Multiple sequence alignment - TraesCS1D01G080300

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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 TraesCS1D01G080300 chr1D 100.000 3099 0 0 1 3099 62856881 62859979 0.000000e+00 5723.0
1 TraesCS1D01G080300 chr1D 94.231 52 3 0 1210 1261 62564158 62564209 2.560000e-11 80.5
2 TraesCS1D01G080300 chr1B 91.623 2268 73 43 108 2315 100307606 100309816 0.000000e+00 3027.0
3 TraesCS1D01G080300 chr1B 95.349 129 5 1 2873 3001 100310626 100310753 1.460000e-48 204.0
4 TraesCS1D01G080300 chr1B 89.431 123 10 3 2529 2651 100309938 100310057 5.350000e-33 152.0
5 TraesCS1D01G080300 chr1B 89.423 104 11 0 2417 2520 572205675 572205778 6.970000e-27 132.0
6 TraesCS1D01G080300 chr1B 85.586 111 6 2 2659 2769 100310359 100310459 1.180000e-19 108.0
7 TraesCS1D01G080300 chr1A 89.698 2388 131 56 122 2429 60957173 60954821 0.000000e+00 2940.0
8 TraesCS1D01G080300 chr1A 85.654 237 17 5 2876 3099 60954444 60954212 1.860000e-57 233.0
9 TraesCS1D01G080300 chr1A 90.476 105 9 1 2421 2525 340015098 340014995 1.500000e-28 137.0
10 TraesCS1D01G080300 chr1A 90.291 103 9 1 2420 2522 347943213 347943314 1.940000e-27 134.0
11 TraesCS1D01G080300 chr1A 94.231 52 3 0 1210 1261 60537496 60537547 2.560000e-11 80.5
12 TraesCS1D01G080300 chrUn 73.866 1014 214 45 1112 2103 114968328 114967344 1.060000e-94 357.0
13 TraesCS1D01G080300 chr6B 73.570 1014 203 51 1109 2100 89513776 89514746 8.290000e-86 327.0
14 TraesCS1D01G080300 chr2A 77.598 433 78 10 1318 1742 94157934 94158355 8.580000e-61 244.0
15 TraesCS1D01G080300 chr2A 73.598 428 82 22 1326 1739 94108256 94108666 5.390000e-28 135.0
16 TraesCS1D01G080300 chr2B 77.725 422 74 12 1330 1742 146992844 146993254 1.110000e-59 241.0
17 TraesCS1D01G080300 chr2B 72.523 666 119 45 1116 1739 146964014 146964657 1.150000e-34 158.0
18 TraesCS1D01G080300 chr7B 79.942 344 53 14 1407 1739 535614657 535614995 3.990000e-59 239.0
19 TraesCS1D01G080300 chr7A 79.598 348 54 16 1407 1742 574754186 574754528 1.860000e-57 233.0
20 TraesCS1D01G080300 chr7A 94.231 52 3 0 1210 1261 669727984 669728035 2.560000e-11 80.5
21 TraesCS1D01G080300 chr2D 77.241 435 76 16 1318 1742 95645044 95645465 1.860000e-57 233.0
22 TraesCS1D01G080300 chr2D 75.059 425 81 19 1326 1739 95516167 95516577 1.140000e-39 174.0
23 TraesCS1D01G080300 chr2D 89.091 110 10 2 2416 2525 98693602 98693495 5.390000e-28 135.0
24 TraesCS1D01G080300 chr2D 90.099 101 10 0 2421 2521 30406648 30406748 6.970000e-27 132.0
25 TraesCS1D01G080300 chr2D 79.333 150 23 8 1386 1532 572263412 572263268 7.070000e-17 99.0
26 TraesCS1D01G080300 chr6D 89.720 107 10 1 2418 2524 251235030 251235135 5.390000e-28 135.0
27 TraesCS1D01G080300 chr3D 91.753 97 8 0 2421 2517 556072205 556072109 5.390000e-28 135.0
28 TraesCS1D01G080300 chr3D 75.465 269 55 7 1485 1746 418876252 418876516 1.510000e-23 121.0
29 TraesCS1D01G080300 chr3D 75.465 269 55 7 1485 1746 418891551 418891815 1.510000e-23 121.0
30 TraesCS1D01G080300 chr3D 86.813 91 12 0 1656 1746 419464718 419464808 5.470000e-18 102.0
31 TraesCS1D01G080300 chr3D 86.813 91 12 0 1656 1746 419516269 419516359 5.470000e-18 102.0
32 TraesCS1D01G080300 chr3B 91.753 97 8 0 2421 2517 119469010 119469106 5.390000e-28 135.0
33 TraesCS1D01G080300 chr5B 88.073 109 12 1 2413 2521 382074616 382074723 9.020000e-26 128.0
34 TraesCS1D01G080300 chr6A 80.000 150 28 2 1109 1257 50034678 50034826 3.270000e-20 110.0
35 TraesCS1D01G080300 chr4B 77.500 200 22 17 1328 1523 641408039 641408219 7.070000e-17 99.0
36 TraesCS1D01G080300 chr4B 88.710 62 7 0 1203 1264 641412309 641412370 3.310000e-10 76.8


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 TraesCS1D01G080300 chr1D 62856881 62859979 3098 False 5723.00 5723 100.00000 1 3099 1 chr1D.!!$F2 3098
1 TraesCS1D01G080300 chr1B 100307606 100310753 3147 False 872.75 3027 90.49725 108 3001 4 chr1B.!!$F2 2893
2 TraesCS1D01G080300 chr1A 60954212 60957173 2961 True 1586.50 2940 87.67600 122 3099 2 chr1A.!!$R2 2977
3 TraesCS1D01G080300 chrUn 114967344 114968328 984 True 357.00 357 73.86600 1112 2103 1 chrUn.!!$R1 991
4 TraesCS1D01G080300 chr6B 89513776 89514746 970 False 327.00 327 73.57000 1109 2100 1 chr6B.!!$F1 991

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
70 71 0.037590 TCCCCACCAAAATCGTCCAG 59.962 55.0 0.0 0.0 0.00 3.86 F
851 901 0.041312 GCCAGCCACGTATAAATGCG 60.041 55.0 0.0 0.0 41.71 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1101 0.031585 CAGATCCGCCATTGCCATTG 59.968 55.0 0.00 0.00 0.00 2.82 R
2671 3109 0.744874 TGATCCGTCGGAATCTGGAC 59.255 55.0 19.76 4.87 34.34 4.02 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
18 19 3.435682 TGCCTGGAAAGGTAGGGAT 57.564 52.632 0.00 0.00 34.58 3.85
19 20 1.681229 TGCCTGGAAAGGTAGGGATT 58.319 50.000 0.00 0.00 34.58 3.01
20 21 1.564348 TGCCTGGAAAGGTAGGGATTC 59.436 52.381 0.00 0.00 34.58 2.52
21 22 1.475213 GCCTGGAAAGGTAGGGATTCG 60.475 57.143 0.00 0.00 34.58 3.34
22 23 1.141053 CCTGGAAAGGTAGGGATTCGG 59.859 57.143 0.00 0.00 0.00 4.30
23 24 1.141053 CTGGAAAGGTAGGGATTCGGG 59.859 57.143 0.00 0.00 0.00 5.14
24 25 1.210538 GGAAAGGTAGGGATTCGGGT 58.789 55.000 0.00 0.00 0.00 5.28
25 26 1.562942 GGAAAGGTAGGGATTCGGGTT 59.437 52.381 0.00 0.00 0.00 4.11
26 27 2.640184 GAAAGGTAGGGATTCGGGTTG 58.360 52.381 0.00 0.00 0.00 3.77
27 28 0.916809 AAGGTAGGGATTCGGGTTGG 59.083 55.000 0.00 0.00 0.00 3.77
28 29 0.043637 AGGTAGGGATTCGGGTTGGA 59.956 55.000 0.00 0.00 0.00 3.53
29 30 1.137697 GGTAGGGATTCGGGTTGGAT 58.862 55.000 0.00 0.00 0.00 3.41
30 31 1.071857 GGTAGGGATTCGGGTTGGATC 59.928 57.143 0.00 0.00 0.00 3.36
31 32 2.047830 GTAGGGATTCGGGTTGGATCT 58.952 52.381 0.00 0.00 0.00 2.75
32 33 1.132500 AGGGATTCGGGTTGGATCTC 58.868 55.000 0.00 0.00 0.00 2.75
33 34 0.837272 GGGATTCGGGTTGGATCTCA 59.163 55.000 0.00 0.00 0.00 3.27
34 35 1.211949 GGGATTCGGGTTGGATCTCAA 59.788 52.381 0.00 0.00 0.00 3.02
35 36 2.158608 GGGATTCGGGTTGGATCTCAAT 60.159 50.000 0.00 0.00 37.73 2.57
36 37 3.555966 GGATTCGGGTTGGATCTCAATT 58.444 45.455 0.00 0.00 37.73 2.32
37 38 4.445735 GGGATTCGGGTTGGATCTCAATTA 60.446 45.833 0.00 0.00 37.73 1.40
38 39 4.515567 GGATTCGGGTTGGATCTCAATTAC 59.484 45.833 0.00 0.00 37.73 1.89
39 40 3.173668 TCGGGTTGGATCTCAATTACG 57.826 47.619 0.00 2.92 37.73 3.18
40 41 2.761767 TCGGGTTGGATCTCAATTACGA 59.238 45.455 0.00 12.07 37.73 3.43
41 42 3.123804 CGGGTTGGATCTCAATTACGAG 58.876 50.000 0.00 0.00 37.73 4.18
42 43 3.430374 CGGGTTGGATCTCAATTACGAGT 60.430 47.826 0.00 0.00 37.73 4.18
43 44 3.871594 GGGTTGGATCTCAATTACGAGTG 59.128 47.826 0.00 0.00 37.73 3.51
44 45 4.382685 GGGTTGGATCTCAATTACGAGTGA 60.383 45.833 0.00 0.00 37.73 3.41
45 46 4.567159 GGTTGGATCTCAATTACGAGTGAC 59.433 45.833 0.00 0.00 37.73 3.67
46 47 4.386867 TGGATCTCAATTACGAGTGACC 57.613 45.455 0.00 0.00 34.46 4.02
47 48 3.767131 TGGATCTCAATTACGAGTGACCA 59.233 43.478 0.00 0.00 34.46 4.02
48 49 4.142160 TGGATCTCAATTACGAGTGACCAG 60.142 45.833 0.00 0.00 34.46 4.00
49 50 4.098044 GGATCTCAATTACGAGTGACCAGA 59.902 45.833 0.00 0.00 34.46 3.86
50 51 5.221342 GGATCTCAATTACGAGTGACCAGAT 60.221 44.000 0.00 0.00 34.46 2.90
51 52 5.661056 TCTCAATTACGAGTGACCAGATT 57.339 39.130 0.00 0.00 34.46 2.40
52 53 5.651530 TCTCAATTACGAGTGACCAGATTC 58.348 41.667 0.00 0.00 34.46 2.52
53 54 4.755411 TCAATTACGAGTGACCAGATTCC 58.245 43.478 0.00 0.00 0.00 3.01
54 55 3.821421 ATTACGAGTGACCAGATTCCC 57.179 47.619 0.00 0.00 0.00 3.97
55 56 1.481871 TACGAGTGACCAGATTCCCC 58.518 55.000 0.00 0.00 0.00 4.81
56 57 0.544357 ACGAGTGACCAGATTCCCCA 60.544 55.000 0.00 0.00 0.00 4.96
57 58 0.108138 CGAGTGACCAGATTCCCCAC 60.108 60.000 0.00 0.00 0.00 4.61
58 59 0.253327 GAGTGACCAGATTCCCCACC 59.747 60.000 0.00 0.00 0.00 4.61
59 60 0.475632 AGTGACCAGATTCCCCACCA 60.476 55.000 0.00 0.00 0.00 4.17
60 61 0.404040 GTGACCAGATTCCCCACCAA 59.596 55.000 0.00 0.00 0.00 3.67
61 62 1.153539 TGACCAGATTCCCCACCAAA 58.846 50.000 0.00 0.00 0.00 3.28
62 63 1.501170 TGACCAGATTCCCCACCAAAA 59.499 47.619 0.00 0.00 0.00 2.44
63 64 2.111613 TGACCAGATTCCCCACCAAAAT 59.888 45.455 0.00 0.00 0.00 1.82
64 65 2.760650 GACCAGATTCCCCACCAAAATC 59.239 50.000 0.00 0.00 0.00 2.17
65 66 1.750778 CCAGATTCCCCACCAAAATCG 59.249 52.381 0.00 0.00 35.14 3.34
66 67 2.446435 CAGATTCCCCACCAAAATCGT 58.554 47.619 0.00 0.00 35.14 3.73
67 68 2.423538 CAGATTCCCCACCAAAATCGTC 59.576 50.000 0.00 0.00 35.14 4.20
68 69 1.749063 GATTCCCCACCAAAATCGTCC 59.251 52.381 0.00 0.00 0.00 4.79
69 70 0.478942 TTCCCCACCAAAATCGTCCA 59.521 50.000 0.00 0.00 0.00 4.02
70 71 0.037590 TCCCCACCAAAATCGTCCAG 59.962 55.000 0.00 0.00 0.00 3.86
71 72 0.037590 CCCCACCAAAATCGTCCAGA 59.962 55.000 0.00 0.00 0.00 3.86
72 73 1.340991 CCCCACCAAAATCGTCCAGAT 60.341 52.381 0.00 0.00 42.43 2.90
73 74 2.017049 CCCACCAAAATCGTCCAGATC 58.983 52.381 0.00 0.00 38.98 2.75
74 75 2.017049 CCACCAAAATCGTCCAGATCC 58.983 52.381 0.00 0.00 38.98 3.36
75 76 2.356125 CCACCAAAATCGTCCAGATCCT 60.356 50.000 0.00 0.00 38.98 3.24
76 77 3.118408 CCACCAAAATCGTCCAGATCCTA 60.118 47.826 0.00 0.00 38.98 2.94
77 78 3.871594 CACCAAAATCGTCCAGATCCTAC 59.128 47.826 0.00 0.00 38.98 3.18
78 79 3.775316 ACCAAAATCGTCCAGATCCTACT 59.225 43.478 0.00 0.00 38.98 2.57
79 80 4.141914 ACCAAAATCGTCCAGATCCTACTC 60.142 45.833 0.00 0.00 38.98 2.59
80 81 4.100189 CCAAAATCGTCCAGATCCTACTCT 59.900 45.833 0.00 0.00 38.98 3.24
81 82 5.395768 CCAAAATCGTCCAGATCCTACTCTT 60.396 44.000 0.00 0.00 38.98 2.85
82 83 5.941555 AAATCGTCCAGATCCTACTCTTT 57.058 39.130 0.00 0.00 38.98 2.52
83 84 5.941555 AATCGTCCAGATCCTACTCTTTT 57.058 39.130 0.00 0.00 38.98 2.27
84 85 4.720649 TCGTCCAGATCCTACTCTTTTG 57.279 45.455 0.00 0.00 0.00 2.44
85 86 3.119101 TCGTCCAGATCCTACTCTTTTGC 60.119 47.826 0.00 0.00 0.00 3.68
86 87 3.536570 GTCCAGATCCTACTCTTTTGCC 58.463 50.000 0.00 0.00 0.00 4.52
87 88 3.198853 GTCCAGATCCTACTCTTTTGCCT 59.801 47.826 0.00 0.00 0.00 4.75
88 89 3.198635 TCCAGATCCTACTCTTTTGCCTG 59.801 47.826 0.00 0.00 0.00 4.85
89 90 2.941720 CAGATCCTACTCTTTTGCCTGC 59.058 50.000 0.00 0.00 0.00 4.85
90 91 1.936547 GATCCTACTCTTTTGCCTGCG 59.063 52.381 0.00 0.00 0.00 5.18
91 92 0.973632 TCCTACTCTTTTGCCTGCGA 59.026 50.000 0.00 0.00 0.00 5.10
92 93 1.555075 TCCTACTCTTTTGCCTGCGAT 59.445 47.619 0.00 0.00 0.00 4.58
93 94 2.764010 TCCTACTCTTTTGCCTGCGATA 59.236 45.455 0.00 0.00 0.00 2.92
94 95 3.388024 TCCTACTCTTTTGCCTGCGATAT 59.612 43.478 0.00 0.00 0.00 1.63
95 96 3.743396 CCTACTCTTTTGCCTGCGATATC 59.257 47.826 0.00 0.00 0.00 1.63
96 97 3.550437 ACTCTTTTGCCTGCGATATCT 57.450 42.857 0.34 0.00 0.00 1.98
97 98 4.672587 ACTCTTTTGCCTGCGATATCTA 57.327 40.909 0.34 0.00 0.00 1.98
98 99 5.220710 ACTCTTTTGCCTGCGATATCTAT 57.779 39.130 0.34 0.00 0.00 1.98
99 100 5.233988 ACTCTTTTGCCTGCGATATCTATC 58.766 41.667 0.34 0.00 0.00 2.08
111 112 2.375014 TATCTATCGTGACCCCAGCA 57.625 50.000 0.00 0.00 0.00 4.41
169 170 2.669878 TGGGAAGAAAATGCCCAGC 58.330 52.632 0.00 0.00 46.57 4.85
174 175 1.250840 AAGAAAATGCCCAGCCGGTC 61.251 55.000 1.90 0.00 0.00 4.79
182 183 1.228657 GCCCAGCCGGTCGAATAATC 61.229 60.000 1.90 0.00 0.00 1.75
330 332 1.101331 CCCGACTCCACTACCACTAC 58.899 60.000 0.00 0.00 0.00 2.73
433 439 3.256105 CGCGCCGCCGTATTGTAA 61.256 61.111 2.28 0.00 36.67 2.41
434 440 2.591311 CGCGCCGCCGTATTGTAAT 61.591 57.895 2.28 0.00 36.67 1.89
435 441 1.083015 GCGCCGCCGTATTGTAATG 60.083 57.895 0.00 0.00 36.67 1.90
479 485 2.994995 ATCCCGTCGTGGCAGTGA 60.995 61.111 0.00 0.00 35.87 3.41
480 486 2.501223 GATCCCGTCGTGGCAGTGAA 62.501 60.000 0.00 0.00 35.87 3.18
544 560 2.716017 GGAGAGGGACAGCACGGAG 61.716 68.421 0.00 0.00 0.00 4.63
610 635 4.489771 CGGCGCCCCAAGGAGAAT 62.490 66.667 23.46 0.00 34.21 2.40
622 647 1.490574 AGGAGAATAGAACAGCGGCT 58.509 50.000 0.00 0.00 0.00 5.52
801 851 5.651530 CTCACTAGCTTCCGTTTTCTATCA 58.348 41.667 0.00 0.00 0.00 2.15
813 863 7.937649 TCCGTTTTCTATCAATCTCGAATCTA 58.062 34.615 0.00 0.00 0.00 1.98
835 885 2.575893 TTAGTTGGAGACGCGGCCA 61.576 57.895 9.25 11.41 0.00 5.36
851 901 0.041312 GCCAGCCACGTATAAATGCG 60.041 55.000 0.00 0.00 41.71 4.73
875 929 2.359900 GCACTTGCTGCTGGTATACTT 58.640 47.619 2.25 0.00 43.33 2.24
903 957 5.152306 TCACCCCTAGTACAGATACCAAT 57.848 43.478 0.00 0.00 30.88 3.16
1026 1098 2.429610 CAGCGGTACTGGTATTGGTACT 59.570 50.000 5.98 0.00 43.19 2.73
1027 1099 2.429610 AGCGGTACTGGTATTGGTACTG 59.570 50.000 4.13 0.00 43.92 2.74
1028 1100 2.482490 GCGGTACTGGTATTGGTACTGG 60.482 54.545 3.34 3.60 42.35 4.00
1029 1101 2.482490 CGGTACTGGTATTGGTACTGGC 60.482 54.545 0.00 0.00 39.96 4.85
1030 1102 2.502538 GGTACTGGTATTGGTACTGGCA 59.497 50.000 0.00 0.00 38.52 4.92
1031 1103 3.054948 GGTACTGGTATTGGTACTGGCAA 60.055 47.826 0.00 0.00 38.52 4.52
1284 1365 3.062466 CTCCACCGGACGAGCTCA 61.062 66.667 15.40 0.00 0.00 4.26
1302 1385 4.512944 AGCTCATGTCATGCTTAATTACGG 59.487 41.667 8.03 0.00 32.61 4.02
1327 1427 0.463295 ATGTAGCTGCTGCATTCGCT 60.463 50.000 24.66 17.29 42.74 4.93
1547 1661 3.762293 GCATCATGGGCGGCATAA 58.238 55.556 12.47 0.00 0.00 1.90
1746 1860 1.992277 GCTCCTCCTTCTCCAGCCA 60.992 63.158 0.00 0.00 0.00 4.75
2111 2229 5.416326 AGAGTGAACTAGTAGTAGTGCCAAG 59.584 44.000 11.04 0.00 39.60 3.61
2142 2260 2.419667 TCAGACATCTGCACATGTGTG 58.580 47.619 26.01 21.41 45.27 3.82
2231 2354 2.292569 GCATCGATCATTCATGGCTGTT 59.707 45.455 0.00 0.00 0.00 3.16
2244 2372 3.328382 TGGCTGTTACCTGTGACATAC 57.672 47.619 0.00 0.00 0.00 2.39
2315 2443 0.830023 TTTGTGGGGCTACTTTGGGC 60.830 55.000 0.00 0.00 0.00 5.36
2352 2495 4.034858 GTGTCATGCATACATTCAGAGGTG 59.965 45.833 0.00 0.00 32.87 4.00
2358 2501 3.557595 GCATACATTCAGAGGTGCAGTAC 59.442 47.826 0.00 0.00 33.09 2.73
2393 2536 6.524734 ACAACAACATAGAGATCAACTGTGA 58.475 36.000 18.05 0.00 38.41 3.58
2400 2543 4.468765 AGAGATCAACTGTGACATGGAG 57.531 45.455 0.00 0.00 36.31 3.86
2404 2547 6.155910 AGAGATCAACTGTGACATGGAGTTAT 59.844 38.462 0.00 0.00 36.31 1.89
2407 2550 6.801539 TCAACTGTGACATGGAGTTATTTC 57.198 37.500 0.00 0.00 0.00 2.17
2408 2551 6.533730 TCAACTGTGACATGGAGTTATTTCT 58.466 36.000 0.00 0.00 0.00 2.52
2410 2553 5.171476 ACTGTGACATGGAGTTATTTCTCG 58.829 41.667 0.00 0.00 35.52 4.04
2418 2561 5.654603 TGGAGTTATTTCTCGCTTCAGTA 57.345 39.130 0.00 0.00 35.52 2.74
2422 2565 7.705325 TGGAGTTATTTCTCGCTTCAGTATTAC 59.295 37.037 0.00 0.00 35.52 1.89
2426 2569 8.960075 GTTATTTCTCGCTTCAGTATTACTCTC 58.040 37.037 0.00 0.00 0.00 3.20
2429 2572 4.817464 TCTCGCTTCAGTATTACTCTCTCC 59.183 45.833 0.00 0.00 0.00 3.71
2430 2573 3.560481 TCGCTTCAGTATTACTCTCTCCG 59.440 47.826 0.00 0.00 0.00 4.63
2433 2576 4.261280 GCTTCAGTATTACTCTCTCCGTCC 60.261 50.000 0.00 0.00 0.00 4.79
2434 2577 3.818180 TCAGTATTACTCTCTCCGTCCC 58.182 50.000 0.00 0.00 0.00 4.46
2435 2578 3.201487 TCAGTATTACTCTCTCCGTCCCA 59.799 47.826 0.00 0.00 0.00 4.37
2437 2580 4.401519 CAGTATTACTCTCTCCGTCCCAAA 59.598 45.833 0.00 0.00 0.00 3.28
2439 2582 5.661759 AGTATTACTCTCTCCGTCCCAAAAT 59.338 40.000 0.00 0.00 0.00 1.82
2440 2583 6.837568 AGTATTACTCTCTCCGTCCCAAAATA 59.162 38.462 0.00 0.00 0.00 1.40
2441 2584 6.555463 ATTACTCTCTCCGTCCCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
2442 2585 4.473477 ACTCTCTCCGTCCCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
2443 2586 3.838903 ACTCTCTCCGTCCCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
2444 2587 4.184629 CTCTCTCCGTCCCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
2445 2588 3.581332 TCTCTCCGTCCCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
2446 2589 3.933332 CTCTCCGTCCCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
2447 2590 3.581332 TCTCCGTCCCAAAATAAGTGTCT 59.419 43.478 0.00 0.00 0.00 3.41
2448 2591 4.041198 TCTCCGTCCCAAAATAAGTGTCTT 59.959 41.667 0.00 0.00 0.00 3.01
2449 2592 5.246656 TCTCCGTCCCAAAATAAGTGTCTTA 59.753 40.000 0.00 0.00 0.00 2.10
2450 2593 5.867330 TCCGTCCCAAAATAAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
2451 2594 5.935789 TCCGTCCCAAAATAAGTGTCTTAAG 59.064 40.000 0.00 0.00 0.00 1.85
2452 2595 5.391629 CCGTCCCAAAATAAGTGTCTTAAGC 60.392 44.000 0.00 0.00 0.00 3.09
2453 2596 5.411669 CGTCCCAAAATAAGTGTCTTAAGCT 59.588 40.000 0.00 0.00 0.00 3.74
2454 2597 6.072673 CGTCCCAAAATAAGTGTCTTAAGCTT 60.073 38.462 3.48 3.48 0.00 3.74
2455 2598 7.118680 CGTCCCAAAATAAGTGTCTTAAGCTTA 59.881 37.037 0.86 0.86 0.00 3.09
2456 2599 8.451748 GTCCCAAAATAAGTGTCTTAAGCTTAG 58.548 37.037 6.24 1.77 0.00 2.18
2457 2600 8.161425 TCCCAAAATAAGTGTCTTAAGCTTAGT 58.839 33.333 6.24 0.00 0.00 2.24
2458 2601 9.444600 CCCAAAATAAGTGTCTTAAGCTTAGTA 57.555 33.333 6.24 0.00 0.00 1.82
2465 2608 8.959705 AAGTGTCTTAAGCTTAGTACAACTTT 57.040 30.769 18.98 13.13 0.00 2.66
2466 2609 8.366671 AGTGTCTTAAGCTTAGTACAACTTTG 57.633 34.615 18.98 0.00 0.00 2.77
2467 2610 7.985752 AGTGTCTTAAGCTTAGTACAACTTTGT 59.014 33.333 18.98 0.00 44.86 2.83
2468 2611 9.252962 GTGTCTTAAGCTTAGTACAACTTTGTA 57.747 33.333 18.98 0.00 42.35 2.41
2508 2651 7.653767 AGTTGAGACAGTTATTTTAAGACGG 57.346 36.000 0.00 0.00 0.00 4.79
2509 2652 7.439381 AGTTGAGACAGTTATTTTAAGACGGA 58.561 34.615 0.00 0.00 0.00 4.69
2510 2653 7.599245 AGTTGAGACAGTTATTTTAAGACGGAG 59.401 37.037 0.00 0.00 0.00 4.63
2511 2654 6.395629 TGAGACAGTTATTTTAAGACGGAGG 58.604 40.000 0.00 0.00 0.00 4.30
2512 2655 5.731591 AGACAGTTATTTTAAGACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2513 2656 5.482878 AGACAGTTATTTTAAGACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2514 2657 5.731591 ACAGTTATTTTAAGACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2515 2658 5.247792 ACAGTTATTTTAAGACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2516 2659 6.438425 ACAGTTATTTTAAGACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2517 2660 6.755607 CAGTTATTTTAAGACGGAGGGAGTAC 59.244 42.308 0.00 0.00 0.00 2.73
2518 2661 6.666980 AGTTATTTTAAGACGGAGGGAGTACT 59.333 38.462 0.00 0.00 0.00 2.73
2519 2662 7.179872 AGTTATTTTAAGACGGAGGGAGTACTT 59.820 37.037 0.00 0.00 0.00 2.24
2520 2663 5.813513 TTTTAAGACGGAGGGAGTACTTT 57.186 39.130 0.00 0.00 0.00 2.66
2521 2664 4.796038 TTAAGACGGAGGGAGTACTTTG 57.204 45.455 0.00 0.00 0.00 2.77
2522 2665 2.305858 AGACGGAGGGAGTACTTTGT 57.694 50.000 0.00 0.00 0.00 2.83
2523 2666 2.606378 AGACGGAGGGAGTACTTTGTT 58.394 47.619 0.00 0.00 0.00 2.83
2524 2667 3.771216 AGACGGAGGGAGTACTTTGTTA 58.229 45.455 0.00 0.00 0.00 2.41
2525 2668 3.762823 AGACGGAGGGAGTACTTTGTTAG 59.237 47.826 0.00 0.00 0.00 2.34
2526 2669 3.504375 ACGGAGGGAGTACTTTGTTAGT 58.496 45.455 0.00 0.00 41.04 2.24
2527 2670 3.899980 ACGGAGGGAGTACTTTGTTAGTT 59.100 43.478 0.00 0.00 38.33 2.24
2528 2671 4.243270 CGGAGGGAGTACTTTGTTAGTTG 58.757 47.826 0.00 0.00 38.33 3.16
2529 2672 4.262335 CGGAGGGAGTACTTTGTTAGTTGT 60.262 45.833 0.00 0.00 38.33 3.32
2530 2673 4.995487 GGAGGGAGTACTTTGTTAGTTGTG 59.005 45.833 0.00 0.00 38.33 3.33
2531 2674 5.454329 GGAGGGAGTACTTTGTTAGTTGTGT 60.454 44.000 0.00 0.00 38.33 3.72
2532 2675 5.365619 AGGGAGTACTTTGTTAGTTGTGTG 58.634 41.667 0.00 0.00 38.33 3.82
2533 2676 4.514066 GGGAGTACTTTGTTAGTTGTGTGG 59.486 45.833 0.00 0.00 38.33 4.17
2566 2709 8.072238 TGTGTATTCGCATACATTAAGATGTC 57.928 34.615 11.05 0.00 45.69 3.06
2571 2714 5.912892 TCGCATACATTAAGATGTCTTCCA 58.087 37.500 0.00 0.00 42.83 3.53
2575 2718 6.017605 GCATACATTAAGATGTCTTCCAGGTG 60.018 42.308 0.00 0.00 42.83 4.00
2576 2719 5.505181 ACATTAAGATGTCTTCCAGGTGT 57.495 39.130 0.00 0.00 42.83 4.16
2577 2720 6.620877 ACATTAAGATGTCTTCCAGGTGTA 57.379 37.500 0.00 0.00 42.83 2.90
2671 3109 4.378459 CCTGCCAAACTAAGCTTTAACTCG 60.378 45.833 3.20 0.00 0.00 4.18
2759 3200 5.131308 TGATAATAAGGTTTCCACGGGATGA 59.869 40.000 0.00 0.00 0.00 2.92
2777 3224 6.585416 GGGATGATGCCAAATAATTTTCACT 58.415 36.000 0.00 0.00 0.00 3.41
2786 3233 7.068955 GCCAAATAATTTTCACTTTTTCCACG 58.931 34.615 0.00 0.00 0.00 4.94
2787 3234 7.571892 CCAAATAATTTTCACTTTTTCCACGG 58.428 34.615 0.00 0.00 0.00 4.94
2788 3235 7.307692 CCAAATAATTTTCACTTTTTCCACGGG 60.308 37.037 0.00 0.00 0.00 5.28
2789 3236 6.658188 ATAATTTTCACTTTTTCCACGGGA 57.342 33.333 0.00 0.00 0.00 5.14
2790 3237 5.545063 AATTTTCACTTTTTCCACGGGAT 57.455 34.783 0.00 0.00 0.00 3.85
2791 3238 6.658188 AATTTTCACTTTTTCCACGGGATA 57.342 33.333 0.00 0.00 0.00 2.59
2793 3240 6.658188 TTTTCACTTTTTCCACGGGATAAT 57.342 33.333 0.00 0.00 0.00 1.28
2798 3260 5.067283 CACTTTTTCCACGGGATAATAAGGG 59.933 44.000 0.00 0.00 0.00 3.95
2814 3281 2.243602 AGGGCAATTGCTTTTGTGTG 57.756 45.000 28.42 0.00 41.70 3.82
2856 3329 1.327303 TTGGATTGCAGGAAAACGCT 58.673 45.000 0.00 0.00 0.00 5.07
2870 3343 4.688419 CGCTTGCACGCAACCTGG 62.688 66.667 16.08 0.00 0.00 4.45
2871 3344 4.347453 GCTTGCACGCAACCTGGG 62.347 66.667 10.77 0.00 36.28 4.45
2936 3443 2.173996 ACAGGAAGAACCGGGAGAAAAA 59.826 45.455 6.32 0.00 44.74 1.94
3055 3573 4.083862 GTCCGGGTGTCCCTCTGC 62.084 72.222 0.00 0.00 42.67 4.26
3077 3595 0.688487 CCCGACCCTTCCTTTACACA 59.312 55.000 0.00 0.00 0.00 3.72
3084 3602 2.025887 CCCTTCCTTTACACATCCAGCT 60.026 50.000 0.00 0.00 0.00 4.24
3085 3603 3.562176 CCCTTCCTTTACACATCCAGCTT 60.562 47.826 0.00 0.00 0.00 3.74
3086 3604 3.441572 CCTTCCTTTACACATCCAGCTTG 59.558 47.826 0.00 0.00 0.00 4.01
3087 3605 2.436417 TCCTTTACACATCCAGCTTGC 58.564 47.619 0.00 0.00 0.00 4.01
3088 3606 2.040278 TCCTTTACACATCCAGCTTGCT 59.960 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.564348 GAATCCCTACCTTTCCAGGCA 59.436 52.381 0.00 0.00 45.56 4.75
3 4 1.141053 CCCGAATCCCTACCTTTCCAG 59.859 57.143 0.00 0.00 0.00 3.86
4 5 1.209621 CCCGAATCCCTACCTTTCCA 58.790 55.000 0.00 0.00 0.00 3.53
5 6 1.210538 ACCCGAATCCCTACCTTTCC 58.789 55.000 0.00 0.00 0.00 3.13
6 7 2.640184 CAACCCGAATCCCTACCTTTC 58.360 52.381 0.00 0.00 0.00 2.62
7 8 1.283905 CCAACCCGAATCCCTACCTTT 59.716 52.381 0.00 0.00 0.00 3.11
8 9 0.916809 CCAACCCGAATCCCTACCTT 59.083 55.000 0.00 0.00 0.00 3.50
9 10 0.043637 TCCAACCCGAATCCCTACCT 59.956 55.000 0.00 0.00 0.00 3.08
10 11 1.071857 GATCCAACCCGAATCCCTACC 59.928 57.143 0.00 0.00 0.00 3.18
11 12 2.037381 GAGATCCAACCCGAATCCCTAC 59.963 54.545 0.00 0.00 0.00 3.18
12 13 2.326428 GAGATCCAACCCGAATCCCTA 58.674 52.381 0.00 0.00 0.00 3.53
13 14 1.132500 GAGATCCAACCCGAATCCCT 58.868 55.000 0.00 0.00 0.00 4.20
14 15 0.837272 TGAGATCCAACCCGAATCCC 59.163 55.000 0.00 0.00 0.00 3.85
15 16 2.710096 TTGAGATCCAACCCGAATCC 57.290 50.000 0.00 0.00 0.00 3.01
16 17 4.211374 CGTAATTGAGATCCAACCCGAATC 59.789 45.833 0.00 0.00 37.63 2.52
17 18 4.127171 CGTAATTGAGATCCAACCCGAAT 58.873 43.478 0.00 0.00 37.63 3.34
18 19 3.196039 TCGTAATTGAGATCCAACCCGAA 59.804 43.478 0.00 0.00 37.63 4.30
19 20 2.761767 TCGTAATTGAGATCCAACCCGA 59.238 45.455 0.00 0.70 37.63 5.14
20 21 3.123804 CTCGTAATTGAGATCCAACCCG 58.876 50.000 0.00 0.00 38.28 5.28
21 22 3.871594 CACTCGTAATTGAGATCCAACCC 59.128 47.826 0.07 0.00 39.35 4.11
22 23 4.567159 GTCACTCGTAATTGAGATCCAACC 59.433 45.833 0.07 0.00 39.35 3.77
23 24 4.567159 GGTCACTCGTAATTGAGATCCAAC 59.433 45.833 0.07 0.00 39.35 3.77
24 25 4.221924 TGGTCACTCGTAATTGAGATCCAA 59.778 41.667 0.07 0.00 39.35 3.53
25 26 3.767131 TGGTCACTCGTAATTGAGATCCA 59.233 43.478 0.07 3.23 39.35 3.41
26 27 4.098044 TCTGGTCACTCGTAATTGAGATCC 59.902 45.833 0.07 1.14 39.35 3.36
27 28 5.250235 TCTGGTCACTCGTAATTGAGATC 57.750 43.478 0.07 0.00 39.35 2.75
28 29 5.860941 ATCTGGTCACTCGTAATTGAGAT 57.139 39.130 0.07 0.00 39.35 2.75
29 30 5.394224 GGAATCTGGTCACTCGTAATTGAGA 60.394 44.000 0.07 0.00 39.35 3.27
30 31 4.806247 GGAATCTGGTCACTCGTAATTGAG 59.194 45.833 0.00 0.00 41.86 3.02
31 32 4.382685 GGGAATCTGGTCACTCGTAATTGA 60.383 45.833 0.00 0.00 0.00 2.57
32 33 3.871594 GGGAATCTGGTCACTCGTAATTG 59.128 47.826 0.00 0.00 0.00 2.32
33 34 3.118371 GGGGAATCTGGTCACTCGTAATT 60.118 47.826 0.00 0.00 0.00 1.40
34 35 2.434702 GGGGAATCTGGTCACTCGTAAT 59.565 50.000 0.00 0.00 0.00 1.89
35 36 1.829222 GGGGAATCTGGTCACTCGTAA 59.171 52.381 0.00 0.00 0.00 3.18
36 37 1.272816 TGGGGAATCTGGTCACTCGTA 60.273 52.381 0.00 0.00 0.00 3.43
37 38 0.544357 TGGGGAATCTGGTCACTCGT 60.544 55.000 0.00 0.00 0.00 4.18
38 39 0.108138 GTGGGGAATCTGGTCACTCG 60.108 60.000 0.00 0.00 0.00 4.18
39 40 0.253327 GGTGGGGAATCTGGTCACTC 59.747 60.000 0.00 0.00 0.00 3.51
40 41 0.475632 TGGTGGGGAATCTGGTCACT 60.476 55.000 0.00 0.00 0.00 3.41
41 42 0.404040 TTGGTGGGGAATCTGGTCAC 59.596 55.000 0.00 0.00 0.00 3.67
42 43 1.153539 TTTGGTGGGGAATCTGGTCA 58.846 50.000 0.00 0.00 0.00 4.02
43 44 2.302587 TTTTGGTGGGGAATCTGGTC 57.697 50.000 0.00 0.00 0.00 4.02
44 45 2.820178 GATTTTGGTGGGGAATCTGGT 58.180 47.619 0.00 0.00 0.00 4.00
45 46 1.750778 CGATTTTGGTGGGGAATCTGG 59.249 52.381 0.00 0.00 0.00 3.86
46 47 2.423538 GACGATTTTGGTGGGGAATCTG 59.576 50.000 0.00 0.00 0.00 2.90
47 48 2.620627 GGACGATTTTGGTGGGGAATCT 60.621 50.000 0.00 0.00 0.00 2.40
48 49 1.749063 GGACGATTTTGGTGGGGAATC 59.251 52.381 0.00 0.00 0.00 2.52
49 50 1.076350 TGGACGATTTTGGTGGGGAAT 59.924 47.619 0.00 0.00 0.00 3.01
50 51 0.478942 TGGACGATTTTGGTGGGGAA 59.521 50.000 0.00 0.00 0.00 3.97
51 52 0.037590 CTGGACGATTTTGGTGGGGA 59.962 55.000 0.00 0.00 0.00 4.81
52 53 0.037590 TCTGGACGATTTTGGTGGGG 59.962 55.000 0.00 0.00 0.00 4.96
53 54 2.017049 GATCTGGACGATTTTGGTGGG 58.983 52.381 0.00 0.00 30.84 4.61
54 55 2.017049 GGATCTGGACGATTTTGGTGG 58.983 52.381 0.00 0.00 30.84 4.61
55 56 2.991250 AGGATCTGGACGATTTTGGTG 58.009 47.619 0.00 0.00 30.84 4.17
56 57 3.775316 AGTAGGATCTGGACGATTTTGGT 59.225 43.478 0.00 0.00 30.84 3.67
57 58 4.100189 AGAGTAGGATCTGGACGATTTTGG 59.900 45.833 0.00 0.00 30.84 3.28
58 59 5.269505 AGAGTAGGATCTGGACGATTTTG 57.730 43.478 0.00 0.00 30.84 2.44
59 60 5.941555 AAGAGTAGGATCTGGACGATTTT 57.058 39.130 0.00 0.00 30.84 1.82
60 61 5.941555 AAAGAGTAGGATCTGGACGATTT 57.058 39.130 0.00 0.00 30.84 2.17
61 62 5.665459 CAAAAGAGTAGGATCTGGACGATT 58.335 41.667 0.00 0.00 30.84 3.34
62 63 4.442192 GCAAAAGAGTAGGATCTGGACGAT 60.442 45.833 0.00 0.00 34.25 3.73
63 64 3.119101 GCAAAAGAGTAGGATCTGGACGA 60.119 47.826 0.00 0.00 0.00 4.20
64 65 3.190874 GCAAAAGAGTAGGATCTGGACG 58.809 50.000 0.00 0.00 0.00 4.79
65 66 3.198853 AGGCAAAAGAGTAGGATCTGGAC 59.801 47.826 0.00 0.00 0.00 4.02
66 67 3.198635 CAGGCAAAAGAGTAGGATCTGGA 59.801 47.826 0.00 0.00 0.00 3.86
67 68 3.539604 CAGGCAAAAGAGTAGGATCTGG 58.460 50.000 0.00 0.00 0.00 3.86
68 69 2.941720 GCAGGCAAAAGAGTAGGATCTG 59.058 50.000 0.00 0.00 0.00 2.90
69 70 2.419297 CGCAGGCAAAAGAGTAGGATCT 60.419 50.000 0.00 0.00 0.00 2.75
70 71 1.936547 CGCAGGCAAAAGAGTAGGATC 59.063 52.381 0.00 0.00 0.00 3.36
71 72 1.555075 TCGCAGGCAAAAGAGTAGGAT 59.445 47.619 0.00 0.00 0.00 3.24
72 73 0.973632 TCGCAGGCAAAAGAGTAGGA 59.026 50.000 0.00 0.00 0.00 2.94
73 74 2.029838 ATCGCAGGCAAAAGAGTAGG 57.970 50.000 0.00 0.00 0.00 3.18
74 75 4.626042 AGATATCGCAGGCAAAAGAGTAG 58.374 43.478 0.00 0.00 0.00 2.57
75 76 4.672587 AGATATCGCAGGCAAAAGAGTA 57.327 40.909 0.00 0.00 0.00 2.59
76 77 3.550437 AGATATCGCAGGCAAAAGAGT 57.450 42.857 0.00 0.00 0.00 3.24
77 78 5.776519 GATAGATATCGCAGGCAAAAGAG 57.223 43.478 0.00 0.00 0.00 2.85
90 91 2.826128 TGCTGGGGTCACGATAGATATC 59.174 50.000 0.00 0.00 41.38 1.63
91 92 2.889512 TGCTGGGGTCACGATAGATAT 58.110 47.619 0.00 0.00 41.38 1.63
92 93 2.375014 TGCTGGGGTCACGATAGATA 57.625 50.000 0.00 0.00 41.38 1.98
93 94 1.620819 GATGCTGGGGTCACGATAGAT 59.379 52.381 0.00 0.00 41.38 1.98
94 95 1.040646 GATGCTGGGGTCACGATAGA 58.959 55.000 0.00 0.00 41.38 1.98
95 96 0.319040 CGATGCTGGGGTCACGATAG 60.319 60.000 0.00 0.00 46.19 2.08
96 97 0.753848 TCGATGCTGGGGTCACGATA 60.754 55.000 0.00 0.00 0.00 2.92
97 98 2.021068 CTCGATGCTGGGGTCACGAT 62.021 60.000 0.00 0.00 0.00 3.73
98 99 2.678580 TCGATGCTGGGGTCACGA 60.679 61.111 0.00 0.00 0.00 4.35
99 100 2.202797 CTCGATGCTGGGGTCACG 60.203 66.667 0.00 0.00 0.00 4.35
100 101 2.512515 GCTCGATGCTGGGGTCAC 60.513 66.667 0.00 0.00 38.95 3.67
101 102 3.785859 GGCTCGATGCTGGGGTCA 61.786 66.667 6.78 0.00 42.39 4.02
102 103 4.899239 CGGCTCGATGCTGGGGTC 62.899 72.222 7.54 0.00 44.06 4.46
118 119 1.821332 GCATCTGAAGCTTCCCCCG 60.821 63.158 23.42 10.79 0.00 5.73
119 120 0.323725 TTGCATCTGAAGCTTCCCCC 60.324 55.000 23.42 8.13 0.00 5.40
123 124 2.094854 CCCAGTTTGCATCTGAAGCTTC 60.095 50.000 19.89 19.89 35.20 3.86
174 175 2.863740 TGCTGCGTTGGTAGATTATTCG 59.136 45.455 0.00 0.00 0.00 3.34
182 183 1.350193 CAGTACTGCTGCGTTGGTAG 58.650 55.000 10.54 0.00 38.52 3.18
236 237 0.178921 TTCCTCAGGTCAGGCTGAGT 60.179 55.000 19.38 5.35 43.91 3.41
241 242 3.885901 GGATTAAATTCCTCAGGTCAGGC 59.114 47.826 0.00 0.00 32.91 4.85
306 307 1.215647 GTAGTGGAGTCGGGCAGTG 59.784 63.158 0.00 0.00 0.00 3.66
330 332 3.204827 GGCTACGCATGCTGTGGG 61.205 66.667 17.13 12.79 45.61 4.61
428 434 7.863375 CGTTTTTGAGGGATTACAACATTACAA 59.137 33.333 0.00 0.00 0.00 2.41
429 435 7.013464 ACGTTTTTGAGGGATTACAACATTACA 59.987 33.333 0.00 0.00 0.00 2.41
430 436 7.364970 ACGTTTTTGAGGGATTACAACATTAC 58.635 34.615 0.00 0.00 0.00 1.89
431 437 7.513371 ACGTTTTTGAGGGATTACAACATTA 57.487 32.000 0.00 0.00 0.00 1.90
432 438 6.399639 ACGTTTTTGAGGGATTACAACATT 57.600 33.333 0.00 0.00 0.00 2.71
433 439 7.413657 CGATACGTTTTTGAGGGATTACAACAT 60.414 37.037 0.00 0.00 0.00 2.71
434 440 6.128499 CGATACGTTTTTGAGGGATTACAACA 60.128 38.462 0.00 0.00 0.00 3.33
435 441 6.245724 CGATACGTTTTTGAGGGATTACAAC 58.754 40.000 0.00 0.00 0.00 3.32
479 485 3.788766 GTGCGCGCTTCATCGGTT 61.789 61.111 33.29 0.00 0.00 4.44
523 539 4.459089 GTGCTGTCCCTCTCCGGC 62.459 72.222 0.00 0.00 0.00 6.13
610 635 1.728069 CTCGCTAGCCGCTGTTCTA 59.272 57.895 9.66 0.00 36.73 2.10
622 647 4.457496 GTGCCCTGCAGCTCGCTA 62.457 66.667 8.66 0.00 40.08 4.26
801 851 9.575868 TCTCCAACTAACTATAGATTCGAGATT 57.424 33.333 6.78 0.00 33.15 2.40
813 863 1.202382 GCCGCGTCTCCAACTAACTAT 60.202 52.381 4.92 0.00 0.00 2.12
835 885 2.201732 CAGTCGCATTTATACGTGGCT 58.798 47.619 0.00 0.00 0.00 4.75
871 925 3.959495 ACTAGGGGTGATCGGTAAGTA 57.041 47.619 0.00 0.00 0.00 2.24
875 929 2.779430 TCTGTACTAGGGGTGATCGGTA 59.221 50.000 0.00 0.00 0.00 4.02
880 934 4.827036 TGGTATCTGTACTAGGGGTGAT 57.173 45.455 0.00 0.00 0.00 3.06
881 935 4.613265 TTGGTATCTGTACTAGGGGTGA 57.387 45.455 0.00 0.00 0.00 4.02
882 936 5.047235 GCTATTGGTATCTGTACTAGGGGTG 60.047 48.000 0.00 0.00 0.00 4.61
884 938 4.158025 CGCTATTGGTATCTGTACTAGGGG 59.842 50.000 0.00 0.00 0.00 4.79
885 939 4.158025 CCGCTATTGGTATCTGTACTAGGG 59.842 50.000 0.00 0.00 0.00 3.53
886 940 4.380655 GCCGCTATTGGTATCTGTACTAGG 60.381 50.000 0.00 0.00 0.00 3.02
1026 1098 3.772281 CCGCCATTGCCATTGCCA 61.772 61.111 0.00 0.00 36.33 4.92
1027 1099 2.704342 GATCCGCCATTGCCATTGCC 62.704 60.000 0.00 0.00 36.33 4.52
1028 1100 1.300388 GATCCGCCATTGCCATTGC 60.300 57.895 0.00 0.00 38.26 3.56
1029 1101 0.031585 CAGATCCGCCATTGCCATTG 59.968 55.000 0.00 0.00 0.00 2.82
1030 1102 0.396139 ACAGATCCGCCATTGCCATT 60.396 50.000 0.00 0.00 0.00 3.16
1031 1103 0.820891 GACAGATCCGCCATTGCCAT 60.821 55.000 0.00 0.00 0.00 4.40
1072 1144 3.197790 GATCAGGCACGCGCACAT 61.198 61.111 5.73 0.00 41.24 3.21
1159 1231 0.617535 ACGATGGTGGTGATGAGGGA 60.618 55.000 0.00 0.00 0.00 4.20
1160 1232 0.179073 GACGATGGTGGTGATGAGGG 60.179 60.000 0.00 0.00 0.00 4.30
1270 1351 1.517257 GACATGAGCTCGTCCGGTG 60.517 63.158 5.16 0.00 0.00 4.94
1284 1365 4.199310 AGCACCGTAATTAAGCATGACAT 58.801 39.130 0.00 0.00 0.00 3.06
1547 1661 2.512896 GGAGGGCATGGCGAAGAT 59.487 61.111 13.76 0.00 0.00 2.40
1746 1860 1.102222 GTCGATCTGCGGGTAGAGGT 61.102 60.000 0.00 0.00 41.33 3.85
2111 2229 3.508762 CAGATGTCTGAATTTGGCAAGC 58.491 45.455 3.96 0.00 46.59 4.01
2142 2260 4.109675 ATGTACAGTGGCCGGGGC 62.110 66.667 14.65 14.65 41.06 5.80
2231 2354 5.889853 CCCTTGTACTAGTATGTCACAGGTA 59.110 44.000 5.75 0.00 0.00 3.08
2244 2372 5.202004 ACACCTGATCTACCCTTGTACTAG 58.798 45.833 0.00 0.00 0.00 2.57
2315 2443 3.372206 GCATGACACAGTTTAGCTAGGTG 59.628 47.826 4.27 12.51 35.66 4.00
2358 2501 6.481976 TCTCTATGTTGTTGTTGTACCTGTTG 59.518 38.462 0.00 0.00 0.00 3.33
2375 2518 5.423290 TCCATGTCACAGTTGATCTCTATGT 59.577 40.000 0.00 0.00 33.11 2.29
2376 2519 5.910614 TCCATGTCACAGTTGATCTCTATG 58.089 41.667 0.00 0.00 33.11 2.23
2377 2520 5.660417 ACTCCATGTCACAGTTGATCTCTAT 59.340 40.000 0.00 0.00 33.11 1.98
2393 2536 4.832248 TGAAGCGAGAAATAACTCCATGT 58.168 39.130 0.00 0.00 33.83 3.21
2400 2543 8.859517 AGAGTAATACTGAAGCGAGAAATAAC 57.140 34.615 0.00 0.00 0.00 1.89
2404 2547 6.183360 GGAGAGAGTAATACTGAAGCGAGAAA 60.183 42.308 0.00 0.00 0.00 2.52
2407 2550 4.319190 CGGAGAGAGTAATACTGAAGCGAG 60.319 50.000 0.00 0.00 0.00 5.03
2408 2551 3.560481 CGGAGAGAGTAATACTGAAGCGA 59.440 47.826 0.00 0.00 0.00 4.93
2410 2553 4.261280 GGACGGAGAGAGTAATACTGAAGC 60.261 50.000 0.00 0.00 0.00 3.86
2418 2561 6.156429 ACTTATTTTGGGACGGAGAGAGTAAT 59.844 38.462 0.00 0.00 0.00 1.89
2422 2565 4.184629 CACTTATTTTGGGACGGAGAGAG 58.815 47.826 0.00 0.00 0.00 3.20
2426 2569 3.939066 AGACACTTATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
2429 2572 5.411669 AGCTTAAGACACTTATTTTGGGACG 59.588 40.000 6.67 0.00 0.00 4.79
2430 2573 6.819397 AGCTTAAGACACTTATTTTGGGAC 57.181 37.500 6.67 0.00 0.00 4.46
2440 2583 8.827677 CAAAGTTGTACTAAGCTTAAGACACTT 58.172 33.333 16.07 17.10 0.00 3.16
2441 2584 7.985752 ACAAAGTTGTACTAAGCTTAAGACACT 59.014 33.333 16.07 13.78 40.16 3.55
2442 2585 8.139521 ACAAAGTTGTACTAAGCTTAAGACAC 57.860 34.615 16.07 12.36 40.16 3.67
2482 2625 8.557029 CCGTCTTAAAATAACTGTCTCAACTTT 58.443 33.333 0.00 0.00 0.00 2.66
2483 2626 7.929785 TCCGTCTTAAAATAACTGTCTCAACTT 59.070 33.333 0.00 0.00 0.00 2.66
2484 2627 7.439381 TCCGTCTTAAAATAACTGTCTCAACT 58.561 34.615 0.00 0.00 0.00 3.16
2485 2628 7.148623 CCTCCGTCTTAAAATAACTGTCTCAAC 60.149 40.741 0.00 0.00 0.00 3.18
2486 2629 6.872020 CCTCCGTCTTAAAATAACTGTCTCAA 59.128 38.462 0.00 0.00 0.00 3.02
2487 2630 6.395629 CCTCCGTCTTAAAATAACTGTCTCA 58.604 40.000 0.00 0.00 0.00 3.27
2488 2631 5.811100 CCCTCCGTCTTAAAATAACTGTCTC 59.189 44.000 0.00 0.00 0.00 3.36
2489 2632 5.482878 TCCCTCCGTCTTAAAATAACTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2490 2633 5.727434 TCCCTCCGTCTTAAAATAACTGTC 58.273 41.667 0.00 0.00 0.00 3.51
2491 2634 5.247792 ACTCCCTCCGTCTTAAAATAACTGT 59.752 40.000 0.00 0.00 0.00 3.55
2492 2635 5.731591 ACTCCCTCCGTCTTAAAATAACTG 58.268 41.667 0.00 0.00 0.00 3.16
2493 2636 6.666980 AGTACTCCCTCCGTCTTAAAATAACT 59.333 38.462 0.00 0.00 0.00 2.24
2494 2637 6.871844 AGTACTCCCTCCGTCTTAAAATAAC 58.128 40.000 0.00 0.00 0.00 1.89
2495 2638 7.486407 AAGTACTCCCTCCGTCTTAAAATAA 57.514 36.000 0.00 0.00 0.00 1.40
2496 2639 7.038799 ACAAAGTACTCCCTCCGTCTTAAAATA 60.039 37.037 0.00 0.00 0.00 1.40
2497 2640 6.171213 CAAAGTACTCCCTCCGTCTTAAAAT 58.829 40.000 0.00 0.00 0.00 1.82
2498 2641 5.070847 ACAAAGTACTCCCTCCGTCTTAAAA 59.929 40.000 0.00 0.00 0.00 1.52
2499 2642 4.590222 ACAAAGTACTCCCTCCGTCTTAAA 59.410 41.667 0.00 0.00 0.00 1.52
2500 2643 4.154942 ACAAAGTACTCCCTCCGTCTTAA 58.845 43.478 0.00 0.00 0.00 1.85
2501 2644 3.771216 ACAAAGTACTCCCTCCGTCTTA 58.229 45.455 0.00 0.00 0.00 2.10
2502 2645 2.606378 ACAAAGTACTCCCTCCGTCTT 58.394 47.619 0.00 0.00 0.00 3.01
2503 2646 2.305858 ACAAAGTACTCCCTCCGTCT 57.694 50.000 0.00 0.00 0.00 4.18
2504 2647 3.509184 ACTAACAAAGTACTCCCTCCGTC 59.491 47.826 0.00 0.00 36.36 4.79
2505 2648 3.504375 ACTAACAAAGTACTCCCTCCGT 58.496 45.455 0.00 0.00 36.36 4.69
2506 2649 4.243270 CAACTAACAAAGTACTCCCTCCG 58.757 47.826 0.00 0.00 37.50 4.63
2507 2650 4.995487 CACAACTAACAAAGTACTCCCTCC 59.005 45.833 0.00 0.00 37.50 4.30
2508 2651 5.465724 CACACAACTAACAAAGTACTCCCTC 59.534 44.000 0.00 0.00 37.50 4.30
2509 2652 5.365619 CACACAACTAACAAAGTACTCCCT 58.634 41.667 0.00 0.00 37.50 4.20
2510 2653 4.514066 CCACACAACTAACAAAGTACTCCC 59.486 45.833 0.00 0.00 37.50 4.30
2511 2654 5.121105 ACCACACAACTAACAAAGTACTCC 58.879 41.667 0.00 0.00 37.50 3.85
2512 2655 6.457799 CCAACCACACAACTAACAAAGTACTC 60.458 42.308 0.00 0.00 37.50 2.59
2513 2656 5.355910 CCAACCACACAACTAACAAAGTACT 59.644 40.000 0.00 0.00 37.50 2.73
2514 2657 5.354792 TCCAACCACACAACTAACAAAGTAC 59.645 40.000 0.00 0.00 37.50 2.73
2515 2658 5.498393 TCCAACCACACAACTAACAAAGTA 58.502 37.500 0.00 0.00 37.50 2.24
2516 2659 4.337145 TCCAACCACACAACTAACAAAGT 58.663 39.130 0.00 0.00 41.49 2.66
2517 2660 4.974368 TCCAACCACACAACTAACAAAG 57.026 40.909 0.00 0.00 0.00 2.77
2518 2661 5.923733 ATTCCAACCACACAACTAACAAA 57.076 34.783 0.00 0.00 0.00 2.83
2519 2662 5.186021 ACAATTCCAACCACACAACTAACAA 59.814 36.000 0.00 0.00 0.00 2.83
2520 2663 4.707448 ACAATTCCAACCACACAACTAACA 59.293 37.500 0.00 0.00 0.00 2.41
2521 2664 5.040635 CACAATTCCAACCACACAACTAAC 58.959 41.667 0.00 0.00 0.00 2.34
2522 2665 4.707448 ACACAATTCCAACCACACAACTAA 59.293 37.500 0.00 0.00 0.00 2.24
2523 2666 4.274147 ACACAATTCCAACCACACAACTA 58.726 39.130 0.00 0.00 0.00 2.24
2524 2667 3.096092 ACACAATTCCAACCACACAACT 58.904 40.909 0.00 0.00 0.00 3.16
2525 2668 3.518634 ACACAATTCCAACCACACAAC 57.481 42.857 0.00 0.00 0.00 3.32
2526 2669 5.506483 CGAATACACAATTCCAACCACACAA 60.506 40.000 0.00 0.00 40.91 3.33
2527 2670 4.023622 CGAATACACAATTCCAACCACACA 60.024 41.667 0.00 0.00 40.91 3.72
2528 2671 4.472286 CGAATACACAATTCCAACCACAC 58.528 43.478 0.00 0.00 40.91 3.82
2529 2672 3.057876 GCGAATACACAATTCCAACCACA 60.058 43.478 0.00 0.00 40.91 4.17
2530 2673 3.057876 TGCGAATACACAATTCCAACCAC 60.058 43.478 0.00 0.00 40.91 4.16
2531 2674 3.149981 TGCGAATACACAATTCCAACCA 58.850 40.909 0.00 0.00 40.91 3.67
2532 2675 3.840890 TGCGAATACACAATTCCAACC 57.159 42.857 0.00 0.00 40.91 3.77
2533 2676 5.874831 TGTATGCGAATACACAATTCCAAC 58.125 37.500 12.46 0.00 40.91 3.77
2566 2709 8.842358 TCTTTAAAATGTACTACACCTGGAAG 57.158 34.615 0.00 0.00 0.00 3.46
2571 2714 9.490379 CTCAGTTCTTTAAAATGTACTACACCT 57.510 33.333 0.00 0.00 0.00 4.00
2575 2718 8.989980 AGCACTCAGTTCTTTAAAATGTACTAC 58.010 33.333 0.00 0.00 0.00 2.73
2576 2719 8.988934 CAGCACTCAGTTCTTTAAAATGTACTA 58.011 33.333 0.00 0.00 0.00 1.82
2577 2720 7.715249 TCAGCACTCAGTTCTTTAAAATGTACT 59.285 33.333 0.00 0.00 0.00 2.73
2651 2795 4.378149 GGACGAGTTAAAGCTTAGTTTGGC 60.378 45.833 0.00 0.00 0.00 4.52
2671 3109 0.744874 TGATCCGTCGGAATCTGGAC 59.255 55.000 19.76 4.87 34.34 4.02
2759 3200 8.567104 GTGGAAAAAGTGAAAATTATTTGGCAT 58.433 29.630 0.00 0.00 0.00 4.40
2777 3224 3.955551 GCCCTTATTATCCCGTGGAAAAA 59.044 43.478 0.00 0.00 34.34 1.94
2786 3233 5.551305 AAAGCAATTGCCCTTATTATCCC 57.449 39.130 26.45 0.00 43.38 3.85
2787 3234 6.258507 CACAAAAGCAATTGCCCTTATTATCC 59.741 38.462 26.45 0.00 43.38 2.59
2788 3235 6.818142 ACACAAAAGCAATTGCCCTTATTATC 59.182 34.615 26.45 0.00 43.38 1.75
2789 3236 6.594937 CACACAAAAGCAATTGCCCTTATTAT 59.405 34.615 26.45 2.53 43.38 1.28
2790 3237 5.931146 CACACAAAAGCAATTGCCCTTATTA 59.069 36.000 26.45 0.00 43.38 0.98
2791 3238 4.756135 CACACAAAAGCAATTGCCCTTATT 59.244 37.500 26.45 11.28 43.38 1.40
2793 3240 3.494048 CCACACAAAAGCAATTGCCCTTA 60.494 43.478 26.45 0.00 43.38 2.69
2798 3260 1.003652 GTGCCACACAAAAGCAATTGC 60.004 47.619 23.05 23.05 38.45 3.56
2814 3281 7.465989 CAATTTTGGAATGACAATATTGTGCC 58.534 34.615 25.42 18.91 41.10 5.01
2845 3318 2.010817 GCGTGCAAGCGTTTTCCTG 61.011 57.895 9.33 0.00 0.00 3.86
2856 3329 2.904866 GTCCCAGGTTGCGTGCAA 60.905 61.111 2.58 2.58 0.00 4.08
2870 3343 1.405821 CTCCTGTCGTCCTGTATGTCC 59.594 57.143 0.00 0.00 0.00 4.02
2871 3344 1.202313 GCTCCTGTCGTCCTGTATGTC 60.202 57.143 0.00 0.00 0.00 3.06
2936 3443 0.035630 GGTCTGCCTCATGCTCTGTT 60.036 55.000 0.00 0.00 42.00 3.16
2958 3469 4.424566 TTCGCTGCGTCCGGTACC 62.425 66.667 22.48 0.16 0.00 3.34
3077 3595 0.179062 CTCGCCTAAGCAAGCTGGAT 60.179 55.000 0.00 0.00 39.83 3.41


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

AutoCloner maintained by Alex Coulton.