Multiple sequence alignment - TraesCS3D01G343000

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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 TraesCS3D01G343000 chr3D 100.000 3833 0 0 1 3833 455600129 455596297 0.000000e+00 7079.0
1 TraesCS3D01G343000 chr3D 84.219 602 45 17 151 750 455554372 455553819 1.210000e-149 540.0
2 TraesCS3D01G343000 chr3D 92.058 277 18 4 150 424 278067705 278067431 1.670000e-103 387.0
3 TraesCS3D01G343000 chr3D 78.671 286 30 21 3209 3470 53386208 53385930 1.100000e-35 161.0
4 TraesCS3D01G343000 chr3D 87.218 133 12 3 3467 3598 455596502 455596374 3.090000e-31 147.0
5 TraesCS3D01G343000 chr3D 87.218 133 12 3 3628 3756 455596663 455596532 3.090000e-31 147.0
6 TraesCS3D01G343000 chr3D 95.122 82 4 0 3389 3470 53385312 53385231 3.110000e-26 130.0
7 TraesCS3D01G343000 chr3D 86.441 59 8 0 3401 3459 523769840 523769898 8.890000e-07 65.8
8 TraesCS3D01G343000 chr3D 84.746 59 9 0 3401 3459 348267773 348267831 4.140000e-05 60.2
9 TraesCS3D01G343000 chr3A 93.495 2352 90 33 857 3176 597854460 597852140 0.000000e+00 3437.0
10 TraesCS3D01G343000 chr3A 91.468 504 15 7 3330 3833 597852143 597851668 0.000000e+00 667.0
11 TraesCS3D01G343000 chr3A 87.821 156 8 8 5 149 597877120 597876965 5.090000e-39 172.0
12 TraesCS3D01G343000 chr3A 91.304 115 4 2 749 863 597876974 597876866 6.630000e-33 152.0
13 TraesCS3D01G343000 chr3A 92.553 94 7 0 3663 3756 597851992 597851899 6.680000e-28 135.0
14 TraesCS3D01G343000 chr3A 92.045 88 6 1 3384 3470 64733892 64733805 5.200000e-24 122.0
15 TraesCS3D01G343000 chr3B 94.677 1146 56 3 926 2069 598975088 598973946 0.000000e+00 1773.0
16 TraesCS3D01G343000 chr3B 92.969 1152 57 14 2065 3208 598973677 598972542 0.000000e+00 1657.0
17 TraesCS3D01G343000 chr3B 87.179 390 24 13 3207 3585 598913842 598913468 1.650000e-113 420.0
18 TraesCS3D01G343000 chr3B 94.444 126 7 0 24 149 598977000 598976875 1.090000e-45 195.0
19 TraesCS3D01G343000 chr3B 86.331 139 13 5 3332 3470 83832153 83832021 3.090000e-31 147.0
20 TraesCS3D01G343000 chr3B 89.157 83 8 1 3516 3598 598972621 598972540 6.770000e-18 102.0
21 TraesCS3D01G343000 chr1B 84.171 537 72 7 150 682 471027210 471027737 3.420000e-140 508.0
22 TraesCS3D01G343000 chr6D 91.900 321 24 2 429 748 438812513 438812832 7.550000e-122 448.0
23 TraesCS3D01G343000 chr5D 89.362 329 29 6 426 751 67967286 67967611 3.560000e-110 409.0
24 TraesCS3D01G343000 chr5D 89.024 328 31 5 426 750 67967381 67967056 5.960000e-108 401.0
25 TraesCS3D01G343000 chr5D 92.029 276 18 4 151 424 67967610 67967337 6.010000e-103 385.0
26 TraesCS3D01G343000 chr5D 91.209 273 22 2 151 422 103995592 103995863 1.680000e-98 370.0
27 TraesCS3D01G343000 chr7D 89.362 329 27 8 426 750 461925157 461924833 1.280000e-109 407.0
28 TraesCS3D01G343000 chr7D 91.958 286 16 6 426 707 461925062 461925344 9.980000e-106 394.0
29 TraesCS3D01G343000 chr7D 88.415 328 34 4 426 751 88998624 88998949 3.590000e-105 392.0
30 TraesCS3D01G343000 chr7D 88.073 327 36 3 426 750 125429038 125428713 6.010000e-103 385.0
31 TraesCS3D01G343000 chr7D 87.234 329 36 5 426 750 245405298 245404972 1.680000e-98 370.0
32 TraesCS3D01G343000 chr7D 88.197 305 30 5 150 450 569703494 569703192 3.640000e-95 359.0
33 TraesCS3D01G343000 chr7D 87.713 293 34 2 151 441 569702953 569703245 1.320000e-89 340.0
34 TraesCS3D01G343000 chr7D 84.848 264 34 3 1417 1680 591565155 591565412 1.060000e-65 261.0
35 TraesCS3D01G343000 chr7D 88.158 76 9 0 675 750 637895028 637895103 1.470000e-14 91.6
36 TraesCS3D01G343000 chr1D 88.308 325 35 2 426 750 87090266 87090587 1.670000e-103 387.0
37 TraesCS3D01G343000 chr2D 89.073 302 27 4 152 448 314360907 314361207 1.680000e-98 370.0
38 TraesCS3D01G343000 chr2D 88.722 133 9 5 3339 3470 493001394 493001267 1.430000e-34 158.0
39 TraesCS3D01G343000 chr2D 87.970 133 10 5 3339 3470 492997751 492997624 6.630000e-33 152.0
40 TraesCS3D01G343000 chr2D 100.000 78 0 0 3393 3470 493003817 493003740 1.110000e-30 145.0
41 TraesCS3D01G343000 chr2D 95.122 82 4 0 3389 3470 492996276 492996195 3.110000e-26 130.0
42 TraesCS3D01G343000 chr2D 94.186 86 1 1 3385 3470 493000843 493000762 1.120000e-25 128.0
43 TraesCS3D01G343000 chr2D 93.023 86 2 1 3385 3470 493003537 493003456 5.200000e-24 122.0
44 TraesCS3D01G343000 chr1A 89.643 280 26 3 147 424 589189997 589190275 1.690000e-93 353.0
45 TraesCS3D01G343000 chr2B 88.000 125 9 4 3346 3470 579570689 579570571 3.990000e-30 143.0
46 TraesCS3D01G343000 chr2B 93.333 90 4 2 3382 3470 579570983 579570895 8.640000e-27 132.0
47 TraesCS3D01G343000 chr2B 84.091 132 16 4 3339 3470 579568273 579568147 5.200000e-24 122.0
48 TraesCS3D01G343000 chr2A 94.382 89 5 0 3382 3470 640820674 640820762 1.860000e-28 137.0
49 TraesCS3D01G343000 chr6B 88.136 59 7 0 3401 3459 311376016 311375958 1.910000e-08 71.3
50 TraesCS3D01G343000 chr4D 86.441 59 8 0 3401 3459 241386645 241386703 8.890000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G343000 chr3D 455596297 455600129 3832 True 2457.666667 7079 91.478667 1 3833 3 chr3D.!!$R4 3832
1 TraesCS3D01G343000 chr3D 455553819 455554372 553 True 540.000000 540 84.219000 151 750 1 chr3D.!!$R2 599
2 TraesCS3D01G343000 chr3A 597851668 597854460 2792 True 1413.000000 3437 92.505333 857 3833 3 chr3A.!!$R2 2976
3 TraesCS3D01G343000 chr3B 598972540 598977000 4460 True 931.750000 1773 92.811750 24 3598 4 chr3B.!!$R3 3574
4 TraesCS3D01G343000 chr1B 471027210 471027737 527 False 508.000000 508 84.171000 150 682 1 chr1B.!!$F1 532
5 TraesCS3D01G343000 chr5D 67967056 67967610 554 True 393.000000 401 90.526500 151 750 2 chr5D.!!$R1 599

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
424 429 0.250727 TGCACTAGTGGTTGCCTTCC 60.251 55.0 23.95 4.83 0.0 3.46 F
810 816 0.824109 CATTCTCTGCTGGTCCCGTA 59.176 55.0 0.00 0.00 0.0 4.02 F
2198 4129 1.031571 CGGGCTGGGTACTGTACGTA 61.032 60.0 11.52 0.00 0.0 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 2885 0.107945 GAGCTGGGCTTGAAGTCGAT 60.108 55.0 0.00 0.0 39.88 3.59 R
2321 4252 0.660300 GGCAAGAAAAGCGTCGTTGG 60.660 55.0 0.00 0.0 0.00 3.77 R
3273 5214 0.108804 GATTCGAGTCAACCCTGCGA 60.109 55.0 2.62 0.0 0.00 5.10 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
78 79 1.404986 GGTACTGTGGATTGTAGCGCA 60.405 52.381 11.47 0.00 0.00 6.09
101 102 3.371097 ATGGCGTGATCCGTCGCTT 62.371 57.895 20.23 10.23 46.52 4.68
139 140 1.226603 CGTGCGGTAGCTACCACTC 60.227 63.158 35.98 27.13 46.80 3.51
140 141 1.141234 GTGCGGTAGCTACCACTCC 59.859 63.158 35.98 22.80 46.80 3.85
141 142 1.000019 TGCGGTAGCTACCACTCCT 60.000 57.895 35.98 0.00 46.80 3.69
142 143 1.035932 TGCGGTAGCTACCACTCCTC 61.036 60.000 35.98 19.69 46.80 3.71
143 144 1.736365 GCGGTAGCTACCACTCCTCC 61.736 65.000 35.98 12.49 46.80 4.30
144 145 1.445716 CGGTAGCTACCACTCCTCCG 61.446 65.000 35.98 19.74 46.80 4.63
145 146 1.108132 GGTAGCTACCACTCCTCCGG 61.108 65.000 33.64 0.00 45.73 5.14
146 147 1.108132 GTAGCTACCACTCCTCCGGG 61.108 65.000 13.20 0.00 0.00 5.73
147 148 2.923634 TAGCTACCACTCCTCCGGGC 62.924 65.000 0.00 0.00 0.00 6.13
148 149 2.042843 CTACCACTCCTCCGGGCT 60.043 66.667 0.00 0.00 0.00 5.19
172 173 4.272018 CGGCAAATTTGACAATTTTGACCA 59.728 37.500 27.56 0.00 40.09 4.02
179 180 9.790344 AAATTTGACAATTTTGACCAATGGATA 57.210 25.926 6.16 0.00 39.19 2.59
250 255 1.231958 TTTTTAGTGGCGCCCGACAG 61.232 55.000 26.77 0.00 31.40 3.51
266 271 1.221840 CAGGAAGGCGCCACACTAT 59.778 57.895 31.54 2.66 0.00 2.12
316 321 4.899239 GCCTGGCTAGCGTCGCAT 62.899 66.667 21.09 7.20 0.00 4.73
326 331 1.587876 GCGTCGCATCCGTGTGATA 60.588 57.895 13.44 0.00 45.74 2.15
327 332 1.143373 GCGTCGCATCCGTGTGATAA 61.143 55.000 13.44 0.00 45.74 1.75
420 425 1.574428 CGTTGCACTAGTGGTTGCC 59.426 57.895 23.95 7.68 0.00 4.52
423 428 1.266989 GTTGCACTAGTGGTTGCCTTC 59.733 52.381 23.95 5.53 0.00 3.46
424 429 0.250727 TGCACTAGTGGTTGCCTTCC 60.251 55.000 23.95 4.83 0.00 3.46
514 519 3.361174 CCTAGAGGCTAGGCGCTC 58.639 66.667 25.42 11.50 39.13 5.03
775 781 3.198236 TTTGCTTGCTCGTGCTGGC 62.198 57.895 11.19 14.10 40.48 4.85
776 782 4.631247 TGCTTGCTCGTGCTGGCT 62.631 61.111 20.64 0.00 40.48 4.75
777 783 4.099170 GCTTGCTCGTGCTGGCTG 62.099 66.667 11.19 0.00 40.48 4.85
778 784 3.429141 CTTGCTCGTGCTGGCTGG 61.429 66.667 11.19 0.00 40.48 4.85
779 785 3.889134 CTTGCTCGTGCTGGCTGGA 62.889 63.158 11.19 0.00 40.48 3.86
796 802 2.780414 TGGACCTGGATCCATCATTCT 58.220 47.619 16.63 0.00 44.14 2.40
804 810 2.106166 GGATCCATCATTCTCTGCTGGT 59.894 50.000 6.95 0.00 41.15 4.00
806 812 1.487976 TCCATCATTCTCTGCTGGTCC 59.512 52.381 0.00 0.00 41.15 4.46
807 813 1.476471 CCATCATTCTCTGCTGGTCCC 60.476 57.143 0.00 0.00 36.56 4.46
810 816 0.824109 CATTCTCTGCTGGTCCCGTA 59.176 55.000 0.00 0.00 0.00 4.02
811 817 1.115467 ATTCTCTGCTGGTCCCGTAG 58.885 55.000 0.00 0.00 0.00 3.51
948 2582 2.886081 CTCTGTTGTCTCCGGAATCTG 58.114 52.381 5.23 0.00 0.00 2.90
979 2613 6.093219 GCACACTATCACAGAAGATCAACATT 59.907 38.462 0.00 0.00 0.00 2.71
984 2618 8.196771 ACTATCACAGAAGATCAACATTCTCTC 58.803 37.037 0.00 0.00 33.51 3.20
1051 2693 2.158755 GGTACAGCCATTAGCCAGACAT 60.159 50.000 0.00 0.00 45.47 3.06
1075 2717 1.080093 CGTGCTTCCAGTTCCGCTA 60.080 57.895 0.00 0.00 0.00 4.26
1084 2726 2.070650 AGTTCCGCTACCCCATCCC 61.071 63.158 0.00 0.00 0.00 3.85
1136 2778 2.419198 GAGATCGATGGCCGCTGT 59.581 61.111 0.54 0.00 38.37 4.40
1243 2885 2.037367 CGGAGGAGGAGGTGGTCA 59.963 66.667 0.00 0.00 0.00 4.02
1259 2901 1.363744 GTCATCGACTTCAAGCCCAG 58.636 55.000 0.00 0.00 0.00 4.45
1326 2968 2.434359 CCCGTCGCCTTCAAGGTC 60.434 66.667 5.03 0.00 37.80 3.85
1666 3308 4.316823 ACCTCCTGCCGGTCCTCA 62.317 66.667 1.90 0.00 0.00 3.86
1860 3502 1.229625 AGAGCTGGTGGACATGGGA 60.230 57.895 0.00 0.00 0.00 4.37
1961 3605 3.059393 GTCCTTTTTGTACTGCCGTGTAC 60.059 47.826 0.00 0.00 42.10 2.90
1962 3606 3.135994 CCTTTTTGTACTGCCGTGTACT 58.864 45.455 11.28 0.00 42.22 2.73
1963 3607 4.039004 TCCTTTTTGTACTGCCGTGTACTA 59.961 41.667 11.28 3.64 42.22 1.82
1980 3624 5.515626 GTGTACTAGTAACTTCATGGCTTCG 59.484 44.000 3.61 0.00 0.00 3.79
2095 4025 1.151668 CTCGAAGGTGGCAAGAACAG 58.848 55.000 0.00 0.00 0.00 3.16
2197 4128 2.345760 CGGGCTGGGTACTGTACGT 61.346 63.158 11.52 0.00 0.00 3.57
2198 4129 1.031571 CGGGCTGGGTACTGTACGTA 61.032 60.000 11.52 0.00 0.00 3.57
2265 4196 2.225091 ACAGCATCCAATGTTCTTGGGA 60.225 45.455 4.28 0.00 39.96 4.37
2267 4198 2.042162 AGCATCCAATGTTCTTGGGACT 59.958 45.455 4.28 0.00 39.96 3.85
2268 4199 2.827921 GCATCCAATGTTCTTGGGACTT 59.172 45.455 4.28 0.00 39.96 3.01
2269 4200 3.259123 GCATCCAATGTTCTTGGGACTTT 59.741 43.478 4.28 0.00 39.96 2.66
2270 4201 4.262592 GCATCCAATGTTCTTGGGACTTTT 60.263 41.667 4.28 0.00 39.96 2.27
2271 4202 5.047377 GCATCCAATGTTCTTGGGACTTTTA 60.047 40.000 4.28 0.00 39.96 1.52
2272 4203 6.389906 CATCCAATGTTCTTGGGACTTTTAC 58.610 40.000 4.28 0.00 39.96 2.01
2273 4204 5.450453 TCCAATGTTCTTGGGACTTTTACA 58.550 37.500 4.28 0.00 39.96 2.41
2274 4205 5.534654 TCCAATGTTCTTGGGACTTTTACAG 59.465 40.000 4.28 0.00 39.96 2.74
2321 4252 5.864474 ACATCTCTTGTCAGAATGTAACGAC 59.136 40.000 0.00 0.00 37.40 4.34
2430 4361 2.754658 GACCTCCGGAGCCTCGAA 60.755 66.667 26.87 0.00 0.00 3.71
2838 4772 3.557898 CGATATCCTGTGCATAAGGCCTT 60.558 47.826 24.18 24.18 43.89 4.35
2839 4773 2.355010 ATCCTGTGCATAAGGCCTTC 57.645 50.000 24.49 8.70 43.89 3.46
2918 4853 7.956328 ATAGGTGACAGAAGTGATTACTGTA 57.044 36.000 0.00 0.00 43.49 2.74
2995 4933 5.497474 GTTCCCCTGAGCAGTTCTAAATTA 58.503 41.667 0.00 0.00 0.00 1.40
3185 5126 8.854614 ATTTACTAATATGGAGACCAGATTGC 57.145 34.615 17.31 0.00 43.97 3.56
3186 5127 7.618019 TTACTAATATGGAGACCAGATTGCT 57.382 36.000 17.31 7.42 43.97 3.91
3187 5128 6.107901 ACTAATATGGAGACCAGATTGCTC 57.892 41.667 17.31 0.00 43.97 4.26
3188 5129 5.604231 ACTAATATGGAGACCAGATTGCTCA 59.396 40.000 17.31 1.08 43.97 4.26
3189 5130 5.378230 AATATGGAGACCAGATTGCTCAA 57.622 39.130 9.38 0.00 42.83 3.02
3190 5131 3.726557 ATGGAGACCAGATTGCTCAAA 57.273 42.857 0.00 0.00 36.75 2.69
3191 5132 2.783135 TGGAGACCAGATTGCTCAAAC 58.217 47.619 0.00 0.00 0.00 2.93
3192 5133 2.087646 GGAGACCAGATTGCTCAAACC 58.912 52.381 0.00 0.00 0.00 3.27
3193 5134 2.553028 GGAGACCAGATTGCTCAAACCA 60.553 50.000 0.00 0.00 0.00 3.67
3194 5135 3.149196 GAGACCAGATTGCTCAAACCAA 58.851 45.455 0.00 0.00 0.00 3.67
3195 5136 3.565307 AGACCAGATTGCTCAAACCAAA 58.435 40.909 0.00 0.00 0.00 3.28
3196 5137 3.960102 AGACCAGATTGCTCAAACCAAAA 59.040 39.130 0.00 0.00 0.00 2.44
3197 5138 4.405358 AGACCAGATTGCTCAAACCAAAAA 59.595 37.500 0.00 0.00 0.00 1.94
3198 5139 4.696455 ACCAGATTGCTCAAACCAAAAAG 58.304 39.130 0.00 0.00 0.00 2.27
3199 5140 3.495753 CCAGATTGCTCAAACCAAAAAGC 59.504 43.478 0.00 0.00 35.31 3.51
3200 5141 4.121317 CAGATTGCTCAAACCAAAAAGCA 58.879 39.130 0.00 0.00 42.66 3.91
3201 5142 4.210537 CAGATTGCTCAAACCAAAAAGCAG 59.789 41.667 0.00 0.00 44.79 4.24
3202 5143 3.883830 TTGCTCAAACCAAAAAGCAGA 57.116 38.095 0.00 0.00 44.79 4.26
3203 5144 3.883830 TGCTCAAACCAAAAAGCAGAA 57.116 38.095 0.00 0.00 39.69 3.02
3204 5145 4.405116 TGCTCAAACCAAAAAGCAGAAT 57.595 36.364 0.00 0.00 39.69 2.40
3205 5146 5.528043 TGCTCAAACCAAAAAGCAGAATA 57.472 34.783 0.00 0.00 39.69 1.75
3206 5147 5.531634 TGCTCAAACCAAAAAGCAGAATAG 58.468 37.500 0.00 0.00 39.69 1.73
3207 5148 4.925646 GCTCAAACCAAAAAGCAGAATAGG 59.074 41.667 0.00 0.00 34.86 2.57
3208 5149 5.509670 GCTCAAACCAAAAAGCAGAATAGGT 60.510 40.000 0.00 0.00 34.86 3.08
3209 5150 5.841810 TCAAACCAAAAAGCAGAATAGGTG 58.158 37.500 0.00 0.00 0.00 4.00
3210 5151 5.596361 TCAAACCAAAAAGCAGAATAGGTGA 59.404 36.000 0.00 0.00 0.00 4.02
3211 5152 6.267471 TCAAACCAAAAAGCAGAATAGGTGAT 59.733 34.615 0.00 0.00 0.00 3.06
3212 5153 5.649782 ACCAAAAAGCAGAATAGGTGATG 57.350 39.130 0.00 0.00 0.00 3.07
3213 5154 5.079643 ACCAAAAAGCAGAATAGGTGATGT 58.920 37.500 0.00 0.00 0.00 3.06
3214 5155 6.245408 ACCAAAAAGCAGAATAGGTGATGTA 58.755 36.000 0.00 0.00 0.00 2.29
3215 5156 6.891908 ACCAAAAAGCAGAATAGGTGATGTAT 59.108 34.615 0.00 0.00 0.00 2.29
3216 5157 7.148018 ACCAAAAAGCAGAATAGGTGATGTATG 60.148 37.037 0.00 0.00 0.00 2.39
3217 5158 7.148018 CCAAAAAGCAGAATAGGTGATGTATGT 60.148 37.037 0.00 0.00 0.00 2.29
3218 5159 6.932356 AAAGCAGAATAGGTGATGTATGTG 57.068 37.500 0.00 0.00 0.00 3.21
3219 5160 5.620738 AGCAGAATAGGTGATGTATGTGT 57.379 39.130 0.00 0.00 0.00 3.72
3220 5161 6.731292 AGCAGAATAGGTGATGTATGTGTA 57.269 37.500 0.00 0.00 0.00 2.90
3221 5162 6.516718 AGCAGAATAGGTGATGTATGTGTAC 58.483 40.000 0.00 0.00 0.00 2.90
3222 5163 5.402568 GCAGAATAGGTGATGTATGTGTACG 59.597 44.000 0.00 0.00 33.36 3.67
3223 5164 6.734871 GCAGAATAGGTGATGTATGTGTACGA 60.735 42.308 0.00 0.00 33.36 3.43
3224 5165 6.858478 CAGAATAGGTGATGTATGTGTACGAG 59.142 42.308 0.00 0.00 33.36 4.18
3225 5166 6.771267 AGAATAGGTGATGTATGTGTACGAGA 59.229 38.462 0.00 0.00 33.36 4.04
3226 5167 4.634184 AGGTGATGTATGTGTACGAGAC 57.366 45.455 0.00 0.00 33.36 3.36
3227 5168 4.014406 AGGTGATGTATGTGTACGAGACA 58.986 43.478 0.00 0.00 33.36 3.41
3236 5177 1.875009 TGTACGAGACACACGACTCT 58.125 50.000 0.00 0.00 32.54 3.24
3237 5178 1.797046 TGTACGAGACACACGACTCTC 59.203 52.381 0.00 0.00 32.54 3.20
3238 5179 1.797046 GTACGAGACACACGACTCTCA 59.203 52.381 0.00 0.00 33.73 3.27
3239 5180 0.869068 ACGAGACACACGACTCTCAG 59.131 55.000 0.00 0.00 33.73 3.35
3240 5181 1.149148 CGAGACACACGACTCTCAGA 58.851 55.000 0.00 0.00 33.73 3.27
3241 5182 1.531578 CGAGACACACGACTCTCAGAA 59.468 52.381 0.00 0.00 33.73 3.02
3242 5183 2.160615 CGAGACACACGACTCTCAGAAT 59.839 50.000 0.00 0.00 33.73 2.40
3243 5184 3.371285 CGAGACACACGACTCTCAGAATA 59.629 47.826 0.00 0.00 33.73 1.75
3244 5185 4.142881 CGAGACACACGACTCTCAGAATAA 60.143 45.833 0.00 0.00 33.73 1.40
3245 5186 5.617087 CGAGACACACGACTCTCAGAATAAA 60.617 44.000 0.00 0.00 33.73 1.40
3246 5187 6.085555 AGACACACGACTCTCAGAATAAAA 57.914 37.500 0.00 0.00 0.00 1.52
3247 5188 6.692486 AGACACACGACTCTCAGAATAAAAT 58.308 36.000 0.00 0.00 0.00 1.82
3248 5189 6.587990 AGACACACGACTCTCAGAATAAAATG 59.412 38.462 0.00 0.00 0.00 2.32
3249 5190 5.120830 ACACACGACTCTCAGAATAAAATGC 59.879 40.000 0.00 0.00 0.00 3.56
3250 5191 5.349817 CACACGACTCTCAGAATAAAATGCT 59.650 40.000 0.00 0.00 0.00 3.79
3251 5192 6.531594 CACACGACTCTCAGAATAAAATGCTA 59.468 38.462 0.00 0.00 0.00 3.49
3252 5193 7.063426 CACACGACTCTCAGAATAAAATGCTAA 59.937 37.037 0.00 0.00 0.00 3.09
3253 5194 7.063544 ACACGACTCTCAGAATAAAATGCTAAC 59.936 37.037 0.00 0.00 0.00 2.34
3254 5195 6.253727 ACGACTCTCAGAATAAAATGCTAACG 59.746 38.462 0.00 0.00 0.00 3.18
3255 5196 6.472486 CGACTCTCAGAATAAAATGCTAACGA 59.528 38.462 0.00 0.00 0.00 3.85
3256 5197 7.513814 CGACTCTCAGAATAAAATGCTAACGAC 60.514 40.741 0.00 0.00 0.00 4.34
3257 5198 7.324178 ACTCTCAGAATAAAATGCTAACGACT 58.676 34.615 0.00 0.00 0.00 4.18
3258 5199 7.276658 ACTCTCAGAATAAAATGCTAACGACTG 59.723 37.037 0.00 0.00 0.00 3.51
3259 5200 6.535150 TCTCAGAATAAAATGCTAACGACTGG 59.465 38.462 0.00 0.00 0.00 4.00
3260 5201 6.403049 TCAGAATAAAATGCTAACGACTGGA 58.597 36.000 0.00 0.00 0.00 3.86
3261 5202 6.312918 TCAGAATAAAATGCTAACGACTGGAC 59.687 38.462 0.00 0.00 0.00 4.02
3262 5203 5.585047 AGAATAAAATGCTAACGACTGGACC 59.415 40.000 0.00 0.00 0.00 4.46
3263 5204 2.109425 AAATGCTAACGACTGGACCC 57.891 50.000 0.00 0.00 0.00 4.46
3264 5205 1.276622 AATGCTAACGACTGGACCCT 58.723 50.000 0.00 0.00 0.00 4.34
3265 5206 0.824759 ATGCTAACGACTGGACCCTC 59.175 55.000 0.00 0.00 0.00 4.30
3266 5207 1.255667 TGCTAACGACTGGACCCTCC 61.256 60.000 0.00 0.00 36.96 4.30
3267 5208 1.255667 GCTAACGACTGGACCCTCCA 61.256 60.000 0.00 0.00 45.98 3.86
3275 5216 3.642938 TGGACCCTCCAATTTGTCG 57.357 52.632 0.00 0.00 45.00 4.35
3276 5217 0.608035 TGGACCCTCCAATTTGTCGC 60.608 55.000 0.00 0.00 45.00 5.19
3277 5218 0.608035 GGACCCTCCAATTTGTCGCA 60.608 55.000 0.00 0.00 36.28 5.10
3278 5219 0.804989 GACCCTCCAATTTGTCGCAG 59.195 55.000 0.00 0.00 0.00 5.18
3279 5220 0.609131 ACCCTCCAATTTGTCGCAGG 60.609 55.000 0.00 0.00 0.00 4.85
3280 5221 1.315257 CCCTCCAATTTGTCGCAGGG 61.315 60.000 5.88 5.88 34.83 4.45
3281 5222 0.609131 CCTCCAATTTGTCGCAGGGT 60.609 55.000 0.00 0.00 0.00 4.34
3282 5223 1.247567 CTCCAATTTGTCGCAGGGTT 58.752 50.000 0.00 0.00 0.00 4.11
3283 5224 0.958091 TCCAATTTGTCGCAGGGTTG 59.042 50.000 0.00 0.00 0.00 3.77
3284 5225 0.958091 CCAATTTGTCGCAGGGTTGA 59.042 50.000 0.00 0.00 0.00 3.18
3285 5226 1.335872 CCAATTTGTCGCAGGGTTGAC 60.336 52.381 0.00 0.00 35.67 3.18
3286 5227 1.608590 CAATTTGTCGCAGGGTTGACT 59.391 47.619 0.00 0.00 36.10 3.41
3287 5228 1.523758 ATTTGTCGCAGGGTTGACTC 58.476 50.000 0.00 0.00 36.10 3.36
3288 5229 0.878523 TTTGTCGCAGGGTTGACTCG 60.879 55.000 0.00 0.00 36.10 4.18
3289 5230 1.740332 TTGTCGCAGGGTTGACTCGA 61.740 55.000 0.00 0.00 36.10 4.04
3290 5231 1.006571 GTCGCAGGGTTGACTCGAA 60.007 57.895 0.00 0.00 32.37 3.71
3291 5232 0.389948 GTCGCAGGGTTGACTCGAAT 60.390 55.000 0.00 0.00 32.37 3.34
3292 5233 0.108804 TCGCAGGGTTGACTCGAATC 60.109 55.000 0.00 0.00 0.00 2.52
3293 5234 1.413767 CGCAGGGTTGACTCGAATCG 61.414 60.000 0.00 0.00 0.00 3.34
3294 5235 0.389948 GCAGGGTTGACTCGAATCGT 60.390 55.000 1.52 0.00 0.00 3.73
3295 5236 1.939838 GCAGGGTTGACTCGAATCGTT 60.940 52.381 1.52 0.00 0.00 3.85
3296 5237 2.413837 CAGGGTTGACTCGAATCGTTT 58.586 47.619 1.52 0.00 0.00 3.60
3297 5238 2.806244 CAGGGTTGACTCGAATCGTTTT 59.194 45.455 1.52 0.00 0.00 2.43
3298 5239 3.250040 CAGGGTTGACTCGAATCGTTTTT 59.750 43.478 1.52 0.00 0.00 1.94
3317 5258 4.602340 TTTTGGACTCACAGTACCTCTC 57.398 45.455 0.00 0.00 0.00 3.20
3318 5259 2.217510 TGGACTCACAGTACCTCTCC 57.782 55.000 0.00 0.00 0.00 3.71
3319 5260 1.096416 GGACTCACAGTACCTCTCCG 58.904 60.000 0.00 0.00 0.00 4.63
3320 5261 1.339824 GGACTCACAGTACCTCTCCGA 60.340 57.143 0.00 0.00 0.00 4.55
3321 5262 2.011222 GACTCACAGTACCTCTCCGAG 58.989 57.143 0.00 0.00 0.00 4.63
3322 5263 1.351683 ACTCACAGTACCTCTCCGAGT 59.648 52.381 0.00 0.00 32.86 4.18
3323 5264 2.224818 ACTCACAGTACCTCTCCGAGTT 60.225 50.000 0.00 0.00 33.50 3.01
3324 5265 3.008813 ACTCACAGTACCTCTCCGAGTTA 59.991 47.826 0.00 0.00 33.50 2.24
3325 5266 4.200874 CTCACAGTACCTCTCCGAGTTAT 58.799 47.826 0.00 0.00 0.00 1.89
3326 5267 4.597004 TCACAGTACCTCTCCGAGTTATT 58.403 43.478 0.00 0.00 0.00 1.40
3327 5268 4.639310 TCACAGTACCTCTCCGAGTTATTC 59.361 45.833 0.00 0.00 0.00 1.75
3338 5279 2.114825 CGAGTTATTCGGGAGCGTAAC 58.885 52.381 0.00 0.00 45.54 2.50
3343 5284 0.892755 ATTCGGGAGCGTAACTGTCA 59.107 50.000 0.00 0.00 0.00 3.58
3443 5384 2.945668 GGTCTGATATGCCAAAGGTCAC 59.054 50.000 0.00 0.00 0.00 3.67
3479 5420 0.734889 GGGACCAATTGCGATGACTG 59.265 55.000 0.00 0.00 0.00 3.51
3482 5423 2.228822 GGACCAATTGCGATGACTGTTT 59.771 45.455 0.00 0.00 0.00 2.83
3483 5424 3.305335 GGACCAATTGCGATGACTGTTTT 60.305 43.478 0.00 0.00 0.00 2.43
3484 5425 4.298332 GACCAATTGCGATGACTGTTTTT 58.702 39.130 0.00 0.00 0.00 1.94
3543 5484 7.253905 AGTTACCTGAAAGAGCCAATTACTA 57.746 36.000 0.00 0.00 34.07 1.82
3749 5690 2.224606 TGCTCAAACCAGAAAGCAGAG 58.775 47.619 0.00 0.00 39.69 3.35
3766 5707 3.799420 GCAGAGTAGGCAGACTTTATTCG 59.201 47.826 0.00 0.00 0.00 3.34
3770 5711 5.361285 AGAGTAGGCAGACTTTATTCGATGT 59.639 40.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 3.424300 CGGATCACGCCATGCAAT 58.576 55.556 0.00 0.00 34.82 3.56
111 112 1.663379 CTACCGCACGTCCCATCAGA 61.663 60.000 0.00 0.00 0.00 3.27
143 144 1.154035 GTCAAATTTGCCGAGCCCG 60.154 57.895 13.54 0.00 0.00 6.13
144 145 0.316841 TTGTCAAATTTGCCGAGCCC 59.683 50.000 13.54 0.00 0.00 5.19
145 146 2.368655 ATTGTCAAATTTGCCGAGCC 57.631 45.000 13.54 0.00 0.00 4.70
146 147 4.210955 TCAAAATTGTCAAATTTGCCGAGC 59.789 37.500 17.69 2.20 43.63 5.03
147 148 5.333263 GGTCAAAATTGTCAAATTTGCCGAG 60.333 40.000 17.69 0.00 43.63 4.63
148 149 4.509600 GGTCAAAATTGTCAAATTTGCCGA 59.490 37.500 17.69 2.05 43.63 5.54
179 180 9.341078 AGGCAGTTTATTTTGTGAAATGATTTT 57.659 25.926 0.00 0.00 36.22 1.82
197 198 7.234577 TGGGTGAAATATTTTTAGAGGCAGTTT 59.765 33.333 1.43 0.00 0.00 2.66
250 255 0.464452 AGTATAGTGTGGCGCCTTCC 59.536 55.000 29.70 15.93 0.00 3.46
266 271 1.822371 TCTATGAGGCGTTGCACAGTA 59.178 47.619 0.00 0.00 0.00 2.74
306 311 2.000215 ATCACACGGATGCGACGCTA 62.000 55.000 22.08 7.92 34.06 4.26
316 321 9.362539 GACTTAGTAATTTTCTTATCACACGGA 57.637 33.333 0.00 0.00 0.00 4.69
326 331 7.520614 GCTGCACACTGACTTAGTAATTTTCTT 60.521 37.037 0.00 0.00 37.60 2.52
327 332 6.073003 GCTGCACACTGACTTAGTAATTTTCT 60.073 38.462 0.00 0.00 37.60 2.52
384 389 3.361174 CCTAGAGGCTAGGCGCTC 58.639 66.667 25.42 11.50 39.13 5.03
420 425 0.530744 TAGGCGCTACACTGTGGAAG 59.469 55.000 13.09 10.04 0.00 3.46
423 428 1.519455 GCTAGGCGCTACACTGTGG 60.519 63.158 13.09 0.00 35.14 4.17
424 429 1.519455 GGCTAGGCGCTACACTGTG 60.519 63.158 7.64 6.19 39.13 3.66
442 447 2.169352 ACCACTAGTGCAATGCCTAGAG 59.831 50.000 26.19 20.75 35.00 2.43
444 449 2.679837 CAACCACTAGTGCAATGCCTAG 59.320 50.000 17.86 21.12 36.35 3.02
616 621 0.034756 TACACTGTGCAACGCCTCAT 59.965 50.000 7.90 0.00 42.39 2.90
641 646 2.660552 CGCCCGACACAAAGACGT 60.661 61.111 0.00 0.00 33.56 4.34
644 649 4.243008 TGGCGCCCGACACAAAGA 62.243 61.111 26.77 0.00 0.00 2.52
728 734 7.623770 CCGAGGCAAATTTGATAATTTTGATG 58.376 34.615 22.31 0.00 40.97 3.07
777 783 2.978278 AGAGAATGATGGATCCAGGTCC 59.022 50.000 21.33 9.62 38.81 4.46
778 784 3.806507 GCAGAGAATGATGGATCCAGGTC 60.807 52.174 21.33 14.26 0.00 3.85
779 785 2.106166 GCAGAGAATGATGGATCCAGGT 59.894 50.000 21.33 3.64 0.00 4.00
796 802 0.554305 TATCCTACGGGACCAGCAGA 59.446 55.000 0.00 0.00 45.43 4.26
804 810 3.169512 TGAGCATGATATCCTACGGGA 57.830 47.619 0.00 0.00 46.81 5.14
806 812 3.193263 GCATGAGCATGATATCCTACGG 58.807 50.000 14.27 0.00 41.20 4.02
948 2582 1.019673 CTGTGATAGTGTGCCATGGC 58.980 55.000 30.54 30.54 42.35 4.40
961 2595 6.944096 TGAGAGAATGTTGATCTTCTGTGAT 58.056 36.000 0.01 0.00 31.99 3.06
979 2613 0.755079 CTGGATCGGGCAATGAGAGA 59.245 55.000 0.00 0.00 0.00 3.10
984 2618 1.658114 CATGCTGGATCGGGCAATG 59.342 57.895 13.69 9.57 41.90 2.82
1075 2717 2.324560 GGTGGGAATGGGATGGGGT 61.325 63.158 0.00 0.00 0.00 4.95
1136 2778 4.467084 CGGAGCAGGCGGGCTTAA 62.467 66.667 0.00 0.00 45.99 1.85
1243 2885 0.107945 GAGCTGGGCTTGAAGTCGAT 60.108 55.000 0.00 0.00 39.88 3.59
1326 2968 4.787280 AGCGGGGAGGAGGTCTGG 62.787 72.222 0.00 0.00 0.00 3.86
1739 3381 2.365586 CCCAGCCTCCTCACCTCTG 61.366 68.421 0.00 0.00 0.00 3.35
1836 3478 3.640407 TCCACCAGCTCTGCCACC 61.640 66.667 0.00 0.00 0.00 4.61
1961 3605 4.363999 CTCCGAAGCCATGAAGTTACTAG 58.636 47.826 0.00 0.00 0.00 2.57
1962 3606 3.430374 GCTCCGAAGCCATGAAGTTACTA 60.430 47.826 0.00 0.00 43.10 1.82
1963 3607 2.678190 GCTCCGAAGCCATGAAGTTACT 60.678 50.000 0.00 0.00 43.10 2.24
1980 3624 5.578336 GCAATTTTTGTCCATTCTAAGCTCC 59.422 40.000 0.00 0.00 0.00 4.70
2034 3691 3.562557 GGTTGTTTACTGTGATCGTGGTT 59.437 43.478 0.00 0.00 0.00 3.67
2039 3696 4.750098 ACAGAAGGTTGTTTACTGTGATCG 59.250 41.667 0.00 0.00 39.76 3.69
2095 4025 7.642194 TCAAATTACGTTTCTGACATGACAAAC 59.358 33.333 0.00 1.01 0.00 2.93
2197 4128 4.338118 GCAAGCCACATAAGCCAAGTTATA 59.662 41.667 0.00 0.00 0.00 0.98
2198 4129 3.131046 GCAAGCCACATAAGCCAAGTTAT 59.869 43.478 0.00 0.00 0.00 1.89
2321 4252 0.660300 GGCAAGAAAAGCGTCGTTGG 60.660 55.000 0.00 0.00 0.00 3.77
2427 4358 1.012841 GCTTGCTGAGGAGGAATTCG 58.987 55.000 0.00 0.00 0.00 3.34
2430 4361 1.451028 GCGCTTGCTGAGGAGGAAT 60.451 57.895 0.00 0.00 35.07 3.01
2943 4879 7.213178 AGTCCCATCTTATTGTTAAGTCCAT 57.787 36.000 0.00 0.00 36.87 3.41
2944 4880 6.636454 AGTCCCATCTTATTGTTAAGTCCA 57.364 37.500 0.00 0.00 36.87 4.02
3086 5025 0.179045 ATATCAGGAAGTGCGGTGCC 60.179 55.000 0.00 0.00 0.00 5.01
3091 5032 6.653183 CAAAGTATGAATATCAGGAAGTGCG 58.347 40.000 0.00 0.00 0.00 5.34
3170 5111 3.350833 GTTTGAGCAATCTGGTCTCCAT 58.649 45.455 7.31 0.00 44.58 3.41
3172 5113 2.087646 GGTTTGAGCAATCTGGTCTCC 58.912 52.381 7.31 4.23 44.58 3.71
3173 5114 2.783135 TGGTTTGAGCAATCTGGTCTC 58.217 47.619 7.31 0.00 44.58 3.36
3174 5115 2.957402 TGGTTTGAGCAATCTGGTCT 57.043 45.000 7.31 0.00 44.58 3.85
3175 5116 4.320608 TTTTGGTTTGAGCAATCTGGTC 57.679 40.909 0.00 0.00 44.54 4.02
3176 5117 4.696455 CTTTTTGGTTTGAGCAATCTGGT 58.304 39.130 0.00 0.00 35.34 4.00
3177 5118 3.495753 GCTTTTTGGTTTGAGCAATCTGG 59.504 43.478 0.00 0.00 35.34 3.86
3178 5119 4.121317 TGCTTTTTGGTTTGAGCAATCTG 58.879 39.130 0.00 0.00 41.72 2.90
3179 5120 4.099881 TCTGCTTTTTGGTTTGAGCAATCT 59.900 37.500 0.00 0.00 43.75 2.40
3180 5121 4.370917 TCTGCTTTTTGGTTTGAGCAATC 58.629 39.130 0.00 0.00 43.75 2.67
3181 5122 4.405116 TCTGCTTTTTGGTTTGAGCAAT 57.595 36.364 0.00 0.00 43.75 3.56
3182 5123 3.883830 TCTGCTTTTTGGTTTGAGCAA 57.116 38.095 0.00 0.00 43.75 3.91
3183 5124 3.883830 TTCTGCTTTTTGGTTTGAGCA 57.116 38.095 0.00 0.00 42.36 4.26
3184 5125 4.925646 CCTATTCTGCTTTTTGGTTTGAGC 59.074 41.667 0.00 0.00 35.74 4.26
3185 5126 5.922544 CACCTATTCTGCTTTTTGGTTTGAG 59.077 40.000 0.00 0.00 0.00 3.02
3186 5127 5.596361 TCACCTATTCTGCTTTTTGGTTTGA 59.404 36.000 0.00 0.00 0.00 2.69
3187 5128 5.841810 TCACCTATTCTGCTTTTTGGTTTG 58.158 37.500 0.00 0.00 0.00 2.93
3188 5129 6.041979 ACATCACCTATTCTGCTTTTTGGTTT 59.958 34.615 0.00 0.00 0.00 3.27
3189 5130 5.539955 ACATCACCTATTCTGCTTTTTGGTT 59.460 36.000 0.00 0.00 0.00 3.67
3190 5131 5.079643 ACATCACCTATTCTGCTTTTTGGT 58.920 37.500 0.00 0.00 0.00 3.67
3191 5132 5.649782 ACATCACCTATTCTGCTTTTTGG 57.350 39.130 0.00 0.00 0.00 3.28
3192 5133 7.699391 CACATACATCACCTATTCTGCTTTTTG 59.301 37.037 0.00 0.00 0.00 2.44
3193 5134 7.394359 ACACATACATCACCTATTCTGCTTTTT 59.606 33.333 0.00 0.00 0.00 1.94
3194 5135 6.886459 ACACATACATCACCTATTCTGCTTTT 59.114 34.615 0.00 0.00 0.00 2.27
3195 5136 6.418101 ACACATACATCACCTATTCTGCTTT 58.582 36.000 0.00 0.00 0.00 3.51
3196 5137 5.994250 ACACATACATCACCTATTCTGCTT 58.006 37.500 0.00 0.00 0.00 3.91
3197 5138 5.620738 ACACATACATCACCTATTCTGCT 57.379 39.130 0.00 0.00 0.00 4.24
3198 5139 5.402568 CGTACACATACATCACCTATTCTGC 59.597 44.000 0.00 0.00 0.00 4.26
3199 5140 6.735130 TCGTACACATACATCACCTATTCTG 58.265 40.000 0.00 0.00 0.00 3.02
3200 5141 6.771267 TCTCGTACACATACATCACCTATTCT 59.229 38.462 0.00 0.00 0.00 2.40
3201 5142 6.856938 GTCTCGTACACATACATCACCTATTC 59.143 42.308 0.00 0.00 0.00 1.75
3202 5143 6.320418 TGTCTCGTACACATACATCACCTATT 59.680 38.462 0.00 0.00 31.43 1.73
3203 5144 5.826208 TGTCTCGTACACATACATCACCTAT 59.174 40.000 0.00 0.00 31.43 2.57
3204 5145 5.187687 TGTCTCGTACACATACATCACCTA 58.812 41.667 0.00 0.00 31.43 3.08
3205 5146 4.014406 TGTCTCGTACACATACATCACCT 58.986 43.478 0.00 0.00 31.43 4.00
3206 5147 4.365899 TGTCTCGTACACATACATCACC 57.634 45.455 0.00 0.00 31.43 4.02
3217 5158 1.797046 GAGAGTCGTGTGTCTCGTACA 59.203 52.381 0.00 0.00 35.72 2.90
3218 5159 1.797046 TGAGAGTCGTGTGTCTCGTAC 59.203 52.381 0.00 0.00 41.93 3.67
3219 5160 2.067013 CTGAGAGTCGTGTGTCTCGTA 58.933 52.381 0.00 0.00 41.93 3.43
3220 5161 0.869068 CTGAGAGTCGTGTGTCTCGT 59.131 55.000 0.00 0.00 41.93 4.18
3221 5162 1.149148 TCTGAGAGTCGTGTGTCTCG 58.851 55.000 0.00 0.00 41.93 4.04
3222 5163 3.840890 ATTCTGAGAGTCGTGTGTCTC 57.159 47.619 0.00 0.00 39.83 3.36
3223 5164 5.707242 TTTATTCTGAGAGTCGTGTGTCT 57.293 39.130 0.00 0.00 0.00 3.41
3224 5165 6.670927 GCATTTTATTCTGAGAGTCGTGTGTC 60.671 42.308 0.00 0.00 0.00 3.67
3225 5166 5.120830 GCATTTTATTCTGAGAGTCGTGTGT 59.879 40.000 0.00 0.00 0.00 3.72
3226 5167 5.349817 AGCATTTTATTCTGAGAGTCGTGTG 59.650 40.000 0.00 0.00 0.00 3.82
3227 5168 5.482908 AGCATTTTATTCTGAGAGTCGTGT 58.517 37.500 0.00 0.00 0.00 4.49
3228 5169 7.394872 GTTAGCATTTTATTCTGAGAGTCGTG 58.605 38.462 0.00 0.00 0.00 4.35
3229 5170 6.253727 CGTTAGCATTTTATTCTGAGAGTCGT 59.746 38.462 0.00 0.00 0.00 4.34
3230 5171 6.472486 TCGTTAGCATTTTATTCTGAGAGTCG 59.528 38.462 0.00 0.00 0.00 4.18
3231 5172 7.489757 AGTCGTTAGCATTTTATTCTGAGAGTC 59.510 37.037 0.00 0.00 0.00 3.36
3232 5173 7.276658 CAGTCGTTAGCATTTTATTCTGAGAGT 59.723 37.037 0.00 0.00 0.00 3.24
3233 5174 7.254252 CCAGTCGTTAGCATTTTATTCTGAGAG 60.254 40.741 0.00 0.00 0.00 3.20
3234 5175 6.535150 CCAGTCGTTAGCATTTTATTCTGAGA 59.465 38.462 0.00 0.00 0.00 3.27
3235 5176 6.535150 TCCAGTCGTTAGCATTTTATTCTGAG 59.465 38.462 0.00 0.00 0.00 3.35
3236 5177 6.312918 GTCCAGTCGTTAGCATTTTATTCTGA 59.687 38.462 0.00 0.00 0.00 3.27
3237 5178 6.456988 GGTCCAGTCGTTAGCATTTTATTCTG 60.457 42.308 0.00 0.00 0.00 3.02
3238 5179 5.585047 GGTCCAGTCGTTAGCATTTTATTCT 59.415 40.000 0.00 0.00 0.00 2.40
3239 5180 5.220796 GGGTCCAGTCGTTAGCATTTTATTC 60.221 44.000 0.00 0.00 0.00 1.75
3240 5181 4.638865 GGGTCCAGTCGTTAGCATTTTATT 59.361 41.667 0.00 0.00 0.00 1.40
3241 5182 4.080526 AGGGTCCAGTCGTTAGCATTTTAT 60.081 41.667 0.00 0.00 0.00 1.40
3242 5183 3.262405 AGGGTCCAGTCGTTAGCATTTTA 59.738 43.478 0.00 0.00 0.00 1.52
3243 5184 2.039879 AGGGTCCAGTCGTTAGCATTTT 59.960 45.455 0.00 0.00 0.00 1.82
3244 5185 1.628846 AGGGTCCAGTCGTTAGCATTT 59.371 47.619 0.00 0.00 0.00 2.32
3245 5186 1.207329 GAGGGTCCAGTCGTTAGCATT 59.793 52.381 0.00 0.00 0.00 3.56
3246 5187 0.824759 GAGGGTCCAGTCGTTAGCAT 59.175 55.000 0.00 0.00 0.00 3.79
3247 5188 1.255667 GGAGGGTCCAGTCGTTAGCA 61.256 60.000 0.00 0.00 36.28 3.49
3248 5189 1.255667 TGGAGGGTCCAGTCGTTAGC 61.256 60.000 0.00 0.00 42.67 3.09
3249 5190 2.971676 TGGAGGGTCCAGTCGTTAG 58.028 57.895 0.00 0.00 42.67 2.34
3257 5198 0.608035 GCGACAAATTGGAGGGTCCA 60.608 55.000 0.00 0.00 46.61 4.02
3258 5199 0.608035 TGCGACAAATTGGAGGGTCC 60.608 55.000 0.00 0.00 36.96 4.46
3259 5200 0.804989 CTGCGACAAATTGGAGGGTC 59.195 55.000 0.00 0.00 0.00 4.46
3260 5201 0.609131 CCTGCGACAAATTGGAGGGT 60.609 55.000 0.00 0.00 42.88 4.34
3261 5202 2.183409 CCTGCGACAAATTGGAGGG 58.817 57.895 0.00 0.00 42.88 4.30
3262 5203 0.609131 ACCCTGCGACAAATTGGAGG 60.609 55.000 0.00 0.00 45.56 4.30
3263 5204 1.068333 CAACCCTGCGACAAATTGGAG 60.068 52.381 0.00 0.00 0.00 3.86
3264 5205 0.958091 CAACCCTGCGACAAATTGGA 59.042 50.000 0.00 0.00 0.00 3.53
3265 5206 0.958091 TCAACCCTGCGACAAATTGG 59.042 50.000 0.00 0.00 0.00 3.16
3266 5207 1.608590 AGTCAACCCTGCGACAAATTG 59.391 47.619 0.00 0.00 34.48 2.32
3267 5208 1.880027 GAGTCAACCCTGCGACAAATT 59.120 47.619 0.00 0.00 34.48 1.82
3268 5209 1.523758 GAGTCAACCCTGCGACAAAT 58.476 50.000 0.00 0.00 34.48 2.32
3269 5210 0.878523 CGAGTCAACCCTGCGACAAA 60.879 55.000 0.00 0.00 34.48 2.83
3270 5211 1.300620 CGAGTCAACCCTGCGACAA 60.301 57.895 0.00 0.00 34.48 3.18
3271 5212 1.740332 TTCGAGTCAACCCTGCGACA 61.740 55.000 0.00 0.00 34.48 4.35
3272 5213 0.389948 ATTCGAGTCAACCCTGCGAC 60.390 55.000 0.00 0.00 0.00 5.19
3273 5214 0.108804 GATTCGAGTCAACCCTGCGA 60.109 55.000 2.62 0.00 0.00 5.10
3274 5215 1.413767 CGATTCGAGTCAACCCTGCG 61.414 60.000 8.75 0.00 0.00 5.18
3275 5216 0.389948 ACGATTCGAGTCAACCCTGC 60.390 55.000 13.95 0.00 0.00 4.85
3276 5217 2.080286 AACGATTCGAGTCAACCCTG 57.920 50.000 13.95 0.00 0.00 4.45
3277 5218 2.833631 AAACGATTCGAGTCAACCCT 57.166 45.000 13.95 0.00 0.00 4.34
3278 5219 3.891056 AAAAACGATTCGAGTCAACCC 57.109 42.857 13.95 0.00 0.00 4.11
3295 5236 4.202326 GGAGAGGTACTGTGAGTCCAAAAA 60.202 45.833 0.00 0.00 41.55 1.94
3296 5237 3.323979 GGAGAGGTACTGTGAGTCCAAAA 59.676 47.826 0.00 0.00 41.55 2.44
3297 5238 2.897969 GGAGAGGTACTGTGAGTCCAAA 59.102 50.000 0.00 0.00 41.55 3.28
3298 5239 2.526432 GGAGAGGTACTGTGAGTCCAA 58.474 52.381 0.00 0.00 41.55 3.53
3299 5240 1.613520 CGGAGAGGTACTGTGAGTCCA 60.614 57.143 0.00 0.00 41.55 4.02
3300 5241 1.096416 CGGAGAGGTACTGTGAGTCC 58.904 60.000 0.00 0.00 41.55 3.85
3301 5242 2.110901 TCGGAGAGGTACTGTGAGTC 57.889 55.000 0.00 0.00 41.55 3.36
3319 5260 3.114065 CAGTTACGCTCCCGAATAACTC 58.886 50.000 0.00 0.00 35.42 3.01
3320 5261 2.494870 ACAGTTACGCTCCCGAATAACT 59.505 45.455 0.00 0.00 36.98 2.24
3321 5262 2.856557 GACAGTTACGCTCCCGAATAAC 59.143 50.000 0.00 0.00 38.29 1.89
3322 5263 2.492881 TGACAGTTACGCTCCCGAATAA 59.507 45.455 0.00 0.00 38.29 1.40
3323 5264 2.093890 TGACAGTTACGCTCCCGAATA 58.906 47.619 0.00 0.00 38.29 1.75
3324 5265 0.892755 TGACAGTTACGCTCCCGAAT 59.107 50.000 0.00 0.00 38.29 3.34
3325 5266 0.892755 ATGACAGTTACGCTCCCGAA 59.107 50.000 0.00 0.00 38.29 4.30
3326 5267 0.892755 AATGACAGTTACGCTCCCGA 59.107 50.000 0.00 0.00 38.29 5.14
3327 5268 1.722011 AAATGACAGTTACGCTCCCG 58.278 50.000 0.00 0.00 41.14 5.14
3328 5269 5.616488 TTAAAAATGACAGTTACGCTCCC 57.384 39.130 0.00 0.00 0.00 4.30
3378 5319 7.618512 AGCTACAGGACCTTATTTCTTACTACA 59.381 37.037 0.00 0.00 0.00 2.74
3379 5320 8.009622 AGCTACAGGACCTTATTTCTTACTAC 57.990 38.462 0.00 0.00 0.00 2.73
3382 5323 6.875076 TGAGCTACAGGACCTTATTTCTTAC 58.125 40.000 0.00 0.00 0.00 2.34
3482 5423 7.345691 TGAGGTGCTGGAGAATTATATGAAAA 58.654 34.615 0.00 0.00 0.00 2.29
3483 5424 6.899089 TGAGGTGCTGGAGAATTATATGAAA 58.101 36.000 0.00 0.00 0.00 2.69
3484 5425 6.499106 TGAGGTGCTGGAGAATTATATGAA 57.501 37.500 0.00 0.00 0.00 2.57
3485 5426 6.499106 TTGAGGTGCTGGAGAATTATATGA 57.501 37.500 0.00 0.00 0.00 2.15
3486 5427 6.713903 ACATTGAGGTGCTGGAGAATTATATG 59.286 38.462 0.00 0.00 0.00 1.78
3487 5428 6.845908 ACATTGAGGTGCTGGAGAATTATAT 58.154 36.000 0.00 0.00 0.00 0.86
3488 5429 6.252599 ACATTGAGGTGCTGGAGAATTATA 57.747 37.500 0.00 0.00 0.00 0.98
3489 5430 5.121380 ACATTGAGGTGCTGGAGAATTAT 57.879 39.130 0.00 0.00 0.00 1.28
3490 5431 4.574674 ACATTGAGGTGCTGGAGAATTA 57.425 40.909 0.00 0.00 0.00 1.40
3491 5432 3.446442 ACATTGAGGTGCTGGAGAATT 57.554 42.857 0.00 0.00 0.00 2.17
3492 5433 3.446442 AACATTGAGGTGCTGGAGAAT 57.554 42.857 0.00 0.00 0.00 2.40
3493 5434 2.957402 AACATTGAGGTGCTGGAGAA 57.043 45.000 0.00 0.00 0.00 2.87
3494 5435 2.373169 AGAAACATTGAGGTGCTGGAGA 59.627 45.455 0.00 0.00 0.00 3.71
3495 5436 2.787994 AGAAACATTGAGGTGCTGGAG 58.212 47.619 0.00 0.00 0.00 3.86
3496 5437 2.957402 AGAAACATTGAGGTGCTGGA 57.043 45.000 0.00 0.00 0.00 3.86
3497 5438 3.152341 AGAAGAAACATTGAGGTGCTGG 58.848 45.455 0.00 0.00 0.00 4.85
3498 5439 4.999950 ACTAGAAGAAACATTGAGGTGCTG 59.000 41.667 0.00 0.00 0.00 4.41
3499 5440 5.234466 ACTAGAAGAAACATTGAGGTGCT 57.766 39.130 0.00 0.00 0.00 4.40
3500 5441 5.948992 AACTAGAAGAAACATTGAGGTGC 57.051 39.130 0.00 0.00 0.00 5.01
3501 5442 7.365840 GGTAACTAGAAGAAACATTGAGGTG 57.634 40.000 0.00 0.00 0.00 4.00
3644 5585 7.492524 ACATTGAGCGTCTAGAGAATATGAAA 58.507 34.615 0.00 0.00 0.00 2.69
3681 5622 4.640771 TGAGTAATTGGCTCTTTCAGGT 57.359 40.909 11.44 0.00 34.30 4.00
3686 5627 8.534496 AGCAAAATTATGAGTAATTGGCTCTTT 58.466 29.630 11.44 3.61 42.22 2.52
3720 5661 4.207891 TCTGGTTTGAGCAATCTAGTCC 57.792 45.455 5.09 0.00 0.00 3.85
3749 5690 6.535508 AGAAACATCGAATAAAGTCTGCCTAC 59.464 38.462 0.00 0.00 0.00 3.18
3788 5729 9.578439 GCATAATTGTTTTTATCTTCAAGCTCT 57.422 29.630 0.00 0.00 0.00 4.09
3789 5730 8.811378 GGCATAATTGTTTTTATCTTCAAGCTC 58.189 33.333 0.00 0.00 0.00 4.09
3790 5731 8.534496 AGGCATAATTGTTTTTATCTTCAAGCT 58.466 29.630 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.