Multiple sequence alignment - TraesCS4A01G137500

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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 TraesCS4A01G137500 chr4A 100.000 4504 0 0 851 5354 196782586 196787089 0.000000e+00 8318.0
1 TraesCS4A01G137500 chr4A 100.000 354 0 0 1 354 196781736 196782089 0.000000e+00 654.0
2 TraesCS4A01G137500 chr4A 89.294 411 30 7 1291 1687 13266106 13266516 2.230000e-138 503.0
3 TraesCS4A01G137500 chr4A 88.854 323 29 7 1 318 591541698 591541378 1.810000e-104 390.0
4 TraesCS4A01G137500 chr4A 88.545 323 30 7 1 318 593069795 593070115 8.410000e-103 385.0
5 TraesCS4A01G137500 chr4A 84.615 390 51 9 4453 4833 10025447 10025058 3.910000e-101 379.0
6 TraesCS4A01G137500 chr4A 88.235 323 31 7 1 318 592503415 592503735 3.910000e-101 379.0
7 TraesCS4A01G137500 chr4A 90.816 196 17 1 854 1049 190554819 190554625 1.480000e-65 261.0
8 TraesCS4A01G137500 chr4A 96.850 127 4 0 3002 3128 712891226 712891100 4.200000e-51 213.0
9 TraesCS4A01G137500 chr1A 95.136 3968 160 13 883 4833 525835054 525839005 0.000000e+00 6228.0
10 TraesCS4A01G137500 chr1A 86.925 696 62 19 3957 4631 562584095 562584782 0.000000e+00 754.0
11 TraesCS4A01G137500 chr1A 86.916 535 35 7 3458 3960 74242135 74242666 7.780000e-158 568.0
12 TraesCS4A01G137500 chr1A 88.545 323 30 7 1 318 55282898 55283218 8.410000e-103 385.0
13 TraesCS4A01G137500 chr1A 91.925 161 9 2 4673 4833 584793486 584793330 6.980000e-54 222.0
14 TraesCS4A01G137500 chr2A 95.364 3861 129 17 992 4836 101130268 101126442 0.000000e+00 6093.0
15 TraesCS4A01G137500 chr2A 96.778 2514 60 11 2112 4617 715827555 715825055 0.000000e+00 4174.0
16 TraesCS4A01G137500 chr2A 95.081 1118 41 5 914 2029 715828656 715827551 0.000000e+00 1748.0
17 TraesCS4A01G137500 chr2A 94.677 789 35 5 3176 3960 484994028 484993243 0.000000e+00 1218.0
18 TraesCS4A01G137500 chr2A 95.806 310 13 0 2866 3175 484995501 484995192 8.010000e-138 501.0
19 TraesCS4A01G137500 chr2A 85.376 465 52 10 4386 4836 47572233 47571771 8.120000e-128 468.0
20 TraesCS4A01G137500 chr2A 100.000 67 0 0 851 917 101130760 101130694 2.020000e-24 124.0
21 TraesCS4A01G137500 chr5A 95.714 2333 82 8 2516 4836 146516599 146514273 0.000000e+00 3738.0
22 TraesCS4A01G137500 chr5A 93.956 1638 68 15 906 2520 146519837 146518208 0.000000e+00 2447.0
23 TraesCS4A01G137500 chr5A 90.491 326 28 3 1 323 446314488 446314163 1.380000e-115 427.0
24 TraesCS4A01G137500 chr5A 88.154 363 32 5 4474 4833 669940747 669941101 6.410000e-114 422.0
25 TraesCS4A01G137500 chr5A 87.572 346 37 6 1 344 635646991 635647332 3.890000e-106 396.0
26 TraesCS4A01G137500 chr5A 89.577 307 31 1 1 307 654664322 654664627 6.500000e-104 388.0
27 TraesCS4A01G137500 chr5A 92.073 164 4 1 2965 3128 73207843 73207689 6.980000e-54 222.0
28 TraesCS4A01G137500 chr6A 93.488 1597 84 9 886 2469 132411207 132412796 0.000000e+00 2355.0
29 TraesCS4A01G137500 chr6A 96.846 1395 42 2 1530 2922 576846051 576844657 0.000000e+00 2331.0
30 TraesCS4A01G137500 chr4B 96.487 1395 47 2 1530 2922 669672306 669670912 0.000000e+00 2303.0
31 TraesCS4A01G137500 chr4B 87.800 500 45 8 1227 1717 567470416 567469924 6.020000e-159 571.0
32 TraesCS4A01G137500 chr4B 83.427 531 55 16 4831 5354 364349187 364349691 3.780000e-126 462.0
33 TraesCS4A01G137500 chr4B 94.340 106 5 1 854 959 69135737 69135633 1.540000e-35 161.0
34 TraesCS4A01G137500 chr4B 86.713 143 10 1 2953 3095 101813030 101813163 3.340000e-32 150.0
35 TraesCS4A01G137500 chr3A 94.018 1237 60 6 851 2084 706365626 706364401 0.000000e+00 1862.0
36 TraesCS4A01G137500 chr3A 95.283 954 33 4 3890 4833 242901168 242900217 0.000000e+00 1502.0
37 TraesCS4A01G137500 chr3A 83.718 909 97 32 3957 4833 606612772 606611883 0.000000e+00 811.0
38 TraesCS4A01G137500 chr3A 89.524 315 31 2 4 317 680169378 680169065 1.080000e-106 398.0
39 TraesCS4A01G137500 chr7A 96.196 920 28 6 1554 2469 650073062 650072146 0.000000e+00 1498.0
40 TraesCS4A01G137500 chr7A 87.103 535 34 9 3458 3960 205894865 205895396 1.670000e-159 573.0
41 TraesCS4A01G137500 chr7A 92.105 380 28 2 851 1229 650073446 650073068 7.890000e-148 534.0
42 TraesCS4A01G137500 chr7A 79.661 649 82 28 2139 2761 670237034 670236410 6.410000e-114 422.0
43 TraesCS4A01G137500 chr7A 88.406 345 35 5 1 344 592763040 592763380 1.390000e-110 411.0
44 TraesCS4A01G137500 chr7A 79.487 546 79 19 2222 2761 670567449 670567967 1.830000e-94 357.0
45 TraesCS4A01G137500 chr5D 87.500 904 75 18 3957 4833 27185653 27184761 0.000000e+00 1009.0
46 TraesCS4A01G137500 chr5D 87.086 906 76 21 3957 4833 27230689 27229796 0.000000e+00 987.0
47 TraesCS4A01G137500 chr7B 88.127 817 55 10 3178 3960 684163964 684164772 0.000000e+00 933.0
48 TraesCS4A01G137500 chr7B 85.043 702 61 22 2052 2722 641680601 641681289 0.000000e+00 675.0
49 TraesCS4A01G137500 chr2D 86.016 901 89 25 3957 4833 649857521 649856634 0.000000e+00 931.0
50 TraesCS4A01G137500 chr2D 94.074 540 25 5 3425 3960 576107658 576108194 0.000000e+00 813.0
51 TraesCS4A01G137500 chr2D 96.805 313 9 1 2863 3175 576106535 576106846 6.140000e-144 521.0
52 TraesCS4A01G137500 chr2D 90.747 281 24 2 851 1130 576105366 576105645 1.820000e-99 374.0
53 TraesCS4A01G137500 chr2B 84.738 629 59 12 2019 2628 756118441 756117831 3.570000e-166 595.0
54 TraesCS4A01G137500 chr2B 86.916 535 35 7 3458 3960 88447893 88447362 7.780000e-158 568.0
55 TraesCS4A01G137500 chr4D 92.647 408 26 3 1232 1635 455017470 455017063 7.730000e-163 584.0
56 TraesCS4A01G137500 chr4D 85.028 354 33 11 5001 5354 295416425 295416092 5.130000e-90 342.0
57 TraesCS4A01G137500 chr4D 89.216 204 12 5 856 1049 14582782 14582579 4.140000e-61 246.0
58 TraesCS4A01G137500 chrUn 86.916 535 35 7 3458 3960 766959 766428 7.780000e-158 568.0
59 TraesCS4A01G137500 chr3D 87.466 367 40 6 4470 4832 164650378 164650742 8.290000e-113 418.0
60 TraesCS4A01G137500 chr3D 91.617 167 5 2 2962 3128 480723412 480723569 6.980000e-54 222.0
61 TraesCS4A01G137500 chr3D 91.241 137 10 2 985 1120 33178886 33178751 9.160000e-43 185.0
62 TraesCS4A01G137500 chr3D 93.671 79 5 0 2863 2941 530344382 530344460 9.420000e-23 119.0
63 TraesCS4A01G137500 chr3D 84.058 69 8 3 5078 5146 306732549 306732484 4.480000e-06 63.9
64 TraesCS4A01G137500 chr1B 84.658 365 27 11 3445 3785 44353283 44353642 2.390000e-88 337.0
65 TraesCS4A01G137500 chr1B 93.258 89 6 0 3245 3333 389736031 389736119 1.210000e-26 132.0
66 TraesCS4A01G137500 chr5B 96.850 127 4 0 3002 3128 665599628 665599502 4.200000e-51 213.0
67 TraesCS4A01G137500 chr3B 91.241 137 10 2 985 1120 55730683 55730548 9.160000e-43 185.0
68 TraesCS4A01G137500 chr3B 86.567 67 6 3 5080 5146 414187432 414187495 2.680000e-08 71.3
69 TraesCS4A01G137500 chr1D 88.060 134 7 1 2962 3095 473554848 473554972 3.340000e-32 150.0
70 TraesCS4A01G137500 chr1D 92.473 93 6 1 3245 3336 288148381 288148473 1.210000e-26 132.0


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 TraesCS4A01G137500 chr4A 196781736 196787089 5353 False 4486.000000 8318 100.000000 1 5354 2 chr4A.!!$F4 5353
1 TraesCS4A01G137500 chr1A 525835054 525839005 3951 False 6228.000000 6228 95.136000 883 4833 1 chr1A.!!$F3 3950
2 TraesCS4A01G137500 chr1A 562584095 562584782 687 False 754.000000 754 86.925000 3957 4631 1 chr1A.!!$F4 674
3 TraesCS4A01G137500 chr1A 74242135 74242666 531 False 568.000000 568 86.916000 3458 3960 1 chr1A.!!$F2 502
4 TraesCS4A01G137500 chr2A 101126442 101130760 4318 True 3108.500000 6093 97.682000 851 4836 2 chr2A.!!$R2 3985
5 TraesCS4A01G137500 chr2A 715825055 715828656 3601 True 2961.000000 4174 95.929500 914 4617 2 chr2A.!!$R4 3703
6 TraesCS4A01G137500 chr2A 484993243 484995501 2258 True 859.500000 1218 95.241500 2866 3960 2 chr2A.!!$R3 1094
7 TraesCS4A01G137500 chr5A 146514273 146519837 5564 True 3092.500000 3738 94.835000 906 4836 2 chr5A.!!$R3 3930
8 TraesCS4A01G137500 chr6A 132411207 132412796 1589 False 2355.000000 2355 93.488000 886 2469 1 chr6A.!!$F1 1583
9 TraesCS4A01G137500 chr6A 576844657 576846051 1394 True 2331.000000 2331 96.846000 1530 2922 1 chr6A.!!$R1 1392
10 TraesCS4A01G137500 chr4B 669670912 669672306 1394 True 2303.000000 2303 96.487000 1530 2922 1 chr4B.!!$R3 1392
11 TraesCS4A01G137500 chr4B 364349187 364349691 504 False 462.000000 462 83.427000 4831 5354 1 chr4B.!!$F2 523
12 TraesCS4A01G137500 chr3A 706364401 706365626 1225 True 1862.000000 1862 94.018000 851 2084 1 chr3A.!!$R4 1233
13 TraesCS4A01G137500 chr3A 242900217 242901168 951 True 1502.000000 1502 95.283000 3890 4833 1 chr3A.!!$R1 943
14 TraesCS4A01G137500 chr3A 606611883 606612772 889 True 811.000000 811 83.718000 3957 4833 1 chr3A.!!$R2 876
15 TraesCS4A01G137500 chr7A 650072146 650073446 1300 True 1016.000000 1498 94.150500 851 2469 2 chr7A.!!$R2 1618
16 TraesCS4A01G137500 chr7A 205894865 205895396 531 False 573.000000 573 87.103000 3458 3960 1 chr7A.!!$F1 502
17 TraesCS4A01G137500 chr7A 670236410 670237034 624 True 422.000000 422 79.661000 2139 2761 1 chr7A.!!$R1 622
18 TraesCS4A01G137500 chr7A 670567449 670567967 518 False 357.000000 357 79.487000 2222 2761 1 chr7A.!!$F3 539
19 TraesCS4A01G137500 chr5D 27184761 27185653 892 True 1009.000000 1009 87.500000 3957 4833 1 chr5D.!!$R1 876
20 TraesCS4A01G137500 chr5D 27229796 27230689 893 True 987.000000 987 87.086000 3957 4833 1 chr5D.!!$R2 876
21 TraesCS4A01G137500 chr7B 684163964 684164772 808 False 933.000000 933 88.127000 3178 3960 1 chr7B.!!$F2 782
22 TraesCS4A01G137500 chr7B 641680601 641681289 688 False 675.000000 675 85.043000 2052 2722 1 chr7B.!!$F1 670
23 TraesCS4A01G137500 chr2D 649856634 649857521 887 True 931.000000 931 86.016000 3957 4833 1 chr2D.!!$R1 876
24 TraesCS4A01G137500 chr2D 576105366 576108194 2828 False 569.333333 813 93.875333 851 3960 3 chr2D.!!$F1 3109
25 TraesCS4A01G137500 chr2B 756117831 756118441 610 True 595.000000 595 84.738000 2019 2628 1 chr2B.!!$R2 609
26 TraesCS4A01G137500 chr2B 88447362 88447893 531 True 568.000000 568 86.916000 3458 3960 1 chr2B.!!$R1 502
27 TraesCS4A01G137500 chrUn 766428 766959 531 True 568.000000 568 86.916000 3458 3960 1 chrUn.!!$R1 502

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
283 284 0.041982 AACTCAGACCCCCTCCTCTC 59.958 60.0 0.0 0.0 0.00 3.20 F
285 286 0.106217 CTCAGACCCCCTCCTCTCTC 60.106 65.0 0.0 0.0 0.00 3.20 F
965 968 0.252927 CCCTCTCCCTCCCACTTCTT 60.253 60.0 0.0 0.0 0.00 2.52 F
1940 2812 0.740149 CAAGCACACACAGCCTCAAA 59.260 50.0 0.0 0.0 0.00 2.69 F
3036 5587 0.980231 ACTCCTGGACATCAGCTCCC 60.980 60.0 0.0 0.0 42.05 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1950 0.251916 AGCATCGTCGGGGAATCAAA 59.748 50.000 0.00 0.0 0.00 2.69 R
1483 2093 1.064166 CCTGCTTGTTCCCCATGATCT 60.064 52.381 0.00 0.0 0.00 2.75 R
2656 5206 1.140161 GCATGCATCACACGCCAAT 59.860 52.632 14.21 0.0 0.00 3.16 R
3579 7574 1.244019 AAGACCGCAAGACCATTGCC 61.244 55.000 6.98 0.0 42.10 4.52 R
4685 8747 0.959553 GAGTGAGAAGGTCGTGGACA 59.040 55.000 0.00 0.0 33.68 4.02 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
38 39 8.877864 ACCATTTGAACAAGTATTTGATAGGA 57.122 30.769 4.81 0.00 37.73 2.94
39 40 8.739972 ACCATTTGAACAAGTATTTGATAGGAC 58.260 33.333 4.81 0.00 37.73 3.85
40 41 8.739039 CCATTTGAACAAGTATTTGATAGGACA 58.261 33.333 4.81 0.00 37.73 4.02
44 45 9.513906 TTGAACAAGTATTTGATAGGACATTCA 57.486 29.630 4.81 0.00 37.73 2.57
45 46 8.946085 TGAACAAGTATTTGATAGGACATTCAC 58.054 33.333 4.81 0.00 37.73 3.18
46 47 8.862325 AACAAGTATTTGATAGGACATTCACA 57.138 30.769 4.81 0.00 37.73 3.58
47 48 8.862325 ACAAGTATTTGATAGGACATTCACAA 57.138 30.769 4.81 0.00 37.73 3.33
48 49 9.295825 ACAAGTATTTGATAGGACATTCACAAA 57.704 29.630 4.81 0.00 37.73 2.83
104 105 9.489393 TGAAATTTTAATCTTGAATCGATCACG 57.511 29.630 0.00 0.00 37.92 4.35
142 143 8.196771 TGGTCATAAGGTTATCAAATGATTTGC 58.803 33.333 12.86 0.00 40.43 3.68
143 144 8.416329 GGTCATAAGGTTATCAAATGATTTGCT 58.584 33.333 12.86 6.27 40.43 3.91
144 145 9.241317 GTCATAAGGTTATCAAATGATTTGCTG 57.759 33.333 12.86 0.00 40.43 4.41
145 146 7.922278 TCATAAGGTTATCAAATGATTTGCTGC 59.078 33.333 12.86 0.00 40.43 5.25
146 147 4.675510 AGGTTATCAAATGATTTGCTGCG 58.324 39.130 12.86 0.00 40.43 5.18
147 148 4.158394 AGGTTATCAAATGATTTGCTGCGT 59.842 37.500 12.86 2.91 40.43 5.24
148 149 4.864247 GGTTATCAAATGATTTGCTGCGTT 59.136 37.500 12.86 0.00 40.43 4.84
149 150 5.348451 GGTTATCAAATGATTTGCTGCGTTT 59.652 36.000 12.86 0.00 40.43 3.60
150 151 6.128580 GGTTATCAAATGATTTGCTGCGTTTT 60.129 34.615 12.86 0.00 40.43 2.43
151 152 4.712191 TCAAATGATTTGCTGCGTTTTG 57.288 36.364 12.86 0.00 40.43 2.44
152 153 4.366586 TCAAATGATTTGCTGCGTTTTGA 58.633 34.783 12.86 1.92 40.43 2.69
153 154 4.989797 TCAAATGATTTGCTGCGTTTTGAT 59.010 33.333 12.86 0.00 40.43 2.57
154 155 5.466058 TCAAATGATTTGCTGCGTTTTGATT 59.534 32.000 12.86 0.00 40.43 2.57
155 156 4.914312 ATGATTTGCTGCGTTTTGATTG 57.086 36.364 0.00 0.00 0.00 2.67
156 157 3.058450 TGATTTGCTGCGTTTTGATTGG 58.942 40.909 0.00 0.00 0.00 3.16
157 158 2.593346 TTTGCTGCGTTTTGATTGGT 57.407 40.000 0.00 0.00 0.00 3.67
158 159 2.132740 TTGCTGCGTTTTGATTGGTC 57.867 45.000 0.00 0.00 0.00 4.02
159 160 0.313672 TGCTGCGTTTTGATTGGTCC 59.686 50.000 0.00 0.00 0.00 4.46
160 161 0.313672 GCTGCGTTTTGATTGGTCCA 59.686 50.000 0.00 0.00 0.00 4.02
161 162 1.067635 GCTGCGTTTTGATTGGTCCAT 60.068 47.619 0.00 0.00 0.00 3.41
162 163 2.598589 CTGCGTTTTGATTGGTCCATG 58.401 47.619 0.00 0.00 0.00 3.66
163 164 1.271934 TGCGTTTTGATTGGTCCATGG 59.728 47.619 4.97 4.97 0.00 3.66
164 165 1.404047 GCGTTTTGATTGGTCCATGGG 60.404 52.381 13.02 0.00 0.00 4.00
165 166 1.404047 CGTTTTGATTGGTCCATGGGC 60.404 52.381 13.02 10.72 0.00 5.36
166 167 1.622811 GTTTTGATTGGTCCATGGGCA 59.377 47.619 20.13 0.00 0.00 5.36
167 168 2.236893 GTTTTGATTGGTCCATGGGCAT 59.763 45.455 20.13 3.30 0.00 4.40
168 169 3.395054 TTTGATTGGTCCATGGGCATA 57.605 42.857 20.13 5.26 0.00 3.14
169 170 3.616343 TTGATTGGTCCATGGGCATAT 57.384 42.857 20.13 10.51 0.00 1.78
170 171 3.159213 TGATTGGTCCATGGGCATATC 57.841 47.619 20.13 18.96 0.00 1.63
171 172 2.446285 TGATTGGTCCATGGGCATATCA 59.554 45.455 21.90 21.90 0.00 2.15
172 173 2.363306 TTGGTCCATGGGCATATCAC 57.637 50.000 20.13 3.61 0.00 3.06
173 174 0.108396 TGGTCCATGGGCATATCACG 59.892 55.000 20.13 0.00 0.00 4.35
174 175 0.108585 GGTCCATGGGCATATCACGT 59.891 55.000 20.13 0.00 0.00 4.49
175 176 1.229428 GTCCATGGGCATATCACGTG 58.771 55.000 12.68 9.94 0.00 4.49
176 177 0.108396 TCCATGGGCATATCACGTGG 59.892 55.000 17.00 0.00 41.55 4.94
177 178 0.108396 CCATGGGCATATCACGTGGA 59.892 55.000 17.00 4.46 42.54 4.02
178 179 1.271543 CCATGGGCATATCACGTGGAT 60.272 52.381 17.00 10.42 42.54 3.41
179 180 2.079158 CATGGGCATATCACGTGGATC 58.921 52.381 17.00 0.86 37.44 3.36
180 181 1.127343 TGGGCATATCACGTGGATCA 58.873 50.000 17.00 0.00 37.44 2.92
181 182 1.699083 TGGGCATATCACGTGGATCAT 59.301 47.619 17.00 4.06 37.44 2.45
182 183 2.079158 GGGCATATCACGTGGATCATG 58.921 52.381 17.00 14.03 37.44 3.07
183 184 1.466167 GGCATATCACGTGGATCATGC 59.534 52.381 23.95 23.95 39.56 4.06
184 185 2.145536 GCATATCACGTGGATCATGCA 58.854 47.619 25.58 0.00 39.78 3.96
185 186 2.745821 GCATATCACGTGGATCATGCAT 59.254 45.455 25.58 11.59 39.78 3.96
186 187 3.181513 GCATATCACGTGGATCATGCATC 60.182 47.826 25.58 8.60 39.78 3.91
187 188 2.625695 ATCACGTGGATCATGCATCA 57.374 45.000 17.00 0.00 32.33 3.07
188 189 2.399916 TCACGTGGATCATGCATCAA 57.600 45.000 17.00 0.00 32.33 2.57
189 190 2.009051 TCACGTGGATCATGCATCAAC 58.991 47.619 17.00 0.00 32.44 3.18
190 191 1.738908 CACGTGGATCATGCATCAACA 59.261 47.619 7.95 0.00 35.30 3.33
191 192 2.011947 ACGTGGATCATGCATCAACAG 58.988 47.619 0.00 7.58 35.30 3.16
192 193 1.268386 CGTGGATCATGCATCAACAGC 60.268 52.381 0.00 0.00 35.30 4.40
193 194 2.022195 GTGGATCATGCATCAACAGCT 58.978 47.619 0.00 0.00 35.63 4.24
194 195 3.208594 GTGGATCATGCATCAACAGCTA 58.791 45.455 0.00 0.00 35.63 3.32
195 196 3.819337 GTGGATCATGCATCAACAGCTAT 59.181 43.478 0.00 0.00 35.63 2.97
196 197 4.070009 TGGATCATGCATCAACAGCTATC 58.930 43.478 0.00 0.00 32.33 2.08
197 198 4.070009 GGATCATGCATCAACAGCTATCA 58.930 43.478 0.00 0.00 32.33 2.15
198 199 4.154375 GGATCATGCATCAACAGCTATCAG 59.846 45.833 0.00 0.00 32.33 2.90
199 200 4.411256 TCATGCATCAACAGCTATCAGA 57.589 40.909 0.00 0.00 0.00 3.27
200 201 4.969484 TCATGCATCAACAGCTATCAGAT 58.031 39.130 0.00 0.00 0.00 2.90
201 202 4.755123 TCATGCATCAACAGCTATCAGATG 59.245 41.667 0.00 11.23 37.69 2.90
208 209 3.185246 ACAGCTATCAGATGTTTCCGG 57.815 47.619 0.00 0.00 43.03 5.14
209 210 2.766263 ACAGCTATCAGATGTTTCCGGA 59.234 45.455 0.00 0.00 43.03 5.14
210 211 3.389329 ACAGCTATCAGATGTTTCCGGAT 59.611 43.478 4.15 0.00 43.03 4.18
211 212 3.993081 CAGCTATCAGATGTTTCCGGATC 59.007 47.826 4.15 0.00 0.00 3.36
212 213 3.007398 AGCTATCAGATGTTTCCGGATCC 59.993 47.826 4.15 0.00 0.00 3.36
213 214 3.244215 GCTATCAGATGTTTCCGGATCCA 60.244 47.826 13.41 5.35 0.00 3.41
214 215 3.931907 ATCAGATGTTTCCGGATCCAA 57.068 42.857 13.41 0.00 0.00 3.53
215 216 2.985896 TCAGATGTTTCCGGATCCAAC 58.014 47.619 13.41 7.89 0.00 3.77
216 217 1.665679 CAGATGTTTCCGGATCCAACG 59.334 52.381 13.41 0.00 0.00 4.10
224 225 4.115199 GGATCCAACGGCAGCCCT 62.115 66.667 6.95 0.00 0.00 5.19
225 226 2.514824 GATCCAACGGCAGCCCTC 60.515 66.667 5.63 0.00 0.00 4.30
226 227 3.329542 GATCCAACGGCAGCCCTCA 62.330 63.158 5.63 0.00 0.00 3.86
227 228 3.628646 ATCCAACGGCAGCCCTCAC 62.629 63.158 5.63 0.00 0.00 3.51
235 236 3.721706 CAGCCCTCACCCCCTCAC 61.722 72.222 0.00 0.00 0.00 3.51
238 239 4.675303 CCCTCACCCCCTCACCCA 62.675 72.222 0.00 0.00 0.00 4.51
239 240 2.531685 CCTCACCCCCTCACCCAA 60.532 66.667 0.00 0.00 0.00 4.12
240 241 2.757077 CTCACCCCCTCACCCAAC 59.243 66.667 0.00 0.00 0.00 3.77
241 242 2.856988 TCACCCCCTCACCCAACC 60.857 66.667 0.00 0.00 0.00 3.77
242 243 4.344865 CACCCCCTCACCCAACCG 62.345 72.222 0.00 0.00 0.00 4.44
245 246 4.722700 CCCCTCACCCAACCGCAG 62.723 72.222 0.00 0.00 0.00 5.18
252 253 4.974721 CCCAACCGCAGCCCAACT 62.975 66.667 0.00 0.00 0.00 3.16
253 254 2.033448 CCAACCGCAGCCCAACTA 59.967 61.111 0.00 0.00 0.00 2.24
254 255 2.332654 CCAACCGCAGCCCAACTAC 61.333 63.158 0.00 0.00 0.00 2.73
255 256 2.033602 AACCGCAGCCCAACTACC 59.966 61.111 0.00 0.00 0.00 3.18
256 257 3.562732 AACCGCAGCCCAACTACCC 62.563 63.158 0.00 0.00 0.00 3.69
257 258 4.028490 CCGCAGCCCAACTACCCA 62.028 66.667 0.00 0.00 0.00 4.51
258 259 2.033448 CGCAGCCCAACTACCCAA 59.967 61.111 0.00 0.00 0.00 4.12
259 260 1.602323 CGCAGCCCAACTACCCAAA 60.602 57.895 0.00 0.00 0.00 3.28
260 261 1.862602 CGCAGCCCAACTACCCAAAC 61.863 60.000 0.00 0.00 0.00 2.93
261 262 1.532604 GCAGCCCAACTACCCAAACC 61.533 60.000 0.00 0.00 0.00 3.27
262 263 0.898326 CAGCCCAACTACCCAAACCC 60.898 60.000 0.00 0.00 0.00 4.11
263 264 1.071909 AGCCCAACTACCCAAACCCT 61.072 55.000 0.00 0.00 0.00 4.34
264 265 0.699981 GCCCAACTACCCAAACCCTA 59.300 55.000 0.00 0.00 0.00 3.53
265 266 1.075861 GCCCAACTACCCAAACCCTAA 59.924 52.381 0.00 0.00 0.00 2.69
266 267 2.799017 CCCAACTACCCAAACCCTAAC 58.201 52.381 0.00 0.00 0.00 2.34
267 268 2.377531 CCCAACTACCCAAACCCTAACT 59.622 50.000 0.00 0.00 0.00 2.24
268 269 3.560668 CCCAACTACCCAAACCCTAACTC 60.561 52.174 0.00 0.00 0.00 3.01
269 270 3.073356 CCAACTACCCAAACCCTAACTCA 59.927 47.826 0.00 0.00 0.00 3.41
270 271 4.324267 CAACTACCCAAACCCTAACTCAG 58.676 47.826 0.00 0.00 0.00 3.35
271 272 3.865571 ACTACCCAAACCCTAACTCAGA 58.134 45.455 0.00 0.00 0.00 3.27
272 273 3.581770 ACTACCCAAACCCTAACTCAGAC 59.418 47.826 0.00 0.00 0.00 3.51
273 274 1.703513 ACCCAAACCCTAACTCAGACC 59.296 52.381 0.00 0.00 0.00 3.85
274 275 1.004394 CCCAAACCCTAACTCAGACCC 59.996 57.143 0.00 0.00 0.00 4.46
275 276 1.004394 CCAAACCCTAACTCAGACCCC 59.996 57.143 0.00 0.00 0.00 4.95
276 277 1.004394 CAAACCCTAACTCAGACCCCC 59.996 57.143 0.00 0.00 0.00 5.40
277 278 0.496841 AACCCTAACTCAGACCCCCT 59.503 55.000 0.00 0.00 0.00 4.79
278 279 0.042881 ACCCTAACTCAGACCCCCTC 59.957 60.000 0.00 0.00 0.00 4.30
279 280 0.691413 CCCTAACTCAGACCCCCTCC 60.691 65.000 0.00 0.00 0.00 4.30
280 281 0.340208 CCTAACTCAGACCCCCTCCT 59.660 60.000 0.00 0.00 0.00 3.69
281 282 1.689892 CCTAACTCAGACCCCCTCCTC 60.690 61.905 0.00 0.00 0.00 3.71
282 283 1.289530 CTAACTCAGACCCCCTCCTCT 59.710 57.143 0.00 0.00 0.00 3.69
283 284 0.041982 AACTCAGACCCCCTCCTCTC 59.958 60.000 0.00 0.00 0.00 3.20
284 285 0.853586 ACTCAGACCCCCTCCTCTCT 60.854 60.000 0.00 0.00 0.00 3.10
285 286 0.106217 CTCAGACCCCCTCCTCTCTC 60.106 65.000 0.00 0.00 0.00 3.20
286 287 1.075600 CAGACCCCCTCCTCTCTCC 60.076 68.421 0.00 0.00 0.00 3.71
287 288 2.284151 GACCCCCTCCTCTCTCCC 59.716 72.222 0.00 0.00 0.00 4.30
288 289 3.369388 ACCCCCTCCTCTCTCCCC 61.369 72.222 0.00 0.00 0.00 4.81
289 290 4.179599 CCCCCTCCTCTCTCCCCC 62.180 77.778 0.00 0.00 0.00 5.40
290 291 4.548513 CCCCTCCTCTCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
291 292 3.430497 CCCTCCTCTCTCCCCCGA 61.430 72.222 0.00 0.00 0.00 5.14
292 293 2.784654 CCCTCCTCTCTCCCCCGAT 61.785 68.421 0.00 0.00 0.00 4.18
293 294 1.228737 CCTCCTCTCTCCCCCGATC 60.229 68.421 0.00 0.00 0.00 3.69
294 295 1.228737 CTCCTCTCTCCCCCGATCC 60.229 68.421 0.00 0.00 0.00 3.36
295 296 2.012794 TCCTCTCTCCCCCGATCCA 61.013 63.158 0.00 0.00 0.00 3.41
296 297 1.834822 CCTCTCTCCCCCGATCCAC 60.835 68.421 0.00 0.00 0.00 4.02
297 298 1.231641 CTCTCTCCCCCGATCCACT 59.768 63.158 0.00 0.00 0.00 4.00
298 299 0.825840 CTCTCTCCCCCGATCCACTC 60.826 65.000 0.00 0.00 0.00 3.51
299 300 1.834822 CTCTCCCCCGATCCACTCC 60.835 68.421 0.00 0.00 0.00 3.85
300 301 2.844839 CTCCCCCGATCCACTCCC 60.845 72.222 0.00 0.00 0.00 4.30
301 302 4.853142 TCCCCCGATCCACTCCCG 62.853 72.222 0.00 0.00 0.00 5.14
328 329 4.522975 CTCCCCCGCCCCCAAATC 62.523 72.222 0.00 0.00 0.00 2.17
334 335 4.060667 CGCCCCCAAATCCACCCT 62.061 66.667 0.00 0.00 0.00 4.34
335 336 2.042944 GCCCCCAAATCCACCCTC 60.043 66.667 0.00 0.00 0.00 4.30
336 337 2.929964 GCCCCCAAATCCACCCTCA 61.930 63.158 0.00 0.00 0.00 3.86
337 338 1.000359 CCCCCAAATCCACCCTCAC 60.000 63.158 0.00 0.00 0.00 3.51
338 339 1.378514 CCCCAAATCCACCCTCACG 60.379 63.158 0.00 0.00 0.00 4.35
339 340 2.046285 CCCAAATCCACCCTCACGC 61.046 63.158 0.00 0.00 0.00 5.34
340 341 2.046285 CCAAATCCACCCTCACGCC 61.046 63.158 0.00 0.00 0.00 5.68
341 342 2.046314 AAATCCACCCTCACGCCG 60.046 61.111 0.00 0.00 0.00 6.46
342 343 4.778143 AATCCACCCTCACGCCGC 62.778 66.667 0.00 0.00 0.00 6.53
941 942 1.196581 CGATCTCAGATCGCATCGAGT 59.803 52.381 23.65 0.00 40.48 4.18
965 968 0.252927 CCCTCTCCCTCCCACTTCTT 60.253 60.000 0.00 0.00 0.00 2.52
1120 1476 3.155167 GCGGAATCGACCCCCTCT 61.155 66.667 0.00 0.00 39.00 3.69
1162 1728 3.254617 GTTCCCCTTCCCCGTGGT 61.255 66.667 0.00 0.00 0.00 4.16
1435 2045 2.975265 TAGAGGGGGACGAGCACGA 61.975 63.158 11.40 0.00 42.66 4.35
1436 2046 4.131088 GAGGGGGACGAGCACGAC 62.131 72.222 11.40 3.60 42.66 4.34
1550 2309 3.965539 CTTCTCCCAGTGGCGGCAG 62.966 68.421 13.91 0.42 0.00 4.85
1845 2715 3.154710 TGACCACTTAGTCAGACGATGT 58.845 45.455 0.00 0.00 41.78 3.06
1940 2812 0.740149 CAAGCACACACAGCCTCAAA 59.260 50.000 0.00 0.00 0.00 2.69
2017 2889 6.727824 ATAGTGCTGAAACTTGTACATGAC 57.272 37.500 15.13 6.97 0.00 3.06
2445 3360 1.064314 TGGTGCTGTTACAACACCCTT 60.064 47.619 28.27 0.00 46.46 3.95
2541 5082 3.519107 TGTGCAGGATAAACTGATGGAGA 59.481 43.478 0.00 0.00 40.97 3.71
2656 5206 4.021192 TGATTGATCGTGCATATGGCTCTA 60.021 41.667 4.56 0.00 45.15 2.43
3036 5587 0.980231 ACTCCTGGACATCAGCTCCC 60.980 60.000 0.00 0.00 42.05 4.30
3576 7571 2.031163 GCTCGCTTCTGGGTGTGT 59.969 61.111 0.00 0.00 0.00 3.72
3579 7574 0.668706 CTCGCTTCTGGGTGTGTGAG 60.669 60.000 0.00 0.00 0.00 3.51
3580 7575 1.669115 CGCTTCTGGGTGTGTGAGG 60.669 63.158 0.00 0.00 0.00 3.86
3666 7662 6.237901 TGTGATGTTTGCTTATTAGGTCTGT 58.762 36.000 0.00 0.00 0.00 3.41
3667 7663 6.149308 TGTGATGTTTGCTTATTAGGTCTGTG 59.851 38.462 0.00 0.00 0.00 3.66
3739 7737 9.793252 CGATATTGATTCCTTTCTTGTTCAATT 57.207 29.630 0.00 0.00 35.87 2.32
3882 7883 7.387948 ACGAGTTCATGAATAACTAAGCAACTT 59.612 33.333 12.12 0.00 37.31 2.66
3953 7973 4.859304 TTACGACTCCATATACGGCAAT 57.141 40.909 0.00 0.00 0.00 3.56
4114 8138 7.975616 GCAGATATTTTGCCTAAATTCAAGACA 59.024 33.333 2.61 0.00 37.60 3.41
4629 8691 2.348104 ACGCTGGATGCCTACGTGA 61.348 57.895 0.00 0.00 35.29 4.35
4668 8730 6.538945 AGTGACCAAAACAAAACAATAGGT 57.461 33.333 0.00 0.00 0.00 3.08
4873 8950 8.472007 AAATTTAGTGTCAAATAGGGAACACA 57.528 30.769 7.18 0.00 0.00 3.72
4918 8995 6.588348 AGGAATTCTTTCAAAAAGCAAACG 57.412 33.333 5.23 0.00 33.23 3.60
4919 8996 6.337356 AGGAATTCTTTCAAAAAGCAAACGA 58.663 32.000 5.23 0.00 33.23 3.85
4921 8998 7.333174 AGGAATTCTTTCAAAAAGCAAACGAAA 59.667 29.630 5.23 0.00 33.23 3.46
4937 9014 6.289901 CAAACGAAACAGACTCGAAACTATC 58.710 40.000 0.00 0.00 39.60 2.08
4942 9019 6.633634 CGAAACAGACTCGAAACTATCCTATC 59.366 42.308 0.00 0.00 38.61 2.08
4960 9037 0.674269 TCGGCCCAAAATACACGGTC 60.674 55.000 0.00 0.00 0.00 4.79
4971 9048 2.801113 TACACGGTCGTTGTAGGCGC 62.801 60.000 0.00 0.00 0.00 6.53
4989 9066 3.394836 GGTGAGCTTCCCCTCGCT 61.395 66.667 0.00 0.00 41.07 4.93
5059 9136 9.586435 AATCCAAATTATTTGCAGCTTTAGTAC 57.414 29.630 11.82 0.00 39.31 2.73
5068 9145 5.429681 TGCAGCTTTAGTACTTTATCCCA 57.570 39.130 0.00 0.00 0.00 4.37
5076 9153 9.343539 GCTTTAGTACTTTATCCCATGAAATCT 57.656 33.333 0.00 0.00 0.00 2.40
5091 9168 6.292757 CCATGAAATCTGAGAGCAACTAATCG 60.293 42.308 0.00 0.00 0.00 3.34
5093 9170 6.398095 TGAAATCTGAGAGCAACTAATCGAA 58.602 36.000 0.00 0.00 0.00 3.71
5099 9176 6.096987 TCTGAGAGCAACTAATCGAAGGTTAT 59.903 38.462 0.00 0.00 0.00 1.89
5111 9188 1.613061 AGGTTATCCTTTGCGGGGG 59.387 57.895 0.00 0.00 42.12 5.40
5112 9189 2.125326 GGTTATCCTTTGCGGGGGC 61.125 63.158 0.00 0.00 0.00 5.80
5113 9190 2.125326 GTTATCCTTTGCGGGGGCC 61.125 63.158 0.00 0.00 0.00 5.80
5114 9191 2.313427 TTATCCTTTGCGGGGGCCT 61.313 57.895 0.84 0.00 0.00 5.19
5115 9192 1.869824 TTATCCTTTGCGGGGGCCTT 61.870 55.000 0.84 0.00 0.00 4.35
5116 9193 1.869824 TATCCTTTGCGGGGGCCTTT 61.870 55.000 0.84 0.00 0.00 3.11
5126 9203 1.388133 GGGGCCTTTGAAGGGTCAT 59.612 57.895 11.53 0.00 46.56 3.06
5136 9213 2.324541 TGAAGGGTCATTTTTGGTGGG 58.675 47.619 0.00 0.00 0.00 4.61
5179 9256 2.741092 GTGCTGAACGGTCCCTCA 59.259 61.111 0.00 0.00 0.00 3.86
5268 9349 5.891810 TTCGGCTTTTTAATTTTTGACCG 57.108 34.783 0.00 0.00 39.44 4.79
5285 9366 4.581868 TGACCGGTTTTACCTAGGATTTG 58.418 43.478 17.98 0.00 35.66 2.32
5324 9405 4.686191 TTTTGGGCATGAAAGAACATGT 57.314 36.364 0.00 0.00 46.25 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.967451 TCCTATCAAATACTTGTTCAAATGGTA 57.033 29.630 0.00 0.00 33.94 3.25
13 14 8.739972 GTCCTATCAAATACTTGTTCAAATGGT 58.260 33.333 0.00 0.00 33.94 3.55
14 15 8.739039 TGTCCTATCAAATACTTGTTCAAATGG 58.261 33.333 0.00 0.00 33.94 3.16
18 19 9.513906 TGAATGTCCTATCAAATACTTGTTCAA 57.486 29.630 0.00 0.00 33.94 2.69
19 20 8.946085 GTGAATGTCCTATCAAATACTTGTTCA 58.054 33.333 0.00 0.00 33.94 3.18
20 21 8.946085 TGTGAATGTCCTATCAAATACTTGTTC 58.054 33.333 0.00 0.00 33.94 3.18
21 22 8.862325 TGTGAATGTCCTATCAAATACTTGTT 57.138 30.769 0.00 0.00 33.94 2.83
22 23 8.862325 TTGTGAATGTCCTATCAAATACTTGT 57.138 30.769 0.00 0.00 33.94 3.16
78 79 9.489393 CGTGATCGATTCAAGATTAAAATTTCA 57.511 29.630 0.00 0.00 36.07 2.69
79 80 9.702726 TCGTGATCGATTCAAGATTAAAATTTC 57.297 29.630 0.00 0.00 41.35 2.17
93 94 7.117812 ACCATATAAATTGGTCGTGATCGATTC 59.882 37.037 0.00 0.00 44.15 2.52
94 95 6.934645 ACCATATAAATTGGTCGTGATCGATT 59.065 34.615 0.00 0.00 44.15 3.34
95 96 6.464222 ACCATATAAATTGGTCGTGATCGAT 58.536 36.000 0.00 0.00 44.15 3.59
96 97 5.849510 ACCATATAAATTGGTCGTGATCGA 58.150 37.500 0.00 0.00 44.15 3.59
116 117 8.196771 GCAAATCATTTGATAACCTTATGACCA 58.803 33.333 14.65 0.00 43.26 4.02
117 118 8.416329 AGCAAATCATTTGATAACCTTATGACC 58.584 33.333 14.65 0.00 43.26 4.02
118 119 9.241317 CAGCAAATCATTTGATAACCTTATGAC 57.759 33.333 14.65 0.00 43.26 3.06
119 120 7.922278 GCAGCAAATCATTTGATAACCTTATGA 59.078 33.333 14.65 0.00 43.26 2.15
120 121 7.096353 CGCAGCAAATCATTTGATAACCTTATG 60.096 37.037 14.65 0.00 43.26 1.90
121 122 6.919662 CGCAGCAAATCATTTGATAACCTTAT 59.080 34.615 14.65 0.00 43.26 1.73
122 123 6.127758 ACGCAGCAAATCATTTGATAACCTTA 60.128 34.615 14.65 0.00 43.26 2.69
123 124 5.104374 CGCAGCAAATCATTTGATAACCTT 58.896 37.500 14.65 0.00 43.26 3.50
124 125 4.158394 ACGCAGCAAATCATTTGATAACCT 59.842 37.500 14.65 0.00 43.26 3.50
125 126 4.423732 ACGCAGCAAATCATTTGATAACC 58.576 39.130 14.65 0.00 43.26 2.85
126 127 6.393720 AAACGCAGCAAATCATTTGATAAC 57.606 33.333 14.65 2.62 43.26 1.89
127 128 6.644181 TCAAAACGCAGCAAATCATTTGATAA 59.356 30.769 14.65 0.00 43.26 1.75
128 129 6.155136 TCAAAACGCAGCAAATCATTTGATA 58.845 32.000 14.65 0.00 43.26 2.15
129 130 4.989797 TCAAAACGCAGCAAATCATTTGAT 59.010 33.333 14.65 4.39 43.26 2.57
130 131 4.366586 TCAAAACGCAGCAAATCATTTGA 58.633 34.783 14.65 0.00 43.26 2.69
131 132 4.712191 TCAAAACGCAGCAAATCATTTG 57.288 36.364 5.68 5.68 43.44 2.32
132 133 5.334260 CCAATCAAAACGCAGCAAATCATTT 60.334 36.000 0.00 0.00 0.00 2.32
133 134 4.152759 CCAATCAAAACGCAGCAAATCATT 59.847 37.500 0.00 0.00 0.00 2.57
134 135 3.680937 CCAATCAAAACGCAGCAAATCAT 59.319 39.130 0.00 0.00 0.00 2.45
135 136 3.058450 CCAATCAAAACGCAGCAAATCA 58.942 40.909 0.00 0.00 0.00 2.57
136 137 3.059166 ACCAATCAAAACGCAGCAAATC 58.941 40.909 0.00 0.00 0.00 2.17
137 138 3.059166 GACCAATCAAAACGCAGCAAAT 58.941 40.909 0.00 0.00 0.00 2.32
138 139 2.468831 GACCAATCAAAACGCAGCAAA 58.531 42.857 0.00 0.00 0.00 3.68
139 140 1.269517 GGACCAATCAAAACGCAGCAA 60.270 47.619 0.00 0.00 0.00 3.91
140 141 0.313672 GGACCAATCAAAACGCAGCA 59.686 50.000 0.00 0.00 0.00 4.41
141 142 0.313672 TGGACCAATCAAAACGCAGC 59.686 50.000 0.00 0.00 0.00 5.25
142 143 2.598589 CATGGACCAATCAAAACGCAG 58.401 47.619 0.00 0.00 0.00 5.18
143 144 1.271934 CCATGGACCAATCAAAACGCA 59.728 47.619 5.56 0.00 0.00 5.24
144 145 1.404047 CCCATGGACCAATCAAAACGC 60.404 52.381 15.22 0.00 0.00 4.84
145 146 1.404047 GCCCATGGACCAATCAAAACG 60.404 52.381 15.22 0.00 0.00 3.60
146 147 1.622811 TGCCCATGGACCAATCAAAAC 59.377 47.619 15.22 0.00 0.00 2.43
147 148 2.021262 TGCCCATGGACCAATCAAAA 57.979 45.000 15.22 0.00 0.00 2.44
148 149 2.250921 ATGCCCATGGACCAATCAAA 57.749 45.000 15.22 0.00 0.00 2.69
149 150 3.117208 TGATATGCCCATGGACCAATCAA 60.117 43.478 15.22 0.00 0.00 2.57
150 151 2.446285 TGATATGCCCATGGACCAATCA 59.554 45.455 15.22 13.68 0.00 2.57
151 152 2.821969 GTGATATGCCCATGGACCAATC 59.178 50.000 15.22 11.24 0.00 2.67
152 153 2.815215 CGTGATATGCCCATGGACCAAT 60.815 50.000 15.22 0.91 0.00 3.16
153 154 1.476652 CGTGATATGCCCATGGACCAA 60.477 52.381 15.22 0.00 0.00 3.67
154 155 0.108396 CGTGATATGCCCATGGACCA 59.892 55.000 15.22 10.56 0.00 4.02
155 156 0.108585 ACGTGATATGCCCATGGACC 59.891 55.000 15.22 4.18 0.00 4.46
156 157 1.229428 CACGTGATATGCCCATGGAC 58.771 55.000 15.22 0.55 0.00 4.02
157 158 0.108396 CCACGTGATATGCCCATGGA 59.892 55.000 19.30 0.00 0.00 3.41
158 159 0.108396 TCCACGTGATATGCCCATGG 59.892 55.000 19.30 4.14 0.00 3.66
159 160 2.079158 GATCCACGTGATATGCCCATG 58.921 52.381 19.30 0.00 32.41 3.66
160 161 1.699083 TGATCCACGTGATATGCCCAT 59.301 47.619 19.30 0.00 32.41 4.00
161 162 1.127343 TGATCCACGTGATATGCCCA 58.873 50.000 19.30 2.18 32.41 5.36
162 163 2.079158 CATGATCCACGTGATATGCCC 58.921 52.381 19.30 0.00 37.69 5.36
163 164 1.466167 GCATGATCCACGTGATATGCC 59.534 52.381 19.30 8.12 36.04 4.40
164 165 2.145536 TGCATGATCCACGTGATATGC 58.854 47.619 25.38 25.38 38.97 3.14
165 166 3.998341 TGATGCATGATCCACGTGATATG 59.002 43.478 19.30 15.43 37.69 1.78
166 167 4.276058 TGATGCATGATCCACGTGATAT 57.724 40.909 19.30 10.24 37.69 1.63
167 168 3.749665 TGATGCATGATCCACGTGATA 57.250 42.857 19.30 4.90 37.69 2.15
168 169 2.615447 GTTGATGCATGATCCACGTGAT 59.385 45.455 19.30 8.71 37.69 3.06
169 170 2.009051 GTTGATGCATGATCCACGTGA 58.991 47.619 19.30 3.36 37.69 4.35
170 171 1.738908 TGTTGATGCATGATCCACGTG 59.261 47.619 9.08 9.08 38.43 4.49
171 172 2.011947 CTGTTGATGCATGATCCACGT 58.988 47.619 2.46 0.00 30.68 4.49
172 173 1.268386 GCTGTTGATGCATGATCCACG 60.268 52.381 2.46 0.00 30.68 4.94
173 174 2.022195 AGCTGTTGATGCATGATCCAC 58.978 47.619 2.46 0.00 0.00 4.02
174 175 2.430248 AGCTGTTGATGCATGATCCA 57.570 45.000 2.46 0.00 0.00 3.41
175 176 4.070009 TGATAGCTGTTGATGCATGATCC 58.930 43.478 2.46 0.00 0.00 3.36
176 177 4.995487 TCTGATAGCTGTTGATGCATGATC 59.005 41.667 2.46 0.00 0.00 2.92
177 178 4.969484 TCTGATAGCTGTTGATGCATGAT 58.031 39.130 2.46 0.00 0.00 2.45
178 179 4.411256 TCTGATAGCTGTTGATGCATGA 57.589 40.909 2.46 0.00 0.00 3.07
179 180 4.515567 ACATCTGATAGCTGTTGATGCATG 59.484 41.667 19.54 0.00 38.33 4.06
180 181 4.715713 ACATCTGATAGCTGTTGATGCAT 58.284 39.130 19.54 0.00 38.33 3.96
181 182 4.146745 ACATCTGATAGCTGTTGATGCA 57.853 40.909 19.54 0.00 38.33 3.96
182 183 5.496133 AAACATCTGATAGCTGTTGATGC 57.504 39.130 19.54 0.00 35.08 3.91
183 184 5.277202 CGGAAACATCTGATAGCTGTTGATG 60.277 44.000 18.64 18.64 35.08 3.07
184 185 4.813161 CGGAAACATCTGATAGCTGTTGAT 59.187 41.667 0.00 0.00 35.08 2.57
185 186 4.183865 CGGAAACATCTGATAGCTGTTGA 58.816 43.478 0.00 0.00 35.08 3.18
186 187 3.310774 CCGGAAACATCTGATAGCTGTTG 59.689 47.826 0.00 0.00 35.08 3.33
187 188 3.197766 TCCGGAAACATCTGATAGCTGTT 59.802 43.478 0.00 0.00 36.25 3.16
188 189 2.766263 TCCGGAAACATCTGATAGCTGT 59.234 45.455 0.00 0.00 0.00 4.40
189 190 3.459232 TCCGGAAACATCTGATAGCTG 57.541 47.619 0.00 0.00 0.00 4.24
190 191 3.007398 GGATCCGGAAACATCTGATAGCT 59.993 47.826 9.01 0.00 0.00 3.32
191 192 3.244215 TGGATCCGGAAACATCTGATAGC 60.244 47.826 9.01 0.00 0.00 2.97
192 193 4.607293 TGGATCCGGAAACATCTGATAG 57.393 45.455 9.01 0.00 0.00 2.08
193 194 4.703897 GTTGGATCCGGAAACATCTGATA 58.296 43.478 9.01 0.00 0.00 2.15
194 195 3.545703 GTTGGATCCGGAAACATCTGAT 58.454 45.455 9.01 0.00 0.00 2.90
195 196 2.676750 CGTTGGATCCGGAAACATCTGA 60.677 50.000 9.01 0.00 0.00 3.27
196 197 1.665679 CGTTGGATCCGGAAACATCTG 59.334 52.381 9.01 3.29 0.00 2.90
197 198 2.024176 CGTTGGATCCGGAAACATCT 57.976 50.000 9.01 0.00 0.00 2.90
207 208 4.115199 AGGGCTGCCGTTGGATCC 62.115 66.667 13.40 4.20 0.00 3.36
208 209 2.514824 GAGGGCTGCCGTTGGATC 60.515 66.667 15.88 0.00 0.00 3.36
209 210 3.329889 TGAGGGCTGCCGTTGGAT 61.330 61.111 15.88 0.00 0.00 3.41
210 211 4.329545 GTGAGGGCTGCCGTTGGA 62.330 66.667 15.88 0.05 0.00 3.53
218 219 3.721706 GTGAGGGGGTGAGGGCTG 61.722 72.222 0.00 0.00 0.00 4.85
221 222 4.675303 TGGGTGAGGGGGTGAGGG 62.675 72.222 0.00 0.00 0.00 4.30
222 223 2.531685 TTGGGTGAGGGGGTGAGG 60.532 66.667 0.00 0.00 0.00 3.86
223 224 2.757077 GTTGGGTGAGGGGGTGAG 59.243 66.667 0.00 0.00 0.00 3.51
224 225 2.856988 GGTTGGGTGAGGGGGTGA 60.857 66.667 0.00 0.00 0.00 4.02
225 226 4.344865 CGGTTGGGTGAGGGGGTG 62.345 72.222 0.00 0.00 0.00 4.61
228 229 4.722700 CTGCGGTTGGGTGAGGGG 62.723 72.222 0.00 0.00 0.00 4.79
235 236 3.561120 TAGTTGGGCTGCGGTTGGG 62.561 63.158 0.00 0.00 0.00 4.12
236 237 2.033448 TAGTTGGGCTGCGGTTGG 59.967 61.111 0.00 0.00 0.00 3.77
237 238 2.332654 GGTAGTTGGGCTGCGGTTG 61.333 63.158 0.00 0.00 0.00 3.77
238 239 2.033602 GGTAGTTGGGCTGCGGTT 59.966 61.111 0.00 0.00 0.00 4.44
239 240 4.029809 GGGTAGTTGGGCTGCGGT 62.030 66.667 0.00 0.00 0.00 5.68
240 241 3.561120 TTGGGTAGTTGGGCTGCGG 62.561 63.158 0.00 0.00 0.00 5.69
241 242 1.602323 TTTGGGTAGTTGGGCTGCG 60.602 57.895 0.00 0.00 0.00 5.18
242 243 1.532604 GGTTTGGGTAGTTGGGCTGC 61.533 60.000 0.00 0.00 0.00 5.25
243 244 0.898326 GGGTTTGGGTAGTTGGGCTG 60.898 60.000 0.00 0.00 0.00 4.85
244 245 1.071909 AGGGTTTGGGTAGTTGGGCT 61.072 55.000 0.00 0.00 0.00 5.19
245 246 0.699981 TAGGGTTTGGGTAGTTGGGC 59.300 55.000 0.00 0.00 0.00 5.36
246 247 2.377531 AGTTAGGGTTTGGGTAGTTGGG 59.622 50.000 0.00 0.00 0.00 4.12
247 248 3.073356 TGAGTTAGGGTTTGGGTAGTTGG 59.927 47.826 0.00 0.00 0.00 3.77
248 249 4.041198 TCTGAGTTAGGGTTTGGGTAGTTG 59.959 45.833 0.00 0.00 0.00 3.16
249 250 4.041321 GTCTGAGTTAGGGTTTGGGTAGTT 59.959 45.833 0.00 0.00 0.00 2.24
250 251 3.581770 GTCTGAGTTAGGGTTTGGGTAGT 59.418 47.826 0.00 0.00 0.00 2.73
251 252 3.055312 GGTCTGAGTTAGGGTTTGGGTAG 60.055 52.174 0.00 0.00 0.00 3.18
252 253 2.908351 GGTCTGAGTTAGGGTTTGGGTA 59.092 50.000 0.00 0.00 0.00 3.69
253 254 1.703513 GGTCTGAGTTAGGGTTTGGGT 59.296 52.381 0.00 0.00 0.00 4.51
254 255 1.004394 GGGTCTGAGTTAGGGTTTGGG 59.996 57.143 0.00 0.00 0.00 4.12
255 256 1.004394 GGGGTCTGAGTTAGGGTTTGG 59.996 57.143 0.00 0.00 0.00 3.28
256 257 1.004394 GGGGGTCTGAGTTAGGGTTTG 59.996 57.143 0.00 0.00 0.00 2.93
257 258 1.132168 AGGGGGTCTGAGTTAGGGTTT 60.132 52.381 0.00 0.00 0.00 3.27
258 259 0.496841 AGGGGGTCTGAGTTAGGGTT 59.503 55.000 0.00 0.00 0.00 4.11
259 260 0.042881 GAGGGGGTCTGAGTTAGGGT 59.957 60.000 0.00 0.00 0.00 4.34
260 261 0.691413 GGAGGGGGTCTGAGTTAGGG 60.691 65.000 0.00 0.00 0.00 3.53
261 262 0.340208 AGGAGGGGGTCTGAGTTAGG 59.660 60.000 0.00 0.00 0.00 2.69
262 263 1.289530 AGAGGAGGGGGTCTGAGTTAG 59.710 57.143 0.00 0.00 0.00 2.34
263 264 1.288335 GAGAGGAGGGGGTCTGAGTTA 59.712 57.143 0.00 0.00 0.00 2.24
264 265 0.041982 GAGAGGAGGGGGTCTGAGTT 59.958 60.000 0.00 0.00 0.00 3.01
265 266 0.853586 AGAGAGGAGGGGGTCTGAGT 60.854 60.000 0.00 0.00 0.00 3.41
266 267 0.106217 GAGAGAGGAGGGGGTCTGAG 60.106 65.000 0.00 0.00 0.00 3.35
267 268 1.585651 GGAGAGAGGAGGGGGTCTGA 61.586 65.000 0.00 0.00 0.00 3.27
268 269 1.075600 GGAGAGAGGAGGGGGTCTG 60.076 68.421 0.00 0.00 0.00 3.51
269 270 2.329399 GGGAGAGAGGAGGGGGTCT 61.329 68.421 0.00 0.00 0.00 3.85
270 271 2.284151 GGGAGAGAGGAGGGGGTC 59.716 72.222 0.00 0.00 0.00 4.46
271 272 3.369388 GGGGAGAGAGGAGGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
272 273 4.179599 GGGGGAGAGAGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
273 274 4.548513 CGGGGGAGAGAGGAGGGG 62.549 77.778 0.00 0.00 0.00 4.79
274 275 2.723464 GATCGGGGGAGAGAGGAGGG 62.723 70.000 0.00 0.00 0.00 4.30
275 276 1.228737 GATCGGGGGAGAGAGGAGG 60.229 68.421 0.00 0.00 0.00 4.30
276 277 1.228737 GGATCGGGGGAGAGAGGAG 60.229 68.421 0.00 0.00 0.00 3.69
277 278 2.012794 TGGATCGGGGGAGAGAGGA 61.013 63.158 0.00 0.00 0.00 3.71
278 279 1.834822 GTGGATCGGGGGAGAGAGG 60.835 68.421 0.00 0.00 0.00 3.69
279 280 0.825840 GAGTGGATCGGGGGAGAGAG 60.826 65.000 0.00 0.00 0.00 3.20
280 281 1.230497 GAGTGGATCGGGGGAGAGA 59.770 63.158 0.00 0.00 0.00 3.10
281 282 1.834822 GGAGTGGATCGGGGGAGAG 60.835 68.421 0.00 0.00 0.00 3.20
282 283 2.282446 GGAGTGGATCGGGGGAGA 59.718 66.667 0.00 0.00 0.00 3.71
283 284 2.844839 GGGAGTGGATCGGGGGAG 60.845 72.222 0.00 0.00 0.00 4.30
284 285 4.853142 CGGGAGTGGATCGGGGGA 62.853 72.222 0.00 0.00 0.00 4.81
311 312 4.522975 GATTTGGGGGCGGGGGAG 62.523 72.222 0.00 0.00 0.00 4.30
317 318 4.060667 AGGGTGGATTTGGGGGCG 62.061 66.667 0.00 0.00 0.00 6.13
318 319 2.042944 GAGGGTGGATTTGGGGGC 60.043 66.667 0.00 0.00 0.00 5.80
319 320 1.000359 GTGAGGGTGGATTTGGGGG 60.000 63.158 0.00 0.00 0.00 5.40
320 321 1.378514 CGTGAGGGTGGATTTGGGG 60.379 63.158 0.00 0.00 0.00 4.96
321 322 2.046285 GCGTGAGGGTGGATTTGGG 61.046 63.158 0.00 0.00 0.00 4.12
322 323 2.046285 GGCGTGAGGGTGGATTTGG 61.046 63.158 0.00 0.00 0.00 3.28
323 324 2.398554 CGGCGTGAGGGTGGATTTG 61.399 63.158 0.00 0.00 0.00 2.32
324 325 2.046314 CGGCGTGAGGGTGGATTT 60.046 61.111 0.00 0.00 0.00 2.17
325 326 4.778143 GCGGCGTGAGGGTGGATT 62.778 66.667 9.37 0.00 0.00 3.01
965 968 2.525629 TGGGACGTGGGAGCTTCA 60.526 61.111 0.00 0.00 0.00 3.02
1120 1476 3.636458 CGCAACATGTCACGGACA 58.364 55.556 11.51 8.81 46.90 4.02
1341 1950 0.251916 AGCATCGTCGGGGAATCAAA 59.748 50.000 0.00 0.00 0.00 2.69
1368 1978 2.203280 CGGGCTGGACAACACCAA 60.203 61.111 0.00 0.00 39.59 3.67
1474 2084 2.280389 CCATGATCTCCCGCACGG 60.280 66.667 1.02 1.02 0.00 4.94
1477 2087 1.692395 TTCCCCATGATCTCCCGCA 60.692 57.895 0.00 0.00 0.00 5.69
1483 2093 1.064166 CCTGCTTGTTCCCCATGATCT 60.064 52.381 0.00 0.00 0.00 2.75
1550 2309 3.805891 GATGCGGCTGAGCTCCTCC 62.806 68.421 12.15 11.13 38.13 4.30
1845 2715 9.010029 GGATTACAGTCAGAGGTAAATCAAAAA 57.990 33.333 0.00 0.00 33.60 1.94
1940 2812 2.997986 CGGCGACTGGTACTTGTTTAAT 59.002 45.455 0.00 0.00 0.00 1.40
2017 2889 8.177663 ACAGAGACAAGTAATCAAATTTATGCG 58.822 33.333 0.00 0.00 0.00 4.73
2445 3360 3.261580 CGAGGTGAATATTGTGCAGTGA 58.738 45.455 0.00 0.00 0.00 3.41
2541 5082 2.089980 GTGTGATTCATCCAGCTGCTT 58.910 47.619 8.66 0.00 0.00 3.91
2656 5206 1.140161 GCATGCATCACACGCCAAT 59.860 52.632 14.21 0.00 0.00 3.16
2895 5445 3.157087 CCAAACACCCTCTTACAAGCAT 58.843 45.455 0.00 0.00 0.00 3.79
3036 5587 9.006839 ACAGATTATACCTAATGCAACATCATG 57.993 33.333 0.00 0.00 0.00 3.07
3427 7402 1.915078 CTTCCCAGGAACCCGAGCAT 61.915 60.000 0.00 0.00 0.00 3.79
3576 7571 1.675310 CCGCAAGACCATTGCCTCA 60.675 57.895 6.98 0.00 42.10 3.86
3579 7574 1.244019 AAGACCGCAAGACCATTGCC 61.244 55.000 6.98 0.00 42.10 4.52
3580 7575 1.448985 TAAGACCGCAAGACCATTGC 58.551 50.000 2.52 2.52 41.71 3.56
3666 7662 7.493645 CACATCTAGCAAGAACAGATCAATACA 59.506 37.037 0.00 0.00 34.73 2.29
3667 7663 7.518052 GCACATCTAGCAAGAACAGATCAATAC 60.518 40.741 0.00 0.00 34.73 1.89
3762 7760 6.879458 CCAACTCTACTAAAGTTACAATGCCT 59.121 38.462 0.00 0.00 35.25 4.75
4114 8138 4.978580 GCGCTTCTTTGAACATCTTCTTTT 59.021 37.500 0.00 0.00 0.00 2.27
4677 8739 5.104941 TGAGAAGGTCGTGGACATTTATGAT 60.105 40.000 0.00 0.00 36.68 2.45
4685 8747 0.959553 GAGTGAGAAGGTCGTGGACA 59.040 55.000 0.00 0.00 33.68 4.02
4852 8929 8.472007 AAATTGTGTTCCCTATTTGACACTAA 57.528 30.769 6.97 1.49 42.09 2.24
4853 8930 8.472007 AAAATTGTGTTCCCTATTTGACACTA 57.528 30.769 6.97 0.39 42.09 2.74
4857 8934 8.364894 ACCTTAAAATTGTGTTCCCTATTTGAC 58.635 33.333 0.00 0.00 0.00 3.18
4893 8970 6.901357 CGTTTGCTTTTTGAAAGAATTCCTTG 59.099 34.615 0.65 0.00 34.79 3.61
4904 8981 5.465935 AGTCTGTTTCGTTTGCTTTTTGAA 58.534 33.333 0.00 0.00 0.00 2.69
4910 8987 2.546778 TCGAGTCTGTTTCGTTTGCTT 58.453 42.857 0.00 0.00 39.05 3.91
4918 8995 6.633634 CGATAGGATAGTTTCGAGTCTGTTTC 59.366 42.308 2.42 0.00 33.59 2.78
4919 8996 6.496571 CGATAGGATAGTTTCGAGTCTGTTT 58.503 40.000 2.42 0.00 33.59 2.83
4921 8998 5.676532 CGATAGGATAGTTTCGAGTCTGT 57.323 43.478 2.42 0.00 33.59 3.41
4942 9019 1.798087 GACCGTGTATTTTGGGCCG 59.202 57.895 0.00 0.00 0.00 6.13
4960 9037 3.179265 CTCACCGCGCCTACAACG 61.179 66.667 0.00 0.00 0.00 4.10
4989 9066 4.827835 AGGCACTTCTATATCTCGCTTGTA 59.172 41.667 0.00 0.00 27.25 2.41
5027 9104 6.380846 AGCTGCAAATAATTTGGATTGTAGGA 59.619 34.615 1.02 0.00 40.27 2.94
5059 9136 6.060136 TGCTCTCAGATTTCATGGGATAAAG 58.940 40.000 0.00 0.00 0.00 1.85
5068 9145 6.577103 TCGATTAGTTGCTCTCAGATTTCAT 58.423 36.000 0.00 0.00 0.00 2.57
5076 9153 4.537135 AACCTTCGATTAGTTGCTCTCA 57.463 40.909 0.00 0.00 0.00 3.27
5093 9170 2.567664 GCCCCCGCAAAGGATAACCT 62.568 60.000 0.00 0.00 45.00 3.50
5099 9176 3.909651 AAAGGCCCCCGCAAAGGA 61.910 61.111 0.00 0.00 45.00 3.36
5103 9180 2.600173 CTTCAAAGGCCCCCGCAA 60.600 61.111 0.00 0.00 36.38 4.85
5104 9181 4.676951 CCTTCAAAGGCCCCCGCA 62.677 66.667 0.00 0.00 39.76 5.69
5106 9183 3.938637 GACCCTTCAAAGGCCCCCG 62.939 68.421 0.00 0.00 45.10 5.73
5107 9184 2.037367 GACCCTTCAAAGGCCCCC 59.963 66.667 0.00 0.00 45.10 5.40
5108 9185 0.252239 AATGACCCTTCAAAGGCCCC 60.252 55.000 0.00 0.00 45.10 5.80
5109 9186 1.644509 AAATGACCCTTCAAAGGCCC 58.355 50.000 0.00 0.00 45.10 5.80
5110 9187 3.402110 CAAAAATGACCCTTCAAAGGCC 58.598 45.455 0.00 0.00 45.10 5.19
5111 9188 3.181455 ACCAAAAATGACCCTTCAAAGGC 60.181 43.478 3.09 0.00 45.10 4.35
5112 9189 4.379652 CACCAAAAATGACCCTTCAAAGG 58.620 43.478 1.54 1.54 46.06 3.11
5113 9190 4.379652 CCACCAAAAATGACCCTTCAAAG 58.620 43.478 0.00 0.00 34.61 2.77
5114 9191 3.135530 CCCACCAAAAATGACCCTTCAAA 59.864 43.478 0.00 0.00 34.61 2.69
5115 9192 2.703007 CCCACCAAAAATGACCCTTCAA 59.297 45.455 0.00 0.00 34.61 2.69
5116 9193 2.324541 CCCACCAAAAATGACCCTTCA 58.675 47.619 0.00 0.00 35.73 3.02
5126 9203 0.106268 TGCTCTCAGCCCACCAAAAA 60.106 50.000 0.00 0.00 41.51 1.94
5162 9239 1.021390 CATGAGGGACCGTTCAGCAC 61.021 60.000 3.99 0.00 0.00 4.40
5165 9242 2.698855 AATCATGAGGGACCGTTCAG 57.301 50.000 0.09 0.00 0.00 3.02
5168 9245 3.154827 ACAAAATCATGAGGGACCGTT 57.845 42.857 0.09 0.00 0.00 4.44
5169 9246 2.879103 ACAAAATCATGAGGGACCGT 57.121 45.000 0.09 0.00 0.00 4.83
5248 9329 4.052608 ACCGGTCAAAAATTAAAAAGCCG 58.947 39.130 0.00 0.00 36.82 5.52
5256 9337 7.230027 TCCTAGGTAAAACCGGTCAAAAATTA 58.770 34.615 8.04 0.00 44.90 1.40
5258 9339 5.633117 TCCTAGGTAAAACCGGTCAAAAAT 58.367 37.500 8.04 0.00 44.90 1.82
5268 9349 5.318630 TGTGTCCAAATCCTAGGTAAAACC 58.681 41.667 9.08 0.00 38.99 3.27
5302 9383 5.033589 ACATGTTCTTTCATGCCCAAAAA 57.966 34.783 0.00 0.00 46.15 1.94
5304 9385 4.686191 AACATGTTCTTTCATGCCCAAA 57.314 36.364 4.92 0.00 46.15 3.28
5332 9413 2.866156 CAAATCTATGCCTCTCGCGAAA 59.134 45.455 11.33 0.00 42.08 3.46
5333 9414 2.473816 CAAATCTATGCCTCTCGCGAA 58.526 47.619 11.33 0.00 42.08 4.70
5334 9415 2.140065 CAAATCTATGCCTCTCGCGA 57.860 50.000 9.26 9.26 42.08 5.87


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

AutoCloner maintained by Alex Coulton.