Multiple sequence alignment - TraesCS6B01G031600

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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 TraesCS6B01G031600 chr6B 100.000 4827 0 0 1 4827 18659859 18655033 0.000000e+00 8914.0
1 TraesCS6B01G031600 chr6B 80.769 2418 340 66 1504 3841 18648053 18645681 0.000000e+00 1773.0
2 TraesCS6B01G031600 chr6B 87.578 1288 145 7 1142 2425 18734219 18732943 0.000000e+00 1478.0
3 TraesCS6B01G031600 chr6B 86.546 1323 153 15 1122 2426 18593260 18594575 0.000000e+00 1434.0
4 TraesCS6B01G031600 chr6B 85.096 832 118 4 3102 3930 18730798 18729970 0.000000e+00 845.0
5 TraesCS6B01G031600 chr6B 82.505 966 148 16 2969 3927 18595280 18596231 0.000000e+00 828.0
6 TraesCS6B01G031600 chr6B 78.553 788 108 38 686 1424 18648923 18648148 3.400000e-126 462.0
7 TraesCS6B01G031600 chr6B 94.931 217 9 2 2 218 664511 664725 5.980000e-89 339.0
8 TraesCS6B01G031600 chr6B 93.023 215 12 3 1 214 405004892 405004680 1.300000e-80 311.0
9 TraesCS6B01G031600 chr6B 90.991 222 14 2 214 431 18723044 18722825 1.310000e-75 294.0
10 TraesCS6B01G031600 chr6B 91.542 201 6 4 243 432 18715748 18715548 2.860000e-67 267.0
11 TraesCS6B01G031600 chr6B 87.805 82 7 3 4016 4097 18749273 18749195 5.140000e-15 93.5
12 TraesCS6B01G031600 chr6B 80.882 136 9 6 217 349 18650418 18650297 1.850000e-14 91.6
13 TraesCS6B01G031600 chr6B 90.566 53 2 3 4016 4068 18569635 18569684 3.120000e-07 67.6
14 TraesCS6B01G031600 chr6D 90.880 3410 244 34 543 3929 10069521 10066156 0.000000e+00 4512.0
15 TraesCS6B01G031600 chr6D 87.833 1315 145 10 1122 2426 10104097 10102788 0.000000e+00 1528.0
16 TraesCS6B01G031600 chr6D 82.635 1814 223 53 686 2430 10046446 10044656 0.000000e+00 1520.0
17 TraesCS6B01G031600 chr6D 86.465 1027 132 5 1472 2497 10121808 10120788 0.000000e+00 1120.0
18 TraesCS6B01G031600 chr6D 83.881 974 129 21 2971 3930 10102155 10101196 0.000000e+00 904.0
19 TraesCS6B01G031600 chr6D 82.054 1003 152 18 2948 3930 10120092 10119098 0.000000e+00 830.0
20 TraesCS6B01G031600 chr6D 82.625 823 137 6 3034 3855 10043972 10043155 0.000000e+00 723.0
21 TraesCS6B01G031600 chr6D 92.623 366 19 7 4094 4456 10065756 10065396 1.990000e-143 520.0
22 TraesCS6B01G031600 chr6D 87.937 315 35 2 1122 1436 10122199 10121888 7.630000e-98 368.0
23 TraesCS6B01G031600 chr6D 93.151 219 13 1 214 432 10093776 10093560 2.170000e-83 320.0
24 TraesCS6B01G031600 chr6D 89.723 253 18 5 4575 4827 10065373 10065129 2.800000e-82 316.0
25 TraesCS6B01G031600 chr6D 92.760 221 13 3 214 432 10070710 10070491 2.800000e-82 316.0
26 TraesCS6B01G031600 chr6D 87.222 180 6 4 3935 4098 10065968 10065790 6.380000e-44 189.0
27 TraesCS6B01G031600 chr6D 87.805 82 7 3 4016 4097 9985351 9985429 5.140000e-15 93.5
28 TraesCS6B01G031600 chr6A 89.908 3260 248 30 698 3938 11571886 11568689 0.000000e+00 4122.0
29 TraesCS6B01G031600 chr6A 87.423 1304 146 15 1130 2426 11590765 11589473 0.000000e+00 1483.0
30 TraesCS6B01G031600 chr6A 87.311 993 119 4 1484 2476 11557450 11556465 0.000000e+00 1129.0
31 TraesCS6B01G031600 chr6A 85.114 833 118 5 3102 3930 11588664 11587834 0.000000e+00 846.0
32 TraesCS6B01G031600 chr6A 83.758 825 120 6 3035 3855 11555729 11554915 0.000000e+00 769.0
33 TraesCS6B01G031600 chr6A 78.429 955 114 57 531 1426 11558450 11557529 5.500000e-149 538.0
34 TraesCS6B01G031600 chr6A 85.343 423 27 13 4167 4568 11568326 11567918 5.820000e-109 405.0
35 TraesCS6B01G031600 chr6A 88.561 271 17 9 4560 4827 11566450 11566191 2.800000e-82 316.0
36 TraesCS6B01G031600 chr6A 88.053 226 15 5 214 432 11573281 11573061 1.720000e-64 257.0
37 TraesCS6B01G031600 chr6A 86.932 176 11 1 3935 4098 11568588 11568413 2.290000e-43 187.0
38 TraesCS6B01G031600 chr2B 94.009 217 8 4 1 217 198104361 198104572 1.680000e-84 324.0
39 TraesCS6B01G031600 chr3B 92.661 218 13 3 1 217 188231588 188231373 1.300000e-80 311.0
40 TraesCS6B01G031600 chr3B 92.166 217 13 4 1 217 624233487 624233275 2.180000e-78 303.0
41 TraesCS6B01G031600 chr1B 92.661 218 13 3 1 217 280213980 280214195 1.300000e-80 311.0
42 TraesCS6B01G031600 chr1B 92.237 219 13 4 1 219 629667047 629666833 1.690000e-79 307.0
43 TraesCS6B01G031600 chr1B 90.541 74 6 1 461 534 642043798 642043870 3.980000e-16 97.1
44 TraesCS6B01G031600 chr5B 92.237 219 14 3 1 218 513991481 513991697 1.690000e-79 307.0
45 TraesCS6B01G031600 chr5B 91.818 220 15 3 1 219 596887406 596887189 2.180000e-78 303.0
46 TraesCS6B01G031600 chr7D 81.818 264 40 5 2143 2402 4794663 4794922 1.050000e-51 215.0
47 TraesCS6B01G031600 chr7D 87.838 74 8 1 466 539 71571977 71571905 8.610000e-13 86.1
48 TraesCS6B01G031600 chr2D 71.333 900 228 24 1512 2402 486501057 486501935 6.330000e-49 206.0
49 TraesCS6B01G031600 chr2D 97.959 49 1 0 467 515 79882283 79882235 8.610000e-13 86.1
50 TraesCS6B01G031600 chr5A 97.959 49 1 0 465 513 548865323 548865371 8.610000e-13 86.1
51 TraesCS6B01G031600 chr3A 94.545 55 3 0 459 513 735912504 735912558 8.610000e-13 86.1
52 TraesCS6B01G031600 chr3A 88.235 68 5 2 467 534 15333244 15333308 1.440000e-10 78.7
53 TraesCS6B01G031600 chr1D 94.545 55 3 0 459 513 509314 509260 8.610000e-13 86.1
54 TraesCS6B01G031600 chr4D 96.078 51 2 0 463 513 191234796 191234846 3.100000e-12 84.2
55 TraesCS6B01G031600 chr4A 96.078 51 2 0 463 513 12679354 12679304 3.100000e-12 84.2


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 TraesCS6B01G031600 chr6B 18655033 18659859 4826 True 8914.000000 8914 100.000000 1 4827 1 chr6B.!!$R1 4826
1 TraesCS6B01G031600 chr6B 18729970 18734219 4249 True 1161.500000 1478 86.337000 1142 3930 2 chr6B.!!$R7 2788
2 TraesCS6B01G031600 chr6B 18593260 18596231 2971 False 1131.000000 1434 84.525500 1122 3927 2 chr6B.!!$F3 2805
3 TraesCS6B01G031600 chr6B 18645681 18650418 4737 True 775.533333 1773 80.068000 217 3841 3 chr6B.!!$R6 3624
4 TraesCS6B01G031600 chr6D 10101196 10104097 2901 True 1216.000000 1528 85.857000 1122 3930 2 chr6D.!!$R4 2808
5 TraesCS6B01G031600 chr6D 10065129 10070710 5581 True 1170.600000 4512 90.641600 214 4827 5 chr6D.!!$R3 4613
6 TraesCS6B01G031600 chr6D 10043155 10046446 3291 True 1121.500000 1520 82.630000 686 3855 2 chr6D.!!$R2 3169
7 TraesCS6B01G031600 chr6D 10119098 10122199 3101 True 772.666667 1120 85.485333 1122 3930 3 chr6D.!!$R5 2808
8 TraesCS6B01G031600 chr6A 11587834 11590765 2931 True 1164.500000 1483 86.268500 1130 3930 2 chr6A.!!$R3 2800
9 TraesCS6B01G031600 chr6A 11566191 11573281 7090 True 1057.400000 4122 87.759400 214 4827 5 chr6A.!!$R2 4613
10 TraesCS6B01G031600 chr6A 11554915 11558450 3535 True 812.000000 1129 83.166000 531 3855 3 chr6A.!!$R1 3324
11 TraesCS6B01G031600 chr2D 486501057 486501935 878 False 206.000000 206 71.333000 1512 2402 1 chr2D.!!$F1 890

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
91 92 0.030908 TTTTTAAACACGCGCCTGGG 59.969 50.0 5.73 0.00 0.00 4.45 F
187 188 0.036294 GGTGCTTTTAGACGCTCCCT 60.036 55.0 0.00 0.00 34.60 4.20 F
852 2546 0.039180 TACCAGACGCAGAAGGGAGA 59.961 55.0 0.00 0.00 0.00 3.71 F
1016 2728 0.252057 TCAATGGAGACCGGAGACCA 60.252 55.0 9.46 14.58 36.83 4.02 F
2556 4608 0.467290 TTTGCTGGGTTCCACAGACC 60.467 55.0 0.00 0.00 38.20 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 3810 0.179009 CATGGCGGTCATCCTTGGAT 60.179 55.000 0.00 0.0 32.92 3.41 R
2130 4007 0.111134 CACGTGCAACACATCGTCAG 60.111 55.000 0.82 0.0 35.02 3.51 R
2263 4140 0.178912 ACTTCCCCCAGTCGTACCTT 60.179 55.000 0.00 0.0 0.00 3.50 R
2958 6880 2.025226 TCCCAGTTTGGTTGGTACAACA 60.025 45.455 13.40 0.0 38.07 3.33 R
4076 8833 0.108472 GCCAGCTCAAATTTCCCAGC 60.108 55.000 5.50 5.5 0.00 4.85 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
19 20 1.707632 TTTCGCCGAAATTTGCCATG 58.292 45.000 8.43 0.00 0.00 3.66
20 21 0.600557 TTCGCCGAAATTTGCCATGT 59.399 45.000 0.00 0.00 0.00 3.21
21 22 0.600557 TCGCCGAAATTTGCCATGTT 59.399 45.000 0.00 0.00 0.00 2.71
22 23 1.000283 TCGCCGAAATTTGCCATGTTT 60.000 42.857 0.00 0.00 0.00 2.83
23 24 2.229062 TCGCCGAAATTTGCCATGTTTA 59.771 40.909 0.00 0.00 0.00 2.01
24 25 2.598192 CGCCGAAATTTGCCATGTTTAG 59.402 45.455 0.00 0.00 0.00 1.85
25 26 2.348362 GCCGAAATTTGCCATGTTTAGC 59.652 45.455 0.00 0.00 0.00 3.09
26 27 2.929398 CCGAAATTTGCCATGTTTAGCC 59.071 45.455 0.00 0.00 0.00 3.93
27 28 3.583806 CGAAATTTGCCATGTTTAGCCA 58.416 40.909 0.00 0.00 0.00 4.75
28 29 3.993081 CGAAATTTGCCATGTTTAGCCAA 59.007 39.130 0.00 0.00 0.00 4.52
29 30 4.450419 CGAAATTTGCCATGTTTAGCCAAA 59.550 37.500 0.00 0.00 0.00 3.28
30 31 5.049818 CGAAATTTGCCATGTTTAGCCAAAA 60.050 36.000 0.00 0.00 0.00 2.44
31 32 6.348376 CGAAATTTGCCATGTTTAGCCAAAAT 60.348 34.615 0.00 0.00 0.00 1.82
32 33 6.897706 AATTTGCCATGTTTAGCCAAAATT 57.102 29.167 0.00 0.00 0.00 1.82
33 34 6.897706 ATTTGCCATGTTTAGCCAAAATTT 57.102 29.167 0.00 0.00 0.00 1.82
34 35 7.992754 ATTTGCCATGTTTAGCCAAAATTTA 57.007 28.000 0.00 0.00 0.00 1.40
35 36 7.807977 TTTGCCATGTTTAGCCAAAATTTAA 57.192 28.000 0.00 0.00 0.00 1.52
36 37 6.793492 TGCCATGTTTAGCCAAAATTTAAC 57.207 33.333 0.00 0.00 0.00 2.01
37 38 6.529220 TGCCATGTTTAGCCAAAATTTAACT 58.471 32.000 0.00 0.00 0.00 2.24
38 39 7.671302 TGCCATGTTTAGCCAAAATTTAACTA 58.329 30.769 0.00 0.00 0.00 2.24
39 40 7.600752 TGCCATGTTTAGCCAAAATTTAACTAC 59.399 33.333 0.00 0.00 0.00 2.73
40 41 7.817478 GCCATGTTTAGCCAAAATTTAACTACT 59.183 33.333 0.00 0.00 0.00 2.57
41 42 9.705290 CCATGTTTAGCCAAAATTTAACTACTT 57.295 29.630 0.00 0.00 0.00 2.24
59 60 7.230466 ACTACTTTTTATCATAACTTCGCCG 57.770 36.000 0.00 0.00 0.00 6.46
60 61 7.037438 ACTACTTTTTATCATAACTTCGCCGA 58.963 34.615 0.00 0.00 0.00 5.54
61 62 6.730960 ACTTTTTATCATAACTTCGCCGAA 57.269 33.333 0.00 0.00 0.00 4.30
62 63 6.540205 ACTTTTTATCATAACTTCGCCGAAC 58.460 36.000 0.00 0.00 0.00 3.95
63 64 5.473796 TTTTATCATAACTTCGCCGAACC 57.526 39.130 0.00 0.00 0.00 3.62
64 65 1.567504 ATCATAACTTCGCCGAACCG 58.432 50.000 0.00 0.00 0.00 4.44
90 91 3.553597 TTTTTAAACACGCGCCTGG 57.446 47.368 5.73 0.00 0.00 4.45
91 92 0.030908 TTTTTAAACACGCGCCTGGG 59.969 50.000 5.73 0.00 0.00 4.45
92 93 1.797211 TTTTAAACACGCGCCTGGGG 61.797 55.000 5.73 6.36 0.00 4.96
93 94 4.708386 TAAACACGCGCCTGGGGG 62.708 66.667 5.73 5.39 37.49 5.40
136 137 4.742201 CACCGACTCGCCACCAGG 62.742 72.222 0.00 0.00 38.23 4.45
160 161 3.972276 TTTTTGCGCCGGCTCACC 61.972 61.111 26.68 10.54 40.82 4.02
174 175 4.335647 CACCCTCAGGCGGTGCTT 62.336 66.667 0.00 0.00 44.10 3.91
175 176 3.570212 ACCCTCAGGCGGTGCTTT 61.570 61.111 0.00 0.00 36.11 3.51
176 177 2.282462 CCCTCAGGCGGTGCTTTT 60.282 61.111 0.00 0.00 0.00 2.27
177 178 1.002624 CCCTCAGGCGGTGCTTTTA 60.003 57.895 0.00 0.00 0.00 1.52
178 179 1.026718 CCCTCAGGCGGTGCTTTTAG 61.027 60.000 0.00 0.00 0.00 1.85
179 180 0.036388 CCTCAGGCGGTGCTTTTAGA 60.036 55.000 0.00 0.00 0.00 2.10
180 181 1.079503 CTCAGGCGGTGCTTTTAGAC 58.920 55.000 0.00 0.00 0.00 2.59
181 182 0.669318 TCAGGCGGTGCTTTTAGACG 60.669 55.000 0.00 0.00 0.00 4.18
183 184 3.562635 GCGGTGCTTTTAGACGCT 58.437 55.556 0.00 0.00 46.02 5.07
184 185 1.420312 GCGGTGCTTTTAGACGCTC 59.580 57.895 0.00 0.00 46.02 5.03
185 186 1.967597 GCGGTGCTTTTAGACGCTCC 61.968 60.000 0.00 0.00 46.02 4.70
186 187 1.359459 CGGTGCTTTTAGACGCTCCC 61.359 60.000 0.00 0.00 36.67 4.30
187 188 0.036294 GGTGCTTTTAGACGCTCCCT 60.036 55.000 0.00 0.00 34.60 4.20
188 189 1.206371 GGTGCTTTTAGACGCTCCCTA 59.794 52.381 0.00 0.00 34.60 3.53
189 190 2.541556 GTGCTTTTAGACGCTCCCTAG 58.458 52.381 0.00 0.00 0.00 3.02
190 191 1.480954 TGCTTTTAGACGCTCCCTAGG 59.519 52.381 0.06 0.06 0.00 3.02
191 192 1.202545 GCTTTTAGACGCTCCCTAGGG 60.203 57.143 23.22 23.22 41.33 3.53
192 193 1.413077 CTTTTAGACGCTCCCTAGGGG 59.587 57.143 28.19 18.77 46.11 4.79
212 213 3.869272 CAACGGCTGGAGATGCGC 61.869 66.667 0.00 0.00 0.00 6.09
242 243 2.179424 ACCCACGGGAGGAGTAGATTAT 59.821 50.000 9.72 0.00 38.96 1.28
244 245 3.762823 CCCACGGGAGGAGTAGATTATAC 59.237 52.174 0.00 0.00 37.50 1.47
249 252 4.767928 CGGGAGGAGTAGATTATACAGCTT 59.232 45.833 0.00 0.00 0.00 3.74
365 375 4.499357 GGCTTCTAGTACCGGAGTATGTTG 60.499 50.000 9.46 0.00 0.00 3.33
383 393 2.823154 GTTGTTTTAGGCATGCCCACTA 59.177 45.455 33.14 16.55 36.58 2.74
418 428 4.753107 TCTCATATGTACACATGCATGCAG 59.247 41.667 26.69 20.59 37.15 4.41
433 443 3.599584 CAGCATGCACCTTCCCAG 58.400 61.111 21.98 0.00 0.00 4.45
434 444 2.362120 AGCATGCACCTTCCCAGC 60.362 61.111 21.98 0.00 0.00 4.85
436 446 3.818787 CATGCACCTTCCCAGCGC 61.819 66.667 0.00 0.00 0.00 5.92
437 447 4.349503 ATGCACCTTCCCAGCGCA 62.350 61.111 11.47 0.00 36.95 6.09
441 2110 3.560251 ACCTTCCCAGCGCACTGT 61.560 61.111 11.47 0.00 42.81 3.55
471 2142 4.023963 GCTGACCCAACTTGTTTTCTACTC 60.024 45.833 0.00 0.00 0.00 2.59
472 2143 4.457466 TGACCCAACTTGTTTTCTACTCC 58.543 43.478 0.00 0.00 0.00 3.85
473 2144 3.819337 GACCCAACTTGTTTTCTACTCCC 59.181 47.826 0.00 0.00 0.00 4.30
474 2145 3.462205 ACCCAACTTGTTTTCTACTCCCT 59.538 43.478 0.00 0.00 0.00 4.20
475 2146 4.072839 CCCAACTTGTTTTCTACTCCCTC 58.927 47.826 0.00 0.00 0.00 4.30
476 2147 4.072839 CCAACTTGTTTTCTACTCCCTCC 58.927 47.826 0.00 0.00 0.00 4.30
477 2148 3.679824 ACTTGTTTTCTACTCCCTCCG 57.320 47.619 0.00 0.00 0.00 4.63
478 2149 2.970640 ACTTGTTTTCTACTCCCTCCGT 59.029 45.455 0.00 0.00 0.00 4.69
479 2150 4.154942 ACTTGTTTTCTACTCCCTCCGTA 58.845 43.478 0.00 0.00 0.00 4.02
480 2151 4.590222 ACTTGTTTTCTACTCCCTCCGTAA 59.410 41.667 0.00 0.00 0.00 3.18
481 2152 5.070847 ACTTGTTTTCTACTCCCTCCGTAAA 59.929 40.000 0.00 0.00 0.00 2.01
482 2153 4.886579 TGTTTTCTACTCCCTCCGTAAAC 58.113 43.478 0.00 0.00 0.00 2.01
483 2154 4.590222 TGTTTTCTACTCCCTCCGTAAACT 59.410 41.667 0.00 0.00 0.00 2.66
484 2155 5.774690 TGTTTTCTACTCCCTCCGTAAACTA 59.225 40.000 0.00 0.00 0.00 2.24
485 2156 6.267471 TGTTTTCTACTCCCTCCGTAAACTAA 59.733 38.462 0.00 0.00 0.00 2.24
486 2157 7.038799 TGTTTTCTACTCCCTCCGTAAACTAAT 60.039 37.037 0.00 0.00 0.00 1.73
487 2158 8.470002 GTTTTCTACTCCCTCCGTAAACTAATA 58.530 37.037 0.00 0.00 0.00 0.98
488 2159 8.773033 TTTCTACTCCCTCCGTAAACTAATAT 57.227 34.615 0.00 0.00 0.00 1.28
489 2160 9.866655 TTTCTACTCCCTCCGTAAACTAATATA 57.133 33.333 0.00 0.00 0.00 0.86
490 2161 9.866655 TTCTACTCCCTCCGTAAACTAATATAA 57.133 33.333 0.00 0.00 0.00 0.98
491 2162 9.866655 TCTACTCCCTCCGTAAACTAATATAAA 57.133 33.333 0.00 0.00 0.00 1.40
494 2165 9.605275 ACTCCCTCCGTAAACTAATATAAAAAC 57.395 33.333 0.00 0.00 0.00 2.43
495 2166 9.603921 CTCCCTCCGTAAACTAATATAAAAACA 57.396 33.333 0.00 0.00 0.00 2.83
556 2227 0.941463 ACAGAGCAAGCGTGTCTTCG 60.941 55.000 0.59 0.00 31.27 3.79
561 2232 1.687494 GCAAGCGTGTCTTCGGCTAG 61.687 60.000 0.59 0.00 31.27 3.42
575 2246 9.692749 TGTCTTCGGCTAGATAACAATTATTAG 57.307 33.333 0.00 0.00 0.00 1.73
618 2296 3.861840 AGAACCCGAACATGTACAGATG 58.138 45.455 0.00 0.00 0.00 2.90
639 2317 1.756408 ATGAGATCCAGCCTGAGCCG 61.756 60.000 0.00 0.00 41.25 5.52
664 2342 4.340381 CGGGCCGGCTAGTAGTATTATTAT 59.660 45.833 28.56 0.00 0.00 1.28
758 2445 1.863454 GATGATTAGCACTGACAGCCG 59.137 52.381 1.25 0.00 0.00 5.52
834 2528 4.020573 CGGGTGGCATGGAGACTATAAATA 60.021 45.833 0.00 0.00 0.00 1.40
847 2541 6.740110 AGACTATAAATACCAGACGCAGAAG 58.260 40.000 0.00 0.00 0.00 2.85
849 2543 2.403252 AAATACCAGACGCAGAAGGG 57.597 50.000 0.00 0.00 0.00 3.95
852 2546 0.039180 TACCAGACGCAGAAGGGAGA 59.961 55.000 0.00 0.00 0.00 3.71
902 2596 3.244700 ACACCTAGCTTCATCTGCTGTTT 60.245 43.478 0.00 0.00 41.32 2.83
957 2651 1.341383 CCCACCAATTCCTCTCCCTTG 60.341 57.143 0.00 0.00 0.00 3.61
969 2681 0.610687 CTCCCTTGTCTGGTGTCCTC 59.389 60.000 0.00 0.00 0.00 3.71
996 2708 2.297597 CCTCCGCCGATCTCTTTCTATT 59.702 50.000 0.00 0.00 0.00 1.73
1016 2728 0.252057 TCAATGGAGACCGGAGACCA 60.252 55.000 9.46 14.58 36.83 4.02
1038 2762 1.750930 CTCGGTGCCATGCTCCTAT 59.249 57.895 5.73 0.00 39.70 2.57
1041 2765 1.900498 GGTGCCATGCTCCTATGCC 60.900 63.158 0.13 0.00 38.91 4.40
1049 2773 3.117452 GCTCCTATGCCCAGCTGCT 62.117 63.158 8.66 0.00 0.00 4.24
1275 3011 3.036431 TGAGTCTGCCGTCTCAGAA 57.964 52.632 1.22 0.00 43.89 3.02
1287 3023 1.268899 GTCTCAGAAAAGACGTCCGGA 59.731 52.381 13.01 0.00 36.61 5.14
1288 3024 1.958579 TCTCAGAAAAGACGTCCGGAA 59.041 47.619 13.01 0.00 0.00 4.30
1459 3204 5.563592 TCCATCCTCCAGCATATTACATTG 58.436 41.667 0.00 0.00 0.00 2.82
1468 3280 7.210174 TCCAGCATATTACATTGAGTAGTGAC 58.790 38.462 0.00 0.00 33.43 3.67
1543 3417 2.354261 ACTACAAGGGGTGGTACCAT 57.646 50.000 19.72 2.05 39.72 3.55
1654 3528 1.136329 ACCTCCCAGTTGCCATGTCT 61.136 55.000 0.00 0.00 0.00 3.41
1657 3531 1.746615 CCCAGTTGCCATGTCTCCG 60.747 63.158 0.00 0.00 0.00 4.63
1741 3615 0.678684 TCGTCATGCTCTACACCGGA 60.679 55.000 9.46 0.00 0.00 5.14
1780 3654 2.032681 GTCCAGTGCCTCGCCTTT 59.967 61.111 0.00 0.00 0.00 3.11
1837 3711 3.244770 GGACCAAGTATGAGAACAACCCA 60.245 47.826 0.00 0.00 0.00 4.51
1909 3783 0.957395 CTGCATGGTTTGACGGCTCT 60.957 55.000 0.00 0.00 0.00 4.09
1936 3810 3.700970 TGGCGGCTCGTCATTGGA 61.701 61.111 11.43 0.00 36.25 3.53
2130 4007 2.672996 AGTGTCCACCAATGGCGC 60.673 61.111 0.00 0.00 46.80 6.53
2204 4081 1.321474 CTACGCGTTGGGGAGGTATA 58.679 55.000 20.78 0.00 0.00 1.47
2263 4140 2.626780 CGATCTCGGCATCGGGCTA 61.627 63.158 8.54 0.00 41.71 3.93
2454 4366 9.683069 GTACAAGATGTCAAAGTCAATTGATTT 57.317 29.630 12.12 11.05 41.09 2.17
2556 4608 0.467290 TTTGCTGGGTTCCACAGACC 60.467 55.000 0.00 0.00 38.20 3.85
2557 4609 1.640593 TTGCTGGGTTCCACAGACCA 61.641 55.000 0.00 0.00 38.98 4.02
2559 4611 0.467290 GCTGGGTTCCACAGACCAAA 60.467 55.000 0.00 0.00 38.98 3.28
2561 4613 0.923358 TGGGTTCCACAGACCAAACT 59.077 50.000 0.00 0.00 38.98 2.66
2564 4616 1.318576 GTTCCACAGACCAAACTGGG 58.681 55.000 0.00 0.00 43.37 4.45
2565 4617 1.133915 GTTCCACAGACCAAACTGGGA 60.134 52.381 0.00 0.00 43.19 4.37
2566 4618 1.444933 TCCACAGACCAAACTGGGAT 58.555 50.000 0.00 0.00 43.19 3.85
2567 4619 1.780309 TCCACAGACCAAACTGGGATT 59.220 47.619 0.00 0.00 43.19 3.01
2568 4620 2.983192 TCCACAGACCAAACTGGGATTA 59.017 45.455 0.00 0.00 43.19 1.75
2570 4622 3.009033 CCACAGACCAAACTGGGATTAGA 59.991 47.826 0.00 0.00 43.19 2.10
2571 4623 4.324563 CCACAGACCAAACTGGGATTAGAT 60.325 45.833 0.00 0.00 43.19 1.98
2576 4628 5.970640 AGACCAAACTGGGATTAGATAAGGA 59.029 40.000 0.00 0.00 43.37 3.36
2577 4629 6.447084 AGACCAAACTGGGATTAGATAAGGAA 59.553 38.462 0.00 0.00 43.37 3.36
2579 4631 7.475299 ACCAAACTGGGATTAGATAAGGAAAA 58.525 34.615 0.00 0.00 43.37 2.29
2580 4632 7.615757 ACCAAACTGGGATTAGATAAGGAAAAG 59.384 37.037 0.00 0.00 43.37 2.27
2582 4634 7.525158 AACTGGGATTAGATAAGGAAAAGGA 57.475 36.000 0.00 0.00 0.00 3.36
2636 5125 5.731591 TGAATCATGGATAGATAGCAGCTG 58.268 41.667 10.11 10.11 0.00 4.24
2664 6527 1.537202 GTTGCTGTCATCTGGTTGTCC 59.463 52.381 0.00 0.00 0.00 4.02
2769 6661 4.532916 TGGTAATCTGGTGCAAGTACCTAA 59.467 41.667 12.53 0.00 41.43 2.69
2784 6676 9.473640 GCAAGTACCTAACTATAACTGGATAAC 57.526 37.037 0.00 0.00 37.50 1.89
2822 6715 7.439056 ACAATTTTCTGTTAGCATGAACCAAAG 59.561 33.333 0.00 0.00 0.00 2.77
2832 6725 3.131046 GCATGAACCAAAGTGGGATTAGG 59.869 47.826 0.00 0.00 43.37 2.69
2840 6743 6.800890 ACCAAAGTGGGATTAGGTAAGAAAT 58.199 36.000 0.00 0.00 43.37 2.17
2859 6766 3.876309 ATGGGTGTGTCCTACAAACTT 57.124 42.857 0.70 0.00 41.89 2.66
2919 6833 4.947388 TCTAGTGGCAGACAAAAGTTGTTT 59.053 37.500 0.00 0.00 45.52 2.83
3016 7494 2.224548 GGTTGTCTTGTCTGCTTACCCT 60.225 50.000 0.00 0.00 0.00 4.34
3017 7495 2.808543 GTTGTCTTGTCTGCTTACCCTG 59.191 50.000 0.00 0.00 0.00 4.45
3040 7558 7.355332 TGCGGTTAGTTACACTATTTCTTTC 57.645 36.000 0.00 0.00 29.64 2.62
3537 8089 2.303890 ACTTCTGCCATGATGAGACACA 59.696 45.455 0.00 0.00 0.00 3.72
3625 8177 1.072159 GCTGTCAGTGAGGGTGCTT 59.928 57.895 0.93 0.00 0.00 3.91
3933 8490 2.094258 TCTCATTTCTTCGTTGCATCGC 59.906 45.455 12.30 0.00 0.00 4.58
4003 8744 3.003897 GCCGTTGTTTTACACTCATGGAA 59.996 43.478 0.00 0.00 0.00 3.53
4076 8833 6.295802 GGATGGATAGAGAGAGAAAGATTGGG 60.296 46.154 0.00 0.00 0.00 4.12
4081 8838 1.563410 AGAGAGAAAGATTGGGCTGGG 59.437 52.381 0.00 0.00 0.00 4.45
4083 8840 1.995542 AGAGAAAGATTGGGCTGGGAA 59.004 47.619 0.00 0.00 0.00 3.97
4098 8855 2.037511 CTGGGAAATTTGAGCTGGCAAA 59.962 45.455 0.00 0.00 41.49 3.68
4101 8858 3.306919 GGGAAATTTGAGCTGGCAAATCA 60.307 43.478 12.36 0.00 45.09 2.57
4103 8860 4.756135 GGAAATTTGAGCTGGCAAATCAAA 59.244 37.500 21.84 21.84 45.09 2.69
4129 8923 2.288273 CCGGTGATAAGATTCTCGGTCC 60.288 54.545 0.00 0.00 32.51 4.46
4142 8936 0.394488 TCGGTCCTCTCCTAGCTGTG 60.394 60.000 0.00 0.00 0.00 3.66
4143 8937 0.681564 CGGTCCTCTCCTAGCTGTGT 60.682 60.000 0.00 0.00 0.00 3.72
4145 8939 1.107945 GTCCTCTCCTAGCTGTGTCC 58.892 60.000 0.00 0.00 0.00 4.02
4146 8940 0.033011 TCCTCTCCTAGCTGTGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
4147 8941 0.032615 CCTCTCCTAGCTGTGTCCCT 60.033 60.000 0.00 0.00 0.00 4.20
4148 8942 1.110442 CTCTCCTAGCTGTGTCCCTG 58.890 60.000 0.00 0.00 0.00 4.45
4149 8943 0.324738 TCTCCTAGCTGTGTCCCTGG 60.325 60.000 0.00 0.00 0.00 4.45
4150 8944 1.965754 CTCCTAGCTGTGTCCCTGGC 61.966 65.000 0.00 0.00 0.00 4.85
4151 8945 1.992277 CCTAGCTGTGTCCCTGGCT 60.992 63.158 0.00 0.00 38.62 4.75
4250 9044 1.753848 GGTGCTGCCATGCATACCA 60.754 57.895 8.85 4.12 45.23 3.25
4275 9069 3.128068 TCTTGTCTTGATGCATGCATGTC 59.872 43.478 36.73 24.41 36.70 3.06
4323 9118 1.291877 ATTCTTGTGTGCTCGCCGTC 61.292 55.000 0.00 0.00 0.00 4.79
4470 9284 6.127196 GGGGATAGACATGCAAATTTAAACCA 60.127 38.462 0.00 0.00 0.00 3.67
4494 9308 7.177041 CCATAGTACTGTCTACTAATTCCCTCC 59.823 44.444 5.39 0.00 34.18 4.30
4497 9311 7.190501 AGTACTGTCTACTAATTCCCTCCTTT 58.809 38.462 0.00 0.00 0.00 3.11
4514 9329 1.356398 CTTTGGGTTTACTGCCCCCTA 59.644 52.381 0.00 0.00 45.49 3.53
4544 9359 9.589461 TTTTGGGTTAAACTTTGACCATCTATA 57.411 29.630 15.41 0.00 35.11 1.31
4546 9361 7.343357 TGGGTTAAACTTTGACCATCTATAGG 58.657 38.462 15.41 0.00 35.11 2.57
4650 10943 9.887406 CTTTTGGTCACGTATAGTTTACATTTT 57.113 29.630 0.00 0.00 0.00 1.82
4680 10973 7.763985 AGTTAACTTTGTGGTCAAATTTTGAGG 59.236 33.333 12.02 0.00 41.77 3.86
4703 10996 5.243954 GGCAAAATAAGAGGGGCCTTAATAG 59.756 44.000 0.84 0.00 38.37 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000283 ACATGGCAAATTTCGGCGAAA 60.000 42.857 33.79 33.79 35.94 3.46
1 2 0.600557 ACATGGCAAATTTCGGCGAA 59.399 45.000 19.83 19.83 0.00 4.70
3 4 1.427435 AAACATGGCAAATTTCGGCG 58.573 45.000 0.00 0.00 0.00 6.46
4 5 2.348362 GCTAAACATGGCAAATTTCGGC 59.652 45.455 0.00 0.58 0.00 5.54
5 6 2.929398 GGCTAAACATGGCAAATTTCGG 59.071 45.455 0.00 0.00 0.00 4.30
6 7 3.583806 TGGCTAAACATGGCAAATTTCG 58.416 40.909 0.00 0.00 37.05 3.46
12 13 6.995091 AGTTAAATTTTGGCTAAACATGGCAA 59.005 30.769 0.00 0.00 45.88 4.52
13 14 6.529220 AGTTAAATTTTGGCTAAACATGGCA 58.471 32.000 0.00 0.00 38.22 4.92
14 15 7.817478 AGTAGTTAAATTTTGGCTAAACATGGC 59.183 33.333 0.00 0.00 0.00 4.40
15 16 9.705290 AAGTAGTTAAATTTTGGCTAAACATGG 57.295 29.630 0.00 0.00 0.00 3.66
33 34 8.810427 CGGCGAAGTTATGATAAAAAGTAGTTA 58.190 33.333 0.00 0.00 0.00 2.24
34 35 7.546667 TCGGCGAAGTTATGATAAAAAGTAGTT 59.453 33.333 7.35 0.00 0.00 2.24
35 36 7.037438 TCGGCGAAGTTATGATAAAAAGTAGT 58.963 34.615 7.35 0.00 0.00 2.73
36 37 7.459394 TCGGCGAAGTTATGATAAAAAGTAG 57.541 36.000 7.35 0.00 0.00 2.57
37 38 7.201548 GGTTCGGCGAAGTTATGATAAAAAGTA 60.202 37.037 24.41 0.00 0.00 2.24
38 39 6.402875 GGTTCGGCGAAGTTATGATAAAAAGT 60.403 38.462 24.41 0.00 0.00 2.66
39 40 5.963586 GGTTCGGCGAAGTTATGATAAAAAG 59.036 40.000 24.41 0.00 0.00 2.27
40 41 5.446206 CGGTTCGGCGAAGTTATGATAAAAA 60.446 40.000 24.41 0.00 0.00 1.94
41 42 4.033129 CGGTTCGGCGAAGTTATGATAAAA 59.967 41.667 24.41 0.00 0.00 1.52
42 43 3.552699 CGGTTCGGCGAAGTTATGATAAA 59.447 43.478 24.41 0.00 0.00 1.40
43 44 3.117794 CGGTTCGGCGAAGTTATGATAA 58.882 45.455 24.41 0.00 0.00 1.75
44 45 2.544277 CCGGTTCGGCGAAGTTATGATA 60.544 50.000 24.41 0.00 41.17 2.15
45 46 1.567504 CGGTTCGGCGAAGTTATGAT 58.432 50.000 24.41 0.00 0.00 2.45
46 47 0.458889 CCGGTTCGGCGAAGTTATGA 60.459 55.000 24.41 0.00 41.17 2.15
47 48 2.003672 CCGGTTCGGCGAAGTTATG 58.996 57.895 24.41 10.66 41.17 1.90
48 49 4.507879 CCGGTTCGGCGAAGTTAT 57.492 55.556 24.41 0.00 41.17 1.89
72 73 0.030908 CCCAGGCGCGTGTTTAAAAA 59.969 50.000 26.57 0.00 0.00 1.94
73 74 1.655329 CCCAGGCGCGTGTTTAAAA 59.345 52.632 26.57 0.00 0.00 1.52
74 75 2.262303 CCCCAGGCGCGTGTTTAAA 61.262 57.895 26.57 0.00 0.00 1.52
75 76 2.670251 CCCCAGGCGCGTGTTTAA 60.670 61.111 26.57 0.00 0.00 1.52
76 77 4.708386 CCCCCAGGCGCGTGTTTA 62.708 66.667 26.57 0.00 0.00 2.01
119 120 4.742201 CCTGGTGGCGAGTCGGTG 62.742 72.222 15.52 0.00 0.00 4.94
143 144 3.972276 GGTGAGCCGGCGCAAAAA 61.972 61.111 34.87 9.47 37.52 1.94
158 159 1.774894 TAAAAGCACCGCCTGAGGGT 61.775 55.000 0.00 0.00 38.65 4.34
159 160 1.002624 TAAAAGCACCGCCTGAGGG 60.003 57.895 0.00 0.00 35.02 4.30
160 161 0.036388 TCTAAAAGCACCGCCTGAGG 60.036 55.000 0.00 0.00 37.30 3.86
161 162 1.079503 GTCTAAAAGCACCGCCTGAG 58.920 55.000 0.00 0.00 0.00 3.35
162 163 0.669318 CGTCTAAAAGCACCGCCTGA 60.669 55.000 0.00 0.00 0.00 3.86
163 164 1.787847 CGTCTAAAAGCACCGCCTG 59.212 57.895 0.00 0.00 0.00 4.85
164 165 2.033194 GCGTCTAAAAGCACCGCCT 61.033 57.895 0.00 0.00 38.52 5.52
165 166 1.967597 GAGCGTCTAAAAGCACCGCC 61.968 60.000 0.00 0.00 45.06 6.13
166 167 1.420312 GAGCGTCTAAAAGCACCGC 59.580 57.895 0.00 0.00 44.35 5.68
167 168 1.359459 GGGAGCGTCTAAAAGCACCG 61.359 60.000 0.00 0.00 43.52 4.94
168 169 0.036294 AGGGAGCGTCTAAAAGCACC 60.036 55.000 0.00 0.00 42.19 5.01
169 170 2.541556 CTAGGGAGCGTCTAAAAGCAC 58.458 52.381 0.00 0.00 35.48 4.40
170 171 1.480954 CCTAGGGAGCGTCTAAAAGCA 59.519 52.381 0.00 0.00 35.48 3.91
171 172 1.202545 CCCTAGGGAGCGTCTAAAAGC 60.203 57.143 24.99 0.00 37.50 3.51
172 173 2.892784 CCCTAGGGAGCGTCTAAAAG 57.107 55.000 24.99 0.00 37.50 2.27
195 196 3.869272 GCGCATCTCCAGCCGTTG 61.869 66.667 0.30 0.00 0.00 4.10
196 197 2.238847 TAAGCGCATCTCCAGCCGTT 62.239 55.000 11.47 0.00 0.00 4.44
197 198 2.635229 CTAAGCGCATCTCCAGCCGT 62.635 60.000 11.47 0.00 0.00 5.68
198 199 1.953138 CTAAGCGCATCTCCAGCCG 60.953 63.158 11.47 0.00 0.00 5.52
199 200 1.144936 ACTAAGCGCATCTCCAGCC 59.855 57.895 11.47 0.00 0.00 4.85
200 201 0.460987 ACACTAAGCGCATCTCCAGC 60.461 55.000 11.47 0.00 0.00 4.85
201 202 2.860735 GTTACACTAAGCGCATCTCCAG 59.139 50.000 11.47 0.00 0.00 3.86
202 203 2.418197 GGTTACACTAAGCGCATCTCCA 60.418 50.000 11.47 0.00 0.00 3.86
203 204 2.202566 GGTTACACTAAGCGCATCTCC 58.797 52.381 11.47 0.00 0.00 3.71
204 205 2.202566 GGGTTACACTAAGCGCATCTC 58.797 52.381 11.47 0.00 37.05 2.75
205 206 1.553248 TGGGTTACACTAAGCGCATCT 59.447 47.619 11.47 0.00 37.05 2.90
206 207 1.664151 GTGGGTTACACTAAGCGCATC 59.336 52.381 11.47 0.00 46.72 3.91
207 208 1.734163 GTGGGTTACACTAAGCGCAT 58.266 50.000 11.47 0.00 46.72 4.73
208 209 3.220447 GTGGGTTACACTAAGCGCA 57.780 52.632 11.47 0.00 46.72 6.09
310 315 1.916206 GAGAGAGAAACAGGGCCCCC 61.916 65.000 21.43 2.53 0.00 5.40
365 375 2.623416 GGATAGTGGGCATGCCTAAAAC 59.377 50.000 34.70 25.34 36.10 2.43
418 428 3.818787 CGCTGGGAAGGTGCATGC 61.819 66.667 11.82 11.82 0.00 4.06
451 2122 3.819337 GGGAGTAGAAAACAAGTTGGGTC 59.181 47.826 7.96 1.42 0.00 4.46
517 2188 8.035984 GCTCTGTTAATACTTCCTCTGTAAACT 58.964 37.037 0.00 0.00 0.00 2.66
518 2189 7.817962 TGCTCTGTTAATACTTCCTCTGTAAAC 59.182 37.037 0.00 0.00 0.00 2.01
519 2190 7.903145 TGCTCTGTTAATACTTCCTCTGTAAA 58.097 34.615 0.00 0.00 0.00 2.01
520 2191 7.476540 TGCTCTGTTAATACTTCCTCTGTAA 57.523 36.000 0.00 0.00 0.00 2.41
521 2192 7.476540 TTGCTCTGTTAATACTTCCTCTGTA 57.523 36.000 0.00 0.00 0.00 2.74
522 2193 6.360370 TTGCTCTGTTAATACTTCCTCTGT 57.640 37.500 0.00 0.00 0.00 3.41
523 2194 5.293079 GCTTGCTCTGTTAATACTTCCTCTG 59.707 44.000 0.00 0.00 0.00 3.35
524 2195 5.423886 GCTTGCTCTGTTAATACTTCCTCT 58.576 41.667 0.00 0.00 0.00 3.69
525 2196 4.268884 CGCTTGCTCTGTTAATACTTCCTC 59.731 45.833 0.00 0.00 0.00 3.71
526 2197 4.184629 CGCTTGCTCTGTTAATACTTCCT 58.815 43.478 0.00 0.00 0.00 3.36
527 2198 3.933332 ACGCTTGCTCTGTTAATACTTCC 59.067 43.478 0.00 0.00 0.00 3.46
528 2199 4.389077 ACACGCTTGCTCTGTTAATACTTC 59.611 41.667 0.00 0.00 0.00 3.01
529 2200 4.315803 ACACGCTTGCTCTGTTAATACTT 58.684 39.130 0.00 0.00 0.00 2.24
530 2201 3.926616 ACACGCTTGCTCTGTTAATACT 58.073 40.909 0.00 0.00 0.00 2.12
531 2202 3.927142 AGACACGCTTGCTCTGTTAATAC 59.073 43.478 0.00 0.00 0.00 1.89
532 2203 4.188247 AGACACGCTTGCTCTGTTAATA 57.812 40.909 0.00 0.00 0.00 0.98
533 2204 3.045601 AGACACGCTTGCTCTGTTAAT 57.954 42.857 0.00 0.00 0.00 1.40
534 2205 2.526304 AGACACGCTTGCTCTGTTAA 57.474 45.000 0.00 0.00 0.00 2.01
535 2206 2.404215 GAAGACACGCTTGCTCTGTTA 58.596 47.619 0.00 0.00 36.83 2.41
556 2227 7.665974 AGTTGGGCTAATAATTGTTATCTAGCC 59.334 37.037 14.78 14.78 43.02 3.93
561 2232 7.817418 TCCAGTTGGGCTAATAATTGTTATC 57.183 36.000 0.00 0.00 36.21 1.75
575 2246 0.387929 CATGCATGATCCAGTTGGGC 59.612 55.000 22.59 0.00 36.21 5.36
618 2296 0.885596 GCTCAGGCTGGATCTCATGC 60.886 60.000 15.73 3.23 35.22 4.06
624 2302 2.107953 GTCGGCTCAGGCTGGATC 59.892 66.667 15.73 3.90 44.44 3.36
639 2317 0.892814 ATACTACTAGCCGGCCCGTC 60.893 60.000 26.15 0.00 0.00 4.79
643 2321 7.579761 ACTATAATAATACTACTAGCCGGCC 57.420 40.000 26.15 5.07 0.00 6.13
813 2507 5.221843 TGGTATTTATAGTCTCCATGCCACC 60.222 44.000 0.00 0.00 0.00 4.61
834 2528 0.832135 TTCTCCCTTCTGCGTCTGGT 60.832 55.000 0.00 0.00 0.00 4.00
849 2543 2.095252 GTTCGCCGTGGAGCTTCTC 61.095 63.158 0.00 0.00 0.00 2.87
852 2546 2.665185 GTGTTCGCCGTGGAGCTT 60.665 61.111 0.00 0.00 0.00 3.74
864 2558 0.929824 GTGTGTGCATGTGCGTGTTC 60.930 55.000 0.00 0.00 45.83 3.18
902 2596 4.804597 TCACCTCTGCTAAGCCTAATCTA 58.195 43.478 0.00 0.00 0.00 1.98
935 2629 0.548510 GGGAGAGGAATTGGTGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
957 2651 0.899019 GGAGAAGGAGGACACCAGAC 59.101 60.000 0.00 0.00 0.00 3.51
969 2681 1.801309 GAGATCGGCGGAGGAGAAGG 61.801 65.000 7.21 0.00 0.00 3.46
996 2708 0.902531 GGTCTCCGGTCTCCATTGAA 59.097 55.000 0.00 0.00 0.00 2.69
1107 2840 0.744874 CCGCCGAAGTCAGGAGAATA 59.255 55.000 0.00 0.00 0.00 1.75
1275 3011 2.356673 GCGGTTCCGGACGTCTTT 60.357 61.111 16.46 0.00 0.00 2.52
1377 3122 0.909610 TCTCGGGCTGGAAGTGGAAT 60.910 55.000 0.00 0.00 35.30 3.01
1543 3417 3.087031 CGGGTTGTACTGGTAGAAGAGA 58.913 50.000 0.00 0.00 0.00 3.10
1642 3516 1.296715 GTCCGGAGACATGGCAACT 59.703 57.895 3.06 0.00 42.99 3.16
1654 3528 1.574263 TGTCATACCATTGGTCCGGA 58.426 50.000 12.68 0.00 37.09 5.14
1657 3531 4.279169 CCATTGATGTCATACCATTGGTCC 59.721 45.833 12.68 0.00 37.09 4.46
1741 3615 1.224592 GACGGAGGCATTGGTGGAT 59.775 57.895 0.00 0.00 0.00 3.41
1780 3654 1.453379 GTCGGAGGGATCAGTCGGA 60.453 63.158 0.00 0.00 0.00 4.55
1837 3711 2.666098 GGGTGGCGGGTACATCACT 61.666 63.158 0.00 0.00 0.00 3.41
1909 3783 1.450134 GAGCCGCCATGTGTCATCA 60.450 57.895 0.00 0.00 0.00 3.07
1933 3807 1.526887 GCGGTCATCCTTGGATCCA 59.473 57.895 11.44 11.44 0.00 3.41
1936 3810 0.179009 CATGGCGGTCATCCTTGGAT 60.179 55.000 0.00 0.00 32.92 3.41
2130 4007 0.111134 CACGTGCAACACATCGTCAG 60.111 55.000 0.82 0.00 35.02 3.51
2204 4081 1.959226 ATGTGTTCTTCGCCGCGTT 60.959 52.632 13.39 0.00 0.00 4.84
2263 4140 0.178912 ACTTCCCCCAGTCGTACCTT 60.179 55.000 0.00 0.00 0.00 3.50
2556 4608 7.834181 TCCTTTTCCTTATCTAATCCCAGTTTG 59.166 37.037 0.00 0.00 0.00 2.93
2557 4609 7.939781 TCCTTTTCCTTATCTAATCCCAGTTT 58.060 34.615 0.00 0.00 0.00 2.66
2559 4611 7.184753 ACTTCCTTTTCCTTATCTAATCCCAGT 59.815 37.037 0.00 0.00 0.00 4.00
2561 4613 7.346471 CACTTCCTTTTCCTTATCTAATCCCA 58.654 38.462 0.00 0.00 0.00 4.37
2564 4616 7.865706 TGCACTTCCTTTTCCTTATCTAATC 57.134 36.000 0.00 0.00 0.00 1.75
2565 4617 8.650143 TTTGCACTTCCTTTTCCTTATCTAAT 57.350 30.769 0.00 0.00 0.00 1.73
2566 4618 8.650143 ATTTGCACTTCCTTTTCCTTATCTAA 57.350 30.769 0.00 0.00 0.00 2.10
2567 4619 9.747898 TTATTTGCACTTCCTTTTCCTTATCTA 57.252 29.630 0.00 0.00 0.00 1.98
2568 4620 8.650143 TTATTTGCACTTCCTTTTCCTTATCT 57.350 30.769 0.00 0.00 0.00 1.98
2576 4628 9.807649 CTGCTATTATTATTTGCACTTCCTTTT 57.192 29.630 0.00 0.00 0.00 2.27
2577 4629 7.922811 GCTGCTATTATTATTTGCACTTCCTTT 59.077 33.333 0.00 0.00 0.00 3.11
2579 4631 6.015940 GGCTGCTATTATTATTTGCACTTCCT 60.016 38.462 0.00 0.00 0.00 3.36
2580 4632 6.152379 GGCTGCTATTATTATTTGCACTTCC 58.848 40.000 0.00 0.00 0.00 3.46
2582 4634 6.096705 TGTGGCTGCTATTATTATTTGCACTT 59.903 34.615 0.00 0.00 0.00 3.16
2636 5125 3.499048 CAGATGACAGCAACATTTCTGC 58.501 45.455 0.00 0.00 40.24 4.26
2664 6527 6.356757 GCTAAAGGAAGCTAAGAGACAATG 57.643 41.667 0.00 0.00 39.50 2.82
2744 6629 2.200373 ACTTGCACCAGATTACCACC 57.800 50.000 0.00 0.00 0.00 4.61
2822 6715 4.887655 CACCCATTTCTTACCTAATCCCAC 59.112 45.833 0.00 0.00 0.00 4.61
2832 6725 4.901868 TGTAGGACACACCCATTTCTTAC 58.098 43.478 0.00 0.00 40.05 2.34
2840 6743 3.283751 CAAAGTTTGTAGGACACACCCA 58.716 45.455 7.48 0.00 36.69 4.51
2958 6880 2.025226 TCCCAGTTTGGTTGGTACAACA 60.025 45.455 13.40 0.00 38.07 3.33
2959 6881 2.657143 TCCCAGTTTGGTTGGTACAAC 58.343 47.619 3.63 3.63 38.07 3.32
2961 6883 3.603965 AATCCCAGTTTGGTTGGTACA 57.396 42.857 0.00 0.00 35.17 2.90
3040 7558 6.425210 TCCTAGGTATCAATCATTGACAGG 57.575 41.667 9.08 5.06 43.48 4.00
3116 7668 2.482374 GGTCGACTGCAGCAATGC 59.518 61.111 15.27 0.00 0.00 3.56
3117 7669 2.401766 GGGGTCGACTGCAGCAATG 61.402 63.158 15.27 0.74 0.00 2.82
3157 7709 0.611714 GGAGGTTGCTTCCCGTCTTA 59.388 55.000 0.00 0.00 0.00 2.10
3466 8018 1.136305 GCCACATAGAAGTAGACGGCA 59.864 52.381 0.00 0.00 38.20 5.69
3625 8177 3.130340 TCTCAACGATCGAATGATCCACA 59.870 43.478 24.34 2.65 46.89 4.17
3933 8490 2.488545 ACACCTACTCGCACTGTAGAAG 59.511 50.000 8.70 4.55 39.61 2.85
3971 8712 5.463061 GTGTAAAACAACGGCAAGACTACTA 59.537 40.000 0.00 0.00 0.00 1.82
4003 8744 2.649312 TCCCTGGGATCATTGACACTTT 59.351 45.455 12.53 0.00 0.00 2.66
4076 8833 0.108472 GCCAGCTCAAATTTCCCAGC 60.108 55.000 5.50 5.50 0.00 4.85
4081 8838 5.613142 CGTTTGATTTGCCAGCTCAAATTTC 60.613 40.000 13.02 5.15 44.15 2.17
4083 8840 3.742369 CGTTTGATTTGCCAGCTCAAATT 59.258 39.130 13.02 0.52 44.15 1.82
4098 8855 0.741574 TTATCACCGGCGCGTTTGAT 60.742 50.000 17.16 17.16 34.01 2.57
4099 8856 1.355796 CTTATCACCGGCGCGTTTGA 61.356 55.000 8.43 3.31 0.00 2.69
4101 8858 0.461339 ATCTTATCACCGGCGCGTTT 60.461 50.000 8.43 0.00 0.00 3.60
4103 8860 0.874607 GAATCTTATCACCGGCGCGT 60.875 55.000 8.43 0.00 0.00 6.01
4129 8923 1.110442 CAGGGACACAGCTAGGAGAG 58.890 60.000 0.00 0.00 0.00 3.20
4142 8936 2.609610 TGGGTGGTAGCCAGGGAC 60.610 66.667 0.00 0.00 41.50 4.46
4147 8941 2.205749 TCAGGTGGGTGGTAGCCA 59.794 61.111 0.00 0.00 44.64 4.75
4148 8942 2.669240 GTCAGGTGGGTGGTAGCC 59.331 66.667 0.00 0.00 36.00 3.93
4149 8943 2.264794 CGTCAGGTGGGTGGTAGC 59.735 66.667 0.00 0.00 0.00 3.58
4150 8944 2.978824 CCGTCAGGTGGGTGGTAG 59.021 66.667 0.00 0.00 0.00 3.18
4151 8945 3.315949 GCCGTCAGGTGGGTGGTA 61.316 66.667 0.00 0.00 40.50 3.25
4250 9044 3.151554 TGCATGCATCAAGACAAGAACT 58.848 40.909 18.46 0.00 0.00 3.01
4296 9091 4.493220 GCGAGCACACAAGAATAGAATCAC 60.493 45.833 0.00 0.00 0.00 3.06
4297 9092 3.618594 GCGAGCACACAAGAATAGAATCA 59.381 43.478 0.00 0.00 0.00 2.57
4323 9118 8.171840 GCACTGCATTAGTTTAACTTTCTAGAG 58.828 37.037 1.94 0.00 37.60 2.43
4427 9227 2.159028 CCCCGCCAAAAGACAAGAAAAA 60.159 45.455 0.00 0.00 0.00 1.94
4470 9284 8.059565 AGGAGGGAATTAGTAGACAGTACTAT 57.940 38.462 0.00 0.00 30.99 2.12
4476 9290 5.675538 CCAAAGGAGGGAATTAGTAGACAG 58.324 45.833 0.00 0.00 0.00 3.51
4502 9316 4.810345 CCCAAAATATTAGGGGGCAGTAA 58.190 43.478 15.17 0.00 38.98 2.24
4514 9329 9.719355 GATGGTCAAAGTTTAACCCAAAATATT 57.281 29.630 5.43 0.00 31.78 1.28
4660 10953 4.440880 TGCCTCAAAATTTGACCACAAAG 58.559 39.130 4.03 0.00 46.84 2.77
4680 10973 6.016192 GTCTATTAAGGCCCCTCTTATTTTGC 60.016 42.308 0.00 0.00 0.00 3.68
4703 10996 0.670854 GTGCTTCCTTCGTCCAGGTC 60.671 60.000 0.00 0.00 35.15 3.85
4749 11042 5.389859 TGCTGATTAATTGGGTTTCACAG 57.610 39.130 0.00 0.00 0.00 3.66
4781 11074 3.704061 ACACAAAACCACCTACATGCTTT 59.296 39.130 0.00 0.00 0.00 3.51
4783 11076 2.622942 CACACAAAACCACCTACATGCT 59.377 45.455 0.00 0.00 0.00 3.79
4790 11083 2.223803 TGAACCACACAAAACCACCT 57.776 45.000 0.00 0.00 0.00 4.00
4793 11086 3.092301 TGACATGAACCACACAAAACCA 58.908 40.909 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.