Multiple sequence alignment - TraesCS5A01G485600

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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 TraesCS5A01G485600 chr5A 100.000 3673 0 0 1 3673 656938269 656934597 0.000000e+00 6783.0
1 TraesCS5A01G485600 chr5A 91.398 93 7 1 1151 1242 382759427 382759519 3.850000e-25 126.0
2 TraesCS5A01G485600 chr5A 95.000 40 2 0 470 509 169297880 169297919 3.060000e-06 63.9
3 TraesCS5A01G485600 chr5B 95.874 2690 57 16 448 3111 665812462 665809801 0.000000e+00 4303.0
4 TraesCS5A01G485600 chr5B 92.219 347 8 3 1 344 665813128 665812798 1.190000e-129 473.0
5 TraesCS5A01G485600 chr5B 90.909 44 4 0 423 466 347274022 347273979 3.960000e-05 60.2
6 TraesCS5A01G485600 chr5B 100.000 29 0 0 473 501 578372090 578372062 2.000000e-03 54.7
7 TraesCS5A01G485600 chr5B 100.000 27 0 0 337 363 665812786 665812760 2.400000e-02 51.0
8 TraesCS5A01G485600 chr3D 92.039 1432 52 29 1240 2641 108571117 108572516 0.000000e+00 1956.0
9 TraesCS5A01G485600 chr3D 91.198 409 20 6 763 1158 108570713 108571118 3.230000e-150 542.0
10 TraesCS5A01G485600 chr3D 93.805 113 7 0 665 777 108570585 108570697 1.750000e-38 171.0
11 TraesCS5A01G485600 chr3D 91.000 100 8 1 1156 1255 22679058 22679156 2.300000e-27 134.0
12 TraesCS5A01G485600 chr3D 91.000 100 8 1 1156 1255 22767900 22767802 2.300000e-27 134.0
13 TraesCS5A01G485600 chr3D 92.391 92 7 0 1151 1242 429097502 429097593 8.280000e-27 132.0
14 TraesCS5A01G485600 chr3D 90.217 92 7 2 19 109 6467028 6466938 6.440000e-23 119.0
15 TraesCS5A01G485600 chr3B 96.029 982 35 2 1521 2502 160138195 160139172 0.000000e+00 1594.0
16 TraesCS5A01G485600 chr3B 90.101 495 29 7 676 1159 160135571 160136056 3.110000e-175 625.0
17 TraesCS5A01G485600 chr3B 87.281 456 35 9 243 678 160135088 160135540 1.970000e-137 499.0
18 TraesCS5A01G485600 chr3B 90.385 208 15 3 1318 1524 160136214 160136417 6.050000e-68 268.0
19 TraesCS5A01G485600 chr3B 81.466 232 19 12 2618 2826 160139735 160139965 6.310000e-38 169.0
20 TraesCS5A01G485600 chr3B 93.976 83 5 0 1240 1322 160136054 160136136 3.850000e-25 126.0
21 TraesCS5A01G485600 chr3B 88.462 104 11 1 1143 1246 809833139 809833037 1.380000e-24 124.0
22 TraesCS5A01G485600 chr3B 85.841 113 15 1 1137 1249 11069979 11070090 6.440000e-23 119.0
23 TraesCS5A01G485600 chr3B 95.652 69 3 0 41 109 603859052 603859120 1.080000e-20 111.0
24 TraesCS5A01G485600 chr3B 91.803 61 4 1 2506 2566 160139201 160139260 2.350000e-12 84.2
25 TraesCS5A01G485600 chr3B 92.727 55 2 2 1 55 716149057 716149109 1.090000e-10 78.7
26 TraesCS5A01G485600 chr1A 88.707 1160 118 9 1255 2409 24944917 24943766 0.000000e+00 1404.0
27 TraesCS5A01G485600 chr1D 87.565 1150 129 10 1263 2409 23999003 23997865 0.000000e+00 1319.0
28 TraesCS5A01G485600 chr1D 87.511 1161 119 13 1252 2409 24125916 24124779 0.000000e+00 1317.0
29 TraesCS5A01G485600 chr1D 96.875 32 1 0 470 501 256999907 256999938 2.000000e-03 54.7
30 TraesCS5A01G485600 chr1B 87.247 792 91 7 1286 2076 39656580 39655798 0.000000e+00 894.0
31 TraesCS5A01G485600 chr1B 91.018 167 15 0 1910 2076 39582056 39582222 3.690000e-55 226.0
32 TraesCS5A01G485600 chr1B 96.970 33 1 0 473 505 268799918 268799950 5.120000e-04 56.5
33 TraesCS5A01G485600 chr1B 94.444 36 1 1 470 504 507308264 507308299 2.000000e-03 54.7
34 TraesCS5A01G485600 chr4D 91.667 96 8 0 1149 1244 245478431 245478336 2.300000e-27 134.0
35 TraesCS5A01G485600 chr4D 91.667 96 8 0 1149 1244 282079939 282080034 2.300000e-27 134.0
36 TraesCS5A01G485600 chr4D 94.203 69 4 0 41 109 55062306 55062374 5.020000e-19 106.0
37 TraesCS5A01G485600 chr7A 95.775 71 3 0 41 111 701480438 701480508 8.340000e-22 115.0
38 TraesCS5A01G485600 chr4A 95.652 69 3 0 41 109 574212370 574212302 1.080000e-20 111.0
39 TraesCS5A01G485600 chr7B 94.366 71 4 0 42 112 114142846 114142776 3.880000e-20 110.0
40 TraesCS5A01G485600 chr7B 94.231 52 1 2 1 52 748308708 748308757 1.090000e-10 78.7
41 TraesCS5A01G485600 chr7B 96.875 32 1 0 470 501 559531989 559532020 2.000000e-03 54.7
42 TraesCS5A01G485600 chr7D 94.203 69 4 0 41 109 27266999 27266931 5.020000e-19 106.0
43 TraesCS5A01G485600 chr7D 94.203 69 4 0 41 109 126883635 126883567 5.020000e-19 106.0
44 TraesCS5A01G485600 chr6B 96.000 50 1 1 1 50 20869293 20869245 3.040000e-11 80.5
45 TraesCS5A01G485600 chr6B 88.889 63 3 4 1 62 659585041 659584982 1.410000e-09 75.0
46 TraesCS5A01G485600 chr2D 96.000 50 1 1 1 50 352876596 352876548 3.040000e-11 80.5
47 TraesCS5A01G485600 chr6D 92.727 55 2 2 1 55 120839284 120839336 1.090000e-10 78.7
48 TraesCS5A01G485600 chr4B 90.164 61 1 5 1 60 673101979 673101923 1.410000e-09 75.0
49 TraesCS5A01G485600 chr5D 100.000 29 0 0 473 501 471051605 471051577 2.000000e-03 54.7


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 TraesCS5A01G485600 chr5A 656934597 656938269 3672 True 6783.000000 6783 100.000000 1 3673 1 chr5A.!!$R1 3672
1 TraesCS5A01G485600 chr5B 665809801 665813128 3327 True 1609.000000 4303 96.031000 1 3111 3 chr5B.!!$R3 3110
2 TraesCS5A01G485600 chr3D 108570585 108572516 1931 False 889.666667 1956 92.347333 665 2641 3 chr3D.!!$F3 1976
3 TraesCS5A01G485600 chr3B 160135088 160139965 4877 False 480.742857 1594 90.148714 243 2826 7 chr3B.!!$F4 2583
4 TraesCS5A01G485600 chr1A 24943766 24944917 1151 True 1404.000000 1404 88.707000 1255 2409 1 chr1A.!!$R1 1154
5 TraesCS5A01G485600 chr1D 23997865 23999003 1138 True 1319.000000 1319 87.565000 1263 2409 1 chr1D.!!$R1 1146
6 TraesCS5A01G485600 chr1D 24124779 24125916 1137 True 1317.000000 1317 87.511000 1252 2409 1 chr1D.!!$R2 1157
7 TraesCS5A01G485600 chr1B 39655798 39656580 782 True 894.000000 894 87.247000 1286 2076 1 chr1B.!!$R1 790

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
889 1193 0.398522 TATCTGCTGGGGGTGTCGAT 60.399 55.0 0.0 0.0 0.0 3.59 F
1416 1816 0.321653 GCCTGAGGTGGTCAACGAAT 60.322 55.0 0.0 0.0 33.6 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2268 4460 0.396435 TGTTTCCTGTCAGCGACCAT 59.604 50.0 0.0 0.0 0.00 3.55 R
3375 6054 0.040204 AAGAAACAGGGGGCATCCAG 59.960 55.0 0.0 0.0 37.22 3.86 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
213 216 7.938563 TTCGTTTGTTTGGATCAATAAAAGG 57.061 32.000 0.00 0.00 0.00 3.11
220 223 7.961351 TGTTTGGATCAATAAAAGGTGAATGT 58.039 30.769 0.00 0.00 0.00 2.71
236 239 8.055279 AGGTGAATGTGTAAATGGACAAATAG 57.945 34.615 0.00 0.00 0.00 1.73
327 332 6.418057 TTGGATTTTCAGTAGCACCATTTT 57.582 33.333 0.00 0.00 0.00 1.82
328 333 5.782047 TGGATTTTCAGTAGCACCATTTTG 58.218 37.500 0.00 0.00 0.00 2.44
329 334 4.627035 GGATTTTCAGTAGCACCATTTTGC 59.373 41.667 0.00 0.00 43.34 3.68
330 335 4.662468 TTTTCAGTAGCACCATTTTGCA 57.338 36.364 0.00 0.00 45.62 4.08
331 336 4.870123 TTTCAGTAGCACCATTTTGCAT 57.130 36.364 0.00 0.00 45.62 3.96
332 337 3.853831 TCAGTAGCACCATTTTGCATG 57.146 42.857 0.00 0.00 45.62 4.06
375 398 9.671279 AAAATTTTCAACTCAAATTGTCCTCTT 57.329 25.926 0.00 0.00 34.68 2.85
383 406 5.069119 ACTCAAATTGTCCTCTTTTTGGGTC 59.931 40.000 0.00 0.00 38.11 4.46
388 411 1.304134 CCTCTTTTTGGGTCGGGGG 60.304 63.158 0.00 0.00 0.00 5.40
426 449 9.946165 AAAGTTAGTGCTATTACAGTTGTTTTC 57.054 29.630 0.00 0.00 0.00 2.29
446 682 3.985127 TCTACTCCCTCCGTTCCATAAA 58.015 45.455 0.00 0.00 0.00 1.40
471 707 4.087510 TGTCGTGGTCTTAGTTCATACG 57.912 45.455 0.00 0.00 0.00 3.06
589 825 6.259829 GGTTGCAACAATAAGTGGACAATTTT 59.740 34.615 29.55 0.00 0.00 1.82
889 1193 0.398522 TATCTGCTGGGGGTGTCGAT 60.399 55.000 0.00 0.00 0.00 3.59
1015 1329 5.046735 ACACTCATCAGTCTCATAAGCAGTT 60.047 40.000 0.00 0.00 0.00 3.16
1055 1370 9.689976 TGTGATTTTAGGAAACAATGTTGTATG 57.310 29.630 0.00 0.00 41.31 2.39
1163 1478 8.522542 TGTTACAAATTATAACATGTACCCCC 57.477 34.615 0.00 3.17 37.56 5.40
1277 1592 0.606401 ATGAAACACACCCAGCTCCG 60.606 55.000 0.00 0.00 0.00 4.63
1363 1763 8.564574 TGCTTTATTCTTTGACGTAATGTTCTT 58.435 29.630 0.00 0.00 0.00 2.52
1416 1816 0.321653 GCCTGAGGTGGTCAACGAAT 60.322 55.000 0.00 0.00 33.60 3.34
1417 1817 1.066430 GCCTGAGGTGGTCAACGAATA 60.066 52.381 0.00 0.00 33.60 1.75
1418 1818 2.614481 GCCTGAGGTGGTCAACGAATAA 60.614 50.000 0.00 0.00 33.60 1.40
1419 1819 3.000727 CCTGAGGTGGTCAACGAATAAC 58.999 50.000 0.00 0.00 33.60 1.89
1420 1820 3.556213 CCTGAGGTGGTCAACGAATAACA 60.556 47.826 0.00 0.00 33.60 2.41
1421 1821 4.253685 CTGAGGTGGTCAACGAATAACAT 58.746 43.478 0.00 0.00 33.60 2.71
1422 1822 4.647611 TGAGGTGGTCAACGAATAACATT 58.352 39.130 0.00 0.00 29.64 2.71
1423 1823 5.067273 TGAGGTGGTCAACGAATAACATTT 58.933 37.500 0.00 0.00 29.64 2.32
1747 3939 1.722034 ACCTGATGAGTGGACACAGT 58.278 50.000 5.14 0.00 0.00 3.55
1748 3940 2.050144 ACCTGATGAGTGGACACAGTT 58.950 47.619 5.14 0.00 0.00 3.16
2058 4250 1.070786 GTGGAAGCTCACCAACGGA 59.929 57.895 13.07 0.00 39.22 4.69
2184 4376 2.111384 GCCTCTCAGGATGGAACTGTA 58.889 52.381 0.00 0.00 37.67 2.74
2263 4455 0.478507 CAGAACCCCTGTTTGGAGGT 59.521 55.000 0.00 0.00 39.87 3.85
2268 4460 0.184933 CCCCTGTTTGGAGGTTGTCA 59.815 55.000 0.00 0.00 38.35 3.58
2412 4604 7.434492 GTGTTCTACCTCTAGCTGCATTTATA 58.566 38.462 1.02 0.00 0.00 0.98
2413 4605 8.091449 GTGTTCTACCTCTAGCTGCATTTATAT 58.909 37.037 1.02 0.00 0.00 0.86
2606 5229 3.720601 CCTGGCCAGGCAGCTGTA 61.721 66.667 38.39 0.00 42.44 2.74
2607 5230 2.437359 CTGGCCAGGCAGCTGTAC 60.437 66.667 26.14 9.04 0.00 2.90
2611 5234 1.810030 GCCAGGCAGCTGTACGTAC 60.810 63.158 18.90 18.90 0.00 3.67
2614 5237 1.068474 CAGGCAGCTGTACGTACAAC 58.932 55.000 27.16 23.08 35.50 3.32
2653 5305 2.242043 CAAACCTGGCCTGAGACAAAT 58.758 47.619 11.88 0.00 0.00 2.32
2703 5355 0.465824 GCTGAGCTGCATCCCATTCT 60.466 55.000 1.02 0.00 0.00 2.40
2706 5358 3.336468 CTGAGCTGCATCCCATTCTATC 58.664 50.000 1.02 0.00 0.00 2.08
2830 5506 0.321919 GCAACCTGGCACATCTCAGA 60.322 55.000 0.00 0.00 38.20 3.27
2831 5507 1.735386 CAACCTGGCACATCTCAGAG 58.265 55.000 0.00 0.00 38.20 3.35
2902 5578 0.605083 TGTGAGTGCTTGCTCTCGAT 59.395 50.000 16.47 0.00 36.51 3.59
2969 5645 4.510038 AGTTTGCTGATAGTTTGGCAAG 57.490 40.909 0.00 0.00 43.84 4.01
2984 5660 7.373493 AGTTTGGCAAGAAACTCATTTGATAG 58.627 34.615 0.00 0.00 41.38 2.08
3009 5685 4.083271 CGATCTTCTGGTTCTTGGGAAAAC 60.083 45.833 0.00 0.00 32.81 2.43
3012 5688 6.008696 TCTTCTGGTTCTTGGGAAAACTTA 57.991 37.500 0.00 0.00 32.81 2.24
3016 5692 5.472137 TCTGGTTCTTGGGAAAACTTAATCG 59.528 40.000 0.00 0.00 32.81 3.34
3111 5790 3.723235 AATCAGACCTGCGCGCGAT 62.723 57.895 37.18 18.35 0.00 4.58
3112 5791 3.723235 ATCAGACCTGCGCGCGATT 62.723 57.895 37.18 13.85 0.00 3.34
3113 5792 2.349969 ATCAGACCTGCGCGCGATTA 62.350 55.000 37.18 17.86 0.00 1.75
3114 5793 2.582498 AGACCTGCGCGCGATTAC 60.582 61.111 37.18 16.86 0.00 1.89
3115 5794 2.582498 GACCTGCGCGCGATTACT 60.582 61.111 37.18 10.90 0.00 2.24
3116 5795 1.298863 GACCTGCGCGCGATTACTA 60.299 57.895 37.18 10.47 0.00 1.82
3117 5796 0.663568 GACCTGCGCGCGATTACTAT 60.664 55.000 37.18 11.26 0.00 2.12
3118 5797 0.249322 ACCTGCGCGCGATTACTATT 60.249 50.000 37.18 5.07 0.00 1.73
3119 5798 1.001048 ACCTGCGCGCGATTACTATTA 60.001 47.619 37.18 3.05 0.00 0.98
3120 5799 2.259618 CCTGCGCGCGATTACTATTAT 58.740 47.619 37.18 0.00 0.00 1.28
3121 5800 2.279136 CCTGCGCGCGATTACTATTATC 59.721 50.000 37.18 11.63 0.00 1.75
3122 5801 3.172050 CTGCGCGCGATTACTATTATCT 58.828 45.455 37.18 0.00 0.00 1.98
3123 5802 3.571571 TGCGCGCGATTACTATTATCTT 58.428 40.909 37.18 0.00 0.00 2.40
3124 5803 3.363724 TGCGCGCGATTACTATTATCTTG 59.636 43.478 37.18 0.00 0.00 3.02
3125 5804 3.364023 GCGCGCGATTACTATTATCTTGT 59.636 43.478 37.18 0.00 0.00 3.16
3126 5805 4.718444 GCGCGCGATTACTATTATCTTGTG 60.718 45.833 37.18 0.00 0.00 3.33
3127 5806 4.381863 CGCGCGATTACTATTATCTTGTGT 59.618 41.667 28.94 0.00 0.00 3.72
3128 5807 5.566395 CGCGCGATTACTATTATCTTGTGTA 59.434 40.000 28.94 0.00 0.00 2.90
3129 5808 6.236967 CGCGCGATTACTATTATCTTGTGTAG 60.237 42.308 28.94 0.00 0.00 2.74
3130 5809 6.800408 GCGCGATTACTATTATCTTGTGTAGA 59.200 38.462 12.10 0.00 37.28 2.59
3131 5810 7.201249 GCGCGATTACTATTATCTTGTGTAGAC 60.201 40.741 12.10 0.00 35.19 2.59
3132 5811 7.801783 CGCGATTACTATTATCTTGTGTAGACA 59.198 37.037 0.00 0.00 35.19 3.41
3133 5812 9.459640 GCGATTACTATTATCTTGTGTAGACAA 57.540 33.333 5.22 5.22 39.88 3.18
3144 5823 8.955061 ATCTTGTGTAGACAAATTTTTCATCG 57.045 30.769 6.91 0.00 41.62 3.84
3145 5824 7.925993 TCTTGTGTAGACAAATTTTTCATCGT 58.074 30.769 6.91 0.00 41.62 3.73
3146 5825 7.855409 TCTTGTGTAGACAAATTTTTCATCGTG 59.145 33.333 6.91 0.00 41.62 4.35
3147 5826 5.912396 TGTGTAGACAAATTTTTCATCGTGC 59.088 36.000 7.08 0.00 0.00 5.34
3148 5827 6.142817 GTGTAGACAAATTTTTCATCGTGCT 58.857 36.000 7.08 0.00 0.00 4.40
3149 5828 6.636850 GTGTAGACAAATTTTTCATCGTGCTT 59.363 34.615 7.08 0.00 0.00 3.91
3150 5829 7.167468 GTGTAGACAAATTTTTCATCGTGCTTT 59.833 33.333 7.08 0.00 0.00 3.51
3151 5830 8.346300 TGTAGACAAATTTTTCATCGTGCTTTA 58.654 29.630 7.08 0.00 0.00 1.85
3152 5831 7.623268 AGACAAATTTTTCATCGTGCTTTAC 57.377 32.000 7.08 0.00 0.00 2.01
3153 5832 6.640907 AGACAAATTTTTCATCGTGCTTTACC 59.359 34.615 7.08 0.00 0.00 2.85
3154 5833 5.694458 ACAAATTTTTCATCGTGCTTTACCC 59.306 36.000 0.00 0.00 0.00 3.69
3155 5834 3.926821 TTTTTCATCGTGCTTTACCCC 57.073 42.857 0.00 0.00 0.00 4.95
3156 5835 2.871096 TTTCATCGTGCTTTACCCCT 57.129 45.000 0.00 0.00 0.00 4.79
3157 5836 2.871096 TTCATCGTGCTTTACCCCTT 57.129 45.000 0.00 0.00 0.00 3.95
3158 5837 2.871096 TCATCGTGCTTTACCCCTTT 57.129 45.000 0.00 0.00 0.00 3.11
3159 5838 2.706890 TCATCGTGCTTTACCCCTTTC 58.293 47.619 0.00 0.00 0.00 2.62
3160 5839 2.039216 TCATCGTGCTTTACCCCTTTCA 59.961 45.455 0.00 0.00 0.00 2.69
3161 5840 2.871096 TCGTGCTTTACCCCTTTCAT 57.129 45.000 0.00 0.00 0.00 2.57
3162 5841 3.149005 TCGTGCTTTACCCCTTTCATT 57.851 42.857 0.00 0.00 0.00 2.57
3163 5842 2.817258 TCGTGCTTTACCCCTTTCATTG 59.183 45.455 0.00 0.00 0.00 2.82
3164 5843 2.556622 CGTGCTTTACCCCTTTCATTGT 59.443 45.455 0.00 0.00 0.00 2.71
3165 5844 3.754323 CGTGCTTTACCCCTTTCATTGTA 59.246 43.478 0.00 0.00 0.00 2.41
3166 5845 4.216687 CGTGCTTTACCCCTTTCATTGTAA 59.783 41.667 0.00 0.00 0.00 2.41
3167 5846 5.278561 CGTGCTTTACCCCTTTCATTGTAAA 60.279 40.000 0.00 0.00 33.50 2.01
3168 5847 6.517605 GTGCTTTACCCCTTTCATTGTAAAA 58.482 36.000 0.00 0.00 34.01 1.52
3169 5848 7.158697 GTGCTTTACCCCTTTCATTGTAAAAT 58.841 34.615 0.00 0.00 34.01 1.82
3170 5849 8.308207 GTGCTTTACCCCTTTCATTGTAAAATA 58.692 33.333 0.00 0.00 34.01 1.40
3171 5850 8.308207 TGCTTTACCCCTTTCATTGTAAAATAC 58.692 33.333 0.00 0.00 34.01 1.89
3172 5851 8.308207 GCTTTACCCCTTTCATTGTAAAATACA 58.692 33.333 0.00 0.00 34.01 2.29
3173 5852 9.634163 CTTTACCCCTTTCATTGTAAAATACAC 57.366 33.333 0.00 0.00 38.63 2.90
3174 5853 8.707796 TTACCCCTTTCATTGTAAAATACACA 57.292 30.769 0.00 0.00 38.63 3.72
3175 5854 7.604657 ACCCCTTTCATTGTAAAATACACAA 57.395 32.000 0.00 0.00 38.63 3.33
3176 5855 8.024145 ACCCCTTTCATTGTAAAATACACAAA 57.976 30.769 0.00 0.00 39.22 2.83
3177 5856 8.147704 ACCCCTTTCATTGTAAAATACACAAAG 58.852 33.333 0.00 0.85 39.22 2.77
3178 5857 7.117667 CCCCTTTCATTGTAAAATACACAAAGC 59.882 37.037 0.00 0.00 39.22 3.51
3179 5858 7.872483 CCCTTTCATTGTAAAATACACAAAGCT 59.128 33.333 0.00 0.00 39.22 3.74
3180 5859 9.260002 CCTTTCATTGTAAAATACACAAAGCTT 57.740 29.630 0.00 0.00 39.22 3.74
3191 5870 9.777297 AAAATACACAAAGCTTTTAACATGGAT 57.223 25.926 9.53 2.80 0.00 3.41
3192 5871 9.777297 AAATACACAAAGCTTTTAACATGGATT 57.223 25.926 9.53 8.54 0.00 3.01
3193 5872 8.986477 ATACACAAAGCTTTTAACATGGATTC 57.014 30.769 9.53 0.00 0.00 2.52
3194 5873 6.815089 ACACAAAGCTTTTAACATGGATTCA 58.185 32.000 9.53 0.00 0.00 2.57
3195 5874 6.701400 ACACAAAGCTTTTAACATGGATTCAC 59.299 34.615 9.53 0.00 0.00 3.18
3196 5875 6.925165 CACAAAGCTTTTAACATGGATTCACT 59.075 34.615 9.53 0.00 0.00 3.41
3197 5876 7.115378 CACAAAGCTTTTAACATGGATTCACTC 59.885 37.037 9.53 0.00 0.00 3.51
3198 5877 5.904362 AGCTTTTAACATGGATTCACTCC 57.096 39.130 0.00 0.00 45.19 3.85
3199 5878 5.574188 AGCTTTTAACATGGATTCACTCCT 58.426 37.500 0.00 0.00 45.21 3.69
3200 5879 6.721318 AGCTTTTAACATGGATTCACTCCTA 58.279 36.000 0.00 0.00 45.21 2.94
3201 5880 7.175104 AGCTTTTAACATGGATTCACTCCTAA 58.825 34.615 0.00 0.00 45.21 2.69
3202 5881 7.669722 AGCTTTTAACATGGATTCACTCCTAAA 59.330 33.333 0.00 0.00 45.21 1.85
3203 5882 8.303876 GCTTTTAACATGGATTCACTCCTAAAA 58.696 33.333 0.00 0.00 45.21 1.52
3204 5883 9.846248 CTTTTAACATGGATTCACTCCTAAAAG 57.154 33.333 0.00 8.11 45.21 2.27
3205 5884 9.581289 TTTTAACATGGATTCACTCCTAAAAGA 57.419 29.630 0.00 0.00 45.21 2.52
3206 5885 9.753674 TTTAACATGGATTCACTCCTAAAAGAT 57.246 29.630 0.00 0.00 45.21 2.40
3207 5886 7.872113 AACATGGATTCACTCCTAAAAGATC 57.128 36.000 0.00 0.00 45.21 2.75
3208 5887 7.205515 ACATGGATTCACTCCTAAAAGATCT 57.794 36.000 0.00 0.00 45.21 2.75
3209 5888 8.324191 ACATGGATTCACTCCTAAAAGATCTA 57.676 34.615 0.00 0.00 45.21 1.98
3210 5889 8.772250 ACATGGATTCACTCCTAAAAGATCTAA 58.228 33.333 0.00 0.00 45.21 2.10
3211 5890 9.050601 CATGGATTCACTCCTAAAAGATCTAAC 57.949 37.037 0.00 0.00 45.21 2.34
3212 5891 8.380742 TGGATTCACTCCTAAAAGATCTAACT 57.619 34.615 0.00 0.00 45.21 2.24
3213 5892 8.478877 TGGATTCACTCCTAAAAGATCTAACTC 58.521 37.037 0.00 0.00 45.21 3.01
3214 5893 8.478877 GGATTCACTCCTAAAAGATCTAACTCA 58.521 37.037 0.00 0.00 41.29 3.41
3216 5895 9.829507 ATTCACTCCTAAAAGATCTAACTCATG 57.170 33.333 0.00 0.00 0.00 3.07
3217 5896 8.367660 TCACTCCTAAAAGATCTAACTCATGT 57.632 34.615 0.00 0.00 0.00 3.21
3218 5897 8.253810 TCACTCCTAAAAGATCTAACTCATGTG 58.746 37.037 0.00 2.05 0.00 3.21
3219 5898 7.493971 CACTCCTAAAAGATCTAACTCATGTGG 59.506 40.741 0.00 0.00 0.00 4.17
3220 5899 7.400339 ACTCCTAAAAGATCTAACTCATGTGGA 59.600 37.037 0.00 0.00 0.00 4.02
3221 5900 7.556844 TCCTAAAAGATCTAACTCATGTGGAC 58.443 38.462 0.00 0.00 0.00 4.02
3222 5901 7.180229 TCCTAAAAGATCTAACTCATGTGGACA 59.820 37.037 0.00 0.00 0.00 4.02
3223 5902 7.824289 CCTAAAAGATCTAACTCATGTGGACAA 59.176 37.037 0.00 0.00 0.00 3.18
3224 5903 9.219603 CTAAAAGATCTAACTCATGTGGACAAA 57.780 33.333 0.00 0.00 0.00 2.83
3225 5904 7.440523 AAAGATCTAACTCATGTGGACAAAC 57.559 36.000 0.00 0.00 0.00 2.93
3226 5905 6.365970 AGATCTAACTCATGTGGACAAACT 57.634 37.500 0.00 0.00 0.00 2.66
3227 5906 6.773638 AGATCTAACTCATGTGGACAAACTT 58.226 36.000 0.00 0.00 0.00 2.66
3228 5907 6.652481 AGATCTAACTCATGTGGACAAACTTG 59.348 38.462 0.00 0.00 0.00 3.16
3229 5908 5.680619 TCTAACTCATGTGGACAAACTTGT 58.319 37.500 0.00 0.00 45.65 3.16
3230 5909 6.119536 TCTAACTCATGTGGACAAACTTGTT 58.880 36.000 0.00 0.00 42.43 2.83
3231 5910 7.276658 TCTAACTCATGTGGACAAACTTGTTA 58.723 34.615 0.00 0.00 42.43 2.41
3232 5911 6.767524 AACTCATGTGGACAAACTTGTTAA 57.232 33.333 0.00 0.00 42.43 2.01
3233 5912 6.767524 ACTCATGTGGACAAACTTGTTAAA 57.232 33.333 0.00 0.00 42.43 1.52
3234 5913 7.346751 ACTCATGTGGACAAACTTGTTAAAT 57.653 32.000 0.00 0.00 42.43 1.40
3235 5914 7.781056 ACTCATGTGGACAAACTTGTTAAATT 58.219 30.769 0.00 0.00 42.43 1.82
3236 5915 8.257306 ACTCATGTGGACAAACTTGTTAAATTT 58.743 29.630 0.00 0.00 42.43 1.82
3237 5916 9.097257 CTCATGTGGACAAACTTGTTAAATTTT 57.903 29.630 0.00 0.00 42.43 1.82
3238 5917 9.442047 TCATGTGGACAAACTTGTTAAATTTTT 57.558 25.926 0.00 0.00 42.43 1.94
3267 5946 8.142994 TCGATTTTCTTATAAACTGGATCAGC 57.857 34.615 0.00 0.00 34.37 4.26
3268 5947 7.226720 TCGATTTTCTTATAAACTGGATCAGCC 59.773 37.037 0.00 0.00 34.37 4.85
3269 5948 7.227512 CGATTTTCTTATAAACTGGATCAGCCT 59.772 37.037 0.00 0.00 37.63 4.58
3270 5949 8.829373 ATTTTCTTATAAACTGGATCAGCCTT 57.171 30.769 0.00 0.00 37.63 4.35
3271 5950 7.865706 TTTCTTATAAACTGGATCAGCCTTC 57.134 36.000 0.00 0.00 37.63 3.46
3272 5951 6.814954 TCTTATAAACTGGATCAGCCTTCT 57.185 37.500 0.00 0.00 37.63 2.85
3273 5952 6.586344 TCTTATAAACTGGATCAGCCTTCTG 58.414 40.000 0.00 0.00 41.67 3.02
3274 5953 2.503895 AAACTGGATCAGCCTTCTGG 57.496 50.000 0.00 0.00 40.69 3.86
3287 5966 3.303351 CCTTCTGGCATATTGACCCTT 57.697 47.619 0.00 0.00 0.00 3.95
3288 5967 3.635591 CCTTCTGGCATATTGACCCTTT 58.364 45.455 0.00 0.00 0.00 3.11
3289 5968 4.026052 CCTTCTGGCATATTGACCCTTTT 58.974 43.478 0.00 0.00 0.00 2.27
3290 5969 4.467438 CCTTCTGGCATATTGACCCTTTTT 59.533 41.667 0.00 0.00 0.00 1.94
3291 5970 5.656416 CCTTCTGGCATATTGACCCTTTTTA 59.344 40.000 0.00 0.00 0.00 1.52
3292 5971 6.183360 CCTTCTGGCATATTGACCCTTTTTAG 60.183 42.308 0.00 0.00 0.00 1.85
3293 5972 5.826643 TCTGGCATATTGACCCTTTTTAGT 58.173 37.500 0.00 0.00 0.00 2.24
3294 5973 6.964464 TCTGGCATATTGACCCTTTTTAGTA 58.036 36.000 0.00 0.00 0.00 1.82
3295 5974 7.582719 TCTGGCATATTGACCCTTTTTAGTAT 58.417 34.615 0.00 0.00 0.00 2.12
3296 5975 8.719596 TCTGGCATATTGACCCTTTTTAGTATA 58.280 33.333 0.00 0.00 0.00 1.47
3297 5976 9.520515 CTGGCATATTGACCCTTTTTAGTATAT 57.479 33.333 0.00 0.00 0.00 0.86
3298 5977 9.875708 TGGCATATTGACCCTTTTTAGTATATT 57.124 29.630 0.00 0.00 0.00 1.28
3304 5983 8.801882 TTGACCCTTTTTAGTATATTCAGGTG 57.198 34.615 0.00 0.00 0.00 4.00
3305 5984 7.343357 TGACCCTTTTTAGTATATTCAGGTGG 58.657 38.462 0.00 0.00 0.00 4.61
3306 5985 6.669631 ACCCTTTTTAGTATATTCAGGTGGG 58.330 40.000 0.00 0.00 34.89 4.61
3307 5986 6.218938 ACCCTTTTTAGTATATTCAGGTGGGT 59.781 38.462 0.00 0.00 36.95 4.51
3308 5987 6.546034 CCCTTTTTAGTATATTCAGGTGGGTG 59.454 42.308 0.00 0.00 0.00 4.61
3309 5988 7.343357 CCTTTTTAGTATATTCAGGTGGGTGA 58.657 38.462 0.00 0.00 0.00 4.02
3310 5989 7.832187 CCTTTTTAGTATATTCAGGTGGGTGAA 59.168 37.037 0.00 0.00 40.68 3.18
3311 5990 8.570068 TTTTTAGTATATTCAGGTGGGTGAAC 57.430 34.615 0.00 0.00 39.25 3.18
3312 5991 7.504926 TTTAGTATATTCAGGTGGGTGAACT 57.495 36.000 0.00 0.00 39.25 3.01
3313 5992 5.359194 AGTATATTCAGGTGGGTGAACTG 57.641 43.478 0.00 0.00 39.25 3.16
3314 5993 5.030147 AGTATATTCAGGTGGGTGAACTGA 58.970 41.667 0.00 0.00 39.25 3.41
3317 5996 3.374042 TTCAGGTGGGTGAACTGAAAA 57.626 42.857 0.00 0.00 45.26 2.29
3318 5997 2.930950 TCAGGTGGGTGAACTGAAAAG 58.069 47.619 0.00 0.00 38.22 2.27
3319 5998 1.956477 CAGGTGGGTGAACTGAAAAGG 59.044 52.381 0.00 0.00 34.21 3.11
3320 5999 1.133482 AGGTGGGTGAACTGAAAAGGG 60.133 52.381 0.00 0.00 0.00 3.95
3321 6000 1.328279 GTGGGTGAACTGAAAAGGGG 58.672 55.000 0.00 0.00 0.00 4.79
3322 6001 0.930726 TGGGTGAACTGAAAAGGGGT 59.069 50.000 0.00 0.00 0.00 4.95
3323 6002 1.328279 GGGTGAACTGAAAAGGGGTG 58.672 55.000 0.00 0.00 0.00 4.61
3324 6003 0.673985 GGTGAACTGAAAAGGGGTGC 59.326 55.000 0.00 0.00 0.00 5.01
3325 6004 1.398692 GTGAACTGAAAAGGGGTGCA 58.601 50.000 0.00 0.00 0.00 4.57
3326 6005 1.338020 GTGAACTGAAAAGGGGTGCAG 59.662 52.381 0.00 0.00 34.65 4.41
3327 6006 0.315251 GAACTGAAAAGGGGTGCAGC 59.685 55.000 7.55 7.55 31.74 5.25
3328 6007 1.455383 AACTGAAAAGGGGTGCAGCG 61.455 55.000 10.24 0.00 31.74 5.18
3329 6008 3.273080 CTGAAAAGGGGTGCAGCGC 62.273 63.158 23.89 23.89 0.00 5.92
3330 6009 4.404654 GAAAAGGGGTGCAGCGCG 62.405 66.667 24.71 0.00 0.00 6.86
3352 6031 4.483243 CACTACCCCCGCGCCATT 62.483 66.667 0.00 0.00 0.00 3.16
3353 6032 3.723922 ACTACCCCCGCGCCATTT 61.724 61.111 0.00 0.00 0.00 2.32
3354 6033 2.368821 ACTACCCCCGCGCCATTTA 61.369 57.895 0.00 0.00 0.00 1.40
3355 6034 1.597027 CTACCCCCGCGCCATTTAG 60.597 63.158 0.00 0.00 0.00 1.85
3356 6035 3.109592 TACCCCCGCGCCATTTAGG 62.110 63.158 0.00 0.00 41.84 2.69
3380 6059 4.431131 CCTTGTGCGGGGCTGGAT 62.431 66.667 0.00 0.00 0.00 3.41
3381 6060 3.136123 CTTGTGCGGGGCTGGATG 61.136 66.667 0.00 0.00 0.00 3.51
3391 6070 2.037847 GCTGGATGCCCCCTGTTT 59.962 61.111 0.00 0.00 35.15 2.83
3392 6071 2.054453 GCTGGATGCCCCCTGTTTC 61.054 63.158 0.00 0.00 35.15 2.78
3393 6072 1.693640 CTGGATGCCCCCTGTTTCT 59.306 57.895 0.00 0.00 0.00 2.52
3394 6073 0.040204 CTGGATGCCCCCTGTTTCTT 59.960 55.000 0.00 0.00 0.00 2.52
3395 6074 0.486879 TGGATGCCCCCTGTTTCTTT 59.513 50.000 0.00 0.00 0.00 2.52
3396 6075 1.132881 TGGATGCCCCCTGTTTCTTTT 60.133 47.619 0.00 0.00 0.00 2.27
3397 6076 1.977854 GGATGCCCCCTGTTTCTTTTT 59.022 47.619 0.00 0.00 0.00 1.94
3421 6100 9.937175 TTTTTCAATTCGTTTTGTCTTGTTTTT 57.063 22.222 1.22 0.00 0.00 1.94
3476 6155 9.725019 AAATATCTTGGGAATTCAAAAGGTTTC 57.275 29.630 7.93 0.00 0.00 2.78
3477 6156 6.745794 ATCTTGGGAATTCAAAAGGTTTCA 57.254 33.333 7.93 0.00 0.00 2.69
3478 6157 6.552445 TCTTGGGAATTCAAAAGGTTTCAA 57.448 33.333 7.93 0.00 0.00 2.69
3479 6158 6.951971 TCTTGGGAATTCAAAAGGTTTCAAA 58.048 32.000 7.93 0.00 0.00 2.69
3480 6159 7.572814 TCTTGGGAATTCAAAAGGTTTCAAAT 58.427 30.769 7.93 0.00 0.00 2.32
3481 6160 8.709308 TCTTGGGAATTCAAAAGGTTTCAAATA 58.291 29.630 7.93 0.00 0.00 1.40
3482 6161 9.506018 CTTGGGAATTCAAAAGGTTTCAAATAT 57.494 29.630 7.93 0.00 0.00 1.28
3483 6162 9.859152 TTGGGAATTCAAAAGGTTTCAAATATT 57.141 25.926 7.93 0.00 0.00 1.28
3484 6163 9.282569 TGGGAATTCAAAAGGTTTCAAATATTG 57.717 29.630 7.93 0.00 0.00 1.90
3485 6164 9.500785 GGGAATTCAAAAGGTTTCAAATATTGA 57.499 29.630 7.93 0.00 38.04 2.57
3536 6215 8.681486 ATCAAGAAATCATAAATGATCGTGGA 57.319 30.769 5.94 2.47 46.22 4.02
3537 6216 8.681486 TCAAGAAATCATAAATGATCGTGGAT 57.319 30.769 5.94 0.00 46.22 3.41
3538 6217 9.123902 TCAAGAAATCATAAATGATCGTGGATT 57.876 29.630 5.94 0.00 46.22 3.01
3539 6218 9.390795 CAAGAAATCATAAATGATCGTGGATTC 57.609 33.333 5.94 5.57 46.22 2.52
3540 6219 8.681486 AGAAATCATAAATGATCGTGGATTCA 57.319 30.769 5.94 0.00 46.22 2.57
3541 6220 9.123902 AGAAATCATAAATGATCGTGGATTCAA 57.876 29.630 5.94 0.00 46.22 2.69
3542 6221 9.734620 GAAATCATAAATGATCGTGGATTCAAA 57.265 29.630 5.94 0.00 46.22 2.69
3572 6251 9.950680 TTGTTTGTGATTTTTAAAAAGTTTGCA 57.049 22.222 17.72 9.74 0.00 4.08
3624 6303 7.951530 AAAATGCTCTGAAAGGTAACAAATG 57.048 32.000 0.00 0.00 41.41 2.32
3625 6304 6.655078 AATGCTCTGAAAGGTAACAAATGT 57.345 33.333 0.00 0.00 41.41 2.71
3626 6305 6.655078 ATGCTCTGAAAGGTAACAAATGTT 57.345 33.333 4.01 4.01 41.73 2.71
3627 6306 7.759489 ATGCTCTGAAAGGTAACAAATGTTA 57.241 32.000 1.96 1.96 39.31 2.41
3628 6307 7.575414 TGCTCTGAAAGGTAACAAATGTTAA 57.425 32.000 7.53 0.00 41.58 2.01
3629 6308 8.001881 TGCTCTGAAAGGTAACAAATGTTAAA 57.998 30.769 7.53 0.00 41.58 1.52
3630 6309 8.470805 TGCTCTGAAAGGTAACAAATGTTAAAA 58.529 29.630 7.53 0.00 41.58 1.52
3631 6310 9.476202 GCTCTGAAAGGTAACAAATGTTAAAAT 57.524 29.630 7.53 0.00 41.58 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.827677 CCTCCGTTCCTAAATATAAGTCTTTTG 58.172 37.037 0.00 0.00 0.00 2.44
17 18 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
80 81 2.029844 GCCACGTTGAGAGGAGTGC 61.030 63.158 0.00 0.00 33.62 4.40
159 162 2.862541 ACTTTCCAACATGTAGCTGCA 58.137 42.857 7.05 7.05 0.00 4.41
213 216 9.559958 CTTCTATTTGTCCATTTACACATTCAC 57.440 33.333 0.00 0.00 0.00 3.18
220 223 7.398829 TGTAGGCTTCTATTTGTCCATTTACA 58.601 34.615 0.00 0.00 0.00 2.41
236 239 4.303282 GCTAGATAGCTGTTGTAGGCTTC 58.697 47.826 4.58 0.00 45.62 3.86
388 411 3.875125 CACTAACTTTAGAAGCCCCTCC 58.125 50.000 2.95 0.00 34.84 4.30
389 412 3.055021 AGCACTAACTTTAGAAGCCCCTC 60.055 47.826 2.95 0.00 36.63 4.30
390 413 2.913617 AGCACTAACTTTAGAAGCCCCT 59.086 45.455 2.95 0.00 36.63 4.79
397 420 9.991906 AACAACTGTAATAGCACTAACTTTAGA 57.008 29.630 2.95 0.00 34.84 2.10
400 423 9.946165 GAAAACAACTGTAATAGCACTAACTTT 57.054 29.630 0.00 0.00 0.00 2.66
421 444 2.301009 TGGAACGGAGGGAGTAGAAAAC 59.699 50.000 0.00 0.00 0.00 2.43
426 449 4.589374 AGATTTATGGAACGGAGGGAGTAG 59.411 45.833 0.00 0.00 0.00 2.57
446 682 4.866508 TGAACTAAGACCACGACAAGAT 57.133 40.909 0.00 0.00 0.00 2.40
471 707 4.675510 TCCGTTCCATAATACTTGTCGTC 58.324 43.478 0.00 0.00 0.00 4.20
551 787 0.323816 TGCAACCCACAAACCACTGA 60.324 50.000 0.00 0.00 0.00 3.41
1055 1370 4.756084 GCTACCAGCATATCAAATGTCC 57.244 45.455 0.00 0.00 41.89 4.02
1213 1528 6.895756 TCCCTCTGTAAAGAACTATAAGAGCA 59.104 38.462 0.00 0.00 0.00 4.26
1223 1538 6.099159 ACAGTTACTCCCTCTGTAAAGAAC 57.901 41.667 0.00 0.00 40.06 3.01
1416 1816 9.522804 CAGCTTTTAAGTGTTAACCAAATGTTA 57.477 29.630 2.48 0.00 38.42 2.41
1417 1817 8.254508 TCAGCTTTTAAGTGTTAACCAAATGTT 58.745 29.630 2.48 0.00 41.11 2.71
1418 1818 7.704899 GTCAGCTTTTAAGTGTTAACCAAATGT 59.295 33.333 2.48 0.00 0.00 2.71
1419 1819 7.096640 CGTCAGCTTTTAAGTGTTAACCAAATG 60.097 37.037 2.48 2.81 0.00 2.32
1420 1820 6.915843 CGTCAGCTTTTAAGTGTTAACCAAAT 59.084 34.615 2.48 0.00 0.00 2.32
1421 1821 6.127952 ACGTCAGCTTTTAAGTGTTAACCAAA 60.128 34.615 2.48 0.00 0.00 3.28
1422 1822 5.354792 ACGTCAGCTTTTAAGTGTTAACCAA 59.645 36.000 2.48 0.00 0.00 3.67
1423 1823 4.877251 ACGTCAGCTTTTAAGTGTTAACCA 59.123 37.500 2.48 0.00 0.00 3.67
1747 3939 3.342719 TGTGCTCAGTGAAAGTGTGAAA 58.657 40.909 0.00 0.00 38.75 2.69
1748 3940 2.984562 TGTGCTCAGTGAAAGTGTGAA 58.015 42.857 0.00 0.00 38.75 3.18
2058 4250 1.366319 AGCAGTCCATCCTCCAACTT 58.634 50.000 0.00 0.00 0.00 2.66
2184 4376 2.581354 GGCGCTGTCCAGATGACT 59.419 61.111 7.64 0.00 44.75 3.41
2268 4460 0.396435 TGTTTCCTGTCAGCGACCAT 59.604 50.000 0.00 0.00 0.00 3.55
2412 4604 8.144478 ACAGACTACATTTGTTATGATAGCGAT 58.856 33.333 0.00 0.00 0.00 4.58
2413 4605 7.489160 ACAGACTACATTTGTTATGATAGCGA 58.511 34.615 0.00 0.00 0.00 4.93
2690 5342 1.446907 GCCGATAGAATGGGATGCAG 58.553 55.000 0.00 0.00 39.76 4.41
2703 5355 3.434053 GGTCTGGTCTAGGCCGATA 57.566 57.895 9.28 0.00 42.30 2.92
2830 5506 1.979693 GCCTCACCTGACGACCTCT 60.980 63.158 0.00 0.00 0.00 3.69
2831 5507 1.816863 TTGCCTCACCTGACGACCTC 61.817 60.000 0.00 0.00 0.00 3.85
2944 5620 3.005791 GCCAAACTATCAGCAAACTTGGT 59.994 43.478 0.00 0.00 39.91 3.67
2969 5645 8.538856 CAGAAGATCGACTATCAAATGAGTTTC 58.461 37.037 0.00 0.00 37.03 2.78
2984 5660 2.233922 TCCCAAGAACCAGAAGATCGAC 59.766 50.000 0.00 0.00 0.00 4.20
3009 5685 6.169419 TGAGACACAAAATCAGCGATTAAG 57.831 37.500 4.60 3.85 31.46 1.85
3012 5688 4.940046 AGATGAGACACAAAATCAGCGATT 59.060 37.500 0.00 0.00 34.64 3.34
3016 5692 5.876612 AGAAGATGAGACACAAAATCAGC 57.123 39.130 0.00 0.00 0.00 4.26
3090 5769 2.103042 GCGCGCAGGTCTGATTTCT 61.103 57.895 29.10 0.00 0.00 2.52
3095 5774 3.058783 TAATCGCGCGCAGGTCTGA 62.059 57.895 32.61 19.20 0.00 3.27
3119 5798 8.567948 ACGATGAAAAATTTGTCTACACAAGAT 58.432 29.630 9.75 0.00 43.54 2.40
3120 5799 7.855409 CACGATGAAAAATTTGTCTACACAAGA 59.145 33.333 9.75 0.00 43.54 3.02
3121 5800 7.357532 GCACGATGAAAAATTTGTCTACACAAG 60.358 37.037 9.75 0.00 43.54 3.16
3122 5801 6.416455 GCACGATGAAAAATTTGTCTACACAA 59.584 34.615 9.75 0.00 40.97 3.33
3123 5802 5.912396 GCACGATGAAAAATTTGTCTACACA 59.088 36.000 9.75 0.00 0.00 3.72
3124 5803 6.142817 AGCACGATGAAAAATTTGTCTACAC 58.857 36.000 9.75 0.00 0.00 2.90
3125 5804 6.312399 AGCACGATGAAAAATTTGTCTACA 57.688 33.333 9.75 0.00 0.00 2.74
3126 5805 7.623268 AAAGCACGATGAAAAATTTGTCTAC 57.377 32.000 9.75 3.28 0.00 2.59
3127 5806 7.806014 GGTAAAGCACGATGAAAAATTTGTCTA 59.194 33.333 9.75 0.00 0.00 2.59
3128 5807 6.640907 GGTAAAGCACGATGAAAAATTTGTCT 59.359 34.615 9.75 0.00 0.00 3.41
3129 5808 6.128929 GGGTAAAGCACGATGAAAAATTTGTC 60.129 38.462 1.01 1.01 0.00 3.18
3130 5809 5.694458 GGGTAAAGCACGATGAAAAATTTGT 59.306 36.000 0.00 0.00 0.00 2.83
3131 5810 5.120053 GGGGTAAAGCACGATGAAAAATTTG 59.880 40.000 0.00 0.00 0.00 2.32
3132 5811 5.011635 AGGGGTAAAGCACGATGAAAAATTT 59.988 36.000 0.00 0.00 0.00 1.82
3133 5812 4.526650 AGGGGTAAAGCACGATGAAAAATT 59.473 37.500 0.00 0.00 0.00 1.82
3134 5813 4.086457 AGGGGTAAAGCACGATGAAAAAT 58.914 39.130 0.00 0.00 0.00 1.82
3135 5814 3.492337 AGGGGTAAAGCACGATGAAAAA 58.508 40.909 0.00 0.00 0.00 1.94
3136 5815 3.149005 AGGGGTAAAGCACGATGAAAA 57.851 42.857 0.00 0.00 0.00 2.29
3137 5816 2.871096 AGGGGTAAAGCACGATGAAA 57.129 45.000 0.00 0.00 0.00 2.69
3138 5817 2.871096 AAGGGGTAAAGCACGATGAA 57.129 45.000 0.00 0.00 0.00 2.57
3139 5818 2.039216 TGAAAGGGGTAAAGCACGATGA 59.961 45.455 0.00 0.00 0.00 2.92
3140 5819 2.432444 TGAAAGGGGTAAAGCACGATG 58.568 47.619 0.00 0.00 0.00 3.84
3141 5820 2.871096 TGAAAGGGGTAAAGCACGAT 57.129 45.000 0.00 0.00 0.00 3.73
3142 5821 2.817258 CAATGAAAGGGGTAAAGCACGA 59.183 45.455 0.00 0.00 0.00 4.35
3143 5822 2.556622 ACAATGAAAGGGGTAAAGCACG 59.443 45.455 0.00 0.00 0.00 5.34
3144 5823 5.715434 TTACAATGAAAGGGGTAAAGCAC 57.285 39.130 0.00 0.00 0.00 4.40
3145 5824 6.732896 TTTTACAATGAAAGGGGTAAAGCA 57.267 33.333 0.00 0.00 37.13 3.91
3146 5825 8.308207 TGTATTTTACAATGAAAGGGGTAAAGC 58.692 33.333 0.00 0.00 37.13 3.51
3147 5826 9.634163 GTGTATTTTACAATGAAAGGGGTAAAG 57.366 33.333 0.00 0.00 40.93 1.85
3148 5827 9.144298 TGTGTATTTTACAATGAAAGGGGTAAA 57.856 29.630 0.00 0.00 40.93 2.01
3149 5828 8.707796 TGTGTATTTTACAATGAAAGGGGTAA 57.292 30.769 0.00 0.00 40.93 2.85
3150 5829 8.707796 TTGTGTATTTTACAATGAAAGGGGTA 57.292 30.769 0.00 0.00 40.93 3.69
3151 5830 7.604657 TTGTGTATTTTACAATGAAAGGGGT 57.395 32.000 0.00 0.00 40.93 4.95
3152 5831 7.117667 GCTTTGTGTATTTTACAATGAAAGGGG 59.882 37.037 0.00 0.00 40.93 4.79
3153 5832 7.872483 AGCTTTGTGTATTTTACAATGAAAGGG 59.128 33.333 0.00 0.00 40.93 3.95
3154 5833 8.816640 AGCTTTGTGTATTTTACAATGAAAGG 57.183 30.769 0.00 0.00 40.93 3.11
3165 5844 9.777297 ATCCATGTTAAAAGCTTTGTGTATTTT 57.223 25.926 13.54 0.00 0.00 1.82
3166 5845 9.777297 AATCCATGTTAAAAGCTTTGTGTATTT 57.223 25.926 13.54 0.00 0.00 1.40
3167 5846 9.423061 GAATCCATGTTAAAAGCTTTGTGTATT 57.577 29.630 13.54 6.00 0.00 1.89
3168 5847 8.584157 TGAATCCATGTTAAAAGCTTTGTGTAT 58.416 29.630 13.54 3.12 0.00 2.29
3169 5848 7.865385 GTGAATCCATGTTAAAAGCTTTGTGTA 59.135 33.333 13.54 0.00 0.00 2.90
3170 5849 6.701400 GTGAATCCATGTTAAAAGCTTTGTGT 59.299 34.615 13.54 0.00 0.00 3.72
3171 5850 6.925165 AGTGAATCCATGTTAAAAGCTTTGTG 59.075 34.615 13.54 7.07 0.00 3.33
3172 5851 7.054491 AGTGAATCCATGTTAAAAGCTTTGT 57.946 32.000 13.54 5.83 0.00 2.83
3173 5852 7.572502 GAGTGAATCCATGTTAAAAGCTTTG 57.427 36.000 13.54 0.00 0.00 2.77
3190 5869 9.829507 CATGAGTTAGATCTTTTAGGAGTGAAT 57.170 33.333 0.00 0.00 0.00 2.57
3191 5870 8.816894 ACATGAGTTAGATCTTTTAGGAGTGAA 58.183 33.333 0.00 0.00 0.00 3.18
3192 5871 8.253810 CACATGAGTTAGATCTTTTAGGAGTGA 58.746 37.037 0.00 0.00 0.00 3.41
3193 5872 7.493971 CCACATGAGTTAGATCTTTTAGGAGTG 59.506 40.741 0.00 3.70 0.00 3.51
3194 5873 7.400339 TCCACATGAGTTAGATCTTTTAGGAGT 59.600 37.037 0.00 0.00 0.00 3.85
3195 5874 7.708752 GTCCACATGAGTTAGATCTTTTAGGAG 59.291 40.741 0.00 0.00 0.00 3.69
3196 5875 7.180229 TGTCCACATGAGTTAGATCTTTTAGGA 59.820 37.037 0.00 0.00 0.00 2.94
3197 5876 7.331026 TGTCCACATGAGTTAGATCTTTTAGG 58.669 38.462 0.00 0.00 0.00 2.69
3198 5877 8.777865 TTGTCCACATGAGTTAGATCTTTTAG 57.222 34.615 0.00 0.00 0.00 1.85
3199 5878 8.999431 GTTTGTCCACATGAGTTAGATCTTTTA 58.001 33.333 0.00 0.00 0.00 1.52
3200 5879 7.721399 AGTTTGTCCACATGAGTTAGATCTTTT 59.279 33.333 0.00 0.00 0.00 2.27
3201 5880 7.227156 AGTTTGTCCACATGAGTTAGATCTTT 58.773 34.615 0.00 0.00 0.00 2.52
3202 5881 6.773638 AGTTTGTCCACATGAGTTAGATCTT 58.226 36.000 0.00 0.00 0.00 2.40
3203 5882 6.365970 AGTTTGTCCACATGAGTTAGATCT 57.634 37.500 0.00 0.00 0.00 2.75
3204 5883 6.428159 ACAAGTTTGTCCACATGAGTTAGATC 59.572 38.462 0.00 0.00 36.50 2.75
3205 5884 6.299141 ACAAGTTTGTCCACATGAGTTAGAT 58.701 36.000 0.00 0.00 36.50 1.98
3206 5885 5.680619 ACAAGTTTGTCCACATGAGTTAGA 58.319 37.500 0.00 0.00 36.50 2.10
3207 5886 6.377327 AACAAGTTTGTCCACATGAGTTAG 57.623 37.500 0.00 0.00 41.31 2.34
3208 5887 7.867305 TTAACAAGTTTGTCCACATGAGTTA 57.133 32.000 0.00 0.00 41.31 2.24
3209 5888 6.767524 TTAACAAGTTTGTCCACATGAGTT 57.232 33.333 0.00 0.00 41.31 3.01
3210 5889 6.767524 TTTAACAAGTTTGTCCACATGAGT 57.232 33.333 0.00 0.00 41.31 3.41
3211 5890 8.647143 AAATTTAACAAGTTTGTCCACATGAG 57.353 30.769 0.00 0.00 41.31 2.90
3212 5891 9.442047 AAAAATTTAACAAGTTTGTCCACATGA 57.558 25.926 0.00 0.00 41.31 3.07
3241 5920 8.612619 GCTGATCCAGTTTATAAGAAAATCGAA 58.387 33.333 0.00 0.00 33.43 3.71
3242 5921 7.226720 GGCTGATCCAGTTTATAAGAAAATCGA 59.773 37.037 0.00 0.00 33.43 3.59
3243 5922 7.227512 AGGCTGATCCAGTTTATAAGAAAATCG 59.772 37.037 0.00 0.00 37.29 3.34
3244 5923 8.457238 AGGCTGATCCAGTTTATAAGAAAATC 57.543 34.615 0.00 0.00 37.29 2.17
3245 5924 8.829373 AAGGCTGATCCAGTTTATAAGAAAAT 57.171 30.769 0.00 0.00 37.29 1.82
3246 5925 8.109634 AGAAGGCTGATCCAGTTTATAAGAAAA 58.890 33.333 0.00 0.00 37.29 2.29
3247 5926 7.554118 CAGAAGGCTGATCCAGTTTATAAGAAA 59.446 37.037 0.00 0.00 45.17 2.52
3248 5927 7.050377 CAGAAGGCTGATCCAGTTTATAAGAA 58.950 38.462 0.00 0.00 45.17 2.52
3249 5928 6.408548 CCAGAAGGCTGATCCAGTTTATAAGA 60.409 42.308 0.00 0.00 45.17 2.10
3250 5929 5.762218 CCAGAAGGCTGATCCAGTTTATAAG 59.238 44.000 0.00 0.00 45.17 1.73
3251 5930 5.684704 CCAGAAGGCTGATCCAGTTTATAA 58.315 41.667 0.00 0.00 45.17 0.98
3252 5931 5.296151 CCAGAAGGCTGATCCAGTTTATA 57.704 43.478 0.00 0.00 45.17 0.98
3253 5932 4.162040 CCAGAAGGCTGATCCAGTTTAT 57.838 45.455 0.00 0.00 45.17 1.40
3254 5933 3.634397 CCAGAAGGCTGATCCAGTTTA 57.366 47.619 0.00 0.00 45.17 2.01
3255 5934 2.503895 CCAGAAGGCTGATCCAGTTT 57.496 50.000 0.00 0.00 45.17 2.66
3267 5946 3.303351 AAGGGTCAATATGCCAGAAGG 57.697 47.619 0.00 0.00 38.23 3.46
3268 5947 5.665916 AAAAAGGGTCAATATGCCAGAAG 57.334 39.130 0.00 0.00 0.00 2.85
3269 5948 6.252995 ACTAAAAAGGGTCAATATGCCAGAA 58.747 36.000 0.00 0.00 0.00 3.02
3270 5949 5.826643 ACTAAAAAGGGTCAATATGCCAGA 58.173 37.500 0.00 0.00 0.00 3.86
3271 5950 7.823745 ATACTAAAAAGGGTCAATATGCCAG 57.176 36.000 0.00 0.00 0.00 4.85
3272 5951 9.875708 AATATACTAAAAAGGGTCAATATGCCA 57.124 29.630 0.00 0.00 0.00 4.92
3278 5957 9.408648 CACCTGAATATACTAAAAAGGGTCAAT 57.591 33.333 0.00 0.00 0.00 2.57
3279 5958 7.832187 CCACCTGAATATACTAAAAAGGGTCAA 59.168 37.037 0.00 0.00 0.00 3.18
3280 5959 7.343357 CCACCTGAATATACTAAAAAGGGTCA 58.657 38.462 0.00 0.00 0.00 4.02
3281 5960 6.771267 CCCACCTGAATATACTAAAAAGGGTC 59.229 42.308 0.00 0.00 0.00 4.46
3282 5961 6.218938 ACCCACCTGAATATACTAAAAAGGGT 59.781 38.462 0.00 0.00 38.39 4.34
3283 5962 6.546034 CACCCACCTGAATATACTAAAAAGGG 59.454 42.308 0.00 0.00 36.17 3.95
3284 5963 7.343357 TCACCCACCTGAATATACTAAAAAGG 58.657 38.462 0.00 0.00 0.00 3.11
3285 5964 8.674607 GTTCACCCACCTGAATATACTAAAAAG 58.325 37.037 0.00 0.00 32.78 2.27
3286 5965 8.387813 AGTTCACCCACCTGAATATACTAAAAA 58.612 33.333 0.00 0.00 32.78 1.94
3287 5966 7.827236 CAGTTCACCCACCTGAATATACTAAAA 59.173 37.037 0.00 0.00 32.78 1.52
3288 5967 7.181305 TCAGTTCACCCACCTGAATATACTAAA 59.819 37.037 0.00 0.00 32.78 1.85
3289 5968 6.670464 TCAGTTCACCCACCTGAATATACTAA 59.330 38.462 0.00 0.00 32.78 2.24
3290 5969 6.199376 TCAGTTCACCCACCTGAATATACTA 58.801 40.000 0.00 0.00 32.78 1.82
3291 5970 5.030147 TCAGTTCACCCACCTGAATATACT 58.970 41.667 0.00 0.00 32.78 2.12
3292 5971 5.353394 TCAGTTCACCCACCTGAATATAC 57.647 43.478 0.00 0.00 32.78 1.47
3293 5972 6.381498 TTTCAGTTCACCCACCTGAATATA 57.619 37.500 0.00 0.00 42.84 0.86
3294 5973 4.927267 TTCAGTTCACCCACCTGAATAT 57.073 40.909 0.00 0.00 39.58 1.28
3295 5974 4.715534 TTTCAGTTCACCCACCTGAATA 57.284 40.909 0.00 0.00 42.84 1.75
3296 5975 3.593442 TTTCAGTTCACCCACCTGAAT 57.407 42.857 0.00 0.00 42.84 2.57
3297 5976 3.287222 CTTTTCAGTTCACCCACCTGAA 58.713 45.455 0.00 0.00 41.95 3.02
3298 5977 2.422803 CCTTTTCAGTTCACCCACCTGA 60.423 50.000 0.00 0.00 33.59 3.86
3299 5978 1.956477 CCTTTTCAGTTCACCCACCTG 59.044 52.381 0.00 0.00 0.00 4.00
3300 5979 1.133482 CCCTTTTCAGTTCACCCACCT 60.133 52.381 0.00 0.00 0.00 4.00
3301 5980 1.328279 CCCTTTTCAGTTCACCCACC 58.672 55.000 0.00 0.00 0.00 4.61
3302 5981 1.328279 CCCCTTTTCAGTTCACCCAC 58.672 55.000 0.00 0.00 0.00 4.61
3303 5982 0.930726 ACCCCTTTTCAGTTCACCCA 59.069 50.000 0.00 0.00 0.00 4.51
3304 5983 1.328279 CACCCCTTTTCAGTTCACCC 58.672 55.000 0.00 0.00 0.00 4.61
3305 5984 0.673985 GCACCCCTTTTCAGTTCACC 59.326 55.000 0.00 0.00 0.00 4.02
3306 5985 1.338020 CTGCACCCCTTTTCAGTTCAC 59.662 52.381 0.00 0.00 0.00 3.18
3307 5986 1.691196 CTGCACCCCTTTTCAGTTCA 58.309 50.000 0.00 0.00 0.00 3.18
3308 5987 0.315251 GCTGCACCCCTTTTCAGTTC 59.685 55.000 0.00 0.00 0.00 3.01
3309 5988 1.455383 CGCTGCACCCCTTTTCAGTT 61.455 55.000 0.00 0.00 0.00 3.16
3310 5989 1.898574 CGCTGCACCCCTTTTCAGT 60.899 57.895 0.00 0.00 0.00 3.41
3311 5990 2.956987 CGCTGCACCCCTTTTCAG 59.043 61.111 0.00 0.00 0.00 3.02
3312 5991 3.294493 GCGCTGCACCCCTTTTCA 61.294 61.111 0.00 0.00 0.00 2.69
3313 5992 4.404654 CGCGCTGCACCCCTTTTC 62.405 66.667 5.56 0.00 0.00 2.29
3335 6014 2.596553 TAAATGGCGCGGGGGTAGTG 62.597 60.000 8.83 0.00 0.00 2.74
3336 6015 2.319890 CTAAATGGCGCGGGGGTAGT 62.320 60.000 8.83 0.00 0.00 2.73
3337 6016 1.597027 CTAAATGGCGCGGGGGTAG 60.597 63.158 8.83 0.00 0.00 3.18
3338 6017 2.506962 CTAAATGGCGCGGGGGTA 59.493 61.111 8.83 0.00 0.00 3.69
3339 6018 4.499633 CCTAAATGGCGCGGGGGT 62.500 66.667 8.83 0.00 0.00 4.95
3363 6042 4.431131 ATCCAGCCCCGCACAAGG 62.431 66.667 0.00 0.00 0.00 3.61
3364 6043 3.136123 CATCCAGCCCCGCACAAG 61.136 66.667 0.00 0.00 0.00 3.16
3374 6053 2.037847 AAACAGGGGGCATCCAGC 59.962 61.111 0.00 0.00 44.65 4.85
3375 6054 0.040204 AAGAAACAGGGGGCATCCAG 59.960 55.000 0.00 0.00 37.22 3.86
3376 6055 0.486879 AAAGAAACAGGGGGCATCCA 59.513 50.000 0.00 0.00 37.22 3.41
3377 6056 1.644509 AAAAGAAACAGGGGGCATCC 58.355 50.000 0.00 0.00 0.00 3.51
3395 6074 9.937175 AAAAACAAGACAAAACGAATTGAAAAA 57.063 22.222 10.96 0.00 34.38 1.94
3450 6129 9.725019 GAAACCTTTTGAATTCCCAAGATATTT 57.275 29.630 13.03 10.50 0.00 1.40
3451 6130 8.879227 TGAAACCTTTTGAATTCCCAAGATATT 58.121 29.630 13.03 6.74 0.00 1.28
3452 6131 8.434589 TGAAACCTTTTGAATTCCCAAGATAT 57.565 30.769 13.03 1.97 0.00 1.63
3453 6132 7.847711 TGAAACCTTTTGAATTCCCAAGATA 57.152 32.000 13.03 0.00 0.00 1.98
3454 6133 6.745794 TGAAACCTTTTGAATTCCCAAGAT 57.254 33.333 13.03 0.00 0.00 2.40
3455 6134 6.552445 TTGAAACCTTTTGAATTCCCAAGA 57.448 33.333 13.03 0.00 0.00 3.02
3456 6135 7.806409 ATTTGAAACCTTTTGAATTCCCAAG 57.194 32.000 2.27 4.99 0.00 3.61
3457 6136 9.859152 AATATTTGAAACCTTTTGAATTCCCAA 57.141 25.926 2.27 0.00 0.00 4.12
3458 6137 9.282569 CAATATTTGAAACCTTTTGAATTCCCA 57.717 29.630 2.27 0.00 0.00 4.37
3459 6138 9.500785 TCAATATTTGAAACCTTTTGAATTCCC 57.499 29.630 2.27 0.00 36.59 3.97
3510 6189 9.123902 TCCACGATCATTTATGATTTCTTGATT 57.876 29.630 6.67 0.00 46.84 2.57
3511 6190 8.681486 TCCACGATCATTTATGATTTCTTGAT 57.319 30.769 6.67 0.00 46.84 2.57
3512 6191 8.681486 ATCCACGATCATTTATGATTTCTTGA 57.319 30.769 6.67 2.35 46.84 3.02
3513 6192 9.390795 GAATCCACGATCATTTATGATTTCTTG 57.609 33.333 6.67 1.07 46.84 3.02
3514 6193 9.123902 TGAATCCACGATCATTTATGATTTCTT 57.876 29.630 6.67 0.00 46.84 2.52
3515 6194 8.681486 TGAATCCACGATCATTTATGATTTCT 57.319 30.769 6.67 0.00 46.84 2.52
3516 6195 9.734620 TTTGAATCCACGATCATTTATGATTTC 57.265 29.630 6.67 6.25 46.84 2.17
3546 6225 9.950680 TGCAAACTTTTTAAAAATCACAAACAA 57.049 22.222 13.55 0.00 0.00 2.83
3599 6278 7.986889 ACATTTGTTACCTTTCAGAGCATTTTT 59.013 29.630 0.00 0.00 0.00 1.94
3600 6279 7.500141 ACATTTGTTACCTTTCAGAGCATTTT 58.500 30.769 0.00 0.00 0.00 1.82
3601 6280 7.054491 ACATTTGTTACCTTTCAGAGCATTT 57.946 32.000 0.00 0.00 0.00 2.32
3602 6281 6.655078 ACATTTGTTACCTTTCAGAGCATT 57.345 33.333 0.00 0.00 0.00 3.56
3603 6282 6.655078 AACATTTGTTACCTTTCAGAGCAT 57.345 33.333 0.00 0.00 36.32 3.79
3604 6283 7.575414 TTAACATTTGTTACCTTTCAGAGCA 57.425 32.000 2.71 0.00 39.92 4.26
3605 6284 8.865590 TTTTAACATTTGTTACCTTTCAGAGC 57.134 30.769 2.71 0.00 39.92 4.09


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

AutoCloner maintained by Alex Coulton.