Multiple sequence alignment - TraesCS7B01G075500

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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 TraesCS7B01G075500 chr7B 100.000 3524 0 0 1 3524 84766492 84762969 0.000000e+00 6508
1 TraesCS7B01G075500 chr7B 90.455 1823 160 7 701 2513 84650993 84652811 0.000000e+00 2390
2 TraesCS7B01G075500 chr7B 89.248 1916 156 20 605 2514 84700603 84702474 0.000000e+00 2351
3 TraesCS7B01G075500 chr7B 92.459 915 48 7 2160 3073 84733260 84732366 0.000000e+00 1288
4 TraesCS7B01G075500 chr7B 95.469 309 12 2 3065 3373 84732340 84732034 3.160000e-135 492
5 TraesCS7B01G075500 chr7B 94.000 150 9 0 3375 3524 84764994 84764845 9.840000e-56 228
6 TraesCS7B01G075500 chr7B 90.667 150 14 0 3375 3524 84701459 84701608 2.150000e-47 200
7 TraesCS7B01G075500 chr7B 90.000 150 15 0 3375 3524 84651797 84651946 9.980000e-46 195
8 TraesCS7B01G075500 chr7B 86.301 146 20 0 2894 3039 511308809 511308954 3.640000e-35 159
9 TraesCS7B01G075500 chr7A 92.679 2240 135 16 340 2565 126368300 126366076 0.000000e+00 3201
10 TraesCS7B01G075500 chr7A 88.962 1975 154 28 547 2514 126195364 126197281 0.000000e+00 2381
11 TraesCS7B01G075500 chr7A 88.059 2035 180 27 576 2597 126190917 126192901 0.000000e+00 2353
12 TraesCS7B01G075500 chr7A 92.667 150 11 0 3375 3524 126367145 126366996 2.130000e-52 217
13 TraesCS7B01G075500 chr7A 92.000 150 12 0 3375 3524 126196266 126196415 9.910000e-51 211
14 TraesCS7B01G075500 chr7A 90.667 150 14 0 3375 3524 126191804 126191953 2.150000e-47 200
15 TraesCS7B01G075500 chr7D 92.612 2098 129 13 492 2565 123491232 123489137 0.000000e+00 2992
16 TraesCS7B01G075500 chr7D 89.989 1808 163 14 803 2597 123454996 123456798 0.000000e+00 2320
17 TraesCS7B01G075500 chr7D 89.510 1430 148 2 1084 2512 123462138 123463566 0.000000e+00 1808
18 TraesCS7B01G075500 chr7D 86.884 1136 142 3 1407 2541 123484830 123483701 0.000000e+00 1266
19 TraesCS7B01G075500 chr7D 87.052 363 39 4 145 506 123493012 123492657 1.520000e-108 403
20 TraesCS7B01G075500 chr7D 82.697 445 38 8 605 1037 123460891 123461308 3.340000e-95 359
21 TraesCS7B01G075500 chr7D 89.865 148 15 0 3375 3522 123462553 123462700 1.290000e-44 191
22 TraesCS7B01G075500 chr7D 88.667 150 17 0 3375 3524 123484738 123484589 2.160000e-42 183
23 TraesCS7B01G075500 chr3B 89.571 163 15 1 2894 3056 815037954 815038114 4.610000e-49 206
24 TraesCS7B01G075500 chr6D 85.417 144 21 0 2894 3037 11286544 11286401 2.190000e-32 150
25 TraesCS7B01G075500 chr4D 84.932 146 21 1 2894 3039 6711547 6711691 2.830000e-31 147
26 TraesCS7B01G075500 chr2D 86.131 137 16 3 2893 3027 552907875 552908010 1.020000e-30 145
27 TraesCS7B01G075500 chr6B 84.247 146 23 0 2894 3039 526964425 526964570 3.670000e-30 143
28 TraesCS7B01G075500 chr5A 84.138 145 23 0 3375 3519 457567104 457566960 1.320000e-29 141
29 TraesCS7B01G075500 chr5B 81.325 166 21 9 2874 3033 544781984 544782145 3.690000e-25 126
30 TraesCS7B01G075500 chr1A 79.310 174 36 0 2893 3066 20156128 20156301 4.780000e-24 122


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 TraesCS7B01G075500 chr7B 84762969 84766492 3523 True 3368.00 6508 97.000000 1 3524 2 chr7B.!!$R2 3523
1 TraesCS7B01G075500 chr7B 84650993 84652811 1818 False 1292.50 2390 90.227500 701 3524 2 chr7B.!!$F2 2823
2 TraesCS7B01G075500 chr7B 84700603 84702474 1871 False 1275.50 2351 89.957500 605 3524 2 chr7B.!!$F3 2919
3 TraesCS7B01G075500 chr7B 84732034 84733260 1226 True 890.00 1288 93.964000 2160 3373 2 chr7B.!!$R1 1213
4 TraesCS7B01G075500 chr7A 126366076 126368300 2224 True 1709.00 3201 92.673000 340 3524 2 chr7A.!!$R1 3184
5 TraesCS7B01G075500 chr7A 126190917 126197281 6364 False 1286.25 2381 89.922000 547 3524 4 chr7A.!!$F1 2977
6 TraesCS7B01G075500 chr7D 123454996 123456798 1802 False 2320.00 2320 89.989000 803 2597 1 chr7D.!!$F1 1794
7 TraesCS7B01G075500 chr7D 123489137 123493012 3875 True 1697.50 2992 89.832000 145 2565 2 chr7D.!!$R2 2420
8 TraesCS7B01G075500 chr7D 123460891 123463566 2675 False 786.00 1808 87.357333 605 3522 3 chr7D.!!$F2 2917
9 TraesCS7B01G075500 chr7D 123483701 123484830 1129 True 724.50 1266 87.775500 1407 3524 2 chr7D.!!$R1 2117

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
234 235 0.031585 CACAACCGACCTCGAACTCA 59.968 55.0 0.00 0.0 43.02 3.41 F
479 486 0.036388 GTCATCCGGAGTGCCAAGAA 60.036 55.0 11.34 0.0 0.00 2.52 F
1437 3718 0.965866 TCGTCTCCGACTTCTGCCAT 60.966 55.0 0.00 0.0 38.40 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 8408 0.028110 GCGCCAACTCGATTTCATCC 59.972 55.0 0.00 0.0 0.0 3.51 R
2007 8751 0.736325 CGTACTGCTCGGGGTTCTTG 60.736 60.0 0.00 0.0 0.0 3.02 R
3397 10184 0.039798 TGTACCTCTCGACGTTGTGC 60.040 55.0 1.96 0.0 0.0 4.57 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
22 23 4.873129 CGCGCCGTGGTAGCTCAT 62.873 66.667 0.00 0.00 0.00 2.90
23 24 3.264897 GCGCCGTGGTAGCTCATG 61.265 66.667 0.00 0.00 0.00 3.07
24 25 2.184322 CGCCGTGGTAGCTCATGT 59.816 61.111 0.00 0.00 0.00 3.21
25 26 2.167219 CGCCGTGGTAGCTCATGTG 61.167 63.158 0.00 0.00 0.00 3.21
26 27 1.079127 GCCGTGGTAGCTCATGTGT 60.079 57.895 0.00 0.00 0.00 3.72
27 28 1.361668 GCCGTGGTAGCTCATGTGTG 61.362 60.000 0.00 0.00 0.00 3.82
28 29 0.740868 CCGTGGTAGCTCATGTGTGG 60.741 60.000 0.00 0.00 0.00 4.17
29 30 0.246360 CGTGGTAGCTCATGTGTGGA 59.754 55.000 0.00 0.00 0.00 4.02
30 31 1.134699 CGTGGTAGCTCATGTGTGGAT 60.135 52.381 0.00 0.00 0.00 3.41
31 32 2.283298 GTGGTAGCTCATGTGTGGATG 58.717 52.381 0.00 0.00 0.00 3.51
32 33 1.210234 TGGTAGCTCATGTGTGGATGG 59.790 52.381 0.00 0.00 0.00 3.51
33 34 1.486310 GGTAGCTCATGTGTGGATGGA 59.514 52.381 0.00 0.00 0.00 3.41
34 35 2.555199 GTAGCTCATGTGTGGATGGAC 58.445 52.381 0.00 0.00 0.00 4.02
35 36 0.254178 AGCTCATGTGTGGATGGACC 59.746 55.000 0.00 0.00 39.54 4.46
36 37 1.091771 GCTCATGTGTGGATGGACCG 61.092 60.000 0.00 0.00 42.61 4.79
42 43 2.109181 GTGGATGGACCGCCTAGC 59.891 66.667 4.97 0.00 42.81 3.42
53 54 3.188786 GCCTAGCGTGCGGAGTTG 61.189 66.667 0.00 0.00 0.00 3.16
54 55 3.188786 CCTAGCGTGCGGAGTTGC 61.189 66.667 0.00 0.00 0.00 4.17
55 56 3.545481 CTAGCGTGCGGAGTTGCG 61.545 66.667 0.00 0.00 37.81 4.85
63 64 3.499737 CGGAGTTGCGCCCATGAC 61.500 66.667 4.18 0.00 0.00 3.06
64 65 2.359850 GGAGTTGCGCCCATGACA 60.360 61.111 4.18 0.00 0.00 3.58
65 66 1.971167 GGAGTTGCGCCCATGACAA 60.971 57.895 4.18 0.00 0.00 3.18
66 67 1.523154 GGAGTTGCGCCCATGACAAA 61.523 55.000 4.18 0.00 0.00 2.83
67 68 0.387239 GAGTTGCGCCCATGACAAAC 60.387 55.000 4.18 0.00 0.00 2.93
68 69 0.823356 AGTTGCGCCCATGACAAACT 60.823 50.000 4.18 1.73 0.00 2.66
69 70 0.387239 GTTGCGCCCATGACAAACTC 60.387 55.000 4.18 0.00 0.00 3.01
70 71 0.821301 TTGCGCCCATGACAAACTCA 60.821 50.000 4.18 0.00 0.00 3.41
71 72 1.210155 GCGCCCATGACAAACTCAC 59.790 57.895 0.00 0.00 0.00 3.51
72 73 1.497278 CGCCCATGACAAACTCACG 59.503 57.895 0.00 0.00 0.00 4.35
73 74 1.210155 GCCCATGACAAACTCACGC 59.790 57.895 0.00 0.00 0.00 5.34
74 75 1.875963 CCCATGACAAACTCACGCC 59.124 57.895 0.00 0.00 0.00 5.68
75 76 1.586154 CCCATGACAAACTCACGCCC 61.586 60.000 0.00 0.00 0.00 6.13
76 77 1.497278 CATGACAAACTCACGCCCG 59.503 57.895 0.00 0.00 0.00 6.13
77 78 2.325082 ATGACAAACTCACGCCCGC 61.325 57.895 0.00 0.00 0.00 6.13
78 79 3.723348 GACAAACTCACGCCCGCC 61.723 66.667 0.00 0.00 0.00 6.13
96 97 4.463879 CTGGCCGACTGGGAGCAG 62.464 72.222 0.00 0.00 38.47 4.24
100 101 4.069232 CCGACTGGGAGCAGCGAA 62.069 66.667 0.00 0.00 38.47 4.70
101 102 2.811317 CGACTGGGAGCAGCGAAC 60.811 66.667 0.00 0.00 0.00 3.95
102 103 2.435059 GACTGGGAGCAGCGAACC 60.435 66.667 0.00 0.00 0.00 3.62
103 104 2.925170 ACTGGGAGCAGCGAACCT 60.925 61.111 4.95 0.00 0.00 3.50
104 105 2.125350 CTGGGAGCAGCGAACCTC 60.125 66.667 4.95 0.00 0.00 3.85
105 106 3.672295 CTGGGAGCAGCGAACCTCC 62.672 68.421 7.03 7.03 45.52 4.30
107 108 4.475135 GGAGCAGCGAACCTCCCC 62.475 72.222 4.81 0.00 41.42 4.81
108 109 4.475135 GAGCAGCGAACCTCCCCC 62.475 72.222 0.00 0.00 0.00 5.40
110 111 4.475135 GCAGCGAACCTCCCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
111 112 3.787001 CAGCGAACCTCCCCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
112 113 4.332543 AGCGAACCTCCCCCTCCA 62.333 66.667 0.00 0.00 0.00 3.86
113 114 3.787001 GCGAACCTCCCCCTCCAG 61.787 72.222 0.00 0.00 0.00 3.86
114 115 3.787001 CGAACCTCCCCCTCCAGC 61.787 72.222 0.00 0.00 0.00 4.85
115 116 3.787001 GAACCTCCCCCTCCAGCG 61.787 72.222 0.00 0.00 0.00 5.18
116 117 4.332543 AACCTCCCCCTCCAGCGA 62.333 66.667 0.00 0.00 0.00 4.93
119 120 4.787280 CTCCCCCTCCAGCGACCT 62.787 72.222 0.00 0.00 0.00 3.85
120 121 3.352748 TCCCCCTCCAGCGACCTA 61.353 66.667 0.00 0.00 0.00 3.08
121 122 2.365105 CCCCCTCCAGCGACCTAA 60.365 66.667 0.00 0.00 0.00 2.69
122 123 1.766461 CCCCCTCCAGCGACCTAAT 60.766 63.158 0.00 0.00 0.00 1.73
123 124 1.447643 CCCCTCCAGCGACCTAATG 59.552 63.158 0.00 0.00 0.00 1.90
124 125 1.338136 CCCCTCCAGCGACCTAATGT 61.338 60.000 0.00 0.00 0.00 2.71
125 126 0.179073 CCCTCCAGCGACCTAATGTG 60.179 60.000 0.00 0.00 0.00 3.21
126 127 0.179073 CCTCCAGCGACCTAATGTGG 60.179 60.000 0.00 0.00 0.00 4.17
130 131 3.102097 GCGACCTAATGTGGCTGC 58.898 61.111 0.00 0.00 44.47 5.25
131 132 2.813179 GCGACCTAATGTGGCTGCG 61.813 63.158 0.00 0.00 44.47 5.18
132 133 2.813179 CGACCTAATGTGGCTGCGC 61.813 63.158 0.00 0.00 0.00 6.09
193 194 0.117140 TGGACCACCTCCATCTCTGT 59.883 55.000 0.00 0.00 44.99 3.41
207 208 3.190849 CTGTGCTCATCGGTGGCG 61.191 66.667 0.00 0.00 0.00 5.69
222 223 4.659874 GCGCCGACAACACAACCG 62.660 66.667 0.00 0.00 0.00 4.44
234 235 0.031585 CACAACCGACCTCGAACTCA 59.968 55.000 0.00 0.00 43.02 3.41
236 237 1.336887 ACAACCGACCTCGAACTCATG 60.337 52.381 0.00 0.00 43.02 3.07
238 239 0.526662 ACCGACCTCGAACTCATGTC 59.473 55.000 0.00 0.00 43.02 3.06
249 250 1.519455 CTCATGTCCGTCGCCTTCC 60.519 63.158 0.00 0.00 0.00 3.46
289 291 3.374402 CCTCGTCTCCACCGTGCT 61.374 66.667 0.00 0.00 0.00 4.40
296 298 4.451150 TCCACCGTGCTCCGCATC 62.451 66.667 0.00 0.00 41.91 3.91
353 355 2.948979 AGAGTGAGTGAATAGAGAGCGG 59.051 50.000 0.00 0.00 0.00 5.52
363 365 1.323412 TAGAGAGCGGAGAGGAATGC 58.677 55.000 0.00 0.00 0.00 3.56
373 375 2.228343 GGAGAGGAATGCATGCATAAGC 59.772 50.000 32.36 22.84 42.57 3.09
381 383 1.151668 GCATGCATAAGCTAGTCCCG 58.848 55.000 14.21 0.00 42.74 5.14
386 388 1.571919 CATAAGCTAGTCCCGTGCAC 58.428 55.000 6.82 6.82 0.00 4.57
441 443 2.202676 GAGCGAACGCCTCTGGAG 60.203 66.667 15.44 0.00 43.17 3.86
442 444 2.992114 AGCGAACGCCTCTGGAGT 60.992 61.111 15.44 0.00 43.17 3.85
444 446 2.995872 GCGAACGCCTCTGGAGTCT 61.996 63.158 8.03 0.00 33.90 3.24
445 447 1.153939 CGAACGCCTCTGGAGTCTG 60.154 63.158 0.00 0.00 33.90 3.51
446 448 1.216710 GAACGCCTCTGGAGTCTGG 59.783 63.158 0.00 0.00 33.90 3.86
447 449 1.228894 AACGCCTCTGGAGTCTGGA 60.229 57.895 0.00 0.00 33.90 3.86
448 450 1.536943 AACGCCTCTGGAGTCTGGAC 61.537 60.000 0.00 0.00 33.90 4.02
449 451 1.979155 CGCCTCTGGAGTCTGGACA 60.979 63.158 3.51 0.00 0.00 4.02
450 452 1.326213 CGCCTCTGGAGTCTGGACAT 61.326 60.000 3.51 0.00 0.00 3.06
457 459 4.352893 TCTGGAGTCTGGACATCAATGTA 58.647 43.478 3.51 0.00 41.95 2.29
469 476 3.118920 ACATCAATGTAACGTCATCCGGA 60.119 43.478 6.61 6.61 39.68 5.14
479 486 0.036388 GTCATCCGGAGTGCCAAGAA 60.036 55.000 11.34 0.00 0.00 2.52
528 1974 2.684001 TATTCAGGCCGAACGTCAAT 57.316 45.000 11.39 0.43 36.12 2.57
544 1990 6.214191 ACGTCAATAAGACTGATGTCAGAT 57.786 37.500 16.41 5.28 46.59 2.90
663 2110 3.446873 AGTGACAAGTGACAAATTTGCCA 59.553 39.130 18.12 10.78 0.00 4.92
672 2119 3.058293 TGACAAATTTGCCATCACTCGTC 60.058 43.478 18.12 4.83 0.00 4.20
761 2209 1.946156 CACGCCTCCGTCATCATCG 60.946 63.158 0.00 0.00 46.39 3.84
788 2236 8.661257 TCAACATAATAACGGACAAACACTATG 58.339 33.333 0.00 0.00 0.00 2.23
790 2238 7.332557 ACATAATAACGGACAAACACTATGGA 58.667 34.615 0.00 0.00 0.00 3.41
816 2269 6.955963 GCATAACTGAAAATCTTGTAGTGACG 59.044 38.462 0.00 0.00 0.00 4.35
846 2299 1.736586 GTCACCTCGCCATCTCGAT 59.263 57.895 0.00 0.00 37.87 3.59
1065 2542 3.458163 GGGCATGAGGACGTCGGA 61.458 66.667 9.92 0.00 0.00 4.55
1437 3718 0.965866 TCGTCTCCGACTTCTGCCAT 60.966 55.000 0.00 0.00 38.40 4.40
1539 8282 1.135373 CAGCACAACGTCGAGAGGTAT 60.135 52.381 0.00 0.00 0.00 2.73
1665 8408 1.586564 CGGGTTCGAGAAGCTAGCG 60.587 63.158 9.55 6.43 38.72 4.26
1722 8465 3.452474 CATCGTCATGAACTCCTTCCTC 58.548 50.000 0.00 0.00 30.57 3.71
1746 8489 4.549516 GAGCCGGAGTACGTCGCC 62.550 72.222 5.05 0.00 42.24 5.54
1830 8573 2.092291 CGCCGAGACGCTAGCAAAA 61.092 57.895 16.45 0.00 0.00 2.44
1872 8615 4.719369 GACGCCGACGAGTGCCTT 62.719 66.667 0.00 0.00 43.93 4.35
2007 8751 1.080025 CCCGTTCGTCTGGGTTCTC 60.080 63.158 1.19 0.00 40.76 2.87
2518 9268 2.358737 CGGGAGGTTGCACCACTC 60.359 66.667 7.86 5.69 41.95 3.51
2577 9330 0.818296 AGAGCGCCGAATGTTCTAGT 59.182 50.000 2.29 0.00 0.00 2.57
2603 9356 5.068215 TCAGAAGATTGTTTGGGGGTTAA 57.932 39.130 0.00 0.00 0.00 2.01
2607 9360 7.898636 TCAGAAGATTGTTTGGGGGTTAAATAT 59.101 33.333 0.00 0.00 0.00 1.28
2615 9368 7.348033 TGTTTGGGGGTTAAATATACTACAGG 58.652 38.462 0.00 0.00 0.00 4.00
2617 9370 6.752285 TGGGGGTTAAATATACTACAGGTC 57.248 41.667 0.00 0.00 0.00 3.85
2630 9383 2.417719 ACAGGTCCCCTAACTTGTCT 57.582 50.000 0.00 0.00 34.74 3.41
2632 9385 1.978580 CAGGTCCCCTAACTTGTCTGT 59.021 52.381 0.00 0.00 29.64 3.41
2636 9389 1.975680 TCCCCTAACTTGTCTGTGACC 59.024 52.381 0.00 0.00 0.00 4.02
2646 9399 1.478916 TGTCTGTGACCGTCAGTTTCA 59.521 47.619 0.08 0.00 34.86 2.69
2658 9411 4.748102 CCGTCAGTTTCAGTGCTTAAACTA 59.252 41.667 10.13 0.30 42.52 2.24
2702 9455 4.223556 TGTAACTTGTCTGGGTGTTCAA 57.776 40.909 0.00 0.00 0.00 2.69
2706 9459 5.767816 AACTTGTCTGGGTGTTCAAATAC 57.232 39.130 0.00 0.00 0.00 1.89
2708 9461 3.755112 TGTCTGGGTGTTCAAATACGA 57.245 42.857 0.00 0.00 0.00 3.43
2732 9485 2.288579 CCTATGAAAGTATGGCGCCGTA 60.289 50.000 24.54 24.54 0.00 4.02
2735 9488 1.137282 TGAAAGTATGGCGCCGTATCA 59.863 47.619 30.13 25.16 0.00 2.15
2825 9578 6.506200 CGTTTTGAGCTATGTGTGTTGTTTTG 60.506 38.462 0.00 0.00 0.00 2.44
2832 9585 7.316640 AGCTATGTGTGTTGTTTTGTTACAAA 58.683 30.769 6.41 6.41 39.54 2.83
2840 9593 5.123979 TGTTGTTTTGTTACAAAAATGCCCC 59.876 36.000 22.51 11.16 39.54 5.80
2915 9668 0.099259 TACTGGAATCGCCACGTACG 59.901 55.000 15.01 15.01 43.33 3.67
2928 9681 3.755628 GTACGCCGAGTGCCAGGA 61.756 66.667 0.00 0.00 36.24 3.86
2929 9682 2.992689 TACGCCGAGTGCCAGGAA 60.993 61.111 0.00 0.00 36.24 3.36
2930 9683 3.291101 TACGCCGAGTGCCAGGAAC 62.291 63.158 0.00 0.00 36.24 3.62
2931 9684 4.680237 CGCCGAGTGCCAGGAACA 62.680 66.667 0.00 0.00 36.24 3.18
2932 9685 3.050275 GCCGAGTGCCAGGAACAC 61.050 66.667 0.00 0.00 38.35 3.32
3011 9764 3.066814 ACCCGGCGTACACCTCTC 61.067 66.667 6.01 0.00 0.00 3.20
3028 9781 5.241506 CACCTCTCAGGCAAACAGATTTTTA 59.758 40.000 0.00 0.00 39.63 1.52
3031 9784 4.215399 TCTCAGGCAAACAGATTTTTACCG 59.785 41.667 0.00 0.00 0.00 4.02
3033 9786 4.023536 TCAGGCAAACAGATTTTTACCGAC 60.024 41.667 0.00 0.00 0.00 4.79
3044 9797 4.657436 TTTTTACCGACAGCCATTTGTT 57.343 36.364 0.00 0.00 0.00 2.83
3073 9827 2.221055 CGGCTAAGACTTTGTGTGTGTC 59.779 50.000 0.00 0.00 0.00 3.67
3074 9828 2.221055 GGCTAAGACTTTGTGTGTGTCG 59.779 50.000 0.00 0.00 36.01 4.35
3075 9829 2.348591 GCTAAGACTTTGTGTGTGTCGC 60.349 50.000 0.00 0.00 36.01 5.19
3076 9830 0.650512 AAGACTTTGTGTGTGTCGCG 59.349 50.000 0.00 0.00 36.01 5.87
3077 9831 1.367665 GACTTTGTGTGTGTCGCGC 60.368 57.895 0.00 0.00 0.00 6.86
3078 9832 2.423517 CTTTGTGTGTGTCGCGCG 60.424 61.111 26.76 26.76 0.00 6.86
3079 9833 4.583254 TTTGTGTGTGTCGCGCGC 62.583 61.111 27.95 23.91 38.49 6.86
3236 10023 5.823861 AAGGGCCACATGTCTTTTTATTT 57.176 34.783 6.18 0.00 0.00 1.40
3237 10024 5.823861 AGGGCCACATGTCTTTTTATTTT 57.176 34.783 6.18 0.00 0.00 1.82
3240 10027 5.512232 GGGCCACATGTCTTTTTATTTTCCA 60.512 40.000 4.39 0.00 0.00 3.53
3373 10160 9.444600 AAGTCTATAACCATACGATTTGTTTGT 57.555 29.630 0.00 0.00 0.00 2.83
3374 10161 9.444600 AGTCTATAACCATACGATTTGTTTGTT 57.555 29.630 0.00 0.00 0.00 2.83
3375 10162 9.485591 GTCTATAACCATACGATTTGTTTGTTG 57.514 33.333 0.00 0.00 0.00 3.33
3376 10163 8.178964 TCTATAACCATACGATTTGTTTGTTGC 58.821 33.333 0.00 0.00 0.00 4.17
3377 10164 3.560503 ACCATACGATTTGTTTGTTGCG 58.439 40.909 0.00 0.00 0.00 4.85
3378 10165 2.341168 CCATACGATTTGTTTGTTGCGC 59.659 45.455 0.00 0.00 0.00 6.09
3379 10166 2.039327 TACGATTTGTTTGTTGCGCC 57.961 45.000 4.18 0.00 0.00 6.53
3380 10167 0.383949 ACGATTTGTTTGTTGCGCCT 59.616 45.000 4.18 0.00 0.00 5.52
3381 10168 1.202359 ACGATTTGTTTGTTGCGCCTT 60.202 42.857 4.18 0.00 0.00 4.35
3382 10169 1.451651 CGATTTGTTTGTTGCGCCTTC 59.548 47.619 4.18 0.00 0.00 3.46
3383 10170 2.742774 GATTTGTTTGTTGCGCCTTCT 58.257 42.857 4.18 0.00 0.00 2.85
3384 10171 1.919918 TTTGTTTGTTGCGCCTTCTG 58.080 45.000 4.18 0.00 0.00 3.02
3385 10172 0.527385 TTGTTTGTTGCGCCTTCTGC 60.527 50.000 4.18 0.00 0.00 4.26
3394 10181 2.817396 GCCTTCTGCGTCCTCTGC 60.817 66.667 0.00 0.00 0.00 4.26
3395 10182 2.125350 CCTTCTGCGTCCTCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
3396 10183 2.659016 CTTCTGCGTCCTCTGCCA 59.341 61.111 0.00 0.00 0.00 4.92
3397 10184 1.447489 CTTCTGCGTCCTCTGCCAG 60.447 63.158 0.00 0.00 0.00 4.85
3398 10185 3.596066 TTCTGCGTCCTCTGCCAGC 62.596 63.158 0.00 0.00 0.00 4.85
3399 10186 4.383861 CTGCGTCCTCTGCCAGCA 62.384 66.667 0.00 0.00 36.34 4.41
3400 10187 4.687215 TGCGTCCTCTGCCAGCAC 62.687 66.667 0.00 0.00 32.43 4.40
3401 10188 4.687215 GCGTCCTCTGCCAGCACA 62.687 66.667 0.00 0.00 0.00 4.57
3402 10189 2.031012 CGTCCTCTGCCAGCACAA 59.969 61.111 0.00 0.00 0.00 3.33
3403 10190 2.320587 CGTCCTCTGCCAGCACAAC 61.321 63.158 0.00 0.00 0.00 3.32
3404 10191 2.031012 TCCTCTGCCAGCACAACG 59.969 61.111 0.00 0.00 0.00 4.10
3405 10192 2.281070 CCTCTGCCAGCACAACGT 60.281 61.111 0.00 0.00 0.00 3.99
3406 10193 2.320587 CCTCTGCCAGCACAACGTC 61.321 63.158 0.00 0.00 0.00 4.34
3407 10194 2.661537 TCTGCCAGCACAACGTCG 60.662 61.111 0.00 0.00 0.00 5.12
3408 10195 2.661537 CTGCCAGCACAACGTCGA 60.662 61.111 0.00 0.00 0.00 4.20
3409 10196 2.661537 TGCCAGCACAACGTCGAG 60.662 61.111 0.00 0.00 0.00 4.04
3410 10197 2.355837 GCCAGCACAACGTCGAGA 60.356 61.111 0.00 0.00 0.00 4.04
3411 10198 2.375766 GCCAGCACAACGTCGAGAG 61.376 63.158 0.00 0.00 0.00 3.20
3412 10199 1.734477 CCAGCACAACGTCGAGAGG 60.734 63.158 0.00 0.00 0.00 3.69
3413 10200 1.007271 CAGCACAACGTCGAGAGGT 60.007 57.895 0.00 0.00 0.00 3.85
3414 10201 0.240145 CAGCACAACGTCGAGAGGTA 59.760 55.000 0.00 0.00 0.00 3.08
3415 10202 0.240411 AGCACAACGTCGAGAGGTAC 59.760 55.000 0.00 0.00 0.00 3.34
3416 10203 0.039798 GCACAACGTCGAGAGGTACA 60.040 55.000 0.00 0.00 0.00 2.90
3417 10204 1.601162 GCACAACGTCGAGAGGTACAA 60.601 52.381 0.00 0.00 0.00 2.41
3418 10205 2.049228 CACAACGTCGAGAGGTACAAC 58.951 52.381 0.00 0.00 0.00 3.32
3419 10206 1.952296 ACAACGTCGAGAGGTACAACT 59.048 47.619 0.00 0.00 0.00 3.16
3420 10207 2.031333 ACAACGTCGAGAGGTACAACTC 60.031 50.000 0.00 1.88 37.77 3.01
3421 10208 1.163554 ACGTCGAGAGGTACAACTCC 58.836 55.000 0.00 1.04 38.26 3.85
3422 10209 1.271271 ACGTCGAGAGGTACAACTCCT 60.271 52.381 0.00 0.00 38.26 3.69
3423 10210 2.027745 ACGTCGAGAGGTACAACTCCTA 60.028 50.000 0.00 0.73 38.26 2.94
3424 10211 2.351111 CGTCGAGAGGTACAACTCCTAC 59.649 54.545 11.20 9.31 38.26 3.18
3425 10212 2.351111 GTCGAGAGGTACAACTCCTACG 59.649 54.545 11.20 8.07 38.26 3.51
3426 10213 1.669779 CGAGAGGTACAACTCCTACGG 59.330 57.143 11.20 0.00 38.26 4.02
3427 10214 1.404748 GAGAGGTACAACTCCTACGGC 59.595 57.143 0.00 0.00 38.26 5.68
3428 10215 1.180029 GAGGTACAACTCCTACGGCA 58.820 55.000 0.00 0.00 35.20 5.69
3429 10216 1.134560 GAGGTACAACTCCTACGGCAG 59.865 57.143 0.00 0.00 35.20 4.85
3430 10217 0.459759 GGTACAACTCCTACGGCAGC 60.460 60.000 0.00 0.00 0.00 5.25
3431 10218 0.245539 GTACAACTCCTACGGCAGCA 59.754 55.000 0.00 0.00 0.00 4.41
3432 10219 1.134788 GTACAACTCCTACGGCAGCAT 60.135 52.381 0.00 0.00 0.00 3.79
3433 10220 0.391661 ACAACTCCTACGGCAGCATG 60.392 55.000 0.00 0.00 40.87 4.06
3434 10221 1.091771 CAACTCCTACGGCAGCATGG 61.092 60.000 0.00 0.00 35.86 3.66
3444 10231 2.741985 CAGCATGGCCGACGACAA 60.742 61.111 0.00 0.00 0.00 3.18
3445 10232 2.742372 AGCATGGCCGACGACAAC 60.742 61.111 0.00 0.00 0.00 3.32
3446 10233 4.147322 GCATGGCCGACGACAACG 62.147 66.667 0.00 0.00 45.75 4.10
3447 10234 2.431771 CATGGCCGACGACAACGA 60.432 61.111 0.00 0.00 42.66 3.85
3448 10235 2.126071 ATGGCCGACGACAACGAG 60.126 61.111 0.00 0.00 42.66 4.18
3457 10244 4.754667 GACAACGAGCCGGGGGTC 62.755 72.222 2.18 6.84 39.05 4.46
3481 10268 2.586357 GGCGTGGAGAGGCGAATC 60.586 66.667 0.00 0.00 33.56 2.52
3482 10269 2.184322 GCGTGGAGAGGCGAATCA 59.816 61.111 0.00 0.00 0.00 2.57
3483 10270 1.447838 GCGTGGAGAGGCGAATCAA 60.448 57.895 0.00 0.00 0.00 2.57
3484 10271 1.424493 GCGTGGAGAGGCGAATCAAG 61.424 60.000 0.00 0.00 0.00 3.02
3485 10272 0.807667 CGTGGAGAGGCGAATCAAGG 60.808 60.000 0.00 0.00 0.00 3.61
3486 10273 0.250513 GTGGAGAGGCGAATCAAGGT 59.749 55.000 0.00 0.00 0.00 3.50
3487 10274 0.250234 TGGAGAGGCGAATCAAGGTG 59.750 55.000 0.00 0.00 0.00 4.00
3488 10275 0.537188 GGAGAGGCGAATCAAGGTGA 59.463 55.000 0.00 0.00 0.00 4.02
3489 10276 1.646189 GAGAGGCGAATCAAGGTGAC 58.354 55.000 0.00 0.00 0.00 3.67
3490 10277 0.250513 AGAGGCGAATCAAGGTGACC 59.749 55.000 0.00 0.00 0.00 4.02
3491 10278 0.036388 GAGGCGAATCAAGGTGACCA 60.036 55.000 3.63 0.00 0.00 4.02
3492 10279 0.036010 AGGCGAATCAAGGTGACCAG 60.036 55.000 3.63 0.00 0.00 4.00
3493 10280 1.026718 GGCGAATCAAGGTGACCAGG 61.027 60.000 3.63 0.00 0.00 4.45
3494 10281 1.026718 GCGAATCAAGGTGACCAGGG 61.027 60.000 3.63 0.00 0.00 4.45
3495 10282 1.026718 CGAATCAAGGTGACCAGGGC 61.027 60.000 3.63 0.00 0.00 5.19
3496 10283 1.002134 AATCAAGGTGACCAGGGCG 60.002 57.895 3.63 0.00 0.00 6.13
3497 10284 3.628646 ATCAAGGTGACCAGGGCGC 62.629 63.158 3.63 0.00 0.00 6.53
3498 10285 4.641645 CAAGGTGACCAGGGCGCA 62.642 66.667 10.83 0.00 0.00 6.09
3499 10286 3.884774 AAGGTGACCAGGGCGCAA 61.885 61.111 10.83 0.00 0.00 4.85
3500 10287 3.850098 AAGGTGACCAGGGCGCAAG 62.850 63.158 10.83 0.00 43.44 4.01
3513 10300 4.678743 GCAAGCCCCCGGGTTCTT 62.679 66.667 21.85 18.55 41.85 2.52
3514 10301 2.361230 CAAGCCCCCGGGTTCTTC 60.361 66.667 21.85 3.03 41.85 2.87
3515 10302 2.531942 AAGCCCCCGGGTTCTTCT 60.532 61.111 21.85 5.54 39.37 2.85
3516 10303 2.907179 AAGCCCCCGGGTTCTTCTG 61.907 63.158 21.85 0.91 39.37 3.02
3517 10304 4.426313 GCCCCCGGGTTCTTCTGG 62.426 72.222 21.85 12.83 37.65 3.86
3520 10307 4.778143 CCCGGGTTCTTCTGGGCG 62.778 72.222 14.18 0.00 45.48 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.873129 ATGAGCTACCACGGCGCG 62.873 66.667 6.90 0.00 32.38 6.86
6 7 3.264897 CATGAGCTACCACGGCGC 61.265 66.667 6.90 0.00 34.52 6.53
9 10 0.740868 CCACACATGAGCTACCACGG 60.741 60.000 0.00 0.00 0.00 4.94
10 11 0.246360 TCCACACATGAGCTACCACG 59.754 55.000 0.00 0.00 0.00 4.94
12 13 1.210234 CCATCCACACATGAGCTACCA 59.790 52.381 0.00 0.00 0.00 3.25
13 14 1.486310 TCCATCCACACATGAGCTACC 59.514 52.381 0.00 0.00 0.00 3.18
14 15 2.555199 GTCCATCCACACATGAGCTAC 58.445 52.381 0.00 0.00 0.00 3.58
16 17 0.254178 GGTCCATCCACACATGAGCT 59.746 55.000 0.00 0.00 35.97 4.09
17 18 1.091771 CGGTCCATCCACACATGAGC 61.092 60.000 0.00 0.00 35.57 4.26
18 19 1.091771 GCGGTCCATCCACACATGAG 61.092 60.000 0.00 0.00 35.57 2.90
19 20 1.078497 GCGGTCCATCCACACATGA 60.078 57.895 0.00 0.00 35.57 3.07
20 21 2.114670 GGCGGTCCATCCACACATG 61.115 63.158 0.00 0.00 35.57 3.21
21 22 0.980754 TAGGCGGTCCATCCACACAT 60.981 55.000 0.49 0.00 35.57 3.21
22 23 1.610967 TAGGCGGTCCATCCACACA 60.611 57.895 0.49 0.00 35.57 3.72
23 24 1.144057 CTAGGCGGTCCATCCACAC 59.856 63.158 0.49 0.00 35.57 3.82
24 25 2.731571 GCTAGGCGGTCCATCCACA 61.732 63.158 0.00 0.00 35.57 4.17
25 26 2.109181 GCTAGGCGGTCCATCCAC 59.891 66.667 0.00 0.00 35.57 4.02
36 37 3.188786 CAACTCCGCACGCTAGGC 61.189 66.667 0.00 0.00 0.00 3.93
37 38 3.188786 GCAACTCCGCACGCTAGG 61.189 66.667 0.00 0.00 0.00 3.02
38 39 3.545481 CGCAACTCCGCACGCTAG 61.545 66.667 0.00 0.00 0.00 3.42
46 47 3.499737 GTCATGGGCGCAACTCCG 61.500 66.667 10.83 0.00 0.00 4.63
47 48 1.523154 TTTGTCATGGGCGCAACTCC 61.523 55.000 10.83 0.47 0.00 3.85
48 49 0.387239 GTTTGTCATGGGCGCAACTC 60.387 55.000 10.83 1.53 0.00 3.01
49 50 0.823356 AGTTTGTCATGGGCGCAACT 60.823 50.000 10.83 4.51 0.00 3.16
50 51 0.387239 GAGTTTGTCATGGGCGCAAC 60.387 55.000 10.83 2.70 0.00 4.17
51 52 0.821301 TGAGTTTGTCATGGGCGCAA 60.821 50.000 10.83 0.00 0.00 4.85
52 53 1.228094 TGAGTTTGTCATGGGCGCA 60.228 52.632 10.83 5.70 0.00 6.09
53 54 1.210155 GTGAGTTTGTCATGGGCGC 59.790 57.895 0.00 0.00 37.56 6.53
54 55 1.497278 CGTGAGTTTGTCATGGGCG 59.503 57.895 0.00 0.00 38.40 6.13
55 56 1.210155 GCGTGAGTTTGTCATGGGC 59.790 57.895 0.00 0.00 41.90 5.36
56 57 1.586154 GGGCGTGAGTTTGTCATGGG 61.586 60.000 0.00 0.00 41.90 4.00
57 58 1.875963 GGGCGTGAGTTTGTCATGG 59.124 57.895 0.00 0.00 41.90 3.66
58 59 1.497278 CGGGCGTGAGTTTGTCATG 59.503 57.895 0.00 0.00 44.15 3.07
59 60 2.325082 GCGGGCGTGAGTTTGTCAT 61.325 57.895 0.00 0.00 37.56 3.06
60 61 2.970324 GCGGGCGTGAGTTTGTCA 60.970 61.111 0.00 0.00 0.00 3.58
61 62 3.723348 GGCGGGCGTGAGTTTGTC 61.723 66.667 0.00 0.00 0.00 3.18
79 80 4.463879 CTGCTCCCAGTCGGCCAG 62.464 72.222 2.24 0.00 34.31 4.85
83 84 4.069232 TTCGCTGCTCCCAGTCGG 62.069 66.667 0.00 0.00 41.26 4.79
84 85 2.811317 GTTCGCTGCTCCCAGTCG 60.811 66.667 0.00 0.00 41.26 4.18
85 86 2.435059 GGTTCGCTGCTCCCAGTC 60.435 66.667 0.00 0.00 41.26 3.51
86 87 2.925170 AGGTTCGCTGCTCCCAGT 60.925 61.111 0.00 0.00 41.26 4.00
87 88 2.125350 GAGGTTCGCTGCTCCCAG 60.125 66.667 0.00 0.00 42.13 4.45
88 89 3.706373 GGAGGTTCGCTGCTCCCA 61.706 66.667 0.00 0.00 0.00 4.37
90 91 4.475135 GGGGAGGTTCGCTGCTCC 62.475 72.222 0.00 0.00 35.38 4.70
91 92 4.475135 GGGGGAGGTTCGCTGCTC 62.475 72.222 0.00 0.00 0.00 4.26
93 94 4.475135 GAGGGGGAGGTTCGCTGC 62.475 72.222 0.00 0.00 0.00 5.25
94 95 3.787001 GGAGGGGGAGGTTCGCTG 61.787 72.222 0.00 0.00 0.00 5.18
95 96 4.332543 TGGAGGGGGAGGTTCGCT 62.333 66.667 0.00 0.00 0.00 4.93
96 97 3.787001 CTGGAGGGGGAGGTTCGC 61.787 72.222 0.00 0.00 0.00 4.70
97 98 3.787001 GCTGGAGGGGGAGGTTCG 61.787 72.222 0.00 0.00 0.00 3.95
98 99 3.787001 CGCTGGAGGGGGAGGTTC 61.787 72.222 0.00 0.00 0.00 3.62
99 100 4.332543 TCGCTGGAGGGGGAGGTT 62.333 66.667 0.00 0.00 0.00 3.50
102 103 2.873557 TTAGGTCGCTGGAGGGGGAG 62.874 65.000 0.00 0.00 0.00 4.30
103 104 2.252012 ATTAGGTCGCTGGAGGGGGA 62.252 60.000 0.00 0.00 0.00 4.81
104 105 1.766461 ATTAGGTCGCTGGAGGGGG 60.766 63.158 0.00 0.00 0.00 5.40
105 106 1.338136 ACATTAGGTCGCTGGAGGGG 61.338 60.000 0.00 0.00 0.00 4.79
106 107 0.179073 CACATTAGGTCGCTGGAGGG 60.179 60.000 0.00 0.00 0.00 4.30
107 108 0.179073 CCACATTAGGTCGCTGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
108 109 0.811616 GCCACATTAGGTCGCTGGAG 60.812 60.000 0.00 0.00 30.18 3.86
109 110 1.220749 GCCACATTAGGTCGCTGGA 59.779 57.895 0.00 0.00 30.18 3.86
110 111 1.221840 AGCCACATTAGGTCGCTGG 59.778 57.895 0.00 0.00 42.70 4.85
111 112 4.941609 AGCCACATTAGGTCGCTG 57.058 55.556 0.00 0.00 42.70 5.18
112 113 1.450312 GCAGCCACATTAGGTCGCT 60.450 57.895 0.00 0.00 45.38 4.93
113 114 2.813179 CGCAGCCACATTAGGTCGC 61.813 63.158 0.00 0.00 33.34 5.19
114 115 3.398920 CGCAGCCACATTAGGTCG 58.601 61.111 0.00 0.00 0.00 4.79
142 143 3.698463 GTGTCGTGGTGGTTCGCG 61.698 66.667 0.00 0.00 41.41 5.87
143 144 2.279918 AGTGTCGTGGTGGTTCGC 60.280 61.111 0.00 0.00 0.00 4.70
176 177 0.107945 GCACAGAGATGGAGGTGGTC 60.108 60.000 0.00 0.00 0.00 4.02
178 179 0.177604 GAGCACAGAGATGGAGGTGG 59.822 60.000 0.00 0.00 0.00 4.61
187 188 1.893062 CCACCGATGAGCACAGAGA 59.107 57.895 0.00 0.00 0.00 3.10
207 208 2.629763 GTCGGTTGTGTTGTCGGC 59.370 61.111 0.00 0.00 0.00 5.54
216 217 0.966920 ATGAGTTCGAGGTCGGTTGT 59.033 50.000 0.00 0.00 40.29 3.32
234 235 4.814294 GCGGAAGGCGACGGACAT 62.814 66.667 0.00 0.00 0.00 3.06
249 250 4.803426 GGCAGTGGAGACGAGGCG 62.803 72.222 0.00 0.00 0.00 5.52
289 291 1.145759 GATTTCAGCGACGATGCGGA 61.146 55.000 8.52 0.00 40.67 5.54
296 298 2.697425 CTGCCGATTTCAGCGACG 59.303 61.111 0.00 0.00 0.00 5.12
322 324 1.348036 TCACTCACTCTCTCCTCACGA 59.652 52.381 0.00 0.00 0.00 4.35
324 326 5.189928 TCTATTCACTCACTCTCTCCTCAC 58.810 45.833 0.00 0.00 0.00 3.51
329 331 4.024893 CGCTCTCTATTCACTCACTCTCTC 60.025 50.000 0.00 0.00 0.00 3.20
353 355 3.147629 AGCTTATGCATGCATTCCTCTC 58.852 45.455 36.23 19.15 42.74 3.20
363 365 2.138320 CACGGGACTAGCTTATGCATG 58.862 52.381 10.16 0.00 42.74 4.06
373 375 2.094659 CAAGCGTGCACGGGACTAG 61.095 63.158 37.47 11.26 40.23 2.57
381 383 2.042520 TTTCGTGGTCAAGCGTGCAC 62.043 55.000 6.82 6.82 0.00 4.57
386 388 4.489683 CGTTTTCGTGGTCAAGCG 57.510 55.556 0.00 0.00 38.65 4.68
441 443 4.242475 TGACGTTACATTGATGTCCAGAC 58.758 43.478 0.00 0.00 41.97 3.51
442 444 4.529109 TGACGTTACATTGATGTCCAGA 57.471 40.909 0.00 0.00 41.97 3.86
444 446 4.188462 GGATGACGTTACATTGATGTCCA 58.812 43.478 0.00 0.00 41.97 4.02
445 447 3.245284 CGGATGACGTTACATTGATGTCC 59.755 47.826 0.00 0.00 38.84 4.02
446 448 3.245284 CCGGATGACGTTACATTGATGTC 59.755 47.826 0.00 0.00 40.61 3.06
447 449 3.118920 TCCGGATGACGTTACATTGATGT 60.119 43.478 0.00 1.84 42.08 3.06
448 450 3.453424 TCCGGATGACGTTACATTGATG 58.547 45.455 0.00 0.00 42.24 3.07
449 451 3.132289 ACTCCGGATGACGTTACATTGAT 59.868 43.478 3.57 0.00 42.24 2.57
450 452 2.494471 ACTCCGGATGACGTTACATTGA 59.506 45.455 3.57 0.00 42.24 2.57
457 459 2.107041 TTGGCACTCCGGATGACGTT 62.107 55.000 3.57 0.00 42.24 3.99
469 476 1.027357 CAAGCACAGTTCTTGGCACT 58.973 50.000 5.10 0.00 37.77 4.40
479 486 1.672356 GTCCGATGGCAAGCACAGT 60.672 57.895 0.00 0.00 0.00 3.55
502 1948 1.940613 GTTCGGCCTGAATATGGTGAC 59.059 52.381 12.13 0.00 39.21 3.67
528 1974 6.542370 TGACGACATATCTGACATCAGTCTTA 59.458 38.462 8.70 1.24 45.20 2.10
544 1990 6.701400 CCAAATGACACATATCTGACGACATA 59.299 38.462 0.00 0.00 0.00 2.29
663 2110 0.322636 ACCGAGGACAGACGAGTGAT 60.323 55.000 0.00 0.00 0.00 3.06
672 2119 1.035932 ACCGATGGTACCGAGGACAG 61.036 60.000 22.11 4.70 32.11 3.51
704 2152 1.227999 TTTGCTCGTCGAAGCTTGGG 61.228 55.000 2.10 0.00 42.94 4.12
711 2159 1.493772 ACGAATGTTTGCTCGTCGAA 58.506 45.000 0.00 0.00 44.64 3.71
717 2165 1.134694 GGGCGACGAATGTTTGCTC 59.865 57.895 0.00 0.00 32.31 4.26
761 2209 6.894828 AGTGTTTGTCCGTTATTATGTTGAC 58.105 36.000 0.00 0.00 0.00 3.18
788 2236 7.334421 TCACTACAAGATTTTCAGTTATGCTCC 59.666 37.037 0.00 0.00 0.00 4.70
790 2238 7.148573 CGTCACTACAAGATTTTCAGTTATGCT 60.149 37.037 0.00 0.00 0.00 3.79
816 2269 1.790838 CGAGGTGACGAGATTGACGAC 60.791 57.143 0.00 0.00 35.09 4.34
862 2315 2.593468 GAACGCCAGCAGCCATCCTA 62.593 60.000 0.00 0.00 38.78 2.94
1045 2522 3.771160 GACGTCCTCATGCCCGGT 61.771 66.667 3.51 0.00 0.00 5.28
1665 8408 0.028110 GCGCCAACTCGATTTCATCC 59.972 55.000 0.00 0.00 0.00 3.51
1722 8465 1.655329 GTACTCCGGCTCCATCTCG 59.345 63.158 0.00 0.00 0.00 4.04
1756 8499 2.989639 CCTCATGTTCCTGGCGGA 59.010 61.111 0.00 0.00 37.60 5.54
1830 8573 1.844130 GGTGGTGGTGTTCCCTCTT 59.156 57.895 0.00 0.00 0.00 2.85
1852 8595 3.764049 GCACTCGTCGGCGTCAAC 61.764 66.667 10.18 0.00 39.49 3.18
1872 8615 3.551496 CTTGCCTTGGAGCCACCGA 62.551 63.158 0.00 0.00 42.61 4.69
1906 8649 1.025812 CTCCCGAAGCTGACGTAGAT 58.974 55.000 11.53 0.00 0.00 1.98
2007 8751 0.736325 CGTACTGCTCGGGGTTCTTG 60.736 60.000 0.00 0.00 0.00 3.02
2019 8763 4.112341 ACGTCCTCGCCGTACTGC 62.112 66.667 0.00 0.00 41.18 4.40
2320 9064 2.055042 CCTCTCTCCCCACCACGAG 61.055 68.421 0.00 0.00 0.00 4.18
2577 9330 5.650283 ACCCCCAAACAATCTTCTGAAATA 58.350 37.500 0.00 0.00 0.00 1.40
2591 9344 7.348815 ACCTGTAGTATATTTAACCCCCAAAC 58.651 38.462 0.00 0.00 0.00 2.93
2615 9368 2.289506 GGTCACAGACAAGTTAGGGGAC 60.290 54.545 0.00 0.00 33.68 4.46
2617 9370 1.337823 CGGTCACAGACAAGTTAGGGG 60.338 57.143 0.00 0.00 33.68 4.79
2630 9383 1.934589 CACTGAAACTGACGGTCACA 58.065 50.000 6.76 2.90 0.00 3.58
2632 9385 0.464036 AGCACTGAAACTGACGGTCA 59.536 50.000 10.88 10.88 0.00 4.02
2636 9389 4.795970 AGTTTAAGCACTGAAACTGACG 57.204 40.909 11.60 0.00 42.77 4.35
2677 9430 4.164843 ACACCCAGACAAGTTACAACAT 57.835 40.909 0.00 0.00 0.00 2.71
2681 9434 3.916359 TGAACACCCAGACAAGTTACA 57.084 42.857 0.00 0.00 0.00 2.41
2702 9455 5.643777 GCCATACTTTCATAGGCATCGTATT 59.356 40.000 0.00 0.00 44.59 1.89
2706 9459 2.413112 CGCCATACTTTCATAGGCATCG 59.587 50.000 0.00 0.00 45.47 3.84
2708 9461 2.154462 GCGCCATACTTTCATAGGCAT 58.846 47.619 0.00 0.00 45.47 4.40
2732 9485 1.246056 ATGCCACGCAAGCACTTGAT 61.246 50.000 14.44 0.00 44.40 2.57
2735 9488 2.646719 CATGCCACGCAAGCACTT 59.353 55.556 0.00 0.00 44.40 3.16
2825 9578 3.769300 AGATCCAGGGGCATTTTTGTAAC 59.231 43.478 0.00 0.00 0.00 2.50
2832 9585 7.348011 ACAATTAATTAAGATCCAGGGGCATTT 59.652 33.333 0.00 0.00 0.00 2.32
2915 9668 3.050275 GTGTTCCTGGCACTCGGC 61.050 66.667 0.00 0.00 43.74 5.54
3011 9764 4.226761 GTCGGTAAAAATCTGTTTGCCTG 58.773 43.478 3.79 0.00 40.12 4.85
3028 9781 2.340427 CCAACAAATGGCTGTCGGT 58.660 52.632 0.00 0.00 43.80 4.69
3044 9797 3.244422 ACAAAGTCTTAGCCGAATGTCCA 60.244 43.478 0.00 0.00 0.00 4.02
3050 9803 2.869801 CACACACAAAGTCTTAGCCGAA 59.130 45.455 0.00 0.00 0.00 4.30
3056 9809 1.855978 CGCGACACACACAAAGTCTTA 59.144 47.619 0.00 0.00 0.00 2.10
3171 9958 8.091449 CCCACTAAATAAAGCCAATACACAAAA 58.909 33.333 0.00 0.00 0.00 2.44
3236 10023 7.817962 TCGAACCAAAATAAACAAAAACTGGAA 59.182 29.630 0.00 0.00 0.00 3.53
3237 10024 7.321153 TCGAACCAAAATAAACAAAAACTGGA 58.679 30.769 0.00 0.00 0.00 3.86
3240 10027 8.974408 GCTATCGAACCAAAATAAACAAAAACT 58.026 29.630 0.00 0.00 0.00 2.66
3308 10095 5.745312 TCTCACTTGGAAGAGATTTAGCA 57.255 39.130 0.00 0.00 36.05 3.49
3367 10154 1.065600 GCAGAAGGCGCAACAAACA 59.934 52.632 10.83 0.00 0.00 2.83
3368 10155 3.922175 GCAGAAGGCGCAACAAAC 58.078 55.556 10.83 0.00 0.00 2.93
3377 10164 2.817396 GCAGAGGACGCAGAAGGC 60.817 66.667 0.00 0.00 39.90 4.35
3378 10165 2.125350 GGCAGAGGACGCAGAAGG 60.125 66.667 0.00 0.00 0.00 3.46
3379 10166 1.447489 CTGGCAGAGGACGCAGAAG 60.447 63.158 9.42 0.00 0.00 2.85
3380 10167 2.659016 CTGGCAGAGGACGCAGAA 59.341 61.111 9.42 0.00 0.00 3.02
3381 10168 4.074526 GCTGGCAGAGGACGCAGA 62.075 66.667 20.86 0.00 0.00 4.26
3382 10169 4.383861 TGCTGGCAGAGGACGCAG 62.384 66.667 20.86 0.00 30.16 5.18
3383 10170 4.687215 GTGCTGGCAGAGGACGCA 62.687 66.667 20.86 5.59 32.76 5.24
3384 10171 4.687215 TGTGCTGGCAGAGGACGC 62.687 66.667 20.86 7.59 45.85 5.19
3385 10172 2.031012 TTGTGCTGGCAGAGGACG 59.969 61.111 20.86 0.00 45.85 4.79
3386 10173 2.320587 CGTTGTGCTGGCAGAGGAC 61.321 63.158 20.86 11.52 43.25 3.85
3387 10174 2.031012 CGTTGTGCTGGCAGAGGA 59.969 61.111 20.86 0.00 0.00 3.71
3388 10175 2.281070 ACGTTGTGCTGGCAGAGG 60.281 61.111 20.86 5.34 0.00 3.69
3389 10176 2.661566 CGACGTTGTGCTGGCAGAG 61.662 63.158 20.86 3.95 0.00 3.35
3390 10177 2.661537 CGACGTTGTGCTGGCAGA 60.662 61.111 20.86 0.00 0.00 4.26
3391 10178 2.661537 TCGACGTTGTGCTGGCAG 60.662 61.111 10.94 10.94 0.00 4.85
3392 10179 2.661537 CTCGACGTTGTGCTGGCA 60.662 61.111 1.96 0.00 0.00 4.92
3393 10180 2.355837 TCTCGACGTTGTGCTGGC 60.356 61.111 1.96 0.00 0.00 4.85
3394 10181 1.734477 CCTCTCGACGTTGTGCTGG 60.734 63.158 1.96 2.93 0.00 4.85
3395 10182 0.240145 TACCTCTCGACGTTGTGCTG 59.760 55.000 1.96 0.00 0.00 4.41
3396 10183 0.240411 GTACCTCTCGACGTTGTGCT 59.760 55.000 1.96 0.00 0.00 4.40
3397 10184 0.039798 TGTACCTCTCGACGTTGTGC 60.040 55.000 1.96 0.00 0.00 4.57
3398 10185 2.049228 GTTGTACCTCTCGACGTTGTG 58.951 52.381 1.96 0.00 0.00 3.33
3399 10186 1.952296 AGTTGTACCTCTCGACGTTGT 59.048 47.619 1.96 0.00 0.00 3.32
3400 10187 2.582687 GAGTTGTACCTCTCGACGTTG 58.417 52.381 0.00 0.00 0.00 4.10
3401 10188 1.538950 GGAGTTGTACCTCTCGACGTT 59.461 52.381 0.00 0.00 0.00 3.99
3402 10189 1.163554 GGAGTTGTACCTCTCGACGT 58.836 55.000 0.00 0.00 0.00 4.34
3403 10190 1.451067 AGGAGTTGTACCTCTCGACG 58.549 55.000 7.85 0.00 31.43 5.12
3404 10191 2.351111 CGTAGGAGTTGTACCTCTCGAC 59.649 54.545 0.00 7.61 38.76 4.20
3405 10192 2.625737 CGTAGGAGTTGTACCTCTCGA 58.374 52.381 0.00 0.00 38.76 4.04
3427 10214 2.741985 TTGTCGTCGGCCATGCTG 60.742 61.111 2.24 0.00 36.06 4.41
3428 10215 2.742372 GTTGTCGTCGGCCATGCT 60.742 61.111 2.24 0.00 0.00 3.79
3429 10216 4.147322 CGTTGTCGTCGGCCATGC 62.147 66.667 2.24 0.00 0.00 4.06
3430 10217 2.431771 TCGTTGTCGTCGGCCATG 60.432 61.111 2.24 0.00 38.33 3.66
3431 10218 2.126071 CTCGTTGTCGTCGGCCAT 60.126 61.111 2.24 0.00 38.33 4.40
3440 10227 4.754667 GACCCCCGGCTCGTTGTC 62.755 72.222 0.00 0.00 0.00 3.18
3463 10250 4.514577 ATTCGCCTCTCCACGCCG 62.515 66.667 0.00 0.00 0.00 6.46
3464 10251 2.586357 GATTCGCCTCTCCACGCC 60.586 66.667 0.00 0.00 0.00 5.68
3465 10252 1.424493 CTTGATTCGCCTCTCCACGC 61.424 60.000 0.00 0.00 0.00 5.34
3466 10253 0.807667 CCTTGATTCGCCTCTCCACG 60.808 60.000 0.00 0.00 0.00 4.94
3467 10254 0.250513 ACCTTGATTCGCCTCTCCAC 59.749 55.000 0.00 0.00 0.00 4.02
3468 10255 0.250234 CACCTTGATTCGCCTCTCCA 59.750 55.000 0.00 0.00 0.00 3.86
3469 10256 0.537188 TCACCTTGATTCGCCTCTCC 59.463 55.000 0.00 0.00 0.00 3.71
3470 10257 1.646189 GTCACCTTGATTCGCCTCTC 58.354 55.000 0.00 0.00 0.00 3.20
3471 10258 0.250513 GGTCACCTTGATTCGCCTCT 59.749 55.000 0.00 0.00 0.00 3.69
3472 10259 0.036388 TGGTCACCTTGATTCGCCTC 60.036 55.000 0.00 0.00 0.00 4.70
3473 10260 0.036010 CTGGTCACCTTGATTCGCCT 60.036 55.000 0.00 0.00 0.00 5.52
3474 10261 1.026718 CCTGGTCACCTTGATTCGCC 61.027 60.000 0.00 0.00 0.00 5.54
3475 10262 1.026718 CCCTGGTCACCTTGATTCGC 61.027 60.000 0.00 0.00 0.00 4.70
3476 10263 1.026718 GCCCTGGTCACCTTGATTCG 61.027 60.000 0.00 0.00 0.00 3.34
3477 10264 1.026718 CGCCCTGGTCACCTTGATTC 61.027 60.000 0.00 0.00 0.00 2.52
3478 10265 1.002134 CGCCCTGGTCACCTTGATT 60.002 57.895 0.00 0.00 0.00 2.57
3479 10266 2.671070 CGCCCTGGTCACCTTGAT 59.329 61.111 0.00 0.00 0.00 2.57
3480 10267 4.329545 GCGCCCTGGTCACCTTGA 62.330 66.667 0.00 0.00 0.00 3.02
3481 10268 4.641645 TGCGCCCTGGTCACCTTG 62.642 66.667 4.18 0.00 0.00 3.61
3482 10269 3.850098 CTTGCGCCCTGGTCACCTT 62.850 63.158 4.18 0.00 0.00 3.50
3483 10270 4.335647 CTTGCGCCCTGGTCACCT 62.336 66.667 4.18 0.00 0.00 4.00
3496 10283 4.678743 AAGAACCCGGGGGCTTGC 62.679 66.667 27.92 0.93 39.32 4.01
3497 10284 2.361230 GAAGAACCCGGGGGCTTG 60.361 66.667 28.30 3.24 39.32 4.01
3498 10285 2.531942 AGAAGAACCCGGGGGCTT 60.532 61.111 27.92 26.12 39.32 4.35
3499 10286 3.330720 CAGAAGAACCCGGGGGCT 61.331 66.667 27.92 18.82 39.32 5.19
3500 10287 4.426313 CCAGAAGAACCCGGGGGC 62.426 72.222 27.92 16.56 39.32 5.80
3501 10288 3.728373 CCCAGAAGAACCCGGGGG 61.728 72.222 27.92 14.41 42.03 5.40
3502 10289 4.426313 GCCCAGAAGAACCCGGGG 62.426 72.222 27.92 12.73 39.26 5.73
3503 10290 4.778143 CGCCCAGAAGAACCCGGG 62.778 72.222 22.25 22.25 42.03 5.73


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

AutoCloner maintained by Alex Coulton.