Multiple sequence alignment - TraesCS1D01G320300

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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 TraesCS1D01G320300 chr1D 100.000 4961 0 0 1 4961 414305194 414300234 0.000000e+00 9162.0
1 TraesCS1D01G320300 chr1D 92.568 296 20 2 5 300 414339464 414339171 1.650000e-114 424.0
2 TraesCS1D01G320300 chr1D 92.806 278 19 1 4 281 414339194 414338918 7.740000e-108 401.0
3 TraesCS1D01G320300 chr1D 88.152 211 18 2 90 300 414339645 414339442 1.380000e-60 244.0
4 TraesCS1D01G320300 chr1A 91.726 4472 218 56 4 4390 511103731 511099327 0.000000e+00 6069.0
5 TraesCS1D01G320300 chr1A 84.983 293 24 5 4 295 511104422 511104149 3.780000e-71 279.0
6 TraesCS1D01G320300 chr1A 92.593 108 8 0 4709 4816 511099313 511099206 6.650000e-34 156.0
7 TraesCS1D01G320300 chr1B 90.693 3406 191 56 4 3347 559104897 559101556 0.000000e+00 4418.0
8 TraesCS1D01G320300 chr1B 95.172 1015 36 9 3379 4390 559101559 559100555 0.000000e+00 1591.0
9 TraesCS1D01G320300 chr1B 96.047 253 10 0 4709 4961 559100541 559100289 3.570000e-111 412.0
10 TraesCS1D01G320300 chr1B 87.919 298 25 6 4 300 559105161 559104874 1.710000e-89 340.0
11 TraesCS1D01G320300 chr4D 83.088 408 56 11 3546 3945 354036989 354037391 4.720000e-95 359.0
12 TraesCS1D01G320300 chr4D 87.571 177 18 4 4534 4708 13934358 13934532 8.420000e-48 202.0
13 TraesCS1D01G320300 chr4D 100.000 28 0 0 3989 4016 338960403 338960376 9.000000e-03 52.8
14 TraesCS1D01G320300 chr4A 82.310 407 61 9 3546 3945 110910012 110909610 4.760000e-90 342.0
15 TraesCS1D01G320300 chr2B 81.373 408 67 8 3546 3947 111669110 111668706 1.720000e-84 324.0
16 TraesCS1D01G320300 chr2B 89.143 175 13 5 4533 4706 144610748 144610917 3.890000e-51 213.0
17 TraesCS1D01G320300 chr4B 81.281 406 67 7 3546 3945 437748079 437748481 2.230000e-83 320.0
18 TraesCS1D01G320300 chr2D 80.835 407 71 7 3546 3947 73819802 73819398 3.730000e-81 313.0
19 TraesCS1D01G320300 chr2D 80.583 412 70 10 3543 3947 323561664 323562072 4.820000e-80 309.0
20 TraesCS1D01G320300 chr2D 80.098 407 74 6 3546 3947 73591851 73591447 3.760000e-76 296.0
21 TraesCS1D01G320300 chr2D 94.326 141 5 3 4394 4533 157903063 157903201 3.890000e-51 213.0
22 TraesCS1D01G320300 chr2D 90.244 164 13 3 4370 4533 376949578 376949418 1.400000e-50 211.0
23 TraesCS1D01G320300 chr2A 80.835 407 71 7 3546 3947 73183094 73182690 3.730000e-81 313.0
24 TraesCS1D01G320300 chr2A 79.753 405 75 6 3546 3945 73179522 73179120 2.260000e-73 287.0
25 TraesCS1D01G320300 chr2A 89.655 174 12 4 4533 4706 94119275 94119108 3.010000e-52 217.0
26 TraesCS1D01G320300 chr5D 84.419 353 16 22 4388 4708 541946951 541947296 1.340000e-80 311.0
27 TraesCS1D01G320300 chr5D 93.151 146 8 2 4388 4533 388094597 388094740 3.890000e-51 213.0
28 TraesCS1D01G320300 chr5B 84.181 354 17 21 4388 4708 683996015 683996362 1.730000e-79 307.0
29 TraesCS1D01G320300 chr3B 96.026 151 5 1 4384 4533 110230139 110230289 1.380000e-60 244.0
30 TraesCS1D01G320300 chr3B 89.266 177 13 4 4534 4708 453991186 453991014 3.010000e-52 217.0
31 TraesCS1D01G320300 chr3B 87.571 177 14 4 4534 4708 454364153 454363983 1.090000e-46 198.0
32 TraesCS1D01G320300 chr3B 87.151 179 14 7 4534 4708 689416167 689416340 1.410000e-45 195.0
33 TraesCS1D01G320300 chr7D 94.558 147 5 3 4388 4533 590654747 590654603 1.800000e-54 224.0
34 TraesCS1D01G320300 chr7D 93.960 149 5 3 4388 4533 629584945 629584798 6.460000e-54 222.0
35 TraesCS1D01G320300 chr7D 93.197 147 8 2 4388 4533 574876981 574877126 1.080000e-51 215.0
36 TraesCS1D01G320300 chr7D 97.059 34 0 1 3989 4022 557381846 557381814 6.940000e-04 56.5
37 TraesCS1D01G320300 chr6B 93.243 148 8 2 4388 4535 517116748 517116893 3.010000e-52 217.0
38 TraesCS1D01G320300 chr6B 100.000 29 0 0 3988 4016 560198230 560198258 2.000000e-03 54.7
39 TraesCS1D01G320300 chr3D 88.764 178 14 5 4534 4708 370532350 370532176 3.890000e-51 213.0
40 TraesCS1D01G320300 chr3D 100.000 28 0 0 3989 4016 128990228 128990201 9.000000e-03 52.8
41 TraesCS1D01G320300 chrUn 100.000 28 0 0 3989 4016 471689436 471689409 9.000000e-03 52.8
42 TraesCS1D01G320300 chr7A 100.000 28 0 0 3989 4016 708146909 708146936 9.000000e-03 52.8
43 TraesCS1D01G320300 chr6D 100.000 28 0 0 3989 4016 422078613 422078586 9.000000e-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 TraesCS1D01G320300 chr1D 414300234 414305194 4960 True 9162.000000 9162 100.000000 1 4961 1 chr1D.!!$R1 4960
1 TraesCS1D01G320300 chr1D 414338918 414339645 727 True 356.333333 424 91.175333 4 300 3 chr1D.!!$R2 296
2 TraesCS1D01G320300 chr1A 511099206 511104422 5216 True 2168.000000 6069 89.767333 4 4816 3 chr1A.!!$R1 4812
3 TraesCS1D01G320300 chr1B 559100289 559105161 4872 True 1690.250000 4418 92.457750 4 4961 4 chr1B.!!$R1 4957
4 TraesCS1D01G320300 chr2A 73179120 73183094 3974 True 300.000000 313 80.294000 3546 3947 2 chr2A.!!$R2 401

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
724 1648 0.329596 ACAATTGAGAGGCCAGGGAC 59.670 55.0 13.59 0.0 0.00 4.46 F
1213 2173 0.604578 GGCAGCAATCACACACCATT 59.395 50.0 0.00 0.0 0.00 3.16 F
1516 2495 0.815615 GCGCTGTCCCCTTTATCTGG 60.816 60.0 0.00 0.0 0.00 3.86 F
2811 3837 0.392706 GTTTGCCCCAAACCCTTCAG 59.607 55.0 9.13 0.0 45.32 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 3227 1.557269 ATCACAGGAGACAGTGGGGC 61.557 60.000 0.00 0.0 46.80 5.80 R
2560 3586 3.384668 ACGAGTGATGCGAATTGATAGG 58.615 45.455 0.00 0.0 0.00 2.57 R
3350 4378 1.208052 GAGCATCACAGTGGGAGCTTA 59.792 52.381 17.01 0.0 33.17 3.09 R
4677 9283 0.181587 TCTGCACCCGGTCAGAAAAA 59.818 50.000 13.73 0.0 36.50 1.94 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
38 216 7.482654 TGTCAGATTGGATTATTTTCTAGCG 57.517 36.000 0.00 0.00 0.00 4.26
45 223 1.961793 TTATTTTCTAGCGCCGCCAT 58.038 45.000 4.98 0.00 0.00 4.40
46 224 2.823924 TATTTTCTAGCGCCGCCATA 57.176 45.000 4.98 0.00 0.00 2.74
50 229 1.034356 TTCTAGCGCCGCCATAGTTA 58.966 50.000 4.98 0.00 0.00 2.24
175 356 5.940470 ACAATCAGTCCATGGTTTCTCTTAC 59.060 40.000 12.58 0.00 26.05 2.34
176 357 6.176183 CAATCAGTCCATGGTTTCTCTTACT 58.824 40.000 12.58 1.79 26.05 2.24
184 365 9.886132 GTCCATGGTTTCTCTTACTTAATAAGA 57.114 33.333 12.58 6.98 45.85 2.10
233 414 2.027451 CCACAAACGAACAAGCAAAACG 59.973 45.455 0.00 0.00 0.00 3.60
261 455 9.986157 ACAAATTATGATATCTTAGCCATGGAT 57.014 29.630 18.40 13.25 0.00 3.41
267 461 2.042686 TCTTAGCCATGGATGCACAC 57.957 50.000 18.40 0.00 0.00 3.82
270 464 2.607411 TAGCCATGGATGCACACCCG 62.607 60.000 18.40 1.50 0.00 5.28
322 1237 2.691011 TGAGGTTTTGACGGGGAAAAAG 59.309 45.455 0.00 0.00 0.00 2.27
367 1282 7.715265 TTGACATTTGACTAGACTCAAGAAC 57.285 36.000 0.00 0.00 31.76 3.01
441 1360 9.836076 CATTAATTCATCATACGCTGAATGAAT 57.164 29.630 9.57 9.57 40.93 2.57
471 1390 0.454196 AATAACATTTGCGTCCGGCC 59.546 50.000 0.00 0.00 42.61 6.13
472 1391 0.678366 ATAACATTTGCGTCCGGCCA 60.678 50.000 2.24 0.00 42.61 5.36
518 1437 0.736325 GGATGGACCTGTCGAACACG 60.736 60.000 0.00 0.00 35.41 4.49
524 1443 1.591594 CCTGTCGAACACGCACACT 60.592 57.895 0.00 0.00 0.00 3.55
549 1468 2.819608 GAGGAGCACAAGTGGCAAAATA 59.180 45.455 2.00 0.00 0.00 1.40
551 1470 2.352715 GGAGCACAAGTGGCAAAATACC 60.353 50.000 2.00 0.00 0.00 2.73
655 1574 4.022935 ACGATAAAGGTTTCCCCGAAAAAC 60.023 41.667 0.00 0.00 38.74 2.43
724 1648 0.329596 ACAATTGAGAGGCCAGGGAC 59.670 55.000 13.59 0.00 0.00 4.46
726 1650 1.915078 AATTGAGAGGCCAGGGACGG 61.915 60.000 5.01 0.00 0.00 4.79
867 1807 2.332654 CCGCCGGCCTATAAATGCC 61.333 63.158 23.46 0.00 44.41 4.40
1048 2002 2.136878 CCCGCTCCCTCACTGCTAT 61.137 63.158 0.00 0.00 0.00 2.97
1049 2003 1.068753 CCGCTCCCTCACTGCTATG 59.931 63.158 0.00 0.00 0.00 2.23
1050 2004 1.680522 CCGCTCCCTCACTGCTATGT 61.681 60.000 0.00 0.00 0.00 2.29
1051 2005 1.032794 CGCTCCCTCACTGCTATGTA 58.967 55.000 0.00 0.00 0.00 2.29
1052 2006 1.000827 CGCTCCCTCACTGCTATGTAG 60.001 57.143 0.00 0.00 0.00 2.74
1072 2026 0.739462 TACCATCTGTTTCGCTGCCG 60.739 55.000 0.00 0.00 0.00 5.69
1167 2127 7.994194 AGTTGATGATTCTGCCTAGATTTTTC 58.006 34.615 0.00 0.00 31.81 2.29
1186 2146 6.921332 TTTTCTAAATTCGGATTGAAACGC 57.079 33.333 2.27 0.00 40.71 4.84
1207 2167 2.359850 TCCCGGCAGCAATCACAC 60.360 61.111 0.00 0.00 0.00 3.82
1213 2173 0.604578 GGCAGCAATCACACACCATT 59.395 50.000 0.00 0.00 0.00 3.16
1229 2189 4.869215 CACCATTAGTGCACAATTGTTCA 58.131 39.130 21.04 7.73 40.28 3.18
1271 2231 2.809010 GCCTCCGTCTAGAGTGGC 59.191 66.667 8.74 8.74 31.53 5.01
1272 2232 2.787567 GCCTCCGTCTAGAGTGGCC 61.788 68.421 12.01 0.00 34.81 5.36
1350 2321 1.846124 GGTGGGGTGAGGGTTCAGA 60.846 63.158 0.00 0.00 32.98 3.27
1372 2343 1.022735 TCAGAGTCGCGGATAACCTC 58.977 55.000 6.13 2.62 0.00 3.85
1404 2379 9.765795 GATTATTAGCTGTATATGGGGTATCAC 57.234 37.037 0.00 0.00 0.00 3.06
1488 2466 4.950479 GGACCTGATCCTGCACTG 57.050 61.111 0.00 0.00 45.22 3.66
1516 2495 0.815615 GCGCTGTCCCCTTTATCTGG 60.816 60.000 0.00 0.00 0.00 3.86
1532 2513 3.864789 TCTGGATATTTTCCTCCCTGC 57.135 47.619 0.00 0.00 45.68 4.85
1643 2633 4.203226 TGCAGTCAACAACACCTTGATTA 58.797 39.130 0.00 0.00 30.46 1.75
1668 2658 5.709164 CCATCTTTCTGAAGAACATCACCTT 59.291 40.000 0.00 0.00 44.61 3.50
1697 2691 3.067833 GACTGTCCCTAGTTTGTTGCTC 58.932 50.000 0.00 0.00 0.00 4.26
1723 2717 7.057894 TGGGCTACGTTTCCTATATGAATTTT 58.942 34.615 0.00 0.00 0.00 1.82
1970 2979 6.113411 ACTATGTGGAACTTGTGTATTAGGC 58.887 40.000 0.00 0.00 38.04 3.93
1980 2989 3.093814 TGTGTATTAGGCGAGAACTGGA 58.906 45.455 0.00 0.00 0.00 3.86
1981 2990 3.512329 TGTGTATTAGGCGAGAACTGGAA 59.488 43.478 0.00 0.00 0.00 3.53
1984 2993 5.921408 GTGTATTAGGCGAGAACTGGAATAG 59.079 44.000 0.00 0.00 0.00 1.73
2019 3028 6.697641 AATTGTAGTTTACCCCTTCTCTCA 57.302 37.500 0.00 0.00 0.00 3.27
2159 3185 2.050639 TTGTCAGTTGCAGCACAGCG 62.051 55.000 2.55 0.00 37.31 5.18
2240 3266 5.525378 GTGATGGATCTTTGCTTGTAGTAGG 59.475 44.000 0.00 0.00 0.00 3.18
2352 3378 1.753956 GCACAAAAGTAACCAGTGCG 58.246 50.000 0.00 0.00 44.84 5.34
2434 3460 9.485591 CAATACAATTAATCCGTAAAGTGTGAC 57.514 33.333 0.00 0.00 30.59 3.67
2723 3749 5.336451 GGATTGCCCAACTACCAAAAAGTAG 60.336 44.000 0.00 0.00 39.29 2.57
2810 3836 2.522271 GTTTGCCCCAAACCCTTCA 58.478 52.632 9.13 0.00 45.32 3.02
2811 3837 0.392706 GTTTGCCCCAAACCCTTCAG 59.607 55.000 9.13 0.00 45.32 3.02
2829 3855 6.377996 CCCTTCAGGACATTTTGACATCATTA 59.622 38.462 0.00 0.00 38.24 1.90
2923 3949 8.642432 TCACCAATCACCAGATATAGAACTTAG 58.358 37.037 0.00 0.00 33.08 2.18
3023 4050 1.952990 TGATGAACATTTGTGCCGTGT 59.047 42.857 0.00 0.00 0.00 4.49
3092 4119 5.220605 GCCTAGCGTGTTTCCTAAAGTTATG 60.221 44.000 0.00 0.00 0.00 1.90
3168 4196 8.969260 ATATATCATTGTGTCTTGCTTCTTGA 57.031 30.769 0.00 0.00 0.00 3.02
3350 4378 5.645929 TGTTTATCAGTTGACAACAGTGTGT 59.354 36.000 20.08 0.00 38.41 3.72
3403 4434 7.561722 TCAGGCTCAAGAACTATCTAGTGTTAT 59.438 37.037 0.00 0.00 36.50 1.89
3405 4436 8.852135 AGGCTCAAGAACTATCTAGTGTTATAC 58.148 37.037 0.00 0.00 36.50 1.47
3407 4438 9.672086 GCTCAAGAACTATCTAGTGTTATACAG 57.328 37.037 0.00 0.00 36.50 2.74
3897 8500 1.804396 CGGAGATGGAGCTCGAGCAT 61.804 60.000 36.87 22.99 45.16 3.79
4055 8661 5.048782 GCTTAAGTTTGATGTGTGATGTGGA 60.049 40.000 4.02 0.00 0.00 4.02
4200 8806 0.586748 CTCTCGCGCTGTACACGTAG 60.587 60.000 5.56 13.63 0.00 3.51
4318 8924 4.334203 ACAACTGCTGTAATTGTCGTTTGA 59.666 37.500 0.00 0.00 36.10 2.69
4395 9001 0.865769 AAAACTCTACAAGTGCGGCG 59.134 50.000 0.51 0.51 38.58 6.46
4396 9002 0.249741 AAACTCTACAAGTGCGGCGT 60.250 50.000 9.37 0.00 38.58 5.68
4398 9004 0.249741 ACTCTACAAGTGCGGCGTTT 60.250 50.000 9.37 0.00 36.65 3.60
4399 9005 0.438830 CTCTACAAGTGCGGCGTTTC 59.561 55.000 9.37 0.00 0.00 2.78
4408 9014 4.735132 CGGCGTTTCTGCTCCCGA 62.735 66.667 0.00 0.00 41.34 5.14
4409 9015 2.815647 GGCGTTTCTGCTCCCGAG 60.816 66.667 0.00 0.00 34.52 4.63
4419 9025 3.214253 CTCCCGAGCTCATCTGCA 58.786 61.111 15.40 0.00 34.99 4.41
4420 9026 1.227205 CTCCCGAGCTCATCTGCAC 60.227 63.158 15.40 0.00 34.99 4.57
4421 9027 2.202987 CCCGAGCTCATCTGCACC 60.203 66.667 15.40 0.00 34.99 5.01
4422 9028 2.202987 CCGAGCTCATCTGCACCC 60.203 66.667 15.40 0.00 34.99 4.61
4423 9029 2.584418 CGAGCTCATCTGCACCCG 60.584 66.667 15.40 0.00 34.99 5.28
4424 9030 2.894387 GAGCTCATCTGCACCCGC 60.894 66.667 9.40 0.00 39.24 6.13
4425 9031 4.479993 AGCTCATCTGCACCCGCC 62.480 66.667 0.00 0.00 37.32 6.13
4426 9032 4.479993 GCTCATCTGCACCCGCCT 62.480 66.667 0.00 0.00 37.32 5.52
4427 9033 2.270205 CTCATCTGCACCCGCCTT 59.730 61.111 0.00 0.00 37.32 4.35
4428 9034 2.046023 TCATCTGCACCCGCCTTG 60.046 61.111 0.00 0.00 37.32 3.61
4429 9035 2.046023 CATCTGCACCCGCCTTGA 60.046 61.111 0.00 0.00 37.32 3.02
4430 9036 2.045926 ATCTGCACCCGCCTTGAC 60.046 61.111 0.00 0.00 37.32 3.18
4431 9037 3.958147 ATCTGCACCCGCCTTGACG 62.958 63.158 0.00 0.00 37.32 4.35
4432 9038 4.680237 CTGCACCCGCCTTGACGA 62.680 66.667 0.00 0.00 37.32 4.20
4433 9039 4.243008 TGCACCCGCCTTGACGAA 62.243 61.111 0.00 0.00 37.32 3.85
4434 9040 2.975799 GCACCCGCCTTGACGAAA 60.976 61.111 0.00 0.00 34.06 3.46
4435 9041 2.548295 GCACCCGCCTTGACGAAAA 61.548 57.895 0.00 0.00 34.06 2.29
4436 9042 2.026522 CACCCGCCTTGACGAAAAA 58.973 52.632 0.00 0.00 34.06 1.94
4502 9108 5.682943 TTGTGTGGTAGACAAGTTTATGC 57.317 39.130 0.00 0.00 35.91 3.14
4503 9109 3.743911 TGTGTGGTAGACAAGTTTATGCG 59.256 43.478 0.00 0.00 35.91 4.73
4504 9110 3.744426 GTGTGGTAGACAAGTTTATGCGT 59.256 43.478 0.00 0.00 35.91 5.24
4505 9111 3.743911 TGTGGTAGACAAGTTTATGCGTG 59.256 43.478 0.00 0.00 0.00 5.34
4506 9112 3.991773 GTGGTAGACAAGTTTATGCGTGA 59.008 43.478 0.00 0.00 0.00 4.35
4507 9113 4.091509 GTGGTAGACAAGTTTATGCGTGAG 59.908 45.833 0.00 0.00 0.00 3.51
4508 9114 3.617263 GGTAGACAAGTTTATGCGTGAGG 59.383 47.826 0.00 0.00 0.00 3.86
4509 9115 3.402628 AGACAAGTTTATGCGTGAGGT 57.597 42.857 0.00 0.00 0.00 3.85
4510 9116 3.067106 AGACAAGTTTATGCGTGAGGTG 58.933 45.455 0.00 0.00 0.00 4.00
4511 9117 1.535462 ACAAGTTTATGCGTGAGGTGC 59.465 47.619 0.00 0.00 0.00 5.01
4512 9118 0.796312 AAGTTTATGCGTGAGGTGCG 59.204 50.000 0.00 0.00 34.24 5.34
4519 9125 3.114616 CGTGAGGTGCGCTCCAAG 61.115 66.667 28.68 13.43 0.00 3.61
4520 9126 2.031163 GTGAGGTGCGCTCCAAGT 59.969 61.111 28.68 9.86 0.00 3.16
4521 9127 1.598130 GTGAGGTGCGCTCCAAGTT 60.598 57.895 28.68 9.48 0.00 2.66
4522 9128 1.148273 TGAGGTGCGCTCCAAGTTT 59.852 52.632 28.68 9.09 0.00 2.66
4523 9129 0.884704 TGAGGTGCGCTCCAAGTTTC 60.885 55.000 28.68 17.55 0.00 2.78
4524 9130 0.884704 GAGGTGCGCTCCAAGTTTCA 60.885 55.000 28.68 0.00 0.00 2.69
4525 9131 0.465460 AGGTGCGCTCCAAGTTTCAA 60.465 50.000 28.68 0.00 0.00 2.69
4526 9132 0.317854 GGTGCGCTCCAAGTTTCAAC 60.318 55.000 23.09 0.26 0.00 3.18
4527 9133 0.663153 GTGCGCTCCAAGTTTCAACT 59.337 50.000 9.73 0.00 42.04 3.16
4528 9134 0.944386 TGCGCTCCAAGTTTCAACTC 59.056 50.000 9.73 0.00 38.57 3.01
4529 9135 0.944386 GCGCTCCAAGTTTCAACTCA 59.056 50.000 0.00 0.00 38.57 3.41
4530 9136 1.537202 GCGCTCCAAGTTTCAACTCAT 59.463 47.619 0.00 0.00 38.57 2.90
4531 9137 2.030805 GCGCTCCAAGTTTCAACTCATT 60.031 45.455 0.00 0.00 38.57 2.57
4532 9138 3.550842 GCGCTCCAAGTTTCAACTCATTT 60.551 43.478 0.00 0.00 38.57 2.32
4533 9139 4.610945 CGCTCCAAGTTTCAACTCATTTT 58.389 39.130 0.00 0.00 38.57 1.82
4534 9140 4.442073 CGCTCCAAGTTTCAACTCATTTTG 59.558 41.667 0.00 0.00 38.57 2.44
4535 9141 5.351458 GCTCCAAGTTTCAACTCATTTTGT 58.649 37.500 0.00 0.00 38.57 2.83
4536 9142 5.812127 GCTCCAAGTTTCAACTCATTTTGTT 59.188 36.000 0.00 0.00 38.57 2.83
4537 9143 6.019559 GCTCCAAGTTTCAACTCATTTTGTTC 60.020 38.462 0.00 0.00 38.57 3.18
4538 9144 7.169158 TCCAAGTTTCAACTCATTTTGTTCT 57.831 32.000 0.00 0.00 38.57 3.01
4539 9145 7.035004 TCCAAGTTTCAACTCATTTTGTTCTG 58.965 34.615 0.00 0.00 38.57 3.02
4540 9146 7.035004 CCAAGTTTCAACTCATTTTGTTCTGA 58.965 34.615 0.00 0.00 38.57 3.27
4541 9147 7.009540 CCAAGTTTCAACTCATTTTGTTCTGAC 59.990 37.037 0.00 0.00 38.57 3.51
4542 9148 6.564328 AGTTTCAACTCATTTTGTTCTGACC 58.436 36.000 0.00 0.00 32.86 4.02
4543 9149 5.514274 TTCAACTCATTTTGTTCTGACCC 57.486 39.130 0.00 0.00 0.00 4.46
4544 9150 3.563808 TCAACTCATTTTGTTCTGACCCG 59.436 43.478 0.00 0.00 0.00 5.28
4545 9151 3.485463 ACTCATTTTGTTCTGACCCGA 57.515 42.857 0.00 0.00 0.00 5.14
4546 9152 4.021102 ACTCATTTTGTTCTGACCCGAT 57.979 40.909 0.00 0.00 0.00 4.18
4547 9153 4.398319 ACTCATTTTGTTCTGACCCGATT 58.602 39.130 0.00 0.00 0.00 3.34
4548 9154 4.827284 ACTCATTTTGTTCTGACCCGATTT 59.173 37.500 0.00 0.00 0.00 2.17
4549 9155 5.301805 ACTCATTTTGTTCTGACCCGATTTT 59.698 36.000 0.00 0.00 0.00 1.82
4550 9156 5.527951 TCATTTTGTTCTGACCCGATTTTG 58.472 37.500 0.00 0.00 0.00 2.44
4551 9157 4.993029 TTTTGTTCTGACCCGATTTTGT 57.007 36.364 0.00 0.00 0.00 2.83
4552 9158 4.993029 TTTGTTCTGACCCGATTTTGTT 57.007 36.364 0.00 0.00 0.00 2.83
4553 9159 4.993029 TTGTTCTGACCCGATTTTGTTT 57.007 36.364 0.00 0.00 0.00 2.83
4554 9160 4.993029 TGTTCTGACCCGATTTTGTTTT 57.007 36.364 0.00 0.00 0.00 2.43
4555 9161 5.331876 TGTTCTGACCCGATTTTGTTTTT 57.668 34.783 0.00 0.00 0.00 1.94
4577 9183 4.783903 GAGAGCTGCTCAGACGTC 57.216 61.111 29.49 15.14 43.38 4.34
4578 9184 1.138671 GAGAGCTGCTCAGACGTCC 59.861 63.158 29.49 2.47 43.38 4.79
4579 9185 1.590610 GAGAGCTGCTCAGACGTCCA 61.591 60.000 29.49 1.65 43.38 4.02
4580 9186 1.181741 AGAGCTGCTCAGACGTCCAA 61.182 55.000 29.49 0.00 32.06 3.53
4581 9187 0.319900 GAGCTGCTCAGACGTCCAAA 60.320 55.000 24.02 0.00 0.00 3.28
4582 9188 0.322975 AGCTGCTCAGACGTCCAAAT 59.677 50.000 13.01 0.00 0.00 2.32
4583 9189 1.550524 AGCTGCTCAGACGTCCAAATA 59.449 47.619 13.01 0.00 0.00 1.40
4584 9190 2.028112 AGCTGCTCAGACGTCCAAATAA 60.028 45.455 13.01 0.00 0.00 1.40
4585 9191 2.349886 GCTGCTCAGACGTCCAAATAAG 59.650 50.000 13.01 4.73 0.00 1.73
4586 9192 3.589988 CTGCTCAGACGTCCAAATAAGT 58.410 45.455 13.01 0.00 0.00 2.24
4587 9193 3.997021 CTGCTCAGACGTCCAAATAAGTT 59.003 43.478 13.01 0.00 0.00 2.66
4588 9194 3.745975 TGCTCAGACGTCCAAATAAGTTG 59.254 43.478 13.01 0.20 36.94 3.16
4589 9195 3.994392 GCTCAGACGTCCAAATAAGTTGA 59.006 43.478 13.01 5.07 39.87 3.18
4590 9196 4.451096 GCTCAGACGTCCAAATAAGTTGAA 59.549 41.667 13.01 0.00 39.87 2.69
4591 9197 5.049680 GCTCAGACGTCCAAATAAGTTGAAA 60.050 40.000 13.01 0.00 39.87 2.69
4592 9198 6.348540 GCTCAGACGTCCAAATAAGTTGAAAT 60.349 38.462 13.01 0.00 39.87 2.17
4593 9199 7.504924 TCAGACGTCCAAATAAGTTGAAATT 57.495 32.000 13.01 0.00 39.87 1.82
4594 9200 7.936584 TCAGACGTCCAAATAAGTTGAAATTT 58.063 30.769 13.01 0.00 39.87 1.82
4595 9201 7.860373 TCAGACGTCCAAATAAGTTGAAATTTG 59.140 33.333 13.01 0.00 39.87 2.32
4596 9202 7.860373 CAGACGTCCAAATAAGTTGAAATTTGA 59.140 33.333 13.01 0.00 42.90 2.69
4597 9203 8.410141 AGACGTCCAAATAAGTTGAAATTTGAA 58.590 29.630 13.01 0.00 42.90 2.69
4598 9204 8.574196 ACGTCCAAATAAGTTGAAATTTGAAG 57.426 30.769 10.02 5.06 42.90 3.02
4599 9205 7.169140 ACGTCCAAATAAGTTGAAATTTGAAGC 59.831 33.333 10.02 0.00 42.90 3.86
4600 9206 7.501515 GTCCAAATAAGTTGAAATTTGAAGCG 58.498 34.615 10.02 0.00 42.90 4.68
4601 9207 6.145371 TCCAAATAAGTTGAAATTTGAAGCGC 59.855 34.615 0.00 0.00 42.90 5.92
4602 9208 6.073873 CCAAATAAGTTGAAATTTGAAGCGCA 60.074 34.615 11.47 0.00 42.90 6.09
4603 9209 6.452244 AATAAGTTGAAATTTGAAGCGCAC 57.548 33.333 11.47 3.52 0.00 5.34
4604 9210 2.742774 AGTTGAAATTTGAAGCGCACC 58.257 42.857 11.47 0.05 0.00 5.01
4605 9211 2.362077 AGTTGAAATTTGAAGCGCACCT 59.638 40.909 11.47 0.00 0.00 4.00
4606 9212 2.704725 TGAAATTTGAAGCGCACCTC 57.295 45.000 11.47 3.36 0.00 3.85
4607 9213 1.952990 TGAAATTTGAAGCGCACCTCA 59.047 42.857 11.47 6.45 0.00 3.86
4608 9214 2.287547 TGAAATTTGAAGCGCACCTCAC 60.288 45.455 11.47 0.00 0.00 3.51
4609 9215 0.238289 AATTTGAAGCGCACCTCACG 59.762 50.000 11.47 0.00 0.00 4.35
4618 9224 2.542766 CGCACCTCACGCATAAAATT 57.457 45.000 0.00 0.00 0.00 1.82
4619 9225 3.666883 CGCACCTCACGCATAAAATTA 57.333 42.857 0.00 0.00 0.00 1.40
4620 9226 4.209452 CGCACCTCACGCATAAAATTAT 57.791 40.909 0.00 0.00 0.00 1.28
4621 9227 4.211389 CGCACCTCACGCATAAAATTATC 58.789 43.478 0.00 0.00 0.00 1.75
4622 9228 4.024893 CGCACCTCACGCATAAAATTATCT 60.025 41.667 0.00 0.00 0.00 1.98
4623 9229 5.176774 CGCACCTCACGCATAAAATTATCTA 59.823 40.000 0.00 0.00 0.00 1.98
4624 9230 6.128553 CGCACCTCACGCATAAAATTATCTAT 60.129 38.462 0.00 0.00 0.00 1.98
4625 9231 7.237173 GCACCTCACGCATAAAATTATCTATC 58.763 38.462 0.00 0.00 0.00 2.08
4626 9232 7.095229 GCACCTCACGCATAAAATTATCTATCA 60.095 37.037 0.00 0.00 0.00 2.15
4627 9233 8.223769 CACCTCACGCATAAAATTATCTATCAC 58.776 37.037 0.00 0.00 0.00 3.06
4628 9234 7.931407 ACCTCACGCATAAAATTATCTATCACA 59.069 33.333 0.00 0.00 0.00 3.58
4629 9235 8.223769 CCTCACGCATAAAATTATCTATCACAC 58.776 37.037 0.00 0.00 0.00 3.82
4630 9236 8.655651 TCACGCATAAAATTATCTATCACACA 57.344 30.769 0.00 0.00 0.00 3.72
4631 9237 9.103861 TCACGCATAAAATTATCTATCACACAA 57.896 29.630 0.00 0.00 0.00 3.33
4632 9238 9.715123 CACGCATAAAATTATCTATCACACAAA 57.285 29.630 0.00 0.00 0.00 2.83
4694 9300 4.988744 TTTTTCTGACCGGGTGCA 57.011 50.000 3.30 1.51 0.00 4.57
4695 9301 2.714259 TTTTTCTGACCGGGTGCAG 58.286 52.632 3.30 12.02 0.00 4.41
4696 9302 0.181587 TTTTTCTGACCGGGTGCAGA 59.818 50.000 19.03 19.03 39.24 4.26
4697 9303 0.400213 TTTTCTGACCGGGTGCAGAT 59.600 50.000 21.76 0.00 40.51 2.90
4698 9304 0.321564 TTTCTGACCGGGTGCAGATG 60.322 55.000 21.76 4.84 40.51 2.90
4699 9305 1.191489 TTCTGACCGGGTGCAGATGA 61.191 55.000 21.76 11.19 40.51 2.92
4700 9306 1.153489 CTGACCGGGTGCAGATGAG 60.153 63.158 3.30 0.00 34.06 2.90
4701 9307 2.512515 GACCGGGTGCAGATGAGC 60.513 66.667 3.30 0.00 0.00 4.26
4702 9308 4.101448 ACCGGGTGCAGATGAGCC 62.101 66.667 6.32 0.00 0.00 4.70
4703 9309 3.790437 CCGGGTGCAGATGAGCCT 61.790 66.667 0.00 0.00 0.00 4.58
4704 9310 2.513204 CGGGTGCAGATGAGCCTG 60.513 66.667 0.00 0.00 37.23 4.85
4705 9311 2.124403 GGGTGCAGATGAGCCTGG 60.124 66.667 0.00 0.00 34.82 4.45
4706 9312 2.124403 GGTGCAGATGAGCCTGGG 60.124 66.667 0.00 0.00 34.82 4.45
4707 9313 2.827642 GTGCAGATGAGCCTGGGC 60.828 66.667 3.00 3.00 42.33 5.36
4752 9358 5.003804 ACAAGTCACCAAGATACAATGTCC 58.996 41.667 0.00 0.00 0.00 4.02
4759 9365 3.062099 CCAAGATACAATGTCCGTTCACG 59.938 47.826 0.00 0.00 39.44 4.35
4876 9482 0.389948 GTTTCGTCCTCGGCTCATGT 60.390 55.000 0.00 0.00 37.69 3.21
4887 9493 0.983378 GGCTCATGTGGGACTAGGGT 60.983 60.000 0.00 0.00 0.00 4.34
4919 9525 3.614870 GCTTTACAGGAAGTTGGCATTGG 60.615 47.826 0.00 0.00 0.00 3.16
4922 9528 1.075374 ACAGGAAGTTGGCATTGGCTA 59.925 47.619 11.84 0.48 40.87 3.93
4944 9550 3.675348 TGAGCATTGATCCCCTTTCAT 57.325 42.857 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.727100 TCCAATCTGACATATAAGGTATCACT 57.273 34.615 0.00 0.00 0.00 3.41
1 2 9.950496 AATCCAATCTGACATATAAGGTATCAC 57.050 33.333 0.00 0.00 0.00 3.06
16 194 5.470098 GGCGCTAGAAAATAATCCAATCTGA 59.530 40.000 7.64 0.00 0.00 3.27
17 195 5.615544 CGGCGCTAGAAAATAATCCAATCTG 60.616 44.000 7.64 0.00 0.00 2.90
18 196 4.452455 CGGCGCTAGAAAATAATCCAATCT 59.548 41.667 7.64 0.00 0.00 2.40
38 216 3.551890 CGATATCATGTAACTATGGCGGC 59.448 47.826 0.00 0.00 0.00 6.53
50 229 7.175347 AGCATCCATAGTTACGATATCATGT 57.825 36.000 3.12 0.00 0.00 3.21
83 264 4.790718 AAGAATCCATAGTTACACCCCC 57.209 45.455 0.00 0.00 0.00 5.40
101 282 8.874156 AGATAAAGATAGGATGTGCATGTAAGA 58.126 33.333 0.00 0.00 0.00 2.10
261 455 0.958382 GTATCTTTGGCGGGTGTGCA 60.958 55.000 0.00 0.00 36.28 4.57
262 456 1.654023 GGTATCTTTGGCGGGTGTGC 61.654 60.000 0.00 0.00 0.00 4.57
267 461 2.702592 TACAAGGTATCTTTGGCGGG 57.297 50.000 0.00 0.00 0.00 6.13
270 464 3.316308 CCAGCATACAAGGTATCTTTGGC 59.684 47.826 0.00 0.00 0.00 4.52
405 1324 9.964253 CGTATGATGAATTAATGATTGTAGAGC 57.036 33.333 0.00 0.00 0.00 4.09
441 1360 9.042008 GGACGCAAATGTTATTTCTATTCTCTA 57.958 33.333 0.00 0.00 0.00 2.43
463 1382 2.635443 ATTTTTGGCTGGCCGGACG 61.635 57.895 18.31 0.00 39.42 4.79
471 1390 7.035612 GGTCCTAAACTATTCATTTTTGGCTG 58.964 38.462 0.00 0.00 30.41 4.85
472 1391 6.723977 TGGTCCTAAACTATTCATTTTTGGCT 59.276 34.615 0.00 0.00 30.41 4.75
518 1437 0.321034 TGTGCTCCTCATCAGTGTGC 60.321 55.000 0.00 0.00 0.00 4.57
524 1443 0.321919 GCCACTTGTGCTCCTCATCA 60.322 55.000 0.00 0.00 0.00 3.07
549 1468 2.375014 AATTTGGACCGTTTCTGGGT 57.625 45.000 0.00 0.00 41.48 4.51
588 1507 7.962995 ATTTCTAGTACTCTCTTCACCATCA 57.037 36.000 0.00 0.00 0.00 3.07
621 1540 6.526674 GGAAACCTTTATCGTATTTGCAACAG 59.473 38.462 0.00 0.00 0.00 3.16
668 1588 0.036022 GACAGCAGGCCTCAAACTCT 59.964 55.000 0.00 0.00 0.00 3.24
669 1589 0.957888 GGACAGCAGGCCTCAAACTC 60.958 60.000 0.00 0.00 0.00 3.01
699 1619 3.575687 CCTGGCCTCTCAATTGTTTTTCT 59.424 43.478 3.32 0.00 0.00 2.52
726 1650 4.017877 GCTGTGTCACGTGCTGCC 62.018 66.667 11.67 0.00 0.00 4.85
850 1790 3.263941 GGCATTTATAGGCCGGCG 58.736 61.111 22.54 4.62 42.00 6.46
1041 1995 6.546428 AAACAGATGGTACTACATAGCAGT 57.454 37.500 0.00 0.00 44.30 4.40
1048 2002 3.845178 CAGCGAAACAGATGGTACTACA 58.155 45.455 0.00 0.00 0.00 2.74
1049 2003 2.603560 GCAGCGAAACAGATGGTACTAC 59.396 50.000 0.00 0.00 0.00 2.73
1050 2004 2.418197 GGCAGCGAAACAGATGGTACTA 60.418 50.000 0.00 0.00 0.00 1.82
1051 2005 1.676014 GGCAGCGAAACAGATGGTACT 60.676 52.381 0.00 0.00 0.00 2.73
1052 2006 0.727398 GGCAGCGAAACAGATGGTAC 59.273 55.000 0.00 0.00 0.00 3.34
1072 2026 3.450457 TGTGAATGAATTGTAATGGGGGC 59.550 43.478 0.00 0.00 0.00 5.80
1167 2127 5.331902 ACATGCGTTTCAATCCGAATTTAG 58.668 37.500 0.00 0.00 32.32 1.85
1186 2146 1.750018 TGATTGCTGCCGGGACATG 60.750 57.895 2.18 0.00 0.00 3.21
1213 2173 2.746904 CCCGATGAACAATTGTGCACTA 59.253 45.455 21.75 11.52 36.19 2.74
1268 2228 5.437060 GAATGATCAAAACTACTAGGGCCA 58.563 41.667 6.18 0.00 0.00 5.36
1271 2231 4.209288 CGCGAATGATCAAAACTACTAGGG 59.791 45.833 0.00 0.00 0.00 3.53
1272 2232 4.804139 ACGCGAATGATCAAAACTACTAGG 59.196 41.667 15.93 0.00 0.00 3.02
1350 2321 1.134560 GGTTATCCGCGACTCTGAAGT 59.865 52.381 8.23 0.00 38.88 3.01
1363 2334 5.808030 GCTAATAATCGAGCAGAGGTTATCC 59.192 44.000 0.00 0.00 38.62 2.59
1372 2343 6.699204 CCCATATACAGCTAATAATCGAGCAG 59.301 42.308 0.00 0.00 41.36 4.24
1404 2379 4.279169 AGCACGGATTAAATCCATGATTGG 59.721 41.667 0.00 0.00 45.08 3.16
1488 2466 1.523938 GGGACAGCGCAGGATTACC 60.524 63.158 11.47 2.62 0.00 2.85
1516 2495 2.222027 CACGGCAGGGAGGAAAATATC 58.778 52.381 0.00 0.00 0.00 1.63
1643 2633 5.006386 GGTGATGTTCTTCAGAAAGATGGT 58.994 41.667 0.00 0.00 41.12 3.55
1668 2658 2.404559 ACTAGGGACAGTCAACAACCA 58.595 47.619 2.17 0.00 0.00 3.67
1697 2691 4.866508 TCATATAGGAAACGTAGCCCAG 57.133 45.455 3.21 0.00 0.00 4.45
1726 2720 9.712305 CAGGGTAAATGGTAAAGATATACTCAG 57.288 37.037 0.00 0.00 0.00 3.35
1727 2721 9.220906 ACAGGGTAAATGGTAAAGATATACTCA 57.779 33.333 0.00 0.00 0.00 3.41
1970 2979 8.648557 TGATTAAACATCTATTCCAGTTCTCG 57.351 34.615 0.00 0.00 0.00 4.04
2092 3118 8.866970 AAGGCCATCAAAAATTTAATCAACAT 57.133 26.923 5.01 0.00 0.00 2.71
2095 3121 9.571816 AAAGAAGGCCATCAAAAATTTAATCAA 57.428 25.926 11.19 0.00 0.00 2.57
2104 3130 3.642848 AGCTGAAAGAAGGCCATCAAAAA 59.357 39.130 11.19 0.00 34.07 1.94
2110 3136 3.439857 TGTAAGCTGAAAGAAGGCCAT 57.560 42.857 5.01 0.00 34.07 4.40
2159 3185 9.002600 ACATCAAAAGAAAATGGCCTTTTAATC 57.997 29.630 16.35 11.42 39.69 1.75
2201 3227 1.557269 ATCACAGGAGACAGTGGGGC 61.557 60.000 0.00 0.00 46.80 5.80
2240 3266 6.599638 ACACTAGGAAGCAATAAGATTGAACC 59.400 38.462 3.38 3.35 0.00 3.62
2434 3460 5.366829 TCTTCAAATGCTGATGTGAGTTG 57.633 39.130 0.00 0.00 32.78 3.16
2560 3586 3.384668 ACGAGTGATGCGAATTGATAGG 58.615 45.455 0.00 0.00 0.00 2.57
2810 3836 9.028284 AGTTTGATAATGATGTCAAAATGTCCT 57.972 29.630 7.53 0.36 44.78 3.85
2811 3837 9.643693 AAGTTTGATAATGATGTCAAAATGTCC 57.356 29.630 7.53 0.00 44.78 4.02
2923 3949 9.819267 ATAACTACTTCAGTAAACTTATGGCTC 57.181 33.333 0.00 0.00 36.04 4.70
2997 4024 6.145209 CACGGCACAAATGTTCATCAATTAAA 59.855 34.615 0.00 0.00 0.00 1.52
3023 4050 5.919755 TCATGAACCAACTAGTGTGTTACA 58.080 37.500 9.56 9.74 0.00 2.41
3092 4119 4.321480 ACTTTTTGTTTACGCGTGTTTCAC 59.679 37.500 24.59 11.26 0.00 3.18
3131 4159 9.896645 GACACAATGATATATCTTGTCCCATAT 57.103 33.333 19.26 0.95 30.96 1.78
3281 4309 1.271217 ACTTTAACCTCCACGCCTTCC 60.271 52.381 0.00 0.00 0.00 3.46
3350 4378 1.208052 GAGCATCACAGTGGGAGCTTA 59.792 52.381 17.01 0.00 33.17 3.09
3454 4485 6.209774 TCAGGATCTCAGGGACCTTTAATAA 58.790 40.000 0.00 0.00 0.00 1.40
3510 4541 4.309950 GGCACGTCGGTCTTGGGT 62.310 66.667 0.00 0.00 0.00 4.51
3681 8284 1.580845 GCGTGCCTGTGCTGAAGAAT 61.581 55.000 0.00 0.00 38.71 2.40
3891 8494 2.046023 TGGTGGAAGGCATGCTCG 60.046 61.111 18.92 0.00 0.00 5.03
4150 8756 4.037565 CAGTCCACCGCTATCACTTGTATA 59.962 45.833 0.00 0.00 0.00 1.47
4330 8936 9.847706 AAGACTGCACGTGAATATATAGATAAG 57.152 33.333 22.23 0.00 0.00 1.73
4384 8990 3.022287 CAGAAACGCCGCACTTGT 58.978 55.556 0.00 0.00 0.00 3.16
4391 8997 4.735132 TCGGGAGCAGAAACGCCG 62.735 66.667 0.00 0.00 0.00 6.46
4402 9008 1.227205 GTGCAGATGAGCTCGGGAG 60.227 63.158 9.64 0.30 34.99 4.30
4403 9009 2.725312 GGTGCAGATGAGCTCGGGA 61.725 63.158 9.64 0.00 34.99 5.14
4404 9010 2.202987 GGTGCAGATGAGCTCGGG 60.203 66.667 9.64 0.00 34.99 5.14
4405 9011 2.202987 GGGTGCAGATGAGCTCGG 60.203 66.667 9.64 0.00 34.99 4.63
4406 9012 2.584418 CGGGTGCAGATGAGCTCG 60.584 66.667 9.64 0.00 34.99 5.03
4407 9013 2.894387 GCGGGTGCAGATGAGCTC 60.894 66.667 6.82 6.82 42.15 4.09
4408 9014 4.479993 GGCGGGTGCAGATGAGCT 62.480 66.667 0.00 0.00 45.35 4.09
4409 9015 3.984193 AAGGCGGGTGCAGATGAGC 62.984 63.158 0.00 0.00 45.35 4.26
4410 9016 2.110967 CAAGGCGGGTGCAGATGAG 61.111 63.158 0.00 0.00 45.35 2.90
4411 9017 2.046023 CAAGGCGGGTGCAGATGA 60.046 61.111 0.00 0.00 45.35 2.92
4412 9018 2.046023 TCAAGGCGGGTGCAGATG 60.046 61.111 0.00 0.00 45.35 2.90
4413 9019 2.045926 GTCAAGGCGGGTGCAGAT 60.046 61.111 0.00 0.00 45.35 2.90
4414 9020 4.680237 CGTCAAGGCGGGTGCAGA 62.680 66.667 0.00 0.00 45.35 4.26
4415 9021 4.680237 TCGTCAAGGCGGGTGCAG 62.680 66.667 0.00 0.00 45.35 4.41
4416 9022 3.758973 TTTCGTCAAGGCGGGTGCA 62.759 57.895 0.00 0.00 45.35 4.57
4417 9023 2.065906 TTTTTCGTCAAGGCGGGTGC 62.066 55.000 0.00 0.00 41.71 5.01
4418 9024 2.026522 TTTTTCGTCAAGGCGGGTG 58.973 52.632 0.00 0.00 0.00 4.61
4419 9025 4.563404 TTTTTCGTCAAGGCGGGT 57.437 50.000 0.00 0.00 0.00 5.28
4477 9083 6.975772 GCATAAACTTGTCTACCACACAAAAA 59.024 34.615 0.00 0.00 33.41 1.94
4478 9084 6.500041 GCATAAACTTGTCTACCACACAAAA 58.500 36.000 0.00 0.00 33.41 2.44
4479 9085 5.277586 CGCATAAACTTGTCTACCACACAAA 60.278 40.000 0.00 0.00 33.41 2.83
4480 9086 4.212425 CGCATAAACTTGTCTACCACACAA 59.788 41.667 0.00 0.00 33.41 3.33
4481 9087 3.743911 CGCATAAACTTGTCTACCACACA 59.256 43.478 0.00 0.00 33.41 3.72
4482 9088 3.744426 ACGCATAAACTTGTCTACCACAC 59.256 43.478 0.00 0.00 33.41 3.82
4483 9089 3.743911 CACGCATAAACTTGTCTACCACA 59.256 43.478 0.00 0.00 0.00 4.17
4484 9090 3.991773 TCACGCATAAACTTGTCTACCAC 59.008 43.478 0.00 0.00 0.00 4.16
4485 9091 4.242475 CTCACGCATAAACTTGTCTACCA 58.758 43.478 0.00 0.00 0.00 3.25
4486 9092 3.617263 CCTCACGCATAAACTTGTCTACC 59.383 47.826 0.00 0.00 0.00 3.18
4487 9093 4.091509 CACCTCACGCATAAACTTGTCTAC 59.908 45.833 0.00 0.00 0.00 2.59
4488 9094 4.242475 CACCTCACGCATAAACTTGTCTA 58.758 43.478 0.00 0.00 0.00 2.59
4489 9095 3.067106 CACCTCACGCATAAACTTGTCT 58.933 45.455 0.00 0.00 0.00 3.41
4490 9096 2.412847 GCACCTCACGCATAAACTTGTC 60.413 50.000 0.00 0.00 0.00 3.18
4491 9097 1.535462 GCACCTCACGCATAAACTTGT 59.465 47.619 0.00 0.00 0.00 3.16
4492 9098 1.464023 CGCACCTCACGCATAAACTTG 60.464 52.381 0.00 0.00 0.00 3.16
4493 9099 0.796312 CGCACCTCACGCATAAACTT 59.204 50.000 0.00 0.00 0.00 2.66
4494 9100 2.456000 CGCACCTCACGCATAAACT 58.544 52.632 0.00 0.00 0.00 2.66
4502 9108 3.114616 CTTGGAGCGCACCTCACG 61.115 66.667 24.52 6.65 42.62 4.35
4503 9109 1.166531 AAACTTGGAGCGCACCTCAC 61.167 55.000 24.52 0.00 42.62 3.51
4504 9110 0.884704 GAAACTTGGAGCGCACCTCA 60.885 55.000 24.52 10.48 42.62 3.86
4505 9111 0.884704 TGAAACTTGGAGCGCACCTC 60.885 55.000 24.52 13.56 39.98 3.85
4506 9112 0.465460 TTGAAACTTGGAGCGCACCT 60.465 50.000 24.52 3.63 0.00 4.00
4507 9113 0.317854 GTTGAAACTTGGAGCGCACC 60.318 55.000 17.78 17.78 0.00 5.01
4508 9114 0.663153 AGTTGAAACTTGGAGCGCAC 59.337 50.000 11.47 1.97 35.21 5.34
4509 9115 0.944386 GAGTTGAAACTTGGAGCGCA 59.056 50.000 11.47 0.00 39.88 6.09
4510 9116 0.944386 TGAGTTGAAACTTGGAGCGC 59.056 50.000 0.00 0.00 39.88 5.92
4511 9117 3.904136 AATGAGTTGAAACTTGGAGCG 57.096 42.857 0.00 0.00 39.88 5.03
4512 9118 5.351458 ACAAAATGAGTTGAAACTTGGAGC 58.649 37.500 0.00 0.00 39.88 4.70
4513 9119 7.221452 CAGAACAAAATGAGTTGAAACTTGGAG 59.779 37.037 0.00 0.00 39.88 3.86
4514 9120 7.035004 CAGAACAAAATGAGTTGAAACTTGGA 58.965 34.615 0.00 0.00 39.88 3.53
4515 9121 7.009540 GTCAGAACAAAATGAGTTGAAACTTGG 59.990 37.037 0.00 0.00 39.88 3.61
4516 9122 7.009540 GGTCAGAACAAAATGAGTTGAAACTTG 59.990 37.037 0.00 0.00 39.88 3.16
4517 9123 7.035612 GGTCAGAACAAAATGAGTTGAAACTT 58.964 34.615 0.00 0.00 39.88 2.66
4518 9124 6.405842 GGGTCAGAACAAAATGAGTTGAAACT 60.406 38.462 0.00 0.00 43.16 2.66
4519 9125 5.748630 GGGTCAGAACAAAATGAGTTGAAAC 59.251 40.000 0.00 0.00 32.59 2.78
4520 9126 5.449862 CGGGTCAGAACAAAATGAGTTGAAA 60.450 40.000 0.00 0.00 32.59 2.69
4521 9127 4.036262 CGGGTCAGAACAAAATGAGTTGAA 59.964 41.667 0.00 0.00 32.59 2.69
4522 9128 3.563808 CGGGTCAGAACAAAATGAGTTGA 59.436 43.478 0.00 0.00 32.59 3.18
4523 9129 3.563808 TCGGGTCAGAACAAAATGAGTTG 59.436 43.478 0.00 0.00 34.52 3.16
4524 9130 3.815809 TCGGGTCAGAACAAAATGAGTT 58.184 40.909 0.00 0.00 0.00 3.01
4525 9131 3.485463 TCGGGTCAGAACAAAATGAGT 57.515 42.857 0.00 0.00 0.00 3.41
4526 9132 5.376854 AAATCGGGTCAGAACAAAATGAG 57.623 39.130 0.00 0.00 0.00 2.90
4527 9133 5.068460 ACAAAATCGGGTCAGAACAAAATGA 59.932 36.000 0.00 0.00 0.00 2.57
4528 9134 5.288804 ACAAAATCGGGTCAGAACAAAATG 58.711 37.500 0.00 0.00 0.00 2.32
4529 9135 5.529581 ACAAAATCGGGTCAGAACAAAAT 57.470 34.783 0.00 0.00 0.00 1.82
4530 9136 4.993029 ACAAAATCGGGTCAGAACAAAA 57.007 36.364 0.00 0.00 0.00 2.44
4531 9137 4.993029 AACAAAATCGGGTCAGAACAAA 57.007 36.364 0.00 0.00 0.00 2.83
4532 9138 4.993029 AAACAAAATCGGGTCAGAACAA 57.007 36.364 0.00 0.00 0.00 2.83
4533 9139 4.993029 AAAACAAAATCGGGTCAGAACA 57.007 36.364 0.00 0.00 0.00 3.18
4552 9158 1.971481 TGAGCAGCTCTCAGCAAAAA 58.029 45.000 23.15 0.00 46.34 1.94
4553 9159 3.711937 TGAGCAGCTCTCAGCAAAA 57.288 47.368 23.15 0.00 46.34 2.44
4560 9166 1.138671 GGACGTCTGAGCAGCTCTC 59.861 63.158 23.15 11.57 42.23 3.20
4561 9167 1.181741 TTGGACGTCTGAGCAGCTCT 61.182 55.000 23.15 2.04 0.00 4.09
4562 9168 0.319900 TTTGGACGTCTGAGCAGCTC 60.320 55.000 16.21 16.21 0.00 4.09
4563 9169 0.322975 ATTTGGACGTCTGAGCAGCT 59.677 50.000 16.46 0.00 0.00 4.24
4564 9170 2.010145 TATTTGGACGTCTGAGCAGC 57.990 50.000 16.46 0.00 0.00 5.25
4565 9171 3.589988 ACTTATTTGGACGTCTGAGCAG 58.410 45.455 16.46 7.48 0.00 4.24
4566 9172 3.678056 ACTTATTTGGACGTCTGAGCA 57.322 42.857 16.46 1.36 0.00 4.26
4567 9173 3.994392 TCAACTTATTTGGACGTCTGAGC 59.006 43.478 16.46 0.00 35.69 4.26
4568 9174 6.539649 TTTCAACTTATTTGGACGTCTGAG 57.460 37.500 16.46 4.16 35.69 3.35
4569 9175 7.504924 AATTTCAACTTATTTGGACGTCTGA 57.495 32.000 16.46 4.87 35.69 3.27
4570 9176 7.860373 TCAAATTTCAACTTATTTGGACGTCTG 59.140 33.333 16.46 2.28 40.46 3.51
4571 9177 7.936584 TCAAATTTCAACTTATTTGGACGTCT 58.063 30.769 16.46 0.00 40.46 4.18
4572 9178 8.568732 TTCAAATTTCAACTTATTTGGACGTC 57.431 30.769 7.13 7.13 40.46 4.34
4573 9179 7.169140 GCTTCAAATTTCAACTTATTTGGACGT 59.831 33.333 0.00 0.00 40.46 4.34
4574 9180 7.501515 GCTTCAAATTTCAACTTATTTGGACG 58.498 34.615 0.00 0.00 40.46 4.79
4575 9181 7.501515 CGCTTCAAATTTCAACTTATTTGGAC 58.498 34.615 0.00 0.00 40.46 4.02
4576 9182 6.145371 GCGCTTCAAATTTCAACTTATTTGGA 59.855 34.615 0.00 0.00 40.46 3.53
4577 9183 6.073873 TGCGCTTCAAATTTCAACTTATTTGG 60.074 34.615 9.73 0.00 40.46 3.28
4578 9184 6.787043 GTGCGCTTCAAATTTCAACTTATTTG 59.213 34.615 9.73 0.00 41.08 2.32
4579 9185 6.073819 GGTGCGCTTCAAATTTCAACTTATTT 60.074 34.615 9.73 0.00 0.00 1.40
4580 9186 5.405269 GGTGCGCTTCAAATTTCAACTTATT 59.595 36.000 9.73 0.00 0.00 1.40
4581 9187 4.923281 GGTGCGCTTCAAATTTCAACTTAT 59.077 37.500 9.73 0.00 0.00 1.73
4582 9188 4.037446 AGGTGCGCTTCAAATTTCAACTTA 59.963 37.500 9.73 0.00 0.00 2.24
4583 9189 3.123050 GGTGCGCTTCAAATTTCAACTT 58.877 40.909 9.73 0.00 0.00 2.66
4584 9190 2.362077 AGGTGCGCTTCAAATTTCAACT 59.638 40.909 9.73 0.00 0.00 3.16
4585 9191 2.726241 GAGGTGCGCTTCAAATTTCAAC 59.274 45.455 9.73 0.00 0.00 3.18
4586 9192 2.360483 TGAGGTGCGCTTCAAATTTCAA 59.640 40.909 9.94 0.00 0.00 2.69
4587 9193 1.952990 TGAGGTGCGCTTCAAATTTCA 59.047 42.857 9.94 0.00 0.00 2.69
4588 9194 2.319472 GTGAGGTGCGCTTCAAATTTC 58.681 47.619 14.19 0.00 32.39 2.17
4589 9195 1.334960 CGTGAGGTGCGCTTCAAATTT 60.335 47.619 14.19 0.00 32.39 1.82
4590 9196 0.238289 CGTGAGGTGCGCTTCAAATT 59.762 50.000 14.19 0.00 32.39 1.82
4591 9197 1.868997 CGTGAGGTGCGCTTCAAAT 59.131 52.632 14.19 0.00 32.39 2.32
4592 9198 3.329231 CGTGAGGTGCGCTTCAAA 58.671 55.556 14.19 0.00 32.39 2.69
4599 9205 2.542766 AATTTTATGCGTGAGGTGCG 57.457 45.000 0.00 0.00 34.24 5.34
4600 9206 5.424121 AGATAATTTTATGCGTGAGGTGC 57.576 39.130 0.00 0.00 0.00 5.01
4601 9207 8.223769 GTGATAGATAATTTTATGCGTGAGGTG 58.776 37.037 0.00 0.00 0.00 4.00
4602 9208 7.931407 TGTGATAGATAATTTTATGCGTGAGGT 59.069 33.333 0.00 0.00 0.00 3.85
4603 9209 8.223769 GTGTGATAGATAATTTTATGCGTGAGG 58.776 37.037 0.00 0.00 0.00 3.86
4604 9210 8.764287 TGTGTGATAGATAATTTTATGCGTGAG 58.236 33.333 0.00 0.00 0.00 3.51
4605 9211 8.655651 TGTGTGATAGATAATTTTATGCGTGA 57.344 30.769 0.00 0.00 0.00 4.35
4606 9212 9.715123 TTTGTGTGATAGATAATTTTATGCGTG 57.285 29.630 0.00 0.00 0.00 5.34
4677 9283 0.181587 TCTGCACCCGGTCAGAAAAA 59.818 50.000 13.73 0.00 36.50 1.94
4678 9284 0.400213 ATCTGCACCCGGTCAGAAAA 59.600 50.000 18.21 1.56 41.96 2.29
4679 9285 0.321564 CATCTGCACCCGGTCAGAAA 60.322 55.000 18.21 2.15 41.96 2.52
4680 9286 1.191489 TCATCTGCACCCGGTCAGAA 61.191 55.000 18.21 4.73 41.96 3.02
4681 9287 1.607801 CTCATCTGCACCCGGTCAGA 61.608 60.000 17.08 17.08 42.72 3.27
4682 9288 1.153489 CTCATCTGCACCCGGTCAG 60.153 63.158 0.00 4.93 0.00 3.51
4683 9289 2.981302 CTCATCTGCACCCGGTCA 59.019 61.111 0.00 0.00 0.00 4.02
4684 9290 2.512515 GCTCATCTGCACCCGGTC 60.513 66.667 0.00 0.00 0.00 4.79
4685 9291 4.101448 GGCTCATCTGCACCCGGT 62.101 66.667 0.00 0.00 34.04 5.28
4686 9292 3.790437 AGGCTCATCTGCACCCGG 61.790 66.667 0.00 0.00 34.04 5.73
4687 9293 2.513204 CAGGCTCATCTGCACCCG 60.513 66.667 0.00 0.00 34.04 5.28
4688 9294 2.124403 CCAGGCTCATCTGCACCC 60.124 66.667 0.00 0.00 33.64 4.61
4689 9295 2.124403 CCCAGGCTCATCTGCACC 60.124 66.667 0.00 0.00 33.64 5.01
4690 9296 2.827642 GCCCAGGCTCATCTGCAC 60.828 66.667 0.08 0.00 38.26 4.57
4700 9306 0.676151 CTTCTTGTCTGAGCCCAGGC 60.676 60.000 0.00 0.00 44.99 4.85
4701 9307 0.689623 ACTTCTTGTCTGAGCCCAGG 59.310 55.000 0.00 0.00 40.76 4.45
4702 9308 2.676463 GCTACTTCTTGTCTGAGCCCAG 60.676 54.545 0.00 0.00 41.74 4.45
4703 9309 1.276421 GCTACTTCTTGTCTGAGCCCA 59.724 52.381 0.00 0.00 0.00 5.36
4704 9310 1.406205 GGCTACTTCTTGTCTGAGCCC 60.406 57.143 0.00 0.00 40.38 5.19
4705 9311 1.552792 AGGCTACTTCTTGTCTGAGCC 59.447 52.381 2.44 2.44 44.35 4.70
4706 9312 3.326836 AAGGCTACTTCTTGTCTGAGC 57.673 47.619 0.00 0.00 28.54 4.26
4733 9339 3.596214 ACGGACATTGTATCTTGGTGAC 58.404 45.455 0.00 0.00 0.00 3.67
4752 9358 1.073177 GTTGGACCATACCGTGAACG 58.927 55.000 0.00 0.00 39.44 3.95
4759 9365 4.913784 TGAACCTTAAGTTGGACCATACC 58.086 43.478 0.00 0.00 39.40 2.73
4876 9482 3.054655 GCAAGTTGAATACCCTAGTCCCA 60.055 47.826 7.16 0.00 0.00 4.37
4887 9493 7.817418 AACTTCCTGTAAAGCAAGTTGAATA 57.183 32.000 7.16 0.00 37.62 1.75
4922 9528 3.985127 TGAAAGGGGATCAATGCTCAAT 58.015 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.