Multiple sequence alignment - TraesCS3D01G153200

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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 TraesCS3D01G153200 chr3D 100.000 4345 0 0 1 4345 120104190 120099846 0.000000e+00 8024.0
1 TraesCS3D01G153200 chr3D 100.000 538 0 0 4713 5250 120099478 120098941 0.000000e+00 994.0
2 TraesCS3D01G153200 chr3D 96.970 33 1 0 2093 2125 120101754 120101786 7.340000e-04 56.5
3 TraesCS3D01G153200 chr3D 96.970 33 1 0 2405 2437 120102066 120102098 7.340000e-04 56.5
4 TraesCS3D01G153200 chr3B 89.958 1922 95 29 1 1870 172020417 172018542 0.000000e+00 2390.0
5 TraesCS3D01G153200 chr3B 86.390 1396 81 31 2121 3464 172018203 172016865 0.000000e+00 1424.0
6 TraesCS3D01G153200 chr3B 93.832 843 47 3 3451 4292 172016820 172015982 0.000000e+00 1264.0
7 TraesCS3D01G153200 chr3B 88.618 369 34 6 4761 5123 172015975 172015609 4.830000e-120 442.0
8 TraesCS3D01G153200 chr3B 92.308 208 11 3 1880 2082 172018414 172018207 1.850000e-74 291.0
9 TraesCS3D01G153200 chr3B 100.000 28 0 0 2712 2739 595212013 595212040 1.000000e-02 52.8
10 TraesCS3D01G153200 chr3A 92.355 1465 79 16 637 2082 127059946 127058496 0.000000e+00 2054.0
11 TraesCS3D01G153200 chr3A 91.044 1552 91 15 2122 3647 127058491 127056962 0.000000e+00 2052.0
12 TraesCS3D01G153200 chr3A 92.582 701 49 3 3646 4345 127056581 127055883 0.000000e+00 1003.0
13 TraesCS3D01G153200 chr3A 89.761 293 20 7 330 622 127060581 127060299 2.990000e-97 366.0
14 TraesCS3D01G153200 chr3A 91.188 261 18 4 1 258 127061243 127060985 3.010000e-92 350.0
15 TraesCS3D01G153200 chr3A 82.287 446 33 18 4713 5128 127055709 127055280 1.400000e-90 344.0
16 TraesCS3D01G153200 chr6B 79.353 402 50 21 3008 3397 690969975 690970355 8.730000e-63 252.0
17 TraesCS3D01G153200 chr6B 71.888 249 61 5 394 635 672065471 672065225 4.390000e-06 63.9
18 TraesCS3D01G153200 chr5A 80.751 213 34 5 3185 3396 502785070 502784864 5.440000e-35 159.0
19 TraesCS3D01G153200 chr5A 75.839 149 26 6 694 838 368676935 368677077 3.390000e-07 67.6
20 TraesCS3D01G153200 chr4D 83.212 137 20 3 2986 3120 92660217 92660082 7.140000e-24 122.0
21 TraesCS3D01G153200 chr1A 75.879 199 35 10 3204 3398 148266550 148266361 7.240000e-14 89.8
22 TraesCS3D01G153200 chr1A 94.595 37 2 0 3362 3398 14127756 14127792 2.040000e-04 58.4
23 TraesCS3D01G153200 chr6A 74.000 250 49 7 396 635 592265999 592265756 2.600000e-13 87.9
24 TraesCS3D01G153200 chr1D 75.127 197 39 8 3204 3398 142152912 142153100 3.370000e-12 84.2
25 TraesCS3D01G153200 chr5B 84.091 88 11 2 393 480 655643702 655643786 1.210000e-11 82.4
26 TraesCS3D01G153200 chr1B 74.874 199 36 11 3204 3397 191001184 191000995 1.570000e-10 78.7
27 TraesCS3D01G153200 chr2B 90.385 52 5 0 783 834 382083006 382082955 9.430000e-08 69.4
28 TraesCS3D01G153200 chr2B 84.615 65 6 1 702 762 34438384 34438320 1.580000e-05 62.1
29 TraesCS3D01G153200 chr7A 92.683 41 3 0 719 759 92464969 92464929 5.680000e-05 60.2
30 TraesCS3D01G153200 chr6D 82.192 73 9 4 3327 3396 25917249 25917320 5.680000e-05 60.2


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 TraesCS3D01G153200 chr3D 120098941 120104190 5249 True 4509.000000 8024 100.0000 1 5250 2 chr3D.!!$R1 5249
1 TraesCS3D01G153200 chr3B 172015609 172020417 4808 True 1162.200000 2390 90.2212 1 5123 5 chr3B.!!$R1 5122
2 TraesCS3D01G153200 chr3A 127055280 127061243 5963 True 1028.166667 2054 89.8695 1 5128 6 chr3A.!!$R1 5127

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
57 58 0.489567 AGTCCACTTCACTCCCCTCT 59.510 55.000 0.00 0.00 0.00 3.69 F
359 694 0.955428 GCTTGGCCGACAGAATCACA 60.955 55.000 0.00 0.00 0.00 3.58 F
906 1579 1.227556 ATCCGCCGACATGTAAGGC 60.228 57.895 26.43 26.43 46.88 4.35 F
921 1594 1.534729 AAGGCCTGGATTTGACGAAC 58.465 50.000 5.69 0.00 0.00 3.95 F
2104 2930 0.486879 ATTCTCCTTTTGGGTGGGCA 59.513 50.000 0.00 0.00 40.87 5.36 F
3399 4288 0.179000 CCCGAGACCCAAAGATCCTG 59.821 60.000 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1297 1991 0.103026 CAAGATCTGGTCCGCGATGA 59.897 55.0 8.23 0.0 0.00 2.92 R
2086 2912 0.263172 TTGCCCACCCAAAAGGAGAA 59.737 50.0 0.00 0.0 39.89 2.87 R
2102 2928 0.453390 GACTGTAGCCAAGCCATTGC 59.547 55.0 0.00 0.0 34.91 3.56 R
2106 2932 0.472044 TTGTGACTGTAGCCAAGCCA 59.528 50.0 0.00 0.0 0.00 4.75 R
3549 4498 0.657368 GTTTTCCACACGCTGCTTCG 60.657 55.0 0.00 0.0 0.00 3.79 R
5225 6598 0.033504 GCGACCACCACAAGAGAGAA 59.966 55.0 0.00 0.0 0.00 2.87 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
57 58 0.489567 AGTCCACTTCACTCCCCTCT 59.510 55.000 0.00 0.00 0.00 3.69
117 118 2.442236 CCTTCATGGTGGGCACTATT 57.558 50.000 0.00 0.00 29.60 1.73
118 119 2.301346 CCTTCATGGTGGGCACTATTC 58.699 52.381 0.00 0.00 29.60 1.75
245 249 3.082548 TCCCGCGGTTGAAATTTATTCA 58.917 40.909 26.12 0.00 0.00 2.57
246 250 3.127895 TCCCGCGGTTGAAATTTATTCAG 59.872 43.478 26.12 2.11 0.00 3.02
266 291 2.975489 AGCGGGAATCCATAGAATCAGT 59.025 45.455 0.09 0.00 0.00 3.41
296 321 4.373116 ATGAAGGCGCGTGACCGT 62.373 61.111 8.43 0.00 36.15 4.83
317 342 1.740296 CCTCGCCGAAAACGGTGAT 60.740 57.895 21.69 0.00 45.85 3.06
327 352 1.016627 AAACGGTGATCATCGCATGG 58.983 50.000 27.69 2.08 38.78 3.66
359 694 0.955428 GCTTGGCCGACAGAATCACA 60.955 55.000 0.00 0.00 0.00 3.58
543 878 2.579738 GACACGGGAGGAGGAAGC 59.420 66.667 0.00 0.00 0.00 3.86
547 882 2.689034 CGGGAGGAGGAAGCCCTT 60.689 66.667 0.00 0.00 44.53 3.95
548 883 2.301738 CGGGAGGAGGAAGCCCTTT 61.302 63.158 0.00 0.00 44.53 3.11
555 890 2.203625 GGAAGCCCTTTGTGCCCA 60.204 61.111 0.00 0.00 0.00 5.36
662 1335 4.203950 TCGATTTGTTTTGTGTCTTCGG 57.796 40.909 0.00 0.00 0.00 4.30
665 1338 1.464734 TTGTTTTGTGTCTTCGGCCA 58.535 45.000 2.24 0.00 0.00 5.36
669 1342 2.812011 GTTTTGTGTCTTCGGCCACTAT 59.188 45.455 2.24 0.00 32.76 2.12
671 1344 3.965379 TTGTGTCTTCGGCCACTATTA 57.035 42.857 2.24 0.00 32.76 0.98
677 1350 3.550678 GTCTTCGGCCACTATTAAAGACG 59.449 47.826 2.24 0.00 35.00 4.18
695 1368 1.371558 GACAAGGGCAAGGACGACT 59.628 57.895 0.00 0.00 0.00 4.18
740 1413 5.343058 CGTAGCAGAACATGTCAATTTTTGG 59.657 40.000 0.00 0.00 0.00 3.28
748 1421 5.067273 ACATGTCAATTTTTGGTAGTCCGA 58.933 37.500 0.00 0.00 36.30 4.55
757 1430 9.051679 CAATTTTTGGTAGTCCGATGATATGTA 57.948 33.333 0.00 0.00 36.30 2.29
763 1436 9.475620 TTGGTAGTCCGATGATATGTATCTAAT 57.524 33.333 2.08 0.00 36.30 1.73
833 1506 5.058149 TCAATTTGATGAATCCGGTTGTG 57.942 39.130 0.00 0.00 0.00 3.33
834 1507 3.508744 ATTTGATGAATCCGGTTGTGC 57.491 42.857 0.00 0.00 0.00 4.57
838 1511 1.315257 ATGAATCCGGTTGTGCAGGC 61.315 55.000 0.00 0.00 32.16 4.85
839 1512 1.971167 GAATCCGGTTGTGCAGGCA 60.971 57.895 0.00 0.00 32.16 4.75
863 1536 9.865321 GCATATTTTTAATACCTGCATGATCAT 57.135 29.630 1.18 1.18 0.00 2.45
906 1579 1.227556 ATCCGCCGACATGTAAGGC 60.228 57.895 26.43 26.43 46.88 4.35
918 1591 2.107950 TGTAAGGCCTGGATTTGACG 57.892 50.000 5.69 0.00 0.00 4.35
920 1593 2.039216 TGTAAGGCCTGGATTTGACGAA 59.961 45.455 5.69 0.00 0.00 3.85
921 1594 1.534729 AAGGCCTGGATTTGACGAAC 58.465 50.000 5.69 0.00 0.00 3.95
925 1611 1.739067 CCTGGATTTGACGAACCTCC 58.261 55.000 0.00 0.00 0.00 4.30
983 1669 2.749441 GCCAAGCTGCAGAGGTCC 60.749 66.667 20.43 0.00 0.00 4.46
1024 1718 3.734293 GCGGCAAAGACGAGTTAGATAGT 60.734 47.826 0.00 0.00 35.20 2.12
1374 2068 3.062466 CGCAGGGAGACGTGGAGA 61.062 66.667 0.00 0.00 46.11 3.71
1448 2142 4.459089 GAGGGAGCAGGCGGTGTC 62.459 72.222 0.00 0.00 0.00 3.67
1838 2539 5.620206 AGATGTGATTTGTCAGTTGTACCA 58.380 37.500 0.00 0.00 0.00 3.25
1989 2814 6.985188 TCCAAGAAATTTTAGAGGTCATCG 57.015 37.500 0.00 0.00 0.00 3.84
2031 2857 3.749632 CGGAGTCCAAACCCCTAAAAAGT 60.750 47.826 10.49 0.00 0.00 2.66
2082 2908 4.164030 TCAGTAGATGCTCCCAAATGCTTA 59.836 41.667 0.00 0.00 0.00 3.09
2083 2909 4.883585 CAGTAGATGCTCCCAAATGCTTAA 59.116 41.667 0.00 0.00 0.00 1.85
2084 2910 5.008415 CAGTAGATGCTCCCAAATGCTTAAG 59.992 44.000 0.00 0.00 0.00 1.85
2086 2912 4.801164 AGATGCTCCCAAATGCTTAAGAT 58.199 39.130 6.67 0.00 0.00 2.40
2087 2913 5.206587 AGATGCTCCCAAATGCTTAAGATT 58.793 37.500 6.67 0.68 0.00 2.40
2088 2914 4.989279 TGCTCCCAAATGCTTAAGATTC 57.011 40.909 6.67 0.00 0.00 2.52
2089 2915 4.603131 TGCTCCCAAATGCTTAAGATTCT 58.397 39.130 6.67 0.00 0.00 2.40
2090 2916 4.641989 TGCTCCCAAATGCTTAAGATTCTC 59.358 41.667 6.67 0.00 0.00 2.87
2091 2917 4.037327 GCTCCCAAATGCTTAAGATTCTCC 59.963 45.833 6.67 0.00 0.00 3.71
2092 2918 5.444176 CTCCCAAATGCTTAAGATTCTCCT 58.556 41.667 6.67 0.00 0.00 3.69
2093 2919 5.831103 TCCCAAATGCTTAAGATTCTCCTT 58.169 37.500 6.67 0.00 0.00 3.36
2094 2920 6.256053 TCCCAAATGCTTAAGATTCTCCTTT 58.744 36.000 6.67 0.00 0.00 3.11
2095 2921 6.725834 TCCCAAATGCTTAAGATTCTCCTTTT 59.274 34.615 6.67 0.00 0.00 2.27
2096 2922 6.815142 CCCAAATGCTTAAGATTCTCCTTTTG 59.185 38.462 6.67 7.96 0.00 2.44
2097 2923 6.815142 CCAAATGCTTAAGATTCTCCTTTTGG 59.185 38.462 6.67 12.50 42.21 3.28
2098 2924 6.535963 AATGCTTAAGATTCTCCTTTTGGG 57.464 37.500 6.67 0.00 40.87 4.12
2099 2925 4.998051 TGCTTAAGATTCTCCTTTTGGGT 58.002 39.130 6.67 0.00 40.87 4.51
2100 2926 4.766891 TGCTTAAGATTCTCCTTTTGGGTG 59.233 41.667 6.67 0.00 40.87 4.61
2101 2927 4.158579 GCTTAAGATTCTCCTTTTGGGTGG 59.841 45.833 6.67 0.00 40.87 4.61
2102 2928 2.907458 AGATTCTCCTTTTGGGTGGG 57.093 50.000 0.00 0.00 40.87 4.61
2103 2929 1.186200 GATTCTCCTTTTGGGTGGGC 58.814 55.000 0.00 0.00 40.87 5.36
2104 2930 0.486879 ATTCTCCTTTTGGGTGGGCA 59.513 50.000 0.00 0.00 40.87 5.36
2105 2931 0.263172 TTCTCCTTTTGGGTGGGCAA 59.737 50.000 0.00 0.00 40.87 4.52
2106 2932 0.486879 TCTCCTTTTGGGTGGGCAAT 59.513 50.000 0.00 0.00 40.87 3.56
2107 2933 0.609662 CTCCTTTTGGGTGGGCAATG 59.390 55.000 0.00 0.00 40.87 2.82
2108 2934 0.835543 TCCTTTTGGGTGGGCAATGG 60.836 55.000 0.00 0.00 40.87 3.16
2109 2935 1.003476 CTTTTGGGTGGGCAATGGC 60.003 57.895 0.00 0.00 40.13 4.40
2110 2936 1.461075 TTTTGGGTGGGCAATGGCT 60.461 52.632 6.78 0.00 40.87 4.75
2111 2937 1.059006 TTTTGGGTGGGCAATGGCTT 61.059 50.000 6.78 0.00 40.87 4.35
2112 2938 1.766625 TTTGGGTGGGCAATGGCTTG 61.767 55.000 6.78 0.00 40.87 4.01
2113 2939 3.393106 GGGTGGGCAATGGCTTGG 61.393 66.667 6.78 0.00 40.87 3.61
2180 3019 5.441500 TGTCAAGAAGAATGGTTTGGTACA 58.558 37.500 0.00 0.00 0.00 2.90
2197 3036 3.497942 GGTACATGGGAGGTCTTGTTTGT 60.498 47.826 0.00 0.00 0.00 2.83
2205 3044 4.546570 GGAGGTCTTGTTTGTACATTTGC 58.453 43.478 0.00 0.00 33.44 3.68
2222 3061 0.244450 TGCCGAGTACGTAGGTTTGG 59.756 55.000 0.00 0.00 37.88 3.28
2232 3071 3.460103 ACGTAGGTTTGGTTGTGTAGTG 58.540 45.455 0.00 0.00 0.00 2.74
2260 3101 8.564574 CAACAGTAAGTAAGATTTAGGTTTGCA 58.435 33.333 0.00 0.00 0.00 4.08
2285 3126 2.945668 GTGGCACAGGATCAGGAAATAC 59.054 50.000 13.86 0.00 41.80 1.89
2286 3127 2.092429 TGGCACAGGATCAGGAAATACC 60.092 50.000 0.00 0.00 39.35 2.73
2287 3128 6.451907 GTGGCACAGGATCAGGAAATACCT 62.452 50.000 13.86 0.00 46.79 3.08
2288 3129 7.150774 GTGGCACAGGATCAGGAAATACCTA 62.151 48.000 13.86 0.00 44.57 3.08
2289 3130 8.381906 GTGGCACAGGATCAGGAAATACCTAT 62.382 46.154 13.86 0.00 44.57 2.57
2354 3195 5.431765 ACAGTATGATGGATGTTTGAGGTC 58.568 41.667 0.00 0.00 39.69 3.85
2366 3208 0.319900 TTGAGGTCGCTTCACTGCTC 60.320 55.000 0.00 0.00 0.00 4.26
2370 3212 2.431430 TCGCTTCACTGCTCTGCG 60.431 61.111 0.00 0.00 46.71 5.18
2430 3272 1.682005 TAGCCAAGCCATTGCCCAC 60.682 57.895 0.00 0.00 38.69 4.61
2480 3322 0.250234 TATGACCAGCTCCTGTGTGC 59.750 55.000 0.00 0.00 0.00 4.57
2492 3334 3.660111 GTGTGCGCAGAACCCCAC 61.660 66.667 12.22 11.00 0.00 4.61
2616 3474 3.308053 CCATTTGAGACATAGTGCAGACG 59.692 47.826 0.00 0.00 0.00 4.18
2779 3643 9.832445 TTAATAGGGCTTACAATTTCTCAGTAG 57.168 33.333 0.00 0.00 0.00 2.57
2918 3783 4.149046 GCGGAATTCGTAATTTGCAAAACA 59.851 37.500 17.19 3.86 41.72 2.83
2919 3784 5.164002 GCGGAATTCGTAATTTGCAAAACAT 60.164 36.000 17.19 8.25 41.72 2.71
2920 3785 6.457676 CGGAATTCGTAATTTGCAAAACATC 58.542 36.000 17.19 6.47 0.00 3.06
2921 3786 6.307800 CGGAATTCGTAATTTGCAAAACATCT 59.692 34.615 17.19 0.00 0.00 2.90
3003 3881 2.341846 AGTACATGCCCAAATACCCG 57.658 50.000 0.00 0.00 0.00 5.28
3113 3992 8.635765 AAACATCATTATCAGGTGTTACACTT 57.364 30.769 15.44 4.67 34.40 3.16
3165 4048 4.479993 CGGCTCCAGGGGCAAGAG 62.480 72.222 15.19 0.00 0.00 2.85
3216 4099 8.726988 GTGAATAGAAACTTTTATGTAGTGCCA 58.273 33.333 0.00 0.00 0.00 4.92
3267 4150 3.065786 CCATGGAAGTCATTCATTCACGG 59.934 47.826 5.56 0.00 37.15 4.94
3284 4167 4.951254 TCACGGAACTTTTCACATGAGTA 58.049 39.130 0.00 0.00 0.00 2.59
3302 4185 4.684242 TGAGTACAACACGTGATCATGTTC 59.316 41.667 25.01 17.09 36.92 3.18
3325 4208 8.817100 GTTCGATTCCAAAAAGTTTCAAGATTT 58.183 29.630 0.00 0.00 0.00 2.17
3399 4288 0.179000 CCCGAGACCCAAAGATCCTG 59.821 60.000 0.00 0.00 0.00 3.86
3401 4290 1.195115 CGAGACCCAAAGATCCTGGA 58.805 55.000 12.14 0.00 35.85 3.86
3440 4329 9.125906 GTACACAATTTATCTTCTCGCGTATAT 57.874 33.333 5.77 0.00 0.00 0.86
3491 4440 7.854934 ATTACTCTGTTTTATATCGACGAGC 57.145 36.000 3.01 0.00 0.00 5.03
3494 4443 5.744345 ACTCTGTTTTATATCGACGAGCAAG 59.256 40.000 3.01 0.00 0.00 4.01
3656 4987 4.968259 TGGTATGTACATACTCATTGGCC 58.032 43.478 33.88 21.06 42.42 5.36
3777 5108 2.131067 TACATGATCGCCGAGCCCA 61.131 57.895 0.00 0.00 0.00 5.36
3782 5113 4.162690 ATCGCCGAGCCCAAGGTC 62.163 66.667 0.00 0.00 37.15 3.85
4205 5537 4.023193 ACATTTGCCTTAGTTCTCCGTTTG 60.023 41.667 0.00 0.00 0.00 2.93
4306 5638 1.036707 CGCTCAAACCCTTCCCAAAA 58.963 50.000 0.00 0.00 0.00 2.44
4307 5639 1.000274 CGCTCAAACCCTTCCCAAAAG 60.000 52.381 0.00 0.00 0.00 2.27
4308 5640 2.039418 GCTCAAACCCTTCCCAAAAGT 58.961 47.619 0.00 0.00 0.00 2.66
4311 5643 4.441792 CTCAAACCCTTCCCAAAAGTTTG 58.558 43.478 7.43 7.43 45.40 2.93
4321 5653 0.744281 CAAAAGTTTGGGCGGACAGT 59.256 50.000 0.00 0.00 34.59 3.55
4742 6074 3.148279 GCCGTCGTCCTCCTCCAT 61.148 66.667 0.00 0.00 0.00 3.41
4750 6082 3.055747 GTCGTCCTCCTCCATTCTTTCTT 60.056 47.826 0.00 0.00 0.00 2.52
4751 6083 3.195825 TCGTCCTCCTCCATTCTTTCTTC 59.804 47.826 0.00 0.00 0.00 2.87
4752 6084 3.680196 CGTCCTCCTCCATTCTTTCTTCC 60.680 52.174 0.00 0.00 0.00 3.46
4753 6085 3.521531 GTCCTCCTCCATTCTTTCTTCCT 59.478 47.826 0.00 0.00 0.00 3.36
4754 6086 3.521126 TCCTCCTCCATTCTTTCTTCCTG 59.479 47.826 0.00 0.00 0.00 3.86
4755 6087 3.265479 CCTCCTCCATTCTTTCTTCCTGT 59.735 47.826 0.00 0.00 0.00 4.00
4756 6088 4.512484 CTCCTCCATTCTTTCTTCCTGTC 58.488 47.826 0.00 0.00 0.00 3.51
4757 6089 4.171234 TCCTCCATTCTTTCTTCCTGTCT 58.829 43.478 0.00 0.00 0.00 3.41
4758 6090 4.019860 TCCTCCATTCTTTCTTCCTGTCTG 60.020 45.833 0.00 0.00 0.00 3.51
4759 6091 3.679389 TCCATTCTTTCTTCCTGTCTGC 58.321 45.455 0.00 0.00 0.00 4.26
4800 6132 3.242220 CGTTGTAGATGTTGATGCTGAGC 60.242 47.826 0.00 0.00 0.00 4.26
4831 6163 0.393673 CACCGCCACCATGGACAATA 60.394 55.000 21.47 0.00 40.96 1.90
4833 6165 1.064017 ACCGCCACCATGGACAATATT 60.064 47.619 21.47 0.00 40.96 1.28
4913 6255 3.849951 CCCATCGCTACGGCCACT 61.850 66.667 2.24 0.00 34.44 4.00
4953 6295 4.941263 TCGATGAAATGTCCCAAAGGTAAG 59.059 41.667 0.00 0.00 0.00 2.34
5015 6388 6.954616 AATGCAATTGTGATGTAATGTGTG 57.045 33.333 7.40 0.00 33.44 3.82
5029 6402 8.696043 ATGTAATGTGTGCCTATGTTATTCAT 57.304 30.769 0.00 0.00 40.25 2.57
5030 6403 8.518430 TGTAATGTGTGCCTATGTTATTCATT 57.482 30.769 0.00 0.00 37.91 2.57
5128 6501 4.439860 AGAAACCCCCTCTCAAGAATACT 58.560 43.478 0.00 0.00 0.00 2.12
5129 6502 4.852697 AGAAACCCCCTCTCAAGAATACTT 59.147 41.667 0.00 0.00 36.73 2.24
5130 6503 6.030082 AGAAACCCCCTCTCAAGAATACTTA 58.970 40.000 0.00 0.00 34.70 2.24
5131 6504 5.959583 AACCCCCTCTCAAGAATACTTAG 57.040 43.478 0.00 0.00 34.70 2.18
5132 6505 4.299485 ACCCCCTCTCAAGAATACTTAGG 58.701 47.826 0.00 0.00 34.70 2.69
5133 6506 4.015541 ACCCCCTCTCAAGAATACTTAGGA 60.016 45.833 0.00 0.00 33.53 2.94
5134 6507 4.345547 CCCCCTCTCAAGAATACTTAGGAC 59.654 50.000 0.00 0.00 33.53 3.85
5135 6508 5.212745 CCCCTCTCAAGAATACTTAGGACT 58.787 45.833 0.00 0.00 33.53 3.85
5136 6509 6.374588 CCCCTCTCAAGAATACTTAGGACTA 58.625 44.000 0.00 0.00 33.53 2.59
5137 6510 6.265876 CCCCTCTCAAGAATACTTAGGACTAC 59.734 46.154 0.00 0.00 33.53 2.73
5138 6511 6.265876 CCCTCTCAAGAATACTTAGGACTACC 59.734 46.154 0.00 0.00 33.53 3.18
5139 6512 6.834451 CCTCTCAAGAATACTTAGGACTACCA 59.166 42.308 0.00 0.00 33.53 3.25
5140 6513 7.201839 CCTCTCAAGAATACTTAGGACTACCAC 60.202 44.444 0.00 0.00 33.53 4.16
5141 6514 7.411808 TCTCAAGAATACTTAGGACTACCACT 58.588 38.462 0.00 0.00 34.72 4.00
5142 6515 7.894364 TCTCAAGAATACTTAGGACTACCACTT 59.106 37.037 0.00 0.00 34.72 3.16
5143 6516 8.431910 TCAAGAATACTTAGGACTACCACTTT 57.568 34.615 0.00 0.00 34.72 2.66
5144 6517 8.529476 TCAAGAATACTTAGGACTACCACTTTC 58.471 37.037 0.00 0.00 34.72 2.62
5145 6518 7.421087 AGAATACTTAGGACTACCACTTTCC 57.579 40.000 0.00 0.00 38.94 3.13
5146 6519 6.383436 AGAATACTTAGGACTACCACTTTCCC 59.617 42.308 0.00 0.00 38.94 3.97
5147 6520 3.179685 ACTTAGGACTACCACTTTCCCC 58.820 50.000 0.00 0.00 38.94 4.81
5148 6521 1.856629 TAGGACTACCACTTTCCCCG 58.143 55.000 0.00 0.00 38.94 5.73
5149 6522 1.078637 GGACTACCACTTTCCCCGC 60.079 63.158 0.00 0.00 35.97 6.13
5150 6523 1.675219 GACTACCACTTTCCCCGCA 59.325 57.895 0.00 0.00 0.00 5.69
5151 6524 0.672711 GACTACCACTTTCCCCGCAC 60.673 60.000 0.00 0.00 0.00 5.34
5152 6525 1.373435 CTACCACTTTCCCCGCACA 59.627 57.895 0.00 0.00 0.00 4.57
5153 6526 0.250553 CTACCACTTTCCCCGCACAA 60.251 55.000 0.00 0.00 0.00 3.33
5154 6527 0.183014 TACCACTTTCCCCGCACAAA 59.817 50.000 0.00 0.00 0.00 2.83
5155 6528 0.469144 ACCACTTTCCCCGCACAAAT 60.469 50.000 0.00 0.00 0.00 2.32
5156 6529 0.678950 CCACTTTCCCCGCACAAATT 59.321 50.000 0.00 0.00 0.00 1.82
5157 6530 1.889829 CCACTTTCCCCGCACAAATTA 59.110 47.619 0.00 0.00 0.00 1.40
5158 6531 2.352323 CCACTTTCCCCGCACAAATTAC 60.352 50.000 0.00 0.00 0.00 1.89
5159 6532 1.890489 ACTTTCCCCGCACAAATTACC 59.110 47.619 0.00 0.00 0.00 2.85
5160 6533 1.889829 CTTTCCCCGCACAAATTACCA 59.110 47.619 0.00 0.00 0.00 3.25
5161 6534 1.249407 TTCCCCGCACAAATTACCAC 58.751 50.000 0.00 0.00 0.00 4.16
5162 6535 0.609681 TCCCCGCACAAATTACCACC 60.610 55.000 0.00 0.00 0.00 4.61
5163 6536 1.504446 CCCGCACAAATTACCACCG 59.496 57.895 0.00 0.00 0.00 4.94
5164 6537 1.238625 CCCGCACAAATTACCACCGT 61.239 55.000 0.00 0.00 0.00 4.83
5165 6538 0.167251 CCGCACAAATTACCACCGTC 59.833 55.000 0.00 0.00 0.00 4.79
5166 6539 0.179235 CGCACAAATTACCACCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
5167 6540 0.167251 GCACAAATTACCACCGTCGG 59.833 55.000 10.48 10.48 0.00 4.79
5168 6541 0.167251 CACAAATTACCACCGTCGGC 59.833 55.000 12.28 0.00 0.00 5.54
5169 6542 0.250381 ACAAATTACCACCGTCGGCA 60.250 50.000 12.28 0.00 0.00 5.69
5170 6543 1.091537 CAAATTACCACCGTCGGCAT 58.908 50.000 12.28 0.00 0.00 4.40
5171 6544 1.470890 CAAATTACCACCGTCGGCATT 59.529 47.619 12.28 0.00 0.00 3.56
5172 6545 1.375551 AATTACCACCGTCGGCATTC 58.624 50.000 12.28 0.00 0.00 2.67
5173 6546 0.463116 ATTACCACCGTCGGCATTCC 60.463 55.000 12.28 0.00 0.00 3.01
5174 6547 1.828461 TTACCACCGTCGGCATTCCA 61.828 55.000 12.28 0.00 0.00 3.53
5175 6548 1.828461 TACCACCGTCGGCATTCCAA 61.828 55.000 12.28 0.00 0.00 3.53
5176 6549 2.686816 CCACCGTCGGCATTCCAAC 61.687 63.158 12.28 0.00 0.00 3.77
5177 6550 2.359478 ACCGTCGGCATTCCAACC 60.359 61.111 12.28 0.00 0.00 3.77
5178 6551 2.359354 CCGTCGGCATTCCAACCA 60.359 61.111 0.00 0.00 0.00 3.67
5179 6552 2.398554 CCGTCGGCATTCCAACCAG 61.399 63.158 0.00 0.00 0.00 4.00
5180 6553 1.671054 CGTCGGCATTCCAACCAGT 60.671 57.895 0.00 0.00 0.00 4.00
5181 6554 1.635663 CGTCGGCATTCCAACCAGTC 61.636 60.000 0.00 0.00 0.00 3.51
5182 6555 0.605319 GTCGGCATTCCAACCAGTCA 60.605 55.000 0.00 0.00 0.00 3.41
5183 6556 0.327924 TCGGCATTCCAACCAGTCAT 59.672 50.000 0.00 0.00 0.00 3.06
5184 6557 1.176527 CGGCATTCCAACCAGTCATT 58.823 50.000 0.00 0.00 0.00 2.57
5185 6558 1.135315 CGGCATTCCAACCAGTCATTG 60.135 52.381 0.00 0.00 0.00 2.82
5186 6559 2.170166 GGCATTCCAACCAGTCATTGA 58.830 47.619 0.00 0.00 0.00 2.57
5187 6560 2.762327 GGCATTCCAACCAGTCATTGAT 59.238 45.455 0.00 0.00 0.00 2.57
5188 6561 3.181483 GGCATTCCAACCAGTCATTGATC 60.181 47.826 0.00 0.00 0.00 2.92
5189 6562 3.488047 GCATTCCAACCAGTCATTGATCG 60.488 47.826 0.00 0.00 0.00 3.69
5190 6563 1.737838 TCCAACCAGTCATTGATCGC 58.262 50.000 0.00 0.00 0.00 4.58
5191 6564 1.278985 TCCAACCAGTCATTGATCGCT 59.721 47.619 0.00 0.00 0.00 4.93
5192 6565 1.399440 CCAACCAGTCATTGATCGCTG 59.601 52.381 0.00 0.00 0.00 5.18
5193 6566 1.089920 AACCAGTCATTGATCGCTGC 58.910 50.000 0.00 0.00 0.00 5.25
5194 6567 1.086067 ACCAGTCATTGATCGCTGCG 61.086 55.000 17.25 17.25 0.00 5.18
5195 6568 0.807275 CCAGTCATTGATCGCTGCGA 60.807 55.000 28.01 28.01 41.13 5.10
5197 6570 2.397549 CAGTCATTGATCGCTGCGATA 58.602 47.619 34.31 22.01 47.00 2.92
5198 6571 2.991866 CAGTCATTGATCGCTGCGATAT 59.008 45.455 34.31 23.19 47.00 1.63
5199 6572 3.431233 CAGTCATTGATCGCTGCGATATT 59.569 43.478 34.31 20.02 47.00 1.28
5200 6573 4.060900 AGTCATTGATCGCTGCGATATTT 58.939 39.130 34.31 19.69 47.00 1.40
5201 6574 5.119125 CAGTCATTGATCGCTGCGATATTTA 59.881 40.000 34.31 20.38 47.00 1.40
5202 6575 5.119279 AGTCATTGATCGCTGCGATATTTAC 59.881 40.000 34.31 25.80 47.00 2.01
5203 6576 4.388773 TCATTGATCGCTGCGATATTTACC 59.611 41.667 34.31 21.75 47.00 2.85
5204 6577 3.660501 TGATCGCTGCGATATTTACCT 57.339 42.857 34.31 13.79 47.00 3.08
5205 6578 3.990092 TGATCGCTGCGATATTTACCTT 58.010 40.909 34.31 13.03 47.00 3.50
5206 6579 3.740832 TGATCGCTGCGATATTTACCTTG 59.259 43.478 34.31 0.00 47.00 3.61
5207 6580 1.864711 TCGCTGCGATATTTACCTTGC 59.135 47.619 22.24 0.00 0.00 4.01
5208 6581 1.867233 CGCTGCGATATTTACCTTGCT 59.133 47.619 18.66 0.00 0.00 3.91
5209 6582 2.348872 CGCTGCGATATTTACCTTGCTG 60.349 50.000 18.66 0.00 0.00 4.41
5210 6583 2.031682 GCTGCGATATTTACCTTGCTGG 60.032 50.000 0.00 0.00 42.93 4.85
5219 6592 3.291611 CCTTGCTGGTTGGGATGC 58.708 61.111 0.00 0.00 0.00 3.91
5220 6593 1.304713 CCTTGCTGGTTGGGATGCT 60.305 57.895 0.00 0.00 0.00 3.79
5221 6594 1.318158 CCTTGCTGGTTGGGATGCTC 61.318 60.000 0.00 0.00 0.00 4.26
5222 6595 0.323178 CTTGCTGGTTGGGATGCTCT 60.323 55.000 0.00 0.00 0.00 4.09
5223 6596 0.322816 TTGCTGGTTGGGATGCTCTC 60.323 55.000 0.00 0.00 0.00 3.20
5224 6597 1.452833 GCTGGTTGGGATGCTCTCC 60.453 63.158 0.00 0.00 44.11 3.71
5225 6598 1.919600 GCTGGTTGGGATGCTCTCCT 61.920 60.000 5.96 0.00 44.28 3.69
5226 6599 0.622665 CTGGTTGGGATGCTCTCCTT 59.377 55.000 5.96 0.00 44.28 3.36
5227 6600 0.620556 TGGTTGGGATGCTCTCCTTC 59.379 55.000 5.96 0.00 44.28 3.46
5228 6601 0.915364 GGTTGGGATGCTCTCCTTCT 59.085 55.000 5.96 0.00 44.28 2.85
5229 6602 1.134250 GGTTGGGATGCTCTCCTTCTC 60.134 57.143 5.96 0.00 44.28 2.87
5230 6603 1.836802 GTTGGGATGCTCTCCTTCTCT 59.163 52.381 5.96 0.00 44.28 3.10
5231 6604 1.786937 TGGGATGCTCTCCTTCTCTC 58.213 55.000 5.96 0.00 44.28 3.20
5232 6605 1.290431 TGGGATGCTCTCCTTCTCTCT 59.710 52.381 5.96 0.00 44.28 3.10
5233 6606 2.292785 TGGGATGCTCTCCTTCTCTCTT 60.293 50.000 5.96 0.00 44.28 2.85
5234 6607 2.102925 GGGATGCTCTCCTTCTCTCTTG 59.897 54.545 5.96 0.00 44.28 3.02
5235 6608 2.765699 GGATGCTCTCCTTCTCTCTTGT 59.234 50.000 0.00 0.00 41.29 3.16
5236 6609 3.430651 GGATGCTCTCCTTCTCTCTTGTG 60.431 52.174 0.00 0.00 41.29 3.33
5237 6610 1.898472 TGCTCTCCTTCTCTCTTGTGG 59.102 52.381 0.00 0.00 0.00 4.17
5238 6611 1.899142 GCTCTCCTTCTCTCTTGTGGT 59.101 52.381 0.00 0.00 0.00 4.16
5239 6612 2.353605 GCTCTCCTTCTCTCTTGTGGTG 60.354 54.545 0.00 0.00 0.00 4.17
5240 6613 2.233431 CTCTCCTTCTCTCTTGTGGTGG 59.767 54.545 0.00 0.00 0.00 4.61
5241 6614 1.974236 CTCCTTCTCTCTTGTGGTGGT 59.026 52.381 0.00 0.00 0.00 4.16
5242 6615 1.971357 TCCTTCTCTCTTGTGGTGGTC 59.029 52.381 0.00 0.00 0.00 4.02
5243 6616 1.337260 CCTTCTCTCTTGTGGTGGTCG 60.337 57.143 0.00 0.00 0.00 4.79
5244 6617 0.033504 TTCTCTCTTGTGGTGGTCGC 59.966 55.000 0.00 0.00 0.00 5.19
5245 6618 1.374758 CTCTCTTGTGGTGGTCGCC 60.375 63.158 0.00 0.00 0.00 5.54
5246 6619 1.821061 CTCTCTTGTGGTGGTCGCCT 61.821 60.000 2.07 0.00 0.00 5.52
5247 6620 1.374758 CTCTTGTGGTGGTCGCCTC 60.375 63.158 2.07 0.00 0.00 4.70
5248 6621 2.099652 CTCTTGTGGTGGTCGCCTCA 62.100 60.000 2.07 1.88 0.00 3.86
5249 6622 1.003355 CTTGTGGTGGTCGCCTCAT 60.003 57.895 6.21 0.00 32.85 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.107402 AGAGGAGCTTGGATACTGTGA 57.893 47.619 0.00 0.00 37.61 3.58
118 119 1.096386 ATCCGGACCTCTCGAAGTCG 61.096 60.000 6.12 0.00 41.45 4.18
167 170 1.272480 TGACAGTCATTCCTCCTCGGA 60.272 52.381 0.00 0.00 41.06 4.55
245 249 2.975489 ACTGATTCTATGGATTCCCGCT 59.025 45.455 0.00 0.00 34.29 5.52
246 250 3.330267 GACTGATTCTATGGATTCCCGC 58.670 50.000 0.00 0.00 34.29 6.13
266 291 2.682136 TTCATCCACCGGCCTCGA 60.682 61.111 0.00 0.00 39.00 4.04
339 674 1.377202 TGATTCTGTCGGCCAAGCC 60.377 57.895 2.24 0.00 46.75 4.35
512 847 2.431771 TGTCGGCGTGTGATTCCG 60.432 61.111 6.85 0.00 44.16 4.30
543 878 1.535204 GGTGATGTGGGCACAAAGGG 61.535 60.000 0.00 0.00 45.41 3.95
547 882 1.599518 GTCGGTGATGTGGGCACAA 60.600 57.895 0.00 0.00 45.41 3.33
548 883 2.031919 GTCGGTGATGTGGGCACA 59.968 61.111 0.00 0.00 46.44 4.57
555 890 2.029288 CGCTGCTTGTCGGTGATGT 61.029 57.895 0.00 0.00 33.40 3.06
662 1335 3.621715 CCCTTGTCGTCTTTAATAGTGGC 59.378 47.826 0.00 0.00 0.00 5.01
665 1338 4.546829 TGCCCTTGTCGTCTTTAATAGT 57.453 40.909 0.00 0.00 0.00 2.12
669 1342 2.105134 TCCTTGCCCTTGTCGTCTTTAA 59.895 45.455 0.00 0.00 0.00 1.52
671 1344 0.472471 TCCTTGCCCTTGTCGTCTTT 59.528 50.000 0.00 0.00 0.00 2.52
677 1350 0.250338 AAGTCGTCCTTGCCCTTGTC 60.250 55.000 0.00 0.00 30.18 3.18
707 1380 3.684305 CATGTTCTGCTACGAATGGAACA 59.316 43.478 8.82 8.82 46.22 3.18
813 1486 3.257873 TGCACAACCGGATTCATCAAATT 59.742 39.130 9.46 0.00 0.00 1.82
824 1497 0.034574 AATATGCCTGCACAACCGGA 60.035 50.000 9.46 0.00 0.00 5.14
827 1500 6.478673 GGTATTAAAAATATGCCTGCACAACC 59.521 38.462 0.00 0.00 0.00 3.77
828 1501 7.222611 CAGGTATTAAAAATATGCCTGCACAAC 59.777 37.037 6.97 0.00 44.93 3.32
886 1559 0.104120 CCTTACATGTCGGCGGATGA 59.896 55.000 21.44 7.14 0.00 2.92
894 1567 2.332063 AATCCAGGCCTTACATGTCG 57.668 50.000 0.00 0.00 0.00 4.35
906 1579 1.003118 TGGAGGTTCGTCAAATCCAGG 59.997 52.381 0.00 0.00 35.16 4.45
943 1629 1.672854 CGAATAGTGGTGCCCGAGGA 61.673 60.000 0.00 0.00 0.00 3.71
1223 1917 0.455005 CGAAGACCCCGAAGTAGTCC 59.545 60.000 0.00 0.00 0.00 3.85
1297 1991 0.103026 CAAGATCTGGTCCGCGATGA 59.897 55.000 8.23 0.00 0.00 2.92
1374 2068 3.083997 GGCCGTCCTCCACCATCT 61.084 66.667 0.00 0.00 0.00 2.90
1631 2329 3.293311 TGAAGTACGAACTAGGCACAC 57.707 47.619 0.00 0.00 33.75 3.82
1838 2539 8.636213 CAGATTAATTACTTGCCAGATTTCCAT 58.364 33.333 0.00 0.00 0.00 3.41
1878 2579 3.702045 GGATGGCTTGTGAGTCTACTACT 59.298 47.826 0.00 0.00 42.80 2.57
1880 2581 3.708451 TGGATGGCTTGTGAGTCTACTA 58.292 45.455 0.00 0.00 0.00 1.82
1882 2583 3.550437 ATGGATGGCTTGTGAGTCTAC 57.450 47.619 0.00 0.00 0.00 2.59
1989 2814 2.845967 CGATTAAAGGAATGCGTTGTGC 59.154 45.455 0.00 0.00 46.70 4.57
2031 2857 8.635765 ATTTCAGTTGCAGAGGAAACTATAAA 57.364 30.769 9.86 4.36 41.15 1.40
2063 2889 5.372343 TCTTAAGCATTTGGGAGCATCTA 57.628 39.130 0.00 0.00 33.73 1.98
2070 2896 5.456921 AGGAGAATCTTAAGCATTTGGGA 57.543 39.130 0.00 0.00 33.73 4.37
2082 2908 2.823152 GCCCACCCAAAAGGAGAATCTT 60.823 50.000 0.00 0.00 39.89 2.40
2083 2909 1.272704 GCCCACCCAAAAGGAGAATCT 60.273 52.381 0.00 0.00 39.89 2.40
2084 2910 1.186200 GCCCACCCAAAAGGAGAATC 58.814 55.000 0.00 0.00 39.89 2.52
2086 2912 0.263172 TTGCCCACCCAAAAGGAGAA 59.737 50.000 0.00 0.00 39.89 2.87
2087 2913 0.486879 ATTGCCCACCCAAAAGGAGA 59.513 50.000 0.00 0.00 39.89 3.71
2088 2914 0.609662 CATTGCCCACCCAAAAGGAG 59.390 55.000 0.00 0.00 39.89 3.69
2089 2915 0.835543 CCATTGCCCACCCAAAAGGA 60.836 55.000 0.00 0.00 39.89 3.36
2090 2916 1.678724 CCATTGCCCACCCAAAAGG 59.321 57.895 0.00 0.00 43.78 3.11
2091 2917 1.003476 GCCATTGCCCACCCAAAAG 60.003 57.895 0.00 0.00 0.00 2.27
2092 2918 1.059006 AAGCCATTGCCCACCCAAAA 61.059 50.000 0.00 0.00 38.69 2.44
2093 2919 1.461075 AAGCCATTGCCCACCCAAA 60.461 52.632 0.00 0.00 38.69 3.28
2094 2920 2.203750 AAGCCATTGCCCACCCAA 59.796 55.556 0.00 0.00 38.69 4.12
2095 2921 2.604079 CAAGCCATTGCCCACCCA 60.604 61.111 0.00 0.00 38.69 4.51
2096 2922 3.393106 CCAAGCCATTGCCCACCC 61.393 66.667 0.00 0.00 38.69 4.61
2097 2923 4.086547 GCCAAGCCATTGCCCACC 62.087 66.667 0.00 0.00 38.69 4.61
2098 2924 1.682005 TAGCCAAGCCATTGCCCAC 60.682 57.895 0.00 0.00 38.69 4.61
2099 2925 1.682005 GTAGCCAAGCCATTGCCCA 60.682 57.895 0.00 0.00 38.69 5.36
2100 2926 1.669999 CTGTAGCCAAGCCATTGCCC 61.670 60.000 0.00 0.00 38.69 5.36
2101 2927 0.967380 ACTGTAGCCAAGCCATTGCC 60.967 55.000 0.00 0.00 38.69 4.52
2102 2928 0.453390 GACTGTAGCCAAGCCATTGC 59.547 55.000 0.00 0.00 34.91 3.56
2103 2929 1.470098 GTGACTGTAGCCAAGCCATTG 59.530 52.381 0.00 0.00 36.09 2.82
2104 2930 1.073763 TGTGACTGTAGCCAAGCCATT 59.926 47.619 0.00 0.00 0.00 3.16
2105 2931 0.692476 TGTGACTGTAGCCAAGCCAT 59.308 50.000 0.00 0.00 0.00 4.40
2106 2932 0.472044 TTGTGACTGTAGCCAAGCCA 59.528 50.000 0.00 0.00 0.00 4.75
2107 2933 1.537202 CTTTGTGACTGTAGCCAAGCC 59.463 52.381 0.00 0.00 0.00 4.35
2108 2934 2.494059 TCTTTGTGACTGTAGCCAAGC 58.506 47.619 0.00 0.00 0.00 4.01
2109 2935 3.876914 TGTTCTTTGTGACTGTAGCCAAG 59.123 43.478 0.00 0.00 0.00 3.61
2110 2936 3.625764 GTGTTCTTTGTGACTGTAGCCAA 59.374 43.478 0.00 0.00 0.00 4.52
2111 2937 3.202906 GTGTTCTTTGTGACTGTAGCCA 58.797 45.455 0.00 0.00 0.00 4.75
2112 2938 3.202906 TGTGTTCTTTGTGACTGTAGCC 58.797 45.455 0.00 0.00 0.00 3.93
2113 2939 4.875544 TTGTGTTCTTTGTGACTGTAGC 57.124 40.909 0.00 0.00 0.00 3.58
2114 2940 5.584649 TCCTTTGTGTTCTTTGTGACTGTAG 59.415 40.000 0.00 0.00 0.00 2.74
2115 2941 5.492895 TCCTTTGTGTTCTTTGTGACTGTA 58.507 37.500 0.00 0.00 0.00 2.74
2116 2942 4.331968 TCCTTTGTGTTCTTTGTGACTGT 58.668 39.130 0.00 0.00 0.00 3.55
2117 2943 4.731773 GCTCCTTTGTGTTCTTTGTGACTG 60.732 45.833 0.00 0.00 0.00 3.51
2118 2944 3.378427 GCTCCTTTGTGTTCTTTGTGACT 59.622 43.478 0.00 0.00 0.00 3.41
2119 2945 3.128589 TGCTCCTTTGTGTTCTTTGTGAC 59.871 43.478 0.00 0.00 0.00 3.67
2180 3019 4.657814 ATGTACAAACAAGACCTCCCAT 57.342 40.909 0.00 0.00 39.58 4.00
2197 3036 2.754552 ACCTACGTACTCGGCAAATGTA 59.245 45.455 0.00 0.00 41.85 2.29
2205 3044 2.288395 ACAACCAAACCTACGTACTCGG 60.288 50.000 0.00 0.00 41.85 4.63
2260 3101 0.545171 CCTGATCCTGTGCCACTCAT 59.455 55.000 0.00 0.00 0.00 2.90
2285 3126 6.611381 CCGCATATTTTTATCACACCATAGG 58.389 40.000 0.00 0.00 0.00 2.57
2286 3127 6.086222 GCCGCATATTTTTATCACACCATAG 58.914 40.000 0.00 0.00 0.00 2.23
2287 3128 5.532779 TGCCGCATATTTTTATCACACCATA 59.467 36.000 0.00 0.00 0.00 2.74
2288 3129 4.340666 TGCCGCATATTTTTATCACACCAT 59.659 37.500 0.00 0.00 0.00 3.55
2289 3130 3.696548 TGCCGCATATTTTTATCACACCA 59.303 39.130 0.00 0.00 0.00 4.17
2290 3131 4.300189 TGCCGCATATTTTTATCACACC 57.700 40.909 0.00 0.00 0.00 4.16
2366 3208 2.668279 GCCCTACAAAATTCACACGCAG 60.668 50.000 0.00 0.00 0.00 5.18
2370 3212 4.278419 ACTTCTGCCCTACAAAATTCACAC 59.722 41.667 0.00 0.00 0.00 3.82
2430 3272 3.376859 GGCAAACCAAGAAAAGTTTTGGG 59.623 43.478 5.36 7.11 46.43 4.12
2480 3322 1.228124 TCTTTGGTGGGGTTCTGCG 60.228 57.895 0.00 0.00 0.00 5.18
2492 3334 1.815003 GCTGGTCCTCATTGTCTTTGG 59.185 52.381 0.00 0.00 0.00 3.28
2616 3474 8.761497 TGTATAAAGCTACGAGCATAAATTGAC 58.239 33.333 9.09 0.00 45.56 3.18
2697 3561 2.124085 TGGTGGGTGGAGGGGTAG 59.876 66.667 0.00 0.00 0.00 3.18
2779 3643 8.677148 TTGGAAGAATTAATCTACATGTAGGC 57.323 34.615 28.33 11.95 37.42 3.93
2849 3714 7.476667 ACTTGTATGTTCGAATAGAGACTGAG 58.523 38.462 0.00 4.53 0.00 3.35
2918 3783 7.991174 AGACTATACCCAGTGAGTACATAGAT 58.009 38.462 0.00 0.00 0.00 1.98
2919 3784 7.390013 AGACTATACCCAGTGAGTACATAGA 57.610 40.000 0.00 0.00 0.00 1.98
2920 3785 9.570468 TTTAGACTATACCCAGTGAGTACATAG 57.430 37.037 0.00 0.00 0.00 2.23
2921 3786 9.347240 GTTTAGACTATACCCAGTGAGTACATA 57.653 37.037 0.00 0.00 0.00 2.29
3093 3972 6.426633 CACACAAGTGTAACACCTGATAATGA 59.573 38.462 5.41 0.00 42.83 2.57
3127 4006 3.797256 CGGTCGAAGCTATTCCTTTACAG 59.203 47.826 0.00 0.00 31.21 2.74
3198 4081 8.956533 ACAAAATTGGCACTACATAAAAGTTT 57.043 26.923 0.00 0.00 0.00 2.66
3267 4150 5.901884 CGTGTTGTACTCATGTGAAAAGTTC 59.098 40.000 0.94 0.00 0.00 3.01
3353 4236 6.183360 GCCAATGCACACGAATTGAAAAATAT 60.183 34.615 0.00 0.00 36.13 1.28
3355 4238 4.083908 GCCAATGCACACGAATTGAAAAAT 60.084 37.500 0.00 0.00 36.13 1.82
3491 4440 5.117440 TGTTCGTACGTATTGTAAGCACTTG 59.883 40.000 16.05 0.00 31.96 3.16
3494 4443 5.478001 CATGTTCGTACGTATTGTAAGCAC 58.522 41.667 16.05 0.00 34.07 4.40
3549 4498 0.657368 GTTTTCCACACGCTGCTTCG 60.657 55.000 0.00 0.00 0.00 3.79
3656 4987 2.054363 CAGAAATGGTCGATCGATCCG 58.946 52.381 24.86 14.15 0.00 4.18
3762 5093 2.109799 CTTGGGCTCGGCGATCAT 59.890 61.111 11.27 0.00 0.00 2.45
3937 5268 2.281484 TTGCCGAGACCCTGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
4012 5343 2.579787 GGACGACGATGACGCTGG 60.580 66.667 0.00 0.00 43.96 4.85
4114 5445 2.282251 ACGGAGAGCCACACGAGA 60.282 61.111 0.00 0.00 0.00 4.04
4242 5574 4.900635 AAACGTTGAAGCTCATGAAACT 57.099 36.364 0.00 0.00 0.00 2.66
4306 5638 2.430367 GGACTGTCCGCCCAAACT 59.570 61.111 11.71 0.00 0.00 2.66
4720 6052 2.105128 GGAGGACGACGGCTCATG 59.895 66.667 0.00 0.00 0.00 3.07
4721 6053 2.043852 AGGAGGACGACGGCTCAT 60.044 61.111 0.00 0.00 0.00 2.90
4722 6054 2.750637 GAGGAGGACGACGGCTCA 60.751 66.667 0.00 0.00 0.00 4.26
4742 6074 1.512926 GCGCAGACAGGAAGAAAGAA 58.487 50.000 0.30 0.00 0.00 2.52
4779 6111 3.686241 TGCTCAGCATCAACATCTACAAC 59.314 43.478 0.00 0.00 31.71 3.32
4816 6148 3.705604 CGAAAATATTGTCCATGGTGGC 58.294 45.455 12.58 4.25 37.47 5.01
4934 6276 6.381420 TGTTTTCTTACCTTTGGGACATTTCA 59.619 34.615 0.00 0.00 39.30 2.69
5128 6501 2.181975 CGGGGAAAGTGGTAGTCCTAA 58.818 52.381 0.00 0.00 34.23 2.69
5129 6502 1.856629 CGGGGAAAGTGGTAGTCCTA 58.143 55.000 0.00 0.00 34.23 2.94
5130 6503 1.551019 GCGGGGAAAGTGGTAGTCCT 61.551 60.000 0.00 0.00 34.23 3.85
5131 6504 1.078637 GCGGGGAAAGTGGTAGTCC 60.079 63.158 0.00 0.00 0.00 3.85
5132 6505 0.672711 GTGCGGGGAAAGTGGTAGTC 60.673 60.000 0.00 0.00 0.00 2.59
5133 6506 1.373812 GTGCGGGGAAAGTGGTAGT 59.626 57.895 0.00 0.00 0.00 2.73
5134 6507 0.250553 TTGTGCGGGGAAAGTGGTAG 60.251 55.000 0.00 0.00 0.00 3.18
5135 6508 0.183014 TTTGTGCGGGGAAAGTGGTA 59.817 50.000 0.00 0.00 0.00 3.25
5136 6509 0.469144 ATTTGTGCGGGGAAAGTGGT 60.469 50.000 0.00 0.00 0.00 4.16
5137 6510 0.678950 AATTTGTGCGGGGAAAGTGG 59.321 50.000 0.00 0.00 0.00 4.00
5138 6511 2.352323 GGTAATTTGTGCGGGGAAAGTG 60.352 50.000 0.00 0.00 0.00 3.16
5139 6512 1.890489 GGTAATTTGTGCGGGGAAAGT 59.110 47.619 0.00 0.00 0.00 2.66
5140 6513 1.889829 TGGTAATTTGTGCGGGGAAAG 59.110 47.619 0.00 0.00 0.00 2.62
5141 6514 1.614413 GTGGTAATTTGTGCGGGGAAA 59.386 47.619 0.00 0.00 0.00 3.13
5142 6515 1.249407 GTGGTAATTTGTGCGGGGAA 58.751 50.000 0.00 0.00 0.00 3.97
5143 6516 0.609681 GGTGGTAATTTGTGCGGGGA 60.610 55.000 0.00 0.00 0.00 4.81
5144 6517 1.887301 GGTGGTAATTTGTGCGGGG 59.113 57.895 0.00 0.00 0.00 5.73
5145 6518 1.238625 ACGGTGGTAATTTGTGCGGG 61.239 55.000 0.00 0.00 0.00 6.13
5146 6519 0.167251 GACGGTGGTAATTTGTGCGG 59.833 55.000 0.00 0.00 0.00 5.69
5147 6520 0.179235 CGACGGTGGTAATTTGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
5148 6521 0.167251 CCGACGGTGGTAATTTGTGC 59.833 55.000 5.48 0.00 0.00 4.57
5149 6522 0.167251 GCCGACGGTGGTAATTTGTG 59.833 55.000 16.73 0.00 0.00 3.33
5150 6523 0.250381 TGCCGACGGTGGTAATTTGT 60.250 50.000 16.73 0.00 0.00 2.83
5151 6524 1.091537 ATGCCGACGGTGGTAATTTG 58.908 50.000 16.73 0.00 0.00 2.32
5152 6525 1.741145 GAATGCCGACGGTGGTAATTT 59.259 47.619 16.73 0.00 0.00 1.82
5153 6526 1.375551 GAATGCCGACGGTGGTAATT 58.624 50.000 16.73 8.00 0.00 1.40
5154 6527 0.463116 GGAATGCCGACGGTGGTAAT 60.463 55.000 16.73 0.00 0.00 1.89
5155 6528 1.078988 GGAATGCCGACGGTGGTAA 60.079 57.895 16.73 0.00 0.00 2.85
5156 6529 1.828461 TTGGAATGCCGACGGTGGTA 61.828 55.000 16.73 0.07 36.79 3.25
5157 6530 3.185299 TTGGAATGCCGACGGTGGT 62.185 57.895 16.73 0.00 36.79 4.16
5158 6531 2.359354 TTGGAATGCCGACGGTGG 60.359 61.111 16.73 0.00 36.79 4.61
5159 6532 2.867472 GTTGGAATGCCGACGGTG 59.133 61.111 16.73 0.00 38.76 4.94
5163 6536 0.605319 TGACTGGTTGGAATGCCGAC 60.605 55.000 0.52 0.52 46.30 4.79
5164 6537 0.327924 ATGACTGGTTGGAATGCCGA 59.672 50.000 0.00 0.00 36.79 5.54
5165 6538 1.135315 CAATGACTGGTTGGAATGCCG 60.135 52.381 0.00 0.00 36.79 5.69
5166 6539 2.170166 TCAATGACTGGTTGGAATGCC 58.830 47.619 0.00 0.00 0.00 4.40
5167 6540 3.488047 CGATCAATGACTGGTTGGAATGC 60.488 47.826 0.00 0.00 0.00 3.56
5168 6541 3.488047 GCGATCAATGACTGGTTGGAATG 60.488 47.826 0.00 0.00 0.00 2.67
5169 6542 2.684881 GCGATCAATGACTGGTTGGAAT 59.315 45.455 0.00 0.00 0.00 3.01
5170 6543 2.083774 GCGATCAATGACTGGTTGGAA 58.916 47.619 0.00 0.00 0.00 3.53
5171 6544 1.278985 AGCGATCAATGACTGGTTGGA 59.721 47.619 0.00 0.00 0.00 3.53
5172 6545 1.399440 CAGCGATCAATGACTGGTTGG 59.601 52.381 0.00 0.00 0.00 3.77
5173 6546 1.202110 GCAGCGATCAATGACTGGTTG 60.202 52.381 2.28 0.00 0.00 3.77
5174 6547 1.089920 GCAGCGATCAATGACTGGTT 58.910 50.000 2.28 0.00 0.00 3.67
5175 6548 1.086067 CGCAGCGATCAATGACTGGT 61.086 55.000 9.98 0.00 0.00 4.00
5176 6549 0.807275 TCGCAGCGATCAATGACTGG 60.807 55.000 15.11 0.00 0.00 4.00
5177 6550 1.215244 ATCGCAGCGATCAATGACTG 58.785 50.000 24.88 0.00 43.45 3.51
5178 6551 2.800881 TATCGCAGCGATCAATGACT 57.199 45.000 33.01 11.07 43.45 3.41
5179 6552 4.395581 AAATATCGCAGCGATCAATGAC 57.604 40.909 33.01 0.00 43.45 3.06
5180 6553 4.388773 GGTAAATATCGCAGCGATCAATGA 59.611 41.667 33.01 16.41 43.45 2.57
5181 6554 4.389992 AGGTAAATATCGCAGCGATCAATG 59.610 41.667 33.01 0.00 43.45 2.82
5182 6555 4.569943 AGGTAAATATCGCAGCGATCAAT 58.430 39.130 33.01 19.46 43.45 2.57
5183 6556 3.990092 AGGTAAATATCGCAGCGATCAA 58.010 40.909 33.01 17.96 43.45 2.57
5184 6557 3.660501 AGGTAAATATCGCAGCGATCA 57.339 42.857 33.01 19.23 43.45 2.92
5185 6558 3.423645 GCAAGGTAAATATCGCAGCGATC 60.424 47.826 33.01 18.14 43.45 3.69
5187 6560 1.864711 GCAAGGTAAATATCGCAGCGA 59.135 47.619 22.06 22.06 41.13 4.93
5188 6561 1.867233 AGCAAGGTAAATATCGCAGCG 59.133 47.619 9.06 9.06 0.00 5.18
5189 6562 2.031682 CCAGCAAGGTAAATATCGCAGC 60.032 50.000 0.00 0.00 0.00 5.25
5190 6563 3.885484 CCAGCAAGGTAAATATCGCAG 57.115 47.619 0.00 0.00 0.00 5.18
5202 6575 1.304713 AGCATCCCAACCAGCAAGG 60.305 57.895 0.00 0.00 45.67 3.61
5203 6576 0.323178 AGAGCATCCCAACCAGCAAG 60.323 55.000 0.00 0.00 33.66 4.01
5204 6577 0.322816 GAGAGCATCCCAACCAGCAA 60.323 55.000 0.00 0.00 33.66 3.91
5205 6578 1.300963 GAGAGCATCCCAACCAGCA 59.699 57.895 0.00 0.00 33.66 4.41
5206 6579 1.452833 GGAGAGCATCCCAACCAGC 60.453 63.158 0.00 0.00 43.01 4.85
5207 6580 4.972875 GGAGAGCATCCCAACCAG 57.027 61.111 0.00 0.00 43.01 4.00
5215 6588 3.430651 CCACAAGAGAGAAGGAGAGCATC 60.431 52.174 0.00 0.00 0.00 3.91
5216 6589 2.500910 CCACAAGAGAGAAGGAGAGCAT 59.499 50.000 0.00 0.00 0.00 3.79
5217 6590 1.898472 CCACAAGAGAGAAGGAGAGCA 59.102 52.381 0.00 0.00 0.00 4.26
5218 6591 1.899142 ACCACAAGAGAGAAGGAGAGC 59.101 52.381 0.00 0.00 0.00 4.09
5219 6592 2.233431 CCACCACAAGAGAGAAGGAGAG 59.767 54.545 0.00 0.00 0.00 3.20
5220 6593 2.251818 CCACCACAAGAGAGAAGGAGA 58.748 52.381 0.00 0.00 0.00 3.71
5221 6594 1.974236 ACCACCACAAGAGAGAAGGAG 59.026 52.381 0.00 0.00 0.00 3.69
5222 6595 1.971357 GACCACCACAAGAGAGAAGGA 59.029 52.381 0.00 0.00 0.00 3.36
5223 6596 1.337260 CGACCACCACAAGAGAGAAGG 60.337 57.143 0.00 0.00 0.00 3.46
5224 6597 1.937108 GCGACCACCACAAGAGAGAAG 60.937 57.143 0.00 0.00 0.00 2.85
5225 6598 0.033504 GCGACCACCACAAGAGAGAA 59.966 55.000 0.00 0.00 0.00 2.87
5226 6599 1.666011 GCGACCACCACAAGAGAGA 59.334 57.895 0.00 0.00 0.00 3.10
5227 6600 1.374758 GGCGACCACCACAAGAGAG 60.375 63.158 0.00 0.00 0.00 3.20
5228 6601 1.816863 GAGGCGACCACCACAAGAGA 61.817 60.000 0.00 0.00 0.00 3.10
5229 6602 1.374758 GAGGCGACCACCACAAGAG 60.375 63.158 0.00 0.00 0.00 2.85
5230 6603 1.480212 ATGAGGCGACCACCACAAGA 61.480 55.000 0.00 0.00 33.82 3.02
5231 6604 1.003355 ATGAGGCGACCACCACAAG 60.003 57.895 0.00 0.00 33.82 3.16
5232 6605 3.156714 ATGAGGCGACCACCACAA 58.843 55.556 0.00 0.00 33.82 3.33


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

AutoCloner maintained by Alex Coulton.