Multiple sequence alignment - TraesCS6D01G126500

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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 TraesCS6D01G126500 chr6D 100.000 3299 0 0 1 3299 90192863 90196161 0.000000e+00 6093.0
1 TraesCS6D01G126500 chr6D 85.615 1300 151 16 1040 2304 90347584 90348882 0.000000e+00 1332.0
2 TraesCS6D01G126500 chr6D 82.123 179 26 5 436 610 268058463 268058639 7.380000e-32 148.0
3 TraesCS6D01G126500 chr6B 94.275 2882 85 27 436 3299 172576427 172573608 0.000000e+00 4335.0
4 TraesCS6D01G126500 chr6B 89.288 1335 125 9 1046 2366 172465872 172464542 0.000000e+00 1657.0
5 TraesCS6D01G126500 chr6B 89.623 636 63 1 1667 2299 172368519 172367884 0.000000e+00 806.0
6 TraesCS6D01G126500 chr6B 85.464 571 69 9 1046 1611 172369175 172368614 1.710000e-162 582.0
7 TraesCS6D01G126500 chr6B 86.260 262 35 1 178 438 459599615 459599876 1.940000e-72 283.0
8 TraesCS6D01G126500 chr6B 85.441 261 37 1 178 438 252842731 252842990 1.510000e-68 270.0
9 TraesCS6D01G126500 chr6B 86.325 117 8 4 44 156 49982202 49982090 1.610000e-23 121.0
10 TraesCS6D01G126500 chr6A 96.908 1714 41 4 655 2360 108653375 108651666 0.000000e+00 2861.0
11 TraesCS6D01G126500 chr6A 86.002 1293 141 25 1043 2307 108217288 108216008 0.000000e+00 1349.0
12 TraesCS6D01G126500 chr6A 89.333 675 68 2 1695 2366 108332002 108331329 0.000000e+00 845.0
13 TraesCS6D01G126500 chr6A 87.786 655 61 8 997 1644 108332649 108332007 0.000000e+00 749.0
14 TraesCS6D01G126500 chr6A 91.954 522 36 5 2351 2869 108650403 108649885 0.000000e+00 726.0
15 TraesCS6D01G126500 chr6A 92.519 401 27 1 39 436 108671338 108670938 3.690000e-159 571.0
16 TraesCS6D01G126500 chr6A 90.934 364 30 3 2937 3299 108649869 108649508 1.380000e-133 486.0
17 TraesCS6D01G126500 chr6A 100.000 32 0 0 2873 2904 108649898 108649867 3.560000e-05 60.2
18 TraesCS6D01G126500 chr2B 89.354 263 23 3 178 440 94268455 94268198 3.170000e-85 326.0
19 TraesCS6D01G126500 chr2B 80.737 353 50 11 2896 3232 147489378 147489028 3.270000e-65 259.0
20 TraesCS6D01G126500 chr2B 84.291 261 41 0 178 438 366971658 366971918 4.220000e-64 255.0
21 TraesCS6D01G126500 chr2A 86.207 261 36 0 178 438 711885511 711885251 1.940000e-72 283.0
22 TraesCS6D01G126500 chr2A 81.041 269 41 5 2972 3231 94289155 94288888 4.320000e-49 206.0
23 TraesCS6D01G126500 chr2A 90.164 122 3 6 35 153 536594469 536594584 2.050000e-32 150.0
24 TraesCS6D01G126500 chr2A 85.484 62 9 0 2896 2957 94289264 94289203 7.640000e-07 65.8
25 TraesCS6D01G126500 chr2A 100.000 28 0 0 655 682 691684924 691684951 6.000000e-03 52.8
26 TraesCS6D01G126500 chr5B 83.077 260 44 0 178 437 434058582 434058841 1.530000e-58 237.0
27 TraesCS6D01G126500 chr5B 82.879 257 44 0 182 438 528382232 528381976 7.120000e-57 231.0
28 TraesCS6D01G126500 chr4A 82.129 263 42 4 178 437 12673920 12674180 1.540000e-53 220.0
29 TraesCS6D01G126500 chr7D 78.409 352 59 13 2896 3232 126671972 126672321 2.580000e-51 213.0
30 TraesCS6D01G126500 chr7D 81.707 246 35 7 3045 3281 596573635 596573391 2.600000e-46 196.0
31 TraesCS6D01G126500 chr7D 85.799 169 20 4 451 618 265002590 265002755 3.380000e-40 176.0
32 TraesCS6D01G126500 chr7D 84.940 166 21 3 454 618 364138368 364138530 7.320000e-37 165.0
33 TraesCS6D01G126500 chr7D 93.548 62 1 3 2576 2636 635514265 635514206 4.530000e-14 89.8
34 TraesCS6D01G126500 chr3D 81.452 248 32 10 3045 3282 517738696 517738453 1.210000e-44 191.0
35 TraesCS6D01G126500 chr3D 82.778 180 24 7 442 618 613816430 613816255 1.590000e-33 154.0
36 TraesCS6D01G126500 chr3D 79.793 193 19 10 2 182 511303429 511303613 4.470000e-24 122.0
37 TraesCS6D01G126500 chr3D 83.459 133 9 7 2542 2662 517738829 517738698 9.680000e-21 111.0
38 TraesCS6D01G126500 chr3A 85.119 168 18 7 454 618 750303335 750303172 7.320000e-37 165.0
39 TraesCS6D01G126500 chr7A 86.577 149 14 5 439 585 134010197 134010053 3.410000e-35 159.0
40 TraesCS6D01G126500 chr7A 88.136 118 7 5 41 156 5178762 5178874 2.070000e-27 134.0
41 TraesCS6D01G126500 chr1B 82.418 182 26 5 439 618 270298632 270298455 1.590000e-33 154.0
42 TraesCS6D01G126500 chr1B 75.078 321 48 18 2403 2699 426961338 426961650 1.610000e-23 121.0
43 TraesCS6D01G126500 chr1D 84.615 156 19 4 455 609 24628877 24628726 2.050000e-32 150.0
44 TraesCS6D01G126500 chr1D 79.661 177 26 9 436 609 196612075 196612244 5.780000e-23 119.0
45 TraesCS6D01G126500 chr3B 88.136 118 11 3 45 162 690565860 690565974 1.600000e-28 137.0
46 TraesCS6D01G126500 chr5D 89.908 109 6 3 45 153 419267552 419267449 5.740000e-28 135.0
47 TraesCS6D01G126500 chr5A 88.991 109 7 2 45 153 407950316 407950419 2.670000e-26 130.0
48 TraesCS6D01G126500 chrUn 79.381 194 19 11 2 182 361790376 361790561 2.080000e-22 117.0


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 TraesCS6D01G126500 chr6D 90192863 90196161 3298 False 6093.0 6093 100.0000 1 3299 1 chr6D.!!$F1 3298
1 TraesCS6D01G126500 chr6D 90347584 90348882 1298 False 1332.0 1332 85.6150 1040 2304 1 chr6D.!!$F2 1264
2 TraesCS6D01G126500 chr6B 172573608 172576427 2819 True 4335.0 4335 94.2750 436 3299 1 chr6B.!!$R3 2863
3 TraesCS6D01G126500 chr6B 172464542 172465872 1330 True 1657.0 1657 89.2880 1046 2366 1 chr6B.!!$R2 1320
4 TraesCS6D01G126500 chr6B 172367884 172369175 1291 True 694.0 806 87.5435 1046 2299 2 chr6B.!!$R4 1253
5 TraesCS6D01G126500 chr6A 108216008 108217288 1280 True 1349.0 1349 86.0020 1043 2307 1 chr6A.!!$R1 1264
6 TraesCS6D01G126500 chr6A 108649508 108653375 3867 True 1033.3 2861 94.9490 655 3299 4 chr6A.!!$R4 2644
7 TraesCS6D01G126500 chr6A 108331329 108332649 1320 True 797.0 845 88.5595 997 2366 2 chr6A.!!$R3 1369

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
34 35 0.028902 GCGGCCCATGTACGAAATTC 59.971 55.0 0.00 0.00 0.0 2.17 F
217 218 0.446222 TAAGGCGCGATTGACTTTGC 59.554 50.0 12.10 0.00 0.0 3.68 F
223 224 0.452784 GCGATTGACTTTGCACGGTC 60.453 55.0 10.31 10.31 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 2094 0.744771 GATCTTGACGCCAGGGTTCC 60.745 60.000 0.00 0.0 0.00 3.62 R
2220 2304 3.963428 ACAATCTTGTACGCCTTCTCT 57.037 42.857 0.00 0.0 40.16 3.10 R
2384 3741 5.068198 TGTGTGGGTTCTAGTACCGAATATC 59.932 44.000 11.95 0.0 39.18 1.63 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
24 25 4.403137 CACAACGTGCGGCCCATG 62.403 66.667 10.80 10.80 36.50 3.66
25 26 4.947147 ACAACGTGCGGCCCATGT 62.947 61.111 11.92 11.92 45.44 3.21
26 27 2.744318 CAACGTGCGGCCCATGTA 60.744 61.111 16.49 0.00 42.76 2.29
27 28 2.744709 AACGTGCGGCCCATGTAC 60.745 61.111 16.49 3.78 42.76 2.90
29 30 4.805231 CGTGCGGCCCATGTACGA 62.805 66.667 13.03 0.00 46.29 3.43
30 31 2.435234 GTGCGGCCCATGTACGAA 60.435 61.111 0.00 0.00 0.00 3.85
31 32 2.036006 GTGCGGCCCATGTACGAAA 61.036 57.895 0.00 0.00 0.00 3.46
32 33 1.078072 TGCGGCCCATGTACGAAAT 60.078 52.632 0.00 0.00 0.00 2.17
33 34 0.678366 TGCGGCCCATGTACGAAATT 60.678 50.000 0.00 0.00 0.00 1.82
34 35 0.028902 GCGGCCCATGTACGAAATTC 59.971 55.000 0.00 0.00 0.00 2.17
35 36 1.663695 CGGCCCATGTACGAAATTCT 58.336 50.000 0.00 0.00 0.00 2.40
36 37 1.330521 CGGCCCATGTACGAAATTCTG 59.669 52.381 0.00 0.00 0.00 3.02
37 38 1.676006 GGCCCATGTACGAAATTCTGG 59.324 52.381 0.00 0.00 0.00 3.86
38 39 1.065551 GCCCATGTACGAAATTCTGGC 59.934 52.381 0.00 0.00 0.00 4.85
39 40 1.330521 CCCATGTACGAAATTCTGGCG 59.669 52.381 0.00 0.00 0.00 5.69
40 41 2.276201 CCATGTACGAAATTCTGGCGA 58.724 47.619 0.00 0.00 0.00 5.54
41 42 2.675844 CCATGTACGAAATTCTGGCGAA 59.324 45.455 0.00 0.00 0.00 4.70
42 43 3.312421 CCATGTACGAAATTCTGGCGAAT 59.688 43.478 0.00 0.00 41.53 3.34
43 44 4.509970 CCATGTACGAAATTCTGGCGAATA 59.490 41.667 0.00 0.00 38.89 1.75
44 45 5.432157 CATGTACGAAATTCTGGCGAATAC 58.568 41.667 0.00 1.77 38.89 1.89
45 46 4.496360 TGTACGAAATTCTGGCGAATACA 58.504 39.130 0.00 3.82 38.89 2.29
46 47 4.327898 TGTACGAAATTCTGGCGAATACAC 59.672 41.667 0.00 2.06 38.89 2.90
47 48 3.331150 ACGAAATTCTGGCGAATACACA 58.669 40.909 0.00 0.00 38.89 3.72
48 49 3.749088 ACGAAATTCTGGCGAATACACAA 59.251 39.130 0.00 0.00 38.89 3.33
49 50 4.088648 CGAAATTCTGGCGAATACACAAC 58.911 43.478 5.29 0.00 38.89 3.32
50 51 4.377943 CGAAATTCTGGCGAATACACAACA 60.378 41.667 5.29 0.00 38.89 3.33
51 52 5.446143 AAATTCTGGCGAATACACAACAA 57.554 34.783 5.29 0.00 38.89 2.83
52 53 5.643379 AATTCTGGCGAATACACAACAAT 57.357 34.783 5.29 0.00 38.89 2.71
53 54 5.643379 ATTCTGGCGAATACACAACAATT 57.357 34.783 3.35 0.00 38.07 2.32
54 55 5.446143 TTCTGGCGAATACACAACAATTT 57.554 34.783 0.00 0.00 0.00 1.82
55 56 6.561737 TTCTGGCGAATACACAACAATTTA 57.438 33.333 0.00 0.00 0.00 1.40
56 57 6.176975 TCTGGCGAATACACAACAATTTAG 57.823 37.500 0.00 0.00 0.00 1.85
57 58 5.703592 TCTGGCGAATACACAACAATTTAGT 59.296 36.000 0.00 0.00 0.00 2.24
58 59 6.874664 TCTGGCGAATACACAACAATTTAGTA 59.125 34.615 0.00 0.00 0.00 1.82
59 60 6.833839 TGGCGAATACACAACAATTTAGTAC 58.166 36.000 0.00 0.00 0.00 2.73
60 61 6.128227 TGGCGAATACACAACAATTTAGTACC 60.128 38.462 0.00 0.00 0.00 3.34
61 62 6.128227 GGCGAATACACAACAATTTAGTACCA 60.128 38.462 0.00 0.00 0.00 3.25
62 63 6.739550 GCGAATACACAACAATTTAGTACCAC 59.260 38.462 0.00 0.00 0.00 4.16
63 64 7.238571 CGAATACACAACAATTTAGTACCACC 58.761 38.462 0.00 0.00 0.00 4.61
64 65 7.118680 CGAATACACAACAATTTAGTACCACCT 59.881 37.037 0.00 0.00 0.00 4.00
65 66 7.916914 ATACACAACAATTTAGTACCACCTC 57.083 36.000 0.00 0.00 0.00 3.85
66 67 5.686753 ACACAACAATTTAGTACCACCTCA 58.313 37.500 0.00 0.00 0.00 3.86
67 68 5.763204 ACACAACAATTTAGTACCACCTCAG 59.237 40.000 0.00 0.00 0.00 3.35
68 69 5.995282 CACAACAATTTAGTACCACCTCAGA 59.005 40.000 0.00 0.00 0.00 3.27
69 70 6.655003 CACAACAATTTAGTACCACCTCAGAT 59.345 38.462 0.00 0.00 0.00 2.90
70 71 7.822334 CACAACAATTTAGTACCACCTCAGATA 59.178 37.037 0.00 0.00 0.00 1.98
71 72 8.041323 ACAACAATTTAGTACCACCTCAGATAG 58.959 37.037 0.00 0.00 0.00 2.08
97 98 6.663480 AAAAATTATTTTCGACGGTGAACG 57.337 33.333 3.23 0.00 40.66 3.95
98 99 5.626132 AAAAATTATTTTCGACGGTGAACGG 59.374 36.000 3.23 0.00 39.72 4.44
99 100 6.513066 AAAAATTATTTTCGACGGTGAACGGA 60.513 34.615 3.23 0.00 39.72 4.69
100 101 7.785772 AAAAATTATTTTCGACGGTGAACGGAT 60.786 33.333 3.23 0.00 39.72 4.18
126 127 2.774439 ATTGACGAAACACACCTTGC 57.226 45.000 0.00 0.00 0.00 4.01
127 128 1.745232 TTGACGAAACACACCTTGCT 58.255 45.000 0.00 0.00 0.00 3.91
128 129 1.745232 TGACGAAACACACCTTGCTT 58.255 45.000 0.00 0.00 0.00 3.91
129 130 2.088423 TGACGAAACACACCTTGCTTT 58.912 42.857 0.00 0.00 0.00 3.51
130 131 3.271729 TGACGAAACACACCTTGCTTTA 58.728 40.909 0.00 0.00 0.00 1.85
131 132 3.880490 TGACGAAACACACCTTGCTTTAT 59.120 39.130 0.00 0.00 0.00 1.40
132 133 4.336993 TGACGAAACACACCTTGCTTTATT 59.663 37.500 0.00 0.00 0.00 1.40
133 134 5.527951 TGACGAAACACACCTTGCTTTATTA 59.472 36.000 0.00 0.00 0.00 0.98
134 135 5.997385 ACGAAACACACCTTGCTTTATTAG 58.003 37.500 0.00 0.00 0.00 1.73
135 136 5.529800 ACGAAACACACCTTGCTTTATTAGT 59.470 36.000 0.00 0.00 0.00 2.24
136 137 6.707161 ACGAAACACACCTTGCTTTATTAGTA 59.293 34.615 0.00 0.00 0.00 1.82
137 138 7.227116 ACGAAACACACCTTGCTTTATTAGTAA 59.773 33.333 0.00 0.00 0.00 2.24
138 139 7.744715 CGAAACACACCTTGCTTTATTAGTAAG 59.255 37.037 0.00 0.00 43.75 2.34
148 149 8.802057 TTGCTTTATTAGTAAGGGGGTATAGA 57.198 34.615 0.00 0.00 0.00 1.98
149 150 8.984112 TGCTTTATTAGTAAGGGGGTATAGAT 57.016 34.615 0.00 0.00 0.00 1.98
185 186 7.607615 TGTTATTAGTCTATGTTACTCCCCC 57.392 40.000 0.00 0.00 0.00 5.40
203 204 4.937201 CCCCCTTCACAAAATATAAGGC 57.063 45.455 0.00 0.00 37.71 4.35
204 205 3.317993 CCCCCTTCACAAAATATAAGGCG 59.682 47.826 0.00 0.00 37.71 5.52
205 206 3.243401 CCCCTTCACAAAATATAAGGCGC 60.243 47.826 0.00 0.00 37.71 6.53
206 207 3.548014 CCCTTCACAAAATATAAGGCGCG 60.548 47.826 0.00 0.00 37.71 6.86
207 208 3.311322 CCTTCACAAAATATAAGGCGCGA 59.689 43.478 12.10 0.00 32.66 5.87
208 209 4.024048 CCTTCACAAAATATAAGGCGCGAT 60.024 41.667 12.10 0.00 32.66 4.58
209 210 5.493133 TTCACAAAATATAAGGCGCGATT 57.507 34.783 12.10 6.21 0.00 3.34
210 211 4.843147 TCACAAAATATAAGGCGCGATTG 58.157 39.130 12.10 2.58 0.00 2.67
211 212 4.572795 TCACAAAATATAAGGCGCGATTGA 59.427 37.500 12.10 0.00 0.00 2.57
212 213 4.670621 CACAAAATATAAGGCGCGATTGAC 59.329 41.667 12.10 0.00 0.00 3.18
213 214 4.574828 ACAAAATATAAGGCGCGATTGACT 59.425 37.500 12.10 0.00 0.00 3.41
214 215 5.065988 ACAAAATATAAGGCGCGATTGACTT 59.934 36.000 12.10 7.96 0.00 3.01
215 216 5.751243 AAATATAAGGCGCGATTGACTTT 57.249 34.783 12.10 0.00 0.00 2.66
216 217 4.732285 ATATAAGGCGCGATTGACTTTG 57.268 40.909 12.10 0.00 0.00 2.77
217 218 0.446222 TAAGGCGCGATTGACTTTGC 59.554 50.000 12.10 0.00 0.00 3.68
218 219 1.514678 AAGGCGCGATTGACTTTGCA 61.515 50.000 12.10 0.00 0.00 4.08
219 220 1.797537 GGCGCGATTGACTTTGCAC 60.798 57.895 12.10 0.00 0.00 4.57
220 221 2.139811 GCGCGATTGACTTTGCACG 61.140 57.895 12.10 0.00 0.00 5.34
221 222 1.509787 CGCGATTGACTTTGCACGG 60.510 57.895 0.00 0.00 0.00 4.94
222 223 1.574428 GCGATTGACTTTGCACGGT 59.426 52.632 0.00 0.00 0.00 4.83
223 224 0.452784 GCGATTGACTTTGCACGGTC 60.453 55.000 10.31 10.31 0.00 4.79
224 225 1.148310 CGATTGACTTTGCACGGTCT 58.852 50.000 16.08 1.16 34.01 3.85
225 226 1.531149 CGATTGACTTTGCACGGTCTT 59.469 47.619 16.08 6.80 34.01 3.01
226 227 2.032030 CGATTGACTTTGCACGGTCTTT 60.032 45.455 16.08 6.53 34.01 2.52
227 228 2.842208 TTGACTTTGCACGGTCTTTG 57.158 45.000 16.08 0.00 34.01 2.77
228 229 2.031258 TGACTTTGCACGGTCTTTGA 57.969 45.000 16.08 0.00 34.01 2.69
229 230 2.571212 TGACTTTGCACGGTCTTTGAT 58.429 42.857 16.08 0.00 34.01 2.57
230 231 2.290367 TGACTTTGCACGGTCTTTGATG 59.710 45.455 16.08 0.00 34.01 3.07
231 232 1.001378 ACTTTGCACGGTCTTTGATGC 60.001 47.619 0.00 0.00 38.59 3.91
232 233 1.001487 CTTTGCACGGTCTTTGATGCA 60.001 47.619 0.00 0.00 45.94 3.96
233 234 1.246649 TTGCACGGTCTTTGATGCAT 58.753 45.000 0.00 0.00 46.75 3.96
234 235 0.522626 TGCACGGTCTTTGATGCATG 59.477 50.000 2.46 0.00 42.92 4.06
235 236 0.804364 GCACGGTCTTTGATGCATGA 59.196 50.000 2.46 0.00 38.00 3.07
236 237 1.466360 GCACGGTCTTTGATGCATGAC 60.466 52.381 2.46 4.99 38.00 3.06
237 238 2.079158 CACGGTCTTTGATGCATGACT 58.921 47.619 2.46 0.00 0.00 3.41
238 239 2.485426 CACGGTCTTTGATGCATGACTT 59.515 45.455 2.46 0.00 0.00 3.01
239 240 3.058016 CACGGTCTTTGATGCATGACTTT 60.058 43.478 2.46 0.00 0.00 2.66
240 241 3.058016 ACGGTCTTTGATGCATGACTTTG 60.058 43.478 2.46 2.79 0.00 2.77
241 242 3.189080 CGGTCTTTGATGCATGACTTTGA 59.811 43.478 2.46 0.00 0.00 2.69
242 243 4.142534 CGGTCTTTGATGCATGACTTTGAT 60.143 41.667 2.46 0.00 0.00 2.57
243 244 5.338365 GGTCTTTGATGCATGACTTTGATC 58.662 41.667 2.46 0.00 0.00 2.92
244 245 5.106038 GGTCTTTGATGCATGACTTTGATCA 60.106 40.000 2.46 0.00 0.00 2.92
245 246 6.405508 GGTCTTTGATGCATGACTTTGATCAT 60.406 38.462 2.46 0.00 40.03 2.45
246 247 7.033791 GTCTTTGATGCATGACTTTGATCATT 58.966 34.615 2.46 0.00 37.20 2.57
247 248 8.186163 GTCTTTGATGCATGACTTTGATCATTA 58.814 33.333 2.46 0.00 37.20 1.90
248 249 8.741841 TCTTTGATGCATGACTTTGATCATTAA 58.258 29.630 2.46 0.00 37.20 1.40
249 250 9.529325 CTTTGATGCATGACTTTGATCATTAAT 57.471 29.630 2.46 0.00 37.20 1.40
374 375 8.888716 ACATACAATGCGTTAAAATCATAGTCA 58.111 29.630 0.00 0.00 0.00 3.41
375 376 9.715123 CATACAATGCGTTAAAATCATAGTCAA 57.285 29.630 0.00 0.00 0.00 3.18
377 378 8.673626 ACAATGCGTTAAAATCATAGTCAAAG 57.326 30.769 0.00 0.00 0.00 2.77
378 379 8.296713 ACAATGCGTTAAAATCATAGTCAAAGT 58.703 29.630 0.00 0.00 0.00 2.66
379 380 9.128107 CAATGCGTTAAAATCATAGTCAAAGTT 57.872 29.630 0.00 0.00 0.00 2.66
382 383 9.767684 TGCGTTAAAATCATAGTCAAAGTTATG 57.232 29.630 0.00 0.00 0.00 1.90
383 384 8.734030 GCGTTAAAATCATAGTCAAAGTTATGC 58.266 33.333 0.00 0.00 0.00 3.14
384 385 9.767684 CGTTAAAATCATAGTCAAAGTTATGCA 57.232 29.630 0.00 0.00 0.00 3.96
388 389 9.979578 AAAATCATAGTCAAAGTTATGCAACAA 57.020 25.926 0.00 0.00 37.10 2.83
389 390 9.979578 AAATCATAGTCAAAGTTATGCAACAAA 57.020 25.926 0.00 0.00 37.10 2.83
390 391 9.630098 AATCATAGTCAAAGTTATGCAACAAAG 57.370 29.630 0.00 0.00 37.10 2.77
391 392 7.592938 TCATAGTCAAAGTTATGCAACAAAGG 58.407 34.615 0.00 0.00 37.10 3.11
392 393 5.852282 AGTCAAAGTTATGCAACAAAGGT 57.148 34.783 0.00 0.00 37.10 3.50
393 394 5.831997 AGTCAAAGTTATGCAACAAAGGTC 58.168 37.500 0.00 0.00 37.10 3.85
394 395 5.359576 AGTCAAAGTTATGCAACAAAGGTCA 59.640 36.000 0.00 0.00 37.10 4.02
395 396 6.039616 GTCAAAGTTATGCAACAAAGGTCAA 58.960 36.000 0.00 0.00 37.10 3.18
396 397 6.533367 GTCAAAGTTATGCAACAAAGGTCAAA 59.467 34.615 0.00 0.00 37.10 2.69
397 398 7.064016 GTCAAAGTTATGCAACAAAGGTCAAAA 59.936 33.333 0.00 0.00 37.10 2.44
398 399 7.604164 TCAAAGTTATGCAACAAAGGTCAAAAA 59.396 29.630 0.00 0.00 37.10 1.94
413 414 2.641197 AAAAAGTCAATCCGCGCCT 58.359 47.368 0.00 0.00 0.00 5.52
414 415 0.958822 AAAAAGTCAATCCGCGCCTT 59.041 45.000 0.00 0.00 0.00 4.35
415 416 1.816074 AAAAGTCAATCCGCGCCTTA 58.184 45.000 0.00 0.00 0.00 2.69
416 417 2.038387 AAAGTCAATCCGCGCCTTAT 57.962 45.000 0.00 0.00 0.00 1.73
417 418 2.902705 AAGTCAATCCGCGCCTTATA 57.097 45.000 0.00 0.00 0.00 0.98
418 419 3.402628 AAGTCAATCCGCGCCTTATAT 57.597 42.857 0.00 0.00 0.00 0.86
419 420 3.402628 AGTCAATCCGCGCCTTATATT 57.597 42.857 0.00 0.00 0.00 1.28
420 421 3.740115 AGTCAATCCGCGCCTTATATTT 58.260 40.909 0.00 0.00 0.00 1.40
421 422 4.134563 AGTCAATCCGCGCCTTATATTTT 58.865 39.130 0.00 0.00 0.00 1.82
422 423 4.024048 AGTCAATCCGCGCCTTATATTTTG 60.024 41.667 0.00 0.00 0.00 2.44
423 424 3.252215 TCAATCCGCGCCTTATATTTTGG 59.748 43.478 0.00 0.00 0.00 3.28
424 425 1.600023 TCCGCGCCTTATATTTTGGG 58.400 50.000 0.00 0.00 0.00 4.12
425 426 1.141254 TCCGCGCCTTATATTTTGGGA 59.859 47.619 0.00 0.00 0.00 4.37
426 427 1.950909 CCGCGCCTTATATTTTGGGAA 59.049 47.619 0.00 0.00 0.00 3.97
427 428 2.031157 CCGCGCCTTATATTTTGGGAAG 60.031 50.000 0.00 0.00 0.00 3.46
428 429 2.031157 CGCGCCTTATATTTTGGGAAGG 60.031 50.000 0.00 0.00 41.26 3.46
429 430 2.296190 GCGCCTTATATTTTGGGAAGGG 59.704 50.000 0.00 0.00 39.14 3.95
430 431 2.890945 CGCCTTATATTTTGGGAAGGGG 59.109 50.000 2.66 2.66 43.11 4.79
431 432 3.239449 GCCTTATATTTTGGGAAGGGGG 58.761 50.000 1.95 0.00 39.14 5.40
480 481 5.239359 ACATATGTGTGATGTCATGCAAC 57.761 39.130 7.78 0.00 37.14 4.17
484 485 2.950975 TGTGTGATGTCATGCAACACTT 59.049 40.909 21.63 2.52 46.81 3.16
485 486 3.380954 TGTGTGATGTCATGCAACACTTT 59.619 39.130 21.63 0.00 46.81 2.66
486 487 4.142204 TGTGTGATGTCATGCAACACTTTT 60.142 37.500 21.63 0.00 46.81 2.27
538 539 8.150296 TCTTGATATGTGTGATGTTACCCATAG 58.850 37.037 0.00 0.00 32.56 2.23
548 549 7.093068 TGTGATGTTACCCATAGTGTGAGTAAT 60.093 37.037 0.00 0.00 32.56 1.89
619 620 9.988815 AAATATCATCTCTTTTGCGTAGATACT 57.011 29.630 0.00 0.00 0.00 2.12
621 622 7.938563 ATCATCTCTTTTGCGTAGATACTTC 57.061 36.000 0.00 0.00 0.00 3.01
622 623 6.273825 TCATCTCTTTTGCGTAGATACTTCC 58.726 40.000 0.00 0.00 0.00 3.46
623 624 5.654603 TCTCTTTTGCGTAGATACTTCCA 57.345 39.130 0.00 0.00 0.00 3.53
624 625 5.408356 TCTCTTTTGCGTAGATACTTCCAC 58.592 41.667 0.00 0.00 0.00 4.02
626 627 6.376299 TCTCTTTTGCGTAGATACTTCCACTA 59.624 38.462 0.00 0.00 0.00 2.74
628 629 6.978659 TCTTTTGCGTAGATACTTCCACTATG 59.021 38.462 0.00 0.00 0.00 2.23
629 630 5.847111 TTGCGTAGATACTTCCACTATGT 57.153 39.130 0.00 0.00 0.00 2.29
631 632 6.947644 TGCGTAGATACTTCCACTATGTTA 57.052 37.500 0.00 0.00 0.00 2.41
632 633 6.732154 TGCGTAGATACTTCCACTATGTTAC 58.268 40.000 0.00 0.00 0.00 2.50
633 634 6.319405 TGCGTAGATACTTCCACTATGTTACA 59.681 38.462 0.00 0.00 0.00 2.41
634 635 6.636044 GCGTAGATACTTCCACTATGTTACAC 59.364 42.308 0.00 0.00 0.00 2.90
635 636 7.680350 GCGTAGATACTTCCACTATGTTACACA 60.680 40.741 0.00 0.00 0.00 3.72
637 638 9.865321 GTAGATACTTCCACTATGTTACACAAA 57.135 33.333 0.00 0.00 0.00 2.83
638 639 8.773404 AGATACTTCCACTATGTTACACAAAC 57.227 34.615 0.00 0.00 38.67 2.93
639 640 8.594550 AGATACTTCCACTATGTTACACAAACT 58.405 33.333 0.00 0.00 38.99 2.66
640 641 9.865321 GATACTTCCACTATGTTACACAAACTA 57.135 33.333 0.00 0.00 38.99 2.24
642 643 8.967664 ACTTCCACTATGTTACACAAACTAAA 57.032 30.769 0.00 0.00 38.99 1.85
643 644 9.569122 ACTTCCACTATGTTACACAAACTAAAT 57.431 29.630 0.00 0.00 38.99 1.40
833 834 7.817641 TCCTGAGTTGATACACATATCGATAC 58.182 38.462 7.41 0.00 40.26 2.24
857 861 5.200454 GCATTCTATAAATGTCACGCACAG 58.800 41.667 0.30 0.00 38.85 3.66
930 941 6.012745 ACCCCTCATTTGCATTATTATCCTC 58.987 40.000 0.00 0.00 0.00 3.71
987 998 1.518929 GATGTCGCAGCAGAACGTATC 59.481 52.381 0.00 0.00 0.00 2.24
1032 1043 1.493311 GTGCTTCTCCGCTGTTTCG 59.507 57.895 0.00 0.00 0.00 3.46
1983 2062 1.463553 CCCAGAAACACAACCTGGCC 61.464 60.000 0.00 0.00 44.56 5.36
2220 2304 2.358615 GACGGCCTGCACATGACA 60.359 61.111 0.00 0.00 0.00 3.58
2452 3810 4.349930 ACCCTTACAGGCTTTTTCTCTGTA 59.650 41.667 0.00 0.00 41.37 2.74
2498 3861 6.367695 GCCCAGTAGCGAAACAAATAAAATTT 59.632 34.615 0.00 0.00 0.00 1.82
2499 3862 7.095397 GCCCAGTAGCGAAACAAATAAAATTTT 60.095 33.333 8.75 8.75 0.00 1.82
2500 3863 8.769891 CCCAGTAGCGAAACAAATAAAATTTTT 58.230 29.630 9.06 0.00 0.00 1.94
2792 4156 5.639082 GGCATTATAGGTAAATTTGCCATGC 59.361 40.000 26.50 26.50 40.65 4.06
3066 4432 4.941873 TGCAAATCATGGCAAAAATGCATA 59.058 33.333 0.00 0.00 37.61 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.403137 CATGGGCCGCACGTTGTG 62.403 66.667 0.00 0.00 36.51 3.33
8 9 3.538785 TACATGGGCCGCACGTTGT 62.539 57.895 0.00 6.31 0.00 3.32
9 10 2.744318 TACATGGGCCGCACGTTG 60.744 61.111 0.00 0.00 0.00 4.10
10 11 2.744709 GTACATGGGCCGCACGTT 60.745 61.111 0.00 0.00 0.00 3.99
12 13 4.805231 TCGTACATGGGCCGCACG 62.805 66.667 11.35 11.35 0.00 5.34
13 14 1.373590 ATTTCGTACATGGGCCGCAC 61.374 55.000 0.00 0.00 0.00 5.34
14 15 0.678366 AATTTCGTACATGGGCCGCA 60.678 50.000 0.00 0.00 0.00 5.69
15 16 0.028902 GAATTTCGTACATGGGCCGC 59.971 55.000 0.00 0.00 0.00 6.53
16 17 1.330521 CAGAATTTCGTACATGGGCCG 59.669 52.381 0.00 0.00 0.00 6.13
17 18 1.676006 CCAGAATTTCGTACATGGGCC 59.324 52.381 0.00 0.00 0.00 5.80
18 19 1.065551 GCCAGAATTTCGTACATGGGC 59.934 52.381 0.00 0.00 0.00 5.36
19 20 1.330521 CGCCAGAATTTCGTACATGGG 59.669 52.381 0.00 0.00 0.00 4.00
20 21 2.276201 TCGCCAGAATTTCGTACATGG 58.724 47.619 0.00 0.00 0.00 3.66
21 22 4.536364 ATTCGCCAGAATTTCGTACATG 57.464 40.909 0.00 0.00 44.11 3.21
22 23 5.006358 GTGTATTCGCCAGAATTTCGTACAT 59.994 40.000 0.00 0.00 44.11 2.29
23 24 4.327898 GTGTATTCGCCAGAATTTCGTACA 59.672 41.667 0.00 0.00 44.11 2.90
24 25 4.327898 TGTGTATTCGCCAGAATTTCGTAC 59.672 41.667 0.00 0.00 44.11 3.67
25 26 4.496360 TGTGTATTCGCCAGAATTTCGTA 58.504 39.130 0.00 0.00 44.11 3.43
26 27 3.331150 TGTGTATTCGCCAGAATTTCGT 58.669 40.909 0.00 0.00 44.11 3.85
27 28 4.088648 GTTGTGTATTCGCCAGAATTTCG 58.911 43.478 0.00 0.00 44.11 3.46
28 29 5.041951 TGTTGTGTATTCGCCAGAATTTC 57.958 39.130 0.00 0.00 44.11 2.17
29 30 5.446143 TTGTTGTGTATTCGCCAGAATTT 57.554 34.783 0.00 0.00 44.11 1.82
30 31 5.643379 ATTGTTGTGTATTCGCCAGAATT 57.357 34.783 0.00 0.00 44.11 2.17
32 33 5.446143 AAATTGTTGTGTATTCGCCAGAA 57.554 34.783 0.00 0.00 41.13 3.02
33 34 5.703592 ACTAAATTGTTGTGTATTCGCCAGA 59.296 36.000 0.00 0.00 0.00 3.86
34 35 5.938322 ACTAAATTGTTGTGTATTCGCCAG 58.062 37.500 0.00 0.00 0.00 4.85
35 36 5.950758 ACTAAATTGTTGTGTATTCGCCA 57.049 34.783 0.00 0.00 0.00 5.69
36 37 6.128227 TGGTACTAAATTGTTGTGTATTCGCC 60.128 38.462 0.00 0.00 0.00 5.54
37 38 6.739550 GTGGTACTAAATTGTTGTGTATTCGC 59.260 38.462 0.00 0.00 0.00 4.70
38 39 7.118680 AGGTGGTACTAAATTGTTGTGTATTCG 59.881 37.037 0.00 0.00 0.00 3.34
39 40 8.331730 AGGTGGTACTAAATTGTTGTGTATTC 57.668 34.615 0.00 0.00 0.00 1.75
40 41 7.940137 TGAGGTGGTACTAAATTGTTGTGTATT 59.060 33.333 0.00 0.00 0.00 1.89
41 42 7.455058 TGAGGTGGTACTAAATTGTTGTGTAT 58.545 34.615 0.00 0.00 0.00 2.29
42 43 6.828788 TGAGGTGGTACTAAATTGTTGTGTA 58.171 36.000 0.00 0.00 0.00 2.90
43 44 5.686753 TGAGGTGGTACTAAATTGTTGTGT 58.313 37.500 0.00 0.00 0.00 3.72
44 45 5.995282 TCTGAGGTGGTACTAAATTGTTGTG 59.005 40.000 0.00 0.00 0.00 3.33
45 46 6.182507 TCTGAGGTGGTACTAAATTGTTGT 57.817 37.500 0.00 0.00 0.00 3.32
46 47 7.495934 CCTATCTGAGGTGGTACTAAATTGTTG 59.504 40.741 0.00 0.00 40.98 3.33
47 48 7.402071 TCCTATCTGAGGTGGTACTAAATTGTT 59.598 37.037 0.00 0.00 46.76 2.83
48 49 6.901300 TCCTATCTGAGGTGGTACTAAATTGT 59.099 38.462 0.00 0.00 46.76 2.71
49 50 7.361457 TCCTATCTGAGGTGGTACTAAATTG 57.639 40.000 0.00 0.00 46.76 2.32
50 51 7.989947 TTCCTATCTGAGGTGGTACTAAATT 57.010 36.000 0.00 0.00 46.76 1.82
51 52 7.989947 TTTCCTATCTGAGGTGGTACTAAAT 57.010 36.000 0.00 0.00 46.76 1.40
52 53 7.801893 TTTTCCTATCTGAGGTGGTACTAAA 57.198 36.000 0.00 0.00 46.76 1.85
53 54 7.801893 TTTTTCCTATCTGAGGTGGTACTAA 57.198 36.000 0.00 0.00 46.76 2.24
74 75 5.626132 CCGTTCACCGTCGAAAATAATTTTT 59.374 36.000 0.00 0.00 34.58 1.94
75 76 5.049543 TCCGTTCACCGTCGAAAATAATTTT 60.050 36.000 0.00 0.00 32.72 1.82
76 77 4.451774 TCCGTTCACCGTCGAAAATAATTT 59.548 37.500 0.00 0.00 33.66 1.82
77 78 3.995705 TCCGTTCACCGTCGAAAATAATT 59.004 39.130 0.00 0.00 33.66 1.40
78 79 3.587923 TCCGTTCACCGTCGAAAATAAT 58.412 40.909 0.00 0.00 33.66 1.28
79 80 3.023946 TCCGTTCACCGTCGAAAATAA 57.976 42.857 0.00 0.00 33.66 1.40
80 81 2.721274 TCCGTTCACCGTCGAAAATA 57.279 45.000 0.00 0.00 33.66 1.40
81 82 1.730064 CATCCGTTCACCGTCGAAAAT 59.270 47.619 0.00 0.00 33.66 1.82
82 83 1.141645 CATCCGTTCACCGTCGAAAA 58.858 50.000 0.00 0.00 33.66 2.29
83 84 0.314618 TCATCCGTTCACCGTCGAAA 59.685 50.000 0.00 0.00 33.66 3.46
84 85 0.314618 TTCATCCGTTCACCGTCGAA 59.685 50.000 0.00 0.00 33.66 3.71
85 86 0.314618 TTTCATCCGTTCACCGTCGA 59.685 50.000 0.00 0.00 33.66 4.20
86 87 1.141645 TTTTCATCCGTTCACCGTCG 58.858 50.000 0.00 0.00 33.66 5.12
103 104 4.328712 GCAAGGTGTGTTTCGTCAATTTTT 59.671 37.500 0.00 0.00 0.00 1.94
104 105 3.862845 GCAAGGTGTGTTTCGTCAATTTT 59.137 39.130 0.00 0.00 0.00 1.82
105 106 3.130340 AGCAAGGTGTGTTTCGTCAATTT 59.870 39.130 0.00 0.00 0.00 1.82
106 107 2.687935 AGCAAGGTGTGTTTCGTCAATT 59.312 40.909 0.00 0.00 0.00 2.32
107 108 2.297701 AGCAAGGTGTGTTTCGTCAAT 58.702 42.857 0.00 0.00 0.00 2.57
108 109 1.745232 AGCAAGGTGTGTTTCGTCAA 58.255 45.000 0.00 0.00 0.00 3.18
109 110 1.745232 AAGCAAGGTGTGTTTCGTCA 58.255 45.000 0.00 0.00 0.00 4.35
110 111 2.844122 AAAGCAAGGTGTGTTTCGTC 57.156 45.000 0.00 0.00 29.15 4.20
111 112 4.911514 AATAAAGCAAGGTGTGTTTCGT 57.088 36.364 0.00 0.00 29.15 3.85
112 113 5.997385 ACTAATAAAGCAAGGTGTGTTTCG 58.003 37.500 0.00 0.00 29.15 3.46
113 114 8.021396 CCTTACTAATAAAGCAAGGTGTGTTTC 58.979 37.037 0.00 0.00 42.03 2.78
114 115 7.039993 CCCTTACTAATAAAGCAAGGTGTGTTT 60.040 37.037 3.88 0.00 44.54 2.83
115 116 6.433093 CCCTTACTAATAAAGCAAGGTGTGTT 59.567 38.462 3.88 0.00 44.54 3.32
116 117 5.944007 CCCTTACTAATAAAGCAAGGTGTGT 59.056 40.000 3.88 0.00 44.54 3.72
117 118 5.357032 CCCCTTACTAATAAAGCAAGGTGTG 59.643 44.000 3.88 0.00 44.54 3.82
118 119 5.506708 CCCCTTACTAATAAAGCAAGGTGT 58.493 41.667 3.88 0.00 44.54 4.16
119 120 4.887655 CCCCCTTACTAATAAAGCAAGGTG 59.112 45.833 3.88 0.00 44.54 4.00
120 121 4.542931 ACCCCCTTACTAATAAAGCAAGGT 59.457 41.667 3.88 0.00 44.54 3.50
121 122 5.125367 ACCCCCTTACTAATAAAGCAAGG 57.875 43.478 0.00 0.00 45.31 3.61
122 123 8.877195 TCTATACCCCCTTACTAATAAAGCAAG 58.123 37.037 0.00 0.00 0.00 4.01
123 124 8.802057 TCTATACCCCCTTACTAATAAAGCAA 57.198 34.615 0.00 0.00 0.00 3.91
124 125 8.984112 ATCTATACCCCCTTACTAATAAAGCA 57.016 34.615 0.00 0.00 0.00 3.91
159 160 9.317827 GGGGGAGTAACATAGACTAATAACATA 57.682 37.037 0.00 0.00 0.00 2.29
160 161 8.203681 GGGGGAGTAACATAGACTAATAACAT 57.796 38.462 0.00 0.00 0.00 2.71
161 162 7.607615 GGGGGAGTAACATAGACTAATAACA 57.392 40.000 0.00 0.00 0.00 2.41
182 183 3.317993 CGCCTTATATTTTGTGAAGGGGG 59.682 47.826 8.31 0.00 44.27 5.40
183 184 4.568152 CGCCTTATATTTTGTGAAGGGG 57.432 45.455 2.66 2.66 43.11 4.79
184 185 3.548014 CGCGCCTTATATTTTGTGAAGGG 60.548 47.826 0.00 0.00 39.14 3.95
185 186 3.311322 TCGCGCCTTATATTTTGTGAAGG 59.689 43.478 0.00 0.00 41.26 3.46
186 187 4.530094 TCGCGCCTTATATTTTGTGAAG 57.470 40.909 0.00 0.00 0.00 3.02
187 188 5.065346 TCAATCGCGCCTTATATTTTGTGAA 59.935 36.000 0.00 0.00 0.00 3.18
188 189 4.572795 TCAATCGCGCCTTATATTTTGTGA 59.427 37.500 0.00 0.00 0.00 3.58
189 190 4.670621 GTCAATCGCGCCTTATATTTTGTG 59.329 41.667 0.00 0.00 0.00 3.33
190 191 4.574828 AGTCAATCGCGCCTTATATTTTGT 59.425 37.500 0.00 0.00 0.00 2.83
191 192 5.095691 AGTCAATCGCGCCTTATATTTTG 57.904 39.130 0.00 0.00 0.00 2.44
192 193 5.751243 AAGTCAATCGCGCCTTATATTTT 57.249 34.783 0.00 0.00 0.00 1.82
193 194 5.510671 CAAAGTCAATCGCGCCTTATATTT 58.489 37.500 0.00 0.00 0.00 1.40
194 195 4.554723 GCAAAGTCAATCGCGCCTTATATT 60.555 41.667 0.00 0.00 0.00 1.28
195 196 3.058914 GCAAAGTCAATCGCGCCTTATAT 60.059 43.478 0.00 0.00 0.00 0.86
196 197 2.286833 GCAAAGTCAATCGCGCCTTATA 59.713 45.455 0.00 0.00 0.00 0.98
197 198 1.064060 GCAAAGTCAATCGCGCCTTAT 59.936 47.619 0.00 0.00 0.00 1.73
198 199 0.446222 GCAAAGTCAATCGCGCCTTA 59.554 50.000 0.00 0.00 0.00 2.69
199 200 1.210155 GCAAAGTCAATCGCGCCTT 59.790 52.632 0.00 0.00 0.00 4.35
200 201 1.965930 TGCAAAGTCAATCGCGCCT 60.966 52.632 0.00 0.00 0.00 5.52
201 202 1.797537 GTGCAAAGTCAATCGCGCC 60.798 57.895 0.00 0.00 0.00 6.53
202 203 2.139811 CGTGCAAAGTCAATCGCGC 61.140 57.895 0.00 0.00 0.00 6.86
203 204 1.509787 CCGTGCAAAGTCAATCGCG 60.510 57.895 0.00 0.00 0.00 5.87
204 205 0.452784 GACCGTGCAAAGTCAATCGC 60.453 55.000 11.50 0.00 33.08 4.58
205 206 1.148310 AGACCGTGCAAAGTCAATCG 58.852 50.000 17.12 1.54 35.38 3.34
206 207 3.003275 TCAAAGACCGTGCAAAGTCAATC 59.997 43.478 17.12 0.00 35.38 2.67
207 208 2.948979 TCAAAGACCGTGCAAAGTCAAT 59.051 40.909 17.12 5.35 35.38 2.57
208 209 2.360844 TCAAAGACCGTGCAAAGTCAA 58.639 42.857 17.12 0.64 35.38 3.18
209 210 2.031258 TCAAAGACCGTGCAAAGTCA 57.969 45.000 17.12 0.00 35.38 3.41
210 211 2.918131 GCATCAAAGACCGTGCAAAGTC 60.918 50.000 8.92 8.92 37.52 3.01
211 212 1.001378 GCATCAAAGACCGTGCAAAGT 60.001 47.619 0.00 0.00 37.52 2.66
212 213 1.001487 TGCATCAAAGACCGTGCAAAG 60.001 47.619 0.00 0.00 43.83 2.77
213 214 1.028130 TGCATCAAAGACCGTGCAAA 58.972 45.000 0.00 0.00 43.83 3.68
214 215 2.712984 TGCATCAAAGACCGTGCAA 58.287 47.368 0.00 0.00 43.83 4.08
215 216 4.471761 TGCATCAAAGACCGTGCA 57.528 50.000 0.00 0.00 44.50 4.57
216 217 0.804364 TCATGCATCAAAGACCGTGC 59.196 50.000 0.00 0.00 38.05 5.34
217 218 2.079158 AGTCATGCATCAAAGACCGTG 58.921 47.619 10.40 0.00 0.00 4.94
218 219 2.479566 AGTCATGCATCAAAGACCGT 57.520 45.000 10.40 0.00 0.00 4.83
219 220 3.189080 TCAAAGTCATGCATCAAAGACCG 59.811 43.478 10.40 2.15 0.00 4.79
220 221 4.771590 TCAAAGTCATGCATCAAAGACC 57.228 40.909 10.40 0.00 0.00 3.85
221 222 5.946298 TGATCAAAGTCATGCATCAAAGAC 58.054 37.500 0.00 0.88 0.00 3.01
222 223 6.769134 ATGATCAAAGTCATGCATCAAAGA 57.231 33.333 0.00 0.00 37.44 2.52
223 224 8.920509 TTAATGATCAAAGTCATGCATCAAAG 57.079 30.769 0.00 0.00 38.76 2.77
348 349 8.888716 TGACTATGATTTTAACGCATTGTATGT 58.111 29.630 0.00 0.00 30.36 2.29
349 350 9.715123 TTGACTATGATTTTAACGCATTGTATG 57.285 29.630 0.00 0.00 30.36 2.39
351 352 9.767684 CTTTGACTATGATTTTAACGCATTGTA 57.232 29.630 0.00 0.00 30.36 2.41
352 353 8.296713 ACTTTGACTATGATTTTAACGCATTGT 58.703 29.630 0.00 0.00 32.28 2.71
353 354 8.673626 ACTTTGACTATGATTTTAACGCATTG 57.326 30.769 0.00 0.00 0.00 2.82
356 357 9.767684 CATAACTTTGACTATGATTTTAACGCA 57.232 29.630 0.00 0.00 0.00 5.24
357 358 8.734030 GCATAACTTTGACTATGATTTTAACGC 58.266 33.333 0.00 0.00 0.00 4.84
358 359 9.767684 TGCATAACTTTGACTATGATTTTAACG 57.232 29.630 0.00 0.00 0.00 3.18
362 363 9.979578 TTGTTGCATAACTTTGACTATGATTTT 57.020 25.926 0.00 0.00 37.68 1.82
363 364 9.979578 TTTGTTGCATAACTTTGACTATGATTT 57.020 25.926 0.00 0.00 37.68 2.17
364 365 9.630098 CTTTGTTGCATAACTTTGACTATGATT 57.370 29.630 0.00 0.00 37.68 2.57
365 366 8.246180 CCTTTGTTGCATAACTTTGACTATGAT 58.754 33.333 0.00 0.00 37.68 2.45
366 367 7.230510 ACCTTTGTTGCATAACTTTGACTATGA 59.769 33.333 0.00 0.00 37.68 2.15
367 368 7.370383 ACCTTTGTTGCATAACTTTGACTATG 58.630 34.615 0.00 0.00 37.68 2.23
368 369 7.230510 TGACCTTTGTTGCATAACTTTGACTAT 59.769 33.333 0.00 0.00 37.68 2.12
369 370 6.544197 TGACCTTTGTTGCATAACTTTGACTA 59.456 34.615 0.00 0.00 37.68 2.59
370 371 5.359576 TGACCTTTGTTGCATAACTTTGACT 59.640 36.000 0.00 0.00 37.68 3.41
371 372 5.587289 TGACCTTTGTTGCATAACTTTGAC 58.413 37.500 0.00 0.00 37.68 3.18
372 373 5.843673 TGACCTTTGTTGCATAACTTTGA 57.156 34.783 0.00 0.00 37.68 2.69
373 374 6.900568 TTTGACCTTTGTTGCATAACTTTG 57.099 33.333 0.00 0.00 37.68 2.77
374 375 7.913674 TTTTTGACCTTTGTTGCATAACTTT 57.086 28.000 0.00 0.00 37.68 2.66
395 396 0.958822 AAGGCGCGGATTGACTTTTT 59.041 45.000 8.83 0.00 0.00 1.94
396 397 1.816074 TAAGGCGCGGATTGACTTTT 58.184 45.000 8.83 0.00 0.00 2.27
397 398 2.038387 ATAAGGCGCGGATTGACTTT 57.962 45.000 8.83 0.00 0.00 2.66
398 399 2.902705 TATAAGGCGCGGATTGACTT 57.097 45.000 8.83 0.00 0.00 3.01
399 400 3.402628 AATATAAGGCGCGGATTGACT 57.597 42.857 8.83 0.00 0.00 3.41
400 401 4.219033 CAAAATATAAGGCGCGGATTGAC 58.781 43.478 8.83 0.00 0.00 3.18
401 402 3.252215 CCAAAATATAAGGCGCGGATTGA 59.748 43.478 8.83 0.00 0.00 2.57
402 403 3.564511 CCAAAATATAAGGCGCGGATTG 58.435 45.455 8.83 0.00 0.00 2.67
403 404 2.556622 CCCAAAATATAAGGCGCGGATT 59.443 45.455 8.83 0.00 0.00 3.01
404 405 2.159382 CCCAAAATATAAGGCGCGGAT 58.841 47.619 8.83 0.00 0.00 4.18
405 406 1.141254 TCCCAAAATATAAGGCGCGGA 59.859 47.619 8.83 0.00 0.00 5.54
406 407 1.600023 TCCCAAAATATAAGGCGCGG 58.400 50.000 8.83 0.00 0.00 6.46
407 408 2.031157 CCTTCCCAAAATATAAGGCGCG 60.031 50.000 0.00 0.00 32.66 6.86
408 409 2.296190 CCCTTCCCAAAATATAAGGCGC 59.704 50.000 0.00 0.00 37.71 6.53
409 410 2.890945 CCCCTTCCCAAAATATAAGGCG 59.109 50.000 0.00 0.00 37.71 5.52
410 411 3.239449 CCCCCTTCCCAAAATATAAGGC 58.761 50.000 0.00 0.00 37.71 4.35
428 429 7.899709 TCTTCATTATAGAGGTAATACTCCCCC 59.100 40.741 0.00 0.00 38.26 5.40
429 430 8.896722 TCTTCATTATAGAGGTAATACTCCCC 57.103 38.462 0.00 0.00 38.26 4.81
430 431 9.536510 ACTCTTCATTATAGAGGTAATACTCCC 57.463 37.037 0.00 0.00 42.73 4.30
448 449 8.260114 TGACATCACACATATGTTACTCTTCAT 58.740 33.333 5.37 0.00 37.69 2.57
451 452 7.011763 GCATGACATCACACATATGTTACTCTT 59.988 37.037 5.37 0.00 37.69 2.85
452 453 6.481313 GCATGACATCACACATATGTTACTCT 59.519 38.462 5.37 0.00 37.69 3.24
508 509 9.337396 GGGTAACATCACACATATCAAGATAAA 57.663 33.333 0.00 0.00 39.74 1.40
517 518 6.992123 CACACTATGGGTAACATCACACATAT 59.008 38.462 0.00 0.00 42.44 1.78
593 594 9.988815 AGTATCTACGCAAAAGAGATGATATTT 57.011 29.630 0.00 0.00 32.27 1.40
595 596 9.632807 GAAGTATCTACGCAAAAGAGATGATAT 57.367 33.333 0.00 0.00 32.27 1.63
596 597 8.082852 GGAAGTATCTACGCAAAAGAGATGATA 58.917 37.037 0.00 0.00 32.27 2.15
604 605 6.757010 ACATAGTGGAAGTATCTACGCAAAAG 59.243 38.462 0.00 0.00 41.56 2.27
647 648 8.857098 TCCATAGTGGAAGTAATATACTCACAC 58.143 37.037 12.72 12.72 45.00 3.82
833 834 4.203828 GTGCGTGACATTTATAGAATGCG 58.796 43.478 0.00 0.00 0.00 4.73
857 861 5.180117 GCACTCCATAACATGATGTGGTATC 59.820 44.000 16.60 3.85 38.68 2.24
930 941 6.183361 TGGTATCCTTTTATAGAACTTCCCGG 60.183 42.308 0.00 0.00 0.00 5.73
987 998 2.304180 ACTCCCCATGTCTGAGAAACAG 59.696 50.000 9.56 0.00 46.97 3.16
1032 1043 4.295119 ACGACGGCAGACACACCC 62.295 66.667 0.00 0.00 0.00 4.61
2015 2094 0.744771 GATCTTGACGCCAGGGTTCC 60.745 60.000 0.00 0.00 0.00 3.62
2220 2304 3.963428 ACAATCTTGTACGCCTTCTCT 57.037 42.857 0.00 0.00 40.16 3.10
2384 3741 5.068198 TGTGTGGGTTCTAGTACCGAATATC 59.932 44.000 11.95 0.00 39.18 1.63
2500 3863 9.364989 GGCAAAAGCTGTATTTTATTTATCACA 57.635 29.630 0.00 0.00 31.29 3.58
2732 4096 4.451629 TTACCTCTTTCTTCTGCTACGG 57.548 45.455 0.00 0.00 0.00 4.02
2792 4156 4.883006 CCATGGCAATTTTCCCTTTATTGG 59.117 41.667 0.00 0.00 31.54 3.16
2864 4228 7.416664 GCCAGGACATGTTAATTACAATGACAT 60.417 37.037 0.00 4.32 40.89 3.06
2865 4229 6.127758 GCCAGGACATGTTAATTACAATGACA 60.128 38.462 0.00 2.32 40.89 3.58
2866 4230 6.127758 TGCCAGGACATGTTAATTACAATGAC 60.128 38.462 0.00 6.90 40.89 3.06
2867 4231 5.948758 TGCCAGGACATGTTAATTACAATGA 59.051 36.000 0.00 0.00 40.89 2.57
2868 4232 6.206395 TGCCAGGACATGTTAATTACAATG 57.794 37.500 0.00 5.42 40.89 2.82
2869 4233 6.849085 TTGCCAGGACATGTTAATTACAAT 57.151 33.333 0.00 0.00 40.89 2.71
2870 4234 6.656632 TTTGCCAGGACATGTTAATTACAA 57.343 33.333 0.00 0.00 40.89 2.41
2871 4235 6.656632 TTTTGCCAGGACATGTTAATTACA 57.343 33.333 0.00 0.00 41.97 2.41
2872 4236 6.926272 TGTTTTTGCCAGGACATGTTAATTAC 59.074 34.615 0.00 0.00 0.00 1.89
2873 4237 7.055667 TGTTTTTGCCAGGACATGTTAATTA 57.944 32.000 0.00 0.00 0.00 1.40
2874 4238 5.923204 TGTTTTTGCCAGGACATGTTAATT 58.077 33.333 0.00 0.00 0.00 1.40
2875 4239 5.543507 TGTTTTTGCCAGGACATGTTAAT 57.456 34.783 0.00 0.00 0.00 1.40
2876 4240 5.344743 TTGTTTTTGCCAGGACATGTTAA 57.655 34.783 0.00 0.00 0.00 2.01
2877 4241 5.543507 ATTGTTTTTGCCAGGACATGTTA 57.456 34.783 0.00 0.00 0.00 2.41
2878 4242 3.902881 TTGTTTTTGCCAGGACATGTT 57.097 38.095 0.00 0.00 0.00 2.71
2879 4243 5.543507 TTATTGTTTTTGCCAGGACATGT 57.456 34.783 0.00 0.00 0.00 3.21
2880 4244 5.352016 CCATTATTGTTTTTGCCAGGACATG 59.648 40.000 0.00 0.00 0.00 3.21
2913 4277 8.425703 ACATGGCAAATTCATATTCATTCATCA 58.574 29.630 0.00 0.00 0.00 3.07
3077 4445 3.614616 GCAAATTTGTGTTCCACGTCAAA 59.385 39.130 19.03 1.00 37.14 2.69
3078 4446 3.182967 GCAAATTTGTGTTCCACGTCAA 58.817 40.909 19.03 0.00 37.14 3.18


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

AutoCloner maintained by Alex Coulton.