Multiple sequence alignment - TraesCS5A01G214200

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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 TraesCS5A01G214200 chr5A 100.000 4825 0 0 1 4825 429752996 429757820 0.000000e+00 8911.0
1 TraesCS5A01G214200 chr5A 92.353 170 12 1 4231 4399 376346760 376346929 1.740000e-59 241.0
2 TraesCS5A01G214200 chr5A 78.378 148 28 2 1845 1990 471692696 471692841 5.140000e-15 93.5
3 TraesCS5A01G214200 chr5B 94.214 3405 128 26 885 4240 379336696 379333312 0.000000e+00 5132.0
4 TraesCS5A01G214200 chr5B 91.506 624 40 8 6 623 379337653 379337037 0.000000e+00 846.0
5 TraesCS5A01G214200 chr5B 93.284 268 8 5 631 897 379336985 379336727 2.110000e-103 387.0
6 TraesCS5A01G214200 chr5B 89.439 303 28 4 4398 4697 379333313 379333012 3.520000e-101 379.0
7 TraesCS5A01G214200 chr5B 85.841 113 9 5 4397 4503 573568594 573568705 3.950000e-21 113.0
8 TraesCS5A01G214200 chr5B 85.000 100 9 3 4397 4491 402065673 402065575 3.970000e-16 97.1
9 TraesCS5A01G214200 chr5D 94.413 3329 121 28 885 4152 326736829 326733505 0.000000e+00 5057.0
10 TraesCS5A01G214200 chr5D 92.727 440 14 8 194 623 326737599 326737168 1.910000e-173 619.0
11 TraesCS5A01G214200 chr5D 89.019 428 42 5 4398 4822 326731694 326731269 4.280000e-145 525.0
12 TraesCS5A01G214200 chr5D 92.164 268 13 4 631 897 326737115 326736855 5.900000e-99 372.0
13 TraesCS5A01G214200 chr5D 92.917 240 15 1 1843 2080 524590476 524590237 9.940000e-92 348.0
14 TraesCS5A01G214200 chr5D 92.045 176 12 2 4236 4410 151671545 151671719 3.730000e-61 246.0
15 TraesCS5A01G214200 chr5D 93.293 164 10 1 4238 4400 390354138 390353975 1.740000e-59 241.0
16 TraesCS5A01G214200 chr5D 92.727 165 11 1 4236 4399 334801459 334801295 2.240000e-58 237.0
17 TraesCS5A01G214200 chr5D 90.345 145 11 3 68 210 326737764 326737621 2.290000e-43 187.0
18 TraesCS5A01G214200 chr5D 93.023 86 6 0 4155 4240 326731778 326731693 5.070000e-25 126.0
19 TraesCS5A01G214200 chr5D 79.054 148 27 2 1845 1990 369295537 369295682 1.110000e-16 99.0
20 TraesCS5A01G214200 chr1B 91.030 301 22 4 2243 2541 26338126 26337829 7.520000e-108 401.0
21 TraesCS5A01G214200 chr1B 93.050 259 18 0 1986 2244 26360608 26360350 3.520000e-101 379.0
22 TraesCS5A01G214200 chr1B 85.304 313 20 10 2024 2336 4177949 4177663 2.820000e-77 300.0
23 TraesCS5A01G214200 chr1B 91.509 212 17 1 2331 2541 4156070 4155859 1.700000e-74 291.0
24 TraesCS5A01G214200 chr1B 84.642 293 35 7 4519 4806 277413028 277413315 2.840000e-72 283.0
25 TraesCS5A01G214200 chr1B 84.701 268 19 7 1648 1905 26360862 26360607 1.040000e-61 248.0
26 TraesCS5A01G214200 chr1B 90.698 129 10 2 1778 1905 4178140 4178013 2.310000e-38 171.0
27 TraesCS5A01G214200 chr1B 98.148 54 1 0 1543 1596 4178247 4178194 1.430000e-15 95.3
28 TraesCS5A01G214200 chr1B 96.296 54 2 0 1543 1596 26360914 26360861 6.650000e-14 89.8
29 TraesCS5A01G214200 chr4D 83.149 451 47 13 4397 4823 301120411 301119966 7.580000e-103 385.0
30 TraesCS5A01G214200 chr4D 82.989 435 63 8 4397 4823 80539213 80539644 2.720000e-102 383.0
31 TraesCS5A01G214200 chr4D 82.667 450 50 12 4397 4822 248314914 248314469 1.640000e-99 374.0
32 TraesCS5A01G214200 chr4D 92.727 165 11 1 4239 4402 484111764 484111928 2.240000e-58 237.0
33 TraesCS5A01G214200 chr4B 82.609 437 60 13 4397 4823 112799813 112800243 5.900000e-99 372.0
34 TraesCS5A01G214200 chr4A 81.840 424 49 17 4405 4823 199876401 199876001 1.000000e-86 331.0
35 TraesCS5A01G214200 chr4A 80.045 441 69 15 4397 4825 505066808 505066375 4.690000e-80 309.0
36 TraesCS5A01G214200 chr3D 91.703 229 18 1 1853 2080 47139046 47138818 2.800000e-82 316.0
37 TraesCS5A01G214200 chr3D 92.899 169 10 2 4235 4401 2148559 2148727 1.340000e-60 244.0
38 TraesCS5A01G214200 chr2D 81.325 332 42 6 2420 2749 605094330 605094017 8.020000e-63 252.0
39 TraesCS5A01G214200 chr2D 88.770 187 20 1 4239 4425 579392605 579392420 1.350000e-55 228.0
40 TraesCS5A01G214200 chr2D 85.714 112 11 2 4397 4503 359054058 359054169 3.950000e-21 113.0
41 TraesCS5A01G214200 chr3A 92.727 165 11 1 4236 4399 745031198 745031362 2.240000e-58 237.0
42 TraesCS5A01G214200 chr3A 79.286 140 17 10 4218 4351 328300750 328300883 2.390000e-13 87.9
43 TraesCS5A01G214200 chr1A 93.210 162 10 1 4239 4399 254348915 254349076 2.240000e-58 237.0
44 TraesCS5A01G214200 chr2B 73.856 459 99 14 1612 2064 596410843 596411286 3.860000e-36 163.0
45 TraesCS5A01G214200 chr7B 87.500 112 9 2 4397 4503 335030378 335030267 1.820000e-24 124.0
46 TraesCS5A01G214200 chr7B 85.586 111 11 2 4397 4502 217176071 217176181 1.420000e-20 111.0
47 TraesCS5A01G214200 chr7D 86.364 110 10 2 4399 4503 270687489 270687598 1.100000e-21 115.0
48 TraesCS5A01G214200 chr2A 85.217 115 12 2 4397 4506 483964817 483964703 3.950000e-21 113.0


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 TraesCS5A01G214200 chr5A 429752996 429757820 4824 False 8911.000000 8911 100.00000 1 4825 1 chr5A.!!$F2 4824
1 TraesCS5A01G214200 chr5B 379333012 379337653 4641 True 1686.000000 5132 92.11075 6 4697 4 chr5B.!!$R2 4691
2 TraesCS5A01G214200 chr5D 326731269 326737764 6495 True 1147.666667 5057 91.94850 68 4822 6 chr5D.!!$R4 4754
3 TraesCS5A01G214200 chr1B 26360350 26360914 564 True 238.933333 379 91.34900 1543 2244 3 chr1B.!!$R4 701

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
461 516 0.105408 TATTAGAAAGGGGCGCGGTC 59.895 55.000 8.83 0.0 0.00 4.79 F
942 1091 0.593128 ACTGCAGACATTTTCGGTGC 59.407 50.000 23.35 0.0 34.62 5.01 F
1064 1263 0.874390 TGCTGCACGGAGAAATCAAC 59.126 50.000 0.00 0.0 0.00 3.18 F
2337 2553 1.302271 GGGTGACGACAAGTTCCCC 60.302 63.158 0.00 0.0 39.62 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1401 1607 0.713579 AGGAGTAGAGGAGGTGGCTT 59.286 55.000 0.0 0.0 0.0 4.35 R
2886 3105 1.471287 TGTCGGTCAGTACAATCCTCG 59.529 52.381 0.0 0.0 0.0 4.63 R
2977 3196 3.383825 ACCTAAAGACGACCATAGCGATT 59.616 43.478 0.0 0.0 0.0 3.34 R
4283 6246 0.687920 TTTGCTCCGTATGTGGTCCA 59.312 50.000 0.0 0.0 0.0 4.02 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 2.159382 CTCGGTGGCCTATTTGTGTTT 58.841 47.619 3.32 0.00 0.00 2.83
21 22 1.883275 TCGGTGGCCTATTTGTGTTTG 59.117 47.619 3.32 0.00 0.00 2.93
28 29 5.234116 GTGGCCTATTTGTGTTTGTTTTCAG 59.766 40.000 3.32 0.00 0.00 3.02
37 38 3.433957 GTGTTTGTTTTCAGCCGGTTTTT 59.566 39.130 1.90 0.00 0.00 1.94
39 40 3.594603 TTGTTTTCAGCCGGTTTTTCA 57.405 38.095 1.90 0.00 0.00 2.69
48 49 5.956642 TCAGCCGGTTTTTCATAATTAACC 58.043 37.500 1.90 0.00 37.31 2.85
49 50 5.477291 TCAGCCGGTTTTTCATAATTAACCA 59.523 36.000 1.90 0.00 39.98 3.67
50 51 6.015350 TCAGCCGGTTTTTCATAATTAACCAA 60.015 34.615 1.90 0.00 39.98 3.67
84 90 8.612619 TCTTCTTAATAATCGATGAGGCAAAAC 58.387 33.333 0.00 0.00 0.00 2.43
100 106 2.663826 AAACTTTTGCGCCTGTTTCA 57.336 40.000 4.18 0.00 0.00 2.69
149 156 2.810164 GACTGTGGAGTCCTCTTACCT 58.190 52.381 11.33 0.00 42.66 3.08
158 165 3.997681 GAGTCCTCTTACCTTGCAAAGTC 59.002 47.826 3.41 0.00 44.25 3.01
182 189 1.270893 TGGCATGGCACGTACAAAGTA 60.271 47.619 19.43 0.00 0.00 2.24
210 256 5.168569 CAAAGTTACTAAGCCACGATCTCA 58.831 41.667 0.00 0.00 0.00 3.27
212 258 4.745649 AGTTACTAAGCCACGATCTCAAC 58.254 43.478 0.00 0.00 0.00 3.18
224 270 0.329596 ATCTCAACAGGACCCCTTGC 59.670 55.000 0.00 0.00 0.00 4.01
269 316 2.548057 TGACAAGTGATTTCGCTTCCAC 59.452 45.455 3.46 0.00 44.06 4.02
298 345 3.315470 TCGACTATTGATTCAGAGGACCG 59.685 47.826 3.54 0.00 0.00 4.79
301 348 2.990066 ATTGATTCAGAGGACCGGAC 57.010 50.000 9.46 0.00 0.00 4.79
305 352 4.671590 TCAGAGGACCGGACGGCA 62.672 66.667 9.46 0.00 39.32 5.69
456 511 1.217882 CGCAGTATTAGAAAGGGGCG 58.782 55.000 0.00 0.00 37.17 6.13
461 516 0.105408 TATTAGAAAGGGGCGCGGTC 59.895 55.000 8.83 0.00 0.00 4.79
747 849 4.564116 GCATCATGCACTGCCGGC 62.564 66.667 22.73 22.73 44.26 6.13
748 850 3.896133 CATCATGCACTGCCGGCC 61.896 66.667 26.77 9.02 0.00 6.13
763 865 3.818787 GCCGGGCTGTGCTTGATG 61.819 66.667 12.87 0.00 0.00 3.07
764 866 3.818787 CCGGGCTGTGCTTGATGC 61.819 66.667 0.00 0.00 43.25 3.91
765 867 3.818787 CGGGCTGTGCTTGATGCC 61.819 66.667 0.00 0.00 44.22 4.40
766 868 2.677524 GGGCTGTGCTTGATGCCA 60.678 61.111 5.21 0.00 46.53 4.92
833 939 2.029244 CCACACTATTCGTCGTGCAATC 59.971 50.000 0.00 0.00 34.58 2.67
897 1003 2.158559 TGACACCAACGGAATTCCATG 58.841 47.619 24.09 19.99 35.14 3.66
930 1079 2.049526 CGCCACACGTACTGCAGA 60.050 61.111 23.35 0.48 36.87 4.26
934 1083 1.795768 CCACACGTACTGCAGACATT 58.204 50.000 23.35 0.00 0.00 2.71
942 1091 0.593128 ACTGCAGACATTTTCGGTGC 59.407 50.000 23.35 0.00 34.62 5.01
967 1116 2.094894 CACTGATTGCTGATTCCGTGAC 59.905 50.000 0.00 0.00 0.00 3.67
969 1118 2.941064 CTGATTGCTGATTCCGTGACAT 59.059 45.455 0.00 0.00 0.00 3.06
970 1119 2.679336 TGATTGCTGATTCCGTGACATG 59.321 45.455 0.00 0.00 0.00 3.21
971 1120 2.183478 TTGCTGATTCCGTGACATGT 57.817 45.000 0.00 0.00 0.00 3.21
994 1168 6.978080 TGTGGATTTTTCTTTGCTTTCACTAC 59.022 34.615 0.00 0.00 0.00 2.73
995 1169 7.147915 TGTGGATTTTTCTTTGCTTTCACTACT 60.148 33.333 0.00 0.00 0.00 2.57
996 1170 8.349983 GTGGATTTTTCTTTGCTTTCACTACTA 58.650 33.333 0.00 0.00 0.00 1.82
997 1171 8.567948 TGGATTTTTCTTTGCTTTCACTACTAG 58.432 33.333 0.00 0.00 0.00 2.57
998 1172 8.568794 GGATTTTTCTTTGCTTTCACTACTAGT 58.431 33.333 0.00 0.00 0.00 2.57
1009 1183 6.513806 TTTCACTACTAGTAATGGCGTACA 57.486 37.500 11.22 0.00 0.00 2.90
1011 1185 5.430886 TCACTACTAGTAATGGCGTACAGA 58.569 41.667 11.22 0.00 0.00 3.41
1027 1201 5.005107 GCGTACAGAAGAATTAGGTTTACGG 59.995 44.000 0.00 0.00 0.00 4.02
1029 1203 3.930848 ACAGAAGAATTAGGTTTACGGCG 59.069 43.478 4.80 4.80 0.00 6.46
1032 1231 5.048507 AGAAGAATTAGGTTTACGGCGATC 58.951 41.667 16.62 0.00 0.00 3.69
1064 1263 0.874390 TGCTGCACGGAGAAATCAAC 59.126 50.000 0.00 0.00 0.00 3.18
1195 1398 4.111016 CACGTACGCTGCGAGGGA 62.111 66.667 30.47 7.82 31.91 4.20
1196 1399 3.812019 ACGTACGCTGCGAGGGAG 61.812 66.667 30.47 16.10 31.91 4.30
1197 1400 4.554363 CGTACGCTGCGAGGGAGG 62.554 72.222 30.47 11.92 31.91 4.30
1198 1401 4.208686 GTACGCTGCGAGGGAGGG 62.209 72.222 30.47 0.00 31.91 4.30
1237 1443 3.141488 CACCCCGTCTCCTCCTCG 61.141 72.222 0.00 0.00 0.00 4.63
1258 1464 3.423162 CTCCTCTTCTGCCTCGCCG 62.423 68.421 0.00 0.00 0.00 6.46
1401 1607 2.283529 GCTCTCCGTGGACCCTGAA 61.284 63.158 0.00 0.00 0.00 3.02
1402 1608 1.827399 GCTCTCCGTGGACCCTGAAA 61.827 60.000 0.00 0.00 0.00 2.69
1470 1676 4.436998 CGCCTCCTCCCGTCACAC 62.437 72.222 0.00 0.00 0.00 3.82
1644 1850 4.438346 GTGCTCGACACTGGTGTT 57.562 55.556 7.82 0.00 46.41 3.32
1824 2040 3.406595 GAACGGCTCCTCCCATGGG 62.407 68.421 26.30 26.30 0.00 4.00
2088 2304 3.227276 CTGGGAGGCGGCTCGTAT 61.227 66.667 29.95 0.00 0.00 3.06
2337 2553 1.302271 GGGTGACGACAAGTTCCCC 60.302 63.158 0.00 0.00 39.62 4.81
2876 3092 3.174799 CACGCTTTGCTTCTTCTGTAC 57.825 47.619 0.00 0.00 0.00 2.90
2886 3105 6.604735 TGCTTCTTCTGTACAAAAACTCTC 57.395 37.500 0.00 0.00 0.00 3.20
2927 3146 6.347402 CGACACGTCTTTCTTGAAAATATGGT 60.347 38.462 0.00 0.00 0.00 3.55
3009 3228 2.159099 TCGTCTTTAGGTGCTAGCCATG 60.159 50.000 13.29 0.00 0.00 3.66
3013 3232 2.260844 TTAGGTGCTAGCCATGATGC 57.739 50.000 13.29 0.00 0.00 3.91
3026 3245 3.549625 GCCATGATGCTGTTAGCTTTAGC 60.550 47.826 0.00 0.00 42.97 3.09
3076 3295 6.174720 TCATAGTAATGACAGGCTTTAGGG 57.825 41.667 0.00 0.00 37.20 3.53
3077 3296 3.283259 AGTAATGACAGGCTTTAGGGC 57.717 47.619 0.00 0.00 41.20 5.19
3078 3297 2.576191 AGTAATGACAGGCTTTAGGGCA 59.424 45.455 0.00 0.00 43.56 5.36
3079 3298 2.834638 AATGACAGGCTTTAGGGCAT 57.165 45.000 0.00 0.00 43.56 4.40
3081 3300 0.680921 TGACAGGCTTTAGGGCATGC 60.681 55.000 9.90 9.90 46.16 4.06
3082 3301 1.718757 GACAGGCTTTAGGGCATGCG 61.719 60.000 12.44 0.00 46.16 4.73
3083 3302 2.830370 AGGCTTTAGGGCATGCGC 60.830 61.111 26.04 26.04 43.56 6.09
3098 3322 0.320771 TGCGCTTGGTCTCTTTCTCC 60.321 55.000 9.73 0.00 0.00 3.71
3099 3323 0.036858 GCGCTTGGTCTCTTTCTCCT 60.037 55.000 0.00 0.00 0.00 3.69
3100 3324 1.204941 GCGCTTGGTCTCTTTCTCCTA 59.795 52.381 0.00 0.00 0.00 2.94
3101 3325 2.882324 CGCTTGGTCTCTTTCTCCTAC 58.118 52.381 0.00 0.00 0.00 3.18
3102 3326 2.231478 CGCTTGGTCTCTTTCTCCTACA 59.769 50.000 0.00 0.00 0.00 2.74
3103 3327 3.591023 GCTTGGTCTCTTTCTCCTACAC 58.409 50.000 0.00 0.00 0.00 2.90
3104 3328 3.259625 GCTTGGTCTCTTTCTCCTACACT 59.740 47.826 0.00 0.00 0.00 3.55
3106 3330 4.114015 TGGTCTCTTTCTCCTACACTGA 57.886 45.455 0.00 0.00 0.00 3.41
3108 3332 4.281182 TGGTCTCTTTCTCCTACACTGAAC 59.719 45.833 0.00 0.00 0.00 3.18
3109 3333 4.322123 GGTCTCTTTCTCCTACACTGAACC 60.322 50.000 0.00 0.00 0.00 3.62
3110 3334 4.525100 GTCTCTTTCTCCTACACTGAACCT 59.475 45.833 0.00 0.00 0.00 3.50
3111 3335 5.011227 GTCTCTTTCTCCTACACTGAACCTT 59.989 44.000 0.00 0.00 0.00 3.50
3112 3336 5.011125 TCTCTTTCTCCTACACTGAACCTTG 59.989 44.000 0.00 0.00 0.00 3.61
3113 3337 4.899457 TCTTTCTCCTACACTGAACCTTGA 59.101 41.667 0.00 0.00 0.00 3.02
3114 3338 5.544176 TCTTTCTCCTACACTGAACCTTGAT 59.456 40.000 0.00 0.00 0.00 2.57
3117 3341 2.637382 TCCTACACTGAACCTTGATGCA 59.363 45.455 0.00 0.00 0.00 3.96
3118 3342 3.005554 CCTACACTGAACCTTGATGCAG 58.994 50.000 0.00 0.00 34.65 4.41
3128 3367 6.554419 TGAACCTTGATGCAGAAATAATTCG 58.446 36.000 0.00 0.00 40.63 3.34
3131 3370 5.066505 ACCTTGATGCAGAAATAATTCGGTC 59.933 40.000 0.00 0.00 40.63 4.79
3136 3375 6.427853 TGATGCAGAAATAATTCGGTCTATGG 59.572 38.462 0.00 0.00 40.63 2.74
3164 3403 2.125147 ACATCCATGTCGTGCCCG 60.125 61.111 0.00 0.00 35.87 6.13
3536 3775 2.484203 CCGTCCTTCTCCGTCGTC 59.516 66.667 0.00 0.00 0.00 4.20
3824 4063 2.507484 TCGTATACGTGGGGGATGTAG 58.493 52.381 23.67 0.00 40.80 2.74
3845 4084 1.665916 CCGATGCATGGGCGAGTAG 60.666 63.158 15.33 0.00 45.35 2.57
3951 4190 2.354259 CTCCTGATTTCTGTGCTGTCC 58.646 52.381 0.00 0.00 0.00 4.02
3966 4205 3.768757 TGCTGTCCAAAAATGGATAAGGG 59.231 43.478 0.19 0.00 40.51 3.95
4153 4392 7.506328 ACTAACCTCTGGTTTCATACAAAAC 57.494 36.000 7.32 0.00 44.33 2.43
4207 6170 1.992667 GACGAGATGTGCGATTGAACA 59.007 47.619 0.00 0.00 38.27 3.18
4243 6206 9.804977 TTCAGAAGTACCCTAGTTATATACTCC 57.195 37.037 0.00 0.00 38.33 3.85
4244 6207 8.389366 TCAGAAGTACCCTAGTTATATACTCCC 58.611 40.741 0.00 0.00 38.33 4.30
4245 6208 8.392479 CAGAAGTACCCTAGTTATATACTCCCT 58.608 40.741 0.00 0.00 38.33 4.20
4246 6209 8.613923 AGAAGTACCCTAGTTATATACTCCCTC 58.386 40.741 0.00 0.00 38.33 4.30
4247 6210 7.282689 AGTACCCTAGTTATATACTCCCTCC 57.717 44.000 0.00 0.00 38.33 4.30
4248 6211 6.801632 AGTACCCTAGTTATATACTCCCTCCA 59.198 42.308 0.00 0.00 38.33 3.86
4249 6212 6.754753 ACCCTAGTTATATACTCCCTCCAT 57.245 41.667 0.00 0.00 38.33 3.41
4250 6213 7.129823 ACCCTAGTTATATACTCCCTCCATT 57.870 40.000 0.00 0.00 38.33 3.16
4251 6214 7.190501 ACCCTAGTTATATACTCCCTCCATTC 58.809 42.308 0.00 0.00 38.33 2.67
4252 6215 6.612049 CCCTAGTTATATACTCCCTCCATTCC 59.388 46.154 0.00 0.00 38.33 3.01
4253 6216 7.423341 CCTAGTTATATACTCCCTCCATTCCT 58.577 42.308 0.00 0.00 38.33 3.36
4254 6217 8.566979 CCTAGTTATATACTCCCTCCATTCCTA 58.433 40.741 0.00 0.00 38.33 2.94
4255 6218 9.992442 CTAGTTATATACTCCCTCCATTCCTAA 57.008 37.037 0.00 0.00 38.33 2.69
4257 6220 9.860393 AGTTATATACTCCCTCCATTCCTAAAT 57.140 33.333 0.00 0.00 28.23 1.40
4263 6226 9.860393 ATACTCCCTCCATTCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
4264 6227 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
4265 6228 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
4266 6229 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
4267 6230 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
4268 6231 9.289782 CCCTCCATTCCTAAATATAAGTCTTTG 57.710 37.037 0.00 0.00 0.00 2.77
4269 6232 9.289782 CCTCCATTCCTAAATATAAGTCTTTGG 57.710 37.037 0.00 0.00 0.00 3.28
4280 6243 8.443953 AATATAAGTCTTTGGAGAGATTGCAC 57.556 34.615 0.00 0.00 31.07 4.57
4281 6244 4.363991 AAGTCTTTGGAGAGATTGCACT 57.636 40.909 0.00 0.00 31.07 4.40
4282 6245 5.489792 AAGTCTTTGGAGAGATTGCACTA 57.510 39.130 0.00 0.00 31.07 2.74
4283 6246 5.690464 AGTCTTTGGAGAGATTGCACTAT 57.310 39.130 0.00 0.00 31.07 2.12
4284 6247 5.426504 AGTCTTTGGAGAGATTGCACTATG 58.573 41.667 0.00 0.00 31.07 2.23
4285 6248 4.574013 GTCTTTGGAGAGATTGCACTATGG 59.426 45.833 0.00 0.00 31.07 2.74
4286 6249 4.471025 TCTTTGGAGAGATTGCACTATGGA 59.529 41.667 0.00 0.00 0.00 3.41
4287 6250 3.827008 TGGAGAGATTGCACTATGGAC 57.173 47.619 0.00 0.00 0.00 4.02
4288 6251 2.435805 TGGAGAGATTGCACTATGGACC 59.564 50.000 0.00 0.00 0.00 4.46
4289 6252 2.435805 GGAGAGATTGCACTATGGACCA 59.564 50.000 0.00 0.00 0.00 4.02
4290 6253 3.462021 GAGAGATTGCACTATGGACCAC 58.538 50.000 0.00 0.00 0.00 4.16
4291 6254 2.840038 AGAGATTGCACTATGGACCACA 59.160 45.455 0.00 0.00 0.00 4.17
4292 6255 3.457380 AGAGATTGCACTATGGACCACAT 59.543 43.478 0.00 0.00 43.68 3.21
4293 6256 4.655649 AGAGATTGCACTATGGACCACATA 59.344 41.667 0.00 0.00 41.03 2.29
4294 6257 4.708177 AGATTGCACTATGGACCACATAC 58.292 43.478 0.00 0.00 41.03 2.39
4295 6258 2.595124 TGCACTATGGACCACATACG 57.405 50.000 0.00 0.00 41.03 3.06
4296 6259 1.138069 TGCACTATGGACCACATACGG 59.862 52.381 0.00 0.00 41.03 4.02
4297 6260 1.411246 GCACTATGGACCACATACGGA 59.589 52.381 0.00 0.00 41.03 4.69
4298 6261 2.545952 GCACTATGGACCACATACGGAG 60.546 54.545 0.00 0.00 41.03 4.63
4299 6262 1.687123 ACTATGGACCACATACGGAGC 59.313 52.381 0.00 0.00 41.03 4.70
4300 6263 1.686587 CTATGGACCACATACGGAGCA 59.313 52.381 0.00 0.00 41.03 4.26
4301 6264 0.908910 ATGGACCACATACGGAGCAA 59.091 50.000 0.00 0.00 38.26 3.91
4302 6265 0.687920 TGGACCACATACGGAGCAAA 59.312 50.000 0.00 0.00 0.00 3.68
4303 6266 1.072489 TGGACCACATACGGAGCAAAA 59.928 47.619 0.00 0.00 0.00 2.44
4304 6267 2.290641 TGGACCACATACGGAGCAAAAT 60.291 45.455 0.00 0.00 0.00 1.82
4305 6268 2.097466 GGACCACATACGGAGCAAAATG 59.903 50.000 0.00 0.00 0.00 2.32
4306 6269 3.006940 GACCACATACGGAGCAAAATGA 58.993 45.455 0.00 0.00 0.00 2.57
4307 6270 3.009723 ACCACATACGGAGCAAAATGAG 58.990 45.455 0.00 0.00 0.00 2.90
4308 6271 3.009723 CCACATACGGAGCAAAATGAGT 58.990 45.455 0.00 0.00 0.00 3.41
4309 6272 3.181507 CCACATACGGAGCAAAATGAGTG 60.182 47.826 0.00 0.00 0.00 3.51
4310 6273 3.684305 CACATACGGAGCAAAATGAGTGA 59.316 43.478 0.00 0.00 0.00 3.41
4311 6274 4.154015 CACATACGGAGCAAAATGAGTGAA 59.846 41.667 0.00 0.00 0.00 3.18
4312 6275 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4313 6276 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4314 6277 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4315 6278 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4316 6279 5.431765 ACGGAGCAAAATGAGTGAATCTAT 58.568 37.500 0.00 0.00 0.00 1.98
4317 6280 6.582636 ACGGAGCAAAATGAGTGAATCTATA 58.417 36.000 0.00 0.00 0.00 1.31
4318 6281 6.480320 ACGGAGCAAAATGAGTGAATCTATAC 59.520 38.462 0.00 0.00 0.00 1.47
4319 6282 6.073548 CGGAGCAAAATGAGTGAATCTATACC 60.074 42.308 0.00 0.00 0.00 2.73
4320 6283 6.205658 GGAGCAAAATGAGTGAATCTATACCC 59.794 42.308 0.00 0.00 0.00 3.69
4321 6284 6.904626 AGCAAAATGAGTGAATCTATACCCT 58.095 36.000 0.00 0.00 0.00 4.34
4322 6285 8.034313 AGCAAAATGAGTGAATCTATACCCTA 57.966 34.615 0.00 0.00 0.00 3.53
4323 6286 8.494433 AGCAAAATGAGTGAATCTATACCCTAA 58.506 33.333 0.00 0.00 0.00 2.69
4324 6287 9.120538 GCAAAATGAGTGAATCTATACCCTAAA 57.879 33.333 0.00 0.00 0.00 1.85
4327 6290 8.854614 AATGAGTGAATCTATACCCTAAATGC 57.145 34.615 0.00 0.00 0.00 3.56
4328 6291 7.373617 TGAGTGAATCTATACCCTAAATGCA 57.626 36.000 0.00 0.00 0.00 3.96
4329 6292 7.977818 TGAGTGAATCTATACCCTAAATGCAT 58.022 34.615 0.00 0.00 0.00 3.96
4330 6293 8.097038 TGAGTGAATCTATACCCTAAATGCATC 58.903 37.037 0.00 0.00 0.00 3.91
4331 6294 8.212259 AGTGAATCTATACCCTAAATGCATCT 57.788 34.615 0.00 0.00 0.00 2.90
4332 6295 9.326489 AGTGAATCTATACCCTAAATGCATCTA 57.674 33.333 0.00 0.00 0.00 1.98
4333 6296 9.593134 GTGAATCTATACCCTAAATGCATCTAG 57.407 37.037 0.00 0.00 0.00 2.43
4334 6297 9.547279 TGAATCTATACCCTAAATGCATCTAGA 57.453 33.333 8.70 0.00 0.00 2.43
4338 6301 9.990868 TCTATACCCTAAATGCATCTAGATACA 57.009 33.333 8.70 8.11 0.00 2.29
4342 6305 7.099764 ACCCTAAATGCATCTAGATACATTCG 58.900 38.462 24.92 19.35 34.59 3.34
4343 6306 7.099764 CCCTAAATGCATCTAGATACATTCGT 58.900 38.462 24.92 16.04 34.59 3.85
4344 6307 8.251026 CCCTAAATGCATCTAGATACATTCGTA 58.749 37.037 24.92 16.25 34.59 3.43
4345 6308 9.809096 CCTAAATGCATCTAGATACATTCGTAT 57.191 33.333 24.92 15.21 41.16 3.06
4348 6311 9.494271 AAATGCATCTAGATACATTCGTATGTT 57.506 29.630 24.92 10.13 42.29 2.71
4349 6312 7.873739 TGCATCTAGATACATTCGTATGTTG 57.126 36.000 13.12 4.90 42.29 3.33
4350 6313 7.433680 TGCATCTAGATACATTCGTATGTTGT 58.566 34.615 13.12 2.99 42.29 3.32
4351 6314 7.926018 TGCATCTAGATACATTCGTATGTTGTT 59.074 33.333 13.12 2.30 42.29 2.83
4352 6315 8.428536 GCATCTAGATACATTCGTATGTTGTTC 58.571 37.037 13.12 8.27 42.29 3.18
4353 6316 9.463443 CATCTAGATACATTCGTATGTTGTTCA 57.537 33.333 13.12 0.00 42.29 3.18
4358 6321 9.249457 AGATACATTCGTATGTTGTTCATAGTG 57.751 33.333 13.12 0.00 42.29 2.74
4359 6322 9.244799 GATACATTCGTATGTTGTTCATAGTGA 57.755 33.333 13.12 0.00 42.29 3.41
4360 6323 7.899178 ACATTCGTATGTTGTTCATAGTGAA 57.101 32.000 1.31 0.00 42.29 3.18
4361 6324 8.317891 ACATTCGTATGTTGTTCATAGTGAAA 57.682 30.769 1.31 0.00 42.29 2.69
4362 6325 8.946085 ACATTCGTATGTTGTTCATAGTGAAAT 58.054 29.630 1.31 0.00 42.29 2.17
4363 6326 9.773328 CATTCGTATGTTGTTCATAGTGAAATT 57.227 29.630 0.00 0.00 38.22 1.82
4433 6396 9.784531 ATTATAACTGTGCTTGAGTATGCTTAT 57.215 29.630 0.00 0.00 0.00 1.73
4465 6428 7.701539 TGAACTATGGTTGAATTATGCTTGT 57.298 32.000 0.00 0.00 35.58 3.16
4504 6468 4.700692 TGCCTGAGTACGCTTATATCTAGG 59.299 45.833 0.00 0.00 0.00 3.02
4524 6488 5.975988 AGGTGTGGGATGAGTATGTAATT 57.024 39.130 0.00 0.00 0.00 1.40
4538 6502 9.173021 TGAGTATGTAATTAGTTTGGTTGATGG 57.827 33.333 0.00 0.00 0.00 3.51
4586 6550 2.219080 TGATTGCCCACATCACACAT 57.781 45.000 0.00 0.00 0.00 3.21
4591 6555 1.303309 GCCCACATCACACATAGCTC 58.697 55.000 0.00 0.00 0.00 4.09
4619 6583 5.006358 AGCGCGAATCGTCTATGTTATTTTT 59.994 36.000 12.10 0.00 41.07 1.94
4620 6584 6.199531 AGCGCGAATCGTCTATGTTATTTTTA 59.800 34.615 12.10 0.00 41.07 1.52
4631 6595 8.601476 GTCTATGTTATTTTTAGTCTTCCCACG 58.399 37.037 0.00 0.00 0.00 4.94
4665 6630 1.132643 GCAACCGTTTACCACAACACA 59.867 47.619 0.00 0.00 0.00 3.72
4687 6653 0.034896 CAGCTACGTGTGGAGGGTTT 59.965 55.000 0.00 0.00 0.00 3.27
4689 6655 0.953960 GCTACGTGTGGAGGGTTTGG 60.954 60.000 0.00 0.00 0.00 3.28
4690 6656 0.953960 CTACGTGTGGAGGGTTTGGC 60.954 60.000 0.00 0.00 0.00 4.52
4729 6695 5.105106 CGTATGGTGCATATTAGGGTGGATA 60.105 44.000 0.00 0.00 0.00 2.59
4736 6702 6.884295 GTGCATATTAGGGTGGATATTTAGCA 59.116 38.462 0.00 0.00 0.00 3.49
4754 6720 6.576662 TTAGCATGGGTAAAAATTTCACGA 57.423 33.333 0.00 0.00 0.00 4.35
4761 6727 5.302059 TGGGTAAAAATTTCACGATCAACCA 59.698 36.000 0.00 0.00 0.00 3.67
4763 6729 6.871492 GGGTAAAAATTTCACGATCAACCAAT 59.129 34.615 0.00 0.00 0.00 3.16
4764 6730 7.148656 GGGTAAAAATTTCACGATCAACCAATG 60.149 37.037 0.00 0.00 0.00 2.82
4767 6733 7.642071 AAAATTTCACGATCAACCAATGAAG 57.358 32.000 0.00 0.00 42.54 3.02
4770 6736 6.384258 TTTCACGATCAACCAATGAAGAAA 57.616 33.333 0.00 0.00 42.54 2.52
4783 6749 2.593026 TGAAGAAAATGTGGACCCACC 58.407 47.619 15.86 1.03 45.63 4.61
4806 6772 4.262164 CCTGAAACTTGGTGATTTTCCCAG 60.262 45.833 0.00 0.00 31.04 4.45
4808 6774 4.584325 TGAAACTTGGTGATTTTCCCAGAG 59.416 41.667 0.00 0.00 31.04 3.35
4817 6783 3.717842 TTTCCCAGAGTGGAAACCG 57.282 52.632 1.23 0.00 46.76 4.44
4818 6784 0.841289 TTTCCCAGAGTGGAAACCGT 59.159 50.000 1.23 0.00 46.76 4.83
4819 6785 0.107831 TTCCCAGAGTGGAAACCGTG 59.892 55.000 0.00 0.00 41.40 4.94
4820 6786 1.052124 TCCCAGAGTGGAAACCGTGT 61.052 55.000 0.00 0.00 40.96 4.49
4821 6787 0.884704 CCCAGAGTGGAAACCGTGTG 60.885 60.000 0.00 0.00 40.96 3.82
4822 6788 1.507141 CCAGAGTGGAAACCGTGTGC 61.507 60.000 0.00 0.00 40.96 4.57
4823 6789 0.813610 CAGAGTGGAAACCGTGTGCA 60.814 55.000 0.00 0.00 0.00 4.57
4824 6790 0.107410 AGAGTGGAAACCGTGTGCAA 60.107 50.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.821216 AACACAAATAGGCCACCGAG 58.179 50.000 5.01 0.00 0.00 4.63
1 2 1.883275 CAAACACAAATAGGCCACCGA 59.117 47.619 5.01 0.00 0.00 4.69
2 3 1.611491 ACAAACACAAATAGGCCACCG 59.389 47.619 5.01 0.00 0.00 4.94
3 4 3.744238 AACAAACACAAATAGGCCACC 57.256 42.857 5.01 0.00 0.00 4.61
4 5 5.112686 TGAAAACAAACACAAATAGGCCAC 58.887 37.500 5.01 0.00 0.00 5.01
20 21 3.810310 ATGAAAAACCGGCTGAAAACA 57.190 38.095 0.00 0.00 0.00 2.83
21 22 6.779115 AATTATGAAAAACCGGCTGAAAAC 57.221 33.333 0.00 0.00 0.00 2.43
28 29 6.160684 ACTTGGTTAATTATGAAAAACCGGC 58.839 36.000 0.00 0.00 43.53 6.13
59 60 8.616076 AGTTTTGCCTCATCGATTATTAAGAAG 58.384 33.333 0.00 0.00 0.00 2.85
60 61 8.506168 AGTTTTGCCTCATCGATTATTAAGAA 57.494 30.769 0.00 0.00 0.00 2.52
62 63 9.573133 AAAAGTTTTGCCTCATCGATTATTAAG 57.427 29.630 0.00 0.00 0.00 1.85
65 66 6.311200 GCAAAAGTTTTGCCTCATCGATTATT 59.689 34.615 33.57 0.00 39.38 1.40
149 156 1.068895 CCATGCCACTTGACTTTGCAA 59.931 47.619 0.00 0.00 35.30 4.08
158 165 1.233950 TGTACGTGCCATGCCACTTG 61.234 55.000 5.16 0.00 33.60 3.16
182 189 4.877251 TCGTGGCTTAGTAACTTTGTTGTT 59.123 37.500 0.00 0.00 0.00 2.83
210 256 1.351350 GAACTAGCAAGGGGTCCTGTT 59.649 52.381 0.00 0.00 32.13 3.16
212 258 0.984230 TGAACTAGCAAGGGGTCCTG 59.016 55.000 0.00 0.00 32.13 3.86
224 270 6.589523 CAGTGTTTCCTCTTGATCTGAACTAG 59.410 42.308 0.00 0.00 0.00 2.57
269 316 5.105063 TCTGAATCAATAGTCGACAGCTTG 58.895 41.667 19.50 16.65 0.00 4.01
298 345 2.435059 GCACTTCCTCTGCCGTCC 60.435 66.667 0.00 0.00 0.00 4.79
301 348 2.811317 GACGCACTTCCTCTGCCG 60.811 66.667 0.00 0.00 0.00 5.69
305 352 1.964891 TCGTCGACGCACTTCCTCT 60.965 57.895 32.19 0.00 39.60 3.69
461 516 4.559386 GCGATCGCGTGCCTTTCG 62.559 66.667 26.12 7.86 40.36 3.46
699 801 3.357079 GCCTCCGCGCCCATTATG 61.357 66.667 0.00 0.00 0.00 1.90
747 849 3.818787 GCATCAAGCACAGCCCGG 61.819 66.667 0.00 0.00 44.79 5.73
869 975 1.564622 CGTTGGTGTCAGCGTCAAG 59.435 57.895 0.00 0.00 41.59 3.02
897 1003 3.357079 CGTTCCTGGCCTGCACAC 61.357 66.667 3.32 0.00 0.00 3.82
915 1064 1.795768 AATGTCTGCAGTACGTGTGG 58.204 50.000 14.67 0.00 0.00 4.17
916 1065 3.661678 CGAAAATGTCTGCAGTACGTGTG 60.662 47.826 14.67 0.00 0.00 3.82
930 1079 1.603802 CAGTGTCAGCACCGAAAATGT 59.396 47.619 0.00 0.00 46.35 2.71
934 1083 1.872952 CAATCAGTGTCAGCACCGAAA 59.127 47.619 0.00 0.00 46.35 3.46
942 1091 2.350804 CGGAATCAGCAATCAGTGTCAG 59.649 50.000 0.00 0.00 0.00 3.51
967 1116 6.480981 AGTGAAAGCAAAGAAAAATCCACATG 59.519 34.615 0.00 0.00 0.00 3.21
969 1118 5.976458 AGTGAAAGCAAAGAAAAATCCACA 58.024 33.333 0.00 0.00 0.00 4.17
970 1119 7.203218 AGTAGTGAAAGCAAAGAAAAATCCAC 58.797 34.615 0.00 0.00 0.00 4.02
971 1120 7.346751 AGTAGTGAAAGCAAAGAAAAATCCA 57.653 32.000 0.00 0.00 0.00 3.41
994 1168 7.595502 CCTAATTCTTCTGTACGCCATTACTAG 59.404 40.741 0.00 0.00 0.00 2.57
995 1169 7.069085 ACCTAATTCTTCTGTACGCCATTACTA 59.931 37.037 0.00 0.00 0.00 1.82
996 1170 6.127140 ACCTAATTCTTCTGTACGCCATTACT 60.127 38.462 0.00 0.00 0.00 2.24
997 1171 6.047231 ACCTAATTCTTCTGTACGCCATTAC 58.953 40.000 0.00 0.00 0.00 1.89
998 1172 6.229936 ACCTAATTCTTCTGTACGCCATTA 57.770 37.500 0.00 0.00 0.00 1.90
999 1173 5.099042 ACCTAATTCTTCTGTACGCCATT 57.901 39.130 0.00 0.00 0.00 3.16
1009 1183 4.460948 TCGCCGTAAACCTAATTCTTCT 57.539 40.909 0.00 0.00 0.00 2.85
1011 1185 3.800506 CGATCGCCGTAAACCTAATTCTT 59.199 43.478 0.26 0.00 0.00 2.52
1027 1201 1.869503 CACACATGAACAACGATCGC 58.130 50.000 16.60 0.00 0.00 4.58
1029 1203 2.843077 CAGCACACATGAACAACGATC 58.157 47.619 0.00 0.00 0.00 3.69
1032 1231 0.029167 TGCAGCACACATGAACAACG 59.971 50.000 0.00 0.00 0.00 4.10
1053 1252 6.512415 CGCTAATGGAAGATGTTGATTTCTCC 60.512 42.308 0.00 0.00 0.00 3.71
1237 1443 1.813192 CGAGGCAGAAGAGGAGGAC 59.187 63.158 0.00 0.00 0.00 3.85
1275 1481 4.547367 CCTTCATCCCCGCCGGAC 62.547 72.222 5.05 0.00 46.09 4.79
1398 1604 2.180276 GAGTAGAGGAGGTGGCTTTCA 58.820 52.381 0.00 0.00 0.00 2.69
1401 1607 0.713579 AGGAGTAGAGGAGGTGGCTT 59.286 55.000 0.00 0.00 0.00 4.35
1402 1608 1.215924 GTAGGAGTAGAGGAGGTGGCT 59.784 57.143 0.00 0.00 0.00 4.75
1638 1844 2.429930 CTCTCGGGCCAAACACCA 59.570 61.111 4.39 0.00 0.00 4.17
1821 2037 2.680352 GAGAGCTCGGTGGTCCCA 60.680 66.667 8.37 0.00 43.71 4.37
2337 2553 1.686355 TGCCTTTGTTGTACACCAGG 58.314 50.000 0.00 0.00 33.73 4.45
2410 2626 4.697756 CTTGCCCTTCACCGCCGA 62.698 66.667 0.00 0.00 0.00 5.54
2605 2821 2.202401 GTCCGACTCCACGTACGC 60.202 66.667 16.72 0.00 0.00 4.42
2806 3022 2.278206 CCGCTCGTCGATGGTCAG 60.278 66.667 4.48 0.00 41.67 3.51
2873 3089 6.867293 AGTACAATCCTCGAGAGTTTTTGTAC 59.133 38.462 26.74 26.74 40.95 2.90
2874 3090 6.866770 CAGTACAATCCTCGAGAGTTTTTGTA 59.133 38.462 15.71 15.44 30.72 2.41
2876 3092 5.926542 TCAGTACAATCCTCGAGAGTTTTTG 59.073 40.000 15.71 11.72 0.00 2.44
2886 3105 1.471287 TGTCGGTCAGTACAATCCTCG 59.529 52.381 0.00 0.00 0.00 4.63
2927 3146 4.467438 CCCGTAAAGTCTAGGGTTTTAGGA 59.533 45.833 11.98 0.00 39.05 2.94
2977 3196 3.383825 ACCTAAAGACGACCATAGCGATT 59.616 43.478 0.00 0.00 0.00 3.34
3054 3273 4.757149 GCCCTAAAGCCTGTCATTACTATG 59.243 45.833 0.00 0.00 0.00 2.23
3076 3295 0.179179 GAAAGAGACCAAGCGCATGC 60.179 55.000 11.47 7.91 43.24 4.06
3077 3296 1.396301 GAGAAAGAGACCAAGCGCATG 59.604 52.381 11.47 8.27 0.00 4.06
3078 3297 1.677217 GGAGAAAGAGACCAAGCGCAT 60.677 52.381 11.47 0.00 0.00 4.73
3079 3298 0.320771 GGAGAAAGAGACCAAGCGCA 60.321 55.000 11.47 0.00 0.00 6.09
3080 3299 0.036858 AGGAGAAAGAGACCAAGCGC 60.037 55.000 0.00 0.00 0.00 5.92
3081 3300 2.231478 TGTAGGAGAAAGAGACCAAGCG 59.769 50.000 0.00 0.00 0.00 4.68
3082 3301 3.259625 AGTGTAGGAGAAAGAGACCAAGC 59.740 47.826 0.00 0.00 0.00 4.01
3083 3302 4.524714 TCAGTGTAGGAGAAAGAGACCAAG 59.475 45.833 0.00 0.00 0.00 3.61
3098 3322 3.930336 TCTGCATCAAGGTTCAGTGTAG 58.070 45.455 0.00 0.00 0.00 2.74
3099 3323 4.350368 TTCTGCATCAAGGTTCAGTGTA 57.650 40.909 0.00 0.00 0.00 2.90
3100 3324 2.936919 TCTGCATCAAGGTTCAGTGT 57.063 45.000 0.00 0.00 0.00 3.55
3101 3325 4.778534 ATTTCTGCATCAAGGTTCAGTG 57.221 40.909 0.00 0.00 0.00 3.66
3102 3326 7.472334 AATTATTTCTGCATCAAGGTTCAGT 57.528 32.000 0.00 0.00 0.00 3.41
3103 3327 6.690098 CGAATTATTTCTGCATCAAGGTTCAG 59.310 38.462 0.00 0.00 0.00 3.02
3104 3328 6.404623 CCGAATTATTTCTGCATCAAGGTTCA 60.405 38.462 0.00 0.00 0.00 3.18
3106 3330 5.418840 ACCGAATTATTTCTGCATCAAGGTT 59.581 36.000 0.00 0.00 0.00 3.50
3108 3332 5.297776 AGACCGAATTATTTCTGCATCAAGG 59.702 40.000 0.00 0.00 0.00 3.61
3109 3333 6.369059 AGACCGAATTATTTCTGCATCAAG 57.631 37.500 0.00 0.00 0.00 3.02
3110 3334 7.041167 CCATAGACCGAATTATTTCTGCATCAA 60.041 37.037 0.00 0.00 0.00 2.57
3111 3335 6.427853 CCATAGACCGAATTATTTCTGCATCA 59.572 38.462 0.00 0.00 0.00 3.07
3112 3336 6.428159 ACCATAGACCGAATTATTTCTGCATC 59.572 38.462 0.00 0.00 0.00 3.91
3113 3337 6.205464 CACCATAGACCGAATTATTTCTGCAT 59.795 38.462 0.00 0.00 0.00 3.96
3114 3338 5.527214 CACCATAGACCGAATTATTTCTGCA 59.473 40.000 0.00 0.00 0.00 4.41
3117 3341 6.428159 GCATCACCATAGACCGAATTATTTCT 59.572 38.462 0.00 0.00 0.00 2.52
3118 3342 6.204688 TGCATCACCATAGACCGAATTATTTC 59.795 38.462 0.00 0.00 0.00 2.17
3128 3367 1.131638 TCCCTGCATCACCATAGACC 58.868 55.000 0.00 0.00 0.00 3.85
3131 3370 2.551721 GGATGTCCCTGCATCACCATAG 60.552 54.545 8.11 0.00 45.11 2.23
3136 3375 1.315690 CATGGATGTCCCTGCATCAC 58.684 55.000 8.11 0.00 45.11 3.06
3951 4190 6.070309 TCCAACAATCCCCTTATCCATTTTTG 60.070 38.462 0.00 0.00 0.00 2.44
3966 4205 5.163519 CCCATGAAATGTACTCCAACAATCC 60.164 44.000 0.00 0.00 44.81 3.01
4032 4271 6.270927 TGCTCTATAGGCAGTGAGGAAATTAT 59.729 38.462 10.69 0.00 34.56 1.28
4093 4332 7.834068 TTGAAGTGTCTGCTTCTTGATATAC 57.166 36.000 7.25 0.00 43.74 1.47
4153 4392 5.549347 CCATCTCTGAGAGGAAATGGTATG 58.451 45.833 19.97 8.05 31.21 2.39
4194 6157 4.217334 ACATAACCATTGTTCAATCGCACA 59.783 37.500 0.00 0.00 35.87 4.57
4207 6170 6.388619 AGGGTACTTCTGAACATAACCATT 57.611 37.500 11.65 0.00 0.00 3.16
4240 6203 8.442660 AGACTTATATTTAGGAATGGAGGGAG 57.557 38.462 0.00 0.00 0.00 4.30
4241 6204 8.814448 AAGACTTATATTTAGGAATGGAGGGA 57.186 34.615 0.00 0.00 0.00 4.20
4242 6205 9.289782 CAAAGACTTATATTTAGGAATGGAGGG 57.710 37.037 0.00 0.00 0.00 4.30
4243 6206 9.289782 CCAAAGACTTATATTTAGGAATGGAGG 57.710 37.037 0.00 0.00 0.00 4.30
4254 6217 8.897752 GTGCAATCTCTCCAAAGACTTATATTT 58.102 33.333 0.00 0.00 0.00 1.40
4255 6218 8.270744 AGTGCAATCTCTCCAAAGACTTATATT 58.729 33.333 0.00 0.00 0.00 1.28
4256 6219 7.800092 AGTGCAATCTCTCCAAAGACTTATAT 58.200 34.615 0.00 0.00 0.00 0.86
4257 6220 7.187824 AGTGCAATCTCTCCAAAGACTTATA 57.812 36.000 0.00 0.00 0.00 0.98
4258 6221 6.059787 AGTGCAATCTCTCCAAAGACTTAT 57.940 37.500 0.00 0.00 0.00 1.73
4259 6222 5.489792 AGTGCAATCTCTCCAAAGACTTA 57.510 39.130 0.00 0.00 0.00 2.24
4260 6223 4.363991 AGTGCAATCTCTCCAAAGACTT 57.636 40.909 0.00 0.00 0.00 3.01
4261 6224 5.426504 CATAGTGCAATCTCTCCAAAGACT 58.573 41.667 0.00 0.00 0.00 3.24
4262 6225 4.574013 CCATAGTGCAATCTCTCCAAAGAC 59.426 45.833 0.00 0.00 0.00 3.01
4263 6226 4.471025 TCCATAGTGCAATCTCTCCAAAGA 59.529 41.667 0.00 0.00 0.00 2.52
4264 6227 4.574013 GTCCATAGTGCAATCTCTCCAAAG 59.426 45.833 0.00 0.00 0.00 2.77
4265 6228 4.517285 GTCCATAGTGCAATCTCTCCAAA 58.483 43.478 0.00 0.00 0.00 3.28
4266 6229 3.118261 GGTCCATAGTGCAATCTCTCCAA 60.118 47.826 0.00 0.00 0.00 3.53
4267 6230 2.435805 GGTCCATAGTGCAATCTCTCCA 59.564 50.000 0.00 0.00 0.00 3.86
4268 6231 2.435805 TGGTCCATAGTGCAATCTCTCC 59.564 50.000 0.00 0.00 0.00 3.71
4269 6232 3.118629 TGTGGTCCATAGTGCAATCTCTC 60.119 47.826 0.00 0.00 0.00 3.20
4270 6233 2.840038 TGTGGTCCATAGTGCAATCTCT 59.160 45.455 0.00 0.00 0.00 3.10
4271 6234 3.266510 TGTGGTCCATAGTGCAATCTC 57.733 47.619 0.00 0.00 0.00 2.75
4272 6235 3.939740 ATGTGGTCCATAGTGCAATCT 57.060 42.857 0.00 0.00 29.82 2.40
4273 6236 3.494626 CGTATGTGGTCCATAGTGCAATC 59.505 47.826 0.00 0.00 36.71 2.67
4274 6237 3.466836 CGTATGTGGTCCATAGTGCAAT 58.533 45.455 0.00 0.00 36.71 3.56
4275 6238 2.419436 CCGTATGTGGTCCATAGTGCAA 60.419 50.000 0.00 0.00 36.71 4.08
4276 6239 1.138069 CCGTATGTGGTCCATAGTGCA 59.862 52.381 0.00 0.00 36.71 4.57
4277 6240 1.411246 TCCGTATGTGGTCCATAGTGC 59.589 52.381 0.00 0.00 36.71 4.40
4278 6241 2.545952 GCTCCGTATGTGGTCCATAGTG 60.546 54.545 0.00 0.00 36.71 2.74
4279 6242 1.687123 GCTCCGTATGTGGTCCATAGT 59.313 52.381 0.00 0.00 36.71 2.12
4280 6243 1.686587 TGCTCCGTATGTGGTCCATAG 59.313 52.381 0.00 0.00 36.71 2.23
4281 6244 1.783071 TGCTCCGTATGTGGTCCATA 58.217 50.000 0.00 0.00 34.86 2.74
4282 6245 0.908910 TTGCTCCGTATGTGGTCCAT 59.091 50.000 0.00 0.00 37.58 3.41
4283 6246 0.687920 TTTGCTCCGTATGTGGTCCA 59.312 50.000 0.00 0.00 0.00 4.02
4284 6247 1.816074 TTTTGCTCCGTATGTGGTCC 58.184 50.000 0.00 0.00 0.00 4.46
4285 6248 3.006940 TCATTTTGCTCCGTATGTGGTC 58.993 45.455 0.00 0.00 0.00 4.02
4286 6249 3.009723 CTCATTTTGCTCCGTATGTGGT 58.990 45.455 0.00 0.00 0.00 4.16
4287 6250 3.009723 ACTCATTTTGCTCCGTATGTGG 58.990 45.455 0.00 0.00 0.00 4.17
4288 6251 3.684305 TCACTCATTTTGCTCCGTATGTG 59.316 43.478 0.00 0.00 0.00 3.21
4289 6252 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4290 6253 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4291 6254 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4292 6255 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4293 6256 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4294 6257 5.998454 ATAGATTCACTCATTTTGCTCCG 57.002 39.130 0.00 0.00 0.00 4.63
4295 6258 6.205658 GGGTATAGATTCACTCATTTTGCTCC 59.794 42.308 0.00 0.00 0.00 4.70
4296 6259 6.995091 AGGGTATAGATTCACTCATTTTGCTC 59.005 38.462 0.00 0.00 0.00 4.26
4297 6260 6.904626 AGGGTATAGATTCACTCATTTTGCT 58.095 36.000 0.00 0.00 0.00 3.91
4298 6261 8.677148 TTAGGGTATAGATTCACTCATTTTGC 57.323 34.615 0.00 0.00 0.00 3.68
4301 6264 9.289782 GCATTTAGGGTATAGATTCACTCATTT 57.710 33.333 0.00 0.00 0.00 2.32
4302 6265 8.439971 TGCATTTAGGGTATAGATTCACTCATT 58.560 33.333 0.00 0.00 0.00 2.57
4303 6266 7.977818 TGCATTTAGGGTATAGATTCACTCAT 58.022 34.615 0.00 0.00 0.00 2.90
4304 6267 7.373617 TGCATTTAGGGTATAGATTCACTCA 57.626 36.000 0.00 0.00 0.00 3.41
4305 6268 8.317679 AGATGCATTTAGGGTATAGATTCACTC 58.682 37.037 0.00 0.00 0.00 3.51
4306 6269 8.212259 AGATGCATTTAGGGTATAGATTCACT 57.788 34.615 0.00 0.00 0.00 3.41
4307 6270 9.593134 CTAGATGCATTTAGGGTATAGATTCAC 57.407 37.037 14.97 0.00 0.00 3.18
4308 6271 9.547279 TCTAGATGCATTTAGGGTATAGATTCA 57.453 33.333 20.75 0.00 0.00 2.57
4312 6275 9.990868 TGTATCTAGATGCATTTAGGGTATAGA 57.009 33.333 18.36 9.69 0.00 1.98
4324 6287 8.090831 ACAACATACGAATGTATCTAGATGCAT 58.909 33.333 25.43 25.43 45.79 3.96
4325 6288 7.433680 ACAACATACGAATGTATCTAGATGCA 58.566 34.615 23.38 23.38 45.79 3.96
4326 6289 7.875316 ACAACATACGAATGTATCTAGATGC 57.125 36.000 15.79 14.54 45.79 3.91
4327 6290 9.463443 TGAACAACATACGAATGTATCTAGATG 57.537 33.333 15.79 0.00 45.79 2.90
4332 6295 9.249457 CACTATGAACAACATACGAATGTATCT 57.751 33.333 0.00 0.00 45.79 1.98
4333 6296 9.244799 TCACTATGAACAACATACGAATGTATC 57.755 33.333 0.00 0.00 45.79 2.24
4334 6297 9.594478 TTCACTATGAACAACATACGAATGTAT 57.406 29.630 0.00 0.00 37.08 2.29
4335 6298 8.989653 TTCACTATGAACAACATACGAATGTA 57.010 30.769 0.00 0.00 37.08 2.29
4336 6299 7.899178 TTCACTATGAACAACATACGAATGT 57.101 32.000 0.00 0.00 38.53 2.71
4337 6300 9.773328 AATTTCACTATGAACAACATACGAATG 57.227 29.630 0.00 0.00 35.89 2.67
4367 6330 9.014297 CCTCCATTTCTAAATGTAAGTCTTTGT 57.986 33.333 12.99 0.00 43.24 2.83
4368 6331 8.462016 CCCTCCATTTCTAAATGTAAGTCTTTG 58.538 37.037 12.99 0.00 43.24 2.77
4369 6332 8.390921 TCCCTCCATTTCTAAATGTAAGTCTTT 58.609 33.333 12.99 0.00 43.24 2.52
4370 6333 7.928873 TCCCTCCATTTCTAAATGTAAGTCTT 58.071 34.615 12.99 0.00 43.24 3.01
4371 6334 7.182930 ACTCCCTCCATTTCTAAATGTAAGTCT 59.817 37.037 12.99 0.00 43.24 3.24
4372 6335 7.339482 ACTCCCTCCATTTCTAAATGTAAGTC 58.661 38.462 12.99 0.00 43.24 3.01
4373 6336 7.272144 ACTCCCTCCATTTCTAAATGTAAGT 57.728 36.000 12.99 6.97 43.24 2.24
4374 6337 8.487028 ACTACTCCCTCCATTTCTAAATGTAAG 58.513 37.037 12.99 9.99 43.24 2.34
4375 6338 8.388656 ACTACTCCCTCCATTTCTAAATGTAA 57.611 34.615 12.99 2.38 43.24 2.41
4376 6339 7.989947 ACTACTCCCTCCATTTCTAAATGTA 57.010 36.000 12.99 0.00 43.24 2.29
4377 6340 6.893020 ACTACTCCCTCCATTTCTAAATGT 57.107 37.500 12.99 0.00 43.24 2.71
4378 6341 9.853177 AAATACTACTCCCTCCATTTCTAAATG 57.147 33.333 8.21 8.21 44.12 2.32
4415 6378 7.735917 ACCTATAATAAGCATACTCAAGCACA 58.264 34.615 0.00 0.00 0.00 4.57
4416 6379 8.499162 CAACCTATAATAAGCATACTCAAGCAC 58.501 37.037 0.00 0.00 0.00 4.40
4491 6455 4.462834 TCATCCCACACCTAGATATAAGCG 59.537 45.833 0.00 0.00 0.00 4.68
4504 6468 8.612619 CAAACTAATTACATACTCATCCCACAC 58.387 37.037 0.00 0.00 0.00 3.82
4524 6488 8.133024 AGCATAAAATTCCATCAACCAAACTA 57.867 30.769 0.00 0.00 0.00 2.24
4538 6502 8.730680 TGTTGGTCTAAGAGAAGCATAAAATTC 58.269 33.333 0.00 0.00 0.00 2.17
4591 6555 2.980476 ACATAGACGATTCGCGCTAATG 59.020 45.455 12.36 7.14 46.04 1.90
4620 6584 7.924947 GCTAGTATAAAATTACGTGGGAAGACT 59.075 37.037 0.00 0.00 0.00 3.24
4631 6595 9.920826 GGTAAACGGTTGCTAGTATAAAATTAC 57.079 33.333 0.15 0.00 0.00 1.89
4698 6664 5.177511 CCTAATATGCACCATACGTGTTCAG 59.822 44.000 0.00 0.00 44.97 3.02
4729 6695 7.607250 TCGTGAAATTTTTACCCATGCTAAAT 58.393 30.769 0.00 0.00 0.00 1.40
4736 6702 6.015010 TGGTTGATCGTGAAATTTTTACCCAT 60.015 34.615 0.00 0.00 0.00 4.00
4752 6718 5.574055 CCACATTTTCTTCATTGGTTGATCG 59.426 40.000 0.00 0.00 33.34 3.69
4754 6720 6.458210 GTCCACATTTTCTTCATTGGTTGAT 58.542 36.000 0.00 0.00 33.34 2.57
4761 6727 4.871933 GTGGGTCCACATTTTCTTCATT 57.128 40.909 14.69 0.00 45.53 2.57
4783 6749 3.640967 TGGGAAAATCACCAAGTTTCAGG 59.359 43.478 1.19 0.00 42.37 3.86
4806 6772 2.399856 TTGCACACGGTTTCCACTC 58.600 52.632 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.