Multiple sequence alignment - TraesCS3A01G417000

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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 TraesCS3A01G417000 chr3A 100.000 7953 0 0 1 7953 659391845 659399797 0.000000e+00 14687.0
1 TraesCS3A01G417000 chr3A 86.000 200 22 4 7492 7689 659398821 659399016 8.090000e-50 209.0
2 TraesCS3A01G417000 chr3A 86.000 200 22 4 6977 7172 659399336 659399533 8.090000e-50 209.0
3 TraesCS3A01G417000 chr3D 94.563 4764 176 26 961 5684 524864513 524869233 0.000000e+00 7286.0
4 TraesCS3A01G417000 chr3D 94.783 1725 72 12 5681 7397 524869271 524870985 0.000000e+00 2671.0
5 TraesCS3A01G417000 chr3D 93.483 491 24 6 478 964 524863881 524864367 0.000000e+00 723.0
6 TraesCS3A01G417000 chr3D 84.348 575 67 15 7398 7953 524871030 524871600 7.020000e-150 542.0
7 TraesCS3A01G417000 chr3D 81.231 325 44 12 7638 7952 524870753 524871070 6.160000e-61 246.0
8 TraesCS3A01G417000 chr3D 86.449 214 24 5 7480 7689 524870547 524870759 6.210000e-56 230.0
9 TraesCS3A01G417000 chr3D 86.082 194 22 2 6977 7165 524871133 524871326 3.760000e-48 204.0
10 TraesCS3A01G417000 chr3B 94.739 3022 113 13 1064 4057 692835249 692838252 0.000000e+00 4658.0
11 TraesCS3A01G417000 chr3B 95.221 1716 68 9 5681 7394 692839927 692841630 0.000000e+00 2702.0
12 TraesCS3A01G417000 chr3B 96.493 884 27 2 4055 4937 692838365 692839245 0.000000e+00 1458.0
13 TraesCS3A01G417000 chr3B 97.568 658 11 5 5028 5684 692839235 692839888 0.000000e+00 1122.0
14 TraesCS3A01G417000 chr3B 90.097 515 48 1 67 578 692834178 692834692 0.000000e+00 665.0
15 TraesCS3A01G417000 chr3B 88.620 413 42 3 116 524 59893929 59894340 1.540000e-136 497.0
16 TraesCS3A01G417000 chr3B 81.690 568 50 14 7414 7953 692841684 692842225 2.650000e-114 424.0
17 TraesCS3A01G417000 chr3B 92.473 279 14 4 637 908 692834694 692834972 7.480000e-105 392.0
18 TraesCS3A01G417000 chr3B 84.834 211 24 6 7483 7689 692841202 692841408 1.050000e-48 206.0
19 TraesCS3A01G417000 chr3B 79.859 283 40 13 7638 7911 692841402 692841676 2.930000e-44 191.0
20 TraesCS3A01G417000 chr3B 87.417 151 14 3 6977 7123 692841772 692841921 1.370000e-37 169.0
21 TraesCS3A01G417000 chr5D 79.648 398 67 13 95 485 423077673 423077283 2.830000e-69 274.0
22 TraesCS3A01G417000 chr7A 87.500 216 20 6 1668 1879 8736659 8736871 7.970000e-60 243.0
23 TraesCS3A01G417000 chr7B 90.476 105 8 2 14 118 510592073 510591971 3.870000e-28 137.0
24 TraesCS3A01G417000 chr7B 86.567 67 7 1 405 469 510578143 510578077 1.110000e-08 73.1
25 TraesCS3A01G417000 chr6A 85.294 136 14 4 14 146 70567832 70567964 1.390000e-27 135.0
26 TraesCS3A01G417000 chr6A 84.615 117 18 0 465 581 325258312 325258428 5.040000e-22 117.0
27 TraesCS3A01G417000 chr1B 85.833 120 17 0 465 584 24636131 24636012 2.330000e-25 128.0
28 TraesCS3A01G417000 chr4B 87.500 112 10 3 1667 1775 640313149 640313259 8.380000e-25 126.0


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 TraesCS3A01G417000 chr3A 659391845 659399797 7952 False 5035.000000 14687 90.666667 1 7953 3 chr3A.!!$F1 7952
1 TraesCS3A01G417000 chr3D 524863881 524871600 7719 False 1700.285714 7286 88.705571 478 7953 7 chr3D.!!$F1 7475
2 TraesCS3A01G417000 chr3B 692834178 692842225 8047 False 1198.700000 4658 90.039100 67 7953 10 chr3B.!!$F2 7886

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
457 461 0.030603 AAGGGGATCAGGGAGGAGAC 60.031 60.000 0.00 0.00 0.00 3.36 F
463 467 0.041238 ATCAGGGAGGAGACGGTTGA 59.959 55.000 0.00 0.00 0.00 3.18 F
1279 1462 0.107214 GAAATCTCGGGTCATGGCCA 60.107 55.000 20.13 8.56 0.00 5.36 F
1295 1478 0.739813 GCCACGTTCTAATCGCTGGT 60.740 55.000 0.00 0.00 34.56 4.00 F
1554 1738 1.003464 TGCTGCTTCTGCTGGTATTCA 59.997 47.619 0.00 0.00 40.48 2.57 F
1692 1876 1.208293 CTCAGCCTCAAGGTTACTCCC 59.792 57.143 0.00 0.00 37.57 4.30 F
2739 2940 1.956477 TGTTCTGCTTTCCTTCTTGGC 59.044 47.619 0.00 0.00 35.26 4.52 F
3101 3304 2.165845 CCTGGTTAACACCTCGTAGGAG 59.834 54.545 8.10 5.43 44.61 3.69 F
3561 3764 3.071874 CAGGTAGTGGAAAGGATTGCA 57.928 47.619 0.00 0.00 34.17 4.08 F
4660 5007 2.028020 CACTACTGGAGGGAGAAACACC 60.028 54.545 0.00 0.00 0.00 4.16 F
4856 5203 2.627699 ACCAACACCCAAGTAATTGCAG 59.372 45.455 0.00 0.00 0.00 4.41 F
6014 6410 2.211806 TGCATGTTTTTGCTGCCTTTC 58.788 42.857 0.00 0.00 43.18 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1472 0.040958 GCTCACAGACAAAACCAGCG 60.041 55.000 0.00 0.00 0.00 5.18 R
1992 2180 0.104855 TGGTGTCATAGCGCCATCTC 59.895 55.000 2.29 0.00 43.32 2.75 R
2736 2937 2.094803 CGGCAACAAATTGTATGAGCCA 60.095 45.455 22.24 0.00 40.19 4.75 R
2737 2938 2.163412 TCGGCAACAAATTGTATGAGCC 59.837 45.455 16.54 16.54 38.17 4.70 R
3360 3563 0.541063 TAGCGAAGGAGGTGACACCA 60.541 55.000 26.30 0.00 44.58 4.17 R
3561 3764 5.525378 GCGACAAGGACTCAATCTGATTAAT 59.475 40.000 1.98 0.00 0.00 1.40 R
4244 4582 1.200948 GCCCAAGACTTGCACAAGATC 59.799 52.381 16.95 10.24 40.79 2.75 R
4660 5007 2.031420 TCCTGTAACAACGACAGACTCG 60.031 50.000 4.38 0.00 46.01 4.18 R
5498 5849 0.246635 GCCTCTGTCGGTGTATGTGT 59.753 55.000 0.00 0.00 0.00 3.72 R
5894 6288 0.107703 GGAAGATGCGTCCACCATCA 60.108 55.000 1.23 0.00 41.13 3.07 R
6403 6799 1.106285 GGCCAGTAAATGCAAGGGAG 58.894 55.000 0.00 0.00 0.00 4.30 R
6993 7389 1.076044 AACCCAAGCAACTGCCACT 60.076 52.632 0.00 0.00 43.38 4.00 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
25 26 4.959596 GAGCGGCCGCCATCTCTC 62.960 72.222 44.47 30.44 43.17 3.20
27 28 4.959596 GCGGCCGCCATCTCTCTC 62.960 72.222 39.89 7.71 34.56 3.20
28 29 3.222855 CGGCCGCCATCTCTCTCT 61.223 66.667 14.67 0.00 0.00 3.10
29 30 2.733945 GGCCGCCATCTCTCTCTC 59.266 66.667 3.91 0.00 0.00 3.20
30 31 1.832167 GGCCGCCATCTCTCTCTCT 60.832 63.158 3.91 0.00 0.00 3.10
31 32 1.659794 GCCGCCATCTCTCTCTCTC 59.340 63.158 0.00 0.00 0.00 3.20
32 33 1.106351 GCCGCCATCTCTCTCTCTCA 61.106 60.000 0.00 0.00 0.00 3.27
33 34 1.619654 CCGCCATCTCTCTCTCTCAT 58.380 55.000 0.00 0.00 0.00 2.90
34 35 1.541147 CCGCCATCTCTCTCTCTCATC 59.459 57.143 0.00 0.00 0.00 2.92
35 36 1.197492 CGCCATCTCTCTCTCTCATCG 59.803 57.143 0.00 0.00 0.00 3.84
36 37 1.541147 GCCATCTCTCTCTCTCATCGG 59.459 57.143 0.00 0.00 0.00 4.18
37 38 2.862541 CCATCTCTCTCTCTCATCGGT 58.137 52.381 0.00 0.00 0.00 4.69
38 39 2.553602 CCATCTCTCTCTCTCATCGGTG 59.446 54.545 0.00 0.00 0.00 4.94
39 40 2.340210 TCTCTCTCTCTCATCGGTGG 57.660 55.000 0.00 0.00 0.00 4.61
40 41 0.667993 CTCTCTCTCTCATCGGTGGC 59.332 60.000 0.00 0.00 0.00 5.01
41 42 0.753479 TCTCTCTCTCATCGGTGGCC 60.753 60.000 0.00 0.00 0.00 5.36
42 43 1.000359 TCTCTCTCATCGGTGGCCA 60.000 57.895 0.00 0.00 0.00 5.36
43 44 1.142748 CTCTCTCATCGGTGGCCAC 59.857 63.158 28.57 28.57 0.00 5.01
52 53 4.603535 GGTGGCCACCCAGTGCTT 62.604 66.667 40.65 0.00 45.68 3.91
53 54 3.297620 GTGGCCACCCAGTGCTTG 61.298 66.667 26.31 0.00 43.18 4.01
54 55 3.819652 TGGCCACCCAGTGCTTGT 61.820 61.111 0.00 0.00 35.79 3.16
55 56 2.985847 GGCCACCCAGTGCTTGTC 60.986 66.667 0.00 0.00 31.34 3.18
56 57 2.985847 GCCACCCAGTGCTTGTCC 60.986 66.667 0.00 0.00 31.34 4.02
57 58 2.839098 CCACCCAGTGCTTGTCCT 59.161 61.111 0.00 0.00 31.34 3.85
58 59 1.151450 CCACCCAGTGCTTGTCCTT 59.849 57.895 0.00 0.00 31.34 3.36
59 60 0.468029 CCACCCAGTGCTTGTCCTTT 60.468 55.000 0.00 0.00 31.34 3.11
60 61 0.670162 CACCCAGTGCTTGTCCTTTG 59.330 55.000 0.00 0.00 0.00 2.77
61 62 0.468029 ACCCAGTGCTTGTCCTTTGG 60.468 55.000 0.00 0.00 0.00 3.28
62 63 1.662044 CCAGTGCTTGTCCTTTGGC 59.338 57.895 0.00 0.00 0.00 4.52
63 64 1.662044 CAGTGCTTGTCCTTTGGCC 59.338 57.895 0.00 0.00 0.00 5.36
64 65 0.825010 CAGTGCTTGTCCTTTGGCCT 60.825 55.000 3.32 0.00 0.00 5.19
65 66 0.825010 AGTGCTTGTCCTTTGGCCTG 60.825 55.000 3.32 0.00 0.00 4.85
69 70 1.615384 GCTTGTCCTTTGGCCTGATCT 60.615 52.381 3.32 0.00 0.00 2.75
72 73 1.988107 TGTCCTTTGGCCTGATCTTCT 59.012 47.619 3.32 0.00 0.00 2.85
77 78 0.740868 TTGGCCTGATCTTCTTCGCG 60.741 55.000 3.32 0.00 0.00 5.87
150 151 4.827087 CTGACGGCCGAGCTGCAT 62.827 66.667 35.90 7.12 38.71 3.96
161 162 2.800736 GCTGCATGCGGTTTAGGG 59.199 61.111 26.79 4.24 0.00 3.53
179 180 4.437587 GGCATCCCTGGCAGCTGT 62.438 66.667 16.64 0.00 46.77 4.40
193 194 0.474184 AGCTGTGCAGGTGGTTTAGT 59.526 50.000 2.87 0.00 37.82 2.24
203 204 0.609662 GTGGTTTAGTAGGCGTCCCA 59.390 55.000 0.00 0.00 0.00 4.37
246 247 4.090588 GGCGATGGTTGGGGACGA 62.091 66.667 0.00 0.00 0.00 4.20
282 283 3.423154 GGCGTCCTTGAAGGCGTG 61.423 66.667 22.27 10.24 37.28 5.34
285 286 1.300620 CGTCCTTGAAGGCGTGACA 60.301 57.895 16.31 0.00 34.61 3.58
341 342 1.069513 CCTAATATGTGGCGGGTCGAA 59.930 52.381 0.00 0.00 0.00 3.71
346 347 4.980805 GTGGCGGGTCGAAGTGCA 62.981 66.667 6.39 0.00 0.00 4.57
399 403 2.113986 AAGGCTTGCGGCTGTTCT 59.886 55.556 0.00 0.00 46.62 3.01
413 417 3.378427 GGCTGTTCTCTTGTGTCAGTTTT 59.622 43.478 0.00 0.00 0.00 2.43
457 461 0.030603 AAGGGGATCAGGGAGGAGAC 60.031 60.000 0.00 0.00 0.00 3.36
463 467 0.041238 ATCAGGGAGGAGACGGTTGA 59.959 55.000 0.00 0.00 0.00 3.18
469 473 1.757699 GGAGGAGACGGTTGATTAGCT 59.242 52.381 0.00 0.00 0.00 3.32
525 529 1.698714 GGACGGTTGGATTAACGCGG 61.699 60.000 12.47 0.00 40.28 6.46
688 720 9.901172 TTTTTAACCTACCCTGCAAATTTAAAA 57.099 25.926 0.00 0.00 0.00 1.52
823 856 5.237344 GCCATTATACGAATCTCAAAGCAGT 59.763 40.000 0.00 0.00 0.00 4.40
955 989 1.205055 CCAGTCTCCTAAACCCCTCC 58.795 60.000 0.00 0.00 0.00 4.30
1038 1221 2.759973 CTGGCCGTCCTCCTGCTA 60.760 66.667 0.00 0.00 0.00 3.49
1202 1385 4.394712 CCAGCTTTCGCCCCTCGT 62.395 66.667 0.00 0.00 39.67 4.18
1279 1462 0.107214 GAAATCTCGGGTCATGGCCA 60.107 55.000 20.13 8.56 0.00 5.36
1288 1471 1.408266 GGGTCATGGCCACGTTCTAAT 60.408 52.381 20.13 0.00 0.00 1.73
1289 1472 1.940613 GGTCATGGCCACGTTCTAATC 59.059 52.381 12.68 0.00 0.00 1.75
1295 1478 0.739813 GCCACGTTCTAATCGCTGGT 60.740 55.000 0.00 0.00 34.56 4.00
1305 1488 3.745975 TCTAATCGCTGGTTTTGTCTGTG 59.254 43.478 0.00 0.00 0.00 3.66
1306 1489 2.254546 ATCGCTGGTTTTGTCTGTGA 57.745 45.000 0.00 0.00 0.00 3.58
1363 1547 2.422479 CAGGACGTTCAAGATACTCGGA 59.578 50.000 0.00 0.00 0.00 4.55
1416 1600 3.032609 CAAGCTCGCCGCGGATAG 61.033 66.667 33.48 25.20 45.59 2.08
1554 1738 1.003464 TGCTGCTTCTGCTGGTATTCA 59.997 47.619 0.00 0.00 40.48 2.57
1556 1740 2.012673 CTGCTTCTGCTGGTATTCACC 58.987 52.381 0.00 0.00 40.28 4.02
1587 1771 4.202212 TGGTGTTCTGAGATTCGTTCTTCA 60.202 41.667 0.00 0.00 33.74 3.02
1617 1801 3.255379 GCGTCGAGGCTTAAGGCG 61.255 66.667 22.16 10.15 46.23 5.52
1662 1846 5.330455 TGCTGGAGTTCTACTATTCTGTG 57.670 43.478 0.00 0.00 0.00 3.66
1692 1876 1.208293 CTCAGCCTCAAGGTTACTCCC 59.792 57.143 0.00 0.00 37.57 4.30
1707 1891 5.488341 GTTACTCCCTCTAATGCACTTTCA 58.512 41.667 0.00 0.00 0.00 2.69
1711 1895 3.009473 TCCCTCTAATGCACTTTCAGCTT 59.991 43.478 0.00 0.00 0.00 3.74
1712 1896 3.128242 CCCTCTAATGCACTTTCAGCTTG 59.872 47.826 0.00 0.00 0.00 4.01
1719 1903 4.389890 TGCACTTTCAGCTTGATGTTTT 57.610 36.364 0.00 0.00 0.00 2.43
1762 1948 3.876914 CTGCTGTTAGTTGGTTGTCTGAA 59.123 43.478 0.00 0.00 0.00 3.02
1776 1962 7.685481 TGGTTGTCTGAATTTTATCTGGTAGA 58.315 34.615 0.00 0.00 0.00 2.59
1827 2015 2.270047 CAAGGCCACAGTGTTGTTTTG 58.730 47.619 5.01 0.00 34.62 2.44
1836 2024 3.181487 ACAGTGTTGTTTTGTCTGATGCC 60.181 43.478 0.00 0.00 32.28 4.40
1865 2053 5.631512 GCACATTTCACGCAATTAAGGTTAA 59.368 36.000 0.00 0.00 0.00 2.01
1926 2114 4.946445 TCTTGCAATCACAATTTTGCTCA 58.054 34.783 12.47 1.20 46.50 4.26
2223 2412 6.127338 TGTGTATATGCTCTCTGCTTGTACTT 60.127 38.462 0.00 0.00 41.01 2.24
2302 2491 6.142818 AGAGATGAAGAAGTCGGATAACTG 57.857 41.667 0.00 0.00 0.00 3.16
2318 2507 8.347771 TCGGATAACTGTATAGTACATGTTGTC 58.652 37.037 2.30 13.78 38.15 3.18
2326 2515 9.371136 CTGTATAGTACATGTTGTCTCACAAAT 57.629 33.333 2.30 0.00 37.70 2.32
2327 2516 9.719355 TGTATAGTACATGTTGTCTCACAAATT 57.281 29.630 2.30 0.00 35.19 1.82
2499 2688 5.444663 AACAGGAAGAGCTTGATTTCAAC 57.555 39.130 0.00 0.00 0.00 3.18
2515 2704 3.414549 TCAACACAAAAGAGAAACGGC 57.585 42.857 0.00 0.00 0.00 5.68
2732 2933 3.244078 TGTGTACGATGTTCTGCTTTCCT 60.244 43.478 0.00 0.00 0.00 3.36
2733 2934 3.746492 GTGTACGATGTTCTGCTTTCCTT 59.254 43.478 0.00 0.00 0.00 3.36
2734 2935 3.994392 TGTACGATGTTCTGCTTTCCTTC 59.006 43.478 0.00 0.00 0.00 3.46
2735 2936 3.409026 ACGATGTTCTGCTTTCCTTCT 57.591 42.857 0.00 0.00 0.00 2.85
2736 2937 3.744660 ACGATGTTCTGCTTTCCTTCTT 58.255 40.909 0.00 0.00 0.00 2.52
2737 2938 3.499918 ACGATGTTCTGCTTTCCTTCTTG 59.500 43.478 0.00 0.00 0.00 3.02
2738 2939 3.120060 CGATGTTCTGCTTTCCTTCTTGG 60.120 47.826 0.00 0.00 37.10 3.61
2739 2940 1.956477 TGTTCTGCTTTCCTTCTTGGC 59.044 47.619 0.00 0.00 35.26 4.52
2740 2941 2.234143 GTTCTGCTTTCCTTCTTGGCT 58.766 47.619 0.00 0.00 35.26 4.75
2741 2942 2.191128 TCTGCTTTCCTTCTTGGCTC 57.809 50.000 0.00 0.00 35.26 4.70
2869 3070 5.299279 CACTATTGGCGGTCCTGATTTTTAT 59.701 40.000 0.00 0.00 0.00 1.40
2872 3073 5.570234 TTGGCGGTCCTGATTTTTATTAC 57.430 39.130 0.00 0.00 0.00 1.89
2874 3075 5.991861 TGGCGGTCCTGATTTTTATTACTA 58.008 37.500 0.00 0.00 0.00 1.82
2877 3078 6.485648 GGCGGTCCTGATTTTTATTACTATGT 59.514 38.462 0.00 0.00 0.00 2.29
3101 3304 2.165845 CCTGGTTAACACCTCGTAGGAG 59.834 54.545 8.10 5.43 44.61 3.69
3180 3383 9.852091 GTTAGCAGTACTATTTAGTTAGTGTGT 57.148 33.333 0.00 0.00 37.73 3.72
3360 3563 4.037684 ACAACTTCTGCTTCAGTAGTACGT 59.962 41.667 6.55 0.00 40.30 3.57
3561 3764 3.071874 CAGGTAGTGGAAAGGATTGCA 57.928 47.619 0.00 0.00 34.17 4.08
3698 3901 7.295201 TGTGATGCTTATTTCGTTTCTACAAC 58.705 34.615 0.00 0.00 0.00 3.32
4012 4235 5.352569 GCATATGCATCCTATGTGGTACTTC 59.647 44.000 22.84 0.00 41.59 3.01
4061 4284 8.668510 AGTGTCTGCTAAAAAGATGTATATGG 57.331 34.615 0.00 0.00 0.00 2.74
4062 4285 7.227512 AGTGTCTGCTAAAAAGATGTATATGGC 59.772 37.037 0.00 0.00 0.00 4.40
4184 4522 7.878127 CCAACTCGTGTTCCCTTGATATATATT 59.122 37.037 0.00 0.00 33.52 1.28
4185 4523 9.923143 CAACTCGTGTTCCCTTGATATATATTA 57.077 33.333 0.00 0.00 33.52 0.98
4393 4732 6.317893 CCGTGTTTTAGCTACAATTCCCTAAT 59.682 38.462 0.00 0.00 0.00 1.73
4660 5007 2.028020 CACTACTGGAGGGAGAAACACC 60.028 54.545 0.00 0.00 0.00 4.16
4793 5140 6.755141 CACTTGATTCCATGCCATTAGAAAAG 59.245 38.462 0.00 0.00 0.00 2.27
4814 5161 6.923928 AAGCATGTTTTACAGCAACATTTT 57.076 29.167 0.00 0.00 41.19 1.82
4816 5163 8.430801 AAGCATGTTTTACAGCAACATTTTAA 57.569 26.923 0.00 0.00 41.19 1.52
4856 5203 2.627699 ACCAACACCCAAGTAATTGCAG 59.372 45.455 0.00 0.00 0.00 4.41
4930 5277 7.618137 ACGAATAACACTTCCTAACCTGTTAT 58.382 34.615 0.00 0.00 40.11 1.89
4948 5295 7.824779 ACCTGTTATTATGTGGTTCTTCTCTTC 59.175 37.037 0.00 0.00 0.00 2.87
4996 5343 3.489355 TCCTGCATTGTTTCAGTCATGT 58.511 40.909 0.00 0.00 0.00 3.21
4998 5345 4.696877 TCCTGCATTGTTTCAGTCATGTAG 59.303 41.667 0.00 0.00 0.00 2.74
5002 5349 4.154737 GCATTGTTTCAGTCATGTAGCTGA 59.845 41.667 0.00 11.32 39.66 4.26
5004 5351 4.607293 TGTTTCAGTCATGTAGCTGAGT 57.393 40.909 0.00 0.00 41.93 3.41
5005 5352 4.960938 TGTTTCAGTCATGTAGCTGAGTT 58.039 39.130 0.00 0.00 41.93 3.01
5006 5353 4.751600 TGTTTCAGTCATGTAGCTGAGTTG 59.248 41.667 0.00 0.00 41.93 3.16
5007 5354 4.607293 TTCAGTCATGTAGCTGAGTTGT 57.393 40.909 0.00 0.00 41.93 3.32
5008 5355 3.917988 TCAGTCATGTAGCTGAGTTGTG 58.082 45.455 0.00 0.00 36.89 3.33
5009 5356 3.573967 TCAGTCATGTAGCTGAGTTGTGA 59.426 43.478 0.00 0.00 36.89 3.58
5082 5432 9.834628 TTTAGGTTCTAATTTCATAGCAAAACG 57.165 29.630 0.00 0.00 0.00 3.60
5163 5513 5.866633 AGATACAAAAGTTTCTCTCTCTGCG 59.133 40.000 0.00 0.00 0.00 5.18
5478 5829 7.279750 TGTTTCCATTAGGTTTTAGGTTGTC 57.720 36.000 0.00 0.00 35.89 3.18
5848 6242 4.255510 ACAAGATTATCCAGGTGCCAAT 57.744 40.909 0.00 0.00 0.00 3.16
5860 6254 5.248020 TCCAGGTGCCAATACATTTGAAATT 59.752 36.000 0.00 0.00 0.00 1.82
5866 6260 7.064490 GGTGCCAATACATTTGAAATTAACCTG 59.936 37.037 0.00 0.00 0.00 4.00
5969 6363 4.777366 TCAGATGTGGAGATGAAGTACCAA 59.223 41.667 0.00 0.00 34.11 3.67
5980 6376 8.041323 GGAGATGAAGTACCAAAAGATCACTTA 58.959 37.037 0.00 0.00 35.05 2.24
6013 6409 2.328819 TGCATGTTTTTGCTGCCTTT 57.671 40.000 0.00 0.00 43.18 3.11
6014 6410 2.211806 TGCATGTTTTTGCTGCCTTTC 58.788 42.857 0.00 0.00 43.18 2.62
6015 6411 2.211806 GCATGTTTTTGCTGCCTTTCA 58.788 42.857 0.00 0.00 39.57 2.69
6016 6412 2.222445 GCATGTTTTTGCTGCCTTTCAG 59.778 45.455 0.00 0.00 45.62 3.02
6167 6563 4.343231 TGGTGATGCTTCAATGGTATGTT 58.657 39.130 3.51 0.00 32.48 2.71
6427 6823 1.131126 CTTGCATTTACTGGCCTCACG 59.869 52.381 3.32 0.00 0.00 4.35
6433 6829 1.605058 TTACTGGCCTCACGCTCCTC 61.605 60.000 3.32 0.00 37.74 3.71
6481 6877 5.998363 GGTGAGTCAACAATTCCTACTCTTT 59.002 40.000 2.42 0.00 37.92 2.52
6518 6914 4.456280 TGCTATCACACTTCTGTACTGG 57.544 45.455 0.00 0.00 0.00 4.00
6784 7180 3.256631 GCATCTTCCTTGTGGTGAAACAT 59.743 43.478 0.00 0.00 39.98 2.71
6786 7182 5.126061 GCATCTTCCTTGTGGTGAAACATAT 59.874 40.000 0.00 0.00 39.98 1.78
6787 7183 6.318648 GCATCTTCCTTGTGGTGAAACATATA 59.681 38.462 0.00 0.00 39.98 0.86
6788 7184 7.148086 GCATCTTCCTTGTGGTGAAACATATAA 60.148 37.037 0.00 0.00 39.98 0.98
6789 7185 8.906867 CATCTTCCTTGTGGTGAAACATATAAT 58.093 33.333 0.00 0.00 39.98 1.28
6790 7186 8.877864 TCTTCCTTGTGGTGAAACATATAATT 57.122 30.769 0.00 0.00 39.98 1.40
6791 7187 8.739039 TCTTCCTTGTGGTGAAACATATAATTG 58.261 33.333 0.00 0.00 39.98 2.32
6793 7189 6.435591 TCCTTGTGGTGAAACATATAATTGCA 59.564 34.615 0.00 0.00 39.98 4.08
6794 7190 6.531240 CCTTGTGGTGAAACATATAATTGCAC 59.469 38.462 0.00 3.54 39.98 4.57
6795 7191 6.832520 TGTGGTGAAACATATAATTGCACT 57.167 33.333 9.84 0.00 39.98 4.40
6796 7192 7.929941 TGTGGTGAAACATATAATTGCACTA 57.070 32.000 9.84 3.24 39.98 2.74
6797 7193 8.341892 TGTGGTGAAACATATAATTGCACTAA 57.658 30.769 9.84 0.00 39.98 2.24
6798 7194 8.965819 TGTGGTGAAACATATAATTGCACTAAT 58.034 29.630 9.84 0.00 39.98 1.73
6828 7224 5.900425 TCTGCTCACTATCATTCTTCTGTC 58.100 41.667 0.00 0.00 0.00 3.51
6910 7306 2.432300 CGTCGGCCATAGGACCCTT 61.432 63.158 2.24 0.00 0.00 3.95
6931 7327 1.071542 TCTCATCTTTCCAACACGGCA 59.928 47.619 0.00 0.00 33.14 5.69
6972 7368 1.382522 TGGGAAGATGCGAAGAATGC 58.617 50.000 0.00 0.00 0.00 3.56
6993 7389 2.097304 CGTGATCATCAATTTTCGGGCA 59.903 45.455 0.00 0.00 0.00 5.36
6996 7392 3.129113 TGATCATCAATTTTCGGGCAGTG 59.871 43.478 0.00 0.00 0.00 3.66
7195 7595 4.302067 AGGACCTCACCTTCATGTATGAT 58.698 43.478 0.00 0.00 36.86 2.45
7199 7599 4.141321 ACCTCACCTTCATGTATGATGCAT 60.141 41.667 0.00 0.00 36.56 3.96
7226 7626 8.902806 TGATGTTTACTAAATAGGCTGGATTTG 58.097 33.333 0.00 0.00 0.00 2.32
7314 7716 9.092876 TGATTTACAAACTCACAAAACCAAATC 57.907 29.630 0.00 0.00 32.15 2.17
7397 7800 1.002069 ATGGGAGCAGAACCAATCCA 58.998 50.000 0.00 0.00 40.73 3.41
7398 7801 1.002069 TGGGAGCAGAACCAATCCAT 58.998 50.000 0.00 0.00 32.89 3.41
7400 7803 2.580322 TGGGAGCAGAACCAATCCATAA 59.420 45.455 0.00 0.00 32.89 1.90
7401 7804 3.205056 TGGGAGCAGAACCAATCCATAAT 59.795 43.478 0.00 0.00 32.89 1.28
7403 7806 5.103728 TGGGAGCAGAACCAATCCATAATTA 60.104 40.000 0.00 0.00 32.89 1.40
7440 7886 4.835615 TGCATTTTAGCCCAAACCTAAGAA 59.164 37.500 0.00 0.00 0.00 2.52
7516 7972 0.250553 AATTTTCGGGCGGTCACAGA 60.251 50.000 0.00 0.00 0.00 3.41
7554 8011 0.519077 GCTTTTTGCTCGAGACCCTG 59.481 55.000 18.75 2.02 38.95 4.45
7595 8053 6.460953 GCAACTTGAGTTTTGAGGGACATAAA 60.461 38.462 0.00 0.00 35.83 1.40
7612 8070 8.837389 GGGACATAAAGGTATCATTTTGTAGTC 58.163 37.037 0.00 0.00 0.00 2.59
7621 8079 3.417101 TCATTTTGTAGTCGGTGCCAAT 58.583 40.909 0.00 0.00 0.00 3.16
7622 8080 3.823873 TCATTTTGTAGTCGGTGCCAATT 59.176 39.130 0.00 0.00 0.00 2.32
7623 8081 4.279671 TCATTTTGTAGTCGGTGCCAATTT 59.720 37.500 0.00 0.00 0.00 1.82
7644 8102 4.399483 TTCCTGGTACTAGAGAAGTGGT 57.601 45.455 7.98 0.00 39.39 4.16
7645 8103 5.525454 TTCCTGGTACTAGAGAAGTGGTA 57.475 43.478 7.98 0.00 39.39 3.25
7653 8111 3.592427 ACTAGAGAAGTGGTAGGACCTCA 59.408 47.826 0.00 0.00 39.58 3.86
7660 8118 1.275573 GTGGTAGGACCTCACCTTCAC 59.724 57.143 16.47 0.00 39.58 3.18
7674 8132 3.622612 CACCTTCACGTATGATGCATTGA 59.377 43.478 0.00 0.00 33.85 2.57
7767 8226 7.015195 AGGTTAACTTGTGTTATGCCTTTTGAT 59.985 33.333 5.42 0.00 39.29 2.57
7780 8239 6.214191 TGCCTTTTGATTTACAAACTCACA 57.786 33.333 0.00 0.00 46.32 3.58
7805 8280 2.478831 CAAATTCCCCAACCAAACACG 58.521 47.619 0.00 0.00 0.00 4.49
7819 8294 2.723124 AACACGGAATTGCAACCATC 57.277 45.000 0.00 0.18 0.00 3.51
7837 8312 5.880901 ACCATCACATCCCACCTAATTATC 58.119 41.667 0.00 0.00 0.00 1.75
7839 8314 4.993705 TCACATCCCACCTAATTATCCC 57.006 45.455 0.00 0.00 0.00 3.85
7842 8317 5.072741 CACATCCCACCTAATTATCCCAAG 58.927 45.833 0.00 0.00 0.00 3.61
7848 8323 4.709397 CCACCTAATTATCCCAAGCAAACA 59.291 41.667 0.00 0.00 0.00 2.83
7868 8343 5.982890 ACATAGGAACAAAACCAATCCTG 57.017 39.130 3.49 0.00 42.20 3.86
7887 8362 3.599343 CTGACATTCCATTCCACTTCGA 58.401 45.455 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.959596 GAGAGATGGCGGCCGCTC 62.960 72.222 45.23 35.77 41.60 5.03
10 11 4.959596 GAGAGAGATGGCGGCCGC 62.960 72.222 41.63 41.63 41.06 6.53
11 12 3.206211 GAGAGAGAGATGGCGGCCG 62.206 68.421 24.05 24.05 0.00 6.13
12 13 1.805428 GAGAGAGAGAGATGGCGGCC 61.805 65.000 13.32 13.32 0.00 6.13
13 14 1.106351 TGAGAGAGAGAGATGGCGGC 61.106 60.000 0.00 0.00 0.00 6.53
14 15 1.541147 GATGAGAGAGAGAGATGGCGG 59.459 57.143 0.00 0.00 0.00 6.13
15 16 1.197492 CGATGAGAGAGAGAGATGGCG 59.803 57.143 0.00 0.00 0.00 5.69
16 17 1.541147 CCGATGAGAGAGAGAGATGGC 59.459 57.143 0.00 0.00 0.00 4.40
17 18 2.553602 CACCGATGAGAGAGAGAGATGG 59.446 54.545 0.00 0.00 0.00 3.51
18 19 2.553602 CCACCGATGAGAGAGAGAGATG 59.446 54.545 0.00 0.00 0.00 2.90
19 20 2.862541 CCACCGATGAGAGAGAGAGAT 58.137 52.381 0.00 0.00 0.00 2.75
20 21 1.748939 GCCACCGATGAGAGAGAGAGA 60.749 57.143 0.00 0.00 0.00 3.10
21 22 0.667993 GCCACCGATGAGAGAGAGAG 59.332 60.000 0.00 0.00 0.00 3.20
22 23 0.753479 GGCCACCGATGAGAGAGAGA 60.753 60.000 0.00 0.00 0.00 3.10
23 24 1.039785 TGGCCACCGATGAGAGAGAG 61.040 60.000 0.00 0.00 0.00 3.20
24 25 1.000359 TGGCCACCGATGAGAGAGA 60.000 57.895 0.00 0.00 0.00 3.10
25 26 1.142748 GTGGCCACCGATGAGAGAG 59.857 63.158 26.31 0.00 0.00 3.20
26 27 2.359169 GGTGGCCACCGATGAGAGA 61.359 63.158 38.35 0.00 42.29 3.10
27 28 2.187946 GGTGGCCACCGATGAGAG 59.812 66.667 38.35 0.00 42.29 3.20
36 37 3.297620 CAAGCACTGGGTGGCCAC 61.298 66.667 28.57 28.57 33.64 5.01
37 38 3.790416 GACAAGCACTGGGTGGCCA 62.790 63.158 0.00 0.00 33.64 5.36
38 39 2.985847 GACAAGCACTGGGTGGCC 60.986 66.667 0.00 0.00 33.64 5.36
39 40 2.983725 AAGGACAAGCACTGGGTGGC 62.984 60.000 0.00 0.00 33.64 5.01
40 41 0.468029 AAAGGACAAGCACTGGGTGG 60.468 55.000 0.00 0.00 33.64 4.61
41 42 0.670162 CAAAGGACAAGCACTGGGTG 59.330 55.000 0.00 0.00 36.51 4.61
42 43 0.468029 CCAAAGGACAAGCACTGGGT 60.468 55.000 0.00 0.00 0.00 4.51
43 44 1.809567 GCCAAAGGACAAGCACTGGG 61.810 60.000 0.00 0.00 0.00 4.45
44 45 1.662044 GCCAAAGGACAAGCACTGG 59.338 57.895 0.00 0.00 0.00 4.00
45 46 0.825010 AGGCCAAAGGACAAGCACTG 60.825 55.000 5.01 0.00 29.21 3.66
46 47 0.825010 CAGGCCAAAGGACAAGCACT 60.825 55.000 5.01 0.00 29.21 4.40
47 48 0.823356 TCAGGCCAAAGGACAAGCAC 60.823 55.000 5.01 0.00 29.21 4.40
48 49 0.112995 ATCAGGCCAAAGGACAAGCA 59.887 50.000 5.01 0.00 29.21 3.91
49 50 0.813821 GATCAGGCCAAAGGACAAGC 59.186 55.000 5.01 0.00 29.21 4.01
50 51 2.503895 AGATCAGGCCAAAGGACAAG 57.496 50.000 5.01 0.00 29.21 3.16
51 52 2.376518 AGAAGATCAGGCCAAAGGACAA 59.623 45.455 5.01 0.00 29.21 3.18
52 53 1.988107 AGAAGATCAGGCCAAAGGACA 59.012 47.619 5.01 0.00 29.21 4.02
53 54 2.797177 AGAAGATCAGGCCAAAGGAC 57.203 50.000 5.01 0.00 0.00 3.85
54 55 2.355108 CGAAGAAGATCAGGCCAAAGGA 60.355 50.000 5.01 0.00 0.00 3.36
55 56 2.012673 CGAAGAAGATCAGGCCAAAGG 58.987 52.381 5.01 0.00 0.00 3.11
56 57 1.399791 GCGAAGAAGATCAGGCCAAAG 59.600 52.381 5.01 0.00 0.00 2.77
57 58 1.453155 GCGAAGAAGATCAGGCCAAA 58.547 50.000 5.01 0.00 0.00 3.28
58 59 0.740868 CGCGAAGAAGATCAGGCCAA 60.741 55.000 5.01 0.00 0.00 4.52
59 60 1.153568 CGCGAAGAAGATCAGGCCA 60.154 57.895 5.01 0.00 0.00 5.36
60 61 1.141881 TCGCGAAGAAGATCAGGCC 59.858 57.895 6.20 0.00 0.00 5.19
61 62 1.148759 GGTCGCGAAGAAGATCAGGC 61.149 60.000 12.06 0.00 0.00 4.85
62 63 0.457851 AGGTCGCGAAGAAGATCAGG 59.542 55.000 12.06 0.00 0.00 3.86
63 64 1.923204 CAAGGTCGCGAAGAAGATCAG 59.077 52.381 12.06 0.00 0.00 2.90
64 65 1.996292 CAAGGTCGCGAAGAAGATCA 58.004 50.000 12.06 0.00 0.00 2.92
65 66 0.647925 GCAAGGTCGCGAAGAAGATC 59.352 55.000 12.06 0.00 0.00 2.75
69 70 0.389426 GGTAGCAAGGTCGCGAAGAA 60.389 55.000 12.06 0.00 36.85 2.52
72 73 2.126228 CGGTAGCAAGGTCGCGAA 60.126 61.111 12.06 0.00 36.85 4.70
77 78 0.735287 GGAACGACGGTAGCAAGGTC 60.735 60.000 0.00 0.00 0.00 3.85
124 125 4.779733 GGCCGTCAGGGAGGGAGA 62.780 72.222 9.01 0.00 39.66 3.71
133 134 4.827087 ATGCAGCTCGGCCGTCAG 62.827 66.667 27.15 17.71 0.00 3.51
143 144 1.750399 CCCTAAACCGCATGCAGCT 60.750 57.895 19.57 0.00 42.61 4.24
145 146 2.120909 CCCCCTAAACCGCATGCAG 61.121 63.158 19.57 9.32 0.00 4.41
146 147 2.044451 CCCCCTAAACCGCATGCA 60.044 61.111 19.57 0.00 0.00 3.96
150 151 2.274104 GATGCCCCCTAAACCGCA 59.726 61.111 0.00 0.00 35.35 5.69
170 171 4.960866 CCACCTGCACAGCTGCCA 62.961 66.667 15.27 10.61 43.51 4.92
174 175 0.474184 ACTAAACCACCTGCACAGCT 59.526 50.000 0.00 0.00 0.00 4.24
176 177 2.699954 CCTACTAAACCACCTGCACAG 58.300 52.381 0.00 0.00 0.00 3.66
179 180 0.036765 CGCCTACTAAACCACCTGCA 60.037 55.000 0.00 0.00 0.00 4.41
183 184 0.107993 GGGACGCCTACTAAACCACC 60.108 60.000 0.00 0.00 0.00 4.61
185 186 1.002315 GTTGGGACGCCTACTAAACCA 59.998 52.381 0.00 0.00 0.00 3.67
193 194 4.077184 CGGCAGTTGGGACGCCTA 62.077 66.667 0.00 0.00 40.74 3.93
246 247 2.606587 GCCCCTCACACCTCCATGT 61.607 63.158 0.00 0.00 0.00 3.21
281 282 1.176619 ACCATCGTGTCGACCTGTCA 61.177 55.000 14.12 0.00 39.18 3.58
282 283 0.732880 CACCATCGTGTCGACCTGTC 60.733 60.000 14.12 0.20 39.18 3.51
285 286 2.970639 CCACCATCGTGTCGACCT 59.029 61.111 14.12 0.00 39.18 3.85
394 398 6.206634 ACAAAGAAAACTGACACAAGAGAACA 59.793 34.615 0.00 0.00 0.00 3.18
399 403 4.671508 CGCACAAAGAAAACTGACACAAGA 60.672 41.667 0.00 0.00 0.00 3.02
413 417 2.039216 TCCATACCCTTTCGCACAAAGA 59.961 45.455 6.70 0.00 0.00 2.52
457 461 3.924686 ACACGTTTAGAGCTAATCAACCG 59.075 43.478 0.00 0.00 0.00 4.44
525 529 3.118956 CCAATAGATCTAGGCCATCCGTC 60.119 52.174 5.01 0.00 37.47 4.79
581 585 9.570488 CGATATCGATATCATCTACGGAGTATA 57.430 37.037 33.62 0.74 41.94 1.47
582 586 8.305317 TCGATATCGATATCATCTACGGAGTAT 58.695 37.037 33.62 6.12 42.71 2.12
583 587 7.655490 TCGATATCGATATCATCTACGGAGTA 58.345 38.462 33.62 10.23 44.22 2.59
584 588 6.514063 TCGATATCGATATCATCTACGGAGT 58.486 40.000 33.62 6.19 44.22 3.85
631 635 9.918630 CACTGAATTTTCAATAAAGAGTGGATT 57.081 29.630 0.00 0.00 36.64 3.01
633 637 7.370383 GCACTGAATTTTCAATAAAGAGTGGA 58.630 34.615 0.00 0.00 36.64 4.02
634 638 6.306356 CGCACTGAATTTTCAATAAAGAGTGG 59.694 38.462 0.00 0.00 36.64 4.00
799 831 5.237344 ACTGCTTTGAGATTCGTATAATGGC 59.763 40.000 0.00 0.00 0.00 4.40
876 909 5.758784 GGAAGGGGACGACTAGAAATATTTG 59.241 44.000 5.17 0.00 0.00 2.32
955 989 4.179599 GAGAGGGGAGGGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1165 1348 0.263172 AGATCAGGGGAGACGGTGAT 59.737 55.000 0.00 0.00 36.46 3.06
1202 1385 0.913205 TAGGTCCTTAATTGCGCCCA 59.087 50.000 4.18 0.00 0.00 5.36
1259 1442 1.160329 GGCCATGACCCGAGATTTCG 61.160 60.000 0.00 0.00 46.29 3.46
1279 1462 3.135994 ACAAAACCAGCGATTAGAACGT 58.864 40.909 0.00 0.00 0.00 3.99
1288 1471 1.581934 CTCACAGACAAAACCAGCGA 58.418 50.000 0.00 0.00 0.00 4.93
1289 1472 0.040958 GCTCACAGACAAAACCAGCG 60.041 55.000 0.00 0.00 0.00 5.18
1295 1478 0.657312 CACAGCGCTCACAGACAAAA 59.343 50.000 7.13 0.00 0.00 2.44
1363 1547 1.348775 GGCCCTTATCCCTCTGCACT 61.349 60.000 0.00 0.00 0.00 4.40
1411 1595 1.338655 GAGGACGAAGACAGCCTATCC 59.661 57.143 0.00 0.00 0.00 2.59
1412 1596 1.002251 CGAGGACGAAGACAGCCTATC 60.002 57.143 0.00 0.00 42.66 2.08
1416 1600 1.153997 GACGAGGACGAAGACAGCC 60.154 63.158 0.00 0.00 42.66 4.85
1482 1666 4.289379 CGGCATCGACGCTGCATG 62.289 66.667 23.41 12.41 41.47 4.06
1501 1685 4.391155 AGCTAAAACCCACATCGTAAACA 58.609 39.130 0.00 0.00 0.00 2.83
1554 1738 1.421268 TCAGAACACCATCAAGCAGGT 59.579 47.619 0.00 0.00 39.10 4.00
1556 1740 3.049708 TCTCAGAACACCATCAAGCAG 57.950 47.619 0.00 0.00 0.00 4.24
1680 1864 4.080863 AGTGCATTAGAGGGAGTAACCTTG 60.081 45.833 0.00 0.00 42.10 3.61
1686 1870 4.383118 GCTGAAAGTGCATTAGAGGGAGTA 60.383 45.833 0.00 0.00 35.30 2.59
1692 1876 5.123502 ACATCAAGCTGAAAGTGCATTAGAG 59.876 40.000 0.00 0.00 35.30 2.43
1748 1934 6.777580 ACCAGATAAAATTCAGACAACCAACT 59.222 34.615 0.00 0.00 0.00 3.16
1753 1939 9.383519 TCATCTACCAGATAAAATTCAGACAAC 57.616 33.333 0.00 0.00 32.12 3.32
1836 2024 2.804421 TTGCGTGAAATGTGCTATCG 57.196 45.000 0.00 0.00 0.00 2.92
1865 2053 2.953648 TGCATAGCATATTGCACTGCTT 59.046 40.909 19.29 7.92 46.22 3.91
1926 2114 6.817184 TCAGACAACTCTAGTTTAAACAGCT 58.183 36.000 20.06 2.61 35.83 4.24
1992 2180 0.104855 TGGTGTCATAGCGCCATCTC 59.895 55.000 2.29 0.00 43.32 2.75
2318 2507 7.363268 CCTCTCCCCATTAAAAGAATTTGTGAG 60.363 40.741 0.00 0.00 39.02 3.51
2326 2515 4.355588 TCAACCCTCTCCCCATTAAAAGAA 59.644 41.667 0.00 0.00 0.00 2.52
2327 2516 3.920197 TCAACCCTCTCCCCATTAAAAGA 59.080 43.478 0.00 0.00 0.00 2.52
2499 2688 7.970384 TGTTATATAGCCGTTTCTCTTTTGTG 58.030 34.615 0.00 0.00 0.00 3.33
2571 2762 7.924412 GTGCATTTGTAATTCAGATGAATGGAT 59.076 33.333 8.76 0.00 43.41 3.41
2732 2933 5.229423 GCAACAAATTGTATGAGCCAAGAA 58.771 37.500 0.00 0.00 38.17 2.52
2733 2934 4.321899 GGCAACAAATTGTATGAGCCAAGA 60.322 41.667 19.61 0.00 40.05 3.02
2734 2935 3.928375 GGCAACAAATTGTATGAGCCAAG 59.072 43.478 19.61 0.00 40.05 3.61
2735 2936 3.613671 CGGCAACAAATTGTATGAGCCAA 60.614 43.478 22.24 0.00 40.19 4.52
2736 2937 2.094803 CGGCAACAAATTGTATGAGCCA 60.095 45.455 22.24 0.00 40.19 4.75
2737 2938 2.163412 TCGGCAACAAATTGTATGAGCC 59.837 45.455 16.54 16.54 38.17 4.70
2738 2939 3.485947 TCGGCAACAAATTGTATGAGC 57.514 42.857 0.00 1.85 38.17 4.26
2739 2940 4.266029 GCATTCGGCAACAAATTGTATGAG 59.734 41.667 0.00 0.00 43.97 2.90
2740 2941 4.172505 GCATTCGGCAACAAATTGTATGA 58.827 39.130 0.00 0.00 43.97 2.15
2741 2942 4.503767 GCATTCGGCAACAAATTGTATG 57.496 40.909 0.00 0.00 43.97 2.39
2869 3070 6.321435 ACGACTCCAATCTGATGACATAGTAA 59.679 38.462 0.00 0.00 0.00 2.24
2872 3073 5.193663 ACGACTCCAATCTGATGACATAG 57.806 43.478 0.00 0.00 0.00 2.23
2874 3075 4.478206 AACGACTCCAATCTGATGACAT 57.522 40.909 0.00 0.00 0.00 3.06
2877 3078 7.606073 TCATTTTTAACGACTCCAATCTGATGA 59.394 33.333 0.00 0.00 0.00 2.92
2886 3087 4.992319 ACGATGTCATTTTTAACGACTCCA 59.008 37.500 0.00 0.00 0.00 3.86
2913 3114 4.338879 AGCTCTTGATTGTGCCAAATAGT 58.661 39.130 0.00 0.00 0.00 2.12
3174 3377 8.879759 CGTAATGGAATAGTATCAAAACACACT 58.120 33.333 0.00 0.00 0.00 3.55
3190 3393 6.257193 GTGGTTTCTTCGTATCGTAATGGAAT 59.743 38.462 0.00 0.00 0.00 3.01
3191 3394 5.577945 GTGGTTTCTTCGTATCGTAATGGAA 59.422 40.000 0.00 0.00 0.00 3.53
3264 3467 5.246981 AGGTTCCATCATCTGAGAAAACA 57.753 39.130 0.00 0.00 0.00 2.83
3360 3563 0.541063 TAGCGAAGGAGGTGACACCA 60.541 55.000 26.30 0.00 44.58 4.17
3550 3753 8.411683 ACTCAATCTGATTAATGCAATCCTTTC 58.588 33.333 1.98 0.00 42.17 2.62
3561 3764 5.525378 GCGACAAGGACTCAATCTGATTAAT 59.475 40.000 1.98 0.00 0.00 1.40
3698 3901 4.219070 TCAAAGGAACAAAGATCCTGCATG 59.781 41.667 0.00 0.00 46.65 4.06
3874 4078 7.706607 TCATTAGTGCAATATCGATATGCCTAC 59.293 37.037 24.38 19.53 0.00 3.18
4061 4284 3.040099 GGTACAATTTTCACACACACGC 58.960 45.455 0.00 0.00 0.00 5.34
4062 4285 4.032355 GTGGTACAATTTTCACACACACG 58.968 43.478 0.00 0.00 44.16 4.49
4103 4441 5.108254 CGTCAAAACTCAAAAGCAATACAGC 60.108 40.000 0.00 0.00 0.00 4.40
4143 4481 4.689345 ACGAGTTGGAGTTAATTACACTGC 59.311 41.667 10.31 10.31 33.39 4.40
4186 4524 9.841295 ACTGTAGTTACTTCAACCTGAAAATAA 57.159 29.630 0.00 0.00 35.73 1.40
4244 4582 1.200948 GCCCAAGACTTGCACAAGATC 59.799 52.381 16.95 10.24 40.79 2.75
4393 4732 6.150332 TCCTGATACCAGAAGGAAATGGATA 58.850 40.000 0.00 0.00 43.02 2.59
4633 4980 4.122337 TCTCCCTCCAGTAGTGTAAACA 57.878 45.455 0.00 0.00 0.00 2.83
4660 5007 2.031420 TCCTGTAACAACGACAGACTCG 60.031 50.000 4.38 0.00 46.01 4.18
4672 5019 5.758296 GTCAACTTTGATCAGTCCTGTAACA 59.242 40.000 0.00 0.00 39.73 2.41
4793 5140 8.547069 TCTTTAAAATGTTGCTGTAAAACATGC 58.453 29.630 2.78 0.00 45.25 4.06
4814 5161 9.485206 GTTGGTGTCAGAGTTAGTTTATCTTTA 57.515 33.333 0.00 0.00 0.00 1.85
4816 5163 7.441458 GTGTTGGTGTCAGAGTTAGTTTATCTT 59.559 37.037 0.00 0.00 0.00 2.40
4856 5203 9.732130 ATTTAAAGTGATCAAGGATATAGAGGC 57.268 33.333 0.00 0.00 0.00 4.70
4930 5277 6.875726 CAGATGTGAAGAGAAGAACCACATAA 59.124 38.462 0.00 0.00 45.20 1.90
4948 5295 6.497437 TGTTCTCAAACAAATGTCAGATGTG 58.503 36.000 0.00 0.00 42.34 3.21
4996 5343 4.702831 TGTTCAACATCACAACTCAGCTA 58.297 39.130 0.00 0.00 0.00 3.32
4998 5345 3.969117 TGTTCAACATCACAACTCAGC 57.031 42.857 0.00 0.00 0.00 4.26
5037 5384 6.040504 ACCTAAACTTCCATTCCAAGTTTCAC 59.959 38.462 12.57 0.00 46.49 3.18
5038 5385 6.133356 ACCTAAACTTCCATTCCAAGTTTCA 58.867 36.000 12.57 2.17 46.49 2.69
5039 5386 6.650427 ACCTAAACTTCCATTCCAAGTTTC 57.350 37.500 12.57 0.00 46.49 2.78
5041 5388 6.373759 AGAACCTAAACTTCCATTCCAAGTT 58.626 36.000 0.00 0.00 44.34 2.66
5042 5389 5.953571 AGAACCTAAACTTCCATTCCAAGT 58.046 37.500 0.00 0.00 35.51 3.16
5043 5390 7.996098 TTAGAACCTAAACTTCCATTCCAAG 57.004 36.000 0.00 0.00 0.00 3.61
5082 5432 6.101332 TGAAATGAGACATGCAAAATAAGCC 58.899 36.000 0.00 0.00 0.00 4.35
5163 5513 3.326747 ACGTAACTTCTGCAGATGGTTC 58.673 45.455 27.45 20.71 0.00 3.62
5425 5776 4.665142 CGAGAGAATGACAAGAGCAAAACG 60.665 45.833 0.00 0.00 0.00 3.60
5498 5849 0.246635 GCCTCTGTCGGTGTATGTGT 59.753 55.000 0.00 0.00 0.00 3.72
5808 6202 3.013921 TGTTCAAACCTCACTTGGTCAC 58.986 45.455 0.00 0.00 39.83 3.67
5860 6254 7.668052 ACTTGCTGGACAATATTTAACAGGTTA 59.332 33.333 10.39 0.00 37.72 2.85
5866 6260 9.669353 CATCATACTTGCTGGACAATATTTAAC 57.331 33.333 0.00 0.00 37.72 2.01
5881 6275 2.620115 CCACCATCACCATCATACTTGC 59.380 50.000 0.00 0.00 0.00 4.01
5894 6288 0.107703 GGAAGATGCGTCCACCATCA 60.108 55.000 1.23 0.00 41.13 3.07
6013 6409 1.349026 CTGGAACCCTCAAAGAGCTGA 59.651 52.381 0.00 0.00 0.00 4.26
6014 6410 1.349026 TCTGGAACCCTCAAAGAGCTG 59.651 52.381 0.00 0.00 0.00 4.24
6015 6411 1.734655 TCTGGAACCCTCAAAGAGCT 58.265 50.000 0.00 0.00 0.00 4.09
6016 6412 2.039084 TCTTCTGGAACCCTCAAAGAGC 59.961 50.000 0.00 0.00 0.00 4.09
6017 6413 4.357918 TTCTTCTGGAACCCTCAAAGAG 57.642 45.455 0.00 0.00 0.00 2.85
6018 6414 4.350816 TGATTCTTCTGGAACCCTCAAAGA 59.649 41.667 0.00 0.00 36.70 2.52
6019 6415 4.655963 TGATTCTTCTGGAACCCTCAAAG 58.344 43.478 0.00 0.00 36.70 2.77
6020 6416 4.722526 TGATTCTTCTGGAACCCTCAAA 57.277 40.909 0.00 0.00 36.70 2.69
6118 6514 1.689273 AGCTCGAGGTCATATGTTCCC 59.311 52.381 12.24 1.95 0.00 3.97
6167 6563 7.549134 CAGAACTGTAGAGTTATAAATGTGGCA 59.451 37.037 5.06 0.00 42.80 4.92
6263 6659 1.228124 CCGGCAAGTCCAACTCCAA 60.228 57.895 0.00 0.00 34.01 3.53
6289 6685 2.125766 GAGGACGTGGGGCCTTTTCT 62.126 60.000 0.84 0.00 33.84 2.52
6403 6799 1.106285 GGCCAGTAAATGCAAGGGAG 58.894 55.000 0.00 0.00 0.00 4.30
6406 6802 1.474077 GTGAGGCCAGTAAATGCAAGG 59.526 52.381 5.01 0.00 0.00 3.61
6495 6891 5.221641 ACCAGTACAGAAGTGTGATAGCAAA 60.222 40.000 0.00 0.00 37.52 3.68
6598 6994 6.609533 GCCAGAAGCACATTATTATCATCAG 58.390 40.000 0.00 0.00 42.97 2.90
6786 7182 9.008965 TGAGCAGAACTTTTATTAGTGCAATTA 57.991 29.630 0.00 0.00 0.00 1.40
6787 7183 7.809806 GTGAGCAGAACTTTTATTAGTGCAATT 59.190 33.333 0.00 0.00 0.00 2.32
6788 7184 7.175641 AGTGAGCAGAACTTTTATTAGTGCAAT 59.824 33.333 0.00 0.00 0.00 3.56
6789 7185 6.486657 AGTGAGCAGAACTTTTATTAGTGCAA 59.513 34.615 0.00 0.00 0.00 4.08
6790 7186 5.997746 AGTGAGCAGAACTTTTATTAGTGCA 59.002 36.000 0.00 0.00 0.00 4.57
6791 7187 6.487689 AGTGAGCAGAACTTTTATTAGTGC 57.512 37.500 0.00 0.00 0.00 4.40
6796 7192 9.678260 AGAATGATAGTGAGCAGAACTTTTATT 57.322 29.630 0.00 0.00 0.00 1.40
6797 7193 9.678260 AAGAATGATAGTGAGCAGAACTTTTAT 57.322 29.630 0.00 0.00 0.00 1.40
6798 7194 9.155975 GAAGAATGATAGTGAGCAGAACTTTTA 57.844 33.333 0.00 0.00 0.00 1.52
6799 7195 7.882271 AGAAGAATGATAGTGAGCAGAACTTTT 59.118 33.333 0.00 0.00 0.00 2.27
6804 7200 6.291648 ACAGAAGAATGATAGTGAGCAGAA 57.708 37.500 0.00 0.00 0.00 3.02
6806 7202 4.739228 CGACAGAAGAATGATAGTGAGCAG 59.261 45.833 0.00 0.00 0.00 4.24
6808 7204 4.047822 CCGACAGAAGAATGATAGTGAGC 58.952 47.826 0.00 0.00 0.00 4.26
6828 7224 2.160417 GTGAAAAGATCCAGCTGTTCCG 59.840 50.000 13.81 0.00 32.27 4.30
6910 7306 2.151202 GCCGTGTTGGAAAGATGAGAA 58.849 47.619 0.00 0.00 42.00 2.87
6931 7327 3.282021 TCAAGCAGTCTTCTGTTTTGCT 58.718 40.909 0.00 0.00 46.25 3.91
6972 7368 2.097304 TGCCCGAAAATTGATGATCACG 59.903 45.455 0.00 0.00 0.00 4.35
6993 7389 1.076044 AACCCAAGCAACTGCCACT 60.076 52.632 0.00 0.00 43.38 4.00
6996 7392 1.662044 CAGAACCCAAGCAACTGCC 59.338 57.895 0.00 0.00 43.38 4.85
7195 7595 7.201812 CCAGCCTATTTAGTAAACATCAATGCA 60.202 37.037 0.00 0.00 0.00 3.96
7199 7599 9.474313 AAATCCAGCCTATTTAGTAAACATCAA 57.526 29.630 0.00 0.00 0.00 2.57
7262 7664 8.474831 AGAAGGCATAACACAAGTTAACTTTTT 58.525 29.630 18.25 13.38 43.01 1.94
7266 7668 6.296026 TCAGAAGGCATAACACAAGTTAACT 58.704 36.000 1.12 1.12 43.01 2.24
7274 7676 7.230510 AGTTTGTAAATCAGAAGGCATAACACA 59.769 33.333 0.00 0.00 0.00 3.72
7314 7716 2.818921 TGGGGAGTTCAAATGGAATGG 58.181 47.619 0.00 0.00 37.93 3.16
7463 7909 5.777850 TGTTAGCTCGCATGTATAGGTTA 57.222 39.130 0.00 0.00 0.00 2.85
7516 7972 1.881324 GCATTTGCAAAACCCAAGCAT 59.119 42.857 17.19 0.00 41.59 3.79
7545 8002 2.059541 GAAAAACTCGTCAGGGTCTCG 58.940 52.381 0.00 0.00 0.00 4.04
7554 8011 1.773525 GTTGCGCAAGAAAAACTCGTC 59.226 47.619 25.78 2.81 35.94 4.20
7595 8053 4.189231 GCACCGACTACAAAATGATACCT 58.811 43.478 0.00 0.00 0.00 3.08
7612 8070 1.201414 GTACCAGGAAAATTGGCACCG 59.799 52.381 0.00 0.00 39.39 4.94
7621 8079 5.152934 ACCACTTCTCTAGTACCAGGAAAA 58.847 41.667 0.00 0.00 34.56 2.29
7622 8080 4.748701 ACCACTTCTCTAGTACCAGGAAA 58.251 43.478 0.00 0.00 34.56 3.13
7623 8081 4.399483 ACCACTTCTCTAGTACCAGGAA 57.601 45.455 0.00 0.00 34.56 3.36
7644 8102 2.885135 TACGTGAAGGTGAGGTCCTA 57.115 50.000 0.00 0.00 36.74 2.94
7645 8103 1.825474 CATACGTGAAGGTGAGGTCCT 59.175 52.381 0.00 0.00 39.84 3.85
7653 8111 3.872696 TCAATGCATCATACGTGAAGGT 58.127 40.909 0.00 0.00 38.01 3.50
7660 8118 9.882996 ATTTAGTAAACATCAATGCATCATACG 57.117 29.630 0.00 0.00 0.00 3.06
7674 8132 7.494922 AAAATCCAGCCCATTTAGTAAACAT 57.505 32.000 0.00 0.00 0.00 2.71
7718 8176 8.862085 ACCTTTTCCGATAAGAATGGTTTAAAA 58.138 29.630 0.54 0.00 32.48 1.52
7719 8177 8.411991 ACCTTTTCCGATAAGAATGGTTTAAA 57.588 30.769 0.54 0.00 32.48 1.52
7721 8179 9.517868 TTAACCTTTTCCGATAAGAATGGTTTA 57.482 29.630 13.54 6.16 40.39 2.01
7723 8181 7.668469 AGTTAACCTTTTCCGATAAGAATGGTT 59.332 33.333 0.88 13.12 41.56 3.67
7728 8186 7.499895 ACACAAGTTAACCTTTTCCGATAAGAA 59.500 33.333 0.88 0.00 0.00 2.52
7729 8187 6.993902 ACACAAGTTAACCTTTTCCGATAAGA 59.006 34.615 0.88 0.00 0.00 2.10
7730 8188 7.198306 ACACAAGTTAACCTTTTCCGATAAG 57.802 36.000 0.88 0.00 0.00 1.73
7732 8190 8.723311 CATAACACAAGTTAACCTTTTCCGATA 58.277 33.333 0.88 0.00 43.01 2.92
7733 8191 7.590279 CATAACACAAGTTAACCTTTTCCGAT 58.410 34.615 0.88 0.00 43.01 4.18
7735 8193 5.627780 GCATAACACAAGTTAACCTTTTCCG 59.372 40.000 0.88 0.00 43.01 4.30
7736 8194 5.924254 GGCATAACACAAGTTAACCTTTTCC 59.076 40.000 0.88 0.00 43.01 3.13
7737 8195 6.745116 AGGCATAACACAAGTTAACCTTTTC 58.255 36.000 0.88 0.00 43.12 2.29
7738 8196 6.724893 AGGCATAACACAAGTTAACCTTTT 57.275 33.333 0.88 0.00 43.12 2.27
7767 8226 7.334671 GGGAATTTGGTTTTGTGAGTTTGTAAA 59.665 33.333 0.00 0.00 0.00 2.01
7780 8239 4.263949 TGTTTGGTTGGGGAATTTGGTTTT 60.264 37.500 0.00 0.00 0.00 2.43
7805 8280 2.159057 GGGATGTGATGGTTGCAATTCC 60.159 50.000 0.59 0.00 0.00 3.01
7819 8294 4.722526 TGGGATAATTAGGTGGGATGTG 57.277 45.455 0.00 0.00 0.00 3.21
7837 8312 4.599047 TTTGTTCCTATGTTTGCTTGGG 57.401 40.909 0.00 0.00 0.00 4.12
7839 8314 5.355596 TGGTTTTGTTCCTATGTTTGCTTG 58.644 37.500 0.00 0.00 0.00 4.01
7842 8317 5.408299 GGATTGGTTTTGTTCCTATGTTTGC 59.592 40.000 0.00 0.00 0.00 3.68
7848 8323 5.640147 TGTCAGGATTGGTTTTGTTCCTAT 58.360 37.500 0.00 0.00 36.45 2.57
7868 8343 3.561725 GGATCGAAGTGGAATGGAATGTC 59.438 47.826 0.00 0.00 0.00 3.06
7887 8362 1.468506 GGGCGTGTTTGGTTTGGGAT 61.469 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.