Multiple sequence alignment - TraesCS3A01G495800

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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 TraesCS3A01G495800 chr3A 100.000 4166 0 0 1 4166 721585058 721580893 0.000000e+00 7694.0
1 TraesCS3A01G495800 chr3A 77.049 244 38 13 3067 3309 89387 89161 1.570000e-24 124.0
2 TraesCS3A01G495800 chr3B 93.971 3367 123 38 824 4166 793263685 793266995 0.000000e+00 5020.0
3 TraesCS3A01G495800 chr3B 85.667 300 24 7 850 1137 793168560 793168852 8.760000e-77 298.0
4 TraesCS3A01G495800 chr3B 84.404 218 23 8 1393 1609 509969724 509969517 1.960000e-48 204.0
5 TraesCS3A01G495800 chr3B 97.297 37 1 0 1929 1965 658489579 658489615 3.480000e-06 63.9
6 TraesCS3A01G495800 chr3D 84.345 1961 199 56 2011 3919 591240962 591239058 0.000000e+00 1821.0
7 TraesCS3A01G495800 chr3D 89.155 793 49 14 824 1609 591242196 591241434 0.000000e+00 953.0
8 TraesCS3A01G495800 chr3D 83.022 589 70 17 176 751 591242893 591242322 1.340000e-139 507.0
9 TraesCS3A01G495800 chr3D 87.188 320 33 5 1609 1920 591241385 591241066 1.420000e-94 357.0
10 TraesCS3A01G495800 chr3D 83.262 233 23 4 3918 4137 591238986 591238757 2.540000e-47 200.0
11 TraesCS3A01G495800 chr3D 77.459 244 37 13 3067 3309 562543289 562543063 3.380000e-26 130.0
12 TraesCS3A01G495800 chr3D 94.737 38 1 1 1928 1965 282448118 282448082 1.620000e-04 58.4
13 TraesCS3A01G495800 chr7B 79.061 788 102 33 2433 3174 14874183 14873413 2.250000e-132 483.0
14 TraesCS3A01G495800 chr7B 87.657 397 36 7 1211 1606 153181092 153181476 2.280000e-122 449.0
15 TraesCS3A01G495800 chr7B 86.715 414 40 7 1197 1609 42361117 42360718 2.950000e-121 446.0
16 TraesCS3A01G495800 chr7B 92.641 231 17 0 1256 1486 14875433 14875203 2.400000e-87 333.0
17 TraesCS3A01G495800 chr7B 86.239 218 19 5 1393 1609 707545242 707545035 4.190000e-55 226.0
18 TraesCS3A01G495800 chr7B 97.297 37 1 0 1929 1965 589467130 589467094 3.480000e-06 63.9
19 TraesCS3A01G495800 chr6A 87.923 414 38 6 1197 1609 437702493 437702091 1.050000e-130 477.0
20 TraesCS3A01G495800 chr6A 97.297 37 1 0 1929 1965 92848745 92848709 3.480000e-06 63.9
21 TraesCS3A01G495800 chr4A 87.681 414 38 7 1197 1609 670379751 670379350 1.750000e-128 470.0
22 TraesCS3A01G495800 chr7D 81.271 598 76 22 2603 3174 73130051 73130638 6.350000e-123 451.0
23 TraesCS3A01G495800 chr7D 92.735 234 17 0 1253 1486 73128875 73129108 5.160000e-89 339.0
24 TraesCS3A01G495800 chr2B 78.795 448 57 25 2555 2982 16303283 16302854 2.470000e-67 267.0
25 TraesCS3A01G495800 chr5B 79.512 410 41 21 3201 3591 390011904 390012289 6.910000e-63 252.0
26 TraesCS3A01G495800 chr5B 94.872 39 2 0 1929 1967 687803410 687803372 1.250000e-05 62.1
27 TraesCS3A01G495800 chr1B 85.915 213 19 6 1395 1606 186142229 186142431 2.520000e-52 217.0
28 TraesCS3A01G495800 chr5A 81.600 250 29 9 2558 2793 595011095 595010849 1.530000e-44 191.0
29 TraesCS3A01G495800 chr5A 84.277 159 21 2 2635 2793 84158838 84158992 7.210000e-33 152.0
30 TraesCS3A01G495800 chr7A 80.478 251 33 6 2556 2793 26873464 26873711 1.190000e-40 178.0
31 TraesCS3A01G495800 chr7A 80.080 251 33 7 2556 2793 24773973 24773727 1.990000e-38 171.0
32 TraesCS3A01G495800 chr2A 80.556 252 32 7 2556 2793 690920334 690920582 1.190000e-40 178.0
33 TraesCS3A01G495800 chr2A 85.455 55 8 0 1911 1965 757930345 757930399 1.620000e-04 58.4
34 TraesCS3A01G495800 chr6D 95.000 40 2 0 1927 1966 426154403 426154364 3.480000e-06 63.9
35 TraesCS3A01G495800 chrUn 94.595 37 2 0 1929 1965 321270873 321270837 1.620000e-04 58.4


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 TraesCS3A01G495800 chr3A 721580893 721585058 4165 True 7694.0 7694 100.0000 1 4166 1 chr3A.!!$R2 4165
1 TraesCS3A01G495800 chr3B 793263685 793266995 3310 False 5020.0 5020 93.9710 824 4166 1 chr3B.!!$F3 3342
2 TraesCS3A01G495800 chr3D 591238757 591242893 4136 True 767.6 1821 85.3944 176 4137 5 chr3D.!!$R3 3961
3 TraesCS3A01G495800 chr7B 14873413 14875433 2020 True 408.0 483 85.8510 1256 3174 2 chr7B.!!$R4 1918
4 TraesCS3A01G495800 chr7D 73128875 73130638 1763 False 395.0 451 87.0030 1253 3174 2 chr7D.!!$F1 1921

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
497 510 0.108329 AGGTGTGTGCGCTATGTACC 60.108 55.0 9.73 10.93 31.26 3.34 F
711 725 0.698238 TGGGCCACTAGTTTGAGCAT 59.302 50.0 0.00 0.00 0.00 3.79 F
716 730 0.729116 CACTAGTTTGAGCATGCGGG 59.271 55.0 13.01 0.00 0.00 6.13 F
1239 1328 0.743097 GTCTTGCCTGATTCCATGGC 59.257 55.0 6.96 0.00 46.26 4.40 F
2561 3185 0.607489 ATCACTTGGCCTCACTGCAC 60.607 55.0 3.32 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 2192 0.386838 GCATATTGTCTTGGGCAGCC 59.613 55.000 1.26 1.26 0.00 4.85 R
2516 3140 2.295253 AGAGAAATTACCCTGTCGCG 57.705 50.000 0.00 0.00 0.00 5.87 R
2562 3186 4.442706 AGAACAAAGAGCAACGAAGAAGA 58.557 39.130 0.00 0.00 0.00 2.87 R
3093 3781 1.070758 GAACTGAGGACTTGGTCAGCA 59.929 52.381 0.00 0.00 43.48 4.41 R
4063 4861 0.035056 ATCAGTTCAAAGGCCGAGGG 60.035 55.000 0.00 0.00 0.00 4.30 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
20 21 2.847441 TCTAGCACGATCGATACAGGT 58.153 47.619 24.34 13.06 0.00 4.00
21 22 3.999046 TCTAGCACGATCGATACAGGTA 58.001 45.455 24.34 13.46 0.00 3.08
22 23 3.744942 TCTAGCACGATCGATACAGGTAC 59.255 47.826 24.34 0.00 0.00 3.34
23 24 2.294979 AGCACGATCGATACAGGTACA 58.705 47.619 24.34 0.00 0.00 2.90
24 25 2.033049 AGCACGATCGATACAGGTACAC 59.967 50.000 24.34 0.00 0.00 2.90
25 26 2.857489 GCACGATCGATACAGGTACACC 60.857 54.545 24.34 0.00 0.00 4.16
26 27 1.600957 ACGATCGATACAGGTACACCG 59.399 52.381 24.34 0.00 42.08 4.94
27 28 1.869132 CGATCGATACAGGTACACCGA 59.131 52.381 10.26 0.00 42.08 4.69
28 29 2.483106 CGATCGATACAGGTACACCGAT 59.517 50.000 10.26 10.75 42.08 4.18
29 30 3.424565 CGATCGATACAGGTACACCGATC 60.425 52.174 10.26 19.50 44.93 3.69
30 31 2.921821 TCGATACAGGTACACCGATCA 58.078 47.619 0.00 0.00 42.08 2.92
31 32 3.281158 TCGATACAGGTACACCGATCAA 58.719 45.455 0.00 0.00 42.08 2.57
32 33 3.887110 TCGATACAGGTACACCGATCAAT 59.113 43.478 0.00 0.00 42.08 2.57
33 34 3.981416 CGATACAGGTACACCGATCAATG 59.019 47.826 0.00 0.00 42.08 2.82
34 35 2.691409 ACAGGTACACCGATCAATGG 57.309 50.000 0.00 0.00 42.08 3.16
35 36 1.299541 CAGGTACACCGATCAATGGC 58.700 55.000 0.00 0.00 42.08 4.40
36 37 1.134401 CAGGTACACCGATCAATGGCT 60.134 52.381 0.00 0.00 42.08 4.75
37 38 1.559682 AGGTACACCGATCAATGGCTT 59.440 47.619 0.00 0.00 42.08 4.35
38 39 1.670811 GGTACACCGATCAATGGCTTG 59.329 52.381 0.00 0.00 0.00 4.01
39 40 1.064060 GTACACCGATCAATGGCTTGC 59.936 52.381 0.00 0.00 32.11 4.01
40 41 0.322816 ACACCGATCAATGGCTTGCT 60.323 50.000 0.00 0.00 32.11 3.91
41 42 0.813184 CACCGATCAATGGCTTGCTT 59.187 50.000 0.00 0.00 32.11 3.91
42 43 2.016318 CACCGATCAATGGCTTGCTTA 58.984 47.619 0.00 0.00 32.11 3.09
43 44 2.620115 CACCGATCAATGGCTTGCTTAT 59.380 45.455 0.00 0.00 32.11 1.73
44 45 3.067180 CACCGATCAATGGCTTGCTTATT 59.933 43.478 0.00 0.00 32.11 1.40
45 46 3.701040 ACCGATCAATGGCTTGCTTATTT 59.299 39.130 0.00 0.00 32.11 1.40
46 47 4.887071 ACCGATCAATGGCTTGCTTATTTA 59.113 37.500 0.00 0.00 32.11 1.40
47 48 5.536161 ACCGATCAATGGCTTGCTTATTTAT 59.464 36.000 0.00 0.00 32.11 1.40
48 49 6.040842 ACCGATCAATGGCTTGCTTATTTATT 59.959 34.615 0.00 0.00 32.11 1.40
49 50 6.925165 CCGATCAATGGCTTGCTTATTTATTT 59.075 34.615 0.00 0.00 32.11 1.40
50 51 7.115378 CCGATCAATGGCTTGCTTATTTATTTC 59.885 37.037 0.00 0.00 32.11 2.17
51 52 7.648908 CGATCAATGGCTTGCTTATTTATTTCA 59.351 33.333 0.00 0.00 32.11 2.69
52 53 9.485206 GATCAATGGCTTGCTTATTTATTTCAT 57.515 29.630 0.00 0.00 32.11 2.57
53 54 9.841295 ATCAATGGCTTGCTTATTTATTTCATT 57.159 25.926 0.00 0.00 32.11 2.57
54 55 9.669887 TCAATGGCTTGCTTATTTATTTCATTT 57.330 25.926 0.00 0.00 32.11 2.32
77 78 7.575414 TTTTTATTGAGGTGCAACACTCTAA 57.425 32.000 3.64 0.00 39.78 2.10
78 79 7.575414 TTTTATTGAGGTGCAACACTCTAAA 57.425 32.000 3.64 3.76 39.78 1.85
79 80 7.575414 TTTATTGAGGTGCAACACTCTAAAA 57.425 32.000 3.64 5.19 39.78 1.52
80 81 7.575414 TTATTGAGGTGCAACACTCTAAAAA 57.425 32.000 3.64 0.00 39.78 1.94
156 157 9.844257 AATTATGGATTTGAAAAAGGTTTGTGA 57.156 25.926 0.00 0.00 0.00 3.58
157 158 9.844257 ATTATGGATTTGAAAAAGGTTTGTGAA 57.156 25.926 0.00 0.00 0.00 3.18
158 159 9.844257 TTATGGATTTGAAAAAGGTTTGTGAAT 57.156 25.926 0.00 0.00 0.00 2.57
159 160 8.750515 ATGGATTTGAAAAAGGTTTGTGAATT 57.249 26.923 0.00 0.00 0.00 2.17
160 161 9.844257 ATGGATTTGAAAAAGGTTTGTGAATTA 57.156 25.926 0.00 0.00 0.00 1.40
161 162 9.672673 TGGATTTGAAAAAGGTTTGTGAATTAA 57.327 25.926 0.00 0.00 0.00 1.40
224 225 7.713764 ATTCTTCAATTTGAAAAAGGTTCGG 57.286 32.000 12.62 0.00 35.73 4.30
225 226 5.596845 TCTTCAATTTGAAAAAGGTTCGGG 58.403 37.500 12.62 0.00 35.73 5.14
302 304 7.040062 TGGTGACGATTTTCATAAAAACCTCAT 60.040 33.333 0.00 0.00 37.20 2.90
306 308 9.573133 GACGATTTTCATAAAAACCTCATGATT 57.427 29.630 0.00 0.00 37.20 2.57
377 379 9.620660 ACTAGCAGAAATGGTAAAATAAAAACG 57.379 29.630 0.00 0.00 0.00 3.60
378 380 9.834628 CTAGCAGAAATGGTAAAATAAAAACGA 57.165 29.630 0.00 0.00 0.00 3.85
381 383 9.134734 GCAGAAATGGTAAAATAAAAACGATCA 57.865 29.630 0.00 0.00 0.00 2.92
394 397 3.678056 AACGATCAGAGGCTTGTACAA 57.322 42.857 8.28 8.28 0.00 2.41
412 415 5.472137 TGTACAAGCTTCATAAAACCAGTCC 59.528 40.000 0.00 0.00 0.00 3.85
419 422 5.183140 GCTTCATAAAACCAGTCCAAAGCTA 59.817 40.000 0.00 0.00 35.06 3.32
458 471 6.906157 AAAAAGAGCTCAATCTCCAAATGA 57.094 33.333 17.77 0.00 33.66 2.57
459 472 7.477945 AAAAAGAGCTCAATCTCCAAATGAT 57.522 32.000 17.77 0.00 33.66 2.45
466 479 4.199310 TCAATCTCCAAATGATTCGGTCC 58.801 43.478 0.00 0.00 32.47 4.46
487 500 3.426159 CCATTTTCGTATCAGGTGTGTGC 60.426 47.826 0.00 0.00 0.00 4.57
488 501 1.424403 TTTCGTATCAGGTGTGTGCG 58.576 50.000 0.00 0.00 0.00 5.34
493 506 1.860950 GTATCAGGTGTGTGCGCTATG 59.139 52.381 9.73 0.00 0.00 2.23
494 507 0.250234 ATCAGGTGTGTGCGCTATGT 59.750 50.000 9.73 0.00 0.00 2.29
495 508 0.892063 TCAGGTGTGTGCGCTATGTA 59.108 50.000 9.73 0.00 0.00 2.29
496 509 0.999406 CAGGTGTGTGCGCTATGTAC 59.001 55.000 9.73 0.00 0.00 2.90
497 510 0.108329 AGGTGTGTGCGCTATGTACC 60.108 55.000 9.73 10.93 31.26 3.34
516 529 7.941053 TGTACCAACAATCCTATAACCCTAT 57.059 36.000 0.00 0.00 30.91 2.57
523 536 8.308931 CAACAATCCTATAACCCTATAAGCGTA 58.691 37.037 0.00 0.00 0.00 4.42
577 591 2.107953 GGAGCTGAGCCGGTCATC 59.892 66.667 1.90 1.45 33.51 2.92
578 592 2.107953 GAGCTGAGCCGGTCATCC 59.892 66.667 1.90 0.61 33.51 3.51
618 632 2.244651 CCTATTAGCACGGCGGCAC 61.245 63.158 19.61 5.64 35.83 5.01
634 648 2.821546 GGCACGACATTAGACATGCTA 58.178 47.619 0.00 0.00 33.57 3.49
656 670 4.169696 TGGCACGGGCTAATCGGG 62.170 66.667 10.74 0.00 40.87 5.14
657 671 4.171103 GGCACGGGCTAATCGGGT 62.171 66.667 10.74 0.00 40.87 5.28
663 677 2.960129 GGCTAATCGGGTCGTGCG 60.960 66.667 0.00 0.00 0.00 5.34
686 700 4.502263 CGTCACACGCCATGATCT 57.498 55.556 0.00 0.00 33.65 2.75
711 725 0.698238 TGGGCCACTAGTTTGAGCAT 59.302 50.000 0.00 0.00 0.00 3.79
716 730 0.729116 CACTAGTTTGAGCATGCGGG 59.271 55.000 13.01 0.00 0.00 6.13
719 733 1.026182 TAGTTTGAGCATGCGGGCTG 61.026 55.000 13.01 0.00 45.99 4.85
733 747 1.140161 GGCTGGCACGACACGTATA 59.860 57.895 0.00 0.00 38.32 1.47
735 749 1.129326 GCTGGCACGACACGTATATC 58.871 55.000 0.00 0.00 38.32 1.63
736 750 1.767289 CTGGCACGACACGTATATCC 58.233 55.000 0.00 0.00 38.32 2.59
741 755 3.000925 GGCACGACACGTATATCCTTTTG 59.999 47.826 0.00 0.00 38.32 2.44
742 756 3.861113 GCACGACACGTATATCCTTTTGA 59.139 43.478 0.00 0.00 38.32 2.69
744 758 5.556382 GCACGACACGTATATCCTTTTGATG 60.556 44.000 0.00 0.00 38.32 3.07
745 759 5.518847 CACGACACGTATATCCTTTTGATGT 59.481 40.000 0.00 0.00 38.32 3.06
779 834 3.845178 TGTATATATAGCCGTGCTGTGC 58.155 45.455 8.44 0.00 40.10 4.57
799 854 3.518068 GGCACCATTAGCACGGGC 61.518 66.667 0.00 0.00 41.61 6.13
802 857 3.395702 ACCATTAGCACGGGCCGA 61.396 61.111 35.78 10.47 42.56 5.54
845 914 1.439365 CTGTTCGTTTGCAGCGAGC 60.439 57.895 17.74 17.74 45.96 5.03
985 1054 1.556499 ATCCCCCAGATCTCTCTCCT 58.444 55.000 0.00 0.00 0.00 3.69
1017 1086 3.329542 AATGGCATCGGTGGACGCT 62.330 57.895 0.00 0.00 43.86 5.07
1119 1208 4.364686 TCCCCACTCCCCCTTCCC 62.365 72.222 0.00 0.00 0.00 3.97
1140 1229 1.908483 GCCTCCCTCGATTCTTGGT 59.092 57.895 0.00 0.00 0.00 3.67
1147 1236 1.961394 CCTCGATTCTTGGTATCCGGA 59.039 52.381 6.61 6.61 0.00 5.14
1149 1238 1.684983 TCGATTCTTGGTATCCGGACC 59.315 52.381 6.12 5.66 40.21 4.46
1182 1271 1.207329 GTCGGTAGCTTCTTGGATGGT 59.793 52.381 0.00 0.00 0.00 3.55
1194 1283 4.599041 TCTTGGATGGTTGGATTTGGTAG 58.401 43.478 0.00 0.00 0.00 3.18
1203 1292 3.153369 TGGATTTGGTAGCTTCTTGCA 57.847 42.857 0.00 0.00 45.94 4.08
1205 1294 2.164422 GGATTTGGTAGCTTCTTGCACC 59.836 50.000 0.00 0.00 45.94 5.01
1206 1295 1.616159 TTTGGTAGCTTCTTGCACCC 58.384 50.000 0.00 0.00 45.94 4.61
1207 1296 0.771127 TTGGTAGCTTCTTGCACCCT 59.229 50.000 0.00 0.00 45.94 4.34
1208 1297 1.651737 TGGTAGCTTCTTGCACCCTA 58.348 50.000 0.00 0.00 45.94 3.53
1209 1298 2.196595 TGGTAGCTTCTTGCACCCTAT 58.803 47.619 0.00 0.00 45.94 2.57
1212 1301 2.887151 AGCTTCTTGCACCCTATTGT 57.113 45.000 0.00 0.00 45.94 2.71
1214 1303 3.500343 AGCTTCTTGCACCCTATTGTTT 58.500 40.909 0.00 0.00 45.94 2.83
1215 1304 3.507622 AGCTTCTTGCACCCTATTGTTTC 59.492 43.478 0.00 0.00 45.94 2.78
1216 1305 3.367395 GCTTCTTGCACCCTATTGTTTCC 60.367 47.826 0.00 0.00 42.31 3.13
1217 1306 3.517296 TCTTGCACCCTATTGTTTCCA 57.483 42.857 0.00 0.00 0.00 3.53
1219 1308 4.415596 TCTTGCACCCTATTGTTTCCATT 58.584 39.130 0.00 0.00 0.00 3.16
1220 1309 4.220382 TCTTGCACCCTATTGTTTCCATTG 59.780 41.667 0.00 0.00 0.00 2.82
1221 1310 3.505386 TGCACCCTATTGTTTCCATTGT 58.495 40.909 0.00 0.00 0.00 2.71
1222 1311 3.509575 TGCACCCTATTGTTTCCATTGTC 59.490 43.478 0.00 0.00 0.00 3.18
1224 1313 4.220602 GCACCCTATTGTTTCCATTGTCTT 59.779 41.667 0.00 0.00 0.00 3.01
1225 1314 5.713025 CACCCTATTGTTTCCATTGTCTTG 58.287 41.667 0.00 0.00 0.00 3.02
1226 1315 4.220602 ACCCTATTGTTTCCATTGTCTTGC 59.779 41.667 0.00 0.00 0.00 4.01
1227 1316 4.381932 CCCTATTGTTTCCATTGTCTTGCC 60.382 45.833 0.00 0.00 0.00 4.52
1228 1317 4.463891 CCTATTGTTTCCATTGTCTTGCCT 59.536 41.667 0.00 0.00 0.00 4.75
1229 1318 3.731652 TTGTTTCCATTGTCTTGCCTG 57.268 42.857 0.00 0.00 0.00 4.85
1230 1319 2.942804 TGTTTCCATTGTCTTGCCTGA 58.057 42.857 0.00 0.00 0.00 3.86
1231 1320 3.499338 TGTTTCCATTGTCTTGCCTGAT 58.501 40.909 0.00 0.00 0.00 2.90
1232 1321 3.896888 TGTTTCCATTGTCTTGCCTGATT 59.103 39.130 0.00 0.00 0.00 2.57
1233 1322 4.022068 TGTTTCCATTGTCTTGCCTGATTC 60.022 41.667 0.00 0.00 0.00 2.52
1234 1323 2.726821 TCCATTGTCTTGCCTGATTCC 58.273 47.619 0.00 0.00 0.00 3.01
1235 1324 2.041485 TCCATTGTCTTGCCTGATTCCA 59.959 45.455 0.00 0.00 0.00 3.53
1236 1325 3.028850 CCATTGTCTTGCCTGATTCCAT 58.971 45.455 0.00 0.00 0.00 3.41
1237 1326 3.181479 CCATTGTCTTGCCTGATTCCATG 60.181 47.826 0.00 0.00 0.00 3.66
1238 1327 2.133281 TGTCTTGCCTGATTCCATGG 57.867 50.000 4.97 4.97 0.00 3.66
1239 1328 0.743097 GTCTTGCCTGATTCCATGGC 59.257 55.000 6.96 0.00 46.26 4.40
1511 1628 6.610020 TCGTTTCTCCCCTTCTAATGATAGAA 59.390 38.462 0.00 0.00 44.07 2.10
1520 1637 7.500559 CCCCTTCTAATGATAGAAACTCTTTGG 59.499 40.741 0.54 0.00 45.20 3.28
1523 1640 9.103861 CTTCTAATGATAGAAACTCTTTGGGTC 57.896 37.037 0.54 0.00 45.20 4.46
1531 1648 5.866207 AGAAACTCTTTGGGTCGTTTATCT 58.134 37.500 0.00 0.00 30.47 1.98
1532 1649 5.701290 AGAAACTCTTTGGGTCGTTTATCTG 59.299 40.000 0.00 0.00 30.47 2.90
1633 1808 8.519799 TTGATAATCTGTTAGATGGGGAAAAC 57.480 34.615 0.00 0.00 34.65 2.43
1634 1809 7.638444 TGATAATCTGTTAGATGGGGAAAACA 58.362 34.615 0.00 0.00 34.65 2.83
1636 1811 6.840780 AATCTGTTAGATGGGGAAAACAAG 57.159 37.500 0.00 0.00 34.65 3.16
1637 1812 5.319043 TCTGTTAGATGGGGAAAACAAGT 57.681 39.130 0.00 0.00 31.90 3.16
1685 1861 8.594881 ATCCTTTAAGTCGATGTAATAAGCTG 57.405 34.615 0.00 0.00 0.00 4.24
1687 1863 8.038944 TCCTTTAAGTCGATGTAATAAGCTGTT 58.961 33.333 0.00 0.00 0.00 3.16
1689 1865 8.766000 TTTAAGTCGATGTAATAAGCTGTTCA 57.234 30.769 0.00 0.00 0.00 3.18
1920 2442 5.834460 TGTTCTTATGTACTACTCCCTCCA 58.166 41.667 0.00 0.00 0.00 3.86
1924 2446 6.075984 TCTTATGTACTACTCCCTCCAATCC 58.924 44.000 0.00 0.00 0.00 3.01
1934 2456 2.899256 TCCCTCCAATCCAAAAAGCTTG 59.101 45.455 0.00 0.00 0.00 4.01
2023 2587 8.996651 ATGATTTAGAACGGAATTTAAGGGAT 57.003 30.769 0.00 0.00 0.00 3.85
2272 2894 2.545946 GCAACTGACCACTCAAGAGAAC 59.454 50.000 3.73 0.00 0.00 3.01
2516 3140 5.350365 TGCAAACGAAATACCTATCTGTGTC 59.650 40.000 0.00 0.00 0.00 3.67
2561 3185 0.607489 ATCACTTGGCCTCACTGCAC 60.607 55.000 3.32 0.00 0.00 4.57
2562 3186 1.228063 CACTTGGCCTCACTGCACT 60.228 57.895 3.32 0.00 0.00 4.40
3093 3781 5.525378 GCTGGATGTTTCGTATCAGAAAGAT 59.475 40.000 2.44 2.44 43.74 2.40
3240 3937 5.047164 ACATATGCAAAAGCTGGAATTGTGA 60.047 36.000 1.58 0.00 0.00 3.58
3335 4032 5.732331 TCAATAAAGACCCTCCCATCAAT 57.268 39.130 0.00 0.00 0.00 2.57
3341 4038 3.701664 AGACCCTCCCATCAATTTTGAC 58.298 45.455 0.00 0.00 40.49 3.18
3445 4150 7.434602 GGTATTTGAAGAACACCTATCTCGTAC 59.565 40.741 0.00 0.00 0.00 3.67
3446 4151 6.585695 TTTGAAGAACACCTATCTCGTACT 57.414 37.500 0.00 0.00 0.00 2.73
3447 4152 5.562506 TGAAGAACACCTATCTCGTACTG 57.437 43.478 0.00 0.00 0.00 2.74
3448 4153 5.008331 TGAAGAACACCTATCTCGTACTGT 58.992 41.667 0.00 0.00 0.00 3.55
3449 4154 4.966965 AGAACACCTATCTCGTACTGTG 57.033 45.455 0.00 0.00 0.00 3.66
3478 4183 6.572703 GCTTACTGTTAGCTAAGGAGACAAGT 60.573 42.308 6.38 4.98 35.74 3.16
3480 4185 6.270156 ACTGTTAGCTAAGGAGACAAGTAC 57.730 41.667 6.38 0.00 0.00 2.73
3488 4196 3.662247 AGGAGACAAGTACAGTTTCGG 57.338 47.619 0.00 0.00 0.00 4.30
3489 4197 2.963782 AGGAGACAAGTACAGTTTCGGT 59.036 45.455 0.00 0.00 0.00 4.69
3490 4198 4.147321 AGGAGACAAGTACAGTTTCGGTA 58.853 43.478 0.00 0.00 0.00 4.02
3535 4243 9.739786 GAACTTAAAACTGAACAAAACATTGTG 57.260 29.630 0.00 0.00 34.99 3.33
3539 4247 4.717233 ACTGAACAAAACATTGTGAGCA 57.283 36.364 0.00 0.00 34.99 4.26
3629 4337 6.775594 ACCCTAGTTCTTTGGAATATTTGC 57.224 37.500 0.00 0.00 33.71 3.68
3737 4446 5.582665 CAGGAACGAGGAAAGGAGAAATAAG 59.417 44.000 0.00 0.00 0.00 1.73
3758 4468 1.406539 CATCATTTGCCCACCAGCTAC 59.593 52.381 0.00 0.00 0.00 3.58
4025 4812 2.028112 TGTCTTGGGAATCGTCTCTTGG 60.028 50.000 0.00 0.00 0.00 3.61
4063 4861 6.759497 ATATTTACCTTCTGTCCACAAAGC 57.241 37.500 0.00 0.00 0.00 3.51
4116 4914 6.510638 GCTGTTTCTGCATCCAAAAAGAAAAG 60.511 38.462 7.11 0.00 39.60 2.27
4142 4940 3.197766 TGATCGACCCAGCTCAGTATTTT 59.802 43.478 0.00 0.00 0.00 1.82
4146 4944 3.010420 GACCCAGCTCAGTATTTTGACC 58.990 50.000 0.00 0.00 0.00 4.02
4150 4948 3.941483 CCAGCTCAGTATTTTGACCGAAT 59.059 43.478 0.00 0.00 0.00 3.34
4152 4950 5.235186 CCAGCTCAGTATTTTGACCGAATAG 59.765 44.000 0.00 0.00 0.00 1.73
4154 4952 6.019479 CAGCTCAGTATTTTGACCGAATAGTC 60.019 42.308 0.00 0.00 37.28 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.847441 ACCTGTATCGATCGTGCTAGA 58.153 47.619 15.94 3.74 0.00 2.43
1 2 3.497262 TGTACCTGTATCGATCGTGCTAG 59.503 47.826 15.94 9.67 0.00 3.42
2 3 3.249320 GTGTACCTGTATCGATCGTGCTA 59.751 47.826 15.94 3.00 0.00 3.49
3 4 2.033049 GTGTACCTGTATCGATCGTGCT 59.967 50.000 15.94 4.00 0.00 4.40
4 5 2.382519 GTGTACCTGTATCGATCGTGC 58.617 52.381 15.94 6.90 0.00 5.34
5 6 2.601504 CGGTGTACCTGTATCGATCGTG 60.602 54.545 15.94 1.86 0.00 4.35
6 7 1.600957 CGGTGTACCTGTATCGATCGT 59.399 52.381 15.94 5.23 0.00 3.73
7 8 1.869132 TCGGTGTACCTGTATCGATCG 59.131 52.381 9.36 9.36 0.00 3.69
8 9 4.080969 GATCGGTGTACCTGTATCGATC 57.919 50.000 0.00 9.87 43.47 3.69
9 10 3.483421 TGATCGGTGTACCTGTATCGAT 58.517 45.455 2.16 2.16 39.57 3.59
10 11 2.921821 TGATCGGTGTACCTGTATCGA 58.078 47.619 0.00 0.00 0.00 3.59
11 12 3.703286 TTGATCGGTGTACCTGTATCG 57.297 47.619 0.00 0.00 0.00 2.92
12 13 4.307432 CCATTGATCGGTGTACCTGTATC 58.693 47.826 0.00 1.19 0.00 2.24
13 14 3.494398 GCCATTGATCGGTGTACCTGTAT 60.494 47.826 0.00 0.00 0.00 2.29
14 15 2.159014 GCCATTGATCGGTGTACCTGTA 60.159 50.000 0.00 0.00 0.00 2.74
15 16 1.406887 GCCATTGATCGGTGTACCTGT 60.407 52.381 0.00 0.00 0.00 4.00
16 17 1.134401 AGCCATTGATCGGTGTACCTG 60.134 52.381 0.00 0.00 0.00 4.00
17 18 1.204146 AGCCATTGATCGGTGTACCT 58.796 50.000 0.00 0.00 0.00 3.08
18 19 1.670811 CAAGCCATTGATCGGTGTACC 59.329 52.381 0.00 0.00 38.83 3.34
19 20 1.064060 GCAAGCCATTGATCGGTGTAC 59.936 52.381 0.00 0.00 38.83 2.90
20 21 1.065491 AGCAAGCCATTGATCGGTGTA 60.065 47.619 0.00 0.00 38.83 2.90
21 22 0.322816 AGCAAGCCATTGATCGGTGT 60.323 50.000 0.00 0.00 38.83 4.16
22 23 0.813184 AAGCAAGCCATTGATCGGTG 59.187 50.000 0.00 0.00 38.83 4.94
23 24 2.418368 TAAGCAAGCCATTGATCGGT 57.582 45.000 0.00 0.00 38.83 4.69
24 25 3.996150 AATAAGCAAGCCATTGATCGG 57.004 42.857 0.00 0.00 38.83 4.18
25 26 7.648908 TGAAATAAATAAGCAAGCCATTGATCG 59.351 33.333 0.00 0.00 38.83 3.69
26 27 8.876275 TGAAATAAATAAGCAAGCCATTGATC 57.124 30.769 0.00 0.00 38.83 2.92
27 28 9.841295 AATGAAATAAATAAGCAAGCCATTGAT 57.159 25.926 0.00 0.00 38.83 2.57
28 29 9.669887 AAATGAAATAAATAAGCAAGCCATTGA 57.330 25.926 0.00 0.00 38.83 2.57
53 54 7.575414 TTAGAGTGTTGCACCTCAATAAAAA 57.425 32.000 9.24 0.00 36.99 1.94
54 55 7.575414 TTTAGAGTGTTGCACCTCAATAAAA 57.425 32.000 9.24 3.14 36.99 1.52
55 56 7.575414 TTTTAGAGTGTTGCACCTCAATAAA 57.425 32.000 9.24 4.65 36.99 1.40
56 57 7.575414 TTTTTAGAGTGTTGCACCTCAATAA 57.425 32.000 9.24 0.00 36.99 1.40
130 131 9.844257 TCACAAACCTTTTTCAAATCCATAATT 57.156 25.926 0.00 0.00 0.00 1.40
131 132 9.844257 TTCACAAACCTTTTTCAAATCCATAAT 57.156 25.926 0.00 0.00 0.00 1.28
132 133 9.844257 ATTCACAAACCTTTTTCAAATCCATAA 57.156 25.926 0.00 0.00 0.00 1.90
133 134 9.844257 AATTCACAAACCTTTTTCAAATCCATA 57.156 25.926 0.00 0.00 0.00 2.74
134 135 8.750515 AATTCACAAACCTTTTTCAAATCCAT 57.249 26.923 0.00 0.00 0.00 3.41
135 136 9.672673 TTAATTCACAAACCTTTTTCAAATCCA 57.327 25.926 0.00 0.00 0.00 3.41
200 201 6.705825 CCCGAACCTTTTTCAAATTGAAGAAT 59.294 34.615 11.31 0.00 37.70 2.40
203 204 5.596845 TCCCGAACCTTTTTCAAATTGAAG 58.403 37.500 8.51 0.23 37.70 3.02
204 205 5.599999 TCCCGAACCTTTTTCAAATTGAA 57.400 34.783 4.03 4.03 34.03 2.69
206 207 6.859420 AAATCCCGAACCTTTTTCAAATTG 57.141 33.333 0.00 0.00 0.00 2.32
241 243 9.877178 ATTGGTGTACTTGTTTCATTTTTGTAA 57.123 25.926 0.00 0.00 0.00 2.41
242 244 9.307121 CATTGGTGTACTTGTTTCATTTTTGTA 57.693 29.630 0.00 0.00 0.00 2.41
248 250 9.877178 TTTTTACATTGGTGTACTTGTTTCATT 57.123 25.926 0.00 0.00 40.40 2.57
250 252 9.877178 AATTTTTACATTGGTGTACTTGTTTCA 57.123 25.926 0.00 0.00 40.40 2.69
253 255 8.655651 CCAATTTTTACATTGGTGTACTTGTT 57.344 30.769 4.53 0.00 45.83 2.83
351 353 9.620660 CGTTTTTATTTTACCATTTCTGCTAGT 57.379 29.630 0.00 0.00 0.00 2.57
352 354 9.834628 TCGTTTTTATTTTACCATTTCTGCTAG 57.165 29.630 0.00 0.00 0.00 3.42
355 357 9.134734 TGATCGTTTTTATTTTACCATTTCTGC 57.865 29.630 0.00 0.00 0.00 4.26
363 365 7.085052 AGCCTCTGATCGTTTTTATTTTACC 57.915 36.000 0.00 0.00 0.00 2.85
370 372 5.543714 TGTACAAGCCTCTGATCGTTTTTA 58.456 37.500 0.00 0.00 0.00 1.52
394 397 4.021981 GCTTTGGACTGGTTTTATGAAGCT 60.022 41.667 0.00 0.00 35.39 3.74
438 442 5.296283 CGAATCATTTGGAGATTGAGCTCTT 59.704 40.000 16.19 1.95 35.93 2.85
439 443 4.815308 CGAATCATTTGGAGATTGAGCTCT 59.185 41.667 16.19 0.00 35.93 4.09
440 444 4.024218 CCGAATCATTTGGAGATTGAGCTC 60.024 45.833 6.82 6.82 35.93 4.09
458 471 4.127171 CCTGATACGAAAATGGACCGAAT 58.873 43.478 0.00 0.00 0.00 3.34
459 472 3.055675 ACCTGATACGAAAATGGACCGAA 60.056 43.478 0.00 0.00 0.00 4.30
466 479 3.724716 CGCACACACCTGATACGAAAATG 60.725 47.826 0.00 0.00 0.00 2.32
487 500 6.367969 GGTTATAGGATTGTTGGTACATAGCG 59.632 42.308 0.00 0.00 39.30 4.26
488 501 6.653740 GGGTTATAGGATTGTTGGTACATAGC 59.346 42.308 0.00 0.00 39.30 2.97
493 506 9.939802 CTTATAGGGTTATAGGATTGTTGGTAC 57.060 37.037 0.00 0.00 0.00 3.34
494 507 8.599792 GCTTATAGGGTTATAGGATTGTTGGTA 58.400 37.037 0.00 0.00 0.00 3.25
495 508 7.459234 GCTTATAGGGTTATAGGATTGTTGGT 58.541 38.462 0.00 0.00 0.00 3.67
496 509 6.594159 CGCTTATAGGGTTATAGGATTGTTGG 59.406 42.308 0.00 0.00 0.00 3.77
497 510 7.159372 ACGCTTATAGGGTTATAGGATTGTTG 58.841 38.462 0.00 0.00 38.28 3.33
516 529 6.208007 TCGATGAAATCCCTATTCTACGCTTA 59.792 38.462 0.00 0.00 41.39 3.09
523 536 5.841237 TCCTCTTCGATGAAATCCCTATTCT 59.159 40.000 2.36 0.00 41.39 2.40
571 585 4.832608 GGCACGACCCGGATGACC 62.833 72.222 0.73 0.00 0.00 4.02
573 587 3.770040 CAGGCACGACCCGGATGA 61.770 66.667 0.73 0.00 40.58 2.92
574 588 4.838152 CCAGGCACGACCCGGATG 62.838 72.222 0.73 0.00 40.58 3.51
577 591 4.143333 CTACCAGGCACGACCCGG 62.143 72.222 0.00 0.00 40.58 5.73
578 592 4.143333 CCTACCAGGCACGACCCG 62.143 72.222 0.00 0.00 40.58 5.28
618 632 2.036475 AGGCCTAGCATGTCTAATGTCG 59.964 50.000 1.29 0.00 0.00 4.35
624 638 0.690744 TGCCAGGCCTAGCATGTCTA 60.691 55.000 22.80 0.00 38.76 2.59
646 660 2.960129 CGCACGACCCGATTAGCC 60.960 66.667 0.00 0.00 0.00 3.93
671 685 1.020861 GCACAGATCATGGCGTGTGA 61.021 55.000 19.94 0.00 42.43 3.58
672 686 1.022982 AGCACAGATCATGGCGTGTG 61.023 55.000 6.60 14.36 42.66 3.82
677 691 2.012902 GCCCAAGCACAGATCATGGC 62.013 60.000 0.00 0.00 39.53 4.40
680 694 0.682209 GTGGCCCAAGCACAGATCAT 60.682 55.000 0.00 0.00 42.56 2.45
686 700 0.184933 AAACTAGTGGCCCAAGCACA 59.815 50.000 0.00 0.00 42.56 4.57
716 730 1.129326 GATATACGTGTCGTGCCAGC 58.871 55.000 0.00 0.00 41.39 4.85
718 732 1.395635 AGGATATACGTGTCGTGCCA 58.604 50.000 0.00 0.00 41.39 4.92
719 733 2.503920 AAGGATATACGTGTCGTGCC 57.496 50.000 0.00 2.09 41.39 5.01
722 736 5.657474 ACATCAAAAGGATATACGTGTCGT 58.343 37.500 0.00 0.00 38.08 4.34
753 767 7.224753 GCACAGCACGGCTATATATACATAATT 59.775 37.037 0.00 0.00 36.40 1.40
757 771 4.433615 GCACAGCACGGCTATATATACAT 58.566 43.478 0.00 0.00 36.40 2.29
760 774 3.096852 AGGCACAGCACGGCTATATATA 58.903 45.455 0.00 0.00 36.40 0.86
765 779 2.124983 CAGGCACAGCACGGCTAT 60.125 61.111 0.00 0.00 36.40 2.97
779 834 2.114670 CCGTGCTAATGGTGCCAGG 61.115 63.158 0.00 0.00 0.00 4.45
786 841 2.588877 CTCGGCCCGTGCTAATGG 60.589 66.667 1.63 0.00 37.74 3.16
787 842 3.272334 GCTCGGCCCGTGCTAATG 61.272 66.667 21.93 0.00 42.00 1.90
818 873 2.881513 TGCAAACGAACAGAATGGCTAA 59.118 40.909 0.00 0.00 43.62 3.09
820 875 1.267806 CTGCAAACGAACAGAATGGCT 59.732 47.619 0.00 0.00 43.62 4.75
845 914 1.293924 CAAATCTGCGCCTGTCCTAG 58.706 55.000 4.18 0.00 0.00 3.02
871 940 2.754552 GTGCAGCTTGGAACATTATGGA 59.245 45.455 0.00 0.00 39.30 3.41
905 974 0.877649 CGACCGGATGATTGCTCCAG 60.878 60.000 9.46 0.00 32.72 3.86
1119 1208 2.435693 AAGAATCGAGGGAGGCGGG 61.436 63.158 0.00 0.00 0.00 6.13
1120 1209 1.227380 CAAGAATCGAGGGAGGCGG 60.227 63.158 0.00 0.00 0.00 6.13
1147 1236 3.637273 GACAGCCCAGGAACCGGT 61.637 66.667 0.00 0.00 0.00 5.28
1149 1238 4.760047 CCGACAGCCCAGGAACCG 62.760 72.222 0.00 0.00 0.00 4.44
1182 1271 3.255642 GTGCAAGAAGCTACCAAATCCAA 59.744 43.478 0.00 0.00 45.94 3.53
1194 1283 3.367395 GGAAACAATAGGGTGCAAGAAGC 60.367 47.826 0.00 0.00 45.96 3.86
1212 1301 3.511146 GGAATCAGGCAAGACAATGGAAA 59.489 43.478 0.00 0.00 0.00 3.13
1214 1303 2.041485 TGGAATCAGGCAAGACAATGGA 59.959 45.455 0.00 0.00 0.00 3.41
1215 1304 2.449464 TGGAATCAGGCAAGACAATGG 58.551 47.619 0.00 0.00 0.00 3.16
1216 1305 3.181479 CCATGGAATCAGGCAAGACAATG 60.181 47.826 5.56 0.00 0.00 2.82
1217 1306 3.028850 CCATGGAATCAGGCAAGACAAT 58.971 45.455 5.56 0.00 0.00 2.71
1219 1308 2.133281 CCATGGAATCAGGCAAGACA 57.867 50.000 5.56 0.00 0.00 3.41
1234 1323 3.803082 CGTCCGCACCAAGCCATG 61.803 66.667 0.00 0.00 41.38 3.66
1487 1604 6.406692 TCTATCATTAGAAGGGGAGAAACG 57.593 41.667 0.00 0.00 31.40 3.60
1511 1628 4.755123 CACAGATAAACGACCCAAAGAGTT 59.245 41.667 0.00 0.00 0.00 3.01
1520 1637 7.705325 ACATCACTTATACACAGATAAACGACC 59.295 37.037 0.00 0.00 0.00 4.79
1523 1640 8.407457 ACACATCACTTATACACAGATAAACG 57.593 34.615 0.00 0.00 0.00 3.60
1531 1648 5.793817 AGCTTGACACATCACTTATACACA 58.206 37.500 0.00 0.00 33.38 3.72
1532 1649 6.727824 AAGCTTGACACATCACTTATACAC 57.272 37.500 0.00 0.00 33.38 2.90
1633 1808 7.672983 TCTACAGCTCAAATTCCTTTACTTG 57.327 36.000 0.00 0.00 0.00 3.16
1634 1809 8.157476 TCTTCTACAGCTCAAATTCCTTTACTT 58.843 33.333 0.00 0.00 0.00 2.24
1636 1811 7.907214 TCTTCTACAGCTCAAATTCCTTTAC 57.093 36.000 0.00 0.00 0.00 2.01
1637 1812 7.770897 GGATCTTCTACAGCTCAAATTCCTTTA 59.229 37.037 0.00 0.00 0.00 1.85
1680 1856 3.189287 CCGAAGCAATTACTGAACAGCTT 59.811 43.478 0.00 0.00 39.44 3.74
1685 1861 3.058224 AGCAACCGAAGCAATTACTGAAC 60.058 43.478 0.00 0.00 0.00 3.18
1687 1863 2.778299 AGCAACCGAAGCAATTACTGA 58.222 42.857 0.00 0.00 0.00 3.41
1689 1865 4.202111 ACAAAAGCAACCGAAGCAATTACT 60.202 37.500 0.00 0.00 0.00 2.24
1850 2192 0.386838 GCATATTGTCTTGGGCAGCC 59.613 55.000 1.26 1.26 0.00 4.85
1934 2456 4.453819 GCTAGATACATCCATTTGAGCCAC 59.546 45.833 0.00 0.00 0.00 5.01
2023 2587 6.381420 TGAAACAAAGGACACCCAGAATTAAA 59.619 34.615 0.00 0.00 33.88 1.52
2177 2799 2.529894 CACAAGTTTTGCGTTTTCTCGG 59.470 45.455 0.00 0.00 0.00 4.63
2227 2849 5.263968 TCAGCCTAGTCTTATACAGTTGC 57.736 43.478 0.00 0.00 0.00 4.17
2428 3051 6.231211 ACGATTCATTATCCACCATAACTCC 58.769 40.000 0.00 0.00 29.24 3.85
2429 3052 7.730364 AACGATTCATTATCCACCATAACTC 57.270 36.000 0.00 0.00 29.24 3.01
2430 3053 7.556275 ACAAACGATTCATTATCCACCATAACT 59.444 33.333 0.00 0.00 29.24 2.24
2431 3054 7.703328 ACAAACGATTCATTATCCACCATAAC 58.297 34.615 0.00 0.00 29.24 1.89
2432 3055 7.773224 AGACAAACGATTCATTATCCACCATAA 59.227 33.333 0.00 0.00 0.00 1.90
2433 3056 7.279615 AGACAAACGATTCATTATCCACCATA 58.720 34.615 0.00 0.00 0.00 2.74
2434 3057 6.122277 AGACAAACGATTCATTATCCACCAT 58.878 36.000 0.00 0.00 0.00 3.55
2435 3058 5.496556 AGACAAACGATTCATTATCCACCA 58.503 37.500 0.00 0.00 0.00 4.17
2516 3140 2.295253 AGAGAAATTACCCTGTCGCG 57.705 50.000 0.00 0.00 0.00 5.87
2561 3185 4.509600 AGAACAAAGAGCAACGAAGAAGAG 59.490 41.667 0.00 0.00 0.00 2.85
2562 3186 4.442706 AGAACAAAGAGCAACGAAGAAGA 58.557 39.130 0.00 0.00 0.00 2.87
2803 3463 6.472016 TGTTCTGAAGGACATAGCAATAACA 58.528 36.000 0.00 0.00 0.00 2.41
2804 3464 6.985188 TGTTCTGAAGGACATAGCAATAAC 57.015 37.500 0.00 0.00 0.00 1.89
2805 3465 7.611467 ACAATGTTCTGAAGGACATAGCAATAA 59.389 33.333 4.65 0.00 0.00 1.40
2806 3466 7.066163 CACAATGTTCTGAAGGACATAGCAATA 59.934 37.037 4.65 0.00 0.00 1.90
2807 3467 5.948162 ACAATGTTCTGAAGGACATAGCAAT 59.052 36.000 4.65 0.00 0.00 3.56
3093 3781 1.070758 GAACTGAGGACTTGGTCAGCA 59.929 52.381 0.00 0.00 43.48 4.41
3262 3959 3.807553 TCAGACACAGCAAGAATGTTCA 58.192 40.909 0.00 0.00 0.00 3.18
3335 4032 6.380095 AAATAGTTTAGGCACACGTCAAAA 57.620 33.333 0.00 0.00 0.00 2.44
3445 4150 6.347725 CCTTAGCTAACAGTAAGCAAACACAG 60.348 42.308 0.86 0.00 42.62 3.66
3446 4151 5.468746 CCTTAGCTAACAGTAAGCAAACACA 59.531 40.000 0.86 0.00 42.62 3.72
3447 4152 5.699458 TCCTTAGCTAACAGTAAGCAAACAC 59.301 40.000 0.86 0.00 42.62 3.32
3448 4153 5.860611 TCCTTAGCTAACAGTAAGCAAACA 58.139 37.500 0.86 0.00 42.62 2.83
3449 4154 6.091034 GTCTCCTTAGCTAACAGTAAGCAAAC 59.909 42.308 0.86 0.00 42.62 2.93
3478 4183 4.464951 AGACATGGACATACCGAAACTGTA 59.535 41.667 0.00 0.00 42.61 2.74
3480 4185 3.618594 CAGACATGGACATACCGAAACTG 59.381 47.826 0.00 0.00 42.61 3.16
3488 4196 6.428159 AGTTCAAGTTTCAGACATGGACATAC 59.572 38.462 0.00 0.00 37.81 2.39
3489 4197 6.533730 AGTTCAAGTTTCAGACATGGACATA 58.466 36.000 0.00 0.00 37.81 2.29
3490 4198 5.380043 AGTTCAAGTTTCAGACATGGACAT 58.620 37.500 0.00 0.00 37.81 3.06
3535 4243 5.376854 TCAGGTCTGCTAAATTTTTGCTC 57.623 39.130 14.90 7.08 0.00 4.26
3539 4247 6.144078 ACGTTTCAGGTCTGCTAAATTTTT 57.856 33.333 0.00 0.00 0.00 1.94
3904 4616 8.417884 AGGACTAAGATCTAATGTTCTACAAGC 58.582 37.037 0.00 0.00 0.00 4.01
4025 4812 5.594317 AGGTAAATATTTGAGGGATGTGTGC 59.406 40.000 11.05 0.00 0.00 4.57
4063 4861 0.035056 ATCAGTTCAAAGGCCGAGGG 60.035 55.000 0.00 0.00 0.00 4.30
4116 4914 0.465705 TGAGCTGGGTCGATCAATCC 59.534 55.000 0.00 0.00 0.00 3.01
4142 4940 4.699637 ACTTGTTGTTGACTATTCGGTCA 58.300 39.130 0.00 0.00 43.41 4.02


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

AutoCloner maintained by Alex Coulton.