Multiple sequence alignment - TraesCS2A01G519600

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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 TraesCS2A01G519600 chr2A 100.000 7546 0 0 1 7546 742726950 742719405 0.000000e+00 13935.0
1 TraesCS2A01G519600 chr2A 89.600 250 25 1 4232 4481 549697318 549697070 4.390000e-82 316.0
2 TraesCS2A01G519600 chr2D 95.664 5327 162 29 1553 6836 609780450 609775150 0.000000e+00 8493.0
3 TraesCS2A01G519600 chr2D 84.153 1546 123 59 22 1507 609781946 609780463 0.000000e+00 1386.0
4 TraesCS2A01G519600 chr2D 93.363 678 19 11 6892 7546 609775122 609774448 0.000000e+00 979.0
5 TraesCS2A01G519600 chr2D 90.283 247 21 3 4232 4477 332086858 332086614 3.400000e-83 320.0
6 TraesCS2A01G519600 chr2D 89.328 253 25 2 4226 4478 513258599 513258849 4.390000e-82 316.0
7 TraesCS2A01G519600 chr2B 95.800 3143 92 15 1553 4676 744172126 744169005 0.000000e+00 5036.0
8 TraesCS2A01G519600 chr2B 95.208 2191 74 12 4672 6836 744168758 744166573 0.000000e+00 3435.0
9 TraesCS2A01G519600 chr2B 93.431 685 13 11 6891 7546 744166546 744165865 0.000000e+00 987.0
10 TraesCS2A01G519600 chr2B 90.345 725 42 14 795 1507 744172847 744172139 0.000000e+00 926.0
11 TraesCS2A01G519600 chr2B 87.238 525 31 14 240 755 744173348 744172851 3.950000e-157 566.0
12 TraesCS2A01G519600 chr2B 94.175 103 1 3 69 167 744173697 744173596 1.310000e-32 152.0
13 TraesCS2A01G519600 chr6B 90.688 247 22 1 4232 4478 87994328 87994083 2.030000e-85 327.0
14 TraesCS2A01G519600 chr6B 84.239 184 20 3 583 765 525982445 525982270 3.620000e-38 171.0
15 TraesCS2A01G519600 chr6B 98.000 50 0 1 6842 6891 75029843 75029795 1.350000e-12 86.1
16 TraesCS2A01G519600 chr4A 88.550 262 29 1 4221 4482 573362367 573362627 4.390000e-82 316.0
17 TraesCS2A01G519600 chr4A 91.304 161 10 3 4660 4820 150653466 150653310 4.590000e-52 217.0
18 TraesCS2A01G519600 chr4A 89.759 166 17 0 4659 4824 101750320 101750485 5.930000e-51 213.0
19 TraesCS2A01G519600 chr1B 89.919 248 20 3 4232 4479 651275805 651276047 1.580000e-81 315.0
20 TraesCS2A01G519600 chrUn 88.716 257 27 2 4224 4480 67654941 67654687 5.680000e-81 313.0
21 TraesCS2A01G519600 chr5D 91.824 159 9 3 4659 4817 461072756 461072602 1.270000e-52 219.0
22 TraesCS2A01G519600 chr5B 86.000 200 22 3 7034 7227 61352837 61352638 7.670000e-50 209.0
23 TraesCS2A01G519600 chr3B 89.080 174 9 7 4644 4817 605663437 605663274 2.760000e-49 207.0
24 TraesCS2A01G519600 chr3B 88.757 169 14 4 4649 4817 805684947 805684784 1.280000e-47 202.0
25 TraesCS2A01G519600 chr3B 83.696 184 21 3 583 765 826120861 826121036 1.680000e-36 165.0
26 TraesCS2A01G519600 chr6D 89.634 164 13 1 4654 4817 287021498 287021339 9.930000e-49 206.0
27 TraesCS2A01G519600 chr6D 87.363 182 18 3 4646 4826 65394442 65394265 3.570000e-48 204.0
28 TraesCS2A01G519600 chr7B 82.412 199 25 3 583 781 734092410 734092598 1.680000e-36 165.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G519600 chr2A 742719405 742726950 7545 True 13935.000000 13935 100.0000 1 7546 1 chr2A.!!$R2 7545
1 TraesCS2A01G519600 chr2D 609774448 609781946 7498 True 3619.333333 8493 91.0600 22 7546 3 chr2D.!!$R2 7524
2 TraesCS2A01G519600 chr2B 744165865 744173697 7832 True 1850.333333 5036 92.6995 69 7546 6 chr2B.!!$R1 7477


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
865 1072 0.107410 TTTGTGCAAGGACGGACTGT 60.107 50.000 0.00 0.00 0.00 3.55 F
900 1107 0.107654 ACATCAGCTAAAGGGTCGGC 60.108 55.000 0.00 0.00 0.00 5.54 F
1194 1413 1.202533 ACTCAACACCTTCCTGTCACG 60.203 52.381 0.00 0.00 0.00 4.35 F
1223 1449 1.203187 TCTGGACACCTTCCTGTAGCT 60.203 52.381 0.00 0.00 46.10 3.32 F
2216 2475 2.034053 TGTGTTTCTTCAATTCCGCACC 59.966 45.455 0.00 0.00 0.00 5.01 F
2354 2613 2.633481 ACCACTTCCACAGGTACTTCTC 59.367 50.000 0.00 0.00 34.60 2.87 F
4050 4314 0.031994 GAAAAGCCAACGTGTGCCAT 59.968 50.000 5.99 0.00 0.00 4.40 F
5624 6192 0.249615 AGTGGATGCATCACCGATCG 60.250 55.000 27.25 8.51 35.87 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 2754 1.604278 GAGCCGGGCTATTGAAATGAC 59.396 52.381 23.92 0.84 39.88 3.06 R
2929 3193 8.941977 TCATAGTGTAAAAACGCACAGATAATT 58.058 29.630 0.00 0.00 0.00 1.40 R
2957 3221 4.219944 ACAATGTTTCTACTCGAGGCACTA 59.780 41.667 18.41 0.00 41.55 2.74 R
3122 3386 5.762825 AGTTGACATATTAGCAATGCCTG 57.237 39.130 0.00 0.00 0.00 4.85 R
3754 4018 1.393883 GCCACGAGAGAAATTCCGTTC 59.606 52.381 0.00 0.00 32.71 3.95 R
4191 4455 1.923864 GTTGGGTGCAACTTTTTGACG 59.076 47.619 0.00 0.00 36.74 4.35 R
6009 6577 1.043816 CGGCCTCCATCAGTAGTCAT 58.956 55.000 0.00 0.00 0.00 3.06 R
6767 7344 0.801251 GGCTCAGTGATGTGCAACTC 59.199 55.000 5.34 0.00 38.04 3.01 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
19 20 4.340246 CAGCAGCAGCCAGACCCA 62.340 66.667 0.00 0.00 43.56 4.51
20 21 4.031129 AGCAGCAGCCAGACCCAG 62.031 66.667 0.00 0.00 43.56 4.45
25 26 2.930019 CAGCCAGACCCAGACCCA 60.930 66.667 0.00 0.00 0.00 4.51
40 41 4.340246 CCAGACCCAGCAGCAGCA 62.340 66.667 3.17 0.00 45.49 4.41
42 43 2.282040 AGACCCAGCAGCAGCAAC 60.282 61.111 3.17 0.00 45.49 4.17
43 44 3.368571 GACCCAGCAGCAGCAACC 61.369 66.667 3.17 0.00 45.49 3.77
45 46 4.980702 CCCAGCAGCAGCAACCCA 62.981 66.667 3.17 0.00 45.49 4.51
46 47 2.913578 CCAGCAGCAGCAACCCAA 60.914 61.111 3.17 0.00 45.49 4.12
47 48 2.649034 CAGCAGCAGCAACCCAAG 59.351 61.111 3.17 0.00 45.49 3.61
48 49 3.300765 AGCAGCAGCAACCCAAGC 61.301 61.111 3.17 0.00 45.49 4.01
49 50 4.368543 GCAGCAGCAACCCAAGCC 62.369 66.667 0.00 0.00 41.58 4.35
50 51 4.047059 CAGCAGCAACCCAAGCCG 62.047 66.667 0.00 0.00 0.00 5.52
119 128 3.120191 CCTACCACCCTCCCTCCT 58.880 66.667 0.00 0.00 0.00 3.69
169 178 2.204306 CCTCCCCTTCCCCCAACT 60.204 66.667 0.00 0.00 0.00 3.16
171 180 2.609610 TCCCCTTCCCCCAACTCG 60.610 66.667 0.00 0.00 0.00 4.18
172 181 4.426313 CCCCTTCCCCCAACTCGC 62.426 72.222 0.00 0.00 0.00 5.03
174 183 4.426313 CCTTCCCCCAACTCGCCC 62.426 72.222 0.00 0.00 0.00 6.13
283 469 2.590645 CGTCTCCTCCTCCCTCGA 59.409 66.667 0.00 0.00 0.00 4.04
405 592 4.711949 CGCTTGGTGCTGCTCCCT 62.712 66.667 17.31 0.00 40.11 4.20
406 593 3.060615 GCTTGGTGCTGCTCCCTG 61.061 66.667 17.31 11.04 38.95 4.45
407 594 3.060615 CTTGGTGCTGCTCCCTGC 61.061 66.667 17.31 0.00 43.25 4.85
408 595 4.666253 TTGGTGCTGCTCCCTGCC 62.666 66.667 17.31 3.24 42.00 4.85
594 783 2.774774 CGCAGAGTTTCAGCGCTC 59.225 61.111 7.13 0.00 44.73 5.03
650 849 5.041940 CCGCTCCACTTTACTTACTGTATC 58.958 45.833 0.00 0.00 0.00 2.24
662 862 9.483489 TTTACTTACTGTATCAGGATTCTACCA 57.517 33.333 1.90 0.00 35.51 3.25
666 866 6.919775 ACTGTATCAGGATTCTACCATACC 57.080 41.667 1.90 0.00 35.51 2.73
704 904 0.247460 GGCTTCCCAATTTGAGTGCC 59.753 55.000 0.00 2.91 0.00 5.01
707 907 0.189574 TTCCCAATTTGAGTGCCCCA 59.810 50.000 0.00 0.00 0.00 4.96
718 918 0.853530 AGTGCCCCAGTTCCTTTTCT 59.146 50.000 0.00 0.00 0.00 2.52
731 938 1.880027 CCTTTTCTGTGTGCCACTACC 59.120 52.381 0.00 0.00 35.11 3.18
755 962 6.589907 CCGCATTTGTGCTACATCTATATGTA 59.410 38.462 1.46 1.46 44.66 2.29
756 963 7.278646 CCGCATTTGTGCTACATCTATATGTAT 59.721 37.037 1.78 0.00 45.33 2.29
757 964 9.301153 CGCATTTGTGCTACATCTATATGTATA 57.699 33.333 1.78 0.00 45.33 1.47
787 994 4.442893 GGCTTACCTTGCAACTTCCTTTTT 60.443 41.667 0.00 0.00 0.00 1.94
790 997 6.681865 GCTTACCTTGCAACTTCCTTTTTGTA 60.682 38.462 0.00 0.00 0.00 2.41
865 1072 0.107410 TTTGTGCAAGGACGGACTGT 60.107 50.000 0.00 0.00 0.00 3.55
878 1085 0.534203 GGACTGTGGACGGCTTTTGA 60.534 55.000 0.00 0.00 0.00 2.69
881 1088 1.021202 CTGTGGACGGCTTTTGACAA 58.979 50.000 0.00 0.00 0.00 3.18
900 1107 0.107654 ACATCAGCTAAAGGGTCGGC 60.108 55.000 0.00 0.00 0.00 5.54
932 1139 1.561542 AGTTATTGGAGCTGTGGAGGG 59.438 52.381 0.00 0.00 0.00 4.30
946 1153 2.284258 AGGGTCTCTCGCCAGCTT 60.284 61.111 0.00 0.00 0.00 3.74
1042 1249 6.923508 GGACTTTAAGAGGTTGGTCATTTTTG 59.076 38.462 0.00 0.00 0.00 2.44
1050 1257 7.334858 AGAGGTTGGTCATTTTTGCTTAAAAA 58.665 30.769 0.00 0.00 39.08 1.94
1121 1328 7.386059 ACTTTGAAGTGACAATGTTTTCCTTT 58.614 30.769 0.00 0.00 37.98 3.11
1122 1329 7.877612 ACTTTGAAGTGACAATGTTTTCCTTTT 59.122 29.630 0.00 0.00 37.98 2.27
1123 1330 8.614469 TTTGAAGTGACAATGTTTTCCTTTTT 57.386 26.923 0.00 0.00 0.00 1.94
1124 1331 7.826260 TGAAGTGACAATGTTTTCCTTTTTC 57.174 32.000 0.00 0.00 0.00 2.29
1125 1332 6.816140 TGAAGTGACAATGTTTTCCTTTTTCC 59.184 34.615 0.00 0.00 0.00 3.13
1126 1333 6.544928 AGTGACAATGTTTTCCTTTTTCCT 57.455 33.333 0.00 0.00 0.00 3.36
1127 1334 6.573434 AGTGACAATGTTTTCCTTTTTCCTC 58.427 36.000 0.00 0.00 0.00 3.71
1128 1335 6.381133 AGTGACAATGTTTTCCTTTTTCCTCT 59.619 34.615 0.00 0.00 0.00 3.69
1132 1351 7.619965 ACAATGTTTTCCTTTTTCCTCTTTCA 58.380 30.769 0.00 0.00 0.00 2.69
1175 1394 7.900782 TCTTAAGCCTGAACATTTGTAGTAC 57.099 36.000 0.00 0.00 0.00 2.73
1177 1396 7.817962 TCTTAAGCCTGAACATTTGTAGTACTC 59.182 37.037 0.00 0.00 0.00 2.59
1178 1397 5.483685 AGCCTGAACATTTGTAGTACTCA 57.516 39.130 0.00 0.00 0.00 3.41
1179 1398 5.865085 AGCCTGAACATTTGTAGTACTCAA 58.135 37.500 0.00 0.93 0.00 3.02
1180 1399 5.701290 AGCCTGAACATTTGTAGTACTCAAC 59.299 40.000 0.00 0.00 0.00 3.18
1181 1400 5.468746 GCCTGAACATTTGTAGTACTCAACA 59.531 40.000 0.00 0.00 0.00 3.33
1182 1401 6.565999 GCCTGAACATTTGTAGTACTCAACAC 60.566 42.308 0.00 0.00 0.00 3.32
1183 1402 6.073222 CCTGAACATTTGTAGTACTCAACACC 60.073 42.308 0.00 0.00 0.00 4.16
1184 1403 6.588204 TGAACATTTGTAGTACTCAACACCT 58.412 36.000 0.00 0.00 0.00 4.00
1185 1404 7.051623 TGAACATTTGTAGTACTCAACACCTT 58.948 34.615 0.00 0.00 0.00 3.50
1186 1405 7.225931 TGAACATTTGTAGTACTCAACACCTTC 59.774 37.037 0.00 0.00 0.00 3.46
1187 1406 5.995897 ACATTTGTAGTACTCAACACCTTCC 59.004 40.000 0.00 0.00 0.00 3.46
1188 1407 5.881923 TTTGTAGTACTCAACACCTTCCT 57.118 39.130 0.00 0.00 0.00 3.36
1189 1408 4.866508 TGTAGTACTCAACACCTTCCTG 57.133 45.455 0.00 0.00 0.00 3.86
1190 1409 4.220724 TGTAGTACTCAACACCTTCCTGT 58.779 43.478 0.00 0.00 0.00 4.00
1191 1410 4.280174 TGTAGTACTCAACACCTTCCTGTC 59.720 45.833 0.00 0.00 0.00 3.51
1194 1413 1.202533 ACTCAACACCTTCCTGTCACG 60.203 52.381 0.00 0.00 0.00 4.35
1223 1449 1.203187 TCTGGACACCTTCCTGTAGCT 60.203 52.381 0.00 0.00 46.10 3.32
1227 1453 2.427506 GACACCTTCCTGTAGCTTTGG 58.572 52.381 0.00 0.00 0.00 3.28
1250 1476 7.766628 TGGTTCTCTCCTGTATATAGTGGTAT 58.233 38.462 0.00 0.00 0.00 2.73
1255 1481 8.110271 TCTCTCCTGTATATAGTGGTATTCCTG 58.890 40.741 0.00 0.00 34.23 3.86
1339 1566 2.123554 GGTACCCCCTCGTCCGAT 60.124 66.667 0.00 0.00 0.00 4.18
1383 1642 7.680730 TGTCTTTCTTAGCTTCAATAGGTCTT 58.319 34.615 0.00 0.00 35.80 3.01
1461 1720 6.610741 AGAAATCGATAAAGCCAGTCATTC 57.389 37.500 0.00 0.00 0.00 2.67
1477 1736 6.087555 CCAGTCATTCGTTTTACATTTTTCCG 59.912 38.462 0.00 0.00 0.00 4.30
1490 1749 5.280945 ACATTTTTCCGTCATGTTGAACAG 58.719 37.500 3.74 0.00 0.00 3.16
1525 1784 7.927092 GGTTTTACTTTTACCCATTTTGCTGTA 59.073 33.333 0.00 0.00 0.00 2.74
1526 1785 9.315525 GTTTTACTTTTACCCATTTTGCTGTAA 57.684 29.630 0.00 0.00 0.00 2.41
1527 1786 9.535878 TTTTACTTTTACCCATTTTGCTGTAAG 57.464 29.630 0.00 0.00 0.00 2.34
1528 1787 6.969993 ACTTTTACCCATTTTGCTGTAAGA 57.030 33.333 0.00 0.00 34.07 2.10
1529 1788 6.981722 ACTTTTACCCATTTTGCTGTAAGAG 58.018 36.000 0.00 0.00 34.07 2.85
1530 1789 6.549736 ACTTTTACCCATTTTGCTGTAAGAGT 59.450 34.615 0.00 0.00 35.22 3.24
1531 1790 6.969993 TTTACCCATTTTGCTGTAAGAGTT 57.030 33.333 0.00 0.00 34.07 3.01
1532 1791 4.853924 ACCCATTTTGCTGTAAGAGTTG 57.146 40.909 0.00 0.00 34.07 3.16
1533 1792 3.005791 ACCCATTTTGCTGTAAGAGTTGC 59.994 43.478 0.00 0.00 34.07 4.17
1534 1793 3.005684 CCCATTTTGCTGTAAGAGTTGCA 59.994 43.478 0.00 0.00 34.07 4.08
1535 1794 4.322198 CCCATTTTGCTGTAAGAGTTGCAT 60.322 41.667 0.00 0.00 34.07 3.96
1536 1795 4.860907 CCATTTTGCTGTAAGAGTTGCATC 59.139 41.667 0.00 0.00 34.07 3.91
1537 1796 5.463286 CATTTTGCTGTAAGAGTTGCATCA 58.537 37.500 0.00 0.00 34.07 3.07
1538 1797 5.710513 TTTTGCTGTAAGAGTTGCATCAT 57.289 34.783 0.00 0.00 34.07 2.45
1539 1798 4.690184 TTGCTGTAAGAGTTGCATCATG 57.310 40.909 0.00 0.00 34.07 3.07
1540 1799 3.678289 TGCTGTAAGAGTTGCATCATGT 58.322 40.909 0.00 0.00 34.07 3.21
1541 1800 4.074259 TGCTGTAAGAGTTGCATCATGTT 58.926 39.130 0.00 0.00 34.07 2.71
1542 1801 4.520111 TGCTGTAAGAGTTGCATCATGTTT 59.480 37.500 0.00 0.00 34.07 2.83
1543 1802 5.704978 TGCTGTAAGAGTTGCATCATGTTTA 59.295 36.000 0.00 0.00 34.07 2.01
1544 1803 6.375174 TGCTGTAAGAGTTGCATCATGTTTAT 59.625 34.615 0.00 0.00 34.07 1.40
1545 1804 7.094248 TGCTGTAAGAGTTGCATCATGTTTATT 60.094 33.333 0.00 0.00 34.07 1.40
1546 1805 7.430502 GCTGTAAGAGTTGCATCATGTTTATTC 59.569 37.037 0.00 0.00 34.07 1.75
1547 1806 7.761409 TGTAAGAGTTGCATCATGTTTATTCC 58.239 34.615 0.00 0.00 0.00 3.01
1548 1807 7.611467 TGTAAGAGTTGCATCATGTTTATTCCT 59.389 33.333 0.00 0.00 0.00 3.36
1549 1808 9.109393 GTAAGAGTTGCATCATGTTTATTCCTA 57.891 33.333 0.00 0.00 0.00 2.94
1550 1809 7.798596 AGAGTTGCATCATGTTTATTCCTAG 57.201 36.000 0.00 0.00 0.00 3.02
1551 1810 7.568349 AGAGTTGCATCATGTTTATTCCTAGA 58.432 34.615 0.00 0.00 0.00 2.43
1659 1918 3.214328 TCATAGCACTCTATCAGACGCA 58.786 45.455 0.00 0.00 33.37 5.24
1731 1990 2.359848 ACTTTTGTTTAACCGTGGGCTC 59.640 45.455 0.00 0.00 0.00 4.70
2100 2359 3.173965 CCACTCTTCTTCTTCCTACCCA 58.826 50.000 0.00 0.00 0.00 4.51
2216 2475 2.034053 TGTGTTTCTTCAATTCCGCACC 59.966 45.455 0.00 0.00 0.00 5.01
2300 2559 5.336990 GCTAATTGCGATGCGTTACATTAAG 59.663 40.000 0.00 0.00 39.84 1.85
2354 2613 2.633481 ACCACTTCCACAGGTACTTCTC 59.367 50.000 0.00 0.00 34.60 2.87
2434 2697 9.528018 CTGAAACAATAAGCCTTTTCTTTTACA 57.472 29.630 0.00 0.00 0.00 2.41
2603 2867 9.317936 CTATGATTACTGCATACTTCAAGACAA 57.682 33.333 0.00 0.00 0.00 3.18
2928 3192 7.656412 TCTTCATCTAGAGAGCATTATCACAC 58.344 38.462 0.00 0.00 0.00 3.82
2929 3193 6.966534 TCATCTAGAGAGCATTATCACACA 57.033 37.500 0.00 0.00 0.00 3.72
2957 3221 6.795098 TCTGTGCGTTTTTACACTATGATT 57.205 33.333 0.00 0.00 37.68 2.57
3122 3386 8.092521 AGATTGTGCATAATACTCTACATTGC 57.907 34.615 8.83 0.00 0.00 3.56
3273 3537 3.991773 TGAACATAGTTTGTCGTAGGTGC 59.008 43.478 0.00 0.00 37.68 5.01
3289 3553 3.771216 AGGTGCTCATGTTTTCCTTGAT 58.229 40.909 0.00 0.00 0.00 2.57
3291 3555 5.324409 AGGTGCTCATGTTTTCCTTGATTA 58.676 37.500 0.00 0.00 0.00 1.75
3672 3936 9.574458 CCGTACATCTGTTCATTATTCTATAGG 57.426 37.037 0.00 0.00 0.00 2.57
3733 3997 4.755123 ACTCTGATTTAAACAGTTCCCACG 59.245 41.667 13.77 0.00 36.81 4.94
3810 4074 1.363744 CATTTCACTCCCTGTCTCGC 58.636 55.000 0.00 0.00 0.00 5.03
3924 4188 4.461781 TCTTAGAGACCCGTAAAGGAACTG 59.538 45.833 0.00 0.00 45.00 3.16
3968 4232 4.275689 TGCTGTGGCATACATATAACTTGC 59.724 41.667 0.00 0.00 44.28 4.01
4050 4314 0.031994 GAAAAGCCAACGTGTGCCAT 59.968 50.000 5.99 0.00 0.00 4.40
4191 4455 3.435105 TTCAAATATGATTGCCGTGGC 57.565 42.857 3.30 3.30 37.22 5.01
4343 4639 4.838986 CACTAGGGCCCTACATTACATACT 59.161 45.833 28.66 1.35 0.00 2.12
4459 4755 1.401318 AAGTGTGGCAATGCAAGGCA 61.401 50.000 13.61 13.61 44.86 4.75
4481 4777 3.322191 AGAACCAAACAGCCCCTTAAA 57.678 42.857 0.00 0.00 0.00 1.52
4526 4822 6.916440 ACACTTTTTGATTATCGGGGTTTAC 58.084 36.000 0.00 0.00 0.00 2.01
4545 4841 6.427242 GGTTTACAGAGAACTAAAGGGAACTG 59.573 42.308 0.00 0.00 42.68 3.16
4582 4878 1.537202 GGTTTCCTGTTGTGCTAGCTG 59.463 52.381 17.23 0.00 0.00 4.24
4583 4879 1.068954 GTTTCCTGTTGTGCTAGCTGC 60.069 52.381 17.23 9.49 43.25 5.25
4584 4880 0.606401 TTCCTGTTGTGCTAGCTGCC 60.606 55.000 17.23 4.50 42.00 4.85
4585 4881 1.002868 CCTGTTGTGCTAGCTGCCT 60.003 57.895 17.23 0.00 42.00 4.75
4586 4882 0.250234 CCTGTTGTGCTAGCTGCCTA 59.750 55.000 17.23 0.00 42.00 3.93
4587 4883 1.649664 CTGTTGTGCTAGCTGCCTAG 58.350 55.000 17.23 5.45 43.23 3.02
4652 4948 7.263100 TGCCTTTAACAGAATGCATATACTG 57.737 36.000 19.70 19.70 42.53 2.74
4698 5245 8.829373 AAGCCCTTTTAGATATTTCAATCACT 57.171 30.769 0.00 0.00 0.00 3.41
4795 5342 7.497909 CCGTATTGGAATCTCTAAAAAGGCTTA 59.502 37.037 0.00 0.00 42.00 3.09
4833 5380 4.282195 GGGAGTACTAGTCATCCAAGATGG 59.718 50.000 21.72 0.00 39.43 3.51
4913 5460 4.486125 AAACCAGCCTGTTCACATTTTT 57.514 36.364 0.00 0.00 0.00 1.94
4950 5497 9.793252 TCATGAAATCTAGCAAAAGCTATTTTC 57.207 29.630 17.29 17.29 36.47 2.29
5038 5597 3.954200 TGAGCAGCTATCATTGTTTGGA 58.046 40.909 0.00 0.00 0.00 3.53
5129 5688 8.335532 TGGACCTTCAGTGTATAGAATTTTTG 57.664 34.615 0.00 0.00 0.00 2.44
5174 5733 9.582223 CGTTTTACTAGATCTTTTGTGAGTTTC 57.418 33.333 0.00 0.00 0.00 2.78
5241 5809 6.753107 AAAATAGCAGCTAACGTGGTAATT 57.247 33.333 6.13 0.00 31.96 1.40
5342 5910 9.290988 TGTGCTTGATATGTTTAACTTCCTTTA 57.709 29.630 0.00 0.00 0.00 1.85
5624 6192 0.249615 AGTGGATGCATCACCGATCG 60.250 55.000 27.25 8.51 35.87 3.69
5852 6420 1.039856 TTTCCTCCTGTTTTGCTGCC 58.960 50.000 0.00 0.00 0.00 4.85
6009 6577 3.199442 TCCATGGTTCCTTGGAGAGTA 57.801 47.619 18.53 1.44 36.00 2.59
6146 6714 0.599558 CGGTTTCGTCCAGGACAGTA 59.400 55.000 20.13 1.20 32.09 2.74
6257 6825 1.336755 GTTCAGCACACATTCCGGTTT 59.663 47.619 0.00 0.00 0.00 3.27
6263 6831 2.412325 GCACACATTCCGGTTTTACTCG 60.412 50.000 0.00 0.00 0.00 4.18
6269 6837 0.669318 TCCGGTTTTACTCGCAGCAG 60.669 55.000 0.00 0.00 0.00 4.24
6278 6846 2.917227 TCGCAGCAGTGGAGGACA 60.917 61.111 0.00 0.00 0.00 4.02
6362 6930 2.042435 CGGAGGGAAGAGGAGGCT 60.042 66.667 0.00 0.00 0.00 4.58
6529 7100 1.289109 CCAGATTTTGGCGTCGACGT 61.289 55.000 35.48 17.63 40.87 4.34
6639 7210 3.798337 ACAAAATTCAAAAGACAGCAGCG 59.202 39.130 0.00 0.00 0.00 5.18
6732 7303 4.981806 TGTTTCAGTTTTGCTACTTGCT 57.018 36.364 0.00 0.00 43.37 3.91
6745 7316 1.484038 ACTTGCTGGTTGCCTGAAAA 58.516 45.000 0.00 0.00 42.00 2.29
6767 7344 0.543277 TTGATGCCTCTGCCACCTAG 59.457 55.000 0.00 0.00 36.33 3.02
6787 7364 0.607489 AGTTGCACATCACTGAGCCC 60.607 55.000 0.00 0.00 38.09 5.19
6797 7376 0.883833 CACTGAGCCCAAAAATCGCT 59.116 50.000 0.00 0.00 34.97 4.93
6836 7416 6.528826 CAAGACTGTGACGACATCAAAATAG 58.471 40.000 0.00 0.00 39.72 1.73
6837 7417 6.025749 AGACTGTGACGACATCAAAATAGA 57.974 37.500 0.00 0.00 39.72 1.98
6838 7418 6.634805 AGACTGTGACGACATCAAAATAGAT 58.365 36.000 0.00 0.00 39.72 1.98
6840 7420 6.398095 ACTGTGACGACATCAAAATAGATGA 58.602 36.000 10.59 0.00 46.51 2.92
6841 7421 7.044181 ACTGTGACGACATCAAAATAGATGAT 58.956 34.615 10.59 0.00 46.51 2.45
6842 7422 7.550551 ACTGTGACGACATCAAAATAGATGATT 59.449 33.333 10.59 0.00 46.51 2.57
6843 7423 8.267620 TGTGACGACATCAAAATAGATGATTT 57.732 30.769 10.59 0.00 46.51 2.17
6844 7424 8.729756 TGTGACGACATCAAAATAGATGATTTT 58.270 29.630 10.59 0.00 46.60 1.82
6879 7459 3.092334 GAGCTTCTCTCTCCGATTTCC 57.908 52.381 0.00 0.00 38.78 3.13
6880 7460 2.428890 GAGCTTCTCTCTCCGATTTCCA 59.571 50.000 0.00 0.00 38.78 3.53
6881 7461 3.037549 AGCTTCTCTCTCCGATTTCCAT 58.962 45.455 0.00 0.00 0.00 3.41
6882 7462 3.454082 AGCTTCTCTCTCCGATTTCCATT 59.546 43.478 0.00 0.00 0.00 3.16
6883 7463 4.651503 AGCTTCTCTCTCCGATTTCCATTA 59.348 41.667 0.00 0.00 0.00 1.90
6884 7464 5.129485 AGCTTCTCTCTCCGATTTCCATTAA 59.871 40.000 0.00 0.00 0.00 1.40
6885 7465 5.235401 GCTTCTCTCTCCGATTTCCATTAAC 59.765 44.000 0.00 0.00 0.00 2.01
6886 7466 5.932619 TCTCTCTCCGATTTCCATTAACA 57.067 39.130 0.00 0.00 0.00 2.41
6889 7469 6.154534 TCTCTCTCCGATTTCCATTAACAGAA 59.845 38.462 0.00 0.00 0.00 3.02
7006 7589 3.728385 AAGAGGTTTCAGGATTCAGGG 57.272 47.619 0.00 0.00 0.00 4.45
7007 7590 2.637165 AGAGGTTTCAGGATTCAGGGT 58.363 47.619 0.00 0.00 0.00 4.34
7009 7592 1.279271 AGGTTTCAGGATTCAGGGTCG 59.721 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.340246 TGGGTCTGGCTGCTGCTG 62.340 66.667 15.64 8.88 39.59 4.41
3 4 4.031129 CTGGGTCTGGCTGCTGCT 62.031 66.667 15.64 0.00 39.59 4.24
4 5 4.025858 TCTGGGTCTGGCTGCTGC 62.026 66.667 7.10 7.10 38.76 5.25
5 6 2.046507 GTCTGGGTCTGGCTGCTG 60.047 66.667 0.00 0.00 0.00 4.41
6 7 3.325753 GGTCTGGGTCTGGCTGCT 61.326 66.667 0.00 0.00 0.00 4.24
7 8 4.416738 GGGTCTGGGTCTGGCTGC 62.417 72.222 0.00 0.00 0.00 5.25
8 9 2.930019 TGGGTCTGGGTCTGGCTG 60.930 66.667 0.00 0.00 0.00 4.85
9 10 2.608988 CTGGGTCTGGGTCTGGCT 60.609 66.667 0.00 0.00 0.00 4.75
10 11 2.607750 TCTGGGTCTGGGTCTGGC 60.608 66.667 0.00 0.00 0.00 4.85
11 12 2.294078 GGTCTGGGTCTGGGTCTGG 61.294 68.421 0.00 0.00 0.00 3.86
12 13 2.294078 GGGTCTGGGTCTGGGTCTG 61.294 68.421 0.00 0.00 0.00 3.51
13 14 2.122954 GGGTCTGGGTCTGGGTCT 59.877 66.667 0.00 0.00 0.00 3.85
14 15 2.203938 TGGGTCTGGGTCTGGGTC 60.204 66.667 0.00 0.00 0.00 4.46
15 16 2.203998 CTGGGTCTGGGTCTGGGT 60.204 66.667 0.00 0.00 0.00 4.51
16 17 3.721706 GCTGGGTCTGGGTCTGGG 61.722 72.222 0.00 0.00 0.00 4.45
17 18 2.930019 TGCTGGGTCTGGGTCTGG 60.930 66.667 0.00 0.00 0.00 3.86
18 19 2.667418 CTGCTGGGTCTGGGTCTG 59.333 66.667 0.00 0.00 0.00 3.51
19 20 3.325753 GCTGCTGGGTCTGGGTCT 61.326 66.667 0.00 0.00 0.00 3.85
20 21 3.618780 CTGCTGCTGGGTCTGGGTC 62.619 68.421 0.00 0.00 0.00 4.46
25 26 2.282040 GTTGCTGCTGCTGGGTCT 60.282 61.111 17.00 0.00 40.48 3.85
153 162 2.670148 CGAGTTGGGGGAAGGGGAG 61.670 68.421 0.00 0.00 0.00 4.30
185 194 4.787280 AGGTCTGGAGGGGAGCGG 62.787 72.222 0.00 0.00 36.47 5.52
264 447 2.835895 GAGGGAGGAGGAGACGGC 60.836 72.222 0.00 0.00 0.00 5.68
327 513 1.734885 CAGCATCAAATTCGCTACGC 58.265 50.000 0.00 0.00 33.82 4.42
328 514 1.595489 GGCAGCATCAAATTCGCTACG 60.595 52.381 0.00 0.00 33.82 3.51
329 515 1.401552 TGGCAGCATCAAATTCGCTAC 59.598 47.619 0.00 0.00 33.82 3.58
330 516 1.748950 TGGCAGCATCAAATTCGCTA 58.251 45.000 0.00 0.00 33.82 4.26
331 517 1.108776 ATGGCAGCATCAAATTCGCT 58.891 45.000 0.00 0.00 36.10 4.93
332 518 1.205657 CATGGCAGCATCAAATTCGC 58.794 50.000 0.00 0.00 0.00 4.70
333 519 1.847818 CCATGGCAGCATCAAATTCG 58.152 50.000 0.00 0.00 0.00 3.34
389 576 3.060615 CAGGGAGCAGCACCAAGC 61.061 66.667 11.40 0.00 46.19 4.01
400 587 3.905678 CTACGAGCCGGCAGGGAG 61.906 72.222 31.54 21.75 38.47 4.30
401 588 3.733507 ATCTACGAGCCGGCAGGGA 62.734 63.158 31.54 22.14 38.47 4.20
402 589 3.214250 GATCTACGAGCCGGCAGGG 62.214 68.421 31.54 19.35 38.20 4.45
403 590 2.196925 AGATCTACGAGCCGGCAGG 61.197 63.158 31.54 22.14 41.62 4.85
404 591 1.007964 CAGATCTACGAGCCGGCAG 60.008 63.158 31.54 24.30 0.00 4.85
405 592 2.490148 CCAGATCTACGAGCCGGCA 61.490 63.158 31.54 6.82 0.00 5.69
406 593 1.528292 ATCCAGATCTACGAGCCGGC 61.528 60.000 21.89 21.89 0.00 6.13
407 594 0.523966 GATCCAGATCTACGAGCCGG 59.476 60.000 0.00 0.00 35.04 6.13
408 595 1.198867 CTGATCCAGATCTACGAGCCG 59.801 57.143 8.99 0.00 38.60 5.52
650 849 3.244112 GGAACGGGTATGGTAGAATCCTG 60.244 52.174 0.00 0.00 0.00 3.86
662 862 6.531021 CCTGATACATTTAAGGAACGGGTAT 58.469 40.000 0.00 0.00 30.92 2.73
666 866 4.451900 AGCCTGATACATTTAAGGAACGG 58.548 43.478 0.00 0.00 30.92 4.44
704 904 1.338020 GCACACAGAAAAGGAACTGGG 59.662 52.381 0.00 0.00 40.86 4.45
731 938 6.471976 ACATATAGATGTAGCACAAATGCG 57.528 37.500 0.00 0.00 46.84 4.73
755 962 4.712051 TGCAAGGTAAGCCTCATCATAT 57.288 40.909 0.00 0.00 46.33 1.78
756 963 4.080356 AGTTGCAAGGTAAGCCTCATCATA 60.080 41.667 0.00 0.00 46.33 2.15
757 964 3.019564 GTTGCAAGGTAAGCCTCATCAT 58.980 45.455 0.00 0.00 46.33 2.45
758 965 2.040278 AGTTGCAAGGTAAGCCTCATCA 59.960 45.455 0.00 0.00 46.33 3.07
759 966 2.716217 AGTTGCAAGGTAAGCCTCATC 58.284 47.619 0.00 0.00 46.33 2.92
760 967 2.887151 AGTTGCAAGGTAAGCCTCAT 57.113 45.000 0.00 0.00 46.33 2.90
764 971 1.911057 AGGAAGTTGCAAGGTAAGCC 58.089 50.000 0.00 0.00 0.00 4.35
865 1072 1.606668 GATGTTGTCAAAAGCCGTCCA 59.393 47.619 0.00 0.00 0.00 4.02
878 1085 2.615493 CCGACCCTTTAGCTGATGTTGT 60.615 50.000 0.00 0.00 0.00 3.32
881 1088 0.107654 GCCGACCCTTTAGCTGATGT 60.108 55.000 0.00 0.00 0.00 3.06
900 1107 4.261489 GCTCCAATAACTGCCATCAATCAG 60.261 45.833 0.00 0.00 36.45 2.90
932 1139 1.357991 GAGCAAAGCTGGCGAGAGAC 61.358 60.000 0.00 0.00 39.88 3.36
946 1153 3.347216 GGCTATGTCAAAGGAAGAGCAA 58.653 45.455 0.00 0.00 0.00 3.91
1042 1249 2.354109 GCAGGAGTGCCTTTTTAAGC 57.646 50.000 0.00 0.00 43.90 3.09
1101 1308 7.041721 AGGAAAAAGGAAAACATTGTCACTTC 58.958 34.615 0.00 0.00 0.00 3.01
1121 1328 5.471116 CAGTCATGACATGTGAAAGAGGAAA 59.529 40.000 27.02 0.00 0.00 3.13
1122 1329 4.999311 CAGTCATGACATGTGAAAGAGGAA 59.001 41.667 27.02 0.00 0.00 3.36
1123 1330 4.040829 ACAGTCATGACATGTGAAAGAGGA 59.959 41.667 27.02 0.00 0.00 3.71
1124 1331 4.321718 ACAGTCATGACATGTGAAAGAGG 58.678 43.478 27.02 4.78 0.00 3.69
1125 1332 4.992951 TGACAGTCATGACATGTGAAAGAG 59.007 41.667 27.02 6.50 0.00 2.85
1126 1333 4.959723 TGACAGTCATGACATGTGAAAGA 58.040 39.130 27.02 0.00 0.00 2.52
1127 1334 5.678132 TTGACAGTCATGACATGTGAAAG 57.322 39.130 27.02 8.82 31.23 2.62
1128 1335 6.487668 AGAATTGACAGTCATGACATGTGAAA 59.512 34.615 27.02 20.32 31.23 2.69
1132 1351 7.361542 GCTTAAGAATTGACAGTCATGACATGT 60.362 37.037 27.02 24.50 31.23 3.21
1175 1394 1.068588 TCGTGACAGGAAGGTGTTGAG 59.931 52.381 0.00 0.00 0.00 3.02
1177 1396 1.948104 TTCGTGACAGGAAGGTGTTG 58.052 50.000 6.48 0.00 0.00 3.33
1178 1397 2.930826 ATTCGTGACAGGAAGGTGTT 57.069 45.000 15.17 0.00 0.00 3.32
1179 1398 2.930826 AATTCGTGACAGGAAGGTGT 57.069 45.000 15.17 0.00 0.00 4.16
1180 1399 3.403038 AGAAATTCGTGACAGGAAGGTG 58.597 45.455 15.17 0.00 0.00 4.00
1181 1400 3.325135 AGAGAAATTCGTGACAGGAAGGT 59.675 43.478 15.17 6.32 0.00 3.50
1182 1401 3.929610 GAGAGAAATTCGTGACAGGAAGG 59.070 47.826 15.17 0.00 0.00 3.46
1183 1402 4.624882 CAGAGAGAAATTCGTGACAGGAAG 59.375 45.833 15.17 0.00 0.00 3.46
1184 1403 4.560128 CAGAGAGAAATTCGTGACAGGAA 58.440 43.478 12.62 12.62 0.00 3.36
1185 1404 3.056536 CCAGAGAGAAATTCGTGACAGGA 60.057 47.826 0.00 0.00 0.00 3.86
1186 1405 3.056536 TCCAGAGAGAAATTCGTGACAGG 60.057 47.826 0.00 0.00 0.00 4.00
1187 1406 3.923461 GTCCAGAGAGAAATTCGTGACAG 59.077 47.826 0.00 0.00 0.00 3.51
1188 1407 3.320826 TGTCCAGAGAGAAATTCGTGACA 59.679 43.478 0.00 0.00 31.89 3.58
1189 1408 3.675698 GTGTCCAGAGAGAAATTCGTGAC 59.324 47.826 0.00 0.00 0.00 3.67
1190 1409 3.306088 GGTGTCCAGAGAGAAATTCGTGA 60.306 47.826 0.00 0.00 0.00 4.35
1191 1410 2.996621 GGTGTCCAGAGAGAAATTCGTG 59.003 50.000 0.00 0.00 0.00 4.35
1194 1413 4.257731 GGAAGGTGTCCAGAGAGAAATTC 58.742 47.826 0.00 0.00 46.97 2.17
1223 1449 6.901300 ACCACTATATACAGGAGAGAACCAAA 59.099 38.462 3.32 0.00 0.00 3.28
1227 1453 8.741841 GGAATACCACTATATACAGGAGAGAAC 58.258 40.741 3.32 0.00 35.97 3.01
1255 1481 3.181575 GCAAAAGTGTATGTTTCGGCAAC 59.818 43.478 0.00 0.00 35.71 4.17
1339 1566 2.906389 ACAGTGAGAAAGATGCCAGGTA 59.094 45.455 0.00 0.00 0.00 3.08
1398 1657 7.737869 TGACATAACTCTTACAGGTAAAACCA 58.262 34.615 0.00 0.00 41.95 3.67
1443 1702 3.520290 ACGAATGACTGGCTTTATCGA 57.480 42.857 0.00 0.00 33.42 3.59
1447 1706 6.811253 ATGTAAAACGAATGACTGGCTTTA 57.189 33.333 0.00 0.00 0.00 1.85
1461 1720 6.415280 TCAACATGACGGAAAAATGTAAAACG 59.585 34.615 0.00 0.00 33.48 3.60
1477 1736 5.473504 ACCCAGTTTATCTGTTCAACATGAC 59.526 40.000 0.00 0.00 42.19 3.06
1502 1761 8.915036 TCTTACAGCAAAATGGGTAAAAGTAAA 58.085 29.630 0.00 0.00 0.00 2.01
1503 1762 8.466617 TCTTACAGCAAAATGGGTAAAAGTAA 57.533 30.769 0.00 0.00 0.00 2.24
1504 1763 7.722285 ACTCTTACAGCAAAATGGGTAAAAGTA 59.278 33.333 0.00 0.00 28.28 2.24
1505 1764 6.549736 ACTCTTACAGCAAAATGGGTAAAAGT 59.450 34.615 0.00 0.00 0.00 2.66
1506 1765 6.981722 ACTCTTACAGCAAAATGGGTAAAAG 58.018 36.000 0.00 0.00 0.00 2.27
1507 1766 6.969993 ACTCTTACAGCAAAATGGGTAAAA 57.030 33.333 0.00 0.00 0.00 1.52
1525 1784 8.049117 TCTAGGAATAAACATGATGCAACTCTT 58.951 33.333 0.00 0.00 0.00 2.85
1526 1785 7.568349 TCTAGGAATAAACATGATGCAACTCT 58.432 34.615 0.00 0.00 0.00 3.24
1527 1786 7.792374 TCTAGGAATAAACATGATGCAACTC 57.208 36.000 0.00 0.00 0.00 3.01
1528 1787 8.757982 ATTCTAGGAATAAACATGATGCAACT 57.242 30.769 0.00 0.00 0.00 3.16
1541 1800 9.823647 CTGCTTCTCTGTTTATTCTAGGAATAA 57.176 33.333 8.17 8.17 0.00 1.40
1542 1801 7.928706 GCTGCTTCTCTGTTTATTCTAGGAATA 59.071 37.037 0.00 0.00 0.00 1.75
1543 1802 6.765512 GCTGCTTCTCTGTTTATTCTAGGAAT 59.234 38.462 0.00 0.00 0.00 3.01
1544 1803 6.109359 GCTGCTTCTCTGTTTATTCTAGGAA 58.891 40.000 0.00 0.00 0.00 3.36
1545 1804 5.395768 GGCTGCTTCTCTGTTTATTCTAGGA 60.396 44.000 0.00 0.00 0.00 2.94
1546 1805 4.813697 GGCTGCTTCTCTGTTTATTCTAGG 59.186 45.833 0.00 0.00 0.00 3.02
1547 1806 5.423015 TGGCTGCTTCTCTGTTTATTCTAG 58.577 41.667 0.00 0.00 0.00 2.43
1548 1807 5.046304 ACTGGCTGCTTCTCTGTTTATTCTA 60.046 40.000 0.00 0.00 0.00 2.10
1549 1808 4.260170 CTGGCTGCTTCTCTGTTTATTCT 58.740 43.478 0.00 0.00 0.00 2.40
1550 1809 4.006319 ACTGGCTGCTTCTCTGTTTATTC 58.994 43.478 0.00 0.00 0.00 1.75
1551 1810 4.026356 ACTGGCTGCTTCTCTGTTTATT 57.974 40.909 0.00 0.00 0.00 1.40
1594 1853 5.363562 TTCTACATCATCACTCCAGCATT 57.636 39.130 0.00 0.00 0.00 3.56
1919 2178 2.507407 TGGGGTGCCTAAGTGATTTC 57.493 50.000 0.00 0.00 0.00 2.17
2100 2359 5.571784 ATGCAATTTGAGTTGTCGATGAT 57.428 34.783 0.00 0.00 0.00 2.45
2216 2475 3.201290 AGAAGATGGAGCAACATAAGCG 58.799 45.455 0.00 0.00 37.01 4.68
2300 2559 8.231161 GCAAAGAAGTCCATTAGAAAGTAACTC 58.769 37.037 0.00 0.00 0.00 3.01
2441 2704 9.738832 GTGTAAAAGCACTTAAAAGGTTTATCA 57.261 29.630 4.91 5.18 34.69 2.15
2491 2754 1.604278 GAGCCGGGCTATTGAAATGAC 59.396 52.381 23.92 0.84 39.88 3.06
2928 3192 8.998989 CATAGTGTAAAAACGCACAGATAATTG 58.001 33.333 0.00 0.00 0.00 2.32
2929 3193 8.941977 TCATAGTGTAAAAACGCACAGATAATT 58.058 29.630 0.00 0.00 0.00 1.40
2957 3221 4.219944 ACAATGTTTCTACTCGAGGCACTA 59.780 41.667 18.41 0.00 41.55 2.74
3122 3386 5.762825 AGTTGACATATTAGCAATGCCTG 57.237 39.130 0.00 0.00 0.00 4.85
3230 3494 9.399797 TGTTCAGAGAATTATGCTTAACATGAT 57.600 29.630 0.00 0.00 40.06 2.45
3273 3537 6.209391 ACAGGGTTAATCAAGGAAAACATGAG 59.791 38.462 0.00 0.00 29.25 2.90
3289 3553 8.885722 CAGCGTATAGAAAAATTACAGGGTTAA 58.114 33.333 0.00 0.00 0.00 2.01
3291 3555 6.882678 ACAGCGTATAGAAAAATTACAGGGTT 59.117 34.615 0.00 0.00 0.00 4.11
3417 3681 8.759641 CATGATTCTCACTACAATACAAGTAGC 58.240 37.037 0.00 0.00 42.04 3.58
3672 3936 5.173774 TCTTGTGCACAATGAAAGACTTC 57.826 39.130 31.17 0.00 35.02 3.01
3754 4018 1.393883 GCCACGAGAGAAATTCCGTTC 59.606 52.381 0.00 0.00 32.71 3.95
3770 4034 2.143925 GACTTTACACACTCCTGCCAC 58.856 52.381 0.00 0.00 0.00 5.01
3832 4096 2.158798 AGTGGTCATCATGCAGATCCAG 60.159 50.000 0.00 0.00 32.84 3.86
3924 4188 5.880887 AGCATACAAAGTTAGGAAAGTAGGC 59.119 40.000 0.00 0.00 38.91 3.93
3995 4259 9.226606 GTATAACCAATATTAACTGGCATGCTA 57.773 33.333 18.92 11.28 36.03 3.49
4191 4455 1.923864 GTTGGGTGCAACTTTTTGACG 59.076 47.619 0.00 0.00 36.74 4.35
4392 4688 9.573133 CTTGCCTAAGGTTAGTTCAATAAAATG 57.427 33.333 0.00 0.00 0.00 2.32
4398 4694 4.923415 AGCTTGCCTAAGGTTAGTTCAAT 58.077 39.130 0.00 0.00 41.61 2.57
4426 4722 3.857010 GCCACACTTTGCCATACACTTTC 60.857 47.826 0.00 0.00 0.00 2.62
4430 4726 0.958091 TGCCACACTTTGCCATACAC 59.042 50.000 0.00 0.00 0.00 2.90
4459 4755 4.668138 TTAAGGGGCTGTTTGGTTCTAT 57.332 40.909 0.00 0.00 0.00 1.98
4499 4795 5.562635 ACCCCGATAATCAAAAAGTGTACA 58.437 37.500 0.00 0.00 0.00 2.90
4526 4822 3.339141 GCCAGTTCCCTTTAGTTCTCTG 58.661 50.000 0.00 0.00 0.00 3.35
4554 4850 1.569072 ACAACAGGAAACCCAGAACCT 59.431 47.619 0.00 0.00 0.00 3.50
4582 4878 5.880054 TTTTCAAGTGTATTGAGCTAGGC 57.120 39.130 0.00 0.00 0.00 3.93
4583 4879 7.227512 CCCTATTTTCAAGTGTATTGAGCTAGG 59.772 40.741 0.00 11.44 32.00 3.02
4584 4880 7.770897 ACCCTATTTTCAAGTGTATTGAGCTAG 59.229 37.037 0.00 0.00 0.00 3.42
4585 4881 7.552687 CACCCTATTTTCAAGTGTATTGAGCTA 59.447 37.037 0.00 0.00 0.00 3.32
4586 4882 6.375455 CACCCTATTTTCAAGTGTATTGAGCT 59.625 38.462 0.00 0.00 0.00 4.09
4587 4883 6.404734 CCACCCTATTTTCAAGTGTATTGAGC 60.405 42.308 0.00 0.00 0.00 4.26
4588 4884 6.659242 ACCACCCTATTTTCAAGTGTATTGAG 59.341 38.462 0.00 0.00 0.00 3.02
4589 4885 6.548321 ACCACCCTATTTTCAAGTGTATTGA 58.452 36.000 0.00 0.00 0.00 2.57
4652 4948 7.353497 GGCTTATATTTAGAAACGGAAAGAGC 58.647 38.462 0.00 0.00 0.00 4.09
4695 5242 5.723672 ACATCCCTATGTATTCCGTAGTG 57.276 43.478 0.00 0.00 44.66 2.74
4755 5302 3.567164 CCAATACGGACTACATACGGAGT 59.433 47.826 0.00 0.00 41.15 3.85
4795 5342 8.465971 ACTAGTACTCCCTCCATTCCTAAATAT 58.534 37.037 0.00 0.00 0.00 1.28
4833 5380 7.382898 AGGAACTTAAGATCTTGTGTTCTCTC 58.617 38.462 31.28 23.03 36.87 3.20
4913 5460 5.453903 GCTAGATTTCATGACCTAAGCCAGA 60.454 44.000 0.00 0.00 0.00 3.86
5129 5688 2.358898 ACGAATTCCATGCTGCCAATAC 59.641 45.455 0.00 0.00 0.00 1.89
5229 5797 6.315642 TGTGAAGACAAACAATTACCACGTTA 59.684 34.615 0.00 0.00 0.00 3.18
5232 5800 5.163302 TGTGAAGACAAACAATTACCACG 57.837 39.130 0.00 0.00 0.00 4.94
5342 5910 3.181427 TGGCCAAGGGTACTGTTAAATGT 60.181 43.478 0.61 0.00 0.00 2.71
5538 6106 4.777896 AGCAACTGATTGAAGGTAGGTCTA 59.222 41.667 0.00 0.00 38.15 2.59
5624 6192 2.740055 CTGATATCCGGCGGCAGC 60.740 66.667 23.83 14.95 44.18 5.25
5852 6420 7.611213 ATTCTCAAACAAAGGTACCTATTCG 57.389 36.000 16.67 6.55 0.00 3.34
6009 6577 1.043816 CGGCCTCCATCAGTAGTCAT 58.956 55.000 0.00 0.00 0.00 3.06
6146 6714 0.173708 CGACCTCGCTAAGAGCCTTT 59.826 55.000 0.00 0.00 45.54 3.11
6257 6825 0.898326 TCCTCCACTGCTGCGAGTAA 60.898 55.000 4.79 0.00 0.00 2.24
6263 6831 1.748122 CCATGTCCTCCACTGCTGC 60.748 63.158 0.00 0.00 0.00 5.25
6269 6837 2.592308 GCTCCCCATGTCCTCCAC 59.408 66.667 0.00 0.00 0.00 4.02
6278 6846 1.535685 GATGAAGCAGGCTCCCCAT 59.464 57.895 0.00 0.00 0.00 4.00
6437 7008 4.753662 CGGTGGACTCCCCGGAGA 62.754 72.222 17.73 0.00 44.53 3.71
6529 7100 1.840630 TTGTTAGTCCGCGTCGTCGA 61.841 55.000 4.92 0.00 39.71 4.20
6732 7303 3.814283 GCATCAAAATTTTCAGGCAACCA 59.186 39.130 6.57 0.00 37.17 3.67
6745 7316 1.188863 GGTGGCAGAGGCATCAAAAT 58.811 50.000 0.00 0.00 43.71 1.82
6767 7344 0.801251 GGCTCAGTGATGTGCAACTC 59.199 55.000 5.34 0.00 38.04 3.01
6787 7364 1.764851 TTTCGGCACAGCGATTTTTG 58.235 45.000 0.00 0.00 0.00 2.44
6797 7376 1.266718 GTCTTGCAGATTTTCGGCACA 59.733 47.619 1.79 0.00 46.55 4.57
6859 7439 2.428890 TGGAAATCGGAGAGAGAAGCTC 59.571 50.000 0.00 0.00 43.63 4.09
6860 7440 2.461695 TGGAAATCGGAGAGAGAAGCT 58.538 47.619 0.00 0.00 43.63 3.74
6861 7441 2.969628 TGGAAATCGGAGAGAGAAGC 57.030 50.000 0.00 0.00 43.63 3.86
6862 7442 6.341316 TGTTAATGGAAATCGGAGAGAGAAG 58.659 40.000 0.00 0.00 43.63 2.85
6863 7443 6.154534 TCTGTTAATGGAAATCGGAGAGAGAA 59.845 38.462 0.00 0.00 43.63 2.87
6864 7444 5.656859 TCTGTTAATGGAAATCGGAGAGAGA 59.343 40.000 0.00 0.00 43.63 3.10
6865 7445 5.907207 TCTGTTAATGGAAATCGGAGAGAG 58.093 41.667 0.00 0.00 43.63 3.20
6866 7446 5.932619 TCTGTTAATGGAAATCGGAGAGA 57.067 39.130 0.00 0.00 43.63 3.10
6867 7447 6.985188 TTTCTGTTAATGGAAATCGGAGAG 57.015 37.500 2.92 0.00 43.63 3.20
6868 7448 7.938140 AATTTCTGTTAATGGAAATCGGAGA 57.062 32.000 14.56 0.00 40.06 3.71
6869 7449 8.028938 ACAAATTTCTGTTAATGGAAATCGGAG 58.971 33.333 14.56 9.79 40.06 4.63
6870 7450 7.891561 ACAAATTTCTGTTAATGGAAATCGGA 58.108 30.769 14.56 0.00 40.06 4.55
6871 7451 8.434661 CAACAAATTTCTGTTAATGGAAATCGG 58.565 33.333 14.56 12.65 40.06 4.18
6872 7452 9.190858 TCAACAAATTTCTGTTAATGGAAATCG 57.809 29.630 14.56 12.28 40.06 3.34
6883 7463 9.447157 TTTCCAGAATTTCAACAAATTTCTGTT 57.553 25.926 15.59 0.00 41.47 3.16
6884 7464 9.617523 ATTTCCAGAATTTCAACAAATTTCTGT 57.382 25.926 15.59 0.00 41.47 3.41
6942 7522 6.096705 TGAAACTTCTTCAAATCTCAGCCAAA 59.903 34.615 0.00 0.00 0.00 3.28
6943 7523 5.593909 TGAAACTTCTTCAAATCTCAGCCAA 59.406 36.000 0.00 0.00 0.00 4.52
6944 7524 5.132502 TGAAACTTCTTCAAATCTCAGCCA 58.867 37.500 0.00 0.00 0.00 4.75
6957 7537 4.455606 CTTGACCTGACCTGAAACTTCTT 58.544 43.478 0.00 0.00 0.00 2.52



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

AutoCloner maintained by Alex Coulton.