Multiple sequence alignment - TraesCS2A01G017500

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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 TraesCS2A01G017500 chr2A 100.000 7529 0 0 1 7529 8173083 8180611 0.000000e+00 13904.0
1 TraesCS2A01G017500 chr2A 97.130 3380 88 4 2034 5406 8349093 8352470 0.000000e+00 5696.0
2 TraesCS2A01G017500 chr2A 94.783 575 12 4 1268 1842 8348413 8348969 0.000000e+00 880.0
3 TraesCS2A01G017500 chr2A 95.616 479 18 2 279 757 8347924 8348399 0.000000e+00 765.0
4 TraesCS2A01G017500 chr2A 91.102 236 19 1 1 234 8347691 8347926 1.220000e-82 318.0
5 TraesCS2A01G017500 chr2A 82.016 367 33 14 7173 7524 7922132 7921784 1.600000e-71 281.0
6 TraesCS2A01G017500 chr2A 94.495 109 6 0 2867 2975 7925909 7925801 1.300000e-37 169.0
7 TraesCS2A01G017500 chr2A 95.918 49 2 0 946 994 7928840 7928792 6.260000e-11 80.5
8 TraesCS2A01G017500 chr2B 97.570 3375 75 3 2034 5406 12010713 12014082 0.000000e+00 5771.0
9 TraesCS2A01G017500 chr2B 92.344 1254 53 9 812 2035 12008182 12009422 0.000000e+00 1744.0
10 TraesCS2A01G017500 chr2B 90.236 594 22 13 276 844 12007578 12008160 0.000000e+00 743.0
11 TraesCS2A01G017500 chr2B 86.383 235 21 9 1 233 12007356 12007581 5.830000e-61 246.0
12 TraesCS2A01G017500 chr2B 95.918 49 2 0 946 994 12051798 12051846 6.260000e-11 80.5
13 TraesCS2A01G017500 chr2B 91.071 56 5 0 2034 2089 12010638 12010693 8.100000e-10 76.8
14 TraesCS2A01G017500 chr2D 98.160 2283 39 2 2034 4316 8777472 8775193 0.000000e+00 3980.0
15 TraesCS2A01G017500 chr2D 98.089 1099 21 0 4308 5406 8770908 8769810 0.000000e+00 1914.0
16 TraesCS2A01G017500 chr2D 94.678 977 37 4 5645 6619 8932047 8931084 0.000000e+00 1502.0
17 TraesCS2A01G017500 chr2D 89.641 1004 24 13 344 1306 8779203 8778239 0.000000e+00 1205.0
18 TraesCS2A01G017500 chr2D 96.256 454 13 1 1389 1842 8778241 8777792 0.000000e+00 741.0
19 TraesCS2A01G017500 chr2D 97.398 269 6 1 6616 6884 8930940 8930673 2.480000e-124 457.0
20 TraesCS2A01G017500 chr2D 91.915 235 17 1 1 233 8779478 8779244 2.030000e-85 327.0
21 TraesCS2A01G017500 chr2D 97.872 141 3 0 7389 7529 8930104 8929964 2.100000e-60 244.0
22 TraesCS2A01G017500 chr2D 92.105 152 11 1 6958 7109 8930623 8930473 5.920000e-51 213.0
23 TraesCS2A01G017500 chr2D 93.578 109 7 0 7159 7267 8930455 8930347 6.040000e-36 163.0
24 TraesCS2A01G017500 chr2D 97.403 77 2 0 7288 7364 8930357 8930281 1.700000e-26 132.0
25 TraesCS2A01G017500 chr7A 96.446 1210 39 1 5410 6619 466512345 466511140 0.000000e+00 1993.0
26 TraesCS2A01G017500 chr7A 97.692 260 4 2 6616 6875 466510958 466510701 5.360000e-121 446.0
27 TraesCS2A01G017500 chr7A 95.906 171 5 2 7361 7529 466510428 466510258 7.440000e-70 276.0
28 TraesCS2A01G017500 chr7A 91.241 137 9 2 6974 7107 466510647 466510511 4.640000e-42 183.0
29 TraesCS2A01G017500 chr6A 85.156 768 78 21 2034 2778 11271957 11272711 0.000000e+00 754.0
30 TraesCS2A01G017500 chr6A 83.848 421 47 11 1598 2014 11270949 11271352 1.530000e-101 381.0
31 TraesCS2A01G017500 chr6A 89.032 155 16 1 2880 3034 11273046 11273199 2.770000e-44 191.0
32 TraesCS2A01G017500 chr6D 85.071 777 72 27 2034 2778 9249815 9249051 0.000000e+00 752.0
33 TraesCS2A01G017500 chr6D 84.086 421 46 11 1598 2014 9250824 9250421 3.290000e-103 387.0
34 TraesCS2A01G017500 chr6D 88.199 161 18 1 2874 3034 9248724 9248565 2.770000e-44 191.0
35 TraesCS2A01G017500 chr6B 85.052 776 75 21 2034 2778 17228658 17227893 0.000000e+00 752.0
36 TraesCS2A01G017500 chr6B 84.323 421 47 11 1598 2014 17229668 17229263 1.970000e-105 394.0
37 TraesCS2A01G017500 chr6B 88.272 162 17 2 2874 3034 17227566 17227406 7.710000e-45 193.0
38 TraesCS2A01G017500 chr3D 81.471 367 35 14 7173 7524 563862409 563862061 3.460000e-68 270.0
39 TraesCS2A01G017500 chr3D 94.495 109 6 0 2867 2975 563866300 563866192 1.300000e-37 169.0
40 TraesCS2A01G017500 chr3D 91.837 49 4 0 946 994 563869275 563869227 1.360000e-07 69.4
41 TraesCS2A01G017500 chr5B 97.222 36 1 0 5364 5399 655302650 655302685 2.270000e-05 62.1


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 TraesCS2A01G017500 chr2A 8173083 8180611 7528 False 13904.000000 13904 100.000000 1 7529 1 chr2A.!!$F1 7528
1 TraesCS2A01G017500 chr2A 8347691 8352470 4779 False 1914.750000 5696 94.657750 1 5406 4 chr2A.!!$F2 5405
2 TraesCS2A01G017500 chr2B 12007356 12014082 6726 False 1716.160000 5771 91.520800 1 5406 5 chr2B.!!$F2 5405
3 TraesCS2A01G017500 chr2D 8769810 8770908 1098 True 1914.000000 1914 98.089000 4308 5406 1 chr2D.!!$R1 1098
4 TraesCS2A01G017500 chr2D 8775193 8779478 4285 True 1563.250000 3980 93.993000 1 4316 4 chr2D.!!$R2 4315
5 TraesCS2A01G017500 chr2D 8929964 8932047 2083 True 451.833333 1502 95.505667 5645 7529 6 chr2D.!!$R3 1884
6 TraesCS2A01G017500 chr7A 466510258 466512345 2087 True 724.500000 1993 95.321250 5410 7529 4 chr7A.!!$R1 2119
7 TraesCS2A01G017500 chr6A 11270949 11273199 2250 False 442.000000 754 86.012000 1598 3034 3 chr6A.!!$F1 1436
8 TraesCS2A01G017500 chr6D 9248565 9250824 2259 True 443.333333 752 85.785333 1598 3034 3 chr6D.!!$R1 1436
9 TraesCS2A01G017500 chr6B 17227406 17229668 2262 True 446.333333 752 85.882333 1598 3034 3 chr6B.!!$R1 1436

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
258 262 0.104671 GAGAGCAGCTGGTCCATCTC 59.895 60.000 35.71 24.85 43.11 2.75 F
260 264 0.251354 GAGCAGCTGGTCCATCTCAA 59.749 55.000 31.17 0.00 36.62 3.02 F
261 265 0.694771 AGCAGCTGGTCCATCTCAAA 59.305 50.000 13.85 0.00 0.00 2.69 F
1158 1265 0.967887 CGCCCAAGGTCTCTCTCTCA 60.968 60.000 0.00 0.00 0.00 3.27 F
1159 1266 1.494960 GCCCAAGGTCTCTCTCTCAT 58.505 55.000 0.00 0.00 0.00 2.90 F
2513 4414 1.757699 ACCGCCTCTTAGCCTCTAAAG 59.242 52.381 0.00 0.00 0.00 1.85 F
2980 5117 3.068873 AGAGCGAGGGATAACAGCTTAAG 59.931 47.826 0.00 0.00 38.39 1.85 F
3647 5786 1.937899 GGACCCGTGCATATGTTACAC 59.062 52.381 4.29 3.40 0.00 2.90 F
4078 6223 1.272212 GTAAATGTGGGCAGTGGGTTG 59.728 52.381 0.00 0.00 0.00 3.77 F
5996 8141 1.004504 CGCCTTGATAAAAGCTCTCGC 60.005 52.381 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1172 1.443872 GGTGTACACGCTCCTGTCG 60.444 63.158 19.41 0.0 0.00 4.35 R
1564 1698 1.909986 GTTAGGCTTGGGAGGTTCTCT 59.090 52.381 0.00 0.0 0.00 3.10 R
1810 1944 2.781757 TCTGGGGAATGCAATCAGAGAT 59.218 45.455 3.77 0.0 31.73 2.75 R
2778 4682 0.961019 GCAAACCTTCCACATGAGCA 59.039 50.000 0.00 0.0 0.00 4.26 R
3150 5289 3.181464 GCCTCCCCTATCACTACAGAAAC 60.181 52.174 0.00 0.0 0.00 2.78 R
3625 5764 0.105224 TAACATATGCACGGGTCCGG 59.895 55.000 14.25 0.0 44.69 5.14 R
4078 6223 3.436704 TCGCATTGTTCCAGATCAAGTTC 59.563 43.478 0.00 0.0 0.00 3.01 R
5550 7695 3.321111 GGAGGAGACGTGCCAGATATTTA 59.679 47.826 0.00 0.0 0.00 1.40 R
6076 8221 0.755079 GGGTACCGTATGTTCCCCTC 59.245 60.000 5.65 0.0 46.29 4.30 R
7078 9463 0.234884 GTAGCGTGAACTTGTGGTGC 59.765 55.000 0.00 0.0 0.00 5.01 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
97 100 2.037641 AGAATTTTGGGTTTGGAGCAGC 59.962 45.455 0.00 0.00 0.00 5.25
98 101 0.686789 ATTTTGGGTTTGGAGCAGCC 59.313 50.000 0.00 0.00 37.10 4.85
101 104 4.660938 GGGTTTGGAGCAGCCGGT 62.661 66.667 1.90 0.00 40.66 5.28
109 112 2.594592 AGCAGCCGGTGGAACAAC 60.595 61.111 1.90 0.00 46.71 3.32
140 143 2.755469 TACGTGCCCGTCTACCCC 60.755 66.667 0.00 0.00 46.28 4.95
142 145 2.786512 TACGTGCCCGTCTACCCCTT 62.787 60.000 0.00 0.00 46.28 3.95
147 150 1.295423 CCCGTCTACCCCTTGTGTG 59.705 63.158 0.00 0.00 0.00 3.82
234 238 1.350193 GTATGGCTCGATATGTGGCG 58.650 55.000 0.00 0.00 39.31 5.69
235 239 0.966179 TATGGCTCGATATGTGGCGT 59.034 50.000 0.00 0.00 39.31 5.68
236 240 0.319900 ATGGCTCGATATGTGGCGTC 60.320 55.000 0.00 0.00 39.31 5.19
237 241 1.067416 GGCTCGATATGTGGCGTCA 59.933 57.895 0.00 0.00 0.00 4.35
238 242 0.529773 GGCTCGATATGTGGCGTCAA 60.530 55.000 0.00 0.00 0.00 3.18
239 243 0.855349 GCTCGATATGTGGCGTCAAG 59.145 55.000 0.00 0.00 0.00 3.02
240 244 1.536072 GCTCGATATGTGGCGTCAAGA 60.536 52.381 0.00 0.00 0.00 3.02
241 245 2.389059 CTCGATATGTGGCGTCAAGAG 58.611 52.381 0.00 0.00 0.00 2.85
242 246 2.021457 TCGATATGTGGCGTCAAGAGA 58.979 47.619 0.00 0.00 0.00 3.10
243 247 2.033424 TCGATATGTGGCGTCAAGAGAG 59.967 50.000 0.00 0.00 0.00 3.20
244 248 2.131183 GATATGTGGCGTCAAGAGAGC 58.869 52.381 0.00 0.00 0.00 4.09
245 249 0.894835 TATGTGGCGTCAAGAGAGCA 59.105 50.000 0.00 0.00 0.00 4.26
246 250 0.390866 ATGTGGCGTCAAGAGAGCAG 60.391 55.000 0.00 0.00 0.00 4.24
247 251 2.047844 TGGCGTCAAGAGAGCAGC 60.048 61.111 0.00 0.00 0.00 5.25
248 252 2.264166 GGCGTCAAGAGAGCAGCT 59.736 61.111 0.00 0.00 0.00 4.24
249 253 2.099431 GGCGTCAAGAGAGCAGCTG 61.099 63.158 10.11 10.11 0.00 4.24
250 254 2.099431 GCGTCAAGAGAGCAGCTGG 61.099 63.158 17.12 0.00 0.00 4.85
251 255 1.291588 CGTCAAGAGAGCAGCTGGT 59.708 57.895 20.31 20.31 0.00 4.00
252 256 0.735632 CGTCAAGAGAGCAGCTGGTC 60.736 60.000 33.42 33.42 42.47 4.02
253 257 0.390998 GTCAAGAGAGCAGCTGGTCC 60.391 60.000 35.71 27.32 43.11 4.46
254 258 0.833409 TCAAGAGAGCAGCTGGTCCA 60.833 55.000 35.71 16.37 43.11 4.02
255 259 0.252479 CAAGAGAGCAGCTGGTCCAT 59.748 55.000 35.71 24.45 43.11 3.41
256 260 0.540923 AAGAGAGCAGCTGGTCCATC 59.459 55.000 35.71 28.12 43.11 3.51
257 261 0.325484 AGAGAGCAGCTGGTCCATCT 60.325 55.000 35.71 29.60 43.11 2.90
258 262 0.104671 GAGAGCAGCTGGTCCATCTC 59.895 60.000 35.71 24.85 43.11 2.75
259 263 0.616964 AGAGCAGCTGGTCCATCTCA 60.617 55.000 35.71 0.00 43.11 3.27
260 264 0.251354 GAGCAGCTGGTCCATCTCAA 59.749 55.000 31.17 0.00 36.62 3.02
261 265 0.694771 AGCAGCTGGTCCATCTCAAA 59.305 50.000 13.85 0.00 0.00 2.69
262 266 1.074405 AGCAGCTGGTCCATCTCAAAA 59.926 47.619 13.85 0.00 0.00 2.44
263 267 1.888512 GCAGCTGGTCCATCTCAAAAA 59.111 47.619 17.12 0.00 0.00 1.94
280 284 3.141449 AAAAAGCAGCTGGTGGGC 58.859 55.556 20.97 1.15 0.00 5.36
281 285 2.510551 AAAAAGCAGCTGGTGGGCC 61.511 57.895 20.97 0.00 0.00 5.80
1002 1109 3.250323 CGGACGTGCTCGCAGATG 61.250 66.667 8.29 0.00 41.18 2.90
1005 1112 3.649277 GACGTGCTCGCAGATGGGT 62.649 63.158 8.29 0.00 41.18 4.51
1082 1189 2.087009 GCGACAGGAGCGTGTACAC 61.087 63.158 16.32 16.32 0.00 2.90
1154 1261 3.764466 CGCGCCCAAGGTCTCTCT 61.764 66.667 0.00 0.00 0.00 3.10
1155 1262 2.185608 GCGCCCAAGGTCTCTCTC 59.814 66.667 0.00 0.00 0.00 3.20
1156 1263 2.355193 GCGCCCAAGGTCTCTCTCT 61.355 63.158 0.00 0.00 0.00 3.10
1157 1264 1.813192 CGCCCAAGGTCTCTCTCTC 59.187 63.158 0.00 0.00 0.00 3.20
1158 1265 0.967887 CGCCCAAGGTCTCTCTCTCA 60.968 60.000 0.00 0.00 0.00 3.27
1159 1266 1.494960 GCCCAAGGTCTCTCTCTCAT 58.505 55.000 0.00 0.00 0.00 2.90
1160 1267 1.836802 GCCCAAGGTCTCTCTCTCATT 59.163 52.381 0.00 0.00 0.00 2.57
1245 1377 7.286508 CAGAAGCTAAATTACATCTGTATGCG 58.713 38.462 0.00 0.00 36.50 4.73
1247 1379 5.056480 AGCTAAATTACATCTGTATGCGCA 58.944 37.500 14.96 14.96 36.50 6.09
1272 1406 4.415596 ACATTTAATCAGGGTCAAGCCAA 58.584 39.130 0.44 0.00 39.65 4.52
1369 1503 6.574350 AGTTGGTGAAGTATACATCTACTGC 58.426 40.000 9.35 0.00 34.43 4.40
1454 1588 5.879237 TGCTAACATTGTACTATTGCTTGC 58.121 37.500 0.00 0.00 0.00 4.01
1512 1646 3.576861 TCTGGAAGAAGAAGGTGACAGA 58.423 45.455 0.00 0.00 42.31 3.41
1564 1698 3.132111 TGCAGATGTATCAAAGGCTACGA 59.868 43.478 0.00 0.00 0.00 3.43
1594 1728 5.338871 CCTCCCAAGCCTAACAATGTAAGTA 60.339 44.000 0.00 0.00 0.00 2.24
1871 2007 7.834068 TTCATGTAATCAGTACTTCTTGCTC 57.166 36.000 0.00 0.00 33.46 4.26
1918 2055 6.571150 GCTTGAGTAAATCTTCAGCATTGGTT 60.571 38.462 0.00 0.00 33.99 3.67
2043 3918 4.148825 AGATGCGCCCGGTCTCAC 62.149 66.667 4.18 0.00 0.00 3.51
2103 3978 8.933653 TCCCTATTGTTTCCTTTTCTTTTCATT 58.066 29.630 0.00 0.00 0.00 2.57
2131 4006 4.377021 TCTCTACTTCAAAATGTGTGCGT 58.623 39.130 0.00 0.00 0.00 5.24
2513 4414 1.757699 ACCGCCTCTTAGCCTCTAAAG 59.242 52.381 0.00 0.00 0.00 1.85
2590 4491 5.435686 AGTATGTTTCAGGCCTGATGTTA 57.564 39.130 35.42 18.64 39.64 2.41
2980 5117 3.068873 AGAGCGAGGGATAACAGCTTAAG 59.931 47.826 0.00 0.00 38.39 1.85
3006 5143 5.105351 CCACAAGACTATGAGGTATGTGACA 60.105 44.000 4.69 0.00 38.38 3.58
3106 5245 3.676291 ACATACCCATTGTTTTGCACC 57.324 42.857 0.00 0.00 0.00 5.01
3150 5289 6.755141 CAGGCATTTAGTGATTTTCCAGATTG 59.245 38.462 0.00 0.00 0.00 2.67
3261 5400 4.575236 CAGAGCTTGCATCAATGTACTGAT 59.425 41.667 0.00 0.00 36.45 2.90
3320 5459 7.783119 TGTAGATGAACTATTACTTGAGGGCTA 59.217 37.037 0.00 0.00 33.39 3.93
3322 5461 6.841755 AGATGAACTATTACTTGAGGGCTAGT 59.158 38.462 0.00 0.00 34.51 2.57
3576 5715 5.467035 TCTGATTTTGTTTGGACCCATTC 57.533 39.130 0.00 0.00 0.00 2.67
3625 5764 5.962423 GCTTGTCGCTAATTCTGATTTTCTC 59.038 40.000 0.00 0.00 35.14 2.87
3647 5786 1.937899 GGACCCGTGCATATGTTACAC 59.062 52.381 4.29 3.40 0.00 2.90
3714 5853 5.659463 TGTTGCTATATGTTGGAAAATGCC 58.341 37.500 0.00 0.00 0.00 4.40
3741 5880 7.011109 GTGTTATTATCTGTCCATGTGTGGTAC 59.989 40.741 0.00 0.00 46.16 3.34
4078 6223 1.272212 GTAAATGTGGGCAGTGGGTTG 59.728 52.381 0.00 0.00 0.00 3.77
4673 6818 3.593442 TGTGGAAAAGTGTTGGATCCT 57.407 42.857 14.23 0.00 0.00 3.24
4695 6840 9.775539 ATCCTGAGCAACTTCTATCCTATTATA 57.224 33.333 0.00 0.00 0.00 0.98
4841 6986 6.211584 TCTTGAACTTACTATTCCTCACAGCT 59.788 38.462 0.00 0.00 0.00 4.24
4990 7135 8.629986 CAAATACTGTTGCTTAATTCTGAAACG 58.370 33.333 0.00 0.00 0.00 3.60
5048 7193 8.598924 CAGTATGTGCCGATCATATCTATTTTC 58.401 37.037 0.00 0.00 31.76 2.29
5468 7613 6.823182 CACAACTGGGATTATGTAATCAGTGA 59.177 38.462 13.17 0.00 42.92 3.41
5672 7817 5.132897 TCCCAGCAAATTATGTTTGACAC 57.867 39.130 8.95 0.00 0.00 3.67
5806 7951 7.437267 CAGCTGACAAATATCCAATGGATTTTC 59.563 37.037 21.06 6.69 39.79 2.29
5819 7964 6.423905 CCAATGGATTTTCATCATCTGATTGC 59.576 38.462 0.00 0.00 32.72 3.56
5820 7965 5.177725 TGGATTTTCATCATCTGATTGCG 57.822 39.130 0.00 0.00 32.72 4.85
5984 8129 4.101585 TGAAGATGATCTAACCGCCTTGAT 59.898 41.667 0.00 0.00 0.00 2.57
5990 8135 4.574828 TGATCTAACCGCCTTGATAAAAGC 59.425 41.667 0.00 0.00 0.00 3.51
5996 8141 1.004504 CGCCTTGATAAAAGCTCTCGC 60.005 52.381 0.00 0.00 0.00 5.03
5998 8143 2.540515 CCTTGATAAAAGCTCTCGCGA 58.459 47.619 9.26 9.26 42.32 5.87
6013 8158 4.509616 TCTCGCGAATTTTAATTGGGAGA 58.490 39.130 11.33 18.71 39.73 3.71
6014 8159 4.938832 TCTCGCGAATTTTAATTGGGAGAA 59.061 37.500 11.33 11.19 39.46 2.87
6040 8185 1.030457 GAGGCAGATTCCAGCAATGG 58.970 55.000 1.77 0.00 0.00 3.16
6043 8188 2.444388 AGGCAGATTCCAGCAATGGATA 59.556 45.455 0.00 0.00 37.87 2.59
6076 8221 7.503566 ACACTTATATTTGGTGGGAAGATGATG 59.496 37.037 0.00 0.00 35.53 3.07
6077 8222 7.720957 CACTTATATTTGGTGGGAAGATGATGA 59.279 37.037 0.00 0.00 0.00 2.92
6078 8223 7.941238 ACTTATATTTGGTGGGAAGATGATGAG 59.059 37.037 0.00 0.00 0.00 2.90
6088 8233 4.505742 GGGAAGATGATGAGGGGAACATAC 60.506 50.000 0.00 0.00 0.00 2.39
6296 8441 0.325933 TCTCATTGGTGGTGGCTGAG 59.674 55.000 0.00 0.00 35.71 3.35
6311 8456 5.590259 GGTGGCTGAGAAATATTTTCTAGCA 59.410 40.000 22.06 12.30 32.21 3.49
6312 8457 6.458888 GGTGGCTGAGAAATATTTTCTAGCAC 60.459 42.308 22.06 18.48 32.21 4.40
6313 8458 6.094048 GTGGCTGAGAAATATTTTCTAGCACA 59.906 38.462 22.06 17.16 32.21 4.57
6542 8687 7.360269 CCAAAATAACTGATTTCAAGCGCAATT 60.360 33.333 11.47 0.00 36.71 2.32
6584 8730 1.742146 CTAGATGGCCTGCTACGCA 59.258 57.895 3.32 0.00 36.92 5.24
6692 9046 2.276201 GGTTTTGTTGCACCTTTGGTC 58.724 47.619 0.00 0.00 31.02 4.02
6849 9203 5.451908 CACACTCAAAACAAGCGATTGTAT 58.548 37.500 20.73 9.22 34.24 2.29
6901 9282 0.819582 AAAGAAATCCAGCCATGCCG 59.180 50.000 0.00 0.00 0.00 5.69
6903 9284 2.362760 AAATCCAGCCATGCCGCA 60.363 55.556 0.00 0.00 0.00 5.69
6904 9285 1.741327 GAAATCCAGCCATGCCGCAT 61.741 55.000 0.00 0.00 0.00 4.73
6906 9287 0.467844 AATCCAGCCATGCCGCATAA 60.468 50.000 5.31 0.00 0.00 1.90
6907 9288 0.467844 ATCCAGCCATGCCGCATAAA 60.468 50.000 5.31 0.00 0.00 1.40
6908 9289 1.066257 CCAGCCATGCCGCATAAAC 59.934 57.895 5.31 0.00 0.00 2.01
6909 9290 1.665264 CCAGCCATGCCGCATAAACA 61.665 55.000 5.31 0.00 0.00 2.83
6910 9291 0.173029 CAGCCATGCCGCATAAACAA 59.827 50.000 5.31 0.00 0.00 2.83
6911 9292 0.894141 AGCCATGCCGCATAAACAAA 59.106 45.000 5.31 0.00 0.00 2.83
6912 9293 1.481772 AGCCATGCCGCATAAACAAAT 59.518 42.857 5.31 0.00 0.00 2.32
6913 9294 1.593933 GCCATGCCGCATAAACAAATG 59.406 47.619 5.31 0.00 0.00 2.32
6914 9295 2.891112 CCATGCCGCATAAACAAATGT 58.109 42.857 5.31 0.00 0.00 2.71
6915 9296 3.736433 GCCATGCCGCATAAACAAATGTA 60.736 43.478 5.31 0.00 0.00 2.29
6916 9297 4.428209 CCATGCCGCATAAACAAATGTAA 58.572 39.130 5.31 0.00 0.00 2.41
6928 9309 1.068610 CAAATGTAACCACAGGCCACG 60.069 52.381 5.01 0.00 38.30 4.94
6929 9310 1.241315 AATGTAACCACAGGCCACGC 61.241 55.000 5.01 0.00 38.30 5.34
6931 9312 2.031919 TAACCACAGGCCACGCAG 59.968 61.111 5.01 0.00 0.00 5.18
6934 9315 2.594303 CCACAGGCCACGCAGAAA 60.594 61.111 5.01 0.00 0.00 2.52
6935 9316 1.973281 CCACAGGCCACGCAGAAAT 60.973 57.895 5.01 0.00 0.00 2.17
6936 9317 1.526575 CCACAGGCCACGCAGAAATT 61.527 55.000 5.01 0.00 0.00 1.82
6937 9318 1.164411 CACAGGCCACGCAGAAATTA 58.836 50.000 5.01 0.00 0.00 1.40
6938 9319 1.135689 CACAGGCCACGCAGAAATTAC 60.136 52.381 5.01 0.00 0.00 1.89
6939 9320 1.164411 CAGGCCACGCAGAAATTACA 58.836 50.000 5.01 0.00 0.00 2.41
6940 9321 1.539388 CAGGCCACGCAGAAATTACAA 59.461 47.619 5.01 0.00 0.00 2.41
6941 9322 2.030363 CAGGCCACGCAGAAATTACAAA 60.030 45.455 5.01 0.00 0.00 2.83
6942 9323 2.825532 AGGCCACGCAGAAATTACAAAT 59.174 40.909 5.01 0.00 0.00 2.32
6943 9324 2.923020 GGCCACGCAGAAATTACAAATG 59.077 45.455 0.00 0.00 0.00 2.32
6944 9325 2.923020 GCCACGCAGAAATTACAAATGG 59.077 45.455 0.00 0.00 0.00 3.16
6945 9326 2.923020 CCACGCAGAAATTACAAATGGC 59.077 45.455 0.00 0.00 0.00 4.40
6947 9328 1.583404 CGCAGAAATTACAAATGGCGC 59.417 47.619 0.00 0.00 36.70 6.53
6948 9329 1.583404 GCAGAAATTACAAATGGCGCG 59.417 47.619 0.00 0.00 0.00 6.86
6949 9330 2.730715 GCAGAAATTACAAATGGCGCGA 60.731 45.455 12.10 0.00 0.00 5.87
6950 9331 3.100817 CAGAAATTACAAATGGCGCGAG 58.899 45.455 12.10 0.00 0.00 5.03
7104 9489 3.494626 CACAAGTTCACGCTACAGAACAT 59.505 43.478 7.88 0.00 44.94 2.71
7110 9495 3.036026 CGCTACAGAACATGAGCGT 57.964 52.632 14.17 2.40 43.94 5.07
7111 9496 0.917259 CGCTACAGAACATGAGCGTC 59.083 55.000 14.17 0.34 43.94 5.19
7113 9498 2.337583 GCTACAGAACATGAGCGTCAA 58.662 47.619 0.00 0.00 0.00 3.18
7114 9499 2.346847 GCTACAGAACATGAGCGTCAAG 59.653 50.000 0.00 0.00 0.00 3.02
7115 9500 1.800805 ACAGAACATGAGCGTCAAGG 58.199 50.000 0.00 0.00 0.00 3.61
7116 9501 1.081892 CAGAACATGAGCGTCAAGGG 58.918 55.000 0.00 0.00 0.00 3.95
7117 9502 0.687354 AGAACATGAGCGTCAAGGGT 59.313 50.000 0.00 0.00 0.00 4.34
7119 9504 2.000447 GAACATGAGCGTCAAGGGTAC 59.000 52.381 0.00 0.00 0.00 3.34
7120 9505 0.973632 ACATGAGCGTCAAGGGTACA 59.026 50.000 0.00 0.00 0.00 2.90
7122 9507 1.935873 CATGAGCGTCAAGGGTACATG 59.064 52.381 0.00 0.00 0.00 3.21
7123 9508 0.249120 TGAGCGTCAAGGGTACATGG 59.751 55.000 0.00 0.00 0.00 3.66
7124 9509 0.462047 GAGCGTCAAGGGTACATGGG 60.462 60.000 0.00 0.00 0.00 4.00
7125 9510 2.112815 GCGTCAAGGGTACATGGGC 61.113 63.158 0.00 0.00 0.00 5.36
7126 9511 1.298340 CGTCAAGGGTACATGGGCA 59.702 57.895 0.00 0.00 0.00 5.36
7128 9513 1.681780 CGTCAAGGGTACATGGGCAAT 60.682 52.381 0.00 0.00 0.00 3.56
7132 9517 3.033184 CAAGGGTACATGGGCAATCATT 58.967 45.455 0.00 0.00 0.00 2.57
7134 9519 2.515429 AGGGTACATGGGCAATCATTCT 59.485 45.455 0.00 0.00 0.00 2.40
7136 9521 4.354987 AGGGTACATGGGCAATCATTCTAT 59.645 41.667 0.00 0.00 0.00 1.98
7137 9522 5.079643 GGGTACATGGGCAATCATTCTATT 58.920 41.667 0.00 0.00 0.00 1.73
7138 9523 6.045459 AGGGTACATGGGCAATCATTCTATTA 59.955 38.462 0.00 0.00 0.00 0.98
7139 9524 6.375455 GGGTACATGGGCAATCATTCTATTAG 59.625 42.308 0.00 0.00 0.00 1.73
7140 9525 5.972107 ACATGGGCAATCATTCTATTAGC 57.028 39.130 0.00 0.00 0.00 3.09
7141 9526 5.387788 ACATGGGCAATCATTCTATTAGCA 58.612 37.500 0.00 0.00 0.00 3.49
7142 9527 5.834742 ACATGGGCAATCATTCTATTAGCAA 59.165 36.000 0.00 0.00 0.00 3.91
7143 9528 6.015688 ACATGGGCAATCATTCTATTAGCAAG 60.016 38.462 0.00 0.00 0.00 4.01
7144 9529 5.448654 TGGGCAATCATTCTATTAGCAAGT 58.551 37.500 0.00 0.00 0.00 3.16
7145 9530 6.600388 TGGGCAATCATTCTATTAGCAAGTA 58.400 36.000 0.00 0.00 0.00 2.24
7146 9531 7.233632 TGGGCAATCATTCTATTAGCAAGTAT 58.766 34.615 0.00 0.00 0.00 2.12
7147 9532 7.175467 TGGGCAATCATTCTATTAGCAAGTATG 59.825 37.037 0.00 0.00 0.00 2.39
7148 9533 7.391554 GGGCAATCATTCTATTAGCAAGTATGA 59.608 37.037 0.00 0.00 35.89 2.15
7149 9534 8.786898 GGCAATCATTCTATTAGCAAGTATGAA 58.213 33.333 0.00 0.00 35.33 2.57
7157 9542 7.851508 TCTATTAGCAAGTATGAAAATCACGC 58.148 34.615 0.00 0.00 0.00 5.34
7172 9557 8.346300 TGAAAATCACGCTAGTTAACAAATTGA 58.654 29.630 8.61 4.13 0.00 2.57
7244 9629 3.139850 CAAATCATGGGCAAGCAAACAA 58.860 40.909 0.00 0.00 0.00 2.83
7262 9647 0.625849 AACGGAGGGAGGCATCAAAT 59.374 50.000 0.00 0.00 0.00 2.32
7271 9656 4.476479 AGGGAGGCATCAAATTAGTTCTCT 59.524 41.667 0.00 0.00 0.00 3.10
7272 9657 5.667626 AGGGAGGCATCAAATTAGTTCTCTA 59.332 40.000 0.00 0.00 0.00 2.43
7274 9659 7.001073 GGGAGGCATCAAATTAGTTCTCTAAT 58.999 38.462 0.00 0.00 45.43 1.73
7279 9664 9.617975 GGCATCAAATTAGTTCTCTAATATTGC 57.382 33.333 0.00 7.75 43.52 3.56
7341 9726 6.015603 TGACAATGATGCAAGTTACAATCCAA 60.016 34.615 0.00 0.00 0.00 3.53
7350 9735 5.738783 GCAAGTTACAATCCAAAAGAAGCCA 60.739 40.000 0.00 0.00 0.00 4.75
7353 9738 5.241728 AGTTACAATCCAAAAGAAGCCACTC 59.758 40.000 0.00 0.00 0.00 3.51
7354 9739 3.565307 ACAATCCAAAAGAAGCCACTCA 58.435 40.909 0.00 0.00 0.00 3.41
7355 9740 3.319122 ACAATCCAAAAGAAGCCACTCAC 59.681 43.478 0.00 0.00 0.00 3.51
7356 9741 3.515602 ATCCAAAAGAAGCCACTCACT 57.484 42.857 0.00 0.00 0.00 3.41
7357 9742 4.640771 ATCCAAAAGAAGCCACTCACTA 57.359 40.909 0.00 0.00 0.00 2.74
7358 9743 4.008074 TCCAAAAGAAGCCACTCACTAG 57.992 45.455 0.00 0.00 0.00 2.57
7359 9744 3.646162 TCCAAAAGAAGCCACTCACTAGA 59.354 43.478 0.00 0.00 0.00 2.43
7360 9745 3.748568 CCAAAAGAAGCCACTCACTAGAC 59.251 47.826 0.00 0.00 0.00 2.59
7361 9746 4.380531 CAAAAGAAGCCACTCACTAGACA 58.619 43.478 0.00 0.00 0.00 3.41
7362 9747 4.899352 AAAGAAGCCACTCACTAGACAT 57.101 40.909 0.00 0.00 0.00 3.06
7363 9748 6.166279 CAAAAGAAGCCACTCACTAGACATA 58.834 40.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 100 1.966451 GCCTCTGTTGTTCCACCGG 60.966 63.158 0.00 0.00 0.00 5.28
98 101 1.966451 GGCCTCTGTTGTTCCACCG 60.966 63.158 0.00 0.00 0.00 4.94
101 104 1.429930 TGTAGGCCTCTGTTGTTCCA 58.570 50.000 9.68 0.00 0.00 3.53
109 112 1.802880 GCACGTACATGTAGGCCTCTG 60.803 57.143 22.23 14.93 0.00 3.35
111 114 0.529992 GGCACGTACATGTAGGCCTC 60.530 60.000 25.15 15.33 38.37 4.70
114 117 1.881252 CGGGCACGTACATGTAGGC 60.881 63.158 22.23 17.40 34.81 3.93
140 143 3.460648 GGCTAGGCCTACACACAAG 57.539 57.895 8.91 0.00 46.69 3.16
204 207 0.249868 GAGCCATACGCCTACATGCA 60.250 55.000 0.00 0.00 38.78 3.96
234 238 0.390998 GGACCAGCTGCTCTCTTGAC 60.391 60.000 8.66 0.00 0.00 3.18
235 239 0.833409 TGGACCAGCTGCTCTCTTGA 60.833 55.000 8.66 0.00 0.00 3.02
236 240 0.252479 ATGGACCAGCTGCTCTCTTG 59.748 55.000 8.66 0.00 0.00 3.02
237 241 0.540923 GATGGACCAGCTGCTCTCTT 59.459 55.000 8.66 0.00 0.00 2.85
238 242 0.325484 AGATGGACCAGCTGCTCTCT 60.325 55.000 12.49 1.44 0.00 3.10
239 243 0.104671 GAGATGGACCAGCTGCTCTC 59.895 60.000 18.99 11.58 26.98 3.20
240 244 0.616964 TGAGATGGACCAGCTGCTCT 60.617 55.000 18.99 5.50 26.98 4.09
241 245 0.251354 TTGAGATGGACCAGCTGCTC 59.749 55.000 18.99 12.50 26.98 4.26
242 246 0.694771 TTTGAGATGGACCAGCTGCT 59.305 50.000 18.99 2.61 26.98 4.24
243 247 1.538047 TTTTGAGATGGACCAGCTGC 58.462 50.000 18.99 9.46 26.98 5.25
263 267 2.510551 GGCCCACCAGCTGCTTTTT 61.511 57.895 8.66 0.00 35.26 1.94
264 268 2.919328 GGCCCACCAGCTGCTTTT 60.919 61.111 8.66 0.00 35.26 2.27
272 276 4.387343 AAGCATGGGGCCCACCAG 62.387 66.667 31.54 21.84 45.20 4.00
273 277 4.380945 GAAGCATGGGGCCCACCA 62.381 66.667 31.54 14.50 46.50 4.17
341 345 1.721664 CGCATTGGAGGCACAGGATG 61.722 60.000 0.00 0.00 46.00 3.51
348 352 2.203056 CCGATCGCATTGGAGGCA 60.203 61.111 10.32 0.00 35.72 4.75
562 566 2.236382 CGCTGCGCATTCCTCTCTC 61.236 63.158 12.24 0.00 0.00 3.20
563 567 2.202851 CGCTGCGCATTCCTCTCT 60.203 61.111 12.24 0.00 0.00 3.10
783 812 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
784 813 2.123033 GGCCTCCTCCTCCTCCTC 60.123 72.222 0.00 0.00 0.00 3.71
785 814 4.150454 CGGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
902 994 4.838486 CGAGCCTCTGGACGACGC 62.838 72.222 0.00 0.00 0.00 5.19
1065 1172 1.443872 GGTGTACACGCTCCTGTCG 60.444 63.158 19.41 0.00 0.00 4.35
1154 1261 2.288763 TGTACGCAGCACAAGAATGAGA 60.289 45.455 0.00 0.00 0.00 3.27
1155 1262 2.068519 TGTACGCAGCACAAGAATGAG 58.931 47.619 0.00 0.00 0.00 2.90
1156 1263 2.162319 TGTACGCAGCACAAGAATGA 57.838 45.000 0.00 0.00 0.00 2.57
1157 1264 3.125829 AGAATGTACGCAGCACAAGAATG 59.874 43.478 0.00 0.00 0.00 2.67
1158 1265 3.338249 AGAATGTACGCAGCACAAGAAT 58.662 40.909 0.00 0.00 0.00 2.40
1159 1266 2.766313 AGAATGTACGCAGCACAAGAA 58.234 42.857 0.00 0.00 0.00 2.52
1160 1267 2.455674 AGAATGTACGCAGCACAAGA 57.544 45.000 0.00 0.00 0.00 3.02
1245 1377 5.449177 GCTTGACCCTGATTAAATGTAGTGC 60.449 44.000 0.00 0.00 0.00 4.40
1247 1379 5.193679 GGCTTGACCCTGATTAAATGTAGT 58.806 41.667 0.00 0.00 0.00 2.73
1272 1406 7.038160 CCTCTTCCATCCATTCTATCTCAGATT 60.038 40.741 0.00 0.00 31.77 2.40
1354 1488 6.583562 GTTCTTTGGGCAGTAGATGTATACT 58.416 40.000 4.17 0.00 36.41 2.12
1564 1698 1.909986 GTTAGGCTTGGGAGGTTCTCT 59.090 52.381 0.00 0.00 0.00 3.10
1594 1728 3.831911 TGCGAAATTTCTGGAAAGGGAAT 59.168 39.130 15.92 0.00 33.32 3.01
1810 1944 2.781757 TCTGGGGAATGCAATCAGAGAT 59.218 45.455 3.77 0.00 31.73 2.75
1871 2007 5.077424 GCGGTCTGTATTTAAGTTTCAACG 58.923 41.667 0.00 0.00 0.00 4.10
2103 3978 8.342634 GCACACATTTTGAAGTAGAGAACTAAA 58.657 33.333 0.00 0.00 37.50 1.85
2513 4414 6.093633 GTCAAGTAGTAATGTGGGATGGTTTC 59.906 42.308 0.00 0.00 0.00 2.78
2590 4491 3.688694 ATGGTCAATTGCATGCTTTGT 57.311 38.095 23.93 9.90 0.00 2.83
2778 4682 0.961019 GCAAACCTTCCACATGAGCA 59.039 50.000 0.00 0.00 0.00 4.26
2980 5117 5.127194 TCACATACCTCATAGTCTTGTGGTC 59.873 44.000 10.23 0.00 41.35 4.02
3014 5151 8.515695 TCAGCATGATTTCATACTTCTCAATT 57.484 30.769 0.00 0.00 42.56 2.32
3106 5245 4.860907 GCCTGCAATGAACAGAAAGTATTG 59.139 41.667 0.00 0.00 37.32 1.90
3150 5289 3.181464 GCCTCCCCTATCACTACAGAAAC 60.181 52.174 0.00 0.00 0.00 2.78
3218 5357 8.263640 AGCTCTGAGATAATTAGTGTGTCAAAT 58.736 33.333 9.28 0.00 0.00 2.32
3576 5715 8.726988 GCTAGACTATATCTTGAAGTAGGACTG 58.273 40.741 0.00 0.00 39.04 3.51
3625 5764 0.105224 TAACATATGCACGGGTCCGG 59.895 55.000 14.25 0.00 44.69 5.14
3647 5786 5.892160 TCTTTCAGCAATGATCAGGAAAG 57.108 39.130 19.71 19.71 41.39 2.62
3714 5853 6.036246 CACACATGGACAGATAATAACACG 57.964 41.667 0.00 0.00 0.00 4.49
3741 5880 5.627499 TTAATTGAAAGGTGCTGCTAGTG 57.373 39.130 0.00 0.00 0.00 2.74
4078 6223 3.436704 TCGCATTGTTCCAGATCAAGTTC 59.563 43.478 0.00 0.00 0.00 3.01
4220 6365 4.518249 AGACATAAAGGTAGCAAGCTTCC 58.482 43.478 9.43 9.43 42.53 3.46
4329 6474 7.165812 CCGAAAAACAATCTATGGCTATTTTCG 59.834 37.037 17.94 17.94 44.01 3.46
4909 7054 9.703892 CCAGGAATTGAACAAAATAACAATGTA 57.296 29.630 0.00 0.00 34.02 2.29
5048 7193 8.134202 ACTTGAATTGTTAGAATTAAAGGGGG 57.866 34.615 14.11 0.00 34.04 5.40
5407 7552 8.994881 GCAAAACAAACAAAATTAGTGCTTTAC 58.005 29.630 0.00 0.00 0.00 2.01
5408 7553 8.721478 TGCAAAACAAACAAAATTAGTGCTTTA 58.279 25.926 0.00 0.00 0.00 1.85
5412 7557 6.465465 CACTGCAAAACAAACAAAATTAGTGC 59.535 34.615 0.00 0.00 0.00 4.40
5550 7695 3.321111 GGAGGAGACGTGCCAGATATTTA 59.679 47.826 0.00 0.00 0.00 1.40
5672 7817 2.058798 CGATACGGACATTTCCATCGG 58.941 52.381 11.10 0.00 41.18 4.18
5806 7951 4.093850 TGACAAGAACGCAATCAGATGATG 59.906 41.667 0.00 0.00 34.49 3.07
5819 7964 2.737252 GGACCTTTAGCTGACAAGAACG 59.263 50.000 0.00 0.00 0.00 3.95
5820 7965 3.740115 TGGACCTTTAGCTGACAAGAAC 58.260 45.455 0.00 0.00 0.00 3.01
5990 8135 4.570772 TCTCCCAATTAAAATTCGCGAGAG 59.429 41.667 9.59 8.07 43.69 3.20
5996 8141 6.267496 ACCTGTTCTCCCAATTAAAATTCG 57.733 37.500 0.00 0.00 0.00 3.34
5998 8143 7.256296 CCTCAACCTGTTCTCCCAATTAAAATT 60.256 37.037 0.00 0.00 0.00 1.82
6013 8158 1.425066 TGGAATCTGCCTCAACCTGTT 59.575 47.619 0.00 0.00 0.00 3.16
6014 8159 1.004044 CTGGAATCTGCCTCAACCTGT 59.996 52.381 0.00 0.00 0.00 4.00
6040 8185 9.925268 CCACCAAATATAAGTGTACGTTTTATC 57.075 33.333 0.00 0.00 0.00 1.75
6043 8188 6.941436 TCCCACCAAATATAAGTGTACGTTTT 59.059 34.615 0.00 0.00 0.00 2.43
6076 8221 0.755079 GGGTACCGTATGTTCCCCTC 59.245 60.000 5.65 0.00 46.29 4.30
6077 8222 2.920708 GGGTACCGTATGTTCCCCT 58.079 57.895 5.65 0.00 46.29 4.79
6584 8730 6.015688 AGACATGCATTCAACTCTCACAAAAT 60.016 34.615 0.00 0.00 0.00 1.82
6692 9046 2.071540 TGTACGTACACGAGGACTCAG 58.928 52.381 24.10 0.00 43.02 3.35
6748 9102 4.633126 CAGTTGGATGACAATCTCGTTGAT 59.367 41.667 0.00 0.00 41.95 2.57
6818 9172 4.261572 GCTTGTTTTGAGTGTGCCTATTCA 60.262 41.667 0.00 0.00 0.00 2.57
6849 9203 2.043551 TGGTTGCACCACAAGGCA 60.044 55.556 4.16 0.00 44.79 4.75
6884 9238 2.123428 GCGGCATGGCTGGATTTCT 61.123 57.895 18.09 0.00 35.15 2.52
6885 9239 1.741327 ATGCGGCATGGCTGGATTTC 61.741 55.000 15.87 0.00 43.17 2.17
6901 9282 4.625311 GCCTGTGGTTACATTTGTTTATGC 59.375 41.667 0.00 0.00 35.97 3.14
6903 9284 4.835615 TGGCCTGTGGTTACATTTGTTTAT 59.164 37.500 3.32 0.00 35.97 1.40
6904 9285 4.038162 GTGGCCTGTGGTTACATTTGTTTA 59.962 41.667 3.32 0.00 35.97 2.01
6906 9287 2.364002 GTGGCCTGTGGTTACATTTGTT 59.636 45.455 3.32 0.00 35.97 2.83
6907 9288 1.960689 GTGGCCTGTGGTTACATTTGT 59.039 47.619 3.32 0.00 35.97 2.83
6908 9289 1.068610 CGTGGCCTGTGGTTACATTTG 60.069 52.381 3.32 0.00 35.97 2.32
6909 9290 1.243902 CGTGGCCTGTGGTTACATTT 58.756 50.000 3.32 0.00 35.97 2.32
6910 9291 1.241315 GCGTGGCCTGTGGTTACATT 61.241 55.000 3.32 0.00 35.97 2.71
6911 9292 1.674322 GCGTGGCCTGTGGTTACAT 60.674 57.895 3.32 0.00 35.97 2.29
6912 9293 2.281208 GCGTGGCCTGTGGTTACA 60.281 61.111 3.32 0.00 35.08 2.41
6913 9294 2.281208 TGCGTGGCCTGTGGTTAC 60.281 61.111 3.32 0.00 0.00 2.50
6914 9295 2.031919 CTGCGTGGCCTGTGGTTA 59.968 61.111 3.32 0.00 0.00 2.85
6915 9296 2.902423 TTTCTGCGTGGCCTGTGGTT 62.902 55.000 3.32 0.00 0.00 3.67
6916 9297 2.697147 ATTTCTGCGTGGCCTGTGGT 62.697 55.000 3.32 0.00 0.00 4.16
6928 9309 1.583404 CGCGCCATTTGTAATTTCTGC 59.417 47.619 0.00 0.00 0.00 4.26
6929 9310 3.100817 CTCGCGCCATTTGTAATTTCTG 58.899 45.455 0.00 0.00 0.00 3.02
6931 9312 1.846175 GCTCGCGCCATTTGTAATTTC 59.154 47.619 0.00 0.00 0.00 2.17
6934 9315 1.351707 CGCTCGCGCCATTTGTAAT 59.648 52.632 0.00 0.00 0.00 1.89
6935 9316 2.781957 CGCTCGCGCCATTTGTAA 59.218 55.556 0.00 0.00 0.00 2.41
6945 9326 4.088762 ATTTGTGGTGCGCTCGCG 62.089 61.111 9.73 6.98 45.51 5.87
6946 9327 1.906994 TACATTTGTGGTGCGCTCGC 61.907 55.000 9.73 7.38 42.35 5.03
6947 9328 0.726827 ATACATTTGTGGTGCGCTCG 59.273 50.000 9.73 0.00 0.00 5.03
6948 9329 4.552166 AATATACATTTGTGGTGCGCTC 57.448 40.909 9.73 4.47 0.00 5.03
6949 9330 4.025229 CGTAATATACATTTGTGGTGCGCT 60.025 41.667 9.73 0.00 0.00 5.92
6950 9331 4.208355 CGTAATATACATTTGTGGTGCGC 58.792 43.478 0.00 0.00 0.00 6.09
6951 9332 5.194657 CACGTAATATACATTTGTGGTGCG 58.805 41.667 0.00 0.00 31.05 5.34
6952 9333 5.963004 CACACGTAATATACATTTGTGGTGC 59.037 40.000 0.00 0.00 35.35 5.01
6953 9334 6.958752 CACACACGTAATATACATTTGTGGTG 59.041 38.462 13.80 0.00 37.65 4.17
6954 9335 6.402766 GCACACACGTAATATACATTTGTGGT 60.403 38.462 13.80 0.00 37.65 4.16
6955 9336 5.963004 GCACACACGTAATATACATTTGTGG 59.037 40.000 13.80 7.63 37.65 4.17
6956 9337 6.538444 TGCACACACGTAATATACATTTGTG 58.462 36.000 0.00 10.18 38.51 3.33
7069 9454 4.869861 GTGAACTTGTGGTGCTTGATTTTT 59.130 37.500 0.00 0.00 0.00 1.94
7070 9455 4.432712 GTGAACTTGTGGTGCTTGATTTT 58.567 39.130 0.00 0.00 0.00 1.82
7071 9456 3.489059 CGTGAACTTGTGGTGCTTGATTT 60.489 43.478 0.00 0.00 0.00 2.17
7072 9457 2.033299 CGTGAACTTGTGGTGCTTGATT 59.967 45.455 0.00 0.00 0.00 2.57
7073 9458 1.603802 CGTGAACTTGTGGTGCTTGAT 59.396 47.619 0.00 0.00 0.00 2.57
7078 9463 0.234884 GTAGCGTGAACTTGTGGTGC 59.765 55.000 0.00 0.00 0.00 5.01
7104 9489 0.249120 CCATGTACCCTTGACGCTCA 59.751 55.000 0.00 0.00 0.00 4.26
7109 9494 2.024414 GATTGCCCATGTACCCTTGAC 58.976 52.381 0.00 0.00 0.00 3.18
7110 9495 1.638070 TGATTGCCCATGTACCCTTGA 59.362 47.619 0.00 0.00 0.00 3.02
7111 9496 2.142356 TGATTGCCCATGTACCCTTG 57.858 50.000 0.00 0.00 0.00 3.61
7113 9498 2.515429 AGAATGATTGCCCATGTACCCT 59.485 45.455 0.00 0.00 0.00 4.34
7114 9499 2.949447 AGAATGATTGCCCATGTACCC 58.051 47.619 0.00 0.00 0.00 3.69
7115 9500 6.127897 GCTAATAGAATGATTGCCCATGTACC 60.128 42.308 0.00 0.00 0.00 3.34
7116 9501 6.430925 TGCTAATAGAATGATTGCCCATGTAC 59.569 38.462 0.00 0.00 0.00 2.90
7117 9502 6.541907 TGCTAATAGAATGATTGCCCATGTA 58.458 36.000 0.00 0.00 0.00 2.29
7119 9504 5.970317 TGCTAATAGAATGATTGCCCATG 57.030 39.130 0.00 0.00 0.00 3.66
7120 9505 6.073314 ACTTGCTAATAGAATGATTGCCCAT 58.927 36.000 0.00 0.00 0.00 4.00
7122 9507 7.391554 TCATACTTGCTAATAGAATGATTGCCC 59.608 37.037 0.00 0.00 0.00 5.36
7123 9508 8.327941 TCATACTTGCTAATAGAATGATTGCC 57.672 34.615 0.00 0.00 0.00 4.52
7132 9517 7.710907 AGCGTGATTTTCATACTTGCTAATAGA 59.289 33.333 0.00 0.00 0.00 1.98
7134 9519 7.786178 AGCGTGATTTTCATACTTGCTAATA 57.214 32.000 0.00 0.00 0.00 0.98
7136 9521 6.816640 ACTAGCGTGATTTTCATACTTGCTAA 59.183 34.615 0.00 0.00 32.64 3.09
7137 9522 6.338146 ACTAGCGTGATTTTCATACTTGCTA 58.662 36.000 0.00 0.00 0.00 3.49
7138 9523 5.178797 ACTAGCGTGATTTTCATACTTGCT 58.821 37.500 0.00 0.00 0.00 3.91
7139 9524 5.470845 ACTAGCGTGATTTTCATACTTGC 57.529 39.130 0.00 0.00 0.00 4.01
7140 9525 8.440059 TGTTAACTAGCGTGATTTTCATACTTG 58.560 33.333 7.22 0.00 0.00 3.16
7141 9526 8.542497 TGTTAACTAGCGTGATTTTCATACTT 57.458 30.769 7.22 0.00 0.00 2.24
7142 9527 8.542497 TTGTTAACTAGCGTGATTTTCATACT 57.458 30.769 7.22 0.00 0.00 2.12
7143 9528 9.769093 ATTTGTTAACTAGCGTGATTTTCATAC 57.231 29.630 7.22 0.00 0.00 2.39
7145 9530 9.128107 CAATTTGTTAACTAGCGTGATTTTCAT 57.872 29.630 7.22 0.00 0.00 2.57
7146 9531 8.346300 TCAATTTGTTAACTAGCGTGATTTTCA 58.654 29.630 7.22 0.00 0.00 2.69
7147 9532 8.722342 TCAATTTGTTAACTAGCGTGATTTTC 57.278 30.769 7.22 0.00 0.00 2.29
7148 9533 9.691362 AATCAATTTGTTAACTAGCGTGATTTT 57.309 25.926 7.22 0.00 31.00 1.82
7149 9534 9.341899 GAATCAATTTGTTAACTAGCGTGATTT 57.658 29.630 17.84 8.72 34.30 2.17
7150 9535 7.968405 GGAATCAATTTGTTAACTAGCGTGATT 59.032 33.333 17.27 17.27 36.24 2.57
7151 9536 7.336931 AGGAATCAATTTGTTAACTAGCGTGAT 59.663 33.333 7.22 6.81 0.00 3.06
7152 9537 6.653320 AGGAATCAATTTGTTAACTAGCGTGA 59.347 34.615 7.22 4.85 0.00 4.35
7153 9538 6.842163 AGGAATCAATTTGTTAACTAGCGTG 58.158 36.000 7.22 0.00 0.00 5.34
7154 9539 7.448748 AAGGAATCAATTTGTTAACTAGCGT 57.551 32.000 7.22 0.00 0.00 5.07
7155 9540 8.742554 AAAAGGAATCAATTTGTTAACTAGCG 57.257 30.769 7.22 0.00 0.00 4.26
7189 9574 9.883142 TTGACAGACCAAAAACAAGATAAATTT 57.117 25.926 0.00 0.00 0.00 1.82
7244 9629 0.625849 AATTTGATGCCTCCCTCCGT 59.374 50.000 0.00 0.00 0.00 4.69
7341 9726 4.899352 ATGTCTAGTGAGTGGCTTCTTT 57.101 40.909 0.00 0.00 0.00 2.52
7350 9735 8.706521 TCTATGTCTAGTGTATGTCTAGTGAGT 58.293 37.037 0.00 0.00 36.99 3.41
7353 9738 7.094975 GGCTCTATGTCTAGTGTATGTCTAGTG 60.095 44.444 0.00 0.00 36.99 2.74
7354 9739 6.938030 GGCTCTATGTCTAGTGTATGTCTAGT 59.062 42.308 0.00 0.00 36.99 2.57
7355 9740 6.937465 TGGCTCTATGTCTAGTGTATGTCTAG 59.063 42.308 0.00 0.00 36.99 2.43
7356 9741 6.838382 TGGCTCTATGTCTAGTGTATGTCTA 58.162 40.000 0.00 0.00 0.00 2.59
7357 9742 5.696030 TGGCTCTATGTCTAGTGTATGTCT 58.304 41.667 0.00 0.00 0.00 3.41
7358 9743 6.207614 TCATGGCTCTATGTCTAGTGTATGTC 59.792 42.308 0.00 0.00 0.00 3.06
7359 9744 6.015856 GTCATGGCTCTATGTCTAGTGTATGT 60.016 42.308 0.00 0.00 0.00 2.29
7360 9745 6.208402 AGTCATGGCTCTATGTCTAGTGTATG 59.792 42.308 0.00 0.00 0.00 2.39
7361 9746 6.310941 AGTCATGGCTCTATGTCTAGTGTAT 58.689 40.000 0.00 0.00 0.00 2.29
7362 9747 5.696030 AGTCATGGCTCTATGTCTAGTGTA 58.304 41.667 0.00 0.00 0.00 2.90
7363 9748 4.541705 AGTCATGGCTCTATGTCTAGTGT 58.458 43.478 0.00 0.00 0.00 3.55
7450 9999 0.967380 GGGTCCACTGGAGGCATTTG 60.967 60.000 0.00 0.00 29.39 2.32
7479 10028 3.884895 TGGACCGCATCATTATCACTTT 58.115 40.909 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.