Multiple sequence alignment - TraesCS6B01G037400

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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 TraesCS6B01G037400 chr6B 100.000 4367 0 0 1 4367 21908509 21912875 0.000000e+00 8065.0
1 TraesCS6B01G037400 chr6B 77.795 1914 284 74 1700 3580 21923035 21924840 0.000000e+00 1050.0
2 TraesCS6B01G037400 chr6D 87.080 3034 314 34 219 3228 12021357 12024336 0.000000e+00 3360.0
3 TraesCS6B01G037400 chr6D 78.636 2874 450 93 973 3794 12061447 12064208 0.000000e+00 1755.0
4 TraesCS6B01G037400 chr6D 89.665 1016 86 10 3358 4367 12024335 12025337 0.000000e+00 1277.0
5 TraesCS6B01G037400 chr6D 75.562 712 131 24 2338 3030 12017665 12018352 1.180000e-80 311.0
6 TraesCS6B01G037400 chr6A 84.354 1470 192 23 2753 4210 13453884 13455327 0.000000e+00 1406.0
7 TraesCS6B01G037400 chr6A 81.527 1218 179 19 1426 2626 13451996 13453184 0.000000e+00 961.0
8 TraesCS6B01G037400 chr6A 85.055 542 52 18 598 1127 13451395 13451919 3.870000e-145 525.0
9 TraesCS6B01G037400 chr6A 84.140 372 42 11 219 585 13449877 13450236 1.160000e-90 344.0
10 TraesCS6B01G037400 chr6A 76.053 380 71 11 2432 2796 13439381 13439755 3.470000e-41 180.0
11 TraesCS6B01G037400 chrUn 92.655 177 12 1 3516 3691 406224551 406224727 2.020000e-63 254.0
12 TraesCS6B01G037400 chrUn 92.655 177 11 2 3516 3691 432962630 432962805 2.020000e-63 254.0
13 TraesCS6B01G037400 chrUn 92.090 177 12 2 3516 3691 429254288 429254463 9.380000e-62 248.0
14 TraesCS6B01G037400 chr7B 92.655 177 11 2 3516 3691 662739555 662739730 2.020000e-63 254.0
15 TraesCS6B01G037400 chr5D 92.222 180 12 2 3516 3694 365229567 365229389 2.020000e-63 254.0
16 TraesCS6B01G037400 chr5D 92.222 180 12 2 3516 3694 503328774 503328596 2.020000e-63 254.0
17 TraesCS6B01G037400 chr5D 100.000 62 0 0 1 62 52574151 52574212 9.920000e-22 115.0
18 TraesCS6B01G037400 chr2D 92.222 180 12 2 3516 3694 630265135 630264957 2.020000e-63 254.0
19 TraesCS6B01G037400 chr2D 98.413 63 1 0 1 63 669741 669679 1.280000e-20 111.0
20 TraesCS6B01G037400 chr2D 98.413 63 1 0 1 63 81465981 81465919 1.280000e-20 111.0
21 TraesCS6B01G037400 chr2A 93.252 163 11 0 59 221 746254780 746254942 1.570000e-59 241.0
22 TraesCS6B01G037400 chr5B 93.168 161 11 0 60 220 425075921 425076081 2.030000e-58 237.0
23 TraesCS6B01G037400 chr5B 93.168 161 11 0 60 220 474640793 474640953 2.030000e-58 237.0
24 TraesCS6B01G037400 chr5B 98.413 63 1 0 1 63 569413799 569413737 1.280000e-20 111.0
25 TraesCS6B01G037400 chr1B 93.168 161 11 0 60 220 149248969 149249129 2.030000e-58 237.0
26 TraesCS6B01G037400 chr1B 93.168 161 11 0 60 220 151922885 151922725 2.030000e-58 237.0
27 TraesCS6B01G037400 chr1B 93.168 161 11 0 60 220 660399417 660399577 2.030000e-58 237.0
28 TraesCS6B01G037400 chr1B 90.909 176 13 2 60 235 24349053 24349225 2.630000e-57 233.0
29 TraesCS6B01G037400 chr1B 91.279 172 14 1 60 230 618752711 618752540 2.630000e-57 233.0
30 TraesCS6B01G037400 chr4B 91.176 170 15 0 60 229 372049001 372048832 9.450000e-57 231.0
31 TraesCS6B01G037400 chr4B 100.000 60 0 0 1 60 653225584 653225643 1.280000e-20 111.0
32 TraesCS6B01G037400 chr5A 98.413 63 1 0 1 63 493659315 493659253 1.280000e-20 111.0
33 TraesCS6B01G037400 chr3D 98.413 63 1 0 1 63 35256697 35256759 1.280000e-20 111.0
34 TraesCS6B01G037400 chr1D 98.413 63 1 0 1 63 379779958 379779896 1.280000e-20 111.0
35 TraesCS6B01G037400 chr1D 77.465 142 24 6 4070 4210 350596686 350596820 1.300000e-10 78.7
36 TraesCS6B01G037400 chr1A 98.413 63 1 0 1 63 497204985 497204923 1.280000e-20 111.0


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 TraesCS6B01G037400 chr6B 21908509 21912875 4366 False 8065.000000 8065 100.000000 1 4367 1 chr6B.!!$F1 4366
1 TraesCS6B01G037400 chr6B 21923035 21924840 1805 False 1050.000000 1050 77.795000 1700 3580 1 chr6B.!!$F2 1880
2 TraesCS6B01G037400 chr6D 12061447 12064208 2761 False 1755.000000 1755 78.636000 973 3794 1 chr6D.!!$F1 2821
3 TraesCS6B01G037400 chr6D 12017665 12025337 7672 False 1649.333333 3360 84.102333 219 4367 3 chr6D.!!$F2 4148
4 TraesCS6B01G037400 chr6A 13449877 13455327 5450 False 809.000000 1406 83.769000 219 4210 4 chr6A.!!$F2 3991

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
887 5518 0.034186 TCCCCGCAGCAGAATGATTT 60.034 50.0 0.0 0.0 39.69 2.17 F
1856 6503 0.179113 CTGTTTGCCTTTGTTGCCGT 60.179 50.0 0.0 0.0 0.00 5.68 F
1991 6638 0.188342 ACTTGCAACACCTGGGGAAT 59.812 50.0 1.1 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2063 6710 0.034767 CTCTGTGTGCCCATCACCAT 60.035 55.0 0.00 0.0 45.03 3.55 R
2900 8163 0.037734 GGAACCTTGACCCGGATTGT 59.962 55.0 0.73 0.0 0.00 2.71 R
3389 8655 0.170339 GTAACCATGCTTTCACCGCC 59.830 55.0 0.00 0.0 0.00 6.13 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
17 18 2.418356 TTGGTCGTGTGTCCCGTC 59.582 61.111 0.00 0.00 0.00 4.79
18 19 2.129146 TTGGTCGTGTGTCCCGTCT 61.129 57.895 0.00 0.00 0.00 4.18
20 21 1.068585 GGTCGTGTGTCCCGTCTTT 59.931 57.895 0.00 0.00 0.00 2.52
22 23 0.857287 GTCGTGTGTCCCGTCTTTTC 59.143 55.000 0.00 0.00 0.00 2.29
25 26 0.942252 GTGTGTCCCGTCTTTTCCAC 59.058 55.000 0.00 0.00 0.00 4.02
33 34 0.794473 CGTCTTTTCCACGGTTAGCC 59.206 55.000 0.00 0.00 33.46 3.93
34 35 1.162698 GTCTTTTCCACGGTTAGCCC 58.837 55.000 0.00 0.00 0.00 5.19
51 52 3.437795 CGGGCCTTGCTGCTCTTG 61.438 66.667 0.84 0.00 0.00 3.02
52 53 3.066814 GGGCCTTGCTGCTCTTGG 61.067 66.667 0.84 0.00 0.00 3.61
53 54 3.756727 GGCCTTGCTGCTCTTGGC 61.757 66.667 14.01 14.01 42.56 4.52
61 62 4.585070 TGCTCTTGGCAGCAAACT 57.415 50.000 0.00 0.00 46.65 2.66
62 63 2.334307 TGCTCTTGGCAGCAAACTC 58.666 52.632 0.00 0.00 46.65 3.01
63 64 1.174712 TGCTCTTGGCAGCAAACTCC 61.175 55.000 0.00 0.00 46.65 3.85
64 65 1.871126 GCTCTTGGCAGCAAACTCCC 61.871 60.000 0.00 0.00 39.43 4.30
65 66 0.251077 CTCTTGGCAGCAAACTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
66 67 0.250901 TCTTGGCAGCAAACTCCCTC 60.251 55.000 0.00 0.00 0.00 4.30
67 68 1.228552 TTGGCAGCAAACTCCCTCC 60.229 57.895 0.00 0.00 0.00 4.30
68 69 2.747855 GGCAGCAAACTCCCTCCG 60.748 66.667 0.00 0.00 0.00 4.63
69 70 2.032681 GCAGCAAACTCCCTCCGT 59.967 61.111 0.00 0.00 0.00 4.69
70 71 1.600916 GCAGCAAACTCCCTCCGTT 60.601 57.895 0.00 0.00 0.00 4.44
71 72 1.578206 GCAGCAAACTCCCTCCGTTC 61.578 60.000 0.00 0.00 0.00 3.95
72 73 0.955919 CAGCAAACTCCCTCCGTTCC 60.956 60.000 0.00 0.00 0.00 3.62
75 76 1.975660 CAAACTCCCTCCGTTCCAAA 58.024 50.000 0.00 0.00 0.00 3.28
78 79 4.076394 CAAACTCCCTCCGTTCCAAAATA 58.924 43.478 0.00 0.00 0.00 1.40
80 81 5.703730 AACTCCCTCCGTTCCAAAATATA 57.296 39.130 0.00 0.00 0.00 0.86
81 82 5.906772 ACTCCCTCCGTTCCAAAATATAT 57.093 39.130 0.00 0.00 0.00 0.86
82 83 5.621193 ACTCCCTCCGTTCCAAAATATATG 58.379 41.667 0.00 0.00 0.00 1.78
83 84 4.980573 TCCCTCCGTTCCAAAATATATGG 58.019 43.478 1.78 1.78 39.41 2.74
84 85 3.506067 CCCTCCGTTCCAAAATATATGGC 59.494 47.826 3.13 0.00 37.88 4.40
85 86 4.398319 CCTCCGTTCCAAAATATATGGCT 58.602 43.478 3.13 0.00 37.88 4.75
86 87 4.827284 CCTCCGTTCCAAAATATATGGCTT 59.173 41.667 3.13 0.00 37.88 4.35
87 88 5.048713 CCTCCGTTCCAAAATATATGGCTTC 60.049 44.000 3.13 0.00 37.88 3.86
88 89 5.690865 TCCGTTCCAAAATATATGGCTTCT 58.309 37.500 3.13 0.00 37.88 2.85
89 90 6.126409 TCCGTTCCAAAATATATGGCTTCTT 58.874 36.000 3.13 0.00 37.88 2.52
91 92 7.444183 TCCGTTCCAAAATATATGGCTTCTTAG 59.556 37.037 3.13 0.00 37.88 2.18
92 93 7.444183 CCGTTCCAAAATATATGGCTTCTTAGA 59.556 37.037 3.13 0.00 37.88 2.10
93 94 8.499162 CGTTCCAAAATATATGGCTTCTTAGAG 58.501 37.037 3.13 0.00 37.88 2.43
104 105 9.941325 ATATGGCTTCTTAGAGATTTCACTATG 57.059 33.333 0.00 0.00 0.00 2.23
106 107 7.851228 TGGCTTCTTAGAGATTTCACTATGAA 58.149 34.615 10.61 10.61 34.57 2.57
107 108 7.766278 TGGCTTCTTAGAGATTTCACTATGAAC 59.234 37.037 8.34 6.82 35.89 3.18
116 117 8.353684 AGAGATTTCACTATGAACTACATACGG 58.646 37.037 0.00 0.00 35.89 4.02
118 119 8.353684 AGATTTCACTATGAACTACATACGGAG 58.646 37.037 0.00 0.00 35.89 4.63
119 120 5.434352 TCACTATGAACTACATACGGAGC 57.566 43.478 0.00 0.00 40.07 4.70
120 121 4.885325 TCACTATGAACTACATACGGAGCA 59.115 41.667 0.00 0.00 40.07 4.26
121 122 5.358725 TCACTATGAACTACATACGGAGCAA 59.641 40.000 0.00 0.00 40.07 3.91
122 123 6.040247 CACTATGAACTACATACGGAGCAAA 58.960 40.000 0.00 0.00 40.07 3.68
123 124 6.533723 CACTATGAACTACATACGGAGCAAAA 59.466 38.462 0.00 0.00 40.07 2.44
125 126 5.794687 TGAACTACATACGGAGCAAAATG 57.205 39.130 0.00 0.00 0.00 2.32
126 127 5.483811 TGAACTACATACGGAGCAAAATGA 58.516 37.500 0.00 0.00 0.00 2.57
127 128 5.580691 TGAACTACATACGGAGCAAAATGAG 59.419 40.000 0.00 0.00 0.00 2.90
128 129 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
129 130 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
130 131 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
131 132 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
132 133 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
133 134 3.837213 ACGGAGCAAAATGAGTGAATG 57.163 42.857 0.00 0.00 0.00 2.67
134 135 3.149196 ACGGAGCAAAATGAGTGAATGT 58.851 40.909 0.00 0.00 0.00 2.71
135 136 4.323417 ACGGAGCAAAATGAGTGAATGTA 58.677 39.130 0.00 0.00 0.00 2.29
136 137 4.154195 ACGGAGCAAAATGAGTGAATGTAC 59.846 41.667 0.00 0.00 0.00 2.90
183 184 9.959721 ACATCCTTATGTAGTTTGTAGTGAAAT 57.040 29.630 0.00 0.00 44.66 2.17
186 187 9.871238 TCCTTATGTAGTTTGTAGTGAAATCTC 57.129 33.333 0.00 0.00 0.00 2.75
214 215 8.543862 AAAAGACTTACATTTAGTAACGGAGG 57.456 34.615 0.00 0.00 37.77 4.30
216 217 5.954150 AGACTTACATTTAGTAACGGAGGGA 59.046 40.000 0.00 0.00 37.77 4.20
217 218 6.096564 AGACTTACATTTAGTAACGGAGGGAG 59.903 42.308 0.00 0.00 37.77 4.30
255 3730 4.207635 GGTGCAATTAATCATGCGTCATTG 59.792 41.667 7.45 0.00 45.47 2.82
264 3739 2.884146 TGCGTCATTGCACAAAAGC 58.116 47.368 0.00 0.00 40.62 3.51
295 3770 3.263681 GCAACCCTACCTTCCTTTACTCT 59.736 47.826 0.00 0.00 0.00 3.24
297 3772 3.451890 ACCCTACCTTCCTTTACTCTGG 58.548 50.000 0.00 0.00 0.00 3.86
302 3779 5.663556 CCTACCTTCCTTTACTCTGGAATCT 59.336 44.000 0.00 0.00 40.98 2.40
370 3849 6.252967 TGAAATCATAAAAGATGTGCGTGT 57.747 33.333 0.00 0.00 0.00 4.49
372 3851 3.469899 TCATAAAAGATGTGCGTGTGC 57.530 42.857 0.00 0.00 43.20 4.57
392 3871 2.755650 CACCACTTTGCTACTTCGAGT 58.244 47.619 0.00 0.00 0.00 4.18
398 3877 5.435557 CACTTTGCTACTTCGAGTGAAAAG 58.564 41.667 0.00 7.50 39.97 2.27
402 3881 6.671614 TTGCTACTTCGAGTGAAAAGAAAA 57.328 33.333 0.00 0.00 32.66 2.29
425 3904 1.594293 AACACCCACGACGCTTCTG 60.594 57.895 0.00 0.00 0.00 3.02
457 3936 4.269603 CCTAAATCTCTGAACACATGAGCG 59.730 45.833 0.00 0.00 0.00 5.03
466 3945 0.036164 ACACATGAGCGCCCTTGTAA 59.964 50.000 10.08 0.00 0.00 2.41
467 3946 1.164411 CACATGAGCGCCCTTGTAAA 58.836 50.000 10.08 0.00 0.00 2.01
474 3953 4.800784 TGAGCGCCCTTGTAAAATTAAAC 58.199 39.130 2.29 0.00 0.00 2.01
479 3958 5.692654 GCGCCCTTGTAAAATTAAACTTCAA 59.307 36.000 0.00 0.00 0.00 2.69
501 3980 3.406595 CTCGGCCAGGTCCCAATCC 62.407 68.421 2.24 0.00 0.00 3.01
558 4037 4.441695 TCCTGCTTCGGCTGCTCG 62.442 66.667 0.00 1.60 42.37 5.03
576 4055 0.868406 CGAGCTTTTGAGTCCCACAC 59.132 55.000 0.00 0.00 0.00 3.82
637 5262 2.167281 TCTCTTCTTCTTGGATCAGCGG 59.833 50.000 0.00 0.00 0.00 5.52
700 5325 1.837439 CATTGGCCACCTAGGTAGTGA 59.163 52.381 15.80 0.12 40.61 3.41
701 5326 2.032965 TTGGCCACCTAGGTAGTGAA 57.967 50.000 15.80 2.77 40.61 3.18
731 5358 6.430000 AGTGATAAAATACTTTGGTTGTCGCT 59.570 34.615 0.00 0.00 0.00 4.93
796 5423 4.478203 TCCAGGAAATTGTCATGAAACCA 58.522 39.130 0.00 0.00 40.61 3.67
797 5424 4.523943 TCCAGGAAATTGTCATGAAACCAG 59.476 41.667 0.00 0.00 40.61 4.00
811 5438 3.774528 CCAGAGCCCGCTACTGCA 61.775 66.667 9.36 0.00 39.64 4.41
828 5455 2.167219 CAACGGCGACAGCGATGAT 61.167 57.895 16.62 0.00 46.35 2.45
832 5459 2.587194 GCGACAGCGATGATGGCT 60.587 61.111 8.12 0.00 42.61 4.75
878 5505 0.038166 AGAAATTTCTCCCCGCAGCA 59.962 50.000 15.11 0.00 29.94 4.41
887 5518 0.034186 TCCCCGCAGCAGAATGATTT 60.034 50.000 0.00 0.00 39.69 2.17
904 5535 9.525826 AGAATGATTTATCTTATTCCCCATCAC 57.474 33.333 0.00 0.00 31.56 3.06
964 5599 1.060713 CTAGAGTGACGCACCAAACG 58.939 55.000 6.39 0.00 34.49 3.60
970 5605 1.263217 GTGACGCACCAAACGAAGAAT 59.737 47.619 0.00 0.00 0.00 2.40
980 5619 0.323629 AACGAAGAATCAAGCCCGGA 59.676 50.000 0.73 0.00 0.00 5.14
982 5621 1.065418 ACGAAGAATCAAGCCCGGAAT 60.065 47.619 0.73 0.00 0.00 3.01
1024 5666 0.462375 CATTGGTGTCGATCGGGGTA 59.538 55.000 16.41 0.00 0.00 3.69
1025 5667 0.462789 ATTGGTGTCGATCGGGGTAC 59.537 55.000 16.41 6.49 0.00 3.34
1114 5756 1.536418 TGTGTGCTACTCCTGGCCT 60.536 57.895 3.32 0.00 0.00 5.19
1128 5770 3.813596 GCCTACTTCACGGCCATG 58.186 61.111 2.24 0.00 40.43 3.66
1222 5864 1.242076 GGTGTTCATCTGCTGCAACT 58.758 50.000 3.02 0.00 0.00 3.16
1226 5868 2.089980 GTTCATCTGCTGCAACTCCAT 58.910 47.619 3.02 0.00 0.00 3.41
1264 5906 1.480954 GGTTCATTCTCCTACGGCTCA 59.519 52.381 0.00 0.00 0.00 4.26
1266 5908 3.432326 GGTTCATTCTCCTACGGCTCAAT 60.432 47.826 0.00 0.00 0.00 2.57
1301 5943 1.164313 ACCCGGGGGATGAGATACTA 58.836 55.000 27.92 0.00 38.96 1.82
1303 5945 2.111384 CCCGGGGGATGAGATACTATG 58.889 57.143 14.71 0.00 37.50 2.23
1312 5954 5.477510 GGATGAGATACTATGACTTGCAGG 58.522 45.833 0.00 0.00 0.00 4.85
1356 5998 1.344763 GGTCTGATTGGCGCCTATAGT 59.655 52.381 29.70 4.81 0.00 2.12
1366 6008 2.049063 CCTATAGTGCCGCGAGCC 60.049 66.667 8.23 3.87 42.71 4.70
1424 6066 1.630148 GTACTGCTCTACGTTGCCAG 58.370 55.000 12.94 12.94 0.00 4.85
1483 6125 1.296715 CTCCCCCACGTGGAAGAAG 59.703 63.158 36.07 21.31 37.39 2.85
1524 6166 1.726853 AATTCCAGAAGCGAGTTCGG 58.273 50.000 3.50 0.00 40.49 4.30
1556 6198 7.414098 GCAAACTATGGTAGTATCAACACAAGG 60.414 40.741 0.00 0.00 38.26 3.61
1569 6211 2.851195 ACACAAGGCAAAGTCGAAGAT 58.149 42.857 0.00 0.00 40.67 2.40
1579 6221 2.103042 GTCGAAGATGCTGCCGCTT 61.103 57.895 0.70 0.00 40.67 4.68
1586 6228 0.455633 GATGCTGCCGCTTTCAAGTG 60.456 55.000 0.70 0.00 36.97 3.16
1591 6233 0.463654 TGCCGCTTTCAAGTGTCTGT 60.464 50.000 0.00 0.00 34.79 3.41
1600 6242 5.470098 GCTTTCAAGTGTCTGTTTCTATCCA 59.530 40.000 0.00 0.00 0.00 3.41
1606 6248 6.155475 AGTGTCTGTTTCTATCCATAGCTC 57.845 41.667 0.00 0.00 0.00 4.09
1629 6271 0.601046 CCACGAGTATGGCATGCGAT 60.601 55.000 19.51 19.51 31.52 4.58
1641 6283 1.268234 GCATGCGATGTTAGAGTTGGC 60.268 52.381 0.00 0.00 0.00 4.52
1684 6331 4.082523 ACCTGGACACCGGCATCG 62.083 66.667 0.00 0.00 0.00 3.84
1768 6415 4.679106 CGCTGATGTTCATTCACCTCTACT 60.679 45.833 0.00 0.00 0.00 2.57
1773 6420 6.667848 TGATGTTCATTCACCTCTACTTCCTA 59.332 38.462 0.00 0.00 0.00 2.94
1796 6443 2.224606 CAGGTCTTTCAGCAAGCAGAA 58.775 47.619 0.00 0.00 31.70 3.02
1803 6450 6.294176 GGTCTTTCAGCAAGCAGAAAATCTTA 60.294 38.462 12.58 0.00 32.52 2.10
1822 6469 1.826340 ATACCGTGCACTGCAGGTCA 61.826 55.000 19.93 12.30 41.98 4.02
1853 6500 1.136891 AGACCTGTTTGCCTTTGTTGC 59.863 47.619 0.00 0.00 0.00 4.17
1856 6503 0.179113 CTGTTTGCCTTTGTTGCCGT 60.179 50.000 0.00 0.00 0.00 5.68
1867 6514 4.143333 TTGCCGTCTCCGCTAGCC 62.143 66.667 9.66 0.00 0.00 3.93
1970 6617 4.321974 GGTTTCCATGTCAGAAATGTTCCC 60.322 45.833 0.00 0.00 35.77 3.97
1979 6626 2.293122 CAGAAATGTTCCCGACTTGCAA 59.707 45.455 0.00 0.00 0.00 4.08
1987 6634 2.260869 CCGACTTGCAACACCTGGG 61.261 63.158 0.00 0.00 0.00 4.45
1991 6638 0.188342 ACTTGCAACACCTGGGGAAT 59.812 50.000 1.10 0.00 0.00 3.01
1995 6642 1.427368 TGCAACACCTGGGGAATAGTT 59.573 47.619 1.10 0.00 0.00 2.24
1999 6646 2.525368 ACACCTGGGGAATAGTTTTGC 58.475 47.619 1.10 0.00 0.00 3.68
2012 6659 1.351017 AGTTTTGCGGGAGAAGATGGA 59.649 47.619 0.00 0.00 0.00 3.41
2060 6707 2.608752 CCAAGTCATTTGAGCTGCCAAC 60.609 50.000 0.00 0.00 39.21 3.77
2061 6708 2.283145 AGTCATTTGAGCTGCCAACT 57.717 45.000 0.00 0.00 0.00 3.16
2062 6709 1.884579 AGTCATTTGAGCTGCCAACTG 59.115 47.619 0.00 11.94 0.00 3.16
2063 6710 1.881973 GTCATTTGAGCTGCCAACTGA 59.118 47.619 14.90 14.90 34.67 3.41
2064 6711 2.490903 GTCATTTGAGCTGCCAACTGAT 59.509 45.455 18.92 4.81 37.80 2.90
2065 6712 2.490509 TCATTTGAGCTGCCAACTGATG 59.509 45.455 14.90 11.02 32.94 3.07
2118 6765 0.258774 CGGGGTGGAATTTGGAGGAT 59.741 55.000 0.00 0.00 0.00 3.24
2129 6776 2.910688 TTGGAGGATTATCGCCAGTC 57.089 50.000 5.76 0.00 0.00 3.51
2201 6860 2.741228 GCATGAGCCTCTCACAGTTAGG 60.741 54.545 0.00 0.00 43.63 2.69
2230 6889 3.654021 TCCTTGTGGTGGACAGCA 58.346 55.556 0.00 0.00 35.44 4.41
2262 6921 8.335532 TCCACTTGAATGAGTTTTATGTAAGG 57.664 34.615 0.00 0.00 0.00 2.69
2278 6937 1.064825 AAGGAACCTCACGGACCAAT 58.935 50.000 0.00 0.00 34.53 3.16
2301 6960 2.764572 CGGTATTAGTTCCCTGTCCAGT 59.235 50.000 0.00 0.00 0.00 4.00
2327 6998 3.137533 GGCAAGAGAATACATCAGGCTC 58.862 50.000 0.00 0.00 0.00 4.70
2407 7084 1.811266 ATCGTGCTGCTGGCTAACG 60.811 57.895 0.00 1.02 40.28 3.18
2408 7085 2.432456 CGTGCTGCTGGCTAACGA 60.432 61.111 0.00 0.00 41.04 3.85
2422 7099 3.490078 GGCTAACGAGAAGATCTGGTCAG 60.490 52.174 0.00 0.00 34.27 3.51
2423 7100 3.378742 GCTAACGAGAAGATCTGGTCAGA 59.621 47.826 0.00 2.93 34.27 3.27
2448 7125 4.260907 GGAATACAGTACTACGTCATGCGA 60.261 45.833 14.88 0.72 44.77 5.10
2474 7151 2.008329 CATGGTTCTTCAGCTGCTCTC 58.992 52.381 9.47 0.00 0.00 3.20
2477 7154 1.675415 GGTTCTTCAGCTGCTCTCCTG 60.675 57.143 9.47 0.00 0.00 3.86
2483 7160 4.385405 GCTGCTCTCCTGCGTGGT 62.385 66.667 0.00 0.00 37.07 4.16
2586 7276 8.972662 TGATTATATTATCAAGAGGTCCCAGA 57.027 34.615 1.94 0.00 31.82 3.86
2587 7277 9.392506 TGATTATATTATCAAGAGGTCCCAGAA 57.607 33.333 1.94 0.00 31.82 3.02
2591 7281 3.990959 ATCAAGAGGTCCCAGAAAGAC 57.009 47.619 0.00 0.00 0.00 3.01
2626 7316 1.690893 TCAGATGGCTCCAGCATACTC 59.309 52.381 6.95 0.00 44.36 2.59
2698 7394 1.965930 GCAGATGGTGGCACGAACA 60.966 57.895 12.17 4.41 0.00 3.18
2709 7410 2.283388 ACGAACAGGGAGCCCGTA 60.283 61.111 0.00 0.00 41.95 4.02
2805 8068 1.191535 CCAGTCCGGTGAAGATGGTA 58.808 55.000 0.00 0.00 0.00 3.25
2809 8072 1.822990 GTCCGGTGAAGATGGTACTGA 59.177 52.381 0.00 0.00 0.00 3.41
2822 8085 5.643777 AGATGGTACTGACATTCTTTTTCGG 59.356 40.000 0.00 0.00 0.00 4.30
2844 8107 0.980423 TAATTGGGGCCAACCTTTGC 59.020 50.000 4.39 0.00 38.88 3.68
2877 8140 1.298859 CCCGTTTACTGCAGGTGCTC 61.299 60.000 19.93 3.53 42.66 4.26
2883 8146 4.383861 CTGCAGGTGCTCGCCAGA 62.384 66.667 5.57 0.00 42.66 3.86
2900 8163 1.885233 CAGAGCTCTCTATCATCGGCA 59.115 52.381 14.96 0.00 37.98 5.69
2904 8167 2.632028 AGCTCTCTATCATCGGCACAAT 59.368 45.455 0.00 0.00 0.00 2.71
2920 8183 0.037590 CAATCCGGGTCAAGGTTCCA 59.962 55.000 0.00 0.00 0.00 3.53
2935 8198 2.594303 CCACGCCAACTGCCTTCA 60.594 61.111 0.00 0.00 36.24 3.02
2936 8199 2.192861 CCACGCCAACTGCCTTCAA 61.193 57.895 0.00 0.00 36.24 2.69
2946 8209 3.423154 GCCTTCAACGCCACCTCG 61.423 66.667 0.00 0.00 0.00 4.63
3003 8266 0.242017 GCAATGGACTGTGCAAGGTC 59.758 55.000 5.98 10.69 40.58 3.85
3100 8363 3.055240 CCTCAAGCTGAAGGTCAAGATCT 60.055 47.826 6.50 0.00 0.00 2.75
3121 8384 4.106502 TCTCCAGTATATCAGCCCTAGTGT 59.893 45.833 0.00 0.00 0.00 3.55
3123 8386 3.306364 CCAGTATATCAGCCCTAGTGTGC 60.306 52.174 0.00 0.00 0.00 4.57
3147 8410 2.153645 CTGATTGCACTTGCTACCACA 58.846 47.619 2.33 0.00 42.66 4.17
3171 8434 1.228521 TACCGTGGACTTCCCGACA 60.229 57.895 7.49 0.00 37.93 4.35
3188 8451 4.461992 CGACAACGGAAACTACAACAAT 57.538 40.909 0.00 0.00 35.72 2.71
3232 8495 2.990066 AACTACAGCTACTGGGATGC 57.010 50.000 0.00 0.00 35.51 3.91
3269 8535 3.157518 TGACTACCTCAGGCACCAA 57.842 52.632 0.00 0.00 37.37 3.67
3272 8538 0.396811 ACTACCTCAGGCACCAACAC 59.603 55.000 0.00 0.00 0.00 3.32
3281 8547 1.827789 GCACCAACACCAGGAGCAA 60.828 57.895 0.00 0.00 41.59 3.91
3285 8551 1.331214 CCAACACCAGGAGCAACAAT 58.669 50.000 0.00 0.00 0.00 2.71
3363 8629 1.186917 TCGGCGAGGAGTGGGTAAAA 61.187 55.000 4.99 0.00 0.00 1.52
3387 8653 2.820197 GTGGATTTCTGGACAGGAAACC 59.180 50.000 11.56 11.56 38.83 3.27
3389 8655 2.084546 GATTTCTGGACAGGAAACCGG 58.915 52.381 0.00 0.00 35.84 5.28
3392 8658 4.323477 TGGACAGGAAACCGGGCG 62.323 66.667 6.32 0.00 0.00 6.13
3530 8813 7.379750 GCTACTATTAAATCCATCTCGAGGTT 58.620 38.462 13.56 0.00 0.00 3.50
3541 8824 4.142600 CCATCTCGAGGTTTTTGGATCAAC 60.143 45.833 13.56 0.00 0.00 3.18
3604 8893 4.336433 CAGATTTGAACTGGTGACACAAGT 59.664 41.667 10.01 10.01 35.60 3.16
3615 8904 5.432645 TGGTGACACAAGTATTTTCAGTCA 58.567 37.500 8.08 0.00 33.40 3.41
3617 8906 6.017192 TGGTGACACAAGTATTTTCAGTCATG 60.017 38.462 8.08 0.00 36.96 3.07
3644 8933 2.540383 ACCAACTGAGCTATCCTGACA 58.460 47.619 0.00 0.00 0.00 3.58
3662 8951 5.105877 CCTGACATTTTCTTGTGCATCATCT 60.106 40.000 0.00 0.00 0.00 2.90
3663 8952 5.946298 TGACATTTTCTTGTGCATCATCTC 58.054 37.500 0.00 0.00 0.00 2.75
3680 8969 9.703892 GCATCATCTCAGTAGAGTATTTGTATT 57.296 33.333 0.00 0.00 42.66 1.89
3794 9083 3.062099 AGCATTCAAACTGTATGTACGCG 59.938 43.478 3.53 3.53 29.35 6.01
3795 9084 3.342269 CATTCAAACTGTATGTACGCGC 58.658 45.455 5.73 0.00 0.00 6.86
3821 9110 8.446273 CGCCCAATGTTCAGAAGATAATTATAG 58.554 37.037 0.00 0.00 0.00 1.31
3822 9111 9.289782 GCCCAATGTTCAGAAGATAATTATAGT 57.710 33.333 0.00 0.00 0.00 2.12
3911 9206 1.063912 CTGCAGTTCACGAGCAACAAA 59.936 47.619 5.25 0.00 37.89 2.83
3938 9236 6.864360 TTGCAGCAATTAAGCAAAGAAATT 57.136 29.167 2.83 0.00 44.39 1.82
3944 9242 9.195411 CAGCAATTAAGCAAAGAAATTGACTTA 57.805 29.630 10.34 0.00 41.14 2.24
3954 9252 7.587629 CAAAGAAATTGACTTACTGCATCAGA 58.412 34.615 0.29 0.00 41.85 3.27
3973 9271 7.416438 GCATCAGATTGAGATGGAAGAATTTGT 60.416 37.037 5.45 0.00 42.38 2.83
4028 9326 0.108186 CAATAGGCAGGAGCACGACA 60.108 55.000 0.00 0.00 44.61 4.35
4039 9337 2.477176 GCACGACAAACCTGTGGCA 61.477 57.895 0.00 0.00 35.30 4.92
4086 9384 1.480545 TCGGTGCTTGCTCTGCTTATA 59.519 47.619 0.00 0.00 0.00 0.98
4087 9385 2.093711 TCGGTGCTTGCTCTGCTTATAA 60.094 45.455 0.00 0.00 0.00 0.98
4088 9386 2.874701 CGGTGCTTGCTCTGCTTATAAT 59.125 45.455 0.00 0.00 0.00 1.28
4095 9393 5.049818 GCTTGCTCTGCTTATAATACCTGTG 60.050 44.000 0.00 0.00 0.00 3.66
4148 9446 2.513897 GATTCCTCCAACCCGCCG 60.514 66.667 0.00 0.00 0.00 6.46
4210 9509 0.119155 TCTCTGTCCCCCAACATCCT 59.881 55.000 0.00 0.00 0.00 3.24
4211 9510 0.995024 CTCTGTCCCCCAACATCCTT 59.005 55.000 0.00 0.00 0.00 3.36
4219 9518 2.436646 CAACATCCTTCGCCCGCT 60.437 61.111 0.00 0.00 0.00 5.52
4237 9536 2.320339 CTAAGTCTCCGTCCGTCCGC 62.320 65.000 0.00 0.00 0.00 5.54
4255 9554 1.790123 CGCGACCAAACCAATCAATCG 60.790 52.381 0.00 0.00 0.00 3.34
4262 9561 0.960364 AACCAATCAATCGCCGCTGT 60.960 50.000 0.00 0.00 0.00 4.40
4263 9562 0.107897 ACCAATCAATCGCCGCTGTA 60.108 50.000 0.00 0.00 0.00 2.74
4271 9570 1.884075 ATCGCCGCTGTAGTGTGGAA 61.884 55.000 0.00 0.00 39.82 3.53
4272 9571 2.380410 CGCCGCTGTAGTGTGGAAC 61.380 63.158 0.00 0.00 39.82 3.62
4277 9576 1.359848 GCTGTAGTGTGGAACCGATG 58.640 55.000 0.00 0.00 34.36 3.84
4302 9601 1.043116 TACCGGTCAGCAGATGGGAG 61.043 60.000 12.40 0.00 0.00 4.30
4324 9624 7.038659 GGAGTGATCCCATAAAGATCGATTAG 58.961 42.308 0.00 0.00 42.57 1.73
4344 9644 6.963117 TTAGGAGGTTGAAGAAAGGGATAA 57.037 37.500 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.678598 AAGACGGGACACACGACCAA 61.679 55.000 0.00 0.00 34.93 3.67
1 2 1.678598 AAAGACGGGACACACGACCA 61.679 55.000 0.00 0.00 34.93 4.02
2 3 0.531311 AAAAGACGGGACACACGACC 60.531 55.000 0.00 0.00 34.93 4.79
3 4 0.857287 GAAAAGACGGGACACACGAC 59.143 55.000 0.00 0.00 34.93 4.34
4 5 0.249573 GGAAAAGACGGGACACACGA 60.250 55.000 0.00 0.00 34.93 4.35
5 6 0.531090 TGGAAAAGACGGGACACACG 60.531 55.000 0.00 0.00 37.36 4.49
6 7 0.942252 GTGGAAAAGACGGGACACAC 59.058 55.000 0.00 0.00 0.00 3.82
7 8 0.531090 CGTGGAAAAGACGGGACACA 60.531 55.000 0.00 0.00 33.08 3.72
8 9 2.231820 CGTGGAAAAGACGGGACAC 58.768 57.895 0.00 0.00 33.08 3.67
14 15 0.794473 GGCTAACCGTGGAAAAGACG 59.206 55.000 0.00 0.00 36.56 4.18
15 16 1.162698 GGGCTAACCGTGGAAAAGAC 58.837 55.000 0.00 0.00 36.48 3.01
27 28 4.426313 AGCAAGGCCCGGGCTAAC 62.426 66.667 42.70 27.64 37.50 2.34
28 29 4.424711 CAGCAAGGCCCGGGCTAA 62.425 66.667 42.70 0.00 37.50 3.09
33 34 4.729918 AAGAGCAGCAAGGCCCGG 62.730 66.667 0.00 0.00 0.00 5.73
34 35 3.437795 CAAGAGCAGCAAGGCCCG 61.438 66.667 0.00 0.00 0.00 6.13
35 36 3.066814 CCAAGAGCAGCAAGGCCC 61.067 66.667 0.00 0.00 0.00 5.80
36 37 3.756727 GCCAAGAGCAGCAAGGCC 61.757 66.667 0.00 0.00 42.97 5.19
52 53 1.578206 GAACGGAGGGAGTTTGCTGC 61.578 60.000 0.00 0.00 31.14 5.25
53 54 0.955919 GGAACGGAGGGAGTTTGCTG 60.956 60.000 0.00 0.00 31.14 4.41
54 55 1.375326 GGAACGGAGGGAGTTTGCT 59.625 57.895 0.00 0.00 31.14 3.91
56 57 1.975660 TTTGGAACGGAGGGAGTTTG 58.024 50.000 0.00 0.00 31.14 2.93
57 58 2.740506 TTTTGGAACGGAGGGAGTTT 57.259 45.000 0.00 0.00 31.14 2.66
58 59 2.971901 ATTTTGGAACGGAGGGAGTT 57.028 45.000 0.00 0.00 34.07 3.01
59 60 5.456186 CCATATATTTTGGAACGGAGGGAGT 60.456 44.000 0.00 0.00 36.26 3.85
60 61 5.003804 CCATATATTTTGGAACGGAGGGAG 58.996 45.833 0.00 0.00 36.26 4.30
61 62 4.748548 GCCATATATTTTGGAACGGAGGGA 60.749 45.833 8.24 0.00 36.26 4.20
62 63 3.506067 GCCATATATTTTGGAACGGAGGG 59.494 47.826 8.24 0.00 36.26 4.30
63 64 4.398319 AGCCATATATTTTGGAACGGAGG 58.602 43.478 8.24 0.00 36.26 4.30
64 65 5.765182 AGAAGCCATATATTTTGGAACGGAG 59.235 40.000 8.24 0.00 36.26 4.63
65 66 5.690865 AGAAGCCATATATTTTGGAACGGA 58.309 37.500 8.24 0.00 36.26 4.69
66 67 6.391227 AAGAAGCCATATATTTTGGAACGG 57.609 37.500 8.24 0.00 36.26 4.44
67 68 8.378172 TCTAAGAAGCCATATATTTTGGAACG 57.622 34.615 8.24 0.00 36.26 3.95
68 69 9.561069 TCTCTAAGAAGCCATATATTTTGGAAC 57.439 33.333 8.24 0.48 36.26 3.62
78 79 9.941325 CATAGTGAAATCTCTAAGAAGCCATAT 57.059 33.333 0.00 0.00 0.00 1.78
80 81 8.027524 TCATAGTGAAATCTCTAAGAAGCCAT 57.972 34.615 0.00 0.00 0.00 4.40
81 82 7.423844 TCATAGTGAAATCTCTAAGAAGCCA 57.576 36.000 0.00 0.00 0.00 4.75
82 83 7.984617 AGTTCATAGTGAAATCTCTAAGAAGCC 59.015 37.037 9.25 2.39 38.22 4.35
83 84 8.940768 AGTTCATAGTGAAATCTCTAAGAAGC 57.059 34.615 9.25 6.36 38.22 3.86
91 92 8.350722 TCCGTATGTAGTTCATAGTGAAATCTC 58.649 37.037 0.00 0.00 38.22 2.75
92 93 8.234136 TCCGTATGTAGTTCATAGTGAAATCT 57.766 34.615 0.00 0.00 38.22 2.40
93 94 7.115095 GCTCCGTATGTAGTTCATAGTGAAATC 59.885 40.741 0.00 0.00 38.22 2.17
95 96 6.127563 TGCTCCGTATGTAGTTCATAGTGAAA 60.128 38.462 0.00 0.00 38.22 2.69
97 98 4.885325 TGCTCCGTATGTAGTTCATAGTGA 59.115 41.667 0.00 0.00 39.36 3.41
99 100 5.847111 TTGCTCCGTATGTAGTTCATAGT 57.153 39.130 0.00 0.00 39.36 2.12
100 101 7.438160 TCATTTTGCTCCGTATGTAGTTCATAG 59.562 37.037 0.00 0.00 39.36 2.23
101 102 7.269316 TCATTTTGCTCCGTATGTAGTTCATA 58.731 34.615 0.00 0.00 37.91 2.15
102 103 6.112734 TCATTTTGCTCCGTATGTAGTTCAT 58.887 36.000 0.00 0.00 40.25 2.57
103 104 5.483811 TCATTTTGCTCCGTATGTAGTTCA 58.516 37.500 0.00 0.00 0.00 3.18
104 105 5.581085 ACTCATTTTGCTCCGTATGTAGTTC 59.419 40.000 0.00 0.00 0.00 3.01
106 107 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
107 108 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
109 110 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
110 111 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
111 112 4.943705 ACATTCACTCATTTTGCTCCGTAT 59.056 37.500 0.00 0.00 0.00 3.06
113 114 3.149196 ACATTCACTCATTTTGCTCCGT 58.851 40.909 0.00 0.00 0.00 4.69
114 115 3.837213 ACATTCACTCATTTTGCTCCG 57.163 42.857 0.00 0.00 0.00 4.63
116 117 6.246420 AGTGTACATTCACTCATTTTGCTC 57.754 37.500 0.00 0.00 44.07 4.26
118 119 8.795786 TTAAAGTGTACATTCACTCATTTTGC 57.204 30.769 0.00 0.00 46.25 3.68
160 161 9.871238 GAGATTTCACTACAAACTACATAAGGA 57.129 33.333 0.00 0.00 0.00 3.36
161 162 9.877178 AGAGATTTCACTACAAACTACATAAGG 57.123 33.333 0.00 0.00 0.00 2.69
188 189 8.996271 CCTCCGTTACTAAATGTAAGTCTTTTT 58.004 33.333 0.00 0.00 41.29 1.94
189 190 7.605309 CCCTCCGTTACTAAATGTAAGTCTTTT 59.395 37.037 0.00 0.00 41.29 2.27
190 191 7.038799 TCCCTCCGTTACTAAATGTAAGTCTTT 60.039 37.037 0.00 0.00 41.29 2.52
191 192 6.438425 TCCCTCCGTTACTAAATGTAAGTCTT 59.562 38.462 0.00 0.00 41.29 3.01
192 193 5.954150 TCCCTCCGTTACTAAATGTAAGTCT 59.046 40.000 0.00 0.00 41.29 3.24
193 194 6.127507 ACTCCCTCCGTTACTAAATGTAAGTC 60.128 42.308 0.00 0.00 41.29 3.01
195 196 6.218108 ACTCCCTCCGTTACTAAATGTAAG 57.782 41.667 0.00 0.00 41.29 2.34
196 197 7.781693 AGATACTCCCTCCGTTACTAAATGTAA 59.218 37.037 0.00 0.00 38.67 2.41
197 198 7.293073 AGATACTCCCTCCGTTACTAAATGTA 58.707 38.462 0.00 0.00 0.00 2.29
199 200 6.651975 AGATACTCCCTCCGTTACTAAATG 57.348 41.667 0.00 0.00 0.00 2.32
200 201 8.953223 AATAGATACTCCCTCCGTTACTAAAT 57.047 34.615 0.00 0.00 0.00 1.40
201 202 8.773033 AAATAGATACTCCCTCCGTTACTAAA 57.227 34.615 0.00 0.00 0.00 1.85
202 203 8.773033 AAAATAGATACTCCCTCCGTTACTAA 57.227 34.615 0.00 0.00 0.00 2.24
204 205 7.343833 TCAAAAATAGATACTCCCTCCGTTACT 59.656 37.037 0.00 0.00 0.00 2.24
206 207 7.664552 TCAAAAATAGATACTCCCTCCGTTA 57.335 36.000 0.00 0.00 0.00 3.18
207 208 6.555463 TCAAAAATAGATACTCCCTCCGTT 57.445 37.500 0.00 0.00 0.00 4.44
209 210 5.934625 CCATCAAAAATAGATACTCCCTCCG 59.065 44.000 0.00 0.00 0.00 4.63
210 211 6.712547 CACCATCAAAAATAGATACTCCCTCC 59.287 42.308 0.00 0.00 0.00 4.30
211 212 6.205658 GCACCATCAAAAATAGATACTCCCTC 59.794 42.308 0.00 0.00 0.00 4.30
212 213 6.064717 GCACCATCAAAAATAGATACTCCCT 58.935 40.000 0.00 0.00 0.00 4.20
213 214 5.827797 TGCACCATCAAAAATAGATACTCCC 59.172 40.000 0.00 0.00 0.00 4.30
214 215 6.942532 TGCACCATCAAAAATAGATACTCC 57.057 37.500 0.00 0.00 0.00 3.85
245 3720 1.269673 TGCTTTTGTGCAATGACGCAT 60.270 42.857 0.00 0.00 45.26 4.73
247 3722 1.207390 TTGCTTTTGTGCAATGACGC 58.793 45.000 0.00 0.00 46.43 5.19
264 3739 2.795329 AGGTAGGGTTGCAATGTCTTG 58.205 47.619 0.59 0.00 35.36 3.02
334 3811 9.987272 CTTTTATGATTTCAAAGAAGGAAACCT 57.013 29.630 0.00 0.00 37.10 3.50
341 3818 8.581263 CGCACATCTTTTATGATTTCAAAGAAG 58.419 33.333 0.00 0.00 39.40 2.85
344 3821 7.326789 ACACGCACATCTTTTATGATTTCAAAG 59.673 33.333 0.00 0.00 0.00 2.77
345 3822 7.114670 CACACGCACATCTTTTATGATTTCAAA 59.885 33.333 0.00 0.00 0.00 2.69
372 3851 2.476619 CACTCGAAGTAGCAAAGTGGTG 59.523 50.000 0.00 0.00 34.96 4.17
373 3852 2.364324 TCACTCGAAGTAGCAAAGTGGT 59.636 45.455 0.00 0.00 38.27 4.16
402 3881 1.027792 AGCGTCGTGGGTGTTGTTTT 61.028 50.000 0.00 0.00 0.00 2.43
404 3883 1.433837 GAAGCGTCGTGGGTGTTGTT 61.434 55.000 0.00 0.00 0.00 2.83
405 3884 1.885850 GAAGCGTCGTGGGTGTTGT 60.886 57.895 0.00 0.00 0.00 3.32
406 3885 1.594293 AGAAGCGTCGTGGGTGTTG 60.594 57.895 0.00 0.00 0.00 3.33
407 3886 1.594293 CAGAAGCGTCGTGGGTGTT 60.594 57.895 0.00 0.00 0.00 3.32
408 3887 2.029073 CAGAAGCGTCGTGGGTGT 59.971 61.111 0.00 0.00 0.00 4.16
409 3888 1.734477 CTCAGAAGCGTCGTGGGTG 60.734 63.158 0.00 0.00 0.00 4.61
410 3889 2.651361 CTCAGAAGCGTCGTGGGT 59.349 61.111 0.00 0.00 0.00 4.51
411 3890 2.811317 GCTCAGAAGCGTCGTGGG 60.811 66.667 0.00 0.00 39.10 4.61
425 3904 7.712639 TGTGTTCAGAGATTTAGGATTATGCTC 59.287 37.037 0.00 0.00 0.00 4.26
431 3910 6.541641 GCTCATGTGTTCAGAGATTTAGGATT 59.458 38.462 0.00 0.00 0.00 3.01
432 3911 6.054295 GCTCATGTGTTCAGAGATTTAGGAT 58.946 40.000 0.00 0.00 0.00 3.24
435 3914 4.260132 GCGCTCATGTGTTCAGAGATTTAG 60.260 45.833 0.00 0.00 0.00 1.85
440 3919 0.390340 GGCGCTCATGTGTTCAGAGA 60.390 55.000 7.64 0.00 0.00 3.10
443 3922 0.957395 AAGGGCGCTCATGTGTTCAG 60.957 55.000 11.40 0.00 0.00 3.02
457 3936 7.214381 AGGTTGAAGTTTAATTTTACAAGGGC 58.786 34.615 0.00 0.00 0.00 5.19
558 4037 1.967319 TGTGTGGGACTCAAAAGCTC 58.033 50.000 0.00 0.00 32.05 4.09
576 4055 7.190191 CAGGCGCTCACTATACTAGTAATATG 58.810 42.308 7.64 5.60 37.23 1.78
700 5325 7.448748 ACCAAAGTATTTTATCACTCGCTTT 57.551 32.000 0.00 0.00 35.03 3.51
701 5326 7.040686 ACAACCAAAGTATTTTATCACTCGCTT 60.041 33.333 0.00 0.00 35.03 4.68
744 5371 1.539496 GCGTACAGTCTGTTTGTCCCA 60.539 52.381 11.54 0.00 0.00 4.37
796 5423 2.266055 GTTGCAGTAGCGGGCTCT 59.734 61.111 0.00 0.00 46.23 4.09
797 5424 3.188786 CGTTGCAGTAGCGGGCTC 61.189 66.667 0.00 0.00 46.23 4.70
811 5438 2.167219 CATCATCGCTGTCGCCGTT 61.167 57.895 0.00 0.00 35.26 4.44
828 5455 2.503382 TATCATGCCGCCGTAGCCA 61.503 57.895 0.00 0.00 34.57 4.75
832 5459 0.394938 ATTGGTATCATGCCGCCGTA 59.605 50.000 0.00 0.00 0.00 4.02
878 5505 9.525826 GTGATGGGGAATAAGATAAATCATTCT 57.474 33.333 0.00 0.00 0.00 2.40
887 5518 4.665009 AGCAAGGTGATGGGGAATAAGATA 59.335 41.667 0.00 0.00 0.00 1.98
904 5535 3.624861 CCAAGCACTTCAGTATAGCAAGG 59.375 47.826 0.00 0.00 0.00 3.61
964 5599 4.646572 AGATATTCCGGGCTTGATTCTTC 58.353 43.478 0.00 0.00 0.00 2.87
970 5605 2.897969 GTCCTAGATATTCCGGGCTTGA 59.102 50.000 0.00 0.00 0.00 3.02
980 5619 3.527507 TCGCCTCTGGTCCTAGATATT 57.472 47.619 0.00 0.00 0.00 1.28
982 5621 2.555448 CCATCGCCTCTGGTCCTAGATA 60.555 54.545 0.00 0.00 0.00 1.98
1046 5688 2.101575 TGGTAGCATCGTCGACGC 59.898 61.111 32.19 18.79 39.60 5.19
1060 5702 2.932234 CGAAGTCCGCCTCTGTGGT 61.932 63.158 0.00 0.00 43.03 4.16
1114 5756 2.270850 GCCCATGGCCGTGAAGTA 59.729 61.111 27.13 0.00 44.06 2.24
1128 5770 1.222936 CAGACTGGGACATGAGCCC 59.777 63.158 17.89 17.89 46.22 5.19
1157 5799 3.277211 CTCACGCCGTCTTTCCCGA 62.277 63.158 0.00 0.00 0.00 5.14
1196 5838 1.667830 CAGATGAACACCACGCCGT 60.668 57.895 0.00 0.00 0.00 5.68
1201 5843 0.953727 TTGCAGCAGATGAACACCAC 59.046 50.000 0.00 0.00 0.00 4.16
1222 5864 2.350895 CACCACAAGGGCGATGGA 59.649 61.111 0.00 0.00 42.05 3.41
1226 5868 2.425592 CAGACACCACAAGGGCGA 59.574 61.111 0.00 0.00 42.05 5.54
1264 5906 3.496160 CGGGTGCCTAATACCTTGCTATT 60.496 47.826 0.00 0.00 38.30 1.73
1266 5908 1.414919 CGGGTGCCTAATACCTTGCTA 59.585 52.381 0.00 0.00 38.30 3.49
1303 5945 2.877168 GGATGATGATGACCTGCAAGTC 59.123 50.000 8.59 8.59 37.28 3.01
1312 5954 3.005261 AGCACGTCTAGGATGATGATGAC 59.995 47.826 0.00 0.00 0.00 3.06
1356 5998 4.742201 GTCTTCAGGCTCGCGGCA 62.742 66.667 18.87 0.00 44.01 5.69
1366 6008 3.114809 CGAGCAAGATAGCTGTCTTCAG 58.885 50.000 21.54 13.28 46.75 3.02
1424 6066 1.202698 ACAAGAACAGCAGGACCTGAC 60.203 52.381 26.25 15.84 36.67 3.51
1493 6135 2.426522 TCTGGAATTTCAGGCACTTCG 58.573 47.619 13.96 0.00 34.60 3.79
1524 6166 0.657840 CTACCATAGTTTGCTGCCGC 59.342 55.000 0.00 0.00 0.00 6.53
1556 6198 0.179179 GGCAGCATCTTCGACTTTGC 60.179 55.000 0.00 4.85 35.34 3.68
1579 6221 6.818644 GCTATGGATAGAAACAGACACTTGAA 59.181 38.462 0.00 0.00 32.05 2.69
1586 6228 5.465056 GCAAGAGCTATGGATAGAAACAGAC 59.535 44.000 0.00 0.00 37.91 3.51
1591 6233 4.708177 GTGGCAAGAGCTATGGATAGAAA 58.292 43.478 0.00 0.00 41.70 2.52
1600 6242 2.036475 CCATACTCGTGGCAAGAGCTAT 59.964 50.000 26.86 19.73 41.70 2.97
1625 6267 1.429148 CGGGCCAACTCTAACATCGC 61.429 60.000 4.39 0.00 0.00 4.58
1629 6271 1.290955 CGTCGGGCCAACTCTAACA 59.709 57.895 4.39 0.00 0.00 2.41
1684 6331 0.606604 TCCGTCACCTTAGGAAGCAC 59.393 55.000 4.77 0.00 0.00 4.40
1750 6397 7.496346 TTAGGAAGTAGAGGTGAATGAACAT 57.504 36.000 0.00 0.00 0.00 2.71
1768 6415 2.371841 TGCTGAAAGACCTGCTTAGGAA 59.628 45.455 0.00 0.00 35.24 3.36
1773 6420 0.957362 GCTTGCTGAAAGACCTGCTT 59.043 50.000 0.00 0.00 38.24 3.91
1796 6443 3.605634 TGCAGTGCACGGTATAAGATTT 58.394 40.909 15.37 0.00 31.71 2.17
1803 6450 1.079127 GACCTGCAGTGCACGGTAT 60.079 57.895 28.17 14.54 39.07 2.73
1822 6469 2.305927 CAAACAGGTCTAGGGTCATGGT 59.694 50.000 0.00 0.00 0.00 3.55
1833 6480 1.136891 GCAACAAAGGCAAACAGGTCT 59.863 47.619 0.00 0.00 0.00 3.85
1856 6503 2.044252 AGTTCCGGCTAGCGGAGA 60.044 61.111 22.71 14.87 36.82 3.71
1867 6514 2.006772 GCAATCGTAGCCAGTTCCG 58.993 57.895 0.00 0.00 0.00 4.30
1875 6522 0.592247 CAAATGCCGGCAATCGTAGC 60.592 55.000 36.33 0.00 37.11 3.58
1880 6527 1.201181 TGTACACAAATGCCGGCAATC 59.799 47.619 36.33 12.71 0.00 2.67
1970 6617 2.260869 CCCCAGGTGTTGCAAGTCG 61.261 63.158 0.00 0.00 0.00 4.18
1979 6626 2.525368 GCAAAACTATTCCCCAGGTGT 58.475 47.619 0.00 0.00 0.00 4.16
1987 6634 3.606687 TCTTCTCCCGCAAAACTATTCC 58.393 45.455 0.00 0.00 0.00 3.01
1991 6638 2.569853 TCCATCTTCTCCCGCAAAACTA 59.430 45.455 0.00 0.00 0.00 2.24
1995 6642 1.073125 TGTTCCATCTTCTCCCGCAAA 59.927 47.619 0.00 0.00 0.00 3.68
1999 6646 2.761208 AGTACTGTTCCATCTTCTCCCG 59.239 50.000 0.00 0.00 0.00 5.14
2012 6659 2.622942 CAATTGGGCACACAGTACTGTT 59.377 45.455 25.89 14.25 42.83 3.16
2060 6707 0.322726 TGTGTGCCCATCACCATCAG 60.323 55.000 0.00 0.00 45.03 2.90
2061 6708 0.322726 CTGTGTGCCCATCACCATCA 60.323 55.000 0.00 0.00 45.03 3.07
2062 6709 0.035152 TCTGTGTGCCCATCACCATC 60.035 55.000 0.00 0.00 45.03 3.51
2063 6710 0.034767 CTCTGTGTGCCCATCACCAT 60.035 55.000 0.00 0.00 45.03 3.55
2064 6711 1.376086 CTCTGTGTGCCCATCACCA 59.624 57.895 0.00 0.00 45.03 4.17
2065 6712 1.377725 CCTCTGTGTGCCCATCACC 60.378 63.158 0.00 0.00 45.03 4.02
2066 6713 0.674895 GTCCTCTGTGTGCCCATCAC 60.675 60.000 0.00 0.00 45.82 3.06
2067 6714 1.126948 TGTCCTCTGTGTGCCCATCA 61.127 55.000 0.00 0.00 0.00 3.07
2068 6715 0.674895 GTGTCCTCTGTGTGCCCATC 60.675 60.000 0.00 0.00 0.00 3.51
2097 6744 0.679960 CCTCCAAATTCCACCCCGTC 60.680 60.000 0.00 0.00 0.00 4.79
2103 6750 3.253432 GGCGATAATCCTCCAAATTCCAC 59.747 47.826 0.00 0.00 0.00 4.02
2118 6765 0.319083 ACAACACCGACTGGCGATAA 59.681 50.000 3.46 0.00 44.57 1.75
2129 6776 1.516453 CAATTGCAACGAACAACACCG 59.484 47.619 0.00 0.00 0.00 4.94
2278 6937 2.292389 TGGACAGGGAACTAATACCGGA 60.292 50.000 9.46 0.00 40.21 5.14
2301 6960 5.532406 GCCTGATGTATTCTCTTGCCATAAA 59.468 40.000 0.00 0.00 0.00 1.40
2327 6998 0.109342 AGCCAGGTTCAGGTTGACAG 59.891 55.000 0.00 0.00 0.00 3.51
2407 7084 5.612725 ATTCCTTCTGACCAGATCTTCTC 57.387 43.478 0.01 0.00 37.29 2.87
2408 7085 5.960811 TGTATTCCTTCTGACCAGATCTTCT 59.039 40.000 0.01 0.00 37.29 2.85
2448 7125 1.202855 AGCTGAAGAACCATGCACAGT 60.203 47.619 0.00 0.00 0.00 3.55
2457 7134 0.612744 AGGAGAGCAGCTGAAGAACC 59.387 55.000 20.43 13.03 0.00 3.62
2483 7160 0.739462 GTTCACATCGGTCATGGCGA 60.739 55.000 0.00 0.00 36.72 5.54
2488 7165 0.541863 GGGAGGTTCACATCGGTCAT 59.458 55.000 0.00 0.00 0.00 3.06
2491 7168 0.768622 TTTGGGAGGTTCACATCGGT 59.231 50.000 0.00 0.00 24.99 4.69
2496 7173 3.146066 CGATTTCTTTGGGAGGTTCACA 58.854 45.455 0.00 0.00 0.00 3.58
2498 7175 3.780804 TCGATTTCTTTGGGAGGTTCA 57.219 42.857 0.00 0.00 0.00 3.18
2586 7276 3.515502 TGAGGATCGATTGGACTGTCTTT 59.484 43.478 7.85 0.00 38.61 2.52
2587 7277 3.099905 TGAGGATCGATTGGACTGTCTT 58.900 45.455 7.85 0.00 38.61 3.01
2591 7281 3.554544 CCATCTGAGGATCGATTGGACTG 60.555 52.174 0.00 0.00 38.61 3.51
2655 7351 0.456995 CGAACTCCAGCTCGTCCTTC 60.457 60.000 0.00 0.00 0.00 3.46
2698 7394 3.077556 CACTGCTACGGGCTCCCT 61.078 66.667 3.11 0.00 42.39 4.20
2709 7410 1.448540 CGCGGAAATCTCCACTGCT 60.449 57.895 0.00 0.00 42.58 4.24
2805 8068 6.575162 ATTAAGCCGAAAAAGAATGTCAGT 57.425 33.333 0.00 0.00 0.00 3.41
2809 8072 5.478407 CCCAATTAAGCCGAAAAAGAATGT 58.522 37.500 0.00 0.00 0.00 2.71
2822 8085 1.275666 AAGGTTGGCCCCAATTAAGC 58.724 50.000 0.00 0.00 38.28 3.09
2877 8140 1.135717 CGATGATAGAGAGCTCTGGCG 60.136 57.143 23.91 9.68 44.37 5.69
2883 8146 1.697284 TGTGCCGATGATAGAGAGCT 58.303 50.000 0.00 0.00 0.00 4.09
2900 8163 0.037734 GGAACCTTGACCCGGATTGT 59.962 55.000 0.73 0.00 0.00 2.71
2904 8167 2.874664 CGTGGAACCTTGACCCGGA 61.875 63.158 0.73 0.00 0.00 5.14
2920 8183 2.542907 CGTTGAAGGCAGTTGGCGT 61.543 57.895 0.00 0.00 46.16 5.68
3003 8266 3.918220 GAACAGAGCGCGCGGATG 61.918 66.667 33.06 25.83 0.00 3.51
3100 8363 4.152647 CACACTAGGGCTGATATACTGGA 58.847 47.826 0.00 0.00 0.00 3.86
3147 8410 1.593296 GGAAGTCCACGGTAGTCGCT 61.593 60.000 0.00 0.00 43.89 4.93
3171 8434 6.294286 CCATGGTAATTGTTGTAGTTTCCGTT 60.294 38.462 2.57 0.00 0.00 4.44
3186 8449 2.434702 GGTCGAGGACTCCATGGTAATT 59.565 50.000 12.58 0.00 32.47 1.40
3188 8451 1.272816 TGGTCGAGGACTCCATGGTAA 60.273 52.381 12.58 0.00 32.47 2.85
3232 8495 2.284798 ATAGCTGTGGTCGAGGTGCG 62.285 60.000 0.00 0.00 42.69 5.34
3269 8535 2.440409 GATGATTGTTGCTCCTGGTGT 58.560 47.619 0.00 0.00 0.00 4.16
3272 8538 1.747355 GTGGATGATTGTTGCTCCTGG 59.253 52.381 0.00 0.00 0.00 4.45
3281 8547 2.567169 TCAACTCGAGGTGGATGATTGT 59.433 45.455 29.35 0.00 0.00 2.71
3285 8551 1.275291 GGTTCAACTCGAGGTGGATGA 59.725 52.381 29.35 15.19 0.00 2.92
3363 8629 5.501156 GTTTCCTGTCCAGAAATCCACTAT 58.499 41.667 0.00 0.00 0.00 2.12
3387 8653 3.814268 CCATGCTTTCACCGCCCG 61.814 66.667 0.00 0.00 0.00 6.13
3389 8655 0.170339 GTAACCATGCTTTCACCGCC 59.830 55.000 0.00 0.00 0.00 6.13
3604 8893 8.812972 AGTTGGTAGAGTACATGACTGAAAATA 58.187 33.333 0.00 0.00 39.06 1.40
3615 8904 5.536916 GGATAGCTCAGTTGGTAGAGTACAT 59.463 44.000 0.00 0.00 34.39 2.29
3617 8906 5.009210 CAGGATAGCTCAGTTGGTAGAGTAC 59.991 48.000 0.00 0.00 34.39 2.73
3644 8933 7.108194 TCTACTGAGATGATGCACAAGAAAAT 58.892 34.615 0.00 0.00 0.00 1.82
3773 9062 3.342269 CGCGTACATACAGTTTGAATGC 58.658 45.455 0.00 0.00 0.00 3.56
3794 9083 1.098050 ATCTTCTGAACATTGGGCGC 58.902 50.000 0.00 0.00 0.00 6.53
3795 9084 5.505173 AATTATCTTCTGAACATTGGGCG 57.495 39.130 0.00 0.00 0.00 6.13
3821 9110 5.092781 TCAACAGCGAAAAACTTCTGAAAC 58.907 37.500 0.00 0.00 0.00 2.78
3822 9111 5.303747 TCAACAGCGAAAAACTTCTGAAA 57.696 34.783 0.00 0.00 0.00 2.69
3922 9217 9.196552 GCAGTAAGTCAATTTCTTTGCTTAATT 57.803 29.630 8.41 0.00 36.55 1.40
3938 9236 5.665916 TCTCAATCTGATGCAGTAAGTCA 57.334 39.130 0.00 0.00 32.61 3.41
3944 9242 4.163649 TCTTCCATCTCAATCTGATGCAGT 59.836 41.667 0.00 0.00 39.76 4.40
3954 9252 7.729124 AATCCACAAATTCTTCCATCTCAAT 57.271 32.000 0.00 0.00 0.00 2.57
3973 9271 1.612199 GGCTGTGGTACGGAAAATCCA 60.612 52.381 0.00 0.00 35.91 3.41
4028 9326 1.302511 CGGTAGCTGCCACAGGTTT 60.303 57.895 21.56 0.00 42.44 3.27
4056 9354 0.745845 CAAGCACCGAAGCATAGCCT 60.746 55.000 2.02 0.00 36.85 4.58
4061 9359 1.002868 AGAGCAAGCACCGAAGCAT 60.003 52.632 2.02 0.00 36.85 3.79
4086 9384 1.282157 GGTCTTCTGCCCACAGGTATT 59.718 52.381 0.00 0.00 44.59 1.89
4087 9385 0.912486 GGTCTTCTGCCCACAGGTAT 59.088 55.000 0.00 0.00 44.59 2.73
4088 9386 0.472925 TGGTCTTCTGCCCACAGGTA 60.473 55.000 0.00 0.00 44.59 3.08
4095 9393 0.178990 AACAACCTGGTCTTCTGCCC 60.179 55.000 0.00 0.00 0.00 5.36
4108 9406 2.129607 CTGCTGCAATGAACAACAACC 58.870 47.619 3.02 0.00 0.00 3.77
4210 9509 2.890371 GGAGACTTAGCGGGCGAA 59.110 61.111 0.00 0.00 0.00 4.70
4211 9510 3.515286 CGGAGACTTAGCGGGCGA 61.515 66.667 0.00 0.00 0.00 5.54
4219 9518 2.401766 GCGGACGGACGGAGACTTA 61.402 63.158 3.28 0.00 0.00 2.24
4237 9536 1.467374 GGCGATTGATTGGTTTGGTCG 60.467 52.381 0.00 0.00 0.00 4.79
4238 9537 1.467374 CGGCGATTGATTGGTTTGGTC 60.467 52.381 0.00 0.00 0.00 4.02
4255 9554 2.033194 GGTTCCACACTACAGCGGC 61.033 63.158 0.00 0.00 0.00 6.53
4262 9561 0.682292 TGTGCATCGGTTCCACACTA 59.318 50.000 0.00 0.00 34.82 2.74
4263 9562 1.449782 TGTGCATCGGTTCCACACT 59.550 52.632 0.00 0.00 34.82 3.55
4271 9570 2.577059 CCGGTAGTGTGCATCGGT 59.423 61.111 0.00 0.00 36.38 4.69
4272 9571 1.518572 GACCGGTAGTGTGCATCGG 60.519 63.158 7.34 0.00 45.42 4.18
4277 9576 1.738099 CTGCTGACCGGTAGTGTGC 60.738 63.158 7.34 8.46 0.00 4.57
4282 9581 1.043116 TCCCATCTGCTGACCGGTAG 61.043 60.000 7.34 6.91 0.00 3.18
4302 9601 6.936279 TCCTAATCGATCTTTATGGGATCAC 58.064 40.000 0.00 0.00 39.42 3.06
4312 9611 6.546428 TCTTCAACCTCCTAATCGATCTTT 57.454 37.500 0.00 0.00 0.00 2.52
4318 9618 4.081087 TCCCTTTCTTCAACCTCCTAATCG 60.081 45.833 0.00 0.00 0.00 3.34
4324 9624 5.180810 ACTTATCCCTTTCTTCAACCTCC 57.819 43.478 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.