Multiple sequence alignment - TraesCS6B01G340100

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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 TraesCS6B01G340100 chr6B 100.000 5889 0 0 1 5889 599447168 599441280 0.000000e+00 10876.0
1 TraesCS6B01G340100 chr6D 95.224 3706 125 24 1548 5232 400549601 400545927 0.000000e+00 5816.0
2 TraesCS6B01G340100 chr6D 88.866 1464 115 25 4 1443 400551045 400549606 0.000000e+00 1757.0
3 TraesCS6B01G340100 chr6D 91.958 659 37 4 5233 5889 400545899 400545255 0.000000e+00 909.0
4 TraesCS6B01G340100 chr6D 82.051 156 25 3 2956 3109 450832118 450831964 4.790000e-26 130.0
5 TraesCS6B01G340100 chr6A 93.708 3719 141 43 1548 5232 546551224 546547565 0.000000e+00 5485.0
6 TraesCS6B01G340100 chr6A 92.178 946 47 8 517 1446 546552155 546551221 0.000000e+00 1312.0
7 TraesCS6B01G340100 chr6A 87.625 598 28 12 5233 5826 546547537 546546982 0.000000e+00 652.0
8 TraesCS6B01G340100 chr6A 85.082 429 34 18 110 530 546553540 546553134 1.530000e-110 411.0
9 TraesCS6B01G340100 chr5B 100.000 111 0 0 1445 1555 558558590 558558700 7.740000e-49 206.0
10 TraesCS6B01G340100 chr5B 98.276 116 1 1 1445 1560 710922398 710922512 1.000000e-47 202.0
11 TraesCS6B01G340100 chr5B 95.763 118 2 3 1435 1551 531199954 531200069 2.800000e-43 187.0
12 TraesCS6B01G340100 chr5B 80.769 156 27 3 2957 3110 291787006 291786852 1.040000e-22 119.0
13 TraesCS6B01G340100 chr5B 73.737 198 44 7 6 197 517411771 517411966 2.940000e-08 71.3
14 TraesCS6B01G340100 chr7A 97.414 116 3 0 1440 1555 97199721 97199606 1.290000e-46 198.0
15 TraesCS6B01G340100 chr7A 87.662 154 13 3 1019 1172 153381523 153381376 2.180000e-39 174.0
16 TraesCS6B01G340100 chr1B 97.436 117 1 2 1443 1558 15616937 15616822 1.290000e-46 198.0
17 TraesCS6B01G340100 chrUn 95.238 126 3 3 1434 1557 37054987 37054863 4.660000e-46 196.0
18 TraesCS6B01G340100 chr3A 93.846 130 7 1 1423 1551 114429421 114429550 1.670000e-45 195.0
19 TraesCS6B01G340100 chr3A 80.263 152 26 4 2956 3105 593355715 593355864 1.730000e-20 111.0
20 TraesCS6B01G340100 chr5D 93.182 132 7 2 1429 1559 529449941 529449811 6.020000e-45 193.0
21 TraesCS6B01G340100 chr5D 90.000 110 9 2 2478 2585 320366569 320366678 2.210000e-29 141.0
22 TraesCS6B01G340100 chr1D 93.130 131 9 0 1437 1567 220210996 220211126 6.020000e-45 193.0
23 TraesCS6B01G340100 chr1D 79.870 154 28 3 2957 3108 418199584 418199432 6.240000e-20 110.0
24 TraesCS6B01G340100 chr7D 88.961 154 11 3 1019 1172 152652756 152652609 1.010000e-42 185.0
25 TraesCS6B01G340100 chr7D 80.795 151 26 3 2957 3105 617790592 617790741 1.340000e-21 115.0
26 TraesCS6B01G340100 chr2D 81.132 159 26 4 2954 3109 215831971 215831814 2.230000e-24 124.0
27 TraesCS6B01G340100 chr3D 81.457 151 25 3 2957 3105 26165695 26165844 2.880000e-23 121.0
28 TraesCS6B01G340100 chr2B 79.429 175 27 7 10 179 3297250 3297420 1.340000e-21 115.0


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 TraesCS6B01G340100 chr6B 599441280 599447168 5888 True 10876.000000 10876 100.00000 1 5889 1 chr6B.!!$R1 5888
1 TraesCS6B01G340100 chr6D 400545255 400551045 5790 True 2827.333333 5816 92.01600 4 5889 3 chr6D.!!$R2 5885
2 TraesCS6B01G340100 chr6A 546546982 546553540 6558 True 1965.000000 5485 89.64825 110 5826 4 chr6A.!!$R1 5716

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
117 128 0.036010 ACCGAGGCACCAGAATTCTG 60.036 55.000 25.75 25.75 43.40 3.02 F
1461 2495 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 F
2077 3119 1.006281 AGCTTCATCTGGGCAAATCCA 59.994 47.619 0.00 0.00 36.21 3.41 F
2508 3550 1.069596 CACACCAAGGCCAAAAGGC 59.930 57.895 5.01 0.00 42.78 4.35 F
3606 4685 0.618458 AATCTTACCGGGAAGCTGCA 59.382 50.000 22.60 4.56 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 2556 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.0 0.00 5.19 R
3056 4110 0.109723 GAGCACCCACCACCTTAACA 59.890 55.000 0.00 0.0 0.00 2.41 R
3064 4118 1.003839 CTAAAGCGAGCACCCACCA 60.004 57.895 0.00 0.0 0.00 4.17 R
4410 5490 1.129437 GCTGTTTCCGTGAGAATCTGC 59.871 52.381 0.00 0.0 40.02 4.26 R
5175 6258 0.460987 GGCAGGACAGATGACCGAAG 60.461 60.000 0.00 0.0 35.05 3.79 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
36 37 0.905357 ATCCTGGAAGACCAACTCGG 59.095 55.000 0.00 0.00 46.32 4.63
38 39 0.037232 CCTGGAAGACCAACTCGGAC 60.037 60.000 0.00 0.00 46.32 4.79
47 48 0.600255 CCAACTCGGACAAGAAGCGT 60.600 55.000 0.00 0.00 36.56 5.07
70 71 4.802051 TCCGCCAGAATGCTGCCC 62.802 66.667 0.00 0.00 40.91 5.36
71 72 4.809496 CCGCCAGAATGCTGCCCT 62.809 66.667 0.00 0.00 40.91 5.19
72 73 3.515286 CGCCAGAATGCTGCCCTG 61.515 66.667 0.00 2.06 40.91 4.45
73 74 2.362120 GCCAGAATGCTGCCCTGT 60.362 61.111 0.00 0.00 40.91 4.00
74 75 2.707849 GCCAGAATGCTGCCCTGTG 61.708 63.158 0.00 0.00 40.91 3.66
75 76 1.001764 CCAGAATGCTGCCCTGTGA 60.002 57.895 0.00 0.00 40.91 3.58
76 77 1.030488 CCAGAATGCTGCCCTGTGAG 61.030 60.000 0.00 0.00 40.91 3.51
78 79 1.203441 AGAATGCTGCCCTGTGAGGA 61.203 55.000 0.00 0.00 37.67 3.71
84 95 0.250513 CTGCCCTGTGAGGACTAACC 59.749 60.000 0.00 0.00 37.67 2.85
103 114 5.397142 AACCTAAACTACTAACCACCGAG 57.603 43.478 0.00 0.00 0.00 4.63
117 128 0.036010 ACCGAGGCACCAGAATTCTG 60.036 55.000 25.75 25.75 43.40 3.02
159 170 1.541588 AGCGACAATCAAAAGGAAGGC 59.458 47.619 0.00 0.00 0.00 4.35
201 216 3.055385 TGTTGCTTAGATGGGAGGTGTAC 60.055 47.826 0.00 0.00 0.00 2.90
216 231 1.553248 GTGTACACCCTAGATGTGGCA 59.447 52.381 15.42 10.60 38.05 4.92
307 322 3.947910 AGGCTGTTTTTGGATGTGATG 57.052 42.857 0.00 0.00 0.00 3.07
336 351 4.850347 AGGTATCCGATACTTTTCCTCG 57.150 45.455 16.40 0.00 36.04 4.63
371 386 9.796120 TGAAAGTGAAAAGTCAAACGATTTAAT 57.204 25.926 0.00 0.00 34.87 1.40
389 404 7.112844 CGATTTAATGTTTTTCGAAAGTCTGCA 59.887 33.333 10.98 7.39 31.74 4.41
437 460 3.343421 GTCACCGGACGCACAACC 61.343 66.667 9.46 0.00 33.68 3.77
453 476 2.897846 CCGCACCGGTCACAAACA 60.898 61.111 2.59 0.00 42.73 2.83
454 477 2.631428 CGCACCGGTCACAAACAG 59.369 61.111 2.59 0.00 0.00 3.16
455 478 1.885388 CGCACCGGTCACAAACAGA 60.885 57.895 2.59 0.00 0.00 3.41
456 479 1.647084 GCACCGGTCACAAACAGAC 59.353 57.895 2.59 0.00 35.29 3.51
543 1558 1.010797 CATTCAAATCGGCTCCGCG 60.011 57.895 0.00 0.00 39.59 6.46
746 1761 2.285889 ATCCCTTCTCCGCTCCTCGA 62.286 60.000 0.00 0.00 41.67 4.04
818 1843 1.125711 GGCGAAATCCCTAGGGCCTA 61.126 60.000 24.42 13.73 37.57 3.93
819 1844 0.763035 GCGAAATCCCTAGGGCCTAA 59.237 55.000 24.42 6.10 34.68 2.69
820 1845 1.142262 GCGAAATCCCTAGGGCCTAAA 59.858 52.381 24.42 5.66 34.68 1.85
833 1858 2.722201 CCTAAACCTCCGGCGCTCT 61.722 63.158 7.64 0.00 0.00 4.09
838 1863 2.598985 CCTCCGGCGCTCTATCCT 60.599 66.667 7.64 0.00 0.00 3.24
991 2025 1.228769 TGCTCGTAGGGTGTGGAGT 60.229 57.895 0.00 0.00 0.00 3.85
1180 2214 2.611518 CCCTCAAGTAAGTCAAGCTCG 58.388 52.381 0.00 0.00 0.00 5.03
1206 2240 4.451652 GCCTCGCGCTCTTGTTGC 62.452 66.667 5.56 0.00 0.00 4.17
1243 2277 2.255406 CCAGCTAGCCAGGATGATACT 58.745 52.381 16.78 0.00 39.69 2.12
1264 2298 9.525409 GATACTAACTGCTAAAATTTCTACCGA 57.475 33.333 0.00 0.00 0.00 4.69
1267 2301 6.481954 AACTGCTAAAATTTCTACCGAGTG 57.518 37.500 0.00 0.00 0.00 3.51
1281 2315 3.444916 ACCGAGTGTAGCGTATTTCATG 58.555 45.455 0.00 0.00 0.00 3.07
1283 2317 4.096833 ACCGAGTGTAGCGTATTTCATGTA 59.903 41.667 0.00 0.00 0.00 2.29
1286 2320 6.200286 CCGAGTGTAGCGTATTTCATGTAAAT 59.800 38.462 0.00 0.80 40.87 1.40
1337 2371 7.962373 GCTAATTTTTGATAATTTTGCCGCTTT 59.038 29.630 0.00 0.00 0.00 3.51
1338 2372 9.264782 CTAATTTTTGATAATTTTGCCGCTTTG 57.735 29.630 0.00 0.00 0.00 2.77
1358 2392 0.315059 CGCAACGACAGACACACAAC 60.315 55.000 0.00 0.00 0.00 3.32
1362 2396 1.556564 ACGACAGACACACAACTTCG 58.443 50.000 0.00 0.00 0.00 3.79
1443 2477 4.671377 CTCTCAGCTAGCTTGTTGAGTAG 58.329 47.826 30.14 23.60 42.99 2.57
1444 2478 4.082845 TCTCAGCTAGCTTGTTGAGTAGT 58.917 43.478 30.14 0.00 42.99 2.73
1445 2479 5.254115 TCTCAGCTAGCTTGTTGAGTAGTA 58.746 41.667 30.14 15.89 42.99 1.82
1446 2480 5.124138 TCTCAGCTAGCTTGTTGAGTAGTAC 59.876 44.000 30.14 0.00 42.99 2.73
1447 2481 5.010933 TCAGCTAGCTTGTTGAGTAGTACT 58.989 41.667 16.46 1.37 0.00 2.73
1448 2482 5.124138 TCAGCTAGCTTGTTGAGTAGTACTC 59.876 44.000 21.35 21.35 45.26 2.59
1449 2483 4.399934 AGCTAGCTTGTTGAGTAGTACTCC 59.600 45.833 24.32 12.50 44.44 3.85
1450 2484 4.440387 GCTAGCTTGTTGAGTAGTACTCCC 60.440 50.000 24.32 16.24 44.44 4.30
1451 2485 3.780626 AGCTTGTTGAGTAGTACTCCCT 58.219 45.455 24.32 10.16 44.44 4.20
1452 2486 3.764972 AGCTTGTTGAGTAGTACTCCCTC 59.235 47.826 24.32 15.54 44.44 4.30
1453 2487 3.119065 GCTTGTTGAGTAGTACTCCCTCC 60.119 52.174 24.32 11.70 44.44 4.30
1454 2488 2.719739 TGTTGAGTAGTACTCCCTCCG 58.280 52.381 24.32 0.00 44.44 4.63
1455 2489 2.040813 TGTTGAGTAGTACTCCCTCCGT 59.959 50.000 24.32 0.00 44.44 4.69
1456 2490 3.087781 GTTGAGTAGTACTCCCTCCGTT 58.912 50.000 24.32 0.00 44.44 4.44
1457 2491 2.996631 TGAGTAGTACTCCCTCCGTTC 58.003 52.381 24.32 1.22 44.44 3.95
1458 2492 1.939255 GAGTAGTACTCCCTCCGTTCG 59.061 57.143 18.10 0.00 39.28 3.95
1459 2493 1.020437 GTAGTACTCCCTCCGTTCGG 58.980 60.000 0.00 4.74 0.00 4.30
1460 2494 0.911769 TAGTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
1461 2495 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
1462 2496 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
1463 2497 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
1464 2498 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1465 2499 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1466 2500 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1467 2501 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1468 2502 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1469 2503 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1470 2504 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1471 2505 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
1472 2506 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
1473 2507 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
1474 2508 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
1475 2509 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
1476 2510 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
1477 2511 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
1478 2512 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
1479 2513 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
1480 2514 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
1481 2515 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
1482 2516 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
1483 2517 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
1484 2518 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
1485 2519 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
1486 2520 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
1487 2521 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
1488 2522 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
1489 2523 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
1490 2524 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
1491 2525 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
1492 2526 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
1493 2527 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
1494 2528 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
1495 2529 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
1496 2530 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
1522 2556 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
1523 2557 5.533482 ACGTCTAGATACATCCATTTCTGC 58.467 41.667 0.00 0.00 0.00 4.26
1524 2558 4.618912 CGTCTAGATACATCCATTTCTGCG 59.381 45.833 0.00 0.00 0.00 5.18
1525 2559 5.562890 CGTCTAGATACATCCATTTCTGCGA 60.563 44.000 0.00 0.00 0.00 5.10
1526 2560 5.631512 GTCTAGATACATCCATTTCTGCGAC 59.368 44.000 0.00 0.00 0.00 5.19
1527 2561 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
1528 2562 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
1529 2563 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
1530 2564 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
1531 2565 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
1532 2566 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
1533 2567 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
1534 2568 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
1535 2569 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
1536 2570 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
1537 2571 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
1538 2572 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
1539 2573 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
1540 2574 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
1541 2575 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
1542 2576 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
1543 2577 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
1544 2578 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
1545 2579 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1546 2580 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1768 2802 7.944729 ATATGGCTTGATTTGAGTAGTTTGT 57.055 32.000 0.00 0.00 0.00 2.83
1798 2832 6.486253 TGTTTCTCATGTGACTAATGCTTC 57.514 37.500 0.00 0.00 0.00 3.86
1832 2866 2.131183 GCCATCGAAGCAGATAGTCAC 58.869 52.381 5.96 0.00 0.00 3.67
1836 2870 3.132629 TCGAAGCAGATAGTCACGAAC 57.867 47.619 0.00 0.00 0.00 3.95
1897 2931 2.618241 TGTTTGCTGCTCTGTTTAGGTG 59.382 45.455 0.00 0.00 0.00 4.00
2077 3119 1.006281 AGCTTCATCTGGGCAAATCCA 59.994 47.619 0.00 0.00 36.21 3.41
2127 3169 4.576053 CCTTCGTTTCATCTCCATGCATTA 59.424 41.667 0.00 0.00 0.00 1.90
2254 3296 4.446719 GGGTTAGTGTGTAGAGTTTGTTCG 59.553 45.833 0.00 0.00 0.00 3.95
2309 3351 4.127907 ACTCGTCGTTAGCATCTATCTGA 58.872 43.478 0.00 0.00 0.00 3.27
2312 3354 4.515567 TCGTCGTTAGCATCTATCTGACAT 59.484 41.667 0.00 0.00 0.00 3.06
2401 3443 7.663905 ACTTGTATTGTTGCACTTGGATAAGTA 59.336 33.333 0.00 0.00 45.12 2.24
2407 3449 7.667043 TGTTGCACTTGGATAAGTAAACTAG 57.333 36.000 14.00 0.00 45.12 2.57
2508 3550 1.069596 CACACCAAGGCCAAAAGGC 59.930 57.895 5.01 0.00 42.78 4.35
2947 3994 7.804129 CCAAACAAACATAATTTCCAGCATTTG 59.196 33.333 0.00 0.00 33.17 2.32
3002 4050 4.242602 GCTTAGGCGGGAAAGCAT 57.757 55.556 10.58 0.00 45.89 3.79
3056 4110 3.705072 AGGCACTTAGTTATCGCTTAGGT 59.295 43.478 0.00 0.00 27.25 3.08
3064 4118 5.672421 AGTTATCGCTTAGGTGTTAAGGT 57.328 39.130 0.00 0.00 39.36 3.50
3113 4171 3.127548 ACCGCATAAGAACATTGCTTCTG 59.872 43.478 0.00 0.00 34.23 3.02
3151 4209 3.758023 TCACCTACCAAGCATGAATTGTG 59.242 43.478 0.00 0.00 0.00 3.33
3195 4253 4.771577 TGCCATCAGCTTTTTATCTTTCCA 59.228 37.500 0.00 0.00 44.23 3.53
3203 4261 9.082313 TCAGCTTTTTATCTTTCCAAAATCTCT 57.918 29.630 0.00 0.00 0.00 3.10
3366 4438 9.829507 ATGTTTCCTTATGTGAATTTTTGAACA 57.170 25.926 0.00 0.00 0.00 3.18
3375 4447 7.176285 TGTGAATTTTTGAACATTAGCTTGC 57.824 32.000 0.00 0.00 0.00 4.01
3376 4448 6.760298 TGTGAATTTTTGAACATTAGCTTGCA 59.240 30.769 0.00 0.00 0.00 4.08
3377 4449 7.279536 TGTGAATTTTTGAACATTAGCTTGCAA 59.720 29.630 0.00 0.00 0.00 4.08
3378 4450 8.284693 GTGAATTTTTGAACATTAGCTTGCAAT 58.715 29.630 0.00 0.00 0.00 3.56
3450 4522 1.217916 TGGTTGGAACTTCCCTCACA 58.782 50.000 5.30 0.00 35.03 3.58
3462 4534 5.611374 ACTTCCCTCACATCGGTATAATTG 58.389 41.667 0.00 0.00 0.00 2.32
3551 4623 6.759272 TCAGGTTTAGATATGGACTGTATGC 58.241 40.000 0.00 0.00 0.00 3.14
3553 4625 5.013183 AGGTTTAGATATGGACTGTATGCCC 59.987 44.000 0.00 0.00 0.00 5.36
3606 4685 0.618458 AATCTTACCGGGAAGCTGCA 59.382 50.000 22.60 4.56 0.00 4.41
3652 4731 8.603242 TTAACAAAGTCTTCTTGTGATCCTAC 57.397 34.615 0.00 0.00 33.79 3.18
3683 4762 4.082125 CAGAAGCTTGGTTAAATCCAGGT 58.918 43.478 2.10 0.00 38.80 4.00
3736 4815 6.611613 AACCAGATCTTCTAGTGTGATTGA 57.388 37.500 0.00 0.00 0.00 2.57
3743 4822 9.688091 AGATCTTCTAGTGTGATTGAAGTAGTA 57.312 33.333 0.00 0.00 37.67 1.82
3756 4835 8.349245 TGATTGAAGTAGTACCAATTTTGTGTG 58.651 33.333 6.32 0.00 31.40 3.82
3904 4983 3.244526 TGCAGGAAGATAGTGCAAAGACA 60.245 43.478 0.00 0.00 44.05 3.41
4029 5108 3.971245 TTGTTTCTTTGTTGGGTTGCT 57.029 38.095 0.00 0.00 0.00 3.91
4036 5115 6.478512 TTCTTTGTTGGGTTGCTTCTTTAT 57.521 33.333 0.00 0.00 0.00 1.40
4040 5119 7.504238 TCTTTGTTGGGTTGCTTCTTTATAAGA 59.496 33.333 0.00 0.00 35.26 2.10
4157 5236 3.374764 AGAAGGGACCCATTATTTTGCC 58.625 45.455 14.60 0.00 0.00 4.52
4300 5380 1.732259 GAGGTTGTATGTGCTGAACCG 59.268 52.381 0.00 0.00 42.34 4.44
4411 5491 0.034089 AGGTATGCCCTCACCTTTGC 60.034 55.000 0.00 0.00 42.68 3.68
4412 5492 0.323360 GGTATGCCCTCACCTTTGCA 60.323 55.000 0.00 0.00 38.23 4.08
4413 5493 1.098050 GTATGCCCTCACCTTTGCAG 58.902 55.000 0.00 0.00 37.12 4.41
4414 5494 0.991146 TATGCCCTCACCTTTGCAGA 59.009 50.000 0.00 0.00 37.12 4.26
4415 5495 0.333993 ATGCCCTCACCTTTGCAGAT 59.666 50.000 0.00 0.00 37.12 2.90
4417 5497 0.813821 GCCCTCACCTTTGCAGATTC 59.186 55.000 0.00 0.00 0.00 2.52
4418 5498 1.615384 GCCCTCACCTTTGCAGATTCT 60.615 52.381 0.00 0.00 0.00 2.40
4419 5499 2.363683 CCCTCACCTTTGCAGATTCTC 58.636 52.381 0.00 0.00 0.00 2.87
4590 5672 5.240183 CCTTGTTCTCACATCATGTTCTTGT 59.760 40.000 0.00 0.00 31.06 3.16
4716 5798 4.662278 TCTAAAGGGTCCAAAAGTGATGG 58.338 43.478 0.00 0.00 39.41 3.51
4936 6019 7.626446 TGTATTATTTTGTGTCGATGATTCCG 58.374 34.615 0.00 0.00 0.00 4.30
4972 6055 5.062528 GCCTTCTCATATCTTTTCTCCCTG 58.937 45.833 0.00 0.00 0.00 4.45
4983 6066 4.514577 CTCCCTGCGCTGTACCGG 62.515 72.222 9.73 0.00 0.00 5.28
4986 6069 3.118454 CCTGCGCTGTACCGGTTG 61.118 66.667 15.04 4.82 0.00 3.77
5024 6107 6.852368 GTCAGGAATCTTGGTAGATTTCGGAA 60.852 42.308 9.57 0.00 45.88 4.30
5040 6123 9.981114 AGATTTCGGAAATGTTGTAAAGAAAAT 57.019 25.926 19.96 0.00 31.47 1.82
5042 6125 7.938563 TTCGGAAATGTTGTAAAGAAAATGG 57.061 32.000 0.00 0.00 0.00 3.16
5043 6126 7.045126 TCGGAAATGTTGTAAAGAAAATGGT 57.955 32.000 0.00 0.00 0.00 3.55
5044 6127 8.167605 TCGGAAATGTTGTAAAGAAAATGGTA 57.832 30.769 0.00 0.00 0.00 3.25
5045 6128 8.798402 TCGGAAATGTTGTAAAGAAAATGGTAT 58.202 29.630 0.00 0.00 0.00 2.73
5046 6129 9.418045 CGGAAATGTTGTAAAGAAAATGGTATT 57.582 29.630 0.00 0.00 0.00 1.89
5156 6239 5.476945 CACTTATATAATCTTGCCCCCAACC 59.523 44.000 0.00 0.00 0.00 3.77
5175 6258 1.079197 CTTTTGATTTGGGGCGGGC 60.079 57.895 0.00 0.00 0.00 6.13
5211 6294 3.095163 CTGGAGGGAGGCCAGCAT 61.095 66.667 5.01 0.00 45.66 3.79
5252 6362 8.017946 GCTGAATAAACAACTTTCTCAAGTAGG 58.982 37.037 0.00 0.00 42.89 3.18
5257 6367 3.072622 ACAACTTTCTCAAGTAGGGTCCC 59.927 47.826 0.00 0.00 42.89 4.46
5333 6443 7.068103 CCAACCAATAATACTTGCTACATGGAA 59.932 37.037 0.00 0.00 0.00 3.53
5345 6455 6.995511 TGCTACATGGAATAAACAGTAACC 57.004 37.500 0.00 0.00 0.00 2.85
5354 6464 8.894768 TGGAATAAACAGTAACCCAAAAATTG 57.105 30.769 0.00 0.00 0.00 2.32
5553 6667 4.822036 TGTTGAACTGGGTTATGTTTCG 57.178 40.909 0.00 0.00 0.00 3.46
5570 6684 6.621316 TGTTTCGGCTAATTTGACAAGTTA 57.379 33.333 3.46 3.46 0.00 2.24
5575 6689 6.607689 TCGGCTAATTTGACAAGTTATGTTG 58.392 36.000 3.87 0.00 44.12 3.33
5581 6695 7.642071 AATTTGACAAGTTATGTTGATGTGC 57.358 32.000 0.00 0.00 44.12 4.57
5595 6709 7.139896 TGTTGATGTGCGACTATTTGTTATT 57.860 32.000 0.00 0.00 0.00 1.40
5605 6719 7.806014 TGCGACTATTTGTTATTCCTTTGAAAC 59.194 33.333 0.00 0.00 33.32 2.78
5770 6886 9.358872 AGATGTACATGATTTATATAGCACACG 57.641 33.333 14.43 0.00 0.00 4.49
5782 6898 6.918892 ATATAGCACACGAGCATGTAAAAA 57.081 33.333 0.00 0.00 36.85 1.94
5862 6978 5.061853 AGTGGCACATCAGCAGAAATATAG 58.938 41.667 21.41 0.00 44.52 1.31
5863 6979 4.214971 GTGGCACATCAGCAGAAATATAGG 59.785 45.833 13.86 0.00 44.52 2.57
5870 6986 7.912250 CACATCAGCAGAAATATAGGACAAAAC 59.088 37.037 0.00 0.00 0.00 2.43
5882 6998 8.888579 ATATAGGACAAAACGAATAACTCCAG 57.111 34.615 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.760580 GGATCCGATCCTTCATGACTT 57.239 47.619 18.84 0.00 46.19 3.01
11 12 1.414158 TGGTCTTCCAGGATCCGATC 58.586 55.000 5.98 0.00 39.03 3.69
15 16 1.134670 CGAGTTGGTCTTCCAGGATCC 60.135 57.143 2.48 2.48 45.22 3.36
18 19 0.178944 TCCGAGTTGGTCTTCCAGGA 60.179 55.000 0.00 0.00 45.22 3.86
20 21 0.679505 TGTCCGAGTTGGTCTTCCAG 59.320 55.000 0.00 0.00 45.22 3.86
36 37 1.696832 GGATGGCGACGCTTCTTGTC 61.697 60.000 20.77 8.62 0.00 3.18
38 39 2.802667 CGGATGGCGACGCTTCTTG 61.803 63.158 20.77 9.94 0.00 3.02
47 48 2.203056 CATTCTGGCGGATGGCGA 60.203 61.111 0.00 0.00 44.92 5.54
57 58 1.001764 TCACAGGGCAGCATTCTGG 60.002 57.895 12.37 4.26 40.65 3.86
59 60 1.203441 TCCTCACAGGGCAGCATTCT 61.203 55.000 0.00 0.00 35.59 2.40
70 71 6.837471 AGTAGTTTAGGTTAGTCCTCACAG 57.163 41.667 0.00 0.00 44.42 3.66
71 72 7.177392 GGTTAGTAGTTTAGGTTAGTCCTCACA 59.823 40.741 0.00 0.00 44.42 3.58
72 73 7.177392 TGGTTAGTAGTTTAGGTTAGTCCTCAC 59.823 40.741 0.00 0.00 44.42 3.51
73 74 7.177392 GTGGTTAGTAGTTTAGGTTAGTCCTCA 59.823 40.741 0.00 0.00 44.42 3.86
74 75 7.363355 GGTGGTTAGTAGTTTAGGTTAGTCCTC 60.363 44.444 0.00 0.00 44.42 3.71
76 77 6.625960 CGGTGGTTAGTAGTTTAGGTTAGTCC 60.626 46.154 0.00 0.00 0.00 3.85
78 79 6.010219 TCGGTGGTTAGTAGTTTAGGTTAGT 58.990 40.000 0.00 0.00 0.00 2.24
84 95 3.194116 TGCCTCGGTGGTTAGTAGTTTAG 59.806 47.826 0.00 0.00 38.35 1.85
95 106 1.779061 AATTCTGGTGCCTCGGTGGT 61.779 55.000 0.00 0.00 38.35 4.16
98 109 0.036010 CAGAATTCTGGTGCCTCGGT 60.036 55.000 25.14 0.00 40.20 4.69
138 149 2.029918 GCCTTCCTTTTGATTGTCGCTT 60.030 45.455 0.00 0.00 0.00 4.68
159 170 2.511600 GGTGAGCCCGTGGATTCG 60.512 66.667 0.00 0.00 0.00 3.34
201 216 2.329267 TCCTATGCCACATCTAGGGTG 58.671 52.381 8.08 8.08 34.09 4.61
277 292 7.992608 ACATCCAAAAACAGCCTAAAAGAAAAT 59.007 29.630 0.00 0.00 0.00 1.82
283 298 5.860941 TCACATCCAAAAACAGCCTAAAA 57.139 34.783 0.00 0.00 0.00 1.52
307 322 4.684484 AGTATCGGATACCTTGGGAAAC 57.316 45.455 21.41 0.00 36.40 2.78
336 351 3.641436 ACTTTTCACTTTCATTCACCCCC 59.359 43.478 0.00 0.00 0.00 5.40
371 386 4.789481 GCTGATGCAGACTTTCGAAAAACA 60.789 41.667 12.41 6.28 39.41 2.83
398 413 1.738030 CGTGTGAGCTCATGCATCAGA 60.738 52.381 21.47 0.00 42.74 3.27
437 460 1.885388 TCTGTTTGTGACCGGTGCG 60.885 57.895 14.63 0.00 0.00 5.34
438 461 1.647084 GTCTGTTTGTGACCGGTGC 59.353 57.895 14.63 5.08 0.00 5.01
446 469 0.466189 AGGTGCAGGGTCTGTTTGTG 60.466 55.000 0.00 0.00 33.43 3.33
447 470 0.258774 AAGGTGCAGGGTCTGTTTGT 59.741 50.000 0.00 0.00 33.43 2.83
448 471 1.067516 CAAAGGTGCAGGGTCTGTTTG 59.932 52.381 0.00 0.00 33.43 2.93
449 472 1.402787 CAAAGGTGCAGGGTCTGTTT 58.597 50.000 0.00 0.00 33.43 2.83
450 473 0.468029 CCAAAGGTGCAGGGTCTGTT 60.468 55.000 0.00 0.00 33.43 3.16
451 474 1.151450 CCAAAGGTGCAGGGTCTGT 59.849 57.895 0.00 0.00 33.43 3.41
452 475 1.604593 CCCAAAGGTGCAGGGTCTG 60.605 63.158 0.00 0.00 37.81 3.51
453 476 2.845345 CCCCAAAGGTGCAGGGTCT 61.845 63.158 7.17 0.00 41.16 3.85
454 477 2.283173 CCCCAAAGGTGCAGGGTC 60.283 66.667 7.17 0.00 41.16 4.46
473 496 0.609662 TGTAAGTGACGGGGTTAGGC 59.390 55.000 0.00 0.00 0.00 3.93
475 498 1.270550 ACGTGTAAGTGACGGGGTTAG 59.729 52.381 0.00 0.00 41.21 2.34
579 1594 2.732658 GTTGTCGTGTCCCGGTCT 59.267 61.111 0.00 0.00 37.11 3.85
746 1761 2.406002 AATTTGGGACGGTGGCGAGT 62.406 55.000 0.00 0.00 0.00 4.18
946 1971 3.305177 CTAACCCCGGACCCACACG 62.305 68.421 0.73 0.00 0.00 4.49
948 1973 2.608368 CCTAACCCCGGACCCACA 60.608 66.667 0.73 0.00 0.00 4.17
949 1974 3.405318 CCCTAACCCCGGACCCAC 61.405 72.222 0.73 0.00 0.00 4.61
950 1975 3.503863 AACCCTAACCCCGGACCCA 62.504 63.158 0.73 0.00 0.00 4.51
951 1976 2.202236 GAAACCCTAACCCCGGACCC 62.202 65.000 0.73 0.00 0.00 4.46
975 2009 1.654954 CCGACTCCACACCCTACGAG 61.655 65.000 0.00 0.00 0.00 4.18
1010 2044 3.049912 GACTTGAACGACCCAAATTTGC 58.950 45.455 12.92 0.00 0.00 3.68
1014 2048 1.071071 TCCGACTTGAACGACCCAAAT 59.929 47.619 0.00 0.00 0.00 2.32
1243 2277 7.156673 ACACTCGGTAGAAATTTTAGCAGTTA 58.843 34.615 0.00 0.00 0.00 2.24
1260 2294 3.119245 ACATGAAATACGCTACACTCGGT 60.119 43.478 0.00 0.00 0.00 4.69
1262 2296 6.563398 TTTACATGAAATACGCTACACTCG 57.437 37.500 0.00 0.00 0.00 4.18
1281 2315 7.093945 TGTTCCCATAGCAGGAGAAAAATTTAC 60.094 37.037 0.00 0.00 34.08 2.01
1283 2317 5.779771 TGTTCCCATAGCAGGAGAAAAATTT 59.220 36.000 0.00 0.00 34.08 1.82
1286 2320 4.380843 TGTTCCCATAGCAGGAGAAAAA 57.619 40.909 0.00 0.00 34.08 1.94
1290 2324 3.071602 GCTAATGTTCCCATAGCAGGAGA 59.928 47.826 0.00 0.00 34.08 3.71
1337 2371 2.202810 TGTGTCTGTCGTTGCGCA 60.203 55.556 5.66 5.66 0.00 6.09
1338 2372 2.031044 TTGTGTGTCTGTCGTTGCGC 62.031 55.000 0.00 0.00 0.00 6.09
1438 2472 1.939255 CGAACGGAGGGAGTACTACTC 59.061 57.143 15.38 15.38 44.32 2.59
1443 2477 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
1444 2478 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
1445 2479 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
1446 2480 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
1447 2481 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
1448 2482 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
1449 2483 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
1450 2484 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
1451 2485 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
1452 2486 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
1453 2487 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
1454 2488 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
1455 2489 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
1456 2490 5.350365 CCATTTTCGAGACAAGTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
1457 2491 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
1458 2492 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
1459 2493 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
1460 2494 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
1461 2495 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
1462 2496 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
1463 2497 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
1464 2498 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
1465 2499 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
1466 2500 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
1467 2501 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
1468 2502 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
1469 2503 8.239038 AGTTCTAGATACATCCATTTTCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
1470 2504 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
1496 2530 9.698309 CAGAAATGGATGTATCTAGACGTATTT 57.302 33.333 0.00 0.00 0.00 1.40
1497 2531 7.815068 GCAGAAATGGATGTATCTAGACGTATT 59.185 37.037 0.00 0.00 0.00 1.89
1498 2532 7.316640 GCAGAAATGGATGTATCTAGACGTAT 58.683 38.462 0.00 0.00 0.00 3.06
1499 2533 6.567891 CGCAGAAATGGATGTATCTAGACGTA 60.568 42.308 0.00 0.00 0.00 3.57
1500 2534 5.533482 GCAGAAATGGATGTATCTAGACGT 58.467 41.667 0.00 0.00 0.00 4.34
1501 2535 4.618912 CGCAGAAATGGATGTATCTAGACG 59.381 45.833 0.00 0.00 0.00 4.18
1502 2536 5.631512 GTCGCAGAAATGGATGTATCTAGAC 59.368 44.000 0.00 0.00 39.69 2.59
1503 2537 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
1504 2538 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
1505 2539 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
1506 2540 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
1507 2541 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
1508 2542 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
1509 2543 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
1510 2544 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
1511 2545 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
1512 2546 5.066505 GGAATTACTTGTCGCAGAAATGGAT 59.933 40.000 0.00 0.00 39.69 3.41
1513 2547 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
1514 2548 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
1515 2549 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
1516 2550 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
1517 2551 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
1518 2552 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
1519 2553 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
1520 2554 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
1521 2555 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
1522 2556 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
1523 2557 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
1524 2558 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
1525 2559 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
1526 2560 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
1527 2561 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
1528 2562 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
1529 2563 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
1530 2564 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
1531 2565 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
1532 2566 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
1533 2567 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
1534 2568 2.092212 ACTATTACTCCCTCCGTTCGGA 60.092 50.000 13.34 13.34 0.00 4.55
1535 2569 2.305009 ACTATTACTCCCTCCGTTCGG 58.695 52.381 4.74 4.74 0.00 4.30
1536 2570 4.110482 CAAACTATTACTCCCTCCGTTCG 58.890 47.826 0.00 0.00 0.00 3.95
1537 2571 5.107824 GTCAAACTATTACTCCCTCCGTTC 58.892 45.833 0.00 0.00 0.00 3.95
1538 2572 4.381292 CGTCAAACTATTACTCCCTCCGTT 60.381 45.833 0.00 0.00 0.00 4.44
1539 2573 3.129988 CGTCAAACTATTACTCCCTCCGT 59.870 47.826 0.00 0.00 0.00 4.69
1540 2574 3.379372 TCGTCAAACTATTACTCCCTCCG 59.621 47.826 0.00 0.00 0.00 4.63
1541 2575 4.996788 TCGTCAAACTATTACTCCCTCC 57.003 45.455 0.00 0.00 0.00 4.30
1542 2576 5.349809 CCTTCGTCAAACTATTACTCCCTC 58.650 45.833 0.00 0.00 0.00 4.30
1543 2577 4.161754 CCCTTCGTCAAACTATTACTCCCT 59.838 45.833 0.00 0.00 0.00 4.20
1544 2578 4.439968 CCCTTCGTCAAACTATTACTCCC 58.560 47.826 0.00 0.00 0.00 4.30
1545 2579 3.869832 GCCCTTCGTCAAACTATTACTCC 59.130 47.826 0.00 0.00 0.00 3.85
1546 2580 4.501071 TGCCCTTCGTCAAACTATTACTC 58.499 43.478 0.00 0.00 0.00 2.59
1768 2802 3.947196 AGTCACATGAGAAACAAGCAACA 59.053 39.130 0.00 0.00 0.00 3.33
1832 2866 3.215151 TGATAGGTCCAGCTCTAGTTCG 58.785 50.000 0.00 0.00 0.00 3.95
1836 2870 4.469657 AGACTTGATAGGTCCAGCTCTAG 58.530 47.826 0.00 0.00 34.56 2.43
1897 2931 2.960819 ACAGCGTATCCTGAACAAGTC 58.039 47.619 0.00 0.00 36.67 3.01
1946 2988 7.389607 ACAAACACAACTATCACTACATAACCC 59.610 37.037 0.00 0.00 0.00 4.11
2077 3119 2.102578 GTTGCCAACCTTCCTGCATAT 58.897 47.619 0.00 0.00 33.08 1.78
2127 3169 9.840427 CCAAAATATTACTCACTCGACAAAAAT 57.160 29.630 0.00 0.00 0.00 1.82
2152 3194 1.895131 ACCTGCCAATGTGTTCAATCC 59.105 47.619 0.00 0.00 0.00 3.01
2254 3296 9.827411 CTAACCTTGAATTTACTTTTAGCAGTC 57.173 33.333 0.00 0.00 0.00 3.51
2401 3443 7.939588 ACCAGAAAAGAACAGATAAGCTAGTTT 59.060 33.333 0.00 0.00 0.00 2.66
2407 3449 8.100508 AGTTAACCAGAAAAGAACAGATAAGC 57.899 34.615 0.88 0.00 0.00 3.09
2489 3531 1.747774 CCTTTTGGCCTTGGTGTGG 59.252 57.895 3.32 0.00 0.00 4.17
2538 3580 4.666512 AGGCTGGACTTCATGTAAAACAT 58.333 39.130 0.00 0.00 39.91 2.71
2539 3581 4.098914 AGGCTGGACTTCATGTAAAACA 57.901 40.909 0.00 0.00 0.00 2.83
2540 3582 5.001232 TGTAGGCTGGACTTCATGTAAAAC 58.999 41.667 0.00 0.00 0.00 2.43
2830 3877 5.964958 TCAAAATAGAGCAACTGAAAGGG 57.035 39.130 0.00 0.00 39.30 3.95
2918 3965 5.988561 GCTGGAAATTATGTTTGTTTGGACA 59.011 36.000 0.00 0.00 0.00 4.02
2947 3994 9.170584 GACGCCTTAAAAATAATGAATAGAAGC 57.829 33.333 0.00 0.00 0.00 3.86
2995 4043 1.139095 GAGCTGCCAGCATGCTTTC 59.861 57.895 19.98 13.18 45.56 2.62
3002 4050 2.133359 ATTGTGAGGAGCTGCCAGCA 62.133 55.000 20.53 0.36 45.56 4.41
3056 4110 0.109723 GAGCACCCACCACCTTAACA 59.890 55.000 0.00 0.00 0.00 2.41
3064 4118 1.003839 CTAAAGCGAGCACCCACCA 60.004 57.895 0.00 0.00 0.00 4.17
3113 4171 6.762661 TGGTAGGTGACAAACTAGTTACAAAC 59.237 38.462 8.92 5.80 30.34 2.93
3151 4209 6.081693 GGCAAGAAACAAATCATGCATTTTC 58.918 36.000 10.09 10.09 43.79 2.29
3195 4253 7.040132 CCCTTTTCAGTAAGAAGCAGAGATTTT 60.040 37.037 0.00 0.00 37.57 1.82
3203 4261 3.882888 CACACCCTTTTCAGTAAGAAGCA 59.117 43.478 0.00 0.00 37.57 3.91
3309 4381 6.388619 AGGAGGGTTGTAATGAAACATAGT 57.611 37.500 0.00 0.00 0.00 2.12
3376 4448 8.042515 ACAAGCTCCAATAATTACAATGCAATT 58.957 29.630 0.00 0.00 36.63 2.32
3377 4449 7.493320 CACAAGCTCCAATAATTACAATGCAAT 59.507 33.333 0.00 0.00 0.00 3.56
3378 4450 6.812656 CACAAGCTCCAATAATTACAATGCAA 59.187 34.615 0.00 0.00 0.00 4.08
3462 4534 7.471721 GCAAAATGCAATATTTTAAGTTCCCC 58.528 34.615 0.00 0.00 44.26 4.81
3493 4565 8.806429 TGGTGAACATATCTGACATTTACATT 57.194 30.769 0.00 0.00 0.00 2.71
3513 4585 1.576577 ACCTGAGATGATGCTGGTGA 58.423 50.000 0.00 0.00 35.39 4.02
3515 4587 3.776969 TCTAAACCTGAGATGATGCTGGT 59.223 43.478 0.00 0.00 37.87 4.00
3551 4623 1.380785 TAGCTGGTGTCCCTACGGG 60.381 63.158 0.00 0.00 46.11 5.28
3553 4625 1.471119 TTCTAGCTGGTGTCCCTACG 58.529 55.000 0.00 0.00 0.00 3.51
3606 4685 4.322057 AGGTTTAGGCCATTCACAGAAT 57.678 40.909 5.01 0.00 0.00 2.40
3736 4815 6.123651 TGACCACACAAAATTGGTACTACTT 58.876 36.000 0.00 0.00 46.56 2.24
3904 4983 2.040412 CCCAGCAGAAGTAACTTTCCCT 59.960 50.000 0.00 0.00 0.00 4.20
3985 5064 8.446273 CAAAAGGATAGACAACAAGACACTATG 58.554 37.037 0.00 0.00 0.00 2.23
4036 5115 5.536161 GCAGCCTGGAAATAATTGGATCTTA 59.464 40.000 0.00 0.00 0.00 2.10
4040 5119 3.640029 CAGCAGCCTGGAAATAATTGGAT 59.360 43.478 0.00 0.00 35.38 3.41
4300 5380 3.550233 GCTTCTCCTTTTCGGTGGAAAAC 60.550 47.826 0.00 0.00 44.86 2.43
4410 5490 1.129437 GCTGTTTCCGTGAGAATCTGC 59.871 52.381 0.00 0.00 40.02 4.26
4411 5491 1.734465 GGCTGTTTCCGTGAGAATCTG 59.266 52.381 0.00 0.00 33.44 2.90
4412 5492 1.625818 AGGCTGTTTCCGTGAGAATCT 59.374 47.619 0.00 0.00 33.44 2.40
4413 5493 2.100605 AGGCTGTTTCCGTGAGAATC 57.899 50.000 0.00 0.00 33.44 2.52
4414 5494 2.568623 AAGGCTGTTTCCGTGAGAAT 57.431 45.000 0.00 0.00 33.44 2.40
4415 5495 2.341846 AAAGGCTGTTTCCGTGAGAA 57.658 45.000 0.00 0.00 0.00 2.87
4417 5497 3.564225 ACTTAAAAGGCTGTTTCCGTGAG 59.436 43.478 0.00 0.00 0.00 3.51
4418 5498 3.314080 CACTTAAAAGGCTGTTTCCGTGA 59.686 43.478 0.00 0.00 0.00 4.35
4419 5499 3.314080 TCACTTAAAAGGCTGTTTCCGTG 59.686 43.478 0.00 1.43 0.00 4.94
4716 5798 6.920569 TCTCTTTTCTTACACTTTGGTCAC 57.079 37.500 0.00 0.00 0.00 3.67
4936 6019 1.328986 GAGAAGGCGAATACTGCAAGC 59.671 52.381 0.00 0.00 37.60 4.01
4983 6066 3.990318 CTGACTTTCCAGGAAACCAAC 57.010 47.619 10.90 3.73 0.00 3.77
5156 6239 1.596408 CCCGCCCCAAATCAAAAGG 59.404 57.895 0.00 0.00 0.00 3.11
5175 6258 0.460987 GGCAGGACAGATGACCGAAG 60.461 60.000 0.00 0.00 35.05 3.79
5203 6286 2.045926 AGACCGTTCATGCTGGCC 60.046 61.111 0.00 0.00 0.00 5.36
5252 6362 2.574450 TGTCAACTTAAAACCGGGACC 58.426 47.619 6.32 0.00 0.00 4.46
5257 6367 8.447833 TCAAGCTATATTGTCAACTTAAAACCG 58.552 33.333 0.00 0.00 0.00 4.44
5354 6464 1.063174 CTAATGCAGAACAAGCTCGCC 59.937 52.381 0.00 0.00 0.00 5.54
5396 6506 6.122277 ACCCATAAGACAATTAGGACACATG 58.878 40.000 0.00 0.00 0.00 3.21
5402 6512 9.762381 ATTTGTTAACCCATAAGACAATTAGGA 57.238 29.630 2.48 0.00 31.15 2.94
5457 6571 7.584123 GCATTAACGATCAAATATGTGACACTC 59.416 37.037 7.20 0.00 0.00 3.51
5553 6667 8.028938 ACATCAACATAACTTGTCAAATTAGCC 58.971 33.333 0.00 0.00 37.68 3.93
5570 6684 5.627499 AACAAATAGTCGCACATCAACAT 57.373 34.783 0.00 0.00 0.00 2.71
5575 6689 6.604735 AGGAATAACAAATAGTCGCACATC 57.395 37.500 0.00 0.00 29.27 3.06
5595 6709 8.794553 TGTTGTGTTTAGTTTAGTTTCAAAGGA 58.205 29.630 0.00 0.00 0.00 3.36
5605 6719 7.700234 TGCAGACATTTGTTGTGTTTAGTTTAG 59.300 33.333 0.00 0.00 39.18 1.85
5610 6726 5.804473 TGTTGCAGACATTTGTTGTGTTTAG 59.196 36.000 0.00 0.00 39.18 1.85
5770 6886 8.741101 TCATATTGTGTTGTTTTTACATGCTC 57.259 30.769 0.00 0.00 0.00 4.26
5782 6898 6.704493 ACTTGTTACGTCTCATATTGTGTTGT 59.296 34.615 0.00 0.00 0.00 3.32
5837 6953 0.397564 TTCTGCTGATGTGCCACTCA 59.602 50.000 0.00 0.00 0.00 3.41
5850 6966 7.865706 ATTCGTTTTGTCCTATATTTCTGCT 57.134 32.000 0.00 0.00 0.00 4.24
5862 6978 6.980051 ATACTGGAGTTATTCGTTTTGTCC 57.020 37.500 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.