Multiple sequence alignment - TraesCS2D01G004000

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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 TraesCS2D01G004000 chr2D 100.000 6404 0 0 1 6404 2475854 2469451 0.000000e+00 11827
1 TraesCS2D01G004000 chr2D 84.940 332 41 8 3025 3350 2375266 2374938 1.720000e-85 327
2 TraesCS2D01G004000 chrUn 91.147 2372 113 35 4076 6401 15908969 15911289 0.000000e+00 3127
3 TraesCS2D01G004000 chrUn 90.813 2264 136 31 1442 3679 15906255 15908472 0.000000e+00 2963
4 TraesCS2D01G004000 chrUn 79.842 1012 59 51 404 1344 15905188 15906125 7.100000e-169 604
5 TraesCS2D01G004000 chrUn 94.000 250 9 1 3891 4134 15908718 15908967 2.180000e-99 374
6 TraesCS2D01G004000 chrUn 84.848 330 43 6 3025 3350 15854362 15854036 6.190000e-85 326
7 TraesCS2D01G004000 chrUn 84.731 334 41 7 3025 3350 352147721 352148052 6.190000e-85 326
8 TraesCS2D01G004000 chrUn 83.483 333 46 6 3025 3350 15637402 15637072 1.040000e-77 302
9 TraesCS2D01G004000 chr2A 90.021 2395 134 45 354 2679 2481347 2483705 0.000000e+00 3001
10 TraesCS2D01G004000 chr2A 92.838 1145 48 17 2673 3790 2483899 2485036 0.000000e+00 1629
11 TraesCS2D01G004000 chr2A 90.774 1073 51 23 5039 6086 2486512 2487561 0.000000e+00 1389
12 TraesCS2D01G004000 chr2A 90.471 997 44 13 4076 5045 2485287 2486259 0.000000e+00 1267
13 TraesCS2D01G004000 chr2A 92.829 251 12 1 3891 4135 2485036 2485286 6.100000e-95 359
14 TraesCS2D01G004000 chr3A 83.492 1575 178 50 3352 4868 13153381 13151831 0.000000e+00 1393
15 TraesCS2D01G004000 chr3A 85.428 748 72 18 2611 3353 13154476 13153761 0.000000e+00 743
16 TraesCS2D01G004000 chr3A 82.469 810 96 31 1469 2264 13155260 13154483 0.000000e+00 667
17 TraesCS2D01G004000 chr3A 82.152 409 25 25 953 1344 13155806 13155429 2.240000e-79 307
18 TraesCS2D01G004000 chr3D 83.633 1558 175 48 3354 4868 7132422 7133942 0.000000e+00 1391
19 TraesCS2D01G004000 chr3D 80.651 1168 130 41 1469 2619 7130271 7131359 0.000000e+00 817
20 TraesCS2D01G004000 chr3D 87.914 604 56 11 2755 3353 7131423 7132014 0.000000e+00 695
21 TraesCS2D01G004000 chr3D 81.995 411 25 26 953 1344 7129729 7130109 2.900000e-78 303
22 TraesCS2D01G004000 chr3B 83.632 1564 166 43 3354 4868 8735483 8737005 0.000000e+00 1387
23 TraesCS2D01G004000 chr3B 82.512 812 95 30 1469 2264 8733885 8734665 0.000000e+00 669
24 TraesCS2D01G004000 chr3B 92.727 385 21 5 2974 3353 8734720 8735102 3.380000e-152 549
25 TraesCS2D01G004000 chr3B 83.288 371 18 22 990 1344 8733378 8733720 1.040000e-77 302
26 TraesCS2D01G004000 chr3B 78.119 489 59 22 92 548 457195455 457195927 3.810000e-67 267
27 TraesCS2D01G004000 chr6D 83.853 737 69 22 3 699 212501957 212501231 0.000000e+00 656
28 TraesCS2D01G004000 chr6D 76.728 434 44 23 95 490 152613879 152613465 8.480000e-44 189
29 TraesCS2D01G004000 chr1D 80.324 864 121 31 1401 2237 60429135 60429976 5.490000e-170 608
30 TraesCS2D01G004000 chr1D 80.588 850 93 34 2514 3353 60430087 60430874 1.990000e-164 590
31 TraesCS2D01G004000 chr1D 92.754 69 5 0 1231 1299 60428962 60429030 4.090000e-17 100
32 TraesCS2D01G004000 chr2B 79.623 849 100 34 2514 3353 757833838 757834622 5.650000e-150 542
33 TraesCS2D01G004000 chr2B 78.996 857 104 34 2514 3353 757705702 757706499 3.420000e-142 516
34 TraesCS2D01G004000 chr2B 84.360 211 27 5 1470 1677 757832987 757833194 1.090000e-47 202
35 TraesCS2D01G004000 chr2B 92.754 69 5 0 1231 1299 757704604 757704672 4.090000e-17 100
36 TraesCS2D01G004000 chr6B 84.022 363 39 7 396 752 633722968 633722619 1.330000e-86 331
37 TraesCS2D01G004000 chr7B 82.254 355 43 9 207 545 583963047 583963397 8.120000e-74 289
38 TraesCS2D01G004000 chr7D 84.053 301 35 6 257 548 470052121 470051825 1.760000e-70 278
39 TraesCS2D01G004000 chr4A 78.465 469 59 22 92 522 281078216 281078680 1.060000e-67 268
40 TraesCS2D01G004000 chr1B 77.111 533 74 25 50 548 348854981 348855499 1.370000e-66 265
41 TraesCS2D01G004000 chr5B 94.203 69 4 0 1231 1299 536510787 536510855 8.780000e-19 106
42 TraesCS2D01G004000 chr4B 92.000 75 6 0 1231 1305 623071212 623071138 8.780000e-19 106


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 TraesCS2D01G004000 chr2D 2469451 2475854 6403 True 11827.000000 11827 100.000000 1 6404 1 chr2D.!!$R2 6403
1 TraesCS2D01G004000 chrUn 15905188 15911289 6101 False 1767.000000 3127 88.950500 404 6401 4 chrUn.!!$F2 5997
2 TraesCS2D01G004000 chr2A 2481347 2487561 6214 False 1529.000000 3001 91.386600 354 6086 5 chr2A.!!$F1 5732
3 TraesCS2D01G004000 chr3A 13151831 13155806 3975 True 777.500000 1393 83.385250 953 4868 4 chr3A.!!$R1 3915
4 TraesCS2D01G004000 chr3D 7129729 7133942 4213 False 801.500000 1391 83.548250 953 4868 4 chr3D.!!$F1 3915
5 TraesCS2D01G004000 chr3B 8733378 8737005 3627 False 726.750000 1387 85.539750 990 4868 4 chr3B.!!$F2 3878
6 TraesCS2D01G004000 chr6D 212501231 212501957 726 True 656.000000 656 83.853000 3 699 1 chr6D.!!$R2 696
7 TraesCS2D01G004000 chr1D 60428962 60430874 1912 False 432.666667 608 84.555333 1231 3353 3 chr1D.!!$F1 2122
8 TraesCS2D01G004000 chr2B 757832987 757834622 1635 False 372.000000 542 81.991500 1470 3353 2 chr2B.!!$F2 1883
9 TraesCS2D01G004000 chr2B 757704604 757706499 1895 False 308.000000 516 85.875000 1231 3353 2 chr2B.!!$F1 2122
10 TraesCS2D01G004000 chr1B 348854981 348855499 518 False 265.000000 265 77.111000 50 548 1 chr1B.!!$F1 498

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
918 1000 0.464554 GCCCAGCCCAGTCTTGTATC 60.465 60.0 0.00 0.00 0.00 2.24 F
1597 1822 0.036732 TTCCATGTGTCCTGGCTCAC 59.963 55.0 12.56 12.56 33.56 3.51 F
1810 2051 1.092345 GGACGCTGAGGGCTGATTTC 61.092 60.0 0.00 0.00 39.13 2.17 F
1924 2171 1.106285 ATCTCATGCCGCCCTTTTTC 58.894 50.0 0.00 0.00 0.00 2.29 F
2017 2266 1.299541 GTGGCAATCACGTATGGGAG 58.700 55.0 0.00 0.00 36.56 4.30 F
3823 4880 0.764890 ACTGAAGTAGCAAGTGCCCA 59.235 50.0 0.00 0.00 43.38 5.36 F
4877 6096 0.463295 CAGGTCAGTATGCTGGGCAG 60.463 60.0 11.15 0.00 43.65 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2051 0.179215 GCAGCCAGAACGATCAAACG 60.179 55.000 0.00 0.0 39.31 3.60 R
2679 3165 2.599659 GACTTTTATGCAGCCACAAGC 58.400 47.619 0.00 0.0 44.25 4.01 R
3239 3755 2.798976 TTGCCATTGACAACAAGAGC 57.201 45.000 0.00 0.0 39.46 4.09 R
3505 4430 3.118261 GGATTTACCTGCTGGTCATCTCA 60.118 47.826 19.71 0.0 44.78 3.27 R
3942 4999 0.760567 TACCAGGAGCATCGCCAGAT 60.761 55.000 0.00 0.0 37.65 2.90 R
5237 6751 0.034670 AAGGACCTGCATCCAGAAGC 60.035 55.000 9.02 0.0 41.77 3.86 R
5869 7389 0.843309 TGCCCACTGGAAAGAAGTCA 59.157 50.000 0.00 0.0 0.00 3.41 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
23 24 6.210287 AGTATAGCAGAAACTGTGGACTAC 57.790 41.667 0.00 0.00 33.43 2.73
36 37 5.159273 TGTGGACTACTATTGCATTGACA 57.841 39.130 0.00 0.00 0.00 3.58
48 49 2.036992 TGCATTGACAAATGACAACCCC 59.963 45.455 2.69 0.00 45.17 4.95
80 81 0.512952 CCCAAAACTCTCGACGCTTG 59.487 55.000 0.00 0.00 0.00 4.01
99 100 1.095807 GGCTCGCCTAAACATGTCCC 61.096 60.000 0.00 0.00 0.00 4.46
118 119 5.815740 TGTCCCTCGACAAGCTTATAAAATC 59.184 40.000 0.00 0.00 46.09 2.17
131 132 9.657419 AAGCTTATAAAATCCATCAAAACCAAG 57.343 29.630 0.00 0.00 0.00 3.61
158 161 1.362224 ACTAACATGGTGGTCAGCCT 58.638 50.000 0.00 0.00 35.27 4.58
197 200 2.453080 GTCAATCGACAATACGCCGTA 58.547 47.619 0.00 0.00 42.13 4.02
198 201 3.047796 GTCAATCGACAATACGCCGTAT 58.952 45.455 3.44 3.44 42.13 3.06
200 203 1.415374 ATCGACAATACGCCGTATGC 58.585 50.000 11.00 3.02 0.00 3.14
201 204 0.595567 TCGACAATACGCCGTATGCC 60.596 55.000 11.00 2.50 36.24 4.40
202 205 0.596600 CGACAATACGCCGTATGCCT 60.597 55.000 11.00 0.00 36.24 4.75
203 206 0.859232 GACAATACGCCGTATGCCTG 59.141 55.000 11.00 8.12 36.24 4.85
204 207 1.157870 ACAATACGCCGTATGCCTGC 61.158 55.000 11.00 0.00 36.24 4.85
205 208 0.880278 CAATACGCCGTATGCCTGCT 60.880 55.000 11.00 0.00 36.24 4.24
206 209 0.880278 AATACGCCGTATGCCTGCTG 60.880 55.000 11.00 0.00 36.24 4.41
222 245 2.270923 TGCTGCGTCTTGCTATACTTG 58.729 47.619 0.00 0.00 46.63 3.16
233 256 4.402056 TGCTATACTTGTTGGGCTACTC 57.598 45.455 0.00 0.00 0.00 2.59
237 260 5.237344 GCTATACTTGTTGGGCTACTCATTG 59.763 44.000 0.00 0.00 0.00 2.82
244 267 4.076394 GTTGGGCTACTCATTGTACCAAA 58.924 43.478 0.00 0.00 38.31 3.28
250 273 6.017109 GGGCTACTCATTGTACCAAATATGTG 60.017 42.308 0.00 0.00 0.00 3.21
252 275 7.254795 GGCTACTCATTGTACCAAATATGTGAC 60.255 40.741 0.00 0.00 0.00 3.67
267 297 9.722056 CAAATATGTGACTTGGAATTACTAAGC 57.278 33.333 0.00 0.00 40.08 3.09
274 304 5.360591 ACTTGGAATTACTAAGCGATGAGG 58.639 41.667 0.00 0.00 40.08 3.86
287 317 1.560923 GATGAGGTCGAACACGATGG 58.439 55.000 1.87 0.00 38.30 3.51
291 321 2.442188 GGTCGAACACGATGGCGAC 61.442 63.158 17.95 17.95 43.50 5.19
311 341 2.213499 CGGAGTCTGAAACAAGCAAGT 58.787 47.619 0.00 0.00 0.00 3.16
313 343 3.430218 CGGAGTCTGAAACAAGCAAGTAG 59.570 47.826 0.00 0.00 0.00 2.57
319 349 5.121454 GTCTGAAACAAGCAAGTAGGATGAG 59.879 44.000 0.00 0.00 0.00 2.90
324 354 2.926200 CAAGCAAGTAGGATGAGTGACG 59.074 50.000 0.00 0.00 0.00 4.35
348 378 3.434641 CACATGACAGAGCTACAGGTTTG 59.565 47.826 0.00 0.00 34.35 2.93
349 379 2.169832 TGACAGAGCTACAGGTTTGC 57.830 50.000 0.00 0.00 31.77 3.68
350 380 1.416030 TGACAGAGCTACAGGTTTGCA 59.584 47.619 0.00 0.00 31.77 4.08
351 381 2.038952 TGACAGAGCTACAGGTTTGCAT 59.961 45.455 0.00 0.00 31.77 3.96
352 382 2.675348 GACAGAGCTACAGGTTTGCATC 59.325 50.000 0.00 0.00 31.77 3.91
382 416 4.715297 GTGAATCTAGAGGGAGGGTAAACA 59.285 45.833 0.00 0.00 0.00 2.83
383 417 5.189145 GTGAATCTAGAGGGAGGGTAAACAA 59.811 44.000 0.00 0.00 0.00 2.83
384 418 5.425539 TGAATCTAGAGGGAGGGTAAACAAG 59.574 44.000 0.00 0.00 0.00 3.16
614 657 1.825622 GTACCCTCCCCCGTACTCG 60.826 68.421 0.00 0.00 33.54 4.18
773 834 2.423446 CCATGGCTCGCTAGGGTC 59.577 66.667 0.00 0.41 0.00 4.46
803 879 2.043953 GAGGGTGTGGGGATTGGC 60.044 66.667 0.00 0.00 0.00 4.52
819 895 2.115291 GGCTTTGACGATGGGCTCC 61.115 63.158 0.00 0.00 0.00 4.70
841 923 4.573087 CCCTCCTCTCTCTTTCCCTTCTAA 60.573 50.000 0.00 0.00 0.00 2.10
843 925 5.515106 CTCCTCTCTCTTTCCCTTCTAAGA 58.485 45.833 0.00 0.00 0.00 2.10
844 926 6.098716 TCCTCTCTCTTTCCCTTCTAAGAT 57.901 41.667 0.00 0.00 30.57 2.40
845 927 7.227355 TCCTCTCTCTTTCCCTTCTAAGATA 57.773 40.000 0.00 0.00 30.57 1.98
847 929 7.782644 TCCTCTCTCTTTCCCTTCTAAGATAAG 59.217 40.741 0.00 0.00 30.57 1.73
848 930 7.782644 CCTCTCTCTTTCCCTTCTAAGATAAGA 59.217 40.741 0.00 0.00 30.57 2.10
860 942 7.772332 TTCTAAGATAAGAAGAATCGTTGGC 57.228 36.000 0.00 0.00 31.85 4.52
883 965 4.760047 CGGCCCGGAAGTGGTCTG 62.760 72.222 0.73 0.00 0.00 3.51
892 974 2.558380 GAAGTGGTCTGGATGGGCCC 62.558 65.000 17.59 17.59 34.97 5.80
893 975 4.489771 GTGGTCTGGATGGGCCCG 62.490 72.222 19.37 1.40 34.97 6.13
897 979 3.407967 TCTGGATGGGCCCGGTTC 61.408 66.667 19.37 13.94 34.97 3.62
916 998 2.602676 GGCCCAGCCCAGTCTTGTA 61.603 63.158 0.00 0.00 44.06 2.41
918 1000 0.464554 GCCCAGCCCAGTCTTGTATC 60.465 60.000 0.00 0.00 0.00 2.24
919 1001 1.207791 CCCAGCCCAGTCTTGTATCT 58.792 55.000 0.00 0.00 0.00 1.98
926 1008 2.100197 CCAGTCTTGTATCTGGGACGA 58.900 52.381 3.58 0.00 45.11 4.20
936 1027 3.611766 ATCTGGGACGAGGTTTGTTAG 57.388 47.619 0.00 0.00 0.00 2.34
970 1069 2.410939 GTGTTAAACCCTCGTCTGGTC 58.589 52.381 0.00 0.00 34.15 4.02
1138 1281 0.399233 GTATGCACCTCTCCCCTCCT 60.399 60.000 0.00 0.00 0.00 3.69
1215 1358 0.787183 GCTGACGTGTTTCTCTCTGC 59.213 55.000 0.00 0.00 0.00 4.26
1224 1367 3.375299 GTGTTTCTCTCTGCTGTTGTGTT 59.625 43.478 0.00 0.00 0.00 3.32
1225 1368 3.374988 TGTTTCTCTCTGCTGTTGTGTTG 59.625 43.478 0.00 0.00 0.00 3.33
1229 1372 2.009051 TCTCTGCTGTTGTGTTGTGTG 58.991 47.619 0.00 0.00 0.00 3.82
1236 1379 0.457681 GTTGTGTTGTGTGGTGTGGC 60.458 55.000 0.00 0.00 0.00 5.01
1381 1552 6.473758 AGTATGTTAGTCTTTTCCCTTCCAC 58.526 40.000 0.00 0.00 0.00 4.02
1445 1651 1.399440 CTTGATTGGTGCAGACGATGG 59.601 52.381 0.00 0.00 0.00 3.51
1564 1785 2.167861 GCGATGAAGCGGTGAGGAC 61.168 63.158 0.00 0.00 0.00 3.85
1565 1786 1.519455 CGATGAAGCGGTGAGGACC 60.519 63.158 0.00 0.00 39.14 4.46
1595 1820 1.541588 GTTTTCCATGTGTCCTGGCTC 59.458 52.381 0.00 0.00 33.56 4.70
1597 1822 0.036732 TTCCATGTGTCCTGGCTCAC 59.963 55.000 12.56 12.56 33.56 3.51
1625 1850 7.925483 AGCATATTTATCTGTCTGTTCTCTGTC 59.075 37.037 0.00 0.00 0.00 3.51
1746 1974 2.225068 AGACCGTGTTCTCACAAGTG 57.775 50.000 0.00 0.00 44.02 3.16
1770 2002 2.835027 ACGGCTTACTTATTGGCTAGC 58.165 47.619 6.04 6.04 0.00 3.42
1810 2051 1.092345 GGACGCTGAGGGCTGATTTC 61.092 60.000 0.00 0.00 39.13 2.17
1822 2063 3.417185 GGCTGATTTCGTTTGATCGTTC 58.583 45.455 0.00 0.00 0.00 3.95
1924 2171 1.106285 ATCTCATGCCGCCCTTTTTC 58.894 50.000 0.00 0.00 0.00 2.29
1928 2175 3.281359 ATGCCGCCCTTTTTCGTGC 62.281 57.895 0.00 0.00 0.00 5.34
1997 2246 2.897436 TGTGCTGTATGAGTCATGAGC 58.103 47.619 22.93 22.93 33.84 4.26
2001 2250 2.467838 CTGTATGAGTCATGAGCGTGG 58.532 52.381 16.15 0.00 0.00 4.94
2017 2266 1.299541 GTGGCAATCACGTATGGGAG 58.700 55.000 0.00 0.00 36.56 4.30
2034 2291 7.063426 CGTATGGGAGCATATGTAGTGTTTATG 59.937 40.741 4.29 0.00 0.00 1.90
2080 2340 2.375174 TGAGCCCTTTGTAGTGGATGTT 59.625 45.455 0.00 0.00 0.00 2.71
2270 2549 3.519107 TGCTCTCTATTTCCACATCACCA 59.481 43.478 0.00 0.00 0.00 4.17
2493 2774 4.631813 ACCGAATGTGTGCTTCTTAATCTC 59.368 41.667 0.00 0.00 0.00 2.75
2550 2831 4.756502 AGTGCGTAGAGAGGGAAAATAAC 58.243 43.478 0.00 0.00 0.00 1.89
3377 4301 5.859521 GCATCACCATTTTAATGCAAACA 57.140 34.783 0.00 0.00 43.10 2.83
3378 4302 6.238610 GCATCACCATTTTAATGCAAACAA 57.761 33.333 0.00 0.00 43.10 2.83
3535 4460 5.665916 CCAGCAGGTAAATCCATTTCTTT 57.334 39.130 0.00 0.00 39.02 2.52
3558 4483 7.734924 TTAGCACTATATGGCTTCTCATTTG 57.265 36.000 3.89 0.00 41.41 2.32
3565 4490 8.216423 ACTATATGGCTTCTCATTTGAAGATGT 58.784 33.333 8.25 0.00 44.40 3.06
3633 4558 8.233190 GCAAGCAGGAGTATAAATTCATACATC 58.767 37.037 1.57 0.00 34.42 3.06
3649 4574 9.896645 ATTCATACATCAATCTGAAACACTACT 57.103 29.630 0.00 0.00 31.92 2.57
3650 4575 9.725019 TTCATACATCAATCTGAAACACTACTT 57.275 29.630 0.00 0.00 0.00 2.24
3666 4673 7.370905 ACACTACTTCTTACCCTTAAAGTGT 57.629 36.000 0.00 0.00 39.97 3.55
3821 4878 6.927294 ATTATAACTGAAGTAGCAAGTGCC 57.073 37.500 0.00 0.00 43.38 5.01
3822 4879 1.897560 AACTGAAGTAGCAAGTGCCC 58.102 50.000 0.00 0.00 43.38 5.36
3823 4880 0.764890 ACTGAAGTAGCAAGTGCCCA 59.235 50.000 0.00 0.00 43.38 5.36
3824 4881 1.142870 ACTGAAGTAGCAAGTGCCCAA 59.857 47.619 0.00 0.00 43.38 4.12
3825 4882 2.224867 ACTGAAGTAGCAAGTGCCCAAT 60.225 45.455 0.00 0.00 43.38 3.16
3826 4883 2.421424 CTGAAGTAGCAAGTGCCCAATC 59.579 50.000 0.00 0.00 43.38 2.67
3827 4884 1.745653 GAAGTAGCAAGTGCCCAATCC 59.254 52.381 0.00 0.00 43.38 3.01
3837 4894 3.624777 AGTGCCCAATCCAATACTTCAG 58.375 45.455 0.00 0.00 0.00 3.02
3941 4998 1.264288 CGACCTGTGCTCCTTGAAAAC 59.736 52.381 0.00 0.00 0.00 2.43
3942 4999 2.297701 GACCTGTGCTCCTTGAAAACA 58.702 47.619 0.00 0.00 0.00 2.83
4189 5381 3.681897 CGAAGAACTTTCCATGAGAGTGG 59.318 47.826 0.00 0.00 40.76 4.00
4213 5405 6.393990 GGATGTTCGATCTACTGATGCTATT 58.606 40.000 0.00 0.00 32.19 1.73
4620 5818 8.831550 GCAGATTACTTTCCTTTATAGGTTGAG 58.168 37.037 0.00 0.00 42.60 3.02
4682 5886 8.466798 ACATTAGCTTATGTGTTAAATTGACCC 58.533 33.333 17.11 0.00 37.36 4.46
4701 5906 7.049799 TGACCCTTTCTTTGTTTTATCCTTG 57.950 36.000 0.00 0.00 0.00 3.61
4725 5943 8.539770 TGTTTCTGTTTGCTCATTTTGTAAAA 57.460 26.923 0.00 0.00 0.00 1.52
4753 5972 6.699642 TGGTTTTGCTGTTACTTATCTTTTGC 59.300 34.615 0.00 0.00 0.00 3.68
4872 6091 4.320129 CGAGAGTATCAGGTCAGTATGCTG 60.320 50.000 4.14 4.14 40.23 4.41
4877 6096 0.463295 CAGGTCAGTATGCTGGGCAG 60.463 60.000 11.15 0.00 43.65 4.85
4906 6125 7.593825 TCTTCTTCTTGTTTTTATAAGCCTGC 58.406 34.615 0.00 0.00 0.00 4.85
4926 6170 5.827797 CCTGCTTAATAATACCTCTTGCCAA 59.172 40.000 0.00 0.00 0.00 4.52
4999 6243 5.183140 TGTCTGAAGCCTAAATTACCAAAGC 59.817 40.000 0.00 0.00 0.00 3.51
5000 6244 5.183140 GTCTGAAGCCTAAATTACCAAAGCA 59.817 40.000 0.00 0.00 0.00 3.91
5100 6612 7.517321 AGCAACAAAATTGGTTTATAAATGCG 58.483 30.769 0.31 0.00 0.00 4.73
5207 6721 8.335532 TCATCTATAAAAACCAGAAACTGTGG 57.664 34.615 0.00 0.00 41.30 4.17
5292 6806 0.518195 CACACATGCAGATGAACGCA 59.482 50.000 6.97 0.00 43.45 5.24
5340 6854 1.002502 GGTACACAAGCCAGACCCC 60.003 63.158 0.00 0.00 0.00 4.95
5342 6856 0.400594 GTACACAAGCCAGACCCCTT 59.599 55.000 0.00 0.00 0.00 3.95
5528 7042 3.498397 GGAAGGACATGTAACATATGCCG 59.502 47.826 0.00 0.00 31.43 5.69
5560 7074 2.912771 CCTGTGTTGTAACTGTGGTCA 58.087 47.619 0.00 0.00 0.00 4.02
5561 7075 3.476552 CCTGTGTTGTAACTGTGGTCAT 58.523 45.455 0.00 0.00 0.00 3.06
5583 7097 7.756722 GTCATTTCACATCCCAGTTTTGATTAG 59.243 37.037 0.00 0.00 0.00 1.73
5639 7154 2.126502 CATGGTTTTCCGCACCGC 60.127 61.111 0.00 0.00 44.36 5.68
5658 7173 0.819582 CCCGTTTACCGCTTCCTCTA 59.180 55.000 0.00 0.00 34.38 2.43
5660 7175 2.537401 CCGTTTACCGCTTCCTCTAAG 58.463 52.381 0.00 0.00 38.32 2.18
5661 7176 2.165030 CCGTTTACCGCTTCCTCTAAGA 59.835 50.000 0.00 0.00 37.38 2.10
5680 7195 7.771183 TCTAAGAAATTTACCACCATGAATGC 58.229 34.615 0.00 0.00 0.00 3.56
5685 7200 6.549433 AATTTACCACCATGAATGCTGAAT 57.451 33.333 0.00 0.00 0.00 2.57
5713 7228 1.421646 AGTGACTTTGCCTAGCCAACT 59.578 47.619 0.00 0.00 0.00 3.16
5739 7255 4.703897 TCTGTTGTCCGAAGAAACTTGAT 58.296 39.130 0.00 0.00 0.00 2.57
5875 7395 9.529325 AAGCTTTGGTAGTAAAATTTTGACTTC 57.471 29.630 13.76 9.98 0.00 3.01
5898 7424 1.457455 CAGTGGGCAAGGTTTGGGT 60.457 57.895 0.00 0.00 0.00 4.51
5902 7428 0.833949 TGGGCAAGGTTTGGGTTTTC 59.166 50.000 0.00 0.00 0.00 2.29
5910 7436 4.011966 AGGTTTGGGTTTTCGGTACTAG 57.988 45.455 0.00 0.00 0.00 2.57
6024 7555 4.891627 TGATTTCAAGCGTGTCAAAAGA 57.108 36.364 0.00 0.00 0.00 2.52
6028 7560 6.417635 TGATTTCAAGCGTGTCAAAAGATTTC 59.582 34.615 0.00 0.00 0.00 2.17
6106 7644 5.888691 TTTGTAGCTTTGACAACACTTGA 57.111 34.783 0.00 0.00 36.55 3.02
6108 7646 3.876914 TGTAGCTTTGACAACACTTGAGG 59.123 43.478 0.00 0.00 0.00 3.86
6114 7652 5.277538 GCTTTGACAACACTTGAGGTAAGAG 60.278 44.000 0.00 0.00 39.76 2.85
6116 7654 4.945246 TGACAACACTTGAGGTAAGAGTC 58.055 43.478 0.00 0.00 38.94 3.36
6123 7662 2.024176 TGAGGTAAGAGTCAAGGCCA 57.976 50.000 5.01 0.00 0.00 5.36
6145 7684 1.963515 GGAAATTATCCCGCCATTGCT 59.036 47.619 0.00 0.00 43.00 3.91
6152 7691 0.178068 TCCCGCCATTGCTAACTCTC 59.822 55.000 0.00 0.00 34.43 3.20
6156 7695 1.440145 GCCATTGCTAACTCTCGCCC 61.440 60.000 0.00 0.00 33.53 6.13
6158 7697 1.475751 CCATTGCTAACTCTCGCCCAT 60.476 52.381 0.00 0.00 0.00 4.00
6159 7698 2.292267 CATTGCTAACTCTCGCCCATT 58.708 47.619 0.00 0.00 0.00 3.16
6161 7700 2.890808 TGCTAACTCTCGCCCATTAG 57.109 50.000 0.00 0.00 0.00 1.73
6162 7701 2.108168 TGCTAACTCTCGCCCATTAGT 58.892 47.619 0.00 0.00 0.00 2.24
6176 7733 5.521010 CGCCCATTAGTTCGAAAACTACATA 59.479 40.000 0.00 0.00 45.43 2.29
6194 7751 5.912149 ACATATGGGTGTGAATATCTGGT 57.088 39.130 7.80 0.00 0.00 4.00
6195 7752 6.266131 ACATATGGGTGTGAATATCTGGTT 57.734 37.500 7.80 0.00 0.00 3.67
6230 7787 3.391049 GGTTATCGCTCCGCTAAGAATT 58.609 45.455 0.00 0.00 0.00 2.17
6265 7822 4.848357 GGATCCTCTCCTGAATTTTGTCA 58.152 43.478 3.84 0.00 41.29 3.58
6266 7823 4.880696 GGATCCTCTCCTGAATTTTGTCAG 59.119 45.833 3.84 0.00 43.98 3.51
6284 7841 9.997482 TTTTGTCAGAAGTACTACATGTTTTTC 57.003 29.630 2.30 1.81 0.00 2.29
6285 7842 7.724305 TGTCAGAAGTACTACATGTTTTTCC 57.276 36.000 2.30 0.00 0.00 3.13
6288 7845 8.092687 GTCAGAAGTACTACATGTTTTTCCCTA 58.907 37.037 2.30 0.00 0.00 3.53
6296 7853 7.110155 ACTACATGTTTTTCCCTACATACTGG 58.890 38.462 2.30 0.00 33.42 4.00
6342 7903 5.664457 TCTGATGATGCTAAGTAGTTGGTG 58.336 41.667 0.00 0.00 0.00 4.17
6343 7904 5.422012 TCTGATGATGCTAAGTAGTTGGTGA 59.578 40.000 0.00 0.00 0.00 4.02
6344 7905 6.048732 TGATGATGCTAAGTAGTTGGTGAA 57.951 37.500 0.00 0.00 0.00 3.18
6345 7906 6.108687 TGATGATGCTAAGTAGTTGGTGAAG 58.891 40.000 0.00 0.00 0.00 3.02
6376 7937 5.003692 TCATGCTAGTTAGAGCTGACAAG 57.996 43.478 0.00 0.00 43.27 3.16
6387 7948 2.977405 GCTGACAAGCCAAGTAACAG 57.023 50.000 0.00 0.00 44.22 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.952947 AGTAGTCCACAGTTTCTGCTATACT 59.047 40.000 0.00 0.00 34.37 2.12
1 2 6.210287 AGTAGTCCACAGTTTCTGCTATAC 57.790 41.667 0.00 0.00 34.37 1.47
10 11 6.149474 GTCAATGCAATAGTAGTCCACAGTTT 59.851 38.462 0.00 0.00 0.00 2.66
13 14 5.178061 TGTCAATGCAATAGTAGTCCACAG 58.822 41.667 0.00 0.00 0.00 3.66
23 24 5.577945 GGGTTGTCATTTGTCAATGCAATAG 59.422 40.000 0.00 0.00 39.90 1.73
36 37 2.178984 TGGAGAAAGGGGGTTGTCATTT 59.821 45.455 0.00 0.00 0.00 2.32
48 49 3.038280 AGTTTTGGGGTTTGGAGAAAGG 58.962 45.455 0.00 0.00 0.00 3.11
80 81 1.095807 GGGACATGTTTAGGCGAGCC 61.096 60.000 5.89 5.89 0.00 4.70
99 100 7.482654 TGATGGATTTTATAAGCTTGTCGAG 57.517 36.000 9.86 0.00 0.00 4.04
118 119 3.749665 TTCCTTGCTTGGTTTTGATGG 57.250 42.857 0.00 0.00 0.00 3.51
131 132 2.890945 ACCACCATGTTAGTTTCCTTGC 59.109 45.455 0.00 0.00 0.00 4.01
158 161 3.245087 TGACCTGGTTTTATTAGCTGGCA 60.245 43.478 0.00 0.00 37.94 4.92
197 200 2.526450 TAGCAAGACGCAGCAGGCAT 62.526 55.000 0.00 0.00 46.13 4.40
198 201 2.526450 ATAGCAAGACGCAGCAGGCA 62.526 55.000 0.00 0.00 46.13 4.75
200 203 1.202463 AGTATAGCAAGACGCAGCAGG 60.202 52.381 0.00 0.00 46.13 4.85
201 204 2.215907 AGTATAGCAAGACGCAGCAG 57.784 50.000 0.00 0.00 46.13 4.24
202 205 2.270923 CAAGTATAGCAAGACGCAGCA 58.729 47.619 0.00 0.00 46.13 4.41
203 206 2.271800 ACAAGTATAGCAAGACGCAGC 58.728 47.619 0.00 0.00 46.13 5.25
204 207 3.062639 CCAACAAGTATAGCAAGACGCAG 59.937 47.826 0.00 0.00 46.13 5.18
205 208 3.000041 CCAACAAGTATAGCAAGACGCA 59.000 45.455 0.00 0.00 46.13 5.24
206 209 2.351726 CCCAACAAGTATAGCAAGACGC 59.648 50.000 0.00 0.00 42.91 5.19
207 210 2.351726 GCCCAACAAGTATAGCAAGACG 59.648 50.000 0.00 0.00 0.00 4.18
237 260 9.174166 AGTAATTCCAAGTCACATATTTGGTAC 57.826 33.333 3.60 0.68 43.66 3.34
244 267 7.497595 TCGCTTAGTAATTCCAAGTCACATAT 58.502 34.615 0.00 0.00 0.00 1.78
250 273 5.463724 CCTCATCGCTTAGTAATTCCAAGTC 59.536 44.000 0.00 0.00 0.00 3.01
252 275 5.360591 ACCTCATCGCTTAGTAATTCCAAG 58.639 41.667 0.00 0.00 0.00 3.61
287 317 0.784778 CTTGTTTCAGACTCCGTCGC 59.215 55.000 0.00 0.00 37.67 5.19
291 321 2.213499 ACTTGCTTGTTTCAGACTCCG 58.787 47.619 0.00 0.00 0.00 4.63
305 335 2.164624 GTCGTCACTCATCCTACTTGCT 59.835 50.000 0.00 0.00 0.00 3.91
311 341 3.128764 GTCATGTGTCGTCACTCATCCTA 59.871 47.826 13.77 0.00 44.14 2.94
313 343 2.263077 GTCATGTGTCGTCACTCATCC 58.737 52.381 13.77 0.00 44.14 3.51
319 349 1.063806 GCTCTGTCATGTGTCGTCAC 58.936 55.000 5.81 5.81 44.08 3.67
324 354 2.232452 ACCTGTAGCTCTGTCATGTGTC 59.768 50.000 0.00 0.00 0.00 3.67
329 359 2.038952 TGCAAACCTGTAGCTCTGTCAT 59.961 45.455 0.00 0.00 0.00 3.06
337 367 2.426522 TCAGTGATGCAAACCTGTAGC 58.573 47.619 0.00 0.00 0.00 3.58
352 382 4.099266 CCTCCCTCTAGATTCACTTCAGTG 59.901 50.000 0.02 0.02 46.91 3.66
371 405 4.072839 CACCTCTTTCTTGTTTACCCTCC 58.927 47.826 0.00 0.00 0.00 4.30
382 416 2.566724 CCTCTGCTCTCACCTCTTTCTT 59.433 50.000 0.00 0.00 0.00 2.52
383 417 2.178580 CCTCTGCTCTCACCTCTTTCT 58.821 52.381 0.00 0.00 0.00 2.52
384 418 2.175202 TCCTCTGCTCTCACCTCTTTC 58.825 52.381 0.00 0.00 0.00 2.62
692 753 1.587613 GCCGTCTCATCTGACTCGC 60.588 63.158 0.00 0.00 35.00 5.03
803 879 0.462759 GAGGGAGCCCATCGTCAAAG 60.463 60.000 8.53 0.00 38.92 2.77
819 895 3.114643 AGAAGGGAAAGAGAGAGGAGG 57.885 52.381 0.00 0.00 0.00 4.30
841 923 3.458189 CCGCCAACGATTCTTCTTATCT 58.542 45.455 0.00 0.00 43.93 1.98
843 925 2.561569 CCCGCCAACGATTCTTCTTAT 58.438 47.619 0.00 0.00 43.93 1.73
844 926 2.010043 GCCCGCCAACGATTCTTCTTA 61.010 52.381 0.00 0.00 43.93 2.10
845 927 1.305930 GCCCGCCAACGATTCTTCTT 61.306 55.000 0.00 0.00 43.93 2.52
847 929 2.761195 GGCCCGCCAACGATTCTTC 61.761 63.158 0.00 0.00 43.93 2.87
848 930 2.750237 GGCCCGCCAACGATTCTT 60.750 61.111 0.00 0.00 43.93 2.52
872 954 1.077429 GCCCATCCAGACCACTTCC 60.077 63.158 0.00 0.00 0.00 3.46
876 958 4.489771 CGGGCCCATCCAGACCAC 62.490 72.222 24.92 0.00 36.21 4.16
916 998 2.354805 GCTAACAAACCTCGTCCCAGAT 60.355 50.000 0.00 0.00 0.00 2.90
918 1000 1.439679 GCTAACAAACCTCGTCCCAG 58.560 55.000 0.00 0.00 0.00 4.45
919 1001 0.320073 CGCTAACAAACCTCGTCCCA 60.320 55.000 0.00 0.00 0.00 4.37
921 1003 1.066136 GTCGCTAACAAACCTCGTCC 58.934 55.000 0.00 0.00 0.00 4.79
922 1004 1.066136 GGTCGCTAACAAACCTCGTC 58.934 55.000 0.00 0.00 0.00 4.20
923 1005 0.320160 GGGTCGCTAACAAACCTCGT 60.320 55.000 0.00 0.00 33.42 4.18
924 1006 1.349259 CGGGTCGCTAACAAACCTCG 61.349 60.000 0.00 0.00 33.42 4.63
926 1008 1.004200 CCGGGTCGCTAACAAACCT 60.004 57.895 0.00 0.00 33.42 3.50
984 1083 4.096003 ATTGGTGTCGGCGGAGGG 62.096 66.667 7.21 0.00 0.00 4.30
985 1084 2.819595 CATTGGTGTCGGCGGAGG 60.820 66.667 7.21 0.00 0.00 4.30
986 1085 2.819595 CCATTGGTGTCGGCGGAG 60.820 66.667 7.21 0.00 0.00 4.63
991 1098 3.803082 CTGCGCCATTGGTGTCGG 61.803 66.667 17.24 10.73 35.34 4.79
1121 1249 0.985490 GAAGGAGGGGAGAGGTGCAT 60.985 60.000 0.00 0.00 0.00 3.96
1122 1250 1.613630 GAAGGAGGGGAGAGGTGCA 60.614 63.158 0.00 0.00 0.00 4.57
1124 1252 1.690985 GGGAAGGAGGGGAGAGGTG 60.691 68.421 0.00 0.00 0.00 4.00
1138 1281 1.282157 GCAGGAAGCTAAAGAGGGGAA 59.718 52.381 0.00 0.00 41.15 3.97
1162 1305 1.112950 AGCTAGCTAGGGTTTCGTCC 58.887 55.000 17.69 2.20 0.00 4.79
1163 1306 1.477295 ACAGCTAGCTAGGGTTTCGTC 59.523 52.381 18.86 2.91 0.00 4.20
1164 1307 1.477295 GACAGCTAGCTAGGGTTTCGT 59.523 52.381 18.86 8.45 0.00 3.85
1165 1308 1.202428 GGACAGCTAGCTAGGGTTTCG 60.202 57.143 18.86 4.81 0.00 3.46
1215 1358 1.135431 CCACACCACACAACACAACAG 60.135 52.381 0.00 0.00 0.00 3.16
1425 1628 1.399440 CCATCGTCTGCACCAATCAAG 59.601 52.381 0.00 0.00 0.00 3.02
1440 1646 1.944676 GTCTCGCGGCTTACCATCG 60.945 63.158 6.13 0.00 34.57 3.84
1466 1687 4.147449 TGGTCTCATCCTGCGCGG 62.147 66.667 9.96 9.96 0.00 6.46
1467 1688 2.584418 CTGGTCTCATCCTGCGCG 60.584 66.667 0.00 0.00 0.00 6.86
1564 1785 2.739671 GGAAAACGGTCGGTCGGG 60.740 66.667 3.69 0.00 0.00 5.14
1565 1786 1.375013 ATGGAAAACGGTCGGTCGG 60.375 57.895 3.69 0.00 0.00 4.79
1595 1820 6.765036 AGAACAGACAGATAAATATGCTGGTG 59.235 38.462 11.15 0.00 34.05 4.17
1597 1822 7.171167 CAGAGAACAGACAGATAAATATGCTGG 59.829 40.741 11.15 0.00 34.05 4.85
1601 1826 9.761504 ATGACAGAGAACAGACAGATAAATATG 57.238 33.333 0.00 0.00 0.00 1.78
1625 1850 4.271049 ACGACGCCAAGATCTCATTAAATG 59.729 41.667 0.00 0.00 0.00 2.32
1746 1974 4.056092 AGCCAATAAGTAAGCCGTACTC 57.944 45.455 0.00 0.00 42.55 2.59
1751 1983 2.802816 CAGCTAGCCAATAAGTAAGCCG 59.197 50.000 12.13 0.00 0.00 5.52
1753 1985 5.180304 GGAATCAGCTAGCCAATAAGTAAGC 59.820 44.000 12.13 0.00 0.00 3.09
1770 2002 3.057033 CCTCCAAAACAGCAAGGAATCAG 60.057 47.826 0.00 0.00 0.00 2.90
1810 2051 0.179215 GCAGCCAGAACGATCAAACG 60.179 55.000 0.00 0.00 39.31 3.60
1822 2063 2.408271 TGTATTTCTCCTGCAGCCAG 57.592 50.000 8.66 6.37 38.85 4.85
1924 2171 7.206981 AGATATTGATATTTTTCCTGGCACG 57.793 36.000 0.00 0.00 0.00 5.34
2001 2250 1.597742 ATGCTCCCATACGTGATTGC 58.402 50.000 0.00 0.00 0.00 3.56
2014 2263 7.786178 TTCACATAAACACTACATATGCTCC 57.214 36.000 1.58 0.00 31.66 4.70
2090 2350 8.006298 AGAGTTCAGAGATATTGGTTCACTAG 57.994 38.462 0.00 0.00 0.00 2.57
2372 2652 6.536688 GTGTATTCAAATGCCTTCAAATTGC 58.463 36.000 0.00 0.00 0.00 3.56
2493 2774 5.840243 ACACCATGTTCCATGTCATATTG 57.160 39.130 3.75 0.00 0.00 1.90
2550 2831 7.962934 TCACAAACATTTCGTTTTAGTCTTG 57.037 32.000 0.00 0.00 45.79 3.02
2679 3165 2.599659 GACTTTTATGCAGCCACAAGC 58.400 47.619 0.00 0.00 44.25 4.01
3002 3508 4.622701 GCTGTAGCATAAAAGGGAACAG 57.377 45.455 0.00 0.00 41.59 3.16
3085 3596 3.939740 AATAGATTGGCTCCAGCAAGA 57.060 42.857 0.03 0.00 44.36 3.02
3239 3755 2.798976 TTGCCATTGACAACAAGAGC 57.201 45.000 0.00 0.00 39.46 4.09
3505 4430 3.118261 GGATTTACCTGCTGGTCATCTCA 60.118 47.826 19.71 0.00 44.78 3.27
3529 4454 7.564793 TGAGAAGCCATATAGTGCTAAAGAAA 58.435 34.615 0.00 0.00 36.66 2.52
3532 4457 7.976135 AATGAGAAGCCATATAGTGCTAAAG 57.024 36.000 0.00 0.00 36.66 1.85
3535 4460 7.066307 TCAAATGAGAAGCCATATAGTGCTA 57.934 36.000 0.00 0.00 36.66 3.49
3633 4558 7.162082 AGGGTAAGAAGTAGTGTTTCAGATTG 58.838 38.462 0.00 0.00 0.00 2.67
3650 4575 8.693625 GCTCTTATAGACACTTTAAGGGTAAGA 58.306 37.037 0.00 5.07 27.47 2.10
3756 4812 9.295825 ACAGTTCCATGTTCATAGTGATAAAAA 57.704 29.630 0.00 0.00 0.00 1.94
3770 4826 4.655963 ACTGCTTCATACAGTTCCATGTT 58.344 39.130 0.00 0.00 46.01 2.71
3795 4851 8.244113 GGCACTTGCTACTTCAGTTATAATTTT 58.756 33.333 0.38 0.00 41.70 1.82
3877 4934 4.823989 CCTGAATGGAGGGTGTTTATGATC 59.176 45.833 0.00 0.00 38.35 2.92
3942 4999 0.760567 TACCAGGAGCATCGCCAGAT 60.761 55.000 0.00 0.00 37.65 2.90
3986 5061 5.068636 ACTGAAAACTCTCGTCTGGTACTA 58.931 41.667 0.00 0.00 0.00 1.82
4003 5078 3.895041 GGTTTTTCCAGGGATGACTGAAA 59.105 43.478 0.00 0.00 40.97 2.69
4189 5381 4.250116 AGCATCAGTAGATCGAACATCC 57.750 45.455 0.00 0.00 30.20 3.51
4213 5405 6.716628 ACTTCCTTTGCAATCTACAGATCAAA 59.283 34.615 0.00 6.15 32.75 2.69
4407 5600 7.168972 GCAGCAACAATCAAACTACATTAACAA 59.831 33.333 0.00 0.00 0.00 2.83
4629 5827 4.654262 AGGGAAGCGACAGGATATTCTTTA 59.346 41.667 0.00 0.00 0.00 1.85
4633 5831 2.365617 TCAGGGAAGCGACAGGATATTC 59.634 50.000 0.00 0.00 0.00 1.75
4682 5886 9.586435 ACAGAAACAAGGATAAAACAAAGAAAG 57.414 29.630 0.00 0.00 0.00 2.62
4725 5943 7.524717 AAGATAAGTAACAGCAAAACCACAT 57.475 32.000 0.00 0.00 0.00 3.21
4753 5972 2.417933 GCTGCATGTAGACACCAGAAAG 59.582 50.000 15.68 0.00 33.15 2.62
4872 6091 4.655762 AACAAGAAGAAGAAAACTGCCC 57.344 40.909 0.00 0.00 0.00 5.36
4906 6125 9.793259 TCCTTATTGGCAAGAGGTATTATTAAG 57.207 33.333 23.74 14.25 35.26 1.85
4999 6243 8.321650 ACAAAATTGGTTTATAAACAGCCATG 57.678 30.769 25.59 18.55 40.63 3.66
5000 6244 8.782144 CAACAAAATTGGTTTATAAACAGCCAT 58.218 29.630 25.59 11.29 40.63 4.40
5127 6640 9.802039 ACAGACCCTTGTTGAATTTATAAGTAA 57.198 29.630 0.00 0.00 0.00 2.24
5237 6751 0.034670 AAGGACCTGCATCCAGAAGC 60.035 55.000 9.02 0.00 41.77 3.86
5292 6806 4.389374 CGCTCAAGATATACCCACCAAAT 58.611 43.478 0.00 0.00 0.00 2.32
5560 7074 7.781324 ACTAATCAAAACTGGGATGTGAAAT 57.219 32.000 0.00 0.00 0.00 2.17
5561 7075 7.286546 TGAACTAATCAAAACTGGGATGTGAAA 59.713 33.333 0.00 0.00 34.30 2.69
5639 7154 0.819582 TAGAGGAAGCGGTAAACGGG 59.180 55.000 0.00 0.00 44.51 5.28
5658 7173 6.610075 AGCATTCATGGTGGTAAATTTCTT 57.390 33.333 0.00 0.00 37.10 2.52
5680 7195 5.525378 GGCAAAGTCACTAGGTATGATTCAG 59.475 44.000 0.00 0.00 0.00 3.02
5685 7200 4.099573 GCTAGGCAAAGTCACTAGGTATGA 59.900 45.833 0.00 0.00 35.79 2.15
5713 7228 4.258543 AGTTTCTTCGGACAACAGAACAA 58.741 39.130 0.00 0.00 0.00 2.83
5739 7255 2.807967 CTCTGATGAACAGCAAAACGGA 59.192 45.455 0.00 0.00 45.38 4.69
5864 7384 4.202253 GCCCACTGGAAAGAAGTCAAAATT 60.202 41.667 0.00 0.00 0.00 1.82
5869 7389 0.843309 TGCCCACTGGAAAGAAGTCA 59.157 50.000 0.00 0.00 0.00 3.41
5875 7395 1.069049 CAAACCTTGCCCACTGGAAAG 59.931 52.381 0.00 0.29 45.92 2.62
5898 7424 8.755977 AGATATTTGAGTTCCTAGTACCGAAAA 58.244 33.333 0.00 0.00 0.00 2.29
5902 7428 7.273320 TCAGATATTTGAGTTCCTAGTACCG 57.727 40.000 0.00 0.00 0.00 4.02
6102 7640 2.303022 TGGCCTTGACTCTTACCTCAAG 59.697 50.000 3.32 0.00 42.08 3.02
6106 7644 1.561542 CCATGGCCTTGACTCTTACCT 59.438 52.381 19.85 0.00 0.00 3.08
6108 7646 3.350219 TTCCATGGCCTTGACTCTTAC 57.650 47.619 19.85 0.00 0.00 2.34
6114 7652 4.590850 GGATAATTTCCATGGCCTTGAC 57.409 45.455 19.85 0.00 44.74 3.18
6141 7680 2.500098 ACTAATGGGCGAGAGTTAGCAA 59.500 45.455 0.00 0.00 34.54 3.91
6145 7684 3.018856 TCGAACTAATGGGCGAGAGTTA 58.981 45.455 0.00 0.00 32.37 2.24
6152 7691 3.680937 TGTAGTTTTCGAACTAATGGGCG 59.319 43.478 0.00 0.00 37.05 6.13
6156 7695 8.335356 CACCCATATGTAGTTTTCGAACTAATG 58.665 37.037 0.00 0.00 37.05 1.90
6158 7697 7.332430 CACACCCATATGTAGTTTTCGAACTAA 59.668 37.037 0.00 0.00 37.05 2.24
6159 7698 6.814644 CACACCCATATGTAGTTTTCGAACTA 59.185 38.462 0.00 0.00 34.37 2.24
6161 7700 5.640357 TCACACCCATATGTAGTTTTCGAAC 59.360 40.000 0.00 0.00 0.00 3.95
6162 7701 5.795972 TCACACCCATATGTAGTTTTCGAA 58.204 37.500 1.24 0.00 0.00 3.71
6194 7751 9.444600 GGAGCGATAACCCTCAAATATATAAAA 57.555 33.333 0.00 0.00 0.00 1.52
6195 7752 7.762615 CGGAGCGATAACCCTCAAATATATAAA 59.237 37.037 0.00 0.00 0.00 1.40
6220 7777 5.371115 TTTTCACCTCCAAATTCTTAGCG 57.629 39.130 0.00 0.00 0.00 4.26
6230 7787 3.260205 AGAGGATCCTTTTCACCTCCAA 58.740 45.455 17.42 0.00 46.88 3.53
6265 7822 7.970102 TGTAGGGAAAAACATGTAGTACTTCT 58.030 34.615 0.00 0.00 0.00 2.85
6266 7823 8.788325 ATGTAGGGAAAAACATGTAGTACTTC 57.212 34.615 0.00 0.00 35.06 3.01
6284 7841 4.800914 GCTTAGCATCACCAGTATGTAGGG 60.801 50.000 0.00 0.00 0.00 3.53
6285 7842 4.202253 TGCTTAGCATCACCAGTATGTAGG 60.202 45.833 1.39 0.00 31.71 3.18
6288 7845 3.452264 TCTGCTTAGCATCACCAGTATGT 59.548 43.478 7.58 0.00 38.13 2.29
6296 7853 3.329386 TGTGTTCTCTGCTTAGCATCAC 58.671 45.455 7.58 12.20 38.13 3.06
6342 7903 7.275920 TCTAACTAGCATGAAATCCTTCCTTC 58.724 38.462 0.00 0.00 0.00 3.46
6343 7904 7.200434 TCTAACTAGCATGAAATCCTTCCTT 57.800 36.000 0.00 0.00 0.00 3.36
6344 7905 6.687647 GCTCTAACTAGCATGAAATCCTTCCT 60.688 42.308 0.00 0.00 42.30 3.36
6345 7906 5.468409 GCTCTAACTAGCATGAAATCCTTCC 59.532 44.000 0.00 0.00 42.30 3.46
6376 7937 4.814771 AGTTACACTGAACTGTTACTTGGC 59.185 41.667 0.00 0.00 38.25 4.52
6378 7939 8.867112 TTCTAGTTACACTGAACTGTTACTTG 57.133 34.615 0.00 0.00 39.96 3.16


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

AutoCloner maintained by Alex Coulton.