Multiple sequence alignment - TraesCS6B01G394400

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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 TraesCS6B01G394400 chr6B 100.000 2919 0 0 836 3754 669532464 669535382 0.000000e+00 5391.0
1 TraesCS6B01G394400 chr6B 100.000 589 0 0 1 589 669531629 669532217 0.000000e+00 1088.0
2 TraesCS6B01G394400 chr6B 97.110 173 5 0 1 173 670012813 670012641 3.670000e-75 292.0
3 TraesCS6B01G394400 chr6B 79.322 295 61 0 3436 3730 669534310 669534604 1.370000e-49 207.0
4 TraesCS6B01G394400 chr3D 97.557 2906 61 4 850 3754 1701429 1698533 0.000000e+00 4964.0
5 TraesCS6B01G394400 chr3D 95.000 420 16 3 174 589 1702257 1701839 0.000000e+00 654.0
6 TraesCS6B01G394400 chr3D 81.695 295 54 0 3436 3730 1699603 1699309 2.900000e-61 246.0
7 TraesCS6B01G394400 chr3D 100.000 34 0 0 1952 1985 1700276 1700243 3.130000e-06 63.9
8 TraesCS6B01G394400 chr5A 97.143 2870 66 7 894 3754 611016733 611013871 0.000000e+00 4831.0
9 TraesCS6B01G394400 chr5A 95.227 419 15 3 175 589 611017475 611017058 0.000000e+00 658.0
10 TraesCS6B01G394400 chr5A 79.183 514 96 11 2477 2984 590560599 590561107 2.780000e-91 346.0
11 TraesCS6B01G394400 chr5A 77.817 568 111 14 2404 2961 552841395 552841957 1.670000e-88 337.0
12 TraesCS6B01G394400 chr5A 81.111 270 51 0 3436 3705 590560805 590561074 2.270000e-52 217.0
13 TraesCS6B01G394400 chr5A 80.080 251 50 0 858 1108 688721438 688721188 1.780000e-43 187.0
14 TraesCS6B01G394400 chr5A 97.059 34 1 0 1952 1985 611015616 611015583 1.460000e-04 58.4
15 TraesCS6B01G394400 chr2A 83.423 742 99 16 1277 2010 32135493 32134768 0.000000e+00 667.0
16 TraesCS6B01G394400 chr2A 80.741 270 50 1 841 1108 677910969 677911238 3.800000e-50 209.0
17 TraesCS6B01G394400 chr5D 83.221 739 103 17 1277 2010 42225068 42224346 0.000000e+00 658.0
18 TraesCS6B01G394400 chr2D 83.266 741 99 19 1277 2010 345275092 345274370 0.000000e+00 658.0
19 TraesCS6B01G394400 chr2D 76.829 574 120 12 2403 2968 110863607 110863039 1.010000e-80 311.0
20 TraesCS6B01G394400 chr2D 97.297 37 1 0 174 210 345276013 345275977 3.130000e-06 63.9
21 TraesCS6B01G394400 chr2D 97.297 37 1 0 174 210 639463359 639463395 3.130000e-06 63.9
22 TraesCS6B01G394400 chr1D 83.221 739 103 16 1277 2010 71308126 71307404 0.000000e+00 658.0
23 TraesCS6B01G394400 chr1D 97.297 37 1 0 174 210 71309049 71309013 3.130000e-06 63.9
24 TraesCS6B01G394400 chr7D 82.815 739 107 16 1277 2010 127417074 127416351 0.000000e+00 643.0
25 TraesCS6B01G394400 chr7D 82.726 741 109 15 1274 2010 58108516 58109241 3.160000e-180 641.0
26 TraesCS6B01G394400 chr1A 81.916 741 109 17 1277 2010 546526397 546525675 1.490000e-168 603.0
27 TraesCS6B01G394400 chr3B 83.106 586 93 6 2404 2986 66886100 66885518 2.570000e-146 529.0
28 TraesCS6B01G394400 chr3B 79.740 385 70 8 3375 3754 11645253 11644872 4.780000e-69 272.0
29 TraesCS6B01G394400 chr3B 79.688 384 72 6 3375 3754 66885884 66885503 4.780000e-69 272.0
30 TraesCS6B01G394400 chr3B 79.876 323 41 7 2046 2344 11645817 11645495 8.170000e-52 215.0
31 TraesCS6B01G394400 chr3B 79.257 323 43 7 2046 2344 66886448 66886126 1.770000e-48 204.0
32 TraesCS6B01G394400 chr2B 76.522 575 120 14 2403 2968 116330281 116329713 2.190000e-77 300.0
33 TraesCS6B01G394400 chr2B 76.562 576 117 15 2403 2968 737854220 737853653 2.190000e-77 300.0
34 TraesCS6B01G394400 chr2B 75.529 425 97 7 1586 2007 642829670 642830090 6.360000e-48 202.0
35 TraesCS6B01G394400 chr7B 79.948 384 71 6 3375 3754 614303263 614302882 1.030000e-70 278.0
36 TraesCS6B01G394400 chr7B 79.876 323 41 7 2046 2344 614303827 614303505 8.170000e-52 215.0
37 TraesCS6B01G394400 chr7A 82.353 272 43 4 1277 1545 128919218 128918949 8.110000e-57 231.0
38 TraesCS6B01G394400 chr7A 88.623 167 10 6 1 159 50141523 50141688 1.060000e-45 195.0
39 TraesCS6B01G394400 chr1B 80.822 292 54 2 2670 2961 145158426 145158715 1.050000e-55 228.0
40 TraesCS6B01G394400 chr3A 81.890 254 46 0 3452 3705 158742612 158742359 8.170000e-52 215.0
41 TraesCS6B01G394400 chr3A 80.000 275 46 7 841 1111 301202467 301202736 1.060000e-45 195.0
42 TraesCS6B01G394400 chr6D 75.524 143 29 4 3211 3348 72222777 72222918 8.700000e-07 65.8


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 TraesCS6B01G394400 chr6B 669531629 669535382 3753 False 2228.666667 5391 93.107333 1 3754 3 chr6B.!!$F1 3753
1 TraesCS6B01G394400 chr3D 1698533 1702257 3724 True 1481.975000 4964 93.563000 174 3754 4 chr3D.!!$R1 3580
2 TraesCS6B01G394400 chr5A 611013871 611017475 3604 True 1849.133333 4831 96.476333 175 3754 3 chr5A.!!$R2 3579
3 TraesCS6B01G394400 chr5A 552841395 552841957 562 False 337.000000 337 77.817000 2404 2961 1 chr5A.!!$F1 557
4 TraesCS6B01G394400 chr5A 590560599 590561107 508 False 281.500000 346 80.147000 2477 3705 2 chr5A.!!$F2 1228
5 TraesCS6B01G394400 chr2A 32134768 32135493 725 True 667.000000 667 83.423000 1277 2010 1 chr2A.!!$R1 733
6 TraesCS6B01G394400 chr5D 42224346 42225068 722 True 658.000000 658 83.221000 1277 2010 1 chr5D.!!$R1 733
7 TraesCS6B01G394400 chr2D 345274370 345276013 1643 True 360.950000 658 90.281500 174 2010 2 chr2D.!!$R2 1836
8 TraesCS6B01G394400 chr2D 110863039 110863607 568 True 311.000000 311 76.829000 2403 2968 1 chr2D.!!$R1 565
9 TraesCS6B01G394400 chr1D 71307404 71309049 1645 True 360.950000 658 90.259000 174 2010 2 chr1D.!!$R1 1836
10 TraesCS6B01G394400 chr7D 127416351 127417074 723 True 643.000000 643 82.815000 1277 2010 1 chr7D.!!$R1 733
11 TraesCS6B01G394400 chr7D 58108516 58109241 725 False 641.000000 641 82.726000 1274 2010 1 chr7D.!!$F1 736
12 TraesCS6B01G394400 chr1A 546525675 546526397 722 True 603.000000 603 81.916000 1277 2010 1 chr1A.!!$R1 733
13 TraesCS6B01G394400 chr3B 66885503 66886448 945 True 335.000000 529 80.683667 2046 3754 3 chr3B.!!$R2 1708
14 TraesCS6B01G394400 chr3B 11644872 11645817 945 True 243.500000 272 79.808000 2046 3754 2 chr3B.!!$R1 1708
15 TraesCS6B01G394400 chr2B 116329713 116330281 568 True 300.000000 300 76.522000 2403 2968 1 chr2B.!!$R1 565
16 TraesCS6B01G394400 chr2B 737853653 737854220 567 True 300.000000 300 76.562000 2403 2968 1 chr2B.!!$R2 565
17 TraesCS6B01G394400 chr7B 614302882 614303827 945 True 246.500000 278 79.912000 2046 3754 2 chr7B.!!$R1 1708

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 0.998928 AGCAGGGAGTGAGAGAGAGA 59.001 55.000 0.00 0.0 0.00 3.10 F
161 162 1.351350 TCCCAGTGAGAAGAGAGACGA 59.649 52.381 0.00 0.0 0.00 4.20 F
1199 1355 0.035881 AGCAGCCGTCCCATGATATG 59.964 55.000 0.00 0.0 0.00 1.78 F
2707 2943 0.685131 TTGGACGAGCCCCTATCGAA 60.685 55.000 1.94 0.0 42.76 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1024 1180 0.397114 TAGATTGCTCGGAGGCTGGA 60.397 55.000 7.2 0.0 0.0 3.86 R
2081 2286 0.109132 GGCTTGCGGGTCATCTTTTG 60.109 55.000 0.0 0.0 0.0 2.44 R
2726 2962 1.021202 TTTTCAAGGGCACACACTCG 58.979 50.000 0.0 0.0 0.0 4.18 R
3587 3824 9.822727 TCCCATGAATATAGATTGTAGTAGTCA 57.177 33.333 0.0 0.0 0.0 3.41 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
21 22 4.464069 AGATTCTTCTGGCTACACTGAC 57.536 45.455 0.00 0.00 0.00 3.51
22 23 3.834813 AGATTCTTCTGGCTACACTGACA 59.165 43.478 0.00 0.00 0.00 3.58
23 24 4.469227 AGATTCTTCTGGCTACACTGACAT 59.531 41.667 0.00 0.00 0.00 3.06
24 25 5.658634 AGATTCTTCTGGCTACACTGACATA 59.341 40.000 0.00 0.00 0.00 2.29
25 26 5.939764 TTCTTCTGGCTACACTGACATAT 57.060 39.130 0.00 0.00 0.00 1.78
26 27 5.939764 TCTTCTGGCTACACTGACATATT 57.060 39.130 0.00 0.00 0.00 1.28
27 28 5.664457 TCTTCTGGCTACACTGACATATTG 58.336 41.667 0.00 0.00 0.00 1.90
28 29 5.187772 TCTTCTGGCTACACTGACATATTGT 59.812 40.000 0.00 0.00 0.00 2.71
29 30 5.420725 TCTGGCTACACTGACATATTGTT 57.579 39.130 0.00 0.00 0.00 2.83
30 31 5.178061 TCTGGCTACACTGACATATTGTTG 58.822 41.667 0.00 0.00 0.00 3.33
31 32 3.689161 TGGCTACACTGACATATTGTTGC 59.311 43.478 8.78 8.78 39.00 4.17
32 33 3.242413 GGCTACACTGACATATTGTTGCG 60.242 47.826 10.21 0.00 40.02 4.85
33 34 3.370978 GCTACACTGACATATTGTTGCGT 59.629 43.478 0.00 0.00 32.99 5.24
34 35 4.492570 GCTACACTGACATATTGTTGCGTC 60.493 45.833 0.00 0.00 32.99 5.19
35 36 2.742053 ACACTGACATATTGTTGCGTCC 59.258 45.455 0.00 0.00 0.00 4.79
36 37 2.741517 CACTGACATATTGTTGCGTCCA 59.258 45.455 0.00 0.00 0.00 4.02
37 38 3.188254 CACTGACATATTGTTGCGTCCAA 59.812 43.478 0.00 0.00 0.00 3.53
48 49 4.773742 GTTGCGTCCAACTACTATTAGC 57.226 45.455 0.00 0.00 46.13 3.09
49 50 4.178540 GTTGCGTCCAACTACTATTAGCA 58.821 43.478 0.00 0.00 46.13 3.49
50 51 4.041740 TGCGTCCAACTACTATTAGCAG 57.958 45.455 0.00 0.00 0.00 4.24
51 52 3.181479 TGCGTCCAACTACTATTAGCAGG 60.181 47.826 0.00 0.00 0.00 4.85
52 53 3.799232 GCGTCCAACTACTATTAGCAGGG 60.799 52.174 0.00 0.00 0.00 4.45
53 54 3.635373 CGTCCAACTACTATTAGCAGGGA 59.365 47.826 0.00 0.00 0.00 4.20
54 55 4.261656 CGTCCAACTACTATTAGCAGGGAG 60.262 50.000 0.00 0.00 0.00 4.30
55 56 4.650131 GTCCAACTACTATTAGCAGGGAGT 59.350 45.833 0.00 0.00 0.00 3.85
56 57 4.649674 TCCAACTACTATTAGCAGGGAGTG 59.350 45.833 0.00 0.00 0.00 3.51
57 58 4.649674 CCAACTACTATTAGCAGGGAGTGA 59.350 45.833 0.00 0.00 0.00 3.41
58 59 5.221342 CCAACTACTATTAGCAGGGAGTGAG 60.221 48.000 0.00 0.00 0.00 3.51
59 60 5.390087 ACTACTATTAGCAGGGAGTGAGA 57.610 43.478 0.00 0.00 0.00 3.27
60 61 5.381757 ACTACTATTAGCAGGGAGTGAGAG 58.618 45.833 0.00 0.00 0.00 3.20
61 62 4.528076 ACTATTAGCAGGGAGTGAGAGA 57.472 45.455 0.00 0.00 0.00 3.10
62 63 4.469657 ACTATTAGCAGGGAGTGAGAGAG 58.530 47.826 0.00 0.00 0.00 3.20
63 64 3.678965 ATTAGCAGGGAGTGAGAGAGA 57.321 47.619 0.00 0.00 0.00 3.10
64 65 2.727123 TAGCAGGGAGTGAGAGAGAG 57.273 55.000 0.00 0.00 0.00 3.20
65 66 0.998928 AGCAGGGAGTGAGAGAGAGA 59.001 55.000 0.00 0.00 0.00 3.10
66 67 1.570501 AGCAGGGAGTGAGAGAGAGAT 59.429 52.381 0.00 0.00 0.00 2.75
67 68 1.682854 GCAGGGAGTGAGAGAGAGATG 59.317 57.143 0.00 0.00 0.00 2.90
68 69 2.686416 GCAGGGAGTGAGAGAGAGATGA 60.686 54.545 0.00 0.00 0.00 2.92
69 70 3.216800 CAGGGAGTGAGAGAGAGATGAG 58.783 54.545 0.00 0.00 0.00 2.90
70 71 3.117926 CAGGGAGTGAGAGAGAGATGAGA 60.118 52.174 0.00 0.00 0.00 3.27
71 72 3.723681 AGGGAGTGAGAGAGAGATGAGAT 59.276 47.826 0.00 0.00 0.00 2.75
72 73 3.822735 GGGAGTGAGAGAGAGATGAGATG 59.177 52.174 0.00 0.00 0.00 2.90
73 74 4.446167 GGGAGTGAGAGAGAGATGAGATGA 60.446 50.000 0.00 0.00 0.00 2.92
74 75 5.132502 GGAGTGAGAGAGAGATGAGATGAA 58.867 45.833 0.00 0.00 0.00 2.57
75 76 5.593909 GGAGTGAGAGAGAGATGAGATGAAA 59.406 44.000 0.00 0.00 0.00 2.69
76 77 6.266103 GGAGTGAGAGAGAGATGAGATGAAAT 59.734 42.308 0.00 0.00 0.00 2.17
77 78 7.201938 GGAGTGAGAGAGAGATGAGATGAAATT 60.202 40.741 0.00 0.00 0.00 1.82
78 79 8.081517 AGTGAGAGAGAGATGAGATGAAATTT 57.918 34.615 0.00 0.00 0.00 1.82
79 80 8.542080 AGTGAGAGAGAGATGAGATGAAATTTT 58.458 33.333 0.00 0.00 0.00 1.82
80 81 8.819974 GTGAGAGAGAGATGAGATGAAATTTTC 58.180 37.037 2.05 2.05 0.00 2.29
81 82 8.760735 TGAGAGAGAGATGAGATGAAATTTTCT 58.239 33.333 10.33 0.00 0.00 2.52
104 105 9.851686 TTCTATGATTATTTGCTTGATGGTACT 57.148 29.630 0.00 0.00 0.00 2.73
105 106 9.494271 TCTATGATTATTTGCTTGATGGTACTC 57.506 33.333 0.00 0.00 0.00 2.59
106 107 9.276590 CTATGATTATTTGCTTGATGGTACTCA 57.723 33.333 0.00 0.00 0.00 3.41
107 108 7.320443 TGATTATTTGCTTGATGGTACTCAC 57.680 36.000 0.00 0.00 0.00 3.51
108 109 6.883756 TGATTATTTGCTTGATGGTACTCACA 59.116 34.615 0.00 0.00 0.00 3.58
109 110 6.741992 TTATTTGCTTGATGGTACTCACAG 57.258 37.500 0.00 0.00 0.00 3.66
110 111 4.350368 TTTGCTTGATGGTACTCACAGA 57.650 40.909 0.00 0.00 0.00 3.41
111 112 4.558226 TTGCTTGATGGTACTCACAGAT 57.442 40.909 0.00 0.00 0.00 2.90
112 113 5.675684 TTGCTTGATGGTACTCACAGATA 57.324 39.130 0.00 0.00 0.00 1.98
113 114 5.675684 TGCTTGATGGTACTCACAGATAA 57.324 39.130 0.00 0.00 0.00 1.75
114 115 5.664457 TGCTTGATGGTACTCACAGATAAG 58.336 41.667 0.00 0.00 0.00 1.73
115 116 5.422012 TGCTTGATGGTACTCACAGATAAGA 59.578 40.000 0.00 0.00 0.00 2.10
116 117 6.098838 TGCTTGATGGTACTCACAGATAAGAT 59.901 38.462 0.00 0.00 0.00 2.40
117 118 7.287696 TGCTTGATGGTACTCACAGATAAGATA 59.712 37.037 0.00 0.00 0.00 1.98
118 119 7.812191 GCTTGATGGTACTCACAGATAAGATAG 59.188 40.741 0.00 0.00 0.00 2.08
119 120 8.768501 TTGATGGTACTCACAGATAAGATAGT 57.231 34.615 0.00 0.00 0.00 2.12
120 121 8.768501 TGATGGTACTCACAGATAAGATAGTT 57.231 34.615 0.00 0.00 0.00 2.24
121 122 9.201989 TGATGGTACTCACAGATAAGATAGTTT 57.798 33.333 0.00 0.00 0.00 2.66
123 124 9.823647 ATGGTACTCACAGATAAGATAGTTTTG 57.176 33.333 0.00 0.00 0.00 2.44
124 125 8.258007 TGGTACTCACAGATAAGATAGTTTTGG 58.742 37.037 0.00 0.00 0.00 3.28
125 126 8.475639 GGTACTCACAGATAAGATAGTTTTGGA 58.524 37.037 0.00 0.00 0.00 3.53
126 127 9.871238 GTACTCACAGATAAGATAGTTTTGGAA 57.129 33.333 0.00 0.00 0.00 3.53
128 129 8.598041 ACTCACAGATAAGATAGTTTTGGAAGT 58.402 33.333 0.00 0.00 0.00 3.01
129 130 8.777865 TCACAGATAAGATAGTTTTGGAAGTG 57.222 34.615 0.00 0.00 0.00 3.16
130 131 7.334421 TCACAGATAAGATAGTTTTGGAAGTGC 59.666 37.037 0.00 0.00 0.00 4.40
131 132 7.119699 CACAGATAAGATAGTTTTGGAAGTGCA 59.880 37.037 0.00 0.00 0.00 4.57
132 133 7.665559 ACAGATAAGATAGTTTTGGAAGTGCAA 59.334 33.333 0.00 0.00 0.00 4.08
133 134 8.180267 CAGATAAGATAGTTTTGGAAGTGCAAG 58.820 37.037 0.00 0.00 0.00 4.01
134 135 8.103305 AGATAAGATAGTTTTGGAAGTGCAAGA 58.897 33.333 0.00 0.00 0.00 3.02
135 136 6.566197 AAGATAGTTTTGGAAGTGCAAGAG 57.434 37.500 0.00 0.00 0.00 2.85
136 137 5.869579 AGATAGTTTTGGAAGTGCAAGAGA 58.130 37.500 0.00 0.00 0.00 3.10
137 138 6.479884 AGATAGTTTTGGAAGTGCAAGAGAT 58.520 36.000 0.00 0.00 0.00 2.75
138 139 6.944862 AGATAGTTTTGGAAGTGCAAGAGATT 59.055 34.615 0.00 0.00 0.00 2.40
139 140 5.192327 AGTTTTGGAAGTGCAAGAGATTG 57.808 39.130 0.00 0.00 0.00 2.67
140 141 4.889409 AGTTTTGGAAGTGCAAGAGATTGA 59.111 37.500 0.00 0.00 0.00 2.57
141 142 5.537674 AGTTTTGGAAGTGCAAGAGATTGAT 59.462 36.000 0.00 0.00 0.00 2.57
142 143 5.633830 TTTGGAAGTGCAAGAGATTGATC 57.366 39.130 0.00 0.00 0.00 2.92
143 144 3.614092 TGGAAGTGCAAGAGATTGATCC 58.386 45.455 0.00 0.00 0.00 3.36
144 145 2.948315 GGAAGTGCAAGAGATTGATCCC 59.052 50.000 0.00 0.00 0.00 3.85
145 146 3.614092 GAAGTGCAAGAGATTGATCCCA 58.386 45.455 0.00 0.00 0.00 4.37
146 147 3.278668 AGTGCAAGAGATTGATCCCAG 57.721 47.619 0.00 0.00 0.00 4.45
147 148 2.575279 AGTGCAAGAGATTGATCCCAGT 59.425 45.455 0.00 0.00 0.00 4.00
148 149 2.681848 GTGCAAGAGATTGATCCCAGTG 59.318 50.000 0.00 0.00 0.00 3.66
149 150 2.573009 TGCAAGAGATTGATCCCAGTGA 59.427 45.455 0.00 0.00 0.00 3.41
150 151 3.204526 GCAAGAGATTGATCCCAGTGAG 58.795 50.000 0.00 0.00 0.00 3.51
151 152 3.118482 GCAAGAGATTGATCCCAGTGAGA 60.118 47.826 0.00 0.00 0.00 3.27
152 153 4.624843 GCAAGAGATTGATCCCAGTGAGAA 60.625 45.833 0.00 0.00 0.00 2.87
153 154 5.117584 CAAGAGATTGATCCCAGTGAGAAG 58.882 45.833 0.00 0.00 0.00 2.85
154 155 4.618635 AGAGATTGATCCCAGTGAGAAGA 58.381 43.478 0.00 0.00 0.00 2.87
155 156 4.650588 AGAGATTGATCCCAGTGAGAAGAG 59.349 45.833 0.00 0.00 0.00 2.85
156 157 4.618635 AGATTGATCCCAGTGAGAAGAGA 58.381 43.478 0.00 0.00 0.00 3.10
157 158 4.650588 AGATTGATCCCAGTGAGAAGAGAG 59.349 45.833 0.00 0.00 0.00 3.20
158 159 3.746792 TGATCCCAGTGAGAAGAGAGA 57.253 47.619 0.00 0.00 0.00 3.10
159 160 3.360867 TGATCCCAGTGAGAAGAGAGAC 58.639 50.000 0.00 0.00 0.00 3.36
160 161 1.827681 TCCCAGTGAGAAGAGAGACG 58.172 55.000 0.00 0.00 0.00 4.18
161 162 1.351350 TCCCAGTGAGAAGAGAGACGA 59.649 52.381 0.00 0.00 0.00 4.20
162 163 1.470890 CCCAGTGAGAAGAGAGACGAC 59.529 57.143 0.00 0.00 0.00 4.34
163 164 2.155279 CCAGTGAGAAGAGAGACGACA 58.845 52.381 0.00 0.00 0.00 4.35
164 165 2.095466 CCAGTGAGAAGAGAGACGACAC 60.095 54.545 0.00 0.00 0.00 3.67
165 166 2.550180 CAGTGAGAAGAGAGACGACACA 59.450 50.000 0.00 0.00 0.00 3.72
166 167 3.190327 CAGTGAGAAGAGAGACGACACAT 59.810 47.826 0.00 0.00 0.00 3.21
167 168 3.190327 AGTGAGAAGAGAGACGACACATG 59.810 47.826 0.00 0.00 0.00 3.21
168 169 2.489722 TGAGAAGAGAGACGACACATGG 59.510 50.000 0.00 0.00 0.00 3.66
169 170 2.750166 GAGAAGAGAGACGACACATGGA 59.250 50.000 0.00 0.00 0.00 3.41
170 171 3.360867 AGAAGAGAGACGACACATGGAT 58.639 45.455 0.00 0.00 0.00 3.41
171 172 3.130164 AGAAGAGAGACGACACATGGATG 59.870 47.826 0.00 0.00 0.00 3.51
172 173 2.451490 AGAGAGACGACACATGGATGT 58.549 47.619 0.00 0.00 42.84 3.06
219 220 4.172512 CGCTCCTGGCAGCTGGAT 62.173 66.667 17.12 0.00 41.91 3.41
350 352 3.349022 GGAACAAATCGGTCCATGGTAA 58.651 45.455 12.58 0.00 0.00 2.85
534 538 2.100197 CTTCGACCACCTCCTGATACA 58.900 52.381 0.00 0.00 0.00 2.29
548 552 3.209410 CTGATACAAGAAGGCCATGGAC 58.791 50.000 18.40 14.73 0.00 4.02
996 1152 4.586001 AGCAGTGGAAAATGACTTGAACAT 59.414 37.500 0.00 0.00 0.00 2.71
1024 1180 2.854420 AGGGGATTGCCCTCTCTGCT 62.854 60.000 10.51 0.00 44.44 4.24
1111 1267 6.003326 TGGATCTACTGCATTGTTTTCTCAA 58.997 36.000 0.00 0.00 0.00 3.02
1199 1355 0.035881 AGCAGCCGTCCCATGATATG 59.964 55.000 0.00 0.00 0.00 1.78
1202 1358 2.688507 CAGCCGTCCCATGATATGTAC 58.311 52.381 0.00 0.00 0.00 2.90
1204 1360 1.271379 GCCGTCCCATGATATGTACGA 59.729 52.381 12.55 0.00 38.96 3.43
1305 1497 4.201724 GCTGGAACTAACAATACGAAGCTG 60.202 45.833 0.00 0.00 0.00 4.24
1362 1554 4.141181 TGCTATGGGAGGCAGTTTTGATAT 60.141 41.667 0.00 0.00 34.22 1.63
1388 1580 6.689177 GCTTGGGGAAGCTTATGATTACTACT 60.689 42.308 0.00 0.00 42.32 2.57
1489 1682 2.093235 GGAGATAGTTTGTGGCTGCTCT 60.093 50.000 0.00 0.00 0.00 4.09
1734 1939 4.565652 GCTCTAACTGAAAGATGTGGGGAA 60.566 45.833 0.00 0.00 37.43 3.97
1915 2120 2.287788 GGTTTGTGTGGCAAGATGAGTG 60.288 50.000 0.00 0.00 38.47 3.51
1994 2199 4.217118 AGCAAAAGATTCAGGCTTGTACTG 59.783 41.667 0.00 0.00 37.30 2.74
2030 2235 2.031120 TGTTTTTGCAGAGTTGGGAGG 58.969 47.619 0.00 0.00 0.00 4.30
2040 2245 3.686726 CAGAGTTGGGAGGAAAAGATTCG 59.313 47.826 0.00 0.00 36.36 3.34
2081 2286 1.070975 CGATTCGCAGCTATCAACAGC 60.071 52.381 0.00 0.00 42.12 4.40
2270 2499 6.581712 ACAAAAGTTGTATTTGGTCATGCTT 58.418 32.000 4.29 0.00 43.27 3.91
2578 2810 8.185003 TCTGAATAATGTAAATGTCTGACACG 57.815 34.615 13.50 0.00 0.00 4.49
2622 2854 6.930164 TGCTCACTTATGAACATTGCATTTTT 59.070 30.769 0.00 0.00 33.30 1.94
2707 2943 0.685131 TTGGACGAGCCCCTATCGAA 60.685 55.000 1.94 0.00 42.76 3.71
2777 3014 5.645497 AGTGGATATGCAGAGAACAAAACTC 59.355 40.000 0.00 0.00 34.95 3.01
2875 3112 3.672241 CGTGGGAAATTGGTTTCGGAATC 60.672 47.826 0.00 0.00 43.73 2.52
2877 3114 3.898123 TGGGAAATTGGTTTCGGAATCAA 59.102 39.130 4.20 4.20 43.73 2.57
2892 3129 5.048643 TCGGAATCAAATACGGAAAAAGCAA 60.049 36.000 0.00 0.00 0.00 3.91
2962 3199 6.737254 TTCTCGGTGAGTGGAAATTAAATC 57.263 37.500 0.00 0.00 0.00 2.17
3068 3305 5.072600 TGGACAAAAAGGTATACCACTCTGT 59.927 40.000 23.87 19.07 38.89 3.41
3170 3407 8.859236 ATGTTGGTCATCTCAATAGATAATGG 57.141 34.615 0.00 0.00 40.65 3.16
3176 3413 7.310299 GGTCATCTCAATAGATAATGGAGAGCA 60.310 40.741 0.00 0.00 45.95 4.26
3304 3541 2.753043 CCCATGTGCTGCCAGGAC 60.753 66.667 9.69 9.69 37.06 3.85
3314 3551 4.459089 GCCAGGACGAGTGCCCTC 62.459 72.222 0.00 0.00 0.00 4.30
3523 3760 3.181482 ACATTGAGAGGATACGCACAGAG 60.181 47.826 0.00 0.00 38.31 3.35
3530 3767 4.649674 AGAGGATACGCACAGAGGAAAATA 59.350 41.667 0.00 0.00 46.39 1.40
3584 3821 0.391130 TTGATTCGTTGGGAGAGGCG 60.391 55.000 0.00 0.00 0.00 5.52
3587 3824 1.068741 GATTCGTTGGGAGAGGCGTAT 59.931 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.193826 TGTCAGTGTAGCCAGAAGAATC 57.806 45.455 0.00 0.00 0.00 2.52
4 5 5.187772 ACAATATGTCAGTGTAGCCAGAAGA 59.812 40.000 0.00 0.00 32.63 2.87
6 7 5.420725 ACAATATGTCAGTGTAGCCAGAA 57.579 39.130 0.00 0.00 32.63 3.02
7 8 5.178061 CAACAATATGTCAGTGTAGCCAGA 58.822 41.667 0.00 0.00 33.44 3.86
8 9 4.201851 GCAACAATATGTCAGTGTAGCCAG 60.202 45.833 0.00 0.00 33.44 4.85
9 10 3.689161 GCAACAATATGTCAGTGTAGCCA 59.311 43.478 0.00 0.00 33.44 4.75
10 11 3.242413 CGCAACAATATGTCAGTGTAGCC 60.242 47.826 0.00 0.00 33.44 3.93
11 12 3.370978 ACGCAACAATATGTCAGTGTAGC 59.629 43.478 0.00 0.00 33.44 3.58
12 13 4.032900 GGACGCAACAATATGTCAGTGTAG 59.967 45.833 0.00 0.00 33.44 2.74
13 14 3.930229 GGACGCAACAATATGTCAGTGTA 59.070 43.478 0.00 0.00 33.44 2.90
14 15 2.742053 GGACGCAACAATATGTCAGTGT 59.258 45.455 0.00 2.94 36.93 3.55
15 16 2.741517 TGGACGCAACAATATGTCAGTG 59.258 45.455 0.00 0.00 33.04 3.66
16 17 3.052455 TGGACGCAACAATATGTCAGT 57.948 42.857 0.00 0.00 33.04 3.41
17 18 3.436704 AGTTGGACGCAACAATATGTCAG 59.563 43.478 8.35 0.00 37.52 3.51
18 19 3.407698 AGTTGGACGCAACAATATGTCA 58.592 40.909 8.35 0.00 37.52 3.58
19 20 4.630069 AGTAGTTGGACGCAACAATATGTC 59.370 41.667 8.35 0.00 37.52 3.06
20 21 4.575885 AGTAGTTGGACGCAACAATATGT 58.424 39.130 8.35 0.00 37.52 2.29
21 22 6.844696 ATAGTAGTTGGACGCAACAATATG 57.155 37.500 8.35 0.00 37.52 1.78
22 23 7.170998 GCTAATAGTAGTTGGACGCAACAATAT 59.829 37.037 8.35 1.91 37.52 1.28
23 24 6.477688 GCTAATAGTAGTTGGACGCAACAATA 59.522 38.462 8.35 0.00 37.52 1.90
24 25 5.293569 GCTAATAGTAGTTGGACGCAACAAT 59.706 40.000 8.35 0.00 37.52 2.71
25 26 4.628333 GCTAATAGTAGTTGGACGCAACAA 59.372 41.667 8.35 0.00 37.52 2.83
26 27 4.178540 GCTAATAGTAGTTGGACGCAACA 58.821 43.478 8.35 0.00 37.52 3.33
27 28 4.178540 TGCTAATAGTAGTTGGACGCAAC 58.821 43.478 0.00 0.00 35.43 4.17
28 29 4.430007 CTGCTAATAGTAGTTGGACGCAA 58.570 43.478 0.00 0.00 0.00 4.85
29 30 3.181479 CCTGCTAATAGTAGTTGGACGCA 60.181 47.826 4.75 0.00 0.00 5.24
30 31 3.381949 CCTGCTAATAGTAGTTGGACGC 58.618 50.000 4.75 0.00 0.00 5.19
31 32 3.635373 TCCCTGCTAATAGTAGTTGGACG 59.365 47.826 4.75 0.00 0.00 4.79
32 33 4.650131 ACTCCCTGCTAATAGTAGTTGGAC 59.350 45.833 4.75 0.00 0.00 4.02
33 34 4.649674 CACTCCCTGCTAATAGTAGTTGGA 59.350 45.833 4.75 4.37 0.00 3.53
34 35 4.649674 TCACTCCCTGCTAATAGTAGTTGG 59.350 45.833 4.75 1.97 0.00 3.77
35 36 5.594725 TCTCACTCCCTGCTAATAGTAGTTG 59.405 44.000 4.75 0.00 0.00 3.16
36 37 5.767670 TCTCACTCCCTGCTAATAGTAGTT 58.232 41.667 4.75 0.00 0.00 2.24
37 38 5.132985 TCTCTCACTCCCTGCTAATAGTAGT 59.867 44.000 4.75 0.00 0.00 2.73
38 39 5.626142 TCTCTCACTCCCTGCTAATAGTAG 58.374 45.833 0.00 0.00 0.00 2.57
39 40 5.369993 TCTCTCTCACTCCCTGCTAATAGTA 59.630 44.000 0.00 0.00 0.00 1.82
40 41 4.167113 TCTCTCTCACTCCCTGCTAATAGT 59.833 45.833 0.00 0.00 0.00 2.12
41 42 4.724399 TCTCTCTCACTCCCTGCTAATAG 58.276 47.826 0.00 0.00 0.00 1.73
42 43 4.413851 TCTCTCTCTCACTCCCTGCTAATA 59.586 45.833 0.00 0.00 0.00 0.98
43 44 3.204158 TCTCTCTCTCACTCCCTGCTAAT 59.796 47.826 0.00 0.00 0.00 1.73
44 45 2.578480 TCTCTCTCTCACTCCCTGCTAA 59.422 50.000 0.00 0.00 0.00 3.09
45 46 2.200955 TCTCTCTCTCACTCCCTGCTA 58.799 52.381 0.00 0.00 0.00 3.49
46 47 0.998928 TCTCTCTCTCACTCCCTGCT 59.001 55.000 0.00 0.00 0.00 4.24
47 48 1.682854 CATCTCTCTCTCACTCCCTGC 59.317 57.143 0.00 0.00 0.00 4.85
48 49 3.117926 TCTCATCTCTCTCTCACTCCCTG 60.118 52.174 0.00 0.00 0.00 4.45
49 50 3.122480 TCTCATCTCTCTCTCACTCCCT 58.878 50.000 0.00 0.00 0.00 4.20
50 51 3.576078 TCTCATCTCTCTCTCACTCCC 57.424 52.381 0.00 0.00 0.00 4.30
51 52 4.717877 TCATCTCATCTCTCTCTCACTCC 58.282 47.826 0.00 0.00 0.00 3.85
52 53 6.698008 TTTCATCTCATCTCTCTCTCACTC 57.302 41.667 0.00 0.00 0.00 3.51
53 54 7.664552 AATTTCATCTCATCTCTCTCTCACT 57.335 36.000 0.00 0.00 0.00 3.41
54 55 8.721019 AAAATTTCATCTCATCTCTCTCTCAC 57.279 34.615 0.00 0.00 0.00 3.51
55 56 8.760735 AGAAAATTTCATCTCATCTCTCTCTCA 58.239 33.333 8.55 0.00 0.00 3.27
78 79 9.851686 AGTACCATCAAGCAAATAATCATAGAA 57.148 29.630 0.00 0.00 0.00 2.10
79 80 9.494271 GAGTACCATCAAGCAAATAATCATAGA 57.506 33.333 0.00 0.00 0.00 1.98
80 81 9.276590 TGAGTACCATCAAGCAAATAATCATAG 57.723 33.333 0.00 0.00 0.00 2.23
81 82 9.056005 GTGAGTACCATCAAGCAAATAATCATA 57.944 33.333 0.00 0.00 0.00 2.15
82 83 7.557358 TGTGAGTACCATCAAGCAAATAATCAT 59.443 33.333 0.00 0.00 0.00 2.45
83 84 6.883756 TGTGAGTACCATCAAGCAAATAATCA 59.116 34.615 0.00 0.00 0.00 2.57
84 85 7.280876 TCTGTGAGTACCATCAAGCAAATAATC 59.719 37.037 0.00 0.00 0.00 1.75
85 86 7.112122 TCTGTGAGTACCATCAAGCAAATAAT 58.888 34.615 0.00 0.00 0.00 1.28
86 87 6.472016 TCTGTGAGTACCATCAAGCAAATAA 58.528 36.000 0.00 0.00 0.00 1.40
87 88 6.048732 TCTGTGAGTACCATCAAGCAAATA 57.951 37.500 0.00 0.00 0.00 1.40
88 89 4.910195 TCTGTGAGTACCATCAAGCAAAT 58.090 39.130 0.00 0.00 0.00 2.32
89 90 4.350368 TCTGTGAGTACCATCAAGCAAA 57.650 40.909 0.00 0.00 0.00 3.68
90 91 4.558226 ATCTGTGAGTACCATCAAGCAA 57.442 40.909 0.00 0.00 0.00 3.91
91 92 5.422012 TCTTATCTGTGAGTACCATCAAGCA 59.578 40.000 0.00 0.00 0.00 3.91
92 93 5.907207 TCTTATCTGTGAGTACCATCAAGC 58.093 41.667 0.00 0.00 0.00 4.01
93 94 8.855110 ACTATCTTATCTGTGAGTACCATCAAG 58.145 37.037 0.00 0.00 0.00 3.02
94 95 8.768501 ACTATCTTATCTGTGAGTACCATCAA 57.231 34.615 0.00 0.00 0.00 2.57
95 96 8.768501 AACTATCTTATCTGTGAGTACCATCA 57.231 34.615 0.00 0.00 0.00 3.07
97 98 9.823647 CAAAACTATCTTATCTGTGAGTACCAT 57.176 33.333 0.00 0.00 0.00 3.55
98 99 8.258007 CCAAAACTATCTTATCTGTGAGTACCA 58.742 37.037 0.00 0.00 0.00 3.25
99 100 8.475639 TCCAAAACTATCTTATCTGTGAGTACC 58.524 37.037 0.00 0.00 0.00 3.34
100 101 9.871238 TTCCAAAACTATCTTATCTGTGAGTAC 57.129 33.333 0.00 0.00 0.00 2.73
102 103 8.598041 ACTTCCAAAACTATCTTATCTGTGAGT 58.402 33.333 0.00 0.00 0.00 3.41
103 104 8.877779 CACTTCCAAAACTATCTTATCTGTGAG 58.122 37.037 0.00 0.00 0.00 3.51
104 105 7.334421 GCACTTCCAAAACTATCTTATCTGTGA 59.666 37.037 0.00 0.00 0.00 3.58
105 106 7.119699 TGCACTTCCAAAACTATCTTATCTGTG 59.880 37.037 0.00 0.00 0.00 3.66
106 107 7.168219 TGCACTTCCAAAACTATCTTATCTGT 58.832 34.615 0.00 0.00 0.00 3.41
107 108 7.615582 TGCACTTCCAAAACTATCTTATCTG 57.384 36.000 0.00 0.00 0.00 2.90
108 109 8.103305 TCTTGCACTTCCAAAACTATCTTATCT 58.897 33.333 0.00 0.00 0.00 1.98
109 110 8.268850 TCTTGCACTTCCAAAACTATCTTATC 57.731 34.615 0.00 0.00 0.00 1.75
110 111 8.103305 TCTCTTGCACTTCCAAAACTATCTTAT 58.897 33.333 0.00 0.00 0.00 1.73
111 112 7.450074 TCTCTTGCACTTCCAAAACTATCTTA 58.550 34.615 0.00 0.00 0.00 2.10
112 113 6.299141 TCTCTTGCACTTCCAAAACTATCTT 58.701 36.000 0.00 0.00 0.00 2.40
113 114 5.869579 TCTCTTGCACTTCCAAAACTATCT 58.130 37.500 0.00 0.00 0.00 1.98
114 115 6.749923 ATCTCTTGCACTTCCAAAACTATC 57.250 37.500 0.00 0.00 0.00 2.08
115 116 6.716628 TCAATCTCTTGCACTTCCAAAACTAT 59.283 34.615 0.00 0.00 32.11 2.12
116 117 6.061441 TCAATCTCTTGCACTTCCAAAACTA 58.939 36.000 0.00 0.00 32.11 2.24
117 118 4.889409 TCAATCTCTTGCACTTCCAAAACT 59.111 37.500 0.00 0.00 32.11 2.66
118 119 5.186996 TCAATCTCTTGCACTTCCAAAAC 57.813 39.130 0.00 0.00 32.11 2.43
119 120 5.047802 GGATCAATCTCTTGCACTTCCAAAA 60.048 40.000 0.00 0.00 32.11 2.44
120 121 4.460382 GGATCAATCTCTTGCACTTCCAAA 59.540 41.667 0.00 0.00 32.11 3.28
121 122 4.012374 GGATCAATCTCTTGCACTTCCAA 58.988 43.478 0.00 0.00 32.11 3.53
122 123 3.614092 GGATCAATCTCTTGCACTTCCA 58.386 45.455 0.00 0.00 32.11 3.53
123 124 2.948315 GGGATCAATCTCTTGCACTTCC 59.052 50.000 0.00 0.00 32.11 3.46
124 125 3.614092 TGGGATCAATCTCTTGCACTTC 58.386 45.455 0.00 0.00 32.11 3.01
125 126 3.009916 ACTGGGATCAATCTCTTGCACTT 59.990 43.478 0.00 0.00 32.11 3.16
126 127 2.575279 ACTGGGATCAATCTCTTGCACT 59.425 45.455 0.00 0.00 32.11 4.40
127 128 2.681848 CACTGGGATCAATCTCTTGCAC 59.318 50.000 0.00 0.00 32.11 4.57
128 129 2.573009 TCACTGGGATCAATCTCTTGCA 59.427 45.455 0.00 0.00 32.11 4.08
129 130 3.118482 TCTCACTGGGATCAATCTCTTGC 60.118 47.826 0.00 0.00 32.11 4.01
130 131 4.750021 TCTCACTGGGATCAATCTCTTG 57.250 45.455 0.00 0.00 0.00 3.02
131 132 5.028802 TCTTCTCACTGGGATCAATCTCTT 58.971 41.667 0.00 0.00 0.00 2.85
132 133 4.618635 TCTTCTCACTGGGATCAATCTCT 58.381 43.478 0.00 0.00 0.00 3.10
133 134 4.648762 TCTCTTCTCACTGGGATCAATCTC 59.351 45.833 0.00 0.00 0.00 2.75
134 135 4.618635 TCTCTTCTCACTGGGATCAATCT 58.381 43.478 0.00 0.00 0.00 2.40
135 136 4.648762 TCTCTCTTCTCACTGGGATCAATC 59.351 45.833 0.00 0.00 0.00 2.67
136 137 4.405358 GTCTCTCTTCTCACTGGGATCAAT 59.595 45.833 0.00 0.00 0.00 2.57
137 138 3.766591 GTCTCTCTTCTCACTGGGATCAA 59.233 47.826 0.00 0.00 0.00 2.57
138 139 3.360867 GTCTCTCTTCTCACTGGGATCA 58.639 50.000 0.00 0.00 0.00 2.92
139 140 2.357637 CGTCTCTCTTCTCACTGGGATC 59.642 54.545 0.00 0.00 0.00 3.36
140 141 2.025793 TCGTCTCTCTTCTCACTGGGAT 60.026 50.000 0.00 0.00 0.00 3.85
141 142 1.351350 TCGTCTCTCTTCTCACTGGGA 59.649 52.381 0.00 0.00 0.00 4.37
142 143 1.470890 GTCGTCTCTCTTCTCACTGGG 59.529 57.143 0.00 0.00 0.00 4.45
143 144 2.095466 GTGTCGTCTCTCTTCTCACTGG 60.095 54.545 0.00 0.00 0.00 4.00
144 145 2.550180 TGTGTCGTCTCTCTTCTCACTG 59.450 50.000 0.00 0.00 0.00 3.66
145 146 2.852449 TGTGTCGTCTCTCTTCTCACT 58.148 47.619 0.00 0.00 0.00 3.41
146 147 3.497118 CATGTGTCGTCTCTCTTCTCAC 58.503 50.000 0.00 0.00 0.00 3.51
147 148 2.489722 CCATGTGTCGTCTCTCTTCTCA 59.510 50.000 0.00 0.00 0.00 3.27
148 149 2.750166 TCCATGTGTCGTCTCTCTTCTC 59.250 50.000 0.00 0.00 0.00 2.87
149 150 2.796557 TCCATGTGTCGTCTCTCTTCT 58.203 47.619 0.00 0.00 0.00 2.85
150 151 3.119316 ACATCCATGTGTCGTCTCTCTTC 60.119 47.826 0.00 0.00 40.03 2.87
151 152 2.828520 ACATCCATGTGTCGTCTCTCTT 59.171 45.455 0.00 0.00 40.03 2.85
152 153 2.451490 ACATCCATGTGTCGTCTCTCT 58.549 47.619 0.00 0.00 40.03 3.10
153 154 2.949451 ACATCCATGTGTCGTCTCTC 57.051 50.000 0.00 0.00 40.03 3.20
154 155 3.621558 TCTACATCCATGTGTCGTCTCT 58.378 45.455 2.26 0.00 41.89 3.10
155 156 3.378742 ACTCTACATCCATGTGTCGTCTC 59.621 47.826 2.26 0.00 41.89 3.36
156 157 3.129462 CACTCTACATCCATGTGTCGTCT 59.871 47.826 2.26 0.00 41.89 4.18
157 158 3.439293 CACTCTACATCCATGTGTCGTC 58.561 50.000 2.26 0.00 41.89 4.20
158 159 2.166459 CCACTCTACATCCATGTGTCGT 59.834 50.000 2.26 0.00 41.89 4.34
159 160 2.814269 CCACTCTACATCCATGTGTCG 58.186 52.381 2.26 0.00 41.89 4.35
160 161 2.555199 GCCACTCTACATCCATGTGTC 58.445 52.381 2.26 0.00 41.89 3.67
161 162 1.134699 CGCCACTCTACATCCATGTGT 60.135 52.381 2.26 0.00 41.89 3.72
162 163 1.136891 TCGCCACTCTACATCCATGTG 59.863 52.381 2.26 0.00 41.89 3.21
163 164 1.485124 TCGCCACTCTACATCCATGT 58.515 50.000 0.00 0.00 44.48 3.21
164 165 2.410939 CATCGCCACTCTACATCCATG 58.589 52.381 0.00 0.00 0.00 3.66
165 166 1.345741 CCATCGCCACTCTACATCCAT 59.654 52.381 0.00 0.00 0.00 3.41
166 167 0.752658 CCATCGCCACTCTACATCCA 59.247 55.000 0.00 0.00 0.00 3.41
167 168 0.601311 GCCATCGCCACTCTACATCC 60.601 60.000 0.00 0.00 0.00 3.51
168 169 0.941463 CGCCATCGCCACTCTACATC 60.941 60.000 0.00 0.00 0.00 3.06
169 170 1.068083 CGCCATCGCCACTCTACAT 59.932 57.895 0.00 0.00 0.00 2.29
170 171 2.494445 CGCCATCGCCACTCTACA 59.506 61.111 0.00 0.00 0.00 2.74
219 220 1.206831 CACGTCGCTCTCTCGTTGA 59.793 57.895 0.00 0.00 35.62 3.18
269 271 0.313043 CCGTATCTACCGGCGATGTT 59.687 55.000 9.30 0.00 38.85 2.71
379 381 1.916000 GGACGTCGTTATGTGCAGTAC 59.084 52.381 9.92 0.00 33.43 2.73
548 552 0.386100 CGGTAGTCGCGATCTCCATG 60.386 60.000 14.06 0.00 0.00 3.66
996 1152 0.034186 GGCAATCCCCTGACATGTGA 60.034 55.000 1.15 0.00 0.00 3.58
1024 1180 0.397114 TAGATTGCTCGGAGGCTGGA 60.397 55.000 7.20 0.00 0.00 3.86
1128 1284 1.193874 GGTTCGCGTTGTGTAAGAAGG 59.806 52.381 5.77 0.00 0.00 3.46
1199 1355 9.722056 TTTTAATTCCTTATCGACTACTCGTAC 57.278 33.333 0.00 0.00 41.02 3.67
1202 1358 8.624701 TGTTTTAATTCCTTATCGACTACTCG 57.375 34.615 0.00 0.00 41.65 4.18
1305 1497 5.863935 ACAGTTTCAGTTTTCTTTTCTGCAC 59.136 36.000 0.00 0.00 0.00 4.57
1388 1580 6.339220 ACCCAACCTCCCATGAATATAGATA 58.661 40.000 0.00 0.00 0.00 1.98
1489 1682 7.548196 AGTGAAAATGAAACGAGTACTTTCA 57.452 32.000 10.18 10.18 40.89 2.69
1659 1856 3.200605 TGTACCAGCCATTGTCAGATGAT 59.799 43.478 0.00 0.00 0.00 2.45
1734 1939 1.497286 TGGGAAGGCCAGTACACTTTT 59.503 47.619 5.01 0.00 35.15 2.27
1915 2120 4.024556 CACATCATTATCGGCTTGTTCTCC 60.025 45.833 0.00 0.00 0.00 3.71
2030 2235 4.214332 ACAAGCTCAACTCCGAATCTTTTC 59.786 41.667 0.00 0.00 0.00 2.29
2040 2245 2.383527 CGCCGACAAGCTCAACTCC 61.384 63.158 0.00 0.00 0.00 3.85
2081 2286 0.109132 GGCTTGCGGGTCATCTTTTG 60.109 55.000 0.00 0.00 0.00 2.44
2303 2532 9.742552 GTTTTACATTCAGAGATCTAAAACGTC 57.257 33.333 0.00 0.00 0.00 4.34
2578 2810 2.863704 GCAACATGGGAGTGCAGTTTTC 60.864 50.000 0.00 0.00 0.00 2.29
2622 2854 3.071892 ACGGTCCCACTATGTTTTCAGAA 59.928 43.478 0.00 0.00 0.00 3.02
2726 2962 1.021202 TTTTCAAGGGCACACACTCG 58.979 50.000 0.00 0.00 0.00 4.18
2875 3112 6.559521 CGTTGAGTTTGCTTTTTCCGTATTTG 60.560 38.462 0.00 0.00 0.00 2.32
2877 3114 4.973663 CGTTGAGTTTGCTTTTTCCGTATT 59.026 37.500 0.00 0.00 0.00 1.89
2892 3129 1.679680 TGGTTCTCTCGACGTTGAGTT 59.320 47.619 27.97 0.00 37.28 3.01
2962 3199 5.916883 GCAATTCCAACGAATGAGATAATGG 59.083 40.000 0.00 0.00 38.75 3.16
3068 3305 4.565022 TGTTCGATCTACAAGCACAATCA 58.435 39.130 0.00 0.00 0.00 2.57
3160 3397 5.494390 TGCACATGCTCTCCATTATCTAT 57.506 39.130 5.31 0.00 42.66 1.98
3170 3407 1.875514 TGAACACTTGCACATGCTCTC 59.124 47.619 5.31 0.00 42.66 3.20
3176 3413 3.760151 ACATGCTATGAACACTTGCACAT 59.240 39.130 0.00 0.00 36.44 3.21
3314 3551 9.430838 CTTTTCTGCATATCTTCTTAATGTTCG 57.569 33.333 0.00 0.00 0.00 3.95
3587 3824 9.822727 TCCCATGAATATAGATTGTAGTAGTCA 57.177 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.