Multiple sequence alignment - TraesCS3D01G419800

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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 TraesCS3D01G419800 chr3D 100.000 4759 0 0 1 4759 532176592 532171834 0.000000e+00 8789.0
1 TraesCS3D01G419800 chr3D 86.692 263 31 3 4499 4759 348731486 348731746 6.030000e-74 289.0
2 TraesCS3D01G419800 chr3A 94.538 2966 113 16 1554 4500 667358259 667355324 0.000000e+00 4534.0
3 TraesCS3D01G419800 chr3A 89.864 1470 74 28 119 1571 667359686 667358275 0.000000e+00 1820.0
4 TraesCS3D01G419800 chr3A 87.266 267 27 6 4496 4759 475281321 475281059 1.000000e-76 298.0
5 TraesCS3D01G419800 chr3A 92.529 174 10 2 37 207 667360385 667360212 3.680000e-61 246.0
6 TraesCS3D01G419800 chr3B 91.336 3024 143 45 1509 4500 704328920 704325984 0.000000e+00 4023.0
7 TraesCS3D01G419800 chr3B 94.307 527 13 5 909 1435 704329427 704328918 0.000000e+00 791.0
8 TraesCS3D01G419800 chr3B 86.940 268 27 7 4496 4759 457574244 457573981 1.300000e-75 294.0
9 TraesCS3D01G419800 chr3B 88.000 250 24 5 4499 4745 394097760 394098006 1.680000e-74 291.0
10 TraesCS3D01G419800 chr3B 86.194 268 28 5 4494 4759 519860916 519860656 1.010000e-71 281.0
11 TraesCS3D01G419800 chr3B 91.262 103 3 5 1 98 258102030 258102131 8.310000e-28 135.0
12 TraesCS3D01G419800 chr3B 90.196 102 6 3 1 98 10615271 10615372 3.870000e-26 130.0
13 TraesCS3D01G419800 chr5B 88.433 268 25 5 4495 4759 121249765 121249501 7.690000e-83 318.0
14 TraesCS3D01G419800 chr5B 90.385 52 1 2 1433 1484 580835512 580835465 1.110000e-06 65.8
15 TraesCS3D01G419800 chr5A 87.732 269 26 5 4495 4759 115095389 115095124 1.660000e-79 307.0
16 TraesCS3D01G419800 chr5A 90.385 52 1 2 1433 1484 593329727 593329680 1.110000e-06 65.8
17 TraesCS3D01G419800 chr4B 86.029 272 28 8 4492 4759 166765781 166765516 2.800000e-72 283.0
18 TraesCS3D01G419800 chrUn 85.662 272 29 7 4492 4759 216298161 216298426 1.300000e-70 278.0
19 TraesCS3D01G419800 chr7D 93.000 100 3 3 3 98 547606719 547606620 4.960000e-30 143.0
20 TraesCS3D01G419800 chr4D 93.684 95 2 4 1 92 223684301 223684394 6.420000e-29 139.0
21 TraesCS3D01G419800 chr4D 91.262 103 5 3 1 99 394912938 394913040 2.310000e-28 137.0
22 TraesCS3D01G419800 chr4D 91.176 102 5 3 1 98 313031031 313030930 8.310000e-28 135.0
23 TraesCS3D01G419800 chr6A 90.196 102 6 3 1 98 324249344 324249445 3.870000e-26 130.0
24 TraesCS3D01G419800 chr1D 90.196 102 6 3 1 98 335101346 335101245 3.870000e-26 130.0
25 TraesCS3D01G419800 chr1B 90.000 50 1 1 1433 1482 411568790 411568745 1.430000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G419800 chr3D 532171834 532176592 4758 True 8789 8789 100.000000 1 4759 1 chr3D.!!$R1 4758
1 TraesCS3D01G419800 chr3A 667355324 667360385 5061 True 2200 4534 92.310333 37 4500 3 chr3A.!!$R2 4463
2 TraesCS3D01G419800 chr3B 704325984 704329427 3443 True 2407 4023 92.821500 909 4500 2 chr3B.!!$R3 3591

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
953 1582 0.177141 AACCGCCACGCATATACAGT 59.823 50.0 0.0 0.0 0.00 3.55 F
1481 2114 0.321671 ACGCAGCCTCTGTACAATGT 59.678 50.0 0.0 0.0 33.43 2.71 F
1482 2115 0.723414 CGCAGCCTCTGTACAATGTG 59.277 55.0 0.0 0.0 33.43 3.21 F
2621 3308 0.984230 CTGGGGCTGTAGGAAACTCA 59.016 55.0 0.0 0.0 43.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2512 0.035152 TCAATCGGACAAGCAGCCAT 60.035 50.0 0.00 0.0 0.00 4.40 R
2598 3285 0.547712 TTTCCTACAGCCCCAGAGCT 60.548 55.0 0.00 0.0 46.45 4.09 R
3413 4100 2.143876 AGCCGCAAATAACTCCCAAT 57.856 45.0 0.00 0.0 0.00 3.16 R
4289 4998 0.248289 TAGGCCTAAGCGGTCAACAC 59.752 55.0 10.98 0.0 40.99 3.32 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
21 22 3.262420 ACGATCTTGTTGTACCATGAGC 58.738 45.455 0.00 0.00 0.00 4.26
22 23 3.055819 ACGATCTTGTTGTACCATGAGCT 60.056 43.478 0.00 0.00 0.00 4.09
23 24 3.935203 CGATCTTGTTGTACCATGAGCTT 59.065 43.478 0.00 0.00 0.00 3.74
24 25 4.393062 CGATCTTGTTGTACCATGAGCTTT 59.607 41.667 0.00 0.00 0.00 3.51
25 26 5.633830 ATCTTGTTGTACCATGAGCTTTG 57.366 39.130 0.00 0.00 0.00 2.77
26 27 4.460263 TCTTGTTGTACCATGAGCTTTGT 58.540 39.130 0.00 0.00 0.00 2.83
27 28 4.887071 TCTTGTTGTACCATGAGCTTTGTT 59.113 37.500 0.00 0.00 0.00 2.83
28 29 6.058833 TCTTGTTGTACCATGAGCTTTGTTA 58.941 36.000 0.00 0.00 0.00 2.41
29 30 6.544197 TCTTGTTGTACCATGAGCTTTGTTAA 59.456 34.615 0.00 0.00 0.00 2.01
30 31 6.892658 TGTTGTACCATGAGCTTTGTTAAT 57.107 33.333 0.00 0.00 0.00 1.40
31 32 7.987750 TGTTGTACCATGAGCTTTGTTAATA 57.012 32.000 0.00 0.00 0.00 0.98
32 33 8.397575 TGTTGTACCATGAGCTTTGTTAATAA 57.602 30.769 0.00 0.00 0.00 1.40
33 34 8.293867 TGTTGTACCATGAGCTTTGTTAATAAC 58.706 33.333 0.00 0.00 0.00 1.89
34 35 7.067532 TGTACCATGAGCTTTGTTAATAACG 57.932 36.000 0.00 0.00 0.00 3.18
35 36 5.560966 ACCATGAGCTTTGTTAATAACGG 57.439 39.130 0.00 0.00 0.00 4.44
73 76 8.655092 GTTCTTCTCTCTATCTTTGTTGTGATG 58.345 37.037 0.00 0.00 0.00 3.07
80 83 9.159364 TCTCTATCTTTGTTGTGATGAATTGAG 57.841 33.333 0.00 0.00 0.00 3.02
86 89 5.112220 TGTTGTGATGAATTGAGTCTTGC 57.888 39.130 0.00 0.00 0.00 4.01
92 95 6.263842 TGTGATGAATTGAGTCTTGCTCTTTT 59.736 34.615 0.00 0.00 44.41 2.27
94 97 7.961827 GTGATGAATTGAGTCTTGCTCTTTTAG 59.038 37.037 0.00 0.00 44.41 1.85
194 198 1.683790 CGTTGTCGCATCGAGGGAAC 61.684 60.000 0.00 0.00 41.26 3.62
195 199 0.669318 GTTGTCGCATCGAGGGAACA 60.669 55.000 0.00 0.00 41.26 3.18
245 862 3.431725 GCAAAGTCTTCGGCCCCG 61.432 66.667 0.00 0.00 41.35 5.73
267 884 1.497278 CATCACAAACGGCTGGTCG 59.503 57.895 0.00 0.00 0.00 4.79
270 887 2.203153 ACAAACGGCTGGTCGCTT 60.203 55.556 0.00 0.00 39.13 4.68
302 919 4.386951 CACCGGGTCATCGTGGCA 62.387 66.667 6.32 0.00 0.00 4.92
312 929 1.206849 TCATCGTGGCATGAAGTAGCA 59.793 47.619 14.29 0.00 29.41 3.49
344 969 2.878406 CAATTTATGGCGGAAGATCGGT 59.122 45.455 0.00 0.00 0.00 4.69
370 995 1.680735 TGAATTGCAGCCAAGTTCGTT 59.319 42.857 0.00 0.00 33.80 3.85
396 1021 2.353889 CTGTTTGCCTCGAAGATCATGG 59.646 50.000 0.00 0.00 33.89 3.66
427 1052 1.288335 AGATCTGGGTACGGGTTCTCT 59.712 52.381 0.00 0.00 0.00 3.10
429 1054 2.905415 TCTGGGTACGGGTTCTCTAA 57.095 50.000 0.00 0.00 0.00 2.10
475 1100 6.091555 TGGAGGGGATTATCTGCTAATTAGT 58.908 40.000 13.91 0.00 29.93 2.24
538 1164 0.613853 TCCCAACTGAGGTAGGTCGG 60.614 60.000 0.00 0.00 0.00 4.79
592 1218 2.204090 TCAAGACCTCCCACCCCC 60.204 66.667 0.00 0.00 0.00 5.40
598 1224 2.444140 CCTCCCACCCCCTCTACG 60.444 72.222 0.00 0.00 0.00 3.51
599 1225 2.444140 CTCCCACCCCCTCTACGG 60.444 72.222 0.00 0.00 0.00 4.02
603 1229 1.305887 CCACCCCCTCTACGGACTT 60.306 63.158 0.00 0.00 33.16 3.01
604 1230 1.328430 CCACCCCCTCTACGGACTTC 61.328 65.000 0.00 0.00 33.16 3.01
614 1240 2.492484 TCTACGGACTTCTCTTGCTTCC 59.508 50.000 0.00 0.00 0.00 3.46
618 1244 2.739379 CGGACTTCTCTTGCTTCCTTTC 59.261 50.000 0.00 0.00 0.00 2.62
620 1246 3.394719 GACTTCTCTTGCTTCCTTTCGT 58.605 45.455 0.00 0.00 0.00 3.85
646 1272 1.108776 CCATGCATCAGTTTGGGGAG 58.891 55.000 0.00 0.00 0.00 4.30
674 1300 4.441695 CTCTTCTCGCTGCCGGCA 62.442 66.667 30.59 30.59 41.91 5.69
675 1301 4.742201 TCTTCTCGCTGCCGGCAC 62.742 66.667 29.03 21.21 41.91 5.01
694 1320 4.684703 GGCACGTGGTATAGATGAATACAC 59.315 45.833 18.88 0.00 34.58 2.90
727 1353 5.963214 TTTATAGGAGGGGTAACTTGGTC 57.037 43.478 0.00 0.00 0.00 4.02
802 1428 1.139163 GCAAATGGTCAAACGGCAAG 58.861 50.000 0.00 0.00 0.00 4.01
814 1440 3.861276 AACGGCAAGTAAAATTAGGGC 57.139 42.857 0.00 0.00 0.00 5.19
826 1452 9.546428 AAGTAAAATTAGGGCAAAATATCATGC 57.454 29.630 4.52 4.52 41.82 4.06
831 1457 7.779754 ATTAGGGCAAAATATCATGCATACA 57.220 32.000 0.00 0.00 44.32 2.29
835 1461 6.042322 AGGGCAAAATATCATGCATACAATGT 59.958 34.615 0.00 0.00 44.32 2.71
950 1579 0.306533 CCAAACCGCCACGCATATAC 59.693 55.000 0.00 0.00 0.00 1.47
952 1581 1.003972 CAAACCGCCACGCATATACAG 60.004 52.381 0.00 0.00 0.00 2.74
953 1582 0.177141 AACCGCCACGCATATACAGT 59.823 50.000 0.00 0.00 0.00 3.55
954 1583 1.034356 ACCGCCACGCATATACAGTA 58.966 50.000 0.00 0.00 0.00 2.74
955 1584 1.616865 ACCGCCACGCATATACAGTAT 59.383 47.619 0.00 0.00 0.00 2.12
956 1585 2.821378 ACCGCCACGCATATACAGTATA 59.179 45.455 2.62 2.62 0.00 1.47
957 1586 3.119602 ACCGCCACGCATATACAGTATAG 60.120 47.826 6.45 0.86 0.00 1.31
1000 1629 1.277440 GCCGCTTCGTTTTCGTTCA 59.723 52.632 0.00 0.00 44.46 3.18
1041 1670 0.598680 CTCCATCCAGATCGCGGAAC 60.599 60.000 6.13 0.00 35.77 3.62
1042 1671 1.595382 CCATCCAGATCGCGGAACC 60.595 63.158 6.13 0.00 35.77 3.62
1043 1672 1.443407 CATCCAGATCGCGGAACCT 59.557 57.895 6.13 0.00 35.77 3.50
1044 1673 0.877649 CATCCAGATCGCGGAACCTG 60.878 60.000 6.13 8.52 35.77 4.00
1045 1674 2.032860 ATCCAGATCGCGGAACCTGG 62.033 60.000 22.01 22.01 45.63 4.45
1046 1675 2.721167 CCAGATCGCGGAACCTGGA 61.721 63.158 22.95 0.00 46.84 3.86
1047 1676 1.519455 CAGATCGCGGAACCTGGAC 60.519 63.158 6.13 0.00 0.00 4.02
1048 1677 2.582498 GATCGCGGAACCTGGACG 60.582 66.667 6.13 3.12 0.00 4.79
1049 1678 3.060020 GATCGCGGAACCTGGACGA 62.060 63.158 6.13 1.84 37.15 4.20
1050 1679 2.938539 GATCGCGGAACCTGGACGAG 62.939 65.000 6.13 4.17 36.05 4.18
1402 2031 6.822073 AAAGTTTCGATTTTTGCTTGGTAC 57.178 33.333 0.00 0.00 0.00 3.34
1403 2032 4.866921 AGTTTCGATTTTTGCTTGGTACC 58.133 39.130 4.43 4.43 0.00 3.34
1444 2077 1.068250 GCATCTGTACTCCCTCCGC 59.932 63.158 0.00 0.00 0.00 5.54
1448 2081 2.439701 TGTACTCCCTCCGCTCCG 60.440 66.667 0.00 0.00 0.00 4.63
1449 2082 2.124403 GTACTCCCTCCGCTCCGA 60.124 66.667 0.00 0.00 0.00 4.55
1450 2083 1.751927 GTACTCCCTCCGCTCCGAA 60.752 63.158 0.00 0.00 0.00 4.30
1451 2084 1.108132 GTACTCCCTCCGCTCCGAAT 61.108 60.000 0.00 0.00 0.00 3.34
1454 2087 1.676678 CTCCCTCCGCTCCGAATGAA 61.677 60.000 0.00 0.00 0.00 2.57
1466 2099 4.495679 GCTCCGAATGAATTAATTGACGCA 60.496 41.667 5.17 0.00 0.00 5.24
1468 2101 3.725740 CCGAATGAATTAATTGACGCAGC 59.274 43.478 5.17 0.00 0.00 5.25
1470 2103 4.496341 CGAATGAATTAATTGACGCAGCCT 60.496 41.667 5.17 0.00 0.00 4.58
1471 2104 4.558538 ATGAATTAATTGACGCAGCCTC 57.441 40.909 5.17 0.00 0.00 4.70
1473 2106 3.374988 TGAATTAATTGACGCAGCCTCTG 59.625 43.478 5.17 0.00 34.12 3.35
1474 2107 2.472695 TTAATTGACGCAGCCTCTGT 57.527 45.000 0.00 0.00 33.43 3.41
1475 2108 3.603158 TTAATTGACGCAGCCTCTGTA 57.397 42.857 0.00 0.00 33.43 2.74
1476 2109 1.726853 AATTGACGCAGCCTCTGTAC 58.273 50.000 0.00 0.00 33.43 2.90
1477 2110 0.608130 ATTGACGCAGCCTCTGTACA 59.392 50.000 0.00 0.00 33.43 2.90
1478 2111 0.391228 TTGACGCAGCCTCTGTACAA 59.609 50.000 0.00 0.00 33.43 2.41
1479 2112 0.608130 TGACGCAGCCTCTGTACAAT 59.392 50.000 0.00 0.00 33.43 2.71
1480 2113 1.002366 GACGCAGCCTCTGTACAATG 58.998 55.000 0.00 0.00 33.43 2.82
1481 2114 0.321671 ACGCAGCCTCTGTACAATGT 59.678 50.000 0.00 0.00 33.43 2.71
1482 2115 0.723414 CGCAGCCTCTGTACAATGTG 59.277 55.000 0.00 0.00 33.43 3.21
1483 2116 1.813513 GCAGCCTCTGTACAATGTGT 58.186 50.000 0.00 0.00 33.43 3.72
1484 2117 1.734465 GCAGCCTCTGTACAATGTGTC 59.266 52.381 0.00 0.00 33.43 3.67
1485 2118 2.871637 GCAGCCTCTGTACAATGTGTCA 60.872 50.000 0.00 0.00 33.43 3.58
1486 2119 3.402110 CAGCCTCTGTACAATGTGTCAA 58.598 45.455 0.00 0.00 0.00 3.18
1487 2120 4.005650 CAGCCTCTGTACAATGTGTCAAT 58.994 43.478 0.00 0.00 0.00 2.57
1488 2121 4.456911 CAGCCTCTGTACAATGTGTCAATT 59.543 41.667 0.00 0.00 0.00 2.32
1489 2122 5.643348 CAGCCTCTGTACAATGTGTCAATTA 59.357 40.000 0.00 0.00 0.00 1.40
1490 2123 5.643777 AGCCTCTGTACAATGTGTCAATTAC 59.356 40.000 0.00 0.00 0.00 1.89
1500 2133 7.250569 ACAATGTGTCAATTACAATTCGGATC 58.749 34.615 0.00 0.00 40.63 3.36
1506 2139 4.100344 TCAATTACAATTCGGATCGGAGGA 59.900 41.667 2.99 0.00 0.00 3.71
1546 2183 7.461182 AAAACTATATGCTGCCTTTACACAA 57.539 32.000 0.00 0.00 0.00 3.33
1605 2275 4.749099 TGAGGTTTGCACATTTGTAATTGC 59.251 37.500 0.00 0.00 35.45 3.56
1610 2280 4.319139 TGCACATTTGTAATTGCACTGT 57.681 36.364 0.00 0.49 40.01 3.55
1634 2304 4.141959 ACCAATGCATATGCTGTAAAACCC 60.142 41.667 27.13 0.00 42.66 4.11
1675 2345 2.124122 GAAGAAATGTTTGCGCCGTTT 58.876 42.857 4.18 3.15 0.00 3.60
1804 2479 5.880901 AGCATGGGGTAATAGAATTGTAGG 58.119 41.667 0.00 0.00 0.00 3.18
1832 2507 4.696479 AACATGGGGTTTAATGTTTGCA 57.304 36.364 0.00 0.00 42.85 4.08
1858 2533 1.427020 GCTGCTTGTCCGATTGAGC 59.573 57.895 0.00 0.00 35.74 4.26
1897 2572 1.060713 CAACGTCTGCTACTGGTTCG 58.939 55.000 0.00 0.00 0.00 3.95
1968 2643 8.579682 AATGCTCTAAAATTGAACTGTTGAAC 57.420 30.769 0.00 0.00 0.00 3.18
1994 2670 2.443255 TGCCTTTCTTTCCTCCACTTCT 59.557 45.455 0.00 0.00 0.00 2.85
1995 2671 2.816672 GCCTTTCTTTCCTCCACTTCTG 59.183 50.000 0.00 0.00 0.00 3.02
2024 2701 2.093890 TGCCAACTTATGCATGTCTGG 58.906 47.619 10.16 11.49 31.31 3.86
2028 2705 4.339247 GCCAACTTATGCATGTCTGGTTAT 59.661 41.667 10.16 0.00 0.00 1.89
2091 2768 6.262049 TGCATGCTTGTTCTCTTTAGTAAACA 59.738 34.615 20.33 0.00 0.00 2.83
2093 2770 7.809806 GCATGCTTGTTCTCTTTAGTAAACAAT 59.190 33.333 11.37 0.00 39.92 2.71
2096 2773 9.555727 TGCTTGTTCTCTTTAGTAAACAATACT 57.444 29.630 10.52 0.00 39.92 2.12
2097 2774 9.813080 GCTTGTTCTCTTTAGTAAACAATACTG 57.187 33.333 10.52 4.24 39.92 2.74
2116 2793 3.323691 ACTGTACATTGTACTCACCTGCA 59.676 43.478 23.58 4.41 0.00 4.41
2133 2810 4.009675 CCTGCATACCACTACACATTTGT 58.990 43.478 0.00 0.00 40.02 2.83
2329 3016 4.425577 AAATGTTGTCTCAAATCGAGCC 57.574 40.909 0.00 0.00 41.98 4.70
2335 3022 2.280628 GTCTCAAATCGAGCCGGATTT 58.719 47.619 5.05 0.00 45.07 2.17
2590 3277 8.052621 AGTCCTACTCCTGAATACTCTTCTAT 57.947 38.462 0.00 0.00 0.00 1.98
2598 3285 9.083422 CTCCTGAATACTCTTCTATACATGGAA 57.917 37.037 0.00 0.00 0.00 3.53
2621 3308 0.984230 CTGGGGCTGTAGGAAACTCA 59.016 55.000 0.00 0.00 43.67 3.41
2624 3311 1.351350 GGGGCTGTAGGAAACTCAAGT 59.649 52.381 0.00 0.00 43.67 3.16
3007 3694 2.584236 GCATGCAGAAATCCTGAGGAT 58.416 47.619 14.21 8.51 45.46 3.24
3210 3897 2.734079 GCTTCTCACTGTCTCTTTTCCG 59.266 50.000 0.00 0.00 0.00 4.30
3550 4237 8.433421 AACTGTTATCCATCTGTTATTTACCG 57.567 34.615 0.00 0.00 0.00 4.02
3687 4374 4.151883 TGGCTTACTTCCATTTGCTTCTT 58.848 39.130 0.00 0.00 0.00 2.52
3769 4456 7.808381 CGAAGTTGAAGTCTGAAGTATCTTGTA 59.192 37.037 0.00 0.00 0.00 2.41
3771 4458 8.994429 AGTTGAAGTCTGAAGTATCTTGTATG 57.006 34.615 0.00 0.00 0.00 2.39
3772 4459 8.037758 AGTTGAAGTCTGAAGTATCTTGTATGG 58.962 37.037 0.00 0.00 0.00 2.74
3817 4504 8.206867 TCTGGAGGAGTAAGATATGTTGAATTG 58.793 37.037 0.00 0.00 0.00 2.32
3822 4509 7.941238 AGGAGTAAGATATGTTGAATTGGATGG 59.059 37.037 0.00 0.00 0.00 3.51
3924 4619 2.424601 TGAAGGTATCAATGCTTGCAGC 59.575 45.455 0.87 1.70 37.07 5.25
3945 4640 1.968540 GGCGGTGCAAGCTTCTTCT 60.969 57.895 14.02 0.00 34.52 2.85
3972 4667 2.423538 GTGAACTTGTGACCTTGCACTT 59.576 45.455 0.00 0.00 39.49 3.16
3973 4668 2.423185 TGAACTTGTGACCTTGCACTTG 59.577 45.455 0.00 0.00 39.49 3.16
3978 4673 0.242017 GTGACCTTGCACTTGGATGC 59.758 55.000 6.59 0.00 46.32 3.91
3986 4681 1.005805 TGCACTTGGATGCCAGGTATT 59.994 47.619 0.66 0.00 41.98 1.89
4059 4754 6.434652 ACAGTATAGTGTTAAGAGTGCAGACT 59.565 38.462 7.42 0.00 33.98 3.24
4060 4755 7.610692 ACAGTATAGTGTTAAGAGTGCAGACTA 59.389 37.037 7.42 0.00 30.16 2.59
4134 4829 4.397420 TGATGCTTTTCTTGCCTCACTTA 58.603 39.130 0.00 0.00 31.93 2.24
4135 4830 5.012239 TGATGCTTTTCTTGCCTCACTTAT 58.988 37.500 0.00 0.00 31.93 1.73
4136 4831 5.477984 TGATGCTTTTCTTGCCTCACTTATT 59.522 36.000 0.00 0.00 31.93 1.40
4137 4832 5.125100 TGCTTTTCTTGCCTCACTTATTG 57.875 39.130 0.00 0.00 0.00 1.90
4138 4833 4.584325 TGCTTTTCTTGCCTCACTTATTGT 59.416 37.500 0.00 0.00 0.00 2.71
4141 4836 5.437289 TTTCTTGCCTCACTTATTGTGTG 57.563 39.130 0.00 0.00 46.27 3.82
4152 4847 9.388506 CCTCACTTATTGTGTGAATTTAGAGAT 57.611 33.333 0.00 0.00 46.27 2.75
4221 4927 7.634649 GCTCTTCTAATCTTTCTCCTGGAATGA 60.635 40.741 0.00 0.00 40.66 2.57
4222 4928 8.329346 TCTTCTAATCTTTCTCCTGGAATGAT 57.671 34.615 0.00 0.00 45.03 2.45
4303 5012 2.753452 TCCTCTAGTGTTGACCGCTTAG 59.247 50.000 0.00 0.00 35.05 2.18
4305 5014 1.203994 TCTAGTGTTGACCGCTTAGGC 59.796 52.381 0.00 0.00 46.52 3.93
4357 5066 4.564372 GCTGTATGCCTGTATGTATGATCG 59.436 45.833 0.00 0.00 35.15 3.69
4401 5110 7.395190 AGCTCAAAAGTATGCACAATTATGA 57.605 32.000 0.00 0.00 0.00 2.15
4427 5136 7.395190 TTCTGCTGAACATAATAGTGCATTT 57.605 32.000 1.33 0.00 0.00 2.32
4428 5137 8.504812 TTCTGCTGAACATAATAGTGCATTTA 57.495 30.769 1.33 0.00 0.00 1.40
4431 5141 9.740239 CTGCTGAACATAATAGTGCATTTATTT 57.260 29.630 10.51 4.21 0.00 1.40
4485 5196 4.578871 TCCCACTCATGTACAGAATTGTG 58.421 43.478 0.33 0.13 38.23 3.33
4500 5211 7.836842 ACAGAATTGTGAACCCCAAATATTAC 58.163 34.615 9.96 0.00 35.83 1.89
4501 5212 7.673926 ACAGAATTGTGAACCCCAAATATTACT 59.326 33.333 9.96 0.00 35.83 2.24
4502 5213 8.190784 CAGAATTGTGAACCCCAAATATTACTC 58.809 37.037 0.00 0.00 0.00 2.59
4503 5214 7.342026 AGAATTGTGAACCCCAAATATTACTCC 59.658 37.037 0.00 0.00 0.00 3.85
4504 5215 4.862371 TGTGAACCCCAAATATTACTCCC 58.138 43.478 0.00 0.00 0.00 4.30
4505 5216 4.542525 TGTGAACCCCAAATATTACTCCCT 59.457 41.667 0.00 0.00 0.00 4.20
4506 5217 5.131067 GTGAACCCCAAATATTACTCCCTC 58.869 45.833 0.00 0.00 0.00 4.30
4507 5218 4.167307 TGAACCCCAAATATTACTCCCTCC 59.833 45.833 0.00 0.00 0.00 4.30
4508 5219 2.709397 ACCCCAAATATTACTCCCTCCG 59.291 50.000 0.00 0.00 0.00 4.63
4509 5220 2.709397 CCCCAAATATTACTCCCTCCGT 59.291 50.000 0.00 0.00 0.00 4.69
4510 5221 3.137728 CCCCAAATATTACTCCCTCCGTT 59.862 47.826 0.00 0.00 0.00 4.44
4511 5222 4.386711 CCCAAATATTACTCCCTCCGTTC 58.613 47.826 0.00 0.00 0.00 3.95
4512 5223 4.386711 CCAAATATTACTCCCTCCGTTCC 58.613 47.826 0.00 0.00 0.00 3.62
4513 5224 4.141574 CCAAATATTACTCCCTCCGTTCCA 60.142 45.833 0.00 0.00 0.00 3.53
4514 5225 5.433526 CAAATATTACTCCCTCCGTTCCAA 58.566 41.667 0.00 0.00 0.00 3.53
4515 5226 5.703730 AATATTACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
4516 5227 5.703730 ATATTACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
4517 5228 2.845363 TACTCCCTCCGTTCCAAAAC 57.155 50.000 0.00 0.00 0.00 2.43
4518 5229 0.841289 ACTCCCTCCGTTCCAAAACA 59.159 50.000 0.00 0.00 34.93 2.83
4519 5230 1.423921 ACTCCCTCCGTTCCAAAACAT 59.576 47.619 0.00 0.00 34.93 2.71
4520 5231 2.640826 ACTCCCTCCGTTCCAAAACATA 59.359 45.455 0.00 0.00 34.93 2.29
4521 5232 3.270877 CTCCCTCCGTTCCAAAACATAG 58.729 50.000 0.00 0.00 34.93 2.23
4522 5233 2.640826 TCCCTCCGTTCCAAAACATAGT 59.359 45.455 0.00 0.00 34.93 2.12
4523 5234 2.747446 CCCTCCGTTCCAAAACATAGTG 59.253 50.000 0.00 0.00 34.93 2.74
4524 5235 2.161609 CCTCCGTTCCAAAACATAGTGC 59.838 50.000 0.00 0.00 34.93 4.40
4525 5236 2.811431 CTCCGTTCCAAAACATAGTGCA 59.189 45.455 0.00 0.00 34.93 4.57
4526 5237 3.417101 TCCGTTCCAAAACATAGTGCAT 58.583 40.909 0.00 0.00 34.93 3.96
4527 5238 4.580868 TCCGTTCCAAAACATAGTGCATA 58.419 39.130 0.00 0.00 34.93 3.14
4528 5239 5.189928 TCCGTTCCAAAACATAGTGCATAT 58.810 37.500 0.00 0.00 34.93 1.78
4529 5240 6.350103 TCCGTTCCAAAACATAGTGCATATA 58.650 36.000 0.00 0.00 34.93 0.86
4530 5241 6.481976 TCCGTTCCAAAACATAGTGCATATAG 59.518 38.462 0.00 0.00 34.93 1.31
4531 5242 6.481976 CCGTTCCAAAACATAGTGCATATAGA 59.518 38.462 0.00 0.00 34.93 1.98
4532 5243 7.173218 CCGTTCCAAAACATAGTGCATATAGAT 59.827 37.037 0.00 0.00 34.93 1.98
4533 5244 8.559536 CGTTCCAAAACATAGTGCATATAGATT 58.440 33.333 0.00 0.00 34.93 2.40
4571 5282 6.816134 AGTTTGCAAACTTTGACCAAATTT 57.184 29.167 33.85 11.83 46.52 1.82
4572 5283 7.913674 AGTTTGCAAACTTTGACCAAATTTA 57.086 28.000 33.85 0.00 46.52 1.40
4573 5284 8.504812 AGTTTGCAAACTTTGACCAAATTTAT 57.495 26.923 33.85 10.80 46.52 1.40
4574 5285 9.606631 AGTTTGCAAACTTTGACCAAATTTATA 57.393 25.926 33.85 0.00 46.52 0.98
4575 5286 9.862585 GTTTGCAAACTTTGACCAAATTTATAG 57.137 29.630 30.49 0.00 36.03 1.31
4576 5287 9.823647 TTTGCAAACTTTGACCAAATTTATAGA 57.176 25.926 8.05 0.00 0.00 1.98
4577 5288 9.474920 TTGCAAACTTTGACCAAATTTATAGAG 57.525 29.630 5.65 0.00 0.00 2.43
4578 5289 8.855110 TGCAAACTTTGACCAAATTTATAGAGA 58.145 29.630 5.65 0.00 0.00 3.10
4579 5290 9.691362 GCAAACTTTGACCAAATTTATAGAGAA 57.309 29.630 5.65 0.00 0.00 2.87
4675 5386 7.701539 TGTTTGGCATTCTAGATGTAAATGT 57.298 32.000 0.00 0.00 33.82 2.71
4676 5387 8.121305 TGTTTGGCATTCTAGATGTAAATGTT 57.879 30.769 0.00 0.00 33.82 2.71
4677 5388 8.584157 TGTTTGGCATTCTAGATGTAAATGTTT 58.416 29.630 0.00 0.00 33.82 2.83
4678 5389 9.423061 GTTTGGCATTCTAGATGTAAATGTTTT 57.577 29.630 0.00 0.00 33.82 2.43
4679 5390 9.995003 TTTGGCATTCTAGATGTAAATGTTTTT 57.005 25.926 0.00 0.00 33.82 1.94
4680 5391 9.638239 TTGGCATTCTAGATGTAAATGTTTTTC 57.362 29.630 0.00 0.00 33.82 2.29
4681 5392 9.023962 TGGCATTCTAGATGTAAATGTTTTTCT 57.976 29.630 0.00 0.00 33.82 2.52
4682 5393 9.860898 GGCATTCTAGATGTAAATGTTTTTCTT 57.139 29.630 0.00 0.00 33.82 2.52
4709 5420 2.654863 CTTGGTCAAAGTTGGTGAGGT 58.345 47.619 0.00 0.00 0.00 3.85
4710 5421 2.818751 TGGTCAAAGTTGGTGAGGTT 57.181 45.000 0.00 0.00 0.00 3.50
4711 5422 3.094484 TGGTCAAAGTTGGTGAGGTTT 57.906 42.857 0.00 0.00 0.00 3.27
4712 5423 2.757868 TGGTCAAAGTTGGTGAGGTTTG 59.242 45.455 0.00 0.00 0.00 2.93
4713 5424 3.020984 GGTCAAAGTTGGTGAGGTTTGA 58.979 45.455 0.00 0.00 36.74 2.69
4714 5425 4.028852 GTCAAAGTTGGTGAGGTTTGAC 57.971 45.455 10.15 10.15 46.75 3.18
4715 5426 3.963129 TCAAAGTTGGTGAGGTTTGACT 58.037 40.909 0.00 0.00 34.72 3.41
4716 5427 3.945285 TCAAAGTTGGTGAGGTTTGACTC 59.055 43.478 0.00 0.00 34.72 3.36
4717 5428 3.933861 AAGTTGGTGAGGTTTGACTCT 57.066 42.857 0.00 0.00 38.32 3.24
4718 5429 3.933861 AGTTGGTGAGGTTTGACTCTT 57.066 42.857 0.00 0.00 38.32 2.85
4719 5430 5.367945 AAGTTGGTGAGGTTTGACTCTTA 57.632 39.130 0.00 0.00 38.32 2.10
4720 5431 5.367945 AGTTGGTGAGGTTTGACTCTTAA 57.632 39.130 0.00 0.00 38.32 1.85
4721 5432 5.751586 AGTTGGTGAGGTTTGACTCTTAAA 58.248 37.500 0.00 0.00 38.32 1.52
4722 5433 6.184789 AGTTGGTGAGGTTTGACTCTTAAAA 58.815 36.000 0.00 0.00 38.32 1.52
4723 5434 6.661805 AGTTGGTGAGGTTTGACTCTTAAAAA 59.338 34.615 0.00 0.00 38.32 1.94
4748 5459 9.672673 AAATCTATATGCACTACATTATGGGAC 57.327 33.333 0.00 0.00 40.38 4.46
4749 5460 6.863275 TCTATATGCACTACATTATGGGACG 58.137 40.000 0.00 0.00 40.38 4.79
4750 5461 2.613026 TGCACTACATTATGGGACGG 57.387 50.000 0.00 0.00 0.00 4.79
4751 5462 2.112190 TGCACTACATTATGGGACGGA 58.888 47.619 0.00 0.00 0.00 4.69
4752 5463 2.102420 TGCACTACATTATGGGACGGAG 59.898 50.000 0.00 0.00 0.00 4.63
4753 5464 2.548067 GCACTACATTATGGGACGGAGG 60.548 54.545 0.00 0.00 0.00 4.30
4754 5465 2.037251 CACTACATTATGGGACGGAGGG 59.963 54.545 0.00 0.00 0.00 4.30
4755 5466 2.090943 ACTACATTATGGGACGGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
4756 5467 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
4757 5468 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
4758 5469 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.314400 TCCGTTATTAACAAAGCTCATGGTAC 59.686 38.462 7.31 0.00 0.00 3.34
12 13 6.408035 TCCGTTATTAACAAAGCTCATGGTA 58.592 36.000 7.31 0.00 0.00 3.25
13 14 5.250200 TCCGTTATTAACAAAGCTCATGGT 58.750 37.500 7.31 0.25 0.00 3.55
14 15 5.811399 TCCGTTATTAACAAAGCTCATGG 57.189 39.130 7.31 0.00 0.00 3.66
15 16 7.471721 TGATTCCGTTATTAACAAAGCTCATG 58.528 34.615 7.31 0.00 0.00 3.07
16 17 7.624360 TGATTCCGTTATTAACAAAGCTCAT 57.376 32.000 7.31 0.00 0.00 2.90
17 18 7.624360 ATGATTCCGTTATTAACAAAGCTCA 57.376 32.000 7.31 3.68 0.00 4.26
18 19 9.599322 CATATGATTCCGTTATTAACAAAGCTC 57.401 33.333 0.00 0.00 0.00 4.09
19 20 8.567948 CCATATGATTCCGTTATTAACAAAGCT 58.432 33.333 3.65 0.00 0.00 3.74
20 21 8.349983 ACCATATGATTCCGTTATTAACAAAGC 58.650 33.333 3.65 4.25 0.00 3.51
21 22 9.663904 CACCATATGATTCCGTTATTAACAAAG 57.336 33.333 3.65 0.00 0.00 2.77
22 23 9.179909 ACACCATATGATTCCGTTATTAACAAA 57.820 29.630 3.65 1.49 0.00 2.83
23 24 8.740123 ACACCATATGATTCCGTTATTAACAA 57.260 30.769 3.65 0.00 0.00 2.83
24 25 8.740123 AACACCATATGATTCCGTTATTAACA 57.260 30.769 3.65 0.00 0.00 2.41
25 26 9.052759 AGAACACCATATGATTCCGTTATTAAC 57.947 33.333 3.65 0.00 0.00 2.01
26 27 9.621629 AAGAACACCATATGATTCCGTTATTAA 57.378 29.630 3.65 0.00 0.00 1.40
27 28 9.268268 GAAGAACACCATATGATTCCGTTATTA 57.732 33.333 3.65 0.00 0.00 0.98
28 29 7.993183 AGAAGAACACCATATGATTCCGTTATT 59.007 33.333 3.65 3.72 0.00 1.40
29 30 7.509546 AGAAGAACACCATATGATTCCGTTAT 58.490 34.615 3.65 0.00 0.00 1.89
30 31 6.884832 AGAAGAACACCATATGATTCCGTTA 58.115 36.000 3.65 0.00 0.00 3.18
31 32 5.745227 AGAAGAACACCATATGATTCCGTT 58.255 37.500 3.65 0.00 0.00 4.44
32 33 5.129485 AGAGAAGAACACCATATGATTCCGT 59.871 40.000 3.65 0.00 0.00 4.69
33 34 5.605534 AGAGAAGAACACCATATGATTCCG 58.394 41.667 3.65 0.00 0.00 4.30
34 35 6.825610 AGAGAGAAGAACACCATATGATTCC 58.174 40.000 3.65 0.00 0.00 3.01
35 36 9.638239 GATAGAGAGAAGAACACCATATGATTC 57.362 37.037 3.65 5.36 0.00 2.52
80 83 3.660865 TCCGAACCTAAAAGAGCAAGAC 58.339 45.455 0.00 0.00 0.00 3.01
111 114 1.804151 CGAAGCGGAATTGTCCTTTGA 59.196 47.619 0.00 0.00 42.44 2.69
132 135 4.912187 GCTTGTCCTTTGAAGTTTCGATTC 59.088 41.667 0.00 0.00 0.00 2.52
137 140 4.336713 ACTCTGCTTGTCCTTTGAAGTTTC 59.663 41.667 0.00 0.00 0.00 2.78
194 198 3.067180 GCCATCAATTAGTGGATGTGGTG 59.933 47.826 11.42 0.00 39.36 4.17
195 199 3.290710 GCCATCAATTAGTGGATGTGGT 58.709 45.455 11.42 0.00 39.36 4.16
245 862 1.081242 CAGCCGTTTGTGATGCCAC 60.081 57.895 0.00 0.00 43.46 5.01
267 884 2.664398 CCACCCCCATGCAAAAGC 59.336 61.111 0.00 0.00 0.00 3.51
270 887 2.921972 GTGCCACCCCCATGCAAA 60.922 61.111 0.00 0.00 36.65 3.68
295 912 0.320050 TGTGCTACTTCATGCCACGA 59.680 50.000 0.00 0.00 0.00 4.35
302 919 2.890945 GGGGTTTGTTGTGCTACTTCAT 59.109 45.455 0.00 0.00 0.00 2.57
312 929 4.014569 GCCATAAATTGGGGTTTGTTGT 57.985 40.909 0.00 0.00 46.55 3.32
344 969 1.536766 CTTGGCTGCAATTCAACGAGA 59.463 47.619 0.50 0.00 0.00 4.04
370 995 3.462483 TCTTCGAGGCAAACAGTGTTA 57.538 42.857 9.37 0.00 0.00 2.41
396 1021 1.078759 CCCAGATCTCGACGCAACAC 61.079 60.000 0.00 0.00 0.00 3.32
443 1068 6.968248 AGCAGATAATCCCCTCCATCTTAATA 59.032 38.462 0.00 0.00 0.00 0.98
445 1070 5.165652 AGCAGATAATCCCCTCCATCTTAA 58.834 41.667 0.00 0.00 0.00 1.85
446 1071 4.767908 AGCAGATAATCCCCTCCATCTTA 58.232 43.478 0.00 0.00 0.00 2.10
447 1072 3.606972 AGCAGATAATCCCCTCCATCTT 58.393 45.455 0.00 0.00 0.00 2.40
448 1073 3.288454 AGCAGATAATCCCCTCCATCT 57.712 47.619 0.00 0.00 0.00 2.90
449 1074 5.707066 ATTAGCAGATAATCCCCTCCATC 57.293 43.478 0.00 0.00 27.00 3.51
450 1075 6.737608 ACTAATTAGCAGATAATCCCCTCCAT 59.262 38.462 12.54 0.00 32.71 3.41
451 1076 6.091555 ACTAATTAGCAGATAATCCCCTCCA 58.908 40.000 12.54 0.00 32.71 3.86
452 1077 6.628644 ACTAATTAGCAGATAATCCCCTCC 57.371 41.667 12.54 0.00 32.71 4.30
592 1218 3.428316 GGAAGCAAGAGAAGTCCGTAGAG 60.428 52.174 0.00 0.00 0.00 2.43
598 1224 2.739379 CGAAAGGAAGCAAGAGAAGTCC 59.261 50.000 0.00 0.00 0.00 3.85
599 1225 3.394719 ACGAAAGGAAGCAAGAGAAGTC 58.605 45.455 0.00 0.00 0.00 3.01
603 1229 3.181465 ACTCAACGAAAGGAAGCAAGAGA 60.181 43.478 0.00 0.00 0.00 3.10
604 1230 3.059325 CACTCAACGAAAGGAAGCAAGAG 60.059 47.826 0.00 0.00 0.00 2.85
614 1240 0.592637 TGCATGGCACTCAACGAAAG 59.407 50.000 0.00 0.00 31.71 2.62
618 1244 0.098200 CTGATGCATGGCACTCAACG 59.902 55.000 2.46 0.00 43.04 4.10
620 1246 1.913778 AACTGATGCATGGCACTCAA 58.086 45.000 2.46 0.00 43.04 3.02
646 1272 1.423395 CGAGAAGAGTGGAGTGTTGC 58.577 55.000 0.00 0.00 0.00 4.17
674 1300 6.984474 CCAAAGTGTATTCATCTATACCACGT 59.016 38.462 0.00 0.00 31.38 4.49
675 1301 6.984474 ACCAAAGTGTATTCATCTATACCACG 59.016 38.462 0.00 0.00 31.38 4.94
677 1303 8.084985 TCACCAAAGTGTATTCATCTATACCA 57.915 34.615 0.00 0.00 44.83 3.25
691 1317 6.663523 CCCTCCTATAAATTTCACCAAAGTGT 59.336 38.462 0.00 0.00 44.83 3.55
694 1320 6.194967 ACCCCTCCTATAAATTTCACCAAAG 58.805 40.000 0.00 0.00 0.00 2.77
707 1333 4.913154 AGACCAAGTTACCCCTCCTATA 57.087 45.455 0.00 0.00 0.00 1.31
712 1338 4.094830 TGAAAAGACCAAGTTACCCCTC 57.905 45.455 0.00 0.00 0.00 4.30
727 1353 7.120285 TCTCCAGAATTTAGCTGACATGAAAAG 59.880 37.037 0.00 0.00 35.39 2.27
767 1393 4.504689 CCATTTGCCTTTTGCCCTTTTCTA 60.505 41.667 0.00 0.00 40.16 2.10
768 1394 3.479489 CATTTGCCTTTTGCCCTTTTCT 58.521 40.909 0.00 0.00 40.16 2.52
769 1395 2.553602 CCATTTGCCTTTTGCCCTTTTC 59.446 45.455 0.00 0.00 40.16 2.29
773 1399 0.686789 GACCATTTGCCTTTTGCCCT 59.313 50.000 0.00 0.00 40.16 5.19
802 1428 8.885494 TGCATGATATTTTGCCCTAATTTTAC 57.115 30.769 0.00 0.00 38.08 2.01
826 1452 9.921637 TTTTTAGCCCTTCTTTTACATTGTATG 57.078 29.630 0.00 0.00 0.00 2.39
856 1482 6.864360 TTTCCAAGCCTTTTGATCATTTTG 57.136 33.333 0.00 0.00 0.00 2.44
898 1527 4.794169 CCGTTGGATTTTCGTTCAGAAAT 58.206 39.130 0.00 0.00 46.98 2.17
900 1529 2.031508 GCCGTTGGATTTTCGTTCAGAA 60.032 45.455 0.00 0.00 37.01 3.02
935 1564 1.034356 TACTGTATATGCGTGGCGGT 58.966 50.000 0.00 0.00 0.00 5.68
950 1579 8.715088 AGTAAACAAAACTAAACGGCTATACTG 58.285 33.333 0.00 0.00 0.00 2.74
952 1581 8.171196 GGAGTAAACAAAACTAAACGGCTATAC 58.829 37.037 0.00 0.00 0.00 1.47
953 1582 7.334171 GGGAGTAAACAAAACTAAACGGCTATA 59.666 37.037 0.00 0.00 0.00 1.31
954 1583 6.149973 GGGAGTAAACAAAACTAAACGGCTAT 59.850 38.462 0.00 0.00 0.00 2.97
955 1584 5.469760 GGGAGTAAACAAAACTAAACGGCTA 59.530 40.000 0.00 0.00 0.00 3.93
956 1585 4.276678 GGGAGTAAACAAAACTAAACGGCT 59.723 41.667 0.00 0.00 0.00 5.52
957 1586 4.036616 TGGGAGTAAACAAAACTAAACGGC 59.963 41.667 0.00 0.00 0.00 5.68
1000 1629 3.400599 GATGGGGAACGGCCGACAT 62.401 63.158 35.90 24.82 37.55 3.06
1041 1670 1.750399 CAAATGGGGCTCGTCCAGG 60.750 63.158 0.00 0.00 37.75 4.45
1042 1671 1.026718 GTCAAATGGGGCTCGTCCAG 61.027 60.000 0.00 0.00 37.75 3.86
1043 1672 1.002624 GTCAAATGGGGCTCGTCCA 60.003 57.895 0.00 0.00 38.82 4.02
1044 1673 0.539986 TAGTCAAATGGGGCTCGTCC 59.460 55.000 0.00 0.00 0.00 4.79
1045 1674 1.207329 AGTAGTCAAATGGGGCTCGTC 59.793 52.381 0.00 0.00 0.00 4.20
1046 1675 1.276622 AGTAGTCAAATGGGGCTCGT 58.723 50.000 0.00 0.00 0.00 4.18
1047 1676 2.483188 GGTAGTAGTCAAATGGGGCTCG 60.483 54.545 0.00 0.00 0.00 5.03
1048 1677 2.483188 CGGTAGTAGTCAAATGGGGCTC 60.483 54.545 0.00 0.00 0.00 4.70
1049 1678 1.485066 CGGTAGTAGTCAAATGGGGCT 59.515 52.381 0.00 0.00 0.00 5.19
1050 1679 1.474498 CCGGTAGTAGTCAAATGGGGC 60.474 57.143 0.00 0.00 0.00 5.80
1403 2032 3.262420 GGACTAGCACAACCATGTAGTG 58.738 50.000 5.37 5.37 37.82 2.74
1430 2063 2.482333 CGGAGCGGAGGGAGTACAG 61.482 68.421 0.00 0.00 0.00 2.74
1444 2077 5.155509 TGCGTCAATTAATTCATTCGGAG 57.844 39.130 0.00 0.00 0.00 4.63
1448 2081 4.925068 AGGCTGCGTCAATTAATTCATTC 58.075 39.130 0.00 0.00 0.00 2.67
1449 2082 4.641989 AGAGGCTGCGTCAATTAATTCATT 59.358 37.500 22.55 0.00 0.00 2.57
1450 2083 4.036027 CAGAGGCTGCGTCAATTAATTCAT 59.964 41.667 22.55 0.00 0.00 2.57
1451 2084 3.374988 CAGAGGCTGCGTCAATTAATTCA 59.625 43.478 22.55 0.00 0.00 2.57
1454 2087 2.991250 ACAGAGGCTGCGTCAATTAAT 58.009 42.857 22.55 0.00 34.37 1.40
1466 2099 3.769739 TTGACACATTGTACAGAGGCT 57.230 42.857 0.00 0.00 0.00 4.58
1468 2101 7.433708 TTGTAATTGACACATTGTACAGAGG 57.566 36.000 0.00 0.00 37.96 3.69
1470 2103 8.227119 CGAATTGTAATTGACACATTGTACAGA 58.773 33.333 0.00 0.00 37.96 3.41
1471 2104 7.481483 CCGAATTGTAATTGACACATTGTACAG 59.519 37.037 0.00 0.00 37.96 2.74
1473 2106 7.523219 TCCGAATTGTAATTGACACATTGTAC 58.477 34.615 0.00 0.00 37.96 2.90
1474 2107 7.674471 TCCGAATTGTAATTGACACATTGTA 57.326 32.000 0.00 0.00 37.96 2.41
1475 2108 6.567687 TCCGAATTGTAATTGACACATTGT 57.432 33.333 0.00 0.00 37.96 2.71
1476 2109 6.411782 CGATCCGAATTGTAATTGACACATTG 59.588 38.462 0.00 0.00 37.96 2.82
1477 2110 6.458206 CCGATCCGAATTGTAATTGACACATT 60.458 38.462 0.00 0.00 37.96 2.71
1478 2111 5.007626 CCGATCCGAATTGTAATTGACACAT 59.992 40.000 0.00 0.00 37.96 3.21
1479 2112 4.331443 CCGATCCGAATTGTAATTGACACA 59.669 41.667 0.00 0.00 37.96 3.72
1480 2113 4.569162 TCCGATCCGAATTGTAATTGACAC 59.431 41.667 0.00 0.00 37.96 3.67
1481 2114 4.760878 TCCGATCCGAATTGTAATTGACA 58.239 39.130 0.00 0.00 35.78 3.58
1482 2115 4.211374 CCTCCGATCCGAATTGTAATTGAC 59.789 45.833 0.00 0.00 0.00 3.18
1483 2116 4.100344 TCCTCCGATCCGAATTGTAATTGA 59.900 41.667 0.00 0.00 0.00 2.57
1484 2117 4.377021 TCCTCCGATCCGAATTGTAATTG 58.623 43.478 0.00 0.00 0.00 2.32
1485 2118 4.682778 TCCTCCGATCCGAATTGTAATT 57.317 40.909 0.00 0.00 0.00 1.40
1486 2119 4.101119 ACTTCCTCCGATCCGAATTGTAAT 59.899 41.667 0.00 0.00 0.00 1.89
1487 2120 3.449737 ACTTCCTCCGATCCGAATTGTAA 59.550 43.478 0.00 0.00 0.00 2.41
1488 2121 3.028850 ACTTCCTCCGATCCGAATTGTA 58.971 45.455 0.00 0.00 0.00 2.41
1489 2122 1.831736 ACTTCCTCCGATCCGAATTGT 59.168 47.619 0.00 0.00 0.00 2.71
1490 2123 2.604046 ACTTCCTCCGATCCGAATTG 57.396 50.000 0.00 0.00 0.00 2.32
1500 2133 6.737254 TTAAAGAAAATGCTACTTCCTCCG 57.263 37.500 0.00 0.00 0.00 4.63
1546 2183 8.783660 TGATGATACTAGGAACTTATCAGGTT 57.216 34.615 0.00 0.00 40.24 3.50
1610 2280 5.068460 GGGTTTTACAGCATATGCATTGGTA 59.932 40.000 28.62 20.07 45.16 3.25
1634 2304 5.677319 TCAGGTTTCTATGTTGACTAGGG 57.323 43.478 0.00 0.00 0.00 3.53
1675 2345 8.485578 AAATTTTGTTCCATGAAACTACCCTA 57.514 30.769 0.00 0.00 0.00 3.53
1698 2369 5.013704 TCTCCTTCCAATAGGCACACTAAAA 59.986 40.000 0.00 0.00 34.79 1.52
1763 2434 5.288712 CCATGCTAGTACAAGTAAACAGTCG 59.711 44.000 0.00 0.00 0.00 4.18
1804 2479 8.716909 CAAACATTAAACCCCATGTTATTTCAC 58.283 33.333 0.00 0.00 41.74 3.18
1832 2507 1.526575 CGGACAAGCAGCCATGGTTT 61.527 55.000 14.67 0.00 44.57 3.27
1837 2512 0.035152 TCAATCGGACAAGCAGCCAT 60.035 50.000 0.00 0.00 0.00 4.40
1858 2533 2.480037 TGCACTAAATCGACAAGCTGTG 59.520 45.455 0.00 0.00 0.00 3.66
1897 2572 7.896782 GGAAATTAGTAACAACGTCGAATCTTC 59.103 37.037 0.00 0.00 0.00 2.87
1968 2643 0.519077 GAGGAAAGAAAGGCAGCACG 59.481 55.000 0.00 0.00 0.00 5.34
1994 2670 3.617045 GCATAAGTTGGCATTGGAAAGCA 60.617 43.478 0.00 0.00 0.00 3.91
1995 2671 2.931969 GCATAAGTTGGCATTGGAAAGC 59.068 45.455 0.00 0.00 0.00 3.51
2024 2701 5.391433 CGAATGAAAACGCGGTGAATATAAC 59.609 40.000 12.47 0.00 0.00 1.89
2028 2705 2.737783 ACGAATGAAAACGCGGTGAATA 59.262 40.909 12.47 0.00 0.00 1.75
2070 2747 9.555727 AGTATTGTTTACTAAAGAGAACAAGCA 57.444 29.630 15.33 7.90 42.93 3.91
2071 2748 9.813080 CAGTATTGTTTACTAAAGAGAACAAGC 57.187 33.333 15.33 12.17 42.93 4.01
2091 2768 6.106673 GCAGGTGAGTACAATGTACAGTATT 58.893 40.000 23.52 4.25 0.00 1.89
2093 2770 4.525100 TGCAGGTGAGTACAATGTACAGTA 59.475 41.667 23.52 8.06 0.00 2.74
2094 2771 3.323691 TGCAGGTGAGTACAATGTACAGT 59.676 43.478 23.52 5.70 0.00 3.55
2095 2772 3.925379 TGCAGGTGAGTACAATGTACAG 58.075 45.455 23.52 8.49 0.00 2.74
2096 2773 4.551702 ATGCAGGTGAGTACAATGTACA 57.448 40.909 23.52 0.00 0.00 2.90
2097 2774 4.809426 GGTATGCAGGTGAGTACAATGTAC 59.191 45.833 15.22 15.22 0.00 2.90
2133 2810 9.775854 ACCATTTAACAAAATGATCATGAAACA 57.224 25.926 9.46 3.81 41.44 2.83
2329 3016 4.627611 ACAGATCTGCATTTCAAATCCG 57.372 40.909 22.83 0.00 0.00 4.18
2335 3022 4.824479 TGAGGTACAGATCTGCATTTCA 57.176 40.909 22.83 17.25 0.00 2.69
2590 3277 0.621571 AGCCCCAGAGCTTCCATGTA 60.622 55.000 0.00 0.00 41.41 2.29
2598 3285 0.547712 TTTCCTACAGCCCCAGAGCT 60.548 55.000 0.00 0.00 46.45 4.09
2621 3308 4.038282 TGATTTTGCAGATCAACAGCACTT 59.962 37.500 11.18 0.00 40.53 3.16
2624 3311 4.794278 ATGATTTTGCAGATCAACAGCA 57.206 36.364 15.91 0.00 35.56 4.41
2670 3357 6.535508 ACAAGTTGACTTTCTACAGAGTTCAC 59.464 38.462 10.54 0.00 33.11 3.18
3007 3694 9.383519 CTGCACTAACAAGGAAATCTATAAGAA 57.616 33.333 0.00 0.00 0.00 2.52
3210 3897 6.926630 AGATTTAGATCCCTGTATGAGGTC 57.073 41.667 0.00 0.00 40.87 3.85
3375 4062 9.507329 GAAAGTTATAGGCATATTTGATCCAGA 57.493 33.333 0.00 0.00 0.00 3.86
3413 4100 2.143876 AGCCGCAAATAACTCCCAAT 57.856 45.000 0.00 0.00 0.00 3.16
3550 4237 6.757897 TTGATATGGAACCATGAAGAACAC 57.242 37.500 15.59 0.92 37.82 3.32
3564 4251 6.888105 TCTTGCTGTGAGTTATTGATATGGA 58.112 36.000 0.00 0.00 0.00 3.41
3687 4374 0.487325 TGGTCCCTCCAGTCAGAGAA 59.513 55.000 0.00 0.00 41.93 2.87
3769 4456 7.256296 CCAGAAGTCCAAAAGGTTTATTTCCAT 60.256 37.037 0.00 0.00 0.00 3.41
3771 4458 6.266786 TCCAGAAGTCCAAAAGGTTTATTTCC 59.733 38.462 0.00 0.00 0.00 3.13
3772 4459 7.284919 TCCAGAAGTCCAAAAGGTTTATTTC 57.715 36.000 0.00 0.00 0.00 2.17
3817 4504 2.206576 AACTTCTGAGGCAACCATCC 57.793 50.000 0.00 0.00 37.17 3.51
3822 4509 5.473504 TCCAAAGATAAACTTCTGAGGCAAC 59.526 40.000 0.00 0.00 37.93 4.17
3924 4619 3.741476 GAAGCTTGCACCGCCTGG 61.741 66.667 2.10 0.00 42.84 4.45
3945 4640 4.095782 GCAAGGTCACAAGTTCACTACAAA 59.904 41.667 0.00 0.00 0.00 2.83
3972 4667 3.882102 AGCATTAATACCTGGCATCCA 57.118 42.857 0.00 0.00 0.00 3.41
3973 4668 4.144297 TGAAGCATTAATACCTGGCATCC 58.856 43.478 0.00 0.00 0.00 3.51
3978 4673 5.343249 GCAAACTGAAGCATTAATACCTGG 58.657 41.667 0.00 0.00 0.00 4.45
3986 4681 8.615878 AATATATACGGCAAACTGAAGCATTA 57.384 30.769 0.00 0.00 0.00 1.90
4059 4754 3.118186 ACAACACAGGTGGCAGTTAACTA 60.118 43.478 8.04 0.00 34.19 2.24
4060 4755 2.297701 CAACACAGGTGGCAGTTAACT 58.702 47.619 1.12 1.12 34.19 2.24
4152 4847 6.014925 TGGTCTGCACTCTTAACACTGTATTA 60.015 38.462 0.00 0.00 0.00 0.98
4221 4927 4.685924 CACAACTGAGGCAAGAAAAACAT 58.314 39.130 0.00 0.00 0.00 2.71
4222 4928 3.675775 GCACAACTGAGGCAAGAAAAACA 60.676 43.478 0.00 0.00 0.00 2.83
4289 4998 0.248289 TAGGCCTAAGCGGTCAACAC 59.752 55.000 10.98 0.00 40.99 3.32
4303 5012 3.118811 TGGCAGCATAAACATTTTAGGCC 60.119 43.478 10.73 0.00 38.16 5.19
4305 5014 6.108015 ACAATGGCAGCATAAACATTTTAGG 58.892 36.000 0.00 0.00 31.67 2.69
4357 5066 7.083858 TGAGCTTTGCATGTAAAATAGTTGAC 58.916 34.615 10.29 0.00 0.00 3.18
4370 5079 4.090930 GTGCATACTTTTGAGCTTTGCATG 59.909 41.667 0.00 0.00 40.32 4.06
4417 5126 9.826574 ATGCAAATGAGAAAATAAATGCACTAT 57.173 25.926 0.00 0.00 44.27 2.12
4428 5137 9.113838 AGACGAACTATATGCAAATGAGAAAAT 57.886 29.630 0.00 0.00 0.00 1.82
4431 5141 8.492673 AAAGACGAACTATATGCAAATGAGAA 57.507 30.769 0.00 0.00 0.00 2.87
4478 5189 7.417456 GGGAGTAATATTTGGGGTTCACAATTC 60.417 40.741 0.00 0.00 0.00 2.17
4485 5196 4.726583 GGAGGGAGTAATATTTGGGGTTC 58.273 47.826 0.00 0.00 0.00 3.62
4500 5211 2.200373 ATGTTTTGGAACGGAGGGAG 57.800 50.000 0.00 0.00 38.65 4.30
4501 5212 2.640826 ACTATGTTTTGGAACGGAGGGA 59.359 45.455 0.00 0.00 38.65 4.20
4502 5213 2.747446 CACTATGTTTTGGAACGGAGGG 59.253 50.000 0.00 0.00 38.65 4.30
4503 5214 2.161609 GCACTATGTTTTGGAACGGAGG 59.838 50.000 0.00 0.00 38.65 4.30
4504 5215 2.811431 TGCACTATGTTTTGGAACGGAG 59.189 45.455 0.00 0.00 38.65 4.63
4505 5216 2.852449 TGCACTATGTTTTGGAACGGA 58.148 42.857 0.00 0.00 38.65 4.69
4506 5217 3.848272 ATGCACTATGTTTTGGAACGG 57.152 42.857 0.00 0.00 38.65 4.44
4507 5218 7.477144 TCTATATGCACTATGTTTTGGAACG 57.523 36.000 0.00 0.00 38.65 3.95
4535 5246 7.489574 AGTTTGCAAACTTTGACTTTTCAAA 57.510 28.000 33.85 2.88 46.52 2.69
4549 5260 9.862585 CTATAAATTTGGTCAAAGTTTGCAAAC 57.137 29.630 30.63 30.63 39.07 2.93
4550 5261 9.823647 TCTATAAATTTGGTCAAAGTTTGCAAA 57.176 25.926 17.93 17.93 39.07 3.68
4551 5262 9.474920 CTCTATAAATTTGGTCAAAGTTTGCAA 57.525 29.630 10.90 7.54 39.07 4.08
4552 5263 8.855110 TCTCTATAAATTTGGTCAAAGTTTGCA 58.145 29.630 10.90 1.36 39.07 4.08
4553 5264 9.691362 TTCTCTATAAATTTGGTCAAAGTTTGC 57.309 29.630 10.90 6.16 39.07 3.68
4649 5360 9.407380 ACATTTACATCTAGAATGCCAAACATA 57.593 29.630 0.00 0.00 38.34 2.29
4650 5361 8.297470 ACATTTACATCTAGAATGCCAAACAT 57.703 30.769 0.00 0.00 42.30 2.71
4651 5362 7.701539 ACATTTACATCTAGAATGCCAAACA 57.298 32.000 0.00 0.00 34.86 2.83
4652 5363 8.986477 AAACATTTACATCTAGAATGCCAAAC 57.014 30.769 0.00 0.00 34.86 2.93
4653 5364 9.995003 AAAAACATTTACATCTAGAATGCCAAA 57.005 25.926 0.00 1.74 34.86 3.28
4654 5365 9.638239 GAAAAACATTTACATCTAGAATGCCAA 57.362 29.630 0.00 0.00 34.86 4.52
4655 5366 9.023962 AGAAAAACATTTACATCTAGAATGCCA 57.976 29.630 0.00 0.00 34.86 4.92
4656 5367 9.860898 AAGAAAAACATTTACATCTAGAATGCC 57.139 29.630 0.00 0.00 34.86 4.40
4675 5386 8.669946 ACTTTGACCAAGTTTTTGAAGAAAAA 57.330 26.923 0.00 0.00 43.89 1.94
4689 5400 2.654863 ACCTCACCAACTTTGACCAAG 58.345 47.619 0.00 0.00 38.64 3.61
4690 5401 2.818751 ACCTCACCAACTTTGACCAA 57.181 45.000 0.00 0.00 0.00 3.67
4691 5402 2.757868 CAAACCTCACCAACTTTGACCA 59.242 45.455 0.00 0.00 0.00 4.02
4692 5403 3.020984 TCAAACCTCACCAACTTTGACC 58.979 45.455 0.00 0.00 29.66 4.02
4693 5404 3.694566 AGTCAAACCTCACCAACTTTGAC 59.305 43.478 12.19 12.19 46.84 3.18
4694 5405 3.945285 GAGTCAAACCTCACCAACTTTGA 59.055 43.478 0.00 0.00 31.68 2.69
4695 5406 3.947834 AGAGTCAAACCTCACCAACTTTG 59.052 43.478 0.00 0.00 33.75 2.77
4696 5407 4.236527 AGAGTCAAACCTCACCAACTTT 57.763 40.909 0.00 0.00 33.75 2.66
4697 5408 3.933861 AGAGTCAAACCTCACCAACTT 57.066 42.857 0.00 0.00 33.75 2.66
4698 5409 3.933861 AAGAGTCAAACCTCACCAACT 57.066 42.857 0.00 0.00 33.75 3.16
4699 5410 6.445357 TTTTAAGAGTCAAACCTCACCAAC 57.555 37.500 0.00 0.00 33.75 3.77
4722 5433 9.672673 GTCCCATAATGTAGTGCATATAGATTT 57.327 33.333 8.82 0.00 36.67 2.17
4723 5434 7.981789 CGTCCCATAATGTAGTGCATATAGATT 59.018 37.037 0.00 8.63 36.67 2.40
4724 5435 7.417911 CCGTCCCATAATGTAGTGCATATAGAT 60.418 40.741 0.00 0.00 36.67 1.98
4725 5436 6.127451 CCGTCCCATAATGTAGTGCATATAGA 60.127 42.308 0.00 0.00 36.67 1.98
4726 5437 6.042777 CCGTCCCATAATGTAGTGCATATAG 58.957 44.000 0.00 0.00 36.67 1.31
4727 5438 5.717654 TCCGTCCCATAATGTAGTGCATATA 59.282 40.000 0.00 0.00 36.67 0.86
4728 5439 4.530553 TCCGTCCCATAATGTAGTGCATAT 59.469 41.667 0.00 0.00 36.67 1.78
4729 5440 3.898741 TCCGTCCCATAATGTAGTGCATA 59.101 43.478 0.00 0.00 36.67 3.14
4730 5441 2.703536 TCCGTCCCATAATGTAGTGCAT 59.296 45.455 0.00 0.00 40.03 3.96
4731 5442 2.102420 CTCCGTCCCATAATGTAGTGCA 59.898 50.000 0.00 0.00 0.00 4.57
4732 5443 2.548067 CCTCCGTCCCATAATGTAGTGC 60.548 54.545 0.00 0.00 0.00 4.40
4733 5444 2.037251 CCCTCCGTCCCATAATGTAGTG 59.963 54.545 0.00 0.00 0.00 2.74
4734 5445 2.090943 TCCCTCCGTCCCATAATGTAGT 60.091 50.000 0.00 0.00 0.00 2.73
4735 5446 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
4736 5447 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
4737 5448 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
4738 5449 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
4739 5450 3.970426 ACTCCCTCCGTCCCATAAT 57.030 52.632 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.