Multiple sequence alignment - TraesCS3B01G461700

Loading Multiple Alignment...

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 TraesCS3B01G461700 chr3B 100.000 3069 0 0 1 3069 704655773 704652705 0.000000e+00 5668.0
1 TraesCS3B01G461700 chr3B 91.503 765 42 13 1646 2395 704577853 704577097 0.000000e+00 1031.0
2 TraesCS3B01G461700 chr3B 75.449 167 30 7 545 707 448581317 448581476 1.530000e-08 71.3
3 TraesCS3B01G461700 chr3D 94.309 2091 82 14 990 3069 532584477 532582413 0.000000e+00 3168.0
4 TraesCS3B01G461700 chr3D 90.289 762 48 13 1646 2395 532343845 532343098 0.000000e+00 974.0
5 TraesCS3B01G461700 chr3D 89.911 674 57 9 308 977 532585523 532584857 0.000000e+00 857.0
6 TraesCS3B01G461700 chr3D 86.885 61 6 2 408 466 195409342 195409402 1.970000e-07 67.6
7 TraesCS3B01G461700 chr3A 94.295 929 41 6 1435 2360 667705087 667704168 0.000000e+00 1411.0
8 TraesCS3B01G461700 chr3A 86.897 725 75 6 2359 3069 667656749 667656031 0.000000e+00 795.0
9 TraesCS3B01G461700 chr3A 90.909 440 29 6 1646 2078 667514136 667513701 5.700000e-162 580.0
10 TraesCS3B01G461700 chr3A 91.329 346 20 6 990 1333 667705857 667705520 5.990000e-127 464.0
11 TraesCS3B01G461700 chr3A 91.071 336 14 8 2070 2395 667513276 667512947 1.010000e-119 440.0
12 TraesCS3B01G461700 chr3A 85.625 320 43 3 308 625 667706789 667706471 1.760000e-87 333.0
13 TraesCS3B01G461700 chr3A 94.783 115 3 2 1329 1443 667705383 667705272 3.150000e-40 176.0
14 TraesCS3B01G461700 chr3A 95.833 48 0 2 998 1045 667705912 667705867 3.280000e-10 76.8
15 TraesCS3B01G461700 chr7A 86.427 641 68 9 2434 3069 3355177 3354551 0.000000e+00 684.0
16 TraesCS3B01G461700 chr2B 85.355 676 81 15 2403 3069 54345220 54344554 0.000000e+00 684.0
17 TraesCS3B01G461700 chr2B 92.491 293 22 0 16 308 507532912 507532620 1.320000e-113 420.0
18 TraesCS3B01G461700 chr2B 91.060 302 25 2 9 308 437035988 437036289 1.020000e-109 407.0
19 TraesCS3B01G461700 chr2B 79.592 98 19 1 683 780 772825564 772825468 5.490000e-08 69.4
20 TraesCS3B01G461700 chr2B 91.667 48 2 2 420 466 32780446 32780492 7.100000e-07 65.8
21 TraesCS3B01G461700 chr4A 85.474 654 79 13 2425 3069 607185216 607184570 0.000000e+00 667.0
22 TraesCS3B01G461700 chr4A 81.818 99 16 2 1099 1195 498698762 498698664 7.050000e-12 82.4
23 TraesCS3B01G461700 chr5B 84.444 630 86 11 2445 3069 170678798 170678176 7.280000e-171 610.0
24 TraesCS3B01G461700 chr5B 82.069 290 41 8 2432 2715 170650143 170649859 1.420000e-58 237.0
25 TraesCS3B01G461700 chr5B 76.243 181 35 8 605 782 653781052 653781227 4.210000e-14 89.8
26 TraesCS3B01G461700 chr5B 76.351 148 32 3 632 777 506198615 506198469 3.280000e-10 76.8
27 TraesCS3B01G461700 chr4B 90.179 448 38 4 2620 3064 249059154 249059598 2.050000e-161 579.0
28 TraesCS3B01G461700 chr4B 81.188 101 17 2 1096 1195 122218294 122218195 2.540000e-11 80.5
29 TraesCS3B01G461700 chr4D 89.357 451 42 4 2620 3067 235508809 235508362 2.070000e-156 562.0
30 TraesCS3B01G461700 chr4D 91.262 309 24 3 2 308 396595106 396595413 4.730000e-113 418.0
31 TraesCS3B01G461700 chr4D 92.150 293 22 1 17 308 387456834 387457126 2.200000e-111 412.0
32 TraesCS3B01G461700 chr4D 90.523 306 25 3 4 307 432593842 432593539 4.770000e-108 401.0
33 TraesCS3B01G461700 chr4D 84.536 97 14 1 1100 1195 85007356 85007260 9.060000e-16 95.3
34 TraesCS3B01G461700 chr4D 77.181 149 28 5 632 777 26156893 26156748 7.050000e-12 82.4
35 TraesCS3B01G461700 chr4D 86.885 61 6 2 408 466 231910618 231910678 1.970000e-07 67.6
36 TraesCS3B01G461700 chr1A 88.767 454 46 4 2617 3068 117249055 117249505 4.470000e-153 551.0
37 TraesCS3B01G461700 chr1A 91.803 305 24 1 4 307 80180247 80180551 1.020000e-114 424.0
38 TraesCS3B01G461700 chr1A 81.132 106 19 1 1096 1200 398666635 398666530 1.960000e-12 84.2
39 TraesCS3B01G461700 chr1D 92.532 308 23 0 1 308 368275826 368275519 2.810000e-120 442.0
40 TraesCS3B01G461700 chr1D 92.542 295 22 0 13 307 43437215 43436921 1.020000e-114 424.0
41 TraesCS3B01G461700 chr1D 84.615 286 37 6 2434 2715 110656203 110656485 8.380000e-71 278.0
42 TraesCS3B01G461700 chr1D 82.203 118 15 6 777 893 18891590 18891478 2.520000e-16 97.1
43 TraesCS3B01G461700 chr6D 90.879 307 26 2 3 307 211884343 211884649 7.920000e-111 411.0
44 TraesCS3B01G461700 chr6D 83.117 77 10 3 634 708 144100188 144100113 1.970000e-07 67.6
45 TraesCS3B01G461700 chr5A 82.175 331 47 10 2445 2769 164201153 164200829 1.080000e-69 274.0
46 TraesCS3B01G461700 chr5A 80.952 315 47 12 2408 2715 368567051 368566743 1.420000e-58 237.0
47 TraesCS3B01G461700 chr5A 86.885 61 6 2 408 466 571121219 571121279 1.970000e-07 67.6
48 TraesCS3B01G461700 chr5A 79.412 102 13 7 369 466 684030943 684031040 7.100000e-07 65.8
49 TraesCS3B01G461700 chr7D 75.154 487 91 15 308 774 484990903 484991379 5.190000e-48 202.0
50 TraesCS3B01G461700 chr7D 76.068 234 45 9 546 777 436480771 436480995 9.000000e-21 111.0
51 TraesCS3B01G461700 chr7D 83.019 106 16 2 313 417 105059500 105059604 9.060000e-16 95.3
52 TraesCS3B01G461700 chr7D 78.641 103 17 5 777 877 55226928 55226829 2.550000e-06 63.9
53 TraesCS3B01G461700 chr7B 76.515 264 48 11 522 780 512475966 512475712 6.900000e-27 132.0
54 TraesCS3B01G461700 chr5D 76.596 188 39 5 599 784 376961216 376961400 7.000000e-17 99.0
55 TraesCS3B01G461700 chr5D 78.523 149 29 3 781 927 30441063 30441210 9.060000e-16 95.3
56 TraesCS3B01G461700 chr5D 79.433 141 20 5 1096 1229 8541077 8541215 1.170000e-14 91.6
57 TraesCS3B01G461700 chr1B 81.132 106 19 1 1096 1200 429700248 429700143 1.960000e-12 84.2
58 TraesCS3B01G461700 chr1B 80.488 82 10 6 781 857 648439785 648439705 1.190000e-04 58.4
59 TraesCS3B01G461700 chr2D 75.138 181 32 9 605 780 568209641 568209813 4.240000e-09 73.1
60 TraesCS3B01G461700 chr2D 92.157 51 3 1 1139 1188 627140476 627140526 1.530000e-08 71.3
61 TraesCS3B01G461700 chr2D 86.885 61 6 2 408 466 568623929 568623869 1.970000e-07 67.6
62 TraesCS3B01G461700 chr6B 86.154 65 8 1 1137 1200 552398549 552398485 5.490000e-08 69.4


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 TraesCS3B01G461700 chr3B 704652705 704655773 3068 True 5668.00 5668 100.000 1 3069 1 chr3B.!!$R2 3068
1 TraesCS3B01G461700 chr3B 704577097 704577853 756 True 1031.00 1031 91.503 1646 2395 1 chr3B.!!$R1 749
2 TraesCS3B01G461700 chr3D 532582413 532585523 3110 True 2012.50 3168 92.110 308 3069 2 chr3D.!!$R2 2761
3 TraesCS3B01G461700 chr3D 532343098 532343845 747 True 974.00 974 90.289 1646 2395 1 chr3D.!!$R1 749
4 TraesCS3B01G461700 chr3A 667656031 667656749 718 True 795.00 795 86.897 2359 3069 1 chr3A.!!$R1 710
5 TraesCS3B01G461700 chr3A 667512947 667514136 1189 True 510.00 580 90.990 1646 2395 2 chr3A.!!$R2 749
6 TraesCS3B01G461700 chr3A 667704168 667706789 2621 True 492.16 1411 92.373 308 2360 5 chr3A.!!$R3 2052
7 TraesCS3B01G461700 chr7A 3354551 3355177 626 True 684.00 684 86.427 2434 3069 1 chr7A.!!$R1 635
8 TraesCS3B01G461700 chr2B 54344554 54345220 666 True 684.00 684 85.355 2403 3069 1 chr2B.!!$R1 666
9 TraesCS3B01G461700 chr4A 607184570 607185216 646 True 667.00 667 85.474 2425 3069 1 chr4A.!!$R2 644
10 TraesCS3B01G461700 chr5B 170678176 170678798 622 True 610.00 610 84.444 2445 3069 1 chr5B.!!$R2 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
65 66 0.035915 GGACTCTTCTGGCCCAACTC 60.036 60.0 0.00 0.0 0.0 3.01 F
88 89 0.037303 TGCTTCAGGGGCTTCTTCTG 59.963 55.0 0.00 0.0 0.0 3.02 F
748 752 0.173481 GCTCCAGACGTATGCAGACA 59.827 55.0 12.67 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1063 1517 0.796312 GGTATGCTTCACCACACGTG 59.204 55.000 15.48 15.48 44.50 4.49 R
1577 2371 1.139520 GCAAATGGCGTGGATCCAC 59.860 57.895 31.59 31.59 43.01 4.02 R
2529 3800 0.531974 TCAATTGTAGATCCCGGCGC 60.532 55.000 0.00 0.00 0.00 6.53 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
33 34 4.209866 GGGGCGCCCTCCATCATT 62.210 66.667 42.70 0.00 41.34 2.57
34 35 2.908940 GGGCGCCCTCCATCATTG 60.909 66.667 38.76 0.00 0.00 2.82
35 36 2.124151 GGCGCCCTCCATCATTGT 60.124 61.111 18.11 0.00 0.00 2.71
36 37 2.484062 GGCGCCCTCCATCATTGTG 61.484 63.158 18.11 0.00 0.00 3.33
37 38 2.484062 GCGCCCTCCATCATTGTGG 61.484 63.158 0.00 0.00 40.76 4.17
38 39 1.077501 CGCCCTCCATCATTGTGGT 60.078 57.895 5.54 0.00 40.27 4.16
39 40 1.378882 CGCCCTCCATCATTGTGGTG 61.379 60.000 5.54 3.88 40.27 4.17
43 44 4.770540 CCATCATTGTGGTGGCCT 57.229 55.556 3.32 0.00 42.45 5.19
44 45 2.496942 CCATCATTGTGGTGGCCTC 58.503 57.895 3.32 0.00 42.45 4.70
45 46 1.378882 CCATCATTGTGGTGGCCTCG 61.379 60.000 3.32 0.00 42.45 4.63
46 47 1.077501 ATCATTGTGGTGGCCTCGG 60.078 57.895 3.32 0.00 0.00 4.63
47 48 2.556840 ATCATTGTGGTGGCCTCGGG 62.557 60.000 3.32 0.00 0.00 5.14
48 49 2.933287 ATTGTGGTGGCCTCGGGA 60.933 61.111 3.32 0.00 0.00 5.14
49 50 3.268103 ATTGTGGTGGCCTCGGGAC 62.268 63.158 3.32 0.00 0.00 4.46
50 51 4.954118 TGTGGTGGCCTCGGGACT 62.954 66.667 3.32 0.00 0.00 3.85
51 52 4.083862 GTGGTGGCCTCGGGACTC 62.084 72.222 3.32 0.00 0.00 3.36
52 53 4.316823 TGGTGGCCTCGGGACTCT 62.317 66.667 3.32 0.00 0.00 3.24
53 54 3.003763 GGTGGCCTCGGGACTCTT 61.004 66.667 3.32 0.00 0.00 2.85
54 55 2.579738 GTGGCCTCGGGACTCTTC 59.420 66.667 3.32 0.00 0.00 2.87
55 56 1.985116 GTGGCCTCGGGACTCTTCT 60.985 63.158 3.32 0.00 0.00 2.85
56 57 1.984570 TGGCCTCGGGACTCTTCTG 60.985 63.158 3.32 0.00 0.00 3.02
57 58 2.726351 GGCCTCGGGACTCTTCTGG 61.726 68.421 0.00 0.00 0.00 3.86
58 59 2.896443 CCTCGGGACTCTTCTGGC 59.104 66.667 0.00 0.00 0.00 4.85
59 60 2.726351 CCTCGGGACTCTTCTGGCC 61.726 68.421 0.00 0.00 0.00 5.36
60 61 2.683933 TCGGGACTCTTCTGGCCC 60.684 66.667 0.00 0.00 37.21 5.80
61 62 3.003173 CGGGACTCTTCTGGCCCA 61.003 66.667 0.00 0.00 40.71 5.36
62 63 2.592993 CGGGACTCTTCTGGCCCAA 61.593 63.158 0.00 0.00 40.71 4.12
63 64 1.002011 GGGACTCTTCTGGCCCAAC 60.002 63.158 0.00 0.00 40.39 3.77
64 65 1.492993 GGGACTCTTCTGGCCCAACT 61.493 60.000 0.00 0.00 40.39 3.16
65 66 0.035915 GGACTCTTCTGGCCCAACTC 60.036 60.000 0.00 0.00 0.00 3.01
66 67 0.980423 GACTCTTCTGGCCCAACTCT 59.020 55.000 0.00 0.00 0.00 3.24
67 68 1.349357 GACTCTTCTGGCCCAACTCTT 59.651 52.381 0.00 0.00 0.00 2.85
68 69 1.777272 ACTCTTCTGGCCCAACTCTTT 59.223 47.619 0.00 0.00 0.00 2.52
69 70 2.175715 ACTCTTCTGGCCCAACTCTTTT 59.824 45.455 0.00 0.00 0.00 2.27
70 71 2.555757 CTCTTCTGGCCCAACTCTTTTG 59.444 50.000 0.00 0.00 0.00 2.44
71 72 1.000171 CTTCTGGCCCAACTCTTTTGC 60.000 52.381 0.00 0.00 0.00 3.68
72 73 0.185901 TCTGGCCCAACTCTTTTGCT 59.814 50.000 0.00 0.00 0.00 3.91
73 74 1.043022 CTGGCCCAACTCTTTTGCTT 58.957 50.000 0.00 0.00 0.00 3.91
74 75 1.000171 CTGGCCCAACTCTTTTGCTTC 60.000 52.381 0.00 0.00 0.00 3.86
75 76 1.039856 GGCCCAACTCTTTTGCTTCA 58.960 50.000 0.00 0.00 0.00 3.02
76 77 1.000171 GGCCCAACTCTTTTGCTTCAG 60.000 52.381 0.00 0.00 0.00 3.02
77 78 1.000171 GCCCAACTCTTTTGCTTCAGG 60.000 52.381 0.00 0.00 0.00 3.86
78 79 1.615392 CCCAACTCTTTTGCTTCAGGG 59.385 52.381 0.00 0.00 0.00 4.45
79 80 1.615392 CCAACTCTTTTGCTTCAGGGG 59.385 52.381 0.00 0.00 0.00 4.79
80 81 1.000171 CAACTCTTTTGCTTCAGGGGC 60.000 52.381 0.00 0.00 0.00 5.80
81 82 0.480252 ACTCTTTTGCTTCAGGGGCT 59.520 50.000 0.00 0.00 0.00 5.19
82 83 1.133356 ACTCTTTTGCTTCAGGGGCTT 60.133 47.619 0.00 0.00 0.00 4.35
83 84 1.543358 CTCTTTTGCTTCAGGGGCTTC 59.457 52.381 0.00 0.00 0.00 3.86
84 85 1.145738 TCTTTTGCTTCAGGGGCTTCT 59.854 47.619 0.00 0.00 0.00 2.85
85 86 1.966354 CTTTTGCTTCAGGGGCTTCTT 59.034 47.619 0.00 0.00 0.00 2.52
86 87 1.620822 TTTGCTTCAGGGGCTTCTTC 58.379 50.000 0.00 0.00 0.00 2.87
87 88 0.773644 TTGCTTCAGGGGCTTCTTCT 59.226 50.000 0.00 0.00 0.00 2.85
88 89 0.037303 TGCTTCAGGGGCTTCTTCTG 59.963 55.000 0.00 0.00 0.00 3.02
89 90 0.679321 GCTTCAGGGGCTTCTTCTGG 60.679 60.000 0.00 0.00 0.00 3.86
90 91 0.695347 CTTCAGGGGCTTCTTCTGGT 59.305 55.000 0.00 0.00 0.00 4.00
91 92 0.693049 TTCAGGGGCTTCTTCTGGTC 59.307 55.000 0.00 0.00 0.00 4.02
92 93 1.201429 TCAGGGGCTTCTTCTGGTCC 61.201 60.000 0.00 0.00 0.00 4.46
93 94 1.151810 AGGGGCTTCTTCTGGTCCA 60.152 57.895 0.00 0.00 0.00 4.02
94 95 0.551131 AGGGGCTTCTTCTGGTCCAT 60.551 55.000 0.00 0.00 0.00 3.41
95 96 1.213296 GGGGCTTCTTCTGGTCCATA 58.787 55.000 0.00 0.00 0.00 2.74
96 97 1.564348 GGGGCTTCTTCTGGTCCATAA 59.436 52.381 0.00 0.00 0.00 1.90
97 98 2.025321 GGGGCTTCTTCTGGTCCATAAA 60.025 50.000 0.00 0.00 0.00 1.40
98 99 3.563479 GGGGCTTCTTCTGGTCCATAAAA 60.563 47.826 0.00 0.00 0.00 1.52
99 100 4.086457 GGGCTTCTTCTGGTCCATAAAAA 58.914 43.478 0.00 0.00 0.00 1.94
125 126 9.439500 AATCACCATAAATTTTCAGGTCATTTG 57.561 29.630 0.00 0.00 0.00 2.32
126 127 7.385267 TCACCATAAATTTTCAGGTCATTTGG 58.615 34.615 0.00 0.00 0.00 3.28
127 128 7.234371 TCACCATAAATTTTCAGGTCATTTGGA 59.766 33.333 0.00 0.00 0.00 3.53
128 129 7.331687 CACCATAAATTTTCAGGTCATTTGGAC 59.668 37.037 0.00 0.00 46.20 4.02
129 130 7.235399 ACCATAAATTTTCAGGTCATTTGGACT 59.765 33.333 0.00 0.00 46.16 3.85
130 131 7.761249 CCATAAATTTTCAGGTCATTTGGACTC 59.239 37.037 0.00 0.00 46.16 3.36
131 132 5.728637 AATTTTCAGGTCATTTGGACTCC 57.271 39.130 0.00 0.00 46.16 3.85
132 133 2.472695 TTCAGGTCATTTGGACTCCG 57.527 50.000 0.00 0.00 46.16 4.63
133 134 1.348064 TCAGGTCATTTGGACTCCGT 58.652 50.000 0.00 0.00 46.16 4.69
134 135 1.697432 TCAGGTCATTTGGACTCCGTT 59.303 47.619 0.00 0.00 46.16 4.44
135 136 2.105821 TCAGGTCATTTGGACTCCGTTT 59.894 45.455 0.00 0.00 46.16 3.60
136 137 2.226437 CAGGTCATTTGGACTCCGTTTG 59.774 50.000 0.00 0.00 46.16 2.93
137 138 1.539827 GGTCATTTGGACTCCGTTTGG 59.460 52.381 0.00 0.00 46.16 3.28
138 139 2.227194 GTCATTTGGACTCCGTTTGGT 58.773 47.619 0.00 0.00 43.46 3.67
139 140 3.404899 GTCATTTGGACTCCGTTTGGTA 58.595 45.455 0.00 0.00 43.46 3.25
140 141 4.007659 GTCATTTGGACTCCGTTTGGTAT 58.992 43.478 0.00 0.00 43.46 2.73
141 142 4.457949 GTCATTTGGACTCCGTTTGGTATT 59.542 41.667 0.00 0.00 43.46 1.89
142 143 4.698304 TCATTTGGACTCCGTTTGGTATTC 59.302 41.667 0.00 0.00 36.30 1.75
143 144 2.773993 TGGACTCCGTTTGGTATTCC 57.226 50.000 0.00 0.00 36.30 3.01
144 145 2.262637 TGGACTCCGTTTGGTATTCCT 58.737 47.619 0.00 0.00 36.30 3.36
145 146 2.640826 TGGACTCCGTTTGGTATTCCTT 59.359 45.455 0.00 0.00 36.30 3.36
146 147 3.073356 TGGACTCCGTTTGGTATTCCTTT 59.927 43.478 0.00 0.00 36.30 3.11
147 148 4.077108 GGACTCCGTTTGGTATTCCTTTT 58.923 43.478 0.00 0.00 36.30 2.27
148 149 4.155462 GGACTCCGTTTGGTATTCCTTTTC 59.845 45.833 0.00 0.00 36.30 2.29
149 150 4.981812 ACTCCGTTTGGTATTCCTTTTCT 58.018 39.130 0.00 0.00 36.30 2.52
150 151 4.760204 ACTCCGTTTGGTATTCCTTTTCTG 59.240 41.667 0.00 0.00 36.30 3.02
151 152 4.721132 TCCGTTTGGTATTCCTTTTCTGT 58.279 39.130 0.00 0.00 36.30 3.41
152 153 5.867330 TCCGTTTGGTATTCCTTTTCTGTA 58.133 37.500 0.00 0.00 36.30 2.74
153 154 6.297582 TCCGTTTGGTATTCCTTTTCTGTAA 58.702 36.000 0.00 0.00 36.30 2.41
154 155 6.771749 TCCGTTTGGTATTCCTTTTCTGTAAA 59.228 34.615 0.00 0.00 36.30 2.01
155 156 7.284944 TCCGTTTGGTATTCCTTTTCTGTAAAA 59.715 33.333 0.00 0.00 36.30 1.52
156 157 7.380333 CCGTTTGGTATTCCTTTTCTGTAAAAC 59.620 37.037 0.00 0.00 31.37 2.43
157 158 8.132995 CGTTTGGTATTCCTTTTCTGTAAAACT 58.867 33.333 0.00 0.00 31.37 2.66
158 159 9.459640 GTTTGGTATTCCTTTTCTGTAAAACTC 57.540 33.333 0.00 0.00 31.37 3.01
159 160 8.754991 TTGGTATTCCTTTTCTGTAAAACTCA 57.245 30.769 0.00 0.00 31.37 3.41
160 161 8.754991 TGGTATTCCTTTTCTGTAAAACTCAA 57.245 30.769 0.00 0.00 31.37 3.02
161 162 9.191479 TGGTATTCCTTTTCTGTAAAACTCAAA 57.809 29.630 0.00 0.00 31.37 2.69
165 166 9.936759 ATTCCTTTTCTGTAAAACTCAAAAACA 57.063 25.926 0.00 0.00 31.37 2.83
166 167 9.765795 TTCCTTTTCTGTAAAACTCAAAAACAA 57.234 25.926 0.00 0.00 31.37 2.83
167 168 9.765795 TCCTTTTCTGTAAAACTCAAAAACAAA 57.234 25.926 0.00 0.00 31.37 2.83
183 184 9.890352 TCAAAAACAAAGAAAAACAGAAAATGG 57.110 25.926 0.00 0.00 0.00 3.16
184 185 8.637704 CAAAAACAAAGAAAAACAGAAAATGGC 58.362 29.630 0.00 0.00 0.00 4.40
185 186 7.446001 AAACAAAGAAAAACAGAAAATGGCA 57.554 28.000 0.00 0.00 0.00 4.92
186 187 7.628769 AACAAAGAAAAACAGAAAATGGCAT 57.371 28.000 0.00 0.00 0.00 4.40
187 188 7.628769 ACAAAGAAAAACAGAAAATGGCATT 57.371 28.000 6.96 6.96 0.00 3.56
188 189 7.474190 ACAAAGAAAAACAGAAAATGGCATTG 58.526 30.769 14.47 4.28 0.00 2.82
189 190 6.622833 AAGAAAAACAGAAAATGGCATTGG 57.377 33.333 14.47 6.69 0.00 3.16
190 191 5.065235 AGAAAAACAGAAAATGGCATTGGG 58.935 37.500 14.47 6.33 0.00 4.12
191 192 2.477845 AACAGAAAATGGCATTGGGC 57.522 45.000 14.47 6.32 43.74 5.36
192 193 1.648116 ACAGAAAATGGCATTGGGCT 58.352 45.000 14.47 8.56 44.01 5.19
193 194 1.551883 ACAGAAAATGGCATTGGGCTC 59.448 47.619 14.47 8.39 44.01 4.70
194 195 1.829222 CAGAAAATGGCATTGGGCTCT 59.171 47.619 14.47 10.45 44.01 4.09
195 196 3.025978 CAGAAAATGGCATTGGGCTCTA 58.974 45.455 14.47 0.00 44.01 2.43
196 197 3.067742 CAGAAAATGGCATTGGGCTCTAG 59.932 47.826 14.47 5.56 44.01 2.43
197 198 2.077687 AAATGGCATTGGGCTCTAGG 57.922 50.000 14.47 0.00 44.01 3.02
198 199 0.929244 AATGGCATTGGGCTCTAGGT 59.071 50.000 12.82 0.00 44.01 3.08
199 200 0.929244 ATGGCATTGGGCTCTAGGTT 59.071 50.000 0.00 0.00 44.01 3.50
200 201 1.590591 TGGCATTGGGCTCTAGGTTA 58.409 50.000 0.00 0.00 44.01 2.85
201 202 1.919654 TGGCATTGGGCTCTAGGTTAA 59.080 47.619 0.00 0.00 44.01 2.01
202 203 2.513738 TGGCATTGGGCTCTAGGTTAAT 59.486 45.455 0.00 0.00 44.01 1.40
203 204 3.719479 TGGCATTGGGCTCTAGGTTAATA 59.281 43.478 0.00 0.00 44.01 0.98
204 205 4.202461 TGGCATTGGGCTCTAGGTTAATAG 60.202 45.833 0.00 0.00 44.01 1.73
205 206 4.327680 GCATTGGGCTCTAGGTTAATAGG 58.672 47.826 0.00 0.00 40.25 2.57
206 207 4.202472 GCATTGGGCTCTAGGTTAATAGGT 60.202 45.833 0.00 0.00 40.25 3.08
207 208 5.690364 GCATTGGGCTCTAGGTTAATAGGTT 60.690 44.000 0.00 0.00 40.25 3.50
208 209 6.465321 GCATTGGGCTCTAGGTTAATAGGTTA 60.465 42.308 0.00 0.00 40.25 2.85
209 210 7.514721 CATTGGGCTCTAGGTTAATAGGTTAA 58.485 38.462 0.00 0.00 0.00 2.01
210 211 7.701257 TTGGGCTCTAGGTTAATAGGTTAAT 57.299 36.000 0.00 0.00 32.76 1.40
211 212 7.312415 TGGGCTCTAGGTTAATAGGTTAATC 57.688 40.000 0.00 0.00 32.76 1.75
212 213 6.271624 TGGGCTCTAGGTTAATAGGTTAATCC 59.728 42.308 0.00 0.00 32.41 3.01
213 214 6.296317 GGGCTCTAGGTTAATAGGTTAATCCC 60.296 46.154 0.00 0.00 32.41 3.85
214 215 6.271624 GGCTCTAGGTTAATAGGTTAATCCCA 59.728 42.308 0.00 0.00 32.41 4.37
215 216 7.202158 GGCTCTAGGTTAATAGGTTAATCCCAA 60.202 40.741 0.00 0.00 32.41 4.12
216 217 8.215736 GCTCTAGGTTAATAGGTTAATCCCAAA 58.784 37.037 0.00 0.00 32.41 3.28
353 354 2.565834 GTGTGGCAGGAGTAGGTTTCTA 59.434 50.000 0.00 0.00 0.00 2.10
354 355 3.007614 GTGTGGCAGGAGTAGGTTTCTAA 59.992 47.826 0.00 0.00 0.00 2.10
366 367 2.104281 AGGTTTCTAAGCTTCCACACGT 59.896 45.455 0.00 0.00 35.27 4.49
379 380 0.306228 CACACGTGTTTGAATGCGGA 59.694 50.000 20.79 0.00 0.00 5.54
487 488 3.510388 TGCATTGAACCGTTTTCAACA 57.490 38.095 10.66 4.47 40.70 3.33
543 546 0.392193 CTTGCGCTGGGAGAGAACAT 60.392 55.000 9.73 0.00 0.00 2.71
551 554 2.125512 GAGAGAACATGCGCGGGT 60.126 61.111 8.83 0.00 0.00 5.28
554 557 2.031919 AGAACATGCGCGGGTGAA 59.968 55.556 8.83 0.00 0.00 3.18
565 568 2.125225 GGGTGAAGGAGGAGGGGT 59.875 66.667 0.00 0.00 0.00 4.95
567 570 1.140772 GGGTGAAGGAGGAGGGGTTT 61.141 60.000 0.00 0.00 0.00 3.27
591 594 0.605589 GTGGGCCAGTGTGGTTAGAC 60.606 60.000 6.40 0.00 40.46 2.59
614 617 4.082523 CGTGGGTGCTGTCCGGAT 62.083 66.667 7.81 0.00 0.00 4.18
625 628 2.933287 TCCGGATGCCCACAAGGT 60.933 61.111 0.00 0.00 38.26 3.50
628 631 2.043953 GGATGCCCACAAGGTCCC 60.044 66.667 0.00 0.00 38.26 4.46
645 649 0.178935 CCCCACCCCATGTTTGTCTT 60.179 55.000 0.00 0.00 0.00 3.01
662 666 1.165270 CTTCGGTTTGCGGGAGAAAT 58.835 50.000 0.00 0.00 0.00 2.17
695 699 1.956170 CTGCGGACGGATACATGCC 60.956 63.158 0.00 0.00 0.00 4.40
696 700 2.665185 GCGGACGGATACATGCCC 60.665 66.667 0.00 0.00 0.00 5.36
707 711 1.031235 TACATGCCCGCATTGAATGG 58.969 50.000 7.35 0.00 33.90 3.16
713 717 0.176219 CCCGCATTGAATGGTGCAAT 59.824 50.000 7.35 0.00 41.32 3.56
716 720 2.159268 CCGCATTGAATGGTGCAATACA 60.159 45.455 7.35 0.00 41.32 2.29
728 732 1.277842 TGCAATACATCCGGACAGTGT 59.722 47.619 18.88 16.26 0.00 3.55
730 734 1.665679 CAATACATCCGGACAGTGTGC 59.334 52.381 17.56 1.28 0.00 4.57
734 738 1.913262 ATCCGGACAGTGTGCTCCA 60.913 57.895 6.12 0.00 0.00 3.86
737 741 1.373497 CGGACAGTGTGCTCCAGAC 60.373 63.158 13.27 0.00 0.00 3.51
742 746 1.067565 ACAGTGTGCTCCAGACGTATG 60.068 52.381 2.43 2.43 32.70 2.39
748 752 0.173481 GCTCCAGACGTATGCAGACA 59.827 55.000 12.67 0.00 0.00 3.41
761 765 0.951040 GCAGACAGTTTGAGGGTCGG 60.951 60.000 0.00 0.00 36.68 4.79
763 767 1.070786 GACAGTTTGAGGGTCGGCA 59.929 57.895 0.00 0.00 0.00 5.69
767 771 0.609131 AGTTTGAGGGTCGGCATTGG 60.609 55.000 0.00 0.00 0.00 3.16
784 788 4.343239 GCATTGGAGATGCCCTTAGAAAAT 59.657 41.667 0.00 0.00 39.01 1.82
794 798 9.034800 AGATGCCCTTAGAAAATGTTAATCAAA 57.965 29.630 0.00 0.00 0.00 2.69
1001 1454 3.731766 AAACAGGCCCAGGCAACGT 62.732 57.895 11.50 0.90 44.11 3.99
1002 1455 2.346284 AAACAGGCCCAGGCAACGTA 62.346 55.000 11.50 0.00 44.11 3.57
1070 1524 6.879188 AAAAAGTTAATGTTTCCACGTGTG 57.121 33.333 15.65 6.24 0.00 3.82
1285 1745 5.886960 AATGAGACTAGTTTGATGTTGCC 57.113 39.130 0.00 0.00 0.00 4.52
1321 1781 8.632679 TCCATAGGCATAATCAAATTTGAAGAC 58.367 33.333 23.91 15.82 41.13 3.01
1502 2296 3.294102 GGACCGAGCAAAGTTTAAAACG 58.706 45.455 0.00 0.00 36.23 3.60
1505 2299 2.466205 CCGAGCAAAGTTTAAAACGCAC 59.534 45.455 0.00 0.00 36.23 5.34
1577 2371 5.813672 CCAATGGCTTCAACATTAGGAATTG 59.186 40.000 0.00 0.00 36.47 2.32
1578 2372 6.400568 CAATGGCTTCAACATTAGGAATTGT 58.599 36.000 0.00 0.00 36.47 2.71
1664 2458 3.077556 CCCACCACCCCTCTCTCG 61.078 72.222 0.00 0.00 0.00 4.04
1751 2547 4.537015 GAATAATCCACCGCAATAAGCAC 58.463 43.478 0.00 0.00 46.13 4.40
1754 2550 2.700722 TCCACCGCAATAAGCACATA 57.299 45.000 0.00 0.00 46.13 2.29
1788 2592 1.004185 CCGCGCAATCTCTCAATCTTG 60.004 52.381 8.75 0.00 0.00 3.02
1791 2595 2.159476 GCGCAATCTCTCAATCTTGCAA 60.159 45.455 0.30 0.00 43.14 4.08
2234 3481 9.834628 TTTGATTAGGTATCGTGATTTTTGTTC 57.165 29.630 0.00 0.00 35.94 3.18
2235 3482 8.786826 TGATTAGGTATCGTGATTTTTGTTCT 57.213 30.769 0.00 0.00 35.94 3.01
2348 3595 5.357878 GTGGCCTCACTGATCATTATGAAAA 59.642 40.000 3.32 0.00 40.58 2.29
2401 3668 4.083431 CGTAGGTGGTCATTAGAGATACGG 60.083 50.000 0.00 0.00 32.19 4.02
2529 3800 4.747108 CACTATATCGAAGGAGGTTGCAAG 59.253 45.833 0.00 0.00 0.00 4.01
2579 3851 2.660236 CTCGTACGGTGACTTACAAAGC 59.340 50.000 16.52 0.00 34.92 3.51
2847 4125 4.708177 TCAACTAAGTCTGAGCAAAGCTT 58.292 39.130 0.00 0.00 39.88 3.74
2903 4181 8.476447 ACATATCAGCAGGATTATCATGAGTAG 58.524 37.037 11.24 0.00 37.44 2.57
2947 4225 1.145738 ACCTTGCTCAACAATGTCCCT 59.854 47.619 0.00 0.00 37.72 4.20
2970 4248 8.567948 CCCTAACATAATGGTATTTGACATCAC 58.432 37.037 0.00 0.00 0.00 3.06
2992 4270 3.405831 TGTGCTTTGTTCTCTCATGGAG 58.594 45.455 5.18 5.18 43.12 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.209866 AATGATGGAGGGCGCCCC 62.210 66.667 41.72 30.78 45.90 5.80
17 18 2.908940 CAATGATGGAGGGCGCCC 60.909 66.667 39.29 39.29 0.00 6.13
18 19 2.124151 ACAATGATGGAGGGCGCC 60.124 61.111 21.18 21.18 0.00 6.53
19 20 2.484062 CCACAATGATGGAGGGCGC 61.484 63.158 0.00 0.00 43.02 6.53
20 21 1.077501 ACCACAATGATGGAGGGCG 60.078 57.895 8.46 0.00 43.02 6.13
21 22 1.039233 CCACCACAATGATGGAGGGC 61.039 60.000 8.46 0.00 44.45 5.19
22 23 3.196040 CCACCACAATGATGGAGGG 57.804 57.895 8.46 6.10 44.45 4.30
24 25 0.033796 AGGCCACCACAATGATGGAG 60.034 55.000 5.01 1.77 43.02 3.86
25 26 0.034186 GAGGCCACCACAATGATGGA 60.034 55.000 5.01 0.00 43.02 3.41
26 27 1.378882 CGAGGCCACCACAATGATGG 61.379 60.000 5.01 0.00 46.10 3.51
27 28 1.378882 CCGAGGCCACCACAATGATG 61.379 60.000 5.01 0.00 0.00 3.07
28 29 1.077501 CCGAGGCCACCACAATGAT 60.078 57.895 5.01 0.00 0.00 2.45
29 30 2.350895 CCGAGGCCACCACAATGA 59.649 61.111 5.01 0.00 0.00 2.57
30 31 2.751436 CCCGAGGCCACCACAATG 60.751 66.667 5.01 0.00 0.00 2.82
31 32 2.933287 TCCCGAGGCCACCACAAT 60.933 61.111 5.01 0.00 0.00 2.71
32 33 3.948719 GTCCCGAGGCCACCACAA 61.949 66.667 5.01 0.00 0.00 3.33
33 34 4.954118 AGTCCCGAGGCCACCACA 62.954 66.667 5.01 0.00 0.00 4.17
34 35 4.083862 GAGTCCCGAGGCCACCAC 62.084 72.222 5.01 0.00 0.00 4.16
35 36 3.846405 AAGAGTCCCGAGGCCACCA 62.846 63.158 5.01 0.00 0.00 4.17
36 37 3.003763 AAGAGTCCCGAGGCCACC 61.004 66.667 5.01 0.00 0.00 4.61
37 38 1.985116 AGAAGAGTCCCGAGGCCAC 60.985 63.158 5.01 0.00 0.00 5.01
38 39 1.984570 CAGAAGAGTCCCGAGGCCA 60.985 63.158 5.01 0.00 0.00 5.36
39 40 2.726351 CCAGAAGAGTCCCGAGGCC 61.726 68.421 0.00 0.00 0.00 5.19
40 41 2.896443 CCAGAAGAGTCCCGAGGC 59.104 66.667 0.00 0.00 0.00 4.70
41 42 2.726351 GGCCAGAAGAGTCCCGAGG 61.726 68.421 0.00 0.00 0.00 4.63
42 43 2.726351 GGGCCAGAAGAGTCCCGAG 61.726 68.421 4.39 0.00 0.00 4.63
43 44 2.683933 GGGCCAGAAGAGTCCCGA 60.684 66.667 4.39 0.00 0.00 5.14
44 45 2.592993 TTGGGCCAGAAGAGTCCCG 61.593 63.158 6.23 0.00 41.65 5.14
45 46 1.002011 GTTGGGCCAGAAGAGTCCC 60.002 63.158 6.23 0.00 39.22 4.46
46 47 0.035915 GAGTTGGGCCAGAAGAGTCC 60.036 60.000 6.23 0.00 0.00 3.85
47 48 0.980423 AGAGTTGGGCCAGAAGAGTC 59.020 55.000 6.23 4.33 0.00 3.36
48 49 1.439543 AAGAGTTGGGCCAGAAGAGT 58.560 50.000 6.23 0.00 0.00 3.24
49 50 2.555757 CAAAAGAGTTGGGCCAGAAGAG 59.444 50.000 6.23 0.00 0.00 2.85
50 51 2.586425 CAAAAGAGTTGGGCCAGAAGA 58.414 47.619 6.23 0.00 0.00 2.87
51 52 1.000171 GCAAAAGAGTTGGGCCAGAAG 60.000 52.381 6.23 0.00 0.00 2.85
52 53 1.039856 GCAAAAGAGTTGGGCCAGAA 58.960 50.000 6.23 0.00 0.00 3.02
53 54 0.185901 AGCAAAAGAGTTGGGCCAGA 59.814 50.000 6.23 0.00 0.00 3.86
54 55 1.000171 GAAGCAAAAGAGTTGGGCCAG 60.000 52.381 6.23 0.00 0.00 4.85
55 56 1.039856 GAAGCAAAAGAGTTGGGCCA 58.960 50.000 0.00 0.00 0.00 5.36
56 57 1.000171 CTGAAGCAAAAGAGTTGGGCC 60.000 52.381 0.00 0.00 0.00 5.80
57 58 1.000171 CCTGAAGCAAAAGAGTTGGGC 60.000 52.381 0.00 0.00 0.00 5.36
58 59 1.615392 CCCTGAAGCAAAAGAGTTGGG 59.385 52.381 0.00 0.00 0.00 4.12
59 60 1.615392 CCCCTGAAGCAAAAGAGTTGG 59.385 52.381 0.00 0.00 0.00 3.77
60 61 1.000171 GCCCCTGAAGCAAAAGAGTTG 60.000 52.381 0.00 0.00 0.00 3.16
61 62 1.133356 AGCCCCTGAAGCAAAAGAGTT 60.133 47.619 0.00 0.00 0.00 3.01
62 63 0.480252 AGCCCCTGAAGCAAAAGAGT 59.520 50.000 0.00 0.00 0.00 3.24
63 64 1.543358 GAAGCCCCTGAAGCAAAAGAG 59.457 52.381 0.00 0.00 0.00 2.85
64 65 1.145738 AGAAGCCCCTGAAGCAAAAGA 59.854 47.619 0.00 0.00 0.00 2.52
65 66 1.625511 AGAAGCCCCTGAAGCAAAAG 58.374 50.000 0.00 0.00 0.00 2.27
66 67 1.963515 GAAGAAGCCCCTGAAGCAAAA 59.036 47.619 0.00 0.00 0.00 2.44
67 68 1.145738 AGAAGAAGCCCCTGAAGCAAA 59.854 47.619 0.00 0.00 0.00 3.68
68 69 0.773644 AGAAGAAGCCCCTGAAGCAA 59.226 50.000 0.00 0.00 0.00 3.91
69 70 0.037303 CAGAAGAAGCCCCTGAAGCA 59.963 55.000 0.00 0.00 0.00 3.91
70 71 0.679321 CCAGAAGAAGCCCCTGAAGC 60.679 60.000 0.00 0.00 0.00 3.86
71 72 0.695347 ACCAGAAGAAGCCCCTGAAG 59.305 55.000 0.00 0.00 0.00 3.02
72 73 0.693049 GACCAGAAGAAGCCCCTGAA 59.307 55.000 0.00 0.00 0.00 3.02
73 74 1.201429 GGACCAGAAGAAGCCCCTGA 61.201 60.000 0.00 0.00 0.00 3.86
74 75 1.301293 GGACCAGAAGAAGCCCCTG 59.699 63.158 0.00 0.00 0.00 4.45
75 76 0.551131 ATGGACCAGAAGAAGCCCCT 60.551 55.000 0.00 0.00 0.00 4.79
76 77 1.213296 TATGGACCAGAAGAAGCCCC 58.787 55.000 0.00 0.00 0.00 5.80
77 78 3.366052 TTTATGGACCAGAAGAAGCCC 57.634 47.619 1.13 0.00 0.00 5.19
99 100 9.439500 CAAATGACCTGAAAATTTATGGTGATT 57.561 29.630 12.47 12.49 36.47 2.57
100 101 8.042515 CCAAATGACCTGAAAATTTATGGTGAT 58.957 33.333 12.47 8.25 0.00 3.06
101 102 7.234371 TCCAAATGACCTGAAAATTTATGGTGA 59.766 33.333 12.47 6.60 0.00 4.02
102 103 7.331687 GTCCAAATGACCTGAAAATTTATGGTG 59.668 37.037 12.47 1.57 38.09 4.17
103 104 7.235399 AGTCCAAATGACCTGAAAATTTATGGT 59.765 33.333 8.74 8.74 45.68 3.55
104 105 7.614494 AGTCCAAATGACCTGAAAATTTATGG 58.386 34.615 0.00 0.00 45.68 2.74
105 106 7.761249 GGAGTCCAAATGACCTGAAAATTTATG 59.239 37.037 3.60 0.00 45.68 1.90
106 107 7.362920 CGGAGTCCAAATGACCTGAAAATTTAT 60.363 37.037 10.49 0.00 45.68 1.40
107 108 6.072175 CGGAGTCCAAATGACCTGAAAATTTA 60.072 38.462 10.49 0.00 45.68 1.40
108 109 5.278957 CGGAGTCCAAATGACCTGAAAATTT 60.279 40.000 10.49 0.00 45.68 1.82
109 110 4.218417 CGGAGTCCAAATGACCTGAAAATT 59.782 41.667 10.49 0.00 45.68 1.82
110 111 3.758554 CGGAGTCCAAATGACCTGAAAAT 59.241 43.478 10.49 0.00 45.68 1.82
111 112 3.146066 CGGAGTCCAAATGACCTGAAAA 58.854 45.455 10.49 0.00 45.68 2.29
112 113 2.105821 ACGGAGTCCAAATGACCTGAAA 59.894 45.455 10.49 0.00 45.68 2.69
113 114 1.697432 ACGGAGTCCAAATGACCTGAA 59.303 47.619 10.49 0.00 45.68 3.02
114 115 1.348064 ACGGAGTCCAAATGACCTGA 58.652 50.000 10.49 0.00 45.68 3.86
115 116 2.185004 AACGGAGTCCAAATGACCTG 57.815 50.000 10.49 0.00 45.00 4.00
116 117 2.504367 CAAACGGAGTCCAAATGACCT 58.496 47.619 10.49 0.00 45.00 3.85
117 118 1.539827 CCAAACGGAGTCCAAATGACC 59.460 52.381 10.49 0.00 45.00 4.02
118 119 2.227194 ACCAAACGGAGTCCAAATGAC 58.773 47.619 10.49 0.00 45.00 3.06
119 120 2.649531 ACCAAACGGAGTCCAAATGA 57.350 45.000 10.49 0.00 45.00 2.57
120 121 4.142469 GGAATACCAAACGGAGTCCAAATG 60.142 45.833 10.49 4.10 36.19 2.32
121 122 4.014406 GGAATACCAAACGGAGTCCAAAT 58.986 43.478 10.49 0.00 36.19 2.32
122 123 3.073356 AGGAATACCAAACGGAGTCCAAA 59.927 43.478 10.49 0.00 38.33 3.28
123 124 2.640826 AGGAATACCAAACGGAGTCCAA 59.359 45.455 10.49 0.00 38.33 3.53
124 125 2.262637 AGGAATACCAAACGGAGTCCA 58.737 47.619 10.49 0.00 38.33 4.02
125 126 3.345508 AAGGAATACCAAACGGAGTCC 57.654 47.619 0.00 0.00 38.33 3.85
126 127 5.001874 AGAAAAGGAATACCAAACGGAGTC 58.998 41.667 0.00 0.00 38.33 3.36
127 128 4.760204 CAGAAAAGGAATACCAAACGGAGT 59.240 41.667 0.00 0.00 40.63 3.85
128 129 4.760204 ACAGAAAAGGAATACCAAACGGAG 59.240 41.667 0.00 0.00 38.94 4.63
129 130 4.721132 ACAGAAAAGGAATACCAAACGGA 58.279 39.130 0.00 0.00 38.94 4.69
130 131 6.563222 TTACAGAAAAGGAATACCAAACGG 57.437 37.500 0.00 0.00 38.94 4.44
131 132 8.132995 AGTTTTACAGAAAAGGAATACCAAACG 58.867 33.333 0.00 0.00 35.21 3.60
132 133 9.459640 GAGTTTTACAGAAAAGGAATACCAAAC 57.540 33.333 0.00 0.00 35.21 2.93
133 134 9.191479 TGAGTTTTACAGAAAAGGAATACCAAA 57.809 29.630 0.00 0.00 35.21 3.28
134 135 8.754991 TGAGTTTTACAGAAAAGGAATACCAA 57.245 30.769 0.00 0.00 35.21 3.67
135 136 8.754991 TTGAGTTTTACAGAAAAGGAATACCA 57.245 30.769 0.00 0.00 35.21 3.25
139 140 9.936759 TGTTTTTGAGTTTTACAGAAAAGGAAT 57.063 25.926 0.00 0.00 35.21 3.01
140 141 9.765795 TTGTTTTTGAGTTTTACAGAAAAGGAA 57.234 25.926 0.00 0.00 35.21 3.36
141 142 9.765795 TTTGTTTTTGAGTTTTACAGAAAAGGA 57.234 25.926 0.00 0.00 35.21 3.36
157 158 9.890352 CCATTTTCTGTTTTTCTTTGTTTTTGA 57.110 25.926 0.00 0.00 0.00 2.69
158 159 8.637704 GCCATTTTCTGTTTTTCTTTGTTTTTG 58.362 29.630 0.00 0.00 0.00 2.44
159 160 8.355913 TGCCATTTTCTGTTTTTCTTTGTTTTT 58.644 25.926 0.00 0.00 0.00 1.94
160 161 7.880105 TGCCATTTTCTGTTTTTCTTTGTTTT 58.120 26.923 0.00 0.00 0.00 2.43
161 162 7.446001 TGCCATTTTCTGTTTTTCTTTGTTT 57.554 28.000 0.00 0.00 0.00 2.83
162 163 7.628769 ATGCCATTTTCTGTTTTTCTTTGTT 57.371 28.000 0.00 0.00 0.00 2.83
163 164 7.415429 CCAATGCCATTTTCTGTTTTTCTTTGT 60.415 33.333 0.00 0.00 0.00 2.83
164 165 6.913673 CCAATGCCATTTTCTGTTTTTCTTTG 59.086 34.615 0.00 0.00 0.00 2.77
165 166 6.039605 CCCAATGCCATTTTCTGTTTTTCTTT 59.960 34.615 0.00 0.00 0.00 2.52
166 167 5.532032 CCCAATGCCATTTTCTGTTTTTCTT 59.468 36.000 0.00 0.00 0.00 2.52
167 168 5.065235 CCCAATGCCATTTTCTGTTTTTCT 58.935 37.500 0.00 0.00 0.00 2.52
168 169 4.320421 GCCCAATGCCATTTTCTGTTTTTC 60.320 41.667 0.00 0.00 0.00 2.29
169 170 3.569277 GCCCAATGCCATTTTCTGTTTTT 59.431 39.130 0.00 0.00 0.00 1.94
170 171 3.148412 GCCCAATGCCATTTTCTGTTTT 58.852 40.909 0.00 0.00 0.00 2.43
171 172 2.372837 AGCCCAATGCCATTTTCTGTTT 59.627 40.909 0.00 0.00 42.71 2.83
172 173 1.980036 AGCCCAATGCCATTTTCTGTT 59.020 42.857 0.00 0.00 42.71 3.16
173 174 1.551883 GAGCCCAATGCCATTTTCTGT 59.448 47.619 0.00 0.00 42.71 3.41
174 175 1.829222 AGAGCCCAATGCCATTTTCTG 59.171 47.619 0.00 0.00 42.71 3.02
175 176 2.242882 AGAGCCCAATGCCATTTTCT 57.757 45.000 0.00 0.00 42.71 2.52
176 177 2.363359 CCTAGAGCCCAATGCCATTTTC 59.637 50.000 0.00 0.00 42.71 2.29
177 178 2.292455 ACCTAGAGCCCAATGCCATTTT 60.292 45.455 0.00 0.00 42.71 1.82
178 179 1.288932 ACCTAGAGCCCAATGCCATTT 59.711 47.619 0.00 0.00 42.71 2.32
179 180 0.929244 ACCTAGAGCCCAATGCCATT 59.071 50.000 0.00 0.00 42.71 3.16
180 181 0.929244 AACCTAGAGCCCAATGCCAT 59.071 50.000 0.00 0.00 42.71 4.40
181 182 1.590591 TAACCTAGAGCCCAATGCCA 58.409 50.000 0.00 0.00 42.71 4.92
182 183 2.729028 TTAACCTAGAGCCCAATGCC 57.271 50.000 0.00 0.00 42.71 4.40
183 184 4.202472 ACCTATTAACCTAGAGCCCAATGC 60.202 45.833 0.00 0.00 41.71 3.56
184 185 5.568620 ACCTATTAACCTAGAGCCCAATG 57.431 43.478 0.00 0.00 0.00 2.82
185 186 7.701257 TTAACCTATTAACCTAGAGCCCAAT 57.299 36.000 0.00 0.00 0.00 3.16
186 187 7.202158 GGATTAACCTATTAACCTAGAGCCCAA 60.202 40.741 0.00 0.00 33.09 4.12
187 188 6.271624 GGATTAACCTATTAACCTAGAGCCCA 59.728 42.308 0.00 0.00 33.09 5.36
188 189 6.296317 GGGATTAACCTATTAACCTAGAGCCC 60.296 46.154 0.00 0.00 38.98 5.19
189 190 6.271624 TGGGATTAACCTATTAACCTAGAGCC 59.728 42.308 0.00 0.00 38.98 4.70
190 191 7.312415 TGGGATTAACCTATTAACCTAGAGC 57.688 40.000 0.00 0.00 38.98 4.09
227 228 9.812347 TCCATCTTGGATGTTTTATATGCTATT 57.188 29.630 6.75 0.00 42.67 1.73
292 293 3.791887 CCGACATTTGATACGTCTCTGAC 59.208 47.826 0.00 0.00 0.00 3.51
293 294 3.733988 GCCGACATTTGATACGTCTCTGA 60.734 47.826 0.00 0.00 0.00 3.27
294 295 2.535984 GCCGACATTTGATACGTCTCTG 59.464 50.000 0.00 0.00 0.00 3.35
295 296 2.481449 GGCCGACATTTGATACGTCTCT 60.481 50.000 0.00 0.00 0.00 3.10
296 297 1.859080 GGCCGACATTTGATACGTCTC 59.141 52.381 0.00 0.00 0.00 3.36
297 298 1.472728 GGGCCGACATTTGATACGTCT 60.473 52.381 0.00 0.00 0.00 4.18
298 299 0.935196 GGGCCGACATTTGATACGTC 59.065 55.000 0.00 0.00 0.00 4.34
299 300 0.808453 CGGGCCGACATTTGATACGT 60.808 55.000 24.41 0.00 0.00 3.57
300 301 1.931551 CGGGCCGACATTTGATACG 59.068 57.895 24.41 0.00 0.00 3.06
301 302 0.814010 AGCGGGCCGACATTTGATAC 60.814 55.000 33.44 7.52 0.00 2.24
302 303 0.531974 GAGCGGGCCGACATTTGATA 60.532 55.000 33.44 0.00 0.00 2.15
303 304 1.819632 GAGCGGGCCGACATTTGAT 60.820 57.895 33.44 3.56 0.00 2.57
304 305 2.435938 GAGCGGGCCGACATTTGA 60.436 61.111 33.44 0.00 0.00 2.69
305 306 3.864686 CGAGCGGGCCGACATTTG 61.865 66.667 33.44 11.43 0.00 2.32
306 307 4.388499 ACGAGCGGGCCGACATTT 62.388 61.111 33.44 8.70 0.00 2.32
353 354 1.745232 TCAAACACGTGTGGAAGCTT 58.255 45.000 24.16 8.72 34.19 3.74
354 355 1.745232 TTCAAACACGTGTGGAAGCT 58.255 45.000 24.16 1.40 34.19 3.74
366 367 1.339055 CCTCCTCTCCGCATTCAAACA 60.339 52.381 0.00 0.00 0.00 2.83
379 380 2.659610 GCAGAACACGCCTCCTCT 59.340 61.111 0.00 0.00 0.00 3.69
459 460 0.454285 CGGTTCAATGCAAACGCGAT 60.454 50.000 15.93 0.00 27.84 4.58
463 464 2.854777 TGAAAACGGTTCAATGCAAACG 59.145 40.909 0.00 0.00 42.43 3.60
511 513 2.813908 GCAAGCTGCCAGCATTGC 60.814 61.111 26.35 26.35 45.56 3.56
512 514 2.506217 CGCAAGCTGCCAGCATTG 60.506 61.111 20.53 19.29 45.56 2.82
531 533 2.125552 CGCGCATGTTCTCTCCCA 60.126 61.111 8.75 0.00 0.00 4.37
551 554 1.146982 CCAAAAACCCCTCCTCCTTCA 59.853 52.381 0.00 0.00 0.00 3.02
554 557 0.704813 ACCCAAAAACCCCTCCTCCT 60.705 55.000 0.00 0.00 0.00 3.69
565 568 1.002274 ACACTGGCCCACCCAAAAA 59.998 52.632 0.00 0.00 44.81 1.94
567 570 2.123511 CACACTGGCCCACCCAAA 60.124 61.111 0.00 0.00 44.81 3.28
625 628 1.071314 AGACAAACATGGGGTGGGGA 61.071 55.000 0.00 0.00 0.00 4.81
628 631 0.881118 CGAAGACAAACATGGGGTGG 59.119 55.000 0.00 0.00 0.00 4.61
645 649 2.078392 GTAATTTCTCCCGCAAACCGA 58.922 47.619 0.00 0.00 40.02 4.69
662 666 4.124351 CAGAGCGGCCGGACGTAA 62.124 66.667 33.66 0.00 35.98 3.18
695 699 2.159268 TGTATTGCACCATTCAATGCGG 60.159 45.455 0.00 0.00 45.13 5.69
696 700 3.148026 TGTATTGCACCATTCAATGCG 57.852 42.857 0.00 0.00 45.13 4.73
707 711 1.665679 CACTGTCCGGATGTATTGCAC 59.334 52.381 7.81 0.00 0.00 4.57
713 717 0.530744 GAGCACACTGTCCGGATGTA 59.469 55.000 7.81 0.00 0.00 2.29
716 720 1.892819 CTGGAGCACACTGTCCGGAT 61.893 60.000 7.81 0.00 41.23 4.18
728 732 0.173481 GTCTGCATACGTCTGGAGCA 59.827 55.000 16.17 8.48 34.84 4.26
730 734 1.474478 ACTGTCTGCATACGTCTGGAG 59.526 52.381 15.05 15.05 36.05 3.86
734 738 3.579709 CTCAAACTGTCTGCATACGTCT 58.420 45.455 0.00 0.00 0.00 4.18
737 741 2.002586 CCCTCAAACTGTCTGCATACG 58.997 52.381 0.00 0.00 0.00 3.06
742 746 0.951040 CCGACCCTCAAACTGTCTGC 60.951 60.000 0.00 0.00 0.00 4.26
748 752 0.609131 CCAATGCCGACCCTCAAACT 60.609 55.000 0.00 0.00 0.00 2.66
761 765 2.645838 TCTAAGGGCATCTCCAATGC 57.354 50.000 1.40 1.40 43.85 3.56
763 767 5.522641 ACATTTTCTAAGGGCATCTCCAAT 58.477 37.500 0.00 0.00 36.21 3.16
767 771 8.225603 TGATTAACATTTTCTAAGGGCATCTC 57.774 34.615 0.00 0.00 0.00 2.75
977 985 1.077005 TGCCTGGGCCTGTTTCTAAAT 59.923 47.619 4.53 0.00 41.09 1.40
978 986 0.480690 TGCCTGGGCCTGTTTCTAAA 59.519 50.000 4.53 0.00 41.09 1.85
979 987 0.480690 TTGCCTGGGCCTGTTTCTAA 59.519 50.000 4.53 0.00 41.09 2.10
980 988 0.251165 GTTGCCTGGGCCTGTTTCTA 60.251 55.000 4.53 0.00 41.09 2.10
981 989 1.531602 GTTGCCTGGGCCTGTTTCT 60.532 57.895 4.53 0.00 41.09 2.52
982 990 2.919494 CGTTGCCTGGGCCTGTTTC 61.919 63.158 4.53 0.00 41.09 2.78
987 995 1.724545 TATATACGTTGCCTGGGCCT 58.275 50.000 4.53 0.00 41.09 5.19
1002 1455 8.845793 TGAGATTAAAACATGCCCCCTATATAT 58.154 33.333 0.00 0.00 0.00 0.86
1063 1517 0.796312 GGTATGCTTCACCACACGTG 59.204 55.000 15.48 15.48 44.50 4.49
1065 1519 2.665649 TAGGTATGCTTCACCACACG 57.334 50.000 5.03 0.00 38.62 4.49
1066 1520 4.324267 AGTTTAGGTATGCTTCACCACAC 58.676 43.478 5.03 0.00 38.62 3.82
1067 1521 4.634012 AGTTTAGGTATGCTTCACCACA 57.366 40.909 5.03 0.00 38.62 4.17
1068 1522 7.335924 TGAAATAGTTTAGGTATGCTTCACCAC 59.664 37.037 5.03 0.00 38.62 4.16
1069 1523 7.398829 TGAAATAGTTTAGGTATGCTTCACCA 58.601 34.615 5.03 0.00 38.62 4.17
1070 1524 7.859325 TGAAATAGTTTAGGTATGCTTCACC 57.141 36.000 0.00 0.00 36.22 4.02
1285 1745 8.667076 TGATTATGCCTATGGATAATTCATCG 57.333 34.615 6.29 0.00 34.12 3.84
1577 2371 1.139520 GCAAATGGCGTGGATCCAC 59.860 57.895 31.59 31.59 43.01 4.02
1578 2372 2.051518 GGCAAATGGCGTGGATCCA 61.052 57.895 11.44 11.44 46.16 3.41
1593 2387 2.611971 CGGTTCTGCTTAAGTGTAGGCA 60.612 50.000 4.02 0.00 39.80 4.75
1664 2458 4.164204 AGGATTTATAGTGGGAGGAGAGC 58.836 47.826 0.00 0.00 0.00 4.09
1751 2547 1.967319 CGGATGGAGGTGGGTTTATG 58.033 55.000 0.00 0.00 0.00 1.90
1754 2550 2.355115 GCGGATGGAGGTGGGTTT 59.645 61.111 0.00 0.00 0.00 3.27
1788 2592 1.519898 CCGCCATTGATGCCTTTGC 60.520 57.895 0.00 0.00 38.26 3.68
1791 2595 3.149648 GCCCGCCATTGATGCCTT 61.150 61.111 0.00 0.00 0.00 4.35
2234 3481 4.869215 TGCACATCCAAATTACACACAAG 58.131 39.130 0.00 0.00 0.00 3.16
2235 3482 4.582240 TCTGCACATCCAAATTACACACAA 59.418 37.500 0.00 0.00 0.00 3.33
2529 3800 0.531974 TCAATTGTAGATCCCGGCGC 60.532 55.000 0.00 0.00 0.00 6.53
2579 3851 9.256228 ACCTAGGTCACCTGTGTTATATATATG 57.744 37.037 9.21 0.00 34.61 1.78
2661 3937 7.986085 ACATAAATGCTAACTTCTGACAAGT 57.014 32.000 0.00 0.00 0.00 3.16
2770 4047 5.381477 GCCAAAAGTGTTTTCTTTGTTGTG 58.619 37.500 0.00 0.00 37.65 3.33
2847 4125 5.925509 AGTCAGTTCCTGTTGCTAAGTTTA 58.074 37.500 0.00 0.00 32.61 2.01
2868 4146 4.910195 TCCTGCTGATATGTTGACAAAGT 58.090 39.130 0.00 0.00 0.00 2.66
2903 4181 9.999009 GGTAAACTAAAAGGTATGCAAGATTAC 57.001 33.333 0.00 0.00 0.00 1.89
2947 4225 9.679661 ACAGTGATGTCAAATACCATTATGTTA 57.320 29.630 0.00 0.00 0.00 2.41
2970 4248 3.405831 TCCATGAGAGAACAAAGCACAG 58.594 45.455 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.