Multiple sequence alignment - TraesCS7A01G563400

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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 TraesCS7A01G563400 chr7A 100.000 1526 0 0 982 2507 733529359 733530884 0.000000e+00 2819.0
1 TraesCS7A01G563400 chr7A 100.000 619 0 0 1 619 733528378 733528996 0.000000e+00 1144.0
2 TraesCS7A01G563400 chr7A 76.349 482 90 15 1079 1549 97410547 97411015 1.160000e-58 237.0
3 TraesCS7A01G563400 chr7D 87.974 1214 85 29 1327 2507 633532682 633531497 0.000000e+00 1376.0
4 TraesCS7A01G563400 chr7D 90.667 150 10 4 1149 1298 633532828 633532683 1.970000e-46 196.0
5 TraesCS7A01G563400 chr7D 94.792 96 4 1 990 1085 633532924 633532830 5.590000e-32 148.0
6 TraesCS7A01G563400 chr7D 79.343 213 37 5 1220 1427 94126487 94126697 2.600000e-30 143.0
7 TraesCS7A01G563400 chr7B 87.325 1215 76 30 1323 2505 749549368 749548200 0.000000e+00 1319.0
8 TraesCS7A01G563400 chr7B 89.666 329 26 6 990 1317 749549889 749549568 1.790000e-111 412.0
9 TraesCS7A01G563400 chr7B 82.768 383 32 17 108 489 749551401 749551052 6.730000e-81 311.0
10 TraesCS7A01G563400 chr2D 94.898 98 4 1 522 619 88309329 88309425 4.320000e-33 152.0
11 TraesCS7A01G563400 chr2A 93.878 98 6 0 522 619 550886053 550885956 5.590000e-32 148.0
12 TraesCS7A01G563400 chr6A 94.737 95 3 1 525 619 600886537 600886629 2.010000e-31 147.0
13 TraesCS7A01G563400 chr6A 90.110 91 8 1 529 619 521486291 521486202 1.580000e-22 117.0
14 TraesCS7A01G563400 chr6D 93.548 93 6 0 526 618 451936695 451936787 3.360000e-29 139.0
15 TraesCS7A01G563400 chr4A 92.553 94 6 1 526 619 594456894 594456986 1.560000e-27 134.0
16 TraesCS7A01G563400 chr3A 91.489 94 8 0 526 619 21162218 21162125 2.020000e-26 130.0
17 TraesCS7A01G563400 chr3B 90.426 94 8 1 526 619 798406758 798406850 3.390000e-24 122.0
18 TraesCS7A01G563400 chr3D 87.097 93 10 2 526 618 260455745 260455655 1.230000e-18 104.0
19 TraesCS7A01G563400 chr6B 90.385 52 2 1 1558 1606 116105428 116105377 5.790000e-07 65.8


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 TraesCS7A01G563400 chr7A 733528378 733530884 2506 False 1981.500000 2819 100.000000 1 2507 2 chr7A.!!$F2 2506
1 TraesCS7A01G563400 chr7D 633531497 633532924 1427 True 573.333333 1376 91.144333 990 2507 3 chr7D.!!$R1 1517
2 TraesCS7A01G563400 chr7B 749548200 749551401 3201 True 680.666667 1319 86.586333 108 2505 3 chr7B.!!$R1 2397

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
549 1689 0.035056 GTGGAGCTACATGCAACCCT 60.035 55.0 0.0 0.0 45.94 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 2867 0.250553 TGAAACAAATCCGGAGCCGT 60.251 50.0 11.34 3.11 37.81 5.68 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.553308 CCGAAGATAAACGGTCGACC 58.447 55.000 25.28 25.28 43.53 4.79
23 24 1.135315 CCGAAGATAAACGGTCGACCA 60.135 52.381 32.80 15.11 43.53 4.02
24 25 2.598589 CGAAGATAAACGGTCGACCAA 58.401 47.619 32.80 15.93 34.51 3.67
25 26 2.988493 CGAAGATAAACGGTCGACCAAA 59.012 45.455 32.80 15.57 34.51 3.28
26 27 3.181537 CGAAGATAAACGGTCGACCAAAC 60.182 47.826 32.80 16.94 34.51 2.93
27 28 2.691927 AGATAAACGGTCGACCAAACC 58.308 47.619 32.80 16.24 35.14 3.27
28 29 2.301009 AGATAAACGGTCGACCAAACCT 59.699 45.455 32.80 18.07 34.45 3.50
29 30 3.511146 AGATAAACGGTCGACCAAACCTA 59.489 43.478 32.80 16.46 34.45 3.08
30 31 2.159327 AAACGGTCGACCAAACCTAG 57.841 50.000 32.80 17.49 34.45 3.02
31 32 0.320160 AACGGTCGACCAAACCTAGC 60.320 55.000 32.80 4.00 34.45 3.42
32 33 1.290955 CGGTCGACCAAACCTAGCA 59.709 57.895 32.80 0.00 34.45 3.49
33 34 0.320073 CGGTCGACCAAACCTAGCAA 60.320 55.000 32.80 0.00 34.45 3.91
34 35 1.154197 GGTCGACCAAACCTAGCAAC 58.846 55.000 29.75 0.00 33.78 4.17
35 36 1.154197 GTCGACCAAACCTAGCAACC 58.846 55.000 3.51 0.00 0.00 3.77
36 37 0.759959 TCGACCAAACCTAGCAACCA 59.240 50.000 0.00 0.00 0.00 3.67
37 38 0.872388 CGACCAAACCTAGCAACCAC 59.128 55.000 0.00 0.00 0.00 4.16
38 39 1.812324 CGACCAAACCTAGCAACCACA 60.812 52.381 0.00 0.00 0.00 4.17
39 40 2.514803 GACCAAACCTAGCAACCACAT 58.485 47.619 0.00 0.00 0.00 3.21
40 41 2.890945 GACCAAACCTAGCAACCACATT 59.109 45.455 0.00 0.00 0.00 2.71
41 42 4.076394 GACCAAACCTAGCAACCACATTA 58.924 43.478 0.00 0.00 0.00 1.90
42 43 3.824443 ACCAAACCTAGCAACCACATTAC 59.176 43.478 0.00 0.00 0.00 1.89
43 44 4.079253 CCAAACCTAGCAACCACATTACT 58.921 43.478 0.00 0.00 0.00 2.24
44 45 5.221966 ACCAAACCTAGCAACCACATTACTA 60.222 40.000 0.00 0.00 0.00 1.82
45 46 5.708230 CCAAACCTAGCAACCACATTACTAA 59.292 40.000 0.00 0.00 0.00 2.24
46 47 6.207810 CCAAACCTAGCAACCACATTACTAAA 59.792 38.462 0.00 0.00 0.00 1.85
47 48 6.812879 AACCTAGCAACCACATTACTAAAC 57.187 37.500 0.00 0.00 0.00 2.01
48 49 5.871834 ACCTAGCAACCACATTACTAAACA 58.128 37.500 0.00 0.00 0.00 2.83
49 50 6.300703 ACCTAGCAACCACATTACTAAACAA 58.699 36.000 0.00 0.00 0.00 2.83
50 51 6.946009 ACCTAGCAACCACATTACTAAACAAT 59.054 34.615 0.00 0.00 0.00 2.71
51 52 7.450323 ACCTAGCAACCACATTACTAAACAATT 59.550 33.333 0.00 0.00 0.00 2.32
52 53 8.303876 CCTAGCAACCACATTACTAAACAATTT 58.696 33.333 0.00 0.00 0.00 1.82
53 54 9.691362 CTAGCAACCACATTACTAAACAATTTT 57.309 29.630 0.00 0.00 0.00 1.82
54 55 8.587952 AGCAACCACATTACTAAACAATTTTC 57.412 30.769 0.00 0.00 0.00 2.29
55 56 8.421002 AGCAACCACATTACTAAACAATTTTCT 58.579 29.630 0.00 0.00 0.00 2.52
56 57 9.685828 GCAACCACATTACTAAACAATTTTCTA 57.314 29.630 0.00 0.00 0.00 2.10
59 60 9.357161 ACCACATTACTAAACAATTTTCTACCA 57.643 29.630 0.00 0.00 0.00 3.25
67 68 6.875948 AAACAATTTTCTACCAAAATGGGC 57.124 33.333 0.87 0.00 43.37 5.36
68 69 4.905429 ACAATTTTCTACCAAAATGGGCC 58.095 39.130 0.00 0.00 43.37 5.80
69 70 4.597075 ACAATTTTCTACCAAAATGGGCCT 59.403 37.500 4.53 0.00 43.37 5.19
70 71 4.824479 ATTTTCTACCAAAATGGGCCTG 57.176 40.909 4.53 0.00 43.37 4.85
71 72 1.555967 TTCTACCAAAATGGGCCTGC 58.444 50.000 4.53 0.00 43.37 4.85
72 73 0.324275 TCTACCAAAATGGGCCTGCC 60.324 55.000 4.53 0.00 43.37 4.85
73 74 1.666209 CTACCAAAATGGGCCTGCCG 61.666 60.000 4.53 0.00 43.37 5.69
74 75 4.455906 CCAAAATGGGCCTGCCGC 62.456 66.667 4.53 0.00 36.85 6.53
75 76 3.384532 CAAAATGGGCCTGCCGCT 61.385 61.111 4.53 0.00 37.74 5.52
76 77 2.051518 CAAAATGGGCCTGCCGCTA 61.052 57.895 4.53 0.00 37.74 4.26
77 78 1.754234 AAAATGGGCCTGCCGCTAG 60.754 57.895 4.53 0.00 37.74 3.42
78 79 2.499303 AAAATGGGCCTGCCGCTAGT 62.499 55.000 4.53 0.00 37.74 2.57
79 80 3.704231 AATGGGCCTGCCGCTAGTG 62.704 63.158 4.53 0.00 37.74 2.74
82 83 4.410400 GGCCTGCCGCTAGTGGTT 62.410 66.667 23.09 0.00 37.74 3.67
83 84 3.127533 GCCTGCCGCTAGTGGTTG 61.128 66.667 23.09 15.26 0.00 3.77
84 85 2.436646 CCTGCCGCTAGTGGTTGG 60.437 66.667 23.09 19.74 0.00 3.77
88 89 4.388499 CCGCTAGTGGTTGGCCGT 62.388 66.667 14.58 0.00 37.67 5.68
89 90 2.813908 CGCTAGTGGTTGGCCGTC 60.814 66.667 0.00 0.00 37.67 4.79
90 91 2.813908 GCTAGTGGTTGGCCGTCG 60.814 66.667 0.00 0.00 37.67 5.12
91 92 2.125673 CTAGTGGTTGGCCGTCGG 60.126 66.667 6.99 6.99 37.67 4.79
101 102 2.105528 GCCGTCGGCGATTTCCTA 59.894 61.111 22.50 0.00 39.62 2.94
102 103 1.300697 GCCGTCGGCGATTTCCTAT 60.301 57.895 22.50 0.00 39.62 2.57
103 104 0.878961 GCCGTCGGCGATTTCCTATT 60.879 55.000 22.50 0.00 39.62 1.73
104 105 1.603678 GCCGTCGGCGATTTCCTATTA 60.604 52.381 22.50 0.00 39.62 0.98
105 106 2.325761 CCGTCGGCGATTTCCTATTAG 58.674 52.381 12.93 0.00 41.33 1.73
106 107 2.030540 CCGTCGGCGATTTCCTATTAGA 60.031 50.000 12.93 0.00 41.33 2.10
164 165 3.058160 CAACCCGCTGCCCTCAAG 61.058 66.667 0.00 0.00 0.00 3.02
165 166 4.351054 AACCCGCTGCCCTCAAGG 62.351 66.667 0.00 0.00 39.47 3.61
201 208 2.943033 GCCGCACCACTACATATTTCTT 59.057 45.455 0.00 0.00 0.00 2.52
223 230 8.343168 TCTTTTCTTTTCTCCTGTGTAAAACA 57.657 30.769 0.00 0.00 37.22 2.83
401 408 7.922505 TTGTTCGGAGAATGTAATTTGTTTG 57.077 32.000 0.00 0.00 45.90 2.93
406 413 7.136119 TCGGAGAATGTAATTTGTTTGTGTTC 58.864 34.615 0.00 0.00 36.07 3.18
418 425 8.647143 ATTTGTTTGTGTTCTCATGGTTTTAG 57.353 30.769 0.00 0.00 0.00 1.85
422 429 7.757624 TGTTTGTGTTCTCATGGTTTTAGAAAC 59.242 33.333 0.00 0.00 31.41 2.78
426 433 7.122055 TGTGTTCTCATGGTTTTAGAAACTGTT 59.878 33.333 0.00 0.00 31.41 3.16
427 434 7.644157 GTGTTCTCATGGTTTTAGAAACTGTTC 59.356 37.037 0.00 0.00 31.41 3.18
428 435 7.338196 TGTTCTCATGGTTTTAGAAACTGTTCA 59.662 33.333 0.00 0.00 36.09 3.18
469 476 9.901724 GAATATGTTCTATAATATTCGGTTGCG 57.098 33.333 0.00 0.00 36.53 4.85
476 483 2.755836 ATATTCGGTTGCGCAATGTC 57.244 45.000 27.79 17.21 0.00 3.06
517 1657 5.615289 ACATTTTTCTAGCCGCTCTATCAT 58.385 37.500 0.00 0.00 0.00 2.45
518 1658 5.468072 ACATTTTTCTAGCCGCTCTATCATG 59.532 40.000 0.00 0.00 0.00 3.07
519 1659 4.672587 TTTTCTAGCCGCTCTATCATGT 57.327 40.909 0.00 0.00 0.00 3.21
520 1660 3.650070 TTCTAGCCGCTCTATCATGTG 57.350 47.619 0.00 0.00 0.00 3.21
521 1661 2.587522 TCTAGCCGCTCTATCATGTGT 58.412 47.619 0.00 0.00 0.00 3.72
522 1662 2.294512 TCTAGCCGCTCTATCATGTGTG 59.705 50.000 0.00 0.00 0.00 3.82
523 1663 1.114627 AGCCGCTCTATCATGTGTGA 58.885 50.000 0.00 0.00 39.04 3.58
524 1664 1.202463 AGCCGCTCTATCATGTGTGAC 60.202 52.381 0.00 0.00 37.14 3.67
525 1665 1.858091 CCGCTCTATCATGTGTGACC 58.142 55.000 0.00 0.00 37.14 4.02
526 1666 1.136891 CCGCTCTATCATGTGTGACCA 59.863 52.381 0.00 0.00 37.14 4.02
527 1667 2.196749 CGCTCTATCATGTGTGACCAC 58.803 52.381 0.00 0.00 42.19 4.16
528 1668 2.159184 CGCTCTATCATGTGTGACCACT 60.159 50.000 1.62 0.00 42.34 4.00
529 1669 3.193263 GCTCTATCATGTGTGACCACTG 58.807 50.000 1.62 0.00 42.34 3.66
530 1670 3.790091 CTCTATCATGTGTGACCACTGG 58.210 50.000 1.62 0.00 42.34 4.00
531 1671 3.173151 TCTATCATGTGTGACCACTGGT 58.827 45.455 0.00 0.00 42.34 4.00
532 1672 2.189594 ATCATGTGTGACCACTGGTG 57.810 50.000 5.10 0.00 42.34 4.17
543 1683 2.772739 CACTGGTGGAGCTACATGC 58.227 57.895 0.00 0.00 43.29 4.06
544 1684 0.036105 CACTGGTGGAGCTACATGCA 60.036 55.000 0.00 0.00 45.94 3.96
545 1685 0.692476 ACTGGTGGAGCTACATGCAA 59.308 50.000 0.00 0.00 45.94 4.08
546 1686 1.089920 CTGGTGGAGCTACATGCAAC 58.910 55.000 0.00 0.00 45.94 4.17
547 1687 0.322456 TGGTGGAGCTACATGCAACC 60.322 55.000 0.00 0.00 45.94 3.77
548 1688 1.032114 GGTGGAGCTACATGCAACCC 61.032 60.000 0.00 0.00 45.94 4.11
549 1689 0.035056 GTGGAGCTACATGCAACCCT 60.035 55.000 0.00 0.00 45.94 4.34
550 1690 0.035152 TGGAGCTACATGCAACCCTG 60.035 55.000 0.00 0.00 45.94 4.45
588 1728 4.707210 CGCAGGTTTGGTAAATTTTGTG 57.293 40.909 0.00 0.00 0.00 3.33
589 1729 4.363999 CGCAGGTTTGGTAAATTTTGTGA 58.636 39.130 0.00 0.00 0.00 3.58
590 1730 4.806247 CGCAGGTTTGGTAAATTTTGTGAA 59.194 37.500 0.00 0.00 0.00 3.18
591 1731 5.051106 CGCAGGTTTGGTAAATTTTGTGAAG 60.051 40.000 0.00 0.00 0.00 3.02
592 1732 6.045955 GCAGGTTTGGTAAATTTTGTGAAGA 58.954 36.000 0.00 0.00 0.00 2.87
593 1733 6.536941 GCAGGTTTGGTAAATTTTGTGAAGAA 59.463 34.615 0.00 0.00 0.00 2.52
594 1734 7.065204 GCAGGTTTGGTAAATTTTGTGAAGAAA 59.935 33.333 0.00 0.00 0.00 2.52
595 1735 9.108284 CAGGTTTGGTAAATTTTGTGAAGAAAT 57.892 29.630 0.00 0.00 0.00 2.17
596 1736 9.679661 AGGTTTGGTAAATTTTGTGAAGAAATT 57.320 25.926 0.00 0.00 38.09 1.82
1017 2157 3.264450 ACCCTATGTTTCTCCCACTTCTG 59.736 47.826 0.00 0.00 0.00 3.02
1027 2167 0.388649 CCCACTTCTGTTCCTCGTCG 60.389 60.000 0.00 0.00 0.00 5.12
1052 2192 0.610687 CTTCTCTTCGGCTCAACCCT 59.389 55.000 0.00 0.00 33.26 4.34
1056 2196 1.672356 CTTCGGCTCAACCCTGTGG 60.672 63.158 0.00 0.00 33.26 4.17
1087 2228 0.111253 CTCAACCCAAAGCTCCCAGT 59.889 55.000 0.00 0.00 0.00 4.00
1092 2233 0.890996 CCCAAAGCTCCCAGTGTCAC 60.891 60.000 0.00 0.00 0.00 3.67
1093 2234 0.890996 CCAAAGCTCCCAGTGTCACC 60.891 60.000 0.00 0.00 0.00 4.02
1123 2264 3.231298 AGGTCATTCCTAGCCGGC 58.769 61.111 21.89 21.89 46.10 6.13
1126 2267 1.451936 GTCATTCCTAGCCGGCCAT 59.548 57.895 26.15 8.44 0.00 4.40
1137 2278 1.001393 CCGGCCATACAACCACCTT 60.001 57.895 2.24 0.00 0.00 3.50
1181 2322 3.879892 GGAATTATCCTCCTTGAGCACAC 59.120 47.826 0.00 0.00 42.93 3.82
1259 2403 4.955811 TGCGATATGGGAGTAGATTGTT 57.044 40.909 0.00 0.00 0.00 2.83
1277 2421 8.650143 AGATTGTTATGGGAAGTATTGTGTTT 57.350 30.769 0.00 0.00 0.00 2.83
1302 2446 5.415221 AGATGAGTTCGTTTGAATCCTCTC 58.585 41.667 0.00 0.00 36.29 3.20
1317 2461 2.510382 TCCTCTCCGTGTATCCTTCTCT 59.490 50.000 0.00 0.00 0.00 3.10
1319 2463 3.546724 CTCTCCGTGTATCCTTCTCTGA 58.453 50.000 0.00 0.00 0.00 3.27
1320 2464 3.948473 CTCTCCGTGTATCCTTCTCTGAA 59.052 47.826 0.00 0.00 0.00 3.02
1321 2465 3.948473 TCTCCGTGTATCCTTCTCTGAAG 59.052 47.826 0.70 0.70 0.00 3.02
1356 2695 1.936547 GACGAAGATGAGGACATTGCC 59.063 52.381 0.00 0.00 36.82 4.52
1365 2704 3.972133 TGAGGACATTGCCTTGATCATT 58.028 40.909 0.00 0.00 38.73 2.57
1366 2705 3.697542 TGAGGACATTGCCTTGATCATTG 59.302 43.478 0.00 0.00 38.73 2.82
1367 2706 2.429610 AGGACATTGCCTTGATCATTGC 59.570 45.455 9.42 9.42 33.46 3.56
1394 2733 2.420022 ACATGCATTAGAACAAGCGACC 59.580 45.455 0.00 0.00 0.00 4.79
1409 2748 1.086696 CGACCGAAGCATGATGGTTT 58.913 50.000 11.49 0.00 38.31 3.27
1419 2758 0.802494 ATGATGGTTTCGTTGTCGGC 59.198 50.000 0.00 0.00 37.69 5.54
1420 2759 0.250124 TGATGGTTTCGTTGTCGGCT 60.250 50.000 0.00 0.00 37.69 5.52
1421 2760 0.165944 GATGGTTTCGTTGTCGGCTG 59.834 55.000 0.00 0.00 37.69 4.85
1436 2775 2.002586 CGGCTGTGAGGTGATTTGTAG 58.997 52.381 0.00 0.00 0.00 2.74
1463 2802 3.264193 AGGCAAGATGGACACAATAGACA 59.736 43.478 0.00 0.00 0.00 3.41
1473 2812 4.331168 GGACACAATAGACAGATGCTCAAC 59.669 45.833 0.00 0.00 0.00 3.18
1483 2822 5.413833 AGACAGATGCTCAACTATTTTGGTG 59.586 40.000 0.00 0.00 0.00 4.17
1490 2829 4.627035 GCTCAACTATTTTGGTGCAAATCC 59.373 41.667 0.00 0.00 33.19 3.01
1497 2836 2.208132 TTGGTGCAAATCCGGTGTAT 57.792 45.000 0.00 0.00 0.00 2.29
1499 2838 1.280710 TGGTGCAAATCCGGTGTATCT 59.719 47.619 0.00 0.00 0.00 1.98
1504 2843 3.704566 TGCAAATCCGGTGTATCTAGAGT 59.295 43.478 0.00 0.00 0.00 3.24
1508 2847 6.294564 GCAAATCCGGTGTATCTAGAGTGATA 60.295 42.308 0.00 0.00 0.00 2.15
1517 2856 7.064674 GTGTATCTAGAGTGATACTTTCGACG 58.935 42.308 13.51 0.00 45.31 5.12
1521 2860 0.524862 AGTGATACTTTCGACGCCGT 59.475 50.000 0.00 0.00 37.05 5.68
1528 2867 1.269726 ACTTTCGACGCCGTTTTAGGA 60.270 47.619 0.00 0.00 37.05 2.94
1538 2877 1.593265 GTTTTAGGACGGCTCCGGA 59.407 57.895 13.31 2.93 42.22 5.14
1545 2884 0.958876 GGACGGCTCCGGATTTGTTT 60.959 55.000 3.57 0.00 44.69 2.83
1556 2895 3.181397 CGGATTTGTTTCATCACATGCC 58.819 45.455 0.00 0.00 0.00 4.40
1578 2917 6.150976 TGCCAACATGTTCTAATAGTTGAAGG 59.849 38.462 8.48 3.29 41.41 3.46
1579 2918 6.555315 CCAACATGTTCTAATAGTTGAAGGC 58.445 40.000 8.48 0.00 41.41 4.35
1580 2919 6.404734 CCAACATGTTCTAATAGTTGAAGGCC 60.405 42.308 8.48 0.00 41.41 5.19
1581 2920 5.815581 ACATGTTCTAATAGTTGAAGGCCA 58.184 37.500 5.01 0.00 0.00 5.36
1582 2921 6.245408 ACATGTTCTAATAGTTGAAGGCCAA 58.755 36.000 5.01 0.00 0.00 4.52
1606 2949 5.606348 TTTTTGGCACCAGTTTTACATCT 57.394 34.783 0.00 0.00 0.00 2.90
1607 2950 6.716934 TTTTTGGCACCAGTTTTACATCTA 57.283 33.333 0.00 0.00 0.00 1.98
1609 2952 3.331150 TGGCACCAGTTTTACATCTACG 58.669 45.455 0.00 0.00 0.00 3.51
1611 2954 2.095372 GCACCAGTTTTACATCTACGGC 59.905 50.000 0.00 0.00 0.00 5.68
1612 2955 2.347452 CACCAGTTTTACATCTACGGCG 59.653 50.000 4.80 4.80 0.00 6.46
1613 2956 1.931172 CCAGTTTTACATCTACGGCGG 59.069 52.381 13.24 0.00 0.00 6.13
1614 2957 2.417651 CCAGTTTTACATCTACGGCGGA 60.418 50.000 13.24 0.00 0.00 5.54
1631 2979 1.202256 CGGAAAATTTTCTAGCGCCCC 60.202 52.381 25.86 10.14 37.35 5.80
1632 2980 1.136305 GGAAAATTTTCTAGCGCCCCC 59.864 52.381 25.86 7.21 37.35 5.40
1653 3001 3.452990 CCCTAAACCTTCTCTCTCCTTCC 59.547 52.174 0.00 0.00 0.00 3.46
1662 3014 6.014070 ACCTTCTCTCTCCTTCCTTAAAACTC 60.014 42.308 0.00 0.00 0.00 3.01
1666 3018 7.672240 TCTCTCTCCTTCCTTAAAACTCTTTC 58.328 38.462 0.00 0.00 0.00 2.62
1674 3026 5.063880 TCCTTAAAACTCTTTCTGAGCACC 58.936 41.667 0.00 0.00 46.41 5.01
1675 3027 4.821805 CCTTAAAACTCTTTCTGAGCACCA 59.178 41.667 0.00 0.00 46.41 4.17
1676 3028 5.299279 CCTTAAAACTCTTTCTGAGCACCAA 59.701 40.000 0.00 0.00 46.41 3.67
1677 3029 4.639135 AAAACTCTTTCTGAGCACCAAC 57.361 40.909 0.00 0.00 46.41 3.77
1678 3030 3.567478 AACTCTTTCTGAGCACCAACT 57.433 42.857 0.00 0.00 46.41 3.16
1679 3031 3.567478 ACTCTTTCTGAGCACCAACTT 57.433 42.857 0.00 0.00 46.41 2.66
1680 3032 3.891049 ACTCTTTCTGAGCACCAACTTT 58.109 40.909 0.00 0.00 46.41 2.66
1681 3033 4.273318 ACTCTTTCTGAGCACCAACTTTT 58.727 39.130 0.00 0.00 46.41 2.27
1682 3034 5.437060 ACTCTTTCTGAGCACCAACTTTTA 58.563 37.500 0.00 0.00 46.41 1.52
1683 3035 5.297029 ACTCTTTCTGAGCACCAACTTTTAC 59.703 40.000 0.00 0.00 46.41 2.01
1684 3036 5.189928 TCTTTCTGAGCACCAACTTTTACA 58.810 37.500 0.00 0.00 0.00 2.41
1685 3037 5.827797 TCTTTCTGAGCACCAACTTTTACAT 59.172 36.000 0.00 0.00 0.00 2.29
1686 3038 5.689383 TTCTGAGCACCAACTTTTACATC 57.311 39.130 0.00 0.00 0.00 3.06
1687 3039 4.713553 TCTGAGCACCAACTTTTACATCA 58.286 39.130 0.00 0.00 0.00 3.07
1688 3040 5.316167 TCTGAGCACCAACTTTTACATCAT 58.684 37.500 0.00 0.00 0.00 2.45
1689 3041 5.181811 TCTGAGCACCAACTTTTACATCATG 59.818 40.000 0.00 0.00 0.00 3.07
1690 3042 4.826733 TGAGCACCAACTTTTACATCATGT 59.173 37.500 0.00 0.00 0.00 3.21
1691 3043 5.125100 AGCACCAACTTTTACATCATGTG 57.875 39.130 0.00 0.00 0.00 3.21
1692 3044 4.584325 AGCACCAACTTTTACATCATGTGT 59.416 37.500 0.00 6.26 44.95 3.72
1693 3045 5.068987 AGCACCAACTTTTACATCATGTGTT 59.931 36.000 0.00 0.00 42.29 3.32
1694 3046 5.175491 GCACCAACTTTTACATCATGTGTTG 59.825 40.000 10.43 10.43 42.29 3.33
1697 3049 6.151691 CCAACTTTTACATCATGTGTTGGAG 58.848 40.000 24.15 8.68 45.72 3.86
1712 3065 6.530120 TGTGTTGGAGATGCTCTAAAAACTA 58.470 36.000 0.00 0.00 33.06 2.24
1724 3077 7.553334 TGCTCTAAAAACTATATCTCCGTTGT 58.447 34.615 0.00 0.00 0.00 3.32
1729 3082 6.811253 AAAACTATATCTCCGTTGTGCAAA 57.189 33.333 0.00 0.00 0.00 3.68
1741 3094 0.404040 TGTGCAAAAGGGGGTAGAGG 59.596 55.000 0.00 0.00 0.00 3.69
1747 3100 3.574395 AAGGGGGTAGAGGCCGGTT 62.574 63.158 1.90 0.00 0.00 4.44
1749 3102 2.686106 GGGGTAGAGGCCGGTTGA 60.686 66.667 1.90 0.00 0.00 3.18
1750 3103 2.295602 GGGGTAGAGGCCGGTTGAA 61.296 63.158 1.90 0.00 0.00 2.69
1760 3113 7.013942 GGTAGAGGCCGGTTGAAAAATAAATAT 59.986 37.037 1.90 0.00 0.00 1.28
1764 3117 9.758651 GAGGCCGGTTGAAAAATAAATATATTT 57.241 29.630 14.86 14.86 42.23 1.40
1797 3150 6.876155 TCATCCCAATGATTACAAACCATTG 58.124 36.000 0.00 0.00 43.89 2.82
1799 3152 6.528537 TCCCAATGATTACAAACCATTGAG 57.471 37.500 13.83 3.36 45.91 3.02
1801 3154 6.896860 TCCCAATGATTACAAACCATTGAGAT 59.103 34.615 13.83 0.00 45.91 2.75
1836 3193 9.381033 TCAACACATCTAGTCTTAGTAGTCTAC 57.619 37.037 1.39 1.39 0.00 2.59
1840 3197 8.995220 CACATCTAGTCTTAGTAGTCTACCATC 58.005 40.741 6.38 0.00 0.00 3.51
1851 3209 4.494091 AGTCTACCATCCCATTTCACAG 57.506 45.455 0.00 0.00 0.00 3.66
1856 3214 6.093633 GTCTACCATCCCATTTCACAGTTTAC 59.906 42.308 0.00 0.00 0.00 2.01
1858 3216 5.144100 ACCATCCCATTTCACAGTTTACAA 58.856 37.500 0.00 0.00 0.00 2.41
1860 3218 6.269769 ACCATCCCATTTCACAGTTTACAAAT 59.730 34.615 0.00 0.00 0.00 2.32
1869 3227 7.921786 TTCACAGTTTACAAATCATAGGAGG 57.078 36.000 0.00 0.00 0.00 4.30
1870 3228 7.016153 TCACAGTTTACAAATCATAGGAGGT 57.984 36.000 0.00 0.00 0.00 3.85
1875 3233 8.830580 CAGTTTACAAATCATAGGAGGTACATG 58.169 37.037 0.00 0.00 0.00 3.21
1876 3234 8.768397 AGTTTACAAATCATAGGAGGTACATGA 58.232 33.333 0.00 0.00 33.47 3.07
1877 3235 9.391006 GTTTACAAATCATAGGAGGTACATGAA 57.609 33.333 0.00 0.00 32.73 2.57
1878 3236 9.613428 TTTACAAATCATAGGAGGTACATGAAG 57.387 33.333 0.00 0.00 32.73 3.02
1909 3280 5.413833 CCCCATCTGTATGCTTGCTAATTAG 59.586 44.000 8.20 8.20 0.00 1.73
1914 3292 4.780815 TGTATGCTTGCTAATTAGGCAGT 58.219 39.130 14.28 7.97 40.90 4.40
1915 3293 4.576053 TGTATGCTTGCTAATTAGGCAGTG 59.424 41.667 14.28 9.80 40.90 3.66
2053 3431 1.338107 TCGGGAAGAAGCAGTTCTGA 58.662 50.000 3.84 0.00 42.59 3.27
2260 3638 2.833227 CCGTTGTGGACCAGGGAA 59.167 61.111 0.00 0.00 42.00 3.97
2362 3740 1.497309 TTCCCCCGTTGCTGAAGGAT 61.497 55.000 0.00 0.00 0.00 3.24
2365 3743 0.107017 CCCCGTTGCTGAAGGATGAT 60.107 55.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.267188 TGGTCGACCGTTTATCTTCG 57.733 50.000 28.70 0.00 39.43 3.79
5 6 3.124128 GGTTTGGTCGACCGTTTATCTTC 59.876 47.826 28.70 11.14 39.43 2.87
6 7 3.069289 GGTTTGGTCGACCGTTTATCTT 58.931 45.455 28.70 0.00 39.43 2.40
7 8 2.301009 AGGTTTGGTCGACCGTTTATCT 59.699 45.455 28.70 16.01 42.11 1.98
8 9 2.691927 AGGTTTGGTCGACCGTTTATC 58.308 47.619 28.70 14.08 42.11 1.75
9 10 2.845363 AGGTTTGGTCGACCGTTTAT 57.155 45.000 28.70 12.48 42.11 1.40
10 11 2.610232 GCTAGGTTTGGTCGACCGTTTA 60.610 50.000 28.70 15.06 42.11 2.01
11 12 1.875157 GCTAGGTTTGGTCGACCGTTT 60.875 52.381 28.70 14.75 42.11 3.60
12 13 0.320160 GCTAGGTTTGGTCGACCGTT 60.320 55.000 28.70 14.41 42.11 4.44
13 14 1.291272 GCTAGGTTTGGTCGACCGT 59.709 57.895 28.70 13.32 42.11 4.83
14 15 0.320073 TTGCTAGGTTTGGTCGACCG 60.320 55.000 28.70 14.02 42.11 4.79
15 16 1.154197 GTTGCTAGGTTTGGTCGACC 58.846 55.000 28.17 28.17 37.44 4.79
16 17 1.154197 GGTTGCTAGGTTTGGTCGAC 58.846 55.000 7.13 7.13 0.00 4.20
17 18 0.759959 TGGTTGCTAGGTTTGGTCGA 59.240 50.000 0.00 0.00 0.00 4.20
18 19 0.872388 GTGGTTGCTAGGTTTGGTCG 59.128 55.000 0.00 0.00 0.00 4.79
19 20 1.975660 TGTGGTTGCTAGGTTTGGTC 58.024 50.000 0.00 0.00 0.00 4.02
20 21 2.675658 ATGTGGTTGCTAGGTTTGGT 57.324 45.000 0.00 0.00 0.00 3.67
21 22 4.079253 AGTAATGTGGTTGCTAGGTTTGG 58.921 43.478 0.00 0.00 30.39 3.28
22 23 6.811253 TTAGTAATGTGGTTGCTAGGTTTG 57.189 37.500 0.00 0.00 36.55 2.93
23 24 6.773685 TGTTTAGTAATGTGGTTGCTAGGTTT 59.226 34.615 0.00 0.00 36.55 3.27
24 25 6.300703 TGTTTAGTAATGTGGTTGCTAGGTT 58.699 36.000 0.00 0.00 36.55 3.50
25 26 5.871834 TGTTTAGTAATGTGGTTGCTAGGT 58.128 37.500 0.00 0.00 36.55 3.08
26 27 6.811253 TTGTTTAGTAATGTGGTTGCTAGG 57.189 37.500 0.00 0.00 36.55 3.02
27 28 9.691362 AAAATTGTTTAGTAATGTGGTTGCTAG 57.309 29.630 0.00 0.00 36.55 3.42
28 29 9.685828 GAAAATTGTTTAGTAATGTGGTTGCTA 57.314 29.630 0.00 0.00 34.42 3.49
29 30 8.421002 AGAAAATTGTTTAGTAATGTGGTTGCT 58.579 29.630 0.00 0.00 36.65 3.91
30 31 8.587952 AGAAAATTGTTTAGTAATGTGGTTGC 57.412 30.769 0.00 0.00 0.00 4.17
33 34 9.357161 TGGTAGAAAATTGTTTAGTAATGTGGT 57.643 29.630 0.00 0.00 0.00 4.16
41 42 7.659799 GCCCATTTTGGTAGAAAATTGTTTAGT 59.340 33.333 0.00 0.00 35.17 2.24
42 43 7.119116 GGCCCATTTTGGTAGAAAATTGTTTAG 59.881 37.037 0.00 0.00 35.17 1.85
43 44 6.937465 GGCCCATTTTGGTAGAAAATTGTTTA 59.063 34.615 0.00 0.00 35.17 2.01
44 45 5.767665 GGCCCATTTTGGTAGAAAATTGTTT 59.232 36.000 0.00 0.00 35.17 2.83
45 46 5.073008 AGGCCCATTTTGGTAGAAAATTGTT 59.927 36.000 0.00 0.00 35.17 2.83
46 47 4.597075 AGGCCCATTTTGGTAGAAAATTGT 59.403 37.500 0.00 0.00 35.17 2.71
47 48 4.937015 CAGGCCCATTTTGGTAGAAAATTG 59.063 41.667 0.00 0.00 35.17 2.32
48 49 4.565444 GCAGGCCCATTTTGGTAGAAAATT 60.565 41.667 0.00 0.00 35.17 1.82
49 50 3.055167 GCAGGCCCATTTTGGTAGAAAAT 60.055 43.478 0.00 0.00 35.17 1.82
50 51 2.301583 GCAGGCCCATTTTGGTAGAAAA 59.698 45.455 0.00 0.00 35.17 2.29
51 52 1.899142 GCAGGCCCATTTTGGTAGAAA 59.101 47.619 0.00 0.00 35.17 2.52
52 53 1.555967 GCAGGCCCATTTTGGTAGAA 58.444 50.000 0.00 0.00 35.17 2.10
53 54 0.324275 GGCAGGCCCATTTTGGTAGA 60.324 55.000 0.00 0.00 35.17 2.59
54 55 1.666209 CGGCAGGCCCATTTTGGTAG 61.666 60.000 0.00 0.00 35.17 3.18
55 56 1.680651 CGGCAGGCCCATTTTGGTA 60.681 57.895 0.00 0.00 35.17 3.25
56 57 2.996734 CGGCAGGCCCATTTTGGT 60.997 61.111 0.00 0.00 35.17 3.67
57 58 4.455906 GCGGCAGGCCCATTTTGG 62.456 66.667 0.00 0.00 37.25 3.28
58 59 2.008268 CTAGCGGCAGGCCCATTTTG 62.008 60.000 0.00 0.00 45.17 2.44
59 60 1.754234 CTAGCGGCAGGCCCATTTT 60.754 57.895 0.00 0.00 45.17 1.82
60 61 2.124151 CTAGCGGCAGGCCCATTT 60.124 61.111 0.00 0.00 45.17 2.32
61 62 3.411517 ACTAGCGGCAGGCCCATT 61.412 61.111 0.00 0.00 45.17 3.16
62 63 4.181010 CACTAGCGGCAGGCCCAT 62.181 66.667 0.00 0.00 45.17 4.00
65 66 4.410400 AACCACTAGCGGCAGGCC 62.410 66.667 1.45 0.00 45.17 5.19
66 67 3.127533 CAACCACTAGCGGCAGGC 61.128 66.667 1.45 0.00 44.05 4.85
67 68 2.436646 CCAACCACTAGCGGCAGG 60.437 66.667 1.45 0.73 0.00 4.85
68 69 3.127533 GCCAACCACTAGCGGCAG 61.128 66.667 1.45 0.01 44.25 4.85
69 70 4.715523 GGCCAACCACTAGCGGCA 62.716 66.667 1.45 0.00 46.75 5.69
71 72 4.388499 ACGGCCAACCACTAGCGG 62.388 66.667 2.24 0.00 34.57 5.52
72 73 2.813908 GACGGCCAACCACTAGCG 60.814 66.667 2.24 0.00 34.57 4.26
73 74 2.813908 CGACGGCCAACCACTAGC 60.814 66.667 2.24 0.00 34.57 3.42
74 75 2.125673 CCGACGGCCAACCACTAG 60.126 66.667 2.24 0.00 34.57 2.57
75 76 4.382320 GCCGACGGCCAACCACTA 62.382 66.667 28.74 0.00 44.06 2.74
84 85 0.878961 AATAGGAAATCGCCGACGGC 60.879 55.000 29.10 29.10 46.75 5.68
85 86 2.030540 TCTAATAGGAAATCGCCGACGG 60.031 50.000 10.29 10.29 40.63 4.79
86 87 3.278367 TCTAATAGGAAATCGCCGACG 57.722 47.619 0.00 0.00 42.01 5.12
87 88 4.807304 TGTTTCTAATAGGAAATCGCCGAC 59.193 41.667 0.00 0.00 37.50 4.79
88 89 4.807304 GTGTTTCTAATAGGAAATCGCCGA 59.193 41.667 0.00 0.00 37.50 5.54
89 90 4.569162 TGTGTTTCTAATAGGAAATCGCCG 59.431 41.667 0.00 0.00 37.50 6.46
90 91 6.619801 ATGTGTTTCTAATAGGAAATCGCC 57.380 37.500 0.00 0.00 37.50 5.54
91 92 7.441458 ACCTATGTGTTTCTAATAGGAAATCGC 59.559 37.037 13.51 0.00 43.85 4.58
92 93 8.765219 CACCTATGTGTTTCTAATAGGAAATCG 58.235 37.037 13.51 0.00 43.85 3.34
120 121 1.136872 GAGAGCACTTCTACAGCGCG 61.137 60.000 0.00 0.00 35.52 6.86
157 158 1.852157 TTACTGGCTGGCCTTGAGGG 61.852 60.000 13.05 0.00 36.94 4.30
158 159 0.257039 ATTACTGGCTGGCCTTGAGG 59.743 55.000 13.05 0.00 36.94 3.86
159 160 1.386533 CATTACTGGCTGGCCTTGAG 58.613 55.000 13.05 4.68 36.94 3.02
160 161 0.034186 CCATTACTGGCTGGCCTTGA 60.034 55.000 13.05 0.00 35.23 3.02
161 162 1.039233 CCCATTACTGGCTGGCCTTG 61.039 60.000 13.05 8.16 41.64 3.61
162 163 1.307647 CCCATTACTGGCTGGCCTT 59.692 57.895 13.05 2.68 41.64 4.35
163 164 3.010144 CCCATTACTGGCTGGCCT 58.990 61.111 13.05 0.00 41.64 5.19
164 165 2.834968 GCCCATTACTGGCTGGCC 60.835 66.667 4.43 4.43 45.70 5.36
170 171 2.828549 GGTGCGGCCCATTACTGG 60.829 66.667 0.00 0.00 42.73 4.00
171 172 2.045438 TGGTGCGGCCCATTACTG 60.045 61.111 0.00 0.00 36.04 2.74
172 173 1.268992 TAGTGGTGCGGCCCATTACT 61.269 55.000 12.33 7.69 36.74 2.24
360 367 8.628882 TCCGAACAATACTATAATATGCGATG 57.371 34.615 0.00 0.00 0.00 3.84
362 369 8.047413 TCTCCGAACAATACTATAATATGCGA 57.953 34.615 0.00 0.00 0.00 5.10
393 400 8.474025 TCTAAAACCATGAGAACACAAACAAAT 58.526 29.630 0.00 0.00 0.00 2.32
394 401 7.831753 TCTAAAACCATGAGAACACAAACAAA 58.168 30.769 0.00 0.00 0.00 2.83
397 404 7.973944 AGTTTCTAAAACCATGAGAACACAAAC 59.026 33.333 0.00 0.00 0.00 2.93
401 408 7.027778 ACAGTTTCTAAAACCATGAGAACAC 57.972 36.000 0.00 0.00 0.00 3.32
406 413 8.783093 TGTATGAACAGTTTCTAAAACCATGAG 58.217 33.333 0.00 0.00 32.36 2.90
443 450 9.901724 CGCAACCGAATATTATAGAACATATTC 57.098 33.333 5.38 5.38 38.33 1.75
453 460 5.467063 TGACATTGCGCAACCGAATATTATA 59.533 36.000 27.64 0.00 36.29 0.98
455 462 3.623510 TGACATTGCGCAACCGAATATTA 59.376 39.130 27.64 0.00 36.29 0.98
462 469 1.203928 TTTTTGACATTGCGCAACCG 58.796 45.000 27.64 21.65 37.57 4.44
500 1640 2.959030 ACACATGATAGAGCGGCTAGAA 59.041 45.455 0.60 0.00 31.33 2.10
501 1641 2.294512 CACACATGATAGAGCGGCTAGA 59.705 50.000 0.60 0.00 31.33 2.43
524 1664 3.393138 TGCATGTAGCTCCACCAGTGG 62.393 57.143 7.91 7.91 46.33 4.00
525 1665 0.036105 TGCATGTAGCTCCACCAGTG 60.036 55.000 0.00 0.00 45.94 3.66
526 1666 0.692476 TTGCATGTAGCTCCACCAGT 59.308 50.000 0.00 0.00 45.94 4.00
527 1667 1.089920 GTTGCATGTAGCTCCACCAG 58.910 55.000 0.00 0.00 45.94 4.00
528 1668 0.322456 GGTTGCATGTAGCTCCACCA 60.322 55.000 0.00 0.00 45.94 4.17
529 1669 1.032114 GGGTTGCATGTAGCTCCACC 61.032 60.000 0.00 0.00 45.94 4.61
530 1670 0.035056 AGGGTTGCATGTAGCTCCAC 60.035 55.000 0.00 0.00 45.94 4.02
531 1671 0.035152 CAGGGTTGCATGTAGCTCCA 60.035 55.000 0.00 0.00 45.94 3.86
532 1672 2.785868 CAGGGTTGCATGTAGCTCC 58.214 57.895 0.00 0.00 45.94 4.70
563 1703 0.613572 ATTTACCAAACCTGCGGGGG 60.614 55.000 18.00 10.33 40.03 5.40
564 1704 1.262417 AATTTACCAAACCTGCGGGG 58.738 50.000 18.00 5.11 41.89 5.73
565 1705 3.063485 CAAAATTTACCAAACCTGCGGG 58.937 45.455 11.02 11.02 38.88 6.13
566 1706 3.492756 CACAAAATTTACCAAACCTGCGG 59.507 43.478 0.00 0.00 0.00 5.69
567 1707 4.363999 TCACAAAATTTACCAAACCTGCG 58.636 39.130 0.00 0.00 0.00 5.18
568 1708 6.045955 TCTTCACAAAATTTACCAAACCTGC 58.954 36.000 0.00 0.00 0.00 4.85
569 1709 8.485976 TTTCTTCACAAAATTTACCAAACCTG 57.514 30.769 0.00 0.00 0.00 4.00
570 1710 9.679661 AATTTCTTCACAAAATTTACCAAACCT 57.320 25.926 0.00 0.00 33.62 3.50
985 2125 3.391296 AGAAACATAGGGTCACACACAGT 59.609 43.478 0.00 0.00 0.00 3.55
986 2126 3.997021 GAGAAACATAGGGTCACACACAG 59.003 47.826 0.00 0.00 0.00 3.66
987 2127 3.244422 GGAGAAACATAGGGTCACACACA 60.244 47.826 0.00 0.00 0.00 3.72
988 2128 3.335579 GGAGAAACATAGGGTCACACAC 58.664 50.000 0.00 0.00 0.00 3.82
1017 2157 2.083002 AGAAGTAGGACGACGAGGAAC 58.917 52.381 0.00 0.00 0.00 3.62
1027 2167 2.093106 TGAGCCGAAGAGAAGTAGGAC 58.907 52.381 0.00 0.00 0.00 3.85
1092 2233 3.906980 ACCTCAGGGTGGTCTTGG 58.093 61.111 0.00 0.00 45.43 3.61
1109 2250 0.685097 GTATGGCCGGCTAGGAATGA 59.315 55.000 28.56 0.00 45.00 2.57
1137 2278 1.683707 AGGCTGCTCATCGAGACCA 60.684 57.895 0.00 0.00 0.00 4.02
1142 2283 2.491621 CGACAGGCTGCTCATCGA 59.508 61.111 15.89 0.00 34.77 3.59
1181 2322 1.069906 CAGGCTTTTCTTCGAACACCG 60.070 52.381 0.00 0.00 40.25 4.94
1233 2377 4.746535 TCTACTCCCATATCGCAACAAA 57.253 40.909 0.00 0.00 0.00 2.83
1234 2378 4.955811 ATCTACTCCCATATCGCAACAA 57.044 40.909 0.00 0.00 0.00 2.83
1235 2379 4.100963 ACAATCTACTCCCATATCGCAACA 59.899 41.667 0.00 0.00 0.00 3.33
1236 2380 4.632153 ACAATCTACTCCCATATCGCAAC 58.368 43.478 0.00 0.00 0.00 4.17
1237 2381 4.955811 ACAATCTACTCCCATATCGCAA 57.044 40.909 0.00 0.00 0.00 4.85
1238 2382 4.955811 AACAATCTACTCCCATATCGCA 57.044 40.909 0.00 0.00 0.00 5.10
1246 2390 5.632034 ACTTCCCATAACAATCTACTCCC 57.368 43.478 0.00 0.00 0.00 4.30
1259 2403 9.613428 CTCATCTAAAACACAATACTTCCCATA 57.387 33.333 0.00 0.00 0.00 2.74
1277 2421 6.936279 AGAGGATTCAAACGAACTCATCTAA 58.064 36.000 0.00 0.00 28.51 2.10
1302 2446 3.067461 CCTCTTCAGAGAAGGATACACGG 59.933 52.174 5.33 0.00 44.74 4.94
1317 2461 5.140454 TCGTCCATCTCATATTCCTCTTCA 58.860 41.667 0.00 0.00 0.00 3.02
1319 2463 5.835819 TCTTCGTCCATCTCATATTCCTCTT 59.164 40.000 0.00 0.00 0.00 2.85
1320 2464 5.389520 TCTTCGTCCATCTCATATTCCTCT 58.610 41.667 0.00 0.00 0.00 3.69
1321 2465 5.713792 TCTTCGTCCATCTCATATTCCTC 57.286 43.478 0.00 0.00 0.00 3.71
1356 2695 2.836479 TGTGCATCGCAATGATCAAG 57.164 45.000 0.00 0.00 41.47 3.02
1394 2733 2.095768 ACAACGAAACCATCATGCTTCG 60.096 45.455 15.08 15.08 44.69 3.79
1409 2748 2.338620 CCTCACAGCCGACAACGA 59.661 61.111 0.00 0.00 42.66 3.85
1419 2758 4.641396 TCAACCTACAAATCACCTCACAG 58.359 43.478 0.00 0.00 0.00 3.66
1420 2759 4.504864 CCTCAACCTACAAATCACCTCACA 60.505 45.833 0.00 0.00 0.00 3.58
1421 2760 4.003648 CCTCAACCTACAAATCACCTCAC 58.996 47.826 0.00 0.00 0.00 3.51
1436 2775 1.168714 GTGTCCATCTTGCCTCAACC 58.831 55.000 0.00 0.00 0.00 3.77
1463 2802 4.081406 TGCACCAAAATAGTTGAGCATCT 58.919 39.130 0.00 0.00 34.92 2.90
1473 2812 3.056891 ACACCGGATTTGCACCAAAATAG 60.057 43.478 9.46 0.00 36.90 1.73
1483 2822 4.051922 CACTCTAGATACACCGGATTTGC 58.948 47.826 9.46 0.00 0.00 3.68
1497 2836 3.311871 GGCGTCGAAAGTATCACTCTAGA 59.688 47.826 0.00 0.00 0.00 2.43
1499 2838 2.031314 CGGCGTCGAAAGTATCACTCTA 59.969 50.000 1.44 0.00 39.00 2.43
1504 2843 2.068837 AAACGGCGTCGAAAGTATCA 57.931 45.000 20.03 0.00 40.11 2.15
1508 2847 1.142474 CCTAAAACGGCGTCGAAAGT 58.858 50.000 20.03 0.00 40.11 2.66
1521 2860 0.906775 AATCCGGAGCCGTCCTAAAA 59.093 50.000 11.34 0.00 41.34 1.52
1528 2867 0.250553 TGAAACAAATCCGGAGCCGT 60.251 50.000 11.34 3.11 37.81 5.68
1538 2877 4.958509 TGTTGGCATGTGATGAAACAAAT 58.041 34.783 0.00 0.00 36.26 2.32
1556 2895 6.150976 TGGCCTTCAACTATTAGAACATGTTG 59.849 38.462 17.58 2.57 39.23 3.33
1606 2949 2.349275 CGCTAGAAAATTTTCCGCCGTA 59.651 45.455 24.01 10.90 37.92 4.02
1607 2950 1.129811 CGCTAGAAAATTTTCCGCCGT 59.870 47.619 24.01 10.37 37.92 5.68
1609 2952 1.545759 GCGCTAGAAAATTTTCCGCC 58.454 50.000 28.02 19.49 38.51 6.13
1611 2954 1.202256 GGGGCGCTAGAAAATTTTCCG 60.202 52.381 24.01 20.73 37.92 4.30
1612 2955 1.136305 GGGGGCGCTAGAAAATTTTCC 59.864 52.381 24.01 10.71 37.92 3.13
1613 2956 2.579207 GGGGGCGCTAGAAAATTTTC 57.421 50.000 21.00 21.00 37.45 2.29
1631 2979 3.452990 GGAAGGAGAGAGAAGGTTTAGGG 59.547 52.174 0.00 0.00 0.00 3.53
1632 2980 4.358214 AGGAAGGAGAGAGAAGGTTTAGG 58.642 47.826 0.00 0.00 0.00 2.69
1633 2981 7.483580 TTAAGGAAGGAGAGAGAAGGTTTAG 57.516 40.000 0.00 0.00 0.00 1.85
1634 2982 7.867160 TTTAAGGAAGGAGAGAGAAGGTTTA 57.133 36.000 0.00 0.00 0.00 2.01
1653 3001 6.038714 AGTTGGTGCTCAGAAAGAGTTTTAAG 59.961 38.462 0.00 0.00 46.47 1.85
1662 3014 5.499139 TGTAAAAGTTGGTGCTCAGAAAG 57.501 39.130 0.00 0.00 0.00 2.62
1666 3018 5.048504 ACATGATGTAAAAGTTGGTGCTCAG 60.049 40.000 0.00 0.00 0.00 3.35
1674 3026 6.969366 TCTCCAACACATGATGTAAAAGTTG 58.031 36.000 15.51 15.51 42.31 3.16
1675 3027 7.596494 CATCTCCAACACATGATGTAAAAGTT 58.404 34.615 0.00 0.00 42.31 2.66
1676 3028 6.349611 GCATCTCCAACACATGATGTAAAAGT 60.350 38.462 0.00 0.00 42.31 2.66
1677 3029 6.032094 GCATCTCCAACACATGATGTAAAAG 58.968 40.000 0.00 0.00 42.31 2.27
1678 3030 5.711506 AGCATCTCCAACACATGATGTAAAA 59.288 36.000 0.00 0.00 42.31 1.52
1679 3031 5.255687 AGCATCTCCAACACATGATGTAAA 58.744 37.500 0.00 0.00 42.31 2.01
1680 3032 4.847198 AGCATCTCCAACACATGATGTAA 58.153 39.130 0.00 0.00 42.31 2.41
1681 3033 4.445453 GAGCATCTCCAACACATGATGTA 58.555 43.478 0.00 0.00 42.31 2.29
1682 3034 3.276857 GAGCATCTCCAACACATGATGT 58.723 45.455 0.00 0.00 46.42 3.06
1683 3035 3.965292 GAGCATCTCCAACACATGATG 57.035 47.619 0.00 0.00 39.24 3.07
1697 3049 8.704234 CAACGGAGATATAGTTTTTAGAGCATC 58.296 37.037 0.00 0.00 0.00 3.91
1712 3065 3.016736 CCCTTTTGCACAACGGAGATAT 58.983 45.455 0.00 0.00 0.00 1.63
1724 3077 1.382629 GCCTCTACCCCCTTTTGCA 59.617 57.895 0.00 0.00 0.00 4.08
1729 3082 3.574395 AACCGGCCTCTACCCCCTT 62.574 63.158 0.00 0.00 0.00 3.95
1760 3113 7.715266 TCATTGGGATGATGAACACAAAATA 57.285 32.000 0.00 0.00 37.37 1.40
1774 3127 6.876155 TCAATGGTTTGTAATCATTGGGATG 58.124 36.000 19.65 1.71 44.45 3.51
1820 3177 6.836714 TGGGATGGTAGACTACTAAGACTA 57.163 41.667 12.31 0.00 0.00 2.59
1824 3181 7.147724 TGTGAAATGGGATGGTAGACTACTAAG 60.148 40.741 12.31 0.00 0.00 2.18
1825 3182 6.670464 TGTGAAATGGGATGGTAGACTACTAA 59.330 38.462 12.31 2.22 0.00 2.24
1826 3183 6.199376 TGTGAAATGGGATGGTAGACTACTA 58.801 40.000 12.31 6.87 0.00 1.82
1827 3184 5.030147 TGTGAAATGGGATGGTAGACTACT 58.970 41.667 12.31 0.00 0.00 2.57
1828 3185 5.104900 ACTGTGAAATGGGATGGTAGACTAC 60.105 44.000 3.86 3.86 0.00 2.73
1829 3186 5.030147 ACTGTGAAATGGGATGGTAGACTA 58.970 41.667 0.00 0.00 0.00 2.59
1830 3187 3.846588 ACTGTGAAATGGGATGGTAGACT 59.153 43.478 0.00 0.00 0.00 3.24
1836 3193 5.720371 TTGTAAACTGTGAAATGGGATGG 57.280 39.130 0.00 0.00 0.00 3.51
1840 3197 7.975616 CCTATGATTTGTAAACTGTGAAATGGG 59.024 37.037 0.00 0.00 0.00 4.00
1851 3209 8.958119 TCATGTACCTCCTATGATTTGTAAAC 57.042 34.615 0.00 0.00 0.00 2.01
1856 3214 7.989741 AGTTCTTCATGTACCTCCTATGATTTG 59.010 37.037 0.00 0.00 31.54 2.32
1858 3216 7.345653 TCAGTTCTTCATGTACCTCCTATGATT 59.654 37.037 0.00 0.00 31.54 2.57
1860 3218 6.096987 GTCAGTTCTTCATGTACCTCCTATGA 59.903 42.308 0.00 0.00 0.00 2.15
1869 3227 3.695830 TGGGGTCAGTTCTTCATGTAC 57.304 47.619 0.00 0.00 0.00 2.90
1870 3228 4.080919 CAGATGGGGTCAGTTCTTCATGTA 60.081 45.833 0.00 0.00 0.00 2.29
1875 3233 4.446371 CATACAGATGGGGTCAGTTCTTC 58.554 47.826 0.00 0.00 0.00 2.87
1876 3234 3.370953 GCATACAGATGGGGTCAGTTCTT 60.371 47.826 0.00 0.00 33.26 2.52
1877 3235 2.171448 GCATACAGATGGGGTCAGTTCT 59.829 50.000 0.00 0.00 33.26 3.01
1878 3236 2.171448 AGCATACAGATGGGGTCAGTTC 59.829 50.000 0.00 0.00 33.26 3.01
1909 3280 2.034687 ACCAGCCATCACACTGCC 59.965 61.111 0.00 0.00 32.37 4.85
2053 3431 1.004200 GTTGACCGACGTGGGGATT 60.004 57.895 21.41 0.00 44.64 3.01
2138 3516 1.065636 CATCTTGCCAGAGCTGAGGAA 60.066 52.381 5.23 0.00 40.80 3.36
2141 3519 1.654317 GACATCTTGCCAGAGCTGAG 58.346 55.000 0.00 0.00 40.80 3.35
2149 3527 2.612972 GGAGTTCTTCGACATCTTGCCA 60.613 50.000 0.00 0.00 0.00 4.92
2344 3722 1.923395 ATCCTTCAGCAACGGGGGA 60.923 57.895 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.