Multiple sequence alignment - TraesCS2D01G165100

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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 TraesCS2D01G165100 chr2D 100.000 3431 0 0 1 3431 109553242 109556672 0.000000e+00 6336.0
1 TraesCS2D01G165100 chr2D 91.919 1782 136 8 922 2702 109030644 109032418 0.000000e+00 2486.0
2 TraesCS2D01G165100 chr2D 90.270 1223 109 10 1484 2702 109129686 109130902 0.000000e+00 1591.0
3 TraesCS2D01G165100 chr2D 78.065 1354 274 18 1048 2385 28915475 28914129 0.000000e+00 833.0
4 TraesCS2D01G165100 chr2D 77.212 1356 289 17 1034 2376 28965049 28966397 0.000000e+00 774.0
5 TraesCS2D01G165100 chr2D 90.305 557 51 3 948 1504 109128717 109128164 0.000000e+00 726.0
6 TraesCS2D01G165100 chr2D 80.788 406 42 22 506 881 109030254 109030653 5.600000e-73 285.0
7 TraesCS2D01G165100 chr2D 93.333 150 10 0 3279 3428 563098558 563098707 4.460000e-54 222.0
8 TraesCS2D01G165100 chr2D 81.757 296 22 16 618 891 109129011 109128726 5.760000e-53 219.0
9 TraesCS2D01G165100 chr2B 91.476 1748 126 12 957 2702 159098362 159100088 0.000000e+00 2381.0
10 TraesCS2D01G165100 chr2B 86.903 1466 131 38 575 2020 158863178 158864602 0.000000e+00 1587.0
11 TraesCS2D01G165100 chr2B 78.178 1361 279 15 1034 2382 46677668 46679022 0.000000e+00 852.0
12 TraesCS2D01G165100 chr2B 76.783 1374 278 26 1040 2382 6178715 6180078 0.000000e+00 732.0
13 TraesCS2D01G165100 chr2B 90.311 547 53 0 2018 2564 158869145 158869691 0.000000e+00 717.0
14 TraesCS2D01G165100 chr2B 88.889 63 6 1 575 637 159097878 159097939 3.670000e-10 76.8
15 TraesCS2D01G165100 chr2A 92.406 1646 110 6 924 2563 105407315 105408951 0.000000e+00 2333.0
16 TraesCS2D01G165100 chr2A 77.199 1364 287 19 1034 2382 30864710 30866064 0.000000e+00 774.0
17 TraesCS2D01G165100 chr2A 90.608 543 22 11 42 563 105406188 105406722 0.000000e+00 693.0
18 TraesCS2D01G165100 chr3D 82.306 1509 238 15 932 2434 22272516 22274001 0.000000e+00 1280.0
19 TraesCS2D01G165100 chr3D 81.992 1516 240 19 929 2434 22223206 22224698 0.000000e+00 1256.0
20 TraesCS2D01G165100 chr3D 94.268 157 5 3 3279 3431 10143053 10143209 1.590000e-58 237.0
21 TraesCS2D01G165100 chr3D 92.258 155 10 2 3279 3431 122940778 122940932 5.760000e-53 219.0
22 TraesCS2D01G165100 chr3B 81.271 1511 256 16 929 2434 39440905 39442393 0.000000e+00 1197.0
23 TraesCS2D01G165100 chr3B 81.717 1444 234 15 999 2433 39451833 39453255 0.000000e+00 1177.0
24 TraesCS2D01G165100 chr3A 81.176 1514 253 20 929 2436 31847886 31849373 0.000000e+00 1188.0
25 TraesCS2D01G165100 chr3A 82.290 751 123 5 990 1732 31962940 31962192 2.890000e-180 641.0
26 TraesCS2D01G165100 chr3A 83.377 379 63 0 2056 2434 31944339 31944717 5.450000e-93 351.0
27 TraesCS2D01G165100 chr7D 96.354 576 21 0 2704 3279 400188245 400187670 0.000000e+00 948.0
28 TraesCS2D01G165100 chr7D 95.486 576 26 0 2704 3279 35188328 35187753 0.000000e+00 920.0
29 TraesCS2D01G165100 chr7D 94.774 574 30 0 2704 3277 513327775 513327202 0.000000e+00 894.0
30 TraesCS2D01G165100 chr7D 95.541 157 3 1 3279 3431 190380233 190380389 7.350000e-62 248.0
31 TraesCS2D01G165100 chr5D 95.660 576 24 1 2704 3279 473443912 473444486 0.000000e+00 924.0
32 TraesCS2D01G165100 chr1D 95.660 576 23 2 2704 3279 18119568 18118995 0.000000e+00 924.0
33 TraesCS2D01G165100 chr1D 95.139 576 28 0 2704 3279 481679191 481679766 0.000000e+00 909.0
34 TraesCS2D01G165100 chr1D 94.792 576 30 0 2704 3279 315985377 315984802 0.000000e+00 898.0
35 TraesCS2D01G165100 chr1D 94.792 576 28 2 2704 3279 18113253 18112680 0.000000e+00 896.0
36 TraesCS2D01G165100 chr6B 94.965 576 28 1 2704 3279 56388984 56389558 0.000000e+00 902.0
37 TraesCS2D01G165100 chr6D 94.156 154 8 1 3279 3431 8998052 8998205 2.060000e-57 233.0
38 TraesCS2D01G165100 chr1A 93.082 159 4 2 3279 3431 95471289 95471446 3.450000e-55 226.0
39 TraesCS2D01G165100 chr5B 92.949 156 7 4 3279 3431 64792048 64791894 1.240000e-54 224.0
40 TraesCS2D01G165100 chr5A 92.453 159 6 1 3279 3431 639363439 639363597 4.460000e-54 222.0
41 TraesCS2D01G165100 chr4B 92.308 156 10 1 3278 3431 292567244 292567399 1.600000e-53 220.0
42 TraesCS2D01G165100 chr7B 97.222 36 1 0 2 37 455758553 455758588 1.030000e-05 62.1


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 TraesCS2D01G165100 chr2D 109553242 109556672 3430 False 6336.0 6336 100.0000 1 3431 1 chr2D.!!$F3 3430
1 TraesCS2D01G165100 chr2D 109129686 109130902 1216 False 1591.0 1591 90.2700 1484 2702 1 chr2D.!!$F2 1218
2 TraesCS2D01G165100 chr2D 109030254 109032418 2164 False 1385.5 2486 86.3535 506 2702 2 chr2D.!!$F5 2196
3 TraesCS2D01G165100 chr2D 28914129 28915475 1346 True 833.0 833 78.0650 1048 2385 1 chr2D.!!$R1 1337
4 TraesCS2D01G165100 chr2D 28965049 28966397 1348 False 774.0 774 77.2120 1034 2376 1 chr2D.!!$F1 1342
5 TraesCS2D01G165100 chr2D 109128164 109129011 847 True 472.5 726 86.0310 618 1504 2 chr2D.!!$R2 886
6 TraesCS2D01G165100 chr2B 158863178 158864602 1424 False 1587.0 1587 86.9030 575 2020 1 chr2B.!!$F3 1445
7 TraesCS2D01G165100 chr2B 159097878 159100088 2210 False 1228.9 2381 90.1825 575 2702 2 chr2B.!!$F5 2127
8 TraesCS2D01G165100 chr2B 46677668 46679022 1354 False 852.0 852 78.1780 1034 2382 1 chr2B.!!$F2 1348
9 TraesCS2D01G165100 chr2B 6178715 6180078 1363 False 732.0 732 76.7830 1040 2382 1 chr2B.!!$F1 1342
10 TraesCS2D01G165100 chr2B 158869145 158869691 546 False 717.0 717 90.3110 2018 2564 1 chr2B.!!$F4 546
11 TraesCS2D01G165100 chr2A 105406188 105408951 2763 False 1513.0 2333 91.5070 42 2563 2 chr2A.!!$F2 2521
12 TraesCS2D01G165100 chr2A 30864710 30866064 1354 False 774.0 774 77.1990 1034 2382 1 chr2A.!!$F1 1348
13 TraesCS2D01G165100 chr3D 22272516 22274001 1485 False 1280.0 1280 82.3060 932 2434 1 chr3D.!!$F3 1502
14 TraesCS2D01G165100 chr3D 22223206 22224698 1492 False 1256.0 1256 81.9920 929 2434 1 chr3D.!!$F2 1505
15 TraesCS2D01G165100 chr3B 39440905 39442393 1488 False 1197.0 1197 81.2710 929 2434 1 chr3B.!!$F1 1505
16 TraesCS2D01G165100 chr3B 39451833 39453255 1422 False 1177.0 1177 81.7170 999 2433 1 chr3B.!!$F2 1434
17 TraesCS2D01G165100 chr3A 31847886 31849373 1487 False 1188.0 1188 81.1760 929 2436 1 chr3A.!!$F1 1507
18 TraesCS2D01G165100 chr3A 31962192 31962940 748 True 641.0 641 82.2900 990 1732 1 chr3A.!!$R1 742
19 TraesCS2D01G165100 chr7D 400187670 400188245 575 True 948.0 948 96.3540 2704 3279 1 chr7D.!!$R2 575
20 TraesCS2D01G165100 chr7D 35187753 35188328 575 True 920.0 920 95.4860 2704 3279 1 chr7D.!!$R1 575
21 TraesCS2D01G165100 chr7D 513327202 513327775 573 True 894.0 894 94.7740 2704 3277 1 chr7D.!!$R3 573
22 TraesCS2D01G165100 chr5D 473443912 473444486 574 False 924.0 924 95.6600 2704 3279 1 chr5D.!!$F1 575
23 TraesCS2D01G165100 chr1D 18118995 18119568 573 True 924.0 924 95.6600 2704 3279 1 chr1D.!!$R2 575
24 TraesCS2D01G165100 chr1D 481679191 481679766 575 False 909.0 909 95.1390 2704 3279 1 chr1D.!!$F1 575
25 TraesCS2D01G165100 chr1D 315984802 315985377 575 True 898.0 898 94.7920 2704 3279 1 chr1D.!!$R3 575
26 TraesCS2D01G165100 chr1D 18112680 18113253 573 True 896.0 896 94.7920 2704 3279 1 chr1D.!!$R1 575
27 TraesCS2D01G165100 chr6B 56388984 56389558 574 False 902.0 902 94.9650 2704 3279 1 chr6B.!!$F1 575

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
26 27 0.108041 TAAAAGATCCACCGGCCGAC 60.108 55.0 30.73 10.34 0.0 4.79 F
930 1302 0.179227 CACACACACACACACACACG 60.179 55.0 0.00 0.00 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2226 0.321671 TGCCAAAGGAGAGGAAGACG 59.678 55.000 0.0 0.0 0.0 4.18 R
2750 3173 1.066918 ACTTTTGTCCGCGTCGACT 59.933 52.632 14.7 0.0 33.7 4.18 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
22 23 4.776795 TCTTTTTAAAAGATCCACCGGC 57.223 40.909 15.24 0.00 0.00 6.13
23 24 3.508402 TCTTTTTAAAAGATCCACCGGCC 59.492 43.478 15.24 0.00 0.00 6.13
24 25 1.455248 TTTAAAAGATCCACCGGCCG 58.545 50.000 21.04 21.04 0.00 6.13
25 26 0.614294 TTAAAAGATCCACCGGCCGA 59.386 50.000 30.73 6.75 0.00 5.54
26 27 0.108041 TAAAAGATCCACCGGCCGAC 60.108 55.000 30.73 10.34 0.00 4.79
27 28 1.838073 AAAAGATCCACCGGCCGACT 61.838 55.000 30.73 8.37 0.00 4.18
28 29 2.240162 AAAGATCCACCGGCCGACTC 62.240 60.000 30.73 14.94 0.00 3.36
29 30 4.570663 GATCCACCGGCCGACTCG 62.571 72.222 30.73 12.89 0.00 4.18
31 32 4.720902 TCCACCGGCCGACTCGTA 62.721 66.667 30.73 3.42 0.00 3.43
32 33 4.189188 CCACCGGCCGACTCGTAG 62.189 72.222 30.73 10.69 0.00 3.51
33 34 4.849329 CACCGGCCGACTCGTAGC 62.849 72.222 30.73 0.00 0.00 3.58
35 36 4.554363 CCGGCCGACTCGTAGCAG 62.554 72.222 30.73 0.44 0.00 4.24
37 38 4.874977 GGCCGACTCGTAGCAGCC 62.875 72.222 0.00 0.00 0.00 4.85
38 39 4.874977 GCCGACTCGTAGCAGCCC 62.875 72.222 0.00 0.00 0.00 5.19
39 40 4.208686 CCGACTCGTAGCAGCCCC 62.209 72.222 0.00 0.00 0.00 5.80
40 41 4.208686 CGACTCGTAGCAGCCCCC 62.209 72.222 0.00 0.00 0.00 5.40
43 44 1.900545 GACTCGTAGCAGCCCCCTTT 61.901 60.000 0.00 0.00 0.00 3.11
56 57 8.422577 AGCAGCCCCCTTTAAATATATAAAAG 57.577 34.615 11.15 11.15 0.00 2.27
120 121 7.609960 AGAGAGATAGTGGTATAACATGCATG 58.390 38.462 25.09 25.09 0.00 4.06
139 140 3.124578 TGTGCAGACATACACACACAT 57.875 42.857 0.00 0.00 41.67 3.21
171 172 2.098117 GCCTTTACATGTGGCATCACTC 59.902 50.000 18.26 0.00 45.46 3.51
175 176 2.519771 ACATGTGGCATCACTCCAAT 57.480 45.000 0.00 0.00 43.94 3.16
198 199 2.041153 CCAAAACCACCACTGCCTC 58.959 57.895 0.00 0.00 0.00 4.70
268 283 2.747446 TCCGTAGAAGAAAGGCATTTGC 59.253 45.455 0.00 0.00 41.14 3.68
335 350 1.132643 ACGAGATAGACGTGAGCCAAC 59.867 52.381 0.00 0.00 42.37 3.77
347 362 0.955428 GAGCCAACCATCAACGAGCA 60.955 55.000 0.00 0.00 0.00 4.26
348 363 1.210155 GCCAACCATCAACGAGCAC 59.790 57.895 0.00 0.00 0.00 4.40
349 364 1.237285 GCCAACCATCAACGAGCACT 61.237 55.000 0.00 0.00 0.00 4.40
350 365 1.943968 GCCAACCATCAACGAGCACTA 60.944 52.381 0.00 0.00 0.00 2.74
377 392 6.371548 TCTGGAGTATGTTGTTTTACATGAGC 59.628 38.462 0.00 0.00 39.06 4.26
386 401 4.242475 TGTTTTACATGAGCAGGAGTACG 58.758 43.478 0.00 0.00 0.00 3.67
493 513 2.667473 AGCTTAAGACATACGCCGTT 57.333 45.000 6.67 0.00 29.27 4.44
504 524 4.365723 ACATACGCCGTTTGGTAGATTAG 58.634 43.478 12.17 0.00 37.67 1.73
512 532 4.351192 CGTTTGGTAGATTAGCAATTGGC 58.649 43.478 7.72 0.00 44.53 4.52
699 1046 3.103447 TCACTCTCTGTTTGTCTGCTG 57.897 47.619 0.00 0.00 0.00 4.41
700 1047 2.695147 TCACTCTCTGTTTGTCTGCTGA 59.305 45.455 0.00 0.00 0.00 4.26
702 1049 2.697751 ACTCTCTGTTTGTCTGCTGAGT 59.302 45.455 0.00 0.00 33.98 3.41
703 1050 3.891977 ACTCTCTGTTTGTCTGCTGAGTA 59.108 43.478 0.00 0.00 33.98 2.59
704 1051 4.022416 ACTCTCTGTTTGTCTGCTGAGTAG 60.022 45.833 0.00 0.00 33.98 2.57
705 1052 4.145052 TCTCTGTTTGTCTGCTGAGTAGA 58.855 43.478 0.00 0.00 33.98 2.59
706 1053 4.217334 TCTCTGTTTGTCTGCTGAGTAGAG 59.783 45.833 0.00 3.87 33.98 2.43
707 1054 2.992543 CTGTTTGTCTGCTGAGTAGAGC 59.007 50.000 0.00 0.00 39.62 4.09
708 1055 2.630098 TGTTTGTCTGCTGAGTAGAGCT 59.370 45.455 0.00 0.00 39.90 4.09
709 1056 2.992543 GTTTGTCTGCTGAGTAGAGCTG 59.007 50.000 0.00 0.00 39.90 4.24
710 1057 2.206576 TGTCTGCTGAGTAGAGCTGA 57.793 50.000 0.00 0.00 42.63 4.26
711 1058 2.090760 TGTCTGCTGAGTAGAGCTGAG 58.909 52.381 0.00 0.00 44.64 3.35
714 1061 2.238395 TCTGCTGAGTAGAGCTGAGAGA 59.762 50.000 0.00 0.00 40.73 3.10
725 1072 0.391661 GCTGAGAGATTCGGTGCCAA 60.392 55.000 0.00 0.00 34.46 4.52
735 1082 2.570415 TCGGTGCCAAATTGGAGTTA 57.430 45.000 17.47 0.00 40.96 2.24
790 1147 1.227823 CCTGAACACCAAGCCGTCA 60.228 57.895 0.00 0.00 0.00 4.35
796 1161 4.373116 ACCAAGCCGTCATCGCGT 62.373 61.111 5.77 0.00 35.54 6.01
869 1241 3.430453 CCTCTCTCTCTTCCTCACTGTT 58.570 50.000 0.00 0.00 0.00 3.16
884 1256 2.225255 CACTGTTTCACACACACACACA 59.775 45.455 0.00 0.00 0.00 3.72
885 1257 2.225491 ACTGTTTCACACACACACACAC 59.775 45.455 0.00 0.00 0.00 3.82
886 1258 2.222027 TGTTTCACACACACACACACA 58.778 42.857 0.00 0.00 0.00 3.72
887 1259 2.031595 TGTTTCACACACACACACACAC 60.032 45.455 0.00 0.00 0.00 3.82
888 1260 1.884235 TTCACACACACACACACACA 58.116 45.000 0.00 0.00 0.00 3.72
889 1261 1.152510 TCACACACACACACACACAC 58.847 50.000 0.00 0.00 0.00 3.82
890 1262 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
891 1263 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
892 1264 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
893 1265 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
894 1266 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
895 1267 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
896 1268 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
897 1269 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
898 1270 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
899 1271 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
930 1302 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
971 1346 1.133761 TCCAAAAATCCACACCACCGA 60.134 47.619 0.00 0.00 0.00 4.69
1009 1384 2.047655 TCGTCAACATGGTCGGCC 60.048 61.111 0.00 0.00 0.00 6.13
1227 1614 2.041620 CAACCCCTCCATCTCTTTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
1362 1761 2.417719 GTCATCGTGCTGGACTTCTTT 58.582 47.619 0.00 0.00 0.00 2.52
1484 1883 3.345808 GCACGGCAAGAGCACGAA 61.346 61.111 0.00 0.00 44.61 3.85
1718 2117 4.776322 CGCACCATCCGGCCTCAA 62.776 66.667 0.00 0.00 34.57 3.02
2130 2529 1.071471 CGGGTGGAACTCAGTGCTT 59.929 57.895 0.00 0.00 36.87 3.91
2151 2550 1.743995 GTCGGTTATGGCAGGCGTT 60.744 57.895 0.00 0.00 0.00 4.84
2245 2644 1.514087 GTCGCGATGGAAGGGTACA 59.486 57.895 14.06 0.00 0.00 2.90
2395 2800 1.153349 GGGGAATCAGAGGCGACAC 60.153 63.158 0.00 0.00 0.00 3.67
2445 2850 6.751157 TCATGCTTGACATTTTGAATTGACT 58.249 32.000 0.00 0.00 36.64 3.41
2448 2853 6.339730 TGCTTGACATTTTGAATTGACTGTT 58.660 32.000 0.00 0.00 0.00 3.16
2465 2878 8.564648 TTGACTGTTGGTATAATCGTATAACG 57.435 34.615 0.00 0.00 44.19 3.18
2601 3022 9.300681 AGAATTCCTCATAAGACAATCAAAACA 57.699 29.630 0.65 0.00 0.00 2.83
2602 3023 9.912634 GAATTCCTCATAAGACAATCAAAACAA 57.087 29.630 0.00 0.00 0.00 2.83
2702 3125 5.633996 TCACAATCAATTTGCGTTTGTTC 57.366 34.783 8.52 0.00 39.03 3.18
2744 3167 1.374252 ATTTCGTTCGCCTGCGTCT 60.374 52.632 11.68 0.00 40.74 4.18
2750 3173 1.227409 TTCGCCTGCGTCTGTTTGA 60.227 52.632 11.68 0.00 40.74 2.69
2755 3178 0.318699 CCTGCGTCTGTTTGAGTCGA 60.319 55.000 0.00 0.00 35.50 4.20
2908 3331 3.129300 CCTTCTCGCTATCCGCCA 58.871 61.111 0.00 0.00 36.73 5.69
3022 3445 2.446753 TTTTTAAGCCGACCGTGCGC 62.447 55.000 0.00 0.00 0.00 6.09
3060 3483 1.816863 AACTCGCCGTCCACATCTGT 61.817 55.000 0.00 0.00 0.00 3.41
3282 3705 3.625897 ACTGGCAGCACCGCACTA 61.626 61.111 15.89 0.00 43.94 2.74
3283 3706 3.121030 CTGGCAGCACCGCACTAC 61.121 66.667 0.00 0.00 43.94 2.73
3284 3707 3.596066 CTGGCAGCACCGCACTACT 62.596 63.158 0.00 0.00 43.94 2.57
3285 3708 2.225791 CTGGCAGCACCGCACTACTA 62.226 60.000 0.00 0.00 43.94 1.82
3286 3709 1.519455 GGCAGCACCGCACTACTAG 60.519 63.158 0.00 0.00 0.00 2.57
3287 3710 1.519455 GCAGCACCGCACTACTAGG 60.519 63.158 0.00 0.00 0.00 3.02
3288 3711 1.945354 GCAGCACCGCACTACTAGGA 61.945 60.000 0.00 0.00 0.00 2.94
3289 3712 0.530744 CAGCACCGCACTACTAGGAA 59.469 55.000 0.00 0.00 0.00 3.36
3290 3713 1.067142 CAGCACCGCACTACTAGGAAA 60.067 52.381 0.00 0.00 0.00 3.13
3291 3714 1.621814 AGCACCGCACTACTAGGAAAA 59.378 47.619 0.00 0.00 0.00 2.29
3292 3715 2.000447 GCACCGCACTACTAGGAAAAG 59.000 52.381 0.00 0.00 0.00 2.27
3293 3716 2.618053 CACCGCACTACTAGGAAAAGG 58.382 52.381 0.00 0.00 0.00 3.11
3294 3717 1.066358 ACCGCACTACTAGGAAAAGGC 60.066 52.381 0.00 0.00 0.00 4.35
3295 3718 1.207329 CCGCACTACTAGGAAAAGGCT 59.793 52.381 0.00 0.00 0.00 4.58
3296 3719 2.429610 CCGCACTACTAGGAAAAGGCTA 59.570 50.000 0.00 0.00 0.00 3.93
3297 3720 3.118884 CCGCACTACTAGGAAAAGGCTAA 60.119 47.826 0.00 0.00 0.00 3.09
3298 3721 4.443034 CCGCACTACTAGGAAAAGGCTAAT 60.443 45.833 0.00 0.00 0.00 1.73
3299 3722 5.116882 CGCACTACTAGGAAAAGGCTAATT 58.883 41.667 0.00 0.00 0.00 1.40
3300 3723 6.278363 CGCACTACTAGGAAAAGGCTAATTA 58.722 40.000 0.00 0.00 0.00 1.40
3301 3724 6.421202 CGCACTACTAGGAAAAGGCTAATTAG 59.579 42.308 8.20 8.20 0.00 1.73
3302 3725 7.273712 GCACTACTAGGAAAAGGCTAATTAGT 58.726 38.462 13.91 0.00 0.00 2.24
3303 3726 7.224949 GCACTACTAGGAAAAGGCTAATTAGTG 59.775 40.741 13.91 2.41 37.06 2.74
3304 3727 7.711339 CACTACTAGGAAAAGGCTAATTAGTGG 59.289 40.741 13.91 0.00 32.57 4.00
3305 3728 5.437946 ACTAGGAAAAGGCTAATTAGTGGC 58.562 41.667 13.91 2.45 0.00 5.01
3306 3729 4.316025 AGGAAAAGGCTAATTAGTGGCA 57.684 40.909 13.91 0.00 0.00 4.92
3307 3730 4.017126 AGGAAAAGGCTAATTAGTGGCAC 58.983 43.478 10.29 10.29 0.00 5.01
3308 3731 3.761752 GGAAAAGGCTAATTAGTGGCACA 59.238 43.478 21.41 0.00 0.00 4.57
3319 3742 3.215245 TGGCACACCTGTTTTGGC 58.785 55.556 0.00 0.00 36.63 4.52
3320 3743 2.421314 GGCACACCTGTTTTGGCC 59.579 61.111 0.00 0.00 0.00 5.36
3321 3744 2.430610 GGCACACCTGTTTTGGCCA 61.431 57.895 0.00 0.00 41.02 5.36
3322 3745 1.747774 GCACACCTGTTTTGGCCAT 59.252 52.632 6.09 0.00 0.00 4.40
3323 3746 0.106521 GCACACCTGTTTTGGCCATT 59.893 50.000 6.09 0.00 0.00 3.16
3324 3747 1.342819 GCACACCTGTTTTGGCCATTA 59.657 47.619 6.09 0.00 0.00 1.90
3325 3748 2.224161 GCACACCTGTTTTGGCCATTAA 60.224 45.455 6.09 0.50 0.00 1.40
3326 3749 3.556843 GCACACCTGTTTTGGCCATTAAT 60.557 43.478 6.09 0.00 0.00 1.40
3327 3750 3.995705 CACACCTGTTTTGGCCATTAATG 59.004 43.478 6.09 8.58 0.00 1.90
3339 3762 1.603802 CCATTAATGGCGCACTACAGG 59.396 52.381 21.32 0.00 41.75 4.00
3340 3763 2.288666 CATTAATGGCGCACTACAGGT 58.711 47.619 10.83 0.00 0.00 4.00
3341 3764 5.085904 CCATTAATGGCGCACTACAGGTG 62.086 52.174 21.32 0.00 43.83 4.00
3348 3771 2.343758 CACTACAGGTGCGCCACT 59.656 61.111 20.59 4.91 39.22 4.00
3349 3772 1.589630 CACTACAGGTGCGCCACTA 59.410 57.895 20.59 5.92 39.22 2.74
3350 3773 0.175760 CACTACAGGTGCGCCACTAT 59.824 55.000 20.59 2.84 39.22 2.12
3351 3774 0.460311 ACTACAGGTGCGCCACTATC 59.540 55.000 20.59 0.00 37.19 2.08
3352 3775 0.459899 CTACAGGTGCGCCACTATCA 59.540 55.000 20.59 0.00 37.19 2.15
3353 3776 1.069204 CTACAGGTGCGCCACTATCAT 59.931 52.381 20.59 0.00 37.19 2.45
3354 3777 0.179073 ACAGGTGCGCCACTATCATC 60.179 55.000 20.59 0.00 37.19 2.92
3355 3778 0.179076 CAGGTGCGCCACTATCATCA 60.179 55.000 20.59 0.00 37.19 3.07
3356 3779 0.179073 AGGTGCGCCACTATCATCAC 60.179 55.000 20.59 0.00 37.19 3.06
3357 3780 1.490693 GGTGCGCCACTATCATCACG 61.491 60.000 12.58 0.00 34.40 4.35
3358 3781 1.882625 TGCGCCACTATCATCACGC 60.883 57.895 4.18 0.00 46.05 5.34
3359 3782 2.598632 GCGCCACTATCATCACGCC 61.599 63.158 0.00 0.00 40.43 5.68
3360 3783 1.227234 CGCCACTATCATCACGCCA 60.227 57.895 0.00 0.00 0.00 5.69
3361 3784 1.490693 CGCCACTATCATCACGCCAC 61.491 60.000 0.00 0.00 0.00 5.01
3362 3785 0.179073 GCCACTATCATCACGCCACT 60.179 55.000 0.00 0.00 0.00 4.00
3363 3786 1.068588 GCCACTATCATCACGCCACTA 59.931 52.381 0.00 0.00 0.00 2.74
3364 3787 2.864097 GCCACTATCATCACGCCACTAG 60.864 54.545 0.00 0.00 0.00 2.57
3365 3788 2.362397 CCACTATCATCACGCCACTAGT 59.638 50.000 0.00 0.00 0.00 2.57
3366 3789 3.568430 CCACTATCATCACGCCACTAGTA 59.432 47.826 0.00 0.00 0.00 1.82
3367 3790 4.037565 CCACTATCATCACGCCACTAGTAA 59.962 45.833 0.00 0.00 0.00 2.24
3368 3791 4.976731 CACTATCATCACGCCACTAGTAAC 59.023 45.833 0.00 0.00 0.00 2.50
3369 3792 4.888239 ACTATCATCACGCCACTAGTAACT 59.112 41.667 0.00 0.00 0.00 2.24
3370 3793 6.017357 CACTATCATCACGCCACTAGTAACTA 60.017 42.308 0.00 0.00 0.00 2.24
3371 3794 5.847111 ATCATCACGCCACTAGTAACTAA 57.153 39.130 0.00 0.00 0.00 2.24
3372 3795 5.847111 TCATCACGCCACTAGTAACTAAT 57.153 39.130 0.00 0.00 0.00 1.73
3373 3796 6.947644 TCATCACGCCACTAGTAACTAATA 57.052 37.500 0.00 0.00 0.00 0.98
3374 3797 6.732154 TCATCACGCCACTAGTAACTAATAC 58.268 40.000 0.00 0.00 34.52 1.89
3375 3798 6.544931 TCATCACGCCACTAGTAACTAATACT 59.455 38.462 0.00 0.00 46.62 2.12
3376 3799 7.716560 TCATCACGCCACTAGTAACTAATACTA 59.283 37.037 0.00 0.00 43.16 1.82
3377 3800 7.864108 TCACGCCACTAGTAACTAATACTAA 57.136 36.000 0.00 0.00 44.50 2.24
3378 3801 8.455903 TCACGCCACTAGTAACTAATACTAAT 57.544 34.615 0.00 0.00 44.50 1.73
3379 3802 8.347771 TCACGCCACTAGTAACTAATACTAATG 58.652 37.037 0.00 0.00 44.50 1.90
3383 3806 7.564044 CACTAGTAACTAATACTAATGGCGC 57.436 40.000 0.00 0.00 44.50 6.53
3384 3807 7.143340 CACTAGTAACTAATACTAATGGCGCA 58.857 38.462 10.83 0.00 44.50 6.09
3385 3808 7.114529 CACTAGTAACTAATACTAATGGCGCAC 59.885 40.741 10.83 0.00 44.50 5.34
3386 3809 5.295152 AGTAACTAATACTAATGGCGCACC 58.705 41.667 10.83 0.00 43.16 5.01
3387 3810 2.750948 ACTAATACTAATGGCGCACCG 58.249 47.619 10.83 0.00 39.70 4.94
3388 3811 2.101917 ACTAATACTAATGGCGCACCGT 59.898 45.455 10.83 0.65 39.70 4.83
3389 3812 2.894763 AATACTAATGGCGCACCGTA 57.105 45.000 10.83 3.16 39.70 4.02
3390 3813 3.396260 AATACTAATGGCGCACCGTAT 57.604 42.857 10.83 5.53 39.70 3.06
3391 3814 4.524316 AATACTAATGGCGCACCGTATA 57.476 40.909 10.83 0.00 39.70 1.47
3392 3815 2.144482 ACTAATGGCGCACCGTATAC 57.856 50.000 10.83 0.00 39.70 1.47
3393 3816 1.269936 ACTAATGGCGCACCGTATACC 60.270 52.381 10.83 0.00 39.70 2.73
3394 3817 0.751452 TAATGGCGCACCGTATACCA 59.249 50.000 10.83 0.00 39.70 3.25
3395 3818 0.531974 AATGGCGCACCGTATACCAG 60.532 55.000 10.83 0.00 39.70 4.00
3396 3819 1.396607 ATGGCGCACCGTATACCAGA 61.397 55.000 10.83 0.00 39.70 3.86
3397 3820 1.590792 GGCGCACCGTATACCAGAC 60.591 63.158 10.83 0.00 0.00 3.51
3398 3821 1.140161 GCGCACCGTATACCAGACA 59.860 57.895 0.30 0.00 0.00 3.41
3399 3822 0.458889 GCGCACCGTATACCAGACAA 60.459 55.000 0.30 0.00 0.00 3.18
3400 3823 1.805120 GCGCACCGTATACCAGACAAT 60.805 52.381 0.30 0.00 0.00 2.71
3401 3824 2.544277 GCGCACCGTATACCAGACAATA 60.544 50.000 0.30 0.00 0.00 1.90
3402 3825 3.305964 CGCACCGTATACCAGACAATAG 58.694 50.000 0.00 0.00 0.00 1.73
3403 3826 3.243301 CGCACCGTATACCAGACAATAGT 60.243 47.826 0.00 0.00 0.00 2.12
3404 3827 4.049186 GCACCGTATACCAGACAATAGTG 58.951 47.826 0.00 0.00 0.00 2.74
3405 3828 4.617959 CACCGTATACCAGACAATAGTGG 58.382 47.826 0.00 0.00 39.98 4.00
3406 3829 3.069158 ACCGTATACCAGACAATAGTGGC 59.931 47.826 0.00 0.00 37.34 5.01
3407 3830 3.305964 CGTATACCAGACAATAGTGGCG 58.694 50.000 0.00 0.00 38.10 5.69
3408 3831 2.240493 ATACCAGACAATAGTGGCGC 57.760 50.000 0.00 0.00 38.10 6.53
3409 3832 0.899019 TACCAGACAATAGTGGCGCA 59.101 50.000 10.83 0.00 38.10 6.09
3410 3833 0.673644 ACCAGACAATAGTGGCGCAC 60.674 55.000 10.83 5.73 38.10 5.34
3411 3834 1.369091 CCAGACAATAGTGGCGCACC 61.369 60.000 10.83 0.00 38.10 5.01
3412 3835 0.673333 CAGACAATAGTGGCGCACCA 60.673 55.000 10.83 0.00 46.51 4.17
3425 3848 4.415150 CACCAGGGAGTGCGCCAT 62.415 66.667 4.18 0.00 0.00 4.40
3426 3849 3.650950 ACCAGGGAGTGCGCCATT 61.651 61.111 4.18 0.00 0.00 3.16
3427 3850 2.297895 ACCAGGGAGTGCGCCATTA 61.298 57.895 4.18 0.00 0.00 1.90
3428 3851 1.524621 CCAGGGAGTGCGCCATTAG 60.525 63.158 4.18 0.00 0.00 1.73
3429 3852 1.221840 CAGGGAGTGCGCCATTAGT 59.778 57.895 4.18 0.00 0.00 2.24
3430 3853 0.464036 CAGGGAGTGCGCCATTAGTA 59.536 55.000 4.18 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.508402 GGCCGGTGGATCTTTTAAAAAGA 59.492 43.478 1.90 0.00 0.00 2.52
4 5 1.813786 CGGCCGGTGGATCTTTTAAAA 59.186 47.619 20.10 0.00 0.00 1.52
5 6 1.003349 TCGGCCGGTGGATCTTTTAAA 59.997 47.619 27.83 0.00 0.00 1.52
7 8 0.108041 GTCGGCCGGTGGATCTTTTA 60.108 55.000 27.83 0.00 0.00 1.52
8 9 1.376812 GTCGGCCGGTGGATCTTTT 60.377 57.895 27.83 0.00 0.00 2.27
9 10 2.240162 GAGTCGGCCGGTGGATCTTT 62.240 60.000 27.83 0.00 0.00 2.52
10 11 2.683933 AGTCGGCCGGTGGATCTT 60.684 61.111 27.83 0.00 0.00 2.40
11 12 3.148279 GAGTCGGCCGGTGGATCT 61.148 66.667 27.83 13.73 0.00 2.75
12 13 4.570663 CGAGTCGGCCGGTGGATC 62.571 72.222 27.83 14.75 0.00 3.36
14 15 4.720902 TACGAGTCGGCCGGTGGA 62.721 66.667 27.83 6.47 0.00 4.02
15 16 4.189188 CTACGAGTCGGCCGGTGG 62.189 72.222 27.83 16.70 0.00 4.61
16 17 4.849329 GCTACGAGTCGGCCGGTG 62.849 72.222 27.83 14.99 0.00 4.94
18 19 4.554363 CTGCTACGAGTCGGCCGG 62.554 72.222 27.83 11.94 0.00 6.13
20 21 4.874977 GGCTGCTACGAGTCGGCC 62.875 72.222 18.30 15.30 46.19 6.13
21 22 4.874977 GGGCTGCTACGAGTCGGC 62.875 72.222 18.30 12.06 0.00 5.54
22 23 4.208686 GGGGCTGCTACGAGTCGG 62.209 72.222 18.30 0.41 0.00 4.79
23 24 4.208686 GGGGGCTGCTACGAGTCG 62.209 72.222 11.85 11.85 0.00 4.18
24 25 1.900545 AAAGGGGGCTGCTACGAGTC 61.901 60.000 0.00 0.00 0.00 3.36
25 26 0.616679 TAAAGGGGGCTGCTACGAGT 60.617 55.000 0.00 0.00 0.00 4.18
26 27 0.539986 TTAAAGGGGGCTGCTACGAG 59.460 55.000 0.00 0.00 0.00 4.18
27 28 0.985760 TTTAAAGGGGGCTGCTACGA 59.014 50.000 0.00 0.00 0.00 3.43
28 29 2.052782 ATTTAAAGGGGGCTGCTACG 57.947 50.000 0.00 0.00 0.00 3.51
29 30 8.873186 TTTATATATTTAAAGGGGGCTGCTAC 57.127 34.615 0.00 0.00 0.00 3.58
30 31 9.528489 CTTTTATATATTTAAAGGGGGCTGCTA 57.472 33.333 0.00 0.00 0.00 3.49
31 32 8.010697 ACTTTTATATATTTAAAGGGGGCTGCT 58.989 33.333 17.44 0.00 34.10 4.24
32 33 8.190326 ACTTTTATATATTTAAAGGGGGCTGC 57.810 34.615 17.44 0.00 34.10 5.25
100 101 5.931532 GCACATGCATGTTATACCACTATC 58.068 41.667 29.48 3.93 39.39 2.08
120 121 2.807967 ACATGTGTGTGTATGTCTGCAC 59.192 45.455 0.00 0.00 37.14 4.57
133 134 1.282570 GCGTGGAACCACATGTGTG 59.717 57.895 23.79 17.05 46.47 3.82
139 140 0.180642 TGTAAAGGCGTGGAACCACA 59.819 50.000 21.41 0.66 46.47 4.17
175 176 1.000993 AGTGGTGGTTTTGGCACCA 59.999 52.632 0.00 0.00 45.13 4.17
198 199 9.739276 TGCTTGATCCTAAATATTAATACCAGG 57.261 33.333 0.00 5.13 0.00 4.45
347 362 7.959175 TGTAAAACAACATACTCCAGAGTAGT 58.041 34.615 12.72 8.35 45.94 2.73
348 363 8.873830 CATGTAAAACAACATACTCCAGAGTAG 58.126 37.037 12.72 7.82 45.94 2.57
349 364 8.590204 TCATGTAAAACAACATACTCCAGAGTA 58.410 33.333 9.84 9.84 46.68 2.59
350 365 7.450074 TCATGTAAAACAACATACTCCAGAGT 58.550 34.615 5.50 5.50 45.02 3.24
377 392 1.792993 CGCCGTTAACTCGTACTCCTG 60.793 57.143 3.71 0.00 0.00 3.86
386 401 0.110373 CCTTTGCACGCCGTTAACTC 60.110 55.000 3.71 0.00 0.00 3.01
415 430 2.220824 TCGAGAACGACAATGTTTGCAG 59.779 45.455 0.00 0.00 43.81 4.41
471 491 5.443185 AACGGCGTATGTCTTAAGCTATA 57.557 39.130 15.20 0.00 35.83 1.31
472 492 4.317671 AACGGCGTATGTCTTAAGCTAT 57.682 40.909 15.20 0.00 35.83 2.97
480 500 1.820519 TCTACCAAACGGCGTATGTCT 59.179 47.619 15.20 0.00 0.00 3.41
481 501 2.282701 TCTACCAAACGGCGTATGTC 57.717 50.000 15.20 0.00 0.00 3.06
504 524 5.695816 TCAGTTCAACATAAAAGCCAATTGC 59.304 36.000 0.00 0.00 41.71 3.56
512 532 6.371548 TCGAGGGAATCAGTTCAACATAAAAG 59.628 38.462 0.00 0.00 36.01 2.27
517 537 3.369892 CCTCGAGGGAATCAGTTCAACAT 60.370 47.826 24.62 0.00 36.01 2.71
596 643 1.732259 CCGATGAAACGAAAGGGTGAG 59.268 52.381 0.00 0.00 35.09 3.51
699 1046 3.003275 CACCGAATCTCTCAGCTCTACTC 59.997 52.174 0.00 0.00 0.00 2.59
700 1047 2.948979 CACCGAATCTCTCAGCTCTACT 59.051 50.000 0.00 0.00 0.00 2.57
702 1049 1.678627 GCACCGAATCTCTCAGCTCTA 59.321 52.381 0.00 0.00 0.00 2.43
703 1050 0.459489 GCACCGAATCTCTCAGCTCT 59.541 55.000 0.00 0.00 0.00 4.09
704 1051 0.529555 GGCACCGAATCTCTCAGCTC 60.530 60.000 0.00 0.00 0.00 4.09
705 1052 1.260538 TGGCACCGAATCTCTCAGCT 61.261 55.000 0.00 0.00 0.00 4.24
706 1053 0.391661 TTGGCACCGAATCTCTCAGC 60.392 55.000 0.00 0.00 0.00 4.26
707 1054 2.099141 TTTGGCACCGAATCTCTCAG 57.901 50.000 0.00 0.00 0.00 3.35
708 1055 2.749076 CAATTTGGCACCGAATCTCTCA 59.251 45.455 2.56 0.00 0.00 3.27
709 1056 2.098117 CCAATTTGGCACCGAATCTCTC 59.902 50.000 1.71 0.00 0.00 3.20
710 1057 2.094675 CCAATTTGGCACCGAATCTCT 58.905 47.619 1.71 0.00 0.00 3.10
711 1058 2.091541 TCCAATTTGGCACCGAATCTC 58.908 47.619 10.76 0.00 37.47 2.75
714 1061 1.923356 ACTCCAATTTGGCACCGAAT 58.077 45.000 10.76 0.00 37.47 3.34
725 1072 5.104109 TCGATCCTTCCCATTAACTCCAATT 60.104 40.000 0.00 0.00 0.00 2.32
735 1082 0.251916 TTGCGTCGATCCTTCCCATT 59.748 50.000 0.00 0.00 0.00 3.16
790 1147 3.367498 GCAGAGATTTATAGGGACGCGAT 60.367 47.826 15.93 0.00 0.00 4.58
796 1161 5.721225 AGAGGAAGCAGAGATTTATAGGGA 58.279 41.667 0.00 0.00 0.00 4.20
869 1241 1.533299 GTGTGTGTGTGTGTGTGTGAA 59.467 47.619 0.00 0.00 0.00 3.18
884 1256 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
885 1257 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
886 1258 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
887 1259 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
888 1260 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
889 1261 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
890 1262 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
891 1263 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
892 1264 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
893 1265 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
894 1266 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
895 1267 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
896 1268 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
897 1269 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
898 1270 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
899 1271 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
971 1346 3.873952 GACAATAGCTTTCGCTCCTGATT 59.126 43.478 0.00 0.00 45.15 2.57
1362 1761 4.733371 TCGATGGCGACGCTGCAA 62.733 61.111 20.77 3.65 42.51 4.08
1386 1785 4.166888 GGGATGCCGAGCTCTGCA 62.167 66.667 31.06 31.06 40.24 4.41
1484 1883 1.609783 CCCATTTCCCCGAAGCTCT 59.390 57.895 0.00 0.00 0.00 4.09
1827 2226 0.321671 TGCCAAAGGAGAGGAAGACG 59.678 55.000 0.00 0.00 0.00 4.18
2044 2443 2.514592 CGGCGCCCATGACTTCAT 60.515 61.111 23.46 0.00 36.96 2.57
2130 2529 1.220749 GCCTGCCATAACCGACTCA 59.779 57.895 0.00 0.00 0.00 3.41
2151 2550 2.185867 GGCCACGCTAACATCGGA 59.814 61.111 0.00 0.00 0.00 4.55
2245 2644 2.069165 GCCTCCACCACCTCCTTGTT 62.069 60.000 0.00 0.00 0.00 2.83
2330 2735 1.326213 CCTCATCACCGCCAGAGTCT 61.326 60.000 0.00 0.00 0.00 3.24
2355 2760 2.104170 CCCTCGAGTAGAGCCTCTTTT 58.896 52.381 12.31 0.00 45.54 2.27
2395 2800 4.394712 GTCCACCACCCTCGCCAG 62.395 72.222 0.00 0.00 0.00 4.85
2404 2809 2.358247 AATCCACGCGTCCACCAC 60.358 61.111 9.86 0.00 0.00 4.16
2464 2877 2.289072 ACATTGACTTCACCCTCACTCG 60.289 50.000 0.00 0.00 0.00 4.18
2465 2878 3.070018 CACATTGACTTCACCCTCACTC 58.930 50.000 0.00 0.00 0.00 3.51
2472 2885 6.970484 ACTAAAATCACACATTGACTTCACC 58.030 36.000 0.00 0.00 36.92 4.02
2576 2996 9.912634 TTGTTTTGATTGTCTTATGAGGAATTC 57.087 29.630 0.00 0.00 0.00 2.17
2610 3031 2.051334 TTGATTGTCTTATGGGCCCG 57.949 50.000 19.37 1.86 0.00 6.13
2614 3035 5.170748 GGCAAGTTTTGATTGTCTTATGGG 58.829 41.667 0.00 0.00 29.60 4.00
2615 3036 5.170748 GGGCAAGTTTTGATTGTCTTATGG 58.829 41.667 0.00 0.00 32.82 2.74
2618 3040 5.304101 ACATGGGCAAGTTTTGATTGTCTTA 59.696 36.000 0.00 0.00 32.82 2.10
2684 3107 3.425193 GCTCGAACAAACGCAAATTGATT 59.575 39.130 0.00 0.00 0.00 2.57
2702 3125 2.335712 GGCCCTTTGGAGTTGCTCG 61.336 63.158 0.00 0.00 0.00 5.03
2733 3156 1.664649 CTCAAACAGACGCAGGCGA 60.665 57.895 21.62 0.00 42.83 5.54
2744 3167 1.659335 GTCCGCGTCGACTCAAACA 60.659 57.895 14.70 0.00 0.00 2.83
2750 3173 1.066918 ACTTTTGTCCGCGTCGACT 59.933 52.632 14.70 0.00 33.70 4.18
2755 3178 3.645975 CGCCACTTTTGTCCGCGT 61.646 61.111 4.92 0.00 40.96 6.01
3002 3425 0.167251 CGCACGGTCGGCTTAAAAAT 59.833 50.000 0.00 0.00 0.00 1.82
3060 3483 0.537188 GACGAGGGAGCAAAGGATGA 59.463 55.000 0.00 0.00 0.00 2.92
3087 3510 1.303317 GGTTGTGGTGGCTAGGGTG 60.303 63.158 0.00 0.00 0.00 4.61
3279 3702 7.635309 GCCACTAATTAGCCTTTTCCTAGTAGT 60.635 40.741 12.54 0.00 0.00 2.73
3280 3703 6.706716 GCCACTAATTAGCCTTTTCCTAGTAG 59.293 42.308 12.54 0.00 0.00 2.57
3281 3704 6.157297 TGCCACTAATTAGCCTTTTCCTAGTA 59.843 38.462 12.54 0.00 0.00 1.82
3282 3705 5.045140 TGCCACTAATTAGCCTTTTCCTAGT 60.045 40.000 12.54 0.00 0.00 2.57
3283 3706 5.297029 GTGCCACTAATTAGCCTTTTCCTAG 59.703 44.000 12.54 0.00 0.00 3.02
3284 3707 5.190677 GTGCCACTAATTAGCCTTTTCCTA 58.809 41.667 12.54 0.00 0.00 2.94
3285 3708 4.017126 GTGCCACTAATTAGCCTTTTCCT 58.983 43.478 12.54 0.00 0.00 3.36
3286 3709 3.761752 TGTGCCACTAATTAGCCTTTTCC 59.238 43.478 12.54 0.00 0.00 3.13
3287 3710 4.380550 GGTGTGCCACTAATTAGCCTTTTC 60.381 45.833 12.54 0.73 34.40 2.29
3288 3711 3.509967 GGTGTGCCACTAATTAGCCTTTT 59.490 43.478 12.54 0.00 34.40 2.27
3289 3712 3.089284 GGTGTGCCACTAATTAGCCTTT 58.911 45.455 12.54 0.00 34.40 3.11
3290 3713 2.308866 AGGTGTGCCACTAATTAGCCTT 59.691 45.455 12.54 0.00 37.19 4.35
3291 3714 1.916181 AGGTGTGCCACTAATTAGCCT 59.084 47.619 12.54 6.12 37.19 4.58
3292 3715 2.017049 CAGGTGTGCCACTAATTAGCC 58.983 52.381 12.54 3.90 37.19 3.93
3293 3716 2.711542 ACAGGTGTGCCACTAATTAGC 58.288 47.619 12.54 0.26 37.19 3.09
3294 3717 5.460646 CAAAACAGGTGTGCCACTAATTAG 58.539 41.667 11.05 11.05 37.19 1.73
3295 3718 4.279671 CCAAAACAGGTGTGCCACTAATTA 59.720 41.667 0.00 0.00 37.19 1.40
3296 3719 3.069443 CCAAAACAGGTGTGCCACTAATT 59.931 43.478 0.00 0.00 37.19 1.40
3297 3720 2.627699 CCAAAACAGGTGTGCCACTAAT 59.372 45.455 0.00 0.00 37.19 1.73
3298 3721 2.028130 CCAAAACAGGTGTGCCACTAA 58.972 47.619 0.00 0.00 37.19 2.24
3299 3722 1.686355 CCAAAACAGGTGTGCCACTA 58.314 50.000 0.00 0.00 37.19 2.74
3300 3723 1.675720 GCCAAAACAGGTGTGCCACT 61.676 55.000 0.00 0.00 37.19 4.00
3301 3724 1.227234 GCCAAAACAGGTGTGCCAC 60.227 57.895 0.00 0.00 37.19 5.01
3302 3725 2.430610 GGCCAAAACAGGTGTGCCA 61.431 57.895 0.00 0.00 38.73 4.92
3303 3726 1.757423 ATGGCCAAAACAGGTGTGCC 61.757 55.000 10.96 2.91 39.33 5.01
3304 3727 0.106521 AATGGCCAAAACAGGTGTGC 59.893 50.000 10.96 0.00 0.00 4.57
3305 3728 3.742433 TTAATGGCCAAAACAGGTGTG 57.258 42.857 10.96 0.00 0.00 3.82
3306 3729 3.007831 CCATTAATGGCCAAAACAGGTGT 59.992 43.478 21.32 0.00 41.75 4.16
3307 3730 3.598299 CCATTAATGGCCAAAACAGGTG 58.402 45.455 21.32 2.58 41.75 4.00
3308 3731 3.979101 CCATTAATGGCCAAAACAGGT 57.021 42.857 21.32 0.00 41.75 4.00
3319 3742 5.085904 CACCTGTAGTGCGCCATTAATGG 62.086 52.174 27.35 27.35 44.70 3.16
3320 3743 2.032054 CACCTGTAGTGCGCCATTAATG 59.968 50.000 4.18 8.58 40.28 1.90
3321 3744 2.288666 CACCTGTAGTGCGCCATTAAT 58.711 47.619 4.18 0.00 40.28 1.40
3322 3745 1.732941 CACCTGTAGTGCGCCATTAA 58.267 50.000 4.18 0.00 40.28 1.40
3323 3746 3.451793 CACCTGTAGTGCGCCATTA 57.548 52.632 4.18 0.00 40.28 1.90
3324 3747 4.301505 CACCTGTAGTGCGCCATT 57.698 55.556 4.18 0.00 40.28 3.16
3332 3755 0.460311 GATAGTGGCGCACCTGTAGT 59.540 55.000 10.83 0.00 34.49 2.73
3333 3756 0.459899 TGATAGTGGCGCACCTGTAG 59.540 55.000 10.83 0.00 34.49 2.74
3334 3757 1.068588 GATGATAGTGGCGCACCTGTA 59.931 52.381 10.83 0.00 34.49 2.74
3335 3758 0.179073 GATGATAGTGGCGCACCTGT 60.179 55.000 10.83 1.42 34.49 4.00
3336 3759 0.179076 TGATGATAGTGGCGCACCTG 60.179 55.000 10.83 0.00 34.49 4.00
3337 3760 0.179073 GTGATGATAGTGGCGCACCT 60.179 55.000 10.83 6.50 34.49 4.00
3338 3761 1.490693 CGTGATGATAGTGGCGCACC 61.491 60.000 10.83 0.00 34.49 5.01
3339 3762 1.927210 CGTGATGATAGTGGCGCAC 59.073 57.895 10.83 5.73 34.10 5.34
3340 3763 1.882625 GCGTGATGATAGTGGCGCA 60.883 57.895 10.83 0.00 43.62 6.09
3341 3764 2.598632 GGCGTGATGATAGTGGCGC 61.599 63.158 0.00 0.00 43.46 6.53
3342 3765 1.227234 TGGCGTGATGATAGTGGCG 60.227 57.895 0.00 0.00 0.00 5.69
3343 3766 0.179073 AGTGGCGTGATGATAGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
3344 3767 2.362397 ACTAGTGGCGTGATGATAGTGG 59.638 50.000 0.00 0.00 0.00 4.00
3345 3768 3.717400 ACTAGTGGCGTGATGATAGTG 57.283 47.619 0.00 0.00 0.00 2.74
3346 3769 4.888239 AGTTACTAGTGGCGTGATGATAGT 59.112 41.667 5.39 0.00 0.00 2.12
3347 3770 5.440234 AGTTACTAGTGGCGTGATGATAG 57.560 43.478 5.39 0.00 0.00 2.08
3348 3771 6.947644 TTAGTTACTAGTGGCGTGATGATA 57.052 37.500 5.39 0.00 0.00 2.15
3349 3772 5.847111 TTAGTTACTAGTGGCGTGATGAT 57.153 39.130 5.39 0.00 0.00 2.45
3350 3773 5.847111 ATTAGTTACTAGTGGCGTGATGA 57.153 39.130 5.39 0.00 0.00 2.92
3351 3774 6.736123 AGTATTAGTTACTAGTGGCGTGATG 58.264 40.000 5.39 0.00 39.44 3.07
3352 3775 6.956202 AGTATTAGTTACTAGTGGCGTGAT 57.044 37.500 5.39 0.00 39.44 3.06
3353 3776 7.864108 TTAGTATTAGTTACTAGTGGCGTGA 57.136 36.000 5.39 0.00 42.83 4.35
3354 3777 8.503486 CATTAGTATTAGTTACTAGTGGCGTG 57.497 38.462 5.39 0.00 42.82 5.34
3359 3782 7.114529 GTGCGCCATTAGTATTAGTTACTAGTG 59.885 40.741 4.18 7.81 44.61 2.74
3360 3783 7.144000 GTGCGCCATTAGTATTAGTTACTAGT 58.856 38.462 4.18 0.00 42.83 2.57
3361 3784 6.585322 GGTGCGCCATTAGTATTAGTTACTAG 59.415 42.308 12.58 0.00 38.35 2.57
3362 3785 6.449698 GGTGCGCCATTAGTATTAGTTACTA 58.550 40.000 12.58 0.00 37.25 1.82
3363 3786 5.295152 GGTGCGCCATTAGTATTAGTTACT 58.705 41.667 12.58 0.00 38.53 2.24
3364 3787 4.149396 CGGTGCGCCATTAGTATTAGTTAC 59.851 45.833 18.18 0.00 34.09 2.50
3365 3788 4.202141 ACGGTGCGCCATTAGTATTAGTTA 60.202 41.667 18.18 0.00 34.09 2.24
3366 3789 3.128349 CGGTGCGCCATTAGTATTAGTT 58.872 45.455 18.18 0.00 34.09 2.24
3367 3790 2.101917 ACGGTGCGCCATTAGTATTAGT 59.898 45.455 18.18 0.00 34.09 2.24
3368 3791 2.750948 ACGGTGCGCCATTAGTATTAG 58.249 47.619 18.18 0.00 34.09 1.73
3369 3792 2.894763 ACGGTGCGCCATTAGTATTA 57.105 45.000 18.18 0.00 34.09 0.98
3370 3793 2.894763 TACGGTGCGCCATTAGTATT 57.105 45.000 18.18 0.00 34.09 1.89
3371 3794 3.367703 GGTATACGGTGCGCCATTAGTAT 60.368 47.826 18.18 16.74 34.09 2.12
3372 3795 2.030007 GGTATACGGTGCGCCATTAGTA 60.030 50.000 18.18 10.56 34.09 1.82
3373 3796 1.269936 GGTATACGGTGCGCCATTAGT 60.270 52.381 18.18 8.48 34.09 2.24
3374 3797 1.269883 TGGTATACGGTGCGCCATTAG 60.270 52.381 18.18 1.79 34.09 1.73
3375 3798 0.751452 TGGTATACGGTGCGCCATTA 59.249 50.000 18.18 7.11 34.09 1.90
3376 3799 0.531974 CTGGTATACGGTGCGCCATT 60.532 55.000 18.18 4.74 34.09 3.16
3377 3800 1.069090 CTGGTATACGGTGCGCCAT 59.931 57.895 18.18 2.70 34.09 4.40
3378 3801 2.053277 TCTGGTATACGGTGCGCCA 61.053 57.895 18.18 0.00 34.09 5.69
3379 3802 1.590792 GTCTGGTATACGGTGCGCC 60.591 63.158 6.11 6.11 0.00 6.53
3380 3803 0.458889 TTGTCTGGTATACGGTGCGC 60.459 55.000 0.00 0.00 0.00 6.09
3381 3804 2.218953 ATTGTCTGGTATACGGTGCG 57.781 50.000 0.00 0.00 0.00 5.34
3382 3805 4.049186 CACTATTGTCTGGTATACGGTGC 58.951 47.826 0.00 0.00 0.00 5.01
3383 3806 4.617959 CCACTATTGTCTGGTATACGGTG 58.382 47.826 0.00 0.00 0.00 4.94
3384 3807 3.069158 GCCACTATTGTCTGGTATACGGT 59.931 47.826 0.00 0.00 0.00 4.83
3385 3808 3.650139 GCCACTATTGTCTGGTATACGG 58.350 50.000 0.00 0.00 0.00 4.02
3386 3809 3.305964 CGCCACTATTGTCTGGTATACG 58.694 50.000 0.00 0.00 0.00 3.06
3387 3810 3.057734 GCGCCACTATTGTCTGGTATAC 58.942 50.000 0.00 0.00 0.00 1.47
3388 3811 2.696187 TGCGCCACTATTGTCTGGTATA 59.304 45.455 4.18 0.00 0.00 1.47
3389 3812 1.484653 TGCGCCACTATTGTCTGGTAT 59.515 47.619 4.18 0.00 0.00 2.73
3390 3813 0.899019 TGCGCCACTATTGTCTGGTA 59.101 50.000 4.18 0.00 0.00 3.25
3391 3814 0.673644 GTGCGCCACTATTGTCTGGT 60.674 55.000 4.18 0.00 0.00 4.00
3392 3815 1.369091 GGTGCGCCACTATTGTCTGG 61.369 60.000 12.58 0.00 34.40 3.86
3393 3816 0.673333 TGGTGCGCCACTATTGTCTG 60.673 55.000 16.89 0.00 40.46 3.51
3394 3817 0.391661 CTGGTGCGCCACTATTGTCT 60.392 55.000 16.89 0.00 40.46 3.41
3395 3818 1.369091 CCTGGTGCGCCACTATTGTC 61.369 60.000 16.89 0.00 40.46 3.18
3396 3819 1.377202 CCTGGTGCGCCACTATTGT 60.377 57.895 16.89 0.00 40.46 2.71
3397 3820 2.114670 CCCTGGTGCGCCACTATTG 61.115 63.158 16.89 5.06 40.46 1.90
3398 3821 2.257409 CTCCCTGGTGCGCCACTATT 62.257 60.000 16.89 0.00 40.46 1.73
3399 3822 2.687200 TCCCTGGTGCGCCACTAT 60.687 61.111 16.89 0.00 40.46 2.12
3400 3823 3.390521 CTCCCTGGTGCGCCACTA 61.391 66.667 16.89 2.40 40.46 2.74
3408 3831 2.535485 TAATGGCGCACTCCCTGGTG 62.535 60.000 10.83 0.00 39.91 4.17
3409 3832 2.257409 CTAATGGCGCACTCCCTGGT 62.257 60.000 10.83 0.00 0.00 4.00
3410 3833 1.524621 CTAATGGCGCACTCCCTGG 60.525 63.158 10.83 0.00 0.00 4.45
3411 3834 0.464036 TACTAATGGCGCACTCCCTG 59.536 55.000 10.83 0.00 0.00 4.45
3412 3835 2.910579 TACTAATGGCGCACTCCCT 58.089 52.632 10.83 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.