Multiple sequence alignment - TraesCS4B01G163400

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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 TraesCS4B01G163400 chr4B 100.000 3422 0 0 1 3422 333757080 333760501 0.000000e+00 6320
1 TraesCS4B01G163400 chr4B 93.299 2298 131 9 1005 3284 200979569 200981861 0.000000e+00 3369
2 TraesCS4B01G163400 chr4B 91.826 991 72 6 25 1009 200962967 200963954 0.000000e+00 1373
3 TraesCS4B01G163400 chr4B 89.744 351 26 6 287 629 620609638 620609986 1.130000e-119 440
4 TraesCS4B01G163400 chr4B 89.174 351 27 7 287 629 620610441 620610788 8.780000e-116 427
5 TraesCS4B01G163400 chr4B 98.519 135 2 0 3288 3422 200981649 200981783 4.410000e-59 239
6 TraesCS4B01G163400 chr4B 85.906 149 13 5 489 629 485277004 485277152 5.910000e-33 152
7 TraesCS4B01G163400 chr7B 91.350 3318 241 20 1 3288 172908544 172905243 0.000000e+00 4495
8 TraesCS4B01G163400 chr7B 90.620 1386 117 9 132 1506 253131193 253132576 0.000000e+00 1827
9 TraesCS4B01G163400 chr7B 90.339 1387 117 9 132 1506 292477863 292479244 0.000000e+00 1803
10 TraesCS4B01G163400 chr7B 98.519 135 2 0 3288 3422 253134030 253134164 4.410000e-59 239
11 TraesCS4B01G163400 chr2B 92.144 3144 213 16 171 3287 486052768 486049632 0.000000e+00 4407
12 TraesCS4B01G163400 chr2B 92.536 2894 192 14 415 3287 161617275 161614385 0.000000e+00 4126
13 TraesCS4B01G163400 chr2B 91.934 1748 102 13 1564 3287 570354941 570356673 0.000000e+00 2410
14 TraesCS4B01G163400 chr2B 92.069 1513 109 9 2 1506 433375252 433376761 0.000000e+00 2119
15 TraesCS4B01G163400 chr2B 90.713 1389 112 10 128 1505 515534111 515535493 0.000000e+00 1834
16 TraesCS4B01G163400 chr2B 94.799 423 22 0 1 423 161618899 161618477 0.000000e+00 660
17 TraesCS4B01G163400 chr2B 98.519 135 2 0 3288 3422 251176783 251176649 4.410000e-59 239
18 TraesCS4B01G163400 chr7D 91.898 3024 207 21 246 3238 452783928 452786944 0.000000e+00 4193
19 TraesCS4B01G163400 chr7D 90.791 3073 244 23 246 3287 536624251 536627315 0.000000e+00 4071
20 TraesCS4B01G163400 chr7D 85.892 2814 316 48 246 3022 588646898 588644129 0.000000e+00 2922
21 TraesCS4B01G163400 chr7D 99.259 135 1 0 3288 3422 536627100 536627234 9.490000e-61 244
22 TraesCS4B01G163400 chr1B 91.324 3066 226 22 244 3287 497537053 497540100 0.000000e+00 4152
23 TraesCS4B01G163400 chr1B 95.473 243 11 0 3 245 409871630 409871872 4.140000e-104 388
24 TraesCS4B01G163400 chr3D 90.548 3068 252 22 246 3285 110918430 110921487 0.000000e+00 4024
25 TraesCS4B01G163400 chr3D 90.413 3077 237 30 246 3287 364947049 364943996 0.000000e+00 3995
26 TraesCS4B01G163400 chr3D 99.259 135 1 0 3288 3422 110921274 110921408 9.490000e-61 244
27 TraesCS4B01G163400 chr3D 99.259 135 1 0 3288 3422 364944208 364944074 9.490000e-61 244
28 TraesCS4B01G163400 chr5B 90.211 3075 239 22 244 3287 139268516 139265473 0.000000e+00 3954
29 TraesCS4B01G163400 chr5B 92.655 953 60 7 1 947 98917578 98918526 0.000000e+00 1363
30 TraesCS4B01G163400 chr5B 98.519 135 2 0 3288 3422 139265691 139265557 4.410000e-59 239
31 TraesCS4B01G163400 chr4A 89.457 3073 284 25 246 3287 278181028 278177965 0.000000e+00 3843
32 TraesCS4B01G163400 chr4A 87.990 2781 276 33 267 3015 538142811 538145565 0.000000e+00 3232
33 TraesCS4B01G163400 chr2A 89.254 3071 289 23 246 3287 204478881 204481939 0.000000e+00 3805
34 TraesCS4B01G163400 chr2D 87.811 3093 307 46 246 3287 273051987 273055060 0.000000e+00 3559
35 TraesCS4B01G163400 chr2D 92.268 1746 95 18 1564 3287 463054686 463056413 0.000000e+00 2440
36 TraesCS4B01G163400 chr2D 99.259 135 1 0 3288 3422 463056196 463056330 9.490000e-61 244
37 TraesCS4B01G163400 chr2D 98.519 135 2 0 3288 3422 376029653 376029519 4.410000e-59 239
38 TraesCS4B01G163400 chr3B 91.413 1514 116 8 1 1506 310884301 310885808 0.000000e+00 2063
39 TraesCS4B01G163400 chr3B 90.556 1546 112 15 1764 3286 171422645 171421111 0.000000e+00 2015
40 TraesCS4B01G163400 chr3B 90.726 744 51 8 1 737 483476254 483475522 0.000000e+00 976
41 TraesCS4B01G163400 chr5A 86.294 1897 229 23 406 2281 686267556 686265670 0.000000e+00 2034
42 TraesCS4B01G163400 chr4D 91.167 1483 109 8 1815 3285 285422001 285420529 0.000000e+00 1993


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 TraesCS4B01G163400 chr4B 333757080 333760501 3421 False 6320.0 6320 100.0000 1 3422 1 chr4B.!!$F2 3421
1 TraesCS4B01G163400 chr4B 200979569 200981861 2292 False 1804.0 3369 95.9090 1005 3422 2 chr4B.!!$F4 2417
2 TraesCS4B01G163400 chr4B 200962967 200963954 987 False 1373.0 1373 91.8260 25 1009 1 chr4B.!!$F1 984
3 TraesCS4B01G163400 chr4B 620609638 620610788 1150 False 433.5 440 89.4590 287 629 2 chr4B.!!$F5 342
4 TraesCS4B01G163400 chr7B 172905243 172908544 3301 True 4495.0 4495 91.3500 1 3288 1 chr7B.!!$R1 3287
5 TraesCS4B01G163400 chr7B 292477863 292479244 1381 False 1803.0 1803 90.3390 132 1506 1 chr7B.!!$F1 1374
6 TraesCS4B01G163400 chr7B 253131193 253134164 2971 False 1033.0 1827 94.5695 132 3422 2 chr7B.!!$F2 3290
7 TraesCS4B01G163400 chr2B 486049632 486052768 3136 True 4407.0 4407 92.1440 171 3287 1 chr2B.!!$R2 3116
8 TraesCS4B01G163400 chr2B 570354941 570356673 1732 False 2410.0 2410 91.9340 1564 3287 1 chr2B.!!$F3 1723
9 TraesCS4B01G163400 chr2B 161614385 161618899 4514 True 2393.0 4126 93.6675 1 3287 2 chr2B.!!$R3 3286
10 TraesCS4B01G163400 chr2B 433375252 433376761 1509 False 2119.0 2119 92.0690 2 1506 1 chr2B.!!$F1 1504
11 TraesCS4B01G163400 chr2B 515534111 515535493 1382 False 1834.0 1834 90.7130 128 1505 1 chr2B.!!$F2 1377
12 TraesCS4B01G163400 chr7D 452783928 452786944 3016 False 4193.0 4193 91.8980 246 3238 1 chr7D.!!$F1 2992
13 TraesCS4B01G163400 chr7D 588644129 588646898 2769 True 2922.0 2922 85.8920 246 3022 1 chr7D.!!$R1 2776
14 TraesCS4B01G163400 chr7D 536624251 536627315 3064 False 2157.5 4071 95.0250 246 3422 2 chr7D.!!$F2 3176
15 TraesCS4B01G163400 chr1B 497537053 497540100 3047 False 4152.0 4152 91.3240 244 3287 1 chr1B.!!$F2 3043
16 TraesCS4B01G163400 chr3D 110918430 110921487 3057 False 2134.0 4024 94.9035 246 3422 2 chr3D.!!$F1 3176
17 TraesCS4B01G163400 chr3D 364943996 364947049 3053 True 2119.5 3995 94.8360 246 3422 2 chr3D.!!$R1 3176
18 TraesCS4B01G163400 chr5B 139265473 139268516 3043 True 2096.5 3954 94.3650 244 3422 2 chr5B.!!$R1 3178
19 TraesCS4B01G163400 chr5B 98917578 98918526 948 False 1363.0 1363 92.6550 1 947 1 chr5B.!!$F1 946
20 TraesCS4B01G163400 chr4A 278177965 278181028 3063 True 3843.0 3843 89.4570 246 3287 1 chr4A.!!$R1 3041
21 TraesCS4B01G163400 chr4A 538142811 538145565 2754 False 3232.0 3232 87.9900 267 3015 1 chr4A.!!$F1 2748
22 TraesCS4B01G163400 chr2A 204478881 204481939 3058 False 3805.0 3805 89.2540 246 3287 1 chr2A.!!$F1 3041
23 TraesCS4B01G163400 chr2D 273051987 273055060 3073 False 3559.0 3559 87.8110 246 3287 1 chr2D.!!$F1 3041
24 TraesCS4B01G163400 chr2D 463054686 463056413 1727 False 1342.0 2440 95.7635 1564 3422 2 chr2D.!!$F2 1858
25 TraesCS4B01G163400 chr3B 310884301 310885808 1507 False 2063.0 2063 91.4130 1 1506 1 chr3B.!!$F1 1505
26 TraesCS4B01G163400 chr3B 171421111 171422645 1534 True 2015.0 2015 90.5560 1764 3286 1 chr3B.!!$R1 1522
27 TraesCS4B01G163400 chr3B 483475522 483476254 732 True 976.0 976 90.7260 1 737 1 chr3B.!!$R2 736
28 TraesCS4B01G163400 chr5A 686265670 686267556 1886 True 2034.0 2034 86.2940 406 2281 1 chr5A.!!$R1 1875
29 TraesCS4B01G163400 chr4D 285420529 285422001 1472 True 1993.0 1993 91.1670 1815 3285 1 chr4D.!!$R1 1470

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
480 1714 0.464036 ACATGACACACACAGTCCGT 59.536 50.0 0.0 0.0 35.15 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2433 4444 0.610232 AGCGAAGGCAGGCTTTGATT 60.61 50.0 25.05 11.0 43.41 2.57 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
35 36 7.939039 TGAGGAAACATTTCAGAAACACTATCT 59.061 33.333 0.00 0.00 38.92 1.98
85 86 9.000486 TCGTCGATTTCTCAATCAGTACTATAT 58.000 33.333 0.00 0.00 39.14 0.86
220 222 7.201661 GGATTTATGTAACGCCAACATTACTGA 60.202 37.037 3.58 0.00 38.49 3.41
222 224 3.729966 TGTAACGCCAACATTACTGACA 58.270 40.909 0.00 0.00 33.32 3.58
379 388 7.492352 ACACCTGTACTGATGAAAAACTAAC 57.508 36.000 0.34 0.00 0.00 2.34
480 1714 0.464036 ACATGACACACACAGTCCGT 59.536 50.000 0.00 0.00 35.15 4.69
563 1804 2.170607 ACGGATCATCACCAACCCTAAG 59.829 50.000 0.00 0.00 0.00 2.18
674 2630 0.740737 GCGCAGTGGGATAAAGCAAT 59.259 50.000 12.03 0.00 0.00 3.56
675 2631 1.946768 GCGCAGTGGGATAAAGCAATA 59.053 47.619 12.03 0.00 0.00 1.90
821 2780 3.578272 GCAAACGGCGACACCACA 61.578 61.111 16.62 0.00 39.03 4.17
866 2837 3.402681 CGCCTCCCACACATCCCT 61.403 66.667 0.00 0.00 0.00 4.20
869 2840 1.271840 GCCTCCCACACATCCCTGTA 61.272 60.000 0.00 0.00 33.14 2.74
1262 3240 0.396811 GTGCACTACACCAGGGAAGT 59.603 55.000 10.32 0.00 44.02 3.01
1285 3263 0.401105 ACCTCCCTAGATGGCAGCAT 60.401 55.000 5.19 0.00 0.00 3.79
1357 3336 2.561569 CTACGAAATGGTGACCATCCC 58.438 52.381 18.84 11.43 44.40 3.85
1399 3384 8.697846 TGGTTCATCTGTTTAATTAGTACTCG 57.302 34.615 0.00 0.00 0.00 4.18
1453 3447 7.311364 TGTACTAGTGTGGTTTTTGAAAGTC 57.689 36.000 5.39 0.00 0.00 3.01
1615 3611 9.793252 TCCGATAGTGTAGTTTTTATACTCAAC 57.207 33.333 0.00 0.00 0.00 3.18
1728 3729 2.554032 GCTGAAGCACTGGTATGTGTTT 59.446 45.455 0.00 0.00 42.48 2.83
2017 4025 1.016130 CAAGCGCCTCAACGAGATGT 61.016 55.000 2.29 0.00 34.06 3.06
2062 4070 3.347958 TTGTCGGTTTCAGCATTGAAC 57.652 42.857 0.00 0.00 42.79 3.18
2085 4093 5.037385 CGCGACAAAGAGAAGATGAAGATA 58.963 41.667 0.00 0.00 0.00 1.98
2190 4198 1.072806 TCCTTGACTGATGTTGCAGCT 59.927 47.619 1.17 0.00 39.51 4.24
2238 4247 4.022935 GGCATGAAGAAGAACATTGACACA 60.023 41.667 0.00 0.00 0.00 3.72
2292 4302 0.390340 TGCCAGACAAGCTCATCGAC 60.390 55.000 0.00 0.00 0.00 4.20
2367 4378 5.920193 ACATCACAAATGGTAGGGAAATG 57.080 39.130 0.00 0.00 0.00 2.32
2376 4387 3.161866 TGGTAGGGAAATGGCAAAAGTC 58.838 45.455 0.00 0.00 0.00 3.01
2395 4406 2.358039 CGGGAGGTTGACCACTACA 58.642 57.895 2.56 0.00 38.89 2.74
2540 4551 2.108168 ACCAGTATGACTATGCCGTGT 58.892 47.619 0.00 0.00 39.69 4.49
2556 4567 4.561735 CCGTGTTTGTCATGGTTAAACT 57.438 40.909 15.96 0.00 45.46 2.66
2659 4672 7.022055 TCGTTTCAAATTCAAAGTAGCTTCA 57.978 32.000 0.00 0.00 0.00 3.02
3085 5170 7.972527 ACTATCAGTACAACTTAGTCTACACG 58.027 38.462 0.00 0.00 0.00 4.49
3086 5171 5.039480 TCAGTACAACTTAGTCTACACGC 57.961 43.478 0.00 0.00 0.00 5.34
3087 5172 4.516321 TCAGTACAACTTAGTCTACACGCA 59.484 41.667 0.00 0.00 0.00 5.24
3088 5173 5.008911 TCAGTACAACTTAGTCTACACGCAA 59.991 40.000 0.00 0.00 0.00 4.85
3103 5188 2.293677 CGCAAGTACCATAGTGCTGA 57.706 50.000 0.00 0.00 39.11 4.26
3104 5189 2.616960 CGCAAGTACCATAGTGCTGAA 58.383 47.619 0.00 0.00 39.11 3.02
3105 5190 3.000041 CGCAAGTACCATAGTGCTGAAA 59.000 45.455 0.00 0.00 39.11 2.69
3106 5191 3.435327 CGCAAGTACCATAGTGCTGAAAA 59.565 43.478 0.00 0.00 39.11 2.29
3107 5192 4.094887 CGCAAGTACCATAGTGCTGAAAAT 59.905 41.667 0.00 0.00 39.11 1.82
3108 5193 5.335127 GCAAGTACCATAGTGCTGAAAATG 58.665 41.667 0.00 0.00 39.11 2.32
3109 5194 5.123820 GCAAGTACCATAGTGCTGAAAATGA 59.876 40.000 0.00 0.00 39.11 2.57
3110 5195 6.183360 GCAAGTACCATAGTGCTGAAAATGAT 60.183 38.462 0.00 0.00 39.11 2.45
3111 5196 7.012327 GCAAGTACCATAGTGCTGAAAATGATA 59.988 37.037 0.00 0.00 39.11 2.15
3112 5197 8.338259 CAAGTACCATAGTGCTGAAAATGATAC 58.662 37.037 0.00 0.00 39.11 2.24
3113 5198 6.992715 AGTACCATAGTGCTGAAAATGATACC 59.007 38.462 0.00 0.00 37.57 2.73
3114 5199 5.754782 ACCATAGTGCTGAAAATGATACCA 58.245 37.500 0.00 0.00 0.00 3.25
3115 5200 6.367983 ACCATAGTGCTGAAAATGATACCAT 58.632 36.000 0.00 0.00 33.66 3.55
3116 5201 7.517320 ACCATAGTGCTGAAAATGATACCATA 58.483 34.615 0.00 0.00 31.59 2.74
3117 5202 7.998383 ACCATAGTGCTGAAAATGATACCATAA 59.002 33.333 0.00 0.00 31.59 1.90
3118 5203 8.509690 CCATAGTGCTGAAAATGATACCATAAG 58.490 37.037 0.00 0.00 31.59 1.73
3119 5204 6.949352 AGTGCTGAAAATGATACCATAAGG 57.051 37.500 0.00 0.00 42.21 2.69
3120 5205 5.300286 AGTGCTGAAAATGATACCATAAGGC 59.700 40.000 0.00 0.00 39.06 4.35
3121 5206 4.584325 TGCTGAAAATGATACCATAAGGCC 59.416 41.667 0.00 0.00 39.06 5.19
3122 5207 4.021981 GCTGAAAATGATACCATAAGGCCC 60.022 45.833 0.00 0.00 39.06 5.80
3123 5208 5.388654 CTGAAAATGATACCATAAGGCCCT 58.611 41.667 0.00 0.00 39.06 5.19
3124 5209 5.776358 TGAAAATGATACCATAAGGCCCTT 58.224 37.500 0.00 0.00 39.06 3.95
3125 5210 5.598005 TGAAAATGATACCATAAGGCCCTTG 59.402 40.000 6.16 0.00 39.06 3.61
3126 5211 5.402054 AAATGATACCATAAGGCCCTTGA 57.598 39.130 6.16 0.00 39.06 3.02
3127 5212 4.647564 ATGATACCATAAGGCCCTTGAG 57.352 45.455 6.16 0.00 39.06 3.02
3128 5213 3.664320 TGATACCATAAGGCCCTTGAGA 58.336 45.455 6.16 0.00 39.06 3.27
3129 5214 4.044308 TGATACCATAAGGCCCTTGAGAA 58.956 43.478 6.16 0.00 39.06 2.87
3130 5215 4.665009 TGATACCATAAGGCCCTTGAGAAT 59.335 41.667 6.16 0.00 39.06 2.40
3131 5216 5.849475 TGATACCATAAGGCCCTTGAGAATA 59.151 40.000 6.16 0.00 39.06 1.75
3132 5217 6.331572 TGATACCATAAGGCCCTTGAGAATAA 59.668 38.462 6.16 0.00 39.06 1.40
3133 5218 5.669798 ACCATAAGGCCCTTGAGAATAAT 57.330 39.130 6.16 0.00 39.06 1.28
3134 5219 5.635120 ACCATAAGGCCCTTGAGAATAATC 58.365 41.667 6.16 0.00 39.06 1.75
3135 5220 5.134339 ACCATAAGGCCCTTGAGAATAATCA 59.866 40.000 6.16 0.00 39.06 2.57
3136 5221 5.474876 CCATAAGGCCCTTGAGAATAATCAC 59.525 44.000 6.16 0.00 0.00 3.06
3137 5222 4.591321 AAGGCCCTTGAGAATAATCACA 57.409 40.909 0.00 0.00 0.00 3.58
3138 5223 4.591321 AGGCCCTTGAGAATAATCACAA 57.409 40.909 0.00 0.00 31.78 3.33
3139 5224 4.934356 AGGCCCTTGAGAATAATCACAAA 58.066 39.130 0.00 0.00 31.78 2.83
3140 5225 5.332743 AGGCCCTTGAGAATAATCACAAAA 58.667 37.500 0.00 0.00 31.78 2.44
3141 5226 5.779771 AGGCCCTTGAGAATAATCACAAAAA 59.220 36.000 0.00 0.00 31.78 1.94
3142 5227 5.869344 GGCCCTTGAGAATAATCACAAAAAC 59.131 40.000 0.00 0.00 31.78 2.43
3143 5228 6.454795 GCCCTTGAGAATAATCACAAAAACA 58.545 36.000 0.00 0.00 31.78 2.83
3144 5229 6.928492 GCCCTTGAGAATAATCACAAAAACAA 59.072 34.615 0.00 0.00 31.78 2.83
3145 5230 7.440856 GCCCTTGAGAATAATCACAAAAACAAA 59.559 33.333 0.00 0.00 31.78 2.83
3146 5231 8.764287 CCCTTGAGAATAATCACAAAAACAAAC 58.236 33.333 0.00 0.00 31.78 2.93
3147 5232 9.311916 CCTTGAGAATAATCACAAAAACAAACA 57.688 29.630 0.00 0.00 31.78 2.83
3149 5234 9.645059 TTGAGAATAATCACAAAAACAAACACA 57.355 25.926 0.00 0.00 31.78 3.72
3150 5235 9.645059 TGAGAATAATCACAAAAACAAACACAA 57.355 25.926 0.00 0.00 0.00 3.33
3154 5239 9.818796 AATAATCACAAAAACAAACACAAACAC 57.181 25.926 0.00 0.00 0.00 3.32
3155 5240 6.851222 ATCACAAAAACAAACACAAACACA 57.149 29.167 0.00 0.00 0.00 3.72
3156 5241 6.662414 TCACAAAAACAAACACAAACACAA 57.338 29.167 0.00 0.00 0.00 3.33
3157 5242 6.709643 TCACAAAAACAAACACAAACACAAG 58.290 32.000 0.00 0.00 0.00 3.16
3158 5243 5.906285 CACAAAAACAAACACAAACACAAGG 59.094 36.000 0.00 0.00 0.00 3.61
3159 5244 4.740741 AAAACAAACACAAACACAAGGC 57.259 36.364 0.00 0.00 0.00 4.35
3160 5245 3.393089 AACAAACACAAACACAAGGCA 57.607 38.095 0.00 0.00 0.00 4.75
3161 5246 3.393089 ACAAACACAAACACAAGGCAA 57.607 38.095 0.00 0.00 0.00 4.52
3162 5247 3.733337 ACAAACACAAACACAAGGCAAA 58.267 36.364 0.00 0.00 0.00 3.68
3163 5248 4.130118 ACAAACACAAACACAAGGCAAAA 58.870 34.783 0.00 0.00 0.00 2.44
3164 5249 4.576463 ACAAACACAAACACAAGGCAAAAA 59.424 33.333 0.00 0.00 0.00 1.94
3200 5285 7.440523 AAAAATAGCACTTCCACAGAACTAG 57.559 36.000 0.00 0.00 0.00 2.57
3201 5286 6.360370 AAATAGCACTTCCACAGAACTAGA 57.640 37.500 0.00 0.00 0.00 2.43
3202 5287 6.360370 AATAGCACTTCCACAGAACTAGAA 57.640 37.500 0.00 0.00 0.00 2.10
3203 5288 3.996480 AGCACTTCCACAGAACTAGAAC 58.004 45.455 0.00 0.00 0.00 3.01
3204 5289 3.388024 AGCACTTCCACAGAACTAGAACA 59.612 43.478 0.00 0.00 0.00 3.18
3205 5290 4.127171 GCACTTCCACAGAACTAGAACAA 58.873 43.478 0.00 0.00 0.00 2.83
3206 5291 4.574828 GCACTTCCACAGAACTAGAACAAA 59.425 41.667 0.00 0.00 0.00 2.83
3207 5292 5.065988 GCACTTCCACAGAACTAGAACAAAA 59.934 40.000 0.00 0.00 0.00 2.44
3208 5293 6.404293 GCACTTCCACAGAACTAGAACAAAAA 60.404 38.462 0.00 0.00 0.00 1.94
3209 5294 7.189512 CACTTCCACAGAACTAGAACAAAAAG 58.810 38.462 0.00 0.00 0.00 2.27
3210 5295 6.884836 ACTTCCACAGAACTAGAACAAAAAGT 59.115 34.615 0.00 0.00 0.00 2.66
3211 5296 8.044908 ACTTCCACAGAACTAGAACAAAAAGTA 58.955 33.333 0.00 0.00 0.00 2.24
3212 5297 8.974060 TTCCACAGAACTAGAACAAAAAGTAT 57.026 30.769 0.00 0.00 0.00 2.12
3213 5298 8.603242 TCCACAGAACTAGAACAAAAAGTATC 57.397 34.615 0.00 0.00 0.00 2.24
3214 5299 8.208224 TCCACAGAACTAGAACAAAAAGTATCA 58.792 33.333 0.00 0.00 0.00 2.15
3215 5300 8.499162 CCACAGAACTAGAACAAAAAGTATCAG 58.501 37.037 0.00 0.00 0.00 2.90
3216 5301 9.046296 CACAGAACTAGAACAAAAAGTATCAGT 57.954 33.333 0.00 0.00 0.00 3.41
3217 5302 9.262358 ACAGAACTAGAACAAAAAGTATCAGTC 57.738 33.333 0.00 0.00 0.00 3.51
3218 5303 8.713271 CAGAACTAGAACAAAAAGTATCAGTCC 58.287 37.037 0.00 0.00 0.00 3.85
3219 5304 8.429641 AGAACTAGAACAAAAAGTATCAGTCCA 58.570 33.333 0.00 0.00 0.00 4.02
3220 5305 8.974060 AACTAGAACAAAAAGTATCAGTCCAA 57.026 30.769 0.00 0.00 0.00 3.53
3221 5306 8.608844 ACTAGAACAAAAAGTATCAGTCCAAG 57.391 34.615 0.00 0.00 0.00 3.61
3222 5307 8.211629 ACTAGAACAAAAAGTATCAGTCCAAGT 58.788 33.333 0.00 0.00 0.00 3.16
3223 5308 7.881775 AGAACAAAAAGTATCAGTCCAAGTT 57.118 32.000 0.00 0.00 0.00 2.66
3224 5309 8.974060 AGAACAAAAAGTATCAGTCCAAGTTA 57.026 30.769 0.00 0.00 0.00 2.24
3225 5310 8.837389 AGAACAAAAAGTATCAGTCCAAGTTAC 58.163 33.333 0.00 0.00 0.00 2.50
3226 5311 8.747538 AACAAAAAGTATCAGTCCAAGTTACT 57.252 30.769 0.00 0.00 0.00 2.24
3227 5312 8.154649 ACAAAAAGTATCAGTCCAAGTTACTG 57.845 34.615 0.05 0.05 44.66 2.74
3228 5313 7.228706 ACAAAAAGTATCAGTCCAAGTTACTGG 59.771 37.037 6.05 0.00 43.69 4.00
3229 5314 6.435292 AAAGTATCAGTCCAAGTTACTGGT 57.565 37.500 6.05 2.02 43.69 4.00
3230 5315 5.407407 AGTATCAGTCCAAGTTACTGGTG 57.593 43.478 6.05 0.00 43.69 4.17
3231 5316 3.703001 ATCAGTCCAAGTTACTGGTGG 57.297 47.619 6.05 0.00 43.69 4.61
3232 5317 2.684943 TCAGTCCAAGTTACTGGTGGA 58.315 47.619 1.91 1.91 43.69 4.02
3233 5318 2.632996 TCAGTCCAAGTTACTGGTGGAG 59.367 50.000 6.07 0.00 42.07 3.86
3234 5319 2.368875 CAGTCCAAGTTACTGGTGGAGT 59.631 50.000 6.07 6.80 44.32 3.85
3235 5320 2.633481 AGTCCAAGTTACTGGTGGAGTC 59.367 50.000 6.07 0.00 40.39 3.36
3236 5321 2.367567 GTCCAAGTTACTGGTGGAGTCA 59.632 50.000 6.07 0.00 42.07 3.41
3237 5322 3.042682 TCCAAGTTACTGGTGGAGTCAA 58.957 45.455 1.91 0.00 36.51 3.18
3238 5323 3.071023 TCCAAGTTACTGGTGGAGTCAAG 59.929 47.826 1.91 0.00 36.51 3.02
3239 5324 3.181454 CCAAGTTACTGGTGGAGTCAAGT 60.181 47.826 0.00 0.00 35.96 3.16
3240 5325 4.039973 CCAAGTTACTGGTGGAGTCAAGTA 59.960 45.833 0.00 0.00 35.96 2.24
3241 5326 4.868314 AGTTACTGGTGGAGTCAAGTAC 57.132 45.455 0.00 0.00 35.96 2.73
3242 5327 4.481072 AGTTACTGGTGGAGTCAAGTACT 58.519 43.478 0.00 0.00 42.80 2.73
3243 5328 5.638133 AGTTACTGGTGGAGTCAAGTACTA 58.362 41.667 0.00 0.00 39.07 1.82
3244 5329 5.711036 AGTTACTGGTGGAGTCAAGTACTAG 59.289 44.000 0.00 0.00 39.07 2.57
3245 5330 4.383931 ACTGGTGGAGTCAAGTACTAGA 57.616 45.455 0.00 0.00 39.07 2.43
3246 5331 4.936802 ACTGGTGGAGTCAAGTACTAGAT 58.063 43.478 0.00 0.00 39.07 1.98
3247 5332 4.951094 ACTGGTGGAGTCAAGTACTAGATC 59.049 45.833 0.00 0.00 39.07 2.75
3248 5333 4.279145 TGGTGGAGTCAAGTACTAGATCC 58.721 47.826 0.00 2.64 39.07 3.36
3249 5334 4.264217 TGGTGGAGTCAAGTACTAGATCCA 60.264 45.833 12.56 12.56 39.07 3.41
3250 5335 4.710375 GGTGGAGTCAAGTACTAGATCCAA 59.290 45.833 16.35 3.81 39.07 3.53
3251 5336 5.187186 GGTGGAGTCAAGTACTAGATCCAAA 59.813 44.000 16.35 0.00 39.07 3.28
3252 5337 6.100668 GTGGAGTCAAGTACTAGATCCAAAC 58.899 44.000 16.35 6.12 39.07 2.93
3253 5338 5.187186 TGGAGTCAAGTACTAGATCCAAACC 59.813 44.000 13.67 3.63 39.07 3.27
3254 5339 5.187186 GGAGTCAAGTACTAGATCCAAACCA 59.813 44.000 0.00 0.00 39.07 3.67
3255 5340 6.295688 GGAGTCAAGTACTAGATCCAAACCAA 60.296 42.308 0.00 0.00 39.07 3.67
3256 5341 7.074653 AGTCAAGTACTAGATCCAAACCAAA 57.925 36.000 0.00 0.00 36.36 3.28
3257 5342 7.514721 AGTCAAGTACTAGATCCAAACCAAAA 58.485 34.615 0.00 0.00 36.36 2.44
3258 5343 7.996644 AGTCAAGTACTAGATCCAAACCAAAAA 59.003 33.333 0.00 0.00 36.36 1.94
3279 5364 3.653539 AAAAGTACAAATTGACCGCCC 57.346 42.857 0.00 0.00 0.00 6.13
3280 5365 2.279935 AAGTACAAATTGACCGCCCA 57.720 45.000 0.00 0.00 0.00 5.36
3281 5366 2.279935 AGTACAAATTGACCGCCCAA 57.720 45.000 0.00 0.00 0.00 4.12
3282 5367 2.159382 AGTACAAATTGACCGCCCAAG 58.841 47.619 0.00 0.00 0.00 3.61
3283 5368 1.201414 GTACAAATTGACCGCCCAAGG 59.799 52.381 0.00 0.00 37.30 3.61
3284 5369 0.178975 ACAAATTGACCGCCCAAGGA 60.179 50.000 0.00 0.00 34.73 3.36
3285 5370 0.243636 CAAATTGACCGCCCAAGGAC 59.756 55.000 0.00 0.00 34.73 3.85
3286 5371 0.178975 AAATTGACCGCCCAAGGACA 60.179 50.000 0.00 0.00 34.38 4.02
3287 5372 0.039618 AATTGACCGCCCAAGGACAT 59.960 50.000 0.00 0.00 36.00 3.06
3288 5373 0.916086 ATTGACCGCCCAAGGACATA 59.084 50.000 0.00 0.00 36.00 2.29
3289 5374 0.035820 TTGACCGCCCAAGGACATAC 60.036 55.000 0.00 0.00 36.00 2.39
3290 5375 1.195442 TGACCGCCCAAGGACATACA 61.195 55.000 0.00 0.00 31.45 2.29
3291 5376 0.035820 GACCGCCCAAGGACATACAA 60.036 55.000 0.00 0.00 34.73 2.41
3292 5377 0.322187 ACCGCCCAAGGACATACAAC 60.322 55.000 0.00 0.00 34.73 3.32
3293 5378 0.035439 CCGCCCAAGGACATACAACT 60.035 55.000 0.00 0.00 0.00 3.16
3294 5379 1.613255 CCGCCCAAGGACATACAACTT 60.613 52.381 0.00 0.00 0.00 2.66
3295 5380 2.355310 CCGCCCAAGGACATACAACTTA 60.355 50.000 0.00 0.00 0.00 2.24
3296 5381 2.936498 CGCCCAAGGACATACAACTTAG 59.064 50.000 0.00 0.00 0.00 2.18
3297 5382 3.618997 CGCCCAAGGACATACAACTTAGT 60.619 47.826 0.00 0.00 0.00 2.24
3298 5383 3.939592 GCCCAAGGACATACAACTTAGTC 59.060 47.826 0.00 0.00 0.00 2.59
3299 5384 4.323562 GCCCAAGGACATACAACTTAGTCT 60.324 45.833 0.00 0.00 0.00 3.24
3300 5385 5.105064 GCCCAAGGACATACAACTTAGTCTA 60.105 44.000 0.00 0.00 0.00 2.59
3301 5386 6.338937 CCCAAGGACATACAACTTAGTCTAC 58.661 44.000 0.00 0.00 0.00 2.59
3302 5387 6.070995 CCCAAGGACATACAACTTAGTCTACA 60.071 42.308 0.00 0.00 0.00 2.74
3303 5388 6.812160 CCAAGGACATACAACTTAGTCTACAC 59.188 42.308 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 222 4.270008 AGTTTTGCTGAGTTACTGGTTGT 58.730 39.130 0.00 0.00 0.00 3.32
222 224 5.705905 GGATAGTTTTGCTGAGTTACTGGTT 59.294 40.000 0.00 0.00 0.00 3.67
457 1687 3.059868 CGGACTGTGTGTGTCATGTTAAC 60.060 47.826 0.00 0.00 36.26 2.01
480 1714 7.658575 GTGTAGTTGAACTTACCAAATACCAGA 59.341 37.037 1.97 0.00 41.56 3.86
537 1772 2.615493 GGTTGGTGATGATCCGTCTTGT 60.615 50.000 0.00 0.00 0.00 3.16
538 1773 2.009774 GGTTGGTGATGATCCGTCTTG 58.990 52.381 0.00 0.00 0.00 3.02
540 1775 0.541863 GGGTTGGTGATGATCCGTCT 59.458 55.000 0.00 0.00 0.00 4.18
541 1776 0.541863 AGGGTTGGTGATGATCCGTC 59.458 55.000 0.00 0.00 0.00 4.79
544 1779 3.199946 TGTCTTAGGGTTGGTGATGATCC 59.800 47.826 0.00 0.00 0.00 3.36
563 1804 3.428045 GCTGTTTATCCCACTTGCATGTC 60.428 47.826 1.56 0.00 0.00 3.06
675 2631 9.469097 AGTAGTCTTGTCAAGATGTACTTATCT 57.531 33.333 22.92 14.14 40.18 1.98
821 2780 0.761702 AGGACGTGGGTGTAGTGGTT 60.762 55.000 0.00 0.00 0.00 3.67
866 2837 2.616001 GGTTATTTCCAGGGCGTGTACA 60.616 50.000 6.43 0.00 0.00 2.90
869 2840 0.323087 GGGTTATTTCCAGGGCGTGT 60.323 55.000 6.43 0.00 0.00 4.49
1262 3240 0.032515 TGCCATCTAGGGAGGTTCGA 60.033 55.000 0.00 0.00 38.09 3.71
1357 3336 4.099266 TGAACCAAACAGGGAAAATGAGTG 59.901 41.667 0.00 0.00 43.89 3.51
1506 3501 8.523915 TTTCAAATAGTAATCCAGTGCATCAT 57.476 30.769 0.00 0.00 0.00 2.45
1759 3762 5.653507 CCAATGTTGTATGTGCTGCTTTAT 58.346 37.500 0.00 0.00 0.00 1.40
1954 3960 9.143631 ACATTTTGAAGATTAGCATTACTTTGC 57.856 29.630 0.00 0.00 43.09 3.68
2017 4025 4.639755 TGTGAACAACTTCTCATGCTTCAA 59.360 37.500 0.00 0.00 0.00 2.69
2062 4070 3.245797 TCTTCATCTTCTCTTTGTCGCG 58.754 45.455 0.00 0.00 0.00 5.87
2085 4093 3.294214 GTTGATCATTGGAAGGCCAGAT 58.706 45.455 5.01 0.00 46.91 2.90
2190 4198 1.496060 AGAACGGGTGGATGATGCTA 58.504 50.000 0.00 0.00 0.00 3.49
2238 4247 2.643551 CACAGTTTGTGGTCTTCCTGT 58.356 47.619 1.31 0.00 44.27 4.00
2260 4270 3.769369 CTGGCAGCGGGCTGATCAT 62.769 63.158 23.89 0.00 46.30 2.45
2367 4378 1.228459 AACCTCCCGGACTTTTGCC 60.228 57.895 0.73 0.00 0.00 4.52
2376 4387 1.189524 TGTAGTGGTCAACCTCCCGG 61.190 60.000 0.00 0.00 36.82 5.73
2433 4444 0.610232 AGCGAAGGCAGGCTTTGATT 60.610 50.000 25.05 11.00 43.41 2.57
2626 4637 9.757227 ACTTTGAATTTGAAACGATGGATTAAA 57.243 25.926 0.00 0.00 0.00 1.52
2637 4648 7.985634 TGTGAAGCTACTTTGAATTTGAAAC 57.014 32.000 0.00 0.00 0.00 2.78
2659 4672 1.069049 GCAGCCACAAAGTTCCATTGT 59.931 47.619 0.00 0.00 41.50 2.71
3037 5110 7.437748 AGTCCATTCATAGTAGCATTACAGAC 58.562 38.462 0.00 0.00 31.96 3.51
3038 5111 7.603180 AGTCCATTCATAGTAGCATTACAGA 57.397 36.000 0.00 0.00 31.96 3.41
3041 5114 9.579768 CTGATAGTCCATTCATAGTAGCATTAC 57.420 37.037 0.00 0.00 0.00 1.89
3042 5115 9.314133 ACTGATAGTCCATTCATAGTAGCATTA 57.686 33.333 0.00 0.00 0.00 1.90
3085 5170 5.123820 TCATTTTCAGCACTATGGTACTTGC 59.876 40.000 0.00 0.00 35.08 4.01
3086 5171 6.741992 TCATTTTCAGCACTATGGTACTTG 57.258 37.500 0.00 0.00 0.00 3.16
3087 5172 7.499232 GGTATCATTTTCAGCACTATGGTACTT 59.501 37.037 0.00 0.00 35.76 2.24
3088 5173 6.992715 GGTATCATTTTCAGCACTATGGTACT 59.007 38.462 0.00 0.00 35.76 2.73
3089 5174 6.765989 TGGTATCATTTTCAGCACTATGGTAC 59.234 38.462 0.00 0.00 35.07 3.34
3090 5175 6.894682 TGGTATCATTTTCAGCACTATGGTA 58.105 36.000 0.00 0.00 0.00 3.25
3091 5176 5.754782 TGGTATCATTTTCAGCACTATGGT 58.245 37.500 0.00 0.00 0.00 3.55
3092 5177 6.889301 ATGGTATCATTTTCAGCACTATGG 57.111 37.500 0.00 0.00 0.00 2.74
3093 5178 8.509690 CCTTATGGTATCATTTTCAGCACTATG 58.490 37.037 0.00 0.00 34.96 2.23
3094 5179 7.175641 GCCTTATGGTATCATTTTCAGCACTAT 59.824 37.037 0.00 0.00 34.96 2.12
3095 5180 6.486657 GCCTTATGGTATCATTTTCAGCACTA 59.513 38.462 0.00 0.00 34.96 2.74
3096 5181 5.300286 GCCTTATGGTATCATTTTCAGCACT 59.700 40.000 0.00 0.00 34.96 4.40
3097 5182 5.507985 GGCCTTATGGTATCATTTTCAGCAC 60.508 44.000 0.00 0.00 34.96 4.40
3098 5183 4.584325 GGCCTTATGGTATCATTTTCAGCA 59.416 41.667 0.00 0.00 34.96 4.41
3099 5184 4.021981 GGGCCTTATGGTATCATTTTCAGC 60.022 45.833 0.84 0.00 34.96 4.26
3100 5185 5.388654 AGGGCCTTATGGTATCATTTTCAG 58.611 41.667 0.00 0.00 34.96 3.02
3101 5186 5.402054 AGGGCCTTATGGTATCATTTTCA 57.598 39.130 0.00 0.00 34.96 2.69
3102 5187 5.833131 TCAAGGGCCTTATGGTATCATTTTC 59.167 40.000 20.44 0.00 34.96 2.29
3103 5188 5.776358 TCAAGGGCCTTATGGTATCATTTT 58.224 37.500 20.44 0.00 34.96 1.82
3104 5189 5.134339 TCTCAAGGGCCTTATGGTATCATTT 59.866 40.000 20.44 0.00 34.96 2.32
3105 5190 4.665009 TCTCAAGGGCCTTATGGTATCATT 59.335 41.667 20.44 0.00 34.96 2.57
3106 5191 4.242811 TCTCAAGGGCCTTATGGTATCAT 58.757 43.478 20.44 0.00 37.40 2.45
3107 5192 3.664320 TCTCAAGGGCCTTATGGTATCA 58.336 45.455 20.44 0.00 35.27 2.15
3108 5193 4.706842 TTCTCAAGGGCCTTATGGTATC 57.293 45.455 20.44 0.00 35.27 2.24
3109 5194 6.780198 TTATTCTCAAGGGCCTTATGGTAT 57.220 37.500 20.44 12.74 35.27 2.73
3110 5195 6.331572 TGATTATTCTCAAGGGCCTTATGGTA 59.668 38.462 20.44 6.01 35.27 3.25
3111 5196 5.134339 TGATTATTCTCAAGGGCCTTATGGT 59.866 40.000 20.44 7.01 35.27 3.55
3112 5197 5.474876 GTGATTATTCTCAAGGGCCTTATGG 59.525 44.000 20.44 11.84 0.00 2.74
3113 5198 6.064060 TGTGATTATTCTCAAGGGCCTTATG 58.936 40.000 20.44 14.47 0.00 1.90
3114 5199 6.266131 TGTGATTATTCTCAAGGGCCTTAT 57.734 37.500 20.44 11.51 0.00 1.73
3115 5200 5.708736 TGTGATTATTCTCAAGGGCCTTA 57.291 39.130 20.44 3.20 0.00 2.69
3116 5201 4.591321 TGTGATTATTCTCAAGGGCCTT 57.409 40.909 14.48 14.48 0.00 4.35
3117 5202 4.591321 TTGTGATTATTCTCAAGGGCCT 57.409 40.909 0.00 0.00 32.07 5.19
3118 5203 5.659440 TTTTGTGATTATTCTCAAGGGCC 57.341 39.130 0.00 0.00 36.87 5.80
3119 5204 6.454795 TGTTTTTGTGATTATTCTCAAGGGC 58.545 36.000 3.26 0.00 36.87 5.19
3120 5205 8.764287 GTTTGTTTTTGTGATTATTCTCAAGGG 58.236 33.333 3.26 0.00 36.87 3.95
3121 5206 9.311916 TGTTTGTTTTTGTGATTATTCTCAAGG 57.688 29.630 3.26 0.00 36.87 3.61
3123 5208 9.645059 TGTGTTTGTTTTTGTGATTATTCTCAA 57.355 25.926 0.00 0.00 34.46 3.02
3124 5209 9.645059 TTGTGTTTGTTTTTGTGATTATTCTCA 57.355 25.926 0.00 0.00 0.00 3.27
3128 5213 9.818796 GTGTTTGTGTTTGTTTTTGTGATTATT 57.181 25.926 0.00 0.00 0.00 1.40
3129 5214 8.993121 TGTGTTTGTGTTTGTTTTTGTGATTAT 58.007 25.926 0.00 0.00 0.00 1.28
3130 5215 8.365399 TGTGTTTGTGTTTGTTTTTGTGATTA 57.635 26.923 0.00 0.00 0.00 1.75
3131 5216 7.251704 TGTGTTTGTGTTTGTTTTTGTGATT 57.748 28.000 0.00 0.00 0.00 2.57
3132 5217 6.851222 TGTGTTTGTGTTTGTTTTTGTGAT 57.149 29.167 0.00 0.00 0.00 3.06
3133 5218 6.238211 CCTTGTGTTTGTGTTTGTTTTTGTGA 60.238 34.615 0.00 0.00 0.00 3.58
3134 5219 5.906285 CCTTGTGTTTGTGTTTGTTTTTGTG 59.094 36.000 0.00 0.00 0.00 3.33
3135 5220 5.504830 GCCTTGTGTTTGTGTTTGTTTTTGT 60.505 36.000 0.00 0.00 0.00 2.83
3136 5221 4.908730 GCCTTGTGTTTGTGTTTGTTTTTG 59.091 37.500 0.00 0.00 0.00 2.44
3137 5222 4.576463 TGCCTTGTGTTTGTGTTTGTTTTT 59.424 33.333 0.00 0.00 0.00 1.94
3138 5223 4.130118 TGCCTTGTGTTTGTGTTTGTTTT 58.870 34.783 0.00 0.00 0.00 2.43
3139 5224 3.733337 TGCCTTGTGTTTGTGTTTGTTT 58.267 36.364 0.00 0.00 0.00 2.83
3140 5225 3.393089 TGCCTTGTGTTTGTGTTTGTT 57.607 38.095 0.00 0.00 0.00 2.83
3141 5226 3.393089 TTGCCTTGTGTTTGTGTTTGT 57.607 38.095 0.00 0.00 0.00 2.83
3142 5227 4.739046 TTTTGCCTTGTGTTTGTGTTTG 57.261 36.364 0.00 0.00 0.00 2.93
3176 5261 7.224297 TCTAGTTCTGTGGAAGTGCTATTTTT 58.776 34.615 0.00 0.00 36.59 1.94
3177 5262 6.769512 TCTAGTTCTGTGGAAGTGCTATTTT 58.230 36.000 0.00 0.00 36.59 1.82
3178 5263 6.360370 TCTAGTTCTGTGGAAGTGCTATTT 57.640 37.500 0.00 0.00 36.59 1.40
3179 5264 6.166982 GTTCTAGTTCTGTGGAAGTGCTATT 58.833 40.000 0.00 0.00 36.59 1.73
3180 5265 5.246203 TGTTCTAGTTCTGTGGAAGTGCTAT 59.754 40.000 0.00 0.00 36.59 2.97
3181 5266 4.587262 TGTTCTAGTTCTGTGGAAGTGCTA 59.413 41.667 0.00 0.00 36.59 3.49
3182 5267 3.388024 TGTTCTAGTTCTGTGGAAGTGCT 59.612 43.478 0.00 0.00 36.59 4.40
3183 5268 3.728845 TGTTCTAGTTCTGTGGAAGTGC 58.271 45.455 0.00 0.00 36.59 4.40
3184 5269 6.677781 TTTTGTTCTAGTTCTGTGGAAGTG 57.322 37.500 0.00 0.00 36.59 3.16
3185 5270 6.884836 ACTTTTTGTTCTAGTTCTGTGGAAGT 59.115 34.615 0.00 0.00 38.51 3.01
3186 5271 7.321745 ACTTTTTGTTCTAGTTCTGTGGAAG 57.678 36.000 0.00 0.00 31.46 3.46
3187 5272 8.974060 ATACTTTTTGTTCTAGTTCTGTGGAA 57.026 30.769 0.00 0.00 0.00 3.53
3188 5273 8.208224 TGATACTTTTTGTTCTAGTTCTGTGGA 58.792 33.333 0.00 0.00 0.00 4.02
3189 5274 8.378172 TGATACTTTTTGTTCTAGTTCTGTGG 57.622 34.615 0.00 0.00 0.00 4.17
3190 5275 9.046296 ACTGATACTTTTTGTTCTAGTTCTGTG 57.954 33.333 0.00 0.00 0.00 3.66
3191 5276 9.262358 GACTGATACTTTTTGTTCTAGTTCTGT 57.738 33.333 0.00 0.00 0.00 3.41
3192 5277 8.713271 GGACTGATACTTTTTGTTCTAGTTCTG 58.287 37.037 0.00 0.00 0.00 3.02
3193 5278 8.429641 TGGACTGATACTTTTTGTTCTAGTTCT 58.570 33.333 0.00 0.00 0.00 3.01
3194 5279 8.603242 TGGACTGATACTTTTTGTTCTAGTTC 57.397 34.615 0.00 0.00 0.00 3.01
3195 5280 8.974060 TTGGACTGATACTTTTTGTTCTAGTT 57.026 30.769 0.00 0.00 0.00 2.24
3196 5281 8.211629 ACTTGGACTGATACTTTTTGTTCTAGT 58.788 33.333 0.00 0.00 0.00 2.57
3197 5282 8.608844 ACTTGGACTGATACTTTTTGTTCTAG 57.391 34.615 0.00 0.00 0.00 2.43
3198 5283 8.974060 AACTTGGACTGATACTTTTTGTTCTA 57.026 30.769 0.00 0.00 0.00 2.10
3199 5284 7.881775 AACTTGGACTGATACTTTTTGTTCT 57.118 32.000 0.00 0.00 0.00 3.01
3200 5285 8.837389 AGTAACTTGGACTGATACTTTTTGTTC 58.163 33.333 0.00 0.00 0.00 3.18
3201 5286 8.621286 CAGTAACTTGGACTGATACTTTTTGTT 58.379 33.333 0.00 0.00 46.01 2.83
3202 5287 7.228706 CCAGTAACTTGGACTGATACTTTTTGT 59.771 37.037 4.38 0.00 46.01 2.83
3203 5288 7.228706 ACCAGTAACTTGGACTGATACTTTTTG 59.771 37.037 4.38 0.00 46.01 2.44
3204 5289 7.228706 CACCAGTAACTTGGACTGATACTTTTT 59.771 37.037 4.38 0.00 46.01 1.94
3205 5290 6.710744 CACCAGTAACTTGGACTGATACTTTT 59.289 38.462 4.38 0.00 46.01 2.27
3206 5291 6.231211 CACCAGTAACTTGGACTGATACTTT 58.769 40.000 4.38 0.00 46.01 2.66
3207 5292 5.280011 CCACCAGTAACTTGGACTGATACTT 60.280 44.000 4.38 0.00 46.01 2.24
3208 5293 4.223032 CCACCAGTAACTTGGACTGATACT 59.777 45.833 4.38 0.00 46.01 2.12
3209 5294 4.222145 TCCACCAGTAACTTGGACTGATAC 59.778 45.833 4.38 0.00 46.01 2.24
3210 5295 4.422057 TCCACCAGTAACTTGGACTGATA 58.578 43.478 4.38 0.00 46.01 2.15
3211 5296 3.248024 TCCACCAGTAACTTGGACTGAT 58.752 45.455 4.38 0.00 46.01 2.90
3212 5297 2.632996 CTCCACCAGTAACTTGGACTGA 59.367 50.000 4.38 0.00 46.01 3.41
3213 5298 2.368875 ACTCCACCAGTAACTTGGACTG 59.631 50.000 0.00 0.00 43.32 3.51
3214 5299 2.633481 GACTCCACCAGTAACTTGGACT 59.367 50.000 0.00 0.00 40.87 3.85
3215 5300 2.367567 TGACTCCACCAGTAACTTGGAC 59.632 50.000 0.00 0.00 40.87 4.02
3216 5301 2.684943 TGACTCCACCAGTAACTTGGA 58.315 47.619 0.00 0.00 40.87 3.53
3217 5302 3.181454 ACTTGACTCCACCAGTAACTTGG 60.181 47.826 0.00 0.00 44.09 3.61
3218 5303 4.073293 ACTTGACTCCACCAGTAACTTG 57.927 45.455 0.00 0.00 34.41 3.16
3219 5304 4.900054 AGTACTTGACTCCACCAGTAACTT 59.100 41.667 0.00 0.00 34.41 2.66
3220 5305 4.481072 AGTACTTGACTCCACCAGTAACT 58.519 43.478 0.00 0.00 34.41 2.24
3221 5306 4.868314 AGTACTTGACTCCACCAGTAAC 57.132 45.455 0.00 0.00 34.41 2.50
3222 5307 5.884322 TCTAGTACTTGACTCCACCAGTAA 58.116 41.667 0.00 0.00 39.81 2.24
3223 5308 5.509832 TCTAGTACTTGACTCCACCAGTA 57.490 43.478 0.00 0.00 39.81 2.74
3224 5309 4.383931 TCTAGTACTTGACTCCACCAGT 57.616 45.455 0.00 0.00 39.81 4.00
3225 5310 4.339814 GGATCTAGTACTTGACTCCACCAG 59.660 50.000 20.18 4.16 39.81 4.00
3226 5311 4.264217 TGGATCTAGTACTTGACTCCACCA 60.264 45.833 22.12 16.98 39.81 4.17
3227 5312 4.279145 TGGATCTAGTACTTGACTCCACC 58.721 47.826 22.12 15.44 39.81 4.61
3228 5313 5.916661 TTGGATCTAGTACTTGACTCCAC 57.083 43.478 23.99 10.79 39.81 4.02
3229 5314 5.187186 GGTTTGGATCTAGTACTTGACTCCA 59.813 44.000 22.12 22.12 39.81 3.86
3230 5315 5.187186 TGGTTTGGATCTAGTACTTGACTCC 59.813 44.000 19.19 19.19 39.81 3.85
3231 5316 6.282199 TGGTTTGGATCTAGTACTTGACTC 57.718 41.667 9.25 8.25 39.81 3.36
3232 5317 6.681729 TTGGTTTGGATCTAGTACTTGACT 57.318 37.500 9.25 0.00 42.69 3.41
3233 5318 7.739498 TTTTGGTTTGGATCTAGTACTTGAC 57.261 36.000 9.25 4.20 0.00 3.18
3258 5343 3.385111 TGGGCGGTCAATTTGTACTTTTT 59.615 39.130 0.00 0.00 0.00 1.94
3259 5344 2.959707 TGGGCGGTCAATTTGTACTTTT 59.040 40.909 0.00 0.00 0.00 2.27
3260 5345 2.588620 TGGGCGGTCAATTTGTACTTT 58.411 42.857 0.00 0.00 0.00 2.66
3261 5346 2.279935 TGGGCGGTCAATTTGTACTT 57.720 45.000 0.00 0.00 0.00 2.24
3262 5347 2.159382 CTTGGGCGGTCAATTTGTACT 58.841 47.619 0.00 0.00 0.00 2.73
3263 5348 1.201414 CCTTGGGCGGTCAATTTGTAC 59.799 52.381 0.00 0.00 0.00 2.90
3264 5349 1.074084 TCCTTGGGCGGTCAATTTGTA 59.926 47.619 0.00 0.00 0.00 2.41
3265 5350 0.178975 TCCTTGGGCGGTCAATTTGT 60.179 50.000 0.00 0.00 0.00 2.83
3266 5351 0.243636 GTCCTTGGGCGGTCAATTTG 59.756 55.000 0.00 0.00 0.00 2.32
3267 5352 0.178975 TGTCCTTGGGCGGTCAATTT 60.179 50.000 0.00 0.00 0.00 1.82
3268 5353 0.039618 ATGTCCTTGGGCGGTCAATT 59.960 50.000 0.00 0.00 0.00 2.32
3269 5354 0.916086 TATGTCCTTGGGCGGTCAAT 59.084 50.000 0.00 0.00 0.00 2.57
3270 5355 0.035820 GTATGTCCTTGGGCGGTCAA 60.036 55.000 0.00 0.00 0.00 3.18
3271 5356 1.195442 TGTATGTCCTTGGGCGGTCA 61.195 55.000 0.00 0.00 0.00 4.02
3272 5357 0.035820 TTGTATGTCCTTGGGCGGTC 60.036 55.000 0.00 0.00 0.00 4.79
3273 5358 0.322187 GTTGTATGTCCTTGGGCGGT 60.322 55.000 0.00 0.00 0.00 5.68
3274 5359 0.035439 AGTTGTATGTCCTTGGGCGG 60.035 55.000 0.00 0.00 0.00 6.13
3275 5360 1.821216 AAGTTGTATGTCCTTGGGCG 58.179 50.000 0.00 0.00 0.00 6.13
3276 5361 3.939592 GACTAAGTTGTATGTCCTTGGGC 59.060 47.826 0.00 0.00 0.00 5.36
3277 5362 5.422214 AGACTAAGTTGTATGTCCTTGGG 57.578 43.478 0.00 0.00 0.00 4.12
3278 5363 6.812160 GTGTAGACTAAGTTGTATGTCCTTGG 59.188 42.308 0.00 0.00 0.00 3.61
3279 5364 6.527023 CGTGTAGACTAAGTTGTATGTCCTTG 59.473 42.308 0.00 0.00 0.00 3.61
3280 5365 6.618811 CGTGTAGACTAAGTTGTATGTCCTT 58.381 40.000 0.00 0.00 0.00 3.36
3281 5366 5.392811 GCGTGTAGACTAAGTTGTATGTCCT 60.393 44.000 0.00 0.00 0.00 3.85
3282 5367 4.797349 GCGTGTAGACTAAGTTGTATGTCC 59.203 45.833 0.00 0.00 0.00 4.02
3283 5368 5.396484 TGCGTGTAGACTAAGTTGTATGTC 58.604 41.667 0.00 0.00 0.00 3.06
3284 5369 5.381174 TGCGTGTAGACTAAGTTGTATGT 57.619 39.130 0.00 0.00 0.00 2.29
3285 5370 5.862323 ACTTGCGTGTAGACTAAGTTGTATG 59.138 40.000 4.40 0.00 0.00 2.39
3286 5371 6.022163 ACTTGCGTGTAGACTAAGTTGTAT 57.978 37.500 4.40 0.00 0.00 2.29
3287 5372 5.443185 ACTTGCGTGTAGACTAAGTTGTA 57.557 39.130 4.40 0.00 0.00 2.41
3288 5373 4.317671 ACTTGCGTGTAGACTAAGTTGT 57.682 40.909 4.40 0.00 0.00 3.32
3289 5374 4.620184 GGTACTTGCGTGTAGACTAAGTTG 59.380 45.833 12.50 0.00 32.58 3.16
3290 5375 4.279169 TGGTACTTGCGTGTAGACTAAGTT 59.721 41.667 12.50 0.00 32.58 2.66
3291 5376 3.822735 TGGTACTTGCGTGTAGACTAAGT 59.177 43.478 12.10 12.10 33.94 2.24
3292 5377 4.430137 TGGTACTTGCGTGTAGACTAAG 57.570 45.455 0.00 3.38 0.00 2.18
3293 5378 5.649395 ACTATGGTACTTGCGTGTAGACTAA 59.351 40.000 0.00 0.00 0.00 2.24
3294 5379 5.065602 CACTATGGTACTTGCGTGTAGACTA 59.934 44.000 0.00 0.00 0.00 2.59
3295 5380 4.015084 ACTATGGTACTTGCGTGTAGACT 58.985 43.478 0.00 0.00 0.00 3.24
3296 5381 4.103357 CACTATGGTACTTGCGTGTAGAC 58.897 47.826 0.00 0.00 0.00 2.59
3297 5382 3.428452 GCACTATGGTACTTGCGTGTAGA 60.428 47.826 0.00 0.00 0.00 2.59
3298 5383 2.858344 GCACTATGGTACTTGCGTGTAG 59.142 50.000 0.00 0.00 0.00 2.74
3299 5384 2.494471 AGCACTATGGTACTTGCGTGTA 59.506 45.455 0.00 0.00 40.04 2.90
3300 5385 1.275291 AGCACTATGGTACTTGCGTGT 59.725 47.619 0.00 0.00 40.04 4.49
3301 5386 1.660607 CAGCACTATGGTACTTGCGTG 59.339 52.381 0.00 0.00 40.04 5.34
3302 5387 1.548719 TCAGCACTATGGTACTTGCGT 59.451 47.619 0.00 0.00 40.04 5.24
3303 5388 2.293677 TCAGCACTATGGTACTTGCG 57.706 50.000 0.00 0.00 40.04 4.85


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

AutoCloner maintained by Alex Coulton.