Multiple sequence alignment - TraesCS1A01G269200

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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 TraesCS1A01G269200 chr1A 100.000 4310 0 0 1 4310 463831200 463826891 0.000000e+00 7960.0
1 TraesCS1A01G269200 chr1B 91.581 3611 156 37 751 4310 488218554 488215041 0.000000e+00 4848.0
2 TraesCS1A01G269200 chr1B 83.208 530 62 16 218 726 530483554 530483031 1.090000e-125 460.0
3 TraesCS1A01G269200 chr1B 82.852 554 52 25 218 731 62721832 62721282 1.410000e-124 457.0
4 TraesCS1A01G269200 chr1D 93.658 2570 86 24 1773 4310 364772417 364769893 0.000000e+00 3771.0
5 TraesCS1A01G269200 chr1D 92.265 1086 55 11 732 1791 364773514 364772432 0.000000e+00 1513.0
6 TraesCS1A01G269200 chr4A 88.192 542 35 15 218 736 699937404 699936869 1.700000e-173 619.0
7 TraesCS1A01G269200 chr4A 83.551 535 63 13 218 731 118627369 118626839 1.080000e-130 477.0
8 TraesCS1A01G269200 chr4A 97.222 108 3 0 1 108 455584563 455584670 2.650000e-42 183.0
9 TraesCS1A01G269200 chr4A 98.095 105 2 0 1 105 590522751 590522855 2.650000e-42 183.0
10 TraesCS1A01G269200 chr4A 94.737 114 5 1 1 114 171275612 171275500 4.430000e-40 176.0
11 TraesCS1A01G269200 chr4A 95.455 44 2 0 169 212 699937497 699937454 2.150000e-08 71.3
12 TraesCS1A01G269200 chr5A 87.500 512 57 7 218 726 338923361 338923868 6.210000e-163 584.0
13 TraesCS1A01G269200 chr5A 84.645 521 59 15 218 726 37633088 37633599 2.310000e-137 499.0
14 TraesCS1A01G269200 chr7D 87.238 525 38 11 218 720 626548328 626548845 4.840000e-159 571.0
15 TraesCS1A01G269200 chr7D 92.562 121 7 2 1 121 78512594 78512476 5.730000e-39 172.0
16 TraesCS1A01G269200 chrUn 86.567 536 49 12 218 732 85387321 85386788 1.740000e-158 569.0
17 TraesCS1A01G269200 chrUn 88.953 172 19 0 1945 2116 300810632 300810803 3.380000e-51 213.0
18 TraesCS1A01G269200 chrUn 95.745 47 2 0 167 213 42253359 42253313 4.620000e-10 76.8
19 TraesCS1A01G269200 chr4D 87.308 520 36 18 218 710 202238872 202238356 6.250000e-158 568.0
20 TraesCS1A01G269200 chr4D 76.923 520 90 18 229 742 312749789 312750284 7.100000e-68 268.0
21 TraesCS1A01G269200 chr4B 87.123 497 49 14 218 710 622759466 622758981 2.270000e-152 549.0
22 TraesCS1A01G269200 chr4B 85.413 521 55 16 218 726 381399625 381399114 4.940000e-144 521.0
23 TraesCS1A01G269200 chr4B 95.556 45 2 0 169 213 622759560 622759516 5.980000e-09 73.1
24 TraesCS1A01G269200 chr2B 85.135 518 70 7 218 732 132499004 132498491 1.370000e-144 523.0
25 TraesCS1A01G269200 chr2B 90.625 128 12 0 1 128 465147505 465147378 2.060000e-38 171.0
26 TraesCS1A01G269200 chr5D 82.136 515 56 18 2331 2816 142542095 142542602 4.010000e-110 409.0
27 TraesCS1A01G269200 chr5D 95.652 46 2 0 168 213 478597890 478597845 1.660000e-09 75.0
28 TraesCS1A01G269200 chr2D 81.532 509 58 22 2337 2816 321610038 321609537 1.880000e-103 387.0
29 TraesCS1A01G269200 chr7A 80.194 515 56 25 2331 2816 616160027 616160524 1.150000e-90 344.0
30 TraesCS1A01G269200 chr7A 94.783 115 4 2 1 114 524674371 524674484 1.230000e-40 178.0
31 TraesCS1A01G269200 chr6D 83.612 299 34 12 2008 2300 384363757 384364046 2.560000e-67 267.0
32 TraesCS1A01G269200 chr6D 83.612 299 34 10 2008 2300 384368795 384369084 2.560000e-67 267.0
33 TraesCS1A01G269200 chr6D 82.724 301 32 17 2008 2300 384366940 384367228 2.570000e-62 250.0
34 TraesCS1A01G269200 chr6B 90.116 172 17 0 1945 2116 383821979 383821808 1.560000e-54 224.0
35 TraesCS1A01G269200 chr6B 88.660 97 10 1 642 738 231144174 231144269 2.720000e-22 117.0
36 TraesCS1A01G269200 chr6B 97.778 45 1 0 169 213 601119730 601119774 1.290000e-10 78.7
37 TraesCS1A01G269200 chr2A 98.095 105 2 0 1 105 677752485 677752381 2.650000e-42 183.0
38 TraesCS1A01G269200 chr2A 95.575 113 5 0 1 113 234405762 234405874 9.520000e-42 182.0
39 TraesCS1A01G269200 chr2A 94.167 120 6 1 1 120 552941837 552941955 9.520000e-42 182.0
40 TraesCS1A01G269200 chr7B 95.745 47 2 0 167 213 488389609 488389563 4.620000e-10 76.8
41 TraesCS1A01G269200 chr7B 95.652 46 2 0 168 213 137448795 137448750 1.660000e-09 75.0
42 TraesCS1A01G269200 chr3B 93.878 49 3 0 165 213 391488232 391488184 1.660000e-09 75.0


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 TraesCS1A01G269200 chr1A 463826891 463831200 4309 True 7960.000000 7960 100.0000 1 4310 1 chr1A.!!$R1 4309
1 TraesCS1A01G269200 chr1B 488215041 488218554 3513 True 4848.000000 4848 91.5810 751 4310 1 chr1B.!!$R2 3559
2 TraesCS1A01G269200 chr1B 530483031 530483554 523 True 460.000000 460 83.2080 218 726 1 chr1B.!!$R3 508
3 TraesCS1A01G269200 chr1B 62721282 62721832 550 True 457.000000 457 82.8520 218 731 1 chr1B.!!$R1 513
4 TraesCS1A01G269200 chr1D 364769893 364773514 3621 True 2642.000000 3771 92.9615 732 4310 2 chr1D.!!$R1 3578
5 TraesCS1A01G269200 chr4A 118626839 118627369 530 True 477.000000 477 83.5510 218 731 1 chr4A.!!$R1 513
6 TraesCS1A01G269200 chr4A 699936869 699937497 628 True 345.150000 619 91.8235 169 736 2 chr4A.!!$R3 567
7 TraesCS1A01G269200 chr5A 338923361 338923868 507 False 584.000000 584 87.5000 218 726 1 chr5A.!!$F2 508
8 TraesCS1A01G269200 chr5A 37633088 37633599 511 False 499.000000 499 84.6450 218 726 1 chr5A.!!$F1 508
9 TraesCS1A01G269200 chr7D 626548328 626548845 517 False 571.000000 571 87.2380 218 720 1 chr7D.!!$F1 502
10 TraesCS1A01G269200 chrUn 85386788 85387321 533 True 569.000000 569 86.5670 218 732 1 chrUn.!!$R2 514
11 TraesCS1A01G269200 chr4D 202238356 202238872 516 True 568.000000 568 87.3080 218 710 1 chr4D.!!$R1 492
12 TraesCS1A01G269200 chr4B 381399114 381399625 511 True 521.000000 521 85.4130 218 726 1 chr4B.!!$R1 508
13 TraesCS1A01G269200 chr4B 622758981 622759560 579 True 311.050000 549 91.3395 169 710 2 chr4B.!!$R2 541
14 TraesCS1A01G269200 chr2B 132498491 132499004 513 True 523.000000 523 85.1350 218 732 1 chr2B.!!$R1 514
15 TraesCS1A01G269200 chr5D 142542095 142542602 507 False 409.000000 409 82.1360 2331 2816 1 chr5D.!!$F1 485
16 TraesCS1A01G269200 chr2D 321609537 321610038 501 True 387.000000 387 81.5320 2337 2816 1 chr2D.!!$R1 479
17 TraesCS1A01G269200 chr6D 384363757 384369084 5327 False 261.333333 267 83.3160 2008 2300 3 chr6D.!!$F1 292

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
749 866 0.036875 AGGTAGGACTGCTTGTTGGC 59.963 55.0 0.0 0.0 0.0 4.52 F
915 1056 0.610687 GCCATAATCCCTCTCCCTCG 59.389 60.0 0.0 0.0 0.0 4.63 F
1941 2131 0.254178 AGCTGGGCATGGTAAGACAG 59.746 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 1907 0.453282 CTCAGCACAATCAAACGCCG 60.453 55.000 0.00 0.0 0.0 6.46 R
2603 7839 2.289133 TGTTAAGACCACGTATGCAGCA 60.289 45.455 0.00 0.0 0.0 4.41 R
3508 8799 0.031616 CTCAGACCCCTAGAGGCCTT 60.032 60.000 6.77 0.0 0.0 4.35 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
26 27 9.771534 GATAGAACTTGAGGTAATATTTGCTCT 57.228 33.333 0.00 0.00 0.00 4.09
28 29 8.950208 AGAACTTGAGGTAATATTTGCTCTAC 57.050 34.615 0.00 0.00 0.00 2.59
29 30 7.988028 AGAACTTGAGGTAATATTTGCTCTACC 59.012 37.037 0.00 0.00 35.08 3.18
30 31 7.439108 ACTTGAGGTAATATTTGCTCTACCT 57.561 36.000 5.23 5.23 45.45 3.08
31 32 7.862675 ACTTGAGGTAATATTTGCTCTACCTT 58.137 34.615 6.76 0.00 43.34 3.50
32 33 8.329502 ACTTGAGGTAATATTTGCTCTACCTTT 58.670 33.333 6.76 0.00 43.34 3.11
33 34 9.832445 CTTGAGGTAATATTTGCTCTACCTTTA 57.168 33.333 6.76 0.00 43.34 1.85
34 35 9.832445 TTGAGGTAATATTTGCTCTACCTTTAG 57.168 33.333 6.76 0.00 43.34 1.85
35 36 7.931948 TGAGGTAATATTTGCTCTACCTTTAGC 59.068 37.037 6.76 0.00 43.34 3.09
36 37 8.035448 AGGTAATATTTGCTCTACCTTTAGCT 57.965 34.615 0.00 0.00 41.07 3.32
37 38 8.151596 AGGTAATATTTGCTCTACCTTTAGCTC 58.848 37.037 0.00 0.00 41.07 4.09
38 39 7.388224 GGTAATATTTGCTCTACCTTTAGCTCC 59.612 40.741 0.00 0.00 39.53 4.70
39 40 6.755542 ATATTTGCTCTACCTTTAGCTCCT 57.244 37.500 0.00 0.00 39.53 3.69
40 41 4.910458 TTTGCTCTACCTTTAGCTCCTT 57.090 40.909 0.00 0.00 39.53 3.36
41 42 3.895232 TGCTCTACCTTTAGCTCCTTG 57.105 47.619 0.00 0.00 39.53 3.61
42 43 3.173965 TGCTCTACCTTTAGCTCCTTGT 58.826 45.455 0.00 0.00 39.53 3.16
43 44 3.583086 TGCTCTACCTTTAGCTCCTTGTT 59.417 43.478 0.00 0.00 39.53 2.83
44 45 3.935828 GCTCTACCTTTAGCTCCTTGTTG 59.064 47.826 0.00 0.00 35.80 3.33
45 46 4.508662 CTCTACCTTTAGCTCCTTGTTGG 58.491 47.826 0.00 0.00 37.10 3.77
46 47 2.586648 ACCTTTAGCTCCTTGTTGGG 57.413 50.000 0.00 0.00 36.20 4.12
47 48 1.780919 ACCTTTAGCTCCTTGTTGGGT 59.219 47.619 0.00 0.00 36.20 4.51
48 49 2.177016 ACCTTTAGCTCCTTGTTGGGTT 59.823 45.455 0.00 0.00 36.20 4.11
49 50 2.820197 CCTTTAGCTCCTTGTTGGGTTC 59.180 50.000 0.00 0.00 36.20 3.62
50 51 2.178912 TTAGCTCCTTGTTGGGTTCG 57.821 50.000 0.00 0.00 36.20 3.95
51 52 1.344065 TAGCTCCTTGTTGGGTTCGA 58.656 50.000 0.00 0.00 36.20 3.71
52 53 0.250338 AGCTCCTTGTTGGGTTCGAC 60.250 55.000 0.00 0.00 36.20 4.20
53 54 0.534203 GCTCCTTGTTGGGTTCGACA 60.534 55.000 0.00 0.00 35.60 4.35
54 55 1.226746 CTCCTTGTTGGGTTCGACAC 58.773 55.000 0.00 0.00 37.04 3.67
55 56 0.834612 TCCTTGTTGGGTTCGACACT 59.165 50.000 0.00 0.00 37.04 3.55
56 57 1.202604 TCCTTGTTGGGTTCGACACTC 60.203 52.381 0.00 0.00 37.04 3.51
57 58 1.202651 CCTTGTTGGGTTCGACACTCT 60.203 52.381 0.00 0.00 37.04 3.24
58 59 2.561569 CTTGTTGGGTTCGACACTCTT 58.438 47.619 0.00 0.00 37.04 2.85
59 60 3.493699 CCTTGTTGGGTTCGACACTCTTA 60.494 47.826 0.00 0.00 37.04 2.10
60 61 3.102052 TGTTGGGTTCGACACTCTTAC 57.898 47.619 0.00 0.00 32.62 2.34
61 62 2.696707 TGTTGGGTTCGACACTCTTACT 59.303 45.455 0.00 0.00 32.62 2.24
62 63 3.133362 TGTTGGGTTCGACACTCTTACTT 59.867 43.478 0.00 0.00 32.62 2.24
63 64 4.341806 TGTTGGGTTCGACACTCTTACTTA 59.658 41.667 0.00 0.00 32.62 2.24
64 65 5.011329 TGTTGGGTTCGACACTCTTACTTAT 59.989 40.000 0.00 0.00 32.62 1.73
65 66 5.320549 TGGGTTCGACACTCTTACTTATC 57.679 43.478 0.00 0.00 0.00 1.75
66 67 4.142534 TGGGTTCGACACTCTTACTTATCG 60.143 45.833 0.00 0.00 0.00 2.92
67 68 4.095483 GGGTTCGACACTCTTACTTATCGA 59.905 45.833 0.00 0.00 36.85 3.59
68 69 5.392380 GGGTTCGACACTCTTACTTATCGAA 60.392 44.000 2.99 2.99 43.90 3.71
69 70 6.088824 GGTTCGACACTCTTACTTATCGAAA 58.911 40.000 8.30 0.00 46.48 3.46
70 71 6.583806 GGTTCGACACTCTTACTTATCGAAAA 59.416 38.462 8.30 0.00 46.48 2.29
71 72 7.410193 GGTTCGACACTCTTACTTATCGAAAAC 60.410 40.741 8.30 2.36 46.48 2.43
72 73 6.906659 TCGACACTCTTACTTATCGAAAACT 58.093 36.000 0.00 0.00 35.80 2.66
73 74 6.800408 TCGACACTCTTACTTATCGAAAACTG 59.200 38.462 0.00 0.00 35.80 3.16
74 75 6.581542 CGACACTCTTACTTATCGAAAACTGT 59.418 38.462 0.00 0.00 0.00 3.55
75 76 7.114529 CGACACTCTTACTTATCGAAAACTGTT 59.885 37.037 0.00 0.00 0.00 3.16
76 77 8.073355 ACACTCTTACTTATCGAAAACTGTTG 57.927 34.615 0.00 0.00 0.00 3.33
77 78 7.010023 CACTCTTACTTATCGAAAACTGTTGC 58.990 38.462 0.00 0.00 0.00 4.17
78 79 6.128902 ACTCTTACTTATCGAAAACTGTTGCG 60.129 38.462 9.05 9.05 37.10 4.85
83 84 1.153353 TCGAAAACTGTTGCGATCCC 58.847 50.000 12.71 0.00 39.99 3.85
84 85 0.168128 CGAAAACTGTTGCGATCCCC 59.832 55.000 9.57 0.00 38.11 4.81
85 86 1.534729 GAAAACTGTTGCGATCCCCT 58.465 50.000 0.00 0.00 0.00 4.79
86 87 2.706890 GAAAACTGTTGCGATCCCCTA 58.293 47.619 0.00 0.00 0.00 3.53
87 88 3.279434 GAAAACTGTTGCGATCCCCTAT 58.721 45.455 0.00 0.00 0.00 2.57
88 89 4.448210 GAAAACTGTTGCGATCCCCTATA 58.552 43.478 0.00 0.00 0.00 1.31
89 90 3.470645 AACTGTTGCGATCCCCTATAC 57.529 47.619 0.00 0.00 0.00 1.47
90 91 2.679082 ACTGTTGCGATCCCCTATACT 58.321 47.619 0.00 0.00 0.00 2.12
91 92 3.039011 ACTGTTGCGATCCCCTATACTT 58.961 45.455 0.00 0.00 0.00 2.24
92 93 3.181465 ACTGTTGCGATCCCCTATACTTG 60.181 47.826 0.00 0.00 0.00 3.16
93 94 2.769663 TGTTGCGATCCCCTATACTTGT 59.230 45.455 0.00 0.00 0.00 3.16
94 95 3.131396 GTTGCGATCCCCTATACTTGTG 58.869 50.000 0.00 0.00 0.00 3.33
95 96 1.691976 TGCGATCCCCTATACTTGTGG 59.308 52.381 0.00 0.00 0.00 4.17
96 97 1.002087 GCGATCCCCTATACTTGTGGG 59.998 57.143 0.00 0.00 40.59 4.61
97 98 2.326428 CGATCCCCTATACTTGTGGGT 58.674 52.381 0.00 0.00 39.31 4.51
98 99 2.704065 CGATCCCCTATACTTGTGGGTT 59.296 50.000 0.00 0.00 39.31 4.11
99 100 3.899360 CGATCCCCTATACTTGTGGGTTA 59.101 47.826 0.00 0.00 39.31 2.85
100 101 4.530946 CGATCCCCTATACTTGTGGGTTAT 59.469 45.833 0.00 0.00 39.31 1.89
101 102 5.337330 CGATCCCCTATACTTGTGGGTTATC 60.337 48.000 0.00 0.00 39.31 1.75
102 103 4.898268 TCCCCTATACTTGTGGGTTATCA 58.102 43.478 0.00 0.00 39.31 2.15
103 104 5.290335 TCCCCTATACTTGTGGGTTATCAA 58.710 41.667 0.00 0.00 39.31 2.57
104 105 5.914716 TCCCCTATACTTGTGGGTTATCAAT 59.085 40.000 0.00 0.00 39.31 2.57
105 106 6.391649 TCCCCTATACTTGTGGGTTATCAATT 59.608 38.462 0.00 0.00 39.31 2.32
106 107 7.573238 TCCCCTATACTTGTGGGTTATCAATTA 59.427 37.037 0.00 0.00 39.31 1.40
107 108 7.664318 CCCCTATACTTGTGGGTTATCAATTAC 59.336 40.741 0.00 0.00 39.31 1.89
108 109 8.437575 CCCTATACTTGTGGGTTATCAATTACT 58.562 37.037 0.00 0.00 36.32 2.24
109 110 9.847224 CCTATACTTGTGGGTTATCAATTACTT 57.153 33.333 0.00 0.00 0.00 2.24
112 113 7.214467 ACTTGTGGGTTATCAATTACTTGTG 57.786 36.000 0.00 0.00 33.87 3.33
113 114 7.001674 ACTTGTGGGTTATCAATTACTTGTGA 58.998 34.615 0.00 0.00 33.87 3.58
114 115 7.504238 ACTTGTGGGTTATCAATTACTTGTGAA 59.496 33.333 0.00 0.00 33.87 3.18
115 116 7.209471 TGTGGGTTATCAATTACTTGTGAAC 57.791 36.000 0.00 0.00 33.87 3.18
116 117 6.773200 TGTGGGTTATCAATTACTTGTGAACA 59.227 34.615 11.61 0.00 33.50 3.18
117 118 7.450014 TGTGGGTTATCAATTACTTGTGAACAT 59.550 33.333 11.61 0.00 33.50 2.71
118 119 8.952278 GTGGGTTATCAATTACTTGTGAACATA 58.048 33.333 11.61 0.00 33.50 2.29
119 120 9.521841 TGGGTTATCAATTACTTGTGAACATAA 57.478 29.630 11.61 0.00 33.50 1.90
125 126 8.415950 TCAATTACTTGTGAACATAATTGGGT 57.584 30.769 19.59 3.65 41.87 4.51
126 127 8.865090 TCAATTACTTGTGAACATAATTGGGTT 58.135 29.630 19.59 0.00 41.87 4.11
129 130 8.693120 TTACTTGTGAACATAATTGGGTTACA 57.307 30.769 0.00 0.00 0.00 2.41
130 131 7.214467 ACTTGTGAACATAATTGGGTTACAG 57.786 36.000 0.00 0.00 0.00 2.74
131 132 7.001674 ACTTGTGAACATAATTGGGTTACAGA 58.998 34.615 0.00 0.00 0.00 3.41
132 133 6.811253 TGTGAACATAATTGGGTTACAGAC 57.189 37.500 0.00 0.00 0.00 3.51
133 134 6.539173 TGTGAACATAATTGGGTTACAGACT 58.461 36.000 0.00 0.00 0.00 3.24
134 135 6.429692 TGTGAACATAATTGGGTTACAGACTG 59.570 38.462 0.00 0.00 0.00 3.51
135 136 6.430000 GTGAACATAATTGGGTTACAGACTGT 59.570 38.462 13.68 13.68 0.00 3.55
136 137 6.653320 TGAACATAATTGGGTTACAGACTGTC 59.347 38.462 12.39 0.00 0.00 3.51
137 138 6.374417 ACATAATTGGGTTACAGACTGTCT 57.626 37.500 12.39 4.06 0.00 3.41
138 139 7.490657 ACATAATTGGGTTACAGACTGTCTA 57.509 36.000 12.39 0.00 0.00 2.59
139 140 7.556844 ACATAATTGGGTTACAGACTGTCTAG 58.443 38.462 12.39 7.73 0.00 2.43
140 141 3.955650 TTGGGTTACAGACTGTCTAGC 57.044 47.619 12.39 10.89 0.00 3.42
141 142 3.170991 TGGGTTACAGACTGTCTAGCT 57.829 47.619 12.39 0.00 0.00 3.32
142 143 2.826128 TGGGTTACAGACTGTCTAGCTG 59.174 50.000 12.39 1.51 35.53 4.24
143 144 2.166664 GGGTTACAGACTGTCTAGCTGG 59.833 54.545 12.39 0.00 34.47 4.85
144 145 2.417515 GGTTACAGACTGTCTAGCTGGC 60.418 54.545 12.39 0.00 34.47 4.85
145 146 1.475403 TACAGACTGTCTAGCTGGCC 58.525 55.000 12.39 0.00 34.47 5.36
146 147 0.542938 ACAGACTGTCTAGCTGGCCA 60.543 55.000 10.47 4.71 34.47 5.36
147 148 0.829333 CAGACTGTCTAGCTGGCCAT 59.171 55.000 5.51 0.00 0.00 4.40
148 149 0.829333 AGACTGTCTAGCTGGCCATG 59.171 55.000 5.51 1.08 0.00 3.66
149 150 0.179062 GACTGTCTAGCTGGCCATGG 60.179 60.000 5.51 7.63 0.00 3.66
150 151 0.618680 ACTGTCTAGCTGGCCATGGA 60.619 55.000 18.40 0.00 0.00 3.41
151 152 0.543277 CTGTCTAGCTGGCCATGGAA 59.457 55.000 18.40 0.87 0.00 3.53
152 153 0.543277 TGTCTAGCTGGCCATGGAAG 59.457 55.000 18.40 13.30 0.00 3.46
153 154 0.833287 GTCTAGCTGGCCATGGAAGA 59.167 55.000 18.40 4.37 0.00 2.87
154 155 1.210478 GTCTAGCTGGCCATGGAAGAA 59.790 52.381 18.40 3.32 0.00 2.52
155 156 2.130193 TCTAGCTGGCCATGGAAGAAT 58.870 47.619 18.40 7.05 0.00 2.40
156 157 2.158711 TCTAGCTGGCCATGGAAGAATG 60.159 50.000 18.40 5.66 0.00 2.67
165 166 3.498774 CATGGAAGAATGGAGGGTAGG 57.501 52.381 0.00 0.00 0.00 3.18
166 167 2.961536 TGGAAGAATGGAGGGTAGGA 57.038 50.000 0.00 0.00 0.00 2.94
167 168 2.478292 TGGAAGAATGGAGGGTAGGAC 58.522 52.381 0.00 0.00 0.00 3.85
205 206 2.785713 AACCGAACCGAAAAACCATG 57.214 45.000 0.00 0.00 0.00 3.66
208 209 0.312416 CGAACCGAAAAACCATGCCA 59.688 50.000 0.00 0.00 0.00 4.92
213 214 2.939756 ACCGAAAAACCATGCCAAAAAC 59.060 40.909 0.00 0.00 0.00 2.43
214 215 2.289274 CCGAAAAACCATGCCAAAAACC 59.711 45.455 0.00 0.00 0.00 3.27
215 216 2.033322 CGAAAAACCATGCCAAAAACCG 60.033 45.455 0.00 0.00 0.00 4.44
255 301 8.494016 TTCATACCGTTTTGAATTTTGGTTTT 57.506 26.923 0.00 0.00 0.00 2.43
299 346 8.850454 ACCGAATGATTAACCAAATAAAATCG 57.150 30.769 0.00 0.00 32.23 3.34
392 454 2.427232 TCACTACCAAGCACGTACAC 57.573 50.000 0.00 0.00 0.00 2.90
445 508 8.883789 TTTAAAACATGCTAAGCACGTTATAC 57.116 30.769 0.00 0.00 44.08 1.47
446 509 6.737254 AAAACATGCTAAGCACGTTATACT 57.263 33.333 0.00 0.00 44.08 2.12
449 512 6.823678 ACATGCTAAGCACGTTATACTAAC 57.176 37.500 0.00 0.00 43.04 2.34
572 670 9.713713 ATTGTCATGATGTCATTTTCAAATTCA 57.286 25.926 0.00 0.00 33.61 2.57
687 804 2.405025 CGTACAGACCGAAAAACCGTAC 59.595 50.000 0.00 0.00 0.00 3.67
749 866 0.036875 AGGTAGGACTGCTTGTTGGC 59.963 55.000 0.00 0.00 0.00 4.52
915 1056 0.610687 GCCATAATCCCTCTCCCTCG 59.389 60.000 0.00 0.00 0.00 4.63
978 1130 2.362632 AGACCTACTTCGCCGGCT 60.363 61.111 26.68 8.22 0.00 5.52
1174 1326 1.667154 CTCCTGCCTCGTGGATTCGA 61.667 60.000 7.92 0.00 38.19 3.71
1181 1333 1.212616 CTCGTGGATTCGATTCCTGC 58.787 55.000 23.12 15.88 39.12 4.85
1196 1348 5.525012 CGATTCCTGCAGATAATCAAACAGA 59.475 40.000 27.24 8.91 31.37 3.41
1215 1367 9.542462 CAAACAGAGAATTAGGGTATCGAATTA 57.458 33.333 0.00 0.00 32.18 1.40
1221 1373 7.852263 AGAATTAGGGTATCGAATTAGGGATG 58.148 38.462 0.00 0.00 32.18 3.51
1478 1633 9.914834 AGGTATAAATCAGGTGTGCTTTAATAA 57.085 29.630 0.00 0.00 30.20 1.40
1513 1668 8.357402 ACACTCATTACATATATGCTCAACGTA 58.643 33.333 12.79 0.00 0.00 3.57
1527 1682 5.240183 TGCTCAACGTAGTAACAGTTCTAGT 59.760 40.000 0.00 0.00 45.00 2.57
1530 1685 7.805071 GCTCAACGTAGTAACAGTTCTAGTTTA 59.195 37.037 0.00 0.00 45.00 2.01
1532 1687 9.831737 TCAACGTAGTAACAGTTCTAGTTTATC 57.168 33.333 0.00 0.00 45.00 1.75
1533 1688 9.616634 CAACGTAGTAACAGTTCTAGTTTATCA 57.383 33.333 0.00 0.00 45.00 2.15
1565 1722 8.094548 AGCTACTAATGTTCAGTGTGTTCATTA 58.905 33.333 0.00 0.00 32.27 1.90
1566 1723 8.883731 GCTACTAATGTTCAGTGTGTTCATTAT 58.116 33.333 0.00 0.00 32.88 1.28
1581 1738 7.041576 TGTGTTCATTATCTCATTGCTATCTGC 60.042 37.037 0.00 0.00 43.25 4.26
1750 1907 3.615496 TCGTGTTTATTTCTAGAAGCGGC 59.385 43.478 5.12 0.00 0.00 6.53
1757 1914 2.775032 TTCTAGAAGCGGCGGCGTTT 62.775 55.000 31.76 31.76 46.35 3.60
1810 2000 0.255890 GGATTCCTGGCTAGGCAACA 59.744 55.000 20.64 6.59 44.22 3.33
1941 2131 0.254178 AGCTGGGCATGGTAAGACAG 59.746 55.000 0.00 0.00 0.00 3.51
1980 2170 4.471747 TGTTGCCAACTGGTCAGGTATATA 59.528 41.667 9.30 0.00 37.57 0.86
1985 2175 4.503296 CCAACTGGTCAGGTATATACTGGC 60.503 50.000 12.54 9.83 39.76 4.85
2146 7374 7.548427 TCAATTGATTTGTTTTGCTTTCTGTCA 59.452 29.630 3.38 0.00 36.65 3.58
2209 7438 8.834749 ACTTTTCAATAAGAAGAGGTACACTC 57.165 34.615 0.00 0.00 46.98 3.51
2365 7598 5.649782 AGATTTATTTGGCAGACTTGTGG 57.350 39.130 0.00 0.00 0.00 4.17
2411 7647 8.034804 CCTTTTTCAATTAAGTAACCATCCAGG 58.965 37.037 0.00 0.00 45.67 4.45
2442 7678 8.197988 ACGATCTGTTTACCTTATTCATTGTC 57.802 34.615 0.00 0.00 0.00 3.18
2447 7683 8.375506 TCTGTTTACCTTATTCATTGTCTCTGT 58.624 33.333 0.00 0.00 0.00 3.41
2448 7684 8.918202 TGTTTACCTTATTCATTGTCTCTGTT 57.082 30.769 0.00 0.00 0.00 3.16
2449 7685 8.783093 TGTTTACCTTATTCATTGTCTCTGTTG 58.217 33.333 0.00 0.00 0.00 3.33
2450 7686 8.784043 GTTTACCTTATTCATTGTCTCTGTTGT 58.216 33.333 0.00 0.00 0.00 3.32
2452 7688 7.907214 ACCTTATTCATTGTCTCTGTTGTAC 57.093 36.000 0.00 0.00 0.00 2.90
2603 7839 6.322712 ACAAGAGAACTGAAGTGAGTTACTCT 59.677 38.462 13.86 0.00 39.50 3.24
2637 7899 6.149633 GTGGTCTTAACATTGATGGTTGTTC 58.850 40.000 0.00 0.00 37.29 3.18
2794 8057 5.128205 TGCCAATGAGAATTAGTGATCAGG 58.872 41.667 0.00 0.00 0.00 3.86
2955 8236 3.373439 GCATACTCTCTCCAGTTGCAAAG 59.627 47.826 0.00 0.00 33.85 2.77
2961 8242 5.595952 ACTCTCTCCAGTTGCAAAGAAAAAT 59.404 36.000 0.00 0.00 0.00 1.82
2995 8276 4.191544 CGTACCATTCCATCATCAAGTGT 58.808 43.478 0.00 0.00 0.00 3.55
3013 8294 2.030363 GTGTGGGTGCGAATCAAAATCA 60.030 45.455 0.00 0.00 0.00 2.57
3019 8300 5.883115 TGGGTGCGAATCAAAATCATTACTA 59.117 36.000 0.00 0.00 0.00 1.82
3105 8386 3.987220 GACTGCGGCAAATTGTATGTTTT 59.013 39.130 3.44 0.00 0.00 2.43
3349 8631 1.683917 ACCAGAGATCATACTCACCGC 59.316 52.381 0.00 0.00 39.14 5.68
3351 8633 2.101415 CCAGAGATCATACTCACCGCAA 59.899 50.000 0.00 0.00 39.14 4.85
3417 8708 3.517901 TGGACCTTAACCTATGTGTGGAG 59.482 47.826 0.00 0.00 0.00 3.86
3434 8725 4.141846 TGTGGAGTGAGGAATCTATTGAGC 60.142 45.833 0.00 0.00 0.00 4.26
3450 8741 5.786121 ATTGAGCATAGGGTGGCTATATT 57.214 39.130 0.00 0.00 41.22 1.28
3467 8758 7.071196 TGGCTATATTCCTACATCACAAGTCTT 59.929 37.037 0.00 0.00 0.00 3.01
3512 8803 4.069304 TGTAGTTACATGGTTGTCAAGGC 58.931 43.478 0.00 0.00 37.28 4.35
3513 8804 2.514803 AGTTACATGGTTGTCAAGGCC 58.485 47.619 0.00 0.00 37.28 5.19
3514 8805 2.108250 AGTTACATGGTTGTCAAGGCCT 59.892 45.455 0.00 0.00 37.28 5.19
3545 8836 5.048154 GTCTGAGCTGATCTGTATGAGCATA 60.048 44.000 0.00 0.00 44.02 3.14
3556 8847 6.653020 TCTGTATGAGCATATGAAAGTTGGT 58.347 36.000 6.97 0.00 0.00 3.67
3649 8941 1.079474 TGCTCGCTCGCATTTACCA 60.079 52.632 0.00 0.00 34.44 3.25
3682 8974 6.418057 TGGCTACTTTGGTGAAATTTGATT 57.582 33.333 0.00 0.00 0.00 2.57
3718 9010 8.363390 TCCACATTTGAAATGTTATGCTGTTAA 58.637 29.630 20.00 0.00 0.00 2.01
3730 9022 9.926158 ATGTTATGCTGTTAAACAATTCATCAA 57.074 25.926 0.00 0.00 36.75 2.57
3861 9153 2.161211 GCTCTTCTGTTCAGAACATGGC 59.839 50.000 16.53 11.89 41.26 4.40
4086 9378 2.681848 CAGACCATCAAGCCTGTCAATC 59.318 50.000 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.771534 AGAGCAAATATTACCTCAAGTTCTATC 57.228 33.333 14.28 0.00 0.00 2.08
3 4 7.988028 GGTAGAGCAAATATTACCTCAAGTTCT 59.012 37.037 14.28 0.00 34.17 3.01
4 5 7.988028 AGGTAGAGCAAATATTACCTCAAGTTC 59.012 37.037 14.28 0.00 41.48 3.01
5 6 7.862675 AGGTAGAGCAAATATTACCTCAAGTT 58.137 34.615 14.28 1.39 41.48 2.66
6 7 7.439108 AGGTAGAGCAAATATTACCTCAAGT 57.561 36.000 14.28 1.64 41.48 3.16
7 8 8.738645 AAAGGTAGAGCAAATATTACCTCAAG 57.261 34.615 14.28 0.00 43.80 3.02
8 9 9.832445 CTAAAGGTAGAGCAAATATTACCTCAA 57.168 33.333 14.28 3.80 43.80 3.02
9 10 7.931948 GCTAAAGGTAGAGCAAATATTACCTCA 59.068 37.037 14.28 3.80 43.80 3.86
10 11 8.151596 AGCTAAAGGTAGAGCAAATATTACCTC 58.848 37.037 5.93 6.51 43.80 3.85
11 12 8.035448 AGCTAAAGGTAGAGCAAATATTACCT 57.965 34.615 0.29 0.29 45.89 3.08
12 13 7.388224 GGAGCTAAAGGTAGAGCAAATATTACC 59.612 40.741 0.00 0.00 41.36 2.85
13 14 8.151596 AGGAGCTAAAGGTAGAGCAAATATTAC 58.848 37.037 0.00 0.00 41.36 1.89
14 15 8.263854 AGGAGCTAAAGGTAGAGCAAATATTA 57.736 34.615 0.00 0.00 41.36 0.98
15 16 7.142995 AGGAGCTAAAGGTAGAGCAAATATT 57.857 36.000 0.00 0.00 41.36 1.28
16 17 6.755542 AGGAGCTAAAGGTAGAGCAAATAT 57.244 37.500 0.00 0.00 41.36 1.28
17 18 6.070194 ACAAGGAGCTAAAGGTAGAGCAAATA 60.070 38.462 0.00 0.00 41.36 1.40
18 19 5.189180 CAAGGAGCTAAAGGTAGAGCAAAT 58.811 41.667 0.00 0.00 41.36 2.32
19 20 4.041691 ACAAGGAGCTAAAGGTAGAGCAAA 59.958 41.667 0.00 0.00 41.36 3.68
20 21 3.583086 ACAAGGAGCTAAAGGTAGAGCAA 59.417 43.478 0.00 0.00 41.36 3.91
21 22 3.173965 ACAAGGAGCTAAAGGTAGAGCA 58.826 45.455 0.00 0.00 41.36 4.26
22 23 3.897141 ACAAGGAGCTAAAGGTAGAGC 57.103 47.619 0.00 0.00 39.08 4.09
23 24 4.508662 CCAACAAGGAGCTAAAGGTAGAG 58.491 47.826 0.00 0.00 41.22 2.43
24 25 3.263425 CCCAACAAGGAGCTAAAGGTAGA 59.737 47.826 0.00 0.00 41.22 2.59
25 26 3.009143 ACCCAACAAGGAGCTAAAGGTAG 59.991 47.826 0.00 0.00 41.22 3.18
26 27 2.983898 ACCCAACAAGGAGCTAAAGGTA 59.016 45.455 0.00 0.00 41.22 3.08
27 28 1.780919 ACCCAACAAGGAGCTAAAGGT 59.219 47.619 0.00 0.00 41.22 3.50
28 29 2.586648 ACCCAACAAGGAGCTAAAGG 57.413 50.000 0.00 0.00 41.22 3.11
29 30 2.484264 CGAACCCAACAAGGAGCTAAAG 59.516 50.000 0.00 0.00 41.22 1.85
30 31 2.105134 TCGAACCCAACAAGGAGCTAAA 59.895 45.455 0.00 0.00 41.22 1.85
31 32 1.695242 TCGAACCCAACAAGGAGCTAA 59.305 47.619 0.00 0.00 41.22 3.09
32 33 1.001633 GTCGAACCCAACAAGGAGCTA 59.998 52.381 0.00 0.00 41.22 3.32
33 34 0.250338 GTCGAACCCAACAAGGAGCT 60.250 55.000 0.00 0.00 41.22 4.09
34 35 0.534203 TGTCGAACCCAACAAGGAGC 60.534 55.000 0.00 0.00 41.22 4.70
35 36 1.202651 AGTGTCGAACCCAACAAGGAG 60.203 52.381 0.00 0.00 41.22 3.69
36 37 0.834612 AGTGTCGAACCCAACAAGGA 59.165 50.000 0.00 0.00 41.22 3.36
37 38 1.202651 AGAGTGTCGAACCCAACAAGG 60.203 52.381 0.00 0.00 37.03 3.61
38 39 2.240493 AGAGTGTCGAACCCAACAAG 57.760 50.000 0.00 0.00 0.00 3.16
39 40 2.702592 AAGAGTGTCGAACCCAACAA 57.297 45.000 0.00 0.00 0.00 2.83
40 41 2.696707 AGTAAGAGTGTCGAACCCAACA 59.303 45.455 0.00 0.00 0.00 3.33
41 42 3.382048 AGTAAGAGTGTCGAACCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
42 43 5.620654 CGATAAGTAAGAGTGTCGAACCCAA 60.621 44.000 0.00 0.00 0.00 4.12
43 44 4.142534 CGATAAGTAAGAGTGTCGAACCCA 60.143 45.833 0.00 0.00 0.00 4.51
44 45 4.095483 TCGATAAGTAAGAGTGTCGAACCC 59.905 45.833 0.00 0.00 35.48 4.11
45 46 5.227238 TCGATAAGTAAGAGTGTCGAACC 57.773 43.478 0.00 0.00 35.48 3.62
46 47 7.325579 AGTTTTCGATAAGTAAGAGTGTCGAAC 59.674 37.037 7.42 0.00 44.53 3.95
47 48 7.325338 CAGTTTTCGATAAGTAAGAGTGTCGAA 59.675 37.037 4.17 4.17 43.60 3.71
48 49 6.800408 CAGTTTTCGATAAGTAAGAGTGTCGA 59.200 38.462 0.00 0.00 36.46 4.20
49 50 6.581542 ACAGTTTTCGATAAGTAAGAGTGTCG 59.418 38.462 0.00 0.00 0.00 4.35
50 51 7.870588 ACAGTTTTCGATAAGTAAGAGTGTC 57.129 36.000 0.00 0.00 0.00 3.67
51 52 7.307219 GCAACAGTTTTCGATAAGTAAGAGTGT 60.307 37.037 0.00 0.00 0.00 3.55
52 53 7.010023 GCAACAGTTTTCGATAAGTAAGAGTG 58.990 38.462 0.00 0.00 0.00 3.51
53 54 6.128902 CGCAACAGTTTTCGATAAGTAAGAGT 60.129 38.462 0.00 0.00 0.00 3.24
54 55 6.089016 TCGCAACAGTTTTCGATAAGTAAGAG 59.911 38.462 3.87 0.00 0.00 2.85
55 56 5.921976 TCGCAACAGTTTTCGATAAGTAAGA 59.078 36.000 3.87 0.00 0.00 2.10
56 57 6.148270 TCGCAACAGTTTTCGATAAGTAAG 57.852 37.500 3.87 0.00 0.00 2.34
57 58 6.183360 GGATCGCAACAGTTTTCGATAAGTAA 60.183 38.462 16.17 0.00 41.11 2.24
58 59 5.290158 GGATCGCAACAGTTTTCGATAAGTA 59.710 40.000 16.17 0.00 41.11 2.24
59 60 4.092968 GGATCGCAACAGTTTTCGATAAGT 59.907 41.667 16.17 0.00 41.11 2.24
60 61 4.494199 GGGATCGCAACAGTTTTCGATAAG 60.494 45.833 16.17 0.00 41.11 1.73
61 62 3.372822 GGGATCGCAACAGTTTTCGATAA 59.627 43.478 16.17 0.00 41.11 1.75
62 63 2.933906 GGGATCGCAACAGTTTTCGATA 59.066 45.455 16.17 0.00 41.11 2.92
63 64 1.737793 GGGATCGCAACAGTTTTCGAT 59.262 47.619 16.15 16.15 43.33 3.59
64 65 1.153353 GGGATCGCAACAGTTTTCGA 58.847 50.000 4.64 9.18 35.34 3.71
65 66 0.168128 GGGGATCGCAACAGTTTTCG 59.832 55.000 12.32 0.00 0.00 3.46
66 67 1.534729 AGGGGATCGCAACAGTTTTC 58.465 50.000 12.32 0.00 0.00 2.29
67 68 2.871096 TAGGGGATCGCAACAGTTTT 57.129 45.000 12.32 0.00 0.00 2.43
68 69 3.454812 AGTATAGGGGATCGCAACAGTTT 59.545 43.478 12.32 0.00 0.00 2.66
69 70 3.039011 AGTATAGGGGATCGCAACAGTT 58.961 45.455 12.32 0.00 0.00 3.16
70 71 2.679082 AGTATAGGGGATCGCAACAGT 58.321 47.619 12.32 0.00 0.00 3.55
71 72 3.181465 ACAAGTATAGGGGATCGCAACAG 60.181 47.826 12.32 4.14 0.00 3.16
72 73 2.769663 ACAAGTATAGGGGATCGCAACA 59.230 45.455 12.32 0.00 0.00 3.33
73 74 3.131396 CACAAGTATAGGGGATCGCAAC 58.869 50.000 12.32 4.19 0.00 4.17
74 75 2.104111 CCACAAGTATAGGGGATCGCAA 59.896 50.000 12.32 0.00 0.00 4.85
75 76 1.691976 CCACAAGTATAGGGGATCGCA 59.308 52.381 12.32 0.00 0.00 5.10
76 77 1.002087 CCCACAAGTATAGGGGATCGC 59.998 57.143 0.06 0.06 43.57 4.58
83 84 9.847224 AAGTAATTGATAACCCACAAGTATAGG 57.153 33.333 0.00 0.00 31.33 2.57
86 87 8.956426 CACAAGTAATTGATAACCCACAAGTAT 58.044 33.333 10.35 0.00 31.33 2.12
87 88 8.158132 TCACAAGTAATTGATAACCCACAAGTA 58.842 33.333 10.35 0.00 0.00 2.24
88 89 7.001674 TCACAAGTAATTGATAACCCACAAGT 58.998 34.615 10.35 0.00 0.00 3.16
89 90 7.447374 TCACAAGTAATTGATAACCCACAAG 57.553 36.000 10.35 0.00 0.00 3.16
90 91 7.285629 TGTTCACAAGTAATTGATAACCCACAA 59.714 33.333 10.35 0.00 0.00 3.33
91 92 6.773200 TGTTCACAAGTAATTGATAACCCACA 59.227 34.615 10.35 0.27 0.00 4.17
92 93 7.209471 TGTTCACAAGTAATTGATAACCCAC 57.791 36.000 10.35 0.00 0.00 4.61
93 94 9.521841 TTATGTTCACAAGTAATTGATAACCCA 57.478 29.630 10.35 0.00 0.00 4.51
99 100 9.034800 ACCCAATTATGTTCACAAGTAATTGAT 57.965 29.630 19.02 9.91 42.70 2.57
100 101 8.415950 ACCCAATTATGTTCACAAGTAATTGA 57.584 30.769 19.02 0.00 42.70 2.57
103 104 9.303116 TGTAACCCAATTATGTTCACAAGTAAT 57.697 29.630 0.00 0.00 0.00 1.89
104 105 8.693120 TGTAACCCAATTATGTTCACAAGTAA 57.307 30.769 0.00 0.00 0.00 2.24
105 106 8.158132 TCTGTAACCCAATTATGTTCACAAGTA 58.842 33.333 0.00 0.00 0.00 2.24
106 107 7.001674 TCTGTAACCCAATTATGTTCACAAGT 58.998 34.615 0.00 0.00 0.00 3.16
107 108 7.174946 AGTCTGTAACCCAATTATGTTCACAAG 59.825 37.037 0.00 0.00 0.00 3.16
108 109 7.001674 AGTCTGTAACCCAATTATGTTCACAA 58.998 34.615 0.00 0.00 0.00 3.33
109 110 6.429692 CAGTCTGTAACCCAATTATGTTCACA 59.570 38.462 0.00 0.00 0.00 3.58
110 111 6.430000 ACAGTCTGTAACCCAATTATGTTCAC 59.570 38.462 2.87 0.00 0.00 3.18
111 112 6.539173 ACAGTCTGTAACCCAATTATGTTCA 58.461 36.000 2.87 0.00 0.00 3.18
112 113 6.879458 AGACAGTCTGTAACCCAATTATGTTC 59.121 38.462 5.21 0.00 0.00 3.18
113 114 6.779860 AGACAGTCTGTAACCCAATTATGTT 58.220 36.000 5.21 0.00 0.00 2.71
114 115 6.374417 AGACAGTCTGTAACCCAATTATGT 57.626 37.500 5.21 0.00 0.00 2.29
115 116 6.480320 GCTAGACAGTCTGTAACCCAATTATG 59.520 42.308 13.84 0.00 0.00 1.90
116 117 6.384305 AGCTAGACAGTCTGTAACCCAATTAT 59.616 38.462 13.84 0.00 0.00 1.28
117 118 5.720041 AGCTAGACAGTCTGTAACCCAATTA 59.280 40.000 13.84 0.00 0.00 1.40
118 119 4.532521 AGCTAGACAGTCTGTAACCCAATT 59.467 41.667 13.84 0.00 0.00 2.32
119 120 4.081420 CAGCTAGACAGTCTGTAACCCAAT 60.081 45.833 13.84 0.00 0.00 3.16
120 121 3.258372 CAGCTAGACAGTCTGTAACCCAA 59.742 47.826 13.84 0.00 0.00 4.12
121 122 2.826128 CAGCTAGACAGTCTGTAACCCA 59.174 50.000 13.84 0.00 0.00 4.51
122 123 2.166664 CCAGCTAGACAGTCTGTAACCC 59.833 54.545 13.84 0.00 0.00 4.11
123 124 2.417515 GCCAGCTAGACAGTCTGTAACC 60.418 54.545 13.84 0.00 0.00 2.85
124 125 2.417515 GGCCAGCTAGACAGTCTGTAAC 60.418 54.545 13.84 0.00 0.00 2.50
125 126 1.825474 GGCCAGCTAGACAGTCTGTAA 59.175 52.381 13.84 0.00 0.00 2.41
126 127 1.272480 TGGCCAGCTAGACAGTCTGTA 60.272 52.381 13.84 0.00 0.00 2.74
127 128 0.542938 TGGCCAGCTAGACAGTCTGT 60.543 55.000 13.84 4.81 0.00 3.41
128 129 0.829333 ATGGCCAGCTAGACAGTCTG 59.171 55.000 13.05 0.00 0.00 3.51
129 130 0.829333 CATGGCCAGCTAGACAGTCT 59.171 55.000 13.05 8.50 0.00 3.24
130 131 0.179062 CCATGGCCAGCTAGACAGTC 60.179 60.000 13.05 0.00 0.00 3.51
131 132 0.618680 TCCATGGCCAGCTAGACAGT 60.619 55.000 13.05 0.00 0.00 3.55
132 133 0.543277 TTCCATGGCCAGCTAGACAG 59.457 55.000 13.05 0.00 0.00 3.51
133 134 0.543277 CTTCCATGGCCAGCTAGACA 59.457 55.000 13.05 0.00 0.00 3.41
134 135 0.833287 TCTTCCATGGCCAGCTAGAC 59.167 55.000 13.05 0.00 0.00 2.59
135 136 1.583556 TTCTTCCATGGCCAGCTAGA 58.416 50.000 13.05 8.55 0.00 2.43
136 137 2.228059 CATTCTTCCATGGCCAGCTAG 58.772 52.381 13.05 6.09 0.00 3.42
137 138 1.133699 CCATTCTTCCATGGCCAGCTA 60.134 52.381 13.05 0.00 37.51 3.32
138 139 0.396695 CCATTCTTCCATGGCCAGCT 60.397 55.000 13.05 0.00 37.51 4.24
139 140 0.396139 TCCATTCTTCCATGGCCAGC 60.396 55.000 13.05 0.00 43.31 4.85
140 141 1.688772 CTCCATTCTTCCATGGCCAG 58.311 55.000 13.05 5.60 43.31 4.85
141 142 0.259647 CCTCCATTCTTCCATGGCCA 59.740 55.000 8.56 8.56 43.31 5.36
142 143 0.468771 CCCTCCATTCTTCCATGGCC 60.469 60.000 6.96 0.00 43.31 5.36
143 144 0.259938 ACCCTCCATTCTTCCATGGC 59.740 55.000 6.96 0.00 43.31 4.40
144 145 2.107204 CCTACCCTCCATTCTTCCATGG 59.893 54.545 4.97 4.97 44.80 3.66
145 146 3.048600 TCCTACCCTCCATTCTTCCATG 58.951 50.000 0.00 0.00 0.00 3.66
146 147 3.049344 GTCCTACCCTCCATTCTTCCAT 58.951 50.000 0.00 0.00 0.00 3.41
147 148 2.045885 AGTCCTACCCTCCATTCTTCCA 59.954 50.000 0.00 0.00 0.00 3.53
148 149 2.701423 GAGTCCTACCCTCCATTCTTCC 59.299 54.545 0.00 0.00 0.00 3.46
149 150 3.133183 GTGAGTCCTACCCTCCATTCTTC 59.867 52.174 0.00 0.00 0.00 2.87
150 151 3.108376 GTGAGTCCTACCCTCCATTCTT 58.892 50.000 0.00 0.00 0.00 2.52
151 152 2.316372 AGTGAGTCCTACCCTCCATTCT 59.684 50.000 0.00 0.00 0.00 2.40
152 153 2.696187 GAGTGAGTCCTACCCTCCATTC 59.304 54.545 0.00 0.00 0.00 2.67
153 154 2.316372 AGAGTGAGTCCTACCCTCCATT 59.684 50.000 0.00 0.00 0.00 3.16
154 155 1.933765 AGAGTGAGTCCTACCCTCCAT 59.066 52.381 0.00 0.00 0.00 3.41
155 156 1.006043 CAGAGTGAGTCCTACCCTCCA 59.994 57.143 0.00 0.00 0.00 3.86
156 157 1.006162 ACAGAGTGAGTCCTACCCTCC 59.994 57.143 0.00 0.00 0.00 4.30
157 158 2.096248 CACAGAGTGAGTCCTACCCTC 58.904 57.143 0.00 0.00 35.23 4.30
158 159 1.893210 GCACAGAGTGAGTCCTACCCT 60.893 57.143 0.58 0.00 35.23 4.34
159 160 0.533032 GCACAGAGTGAGTCCTACCC 59.467 60.000 0.58 0.00 35.23 3.69
160 161 1.257743 TGCACAGAGTGAGTCCTACC 58.742 55.000 0.58 0.00 35.23 3.18
161 162 3.601443 AATGCACAGAGTGAGTCCTAC 57.399 47.619 0.58 0.00 35.23 3.18
162 163 4.040339 TCAAAATGCACAGAGTGAGTCCTA 59.960 41.667 0.58 0.00 35.23 2.94
163 164 3.144506 CAAAATGCACAGAGTGAGTCCT 58.855 45.455 0.58 0.00 35.23 3.85
164 165 3.141398 TCAAAATGCACAGAGTGAGTCC 58.859 45.455 0.58 0.00 35.23 3.85
165 166 4.818534 TTCAAAATGCACAGAGTGAGTC 57.181 40.909 0.58 0.00 35.23 3.36
166 167 4.202050 GGTTTCAAAATGCACAGAGTGAGT 60.202 41.667 0.58 0.00 35.23 3.41
167 168 4.293415 GGTTTCAAAATGCACAGAGTGAG 58.707 43.478 0.58 0.00 35.23 3.51
205 206 3.586100 ACATACCATTCGGTTTTTGGC 57.414 42.857 0.00 0.00 46.31 4.52
208 209 7.942990 TGAAAAGTACATACCATTCGGTTTTT 58.057 30.769 0.00 0.00 46.31 1.94
225 271 9.250624 CCAAAATTCAAAACGGTATGAAAAGTA 57.749 29.630 11.71 0.00 38.88 2.24
255 301 8.991026 CATTCGGTTTTTCGGTATATACCATAA 58.009 33.333 27.58 19.00 46.80 1.90
315 363 6.418057 TGGTTGTTTGCCTCAAGAAATATT 57.582 33.333 0.00 0.00 0.00 1.28
361 423 5.412594 TGCTTGGTAGTGAATTTGACTCATC 59.587 40.000 0.00 0.00 0.00 2.92
551 649 9.145865 TGACATGAATTTGAAAATGACATCATG 57.854 29.630 18.15 18.15 41.33 3.07
572 670 9.841295 ATATACCGTAATAACCAAAGTTGACAT 57.159 29.630 0.00 0.00 36.68 3.06
672 789 2.354199 TGGTTTGTACGGTTTTTCGGTC 59.646 45.455 0.00 0.00 0.00 4.79
687 804 8.879342 TTATTCAGTTTACATGGTTTGGTTTG 57.121 30.769 0.00 0.00 0.00 2.93
749 866 5.063438 CGGTACACACAGGAATTTCACATAG 59.937 44.000 0.00 0.00 0.00 2.23
915 1056 3.969802 GTGCCCACTGTGTGCAGC 61.970 66.667 18.11 9.60 46.30 5.25
941 1082 4.200283 GAGGGGTCGAGCTGAGCG 62.200 72.222 15.18 0.00 46.20 5.03
1045 1197 2.202837 GATGTACGGGTGGACGGC 60.203 66.667 0.00 0.00 38.39 5.68
1050 1202 1.382695 AGGGGAGATGTACGGGTGG 60.383 63.158 0.00 0.00 0.00 4.61
1174 1326 6.656902 TCTCTGTTTGATTATCTGCAGGAAT 58.343 36.000 15.13 13.75 0.00 3.01
1181 1333 8.970859 ACCCTAATTCTCTGTTTGATTATCTG 57.029 34.615 0.00 0.00 0.00 2.90
1196 1348 7.581658 GCATCCCTAATTCGATACCCTAATTCT 60.582 40.741 0.00 0.00 0.00 2.40
1215 1367 3.439857 TTTTCTGTAAGCAGCATCCCT 57.560 42.857 0.00 0.00 42.29 4.20
1242 1394 8.711457 CAATTTTCACCATTCCAACTGATAAAC 58.289 33.333 0.00 0.00 0.00 2.01
1530 1685 8.671921 CACTGAACATTAGTAGCTGATTTTGAT 58.328 33.333 0.00 0.00 0.00 2.57
1532 1687 7.747799 CACACTGAACATTAGTAGCTGATTTTG 59.252 37.037 0.00 0.00 0.00 2.44
1533 1688 7.445402 ACACACTGAACATTAGTAGCTGATTTT 59.555 33.333 0.00 0.00 0.00 1.82
1552 1709 6.432607 AGCAATGAGATAATGAACACACTG 57.567 37.500 0.00 0.00 0.00 3.66
1581 1738 1.679944 CCAGGATACCACTGCAAGGTG 60.680 57.143 18.22 9.60 40.26 4.00
1750 1907 0.453282 CTCAGCACAATCAAACGCCG 60.453 55.000 0.00 0.00 0.00 6.46
1757 1914 4.579753 TCAAAACATGTCTCAGCACAATCA 59.420 37.500 0.00 0.00 0.00 2.57
1810 2000 5.306678 GGTTCATCACTATGATCCTTCTCCT 59.693 44.000 7.81 0.00 44.01 3.69
1812 2002 5.226396 CGGTTCATCACTATGATCCTTCTC 58.774 45.833 11.68 0.00 44.71 2.87
1941 2131 3.002348 GGCAACAGAGATTACATAACGGC 59.998 47.826 0.00 0.00 0.00 5.68
1985 2175 5.583854 GTGATATACTGCATCAGGGCATAAG 59.416 44.000 0.00 0.00 43.97 1.73
2176 7405 7.040686 CCTCTTCTTATTGAAAAGTTCCCGAAA 60.041 37.037 0.00 0.00 33.79 3.46
2180 7409 7.664318 TGTACCTCTTCTTATTGAAAAGTTCCC 59.336 37.037 0.00 0.00 33.79 3.97
2209 7438 5.991328 ATGATATCGTAACCAAGTTGCAG 57.009 39.130 0.00 0.00 0.00 4.41
2349 7582 2.629617 CCTTTCCACAAGTCTGCCAAAT 59.370 45.455 0.00 0.00 0.00 2.32
2365 7598 9.440773 AAAAAGGATCAAGAAATATTGCCTTTC 57.559 29.630 0.00 0.00 39.59 2.62
2411 7647 7.485913 TGAATAAGGTAAACAGATCGTCGTTAC 59.514 37.037 0.00 2.16 0.00 2.50
2415 7651 7.010183 ACAATGAATAAGGTAAACAGATCGTCG 59.990 37.037 0.00 0.00 0.00 5.12
2442 7678 6.920569 AAACAAGGTACAAGTACAACAGAG 57.079 37.500 12.00 0.00 37.78 3.35
2447 7683 8.358148 TCAAACAAAAACAAGGTACAAGTACAA 58.642 29.630 12.00 0.00 37.78 2.41
2448 7684 7.883217 TCAAACAAAAACAAGGTACAAGTACA 58.117 30.769 12.00 0.00 37.78 2.90
2449 7685 8.745464 TTCAAACAAAAACAAGGTACAAGTAC 57.255 30.769 1.77 1.77 35.40 2.73
2450 7686 8.030106 CCTTCAAACAAAAACAAGGTACAAGTA 58.970 33.333 0.00 0.00 30.69 2.24
2451 7687 6.871492 CCTTCAAACAAAAACAAGGTACAAGT 59.129 34.615 0.00 0.00 30.69 3.16
2452 7688 6.871492 ACCTTCAAACAAAAACAAGGTACAAG 59.129 34.615 0.00 0.00 44.12 3.16
2603 7839 2.289133 TGTTAAGACCACGTATGCAGCA 60.289 45.455 0.00 0.00 0.00 4.41
2961 8242 8.041919 TGATGGAATGGTACGTAGAAAATGTTA 58.958 33.333 0.00 0.00 0.00 2.41
2974 8255 4.336433 CCACACTTGATGATGGAATGGTAC 59.664 45.833 0.00 0.00 33.61 3.34
2995 8276 4.704540 AGTAATGATTTTGATTCGCACCCA 59.295 37.500 0.00 0.00 0.00 4.51
3013 8294 7.201785 CCTGTTTCACACAAACCTGTTAGTAAT 60.202 37.037 0.00 0.00 33.87 1.89
3019 8300 3.161866 ACCTGTTTCACACAAACCTGTT 58.838 40.909 0.00 0.00 33.87 3.16
3105 8386 7.806409 TCATTTCAAAGAACTGAGTTGATCA 57.194 32.000 0.90 0.00 36.21 2.92
3349 8631 0.858583 TGTGATTGACGTGCGTCTTG 59.141 50.000 22.54 0.00 44.80 3.02
3351 8633 1.460743 CATTGTGATTGACGTGCGTCT 59.539 47.619 22.54 6.27 44.80 4.18
3417 8708 5.012561 ACCCTATGCTCAATAGATTCCTCAC 59.987 44.000 0.00 0.00 40.83 3.51
3434 8725 6.384015 TGATGTAGGAATATAGCCACCCTATG 59.616 42.308 0.00 0.00 37.34 2.23
3467 8758 3.513680 GCAATTTCTGATGTGCCATCA 57.486 42.857 14.60 14.60 0.00 3.07
3507 8798 0.325671 TCAGACCCCTAGAGGCCTTG 60.326 60.000 6.77 0.00 0.00 3.61
3508 8799 0.031616 CTCAGACCCCTAGAGGCCTT 60.032 60.000 6.77 0.00 0.00 4.35
3509 8800 1.623625 CTCAGACCCCTAGAGGCCT 59.376 63.158 3.86 3.86 0.00 5.19
3510 8801 2.137528 GCTCAGACCCCTAGAGGCC 61.138 68.421 0.00 0.00 0.00 5.19
3511 8802 1.075600 AGCTCAGACCCCTAGAGGC 60.076 63.158 0.00 0.00 0.00 4.70
3512 8803 0.260230 TCAGCTCAGACCCCTAGAGG 59.740 60.000 0.00 0.00 0.00 3.69
3513 8804 2.158475 AGATCAGCTCAGACCCCTAGAG 60.158 54.545 0.00 0.00 0.00 2.43
3514 8805 1.856259 AGATCAGCTCAGACCCCTAGA 59.144 52.381 0.00 0.00 0.00 2.43
3622 8914 1.115639 GCGAGCGAGCATTTAATTGC 58.884 50.000 13.25 13.25 43.09 3.56
3646 8938 1.008449 AGTAGCCATGGGTAGTCTGGT 59.992 52.381 23.83 2.40 32.42 4.00
3649 8941 2.505819 CCAAAGTAGCCATGGGTAGTCT 59.494 50.000 27.36 17.74 32.11 3.24
3682 8974 3.448093 TCAAATGTGGATGTAAGGCCA 57.552 42.857 5.01 0.00 0.00 5.36
3718 9010 5.733620 ATTCCAGTGCTTGATGAATTGTT 57.266 34.783 0.00 0.00 0.00 2.83
3730 9022 1.538687 GGCCTGCAAATTCCAGTGCT 61.539 55.000 0.00 0.00 41.48 4.40
3861 9153 9.882996 CTGGTGTAGCAAACATTGTATTATATG 57.117 33.333 0.00 0.00 41.10 1.78
3938 9230 1.135315 TGTTTACCTACAGGCTACGCG 60.135 52.381 3.53 3.53 39.32 6.01
3941 9233 2.493278 TCGGTGTTTACCTACAGGCTAC 59.507 50.000 0.00 0.00 45.22 3.58
3942 9234 2.493278 GTCGGTGTTTACCTACAGGCTA 59.507 50.000 0.00 0.00 45.22 3.93
3943 9235 1.274447 GTCGGTGTTTACCTACAGGCT 59.726 52.381 0.00 0.00 45.22 4.58
3944 9236 1.274447 AGTCGGTGTTTACCTACAGGC 59.726 52.381 4.30 0.00 43.26 4.85
3945 9237 3.672767 AAGTCGGTGTTTACCTACAGG 57.327 47.619 4.30 0.00 43.26 4.00
3946 9238 5.996669 AAAAAGTCGGTGTTTACCTACAG 57.003 39.130 4.30 0.00 43.26 2.74
3947 9239 6.344500 TGTAAAAAGTCGGTGTTTACCTACA 58.656 36.000 8.28 0.00 43.26 2.74
3948 9240 6.843069 TGTAAAAAGTCGGTGTTTACCTAC 57.157 37.500 8.28 0.00 45.22 3.18
3949 9241 6.650390 GGATGTAAAAAGTCGGTGTTTACCTA 59.350 38.462 8.28 0.00 45.22 3.08
3950 9242 5.471116 GGATGTAAAAAGTCGGTGTTTACCT 59.529 40.000 8.28 1.18 45.22 3.08
3951 9243 5.471116 AGGATGTAAAAAGTCGGTGTTTACC 59.529 40.000 8.28 0.00 43.89 2.85
3952 9244 6.549912 AGGATGTAAAAAGTCGGTGTTTAC 57.450 37.500 5.14 5.14 37.93 2.01
3953 9245 6.513720 GCAAGGATGTAAAAAGTCGGTGTTTA 60.514 38.462 0.00 0.00 0.00 2.01
3954 9246 5.735070 GCAAGGATGTAAAAAGTCGGTGTTT 60.735 40.000 0.00 0.00 0.00 2.83
3955 9247 4.261447 GCAAGGATGTAAAAAGTCGGTGTT 60.261 41.667 0.00 0.00 0.00 3.32
4086 9378 5.185635 TGATAGGACAAAGGCTTTGGATTTG 59.814 40.000 35.57 17.08 44.81 2.32


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

AutoCloner maintained by Alex Coulton.