Multiple sequence alignment - TraesCS3D01G085400

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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 TraesCS3D01G085400 chr3D 100.000 6243 0 0 1 6243 43015913 43009671 0.000000e+00 11529.0
1 TraesCS3D01G085400 chr3D 85.375 547 73 4 5448 5987 388448873 388448327 1.520000e-155 560.0
2 TraesCS3D01G085400 chr3B 93.845 4094 175 30 2194 6243 66880788 66876728 0.000000e+00 6093.0
3 TraesCS3D01G085400 chr3B 86.315 1666 94 72 572 2196 66882387 66880815 0.000000e+00 1690.0
4 TraesCS3D01G085400 chr3B 85.094 530 73 3 5464 5987 505268480 505267951 2.560000e-148 536.0
5 TraesCS3D01G085400 chr3B 93.182 88 4 1 205 292 110230224 110230139 1.830000e-25 128.0
6 TraesCS3D01G085400 chr3B 97.059 68 1 1 293 360 66883932 66883866 5.120000e-21 113.0
7 TraesCS3D01G085400 chr3A 94.453 3263 133 25 3009 6243 55037878 55034636 0.000000e+00 4979.0
8 TraesCS3D01G085400 chr3A 91.254 2481 138 31 533 2968 55040320 55037874 0.000000e+00 3306.0
9 TraesCS3D01G085400 chr3A 84.906 530 74 3 5464 5987 509543736 509543207 1.190000e-146 531.0
10 TraesCS3D01G085400 chr5A 79.336 663 89 32 3621 4275 622418809 622419431 7.480000e-114 422.0
11 TraesCS3D01G085400 chrUn 78.743 668 88 34 3626 4275 410721799 410722430 1.260000e-106 398.0
12 TraesCS3D01G085400 chr2D 78.743 668 87 35 3626 4275 44536921 44536291 4.540000e-106 396.0
13 TraesCS3D01G085400 chr2D 90.323 93 7 1 205 297 31818940 31818850 3.060000e-23 121.0
14 TraesCS3D01G085400 chr2D 89.888 89 7 1 111 199 157903455 157903369 5.120000e-21 113.0
15 TraesCS3D01G085400 chr2D 84.810 79 10 2 117 194 587204991 587204914 1.870000e-10 78.7
16 TraesCS3D01G085400 chr2A 77.726 642 78 35 3621 4245 48441556 48440963 3.610000e-87 333.0
17 TraesCS3D01G085400 chr2A 91.954 87 5 1 203 289 73938669 73938585 3.060000e-23 121.0
18 TraesCS3D01G085400 chr6D 86.932 176 19 4 4289 4463 132304855 132305027 1.780000e-45 195.0
19 TraesCS3D01G085400 chr1D 83.735 166 21 2 6081 6243 316010363 316010201 1.080000e-32 152.0
20 TraesCS3D01G085400 chr1B 83.636 165 21 2 6082 6243 428109127 428108966 3.900000e-32 150.0
21 TraesCS3D01G085400 chr7D 90.722 97 6 2 193 289 590654655 590654748 6.570000e-25 126.0
22 TraesCS3D01G085400 chr7D 91.304 92 6 1 111 202 247320503 247320414 2.360000e-24 124.0
23 TraesCS3D01G085400 chr5B 89.216 102 6 4 112 211 683996385 683996287 8.500000e-24 122.0
24 TraesCS3D01G085400 chr5B 90.476 84 6 2 208 291 513965562 513965481 6.620000e-20 110.0
25 TraesCS3D01G085400 chr5B 86.364 88 8 3 115 201 642146804 642146720 6.660000e-15 93.5
26 TraesCS3D01G085400 chr4A 95.775 71 2 1 219 288 583164622 583164692 5.120000e-21 113.0
27 TraesCS3D01G085400 chr4A 93.333 45 3 0 243 287 595289867 595289823 4.040000e-07 67.6
28 TraesCS3D01G085400 chr7B 90.588 85 6 1 116 200 193054650 193054732 1.840000e-20 111.0
29 TraesCS3D01G085400 chr5D 87.255 102 7 5 112 211 541947319 541947222 1.840000e-20 111.0
30 TraesCS3D01G085400 chr4B 92.958 71 3 1 205 275 53190953 53191021 1.110000e-17 102.0
31 TraesCS3D01G085400 chr2B 84.536 97 8 4 116 211 466187570 466187660 8.620000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G085400 chr3D 43009671 43015913 6242 True 11529.0 11529 100.000000 1 6243 1 chr3D.!!$R1 6242
1 TraesCS3D01G085400 chr3D 388448327 388448873 546 True 560.0 560 85.375000 5448 5987 1 chr3D.!!$R2 539
2 TraesCS3D01G085400 chr3B 66876728 66883932 7204 True 2632.0 6093 92.406333 293 6243 3 chr3B.!!$R3 5950
3 TraesCS3D01G085400 chr3B 505267951 505268480 529 True 536.0 536 85.094000 5464 5987 1 chr3B.!!$R2 523
4 TraesCS3D01G085400 chr3A 55034636 55040320 5684 True 4142.5 4979 92.853500 533 6243 2 chr3A.!!$R2 5710
5 TraesCS3D01G085400 chr3A 509543207 509543736 529 True 531.0 531 84.906000 5464 5987 1 chr3A.!!$R1 523
6 TraesCS3D01G085400 chr5A 622418809 622419431 622 False 422.0 422 79.336000 3621 4275 1 chr5A.!!$F1 654
7 TraesCS3D01G085400 chrUn 410721799 410722430 631 False 398.0 398 78.743000 3626 4275 1 chrUn.!!$F1 649
8 TraesCS3D01G085400 chr2D 44536291 44536921 630 True 396.0 396 78.743000 3626 4275 1 chr2D.!!$R2 649
9 TraesCS3D01G085400 chr2A 48440963 48441556 593 True 333.0 333 77.726000 3621 4245 1 chr2A.!!$R1 624

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
136 137 0.037697 GAAAACCCAATTCGGTGCCC 60.038 55.0 0.00 0.00 35.83 5.36 F
1203 2524 0.034337 TGGCCACCGTCAAGTACTTC 59.966 55.0 0.00 0.00 0.00 3.01 F
1616 2955 0.102300 GTGACCAACCGCTTTTGCTT 59.898 50.0 0.00 0.00 44.80 3.91 F
1810 3149 0.109272 CTGTGTACGTGCACCTCGAT 60.109 55.0 29.93 0.00 38.52 3.59 F
3077 4469 0.967380 CTGCACCAGGATTTCCCCAC 60.967 60.0 0.00 0.00 36.42 4.61 F
3746 5147 0.676466 TGATTGGCGCCGTCATCTTT 60.676 50.0 25.18 3.91 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 2956 0.099259 CACAAATGGCGCACGATGAT 59.901 50.000 10.83 0.0 0.00 2.45 R
2344 3731 1.135689 GGCCTATTCACACGCAACTTG 60.136 52.381 0.00 0.0 0.00 3.16 R
3077 4469 2.612212 CTCGATGGGGTCAATTAAACCG 59.388 50.000 3.73 0.0 37.69 4.44 R
3717 5118 0.109132 GCGCCAATCACAAAAGAGGG 60.109 55.000 0.00 0.0 0.00 4.30 R
4837 6273 1.135721 GCATTGAGGTGCCATCCTTTC 59.864 52.381 0.00 0.0 39.18 2.62 R
5542 7004 0.108615 TAGAGCTGCGCTGGAAGAAC 60.109 55.000 16.38 0.0 39.88 3.01 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.541133 GAGATGTCTGCTATAAAAATCCTACC 57.459 38.462 0.00 0.00 0.00 3.18
26 27 8.034313 AGATGTCTGCTATAAAAATCCTACCA 57.966 34.615 0.00 0.00 0.00 3.25
27 28 8.664079 AGATGTCTGCTATAAAAATCCTACCAT 58.336 33.333 0.00 0.00 0.00 3.55
28 29 8.854614 ATGTCTGCTATAAAAATCCTACCATC 57.145 34.615 0.00 0.00 0.00 3.51
29 30 6.929049 TGTCTGCTATAAAAATCCTACCATCG 59.071 38.462 0.00 0.00 0.00 3.84
30 31 6.369065 GTCTGCTATAAAAATCCTACCATCGG 59.631 42.308 0.00 0.00 0.00 4.18
31 32 6.269077 TCTGCTATAAAAATCCTACCATCGGA 59.731 38.462 0.00 0.00 34.52 4.55
32 33 6.833041 TGCTATAAAAATCCTACCATCGGAA 58.167 36.000 0.00 0.00 33.55 4.30
33 34 7.284074 TGCTATAAAAATCCTACCATCGGAAA 58.716 34.615 0.00 0.00 33.55 3.13
34 35 7.227910 TGCTATAAAAATCCTACCATCGGAAAC 59.772 37.037 0.00 0.00 33.55 2.78
35 36 7.444487 GCTATAAAAATCCTACCATCGGAAACT 59.556 37.037 0.00 0.00 33.55 2.66
36 37 7.803279 ATAAAAATCCTACCATCGGAAACTC 57.197 36.000 0.00 0.00 33.55 3.01
37 38 4.837093 AAATCCTACCATCGGAAACTCA 57.163 40.909 0.00 0.00 33.55 3.41
38 39 5.373812 AAATCCTACCATCGGAAACTCAT 57.626 39.130 0.00 0.00 33.55 2.90
39 40 5.373812 AATCCTACCATCGGAAACTCATT 57.626 39.130 0.00 0.00 33.55 2.57
40 41 4.837093 TCCTACCATCGGAAACTCATTT 57.163 40.909 0.00 0.00 0.00 2.32
41 42 4.766375 TCCTACCATCGGAAACTCATTTC 58.234 43.478 0.00 0.00 43.11 2.17
42 43 4.224147 TCCTACCATCGGAAACTCATTTCA 59.776 41.667 2.48 0.00 45.26 2.69
43 44 5.104527 TCCTACCATCGGAAACTCATTTCAT 60.105 40.000 2.48 0.00 45.26 2.57
44 45 5.590259 CCTACCATCGGAAACTCATTTCATT 59.410 40.000 2.48 0.00 45.26 2.57
45 46 6.765989 CCTACCATCGGAAACTCATTTCATTA 59.234 38.462 2.48 0.00 45.26 1.90
46 47 7.445402 CCTACCATCGGAAACTCATTTCATTAT 59.555 37.037 2.48 0.00 45.26 1.28
47 48 9.489084 CTACCATCGGAAACTCATTTCATTATA 57.511 33.333 2.48 0.00 45.26 0.98
48 49 8.746052 ACCATCGGAAACTCATTTCATTATAA 57.254 30.769 2.48 0.00 45.26 0.98
49 50 8.621286 ACCATCGGAAACTCATTTCATTATAAC 58.379 33.333 2.48 0.00 45.26 1.89
50 51 8.620416 CCATCGGAAACTCATTTCATTATAACA 58.380 33.333 2.48 0.00 45.26 2.41
51 52 9.655769 CATCGGAAACTCATTTCATTATAACAG 57.344 33.333 2.48 0.00 45.26 3.16
52 53 9.613428 ATCGGAAACTCATTTCATTATAACAGA 57.387 29.630 2.48 0.00 45.26 3.41
53 54 8.879759 TCGGAAACTCATTTCATTATAACAGAC 58.120 33.333 2.48 0.00 45.26 3.51
54 55 8.664798 CGGAAACTCATTTCATTATAACAGACA 58.335 33.333 2.48 0.00 45.26 3.41
55 56 9.774742 GGAAACTCATTTCATTATAACAGACAC 57.225 33.333 2.48 0.00 45.26 3.67
56 57 9.478019 GAAACTCATTTCATTATAACAGACACG 57.522 33.333 0.00 0.00 43.29 4.49
57 58 8.547967 AACTCATTTCATTATAACAGACACGT 57.452 30.769 0.00 0.00 0.00 4.49
58 59 8.547967 ACTCATTTCATTATAACAGACACGTT 57.452 30.769 0.00 0.00 0.00 3.99
59 60 9.647797 ACTCATTTCATTATAACAGACACGTTA 57.352 29.630 0.00 0.00 35.89 3.18
70 71 6.662414 AACAGACACGTTATACATGATTGG 57.338 37.500 0.00 0.00 0.00 3.16
71 72 5.730550 ACAGACACGTTATACATGATTGGT 58.269 37.500 0.00 0.00 0.00 3.67
72 73 5.810587 ACAGACACGTTATACATGATTGGTC 59.189 40.000 0.00 0.00 0.00 4.02
73 74 6.042777 CAGACACGTTATACATGATTGGTCT 58.957 40.000 0.00 0.00 32.56 3.85
74 75 7.147966 ACAGACACGTTATACATGATTGGTCTA 60.148 37.037 0.00 0.00 31.32 2.59
75 76 7.704899 CAGACACGTTATACATGATTGGTCTAA 59.295 37.037 0.00 0.00 31.32 2.10
76 77 8.255206 AGACACGTTATACATGATTGGTCTAAA 58.745 33.333 0.00 0.00 30.78 1.85
77 78 8.958119 ACACGTTATACATGATTGGTCTAAAT 57.042 30.769 0.00 0.00 0.00 1.40
86 87 8.821686 ACATGATTGGTCTAAATATTGGTCAA 57.178 30.769 0.00 0.00 0.00 3.18
87 88 9.253832 ACATGATTGGTCTAAATATTGGTCAAA 57.746 29.630 0.00 0.00 0.00 2.69
88 89 9.740239 CATGATTGGTCTAAATATTGGTCAAAG 57.260 33.333 0.00 0.00 0.00 2.77
89 90 8.877864 TGATTGGTCTAAATATTGGTCAAAGT 57.122 30.769 0.00 0.00 0.00 2.66
90 91 9.967451 TGATTGGTCTAAATATTGGTCAAAGTA 57.033 29.630 0.00 0.00 0.00 2.24
99 100 8.801882 AAATATTGGTCAAAGTAAATCTCGGA 57.198 30.769 0.00 0.00 0.00 4.55
100 101 8.801882 AATATTGGTCAAAGTAAATCTCGGAA 57.198 30.769 0.00 0.00 0.00 4.30
101 102 8.980481 ATATTGGTCAAAGTAAATCTCGGAAT 57.020 30.769 0.00 0.00 0.00 3.01
103 104 7.605410 TTGGTCAAAGTAAATCTCGGAATAC 57.395 36.000 0.00 0.00 0.00 1.89
104 105 6.703319 TGGTCAAAGTAAATCTCGGAATACA 58.297 36.000 0.00 0.00 0.00 2.29
105 106 6.592607 TGGTCAAAGTAAATCTCGGAATACAC 59.407 38.462 0.00 0.00 0.00 2.90
106 107 6.036844 GGTCAAAGTAAATCTCGGAATACACC 59.963 42.308 0.00 0.00 0.00 4.16
116 117 2.391879 CGGAATACACCGCTTACTAGC 58.608 52.381 0.00 0.00 46.20 3.42
128 129 4.696899 GCTTACTAGCGAAAACCCAATT 57.303 40.909 0.00 0.00 37.71 2.32
129 130 4.659088 GCTTACTAGCGAAAACCCAATTC 58.341 43.478 0.00 0.00 37.71 2.17
134 135 3.101019 CGAAAACCCAATTCGGTGC 57.899 52.632 0.00 0.00 44.36 5.01
135 136 0.388006 CGAAAACCCAATTCGGTGCC 60.388 55.000 0.00 0.00 44.36 5.01
136 137 0.037697 GAAAACCCAATTCGGTGCCC 60.038 55.000 0.00 0.00 35.83 5.36
137 138 0.760945 AAAACCCAATTCGGTGCCCA 60.761 50.000 0.00 0.00 35.83 5.36
138 139 1.184970 AAACCCAATTCGGTGCCCAG 61.185 55.000 0.00 0.00 35.83 4.45
139 140 2.755469 CCCAATTCGGTGCCCAGG 60.755 66.667 0.00 0.00 0.00 4.45
140 141 3.451894 CCAATTCGGTGCCCAGGC 61.452 66.667 0.38 0.38 42.35 4.85
141 142 2.361610 CAATTCGGTGCCCAGGCT 60.362 61.111 10.58 0.00 42.51 4.58
142 143 2.044946 AATTCGGTGCCCAGGCTC 60.045 61.111 10.58 6.18 42.51 4.70
143 144 3.976701 AATTCGGTGCCCAGGCTCG 62.977 63.158 10.58 13.47 42.51 5.03
160 161 4.612412 GTGTGCACCCGGTCCGAA 62.612 66.667 14.39 0.00 0.00 4.30
161 162 3.862991 TGTGCACCCGGTCCGAAA 61.863 61.111 14.39 0.00 0.00 3.46
162 163 2.592287 GTGCACCCGGTCCGAAAA 60.592 61.111 14.39 0.00 0.00 2.29
163 164 2.188161 GTGCACCCGGTCCGAAAAA 61.188 57.895 14.39 0.00 0.00 1.94
255 256 2.511900 TTTTTCGTCAGGGCGGGT 59.488 55.556 0.00 0.00 0.00 5.28
256 257 1.894756 TTTTTCGTCAGGGCGGGTG 60.895 57.895 0.00 0.00 0.00 4.61
261 262 4.101448 GTCAGGGCGGGTGCAGAT 62.101 66.667 0.00 0.00 45.35 2.90
262 263 4.100084 TCAGGGCGGGTGCAGATG 62.100 66.667 0.00 0.00 45.35 2.90
263 264 4.100084 CAGGGCGGGTGCAGATGA 62.100 66.667 0.00 0.00 45.35 2.92
264 265 3.790437 AGGGCGGGTGCAGATGAG 61.790 66.667 0.00 0.00 45.35 2.90
266 267 4.479993 GGCGGGTGCAGATGAGCT 62.480 66.667 0.00 0.00 45.35 4.09
267 268 2.894387 GCGGGTGCAGATGAGCTC 60.894 66.667 6.82 6.82 42.15 4.09
268 269 2.584418 CGGGTGCAGATGAGCTCG 60.584 66.667 9.64 0.00 34.99 5.03
269 270 2.202987 GGGTGCAGATGAGCTCGG 60.203 66.667 9.64 0.00 34.99 4.63
270 271 2.202987 GGTGCAGATGAGCTCGGG 60.203 66.667 9.64 0.00 34.99 5.14
271 272 2.725312 GGTGCAGATGAGCTCGGGA 61.725 63.158 9.64 0.00 34.99 5.14
272 273 1.227205 GTGCAGATGAGCTCGGGAG 60.227 63.158 9.64 0.30 34.99 4.30
282 283 4.821589 CTCGGGAGCAGGAACGCC 62.822 72.222 0.00 0.00 0.00 5.68
290 291 4.379243 CAGGAACGCCGCACTCCT 62.379 66.667 4.69 4.69 40.33 3.69
291 292 2.678934 AGGAACGCCGCACTCCTA 60.679 61.111 8.23 0.00 37.83 2.94
343 344 1.539280 CGGGGTTTGCGGTTGATTTTT 60.539 47.619 0.00 0.00 0.00 1.94
373 1613 0.252103 AAAGGGCTAGACTCCGGTGA 60.252 55.000 11.17 0.00 0.00 4.02
393 1633 1.202651 ACACCTCCTGTTTCAGTTCCG 60.203 52.381 0.00 0.00 0.00 4.30
400 1640 1.608590 CTGTTTCAGTTCCGCCACATT 59.391 47.619 0.00 0.00 0.00 2.71
401 1641 2.028130 TGTTTCAGTTCCGCCACATTT 58.972 42.857 0.00 0.00 0.00 2.32
402 1642 2.428890 TGTTTCAGTTCCGCCACATTTT 59.571 40.909 0.00 0.00 0.00 1.82
403 1643 3.118956 TGTTTCAGTTCCGCCACATTTTT 60.119 39.130 0.00 0.00 0.00 1.94
424 1664 5.584253 TTTGTTTTGTAAGTAGGCAAGCA 57.416 34.783 0.00 0.00 0.00 3.91
444 1684 1.153353 ACGCATACCTTTGTTGACCG 58.847 50.000 0.00 0.00 0.00 4.79
457 1701 2.241430 TGTTGACCGGGAGAGAGAGATA 59.759 50.000 6.32 0.00 0.00 1.98
473 1717 2.409241 GATAGAGAGGGACGTGGCGC 62.409 65.000 0.00 0.00 0.00 6.53
497 1743 2.495669 CTCTCTCTCTGTTGGGTCTTCC 59.504 54.545 0.00 0.00 0.00 3.46
505 1751 1.532316 TTGGGTCTTCCGTCCGTCT 60.532 57.895 0.00 0.00 38.76 4.18
554 1842 1.338020 CACCACAAACAGAAGGCTTCC 59.662 52.381 23.09 6.13 0.00 3.46
560 1848 3.117888 ACAAACAGAAGGCTTCCAGAAGA 60.118 43.478 23.09 0.00 40.79 2.87
561 1849 3.864789 AACAGAAGGCTTCCAGAAGAA 57.135 42.857 23.09 0.00 40.79 2.52
603 1891 2.034066 CCCGCCTCAGGAAGCAAA 59.966 61.111 0.00 0.00 0.00 3.68
616 1905 2.156310 GGAAGCAAAGCAAATCAAAGCG 59.844 45.455 0.00 0.00 35.48 4.68
619 1908 2.035066 AGCAAAGCAAATCAAAGCGTCT 59.965 40.909 0.00 0.00 35.48 4.18
704 1993 5.086058 CACGCAGTAATAAAACGCAAGAAT 58.914 37.500 0.00 0.00 41.61 2.40
705 1994 5.567534 CACGCAGTAATAAAACGCAAGAATT 59.432 36.000 0.00 0.00 41.61 2.17
706 1995 6.739100 CACGCAGTAATAAAACGCAAGAATTA 59.261 34.615 0.00 0.00 41.61 1.40
707 1996 7.428183 CACGCAGTAATAAAACGCAAGAATTAT 59.572 33.333 0.00 0.00 41.61 1.28
708 1997 8.605746 ACGCAGTAATAAAACGCAAGAATTATA 58.394 29.630 0.00 0.00 41.94 0.98
754 2044 6.759356 TCATTGCAAAAAGCTGGATTATCATG 59.241 34.615 1.71 0.00 45.94 3.07
787 2097 2.694628 TGTTTATATACGCTGACCCGGT 59.305 45.455 0.00 0.00 0.00 5.28
850 2164 3.473647 CAGCTCCTCGGGCCATCA 61.474 66.667 4.39 0.00 0.00 3.07
870 2187 0.538977 TCGTCGTCCCTCCTCTTTGT 60.539 55.000 0.00 0.00 0.00 2.83
886 2204 1.779061 TTGTCACCCCCTTCCTCTGC 61.779 60.000 0.00 0.00 0.00 4.26
893 2211 1.710816 CCCCTTCCTCTGCCTAGTAG 58.289 60.000 0.00 0.00 0.00 2.57
895 2213 2.177233 CCCCTTCCTCTGCCTAGTAGTA 59.823 54.545 0.00 0.00 0.00 1.82
913 2231 6.347696 AGTAGTAGTAGTGCCAGTACTAGTG 58.652 44.000 26.70 0.00 39.41 2.74
914 2232 4.525024 AGTAGTAGTGCCAGTACTAGTGG 58.475 47.826 21.07 5.62 38.30 4.00
1201 2522 0.036388 CATGGCCACCGTCAAGTACT 60.036 55.000 8.16 0.00 0.00 2.73
1203 2524 0.034337 TGGCCACCGTCAAGTACTTC 59.966 55.000 0.00 0.00 0.00 3.01
1226 2547 5.007234 TCTCTCTTCTCGCTTATCTTTCTCG 59.993 44.000 0.00 0.00 0.00 4.04
1227 2548 3.696898 TCTTCTCGCTTATCTTTCTCGC 58.303 45.455 0.00 0.00 0.00 5.03
1242 2563 4.327982 TTCTCGCCTTCATCCTATTCAG 57.672 45.455 0.00 0.00 0.00 3.02
1247 2568 2.289072 GCCTTCATCCTATTCAGCGCTA 60.289 50.000 10.99 0.00 0.00 4.26
1249 2570 3.006323 CCTTCATCCTATTCAGCGCTACT 59.994 47.826 10.99 0.00 0.00 2.57
1251 2572 3.222603 TCATCCTATTCAGCGCTACTCA 58.777 45.455 10.99 0.00 0.00 3.41
1283 2604 7.289782 AGCTACTTCAGTTCATCTATCCAATCT 59.710 37.037 0.00 0.00 0.00 2.40
1298 2619 9.766754 TCTATCCAATCTAATCTAATCTGCTCT 57.233 33.333 0.00 0.00 0.00 4.09
1386 2719 0.611200 TCACCACCACCACCGATTAG 59.389 55.000 0.00 0.00 0.00 1.73
1399 2732 1.021390 CGATTAGCCATCCGCCCATC 61.021 60.000 0.00 0.00 38.78 3.51
1408 2741 3.819652 CCGCCCATCCCATCCCAA 61.820 66.667 0.00 0.00 0.00 4.12
1462 2800 6.773976 TGGGTGGATAATAAGCAAGAAAAG 57.226 37.500 0.00 0.00 0.00 2.27
1551 2889 0.248565 AGACAGCACACGCATCTCAT 59.751 50.000 0.00 0.00 42.27 2.90
1606 2945 1.298859 GCTGACATCGGTGACCAACC 61.299 60.000 0.65 0.00 46.60 3.77
1615 2954 1.733526 GTGACCAACCGCTTTTGCT 59.266 52.632 0.00 0.00 44.80 3.91
1616 2955 0.102300 GTGACCAACCGCTTTTGCTT 59.898 50.000 0.00 0.00 44.80 3.91
1617 2956 1.335496 GTGACCAACCGCTTTTGCTTA 59.665 47.619 0.00 0.00 44.80 3.09
1618 2957 2.030274 GTGACCAACCGCTTTTGCTTAT 60.030 45.455 0.00 0.00 44.80 1.73
1619 2958 2.227865 TGACCAACCGCTTTTGCTTATC 59.772 45.455 0.00 0.00 44.80 1.75
1620 2959 2.227865 GACCAACCGCTTTTGCTTATCA 59.772 45.455 0.00 0.00 44.80 2.15
1621 2960 2.825532 ACCAACCGCTTTTGCTTATCAT 59.174 40.909 0.00 0.00 44.80 2.45
1622 2961 3.119495 ACCAACCGCTTTTGCTTATCATC 60.119 43.478 0.00 0.00 44.80 2.92
1623 2962 3.100817 CAACCGCTTTTGCTTATCATCG 58.899 45.455 0.00 0.00 44.80 3.84
1624 2963 2.356135 ACCGCTTTTGCTTATCATCGT 58.644 42.857 0.00 0.00 44.80 3.73
1625 2964 2.095853 ACCGCTTTTGCTTATCATCGTG 59.904 45.455 0.00 0.00 44.80 4.35
1626 2965 2.104144 CGCTTTTGCTTATCATCGTGC 58.896 47.619 0.00 0.00 44.80 5.34
1627 2966 2.104144 GCTTTTGCTTATCATCGTGCG 58.896 47.619 0.00 0.00 43.35 5.34
1628 2967 2.104144 CTTTTGCTTATCATCGTGCGC 58.896 47.619 0.00 0.00 0.00 6.09
1633 2972 1.002468 GCTTATCATCGTGCGCCATTT 60.002 47.619 4.18 0.00 0.00 2.32
1676 3015 2.104859 CAGTCAGGCAGTGCATCCG 61.105 63.158 18.61 0.00 0.00 4.18
1677 3016 3.503363 GTCAGGCAGTGCATCCGC 61.503 66.667 18.61 0.00 39.24 5.54
1808 3147 1.007734 ACTGTGTACGTGCACCTCG 60.008 57.895 29.93 20.88 38.52 4.63
1810 3149 0.109272 CTGTGTACGTGCACCTCGAT 60.109 55.000 29.93 0.00 38.52 3.59
1824 3163 4.186926 CACCTCGATGACATGATGAACTT 58.813 43.478 0.00 0.00 0.00 2.66
1825 3164 4.033702 CACCTCGATGACATGATGAACTTG 59.966 45.833 0.00 0.00 0.00 3.16
1828 3167 5.526479 CCTCGATGACATGATGAACTTGAAT 59.474 40.000 0.00 0.00 0.00 2.57
1834 3173 6.384224 TGACATGATGAACTTGAATTGCTTC 58.616 36.000 0.00 0.00 0.00 3.86
1838 3177 4.275689 TGATGAACTTGAATTGCTTCGTGT 59.724 37.500 0.00 0.00 33.86 4.49
1850 3189 8.134895 TGAATTGCTTCGTGTTCTTAGAATTTT 58.865 29.630 0.00 0.00 33.86 1.82
1851 3190 7.858052 ATTGCTTCGTGTTCTTAGAATTTTG 57.142 32.000 0.00 0.00 0.00 2.44
1902 3242 5.431420 TGTTTCATGTCAAATAAGCGTGT 57.569 34.783 0.00 0.00 0.00 4.49
1921 3261 2.488545 TGTCTAACTCTGCTCTCGGTTC 59.511 50.000 0.00 0.00 0.00 3.62
2083 3439 6.430925 TCACTTTCCACCTCACATAGAAAATG 59.569 38.462 0.00 0.00 0.00 2.32
2147 3505 4.399219 AGGCGATGACTCTAGCTTATGTA 58.601 43.478 0.00 0.00 0.00 2.29
2177 3535 5.736951 TGTCATATTTGTTTTTCAGGGGG 57.263 39.130 0.00 0.00 0.00 5.40
2396 3784 7.982761 ATATACCTAACCTTCAGACTCGTAG 57.017 40.000 0.00 0.00 0.00 3.51
2400 3788 4.033817 CCTAACCTTCAGACTCGTAGTACG 59.966 50.000 16.65 16.65 44.19 3.67
2428 3816 7.278646 TCTCTAATGACGACTTCCAAATGAATG 59.721 37.037 0.00 0.00 31.06 2.67
2676 4064 3.532641 AAGAAGGGAATCACAAAGCCT 57.467 42.857 0.00 0.00 0.00 4.58
2688 4076 3.565482 TCACAAAGCCTGAAATGTGAGAC 59.435 43.478 3.52 0.00 45.14 3.36
2711 4099 8.584157 AGACAGTGATGCATTTTATTTGGTTTA 58.416 29.630 0.00 0.00 0.00 2.01
2715 4103 9.941325 AGTGATGCATTTTATTTGGTTTATCAA 57.059 25.926 0.00 0.00 0.00 2.57
2954 4346 3.801698 CATCCATTCACCTGAGATTCGT 58.198 45.455 0.00 0.00 0.00 3.85
2974 4366 7.545362 TTCGTGAGACTAGTATGTACCTTAC 57.455 40.000 0.00 0.00 41.84 2.34
2988 4380 2.498167 ACCTTACTGTCTTGCTTGCAG 58.502 47.619 0.00 0.00 36.41 4.41
3009 4401 4.751600 CAGCTCAAATGTGTTGTCTGTCTA 59.248 41.667 0.00 0.00 0.00 2.59
3013 4405 6.544038 TCAAATGTGTTGTCTGTCTATGTG 57.456 37.500 0.00 0.00 0.00 3.21
3015 4407 7.213678 TCAAATGTGTTGTCTGTCTATGTGTA 58.786 34.615 0.00 0.00 0.00 2.90
3016 4408 7.877612 TCAAATGTGTTGTCTGTCTATGTGTAT 59.122 33.333 0.00 0.00 0.00 2.29
3077 4469 0.967380 CTGCACCAGGATTTCCCCAC 60.967 60.000 0.00 0.00 36.42 4.61
3089 4481 4.381185 GGATTTCCCCACGGTTTAATTGAC 60.381 45.833 0.00 0.00 0.00 3.18
3104 4496 4.519906 AATTGACCCCATCGAGGTAAAT 57.480 40.909 0.00 0.00 39.76 1.40
3105 4497 5.640158 AATTGACCCCATCGAGGTAAATA 57.360 39.130 5.55 0.00 37.46 1.40
3106 4498 5.843019 ATTGACCCCATCGAGGTAAATAT 57.157 39.130 3.58 0.00 36.78 1.28
3160 4552 2.022764 GCAAGTTTGGTGGTTGCTTT 57.977 45.000 0.00 0.00 42.70 3.51
3209 4601 2.099756 GGAGTTGGCTTCACAATATGGC 59.900 50.000 0.00 0.00 32.24 4.40
3262 4654 1.543802 CTTTGTATTGCCTTTCGCCCA 59.456 47.619 0.00 0.00 36.24 5.36
3343 4735 2.166459 TCTCTAATTGTGCCCTGACTCG 59.834 50.000 0.00 0.00 0.00 4.18
3386 4778 5.596836 TGTGCCAACTTTGAAGAAATTCT 57.403 34.783 0.00 0.00 0.00 2.40
3695 5089 9.459640 CATGGAATATTTATCTTCAGTTTGCTG 57.540 33.333 0.00 0.00 43.87 4.41
3714 5115 7.551035 TTGCTGTGCAATTTTCTAACATTTT 57.449 28.000 0.45 0.00 43.99 1.82
3715 5116 7.176285 TGCTGTGCAATTTTCTAACATTTTC 57.824 32.000 0.00 0.00 34.76 2.29
3716 5117 6.985645 TGCTGTGCAATTTTCTAACATTTTCT 59.014 30.769 0.00 0.00 34.76 2.52
3717 5118 7.169645 TGCTGTGCAATTTTCTAACATTTTCTC 59.830 33.333 0.00 0.00 34.76 2.87
3718 5119 7.359514 GCTGTGCAATTTTCTAACATTTTCTCC 60.360 37.037 0.00 0.00 0.00 3.71
3746 5147 0.676466 TGATTGGCGCCGTCATCTTT 60.676 50.000 25.18 3.91 0.00 2.52
3861 5273 9.153721 CATTTACTAACTGGACACCGTAATTTA 57.846 33.333 0.00 0.00 0.00 1.40
3963 5377 3.330701 TGTTGGCACTCCCTTTCTCTAAT 59.669 43.478 0.00 0.00 0.00 1.73
3968 5382 8.594550 GTTGGCACTCCCTTTCTCTAATATATA 58.405 37.037 0.00 0.00 0.00 0.86
3975 5389 9.983024 CTCCCTTTCTCTAATATATAGACCTGA 57.017 37.037 0.00 0.00 0.00 3.86
4315 5737 3.072038 CAGCATTCCTGATGTATCCTGGA 59.928 47.826 0.00 0.00 44.64 3.86
4354 5776 4.705023 CCAGGTTATTTGGAAAGTACTGGG 59.295 45.833 0.00 0.00 37.96 4.45
4413 5835 8.512138 AGGGTAAAGAAAACTGTTTGATTATCG 58.488 33.333 6.53 0.00 0.00 2.92
4522 5958 7.621832 TTTTCGCAATAAAAGTTGTGATCTG 57.378 32.000 4.03 0.00 45.04 2.90
4671 6107 6.653526 AAATGTGGAATGACAATGTCTGAA 57.346 33.333 14.97 0.00 33.15 3.02
4677 6113 6.599244 GTGGAATGACAATGTCTGAATCCTTA 59.401 38.462 14.97 0.45 33.15 2.69
4738 6174 6.774354 AATTGTTTGTGCAGAATTGATGAC 57.226 33.333 0.00 0.00 0.00 3.06
4906 6342 6.042143 CCAAATTAACCCGATTTCATCCAAG 58.958 40.000 0.00 0.00 0.00 3.61
5173 6609 2.359230 GCTCCCATCTATGGCGCC 60.359 66.667 22.73 22.73 46.70 6.53
5347 6802 2.195922 GCAAAACTGAAGGCACACAAG 58.804 47.619 0.00 0.00 0.00 3.16
5507 6963 1.539157 CAGCCCTTTCCAGTTTCCTC 58.461 55.000 0.00 0.00 0.00 3.71
5542 7004 2.561373 GCCCTTTTCGCGGACAAG 59.439 61.111 6.13 6.06 0.00 3.16
5614 7076 1.157870 ACGTATATTGCGGCACCAGC 61.158 55.000 0.05 0.00 41.10 4.85
5639 7101 2.071778 ACATGTTCAACACCCTTGCT 57.928 45.000 0.00 0.00 0.00 3.91
5819 7281 4.762289 ACAGCCGAAGAAGAATAGGATT 57.238 40.909 0.00 0.00 0.00 3.01
5837 7299 1.140312 TTGGAGCTGTGGGTTCTCTT 58.860 50.000 0.00 0.00 0.00 2.85
5882 7344 3.112126 AAATGCTCGGAATGGCGCG 62.112 57.895 0.00 0.00 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.150945 TGGTAGGATTTTTATAGCAGACATCTC 58.849 37.037 0.00 0.00 0.00 2.75
1 2 8.034313 TGGTAGGATTTTTATAGCAGACATCT 57.966 34.615 0.00 0.00 0.00 2.90
2 3 8.854614 ATGGTAGGATTTTTATAGCAGACATC 57.145 34.615 0.00 0.00 31.16 3.06
3 4 7.604164 CGATGGTAGGATTTTTATAGCAGACAT 59.396 37.037 0.00 0.00 31.16 3.06
4 5 6.929049 CGATGGTAGGATTTTTATAGCAGACA 59.071 38.462 0.00 0.00 31.16 3.41
5 6 6.369065 CCGATGGTAGGATTTTTATAGCAGAC 59.631 42.308 0.00 0.00 31.16 3.51
6 7 6.269077 TCCGATGGTAGGATTTTTATAGCAGA 59.731 38.462 0.00 0.00 31.86 4.26
7 8 6.464222 TCCGATGGTAGGATTTTTATAGCAG 58.536 40.000 0.00 0.00 31.86 4.24
8 9 6.428083 TCCGATGGTAGGATTTTTATAGCA 57.572 37.500 0.00 0.00 31.86 3.49
9 10 7.444487 AGTTTCCGATGGTAGGATTTTTATAGC 59.556 37.037 0.00 0.00 37.65 2.97
10 11 8.904099 AGTTTCCGATGGTAGGATTTTTATAG 57.096 34.615 0.00 0.00 37.65 1.31
11 12 8.487848 TGAGTTTCCGATGGTAGGATTTTTATA 58.512 33.333 0.00 0.00 37.65 0.98
12 13 7.343357 TGAGTTTCCGATGGTAGGATTTTTAT 58.657 34.615 0.00 0.00 37.65 1.40
13 14 6.713276 TGAGTTTCCGATGGTAGGATTTTTA 58.287 36.000 0.00 0.00 37.65 1.52
14 15 5.566469 TGAGTTTCCGATGGTAGGATTTTT 58.434 37.500 0.00 0.00 37.65 1.94
15 16 5.174037 TGAGTTTCCGATGGTAGGATTTT 57.826 39.130 0.00 0.00 37.65 1.82
16 17 4.837093 TGAGTTTCCGATGGTAGGATTT 57.163 40.909 0.00 0.00 37.65 2.17
17 18 5.373812 AATGAGTTTCCGATGGTAGGATT 57.626 39.130 0.00 0.00 37.65 3.01
18 19 5.104527 TGAAATGAGTTTCCGATGGTAGGAT 60.105 40.000 0.00 0.00 42.44 3.24
19 20 4.224147 TGAAATGAGTTTCCGATGGTAGGA 59.776 41.667 0.00 0.00 42.44 2.94
20 21 4.513442 TGAAATGAGTTTCCGATGGTAGG 58.487 43.478 0.00 0.00 42.44 3.18
21 22 6.683974 AATGAAATGAGTTTCCGATGGTAG 57.316 37.500 0.00 0.00 42.44 3.18
22 23 9.839817 TTATAATGAAATGAGTTTCCGATGGTA 57.160 29.630 0.00 0.00 42.44 3.25
23 24 8.621286 GTTATAATGAAATGAGTTTCCGATGGT 58.379 33.333 0.00 0.00 42.44 3.55
24 25 8.620416 TGTTATAATGAAATGAGTTTCCGATGG 58.380 33.333 0.00 0.00 42.44 3.51
25 26 9.655769 CTGTTATAATGAAATGAGTTTCCGATG 57.344 33.333 0.00 0.00 42.44 3.84
26 27 9.613428 TCTGTTATAATGAAATGAGTTTCCGAT 57.387 29.630 0.00 0.00 42.44 4.18
27 28 8.879759 GTCTGTTATAATGAAATGAGTTTCCGA 58.120 33.333 0.00 0.00 42.44 4.55
28 29 8.664798 TGTCTGTTATAATGAAATGAGTTTCCG 58.335 33.333 0.00 0.00 42.44 4.30
29 30 9.774742 GTGTCTGTTATAATGAAATGAGTTTCC 57.225 33.333 0.00 0.00 42.44 3.13
30 31 9.478019 CGTGTCTGTTATAATGAAATGAGTTTC 57.522 33.333 0.00 0.00 43.22 2.78
31 32 8.999431 ACGTGTCTGTTATAATGAAATGAGTTT 58.001 29.630 0.00 0.00 0.00 2.66
32 33 8.547967 ACGTGTCTGTTATAATGAAATGAGTT 57.452 30.769 0.00 0.00 0.00 3.01
33 34 8.547967 AACGTGTCTGTTATAATGAAATGAGT 57.452 30.769 0.00 0.00 0.00 3.41
44 45 9.471084 CCAATCATGTATAACGTGTCTGTTATA 57.529 33.333 0.00 3.01 41.88 0.98
45 46 7.985184 ACCAATCATGTATAACGTGTCTGTTAT 59.015 33.333 0.00 4.73 44.81 1.89
46 47 7.324935 ACCAATCATGTATAACGTGTCTGTTA 58.675 34.615 0.00 0.00 36.53 2.41
47 48 6.170506 ACCAATCATGTATAACGTGTCTGTT 58.829 36.000 0.00 0.00 36.53 3.16
48 49 5.730550 ACCAATCATGTATAACGTGTCTGT 58.269 37.500 0.00 0.00 36.53 3.41
49 50 6.042777 AGACCAATCATGTATAACGTGTCTG 58.957 40.000 0.00 0.00 36.53 3.51
50 51 6.222038 AGACCAATCATGTATAACGTGTCT 57.778 37.500 0.00 0.00 36.53 3.41
51 52 7.997107 TTAGACCAATCATGTATAACGTGTC 57.003 36.000 0.00 0.00 36.53 3.67
52 53 8.958119 ATTTAGACCAATCATGTATAACGTGT 57.042 30.769 0.00 0.00 36.53 4.49
60 61 9.913310 TTGACCAATATTTAGACCAATCATGTA 57.087 29.630 0.00 0.00 0.00 2.29
61 62 8.821686 TTGACCAATATTTAGACCAATCATGT 57.178 30.769 0.00 0.00 0.00 3.21
62 63 9.740239 CTTTGACCAATATTTAGACCAATCATG 57.260 33.333 0.00 0.00 0.00 3.07
63 64 9.479549 ACTTTGACCAATATTTAGACCAATCAT 57.520 29.630 0.00 0.00 0.00 2.45
64 65 8.877864 ACTTTGACCAATATTTAGACCAATCA 57.122 30.769 0.00 0.00 0.00 2.57
73 74 9.893634 TCCGAGATTTACTTTGACCAATATTTA 57.106 29.630 0.00 0.00 0.00 1.40
74 75 8.801882 TCCGAGATTTACTTTGACCAATATTT 57.198 30.769 0.00 0.00 0.00 1.40
75 76 8.801882 TTCCGAGATTTACTTTGACCAATATT 57.198 30.769 0.00 0.00 0.00 1.28
76 77 8.980481 ATTCCGAGATTTACTTTGACCAATAT 57.020 30.769 0.00 0.00 0.00 1.28
77 78 9.321562 GTATTCCGAGATTTACTTTGACCAATA 57.678 33.333 0.00 0.00 0.00 1.90
78 79 7.827236 TGTATTCCGAGATTTACTTTGACCAAT 59.173 33.333 0.00 0.00 0.00 3.16
79 80 7.118680 GTGTATTCCGAGATTTACTTTGACCAA 59.881 37.037 0.00 0.00 0.00 3.67
80 81 6.592607 GTGTATTCCGAGATTTACTTTGACCA 59.407 38.462 0.00 0.00 0.00 4.02
81 82 6.036844 GGTGTATTCCGAGATTTACTTTGACC 59.963 42.308 0.00 0.00 0.00 4.02
82 83 7.001695 GGTGTATTCCGAGATTTACTTTGAC 57.998 40.000 0.00 0.00 0.00 3.18
107 108 4.659088 GAATTGGGTTTTCGCTAGTAAGC 58.341 43.478 0.00 0.00 45.86 3.09
108 109 4.201783 CCGAATTGGGTTTTCGCTAGTAAG 60.202 45.833 0.00 0.00 43.44 2.34
109 110 3.685756 CCGAATTGGGTTTTCGCTAGTAA 59.314 43.478 0.00 0.00 43.44 2.24
110 111 3.264104 CCGAATTGGGTTTTCGCTAGTA 58.736 45.455 0.00 0.00 43.44 1.82
111 112 2.081462 CCGAATTGGGTTTTCGCTAGT 58.919 47.619 0.00 0.00 43.44 2.57
112 113 2.081462 ACCGAATTGGGTTTTCGCTAG 58.919 47.619 6.28 0.00 43.44 3.42
113 114 1.807742 CACCGAATTGGGTTTTCGCTA 59.192 47.619 9.76 0.00 43.44 4.26
114 115 0.596082 CACCGAATTGGGTTTTCGCT 59.404 50.000 9.76 0.00 43.44 4.93
115 116 1.006825 GCACCGAATTGGGTTTTCGC 61.007 55.000 9.76 6.66 43.44 4.70
116 117 0.388006 GGCACCGAATTGGGTTTTCG 60.388 55.000 9.76 0.00 44.64 3.46
117 118 0.037697 GGGCACCGAATTGGGTTTTC 60.038 55.000 9.76 2.41 44.64 2.29
118 119 2.054458 GGGCACCGAATTGGGTTTT 58.946 52.632 9.76 0.00 44.64 2.43
119 120 3.785982 GGGCACCGAATTGGGTTT 58.214 55.556 9.76 0.00 44.64 3.27
143 144 4.612412 TTCGGACCGGGTGCACAC 62.612 66.667 20.43 15.50 0.00 3.82
144 145 2.888464 TTTTTCGGACCGGGTGCACA 62.888 55.000 20.43 1.14 0.00 4.57
145 146 2.188161 TTTTTCGGACCGGGTGCAC 61.188 57.895 19.13 8.80 0.00 4.57
146 147 2.192443 TTTTTCGGACCGGGTGCA 59.808 55.556 19.13 3.22 0.00 4.57
238 239 1.894756 CACCCGCCCTGACGAAAAA 60.895 57.895 0.00 0.00 34.06 1.94
239 240 2.281208 CACCCGCCCTGACGAAAA 60.281 61.111 0.00 0.00 34.06 2.29
244 245 4.101448 ATCTGCACCCGCCCTGAC 62.101 66.667 0.00 0.00 37.32 3.51
245 246 4.100084 CATCTGCACCCGCCCTGA 62.100 66.667 0.00 0.00 37.32 3.86
246 247 4.100084 TCATCTGCACCCGCCCTG 62.100 66.667 0.00 0.00 37.32 4.45
247 248 3.790437 CTCATCTGCACCCGCCCT 61.790 66.667 0.00 0.00 37.32 5.19
249 250 4.479993 AGCTCATCTGCACCCGCC 62.480 66.667 0.00 0.00 37.32 6.13
250 251 2.894387 GAGCTCATCTGCACCCGC 60.894 66.667 9.40 0.00 39.24 6.13
251 252 2.584418 CGAGCTCATCTGCACCCG 60.584 66.667 15.40 0.00 34.99 5.28
252 253 2.202987 CCGAGCTCATCTGCACCC 60.203 66.667 15.40 0.00 34.99 4.61
253 254 2.202987 CCCGAGCTCATCTGCACC 60.203 66.667 15.40 0.00 34.99 5.01
254 255 1.227205 CTCCCGAGCTCATCTGCAC 60.227 63.158 15.40 0.00 34.99 4.57
255 256 3.214253 CTCCCGAGCTCATCTGCA 58.786 61.111 15.40 0.00 34.99 4.41
265 266 4.821589 GGCGTTCCTGCTCCCGAG 62.822 72.222 0.00 0.00 34.52 4.63
273 274 2.890847 CTAGGAGTGCGGCGTTCCTG 62.891 65.000 27.83 18.40 41.33 3.86
274 275 2.678934 TAGGAGTGCGGCGTTCCT 60.679 61.111 24.99 24.99 43.53 3.36
275 276 2.202756 CTAGGAGTGCGGCGTTCC 60.203 66.667 9.37 13.55 0.00 3.62
276 277 1.226717 CTCTAGGAGTGCGGCGTTC 60.227 63.158 9.37 4.14 0.00 3.95
277 278 0.679002 TACTCTAGGAGTGCGGCGTT 60.679 55.000 9.37 0.00 43.30 4.84
278 279 1.077930 TACTCTAGGAGTGCGGCGT 60.078 57.895 9.37 0.00 43.30 5.68
279 280 1.649815 CTACTCTAGGAGTGCGGCG 59.350 63.158 0.51 0.51 43.30 6.46
289 290 5.068460 CAGGATCACAAACCTCCTACTCTAG 59.932 48.000 0.00 0.00 37.30 2.43
290 291 4.956700 CAGGATCACAAACCTCCTACTCTA 59.043 45.833 0.00 0.00 37.30 2.43
291 292 3.772025 CAGGATCACAAACCTCCTACTCT 59.228 47.826 0.00 0.00 37.30 3.24
343 344 6.433093 GGAGTCTAGCCCTTTCATTTTTACAA 59.567 38.462 0.00 0.00 0.00 2.41
356 357 1.380112 GTCACCGGAGTCTAGCCCT 60.380 63.158 9.46 0.00 0.00 5.19
359 360 0.966370 AGGTGTCACCGGAGTCTAGC 60.966 60.000 16.44 0.99 44.90 3.42
362 1602 1.606889 GGAGGTGTCACCGGAGTCT 60.607 63.158 16.44 0.00 44.90 3.24
373 1613 1.202651 CGGAACTGAAACAGGAGGTGT 60.203 52.381 0.00 0.00 43.24 4.16
400 1640 6.398918 TGCTTGCCTACTTACAAAACAAAAA 58.601 32.000 0.00 0.00 0.00 1.94
401 1641 5.967088 TGCTTGCCTACTTACAAAACAAAA 58.033 33.333 0.00 0.00 0.00 2.44
402 1642 5.584253 TGCTTGCCTACTTACAAAACAAA 57.416 34.783 0.00 0.00 0.00 2.83
403 1643 5.344884 GTTGCTTGCCTACTTACAAAACAA 58.655 37.500 0.00 0.00 0.00 2.83
404 1644 4.496673 CGTTGCTTGCCTACTTACAAAACA 60.497 41.667 0.00 0.00 0.00 2.83
405 1645 3.972502 CGTTGCTTGCCTACTTACAAAAC 59.027 43.478 0.00 0.00 0.00 2.43
406 1646 3.549221 GCGTTGCTTGCCTACTTACAAAA 60.549 43.478 0.00 0.00 0.00 2.44
407 1647 2.031508 GCGTTGCTTGCCTACTTACAAA 60.032 45.455 0.00 0.00 0.00 2.83
413 1653 1.369625 GTATGCGTTGCTTGCCTACT 58.630 50.000 0.00 0.00 32.73 2.57
421 1661 2.031157 GTCAACAAAGGTATGCGTTGCT 60.031 45.455 0.00 0.00 38.85 3.91
424 1664 1.533731 CGGTCAACAAAGGTATGCGTT 59.466 47.619 0.00 0.00 0.00 4.84
444 1684 3.009143 GTCCCTCTCTATCTCTCTCTCCC 59.991 56.522 0.00 0.00 0.00 4.30
473 1717 2.099405 GACCCAACAGAGAGAGAGAGG 58.901 57.143 0.00 0.00 0.00 3.69
474 1718 3.085952 AGACCCAACAGAGAGAGAGAG 57.914 52.381 0.00 0.00 0.00 3.20
475 1719 3.426615 GAAGACCCAACAGAGAGAGAGA 58.573 50.000 0.00 0.00 0.00 3.10
476 1720 2.495669 GGAAGACCCAACAGAGAGAGAG 59.504 54.545 0.00 0.00 34.14 3.20
477 1721 2.530701 GGAAGACCCAACAGAGAGAGA 58.469 52.381 0.00 0.00 34.14 3.10
505 1751 2.632602 TTTGTCTTTGGCTGGCCGGA 62.633 55.000 18.31 0.00 39.42 5.14
528 1774 2.292267 CTTCTGTTTGTGGTGCTCTGT 58.708 47.619 0.00 0.00 0.00 3.41
529 1775 1.605710 CCTTCTGTTTGTGGTGCTCTG 59.394 52.381 0.00 0.00 0.00 3.35
530 1776 1.972872 CCTTCTGTTTGTGGTGCTCT 58.027 50.000 0.00 0.00 0.00 4.09
554 1842 5.391523 CGTCTTCTGGTCTAGTCTTCTTCTG 60.392 48.000 0.00 0.00 0.00 3.02
560 1848 3.191791 GCTTCGTCTTCTGGTCTAGTCTT 59.808 47.826 0.00 0.00 0.00 3.01
561 1849 2.750712 GCTTCGTCTTCTGGTCTAGTCT 59.249 50.000 0.00 0.00 0.00 3.24
562 1850 2.750712 AGCTTCGTCTTCTGGTCTAGTC 59.249 50.000 0.00 0.00 0.00 2.59
603 1891 5.446473 CGATTTCTAGACGCTTTGATTTGCT 60.446 40.000 0.00 0.00 0.00 3.91
616 1905 3.444916 TCAATGCCGTCGATTTCTAGAC 58.555 45.455 0.00 0.00 0.00 2.59
619 1908 4.794248 CAATCAATGCCGTCGATTTCTA 57.206 40.909 0.00 0.00 0.00 2.10
715 2004 9.985318 CTTTTTGCAATGAAAACTTGACATAAA 57.015 25.926 0.00 0.00 0.00 1.40
754 2044 4.989168 CGTATATAAACAGGGGAAGAGTGC 59.011 45.833 0.00 0.00 0.00 4.40
787 2097 1.342975 TGAGGAAGATGATCCGGGTCA 60.343 52.381 22.11 22.11 44.60 4.02
850 2164 0.818296 CAAAGAGGAGGGACGACGAT 59.182 55.000 0.00 0.00 0.00 3.73
870 2187 1.821966 TAGGCAGAGGAAGGGGGTGA 61.822 60.000 0.00 0.00 0.00 4.02
886 2204 5.927819 AGTACTGGCACTACTACTACTAGG 58.072 45.833 5.18 0.00 0.00 3.02
893 2211 4.268359 ACCACTAGTACTGGCACTACTAC 58.732 47.826 5.39 0.00 31.13 2.73
895 2213 3.453059 ACCACTAGTACTGGCACTACT 57.547 47.619 5.39 10.90 31.13 2.57
1189 2510 4.400120 AGAAGAGAGAAGTACTTGACGGT 58.600 43.478 14.14 0.00 0.00 4.83
1201 2522 6.457663 CGAGAAAGATAAGCGAGAAGAGAGAA 60.458 42.308 0.00 0.00 0.00 2.87
1203 2524 5.204833 CGAGAAAGATAAGCGAGAAGAGAG 58.795 45.833 0.00 0.00 0.00 3.20
1226 2547 0.871057 GCGCTGAATAGGATGAAGGC 59.129 55.000 0.00 0.00 0.00 4.35
1227 2548 2.540265 AGCGCTGAATAGGATGAAGG 57.460 50.000 10.39 0.00 0.00 3.46
1242 2563 4.752661 AGTAGCTATAGTTGAGTAGCGC 57.247 45.455 0.00 0.00 46.05 5.92
1247 2568 7.704578 TGAACTGAAGTAGCTATAGTTGAGT 57.295 36.000 15.67 9.03 39.55 3.41
1249 2570 8.526667 AGATGAACTGAAGTAGCTATAGTTGA 57.473 34.615 15.67 10.58 32.23 3.18
1283 2604 4.876125 CGGAGCAAGAGCAGATTAGATTA 58.124 43.478 0.00 0.00 45.49 1.75
1386 2719 4.290622 ATGGGATGGGCGGATGGC 62.291 66.667 0.00 0.00 42.51 4.40
1399 2732 1.305213 CTGGTTGGGTTGGGATGGG 60.305 63.158 0.00 0.00 0.00 4.00
1408 2741 1.973281 CGATTGCTGCTGGTTGGGT 60.973 57.895 0.00 0.00 0.00 4.51
1576 2914 1.070601 CGATGTCAGCATGGATGGGTA 59.929 52.381 0.00 0.00 35.07 3.69
1606 2945 2.104144 GCACGATGATAAGCAAAAGCG 58.896 47.619 0.00 0.00 0.00 4.68
1608 2947 2.104144 GCGCACGATGATAAGCAAAAG 58.896 47.619 0.30 0.00 0.00 2.27
1611 2950 0.742635 TGGCGCACGATGATAAGCAA 60.743 50.000 10.83 0.00 0.00 3.91
1615 2954 2.013400 ACAAATGGCGCACGATGATAA 58.987 42.857 10.83 0.00 0.00 1.75
1616 2955 1.330213 CACAAATGGCGCACGATGATA 59.670 47.619 10.83 0.00 0.00 2.15
1617 2956 0.099259 CACAAATGGCGCACGATGAT 59.901 50.000 10.83 0.00 0.00 2.45
1618 2957 1.501292 CACAAATGGCGCACGATGA 59.499 52.632 10.83 0.00 0.00 2.92
1619 2958 2.153945 GCACAAATGGCGCACGATG 61.154 57.895 10.83 5.25 0.00 3.84
1620 2959 2.179018 GCACAAATGGCGCACGAT 59.821 55.556 10.83 0.00 0.00 3.73
1621 2960 2.977456 AGCACAAATGGCGCACGA 60.977 55.556 10.83 0.00 36.08 4.35
1622 2961 2.801996 CAGCACAAATGGCGCACG 60.802 61.111 10.83 0.00 36.08 5.34
1623 2962 3.107661 GCAGCACAAATGGCGCAC 61.108 61.111 10.83 0.00 36.08 5.34
1624 2963 3.561217 CTGCAGCACAAATGGCGCA 62.561 57.895 10.83 0.00 38.03 6.09
1625 2964 2.807895 CTGCAGCACAAATGGCGC 60.808 61.111 0.00 0.00 36.08 6.53
1626 2965 2.126228 CCTGCAGCACAAATGGCG 60.126 61.111 8.66 0.00 36.08 5.69
1627 2966 0.947180 CAACCTGCAGCACAAATGGC 60.947 55.000 8.66 0.00 0.00 4.40
1628 2967 0.390124 ACAACCTGCAGCACAAATGG 59.610 50.000 8.66 0.00 0.00 3.16
1633 2972 1.727511 GCTCAACAACCTGCAGCACA 61.728 55.000 8.66 0.00 0.00 4.57
1672 3011 0.678048 GCAGGTTCTTCTTGGCGGAT 60.678 55.000 0.00 0.00 0.00 4.18
1676 3015 0.238553 GTTCGCAGGTTCTTCTTGGC 59.761 55.000 0.00 0.00 0.00 4.52
1677 3016 0.875059 GGTTCGCAGGTTCTTCTTGG 59.125 55.000 0.00 0.00 0.00 3.61
1792 3131 0.388006 CATCGAGGTGCACGTACACA 60.388 55.000 20.08 0.13 42.55 3.72
1808 3147 6.561614 AGCAATTCAAGTTCATCATGTCATC 58.438 36.000 0.00 0.00 0.00 2.92
1810 3149 5.970317 AGCAATTCAAGTTCATCATGTCA 57.030 34.783 0.00 0.00 0.00 3.58
1824 3163 6.801539 ATTCTAAGAACACGAAGCAATTCA 57.198 33.333 0.00 0.00 0.00 2.57
1825 3164 8.420189 CAAAATTCTAAGAACACGAAGCAATTC 58.580 33.333 0.00 0.00 0.00 2.17
1828 3167 7.022055 TCAAAATTCTAAGAACACGAAGCAA 57.978 32.000 0.00 0.00 0.00 3.91
1850 3189 9.778741 AATGTGAAAACACTAGAGTAGAATTCA 57.221 29.630 8.44 2.13 0.00 2.57
1883 3223 6.649141 AGTTAGACACGCTTATTTGACATGAA 59.351 34.615 0.00 0.00 0.00 2.57
1902 3242 2.093106 GGAACCGAGAGCAGAGTTAGA 58.907 52.381 0.00 0.00 0.00 2.10
1921 3261 2.146342 CCCAGCGATATAACTGCAAGG 58.854 52.381 0.00 0.00 39.30 3.61
2114 3472 6.596309 AGAGTCATCGCCTATCATTATGAA 57.404 37.500 0.00 0.00 0.00 2.57
2115 3473 6.183360 GCTAGAGTCATCGCCTATCATTATGA 60.183 42.308 0.00 0.00 0.00 2.15
2116 3474 5.976534 GCTAGAGTCATCGCCTATCATTATG 59.023 44.000 0.00 0.00 0.00 1.90
2152 3510 7.167535 CCCCCTGAAAAACAAATATGACATTT 58.832 34.615 0.00 0.00 0.00 2.32
2177 3535 8.860128 GGTAGCATGTAAATTTTAAGAAAGTGC 58.140 33.333 0.00 0.00 0.00 4.40
2344 3731 1.135689 GGCCTATTCACACGCAACTTG 60.136 52.381 0.00 0.00 0.00 3.16
2396 3784 5.027099 GGAAGTCGTCATTAGAGAACGTAC 58.973 45.833 0.00 0.00 0.00 3.67
2400 3788 6.590292 TCATTTGGAAGTCGTCATTAGAGAAC 59.410 38.462 0.00 0.00 0.00 3.01
2445 3833 5.047731 TGTGTGTGAAAACCTGAAAACATGA 60.048 36.000 0.00 0.00 0.00 3.07
2446 3834 5.167121 TGTGTGTGAAAACCTGAAAACATG 58.833 37.500 0.00 0.00 0.00 3.21
2676 4064 3.742385 TGCATCACTGTCTCACATTTCA 58.258 40.909 0.00 0.00 0.00 2.69
2688 4076 9.368674 TGATAAACCAAATAAAATGCATCACTG 57.631 29.630 0.00 0.00 0.00 3.66
2711 4099 5.512921 CCAAAGCAAAAAGGTATGGGTTGAT 60.513 40.000 0.00 0.00 0.00 2.57
2715 4103 3.582164 TCCAAAGCAAAAAGGTATGGGT 58.418 40.909 0.00 0.00 0.00 4.51
2718 4106 3.428534 GCGTTCCAAAGCAAAAAGGTATG 59.571 43.478 0.00 0.00 33.47 2.39
2954 4346 7.859540 AGACAGTAAGGTACATACTAGTCTCA 58.140 38.462 21.24 0.00 41.19 3.27
2988 4380 5.180117 ACATAGACAGACAACACATTTGAGC 59.820 40.000 0.00 0.00 0.00 4.26
3009 4401 8.367156 AGTTTGTTAAAAGGCATCAATACACAT 58.633 29.630 0.00 0.00 0.00 3.21
3016 4408 9.474920 CAATAGAAGTTTGTTAAAAGGCATCAA 57.525 29.630 0.00 0.00 0.00 2.57
3077 4469 2.612212 CTCGATGGGGTCAATTAAACCG 59.388 50.000 3.73 0.00 37.69 4.44
3089 4481 5.160607 TGCTAATATTTACCTCGATGGGG 57.839 43.478 0.00 0.00 41.11 4.96
3104 4496 6.635641 CGCAAGAAGTACGACTAATGCTAATA 59.364 38.462 13.06 0.00 43.02 0.98
3105 4497 5.459107 CGCAAGAAGTACGACTAATGCTAAT 59.541 40.000 13.06 0.00 43.02 1.73
3106 4498 4.796830 CGCAAGAAGTACGACTAATGCTAA 59.203 41.667 13.06 0.00 43.02 3.09
3209 4601 5.051039 GCATAGATCAACATGCAAGCAAATG 60.051 40.000 17.28 0.00 45.51 2.32
3262 4654 6.668283 TGAGAAGAGTAAGTACCCAAGCTTAT 59.332 38.462 0.00 0.00 31.02 1.73
3343 4735 6.455646 GCACATGTATTACTACTGCTGACAAC 60.456 42.308 0.00 0.00 0.00 3.32
3435 4827 8.800370 TCCATTGAAAGTTGTAGCACAATATA 57.200 30.769 5.26 0.00 40.59 0.86
3436 4828 7.701539 TCCATTGAAAGTTGTAGCACAATAT 57.298 32.000 5.26 0.00 40.59 1.28
3537 4931 8.021898 TGACAGAAAAATCAAAAGGAGGAATT 57.978 30.769 0.00 0.00 0.00 2.17
3695 5089 7.154656 AGGGAGAAAATGTTAGAAAATTGCAC 58.845 34.615 0.00 0.00 0.00 4.57
3701 5095 8.977412 ACAAAAGAGGGAGAAAATGTTAGAAAA 58.023 29.630 0.00 0.00 0.00 2.29
3714 5115 2.795329 GCCAATCACAAAAGAGGGAGA 58.205 47.619 0.00 0.00 0.00 3.71
3715 5116 1.470098 CGCCAATCACAAAAGAGGGAG 59.530 52.381 0.00 0.00 0.00 4.30
3716 5117 1.533625 CGCCAATCACAAAAGAGGGA 58.466 50.000 0.00 0.00 0.00 4.20
3717 5118 0.109132 GCGCCAATCACAAAAGAGGG 60.109 55.000 0.00 0.00 0.00 4.30
3718 5119 0.109132 GGCGCCAATCACAAAAGAGG 60.109 55.000 24.80 0.00 0.00 3.69
3746 5147 6.044046 GGTGCTGAATTTGATGCAAATATCA 58.956 36.000 5.88 10.08 42.32 2.15
3810 5211 4.999311 TGAAGTCAGGATCTGATTGTGTTG 59.001 41.667 0.72 0.00 42.73 3.33
3938 5352 1.494721 AGAAAGGGAGTGCCAACAAGA 59.505 47.619 2.50 0.00 35.15 3.02
3939 5353 1.882623 GAGAAAGGGAGTGCCAACAAG 59.117 52.381 2.50 0.00 35.15 3.16
3942 5356 3.418684 TTAGAGAAAGGGAGTGCCAAC 57.581 47.619 2.50 0.00 35.15 3.77
3968 5382 4.465886 CCACTACTATACAGCTCAGGTCT 58.534 47.826 0.00 0.00 0.00 3.85
3975 5389 3.226777 CAGAGGCCACTACTATACAGCT 58.773 50.000 5.01 0.00 0.00 4.24
3989 5403 1.453928 GCCACCATTACCAGAGGCC 60.454 63.158 0.00 0.00 36.17 5.19
4279 5701 7.568349 TCAGGAATGCTGTTCTAATACAGAAT 58.432 34.615 7.88 0.00 44.62 2.40
4315 5737 1.402787 CTGGAAAACAAGCACCAGGT 58.597 50.000 0.00 0.00 44.04 4.00
4354 5776 8.103948 TCTTCTTTGAGACTTCCATGATTTTC 57.896 34.615 0.00 0.00 0.00 2.29
4413 5835 6.986904 ACTTTATAGTAGGCTTTCAAGCAC 57.013 37.500 13.45 4.13 42.67 4.40
4629 6065 7.207383 CACATTTACGAGGACATCTGGTATAA 58.793 38.462 0.00 0.00 36.73 0.98
4640 6076 4.250464 TGTCATTCCACATTTACGAGGAC 58.750 43.478 0.00 0.00 0.00 3.85
4738 6174 6.377996 TCCCAATCACAAATAAACCTGAGATG 59.622 38.462 0.00 0.00 0.00 2.90
4837 6273 1.135721 GCATTGAGGTGCCATCCTTTC 59.864 52.381 0.00 0.00 39.18 2.62
5173 6609 4.161295 TCCGGCATCTTCCCAGCG 62.161 66.667 0.00 0.00 0.00 5.18
5255 6705 9.768662 TGTACGTATACATGTTACAGAGAGATA 57.231 33.333 2.30 0.00 36.34 1.98
5276 6726 1.617755 CTGTCACTGCGGCTTGTACG 61.618 60.000 0.00 0.00 0.00 3.67
5347 6802 6.552445 AGATACATGTCTATATTGGAGGCC 57.448 41.667 0.00 0.00 0.00 5.19
5429 6884 3.761218 TGTCAGAGAGAGCAAGGAAGTAG 59.239 47.826 0.00 0.00 0.00 2.57
5542 7004 0.108615 TAGAGCTGCGCTGGAAGAAC 60.109 55.000 16.38 0.00 39.88 3.01
5614 7076 2.487762 AGGGTGTTGAACATGTTATGCG 59.512 45.455 11.95 0.00 0.00 4.73
5639 7101 1.829849 CACAAGATCAGGGAGCAGAGA 59.170 52.381 0.00 0.00 0.00 3.10
5681 7143 1.626356 CCGCCTTCTCCAGGGATCAA 61.626 60.000 0.00 0.00 44.16 2.57
5819 7281 0.397941 CAAGAGAACCCACAGCTCCA 59.602 55.000 0.00 0.00 0.00 3.86
5882 7344 0.038166 TTGGACCAGGAACAGGATGC 59.962 55.000 0.00 0.00 42.53 3.91
6054 7525 1.376424 TTACTCTGCTGCTGCTGCC 60.376 57.895 25.44 10.66 40.48 4.85


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

AutoCloner maintained by Alex Coulton.