Multiple sequence alignment - TraesCS6D01G020000

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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 TraesCS6D01G020000 chr6D 100.000 3203 0 0 1 3203 7990970 7987768 0.000000e+00 5915.0
1 TraesCS6D01G020000 chr6D 83.689 2765 294 65 322 3012 7718165 7720846 0.000000e+00 2462.0
2 TraesCS6D01G020000 chr6D 78.591 1093 208 22 1128 2204 8899590 8900672 0.000000e+00 699.0
3 TraesCS6D01G020000 chr6D 95.181 83 3 1 637 719 168264083 168264002 2.590000e-26 130.0
4 TraesCS6D01G020000 chr6D 94.737 57 3 0 465 521 270898153 270898209 4.400000e-14 89.8
5 TraesCS6D01G020000 chr6A 83.575 2685 311 49 617 3203 7990821 7993473 0.000000e+00 2396.0
6 TraesCS6D01G020000 chr6A 86.256 1688 136 47 1547 3193 8197967 8196335 0.000000e+00 1744.0
7 TraesCS6D01G020000 chr6A 88.997 718 35 14 846 1536 8199049 8198349 0.000000e+00 848.0
8 TraesCS6D01G020000 chr6A 77.990 1045 216 12 1169 2203 9339065 9340105 0.000000e+00 643.0
9 TraesCS6D01G020000 chr6A 87.726 497 50 8 1721 2212 8395393 8394903 1.290000e-158 569.0
10 TraesCS6D01G020000 chr6A 82.363 601 101 5 1614 2212 8393036 8392439 4.740000e-143 518.0
11 TraesCS6D01G020000 chr6A 77.707 628 79 34 2613 3203 8194601 8193998 8.570000e-86 327.0
12 TraesCS6D01G020000 chr6A 80.308 325 38 16 119 437 7990469 7990773 4.160000e-54 222.0
13 TraesCS6D01G020000 chr6A 82.540 126 22 0 970 1095 9473089 9473214 9.390000e-21 111.0
14 TraesCS6D01G020000 chr6B 83.576 2472 295 44 820 3203 14545638 14543190 0.000000e+00 2213.0
15 TraesCS6D01G020000 chr6B 85.804 1909 203 32 732 2586 14333103 14334997 0.000000e+00 1962.0
16 TraesCS6D01G020000 chr6B 80.110 1277 211 30 960 2204 14550309 14549044 0.000000e+00 911.0
17 TraesCS6D01G020000 chr6B 86.122 526 51 13 416 924 14550907 14550387 6.040000e-152 547.0
18 TraesCS6D01G020000 chr6B 97.211 251 6 1 1 251 14619637 14619388 1.060000e-114 424.0
19 TraesCS6D01G020000 chr6B 94.964 139 5 2 119 257 14547212 14547076 1.930000e-52 217.0
20 TraesCS6D01G020000 chr6B 82.075 106 14 4 979 1079 53077163 53077058 5.690000e-13 86.1
21 TraesCS6D01G020000 chr2B 79.310 1044 195 17 1175 2206 54043889 54042855 0.000000e+00 712.0
22 TraesCS6D01G020000 chr2B 79.083 1047 192 20 1175 2206 54016537 54015503 0.000000e+00 695.0
23 TraesCS6D01G020000 chr2B 95.349 86 3 1 634 719 692664671 692664755 5.570000e-28 135.0
24 TraesCS6D01G020000 chr1B 77.083 1296 224 52 960 2204 27753059 27751786 0.000000e+00 680.0
25 TraesCS6D01G020000 chr1B 83.104 799 71 32 819 1567 27364849 27364065 0.000000e+00 669.0
26 TraesCS6D01G020000 chr3B 82.583 333 27 6 119 420 778245087 778245419 6.810000e-67 265.0
27 TraesCS6D01G020000 chr3B 92.632 95 7 0 23 117 490333784 490333878 1.550000e-28 137.0
28 TraesCS6D01G020000 chr3B 96.386 83 2 1 637 719 6004143 6004062 5.570000e-28 135.0
29 TraesCS6D01G020000 chr3B 91.579 95 8 0 23 117 778244927 778245021 7.210000e-27 132.0
30 TraesCS6D01G020000 chrUn 82.282 333 27 9 119 420 371418613 371418282 3.170000e-65 259.0
31 TraesCS6D01G020000 chrUn 82.282 333 27 9 119 420 386303403 386303072 3.170000e-65 259.0
32 TraesCS6D01G020000 chrUn 81.982 333 29 6 119 420 318761642 318761974 1.470000e-63 254.0
33 TraesCS6D01G020000 chrUn 81.982 333 29 6 119 420 319095082 319095414 1.470000e-63 254.0
34 TraesCS6D01G020000 chrUn 81.982 333 29 6 119 420 341655213 341654881 1.470000e-63 254.0
35 TraesCS6D01G020000 chrUn 92.632 95 7 0 23 117 318761482 318761576 1.550000e-28 137.0
36 TraesCS6D01G020000 chrUn 92.632 95 7 0 23 117 319094922 319095016 1.550000e-28 137.0
37 TraesCS6D01G020000 chrUn 92.632 95 7 0 23 117 341655373 341655279 1.550000e-28 137.0
38 TraesCS6D01G020000 chrUn 95.349 86 3 1 634 719 452335135 452335219 5.570000e-28 135.0
39 TraesCS6D01G020000 chrUn 94.186 86 4 1 634 719 216512181 216512265 2.590000e-26 130.0
40 TraesCS6D01G020000 chrUn 95.181 83 3 1 637 719 286271199 286271118 2.590000e-26 130.0
41 TraesCS6D01G020000 chrUn 96.491 57 1 1 465 521 110373737 110373682 3.400000e-15 93.5
42 TraesCS6D01G020000 chr7B 82.282 333 28 14 119 420 408932341 408932673 3.170000e-65 259.0
43 TraesCS6D01G020000 chr7B 81.381 333 31 14 119 420 408947267 408947599 3.190000e-60 243.0
44 TraesCS6D01G020000 chr7B 81.381 333 30 9 119 420 674546467 674546136 3.190000e-60 243.0
45 TraesCS6D01G020000 chr7B 92.632 95 7 0 23 117 408932181 408932275 1.550000e-28 137.0
46 TraesCS6D01G020000 chr7B 90.526 95 9 0 23 117 408947107 408947201 3.350000e-25 126.0
47 TraesCS6D01G020000 chr4B 81.682 333 30 6 119 420 203526546 203526214 6.860000e-62 248.0
48 TraesCS6D01G020000 chr4B 92.632 95 7 0 23 117 203526706 203526612 1.550000e-28 137.0
49 TraesCS6D01G020000 chr1D 81.737 334 28 9 119 420 350884789 350885121 6.860000e-62 248.0
50 TraesCS6D01G020000 chr1D 96.491 57 1 1 465 521 408675848 408675903 3.400000e-15 93.5
51 TraesCS6D01G020000 chr4D 94.186 86 4 1 634 719 207363843 207363927 2.590000e-26 130.0
52 TraesCS6D01G020000 chr4D 94.186 86 4 1 634 719 285138037 285138121 2.590000e-26 130.0
53 TraesCS6D01G020000 chr4D 94.737 57 1 2 465 521 287863126 287863072 1.580000e-13 87.9
54 TraesCS6D01G020000 chr5D 89.011 91 10 0 544 634 432339218 432339308 2.610000e-21 113.0
55 TraesCS6D01G020000 chr7D 96.491 57 2 0 465 521 427384723 427384779 9.460000e-16 95.3
56 TraesCS6D01G020000 chr7D 96.491 57 1 1 465 521 117426753 117426808 3.400000e-15 93.5
57 TraesCS6D01G020000 chr7D 96.491 57 1 1 465 521 438999999 438999944 3.400000e-15 93.5


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 TraesCS6D01G020000 chr6D 7987768 7990970 3202 True 5915.0 5915 100.0000 1 3203 1 chr6D.!!$R1 3202
1 TraesCS6D01G020000 chr6D 7718165 7720846 2681 False 2462.0 2462 83.6890 322 3012 1 chr6D.!!$F1 2690
2 TraesCS6D01G020000 chr6D 8899590 8900672 1082 False 699.0 699 78.5910 1128 2204 1 chr6D.!!$F2 1076
3 TraesCS6D01G020000 chr6A 7990469 7993473 3004 False 1309.0 2396 81.9415 119 3203 2 chr6A.!!$F3 3084
4 TraesCS6D01G020000 chr6A 8193998 8199049 5051 True 973.0 1744 84.3200 846 3203 3 chr6A.!!$R1 2357
5 TraesCS6D01G020000 chr6A 9339065 9340105 1040 False 643.0 643 77.9900 1169 2203 1 chr6A.!!$F1 1034
6 TraesCS6D01G020000 chr6A 8392439 8395393 2954 True 543.5 569 85.0445 1614 2212 2 chr6A.!!$R2 598
7 TraesCS6D01G020000 chr6B 14333103 14334997 1894 False 1962.0 1962 85.8040 732 2586 1 chr6B.!!$F1 1854
8 TraesCS6D01G020000 chr6B 14543190 14550907 7717 True 972.0 2213 86.1930 119 3203 4 chr6B.!!$R3 3084
9 TraesCS6D01G020000 chr2B 54042855 54043889 1034 True 712.0 712 79.3100 1175 2206 1 chr2B.!!$R2 1031
10 TraesCS6D01G020000 chr2B 54015503 54016537 1034 True 695.0 695 79.0830 1175 2206 1 chr2B.!!$R1 1031
11 TraesCS6D01G020000 chr1B 27751786 27753059 1273 True 680.0 680 77.0830 960 2204 1 chr1B.!!$R2 1244
12 TraesCS6D01G020000 chr1B 27364065 27364849 784 True 669.0 669 83.1040 819 1567 1 chr1B.!!$R1 748

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
21 22 0.034380 AGCACTGCATTGCATCCTCT 60.034 50.0 28.09 6.13 45.62 3.69 F
924 5528 0.257616 GCCCAGCCCACCAGTAAATA 59.742 55.0 0.00 0.00 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1342 6002 1.918800 AGAGGAACTTGGGGTCCCG 60.919 63.158 0.48 0.0 41.55 5.14 R
2636 10190 0.320508 GTTCCAGGTCGTTGGGTCTC 60.321 60.000 4.10 0.0 38.81 3.36 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 4.806571 CAGCACTGCATTGCATCC 57.193 55.556 28.09 3.66 45.62 3.51
19 20 2.189833 CAGCACTGCATTGCATCCT 58.810 52.632 28.09 7.22 45.62 3.24
20 21 0.100682 CAGCACTGCATTGCATCCTC 59.899 55.000 28.09 0.68 45.62 3.71
21 22 0.034380 AGCACTGCATTGCATCCTCT 60.034 50.000 28.09 6.13 45.62 3.69
22 23 0.815734 GCACTGCATTGCATCCTCTT 59.184 50.000 22.74 0.00 42.49 2.85
24 25 2.353406 GCACTGCATTGCATCCTCTTTT 60.353 45.455 22.74 0.00 42.49 2.27
28 29 5.747197 CACTGCATTGCATCCTCTTTTATTC 59.253 40.000 12.53 0.00 38.13 1.75
29 30 5.655532 ACTGCATTGCATCCTCTTTTATTCT 59.344 36.000 12.53 0.00 38.13 2.40
30 31 6.154021 ACTGCATTGCATCCTCTTTTATTCTT 59.846 34.615 12.53 0.00 38.13 2.52
34 35 9.538508 GCATTGCATCCTCTTTTATTCTTTATT 57.461 29.630 3.15 0.00 0.00 1.40
51 52 7.475771 TCTTTATTTTGATTGTTGTGGTTGC 57.524 32.000 0.00 0.00 0.00 4.17
52 53 7.271511 TCTTTATTTTGATTGTTGTGGTTGCT 58.728 30.769 0.00 0.00 0.00 3.91
53 54 7.437862 TCTTTATTTTGATTGTTGTGGTTGCTC 59.562 33.333 0.00 0.00 0.00 4.26
54 55 4.462508 TTTTGATTGTTGTGGTTGCTCA 57.537 36.364 0.00 0.00 0.00 4.26
55 56 4.462508 TTTGATTGTTGTGGTTGCTCAA 57.537 36.364 0.00 0.00 0.00 3.02
56 57 3.435105 TGATTGTTGTGGTTGCTCAAC 57.565 42.857 4.26 4.26 42.62 3.18
59 60 2.937469 TGTTGTGGTTGCTCAACAAG 57.063 45.000 13.89 0.00 46.72 3.16
60 61 2.166829 TGTTGTGGTTGCTCAACAAGT 58.833 42.857 13.89 0.00 46.72 3.16
61 62 2.560542 TGTTGTGGTTGCTCAACAAGTT 59.439 40.909 13.89 0.00 46.72 2.66
63 64 4.400884 TGTTGTGGTTGCTCAACAAGTTAT 59.599 37.500 13.89 0.00 46.72 1.89
64 65 4.829064 TGTGGTTGCTCAACAAGTTATC 57.171 40.909 13.89 0.00 42.85 1.75
65 66 4.460263 TGTGGTTGCTCAACAAGTTATCT 58.540 39.130 13.89 0.00 42.85 1.98
66 67 4.515191 TGTGGTTGCTCAACAAGTTATCTC 59.485 41.667 13.89 0.00 42.85 2.75
67 68 4.757149 GTGGTTGCTCAACAAGTTATCTCT 59.243 41.667 13.89 0.00 42.85 3.10
68 69 4.997395 TGGTTGCTCAACAAGTTATCTCTC 59.003 41.667 13.89 0.00 42.85 3.20
70 71 5.121454 GGTTGCTCAACAAGTTATCTCTCAG 59.879 44.000 13.89 0.00 42.85 3.35
72 73 6.291648 TGCTCAACAAGTTATCTCTCAGAT 57.708 37.500 0.00 0.00 38.70 2.90
73 74 6.705302 TGCTCAACAAGTTATCTCTCAGATT 58.295 36.000 0.00 0.00 36.20 2.40
75 76 8.481314 TGCTCAACAAGTTATCTCTCAGATTAT 58.519 33.333 0.00 0.00 36.20 1.28
76 77 8.977505 GCTCAACAAGTTATCTCTCAGATTATC 58.022 37.037 0.00 0.00 36.20 1.75
78 79 7.649705 TCAACAAGTTATCTCTCAGATTATCGC 59.350 37.037 0.00 0.00 36.20 4.58
79 80 7.283625 ACAAGTTATCTCTCAGATTATCGCT 57.716 36.000 0.00 0.00 36.20 4.93
80 81 7.721402 ACAAGTTATCTCTCAGATTATCGCTT 58.279 34.615 0.00 0.00 36.20 4.68
81 82 8.200792 ACAAGTTATCTCTCAGATTATCGCTTT 58.799 33.333 0.00 0.00 36.20 3.51
82 83 8.698854 CAAGTTATCTCTCAGATTATCGCTTTC 58.301 37.037 0.00 0.00 36.20 2.62
84 85 8.081633 AGTTATCTCTCAGATTATCGCTTTCAG 58.918 37.037 0.00 0.00 36.20 3.02
85 86 5.843673 TCTCTCAGATTATCGCTTTCAGT 57.156 39.130 0.00 0.00 0.00 3.41
87 88 4.115516 TCTCAGATTATCGCTTTCAGTGC 58.884 43.478 0.00 0.00 0.00 4.40
88 89 3.860641 TCAGATTATCGCTTTCAGTGCA 58.139 40.909 0.00 0.00 0.00 4.57
89 90 4.252878 TCAGATTATCGCTTTCAGTGCAA 58.747 39.130 0.00 0.00 0.00 4.08
90 91 4.694982 TCAGATTATCGCTTTCAGTGCAAA 59.305 37.500 0.00 0.00 0.00 3.68
91 92 4.790140 CAGATTATCGCTTTCAGTGCAAAC 59.210 41.667 0.00 0.00 0.00 2.93
92 93 3.552604 TTATCGCTTTCAGTGCAAACC 57.447 42.857 0.00 0.00 0.00 3.27
94 95 1.370414 CGCTTTCAGTGCAAACCGG 60.370 57.895 0.00 0.00 0.00 5.28
97 98 1.308998 CTTTCAGTGCAAACCGGAGT 58.691 50.000 9.46 0.00 0.00 3.85
98 99 2.489971 CTTTCAGTGCAAACCGGAGTA 58.510 47.619 9.46 0.00 0.00 2.59
99 100 2.163818 TTCAGTGCAAACCGGAGTAG 57.836 50.000 9.46 0.00 0.00 2.57
100 101 1.334160 TCAGTGCAAACCGGAGTAGA 58.666 50.000 9.46 0.00 0.00 2.59
102 103 2.301870 TCAGTGCAAACCGGAGTAGATT 59.698 45.455 9.46 0.00 0.00 2.40
103 104 3.512329 TCAGTGCAAACCGGAGTAGATTA 59.488 43.478 9.46 0.00 0.00 1.75
104 105 4.020928 TCAGTGCAAACCGGAGTAGATTAA 60.021 41.667 9.46 0.00 0.00 1.40
105 106 4.876107 CAGTGCAAACCGGAGTAGATTAAT 59.124 41.667 9.46 0.00 0.00 1.40
107 108 6.537301 CAGTGCAAACCGGAGTAGATTAATTA 59.463 38.462 9.46 0.00 0.00 1.40
108 109 7.065324 CAGTGCAAACCGGAGTAGATTAATTAA 59.935 37.037 9.46 0.00 0.00 1.40
109 110 7.773690 AGTGCAAACCGGAGTAGATTAATTAAT 59.226 33.333 9.46 10.51 0.00 1.40
110 111 8.403236 GTGCAAACCGGAGTAGATTAATTAATT 58.597 33.333 9.46 5.89 0.00 1.40
112 113 9.797556 GCAAACCGGAGTAGATTAATTAATTTT 57.202 29.630 9.46 6.74 0.00 1.82
116 117 9.901172 ACCGGAGTAGATTAATTAATTTTGAGT 57.099 29.630 9.46 1.94 0.00 3.41
158 3736 3.117701 TCTGAAAGACACCCCACATTTCA 60.118 43.478 0.00 0.00 38.67 2.69
171 3751 5.466728 CCCCACATTTCAGAAGATACATACG 59.533 44.000 0.00 0.00 0.00 3.06
215 3795 4.503741 TCTGTTTCCAGTTGCAATAAGC 57.496 40.909 0.59 0.00 40.90 3.09
239 3819 6.599356 TTGGTTACTTATCAGCTGAGTACA 57.401 37.500 22.96 10.82 0.00 2.90
255 3835 6.268825 TGAGTACAAGTAGTGGAGATTGAC 57.731 41.667 0.00 0.00 0.00 3.18
256 3836 6.010850 TGAGTACAAGTAGTGGAGATTGACT 58.989 40.000 0.00 0.00 0.00 3.41
257 3837 6.493802 TGAGTACAAGTAGTGGAGATTGACTT 59.506 38.462 0.00 0.00 0.00 3.01
258 3838 7.015292 TGAGTACAAGTAGTGGAGATTGACTTT 59.985 37.037 0.00 0.00 0.00 2.66
259 3839 7.736893 AGTACAAGTAGTGGAGATTGACTTTT 58.263 34.615 0.00 0.00 0.00 2.27
260 3840 8.211629 AGTACAAGTAGTGGAGATTGACTTTTT 58.788 33.333 0.00 0.00 0.00 1.94
261 3841 7.264373 ACAAGTAGTGGAGATTGACTTTTTG 57.736 36.000 0.00 0.00 0.00 2.44
262 3842 6.828785 ACAAGTAGTGGAGATTGACTTTTTGT 59.171 34.615 0.00 0.00 0.00 2.83
263 3843 7.339466 ACAAGTAGTGGAGATTGACTTTTTGTT 59.661 33.333 0.00 0.00 30.02 2.83
264 3844 7.881775 AGTAGTGGAGATTGACTTTTTGTTT 57.118 32.000 0.00 0.00 0.00 2.83
265 3845 7.931275 AGTAGTGGAGATTGACTTTTTGTTTC 58.069 34.615 0.00 0.00 0.00 2.78
266 3846 7.775561 AGTAGTGGAGATTGACTTTTTGTTTCT 59.224 33.333 0.00 0.00 0.00 2.52
267 3847 7.410120 AGTGGAGATTGACTTTTTGTTTCTT 57.590 32.000 0.00 0.00 0.00 2.52
268 3848 7.260603 AGTGGAGATTGACTTTTTGTTTCTTG 58.739 34.615 0.00 0.00 0.00 3.02
269 3849 7.035612 GTGGAGATTGACTTTTTGTTTCTTGT 58.964 34.615 0.00 0.00 0.00 3.16
270 3850 7.009540 GTGGAGATTGACTTTTTGTTTCTTGTG 59.990 37.037 0.00 0.00 0.00 3.33
271 3851 6.019559 GGAGATTGACTTTTTGTTTCTTGTGC 60.020 38.462 0.00 0.00 0.00 4.57
272 3852 6.397272 AGATTGACTTTTTGTTTCTTGTGCA 58.603 32.000 0.00 0.00 0.00 4.57
273 3853 6.532657 AGATTGACTTTTTGTTTCTTGTGCAG 59.467 34.615 0.00 0.00 0.00 4.41
274 3854 4.493547 TGACTTTTTGTTTCTTGTGCAGG 58.506 39.130 0.00 0.00 0.00 4.85
275 3855 3.860641 ACTTTTTGTTTCTTGTGCAGGG 58.139 40.909 0.00 0.00 0.00 4.45
276 3856 3.260632 ACTTTTTGTTTCTTGTGCAGGGT 59.739 39.130 0.00 0.00 0.00 4.34
277 3857 3.971245 TTTTGTTTCTTGTGCAGGGTT 57.029 38.095 0.00 0.00 0.00 4.11
278 3858 3.518634 TTTGTTTCTTGTGCAGGGTTC 57.481 42.857 0.00 0.00 0.00 3.62
279 3859 2.136298 TGTTTCTTGTGCAGGGTTCA 57.864 45.000 0.00 0.00 0.00 3.18
280 3860 1.748493 TGTTTCTTGTGCAGGGTTCAC 59.252 47.619 0.00 0.00 35.14 3.18
281 3861 1.748493 GTTTCTTGTGCAGGGTTCACA 59.252 47.619 0.00 0.00 42.10 3.58
283 3863 1.388547 TCTTGTGCAGGGTTCACAAC 58.611 50.000 4.65 0.00 45.99 3.32
384 3980 5.913514 CGCCGTATATTATATGCAGTCCTAC 59.086 44.000 0.00 0.00 0.00 3.18
413 4517 7.596749 TCTTCTTCTTTTATTTAGGTGAGCG 57.403 36.000 0.00 0.00 0.00 5.03
414 4518 5.796350 TCTTCTTTTATTTAGGTGAGCGC 57.204 39.130 0.00 0.00 0.00 5.92
433 4537 3.377172 GCGCCATCAGGTTTAATAAGTGT 59.623 43.478 0.00 0.00 37.19 3.55
456 4560 6.051717 GTCTAATTATGTGCTCTCACCATGT 58.948 40.000 0.00 0.00 42.46 3.21
534 4638 5.148568 GCAATGTGATTTCAATTTGGTTGC 58.851 37.500 0.00 0.00 37.74 4.17
544 4648 6.647334 TTCAATTTGGTTGCTTACATCTCA 57.353 33.333 0.00 0.00 37.74 3.27
545 4649 6.839124 TCAATTTGGTTGCTTACATCTCAT 57.161 33.333 0.00 0.00 37.74 2.90
547 4651 6.433716 TCAATTTGGTTGCTTACATCTCATGA 59.566 34.615 0.00 0.00 37.74 3.07
548 4652 7.123098 TCAATTTGGTTGCTTACATCTCATGAT 59.877 33.333 0.00 0.00 37.74 2.45
549 4653 8.407832 CAATTTGGTTGCTTACATCTCATGATA 58.592 33.333 0.00 0.00 0.00 2.15
552 4656 6.653020 TGGTTGCTTACATCTCATGATAACT 58.347 36.000 0.00 0.00 0.00 2.24
553 4657 7.791029 TGGTTGCTTACATCTCATGATAACTA 58.209 34.615 0.00 0.00 0.00 2.24
555 4659 7.928706 GGTTGCTTACATCTCATGATAACTAGT 59.071 37.037 0.00 0.00 0.00 2.57
556 4660 9.967346 GTTGCTTACATCTCATGATAACTAGTA 57.033 33.333 0.00 0.00 0.00 1.82
559 4663 9.400638 GCTTACATCTCATGATAACTAGTACAC 57.599 37.037 0.00 0.00 0.00 2.90
560 4664 9.900710 CTTACATCTCATGATAACTAGTACACC 57.099 37.037 0.00 0.00 0.00 4.16
578 5122 1.291877 CCAGAGGTGCGTCTTTTCCG 61.292 60.000 0.00 0.00 0.00 4.30
586 5130 1.003718 CGTCTTTTCCGGCCCTCTT 60.004 57.895 0.00 0.00 0.00 2.85
595 5139 0.396695 CCGGCCCTCTTGTACTAGGA 60.397 60.000 0.00 0.00 34.58 2.94
601 5145 3.263681 GCCCTCTTGTACTAGGAAAAGGT 59.736 47.826 4.97 0.00 34.58 3.50
602 5146 4.468868 GCCCTCTTGTACTAGGAAAAGGTA 59.531 45.833 4.97 0.00 34.58 3.08
603 5147 5.626347 GCCCTCTTGTACTAGGAAAAGGTAC 60.626 48.000 4.97 0.00 34.58 3.34
604 5148 5.720520 CCCTCTTGTACTAGGAAAAGGTACT 59.279 44.000 4.97 0.00 37.35 2.73
605 5149 6.127394 CCCTCTTGTACTAGGAAAAGGTACTC 60.127 46.154 4.97 0.00 37.35 2.59
621 5166 3.181485 GGTACTCTCAATGCTCTAACGCT 60.181 47.826 0.00 0.00 0.00 5.07
624 5169 3.131933 ACTCTCAATGCTCTAACGCTCAT 59.868 43.478 0.00 0.00 0.00 2.90
625 5170 3.451526 TCTCAATGCTCTAACGCTCATG 58.548 45.455 0.00 0.00 0.00 3.07
628 5173 0.877649 ATGCTCTAACGCTCATGCCG 60.878 55.000 4.39 4.39 35.36 5.69
634 5179 2.299013 TCTAACGCTCATGCCGGATATT 59.701 45.455 5.05 0.00 35.36 1.28
681 5233 9.934190 TTTTTATGAAAGCTTTTCATTTGCTTC 57.066 25.926 21.28 5.32 44.94 3.86
687 5239 5.779529 AGCTTTTCATTTGCTTCTCTTCA 57.220 34.783 0.00 0.00 32.61 3.02
692 5244 5.395682 TTCATTTGCTTCTCTTCAATGGG 57.604 39.130 0.00 0.00 0.00 4.00
703 5255 6.824305 TCTCTTCAATGGGAGTTTCATTTC 57.176 37.500 4.69 0.00 33.08 2.17
709 5261 6.418101 TCAATGGGAGTTTCATTTCTCCTAG 58.582 40.000 10.39 0.00 46.56 3.02
720 5272 6.346477 TCATTTCTCCTAGAATGTATCCCG 57.654 41.667 0.00 0.00 33.67 5.14
723 5275 4.035612 TCTCCTAGAATGTATCCCGAGG 57.964 50.000 0.00 0.00 0.00 4.63
760 5312 1.945394 GATGCTCAATGTCGGCTCATT 59.055 47.619 0.00 0.21 38.38 2.57
763 5315 2.557924 TGCTCAATGTCGGCTCATTTTT 59.442 40.909 0.00 0.00 36.10 1.94
852 5440 4.686191 AAAGACAGGGCATCTATCTCTG 57.314 45.455 0.00 0.00 0.00 3.35
857 5445 3.896888 ACAGGGCATCTATCTCTGAAGAG 59.103 47.826 0.58 0.58 43.36 2.85
891 5487 3.741476 GGCAGCCCAGCGTCTTTG 61.741 66.667 0.00 0.00 34.64 2.77
924 5528 0.257616 GCCCAGCCCACCAGTAAATA 59.742 55.000 0.00 0.00 0.00 1.40
926 5530 2.107552 GCCCAGCCCACCAGTAAATATA 59.892 50.000 0.00 0.00 0.00 0.86
931 5536 5.221925 CCAGCCCACCAGTAAATATATGTCT 60.222 44.000 0.00 0.00 0.00 3.41
939 5544 8.777413 CACCAGTAAATATATGTCTGTCAATGG 58.223 37.037 9.58 0.00 0.00 3.16
1161 5821 1.152567 CCTCCTCTCCGGCATCTCT 60.153 63.158 0.00 0.00 0.00 3.10
1164 5824 1.456518 CCTCTCCGGCATCTCTCCA 60.457 63.158 0.00 0.00 0.00 3.86
1167 5827 0.614697 TCTCCGGCATCTCTCCAACA 60.615 55.000 0.00 0.00 0.00 3.33
1245 5905 1.778383 ACTCAAGGCCTCCCCCAAA 60.778 57.895 5.23 0.00 0.00 3.28
2000 7049 4.295407 CCTAGAGGGCCGGATGAA 57.705 61.111 5.05 0.00 0.00 2.57
2161 9674 2.723322 TGCTGAAGATTATGCTGCCT 57.277 45.000 0.00 0.00 0.00 4.75
2239 9764 8.560374 TCTGAGTAATATGTGTAGAATCACGAG 58.440 37.037 0.00 0.00 40.74 4.18
2301 9844 8.948631 TGTAATGGAGAAGAAGATACATGTTC 57.051 34.615 2.30 1.60 0.00 3.18
2335 9878 4.963276 TGTGGCTTTCCAAAATCTATCG 57.037 40.909 0.00 0.00 45.53 2.92
2339 9882 5.800438 GTGGCTTTCCAAAATCTATCGTTTC 59.200 40.000 0.00 0.00 45.53 2.78
2340 9883 5.028375 GGCTTTCCAAAATCTATCGTTTCG 58.972 41.667 0.00 0.00 0.00 3.46
2369 9912 5.750352 ATTGATTTCTCCTTTGTGCCATT 57.250 34.783 0.00 0.00 0.00 3.16
2447 10000 7.383102 AGGTTCACTGCTTCATAAATAGTTG 57.617 36.000 0.00 0.00 0.00 3.16
2448 10001 6.375455 AGGTTCACTGCTTCATAAATAGTTGG 59.625 38.462 0.00 0.00 0.00 3.77
2453 10006 9.461312 TCACTGCTTCATAAATAGTTGGTATTT 57.539 29.630 0.00 0.00 42.81 1.40
2489 10042 8.805175 TGAATTCCATTTCATATCACAGTTGTT 58.195 29.630 2.27 0.00 30.82 2.83
2519 10072 5.648178 TGTAGATTGTTGATTGCAGCATT 57.352 34.783 0.00 0.00 35.11 3.56
2520 10073 5.404096 TGTAGATTGTTGATTGCAGCATTG 58.596 37.500 0.00 0.00 35.11 2.82
2525 10078 3.093814 TGTTGATTGCAGCATTGGAGAT 58.906 40.909 0.00 0.00 29.77 2.75
2526 10079 3.119280 TGTTGATTGCAGCATTGGAGATG 60.119 43.478 0.00 0.00 29.77 2.90
2563 10117 3.964031 TGTAGGTTTGGCCAACTTCAAAT 59.036 39.130 20.35 2.72 40.61 2.32
2567 10121 3.205338 GTTTGGCCAACTTCAAATGCTT 58.795 40.909 20.35 0.00 35.66 3.91
2573 10127 3.243501 GCCAACTTCAAATGCTTGAGACA 60.244 43.478 0.00 0.00 42.48 3.41
2575 10129 4.293415 CAACTTCAAATGCTTGAGACACC 58.707 43.478 0.00 0.00 42.48 4.16
2576 10130 2.887152 ACTTCAAATGCTTGAGACACCC 59.113 45.455 0.00 0.00 42.48 4.61
2577 10131 2.655090 TCAAATGCTTGAGACACCCA 57.345 45.000 0.00 0.00 36.62 4.51
2578 10132 2.507484 TCAAATGCTTGAGACACCCAG 58.493 47.619 0.00 0.00 36.62 4.45
2579 10133 1.542915 CAAATGCTTGAGACACCCAGG 59.457 52.381 0.00 0.00 34.14 4.45
2580 10134 0.773644 AATGCTTGAGACACCCAGGT 59.226 50.000 0.00 0.00 0.00 4.00
2581 10135 0.326264 ATGCTTGAGACACCCAGGTC 59.674 55.000 0.00 0.00 38.08 3.85
2582 10136 1.053835 TGCTTGAGACACCCAGGTCA 61.054 55.000 0.00 0.00 40.29 4.02
2583 10137 0.321122 GCTTGAGACACCCAGGTCAG 60.321 60.000 0.00 0.00 40.29 3.51
2584 10138 0.322975 CTTGAGACACCCAGGTCAGG 59.677 60.000 0.00 0.00 40.29 3.86
2611 10165 0.835276 TGGGAGAGGCACTGATGATG 59.165 55.000 0.00 0.00 41.55 3.07
2615 10169 2.037901 GAGAGGCACTGATGATGGAGA 58.962 52.381 0.00 0.00 41.55 3.71
2618 10172 1.126488 GGCACTGATGATGGAGAGGA 58.874 55.000 0.00 0.00 0.00 3.71
2619 10173 1.202627 GGCACTGATGATGGAGAGGAC 60.203 57.143 0.00 0.00 0.00 3.85
2628 10182 4.828925 GGAGAGGACGCAGCTGGC 62.829 72.222 17.12 6.97 39.90 4.85
2636 10190 3.506096 CGCAGCTGGCAGACATGG 61.506 66.667 20.86 2.80 45.17 3.66
2637 10191 2.045634 GCAGCTGGCAGACATGGA 60.046 61.111 20.86 0.00 43.97 3.41
2659 10213 0.036164 CCCAACGACCTGGAACATCA 59.964 55.000 0.00 0.00 38.96 3.07
2662 10216 2.494059 CAACGACCTGGAACATCAACT 58.506 47.619 0.00 0.00 38.20 3.16
2664 10218 1.002087 ACGACCTGGAACATCAACTCC 59.998 52.381 0.00 0.00 38.20 3.85
2673 10227 5.003804 TGGAACATCAACTCCTAAGCTTTC 58.996 41.667 3.20 0.00 32.51 2.62
2674 10228 5.003804 GGAACATCAACTCCTAAGCTTTCA 58.996 41.667 3.20 0.00 0.00 2.69
2677 10231 7.011857 GGAACATCAACTCCTAAGCTTTCATAG 59.988 40.741 3.20 0.00 0.00 2.23
2702 10256 6.543831 GGAGGTATATGTGATTTTGTCAAGCT 59.456 38.462 0.00 0.00 38.90 3.74
2704 10258 6.886459 AGGTATATGTGATTTTGTCAAGCTGT 59.114 34.615 0.00 0.00 38.90 4.40
2714 10268 5.596836 TTTGTCAAGCTGTTCTTCCAAAT 57.403 34.783 0.00 0.00 32.29 2.32
2717 10271 5.620206 TGTCAAGCTGTTCTTCCAAATCTA 58.380 37.500 0.00 0.00 31.27 1.98
2722 10276 7.502226 TCAAGCTGTTCTTCCAAATCTAAAAGA 59.498 33.333 0.00 0.00 31.27 2.52
2728 10282 9.801873 TGTTCTTCCAAATCTAAAAGAAGTTTG 57.198 29.630 0.00 0.00 38.15 2.93
2763 10317 4.805719 GCAGACGACTTGTGATGATTATCA 59.194 41.667 0.00 0.00 40.92 2.15
2765 10319 5.461407 CAGACGACTTGTGATGATTATCAGG 59.539 44.000 0.00 0.00 43.66 3.86
2843 10397 0.251297 ACCTTGCTATTGTGCCTGCA 60.251 50.000 0.00 0.00 0.00 4.41
2854 10408 1.001764 TGCCTGCAGGTTGAGGATG 60.002 57.895 32.81 5.52 37.57 3.51
2855 10409 1.001641 GCCTGCAGGTTGAGGATGT 60.002 57.895 32.81 0.00 37.57 3.06
2899 10456 2.642311 TGCTAAGGAAACCCATGTGAGA 59.358 45.455 0.00 0.00 0.00 3.27
2909 10466 7.072961 AGGAAACCCATGTGAGATACTTCATAT 59.927 37.037 0.00 0.00 30.16 1.78
2913 10470 7.448420 ACCCATGTGAGATACTTCATATTCTG 58.552 38.462 0.00 0.00 27.90 3.02
2915 10472 6.877855 CCATGTGAGATACTTCATATTCTGGG 59.122 42.308 0.00 0.00 27.90 4.45
2947 10507 5.707764 AGTTTCTCCTTTTTCATCACTAGCC 59.292 40.000 0.00 0.00 0.00 3.93
2949 10509 5.505181 TCTCCTTTTTCATCACTAGCCTT 57.495 39.130 0.00 0.00 0.00 4.35
2950 10510 6.620877 TCTCCTTTTTCATCACTAGCCTTA 57.379 37.500 0.00 0.00 0.00 2.69
2951 10511 7.016153 TCTCCTTTTTCATCACTAGCCTTAA 57.984 36.000 0.00 0.00 0.00 1.85
2952 10512 7.458397 TCTCCTTTTTCATCACTAGCCTTAAA 58.542 34.615 0.00 0.00 0.00 1.52
2953 10513 7.607991 TCTCCTTTTTCATCACTAGCCTTAAAG 59.392 37.037 0.00 0.00 0.00 1.85
2977 10560 7.777095 AGGCATTTACTAAAACAAACTGTGAA 58.223 30.769 0.00 0.00 0.00 3.18
2994 10577 3.066621 TGTGAACTGCATTGGTTTCAGTC 59.933 43.478 0.00 0.00 39.86 3.51
3008 10592 3.114616 AGTCGCACGCATCACTGC 61.115 61.111 0.00 0.00 45.31 4.40
3022 10606 2.241160 TCACTGCATTCATTGTTGCCT 58.759 42.857 10.39 0.00 38.08 4.75
3023 10607 2.029739 TCACTGCATTCATTGTTGCCTG 60.030 45.455 10.39 7.08 38.08 4.85
3024 10608 1.965643 ACTGCATTCATTGTTGCCTGT 59.034 42.857 10.39 7.57 38.08 4.00
3033 10617 4.072131 TCATTGTTGCCTGTACTTCCTTC 58.928 43.478 0.00 0.00 0.00 3.46
3042 10626 4.324267 CCTGTACTTCCTTCCGTGAATTT 58.676 43.478 0.00 0.00 0.00 1.82
3045 10629 5.127491 TGTACTTCCTTCCGTGAATTTTGT 58.873 37.500 0.00 0.00 0.00 2.83
3052 10636 1.606668 TCCGTGAATTTTGTGGTCTGC 59.393 47.619 0.00 0.00 0.00 4.26
3116 10708 6.906157 AATATCCATAGAAAACATGCCCAG 57.094 37.500 0.00 0.00 0.00 4.45
3124 10716 4.265073 AGAAAACATGCCCAGTATCTGAC 58.735 43.478 0.00 0.00 32.44 3.51
3125 10717 2.315925 AACATGCCCAGTATCTGACG 57.684 50.000 0.00 0.00 32.44 4.35
3131 10723 1.207329 GCCCAGTATCTGACGGAACTT 59.793 52.381 0.00 0.00 32.44 2.66
3142 10734 2.289444 TGACGGAACTTCCTCCAATGTC 60.289 50.000 6.25 5.51 34.91 3.06
3169 10764 2.092375 GGTAAACCTTGATAGCTGGGCT 60.092 50.000 0.00 0.00 43.41 5.19
3193 10788 2.957402 AAGAAACTGAGGTGGCATGA 57.043 45.000 0.00 0.00 0.00 3.07
3194 10789 3.446442 AAGAAACTGAGGTGGCATGAT 57.554 42.857 0.00 0.00 0.00 2.45
3198 10793 2.634815 ACTGAGGTGGCATGATGATC 57.365 50.000 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.100682 GAGGATGCAATGCAGTGCTG 59.899 55.000 35.48 11.60 43.65 4.41
2 3 0.034380 AGAGGATGCAATGCAGTGCT 60.034 50.000 35.48 22.79 43.65 4.40
6 7 6.145338 AGAATAAAAGAGGATGCAATGCAG 57.855 37.500 14.98 0.00 43.65 4.41
8 9 9.538508 AATAAAGAATAAAAGAGGATGCAATGC 57.461 29.630 0.00 0.00 33.28 3.56
28 29 7.224362 TGAGCAACCACAACAATCAAAATAAAG 59.776 33.333 0.00 0.00 0.00 1.85
29 30 7.044181 TGAGCAACCACAACAATCAAAATAAA 58.956 30.769 0.00 0.00 0.00 1.40
30 31 6.577103 TGAGCAACCACAACAATCAAAATAA 58.423 32.000 0.00 0.00 0.00 1.40
34 35 4.180057 GTTGAGCAACCACAACAATCAAA 58.820 39.130 0.00 0.00 43.66 2.69
35 36 3.779759 GTTGAGCAACCACAACAATCAA 58.220 40.909 0.00 0.00 43.66 2.57
36 37 3.435105 GTTGAGCAACCACAACAATCA 57.565 42.857 0.00 0.00 43.66 2.57
41 42 2.939460 ACTTGTTGAGCAACCACAAC 57.061 45.000 10.54 0.00 44.21 3.32
42 43 4.887071 AGATAACTTGTTGAGCAACCACAA 59.113 37.500 10.54 0.00 40.46 3.33
44 45 4.757149 AGAGATAACTTGTTGAGCAACCAC 59.243 41.667 10.54 0.00 40.46 4.16
46 47 4.997395 TGAGAGATAACTTGTTGAGCAACC 59.003 41.667 10.54 0.00 40.46 3.77
47 48 5.928839 TCTGAGAGATAACTTGTTGAGCAAC 59.071 40.000 6.41 6.41 41.50 4.17
48 49 6.101650 TCTGAGAGATAACTTGTTGAGCAA 57.898 37.500 0.00 0.00 35.50 3.91
49 50 5.728637 TCTGAGAGATAACTTGTTGAGCA 57.271 39.130 0.00 0.00 0.00 4.26
50 51 8.885494 ATAATCTGAGAGATAACTTGTTGAGC 57.115 34.615 0.00 0.00 32.89 4.26
51 52 9.179552 CGATAATCTGAGAGATAACTTGTTGAG 57.820 37.037 0.00 0.00 32.89 3.02
52 53 7.649705 GCGATAATCTGAGAGATAACTTGTTGA 59.350 37.037 0.00 0.00 32.89 3.18
53 54 7.651304 AGCGATAATCTGAGAGATAACTTGTTG 59.349 37.037 0.00 0.00 32.89 3.33
54 55 7.721402 AGCGATAATCTGAGAGATAACTTGTT 58.279 34.615 0.00 0.00 32.89 2.83
55 56 7.283625 AGCGATAATCTGAGAGATAACTTGT 57.716 36.000 0.00 0.00 32.89 3.16
56 57 8.586570 AAAGCGATAATCTGAGAGATAACTTG 57.413 34.615 0.00 0.00 32.89 3.16
57 58 8.417106 TGAAAGCGATAATCTGAGAGATAACTT 58.583 33.333 0.00 0.00 32.89 2.66
58 59 7.946207 TGAAAGCGATAATCTGAGAGATAACT 58.054 34.615 0.00 0.00 32.89 2.24
59 60 7.865385 ACTGAAAGCGATAATCTGAGAGATAAC 59.135 37.037 0.00 0.00 37.60 1.89
60 61 7.864882 CACTGAAAGCGATAATCTGAGAGATAA 59.135 37.037 0.00 0.00 37.60 1.75
61 62 7.366513 CACTGAAAGCGATAATCTGAGAGATA 58.633 38.462 0.00 0.00 37.60 1.98
63 64 5.586339 CACTGAAAGCGATAATCTGAGAGA 58.414 41.667 0.00 0.00 37.60 3.10
64 65 4.208873 GCACTGAAAGCGATAATCTGAGAG 59.791 45.833 0.00 0.00 37.60 3.20
65 66 4.115516 GCACTGAAAGCGATAATCTGAGA 58.884 43.478 0.00 0.00 37.60 3.27
66 67 3.867493 TGCACTGAAAGCGATAATCTGAG 59.133 43.478 0.00 0.00 37.60 3.35
67 68 3.860641 TGCACTGAAAGCGATAATCTGA 58.139 40.909 0.00 0.00 37.60 3.27
68 69 4.604843 TTGCACTGAAAGCGATAATCTG 57.395 40.909 0.00 0.00 37.60 2.90
70 71 4.098416 GGTTTGCACTGAAAGCGATAATC 58.902 43.478 0.00 0.00 37.60 1.75
72 73 3.552604 GGTTTGCACTGAAAGCGATAA 57.447 42.857 0.00 0.00 37.60 1.75
76 77 4.210447 CGGTTTGCACTGAAAGCG 57.790 55.556 6.11 6.11 46.54 4.68
78 79 1.308998 ACTCCGGTTTGCACTGAAAG 58.691 50.000 0.00 0.00 42.29 2.62
79 80 2.103432 TCTACTCCGGTTTGCACTGAAA 59.897 45.455 0.00 0.00 0.00 2.69
80 81 1.689813 TCTACTCCGGTTTGCACTGAA 59.310 47.619 0.00 0.00 0.00 3.02
81 82 1.334160 TCTACTCCGGTTTGCACTGA 58.666 50.000 0.00 0.00 0.00 3.41
82 83 2.386661 ATCTACTCCGGTTTGCACTG 57.613 50.000 0.00 0.00 0.00 3.66
84 85 5.813080 AATTAATCTACTCCGGTTTGCAC 57.187 39.130 0.00 0.00 0.00 4.57
85 86 8.514330 AATTAATTAATCTACTCCGGTTTGCA 57.486 30.769 11.08 0.00 0.00 4.08
90 91 9.901172 ACTCAAAATTAATTAATCTACTCCGGT 57.099 29.630 11.08 1.97 0.00 5.28
103 104 9.692325 AGAAGCTCCATCTACTCAAAATTAATT 57.308 29.630 0.00 0.00 0.00 1.40
104 105 9.692325 AAGAAGCTCCATCTACTCAAAATTAAT 57.308 29.630 0.00 0.00 0.00 1.40
105 106 9.520515 AAAGAAGCTCCATCTACTCAAAATTAA 57.479 29.630 0.00 0.00 0.00 1.40
107 108 8.414629 AAAAGAAGCTCCATCTACTCAAAATT 57.585 30.769 0.00 0.00 0.00 1.82
108 109 8.414629 AAAAAGAAGCTCCATCTACTCAAAAT 57.585 30.769 0.00 0.00 0.00 1.82
109 110 7.502226 TGAAAAAGAAGCTCCATCTACTCAAAA 59.498 33.333 0.00 0.00 0.00 2.44
110 111 6.998074 TGAAAAAGAAGCTCCATCTACTCAAA 59.002 34.615 0.00 0.00 0.00 2.69
112 113 6.114187 TGAAAAAGAAGCTCCATCTACTCA 57.886 37.500 0.00 0.00 0.00 3.41
113 114 7.011295 CAGATGAAAAAGAAGCTCCATCTACTC 59.989 40.741 0.00 0.00 38.77 2.59
114 115 6.822676 CAGATGAAAAAGAAGCTCCATCTACT 59.177 38.462 0.00 0.00 38.77 2.57
115 116 6.820656 TCAGATGAAAAAGAAGCTCCATCTAC 59.179 38.462 0.00 0.00 38.77 2.59
116 117 6.950842 TCAGATGAAAAAGAAGCTCCATCTA 58.049 36.000 0.00 0.00 38.77 1.98
117 118 5.813383 TCAGATGAAAAAGAAGCTCCATCT 58.187 37.500 0.00 0.00 40.69 2.90
118 119 6.506500 TTCAGATGAAAAAGAAGCTCCATC 57.493 37.500 0.00 0.00 0.00 3.51
119 120 6.718454 TCTTTCAGATGAAAAAGAAGCTCCAT 59.282 34.615 9.16 0.00 42.72 3.41
120 121 6.016777 GTCTTTCAGATGAAAAAGAAGCTCCA 60.017 38.462 9.16 0.00 42.72 3.86
122 123 6.855403 GTGTCTTTCAGATGAAAAAGAAGCTC 59.145 38.462 9.16 0.00 42.72 4.09
158 3736 6.096423 TGAAACTGTAGGCGTATGTATCTTCT 59.904 38.462 0.00 0.00 0.00 2.85
171 3751 2.169832 TCACTGCTGAAACTGTAGGC 57.830 50.000 0.00 0.00 0.00 3.93
215 3795 6.631016 TGTACTCAGCTGATAAGTAACCAAG 58.369 40.000 18.63 3.13 0.00 3.61
239 3819 7.881775 AACAAAAAGTCAATCTCCACTACTT 57.118 32.000 0.00 0.00 31.94 2.24
255 3835 3.860641 ACCCTGCACAAGAAACAAAAAG 58.139 40.909 0.00 0.00 0.00 2.27
256 3836 3.971245 ACCCTGCACAAGAAACAAAAA 57.029 38.095 0.00 0.00 0.00 1.94
257 3837 3.259374 TGAACCCTGCACAAGAAACAAAA 59.741 39.130 0.00 0.00 0.00 2.44
258 3838 2.828520 TGAACCCTGCACAAGAAACAAA 59.171 40.909 0.00 0.00 0.00 2.83
259 3839 2.165437 GTGAACCCTGCACAAGAAACAA 59.835 45.455 0.00 0.00 36.31 2.83
260 3840 1.748493 GTGAACCCTGCACAAGAAACA 59.252 47.619 0.00 0.00 36.31 2.83
261 3841 1.748493 TGTGAACCCTGCACAAGAAAC 59.252 47.619 0.00 0.00 42.75 2.78
262 3842 2.136298 TGTGAACCCTGCACAAGAAA 57.864 45.000 0.00 0.00 42.75 2.52
263 3843 3.892633 TGTGAACCCTGCACAAGAA 57.107 47.368 0.00 0.00 42.75 2.52
267 3847 0.814457 GTTGTTGTGAACCCTGCACA 59.186 50.000 0.00 0.00 43.89 4.57
268 3848 1.102978 AGTTGTTGTGAACCCTGCAC 58.897 50.000 0.00 0.00 36.81 4.57
269 3849 1.102154 CAGTTGTTGTGAACCCTGCA 58.898 50.000 0.00 0.00 0.00 4.41
270 3850 0.385390 CCAGTTGTTGTGAACCCTGC 59.615 55.000 0.00 0.00 31.64 4.85
271 3851 1.405105 CACCAGTTGTTGTGAACCCTG 59.595 52.381 0.00 0.00 34.37 4.45
272 3852 1.005450 ACACCAGTTGTTGTGAACCCT 59.995 47.619 0.00 0.00 33.09 4.34
273 3853 1.470051 ACACCAGTTGTTGTGAACCC 58.530 50.000 0.00 0.00 33.09 4.11
327 3923 1.227999 TTCAAAGCGCCTTCCGTCTG 61.228 55.000 2.29 0.00 39.71 3.51
328 3924 0.534203 TTTCAAAGCGCCTTCCGTCT 60.534 50.000 2.29 0.00 39.71 4.18
390 3986 6.251549 GCGCTCACCTAAATAAAAGAAGAAG 58.748 40.000 0.00 0.00 0.00 2.85
408 4512 2.418368 ATTAAACCTGATGGCGCTCA 57.582 45.000 7.64 2.69 36.63 4.26
413 4517 7.859325 TTAGACACTTATTAAACCTGATGGC 57.141 36.000 0.00 0.00 36.63 4.40
433 4537 6.098838 AGACATGGTGAGAGCACATAATTAGA 59.901 38.462 0.00 0.00 46.96 2.10
447 4551 2.028294 AGTGAGCTTGAGACATGGTGAG 60.028 50.000 0.00 0.00 0.00 3.51
475 4579 8.603181 ACGGTTCTTTCATTTCTTTTCATTTTG 58.397 29.630 0.00 0.00 0.00 2.44
480 4584 6.626302 ACAACGGTTCTTTCATTTCTTTTCA 58.374 32.000 0.00 0.00 0.00 2.69
490 4594 3.065648 GCCTACAAACAACGGTTCTTTCA 59.934 43.478 0.00 0.00 35.82 2.69
534 4638 9.900710 GGTGTACTAGTTATCATGAGATGTAAG 57.099 37.037 0.00 0.00 35.67 2.34
559 4663 1.291877 CGGAAAAGACGCACCTCTGG 61.292 60.000 0.00 0.00 0.00 3.86
560 4664 1.291877 CCGGAAAAGACGCACCTCTG 61.292 60.000 0.00 0.00 0.00 3.35
572 5116 1.061546 AGTACAAGAGGGCCGGAAAA 58.938 50.000 5.05 0.00 0.00 2.29
575 5119 0.396695 CCTAGTACAAGAGGGCCGGA 60.397 60.000 5.05 0.00 0.00 5.14
578 5122 3.370633 CCTTTTCCTAGTACAAGAGGGCC 60.371 52.174 0.00 0.00 33.27 5.80
586 5130 7.578955 GCATTGAGAGTACCTTTTCCTAGTACA 60.579 40.741 0.00 0.00 39.04 2.90
595 5139 5.869888 CGTTAGAGCATTGAGAGTACCTTTT 59.130 40.000 0.00 0.00 0.00 2.27
601 5145 3.694566 TGAGCGTTAGAGCATTGAGAGTA 59.305 43.478 0.00 0.00 40.15 2.59
602 5146 2.493675 TGAGCGTTAGAGCATTGAGAGT 59.506 45.455 0.00 0.00 40.15 3.24
603 5147 3.156511 TGAGCGTTAGAGCATTGAGAG 57.843 47.619 0.00 0.00 40.15 3.20
604 5148 3.451526 CATGAGCGTTAGAGCATTGAGA 58.548 45.455 0.00 0.00 40.15 3.27
605 5149 2.033065 GCATGAGCGTTAGAGCATTGAG 60.033 50.000 0.00 0.00 40.15 3.02
621 5166 3.258123 TCGAGAATCAATATCCGGCATGA 59.742 43.478 0.00 0.00 33.17 3.07
624 5169 3.961480 ATCGAGAATCAATATCCGGCA 57.039 42.857 0.00 0.00 33.17 5.69
625 5170 4.499183 AGAATCGAGAATCAATATCCGGC 58.501 43.478 0.00 0.00 33.17 6.13
668 5220 6.041865 TCCCATTGAAGAGAAGCAAATGAAAA 59.958 34.615 0.00 0.00 0.00 2.29
681 5233 6.127786 GGAGAAATGAAACTCCCATTGAAGAG 60.128 42.308 0.00 3.05 34.75 2.85
687 5239 6.642733 TCTAGGAGAAATGAAACTCCCATT 57.357 37.500 0.00 0.00 35.92 3.16
692 5244 9.267084 GGATACATTCTAGGAGAAATGAAACTC 57.733 37.037 8.45 0.00 37.82 3.01
703 5255 4.035612 TCCTCGGGATACATTCTAGGAG 57.964 50.000 0.00 0.00 39.74 3.69
709 5261 4.082190 TCGATGAATCCTCGGGATACATTC 60.082 45.833 7.99 2.56 42.27 2.67
720 5272 3.717707 TCAATTCGGTCGATGAATCCTC 58.282 45.455 14.00 0.00 35.07 3.71
723 5275 3.496130 AGCATCAATTCGGTCGATGAATC 59.504 43.478 14.00 4.42 39.09 2.52
763 5315 9.814899 TTACATCTTTTTCTTTCTGATTGCAAA 57.185 25.926 1.71 0.00 0.00 3.68
852 5440 3.132111 CCTGGGCTTAGACTCTTCTCTTC 59.868 52.174 0.00 0.00 32.75 2.87
857 5445 0.179234 GCCCTGGGCTTAGACTCTTC 59.821 60.000 30.42 0.00 46.69 2.87
885 5481 2.892613 CTTTTCGTCTGCGTCAAAGAC 58.107 47.619 0.00 0.00 39.49 3.01
891 5487 1.901650 CTGGGCTTTTCGTCTGCGTC 61.902 60.000 0.00 0.00 39.49 5.19
924 5528 5.304101 GTCTCTCTCCCATTGACAGACATAT 59.696 44.000 0.00 0.00 31.08 1.78
926 5530 3.450457 GTCTCTCTCCCATTGACAGACAT 59.550 47.826 0.00 0.00 31.08 3.06
931 5536 2.828520 GTCAGTCTCTCTCCCATTGACA 59.171 50.000 0.00 0.00 34.97 3.58
939 5544 1.316706 CCGTGGGTCAGTCTCTCTCC 61.317 65.000 0.00 0.00 0.00 3.71
1161 5821 2.592287 GCGAACCCGGTTGTTGGA 60.592 61.111 7.78 0.00 36.06 3.53
1245 5905 2.997897 GACCTGAGGTGGGCGAGT 60.998 66.667 9.89 0.00 35.25 4.18
1342 6002 1.918800 AGAGGAACTTGGGGTCCCG 60.919 63.158 0.48 0.00 41.55 5.14
2000 7049 4.278419 ACTTTACAACGTAGTACCGAGGTT 59.722 41.667 0.00 0.00 45.00 3.50
2161 9674 3.068881 CACTTCCCCTCCGCAAGA 58.931 61.111 0.00 0.00 43.02 3.02
2239 9764 3.118592 ACATAGCTGGCTTCAGAACTACC 60.119 47.826 0.00 0.00 40.86 3.18
2301 9844 5.649395 TGGAAAGCCACATAAATCTTCAGAG 59.351 40.000 0.00 0.00 39.92 3.35
2339 9882 7.429340 GCACAAAGGAGAAATCAATACATAACG 59.571 37.037 0.00 0.00 0.00 3.18
2340 9883 7.702348 GGCACAAAGGAGAAATCAATACATAAC 59.298 37.037 0.00 0.00 0.00 1.89
2402 9945 1.078709 CCGTGACGTTCATGAAGCAT 58.921 50.000 8.80 0.00 35.46 3.79
2404 9947 0.669318 TCCCGTGACGTTCATGAAGC 60.669 55.000 8.80 3.29 35.46 3.86
2413 9956 1.831286 AGTGAACCTCCCGTGACGT 60.831 57.895 3.64 0.00 0.00 4.34
2492 10045 7.600960 TGCTGCAATCAACAATCTACAAATTA 58.399 30.769 0.00 0.00 0.00 1.40
2494 10047 6.028146 TGCTGCAATCAACAATCTACAAAT 57.972 33.333 0.00 0.00 0.00 2.32
2498 10051 4.802039 CCAATGCTGCAATCAACAATCTAC 59.198 41.667 6.36 0.00 0.00 2.59
2499 10052 4.705991 TCCAATGCTGCAATCAACAATCTA 59.294 37.500 6.36 0.00 0.00 1.98
2500 10053 3.512329 TCCAATGCTGCAATCAACAATCT 59.488 39.130 6.36 0.00 0.00 2.40
2509 10062 0.384309 CGCATCTCCAATGCTGCAAT 59.616 50.000 6.36 0.00 42.50 3.56
2519 10072 2.110757 TTGTGGCTCACGCATCTCCA 62.111 55.000 0.00 0.00 39.75 3.86
2520 10073 1.364626 CTTGTGGCTCACGCATCTCC 61.365 60.000 0.00 0.00 39.75 3.71
2533 10086 0.598065 GCCAAACCTACAGCTTGTGG 59.402 55.000 0.00 0.00 0.00 4.17
2548 10101 2.433604 TCAAGCATTTGAAGTTGGCCAA 59.566 40.909 16.05 16.05 40.26 4.52
2549 10102 2.036217 CTCAAGCATTTGAAGTTGGCCA 59.964 45.455 0.00 0.00 42.48 5.36
2550 10103 2.297033 TCTCAAGCATTTGAAGTTGGCC 59.703 45.455 0.00 0.00 42.48 5.36
2563 10117 1.053835 TGACCTGGGTGTCTCAAGCA 61.054 55.000 0.00 0.00 36.21 3.91
2567 10121 1.536418 CCCTGACCTGGGTGTCTCA 60.536 63.158 0.00 0.00 42.25 3.27
2590 10144 0.979709 TCATCAGTGCCTCTCCCAGG 60.980 60.000 0.00 0.00 46.82 4.45
2603 10157 0.749049 TGCGTCCTCTCCATCATCAG 59.251 55.000 0.00 0.00 0.00 2.90
2606 10160 1.047596 AGCTGCGTCCTCTCCATCAT 61.048 55.000 0.00 0.00 0.00 2.45
2611 10165 4.828925 GCCAGCTGCGTCCTCTCC 62.829 72.222 8.66 0.00 0.00 3.71
2615 10169 4.385405 GTCTGCCAGCTGCGTCCT 62.385 66.667 8.66 0.00 45.60 3.85
2618 10172 2.745100 CATGTCTGCCAGCTGCGT 60.745 61.111 8.66 0.00 45.60 5.24
2619 10173 3.506096 CCATGTCTGCCAGCTGCG 61.506 66.667 8.66 2.70 45.60 5.18
2628 10182 0.608130 TCGTTGGGTCTCCATGTCTG 59.392 55.000 0.00 0.00 43.63 3.51
2636 10190 0.320508 GTTCCAGGTCGTTGGGTCTC 60.321 60.000 4.10 0.00 38.81 3.36
2637 10191 1.052124 TGTTCCAGGTCGTTGGGTCT 61.052 55.000 4.10 0.00 38.81 3.85
2662 10216 7.956315 ACATATACCTCCTATGAAAGCTTAGGA 59.044 37.037 14.68 14.23 44.33 2.94
2664 10218 8.807118 TCACATATACCTCCTATGAAAGCTTAG 58.193 37.037 0.00 0.00 32.17 2.18
2673 10227 9.559732 TTGACAAAATCACATATACCTCCTATG 57.440 33.333 0.00 0.00 36.92 2.23
2674 10228 9.784531 CTTGACAAAATCACATATACCTCCTAT 57.215 33.333 0.00 0.00 36.92 2.57
2677 10231 6.543831 AGCTTGACAAAATCACATATACCTCC 59.456 38.462 0.00 0.00 36.92 4.30
2681 10235 8.454106 AGAACAGCTTGACAAAATCACATATAC 58.546 33.333 0.00 0.00 36.92 1.47
2702 10256 9.801873 CAAACTTCTTTTAGATTTGGAAGAACA 57.198 29.630 0.00 0.00 37.43 3.18
2704 10258 8.695456 AGCAAACTTCTTTTAGATTTGGAAGAA 58.305 29.630 0.00 0.00 37.43 2.52
2714 10268 8.902540 TTCATAGACAGCAAACTTCTTTTAGA 57.097 30.769 0.00 0.00 0.00 2.10
2717 10271 6.039717 TGCTTCATAGACAGCAAACTTCTTTT 59.960 34.615 0.00 0.00 43.14 2.27
2722 10276 4.453819 GTCTGCTTCATAGACAGCAAACTT 59.546 41.667 0.00 0.00 45.36 2.66
2728 10282 2.159310 AGTCGTCTGCTTCATAGACAGC 60.159 50.000 0.00 0.00 43.65 4.40
2744 10298 5.111989 CACCTGATAATCATCACAAGTCGT 58.888 41.667 0.00 0.00 36.22 4.34
2763 10317 9.739276 TCATCTAAAAGTAATTGAATGACACCT 57.261 29.630 0.00 0.00 0.00 4.00
2792 10346 4.583907 TGAACTGCACAAAAAGATGATGGA 59.416 37.500 0.00 0.00 0.00 3.41
2839 10393 1.808945 GACAACATCCTCAACCTGCAG 59.191 52.381 6.78 6.78 0.00 4.41
2861 10415 1.492176 AGCAAGCCTATACCACTGCAT 59.508 47.619 0.00 0.00 0.00 3.96
2866 10420 4.417426 TTCCTTAGCAAGCCTATACCAC 57.583 45.455 0.00 0.00 0.00 4.16
2869 10423 4.135306 GGGTTTCCTTAGCAAGCCTATAC 58.865 47.826 4.10 0.00 37.54 1.47
2874 10428 1.478105 CATGGGTTTCCTTAGCAAGCC 59.522 52.381 4.32 4.32 40.40 4.35
2899 10456 6.848562 AAAGGTCCCCAGAATATGAAGTAT 57.151 37.500 0.00 0.00 0.00 2.12
2909 10466 3.329814 GGAGAAACTAAAGGTCCCCAGAA 59.670 47.826 0.00 0.00 0.00 3.02
2913 10470 4.383931 AAAGGAGAAACTAAAGGTCCCC 57.616 45.455 0.00 0.00 0.00 4.81
2915 10472 6.954487 TGAAAAAGGAGAAACTAAAGGTCC 57.046 37.500 0.00 0.00 0.00 4.46
2924 10481 5.707764 AGGCTAGTGATGAAAAAGGAGAAAC 59.292 40.000 0.00 0.00 0.00 2.78
2949 10509 9.522804 CACAGTTTGTTTTAGTAAATGCCTTTA 57.477 29.630 0.00 0.00 0.00 1.85
2950 10510 8.254508 TCACAGTTTGTTTTAGTAAATGCCTTT 58.745 29.630 0.00 0.00 0.00 3.11
2951 10511 7.777095 TCACAGTTTGTTTTAGTAAATGCCTT 58.223 30.769 0.00 0.00 0.00 4.35
2952 10512 7.341445 TCACAGTTTGTTTTAGTAAATGCCT 57.659 32.000 0.00 0.00 0.00 4.75
2953 10513 7.704899 AGTTCACAGTTTGTTTTAGTAAATGCC 59.295 33.333 0.00 0.00 0.00 4.40
2962 10545 5.809562 CCAATGCAGTTCACAGTTTGTTTTA 59.190 36.000 0.00 0.00 0.00 1.52
2977 10560 0.593128 GCGACTGAAACCAATGCAGT 59.407 50.000 0.00 0.00 44.87 4.40
2994 10577 1.581912 GAATGCAGTGATGCGTGCG 60.582 57.895 0.00 0.00 42.96 5.34
3008 10592 4.460382 AGGAAGTACAGGCAACAATGAATG 59.540 41.667 0.00 0.00 41.41 2.67
3017 10601 1.053424 ACGGAAGGAAGTACAGGCAA 58.947 50.000 0.00 0.00 0.00 4.52
3022 10606 5.008217 CACAAAATTCACGGAAGGAAGTACA 59.992 40.000 0.00 0.00 0.00 2.90
3023 10607 5.449304 CACAAAATTCACGGAAGGAAGTAC 58.551 41.667 0.00 0.00 0.00 2.73
3024 10608 4.517453 CCACAAAATTCACGGAAGGAAGTA 59.483 41.667 0.00 0.00 0.00 2.24
3033 10617 1.608590 AGCAGACCACAAAATTCACGG 59.391 47.619 0.00 0.00 0.00 4.94
3042 10626 0.546122 ACCAACTCAGCAGACCACAA 59.454 50.000 0.00 0.00 0.00 3.33
3045 10629 1.059098 ATCACCAACTCAGCAGACCA 58.941 50.000 0.00 0.00 0.00 4.02
3099 10691 6.017605 GTCAGATACTGGGCATGTTTTCTATG 60.018 42.308 0.00 0.00 31.51 2.23
3100 10692 6.058183 GTCAGATACTGGGCATGTTTTCTAT 58.942 40.000 0.00 0.00 31.51 1.98
3102 10694 4.265073 GTCAGATACTGGGCATGTTTTCT 58.735 43.478 0.00 0.00 31.51 2.52
3109 10701 1.139058 GTTCCGTCAGATACTGGGCAT 59.861 52.381 0.00 0.00 31.51 4.40
3116 10708 2.758979 TGGAGGAAGTTCCGTCAGATAC 59.241 50.000 16.31 0.00 42.75 2.24
3124 10716 2.472695 TGACATTGGAGGAAGTTCCG 57.527 50.000 16.31 3.57 42.75 4.30
3125 10717 3.019564 CCATGACATTGGAGGAAGTTCC 58.980 50.000 14.54 14.54 39.25 3.62
3169 10764 2.173782 TGCCACCTCAGTTTCTTTACCA 59.826 45.455 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.