Multiple sequence alignment - TraesCS3B01G480700

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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 TraesCS3B01G480700 chr3B 100.000 2924 0 0 1 2924 728755015 728752092 0.000000e+00 5400
1 TraesCS3B01G480700 chr3B 83.603 1238 174 13 1005 2226 728890682 728889458 0.000000e+00 1134
2 TraesCS3B01G480700 chr3B 83.245 1128 132 28 1008 2100 728585803 728584698 0.000000e+00 983
3 TraesCS3B01G480700 chr3B 81.818 1144 167 22 1005 2112 727786563 727787701 0.000000e+00 922
4 TraesCS3B01G480700 chr3B 79.293 1357 186 49 1112 2414 605912628 605911313 0.000000e+00 861
5 TraesCS3B01G480700 chr3B 80.548 365 56 8 2464 2813 728889217 728888853 1.730000e-67 267
6 TraesCS3B01G480700 chr3B 78.947 380 51 20 2462 2818 728509372 728508999 6.300000e-57 231
7 TraesCS3B01G480700 chr3B 75.000 400 71 24 2435 2818 727742052 727742438 1.080000e-34 158
8 TraesCS3B01G480700 chr3B 98.305 59 1 0 2377 2435 728752578 728752636 1.430000e-18 104
9 TraesCS3B01G480700 chr3D 90.425 2214 159 17 226 2414 549127955 549125770 0.000000e+00 2865
10 TraesCS3B01G480700 chr3D 81.476 1301 171 40 1007 2281 549061921 549060665 0.000000e+00 1003
11 TraesCS3B01G480700 chr3D 81.187 1297 191 28 1005 2283 549349765 549348504 0.000000e+00 994
12 TraesCS3B01G480700 chr3D 83.287 1089 158 10 1012 2090 549467961 549466887 0.000000e+00 981
13 TraesCS3B01G480700 chr3D 80.997 1284 175 38 1005 2238 548725595 548726859 0.000000e+00 955
14 TraesCS3B01G480700 chr3D 81.970 1137 154 25 1008 2112 549074036 549072919 0.000000e+00 917
15 TraesCS3B01G480700 chr3D 89.679 436 17 8 2435 2846 549125778 549125347 5.550000e-147 531
16 TraesCS3B01G480700 chr3D 79.474 380 48 21 2462 2818 549060519 549060147 2.910000e-60 243
17 TraesCS3B01G480700 chr3D 77.570 321 54 15 2435 2744 548713320 548713633 8.330000e-41 178
18 TraesCS3B01G480700 chr3D 75.907 386 67 21 2435 2805 548695790 548696164 1.080000e-39 174
19 TraesCS3B01G480700 chr3D 78.652 267 46 8 2447 2702 549463828 549463562 1.800000e-37 167
20 TraesCS3B01G480700 chr3A 88.232 1572 142 26 868 2414 686617527 686615974 0.000000e+00 1838
21 TraesCS3B01G480700 chr3A 83.225 1234 174 23 1010 2226 686749804 686748587 0.000000e+00 1101
22 TraesCS3B01G480700 chr3A 80.274 1460 196 43 1007 2414 601133921 601132502 0.000000e+00 1016
23 TraesCS3B01G480700 chr3A 81.274 1303 175 39 1004 2283 686539218 686537962 0.000000e+00 990
24 TraesCS3B01G480700 chr3A 80.814 1277 185 35 1005 2235 686189757 686191019 0.000000e+00 946
25 TraesCS3B01G480700 chr3A 87.472 439 24 9 2435 2846 686615982 686615548 7.330000e-131 477
26 TraesCS3B01G480700 chr3A 79.262 569 85 16 1732 2283 686549887 686549335 1.660000e-97 366
27 TraesCS3B01G480700 chr3A 79.747 395 57 20 2435 2813 686748359 686747972 6.210000e-67 265
28 TraesCS3B01G480700 chr3A 77.160 324 51 21 2435 2744 686184530 686184844 1.800000e-37 167
29 TraesCS3B01G480700 chr3A 89.691 97 8 2 2822 2918 574452998 574452904 3.960000e-24 122
30 TraesCS3B01G480700 chr7B 84.032 1240 168 16 1005 2226 543187030 543188257 0.000000e+00 1166
31 TraesCS3B01G480700 chr7B 78.421 570 111 7 233 795 585881595 585881031 7.700000e-96 361
32 TraesCS3B01G480700 chr7B 77.365 539 107 12 240 767 704696303 704695769 3.660000e-79 305
33 TraesCS3B01G480700 chr7B 76.252 539 113 12 240 767 663194545 663194011 3.710000e-69 272
34 TraesCS3B01G480700 chr7B 76.067 539 114 12 240 767 428933918 428934452 1.730000e-67 267
35 TraesCS3B01G480700 chr2A 82.394 568 81 10 233 787 486281833 486282394 7.330000e-131 477
36 TraesCS3B01G480700 chr6D 78.821 543 106 5 233 767 102220384 102219843 9.970000e-95 357
37 TraesCS3B01G480700 chr1B 95.305 213 9 1 22 234 563941393 563941182 1.300000e-88 337
38 TraesCS3B01G480700 chr1B 76.446 484 102 7 240 714 666808997 666808517 4.840000e-63 252
39 TraesCS3B01G480700 chr4B 77.737 539 105 12 240 767 647595525 647596059 1.690000e-82 316
40 TraesCS3B01G480700 chr4B 77.162 451 91 9 326 767 444107510 444107063 4.840000e-63 252
41 TraesCS3B01G480700 chr2B 77.593 540 104 14 240 767 768546466 768547000 7.870000e-81 311
42 TraesCS3B01G480700 chr2B 86.667 210 25 3 24 233 214295937 214296143 2.270000e-56 230
43 TraesCS3B01G480700 chr2B 88.571 105 10 2 2821 2923 7641710 7641606 3.060000e-25 126
44 TraesCS3B01G480700 chr2B 93.846 65 4 0 254 318 764871817 764871753 6.670000e-17 99
45 TraesCS3B01G480700 chr5B 83.912 317 38 8 479 788 418925316 418925006 1.030000e-74 291
46 TraesCS3B01G480700 chr5B 85.217 115 13 3 2808 2922 419761942 419761832 6.620000e-22 115
47 TraesCS3B01G480700 chr5A 94.186 86 5 0 2822 2907 280154614 280154699 6.580000e-27 132
48 TraesCS3B01G480700 chr2D 92.222 90 7 0 2817 2906 201441564 201441653 8.510000e-26 128
49 TraesCS3B01G480700 chr2D 91.398 93 7 1 2822 2914 603651252 603651343 3.060000e-25 126
50 TraesCS3B01G480700 chr6B 93.023 86 5 1 2822 2907 374144308 374144392 1.100000e-24 124
51 TraesCS3B01G480700 chr4A 90.526 95 8 1 2822 2915 241152939 241153033 1.100000e-24 124
52 TraesCS3B01G480700 chr7D 88.776 98 10 1 2819 2915 361747032 361747129 5.120000e-23 119


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 TraesCS3B01G480700 chr3B 728752092 728755015 2923 True 5400.0 5400 100.0000 1 2924 1 chr3B.!!$R4 2923
1 TraesCS3B01G480700 chr3B 728584698 728585803 1105 True 983.0 983 83.2450 1008 2100 1 chr3B.!!$R3 1092
2 TraesCS3B01G480700 chr3B 727786563 727787701 1138 False 922.0 922 81.8180 1005 2112 1 chr3B.!!$F2 1107
3 TraesCS3B01G480700 chr3B 605911313 605912628 1315 True 861.0 861 79.2930 1112 2414 1 chr3B.!!$R1 1302
4 TraesCS3B01G480700 chr3B 728888853 728890682 1829 True 700.5 1134 82.0755 1005 2813 2 chr3B.!!$R5 1808
5 TraesCS3B01G480700 chr3D 549125347 549127955 2608 True 1698.0 2865 90.0520 226 2846 2 chr3D.!!$R4 2620
6 TraesCS3B01G480700 chr3D 549348504 549349765 1261 True 994.0 994 81.1870 1005 2283 1 chr3D.!!$R2 1278
7 TraesCS3B01G480700 chr3D 548725595 548726859 1264 False 955.0 955 80.9970 1005 2238 1 chr3D.!!$F3 1233
8 TraesCS3B01G480700 chr3D 549072919 549074036 1117 True 917.0 917 81.9700 1008 2112 1 chr3D.!!$R1 1104
9 TraesCS3B01G480700 chr3D 549060147 549061921 1774 True 623.0 1003 80.4750 1007 2818 2 chr3D.!!$R3 1811
10 TraesCS3B01G480700 chr3D 549463562 549467961 4399 True 574.0 981 80.9695 1012 2702 2 chr3D.!!$R5 1690
11 TraesCS3B01G480700 chr3A 686615548 686617527 1979 True 1157.5 1838 87.8520 868 2846 2 chr3A.!!$R5 1978
12 TraesCS3B01G480700 chr3A 601132502 601133921 1419 True 1016.0 1016 80.2740 1007 2414 1 chr3A.!!$R2 1407
13 TraesCS3B01G480700 chr3A 686537962 686539218 1256 True 990.0 990 81.2740 1004 2283 1 chr3A.!!$R3 1279
14 TraesCS3B01G480700 chr3A 686189757 686191019 1262 False 946.0 946 80.8140 1005 2235 1 chr3A.!!$F2 1230
15 TraesCS3B01G480700 chr3A 686747972 686749804 1832 True 683.0 1101 81.4860 1010 2813 2 chr3A.!!$R6 1803
16 TraesCS3B01G480700 chr3A 686549335 686549887 552 True 366.0 366 79.2620 1732 2283 1 chr3A.!!$R4 551
17 TraesCS3B01G480700 chr7B 543187030 543188257 1227 False 1166.0 1166 84.0320 1005 2226 1 chr7B.!!$F2 1221
18 TraesCS3B01G480700 chr7B 585881031 585881595 564 True 361.0 361 78.4210 233 795 1 chr7B.!!$R1 562
19 TraesCS3B01G480700 chr7B 704695769 704696303 534 True 305.0 305 77.3650 240 767 1 chr7B.!!$R3 527
20 TraesCS3B01G480700 chr7B 663194011 663194545 534 True 272.0 272 76.2520 240 767 1 chr7B.!!$R2 527
21 TraesCS3B01G480700 chr7B 428933918 428934452 534 False 267.0 267 76.0670 240 767 1 chr7B.!!$F1 527
22 TraesCS3B01G480700 chr2A 486281833 486282394 561 False 477.0 477 82.3940 233 787 1 chr2A.!!$F1 554
23 TraesCS3B01G480700 chr6D 102219843 102220384 541 True 357.0 357 78.8210 233 767 1 chr6D.!!$R1 534
24 TraesCS3B01G480700 chr4B 647595525 647596059 534 False 316.0 316 77.7370 240 767 1 chr4B.!!$F1 527
25 TraesCS3B01G480700 chr2B 768546466 768547000 534 False 311.0 311 77.5930 240 767 1 chr2B.!!$F2 527

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
22 23 0.104304 ACACGTCTCAGGGTGACAAC 59.896 55.0 4.07 0.0 37.58 3.32 F
211 212 0.322098 CACCATACCTTCCCGCAACA 60.322 55.0 0.00 0.0 0.00 3.33 F
662 682 0.400213 AAGGTCGCCCATGAACTTGA 59.600 50.0 0.00 0.0 44.04 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1492 0.108615 CTCGAACGACATCCTTGGCT 60.109 55.0 0.00 0.0 0.0 4.75 R
1548 1581 0.248661 CGCCGGTGTCTGATGAGTAG 60.249 60.0 6.91 0.0 0.0 2.57 R
2423 5285 0.250467 CAGTTGTACCCTGCTGTGCT 60.250 55.0 0.00 0.0 0.0 4.40 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
20 21 4.270482 ACACGTCTCAGGGTGACA 57.730 55.556 4.07 0.00 37.58 3.58
21 22 2.511818 ACACGTCTCAGGGTGACAA 58.488 52.632 4.07 0.00 37.58 3.18
22 23 0.104304 ACACGTCTCAGGGTGACAAC 59.896 55.000 4.07 0.00 37.58 3.32
23 24 0.600255 CACGTCTCAGGGTGACAACC 60.600 60.000 0.00 0.00 46.81 3.77
33 34 1.832883 GGTGACAACCCATATGTGCA 58.167 50.000 1.24 0.00 41.04 4.57
34 35 1.745087 GGTGACAACCCATATGTGCAG 59.255 52.381 1.24 0.00 41.04 4.41
35 36 2.617788 GGTGACAACCCATATGTGCAGA 60.618 50.000 1.24 0.00 41.04 4.26
36 37 3.081061 GTGACAACCCATATGTGCAGAA 58.919 45.455 1.24 0.00 0.00 3.02
37 38 3.081061 TGACAACCCATATGTGCAGAAC 58.919 45.455 1.24 0.00 0.00 3.01
38 39 3.244875 TGACAACCCATATGTGCAGAACT 60.245 43.478 1.24 0.00 0.00 3.01
39 40 3.347216 ACAACCCATATGTGCAGAACTC 58.653 45.455 1.24 0.00 0.00 3.01
40 41 3.244875 ACAACCCATATGTGCAGAACTCA 60.245 43.478 1.24 0.00 0.00 3.41
41 42 2.991250 ACCCATATGTGCAGAACTCAC 58.009 47.619 1.24 0.00 35.14 3.51
42 43 2.305635 ACCCATATGTGCAGAACTCACA 59.694 45.455 1.24 0.00 46.86 3.58
47 48 2.618442 TGTGCAGAACTCACATGTGA 57.382 45.000 26.33 26.33 39.29 3.58
58 59 3.198409 TCACATGTGAGTTTCAGTGCT 57.802 42.857 24.56 0.00 34.14 4.40
59 60 4.335400 TCACATGTGAGTTTCAGTGCTA 57.665 40.909 24.56 0.00 34.14 3.49
60 61 4.058124 TCACATGTGAGTTTCAGTGCTAC 58.942 43.478 24.56 0.00 34.14 3.58
61 62 3.059884 ACATGTGAGTTTCAGTGCTACG 58.940 45.455 0.00 0.00 0.00 3.51
62 63 2.882927 TGTGAGTTTCAGTGCTACGT 57.117 45.000 0.00 0.00 0.00 3.57
63 64 2.739292 TGTGAGTTTCAGTGCTACGTC 58.261 47.619 0.00 0.00 0.00 4.34
64 65 2.361119 TGTGAGTTTCAGTGCTACGTCT 59.639 45.455 0.00 0.00 0.00 4.18
65 66 3.181479 TGTGAGTTTCAGTGCTACGTCTT 60.181 43.478 0.00 0.00 0.00 3.01
66 67 4.037089 TGTGAGTTTCAGTGCTACGTCTTA 59.963 41.667 0.00 0.00 0.00 2.10
67 68 4.617645 GTGAGTTTCAGTGCTACGTCTTAG 59.382 45.833 0.00 0.00 0.00 2.18
68 69 4.167268 GAGTTTCAGTGCTACGTCTTAGG 58.833 47.826 0.00 0.00 0.00 2.69
69 70 3.573110 AGTTTCAGTGCTACGTCTTAGGT 59.427 43.478 0.00 0.00 0.00 3.08
70 71 4.038883 AGTTTCAGTGCTACGTCTTAGGTT 59.961 41.667 0.00 0.00 0.00 3.50
71 72 4.595762 TTCAGTGCTACGTCTTAGGTTT 57.404 40.909 0.00 0.00 0.00 3.27
72 73 5.710513 TTCAGTGCTACGTCTTAGGTTTA 57.289 39.130 0.00 0.00 0.00 2.01
73 74 5.306532 TCAGTGCTACGTCTTAGGTTTAG 57.693 43.478 0.00 0.00 0.00 1.85
74 75 4.763793 TCAGTGCTACGTCTTAGGTTTAGT 59.236 41.667 0.00 0.00 0.00 2.24
75 76 5.242393 TCAGTGCTACGTCTTAGGTTTAGTT 59.758 40.000 0.00 0.00 0.00 2.24
76 77 5.924825 CAGTGCTACGTCTTAGGTTTAGTTT 59.075 40.000 0.00 0.00 0.00 2.66
77 78 6.089150 CAGTGCTACGTCTTAGGTTTAGTTTC 59.911 42.308 0.00 0.00 0.00 2.78
78 79 6.015603 AGTGCTACGTCTTAGGTTTAGTTTCT 60.016 38.462 0.00 0.00 0.00 2.52
79 80 6.644181 GTGCTACGTCTTAGGTTTAGTTTCTT 59.356 38.462 0.00 0.00 0.00 2.52
80 81 6.643770 TGCTACGTCTTAGGTTTAGTTTCTTG 59.356 38.462 0.00 0.00 0.00 3.02
81 82 6.865205 GCTACGTCTTAGGTTTAGTTTCTTGA 59.135 38.462 0.00 0.00 0.00 3.02
82 83 7.544915 GCTACGTCTTAGGTTTAGTTTCTTGAT 59.455 37.037 0.00 0.00 0.00 2.57
83 84 7.886405 ACGTCTTAGGTTTAGTTTCTTGATC 57.114 36.000 0.00 0.00 0.00 2.92
84 85 7.439381 ACGTCTTAGGTTTAGTTTCTTGATCA 58.561 34.615 0.00 0.00 0.00 2.92
85 86 7.384387 ACGTCTTAGGTTTAGTTTCTTGATCAC 59.616 37.037 0.00 0.00 0.00 3.06
86 87 7.384115 CGTCTTAGGTTTAGTTTCTTGATCACA 59.616 37.037 0.00 0.00 0.00 3.58
87 88 9.052759 GTCTTAGGTTTAGTTTCTTGATCACAA 57.947 33.333 0.00 0.00 34.65 3.33
88 89 9.621629 TCTTAGGTTTAGTTTCTTGATCACAAA 57.378 29.630 0.00 0.00 35.49 2.83
167 168 7.572523 TCATCCTAAAGCTAAATTCATGTGG 57.427 36.000 0.00 0.00 0.00 4.17
168 169 5.835113 TCCTAAAGCTAAATTCATGTGGC 57.165 39.130 0.00 0.00 0.00 5.01
169 170 5.260424 TCCTAAAGCTAAATTCATGTGGCA 58.740 37.500 0.00 0.00 0.00 4.92
170 171 5.893255 TCCTAAAGCTAAATTCATGTGGCAT 59.107 36.000 0.00 0.00 0.00 4.40
171 172 6.039717 TCCTAAAGCTAAATTCATGTGGCATC 59.960 38.462 0.00 0.00 0.00 3.91
172 173 5.664294 AAAGCTAAATTCATGTGGCATCA 57.336 34.783 0.00 0.00 0.00 3.07
173 174 4.644103 AGCTAAATTCATGTGGCATCAC 57.356 40.909 0.00 0.00 43.87 3.06
183 184 1.668419 GTGGCATCACATAGTGGACC 58.332 55.000 0.00 0.00 43.13 4.46
184 185 1.210478 GTGGCATCACATAGTGGACCT 59.790 52.381 0.00 0.00 43.13 3.85
185 186 1.915489 TGGCATCACATAGTGGACCTT 59.085 47.619 0.00 0.00 33.87 3.50
186 187 2.308570 TGGCATCACATAGTGGACCTTT 59.691 45.455 0.00 0.00 33.87 3.11
187 188 2.945668 GGCATCACATAGTGGACCTTTC 59.054 50.000 0.00 0.00 33.87 2.62
188 189 3.370953 GGCATCACATAGTGGACCTTTCT 60.371 47.826 0.00 0.00 33.87 2.52
189 190 4.265073 GCATCACATAGTGGACCTTTCTT 58.735 43.478 0.00 0.00 33.87 2.52
190 191 4.702131 GCATCACATAGTGGACCTTTCTTT 59.298 41.667 0.00 0.00 33.87 2.52
191 192 5.880332 GCATCACATAGTGGACCTTTCTTTA 59.120 40.000 0.00 0.00 33.87 1.85
192 193 6.183360 GCATCACATAGTGGACCTTTCTTTAC 60.183 42.308 0.00 0.00 33.87 2.01
193 194 6.428083 TCACATAGTGGACCTTTCTTTACA 57.572 37.500 0.00 0.00 33.87 2.41
194 195 6.228258 TCACATAGTGGACCTTTCTTTACAC 58.772 40.000 0.00 0.00 33.87 2.90
195 196 5.411669 CACATAGTGGACCTTTCTTTACACC 59.588 44.000 0.00 0.00 0.00 4.16
196 197 5.072600 ACATAGTGGACCTTTCTTTACACCA 59.927 40.000 0.00 0.00 0.00 4.17
197 198 4.724279 AGTGGACCTTTCTTTACACCAT 57.276 40.909 0.00 0.00 0.00 3.55
198 199 5.836024 AGTGGACCTTTCTTTACACCATA 57.164 39.130 0.00 0.00 0.00 2.74
199 200 5.557866 AGTGGACCTTTCTTTACACCATAC 58.442 41.667 0.00 0.00 0.00 2.39
200 201 4.698780 GTGGACCTTTCTTTACACCATACC 59.301 45.833 0.00 0.00 0.00 2.73
201 202 4.600111 TGGACCTTTCTTTACACCATACCT 59.400 41.667 0.00 0.00 0.00 3.08
202 203 5.073965 TGGACCTTTCTTTACACCATACCTT 59.926 40.000 0.00 0.00 0.00 3.50
203 204 5.646793 GGACCTTTCTTTACACCATACCTTC 59.353 44.000 0.00 0.00 0.00 3.46
204 205 5.567430 ACCTTTCTTTACACCATACCTTCC 58.433 41.667 0.00 0.00 0.00 3.46
205 206 4.948004 CCTTTCTTTACACCATACCTTCCC 59.052 45.833 0.00 0.00 0.00 3.97
206 207 3.899052 TCTTTACACCATACCTTCCCG 57.101 47.619 0.00 0.00 0.00 5.14
207 208 2.093341 TCTTTACACCATACCTTCCCGC 60.093 50.000 0.00 0.00 0.00 6.13
208 209 1.277579 TTACACCATACCTTCCCGCA 58.722 50.000 0.00 0.00 0.00 5.69
209 210 1.277579 TACACCATACCTTCCCGCAA 58.722 50.000 0.00 0.00 0.00 4.85
210 211 0.322187 ACACCATACCTTCCCGCAAC 60.322 55.000 0.00 0.00 0.00 4.17
211 212 0.322098 CACCATACCTTCCCGCAACA 60.322 55.000 0.00 0.00 0.00 3.33
212 213 0.402504 ACCATACCTTCCCGCAACAA 59.597 50.000 0.00 0.00 0.00 2.83
213 214 1.005450 ACCATACCTTCCCGCAACAAT 59.995 47.619 0.00 0.00 0.00 2.71
214 215 1.405105 CCATACCTTCCCGCAACAATG 59.595 52.381 0.00 0.00 0.00 2.82
223 224 2.560861 GCAACAATGCGCGGAGAA 59.439 55.556 8.83 0.00 43.83 2.87
224 225 1.137404 GCAACAATGCGCGGAGAAT 59.863 52.632 8.83 0.00 43.83 2.40
229 230 1.224075 CAATGCGCGGAGAATCATCT 58.776 50.000 8.83 0.00 39.10 2.90
231 232 2.360553 ATGCGCGGAGAATCATCTAG 57.639 50.000 8.83 0.00 35.54 2.43
236 237 4.049186 GCGCGGAGAATCATCTAGTTTTA 58.951 43.478 8.83 0.00 35.54 1.52
252 253 5.184892 AGTTTTATCAATGCTCAGTCCCT 57.815 39.130 0.00 0.00 0.00 4.20
361 363 0.969917 TAGGGTAACAACGGGCGCTA 60.970 55.000 7.64 0.00 39.74 4.26
386 388 6.625873 ACTCAGAGATGACAAAGAAAAACC 57.374 37.500 3.79 0.00 0.00 3.27
394 396 4.138290 TGACAAAGAAAAACCCATCGCTA 58.862 39.130 0.00 0.00 0.00 4.26
421 423 6.723515 TGGAAATTGGAAGATTGATTGGTGTA 59.276 34.615 0.00 0.00 0.00 2.90
445 447 2.855963 GACGTTCTGACAGTTGAAACGA 59.144 45.455 25.19 0.00 0.00 3.85
455 457 4.385825 ACAGTTGAAACGATGGCTCTAAA 58.614 39.130 0.00 0.00 0.00 1.85
475 477 7.765307 TCTAAAATTTGGCTTATCTCTTGCAG 58.235 34.615 0.00 0.00 0.00 4.41
509 512 6.410914 GGTTGCAATCGTCTTGTTATTAATCG 59.589 38.462 0.59 0.00 0.00 3.34
553 561 3.293337 CAATGAAGAATGGAGGATGGCA 58.707 45.455 0.00 0.00 0.00 4.92
579 594 2.950673 CAGCGGCGGCAGTTTTTA 59.049 55.556 19.21 0.00 43.41 1.52
662 682 0.400213 AAGGTCGCCCATGAACTTGA 59.600 50.000 0.00 0.00 44.04 3.02
861 881 6.469782 TTCTTAGGTTATAAATCGACCGGT 57.530 37.500 6.92 6.92 38.48 5.28
966 987 1.303317 ACCAAATCACCGACCTGCC 60.303 57.895 0.00 0.00 0.00 4.85
974 995 0.899720 CACCGACCTGCCCTACTAAA 59.100 55.000 0.00 0.00 0.00 1.85
1207 1236 2.158449 GGCTTCTTCATCGACAACTGTG 59.842 50.000 0.00 0.00 0.00 3.66
1489 1519 3.130516 AGGATGTCGTTCGAGCTATTTCA 59.869 43.478 0.00 0.00 0.00 2.69
1521 1554 0.833287 TAGCCCTTGACAGATGGAGC 59.167 55.000 0.00 0.00 0.00 4.70
1530 1563 2.432146 TGACAGATGGAGCACTCATACC 59.568 50.000 0.00 0.00 0.00 2.73
1538 1571 3.327757 TGGAGCACTCATACCAGAGTTTT 59.672 43.478 0.00 0.00 46.26 2.43
1548 1581 0.449388 CCAGAGTTTTCGCATGCCTC 59.551 55.000 13.15 12.24 0.00 4.70
1587 1620 1.202110 GCATGGAGCAACATCAACTCG 60.202 52.381 0.00 0.00 44.79 4.18
1827 1899 5.075858 TCTCACAATTTCATGGCCAATTC 57.924 39.130 10.96 0.00 0.00 2.17
1978 2060 5.485620 TGTACGAACAGCTTCTAGAGTCTA 58.514 41.667 0.00 0.00 0.00 2.59
1986 2068 4.037446 CAGCTTCTAGAGTCTACATGGTCC 59.963 50.000 0.00 0.00 0.00 4.46
2195 4994 8.241367 TGATCATTGAAGTTCAAATCACATCAG 58.759 33.333 21.57 4.73 40.12 2.90
2262 5081 5.820404 ACTAGTACTTAAGGCCACTGTTT 57.180 39.130 5.01 0.00 0.00 2.83
2287 5107 4.937201 TTCTGTAGGTCATATGCGTCAT 57.063 40.909 0.00 0.00 0.00 3.06
2288 5108 6.399639 TTTCTGTAGGTCATATGCGTCATA 57.600 37.500 0.00 2.73 0.00 2.15
2289 5109 6.590234 TTCTGTAGGTCATATGCGTCATAT 57.410 37.500 0.00 6.54 37.51 1.78
2294 5114 3.262420 GGTCATATGCGTCATATGTCCC 58.738 50.000 26.31 23.33 46.77 4.46
2295 5115 3.055819 GGTCATATGCGTCATATGTCCCT 60.056 47.826 26.31 4.70 46.77 4.20
2296 5116 4.159693 GGTCATATGCGTCATATGTCCCTA 59.840 45.833 26.31 14.00 46.77 3.53
2368 5230 6.552859 TCAATGCAATAGTTTTTCTCACGA 57.447 33.333 0.00 0.00 0.00 4.35
2377 5239 3.118371 AGTTTTTCTCACGAGTGGAAGGT 60.118 43.478 3.19 0.00 0.00 3.50
2426 5288 7.473027 GTTGTACAACTGAACTAACTAAGCA 57.527 36.000 27.69 0.00 38.25 3.91
2427 5289 7.342942 GTTGTACAACTGAACTAACTAAGCAC 58.657 38.462 27.69 0.00 38.25 4.40
2428 5290 6.575267 TGTACAACTGAACTAACTAAGCACA 58.425 36.000 0.00 0.00 0.00 4.57
2429 5291 6.700081 TGTACAACTGAACTAACTAAGCACAG 59.300 38.462 0.00 0.00 37.55 3.66
2430 5292 4.511826 ACAACTGAACTAACTAAGCACAGC 59.488 41.667 0.00 0.00 36.04 4.40
2431 5293 4.336889 ACTGAACTAACTAAGCACAGCA 57.663 40.909 0.00 0.00 36.04 4.41
2432 5294 4.310769 ACTGAACTAACTAAGCACAGCAG 58.689 43.478 0.00 0.00 36.04 4.24
2433 5295 3.664107 TGAACTAACTAAGCACAGCAGG 58.336 45.455 0.00 0.00 0.00 4.85
2434 5296 2.770164 ACTAACTAAGCACAGCAGGG 57.230 50.000 0.00 0.00 0.00 4.45
2435 5297 1.978580 ACTAACTAAGCACAGCAGGGT 59.021 47.619 0.00 0.00 0.00 4.34
2436 5298 3.170717 ACTAACTAAGCACAGCAGGGTA 58.829 45.455 0.00 0.00 0.00 3.69
2437 5299 2.474410 AACTAAGCACAGCAGGGTAC 57.526 50.000 0.00 0.00 0.00 3.34
2438 5300 1.348064 ACTAAGCACAGCAGGGTACA 58.652 50.000 0.00 0.00 0.00 2.90
2439 5301 1.697432 ACTAAGCACAGCAGGGTACAA 59.303 47.619 0.00 0.00 0.00 2.41
2440 5302 2.076863 CTAAGCACAGCAGGGTACAAC 58.923 52.381 0.00 0.00 0.00 3.32
2441 5303 0.474184 AAGCACAGCAGGGTACAACT 59.526 50.000 0.00 0.00 0.00 3.16
2442 5304 0.250467 AGCACAGCAGGGTACAACTG 60.250 55.000 11.29 11.29 38.95 3.16
2443 5305 1.237285 GCACAGCAGGGTACAACTGG 61.237 60.000 15.81 5.59 36.48 4.00
2444 5306 0.396435 CACAGCAGGGTACAACTGGA 59.604 55.000 15.81 0.00 36.48 3.86
2510 5375 5.519722 AGTTTCGGCATGTCTTACTTTTTG 58.480 37.500 0.00 0.00 0.00 2.44
2557 5422 9.658799 TTGAGTTTACTGAAGATGATTTCTAGG 57.341 33.333 0.00 0.00 33.05 3.02
2833 5735 4.317488 CACTAGATAGTACTCCCTCCGTC 58.683 52.174 0.00 0.00 34.13 4.79
2835 5737 2.133520 AGATAGTACTCCCTCCGTCCA 58.866 52.381 0.00 0.00 0.00 4.02
2836 5738 2.512896 AGATAGTACTCCCTCCGTCCAA 59.487 50.000 0.00 0.00 0.00 3.53
2846 5748 5.427481 ACTCCCTCCGTCCAAAAATATAAGA 59.573 40.000 0.00 0.00 0.00 2.10
2847 5749 6.069847 ACTCCCTCCGTCCAAAAATATAAGAA 60.070 38.462 0.00 0.00 0.00 2.52
2848 5750 6.117488 TCCCTCCGTCCAAAAATATAAGAAC 58.883 40.000 0.00 0.00 0.00 3.01
2849 5751 5.007332 CCCTCCGTCCAAAAATATAAGAACG 59.993 44.000 0.00 0.00 0.00 3.95
2850 5752 5.583457 CCTCCGTCCAAAAATATAAGAACGT 59.417 40.000 0.00 0.00 0.00 3.99
2851 5753 6.757947 CCTCCGTCCAAAAATATAAGAACGTA 59.242 38.462 0.00 0.00 0.00 3.57
2852 5754 7.440255 CCTCCGTCCAAAAATATAAGAACGTAT 59.560 37.037 0.00 0.00 0.00 3.06
2853 5755 8.721019 TCCGTCCAAAAATATAAGAACGTATT 57.279 30.769 0.00 0.00 0.00 1.89
2854 5756 9.165035 TCCGTCCAAAAATATAAGAACGTATTT 57.835 29.630 0.00 0.00 33.24 1.40
2855 5757 9.777575 CCGTCCAAAAATATAAGAACGTATTTT 57.222 29.630 0.00 0.00 40.39 1.82
2882 5784 9.485206 ACACTAGTATAATGTCAAAAACGTTCT 57.515 29.630 0.00 0.00 38.14 3.01
2894 5796 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
2895 5797 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
2914 5816 7.451731 TGGGACAGATGGAGTAGATAATTTT 57.548 36.000 0.00 0.00 0.00 1.82
2915 5817 7.282585 TGGGACAGATGGAGTAGATAATTTTG 58.717 38.462 0.00 0.00 0.00 2.44
2916 5818 7.092444 TGGGACAGATGGAGTAGATAATTTTGT 60.092 37.037 0.00 0.00 0.00 2.83
2917 5819 7.775561 GGGACAGATGGAGTAGATAATTTTGTT 59.224 37.037 0.00 0.00 0.00 2.83
2918 5820 8.831550 GGACAGATGGAGTAGATAATTTTGTTC 58.168 37.037 0.00 0.00 0.00 3.18
2919 5821 9.383519 GACAGATGGAGTAGATAATTTTGTTCA 57.616 33.333 0.00 0.00 0.00 3.18
2920 5822 9.911788 ACAGATGGAGTAGATAATTTTGTTCAT 57.088 29.630 0.00 0.00 0.00 2.57
2922 5824 9.911788 AGATGGAGTAGATAATTTTGTTCATGT 57.088 29.630 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.131067 TCACCCTGAGACGTGTGCA 61.131 57.895 0.00 0.00 0.00 4.57
1 2 1.664965 GTCACCCTGAGACGTGTGC 60.665 63.158 0.00 0.00 0.00 4.57
2 3 0.104120 TTGTCACCCTGAGACGTGTG 59.896 55.000 0.00 0.00 38.83 3.82
3 4 0.104304 GTTGTCACCCTGAGACGTGT 59.896 55.000 0.00 0.00 38.83 4.49
4 5 0.600255 GGTTGTCACCCTGAGACGTG 60.600 60.000 0.00 0.00 38.83 4.49
5 6 1.746517 GGTTGTCACCCTGAGACGT 59.253 57.895 0.00 0.00 38.83 4.34
6 7 4.675404 GGTTGTCACCCTGAGACG 57.325 61.111 0.00 0.00 38.83 4.18
14 15 1.745087 CTGCACATATGGGTTGTCACC 59.255 52.381 6.86 0.00 43.37 4.02
15 16 2.710377 TCTGCACATATGGGTTGTCAC 58.290 47.619 6.86 0.00 0.00 3.67
16 17 3.081061 GTTCTGCACATATGGGTTGTCA 58.919 45.455 6.86 0.00 0.00 3.58
17 18 3.347216 AGTTCTGCACATATGGGTTGTC 58.653 45.455 6.86 0.00 0.00 3.18
18 19 3.244875 TGAGTTCTGCACATATGGGTTGT 60.245 43.478 6.86 0.00 0.00 3.32
19 20 3.127548 GTGAGTTCTGCACATATGGGTTG 59.872 47.826 6.86 0.00 36.31 3.77
20 21 3.244875 TGTGAGTTCTGCACATATGGGTT 60.245 43.478 6.86 0.00 41.00 4.11
21 22 2.305635 TGTGAGTTCTGCACATATGGGT 59.694 45.455 6.86 0.00 41.00 4.51
22 23 2.989909 TGTGAGTTCTGCACATATGGG 58.010 47.619 7.80 3.61 41.00 4.00
38 39 3.198409 AGCACTGAAACTCACATGTGA 57.802 42.857 26.33 26.33 38.06 3.58
39 40 3.120889 CGTAGCACTGAAACTCACATGTG 60.121 47.826 20.18 20.18 0.00 3.21
40 41 3.059884 CGTAGCACTGAAACTCACATGT 58.940 45.455 0.00 0.00 0.00 3.21
41 42 3.059884 ACGTAGCACTGAAACTCACATG 58.940 45.455 0.00 0.00 0.00 3.21
42 43 3.005897 AGACGTAGCACTGAAACTCACAT 59.994 43.478 0.00 0.00 0.00 3.21
43 44 2.361119 AGACGTAGCACTGAAACTCACA 59.639 45.455 0.00 0.00 0.00 3.58
44 45 3.014604 AGACGTAGCACTGAAACTCAC 57.985 47.619 0.00 0.00 0.00 3.51
45 46 3.728076 AAGACGTAGCACTGAAACTCA 57.272 42.857 0.00 0.00 0.00 3.41
46 47 4.167268 CCTAAGACGTAGCACTGAAACTC 58.833 47.826 0.00 0.00 0.00 3.01
47 48 3.573110 ACCTAAGACGTAGCACTGAAACT 59.427 43.478 0.00 0.00 0.00 2.66
48 49 3.910648 ACCTAAGACGTAGCACTGAAAC 58.089 45.455 0.00 0.00 0.00 2.78
49 50 4.595762 AACCTAAGACGTAGCACTGAAA 57.404 40.909 0.00 0.00 0.00 2.69
50 51 4.595762 AAACCTAAGACGTAGCACTGAA 57.404 40.909 0.00 0.00 0.00 3.02
51 52 4.763793 ACTAAACCTAAGACGTAGCACTGA 59.236 41.667 0.00 0.00 0.00 3.41
52 53 5.056894 ACTAAACCTAAGACGTAGCACTG 57.943 43.478 0.00 0.00 0.00 3.66
53 54 5.718724 AACTAAACCTAAGACGTAGCACT 57.281 39.130 0.00 0.00 0.00 4.40
54 55 6.155136 AGAAACTAAACCTAAGACGTAGCAC 58.845 40.000 0.00 0.00 0.00 4.40
55 56 6.336842 AGAAACTAAACCTAAGACGTAGCA 57.663 37.500 0.00 0.00 0.00 3.49
56 57 6.865205 TCAAGAAACTAAACCTAAGACGTAGC 59.135 38.462 0.00 0.00 0.00 3.58
57 58 8.983307 ATCAAGAAACTAAACCTAAGACGTAG 57.017 34.615 0.00 0.00 0.00 3.51
58 59 8.579006 TGATCAAGAAACTAAACCTAAGACGTA 58.421 33.333 0.00 0.00 0.00 3.57
59 60 7.384387 GTGATCAAGAAACTAAACCTAAGACGT 59.616 37.037 0.00 0.00 0.00 4.34
60 61 7.384115 TGTGATCAAGAAACTAAACCTAAGACG 59.616 37.037 0.00 0.00 0.00 4.18
61 62 8.603242 TGTGATCAAGAAACTAAACCTAAGAC 57.397 34.615 0.00 0.00 0.00 3.01
62 63 9.621629 TTTGTGATCAAGAAACTAAACCTAAGA 57.378 29.630 0.00 0.00 34.88 2.10
141 142 8.469200 CCACATGAATTTAGCTTTAGGATGAAA 58.531 33.333 0.00 0.00 0.00 2.69
142 143 7.416664 GCCACATGAATTTAGCTTTAGGATGAA 60.417 37.037 0.00 0.00 0.00 2.57
143 144 6.039717 GCCACATGAATTTAGCTTTAGGATGA 59.960 38.462 0.00 0.00 0.00 2.92
144 145 6.183360 TGCCACATGAATTTAGCTTTAGGATG 60.183 38.462 0.00 0.00 0.00 3.51
145 146 5.893255 TGCCACATGAATTTAGCTTTAGGAT 59.107 36.000 0.00 0.00 0.00 3.24
146 147 5.260424 TGCCACATGAATTTAGCTTTAGGA 58.740 37.500 0.00 0.00 0.00 2.94
147 148 5.581126 TGCCACATGAATTTAGCTTTAGG 57.419 39.130 0.00 0.00 0.00 2.69
148 149 6.694411 GTGATGCCACATGAATTTAGCTTTAG 59.306 38.462 0.00 0.00 42.72 1.85
149 150 6.563422 GTGATGCCACATGAATTTAGCTTTA 58.437 36.000 0.00 0.00 42.72 1.85
150 151 5.413499 GTGATGCCACATGAATTTAGCTTT 58.587 37.500 0.00 0.00 42.72 3.51
151 152 5.002464 GTGATGCCACATGAATTTAGCTT 57.998 39.130 0.00 0.00 42.72 3.74
152 153 4.644103 GTGATGCCACATGAATTTAGCT 57.356 40.909 0.00 0.00 42.72 3.32
164 165 1.210478 AGGTCCACTATGTGATGCCAC 59.790 52.381 0.00 0.00 43.46 5.01
165 166 1.583556 AGGTCCACTATGTGATGCCA 58.416 50.000 0.00 0.00 35.23 4.92
166 167 2.717639 AAGGTCCACTATGTGATGCC 57.282 50.000 0.00 0.00 35.23 4.40
167 168 3.878778 AGAAAGGTCCACTATGTGATGC 58.121 45.455 0.00 0.00 35.23 3.91
168 169 6.878923 TGTAAAGAAAGGTCCACTATGTGATG 59.121 38.462 0.00 0.00 35.23 3.07
169 170 6.879458 GTGTAAAGAAAGGTCCACTATGTGAT 59.121 38.462 0.00 0.00 35.23 3.06
170 171 6.228258 GTGTAAAGAAAGGTCCACTATGTGA 58.772 40.000 0.00 0.00 35.23 3.58
171 172 5.411669 GGTGTAAAGAAAGGTCCACTATGTG 59.588 44.000 0.00 0.00 0.00 3.21
172 173 5.072600 TGGTGTAAAGAAAGGTCCACTATGT 59.927 40.000 0.00 0.00 0.00 2.29
173 174 5.556915 TGGTGTAAAGAAAGGTCCACTATG 58.443 41.667 0.00 0.00 0.00 2.23
174 175 5.836024 TGGTGTAAAGAAAGGTCCACTAT 57.164 39.130 0.00 0.00 0.00 2.12
175 176 5.836024 ATGGTGTAAAGAAAGGTCCACTA 57.164 39.130 0.00 0.00 0.00 2.74
176 177 4.724279 ATGGTGTAAAGAAAGGTCCACT 57.276 40.909 0.00 0.00 0.00 4.00
177 178 4.698780 GGTATGGTGTAAAGAAAGGTCCAC 59.301 45.833 0.00 0.00 0.00 4.02
178 179 4.600111 AGGTATGGTGTAAAGAAAGGTCCA 59.400 41.667 0.00 0.00 0.00 4.02
179 180 5.175388 AGGTATGGTGTAAAGAAAGGTCC 57.825 43.478 0.00 0.00 0.00 4.46
180 181 5.646793 GGAAGGTATGGTGTAAAGAAAGGTC 59.353 44.000 0.00 0.00 0.00 3.85
181 182 5.516062 GGGAAGGTATGGTGTAAAGAAAGGT 60.516 44.000 0.00 0.00 0.00 3.50
182 183 4.948004 GGGAAGGTATGGTGTAAAGAAAGG 59.052 45.833 0.00 0.00 0.00 3.11
183 184 4.634443 CGGGAAGGTATGGTGTAAAGAAAG 59.366 45.833 0.00 0.00 0.00 2.62
184 185 4.581868 CGGGAAGGTATGGTGTAAAGAAA 58.418 43.478 0.00 0.00 0.00 2.52
185 186 3.620472 GCGGGAAGGTATGGTGTAAAGAA 60.620 47.826 0.00 0.00 0.00 2.52
186 187 2.093341 GCGGGAAGGTATGGTGTAAAGA 60.093 50.000 0.00 0.00 0.00 2.52
187 188 2.285977 GCGGGAAGGTATGGTGTAAAG 58.714 52.381 0.00 0.00 0.00 1.85
188 189 1.629353 TGCGGGAAGGTATGGTGTAAA 59.371 47.619 0.00 0.00 0.00 2.01
189 190 1.277579 TGCGGGAAGGTATGGTGTAA 58.722 50.000 0.00 0.00 0.00 2.41
190 191 1.065998 GTTGCGGGAAGGTATGGTGTA 60.066 52.381 0.00 0.00 0.00 2.90
191 192 0.322187 GTTGCGGGAAGGTATGGTGT 60.322 55.000 0.00 0.00 0.00 4.16
192 193 0.322098 TGTTGCGGGAAGGTATGGTG 60.322 55.000 0.00 0.00 0.00 4.17
193 194 0.402504 TTGTTGCGGGAAGGTATGGT 59.597 50.000 0.00 0.00 0.00 3.55
194 195 1.405105 CATTGTTGCGGGAAGGTATGG 59.595 52.381 0.00 0.00 0.00 2.74
195 196 1.202290 GCATTGTTGCGGGAAGGTATG 60.202 52.381 0.00 0.00 39.49 2.39
196 197 1.102978 GCATTGTTGCGGGAAGGTAT 58.897 50.000 0.00 0.00 39.49 2.73
197 198 2.562125 GCATTGTTGCGGGAAGGTA 58.438 52.632 0.00 0.00 39.49 3.08
198 199 3.365535 GCATTGTTGCGGGAAGGT 58.634 55.556 0.00 0.00 39.49 3.50
206 207 0.863119 GATTCTCCGCGCATTGTTGC 60.863 55.000 8.75 0.00 45.78 4.17
207 208 0.447406 TGATTCTCCGCGCATTGTTG 59.553 50.000 8.75 0.00 0.00 3.33
208 209 1.331756 GATGATTCTCCGCGCATTGTT 59.668 47.619 8.75 0.00 0.00 2.83
209 210 0.940126 GATGATTCTCCGCGCATTGT 59.060 50.000 8.75 0.00 0.00 2.71
210 211 1.224075 AGATGATTCTCCGCGCATTG 58.776 50.000 8.75 0.00 0.00 2.82
211 212 2.036475 ACTAGATGATTCTCCGCGCATT 59.964 45.455 8.75 0.00 33.17 3.56
212 213 1.615883 ACTAGATGATTCTCCGCGCAT 59.384 47.619 8.75 0.00 33.17 4.73
213 214 1.032794 ACTAGATGATTCTCCGCGCA 58.967 50.000 8.75 0.00 33.17 6.09
214 215 2.141535 AACTAGATGATTCTCCGCGC 57.858 50.000 0.00 0.00 33.17 6.86
215 216 5.920840 TGATAAAACTAGATGATTCTCCGCG 59.079 40.000 0.00 0.00 33.17 6.46
216 217 7.715265 TTGATAAAACTAGATGATTCTCCGC 57.285 36.000 0.00 0.00 33.17 5.54
217 218 8.226448 GCATTGATAAAACTAGATGATTCTCCG 58.774 37.037 0.00 0.00 33.17 4.63
218 219 9.282569 AGCATTGATAAAACTAGATGATTCTCC 57.717 33.333 0.00 0.00 33.17 3.71
220 221 9.842775 TGAGCATTGATAAAACTAGATGATTCT 57.157 29.630 0.00 0.00 35.90 2.40
222 223 9.624373 ACTGAGCATTGATAAAACTAGATGATT 57.376 29.630 0.00 0.00 0.00 2.57
223 224 9.270640 GACTGAGCATTGATAAAACTAGATGAT 57.729 33.333 0.00 0.00 0.00 2.45
224 225 7.712639 GGACTGAGCATTGATAAAACTAGATGA 59.287 37.037 0.00 0.00 0.00 2.92
229 230 6.313519 AGGGACTGAGCATTGATAAAACTA 57.686 37.500 0.00 0.00 37.18 2.24
231 232 5.904362 AAGGGACTGAGCATTGATAAAAC 57.096 39.130 0.00 0.00 40.86 2.43
236 237 3.887716 GCATTAAGGGACTGAGCATTGAT 59.112 43.478 0.00 0.00 40.86 2.57
284 286 4.827284 ACTTGACAAAACCCATAGAAGGTG 59.173 41.667 0.00 0.00 37.78 4.00
289 291 8.472007 ACATTTAACTTGACAAAACCCATAGA 57.528 30.769 0.00 0.00 0.00 1.98
340 342 0.954938 GCGCCCGTTGTTACCCTAAA 60.955 55.000 0.00 0.00 0.00 1.85
361 363 7.391833 GGGTTTTTCTTTGTCATCTCTGAGTAT 59.608 37.037 4.32 0.00 30.18 2.12
394 396 7.107542 CACCAATCAATCTTCCAATTTCCATT 58.892 34.615 0.00 0.00 0.00 3.16
421 423 3.520290 TTCAACTGTCAGAACGTCAGT 57.480 42.857 6.91 1.27 44.51 3.41
437 439 6.155827 CCAAATTTTAGAGCCATCGTTTCAA 58.844 36.000 0.00 0.00 0.00 2.69
445 447 7.065504 AGAGATAAGCCAAATTTTAGAGCCAT 58.934 34.615 0.00 0.00 0.00 4.40
475 477 1.059942 CGATTGCAACCCGCTTTTTC 58.940 50.000 0.00 0.00 43.06 2.29
579 594 4.634443 ACAAGTCAAAAAGTAGCAGTCGTT 59.366 37.500 0.00 0.00 0.00 3.85
616 631 8.514330 TTCGCTTCCCTATTACAATGTTTTAT 57.486 30.769 0.00 0.00 0.00 1.40
662 682 4.873827 TCGCTGAAAATTTCGCTAACCTAT 59.126 37.500 15.99 0.00 0.00 2.57
698 718 0.469070 CTCATCCAAGGGCTCCTCAG 59.531 60.000 0.00 0.00 30.89 3.35
787 807 5.063180 TCGTCATAGGTGTTCGTATTTGT 57.937 39.130 0.00 0.00 0.00 2.83
788 808 6.583912 AATCGTCATAGGTGTTCGTATTTG 57.416 37.500 0.00 0.00 0.00 2.32
801 821 7.275779 CCCGGTCAATATCTTAAATCGTCATAG 59.724 40.741 0.00 0.00 0.00 2.23
807 827 4.389077 GCTCCCGGTCAATATCTTAAATCG 59.611 45.833 0.00 0.00 0.00 3.34
843 863 4.161001 AGTCAACCGGTCGATTTATAACCT 59.839 41.667 8.04 0.00 0.00 3.50
861 881 2.158579 GGGGGTTTGGTCAACTAGTCAA 60.159 50.000 0.00 0.00 35.46 3.18
932 953 1.232216 GGTCGGTAGGGATGAGGGA 59.768 63.158 0.00 0.00 0.00 4.20
933 954 0.689745 TTGGTCGGTAGGGATGAGGG 60.690 60.000 0.00 0.00 0.00 4.30
934 955 1.200519 TTTGGTCGGTAGGGATGAGG 58.799 55.000 0.00 0.00 0.00 3.86
935 956 2.434336 TGATTTGGTCGGTAGGGATGAG 59.566 50.000 0.00 0.00 0.00 2.90
936 957 2.169769 GTGATTTGGTCGGTAGGGATGA 59.830 50.000 0.00 0.00 0.00 2.92
937 958 2.561569 GTGATTTGGTCGGTAGGGATG 58.438 52.381 0.00 0.00 0.00 3.51
938 959 1.489230 GGTGATTTGGTCGGTAGGGAT 59.511 52.381 0.00 0.00 0.00 3.85
966 987 3.199946 TGCTCATTGGAGGGTTTAGTAGG 59.800 47.826 0.00 0.00 41.67 3.18
974 995 2.671070 CCGTGCTCATTGGAGGGT 59.329 61.111 0.00 0.00 41.67 4.34
1345 1374 1.677300 CCCACACAAATAGGCGGCA 60.677 57.895 13.08 0.00 0.00 5.69
1414 1444 2.143122 GAAGATGAACAACTGGTCGCA 58.857 47.619 0.00 0.00 33.57 5.10
1462 1492 0.108615 CTCGAACGACATCCTTGGCT 60.109 55.000 0.00 0.00 0.00 4.75
1521 1554 3.325870 TGCGAAAACTCTGGTATGAGTG 58.674 45.455 0.00 0.00 45.49 3.51
1530 1563 1.446907 AGAGGCATGCGAAAACTCTG 58.553 50.000 18.87 0.00 37.16 3.35
1538 1571 1.339291 CTGATGAGTAGAGGCATGCGA 59.661 52.381 12.44 0.00 0.00 5.10
1548 1581 0.248661 CGCCGGTGTCTGATGAGTAG 60.249 60.000 6.91 0.00 0.00 2.57
1713 1770 2.745379 TGGCAGCTCTGTCACAGTA 58.255 52.632 4.28 0.00 40.71 2.74
1827 1899 3.033184 AGAATCAGGCTCTCTCTTCCAG 58.967 50.000 0.00 0.00 0.00 3.86
1978 2060 1.956869 TGACTGGAGATGGACCATGT 58.043 50.000 12.99 8.04 36.79 3.21
2281 5101 4.142160 TGCAGATATAGGGACATATGACGC 60.142 45.833 10.38 11.93 0.00 5.19
2377 5239 0.690192 TAACTAAGCACAGCAGGGCA 59.310 50.000 5.99 0.00 0.00 5.36
2414 5276 2.372172 ACCCTGCTGTGCTTAGTTAGTT 59.628 45.455 0.00 0.00 0.00 2.24
2415 5277 1.978580 ACCCTGCTGTGCTTAGTTAGT 59.021 47.619 0.00 0.00 0.00 2.24
2416 5278 2.770164 ACCCTGCTGTGCTTAGTTAG 57.230 50.000 0.00 0.00 0.00 2.34
2417 5279 2.901192 TGTACCCTGCTGTGCTTAGTTA 59.099 45.455 0.00 0.00 0.00 2.24
2418 5280 1.697432 TGTACCCTGCTGTGCTTAGTT 59.303 47.619 0.00 0.00 0.00 2.24
2419 5281 1.348064 TGTACCCTGCTGTGCTTAGT 58.652 50.000 0.00 0.00 0.00 2.24
2420 5282 2.076863 GTTGTACCCTGCTGTGCTTAG 58.923 52.381 0.00 0.00 0.00 2.18
2421 5283 1.697432 AGTTGTACCCTGCTGTGCTTA 59.303 47.619 0.00 0.00 0.00 3.09
2422 5284 0.474184 AGTTGTACCCTGCTGTGCTT 59.526 50.000 0.00 0.00 0.00 3.91
2423 5285 0.250467 CAGTTGTACCCTGCTGTGCT 60.250 55.000 0.00 0.00 0.00 4.40
2424 5286 1.237285 CCAGTTGTACCCTGCTGTGC 61.237 60.000 4.52 0.00 0.00 4.57
2425 5287 0.396435 TCCAGTTGTACCCTGCTGTG 59.604 55.000 4.52 0.00 0.00 3.66
2426 5288 1.136828 TTCCAGTTGTACCCTGCTGT 58.863 50.000 4.52 0.00 0.00 4.40
2427 5289 2.270352 TTTCCAGTTGTACCCTGCTG 57.730 50.000 4.52 1.39 0.00 4.41
2428 5290 3.306472 TTTTTCCAGTTGTACCCTGCT 57.694 42.857 4.52 0.00 0.00 4.24
2458 5320 6.010219 ACCTGACACAAAACATAATAGGCTT 58.990 36.000 0.00 0.00 0.00 4.35
2473 5335 3.998341 GCCGAAACTAAATACCTGACACA 59.002 43.478 0.00 0.00 0.00 3.72
2510 5375 0.889186 TCCTTTTCAGACCAAGCGGC 60.889 55.000 0.00 0.00 34.57 6.53
2570 5435 6.656314 TTACCATAACACAATTCACGCTAG 57.344 37.500 0.00 0.00 0.00 3.42
2572 5437 7.801716 ATATTACCATAACACAATTCACGCT 57.198 32.000 0.00 0.00 0.00 5.07
2856 5758 9.485206 AGAACGTTTTTGACATTATACTAGTGT 57.515 29.630 5.39 0.39 0.00 3.55
2868 5770 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
2869 5771 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
2870 5772 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
2871 5773 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
2872 5774 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
2873 5775 9.847224 ATCTGTCCCATAATATAAGAACGTTTT 57.153 29.630 0.46 0.00 0.00 2.43
2874 5776 9.273016 CATCTGTCCCATAATATAAGAACGTTT 57.727 33.333 0.46 0.00 0.00 3.60
2875 5777 7.878127 CCATCTGTCCCATAATATAAGAACGTT 59.122 37.037 0.00 0.00 0.00 3.99
2876 5778 7.234782 TCCATCTGTCCCATAATATAAGAACGT 59.765 37.037 0.00 0.00 0.00 3.99
2877 5779 7.611770 TCCATCTGTCCCATAATATAAGAACG 58.388 38.462 0.00 0.00 0.00 3.95
2878 5780 8.598041 ACTCCATCTGTCCCATAATATAAGAAC 58.402 37.037 0.00 0.00 0.00 3.01
2879 5781 8.742125 ACTCCATCTGTCCCATAATATAAGAA 57.258 34.615 0.00 0.00 0.00 2.52
2880 5782 9.480861 CTACTCCATCTGTCCCATAATATAAGA 57.519 37.037 0.00 0.00 0.00 2.10
2881 5783 9.480861 TCTACTCCATCTGTCCCATAATATAAG 57.519 37.037 0.00 0.00 0.00 1.73
2886 5788 8.923838 ATTATCTACTCCATCTGTCCCATAAT 57.076 34.615 0.00 0.00 0.00 1.28
2887 5789 8.742125 AATTATCTACTCCATCTGTCCCATAA 57.258 34.615 0.00 0.00 0.00 1.90
2888 5790 8.742125 AAATTATCTACTCCATCTGTCCCATA 57.258 34.615 0.00 0.00 0.00 2.74
2889 5791 7.639062 AAATTATCTACTCCATCTGTCCCAT 57.361 36.000 0.00 0.00 0.00 4.00
2890 5792 7.092444 ACAAAATTATCTACTCCATCTGTCCCA 60.092 37.037 0.00 0.00 0.00 4.37
2891 5793 7.283329 ACAAAATTATCTACTCCATCTGTCCC 58.717 38.462 0.00 0.00 0.00 4.46
2892 5794 8.738645 AACAAAATTATCTACTCCATCTGTCC 57.261 34.615 0.00 0.00 0.00 4.02
2893 5795 9.383519 TGAACAAAATTATCTACTCCATCTGTC 57.616 33.333 0.00 0.00 0.00 3.51
2894 5796 9.911788 ATGAACAAAATTATCTACTCCATCTGT 57.088 29.630 0.00 0.00 0.00 3.41
2896 5798 9.911788 ACATGAACAAAATTATCTACTCCATCT 57.088 29.630 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.