Multiple sequence alignment - TraesCS2D01G412600

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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 TraesCS2D01G412600 chr2D 100.000 7403 0 0 1 7403 527385275 527392677 0.000000e+00 13671
1 TraesCS2D01G412600 chr2D 97.673 1332 15 3 4751 6067 136425481 136426811 0.000000e+00 2274
2 TraesCS2D01G412600 chr2D 97.303 1335 20 3 4751 6070 364092662 364091329 0.000000e+00 2252
3 TraesCS2D01G412600 chr2D 98.587 566 8 0 4195 4760 106330782 106331347 0.000000e+00 1002
4 TraesCS2D01G412600 chr2D 98.587 566 8 0 4195 4760 294544152 294543587 0.000000e+00 1002
5 TraesCS2D01G412600 chr2B 92.617 4253 192 54 3 4202 624534823 624539006 0.000000e+00 6002
6 TraesCS2D01G412600 chr2B 95.776 1160 41 4 4911 6065 220436192 220437348 0.000000e+00 1864
7 TraesCS2D01G412600 chr2B 92.212 1284 83 12 4756 6033 270212600 270213872 0.000000e+00 1801
8 TraesCS2D01G412600 chr2B 90.533 1088 52 22 6069 7119 624539003 624540076 0.000000e+00 1391
9 TraesCS2D01G412600 chr2B 80.702 798 125 9 5256 6031 16947614 16948404 1.780000e-165 593
10 TraesCS2D01G412600 chr2B 92.887 239 9 3 7168 7403 624540230 624540463 2.560000e-89 340
11 TraesCS2D01G412600 chr2B 97.115 104 2 1 7078 7181 624540110 624540212 2.750000e-39 174
12 TraesCS2D01G412600 chr2A 92.491 2730 97 46 1531 4201 672343901 672346581 0.000000e+00 3807
13 TraesCS2D01G412600 chr2A 90.972 1451 72 19 3 1425 672342423 672343842 0.000000e+00 1899
14 TraesCS2D01G412600 chr2A 96.744 952 15 3 5135 6070 624463175 624462224 0.000000e+00 1572
15 TraesCS2D01G412600 chr2A 90.316 1012 71 18 6069 7058 672346579 672347585 0.000000e+00 1301
16 TraesCS2D01G412600 chr1D 97.523 1332 17 3 4751 6067 223523247 223524577 0.000000e+00 2263
17 TraesCS2D01G412600 chr1D 98.763 566 7 0 4195 4760 94052573 94052008 0.000000e+00 1007
18 TraesCS2D01G412600 chr1D 98.587 566 8 0 4195 4760 269367851 269367286 0.000000e+00 1002
19 TraesCS2D01G412600 chr5A 97.489 1314 14 4 4751 6049 524722625 524723934 0.000000e+00 2226
20 TraesCS2D01G412600 chr6A 96.781 1336 23 5 4751 6070 134698172 134699503 0.000000e+00 2211
21 TraesCS2D01G412600 chr6A 96.902 807 12 1 5277 6070 410902312 410901506 0.000000e+00 1339
22 TraesCS2D01G412600 chr7A 95.934 1328 44 6 4751 6070 541461873 541460548 0.000000e+00 2145
23 TraesCS2D01G412600 chr7A 90.411 1314 106 15 4751 6061 398925992 398924696 0.000000e+00 1711
24 TraesCS2D01G412600 chr7A 89.617 1175 99 10 4888 6060 245944745 245943592 0.000000e+00 1472
25 TraesCS2D01G412600 chr6B 96.187 813 24 4 5259 6070 192347012 192346206 0.000000e+00 1323
26 TraesCS2D01G412600 chr1B 82.669 1229 179 19 4748 5971 649160505 649161704 0.000000e+00 1059
27 TraesCS2D01G412600 chr7D 98.763 566 7 0 4195 4760 487763869 487764434 0.000000e+00 1007
28 TraesCS2D01G412600 chr7D 98.587 566 8 0 4195 4760 465338646 465339211 0.000000e+00 1002
29 TraesCS2D01G412600 chr4D 98.763 566 7 0 4195 4760 340563578 340564143 0.000000e+00 1007
30 TraesCS2D01G412600 chrUn 98.587 566 8 0 4195 4760 27368530 27367965 0.000000e+00 1002
31 TraesCS2D01G412600 chr1A 98.587 566 8 0 4195 4760 477662604 477662039 0.000000e+00 1002


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 TraesCS2D01G412600 chr2D 527385275 527392677 7402 False 13671.000000 13671 100.000000 1 7403 1 chr2D.!!$F3 7402
1 TraesCS2D01G412600 chr2D 136425481 136426811 1330 False 2274.000000 2274 97.673000 4751 6067 1 chr2D.!!$F2 1316
2 TraesCS2D01G412600 chr2D 364091329 364092662 1333 True 2252.000000 2252 97.303000 4751 6070 1 chr2D.!!$R2 1319
3 TraesCS2D01G412600 chr2D 106330782 106331347 565 False 1002.000000 1002 98.587000 4195 4760 1 chr2D.!!$F1 565
4 TraesCS2D01G412600 chr2D 294543587 294544152 565 True 1002.000000 1002 98.587000 4195 4760 1 chr2D.!!$R1 565
5 TraesCS2D01G412600 chr2B 624534823 624540463 5640 False 1976.750000 6002 93.288000 3 7403 4 chr2B.!!$F4 7400
6 TraesCS2D01G412600 chr2B 220436192 220437348 1156 False 1864.000000 1864 95.776000 4911 6065 1 chr2B.!!$F2 1154
7 TraesCS2D01G412600 chr2B 270212600 270213872 1272 False 1801.000000 1801 92.212000 4756 6033 1 chr2B.!!$F3 1277
8 TraesCS2D01G412600 chr2B 16947614 16948404 790 False 593.000000 593 80.702000 5256 6031 1 chr2B.!!$F1 775
9 TraesCS2D01G412600 chr2A 672342423 672347585 5162 False 2335.666667 3807 91.259667 3 7058 3 chr2A.!!$F1 7055
10 TraesCS2D01G412600 chr2A 624462224 624463175 951 True 1572.000000 1572 96.744000 5135 6070 1 chr2A.!!$R1 935
11 TraesCS2D01G412600 chr1D 223523247 223524577 1330 False 2263.000000 2263 97.523000 4751 6067 1 chr1D.!!$F1 1316
12 TraesCS2D01G412600 chr1D 94052008 94052573 565 True 1007.000000 1007 98.763000 4195 4760 1 chr1D.!!$R1 565
13 TraesCS2D01G412600 chr1D 269367286 269367851 565 True 1002.000000 1002 98.587000 4195 4760 1 chr1D.!!$R2 565
14 TraesCS2D01G412600 chr5A 524722625 524723934 1309 False 2226.000000 2226 97.489000 4751 6049 1 chr5A.!!$F1 1298
15 TraesCS2D01G412600 chr6A 134698172 134699503 1331 False 2211.000000 2211 96.781000 4751 6070 1 chr6A.!!$F1 1319
16 TraesCS2D01G412600 chr6A 410901506 410902312 806 True 1339.000000 1339 96.902000 5277 6070 1 chr6A.!!$R1 793
17 TraesCS2D01G412600 chr7A 541460548 541461873 1325 True 2145.000000 2145 95.934000 4751 6070 1 chr7A.!!$R3 1319
18 TraesCS2D01G412600 chr7A 398924696 398925992 1296 True 1711.000000 1711 90.411000 4751 6061 1 chr7A.!!$R2 1310
19 TraesCS2D01G412600 chr7A 245943592 245944745 1153 True 1472.000000 1472 89.617000 4888 6060 1 chr7A.!!$R1 1172
20 TraesCS2D01G412600 chr6B 192346206 192347012 806 True 1323.000000 1323 96.187000 5259 6070 1 chr6B.!!$R1 811
21 TraesCS2D01G412600 chr1B 649160505 649161704 1199 False 1059.000000 1059 82.669000 4748 5971 1 chr1B.!!$F1 1223
22 TraesCS2D01G412600 chr7D 487763869 487764434 565 False 1007.000000 1007 98.763000 4195 4760 1 chr7D.!!$F2 565
23 TraesCS2D01G412600 chr7D 465338646 465339211 565 False 1002.000000 1002 98.587000 4195 4760 1 chr7D.!!$F1 565
24 TraesCS2D01G412600 chr4D 340563578 340564143 565 False 1007.000000 1007 98.763000 4195 4760 1 chr4D.!!$F1 565
25 TraesCS2D01G412600 chrUn 27367965 27368530 565 True 1002.000000 1002 98.587000 4195 4760 1 chrUn.!!$R1 565
26 TraesCS2D01G412600 chr1A 477662039 477662604 565 True 1002.000000 1002 98.587000 4195 4760 1 chr1A.!!$R1 565

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
301 328 0.037232 AACTCTTGCCGCTCCAGTAC 60.037 55.000 0.00 0.00 0.00 2.73 F
447 483 0.645355 CACAGACGCGCGATGTAAAT 59.355 50.000 39.36 12.67 0.00 1.40 F
921 963 0.835276 AACATAACGGGGTAGGCTCC 59.165 55.000 0.00 0.00 0.00 4.70 F
1497 1550 0.466007 TGGGGTGAATGGCGATGATG 60.466 55.000 0.00 0.00 0.00 3.07 F
1636 1693 0.877743 GTTGCAACTCCCAGAAGCTC 59.122 55.000 22.36 0.00 0.00 4.09 F
2705 2782 1.021390 AGAAGGCGACATCCTTTGCG 61.021 55.000 0.00 0.00 45.92 4.85 F
2919 2996 1.081892 CACTTGTCAGGAATGGCTCG 58.918 55.000 0.00 0.00 0.00 5.03 F
3785 3906 3.069443 TCATGCCACAGTTTTCCCTTTTC 59.931 43.478 0.00 0.00 0.00 2.29 F
4319 4442 3.388024 GCATATGAGGACCTCTACCAACA 59.612 47.826 22.14 0.96 0.00 3.33 F
5798 5957 0.250209 CATATTCAGCGCAGGCCTCT 60.250 55.000 11.47 0.00 41.24 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 1510 0.036952 TGCTACCACTTCAGCTCAGC 60.037 55.000 0.00 0.00 38.63 4.26 R
1472 1525 1.302949 GCCATTCACCCCAGTGCTA 59.697 57.895 0.00 0.00 44.16 3.49 R
2903 2980 2.559698 TTTCGAGCCATTCCTGACAA 57.440 45.000 0.00 0.00 0.00 3.18 R
3349 3456 2.234661 CAGTGGTGAGTTCTATGGCTGA 59.765 50.000 0.00 0.00 0.00 4.26 R
3394 3501 5.437289 TTGCAAATATACCAGTGCATAGC 57.563 39.130 0.00 0.00 45.74 2.97 R
4319 4442 0.036294 GCCTTCCTTCGTGCCTAACT 60.036 55.000 0.00 0.00 0.00 2.24 R
4459 4582 1.067582 CGAAGTACTCCCGCCATCC 59.932 63.158 0.00 0.00 0.00 3.51 R
4630 4753 1.953559 CACACCTCAATGGGGATACG 58.046 55.000 5.97 0.00 43.63 3.06 R
6195 6381 0.610174 TTCCAAGTCGCATGCTCTCT 59.390 50.000 17.13 8.15 0.00 3.10 R
7284 7612 0.179029 GGCCAGGTACCATTACGCAT 60.179 55.000 15.94 0.00 0.00 4.73 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
55 56 3.672241 GCAACTGTGAGGAAACAACGTTT 60.672 43.478 0.00 0.00 0.00 3.60
103 105 9.567848 GACATTCGTCAAATAACATTACCAAAT 57.432 29.630 0.00 0.00 42.13 2.32
104 106 9.567848 ACATTCGTCAAATAACATTACCAAATC 57.432 29.630 0.00 0.00 0.00 2.17
105 107 9.787532 CATTCGTCAAATAACATTACCAAATCT 57.212 29.630 0.00 0.00 0.00 2.40
152 163 6.459670 TTGAGACGAGTACAATGGCTATAA 57.540 37.500 0.00 0.00 0.00 0.98
155 166 5.700846 AGACGAGTACAATGGCTATAATCG 58.299 41.667 0.00 0.49 40.97 3.34
273 300 3.943381 TGATCATGTGAAGCAATCCAGAC 59.057 43.478 0.00 0.00 0.00 3.51
280 307 1.133790 GAAGCAATCCAGACCACATGC 59.866 52.381 0.00 0.00 0.00 4.06
301 328 0.037232 AACTCTTGCCGCTCCAGTAC 60.037 55.000 0.00 0.00 0.00 2.73
440 476 2.428569 GAGAACACAGACGCGCGA 60.429 61.111 39.36 0.00 0.00 5.87
447 483 0.645355 CACAGACGCGCGATGTAAAT 59.355 50.000 39.36 12.67 0.00 1.40
448 484 1.060553 CACAGACGCGCGATGTAAATT 59.939 47.619 39.36 11.73 0.00 1.82
449 485 1.730064 ACAGACGCGCGATGTAAATTT 59.270 42.857 39.36 10.81 0.00 1.82
493 529 4.451150 TCACACGGATGCGAGGGC 62.451 66.667 15.49 0.00 40.52 5.19
497 533 1.153449 CACGGATGCGAGGGCTTTA 60.153 57.895 15.49 0.00 40.82 1.85
499 535 1.327690 ACGGATGCGAGGGCTTTAGA 61.328 55.000 15.49 0.00 40.82 2.10
507 543 1.612442 AGGGCTTTAGACTCCGGCA 60.612 57.895 0.00 0.00 0.00 5.69
763 805 2.357154 GCCGCCGCTAGGGTATTC 60.357 66.667 6.02 0.00 38.44 1.75
867 909 2.173669 GCCGTGTCATGTCCATCCG 61.174 63.158 0.00 0.00 0.00 4.18
898 940 2.983592 CCCGTTGCCAGTTCACCC 60.984 66.667 0.00 0.00 0.00 4.61
920 962 1.474498 CCAACATAACGGGGTAGGCTC 60.474 57.143 0.00 0.00 0.00 4.70
921 963 0.835276 AACATAACGGGGTAGGCTCC 59.165 55.000 0.00 0.00 0.00 4.70
953 995 3.093057 ACCTCTCAGTGATCACCAGTAC 58.907 50.000 22.21 0.00 0.00 2.73
972 1014 2.208872 ACTACTGCCATTCCCCATTCT 58.791 47.619 0.00 0.00 0.00 2.40
1029 1075 1.993391 CAACCCGGGGCTTCTCCTA 60.993 63.158 27.92 0.00 34.39 2.94
1035 1081 2.447714 GGGGCTTCTCCTAGGGCTG 61.448 68.421 9.46 0.00 34.39 4.85
1038 1084 1.631071 GGCTTCTCCTAGGGCTGCTT 61.631 60.000 9.46 0.00 0.00 3.91
1069 1115 2.624838 CTCAATTGGTGCTTGGTGAGTT 59.375 45.455 5.42 0.00 0.00 3.01
1087 1133 2.695666 AGTTGTTGATCCGATCCGATCT 59.304 45.455 20.20 1.80 39.57 2.75
1094 1140 4.560128 TGATCCGATCCGATCTGATTTTC 58.440 43.478 20.20 6.04 39.57 2.29
1106 1152 3.829948 TCTGATTTTCGTACAGGTCGAC 58.170 45.455 7.13 7.13 37.05 4.20
1131 1177 4.308265 TGTTCGTGTTATCGTTGATGGAA 58.692 39.130 0.00 0.00 0.00 3.53
1150 1196 1.125093 ATCGGTGCGATTGGGGGATA 61.125 55.000 0.00 0.00 44.59 2.59
1161 1207 3.983533 TTGGGGGATATTAAACCAGGG 57.016 47.619 0.00 0.00 32.01 4.45
1376 1422 1.739562 GCTGCCGTCCTTCTCTGTG 60.740 63.158 0.00 0.00 0.00 3.66
1444 1497 6.817641 TGTGGCATGGTATCATTTCAATTTTC 59.182 34.615 0.00 0.00 0.00 2.29
1445 1498 6.817641 GTGGCATGGTATCATTTCAATTTTCA 59.182 34.615 0.00 0.00 0.00 2.69
1446 1499 6.817641 TGGCATGGTATCATTTCAATTTTCAC 59.182 34.615 0.00 0.00 0.00 3.18
1447 1500 6.258507 GGCATGGTATCATTTCAATTTTCACC 59.741 38.462 0.00 0.00 0.00 4.02
1448 1501 7.043565 GCATGGTATCATTTCAATTTTCACCT 58.956 34.615 0.00 0.00 0.00 4.00
1449 1502 7.223387 GCATGGTATCATTTCAATTTTCACCTC 59.777 37.037 0.00 0.00 0.00 3.85
1450 1503 7.773489 TGGTATCATTTCAATTTTCACCTCA 57.227 32.000 0.00 0.00 0.00 3.86
1451 1504 7.829725 TGGTATCATTTCAATTTTCACCTCAG 58.170 34.615 0.00 0.00 0.00 3.35
1452 1505 6.753744 GGTATCATTTCAATTTTCACCTCAGC 59.246 38.462 0.00 0.00 0.00 4.26
1453 1506 5.787953 TCATTTCAATTTTCACCTCAGCA 57.212 34.783 0.00 0.00 0.00 4.41
1454 1507 5.531634 TCATTTCAATTTTCACCTCAGCAC 58.468 37.500 0.00 0.00 0.00 4.40
1455 1508 5.302568 TCATTTCAATTTTCACCTCAGCACT 59.697 36.000 0.00 0.00 0.00 4.40
1456 1509 4.836125 TTCAATTTTCACCTCAGCACTC 57.164 40.909 0.00 0.00 0.00 3.51
1457 1510 2.807967 TCAATTTTCACCTCAGCACTCG 59.192 45.455 0.00 0.00 0.00 4.18
1458 1511 1.160137 ATTTTCACCTCAGCACTCGC 58.840 50.000 0.00 0.00 38.99 5.03
1472 1525 1.291588 CTCGCTGAGCTGAAGTGGT 59.708 57.895 1.78 0.00 0.00 4.16
1493 1546 1.077501 CACTGGGGTGAATGGCGAT 60.078 57.895 0.00 0.00 45.61 4.58
1497 1550 0.466007 TGGGGTGAATGGCGATGATG 60.466 55.000 0.00 0.00 0.00 3.07
1500 1553 1.605710 GGGTGAATGGCGATGATGAAG 59.394 52.381 0.00 0.00 0.00 3.02
1504 1557 2.945008 TGAATGGCGATGATGAAGGAAC 59.055 45.455 0.00 0.00 0.00 3.62
1511 1564 3.812053 GCGATGATGAAGGAACTATGCTT 59.188 43.478 0.00 0.00 38.49 3.91
1514 1567 5.985530 CGATGATGAAGGAACTATGCTTGTA 59.014 40.000 0.00 0.00 38.49 2.41
1522 1575 4.775780 AGGAACTATGCTTGTACAGTGGTA 59.224 41.667 0.00 0.00 36.02 3.25
1526 1579 7.120726 GGAACTATGCTTGTACAGTGGTAAAAT 59.879 37.037 0.00 0.00 0.00 1.82
1550 1604 4.451900 AGATGGAAATACCTGCTAAACCG 58.548 43.478 0.00 0.00 39.86 4.44
1551 1605 3.706600 TGGAAATACCTGCTAAACCGT 57.293 42.857 0.00 0.00 39.86 4.83
1552 1606 4.023726 TGGAAATACCTGCTAAACCGTT 57.976 40.909 0.00 0.00 39.86 4.44
1553 1607 5.163281 TGGAAATACCTGCTAAACCGTTA 57.837 39.130 0.00 0.00 39.86 3.18
1554 1608 5.747342 TGGAAATACCTGCTAAACCGTTAT 58.253 37.500 0.00 0.00 39.86 1.89
1563 1620 7.111466 ACCTGCTAAACCGTTATTTAATACCA 58.889 34.615 0.00 0.00 0.00 3.25
1588 1645 9.546428 CAAAGTTAGAAAATCATTTTGTTCCCT 57.454 29.630 0.00 0.00 31.94 4.20
1591 1648 7.290014 AGTTAGAAAATCATTTTGTTCCCTGGT 59.710 33.333 0.00 0.00 31.94 4.00
1632 1689 1.228124 CCGGTTGCAACTCCCAGAA 60.228 57.895 27.64 0.00 0.00 3.02
1636 1693 0.877743 GTTGCAACTCCCAGAAGCTC 59.122 55.000 22.36 0.00 0.00 4.09
1698 1755 7.120051 TGTAAGCAAGCCTATAAATGGGTTTA 58.880 34.615 0.00 0.00 42.57 2.01
1705 1762 8.567948 CAAGCCTATAAATGGGTTTACATACAG 58.432 37.037 0.00 0.00 42.57 2.74
1744 1808 3.326588 ACATACTTGCAGGTACCAGACAA 59.673 43.478 15.94 13.61 0.00 3.18
1763 1827 7.207383 CAGACAACAAAATGATATGGCATCAT 58.793 34.615 1.65 0.00 40.20 2.45
1870 1943 6.677913 TGCAAGCCTACTTAAAACAATTCTC 58.322 36.000 0.00 0.00 33.74 2.87
2108 2183 7.120138 CCCACTCAACCTATTTACAAACGTTAT 59.880 37.037 0.00 0.00 0.00 1.89
2153 2228 8.114331 TCTCTACCTAACATCGTGAAAAACTA 57.886 34.615 0.00 0.00 0.00 2.24
2176 2251 2.159014 AGACAACGGTAAGTGCAGTTGA 60.159 45.455 17.21 0.00 43.70 3.18
2316 2391 1.203052 CAGAACCCCATGATTGTGTGC 59.797 52.381 0.00 0.00 0.00 4.57
2483 2560 7.811282 TCTTATCATGAATGGGGTAAAAGCTA 58.189 34.615 0.00 0.00 0.00 3.32
2528 2605 9.191995 CAGTATATGCTGATGTTTATGTTACGA 57.808 33.333 15.07 0.00 38.70 3.43
2550 2627 7.732025 ACGACATTTATGGTGGATGTAATAGA 58.268 34.615 0.00 0.00 34.38 1.98
2705 2782 1.021390 AGAAGGCGACATCCTTTGCG 61.021 55.000 0.00 0.00 45.92 4.85
2903 2980 5.429762 TGTATGGGAGAATCAAGGAATCACT 59.570 40.000 0.00 0.00 36.25 3.41
2919 2996 1.081892 CACTTGTCAGGAATGGCTCG 58.918 55.000 0.00 0.00 0.00 5.03
3042 3119 3.493503 CGCGTTTAAAGGAAAGTCACTCT 59.506 43.478 11.95 0.00 0.00 3.24
3043 3120 4.025145 CGCGTTTAAAGGAAAGTCACTCTT 60.025 41.667 11.95 0.00 38.10 2.85
3265 3342 4.633565 TGCAATAATGTATGAACGACTGCA 59.366 37.500 0.00 0.00 33.96 4.41
3326 3433 8.034313 AGTTGGCCTTGTATCTTCTATATTCA 57.966 34.615 3.32 0.00 0.00 2.57
3349 3456 8.324191 TCAAACTTCTGTCTGAGGGATAATAT 57.676 34.615 0.00 0.00 0.00 1.28
3394 3501 5.406780 GCCGAATCCTCTTGTAGTATTGATG 59.593 44.000 0.00 0.00 0.00 3.07
3401 3508 6.041979 TCCTCTTGTAGTATTGATGCTATGCA 59.958 38.462 0.00 0.00 44.86 3.96
3433 3540 3.550820 TGCAAAGTCACTAATGTGTGGT 58.449 40.909 0.00 0.00 44.14 4.16
3619 3739 9.926158 TTGTTCAACTTATATTTACGTAGGACA 57.074 29.630 0.00 0.00 0.00 4.02
3620 3740 9.577110 TGTTCAACTTATATTTACGTAGGACAG 57.423 33.333 0.00 0.00 0.00 3.51
3621 3741 9.028185 GTTCAACTTATATTTACGTAGGACAGG 57.972 37.037 0.00 0.00 0.00 4.00
3785 3906 3.069443 TCATGCCACAGTTTTCCCTTTTC 59.931 43.478 0.00 0.00 0.00 2.29
4014 4135 4.090090 TGTTCTTCTTTCCCACAAACCAA 58.910 39.130 0.00 0.00 0.00 3.67
4015 4136 4.714308 TGTTCTTCTTTCCCACAAACCAAT 59.286 37.500 0.00 0.00 0.00 3.16
4016 4137 5.188751 TGTTCTTCTTTCCCACAAACCAATT 59.811 36.000 0.00 0.00 0.00 2.32
4095 4216 5.643777 TCACTAGCAAGCTGTTATTTTCTCC 59.356 40.000 4.53 0.00 0.00 3.71
4101 4222 5.562890 GCAAGCTGTTATTTTCTCCGAACTT 60.563 40.000 0.00 0.00 0.00 2.66
4119 4242 5.163764 CGAACTTGCTTTAATCATGCACCTA 60.164 40.000 0.00 0.00 35.34 3.08
4120 4243 6.458751 CGAACTTGCTTTAATCATGCACCTAT 60.459 38.462 0.00 0.00 35.34 2.57
4121 4244 6.780457 ACTTGCTTTAATCATGCACCTATT 57.220 33.333 0.00 0.00 35.34 1.73
4122 4245 7.880160 ACTTGCTTTAATCATGCACCTATTA 57.120 32.000 0.00 0.00 35.34 0.98
4319 4442 3.388024 GCATATGAGGACCTCTACCAACA 59.612 47.826 22.14 0.96 0.00 3.33
4459 4582 3.742433 AGGACGAGGAGATTAAGCATG 57.258 47.619 0.00 0.00 0.00 4.06
5654 5812 1.264749 TTAGGTGTGGCGGAGATGCT 61.265 55.000 0.00 0.00 34.52 3.79
5798 5957 0.250209 CATATTCAGCGCAGGCCTCT 60.250 55.000 11.47 0.00 41.24 3.69
6067 6240 6.422776 TTGTTGTTGTTGTTGTTGTTGTTT 57.577 29.167 0.00 0.00 0.00 2.83
6234 6420 2.795110 GGAGCCTCGAGATGCTGCT 61.795 63.158 21.96 17.59 42.02 4.24
6315 6501 3.607078 CGCTTAACAAGAAAGGAGTGCAC 60.607 47.826 9.40 9.40 0.00 4.57
6371 6557 1.005097 TGTCAGGAATTCCAGCATGCT 59.995 47.619 26.22 16.30 38.89 3.79
6463 6650 6.447162 GCCAATAAGGTGTATTCCTTTATGC 58.553 40.000 3.31 0.00 44.36 3.14
6504 6691 5.898972 ACTCCCATGGTAATGCAACAATATT 59.101 36.000 11.73 0.00 31.93 1.28
6509 6696 8.149647 CCCATGGTAATGCAACAATATTATGTT 58.850 33.333 11.73 0.00 44.08 2.71
6520 6707 6.220726 ACAATATTATGTTGGGCTTGTTCC 57.779 37.500 6.64 0.00 0.00 3.62
6522 6709 2.990740 TTATGTTGGGCTTGTTCCCT 57.009 45.000 0.12 0.00 46.67 4.20
6523 6710 2.214376 TATGTTGGGCTTGTTCCCTG 57.786 50.000 0.12 0.00 46.67 4.45
6524 6711 0.482446 ATGTTGGGCTTGTTCCCTGA 59.518 50.000 0.12 0.00 46.67 3.86
6525 6712 0.178992 TGTTGGGCTTGTTCCCTGAG 60.179 55.000 0.12 0.00 46.67 3.35
6526 6713 0.178990 GTTGGGCTTGTTCCCTGAGT 60.179 55.000 0.12 0.00 46.67 3.41
6527 6714 0.110486 TTGGGCTTGTTCCCTGAGTC 59.890 55.000 0.12 0.00 46.67 3.36
6528 6715 1.059584 TGGGCTTGTTCCCTGAGTCA 61.060 55.000 0.12 0.00 46.67 3.41
6529 6716 0.329596 GGGCTTGTTCCCTGAGTCAT 59.670 55.000 0.00 0.00 43.13 3.06
6530 6717 1.680249 GGGCTTGTTCCCTGAGTCATC 60.680 57.143 0.00 0.00 43.13 2.92
6543 6730 4.383444 CCTGAGTCATCTATTGGACTGCAA 60.383 45.833 0.00 0.00 44.03 4.08
6606 6799 7.692460 TCATTGAATGCATTGTAGACTTCTT 57.308 32.000 18.59 0.00 0.00 2.52
6694 6890 4.154918 CAGGTGTGCTTCTTTAAGTCATCC 59.845 45.833 0.00 0.00 34.99 3.51
6701 6897 5.115480 GCTTCTTTAAGTCATCCTCAGAGG 58.885 45.833 10.70 10.70 34.99 3.69
6730 6926 5.026121 TGTGGAATAGGTCATCTTCAGAGT 58.974 41.667 0.00 0.00 0.00 3.24
6799 6995 1.199615 CCCAGAGAACCTCCTCCTTC 58.800 60.000 0.00 0.00 33.76 3.46
6814 7011 2.520979 TCCTTCGTTGTTGTTTTTGCG 58.479 42.857 0.00 0.00 0.00 4.85
6826 7023 6.899114 TGTTGTTTTTGCGTTTGGTTTATTT 58.101 28.000 0.00 0.00 0.00 1.40
6844 7041 3.768468 TTTTCGCACGTTTTCTCCTTT 57.232 38.095 0.00 0.00 0.00 3.11
6872 7069 4.980573 ACCTAAGTTTGTTGGCAGTATCA 58.019 39.130 0.00 0.00 0.00 2.15
6902 7099 7.092444 TGACACCCATTTCTTATTCCTCTATGT 60.092 37.037 0.00 0.00 0.00 2.29
6981 7185 1.337703 TGCAAGGTTGTCAGCATTGTC 59.662 47.619 14.27 8.22 31.05 3.18
6982 7186 1.337703 GCAAGGTTGTCAGCATTGTCA 59.662 47.619 14.27 0.00 0.00 3.58
7064 7272 7.792374 TTTATTCTCTGAATATGCACTCACC 57.208 36.000 0.00 0.00 0.00 4.02
7065 7273 5.627182 ATTCTCTGAATATGCACTCACCT 57.373 39.130 0.00 0.00 0.00 4.00
7101 7321 0.828022 ACCTCGGGTTATTGCGATCA 59.172 50.000 0.00 0.00 27.29 2.92
7131 7425 2.677836 GGAGATGAATGCGTGTTGCTTA 59.322 45.455 0.00 0.00 46.63 3.09
7181 7475 4.138290 ACGAAATGAATGTGTACAACCCA 58.862 39.130 0.00 0.00 0.00 4.51
7182 7476 4.023536 ACGAAATGAATGTGTACAACCCAC 60.024 41.667 0.00 0.00 0.00 4.61
7183 7477 4.614993 CGAAATGAATGTGTACAACCCACC 60.615 45.833 0.00 0.00 31.71 4.61
7184 7478 3.517296 ATGAATGTGTACAACCCACCA 57.483 42.857 0.00 0.00 31.71 4.17
7185 7479 2.857483 TGAATGTGTACAACCCACCAG 58.143 47.619 0.00 0.00 31.71 4.00
7188 7482 0.470766 TGTGTACAACCCACCAGGAC 59.529 55.000 0.00 0.00 39.89 3.85
7189 7483 0.763035 GTGTACAACCCACCAGGACT 59.237 55.000 0.00 0.00 39.89 3.85
7284 7612 1.678598 CGGCTCCCGGTACCATTGTA 61.679 60.000 13.54 0.00 44.15 2.41
7303 7631 0.179029 ATGCGTAATGGTACCTGGCC 60.179 55.000 14.36 0.00 0.00 5.36
7379 7707 3.142393 CCGATCGCCTCCATTCCT 58.858 61.111 10.32 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.951602 AGACGGTGGCAGTTTTAAACC 59.048 47.619 4.01 0.00 0.00 3.27
10 11 1.226802 CGAGATCAGACGGTGGCAG 60.227 63.158 0.00 0.00 0.00 4.85
55 56 1.228124 CGGAAGGGGTTGACAAGCA 60.228 57.895 18.44 0.00 0.00 3.91
103 105 5.574891 TGTGAAACTGCTTGCTTAAAAGA 57.425 34.783 0.00 0.00 38.04 2.52
104 106 5.807011 ACTTGTGAAACTGCTTGCTTAAAAG 59.193 36.000 0.00 0.00 38.04 2.27
105 107 5.719173 ACTTGTGAAACTGCTTGCTTAAAA 58.281 33.333 0.00 0.00 38.04 1.52
111 114 3.510719 TCAAACTTGTGAAACTGCTTGC 58.489 40.909 0.00 0.00 38.04 4.01
152 163 3.634397 TTTTGATCCTGCCTTCTCGAT 57.366 42.857 0.00 0.00 0.00 3.59
155 166 3.941483 TCGAATTTTGATCCTGCCTTCTC 59.059 43.478 0.00 0.00 0.00 2.87
280 307 0.886490 ACTGGAGCGGCAAGAGTTTG 60.886 55.000 1.45 0.00 37.36 2.93
296 323 7.443575 CCATGGATTTGATCTAGGAAAGTACTG 59.556 40.741 5.56 0.00 0.00 2.74
301 328 5.135383 TGCCATGGATTTGATCTAGGAAAG 58.865 41.667 18.40 0.00 0.00 2.62
448 484 0.451383 CGATCTGGATGCGGCAAAAA 59.549 50.000 6.82 0.00 0.00 1.94
449 485 0.392327 TCGATCTGGATGCGGCAAAA 60.392 50.000 6.82 0.00 0.00 2.44
493 529 3.259902 GGTAAGTTGCCGGAGTCTAAAG 58.740 50.000 5.05 0.00 0.00 1.85
497 533 1.590147 CGGTAAGTTGCCGGAGTCT 59.410 57.895 23.11 0.00 44.98 3.24
507 543 1.140375 GGCGTCGGATCGGTAAGTT 59.860 57.895 0.00 0.00 0.00 2.66
601 637 1.810853 CAGCGACATGACGATGCCA 60.811 57.895 21.35 0.00 42.22 4.92
758 800 0.107848 CTGTGGTGTCCCCCGAATAC 60.108 60.000 0.00 0.00 0.00 1.89
763 805 4.394712 GAGCTGTGGTGTCCCCCG 62.395 72.222 0.00 0.00 0.00 5.73
867 909 2.436646 CGGGTCCCACATGTCAGC 60.437 66.667 9.12 0.00 0.00 4.26
920 962 0.041833 TGAGAGGTGGGAGAGAAGGG 59.958 60.000 0.00 0.00 0.00 3.95
921 963 1.272985 ACTGAGAGGTGGGAGAGAAGG 60.273 57.143 0.00 0.00 0.00 3.46
953 995 2.487986 GGAGAATGGGGAATGGCAGTAG 60.488 54.545 0.00 0.00 0.00 2.57
972 1014 1.002624 GCGGTTGAGGTGGATTGGA 60.003 57.895 0.00 0.00 0.00 3.53
1035 1081 1.930908 AATTGAGCCGCAGCAGAAGC 61.931 55.000 0.00 0.00 43.56 3.86
1038 1084 2.042259 CCAATTGAGCCGCAGCAGA 61.042 57.895 7.12 0.00 43.56 4.26
1069 1115 2.306847 TCAGATCGGATCGGATCAACA 58.693 47.619 32.62 19.23 44.21 3.33
1087 1133 3.928727 AGTCGACCTGTACGAAAATCA 57.071 42.857 13.01 0.00 41.31 2.57
1094 1140 1.712350 CGAACAAAGTCGACCTGTACG 59.288 52.381 18.30 11.41 43.86 3.67
1106 1152 5.079406 CCATCAACGATAACACGAACAAAG 58.921 41.667 0.00 0.00 37.03 2.77
1135 1181 3.254903 GGTTTAATATCCCCCAATCGCAC 59.745 47.826 0.00 0.00 0.00 5.34
1150 1196 1.684869 CCATCCACGCCCTGGTTTAAT 60.685 52.381 0.00 0.00 41.52 1.40
1376 1422 0.456653 GGCACACATGGACGAATTGC 60.457 55.000 0.00 0.00 0.00 3.56
1451 1504 1.373999 ACTTCAGCTCAGCGAGTGC 60.374 57.895 3.02 3.36 43.24 4.40
1452 1505 1.013005 CCACTTCAGCTCAGCGAGTG 61.013 60.000 18.48 18.48 37.99 3.51
1453 1506 1.291588 CCACTTCAGCTCAGCGAGT 59.708 57.895 0.00 0.00 31.39 4.18
1454 1507 0.528017 TACCACTTCAGCTCAGCGAG 59.472 55.000 0.00 0.00 0.00 5.03
1455 1508 0.528017 CTACCACTTCAGCTCAGCGA 59.472 55.000 0.00 0.00 0.00 4.93
1456 1509 1.080995 GCTACCACTTCAGCTCAGCG 61.081 60.000 0.00 0.00 34.86 5.18
1457 1510 0.036952 TGCTACCACTTCAGCTCAGC 60.037 55.000 0.00 0.00 38.63 4.26
1458 1511 1.719600 GTGCTACCACTTCAGCTCAG 58.280 55.000 0.00 0.00 38.93 3.35
1459 1512 3.914984 GTGCTACCACTTCAGCTCA 57.085 52.632 0.00 0.00 38.93 4.26
1472 1525 1.302949 GCCATTCACCCCAGTGCTA 59.697 57.895 0.00 0.00 44.16 3.49
1493 1546 6.048732 TGTACAAGCATAGTTCCTTCATCA 57.951 37.500 0.00 0.00 0.00 3.07
1497 1550 4.631813 CCACTGTACAAGCATAGTTCCTTC 59.368 45.833 0.00 0.00 0.00 3.46
1500 1553 3.939066 ACCACTGTACAAGCATAGTTCC 58.061 45.455 0.00 0.00 0.00 3.62
1504 1557 9.378551 TCTAATTTTACCACTGTACAAGCATAG 57.621 33.333 0.00 0.00 0.00 2.23
1511 1564 9.747898 ATTTCCATCTAATTTTACCACTGTACA 57.252 29.630 0.00 0.00 0.00 2.90
1514 1567 9.185680 GGTATTTCCATCTAATTTTACCACTGT 57.814 33.333 0.00 0.00 35.97 3.55
1526 1579 6.053005 CGGTTTAGCAGGTATTTCCATCTAA 58.947 40.000 0.00 0.00 39.02 2.10
1563 1620 9.546428 CAGGGAACAAAATGATTTTCTAACTTT 57.454 29.630 0.00 0.00 0.00 2.66
1570 1627 4.996758 CCACCAGGGAACAAAATGATTTTC 59.003 41.667 0.00 0.00 40.01 2.29
1576 1633 2.697751 TCAACCACCAGGGAACAAAATG 59.302 45.455 0.00 0.00 41.15 2.32
1581 1638 1.496857 TCAATCAACCACCAGGGAACA 59.503 47.619 0.00 0.00 41.15 3.18
1591 1648 8.575589 CCGGAAAAATATCATATCAATCAACCA 58.424 33.333 0.00 0.00 0.00 3.67
1632 1689 3.430929 CCTGGTTTCTATGTAAGCGAGCT 60.431 47.826 0.00 0.00 0.00 4.09
1636 1693 3.536956 TCCCTGGTTTCTATGTAAGCG 57.463 47.619 0.00 0.00 0.00 4.68
1698 1755 7.093156 TGTTCATCAGAGATCTTTCCTGTATGT 60.093 37.037 9.14 0.00 0.00 2.29
1705 1762 7.254727 GCAAGTATGTTCATCAGAGATCTTTCC 60.255 40.741 0.00 0.00 0.00 3.13
1710 1767 5.466058 CCTGCAAGTATGTTCATCAGAGATC 59.534 44.000 0.00 0.00 0.00 2.75
1827 1900 4.261801 TGCAAAATCCAGTAGTAAGGCTC 58.738 43.478 0.00 0.00 0.00 4.70
2077 2152 3.525800 AAATAGGTTGAGTGGGCAAGT 57.474 42.857 0.00 0.00 0.00 3.16
2153 2228 2.914059 ACTGCACTTACCGTTGTCTTT 58.086 42.857 0.00 0.00 0.00 2.52
2176 2251 2.729028 ATTTACCTGCGGCATAACCT 57.271 45.000 1.75 0.00 35.61 3.50
2275 2350 9.868277 GTTCTGCTATATCTTTAGTGCATAGAT 57.132 33.333 0.00 0.00 33.46 1.98
2316 2391 7.581011 AGTTGTGAAACTAAAAAGTTGCAAG 57.419 32.000 0.00 0.00 38.89 4.01
2352 2428 4.908601 TGGTTGATTCAGGATACACACT 57.091 40.909 0.00 0.00 41.41 3.55
2435 2512 5.675538 AGCATCTAAGGTAGTTTCACCATC 58.324 41.667 0.00 0.00 41.40 3.51
2437 2514 5.086104 GAGCATCTAAGGTAGTTTCACCA 57.914 43.478 0.00 0.00 41.40 4.17
2483 2560 5.291905 ACTGTAGCTTGAGTGGTTAAAGT 57.708 39.130 0.00 0.00 0.00 2.66
2528 2605 7.517320 TGCTCTATTACATCCACCATAAATGT 58.483 34.615 0.00 0.00 37.40 2.71
2705 2782 3.091545 TCCTGCAAGACCCATTGAAATC 58.908 45.455 0.00 0.00 34.07 2.17
2903 2980 2.559698 TTTCGAGCCATTCCTGACAA 57.440 45.000 0.00 0.00 0.00 3.18
2947 3024 5.643777 CGATTAACAGAGTTGAAATGGGAGT 59.356 40.000 0.00 0.00 0.00 3.85
3219 3296 6.149640 GCAGATGCATTCAATAGACAGATCAT 59.850 38.462 0.00 0.00 41.59 2.45
3326 3433 8.324191 TGATATTATCCCTCAGACAGAAGTTT 57.676 34.615 1.27 0.00 0.00 2.66
3349 3456 2.234661 CAGTGGTGAGTTCTATGGCTGA 59.765 50.000 0.00 0.00 0.00 4.26
3394 3501 5.437289 TTGCAAATATACCAGTGCATAGC 57.563 39.130 0.00 0.00 45.74 2.97
3401 3508 8.677300 CATTAGTGACTTTGCAAATATACCAGT 58.323 33.333 13.23 4.74 0.00 4.00
3433 3540 9.605275 CCATAAAGAAAGTATCATCAAGACTCA 57.395 33.333 0.00 0.00 0.00 3.41
3617 3737 5.485708 AGGAAGCTTCAAGTAGTATTCCTGT 59.514 40.000 27.02 0.00 39.69 4.00
3618 3738 5.983540 AGGAAGCTTCAAGTAGTATTCCTG 58.016 41.667 27.02 0.00 39.69 3.86
3619 3739 6.628644 AAGGAAGCTTCAAGTAGTATTCCT 57.371 37.500 27.02 9.01 41.33 3.36
3620 3740 7.390718 TCAAAAGGAAGCTTCAAGTAGTATTCC 59.609 37.037 27.02 6.67 35.29 3.01
3621 3741 8.324163 TCAAAAGGAAGCTTCAAGTAGTATTC 57.676 34.615 27.02 6.37 0.00 1.75
3756 3877 1.999648 AACTGTGGCATGACACCAAT 58.000 45.000 28.69 11.34 39.39 3.16
3785 3906 1.535462 GTTCCACTTCCACAACATCGG 59.465 52.381 0.00 0.00 0.00 4.18
3988 4109 4.981806 TTGTGGGAAAGAAGAACAACAG 57.018 40.909 0.00 0.00 0.00 3.16
4095 4216 3.853671 GGTGCATGATTAAAGCAAGTTCG 59.146 43.478 0.00 0.00 40.35 3.95
4101 4222 5.534654 GGGTAATAGGTGCATGATTAAAGCA 59.465 40.000 0.00 0.00 35.63 3.91
4119 4242 2.361085 AAGACCACAGAGGGGGTAAT 57.639 50.000 0.00 0.00 43.89 1.89
4120 4243 2.113052 AGTAAGACCACAGAGGGGGTAA 59.887 50.000 0.00 0.00 43.89 2.85
4121 4244 1.720533 AGTAAGACCACAGAGGGGGTA 59.279 52.381 0.00 0.00 43.89 3.69
4122 4245 0.492276 AGTAAGACCACAGAGGGGGT 59.508 55.000 0.00 0.00 43.89 4.95
4319 4442 0.036294 GCCTTCCTTCGTGCCTAACT 60.036 55.000 0.00 0.00 0.00 2.24
4459 4582 1.067582 CGAAGTACTCCCGCCATCC 59.932 63.158 0.00 0.00 0.00 3.51
4630 4753 1.953559 CACACCTCAATGGGGATACG 58.046 55.000 5.97 0.00 43.63 3.06
5654 5812 3.947196 GCCACACATCCATCTCAACATAA 59.053 43.478 0.00 0.00 0.00 1.90
5798 5957 1.067669 CGCTATGCACTGGAGCTTCTA 59.932 52.381 9.31 0.00 33.91 2.10
6067 6240 9.679661 TCATATTACAATACTCAGCCTTTGAAA 57.320 29.630 0.00 0.00 34.81 2.69
6111 6290 6.778559 ACCATTGCTTAACTTGGGTTACTAAA 59.221 34.615 0.00 0.00 37.61 1.85
6118 6297 2.525368 GGACCATTGCTTAACTTGGGT 58.475 47.619 0.00 0.00 33.39 4.51
6180 6366 7.308049 CGCATGCTCTCTACTACTTGATAACTA 60.308 40.741 17.13 0.00 0.00 2.24
6195 6381 0.610174 TTCCAAGTCGCATGCTCTCT 59.390 50.000 17.13 8.15 0.00 3.10
6234 6420 6.301486 AGCAATTCTTGATATAGCATCCACA 58.699 36.000 0.00 0.00 0.00 4.17
6333 6519 5.513094 CCTGACAGAATACTGAAAGGTCCAA 60.513 44.000 3.32 0.00 46.03 3.53
6371 6557 1.556451 CTGTGATGACCTCCACATCCA 59.444 52.381 0.00 0.00 41.75 3.41
6463 6650 3.604582 GGAGTGAATGGAGAGAACTTGG 58.395 50.000 0.00 0.00 0.00 3.61
6520 6707 3.133542 TGCAGTCCAATAGATGACTCAGG 59.866 47.826 0.00 0.00 0.00 3.86
6522 6709 4.824479 TTGCAGTCCAATAGATGACTCA 57.176 40.909 0.00 0.00 0.00 3.41
6523 6710 6.690194 AAATTGCAGTCCAATAGATGACTC 57.310 37.500 0.00 0.00 43.22 3.36
6524 6711 6.888632 AGAAAATTGCAGTCCAATAGATGACT 59.111 34.615 0.00 0.00 43.22 3.41
6525 6712 7.093322 AGAAAATTGCAGTCCAATAGATGAC 57.907 36.000 0.00 0.00 43.22 3.06
6526 6713 8.985315 ATAGAAAATTGCAGTCCAATAGATGA 57.015 30.769 0.00 0.00 43.22 2.92
6527 6714 9.459640 CAATAGAAAATTGCAGTCCAATAGATG 57.540 33.333 0.00 0.00 43.22 2.90
6528 6715 9.412460 TCAATAGAAAATTGCAGTCCAATAGAT 57.588 29.630 0.00 0.00 43.22 1.98
6529 6716 8.806429 TCAATAGAAAATTGCAGTCCAATAGA 57.194 30.769 0.00 0.00 43.22 1.98
6530 6717 9.859427 TTTCAATAGAAAATTGCAGTCCAATAG 57.141 29.630 0.00 0.00 43.22 1.73
6606 6799 2.297033 GTGCAATTCCAGCCTTTTCTCA 59.703 45.455 0.00 0.00 0.00 3.27
6694 6890 4.697352 CCTATTCCACACAAAACCTCTGAG 59.303 45.833 0.00 0.00 0.00 3.35
6701 6897 6.206634 TGAAGATGACCTATTCCACACAAAAC 59.793 38.462 0.00 0.00 0.00 2.43
6730 6926 7.940137 ACGTGAAATATTATATGCCCTTACCAA 59.060 33.333 0.00 0.00 0.00 3.67
6799 6995 2.155924 ACCAAACGCAAAAACAACAACG 59.844 40.909 0.00 0.00 0.00 4.10
6814 7011 5.378351 AAACGTGCGAAAATAAACCAAAC 57.622 34.783 0.00 0.00 0.00 2.93
6826 7023 2.281517 TCAAAGGAGAAAACGTGCGAA 58.718 42.857 0.00 0.00 0.00 4.70
6844 7041 4.211125 TGCCAACAAACTTAGGTTGATCA 58.789 39.130 17.62 5.71 45.50 2.92
6872 7069 6.314917 AGGAATAAGAAATGGGTGTCAACTT 58.685 36.000 0.00 0.00 0.00 2.66
6943 7147 8.621532 ACCTTGCATTATGTCGATAAATATGT 57.378 30.769 0.00 0.00 0.00 2.29
6955 7159 3.156293 TGCTGACAACCTTGCATTATGT 58.844 40.909 0.00 0.00 0.00 2.29
6998 7202 5.871396 ATACAACCGTCATCAAGATACCT 57.129 39.130 0.00 0.00 0.00 3.08
7000 7204 6.145696 GCCTAATACAACCGTCATCAAGATAC 59.854 42.308 0.00 0.00 0.00 2.24
7012 7217 3.006940 TCTTTGCTGCCTAATACAACCG 58.993 45.455 0.00 0.00 0.00 4.44
7016 7221 7.880160 ATAACAATCTTTGCTGCCTAATACA 57.120 32.000 0.00 0.00 0.00 2.29
7058 7266 3.096092 TCAAGCCAAAAACAAGGTGAGT 58.904 40.909 0.00 0.00 0.00 3.41
7059 7267 3.799281 TCAAGCCAAAAACAAGGTGAG 57.201 42.857 0.00 0.00 0.00 3.51
7061 7269 3.865164 GTCTTCAAGCCAAAAACAAGGTG 59.135 43.478 0.00 0.00 0.00 4.00
7062 7270 3.118775 GGTCTTCAAGCCAAAAACAAGGT 60.119 43.478 0.00 0.00 0.00 3.50
7063 7271 3.132824 AGGTCTTCAAGCCAAAAACAAGG 59.867 43.478 1.37 0.00 0.00 3.61
7064 7272 4.363138 GAGGTCTTCAAGCCAAAAACAAG 58.637 43.478 1.37 0.00 0.00 3.16
7065 7273 3.181491 CGAGGTCTTCAAGCCAAAAACAA 60.181 43.478 1.37 0.00 0.00 2.83
7101 7321 2.098607 CGCATTCATCTCCTGCAAACAT 59.901 45.455 0.00 0.00 35.64 2.71
7131 7425 3.773370 TCGCAACCCGACTTCTCT 58.227 55.556 0.00 0.00 41.89 3.10
7183 7477 3.820557 TCCAAGTTTCTTTCCAGTCCTG 58.179 45.455 0.00 0.00 0.00 3.86
7184 7478 4.731313 ATCCAAGTTTCTTTCCAGTCCT 57.269 40.909 0.00 0.00 0.00 3.85
7185 7479 8.575649 TTATTATCCAAGTTTCTTTCCAGTCC 57.424 34.615 0.00 0.00 0.00 3.85
7189 7483 9.581289 TGAGTTTATTATCCAAGTTTCTTTCCA 57.419 29.630 0.00 0.00 0.00 3.53
7219 7544 0.773644 ACAGCAACCCCAACTCTCAT 59.226 50.000 0.00 0.00 0.00 2.90
7231 7556 6.018832 ACAAATGCATTTAGTGAAACAGCAAC 60.019 34.615 23.69 0.00 40.34 4.17
7273 7598 4.742438 CCATTACGCATACAATGGTACC 57.258 45.455 4.43 4.43 44.11 3.34
7284 7612 0.179029 GGCCAGGTACCATTACGCAT 60.179 55.000 15.94 0.00 0.00 4.73
7314 7642 2.670148 CCCTCGGAAGTTCAGGGGG 61.670 68.421 24.45 24.45 45.81 5.40
7355 7683 4.959596 GAGGCGATCGGCAGCTCC 62.960 72.222 38.28 20.07 46.16 4.70
7359 7687 1.958205 GAATGGAGGCGATCGGCAG 60.958 63.158 38.28 2.43 46.16 4.85
7360 7688 2.108976 GAATGGAGGCGATCGGCA 59.891 61.111 38.28 21.99 46.16 5.69
7361 7689 2.666526 GGAATGGAGGCGATCGGC 60.667 66.667 32.17 32.17 42.51 5.54
7362 7690 0.179045 AAAGGAATGGAGGCGATCGG 60.179 55.000 18.30 0.00 0.00 4.18
7363 7691 1.668419 AAAAGGAATGGAGGCGATCG 58.332 50.000 11.69 11.69 0.00 3.69
7379 7707 1.063867 TCCAGTTGTTCCCCGGAAAAA 60.064 47.619 0.73 0.00 35.75 1.94


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

AutoCloner maintained by Alex Coulton.