Multiple sequence alignment - TraesCS4B01G320000

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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 TraesCS4B01G320000 chr4B 100.000 2583 0 0 1 2583 611024545 611027127 0.000000e+00 4771
1 TraesCS4B01G320000 chr4B 95.622 434 17 2 1696 2129 588587214 588587645 0.000000e+00 695
2 TraesCS4B01G320000 chr4B 95.238 441 17 3 1692 2132 629957943 629957507 0.000000e+00 695
3 TraesCS4B01G320000 chr4B 91.188 261 22 1 2260 2519 629957526 629957266 1.140000e-93 353
4 TraesCS4B01G320000 chr4D 96.433 1486 51 2 101 1585 88084835 88086319 0.000000e+00 2449
5 TraesCS4B01G320000 chr4D 96.311 1491 51 4 101 1589 481897207 481898695 0.000000e+00 2446
6 TraesCS4B01G320000 chr4D 95.772 1490 56 4 101 1589 494280533 494279050 0.000000e+00 2396
7 TraesCS4B01G320000 chr4D 95.775 426 16 2 1704 2129 8274419 8274842 0.000000e+00 686
8 TraesCS4B01G320000 chr7D 96.159 1484 55 2 101 1583 602728942 602730424 0.000000e+00 2423
9 TraesCS4B01G320000 chr7D 95.909 1491 58 3 101 1590 140813190 140811702 0.000000e+00 2412
10 TraesCS4B01G320000 chr7D 96.009 426 16 1 1704 2129 101778762 101779186 0.000000e+00 691
11 TraesCS4B01G320000 chr7D 97.826 138 3 0 2125 2262 625517673 625517536 3.320000e-59 239
12 TraesCS4B01G320000 chr3D 95.924 1472 57 3 101 1571 432511545 432513014 0.000000e+00 2383
13 TraesCS4B01G320000 chr3D 92.213 244 19 0 2260 2503 554948822 554948579 1.900000e-91 346
14 TraesCS4B01G320000 chr3D 97.826 138 3 0 2125 2262 531175695 531175558 3.320000e-59 239
15 TraesCS4B01G320000 chr5D 95.424 1486 66 2 101 1585 363307597 363306113 0.000000e+00 2366
16 TraesCS4B01G320000 chr5D 78.928 541 83 23 1743 2262 391865721 391865191 3.180000e-89 339
17 TraesCS4B01G320000 chr5D 99.259 135 1 0 2127 2261 314672817 314672683 7.140000e-61 244
18 TraesCS4B01G320000 chr5A 95.305 1491 67 3 102 1591 707999835 707998347 0.000000e+00 2362
19 TraesCS4B01G320000 chr5A 98.529 136 2 0 2127 2262 459960848 459960983 9.240000e-60 241
20 TraesCS4B01G320000 chr3A 95.127 1498 68 5 102 1596 50111668 50110173 0.000000e+00 2357
21 TraesCS4B01G320000 chr1B 96.714 426 13 1 1704 2129 269218259 269218683 0.000000e+00 708
22 TraesCS4B01G320000 chr6D 96.262 428 15 1 1702 2129 315652518 315652944 0.000000e+00 701
23 TraesCS4B01G320000 chr6B 96.253 427 14 2 1703 2129 611351618 611352042 0.000000e+00 699
24 TraesCS4B01G320000 chr6B 98.529 136 2 0 2127 2262 228607135 228607270 9.240000e-60 241
25 TraesCS4B01G320000 chr2B 96.882 417 12 1 1713 2129 659017651 659018066 0.000000e+00 697
26 TraesCS4B01G320000 chr2B 95.804 429 17 1 1704 2132 156589453 156589026 0.000000e+00 691
27 TraesCS4B01G320000 chr1D 93.916 263 15 1 1334 1596 373120318 373120057 1.860000e-106 396
28 TraesCS4B01G320000 chr1D 95.152 165 8 0 1395 1559 92957960 92957796 7.090000e-66 261
29 TraesCS4B01G320000 chr3B 92.339 248 18 1 2260 2506 416273093 416273340 4.090000e-93 351
30 TraesCS4B01G320000 chr3B 91.935 248 19 1 2260 2506 321772386 321772633 1.900000e-91 346
31 TraesCS4B01G320000 chr3B 94.194 155 4 4 2112 2262 482578191 482578038 5.560000e-57 231
32 TraesCS4B01G320000 chr7B 92.213 244 19 0 2260 2503 130516888 130516645 1.900000e-91 346
33 TraesCS4B01G320000 chr7B 91.270 252 20 2 2256 2506 692876461 692876211 2.460000e-90 342
34 TraesCS4B01G320000 chr5B 91.935 248 19 1 2260 2506 699778771 699779018 1.900000e-91 346
35 TraesCS4B01G320000 chr5B 98.529 136 2 0 2127 2262 582197871 582197736 9.240000e-60 241
36 TraesCS4B01G320000 chr5B 95.238 147 4 3 2118 2262 74229232 74229377 2.000000e-56 230
37 TraesCS4B01G320000 chr4A 91.633 251 20 1 2260 2509 702119271 702119021 1.900000e-91 346
38 TraesCS4B01G320000 chr2D 91.633 251 20 1 2260 2509 548254404 548254154 1.900000e-91 346


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 TraesCS4B01G320000 chr4B 611024545 611027127 2582 False 4771 4771 100.000 1 2583 1 chr4B.!!$F2 2582
1 TraesCS4B01G320000 chr4B 629957266 629957943 677 True 524 695 93.213 1692 2519 2 chr4B.!!$R1 827
2 TraesCS4B01G320000 chr4D 88084835 88086319 1484 False 2449 2449 96.433 101 1585 1 chr4D.!!$F2 1484
3 TraesCS4B01G320000 chr4D 481897207 481898695 1488 False 2446 2446 96.311 101 1589 1 chr4D.!!$F3 1488
4 TraesCS4B01G320000 chr4D 494279050 494280533 1483 True 2396 2396 95.772 101 1589 1 chr4D.!!$R1 1488
5 TraesCS4B01G320000 chr7D 602728942 602730424 1482 False 2423 2423 96.159 101 1583 1 chr7D.!!$F2 1482
6 TraesCS4B01G320000 chr7D 140811702 140813190 1488 True 2412 2412 95.909 101 1590 1 chr7D.!!$R1 1489
7 TraesCS4B01G320000 chr3D 432511545 432513014 1469 False 2383 2383 95.924 101 1571 1 chr3D.!!$F1 1470
8 TraesCS4B01G320000 chr5D 363306113 363307597 1484 True 2366 2366 95.424 101 1585 1 chr5D.!!$R2 1484
9 TraesCS4B01G320000 chr5D 391865191 391865721 530 True 339 339 78.928 1743 2262 1 chr5D.!!$R3 519
10 TraesCS4B01G320000 chr5A 707998347 707999835 1488 True 2362 2362 95.305 102 1591 1 chr5A.!!$R1 1489
11 TraesCS4B01G320000 chr3A 50110173 50111668 1495 True 2357 2357 95.127 102 1596 1 chr3A.!!$R1 1494

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
252 254 0.323725 AGCCATCACACCAACCCATC 60.324 55.0 0.0 0.0 0.0 3.51 F
667 670 0.539438 GACATTTGCCCCCTGTGTGA 60.539 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1304 1307 0.103208 AATCATCGACACCGCCTCTC 59.897 55.0 0.0 0.0 35.37 3.20 R
2197 2223 0.604578 CACCCAAGTTCAAGGCATGG 59.395 55.0 0.0 0.0 0.00 3.66 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
21 22 3.552875 CAGGTCTACGATACTTCCTCCA 58.447 50.000 0.00 0.00 0.00 3.86
22 23 3.315749 CAGGTCTACGATACTTCCTCCAC 59.684 52.174 0.00 0.00 0.00 4.02
23 24 2.290093 GGTCTACGATACTTCCTCCACG 59.710 54.545 0.00 0.00 0.00 4.94
24 25 2.941720 GTCTACGATACTTCCTCCACGT 59.058 50.000 0.00 0.00 37.68 4.49
25 26 3.002144 GTCTACGATACTTCCTCCACGTC 59.998 52.174 0.00 0.00 35.66 4.34
26 27 1.830279 ACGATACTTCCTCCACGTCA 58.170 50.000 0.00 0.00 0.00 4.35
27 28 2.165167 ACGATACTTCCTCCACGTCAA 58.835 47.619 0.00 0.00 0.00 3.18
28 29 2.559668 ACGATACTTCCTCCACGTCAAA 59.440 45.455 0.00 0.00 0.00 2.69
29 30 3.006110 ACGATACTTCCTCCACGTCAAAA 59.994 43.478 0.00 0.00 0.00 2.44
30 31 3.367025 CGATACTTCCTCCACGTCAAAAC 59.633 47.826 0.00 0.00 0.00 2.43
31 32 2.702592 ACTTCCTCCACGTCAAAACA 57.297 45.000 0.00 0.00 0.00 2.83
32 33 3.208747 ACTTCCTCCACGTCAAAACAT 57.791 42.857 0.00 0.00 0.00 2.71
33 34 4.345859 ACTTCCTCCACGTCAAAACATA 57.654 40.909 0.00 0.00 0.00 2.29
34 35 4.315803 ACTTCCTCCACGTCAAAACATAG 58.684 43.478 0.00 0.00 0.00 2.23
35 36 2.695359 TCCTCCACGTCAAAACATAGC 58.305 47.619 0.00 0.00 0.00 2.97
36 37 1.393539 CCTCCACGTCAAAACATAGCG 59.606 52.381 0.00 0.00 0.00 4.26
37 38 0.793861 TCCACGTCAAAACATAGCGC 59.206 50.000 0.00 0.00 0.00 5.92
38 39 0.515127 CCACGTCAAAACATAGCGCA 59.485 50.000 11.47 0.00 0.00 6.09
39 40 1.130373 CCACGTCAAAACATAGCGCAT 59.870 47.619 11.47 0.00 0.00 4.73
40 41 2.350192 CCACGTCAAAACATAGCGCATA 59.650 45.455 11.47 0.00 0.00 3.14
41 42 3.342269 CACGTCAAAACATAGCGCATAC 58.658 45.455 11.47 0.00 0.00 2.39
42 43 3.062099 CACGTCAAAACATAGCGCATACT 59.938 43.478 11.47 0.00 0.00 2.12
43 44 3.062099 ACGTCAAAACATAGCGCATACTG 59.938 43.478 11.47 3.36 0.00 2.74
44 45 3.354397 GTCAAAACATAGCGCATACTGC 58.646 45.455 11.47 0.00 40.69 4.40
45 46 3.006247 TCAAAACATAGCGCATACTGCA 58.994 40.909 11.47 0.00 45.36 4.41
46 47 3.627123 TCAAAACATAGCGCATACTGCAT 59.373 39.130 11.47 0.00 45.36 3.96
47 48 4.096231 TCAAAACATAGCGCATACTGCATT 59.904 37.500 11.47 0.00 45.36 3.56
48 49 4.637483 AAACATAGCGCATACTGCATTT 57.363 36.364 11.47 0.00 45.36 2.32
49 50 3.614159 ACATAGCGCATACTGCATTTG 57.386 42.857 11.47 0.00 45.36 2.32
50 51 2.945008 ACATAGCGCATACTGCATTTGT 59.055 40.909 11.47 0.00 45.36 2.83
51 52 3.002656 ACATAGCGCATACTGCATTTGTC 59.997 43.478 11.47 0.00 45.36 3.18
52 53 1.742761 AGCGCATACTGCATTTGTCT 58.257 45.000 11.47 0.00 45.36 3.41
53 54 2.086869 AGCGCATACTGCATTTGTCTT 58.913 42.857 11.47 0.00 45.36 3.01
54 55 2.159476 AGCGCATACTGCATTTGTCTTG 60.159 45.455 11.47 0.00 45.36 3.02
55 56 2.159531 GCGCATACTGCATTTGTCTTGA 60.160 45.455 0.30 0.00 45.36 3.02
56 57 3.677601 CGCATACTGCATTTGTCTTGAG 58.322 45.455 0.00 0.00 45.36 3.02
57 58 3.125829 CGCATACTGCATTTGTCTTGAGT 59.874 43.478 0.00 0.00 45.36 3.41
58 59 4.656041 GCATACTGCATTTGTCTTGAGTC 58.344 43.478 0.00 0.00 44.26 3.36
59 60 4.726021 GCATACTGCATTTGTCTTGAGTCG 60.726 45.833 0.00 0.00 44.26 4.18
60 61 2.146342 ACTGCATTTGTCTTGAGTCGG 58.854 47.619 0.00 0.00 0.00 4.79
61 62 2.224281 ACTGCATTTGTCTTGAGTCGGA 60.224 45.455 0.00 0.00 0.00 4.55
62 63 3.005554 CTGCATTTGTCTTGAGTCGGAT 58.994 45.455 0.00 0.00 0.00 4.18
63 64 3.411446 TGCATTTGTCTTGAGTCGGATT 58.589 40.909 0.00 0.00 0.00 3.01
64 65 3.820467 TGCATTTGTCTTGAGTCGGATTT 59.180 39.130 0.00 0.00 0.00 2.17
65 66 4.278170 TGCATTTGTCTTGAGTCGGATTTT 59.722 37.500 0.00 0.00 0.00 1.82
66 67 5.471797 TGCATTTGTCTTGAGTCGGATTTTA 59.528 36.000 0.00 0.00 0.00 1.52
67 68 6.150976 TGCATTTGTCTTGAGTCGGATTTTAT 59.849 34.615 0.00 0.00 0.00 1.40
68 69 7.335673 TGCATTTGTCTTGAGTCGGATTTTATA 59.664 33.333 0.00 0.00 0.00 0.98
69 70 8.181573 GCATTTGTCTTGAGTCGGATTTTATAA 58.818 33.333 0.00 0.00 0.00 0.98
72 73 9.496873 TTTGTCTTGAGTCGGATTTTATAAAGA 57.503 29.630 0.00 0.00 0.00 2.52
73 74 9.667107 TTGTCTTGAGTCGGATTTTATAAAGAT 57.333 29.630 0.00 0.00 0.00 2.40
74 75 9.667107 TGTCTTGAGTCGGATTTTATAAAGATT 57.333 29.630 0.00 0.00 0.00 2.40
75 76 9.922305 GTCTTGAGTCGGATTTTATAAAGATTG 57.078 33.333 0.00 0.00 0.00 2.67
76 77 9.884636 TCTTGAGTCGGATTTTATAAAGATTGA 57.115 29.630 0.00 0.00 0.00 2.57
77 78 9.922305 CTTGAGTCGGATTTTATAAAGATTGAC 57.078 33.333 11.61 11.61 0.00 3.18
78 79 8.433421 TGAGTCGGATTTTATAAAGATTGACC 57.567 34.615 14.12 9.45 0.00 4.02
79 80 8.044309 TGAGTCGGATTTTATAAAGATTGACCA 58.956 33.333 14.12 10.97 0.00 4.02
80 81 8.801882 AGTCGGATTTTATAAAGATTGACCAA 57.198 30.769 14.12 0.00 0.00 3.67
81 82 8.893727 AGTCGGATTTTATAAAGATTGACCAAG 58.106 33.333 14.12 0.00 0.00 3.61
82 83 8.674607 GTCGGATTTTATAAAGATTGACCAAGT 58.325 33.333 0.00 0.00 0.00 3.16
83 84 9.238368 TCGGATTTTATAAAGATTGACCAAGTT 57.762 29.630 0.00 0.00 0.00 2.66
84 85 9.503427 CGGATTTTATAAAGATTGACCAAGTTC 57.497 33.333 0.00 0.00 0.00 3.01
95 96 9.696917 AAGATTGACCAAGTTCATATGAAAAAC 57.303 29.630 19.55 8.71 35.58 2.43
96 97 8.859090 AGATTGACCAAGTTCATATGAAAAACA 58.141 29.630 19.55 11.04 35.58 2.83
97 98 9.474920 GATTGACCAAGTTCATATGAAAAACAA 57.525 29.630 19.55 17.43 35.58 2.83
98 99 9.829507 ATTGACCAAGTTCATATGAAAAACAAA 57.170 25.926 19.55 9.10 35.58 2.83
99 100 9.829507 TTGACCAAGTTCATATGAAAAACAAAT 57.170 25.926 19.55 3.08 35.58 2.32
211 213 1.134220 GGCAGGACATCCGTATTTGGA 60.134 52.381 0.00 0.00 43.58 3.53
242 244 0.913934 TTGCCTAGGGAGCCATCACA 60.914 55.000 11.72 0.00 0.00 3.58
252 254 0.323725 AGCCATCACACCAACCCATC 60.324 55.000 0.00 0.00 0.00 3.51
361 364 3.822192 CCCTGCGGATGTCGACGA 61.822 66.667 11.62 0.00 42.43 4.20
537 540 3.567797 GTCGCGCCATCTGGAAGC 61.568 66.667 0.00 3.87 37.39 3.86
567 570 0.978146 GTGCCCTGCTCCTCCTAAGA 60.978 60.000 0.00 0.00 0.00 2.10
660 663 0.817654 GCTTACTGACATTTGCCCCC 59.182 55.000 0.00 0.00 0.00 5.40
667 670 0.539438 GACATTTGCCCCCTGTGTGA 60.539 55.000 0.00 0.00 0.00 3.58
685 688 1.337728 TGATGTTGAACGCGAGGATGT 60.338 47.619 15.93 0.00 0.00 3.06
811 814 1.200948 GTGGATCTTTTCACTGCTGGC 59.799 52.381 0.00 0.00 0.00 4.85
826 829 1.309013 TGGCCCCCTTGGATGAGAT 60.309 57.895 0.00 0.00 35.39 2.75
828 831 1.355718 GGCCCCCTTGGATGAGATGA 61.356 60.000 0.00 0.00 35.39 2.92
869 872 2.105477 GACCATGTGGAGAGTATGGCAT 59.895 50.000 4.88 4.88 44.06 4.40
903 906 4.539083 ACACACGACAAGGCGCCA 62.539 61.111 31.54 0.00 33.86 5.69
955 958 3.448686 CACGGATACATCAACTCACTCC 58.551 50.000 0.00 0.00 0.00 3.85
997 1000 4.037927 TGATGGTAACCTAGAGAAAGGGG 58.962 47.826 0.00 0.00 41.32 4.79
1024 1027 1.380302 GTCCTGCCTTCACCACCAT 59.620 57.895 0.00 0.00 0.00 3.55
1049 1052 2.100631 CAGAAAGTACGGCGCCCAG 61.101 63.158 23.46 10.83 0.00 4.45
1181 1184 3.291584 ACAGAGGCGAGATCATCTACAA 58.708 45.455 0.00 0.00 0.00 2.41
1304 1307 1.207089 TCTGGTTGAGTTGGATAGCGG 59.793 52.381 0.00 0.00 0.00 5.52
1387 1390 2.957006 GAGGAGATTCGTAGGTTGGCTA 59.043 50.000 0.00 0.00 0.00 3.93
1427 1430 7.246171 AGATCTCTTTTACTCTTTGTAGCCA 57.754 36.000 0.00 0.00 32.08 4.75
1438 1441 1.725641 TTGTAGCCATCTGCAGAACG 58.274 50.000 22.50 14.78 44.83 3.95
1484 1487 2.104331 CCGTAGAACTCCGCGCAT 59.896 61.111 8.75 0.00 0.00 4.73
1562 1565 4.479786 AGCCTCCTTGAGTAATGAGAAC 57.520 45.455 0.00 0.00 32.28 3.01
1629 1632 5.881637 AAATGTTTTCATGTTCGGTTTCG 57.118 34.783 0.00 0.00 40.79 3.46
1630 1633 4.822036 ATGTTTTCATGTTCGGTTTCGA 57.178 36.364 0.00 0.00 40.38 3.71
1631 1634 5.176407 ATGTTTTCATGTTCGGTTTCGAA 57.824 34.783 0.00 0.00 44.48 3.71
1632 1635 5.583495 ATGTTTTCATGTTCGGTTTCGAAA 58.417 33.333 6.47 6.47 44.12 3.46
1633 1636 5.685511 ATGTTTTCATGTTCGGTTTCGAAAG 59.314 36.000 11.66 0.29 44.12 2.62
1634 1637 6.459024 ATGTTTTCATGTTCGGTTTCGAAAGA 60.459 34.615 11.66 3.07 44.12 2.52
1635 1638 7.734421 ATGTTTTCATGTTCGGTTTCGAAAGAT 60.734 33.333 11.66 0.00 44.12 2.40
1645 1648 7.192148 TCGGTTTCGAAAGATAATGTTTTCA 57.808 32.000 11.66 0.00 43.03 2.69
1646 1649 7.812648 TCGGTTTCGAAAGATAATGTTTTCAT 58.187 30.769 11.66 0.00 43.03 2.57
1647 1650 7.748683 TCGGTTTCGAAAGATAATGTTTTCATG 59.251 33.333 11.66 0.00 43.03 3.07
1648 1651 7.537306 CGGTTTCGAAAGATAATGTTTTCATGT 59.463 33.333 11.66 0.00 39.44 3.21
1649 1652 8.638565 GGTTTCGAAAGATAATGTTTTCATGTG 58.361 33.333 11.66 0.00 39.44 3.21
1650 1653 9.393249 GTTTCGAAAGATAATGTTTTCATGTGA 57.607 29.630 11.66 0.00 39.44 3.58
1652 1655 9.558648 TTCGAAAGATAATGTTTTCATGTGATG 57.441 29.630 0.00 0.00 39.44 3.07
1653 1656 8.945057 TCGAAAGATAATGTTTTCATGTGATGA 58.055 29.630 0.00 0.00 36.35 2.92
1654 1657 9.558648 CGAAAGATAATGTTTTCATGTGATGAA 57.441 29.630 0.00 0.00 46.77 2.57
1684 1687 7.432350 TGATCTTCTTCTTCTTCTTCTTTGC 57.568 36.000 0.00 0.00 0.00 3.68
1685 1688 5.914085 TCTTCTTCTTCTTCTTCTTTGCG 57.086 39.130 0.00 0.00 0.00 4.85
1686 1689 4.752101 TCTTCTTCTTCTTCTTCTTTGCGG 59.248 41.667 0.00 0.00 0.00 5.69
1687 1690 3.403038 TCTTCTTCTTCTTCTTTGCGGG 58.597 45.455 0.00 0.00 0.00 6.13
1688 1691 2.930826 TCTTCTTCTTCTTTGCGGGT 57.069 45.000 0.00 0.00 0.00 5.28
1689 1692 2.494059 TCTTCTTCTTCTTTGCGGGTG 58.506 47.619 0.00 0.00 0.00 4.61
1690 1693 2.104111 TCTTCTTCTTCTTTGCGGGTGA 59.896 45.455 0.00 0.00 0.00 4.02
1691 1694 2.859165 TCTTCTTCTTTGCGGGTGAT 57.141 45.000 0.00 0.00 0.00 3.06
1692 1695 2.426522 TCTTCTTCTTTGCGGGTGATG 58.573 47.619 0.00 0.00 0.00 3.07
1693 1696 2.038426 TCTTCTTCTTTGCGGGTGATGA 59.962 45.455 0.00 0.00 0.00 2.92
1694 1697 2.559698 TCTTCTTTGCGGGTGATGAA 57.440 45.000 0.00 0.00 0.00 2.57
1695 1698 3.071874 TCTTCTTTGCGGGTGATGAAT 57.928 42.857 0.00 0.00 0.00 2.57
1696 1699 4.214986 TCTTCTTTGCGGGTGATGAATA 57.785 40.909 0.00 0.00 0.00 1.75
1697 1700 4.780815 TCTTCTTTGCGGGTGATGAATAT 58.219 39.130 0.00 0.00 0.00 1.28
1698 1701 5.924356 TCTTCTTTGCGGGTGATGAATATA 58.076 37.500 0.00 0.00 0.00 0.86
1699 1702 6.353323 TCTTCTTTGCGGGTGATGAATATAA 58.647 36.000 0.00 0.00 0.00 0.98
1700 1703 6.998074 TCTTCTTTGCGGGTGATGAATATAAT 59.002 34.615 0.00 0.00 0.00 1.28
1701 1704 6.558771 TCTTTGCGGGTGATGAATATAATG 57.441 37.500 0.00 0.00 0.00 1.90
1702 1705 6.295249 TCTTTGCGGGTGATGAATATAATGA 58.705 36.000 0.00 0.00 0.00 2.57
1749 1752 6.738832 ATCTATTCATCTTCAATCATGGCG 57.261 37.500 0.00 0.00 0.00 5.69
1756 1759 3.884895 TCTTCAATCATGGCGGTACAAT 58.115 40.909 0.00 0.00 0.00 2.71
1766 1769 2.218603 GGCGGTACAATGAATACCAGG 58.781 52.381 0.00 0.00 42.03 4.45
1935 1938 2.505982 CCATAGGACCAGCACCCG 59.494 66.667 0.00 0.00 0.00 5.28
1963 1966 2.686816 AACCGCCGCCGATGAAAAG 61.687 57.895 0.00 0.00 36.29 2.27
1997 2001 2.770164 AGGATCCAAACCGAAGACAG 57.230 50.000 15.82 0.00 0.00 3.51
2092 2117 1.606480 CGCCCATCAACGATGCTAGAT 60.606 52.381 0.00 0.00 38.59 1.98
2119 2144 3.162154 GAACGGGGGCTAGGAGGG 61.162 72.222 0.00 0.00 0.00 4.30
2122 2147 4.944069 CGGGGGCTAGGAGGGGAG 62.944 77.778 0.00 0.00 0.00 4.30
2158 2184 3.074094 AGAAAGACTGTAAAGGAACCCCC 59.926 47.826 0.00 0.00 0.00 5.40
2182 2208 7.027161 CCTACAGTATAATTGGTGCAACAAAC 58.973 38.462 23.14 15.04 39.98 2.93
2183 2209 5.778862 ACAGTATAATTGGTGCAACAAACC 58.221 37.500 23.14 7.62 39.98 3.27
2197 2223 4.260579 GCAACAAACCCAAATTGCAAGTAC 60.261 41.667 4.94 0.00 45.38 2.73
2209 2235 1.885887 TGCAAGTACCATGCCTTGAAC 59.114 47.619 16.17 5.82 43.16 3.18
2210 2236 2.162681 GCAAGTACCATGCCTTGAACT 58.837 47.619 17.22 0.00 40.36 3.01
2242 2268 1.442886 AAGGCATCAACCCCTTCCCA 61.443 55.000 0.00 0.00 36.78 4.37
2393 2420 1.750399 CCCTTGGCAGAATCCACCG 60.750 63.158 0.00 0.00 35.50 4.94
2394 2421 2.409870 CCTTGGCAGAATCCACCGC 61.410 63.158 0.00 0.00 35.50 5.68
2395 2422 1.675310 CTTGGCAGAATCCACCGCA 60.675 57.895 0.00 0.00 35.50 5.69
2430 2457 2.579201 CCACCGAAGACGAGGCAT 59.421 61.111 0.00 0.00 42.66 4.40
2467 2494 0.458025 CGAGAGGCACGAACCCTAAC 60.458 60.000 0.00 0.00 31.41 2.34
2468 2495 0.108281 GAGAGGCACGAACCCTAACC 60.108 60.000 0.00 0.00 31.41 2.85
2482 2509 3.330998 ACCCTAACCTTCTTTCTTGGAGG 59.669 47.826 0.00 0.00 0.00 4.30
2510 2537 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
2531 2558 3.130227 GCCCTGGCTCTAGGTACG 58.870 66.667 0.00 0.00 36.02 3.67
2532 2559 1.757340 GCCCTGGCTCTAGGTACGT 60.757 63.158 0.00 0.00 36.02 3.57
2533 2560 2.017559 GCCCTGGCTCTAGGTACGTG 62.018 65.000 0.00 0.00 36.02 4.49
2534 2561 1.437986 CCTGGCTCTAGGTACGTGC 59.562 63.158 0.00 0.00 32.99 5.34
2535 2562 1.038130 CCTGGCTCTAGGTACGTGCT 61.038 60.000 3.01 0.00 32.99 4.40
2536 2563 0.101399 CTGGCTCTAGGTACGTGCTG 59.899 60.000 3.01 0.00 0.00 4.41
2537 2564 0.323087 TGGCTCTAGGTACGTGCTGA 60.323 55.000 3.01 0.00 0.00 4.26
2538 2565 1.033574 GGCTCTAGGTACGTGCTGAT 58.966 55.000 3.01 0.00 0.00 2.90
2539 2566 1.269309 GGCTCTAGGTACGTGCTGATG 60.269 57.143 3.01 0.00 0.00 3.07
2540 2567 1.405821 GCTCTAGGTACGTGCTGATGT 59.594 52.381 3.01 0.00 0.00 3.06
2541 2568 2.796383 GCTCTAGGTACGTGCTGATGTG 60.796 54.545 3.01 0.00 0.00 3.21
2542 2569 2.683362 CTCTAGGTACGTGCTGATGTGA 59.317 50.000 3.01 0.00 0.00 3.58
2543 2570 3.288092 TCTAGGTACGTGCTGATGTGAT 58.712 45.455 3.01 0.00 0.00 3.06
2544 2571 3.699538 TCTAGGTACGTGCTGATGTGATT 59.300 43.478 3.01 0.00 0.00 2.57
2545 2572 3.334583 AGGTACGTGCTGATGTGATTT 57.665 42.857 3.01 0.00 0.00 2.17
2546 2573 4.465632 AGGTACGTGCTGATGTGATTTA 57.534 40.909 3.01 0.00 0.00 1.40
2547 2574 5.023533 AGGTACGTGCTGATGTGATTTAT 57.976 39.130 3.01 0.00 0.00 1.40
2548 2575 6.156748 AGGTACGTGCTGATGTGATTTATA 57.843 37.500 3.01 0.00 0.00 0.98
2549 2576 6.578944 AGGTACGTGCTGATGTGATTTATAA 58.421 36.000 3.01 0.00 0.00 0.98
2550 2577 7.217200 AGGTACGTGCTGATGTGATTTATAAT 58.783 34.615 3.01 0.00 0.00 1.28
2551 2578 7.171508 AGGTACGTGCTGATGTGATTTATAATG 59.828 37.037 3.01 0.00 0.00 1.90
2552 2579 7.170828 GGTACGTGCTGATGTGATTTATAATGA 59.829 37.037 3.01 0.00 0.00 2.57
2553 2580 7.734924 ACGTGCTGATGTGATTTATAATGAT 57.265 32.000 0.00 0.00 0.00 2.45
2554 2581 7.800767 ACGTGCTGATGTGATTTATAATGATC 58.199 34.615 0.00 0.00 0.00 2.92
2555 2582 7.658982 ACGTGCTGATGTGATTTATAATGATCT 59.341 33.333 0.00 0.00 0.00 2.75
2556 2583 8.501580 CGTGCTGATGTGATTTATAATGATCTT 58.498 33.333 0.00 0.00 0.00 2.40
2557 2584 9.608617 GTGCTGATGTGATTTATAATGATCTTG 57.391 33.333 0.00 0.00 0.00 3.02
2558 2585 9.563748 TGCTGATGTGATTTATAATGATCTTGA 57.436 29.630 0.00 0.00 0.00 3.02
2565 2592 9.622004 GTGATTTATAATGATCTTGATGCAAGG 57.378 33.333 7.27 0.00 41.33 3.61
2566 2593 8.301720 TGATTTATAATGATCTTGATGCAAGGC 58.698 33.333 7.27 1.76 41.33 4.35
2567 2594 7.585579 TTTATAATGATCTTGATGCAAGGCA 57.414 32.000 7.27 6.69 44.86 4.75
2576 2603 3.057548 TGCAAGGCATGGCACTCG 61.058 61.111 22.64 7.42 34.58 4.18
2577 2604 4.487412 GCAAGGCATGGCACTCGC 62.487 66.667 22.64 13.57 37.44 5.03
2578 2605 3.057548 CAAGGCATGGCACTCGCA 61.058 61.111 22.64 0.00 41.24 5.10
2579 2606 2.282391 AAGGCATGGCACTCGCAA 60.282 55.556 22.64 0.00 41.24 4.85
2580 2607 1.902918 AAGGCATGGCACTCGCAAA 60.903 52.632 22.64 0.00 41.24 3.68
2581 2608 1.870055 AAGGCATGGCACTCGCAAAG 61.870 55.000 22.64 0.00 41.24 2.77
2582 2609 2.505557 GCATGGCACTCGCAAAGC 60.506 61.111 0.00 0.00 41.24 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.315749 GTGGAGGAAGTATCGTAGACCTG 59.684 52.174 0.00 0.00 42.51 4.00
1 2 3.553904 GTGGAGGAAGTATCGTAGACCT 58.446 50.000 0.00 0.00 42.51 3.85
2 3 2.290093 CGTGGAGGAAGTATCGTAGACC 59.710 54.545 0.00 0.00 42.51 3.85
3 4 2.941720 ACGTGGAGGAAGTATCGTAGAC 59.058 50.000 0.00 0.00 42.51 2.59
5 6 2.941064 TGACGTGGAGGAAGTATCGTAG 59.059 50.000 0.00 0.00 0.00 3.51
6 7 2.989909 TGACGTGGAGGAAGTATCGTA 58.010 47.619 0.00 0.00 0.00 3.43
8 9 2.933495 TTGACGTGGAGGAAGTATCG 57.067 50.000 0.00 0.00 0.00 2.92
9 10 4.312443 TGTTTTGACGTGGAGGAAGTATC 58.688 43.478 0.00 0.00 0.00 2.24
10 11 4.345859 TGTTTTGACGTGGAGGAAGTAT 57.654 40.909 0.00 0.00 0.00 2.12
11 12 3.823281 TGTTTTGACGTGGAGGAAGTA 57.177 42.857 0.00 0.00 0.00 2.24
12 13 2.702592 TGTTTTGACGTGGAGGAAGT 57.297 45.000 0.00 0.00 0.00 3.01
13 14 3.125316 GCTATGTTTTGACGTGGAGGAAG 59.875 47.826 0.00 0.00 0.00 3.46
14 15 3.071479 GCTATGTTTTGACGTGGAGGAA 58.929 45.455 0.00 0.00 0.00 3.36
15 16 2.695359 GCTATGTTTTGACGTGGAGGA 58.305 47.619 0.00 0.00 0.00 3.71
16 17 1.393539 CGCTATGTTTTGACGTGGAGG 59.606 52.381 0.00 0.00 0.00 4.30
17 18 1.201921 GCGCTATGTTTTGACGTGGAG 60.202 52.381 0.00 0.00 0.00 3.86
18 19 0.793861 GCGCTATGTTTTGACGTGGA 59.206 50.000 0.00 0.00 0.00 4.02
19 20 0.515127 TGCGCTATGTTTTGACGTGG 59.485 50.000 9.73 0.00 0.00 4.94
20 21 2.525750 ATGCGCTATGTTTTGACGTG 57.474 45.000 9.73 0.00 0.00 4.49
21 22 3.062099 CAGTATGCGCTATGTTTTGACGT 59.938 43.478 9.73 0.00 0.00 4.34
22 23 3.597324 CAGTATGCGCTATGTTTTGACG 58.403 45.455 9.73 0.00 0.00 4.35
37 38 4.201753 CCGACTCAAGACAAATGCAGTATG 60.202 45.833 0.00 0.00 40.87 2.39
38 39 3.935203 CCGACTCAAGACAAATGCAGTAT 59.065 43.478 0.00 0.00 0.00 2.12
39 40 3.006430 TCCGACTCAAGACAAATGCAGTA 59.994 43.478 0.00 0.00 0.00 2.74
40 41 2.146342 CCGACTCAAGACAAATGCAGT 58.854 47.619 0.00 0.00 0.00 4.40
41 42 2.416747 TCCGACTCAAGACAAATGCAG 58.583 47.619 0.00 0.00 0.00 4.41
42 43 2.542020 TCCGACTCAAGACAAATGCA 57.458 45.000 0.00 0.00 0.00 3.96
43 44 4.425577 AAATCCGACTCAAGACAAATGC 57.574 40.909 0.00 0.00 0.00 3.56
46 47 9.496873 TCTTTATAAAATCCGACTCAAGACAAA 57.503 29.630 0.00 0.00 0.00 2.83
47 48 9.667107 ATCTTTATAAAATCCGACTCAAGACAA 57.333 29.630 0.00 0.00 0.00 3.18
48 49 9.667107 AATCTTTATAAAATCCGACTCAAGACA 57.333 29.630 0.00 0.00 0.00 3.41
49 50 9.922305 CAATCTTTATAAAATCCGACTCAAGAC 57.078 33.333 0.00 0.00 0.00 3.01
50 51 9.884636 TCAATCTTTATAAAATCCGACTCAAGA 57.115 29.630 0.00 0.00 0.00 3.02
51 52 9.922305 GTCAATCTTTATAAAATCCGACTCAAG 57.078 33.333 0.00 0.00 0.00 3.02
52 53 8.889717 GGTCAATCTTTATAAAATCCGACTCAA 58.110 33.333 0.00 0.00 0.00 3.02
53 54 8.044309 TGGTCAATCTTTATAAAATCCGACTCA 58.956 33.333 0.00 3.26 0.00 3.41
54 55 8.433421 TGGTCAATCTTTATAAAATCCGACTC 57.567 34.615 0.00 1.22 0.00 3.36
55 56 8.801882 TTGGTCAATCTTTATAAAATCCGACT 57.198 30.769 0.00 0.00 0.00 4.18
56 57 8.674607 ACTTGGTCAATCTTTATAAAATCCGAC 58.325 33.333 0.00 4.60 0.00 4.79
57 58 8.801882 ACTTGGTCAATCTTTATAAAATCCGA 57.198 30.769 0.00 0.00 0.00 4.55
58 59 9.503427 GAACTTGGTCAATCTTTATAAAATCCG 57.497 33.333 0.00 0.00 0.00 4.18
69 70 9.696917 GTTTTTCATATGAACTTGGTCAATCTT 57.303 29.630 17.76 0.00 33.13 2.40
70 71 8.859090 TGTTTTTCATATGAACTTGGTCAATCT 58.141 29.630 17.76 0.00 33.13 2.40
71 72 9.474920 TTGTTTTTCATATGAACTTGGTCAATC 57.525 29.630 17.76 7.54 33.13 2.67
72 73 9.829507 TTTGTTTTTCATATGAACTTGGTCAAT 57.170 25.926 17.76 0.00 33.13 2.57
73 74 9.829507 ATTTGTTTTTCATATGAACTTGGTCAA 57.170 25.926 17.76 13.24 33.13 3.18
74 75 9.258826 CATTTGTTTTTCATATGAACTTGGTCA 57.741 29.630 17.76 8.70 37.57 4.02
75 76 9.260002 ACATTTGTTTTTCATATGAACTTGGTC 57.740 29.630 17.76 6.50 38.33 4.02
84 85 9.236691 CCCGAGAATACATTTGTTTTTCATATG 57.763 33.333 0.00 0.00 39.94 1.78
85 86 8.413229 CCCCGAGAATACATTTGTTTTTCATAT 58.587 33.333 8.08 0.00 0.00 1.78
86 87 7.612244 TCCCCGAGAATACATTTGTTTTTCATA 59.388 33.333 8.08 0.00 0.00 2.15
87 88 6.435904 TCCCCGAGAATACATTTGTTTTTCAT 59.564 34.615 8.08 0.00 0.00 2.57
88 89 5.770663 TCCCCGAGAATACATTTGTTTTTCA 59.229 36.000 8.08 0.00 0.00 2.69
89 90 6.262193 TCCCCGAGAATACATTTGTTTTTC 57.738 37.500 0.00 0.00 0.00 2.29
90 91 6.658188 TTCCCCGAGAATACATTTGTTTTT 57.342 33.333 0.00 0.00 0.00 1.94
91 92 6.630071 CATTCCCCGAGAATACATTTGTTTT 58.370 36.000 1.01 0.00 43.63 2.43
92 93 5.394115 GCATTCCCCGAGAATACATTTGTTT 60.394 40.000 1.01 0.00 43.63 2.83
93 94 4.097892 GCATTCCCCGAGAATACATTTGTT 59.902 41.667 1.01 0.00 43.63 2.83
94 95 3.632145 GCATTCCCCGAGAATACATTTGT 59.368 43.478 1.01 0.00 43.63 2.83
95 96 3.631686 TGCATTCCCCGAGAATACATTTG 59.368 43.478 1.01 0.00 43.63 2.32
96 97 3.897239 TGCATTCCCCGAGAATACATTT 58.103 40.909 1.01 0.00 43.63 2.32
97 98 3.576078 TGCATTCCCCGAGAATACATT 57.424 42.857 1.01 0.00 43.63 2.71
98 99 3.795688 ATGCATTCCCCGAGAATACAT 57.204 42.857 0.00 7.61 43.63 2.29
99 100 2.705658 AGATGCATTCCCCGAGAATACA 59.294 45.455 0.00 4.24 43.63 2.29
204 206 1.946984 ACCACCGGTCTCTCCAAATA 58.053 50.000 2.59 0.00 35.57 1.40
211 213 1.229082 TAGGCAACCACCGGTCTCT 60.229 57.895 2.59 0.00 33.12 3.10
242 244 1.852157 TGCAGGGAGATGGGTTGGT 60.852 57.895 0.00 0.00 0.00 3.67
331 334 2.359967 GCAGGGAGGAAGTAGCGGT 61.360 63.158 0.00 0.00 0.00 5.68
361 364 2.357009 GACGTACGGATACTGGTGATGT 59.643 50.000 21.06 0.00 0.00 3.06
419 422 3.025262 GGTGAAGATACCGTTCCTCTCT 58.975 50.000 0.00 0.00 0.00 3.10
560 563 1.532505 GCGAACACGCGTATCTTAGGA 60.533 52.381 13.44 0.00 42.84 2.94
660 663 0.858583 TCGCGTTCAACATCACACAG 59.141 50.000 5.77 0.00 0.00 3.66
667 670 2.665649 TACATCCTCGCGTTCAACAT 57.334 45.000 5.77 0.00 0.00 2.71
811 814 0.107456 CGTCATCTCATCCAAGGGGG 59.893 60.000 0.00 0.00 38.37 5.40
826 829 1.806461 GAGCACCACCAGTCTCGTCA 61.806 60.000 0.00 0.00 0.00 4.35
828 831 1.188219 ATGAGCACCACCAGTCTCGT 61.188 55.000 0.00 0.00 0.00 4.18
869 872 2.301583 TGTGTGATCTCATTCCGGACAA 59.698 45.455 1.83 0.00 0.00 3.18
903 906 4.021925 GAGGCTTCGGCAGTGGGT 62.022 66.667 0.00 0.00 43.96 4.51
955 958 3.752747 TCAGGATGTTGTTGTATGCACAG 59.247 43.478 0.00 0.00 34.62 3.66
997 1000 0.107459 GAAGGCAGGACCACCATCTC 60.107 60.000 6.36 0.00 43.14 2.75
1024 1027 1.080093 CCGTACTTTCTGGAGCGCA 60.080 57.895 11.47 0.00 0.00 6.09
1134 1137 1.825242 CGCAGGATCATACCTCCTCCT 60.825 57.143 0.00 0.00 41.29 3.69
1155 1158 1.035923 TGATCTCGCCTCTGTCATCC 58.964 55.000 0.00 0.00 0.00 3.51
1181 1184 1.414158 ACGTAGCTCCCTACATGCAT 58.586 50.000 0.00 0.00 43.33 3.96
1230 1233 3.123620 CCTTCTCTGCACGCTGCC 61.124 66.667 7.38 0.00 44.23 4.85
1304 1307 0.103208 AATCATCGACACCGCCTCTC 59.897 55.000 0.00 0.00 35.37 3.20
1387 1390 1.892474 GATCTCCCTAGCATCGCTTCT 59.108 52.381 0.00 0.00 40.44 2.85
1427 1430 2.766263 TGACTAATCCCGTTCTGCAGAT 59.234 45.455 19.04 2.75 0.00 2.90
1438 1441 2.576615 GGCCAACTCATGACTAATCCC 58.423 52.381 0.00 0.00 0.00 3.85
1503 1506 3.892588 GGTTTACAACAAAGTCCATCCCA 59.107 43.478 0.00 0.00 0.00 4.37
1562 1565 2.900716 TTTTTGCGGGGAAAAAGGAG 57.099 45.000 6.72 0.00 32.36 3.69
1605 1608 6.531948 TCGAAACCGAACATGAAAACATTTTT 59.468 30.769 0.00 0.00 32.51 1.94
1606 1609 6.037098 TCGAAACCGAACATGAAAACATTTT 58.963 32.000 0.00 0.00 32.51 1.82
1607 1610 5.583495 TCGAAACCGAACATGAAAACATTT 58.417 33.333 0.00 0.00 32.51 2.32
1608 1611 5.176407 TCGAAACCGAACATGAAAACATT 57.824 34.783 0.00 0.00 32.51 2.71
1609 1612 4.822036 TCGAAACCGAACATGAAAACAT 57.178 36.364 0.00 0.00 32.51 2.71
1610 1613 4.617808 TTCGAAACCGAACATGAAAACA 57.382 36.364 0.00 0.00 40.65 2.83
1611 1614 5.267776 TCTTTCGAAACCGAACATGAAAAC 58.732 37.500 6.47 0.00 44.58 2.43
1612 1615 5.487153 TCTTTCGAAACCGAACATGAAAA 57.513 34.783 6.47 0.00 44.58 2.29
1613 1616 5.682943 ATCTTTCGAAACCGAACATGAAA 57.317 34.783 6.47 0.00 44.58 2.69
1614 1617 6.788684 TTATCTTTCGAAACCGAACATGAA 57.211 33.333 6.47 0.00 44.58 2.57
1615 1618 6.370442 ACATTATCTTTCGAAACCGAACATGA 59.630 34.615 18.79 10.11 44.58 3.07
1616 1619 6.542852 ACATTATCTTTCGAAACCGAACATG 58.457 36.000 6.47 11.82 44.58 3.21
1617 1620 6.737254 ACATTATCTTTCGAAACCGAACAT 57.263 33.333 6.47 0.00 44.58 2.71
1618 1621 6.548441 AACATTATCTTTCGAAACCGAACA 57.452 33.333 6.47 0.00 44.58 3.18
1619 1622 7.588488 TGAAAACATTATCTTTCGAAACCGAAC 59.412 33.333 6.47 0.00 44.58 3.95
1620 1623 7.640852 TGAAAACATTATCTTTCGAAACCGAA 58.359 30.769 6.47 1.44 43.40 4.30
1621 1624 7.192148 TGAAAACATTATCTTTCGAAACCGA 57.808 32.000 6.47 4.31 34.84 4.69
1622 1625 7.537306 ACATGAAAACATTATCTTTCGAAACCG 59.463 33.333 6.47 0.00 34.84 4.44
1623 1626 8.638565 CACATGAAAACATTATCTTTCGAAACC 58.361 33.333 6.47 0.00 34.84 3.27
1624 1627 9.393249 TCACATGAAAACATTATCTTTCGAAAC 57.607 29.630 6.47 0.00 34.84 2.78
1626 1629 9.558648 CATCACATGAAAACATTATCTTTCGAA 57.441 29.630 0.00 0.00 34.84 3.71
1627 1630 8.945057 TCATCACATGAAAACATTATCTTTCGA 58.055 29.630 0.00 0.00 36.11 3.71
1628 1631 9.558648 TTCATCACATGAAAACATTATCTTTCG 57.441 29.630 0.00 0.00 45.57 3.46
1658 1661 8.513774 GCAAAGAAGAAGAAGAAGAAGATCATT 58.486 33.333 0.00 0.00 0.00 2.57
1659 1662 7.148440 CGCAAAGAAGAAGAAGAAGAAGATCAT 60.148 37.037 0.00 0.00 0.00 2.45
1660 1663 6.146837 CGCAAAGAAGAAGAAGAAGAAGATCA 59.853 38.462 0.00 0.00 0.00 2.92
1661 1664 6.402011 CCGCAAAGAAGAAGAAGAAGAAGATC 60.402 42.308 0.00 0.00 0.00 2.75
1662 1665 5.411053 CCGCAAAGAAGAAGAAGAAGAAGAT 59.589 40.000 0.00 0.00 0.00 2.40
1663 1666 4.752101 CCGCAAAGAAGAAGAAGAAGAAGA 59.248 41.667 0.00 0.00 0.00 2.87
1664 1667 4.083590 CCCGCAAAGAAGAAGAAGAAGAAG 60.084 45.833 0.00 0.00 0.00 2.85
1665 1668 3.815401 CCCGCAAAGAAGAAGAAGAAGAA 59.185 43.478 0.00 0.00 0.00 2.52
1666 1669 3.181454 ACCCGCAAAGAAGAAGAAGAAGA 60.181 43.478 0.00 0.00 0.00 2.87
1667 1670 3.058639 CACCCGCAAAGAAGAAGAAGAAG 60.059 47.826 0.00 0.00 0.00 2.85
1668 1671 2.878406 CACCCGCAAAGAAGAAGAAGAA 59.122 45.455 0.00 0.00 0.00 2.52
1669 1672 2.104111 TCACCCGCAAAGAAGAAGAAGA 59.896 45.455 0.00 0.00 0.00 2.87
1670 1673 2.494059 TCACCCGCAAAGAAGAAGAAG 58.506 47.619 0.00 0.00 0.00 2.85
1671 1674 2.631160 TCACCCGCAAAGAAGAAGAA 57.369 45.000 0.00 0.00 0.00 2.52
1672 1675 2.038426 TCATCACCCGCAAAGAAGAAGA 59.962 45.455 0.00 0.00 0.00 2.87
1673 1676 2.426522 TCATCACCCGCAAAGAAGAAG 58.573 47.619 0.00 0.00 0.00 2.85
1674 1677 2.559698 TCATCACCCGCAAAGAAGAA 57.440 45.000 0.00 0.00 0.00 2.52
1675 1678 2.559698 TTCATCACCCGCAAAGAAGA 57.440 45.000 0.00 0.00 0.00 2.87
1676 1679 6.618287 TTATATTCATCACCCGCAAAGAAG 57.382 37.500 0.00 0.00 0.00 2.85
1677 1680 6.770303 TCATTATATTCATCACCCGCAAAGAA 59.230 34.615 0.00 0.00 0.00 2.52
1678 1681 6.295249 TCATTATATTCATCACCCGCAAAGA 58.705 36.000 0.00 0.00 0.00 2.52
1679 1682 6.558771 TCATTATATTCATCACCCGCAAAG 57.441 37.500 0.00 0.00 0.00 2.77
1680 1683 7.523293 AATCATTATATTCATCACCCGCAAA 57.477 32.000 0.00 0.00 0.00 3.68
1681 1684 7.523293 AAATCATTATATTCATCACCCGCAA 57.477 32.000 0.00 0.00 0.00 4.85
1682 1685 7.523293 AAAATCATTATATTCATCACCCGCA 57.477 32.000 0.00 0.00 0.00 5.69
1935 1938 2.556287 CGGCGGTTGCTGTTTCTC 59.444 61.111 0.00 0.00 42.79 2.87
1963 1966 3.567164 TGGATCCTTCCGATCTACGTTAC 59.433 47.826 14.23 0.00 45.90 2.50
1997 2001 1.376856 CGTTGTTCGTCTACGTTCGTC 59.623 52.381 0.00 0.00 39.58 4.20
2133 2159 6.157471 GGGGGTTCCTTTACAGTCTTTCTATA 59.843 42.308 0.00 0.00 0.00 1.31
2151 2177 5.374071 CACCAATTATACTGTAGGGGGTTC 58.626 45.833 0.00 0.00 0.00 3.62
2158 2184 7.027161 GGTTTGTTGCACCAATTATACTGTAG 58.973 38.462 0.00 0.00 34.04 2.74
2161 2187 5.167845 GGGTTTGTTGCACCAATTATACTG 58.832 41.667 0.00 0.00 35.80 2.74
2182 2208 2.620242 GCATGGTACTTGCAATTTGGG 58.380 47.619 14.01 0.00 39.90 4.12
2183 2209 2.234414 AGGCATGGTACTTGCAATTTGG 59.766 45.455 18.60 0.00 41.95 3.28
2197 2223 0.604578 CACCCAAGTTCAAGGCATGG 59.395 55.000 0.00 0.00 0.00 3.66
2209 2235 2.440599 CCTTCCCACCCACCCAAG 59.559 66.667 0.00 0.00 0.00 3.61
2210 2236 3.909651 GCCTTCCCACCCACCCAA 61.910 66.667 0.00 0.00 0.00 4.12
2262 2288 5.638530 AGATGAAATAAAGGTCTCCCCTC 57.361 43.478 0.00 0.00 45.47 4.30
2279 2305 2.735772 GGCGGCTCCCTGAAGATGA 61.736 63.158 0.00 0.00 0.00 2.92
2348 2375 3.685550 CGGGATGGCTCCATTTTTAGTCT 60.686 47.826 2.53 0.00 44.08 3.24
2381 2408 2.045926 AGGTGCGGTGGATTCTGC 60.046 61.111 0.00 0.00 39.84 4.26
2385 2412 1.077501 CATGGAGGTGCGGTGGATT 60.078 57.895 0.00 0.00 0.00 3.01
2393 2420 2.512896 CTAGGGCCATGGAGGTGC 59.487 66.667 18.40 0.00 40.61 5.01
2394 2421 2.455565 CCCTAGGGCCATGGAGGTG 61.456 68.421 16.90 3.76 40.61 4.00
2395 2422 2.039405 CCCTAGGGCCATGGAGGT 60.039 66.667 16.90 0.00 40.61 3.85
2446 2473 4.070552 GGGTTCGTGCCTCTCGCT 62.071 66.667 0.00 0.00 38.78 4.93
2459 2486 4.202577 CCTCCAAGAAAGAAGGTTAGGGTT 60.203 45.833 0.00 0.00 0.00 4.11
2462 2489 4.323868 CCTCCTCCAAGAAAGAAGGTTAGG 60.324 50.000 0.00 0.00 0.00 2.69
2467 2494 2.238395 CCTCCTCCTCCAAGAAAGAAGG 59.762 54.545 0.00 0.00 0.00 3.46
2468 2495 3.177228 TCCTCCTCCTCCAAGAAAGAAG 58.823 50.000 0.00 0.00 0.00 2.85
2482 2509 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
2519 2546 1.033574 ATCAGCACGTACCTAGAGCC 58.966 55.000 0.00 0.00 0.00 4.70
2520 2547 1.405821 ACATCAGCACGTACCTAGAGC 59.594 52.381 0.00 0.00 0.00 4.09
2521 2548 2.683362 TCACATCAGCACGTACCTAGAG 59.317 50.000 0.00 0.00 0.00 2.43
2522 2549 2.718563 TCACATCAGCACGTACCTAGA 58.281 47.619 0.00 0.00 0.00 2.43
2523 2550 3.717400 ATCACATCAGCACGTACCTAG 57.283 47.619 0.00 0.00 0.00 3.02
2524 2551 4.465632 AAATCACATCAGCACGTACCTA 57.534 40.909 0.00 0.00 0.00 3.08
2525 2552 3.334583 AAATCACATCAGCACGTACCT 57.665 42.857 0.00 0.00 0.00 3.08
2526 2553 6.838198 TTATAAATCACATCAGCACGTACC 57.162 37.500 0.00 0.00 0.00 3.34
2527 2554 8.072238 TCATTATAAATCACATCAGCACGTAC 57.928 34.615 0.00 0.00 0.00 3.67
2528 2555 8.831715 ATCATTATAAATCACATCAGCACGTA 57.168 30.769 0.00 0.00 0.00 3.57
2529 2556 7.658982 AGATCATTATAAATCACATCAGCACGT 59.341 33.333 0.00 0.00 0.00 4.49
2530 2557 8.026341 AGATCATTATAAATCACATCAGCACG 57.974 34.615 0.00 0.00 0.00 5.34
2531 2558 9.608617 CAAGATCATTATAAATCACATCAGCAC 57.391 33.333 0.00 0.00 0.00 4.40
2532 2559 9.563748 TCAAGATCATTATAAATCACATCAGCA 57.436 29.630 0.00 0.00 0.00 4.41
2539 2566 9.622004 CCTTGCATCAAGATCATTATAAATCAC 57.378 33.333 8.04 0.00 43.42 3.06
2540 2567 8.301720 GCCTTGCATCAAGATCATTATAAATCA 58.698 33.333 8.04 0.00 43.42 2.57
2541 2568 8.301720 TGCCTTGCATCAAGATCATTATAAATC 58.698 33.333 8.04 0.00 43.42 2.17
2542 2569 8.185506 TGCCTTGCATCAAGATCATTATAAAT 57.814 30.769 8.04 0.00 43.42 1.40
2543 2570 7.585579 TGCCTTGCATCAAGATCATTATAAA 57.414 32.000 8.04 0.00 43.42 1.40
2559 2586 3.057548 CGAGTGCCATGCCTTGCA 61.058 61.111 0.00 0.00 44.86 4.08
2560 2587 4.487412 GCGAGTGCCATGCCTTGC 62.487 66.667 0.00 0.00 32.39 4.01
2561 2588 2.144833 TTTGCGAGTGCCATGCCTTG 62.145 55.000 0.00 0.00 41.78 3.61
2562 2589 1.870055 CTTTGCGAGTGCCATGCCTT 61.870 55.000 0.00 0.00 41.78 4.35
2563 2590 2.282391 TTTGCGAGTGCCATGCCT 60.282 55.556 0.00 0.00 41.78 4.75
2564 2591 2.180017 CTTTGCGAGTGCCATGCC 59.820 61.111 0.00 0.00 41.78 4.40
2565 2592 2.505557 GCTTTGCGAGTGCCATGC 60.506 61.111 0.00 0.00 41.78 4.06


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

AutoCloner maintained by Alex Coulton.