Multiple sequence alignment - TraesCS2D01G144500

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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 TraesCS2D01G144500 chr2D 100.000 5684 0 0 1 5684 85920508 85926191 0.000000e+00 10497.0
1 TraesCS2D01G144500 chr2D 94.000 100 4 2 5395 5493 17163430 17163528 3.550000e-32 150.0
2 TraesCS2D01G144500 chr2D 94.792 96 5 0 5393 5488 436111431 436111336 3.550000e-32 150.0
3 TraesCS2D01G144500 chr2D 78.629 248 37 10 367 601 558791356 558791112 3.550000e-32 150.0
4 TraesCS2D01G144500 chr2D 88.000 125 8 5 5379 5498 15192987 15192865 2.140000e-29 141.0
5 TraesCS2D01G144500 chr2A 90.465 3010 194 36 2388 5339 86380975 86383949 0.000000e+00 3882.0
6 TraesCS2D01G144500 chr2A 93.110 1553 43 29 585 2091 86379086 86380620 0.000000e+00 2217.0
7 TraesCS2D01G144500 chr2A 92.035 565 36 4 1 556 86378315 86378879 0.000000e+00 785.0
8 TraesCS2D01G144500 chr2A 94.949 99 3 2 5393 5489 115434512 115434414 2.740000e-33 154.0
9 TraesCS2D01G144500 chr2A 91.071 112 8 2 2313 2423 86380854 86380964 3.550000e-32 150.0
10 TraesCS2D01G144500 chr2A 93.069 101 5 2 5395 5493 18632649 18632749 4.590000e-31 147.0
11 TraesCS2D01G144500 chr2A 80.606 165 13 4 2042 2190 86380761 86380922 6.020000e-20 110.0
12 TraesCS2D01G144500 chr2A 82.836 134 7 3 2092 2209 86380646 86380779 7.790000e-19 106.0
13 TraesCS2D01G144500 chr2A 91.667 72 6 0 1282 1353 722813468 722813397 3.620000e-17 100.0
14 TraesCS2D01G144500 chr2B 91.955 2399 101 30 3040 5401 138965889 138968232 0.000000e+00 3277.0
15 TraesCS2D01G144500 chr2B 90.737 1846 96 32 420 2209 138963448 138965274 0.000000e+00 2392.0
16 TraesCS2D01G144500 chr2B 90.604 149 14 0 1112 1260 182609198 182609346 1.250000e-46 198.0
17 TraesCS2D01G144500 chr2B 94.783 115 6 0 2488 2602 138965758 138965872 4.520000e-41 180.0
18 TraesCS2D01G144500 chr2B 91.736 121 10 0 5564 5684 138972056 138972176 9.790000e-38 169.0
19 TraesCS2D01G144500 chr2B 86.184 152 10 2 1 151 138963298 138963439 2.740000e-33 154.0
20 TraesCS2D01G144500 chr2B 80.247 162 15 8 2042 2190 138965256 138965413 7.790000e-19 106.0
21 TraesCS2D01G144500 chr2B 94.595 37 2 0 2227 2263 553006515 553006551 2.210000e-04 58.4
22 TraesCS2D01G144500 chr5B 87.648 1012 80 13 1001 2003 343135840 343136815 0.000000e+00 1134.0
23 TraesCS2D01G144500 chr5B 87.512 1009 77 15 1001 2003 406980197 406981162 0.000000e+00 1120.0
24 TraesCS2D01G144500 chr5B 91.667 72 6 0 1282 1353 479039659 479039730 3.620000e-17 100.0
25 TraesCS2D01G144500 chr5B 91.667 72 6 0 1282 1353 700066514 700066443 3.620000e-17 100.0
26 TraesCS2D01G144500 chr5B 80.612 98 15 4 495 590 367078996 367079091 7.900000e-09 73.1
27 TraesCS2D01G144500 chr7B 86.125 1009 76 17 1001 2003 629432069 629431119 0.000000e+00 1029.0
28 TraesCS2D01G144500 chr7B 74.910 279 38 21 333 598 494600824 494600565 1.300000e-16 99.0
29 TraesCS2D01G144500 chr7B 88.750 80 7 1 233 310 73300141 73300220 4.690000e-16 97.1
30 TraesCS2D01G144500 chr7B 74.879 207 39 7 396 596 502671206 502671405 1.310000e-11 82.4
31 TraesCS2D01G144500 chr1D 87.149 677 68 6 1101 1776 265799313 265799971 0.000000e+00 750.0
32 TraesCS2D01G144500 chr1D 97.222 180 4 1 1819 1997 265799971 265800150 2.570000e-78 303.0
33 TraesCS2D01G144500 chr5A 90.988 344 30 1 1434 1776 671883335 671882992 4.010000e-126 462.0
34 TraesCS2D01G144500 chr5A 78.073 301 51 12 308 597 600354720 600354424 5.850000e-40 176.0
35 TraesCS2D01G144500 chr5A 97.701 87 2 0 1819 1905 671882992 671882906 3.550000e-32 150.0
36 TraesCS2D01G144500 chr6B 77.592 299 51 10 308 592 717633556 717633260 3.520000e-37 167.0
37 TraesCS2D01G144500 chr4D 89.516 124 12 1 1390 1512 20314745 20314868 7.630000e-34 156.0
38 TraesCS2D01G144500 chr4D 81.061 132 23 2 308 438 72661307 72661177 2.800000e-18 104.0
39 TraesCS2D01G144500 chr4B 94.949 99 3 2 5393 5489 438099455 438099357 2.740000e-33 154.0
40 TraesCS2D01G144500 chr3D 76.689 296 55 10 308 591 516183096 516183389 9.860000e-33 152.0
41 TraesCS2D01G144500 chr5D 94.000 100 5 1 5387 5486 382868508 382868410 3.550000e-32 150.0
42 TraesCS2D01G144500 chr5D 77.273 242 39 9 367 598 409689722 409689487 1.660000e-25 128.0
43 TraesCS2D01G144500 chr7A 93.939 99 4 2 5393 5489 611771870 611771772 1.280000e-31 148.0
44 TraesCS2D01G144500 chr7A 87.805 123 15 0 1390 1512 193563281 193563159 1.650000e-30 145.0
45 TraesCS2D01G144500 chr7A 94.118 51 3 0 2223 2273 695037446 695037496 1.700000e-10 78.7
46 TraesCS2D01G144500 chr1B 94.000 100 3 2 5393 5489 93954393 93954294 1.280000e-31 148.0
47 TraesCS2D01G144500 chrUn 87.805 123 15 0 1390 1512 42466393 42466271 1.650000e-30 145.0
48 TraesCS2D01G144500 chrUn 94.118 51 3 0 2223 2273 83173842 83173792 1.700000e-10 78.7
49 TraesCS2D01G144500 chrUn 94.118 51 3 0 2223 2273 331430283 331430333 1.700000e-10 78.7
50 TraesCS2D01G144500 chrUn 94.118 51 3 0 2223 2273 332318048 332318098 1.700000e-10 78.7
51 TraesCS2D01G144500 chrUn 92.157 51 4 0 2223 2273 83145196 83145146 7.900000e-09 73.1
52 TraesCS2D01G144500 chr3A 76.080 301 59 7 308 596 73570129 73569830 1.650000e-30 145.0
53 TraesCS2D01G144500 chr3A 82.192 146 19 7 458 598 691295284 691295141 1.000000e-22 119.0
54 TraesCS2D01G144500 chr3A 77.941 136 23 2 421 549 70802849 70802714 1.700000e-10 78.7
55 TraesCS2D01G144500 chr4A 100.000 28 0 0 396 423 514744251 514744278 1.000000e-02 52.8


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 TraesCS2D01G144500 chr2D 85920508 85926191 5683 False 10497.000000 10497 100.000000 1 5684 1 chr2D.!!$F2 5683
1 TraesCS2D01G144500 chr2A 86378315 86383949 5634 False 1208.333333 3882 88.353833 1 5339 6 chr2A.!!$F2 5338
2 TraesCS2D01G144500 chr2B 138963298 138972176 8878 False 1046.333333 3277 89.273667 1 5684 6 chr2B.!!$F3 5683
3 TraesCS2D01G144500 chr5B 343135840 343136815 975 False 1134.000000 1134 87.648000 1001 2003 1 chr5B.!!$F1 1002
4 TraesCS2D01G144500 chr5B 406980197 406981162 965 False 1120.000000 1120 87.512000 1001 2003 1 chr5B.!!$F3 1002
5 TraesCS2D01G144500 chr7B 629431119 629432069 950 True 1029.000000 1029 86.125000 1001 2003 1 chr7B.!!$R2 1002
6 TraesCS2D01G144500 chr1D 265799313 265800150 837 False 526.500000 750 92.185500 1101 1997 2 chr1D.!!$F1 896

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
947 1167 0.034089 CAAACTCCCATCCCCCACTC 60.034 60.0 0.00 0.00 0.00 3.51 F
2243 2563 0.537653 GCAAGTACTCCCTCTGTCCC 59.462 60.0 0.00 0.00 0.00 4.46 F
2627 3226 0.381089 CGAGTGGCGTAGGGTTAGAG 59.619 60.0 0.00 0.00 34.64 2.43 F
4413 5035 0.026674 CGATAGCATTGCACACGGTG 59.973 55.0 11.91 6.58 36.51 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2608 3207 0.381089 CTCTAACCCTACGCCACTCG 59.619 60.000 0.0 0.0 45.38 4.18 R
3573 4193 1.531149 CGGCAGTACAACAGGAAAGTG 59.469 52.381 0.0 0.0 0.00 3.16 R
4560 5206 1.004277 TCCAATGCTTTACCGCCTTCT 59.996 47.619 0.0 0.0 0.00 2.85 R
5255 5910 1.541620 ACAAAGACCCCTCCCTCCC 60.542 63.158 0.0 0.0 0.00 4.30 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
23 25 3.655615 AACCACCTAAACTTCACCACA 57.344 42.857 0.00 0.00 0.00 4.17
117 119 3.356639 CTCGTGCTGCCCTTCGCTA 62.357 63.158 0.00 0.00 38.78 4.26
145 147 3.381045 GTCACGAGTGTCACTGATTGAA 58.619 45.455 11.04 0.00 35.39 2.69
151 153 0.038166 TGTCACTGATTGAAGGGCCC 59.962 55.000 16.46 16.46 35.39 5.80
156 158 0.475906 CTGATTGAAGGGCCCTAGGG 59.524 60.000 28.96 24.89 38.57 3.53
347 350 4.314961 ACGCTGACACTCATACATTTCAA 58.685 39.130 0.00 0.00 0.00 2.69
359 362 7.826252 ACTCATACATTTCAAATACACTCAGCT 59.174 33.333 0.00 0.00 0.00 4.24
360 363 8.565896 TCATACATTTCAAATACACTCAGCTT 57.434 30.769 0.00 0.00 0.00 3.74
363 366 5.922544 ACATTTCAAATACACTCAGCTTTGC 59.077 36.000 0.00 0.00 0.00 3.68
367 370 4.455533 TCAAATACACTCAGCTTTGCGAAT 59.544 37.500 0.00 0.00 0.00 3.34
382 385 4.664864 AATGCACGCACGCACACG 62.665 61.111 0.00 0.00 46.56 4.49
386 389 4.409588 CACGCACGCACACGCTAC 62.410 66.667 0.00 0.00 45.53 3.58
391 394 2.677524 ACGCACACGCTACCCCTA 60.678 61.111 0.00 0.00 45.53 3.53
393 396 0.752743 ACGCACACGCTACCCCTATA 60.753 55.000 0.00 0.00 45.53 1.31
394 397 0.601558 CGCACACGCTACCCCTATAT 59.398 55.000 0.00 0.00 35.30 0.86
402 405 2.353803 CGCTACCCCTATATGCACCTTC 60.354 54.545 0.00 0.00 0.00 3.46
413 416 1.328279 TGCACCTTCGAGAGACTGAA 58.672 50.000 0.00 0.00 41.84 3.02
414 417 1.000163 TGCACCTTCGAGAGACTGAAC 60.000 52.381 0.00 0.00 41.84 3.18
417 420 0.171455 CCTTCGAGAGACTGAACCGG 59.829 60.000 0.00 0.00 41.84 5.28
418 421 0.882474 CTTCGAGAGACTGAACCGGT 59.118 55.000 0.00 0.00 41.84 5.28
438 441 5.351458 CGGTACATCATCTTGAGATTGACA 58.649 41.667 0.00 0.00 31.21 3.58
453 456 6.025749 AGATTGACAAAGTCGTCATAGACA 57.974 37.500 0.00 0.00 45.03 3.41
480 489 1.889530 CTGGAACGTCTCCTCCCACC 61.890 65.000 14.95 0.00 45.64 4.61
503 513 1.464608 GCGCACATGCTGAAAGTTCTA 59.535 47.619 0.30 0.00 39.32 2.10
544 554 0.603569 AGCACCCGTGTCAAGTCTAG 59.396 55.000 0.00 0.00 0.00 2.43
562 735 0.038310 AGAGCTTAAACCCTGGTGGC 59.962 55.000 0.00 0.00 37.83 5.01
576 751 1.696097 GGTGGCCGGGATATCACTGT 61.696 60.000 2.18 0.00 0.00 3.55
586 761 4.484912 GGGATATCACTGTCCTCCTAACT 58.515 47.826 4.83 0.00 33.34 2.24
668 857 2.981859 AGCTAATCCATTTCGACCGT 57.018 45.000 0.00 0.00 0.00 4.83
706 895 3.242739 CCAAGTGTATGGCGCTGATTTAC 60.243 47.826 7.64 3.25 38.09 2.01
756 946 4.292784 GCACAAGCCTCACTCTCC 57.707 61.111 0.00 0.00 33.58 3.71
769 966 0.111253 ACTCTCCCCCTTTTGCAGTG 59.889 55.000 0.00 0.00 0.00 3.66
778 975 0.598065 CTTTTGCAGTGTGGCCTACC 59.402 55.000 3.32 0.00 0.00 3.18
811 1008 3.981212 ACAGGAAAACCCCCAGAATATG 58.019 45.455 0.00 0.00 34.66 1.78
903 1122 1.355720 CATTCCACCCAACCTCTTCCT 59.644 52.381 0.00 0.00 0.00 3.36
946 1166 1.509548 CCAAACTCCCATCCCCCACT 61.510 60.000 0.00 0.00 0.00 4.00
947 1167 0.034089 CAAACTCCCATCCCCCACTC 60.034 60.000 0.00 0.00 0.00 3.51
948 1168 1.214992 AAACTCCCATCCCCCACTCC 61.215 60.000 0.00 0.00 0.00 3.85
949 1169 2.774351 CTCCCATCCCCCACTCCC 60.774 72.222 0.00 0.00 0.00 4.30
950 1170 4.448340 TCCCATCCCCCACTCCCC 62.448 72.222 0.00 0.00 0.00 4.81
952 1172 4.455137 CCATCCCCCACTCCCCCT 62.455 72.222 0.00 0.00 0.00 4.79
953 1173 3.099170 CATCCCCCACTCCCCCTG 61.099 72.222 0.00 0.00 0.00 4.45
994 1214 4.123545 CCCCCAAACCCTAGCCCG 62.124 72.222 0.00 0.00 0.00 6.13
2064 2342 3.265791 CTTCTAGTGTGGTGAATCTGGC 58.734 50.000 0.00 0.00 0.00 4.85
2132 2437 7.554118 CACCAGTTACTCATATTTGTTGATCCT 59.446 37.037 0.00 0.00 0.00 3.24
2155 2467 6.294675 CCTTGTCTGATTGCCTTGATGTAAAA 60.295 38.462 0.00 0.00 0.00 1.52
2179 2499 3.350219 TGGATCTTGGAAGTAGCCAAC 57.650 47.619 0.00 0.00 42.75 3.77
2181 2501 2.280628 GATCTTGGAAGTAGCCAACGG 58.719 52.381 0.00 0.00 42.75 4.44
2190 2510 1.068055 AGTAGCCAACGGTAGTGAACG 60.068 52.381 0.00 0.00 0.00 3.95
2191 2511 0.961019 TAGCCAACGGTAGTGAACGT 59.039 50.000 0.00 0.00 46.48 3.99
2198 2518 3.549299 ACGGTAGTGAACGTACTTCTG 57.451 47.619 0.00 0.00 42.15 3.02
2199 2519 2.880890 ACGGTAGTGAACGTACTTCTGT 59.119 45.455 4.30 4.30 42.15 3.41
2200 2520 3.231965 CGGTAGTGAACGTACTTCTGTG 58.768 50.000 0.00 0.00 32.19 3.66
2201 2521 3.304257 CGGTAGTGAACGTACTTCTGTGT 60.304 47.826 0.00 0.00 32.19 3.72
2202 2522 3.979495 GGTAGTGAACGTACTTCTGTGTG 59.021 47.826 0.00 0.00 32.19 3.82
2204 2524 2.429610 AGTGAACGTACTTCTGTGTGGT 59.570 45.455 0.00 0.00 0.00 4.16
2205 2525 2.538449 GTGAACGTACTTCTGTGTGGTG 59.462 50.000 0.00 0.00 0.00 4.17
2206 2526 2.427812 TGAACGTACTTCTGTGTGGTGA 59.572 45.455 0.00 0.00 0.00 4.02
2207 2527 3.119065 TGAACGTACTTCTGTGTGGTGAA 60.119 43.478 0.00 0.00 0.00 3.18
2208 2528 3.746045 ACGTACTTCTGTGTGGTGAAT 57.254 42.857 0.00 0.00 0.00 2.57
2209 2529 3.650139 ACGTACTTCTGTGTGGTGAATC 58.350 45.455 0.00 0.00 0.00 2.52
2210 2530 2.993899 CGTACTTCTGTGTGGTGAATCC 59.006 50.000 0.00 0.00 0.00 3.01
2232 2552 4.142227 CCGTGAATGTAGGTAGCAAGTACT 60.142 45.833 0.00 0.00 0.00 2.73
2233 2553 5.035443 CGTGAATGTAGGTAGCAAGTACTC 58.965 45.833 0.00 0.00 0.00 2.59
2234 2554 5.349809 GTGAATGTAGGTAGCAAGTACTCC 58.650 45.833 0.00 0.00 0.00 3.85
2235 2555 4.404715 TGAATGTAGGTAGCAAGTACTCCC 59.595 45.833 0.00 0.00 0.00 4.30
2236 2556 3.752359 TGTAGGTAGCAAGTACTCCCT 57.248 47.619 0.00 0.00 0.00 4.20
2237 2557 3.629087 TGTAGGTAGCAAGTACTCCCTC 58.371 50.000 0.00 0.00 0.00 4.30
2238 2558 3.268856 TGTAGGTAGCAAGTACTCCCTCT 59.731 47.826 0.00 0.00 0.00 3.69
2239 2559 2.741145 AGGTAGCAAGTACTCCCTCTG 58.259 52.381 0.00 0.00 0.00 3.35
2240 2560 2.043252 AGGTAGCAAGTACTCCCTCTGT 59.957 50.000 0.00 0.00 0.00 3.41
2241 2561 2.427812 GGTAGCAAGTACTCCCTCTGTC 59.572 54.545 0.00 0.00 0.00 3.51
2242 2562 1.562783 AGCAAGTACTCCCTCTGTCC 58.437 55.000 0.00 0.00 0.00 4.02
2243 2563 0.537653 GCAAGTACTCCCTCTGTCCC 59.462 60.000 0.00 0.00 0.00 4.46
2244 2564 1.938585 CAAGTACTCCCTCTGTCCCA 58.061 55.000 0.00 0.00 0.00 4.37
2245 2565 2.472029 CAAGTACTCCCTCTGTCCCAT 58.528 52.381 0.00 0.00 0.00 4.00
2246 2566 3.643237 CAAGTACTCCCTCTGTCCCATA 58.357 50.000 0.00 0.00 0.00 2.74
2247 2567 4.030913 CAAGTACTCCCTCTGTCCCATAA 58.969 47.826 0.00 0.00 0.00 1.90
2248 2568 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
2249 2569 4.227197 AGTACTCCCTCTGTCCCATAATG 58.773 47.826 0.00 0.00 0.00 1.90
2250 2570 1.771255 ACTCCCTCTGTCCCATAATGC 59.229 52.381 0.00 0.00 0.00 3.56
2251 2571 1.770658 CTCCCTCTGTCCCATAATGCA 59.229 52.381 0.00 0.00 0.00 3.96
2252 2572 2.173356 CTCCCTCTGTCCCATAATGCAA 59.827 50.000 0.00 0.00 0.00 4.08
2253 2573 2.173356 TCCCTCTGTCCCATAATGCAAG 59.827 50.000 0.00 0.00 0.00 4.01
2254 2574 2.173356 CCCTCTGTCCCATAATGCAAGA 59.827 50.000 0.00 0.00 0.00 3.02
2255 2575 3.181436 CCCTCTGTCCCATAATGCAAGAT 60.181 47.826 0.00 0.00 0.00 2.40
2256 2576 4.070716 CCTCTGTCCCATAATGCAAGATC 58.929 47.826 0.00 0.00 0.00 2.75
2257 2577 4.202440 CCTCTGTCCCATAATGCAAGATCT 60.202 45.833 0.00 0.00 0.00 2.75
2258 2578 5.374921 CTCTGTCCCATAATGCAAGATCTT 58.625 41.667 0.88 0.88 0.00 2.40
2259 2579 5.759059 TCTGTCCCATAATGCAAGATCTTT 58.241 37.500 4.86 0.00 0.00 2.52
2260 2580 6.189859 TCTGTCCCATAATGCAAGATCTTTT 58.810 36.000 4.86 0.37 0.00 2.27
2261 2581 6.664816 TCTGTCCCATAATGCAAGATCTTTTT 59.335 34.615 4.86 2.97 0.00 1.94
2279 2599 4.647424 TTTTTGACACCACACCAAGATC 57.353 40.909 0.00 0.00 0.00 2.75
2280 2600 3.576078 TTTGACACCACACCAAGATCT 57.424 42.857 0.00 0.00 0.00 2.75
2281 2601 3.576078 TTGACACCACACCAAGATCTT 57.424 42.857 0.88 0.88 0.00 2.40
2282 2602 3.576078 TGACACCACACCAAGATCTTT 57.424 42.857 4.86 0.00 0.00 2.52
2283 2603 3.897239 TGACACCACACCAAGATCTTTT 58.103 40.909 4.86 0.00 0.00 2.27
2284 2604 4.277476 TGACACCACACCAAGATCTTTTT 58.723 39.130 4.86 0.00 0.00 1.94
2325 2680 9.058174 TGGTAATTAAGAATGACTTTGTTCGAA 57.942 29.630 0.00 0.00 39.72 3.71
2343 2698 4.021229 TCGAATAACCTAGAGCCTTGACA 58.979 43.478 0.00 0.00 0.00 3.58
2391 2748 6.324819 CCAATAATAGTGAACCAACTGCTTG 58.675 40.000 0.00 0.00 0.00 4.01
2407 2764 2.572556 TGCTTGCCATGAATTCCCATTT 59.427 40.909 2.27 0.00 0.00 2.32
2416 2773 5.300286 CCATGAATTCCCATTTCCTCAGTAC 59.700 44.000 2.27 0.00 0.00 2.73
2417 2774 5.779241 TGAATTCCCATTTCCTCAGTACT 57.221 39.130 2.27 0.00 0.00 2.73
2449 2858 7.069455 TGCTTATTAGTAGCACATAGGAGTTGA 59.931 37.037 0.00 0.00 43.30 3.18
2461 2870 8.677300 GCACATAGGAGTTGAAGAAAATTATCA 58.323 33.333 0.00 0.00 0.00 2.15
2545 3144 9.472361 CGCTACTACCTTTAATGAGCTAATAAA 57.528 33.333 0.00 0.00 0.00 1.40
2564 3163 3.963428 AAATGTAGAGCGACTCCAACT 57.037 42.857 3.66 0.00 0.00 3.16
2624 3223 2.713967 GGCGAGTGGCGTAGGGTTA 61.714 63.158 0.00 0.00 44.92 2.85
2627 3226 0.381089 CGAGTGGCGTAGGGTTAGAG 59.619 60.000 0.00 0.00 34.64 2.43
2685 3284 7.328737 GGATAGTTGGAGTTGCTCTTTAAGTA 58.671 38.462 0.00 0.00 0.00 2.24
2709 3308 9.705290 GTATCATTTTAGGTCCAAACATGTTTT 57.295 29.630 21.10 9.21 0.00 2.43
2710 3309 8.606040 ATCATTTTAGGTCCAAACATGTTTTG 57.394 30.769 21.10 17.60 0.00 2.44
2807 3406 6.006449 ACCTATGATGATATTGAAGCCCAAC 58.994 40.000 0.00 0.00 37.63 3.77
2809 3408 6.150641 CCTATGATGATATTGAAGCCCAACTG 59.849 42.308 0.00 0.00 37.63 3.16
2812 3411 3.620488 TGATATTGAAGCCCAACTGGAC 58.380 45.455 0.00 0.00 37.63 4.02
2837 3436 1.071385 ACCTTGACTTGCTCTGTCCAG 59.929 52.381 0.00 0.00 33.83 3.86
2845 3444 0.966179 TGCTCTGTCCAGCGAAAGTA 59.034 50.000 0.00 0.00 42.92 2.24
2846 3445 1.067565 TGCTCTGTCCAGCGAAAGTAG 60.068 52.381 0.00 0.00 42.92 2.57
2847 3446 1.067495 GCTCTGTCCAGCGAAAGTAGT 60.067 52.381 0.00 0.00 0.00 2.73
2856 3455 6.092122 TGTCCAGCGAAAGTAGTATGAAATTG 59.908 38.462 0.00 0.00 0.00 2.32
2859 3458 7.820386 TCCAGCGAAAGTAGTATGAAATTGTTA 59.180 33.333 0.00 0.00 0.00 2.41
2860 3459 7.903431 CCAGCGAAAGTAGTATGAAATTGTTAC 59.097 37.037 0.00 0.00 0.00 2.50
2925 3527 1.971357 AGGTCGAATAGTAGGGCATGG 59.029 52.381 0.00 0.00 0.00 3.66
2950 3552 7.201705 GGGATGTTAAGCATTAAACCTGTAGTC 60.202 40.741 0.00 0.00 43.05 2.59
2951 3553 6.715344 TGTTAAGCATTAAACCTGTAGTCG 57.285 37.500 0.00 0.00 43.05 4.18
3035 3637 4.520492 GGAATGTGTTGAGAAGTGGATGTT 59.480 41.667 0.00 0.00 0.00 2.71
3038 3640 5.545063 TGTGTTGAGAAGTGGATGTTCTA 57.455 39.130 0.00 0.00 34.30 2.10
3056 3671 5.128663 TGTTCTAGAGCCAGTAATGCATACA 59.871 40.000 0.00 0.00 36.94 2.29
3103 3719 5.414360 TGAGAATATTGACAGTCTGCAGAC 58.586 41.667 34.82 34.82 45.08 3.51
3128 3744 6.991938 TGCACAATTATTTCAGCCTTTTACT 58.008 32.000 0.00 0.00 0.00 2.24
3142 3758 5.104900 AGCCTTTTACTGATTATCGTGGAGT 60.105 40.000 0.00 0.00 0.00 3.85
3151 3767 7.612677 ACTGATTATCGTGGAGTTATATTCCC 58.387 38.462 2.32 0.00 33.62 3.97
3154 3770 8.040727 TGATTATCGTGGAGTTATATTCCCATG 58.959 37.037 0.00 0.00 37.11 3.66
3182 3799 7.275920 AGGTTATGAGCTTAGTATTGAGTTGG 58.724 38.462 0.00 0.00 0.00 3.77
3197 3814 5.677319 TGAGTTGGTGGGAATCTAGTAAG 57.323 43.478 0.00 0.00 0.00 2.34
3198 3815 5.338632 TGAGTTGGTGGGAATCTAGTAAGA 58.661 41.667 0.00 0.00 35.80 2.10
3199 3816 5.964477 TGAGTTGGTGGGAATCTAGTAAGAT 59.036 40.000 0.00 0.00 44.67 2.40
3200 3817 6.127054 TGAGTTGGTGGGAATCTAGTAAGATG 60.127 42.308 0.00 0.00 41.81 2.90
3201 3818 5.726793 AGTTGGTGGGAATCTAGTAAGATGT 59.273 40.000 0.00 0.00 41.81 3.06
3202 3819 6.901300 AGTTGGTGGGAATCTAGTAAGATGTA 59.099 38.462 0.00 0.00 41.81 2.29
3203 3820 6.978674 TGGTGGGAATCTAGTAAGATGTAG 57.021 41.667 0.00 0.00 41.81 2.74
3205 3822 6.901300 TGGTGGGAATCTAGTAAGATGTAGTT 59.099 38.462 0.00 0.00 41.81 2.24
3206 3823 7.402071 TGGTGGGAATCTAGTAAGATGTAGTTT 59.598 37.037 0.00 0.00 41.81 2.66
3254 3874 5.183228 ACTCGTGGGGTCAACTTTTATATG 58.817 41.667 0.00 0.00 0.00 1.78
3264 3884 7.029563 GGTCAACTTTTATATGCAGGAAACAG 58.970 38.462 0.00 0.00 0.00 3.16
3286 3906 3.015675 TGCAAATGGTCCTGCATATCA 57.984 42.857 0.23 0.00 43.44 2.15
3365 3985 9.120538 GATGTGTAGGTTGGTGTAATGATTATT 57.879 33.333 0.00 0.00 0.00 1.40
3524 4144 4.819105 TGACTAATCCGAAATGTGTCCT 57.181 40.909 0.00 0.00 0.00 3.85
3609 4229 6.876789 TGTACTGCCGATGAAGAAAAAGATAA 59.123 34.615 0.00 0.00 0.00 1.75
3630 4250 7.564660 AGATAATGGCCATTTTATTGGTCTTGA 59.435 33.333 34.85 13.41 42.12 3.02
3641 4261 4.574599 ATTGGTCTTGAAACTGACAAGC 57.425 40.909 0.00 0.00 42.76 4.01
3682 4302 5.987953 GCTGATTGCTGAATCACTAGTGATA 59.012 40.000 33.11 20.36 42.56 2.15
3702 4322 6.974048 GTGATATGCTTGCATGTTGTCAATTA 59.026 34.615 17.26 0.00 0.00 1.40
3781 4401 3.053245 TCTTTTCCTTTCCACCACTTCCA 60.053 43.478 0.00 0.00 0.00 3.53
3798 4418 6.092259 CCACTTCCATAACTAGTGCACTTAAC 59.908 42.308 27.06 0.00 38.32 2.01
3873 4493 1.105759 GCATGATGCCCTCCTTGTCC 61.106 60.000 6.04 0.00 37.42 4.02
4005 4625 6.483405 TCTATGCCATATCATGCACCATTTA 58.517 36.000 0.00 0.00 40.88 1.40
4095 4716 0.984230 TCTGCCTCCAGTCCGAAATT 59.016 50.000 0.00 0.00 40.09 1.82
4098 4719 1.066143 TGCCTCCAGTCCGAAATTCTC 60.066 52.381 0.00 0.00 0.00 2.87
4155 4776 1.066573 CAAGACCCTCGAGATGCTTGT 60.067 52.381 15.71 0.67 0.00 3.16
4212 4833 3.406764 AGAGCATGAAAACAGGACAGAC 58.593 45.455 0.00 0.00 0.00 3.51
4262 4883 3.356290 GGGATGCTCAAAATGTAGGTGT 58.644 45.455 0.00 0.00 0.00 4.16
4316 4938 0.459489 TTGTTGGTGGCTTTGCAGAC 59.541 50.000 0.00 0.00 0.00 3.51
4413 5035 0.026674 CGATAGCATTGCACACGGTG 59.973 55.000 11.91 6.58 36.51 4.94
4560 5206 4.383335 CCTTCGCCTACACACCCTTTATTA 60.383 45.833 0.00 0.00 0.00 0.98
4730 5376 3.523564 TCTCCTTCTAACTGGGAAATGGG 59.476 47.826 0.00 0.00 0.00 4.00
4769 5416 5.412594 GCTCATATCAGTTCACCTGTTTCAA 59.587 40.000 0.00 0.00 42.19 2.69
4776 5423 3.701040 AGTTCACCTGTTTCAATGCAGTT 59.299 39.130 0.00 0.00 0.00 3.16
4779 5429 3.953612 TCACCTGTTTCAATGCAGTTCTT 59.046 39.130 0.00 0.00 0.00 2.52
4786 5436 5.978919 TGTTTCAATGCAGTTCTTTAGCTTG 59.021 36.000 0.00 0.00 0.00 4.01
4809 5459 1.572085 CTCACAACAGAAGCGGCAGG 61.572 60.000 1.45 0.00 0.00 4.85
4860 5510 5.722021 TGCCCTAATCAAGTTTCTTTTCC 57.278 39.130 0.00 0.00 0.00 3.13
4863 5513 5.476945 GCCCTAATCAAGTTTCTTTTCCTCA 59.523 40.000 0.00 0.00 0.00 3.86
4874 5524 8.572855 AGTTTCTTTTCCTCATATTTCTGGAG 57.427 34.615 0.00 0.00 0.00 3.86
4880 5530 3.134458 CCTCATATTTCTGGAGCGGTTC 58.866 50.000 0.00 0.00 0.00 3.62
4943 5594 1.174712 AACAGTGGGTGTGATGCAGC 61.175 55.000 0.00 0.00 40.26 5.25
4961 5612 2.278596 CATGCAGGCTCGCAATGC 60.279 61.111 14.01 10.31 46.87 3.56
5022 5673 1.135575 GCACCTGCTTACTGACAATGC 60.136 52.381 0.00 0.00 38.21 3.56
5061 5712 6.074544 CCAAACAGGGTCGTTTAACATAAA 57.925 37.500 0.00 0.00 36.98 1.40
5077 5728 8.537728 TTAACATAAAGATTGATGGGCTTGAT 57.462 30.769 0.00 0.00 0.00 2.57
5121 5773 6.472887 CCAAGAGTTAACTGGAAATGGAGTA 58.527 40.000 14.14 0.00 0.00 2.59
5141 5793 9.431887 TGGAGTAAAGTGTCAGATAATTTGTAC 57.568 33.333 3.11 0.00 0.00 2.90
5188 5843 5.745312 TGAGTTGATGATTACAGACCTGT 57.255 39.130 7.86 7.86 46.87 4.00
5209 5864 4.588528 TGTAGTCATATGGTATCAGCTGCA 59.411 41.667 9.47 0.77 0.00 4.41
5255 5910 6.682863 CGAATAATTGTTGCTTCCTCTTAACG 59.317 38.462 0.00 0.00 0.00 3.18
5270 5939 1.818669 TAACGGGAGGGAGGGGTCTT 61.819 60.000 0.00 0.00 0.00 3.01
5271 5940 2.285442 CGGGAGGGAGGGGTCTTT 60.285 66.667 0.00 0.00 0.00 2.52
5272 5941 2.670148 CGGGAGGGAGGGGTCTTTG 61.670 68.421 0.00 0.00 0.00 2.77
5273 5942 1.541620 GGGAGGGAGGGGTCTTTGT 60.542 63.158 0.00 0.00 0.00 2.83
5274 5943 1.685820 GGAGGGAGGGGTCTTTGTG 59.314 63.158 0.00 0.00 0.00 3.33
5275 5944 0.840722 GGAGGGAGGGGTCTTTGTGA 60.841 60.000 0.00 0.00 0.00 3.58
5276 5945 0.325272 GAGGGAGGGGTCTTTGTGAC 59.675 60.000 0.00 0.00 44.63 3.67
5305 5974 5.128919 AGTTGGATATCAGTGAGAAATGCC 58.871 41.667 4.83 0.00 0.00 4.40
5360 6029 2.094286 TCCAAAATGCTTATGGTTGCCG 60.094 45.455 4.80 0.00 35.66 5.69
5383 6053 4.275196 GGAGGGCGAAAATTCCATTACTAC 59.725 45.833 0.00 0.00 0.00 2.73
5392 6062 3.603158 TTCCATTACTACGCTTGCTCA 57.397 42.857 0.00 0.00 0.00 4.26
5401 6071 8.978539 CATTACTACGCTTGCTCATAAAATCTA 58.021 33.333 0.00 0.00 0.00 1.98
5402 6072 6.830114 ACTACGCTTGCTCATAAAATCTAC 57.170 37.500 0.00 0.00 0.00 2.59
5404 6074 5.975410 ACGCTTGCTCATAAAATCTACTC 57.025 39.130 0.00 0.00 0.00 2.59
5406 6076 4.212214 CGCTTGCTCATAAAATCTACTCCC 59.788 45.833 0.00 0.00 0.00 4.30
5408 6078 5.468409 GCTTGCTCATAAAATCTACTCCCTC 59.532 44.000 0.00 0.00 0.00 4.30
5409 6079 5.552870 TGCTCATAAAATCTACTCCCTCC 57.447 43.478 0.00 0.00 0.00 4.30
5410 6080 4.039245 TGCTCATAAAATCTACTCCCTCCG 59.961 45.833 0.00 0.00 0.00 4.63
5411 6081 4.039366 GCTCATAAAATCTACTCCCTCCGT 59.961 45.833 0.00 0.00 0.00 4.69
5412 6082 5.774630 CTCATAAAATCTACTCCCTCCGTC 58.225 45.833 0.00 0.00 0.00 4.79
5413 6083 4.587684 TCATAAAATCTACTCCCTCCGTCC 59.412 45.833 0.00 0.00 0.00 4.79
5414 6084 1.790818 AAATCTACTCCCTCCGTCCC 58.209 55.000 0.00 0.00 0.00 4.46
5415 6085 0.635009 AATCTACTCCCTCCGTCCCA 59.365 55.000 0.00 0.00 0.00 4.37
5416 6086 0.861155 ATCTACTCCCTCCGTCCCAT 59.139 55.000 0.00 0.00 0.00 4.00
5417 6087 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
5418 6088 1.854939 TCTACTCCCTCCGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
5419 6089 2.449730 TCTACTCCCTCCGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
5420 6090 3.659195 TCTACTCCCTCCGTCCCATAATA 59.341 47.826 0.00 0.00 0.00 0.98
5421 6091 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
5422 6092 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
5423 6093 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
5424 6094 5.408824 ACTCCCTCCGTCCCATAATATAAA 58.591 41.667 0.00 0.00 0.00 1.40
5425 6095 5.847817 ACTCCCTCCGTCCCATAATATAAAA 59.152 40.000 0.00 0.00 0.00 1.52
5426 6096 6.013639 ACTCCCTCCGTCCCATAATATAAAAG 60.014 42.308 0.00 0.00 0.00 2.27
5427 6097 4.941873 CCCTCCGTCCCATAATATAAAAGC 59.058 45.833 0.00 0.00 0.00 3.51
5428 6098 4.630069 CCTCCGTCCCATAATATAAAAGCG 59.370 45.833 0.00 0.00 0.00 4.68
5429 6099 5.217978 TCCGTCCCATAATATAAAAGCGT 57.782 39.130 0.00 0.00 0.00 5.07
5430 6100 5.613329 TCCGTCCCATAATATAAAAGCGTT 58.387 37.500 0.00 0.00 0.00 4.84
5431 6101 6.056884 TCCGTCCCATAATATAAAAGCGTTT 58.943 36.000 2.53 2.53 0.00 3.60
5432 6102 6.543100 TCCGTCCCATAATATAAAAGCGTTTT 59.457 34.615 2.19 1.29 36.67 2.43
5433 6103 7.067251 TCCGTCCCATAATATAAAAGCGTTTTT 59.933 33.333 14.50 14.50 39.69 1.94
5460 6130 6.787085 ACTAGTGTAGTGTCAAAAATGCTC 57.213 37.500 0.00 0.00 37.69 4.26
5461 6131 6.525629 ACTAGTGTAGTGTCAAAAATGCTCT 58.474 36.000 0.00 0.00 37.69 4.09
5462 6132 6.992715 ACTAGTGTAGTGTCAAAAATGCTCTT 59.007 34.615 0.00 0.00 37.69 2.85
5463 6133 8.148351 ACTAGTGTAGTGTCAAAAATGCTCTTA 58.852 33.333 0.00 0.00 37.69 2.10
5464 6134 7.986085 AGTGTAGTGTCAAAAATGCTCTTAT 57.014 32.000 0.00 0.00 0.00 1.73
5466 6136 9.672673 AGTGTAGTGTCAAAAATGCTCTTATAT 57.327 29.630 0.00 0.00 0.00 0.86
5472 6142 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
5473 6143 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
5474 6144 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
5491 6161 3.012502 TGGGACAGAGGGAGTATTACTGT 59.987 47.826 0.00 0.00 43.10 3.55
5546 6216 8.119226 GCTACAAAAATAGCAATGACTCACTAG 58.881 37.037 0.00 0.00 45.83 2.57
5551 6221 9.890629 AAAAATAGCAATGACTCACTAGTATGA 57.109 29.630 0.00 0.00 35.56 2.15
5552 6222 8.879342 AAATAGCAATGACTCACTAGTATGAC 57.121 34.615 0.00 0.00 35.56 3.06
5553 6223 7.831691 ATAGCAATGACTCACTAGTATGACT 57.168 36.000 0.00 0.00 35.56 3.41
5554 6224 6.142818 AGCAATGACTCACTAGTATGACTC 57.857 41.667 0.00 0.00 35.56 3.36
5556 6226 5.746245 GCAATGACTCACTAGTATGACTCAC 59.254 44.000 0.00 0.00 35.56 3.51
5557 6227 6.269315 CAATGACTCACTAGTATGACTCACC 58.731 44.000 0.00 0.00 35.56 4.02
5559 6229 5.571285 TGACTCACTAGTATGACTCACCTT 58.429 41.667 0.00 0.00 35.56 3.50
5560 6230 6.718294 TGACTCACTAGTATGACTCACCTTA 58.282 40.000 0.00 0.00 35.56 2.69
5597 10009 9.139174 CACTTTGGATGTTGTTATTTGTTATCC 57.861 33.333 0.00 0.00 34.60 2.59
5675 10087 4.634012 TTACTGCACAGTAATTGGGACT 57.366 40.909 17.17 0.00 45.82 3.85
5678 10090 3.149196 CTGCACAGTAATTGGGACTTGT 58.851 45.455 0.00 0.00 28.76 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 0.253160 TCTGGCATTGAGGGTAGGGT 60.253 55.000 0.00 0.00 0.00 4.34
117 119 1.283181 GACACTCGTGACGACAGCT 59.717 57.895 2.39 0.00 0.00 4.24
320 323 3.769536 TGTATGAGTGTCAGCGTATGTG 58.230 45.455 0.00 0.00 0.00 3.21
324 327 5.066968 TGAAATGTATGAGTGTCAGCGTA 57.933 39.130 0.00 0.00 0.00 4.42
333 336 7.826252 AGCTGAGTGTATTTGAAATGTATGAGT 59.174 33.333 0.00 0.00 0.00 3.41
347 350 3.426695 GCATTCGCAAAGCTGAGTGTATT 60.427 43.478 0.00 0.00 38.36 1.89
382 385 2.353803 CGAAGGTGCATATAGGGGTAGC 60.354 54.545 0.00 0.00 0.00 3.58
386 389 2.232452 CTCTCGAAGGTGCATATAGGGG 59.768 54.545 0.00 0.00 0.00 4.79
391 394 3.291584 TCAGTCTCTCGAAGGTGCATAT 58.708 45.455 0.00 0.00 0.00 1.78
393 396 1.550327 TCAGTCTCTCGAAGGTGCAT 58.450 50.000 0.00 0.00 0.00 3.96
394 397 1.000163 GTTCAGTCTCTCGAAGGTGCA 60.000 52.381 0.00 0.00 0.00 4.57
402 405 1.162698 TGTACCGGTTCAGTCTCTCG 58.837 55.000 15.04 0.00 0.00 4.04
413 416 4.405680 TCAATCTCAAGATGATGTACCGGT 59.594 41.667 13.98 13.98 34.49 5.28
414 417 4.747108 GTCAATCTCAAGATGATGTACCGG 59.253 45.833 0.00 0.00 34.49 5.28
417 420 8.261492 ACTTTGTCAATCTCAAGATGATGTAC 57.739 34.615 0.00 0.00 34.49 2.90
418 421 7.276438 CGACTTTGTCAATCTCAAGATGATGTA 59.724 37.037 0.00 0.00 34.49 2.29
438 441 3.501062 TCGACTGTGTCTATGACGACTTT 59.499 43.478 0.00 0.00 34.95 2.66
453 456 0.592148 GAGACGTTCCAGTCGACTGT 59.408 55.000 36.37 22.37 45.26 3.55
503 513 8.031277 GTGCTCACATTTTTCTGGATTTATTCT 58.969 33.333 0.00 0.00 0.00 2.40
544 554 0.965866 GGCCACCAGGGTTTAAGCTC 60.966 60.000 0.00 0.00 39.65 4.09
562 735 0.969894 GGAGGACAGTGATATCCCGG 59.030 60.000 0.00 0.00 0.00 5.73
576 751 2.023404 TGTGGCTGGATAGTTAGGAGGA 60.023 50.000 0.00 0.00 0.00 3.71
586 761 0.613260 AAGCGAGTTGTGGCTGGATA 59.387 50.000 0.00 0.00 37.87 2.59
668 857 4.009675 CACTTGGCTTGCAGGAGTAAATA 58.990 43.478 0.00 0.00 0.00 1.40
706 895 6.020121 CAGCTTGTGTGTCTTTGAGATTTTTG 60.020 38.462 0.00 0.00 0.00 2.44
721 911 2.558286 CCACCTGGCAGCTTGTGTG 61.558 63.158 9.56 11.20 0.00 3.82
756 946 2.736531 GCCACACTGCAAAAGGGG 59.263 61.111 0.00 0.00 31.29 4.79
780 977 0.879090 GTTTTCCTGTTGCCGGTAGG 59.121 55.000 1.90 6.59 41.62 3.18
782 979 0.537828 GGGTTTTCCTGTTGCCGGTA 60.538 55.000 1.90 0.00 40.46 4.02
785 982 2.570284 GGGGGTTTTCCTGTTGCCG 61.570 63.158 0.00 0.00 40.46 5.69
788 985 2.080654 TTCTGGGGGTTTTCCTGTTG 57.919 50.000 0.00 0.00 40.46 3.33
789 986 4.202781 ACATATTCTGGGGGTTTTCCTGTT 60.203 41.667 0.00 0.00 40.46 3.16
790 987 3.336694 ACATATTCTGGGGGTTTTCCTGT 59.663 43.478 0.00 0.00 40.46 4.00
791 988 3.701040 CACATATTCTGGGGGTTTTCCTG 59.299 47.826 0.00 0.00 40.46 3.86
792 989 3.881713 GCACATATTCTGGGGGTTTTCCT 60.882 47.826 0.00 0.00 40.46 3.36
793 990 2.430694 GCACATATTCTGGGGGTTTTCC 59.569 50.000 0.00 0.00 39.75 3.13
794 991 2.099098 CGCACATATTCTGGGGGTTTTC 59.901 50.000 0.00 0.00 36.49 2.29
903 1122 1.230182 GGAAGGGGAGGGGAAGGAA 60.230 63.158 0.00 0.00 0.00 3.36
946 1166 3.943137 ATGGACGGAAGCAGGGGGA 62.943 63.158 0.00 0.00 0.00 4.81
947 1167 3.406595 GATGGACGGAAGCAGGGGG 62.407 68.421 0.00 0.00 0.00 5.40
948 1168 2.190578 GATGGACGGAAGCAGGGG 59.809 66.667 0.00 0.00 0.00 4.79
949 1169 1.450312 GTGATGGACGGAAGCAGGG 60.450 63.158 0.00 0.00 0.00 4.45
950 1170 1.811266 CGTGATGGACGGAAGCAGG 60.811 63.158 0.00 0.00 44.85 4.85
951 1171 3.786101 CGTGATGGACGGAAGCAG 58.214 61.111 0.00 0.00 44.85 4.24
1129 1360 4.415332 CGTGGCGTACTCCAGCGT 62.415 66.667 4.41 0.00 36.67 5.07
1452 1699 2.668632 GTGGTCCCGCTCATGGAA 59.331 61.111 0.00 0.00 32.59 3.53
1581 1828 3.934391 GAACGGCGTCTGGTCCCAG 62.934 68.421 15.17 7.02 44.86 4.45
2064 2342 9.865321 TTACCAATTTACTACTGTACTTGCTAG 57.135 33.333 0.00 0.00 0.00 3.42
2132 2437 6.265196 AGTTTTACATCAAGGCAATCAGACAA 59.735 34.615 0.00 0.00 0.00 3.18
2155 2467 3.330701 TGGCTACTTCCAAGATCCAAAGT 59.669 43.478 0.00 0.00 36.09 2.66
2179 2499 3.231965 CACAGAAGTACGTTCACTACCG 58.768 50.000 0.00 0.00 37.67 4.02
2181 2501 3.979495 CCACACAGAAGTACGTTCACTAC 59.021 47.826 0.00 0.00 37.67 2.73
2190 2510 2.993899 CGGATTCACCACACAGAAGTAC 59.006 50.000 0.00 0.00 38.90 2.73
2191 2511 2.631062 ACGGATTCACCACACAGAAGTA 59.369 45.455 0.00 0.00 38.90 2.24
2198 2518 2.151202 ACATTCACGGATTCACCACAC 58.849 47.619 0.00 0.00 38.90 3.82
2199 2519 2.559698 ACATTCACGGATTCACCACA 57.440 45.000 0.00 0.00 38.90 4.17
2200 2520 2.936498 CCTACATTCACGGATTCACCAC 59.064 50.000 0.00 0.00 38.90 4.16
2201 2521 2.569853 ACCTACATTCACGGATTCACCA 59.430 45.455 0.00 0.00 38.90 4.17
2202 2522 3.261981 ACCTACATTCACGGATTCACC 57.738 47.619 0.00 0.00 0.00 4.02
2204 2524 3.449377 TGCTACCTACATTCACGGATTCA 59.551 43.478 0.00 0.00 0.00 2.57
2205 2525 4.054780 TGCTACCTACATTCACGGATTC 57.945 45.455 0.00 0.00 0.00 2.52
2206 2526 4.081087 ACTTGCTACCTACATTCACGGATT 60.081 41.667 0.00 0.00 0.00 3.01
2207 2527 3.451178 ACTTGCTACCTACATTCACGGAT 59.549 43.478 0.00 0.00 0.00 4.18
2208 2528 2.829720 ACTTGCTACCTACATTCACGGA 59.170 45.455 0.00 0.00 0.00 4.69
2209 2529 3.247006 ACTTGCTACCTACATTCACGG 57.753 47.619 0.00 0.00 0.00 4.94
2210 2530 4.995124 AGTACTTGCTACCTACATTCACG 58.005 43.478 0.00 0.00 0.00 4.35
2258 2578 4.277476 AGATCTTGGTGTGGTGTCAAAAA 58.723 39.130 0.00 0.00 0.00 1.94
2259 2579 3.897239 AGATCTTGGTGTGGTGTCAAAA 58.103 40.909 0.00 0.00 0.00 2.44
2260 2580 3.576078 AGATCTTGGTGTGGTGTCAAA 57.424 42.857 0.00 0.00 0.00 2.69
2261 2581 3.576078 AAGATCTTGGTGTGGTGTCAA 57.424 42.857 7.30 0.00 0.00 3.18
2262 2582 3.576078 AAAGATCTTGGTGTGGTGTCA 57.424 42.857 9.17 0.00 0.00 3.58
2263 2583 4.918810 AAAAAGATCTTGGTGTGGTGTC 57.081 40.909 9.17 0.00 0.00 3.67
2283 2603 9.906660 CTTAATTACCAATTTACTGCTGTCAAA 57.093 29.630 0.00 0.70 32.38 2.69
2284 2604 9.290988 TCTTAATTACCAATTTACTGCTGTCAA 57.709 29.630 0.00 0.00 32.38 3.18
2285 2605 8.856153 TCTTAATTACCAATTTACTGCTGTCA 57.144 30.769 0.00 0.00 32.38 3.58
2308 2628 8.311836 TCTAGGTTATTCGAACAAAGTCATTCT 58.688 33.333 0.00 0.00 0.00 2.40
2325 2680 6.100424 AGCTTTATGTCAAGGCTCTAGGTTAT 59.900 38.462 0.00 0.00 0.00 1.89
2343 2698 6.127338 GGCTACTTTCCAATCCAAAGCTTTAT 60.127 38.462 12.25 0.00 34.67 1.40
2391 2748 3.033184 TGAGGAAATGGGAATTCATGGC 58.967 45.455 7.93 0.00 0.00 4.40
2407 2764 1.763968 AGCATGCGTAGTACTGAGGA 58.236 50.000 13.01 0.49 0.00 3.71
2545 3144 4.890581 AGATAGTTGGAGTCGCTCTACATT 59.109 41.667 6.78 0.00 36.80 2.71
2555 3154 3.033659 TCAGGGGAGATAGTTGGAGTC 57.966 52.381 0.00 0.00 0.00 3.36
2564 3163 2.443255 GGAGGCAAATTCAGGGGAGATA 59.557 50.000 0.00 0.00 0.00 1.98
2608 3207 0.381089 CTCTAACCCTACGCCACTCG 59.619 60.000 0.00 0.00 45.38 4.18
2613 3212 1.472188 ACTCACTCTAACCCTACGCC 58.528 55.000 0.00 0.00 0.00 5.68
2614 3213 3.589495 AAACTCACTCTAACCCTACGC 57.411 47.619 0.00 0.00 0.00 4.42
2661 3260 8.950208 ATACTTAAAGAGCAACTCCAACTATC 57.050 34.615 0.00 0.00 0.00 2.08
2685 3284 8.210265 ACAAAACATGTTTGGACCTAAAATGAT 58.790 29.630 28.58 10.05 40.06 2.45
2709 3308 7.609918 AGAATATTTACTGTGTATGTTGCCACA 59.390 33.333 0.00 0.00 39.16 4.17
2710 3309 7.985476 AGAATATTTACTGTGTATGTTGCCAC 58.015 34.615 0.00 0.00 0.00 5.01
2743 3342 9.999009 TGAAGTCTATAAACTCGTAAGTGTATG 57.001 33.333 0.00 0.00 44.35 2.39
2764 3363 3.900601 AGGTCAGACAGACTTGATGAAGT 59.099 43.478 0.00 0.00 46.72 3.01
2768 3367 5.588958 TCATAGGTCAGACAGACTTGATG 57.411 43.478 2.17 0.82 46.72 3.07
2783 3382 5.848286 TGGGCTTCAATATCATCATAGGT 57.152 39.130 0.00 0.00 0.00 3.08
2807 3406 1.867233 CAAGTCAAGGTCAACGTCCAG 59.133 52.381 0.00 0.00 0.00 3.86
2809 3408 0.586802 GCAAGTCAAGGTCAACGTCC 59.413 55.000 0.00 0.00 0.00 4.79
2812 3411 1.528586 CAGAGCAAGTCAAGGTCAACG 59.471 52.381 0.00 0.00 36.03 4.10
2837 3436 7.971455 AGGTAACAATTTCATACTACTTTCGC 58.029 34.615 0.00 0.00 41.41 4.70
2909 3511 2.303022 ACATCCCATGCCCTACTATTCG 59.697 50.000 0.00 0.00 0.00 3.34
2913 3515 3.072476 GCTTAACATCCCATGCCCTACTA 59.928 47.826 0.00 0.00 0.00 1.82
2925 3527 7.465513 CGACTACAGGTTTAATGCTTAACATCC 60.466 40.741 0.00 0.00 38.34 3.51
2997 3599 6.515272 ACACATTCCACTGAAATTATCACC 57.485 37.500 0.00 0.00 33.32 4.02
3005 3607 5.066375 CACTTCTCAACACATTCCACTGAAA 59.934 40.000 0.00 0.00 33.32 2.69
3011 3613 3.855255 TCCACTTCTCAACACATTCCA 57.145 42.857 0.00 0.00 0.00 3.53
3035 3637 4.281941 CCTGTATGCATTACTGGCTCTAGA 59.718 45.833 3.54 0.00 41.35 2.43
3038 3640 2.105477 CCCTGTATGCATTACTGGCTCT 59.895 50.000 3.54 0.00 44.52 4.09
3056 3671 7.240405 TCATCCATGATCATTTTAGGTATCCCT 59.760 37.037 5.16 0.00 45.51 4.20
3070 3685 7.742767 ACTGTCAATATTCTCATCCATGATCA 58.257 34.615 0.00 0.00 36.02 2.92
3071 3686 8.095792 AGACTGTCAATATTCTCATCCATGATC 58.904 37.037 10.88 0.00 36.02 2.92
3072 3687 7.878644 CAGACTGTCAATATTCTCATCCATGAT 59.121 37.037 10.88 0.00 36.02 2.45
3078 3693 6.200665 GTCTGCAGACTGTCAATATTCTCATC 59.799 42.308 34.54 6.10 41.65 2.92
3103 3719 7.062605 CAGTAAAAGGCTGAAATAATTGTGCAG 59.937 37.037 0.00 0.00 36.12 4.41
3128 3744 7.547697 TGGGAATATAACTCCACGATAATCA 57.452 36.000 6.57 0.00 34.34 2.57
3142 3758 8.890472 AGCTCATAACCTTACATGGGAATATAA 58.110 33.333 0.00 0.00 0.00 0.98
3149 3765 5.930135 ACTAAGCTCATAACCTTACATGGG 58.070 41.667 0.00 0.00 0.00 4.00
3151 3767 9.764363 TCAATACTAAGCTCATAACCTTACATG 57.236 33.333 0.00 0.00 0.00 3.21
3154 3770 9.819267 AACTCAATACTAAGCTCATAACCTTAC 57.181 33.333 0.00 0.00 0.00 2.34
3182 3799 9.968870 CTAAACTACATCTTACTAGATTCCCAC 57.031 37.037 0.00 0.00 39.11 4.61
3197 3814 8.788325 ATTCCTTGTACCAACTAAACTACATC 57.212 34.615 0.00 0.00 0.00 3.06
3210 3830 9.287373 ACGAGTTATTTTTAATTCCTTGTACCA 57.713 29.630 0.00 0.00 0.00 3.25
3254 3874 2.028748 ACCATTTGCATCTGTTTCCTGC 60.029 45.455 0.00 0.00 36.45 4.85
3286 3906 7.346751 ACACACAAGAATGGAGTAAAAATGT 57.653 32.000 0.00 0.00 0.00 2.71
3365 3985 6.310941 TCAACCTCAAATTCCTGACCATTTA 58.689 36.000 0.00 0.00 0.00 1.40
3524 4144 6.419413 GTCCATTTTATCACGTTCTTTTTGCA 59.581 34.615 0.00 0.00 0.00 4.08
3573 4193 1.531149 CGGCAGTACAACAGGAAAGTG 59.469 52.381 0.00 0.00 0.00 3.16
3609 4229 6.013466 AGTTTCAAGACCAATAAAATGGCCAT 60.013 34.615 14.09 14.09 44.75 4.40
3630 4250 3.281727 TCTGAAGTGGCTTGTCAGTTT 57.718 42.857 10.30 0.00 39.82 2.66
3641 4261 3.405831 TCAGCAGTCAATTCTGAAGTGG 58.594 45.455 16.68 3.55 37.61 4.00
3682 4302 5.726397 ACATAATTGACAACATGCAAGCAT 58.274 33.333 0.86 0.86 37.08 3.79
3747 4367 5.473846 GGAAAGGAAAAGAGAGGGTTTACAG 59.526 44.000 0.00 0.00 0.00 2.74
3781 4401 6.225318 TGGTTTCGTTAAGTGCACTAGTTAT 58.775 36.000 22.01 6.49 0.00 1.89
3873 4493 3.813724 CACTTCATGGAGATGCATACTGG 59.186 47.826 8.39 0.00 0.00 4.00
4095 4716 7.877612 TGTAGCAATTGAGACAAATGTTAGAGA 59.122 33.333 10.34 0.00 0.00 3.10
4098 4719 7.094634 ACCTGTAGCAATTGAGACAAATGTTAG 60.095 37.037 10.34 0.00 0.00 2.34
4262 4883 9.616156 TTATGCCTAAATAATCGAAGGTTTGTA 57.384 29.630 0.00 0.00 0.00 2.41
4534 5180 1.542187 GGGTGTGTAGGCGAAGGAGT 61.542 60.000 0.00 0.00 0.00 3.85
4560 5206 1.004277 TCCAATGCTTTACCGCCTTCT 59.996 47.619 0.00 0.00 0.00 2.85
4730 5376 2.766970 TGAGCTTGTTTGCGTTTACC 57.233 45.000 0.00 0.00 38.13 2.85
4769 5416 5.942236 TGAGATTCAAGCTAAAGAACTGCAT 59.058 36.000 0.00 0.00 0.00 3.96
4776 5423 6.524734 TCTGTTGTGAGATTCAAGCTAAAGA 58.475 36.000 0.00 0.00 0.00 2.52
4779 5429 5.180117 GCTTCTGTTGTGAGATTCAAGCTAA 59.820 40.000 0.00 0.00 0.00 3.09
4786 5436 1.129437 GCCGCTTCTGTTGTGAGATTC 59.871 52.381 0.00 0.00 0.00 2.52
4809 5459 1.139095 GAGGATGACGACGGGTGTC 59.861 63.158 0.00 0.00 41.91 3.67
4838 5488 5.393866 AGGAAAAGAAACTTGATTAGGGCA 58.606 37.500 0.00 0.00 0.00 5.36
4860 5510 2.797156 CGAACCGCTCCAGAAATATGAG 59.203 50.000 0.00 0.00 0.00 2.90
4943 5594 2.411701 CATTGCGAGCCTGCATGG 59.588 61.111 0.85 0.00 45.78 3.66
4944 5595 2.278596 GCATTGCGAGCCTGCATG 60.279 61.111 12.74 4.13 45.78 4.06
4945 5596 2.050350 AAGCATTGCGAGCCTGCAT 61.050 52.632 17.72 6.97 45.78 3.96
4946 5597 2.674033 AAGCATTGCGAGCCTGCA 60.674 55.556 17.72 0.00 44.61 4.41
4947 5598 2.202570 CAAGCATTGCGAGCCTGC 60.203 61.111 2.38 10.49 40.39 4.85
4961 5612 2.252260 CAACCGGCGCAGAACAAG 59.748 61.111 10.83 0.00 0.00 3.16
5011 5662 6.489700 TCAGAATCCTTTTTGCATTGTCAGTA 59.510 34.615 0.00 0.00 0.00 2.74
5022 5673 5.275067 TGTTTGGGTCAGAATCCTTTTTG 57.725 39.130 0.00 0.00 0.00 2.44
5061 5712 3.889538 CACATGATCAAGCCCATCAATCT 59.110 43.478 0.00 0.00 33.94 2.40
5077 5728 3.589579 GCGTCCAATGCCACATGA 58.410 55.556 0.00 0.00 0.00 3.07
5167 5822 6.868622 ACTACAGGTCTGTAATCATCAACTC 58.131 40.000 11.39 0.00 44.47 3.01
5176 5831 8.958060 ATACCATATGACTACAGGTCTGTAAT 57.042 34.615 3.65 2.29 44.47 1.89
5179 5834 6.373759 TGATACCATATGACTACAGGTCTGT 58.626 40.000 3.65 8.74 44.74 3.41
5188 5843 4.835056 ACTGCAGCTGATACCATATGACTA 59.165 41.667 20.43 0.00 0.00 2.59
5255 5910 1.541620 ACAAAGACCCCTCCCTCCC 60.542 63.158 0.00 0.00 0.00 4.30
5270 5939 5.863965 TGATATCCAACTCACAAGTCACAA 58.136 37.500 0.00 0.00 33.48 3.33
5271 5940 5.012046 ACTGATATCCAACTCACAAGTCACA 59.988 40.000 0.00 0.00 33.48 3.58
5272 5941 5.349817 CACTGATATCCAACTCACAAGTCAC 59.650 44.000 0.00 0.00 33.48 3.67
5273 5942 5.245977 TCACTGATATCCAACTCACAAGTCA 59.754 40.000 0.00 0.00 33.48 3.41
5274 5943 5.724328 TCACTGATATCCAACTCACAAGTC 58.276 41.667 0.00 0.00 33.48 3.01
5275 5944 5.481824 TCTCACTGATATCCAACTCACAAGT 59.518 40.000 0.00 0.00 37.32 3.16
5276 5945 5.970592 TCTCACTGATATCCAACTCACAAG 58.029 41.667 0.00 0.00 0.00 3.16
5305 5974 4.084328 CGTGTTTCTTTCAGTAAGCTCTGG 60.084 45.833 2.82 0.00 36.25 3.86
5360 6029 3.288092 AGTAATGGAATTTTCGCCCTCC 58.712 45.455 0.00 0.00 37.87 4.30
5383 6053 4.212214 GGGAGTAGATTTTATGAGCAAGCG 59.788 45.833 0.00 0.00 0.00 4.68
5392 6062 3.902467 GGGACGGAGGGAGTAGATTTTAT 59.098 47.826 0.00 0.00 0.00 1.40
5401 6071 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
5402 6072 6.368779 TTTTATATTATGGGACGGAGGGAG 57.631 41.667 0.00 0.00 0.00 4.30
5404 6074 4.941873 GCTTTTATATTATGGGACGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
5406 6076 5.235516 ACGCTTTTATATTATGGGACGGAG 58.764 41.667 0.00 0.00 0.00 4.63
5408 6078 5.934935 AACGCTTTTATATTATGGGACGG 57.065 39.130 0.00 0.00 0.00 4.79
5437 6107 6.525629 AGAGCATTTTTGACACTACACTAGT 58.474 36.000 0.00 0.00 40.28 2.57
5438 6108 7.426929 AAGAGCATTTTTGACACTACACTAG 57.573 36.000 0.00 0.00 0.00 2.57
5440 6110 7.986085 ATAAGAGCATTTTTGACACTACACT 57.014 32.000 0.00 0.00 0.00 3.55
5446 6116 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
5447 6117 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
5448 6118 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
5449 6119 9.639563 TGTCCCATAATATAAGAGCATTTTTGA 57.360 29.630 0.00 0.00 0.00 2.69
5450 6120 9.903682 CTGTCCCATAATATAAGAGCATTTTTG 57.096 33.333 0.00 0.00 0.00 2.44
5451 6121 9.866655 TCTGTCCCATAATATAAGAGCATTTTT 57.133 29.630 0.00 0.00 0.00 1.94
5452 6122 9.512588 CTCTGTCCCATAATATAAGAGCATTTT 57.487 33.333 0.00 0.00 0.00 1.82
5453 6123 8.105829 CCTCTGTCCCATAATATAAGAGCATTT 58.894 37.037 0.00 0.00 0.00 2.32
5454 6124 7.311549 CCCTCTGTCCCATAATATAAGAGCATT 60.312 40.741 0.00 0.00 0.00 3.56
5455 6125 6.157645 CCCTCTGTCCCATAATATAAGAGCAT 59.842 42.308 0.00 0.00 0.00 3.79
5456 6126 5.485353 CCCTCTGTCCCATAATATAAGAGCA 59.515 44.000 0.00 0.00 0.00 4.26
5457 6127 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
5458 6128 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
5459 6129 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
5460 6130 8.846423 ATACTCCCTCTGTCCCATAATATAAG 57.154 38.462 0.00 0.00 0.00 1.73
5462 6132 9.710818 GTAATACTCCCTCTGTCCCATAATATA 57.289 37.037 0.00 0.00 0.00 0.86
5463 6133 8.410623 AGTAATACTCCCTCTGTCCCATAATAT 58.589 37.037 0.00 0.00 0.00 1.28
5464 6134 7.674348 CAGTAATACTCCCTCTGTCCCATAATA 59.326 40.741 0.00 0.00 0.00 0.98
5465 6135 6.498651 CAGTAATACTCCCTCTGTCCCATAAT 59.501 42.308 0.00 0.00 0.00 1.28
5466 6136 5.839063 CAGTAATACTCCCTCTGTCCCATAA 59.161 44.000 0.00 0.00 0.00 1.90
5467 6137 5.103215 ACAGTAATACTCCCTCTGTCCCATA 60.103 44.000 0.00 0.00 34.87 2.74
5468 6138 4.227197 CAGTAATACTCCCTCTGTCCCAT 58.773 47.826 0.00 0.00 0.00 4.00
5469 6139 3.012502 ACAGTAATACTCCCTCTGTCCCA 59.987 47.826 0.00 0.00 34.87 4.37
5470 6140 3.637694 GACAGTAATACTCCCTCTGTCCC 59.362 52.174 11.11 0.00 44.98 4.46
5471 6141 4.922471 GACAGTAATACTCCCTCTGTCC 57.078 50.000 11.11 0.00 44.98 4.02
5473 6143 6.330178 ACTAGACAGTAATACTCCCTCTGT 57.670 41.667 0.00 0.00 41.18 3.41
5517 6187 6.377996 TGAGTCATTGCTATTTTTGTAGCCAT 59.622 34.615 3.72 0.00 45.07 4.40
5521 6191 9.155975 ACTAGTGAGTCATTGCTATTTTTGTAG 57.844 33.333 0.00 0.00 0.00 2.74
5567 9979 4.789012 ATAACAACATCCAAAGTGGCAG 57.211 40.909 0.00 0.00 37.47 4.85
5577 9989 9.573133 CTTCTTGGATAACAAATAACAACATCC 57.427 33.333 0.00 0.00 38.91 3.51
5597 10009 5.741388 ATCCAGCGCTATTAAACTTCTTG 57.259 39.130 10.99 0.00 0.00 3.02
5600 10012 7.041372 TCCAATAATCCAGCGCTATTAAACTTC 60.041 37.037 10.99 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.