Multiple sequence alignment - TraesCS5D01G396800

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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 TraesCS5D01G396800 chr5D 100.000 5034 0 0 1 5034 464077774 464072741 0.000000e+00 9297
1 TraesCS5D01G396800 chr5D 82.818 1100 179 10 2952 4047 544701284 544702377 0.000000e+00 976
2 TraesCS5D01G396800 chr5B 93.667 2921 134 29 1413 4314 570933752 570930864 0.000000e+00 4322
3 TraesCS5D01G396800 chr5B 84.810 1422 152 31 4 1383 571123225 571121826 0.000000e+00 1371
4 TraesCS5D01G396800 chr5B 88.745 924 50 14 499 1383 570934657 570933749 0.000000e+00 1081
5 TraesCS5D01G396800 chr5B 90.792 467 37 3 4 464 570935220 570934754 1.990000e-173 619
6 TraesCS5D01G396800 chr5B 92.265 362 20 3 4681 5034 570930792 570930431 1.620000e-139 507
7 TraesCS5D01G396800 chr5A 91.975 1757 78 21 2689 4425 584458229 584456516 0.000000e+00 2405
8 TraesCS5D01G396800 chr5A 91.220 877 56 8 1415 2290 584491055 584490199 0.000000e+00 1173
9 TraesCS5D01G396800 chr5A 91.760 716 37 14 676 1383 584491755 584491054 0.000000e+00 976
10 TraesCS5D01G396800 chr5A 89.258 633 43 9 4422 5034 584456411 584455784 0.000000e+00 769
11 TraesCS5D01G396800 chr5A 90.598 468 37 6 2 464 584507520 584507055 9.260000e-172 614
12 TraesCS5D01G396800 chr5A 88.060 402 29 11 2293 2690 584490156 584489770 4.590000e-125 459
13 TraesCS5D01G396800 chr2B 87.256 1381 151 17 2676 4048 752833541 752834904 0.000000e+00 1552
14 TraesCS5D01G396800 chr2B 83.636 770 91 20 614 1383 752831013 752831747 0.000000e+00 691
15 TraesCS5D01G396800 chr2B 84.990 493 69 3 1415 1906 752831746 752832234 3.500000e-136 496
16 TraesCS5D01G396800 chr2B 79.079 478 75 9 1 460 752830419 752830889 6.330000e-79 305
17 TraesCS5D01G396800 chr2D 86.931 1385 157 17 2672 4048 617076528 617077896 0.000000e+00 1533
18 TraesCS5D01G396800 chr2D 81.771 768 97 25 614 1381 617074004 617074728 2.000000e-168 603
19 TraesCS5D01G396800 chr2D 85.743 491 67 1 1416 1906 617074730 617075217 2.690000e-142 516
20 TraesCS5D01G396800 chr2D 79.955 444 68 7 1 426 617073411 617073851 1.760000e-79 307
21 TraesCS5D01G396800 chr2A 85.961 1446 172 24 2663 4095 746980925 746982352 0.000000e+00 1517
22 TraesCS5D01G396800 chr2A 79.690 1162 161 47 1415 2528 746978596 746979730 0.000000e+00 769
23 TraesCS5D01G396800 chr2A 81.582 771 101 25 614 1383 747144890 747145620 2.590000e-167 599
24 TraesCS5D01G396800 chr2A 85.311 354 46 5 1424 1777 747145625 747145972 1.330000e-95 361
25 TraesCS5D01G396800 chr2A 79.079 478 75 13 1 460 747144296 747144766 6.330000e-79 305
26 TraesCS5D01G396800 chr2A 83.846 260 38 4 87 344 746977261 746977518 1.400000e-60 244
27 TraesCS5D01G396800 chr3A 84.498 1045 158 4 2979 4021 11413903 11414945 0.000000e+00 1029
28 TraesCS5D01G396800 chr1B 81.028 1323 212 27 2731 4033 9594797 9593494 0.000000e+00 1016
29 TraesCS5D01G396800 chr1B 83.303 1096 174 9 2955 4045 10084760 10085851 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 TraesCS5D01G396800 chr5D 464072741 464077774 5033 True 9297.000000 9297 100.000000 1 5034 1 chr5D.!!$R1 5033
1 TraesCS5D01G396800 chr5D 544701284 544702377 1093 False 976.000000 976 82.818000 2952 4047 1 chr5D.!!$F1 1095
2 TraesCS5D01G396800 chr5B 570930431 570935220 4789 True 1632.250000 4322 91.367250 4 5034 4 chr5B.!!$R2 5030
3 TraesCS5D01G396800 chr5B 571121826 571123225 1399 True 1371.000000 1371 84.810000 4 1383 1 chr5B.!!$R1 1379
4 TraesCS5D01G396800 chr5A 584455784 584458229 2445 True 1587.000000 2405 90.616500 2689 5034 2 chr5A.!!$R2 2345
5 TraesCS5D01G396800 chr5A 584489770 584491755 1985 True 869.333333 1173 90.346667 676 2690 3 chr5A.!!$R3 2014
6 TraesCS5D01G396800 chr2B 752830419 752834904 4485 False 761.000000 1552 83.740250 1 4048 4 chr2B.!!$F1 4047
7 TraesCS5D01G396800 chr2D 617073411 617077896 4485 False 739.750000 1533 83.600000 1 4048 4 chr2D.!!$F1 4047
8 TraesCS5D01G396800 chr2A 746977261 746982352 5091 False 843.333333 1517 83.165667 87 4095 3 chr2A.!!$F1 4008
9 TraesCS5D01G396800 chr2A 747144296 747145972 1676 False 421.666667 599 81.990667 1 1777 3 chr2A.!!$F2 1776
10 TraesCS5D01G396800 chr3A 11413903 11414945 1042 False 1029.000000 1029 84.498000 2979 4021 1 chr3A.!!$F1 1042
11 TraesCS5D01G396800 chr1B 9593494 9594797 1303 True 1016.000000 1016 81.028000 2731 4033 1 chr1B.!!$R1 1302
12 TraesCS5D01G396800 chr1B 10084760 10085851 1091 False 1002.000000 1002 83.303000 2955 4045 1 chr1B.!!$F1 1090

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
501 648 0.472471 ACAAAGGGACGCTGGAGAAA 59.528 50.0 0.00 0.0 0.0 2.52 F
1927 2175 0.106918 ACTTGACAAAACCGAGGCCA 60.107 50.0 5.01 0.0 0.0 5.36 F
1930 2178 0.608035 TGACAAAACCGAGGCCATCC 60.608 55.0 5.01 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2251 0.037590 TGGAAAGGCCGCACAGTTAT 59.962 50.0 0.0 0.0 40.66 1.89 R
3886 5447 0.036164 ACCAAAGTGCCACGATAGCA 59.964 50.0 0.0 0.0 42.67 3.49 R
4095 5664 5.220228 GCTACTGTAAAGAGCAATACACACG 60.220 44.0 0.0 0.0 36.20 4.49 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
35 36 2.035321 ACAAAGTTTGCCCATGTAACCG 59.965 45.455 15.59 0.00 0.00 4.44
36 37 0.601057 AAGTTTGCCCATGTAACCGC 59.399 50.000 0.00 0.00 0.00 5.68
142 146 1.303561 GCTCATGTCCAGGTTGGCA 60.304 57.895 0.00 0.00 37.47 4.92
153 157 3.124921 GTTGGCATCCACGACCCG 61.125 66.667 0.00 0.00 30.78 5.28
278 282 1.086634 GCACTCAGTTGGATCGCCTC 61.087 60.000 0.00 0.00 34.31 4.70
326 330 1.478105 GGAGATGGCCGCAAGAAAAAT 59.522 47.619 0.00 0.00 43.02 1.82
366 397 1.224592 GTCGCCCCTCAACATCCAT 59.775 57.895 0.00 0.00 0.00 3.41
369 400 1.307647 GCCCCTCAACATCCATGGT 59.692 57.895 12.58 0.00 0.00 3.55
376 407 4.567537 CCCTCAACATCCATGGTAAGAACA 60.568 45.833 12.58 0.00 0.00 3.18
386 417 2.046314 TAAGAACAGCGGCCAGGC 60.046 61.111 1.26 1.26 0.00 4.85
408 442 2.270257 GCAGCAGCAACCACCATGA 61.270 57.895 0.00 0.00 41.58 3.07
442 480 7.166628 CGATAGTCGATTGATTGTTTAGCTT 57.833 36.000 0.00 0.00 43.74 3.74
479 618 5.277345 CGTTGTAGAAGAAGGGTGAAAACAG 60.277 44.000 0.00 0.00 0.00 3.16
491 638 3.181490 GGTGAAAACAGACACAAAGGGAC 60.181 47.826 0.00 0.00 38.57 4.46
498 645 0.951040 GACACAAAGGGACGCTGGAG 60.951 60.000 0.00 0.00 0.00 3.86
501 648 0.472471 ACAAAGGGACGCTGGAGAAA 59.528 50.000 0.00 0.00 0.00 2.52
505 652 2.586648 AGGGACGCTGGAGAAAATTT 57.413 45.000 0.00 0.00 0.00 1.82
538 700 4.342359 TGTAGAAAGACCTGGTAGGAGAC 58.658 47.826 0.00 0.00 37.67 3.36
560 722 0.943835 TGAACGTCCACATCACTGCG 60.944 55.000 0.00 0.00 0.00 5.18
568 730 2.962421 TCCACATCACTGCGTCCATATA 59.038 45.455 0.00 0.00 0.00 0.86
569 731 3.578282 TCCACATCACTGCGTCCATATAT 59.422 43.478 0.00 0.00 0.00 0.86
570 732 4.770010 TCCACATCACTGCGTCCATATATA 59.230 41.667 0.00 0.00 0.00 0.86
571 733 5.422012 TCCACATCACTGCGTCCATATATAT 59.578 40.000 0.00 0.00 0.00 0.86
596 758 4.094739 TCATCACAATGAAATACGTGCCAG 59.905 41.667 0.00 0.00 38.97 4.85
600 762 5.523552 TCACAATGAAATACGTGCCAGATAG 59.476 40.000 0.00 0.00 31.82 2.08
606 768 9.587772 AATGAAATACGTGCCAGATAGATATAC 57.412 33.333 0.00 0.00 0.00 1.47
754 962 4.332819 GCCAAGGTAGTTGATACATGTCAC 59.667 45.833 0.00 0.00 38.60 3.67
809 1019 4.336993 AGTCTACCGAAGCTTGATCTACAG 59.663 45.833 2.10 0.00 0.00 2.74
987 1219 1.830587 TTCATCCACCTCTGCAGCGT 61.831 55.000 9.47 4.48 0.00 5.07
1086 1318 2.262774 CTTCGGCAGCTTGGGAGGAT 62.263 60.000 0.00 0.00 0.00 3.24
1104 1336 6.832900 GGGAGGATCAAGATTTCTTCAGAAAT 59.167 38.462 13.54 13.54 46.53 2.17
1188 1420 5.754890 TGATTCCAGTAACACATCATCATCG 59.245 40.000 0.00 0.00 0.00 3.84
1194 1426 4.978580 AGTAACACATCATCATCGTCATCG 59.021 41.667 0.00 0.00 38.55 3.84
1383 1628 2.203294 ACAAGTTCACCACCGGCC 60.203 61.111 0.00 0.00 0.00 6.13
1384 1629 2.203280 CAAGTTCACCACCGGCCA 60.203 61.111 0.00 0.00 0.00 5.36
1385 1630 1.603455 CAAGTTCACCACCGGCCAT 60.603 57.895 0.00 0.00 0.00 4.40
1386 1631 1.303317 AAGTTCACCACCGGCCATC 60.303 57.895 0.00 0.00 0.00 3.51
1387 1632 2.750237 GTTCACCACCGGCCATCC 60.750 66.667 0.00 0.00 0.00 3.51
1388 1633 3.253061 TTCACCACCGGCCATCCA 61.253 61.111 0.00 0.00 0.00 3.41
1389 1634 2.611505 TTCACCACCGGCCATCCAT 61.612 57.895 0.00 0.00 0.00 3.41
1390 1635 1.275421 TTCACCACCGGCCATCCATA 61.275 55.000 0.00 0.00 0.00 2.74
1391 1636 1.525995 CACCACCGGCCATCCATAC 60.526 63.158 0.00 0.00 0.00 2.39
1392 1637 1.998438 ACCACCGGCCATCCATACA 60.998 57.895 0.00 0.00 0.00 2.29
1393 1638 1.225983 CCACCGGCCATCCATACAA 59.774 57.895 0.00 0.00 0.00 2.41
1394 1639 0.178992 CCACCGGCCATCCATACAAT 60.179 55.000 0.00 0.00 0.00 2.71
1395 1640 1.238439 CACCGGCCATCCATACAATC 58.762 55.000 0.00 0.00 0.00 2.67
1396 1641 0.110486 ACCGGCCATCCATACAATCC 59.890 55.000 0.00 0.00 0.00 3.01
1397 1642 0.609131 CCGGCCATCCATACAATCCC 60.609 60.000 2.24 0.00 0.00 3.85
1398 1643 0.110295 CGGCCATCCATACAATCCCA 59.890 55.000 2.24 0.00 0.00 4.37
1399 1644 1.620822 GGCCATCCATACAATCCCAC 58.379 55.000 0.00 0.00 0.00 4.61
1400 1645 1.133513 GGCCATCCATACAATCCCACA 60.134 52.381 0.00 0.00 0.00 4.17
1401 1646 2.665165 GCCATCCATACAATCCCACAA 58.335 47.619 0.00 0.00 0.00 3.33
1402 1647 2.362077 GCCATCCATACAATCCCACAAC 59.638 50.000 0.00 0.00 0.00 3.32
1403 1648 3.630168 CCATCCATACAATCCCACAACA 58.370 45.455 0.00 0.00 0.00 3.33
1404 1649 4.217510 CCATCCATACAATCCCACAACAT 58.782 43.478 0.00 0.00 0.00 2.71
1405 1650 4.650588 CCATCCATACAATCCCACAACATT 59.349 41.667 0.00 0.00 0.00 2.71
1406 1651 5.221303 CCATCCATACAATCCCACAACATTC 60.221 44.000 0.00 0.00 0.00 2.67
1407 1652 3.944650 TCCATACAATCCCACAACATTCG 59.055 43.478 0.00 0.00 0.00 3.34
1408 1653 3.944650 CCATACAATCCCACAACATTCGA 59.055 43.478 0.00 0.00 0.00 3.71
1409 1654 4.580167 CCATACAATCCCACAACATTCGAT 59.420 41.667 0.00 0.00 0.00 3.59
1410 1655 5.277974 CCATACAATCCCACAACATTCGATC 60.278 44.000 0.00 0.00 0.00 3.69
1411 1656 3.684908 ACAATCCCACAACATTCGATCA 58.315 40.909 0.00 0.00 0.00 2.92
1412 1657 3.440173 ACAATCCCACAACATTCGATCAC 59.560 43.478 0.00 0.00 0.00 3.06
1413 1658 2.849294 TCCCACAACATTCGATCACA 57.151 45.000 0.00 0.00 0.00 3.58
1414 1659 2.698803 TCCCACAACATTCGATCACAG 58.301 47.619 0.00 0.00 0.00 3.66
1415 1660 1.131126 CCCACAACATTCGATCACAGC 59.869 52.381 0.00 0.00 0.00 4.40
1429 1674 2.421314 CAGCTGACACCGACCACA 59.579 61.111 8.42 0.00 0.00 4.17
1606 1851 1.206831 GGCAACGAAACTCGCTTCC 59.793 57.895 0.00 0.00 45.12 3.46
1672 1917 3.386078 GGACTGCAAGGTCATCTCAGATA 59.614 47.826 8.22 0.00 39.30 1.98
1782 2029 1.070758 GCTGACTGGAGTGAACAGGAA 59.929 52.381 0.00 0.00 40.23 3.36
1850 2098 3.559024 CTGTGCCTTCAGCTCACG 58.441 61.111 0.00 0.00 44.23 4.35
1863 2111 3.070018 CAGCTCACGAAGGAATGAAACT 58.930 45.455 0.00 0.00 0.00 2.66
1920 2168 7.708998 TCAATTACTACCAACTTGACAAAACC 58.291 34.615 0.00 0.00 0.00 3.27
1921 2169 5.738118 TTACTACCAACTTGACAAAACCG 57.262 39.130 0.00 0.00 0.00 4.44
1922 2170 3.876341 ACTACCAACTTGACAAAACCGA 58.124 40.909 0.00 0.00 0.00 4.69
1923 2171 3.875134 ACTACCAACTTGACAAAACCGAG 59.125 43.478 0.00 0.00 0.00 4.63
1924 2172 2.021457 ACCAACTTGACAAAACCGAGG 58.979 47.619 0.00 0.00 0.00 4.63
1925 2173 1.269051 CCAACTTGACAAAACCGAGGC 60.269 52.381 0.00 0.00 0.00 4.70
1926 2174 1.029681 AACTTGACAAAACCGAGGCC 58.970 50.000 0.00 0.00 0.00 5.19
1927 2175 0.106918 ACTTGACAAAACCGAGGCCA 60.107 50.000 5.01 0.00 0.00 5.36
1928 2176 1.247567 CTTGACAAAACCGAGGCCAT 58.752 50.000 5.01 0.00 0.00 4.40
1929 2177 1.200020 CTTGACAAAACCGAGGCCATC 59.800 52.381 5.01 0.00 0.00 3.51
1930 2178 0.608035 TGACAAAACCGAGGCCATCC 60.608 55.000 5.01 0.00 0.00 3.51
1932 2180 0.988832 ACAAAACCGAGGCCATCCTA 59.011 50.000 5.01 0.00 44.46 2.94
1933 2181 1.564348 ACAAAACCGAGGCCATCCTAT 59.436 47.619 5.01 0.00 44.46 2.57
1934 2182 2.775384 ACAAAACCGAGGCCATCCTATA 59.225 45.455 5.01 0.00 44.46 1.31
1935 2183 3.394606 ACAAAACCGAGGCCATCCTATAT 59.605 43.478 5.01 0.00 44.46 0.86
1936 2184 4.141251 ACAAAACCGAGGCCATCCTATATT 60.141 41.667 5.01 0.00 44.46 1.28
1937 2185 5.072600 ACAAAACCGAGGCCATCCTATATTA 59.927 40.000 5.01 0.00 44.46 0.98
1938 2186 6.180472 CAAAACCGAGGCCATCCTATATTAT 58.820 40.000 5.01 0.00 44.46 1.28
1939 2187 6.388619 AAACCGAGGCCATCCTATATTATT 57.611 37.500 5.01 0.00 44.46 1.40
1940 2188 5.359194 ACCGAGGCCATCCTATATTATTG 57.641 43.478 5.01 0.00 44.46 1.90
1941 2189 4.783227 ACCGAGGCCATCCTATATTATTGT 59.217 41.667 5.01 0.00 44.46 2.71
1942 2190 5.118990 CCGAGGCCATCCTATATTATTGTG 58.881 45.833 5.01 0.00 44.46 3.33
1943 2191 5.338381 CCGAGGCCATCCTATATTATTGTGT 60.338 44.000 5.01 0.00 44.46 3.72
1944 2192 6.173339 CGAGGCCATCCTATATTATTGTGTT 58.827 40.000 5.01 0.00 44.46 3.32
1945 2193 7.327975 CGAGGCCATCCTATATTATTGTGTTA 58.672 38.462 5.01 0.00 44.46 2.41
1946 2194 7.822334 CGAGGCCATCCTATATTATTGTGTTAA 59.178 37.037 5.01 0.00 44.46 2.01
1947 2195 9.686683 GAGGCCATCCTATATTATTGTGTTAAT 57.313 33.333 5.01 0.00 44.46 1.40
1960 2208 9.975218 ATTATTGTGTTAATTCCTAGTCTTGGT 57.025 29.630 0.00 0.00 0.00 3.67
1963 2211 7.549147 TGTGTTAATTCCTAGTCTTGGTAGT 57.451 36.000 0.00 0.00 0.00 2.73
1964 2212 7.970102 TGTGTTAATTCCTAGTCTTGGTAGTT 58.030 34.615 0.00 0.00 0.00 2.24
1965 2213 9.092338 TGTGTTAATTCCTAGTCTTGGTAGTTA 57.908 33.333 0.00 0.00 0.00 2.24
1966 2214 9.933723 GTGTTAATTCCTAGTCTTGGTAGTTAA 57.066 33.333 0.00 2.98 0.00 2.01
1972 2220 9.668497 ATTCCTAGTCTTGGTAGTTAAAATCAC 57.332 33.333 0.00 0.00 0.00 3.06
1973 2221 8.431910 TCCTAGTCTTGGTAGTTAAAATCACT 57.568 34.615 0.00 0.00 0.00 3.41
1974 2222 8.311836 TCCTAGTCTTGGTAGTTAAAATCACTG 58.688 37.037 0.00 0.00 0.00 3.66
1975 2223 8.311836 CCTAGTCTTGGTAGTTAAAATCACTGA 58.688 37.037 0.00 0.00 0.00 3.41
1976 2224 9.360093 CTAGTCTTGGTAGTTAAAATCACTGAG 57.640 37.037 0.00 0.00 0.00 3.35
1977 2225 7.963532 AGTCTTGGTAGTTAAAATCACTGAGA 58.036 34.615 0.00 0.00 0.00 3.27
1978 2226 8.429641 AGTCTTGGTAGTTAAAATCACTGAGAA 58.570 33.333 0.00 0.00 0.00 2.87
1979 2227 9.220767 GTCTTGGTAGTTAAAATCACTGAGAAT 57.779 33.333 0.00 0.00 0.00 2.40
1980 2228 9.793259 TCTTGGTAGTTAAAATCACTGAGAATT 57.207 29.630 0.00 0.00 0.00 2.17
1983 2231 9.010029 TGGTAGTTAAAATCACTGAGAATTTCC 57.990 33.333 0.00 0.00 31.93 3.13
1984 2232 9.232473 GGTAGTTAAAATCACTGAGAATTTCCT 57.768 33.333 0.00 0.00 31.93 3.36
2016 2371 1.287425 GTACTCATAACTGTGCGGCC 58.713 55.000 0.00 0.00 0.00 6.13
2512 2941 3.578688 GCCAACTGCATTCCTTAAAGTG 58.421 45.455 0.00 0.00 40.77 3.16
3233 4794 1.427020 GCCGTCAAGATGCTTGAGC 59.573 57.895 9.91 7.67 42.50 4.26
3319 4880 1.002134 CATTGTCCGCCTCCTTGGT 60.002 57.895 0.00 0.00 38.35 3.67
3383 4944 5.135383 TCATGCCTAAAGATTCATTGGAGG 58.865 41.667 0.00 0.00 0.00 4.30
3449 5010 4.634004 TGGTACCGAACAAAATGCTAGATG 59.366 41.667 7.57 0.00 0.00 2.90
3553 5114 7.050970 TCGCAATATCTTACTGGACTACAAT 57.949 36.000 0.00 0.00 0.00 2.71
3886 5447 3.810386 GGAAAGAAAAGACGAGACAGCTT 59.190 43.478 0.00 0.00 0.00 3.74
3985 5546 4.005650 CTGGAAGCTTACAGAATCTGCAA 58.994 43.478 31.64 2.64 41.85 4.08
4095 5664 6.375455 ACATTTGAGGGACATAGTTGATTCAC 59.625 38.462 0.00 0.00 0.00 3.18
4114 5683 4.623002 TCACGTGTGTATTGCTCTTTACA 58.377 39.130 16.51 0.00 0.00 2.41
4135 5708 1.933853 GTAGCACGGTTTCTAGCATGG 59.066 52.381 0.00 0.00 0.00 3.66
4139 5712 2.802816 GCACGGTTTCTAGCATGGATAG 59.197 50.000 0.00 0.00 0.00 2.08
4164 5747 7.986889 AGAAAAATTATTGCCAAGTCAACTGTT 59.013 29.630 0.00 0.00 0.00 3.16
4187 5770 3.118775 TGTGTGTTAGCTAGCATACCTGG 60.119 47.826 26.63 0.00 29.84 4.45
4189 5772 4.098960 GTGTGTTAGCTAGCATACCTGGTA 59.901 45.833 21.66 9.36 34.31 3.25
4220 5803 9.664332 GATCTAGTTCATGAGCCATTATATTGT 57.336 33.333 5.87 0.00 0.00 2.71
4282 5865 4.247258 GCCATTGCTGTGATTTTGATGAA 58.753 39.130 0.00 0.00 33.53 2.57
4285 5868 5.929992 CCATTGCTGTGATTTTGATGAAGTT 59.070 36.000 0.00 0.00 0.00 2.66
4286 5869 7.092079 CCATTGCTGTGATTTTGATGAAGTTA 58.908 34.615 0.00 0.00 0.00 2.24
4287 5870 7.762615 CCATTGCTGTGATTTTGATGAAGTTAT 59.237 33.333 0.00 0.00 0.00 1.89
4288 5871 9.146984 CATTGCTGTGATTTTGATGAAGTTATT 57.853 29.630 0.00 0.00 0.00 1.40
4316 5905 5.578005 TCAGTTGTGTAGTATCCACTAGC 57.422 43.478 0.00 0.00 37.94 3.42
4399 5988 7.654520 CACAATCACAAGAGGATTTTCAATTGT 59.345 33.333 5.13 0.00 34.83 2.71
4400 5989 7.869429 ACAATCACAAGAGGATTTTCAATTGTC 59.131 33.333 5.13 0.00 32.86 3.18
4402 5991 7.206981 TCACAAGAGGATTTTCAATTGTCTC 57.793 36.000 5.13 4.86 0.00 3.36
4404 5993 7.040892 TCACAAGAGGATTTTCAATTGTCTCTG 60.041 37.037 5.13 3.80 31.47 3.35
4432 6129 9.817809 ATCTAGTGAACGATTAAAAGATGCTTA 57.182 29.630 0.00 0.00 0.00 3.09
4452 6149 5.863935 GCTTACCTCCTGCTATTTTGTTTTG 59.136 40.000 0.00 0.00 0.00 2.44
4456 6153 4.321974 CCTCCTGCTATTTTGTTTTGGGAC 60.322 45.833 0.00 0.00 0.00 4.46
4458 6155 2.986479 CTGCTATTTTGTTTTGGGACGC 59.014 45.455 0.00 0.00 0.00 5.19
4481 6178 1.597027 CCCCAGCGAACGTTCACTT 60.597 57.895 26.71 9.47 0.00 3.16
4497 6194 5.232463 GTTCACTTCCATGCATGACATTTT 58.768 37.500 28.31 4.07 36.64 1.82
4511 6219 6.621164 GCATGACATTTTGGTGGCAATTTTAG 60.621 38.462 0.00 0.00 41.24 1.85
4524 6232 3.194755 GCAATTTTAGTGTTAGGGGGTGG 59.805 47.826 0.00 0.00 0.00 4.61
4527 6235 0.988832 TTAGTGTTAGGGGGTGGCAG 59.011 55.000 0.00 0.00 0.00 4.85
4534 6242 0.854218 TAGGGGGTGGCAGTTTTCAA 59.146 50.000 0.00 0.00 0.00 2.69
4537 6245 1.474320 GGGGGTGGCAGTTTTCAAAAC 60.474 52.381 4.72 4.72 0.00 2.43
4541 6249 3.753797 GGGTGGCAGTTTTCAAAACAAAA 59.246 39.130 15.41 0.00 0.00 2.44
4586 6298 7.304735 CAATTTTCGTCAATTACTGTCATCCA 58.695 34.615 0.00 0.00 0.00 3.41
4588 6300 6.662414 TTTCGTCAATTACTGTCATCCATC 57.338 37.500 0.00 0.00 0.00 3.51
4596 6308 2.670939 ACTGTCATCCATCGGATCTGA 58.329 47.619 6.72 6.72 40.98 3.27
4603 6315 2.031870 TCCATCGGATCTGAATCGTGT 58.968 47.619 8.65 0.00 32.24 4.49
4621 6333 4.821589 GGCTCTGGAGGCGTTCGG 62.822 72.222 8.34 0.00 44.15 4.30
4659 6371 2.090195 GCGAACGTCAGCTAGTTAACAC 59.910 50.000 8.61 0.00 0.00 3.32
4661 6373 4.715896 CGAACGTCAGCTAGTTAACACTA 58.284 43.478 8.61 0.00 34.06 2.74
4672 6384 8.995220 CAGCTAGTTAACACTACCATTGTTTTA 58.005 33.333 8.61 0.00 38.21 1.52
4673 6385 9.734984 AGCTAGTTAACACTACCATTGTTTTAT 57.265 29.630 8.61 0.00 38.21 1.40
4723 6439 3.627395 AATATCGAAGAGGCCACACAA 57.373 42.857 5.01 0.00 43.63 3.33
4725 6441 2.270352 ATCGAAGAGGCCACACAAAA 57.730 45.000 5.01 0.00 43.63 2.44
4726 6442 1.593196 TCGAAGAGGCCACACAAAAG 58.407 50.000 5.01 0.00 0.00 2.27
4727 6443 1.140052 TCGAAGAGGCCACACAAAAGA 59.860 47.619 5.01 0.00 0.00 2.52
4729 6445 2.357637 CGAAGAGGCCACACAAAAGAAA 59.642 45.455 5.01 0.00 0.00 2.52
4731 6447 4.499696 CGAAGAGGCCACACAAAAGAAAAT 60.500 41.667 5.01 0.00 0.00 1.82
4732 6448 4.590850 AGAGGCCACACAAAAGAAAATC 57.409 40.909 5.01 0.00 0.00 2.17
4733 6449 4.218312 AGAGGCCACACAAAAGAAAATCT 58.782 39.130 5.01 0.00 0.00 2.40
4734 6450 4.279420 AGAGGCCACACAAAAGAAAATCTC 59.721 41.667 5.01 0.00 0.00 2.75
4779 6503 1.067416 TGCAGATAAGGCTACCGCG 59.933 57.895 0.00 0.00 36.88 6.46
4903 6627 0.907486 CCATCACCTTCCTCAGCTCA 59.093 55.000 0.00 0.00 0.00 4.26
4916 6640 2.295629 CTCAGCTCATCGAGGCTAATCA 59.704 50.000 9.43 0.00 37.00 2.57
5011 6735 3.372554 CTTCCCTCCTCCGAACGCC 62.373 68.421 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.787286 CCCGCGGTTACATGGGCA 62.787 66.667 26.12 0.00 34.25 5.36
45 49 1.538276 CAACGGCTTCATCGATTTGC 58.462 50.000 0.00 0.00 0.00 3.68
49 53 4.540153 CCCAACGGCTTCATCGAT 57.460 55.556 0.00 0.00 0.00 3.59
142 146 0.750850 CATACTTCCGGGTCGTGGAT 59.249 55.000 0.00 0.00 34.91 3.41
153 157 5.634896 TCGACTACGAACTTTCATACTTCC 58.365 41.667 0.00 0.00 45.74 3.46
236 240 0.393944 TCTCCGTCATACGAGCTGGT 60.394 55.000 6.61 6.61 46.05 4.00
278 282 2.511600 CTACCCTTTCCGCCTGCG 60.512 66.667 4.20 4.20 39.44 5.18
326 330 1.075525 ATAGGTACGCCTGCCCTCA 60.076 57.895 0.00 0.00 46.47 3.86
366 397 1.003839 CTGGCCGCTGTTCTTACCA 60.004 57.895 0.00 0.00 0.00 3.25
369 400 2.046314 GCCTGGCCGCTGTTCTTA 60.046 61.111 7.66 0.00 0.00 2.10
426 464 7.293018 CCAAAGCAAAAGCTAAACAATCAATC 58.707 34.615 0.00 0.00 0.00 2.67
427 465 6.293571 GCCAAAGCAAAAGCTAAACAATCAAT 60.294 34.615 0.00 0.00 39.53 2.57
428 466 5.007528 GCCAAAGCAAAAGCTAAACAATCAA 59.992 36.000 0.00 0.00 39.53 2.57
429 467 4.511082 GCCAAAGCAAAAGCTAAACAATCA 59.489 37.500 0.00 0.00 39.53 2.57
442 480 2.946329 TCTACAACGAAGCCAAAGCAAA 59.054 40.909 0.00 0.00 43.56 3.68
455 493 4.573201 TGTTTTCACCCTTCTTCTACAACG 59.427 41.667 0.00 0.00 0.00 4.10
479 618 0.951040 CTCCAGCGTCCCTTTGTGTC 60.951 60.000 0.00 0.00 0.00 3.67
491 638 5.346011 GGCTCTTTTTAAATTTTCTCCAGCG 59.654 40.000 0.00 0.00 0.00 5.18
501 648 8.577296 GGTCTTTCTACAGGCTCTTTTTAAATT 58.423 33.333 0.00 0.00 0.00 1.82
505 652 6.231211 CAGGTCTTTCTACAGGCTCTTTTTA 58.769 40.000 0.00 0.00 0.00 1.52
538 700 0.319555 AGTGATGTGGACGTTCACCG 60.320 55.000 24.06 0.00 44.03 4.94
568 730 7.355017 GCACGTATTTCATTGTGATGACATAT 58.645 34.615 0.00 0.00 41.84 1.78
569 731 6.238347 GGCACGTATTTCATTGTGATGACATA 60.238 38.462 0.00 0.00 41.84 2.29
570 732 5.449041 GGCACGTATTTCATTGTGATGACAT 60.449 40.000 0.00 0.00 41.84 3.06
571 733 4.142708 GGCACGTATTTCATTGTGATGACA 60.143 41.667 0.00 0.00 41.84 3.58
600 762 6.854892 GCAGCAGTGATGTTTTCATGTATATC 59.145 38.462 10.56 0.00 41.05 1.63
606 768 2.029739 TGGCAGCAGTGATGTTTTCATG 60.030 45.455 10.56 0.00 41.05 3.07
754 962 4.163078 ACATTAGAATCCCAGACCTGACAG 59.837 45.833 0.00 0.00 0.00 3.51
793 1003 1.849219 GTCGCTGTAGATCAAGCTTCG 59.151 52.381 0.00 0.00 0.00 3.79
856 1079 4.567537 CCCTGTCCATGAGTCAATACCAAA 60.568 45.833 0.00 0.00 0.00 3.28
859 1082 2.158755 CCCCTGTCCATGAGTCAATACC 60.159 54.545 0.00 0.00 0.00 2.73
987 1219 7.451877 AGAAATATACTCATCTTTCTCCCGCTA 59.548 37.037 0.00 0.00 34.27 4.26
1038 1270 2.438434 CCGGTTCCATGGCTGACC 60.438 66.667 6.96 13.65 0.00 4.02
1104 1336 2.180769 CATCGAGACGGCGGACAA 59.819 61.111 13.24 0.00 0.00 3.18
1383 1628 5.506151 CGAATGTTGTGGGATTGTATGGATG 60.506 44.000 0.00 0.00 0.00 3.51
1384 1629 4.580167 CGAATGTTGTGGGATTGTATGGAT 59.420 41.667 0.00 0.00 0.00 3.41
1385 1630 3.944650 CGAATGTTGTGGGATTGTATGGA 59.055 43.478 0.00 0.00 0.00 3.41
1386 1631 3.944650 TCGAATGTTGTGGGATTGTATGG 59.055 43.478 0.00 0.00 0.00 2.74
1387 1632 5.296531 TGATCGAATGTTGTGGGATTGTATG 59.703 40.000 0.00 0.00 0.00 2.39
1388 1633 5.296780 GTGATCGAATGTTGTGGGATTGTAT 59.703 40.000 0.00 0.00 0.00 2.29
1389 1634 4.634004 GTGATCGAATGTTGTGGGATTGTA 59.366 41.667 0.00 0.00 0.00 2.41
1390 1635 3.440173 GTGATCGAATGTTGTGGGATTGT 59.560 43.478 0.00 0.00 0.00 2.71
1391 1636 3.439825 TGTGATCGAATGTTGTGGGATTG 59.560 43.478 0.00 0.00 0.00 2.67
1392 1637 3.684908 TGTGATCGAATGTTGTGGGATT 58.315 40.909 0.00 0.00 0.00 3.01
1393 1638 3.273434 CTGTGATCGAATGTTGTGGGAT 58.727 45.455 0.00 0.00 0.00 3.85
1394 1639 2.698803 CTGTGATCGAATGTTGTGGGA 58.301 47.619 0.00 0.00 0.00 4.37
1395 1640 1.131126 GCTGTGATCGAATGTTGTGGG 59.869 52.381 0.00 0.00 0.00 4.61
1396 1641 2.079158 AGCTGTGATCGAATGTTGTGG 58.921 47.619 0.00 0.00 0.00 4.17
1397 1642 2.738314 TCAGCTGTGATCGAATGTTGTG 59.262 45.455 14.67 0.00 0.00 3.33
1398 1643 2.738846 GTCAGCTGTGATCGAATGTTGT 59.261 45.455 14.67 0.00 34.36 3.32
1399 1644 2.738314 TGTCAGCTGTGATCGAATGTTG 59.262 45.455 14.67 0.00 34.36 3.33
1400 1645 2.738846 GTGTCAGCTGTGATCGAATGTT 59.261 45.455 14.67 0.00 34.36 2.71
1401 1646 2.341257 GTGTCAGCTGTGATCGAATGT 58.659 47.619 14.67 0.00 34.36 2.71
1402 1647 1.662629 GGTGTCAGCTGTGATCGAATG 59.337 52.381 14.67 0.00 34.36 2.67
1403 1648 1.737029 CGGTGTCAGCTGTGATCGAAT 60.737 52.381 14.67 0.00 34.36 3.34
1404 1649 0.388520 CGGTGTCAGCTGTGATCGAA 60.389 55.000 14.67 0.00 34.36 3.71
1405 1650 1.212751 CGGTGTCAGCTGTGATCGA 59.787 57.895 14.67 0.00 34.36 3.59
1406 1651 1.073216 GTCGGTGTCAGCTGTGATCG 61.073 60.000 14.67 13.31 34.36 3.69
1407 1652 0.737715 GGTCGGTGTCAGCTGTGATC 60.738 60.000 14.67 0.55 34.36 2.92
1408 1653 1.293498 GGTCGGTGTCAGCTGTGAT 59.707 57.895 14.67 0.00 34.36 3.06
1409 1654 2.131067 TGGTCGGTGTCAGCTGTGA 61.131 57.895 14.67 2.60 0.00 3.58
1410 1655 1.956170 GTGGTCGGTGTCAGCTGTG 60.956 63.158 14.67 0.10 0.00 3.66
1411 1656 2.369257 CTGTGGTCGGTGTCAGCTGT 62.369 60.000 14.67 0.00 0.00 4.40
1412 1657 1.665916 CTGTGGTCGGTGTCAGCTG 60.666 63.158 7.63 7.63 0.00 4.24
1413 1658 2.737180 CTGTGGTCGGTGTCAGCT 59.263 61.111 0.00 0.00 0.00 4.24
1414 1659 3.044305 GCTGTGGTCGGTGTCAGC 61.044 66.667 0.00 0.00 44.50 4.26
1415 1660 1.665916 CAGCTGTGGTCGGTGTCAG 60.666 63.158 5.25 0.00 0.00 3.51
1464 1709 1.142748 CTCCCTTGAGCAGCCTACG 59.857 63.158 0.00 0.00 0.00 3.51
1606 1851 1.529226 TCAGTTGCCACCAAATACGG 58.471 50.000 0.00 0.00 31.68 4.02
1850 2098 5.836347 ACAAGCAGAAAGTTTCATTCCTTC 58.164 37.500 17.65 0.00 0.00 3.46
1863 2111 3.558931 TGAGGTTGAGACAAGCAGAAA 57.441 42.857 14.38 0.00 0.00 2.52
1901 2149 3.875134 CTCGGTTTTGTCAAGTTGGTAGT 59.125 43.478 2.34 0.00 0.00 2.73
1904 2152 2.021457 CCTCGGTTTTGTCAAGTTGGT 58.979 47.619 2.34 0.00 0.00 3.67
1905 2153 1.269051 GCCTCGGTTTTGTCAAGTTGG 60.269 52.381 2.34 0.00 0.00 3.77
1906 2154 1.269051 GGCCTCGGTTTTGTCAAGTTG 60.269 52.381 0.00 0.00 0.00 3.16
1907 2155 1.029681 GGCCTCGGTTTTGTCAAGTT 58.970 50.000 0.00 0.00 0.00 2.66
1908 2156 0.106918 TGGCCTCGGTTTTGTCAAGT 60.107 50.000 3.32 0.00 0.00 3.16
1909 2157 1.200020 GATGGCCTCGGTTTTGTCAAG 59.800 52.381 3.32 0.00 0.00 3.02
1910 2158 1.243902 GATGGCCTCGGTTTTGTCAA 58.756 50.000 3.32 0.00 0.00 3.18
1911 2159 0.608035 GGATGGCCTCGGTTTTGTCA 60.608 55.000 3.32 0.00 0.00 3.58
1912 2160 0.322546 AGGATGGCCTCGGTTTTGTC 60.323 55.000 3.32 0.00 42.19 3.18
1913 2161 0.988832 TAGGATGGCCTCGGTTTTGT 59.011 50.000 3.32 0.00 45.54 2.83
1914 2162 2.348411 ATAGGATGGCCTCGGTTTTG 57.652 50.000 3.32 0.00 45.54 2.44
1915 2163 4.724279 AATATAGGATGGCCTCGGTTTT 57.276 40.909 3.32 0.00 45.54 2.43
1916 2164 6.180472 CAATAATATAGGATGGCCTCGGTTT 58.820 40.000 3.32 0.00 45.54 3.27
1917 2165 5.250774 ACAATAATATAGGATGGCCTCGGTT 59.749 40.000 3.32 0.00 45.54 4.44
1918 2166 4.783227 ACAATAATATAGGATGGCCTCGGT 59.217 41.667 3.32 0.00 45.54 4.69
1919 2167 5.118990 CACAATAATATAGGATGGCCTCGG 58.881 45.833 3.32 0.00 45.54 4.63
1920 2168 5.734720 ACACAATAATATAGGATGGCCTCG 58.265 41.667 3.32 0.00 45.54 4.63
1921 2169 9.686683 ATTAACACAATAATATAGGATGGCCTC 57.313 33.333 3.32 0.00 45.54 4.70
1934 2182 9.975218 ACCAAGACTAGGAATTAACACAATAAT 57.025 29.630 0.00 0.00 0.00 1.28
1937 2185 8.603304 ACTACCAAGACTAGGAATTAACACAAT 58.397 33.333 0.00 0.00 0.00 2.71
1938 2186 7.970102 ACTACCAAGACTAGGAATTAACACAA 58.030 34.615 0.00 0.00 0.00 3.33
1939 2187 7.549147 ACTACCAAGACTAGGAATTAACACA 57.451 36.000 0.00 0.00 0.00 3.72
1940 2188 9.933723 TTAACTACCAAGACTAGGAATTAACAC 57.066 33.333 0.00 0.00 0.00 3.32
1946 2194 9.668497 GTGATTTTAACTACCAAGACTAGGAAT 57.332 33.333 0.00 0.00 0.00 3.01
1947 2195 8.877195 AGTGATTTTAACTACCAAGACTAGGAA 58.123 33.333 0.00 0.00 0.00 3.36
1948 2196 8.311836 CAGTGATTTTAACTACCAAGACTAGGA 58.688 37.037 0.00 0.00 0.00 2.94
1949 2197 8.311836 TCAGTGATTTTAACTACCAAGACTAGG 58.688 37.037 0.00 0.00 0.00 3.02
1950 2198 9.360093 CTCAGTGATTTTAACTACCAAGACTAG 57.640 37.037 0.00 0.00 0.00 2.57
1951 2199 9.085645 TCTCAGTGATTTTAACTACCAAGACTA 57.914 33.333 0.00 0.00 0.00 2.59
1952 2200 7.963532 TCTCAGTGATTTTAACTACCAAGACT 58.036 34.615 0.00 0.00 0.00 3.24
1953 2201 8.603242 TTCTCAGTGATTTTAACTACCAAGAC 57.397 34.615 0.00 0.00 0.00 3.01
1954 2202 9.793259 AATTCTCAGTGATTTTAACTACCAAGA 57.207 29.630 0.00 0.00 0.00 3.02
1957 2205 9.010029 GGAAATTCTCAGTGATTTTAACTACCA 57.990 33.333 0.00 0.00 31.00 3.25
1958 2206 9.232473 AGGAAATTCTCAGTGATTTTAACTACC 57.768 33.333 0.00 0.00 31.00 3.18
1987 2235 9.244799 CGCACAGTTATGAGTACATTCTAAATA 57.755 33.333 0.00 0.00 37.87 1.40
1988 2236 7.224753 CCGCACAGTTATGAGTACATTCTAAAT 59.775 37.037 0.00 0.00 37.87 1.40
1989 2237 6.533723 CCGCACAGTTATGAGTACATTCTAAA 59.466 38.462 0.00 0.00 37.87 1.85
1990 2238 6.040247 CCGCACAGTTATGAGTACATTCTAA 58.960 40.000 0.00 0.00 37.87 2.10
1991 2239 5.588240 CCGCACAGTTATGAGTACATTCTA 58.412 41.667 0.00 0.00 37.87 2.10
1992 2240 4.433615 CCGCACAGTTATGAGTACATTCT 58.566 43.478 0.00 0.00 37.87 2.40
1993 2241 3.001330 GCCGCACAGTTATGAGTACATTC 59.999 47.826 0.00 0.00 37.87 2.67
1994 2242 2.936498 GCCGCACAGTTATGAGTACATT 59.064 45.455 0.00 0.00 37.87 2.71
1995 2243 2.550978 GCCGCACAGTTATGAGTACAT 58.449 47.619 0.00 0.00 40.16 2.29
1996 2244 1.404986 GGCCGCACAGTTATGAGTACA 60.405 52.381 0.00 0.00 0.00 2.90
1997 2245 1.134788 AGGCCGCACAGTTATGAGTAC 60.135 52.381 0.00 0.00 0.00 2.73
1998 2246 1.191535 AGGCCGCACAGTTATGAGTA 58.808 50.000 0.00 0.00 0.00 2.59
1999 2247 0.324943 AAGGCCGCACAGTTATGAGT 59.675 50.000 0.00 0.00 0.00 3.41
2000 2248 1.398390 GAAAGGCCGCACAGTTATGAG 59.602 52.381 0.00 0.00 0.00 2.90
2001 2249 1.448985 GAAAGGCCGCACAGTTATGA 58.551 50.000 0.00 0.00 0.00 2.15
2002 2250 0.451783 GGAAAGGCCGCACAGTTATG 59.548 55.000 0.00 0.00 0.00 1.90
2003 2251 0.037590 TGGAAAGGCCGCACAGTTAT 59.962 50.000 0.00 0.00 40.66 1.89
2004 2252 0.605319 CTGGAAAGGCCGCACAGTTA 60.605 55.000 0.00 0.00 40.66 2.24
2005 2253 1.898574 CTGGAAAGGCCGCACAGTT 60.899 57.895 0.00 0.00 40.66 3.16
2016 2371 8.716646 AATTTAACAACAAAACTCCTGGAAAG 57.283 30.769 0.00 0.00 0.00 2.62
3233 4794 2.158842 CCTGCCCTTCTCCATTAGAGTG 60.159 54.545 0.00 0.00 43.71 3.51
3319 4880 3.897239 TCTTGTCCCTTCAGAGCAAAAA 58.103 40.909 0.00 0.00 0.00 1.94
3553 5114 3.578716 AGTCTGAGATCTTCGGGTTGAAA 59.421 43.478 0.00 0.00 35.79 2.69
3886 5447 0.036164 ACCAAAGTGCCACGATAGCA 59.964 50.000 0.00 0.00 42.67 3.49
4095 5664 5.220228 GCTACTGTAAAGAGCAATACACACG 60.220 44.000 0.00 0.00 36.20 4.49
4114 5683 2.418746 CCATGCTAGAAACCGTGCTACT 60.419 50.000 0.00 0.00 0.00 2.57
4135 5708 9.860898 AGTTGACTTGGCAATAATTTTTCTATC 57.139 29.630 0.00 0.00 0.00 2.08
4139 5712 7.713764 ACAGTTGACTTGGCAATAATTTTTC 57.286 32.000 0.00 0.00 0.00 2.29
4164 5747 4.503910 CAGGTATGCTAGCTAACACACAA 58.496 43.478 17.23 0.00 34.67 3.33
4187 5770 5.244851 TGGCTCATGAACTAGATCAGGATAC 59.755 44.000 16.33 12.72 39.18 2.24
4189 5772 4.229639 TGGCTCATGAACTAGATCAGGAT 58.770 43.478 16.33 0.00 39.18 3.24
4220 5803 9.571816 TCAATGCACATCAAATCCAGTATTATA 57.428 29.630 0.00 0.00 0.00 0.98
4221 5804 8.467963 TCAATGCACATCAAATCCAGTATTAT 57.532 30.769 0.00 0.00 0.00 1.28
4287 5870 9.787435 AGTGGATACTACACAACTGAAAATTAA 57.213 29.630 0.00 0.00 41.21 1.40
4290 5873 7.549488 GCTAGTGGATACTACACAACTGAAAAT 59.451 37.037 0.00 0.00 41.21 1.82
4314 5903 4.579869 ACATTACTCGAGTTCATTTGGCT 58.420 39.130 25.44 0.00 0.00 4.75
4316 5905 5.347635 TCGAACATTACTCGAGTTCATTTGG 59.652 40.000 25.44 13.14 40.25 3.28
4404 5993 9.250624 AGCATCTTTTAATCGTTCACTAGATAC 57.749 33.333 0.00 0.00 0.00 2.24
4428 6125 5.644977 AAACAAAATAGCAGGAGGTAAGC 57.355 39.130 0.00 0.00 0.00 3.09
4432 6129 3.578282 CCCAAAACAAAATAGCAGGAGGT 59.422 43.478 0.00 0.00 0.00 3.85
4458 6155 1.287425 GAACGTTCGCTGGGGATTAG 58.713 55.000 13.36 0.00 0.00 1.73
4481 6178 2.234168 CCACCAAAATGTCATGCATGGA 59.766 45.455 25.97 13.72 37.96 3.41
4497 6194 3.829601 CCCTAACACTAAAATTGCCACCA 59.170 43.478 0.00 0.00 0.00 4.17
4511 6219 0.178973 AAACTGCCACCCCCTAACAC 60.179 55.000 0.00 0.00 0.00 3.32
4544 6252 9.260002 ACGAAAATTGCATTGAAACTAAAGATT 57.740 25.926 0.00 0.00 0.00 2.40
4545 6253 8.816640 ACGAAAATTGCATTGAAACTAAAGAT 57.183 26.923 0.00 0.00 0.00 2.40
4552 6264 8.487176 AGTAATTGACGAAAATTGCATTGAAAC 58.513 29.630 14.21 3.29 35.37 2.78
4556 6268 7.114670 TGACAGTAATTGACGAAAATTGCATTG 59.885 33.333 14.21 9.24 35.37 2.82
4586 6298 1.539065 GCCACACGATTCAGATCCGAT 60.539 52.381 0.00 0.00 0.00 4.18
4588 6300 0.179100 AGCCACACGATTCAGATCCG 60.179 55.000 0.00 0.00 0.00 4.18
4596 6308 1.599047 CCTCCAGAGCCACACGATT 59.401 57.895 0.00 0.00 0.00 3.34
4603 6315 4.069232 CGAACGCCTCCAGAGCCA 62.069 66.667 0.00 0.00 0.00 4.75
4616 6328 4.934989 GGTGAGATCCCACCGAAC 57.065 61.111 11.00 0.00 46.00 3.95
4636 6348 2.257974 TAACTAGCTGACGTTCGCTG 57.742 50.000 19.01 12.60 37.05 5.18
4672 6384 8.792830 TCGTCTTTCCTTTCATTTCTTGATAT 57.207 30.769 0.00 0.00 33.34 1.63
4673 6385 8.792830 ATCGTCTTTCCTTTCATTTCTTGATA 57.207 30.769 0.00 0.00 33.34 2.15
4674 6386 7.148171 GGATCGTCTTTCCTTTCATTTCTTGAT 60.148 37.037 0.00 0.00 33.34 2.57
4675 6387 6.149474 GGATCGTCTTTCCTTTCATTTCTTGA 59.851 38.462 0.00 0.00 0.00 3.02
4676 6388 6.072508 TGGATCGTCTTTCCTTTCATTTCTTG 60.073 38.462 0.00 0.00 34.17 3.02
4677 6389 6.003950 TGGATCGTCTTTCCTTTCATTTCTT 58.996 36.000 0.00 0.00 34.17 2.52
4678 6390 5.560724 TGGATCGTCTTTCCTTTCATTTCT 58.439 37.500 0.00 0.00 34.17 2.52
4679 6391 5.880054 TGGATCGTCTTTCCTTTCATTTC 57.120 39.130 0.00 0.00 34.17 2.17
4693 6409 4.150804 GCCTCTTCGATATTTTGGATCGTC 59.849 45.833 5.08 0.00 45.09 4.20
4723 6439 4.398319 TCCTTCGGCTTGAGATTTTCTTT 58.602 39.130 0.00 0.00 0.00 2.52
4725 6441 3.703001 TCCTTCGGCTTGAGATTTTCT 57.297 42.857 0.00 0.00 0.00 2.52
4726 6442 4.766404 TTTCCTTCGGCTTGAGATTTTC 57.234 40.909 0.00 0.00 0.00 2.29
4727 6443 5.529581 TTTTTCCTTCGGCTTGAGATTTT 57.470 34.783 0.00 0.00 0.00 1.82
4967 6691 1.730902 CCGCAGTCGCCGATGATAG 60.731 63.158 0.00 0.00 33.11 2.08


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

AutoCloner maintained by Alex Coulton.