Multiple sequence alignment - TraesCS3D01G453500

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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 TraesCS3D01G453500 chr3D 100.000 3891 0 0 1 3891 560639125 560643015 0.000000e+00 7186.0
1 TraesCS3D01G453500 chr3D 88.634 1654 99 29 850 2432 560551399 560553034 0.000000e+00 1930.0
2 TraesCS3D01G453500 chr3D 83.726 1868 256 33 1107 2956 560752705 560754542 0.000000e+00 1722.0
3 TraesCS3D01G453500 chr3D 86.926 1285 135 14 1043 2321 560826932 560828189 0.000000e+00 1411.0
4 TraesCS3D01G453500 chr3D 88.181 973 111 4 1080 2050 560785780 560784810 0.000000e+00 1157.0
5 TraesCS3D01G453500 chr3D 92.500 680 42 4 2348 3023 560553027 560553701 0.000000e+00 965.0
6 TraesCS3D01G453500 chr3D 80.802 823 114 31 2103 2903 560784655 560783855 4.300000e-169 604.0
7 TraesCS3D01G453500 chr3D 80.376 744 98 28 59 777 560550425 560551145 4.460000e-144 521.0
8 TraesCS3D01G453500 chr3D 79.385 781 93 27 3148 3891 560553791 560554540 4.520000e-134 488.0
9 TraesCS3D01G453500 chr3D 83.757 511 69 11 2454 2955 560285189 560284684 4.550000e-129 472.0
10 TraesCS3D01G453500 chr3D 88.546 227 19 2 2074 2293 560867914 560868140 6.410000e-68 268.0
11 TraesCS3D01G453500 chr3D 87.755 49 4 2 582 629 6294518 6294471 5.430000e-04 56.5
12 TraesCS3D01G453500 chr3D 86.000 50 5 1 582 629 32704454 32704503 7.000000e-03 52.8
13 TraesCS3D01G453500 chr3B 90.475 2887 185 38 850 3658 744728402 744731276 0.000000e+00 3725.0
14 TraesCS3D01G453500 chr3B 89.491 1494 108 18 850 2297 744846975 744848465 0.000000e+00 1844.0
15 TraesCS3D01G453500 chr3B 85.382 1245 158 17 1088 2320 745474763 745473531 0.000000e+00 1269.0
16 TraesCS3D01G453500 chr3B 85.489 1268 126 34 1043 2303 745540181 745541397 0.000000e+00 1269.0
17 TraesCS3D01G453500 chr3B 90.359 975 64 14 1968 2919 746286036 746287003 0.000000e+00 1253.0
18 TraesCS3D01G453500 chr3B 88.173 947 108 4 1080 2024 745450369 745449425 0.000000e+00 1125.0
19 TraesCS3D01G453500 chr3B 91.765 765 46 6 2348 3107 744848553 744849305 0.000000e+00 1048.0
20 TraesCS3D01G453500 chr3B 90.186 591 34 10 3310 3891 746287299 746287874 0.000000e+00 749.0
21 TraesCS3D01G453500 chr3B 88.673 565 39 9 3337 3891 744849300 744849849 0.000000e+00 665.0
22 TraesCS3D01G453500 chr3B 79.673 733 105 24 59 774 744732841 744733546 4.520000e-134 488.0
23 TraesCS3D01G453500 chr3B 85.144 451 64 3 2454 2903 745473286 745472838 3.540000e-125 459.0
24 TraesCS3D01G453500 chr3B 83.137 510 72 7 2390 2899 746854518 746854023 1.650000e-123 453.0
25 TraesCS3D01G453500 chr3B 82.524 515 77 10 2454 2960 744545189 744544680 1.280000e-119 440.0
26 TraesCS3D01G453500 chr3B 79.338 634 80 29 2177 2778 744598119 744597505 7.830000e-107 398.0
27 TraesCS3D01G453500 chr3B 92.771 249 12 4 3508 3750 745720334 745720582 4.780000e-94 355.0
28 TraesCS3D01G453500 chr3B 87.889 289 13 6 2967 3241 746287021 746287301 1.740000e-83 320.0
29 TraesCS3D01G453500 chr3B 91.753 194 16 0 2100 2293 745548018 745548211 1.780000e-68 270.0
30 TraesCS3D01G453500 chr3B 85.333 225 20 7 3677 3890 745192854 745193076 1.820000e-53 220.0
31 TraesCS3D01G453500 chr3B 83.146 178 27 3 333 507 162727527 162727350 4.020000e-35 159.0
32 TraesCS3D01G453500 chr3B 82.123 179 18 8 3152 3319 746849099 746849274 1.460000e-29 141.0
33 TraesCS3D01G453500 chr3B 80.097 206 21 12 3152 3341 744597049 744596848 6.780000e-28 135.0
34 TraesCS3D01G453500 chr3B 88.506 87 5 4 3340 3421 565270281 565270195 2.470000e-17 100.0
35 TraesCS3D01G453500 chr3B 88.372 86 5 2 2348 2432 744848479 744848560 8.900000e-17 99.0
36 TraesCS3D01G453500 chr3B 84.259 108 5 7 644 746 744727807 744727907 1.150000e-15 95.3
37 TraesCS3D01G453500 chr3A 82.251 1724 208 56 1081 2778 696477932 696476281 0.000000e+00 1399.0
38 TraesCS3D01G453500 chr3A 85.470 1287 143 22 1043 2321 696637274 696638524 0.000000e+00 1301.0
39 TraesCS3D01G453500 chr3A 88.235 85 6 4 3340 3420 679696560 679696644 8.900000e-17 99.0
40 TraesCS3D01G453500 chrUn 84.951 1236 155 23 1080 2297 301717246 301718468 0.000000e+00 1223.0
41 TraesCS3D01G453500 chrUn 93.103 58 4 0 3504 3561 45118613 45118556 6.930000e-13 86.1
42 TraesCS3D01G453500 chrUn 93.103 58 4 0 3504 3561 222665902 222665959 6.930000e-13 86.1
43 TraesCS3D01G453500 chrUn 93.103 58 4 0 3504 3561 423257095 423257152 6.930000e-13 86.1
44 TraesCS3D01G453500 chrUn 93.103 58 4 0 3504 3561 441344226 441344169 6.930000e-13 86.1
45 TraesCS3D01G453500 chr1B 77.252 444 65 22 58 496 686781938 686781526 1.090000e-55 228.0
46 TraesCS3D01G453500 chr5D 73.666 581 106 30 55 630 385601026 385601564 8.590000e-42 182.0
47 TraesCS3D01G453500 chr5D 86.301 73 8 2 367 438 320370457 320370528 1.160000e-10 78.7
48 TraesCS3D01G453500 chr5B 84.153 183 26 3 372 553 462880040 462880220 1.440000e-39 174.0
49 TraesCS3D01G453500 chr5B 87.500 88 6 4 3338 3420 215889770 215889683 3.200000e-16 97.1
50 TraesCS3D01G453500 chr5B 88.136 59 2 4 575 629 474528994 474529051 9.020000e-07 65.8
51 TraesCS3D01G453500 chr2A 83.696 184 24 6 387 568 748076851 748077030 6.690000e-38 169.0
52 TraesCS3D01G453500 chr7A 78.707 263 47 4 59 318 641704430 641704686 2.400000e-37 167.0
53 TraesCS3D01G453500 chr7A 76.991 226 45 5 58 280 641489477 641489256 5.280000e-24 122.0
54 TraesCS3D01G453500 chr7A 78.333 180 33 6 270 446 164809587 164809763 1.140000e-20 111.0
55 TraesCS3D01G453500 chr7D 80.663 181 35 0 67 247 555739368 555739188 1.460000e-29 141.0
56 TraesCS3D01G453500 chr6B 83.803 142 16 7 360 497 288163751 288163613 1.130000e-25 128.0
57 TraesCS3D01G453500 chr6B 88.000 50 4 2 582 629 23634650 23634699 1.510000e-04 58.4
58 TraesCS3D01G453500 chr6D 82.812 128 13 8 375 497 158585144 158585267 5.320000e-19 106.0
59 TraesCS3D01G453500 chr2B 88.764 89 5 3 3340 3423 764537697 764537609 1.910000e-18 104.0
60 TraesCS3D01G453500 chr2B 88.764 89 5 3 3337 3420 764537609 764537697 1.910000e-18 104.0
61 TraesCS3D01G453500 chr2B 78.065 155 30 3 58 210 463213627 463213779 1.150000e-15 95.3
62 TraesCS3D01G453500 chr2B 82.432 74 9 4 560 630 241106844 241106916 1.170000e-05 62.1
63 TraesCS3D01G453500 chr4B 88.506 87 7 2 3340 3423 168988627 168988541 6.880000e-18 102.0
64 TraesCS3D01G453500 chr4B 88.235 51 4 1 582 630 616267261 616267211 4.200000e-05 60.2
65 TraesCS3D01G453500 chr1A 81.513 119 13 5 379 496 405865373 405865263 5.350000e-14 89.8
66 TraesCS3D01G453500 chr4D 100.000 30 0 0 601 630 484333284 484333255 5.430000e-04 56.5
67 TraesCS3D01G453500 chr4D 100.000 30 0 0 601 630 507167844 507167815 5.430000e-04 56.5


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 TraesCS3D01G453500 chr3D 560639125 560643015 3890 False 7186.0 7186 100.000000 1 3891 1 chr3D.!!$F2 3890
1 TraesCS3D01G453500 chr3D 560752705 560754542 1837 False 1722.0 1722 83.726000 1107 2956 1 chr3D.!!$F3 1849
2 TraesCS3D01G453500 chr3D 560826932 560828189 1257 False 1411.0 1411 86.926000 1043 2321 1 chr3D.!!$F4 1278
3 TraesCS3D01G453500 chr3D 560550425 560554540 4115 False 976.0 1930 85.223750 59 3891 4 chr3D.!!$F6 3832
4 TraesCS3D01G453500 chr3D 560783855 560785780 1925 True 880.5 1157 84.491500 1080 2903 2 chr3D.!!$R3 1823
5 TraesCS3D01G453500 chr3D 560284684 560285189 505 True 472.0 472 83.757000 2454 2955 1 chr3D.!!$R2 501
6 TraesCS3D01G453500 chr3B 744727807 744733546 5739 False 1436.1 3725 84.802333 59 3658 3 chr3B.!!$F6 3599
7 TraesCS3D01G453500 chr3B 745540181 745541397 1216 False 1269.0 1269 85.489000 1043 2303 1 chr3B.!!$F2 1260
8 TraesCS3D01G453500 chr3B 745449425 745450369 944 True 1125.0 1125 88.173000 1080 2024 1 chr3B.!!$R4 944
9 TraesCS3D01G453500 chr3B 744846975 744849849 2874 False 914.0 1844 89.575250 850 3891 4 chr3B.!!$F7 3041
10 TraesCS3D01G453500 chr3B 745472838 745474763 1925 True 864.0 1269 85.263000 1088 2903 2 chr3B.!!$R7 1815
11 TraesCS3D01G453500 chr3B 746286036 746287874 1838 False 774.0 1253 89.478000 1968 3891 3 chr3B.!!$F8 1923
12 TraesCS3D01G453500 chr3B 744544680 744545189 509 True 440.0 440 82.524000 2454 2960 1 chr3B.!!$R3 506
13 TraesCS3D01G453500 chr3B 744596848 744598119 1271 True 266.5 398 79.717500 2177 3341 2 chr3B.!!$R6 1164
14 TraesCS3D01G453500 chr3A 696476281 696477932 1651 True 1399.0 1399 82.251000 1081 2778 1 chr3A.!!$R1 1697
15 TraesCS3D01G453500 chr3A 696637274 696638524 1250 False 1301.0 1301 85.470000 1043 2321 1 chr3A.!!$F2 1278
16 TraesCS3D01G453500 chrUn 301717246 301718468 1222 False 1223.0 1223 84.951000 1080 2297 1 chrUn.!!$F2 1217

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
69 70 0.035439 GGCAATTGAGAAGGTCCGGA 60.035 55.0 10.34 0.0 0.00 5.14 F
356 358 0.100682 CGTCGACCAATGATCCGTCT 59.899 55.0 10.58 0.0 0.00 4.18 F
365 367 0.250038 ATGATCCGTCTGGCGATTGG 60.250 55.0 1.87 0.0 44.77 3.16 F
550 562 0.466189 CAGCAAATATGAGGGGCCGT 60.466 55.0 0.00 0.0 0.00 5.68 F
921 1343 0.894835 ATTCGGACATTTGGCCCAAC 59.105 50.0 0.00 0.0 41.34 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1027 1489 1.145900 TCCAAATTGCTCCTGGGGGA 61.146 55.000 0.00 0.00 39.70 4.81 R
1314 1800 1.203523 AGATGACTGTCGACAAGAGCC 59.796 52.381 20.49 9.01 0.00 4.70 R
1585 2089 1.220477 GGGAGGAGCAGCTGAAGAC 59.780 63.158 20.43 3.82 0.00 3.01 R
2374 3199 0.612453 TGCAGCAGGCCATCAATCAA 60.612 50.000 5.01 0.00 43.89 2.57 R
2892 3897 0.462047 GGCACGGCATACTGCTACTT 60.462 55.000 0.00 0.00 44.28 2.24 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
28 29 9.226345 GCAAAAAGAAAGAATAGATTGATACCG 57.774 33.333 0.00 0.00 0.00 4.02
32 33 9.757227 AAAGAAAGAATAGATTGATACCGAGAG 57.243 33.333 0.00 0.00 0.00 3.20
33 34 8.698973 AGAAAGAATAGATTGATACCGAGAGA 57.301 34.615 0.00 0.00 0.00 3.10
34 35 8.792633 AGAAAGAATAGATTGATACCGAGAGAG 58.207 37.037 0.00 0.00 0.00 3.20
35 36 7.461182 AAGAATAGATTGATACCGAGAGAGG 57.539 40.000 0.00 0.00 37.30 3.69
36 37 5.949354 AGAATAGATTGATACCGAGAGAGGG 59.051 44.000 0.00 0.00 35.02 4.30
37 38 3.603965 AGATTGATACCGAGAGAGGGT 57.396 47.619 0.00 0.00 41.62 4.34
38 39 3.226777 AGATTGATACCGAGAGAGGGTG 58.773 50.000 0.00 0.00 38.50 4.61
39 40 2.820728 TTGATACCGAGAGAGGGTGA 57.179 50.000 0.00 0.00 38.50 4.02
40 41 2.820728 TGATACCGAGAGAGGGTGAA 57.179 50.000 0.00 0.00 38.50 3.18
41 42 2.376109 TGATACCGAGAGAGGGTGAAC 58.624 52.381 0.00 0.00 38.50 3.18
42 43 2.291346 TGATACCGAGAGAGGGTGAACA 60.291 50.000 0.00 0.00 38.50 3.18
43 44 2.297698 TACCGAGAGAGGGTGAACAA 57.702 50.000 0.00 0.00 38.50 2.83
44 45 0.680061 ACCGAGAGAGGGTGAACAAC 59.320 55.000 0.00 0.00 36.14 3.32
45 46 0.679505 CCGAGAGAGGGTGAACAACA 59.320 55.000 0.00 0.00 0.00 3.33
46 47 1.070134 CCGAGAGAGGGTGAACAACAA 59.930 52.381 0.00 0.00 0.00 2.83
47 48 2.408050 CGAGAGAGGGTGAACAACAAG 58.592 52.381 0.00 0.00 0.00 3.16
48 49 2.224066 CGAGAGAGGGTGAACAACAAGT 60.224 50.000 0.00 0.00 0.00 3.16
49 50 3.741388 CGAGAGAGGGTGAACAACAAGTT 60.741 47.826 0.00 0.00 44.93 2.66
50 51 3.545703 AGAGAGGGTGAACAACAAGTTG 58.454 45.455 11.16 11.16 41.51 3.16
51 52 2.618709 GAGAGGGTGAACAACAAGTTGG 59.381 50.000 16.45 0.00 44.45 3.77
52 53 1.067060 GAGGGTGAACAACAAGTTGGC 59.933 52.381 16.45 8.96 44.45 4.52
53 54 0.820871 GGGTGAACAACAAGTTGGCA 59.179 50.000 16.45 11.17 44.45 4.92
54 55 1.205893 GGGTGAACAACAAGTTGGCAA 59.794 47.619 16.45 0.00 44.45 4.52
55 56 2.158971 GGGTGAACAACAAGTTGGCAAT 60.159 45.455 16.45 1.06 44.45 3.56
56 57 3.530535 GGTGAACAACAAGTTGGCAATT 58.469 40.909 16.45 0.00 44.45 2.32
57 58 3.309410 GGTGAACAACAAGTTGGCAATTG 59.691 43.478 16.45 11.41 44.45 2.32
61 62 4.734398 ACAACAAGTTGGCAATTGAGAA 57.266 36.364 21.19 0.00 44.45 2.87
65 66 3.319122 ACAAGTTGGCAATTGAGAAGGTC 59.681 43.478 21.19 0.50 0.00 3.85
67 68 1.200020 GTTGGCAATTGAGAAGGTCCG 59.800 52.381 10.34 0.00 0.00 4.79
69 70 0.035439 GGCAATTGAGAAGGTCCGGA 60.035 55.000 10.34 0.00 0.00 5.14
78 79 1.985895 AGAAGGTCCGGACTTTTGGAT 59.014 47.619 30.06 15.41 36.48 3.41
79 80 2.027100 AGAAGGTCCGGACTTTTGGATC 60.027 50.000 30.06 18.41 36.48 3.36
83 84 2.423538 GGTCCGGACTTTTGGATCAATG 59.576 50.000 32.52 0.00 35.37 2.82
114 115 1.699634 AGGAGAGGTTGCAACTTGCTA 59.300 47.619 27.64 4.54 45.31 3.49
123 124 1.339929 TGCAACTTGCTAGAGACACGA 59.660 47.619 14.78 0.00 45.31 4.35
125 126 2.996621 GCAACTTGCTAGAGACACGAAT 59.003 45.455 6.50 0.00 40.96 3.34
128 129 3.839293 ACTTGCTAGAGACACGAATGAC 58.161 45.455 1.04 0.00 0.00 3.06
158 159 0.670546 TGTTAGCAGACGCAAGCCTC 60.671 55.000 0.00 0.00 42.27 4.70
168 169 1.712977 CGCAAGCCTCTTGGATGAGC 61.713 60.000 8.43 0.00 34.57 4.26
178 179 4.578105 CCTCTTGGATGAGCAAGGAAATAC 59.422 45.833 0.00 0.00 34.57 1.89
224 225 6.072286 AGGAGATCAACGAACGTAGAAAGTAA 60.072 38.462 0.00 0.00 0.00 2.24
233 234 1.135199 CGTAGAAAGTAAGAGGCGGCA 60.135 52.381 13.08 0.00 0.00 5.69
234 235 2.541556 GTAGAAAGTAAGAGGCGGCAG 58.458 52.381 13.08 0.00 0.00 4.85
238 239 0.905337 AAGTAAGAGGCGGCAGGAGT 60.905 55.000 13.08 0.00 0.00 3.85
239 240 1.153549 GTAAGAGGCGGCAGGAGTG 60.154 63.158 13.08 0.00 0.00 3.51
248 249 3.818787 GCAGGAGTGGCAATGGCG 61.819 66.667 1.51 0.00 42.47 5.69
249 250 2.046023 CAGGAGTGGCAATGGCGA 60.046 61.111 1.51 0.00 42.47 5.54
264 265 2.507992 CGACAGAGGAGCAAGCGG 60.508 66.667 0.00 0.00 0.00 5.52
280 281 2.897350 GGCACGGATGGTAGCAGC 60.897 66.667 0.49 0.49 0.00 5.25
282 283 2.494445 CACGGATGGTAGCAGCGA 59.506 61.111 3.82 0.00 0.00 4.93
285 286 0.739813 ACGGATGGTAGCAGCGAAAC 60.740 55.000 3.82 0.00 0.00 2.78
287 288 1.009829 GGATGGTAGCAGCGAAACAG 58.990 55.000 3.82 0.00 0.00 3.16
290 291 2.740714 GGTAGCAGCGAAACAGGCG 61.741 63.158 0.00 0.00 35.00 5.52
294 295 3.434319 CAGCGAAACAGGCGGCAT 61.434 61.111 13.08 0.00 35.00 4.40
295 296 3.434319 AGCGAAACAGGCGGCATG 61.434 61.111 13.73 13.73 35.00 4.06
303 304 2.769621 AGGCGGCATGGATGGAGA 60.770 61.111 13.08 0.00 0.00 3.71
305 306 2.969238 GCGGCATGGATGGAGACG 60.969 66.667 0.00 0.00 0.00 4.18
313 314 2.107953 GATGGAGACGGAGCAGGC 59.892 66.667 0.00 0.00 0.00 4.85
316 317 4.500116 GGAGACGGAGCAGGCGAC 62.500 72.222 0.00 0.00 0.00 5.19
321 322 3.443925 CGGAGCAGGCGACAGAGA 61.444 66.667 0.00 0.00 0.00 3.10
331 332 2.169789 CGACAGAGAAGGCGGCATG 61.170 63.158 13.08 4.18 0.00 4.06
352 354 0.532862 ATGGCGTCGACCAATGATCC 60.533 55.000 10.58 0.90 44.65 3.36
354 356 1.518572 GCGTCGACCAATGATCCGT 60.519 57.895 10.58 0.00 0.00 4.69
356 358 0.100682 CGTCGACCAATGATCCGTCT 59.899 55.000 10.58 0.00 0.00 4.18
358 360 0.459899 TCGACCAATGATCCGTCTGG 59.540 55.000 0.00 0.00 34.95 3.86
359 361 1.154205 CGACCAATGATCCGTCTGGC 61.154 60.000 0.00 0.00 34.14 4.85
365 367 0.250038 ATGATCCGTCTGGCGATTGG 60.250 55.000 1.87 0.00 44.77 3.16
378 380 2.514592 ATTGGTCCGCCATGCTCG 60.515 61.111 0.00 0.00 45.56 5.03
379 381 4.776322 TTGGTCCGCCATGCTCGG 62.776 66.667 15.79 15.79 45.56 4.63
385 387 2.434884 CGCCATGCTCGGACTTGT 60.435 61.111 0.00 0.00 0.00 3.16
396 398 5.698832 TGCTCGGACTTGTATTTCATTTTG 58.301 37.500 0.00 0.00 0.00 2.44
400 402 5.184864 TCGGACTTGTATTTCATTTTGCCAT 59.815 36.000 0.00 0.00 0.00 4.40
401 403 5.289193 CGGACTTGTATTTCATTTTGCCATG 59.711 40.000 0.00 0.00 0.00 3.66
402 404 6.165577 GGACTTGTATTTCATTTTGCCATGT 58.834 36.000 0.00 0.00 0.00 3.21
403 405 6.311200 GGACTTGTATTTCATTTTGCCATGTC 59.689 38.462 0.00 0.00 0.00 3.06
404 406 6.165577 ACTTGTATTTCATTTTGCCATGTCC 58.834 36.000 0.00 0.00 0.00 4.02
405 407 4.742417 TGTATTTCATTTTGCCATGTCCG 58.258 39.130 0.00 0.00 0.00 4.79
406 408 2.739885 TTTCATTTTGCCATGTCCGG 57.260 45.000 0.00 0.00 0.00 5.14
407 409 1.916506 TTCATTTTGCCATGTCCGGA 58.083 45.000 0.00 0.00 0.00 5.14
408 410 2.142356 TCATTTTGCCATGTCCGGAT 57.858 45.000 7.81 0.00 0.00 4.18
416 418 1.135402 GCCATGTCCGGATTGTTGAAC 60.135 52.381 7.81 0.00 0.00 3.18
429 431 9.801873 CCGGATTGTTGAACTATGATTTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
450 452 3.230743 ACTGTGTTGCTTTGTTGAACC 57.769 42.857 0.00 0.00 0.00 3.62
464 466 4.605968 TGTTGAACCGTTGAATTGTGATG 58.394 39.130 0.00 0.00 0.00 3.07
474 477 6.129115 CCGTTGAATTGTGATGAATTTGTGTC 60.129 38.462 0.00 0.00 0.00 3.67
486 489 7.556996 TGATGAATTTGTGTCATATGATCCACA 59.443 33.333 19.79 19.79 35.84 4.17
500 512 2.632987 TCCACATGCATGGATCTGAG 57.367 50.000 29.41 12.69 44.14 3.35
501 513 1.142262 TCCACATGCATGGATCTGAGG 59.858 52.381 29.41 17.72 44.14 3.86
510 522 2.133281 TGGATCTGAGGGTTTGCATG 57.867 50.000 0.00 0.00 0.00 4.06
511 523 0.743097 GGATCTGAGGGTTTGCATGC 59.257 55.000 11.82 11.82 0.00 4.06
522 534 2.859538 GGTTTGCATGCGATAATTGTGG 59.140 45.455 14.09 0.00 0.00 4.17
529 541 1.383456 GCGATAATTGTGGCTGCCCA 61.383 55.000 17.53 10.98 39.32 5.36
530 542 1.102154 CGATAATTGTGGCTGCCCAA 58.898 50.000 17.53 19.01 44.33 4.12
550 562 0.466189 CAGCAAATATGAGGGGCCGT 60.466 55.000 0.00 0.00 0.00 5.68
554 566 0.923358 AAATATGAGGGGCCGTCCAA 59.077 50.000 22.54 11.43 37.22 3.53
555 567 1.149101 AATATGAGGGGCCGTCCAAT 58.851 50.000 22.54 13.09 37.22 3.16
557 569 1.415672 TATGAGGGGCCGTCCAATCC 61.416 60.000 22.54 0.00 37.22 3.01
558 570 4.547367 GAGGGGCCGTCCAATCCG 62.547 72.222 15.31 0.00 37.22 4.18
580 592 4.778415 CGGACGCGTCAGGGTGAG 62.778 72.222 37.26 16.51 43.97 3.51
593 605 4.409218 GTGAGCCGCGGACGTGTA 62.409 66.667 33.48 4.95 37.70 2.90
594 606 3.672447 TGAGCCGCGGACGTGTAA 61.672 61.111 33.48 2.77 37.70 2.41
595 607 2.879462 GAGCCGCGGACGTGTAAG 60.879 66.667 33.48 0.00 37.70 2.34
596 608 3.332493 GAGCCGCGGACGTGTAAGA 62.332 63.158 33.48 0.00 37.70 2.10
599 611 2.564975 CGCGGACGTGTAAGAGGT 59.435 61.111 0.00 0.00 33.53 3.85
607 619 3.326747 GACGTGTAAGAGGTGATTTGCT 58.673 45.455 0.00 0.00 0.00 3.91
642 658 8.079211 TGTAGATGCTCTTCTTGGTTTACTAT 57.921 34.615 0.00 0.00 0.00 2.12
660 676 9.442033 GTTTACTATTATGTAATTCGGTTTGCC 57.558 33.333 0.00 0.00 33.16 4.52
666 682 7.644986 TTATGTAATTCGGTTTGCCTTTTTG 57.355 32.000 0.00 0.00 0.00 2.44
667 683 5.012328 TGTAATTCGGTTTGCCTTTTTGT 57.988 34.783 0.00 0.00 0.00 2.83
670 686 6.697892 TGTAATTCGGTTTGCCTTTTTGTAAG 59.302 34.615 0.00 0.00 0.00 2.34
673 689 4.927422 TCGGTTTGCCTTTTTGTAAGAAG 58.073 39.130 0.00 0.00 0.00 2.85
674 690 4.399934 TCGGTTTGCCTTTTTGTAAGAAGT 59.600 37.500 0.00 0.00 0.00 3.01
741 760 8.278639 TCTATAGGTTGCATTCTTTTATTGGGA 58.721 33.333 0.00 0.00 0.00 4.37
806 1024 5.560966 AATACACAAGGTAAATGGAAGCG 57.439 39.130 0.00 0.00 35.14 4.68
807 1025 2.858745 ACACAAGGTAAATGGAAGCGT 58.141 42.857 0.00 0.00 0.00 5.07
808 1026 4.010667 ACACAAGGTAAATGGAAGCGTA 57.989 40.909 0.00 0.00 0.00 4.42
809 1027 4.585879 ACACAAGGTAAATGGAAGCGTAT 58.414 39.130 0.00 0.00 0.00 3.06
810 1028 4.394920 ACACAAGGTAAATGGAAGCGTATG 59.605 41.667 0.00 0.00 0.00 2.39
811 1029 3.945285 ACAAGGTAAATGGAAGCGTATGG 59.055 43.478 0.00 0.00 0.00 2.74
813 1031 5.120399 CAAGGTAAATGGAAGCGTATGGTA 58.880 41.667 0.00 0.00 0.00 3.25
814 1032 5.562298 AGGTAAATGGAAGCGTATGGTAT 57.438 39.130 0.00 0.00 0.00 2.73
816 1034 7.253905 AGGTAAATGGAAGCGTATGGTATAT 57.746 36.000 0.00 0.00 0.00 0.86
817 1035 7.686434 AGGTAAATGGAAGCGTATGGTATATT 58.314 34.615 0.00 0.00 0.00 1.28
818 1036 8.161425 AGGTAAATGGAAGCGTATGGTATATTT 58.839 33.333 0.00 0.00 0.00 1.40
819 1037 8.234546 GGTAAATGGAAGCGTATGGTATATTTG 58.765 37.037 10.77 0.00 0.00 2.32
820 1038 6.817765 AATGGAAGCGTATGGTATATTTGG 57.182 37.500 0.00 0.00 0.00 3.28
821 1039 5.554437 TGGAAGCGTATGGTATATTTGGA 57.446 39.130 0.00 0.00 0.00 3.53
822 1040 5.931294 TGGAAGCGTATGGTATATTTGGAA 58.069 37.500 0.00 0.00 0.00 3.53
824 1042 7.681679 TGGAAGCGTATGGTATATTTGGAATA 58.318 34.615 0.00 0.00 0.00 1.75
825 1043 8.325787 TGGAAGCGTATGGTATATTTGGAATAT 58.674 33.333 0.00 0.00 0.00 1.28
826 1044 8.612619 GGAAGCGTATGGTATATTTGGAATATG 58.387 37.037 3.97 0.00 0.00 1.78
827 1045 8.506168 AAGCGTATGGTATATTTGGAATATGG 57.494 34.615 3.97 0.00 0.00 2.74
828 1046 7.630082 AGCGTATGGTATATTTGGAATATGGT 58.370 34.615 3.97 0.00 0.00 3.55
829 1047 8.764558 AGCGTATGGTATATTTGGAATATGGTA 58.235 33.333 3.97 0.00 0.00 3.25
830 1048 8.823818 GCGTATGGTATATTTGGAATATGGTAC 58.176 37.037 3.97 0.00 0.00 3.34
839 1057 6.877668 TTTGGAATATGGTACTACTCCACA 57.122 37.500 6.15 0.00 37.81 4.17
840 1058 6.877668 TTGGAATATGGTACTACTCCACAA 57.122 37.500 6.15 0.00 37.81 3.33
841 1059 6.877668 TGGAATATGGTACTACTCCACAAA 57.122 37.500 3.26 0.00 37.81 2.83
842 1060 6.646267 TGGAATATGGTACTACTCCACAAAC 58.354 40.000 3.26 0.00 37.81 2.93
843 1061 6.442564 TGGAATATGGTACTACTCCACAAACT 59.557 38.462 3.26 0.00 37.81 2.66
844 1062 6.761714 GGAATATGGTACTACTCCACAAACTG 59.238 42.308 0.00 0.00 37.81 3.16
845 1063 7.364408 GGAATATGGTACTACTCCACAAACTGA 60.364 40.741 0.00 0.00 37.81 3.41
846 1064 7.676683 ATATGGTACTACTCCACAAACTGAT 57.323 36.000 0.00 0.00 37.81 2.90
848 1066 5.790593 TGGTACTACTCCACAAACTGATTC 58.209 41.667 0.00 0.00 0.00 2.52
849 1067 4.863131 GGTACTACTCCACAAACTGATTCG 59.137 45.833 0.00 0.00 0.00 3.34
851 1069 3.576982 ACTACTCCACAAACTGATTCGGA 59.423 43.478 0.00 0.00 0.00 4.55
853 1071 1.726791 CTCCACAAACTGATTCGGACG 59.273 52.381 0.00 0.00 0.00 4.79
854 1072 1.069513 TCCACAAACTGATTCGGACGT 59.930 47.619 0.00 0.00 0.00 4.34
855 1073 1.871039 CCACAAACTGATTCGGACGTT 59.129 47.619 0.00 0.00 0.00 3.99
856 1074 2.349438 CCACAAACTGATTCGGACGTTG 60.349 50.000 0.00 3.64 0.00 4.10
857 1075 1.871039 ACAAACTGATTCGGACGTTGG 59.129 47.619 0.00 0.00 0.00 3.77
921 1343 0.894835 ATTCGGACATTTGGCCCAAC 59.105 50.000 0.00 0.00 41.34 3.77
959 1392 1.144936 CCTCGCCTCCATTCCTCAC 59.855 63.158 0.00 0.00 0.00 3.51
960 1393 1.144936 CTCGCCTCCATTCCTCACC 59.855 63.158 0.00 0.00 0.00 4.02
961 1394 1.306141 TCGCCTCCATTCCTCACCT 60.306 57.895 0.00 0.00 0.00 4.00
962 1395 1.144936 CGCCTCCATTCCTCACCTC 59.855 63.158 0.00 0.00 0.00 3.85
963 1396 1.617018 CGCCTCCATTCCTCACCTCA 61.617 60.000 0.00 0.00 0.00 3.86
975 1408 2.358957 CTCACCTCAATCATTCCGCAA 58.641 47.619 0.00 0.00 0.00 4.85
986 1419 0.898326 ATTCCGCAAGACCAAACCCC 60.898 55.000 0.00 0.00 43.02 4.95
987 1420 2.002018 TTCCGCAAGACCAAACCCCT 62.002 55.000 0.00 0.00 43.02 4.79
989 1422 1.971695 CGCAAGACCAAACCCCTCC 60.972 63.158 0.00 0.00 43.02 4.30
990 1423 1.971695 GCAAGACCAAACCCCTCCG 60.972 63.158 0.00 0.00 0.00 4.63
992 1425 3.205851 AAGACCAAACCCCTCCGCC 62.206 63.158 0.00 0.00 0.00 6.13
1027 1489 3.812019 CGCAGTACCTCGTCGGCT 61.812 66.667 0.00 0.00 35.61 5.52
1050 1524 0.962356 CCAGGAGCAATTTGGAGCGT 60.962 55.000 0.00 0.00 33.76 5.07
1123 1597 1.064463 TCGTGTACGATTACCTCCCCT 60.064 52.381 2.55 0.00 44.22 4.79
1230 1716 1.409064 GATGTGCTCCTCCGTGACATA 59.591 52.381 0.00 0.00 0.00 2.29
1818 2322 2.493973 CTCGTCAGCCAGAGCCTC 59.506 66.667 0.00 0.00 41.25 4.70
1901 2405 1.671901 GAGAGGCTCTTCCAGTCGGG 61.672 65.000 19.80 0.00 37.29 5.14
1903 2407 4.821589 GGCTCTTCCAGTCGGGCG 62.822 72.222 0.00 0.00 36.21 6.13
2050 2571 1.605968 CCAACACCGTCATCGTGGTAA 60.606 52.381 0.00 0.00 36.50 2.85
2051 2572 1.458064 CAACACCGTCATCGTGGTAAC 59.542 52.381 0.00 0.00 36.50 2.50
2210 2856 1.331756 CATAGAGGTGCAATTCGGTGC 59.668 52.381 0.00 0.42 45.15 5.01
2248 2894 3.297134 AAGTGCCTGGTTTTCTCAGAA 57.703 42.857 0.00 0.00 34.36 3.02
2293 2939 3.995705 CCATGTGCAGGTAAAATTGGTTG 59.004 43.478 0.00 0.00 0.00 3.77
2336 3015 9.399797 TGCATTGTCAGAACTGATTATTTATCT 57.600 29.630 7.77 0.00 42.18 1.98
2359 3184 4.093011 AGCAAGGTCAGAACTATGAGTCT 58.907 43.478 0.00 0.00 0.00 3.24
2634 3632 1.133216 CAAGTTCATCGCGGAGAGAGA 59.867 52.381 6.13 0.00 41.36 3.10
2856 3861 0.685660 GACCCCTTTGACCTCGAGTT 59.314 55.000 12.31 0.00 0.00 3.01
2869 3874 2.356382 CCTCGAGTTCTACTGCGAATCT 59.644 50.000 12.31 0.00 31.30 2.40
2941 3956 4.220163 GGTGCAAGACTACTGGTAACTAGT 59.780 45.833 0.00 0.00 30.80 2.57
2964 3979 3.139077 AGACTTTGTGTTGTCGGGAATC 58.861 45.455 0.00 0.00 38.16 2.52
2992 4014 7.283127 CAGGAGCTAAAAATACCTGCATTTCTA 59.717 37.037 2.71 0.00 40.90 2.10
3024 4046 4.771590 TTCTGCATGATGAGGTTGTTTC 57.228 40.909 0.00 0.00 0.00 2.78
3028 4050 3.890756 TGCATGATGAGGTTGTTTCTTGT 59.109 39.130 0.00 0.00 0.00 3.16
3029 4051 4.341806 TGCATGATGAGGTTGTTTCTTGTT 59.658 37.500 0.00 0.00 0.00 2.83
3030 4052 5.163426 TGCATGATGAGGTTGTTTCTTGTTT 60.163 36.000 0.00 0.00 0.00 2.83
3257 4377 5.788450 CATTAGAAAGGTGTCACTCTCAGT 58.212 41.667 2.35 0.00 0.00 3.41
3364 4513 3.139077 CCCTCGGTTCCATAATAAGTGC 58.861 50.000 0.00 0.00 0.00 4.40
3433 4584 7.288158 GGAAGAGGGAGTATTACTGATTACTGT 59.712 40.741 0.00 0.00 0.00 3.55
3440 4591 7.378995 GGAGTATTACTGATTACTGTAGTTGCG 59.621 40.741 0.00 0.00 33.38 4.85
3443 4594 2.993899 ACTGATTACTGTAGTTGCGCAC 59.006 45.455 11.12 5.61 0.00 5.34
3445 4596 3.595173 TGATTACTGTAGTTGCGCACAT 58.405 40.909 11.12 3.66 0.00 3.21
3502 4653 4.150897 TCACCTGTTGAGCACTAAAACT 57.849 40.909 0.00 0.00 0.00 2.66
3644 4805 2.358898 AGCACACTGTGAAAACATGGAC 59.641 45.455 15.86 0.00 35.23 4.02
3682 4983 7.771826 ACTTTTAAAGTAGCACAGACCAAACTA 59.228 33.333 8.76 0.00 40.69 2.24
3725 5026 0.318869 CTGCAATTGAAGCGGCACAA 60.319 50.000 10.34 13.11 33.85 3.33
3728 5029 1.070643 GCAATTGAAGCGGCACAAAAC 60.071 47.619 10.34 5.89 0.00 2.43
3753 5054 3.602483 TCAAATGTACTCCTTTACGGCC 58.398 45.455 0.00 0.00 0.00 6.13
3774 5400 3.677121 CCTATCGATCCGATTCAGCTTTG 59.323 47.826 0.00 0.00 44.59 2.77
3778 5404 4.191544 TCGATCCGATTCAGCTTTGATTT 58.808 39.130 0.00 0.00 0.00 2.17
3780 5406 5.815222 TCGATCCGATTCAGCTTTGATTTAA 59.185 36.000 0.00 0.00 0.00 1.52
3781 5407 5.904080 CGATCCGATTCAGCTTTGATTTAAC 59.096 40.000 0.00 0.00 0.00 2.01
3824 6732 8.190784 AGTTGAATTTAGTTTGTTCTGGTTCAG 58.809 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.226345 CGGTATCAATCTATTCTTTCTTTTTGC 57.774 33.333 0.00 0.00 0.00 3.68
6 7 9.757227 CTCTCGGTATCAATCTATTCTTTCTTT 57.243 33.333 0.00 0.00 0.00 2.52
7 8 9.137459 TCTCTCGGTATCAATCTATTCTTTCTT 57.863 33.333 0.00 0.00 0.00 2.52
8 9 8.698973 TCTCTCGGTATCAATCTATTCTTTCT 57.301 34.615 0.00 0.00 0.00 2.52
9 10 8.026607 CCTCTCTCGGTATCAATCTATTCTTTC 58.973 40.741 0.00 0.00 0.00 2.62
10 11 7.039363 CCCTCTCTCGGTATCAATCTATTCTTT 60.039 40.741 0.00 0.00 0.00 2.52
11 12 6.435904 CCCTCTCTCGGTATCAATCTATTCTT 59.564 42.308 0.00 0.00 0.00 2.52
12 13 5.949354 CCCTCTCTCGGTATCAATCTATTCT 59.051 44.000 0.00 0.00 0.00 2.40
13 14 5.712917 ACCCTCTCTCGGTATCAATCTATTC 59.287 44.000 0.00 0.00 0.00 1.75
14 15 5.478679 CACCCTCTCTCGGTATCAATCTATT 59.521 44.000 0.00 0.00 30.42 1.73
15 16 5.013547 CACCCTCTCTCGGTATCAATCTAT 58.986 45.833 0.00 0.00 30.42 1.98
16 17 4.104261 TCACCCTCTCTCGGTATCAATCTA 59.896 45.833 0.00 0.00 30.42 1.98
17 18 3.117474 TCACCCTCTCTCGGTATCAATCT 60.117 47.826 0.00 0.00 30.42 2.40
18 19 3.223435 TCACCCTCTCTCGGTATCAATC 58.777 50.000 0.00 0.00 30.42 2.67
19 20 3.314307 TCACCCTCTCTCGGTATCAAT 57.686 47.619 0.00 0.00 30.42 2.57
20 21 2.758979 GTTCACCCTCTCTCGGTATCAA 59.241 50.000 0.00 0.00 30.42 2.57
21 22 2.291346 TGTTCACCCTCTCTCGGTATCA 60.291 50.000 0.00 0.00 30.42 2.15
22 23 2.376109 TGTTCACCCTCTCTCGGTATC 58.624 52.381 0.00 0.00 30.42 2.24
23 24 2.496470 GTTGTTCACCCTCTCTCGGTAT 59.504 50.000 0.00 0.00 30.42 2.73
24 25 1.891150 GTTGTTCACCCTCTCTCGGTA 59.109 52.381 0.00 0.00 30.42 4.02
25 26 0.680061 GTTGTTCACCCTCTCTCGGT 59.320 55.000 0.00 0.00 0.00 4.69
26 27 0.679505 TGTTGTTCACCCTCTCTCGG 59.320 55.000 0.00 0.00 0.00 4.63
27 28 2.224066 ACTTGTTGTTCACCCTCTCTCG 60.224 50.000 0.00 0.00 0.00 4.04
28 29 3.477210 ACTTGTTGTTCACCCTCTCTC 57.523 47.619 0.00 0.00 0.00 3.20
29 30 3.545703 CAACTTGTTGTTCACCCTCTCT 58.454 45.455 5.42 0.00 36.63 3.10
30 31 2.618709 CCAACTTGTTGTTCACCCTCTC 59.381 50.000 11.82 0.00 36.63 3.20
31 32 2.654863 CCAACTTGTTGTTCACCCTCT 58.345 47.619 11.82 0.00 36.63 3.69
32 33 1.067060 GCCAACTTGTTGTTCACCCTC 59.933 52.381 11.82 0.00 36.63 4.30
33 34 1.111277 GCCAACTTGTTGTTCACCCT 58.889 50.000 11.82 0.00 36.63 4.34
34 35 0.820871 TGCCAACTTGTTGTTCACCC 59.179 50.000 11.82 0.00 36.63 4.61
35 36 2.663826 TTGCCAACTTGTTGTTCACC 57.336 45.000 11.82 0.00 36.63 4.02
36 37 4.180057 TCAATTGCCAACTTGTTGTTCAC 58.820 39.130 11.82 0.91 36.63 3.18
37 38 4.159321 TCTCAATTGCCAACTTGTTGTTCA 59.841 37.500 11.82 7.05 36.63 3.18
38 39 4.681744 TCTCAATTGCCAACTTGTTGTTC 58.318 39.130 11.82 4.86 36.63 3.18
39 40 4.734398 TCTCAATTGCCAACTTGTTGTT 57.266 36.364 11.82 0.00 39.92 2.83
40 41 4.441913 CCTTCTCAATTGCCAACTTGTTGT 60.442 41.667 11.82 0.00 0.00 3.32
41 42 4.053295 CCTTCTCAATTGCCAACTTGTTG 58.947 43.478 0.00 6.52 0.00 3.33
42 43 3.706086 ACCTTCTCAATTGCCAACTTGTT 59.294 39.130 0.00 0.00 0.00 2.83
43 44 3.299503 ACCTTCTCAATTGCCAACTTGT 58.700 40.909 0.00 0.00 0.00 3.16
44 45 3.305608 GGACCTTCTCAATTGCCAACTTG 60.306 47.826 0.00 0.00 0.00 3.16
45 46 2.893489 GGACCTTCTCAATTGCCAACTT 59.107 45.455 0.00 0.00 0.00 2.66
46 47 2.519013 GGACCTTCTCAATTGCCAACT 58.481 47.619 0.00 0.00 0.00 3.16
47 48 1.200020 CGGACCTTCTCAATTGCCAAC 59.800 52.381 0.00 0.00 0.00 3.77
48 49 1.533625 CGGACCTTCTCAATTGCCAA 58.466 50.000 0.00 0.00 0.00 4.52
49 50 0.322456 CCGGACCTTCTCAATTGCCA 60.322 55.000 0.00 0.00 0.00 4.92
50 51 0.035439 TCCGGACCTTCTCAATTGCC 60.035 55.000 0.00 0.00 0.00 4.52
51 52 1.087501 GTCCGGACCTTCTCAATTGC 58.912 55.000 24.75 0.00 0.00 3.56
52 53 2.770164 AGTCCGGACCTTCTCAATTG 57.230 50.000 30.82 0.00 0.00 2.32
53 54 3.790089 AAAGTCCGGACCTTCTCAATT 57.210 42.857 30.82 13.13 0.00 2.32
54 55 3.412386 CAAAAGTCCGGACCTTCTCAAT 58.588 45.455 30.82 6.96 0.00 2.57
55 56 2.486548 CCAAAAGTCCGGACCTTCTCAA 60.487 50.000 30.82 0.00 0.00 3.02
56 57 1.071699 CCAAAAGTCCGGACCTTCTCA 59.928 52.381 30.82 0.00 0.00 3.27
57 58 1.346722 TCCAAAAGTCCGGACCTTCTC 59.653 52.381 30.82 5.02 0.00 2.87
61 62 1.358152 TGATCCAAAAGTCCGGACCT 58.642 50.000 30.82 16.53 33.05 3.85
65 66 2.684881 CTCCATTGATCCAAAAGTCCGG 59.315 50.000 0.00 0.00 0.00 5.14
67 68 5.653769 TCAATCTCCATTGATCCAAAAGTCC 59.346 40.000 0.00 0.00 42.99 3.85
69 70 6.487828 TCTCAATCTCCATTGATCCAAAAGT 58.512 36.000 0.00 0.00 46.01 2.66
78 79 4.408270 CCTCTCCTTCTCAATCTCCATTGA 59.592 45.833 0.00 0.00 45.20 2.57
79 80 4.163839 ACCTCTCCTTCTCAATCTCCATTG 59.836 45.833 0.00 0.00 40.91 2.82
83 84 3.681313 GCAACCTCTCCTTCTCAATCTCC 60.681 52.174 0.00 0.00 0.00 3.71
123 124 6.040955 TCTGCTAACATTATCCTCGAGTCATT 59.959 38.462 12.31 0.00 0.00 2.57
125 126 4.887655 TCTGCTAACATTATCCTCGAGTCA 59.112 41.667 12.31 0.00 0.00 3.41
128 129 4.222886 CGTCTGCTAACATTATCCTCGAG 58.777 47.826 5.13 5.13 0.00 4.04
134 135 3.303395 GGCTTGCGTCTGCTAACATTATC 60.303 47.826 0.00 0.00 43.34 1.75
158 159 5.591472 TCATGTATTTCCTTGCTCATCCAAG 59.409 40.000 0.00 0.00 41.40 3.61
168 169 3.270027 TGGCGAGTCATGTATTTCCTTG 58.730 45.455 0.00 0.00 0.00 3.61
178 179 1.205655 TCTTCCTCTTGGCGAGTCATG 59.794 52.381 0.77 0.00 38.11 3.07
233 234 2.045926 GTCGCCATTGCCACTCCT 60.046 61.111 0.00 0.00 0.00 3.69
234 235 2.359850 TGTCGCCATTGCCACTCC 60.360 61.111 0.00 0.00 29.05 3.85
238 239 2.046023 CCTCTGTCGCCATTGCCA 60.046 61.111 0.00 0.00 0.00 4.92
239 240 1.817099 CTCCTCTGTCGCCATTGCC 60.817 63.158 0.00 0.00 0.00 4.52
241 242 0.674581 TTGCTCCTCTGTCGCCATTG 60.675 55.000 0.00 0.00 0.00 2.82
242 243 0.392193 CTTGCTCCTCTGTCGCCATT 60.392 55.000 0.00 0.00 0.00 3.16
245 246 2.817396 GCTTGCTCCTCTGTCGCC 60.817 66.667 0.00 0.00 0.00 5.54
247 248 2.507992 CCGCTTGCTCCTCTGTCG 60.508 66.667 0.00 0.00 0.00 4.35
248 249 2.817396 GCCGCTTGCTCCTCTGTC 60.817 66.667 0.00 0.00 36.87 3.51
249 250 3.630013 TGCCGCTTGCTCCTCTGT 61.630 61.111 0.00 0.00 42.00 3.41
260 261 4.530857 GCTACCATCCGTGCCGCT 62.531 66.667 0.00 0.00 0.00 5.52
264 265 3.264897 CGCTGCTACCATCCGTGC 61.265 66.667 0.00 0.00 0.00 5.34
269 270 1.009829 CCTGTTTCGCTGCTACCATC 58.990 55.000 0.00 0.00 0.00 3.51
280 281 2.114670 ATCCATGCCGCCTGTTTCG 61.115 57.895 0.00 0.00 0.00 3.46
282 283 2.053865 CCATCCATGCCGCCTGTTT 61.054 57.895 0.00 0.00 0.00 2.83
285 286 2.593725 CTCCATCCATGCCGCCTG 60.594 66.667 0.00 0.00 0.00 4.85
287 288 2.592861 GTCTCCATCCATGCCGCC 60.593 66.667 0.00 0.00 0.00 6.13
290 291 1.070445 CTCCGTCTCCATCCATGCC 59.930 63.158 0.00 0.00 0.00 4.40
294 295 2.060383 CCTGCTCCGTCTCCATCCA 61.060 63.158 0.00 0.00 0.00 3.41
295 296 2.818132 CCTGCTCCGTCTCCATCC 59.182 66.667 0.00 0.00 0.00 3.51
303 304 3.753434 CTCTGTCGCCTGCTCCGT 61.753 66.667 0.00 0.00 0.00 4.69
305 306 1.153667 CTTCTCTGTCGCCTGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
313 314 2.169789 CATGCCGCCTTCTCTGTCG 61.170 63.158 0.00 0.00 0.00 4.35
316 317 1.147824 ATCCATGCCGCCTTCTCTG 59.852 57.895 0.00 0.00 0.00 3.35
331 332 0.532862 ATCATTGGTCGACGCCATCC 60.533 55.000 9.92 0.00 38.48 3.51
338 339 1.560923 CAGACGGATCATTGGTCGAC 58.439 55.000 7.13 7.13 35.87 4.20
342 344 1.153369 CGCCAGACGGATCATTGGT 60.153 57.895 0.00 0.00 38.44 3.67
352 354 2.885644 CGGACCAATCGCCAGACG 60.886 66.667 0.00 0.00 45.62 4.18
378 380 6.165577 ACATGGCAAAATGAAATACAAGTCC 58.834 36.000 0.00 0.00 0.00 3.85
379 381 6.311200 GGACATGGCAAAATGAAATACAAGTC 59.689 38.462 0.00 0.00 0.00 3.01
385 387 4.019858 TCCGGACATGGCAAAATGAAATA 58.980 39.130 0.00 0.00 0.00 1.40
396 398 1.135402 GTTCAACAATCCGGACATGGC 60.135 52.381 20.00 0.00 0.00 4.40
400 402 4.545208 TCATAGTTCAACAATCCGGACA 57.455 40.909 6.12 0.00 0.00 4.02
401 403 6.436843 AAATCATAGTTCAACAATCCGGAC 57.563 37.500 6.12 0.00 0.00 4.79
402 404 8.746052 AATAAATCATAGTTCAACAATCCGGA 57.254 30.769 6.61 6.61 0.00 5.14
403 405 9.801873 AAAATAAATCATAGTTCAACAATCCGG 57.198 29.630 0.00 0.00 0.00 5.14
429 431 3.181505 CGGTTCAACAAAGCAACACAGTA 60.182 43.478 0.00 0.00 34.98 2.74
433 435 2.271821 ACGGTTCAACAAAGCAACAC 57.728 45.000 0.00 0.00 34.98 3.32
438 440 3.862845 ACAATTCAACGGTTCAACAAAGC 59.137 39.130 0.00 0.00 0.00 3.51
442 444 4.336713 TCATCACAATTCAACGGTTCAACA 59.663 37.500 0.00 0.00 0.00 3.33
443 445 4.854399 TCATCACAATTCAACGGTTCAAC 58.146 39.130 0.00 0.00 0.00 3.18
450 452 6.417339 TGACACAAATTCATCACAATTCAACG 59.583 34.615 0.00 0.00 0.00 4.10
464 466 6.639686 GCATGTGGATCATATGACACAAATTC 59.360 38.462 24.68 12.08 45.65 2.17
486 489 2.662866 CAAACCCTCAGATCCATGCAT 58.337 47.619 0.00 0.00 0.00 3.96
496 508 1.667236 TATCGCATGCAAACCCTCAG 58.333 50.000 19.57 0.00 0.00 3.35
500 512 2.859538 CACAATTATCGCATGCAAACCC 59.140 45.455 19.57 0.00 0.00 4.11
501 513 2.859538 CCACAATTATCGCATGCAAACC 59.140 45.455 19.57 0.00 0.00 3.27
510 522 1.360192 GGGCAGCCACAATTATCGC 59.640 57.895 15.19 0.00 0.00 4.58
511 523 1.102154 TTGGGCAGCCACAATTATCG 58.898 50.000 15.19 0.00 0.00 2.92
529 541 1.780503 GGCCCCTCATATTTGCTGTT 58.219 50.000 0.00 0.00 0.00 3.16
530 542 0.466189 CGGCCCCTCATATTTGCTGT 60.466 55.000 0.00 0.00 0.00 4.40
534 546 0.182537 TGGACGGCCCCTCATATTTG 59.817 55.000 3.83 0.00 0.00 2.32
563 575 4.778415 CTCACCCTGACGCGTCCG 62.778 72.222 34.34 28.10 41.14 4.79
577 589 3.620300 CTTACACGTCCGCGGCTCA 62.620 63.158 23.51 0.00 43.45 4.26
578 590 2.879462 CTTACACGTCCGCGGCTC 60.879 66.667 23.51 15.19 43.45 4.70
579 591 3.338126 CTCTTACACGTCCGCGGCT 62.338 63.158 23.51 1.28 43.45 5.52
580 592 2.879462 CTCTTACACGTCCGCGGC 60.879 66.667 23.51 15.21 43.45 6.53
581 593 2.202570 CCTCTTACACGTCCGCGG 60.203 66.667 22.12 22.12 43.45 6.46
582 594 1.800315 CACCTCTTACACGTCCGCG 60.800 63.158 0.00 0.00 44.93 6.46
583 595 0.172803 ATCACCTCTTACACGTCCGC 59.827 55.000 0.00 0.00 0.00 5.54
585 597 2.415512 GCAAATCACCTCTTACACGTCC 59.584 50.000 0.00 0.00 0.00 4.79
586 598 3.326747 AGCAAATCACCTCTTACACGTC 58.673 45.455 0.00 0.00 0.00 4.34
587 599 3.402628 AGCAAATCACCTCTTACACGT 57.597 42.857 0.00 0.00 0.00 4.49
588 600 4.929808 ACTTAGCAAATCACCTCTTACACG 59.070 41.667 0.00 0.00 0.00 4.49
589 601 5.351740 GGACTTAGCAAATCACCTCTTACAC 59.648 44.000 0.00 0.00 0.00 2.90
590 602 5.488341 GGACTTAGCAAATCACCTCTTACA 58.512 41.667 0.00 0.00 0.00 2.41
591 603 4.567159 CGGACTTAGCAAATCACCTCTTAC 59.433 45.833 0.00 0.00 0.00 2.34
593 605 3.600388 CGGACTTAGCAAATCACCTCTT 58.400 45.455 0.00 0.00 0.00 2.85
594 606 2.093447 CCGGACTTAGCAAATCACCTCT 60.093 50.000 0.00 0.00 0.00 3.69
595 607 2.280628 CCGGACTTAGCAAATCACCTC 58.719 52.381 0.00 0.00 0.00 3.85
596 608 1.628846 ACCGGACTTAGCAAATCACCT 59.371 47.619 9.46 0.00 0.00 4.00
599 611 3.134574 ACAACCGGACTTAGCAAATCA 57.865 42.857 9.46 0.00 0.00 2.57
607 619 3.795623 GAGCATCTACAACCGGACTTA 57.204 47.619 9.46 0.00 0.00 2.24
642 658 7.210873 ACAAAAAGGCAAACCGAATTACATAA 58.789 30.769 0.00 0.00 42.76 1.90
652 668 4.678622 ACTTCTTACAAAAAGGCAAACCG 58.321 39.130 0.00 0.00 42.76 4.44
714 733 9.082313 CCCAATAAAAGAATGCAACCTATAGAT 57.918 33.333 0.00 0.00 0.00 1.98
721 740 7.503521 TTTTTCCCAATAAAAGAATGCAACC 57.496 32.000 0.00 0.00 30.47 3.77
780 799 8.832521 CGCTTCCATTTACCTTGTGTATTAATA 58.167 33.333 0.00 0.00 0.00 0.98
782 801 6.655848 ACGCTTCCATTTACCTTGTGTATTAA 59.344 34.615 0.00 0.00 0.00 1.40
785 804 4.585879 ACGCTTCCATTTACCTTGTGTAT 58.414 39.130 0.00 0.00 0.00 2.29
793 1011 7.916914 AATATACCATACGCTTCCATTTACC 57.083 36.000 0.00 0.00 0.00 2.85
794 1012 8.234546 CCAAATATACCATACGCTTCCATTTAC 58.765 37.037 0.00 0.00 0.00 2.01
803 1021 7.630082 ACCATATTCCAAATATACCATACGCT 58.370 34.615 0.00 0.00 0.00 5.07
813 1031 9.166222 TGTGGAGTAGTACCATATTCCAAATAT 57.834 33.333 9.21 0.00 41.56 1.28
814 1032 8.555896 TGTGGAGTAGTACCATATTCCAAATA 57.444 34.615 9.21 0.00 41.56 1.40
816 1034 6.877668 TGTGGAGTAGTACCATATTCCAAA 57.122 37.500 9.21 2.76 41.56 3.28
817 1035 6.877668 TTGTGGAGTAGTACCATATTCCAA 57.122 37.500 9.21 0.30 41.56 3.53
818 1036 6.442564 AGTTTGTGGAGTAGTACCATATTCCA 59.557 38.462 4.51 4.51 38.74 3.53
819 1037 6.761714 CAGTTTGTGGAGTAGTACCATATTCC 59.238 42.308 0.00 0.00 39.69 3.01
820 1038 7.553334 TCAGTTTGTGGAGTAGTACCATATTC 58.447 38.462 0.00 0.00 39.69 1.75
821 1039 7.490657 TCAGTTTGTGGAGTAGTACCATATT 57.509 36.000 0.00 0.00 39.69 1.28
822 1040 7.676683 ATCAGTTTGTGGAGTAGTACCATAT 57.323 36.000 0.00 0.00 39.69 1.78
824 1042 6.374417 AATCAGTTTGTGGAGTAGTACCAT 57.626 37.500 0.00 0.00 39.69 3.55
825 1043 5.566032 CGAATCAGTTTGTGGAGTAGTACCA 60.566 44.000 0.00 0.00 34.84 3.25
826 1044 4.863131 CGAATCAGTTTGTGGAGTAGTACC 59.137 45.833 0.00 0.00 0.00 3.34
827 1045 4.863131 CCGAATCAGTTTGTGGAGTAGTAC 59.137 45.833 0.00 0.00 0.00 2.73
828 1046 4.768448 TCCGAATCAGTTTGTGGAGTAGTA 59.232 41.667 0.00 0.00 0.00 1.82
829 1047 3.576982 TCCGAATCAGTTTGTGGAGTAGT 59.423 43.478 0.00 0.00 0.00 2.73
830 1048 3.927142 GTCCGAATCAGTTTGTGGAGTAG 59.073 47.826 0.00 0.00 0.00 2.57
831 1049 3.613193 CGTCCGAATCAGTTTGTGGAGTA 60.613 47.826 0.00 0.00 0.00 2.59
832 1050 2.767505 GTCCGAATCAGTTTGTGGAGT 58.232 47.619 0.00 0.00 0.00 3.85
833 1051 1.726791 CGTCCGAATCAGTTTGTGGAG 59.273 52.381 0.00 0.00 0.00 3.86
834 1052 1.069513 ACGTCCGAATCAGTTTGTGGA 59.930 47.619 0.00 0.00 0.00 4.02
836 1054 2.349438 CCAACGTCCGAATCAGTTTGTG 60.349 50.000 0.00 0.00 0.00 3.33
837 1055 1.871039 CCAACGTCCGAATCAGTTTGT 59.129 47.619 0.00 0.00 0.00 2.83
838 1056 2.139917 TCCAACGTCCGAATCAGTTTG 58.860 47.619 0.00 0.00 0.00 2.93
839 1057 2.536761 TCCAACGTCCGAATCAGTTT 57.463 45.000 0.00 0.00 0.00 2.66
840 1058 2.536761 TTCCAACGTCCGAATCAGTT 57.463 45.000 0.00 0.00 0.00 3.16
841 1059 2.742053 CAATTCCAACGTCCGAATCAGT 59.258 45.455 9.71 0.00 0.00 3.41
842 1060 3.000041 TCAATTCCAACGTCCGAATCAG 59.000 45.455 9.71 6.93 0.00 2.90
843 1061 3.046968 TCAATTCCAACGTCCGAATCA 57.953 42.857 9.71 0.00 0.00 2.57
844 1062 3.682858 TCTTCAATTCCAACGTCCGAATC 59.317 43.478 9.71 0.00 0.00 2.52
845 1063 3.670625 TCTTCAATTCCAACGTCCGAAT 58.329 40.909 4.64 4.64 0.00 3.34
846 1064 3.064207 CTCTTCAATTCCAACGTCCGAA 58.936 45.455 0.00 0.00 0.00 4.30
848 1066 2.683968 TCTCTTCAATTCCAACGTCCG 58.316 47.619 0.00 0.00 0.00 4.79
849 1067 3.120165 GCTTCTCTTCAATTCCAACGTCC 60.120 47.826 0.00 0.00 0.00 4.79
851 1069 3.499918 CAGCTTCTCTTCAATTCCAACGT 59.500 43.478 0.00 0.00 0.00 3.99
853 1071 5.444663 AACAGCTTCTCTTCAATTCCAAC 57.555 39.130 0.00 0.00 0.00 3.77
854 1072 5.593909 TGAAACAGCTTCTCTTCAATTCCAA 59.406 36.000 0.00 0.00 34.86 3.53
855 1073 5.132502 TGAAACAGCTTCTCTTCAATTCCA 58.867 37.500 0.00 0.00 34.86 3.53
856 1074 5.695851 TGAAACAGCTTCTCTTCAATTCC 57.304 39.130 0.00 0.00 34.86 3.01
857 1075 6.091437 CCATGAAACAGCTTCTCTTCAATTC 58.909 40.000 0.00 0.00 34.86 2.17
898 1316 0.740737 GGCCAAATGTCCGAATCAGG 59.259 55.000 0.00 0.00 0.00 3.86
899 1317 0.740737 GGGCCAAATGTCCGAATCAG 59.259 55.000 4.39 0.00 0.00 2.90
900 1318 0.038890 TGGGCCAAATGTCCGAATCA 59.961 50.000 2.13 0.00 0.00 2.57
901 1319 1.135112 GTTGGGCCAAATGTCCGAATC 60.135 52.381 22.82 0.00 0.00 2.52
921 1343 0.247301 GTTTCGGCGAGCGAGAAATG 60.247 55.000 10.46 0.00 36.45 2.32
959 1392 1.672881 GGTCTTGCGGAATGATTGAGG 59.327 52.381 0.00 0.00 0.00 3.86
960 1393 2.358957 TGGTCTTGCGGAATGATTGAG 58.641 47.619 0.00 0.00 0.00 3.02
961 1394 2.488204 TGGTCTTGCGGAATGATTGA 57.512 45.000 0.00 0.00 0.00 2.57
962 1395 3.244976 GTTTGGTCTTGCGGAATGATTG 58.755 45.455 0.00 0.00 0.00 2.67
963 1396 2.231235 GGTTTGGTCTTGCGGAATGATT 59.769 45.455 0.00 0.00 0.00 2.57
975 1408 3.647771 GGCGGAGGGGTTTGGTCT 61.648 66.667 0.00 0.00 0.00 3.85
1027 1489 1.145900 TCCAAATTGCTCCTGGGGGA 61.146 55.000 0.00 0.00 39.70 4.81
1076 1550 1.267806 GCATCAGGTTTATGCCGATGG 59.732 52.381 13.98 0.00 43.17 3.51
1113 1587 2.041612 GGCGGGTAGGGGAGGTAA 60.042 66.667 0.00 0.00 0.00 2.85
1314 1800 1.203523 AGATGACTGTCGACAAGAGCC 59.796 52.381 20.49 9.01 0.00 4.70
1585 2089 1.220477 GGGAGGAGCAGCTGAAGAC 59.780 63.158 20.43 3.82 0.00 3.01
1818 2322 1.903877 ATCCCAGCTGAAGACACCGG 61.904 60.000 17.39 0.00 0.00 5.28
2050 2571 8.480501 AGAGATGCAAATTAAATTAGGCATTGT 58.519 29.630 9.78 3.07 40.91 2.71
2051 2572 8.761497 CAGAGATGCAAATTAAATTAGGCATTG 58.239 33.333 9.78 3.18 40.91 2.82
2210 2856 2.034558 ACTTTCTTGACACAATTGCGGG 59.965 45.455 5.05 0.00 0.00 6.13
2219 2865 1.680338 ACCAGGCACTTTCTTGACAC 58.320 50.000 0.00 0.00 34.60 3.67
2248 2894 1.909986 GGTCTCCAGGTTAGGAAAGCT 59.090 52.381 0.00 0.00 44.16 3.74
2293 2939 5.049405 ACAATGCAGCAAGTGTAGTTAAGTC 60.049 40.000 12.32 0.00 0.00 3.01
2336 3015 5.126222 CAGACTCATAGTTCTGACCTTGCTA 59.874 44.000 0.00 0.00 30.29 3.49
2371 3196 2.028876 CAGCAGGCCATCAATCAATCA 58.971 47.619 5.01 0.00 0.00 2.57
2372 3197 1.269621 GCAGCAGGCCATCAATCAATC 60.270 52.381 5.01 0.00 36.11 2.67
2373 3198 0.750850 GCAGCAGGCCATCAATCAAT 59.249 50.000 5.01 0.00 36.11 2.57
2374 3199 0.612453 TGCAGCAGGCCATCAATCAA 60.612 50.000 5.01 0.00 43.89 2.57
2405 3321 9.473007 CATAGTTCAGGGATCTTATCTATGAGA 57.527 37.037 0.00 0.00 37.03 3.27
2856 3861 3.842732 TCGTTTCAGATTCGCAGTAGA 57.157 42.857 0.00 0.00 0.00 2.59
2892 3897 0.462047 GGCACGGCATACTGCTACTT 60.462 55.000 0.00 0.00 44.28 2.24
2941 3956 3.823281 TCCCGACAACACAAAGTCTAA 57.177 42.857 0.00 0.00 32.68 2.10
2964 3979 4.009675 TGCAGGTATTTTTAGCTCCTGTG 58.990 43.478 14.78 0.00 44.99 3.66
2992 4014 1.897133 TCATGCAGAAAGCTTGCCAAT 59.103 42.857 0.00 0.00 45.30 3.16
3030 4052 3.814842 CACATAAGTCTTGACTTGGCACA 59.185 43.478 21.97 5.96 0.00 4.57
3057 4079 4.074970 CTGTTACTTCTTCCACCAGCATT 58.925 43.478 0.00 0.00 0.00 3.56
3110 4137 2.718073 GCCCTGCTGATTGGCTTGG 61.718 63.158 2.73 0.00 42.01 3.61
3241 4361 4.487714 TTCAAACTGAGAGTGACACCTT 57.512 40.909 0.84 0.00 0.00 3.50
3302 4427 9.803315 AAAGGAAACTGTAAAAGTCTGAAAATC 57.197 29.630 0.00 0.00 42.68 2.17
3364 4513 9.757227 TTTTAGTTCAAATGACTAAAACCATGG 57.243 29.630 11.19 11.19 39.51 3.66
3443 4594 8.929827 TGTTTTGCCAAGATTTCACATATATG 57.070 30.769 11.29 11.29 0.00 1.78
3445 4596 8.801299 TCTTGTTTTGCCAAGATTTCACATATA 58.199 29.630 0.00 0.00 44.39 0.86
3460 4611 6.753744 GGTGAAGATATGATTCTTGTTTTGCC 59.246 38.462 0.00 0.00 36.10 4.52
3502 4653 3.097614 GAGAGGTAGGCAAACCAGAGTA 58.902 50.000 11.12 0.00 42.40 2.59
3644 4805 9.151471 TGCTACTTTAAAAGTGCTATTCTGTAG 57.849 33.333 0.00 0.00 42.84 2.74
3682 4983 4.584325 TGCACTTGCTACCTTCATTTTTCT 59.416 37.500 2.33 0.00 42.66 2.52
3725 5026 7.308951 CCGTAAAGGAGTACATTTGATTGGTTT 60.309 37.037 0.00 0.00 45.00 3.27
3728 5029 5.448632 GCCGTAAAGGAGTACATTTGATTGG 60.449 44.000 0.00 0.00 45.00 3.16
3753 5054 4.550422 TCAAAGCTGAATCGGATCGATAG 58.450 43.478 0.00 0.00 46.30 2.08
3774 5400 9.915629 ACTCATGGATATCTAACTCGTTAAATC 57.084 33.333 2.05 0.00 0.00 2.17
3778 5404 8.459911 TCAACTCATGGATATCTAACTCGTTA 57.540 34.615 2.05 0.00 0.00 3.18
3780 5406 6.961360 TCAACTCATGGATATCTAACTCGT 57.039 37.500 2.05 0.00 0.00 4.18
3781 5407 8.824159 AATTCAACTCATGGATATCTAACTCG 57.176 34.615 2.05 0.00 0.00 4.18
3824 6732 0.099436 CAGCTGGCCTGCGAAAATAC 59.901 55.000 26.64 0.38 38.13 1.89


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

AutoCloner maintained by Alex Coulton.