Multiple sequence alignment - TraesCS6D01G311900

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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 TraesCS6D01G311900 chr6D 100.000 4235 0 0 1 4235 421475927 421471693 0.000000e+00 7821.0
1 TraesCS6D01G311900 chr6D 86.832 805 87 12 2444 3246 421789790 421790577 0.000000e+00 881.0
2 TraesCS6D01G311900 chr6D 81.805 687 99 20 2573 3242 421800355 421801032 1.720000e-153 553.0
3 TraesCS6D01G311900 chr6D 86.792 424 41 7 982 1405 421788325 421788733 3.860000e-125 459.0
4 TraesCS6D01G311900 chr6D 86.025 322 36 8 1979 2294 421789445 421789763 1.890000e-88 337.0
5 TraesCS6D01G311900 chr6D 87.857 280 33 1 3957 4235 411814508 411814229 1.140000e-85 327.0
6 TraesCS6D01G311900 chr6D 85.971 278 33 4 1143 1415 421798744 421799020 4.140000e-75 292.0
7 TraesCS6D01G311900 chr6D 99.248 133 1 0 3518 3650 421472278 421472146 1.520000e-59 241.0
8 TraesCS6D01G311900 chr6D 92.784 97 4 1 3309 3405 421790573 421790666 2.050000e-28 137.0
9 TraesCS6D01G311900 chr6D 95.556 45 2 0 3600 3644 321996941 321996985 5.870000e-09 73.1
10 TraesCS6D01G311900 chr6B 93.206 1516 66 19 1916 3415 634641144 634642638 0.000000e+00 2194.0
11 TraesCS6D01G311900 chr6B 92.286 1413 73 18 178 1576 634638904 634640294 0.000000e+00 1973.0
12 TraesCS6D01G311900 chr6B 83.834 1299 164 29 1967 3248 634941183 634942452 0.000000e+00 1194.0
13 TraesCS6D01G311900 chr6B 80.655 672 105 17 2573 3231 634978753 634979412 8.180000e-137 497.0
14 TraesCS6D01G311900 chr6B 93.525 278 17 1 1132 1408 634940037 634940314 3.050000e-111 412.0
15 TraesCS6D01G311900 chr6B 88.814 295 20 9 1639 1932 634640846 634641128 2.420000e-92 350.0
16 TraesCS6D01G311900 chr6B 88.104 269 24 6 1143 1405 634976863 634977129 3.180000e-81 313.0
17 TraesCS6D01G311900 chr6B 93.855 179 6 2 1 176 634638687 634638863 9.030000e-67 265.0
18 TraesCS6D01G311900 chr6B 90.678 118 7 2 3288 3405 634942767 634942880 2.040000e-33 154.0
19 TraesCS6D01G311900 chr6A 89.083 1658 113 35 1792 3415 564404054 564405677 0.000000e+00 1997.0
20 TraesCS6D01G311900 chr6A 90.476 1386 75 21 475 1840 564402722 564404070 0.000000e+00 1775.0
21 TraesCS6D01G311900 chr6A 86.218 965 105 19 2444 3405 564509411 564510350 0.000000e+00 1020.0
22 TraesCS6D01G311900 chr6A 88.690 504 45 9 3650 4146 73842398 73841900 4.680000e-169 604.0
23 TraesCS6D01G311900 chr6A 84.762 630 62 17 782 1408 564507684 564508282 6.060000e-168 601.0
24 TraesCS6D01G311900 chr6A 80.210 667 104 17 2573 3231 564586278 564586924 3.830000e-130 475.0
25 TraesCS6D01G311900 chr6A 94.372 231 11 2 243 472 564402444 564402673 1.870000e-93 353.0
26 TraesCS6D01G311900 chr6A 82.118 425 52 8 3816 4233 611553498 611553905 4.050000e-90 342.0
27 TraesCS6D01G311900 chr6A 85.448 268 33 4 1143 1405 564584662 564584928 1.500000e-69 274.0
28 TraesCS6D01G311900 chr6A 93.750 176 7 2 1 176 564402136 564402307 1.170000e-65 261.0
29 TraesCS6D01G311900 chr6A 81.295 278 26 12 2069 2346 564509118 564509369 7.180000e-48 202.0
30 TraesCS6D01G311900 chr6A 87.838 148 12 5 1985 2129 564508975 564509119 7.280000e-38 169.0
31 TraesCS6D01G311900 chr6A 97.059 34 0 1 3458 3491 103960617 103960649 5.920000e-04 56.5
32 TraesCS6D01G311900 chr3B 88.605 588 63 3 3650 4233 828526134 828526721 0.000000e+00 712.0
33 TraesCS6D01G311900 chr1A 87.966 590 61 7 3650 4235 574300380 574300963 0.000000e+00 688.0
34 TraesCS6D01G311900 chrUn 87.627 590 65 7 3650 4235 37076514 37075929 0.000000e+00 678.0
35 TraesCS6D01G311900 chrUn 88.235 187 22 0 3464 3650 320717716 320717530 1.530000e-54 224.0
36 TraesCS6D01G311900 chrUn 87.166 187 24 0 3464 3650 267642608 267642422 3.320000e-51 213.0
37 TraesCS6D01G311900 chr4A 86.078 589 63 13 3650 4235 211390221 211389649 2.160000e-172 616.0
38 TraesCS6D01G311900 chr4A 84.823 593 61 12 3646 4233 11309344 11309912 1.710000e-158 569.0
39 TraesCS6D01G311900 chr3D 87.316 544 61 6 3696 4235 589415694 589416233 2.160000e-172 616.0
40 TraesCS6D01G311900 chr7A 90.391 281 23 4 3957 4235 33879723 33879445 2.410000e-97 366.0
41 TraesCS6D01G311900 chr4D 86.552 290 29 6 3650 3937 15773261 15772980 1.140000e-80 311.0
42 TraesCS6D01G311900 chr4D 84.699 183 16 4 3468 3650 378254106 378253936 5.630000e-39 172.0
43 TraesCS6D01G311900 chr2D 85.862 290 31 5 3650 3937 469269052 469269333 2.480000e-77 300.0
44 TraesCS6D01G311900 chr2D 83.793 290 34 8 3649 3934 72573833 72573553 3.250000e-66 263.0
45 TraesCS6D01G311900 chr2D 78.095 105 16 6 3464 3565 10432104 10432004 4.570000e-05 60.2
46 TraesCS6D01G311900 chr2D 94.595 37 1 1 3456 3491 131272818 131272854 5.920000e-04 56.5
47 TraesCS6D01G311900 chr5A 85.052 194 23 2 3452 3644 453842601 453842789 4.320000e-45 193.0
48 TraesCS6D01G311900 chr5A 85.635 181 21 1 3464 3644 702896335 702896510 7.230000e-43 185.0
49 TraesCS6D01G311900 chr5D 96.774 31 1 0 3461 3491 340103165 340103195 8.000000e-03 52.8


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 TraesCS6D01G311900 chr6D 421471693 421475927 4234 True 4031.000000 7821 99.624000 1 4235 2 chr6D.!!$R2 4234
1 TraesCS6D01G311900 chr6D 421788325 421790666 2341 False 453.500000 881 88.108250 982 3405 4 chr6D.!!$F2 2423
2 TraesCS6D01G311900 chr6D 421798744 421801032 2288 False 422.500000 553 83.888000 1143 3242 2 chr6D.!!$F3 2099
3 TraesCS6D01G311900 chr6B 634638687 634642638 3951 False 1195.500000 2194 92.040250 1 3415 4 chr6B.!!$F1 3414
4 TraesCS6D01G311900 chr6B 634940037 634942880 2843 False 586.666667 1194 89.345667 1132 3405 3 chr6B.!!$F2 2273
5 TraesCS6D01G311900 chr6B 634976863 634979412 2549 False 405.000000 497 84.379500 1143 3231 2 chr6B.!!$F3 2088
6 TraesCS6D01G311900 chr6A 564402136 564405677 3541 False 1096.500000 1997 91.920250 1 3415 4 chr6A.!!$F3 3414
7 TraesCS6D01G311900 chr6A 564507684 564510350 2666 False 498.000000 1020 85.028250 782 3405 4 chr6A.!!$F4 2623
8 TraesCS6D01G311900 chr6A 564584662 564586924 2262 False 374.500000 475 82.829000 1143 3231 2 chr6A.!!$F5 2088
9 TraesCS6D01G311900 chr3B 828526134 828526721 587 False 712.000000 712 88.605000 3650 4233 1 chr3B.!!$F1 583
10 TraesCS6D01G311900 chr1A 574300380 574300963 583 False 688.000000 688 87.966000 3650 4235 1 chr1A.!!$F1 585
11 TraesCS6D01G311900 chrUn 37075929 37076514 585 True 678.000000 678 87.627000 3650 4235 1 chrUn.!!$R1 585
12 TraesCS6D01G311900 chr4A 211389649 211390221 572 True 616.000000 616 86.078000 3650 4235 1 chr4A.!!$R1 585
13 TraesCS6D01G311900 chr4A 11309344 11309912 568 False 569.000000 569 84.823000 3646 4233 1 chr4A.!!$F1 587
14 TraesCS6D01G311900 chr3D 589415694 589416233 539 False 616.000000 616 87.316000 3696 4235 1 chr3D.!!$F1 539

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
473 549 0.673644 ACGGCCTCTTCAAACATCCG 60.674 55.0 0.00 0.0 40.98 4.18 F
2037 3762 0.248134 GGACTCGACTTCGTGATCGG 60.248 60.0 7.64 0.7 38.86 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 4034 1.256376 GAGTGCACGCGATTAGTCATG 59.744 52.381 15.93 0.00 0.0 3.07 R
3615 6028 0.035152 AGGCTCGGATGATTGCAACA 60.035 50.000 0.00 2.38 0.0 3.33 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
56 57 3.669251 AAGAGAGAGTGAAAACTCCCG 57.331 47.619 2.32 0.00 37.46 5.14
57 58 1.896465 AGAGAGAGTGAAAACTCCCGG 59.104 52.381 0.00 0.00 37.46 5.73
169 173 9.399403 CTCCTTTTTGTAAGTTTCTATTTCAGC 57.601 33.333 0.00 0.00 0.00 4.26
176 180 5.864628 AAGTTTCTATTTCAGCTTCCGTC 57.135 39.130 0.00 0.00 0.00 4.79
277 352 4.235762 AACGCGTCCTGTGCCTGT 62.236 61.111 14.44 0.00 0.00 4.00
278 353 4.969196 ACGCGTCCTGTGCCTGTG 62.969 66.667 5.58 0.00 0.00 3.66
285 360 2.675423 CTGTGCCTGTGCCTGCAT 60.675 61.111 0.00 0.00 40.07 3.96
333 409 2.176247 ACCCCGAGTTGTAGGATGAT 57.824 50.000 0.00 0.00 0.00 2.45
467 543 2.676076 GTACGTAACGGCCTCTTCAAA 58.324 47.619 0.00 0.00 0.00 2.69
468 544 1.505425 ACGTAACGGCCTCTTCAAAC 58.495 50.000 0.00 0.00 0.00 2.93
469 545 1.202557 ACGTAACGGCCTCTTCAAACA 60.203 47.619 0.00 0.00 0.00 2.83
470 546 2.073816 CGTAACGGCCTCTTCAAACAT 58.926 47.619 0.00 0.00 0.00 2.71
471 547 2.093783 CGTAACGGCCTCTTCAAACATC 59.906 50.000 0.00 0.00 0.00 3.06
472 548 1.534729 AACGGCCTCTTCAAACATCC 58.465 50.000 0.00 0.00 0.00 3.51
473 549 0.673644 ACGGCCTCTTCAAACATCCG 60.674 55.000 0.00 0.00 40.98 4.18
527 648 6.148480 GCACATCCTGATCTACACAATTATCC 59.852 42.308 0.00 0.00 0.00 2.59
615 736 7.431249 CAGAGTAATGGCAATTATTTCATGCT 58.569 34.615 0.00 0.00 39.94 3.79
686 810 3.058293 TGCCAAAGTAAGCTTGTTCATCG 60.058 43.478 9.86 0.00 34.71 3.84
750 874 4.342674 CGTACGCAACGCAACGCA 62.343 61.111 0.52 0.00 46.10 5.24
760 890 2.649349 GCAACGCAAACGCAACGA 60.649 55.556 0.00 0.00 45.53 3.85
797 927 2.514592 CATGCCGGTCGATTGCCT 60.515 61.111 1.90 0.00 0.00 4.75
881 1011 2.125952 TCGTCTCCATGCACAGCG 60.126 61.111 0.00 0.00 0.00 5.18
935 1067 1.347097 CTGATCACCTGCACGACGTG 61.347 60.000 23.43 23.43 36.51 4.49
967 1099 5.923114 CAGCTCTAGTTTCGCATACATACAT 59.077 40.000 0.00 0.00 0.00 2.29
968 1100 7.084486 CAGCTCTAGTTTCGCATACATACATA 58.916 38.462 0.00 0.00 0.00 2.29
969 1101 7.061210 CAGCTCTAGTTTCGCATACATACATAC 59.939 40.741 0.00 0.00 0.00 2.39
970 1102 6.861572 GCTCTAGTTTCGCATACATACATACA 59.138 38.462 0.00 0.00 0.00 2.29
971 1103 7.148950 GCTCTAGTTTCGCATACATACATACAC 60.149 40.741 0.00 0.00 0.00 2.90
972 1104 7.708998 TCTAGTTTCGCATACATACATACACA 58.291 34.615 0.00 0.00 0.00 3.72
973 1105 6.583912 AGTTTCGCATACATACATACACAC 57.416 37.500 0.00 0.00 0.00 3.82
974 1106 6.103330 AGTTTCGCATACATACATACACACA 58.897 36.000 0.00 0.00 0.00 3.72
975 1107 6.761242 AGTTTCGCATACATACATACACACAT 59.239 34.615 0.00 0.00 0.00 3.21
994 1126 8.646900 ACACACATACATACATACATCCATACA 58.353 33.333 0.00 0.00 0.00 2.29
1035 1167 4.201679 CGGCGGCTGATGGTCGTA 62.202 66.667 7.61 0.00 45.81 3.43
1146 1281 2.365237 AACGGGGGAGTAGAGGCC 60.365 66.667 0.00 0.00 0.00 5.19
1450 1608 6.018669 CGCTAGAGTAAATCTTTGGAACATCC 60.019 42.308 0.00 0.00 37.62 3.51
1455 1613 8.797438 AGAGTAAATCTTTGGAACATCCTTTTC 58.203 33.333 0.00 0.00 39.30 2.29
1462 1620 7.047271 TCTTTGGAACATCCTTTTCTTTTTGG 58.953 34.615 0.00 0.00 39.30 3.28
1465 1623 4.102524 GGAACATCCTTTTCTTTTTGGGGT 59.897 41.667 0.00 0.00 32.53 4.95
1466 1624 5.305902 GGAACATCCTTTTCTTTTTGGGGTA 59.694 40.000 0.00 0.00 32.53 3.69
1470 1628 8.499288 ACATCCTTTTCTTTTTGGGGTAAATA 57.501 30.769 0.00 0.00 0.00 1.40
1472 1630 9.958180 CATCCTTTTCTTTTTGGGGTAAATATT 57.042 29.630 0.00 0.00 0.00 1.28
1475 1633 9.008965 CCTTTTCTTTTTGGGGTAAATATTTGG 57.991 33.333 11.05 0.00 0.00 3.28
1476 1634 9.785982 CTTTTCTTTTTGGGGTAAATATTTGGA 57.214 29.630 11.05 0.00 0.00 3.53
1579 1749 7.442364 TCCGTCGCAGTAAAGTTATAGTAGTAT 59.558 37.037 0.00 0.00 0.00 2.12
1690 2363 8.661352 AAAATAACCACATGTTCTTTTTCTGG 57.339 30.769 0.00 0.00 39.06 3.86
1785 3243 8.887264 AAAAGTTTCCATTGTATATACCACCA 57.113 30.769 10.38 0.00 0.00 4.17
1786 3244 8.887264 AAAGTTTCCATTGTATATACCACCAA 57.113 30.769 10.38 0.00 0.00 3.67
1787 3245 9.487442 AAAGTTTCCATTGTATATACCACCAAT 57.513 29.630 10.38 0.99 0.00 3.16
1788 3246 9.487442 AAGTTTCCATTGTATATACCACCAATT 57.513 29.630 10.38 0.00 0.00 2.32
1933 3555 6.566141 TGCACCAATTCATGATGAACATTAG 58.434 36.000 10.45 2.57 39.45 1.73
1945 3608 9.920826 CATGATGAACATTAGTAACATACACAC 57.079 33.333 0.00 0.00 37.07 3.82
2023 3748 8.740906 TGTCTCGATATATTAATTCAGGGACTC 58.259 37.037 0.00 0.00 34.60 3.36
2037 3762 0.248134 GGACTCGACTTCGTGATCGG 60.248 60.000 7.64 0.70 38.86 4.18
2232 4018 3.450115 CAGTCCCGTCCCGTCCTC 61.450 72.222 0.00 0.00 0.00 3.71
2347 4159 1.803334 TCGTTGGCATCTTGTGTACC 58.197 50.000 0.00 0.00 0.00 3.34
2348 4160 0.442310 CGTTGGCATCTTGTGTACCG 59.558 55.000 0.00 0.00 0.00 4.02
2349 4161 1.519408 GTTGGCATCTTGTGTACCGT 58.481 50.000 0.00 0.00 0.00 4.83
2350 4162 2.690786 GTTGGCATCTTGTGTACCGTA 58.309 47.619 0.00 0.00 0.00 4.02
2352 4164 4.435425 GTTGGCATCTTGTGTACCGTATA 58.565 43.478 0.00 0.00 0.00 1.47
2355 4167 3.069158 GGCATCTTGTGTACCGTATACCT 59.931 47.826 3.27 0.00 0.00 3.08
2357 4169 5.114081 GCATCTTGTGTACCGTATACCTTT 58.886 41.667 3.27 0.00 0.00 3.11
2358 4170 5.583457 GCATCTTGTGTACCGTATACCTTTT 59.417 40.000 3.27 0.00 0.00 2.27
2437 4274 1.381429 GCTTCGTGTCGTTAACTCGTC 59.619 52.381 3.71 0.00 43.50 4.20
2485 4324 2.822764 ACGAGAGTCAACAACTTCACC 58.177 47.619 0.00 0.00 44.19 4.02
2491 4330 2.093128 AGTCAACAACTTCACCGGAGTT 60.093 45.455 9.46 4.47 33.03 3.01
2943 4946 0.464373 AGAAATGGATGGCGTCGCAT 60.464 50.000 20.50 10.56 0.00 4.73
3248 5654 1.226435 CGTGAGTCTAGCCTGCGTC 60.226 63.158 0.00 0.00 0.00 5.19
3250 5656 0.179150 GTGAGTCTAGCCTGCGTCTG 60.179 60.000 0.00 0.00 0.00 3.51
3251 5657 1.226831 GAGTCTAGCCTGCGTCTGC 60.227 63.158 0.00 0.00 43.20 4.26
3415 5828 4.041740 ACACATGTAGTACGTGGCATAG 57.958 45.455 23.22 11.63 39.36 2.23
3416 5829 3.446161 ACACATGTAGTACGTGGCATAGT 59.554 43.478 23.22 12.14 39.36 2.12
3417 5830 4.641541 ACACATGTAGTACGTGGCATAGTA 59.358 41.667 23.22 0.00 39.36 1.82
3418 5831 5.125900 ACACATGTAGTACGTGGCATAGTAA 59.874 40.000 23.22 0.00 39.36 2.24
3419 5832 6.183360 ACACATGTAGTACGTGGCATAGTAAT 60.183 38.462 23.22 10.04 39.36 1.89
3420 5833 7.013559 ACACATGTAGTACGTGGCATAGTAATA 59.986 37.037 23.22 7.90 39.36 0.98
3421 5834 7.863877 CACATGTAGTACGTGGCATAGTAATAA 59.136 37.037 23.22 6.46 39.36 1.40
3422 5835 8.415553 ACATGTAGTACGTGGCATAGTAATAAA 58.584 33.333 23.22 9.27 39.36 1.40
3423 5836 8.912658 CATGTAGTACGTGGCATAGTAATAAAG 58.087 37.037 13.81 5.12 31.65 1.85
3424 5837 8.224389 TGTAGTACGTGGCATAGTAATAAAGA 57.776 34.615 12.42 1.80 0.00 2.52
3425 5838 8.853126 TGTAGTACGTGGCATAGTAATAAAGAT 58.147 33.333 12.42 0.00 0.00 2.40
3426 5839 9.688592 GTAGTACGTGGCATAGTAATAAAGATT 57.311 33.333 12.42 0.00 0.00 2.40
3430 5843 8.374327 ACGTGGCATAGTAATAAAGATTTACC 57.626 34.615 0.00 0.00 31.31 2.85
3431 5844 8.208903 ACGTGGCATAGTAATAAAGATTTACCT 58.791 33.333 0.00 0.00 31.31 3.08
3432 5845 8.709646 CGTGGCATAGTAATAAAGATTTACCTC 58.290 37.037 0.00 0.00 31.31 3.85
3433 5846 9.000486 GTGGCATAGTAATAAAGATTTACCTCC 58.000 37.037 0.00 0.00 31.31 4.30
3434 5847 8.945193 TGGCATAGTAATAAAGATTTACCTCCT 58.055 33.333 0.00 0.00 31.31 3.69
3476 5889 1.283736 AAAAATAGGGCGACGCTACG 58.716 50.000 20.77 0.00 31.96 3.51
3498 5911 2.817834 CGCCGGCGGAGATTCAAA 60.818 61.111 40.50 0.00 35.56 2.69
3499 5912 2.813179 CGCCGGCGGAGATTCAAAG 61.813 63.158 40.50 8.19 35.56 2.77
3500 5913 1.449601 GCCGGCGGAGATTCAAAGA 60.450 57.895 33.44 0.00 0.00 2.52
3501 5914 1.432270 GCCGGCGGAGATTCAAAGAG 61.432 60.000 33.44 0.00 0.00 2.85
3502 5915 0.811616 CCGGCGGAGATTCAAAGAGG 60.812 60.000 24.41 0.00 0.00 3.69
3503 5916 0.175760 CGGCGGAGATTCAAAGAGGA 59.824 55.000 0.00 0.00 0.00 3.71
3504 5917 1.202580 CGGCGGAGATTCAAAGAGGAT 60.203 52.381 0.00 0.00 0.00 3.24
3505 5918 2.488952 GGCGGAGATTCAAAGAGGATC 58.511 52.381 0.00 0.00 0.00 3.36
3506 5919 2.488952 GCGGAGATTCAAAGAGGATCC 58.511 52.381 2.48 2.48 33.66 3.36
3507 5920 2.748605 CGGAGATTCAAAGAGGATCCG 58.251 52.381 5.98 0.00 41.80 4.18
3508 5921 2.101582 CGGAGATTCAAAGAGGATCCGT 59.898 50.000 5.98 0.00 42.40 4.69
3509 5922 3.723260 GGAGATTCAAAGAGGATCCGTC 58.277 50.000 5.98 4.61 33.66 4.79
3510 5923 3.133003 GGAGATTCAAAGAGGATCCGTCA 59.867 47.826 5.98 0.00 33.66 4.35
3511 5924 4.116238 GAGATTCAAAGAGGATCCGTCAC 58.884 47.826 5.98 0.00 33.66 3.67
3512 5925 2.762535 TTCAAAGAGGATCCGTCACC 57.237 50.000 5.98 0.00 33.66 4.02
3513 5926 1.938585 TCAAAGAGGATCCGTCACCT 58.061 50.000 5.98 0.00 39.41 4.00
3514 5927 2.257207 TCAAAGAGGATCCGTCACCTT 58.743 47.619 5.98 3.59 36.57 3.50
3515 5928 2.028112 TCAAAGAGGATCCGTCACCTTG 60.028 50.000 5.98 5.99 36.57 3.61
3516 5929 0.250513 AAGAGGATCCGTCACCTTGC 59.749 55.000 5.98 0.00 36.57 4.01
3517 5930 0.616111 AGAGGATCCGTCACCTTGCT 60.616 55.000 5.98 0.00 36.57 3.91
3518 5931 0.460987 GAGGATCCGTCACCTTGCTG 60.461 60.000 5.98 0.00 36.57 4.41
3519 5932 0.904865 AGGATCCGTCACCTTGCTGA 60.905 55.000 5.98 0.00 31.95 4.26
3520 5933 0.741221 GGATCCGTCACCTTGCTGAC 60.741 60.000 0.00 0.00 37.75 3.51
3521 5934 0.741221 GATCCGTCACCTTGCTGACC 60.741 60.000 0.00 0.00 37.83 4.02
3522 5935 1.480212 ATCCGTCACCTTGCTGACCA 61.480 55.000 0.00 0.00 37.83 4.02
3523 5936 1.003355 CCGTCACCTTGCTGACCAT 60.003 57.895 0.00 0.00 37.83 3.55
3524 5937 0.606401 CCGTCACCTTGCTGACCATT 60.606 55.000 0.00 0.00 37.83 3.16
3525 5938 0.518636 CGTCACCTTGCTGACCATTG 59.481 55.000 0.00 0.00 37.83 2.82
3526 5939 0.883833 GTCACCTTGCTGACCATTGG 59.116 55.000 0.00 0.00 35.44 3.16
3527 5940 0.770499 TCACCTTGCTGACCATTGGA 59.230 50.000 10.37 0.00 0.00 3.53
3528 5941 1.355381 TCACCTTGCTGACCATTGGAT 59.645 47.619 10.37 0.00 0.00 3.41
3529 5942 1.747355 CACCTTGCTGACCATTGGATC 59.253 52.381 10.37 4.12 0.00 3.36
3530 5943 1.019673 CCTTGCTGACCATTGGATCG 58.980 55.000 10.37 0.00 0.00 3.69
3531 5944 1.407299 CCTTGCTGACCATTGGATCGA 60.407 52.381 10.37 0.00 0.00 3.59
3532 5945 1.667724 CTTGCTGACCATTGGATCGAC 59.332 52.381 10.37 0.96 0.00 4.20
3533 5946 0.612744 TGCTGACCATTGGATCGACA 59.387 50.000 10.37 3.38 0.00 4.35
3534 5947 1.009829 GCTGACCATTGGATCGACAC 58.990 55.000 10.37 0.00 0.00 3.67
3535 5948 1.675714 GCTGACCATTGGATCGACACA 60.676 52.381 10.37 0.00 0.00 3.72
3536 5949 2.910199 CTGACCATTGGATCGACACAT 58.090 47.619 10.37 0.00 0.00 3.21
3537 5950 3.273434 CTGACCATTGGATCGACACATT 58.727 45.455 10.37 0.00 0.00 2.71
3538 5951 4.441792 CTGACCATTGGATCGACACATTA 58.558 43.478 10.37 0.00 0.00 1.90
3539 5952 4.837972 TGACCATTGGATCGACACATTAA 58.162 39.130 10.37 0.00 0.00 1.40
3540 5953 5.436175 TGACCATTGGATCGACACATTAAT 58.564 37.500 10.37 0.00 0.00 1.40
3541 5954 5.296531 TGACCATTGGATCGACACATTAATG 59.703 40.000 14.01 14.01 0.00 1.90
3542 5955 5.436175 ACCATTGGATCGACACATTAATGA 58.564 37.500 22.16 0.00 0.00 2.57
3543 5956 5.296780 ACCATTGGATCGACACATTAATGAC 59.703 40.000 22.16 11.17 0.00 3.06
3544 5957 5.277974 CCATTGGATCGACACATTAATGACC 60.278 44.000 22.16 12.14 0.00 4.02
3545 5958 3.453424 TGGATCGACACATTAATGACCG 58.547 45.455 22.16 18.75 0.00 4.79
3546 5959 3.118920 TGGATCGACACATTAATGACCGT 60.119 43.478 22.16 14.57 0.00 4.83
3547 5960 3.489785 GGATCGACACATTAATGACCGTC 59.510 47.826 22.16 20.11 0.00 4.79
3548 5961 2.883574 TCGACACATTAATGACCGTCC 58.116 47.619 22.16 8.75 0.00 4.79
3549 5962 1.586578 CGACACATTAATGACCGTCCG 59.413 52.381 22.16 14.77 0.00 4.79
3550 5963 2.732912 CGACACATTAATGACCGTCCGA 60.733 50.000 22.16 0.00 0.00 4.55
3551 5964 3.454375 GACACATTAATGACCGTCCGAT 58.546 45.455 22.16 0.00 0.00 4.18
3552 5965 3.454375 ACACATTAATGACCGTCCGATC 58.546 45.455 22.16 0.00 0.00 3.69
3553 5966 3.132289 ACACATTAATGACCGTCCGATCT 59.868 43.478 22.16 0.00 0.00 2.75
3554 5967 4.340097 ACACATTAATGACCGTCCGATCTA 59.660 41.667 22.16 0.00 0.00 1.98
3555 5968 4.680110 CACATTAATGACCGTCCGATCTAC 59.320 45.833 22.16 0.00 0.00 2.59
3556 5969 3.996150 TTAATGACCGTCCGATCTACC 57.004 47.619 0.00 0.00 0.00 3.18
3557 5970 1.771565 AATGACCGTCCGATCTACCA 58.228 50.000 0.00 0.00 0.00 3.25
3558 5971 1.771565 ATGACCGTCCGATCTACCAA 58.228 50.000 0.00 0.00 0.00 3.67
3559 5972 0.813184 TGACCGTCCGATCTACCAAC 59.187 55.000 0.00 0.00 0.00 3.77
3560 5973 0.248377 GACCGTCCGATCTACCAACG 60.248 60.000 0.00 0.00 0.00 4.10
3561 5974 0.962356 ACCGTCCGATCTACCAACGT 60.962 55.000 0.00 0.00 0.00 3.99
3562 5975 1.016627 CCGTCCGATCTACCAACGTA 58.983 55.000 0.00 0.00 0.00 3.57
3563 5976 1.401552 CCGTCCGATCTACCAACGTAA 59.598 52.381 0.00 0.00 0.00 3.18
3564 5977 2.444351 CGTCCGATCTACCAACGTAAC 58.556 52.381 0.00 0.00 0.00 2.50
3565 5978 2.096496 CGTCCGATCTACCAACGTAACT 59.904 50.000 0.00 0.00 0.00 2.24
3566 5979 3.426695 CGTCCGATCTACCAACGTAACTT 60.427 47.826 0.00 0.00 0.00 2.66
3567 5980 4.201812 CGTCCGATCTACCAACGTAACTTA 60.202 45.833 0.00 0.00 0.00 2.24
3568 5981 5.640732 GTCCGATCTACCAACGTAACTTAA 58.359 41.667 0.00 0.00 0.00 1.85
3569 5982 5.741040 GTCCGATCTACCAACGTAACTTAAG 59.259 44.000 0.00 0.00 0.00 1.85
3570 5983 4.501921 CCGATCTACCAACGTAACTTAAGC 59.498 45.833 1.29 0.00 0.00 3.09
3571 5984 5.097529 CGATCTACCAACGTAACTTAAGCA 58.902 41.667 1.29 0.00 0.00 3.91
3572 5985 5.229469 CGATCTACCAACGTAACTTAAGCAG 59.771 44.000 1.29 0.00 0.00 4.24
3573 5986 4.240096 TCTACCAACGTAACTTAAGCAGC 58.760 43.478 1.29 0.00 0.00 5.25
3574 5987 2.148768 ACCAACGTAACTTAAGCAGCC 58.851 47.619 1.29 0.00 0.00 4.85
3575 5988 2.147958 CCAACGTAACTTAAGCAGCCA 58.852 47.619 1.29 0.00 0.00 4.75
3576 5989 2.095919 CCAACGTAACTTAAGCAGCCAC 60.096 50.000 1.29 0.00 0.00 5.01
3577 5990 1.804601 ACGTAACTTAAGCAGCCACC 58.195 50.000 1.29 0.00 0.00 4.61
3578 5991 1.084289 CGTAACTTAAGCAGCCACCC 58.916 55.000 1.29 0.00 0.00 4.61
3579 5992 1.338769 CGTAACTTAAGCAGCCACCCT 60.339 52.381 1.29 0.00 0.00 4.34
3580 5993 2.791655 GTAACTTAAGCAGCCACCCTT 58.208 47.619 1.29 0.00 0.00 3.95
3581 5994 2.381752 AACTTAAGCAGCCACCCTTT 57.618 45.000 1.29 0.00 0.00 3.11
3582 5995 1.620822 ACTTAAGCAGCCACCCTTTG 58.379 50.000 1.29 0.00 0.00 2.77
3583 5996 0.244721 CTTAAGCAGCCACCCTTTGC 59.755 55.000 0.00 0.00 38.09 3.68
3584 5997 0.468958 TTAAGCAGCCACCCTTTGCA 60.469 50.000 0.00 0.00 40.22 4.08
3585 5998 0.468958 TAAGCAGCCACCCTTTGCAA 60.469 50.000 0.00 0.00 40.22 4.08
3586 5999 2.029518 GCAGCCACCCTTTGCAAC 59.970 61.111 0.00 0.00 37.75 4.17
3587 6000 2.795110 GCAGCCACCCTTTGCAACA 61.795 57.895 0.00 0.00 37.75 3.33
3588 6001 1.821936 CAGCCACCCTTTGCAACAA 59.178 52.632 0.00 0.00 0.00 2.83
3589 6002 0.249573 CAGCCACCCTTTGCAACAAG 60.250 55.000 0.00 0.00 0.00 3.16
3590 6003 0.396974 AGCCACCCTTTGCAACAAGA 60.397 50.000 0.00 0.00 0.00 3.02
3591 6004 0.463620 GCCACCCTTTGCAACAAGAA 59.536 50.000 0.00 0.00 0.00 2.52
3592 6005 1.806247 GCCACCCTTTGCAACAAGAAC 60.806 52.381 0.00 0.00 0.00 3.01
3593 6006 1.535860 CCACCCTTTGCAACAAGAACG 60.536 52.381 0.00 0.00 0.00 3.95
3594 6007 0.744281 ACCCTTTGCAACAAGAACGG 59.256 50.000 0.00 0.00 0.00 4.44
3595 6008 0.744281 CCCTTTGCAACAAGAACGGT 59.256 50.000 0.00 0.00 0.00 4.83
3596 6009 1.535860 CCCTTTGCAACAAGAACGGTG 60.536 52.381 0.00 0.00 0.00 4.94
3597 6010 1.134175 CCTTTGCAACAAGAACGGTGT 59.866 47.619 0.00 0.00 0.00 4.16
3598 6011 2.416701 CCTTTGCAACAAGAACGGTGTT 60.417 45.455 0.00 0.00 39.79 3.32
3599 6012 3.249917 CTTTGCAACAAGAACGGTGTTT 58.750 40.909 0.00 0.00 37.09 2.83
3600 6013 2.553079 TGCAACAAGAACGGTGTTTC 57.447 45.000 0.00 0.00 37.09 2.78
3601 6014 2.088423 TGCAACAAGAACGGTGTTTCT 58.912 42.857 0.00 0.00 37.09 2.52
3602 6015 2.159448 TGCAACAAGAACGGTGTTTCTG 60.159 45.455 0.00 0.00 37.09 3.02
3603 6016 2.159435 GCAACAAGAACGGTGTTTCTGT 60.159 45.455 0.00 0.00 37.09 3.41
3604 6017 3.064271 GCAACAAGAACGGTGTTTCTGTA 59.936 43.478 0.00 0.00 37.09 2.74
3605 6018 4.437659 GCAACAAGAACGGTGTTTCTGTAA 60.438 41.667 0.00 0.00 37.09 2.41
3606 6019 4.870221 ACAAGAACGGTGTTTCTGTAAC 57.130 40.909 0.00 0.00 35.92 2.50
3607 6020 4.255301 ACAAGAACGGTGTTTCTGTAACA 58.745 39.130 0.00 0.00 44.31 2.41
3608 6021 4.331717 ACAAGAACGGTGTTTCTGTAACAG 59.668 41.667 0.00 0.00 46.95 3.16
3609 6022 4.133013 AGAACGGTGTTTCTGTAACAGT 57.867 40.909 0.00 0.00 46.95 3.55
3610 6023 4.117685 AGAACGGTGTTTCTGTAACAGTC 58.882 43.478 0.00 0.00 46.95 3.51
3611 6024 3.814005 ACGGTGTTTCTGTAACAGTCT 57.186 42.857 0.00 0.00 46.95 3.24
3612 6025 3.454375 ACGGTGTTTCTGTAACAGTCTG 58.546 45.455 0.00 0.00 46.95 3.51
3613 6026 2.221055 CGGTGTTTCTGTAACAGTCTGC 59.779 50.000 0.00 0.00 46.95 4.26
3614 6027 3.467803 GGTGTTTCTGTAACAGTCTGCT 58.532 45.455 0.00 0.00 46.95 4.24
3615 6028 3.877508 GGTGTTTCTGTAACAGTCTGCTT 59.122 43.478 0.00 0.00 46.95 3.91
3616 6029 4.260784 GGTGTTTCTGTAACAGTCTGCTTG 60.261 45.833 0.00 0.00 46.95 4.01
3617 6030 4.332819 GTGTTTCTGTAACAGTCTGCTTGT 59.667 41.667 0.00 0.00 46.95 3.16
3618 6031 4.941263 TGTTTCTGTAACAGTCTGCTTGTT 59.059 37.500 0.00 0.00 41.73 2.83
3619 6032 5.163764 TGTTTCTGTAACAGTCTGCTTGTTG 60.164 40.000 0.00 0.00 41.73 3.33
3620 6033 2.872245 TCTGTAACAGTCTGCTTGTTGC 59.128 45.455 0.00 0.69 36.06 4.17
3621 6034 3.681313 TCTGTAACAGTCTGCTTGTTGCA 60.681 43.478 0.00 8.25 39.98 4.08
3622 6035 5.160721 TCTGTAACAGTCTGCTTGTTGCAA 61.161 41.667 0.00 0.00 40.90 4.08
3623 6036 6.433522 TCTGTAACAGTCTGCTTGTTGCAAT 61.434 40.000 0.59 0.00 40.90 3.56
3624 6037 8.159645 TCTGTAACAGTCTGCTTGTTGCAATC 62.160 42.308 0.59 0.00 40.90 2.67
3631 6044 2.184385 GCTTGTTGCAATCATCCGAG 57.816 50.000 0.59 0.00 42.31 4.63
3632 6045 1.796617 GCTTGTTGCAATCATCCGAGC 60.797 52.381 0.59 6.44 42.31 5.03
3633 6046 0.810648 TTGTTGCAATCATCCGAGCC 59.189 50.000 0.59 0.00 0.00 4.70
3634 6047 0.035152 TGTTGCAATCATCCGAGCCT 60.035 50.000 0.59 0.00 0.00 4.58
3635 6048 0.379669 GTTGCAATCATCCGAGCCTG 59.620 55.000 0.59 0.00 0.00 4.85
3636 6049 0.035152 TTGCAATCATCCGAGCCTGT 60.035 50.000 0.00 0.00 0.00 4.00
3637 6050 0.829990 TGCAATCATCCGAGCCTGTA 59.170 50.000 0.00 0.00 0.00 2.74
3638 6051 1.417517 TGCAATCATCCGAGCCTGTAT 59.582 47.619 0.00 0.00 0.00 2.29
3639 6052 2.158769 TGCAATCATCCGAGCCTGTATT 60.159 45.455 0.00 0.00 0.00 1.89
3640 6053 2.880890 GCAATCATCCGAGCCTGTATTT 59.119 45.455 0.00 0.00 0.00 1.40
3641 6054 3.316308 GCAATCATCCGAGCCTGTATTTT 59.684 43.478 0.00 0.00 0.00 1.82
3642 6055 4.202050 GCAATCATCCGAGCCTGTATTTTT 60.202 41.667 0.00 0.00 0.00 1.94
3697 6110 2.096496 CGTCCGATCTACCAACGTAACT 59.904 50.000 0.00 0.00 0.00 2.24
3714 6127 3.518992 AACTTAAGCAGCCACCCTTTA 57.481 42.857 1.29 0.00 0.00 1.85
3723 6136 2.955660 CAGCCACCCTTTACAACAAGAA 59.044 45.455 0.00 0.00 0.00 2.52
3724 6137 2.956333 AGCCACCCTTTACAACAAGAAC 59.044 45.455 0.00 0.00 0.00 3.01
3735 6148 3.078837 ACAACAAGAACGGTGTTTCTGT 58.921 40.909 0.00 0.00 37.09 3.41
3845 6260 8.822652 AGATCTTGTTGCAGAAATTTTAAAGG 57.177 30.769 0.00 0.00 0.00 3.11
3848 6263 6.695278 TCTTGTTGCAGAAATTTTAAAGGTCG 59.305 34.615 0.00 0.00 0.00 4.79
3851 6266 3.319405 TGCAGAAATTTTAAAGGTCGCCA 59.681 39.130 0.00 0.00 0.00 5.69
3856 6271 4.929819 AATTTTAAAGGTCGCCAGTGTT 57.070 36.364 0.00 0.00 0.00 3.32
3886 6301 9.301153 GTTCTTTTTATTTTCTGCAACAGAGAA 57.699 29.630 3.40 3.40 41.75 2.87
3974 6391 4.036734 CCTCTTTGCAACAAGAGCTTTGTA 59.963 41.667 18.82 0.00 40.80 2.41
3978 6395 4.488126 TGCAACAAGAGCTTTGTATCAC 57.512 40.909 12.60 5.89 31.50 3.06
3984 6401 6.449635 ACAAGAGCTTTGTATCACAAACAA 57.550 33.333 11.11 0.00 42.55 2.83
4032 6451 1.885887 CAGAAACATGCTCCCCGAAAA 59.114 47.619 0.00 0.00 0.00 2.29
4190 6609 7.254137 CGTTTTCTTCATCTCTCTGTATCTCA 58.746 38.462 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 0.676466 TTCCGCATCCACACATGTCC 60.676 55.000 0.00 0.00 0.00 4.02
57 58 1.382522 ATTCCGCATCCACACATGTC 58.617 50.000 0.00 0.00 0.00 3.06
169 173 1.281899 GAGCGGAATCTTGACGGAAG 58.718 55.000 0.00 0.00 0.00 3.46
176 180 4.498682 GGATCAAAATGGAGCGGAATCTTG 60.499 45.833 0.00 0.00 0.00 3.02
321 397 6.157211 CGGTTATCTGGTATCATCCTACAAC 58.843 44.000 0.00 0.00 0.00 3.32
333 409 0.263765 AGGAGGGCGGTTATCTGGTA 59.736 55.000 0.00 0.00 0.00 3.25
399 475 2.354510 CGTACGTTCCATACCTCCGTTA 59.645 50.000 7.22 0.00 33.32 3.18
486 607 1.601903 TGTGCATGAGAAACGACCAAC 59.398 47.619 0.00 0.00 0.00 3.77
615 736 6.373005 TGCAGGCTTTCCTTAGCATATATA 57.627 37.500 0.00 0.00 41.93 0.86
881 1011 6.461816 CAATATATCTTCGCTGCGAATGTAC 58.538 40.000 33.97 0.00 44.85 2.90
935 1067 0.322008 AAACTAGAGCTGCTGTGGCC 60.322 55.000 7.01 0.00 37.74 5.36
968 1100 8.646900 TGTATGGATGTATGTATGTATGTGTGT 58.353 33.333 0.00 0.00 0.00 3.72
969 1101 9.657419 ATGTATGGATGTATGTATGTATGTGTG 57.343 33.333 0.00 0.00 0.00 3.82
973 1105 9.481340 GCCTATGTATGGATGTATGTATGTATG 57.519 37.037 0.00 0.00 0.00 2.39
974 1106 9.212593 TGCCTATGTATGGATGTATGTATGTAT 57.787 33.333 0.00 0.00 0.00 2.29
975 1107 8.602472 TGCCTATGTATGGATGTATGTATGTA 57.398 34.615 0.00 0.00 0.00 2.29
994 1126 2.196776 GCTGGTGCCCATGCCTAT 59.803 61.111 0.00 0.00 36.33 2.57
1360 1498 4.195334 GCCGGGGGTGATCTGCAT 62.195 66.667 2.18 0.00 0.00 3.96
1420 1575 3.906720 AAGATTTACTCTAGCGCCCAA 57.093 42.857 2.29 0.00 32.41 4.12
1422 1577 2.872858 CCAAAGATTTACTCTAGCGCCC 59.127 50.000 2.29 0.00 32.41 6.13
1450 1608 9.785982 TCCAAATATTTACCCCAAAAAGAAAAG 57.214 29.630 0.00 0.00 0.00 2.27
1470 1628 9.877178 TTGGCGTGTAATTAATATTTTCCAAAT 57.123 25.926 0.00 0.00 0.00 2.32
1472 1630 9.360093 CTTTGGCGTGTAATTAATATTTTCCAA 57.640 29.630 0.00 0.00 0.00 3.53
1473 1631 8.740906 TCTTTGGCGTGTAATTAATATTTTCCA 58.259 29.630 0.00 0.00 0.00 3.53
1477 1635 9.893305 GCTATCTTTGGCGTGTAATTAATATTT 57.107 29.630 0.00 0.00 0.00 1.40
1478 1636 9.284968 AGCTATCTTTGGCGTGTAATTAATATT 57.715 29.630 0.00 0.00 33.93 1.28
1579 1749 3.748083 AGCGTATCCGTCTATCTAACCA 58.252 45.455 0.00 0.00 36.15 3.67
1672 2338 4.262164 CCTTCCCAGAAAAAGAACATGTGG 60.262 45.833 0.00 0.00 0.00 4.17
1687 2360 8.469309 AATTACATGTGATTATTCCTTCCCAG 57.531 34.615 13.74 0.00 0.00 4.45
1782 3240 6.043822 AGCAAACTTTTACCCCATTAATTGGT 59.956 34.615 10.48 10.48 44.83 3.67
1785 3243 7.553504 AGAGCAAACTTTTACCCCATTAATT 57.446 32.000 0.00 0.00 0.00 1.40
1786 3244 7.553504 AAGAGCAAACTTTTACCCCATTAAT 57.446 32.000 0.00 0.00 0.00 1.40
1787 3245 6.987403 AAGAGCAAACTTTTACCCCATTAA 57.013 33.333 0.00 0.00 0.00 1.40
1788 3246 6.987403 AAAGAGCAAACTTTTACCCCATTA 57.013 33.333 0.00 0.00 36.84 1.90
1789 3247 5.887214 AAAGAGCAAACTTTTACCCCATT 57.113 34.783 0.00 0.00 36.84 3.16
2023 3748 1.513373 TTCGCCGATCACGAAGTCG 60.513 57.895 14.58 0.00 44.01 4.18
2037 3762 2.692109 CTCGCTTCTTCGCTTCGC 59.308 61.111 0.00 0.00 0.00 4.70
2238 4026 2.190161 GCGATTAGTCATGCACGTGTA 58.810 47.619 18.38 14.09 0.00 2.90
2246 4034 1.256376 GAGTGCACGCGATTAGTCATG 59.744 52.381 15.93 0.00 0.00 3.07
2365 4177 2.259618 CAGTGCGTATATATGTCCCGC 58.740 52.381 7.51 7.51 44.27 6.13
2366 4178 3.570926 ACAGTGCGTATATATGTCCCG 57.429 47.619 3.92 0.00 0.00 5.14
2367 4179 6.197276 CGTATACAGTGCGTATATATGTCCC 58.803 44.000 3.32 0.00 43.37 4.46
2397 4222 5.405935 AGCATATACGGTGCATATCAAGA 57.594 39.130 0.00 0.00 44.87 3.02
2400 4225 4.173256 CGAAGCATATACGGTGCATATCA 58.827 43.478 0.00 0.00 44.87 2.15
2437 4274 2.394708 CTCTGTTCCACACACGTACAG 58.605 52.381 6.12 6.12 38.00 2.74
2485 4324 1.342082 CGTCCTTGTACGCAACTCCG 61.342 60.000 0.00 0.00 35.87 4.63
2491 4330 2.260434 GGCTCGTCCTTGTACGCA 59.740 61.111 0.00 0.00 42.56 5.24
2797 4774 4.448005 GAAAAATTCGTGCGTCGTTTCTA 58.552 39.130 0.00 0.00 40.80 2.10
2870 4873 1.228245 GGCACCCTGACACACACAT 60.228 57.895 0.00 0.00 0.00 3.21
2982 4985 2.885644 CATCCGAACTCCGCCACG 60.886 66.667 0.00 0.00 36.84 4.94
3025 5034 1.868251 GGAAGTAGTCGTCGCGCTG 60.868 63.158 5.56 0.00 0.00 5.18
3026 5035 2.484203 GGAAGTAGTCGTCGCGCT 59.516 61.111 5.56 0.00 0.00 5.92
3251 5657 1.153449 ACCCATGGATGCGTACACG 60.153 57.895 15.22 0.00 43.27 4.49
3253 5659 0.392327 CACACCCATGGATGCGTACA 60.392 55.000 15.22 0.00 0.00 2.90
3257 5663 1.669049 AATGCACACCCATGGATGCG 61.669 55.000 22.69 10.01 39.74 4.73
3457 5870 1.283736 CGTAGCGTCGCCCTATTTTT 58.716 50.000 14.86 0.00 0.00 1.94
3458 5871 2.967740 CGTAGCGTCGCCCTATTTT 58.032 52.632 14.86 0.00 0.00 1.82
3459 5872 4.724022 CGTAGCGTCGCCCTATTT 57.276 55.556 14.86 0.00 0.00 1.40
3481 5894 2.813179 CTTTGAATCTCCGCCGGCG 61.813 63.158 41.00 41.00 39.44 6.46
3482 5895 1.432270 CTCTTTGAATCTCCGCCGGC 61.432 60.000 19.07 19.07 0.00 6.13
3483 5896 0.811616 CCTCTTTGAATCTCCGCCGG 60.812 60.000 0.00 0.00 0.00 6.13
3484 5897 0.175760 TCCTCTTTGAATCTCCGCCG 59.824 55.000 0.00 0.00 0.00 6.46
3485 5898 2.488952 GATCCTCTTTGAATCTCCGCC 58.511 52.381 0.00 0.00 0.00 6.13
3486 5899 2.488952 GGATCCTCTTTGAATCTCCGC 58.511 52.381 3.84 0.00 0.00 5.54
3487 5900 2.748605 CGGATCCTCTTTGAATCTCCG 58.251 52.381 10.75 0.00 38.31 4.63
3488 5901 3.133003 TGACGGATCCTCTTTGAATCTCC 59.867 47.826 10.75 0.00 0.00 3.71
3489 5902 4.116238 GTGACGGATCCTCTTTGAATCTC 58.884 47.826 10.75 0.00 0.00 2.75
3490 5903 3.118592 GGTGACGGATCCTCTTTGAATCT 60.119 47.826 10.75 0.00 0.00 2.40
3491 5904 3.118592 AGGTGACGGATCCTCTTTGAATC 60.119 47.826 10.75 0.00 0.00 2.52
3492 5905 2.840651 AGGTGACGGATCCTCTTTGAAT 59.159 45.455 10.75 0.00 0.00 2.57
3493 5906 2.257207 AGGTGACGGATCCTCTTTGAA 58.743 47.619 10.75 0.00 0.00 2.69
3494 5907 1.938585 AGGTGACGGATCCTCTTTGA 58.061 50.000 10.75 0.00 0.00 2.69
3495 5908 2.350522 CAAGGTGACGGATCCTCTTTG 58.649 52.381 10.75 6.83 33.09 2.77
3496 5909 1.339151 GCAAGGTGACGGATCCTCTTT 60.339 52.381 10.75 0.00 33.09 2.52
3497 5910 0.250513 GCAAGGTGACGGATCCTCTT 59.749 55.000 10.75 3.11 33.09 2.85
3498 5911 0.616111 AGCAAGGTGACGGATCCTCT 60.616 55.000 10.75 0.00 33.09 3.69
3499 5912 0.460987 CAGCAAGGTGACGGATCCTC 60.461 60.000 10.75 7.19 33.09 3.71
3500 5913 0.904865 TCAGCAAGGTGACGGATCCT 60.905 55.000 10.75 0.00 35.34 3.24
3501 5914 0.741221 GTCAGCAAGGTGACGGATCC 60.741 60.000 15.51 0.00 37.69 3.36
3502 5915 0.741221 GGTCAGCAAGGTGACGGATC 60.741 60.000 21.68 8.08 46.72 3.36
3503 5916 1.296715 GGTCAGCAAGGTGACGGAT 59.703 57.895 21.68 0.00 46.72 4.18
3504 5917 1.480212 ATGGTCAGCAAGGTGACGGA 61.480 55.000 21.68 13.53 46.72 4.69
3505 5918 0.606401 AATGGTCAGCAAGGTGACGG 60.606 55.000 21.68 0.00 46.72 4.79
3506 5919 0.518636 CAATGGTCAGCAAGGTGACG 59.481 55.000 21.68 8.08 46.72 4.35
3507 5920 0.883833 CCAATGGTCAGCAAGGTGAC 59.116 55.000 20.75 20.75 45.30 3.67
3508 5921 0.770499 TCCAATGGTCAGCAAGGTGA 59.230 50.000 0.00 0.00 0.00 4.02
3509 5922 1.747355 GATCCAATGGTCAGCAAGGTG 59.253 52.381 0.00 0.00 0.00 4.00
3510 5923 1.679944 CGATCCAATGGTCAGCAAGGT 60.680 52.381 0.00 0.00 0.00 3.50
3511 5924 1.019673 CGATCCAATGGTCAGCAAGG 58.980 55.000 0.00 0.00 0.00 3.61
3512 5925 1.667724 GTCGATCCAATGGTCAGCAAG 59.332 52.381 0.00 0.00 0.00 4.01
3513 5926 1.003003 TGTCGATCCAATGGTCAGCAA 59.997 47.619 0.00 0.00 0.00 3.91
3514 5927 0.612744 TGTCGATCCAATGGTCAGCA 59.387 50.000 0.00 0.00 0.00 4.41
3515 5928 1.009829 GTGTCGATCCAATGGTCAGC 58.990 55.000 0.00 0.00 0.00 4.26
3516 5929 2.385013 TGTGTCGATCCAATGGTCAG 57.615 50.000 0.00 0.00 0.00 3.51
3517 5930 3.348647 AATGTGTCGATCCAATGGTCA 57.651 42.857 0.00 0.00 0.00 4.02
3518 5931 5.527214 TCATTAATGTGTCGATCCAATGGTC 59.473 40.000 14.97 0.00 0.00 4.02
3519 5932 5.296780 GTCATTAATGTGTCGATCCAATGGT 59.703 40.000 14.97 0.00 0.00 3.55
3520 5933 5.277974 GGTCATTAATGTGTCGATCCAATGG 60.278 44.000 14.97 0.00 0.00 3.16
3521 5934 5.558844 CGGTCATTAATGTGTCGATCCAATG 60.559 44.000 14.97 0.00 0.00 2.82
3522 5935 4.511454 CGGTCATTAATGTGTCGATCCAAT 59.489 41.667 14.97 0.00 0.00 3.16
3523 5936 3.868661 CGGTCATTAATGTGTCGATCCAA 59.131 43.478 14.97 0.00 0.00 3.53
3524 5937 3.118920 ACGGTCATTAATGTGTCGATCCA 60.119 43.478 23.30 0.00 0.00 3.41
3525 5938 3.454375 ACGGTCATTAATGTGTCGATCC 58.546 45.455 23.30 12.66 0.00 3.36
3526 5939 3.489785 GGACGGTCATTAATGTGTCGATC 59.510 47.826 23.30 18.07 0.00 3.69
3527 5940 3.454375 GGACGGTCATTAATGTGTCGAT 58.546 45.455 23.30 13.61 0.00 3.59
3528 5941 2.732912 CGGACGGTCATTAATGTGTCGA 60.733 50.000 23.30 3.15 0.00 4.20
3529 5942 1.586578 CGGACGGTCATTAATGTGTCG 59.413 52.381 14.97 17.12 0.00 4.35
3530 5943 2.883574 TCGGACGGTCATTAATGTGTC 58.116 47.619 14.97 18.21 0.00 3.67
3531 5944 3.132289 AGATCGGACGGTCATTAATGTGT 59.868 43.478 14.97 11.82 0.00 3.72
3532 5945 3.717707 AGATCGGACGGTCATTAATGTG 58.282 45.455 14.97 8.97 0.00 3.21
3533 5946 4.261909 GGTAGATCGGACGGTCATTAATGT 60.262 45.833 14.97 0.00 0.00 2.71
3534 5947 4.235360 GGTAGATCGGACGGTCATTAATG 58.765 47.826 9.29 9.29 0.00 1.90
3535 5948 3.893200 TGGTAGATCGGACGGTCATTAAT 59.107 43.478 10.76 0.00 0.00 1.40
3536 5949 3.289836 TGGTAGATCGGACGGTCATTAA 58.710 45.455 10.76 0.00 0.00 1.40
3537 5950 2.934887 TGGTAGATCGGACGGTCATTA 58.065 47.619 10.76 0.00 0.00 1.90
3538 5951 1.771565 TGGTAGATCGGACGGTCATT 58.228 50.000 10.76 0.00 0.00 2.57
3539 5952 1.407979 GTTGGTAGATCGGACGGTCAT 59.592 52.381 10.76 0.00 0.00 3.06
3540 5953 0.813184 GTTGGTAGATCGGACGGTCA 59.187 55.000 10.76 0.00 0.00 4.02
3541 5954 0.248377 CGTTGGTAGATCGGACGGTC 60.248 60.000 0.00 0.00 0.00 4.79
3542 5955 0.962356 ACGTTGGTAGATCGGACGGT 60.962 55.000 11.74 0.00 37.99 4.83
3543 5956 1.016627 TACGTTGGTAGATCGGACGG 58.983 55.000 0.00 0.00 37.99 4.79
3544 5957 2.096496 AGTTACGTTGGTAGATCGGACG 59.904 50.000 0.00 7.47 39.43 4.79
3545 5958 3.772060 AGTTACGTTGGTAGATCGGAC 57.228 47.619 0.00 0.00 0.00 4.79
3546 5959 5.677091 GCTTAAGTTACGTTGGTAGATCGGA 60.677 44.000 4.02 0.00 0.00 4.55
3547 5960 4.501921 GCTTAAGTTACGTTGGTAGATCGG 59.498 45.833 4.02 0.00 0.00 4.18
3548 5961 5.097529 TGCTTAAGTTACGTTGGTAGATCG 58.902 41.667 4.02 0.00 0.00 3.69
3549 5962 5.005490 GCTGCTTAAGTTACGTTGGTAGATC 59.995 44.000 4.02 0.00 0.00 2.75
3550 5963 4.868734 GCTGCTTAAGTTACGTTGGTAGAT 59.131 41.667 4.02 0.00 0.00 1.98
3551 5964 4.240096 GCTGCTTAAGTTACGTTGGTAGA 58.760 43.478 4.02 0.00 0.00 2.59
3552 5965 3.370061 GGCTGCTTAAGTTACGTTGGTAG 59.630 47.826 4.02 0.00 0.00 3.18
3553 5966 3.244146 TGGCTGCTTAAGTTACGTTGGTA 60.244 43.478 4.02 0.00 0.00 3.25
3554 5967 2.148768 GGCTGCTTAAGTTACGTTGGT 58.851 47.619 4.02 0.00 0.00 3.67
3555 5968 2.095919 GTGGCTGCTTAAGTTACGTTGG 60.096 50.000 4.02 0.00 0.00 3.77
3556 5969 2.095919 GGTGGCTGCTTAAGTTACGTTG 60.096 50.000 4.02 0.00 0.00 4.10
3557 5970 2.148768 GGTGGCTGCTTAAGTTACGTT 58.851 47.619 4.02 0.00 0.00 3.99
3558 5971 1.609841 GGGTGGCTGCTTAAGTTACGT 60.610 52.381 4.02 0.00 0.00 3.57
3559 5972 1.084289 GGGTGGCTGCTTAAGTTACG 58.916 55.000 4.02 0.00 0.00 3.18
3560 5973 2.491675 AGGGTGGCTGCTTAAGTTAC 57.508 50.000 4.02 0.00 0.00 2.50
3561 5974 3.153919 CAAAGGGTGGCTGCTTAAGTTA 58.846 45.455 4.02 0.00 0.00 2.24
3562 5975 1.963515 CAAAGGGTGGCTGCTTAAGTT 59.036 47.619 4.02 0.00 0.00 2.66
3563 5976 1.620822 CAAAGGGTGGCTGCTTAAGT 58.379 50.000 4.02 0.00 0.00 2.24
3564 5977 0.244721 GCAAAGGGTGGCTGCTTAAG 59.755 55.000 0.00 0.00 33.20 1.85
3565 5978 0.468958 TGCAAAGGGTGGCTGCTTAA 60.469 50.000 0.00 0.00 37.00 1.85
3566 5979 0.468958 TTGCAAAGGGTGGCTGCTTA 60.469 50.000 0.00 0.00 37.00 3.09
3567 5980 1.761667 TTGCAAAGGGTGGCTGCTT 60.762 52.632 0.00 0.00 37.00 3.91
3568 5981 2.123338 TTGCAAAGGGTGGCTGCT 60.123 55.556 0.00 0.00 37.00 4.24
3569 5982 2.029518 GTTGCAAAGGGTGGCTGC 59.970 61.111 0.00 0.00 36.60 5.25
3570 5983 0.249573 CTTGTTGCAAAGGGTGGCTG 60.250 55.000 0.00 0.00 0.00 4.85
3571 5984 0.396974 TCTTGTTGCAAAGGGTGGCT 60.397 50.000 0.00 0.00 0.00 4.75
3572 5985 0.463620 TTCTTGTTGCAAAGGGTGGC 59.536 50.000 0.00 0.00 0.00 5.01
3573 5986 1.535860 CGTTCTTGTTGCAAAGGGTGG 60.536 52.381 0.00 0.00 0.00 4.61
3574 5987 1.535860 CCGTTCTTGTTGCAAAGGGTG 60.536 52.381 0.00 0.00 0.00 4.61
3575 5988 0.744281 CCGTTCTTGTTGCAAAGGGT 59.256 50.000 0.00 0.00 0.00 4.34
3576 5989 0.744281 ACCGTTCTTGTTGCAAAGGG 59.256 50.000 0.00 2.68 34.81 3.95
3577 5990 1.134175 ACACCGTTCTTGTTGCAAAGG 59.866 47.619 0.00 0.00 0.00 3.11
3578 5991 2.559998 ACACCGTTCTTGTTGCAAAG 57.440 45.000 0.00 0.00 0.00 2.77
3579 5992 3.057174 AGAAACACCGTTCTTGTTGCAAA 60.057 39.130 0.00 0.00 37.26 3.68
3580 5993 2.490115 AGAAACACCGTTCTTGTTGCAA 59.510 40.909 0.00 0.00 37.26 4.08
3581 5994 2.088423 AGAAACACCGTTCTTGTTGCA 58.912 42.857 0.00 0.00 37.26 4.08
3582 5995 2.159435 ACAGAAACACCGTTCTTGTTGC 60.159 45.455 0.00 0.00 37.26 4.17
3583 5996 3.757745 ACAGAAACACCGTTCTTGTTG 57.242 42.857 0.00 0.00 37.26 3.33
3584 5997 4.696402 TGTTACAGAAACACCGTTCTTGTT 59.304 37.500 0.00 0.00 43.22 2.83
3585 5998 4.255301 TGTTACAGAAACACCGTTCTTGT 58.745 39.130 0.00 0.00 43.22 3.16
3586 5999 4.331717 ACTGTTACAGAAACACCGTTCTTG 59.668 41.667 20.07 0.00 43.22 3.02
3587 6000 4.510571 ACTGTTACAGAAACACCGTTCTT 58.489 39.130 20.07 0.00 43.22 2.52
3588 6001 4.117685 GACTGTTACAGAAACACCGTTCT 58.882 43.478 20.07 0.00 43.22 3.01
3589 6002 4.025979 CAGACTGTTACAGAAACACCGTTC 60.026 45.833 20.07 2.65 43.22 3.95
3590 6003 3.869246 CAGACTGTTACAGAAACACCGTT 59.131 43.478 20.07 0.00 43.22 4.44
3591 6004 3.454375 CAGACTGTTACAGAAACACCGT 58.546 45.455 20.07 0.00 43.22 4.83
3592 6005 2.221055 GCAGACTGTTACAGAAACACCG 59.779 50.000 20.07 1.48 43.22 4.94
3593 6006 3.467803 AGCAGACTGTTACAGAAACACC 58.532 45.455 20.07 2.39 43.22 4.16
3594 6007 4.332819 ACAAGCAGACTGTTACAGAAACAC 59.667 41.667 20.07 4.43 43.22 3.32
3595 6008 4.513442 ACAAGCAGACTGTTACAGAAACA 58.487 39.130 20.07 0.00 45.90 2.83
3596 6009 5.266242 CAACAAGCAGACTGTTACAGAAAC 58.734 41.667 20.07 9.65 38.67 2.78
3597 6010 4.201910 GCAACAAGCAGACTGTTACAGAAA 60.202 41.667 20.07 0.00 44.79 2.52
3598 6011 3.312421 GCAACAAGCAGACTGTTACAGAA 59.688 43.478 20.07 0.00 44.79 3.02
3599 6012 2.872245 GCAACAAGCAGACTGTTACAGA 59.128 45.455 20.07 0.00 44.79 3.41
3600 6013 3.259207 GCAACAAGCAGACTGTTACAG 57.741 47.619 11.21 11.21 44.79 2.74
3612 6025 1.796617 GCTCGGATGATTGCAACAAGC 60.797 52.381 0.00 4.67 45.96 4.01
3613 6026 1.202222 GGCTCGGATGATTGCAACAAG 60.202 52.381 0.00 0.00 0.00 3.16
3614 6027 0.810648 GGCTCGGATGATTGCAACAA 59.189 50.000 0.00 0.00 0.00 2.83
3615 6028 0.035152 AGGCTCGGATGATTGCAACA 60.035 50.000 0.00 2.38 0.00 3.33
3616 6029 0.379669 CAGGCTCGGATGATTGCAAC 59.620 55.000 0.00 0.00 0.00 4.17
3617 6030 0.035152 ACAGGCTCGGATGATTGCAA 60.035 50.000 0.00 0.00 0.00 4.08
3618 6031 0.829990 TACAGGCTCGGATGATTGCA 59.170 50.000 0.00 0.00 0.00 4.08
3619 6032 2.175878 ATACAGGCTCGGATGATTGC 57.824 50.000 0.00 0.00 0.00 3.56
3620 6033 5.505173 AAAAATACAGGCTCGGATGATTG 57.495 39.130 0.00 0.00 0.00 2.67
3639 6052 8.144478 TGTCGATCCAATGGTCAAAAATAAAAA 58.856 29.630 0.00 0.00 0.00 1.94
3640 6053 7.596995 GTGTCGATCCAATGGTCAAAAATAAAA 59.403 33.333 0.00 0.00 0.00 1.52
3641 6054 7.087639 GTGTCGATCCAATGGTCAAAAATAAA 58.912 34.615 0.00 0.00 0.00 1.40
3642 6055 6.207614 TGTGTCGATCCAATGGTCAAAAATAA 59.792 34.615 0.00 0.00 0.00 1.40
3643 6056 5.707764 TGTGTCGATCCAATGGTCAAAAATA 59.292 36.000 0.00 0.00 0.00 1.40
3644 6057 4.522405 TGTGTCGATCCAATGGTCAAAAAT 59.478 37.500 0.00 0.00 0.00 1.82
3647 6060 3.133141 TGTGTCGATCCAATGGTCAAA 57.867 42.857 0.00 0.00 0.00 2.69
3697 6110 2.888414 GTTGTAAAGGGTGGCTGCTTAA 59.112 45.455 0.00 0.00 0.00 1.85
3714 6127 3.078837 ACAGAAACACCGTTCTTGTTGT 58.921 40.909 0.00 0.00 37.26 3.32
3723 6136 3.454375 CAGACTGTTACAGAAACACCGT 58.546 45.455 20.07 0.00 43.22 4.83
3724 6137 2.221055 GCAGACTGTTACAGAAACACCG 59.779 50.000 20.07 1.48 43.22 4.94
3782 6196 7.919313 ATTCTGCAATAAAATATCTGTTGCG 57.081 32.000 11.88 8.50 45.94 4.85
3845 6260 1.014352 AGAACACAAACACTGGCGAC 58.986 50.000 0.00 0.00 0.00 5.19
3848 6263 6.902224 AATAAAAAGAACACAAACACTGGC 57.098 33.333 0.00 0.00 0.00 4.85
3851 6266 8.655970 GCAGAAAATAAAAAGAACACAAACACT 58.344 29.630 0.00 0.00 0.00 3.55
3856 6271 8.539770 TGTTGCAGAAAATAAAAAGAACACAA 57.460 26.923 0.00 0.00 0.00 3.33
3886 6301 5.177326 TGTTGCAAAAATTCTGAAGCAAGT 58.823 33.333 12.48 0.00 41.91 3.16
3974 6391 4.520111 TGCAATAGTCAGCTTGTTTGTGAT 59.480 37.500 0.00 0.00 0.00 3.06
3978 6395 4.609947 TGTTGCAATAGTCAGCTTGTTTG 58.390 39.130 0.59 0.00 0.00 2.93
3984 6401 2.746362 GCTCTTGTTGCAATAGTCAGCT 59.254 45.455 0.59 0.00 0.00 4.24
4123 6542 0.966920 GAGGTGACTTTGGTCGGAGA 59.033 55.000 0.00 0.00 44.43 3.71


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

AutoCloner maintained by Alex Coulton.