Multiple sequence alignment - TraesCS5D01G178500

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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 TraesCS5D01G178500 chr5D 100.000 6216 0 0 1 6216 277823313 277829528 0.000000e+00 11479.0
1 TraesCS5D01G178500 chr5D 79.540 435 72 9 336 754 549551896 549551463 1.690000e-75 294.0
2 TraesCS5D01G178500 chr5D 79.420 345 64 4 326 664 352217718 352218061 2.900000e-58 237.0
3 TraesCS5D01G178500 chr5B 92.184 5284 282 63 326 5533 315942381 315947609 0.000000e+00 7348.0
4 TraesCS5D01G178500 chr5B 94.097 288 5 3 5623 5898 315948007 315948294 1.600000e-115 427.0
5 TraesCS5D01G178500 chr5B 86.686 338 35 3 1 331 315941435 315941769 3.540000e-97 366.0
6 TraesCS5D01G178500 chr5B 89.732 224 18 3 5994 6216 316024367 316024586 1.320000e-71 281.0
7 TraesCS5D01G178500 chr5B 97.674 86 2 0 5523 5608 315947934 315948019 1.400000e-31 148.0
8 TraesCS5D01G178500 chr5B 92.857 42 2 1 5893 5934 316024060 316024100 6.730000e-05 60.2
9 TraesCS5D01G178500 chr5A 95.887 3477 106 17 2519 5974 367140690 367144150 0.000000e+00 5594.0
10 TraesCS5D01G178500 chr5A 93.171 1684 79 20 873 2537 367135717 367137383 0.000000e+00 2440.0
11 TraesCS5D01G178500 chr5A 90.359 529 37 4 335 852 367135202 367135727 0.000000e+00 682.0
12 TraesCS5D01G178500 chr5A 93.636 330 21 0 1 330 367134354 367134683 1.560000e-135 494.0
13 TraesCS5D01G178500 chr5A 77.931 435 76 13 337 753 589002188 589002620 2.880000e-63 254.0
14 TraesCS5D01G178500 chr2D 81.250 432 64 4 337 751 638817503 638817934 3.590000e-87 333.0
15 TraesCS5D01G178500 chr2D 83.140 172 25 2 161 331 102275201 102275369 3.000000e-33 154.0
16 TraesCS5D01G178500 chr6D 79.808 416 67 10 336 735 62884283 62884697 2.840000e-73 287.0
17 TraesCS5D01G178500 chr7A 79.128 436 71 16 330 752 718513014 718512586 3.670000e-72 283.0
18 TraesCS5D01G178500 chr4D 79.236 419 69 8 340 741 399730955 399730538 6.140000e-70 276.0
19 TraesCS5D01G178500 chr7D 78.507 442 68 14 326 741 47425548 47425988 1.330000e-66 265.0
20 TraesCS5D01G178500 chr3D 91.954 174 12 2 2151 2324 427803824 427803995 6.230000e-60 243.0
21 TraesCS5D01G178500 chr3D 81.871 171 25 4 161 331 600600273 600600109 8.400000e-29 139.0
22 TraesCS5D01G178500 chr3A 89.143 175 17 2 2150 2324 557962865 557962693 3.770000e-52 217.0
23 TraesCS5D01G178500 chr3A 84.916 179 13 8 2329 2495 557962647 557962471 1.070000e-37 169.0
24 TraesCS5D01G178500 chr3A 97.143 35 1 0 674 708 721880957 721880923 6.730000e-05 60.2
25 TraesCS5D01G178500 chrUn 85.465 172 21 3 161 331 18809031 18808863 6.400000e-40 176.0
26 TraesCS5D01G178500 chr3B 85.465 172 21 4 161 331 179668680 179668848 6.400000e-40 176.0
27 TraesCS5D01G178500 chr3B 87.413 143 6 6 2329 2460 559328364 559328505 3.000000e-33 154.0
28 TraesCS5D01G178500 chr4A 84.416 154 21 3 161 314 591452558 591452708 1.400000e-31 148.0
29 TraesCS5D01G178500 chr4A 84.416 154 21 3 161 314 593162882 593162732 1.400000e-31 148.0
30 TraesCS5D01G178500 chr1D 82.081 173 25 5 161 331 46338352 46338184 6.500000e-30 143.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G178500 chr5D 277823313 277829528 6215 False 11479.00 11479 100.00000 1 6216 1 chr5D.!!$F1 6215
1 TraesCS5D01G178500 chr5B 315941435 315948294 6859 False 2072.25 7348 92.66025 1 5898 4 chr5B.!!$F1 5897
2 TraesCS5D01G178500 chr5A 367134354 367144150 9796 False 2302.50 5594 93.26325 1 5974 4 chr5A.!!$F2 5973

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
571 1203 0.317020 GGCACGTGCACAAAGACTTC 60.317 55.000 38.60 15.88 44.36 3.01 F
572 1204 0.317020 GCACGTGCACAAAGACTTCC 60.317 55.000 34.52 0.00 41.59 3.46 F
578 1210 0.321298 GCACAAAGACTTCCCGGCTA 60.321 55.000 0.00 0.00 0.00 3.93 F
1581 2295 0.040958 CCAAGTGTTTCACTCGCTGC 60.041 55.000 2.86 0.00 44.62 5.25 F
1585 2299 0.233332 GTGTTTCACTCGCTGCTGTC 59.767 55.000 0.00 0.00 0.00 3.51 F
1641 2355 0.333993 AGGCAGGGAAGCATGTGATT 59.666 50.000 0.00 0.00 35.83 2.57 F
1988 2705 1.703411 TTTCCAAACAAGCTCCCCTG 58.297 50.000 0.00 0.00 0.00 4.45 F
2281 2998 1.804151 TCAGTGCAACGTGCTTTATCC 59.196 47.619 10.54 0.00 45.31 2.59 F
2719 6764 2.622942 TCTGTTGGCATTGAAGTGGAAC 59.377 45.455 0.00 0.00 0.00 3.62 F
3199 7250 3.876914 ACACATCACAAGTACACAACTGG 59.123 43.478 0.00 0.00 38.88 4.00 F
4489 8544 0.813821 GATGCAGGCTTTCCTTGTCC 59.186 55.000 0.00 0.00 41.93 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1571 2285 0.035317 ATTTGGACAGCAGCGAGTGA 59.965 50.000 0.00 0.00 0.00 3.41 R
1577 2291 0.388134 CTGCACATTTGGACAGCAGC 60.388 55.000 0.00 0.00 44.98 5.25 R
1585 2299 0.963962 AGCTCAACCTGCACATTTGG 59.036 50.000 0.00 0.00 0.00 3.28 R
3366 7417 4.644685 ACCAACAAGCTGTTACAAATGAGT 59.355 37.500 0.00 0.00 38.77 3.41 R
3392 7443 6.768861 AGATAGACGATACAGTTGCTACTTCT 59.231 38.462 0.00 0.78 30.26 2.85 R
3594 7645 0.899720 TAACCTTTGGCGACCTCGAT 59.100 50.000 0.00 0.00 43.02 3.59 R
3833 7886 2.694628 AGTTCATTTGGCACTTGCAGAA 59.305 40.909 3.15 0.00 44.36 3.02 R
4168 8223 0.108186 TGCCTCAGTAACATCCTGCG 60.108 55.000 0.00 0.00 0.00 5.18 R
4169 8224 1.065854 ACTGCCTCAGTAACATCCTGC 60.066 52.381 0.00 0.00 43.46 4.85 R
4649 8704 1.281867 ACTTTGCTAGCCTGCACCATA 59.718 47.619 13.29 0.00 43.20 2.74 R
5362 9422 0.107557 ACATCGCATGCCACATCAGA 60.108 50.000 13.15 1.42 0.00 3.27 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
141 149 7.042797 AGTTTAGCAGCCACCATAATTAATG 57.957 36.000 0.00 0.00 35.15 1.90
208 216 5.496133 AGCGAATGAGAATTGAAGGAATG 57.504 39.130 0.00 0.00 0.00 2.67
248 256 9.765795 CTAGTATTGTTTAGTTAGGGAGATTGG 57.234 37.037 0.00 0.00 0.00 3.16
254 262 7.475299 TGTTTAGTTAGGGAGATTGGGAATTT 58.525 34.615 0.00 0.00 0.00 1.82
261 269 9.862149 GTTAGGGAGATTGGGAATTTATAAGAA 57.138 33.333 0.00 0.00 0.00 2.52
294 302 4.646572 AGACTTGAGACTTCAATTCCCAC 58.353 43.478 4.61 0.00 41.44 4.61
304 312 6.266786 AGACTTCAATTCCCACCGTTTTATTT 59.733 34.615 0.00 0.00 0.00 1.40
331 339 2.361737 GGGCAGGAGTTGGAAGGC 60.362 66.667 0.00 0.00 0.00 4.35
332 340 2.747855 GGCAGGAGTTGGAAGGCG 60.748 66.667 0.00 0.00 0.00 5.52
333 341 2.032681 GCAGGAGTTGGAAGGCGT 59.967 61.111 0.00 0.00 0.00 5.68
406 1037 1.134037 AGACGGATTAGACGGAGCTCT 60.134 52.381 14.64 0.00 35.23 4.09
409 1040 2.158784 ACGGATTAGACGGAGCTCTAGT 60.159 50.000 14.64 14.08 35.23 2.57
460 1092 1.549170 AGATTAGGTTTCTCGCCGTGT 59.451 47.619 0.00 0.00 0.00 4.49
510 1142 6.342111 AGGTTCTTCAGATCGATTTAAGGAC 58.658 40.000 14.07 14.07 0.00 3.85
514 1146 6.800543 TCTTCAGATCGATTTAAGGACTCAG 58.199 40.000 0.00 0.00 0.00 3.35
571 1203 0.317020 GGCACGTGCACAAAGACTTC 60.317 55.000 38.60 15.88 44.36 3.01
572 1204 0.317020 GCACGTGCACAAAGACTTCC 60.317 55.000 34.52 0.00 41.59 3.46
578 1210 0.321298 GCACAAAGACTTCCCGGCTA 60.321 55.000 0.00 0.00 0.00 3.93
583 1215 1.286248 AAGACTTCCCGGCTACCATT 58.714 50.000 0.00 0.00 0.00 3.16
595 1227 2.027192 GGCTACCATTGACAAGGTCAGA 60.027 50.000 11.20 0.00 43.69 3.27
635 1267 3.047280 GACAACGGCATGTCGGCA 61.047 61.111 25.37 0.00 40.23 5.69
701 1344 7.867445 ATTTTTATTACGTTTGAGGTGCTTG 57.133 32.000 0.00 0.00 0.00 4.01
708 1351 2.223377 CGTTTGAGGTGCTTGGTACTTC 59.777 50.000 0.00 0.00 0.00 3.01
709 1352 3.477530 GTTTGAGGTGCTTGGTACTTCT 58.522 45.455 0.00 0.00 0.00 2.85
716 1359 2.548480 GTGCTTGGTACTTCTGGTGAAC 59.452 50.000 0.00 0.00 0.00 3.18
723 1366 6.195600 TGGTACTTCTGGTGAACCTTTATT 57.804 37.500 0.37 0.00 36.82 1.40
835 1524 9.638239 TGCCAAACAGATAATTGAGAATAAAAC 57.362 29.630 0.00 0.00 0.00 2.43
846 1535 7.921786 ATTGAGAATAAAACGAACCATCTCA 57.078 32.000 0.00 0.00 39.82 3.27
847 1536 7.921786 TTGAGAATAAAACGAACCATCTCAT 57.078 32.000 3.69 0.00 40.81 2.90
848 1537 7.307493 TGAGAATAAAACGAACCATCTCATG 57.693 36.000 0.00 0.00 37.49 3.07
849 1538 6.878923 TGAGAATAAAACGAACCATCTCATGT 59.121 34.615 0.00 0.00 37.49 3.21
850 1539 7.064609 TGAGAATAAAACGAACCATCTCATGTC 59.935 37.037 0.00 0.00 37.49 3.06
851 1540 7.106239 AGAATAAAACGAACCATCTCATGTCT 58.894 34.615 0.00 0.00 0.00 3.41
852 1541 6.910536 ATAAAACGAACCATCTCATGTCTC 57.089 37.500 0.00 0.00 0.00 3.36
853 1542 3.961480 AACGAACCATCTCATGTCTCA 57.039 42.857 0.00 0.00 0.00 3.27
854 1543 4.478206 AACGAACCATCTCATGTCTCAT 57.522 40.909 0.00 0.00 0.00 2.90
855 1544 4.052159 ACGAACCATCTCATGTCTCATC 57.948 45.455 0.00 0.00 0.00 2.92
856 1545 3.703556 ACGAACCATCTCATGTCTCATCT 59.296 43.478 0.00 0.00 0.00 2.90
857 1546 4.161189 ACGAACCATCTCATGTCTCATCTT 59.839 41.667 0.00 0.00 0.00 2.40
858 1547 5.114780 CGAACCATCTCATGTCTCATCTTT 58.885 41.667 0.00 0.00 0.00 2.52
859 1548 5.583854 CGAACCATCTCATGTCTCATCTTTT 59.416 40.000 0.00 0.00 0.00 2.27
860 1549 6.093219 CGAACCATCTCATGTCTCATCTTTTT 59.907 38.462 0.00 0.00 0.00 1.94
888 1577 6.183361 GGGAGGGAAATCTCATGTCTAATCTT 60.183 42.308 0.00 0.00 35.58 2.40
925 1614 6.180472 TGCTCTAAACTCCTATTCCCTTTTG 58.820 40.000 0.00 0.00 0.00 2.44
950 1639 5.574891 AATATTGCCAAACACGCTATGAA 57.425 34.783 0.00 0.00 0.00 2.57
954 1643 4.250116 TGCCAAACACGCTATGAAAAAT 57.750 36.364 0.00 0.00 0.00 1.82
955 1644 5.378292 TGCCAAACACGCTATGAAAAATA 57.622 34.783 0.00 0.00 0.00 1.40
956 1645 5.773575 TGCCAAACACGCTATGAAAAATAA 58.226 33.333 0.00 0.00 0.00 1.40
1193 1896 3.706373 CCAGGTCAGGTGTCCCCG 61.706 72.222 0.00 0.00 38.74 5.73
1402 2105 1.697291 ATGGGAGACCCTTCCATCCTC 60.697 57.143 8.34 0.00 46.20 3.71
1408 2111 2.584608 CCTTCCATCCTCGGCGTT 59.415 61.111 6.85 0.00 0.00 4.84
1440 2143 0.464554 GCAGGCCAAGTCCAGGTATC 60.465 60.000 5.01 0.00 0.00 2.24
1442 2145 1.134280 CAGGCCAAGTCCAGGTATCTG 60.134 57.143 5.01 0.00 40.59 2.90
1446 2157 1.210478 CCAAGTCCAGGTATCTGTGGG 59.790 57.143 1.52 0.00 39.31 4.61
1451 2162 2.505819 GTCCAGGTATCTGTGGGTCATT 59.494 50.000 1.52 0.00 39.31 2.57
1462 2173 3.944015 CTGTGGGTCATTGAGAATTCCTC 59.056 47.826 0.65 0.09 42.30 3.71
1492 2206 4.201792 CCGAGTTGATGCTCTGAGAATTTG 60.202 45.833 9.28 0.00 33.55 2.32
1499 2213 5.410746 TGATGCTCTGAGAATTTGACTTCAC 59.589 40.000 9.28 0.00 0.00 3.18
1503 2217 5.238214 GCTCTGAGAATTTGACTTCACTGTT 59.762 40.000 9.28 0.00 0.00 3.16
1504 2218 6.238593 GCTCTGAGAATTTGACTTCACTGTTT 60.239 38.462 9.28 0.00 0.00 2.83
1508 2222 8.142994 TGAGAATTTGACTTCACTGTTTACTC 57.857 34.615 0.00 0.00 0.00 2.59
1571 2285 3.383505 GTCCAAAACCTAGCCAAGTGTTT 59.616 43.478 0.00 0.00 32.97 2.83
1577 2291 2.069273 CCTAGCCAAGTGTTTCACTCG 58.931 52.381 2.86 0.00 44.62 4.18
1581 2295 0.040958 CCAAGTGTTTCACTCGCTGC 60.041 55.000 2.86 0.00 44.62 5.25
1585 2299 0.233332 GTGTTTCACTCGCTGCTGTC 59.767 55.000 0.00 0.00 0.00 3.51
1641 2355 0.333993 AGGCAGGGAAGCATGTGATT 59.666 50.000 0.00 0.00 35.83 2.57
1650 2364 4.142381 GGGAAGCATGTGATTCAAGGTAAC 60.142 45.833 12.40 0.00 41.81 2.50
1665 2379 3.936372 GGTAACTGGGAAAAGGAAAGC 57.064 47.619 0.00 0.00 0.00 3.51
1676 2392 6.101997 GGGAAAAGGAAAGCATATGAAACTG 58.898 40.000 6.97 0.00 0.00 3.16
1707 2423 5.303078 ACGGTCTGATTTGAGCTATATGACT 59.697 40.000 0.00 0.00 32.83 3.41
1710 2426 6.463614 GGTCTGATTTGAGCTATATGACTGGT 60.464 42.308 0.00 0.00 0.00 4.00
1845 2562 3.430929 CCTGCCTCTGGATGTAAGTACAC 60.431 52.174 0.00 0.00 39.30 2.90
1888 2605 4.568956 TCATGAGCACCATAATGGATACG 58.431 43.478 0.00 0.00 40.96 3.06
1889 2606 4.283212 TCATGAGCACCATAATGGATACGA 59.717 41.667 0.00 0.00 40.96 3.43
1890 2607 3.990092 TGAGCACCATAATGGATACGAC 58.010 45.455 0.00 0.00 40.96 4.34
1891 2608 2.987149 GAGCACCATAATGGATACGACG 59.013 50.000 0.00 0.00 40.96 5.12
1892 2609 2.626266 AGCACCATAATGGATACGACGA 59.374 45.455 0.00 0.00 40.96 4.20
1893 2610 3.069016 AGCACCATAATGGATACGACGAA 59.931 43.478 0.00 0.00 40.96 3.85
1894 2611 3.994392 GCACCATAATGGATACGACGAAT 59.006 43.478 0.00 0.00 40.96 3.34
1930 2647 3.769536 CTTTGTCCAAAAACTTCAGCGT 58.230 40.909 0.00 0.00 0.00 5.07
1935 2652 3.013921 TCCAAAAACTTCAGCGTCAACT 58.986 40.909 0.00 0.00 0.00 3.16
1981 2698 5.458779 GTGTACAACTCATTTCCAAACAAGC 59.541 40.000 0.00 0.00 0.00 4.01
1988 2705 1.703411 TTTCCAAACAAGCTCCCCTG 58.297 50.000 0.00 0.00 0.00 4.45
1992 2709 2.175931 TCCAAACAAGCTCCCCTGTAAA 59.824 45.455 0.00 0.00 0.00 2.01
2005 2722 2.028203 CCCTGTAAACCAATTTGGGCTG 60.028 50.000 19.39 9.85 43.37 4.85
2127 2844 3.316029 TCAACAGTCAAGCAAGTTGATGG 59.684 43.478 7.16 0.00 46.99 3.51
2243 2960 2.007608 GTGGTAAGGAATCAAGTCGCC 58.992 52.381 0.00 0.00 0.00 5.54
2281 2998 1.804151 TCAGTGCAACGTGCTTTATCC 59.196 47.619 10.54 0.00 45.31 2.59
2449 3168 5.237127 GGATGATTTCGTATGCACATCTTGA 59.763 40.000 8.89 0.00 35.80 3.02
2598 6643 5.422878 CGCAAGTTTGTCTAATTTTTGTGC 58.577 37.500 0.00 0.00 0.00 4.57
2719 6764 2.622942 TCTGTTGGCATTGAAGTGGAAC 59.377 45.455 0.00 0.00 0.00 3.62
2903 6953 9.832445 TGACAAGTATTTTATCCTAATGAGTCC 57.168 33.333 0.00 0.00 0.00 3.85
3106 7157 7.870509 TCCATTTGAAGGATTTGATACTCAG 57.129 36.000 0.00 0.00 0.00 3.35
3199 7250 3.876914 ACACATCACAAGTACACAACTGG 59.123 43.478 0.00 0.00 38.88 4.00
3392 7443 5.126222 TCATTTGTAACAGCTTGTTGGTTCA 59.874 36.000 10.59 4.13 41.30 3.18
3594 7645 6.544650 TGGGGTCTTAGTATTTGCAGTTAAA 58.455 36.000 0.00 0.00 0.00 1.52
3833 7886 5.270794 TGGTTACCAGGTAAAACCACTTTT 58.729 37.500 19.55 0.00 45.85 2.27
3995 8049 5.956068 TCACAGTGCATTGCTACAAATAA 57.044 34.783 9.42 0.00 0.00 1.40
3996 8050 6.513806 TCACAGTGCATTGCTACAAATAAT 57.486 33.333 9.42 0.00 0.00 1.28
3997 8051 7.622893 TCACAGTGCATTGCTACAAATAATA 57.377 32.000 9.42 0.00 0.00 0.98
4016 8071 5.479124 AATAGTTACTCGGACAAAGGTGT 57.521 39.130 0.00 0.00 42.10 4.16
4034 8089 5.276440 AGGTGTGGAGTCTATCTCTGATTT 58.724 41.667 0.00 0.00 42.40 2.17
4061 8116 9.554395 GGAAAAAGGACTTTGGATTTGAAAATA 57.446 29.630 0.00 0.00 32.36 1.40
4169 8224 1.081892 CTGAAGTCATGTTCAGGCCG 58.918 55.000 15.14 0.00 46.64 6.13
4170 8225 0.955428 TGAAGTCATGTTCAGGCCGC 60.955 55.000 0.00 0.00 32.54 6.53
4489 8544 0.813821 GATGCAGGCTTTCCTTGTCC 59.186 55.000 0.00 0.00 41.93 4.02
4574 8629 4.370364 TTCACAGGTGCTTTTCTCAAAC 57.630 40.909 0.00 0.00 0.00 2.93
4649 8704 5.479375 AGAACTGAAAGCATTTGTCCATGAT 59.521 36.000 0.00 0.00 39.27 2.45
4712 8767 8.230486 TCAATCTCTATTTTTCTTTTCTCGCAC 58.770 33.333 0.00 0.00 0.00 5.34
4791 8846 9.125026 CCTATATTCCACAGAATGCTTAAAAGT 57.875 33.333 0.00 0.00 42.78 2.66
5020 9077 4.211125 TCTTCTGCTAGAATGATCGGTCT 58.789 43.478 0.00 3.69 33.13 3.85
5157 9214 9.722184 CCATCATTCTTTCACACAGATCTATAT 57.278 33.333 0.00 0.00 0.00 0.86
5287 9347 5.733676 ACTCTTGCTTGTTGTTTTCCATTT 58.266 33.333 0.00 0.00 0.00 2.32
5311 9371 2.487934 CTGCATATACAGGTGGCTGAC 58.512 52.381 0.00 0.00 33.85 3.51
5362 9422 5.975693 TGACAGTTTGGAGAGTTGTTTTT 57.024 34.783 0.00 0.00 0.00 1.94
5409 9469 8.637986 GGTGGCACATAATTATTGGATTTCTTA 58.362 33.333 20.82 0.00 44.52 2.10
5460 9520 9.657419 AAACACTGAACAAGATTCTGAAAATTT 57.343 25.926 0.00 0.00 0.00 1.82
5557 9952 4.578105 GCATGTTGTTGGGATTTTGGAAAA 59.422 37.500 0.00 0.00 0.00 2.29
5616 10037 9.913451 TTCTGAAGTTTGATTTTTATTTTTGCG 57.087 25.926 0.00 0.00 0.00 4.85
5617 10038 8.547069 TCTGAAGTTTGATTTTTATTTTTGCGG 58.453 29.630 0.00 0.00 0.00 5.69
5618 10039 7.634522 TGAAGTTTGATTTTTATTTTTGCGGG 58.365 30.769 0.00 0.00 0.00 6.13
5619 10040 7.281100 TGAAGTTTGATTTTTATTTTTGCGGGT 59.719 29.630 0.00 0.00 0.00 5.28
5620 10041 8.664211 AAGTTTGATTTTTATTTTTGCGGGTA 57.336 26.923 0.00 0.00 0.00 3.69
5621 10042 8.664211 AGTTTGATTTTTATTTTTGCGGGTAA 57.336 26.923 0.00 0.00 0.00 2.85
5622 10043 9.110502 AGTTTGATTTTTATTTTTGCGGGTAAA 57.889 25.926 0.00 0.00 0.00 2.01
5623 10044 9.717892 GTTTGATTTTTATTTTTGCGGGTAAAA 57.282 25.926 0.00 0.00 0.00 1.52
5624 10045 9.937175 TTTGATTTTTATTTTTGCGGGTAAAAG 57.063 25.926 0.00 0.00 31.80 2.27
5625 10046 8.664211 TGATTTTTATTTTTGCGGGTAAAAGT 57.336 26.923 0.00 0.00 31.80 2.66
5626 10047 9.110502 TGATTTTTATTTTTGCGGGTAAAAGTT 57.889 25.926 0.00 0.00 31.80 2.66
5627 10048 9.938670 GATTTTTATTTTTGCGGGTAAAAGTTT 57.061 25.926 0.00 0.00 31.80 2.66
5628 10049 9.723447 ATTTTTATTTTTGCGGGTAAAAGTTTG 57.277 25.926 0.00 0.00 31.80 2.93
5629 10050 8.488651 TTTTATTTTTGCGGGTAAAAGTTTGA 57.511 26.923 0.00 0.00 31.80 2.69
5630 10051 8.664211 TTTATTTTTGCGGGTAAAAGTTTGAT 57.336 26.923 0.00 0.00 31.80 2.57
5631 10052 8.664211 TTATTTTTGCGGGTAAAAGTTTGATT 57.336 26.923 0.00 0.00 31.80 2.57
5911 10344 2.488545 TCTTTGTCGCTAGAGGTGAGAC 59.511 50.000 0.00 0.00 34.88 3.36
5931 10364 4.813161 AGACAAATCGACTAGCATCAATGG 59.187 41.667 0.00 0.00 0.00 3.16
5935 10368 3.349488 TCGACTAGCATCAATGGTACG 57.651 47.619 0.00 2.70 39.52 3.67
5974 10407 1.610522 ACAGTTTGGTGCTCAATGCTC 59.389 47.619 0.00 0.00 43.37 4.26
5978 10411 3.181367 GGTGCTCAATGCTCCGTG 58.819 61.111 0.00 0.00 44.08 4.94
5979 10412 1.375908 GGTGCTCAATGCTCCGTGA 60.376 57.895 0.00 0.00 44.08 4.35
5980 10413 0.745845 GGTGCTCAATGCTCCGTGAT 60.746 55.000 0.00 0.00 44.08 3.06
5981 10414 1.473257 GGTGCTCAATGCTCCGTGATA 60.473 52.381 0.00 0.00 44.08 2.15
5982 10415 2.487934 GTGCTCAATGCTCCGTGATAT 58.512 47.619 0.00 0.00 43.37 1.63
5983 10416 2.222678 GTGCTCAATGCTCCGTGATATG 59.777 50.000 0.00 0.00 43.37 1.78
5984 10417 2.102925 TGCTCAATGCTCCGTGATATGA 59.897 45.455 0.00 0.00 43.37 2.15
5985 10418 2.735663 GCTCAATGCTCCGTGATATGAG 59.264 50.000 0.00 0.00 38.95 2.90
5986 10419 3.801638 GCTCAATGCTCCGTGATATGAGT 60.802 47.826 0.00 0.00 38.95 3.41
5987 10420 3.721035 TCAATGCTCCGTGATATGAGTG 58.279 45.455 0.00 0.00 0.00 3.51
5988 10421 2.160822 ATGCTCCGTGATATGAGTGC 57.839 50.000 0.00 0.00 0.00 4.40
5989 10422 0.249031 TGCTCCGTGATATGAGTGCG 60.249 55.000 0.00 0.00 0.00 5.34
5990 10423 0.030773 GCTCCGTGATATGAGTGCGA 59.969 55.000 0.00 0.00 0.00 5.10
5991 10424 1.536072 GCTCCGTGATATGAGTGCGAA 60.536 52.381 0.00 0.00 0.00 4.70
5992 10425 2.389059 CTCCGTGATATGAGTGCGAAG 58.611 52.381 0.00 0.00 0.00 3.79
5993 10426 1.067060 TCCGTGATATGAGTGCGAAGG 59.933 52.381 0.00 0.00 0.00 3.46
5994 10427 1.491670 CGTGATATGAGTGCGAAGGG 58.508 55.000 0.00 0.00 0.00 3.95
5995 10428 1.067060 CGTGATATGAGTGCGAAGGGA 59.933 52.381 0.00 0.00 0.00 4.20
5996 10429 2.288457 CGTGATATGAGTGCGAAGGGAT 60.288 50.000 0.00 0.00 0.00 3.85
5997 10430 3.062763 GTGATATGAGTGCGAAGGGATG 58.937 50.000 0.00 0.00 0.00 3.51
5998 10431 2.037641 TGATATGAGTGCGAAGGGATGG 59.962 50.000 0.00 0.00 0.00 3.51
5999 10432 0.758734 TATGAGTGCGAAGGGATGGG 59.241 55.000 0.00 0.00 0.00 4.00
6000 10433 2.514824 GAGTGCGAAGGGATGGGC 60.515 66.667 0.00 0.00 0.00 5.36
6001 10434 3.011517 AGTGCGAAGGGATGGGCT 61.012 61.111 0.00 0.00 0.00 5.19
6002 10435 2.514824 GTGCGAAGGGATGGGCTC 60.515 66.667 0.00 0.00 0.00 4.70
6003 10436 2.688666 TGCGAAGGGATGGGCTCT 60.689 61.111 0.00 0.00 0.00 4.09
6004 10437 2.300967 TGCGAAGGGATGGGCTCTT 61.301 57.895 0.00 0.00 41.00 2.85
6005 10438 1.077429 GCGAAGGGATGGGCTCTTT 60.077 57.895 0.00 0.00 37.47 2.52
6006 10439 1.379642 GCGAAGGGATGGGCTCTTTG 61.380 60.000 0.00 0.00 37.47 2.77
6007 10440 0.749454 CGAAGGGATGGGCTCTTTGG 60.749 60.000 0.00 0.00 37.47 3.28
6008 10441 0.625849 GAAGGGATGGGCTCTTTGGA 59.374 55.000 0.00 0.00 37.47 3.53
6009 10442 0.627986 AAGGGATGGGCTCTTTGGAG 59.372 55.000 0.00 0.00 31.70 3.86
6017 10450 4.423231 CTCTTTGGAGCCAACCCC 57.577 61.111 0.50 0.00 35.46 4.95
6018 10451 1.304464 CTCTTTGGAGCCAACCCCC 60.304 63.158 0.50 0.00 35.46 5.40
6040 10473 3.313012 CCCCCGTTCCTTTTGAATTTC 57.687 47.619 0.00 0.00 34.90 2.17
6041 10474 2.897326 CCCCCGTTCCTTTTGAATTTCT 59.103 45.455 0.00 0.00 34.90 2.52
6042 10475 3.323691 CCCCCGTTCCTTTTGAATTTCTT 59.676 43.478 0.00 0.00 34.90 2.52
6043 10476 4.202315 CCCCCGTTCCTTTTGAATTTCTTT 60.202 41.667 0.00 0.00 34.90 2.52
6044 10477 5.364778 CCCCGTTCCTTTTGAATTTCTTTT 58.635 37.500 0.00 0.00 34.90 2.27
6045 10478 5.236263 CCCCGTTCCTTTTGAATTTCTTTTG 59.764 40.000 0.00 0.00 34.90 2.44
6046 10479 6.045955 CCCGTTCCTTTTGAATTTCTTTTGA 58.954 36.000 0.00 0.00 34.90 2.69
6047 10480 6.536941 CCCGTTCCTTTTGAATTTCTTTTGAA 59.463 34.615 0.00 0.00 34.90 2.69
6081 10514 9.604626 TTTAAAAGTTTCAAACAAATGCAGTTG 57.395 25.926 24.24 24.24 34.52 3.16
6082 10515 6.799926 AAAGTTTCAAACAAATGCAGTTGT 57.200 29.167 25.66 25.66 43.58 3.32
6090 10523 5.738118 AACAAATGCAGTTGTTTTCCATG 57.262 34.783 32.91 7.26 46.97 3.66
6091 10524 5.021033 ACAAATGCAGTTGTTTTCCATGA 57.979 34.783 25.66 0.00 38.60 3.07
6092 10525 5.426504 ACAAATGCAGTTGTTTTCCATGAA 58.573 33.333 25.66 0.00 38.60 2.57
6093 10526 5.879223 ACAAATGCAGTTGTTTTCCATGAAA 59.121 32.000 25.66 0.00 38.60 2.69
6094 10527 6.373774 ACAAATGCAGTTGTTTTCCATGAAAA 59.626 30.769 25.66 0.00 38.60 2.29
6107 10540 8.641499 TTTTCCATGAAAACAAGTACATGTTC 57.359 30.769 16.17 6.47 42.49 3.18
6108 10541 6.951062 TCCATGAAAACAAGTACATGTTCA 57.049 33.333 16.17 11.67 42.49 3.18
6109 10542 6.734137 TCCATGAAAACAAGTACATGTTCAC 58.266 36.000 16.17 13.12 42.49 3.18
6110 10543 6.545666 TCCATGAAAACAAGTACATGTTCACT 59.454 34.615 16.17 0.00 42.49 3.41
6111 10544 7.717436 TCCATGAAAACAAGTACATGTTCACTA 59.283 33.333 16.17 5.12 42.49 2.74
6112 10545 8.514594 CCATGAAAACAAGTACATGTTCACTAT 58.485 33.333 16.17 6.94 42.49 2.12
6113 10546 9.333497 CATGAAAACAAGTACATGTTCACTATG 57.667 33.333 16.17 13.61 42.49 2.23
6114 10547 8.669946 TGAAAACAAGTACATGTTCACTATGA 57.330 30.769 16.17 0.00 42.49 2.15
6115 10548 9.114952 TGAAAACAAGTACATGTTCACTATGAA 57.885 29.630 16.17 0.00 42.49 2.57
6118 10551 9.507329 AAACAAGTACATGTTCACTATGAATCT 57.493 29.630 16.17 0.00 42.49 2.40
6119 10552 8.484641 ACAAGTACATGTTCACTATGAATCTG 57.515 34.615 2.30 0.00 38.79 2.90
6120 10553 8.097038 ACAAGTACATGTTCACTATGAATCTGT 58.903 33.333 2.30 0.00 38.79 3.41
6121 10554 9.586435 CAAGTACATGTTCACTATGAATCTGTA 57.414 33.333 2.30 10.00 38.79 2.74
6153 10586 9.982291 TCGTTGAAAATATAGTGATTTGTAAGC 57.018 29.630 0.00 0.00 0.00 3.09
6154 10587 9.988350 CGTTGAAAATATAGTGATTTGTAAGCT 57.012 29.630 0.00 0.00 0.00 3.74
6171 10604 8.433421 TTGTAAGCTAGAAAAATAATCTCGGG 57.567 34.615 0.00 0.00 0.00 5.14
6172 10605 6.482308 TGTAAGCTAGAAAAATAATCTCGGGC 59.518 38.462 0.00 0.00 0.00 6.13
6173 10606 4.390264 AGCTAGAAAAATAATCTCGGGCC 58.610 43.478 0.00 0.00 0.00 5.80
6174 10607 4.134563 GCTAGAAAAATAATCTCGGGCCA 58.865 43.478 4.39 0.00 0.00 5.36
6175 10608 4.762251 GCTAGAAAAATAATCTCGGGCCAT 59.238 41.667 4.39 0.00 0.00 4.40
6176 10609 5.241728 GCTAGAAAAATAATCTCGGGCCATT 59.758 40.000 4.39 0.00 0.00 3.16
6177 10610 6.430000 GCTAGAAAAATAATCTCGGGCCATTA 59.570 38.462 4.39 0.00 0.00 1.90
6178 10611 7.040686 GCTAGAAAAATAATCTCGGGCCATTAA 60.041 37.037 4.39 0.00 0.00 1.40
6179 10612 7.654022 AGAAAAATAATCTCGGGCCATTAAA 57.346 32.000 4.39 0.00 0.00 1.52
6180 10613 8.073467 AGAAAAATAATCTCGGGCCATTAAAA 57.927 30.769 4.39 0.00 0.00 1.52
6181 10614 8.536175 AGAAAAATAATCTCGGGCCATTAAAAA 58.464 29.630 4.39 0.00 0.00 1.94
6202 10635 6.399639 AAAAAGACCCATTTTGATGTACGT 57.600 33.333 0.00 0.00 32.81 3.57
6203 10636 5.371115 AAAGACCCATTTTGATGTACGTG 57.629 39.130 0.00 0.00 0.00 4.49
6204 10637 4.015872 AGACCCATTTTGATGTACGTGT 57.984 40.909 0.00 0.00 0.00 4.49
6205 10638 4.394729 AGACCCATTTTGATGTACGTGTT 58.605 39.130 0.00 0.00 0.00 3.32
6206 10639 4.825085 AGACCCATTTTGATGTACGTGTTT 59.175 37.500 0.00 0.00 0.00 2.83
6207 10640 4.865776 ACCCATTTTGATGTACGTGTTTG 58.134 39.130 0.00 0.00 0.00 2.93
6208 10641 4.339814 ACCCATTTTGATGTACGTGTTTGT 59.660 37.500 0.00 0.00 0.00 2.83
6209 10642 5.163499 ACCCATTTTGATGTACGTGTTTGTT 60.163 36.000 0.00 0.00 0.00 2.83
6210 10643 5.751028 CCCATTTTGATGTACGTGTTTGTTT 59.249 36.000 0.00 0.00 0.00 2.83
6211 10644 6.256757 CCCATTTTGATGTACGTGTTTGTTTT 59.743 34.615 0.00 0.00 0.00 2.43
6212 10645 7.201565 CCCATTTTGATGTACGTGTTTGTTTTT 60.202 33.333 0.00 0.00 0.00 1.94
6213 10646 7.843686 CCATTTTGATGTACGTGTTTGTTTTTC 59.156 33.333 0.00 0.00 0.00 2.29
6214 10647 8.591312 CATTTTGATGTACGTGTTTGTTTTTCT 58.409 29.630 0.00 0.00 0.00 2.52
6215 10648 8.522178 TTTTGATGTACGTGTTTGTTTTTCTT 57.478 26.923 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 149 5.382618 ACACATTCAAGAGAAATTGCTCC 57.617 39.130 10.04 0.00 37.29 4.70
158 166 2.777459 TTACCCCCAACCAAACACAT 57.223 45.000 0.00 0.00 0.00 3.21
159 167 2.777459 ATTACCCCCAACCAAACACA 57.223 45.000 0.00 0.00 0.00 3.72
208 216 7.527084 AACAATACTAGATTTCAAGTCTCGC 57.473 36.000 0.00 0.00 0.00 5.03
277 285 1.697432 ACGGTGGGAATTGAAGTCTCA 59.303 47.619 0.00 0.00 0.00 3.27
294 302 4.196971 CCCCTCCTCTGTAAATAAAACGG 58.803 47.826 0.00 0.00 0.00 4.44
304 312 1.311403 CTCCTGCCCCTCCTCTGTA 59.689 63.158 0.00 0.00 0.00 2.74
331 339 1.335964 TGACTCGAAGAAGGAGCAACG 60.336 52.381 0.00 0.00 34.09 4.10
332 340 2.288518 ACTGACTCGAAGAAGGAGCAAC 60.289 50.000 0.00 0.00 34.09 4.17
333 341 1.964223 ACTGACTCGAAGAAGGAGCAA 59.036 47.619 0.00 0.00 34.09 3.91
406 1037 5.004361 AGAGCTGGCAGGAATCTATACTA 57.996 43.478 17.64 0.00 0.00 1.82
409 1040 4.202398 CCAAAGAGCTGGCAGGAATCTATA 60.202 45.833 17.64 0.00 0.00 1.31
510 1142 2.872001 GCAGTCGTCGTCGCTGAG 60.872 66.667 22.30 5.38 40.64 3.35
514 1146 2.708059 GAGTTGCAGTCGTCGTCGC 61.708 63.158 0.00 0.00 36.96 5.19
563 1195 1.286248 ATGGTAGCCGGGAAGTCTTT 58.714 50.000 2.18 0.00 0.00 2.52
571 1203 0.748005 CCTTGTCAATGGTAGCCGGG 60.748 60.000 2.18 0.00 0.00 5.73
572 1204 0.035439 ACCTTGTCAATGGTAGCCGG 60.035 55.000 0.00 0.00 34.36 6.13
578 1210 1.270839 CGGTCTGACCTTGTCAATGGT 60.271 52.381 23.49 6.45 42.26 3.55
583 1215 1.816863 GAGCCGGTCTGACCTTGTCA 61.817 60.000 23.49 0.00 40.50 3.58
633 1265 3.885521 GCCGCCAGAATGAGCTGC 61.886 66.667 0.00 0.00 39.69 5.25
635 1267 1.617018 TACTGCCGCCAGAATGAGCT 61.617 55.000 0.00 0.00 41.77 4.09
687 1330 1.878953 AGTACCAAGCACCTCAAACG 58.121 50.000 0.00 0.00 0.00 3.60
701 1344 9.543783 CTATAATAAAGGTTCACCAGAAGTACC 57.456 37.037 0.00 0.00 38.89 3.34
801 1444 8.291191 TCAATTATCTGTTTGGCACATGATAA 57.709 30.769 0.00 11.57 39.30 1.75
835 1524 4.319139 AGATGAGACATGAGATGGTTCG 57.681 45.455 0.00 0.00 33.60 3.95
858 1547 4.750941 ACATGAGATTTCCCTCCCAAAAA 58.249 39.130 0.00 0.00 32.32 1.94
859 1548 4.044571 AGACATGAGATTTCCCTCCCAAAA 59.955 41.667 0.00 0.00 32.32 2.44
860 1549 3.593328 AGACATGAGATTTCCCTCCCAAA 59.407 43.478 0.00 0.00 32.32 3.28
861 1550 3.192944 AGACATGAGATTTCCCTCCCAA 58.807 45.455 0.00 0.00 32.32 4.12
862 1551 2.850833 AGACATGAGATTTCCCTCCCA 58.149 47.619 0.00 0.00 32.32 4.37
863 1552 5.309282 AGATTAGACATGAGATTTCCCTCCC 59.691 44.000 0.00 0.00 32.32 4.30
864 1553 6.432403 AGATTAGACATGAGATTTCCCTCC 57.568 41.667 0.00 0.00 32.32 4.30
865 1554 7.504403 TCAAGATTAGACATGAGATTTCCCTC 58.496 38.462 0.00 0.00 0.00 4.30
866 1555 7.443302 TCAAGATTAGACATGAGATTTCCCT 57.557 36.000 0.00 0.00 0.00 4.20
867 1556 9.213799 GTATCAAGATTAGACATGAGATTTCCC 57.786 37.037 0.00 0.00 0.00 3.97
868 1557 9.770097 TGTATCAAGATTAGACATGAGATTTCC 57.230 33.333 0.00 0.00 0.00 3.13
888 1577 6.360370 AGTTTAGAGCAGGAAGTTGTATCA 57.640 37.500 0.00 0.00 0.00 2.15
1193 1896 4.423209 AGAGGGGACAGGGGAGGC 62.423 72.222 0.00 0.00 0.00 4.70
1285 1988 1.133167 TCTGCGGATTCCTGGAGGATA 60.133 52.381 13.17 0.00 44.98 2.59
1408 2111 2.844451 GCCTGCAAGAACAACGGCA 61.844 57.895 4.59 0.00 37.48 5.69
1440 2143 3.944015 GAGGAATTCTCAATGACCCACAG 59.056 47.826 5.23 0.00 42.02 3.66
1442 2145 4.227864 AGAGGAATTCTCAATGACCCAC 57.772 45.455 5.23 0.00 44.81 4.61
1462 2173 3.309138 CAGAGCATCAACTCGGAAATGAG 59.691 47.826 0.00 0.00 41.77 2.90
1464 2175 3.264947 TCAGAGCATCAACTCGGAAATG 58.735 45.455 0.00 0.00 41.77 2.32
1465 2176 3.196469 TCTCAGAGCATCAACTCGGAAAT 59.804 43.478 0.00 0.00 39.81 2.17
1492 2206 8.961294 TCTTTATACGAGTAAACAGTGAAGTC 57.039 34.615 0.00 0.00 0.00 3.01
1499 2213 7.201444 CCAACAGCTCTTTATACGAGTAAACAG 60.201 40.741 0.00 0.00 0.00 3.16
1503 2217 6.276832 ACCAACAGCTCTTTATACGAGTAA 57.723 37.500 0.00 0.00 0.00 2.24
1504 2218 5.909621 ACCAACAGCTCTTTATACGAGTA 57.090 39.130 0.00 0.00 0.00 2.59
1508 2222 6.705782 CATTGTACCAACAGCTCTTTATACG 58.294 40.000 0.00 0.00 36.83 3.06
1571 2285 0.035317 ATTTGGACAGCAGCGAGTGA 59.965 50.000 0.00 0.00 0.00 3.41
1577 2291 0.388134 CTGCACATTTGGACAGCAGC 60.388 55.000 0.00 0.00 44.98 5.25
1581 2295 1.955778 TCAACCTGCACATTTGGACAG 59.044 47.619 0.00 0.00 0.00 3.51
1585 2299 0.963962 AGCTCAACCTGCACATTTGG 59.036 50.000 0.00 0.00 0.00 3.28
1629 2343 5.392380 CCAGTTACCTTGAATCACATGCTTC 60.392 44.000 0.00 0.00 0.00 3.86
1641 2355 4.799715 TTCCTTTTCCCAGTTACCTTGA 57.200 40.909 0.00 0.00 0.00 3.02
1650 2364 5.920193 TTCATATGCTTTCCTTTTCCCAG 57.080 39.130 0.00 0.00 0.00 4.45
1659 2373 7.852945 CGTTAAGATCAGTTTCATATGCTTTCC 59.147 37.037 0.00 0.00 0.00 3.13
1660 2374 7.852945 CCGTTAAGATCAGTTTCATATGCTTTC 59.147 37.037 0.00 0.00 0.00 2.62
1661 2375 7.336931 ACCGTTAAGATCAGTTTCATATGCTTT 59.663 33.333 0.00 0.00 0.00 3.51
1663 2377 6.349300 ACCGTTAAGATCAGTTTCATATGCT 58.651 36.000 0.00 0.00 0.00 3.79
1665 2379 7.706607 TCAGACCGTTAAGATCAGTTTCATATG 59.293 37.037 0.00 0.00 0.00 1.78
1676 2392 5.112686 AGCTCAAATCAGACCGTTAAGATC 58.887 41.667 0.00 0.00 0.00 2.75
1759 2476 8.504005 CGCGAGAAACCAATTAGGATATTTTAT 58.496 33.333 0.00 0.00 41.22 1.40
1845 2562 1.071605 AGAAGCGCTGAAAAGCTACG 58.928 50.000 12.58 0.00 43.78 3.51
1890 2607 5.232202 ACAAAGCTGATCACATACGTATTCG 59.768 40.000 5.03 0.00 43.34 3.34
1891 2608 6.292381 GGACAAAGCTGATCACATACGTATTC 60.292 42.308 5.03 1.56 0.00 1.75
1892 2609 5.523916 GGACAAAGCTGATCACATACGTATT 59.476 40.000 5.03 0.00 0.00 1.89
1893 2610 5.050490 GGACAAAGCTGATCACATACGTAT 58.950 41.667 1.14 1.14 0.00 3.06
1894 2611 4.081917 TGGACAAAGCTGATCACATACGTA 60.082 41.667 0.00 0.00 0.00 3.57
1950 2667 7.004555 TGGAAATGAGTTGTACACTGATAGT 57.995 36.000 0.00 0.00 35.01 2.12
1959 2676 5.831997 AGCTTGTTTGGAAATGAGTTGTAC 58.168 37.500 0.00 0.00 0.00 2.90
1971 2688 1.440618 TACAGGGGAGCTTGTTTGGA 58.559 50.000 0.00 0.00 0.00 3.53
1981 2698 2.831526 CCCAAATTGGTTTACAGGGGAG 59.168 50.000 11.52 0.00 35.17 4.30
1988 2705 3.070302 TCCAACAGCCCAAATTGGTTTAC 59.930 43.478 11.52 0.00 42.95 2.01
1992 2709 1.133199 TCTCCAACAGCCCAAATTGGT 60.133 47.619 11.52 0.00 42.95 3.67
2005 2722 6.147985 GGTTCAAATCTGTAGTTCTCTCCAAC 59.852 42.308 0.00 0.00 0.00 3.77
2079 2796 9.875708 ATAGAAGTCCAGAGATTACAGAAGTAT 57.124 33.333 0.00 0.00 0.00 2.12
2127 2844 7.889589 TGTTCATCATATCACCAATATCGTC 57.110 36.000 0.00 0.00 0.00 4.20
2243 2960 3.065371 ACTGAAAGAAAAAGGACGCTGTG 59.935 43.478 0.00 0.00 37.43 3.66
2252 2969 3.000773 GCACGTTGCACTGAAAGAAAAAG 60.001 43.478 5.30 0.00 44.26 2.27
2281 2998 3.520290 TGTATGGTAAGGAGAACTGCG 57.480 47.619 0.00 0.00 0.00 5.18
2449 3168 9.469097 TTGCTATGGTATAAAAGTATTGGTTGT 57.531 29.630 0.00 0.00 0.00 3.32
2598 6643 4.866921 TCCATGGATTTCGAGTATGTACG 58.133 43.478 11.44 0.00 0.00 3.67
2719 6764 7.443575 ACCTAGCTATTGCAGAATTGTATGAAG 59.556 37.037 1.12 0.00 42.74 3.02
2721 6766 6.830912 ACCTAGCTATTGCAGAATTGTATGA 58.169 36.000 1.12 0.00 42.74 2.15
2722 6767 6.707608 TGACCTAGCTATTGCAGAATTGTATG 59.292 38.462 1.12 0.00 42.74 2.39
2723 6768 6.830912 TGACCTAGCTATTGCAGAATTGTAT 58.169 36.000 1.12 0.00 42.74 2.29
2724 6769 6.233905 TGACCTAGCTATTGCAGAATTGTA 57.766 37.500 1.12 0.00 42.74 2.41
2725 6770 5.102953 TGACCTAGCTATTGCAGAATTGT 57.897 39.130 1.12 0.00 42.74 2.71
2729 6779 5.357742 TGAATGACCTAGCTATTGCAGAA 57.642 39.130 1.12 0.00 42.74 3.02
2889 6939 9.647918 GGATAGACATATGGACTCATTAGGATA 57.352 37.037 7.80 0.00 34.96 2.59
2903 6953 5.946972 AGTAAGGACCGAGGATAGACATATG 59.053 44.000 0.00 0.00 0.00 1.78
3058 7109 8.147058 GGATTATGATGACTACTCACATGACTT 58.853 37.037 0.00 0.00 0.00 3.01
3059 7110 7.288621 TGGATTATGATGACTACTCACATGACT 59.711 37.037 0.00 0.00 0.00 3.41
3105 7156 9.640963 GGATAATATTTCTTATGTCTGCGTACT 57.359 33.333 0.00 0.00 0.00 2.73
3106 7157 9.419297 TGGATAATATTTCTTATGTCTGCGTAC 57.581 33.333 0.00 0.00 0.00 3.67
3221 7272 6.183361 TGGGCAACTGGAAAATCAAACTTAAT 60.183 34.615 0.00 0.00 0.00 1.40
3366 7417 4.644685 ACCAACAAGCTGTTACAAATGAGT 59.355 37.500 0.00 0.00 38.77 3.41
3392 7443 6.768861 AGATAGACGATACAGTTGCTACTTCT 59.231 38.462 0.00 0.78 30.26 2.85
3594 7645 0.899720 TAACCTTTGGCGACCTCGAT 59.100 50.000 0.00 0.00 43.02 3.59
3833 7886 2.694628 AGTTCATTTGGCACTTGCAGAA 59.305 40.909 3.15 0.00 44.36 3.02
3995 8049 4.322499 CCACACCTTTGTCCGAGTAACTAT 60.322 45.833 0.00 0.00 31.66 2.12
3996 8050 3.006110 CCACACCTTTGTCCGAGTAACTA 59.994 47.826 0.00 0.00 31.66 2.24
3997 8051 2.224209 CCACACCTTTGTCCGAGTAACT 60.224 50.000 0.00 0.00 31.66 2.24
4016 8071 6.874278 TTTCCAAATCAGAGATAGACTCCA 57.126 37.500 0.00 0.00 45.96 3.86
4034 8089 6.552445 TTCAAATCCAAAGTCCTTTTTCCA 57.448 33.333 0.00 0.00 0.00 3.53
4061 8116 3.447586 ACAAGTGTGCATATCCGAGTAGT 59.552 43.478 0.00 0.00 0.00 2.73
4168 8223 0.108186 TGCCTCAGTAACATCCTGCG 60.108 55.000 0.00 0.00 0.00 5.18
4169 8224 1.065854 ACTGCCTCAGTAACATCCTGC 60.066 52.381 0.00 0.00 43.46 4.85
4170 8225 2.027745 ACACTGCCTCAGTAACATCCTG 60.028 50.000 0.00 0.00 43.43 3.86
4184 8239 6.560253 TTCTCAAGAAAAAGATACACTGCC 57.440 37.500 0.00 0.00 0.00 4.85
4306 8361 4.962362 TGCTGGTAAATGACTGAGATAGGA 59.038 41.667 0.00 0.00 0.00 2.94
4315 8370 3.261897 AGCTACTGTGCTGGTAAATGACT 59.738 43.478 4.36 0.00 42.33 3.41
4489 8544 1.475280 CAATCATGTGGGCAGTTGGAG 59.525 52.381 0.00 0.00 0.00 3.86
4574 8629 1.672356 CTGGCACTCCCCACTTTCG 60.672 63.158 0.00 0.00 0.00 3.46
4649 8704 1.281867 ACTTTGCTAGCCTGCACCATA 59.718 47.619 13.29 0.00 43.20 2.74
4695 8750 5.049405 ACGATCTGTGCGAGAAAAGAAAAAT 60.049 36.000 0.00 0.00 33.12 1.82
4712 8767 2.967599 TCATCAGAACCCACGATCTG 57.032 50.000 0.00 0.00 43.51 2.90
4743 8798 5.071653 AGGCAAATGTTCTTTGGTTTATGGT 59.928 36.000 0.44 0.00 0.00 3.55
4791 8846 7.251936 AGAGAGTATGATGAAATCCTGGGATA 58.748 38.462 2.24 0.00 44.73 2.59
4923 8980 2.042259 CATGGCTCCTTGCTTCGCA 61.042 57.895 0.00 0.00 42.39 5.10
5020 9077 4.453136 GCTACAAATTTTCACGTCCTACCA 59.547 41.667 0.00 0.00 0.00 3.25
5157 9214 6.538742 GGTAAATAAATCTGTAGCAGCTGTCA 59.461 38.462 16.64 11.32 0.00 3.58
5253 9310 5.453567 ACAAGCAAGAGTACATTTTTCCC 57.546 39.130 0.00 0.00 0.00 3.97
5287 9347 1.202687 GCCACCTGTATATGCAGCTGA 60.203 52.381 20.43 2.70 35.28 4.26
5311 9371 1.002468 CACTTTCGCAAGTTGAGGGTG 60.002 52.381 7.16 9.84 40.66 4.61
5362 9422 0.107557 ACATCGCATGCCACATCAGA 60.108 50.000 13.15 1.42 0.00 3.27
5605 10026 8.664211 ATCAAACTTTTACCCGCAAAAATAAA 57.336 26.923 0.00 0.00 0.00 1.40
5606 10027 8.664211 AATCAAACTTTTACCCGCAAAAATAA 57.336 26.923 0.00 0.00 0.00 1.40
5607 10028 8.664211 AAATCAAACTTTTACCCGCAAAAATA 57.336 26.923 0.00 0.00 0.00 1.40
5608 10029 7.561021 AAATCAAACTTTTACCCGCAAAAAT 57.439 28.000 0.00 0.00 0.00 1.82
5609 10030 6.986904 AAATCAAACTTTTACCCGCAAAAA 57.013 29.167 0.00 0.00 0.00 1.94
5610 10031 6.986904 AAAATCAAACTTTTACCCGCAAAA 57.013 29.167 0.00 0.00 0.00 2.44
5611 10032 6.819146 AGAAAAATCAAACTTTTACCCGCAAA 59.181 30.769 0.00 0.00 0.00 3.68
5612 10033 6.342111 AGAAAAATCAAACTTTTACCCGCAA 58.658 32.000 0.00 0.00 0.00 4.85
5613 10034 5.908341 AGAAAAATCAAACTTTTACCCGCA 58.092 33.333 0.00 0.00 0.00 5.69
5614 10035 6.700081 AGAAGAAAAATCAAACTTTTACCCGC 59.300 34.615 0.00 0.00 0.00 6.13
5615 10036 8.642908 AAGAAGAAAAATCAAACTTTTACCCG 57.357 30.769 0.00 0.00 0.00 5.28
5616 10037 9.042008 GGAAGAAGAAAAATCAAACTTTTACCC 57.958 33.333 0.00 0.00 0.00 3.69
5617 10038 9.594478 TGGAAGAAGAAAAATCAAACTTTTACC 57.406 29.630 0.00 0.00 0.00 2.85
5619 10040 9.313118 GCTGGAAGAAGAAAAATCAAACTTTTA 57.687 29.630 0.00 0.00 34.07 1.52
5620 10041 8.043113 AGCTGGAAGAAGAAAAATCAAACTTTT 58.957 29.630 0.00 0.00 34.07 2.27
5621 10042 7.559486 AGCTGGAAGAAGAAAAATCAAACTTT 58.441 30.769 0.00 0.00 34.07 2.66
5622 10043 7.117285 AGCTGGAAGAAGAAAAATCAAACTT 57.883 32.000 0.00 0.00 34.07 2.66
5623 10044 6.721704 AGCTGGAAGAAGAAAAATCAAACT 57.278 33.333 0.00 0.00 34.07 2.66
5624 10045 7.776933 AAAGCTGGAAGAAGAAAAATCAAAC 57.223 32.000 0.00 0.00 34.07 2.93
5625 10046 8.260114 AGAAAAGCTGGAAGAAGAAAAATCAAA 58.740 29.630 0.00 0.00 34.07 2.69
5626 10047 7.785033 AGAAAAGCTGGAAGAAGAAAAATCAA 58.215 30.769 0.00 0.00 34.07 2.57
5627 10048 7.352079 AGAAAAGCTGGAAGAAGAAAAATCA 57.648 32.000 0.00 0.00 34.07 2.57
5628 10049 9.920133 ATTAGAAAAGCTGGAAGAAGAAAAATC 57.080 29.630 0.00 0.00 34.07 2.17
5631 10052 9.750125 GAAATTAGAAAAGCTGGAAGAAGAAAA 57.250 29.630 0.00 0.00 34.07 2.29
5883 10316 3.063180 CCTCTAGCGACAAAGAATGCAAG 59.937 47.826 0.00 0.00 0.00 4.01
5911 10344 5.332581 CGTACCATTGATGCTAGTCGATTTG 60.333 44.000 0.00 0.00 0.00 2.32
5931 10364 3.344904 ACTGCCATATCACGTACGTAC 57.655 47.619 22.34 15.90 0.00 3.67
5935 10368 4.036498 ACTGTCTACTGCCATATCACGTAC 59.964 45.833 0.00 0.00 0.00 3.67
5974 10407 1.491670 CCTTCGCACTCATATCACGG 58.508 55.000 0.00 0.00 0.00 4.94
5975 10408 1.067060 TCCCTTCGCACTCATATCACG 59.933 52.381 0.00 0.00 0.00 4.35
5976 10409 2.890808 TCCCTTCGCACTCATATCAC 57.109 50.000 0.00 0.00 0.00 3.06
5977 10410 2.037641 CCATCCCTTCGCACTCATATCA 59.962 50.000 0.00 0.00 0.00 2.15
5978 10411 2.613977 CCCATCCCTTCGCACTCATATC 60.614 54.545 0.00 0.00 0.00 1.63
5979 10412 1.349026 CCCATCCCTTCGCACTCATAT 59.651 52.381 0.00 0.00 0.00 1.78
5980 10413 0.758734 CCCATCCCTTCGCACTCATA 59.241 55.000 0.00 0.00 0.00 2.15
5981 10414 1.528824 CCCATCCCTTCGCACTCAT 59.471 57.895 0.00 0.00 0.00 2.90
5982 10415 2.989639 CCCATCCCTTCGCACTCA 59.010 61.111 0.00 0.00 0.00 3.41
5983 10416 2.514824 GCCCATCCCTTCGCACTC 60.515 66.667 0.00 0.00 0.00 3.51
5984 10417 3.011517 AGCCCATCCCTTCGCACT 61.012 61.111 0.00 0.00 0.00 4.40
5985 10418 2.514824 GAGCCCATCCCTTCGCAC 60.515 66.667 0.00 0.00 0.00 5.34
5986 10419 1.852157 AAAGAGCCCATCCCTTCGCA 61.852 55.000 0.00 0.00 0.00 5.10
5987 10420 1.077429 AAAGAGCCCATCCCTTCGC 60.077 57.895 0.00 0.00 0.00 4.70
5988 10421 0.749454 CCAAAGAGCCCATCCCTTCG 60.749 60.000 0.00 0.00 0.00 3.79
5989 10422 0.625849 TCCAAAGAGCCCATCCCTTC 59.374 55.000 0.00 0.00 0.00 3.46
5990 10423 0.627986 CTCCAAAGAGCCCATCCCTT 59.372 55.000 0.00 0.00 32.13 3.95
5991 10424 2.315443 CTCCAAAGAGCCCATCCCT 58.685 57.895 0.00 0.00 32.13 4.20
5992 10425 4.995594 CTCCAAAGAGCCCATCCC 57.004 61.111 0.00 0.00 32.13 3.85
6000 10433 1.304464 GGGGGTTGGCTCCAAAGAG 60.304 63.158 2.45 0.00 43.57 2.85
6001 10434 2.851045 GGGGGTTGGCTCCAAAGA 59.149 61.111 2.45 0.00 36.82 2.52
6020 10453 2.897326 AGAAATTCAAAAGGAACGGGGG 59.103 45.455 0.00 0.00 38.60 5.40
6021 10454 4.600692 AAGAAATTCAAAAGGAACGGGG 57.399 40.909 0.00 0.00 38.60 5.73
6022 10455 6.045955 TCAAAAGAAATTCAAAAGGAACGGG 58.954 36.000 0.00 0.00 38.60 5.28
6023 10456 7.532682 TTCAAAAGAAATTCAAAAGGAACGG 57.467 32.000 0.00 0.00 38.60 4.44
6024 10457 9.261318 GTTTTCAAAAGAAATTCAAAAGGAACG 57.739 29.630 0.00 0.00 38.60 3.95
6025 10458 9.261318 CGTTTTCAAAAGAAATTCAAAAGGAAC 57.739 29.630 0.00 0.00 38.60 3.62
6026 10459 9.209175 TCGTTTTCAAAAGAAATTCAAAAGGAA 57.791 25.926 7.78 0.00 40.46 3.36
6027 10460 8.764524 TCGTTTTCAAAAGAAATTCAAAAGGA 57.235 26.923 0.00 1.96 31.69 3.36
6055 10488 9.604626 CAACTGCATTTGTTTGAAACTTTTAAA 57.395 25.926 9.69 2.00 0.00 1.52
6056 10489 8.778358 ACAACTGCATTTGTTTGAAACTTTTAA 58.222 25.926 15.99 0.00 36.22 1.52
6057 10490 8.316640 ACAACTGCATTTGTTTGAAACTTTTA 57.683 26.923 15.99 0.00 36.22 1.52
6058 10491 7.200778 ACAACTGCATTTGTTTGAAACTTTT 57.799 28.000 15.99 0.00 36.22 2.27
6059 10492 6.799926 ACAACTGCATTTGTTTGAAACTTT 57.200 29.167 15.99 0.00 36.22 2.66
6060 10493 6.799926 AACAACTGCATTTGTTTGAAACTT 57.200 29.167 24.65 5.23 45.45 2.66
6069 10502 5.021033 TCATGGAAAACAACTGCATTTGT 57.979 34.783 15.99 15.99 41.62 2.83
6070 10503 5.987777 TTCATGGAAAACAACTGCATTTG 57.012 34.783 14.64 14.64 0.00 2.32
6071 10504 6.998968 TTTTCATGGAAAACAACTGCATTT 57.001 29.167 0.00 0.00 36.73 2.32
6082 10515 8.253810 TGAACATGTACTTGTTTTCATGGAAAA 58.746 29.630 23.40 0.12 39.85 2.29
6083 10516 7.704472 GTGAACATGTACTTGTTTTCATGGAAA 59.296 33.333 23.40 0.00 39.85 3.13
6084 10517 7.068103 AGTGAACATGTACTTGTTTTCATGGAA 59.932 33.333 23.40 0.00 39.85 3.53
6085 10518 6.545666 AGTGAACATGTACTTGTTTTCATGGA 59.454 34.615 23.40 4.79 39.85 3.41
6086 10519 6.738114 AGTGAACATGTACTTGTTTTCATGG 58.262 36.000 23.40 0.00 39.85 3.66
6087 10520 9.333497 CATAGTGAACATGTACTTGTTTTCATG 57.667 33.333 23.40 19.08 39.85 3.07
6088 10521 9.283768 TCATAGTGAACATGTACTTGTTTTCAT 57.716 29.630 23.40 14.40 39.85 2.57
6089 10522 8.669946 TCATAGTGAACATGTACTTGTTTTCA 57.330 30.769 23.40 16.81 39.85 2.69
6092 10525 9.507329 AGATTCATAGTGAACATGTACTTGTTT 57.493 29.630 23.40 13.30 39.45 2.83
6093 10526 8.939929 CAGATTCATAGTGAACATGTACTTGTT 58.060 33.333 22.93 22.93 39.45 2.83
6094 10527 8.097038 ACAGATTCATAGTGAACATGTACTTGT 58.903 33.333 8.51 8.51 39.45 3.16
6095 10528 8.484641 ACAGATTCATAGTGAACATGTACTTG 57.515 34.615 6.59 7.18 39.45 3.16
6127 10560 9.982291 GCTTACAAATCACTATATTTTCAACGA 57.018 29.630 0.00 0.00 0.00 3.85
6128 10561 9.988350 AGCTTACAAATCACTATATTTTCAACG 57.012 29.630 0.00 0.00 0.00 4.10
6145 10578 8.889717 CCCGAGATTATTTTTCTAGCTTACAAA 58.110 33.333 0.00 0.00 0.00 2.83
6146 10579 7.012044 GCCCGAGATTATTTTTCTAGCTTACAA 59.988 37.037 0.00 0.00 0.00 2.41
6147 10580 6.482308 GCCCGAGATTATTTTTCTAGCTTACA 59.518 38.462 0.00 0.00 0.00 2.41
6148 10581 6.073167 GGCCCGAGATTATTTTTCTAGCTTAC 60.073 42.308 0.00 0.00 0.00 2.34
6149 10582 5.995897 GGCCCGAGATTATTTTTCTAGCTTA 59.004 40.000 0.00 0.00 0.00 3.09
6150 10583 4.822350 GGCCCGAGATTATTTTTCTAGCTT 59.178 41.667 0.00 0.00 0.00 3.74
6151 10584 4.141482 TGGCCCGAGATTATTTTTCTAGCT 60.141 41.667 0.00 0.00 0.00 3.32
6152 10585 4.134563 TGGCCCGAGATTATTTTTCTAGC 58.865 43.478 0.00 0.00 0.00 3.42
6153 10586 6.884280 AATGGCCCGAGATTATTTTTCTAG 57.116 37.500 0.00 0.00 0.00 2.43
6154 10587 8.754991 TTTAATGGCCCGAGATTATTTTTCTA 57.245 30.769 0.00 0.00 0.00 2.10
6155 10588 7.654022 TTTAATGGCCCGAGATTATTTTTCT 57.346 32.000 0.00 0.00 0.00 2.52
6156 10589 8.710835 TTTTTAATGGCCCGAGATTATTTTTC 57.289 30.769 0.00 0.00 0.00 2.29
6179 10612 6.183360 ACACGTACATCAAAATGGGTCTTTTT 60.183 34.615 0.00 0.00 37.19 1.94
6180 10613 5.300792 ACACGTACATCAAAATGGGTCTTTT 59.699 36.000 0.00 0.00 37.19 2.27
6181 10614 4.825085 ACACGTACATCAAAATGGGTCTTT 59.175 37.500 0.00 0.00 37.19 2.52
6182 10615 4.394729 ACACGTACATCAAAATGGGTCTT 58.605 39.130 0.00 0.00 37.19 3.01
6183 10616 4.015872 ACACGTACATCAAAATGGGTCT 57.984 40.909 0.00 0.00 37.19 3.85
6184 10617 4.759516 AACACGTACATCAAAATGGGTC 57.240 40.909 0.00 0.00 37.19 4.46
6185 10618 4.339814 ACAAACACGTACATCAAAATGGGT 59.660 37.500 0.00 0.00 37.19 4.51
6186 10619 4.865776 ACAAACACGTACATCAAAATGGG 58.134 39.130 0.00 0.00 37.19 4.00
6187 10620 6.820470 AAACAAACACGTACATCAAAATGG 57.180 33.333 0.00 0.00 37.19 3.16
6188 10621 8.591312 AGAAAAACAAACACGTACATCAAAATG 58.409 29.630 0.00 0.00 38.93 2.32
6189 10622 8.696410 AGAAAAACAAACACGTACATCAAAAT 57.304 26.923 0.00 0.00 0.00 1.82
6190 10623 8.522178 AAGAAAAACAAACACGTACATCAAAA 57.478 26.923 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.