Multiple sequence alignment - TraesCS2D01G108300

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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 TraesCS2D01G108300 chr2D 100.000 3227 0 0 1 3227 60109784 60106558 0.000000e+00 5960.0
1 TraesCS2D01G108300 chr2D 75.758 363 54 23 887 1222 59726964 59727319 5.580000e-33 152.0
2 TraesCS2D01G108300 chr2D 93.939 66 4 0 1503 1568 59658293 59658358 2.050000e-17 100.0
3 TraesCS2D01G108300 chr2D 89.231 65 6 1 892 956 60139079 60139016 2.670000e-11 80.5
4 TraesCS2D01G108300 chr2B 92.385 2495 102 41 1 2449 93935598 93933146 0.000000e+00 3474.0
5 TraesCS2D01G108300 chr2B 80.227 617 104 11 1637 2243 94202759 94202151 6.350000e-122 448.0
6 TraesCS2D01G108300 chr2B 78.748 687 101 21 877 1557 94203511 94202864 4.980000e-113 418.0
7 TraesCS2D01G108300 chr2B 82.804 378 44 9 2850 3225 93932733 93932375 5.200000e-83 318.0
8 TraesCS2D01G108300 chr2B 89.140 221 22 1 2452 2670 93932981 93932761 1.140000e-69 274.0
9 TraesCS2D01G108300 chr2B 76.140 570 97 25 1646 2203 94224400 94223858 2.470000e-66 263.0
10 TraesCS2D01G108300 chr2B 89.109 202 17 4 57 256 93935008 93934810 2.490000e-61 246.0
11 TraesCS2D01G108300 chr2B 75.395 569 103 23 1646 2203 94033770 94033228 1.160000e-59 241.0
12 TraesCS2D01G108300 chr2B 85.000 100 11 1 491 586 94204370 94204271 7.370000e-17 99.0
13 TraesCS2D01G108300 chr2B 91.935 62 4 1 887 948 93111844 93111904 5.740000e-13 86.1
14 TraesCS2D01G108300 chr2B 91.111 45 2 2 349 392 94204563 94204520 3.480000e-05 60.2
15 TraesCS2D01G108300 chr1D 88.953 869 67 12 786 1641 247868012 247867160 0.000000e+00 1046.0
16 TraesCS2D01G108300 chr1D 94.243 608 35 0 1719 2326 247859571 247858964 0.000000e+00 929.0
17 TraesCS2D01G108300 chr1D 87.647 170 19 2 103 272 247868198 247868031 2.540000e-46 196.0
18 TraesCS2D01G108300 chr1D 88.820 161 9 3 620 780 247868198 247868047 4.250000e-44 189.0
19 TraesCS2D01G108300 chr1A 93.695 682 41 1 1647 2326 299267823 299268504 0.000000e+00 1020.0
20 TraesCS2D01G108300 chr1A 87.582 612 50 9 786 1383 299261288 299261887 0.000000e+00 686.0
21 TraesCS2D01G108300 chr1A 91.418 268 20 2 1370 1637 299267381 299267645 6.580000e-97 364.0
22 TraesCS2D01G108300 chr1A 86.145 166 18 4 107 272 299261109 299261269 1.190000e-39 174.0
23 TraesCS2D01G108300 chr1A 86.076 158 10 4 623 780 299261108 299261253 3.330000e-35 159.0
24 TraesCS2D01G108300 chr1B 85.897 858 76 15 786 1629 329763181 329764007 0.000000e+00 872.0
25 TraesCS2D01G108300 chr1B 91.275 596 48 4 1650 2244 329764642 329765234 0.000000e+00 809.0
26 TraesCS2D01G108300 chr1B 96.970 99 3 0 2228 2326 329765384 329765482 1.990000e-37 167.0
27 TraesCS2D01G108300 chr1B 95.455 88 4 0 693 780 329763059 329763146 1.210000e-29 141.0
28 TraesCS2D01G108300 chr1B 83.607 122 11 3 609 730 329762891 329763003 4.400000e-19 106.0
29 TraesCS2D01G108300 chr1B 97.959 49 1 0 344 392 329761471 329761519 5.740000e-13 86.1
30 TraesCS2D01G108300 chr2A 84.547 783 67 25 827 1577 60101216 60100456 0.000000e+00 726.0
31 TraesCS2D01G108300 chr2A 76.974 1355 214 48 887 2203 60609934 60608640 0.000000e+00 684.0
32 TraesCS2D01G108300 chr2A 76.331 1390 229 49 887 2236 60195915 60194586 0.000000e+00 652.0
33 TraesCS2D01G108300 chr2A 75.986 583 101 26 1646 2216 60711238 60710683 6.860000e-67 265.0
34 TraesCS2D01G108300 chr2A 79.939 329 43 13 453 780 60196432 60196126 1.510000e-53 220.0
35 TraesCS2D01G108300 chr2A 76.812 345 59 17 892 1222 60711924 60711587 1.190000e-39 174.0
36 TraesCS2D01G108300 chrUn 81.366 322 41 12 911 1215 109056546 109056865 8.940000e-61 244.0
37 TraesCS2D01G108300 chrUn 96.552 58 2 0 1503 1560 109057065 109057122 2.650000e-16 97.1
38 TraesCS2D01G108300 chr5A 80.247 324 47 12 912 1220 703952220 703951899 9.010000e-56 228.0
39 TraesCS2D01G108300 chr5A 96.552 58 2 0 1503 1560 703951701 703951644 2.650000e-16 97.1
40 TraesCS2D01G108300 chr5A 91.304 46 4 0 519 564 704016606 704016561 2.690000e-06 63.9
41 TraesCS2D01G108300 chr4B 83.260 227 33 4 998 1220 664051602 664051827 1.520000e-48 204.0
42 TraesCS2D01G108300 chr4B 76.763 241 18 15 1321 1560 664051878 664052081 2.050000e-17 100.0


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 TraesCS2D01G108300 chr2D 60106558 60109784 3226 True 5960.000000 5960 100.000000 1 3227 1 chr2D.!!$R1 3226
1 TraesCS2D01G108300 chr2B 93932375 93935598 3223 True 1078.000000 3474 88.359500 1 3225 4 chr2B.!!$R3 3224
2 TraesCS2D01G108300 chr2B 94223858 94224400 542 True 263.000000 263 76.140000 1646 2203 1 chr2B.!!$R2 557
3 TraesCS2D01G108300 chr2B 94202151 94204563 2412 True 256.300000 448 83.771500 349 2243 4 chr2B.!!$R4 1894
4 TraesCS2D01G108300 chr2B 94033228 94033770 542 True 241.000000 241 75.395000 1646 2203 1 chr2B.!!$R1 557
5 TraesCS2D01G108300 chr1D 247858964 247859571 607 True 929.000000 929 94.243000 1719 2326 1 chr1D.!!$R1 607
6 TraesCS2D01G108300 chr1D 247867160 247868198 1038 True 477.000000 1046 88.473333 103 1641 3 chr1D.!!$R2 1538
7 TraesCS2D01G108300 chr1A 299267381 299268504 1123 False 692.000000 1020 92.556500 1370 2326 2 chr1A.!!$F2 956
8 TraesCS2D01G108300 chr1A 299261108 299261887 779 False 339.666667 686 86.601000 107 1383 3 chr1A.!!$F1 1276
9 TraesCS2D01G108300 chr1B 329761471 329765482 4011 False 363.516667 872 91.860500 344 2326 6 chr1B.!!$F1 1982
10 TraesCS2D01G108300 chr2A 60100456 60101216 760 True 726.000000 726 84.547000 827 1577 1 chr2A.!!$R1 750
11 TraesCS2D01G108300 chr2A 60608640 60609934 1294 True 684.000000 684 76.974000 887 2203 1 chr2A.!!$R2 1316
12 TraesCS2D01G108300 chr2A 60194586 60196432 1846 True 436.000000 652 78.135000 453 2236 2 chr2A.!!$R3 1783
13 TraesCS2D01G108300 chr2A 60710683 60711924 1241 True 219.500000 265 76.399000 892 2216 2 chr2A.!!$R4 1324

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
427 463 0.322546 ATGTCCAAGGTTTCGAGCCC 60.323 55.0 4.72 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 4634 0.106918 ACCACAACGGGCTGAAAAGA 60.107 50.0 0.0 0.0 40.22 2.52 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
19 20 2.251409 GCTAGCTTGCAGATGGATGA 57.749 50.000 15.53 0.00 0.00 2.92
21 22 2.492012 CTAGCTTGCAGATGGATGACC 58.508 52.381 0.00 0.00 0.00 4.02
120 122 6.149973 TGAGTACATTCCTTTTGAGCATTCAG 59.850 38.462 0.00 0.00 34.15 3.02
133 135 7.765695 TTGAGCATTCAGAAGGAAAATAGTT 57.234 32.000 0.00 0.00 39.39 2.24
182 184 4.564782 ATGCACCCTATGGATGATACAG 57.435 45.455 0.00 0.00 38.09 2.74
223 225 6.884280 AAACATGGCTACTTGCTAATATCC 57.116 37.500 0.00 0.00 42.39 2.59
226 228 6.546484 ACATGGCTACTTGCTAATATCCAAT 58.454 36.000 0.00 0.00 42.39 3.16
241 243 9.859427 CTAATATCCAATTCAACTTCTTGCAAA 57.141 29.630 0.00 0.00 0.00 3.68
259 261 3.122948 GCAAAATCATTCTGCAACAGCTG 59.877 43.478 13.48 13.48 36.09 4.24
278 280 7.765307 ACAGCTGGTTAATTTGACTATTCATG 58.235 34.615 19.93 0.00 0.00 3.07
280 282 7.912250 CAGCTGGTTAATTTGACTATTCATGAC 59.088 37.037 5.57 0.00 0.00 3.06
311 313 2.945315 GATGCACTCGACCTACACG 58.055 57.895 0.00 0.00 0.00 4.49
346 348 3.295973 TGACACCCAGAAAAAGGAAAGG 58.704 45.455 0.00 0.00 0.00 3.11
392 394 1.186200 TCGAACAGCTAGCAGGATGT 58.814 50.000 18.83 9.61 39.31 3.06
393 395 1.134995 TCGAACAGCTAGCAGGATGTG 60.135 52.381 18.83 7.70 39.31 3.21
394 396 1.661341 GAACAGCTAGCAGGATGTGG 58.339 55.000 18.83 0.00 39.31 4.17
395 397 1.208052 GAACAGCTAGCAGGATGTGGA 59.792 52.381 18.83 0.00 39.31 4.02
396 398 1.504912 ACAGCTAGCAGGATGTGGAT 58.495 50.000 18.83 0.00 39.31 3.41
397 399 1.140452 ACAGCTAGCAGGATGTGGATG 59.860 52.381 18.83 4.58 39.31 3.51
398 400 1.140452 CAGCTAGCAGGATGTGGATGT 59.860 52.381 18.83 0.00 39.31 3.06
399 401 1.140452 AGCTAGCAGGATGTGGATGTG 59.860 52.381 18.83 0.00 39.31 3.21
404 440 0.750546 CAGGATGTGGATGTGCCCTG 60.751 60.000 0.00 0.00 35.75 4.45
427 463 0.322546 ATGTCCAAGGTTTCGAGCCC 60.323 55.000 4.72 0.00 0.00 5.19
428 464 2.033194 GTCCAAGGTTTCGAGCCCG 61.033 63.158 4.72 0.00 37.07 6.13
429 465 2.746277 CCAAGGTTTCGAGCCCGG 60.746 66.667 0.00 0.00 36.24 5.73
430 466 3.431725 CAAGGTTTCGAGCCCGGC 61.432 66.667 0.00 0.00 36.24 6.13
431 467 4.717313 AAGGTTTCGAGCCCGGCC 62.717 66.667 5.55 0.00 36.24 6.13
477 513 1.636340 GTACATCCGTGCACGATGC 59.364 57.895 39.10 21.68 45.29 3.91
618 1221 3.119424 ACTTCTAGGAAGTAAGAGCACGC 60.119 47.826 10.68 0.00 0.00 5.34
620 1223 3.024547 TCTAGGAAGTAAGAGCACGCAT 58.975 45.455 0.00 0.00 0.00 4.73
679 1867 4.086706 AGAATTTCGTTGAGTCCAAGGT 57.913 40.909 0.00 0.00 38.78 3.50
681 1869 5.238583 AGAATTTCGTTGAGTCCAAGGTAG 58.761 41.667 0.00 0.00 38.78 3.18
682 1870 3.396260 TTTCGTTGAGTCCAAGGTAGG 57.604 47.619 0.00 0.00 38.78 3.18
683 1871 1.263356 TCGTTGAGTCCAAGGTAGGG 58.737 55.000 0.00 0.00 38.78 3.53
684 1872 0.391263 CGTTGAGTCCAAGGTAGGGC 60.391 60.000 0.00 0.00 34.47 5.19
685 1873 0.391263 GTTGAGTCCAAGGTAGGGCG 60.391 60.000 0.00 0.00 38.64 6.13
686 1874 2.180159 TTGAGTCCAAGGTAGGGCGC 62.180 60.000 0.00 0.00 38.64 6.53
687 1875 2.284699 AGTCCAAGGTAGGGCGCT 60.285 61.111 7.64 8.86 38.64 5.92
688 1876 2.187163 GTCCAAGGTAGGGCGCTC 59.813 66.667 6.54 1.48 0.00 5.03
689 1877 2.038975 TCCAAGGTAGGGCGCTCT 59.961 61.111 17.29 17.29 0.00 4.09
690 1878 2.187946 CCAAGGTAGGGCGCTCTG 59.812 66.667 23.04 2.57 0.00 3.35
691 1879 2.187946 CAAGGTAGGGCGCTCTGG 59.812 66.667 23.04 0.00 0.00 3.86
701 1889 1.890979 GCGCTCTGGCTATGCATGT 60.891 57.895 10.16 0.00 36.09 3.21
861 2258 3.345808 CGCCAGTTGGACACCACG 61.346 66.667 1.45 0.00 37.39 4.94
879 2300 2.820479 TTATTTGCCGTCCGCCCG 60.820 61.111 0.00 0.00 36.24 6.13
1035 2476 5.117584 TCTCTATCAGTCGTGTTACTCCTC 58.882 45.833 0.00 0.00 0.00 3.71
1272 2735 4.358851 TCGGTTTTGTTCATTTGCTGAAG 58.641 39.130 0.00 0.00 44.44 3.02
1273 2736 3.490526 CGGTTTTGTTCATTTGCTGAAGG 59.509 43.478 0.00 0.00 44.44 3.46
1274 2737 3.809279 GGTTTTGTTCATTTGCTGAAGGG 59.191 43.478 0.00 0.00 44.44 3.95
1275 2738 4.441792 GTTTTGTTCATTTGCTGAAGGGT 58.558 39.130 0.00 0.00 44.44 4.34
1276 2739 5.452636 GGTTTTGTTCATTTGCTGAAGGGTA 60.453 40.000 0.00 0.00 44.44 3.69
1277 2740 4.846779 TTGTTCATTTGCTGAAGGGTAC 57.153 40.909 0.00 0.00 44.44 3.34
1278 2741 3.826524 TGTTCATTTGCTGAAGGGTACA 58.173 40.909 0.00 0.00 44.44 2.90
1279 2742 3.568007 TGTTCATTTGCTGAAGGGTACAC 59.432 43.478 0.00 0.00 44.44 2.90
1280 2743 2.790433 TCATTTGCTGAAGGGTACACC 58.210 47.619 0.00 0.00 40.67 4.16
1314 2777 1.064952 GCTAACGGCCGTGCATATTTT 59.935 47.619 34.95 16.43 34.27 1.82
1315 2778 2.478879 GCTAACGGCCGTGCATATTTTT 60.479 45.455 34.95 15.59 34.27 1.94
1496 2967 2.332654 GCCCTACAGCAACAACGGG 61.333 63.158 0.00 0.00 34.79 5.28
1582 3053 4.129380 TCATGATCGATCGCCTCAATTTT 58.871 39.130 20.03 5.33 0.00 1.82
1584 3055 5.177511 TCATGATCGATCGCCTCAATTTTAC 59.822 40.000 20.03 0.00 0.00 2.01
1585 3056 4.693283 TGATCGATCGCCTCAATTTTACT 58.307 39.130 20.03 0.00 0.00 2.24
1586 3057 4.745125 TGATCGATCGCCTCAATTTTACTC 59.255 41.667 20.03 0.00 0.00 2.59
1587 3058 3.113322 TCGATCGCCTCAATTTTACTCG 58.887 45.455 11.09 0.00 0.00 4.18
1797 3890 1.376037 GGGGTTCAGCTTGACCGAG 60.376 63.158 8.72 0.00 0.00 4.63
2305 4580 0.944311 TGCTTTGAGAGTCGAACCGC 60.944 55.000 0.00 0.00 0.00 5.68
2326 4601 3.249080 GCATTTTTGCTGCACAATGAACT 59.751 39.130 26.52 3.19 38.31 3.01
2327 4602 4.260866 GCATTTTTGCTGCACAATGAACTT 60.261 37.500 26.52 0.32 38.31 2.66
2328 4603 5.437263 CATTTTTGCTGCACAATGAACTTC 58.563 37.500 21.25 0.00 38.31 3.01
2329 4604 3.797451 TTTGCTGCACAATGAACTTCA 57.203 38.095 0.00 0.00 38.31 3.02
2330 4605 3.358707 TTGCTGCACAATGAACTTCAG 57.641 42.857 0.00 0.00 31.73 3.02
2334 4609 2.295349 CTGCACAATGAACTTCAGCCTT 59.705 45.455 0.00 0.00 0.00 4.35
2337 4612 3.492011 GCACAATGAACTTCAGCCTTTTG 59.508 43.478 0.00 0.00 0.00 2.44
2338 4613 4.053295 CACAATGAACTTCAGCCTTTTGG 58.947 43.478 0.00 0.00 44.18 3.28
2339 4614 3.706086 ACAATGAACTTCAGCCTTTTGGT 59.294 39.130 0.00 0.00 42.99 3.67
2342 4624 6.127196 ACAATGAACTTCAGCCTTTTGGTTTA 60.127 34.615 0.00 0.00 42.99 2.01
2368 4650 6.827586 TTATTTATCTTTTCAGCCCGTTGT 57.172 33.333 0.00 0.00 0.00 3.32
2395 4677 6.037830 GTGCCACGTATTCCATTATTTGTAGT 59.962 38.462 0.00 0.00 0.00 2.73
2480 4926 4.034626 CACGGTGTCATGACAAAAGTTGTA 59.965 41.667 29.42 1.05 45.52 2.41
2487 4933 6.021596 GTCATGACAAAAGTTGTATAAGCCG 58.978 40.000 21.07 0.00 45.52 5.52
2506 4954 0.179169 GAGTACGGTTCTCGGCAGAC 60.179 60.000 0.00 0.00 44.45 3.51
2520 4968 1.603842 CAGACAGTAGGGCATGCCA 59.396 57.895 36.56 16.33 37.98 4.92
2546 4994 2.686106 ATGTTACCGAGCCCCCGT 60.686 61.111 0.00 0.00 0.00 5.28
2568 5016 2.480100 GACGAACTCGGCCTAGACT 58.520 57.895 11.98 0.00 42.67 3.24
2574 5022 3.128242 CGAACTCGGCCTAGACTAAAGAA 59.872 47.826 11.98 0.00 35.37 2.52
2577 5025 4.087907 ACTCGGCCTAGACTAAAGAACTT 58.912 43.478 11.98 0.00 0.00 2.66
2606 5054 2.814919 AGAACGTATGCCGAGATCCTAG 59.185 50.000 0.00 0.00 40.70 3.02
2658 5106 1.136085 CACGGCCGTTTGTAGTTGATG 60.136 52.381 32.11 9.06 0.00 3.07
2659 5107 0.446222 CGGCCGTTTGTAGTTGATGG 59.554 55.000 19.50 0.00 0.00 3.51
2660 5108 0.170339 GGCCGTTTGTAGTTGATGGC 59.830 55.000 0.00 0.00 43.22 4.40
2661 5109 0.878416 GCCGTTTGTAGTTGATGGCA 59.122 50.000 0.00 0.00 43.39 4.92
2662 5110 1.401018 GCCGTTTGTAGTTGATGGCAC 60.401 52.381 0.00 0.00 43.39 5.01
2663 5111 1.199097 CCGTTTGTAGTTGATGGCACC 59.801 52.381 0.00 0.00 0.00 5.01
2664 5112 1.136085 CGTTTGTAGTTGATGGCACCG 60.136 52.381 0.00 0.00 0.00 4.94
2665 5113 1.877443 GTTTGTAGTTGATGGCACCGT 59.123 47.619 0.00 0.00 0.00 4.83
2666 5114 1.518325 TTGTAGTTGATGGCACCGTG 58.482 50.000 0.00 0.00 0.00 4.94
2667 5115 0.682292 TGTAGTTGATGGCACCGTGA 59.318 50.000 1.65 0.00 0.00 4.35
2668 5116 1.076332 GTAGTTGATGGCACCGTGAC 58.924 55.000 1.65 0.00 0.00 3.67
2680 5128 2.335011 CGTGACGGCTCTGTGACA 59.665 61.111 0.00 0.00 0.00 3.58
2697 5145 3.059352 GACATACAGTCCACCTTTGCT 57.941 47.619 0.00 0.00 41.56 3.91
2704 5152 1.771255 AGTCCACCTTTGCTGAGACTT 59.229 47.619 0.00 0.00 30.65 3.01
2706 5154 2.952310 GTCCACCTTTGCTGAGACTTTT 59.048 45.455 0.00 0.00 0.00 2.27
2707 5155 3.381590 GTCCACCTTTGCTGAGACTTTTT 59.618 43.478 0.00 0.00 0.00 1.94
2741 5189 6.920569 AAGCATAACTTTATTACGACAGGG 57.079 37.500 0.00 0.00 33.71 4.45
2742 5190 6.229936 AGCATAACTTTATTACGACAGGGA 57.770 37.500 0.00 0.00 0.00 4.20
2743 5191 6.281405 AGCATAACTTTATTACGACAGGGAG 58.719 40.000 0.00 0.00 0.00 4.30
2744 5192 6.047231 GCATAACTTTATTACGACAGGGAGT 58.953 40.000 0.00 0.00 0.00 3.85
2745 5193 6.200475 GCATAACTTTATTACGACAGGGAGTC 59.800 42.308 0.00 0.00 44.02 3.36
2753 5201 3.965888 GACAGGGAGTCAGGCAATT 57.034 52.632 0.00 0.00 46.77 2.32
2754 5202 1.743996 GACAGGGAGTCAGGCAATTC 58.256 55.000 0.00 0.00 46.77 2.17
2755 5203 0.036010 ACAGGGAGTCAGGCAATTCG 60.036 55.000 0.00 0.00 0.00 3.34
2756 5204 1.078143 AGGGAGTCAGGCAATTCGC 60.078 57.895 0.00 0.00 41.28 4.70
2765 5213 3.680156 GCAATTCGCCCAGGACAA 58.320 55.556 0.00 0.00 32.94 3.18
2766 5214 1.212751 GCAATTCGCCCAGGACAAC 59.787 57.895 0.00 0.00 32.94 3.32
2767 5215 1.244019 GCAATTCGCCCAGGACAACT 61.244 55.000 0.00 0.00 32.94 3.16
2768 5216 1.948611 GCAATTCGCCCAGGACAACTA 60.949 52.381 0.00 0.00 32.94 2.24
2769 5217 2.643551 CAATTCGCCCAGGACAACTAT 58.356 47.619 0.00 0.00 0.00 2.12
2770 5218 2.332063 ATTCGCCCAGGACAACTATG 57.668 50.000 0.00 0.00 0.00 2.23
2771 5219 0.251916 TTCGCCCAGGACAACTATGG 59.748 55.000 0.00 0.00 0.00 2.74
2773 5221 4.986467 CCCAGGACAACTATGGGC 57.014 61.111 0.00 0.00 46.86 5.36
2774 5222 1.998530 CCCAGGACAACTATGGGCA 59.001 57.895 0.00 0.00 46.86 5.36
2775 5223 0.394352 CCCAGGACAACTATGGGCAC 60.394 60.000 0.00 0.00 46.86 5.01
2776 5224 0.327924 CCAGGACAACTATGGGCACA 59.672 55.000 0.00 0.00 0.00 4.57
2777 5225 1.679944 CCAGGACAACTATGGGCACAG 60.680 57.143 0.00 0.00 0.00 3.66
2778 5226 1.278985 CAGGACAACTATGGGCACAGA 59.721 52.381 0.00 0.00 0.00 3.41
2779 5227 2.092753 CAGGACAACTATGGGCACAGAT 60.093 50.000 0.00 0.00 0.00 2.90
2780 5228 2.092753 AGGACAACTATGGGCACAGATG 60.093 50.000 0.00 0.00 0.00 2.90
2781 5229 2.292267 GACAACTATGGGCACAGATGG 58.708 52.381 0.00 0.00 0.00 3.51
2788 5236 2.267642 GGCACAGATGGCGGTACA 59.732 61.111 0.00 0.00 42.22 2.90
2789 5237 1.153168 GGCACAGATGGCGGTACAT 60.153 57.895 0.00 0.00 42.22 2.29
2790 5238 1.160329 GGCACAGATGGCGGTACATC 61.160 60.000 0.00 6.69 45.91 3.06
2795 5243 3.386543 GATGGCGGTACATCAGCTT 57.613 52.632 9.07 0.00 45.11 3.74
2796 5244 1.221414 GATGGCGGTACATCAGCTTC 58.779 55.000 9.07 0.00 45.11 3.86
2797 5245 0.179045 ATGGCGGTACATCAGCTTCC 60.179 55.000 0.00 0.00 37.40 3.46
2798 5246 1.523938 GGCGGTACATCAGCTTCCC 60.524 63.158 0.00 0.00 37.40 3.97
2799 5247 1.220749 GCGGTACATCAGCTTCCCA 59.779 57.895 0.00 0.00 34.56 4.37
2800 5248 1.090052 GCGGTACATCAGCTTCCCAC 61.090 60.000 0.00 0.00 34.56 4.61
2801 5249 0.249120 CGGTACATCAGCTTCCCACA 59.751 55.000 0.00 0.00 0.00 4.17
2802 5250 1.338674 CGGTACATCAGCTTCCCACAA 60.339 52.381 0.00 0.00 0.00 3.33
2803 5251 2.084546 GGTACATCAGCTTCCCACAAC 58.915 52.381 0.00 0.00 0.00 3.32
2804 5252 2.552155 GGTACATCAGCTTCCCACAACA 60.552 50.000 0.00 0.00 0.00 3.33
2805 5253 2.592102 ACATCAGCTTCCCACAACAT 57.408 45.000 0.00 0.00 0.00 2.71
2806 5254 2.440409 ACATCAGCTTCCCACAACATC 58.560 47.619 0.00 0.00 0.00 3.06
2807 5255 2.224843 ACATCAGCTTCCCACAACATCA 60.225 45.455 0.00 0.00 0.00 3.07
2808 5256 2.189594 TCAGCTTCCCACAACATCAG 57.810 50.000 0.00 0.00 0.00 2.90
2809 5257 1.421268 TCAGCTTCCCACAACATCAGT 59.579 47.619 0.00 0.00 0.00 3.41
2810 5258 2.637382 TCAGCTTCCCACAACATCAGTA 59.363 45.455 0.00 0.00 0.00 2.74
2811 5259 3.005554 CAGCTTCCCACAACATCAGTAG 58.994 50.000 0.00 0.00 0.00 2.57
2812 5260 2.906389 AGCTTCCCACAACATCAGTAGA 59.094 45.455 0.00 0.00 0.00 2.59
2813 5261 3.521126 AGCTTCCCACAACATCAGTAGAT 59.479 43.478 0.00 0.00 33.87 1.98
2814 5262 4.018960 AGCTTCCCACAACATCAGTAGATT 60.019 41.667 0.00 0.00 30.20 2.40
2815 5263 5.189736 AGCTTCCCACAACATCAGTAGATTA 59.810 40.000 0.00 0.00 30.20 1.75
2816 5264 5.880332 GCTTCCCACAACATCAGTAGATTAA 59.120 40.000 0.00 0.00 30.20 1.40
2817 5265 6.183360 GCTTCCCACAACATCAGTAGATTAAC 60.183 42.308 0.00 0.00 30.20 2.01
2818 5266 6.367374 TCCCACAACATCAGTAGATTAACA 57.633 37.500 0.00 0.00 30.20 2.41
2819 5267 6.774673 TCCCACAACATCAGTAGATTAACAA 58.225 36.000 0.00 0.00 30.20 2.83
2820 5268 6.653320 TCCCACAACATCAGTAGATTAACAAC 59.347 38.462 0.00 0.00 30.20 3.32
2821 5269 6.655003 CCCACAACATCAGTAGATTAACAACT 59.345 38.462 0.00 0.00 30.20 3.16
2822 5270 7.148407 CCCACAACATCAGTAGATTAACAACTC 60.148 40.741 0.00 0.00 30.20 3.01
2823 5271 7.387673 CCACAACATCAGTAGATTAACAACTCA 59.612 37.037 0.00 0.00 30.20 3.41
2824 5272 8.939929 CACAACATCAGTAGATTAACAACTCAT 58.060 33.333 0.00 0.00 30.20 2.90
2827 5275 8.879342 ACATCAGTAGATTAACAACTCATAGC 57.121 34.615 0.00 0.00 30.20 2.97
2828 5276 7.928706 ACATCAGTAGATTAACAACTCATAGCC 59.071 37.037 0.00 0.00 30.20 3.93
2829 5277 7.418337 TCAGTAGATTAACAACTCATAGCCA 57.582 36.000 0.00 0.00 0.00 4.75
2830 5278 7.847096 TCAGTAGATTAACAACTCATAGCCAA 58.153 34.615 0.00 0.00 0.00 4.52
2831 5279 8.486210 TCAGTAGATTAACAACTCATAGCCAAT 58.514 33.333 0.00 0.00 0.00 3.16
2832 5280 8.768955 CAGTAGATTAACAACTCATAGCCAATC 58.231 37.037 0.00 0.00 0.00 2.67
2833 5281 8.709308 AGTAGATTAACAACTCATAGCCAATCT 58.291 33.333 0.00 0.00 36.01 2.40
2834 5282 9.331282 GTAGATTAACAACTCATAGCCAATCTT 57.669 33.333 0.00 0.00 34.35 2.40
2835 5283 8.814038 AGATTAACAACTCATAGCCAATCTTT 57.186 30.769 0.00 0.00 29.52 2.52
2836 5284 8.897752 AGATTAACAACTCATAGCCAATCTTTC 58.102 33.333 0.00 0.00 29.52 2.62
2837 5285 7.994425 TTAACAACTCATAGCCAATCTTTCA 57.006 32.000 0.00 0.00 0.00 2.69
2838 5286 6.899393 AACAACTCATAGCCAATCTTTCAA 57.101 33.333 0.00 0.00 0.00 2.69
2839 5287 6.899393 ACAACTCATAGCCAATCTTTCAAA 57.101 33.333 0.00 0.00 0.00 2.69
2840 5288 6.917533 ACAACTCATAGCCAATCTTTCAAAG 58.082 36.000 0.00 0.00 0.00 2.77
2841 5289 6.491403 ACAACTCATAGCCAATCTTTCAAAGT 59.509 34.615 0.00 0.00 0.00 2.66
2842 5290 7.014615 ACAACTCATAGCCAATCTTTCAAAGTT 59.985 33.333 0.00 0.00 0.00 2.66
2843 5291 7.150783 ACTCATAGCCAATCTTTCAAAGTTC 57.849 36.000 0.00 0.00 0.00 3.01
2844 5292 6.716628 ACTCATAGCCAATCTTTCAAAGTTCA 59.283 34.615 0.00 0.00 0.00 3.18
2845 5293 7.395489 ACTCATAGCCAATCTTTCAAAGTTCAT 59.605 33.333 0.00 0.00 0.00 2.57
2846 5294 7.541162 TCATAGCCAATCTTTCAAAGTTCATG 58.459 34.615 0.00 0.00 0.00 3.07
2847 5295 7.394077 TCATAGCCAATCTTTCAAAGTTCATGA 59.606 33.333 0.00 0.00 0.00 3.07
2848 5296 6.022163 AGCCAATCTTTCAAAGTTCATGAG 57.978 37.500 0.00 0.00 0.00 2.90
2853 5301 4.717877 TCTTTCAAAGTTCATGAGCTCCA 58.282 39.130 12.88 0.00 0.00 3.86
2874 5322 5.291614 TCCACGTACTCGGCAAAATATTTAC 59.708 40.000 0.01 0.00 41.85 2.01
2882 5330 8.825667 ACTCGGCAAAATATTTACAAAAACAT 57.174 26.923 0.01 0.00 0.00 2.71
2908 5356 6.548441 TTTCCTCACAGTAAATGTTTACCG 57.452 37.500 11.03 5.02 43.03 4.02
2910 5358 5.475719 TCCTCACAGTAAATGTTTACCGAG 58.524 41.667 11.03 12.98 43.03 4.63
2915 5363 3.749088 CAGTAAATGTTTACCGAGCACCA 59.251 43.478 11.03 0.00 43.03 4.17
2921 5369 2.271800 GTTTACCGAGCACCATCTCTG 58.728 52.381 0.00 0.00 0.00 3.35
2922 5370 1.847328 TTACCGAGCACCATCTCTGA 58.153 50.000 0.00 0.00 0.00 3.27
2930 5378 3.888323 GAGCACCATCTCTGAGATACTCA 59.112 47.826 19.16 0.00 38.25 3.41
2950 5398 4.560128 TCAGTAGAGTTGTTCAGATGTGC 58.440 43.478 0.00 0.00 0.00 4.57
2951 5399 4.281941 TCAGTAGAGTTGTTCAGATGTGCT 59.718 41.667 0.00 0.00 0.00 4.40
2952 5400 4.624882 CAGTAGAGTTGTTCAGATGTGCTC 59.375 45.833 0.00 0.00 0.00 4.26
2953 5401 3.758755 AGAGTTGTTCAGATGTGCTCA 57.241 42.857 0.00 0.00 0.00 4.26
2954 5402 4.077300 AGAGTTGTTCAGATGTGCTCAA 57.923 40.909 0.00 0.00 0.00 3.02
2955 5403 3.812053 AGAGTTGTTCAGATGTGCTCAAC 59.188 43.478 16.21 16.21 37.30 3.18
2956 5404 3.812053 GAGTTGTTCAGATGTGCTCAACT 59.188 43.478 22.18 22.18 43.37 3.16
2957 5405 3.812053 AGTTGTTCAGATGTGCTCAACTC 59.188 43.478 18.91 4.67 40.18 3.01
2958 5406 3.758755 TGTTCAGATGTGCTCAACTCT 57.241 42.857 0.00 0.00 0.00 3.24
2959 5407 4.077300 TGTTCAGATGTGCTCAACTCTT 57.923 40.909 0.00 0.00 0.00 2.85
2960 5408 3.811497 TGTTCAGATGTGCTCAACTCTTG 59.189 43.478 0.00 0.00 0.00 3.02
2961 5409 2.420642 TCAGATGTGCTCAACTCTTGC 58.579 47.619 0.00 0.00 0.00 4.01
2962 5410 1.467734 CAGATGTGCTCAACTCTTGCC 59.532 52.381 0.00 0.00 0.00 4.52
2963 5411 1.072806 AGATGTGCTCAACTCTTGCCA 59.927 47.619 0.00 0.00 0.00 4.92
2964 5412 1.198637 GATGTGCTCAACTCTTGCCAC 59.801 52.381 0.00 0.00 35.00 5.01
2965 5413 0.107263 TGTGCTCAACTCTTGCCACA 60.107 50.000 0.00 0.00 38.96 4.17
2969 5417 1.198637 GCTCAACTCTTGCCACATGTC 59.801 52.381 0.00 0.00 0.00 3.06
2982 5430 3.599343 CCACATGTCATCTCTTTCCGAA 58.401 45.455 0.00 0.00 0.00 4.30
2987 5435 3.525537 TGTCATCTCTTTCCGAATGCTC 58.474 45.455 0.00 0.00 0.00 4.26
2996 5444 2.169789 CCGAATGCTCCAGTGCTCG 61.170 63.158 0.00 0.00 32.73 5.03
2997 5445 2.169789 CGAATGCTCCAGTGCTCGG 61.170 63.158 0.00 0.00 30.43 4.63
3006 5454 0.036010 CCAGTGCTCGGGAAAGATGT 60.036 55.000 0.00 0.00 0.00 3.06
3007 5455 1.081892 CAGTGCTCGGGAAAGATGTG 58.918 55.000 0.00 0.00 0.00 3.21
3013 5461 2.814336 GCTCGGGAAAGATGTGAAGTTT 59.186 45.455 0.00 0.00 0.00 2.66
3027 5475 2.025898 GAAGTTTCCAACGGAACCCAA 58.974 47.619 0.00 0.00 41.87 4.12
3030 5478 1.448922 TTTCCAACGGAACCCAAGCG 61.449 55.000 0.00 0.00 41.87 4.68
3063 5511 2.866762 GAGATGTGTACTCGGCAAATCC 59.133 50.000 0.00 0.00 32.43 3.01
3094 5542 1.194772 GAGTGCAGTACTCGGCAAAAC 59.805 52.381 9.29 0.00 45.77 2.43
3097 5545 1.269673 TGCAGTACTCGGCAAAACGTA 60.270 47.619 5.46 0.00 41.28 3.57
3099 5547 1.723003 CAGTACTCGGCAAAACGTACC 59.277 52.381 0.00 0.00 34.30 3.34
3101 5549 1.723003 GTACTCGGCAAAACGTACCAG 59.277 52.381 0.00 0.00 34.94 4.00
3106 5554 0.596082 GGCAAAACGTACCAGCACAT 59.404 50.000 0.00 0.00 0.00 3.21
3110 5558 1.519408 AAACGTACCAGCACATCACC 58.481 50.000 0.00 0.00 0.00 4.02
3114 5562 1.880221 CGTACCAGCACATCACCCAAA 60.880 52.381 0.00 0.00 0.00 3.28
3118 5566 4.518278 ACCAGCACATCACCCAAATATA 57.482 40.909 0.00 0.00 0.00 0.86
3138 5586 8.783660 AATATATGTTCTCTGTCCTAAGTCCA 57.216 34.615 0.00 0.00 0.00 4.02
3146 5594 4.517285 TCTGTCCTAAGTCCATGCAATTC 58.483 43.478 0.00 0.00 0.00 2.17
3148 5596 4.661222 TGTCCTAAGTCCATGCAATTCAA 58.339 39.130 0.00 0.00 0.00 2.69
3161 5611 7.042187 TCCATGCAATTCAAAAACAACACATAC 60.042 33.333 0.00 0.00 0.00 2.39
3166 5616 8.121708 GCAATTCAAAAACAACACATACATTGT 58.878 29.630 0.00 0.00 40.76 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 89 7.918076 TCAAAAGGAATGTACTCATACTTCCT 58.082 34.615 10.13 10.13 43.47 3.36
133 135 9.925268 GAAGTCAACGAAATTCTAAAACTACAA 57.075 29.630 0.00 0.00 0.00 2.41
182 184 2.276472 TTTGCTAAATCATGCACGGC 57.724 45.000 0.00 0.00 39.05 5.68
223 225 8.770828 AGAATGATTTTGCAAGAAGTTGAATTG 58.229 29.630 0.00 0.00 35.46 2.32
226 228 6.201425 GCAGAATGATTTTGCAAGAAGTTGAA 59.799 34.615 14.86 0.00 39.69 2.69
241 243 2.522185 ACCAGCTGTTGCAGAATGATT 58.478 42.857 13.81 0.00 39.69 2.57
278 280 1.606668 TGCATCGTCCAAGGTTTTGTC 59.393 47.619 0.00 0.00 32.21 3.18
280 282 1.608590 AGTGCATCGTCCAAGGTTTTG 59.391 47.619 0.00 0.00 0.00 2.44
311 313 2.290641 GGGTGTCATGATGCCGTATTTC 59.709 50.000 0.00 0.00 0.00 2.17
346 348 4.218417 TGGTTGCTGCTCTTAATCTTTTCC 59.782 41.667 0.00 0.00 0.00 3.13
392 394 1.307309 CATTCCCAGGGCACATCCA 59.693 57.895 0.00 0.00 36.21 3.41
393 395 0.753111 GACATTCCCAGGGCACATCC 60.753 60.000 0.00 0.00 0.00 3.51
394 396 0.753111 GGACATTCCCAGGGCACATC 60.753 60.000 0.00 0.00 0.00 3.06
395 397 1.307647 GGACATTCCCAGGGCACAT 59.692 57.895 0.00 0.00 0.00 3.21
396 398 1.724148 TTGGACATTCCCAGGGCACA 61.724 55.000 0.00 0.00 37.53 4.57
397 399 0.967380 CTTGGACATTCCCAGGGCAC 60.967 60.000 0.00 0.00 37.53 5.01
398 400 1.383799 CTTGGACATTCCCAGGGCA 59.616 57.895 0.00 0.00 37.53 5.36
399 401 1.380380 CCTTGGACATTCCCAGGGC 60.380 63.158 0.00 0.00 43.76 5.19
404 440 2.084546 CTCGAAACCTTGGACATTCCC 58.915 52.381 0.00 0.00 35.03 3.97
428 464 4.228567 GTAGCTGGAGAGGCGGCC 62.229 72.222 12.11 12.11 34.52 6.13
429 465 1.801309 CTAGTAGCTGGAGAGGCGGC 61.801 65.000 0.00 0.00 34.52 6.53
430 466 1.801309 GCTAGTAGCTGGAGAGGCGG 61.801 65.000 15.16 0.00 38.45 6.13
431 467 1.657556 GCTAGTAGCTGGAGAGGCG 59.342 63.158 15.16 0.00 38.45 5.52
450 486 2.099427 TGCACGGATGTACGCATACTAA 59.901 45.455 0.00 0.00 33.76 2.24
451 487 1.677052 TGCACGGATGTACGCATACTA 59.323 47.619 0.00 0.00 33.76 1.82
511 570 9.197694 CCAAGTCAACTTCTCTATATTAATCCG 57.802 37.037 0.00 0.00 33.11 4.18
671 1859 2.187163 GAGCGCCCTACCTTGGAC 59.813 66.667 2.29 0.00 0.00 4.02
673 1861 2.187946 CAGAGCGCCCTACCTTGG 59.812 66.667 2.29 0.00 0.00 3.61
679 1867 2.872388 GCATAGCCAGAGCGCCCTA 61.872 63.158 2.29 0.00 46.67 3.53
681 1869 3.839353 ATGCATAGCCAGAGCGCCC 62.839 63.158 2.29 0.00 46.67 6.13
682 1870 2.281345 ATGCATAGCCAGAGCGCC 60.281 61.111 2.29 0.00 46.67 6.53
683 1871 1.442526 AACATGCATAGCCAGAGCGC 61.443 55.000 0.00 0.00 46.67 5.92
684 1872 1.528586 GTAACATGCATAGCCAGAGCG 59.471 52.381 0.00 0.00 46.67 5.03
685 1873 2.564771 TGTAACATGCATAGCCAGAGC 58.435 47.619 0.00 0.00 40.32 4.09
686 1874 3.750130 GGATGTAACATGCATAGCCAGAG 59.250 47.826 0.00 0.00 0.00 3.35
687 1875 3.743521 GGATGTAACATGCATAGCCAGA 58.256 45.455 0.00 0.00 0.00 3.86
688 1876 2.481568 CGGATGTAACATGCATAGCCAG 59.518 50.000 0.00 0.00 0.00 4.85
689 1877 2.158827 ACGGATGTAACATGCATAGCCA 60.159 45.455 0.00 0.00 0.00 4.75
690 1878 2.224079 CACGGATGTAACATGCATAGCC 59.776 50.000 0.00 0.00 0.00 3.93
691 1879 2.349817 GCACGGATGTAACATGCATAGC 60.350 50.000 0.00 0.00 36.30 2.97
701 1889 3.696548 TGCCAAATAATGCACGGATGTAA 59.303 39.130 0.00 0.00 31.31 2.41
780 2061 4.410555 CCTTTTTCTAGGCTGTCCTCCTAT 59.589 45.833 0.00 0.00 43.06 2.57
781 2062 3.775316 CCTTTTTCTAGGCTGTCCTCCTA 59.225 47.826 0.00 0.00 43.06 2.94
782 2063 2.573915 CCTTTTTCTAGGCTGTCCTCCT 59.426 50.000 0.00 0.00 43.06 3.69
819 2207 0.245266 TGTGCTAGCCGTTCGATCAA 59.755 50.000 13.29 0.00 0.00 2.57
820 2208 0.459899 ATGTGCTAGCCGTTCGATCA 59.540 50.000 13.29 0.00 0.00 2.92
861 2258 2.795973 GGGCGGACGGCAAATAAC 59.204 61.111 19.72 0.00 46.16 1.89
879 2300 0.544120 TGGCCATTCCTGGGGTTTTC 60.544 55.000 0.00 0.00 43.36 2.29
1273 2736 4.558871 GCCACTAGCTAGGTAGGTGTACC 61.559 56.522 27.89 12.74 43.29 3.34
1274 2737 2.622470 GCCACTAGCTAGGTAGGTGTAC 59.378 54.545 27.89 15.36 38.99 2.90
1275 2738 2.941480 GCCACTAGCTAGGTAGGTGTA 58.059 52.381 27.89 0.00 38.99 2.90
1276 2739 1.777941 GCCACTAGCTAGGTAGGTGT 58.222 55.000 27.89 9.73 38.99 4.16
1314 2777 3.927854 TGTACGTAGCCAAGCAACATAA 58.072 40.909 0.00 0.00 0.00 1.90
1315 2778 3.596310 TGTACGTAGCCAAGCAACATA 57.404 42.857 0.00 0.00 0.00 2.29
1432 2903 4.436050 CCTTCTTGATTTGTTCGATGACCG 60.436 45.833 0.00 0.00 40.25 4.79
1584 3055 1.080772 TCTACTTGGCACACGCGAG 60.081 57.895 15.93 7.88 39.29 5.03
1585 3056 1.372499 GTCTACTTGGCACACGCGA 60.372 57.895 15.93 0.00 39.29 5.87
1586 3057 2.380410 GGTCTACTTGGCACACGCG 61.380 63.158 3.53 3.53 39.29 6.01
1587 3058 2.380410 CGGTCTACTTGGCACACGC 61.380 63.158 0.00 0.00 39.29 5.34
2305 4580 5.006844 TGAAGTTCATTGTGCAGCAAAAATG 59.993 36.000 19.56 19.56 40.91 2.32
2342 4624 8.311109 ACAACGGGCTGAAAAGATAAATAAAAT 58.689 29.630 0.00 0.00 0.00 1.82
2351 4633 1.247567 CCACAACGGGCTGAAAAGAT 58.752 50.000 0.00 0.00 0.00 2.40
2352 4634 0.106918 ACCACAACGGGCTGAAAAGA 60.107 50.000 0.00 0.00 40.22 2.52
2354 4636 2.010582 GCACCACAACGGGCTGAAAA 62.011 55.000 0.00 0.00 40.22 2.29
2364 4646 0.519961 GGAATACGTGGCACCACAAC 59.480 55.000 19.38 1.26 46.47 3.32
2368 4650 3.569194 ATAATGGAATACGTGGCACCA 57.431 42.857 12.86 3.03 35.09 4.17
2419 4701 7.748677 AGAAGAATGTTTGGGATCCAATTTTT 58.251 30.769 15.23 6.48 43.55 1.94
2420 4702 7.320384 AGAAGAATGTTTGGGATCCAATTTT 57.680 32.000 15.23 0.00 43.55 1.82
2421 4703 6.940430 AGAAGAATGTTTGGGATCCAATTT 57.060 33.333 15.23 0.00 43.55 1.82
2436 4720 9.273016 ACCGTGTTTCCATAATATAGAAGAATG 57.727 33.333 0.00 0.00 0.00 2.67
2449 4733 3.244249 TGTCATGACACCGTGTTTCCATA 60.244 43.478 24.56 0.00 36.21 2.74
2450 4734 2.151202 GTCATGACACCGTGTTTCCAT 58.849 47.619 21.07 2.14 0.00 3.41
2454 4900 3.442273 ACTTTTGTCATGACACCGTGTTT 59.558 39.130 27.88 6.36 41.67 2.83
2462 4908 6.348132 CGGCTTATACAACTTTTGTCATGACA 60.348 38.462 24.56 24.56 44.12 3.58
2463 4909 6.021596 CGGCTTATACAACTTTTGTCATGAC 58.978 40.000 19.27 19.27 44.12 3.06
2467 4913 5.302360 ACTCGGCTTATACAACTTTTGTCA 58.698 37.500 0.00 0.00 44.12 3.58
2487 4933 0.179169 GTCTGCCGAGAACCGTACTC 60.179 60.000 0.00 0.00 36.31 2.59
2506 4954 2.156917 CACATATGGCATGCCCTACTG 58.843 52.381 33.44 24.79 34.56 2.74
2520 4968 3.006967 GGGCTCGGTAACATCTCACATAT 59.993 47.826 0.00 0.00 0.00 1.78
2546 4994 1.001764 TAGGCCGAGTTCGTCCAGA 60.002 57.895 4.32 0.00 40.28 3.86
2551 4999 2.119801 TTAGTCTAGGCCGAGTTCGT 57.880 50.000 13.04 0.00 37.74 3.85
2552 5000 2.681848 TCTTTAGTCTAGGCCGAGTTCG 59.318 50.000 13.04 0.00 39.44 3.95
2558 5006 3.522553 CCAAGTTCTTTAGTCTAGGCCG 58.477 50.000 0.00 0.00 0.00 6.13
2568 5016 5.362263 ACGTTCTGTAAGCCAAGTTCTTTA 58.638 37.500 0.00 0.00 0.00 1.85
2574 5022 3.000727 GCATACGTTCTGTAAGCCAAGT 58.999 45.455 0.00 0.00 40.90 3.16
2640 5088 0.446222 CCATCAACTACAAACGGCCG 59.554 55.000 26.86 26.86 0.00 6.13
2645 5093 1.877443 ACGGTGCCATCAACTACAAAC 59.123 47.619 0.00 0.00 0.00 2.93
2650 5098 0.389296 CGTCACGGTGCCATCAACTA 60.389 55.000 2.51 0.00 0.00 2.24
2663 5111 0.170339 TATGTCACAGAGCCGTCACG 59.830 55.000 0.00 0.00 0.00 4.35
2664 5112 1.067846 TGTATGTCACAGAGCCGTCAC 60.068 52.381 0.00 0.00 31.89 3.67
2665 5113 1.253100 TGTATGTCACAGAGCCGTCA 58.747 50.000 0.00 0.00 31.89 4.35
2680 5128 2.906389 TCTCAGCAAAGGTGGACTGTAT 59.094 45.455 0.00 0.00 0.00 2.29
2685 5133 2.262423 AAGTCTCAGCAAAGGTGGAC 57.738 50.000 8.67 8.67 34.22 4.02
2718 5166 6.646267 TCCCTGTCGTAATAAAGTTATGCTT 58.354 36.000 0.00 0.00 39.52 3.91
2719 5167 6.127140 ACTCCCTGTCGTAATAAAGTTATGCT 60.127 38.462 0.00 0.00 0.00 3.79
2720 5168 6.047231 ACTCCCTGTCGTAATAAAGTTATGC 58.953 40.000 0.00 0.00 0.00 3.14
2721 5169 7.695869 GACTCCCTGTCGTAATAAAGTTATG 57.304 40.000 0.00 0.00 35.81 1.90
2735 5183 1.743996 GAATTGCCTGACTCCCTGTC 58.256 55.000 0.00 0.00 45.54 3.51
2736 5184 0.036010 CGAATTGCCTGACTCCCTGT 60.036 55.000 0.00 0.00 0.00 4.00
2737 5185 1.372087 GCGAATTGCCTGACTCCCTG 61.372 60.000 0.00 0.00 37.76 4.45
2738 5186 1.078143 GCGAATTGCCTGACTCCCT 60.078 57.895 0.00 0.00 37.76 4.20
2739 5187 3.502572 GCGAATTGCCTGACTCCC 58.497 61.111 0.00 0.00 37.76 4.30
2748 5196 1.212751 GTTGTCCTGGGCGAATTGC 59.787 57.895 0.00 0.00 45.38 3.56
2749 5197 2.107950 TAGTTGTCCTGGGCGAATTG 57.892 50.000 0.00 0.00 0.00 2.32
2750 5198 2.643551 CATAGTTGTCCTGGGCGAATT 58.356 47.619 0.00 0.00 0.00 2.17
2751 5199 1.134098 CCATAGTTGTCCTGGGCGAAT 60.134 52.381 0.00 0.00 0.00 3.34
2752 5200 0.251916 CCATAGTTGTCCTGGGCGAA 59.748 55.000 0.00 0.00 0.00 4.70
2753 5201 1.622607 CCCATAGTTGTCCTGGGCGA 61.623 60.000 0.00 0.00 43.02 5.54
2754 5202 1.153168 CCCATAGTTGTCCTGGGCG 60.153 63.158 0.00 0.00 43.02 6.13
2755 5203 4.986467 CCCATAGTTGTCCTGGGC 57.014 61.111 0.00 0.00 43.02 5.36
2757 5205 0.327924 TGTGCCCATAGTTGTCCTGG 59.672 55.000 0.00 0.00 0.00 4.45
2758 5206 1.278985 TCTGTGCCCATAGTTGTCCTG 59.721 52.381 0.00 0.00 0.00 3.86
2759 5207 1.656587 TCTGTGCCCATAGTTGTCCT 58.343 50.000 0.00 0.00 0.00 3.85
2760 5208 2.292267 CATCTGTGCCCATAGTTGTCC 58.708 52.381 0.00 0.00 0.00 4.02
2761 5209 2.292267 CCATCTGTGCCCATAGTTGTC 58.708 52.381 3.51 0.00 0.00 3.18
2762 5210 1.683011 GCCATCTGTGCCCATAGTTGT 60.683 52.381 3.51 0.00 0.00 3.32
2763 5211 1.027357 GCCATCTGTGCCCATAGTTG 58.973 55.000 0.00 0.00 0.00 3.16
2764 5212 0.464373 CGCCATCTGTGCCCATAGTT 60.464 55.000 0.00 0.00 0.00 2.24
2765 5213 1.146930 CGCCATCTGTGCCCATAGT 59.853 57.895 0.00 0.00 0.00 2.12
2766 5214 1.598962 CCGCCATCTGTGCCCATAG 60.599 63.158 0.00 0.00 0.00 2.23
2767 5215 1.051556 TACCGCCATCTGTGCCCATA 61.052 55.000 0.00 0.00 0.00 2.74
2768 5216 2.374525 TACCGCCATCTGTGCCCAT 61.375 57.895 0.00 0.00 0.00 4.00
2769 5217 3.006133 TACCGCCATCTGTGCCCA 61.006 61.111 0.00 0.00 0.00 5.36
2770 5218 2.513897 GTACCGCCATCTGTGCCC 60.514 66.667 0.00 0.00 0.00 5.36
2771 5219 1.153168 ATGTACCGCCATCTGTGCC 60.153 57.895 0.00 0.00 0.00 5.01
2772 5220 0.461870 TGATGTACCGCCATCTGTGC 60.462 55.000 8.70 0.00 41.47 4.57
2773 5221 1.575244 CTGATGTACCGCCATCTGTG 58.425 55.000 8.70 0.00 41.47 3.66
2774 5222 0.179073 GCTGATGTACCGCCATCTGT 60.179 55.000 12.75 0.00 41.47 3.41
2775 5223 0.105593 AGCTGATGTACCGCCATCTG 59.894 55.000 8.70 8.93 41.47 2.90
2776 5224 0.833287 AAGCTGATGTACCGCCATCT 59.167 50.000 0.00 0.00 41.47 2.90
2777 5225 1.221414 GAAGCTGATGTACCGCCATC 58.779 55.000 0.00 0.00 41.32 3.51
2778 5226 0.179045 GGAAGCTGATGTACCGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
2779 5227 1.220749 GGAAGCTGATGTACCGCCA 59.779 57.895 0.00 0.00 0.00 5.69
2780 5228 1.523938 GGGAAGCTGATGTACCGCC 60.524 63.158 0.00 0.00 0.00 6.13
2781 5229 1.090052 GTGGGAAGCTGATGTACCGC 61.090 60.000 0.00 0.00 0.00 5.68
2782 5230 0.249120 TGTGGGAAGCTGATGTACCG 59.751 55.000 0.00 0.00 0.00 4.02
2783 5231 2.084546 GTTGTGGGAAGCTGATGTACC 58.915 52.381 0.00 0.00 0.00 3.34
2784 5232 2.778299 TGTTGTGGGAAGCTGATGTAC 58.222 47.619 0.00 0.00 0.00 2.90
2785 5233 3.008923 TGATGTTGTGGGAAGCTGATGTA 59.991 43.478 0.00 0.00 0.00 2.29
2786 5234 2.224843 TGATGTTGTGGGAAGCTGATGT 60.225 45.455 0.00 0.00 0.00 3.06
2787 5235 2.422479 CTGATGTTGTGGGAAGCTGATG 59.578 50.000 0.00 0.00 0.00 3.07
2788 5236 2.040813 ACTGATGTTGTGGGAAGCTGAT 59.959 45.455 0.00 0.00 0.00 2.90
2789 5237 1.421268 ACTGATGTTGTGGGAAGCTGA 59.579 47.619 0.00 0.00 0.00 4.26
2790 5238 1.901591 ACTGATGTTGTGGGAAGCTG 58.098 50.000 0.00 0.00 0.00 4.24
2791 5239 2.906389 TCTACTGATGTTGTGGGAAGCT 59.094 45.455 0.00 0.00 0.00 3.74
2792 5240 3.334583 TCTACTGATGTTGTGGGAAGC 57.665 47.619 0.00 0.00 0.00 3.86
2793 5241 6.878923 TGTTAATCTACTGATGTTGTGGGAAG 59.121 38.462 0.00 0.00 32.44 3.46
2794 5242 6.774673 TGTTAATCTACTGATGTTGTGGGAA 58.225 36.000 0.00 0.00 32.44 3.97
2795 5243 6.367374 TGTTAATCTACTGATGTTGTGGGA 57.633 37.500 0.00 0.00 32.44 4.37
2796 5244 6.655003 AGTTGTTAATCTACTGATGTTGTGGG 59.345 38.462 0.00 0.00 31.55 4.61
2797 5245 7.387673 TGAGTTGTTAATCTACTGATGTTGTGG 59.612 37.037 0.00 0.00 32.78 4.17
2798 5246 8.310406 TGAGTTGTTAATCTACTGATGTTGTG 57.690 34.615 0.00 0.00 32.78 3.33
2801 5249 9.319143 GCTATGAGTTGTTAATCTACTGATGTT 57.681 33.333 0.00 0.00 32.78 2.71
2802 5250 7.928706 GGCTATGAGTTGTTAATCTACTGATGT 59.071 37.037 0.00 0.00 32.78 3.06
2803 5251 7.928167 TGGCTATGAGTTGTTAATCTACTGATG 59.072 37.037 0.00 0.00 32.78 3.07
2804 5252 8.023021 TGGCTATGAGTTGTTAATCTACTGAT 57.977 34.615 0.00 0.00 32.78 2.90
2805 5253 7.418337 TGGCTATGAGTTGTTAATCTACTGA 57.582 36.000 0.00 0.00 32.78 3.41
2806 5254 8.668510 ATTGGCTATGAGTTGTTAATCTACTG 57.331 34.615 0.00 0.00 32.78 2.74
2807 5255 8.709308 AGATTGGCTATGAGTTGTTAATCTACT 58.291 33.333 0.00 0.00 33.34 2.57
2808 5256 8.894768 AGATTGGCTATGAGTTGTTAATCTAC 57.105 34.615 0.00 0.00 33.34 2.59
2809 5257 9.905713 AAAGATTGGCTATGAGTTGTTAATCTA 57.094 29.630 0.00 0.00 33.81 1.98
2810 5258 8.814038 AAAGATTGGCTATGAGTTGTTAATCT 57.186 30.769 0.00 0.00 35.75 2.40
2811 5259 8.677300 TGAAAGATTGGCTATGAGTTGTTAATC 58.323 33.333 0.00 0.00 0.00 1.75
2812 5260 8.579850 TGAAAGATTGGCTATGAGTTGTTAAT 57.420 30.769 0.00 0.00 0.00 1.40
2813 5261 7.994425 TGAAAGATTGGCTATGAGTTGTTAA 57.006 32.000 0.00 0.00 0.00 2.01
2814 5262 7.994425 TTGAAAGATTGGCTATGAGTTGTTA 57.006 32.000 0.00 0.00 0.00 2.41
2815 5263 6.899393 TTGAAAGATTGGCTATGAGTTGTT 57.101 33.333 0.00 0.00 0.00 2.83
2816 5264 6.491403 ACTTTGAAAGATTGGCTATGAGTTGT 59.509 34.615 12.53 0.00 0.00 3.32
2817 5265 6.917533 ACTTTGAAAGATTGGCTATGAGTTG 58.082 36.000 12.53 0.00 0.00 3.16
2818 5266 7.231317 TGAACTTTGAAAGATTGGCTATGAGTT 59.769 33.333 12.53 0.00 0.00 3.01
2819 5267 6.716628 TGAACTTTGAAAGATTGGCTATGAGT 59.283 34.615 12.53 0.00 0.00 3.41
2820 5268 7.149569 TGAACTTTGAAAGATTGGCTATGAG 57.850 36.000 12.53 0.00 0.00 2.90
2821 5269 7.394077 TCATGAACTTTGAAAGATTGGCTATGA 59.606 33.333 12.53 8.31 0.00 2.15
2822 5270 7.541162 TCATGAACTTTGAAAGATTGGCTATG 58.459 34.615 12.53 6.39 0.00 2.23
2823 5271 7.630082 GCTCATGAACTTTGAAAGATTGGCTAT 60.630 37.037 12.53 0.00 0.00 2.97
2824 5272 6.349611 GCTCATGAACTTTGAAAGATTGGCTA 60.350 38.462 12.53 0.00 0.00 3.93
2825 5273 5.566230 GCTCATGAACTTTGAAAGATTGGCT 60.566 40.000 12.53 0.00 0.00 4.75
2826 5274 4.624452 GCTCATGAACTTTGAAAGATTGGC 59.376 41.667 12.53 3.17 0.00 4.52
2827 5275 6.022163 AGCTCATGAACTTTGAAAGATTGG 57.978 37.500 12.53 0.00 0.00 3.16
2828 5276 6.091437 GGAGCTCATGAACTTTGAAAGATTG 58.909 40.000 17.19 3.80 0.00 2.67
2829 5277 5.771666 TGGAGCTCATGAACTTTGAAAGATT 59.228 36.000 17.19 2.35 0.00 2.40
2830 5278 5.182760 GTGGAGCTCATGAACTTTGAAAGAT 59.817 40.000 17.19 0.00 0.00 2.40
2831 5279 4.516698 GTGGAGCTCATGAACTTTGAAAGA 59.483 41.667 17.19 0.00 0.00 2.52
2832 5280 4.612259 CGTGGAGCTCATGAACTTTGAAAG 60.612 45.833 17.19 2.89 34.35 2.62
2833 5281 3.250762 CGTGGAGCTCATGAACTTTGAAA 59.749 43.478 17.19 0.00 34.35 2.69
2834 5282 2.807967 CGTGGAGCTCATGAACTTTGAA 59.192 45.455 17.19 0.00 34.35 2.69
2835 5283 2.224281 ACGTGGAGCTCATGAACTTTGA 60.224 45.455 17.19 0.00 36.29 2.69
2836 5284 2.146342 ACGTGGAGCTCATGAACTTTG 58.854 47.619 17.19 0.00 36.29 2.77
2837 5285 2.550830 ACGTGGAGCTCATGAACTTT 57.449 45.000 17.19 0.00 36.29 2.66
2838 5286 2.563179 AGTACGTGGAGCTCATGAACTT 59.437 45.455 17.19 4.39 36.29 2.66
2839 5287 2.164624 GAGTACGTGGAGCTCATGAACT 59.835 50.000 17.19 11.45 36.29 3.01
2840 5288 2.531206 GAGTACGTGGAGCTCATGAAC 58.469 52.381 17.19 7.01 36.29 3.18
2841 5289 1.132453 CGAGTACGTGGAGCTCATGAA 59.868 52.381 17.19 0.00 36.29 2.57
2842 5290 0.733150 CGAGTACGTGGAGCTCATGA 59.267 55.000 17.19 0.00 36.29 3.07
2843 5291 0.248661 CCGAGTACGTGGAGCTCATG 60.249 60.000 17.19 9.67 37.88 3.07
2844 5292 2.005960 GCCGAGTACGTGGAGCTCAT 62.006 60.000 17.19 0.00 37.88 2.90
2845 5293 2.697761 GCCGAGTACGTGGAGCTCA 61.698 63.158 17.19 0.00 37.88 4.26
2846 5294 2.102553 GCCGAGTACGTGGAGCTC 59.897 66.667 4.71 4.71 37.88 4.09
2847 5295 1.812686 TTTGCCGAGTACGTGGAGCT 61.813 55.000 10.24 0.00 37.88 4.09
2848 5296 0.947180 TTTTGCCGAGTACGTGGAGC 60.947 55.000 10.24 0.00 37.88 4.70
2853 5301 6.724694 TTGTAAATATTTTGCCGAGTACGT 57.275 33.333 5.91 0.00 37.88 3.57
2885 5333 6.289834 TCGGTAAACATTTACTGTGAGGAAA 58.710 36.000 18.43 0.00 45.68 3.13
2887 5335 5.471556 TCGGTAAACATTTACTGTGAGGA 57.528 39.130 18.43 1.82 45.68 3.71
2888 5336 4.092968 GCTCGGTAAACATTTACTGTGAGG 59.907 45.833 21.29 12.67 45.68 3.86
2894 5342 4.010667 TGGTGCTCGGTAAACATTTACT 57.989 40.909 12.90 0.00 42.00 2.24
2902 5350 2.166459 CTCAGAGATGGTGCTCGGTAAA 59.834 50.000 0.00 0.00 39.87 2.01
2908 5356 3.888323 TGAGTATCTCAGAGATGGTGCTC 59.112 47.826 21.58 19.96 35.39 4.26
2930 5378 4.281941 TGAGCACATCTGAACAACTCTACT 59.718 41.667 0.00 0.00 0.00 2.57
2932 5380 4.871933 TGAGCACATCTGAACAACTCTA 57.128 40.909 0.00 0.00 0.00 2.43
2940 5388 2.810274 GCAAGAGTTGAGCACATCTGAA 59.190 45.455 0.00 0.00 0.00 3.02
2943 5391 1.072806 TGGCAAGAGTTGAGCACATCT 59.927 47.619 0.00 0.00 0.00 2.90
2945 5393 1.242076 GTGGCAAGAGTTGAGCACAT 58.758 50.000 0.00 0.00 0.00 3.21
2950 5398 2.497138 TGACATGTGGCAAGAGTTGAG 58.503 47.619 1.15 0.00 0.00 3.02
2951 5399 2.636647 TGACATGTGGCAAGAGTTGA 57.363 45.000 1.15 0.00 0.00 3.18
2952 5400 3.079578 AGATGACATGTGGCAAGAGTTG 58.920 45.455 1.15 0.00 36.16 3.16
2953 5401 3.008813 AGAGATGACATGTGGCAAGAGTT 59.991 43.478 1.15 0.00 36.16 3.01
2954 5402 2.570752 AGAGATGACATGTGGCAAGAGT 59.429 45.455 1.15 0.00 36.16 3.24
2955 5403 3.263489 AGAGATGACATGTGGCAAGAG 57.737 47.619 1.15 0.00 36.16 2.85
2956 5404 3.708403 AAGAGATGACATGTGGCAAGA 57.292 42.857 1.15 0.00 36.16 3.02
2957 5405 3.128242 GGAAAGAGATGACATGTGGCAAG 59.872 47.826 1.15 0.00 36.16 4.01
2958 5406 3.084039 GGAAAGAGATGACATGTGGCAA 58.916 45.455 1.15 0.00 36.16 4.52
2959 5407 2.715046 GGAAAGAGATGACATGTGGCA 58.285 47.619 1.15 0.00 37.54 4.92
2960 5408 1.667724 CGGAAAGAGATGACATGTGGC 59.332 52.381 1.15 0.00 0.00 5.01
2961 5409 3.251479 TCGGAAAGAGATGACATGTGG 57.749 47.619 1.15 0.00 0.00 4.17
2962 5410 4.495349 GCATTCGGAAAGAGATGACATGTG 60.495 45.833 1.15 0.00 0.00 3.21
2963 5411 3.624861 GCATTCGGAAAGAGATGACATGT 59.375 43.478 0.00 0.00 0.00 3.21
2964 5412 3.875727 AGCATTCGGAAAGAGATGACATG 59.124 43.478 0.00 0.00 0.00 3.21
2965 5413 4.125703 GAGCATTCGGAAAGAGATGACAT 58.874 43.478 0.00 0.00 0.00 3.06
2969 5417 2.871022 CTGGAGCATTCGGAAAGAGATG 59.129 50.000 0.00 0.00 0.00 2.90
2982 5430 1.841302 TTTCCCGAGCACTGGAGCAT 61.841 55.000 0.00 0.00 36.85 3.79
2987 5435 0.036010 ACATCTTTCCCGAGCACTGG 60.036 55.000 0.00 0.00 0.00 4.00
2996 5444 4.556699 CGTTGGAAACTTCACATCTTTCCC 60.557 45.833 6.05 0.00 46.99 3.97
2997 5445 4.537015 CGTTGGAAACTTCACATCTTTCC 58.463 43.478 0.00 0.00 46.99 3.13
3013 5461 2.281208 CGCTTGGGTTCCGTTGGA 60.281 61.111 0.00 0.00 0.00 3.53
3034 5482 3.933155 GAGTACACATCTCGGCAAATG 57.067 47.619 0.00 0.00 0.00 2.32
3044 5492 2.906354 AGGATTTGCCGAGTACACATC 58.094 47.619 0.00 0.00 43.43 3.06
3081 5529 1.723003 CTGGTACGTTTTGCCGAGTAC 59.277 52.381 0.00 0.00 38.83 2.73
3094 5542 0.321210 TTGGGTGATGTGCTGGTACG 60.321 55.000 0.00 0.00 0.00 3.67
3097 5545 2.897271 TATTTGGGTGATGTGCTGGT 57.103 45.000 0.00 0.00 0.00 4.00
3099 5547 6.263842 AGAACATATATTTGGGTGATGTGCTG 59.736 38.462 0.00 0.00 35.48 4.41
3101 5549 6.488006 AGAGAACATATATTTGGGTGATGTGC 59.512 38.462 0.00 0.00 31.29 4.57
3106 5554 6.386927 AGGACAGAGAACATATATTTGGGTGA 59.613 38.462 0.00 0.00 0.00 4.02
3110 5558 9.482627 GACTTAGGACAGAGAACATATATTTGG 57.517 37.037 0.00 0.00 0.00 3.28
3114 5562 8.811017 CATGGACTTAGGACAGAGAACATATAT 58.189 37.037 0.00 0.00 0.00 0.86
3118 5566 4.383552 GCATGGACTTAGGACAGAGAACAT 60.384 45.833 0.00 0.00 0.00 2.71
3138 5586 7.783090 TGTATGTGTTGTTTTTGAATTGCAT 57.217 28.000 0.00 0.00 0.00 3.96
3161 5611 7.440556 TGTGTTGTGAAATTATCCCAAACAATG 59.559 33.333 0.00 0.00 26.71 2.82
3166 5616 6.758886 GTGTTGTGTTGTGAAATTATCCCAAA 59.241 34.615 0.00 0.00 26.71 3.28


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

AutoCloner maintained by Alex Coulton.