Multiple sequence alignment - TraesCS5D01G382400

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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 TraesCS5D01G382400 chr5D 100.000 6027 0 0 1 6027 452222395 452216369 0.000000e+00 11130.0
1 TraesCS5D01G382400 chr5D 89.241 158 10 3 5870 6027 451979113 451978963 2.220000e-44 191.0
2 TraesCS5D01G382400 chr5D 87.117 163 17 4 1537 1696 489774790 489774951 1.330000e-41 182.0
3 TraesCS5D01G382400 chr5D 93.548 93 5 1 2915 3006 128577672 128577580 2.930000e-28 137.0
4 TraesCS5D01G382400 chr5D 81.208 149 17 8 129 271 67044749 67044606 6.390000e-20 110.0
5 TraesCS5D01G382400 chr5D 79.605 152 24 6 124 271 30433095 30432947 1.070000e-17 102.0
6 TraesCS5D01G382400 chr5D 81.250 80 11 3 201 276 429301575 429301496 1.810000e-05 62.1
7 TraesCS5D01G382400 chr5B 95.069 2839 100 20 3206 6027 552295723 552292908 0.000000e+00 4431.0
8 TraesCS5D01G382400 chr5B 91.085 1862 99 34 974 2813 552297778 552295962 0.000000e+00 2457.0
9 TraesCS5D01G382400 chr5B 95.793 618 26 0 350 967 680927260 680927877 0.000000e+00 998.0
10 TraesCS5D01G382400 chr5B 82.836 268 41 4 1 266 552298173 552297909 1.010000e-57 235.0
11 TraesCS5D01G382400 chr5B 90.116 172 12 3 2999 3170 552295895 552295729 1.020000e-52 219.0
12 TraesCS5D01G382400 chr5B 87.730 163 16 4 1537 1696 603954030 603954191 2.870000e-43 187.0
13 TraesCS5D01G382400 chr5B 97.753 89 2 0 2914 3002 428577432 428577344 2.910000e-33 154.0
14 TraesCS5D01G382400 chr5B 91.262 103 8 1 2914 3015 541093231 541093333 8.150000e-29 139.0
15 TraesCS5D01G382400 chr5B 93.548 93 5 1 2915 3006 140966014 140965922 2.930000e-28 137.0
16 TraesCS5D01G382400 chr5B 83.750 80 12 1 134 213 561974586 561974508 2.330000e-09 75.0
17 TraesCS5D01G382400 chr5A 91.185 3063 169 40 2999 6027 570939920 570936925 0.000000e+00 4067.0
18 TraesCS5D01G382400 chr5A 91.909 1891 107 25 1051 2913 570941795 570939923 0.000000e+00 2603.0
19 TraesCS5D01G382400 chr5A 87.730 163 16 4 1537 1696 611339333 611339494 2.870000e-43 187.0
20 TraesCS5D01G382400 chr5A 89.000 100 9 2 2915 3013 578056663 578056761 8.200000e-24 122.0
21 TraesCS5D01G382400 chrUn 96.434 617 21 1 350 965 83929027 83928411 0.000000e+00 1016.0
22 TraesCS5D01G382400 chr6D 96.141 622 22 2 350 970 464465386 464466006 0.000000e+00 1014.0
23 TraesCS5D01G382400 chr6D 96.260 615 23 0 350 964 14615552 14616166 0.000000e+00 1009.0
24 TraesCS5D01G382400 chr3B 95.779 616 25 1 350 964 59705304 59704689 0.000000e+00 992.0
25 TraesCS5D01G382400 chr3B 100.000 85 0 0 2915 2999 551513888 551513972 2.250000e-34 158.0
26 TraesCS5D01G382400 chr3B 88.785 107 11 1 2915 3020 409602640 409602534 4.900000e-26 130.0
27 TraesCS5D01G382400 chr7D 95.484 620 27 1 350 968 29788841 29789460 0.000000e+00 989.0
28 TraesCS5D01G382400 chr7D 88.182 110 7 5 2914 3023 57777666 57777563 6.340000e-25 126.0
29 TraesCS5D01G382400 chr6B 95.624 617 26 1 350 965 117774665 117774049 0.000000e+00 989.0
30 TraesCS5D01G382400 chr1D 95.338 622 29 0 350 971 406828813 406828192 0.000000e+00 989.0
31 TraesCS5D01G382400 chr1D 83.133 83 9 4 198 276 459524443 459524362 3.010000e-08 71.3
32 TraesCS5D01G382400 chr1D 83.133 83 9 4 198 276 459623620 459623701 3.010000e-08 71.3
33 TraesCS5D01G382400 chr1D 82.051 78 14 0 271 348 420094233 420094156 3.900000e-07 67.6
34 TraesCS5D01G382400 chr4D 95.484 620 25 3 350 969 47729321 47728705 0.000000e+00 987.0
35 TraesCS5D01G382400 chr4D 95.604 91 4 0 2915 3005 252173788 252173698 4.870000e-31 147.0
36 TraesCS5D01G382400 chr3A 95.833 96 4 0 2904 2999 99426174 99426269 8.090000e-34 156.0
37 TraesCS5D01G382400 chr3A 86.916 107 13 1 2915 3020 420745307 420745201 1.060000e-22 119.0
38 TraesCS5D01G382400 chr7B 97.753 89 2 0 2915 3003 428966927 428966839 2.910000e-33 154.0
39 TraesCS5D01G382400 chr7B 89.720 107 7 3 2915 3020 93439151 93439048 3.790000e-27 134.0
40 TraesCS5D01G382400 chr7B 89.423 104 9 2 2915 3016 503119604 503119501 4.900000e-26 130.0
41 TraesCS5D01G382400 chr7B 97.368 38 0 1 270 306 513068477 513068440 5.040000e-06 63.9
42 TraesCS5D01G382400 chr2D 91.509 106 5 3 2900 3003 208540243 208540140 6.300000e-30 143.0
43 TraesCS5D01G382400 chr2D 80.723 83 12 3 198 276 628333882 628333964 1.810000e-05 62.1
44 TraesCS5D01G382400 chr2D 80.723 83 12 3 198 276 628347854 628347936 1.810000e-05 62.1
45 TraesCS5D01G382400 chr2A 89.474 114 9 2 2889 3002 57459144 57459034 2.260000e-29 141.0
46 TraesCS5D01G382400 chr2A 83.544 79 13 0 270 348 89536489 89536411 2.330000e-09 75.0
47 TraesCS5D01G382400 chr2A 82.278 79 14 0 270 348 68322314 68322236 1.080000e-07 69.4
48 TraesCS5D01G382400 chr4A 91.262 103 7 2 2915 3016 259379673 259379572 8.150000e-29 139.0
49 TraesCS5D01G382400 chr4B 87.619 105 10 3 2914 3015 21543450 21543554 1.060000e-22 119.0
50 TraesCS5D01G382400 chr4B 77.358 106 17 6 169 271 77649460 77649561 8.440000e-04 56.5
51 TraesCS5D01G382400 chr7A 82.278 79 14 0 270 348 174220071 174220149 1.080000e-07 69.4
52 TraesCS5D01G382400 chr7A 84.058 69 11 0 270 338 99678060 99678128 3.900000e-07 67.6
53 TraesCS5D01G382400 chr1B 81.928 83 11 4 198 276 575640805 575640723 3.900000e-07 67.6


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 TraesCS5D01G382400 chr5D 452216369 452222395 6026 True 11130.0 11130 100.0000 1 6027 1 chr5D.!!$R6 6026
1 TraesCS5D01G382400 chr5B 552292908 552298173 5265 True 1835.5 4431 89.7765 1 6027 4 chr5B.!!$R4 6026
2 TraesCS5D01G382400 chr5B 680927260 680927877 617 False 998.0 998 95.7930 350 967 1 chr5B.!!$F3 617
3 TraesCS5D01G382400 chr5A 570936925 570941795 4870 True 3335.0 4067 91.5470 1051 6027 2 chr5A.!!$R1 4976
4 TraesCS5D01G382400 chrUn 83928411 83929027 616 True 1016.0 1016 96.4340 350 965 1 chrUn.!!$R1 615
5 TraesCS5D01G382400 chr6D 464465386 464466006 620 False 1014.0 1014 96.1410 350 970 1 chr6D.!!$F2 620
6 TraesCS5D01G382400 chr6D 14615552 14616166 614 False 1009.0 1009 96.2600 350 964 1 chr6D.!!$F1 614
7 TraesCS5D01G382400 chr3B 59704689 59705304 615 True 992.0 992 95.7790 350 964 1 chr3B.!!$R1 614
8 TraesCS5D01G382400 chr7D 29788841 29789460 619 False 989.0 989 95.4840 350 968 1 chr7D.!!$F1 618
9 TraesCS5D01G382400 chr6B 117774049 117774665 616 True 989.0 989 95.6240 350 965 1 chr6B.!!$R1 615
10 TraesCS5D01G382400 chr1D 406828192 406828813 621 True 989.0 989 95.3380 350 971 1 chr1D.!!$R1 621
11 TraesCS5D01G382400 chr4D 47728705 47729321 616 True 987.0 987 95.4840 350 969 1 chr4D.!!$R1 619

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
297 338 0.108424 CCGGCTCAGTCTTTCAGAGG 60.108 60.0 0.00 0.0 31.57 3.69 F
1136 1179 0.805322 GAGGACACAGATGCAGAGCG 60.805 60.0 0.00 0.0 0.00 5.03 F
2101 2171 0.036577 CTGCAGAGTGCTGGCTACTT 60.037 55.0 8.42 0.0 45.31 2.24 F
3202 3281 0.332972 GGGATTCTGCCTGGAAAGGT 59.667 55.0 0.00 0.0 0.00 3.50 F
3920 4007 0.329596 AGGGGTCAGGCATGAAAGTC 59.670 55.0 0.92 0.0 37.14 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 1979 0.881796 GCTACAAACCCCAGCAGAAC 59.118 55.0 0.00 0.0 35.35 3.01 R
2401 2472 0.615850 TGTGGTGTGTGAGGTGACAA 59.384 50.0 0.00 0.0 0.00 3.18 R
3920 4007 0.811616 GCCCCAGCTGACGAATAGTG 60.812 60.0 17.39 0.0 35.50 2.74 R
4837 4928 0.040204 AAGCTTGCTGCCCAACCTAT 59.960 50.0 0.00 0.0 44.23 2.57 R
5837 5963 0.386985 GTTCCTTCGCGACTCGTCTT 60.387 55.0 9.15 0.0 39.67 3.01 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
66 67 3.634397 TCTAGCCAAGGGACATTTCTG 57.366 47.619 0.00 0.00 0.00 3.02
70 71 1.815003 GCCAAGGGACATTTCTGTGAG 59.185 52.381 0.00 0.00 35.14 3.51
81 82 7.355778 GGACATTTCTGTGAGTTGAGTTTAAG 58.644 38.462 0.00 0.00 35.14 1.85
98 99 0.593128 AAGAACATGGAAGCACGTGC 59.407 50.000 32.79 32.79 42.49 5.34
100 101 0.310543 GAACATGGAAGCACGTGCAA 59.689 50.000 39.21 22.95 45.16 4.08
126 127 8.625786 AAAAATAAGCCTTTCAGCAAATCAAT 57.374 26.923 0.00 0.00 34.23 2.57
127 128 8.625786 AAAATAAGCCTTTCAGCAAATCAATT 57.374 26.923 0.00 0.00 34.23 2.32
132 133 4.751098 GCCTTTCAGCAAATCAATTTGTGA 59.249 37.500 14.97 13.59 46.63 3.58
145 146 7.959658 ATCAATTTGTGATTGGATGGTTAGA 57.040 32.000 0.00 0.00 45.13 2.10
147 148 7.601856 TCAATTTGTGATTGGATGGTTAGAAC 58.398 34.615 0.00 0.00 0.00 3.01
148 149 7.232330 TCAATTTGTGATTGGATGGTTAGAACA 59.768 33.333 0.00 0.00 0.00 3.18
152 153 5.473162 TGTGATTGGATGGTTAGAACAACAG 59.527 40.000 0.00 0.00 0.00 3.16
153 154 5.473504 GTGATTGGATGGTTAGAACAACAGT 59.526 40.000 0.00 0.00 0.00 3.55
156 157 3.392947 TGGATGGTTAGAACAACAGTGGA 59.607 43.478 0.00 0.00 0.00 4.02
160 161 5.042463 TGGTTAGAACAACAGTGGAATCA 57.958 39.130 0.00 0.00 0.00 2.57
161 162 5.630121 TGGTTAGAACAACAGTGGAATCAT 58.370 37.500 0.00 0.00 0.00 2.45
165 166 4.978099 AGAACAACAGTGGAATCATCAGT 58.022 39.130 0.00 0.00 0.00 3.41
175 176 4.035814 TGGAATCATCAGTCCATCAGAGT 58.964 43.478 0.00 0.00 41.99 3.24
187 188 8.647796 TCAGTCCATCAGAGTTTTAAGTCTTAA 58.352 33.333 0.65 0.65 36.59 1.85
205 206 5.008613 GTCTTAAACTTGACATTGGTGCTCA 59.991 40.000 0.00 0.00 33.75 4.26
212 213 4.669206 TGACATTGGTGCTCACATTTTT 57.331 36.364 2.21 0.00 0.00 1.94
213 214 4.370049 TGACATTGGTGCTCACATTTTTG 58.630 39.130 2.21 0.00 0.00 2.44
216 217 4.571580 ACATTGGTGCTCACATTTTTGTTG 59.428 37.500 2.21 0.00 0.00 3.33
218 219 3.779759 TGGTGCTCACATTTTTGTTGAC 58.220 40.909 2.21 0.00 0.00 3.18
221 222 4.268405 GGTGCTCACATTTTTGTTGACTTG 59.732 41.667 2.21 0.00 0.00 3.16
228 229 6.589523 TCACATTTTTGTTGACTTGTTTCAGG 59.410 34.615 0.00 0.00 0.00 3.86
233 234 2.687935 TGTTGACTTGTTTCAGGCCTTC 59.312 45.455 0.00 0.00 0.00 3.46
234 235 1.981256 TGACTTGTTTCAGGCCTTCC 58.019 50.000 0.00 0.00 0.00 3.46
251 254 1.244816 TCCGGCGATGTATCTAGTGG 58.755 55.000 9.30 0.00 0.00 4.00
259 262 4.594970 CGATGTATCTAGTGGGAGGAGAT 58.405 47.826 0.00 0.00 34.36 2.75
262 265 5.144159 TGTATCTAGTGGGAGGAGATGTT 57.856 43.478 0.00 0.00 32.27 2.71
275 316 2.398498 GAGATGTTCCCGTCGATGATG 58.602 52.381 6.11 0.00 0.00 3.07
281 322 2.961721 CCGTCGATGATGTGCCGG 60.962 66.667 6.11 0.00 0.00 6.13
286 327 2.242572 CGATGATGTGCCGGCTCAG 61.243 63.158 32.06 17.06 0.00 3.35
288 329 1.153289 ATGATGTGCCGGCTCAGTC 60.153 57.895 32.06 26.67 0.00 3.51
290 331 1.078848 GATGTGCCGGCTCAGTCTT 60.079 57.895 32.06 18.34 0.00 3.01
297 338 0.108424 CCGGCTCAGTCTTTCAGAGG 60.108 60.000 0.00 0.00 31.57 3.69
300 341 1.346068 GGCTCAGTCTTTCAGAGGTGT 59.654 52.381 0.00 0.00 31.57 4.16
305 346 5.567623 GCTCAGTCTTTCAGAGGTGTTCATA 60.568 44.000 0.00 0.00 31.57 2.15
306 347 6.419484 TCAGTCTTTCAGAGGTGTTCATAA 57.581 37.500 0.00 0.00 0.00 1.90
310 351 7.605691 CAGTCTTTCAGAGGTGTTCATAAAGAT 59.394 37.037 0.00 0.00 39.21 2.40
316 357 7.730084 TCAGAGGTGTTCATAAAGATAGGATG 58.270 38.462 0.00 0.00 0.00 3.51
317 358 7.565029 TCAGAGGTGTTCATAAAGATAGGATGA 59.435 37.037 0.00 0.00 0.00 2.92
318 359 7.871973 CAGAGGTGTTCATAAAGATAGGATGAG 59.128 40.741 0.00 0.00 31.50 2.90
321 362 6.939163 GGTGTTCATAAAGATAGGATGAGCAT 59.061 38.462 4.35 0.00 41.09 3.79
337 378 8.045507 AGGATGAGCATGTATACATTCATAAGG 58.954 37.037 23.71 11.19 35.25 2.69
342 383 9.155975 GAGCATGTATACATTCATAAGGGTAAG 57.844 37.037 15.85 1.60 33.61 2.34
344 385 9.938280 GCATGTATACATTCATAAGGGTAAGTA 57.062 33.333 15.85 0.00 33.61 2.24
600 641 1.374885 CATCGTTGGTGGGCGTGTA 60.375 57.895 0.00 0.00 0.00 2.90
649 690 1.134401 GGTGGATTTGCTCGGATCTCA 60.134 52.381 0.00 0.00 0.00 3.27
664 705 4.554919 CGGATCTCATCGTTGTTCGTCTAT 60.555 45.833 0.00 0.00 40.80 1.98
670 711 1.980844 TCGTTGTTCGTCTATGTTCGC 59.019 47.619 0.00 0.00 40.80 4.70
713 754 6.598064 CCTTCCAACCTACGTTATTCTTCATT 59.402 38.462 0.00 0.00 0.00 2.57
1002 1043 1.887320 GCATCTGCACTGCGTTAAAG 58.113 50.000 1.04 0.00 41.59 1.85
1054 1097 3.227276 CGATGGAGAGGGGTCCGG 61.227 72.222 0.00 0.00 39.81 5.14
1061 1104 4.097361 GAGGGGTCCGGTGGCTTC 62.097 72.222 0.00 0.00 0.00 3.86
1079 1122 4.354587 GCTTCTGTCTTTTGGAACTGTTG 58.645 43.478 0.00 0.00 0.00 3.33
1080 1123 4.142381 GCTTCTGTCTTTTGGAACTGTTGT 60.142 41.667 0.00 0.00 0.00 3.32
1118 1161 4.838152 GCCTGAATCAGCCGGCGA 62.838 66.667 23.20 21.50 32.22 5.54
1136 1179 0.805322 GAGGACACAGATGCAGAGCG 60.805 60.000 0.00 0.00 0.00 5.03
1179 1236 1.003223 GTGCTAAACCGTCACAACACC 60.003 52.381 0.00 0.00 0.00 4.16
1247 1309 1.965754 GAATCTCTGGCCAGCGACCT 61.966 60.000 27.20 17.24 0.00 3.85
1248 1310 1.965754 AATCTCTGGCCAGCGACCTC 61.966 60.000 27.20 0.00 0.00 3.85
1360 1423 3.695606 GCCAGCTCACGGACTCCA 61.696 66.667 0.00 0.00 0.00 3.86
1704 1771 2.722487 CGAGAAGGTCCGATCCCG 59.278 66.667 0.00 0.00 0.00 5.14
1708 1775 4.798682 AAGGTCCGATCCCGCCCT 62.799 66.667 0.00 0.00 0.00 5.19
1786 1855 1.483827 TCTGGTGTGATCTGATCTGCC 59.516 52.381 17.82 15.79 0.00 4.85
1886 1956 2.819595 TGGCCGAGCTGCGAATTC 60.820 61.111 0.00 0.00 44.57 2.17
1909 1979 2.868583 GTGTGGATTCATGACGATCTGG 59.131 50.000 0.00 0.00 0.00 3.86
1964 2034 0.813184 AGGATTTGCTGTGGCGATTG 59.187 50.000 0.00 0.00 42.25 2.67
2002 2072 2.012673 GGATTTGCTGTGGCTAGTCAG 58.987 52.381 0.00 2.37 39.59 3.51
2003 2073 2.012673 GATTTGCTGTGGCTAGTCAGG 58.987 52.381 0.00 0.00 39.59 3.86
2004 2074 0.036732 TTTGCTGTGGCTAGTCAGGG 59.963 55.000 0.00 0.00 39.59 4.45
2063 2133 2.219674 GTGGTCATGATCGCGATCTTTC 59.780 50.000 39.74 28.34 38.60 2.62
2101 2171 0.036577 CTGCAGAGTGCTGGCTACTT 60.037 55.000 8.42 0.00 45.31 2.24
2103 2173 1.066858 TGCAGAGTGCTGGCTACTTAC 60.067 52.381 0.00 0.00 45.31 2.34
2295 2366 8.540388 TCTAGGGATAATGCATATTTGTAGACC 58.460 37.037 0.00 0.00 0.00 3.85
2340 2411 2.614983 TGGACAACCGTTTTCTTAGTGC 59.385 45.455 0.00 0.00 39.42 4.40
2354 2425 3.266772 TCTTAGTGCCATGGGAAGACATT 59.733 43.478 15.13 1.62 0.00 2.71
2367 2438 4.219288 GGGAAGACATTTGATGCTTCTTGT 59.781 41.667 16.79 2.77 40.26 3.16
2368 2439 5.279156 GGGAAGACATTTGATGCTTCTTGTT 60.279 40.000 16.79 0.00 40.26 2.83
2369 2440 6.218746 GGAAGACATTTGATGCTTCTTGTTT 58.781 36.000 16.79 0.00 40.26 2.83
2376 2447 6.889301 TTTGATGCTTCTTGTTTCTCTGAT 57.111 33.333 0.88 0.00 0.00 2.90
2380 2451 4.067896 TGCTTCTTGTTTCTCTGATGTCC 58.932 43.478 0.00 0.00 0.00 4.02
2385 2456 2.054021 TGTTTCTCTGATGTCCCCACA 58.946 47.619 0.00 0.00 36.78 4.17
2401 2472 4.474651 TCCCCACAAGTCATACATGAGAAT 59.525 41.667 0.00 0.00 37.51 2.40
2425 2496 2.172505 TCACCTCACACACCACAATTCT 59.827 45.455 0.00 0.00 0.00 2.40
2426 2497 2.549754 CACCTCACACACCACAATTCTC 59.450 50.000 0.00 0.00 0.00 2.87
2435 2506 0.409484 CCACAATTCTCCCACCCCTT 59.591 55.000 0.00 0.00 0.00 3.95
2441 2512 1.779061 TTCTCCCACCCCTTGACAGC 61.779 60.000 0.00 0.00 0.00 4.40
2511 2586 0.614415 TGGGACATGCAACATTCCCC 60.614 55.000 17.99 11.25 46.53 4.81
2645 2721 5.449107 GCTGATGGCAGAAAATGATATGT 57.551 39.130 0.00 0.00 45.17 2.29
2668 2744 8.306313 TGTGTCTAGTCTGTATTTCATACCAT 57.694 34.615 0.00 0.00 34.86 3.55
2673 2749 9.822727 TCTAGTCTGTATTTCATACCATGGATA 57.177 33.333 21.47 7.65 34.86 2.59
2701 2777 7.488322 TCACCTTATCTGTTTTTGGACTTTTG 58.512 34.615 0.00 0.00 0.00 2.44
2721 2797 8.454106 ACTTTTGTGAAGCTTATCATATGACAC 58.546 33.333 7.78 10.12 0.00 3.67
2793 2869 5.222048 TGCAGATTCCCTTACTAAAAGTGGT 60.222 40.000 0.00 0.00 0.00 4.16
2795 2871 5.880887 CAGATTCCCTTACTAAAAGTGGTCC 59.119 44.000 0.00 0.00 0.00 4.46
2796 2872 5.550403 AGATTCCCTTACTAAAAGTGGTCCA 59.450 40.000 0.00 0.00 0.00 4.02
2797 2873 4.628963 TCCCTTACTAAAAGTGGTCCAC 57.371 45.455 14.68 14.68 34.10 4.02
2864 2941 6.659242 CAGGGTAATTATCTGTTGGACAGTTT 59.341 38.462 7.85 1.01 46.03 2.66
2884 2961 5.237344 AGTTTTTAGATCTGTATGATGCCGC 59.763 40.000 5.18 0.00 35.14 6.53
2901 2980 7.432869 TGATGCCGCTTTATTTATTATGCTTT 58.567 30.769 0.00 0.00 0.00 3.51
2916 2995 9.950680 TTATTATGCTTTTTGCTTATCTGCTAC 57.049 29.630 0.00 0.00 43.37 3.58
2917 2996 7.630242 TTATGCTTTTTGCTTATCTGCTACT 57.370 32.000 0.00 0.00 43.37 2.57
2918 2997 5.551760 TGCTTTTTGCTTATCTGCTACTC 57.448 39.130 0.00 0.00 43.37 2.59
2919 2998 4.396166 TGCTTTTTGCTTATCTGCTACTCC 59.604 41.667 0.00 0.00 43.37 3.85
2920 2999 4.201960 GCTTTTTGCTTATCTGCTACTCCC 60.202 45.833 0.00 0.00 38.95 4.30
2921 3000 4.844349 TTTTGCTTATCTGCTACTCCCT 57.156 40.909 0.00 0.00 0.00 4.20
2922 3001 4.408182 TTTGCTTATCTGCTACTCCCTC 57.592 45.455 0.00 0.00 0.00 4.30
2923 3002 2.320781 TGCTTATCTGCTACTCCCTCC 58.679 52.381 0.00 0.00 0.00 4.30
2924 3003 1.271102 GCTTATCTGCTACTCCCTCCG 59.729 57.143 0.00 0.00 0.00 4.63
2925 3004 2.588620 CTTATCTGCTACTCCCTCCGT 58.411 52.381 0.00 0.00 0.00 4.69
2926 3005 3.752665 CTTATCTGCTACTCCCTCCGTA 58.247 50.000 0.00 0.00 0.00 4.02
2927 3006 2.750141 ATCTGCTACTCCCTCCGTAA 57.250 50.000 0.00 0.00 0.00 3.18
2928 3007 2.519771 TCTGCTACTCCCTCCGTAAA 57.480 50.000 0.00 0.00 0.00 2.01
2929 3008 2.376109 TCTGCTACTCCCTCCGTAAAG 58.624 52.381 0.00 0.00 0.00 1.85
2930 3009 2.025605 TCTGCTACTCCCTCCGTAAAGA 60.026 50.000 0.00 0.00 0.00 2.52
2931 3010 2.758979 CTGCTACTCCCTCCGTAAAGAA 59.241 50.000 0.00 0.00 0.00 2.52
2932 3011 3.167485 TGCTACTCCCTCCGTAAAGAAA 58.833 45.455 0.00 0.00 0.00 2.52
2933 3012 3.773119 TGCTACTCCCTCCGTAAAGAAAT 59.227 43.478 0.00 0.00 0.00 2.17
2934 3013 4.957954 TGCTACTCCCTCCGTAAAGAAATA 59.042 41.667 0.00 0.00 0.00 1.40
2935 3014 5.601313 TGCTACTCCCTCCGTAAAGAAATAT 59.399 40.000 0.00 0.00 0.00 1.28
2936 3015 6.779049 TGCTACTCCCTCCGTAAAGAAATATA 59.221 38.462 0.00 0.00 0.00 0.86
2937 3016 7.288389 TGCTACTCCCTCCGTAAAGAAATATAA 59.712 37.037 0.00 0.00 0.00 0.98
2938 3017 7.813627 GCTACTCCCTCCGTAAAGAAATATAAG 59.186 40.741 0.00 0.00 0.00 1.73
2939 3018 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2940 3019 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2941 3020 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2942 3021 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2943 3022 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2944 3023 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2945 3024 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2946 3025 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2947 3026 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2948 3027 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2960 3039 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
2961 3040 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2994 3073 8.682936 ATGCTCTTATATTTGTTTACAGAGGG 57.317 34.615 0.00 0.00 0.00 4.30
2995 3074 7.857456 TGCTCTTATATTTGTTTACAGAGGGA 58.143 34.615 0.00 0.00 0.00 4.20
2996 3075 7.987458 TGCTCTTATATTTGTTTACAGAGGGAG 59.013 37.037 0.00 0.00 0.00 4.30
2997 3076 7.988028 GCTCTTATATTTGTTTACAGAGGGAGT 59.012 37.037 0.00 0.00 0.00 3.85
3014 3093 9.629878 CAGAGGGAGTATATATTAGGTAATCGT 57.370 37.037 0.00 0.00 0.00 3.73
3076 3155 3.064931 GCTGTAGTGGAGTGGTACAAAC 58.935 50.000 0.00 0.00 44.16 2.93
3079 3158 4.952460 TGTAGTGGAGTGGTACAAACTTC 58.048 43.478 0.00 0.00 44.16 3.01
3171 3250 6.846350 ACTCTTTGAACTGTGAAAGAACTTG 58.154 36.000 13.31 7.09 37.66 3.16
3176 3255 5.007034 TGAACTGTGAAAGAACTTGTTGGA 58.993 37.500 0.00 0.00 0.00 3.53
3177 3256 4.965119 ACTGTGAAAGAACTTGTTGGAC 57.035 40.909 0.00 0.00 0.00 4.02
3178 3257 4.331968 ACTGTGAAAGAACTTGTTGGACA 58.668 39.130 0.00 0.00 0.00 4.02
3179 3258 4.949856 ACTGTGAAAGAACTTGTTGGACAT 59.050 37.500 0.00 0.00 0.00 3.06
3180 3259 5.418840 ACTGTGAAAGAACTTGTTGGACATT 59.581 36.000 0.00 0.00 0.00 2.71
3197 3276 2.785269 ACATTATGGGATTCTGCCTGGA 59.215 45.455 0.00 0.00 0.00 3.86
3202 3281 0.332972 GGGATTCTGCCTGGAAAGGT 59.667 55.000 0.00 0.00 0.00 3.50
3203 3282 1.683319 GGGATTCTGCCTGGAAAGGTC 60.683 57.143 0.00 0.00 0.00 3.85
3223 3303 4.441634 GGTCCAAATGTATCTAGTGAGCGT 60.442 45.833 0.00 0.00 0.00 5.07
3282 3365 6.771749 AGCTCTCATGCTAAATCTATTTGCTT 59.228 34.615 0.00 0.00 42.10 3.91
3322 3405 5.420104 CAGAATGGAAGGCTTATTTCAGGTT 59.580 40.000 0.00 0.00 0.00 3.50
3740 3827 1.931635 AGAAGCTCTCTCTTTCCCGT 58.068 50.000 0.00 0.00 0.00 5.28
3743 3830 2.517998 AGCTCTCTCTTTCCCGTAGT 57.482 50.000 0.00 0.00 0.00 2.73
3920 4007 0.329596 AGGGGTCAGGCATGAAAGTC 59.670 55.000 0.92 0.00 37.14 3.01
4287 4376 1.766496 AGGAACACCCGAAGTTCAAGA 59.234 47.619 3.32 0.00 45.45 3.02
4410 4499 6.588719 TCATTAAATCAAACCCTGGTGAAG 57.411 37.500 0.00 0.00 0.00 3.02
4444 4533 4.093011 GGTATGGCCTCATAGATCTCAGT 58.907 47.826 3.32 0.00 36.62 3.41
4461 4550 6.456795 TCTCAGTGACCAATCTGTATACTG 57.543 41.667 4.17 3.79 36.03 2.74
4496 4587 8.177119 TGTACTTGCTGATAATCTTTGGTTTT 57.823 30.769 0.00 0.00 0.00 2.43
4559 4650 2.435693 GCCGATGTACCAGAGGCCT 61.436 63.158 3.86 3.86 41.81 5.19
4601 4692 3.888930 ACATTCATTTCACGGTGGAGTTT 59.111 39.130 8.50 0.00 0.00 2.66
4691 4782 1.037579 TGACCGACATGGAGCTCGAT 61.038 55.000 7.83 6.51 42.00 3.59
4709 4800 0.817654 ATGAATGCGAGGAGACGACA 59.182 50.000 0.00 0.00 35.09 4.35
4718 4809 1.929836 GAGGAGACGACAATGCATGAC 59.070 52.381 0.00 0.00 0.00 3.06
4837 4928 1.217001 CAGTGCGCACAACAGTAAGA 58.783 50.000 39.21 0.00 0.00 2.10
4892 4983 2.976490 AAGATGCCTGCCCGCTCTT 61.976 57.895 0.00 0.00 0.00 2.85
4904 4998 1.006220 CGCTCTTTGGGGTTTTGGC 60.006 57.895 0.00 0.00 0.00 4.52
5044 5148 1.004398 TGTGAAAACTAACGCACGCTG 60.004 47.619 0.00 0.00 34.12 5.18
5046 5150 1.259507 TGAAAACTAACGCACGCTGTC 59.740 47.619 0.00 0.00 0.00 3.51
5079 5183 5.183331 TCTCTGAATACGTTGTCTAAGCAGT 59.817 40.000 0.00 0.00 0.00 4.40
5209 5313 5.294306 TGTCGATCTAAGCACAATTCCATTC 59.706 40.000 0.00 0.00 0.00 2.67
5266 5373 8.779354 AGTAGCAGTTGAAAGGAGTTTATTAG 57.221 34.615 0.00 0.00 0.00 1.73
5906 6037 4.465512 CATGCAACAGCGGGCGTC 62.466 66.667 0.00 0.00 0.00 5.19
5979 6113 1.526917 CATGGGCCTTAGAAGCGGG 60.527 63.158 4.53 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.330701 ACAGAAATGTCCCTTGGCTAGAA 59.669 43.478 0.00 0.00 0.00 2.10
52 53 4.136796 TCAACTCACAGAAATGTCCCTTG 58.863 43.478 0.00 0.00 0.00 3.61
66 67 6.861065 TCCATGTTCTTAAACTCAACTCAC 57.139 37.500 0.00 0.00 36.30 3.51
70 71 5.915196 GTGCTTCCATGTTCTTAAACTCAAC 59.085 40.000 0.00 0.00 36.30 3.18
81 82 0.310543 TTGCACGTGCTTCCATGTTC 59.689 50.000 37.59 8.73 39.12 3.18
107 108 5.934935 CAAATTGATTTGCTGAAAGGCTT 57.065 34.783 0.00 0.00 40.42 4.35
126 127 6.322456 TGTTGTTCTAACCATCCAATCACAAA 59.678 34.615 0.00 0.00 0.00 2.83
127 128 5.830457 TGTTGTTCTAACCATCCAATCACAA 59.170 36.000 0.00 0.00 0.00 3.33
132 133 4.766891 CCACTGTTGTTCTAACCATCCAAT 59.233 41.667 0.00 0.00 0.00 3.16
135 136 4.015872 TCCACTGTTGTTCTAACCATCC 57.984 45.455 0.00 0.00 0.00 3.51
145 146 4.074970 GGACTGATGATTCCACTGTTGTT 58.925 43.478 0.00 0.00 0.00 2.83
147 148 3.678289 TGGACTGATGATTCCACTGTTG 58.322 45.455 0.00 0.00 36.96 3.33
148 149 4.019051 TGATGGACTGATGATTCCACTGTT 60.019 41.667 0.00 0.00 44.80 3.16
152 153 4.141756 ACTCTGATGGACTGATGATTCCAC 60.142 45.833 0.00 0.00 44.80 4.02
153 154 4.035814 ACTCTGATGGACTGATGATTCCA 58.964 43.478 0.00 0.00 46.06 3.53
156 157 8.105829 ACTTAAAACTCTGATGGACTGATGATT 58.894 33.333 0.00 0.00 0.00 2.57
160 161 7.251321 AGACTTAAAACTCTGATGGACTGAT 57.749 36.000 0.00 0.00 0.00 2.90
161 162 6.672266 AGACTTAAAACTCTGATGGACTGA 57.328 37.500 0.00 0.00 0.00 3.41
165 166 9.847224 AAGTTTAAGACTTAAAACTCTGATGGA 57.153 29.630 19.48 0.00 46.61 3.41
175 176 9.796120 CACCAATGTCAAGTTTAAGACTTAAAA 57.204 29.630 19.48 6.07 46.75 1.52
187 188 2.653726 TGTGAGCACCAATGTCAAGTT 58.346 42.857 0.00 0.00 0.00 2.66
194 195 4.809958 TCAACAAAAATGTGAGCACCAATG 59.190 37.500 0.00 0.00 0.00 2.82
196 197 4.081752 AGTCAACAAAAATGTGAGCACCAA 60.082 37.500 0.00 0.00 0.00 3.67
197 198 3.446873 AGTCAACAAAAATGTGAGCACCA 59.553 39.130 0.00 0.00 0.00 4.17
205 206 5.351189 GCCTGAAACAAGTCAACAAAAATGT 59.649 36.000 0.00 0.00 0.00 2.71
212 213 2.435372 AGGCCTGAAACAAGTCAACA 57.565 45.000 3.11 0.00 0.00 3.33
213 214 2.034685 GGAAGGCCTGAAACAAGTCAAC 59.965 50.000 5.69 0.00 0.00 3.18
216 217 0.875059 CGGAAGGCCTGAAACAAGTC 59.125 55.000 5.69 0.00 0.00 3.01
233 234 0.243907 CCCACTAGATACATCGCCGG 59.756 60.000 0.00 0.00 0.00 6.13
234 235 1.200252 CTCCCACTAGATACATCGCCG 59.800 57.143 0.00 0.00 0.00 6.46
237 238 4.022413 TCTCCTCCCACTAGATACATCG 57.978 50.000 0.00 0.00 0.00 3.84
251 254 1.035932 TCGACGGGAACATCTCCTCC 61.036 60.000 0.00 0.00 44.68 4.30
259 262 0.739462 GCACATCATCGACGGGAACA 60.739 55.000 0.00 0.00 0.00 3.18
262 265 2.499205 GGCACATCATCGACGGGA 59.501 61.111 0.00 0.00 0.00 5.14
265 268 3.630148 GCCGGCACATCATCGACG 61.630 66.667 24.80 0.00 0.00 5.12
266 269 2.202932 AGCCGGCACATCATCGAC 60.203 61.111 31.54 0.00 0.00 4.20
268 271 2.202919 TGAGCCGGCACATCATCG 60.203 61.111 31.54 0.00 0.00 3.84
275 316 1.294659 CTGAAAGACTGAGCCGGCAC 61.295 60.000 31.54 24.60 34.07 5.01
281 322 2.829741 ACACCTCTGAAAGACTGAGC 57.170 50.000 0.00 0.00 38.67 4.26
286 327 7.913674 ATCTTTATGAACACCTCTGAAAGAC 57.086 36.000 0.00 0.00 38.67 3.01
288 329 8.260818 TCCTATCTTTATGAACACCTCTGAAAG 58.739 37.037 0.00 0.00 32.21 2.62
290 331 7.733773 TCCTATCTTTATGAACACCTCTGAA 57.266 36.000 0.00 0.00 0.00 3.02
297 338 7.443575 ACATGCTCATCCTATCTTTATGAACAC 59.556 37.037 0.00 0.00 30.84 3.32
305 346 9.664332 GAATGTATACATGCTCATCCTATCTTT 57.336 33.333 18.94 0.00 36.56 2.52
306 347 8.819845 TGAATGTATACATGCTCATCCTATCTT 58.180 33.333 22.00 2.33 36.56 2.40
316 357 9.155975 CTTACCCTTATGAATGTATACATGCTC 57.844 37.037 22.00 15.63 36.56 4.26
317 358 8.660435 ACTTACCCTTATGAATGTATACATGCT 58.340 33.333 22.00 7.50 36.56 3.79
318 359 8.848474 ACTTACCCTTATGAATGTATACATGC 57.152 34.615 18.94 17.42 36.56 4.06
337 378 6.382282 AGGCGGAAACCCTATATATACTTACC 59.618 42.308 0.00 0.00 30.32 2.85
342 383 5.221009 CGAGAGGCGGAAACCCTATATATAC 60.221 48.000 0.00 0.00 36.03 1.47
344 385 3.700038 CGAGAGGCGGAAACCCTATATAT 59.300 47.826 0.00 0.00 36.03 0.86
600 641 3.374402 CGCCGGAGACACACCTCT 61.374 66.667 5.05 0.00 33.79 3.69
649 690 2.597305 GCGAACATAGACGAACAACGAT 59.403 45.455 0.00 0.00 45.77 3.73
664 705 2.355363 CCCGAAGACACGCGAACA 60.355 61.111 15.93 0.00 0.00 3.18
670 711 1.076332 GGATTCAACCCGAAGACACG 58.924 55.000 0.00 0.00 36.95 4.49
983 1024 1.464608 TCTTTAACGCAGTGCAGATGC 59.535 47.619 16.83 12.76 45.00 3.91
1002 1043 8.771920 TTTTCCTTGGAAGAAAGAAAGTTTTC 57.228 30.769 2.16 0.00 34.84 2.29
1037 1080 3.227276 CCGGACCCCTCTCCATCG 61.227 72.222 0.00 0.00 0.00 3.84
1054 1097 2.952310 AGTTCCAAAAGACAGAAGCCAC 59.048 45.455 0.00 0.00 0.00 5.01
1118 1161 1.217511 CGCTCTGCATCTGTGTCCT 59.782 57.895 0.00 0.00 0.00 3.85
1174 1217 1.337823 CCTCTTTGATCGGTCGGTGTT 60.338 52.381 0.00 0.00 0.00 3.32
1179 1236 2.164624 AGAACTCCTCTTTGATCGGTCG 59.835 50.000 0.00 0.00 0.00 4.79
1216 1278 1.407979 CAGAGATTCCAGCCCAAATGC 59.592 52.381 0.00 0.00 0.00 3.56
1247 1309 1.073763 CTGGATTGTTGGACCTGGTGA 59.926 52.381 2.82 0.00 0.00 4.02
1248 1310 1.538047 CTGGATTGTTGGACCTGGTG 58.462 55.000 2.82 0.00 0.00 4.17
1325 1388 2.202878 TGCGGAGGCGTATTCTGC 60.203 61.111 9.03 9.03 45.16 4.26
1354 1417 4.591072 AGGGCTAATGTAGAGAATGGAGTC 59.409 45.833 0.00 0.00 0.00 3.36
1360 1423 2.037772 CGCCAGGGCTAATGTAGAGAAT 59.962 50.000 8.91 0.00 39.32 2.40
1509 1572 2.694616 TGGGATGGGTGGGTAGGC 60.695 66.667 0.00 0.00 0.00 3.93
1510 1573 2.383601 GGTGGGATGGGTGGGTAGG 61.384 68.421 0.00 0.00 0.00 3.18
1511 1574 1.618143 TGGTGGGATGGGTGGGTAG 60.618 63.158 0.00 0.00 0.00 3.18
1512 1575 1.926489 GTGGTGGGATGGGTGGGTA 60.926 63.158 0.00 0.00 0.00 3.69
1513 1576 3.264845 GTGGTGGGATGGGTGGGT 61.265 66.667 0.00 0.00 0.00 4.51
1516 1579 4.060667 GGGGTGGTGGGATGGGTG 62.061 72.222 0.00 0.00 0.00 4.61
1708 1775 1.748329 CGATGATCGCAGGGGAGGAA 61.748 60.000 0.41 0.00 31.14 3.36
1786 1855 6.656632 TCTATCTAGTTCTACCTTGCCATG 57.343 41.667 0.00 0.00 0.00 3.66
1833 1902 2.802667 CGCGAATTGACTCCCTGCG 61.803 63.158 0.00 0.00 38.04 5.18
1886 1956 3.554731 CAGATCGTCATGAATCCACACAG 59.445 47.826 0.00 0.00 0.00 3.66
1909 1979 0.881796 GCTACAAACCCCAGCAGAAC 59.118 55.000 0.00 0.00 35.35 3.01
1964 2034 5.973899 AATCCTCTTCTTTTCTTTCTGCC 57.026 39.130 0.00 0.00 0.00 4.85
2003 2073 4.748144 CAGGGCAAGCACTCCCCC 62.748 72.222 0.00 1.13 43.67 5.40
2022 2092 4.353737 CACTTCACATCAAACCACAACAG 58.646 43.478 0.00 0.00 0.00 3.16
2065 2135 1.068610 GCAGAAAGCAATACACGCCAA 60.069 47.619 0.00 0.00 44.79 4.52
2086 2156 1.202582 CGTGTAAGTAGCCAGCACTCT 59.797 52.381 0.00 0.00 0.00 3.24
2128 2198 3.053991 TCCCCGAATCTAGCCAAATTCAA 60.054 43.478 3.59 0.00 32.55 2.69
2272 2343 7.238514 AGAGGTCTACAAATATGCATTATCCCT 59.761 37.037 3.54 0.00 0.00 4.20
2333 2404 2.787473 TGTCTTCCCATGGCACTAAG 57.213 50.000 6.09 7.10 0.00 2.18
2340 2411 3.028850 AGCATCAAATGTCTTCCCATGG 58.971 45.455 4.14 4.14 0.00 3.66
2354 2425 5.766670 ACATCAGAGAAACAAGAAGCATCAA 59.233 36.000 0.00 0.00 0.00 2.57
2367 2438 2.711009 ACTTGTGGGGACATCAGAGAAA 59.289 45.455 0.00 0.00 46.14 2.52
2368 2439 2.303022 GACTTGTGGGGACATCAGAGAA 59.697 50.000 0.00 0.00 46.14 2.87
2369 2440 1.902508 GACTTGTGGGGACATCAGAGA 59.097 52.381 0.00 0.00 46.14 3.10
2376 2447 2.909662 TCATGTATGACTTGTGGGGACA 59.090 45.455 0.00 0.00 38.70 4.02
2380 2451 5.649395 ACAATTCTCATGTATGACTTGTGGG 59.351 40.000 15.02 0.00 32.34 4.61
2385 2456 6.715280 AGGTGACAATTCTCATGTATGACTT 58.285 36.000 0.00 0.00 32.50 3.01
2401 2472 0.615850 TGTGGTGTGTGAGGTGACAA 59.384 50.000 0.00 0.00 0.00 3.18
2425 2496 3.636231 CGCTGTCAAGGGGTGGGA 61.636 66.667 0.00 0.00 32.81 4.37
2426 2497 3.636231 TCGCTGTCAAGGGGTGGG 61.636 66.667 0.00 0.00 36.99 4.61
2435 2506 3.519973 CTGGGCACAGTCGCTGTCA 62.520 63.158 8.15 5.08 43.43 3.58
2668 2744 8.748412 CCAAAAACAGATAAGGTGAATTATCCA 58.252 33.333 3.48 0.00 41.24 3.41
2673 2749 7.839680 AGTCCAAAAACAGATAAGGTGAATT 57.160 32.000 0.00 0.00 0.00 2.17
2701 2777 7.875041 ACATAGGTGTCATATGATAAGCTTCAC 59.125 37.037 21.16 16.01 35.15 3.18
2864 2941 4.607293 AGCGGCATCATACAGATCTAAA 57.393 40.909 1.45 0.00 33.72 1.85
2901 2980 3.134804 GGAGGGAGTAGCAGATAAGCAAA 59.865 47.826 0.00 0.00 36.85 3.68
2913 2992 9.075678 TCTTATATTTCTTTACGGAGGGAGTAG 57.924 37.037 0.00 0.00 0.00 2.57
2914 2993 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2915 2994 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
2916 2995 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2917 2996 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2918 2997 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2919 2998 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2920 2999 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2921 3000 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
2922 3001 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
2934 3013 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
2935 3014 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
2936 3015 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
2937 3016 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2968 3047 9.125026 CCCTCTGTAAACAAATATAAGAGCATT 57.875 33.333 0.00 0.00 0.00 3.56
2969 3048 8.494433 TCCCTCTGTAAACAAATATAAGAGCAT 58.506 33.333 0.00 0.00 0.00 3.79
2970 3049 7.857456 TCCCTCTGTAAACAAATATAAGAGCA 58.143 34.615 0.00 0.00 0.00 4.26
2971 3050 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
2987 3066 9.629878 CGATTACCTAATATATACTCCCTCTGT 57.370 37.037 0.00 0.00 0.00 3.41
2988 3067 9.629878 ACGATTACCTAATATATACTCCCTCTG 57.370 37.037 0.00 0.00 0.00 3.35
2993 3072 9.733219 GCAGAACGATTACCTAATATATACTCC 57.267 37.037 0.00 0.00 0.00 3.85
3005 3084 3.678056 TGTCAAGCAGAACGATTACCT 57.322 42.857 0.00 0.00 0.00 3.08
3014 3093 6.352016 AGAGATTAGAGTTGTCAAGCAGAA 57.648 37.500 0.00 0.00 0.00 3.02
3154 3233 5.106317 TGTCCAACAAGTTCTTTCACAGTTC 60.106 40.000 0.00 0.00 0.00 3.01
3171 3250 3.319122 GGCAGAATCCCATAATGTCCAAC 59.681 47.826 0.00 0.00 0.00 3.77
3176 3255 2.785269 TCCAGGCAGAATCCCATAATGT 59.215 45.455 0.00 0.00 0.00 2.71
3177 3256 3.513909 TCCAGGCAGAATCCCATAATG 57.486 47.619 0.00 0.00 0.00 1.90
3178 3257 4.477249 CTTTCCAGGCAGAATCCCATAAT 58.523 43.478 0.00 0.00 0.00 1.28
3179 3258 3.373001 CCTTTCCAGGCAGAATCCCATAA 60.373 47.826 0.00 0.00 31.53 1.90
3180 3259 2.175499 CCTTTCCAGGCAGAATCCCATA 59.825 50.000 0.00 0.00 31.53 2.74
3197 3276 6.116126 GCTCACTAGATACATTTGGACCTTT 58.884 40.000 0.00 0.00 0.00 3.11
3202 3281 6.459670 TTACGCTCACTAGATACATTTGGA 57.540 37.500 0.00 0.00 0.00 3.53
3203 3282 7.715265 ATTTACGCTCACTAGATACATTTGG 57.285 36.000 0.00 0.00 0.00 3.28
3273 3356 8.570488 TGCTGATCATGGTAAATAAGCAAATAG 58.430 33.333 0.00 0.00 36.60 1.73
3277 3360 6.121590 TCTGCTGATCATGGTAAATAAGCAA 58.878 36.000 0.00 0.00 38.59 3.91
3282 3365 6.840527 TCCATTCTGCTGATCATGGTAAATA 58.159 36.000 18.55 2.76 37.92 1.40
3296 3379 4.603131 TGAAATAAGCCTTCCATTCTGCT 58.397 39.130 0.00 0.00 35.08 4.24
3740 3827 1.895798 CACTTGGAGCAGAGGACACTA 59.104 52.381 0.00 0.00 0.00 2.74
3743 3830 1.372683 GCACTTGGAGCAGAGGACA 59.627 57.895 0.00 0.00 0.00 4.02
3920 4007 0.811616 GCCCCAGCTGACGAATAGTG 60.812 60.000 17.39 0.00 35.50 2.74
4287 4376 3.037549 AGAAGAGATCATCGCCCTTTCT 58.962 45.455 0.00 0.00 0.00 2.52
4444 4533 9.952030 TTTTTACATCAGTATACAGATTGGTCA 57.048 29.630 7.97 0.00 0.00 4.02
4559 4650 2.592102 AGAGCTTGCCCTTCATGAAA 57.408 45.000 9.88 0.00 0.00 2.69
4691 4782 0.601057 TTGTCGTCTCCTCGCATTCA 59.399 50.000 0.00 0.00 0.00 2.57
4709 4800 2.421073 CTCCATGTTGACGTCATGCATT 59.579 45.455 24.42 13.02 40.63 3.56
4718 4809 1.186200 TCTCCTCCTCCATGTTGACG 58.814 55.000 0.00 0.00 0.00 4.35
4837 4928 0.040204 AAGCTTGCTGCCCAACCTAT 59.960 50.000 0.00 0.00 44.23 2.57
4892 4983 0.396695 TAACACCGCCAAAACCCCAA 60.397 50.000 0.00 0.00 0.00 4.12
4904 4998 2.809446 TCAGCTTCATCGATAACACCG 58.191 47.619 0.00 0.00 0.00 4.94
5044 5148 4.393680 ACGTATTCAGAGAGACAGACAGAC 59.606 45.833 0.00 0.00 0.00 3.51
5046 5150 4.955925 ACGTATTCAGAGAGACAGACAG 57.044 45.455 0.00 0.00 0.00 3.51
5079 5183 3.797184 GCTTTGCAAAATTGTCCACGGTA 60.797 43.478 13.84 0.00 0.00 4.02
5233 5339 6.014647 TCCTTTCAACTGCTACTCCTACTAA 58.985 40.000 0.00 0.00 0.00 2.24
5837 5963 0.386985 GTTCCTTCGCGACTCGTCTT 60.387 55.000 9.15 0.00 39.67 3.01
5889 6020 4.465512 GACGCCCGCTGTTGCATG 62.466 66.667 0.00 0.00 39.64 4.06
5892 6023 4.465512 CATGACGCCCGCTGTTGC 62.466 66.667 0.00 0.00 0.00 4.17
5893 6024 4.465512 GCATGACGCCCGCTGTTG 62.466 66.667 0.00 0.00 32.94 3.33
5894 6025 4.704833 AGCATGACGCCCGCTGTT 62.705 61.111 0.00 0.00 44.04 3.16
5944 6075 2.910482 CCATGAATTGCGTTTCGTTCTG 59.090 45.455 0.00 0.00 0.00 3.02
5946 6077 2.250188 CCCATGAATTGCGTTTCGTTC 58.750 47.619 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.