Multiple sequence alignment - TraesCS6D01G398900

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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 TraesCS6D01G398900 chr6D 100.000 3365 0 0 1 3365 469814092 469810728 0.000000e+00 6215.0
1 TraesCS6D01G398900 chr6D 90.187 907 85 4 2461 3365 469917948 469918852 0.000000e+00 1179.0
2 TraesCS6D01G398900 chr6D 88.060 201 23 1 658 857 456453760 456453560 1.560000e-58 237.0
3 TraesCS6D01G398900 chr6D 83.628 226 33 4 648 872 436237878 436238100 3.400000e-50 209.0
4 TraesCS6D01G398900 chr6D 83.077 195 24 5 2151 2343 469917355 469917542 5.770000e-38 169.0
5 TraesCS6D01G398900 chr6A 87.583 1498 153 21 987 2468 614678409 614676929 0.000000e+00 1705.0
6 TraesCS6D01G398900 chr6A 86.724 1514 161 13 965 2467 614795202 614793718 0.000000e+00 1646.0
7 TraesCS6D01G398900 chr6A 90.055 905 90 0 2461 3365 614676118 614675214 0.000000e+00 1173.0
8 TraesCS6D01G398900 chr6A 86.347 813 108 1 1005 1814 614697827 614697015 0.000000e+00 883.0
9 TraesCS6D01G398900 chr6A 86.389 529 61 5 873 1399 614704987 614704468 4.870000e-158 568.0
10 TraesCS6D01G398900 chr6A 87.288 118 14 1 757 874 603179836 603179720 2.110000e-27 134.0
11 TraesCS6D01G398900 chrUn 89.915 1170 105 5 873 2042 75076808 75075652 0.000000e+00 1495.0
12 TraesCS6D01G398900 chrUn 91.050 905 81 0 2461 3365 325009657 325008753 0.000000e+00 1223.0
13 TraesCS6D01G398900 chrUn 90.177 906 87 2 2461 3365 307483832 307484736 0.000000e+00 1179.0
14 TraesCS6D01G398900 chrUn 83.293 1251 177 26 981 2218 62146627 62147858 0.000000e+00 1123.0
15 TraesCS6D01G398900 chrUn 88.479 894 101 2 2461 3353 62149201 62150093 0.000000e+00 1079.0
16 TraesCS6D01G398900 chrUn 82.869 1004 150 15 981 1978 331544464 331545451 0.000000e+00 881.0
17 TraesCS6D01G398900 chrUn 86.029 816 111 1 1002 1814 305405291 305406106 0.000000e+00 872.0
18 TraesCS6D01G398900 chrUn 89.541 392 33 3 2078 2467 75075653 75075268 1.080000e-134 490.0
19 TraesCS6D01G398900 chrUn 80.243 658 62 36 2 606 75077459 75076817 1.850000e-117 433.0
20 TraesCS6D01G398900 chrUn 82.990 194 25 4 2144 2335 331545461 331545648 5.770000e-38 169.0
21 TraesCS6D01G398900 chr6B 93.591 905 58 0 2461 3365 716107238 716106334 0.000000e+00 1351.0
22 TraesCS6D01G398900 chr6B 86.289 1218 140 15 1005 2216 715817188 715815992 0.000000e+00 1299.0
23 TraesCS6D01G398900 chr6B 92.102 899 71 0 2467 3365 715813467 715812569 0.000000e+00 1267.0
24 TraesCS6D01G398900 chr6B 82.913 1387 186 31 981 2343 716109954 716108595 0.000000e+00 1201.0
25 TraesCS6D01G398900 chr6B 89.834 905 90 2 2461 3365 648359669 648360571 0.000000e+00 1160.0
26 TraesCS6D01G398900 chr6B 88.631 906 98 5 2461 3365 715860464 715859563 0.000000e+00 1098.0
27 TraesCS6D01G398900 chr6B 84.535 860 130 2 1005 1861 715980264 715979405 0.000000e+00 848.0
28 TraesCS6D01G398900 chr6B 80.928 194 29 4 2144 2335 715770855 715770668 2.710000e-31 147.0
29 TraesCS6D01G398900 chr6B 84.615 65 9 1 2254 2317 715814443 715814379 2.800000e-06 63.9
30 TraesCS6D01G398900 chr3B 88.034 234 23 5 648 878 143663787 143664018 4.280000e-69 272.0
31 TraesCS6D01G398900 chr3A 87.671 219 26 1 657 874 681520247 681520465 1.550000e-63 254.0
32 TraesCS6D01G398900 chr2D 91.803 183 13 2 651 833 425475213 425475393 1.550000e-63 254.0
33 TraesCS6D01G398900 chr3D 84.141 227 33 3 648 873 544442635 544442859 2.030000e-52 217.0
34 TraesCS6D01G398900 chr7B 87.879 132 16 0 746 877 13309286 13309155 4.500000e-34 156.0
35 TraesCS6D01G398900 chr4D 93.671 79 4 1 794 872 8988924 8988847 2.120000e-22 117.0


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 TraesCS6D01G398900 chr6D 469810728 469814092 3364 True 6215.000000 6215 100.000000 1 3365 1 chr6D.!!$R2 3364
1 TraesCS6D01G398900 chr6D 469917355 469918852 1497 False 674.000000 1179 86.632000 2151 3365 2 chr6D.!!$F2 1214
2 TraesCS6D01G398900 chr6A 614793718 614795202 1484 True 1646.000000 1646 86.724000 965 2467 1 chr6A.!!$R4 1502
3 TraesCS6D01G398900 chr6A 614675214 614678409 3195 True 1439.000000 1705 88.819000 987 3365 2 chr6A.!!$R5 2378
4 TraesCS6D01G398900 chr6A 614697015 614697827 812 True 883.000000 883 86.347000 1005 1814 1 chr6A.!!$R2 809
5 TraesCS6D01G398900 chr6A 614704468 614704987 519 True 568.000000 568 86.389000 873 1399 1 chr6A.!!$R3 526
6 TraesCS6D01G398900 chrUn 325008753 325009657 904 True 1223.000000 1223 91.050000 2461 3365 1 chrUn.!!$R1 904
7 TraesCS6D01G398900 chrUn 307483832 307484736 904 False 1179.000000 1179 90.177000 2461 3365 1 chrUn.!!$F2 904
8 TraesCS6D01G398900 chrUn 62146627 62150093 3466 False 1101.000000 1123 85.886000 981 3353 2 chrUn.!!$F3 2372
9 TraesCS6D01G398900 chrUn 305405291 305406106 815 False 872.000000 872 86.029000 1002 1814 1 chrUn.!!$F1 812
10 TraesCS6D01G398900 chrUn 75075268 75077459 2191 True 806.000000 1495 86.566333 2 2467 3 chrUn.!!$R2 2465
11 TraesCS6D01G398900 chrUn 331544464 331545648 1184 False 525.000000 881 82.929500 981 2335 2 chrUn.!!$F4 1354
12 TraesCS6D01G398900 chr6B 716106334 716109954 3620 True 1276.000000 1351 88.252000 981 3365 2 chr6B.!!$R5 2384
13 TraesCS6D01G398900 chr6B 648359669 648360571 902 False 1160.000000 1160 89.834000 2461 3365 1 chr6B.!!$F1 904
14 TraesCS6D01G398900 chr6B 715859563 715860464 901 True 1098.000000 1098 88.631000 2461 3365 1 chr6B.!!$R2 904
15 TraesCS6D01G398900 chr6B 715812569 715817188 4619 True 876.633333 1299 87.668667 1005 3365 3 chr6B.!!$R4 2360
16 TraesCS6D01G398900 chr6B 715979405 715980264 859 True 848.000000 848 84.535000 1005 1861 1 chr6B.!!$R3 856

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
567 639 0.034059 CATCCTCCTCGTATGCCACC 59.966 60.0 0.0 0.0 0.0 4.61 F
806 879 0.105593 GCTGCCCATTCGATCTCAGA 59.894 55.0 0.0 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2323 0.678950 AAAATGGAGTGTTTGGGCCG 59.321 50.0 0.0 0.0 0.00 6.13 R
2569 5662 0.693622 TCGCCAAAGGTAACCCATGA 59.306 50.0 0.0 0.0 37.17 3.07 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 1.528129 CTGTCTTGGCCACTTCCTTC 58.472 55.000 3.88 0.00 0.00 3.46
27 28 0.957888 GGCCACTTCCTTCTGTCAGC 60.958 60.000 0.00 0.00 0.00 4.26
28 29 0.250467 GCCACTTCCTTCTGTCAGCA 60.250 55.000 0.00 0.00 0.00 4.41
72 80 2.373540 AGGATTAGTGTTAACGCGCA 57.626 45.000 5.73 4.79 0.00 6.09
75 83 2.033151 GGATTAGTGTTAACGCGCATCC 60.033 50.000 24.85 24.85 34.77 3.51
76 84 1.361793 TTAGTGTTAACGCGCATCCC 58.638 50.000 5.73 0.00 0.00 3.85
83 91 2.025589 TAACGCGCATCCCATGTTAA 57.974 45.000 5.73 0.00 0.00 2.01
111 119 6.924111 ACTAGCCAATAATTTCACAACTTGG 58.076 36.000 0.00 0.00 36.94 3.61
113 121 5.540911 AGCCAATAATTTCACAACTTGGTG 58.459 37.500 0.00 0.00 40.16 4.17
116 124 6.586082 GCCAATAATTTCACAACTTGGTGTAG 59.414 38.462 0.00 0.00 39.76 2.74
148 163 0.381801 AAAGCAACAGCGTGTGAAGG 59.618 50.000 0.00 0.00 0.00 3.46
162 177 5.670341 GCGTGTGAAGGTATAACAATGACAC 60.670 44.000 6.34 6.34 0.00 3.67
163 178 5.407084 CGTGTGAAGGTATAACAATGACACA 59.593 40.000 13.71 8.45 32.54 3.72
164 179 6.092122 CGTGTGAAGGTATAACAATGACACAT 59.908 38.462 13.71 0.00 37.87 3.21
165 180 7.464358 GTGTGAAGGTATAACAATGACACATC 58.536 38.462 10.11 0.00 37.87 3.06
167 182 7.882791 TGTGAAGGTATAACAATGACACATCTT 59.117 33.333 0.00 0.00 32.23 2.40
168 183 8.730680 GTGAAGGTATAACAATGACACATCTTT 58.269 33.333 0.00 0.00 0.00 2.52
170 185 7.630242 AGGTATAACAATGACACATCTTTGG 57.370 36.000 7.55 0.00 41.89 3.28
171 186 7.402054 AGGTATAACAATGACACATCTTTGGA 58.598 34.615 7.55 0.00 41.89 3.53
172 187 7.888021 AGGTATAACAATGACACATCTTTGGAA 59.112 33.333 7.55 0.00 41.89 3.53
173 188 7.968405 GGTATAACAATGACACATCTTTGGAAC 59.032 37.037 7.55 1.73 41.89 3.62
192 208 1.133792 ACTATTAAGCAGGCGGGCATT 60.134 47.619 3.78 0.00 35.83 3.56
197 213 1.598701 AAGCAGGCGGGCATTCTTTC 61.599 55.000 3.78 0.00 35.83 2.62
221 264 1.131504 CCCTTCTCGTCTCTTCTCACG 59.868 57.143 0.00 0.00 37.36 4.35
222 265 1.466697 CCTTCTCGTCTCTTCTCACGC 60.467 57.143 0.00 0.00 35.93 5.34
223 266 1.197949 CTTCTCGTCTCTTCTCACGCA 59.802 52.381 0.00 0.00 35.93 5.24
224 267 1.454201 TCTCGTCTCTTCTCACGCAT 58.546 50.000 0.00 0.00 35.93 4.73
225 268 1.398739 TCTCGTCTCTTCTCACGCATC 59.601 52.381 0.00 0.00 35.93 3.91
229 272 2.159448 CGTCTCTTCTCACGCATCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
230 273 3.178267 GTCTCTTCTCACGCATCTTCTG 58.822 50.000 0.00 0.00 0.00 3.02
232 275 1.895798 TCTTCTCACGCATCTTCTGGT 59.104 47.619 0.00 0.00 0.00 4.00
233 276 2.094494 TCTTCTCACGCATCTTCTGGTC 60.094 50.000 0.00 0.00 0.00 4.02
234 277 1.550327 TCTCACGCATCTTCTGGTCT 58.450 50.000 0.00 0.00 0.00 3.85
235 278 1.895798 TCTCACGCATCTTCTGGTCTT 59.104 47.619 0.00 0.00 0.00 3.01
236 279 1.998315 CTCACGCATCTTCTGGTCTTG 59.002 52.381 0.00 0.00 0.00 3.02
237 280 0.445436 CACGCATCTTCTGGTCTTGC 59.555 55.000 0.00 0.00 0.00 4.01
239 282 2.093216 GCATCTTCTGGTCTTGCGG 58.907 57.895 0.00 0.00 0.00 5.69
240 283 0.674895 GCATCTTCTGGTCTTGCGGT 60.675 55.000 0.00 0.00 0.00 5.68
241 284 1.081892 CATCTTCTGGTCTTGCGGTG 58.918 55.000 0.00 0.00 0.00 4.94
242 285 0.674895 ATCTTCTGGTCTTGCGGTGC 60.675 55.000 0.00 0.00 0.00 5.01
243 286 1.597854 CTTCTGGTCTTGCGGTGCA 60.598 57.895 0.00 0.00 36.47 4.57
244 287 1.845809 CTTCTGGTCTTGCGGTGCAC 61.846 60.000 8.80 8.80 38.71 4.57
245 288 2.591429 CTGGTCTTGCGGTGCACA 60.591 61.111 20.43 0.00 38.71 4.57
246 289 2.896801 CTGGTCTTGCGGTGCACAC 61.897 63.158 20.43 10.78 38.71 3.82
247 290 4.012895 GGTCTTGCGGTGCACACG 62.013 66.667 20.43 19.79 38.71 4.49
297 340 0.322546 CAAGGTGCCTGGGTTACTCC 60.323 60.000 0.00 0.00 0.00 3.85
324 367 3.633418 GGATCCATCCGCTAGGTATACT 58.367 50.000 6.95 0.00 37.19 2.12
325 368 4.024670 GGATCCATCCGCTAGGTATACTT 58.975 47.826 6.95 0.00 37.19 2.24
326 369 4.142138 GGATCCATCCGCTAGGTATACTTG 60.142 50.000 6.95 0.00 37.19 3.16
338 381 4.978099 AGGTATACTTGCATCTCCCATTG 58.022 43.478 2.25 0.00 0.00 2.82
340 383 2.057137 TACTTGCATCTCCCATTGCC 57.943 50.000 0.00 0.00 38.08 4.52
390 454 0.387622 CTTGTTCGGTGCAGCAATGG 60.388 55.000 17.33 0.00 0.00 3.16
403 467 3.736126 GCAGCAATGGTTGGCTTTATCTC 60.736 47.826 0.00 0.00 38.56 2.75
418 482 7.007116 GGCTTTATCTCCTTTAATCCATCCTT 58.993 38.462 0.00 0.00 0.00 3.36
439 508 4.301072 TTTTCCAGGGTTTCAGATCGAT 57.699 40.909 0.00 0.00 0.00 3.59
487 556 6.758416 TGATTCAGATCAGTTAATCCGTTCTG 59.242 38.462 0.00 0.00 37.37 3.02
492 561 5.875359 AGATCAGTTAATCCGTTCTGTTTCC 59.125 40.000 0.00 0.00 0.00 3.13
502 571 2.553086 GTTCTGTTTCCGTGTACACCA 58.447 47.619 20.11 10.62 0.00 4.17
529 598 1.711206 GTTGGTCCGACTCTGCTAAC 58.289 55.000 1.48 0.00 0.00 2.34
530 599 0.606604 TTGGTCCGACTCTGCTAACC 59.393 55.000 0.00 0.00 0.00 2.85
537 609 2.520979 CGACTCTGCTAACCGAGAAAG 58.479 52.381 0.00 0.00 0.00 2.62
552 624 3.475575 GAGAAAGATCCAGCTTCCATCC 58.524 50.000 0.00 0.00 0.00 3.51
567 639 0.034059 CATCCTCCTCGTATGCCACC 59.966 60.000 0.00 0.00 0.00 4.61
571 643 4.910585 CCTCGTATGCCACCGCCC 62.911 72.222 0.00 0.00 0.00 6.13
596 669 1.798223 GCACAGTGTCGATTTGTAGCA 59.202 47.619 1.61 0.00 0.00 3.49
606 679 4.554973 GTCGATTTGTAGCATTTTCAGTGC 59.445 41.667 0.00 0.00 42.81 4.40
617 690 6.238610 GCATTTTCAGTGCTGGATATCTAG 57.761 41.667 11.56 11.56 39.45 2.43
618 691 5.762218 GCATTTTCAGTGCTGGATATCTAGT 59.238 40.000 16.53 0.00 39.45 2.57
619 692 6.293298 GCATTTTCAGTGCTGGATATCTAGTG 60.293 42.308 16.53 8.11 39.45 2.74
620 693 6.544928 TTTTCAGTGCTGGATATCTAGTGA 57.455 37.500 16.53 10.13 0.00 3.41
621 694 6.544928 TTTCAGTGCTGGATATCTAGTGAA 57.455 37.500 16.53 14.73 0.00 3.18
622 695 6.737720 TTCAGTGCTGGATATCTAGTGAAT 57.262 37.500 16.53 1.89 0.00 2.57
623 696 6.094193 TCAGTGCTGGATATCTAGTGAATG 57.906 41.667 16.53 12.68 0.00 2.67
624 697 5.011431 TCAGTGCTGGATATCTAGTGAATGG 59.989 44.000 16.53 3.84 0.00 3.16
625 698 4.904251 AGTGCTGGATATCTAGTGAATGGT 59.096 41.667 16.53 0.00 0.00 3.55
626 699 5.011533 AGTGCTGGATATCTAGTGAATGGTC 59.988 44.000 16.53 0.00 0.00 4.02
627 700 4.284490 TGCTGGATATCTAGTGAATGGTCC 59.716 45.833 16.53 0.00 0.00 4.46
628 701 4.284490 GCTGGATATCTAGTGAATGGTCCA 59.716 45.833 16.53 0.00 33.77 4.02
629 702 5.221722 GCTGGATATCTAGTGAATGGTCCAA 60.222 44.000 16.53 0.00 34.42 3.53
630 703 6.688922 GCTGGATATCTAGTGAATGGTCCAAA 60.689 42.308 16.53 0.00 34.42 3.28
631 704 7.206789 TGGATATCTAGTGAATGGTCCAAAA 57.793 36.000 2.05 0.00 32.02 2.44
632 705 7.638444 TGGATATCTAGTGAATGGTCCAAAAA 58.362 34.615 2.05 0.00 32.02 1.94
633 706 8.281531 TGGATATCTAGTGAATGGTCCAAAAAT 58.718 33.333 2.05 0.00 32.02 1.82
634 707 8.787852 GGATATCTAGTGAATGGTCCAAAAATC 58.212 37.037 2.05 0.00 0.00 2.17
635 708 8.697507 ATATCTAGTGAATGGTCCAAAAATCC 57.302 34.615 0.00 0.00 0.00 3.01
636 709 4.941263 TCTAGTGAATGGTCCAAAAATCCG 59.059 41.667 0.00 0.00 0.00 4.18
637 710 3.761897 AGTGAATGGTCCAAAAATCCGA 58.238 40.909 0.00 0.00 0.00 4.55
638 711 4.148838 AGTGAATGGTCCAAAAATCCGAA 58.851 39.130 0.00 0.00 0.00 4.30
639 712 4.586841 AGTGAATGGTCCAAAAATCCGAAA 59.413 37.500 0.00 0.00 0.00 3.46
640 713 5.069781 AGTGAATGGTCCAAAAATCCGAAAA 59.930 36.000 0.00 0.00 0.00 2.29
641 714 5.755861 GTGAATGGTCCAAAAATCCGAAAAA 59.244 36.000 0.00 0.00 0.00 1.94
663 736 5.859205 AAATTCTGGATGTTAGCAATCCC 57.141 39.130 0.18 0.00 33.65 3.85
664 737 4.803329 ATTCTGGATGTTAGCAATCCCT 57.197 40.909 0.18 0.00 33.65 4.20
665 738 5.912149 ATTCTGGATGTTAGCAATCCCTA 57.088 39.130 0.18 0.00 33.65 3.53
666 739 5.708736 TTCTGGATGTTAGCAATCCCTAA 57.291 39.130 0.18 0.00 33.65 2.69
667 740 5.708736 TCTGGATGTTAGCAATCCCTAAA 57.291 39.130 0.18 0.00 33.65 1.85
668 741 6.073447 TCTGGATGTTAGCAATCCCTAAAA 57.927 37.500 0.18 0.00 33.65 1.52
669 742 6.489603 TCTGGATGTTAGCAATCCCTAAAAA 58.510 36.000 0.18 0.00 33.65 1.94
731 804 8.441312 AAAAAGACAAATCTTGCATGAATGTT 57.559 26.923 18.96 7.79 44.82 2.71
732 805 8.441312 AAAAGACAAATCTTGCATGAATGTTT 57.559 26.923 18.96 13.68 44.82 2.83
733 806 8.441312 AAAGACAAATCTTGCATGAATGTTTT 57.559 26.923 18.96 17.15 44.82 2.43
734 807 7.416154 AGACAAATCTTGCATGAATGTTTTG 57.584 32.000 18.96 18.43 0.00 2.44
735 808 5.992729 ACAAATCTTGCATGAATGTTTTGC 58.007 33.333 18.82 0.00 36.91 3.68
736 809 5.527951 ACAAATCTTGCATGAATGTTTTGCA 59.472 32.000 18.82 0.00 44.12 4.08
737 810 5.856126 AATCTTGCATGAATGTTTTGCAG 57.144 34.783 6.36 0.00 46.10 4.41
738 811 4.587584 TCTTGCATGAATGTTTTGCAGA 57.412 36.364 0.00 0.00 46.10 4.26
739 812 4.946445 TCTTGCATGAATGTTTTGCAGAA 58.054 34.783 0.00 0.00 46.10 3.02
740 813 5.358090 TCTTGCATGAATGTTTTGCAGAAA 58.642 33.333 0.00 0.00 46.10 2.52
741 814 5.816258 TCTTGCATGAATGTTTTGCAGAAAA 59.184 32.000 0.00 0.00 46.10 2.29
748 821 2.700722 GTTTTGCAGAAAACCCCCAA 57.299 45.000 3.08 0.00 43.54 4.12
749 822 2.992593 GTTTTGCAGAAAACCCCCAAA 58.007 42.857 3.08 0.00 43.54 3.28
750 823 2.680841 GTTTTGCAGAAAACCCCCAAAC 59.319 45.455 3.08 0.00 43.54 2.93
751 824 1.573108 TTGCAGAAAACCCCCAAACA 58.427 45.000 0.00 0.00 0.00 2.83
752 825 1.799933 TGCAGAAAACCCCCAAACAT 58.200 45.000 0.00 0.00 0.00 2.71
753 826 1.691434 TGCAGAAAACCCCCAAACATC 59.309 47.619 0.00 0.00 0.00 3.06
754 827 1.001974 GCAGAAAACCCCCAAACATCC 59.998 52.381 0.00 0.00 0.00 3.51
755 828 1.623311 CAGAAAACCCCCAAACATCCC 59.377 52.381 0.00 0.00 0.00 3.85
756 829 0.981183 GAAAACCCCCAAACATCCCC 59.019 55.000 0.00 0.00 0.00 4.81
757 830 0.834261 AAAACCCCCAAACATCCCCG 60.834 55.000 0.00 0.00 0.00 5.73
758 831 1.731324 AAACCCCCAAACATCCCCGA 61.731 55.000 0.00 0.00 0.00 5.14
759 832 1.731324 AACCCCCAAACATCCCCGAA 61.731 55.000 0.00 0.00 0.00 4.30
760 833 1.077625 CCCCCAAACATCCCCGAAA 59.922 57.895 0.00 0.00 0.00 3.46
761 834 0.325203 CCCCCAAACATCCCCGAAAT 60.325 55.000 0.00 0.00 0.00 2.17
762 835 0.823460 CCCCAAACATCCCCGAAATG 59.177 55.000 0.00 0.00 0.00 2.32
763 836 1.618345 CCCCAAACATCCCCGAAATGA 60.618 52.381 0.00 0.00 0.00 2.57
764 837 1.476488 CCCAAACATCCCCGAAATGAC 59.524 52.381 0.00 0.00 0.00 3.06
765 838 2.166829 CCAAACATCCCCGAAATGACA 58.833 47.619 0.00 0.00 0.00 3.58
766 839 2.760092 CCAAACATCCCCGAAATGACAT 59.240 45.455 0.00 0.00 0.00 3.06
767 840 3.429272 CCAAACATCCCCGAAATGACATG 60.429 47.826 0.00 0.00 0.00 3.21
768 841 2.806945 ACATCCCCGAAATGACATGT 57.193 45.000 0.00 0.00 0.00 3.21
769 842 3.085952 ACATCCCCGAAATGACATGTT 57.914 42.857 0.00 0.00 0.00 2.71
770 843 4.229304 ACATCCCCGAAATGACATGTTA 57.771 40.909 0.00 0.00 0.00 2.41
771 844 4.199310 ACATCCCCGAAATGACATGTTAG 58.801 43.478 0.00 0.00 0.00 2.34
772 845 3.992943 TCCCCGAAATGACATGTTAGT 57.007 42.857 0.00 0.00 0.00 2.24
773 846 3.869065 TCCCCGAAATGACATGTTAGTC 58.131 45.455 0.00 0.00 38.99 2.59
774 847 2.943033 CCCCGAAATGACATGTTAGTCC 59.057 50.000 0.00 0.00 37.73 3.85
775 848 3.605634 CCCGAAATGACATGTTAGTCCA 58.394 45.455 0.00 0.00 37.73 4.02
776 849 3.374058 CCCGAAATGACATGTTAGTCCAC 59.626 47.826 0.00 0.00 37.73 4.02
777 850 4.000325 CCGAAATGACATGTTAGTCCACA 59.000 43.478 0.00 0.00 37.73 4.17
778 851 4.635765 CCGAAATGACATGTTAGTCCACAT 59.364 41.667 0.00 0.00 37.93 3.21
779 852 5.220662 CCGAAATGACATGTTAGTCCACATC 60.221 44.000 0.00 0.00 35.03 3.06
780 853 5.351189 CGAAATGACATGTTAGTCCACATCA 59.649 40.000 0.00 0.00 35.03 3.07
781 854 6.037500 CGAAATGACATGTTAGTCCACATCAT 59.962 38.462 0.00 0.00 35.03 2.45
782 855 6.688637 AATGACATGTTAGTCCACATCATG 57.311 37.500 0.00 0.00 40.80 3.07
783 856 5.419239 TGACATGTTAGTCCACATCATGA 57.581 39.130 0.00 0.00 39.07 3.07
784 857 5.422145 TGACATGTTAGTCCACATCATGAG 58.578 41.667 0.00 0.00 39.07 2.90
785 858 5.187576 TGACATGTTAGTCCACATCATGAGA 59.812 40.000 0.00 0.00 39.07 3.27
786 859 6.126968 TGACATGTTAGTCCACATCATGAGAT 60.127 38.462 0.00 0.00 39.07 2.75
787 860 6.202379 GACATGTTAGTCCACATCATGAGATG 59.798 42.308 0.00 1.59 43.27 2.90
788 861 9.106396 GACATGTTAGTCCACATCATGAGATGC 62.106 44.444 0.00 0.00 42.43 3.91
794 867 3.414486 CATCATGAGATGCTGCCCA 57.586 52.632 0.09 0.00 44.61 5.36
795 868 1.911057 CATCATGAGATGCTGCCCAT 58.089 50.000 0.09 0.00 44.61 4.00
796 869 2.239400 CATCATGAGATGCTGCCCATT 58.761 47.619 0.09 0.00 44.61 3.16
797 870 1.977056 TCATGAGATGCTGCCCATTC 58.023 50.000 0.00 0.00 33.29 2.67
798 871 0.591659 CATGAGATGCTGCCCATTCG 59.408 55.000 0.00 0.00 33.29 3.34
799 872 0.471191 ATGAGATGCTGCCCATTCGA 59.529 50.000 0.00 0.00 33.29 3.71
800 873 0.471191 TGAGATGCTGCCCATTCGAT 59.529 50.000 0.00 0.00 33.29 3.59
801 874 1.155042 GAGATGCTGCCCATTCGATC 58.845 55.000 0.00 0.00 33.29 3.69
802 875 0.763652 AGATGCTGCCCATTCGATCT 59.236 50.000 0.00 0.00 33.29 2.75
803 876 1.155042 GATGCTGCCCATTCGATCTC 58.845 55.000 0.00 0.00 33.29 2.75
804 877 0.471191 ATGCTGCCCATTCGATCTCA 59.529 50.000 0.00 0.00 0.00 3.27
805 878 0.179065 TGCTGCCCATTCGATCTCAG 60.179 55.000 0.00 0.00 0.00 3.35
806 879 0.105593 GCTGCCCATTCGATCTCAGA 59.894 55.000 0.00 0.00 0.00 3.27
807 880 1.473965 GCTGCCCATTCGATCTCAGAA 60.474 52.381 0.00 0.00 0.00 3.02
808 881 2.208431 CTGCCCATTCGATCTCAGAAC 58.792 52.381 0.00 0.00 0.00 3.01
809 882 1.212616 GCCCATTCGATCTCAGAACG 58.787 55.000 0.00 0.00 0.00 3.95
810 883 1.202417 GCCCATTCGATCTCAGAACGA 60.202 52.381 2.36 2.36 35.25 3.85
811 884 2.464865 CCCATTCGATCTCAGAACGAC 58.535 52.381 6.52 0.00 36.66 4.34
812 885 2.112522 CCATTCGATCTCAGAACGACG 58.887 52.381 6.52 1.44 36.66 5.12
813 886 2.112522 CATTCGATCTCAGAACGACGG 58.887 52.381 6.52 0.00 36.66 4.79
814 887 0.179171 TTCGATCTCAGAACGACGGC 60.179 55.000 6.52 0.00 36.66 5.68
815 888 1.586564 CGATCTCAGAACGACGGCC 60.587 63.158 0.00 0.00 29.49 6.13
816 889 1.586564 GATCTCAGAACGACGGCCG 60.587 63.158 26.86 26.86 45.44 6.13
817 890 1.989966 GATCTCAGAACGACGGCCGA 61.990 60.000 35.90 4.92 41.76 5.54
818 891 1.994507 ATCTCAGAACGACGGCCGAG 61.995 60.000 35.90 26.65 41.76 4.63
819 892 3.685214 CTCAGAACGACGGCCGAGG 62.685 68.421 35.90 24.63 41.76 4.63
820 893 4.052229 CAGAACGACGGCCGAGGT 62.052 66.667 35.90 25.36 41.76 3.85
821 894 3.300765 AGAACGACGGCCGAGGTT 61.301 61.111 35.90 31.65 41.76 3.50
822 895 3.110178 GAACGACGGCCGAGGTTG 61.110 66.667 35.90 16.58 41.76 3.77
851 924 3.788672 CCTAATGTGAGGTGCTCCC 57.211 57.895 0.00 0.00 0.00 4.30
852 925 0.179073 CCTAATGTGAGGTGCTCCCG 60.179 60.000 0.00 0.00 38.74 5.14
853 926 0.537188 CTAATGTGAGGTGCTCCCGT 59.463 55.000 0.00 0.00 38.74 5.28
854 927 1.754803 CTAATGTGAGGTGCTCCCGTA 59.245 52.381 0.00 0.00 38.74 4.02
855 928 0.537188 AATGTGAGGTGCTCCCGTAG 59.463 55.000 0.00 0.00 38.74 3.51
867 940 3.305398 CTCCCGTAGCACCAGATATTC 57.695 52.381 0.00 0.00 0.00 1.75
868 941 2.894126 CTCCCGTAGCACCAGATATTCT 59.106 50.000 0.00 0.00 0.00 2.40
869 942 2.891580 TCCCGTAGCACCAGATATTCTC 59.108 50.000 0.00 0.00 0.00 2.87
870 943 2.028930 CCCGTAGCACCAGATATTCTCC 60.029 54.545 0.00 0.00 0.00 3.71
871 944 2.028930 CCGTAGCACCAGATATTCTCCC 60.029 54.545 0.00 0.00 0.00 4.30
917 990 6.049149 CGATTAATCCTCTTTTCAGGCTGTA 58.951 40.000 15.27 1.01 32.91 2.74
918 991 6.018669 CGATTAATCCTCTTTTCAGGCTGTAC 60.019 42.308 15.27 0.00 32.91 2.90
929 1002 2.233676 TCAGGCTGTACATTGACGACAT 59.766 45.455 15.27 0.00 0.00 3.06
947 1020 2.027745 ACATTCTCGGTGCATTCTGAGT 60.028 45.455 11.72 0.00 40.53 3.41
948 1021 2.839486 TTCTCGGTGCATTCTGAGTT 57.161 45.000 11.72 0.00 40.53 3.01
949 1022 2.839486 TCTCGGTGCATTCTGAGTTT 57.161 45.000 11.72 0.00 40.53 2.66
950 1023 2.688507 TCTCGGTGCATTCTGAGTTTC 58.311 47.619 11.72 0.00 40.53 2.78
951 1024 2.300152 TCTCGGTGCATTCTGAGTTTCT 59.700 45.455 11.72 0.00 40.53 2.52
952 1025 2.414481 CTCGGTGCATTCTGAGTTTCTG 59.586 50.000 5.23 0.00 36.43 3.02
953 1026 2.037121 TCGGTGCATTCTGAGTTTCTGA 59.963 45.455 0.00 0.00 0.00 3.27
954 1027 2.158449 CGGTGCATTCTGAGTTTCTGAC 59.842 50.000 0.00 0.00 0.00 3.51
963 1036 3.004839 TCTGAGTTTCTGACGACTTGAGG 59.995 47.826 0.00 0.00 0.00 3.86
972 1045 1.079819 CGACTTGAGGTCCACGCAT 60.080 57.895 0.00 0.00 41.64 4.73
981 1054 1.559682 AGGTCCACGCATAATCCACTT 59.440 47.619 0.00 0.00 0.00 3.16
982 1055 1.670811 GGTCCACGCATAATCCACTTG 59.329 52.381 0.00 0.00 0.00 3.16
1267 1344 0.460109 TGCCATCGACGACTTCATGG 60.460 55.000 9.58 9.58 36.61 3.66
1336 1415 1.827969 TCAAGAGCTCACTAGGGAAGC 59.172 52.381 17.77 2.10 0.00 3.86
1360 1439 2.914777 GAAGATGAAGGCTCGCCGCT 62.915 60.000 1.69 0.00 41.95 5.52
1436 1515 5.181009 CAGGAATGCAAGATACAAGAGTCA 58.819 41.667 0.00 0.00 0.00 3.41
1529 1608 3.411446 AGCTTGTTGGAATCGATGAACA 58.589 40.909 0.00 6.25 0.00 3.18
1534 1613 4.384940 TGTTGGAATCGATGAACACAAGA 58.615 39.130 0.00 0.00 0.00 3.02
1629 1720 0.621571 CTGGACCTGGAGGAATGGGA 60.622 60.000 0.00 0.00 38.94 4.37
1686 1777 2.143876 AAGGGCAGTTTGAGTGTTGT 57.856 45.000 0.00 0.00 0.00 3.32
1731 1822 4.353191 AGCCCAGACATGATGAATATCCTT 59.647 41.667 0.00 0.00 32.09 3.36
1893 1988 1.468520 TGCTAGGCGTTCTTTGAATGC 59.531 47.619 14.08 14.08 0.00 3.56
1994 2090 3.198068 TCTTCGCAGTTTCTCCATATGC 58.802 45.455 0.00 0.00 0.00 3.14
1998 2094 2.031314 CGCAGTTTCTCCATATGCTGTG 59.969 50.000 0.00 1.31 34.75 3.66
2005 2101 6.888632 AGTTTCTCCATATGCTGTGAGAAAAT 59.111 34.615 24.40 22.24 44.11 1.82
2021 2117 7.866898 TGTGAGAAAATGTAATGGTCAAATGTG 59.133 33.333 0.00 0.00 0.00 3.21
2194 2300 8.956426 TCCCTTTATTGTGTAAGAATTGACATC 58.044 33.333 0.00 0.00 29.89 3.06
2216 2322 3.743396 CAGTTTGTGTCAAGAGTAGAGCC 59.257 47.826 0.00 0.00 0.00 4.70
2217 2323 3.067833 GTTTGTGTCAAGAGTAGAGCCC 58.932 50.000 0.00 0.00 0.00 5.19
2218 2324 0.888619 TGTGTCAAGAGTAGAGCCCG 59.111 55.000 0.00 0.00 0.00 6.13
2219 2325 0.173708 GTGTCAAGAGTAGAGCCCGG 59.826 60.000 0.00 0.00 0.00 5.73
2242 2777 3.304659 CCCAAACACTCCATTTTCTCACG 60.305 47.826 0.00 0.00 0.00 4.35
2281 3902 6.402658 GGCTCACTTTTCTTTCTAATTCTCCG 60.403 42.308 0.00 0.00 0.00 4.63
2284 3905 6.426937 TCACTTTTCTTTCTAATTCTCCGTGG 59.573 38.462 0.00 0.00 0.00 4.94
2289 3910 2.160721 TCTAATTCTCCGTGGGCTCT 57.839 50.000 0.00 0.00 0.00 4.09
2336 3960 2.105649 TGTGCACTTTACCTCATGACCA 59.894 45.455 19.41 0.00 0.00 4.02
2403 4029 1.298667 GCATCCACGTTACCCTGGT 59.701 57.895 0.00 0.00 0.00 4.00
2404 4030 0.322187 GCATCCACGTTACCCTGGTT 60.322 55.000 0.00 0.00 0.00 3.67
2445 4081 3.634448 CACACACATAACCTTTTCCCACA 59.366 43.478 0.00 0.00 0.00 4.17
2569 5662 7.707624 TTCTGAGCAGATATTGGAAAAATGT 57.292 32.000 0.37 0.00 37.29 2.71
2608 5701 5.182001 GGCGATCATTGCTATATCTGGTTTT 59.818 40.000 0.00 0.00 0.00 2.43
2683 5776 2.096819 TGGTCGTGCACTTGAAAGAAAC 59.903 45.455 16.19 1.33 0.00 2.78
2761 5854 8.449397 CCTCTTTATCTGAAAACATGTCTCTTG 58.551 37.037 0.00 0.00 0.00 3.02
2968 6061 6.294473 AGTGAAGAGTTGTCAAGTTCATGAT 58.706 36.000 0.00 0.00 30.27 2.45
2974 6067 8.261492 AGAGTTGTCAAGTTCATGATACAATC 57.739 34.615 0.00 3.95 0.00 2.67
3098 6193 5.984725 TCTGTCTACAAGGTGTCAAGAAAA 58.015 37.500 0.00 0.00 0.00 2.29
3165 6260 7.555195 TGTTCGATCACTTACTATGGTTAGAGA 59.445 37.037 1.96 0.13 0.00 3.10
3168 6263 7.390996 TCGATCACTTACTATGGTTAGAGATCC 59.609 40.741 21.11 10.23 41.51 3.36
3206 6301 4.963318 TTGGAAGAGTTCAGACATCTGT 57.037 40.909 8.70 0.00 44.12 3.41
3278 6373 7.685481 TGAAAATATAGTGAGGTTGTTCCAGA 58.315 34.615 0.00 0.00 39.02 3.86
3284 6379 1.003580 TGAGGTTGTTCCAGATGAGGC 59.996 52.381 0.00 0.00 39.02 4.70
3305 6400 3.684788 GCACCTGAATCTCAAACGTACAT 59.315 43.478 0.00 0.00 0.00 2.29
3327 6422 2.029838 ATAAGCAAGCTCCCAGAACG 57.970 50.000 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.538287 AAGGAAGTGGCCAAGACAGC 60.538 55.000 7.24 0.00 0.00 4.40
1 2 1.072965 AGAAGGAAGTGGCCAAGACAG 59.927 52.381 7.24 0.00 0.00 3.51
2 3 1.140312 AGAAGGAAGTGGCCAAGACA 58.860 50.000 7.24 0.00 0.00 3.41
3 4 1.202818 ACAGAAGGAAGTGGCCAAGAC 60.203 52.381 7.24 0.59 0.00 3.01
5 6 1.202806 TGACAGAAGGAAGTGGCCAAG 60.203 52.381 7.24 0.00 0.00 3.61
6 7 0.843309 TGACAGAAGGAAGTGGCCAA 59.157 50.000 7.24 0.00 0.00 4.52
12 13 3.584848 ACCTATTGCTGACAGAAGGAAGT 59.415 43.478 6.65 0.00 34.90 3.01
43 44 8.715088 GCGTTAACACTAATCCTTTCTCTTTAA 58.285 33.333 6.39 0.00 0.00 1.52
44 45 7.062605 CGCGTTAACACTAATCCTTTCTCTTTA 59.937 37.037 6.39 0.00 0.00 1.85
45 46 6.128634 CGCGTTAACACTAATCCTTTCTCTTT 60.129 38.462 6.39 0.00 0.00 2.52
48 49 4.492085 GCGCGTTAACACTAATCCTTTCTC 60.492 45.833 8.43 0.00 0.00 2.87
50 51 3.123959 TGCGCGTTAACACTAATCCTTTC 59.876 43.478 8.43 0.00 0.00 2.62
53 54 2.373540 TGCGCGTTAACACTAATCCT 57.626 45.000 8.43 0.00 0.00 3.24
55 56 2.033151 GGGATGCGCGTTAACACTAATC 60.033 50.000 8.43 3.51 0.00 1.75
56 57 1.937899 GGGATGCGCGTTAACACTAAT 59.062 47.619 8.43 0.00 0.00 1.73
63 71 2.025589 TAACATGGGATGCGCGTTAA 57.974 45.000 8.43 0.00 0.00 2.01
72 80 9.875708 TTATTGGCTAGTAAATTAACATGGGAT 57.124 29.630 0.00 0.00 0.00 3.85
101 109 4.935205 GTGATATGCTACACCAAGTTGTGA 59.065 41.667 1.45 0.00 39.57 3.58
106 114 5.932619 TGTAGTGATATGCTACACCAAGT 57.067 39.130 10.88 0.00 42.45 3.16
111 119 6.662414 TGCTTTTGTAGTGATATGCTACAC 57.338 37.500 13.35 0.00 45.62 2.90
113 121 7.072177 TGTTGCTTTTGTAGTGATATGCTAC 57.928 36.000 6.96 6.96 39.26 3.58
116 124 4.795278 GCTGTTGCTTTTGTAGTGATATGC 59.205 41.667 0.00 0.00 36.03 3.14
148 163 8.730680 AGTTCCAAAGATGTGTCATTGTTATAC 58.269 33.333 0.00 0.00 32.58 1.47
162 177 5.504665 CGCCTGCTTAATAGTTCCAAAGATG 60.505 44.000 0.00 0.00 0.00 2.90
163 178 4.576463 CGCCTGCTTAATAGTTCCAAAGAT 59.424 41.667 0.00 0.00 0.00 2.40
164 179 3.938963 CGCCTGCTTAATAGTTCCAAAGA 59.061 43.478 0.00 0.00 0.00 2.52
165 180 3.065371 CCGCCTGCTTAATAGTTCCAAAG 59.935 47.826 0.00 0.00 0.00 2.77
167 182 2.639065 CCGCCTGCTTAATAGTTCCAA 58.361 47.619 0.00 0.00 0.00 3.53
168 183 1.134220 CCCGCCTGCTTAATAGTTCCA 60.134 52.381 0.00 0.00 0.00 3.53
170 185 0.945099 GCCCGCCTGCTTAATAGTTC 59.055 55.000 0.00 0.00 0.00 3.01
171 186 0.254747 TGCCCGCCTGCTTAATAGTT 59.745 50.000 0.00 0.00 0.00 2.24
172 187 0.474184 ATGCCCGCCTGCTTAATAGT 59.526 50.000 0.00 0.00 0.00 2.12
173 188 1.537202 GAATGCCCGCCTGCTTAATAG 59.463 52.381 0.00 0.00 0.00 1.73
221 264 0.674895 ACCGCAAGACCAGAAGATGC 60.675 55.000 0.00 0.00 43.02 3.91
222 265 1.081892 CACCGCAAGACCAGAAGATG 58.918 55.000 0.00 0.00 43.02 2.90
223 266 0.674895 GCACCGCAAGACCAGAAGAT 60.675 55.000 0.00 0.00 43.02 2.40
224 267 1.301716 GCACCGCAAGACCAGAAGA 60.302 57.895 0.00 0.00 43.02 2.87
225 268 1.597854 TGCACCGCAAGACCAGAAG 60.598 57.895 0.00 0.00 43.02 2.85
229 272 2.899838 GTGTGCACCGCAAGACCA 60.900 61.111 15.69 0.00 41.47 4.02
230 273 4.012895 CGTGTGCACCGCAAGACC 62.013 66.667 15.69 0.00 41.47 3.85
252 295 2.077821 GAGGAGAATCTCGGACGCCC 62.078 65.000 3.96 0.00 33.73 6.13
253 296 1.360911 GAGGAGAATCTCGGACGCC 59.639 63.158 3.96 0.00 33.73 5.68
260 303 2.731374 CCCGGCGAGGAGAATCTC 59.269 66.667 9.30 0.71 45.00 2.75
261 304 3.541713 GCCCGGCGAGGAGAATCT 61.542 66.667 9.30 0.00 45.00 2.40
262 305 3.385749 TTGCCCGGCGAGGAGAATC 62.386 63.158 9.30 0.00 45.00 2.52
263 306 3.391665 CTTGCCCGGCGAGGAGAAT 62.392 63.158 18.12 0.00 45.00 2.40
309 352 4.090090 AGATGCAAGTATACCTAGCGGAT 58.910 43.478 0.00 0.00 0.00 4.18
310 353 3.497332 AGATGCAAGTATACCTAGCGGA 58.503 45.455 0.00 0.00 0.00 5.54
311 354 3.367498 GGAGATGCAAGTATACCTAGCGG 60.367 52.174 0.00 0.00 0.00 5.52
312 355 3.367498 GGGAGATGCAAGTATACCTAGCG 60.367 52.174 0.00 0.00 0.00 4.26
324 367 1.001020 ACGGCAATGGGAGATGCAA 60.001 52.632 0.00 0.00 44.32 4.08
325 368 1.750018 CACGGCAATGGGAGATGCA 60.750 57.895 0.00 0.00 44.32 3.96
326 369 3.113745 CACGGCAATGGGAGATGC 58.886 61.111 0.00 0.00 41.82 3.91
338 381 3.426568 GCCAGACTGAAGCACGGC 61.427 66.667 3.32 0.00 0.00 5.68
340 383 3.114616 CGGCCAGACTGAAGCACG 61.115 66.667 2.24 2.60 0.00 5.34
362 405 0.319555 CACCGAACAAGCGAGAGGAA 60.320 55.000 0.00 0.00 0.00 3.36
371 414 0.387622 CCATTGCTGCACCGAACAAG 60.388 55.000 0.00 0.00 0.00 3.16
390 454 7.255625 GGATGGATTAAAGGAGATAAAGCCAAC 60.256 40.741 0.00 0.00 30.00 3.77
403 467 5.129320 CCCTGGAAAAAGGATGGATTAAAGG 59.871 44.000 0.00 0.00 40.02 3.11
418 482 3.780804 TCGATCTGAAACCCTGGAAAA 57.219 42.857 0.00 0.00 0.00 2.29
487 556 2.762745 ACTGATGGTGTACACGGAAAC 58.237 47.619 19.41 6.11 0.00 2.78
492 561 2.060326 ACGAACTGATGGTGTACACG 57.940 50.000 19.41 8.01 0.00 4.49
502 571 0.966920 AGTCGGACCAACGAACTGAT 59.033 50.000 4.14 0.00 45.38 2.90
529 598 1.208052 TGGAAGCTGGATCTTTCTCGG 59.792 52.381 0.00 0.00 0.00 4.63
530 599 2.680312 TGGAAGCTGGATCTTTCTCG 57.320 50.000 0.00 0.00 0.00 4.04
537 609 1.347378 GAGGAGGATGGAAGCTGGATC 59.653 57.143 0.00 0.00 0.00 3.36
552 624 2.279517 GCGGTGGCATACGAGGAG 60.280 66.667 16.91 0.00 39.62 3.69
571 643 3.605749 AATCGACACTGTGCCGGGG 62.606 63.158 16.20 0.00 0.00 5.73
575 647 1.128692 GCTACAAATCGACACTGTGCC 59.871 52.381 7.90 0.00 0.00 5.01
576 648 1.798223 TGCTACAAATCGACACTGTGC 59.202 47.619 7.90 0.00 0.00 4.57
596 669 7.129457 TCACTAGATATCCAGCACTGAAAAT 57.871 36.000 0.00 0.00 0.00 1.82
606 679 6.425210 TTGGACCATTCACTAGATATCCAG 57.575 41.667 0.00 0.00 36.41 3.86
607 680 6.823286 TTTGGACCATTCACTAGATATCCA 57.177 37.500 0.00 0.00 33.21 3.41
608 681 8.697507 ATTTTTGGACCATTCACTAGATATCC 57.302 34.615 0.00 0.00 0.00 2.59
609 682 8.787852 GGATTTTTGGACCATTCACTAGATATC 58.212 37.037 0.00 0.00 0.00 1.63
611 684 6.765989 CGGATTTTTGGACCATTCACTAGATA 59.234 38.462 0.00 0.00 0.00 1.98
612 685 5.590259 CGGATTTTTGGACCATTCACTAGAT 59.410 40.000 0.00 0.00 0.00 1.98
613 686 4.941263 CGGATTTTTGGACCATTCACTAGA 59.059 41.667 0.00 0.00 0.00 2.43
614 687 4.941263 TCGGATTTTTGGACCATTCACTAG 59.059 41.667 0.00 0.00 0.00 2.57
615 688 4.912586 TCGGATTTTTGGACCATTCACTA 58.087 39.130 0.00 0.00 0.00 2.74
616 689 3.761897 TCGGATTTTTGGACCATTCACT 58.238 40.909 0.00 0.00 0.00 3.41
617 690 4.513198 TTCGGATTTTTGGACCATTCAC 57.487 40.909 0.00 0.00 0.00 3.18
618 691 5.537300 TTTTCGGATTTTTGGACCATTCA 57.463 34.783 0.00 0.00 0.00 2.57
639 712 6.441604 AGGGATTGCTAACATCCAGAATTTTT 59.558 34.615 1.50 0.00 36.22 1.94
640 713 5.960202 AGGGATTGCTAACATCCAGAATTTT 59.040 36.000 1.50 0.00 36.22 1.82
641 714 5.522641 AGGGATTGCTAACATCCAGAATTT 58.477 37.500 1.50 0.00 36.22 1.82
642 715 5.134725 AGGGATTGCTAACATCCAGAATT 57.865 39.130 1.50 0.00 36.22 2.17
643 716 4.803329 AGGGATTGCTAACATCCAGAAT 57.197 40.909 1.50 0.00 36.22 2.40
644 717 5.708736 TTAGGGATTGCTAACATCCAGAA 57.291 39.130 1.50 0.00 36.22 3.02
645 718 5.708736 TTTAGGGATTGCTAACATCCAGA 57.291 39.130 1.50 0.00 36.22 3.86
646 719 6.773976 TTTTTAGGGATTGCTAACATCCAG 57.226 37.500 1.50 0.00 36.22 3.86
706 779 8.441312 AACATTCATGCAAGATTTGTCTTTTT 57.559 26.923 8.06 0.00 0.00 1.94
707 780 8.441312 AAACATTCATGCAAGATTTGTCTTTT 57.559 26.923 8.06 0.00 0.00 2.27
708 781 8.339714 CAAAACATTCATGCAAGATTTGTCTTT 58.660 29.630 8.06 8.20 0.00 2.52
709 782 7.519328 GCAAAACATTCATGCAAGATTTGTCTT 60.519 33.333 13.97 3.92 39.81 3.01
710 783 6.073440 GCAAAACATTCATGCAAGATTTGTCT 60.073 34.615 13.97 0.00 39.81 3.41
711 784 6.075280 GCAAAACATTCATGCAAGATTTGTC 58.925 36.000 13.97 6.22 39.81 3.18
712 785 5.527951 TGCAAAACATTCATGCAAGATTTGT 59.472 32.000 13.97 9.02 46.23 2.83
713 786 5.991568 TGCAAAACATTCATGCAAGATTTG 58.008 33.333 10.05 10.05 46.23 2.32
730 803 2.305927 TGTTTGGGGGTTTTCTGCAAAA 59.694 40.909 0.00 0.00 0.00 2.44
731 804 1.909302 TGTTTGGGGGTTTTCTGCAAA 59.091 42.857 0.00 0.00 0.00 3.68
732 805 1.573108 TGTTTGGGGGTTTTCTGCAA 58.427 45.000 0.00 0.00 0.00 4.08
733 806 1.691434 GATGTTTGGGGGTTTTCTGCA 59.309 47.619 0.00 0.00 0.00 4.41
734 807 1.001974 GGATGTTTGGGGGTTTTCTGC 59.998 52.381 0.00 0.00 0.00 4.26
735 808 1.623311 GGGATGTTTGGGGGTTTTCTG 59.377 52.381 0.00 0.00 0.00 3.02
736 809 1.484256 GGGGATGTTTGGGGGTTTTCT 60.484 52.381 0.00 0.00 0.00 2.52
737 810 0.981183 GGGGATGTTTGGGGGTTTTC 59.019 55.000 0.00 0.00 0.00 2.29
738 811 0.834261 CGGGGATGTTTGGGGGTTTT 60.834 55.000 0.00 0.00 0.00 2.43
739 812 1.229051 CGGGGATGTTTGGGGGTTT 60.229 57.895 0.00 0.00 0.00 3.27
740 813 1.731324 TTCGGGGATGTTTGGGGGTT 61.731 55.000 0.00 0.00 0.00 4.11
741 814 1.731324 TTTCGGGGATGTTTGGGGGT 61.731 55.000 0.00 0.00 0.00 4.95
742 815 0.325203 ATTTCGGGGATGTTTGGGGG 60.325 55.000 0.00 0.00 0.00 5.40
743 816 0.823460 CATTTCGGGGATGTTTGGGG 59.177 55.000 0.00 0.00 0.00 4.96
744 817 1.476488 GTCATTTCGGGGATGTTTGGG 59.524 52.381 0.00 0.00 0.00 4.12
745 818 2.166829 TGTCATTTCGGGGATGTTTGG 58.833 47.619 0.00 0.00 0.00 3.28
746 819 3.193267 ACATGTCATTTCGGGGATGTTTG 59.807 43.478 0.00 0.00 0.00 2.93
747 820 3.430453 ACATGTCATTTCGGGGATGTTT 58.570 40.909 0.00 0.00 0.00 2.83
748 821 3.085952 ACATGTCATTTCGGGGATGTT 57.914 42.857 0.00 0.00 0.00 2.71
749 822 2.806945 ACATGTCATTTCGGGGATGT 57.193 45.000 0.00 0.00 0.00 3.06
750 823 4.199310 ACTAACATGTCATTTCGGGGATG 58.801 43.478 0.00 0.00 0.00 3.51
751 824 4.451900 GACTAACATGTCATTTCGGGGAT 58.548 43.478 0.00 0.00 36.97 3.85
752 825 3.370103 GGACTAACATGTCATTTCGGGGA 60.370 47.826 0.00 0.00 38.61 4.81
753 826 2.943033 GGACTAACATGTCATTTCGGGG 59.057 50.000 0.00 0.00 38.61 5.73
754 827 3.374058 GTGGACTAACATGTCATTTCGGG 59.626 47.826 0.00 0.00 38.61 5.14
755 828 4.000325 TGTGGACTAACATGTCATTTCGG 59.000 43.478 0.00 0.00 38.61 4.30
756 829 5.351189 TGATGTGGACTAACATGTCATTTCG 59.649 40.000 0.00 0.00 40.87 3.46
757 830 6.741992 TGATGTGGACTAACATGTCATTTC 57.258 37.500 0.00 0.00 40.87 2.17
758 831 6.885918 TCATGATGTGGACTAACATGTCATTT 59.114 34.615 0.00 0.00 40.87 2.32
759 832 6.417258 TCATGATGTGGACTAACATGTCATT 58.583 36.000 0.00 0.00 40.87 2.57
760 833 5.993055 TCATGATGTGGACTAACATGTCAT 58.007 37.500 0.00 0.00 40.87 3.06
761 834 5.187576 TCTCATGATGTGGACTAACATGTCA 59.812 40.000 0.00 0.00 40.87 3.58
762 835 5.664457 TCTCATGATGTGGACTAACATGTC 58.336 41.667 0.00 0.00 40.87 3.06
763 836 5.682234 TCTCATGATGTGGACTAACATGT 57.318 39.130 0.00 0.00 40.87 3.21
764 837 6.541111 CATCTCATGATGTGGACTAACATG 57.459 41.667 0.00 0.00 43.68 3.21
777 850 2.515854 GAATGGGCAGCATCTCATGAT 58.484 47.619 0.00 0.00 0.00 2.45
778 851 1.812708 CGAATGGGCAGCATCTCATGA 60.813 52.381 0.00 0.00 0.00 3.07
779 852 0.591659 CGAATGGGCAGCATCTCATG 59.408 55.000 0.00 0.00 0.00 3.07
780 853 0.471191 TCGAATGGGCAGCATCTCAT 59.529 50.000 0.00 0.00 0.00 2.90
781 854 0.471191 ATCGAATGGGCAGCATCTCA 59.529 50.000 0.00 0.00 0.00 3.27
782 855 1.155042 GATCGAATGGGCAGCATCTC 58.845 55.000 0.00 0.00 0.00 2.75
783 856 0.763652 AGATCGAATGGGCAGCATCT 59.236 50.000 0.00 0.00 0.00 2.90
784 857 1.155042 GAGATCGAATGGGCAGCATC 58.845 55.000 0.00 0.00 0.00 3.91
785 858 0.471191 TGAGATCGAATGGGCAGCAT 59.529 50.000 0.00 0.00 0.00 3.79
786 859 0.179065 CTGAGATCGAATGGGCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
787 860 0.105593 TCTGAGATCGAATGGGCAGC 59.894 55.000 0.00 0.00 0.00 5.25
788 861 2.208431 GTTCTGAGATCGAATGGGCAG 58.792 52.381 0.00 0.00 0.00 4.85
789 862 1.471501 CGTTCTGAGATCGAATGGGCA 60.472 52.381 7.10 0.00 0.00 5.36
790 863 1.202417 TCGTTCTGAGATCGAATGGGC 60.202 52.381 12.69 0.00 32.08 5.36
791 864 2.464865 GTCGTTCTGAGATCGAATGGG 58.535 52.381 16.20 0.00 35.92 4.00
792 865 2.112522 CGTCGTTCTGAGATCGAATGG 58.887 52.381 16.20 6.40 35.92 3.16
793 866 2.112522 CCGTCGTTCTGAGATCGAATG 58.887 52.381 16.20 11.87 35.92 2.67
794 867 1.534175 GCCGTCGTTCTGAGATCGAAT 60.534 52.381 16.20 0.00 35.92 3.34
795 868 0.179171 GCCGTCGTTCTGAGATCGAA 60.179 55.000 16.20 0.01 35.92 3.71
796 869 1.428219 GCCGTCGTTCTGAGATCGA 59.572 57.895 11.22 11.22 32.48 3.59
797 870 1.586564 GGCCGTCGTTCTGAGATCG 60.587 63.158 6.59 6.59 0.00 3.69
798 871 1.586564 CGGCCGTCGTTCTGAGATC 60.587 63.158 19.50 0.00 0.00 2.75
799 872 1.994507 CTCGGCCGTCGTTCTGAGAT 61.995 60.000 27.15 0.00 37.80 2.75
800 873 2.670592 TCGGCCGTCGTTCTGAGA 60.671 61.111 27.15 0.00 40.32 3.27
801 874 2.202492 CTCGGCCGTCGTTCTGAG 60.202 66.667 27.15 8.60 40.32 3.35
802 875 3.744719 CCTCGGCCGTCGTTCTGA 61.745 66.667 27.15 1.04 40.32 3.27
803 876 3.569049 AACCTCGGCCGTCGTTCTG 62.569 63.158 27.15 9.17 40.32 3.02
804 877 3.300765 AACCTCGGCCGTCGTTCT 61.301 61.111 27.15 5.40 40.32 3.01
805 878 3.110178 CAACCTCGGCCGTCGTTC 61.110 66.667 27.15 0.00 40.32 3.95
822 895 3.272334 CATTAGGTGCTCCCGCGC 61.272 66.667 0.00 0.00 45.74 6.86
823 896 2.173669 CACATTAGGTGCTCCCGCG 61.174 63.158 0.00 0.00 41.36 6.46
824 897 3.813596 CACATTAGGTGCTCCCGC 58.186 61.111 0.00 0.00 41.36 6.13
833 906 0.179073 CGGGAGCACCTCACATTAGG 60.179 60.000 0.00 0.00 42.82 2.69
834 907 0.537188 ACGGGAGCACCTCACATTAG 59.463 55.000 0.00 0.00 32.66 1.73
835 908 1.754803 CTACGGGAGCACCTCACATTA 59.245 52.381 0.00 0.00 32.66 1.90
836 909 0.537188 CTACGGGAGCACCTCACATT 59.463 55.000 0.00 0.00 32.66 2.71
837 910 2.202866 CTACGGGAGCACCTCACAT 58.797 57.895 0.00 0.00 32.66 3.21
838 911 3.694746 CTACGGGAGCACCTCACA 58.305 61.111 0.00 0.00 32.66 3.58
847 920 2.894126 AGAATATCTGGTGCTACGGGAG 59.106 50.000 0.00 0.00 0.00 4.30
848 921 2.891580 GAGAATATCTGGTGCTACGGGA 59.108 50.000 0.00 0.00 0.00 5.14
849 922 2.028930 GGAGAATATCTGGTGCTACGGG 60.029 54.545 0.00 0.00 0.00 5.28
850 923 2.028930 GGGAGAATATCTGGTGCTACGG 60.029 54.545 0.00 0.00 0.00 4.02
851 924 2.028930 GGGGAGAATATCTGGTGCTACG 60.029 54.545 0.00 0.00 0.00 3.51
852 925 3.243724 AGGGGAGAATATCTGGTGCTAC 58.756 50.000 0.00 0.00 0.00 3.58
853 926 3.637821 AGGGGAGAATATCTGGTGCTA 57.362 47.619 0.00 0.00 0.00 3.49
854 927 2.441001 CAAGGGGAGAATATCTGGTGCT 59.559 50.000 0.00 0.00 0.00 4.40
855 928 2.487986 CCAAGGGGAGAATATCTGGTGC 60.488 54.545 0.00 0.00 35.59 5.01
856 929 3.048600 TCCAAGGGGAGAATATCTGGTG 58.951 50.000 0.00 0.00 38.64 4.17
857 930 3.049344 GTCCAAGGGGAGAATATCTGGT 58.951 50.000 0.00 0.00 46.12 4.00
858 931 3.048600 TGTCCAAGGGGAGAATATCTGG 58.951 50.000 0.00 0.00 46.12 3.86
859 932 4.989875 ATGTCCAAGGGGAGAATATCTG 57.010 45.455 0.00 0.00 46.12 2.90
860 933 5.545723 CACTATGTCCAAGGGGAGAATATCT 59.454 44.000 0.00 0.00 46.12 1.98
861 934 5.280215 CCACTATGTCCAAGGGGAGAATATC 60.280 48.000 0.00 0.00 46.12 1.63
862 935 4.599241 CCACTATGTCCAAGGGGAGAATAT 59.401 45.833 0.00 0.00 46.12 1.28
863 936 3.973973 CCACTATGTCCAAGGGGAGAATA 59.026 47.826 0.00 0.00 46.12 1.75
864 937 2.780010 CCACTATGTCCAAGGGGAGAAT 59.220 50.000 0.00 0.00 46.12 2.40
865 938 2.196595 CCACTATGTCCAAGGGGAGAA 58.803 52.381 0.00 0.00 46.12 2.87
866 939 1.879575 CCACTATGTCCAAGGGGAGA 58.120 55.000 0.00 0.00 46.12 3.71
867 940 0.181350 GCCACTATGTCCAAGGGGAG 59.819 60.000 0.00 0.00 46.12 4.30
868 941 0.253160 AGCCACTATGTCCAAGGGGA 60.253 55.000 0.00 0.00 40.22 4.81
869 942 0.625849 AAGCCACTATGTCCAAGGGG 59.374 55.000 0.00 0.00 40.80 4.79
870 943 2.238646 TGTAAGCCACTATGTCCAAGGG 59.761 50.000 0.00 0.00 0.00 3.95
871 944 3.627395 TGTAAGCCACTATGTCCAAGG 57.373 47.619 0.00 0.00 0.00 3.61
929 1002 2.839486 AACTCAGAATGCACCGAGAA 57.161 45.000 9.70 0.00 34.76 2.87
963 1036 1.670811 CCAAGTGGATTATGCGTGGAC 59.329 52.381 0.00 0.00 37.39 4.02
972 1045 1.137086 GAGAGCTCGCCAAGTGGATTA 59.863 52.381 8.37 0.00 37.39 1.75
1267 1344 2.411547 CGTCTTTGTCACCGATGCTTTC 60.412 50.000 0.00 0.00 0.00 2.62
1336 1415 0.179062 CGAGCCTTCATCTTCCCCAG 60.179 60.000 0.00 0.00 0.00 4.45
1360 1439 2.420547 CCTGAATCTCTTTGCCGATCCA 60.421 50.000 0.00 0.00 0.00 3.41
1436 1515 1.827969 CGGTCTTGGAGAAGGTCTCAT 59.172 52.381 7.52 0.00 45.12 2.90
1529 1608 5.068636 ACAATTTGATCAGCTCAGTCTTGT 58.931 37.500 2.79 0.00 34.68 3.16
1534 1613 4.083643 CGTCAACAATTTGATCAGCTCAGT 60.084 41.667 2.79 0.00 43.72 3.41
1629 1720 5.179182 CACTTGGTTTGCAAGAGTTGTTTTT 59.821 36.000 0.00 0.00 34.08 1.94
1686 1777 1.813859 CGACACGGATAGGAAGGCA 59.186 57.895 0.00 0.00 0.00 4.75
1731 1822 7.013083 CCGCTAACTTCACTAAGAATAGTCCTA 59.987 40.741 0.00 0.00 40.44 2.94
1871 1966 3.492313 CATTCAAAGAACGCCTAGCAAC 58.508 45.455 0.00 0.00 0.00 4.17
1917 2012 8.099537 CCACTAGCATAATCTTCCTAATGACAT 58.900 37.037 0.00 0.00 0.00 3.06
1918 2013 7.290014 TCCACTAGCATAATCTTCCTAATGACA 59.710 37.037 0.00 0.00 0.00 3.58
1936 2032 7.923878 TGGAACTTTTTAACAAATTCCACTAGC 59.076 33.333 12.08 0.00 40.44 3.42
1964 2060 6.757010 TGGAGAAACTGCGAAGATAGAATTAC 59.243 38.462 0.00 0.00 0.00 1.89
1994 2090 8.084073 ACATTTGACCATTACATTTTCTCACAG 58.916 33.333 0.00 0.00 0.00 3.66
1998 2094 7.867403 ACACACATTTGACCATTACATTTTCTC 59.133 33.333 0.00 0.00 0.00 2.87
2005 2101 8.856153 ATTAGTACACACATTTGACCATTACA 57.144 30.769 0.00 0.00 0.00 2.41
2089 2186 6.656632 ATCATGAACGTACTCCTGACATAT 57.343 37.500 0.00 0.00 0.00 1.78
2090 2187 6.465439 AATCATGAACGTACTCCTGACATA 57.535 37.500 0.00 0.00 0.00 2.29
2194 2300 3.743396 GGCTCTACTCTTGACACAAACTG 59.257 47.826 0.00 0.00 0.00 3.16
2216 2322 1.184970 AAATGGAGTGTTTGGGCCGG 61.185 55.000 0.00 0.00 0.00 6.13
2217 2323 0.678950 AAAATGGAGTGTTTGGGCCG 59.321 50.000 0.00 0.00 0.00 6.13
2218 2324 1.970640 AGAAAATGGAGTGTTTGGGCC 59.029 47.619 0.00 0.00 0.00 5.80
2219 2325 2.627699 TGAGAAAATGGAGTGTTTGGGC 59.372 45.455 0.00 0.00 0.00 5.36
2242 2777 2.302157 AGTGAGCCAAGGTGTTAGTACC 59.698 50.000 0.00 0.00 41.17 3.34
2281 3902 6.116126 AGTTTATCATGTTAAGAGAGCCCAC 58.884 40.000 0.00 0.00 0.00 4.61
2368 3992 3.592059 GATGCCACACTTGCAAAATCAT 58.408 40.909 0.00 0.00 42.92 2.45
2371 3995 1.693062 TGGATGCCACACTTGCAAAAT 59.307 42.857 0.00 0.00 42.92 1.82
2404 4030 5.126222 TGTGTGGTAGCTTTCATGTGAAAAA 59.874 36.000 9.24 0.00 42.72 1.94
2445 4081 2.476199 CAAGAGAAGGGAGAGGTGGAT 58.524 52.381 0.00 0.00 0.00 3.41
2519 5612 4.934356 TCTTGAAGGTATGAAGGGCAATT 58.066 39.130 0.00 0.00 0.00 2.32
2569 5662 0.693622 TCGCCAAAGGTAACCCATGA 59.306 50.000 0.00 0.00 37.17 3.07
2683 5776 4.960938 TCATCATTCCTTCGATGTTAGGG 58.039 43.478 1.09 0.00 39.99 3.53
2842 5935 1.609555 GCCGTGTATCTACCCTCTCTG 59.390 57.143 0.00 0.00 0.00 3.35
3098 6193 5.368145 TGCTGTCAGTACTGTTGAATTTCT 58.632 37.500 21.99 0.00 0.00 2.52
3165 6260 3.739401 AAGAAGGGATTTCCAACGGAT 57.261 42.857 0.00 0.00 36.40 4.18
3168 6263 3.153919 TCCAAAGAAGGGATTTCCAACG 58.846 45.455 0.00 0.00 36.40 4.10
3206 6301 4.036734 GCAATCCTTCAAGTTGAGAACACA 59.963 41.667 5.56 0.00 0.00 3.72
3278 6373 3.350833 GTTTGAGATTCAGGTGCCTCAT 58.649 45.455 0.00 0.00 35.82 2.90
3284 6379 4.929211 TCATGTACGTTTGAGATTCAGGTG 59.071 41.667 0.00 0.00 0.00 4.00
3305 6400 3.347216 GTTCTGGGAGCTTGCTTATTCA 58.653 45.455 0.00 0.00 0.00 2.57
3327 6422 4.965119 AAGCATCCTAAACGACCAATTC 57.035 40.909 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.