Multiple sequence alignment - TraesCS5B01G226900

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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 TraesCS5B01G226900 chr5B 100.000 6195 0 0 1 6195 403716478 403710284 0.000000e+00 11441.0
1 TraesCS5B01G226900 chr5B 92.960 625 38 5 1422 2040 522925551 522924927 0.000000e+00 905.0
2 TraesCS5B01G226900 chr5B 100.000 28 0 0 6106 6133 271955443 271955416 1.100000e-02 52.8
3 TraesCS5B01G226900 chr5D 95.818 2678 61 17 3460 6112 347439540 347442191 0.000000e+00 4277.0
4 TraesCS5B01G226900 chr5D 95.208 1106 40 8 2080 3180 347438147 347439244 0.000000e+00 1736.0
5 TraesCS5B01G226900 chr5D 93.540 1130 46 11 168 1286 347436877 347437990 0.000000e+00 1657.0
6 TraesCS5B01G226900 chr5D 97.183 213 6 0 3232 3444 347439344 347439556 1.640000e-95 361.0
7 TraesCS5B01G226900 chr5D 89.119 193 9 5 1 185 347436658 347436846 4.830000e-56 230.0
8 TraesCS5B01G226900 chr5A 96.077 1810 51 9 4308 6112 444536620 444534826 0.000000e+00 2931.0
9 TraesCS5B01G226900 chr5A 94.799 1365 50 10 2080 3428 444539127 444537768 0.000000e+00 2108.0
10 TraesCS5B01G226900 chr5A 92.438 1296 74 13 1 1286 444540565 444539284 0.000000e+00 1829.0
11 TraesCS5B01G226900 chr5A 93.187 866 26 11 3469 4310 444537779 444536923 0.000000e+00 1242.0
12 TraesCS5B01G226900 chr5A 100.000 29 0 0 6164 6192 367133235 367133263 3.000000e-03 54.7
13 TraesCS5B01G226900 chr5A 90.244 41 2 2 6153 6192 462868827 462868866 1.100000e-02 52.8
14 TraesCS5B01G226900 chr1D 93.291 626 36 5 1415 2034 67978133 67977508 0.000000e+00 918.0
15 TraesCS5B01G226900 chr1D 96.875 32 1 0 6164 6195 439878892 439878861 3.000000e-03 54.7
16 TraesCS5B01G226900 chr2D 92.994 628 37 6 1415 2036 607135670 607135044 0.000000e+00 909.0
17 TraesCS5B01G226900 chr2D 92.698 630 39 6 1415 2038 36579045 36579673 0.000000e+00 902.0
18 TraesCS5B01G226900 chr2D 100.000 29 0 0 6164 6192 427150391 427150419 3.000000e-03 54.7
19 TraesCS5B01G226900 chr2D 100.000 29 0 0 6164 6192 547203553 547203581 3.000000e-03 54.7
20 TraesCS5B01G226900 chr2D 100.000 28 0 0 6106 6133 189528074 189528047 1.100000e-02 52.8
21 TraesCS5B01G226900 chr2D 100.000 28 0 0 6106 6133 300887312 300887339 1.100000e-02 52.8
22 TraesCS5B01G226900 chr4A 92.960 625 38 5 1417 2035 715314929 715315553 0.000000e+00 905.0
23 TraesCS5B01G226900 chr7D 92.823 627 39 5 1415 2035 618704986 618705612 0.000000e+00 904.0
24 TraesCS5B01G226900 chr3B 92.504 627 41 5 1415 2035 13762166 13761540 0.000000e+00 893.0
25 TraesCS5B01G226900 chr3B 91.969 635 42 8 1410 2036 661776664 661777297 0.000000e+00 881.0
26 TraesCS5B01G226900 chr3B 94.737 38 0 1 2970 3005 376633593 376633630 2.410000e-04 58.4
27 TraesCS5B01G226900 chr6B 92.222 630 41 6 1415 2036 72329187 72328558 0.000000e+00 885.0
28 TraesCS5B01G226900 chr4B 97.500 40 0 1 2966 3005 650458871 650458909 4.010000e-07 67.6
29 TraesCS5B01G226900 chr4B 100.000 29 0 0 6105 6133 483907013 483906985 3.000000e-03 54.7
30 TraesCS5B01G226900 chr3D 97.500 40 0 1 2966 3005 371845574 371845612 4.010000e-07 67.6
31 TraesCS5B01G226900 chr3D 96.875 32 1 0 6164 6195 251316068 251316037 3.000000e-03 54.7
32 TraesCS5B01G226900 chr2B 95.000 40 1 1 2966 3005 535576315 535576277 1.860000e-05 62.1
33 TraesCS5B01G226900 chr2A 94.444 36 2 0 6160 6195 534626484 534626449 8.680000e-04 56.5
34 TraesCS5B01G226900 chr4D 96.875 32 1 0 6164 6195 29829521 29829490 3.000000e-03 54.7
35 TraesCS5B01G226900 chr1B 100.000 29 0 0 6164 6192 654813331 654813359 3.000000e-03 54.7


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 TraesCS5B01G226900 chr5B 403710284 403716478 6194 True 11441.0 11441 100.00000 1 6195 1 chr5B.!!$R2 6194
1 TraesCS5B01G226900 chr5B 522924927 522925551 624 True 905.0 905 92.96000 1422 2040 1 chr5B.!!$R3 618
2 TraesCS5B01G226900 chr5D 347436658 347442191 5533 False 1652.2 4277 94.17360 1 6112 5 chr5D.!!$F1 6111
3 TraesCS5B01G226900 chr5A 444534826 444540565 5739 True 2027.5 2931 94.12525 1 6112 4 chr5A.!!$R1 6111
4 TraesCS5B01G226900 chr1D 67977508 67978133 625 True 918.0 918 93.29100 1415 2034 1 chr1D.!!$R1 619
5 TraesCS5B01G226900 chr2D 607135044 607135670 626 True 909.0 909 92.99400 1415 2036 1 chr2D.!!$R2 621
6 TraesCS5B01G226900 chr2D 36579045 36579673 628 False 902.0 902 92.69800 1415 2038 1 chr2D.!!$F1 623
7 TraesCS5B01G226900 chr4A 715314929 715315553 624 False 905.0 905 92.96000 1417 2035 1 chr4A.!!$F1 618
8 TraesCS5B01G226900 chr7D 618704986 618705612 626 False 904.0 904 92.82300 1415 2035 1 chr7D.!!$F1 620
9 TraesCS5B01G226900 chr3B 13761540 13762166 626 True 893.0 893 92.50400 1415 2035 1 chr3B.!!$R1 620
10 TraesCS5B01G226900 chr3B 661776664 661777297 633 False 881.0 881 91.96900 1410 2036 1 chr3B.!!$F2 626
11 TraesCS5B01G226900 chr6B 72328558 72329187 629 True 885.0 885 92.22200 1415 2036 1 chr6B.!!$R1 621

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
22 23 0.038310 AAGACAAGGGCAGGCTAACC 59.962 55.000 0.00 0.00 0.00 2.85 F
797 865 0.106149 AAAAGAACGGGCGTCTGTCT 59.894 50.000 0.00 0.00 0.00 3.41 F
856 924 0.193574 AAAGGGTCTCCACTCTCCCA 59.806 55.000 0.00 0.00 42.12 4.37 F
1413 1490 0.321210 AACATGTCGAATGCGTCCCA 60.321 50.000 0.00 0.00 38.98 4.37 F
1583 1660 0.674581 TGTTGCTTGGAGATGGCTCG 60.675 55.000 0.00 0.00 42.25 5.03 F
1909 1992 0.690411 AGGAGTAGCTGCAGATGCCT 60.690 55.000 20.43 16.86 41.18 4.75 F
3443 3611 1.362224 TCTTAAGCCCACTTGAGCCT 58.638 50.000 0.00 0.00 38.93 4.58 F
3444 3612 1.705186 TCTTAAGCCCACTTGAGCCTT 59.295 47.619 0.00 0.00 38.93 4.35 F
3447 3615 1.793414 AAGCCCACTTGAGCCTTTTT 58.207 45.000 0.00 0.00 33.84 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1411 0.031178 GCACCAAGCAACAAGACAGG 59.969 55.000 0.00 0.0 44.79 4.00 R
1899 1982 0.106868 CCATCTTGGAGGCATCTGCA 60.107 55.000 4.33 0.0 40.96 4.41 R
1909 1992 0.181114 CCTGAATCCGCCATCTTGGA 59.819 55.000 0.00 0.0 40.96 3.53 R
2463 2570 1.669760 CGCGGCTGAAAACCCTACA 60.670 57.895 0.00 0.0 0.00 2.74 R
3462 3630 0.322906 AAAGCTAGGCTCAAGTGGGC 60.323 55.000 0.00 0.0 38.25 5.36 R
3463 3631 3.209410 CATAAAGCTAGGCTCAAGTGGG 58.791 50.000 0.00 0.0 38.25 4.61 R
4310 4508 0.179124 GGCAAAGTTTGTCGGCAACA 60.179 50.000 16.70 0.0 33.82 3.33 R
4430 4934 1.776034 GCTTCCCTAAAGATGCGCGG 61.776 60.000 8.83 0.0 37.12 6.46 R
5311 5816 2.013400 CATACATTGCGTGCCTTACCA 58.987 47.619 0.00 0.0 0.00 3.25 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 0.038310 AAGACAAGGGCAGGCTAACC 59.962 55.000 0.00 0.00 0.00 2.85
54 55 9.372369 CTAGTCTAAGTTTCCCTTAAAGATGTG 57.628 37.037 0.00 0.00 35.25 3.21
85 86 0.179089 AGCTCTACATTGCCAGCGAG 60.179 55.000 0.00 0.00 36.95 5.03
140 149 5.764686 AGATGCTCAAAACATACTGACAACA 59.235 36.000 0.00 0.00 0.00 3.33
142 151 4.222114 GCTCAAAACATACTGACAACAGC 58.778 43.478 0.00 0.00 46.95 4.40
147 156 5.362556 AAACATACTGACAACAGCACATC 57.637 39.130 0.00 0.00 46.95 3.06
153 162 1.948834 TGACAACAGCACATCAGGTTG 59.051 47.619 0.00 0.00 44.57 3.77
156 165 0.956633 AACAGCACATCAGGTTGCAG 59.043 50.000 0.00 0.00 0.00 4.41
162 171 2.439409 CACATCAGGTTGCAGAATGGA 58.561 47.619 0.00 0.00 35.86 3.41
367 425 2.266554 CTCTGAAGGTTGATCTGACGC 58.733 52.381 0.00 0.00 0.00 5.19
431 490 5.770162 CACAAACCCTAATCTGAGAAAACCT 59.230 40.000 0.00 0.00 0.00 3.50
434 493 3.523972 ACCCTAATCTGAGAAAACCTCCC 59.476 47.826 0.00 0.00 41.25 4.30
438 497 1.064825 TCTGAGAAAACCTCCCACCC 58.935 55.000 0.00 0.00 41.25 4.61
792 860 0.165295 GCAGTAAAAGAACGGGCGTC 59.835 55.000 0.00 0.00 0.00 5.19
797 865 0.106149 AAAAGAACGGGCGTCTGTCT 59.894 50.000 0.00 0.00 0.00 3.41
806 874 0.944386 GGCGTCTGTCTCTTTGCAAA 59.056 50.000 12.14 12.14 0.00 3.68
848 916 4.721132 ACAAATAAACGAAAGGGTCTCCA 58.279 39.130 0.00 0.00 34.83 3.86
849 917 4.517832 ACAAATAAACGAAAGGGTCTCCAC 59.482 41.667 0.00 0.00 34.83 4.02
852 920 1.718280 AACGAAAGGGTCTCCACTCT 58.282 50.000 0.00 0.00 33.12 3.24
853 921 1.258676 ACGAAAGGGTCTCCACTCTC 58.741 55.000 0.00 0.00 28.72 3.20
854 922 0.533032 CGAAAGGGTCTCCACTCTCC 59.467 60.000 0.00 0.00 28.72 3.71
855 923 0.906066 GAAAGGGTCTCCACTCTCCC 59.094 60.000 0.00 0.00 40.16 4.30
856 924 0.193574 AAAGGGTCTCCACTCTCCCA 59.806 55.000 0.00 0.00 42.12 4.37
857 925 0.419459 AAGGGTCTCCACTCTCCCAT 59.581 55.000 0.00 0.00 42.12 4.00
858 926 0.419459 AGGGTCTCCACTCTCCCATT 59.581 55.000 0.00 0.00 42.12 3.16
901 969 7.096477 GCGCTTGCATTTTATCTAATTTACAGG 60.096 37.037 0.00 0.00 38.92 4.00
927 995 1.696097 CCCACCTTATCCCCACGAGG 61.696 65.000 0.00 0.00 35.39 4.63
928 996 1.146263 CACCTTATCCCCACGAGGC 59.854 63.158 0.00 0.00 32.42 4.70
929 997 2.070650 ACCTTATCCCCACGAGGCC 61.071 63.158 0.00 0.00 32.42 5.19
930 998 2.070039 CCTTATCCCCACGAGGCCA 61.070 63.158 5.01 0.00 0.00 5.36
931 999 1.146263 CTTATCCCCACGAGGCCAC 59.854 63.158 5.01 0.00 0.00 5.01
932 1000 2.644555 CTTATCCCCACGAGGCCACG 62.645 65.000 21.59 21.59 39.31 4.94
933 1001 3.665515 TATCCCCACGAGGCCACGA 62.666 63.158 29.67 6.47 37.03 4.35
1073 1149 0.341258 TGCAGATCCCTCCTCCTCTT 59.659 55.000 0.00 0.00 0.00 2.85
1107 1183 1.203174 CCATTTCCCACCCCAAGAACT 60.203 52.381 0.00 0.00 0.00 3.01
1116 1192 2.668632 CCAAGAACTGGCCGCCTA 59.331 61.111 11.61 0.00 38.76 3.93
1230 1306 2.607635 CGCGTGCTTATCCTACAACAAT 59.392 45.455 0.00 0.00 0.00 2.71
1286 1362 2.883386 GCTCCATTTCTTGATGCCCTAG 59.117 50.000 0.00 0.00 0.00 3.02
1297 1373 2.996985 TGCCCTAGCACTGATCAGT 58.003 52.632 22.89 22.89 46.52 3.41
1298 1374 2.159179 TGCCCTAGCACTGATCAGTA 57.841 50.000 27.44 12.09 46.52 2.74
1299 1375 2.682594 TGCCCTAGCACTGATCAGTAT 58.317 47.619 27.44 20.41 46.52 2.12
1300 1376 2.630098 TGCCCTAGCACTGATCAGTATC 59.370 50.000 27.44 20.68 46.52 2.24
1301 1377 2.630098 GCCCTAGCACTGATCAGTATCA 59.370 50.000 27.44 13.91 40.20 2.15
1315 1391 7.661968 TGATCAGTATCAGTTGTATTCCTAGC 58.338 38.462 0.00 0.00 37.20 3.42
1323 1399 4.100189 CAGTTGTATTCCTAGCAGGCTAGT 59.900 45.833 22.80 10.39 43.22 2.57
1324 1400 4.100189 AGTTGTATTCCTAGCAGGCTAGTG 59.900 45.833 22.80 15.64 43.22 2.74
1333 1409 1.002868 CAGGCTAGTGGCAGTGCTT 60.003 57.895 16.11 3.85 44.01 3.91
1334 1410 1.023513 CAGGCTAGTGGCAGTGCTTC 61.024 60.000 16.11 8.44 44.01 3.86
1335 1411 1.746991 GGCTAGTGGCAGTGCTTCC 60.747 63.158 16.11 3.08 44.01 3.46
1336 1412 1.746991 GCTAGTGGCAGTGCTTCCC 60.747 63.158 16.11 0.00 41.35 3.97
1337 1413 1.986413 CTAGTGGCAGTGCTTCCCT 59.014 57.895 16.11 8.17 0.00 4.20
1338 1414 0.392193 CTAGTGGCAGTGCTTCCCTG 60.392 60.000 16.11 0.00 0.00 4.45
1387 1464 8.281212 AGCTTCTTGAAAAACAGAAGAACTTA 57.719 30.769 12.15 0.00 36.66 2.24
1388 1465 8.401709 AGCTTCTTGAAAAACAGAAGAACTTAG 58.598 33.333 12.15 0.00 36.66 2.18
1389 1466 8.184848 GCTTCTTGAAAAACAGAAGAACTTAGT 58.815 33.333 12.15 0.00 36.66 2.24
1390 1467 9.709600 CTTCTTGAAAAACAGAAGAACTTAGTC 57.290 33.333 3.26 0.00 36.66 2.59
1400 1477 9.614792 AACAGAAGAACTTAGTCTAAAACATGT 57.385 29.630 0.00 0.00 0.00 3.21
1401 1478 9.262358 ACAGAAGAACTTAGTCTAAAACATGTC 57.738 33.333 0.00 0.00 0.00 3.06
1402 1479 8.428536 CAGAAGAACTTAGTCTAAAACATGTCG 58.571 37.037 0.00 0.00 0.00 4.35
1403 1480 8.358148 AGAAGAACTTAGTCTAAAACATGTCGA 58.642 33.333 0.00 0.00 0.00 4.20
1404 1481 8.882415 AAGAACTTAGTCTAAAACATGTCGAA 57.118 30.769 0.00 0.00 0.00 3.71
1405 1482 9.490379 AAGAACTTAGTCTAAAACATGTCGAAT 57.510 29.630 0.00 0.00 0.00 3.34
1406 1483 8.926710 AGAACTTAGTCTAAAACATGTCGAATG 58.073 33.333 0.00 0.00 0.00 2.67
1407 1484 7.061752 ACTTAGTCTAAAACATGTCGAATGC 57.938 36.000 0.00 0.00 0.00 3.56
1408 1485 4.584029 AGTCTAAAACATGTCGAATGCG 57.416 40.909 0.00 0.00 39.35 4.73
1409 1486 3.994392 AGTCTAAAACATGTCGAATGCGT 59.006 39.130 0.00 0.00 38.98 5.24
1410 1487 4.091509 AGTCTAAAACATGTCGAATGCGTC 59.908 41.667 0.00 0.00 38.98 5.19
1411 1488 2.611974 AAAACATGTCGAATGCGTCC 57.388 45.000 0.00 0.00 38.98 4.79
1412 1489 0.802494 AAACATGTCGAATGCGTCCC 59.198 50.000 0.00 0.00 38.98 4.46
1413 1490 0.321210 AACATGTCGAATGCGTCCCA 60.321 50.000 0.00 0.00 38.98 4.37
1420 1497 1.873165 GAATGCGTCCCAGCGAAAA 59.127 52.632 0.00 0.00 40.67 2.29
1428 1505 0.766131 TCCCAGCGAAAACCCTAACA 59.234 50.000 0.00 0.00 0.00 2.41
1555 1632 1.615262 GGCCCTTTCCTAGCATGGT 59.385 57.895 1.62 1.62 0.00 3.55
1580 1657 0.807496 GTCTGTTGCTTGGAGATGGC 59.193 55.000 0.00 0.00 0.00 4.40
1581 1658 0.694771 TCTGTTGCTTGGAGATGGCT 59.305 50.000 0.00 0.00 0.00 4.75
1582 1659 1.093159 CTGTTGCTTGGAGATGGCTC 58.907 55.000 0.00 0.00 40.54 4.70
1583 1660 0.674581 TGTTGCTTGGAGATGGCTCG 60.675 55.000 0.00 0.00 42.25 5.03
1585 1662 1.841302 TTGCTTGGAGATGGCTCGGT 61.841 55.000 0.00 0.00 42.25 4.69
1586 1663 1.522580 GCTTGGAGATGGCTCGGTC 60.523 63.158 0.00 0.00 42.25 4.79
1587 1664 1.227089 CTTGGAGATGGCTCGGTCG 60.227 63.158 0.00 0.00 42.25 4.79
1588 1665 2.635229 CTTGGAGATGGCTCGGTCGG 62.635 65.000 0.00 0.00 42.25 4.79
1835 1918 3.261137 GCCTCCGGCTTTAGATATTAGGT 59.739 47.826 0.00 0.00 46.69 3.08
1853 1936 2.772515 AGGTTTAGGTGAGAGGTATGGC 59.227 50.000 0.00 0.00 0.00 4.40
1899 1982 6.239829 CCTTCATCATTTGGATAGGAGTAGCT 60.240 42.308 0.00 0.00 34.78 3.32
1908 1991 1.043816 TAGGAGTAGCTGCAGATGCC 58.956 55.000 20.43 14.75 41.18 4.40
1909 1992 0.690411 AGGAGTAGCTGCAGATGCCT 60.690 55.000 20.43 16.86 41.18 4.75
2058 2141 9.912634 AAAATGTCGAATGTGTCAATAGAAAAT 57.087 25.926 0.00 0.00 0.00 1.82
2059 2142 8.900511 AATGTCGAATGTGTCAATAGAAAATG 57.099 30.769 0.00 0.00 0.00 2.32
2060 2143 7.433708 TGTCGAATGTGTCAATAGAAAATGT 57.566 32.000 0.00 0.00 0.00 2.71
2061 2144 7.297391 TGTCGAATGTGTCAATAGAAAATGTG 58.703 34.615 0.00 0.00 0.00 3.21
2062 2145 7.041440 TGTCGAATGTGTCAATAGAAAATGTGT 60.041 33.333 0.00 0.00 0.00 3.72
2063 2146 7.478667 GTCGAATGTGTCAATAGAAAATGTGTC 59.521 37.037 0.00 0.00 0.00 3.67
2064 2147 6.462636 CGAATGTGTCAATAGAAAATGTGTCG 59.537 38.462 0.00 0.00 0.00 4.35
2065 2148 5.605564 TGTGTCAATAGAAAATGTGTCGG 57.394 39.130 0.00 0.00 0.00 4.79
2066 2149 5.301555 TGTGTCAATAGAAAATGTGTCGGA 58.698 37.500 0.00 0.00 0.00 4.55
2067 2150 5.937540 TGTGTCAATAGAAAATGTGTCGGAT 59.062 36.000 0.00 0.00 0.00 4.18
2068 2151 6.128309 TGTGTCAATAGAAAATGTGTCGGATG 60.128 38.462 0.00 0.00 0.00 3.51
2069 2152 5.937540 TGTCAATAGAAAATGTGTCGGATGT 59.062 36.000 0.00 0.00 0.00 3.06
2070 2153 7.064134 GTGTCAATAGAAAATGTGTCGGATGTA 59.936 37.037 0.00 0.00 0.00 2.29
2071 2154 7.064134 TGTCAATAGAAAATGTGTCGGATGTAC 59.936 37.037 0.00 0.00 0.00 2.90
2072 2155 7.064134 GTCAATAGAAAATGTGTCGGATGTACA 59.936 37.037 0.00 0.00 0.00 2.90
2074 2157 7.715265 ATAGAAAATGTGTCGGATGTACATC 57.285 36.000 24.95 24.95 34.18 3.06
2075 2158 5.487433 AGAAAATGTGTCGGATGTACATCA 58.513 37.500 31.51 15.13 39.54 3.07
2076 2159 5.582269 AGAAAATGTGTCGGATGTACATCAG 59.418 40.000 31.51 28.17 39.54 2.90
2077 2160 4.471904 AATGTGTCGGATGTACATCAGT 57.528 40.909 31.51 12.89 39.54 3.41
2098 2202 8.327941 TCAGTAATATTATCTTGCCATGAAGC 57.672 34.615 0.00 0.00 0.00 3.86
2099 2203 7.938490 TCAGTAATATTATCTTGCCATGAAGCA 59.062 33.333 0.00 0.00 42.17 3.91
2102 2206 9.350357 GTAATATTATCTTGCCATGAAGCATTG 57.650 33.333 0.00 0.00 43.64 2.82
2103 2207 4.659111 TTATCTTGCCATGAAGCATTGG 57.341 40.909 0.00 0.00 43.64 3.16
2111 2215 2.821378 CCATGAAGCATTGGTGAACTCA 59.179 45.455 0.00 0.00 0.00 3.41
2122 2226 2.503765 TGGTGAACTCAAGTTGGACTGA 59.496 45.455 2.34 0.00 38.56 3.41
2299 2403 3.802948 AAGGTACTCTTATCCTGCACG 57.197 47.619 0.00 0.00 38.49 5.34
2307 2411 3.807631 TATCCTGCACGCCGGATGC 62.808 63.158 21.22 20.96 40.17 3.91
2320 2424 3.447742 GCCGGATGCTTATTTTCAAAGG 58.552 45.455 5.05 0.00 36.87 3.11
2365 2472 2.292267 CTGTGGTTGGTGATGCCTATC 58.708 52.381 0.00 0.00 38.35 2.08
2407 2514 7.092979 GGTTAACCCTAAGAAAGTATCCTGAGT 60.093 40.741 14.16 0.00 0.00 3.41
2567 2674 7.719633 TCTTGCTTGATACTTTTTCTGGTAGTT 59.280 33.333 0.00 0.00 0.00 2.24
2569 2676 8.232913 TGCTTGATACTTTTTCTGGTAGTTTT 57.767 30.769 0.00 0.00 0.00 2.43
2742 2849 7.114529 CGTTACGGTCAGGACATTATCTTATTC 59.885 40.741 0.00 0.00 0.00 1.75
2805 2916 7.119846 GTGGTGCATTCTTTCTTGTAGACTAAT 59.880 37.037 0.00 0.00 0.00 1.73
2993 3113 2.593026 TGGGACTAAAGGCTTTGTTGG 58.407 47.619 22.32 11.54 0.00 3.77
2994 3114 2.091555 TGGGACTAAAGGCTTTGTTGGT 60.092 45.455 22.32 14.35 0.00 3.67
2995 3115 2.296190 GGGACTAAAGGCTTTGTTGGTG 59.704 50.000 22.32 7.79 0.00 4.17
2996 3116 2.956333 GGACTAAAGGCTTTGTTGGTGT 59.044 45.455 22.32 10.58 0.00 4.16
2997 3117 3.383505 GGACTAAAGGCTTTGTTGGTGTT 59.616 43.478 22.32 0.00 0.00 3.32
2998 3118 4.359706 GACTAAAGGCTTTGTTGGTGTTG 58.640 43.478 22.32 0.00 0.00 3.33
3078 3198 1.820519 CTGCAAAATGGCTGGCTTCTA 59.179 47.619 2.00 0.00 34.04 2.10
3156 3276 2.602257 TGACCTATCTGAATGGTGCG 57.398 50.000 9.22 0.00 33.74 5.34
3186 3311 3.161067 GAGAGAGGTCAGGCTATATGCA 58.839 50.000 0.00 0.00 45.15 3.96
3188 3313 3.768757 AGAGAGGTCAGGCTATATGCATC 59.231 47.826 0.19 0.00 45.15 3.91
3215 3340 3.496130 AGACAGACTTTTCTTGTGCATCG 59.504 43.478 0.00 0.00 0.00 3.84
3221 3346 3.120546 ACTTTTCTTGTGCATCGTCATCG 60.121 43.478 0.00 0.00 38.55 3.84
3303 3471 2.094752 CACCTTTAATTTGCACCCCGAG 60.095 50.000 0.00 0.00 0.00 4.63
3408 3576 7.707624 AGAATCTGCTTTGTTTTCATATGGA 57.292 32.000 2.13 0.00 0.00 3.41
3409 3577 8.302515 AGAATCTGCTTTGTTTTCATATGGAT 57.697 30.769 2.13 0.00 0.00 3.41
3433 3601 6.679327 AATCTTTTGACGTATCTTAAGCCC 57.321 37.500 0.00 0.00 0.00 5.19
3434 3602 5.155278 TCTTTTGACGTATCTTAAGCCCA 57.845 39.130 0.00 0.00 0.00 5.36
3435 3603 4.933400 TCTTTTGACGTATCTTAAGCCCAC 59.067 41.667 0.00 0.00 0.00 4.61
3436 3604 4.546829 TTTGACGTATCTTAAGCCCACT 57.453 40.909 0.00 0.00 0.00 4.00
3437 3605 4.546829 TTGACGTATCTTAAGCCCACTT 57.453 40.909 0.00 0.00 40.07 3.16
3438 3606 3.857052 TGACGTATCTTAAGCCCACTTG 58.143 45.455 0.00 0.00 36.57 3.16
3439 3607 3.512329 TGACGTATCTTAAGCCCACTTGA 59.488 43.478 0.00 0.00 36.57 3.02
3440 3608 4.113354 GACGTATCTTAAGCCCACTTGAG 58.887 47.826 0.00 0.00 40.09 3.02
3441 3609 2.866762 CGTATCTTAAGCCCACTTGAGC 59.133 50.000 0.00 0.00 38.93 4.26
3442 3610 2.426842 ATCTTAAGCCCACTTGAGCC 57.573 50.000 0.00 0.00 38.93 4.70
3443 3611 1.362224 TCTTAAGCCCACTTGAGCCT 58.638 50.000 0.00 0.00 38.93 4.58
3444 3612 1.705186 TCTTAAGCCCACTTGAGCCTT 59.295 47.619 0.00 0.00 38.93 4.35
3445 3613 2.108250 TCTTAAGCCCACTTGAGCCTTT 59.892 45.455 0.00 0.00 38.93 3.11
3446 3614 2.675658 TAAGCCCACTTGAGCCTTTT 57.324 45.000 0.00 0.00 36.57 2.27
3447 3615 1.793414 AAGCCCACTTGAGCCTTTTT 58.207 45.000 0.00 0.00 33.84 1.94
3592 3761 8.890410 TTGTCCTATACTTTGGAGTTAGTACT 57.110 34.615 0.00 0.00 37.33 2.73
3593 3762 8.890410 TGTCCTATACTTTGGAGTTAGTACTT 57.110 34.615 0.00 0.00 37.33 2.24
3594 3763 9.979897 TGTCCTATACTTTGGAGTTAGTACTTA 57.020 33.333 0.00 0.00 37.33 2.24
3690 3859 9.667107 AACATAGATTCTCTTATTTTCGGTTGA 57.333 29.630 0.00 0.00 0.00 3.18
3698 3867 7.581476 TCTCTTATTTTCGGTTGACAATTGAC 58.419 34.615 13.59 6.72 0.00 3.18
3768 3966 7.747958 ACTACTGCAGTTAACCCATTTAATGGA 60.748 37.037 27.06 2.63 43.88 3.41
3889 4087 4.026744 TCAGGTAGCATCTCACTAGCTTT 58.973 43.478 0.00 0.00 43.97 3.51
3910 4108 4.650754 TTTTTGTTTTACTTGCCGGCTA 57.349 36.364 29.70 20.51 0.00 3.93
4155 4353 3.581770 GGTACAGGTTTCCTACTCCAGTT 59.418 47.826 0.00 0.00 29.64 3.16
4310 4508 4.142315 GCCATCTGTGCATGAACATACTTT 60.142 41.667 7.07 0.00 0.00 2.66
4430 4934 0.171455 CACCAGTAGCGAGTCCAGTC 59.829 60.000 0.00 0.00 0.00 3.51
4540 5044 7.222999 CAGTTCAGGATAATTAGGAAAGACGTC 59.777 40.741 7.70 7.70 0.00 4.34
4541 5045 6.785337 TCAGGATAATTAGGAAAGACGTCA 57.215 37.500 19.50 0.00 0.00 4.35
4601 5106 6.689561 TCTTAGGGATCAGATTAGGTGGTAA 58.310 40.000 0.00 0.00 0.00 2.85
4907 5412 0.309612 GTGTTGCACTGGGGTTTACG 59.690 55.000 0.00 0.00 0.00 3.18
5034 5539 5.534278 TGTGTCAGTAATTTGCTGGATGAAA 59.466 36.000 13.55 0.00 34.89 2.69
5116 5621 5.044550 AGCTAATTCATGTTCCCTTCTTCCT 60.045 40.000 0.00 0.00 0.00 3.36
5117 5622 6.158695 AGCTAATTCATGTTCCCTTCTTCCTA 59.841 38.462 0.00 0.00 0.00 2.94
5118 5623 7.001073 GCTAATTCATGTTCCCTTCTTCCTAT 58.999 38.462 0.00 0.00 0.00 2.57
5164 5669 2.584835 TGCTTCAGTTGCAAGGGTAT 57.415 45.000 0.00 0.00 37.51 2.73
5311 5816 7.067129 TCGACTGCTTAGTGTATGATCTTACTT 59.933 37.037 17.02 9.69 0.00 2.24
5337 5842 2.104792 AGGCACGCAATGTATGGTCTAT 59.895 45.455 0.00 0.00 0.00 1.98
5582 6087 8.439971 ACCAATAAATCTATCTCACTGGCATTA 58.560 33.333 0.00 0.00 0.00 1.90
5766 6271 3.006247 GGAGGTCAGATGTTGCTTTCTC 58.994 50.000 0.00 0.00 0.00 2.87
5847 6357 4.799564 TGGGCAAACAAATTATGAGGAC 57.200 40.909 0.00 0.00 0.00 3.85
5930 6440 6.493458 ACATATTTGCTCAAAAGGGTTGTAGT 59.507 34.615 0.00 0.00 33.56 2.73
6112 6622 8.813643 ACATTTCACAGTAACTCAGTAAGTAC 57.186 34.615 0.00 0.00 37.17 2.73
6113 6623 8.639761 ACATTTCACAGTAACTCAGTAAGTACT 58.360 33.333 0.00 0.00 37.17 2.73
6114 6624 9.130312 CATTTCACAGTAACTCAGTAAGTACTC 57.870 37.037 0.00 0.00 37.17 2.59
6115 6625 6.814506 TCACAGTAACTCAGTAAGTACTCC 57.185 41.667 0.00 0.00 37.17 3.85
6116 6626 5.709164 TCACAGTAACTCAGTAAGTACTCCC 59.291 44.000 0.00 0.00 37.17 4.30
6117 6627 5.711036 CACAGTAACTCAGTAAGTACTCCCT 59.289 44.000 0.00 0.00 37.17 4.20
6118 6628 5.945191 ACAGTAACTCAGTAAGTACTCCCTC 59.055 44.000 0.00 0.00 37.17 4.30
6119 6629 5.357596 CAGTAACTCAGTAAGTACTCCCTCC 59.642 48.000 0.00 0.00 37.17 4.30
6120 6630 3.002038 ACTCAGTAAGTACTCCCTCCG 57.998 52.381 0.00 0.00 36.07 4.63
6121 6631 2.308275 ACTCAGTAAGTACTCCCTCCGT 59.692 50.000 0.00 0.00 36.07 4.69
6122 6632 2.944349 CTCAGTAAGTACTCCCTCCGTC 59.056 54.545 0.00 0.00 33.46 4.79
6123 6633 2.022934 CAGTAAGTACTCCCTCCGTCC 58.977 57.143 0.00 0.00 33.46 4.79
6124 6634 1.064091 AGTAAGTACTCCCTCCGTCCC 60.064 57.143 0.00 0.00 0.00 4.46
6125 6635 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
6126 6636 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
6127 6637 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
6128 6638 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
6129 6639 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
6130 6640 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
6131 6641 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
6132 6642 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
6133 6643 2.504175 CTCCCTCCGTCCCAAAATTCTA 59.496 50.000 0.00 0.00 0.00 2.10
6134 6644 3.120108 TCCCTCCGTCCCAAAATTCTAT 58.880 45.455 0.00 0.00 0.00 1.98
6135 6645 3.118038 TCCCTCCGTCCCAAAATTCTATG 60.118 47.826 0.00 0.00 0.00 2.23
6136 6646 3.118038 CCCTCCGTCCCAAAATTCTATGA 60.118 47.826 0.00 0.00 0.00 2.15
6137 6647 3.877508 CCTCCGTCCCAAAATTCTATGAC 59.122 47.826 0.00 0.00 0.00 3.06
6138 6648 4.513442 CTCCGTCCCAAAATTCTATGACA 58.487 43.478 0.00 0.00 0.00 3.58
6139 6649 4.912586 TCCGTCCCAAAATTCTATGACAA 58.087 39.130 0.00 0.00 0.00 3.18
6140 6650 5.317808 TCCGTCCCAAAATTCTATGACAAA 58.682 37.500 0.00 0.00 0.00 2.83
6141 6651 5.949354 TCCGTCCCAAAATTCTATGACAAAT 59.051 36.000 0.00 0.00 0.00 2.32
6142 6652 6.094881 TCCGTCCCAAAATTCTATGACAAATC 59.905 38.462 0.00 0.00 0.00 2.17
6143 6653 6.095440 CCGTCCCAAAATTCTATGACAAATCT 59.905 38.462 0.00 0.00 0.00 2.40
6144 6654 7.282224 CCGTCCCAAAATTCTATGACAAATCTA 59.718 37.037 0.00 0.00 0.00 1.98
6145 6655 8.840321 CGTCCCAAAATTCTATGACAAATCTAT 58.160 33.333 0.00 0.00 0.00 1.98
6146 6656 9.956720 GTCCCAAAATTCTATGACAAATCTATG 57.043 33.333 0.00 0.00 0.00 2.23
6147 6657 9.919416 TCCCAAAATTCTATGACAAATCTATGA 57.081 29.630 0.00 0.00 0.00 2.15
6148 6658 9.956720 CCCAAAATTCTATGACAAATCTATGAC 57.043 33.333 0.00 0.00 0.00 3.06
6159 6669 7.874940 TGACAAATCTATGACAAGAAGTTTGG 58.125 34.615 12.84 2.02 33.04 3.28
6160 6670 7.502226 TGACAAATCTATGACAAGAAGTTTGGT 59.498 33.333 12.84 4.12 33.04 3.67
6161 6671 8.918202 ACAAATCTATGACAAGAAGTTTGGTA 57.082 30.769 12.84 0.00 33.04 3.25
6162 6672 9.349713 ACAAATCTATGACAAGAAGTTTGGTAA 57.650 29.630 12.84 0.00 33.04 2.85
6163 6673 9.612620 CAAATCTATGACAAGAAGTTTGGTAAC 57.387 33.333 0.00 0.00 28.49 2.50
6164 6674 9.574516 AAATCTATGACAAGAAGTTTGGTAACT 57.425 29.630 0.00 0.00 46.44 2.24
6166 6676 9.877178 ATCTATGACAAGAAGTTTGGTAACTAG 57.123 33.333 0.00 0.00 43.74 2.57
6167 6677 9.085645 TCTATGACAAGAAGTTTGGTAACTAGA 57.914 33.333 0.00 0.00 43.74 2.43
6168 6678 9.877178 CTATGACAAGAAGTTTGGTAACTAGAT 57.123 33.333 0.00 0.00 43.74 1.98
6176 6686 9.364653 AGAAGTTTGGTAACTAGATATATCCGT 57.635 33.333 9.18 4.47 43.74 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.091261 AGGGAAACTTAGACTAGTGCATG 57.909 43.478 0.00 0.00 0.00 4.06
54 55 5.461737 GCAATGTAGAGCTTGAGATGTAGTC 59.538 44.000 0.00 0.00 0.00 2.59
111 120 7.280876 TGTCAGTATGTTTTGAGCATCTTATCC 59.719 37.037 0.00 0.00 37.40 2.59
140 149 1.816835 CATTCTGCAACCTGATGTGCT 59.183 47.619 0.00 0.00 0.00 4.40
141 150 1.135199 CCATTCTGCAACCTGATGTGC 60.135 52.381 0.00 0.00 0.00 4.57
142 151 2.439409 TCCATTCTGCAACCTGATGTG 58.561 47.619 0.00 0.00 0.00 3.21
147 156 4.158949 TCATGAATTCCATTCTGCAACCTG 59.841 41.667 2.27 0.00 39.96 4.00
153 162 7.093902 ACCATATCATCATGAATTCCATTCTGC 60.094 37.037 0.00 0.00 39.96 4.26
156 165 9.021807 AGAACCATATCATCATGAATTCCATTC 57.978 33.333 0.00 0.00 39.70 2.67
178 187 4.518970 TGGAGAACATGGTGCTTAAAGAAC 59.481 41.667 0.00 0.00 0.00 3.01
367 425 2.093783 GCTGACGTTAGGATTGGTTTCG 59.906 50.000 9.62 0.00 0.00 3.46
431 490 1.688884 TGATCTGCATCGGGTGGGA 60.689 57.895 0.00 0.00 0.00 4.37
438 497 3.344215 GCGGCCTGATCTGCATCG 61.344 66.667 0.00 6.23 38.21 3.84
478 537 3.254166 GCCTTCTGATTTGAGCTTGTTGA 59.746 43.478 0.00 0.00 0.00 3.18
481 540 2.165998 GGCCTTCTGATTTGAGCTTGT 58.834 47.619 0.00 0.00 0.00 3.16
520 579 5.220416 GGAACGATAACTTACAGCACATGTC 60.220 44.000 0.00 0.00 42.70 3.06
521 580 4.630069 GGAACGATAACTTACAGCACATGT 59.370 41.667 0.00 0.00 46.45 3.21
769 829 1.938016 GCCCGTTCTTTTACTGCGAGA 60.938 52.381 0.00 0.00 0.00 4.04
792 860 3.305608 GGGTCCAATTTGCAAAGAGACAG 60.306 47.826 26.88 12.13 0.00 3.51
797 865 0.965439 CGGGGTCCAATTTGCAAAGA 59.035 50.000 18.19 6.77 0.00 2.52
806 874 2.363359 GTCGTATAACTCGGGGTCCAAT 59.637 50.000 0.00 0.00 0.00 3.16
848 916 4.324267 CCAGAAAACGTAAATGGGAGAGT 58.676 43.478 0.00 0.00 0.00 3.24
849 917 3.127030 GCCAGAAAACGTAAATGGGAGAG 59.873 47.826 10.04 0.00 0.00 3.20
852 920 3.149005 AGCCAGAAAACGTAAATGGGA 57.851 42.857 10.04 0.00 0.00 4.37
853 921 3.934457 AAGCCAGAAAACGTAAATGGG 57.066 42.857 10.04 2.00 0.00 4.00
854 922 3.428534 GCAAAGCCAGAAAACGTAAATGG 59.571 43.478 0.00 0.00 0.00 3.16
855 923 3.119463 CGCAAAGCCAGAAAACGTAAATG 59.881 43.478 0.00 0.00 0.00 2.32
856 924 3.305110 CGCAAAGCCAGAAAACGTAAAT 58.695 40.909 0.00 0.00 0.00 1.40
857 925 2.722071 CGCAAAGCCAGAAAACGTAAA 58.278 42.857 0.00 0.00 0.00 2.01
858 926 1.598430 GCGCAAAGCCAGAAAACGTAA 60.598 47.619 0.30 0.00 40.81 3.18
953 1029 1.936436 CTGCTCTCTCTGCTCGCTGT 61.936 60.000 0.00 0.00 0.00 4.40
1073 1149 1.888512 GAAATGGCTTCCTGTGCTTGA 59.111 47.619 0.00 0.00 0.00 3.02
1290 1366 7.287696 TGCTAGGAATACAACTGATACTGATCA 59.712 37.037 0.00 0.00 39.88 2.92
1291 1367 7.661968 TGCTAGGAATACAACTGATACTGATC 58.338 38.462 0.00 0.00 0.00 2.92
1292 1368 7.256119 CCTGCTAGGAATACAACTGATACTGAT 60.256 40.741 0.00 0.00 37.67 2.90
1293 1369 6.040955 CCTGCTAGGAATACAACTGATACTGA 59.959 42.308 0.00 0.00 37.67 3.41
1294 1370 6.219473 CCTGCTAGGAATACAACTGATACTG 58.781 44.000 0.00 0.00 37.67 2.74
1295 1371 5.221541 GCCTGCTAGGAATACAACTGATACT 60.222 44.000 6.40 0.00 37.67 2.12
1296 1372 4.991687 GCCTGCTAGGAATACAACTGATAC 59.008 45.833 6.40 0.00 37.67 2.24
1297 1373 4.901849 AGCCTGCTAGGAATACAACTGATA 59.098 41.667 6.40 0.00 37.67 2.15
1298 1374 3.713764 AGCCTGCTAGGAATACAACTGAT 59.286 43.478 6.40 0.00 37.67 2.90
1299 1375 3.107601 AGCCTGCTAGGAATACAACTGA 58.892 45.455 6.40 0.00 37.67 3.41
1300 1376 3.550437 AGCCTGCTAGGAATACAACTG 57.450 47.619 6.40 0.00 37.67 3.16
1301 1377 4.946478 CTAGCCTGCTAGGAATACAACT 57.054 45.455 16.69 0.00 41.58 3.16
1312 1388 1.900351 CACTGCCACTAGCCTGCTA 59.100 57.895 0.00 0.00 42.71 3.49
1313 1389 2.667418 CACTGCCACTAGCCTGCT 59.333 61.111 0.00 0.00 42.71 4.24
1314 1390 3.130160 GCACTGCCACTAGCCTGC 61.130 66.667 0.00 0.00 42.71 4.85
1315 1391 1.002868 AAGCACTGCCACTAGCCTG 60.003 57.895 0.00 0.00 42.71 4.85
1323 1399 1.708993 AAGACAGGGAAGCACTGCCA 61.709 55.000 0.00 0.00 38.23 4.92
1324 1400 1.073897 AAGACAGGGAAGCACTGCC 59.926 57.895 0.00 0.00 39.55 4.85
1333 1409 0.550914 ACCAAGCAACAAGACAGGGA 59.449 50.000 0.00 0.00 0.00 4.20
1334 1410 0.670162 CACCAAGCAACAAGACAGGG 59.330 55.000 0.00 0.00 0.00 4.45
1335 1411 0.031178 GCACCAAGCAACAAGACAGG 59.969 55.000 0.00 0.00 44.79 4.00
1336 1412 3.557207 GCACCAAGCAACAAGACAG 57.443 52.632 0.00 0.00 44.79 3.51
1356 1432 9.391006 TCTTCTGTTTTTCAAGAAGCTAAACTA 57.609 29.630 7.41 0.00 38.05 2.24
1358 1434 8.799091 GTTCTTCTGTTTTTCAAGAAGCTAAAC 58.201 33.333 7.41 0.00 38.05 2.01
1387 1464 3.994392 ACGCATTCGACATGTTTTAGACT 59.006 39.130 0.00 0.00 39.41 3.24
1388 1465 4.322101 ACGCATTCGACATGTTTTAGAC 57.678 40.909 0.00 0.00 39.41 2.59
1389 1466 3.369756 GGACGCATTCGACATGTTTTAGA 59.630 43.478 0.00 0.00 39.41 2.10
1390 1467 3.485216 GGGACGCATTCGACATGTTTTAG 60.485 47.826 0.00 0.00 39.41 1.85
1392 1469 1.199097 GGGACGCATTCGACATGTTTT 59.801 47.619 0.00 0.00 39.41 2.43
1396 1473 2.009108 CTGGGACGCATTCGACATG 58.991 57.895 0.00 0.00 39.41 3.21
1397 1474 1.815421 GCTGGGACGCATTCGACAT 60.815 57.895 0.00 0.00 39.41 3.06
1400 1477 2.773397 TTTCGCTGGGACGCATTCGA 62.773 55.000 11.21 11.21 39.41 3.71
1401 1478 1.906994 TTTTCGCTGGGACGCATTCG 61.907 55.000 0.00 7.63 42.43 3.34
1402 1479 0.454452 GTTTTCGCTGGGACGCATTC 60.454 55.000 0.00 0.00 0.00 2.67
1403 1480 1.579429 GTTTTCGCTGGGACGCATT 59.421 52.632 0.00 0.00 0.00 3.56
1404 1481 2.332654 GGTTTTCGCTGGGACGCAT 61.333 57.895 0.00 0.00 0.00 4.73
1405 1482 2.975799 GGTTTTCGCTGGGACGCA 60.976 61.111 0.00 0.00 0.00 5.24
1406 1483 2.791501 TAGGGTTTTCGCTGGGACGC 62.792 60.000 0.00 0.00 43.01 5.19
1407 1484 0.320946 TTAGGGTTTTCGCTGGGACG 60.321 55.000 0.00 0.00 43.01 4.79
1408 1485 1.162698 GTTAGGGTTTTCGCTGGGAC 58.837 55.000 0.00 0.00 43.01 4.46
1409 1486 0.766131 TGTTAGGGTTTTCGCTGGGA 59.234 50.000 0.00 0.00 43.01 4.37
1410 1487 0.879090 GTGTTAGGGTTTTCGCTGGG 59.121 55.000 0.00 0.00 43.01 4.45
1411 1488 1.535462 CAGTGTTAGGGTTTTCGCTGG 59.465 52.381 0.00 0.00 43.01 4.85
1412 1489 2.218603 ACAGTGTTAGGGTTTTCGCTG 58.781 47.619 0.00 0.00 43.01 5.18
1413 1490 2.616842 CAACAGTGTTAGGGTTTTCGCT 59.383 45.455 8.49 0.00 45.12 4.93
1420 1497 1.072505 CGCCCAACAGTGTTAGGGT 59.927 57.895 28.98 2.60 43.42 4.34
1504 1581 4.579384 CCCACCACCCACAAGCGT 62.579 66.667 0.00 0.00 0.00 5.07
1555 1632 3.799366 TCTCCAAGCAACAGACGTAAAA 58.201 40.909 0.00 0.00 0.00 1.52
1716 1799 3.087031 CACTGGTCCATCTTCAAAGCAT 58.913 45.455 0.00 0.00 0.00 3.79
1789 1872 4.473520 CGAGCCATCTGCCGGGTT 62.474 66.667 2.18 0.00 42.71 4.11
1829 1912 5.071923 GCCATACCTCTCACCTAAACCTAAT 59.928 44.000 0.00 0.00 0.00 1.73
1835 1918 5.070446 CACATAGCCATACCTCTCACCTAAA 59.930 44.000 0.00 0.00 0.00 1.85
1853 1936 1.378911 TGCAAGCTGGGCCACATAG 60.379 57.895 0.00 0.00 0.00 2.23
1899 1982 0.106868 CCATCTTGGAGGCATCTGCA 60.107 55.000 4.33 0.00 40.96 4.41
1908 1991 1.590932 CTGAATCCGCCATCTTGGAG 58.409 55.000 0.00 0.00 40.96 3.86
1909 1992 0.181114 CCTGAATCCGCCATCTTGGA 59.819 55.000 0.00 0.00 40.96 3.53
1948 2031 9.973661 TTTATTGATCATTCTTGAGGACCTTAA 57.026 29.630 0.00 0.00 34.73 1.85
1965 2048 5.119931 TGCATACGGCCATTTTATTGATC 57.880 39.130 2.24 0.00 43.89 2.92
2040 2123 6.742718 CCGACACATTTTCTATTGACACATTC 59.257 38.462 0.00 0.00 0.00 2.67
2042 2125 5.937540 TCCGACACATTTTCTATTGACACAT 59.062 36.000 0.00 0.00 0.00 3.21
2045 2128 5.937540 ACATCCGACACATTTTCTATTGACA 59.062 36.000 0.00 0.00 0.00 3.58
2046 2129 6.422776 ACATCCGACACATTTTCTATTGAC 57.577 37.500 0.00 0.00 0.00 3.18
2058 2141 5.592104 ATTACTGATGTACATCCGACACA 57.408 39.130 28.64 12.00 37.02 3.72
2059 2142 9.856488 ATAATATTACTGATGTACATCCGACAC 57.144 33.333 28.64 8.05 37.02 3.67
2070 2153 9.797642 TTCATGGCAAGATAATATTACTGATGT 57.202 29.630 0.00 0.00 0.00 3.06
2072 2155 8.954350 GCTTCATGGCAAGATAATATTACTGAT 58.046 33.333 0.00 0.00 0.00 2.90
2074 2157 8.102800 TGCTTCATGGCAAGATAATATTACTG 57.897 34.615 0.00 0.00 39.43 2.74
2075 2158 8.874744 ATGCTTCATGGCAAGATAATATTACT 57.125 30.769 0.00 0.00 45.68 2.24
2076 2159 9.350357 CAATGCTTCATGGCAAGATAATATTAC 57.650 33.333 0.00 0.00 45.68 1.89
2077 2160 8.525316 CCAATGCTTCATGGCAAGATAATATTA 58.475 33.333 0.58 0.00 45.68 0.98
2088 2192 1.273048 GTTCACCAATGCTTCATGGCA 59.727 47.619 0.00 0.00 46.63 4.92
2095 2199 3.068590 CCAACTTGAGTTCACCAATGCTT 59.931 43.478 0.00 0.00 35.83 3.91
2097 2201 2.622942 TCCAACTTGAGTTCACCAATGC 59.377 45.455 0.00 0.00 35.83 3.56
2098 2202 3.885297 AGTCCAACTTGAGTTCACCAATG 59.115 43.478 0.00 0.00 35.83 2.82
2099 2203 3.885297 CAGTCCAACTTGAGTTCACCAAT 59.115 43.478 0.00 0.00 35.83 3.16
2102 2206 3.134458 CTCAGTCCAACTTGAGTTCACC 58.866 50.000 0.00 0.00 35.83 4.02
2103 2207 4.060038 TCTCAGTCCAACTTGAGTTCAC 57.940 45.455 0.00 0.00 35.83 3.18
2111 2215 6.214412 AGACAGGAATATTCTCAGTCCAACTT 59.786 38.462 21.07 8.71 35.09 2.66
2122 2226 7.066766 GCAACATCAGAAAGACAGGAATATTCT 59.933 37.037 14.95 0.00 0.00 2.40
2174 2278 5.508489 CGAATCCTGCTTGCATCCAAATAAT 60.508 40.000 0.00 0.00 0.00 1.28
2186 2290 1.391485 CACTCGTTCGAATCCTGCTTG 59.609 52.381 0.00 0.00 0.00 4.01
2299 2403 3.130340 TCCTTTGAAAATAAGCATCCGGC 59.870 43.478 0.00 0.00 45.30 6.13
2320 2424 6.402983 GCCAGCATGCATATACAAAGATACTC 60.403 42.308 21.98 0.00 31.97 2.59
2365 2472 4.485163 GTTAACCATGCCTAAAACTGCAG 58.515 43.478 13.48 13.48 41.46 4.41
2407 2514 4.512944 CAGAGCAAAGCTGTCTAAAGAACA 59.487 41.667 0.00 0.00 39.88 3.18
2463 2570 1.669760 CGCGGCTGAAAACCCTACA 60.670 57.895 0.00 0.00 0.00 2.74
2569 2676 7.615365 GGGCAATATCCATCCTTTCATATGTAA 59.385 37.037 1.90 0.00 0.00 2.41
2576 2683 3.969466 TGGGCAATATCCATCCTTTCA 57.031 42.857 0.00 0.00 0.00 2.69
2614 2721 9.762933 ACTGCATAAGACAACAAAAATAAACAT 57.237 25.926 0.00 0.00 0.00 2.71
2817 2928 3.678056 ATAACCGACAGCACTTCTGAA 57.322 42.857 0.00 0.00 45.72 3.02
2993 3113 6.375377 TGTCAACTTACTTCAACAACAACAC 58.625 36.000 0.00 0.00 0.00 3.32
2994 3114 6.561737 TGTCAACTTACTTCAACAACAACA 57.438 33.333 0.00 0.00 0.00 3.33
2995 3115 7.540745 ACAATGTCAACTTACTTCAACAACAAC 59.459 33.333 0.00 0.00 0.00 3.32
2996 3116 7.598278 ACAATGTCAACTTACTTCAACAACAA 58.402 30.769 0.00 0.00 0.00 2.83
2997 3117 7.151999 ACAATGTCAACTTACTTCAACAACA 57.848 32.000 0.00 0.00 0.00 3.33
2998 3118 9.730420 ATTACAATGTCAACTTACTTCAACAAC 57.270 29.630 0.00 0.00 0.00 3.32
3186 3311 5.931146 CACAAGAAAAGTCTGTCTGCTAGAT 59.069 40.000 0.00 0.00 33.05 1.98
3188 3313 4.084118 GCACAAGAAAAGTCTGTCTGCTAG 60.084 45.833 0.00 0.00 33.05 3.42
3215 3340 2.284417 GGAGCAACGGTTAATCGATGAC 59.716 50.000 20.96 13.20 35.42 3.06
3221 3346 4.251268 AGTGTAAGGAGCAACGGTTAATC 58.749 43.478 0.00 0.00 0.00 1.75
3260 3428 6.295123 GGTGAATGGAGTCAGACTAGTGTAAA 60.295 42.308 2.00 0.00 0.00 2.01
3408 3576 7.990886 TGGGCTTAAGATACGTCAAAAGATTAT 59.009 33.333 6.67 0.00 0.00 1.28
3409 3577 7.279313 GTGGGCTTAAGATACGTCAAAAGATTA 59.721 37.037 6.67 0.00 0.00 1.75
3448 3616 4.707448 TCAAGTGGGCTTAGTTGTCAAAAA 59.293 37.500 8.82 0.00 33.67 1.94
3449 3617 4.274147 TCAAGTGGGCTTAGTTGTCAAAA 58.726 39.130 8.82 0.00 33.67 2.44
3450 3618 3.882888 CTCAAGTGGGCTTAGTTGTCAAA 59.117 43.478 8.82 0.00 33.67 2.69
3451 3619 3.476552 CTCAAGTGGGCTTAGTTGTCAA 58.523 45.455 8.82 0.00 33.67 3.18
3452 3620 2.810400 GCTCAAGTGGGCTTAGTTGTCA 60.810 50.000 0.00 0.00 33.67 3.58
3453 3621 1.807142 GCTCAAGTGGGCTTAGTTGTC 59.193 52.381 0.00 1.89 33.67 3.18
3454 3622 1.545651 GGCTCAAGTGGGCTTAGTTGT 60.546 52.381 2.65 0.00 33.67 3.32
3455 3623 1.168714 GGCTCAAGTGGGCTTAGTTG 58.831 55.000 2.65 4.26 32.87 3.16
3456 3624 1.068121 AGGCTCAAGTGGGCTTAGTT 58.932 50.000 2.65 0.00 36.12 2.24
3457 3625 1.834263 CTAGGCTCAAGTGGGCTTAGT 59.166 52.381 12.85 0.00 40.13 2.24
3458 3626 1.474143 GCTAGGCTCAAGTGGGCTTAG 60.474 57.143 15.93 15.93 39.87 2.18
3459 3627 0.541863 GCTAGGCTCAAGTGGGCTTA 59.458 55.000 2.65 0.00 40.13 3.09
3460 3628 1.204113 AGCTAGGCTCAAGTGGGCTT 61.204 55.000 2.65 0.00 40.13 4.35
3461 3629 1.204113 AAGCTAGGCTCAAGTGGGCT 61.204 55.000 2.65 2.51 38.25 5.19
3462 3630 0.322906 AAAGCTAGGCTCAAGTGGGC 60.323 55.000 0.00 0.00 38.25 5.36
3463 3631 3.209410 CATAAAGCTAGGCTCAAGTGGG 58.791 50.000 0.00 0.00 38.25 4.61
3464 3632 3.878778 ACATAAAGCTAGGCTCAAGTGG 58.121 45.455 0.00 0.00 38.25 4.00
3546 3714 8.355913 GGACAATCTTTCTTTTTGACAGAGAAT 58.644 33.333 0.00 0.00 35.27 2.40
3567 3736 8.890410 AGTACTAACTCCAAAGTATAGGACAA 57.110 34.615 0.00 0.00 35.07 3.18
3592 3761 7.640616 TGATTTGACAATCGTTTCGTACTAA 57.359 32.000 0.00 0.00 41.77 2.24
3593 3762 7.640616 TTGATTTGACAATCGTTTCGTACTA 57.359 32.000 0.00 0.00 41.77 1.82
3594 3763 6.533819 TTGATTTGACAATCGTTTCGTACT 57.466 33.333 0.00 0.00 41.77 2.73
3595 3764 7.584847 TCTTTTGATTTGACAATCGTTTCGTAC 59.415 33.333 0.00 0.00 41.77 3.67
3596 3765 7.631822 TCTTTTGATTTGACAATCGTTTCGTA 58.368 30.769 0.00 0.00 41.77 3.43
3597 3766 6.491394 TCTTTTGATTTGACAATCGTTTCGT 58.509 32.000 0.00 0.00 41.77 3.85
3598 3767 6.968004 TCTTTTGATTTGACAATCGTTTCG 57.032 33.333 0.00 0.00 41.77 3.46
3690 3859 6.528321 TGAACATCTCAGAGAAGTCAATTGT 58.472 36.000 8.75 2.04 0.00 2.71
3774 3972 9.421399 TCCAGAAATAGATCAGTAGTCATGTAA 57.579 33.333 0.00 0.00 0.00 2.41
3889 4087 3.528597 AGCCGGCAAGTAAAACAAAAA 57.471 38.095 31.54 0.00 0.00 1.94
3910 4108 6.318913 AGTTCTGATAGCCTGGTGTATAGAT 58.681 40.000 0.00 0.00 0.00 1.98
3947 4145 6.368516 GGCAGTGCTAGCAATTTTAAAATTCA 59.631 34.615 21.29 13.55 36.52 2.57
3948 4146 6.591448 AGGCAGTGCTAGCAATTTTAAAATTC 59.409 34.615 21.29 15.57 36.52 2.17
3962 4160 2.292267 CCACCAAATAGGCAGTGCTAG 58.708 52.381 16.11 0.00 43.14 3.42
4155 4353 1.150827 CAGCACTGAGAATCACGCAA 58.849 50.000 0.00 0.00 42.56 4.85
4310 4508 0.179124 GGCAAAGTTTGTCGGCAACA 60.179 50.000 16.70 0.00 33.82 3.33
4430 4934 1.776034 GCTTCCCTAAAGATGCGCGG 61.776 60.000 8.83 0.00 37.12 6.46
4540 5044 8.432805 ACTGGGAACTAATTCAAGTCCTATATG 58.567 37.037 0.00 0.00 36.46 1.78
4541 5045 8.568617 ACTGGGAACTAATTCAAGTCCTATAT 57.431 34.615 0.00 0.00 36.46 0.86
4907 5412 4.331168 AGAAGATTGCGAGTTTGAGCATAC 59.669 41.667 0.00 0.00 43.42 2.39
5164 5669 3.588842 CCCCCAATAGCTCCTTGATATCA 59.411 47.826 0.00 0.00 0.00 2.15
5270 5775 3.242123 GCAGTCGAATAAAGGAAAGCTCG 60.242 47.826 0.00 0.00 0.00 5.03
5311 5816 2.013400 CATACATTGCGTGCCTTACCA 58.987 47.619 0.00 0.00 0.00 3.25
5372 5877 4.804139 CGTAGGTTGGCAGTAGTATGAAAG 59.196 45.833 0.00 0.00 0.00 2.62
5603 6108 2.301870 TCCCTCCATTCACACAGTACAC 59.698 50.000 0.00 0.00 0.00 2.90
5766 6271 2.409870 GGCTGAAATGGACTGGCCG 61.410 63.158 0.00 0.00 40.66 6.13
5793 6303 2.710096 ACTTACATTGCACGGCCTAT 57.290 45.000 0.00 0.00 0.00 2.57
5900 6410 4.497300 CCTTTTGAGCAAATATGTGGTGG 58.503 43.478 1.35 0.00 0.00 4.61
5930 6440 8.189119 ACTCCAGTTTTTATGCATTCCTTTTA 57.811 30.769 3.54 0.00 0.00 1.52
6112 6622 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
6113 6623 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
6114 6624 3.118038 TCATAGAATTTTGGGACGGAGGG 60.118 47.826 0.00 0.00 0.00 4.30
6115 6625 3.877508 GTCATAGAATTTTGGGACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
6116 6626 4.513442 TGTCATAGAATTTTGGGACGGAG 58.487 43.478 0.00 0.00 0.00 4.63
6117 6627 4.561500 TGTCATAGAATTTTGGGACGGA 57.438 40.909 0.00 0.00 0.00 4.69
6118 6628 5.637006 TTTGTCATAGAATTTTGGGACGG 57.363 39.130 0.00 0.00 0.00 4.79
6119 6629 7.088589 AGATTTGTCATAGAATTTTGGGACG 57.911 36.000 0.00 0.00 0.00 4.79
6120 6630 9.956720 CATAGATTTGTCATAGAATTTTGGGAC 57.043 33.333 0.00 0.00 0.00 4.46
6121 6631 9.919416 TCATAGATTTGTCATAGAATTTTGGGA 57.081 29.630 0.00 0.00 0.00 4.37
6122 6632 9.956720 GTCATAGATTTGTCATAGAATTTTGGG 57.043 33.333 0.00 0.00 0.00 4.12
6133 6643 8.517878 CCAAACTTCTTGTCATAGATTTGTCAT 58.482 33.333 0.00 0.00 28.79 3.06
6134 6644 7.502226 ACCAAACTTCTTGTCATAGATTTGTCA 59.498 33.333 0.00 0.00 28.79 3.58
6135 6645 7.875971 ACCAAACTTCTTGTCATAGATTTGTC 58.124 34.615 0.00 0.00 28.79 3.18
6136 6646 7.823745 ACCAAACTTCTTGTCATAGATTTGT 57.176 32.000 0.00 0.00 28.79 2.83
6137 6647 9.612620 GTTACCAAACTTCTTGTCATAGATTTG 57.387 33.333 0.00 0.00 32.54 2.32
6138 6648 9.574516 AGTTACCAAACTTCTTGTCATAGATTT 57.425 29.630 0.00 0.00 43.60 2.17
6140 6650 9.877178 CTAGTTACCAAACTTCTTGTCATAGAT 57.123 33.333 0.00 0.00 43.60 1.98
6141 6651 9.085645 TCTAGTTACCAAACTTCTTGTCATAGA 57.914 33.333 0.00 0.00 43.60 1.98
6142 6652 9.877178 ATCTAGTTACCAAACTTCTTGTCATAG 57.123 33.333 0.00 0.00 43.60 2.23
6150 6660 9.364653 ACGGATATATCTAGTTACCAAACTTCT 57.635 33.333 12.42 0.00 43.60 2.85


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

AutoCloner maintained by Alex Coulton.