Multiple sequence alignment - TraesCS4A01G440200

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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 TraesCS4A01G440200 chr4A 100.000 2285 0 0 1 2285 709202520 709204804 0.000000e+00 4220
1 TraesCS4A01G440200 chr4A 88.000 325 37 2 962 1285 709264440 709264763 1.280000e-102 383
2 TraesCS4A01G440200 chr7D 90.923 639 36 6 667 1294 25276562 25277189 0.000000e+00 839
3 TraesCS4A01G440200 chr7D 86.573 499 42 6 795 1285 25285620 25286101 5.590000e-146 527
4 TraesCS4A01G440200 chr7D 91.826 367 19 7 329 688 25276189 25276551 3.390000e-138 501
5 TraesCS4A01G440200 chr7D 90.037 271 16 8 40 307 25275944 25276206 7.820000e-90 340
6 TraesCS4A01G440200 chr7D 86.182 275 27 6 1299 1571 25277223 25277488 1.030000e-73 287
7 TraesCS4A01G440200 chr7D 73.496 615 85 38 1691 2285 25277712 25278268 6.530000e-36 161
8 TraesCS4A01G440200 chr7A 92.135 534 31 5 760 1291 26049363 26049887 0.000000e+00 743
9 TraesCS4A01G440200 chr7A 92.075 265 21 0 1021 1285 26099657 26099921 7.710000e-100 374
10 TraesCS4A01G440200 chr7A 82.547 212 24 8 2039 2240 26051296 26051504 8.390000e-40 174
11 TraesCS4A01G440200 chr7A 85.271 129 15 3 795 920 26099527 26099654 1.840000e-26 130


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 TraesCS4A01G440200 chr4A 709202520 709204804 2284 False 4220.0 4220 100.0000 1 2285 1 chr4A.!!$F1 2284
1 TraesCS4A01G440200 chr7D 25275944 25278268 2324 False 425.6 839 86.4928 40 2285 5 chr7D.!!$F2 2245
2 TraesCS4A01G440200 chr7A 26049363 26051504 2141 False 458.5 743 87.3410 760 2240 2 chr7A.!!$F1 1480

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
968 1018 0.109342 CTGGTGGTTGCAGGAAGACT 59.891 55.0 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 2069 0.11714 TCATGGTGTCTCCCTCCTGT 59.883 55.0 0.0 0.0 34.77 4.0 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
26 27 7.953158 TGACTTTTCAAAACACACAATGAAA 57.047 28.000 0.00 0.00 39.33 2.69
27 28 8.370493 TGACTTTTCAAAACACACAATGAAAA 57.630 26.923 10.86 10.86 44.80 2.29
28 29 8.997323 TGACTTTTCAAAACACACAATGAAAAT 58.003 25.926 11.53 4.58 45.43 1.82
29 30 9.824534 GACTTTTCAAAACACACAATGAAAATT 57.175 25.926 11.53 7.44 45.43 1.82
30 31 9.824534 ACTTTTCAAAACACACAATGAAAATTC 57.175 25.926 11.53 0.00 45.43 2.17
31 32 9.823098 CTTTTCAAAACACACAATGAAAATTCA 57.177 25.926 11.53 0.00 45.43 2.57
32 33 9.604626 TTTTCAAAACACACAATGAAAATTCAC 57.395 25.926 8.07 0.00 43.18 3.18
33 34 7.301068 TCAAAACACACAATGAAAATTCACC 57.699 32.000 0.00 0.00 40.49 4.02
34 35 6.875726 TCAAAACACACAATGAAAATTCACCA 59.124 30.769 0.00 0.00 40.49 4.17
35 36 6.660887 AAACACACAATGAAAATTCACCAC 57.339 33.333 0.00 0.00 40.49 4.16
36 37 4.358851 ACACACAATGAAAATTCACCACG 58.641 39.130 0.00 0.00 40.49 4.94
37 38 4.097135 ACACACAATGAAAATTCACCACGA 59.903 37.500 0.00 0.00 40.49 4.35
38 39 4.440758 CACACAATGAAAATTCACCACGAC 59.559 41.667 0.00 0.00 40.49 4.34
39 40 4.097135 ACACAATGAAAATTCACCACGACA 59.903 37.500 0.00 0.00 40.49 4.35
40 41 5.039984 CACAATGAAAATTCACCACGACAA 58.960 37.500 0.00 0.00 40.49 3.18
41 42 5.518128 CACAATGAAAATTCACCACGACAAA 59.482 36.000 0.00 0.00 40.49 2.83
42 43 6.035435 CACAATGAAAATTCACCACGACAAAA 59.965 34.615 0.00 0.00 40.49 2.44
43 44 6.591834 ACAATGAAAATTCACCACGACAAAAA 59.408 30.769 0.00 0.00 40.49 1.94
76 77 1.414158 AGGTCCTGGTCGTGGATATG 58.586 55.000 0.00 0.00 35.87 1.78
89 90 1.142262 TGGATATGACGACGAGGAGGA 59.858 52.381 0.00 0.00 0.00 3.71
115 116 2.354704 CGTTCTCCCTTGTGCTGGATAA 60.355 50.000 0.00 0.00 0.00 1.75
119 120 5.489792 TCTCCCTTGTGCTGGATAATATC 57.510 43.478 0.00 0.00 0.00 1.63
132 133 5.345418 TGGATAATATCAGGGCTAGAGCTT 58.655 41.667 2.41 0.00 41.70 3.74
153 154 2.032550 TGAGCGTACTGTACTATTCGGC 59.967 50.000 15.35 10.07 0.00 5.54
164 165 2.199236 ACTATTCGGCCGTTCGATTTC 58.801 47.619 27.15 0.00 39.03 2.17
182 183 4.627611 TTTCGAGTATACTACTTGCGCT 57.372 40.909 9.73 0.00 39.59 5.92
222 223 3.399330 TCCTCTCTGTTGTTTTTAGCCG 58.601 45.455 0.00 0.00 0.00 5.52
241 242 9.830294 TTTAGCCGCTTAACTTTAATAAAGAAC 57.170 29.630 18.55 3.33 41.02 3.01
242 243 7.443259 AGCCGCTTAACTTTAATAAAGAACA 57.557 32.000 18.55 1.52 41.02 3.18
243 244 7.527457 AGCCGCTTAACTTTAATAAAGAACAG 58.473 34.615 18.55 11.14 41.02 3.16
244 245 7.174426 AGCCGCTTAACTTTAATAAAGAACAGT 59.826 33.333 18.55 0.00 41.02 3.55
245 246 7.806487 GCCGCTTAACTTTAATAAAGAACAGTT 59.194 33.333 18.55 6.09 41.02 3.16
266 267 7.328493 ACAGTTTAACTTTTGAAAGCAACACTC 59.672 33.333 0.00 0.00 39.63 3.51
269 270 7.810766 TTAACTTTTGAAAGCAACACTCTTG 57.189 32.000 3.48 0.00 39.63 3.02
314 315 3.411415 GCATGAGCACCTTGAATGTAC 57.589 47.619 0.00 0.00 41.58 2.90
315 316 2.749076 GCATGAGCACCTTGAATGTACA 59.251 45.455 0.00 0.00 41.58 2.90
316 317 3.191162 GCATGAGCACCTTGAATGTACAA 59.809 43.478 0.00 0.00 41.58 2.41
317 318 4.321156 GCATGAGCACCTTGAATGTACAAA 60.321 41.667 0.00 0.00 41.58 2.83
318 319 4.829064 TGAGCACCTTGAATGTACAAAC 57.171 40.909 0.00 0.00 0.00 2.93
319 320 4.203226 TGAGCACCTTGAATGTACAAACA 58.797 39.130 0.00 0.00 40.69 2.83
320 321 4.036262 TGAGCACCTTGAATGTACAAACAC 59.964 41.667 0.00 0.00 38.78 3.32
321 322 3.317993 AGCACCTTGAATGTACAAACACC 59.682 43.478 0.00 0.00 38.78 4.16
322 323 3.552068 GCACCTTGAATGTACAAACACCC 60.552 47.826 0.00 0.00 38.78 4.61
323 324 3.888930 CACCTTGAATGTACAAACACCCT 59.111 43.478 0.00 0.00 38.78 4.34
324 325 3.888930 ACCTTGAATGTACAAACACCCTG 59.111 43.478 0.00 0.00 38.78 4.45
325 326 3.305335 CCTTGAATGTACAAACACCCTGC 60.305 47.826 0.00 0.00 38.78 4.85
326 327 2.937519 TGAATGTACAAACACCCTGCA 58.062 42.857 0.00 0.00 38.78 4.41
327 328 3.291584 TGAATGTACAAACACCCTGCAA 58.708 40.909 0.00 0.00 38.78 4.08
328 329 3.894427 TGAATGTACAAACACCCTGCAAT 59.106 39.130 0.00 0.00 38.78 3.56
329 330 4.343526 TGAATGTACAAACACCCTGCAATT 59.656 37.500 0.00 0.00 38.78 2.32
330 331 4.953940 ATGTACAAACACCCTGCAATTT 57.046 36.364 0.00 0.00 38.78 1.82
331 332 4.744795 TGTACAAACACCCTGCAATTTT 57.255 36.364 0.00 0.00 0.00 1.82
332 333 4.437239 TGTACAAACACCCTGCAATTTTG 58.563 39.130 0.00 0.00 34.10 2.44
333 334 6.482028 ATGTACAAACACCCTGCAATTTTGC 61.482 40.000 8.32 8.32 45.94 3.68
367 368 3.667960 GCTTTTGAGTATCTTGCACCACG 60.668 47.826 0.00 0.00 34.92 4.94
416 420 9.757227 TTTTTATGATTTTTACTGTTCACCAGG 57.243 29.630 0.00 0.00 46.06 4.45
421 425 1.961793 TTACTGTTCACCAGGTGCAC 58.038 50.000 15.64 15.30 46.06 4.57
514 518 3.880047 ATGGCATTTTGTCACCATCTG 57.120 42.857 0.00 0.00 38.55 2.90
525 529 4.148079 TGTCACCATCTGTTAAATGCCAA 58.852 39.130 0.00 0.00 0.00 4.52
588 592 2.865551 AGCATTTTGTTTGTTTGCTCCG 59.134 40.909 0.00 0.00 39.32 4.63
599 603 3.246619 TGTTTGCTCCGTTGTTTTGTTC 58.753 40.909 0.00 0.00 0.00 3.18
633 637 5.197451 TGCTAGTTGAAAAACTTCCCAAGA 58.803 37.500 0.00 0.00 34.37 3.02
640 644 7.343057 AGTTGAAAAACTTCCCAAGAATCTTCT 59.657 33.333 0.00 0.00 39.74 2.85
689 728 3.829601 ACGGCCAAATCCACTTTGATTAA 59.170 39.130 2.24 0.00 45.96 1.40
696 735 6.366877 CCAAATCCACTTTGATTAACAGCTTG 59.633 38.462 0.00 0.00 45.96 4.01
721 760 3.243101 ACGTTATCATGTCTCACCGCTAG 60.243 47.826 0.00 0.00 0.00 3.42
722 761 3.243101 CGTTATCATGTCTCACCGCTAGT 60.243 47.826 0.00 0.00 0.00 2.57
803 845 3.314331 ACCGACAGCAGGTCCCTG 61.314 66.667 9.04 9.04 43.95 4.45
824 866 2.343758 GCCGACCTCTCAACAGCA 59.656 61.111 0.00 0.00 0.00 4.41
846 888 2.358737 CTCACCCGTCACCCTTGC 60.359 66.667 0.00 0.00 0.00 4.01
863 905 2.663852 CCACGACGGTTCACCCAC 60.664 66.667 0.00 0.00 0.00 4.61
871 913 2.032071 GTTCACCCACCTGGACCG 59.968 66.667 0.00 0.00 37.39 4.79
900 942 5.840149 TCCGCCTATATAAAAACTCACCCTA 59.160 40.000 0.00 0.00 0.00 3.53
950 1000 3.518634 GCTCAAGCTAGCTAGACAACT 57.481 47.619 25.15 8.82 39.50 3.16
953 1003 3.165875 TCAAGCTAGCTAGACAACTGGT 58.834 45.455 25.15 0.00 0.00 4.00
956 1006 1.550976 GCTAGCTAGACAACTGGTGGT 59.449 52.381 25.15 0.00 0.00 4.16
963 1013 4.577152 CAACTGGTGGTTGCAGGA 57.423 55.556 0.00 0.00 46.89 3.86
964 1014 2.805897 CAACTGGTGGTTGCAGGAA 58.194 52.632 0.00 0.00 46.89 3.36
965 1015 0.670162 CAACTGGTGGTTGCAGGAAG 59.330 55.000 0.00 0.00 46.89 3.46
967 1017 0.179018 ACTGGTGGTTGCAGGAAGAC 60.179 55.000 0.00 0.00 0.00 3.01
968 1018 0.109342 CTGGTGGTTGCAGGAAGACT 59.891 55.000 0.00 0.00 0.00 3.24
969 1019 1.347707 CTGGTGGTTGCAGGAAGACTA 59.652 52.381 0.00 0.00 0.00 2.59
970 1020 1.985159 TGGTGGTTGCAGGAAGACTAT 59.015 47.619 0.00 0.00 0.00 2.12
975 1025 3.073798 TGGTTGCAGGAAGACTATCCAAA 59.926 43.478 6.49 0.00 42.27 3.28
997 1047 2.746279 AACCACAAGGATCACCAACA 57.254 45.000 0.00 0.00 38.69 3.33
1011 1061 0.389426 CCAACAAGATGCAGCAAGCC 60.389 55.000 4.07 0.00 44.83 4.35
1029 1079 1.272147 GCCAAGGTGAAGGTGAAGGAT 60.272 52.381 0.00 0.00 0.00 3.24
1062 1112 0.980754 TGAGGGCCAAGGCGAAGATA 60.981 55.000 6.18 0.00 43.06 1.98
1095 1145 3.394836 GCGGAGAAGGTGGAGGCT 61.395 66.667 0.00 0.00 0.00 4.58
1311 1392 5.510671 GTGGCGTGTATATTCTTTCCATTG 58.489 41.667 0.00 0.00 0.00 2.82
1333 1414 4.860352 TGATGTACTGTTACATACGTGTGC 59.140 41.667 12.67 0.00 47.00 4.57
1369 1450 4.811557 GTCAAGTTATATCTGGAGTGCCAC 59.188 45.833 0.00 0.00 39.92 5.01
1386 1467 3.160545 GCCACGTGAATTATTGACGTTG 58.839 45.455 18.77 16.45 43.51 4.10
1391 1472 4.693566 ACGTGAATTATTGACGTTGTGGAT 59.306 37.500 16.03 0.00 43.51 3.41
1405 1486 6.155827 ACGTTGTGGATGTTTTTATGATTGG 58.844 36.000 0.00 0.00 0.00 3.16
1406 1487 6.155827 CGTTGTGGATGTTTTTATGATTGGT 58.844 36.000 0.00 0.00 0.00 3.67
1408 1489 7.359097 CGTTGTGGATGTTTTTATGATTGGTTG 60.359 37.037 0.00 0.00 0.00 3.77
1411 1492 7.151308 GTGGATGTTTTTATGATTGGTTGACA 58.849 34.615 0.00 0.00 0.00 3.58
1413 1494 7.871973 TGGATGTTTTTATGATTGGTTGACAAG 59.128 33.333 0.00 0.00 43.48 3.16
1414 1495 7.148590 GGATGTTTTTATGATTGGTTGACAAGC 60.149 37.037 10.46 10.46 45.46 4.01
1415 1496 6.815089 TGTTTTTATGATTGGTTGACAAGCT 58.185 32.000 17.62 0.00 45.46 3.74
1418 1499 9.255304 GTTTTTATGATTGGTTGACAAGCTAAA 57.745 29.630 17.62 10.69 45.46 1.85
1419 1500 9.823647 TTTTTATGATTGGTTGACAAGCTAAAA 57.176 25.926 17.62 15.05 45.46 1.52
1420 1501 9.995003 TTTTATGATTGGTTGACAAGCTAAAAT 57.005 25.926 17.62 9.52 45.46 1.82
1501 1582 8.102676 TCACTTCATCTCTTATCCATGTTTTCA 58.897 33.333 0.00 0.00 0.00 2.69
1505 1586 7.050377 TCATCTCTTATCCATGTTTTCACTCC 58.950 38.462 0.00 0.00 0.00 3.85
1510 1591 7.054124 TCTTATCCATGTTTTCACTCCCATAC 58.946 38.462 0.00 0.00 0.00 2.39
1514 1595 5.835819 TCCATGTTTTCACTCCCATACAAAA 59.164 36.000 0.00 0.00 0.00 2.44
1546 1627 3.121929 TCCTCAGTTCAAGGGAGCTAT 57.878 47.619 0.00 0.00 32.27 2.97
1574 1655 8.880878 ATTATAATTTTGTAATCAAACCGGGC 57.119 30.769 6.32 0.00 42.28 6.13
1575 1656 4.608948 AATTTTGTAATCAAACCGGGCA 57.391 36.364 6.32 0.00 42.28 5.36
1576 1657 4.608948 ATTTTGTAATCAAACCGGGCAA 57.391 36.364 6.32 0.00 42.28 4.52
1577 1658 3.651803 TTTGTAATCAAACCGGGCAAG 57.348 42.857 6.32 0.00 38.44 4.01
1578 1659 1.540267 TGTAATCAAACCGGGCAAGG 58.460 50.000 6.32 0.00 37.30 3.61
1579 1660 1.074084 TGTAATCAAACCGGGCAAGGA 59.926 47.619 6.32 0.00 34.73 3.36
1580 1661 1.743394 GTAATCAAACCGGGCAAGGAG 59.257 52.381 6.32 0.00 34.73 3.69
1581 1662 1.250840 AATCAAACCGGGCAAGGAGC 61.251 55.000 6.32 0.00 44.65 4.70
1582 1663 2.142292 ATCAAACCGGGCAAGGAGCT 62.142 55.000 6.32 0.00 44.79 4.09
1583 1664 1.002624 CAAACCGGGCAAGGAGCTA 60.003 57.895 6.32 0.00 44.79 3.32
1584 1665 1.002502 AAACCGGGCAAGGAGCTAC 60.003 57.895 6.32 0.00 44.79 3.58
1585 1666 1.774894 AAACCGGGCAAGGAGCTACA 61.775 55.000 6.32 0.00 44.79 2.74
1586 1667 1.774894 AACCGGGCAAGGAGCTACAA 61.775 55.000 6.32 0.00 44.79 2.41
1587 1668 1.002624 CCGGGCAAGGAGCTACAAA 60.003 57.895 0.00 0.00 44.79 2.83
1588 1669 0.394352 CCGGGCAAGGAGCTACAAAT 60.394 55.000 0.00 0.00 44.79 2.32
1589 1670 1.463674 CGGGCAAGGAGCTACAAATT 58.536 50.000 0.00 0.00 44.79 1.82
1590 1671 2.639065 CGGGCAAGGAGCTACAAATTA 58.361 47.619 0.00 0.00 44.79 1.40
1591 1672 3.214328 CGGGCAAGGAGCTACAAATTAT 58.786 45.455 0.00 0.00 44.79 1.28
1592 1673 4.385825 CGGGCAAGGAGCTACAAATTATA 58.614 43.478 0.00 0.00 44.79 0.98
1593 1674 4.819630 CGGGCAAGGAGCTACAAATTATAA 59.180 41.667 0.00 0.00 44.79 0.98
1594 1675 5.473504 CGGGCAAGGAGCTACAAATTATAAT 59.526 40.000 0.00 0.00 44.79 1.28
1595 1676 6.016276 CGGGCAAGGAGCTACAAATTATAATT 60.016 38.462 4.81 4.81 44.79 1.40
1596 1677 7.470009 CGGGCAAGGAGCTACAAATTATAATTT 60.470 37.037 16.15 16.15 44.79 1.82
1597 1678 8.204160 GGGCAAGGAGCTACAAATTATAATTTT 58.796 33.333 18.72 13.18 44.79 1.82
1598 1679 9.034544 GGCAAGGAGCTACAAATTATAATTTTG 57.965 33.333 18.72 15.91 44.79 2.44
1599 1680 9.586435 GCAAGGAGCTACAAATTATAATTTTGT 57.414 29.630 18.72 19.56 41.15 2.83
1612 1693 5.993748 ATAATTTTGTGATCAAACCGGGT 57.006 34.783 6.32 0.00 42.28 5.28
1615 1696 5.993748 ATTTTGTGATCAAACCGGGTAAT 57.006 34.783 6.32 0.00 42.28 1.89
1640 1721 6.895782 ACGGTTCATCTTGATCCCTAAAATA 58.104 36.000 0.00 0.00 33.69 1.40
1644 1798 7.177392 GGTTCATCTTGATCCCTAAAATATGGG 59.823 40.741 0.00 0.00 44.66 4.00
1651 1805 9.686683 CTTGATCCCTAAAATATGGGTATAAGG 57.313 37.037 0.00 0.00 43.74 2.69
1673 1929 8.941995 AAGGCTATTACTATGTCTATGACTCA 57.058 34.615 0.00 0.00 33.15 3.41
1676 1932 7.704472 GGCTATTACTATGTCTATGACTCATGC 59.296 40.741 1.42 0.00 33.15 4.06
1680 1936 5.392995 ACTATGTCTATGACTCATGCTCCT 58.607 41.667 1.42 0.00 33.15 3.69
1687 1943 1.039856 GACTCATGCTCCTCCTCCTC 58.960 60.000 0.00 0.00 0.00 3.71
1688 1944 0.398381 ACTCATGCTCCTCCTCCTCC 60.398 60.000 0.00 0.00 0.00 4.30
1689 1945 0.105555 CTCATGCTCCTCCTCCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
1690 1946 0.105760 TCATGCTCCTCCTCCTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
1691 1947 0.105555 CATGCTCCTCCTCCTCCTCT 60.106 60.000 0.00 0.00 0.00 3.69
1692 1948 0.188342 ATGCTCCTCCTCCTCCTCTC 59.812 60.000 0.00 0.00 0.00 3.20
1693 1949 1.217747 TGCTCCTCCTCCTCCTCTCA 61.218 60.000 0.00 0.00 0.00 3.27
1704 1960 1.949847 CTCCTCTCAACCGCATCCGT 61.950 60.000 0.00 0.00 0.00 4.69
1745 2003 0.037303 CCATGGAGGGATCCGATTGG 59.963 60.000 5.56 4.66 0.00 3.16
1754 2012 2.717139 GATCCGATTGGTCCTCCGGC 62.717 65.000 0.00 0.00 41.55 6.13
1756 2014 3.833645 CGATTGGTCCTCCGGCGA 61.834 66.667 9.30 0.00 36.30 5.54
1759 2017 1.749334 GATTGGTCCTCCGGCGAGAT 61.749 60.000 9.30 0.00 38.52 2.75
1760 2018 1.749334 ATTGGTCCTCCGGCGAGATC 61.749 60.000 9.30 2.84 38.52 2.75
1766 2024 3.064987 CTCCGGCGAGATCGGTGTT 62.065 63.158 9.30 0.00 46.82 3.32
1772 2030 0.526524 GCGAGATCGGTGTTGAGGAG 60.527 60.000 4.18 0.00 40.23 3.69
1774 2032 1.475403 GAGATCGGTGTTGAGGAGGA 58.525 55.000 0.00 0.00 0.00 3.71
1775 2033 2.035632 GAGATCGGTGTTGAGGAGGAT 58.964 52.381 0.00 0.00 0.00 3.24
1777 2035 1.482593 GATCGGTGTTGAGGAGGATGT 59.517 52.381 0.00 0.00 0.00 3.06
1783 2041 2.054021 TGTTGAGGAGGATGTTGGTGA 58.946 47.619 0.00 0.00 0.00 4.02
1787 2045 3.689347 TGAGGAGGATGTTGGTGAATTG 58.311 45.455 0.00 0.00 0.00 2.32
1808 2069 1.982958 GAAGAGGTACCCAAGGGAACA 59.017 52.381 13.15 0.00 38.96 3.18
1809 2070 1.359168 AGAGGTACCCAAGGGAACAC 58.641 55.000 13.15 6.46 38.96 3.32
1811 2072 1.003233 GAGGTACCCAAGGGAACACAG 59.997 57.143 13.15 0.00 38.96 3.66
1818 2079 0.326264 CAAGGGAACACAGGAGGGAG 59.674 60.000 0.00 0.00 0.00 4.30
1820 2081 0.545548 AGGGAACACAGGAGGGAGAC 60.546 60.000 0.00 0.00 0.00 3.36
1821 2082 0.836400 GGGAACACAGGAGGGAGACA 60.836 60.000 0.00 0.00 0.00 3.41
1833 2094 1.276421 AGGGAGACACCATGACGAAAG 59.724 52.381 0.00 0.00 41.20 2.62
1840 2101 2.079158 CACCATGACGAAAGCACTGAT 58.921 47.619 0.00 0.00 0.00 2.90
1841 2102 2.079158 ACCATGACGAAAGCACTGATG 58.921 47.619 0.00 0.00 0.00 3.07
1842 2103 2.289631 ACCATGACGAAAGCACTGATGA 60.290 45.455 0.00 0.00 0.00 2.92
1843 2104 2.094894 CCATGACGAAAGCACTGATGAC 59.905 50.000 0.00 0.00 0.00 3.06
1866 2127 1.534476 TAAGTCCTGGACACCGGCA 60.534 57.895 27.48 4.07 34.60 5.69
1883 2144 3.017581 AAGGCGGGCAGGGAGAAT 61.018 61.111 3.78 0.00 0.00 2.40
1884 2145 2.616458 AAGGCGGGCAGGGAGAATT 61.616 57.895 3.78 0.00 0.00 2.17
1885 2146 2.517166 GGCGGGCAGGGAGAATTC 60.517 66.667 0.00 0.00 0.00 2.17
1886 2147 2.272146 GCGGGCAGGGAGAATTCA 59.728 61.111 8.44 0.00 0.00 2.57
1887 2148 2.115291 GCGGGCAGGGAGAATTCAC 61.115 63.158 8.44 0.52 0.00 3.18
1888 2149 1.815421 CGGGCAGGGAGAATTCACG 60.815 63.158 8.44 0.00 0.00 4.35
1889 2150 1.602237 GGGCAGGGAGAATTCACGA 59.398 57.895 8.44 0.00 0.00 4.35
1890 2151 0.181350 GGGCAGGGAGAATTCACGAT 59.819 55.000 8.44 0.00 0.00 3.73
1891 2152 1.408822 GGGCAGGGAGAATTCACGATT 60.409 52.381 8.44 0.00 0.00 3.34
1892 2153 1.943340 GGCAGGGAGAATTCACGATTC 59.057 52.381 8.44 0.00 43.71 2.52
1904 2165 4.427096 TTCACGATTCTCTCTCAGTGAC 57.573 45.455 0.00 0.00 38.18 3.67
1910 2171 4.142513 CGATTCTCTCTCAGTGACATGTGA 60.143 45.833 1.15 0.00 0.00 3.58
1914 2175 2.230750 TCTCTCAGTGACATGTGAGCAG 59.769 50.000 1.15 4.01 40.13 4.24
1930 2191 0.610232 GCAGCACCAGACAAGGGAAT 60.610 55.000 0.00 0.00 0.00 3.01
1933 2194 1.168714 GCACCAGACAAGGGAATCAC 58.831 55.000 0.00 0.00 0.00 3.06
1945 2206 3.379452 AGGGAATCACGAGAAAGGAGAT 58.621 45.455 0.00 0.00 0.00 2.75
1951 2212 3.020274 TCACGAGAAAGGAGATGAGAGG 58.980 50.000 0.00 0.00 0.00 3.69
1953 2214 3.066621 CACGAGAAAGGAGATGAGAGGAG 59.933 52.174 0.00 0.00 0.00 3.69
1958 2219 1.719529 AGGAGATGAGAGGAGCATGG 58.280 55.000 0.00 0.00 0.00 3.66
1961 2222 1.767681 GAGATGAGAGGAGCATGGGTT 59.232 52.381 0.00 0.00 0.00 4.11
1965 2226 1.839994 TGAGAGGAGCATGGGTTTAGG 59.160 52.381 0.00 0.00 0.00 2.69
1969 2230 2.708325 GAGGAGCATGGGTTTAGGAGAT 59.292 50.000 0.00 0.00 0.00 2.75
1976 2237 1.757118 TGGGTTTAGGAGATGAGAGCG 59.243 52.381 0.00 0.00 0.00 5.03
1977 2238 1.069358 GGGTTTAGGAGATGAGAGCGG 59.931 57.143 0.00 0.00 0.00 5.52
1978 2239 1.539280 GGTTTAGGAGATGAGAGCGGC 60.539 57.143 0.00 0.00 0.00 6.53
1979 2240 1.137086 GTTTAGGAGATGAGAGCGGCA 59.863 52.381 1.45 0.00 0.00 5.69
1980 2241 1.485124 TTAGGAGATGAGAGCGGCAA 58.515 50.000 1.45 0.00 0.00 4.52
1981 2242 1.035923 TAGGAGATGAGAGCGGCAAG 58.964 55.000 1.45 0.00 0.00 4.01
1982 2243 0.685785 AGGAGATGAGAGCGGCAAGA 60.686 55.000 1.45 0.00 0.00 3.02
1983 2244 0.176680 GGAGATGAGAGCGGCAAGAA 59.823 55.000 1.45 0.00 0.00 2.52
1984 2245 1.202627 GGAGATGAGAGCGGCAAGAAT 60.203 52.381 1.45 0.00 0.00 2.40
1985 2246 2.134346 GAGATGAGAGCGGCAAGAATC 58.866 52.381 1.45 0.20 0.00 2.52
1986 2247 1.761784 AGATGAGAGCGGCAAGAATCT 59.238 47.619 1.45 2.68 0.00 2.40
1987 2248 2.170187 AGATGAGAGCGGCAAGAATCTT 59.830 45.455 1.45 0.00 0.00 2.40
1988 2249 3.386078 AGATGAGAGCGGCAAGAATCTTA 59.614 43.478 1.45 0.00 0.00 2.10
1989 2250 3.827008 TGAGAGCGGCAAGAATCTTAT 57.173 42.857 1.45 0.00 0.00 1.73
1990 2251 4.937201 TGAGAGCGGCAAGAATCTTATA 57.063 40.909 1.45 0.00 0.00 0.98
1991 2252 4.876125 TGAGAGCGGCAAGAATCTTATAG 58.124 43.478 1.45 0.00 0.00 1.31
1992 2253 4.241681 GAGAGCGGCAAGAATCTTATAGG 58.758 47.826 1.45 0.00 0.00 2.57
1993 2254 2.739379 GAGCGGCAAGAATCTTATAGGC 59.261 50.000 1.45 0.00 0.00 3.93
1994 2255 2.104792 AGCGGCAAGAATCTTATAGGCA 59.895 45.455 1.45 0.00 0.00 4.75
1995 2256 2.224314 GCGGCAAGAATCTTATAGGCAC 59.776 50.000 0.00 0.00 0.00 5.01
1996 2257 2.476619 CGGCAAGAATCTTATAGGCACG 59.523 50.000 0.00 0.00 0.00 5.34
2014 2275 4.772687 GGGGAGGCCGAAACGTCC 62.773 72.222 0.00 0.00 42.62 4.79
2022 2283 0.040692 GCCGAAACGTCCCTTTGTTC 60.041 55.000 0.00 0.00 0.00 3.18
2027 2288 3.250040 CGAAACGTCCCTTTGTTCAGAAT 59.750 43.478 0.00 0.00 0.00 2.40
2028 2289 4.537015 GAAACGTCCCTTTGTTCAGAATG 58.463 43.478 0.00 0.00 37.54 2.67
2035 2296 3.998341 CCCTTTGTTCAGAATGCCATTTG 59.002 43.478 0.00 0.00 34.76 2.32
2036 2297 3.434299 CCTTTGTTCAGAATGCCATTTGC 59.566 43.478 0.00 0.00 41.77 3.68
2063 2867 1.821753 AGACTGACCGATCAAGACTGG 59.178 52.381 0.00 0.00 33.30 4.00
2078 2882 1.895131 GACTGGGACATGGCAAACAAT 59.105 47.619 0.00 0.00 38.20 2.71
2079 2883 3.088532 GACTGGGACATGGCAAACAATA 58.911 45.455 0.00 0.00 38.20 1.90
2080 2884 3.505386 ACTGGGACATGGCAAACAATAA 58.495 40.909 0.00 0.00 38.20 1.40
2081 2885 4.095946 ACTGGGACATGGCAAACAATAAT 58.904 39.130 0.00 0.00 38.20 1.28
2090 2894 2.094752 GGCAAACAATAATGTCAGCGGT 60.095 45.455 2.61 0.00 39.40 5.68
2105 2909 1.218047 CGGTGCCTCGATTCCTCAA 59.782 57.895 0.00 0.00 0.00 3.02
2109 2913 0.909610 TGCCTCGATTCCTCAACCCT 60.910 55.000 0.00 0.00 0.00 4.34
2111 2915 0.103208 CCTCGATTCCTCAACCCTCG 59.897 60.000 0.00 0.00 0.00 4.63
2124 2928 2.573869 CCTCGGTCAGCGTCATGT 59.426 61.111 0.00 0.00 0.00 3.21
2128 2932 2.358615 GGTCAGCGTCATGTGGCA 60.359 61.111 12.07 0.00 0.00 4.92
2131 2935 1.003476 TCAGCGTCATGTGGCACAT 60.003 52.632 26.78 26.78 44.52 3.21
2149 2953 3.313526 CACATGATTCCCCTTCAACGATC 59.686 47.826 0.00 0.00 0.00 3.69
2150 2954 2.710096 TGATTCCCCTTCAACGATCC 57.290 50.000 0.00 0.00 0.00 3.36
2151 2955 1.134521 TGATTCCCCTTCAACGATCCG 60.135 52.381 0.00 0.00 0.00 4.18
2152 2956 0.909623 ATTCCCCTTCAACGATCCGT 59.090 50.000 0.00 0.00 43.97 4.69
2157 2961 1.571919 CCTTCAACGATCCGTCCATC 58.428 55.000 0.00 0.00 39.99 3.51
2158 2962 1.134818 CCTTCAACGATCCGTCCATCA 60.135 52.381 0.00 0.00 39.99 3.07
2159 2963 2.483714 CCTTCAACGATCCGTCCATCAT 60.484 50.000 0.00 0.00 39.99 2.45
2162 2974 2.093711 TCAACGATCCGTCCATCATTGT 60.094 45.455 0.00 0.00 39.99 2.71
2164 2976 3.371102 ACGATCCGTCCATCATTGTAG 57.629 47.619 0.00 0.00 33.69 2.74
2166 2978 3.243434 ACGATCCGTCCATCATTGTAGTC 60.243 47.826 0.00 0.00 33.69 2.59
2181 2993 3.812262 TGTAGTCGAGATCGTGGGAATA 58.188 45.455 1.70 0.00 40.80 1.75
2197 3010 4.276058 GGAATATTTTCCCATGGCCATG 57.724 45.455 34.82 34.82 44.96 3.66
2244 3058 5.445069 TCAACCACTGAAATTCCTTCTTGA 58.555 37.500 0.00 0.00 34.86 3.02
2252 3066 7.001073 ACTGAAATTCCTTCTTGAGTAGCTTT 58.999 34.615 0.00 0.00 34.86 3.51
2254 3068 6.431234 TGAAATTCCTTCTTGAGTAGCTTTCC 59.569 38.462 0.00 0.00 34.86 3.13
2265 3079 3.870606 GCTTTCCGCTAGACGCAA 58.129 55.556 0.00 0.00 41.76 4.85
2274 3088 2.159421 CCGCTAGACGCAAAGAGACTTA 60.159 50.000 0.00 0.00 41.76 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.645059 TTTCATTGTGTGTTTTGAAAAGTCATA 57.355 25.926 0.00 0.00 35.71 2.15
2 3 7.953158 TTTCATTGTGTGTTTTGAAAAGTCA 57.047 28.000 0.00 0.00 35.71 3.41
3 4 9.824534 AATTTTCATTGTGTGTTTTGAAAAGTC 57.175 25.926 13.16 0.00 45.74 3.01
4 5 9.824534 GAATTTTCATTGTGTGTTTTGAAAAGT 57.175 25.926 13.16 11.15 45.74 2.66
5 6 9.823098 TGAATTTTCATTGTGTGTTTTGAAAAG 57.177 25.926 13.16 0.00 45.74 2.27
6 7 9.604626 GTGAATTTTCATTGTGTGTTTTGAAAA 57.395 25.926 10.88 10.88 46.25 2.29
7 8 8.233190 GGTGAATTTTCATTGTGTGTTTTGAAA 58.767 29.630 0.00 0.00 39.73 2.69
8 9 7.388776 TGGTGAATTTTCATTGTGTGTTTTGAA 59.611 29.630 0.00 0.00 39.73 2.69
9 10 6.875726 TGGTGAATTTTCATTGTGTGTTTTGA 59.124 30.769 0.00 0.00 39.73 2.69
10 11 6.960431 GTGGTGAATTTTCATTGTGTGTTTTG 59.040 34.615 0.00 0.00 39.73 2.44
11 12 6.183360 CGTGGTGAATTTTCATTGTGTGTTTT 60.183 34.615 0.00 0.00 39.73 2.43
12 13 5.290643 CGTGGTGAATTTTCATTGTGTGTTT 59.709 36.000 0.00 0.00 39.73 2.83
13 14 4.803088 CGTGGTGAATTTTCATTGTGTGTT 59.197 37.500 0.00 0.00 39.73 3.32
14 15 4.097135 TCGTGGTGAATTTTCATTGTGTGT 59.903 37.500 0.00 0.00 39.73 3.72
15 16 4.440758 GTCGTGGTGAATTTTCATTGTGTG 59.559 41.667 0.00 0.00 39.73 3.82
16 17 4.097135 TGTCGTGGTGAATTTTCATTGTGT 59.903 37.500 0.00 0.00 39.73 3.72
17 18 4.605968 TGTCGTGGTGAATTTTCATTGTG 58.394 39.130 0.00 0.00 39.73 3.33
18 19 4.909696 TGTCGTGGTGAATTTTCATTGT 57.090 36.364 0.00 0.00 39.73 2.71
19 20 6.580963 TTTTGTCGTGGTGAATTTTCATTG 57.419 33.333 0.00 0.00 39.73 2.82
42 43 7.309194 CGACCAGGACCTTCTATTTGAATTTTT 60.309 37.037 0.00 0.00 33.71 1.94
43 44 6.151144 CGACCAGGACCTTCTATTTGAATTTT 59.849 38.462 0.00 0.00 33.71 1.82
76 77 0.179194 CGAAGTTCCTCCTCGTCGTC 60.179 60.000 0.00 0.00 32.79 4.20
115 116 2.566724 GCTCAAGCTCTAGCCCTGATAT 59.433 50.000 8.69 0.00 43.38 1.63
119 120 1.227205 CGCTCAAGCTCTAGCCCTG 60.227 63.158 13.10 0.00 43.38 4.45
132 133 2.032550 GCCGAATAGTACAGTACGCTCA 59.967 50.000 5.02 0.00 0.00 4.26
145 146 1.189446 CGAAATCGAACGGCCGAATAG 59.811 52.381 35.90 19.96 42.22 1.73
149 150 2.567569 TCGAAATCGAACGGCCGA 59.432 55.556 35.90 10.13 46.30 5.54
182 183 2.365293 GGAAAGAAAAGGCCAGCTGAAA 59.635 45.455 17.39 0.00 0.00 2.69
238 239 7.949962 GTGTTGCTTTCAAAAGTTAAACTGTTC 59.050 33.333 4.54 0.00 38.28 3.18
241 242 7.542130 AGAGTGTTGCTTTCAAAAGTTAAACTG 59.458 33.333 4.54 0.00 38.28 3.16
242 243 7.602753 AGAGTGTTGCTTTCAAAAGTTAAACT 58.397 30.769 4.54 3.74 38.28 2.66
243 244 7.812309 AGAGTGTTGCTTTCAAAAGTTAAAC 57.188 32.000 4.54 7.34 38.28 2.01
244 245 8.085296 TCAAGAGTGTTGCTTTCAAAAGTTAAA 58.915 29.630 4.54 0.00 38.28 1.52
245 246 7.540745 GTCAAGAGTGTTGCTTTCAAAAGTTAA 59.459 33.333 4.54 0.00 38.28 2.01
247 248 5.863935 GTCAAGAGTGTTGCTTTCAAAAGTT 59.136 36.000 4.54 0.00 38.28 2.66
249 250 5.287035 GTGTCAAGAGTGTTGCTTTCAAAAG 59.713 40.000 0.00 0.00 39.03 2.27
250 251 5.160641 GTGTCAAGAGTGTTGCTTTCAAAA 58.839 37.500 0.00 0.00 33.37 2.44
253 254 2.682856 GGTGTCAAGAGTGTTGCTTTCA 59.317 45.455 0.00 0.00 0.00 2.69
254 255 2.033424 GGGTGTCAAGAGTGTTGCTTTC 59.967 50.000 0.00 0.00 0.00 2.62
255 256 2.024414 GGGTGTCAAGAGTGTTGCTTT 58.976 47.619 0.00 0.00 0.00 3.51
294 295 2.749076 TGTACATTCAAGGTGCTCATGC 59.251 45.455 0.00 0.00 40.20 4.06
296 297 4.826733 TGTTTGTACATTCAAGGTGCTCAT 59.173 37.500 0.00 0.00 0.00 2.90
297 298 4.036262 GTGTTTGTACATTCAAGGTGCTCA 59.964 41.667 0.00 0.00 36.50 4.26
298 299 4.537015 GTGTTTGTACATTCAAGGTGCTC 58.463 43.478 0.00 0.00 36.50 4.26
299 300 3.317993 GGTGTTTGTACATTCAAGGTGCT 59.682 43.478 0.00 0.00 36.50 4.40
300 301 3.552068 GGGTGTTTGTACATTCAAGGTGC 60.552 47.826 0.00 0.00 36.50 5.01
301 302 3.888930 AGGGTGTTTGTACATTCAAGGTG 59.111 43.478 0.00 0.00 36.50 4.00
302 303 3.888930 CAGGGTGTTTGTACATTCAAGGT 59.111 43.478 0.00 0.00 36.50 3.50
303 304 3.305335 GCAGGGTGTTTGTACATTCAAGG 60.305 47.826 0.00 0.00 36.50 3.61
304 305 3.317711 TGCAGGGTGTTTGTACATTCAAG 59.682 43.478 0.00 0.00 36.50 3.02
305 306 3.291584 TGCAGGGTGTTTGTACATTCAA 58.708 40.909 0.00 0.00 36.50 2.69
306 307 2.937519 TGCAGGGTGTTTGTACATTCA 58.062 42.857 0.00 0.00 36.50 2.57
307 308 4.519540 ATTGCAGGGTGTTTGTACATTC 57.480 40.909 0.00 0.00 36.50 2.67
308 309 4.953940 AATTGCAGGGTGTTTGTACATT 57.046 36.364 0.00 0.00 36.50 2.71
309 310 4.953940 AAATTGCAGGGTGTTTGTACAT 57.046 36.364 0.00 0.00 36.50 2.29
310 311 4.437239 CAAAATTGCAGGGTGTTTGTACA 58.563 39.130 0.00 0.00 0.00 2.90
325 326 1.978097 CGTGATGTCCGTGCAAAATTG 59.022 47.619 0.00 0.00 0.00 2.32
326 327 1.665735 GCGTGATGTCCGTGCAAAATT 60.666 47.619 0.00 0.00 0.00 1.82
327 328 0.109781 GCGTGATGTCCGTGCAAAAT 60.110 50.000 0.00 0.00 0.00 1.82
328 329 1.163420 AGCGTGATGTCCGTGCAAAA 61.163 50.000 0.00 0.00 0.00 2.44
329 330 1.163420 AAGCGTGATGTCCGTGCAAA 61.163 50.000 0.00 0.00 0.00 3.68
330 331 1.163420 AAAGCGTGATGTCCGTGCAA 61.163 50.000 0.00 0.00 0.00 4.08
331 332 1.163420 AAAAGCGTGATGTCCGTGCA 61.163 50.000 0.00 0.00 0.00 4.57
332 333 0.725784 CAAAAGCGTGATGTCCGTGC 60.726 55.000 0.00 0.00 0.00 5.34
333 334 0.865111 TCAAAAGCGTGATGTCCGTG 59.135 50.000 0.00 0.00 0.00 4.94
334 335 1.148310 CTCAAAAGCGTGATGTCCGT 58.852 50.000 0.00 0.00 0.00 4.69
335 336 1.148310 ACTCAAAAGCGTGATGTCCG 58.852 50.000 0.00 0.00 0.00 4.79
336 337 4.184629 AGATACTCAAAAGCGTGATGTCC 58.815 43.478 0.00 0.00 0.00 4.02
337 338 5.554636 CAAGATACTCAAAAGCGTGATGTC 58.445 41.667 0.00 0.00 0.00 3.06
338 339 4.142816 GCAAGATACTCAAAAGCGTGATGT 60.143 41.667 0.00 0.00 0.00 3.06
339 340 4.142838 TGCAAGATACTCAAAAGCGTGATG 60.143 41.667 0.00 0.00 0.00 3.07
424 428 1.814772 TTCAATTTGGTGCCGGGCTG 61.815 55.000 21.46 8.22 0.00 4.85
436 440 9.358872 GAGGATAGAAAAGCGAAAATTCAATTT 57.641 29.630 0.00 0.00 0.00 1.82
611 615 5.767816 TCTTGGGAAGTTTTTCAACTAGC 57.232 39.130 0.00 0.00 42.89 3.42
653 660 2.364632 TGGCCGTAATGACATCCAAAG 58.635 47.619 0.00 0.00 0.00 2.77
654 661 2.498644 TGGCCGTAATGACATCCAAA 57.501 45.000 0.00 0.00 0.00 3.28
657 664 2.293399 GGATTTGGCCGTAATGACATCC 59.707 50.000 7.57 0.00 0.00 3.51
689 728 1.739466 CATGATAACGTGGCAAGCTGT 59.261 47.619 0.00 0.00 0.00 4.40
696 735 1.933853 GGTGAGACATGATAACGTGGC 59.066 52.381 0.00 0.00 41.06 5.01
721 760 2.195922 CAAACTGCAAAGCCACTTCAC 58.804 47.619 0.00 0.00 0.00 3.18
722 761 1.471327 GCAAACTGCAAAGCCACTTCA 60.471 47.619 0.00 0.00 44.26 3.02
724 763 3.367678 GCAAACTGCAAAGCCACTT 57.632 47.368 0.00 0.00 44.26 3.16
803 845 2.126031 GTTGAGAGGTCGGCCGAC 60.126 66.667 43.30 43.30 43.87 4.79
824 866 2.214920 GGGTGACGGGTGAGAGGTT 61.215 63.158 0.00 0.00 0.00 3.50
846 888 2.663852 GTGGGTGAACCGTCGTGG 60.664 66.667 0.00 0.00 44.64 4.94
871 913 4.386711 AGTTTTTATATAGGCGGAGTGGC 58.613 43.478 0.00 0.00 45.27 5.01
900 942 7.062957 TCTTCCTCTTTGTTTTCTTCTGGATT 58.937 34.615 0.00 0.00 0.00 3.01
950 1000 1.429930 TAGTCTTCCTGCAACCACCA 58.570 50.000 0.00 0.00 0.00 4.17
953 1003 2.265367 TGGATAGTCTTCCTGCAACCA 58.735 47.619 0.00 0.00 36.68 3.67
975 1025 3.772025 TGTTGGTGATCCTTGTGGTTTTT 59.228 39.130 0.00 0.00 34.23 1.94
997 1047 0.541296 ACCTTGGCTTGCTGCATCTT 60.541 50.000 1.84 0.00 45.15 2.40
1011 1061 2.440409 CCATCCTTCACCTTCACCTTG 58.560 52.381 0.00 0.00 0.00 3.61
1311 1392 4.266976 GGCACACGTATGTAACAGTACATC 59.733 45.833 0.00 0.00 46.01 3.06
1333 1414 5.890424 ATAACTTGACCAAATAACCACGG 57.110 39.130 0.00 0.00 0.00 4.94
1369 1450 4.655440 TCCACAACGTCAATAATTCACG 57.345 40.909 0.00 0.00 39.48 4.35
1386 1467 7.151308 TGTCAACCAATCATAAAAACATCCAC 58.849 34.615 0.00 0.00 0.00 4.02
1391 1472 6.815089 AGCTTGTCAACCAATCATAAAAACA 58.185 32.000 0.00 0.00 31.20 2.83
1487 1568 6.726379 TGTATGGGAGTGAAAACATGGATAA 58.274 36.000 0.00 0.00 0.00 1.75
1489 1570 5.191727 TGTATGGGAGTGAAAACATGGAT 57.808 39.130 0.00 0.00 0.00 3.41
1518 1599 2.572290 CTTGAACTGAGGAACCGGTTT 58.428 47.619 23.22 6.19 35.90 3.27
1519 1600 1.202770 CCTTGAACTGAGGAACCGGTT 60.203 52.381 22.50 22.50 38.27 4.44
1521 1602 0.321653 CCCTTGAACTGAGGAACCGG 60.322 60.000 0.00 0.00 36.33 5.28
1522 1603 0.685097 TCCCTTGAACTGAGGAACCG 59.315 55.000 0.00 0.00 36.33 4.44
1523 1604 1.611936 GCTCCCTTGAACTGAGGAACC 60.612 57.143 0.00 0.00 36.33 3.62
1529 1610 5.441718 AATTCATAGCTCCCTTGAACTGA 57.558 39.130 0.00 0.00 32.61 3.41
1565 1646 1.002624 TAGCTCCTTGCCCGGTTTG 60.003 57.895 0.00 0.00 44.23 2.93
1566 1647 1.002502 GTAGCTCCTTGCCCGGTTT 60.003 57.895 0.00 0.00 44.23 3.27
1567 1648 1.774894 TTGTAGCTCCTTGCCCGGTT 61.775 55.000 0.00 0.00 44.23 4.44
1568 1649 1.774894 TTTGTAGCTCCTTGCCCGGT 61.775 55.000 0.00 0.00 44.23 5.28
1569 1650 0.394352 ATTTGTAGCTCCTTGCCCGG 60.394 55.000 0.00 0.00 44.23 5.73
1570 1651 1.463674 AATTTGTAGCTCCTTGCCCG 58.536 50.000 0.00 0.00 44.23 6.13
1571 1652 6.901081 ATTATAATTTGTAGCTCCTTGCCC 57.099 37.500 0.00 0.00 44.23 5.36
1572 1653 9.034544 CAAAATTATAATTTGTAGCTCCTTGCC 57.965 33.333 21.23 0.00 39.37 4.52
1573 1654 9.586435 ACAAAATTATAATTTGTAGCTCCTTGC 57.414 29.630 21.23 0.00 46.21 4.01
1585 1666 9.377312 CCCGGTTTGATCACAAAATTATAATTT 57.623 29.630 16.15 16.15 45.65 1.82
1586 1667 8.536175 ACCCGGTTTGATCACAAAATTATAATT 58.464 29.630 4.81 4.81 45.65 1.40
1587 1668 8.073467 ACCCGGTTTGATCACAAAATTATAAT 57.927 30.769 0.00 0.00 45.65 1.28
1588 1669 7.469537 ACCCGGTTTGATCACAAAATTATAA 57.530 32.000 0.00 0.00 45.65 0.98
1589 1670 8.577048 TTACCCGGTTTGATCACAAAATTATA 57.423 30.769 0.00 0.00 45.65 0.98
1590 1671 5.993748 ACCCGGTTTGATCACAAAATTAT 57.006 34.783 0.00 0.00 45.65 1.28
1591 1672 6.896021 TTACCCGGTTTGATCACAAAATTA 57.104 33.333 0.00 0.00 45.65 1.40
1592 1673 5.793030 TTACCCGGTTTGATCACAAAATT 57.207 34.783 0.00 0.00 45.65 1.82
1593 1674 5.993748 ATTACCCGGTTTGATCACAAAAT 57.006 34.783 0.00 0.00 45.65 1.82
1594 1675 5.106634 CGTATTACCCGGTTTGATCACAAAA 60.107 40.000 0.00 0.00 45.65 2.44
1595 1676 4.392445 CGTATTACCCGGTTTGATCACAAA 59.608 41.667 0.00 0.00 42.66 2.83
1596 1677 3.933955 CGTATTACCCGGTTTGATCACAA 59.066 43.478 0.00 0.00 0.00 3.33
1597 1678 3.523547 CGTATTACCCGGTTTGATCACA 58.476 45.455 0.00 0.00 0.00 3.58
1598 1679 2.867975 CCGTATTACCCGGTTTGATCAC 59.132 50.000 0.00 0.00 40.59 3.06
1599 1680 3.182341 CCGTATTACCCGGTTTGATCA 57.818 47.619 0.00 0.00 40.59 2.92
1609 1690 4.995487 GGATCAAGATGAACCGTATTACCC 59.005 45.833 0.00 0.00 29.57 3.69
1612 1693 7.606135 TTAGGGATCAAGATGAACCGTATTA 57.394 36.000 9.06 0.00 39.90 0.98
1615 1696 5.943349 TTTAGGGATCAAGATGAACCGTA 57.057 39.130 5.34 5.34 39.90 4.02
1651 1805 8.465999 AGCATGAGTCATAGACATAGTAATAGC 58.534 37.037 5.03 0.00 34.60 2.97
1662 1816 3.230134 AGGAGGAGCATGAGTCATAGAC 58.770 50.000 5.03 0.00 0.00 2.59
1664 1818 2.562298 GGAGGAGGAGCATGAGTCATAG 59.438 54.545 5.03 1.94 0.00 2.23
1665 1819 2.178764 AGGAGGAGGAGCATGAGTCATA 59.821 50.000 5.03 0.00 0.00 2.15
1673 1929 0.188342 GAGAGGAGGAGGAGGAGCAT 59.812 60.000 0.00 0.00 0.00 3.79
1676 1932 1.687996 GGTTGAGAGGAGGAGGAGGAG 60.688 61.905 0.00 0.00 0.00 3.69
1680 1936 1.682684 GCGGTTGAGAGGAGGAGGA 60.683 63.158 0.00 0.00 0.00 3.71
1687 1943 1.811266 CACGGATGCGGTTGAGAGG 60.811 63.158 12.44 0.00 0.00 3.69
1688 1944 2.456119 GCACGGATGCGGTTGAGAG 61.456 63.158 12.44 0.00 43.33 3.20
1689 1945 2.434185 GCACGGATGCGGTTGAGA 60.434 61.111 12.44 0.00 43.33 3.27
1727 1983 0.767375 ACCAATCGGATCCCTCCATG 59.233 55.000 6.06 0.00 42.19 3.66
1728 1984 1.059913 GACCAATCGGATCCCTCCAT 58.940 55.000 6.06 0.00 42.19 3.41
1729 1985 1.054406 GGACCAATCGGATCCCTCCA 61.054 60.000 6.06 0.00 42.19 3.86
1731 1987 0.682292 GAGGACCAATCGGATCCCTC 59.318 60.000 6.06 0.15 38.62 4.30
1732 1988 0.764752 GGAGGACCAATCGGATCCCT 60.765 60.000 6.06 0.00 34.45 4.20
1754 2012 0.101399 CCTCCTCAACACCGATCTCG 59.899 60.000 0.00 0.00 39.44 4.04
1756 2014 1.759445 CATCCTCCTCAACACCGATCT 59.241 52.381 0.00 0.00 0.00 2.75
1759 2017 1.001974 CAACATCCTCCTCAACACCGA 59.998 52.381 0.00 0.00 0.00 4.69
1760 2018 1.442769 CAACATCCTCCTCAACACCG 58.557 55.000 0.00 0.00 0.00 4.94
1766 2024 3.561960 CCAATTCACCAACATCCTCCTCA 60.562 47.826 0.00 0.00 0.00 3.86
1772 2030 3.445096 CCTCTTCCAATTCACCAACATCC 59.555 47.826 0.00 0.00 0.00 3.51
1774 2032 4.118168 ACCTCTTCCAATTCACCAACAT 57.882 40.909 0.00 0.00 0.00 2.71
1775 2033 3.593442 ACCTCTTCCAATTCACCAACA 57.407 42.857 0.00 0.00 0.00 3.33
1777 2035 4.028993 GGTACCTCTTCCAATTCACCAA 57.971 45.455 4.06 0.00 0.00 3.67
1808 2069 0.117140 TCATGGTGTCTCCCTCCTGT 59.883 55.000 0.00 0.00 34.77 4.00
1809 2070 0.539051 GTCATGGTGTCTCCCTCCTG 59.461 60.000 0.00 0.00 34.77 3.86
1811 2072 0.970937 TCGTCATGGTGTCTCCCTCC 60.971 60.000 0.00 0.00 34.77 4.30
1818 2079 1.195448 CAGTGCTTTCGTCATGGTGTC 59.805 52.381 0.00 0.00 0.00 3.67
1820 2081 1.511850 TCAGTGCTTTCGTCATGGTG 58.488 50.000 0.00 0.00 0.00 4.17
1821 2082 2.079158 CATCAGTGCTTTCGTCATGGT 58.921 47.619 0.00 0.00 0.00 3.55
1833 2094 1.656095 GACTTACTGCGTCATCAGTGC 59.344 52.381 6.67 0.00 45.95 4.40
1840 2101 0.601558 GTCCAGGACTTACTGCGTCA 59.398 55.000 12.94 0.00 37.16 4.35
1841 2102 0.601558 TGTCCAGGACTTACTGCGTC 59.398 55.000 20.82 0.00 37.16 5.19
1842 2103 0.317479 GTGTCCAGGACTTACTGCGT 59.683 55.000 20.82 0.00 37.16 5.24
1843 2104 0.389948 GGTGTCCAGGACTTACTGCG 60.390 60.000 20.82 0.00 37.16 5.18
1866 2127 2.558380 GAATTCTCCCTGCCCGCCTT 62.558 60.000 0.00 0.00 0.00 4.35
1872 2133 1.943340 GAATCGTGAATTCTCCCTGCC 59.057 52.381 7.05 0.00 40.62 4.85
1881 2142 5.047731 TGTCACTGAGAGAGAATCGTGAATT 60.048 40.000 0.00 0.00 42.67 2.17
1883 2144 3.821033 TGTCACTGAGAGAGAATCGTGAA 59.179 43.478 0.00 0.00 42.67 3.18
1884 2145 3.412386 TGTCACTGAGAGAGAATCGTGA 58.588 45.455 0.00 0.00 42.67 4.35
1885 2146 3.839051 TGTCACTGAGAGAGAATCGTG 57.161 47.619 0.00 0.00 42.67 4.35
1886 2147 3.761218 ACATGTCACTGAGAGAGAATCGT 59.239 43.478 0.00 0.00 42.67 3.73
1887 2148 4.104066 CACATGTCACTGAGAGAGAATCG 58.896 47.826 0.00 0.00 42.67 3.34
1888 2149 5.321959 TCACATGTCACTGAGAGAGAATC 57.678 43.478 0.00 0.00 0.00 2.52
1889 2150 4.381825 GCTCACATGTCACTGAGAGAGAAT 60.382 45.833 13.65 0.00 36.35 2.40
1890 2151 3.056962 GCTCACATGTCACTGAGAGAGAA 60.057 47.826 13.65 0.00 36.35 2.87
1891 2152 2.491298 GCTCACATGTCACTGAGAGAGA 59.509 50.000 13.65 0.00 36.35 3.10
1892 2153 2.230750 TGCTCACATGTCACTGAGAGAG 59.769 50.000 13.65 7.93 36.35 3.20
1893 2154 2.230750 CTGCTCACATGTCACTGAGAGA 59.769 50.000 13.65 0.00 36.35 3.10
1899 2160 2.924185 GTGCTGCTCACATGTCACT 58.076 52.632 0.00 0.00 44.98 3.41
1910 2171 1.708993 TTCCCTTGTCTGGTGCTGCT 61.709 55.000 0.00 0.00 0.00 4.24
1914 2175 1.168714 GTGATTCCCTTGTCTGGTGC 58.831 55.000 0.00 0.00 0.00 5.01
1918 2179 3.319137 TTCTCGTGATTCCCTTGTCTG 57.681 47.619 0.00 0.00 0.00 3.51
1930 2191 3.020274 CCTCTCATCTCCTTTCTCGTGA 58.980 50.000 0.00 0.00 0.00 4.35
1933 2194 2.034558 GCTCCTCTCATCTCCTTTCTCG 59.965 54.545 0.00 0.00 0.00 4.04
1945 2206 1.839994 CCTAAACCCATGCTCCTCTCA 59.160 52.381 0.00 0.00 0.00 3.27
1951 2212 3.389329 TCTCATCTCCTAAACCCATGCTC 59.611 47.826 0.00 0.00 0.00 4.26
1953 2214 3.737850 CTCTCATCTCCTAAACCCATGC 58.262 50.000 0.00 0.00 0.00 4.06
1958 2219 1.539280 GCCGCTCTCATCTCCTAAACC 60.539 57.143 0.00 0.00 0.00 3.27
1961 2222 1.410517 CTTGCCGCTCTCATCTCCTAA 59.589 52.381 0.00 0.00 0.00 2.69
1965 2226 2.134346 GATTCTTGCCGCTCTCATCTC 58.866 52.381 0.00 0.00 0.00 2.75
1969 2230 3.827008 ATAAGATTCTTGCCGCTCTCA 57.173 42.857 9.22 0.00 0.00 3.27
1976 2237 2.808543 CCGTGCCTATAAGATTCTTGCC 59.191 50.000 9.22 0.00 0.00 4.52
1977 2238 2.808543 CCCGTGCCTATAAGATTCTTGC 59.191 50.000 9.22 4.54 0.00 4.01
1978 2239 3.403038 CCCCGTGCCTATAAGATTCTTG 58.597 50.000 9.22 0.00 0.00 3.02
1979 2240 2.372172 CCCCCGTGCCTATAAGATTCTT 59.628 50.000 4.03 4.03 0.00 2.52
1980 2241 1.978580 CCCCCGTGCCTATAAGATTCT 59.021 52.381 0.00 0.00 0.00 2.40
1981 2242 1.975680 TCCCCCGTGCCTATAAGATTC 59.024 52.381 0.00 0.00 0.00 2.52
1982 2243 1.978580 CTCCCCCGTGCCTATAAGATT 59.021 52.381 0.00 0.00 0.00 2.40
1983 2244 1.645710 CTCCCCCGTGCCTATAAGAT 58.354 55.000 0.00 0.00 0.00 2.40
1984 2245 0.471211 CCTCCCCCGTGCCTATAAGA 60.471 60.000 0.00 0.00 0.00 2.10
1985 2246 2.058675 CCTCCCCCGTGCCTATAAG 58.941 63.158 0.00 0.00 0.00 1.73
1986 2247 2.144738 GCCTCCCCCGTGCCTATAA 61.145 63.158 0.00 0.00 0.00 0.98
1987 2248 2.525877 GCCTCCCCCGTGCCTATA 60.526 66.667 0.00 0.00 0.00 1.31
1996 2257 4.772687 GACGTTTCGGCCTCCCCC 62.773 72.222 0.00 0.00 0.00 5.40
2014 2275 3.434299 GCAAATGGCATTCTGAACAAAGG 59.566 43.478 14.04 0.00 43.97 3.11
2028 2289 1.068055 CAGTCTTGACTGGCAAATGGC 60.068 52.381 19.75 0.00 43.74 4.40
2063 2867 5.070770 TGACATTATTGTTTGCCATGTCC 57.929 39.130 7.86 0.00 42.04 4.02
2078 2882 1.153647 CGAGGCACCGCTGACATTA 60.154 57.895 0.00 0.00 0.00 1.90
2079 2883 2.244117 ATCGAGGCACCGCTGACATT 62.244 55.000 0.00 0.00 0.00 2.71
2080 2884 2.244117 AATCGAGGCACCGCTGACAT 62.244 55.000 0.00 0.00 0.00 3.06
2081 2885 2.835701 GAATCGAGGCACCGCTGACA 62.836 60.000 0.00 0.00 0.00 3.58
2090 2894 0.909610 AGGGTTGAGGAATCGAGGCA 60.910 55.000 0.00 0.00 0.00 4.75
2109 2913 2.261361 CCACATGACGCTGACCGA 59.739 61.111 0.00 0.00 41.02 4.69
2111 2915 2.358615 TGCCACATGACGCTGACC 60.359 61.111 0.00 0.00 0.00 4.02
2124 2928 0.703488 TGAAGGGGAATCATGTGCCA 59.297 50.000 0.00 0.00 0.00 4.92
2128 2932 3.545703 GATCGTTGAAGGGGAATCATGT 58.454 45.455 0.00 0.00 0.00 3.21
2131 2935 1.134521 CGGATCGTTGAAGGGGAATCA 60.135 52.381 0.00 0.00 0.00 2.57
2149 2953 2.357952 TCTCGACTACAATGATGGACGG 59.642 50.000 0.00 0.00 0.00 4.79
2150 2954 3.692791 TCTCGACTACAATGATGGACG 57.307 47.619 0.00 0.00 0.00 4.79
2151 2955 4.222886 CGATCTCGACTACAATGATGGAC 58.777 47.826 0.00 0.00 43.02 4.02
2152 2956 3.883489 ACGATCTCGACTACAATGATGGA 59.117 43.478 6.60 0.00 43.02 3.41
2157 2961 2.357952 TCCCACGATCTCGACTACAATG 59.642 50.000 6.60 0.00 43.02 2.82
2158 2962 2.651455 TCCCACGATCTCGACTACAAT 58.349 47.619 6.60 0.00 43.02 2.71
2159 2963 2.118313 TCCCACGATCTCGACTACAA 57.882 50.000 6.60 0.00 43.02 2.41
2162 2974 6.401047 AAAATATTCCCACGATCTCGACTA 57.599 37.500 6.60 0.00 43.02 2.59
2164 2976 5.577860 GAAAATATTCCCACGATCTCGAC 57.422 43.478 6.60 0.00 43.02 4.20
2190 3003 2.271821 CATCCGGTCACATGGCCA 59.728 61.111 8.56 8.56 40.62 5.36
2192 3005 2.124570 AGCATCCGGTCACATGGC 60.125 61.111 0.00 0.00 0.00 4.40
2195 3008 2.124570 GGCAGCATCCGGTCACAT 60.125 61.111 0.00 0.00 0.00 3.21
2257 3071 5.839621 ACTTGTTAAGTCTCTTTGCGTCTA 58.160 37.500 0.00 0.00 37.02 2.59
2258 3072 4.694339 ACTTGTTAAGTCTCTTTGCGTCT 58.306 39.130 0.00 0.00 37.02 4.18


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

AutoCloner maintained by Alex Coulton.