Multiple sequence alignment - TraesCS5D01G449600

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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 TraesCS5D01G449600 chr5D 100.000 7138 0 0 1 7138 498494923 498487786 0.000000e+00 13182
1 TraesCS5D01G449600 chr5D 98.824 170 2 0 2410 2579 434334838 434335007 3.240000e-78 303
2 TraesCS5D01G449600 chr5D 99.387 163 1 0 2410 2572 297115773 297115611 5.410000e-76 296
3 TraesCS5D01G449600 chr5D 98.802 167 1 1 2408 2573 302016701 302016867 5.410000e-76 296
4 TraesCS5D01G449600 chr5B 94.185 4437 186 32 2533 6932 617823408 617819007 0.000000e+00 6698
5 TraesCS5D01G449600 chr5B 90.723 2490 122 50 1 2422 617825911 617823463 0.000000e+00 3217
6 TraesCS5D01G449600 chr5A 95.342 3585 120 17 2629 6190 622772064 622768504 0.000000e+00 5651
7 TraesCS5D01G449600 chr5A 87.787 2440 142 72 44 2409 622774454 622772097 0.000000e+00 2712
8 TraesCS5D01G449600 chr5A 92.288 389 25 3 6548 6932 622768097 622767710 1.350000e-151 547
9 TraesCS5D01G449600 chr5A 93.272 327 15 5 6194 6513 622768423 622768097 6.480000e-130 475
10 TraesCS5D01G449600 chr5A 88.372 129 15 0 4615 4743 571787674 571787546 9.590000e-34 156
11 TraesCS5D01G449600 chr5A 86.719 128 16 1 4615 4741 540392383 540392256 2.680000e-29 141
12 TraesCS5D01G449600 chr5A 87.705 122 12 3 6949 7070 622767645 622767527 9.660000e-29 139
13 TraesCS5D01G449600 chr3D 98.204 167 2 1 2406 2572 274337951 274337786 2.520000e-74 291
14 TraesCS5D01G449600 chr3D 97.546 163 4 0 2410 2572 486424949 486424787 5.450000e-71 279
15 TraesCS5D01G449600 chr3D 86.719 128 17 0 4615 4742 75116604 75116731 7.460000e-30 143
16 TraesCS5D01G449600 chr6D 92.857 196 12 2 2410 2604 359354779 359354973 4.220000e-72 283
17 TraesCS5D01G449600 chr6D 86.364 132 16 2 4615 4745 94767424 94767554 7.460000e-30 143
18 TraesCS5D01G449600 chr4D 97.576 165 4 0 2402 2566 424572386 424572550 4.220000e-72 283
19 TraesCS5D01G449600 chr4D 87.903 124 15 0 4615 4738 359681036 359681159 5.770000e-31 147
20 TraesCS5D01G449600 chr1D 97.024 168 5 0 2407 2574 311986609 311986776 4.220000e-72 283
21 TraesCS5D01G449600 chr2D 97.006 167 5 0 2408 2574 391812510 391812344 1.520000e-71 281
22 TraesCS5D01G449600 chr7A 93.023 129 9 0 4615 4743 701309112 701309240 9.450000e-44 189
23 TraesCS5D01G449600 chr1B 84.559 136 21 0 4614 4749 59996060 59996195 1.250000e-27 135


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 TraesCS5D01G449600 chr5D 498487786 498494923 7137 True 13182.0 13182 100.0000 1 7138 1 chr5D.!!$R2 7137
1 TraesCS5D01G449600 chr5B 617819007 617825911 6904 True 4957.5 6698 92.4540 1 6932 2 chr5B.!!$R1 6931
2 TraesCS5D01G449600 chr5A 622767527 622774454 6927 True 1904.8 5651 91.2788 44 7070 5 chr5A.!!$R3 7026

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
108 109 0.035820 TCCATAGCCCACCAACGAAC 60.036 55.000 0.00 0.0 0.00 3.95 F
784 824 0.172352 AAGAGAGAGAAGCGAAGGCG 59.828 55.000 0.00 0.0 46.35 5.52 F
1662 1747 0.250338 GGCTCAAGACCCTTGACGTT 60.250 55.000 5.38 0.0 0.00 3.99 F
2526 2628 0.533491 TGCACCGTATGTAGTCCACC 59.467 55.000 0.00 0.0 0.00 4.61 F
3326 3432 0.765510 AGGCTTTCGTCTCCCAACTT 59.234 50.000 0.00 0.0 0.00 2.66 F
3693 3799 2.523325 TTGTTATGGGTGTGGATGGG 57.477 50.000 0.00 0.0 0.00 4.00 F
5212 5323 1.801025 CGTTGGGTTTGTGCCTTTGTC 60.801 52.381 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1726 0.895530 CGTCAAGGGTCTTGAGCCTA 59.104 55.000 19.95 4.7 0.00 3.93 R
2595 2697 0.532115 GCAGGCCCAAAATCAATCGT 59.468 50.000 0.00 0.0 0.00 3.73 R
2596 2698 0.819582 AGCAGGCCCAAAATCAATCG 59.180 50.000 0.00 0.0 0.00 3.34 R
3351 3457 1.878211 TCTATGGTGATGGCTGGTCA 58.122 50.000 0.00 0.0 0.00 4.02 R
4245 4351 2.035632 TCCAATCCACCAACAACCAAC 58.964 47.619 0.00 0.0 0.00 3.77 R
5256 5367 2.747989 GGCCCACTAGCTGTTAAAAGAC 59.252 50.000 0.00 0.0 0.00 3.01 R
6942 7159 0.042581 TCTCCACTGCCACCCAGATA 59.957 55.000 0.00 0.0 44.64 1.98 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
34 35 8.334632 CAGCGATTAACATTACATAATCACACA 58.665 33.333 6.40 0.00 38.05 3.72
100 101 3.891049 AGAGACAATTTCCATAGCCCAC 58.109 45.455 0.00 0.00 0.00 4.61
104 105 2.831526 ACAATTTCCATAGCCCACCAAC 59.168 45.455 0.00 0.00 0.00 3.77
108 109 0.035820 TCCATAGCCCACCAACGAAC 60.036 55.000 0.00 0.00 0.00 3.95
169 172 2.180276 TCCTAACCAGAGACCAGAAGC 58.820 52.381 0.00 0.00 0.00 3.86
170 173 1.134965 CCTAACCAGAGACCAGAAGCG 60.135 57.143 0.00 0.00 0.00 4.68
178 181 1.817099 GACCAGAAGCGGCATCCTG 60.817 63.158 1.45 6.06 0.00 3.86
181 184 1.144716 CAGAAGCGGCATCCTGCTA 59.855 57.895 1.45 0.00 44.28 3.49
221 225 1.630878 GAGAAGAGGGGAAAGGAAGCA 59.369 52.381 0.00 0.00 0.00 3.91
227 231 0.318441 GGGGAAAGGAAGCAGCAAAC 59.682 55.000 0.00 0.00 0.00 2.93
336 340 1.039233 AAGGCAACACACAGCAAGCT 61.039 50.000 0.00 0.00 41.41 3.74
337 341 0.179020 AGGCAACACACAGCAAGCTA 60.179 50.000 0.00 0.00 41.41 3.32
338 342 0.883833 GGCAACACACAGCAAGCTAT 59.116 50.000 0.00 0.00 0.00 2.97
384 399 1.003580 ACCAATCGAGTCAGCACCAAT 59.996 47.619 0.00 0.00 0.00 3.16
408 423 1.679898 GAACCAGCAGCCTACCTGT 59.320 57.895 0.00 0.00 43.71 4.00
468 483 1.481772 CTCTCCTTCCTCTTGGAGCTG 59.518 57.143 0.00 0.00 46.90 4.24
545 564 1.902938 TCGCAACCATTCCAACATCA 58.097 45.000 0.00 0.00 0.00 3.07
548 567 2.730928 CGCAACCATTCCAACATCAAAC 59.269 45.455 0.00 0.00 0.00 2.93
550 569 3.663025 CAACCATTCCAACATCAAACCC 58.337 45.455 0.00 0.00 0.00 4.11
551 570 1.892474 ACCATTCCAACATCAAACCCG 59.108 47.619 0.00 0.00 0.00 5.28
552 571 1.204467 CCATTCCAACATCAAACCCGG 59.796 52.381 0.00 0.00 0.00 5.73
553 572 1.204467 CATTCCAACATCAAACCCGGG 59.796 52.381 22.25 22.25 0.00 5.73
784 824 0.172352 AAGAGAGAGAAGCGAAGGCG 59.828 55.000 0.00 0.00 46.35 5.52
821 861 1.686325 TAGACCAGCTCGGCCCATTC 61.686 60.000 0.00 0.00 39.03 2.67
826 866 1.097547 CAGCTCGGCCCATTCGAAAT 61.098 55.000 0.00 0.00 36.15 2.17
830 870 2.135933 CTCGGCCCATTCGAAATACTC 58.864 52.381 0.00 0.00 36.15 2.59
957 1000 2.234908 CTCTCCGTAATCCCATCCATCC 59.765 54.545 0.00 0.00 0.00 3.51
983 1029 2.056223 CCCTCGGCGAAACCCTAGA 61.056 63.158 12.13 0.00 33.26 2.43
1133 1182 0.824759 GCCTCCTTCCTCGCTTCTTA 59.175 55.000 0.00 0.00 0.00 2.10
1137 1186 4.623002 CCTCCTTCCTCGCTTCTTATTAC 58.377 47.826 0.00 0.00 0.00 1.89
1181 1230 0.941463 CGTCGTCTGCTCTTGCTTGT 60.941 55.000 0.00 0.00 40.48 3.16
1215 1273 1.068055 GGCTCTTGATTGTTGGCTGTG 60.068 52.381 0.00 0.00 0.00 3.66
1302 1360 3.701040 CTCAAGGAGGAGGAGAAGAAGAG 59.299 52.174 0.00 0.00 0.00 2.85
1325 1383 1.168714 GGTGTGATGCTGACCCTTTC 58.831 55.000 0.00 0.00 0.00 2.62
1345 1404 4.585955 TCTTCTGTCGTGCTACTTTTCT 57.414 40.909 0.00 0.00 0.00 2.52
1346 1405 4.299155 TCTTCTGTCGTGCTACTTTTCTG 58.701 43.478 0.00 0.00 0.00 3.02
1347 1406 4.037565 TCTTCTGTCGTGCTACTTTTCTGA 59.962 41.667 0.00 0.00 0.00 3.27
1348 1407 4.521130 TCTGTCGTGCTACTTTTCTGAT 57.479 40.909 0.00 0.00 0.00 2.90
1349 1408 4.237724 TCTGTCGTGCTACTTTTCTGATG 58.762 43.478 0.00 0.00 0.00 3.07
1350 1409 2.736721 TGTCGTGCTACTTTTCTGATGC 59.263 45.455 0.00 0.00 0.00 3.91
1351 1410 2.736721 GTCGTGCTACTTTTCTGATGCA 59.263 45.455 0.00 0.00 0.00 3.96
1352 1411 2.995939 TCGTGCTACTTTTCTGATGCAG 59.004 45.455 0.00 0.00 0.00 4.41
1353 1412 2.995939 CGTGCTACTTTTCTGATGCAGA 59.004 45.455 0.00 0.00 38.87 4.26
1354 1413 3.620374 CGTGCTACTTTTCTGATGCAGAT 59.380 43.478 0.00 0.00 40.39 2.90
1355 1414 4.805719 CGTGCTACTTTTCTGATGCAGATA 59.194 41.667 0.00 0.00 40.39 1.98
1356 1415 5.291858 CGTGCTACTTTTCTGATGCAGATAA 59.708 40.000 0.00 0.00 40.39 1.75
1357 1416 6.018425 CGTGCTACTTTTCTGATGCAGATAAT 60.018 38.462 0.00 0.00 40.39 1.28
1358 1417 7.130917 GTGCTACTTTTCTGATGCAGATAATG 58.869 38.462 0.00 2.31 40.39 1.90
1359 1418 6.825213 TGCTACTTTTCTGATGCAGATAATGT 59.175 34.615 0.00 6.91 40.39 2.71
1363 1422 7.533426 ACTTTTCTGATGCAGATAATGTTGAC 58.467 34.615 0.00 0.00 40.39 3.18
1420 1479 3.117491 TCTCTCTGTCTTGTTTGCTGG 57.883 47.619 0.00 0.00 0.00 4.85
1429 1488 4.095782 TGTCTTGTTTGCTGGAACACTAAC 59.904 41.667 1.30 0.00 39.11 2.34
1459 1521 7.012515 TCCGTGTGTGTCTTTTAATTGTTGTAT 59.987 33.333 0.00 0.00 0.00 2.29
1461 1523 7.642194 CGTGTGTGTCTTTTAATTGTTGTATGT 59.358 33.333 0.00 0.00 0.00 2.29
1462 1524 9.938670 GTGTGTGTCTTTTAATTGTTGTATGTA 57.061 29.630 0.00 0.00 0.00 2.29
1464 1526 9.607285 GTGTGTCTTTTAATTGTTGTATGTAGG 57.393 33.333 0.00 0.00 0.00 3.18
1465 1527 8.293867 TGTGTCTTTTAATTGTTGTATGTAGGC 58.706 33.333 0.00 0.00 0.00 3.93
1466 1528 7.480542 GTGTCTTTTAATTGTTGTATGTAGGCG 59.519 37.037 0.00 0.00 0.00 5.52
1467 1529 6.964934 GTCTTTTAATTGTTGTATGTAGGCGG 59.035 38.462 0.00 0.00 0.00 6.13
1468 1530 4.886247 TTAATTGTTGTATGTAGGCGGC 57.114 40.909 0.00 0.00 0.00 6.53
1469 1531 1.295792 ATTGTTGTATGTAGGCGGCG 58.704 50.000 0.51 0.51 0.00 6.46
1470 1532 0.741574 TTGTTGTATGTAGGCGGCGG 60.742 55.000 9.78 0.00 0.00 6.13
1471 1533 1.153509 GTTGTATGTAGGCGGCGGT 60.154 57.895 9.78 0.00 0.00 5.68
1472 1534 1.153529 TTGTATGTAGGCGGCGGTG 60.154 57.895 9.78 0.00 0.00 4.94
1569 1640 3.726517 GCGCCGCTTTCTTGCTGA 61.727 61.111 0.00 0.00 0.00 4.26
1574 1645 1.672881 GCCGCTTTCTTGCTGATGTAT 59.327 47.619 0.00 0.00 0.00 2.29
1580 1651 7.072030 CCGCTTTCTTGCTGATGTATTATTAC 58.928 38.462 0.00 0.00 0.00 1.89
1581 1652 7.041780 CCGCTTTCTTGCTGATGTATTATTACT 60.042 37.037 0.00 0.00 0.00 2.24
1582 1653 7.795734 CGCTTTCTTGCTGATGTATTATTACTG 59.204 37.037 0.00 0.00 0.00 2.74
1604 1689 4.181578 GGCTGAATTGCGTTCTAGTTCTA 58.818 43.478 3.71 0.00 37.72 2.10
1649 1734 7.120285 GCAGCAATATTATGAGAATAGGCTCAA 59.880 37.037 5.99 0.00 46.94 3.02
1661 1746 1.122019 AGGCTCAAGACCCTTGACGT 61.122 55.000 5.38 0.00 0.00 4.34
1662 1747 0.250338 GGCTCAAGACCCTTGACGTT 60.250 55.000 5.38 0.00 0.00 3.99
1683 1768 3.021263 AAGGCCGGGGGTGCTAAT 61.021 61.111 2.18 0.00 0.00 1.73
1974 2060 3.221964 GCTGATGCCAGGTAAACTTTG 57.778 47.619 0.00 0.00 40.72 2.77
1975 2061 2.819608 GCTGATGCCAGGTAAACTTTGA 59.180 45.455 0.00 0.00 40.72 2.69
1980 2066 4.164843 TGCCAGGTAAACTTTGAAGACT 57.835 40.909 0.00 0.00 0.00 3.24
1981 2067 5.298989 TGCCAGGTAAACTTTGAAGACTA 57.701 39.130 0.00 0.00 0.00 2.59
2006 2092 1.541588 GGTGTCTGTTTGGATGGCTTC 59.458 52.381 0.00 0.00 0.00 3.86
2007 2093 2.229792 GTGTCTGTTTGGATGGCTTCA 58.770 47.619 2.60 0.00 0.00 3.02
2017 2103 3.565307 TGGATGGCTTCAGTCACTTTTT 58.435 40.909 2.60 0.00 29.57 1.94
2021 2107 3.820557 TGGCTTCAGTCACTTTTTAGCT 58.179 40.909 0.00 0.00 0.00 3.32
2044 2132 7.041235 AGCTTGTCTATTACTATCAGTACCGAC 60.041 40.741 0.00 0.00 28.93 4.79
2207 2297 4.947645 AGCTTTGCTTGCAACTTAATTGA 58.052 34.783 7.60 0.00 36.43 2.57
2208 2298 5.544650 AGCTTTGCTTGCAACTTAATTGAT 58.455 33.333 7.60 0.00 36.43 2.57
2209 2299 5.993441 AGCTTTGCTTGCAACTTAATTGATT 59.007 32.000 7.60 0.00 36.43 2.57
2216 2306 9.449550 TGCTTGCAACTTAATTGATTATTATCG 57.550 29.630 0.00 0.00 41.23 2.92
2278 2368 4.336713 AGTTCTTGGCTTCTGAGTTTTCAC 59.663 41.667 0.00 0.00 0.00 3.18
2344 2434 5.045215 CAGTTCAGTCAATTGTGTTTGCAT 58.955 37.500 5.13 0.00 0.00 3.96
2363 2453 4.947388 TGCATTCTGGTTTTATACTGGGTC 59.053 41.667 0.00 0.00 0.00 4.46
2364 2454 4.338400 GCATTCTGGTTTTATACTGGGTCC 59.662 45.833 0.00 0.00 0.00 4.46
2365 2455 5.755849 CATTCTGGTTTTATACTGGGTCCT 58.244 41.667 0.00 0.00 0.00 3.85
2366 2456 5.853572 TTCTGGTTTTATACTGGGTCCTT 57.146 39.130 0.00 0.00 0.00 3.36
2367 2457 5.174037 TCTGGTTTTATACTGGGTCCTTG 57.826 43.478 0.00 0.00 0.00 3.61
2368 2458 4.600111 TCTGGTTTTATACTGGGTCCTTGT 59.400 41.667 0.00 0.00 0.00 3.16
2369 2459 5.073965 TCTGGTTTTATACTGGGTCCTTGTT 59.926 40.000 0.00 0.00 0.00 2.83
2370 2460 5.707495 TGGTTTTATACTGGGTCCTTGTTT 58.293 37.500 0.00 0.00 0.00 2.83
2371 2461 6.137559 TGGTTTTATACTGGGTCCTTGTTTT 58.862 36.000 0.00 0.00 0.00 2.43
2372 2462 7.296098 TGGTTTTATACTGGGTCCTTGTTTTA 58.704 34.615 0.00 0.00 0.00 1.52
2423 2525 9.433153 CTTTATAAAATATACTCCCTCCGTTCC 57.567 37.037 0.00 0.00 0.00 3.62
2425 2527 9.827198 TTATAAAATATACTCCCTCCGTTCCTA 57.173 33.333 0.00 0.00 0.00 2.94
2426 2528 8.731591 ATAAAATATACTCCCTCCGTTCCTAA 57.268 34.615 0.00 0.00 0.00 2.69
2427 2529 7.441903 AAAATATACTCCCTCCGTTCCTAAA 57.558 36.000 0.00 0.00 0.00 1.85
2434 2536 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2435 2537 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2436 2538 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2439 2541 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2440 2542 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
2462 2564 9.616156 TTTGTAGAGTTTTCACTATAAACCACA 57.384 29.630 0.00 0.00 36.40 4.17
2466 2568 8.475331 AGAGTTTTCACTATAAACCACATACG 57.525 34.615 0.00 0.00 36.40 3.06
2467 2569 7.548075 AGAGTTTTCACTATAAACCACATACGG 59.452 37.037 0.00 0.00 36.40 4.02
2468 2570 7.388437 AGTTTTCACTATAAACCACATACGGA 58.612 34.615 0.00 0.00 36.40 4.69
2469 2571 8.044908 AGTTTTCACTATAAACCACATACGGAT 58.955 33.333 0.00 0.00 36.40 4.18
2472 2574 7.585579 TCACTATAAACCACATACGGATGTA 57.414 36.000 14.23 0.00 44.82 2.29
2474 2576 9.299465 TCACTATAAACCACATACGGATGTATA 57.701 33.333 14.23 6.48 44.82 1.47
2481 2583 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
2482 2584 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
2483 2585 7.069950 ACCACATACGGATGTATATAGATGCAT 59.930 37.037 14.23 0.00 44.82 3.96
2484 2586 7.928167 CCACATACGGATGTATATAGATGCATT 59.072 37.037 14.23 1.23 44.82 3.56
2485 2587 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
2486 2588 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
2490 2592 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
2511 2613 9.624697 TTAAGTGTAGATTCATTCATTTTGCAC 57.375 29.630 0.00 0.00 0.00 4.57
2512 2614 6.624423 AGTGTAGATTCATTCATTTTGCACC 58.376 36.000 0.00 0.00 0.00 5.01
2513 2615 5.512788 GTGTAGATTCATTCATTTTGCACCG 59.487 40.000 0.00 0.00 0.00 4.94
2514 2616 4.789012 AGATTCATTCATTTTGCACCGT 57.211 36.364 0.00 0.00 0.00 4.83
2515 2617 5.895636 AGATTCATTCATTTTGCACCGTA 57.104 34.783 0.00 0.00 0.00 4.02
2516 2618 6.455360 AGATTCATTCATTTTGCACCGTAT 57.545 33.333 0.00 0.00 0.00 3.06
2517 2619 6.267817 AGATTCATTCATTTTGCACCGTATG 58.732 36.000 0.00 0.00 0.00 2.39
2518 2620 5.384063 TTCATTCATTTTGCACCGTATGT 57.616 34.783 0.00 0.00 0.00 2.29
2519 2621 6.502136 TTCATTCATTTTGCACCGTATGTA 57.498 33.333 0.00 0.00 0.00 2.29
2520 2622 6.117911 TCATTCATTTTGCACCGTATGTAG 57.882 37.500 0.00 0.00 0.00 2.74
2521 2623 5.645929 TCATTCATTTTGCACCGTATGTAGT 59.354 36.000 0.00 0.00 0.00 2.73
2522 2624 5.539582 TTCATTTTGCACCGTATGTAGTC 57.460 39.130 0.00 0.00 0.00 2.59
2523 2625 3.936453 TCATTTTGCACCGTATGTAGTCC 59.064 43.478 0.00 0.00 0.00 3.85
2524 2626 3.404224 TTTTGCACCGTATGTAGTCCA 57.596 42.857 0.00 0.00 0.00 4.02
2525 2627 2.373540 TTGCACCGTATGTAGTCCAC 57.626 50.000 0.00 0.00 0.00 4.02
2526 2628 0.533491 TGCACCGTATGTAGTCCACC 59.467 55.000 0.00 0.00 0.00 4.61
2527 2629 0.822164 GCACCGTATGTAGTCCACCT 59.178 55.000 0.00 0.00 0.00 4.00
2528 2630 2.026641 GCACCGTATGTAGTCCACCTA 58.973 52.381 0.00 0.00 0.00 3.08
2529 2631 2.034305 GCACCGTATGTAGTCCACCTAG 59.966 54.545 0.00 0.00 0.00 3.02
2530 2632 3.285484 CACCGTATGTAGTCCACCTAGT 58.715 50.000 0.00 0.00 0.00 2.57
2531 2633 3.066342 CACCGTATGTAGTCCACCTAGTG 59.934 52.174 0.00 0.00 0.00 2.74
2546 2648 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
2567 2669 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2622 2724 7.309133 CGATTGATTTTGGGCCTGCTATTATAA 60.309 37.037 4.53 0.00 0.00 0.98
2626 2728 7.447238 TGATTTTGGGCCTGCTATTATAAGTAC 59.553 37.037 4.53 0.00 0.00 2.73
2904 3007 7.090173 TCTGTTTGAAAGTTGGTTCTTGAAAG 58.910 34.615 0.00 0.00 0.00 2.62
3121 3227 4.263331 GGGACCAGGTTTGTTCTCATTCTA 60.263 45.833 0.00 0.00 0.00 2.10
3125 3231 5.765182 ACCAGGTTTGTTCTCATTCTAACTG 59.235 40.000 0.00 0.00 0.00 3.16
3168 3274 1.186200 TTCTGCGATGTGGAGTAGCT 58.814 50.000 0.00 0.00 37.31 3.32
3174 3280 2.930887 GCGATGTGGAGTAGCTGTCAAA 60.931 50.000 0.00 0.00 0.00 2.69
3221 3327 8.985315 ATTCCATAGGGTGTTATATGCATATG 57.015 34.615 26.21 10.08 34.93 1.78
3247 3353 9.457436 GTTCCTTCTTATTTACATGTAGGGAAA 57.543 33.333 5.56 0.00 31.22 3.13
3326 3432 0.765510 AGGCTTTCGTCTCCCAACTT 59.234 50.000 0.00 0.00 0.00 2.66
3385 3491 3.990245 ACCATAGATTAAGGCCCATTCCT 59.010 43.478 0.00 0.00 38.31 3.36
3398 3504 7.642094 AGGCCCATTCCTAATAGTAACATTA 57.358 36.000 0.00 0.00 33.95 1.90
3507 3613 9.029243 CACATTTTTGCACTTTACTTTCACATA 57.971 29.630 0.00 0.00 0.00 2.29
3508 3614 9.030301 ACATTTTTGCACTTTACTTTCACATAC 57.970 29.630 0.00 0.00 0.00 2.39
3663 3769 2.939103 CCTCTTTGCTAAATCTCACCCG 59.061 50.000 0.00 0.00 0.00 5.28
3679 3785 3.945921 TCACCCGTTTGTTCACATTGTTA 59.054 39.130 0.00 0.00 0.00 2.41
3693 3799 2.523325 TTGTTATGGGTGTGGATGGG 57.477 50.000 0.00 0.00 0.00 4.00
3713 3819 3.939592 GGGTAGTACAATGCCAGTTTCTC 59.060 47.826 2.06 0.00 0.00 2.87
3735 3841 7.224297 TCTCTACCAACTTAATTTGCTGAGTT 58.776 34.615 14.16 0.00 32.89 3.01
3769 3875 4.944962 TCTAATTTGCATGACCAAGTCG 57.055 40.909 0.00 0.00 34.95 4.18
3789 3895 2.930040 CGTAGTGTTGATGGATGTGACC 59.070 50.000 0.00 0.00 0.00 4.02
4068 4174 8.752005 TTTGGAGGTAGGATTCTTCAAATATG 57.248 34.615 0.00 0.00 34.58 1.78
4239 4345 4.572389 CGTATTGCACCTGAGCTTTATCTT 59.428 41.667 0.00 0.00 34.99 2.40
4245 4351 4.813697 GCACCTGAGCTTTATCTTAAGGAG 59.186 45.833 1.85 0.00 0.00 3.69
4359 4465 6.657836 ACAGTTGAGTTTTATATGGCGTAC 57.342 37.500 0.00 0.00 0.00 3.67
4424 4530 9.299963 GATATCTGGTGAGAATCTATTTCATCG 57.700 37.037 0.00 0.00 36.75 3.84
4443 4549 8.438676 TTCATCGATATTTTCCTTCTTCCTTC 57.561 34.615 0.00 0.00 0.00 3.46
4447 4553 6.976925 TCGATATTTTCCTTCTTCCTTCGTAC 59.023 38.462 0.00 0.00 0.00 3.67
4512 4618 3.452627 CAGGTATGGTTAAGGAGCTGACT 59.547 47.826 0.00 0.00 39.26 3.41
4979 5087 6.270064 GCTGCTTGACAAGGTTTTACTTTTA 58.730 36.000 16.80 0.00 0.00 1.52
5016 5124 3.885724 TCCGATGCTGTGTCTTCATTA 57.114 42.857 0.00 0.00 0.00 1.90
5180 5291 8.267620 TCTCAGTGGTATTATTTGTTGTCATG 57.732 34.615 0.00 0.00 0.00 3.07
5181 5292 7.336679 TCTCAGTGGTATTATTTGTTGTCATGG 59.663 37.037 0.00 0.00 0.00 3.66
5182 5293 6.945435 TCAGTGGTATTATTTGTTGTCATGGT 59.055 34.615 0.00 0.00 0.00 3.55
5212 5323 1.801025 CGTTGGGTTTGTGCCTTTGTC 60.801 52.381 0.00 0.00 0.00 3.18
5256 5367 6.862209 TGTTAGCTAATTTTACAAGCCATGG 58.138 36.000 9.88 7.63 36.92 3.66
5454 5565 2.159085 GGTCCTTTGATACCTGGTCTCG 60.159 54.545 0.63 0.00 32.72 4.04
5578 5689 7.891498 ACAACTAAAGGTACCTGTTTGAATT 57.109 32.000 17.14 6.58 0.00 2.17
5588 5699 3.960102 ACCTGTTTGAATTTGCCTGAGAA 59.040 39.130 0.00 0.00 0.00 2.87
5591 5702 5.452356 CCTGTTTGAATTTGCCTGAGAACTT 60.452 40.000 0.00 0.00 0.00 2.66
5631 5742 3.749088 TGTAATTCTTGCTGTAACCACCG 59.251 43.478 0.00 0.00 0.00 4.94
5634 5745 0.882927 TCTTGCTGTAACCACCGCAC 60.883 55.000 0.00 0.00 43.50 5.34
5748 5861 6.890663 ATGTTGTGCATATATTTTGTGTGC 57.109 33.333 0.00 0.00 35.74 4.57
5811 5935 2.503895 AGCCTGCATTGCTCTACTTT 57.496 45.000 10.49 0.00 32.41 2.66
6041 6168 6.311200 GGCTATTTCCATCATTTGTGTTTCAC 59.689 38.462 0.00 0.00 34.56 3.18
6070 6197 4.093261 GCAACACTTTTTGACTTGCATTGT 59.907 37.500 0.00 0.00 37.70 2.71
6162 6289 2.666272 TGCAAACCCATCAACAGGTA 57.334 45.000 0.00 0.00 34.45 3.08
6190 6317 9.771915 GTGAACACACTACTTTATCTAGTACTC 57.228 37.037 0.00 0.00 0.00 2.59
6192 6319 7.551035 ACACACTACTTTATCTAGTACTCCG 57.449 40.000 0.00 0.00 0.00 4.63
6318 6523 4.012374 AGTCTTGCGGATCATGAAATGTT 58.988 39.130 0.00 0.00 46.80 2.71
6372 6577 3.753272 GCTCAGATTTCTTGTTGCACCTA 59.247 43.478 0.00 0.00 0.00 3.08
6407 6618 8.333235 AGTATTTTGACCTGTTATACCATGGAA 58.667 33.333 21.47 0.00 0.00 3.53
6448 6659 2.069273 GTGCGTCTATGCTGTTTCTGT 58.931 47.619 0.00 0.00 35.36 3.41
6477 6688 2.682256 TTTGTTTGCTGCGCTGAGGC 62.682 55.000 19.32 12.73 0.00 4.70
6520 6733 6.546034 ACAATACAAGGAGTTTTAACTGTGCT 59.454 34.615 0.00 0.00 39.88 4.40
6595 6808 5.425217 AGGGTTGTTGAAAATTTGAACTCCT 59.575 36.000 9.26 9.83 0.00 3.69
6600 6813 8.807581 GTTGTTGAAAATTTGAACTCCTGTTAG 58.192 33.333 9.26 0.00 36.39 2.34
6632 6845 5.067413 CAGTGAGGCATATGAAGCAAGAATT 59.933 40.000 6.97 0.00 0.00 2.17
6705 6921 7.650834 TTCAAAATTTAGTGCTTGGTATTGC 57.349 32.000 0.00 0.00 0.00 3.56
6716 6932 6.316390 AGTGCTTGGTATTGCTATACACTTTC 59.684 38.462 18.03 3.32 38.71 2.62
6770 6986 7.210873 GTCTTATTTGTATGGACCACTAGAGG 58.789 42.308 4.44 4.44 0.00 3.69
6781 6997 1.063567 CCACTAGAGGTAGAGGTGCCT 60.064 57.143 0.00 0.00 42.50 4.75
6848 7064 1.283321 AGGATGAAAGGTCCCAGAAGC 59.717 52.381 0.00 0.00 36.36 3.86
6899 7116 9.945904 ATACTAACTGGAGGAACTTAAAGAAAG 57.054 33.333 0.00 0.00 41.55 2.62
6907 7124 8.793592 TGGAGGAACTTAAAGAAAGCTAAAATC 58.206 33.333 0.00 0.00 41.55 2.17
6926 7143 4.882671 ATCAACTAAATACAAGCTGCCG 57.117 40.909 0.00 0.00 0.00 5.69
6940 7157 4.179579 GCCGTGGCCGCAATCTTC 62.180 66.667 18.18 0.00 34.56 2.87
6941 7158 2.745884 CCGTGGCCGCAATCTTCA 60.746 61.111 18.18 0.00 0.00 3.02
6942 7159 2.114670 CCGTGGCCGCAATCTTCAT 61.115 57.895 18.18 0.00 0.00 2.57
6943 7160 0.813610 CCGTGGCCGCAATCTTCATA 60.814 55.000 18.18 0.00 0.00 2.15
6944 7161 1.229428 CGTGGCCGCAATCTTCATAT 58.771 50.000 18.18 0.00 0.00 1.78
6945 7162 1.195448 CGTGGCCGCAATCTTCATATC 59.805 52.381 18.18 0.00 0.00 1.63
6967 7232 2.301346 GGGTGGCAGTGGAGATATTTG 58.699 52.381 0.00 0.00 0.00 2.32
6976 7241 6.481644 GGCAGTGGAGATATTTGAAGTTCTAG 59.518 42.308 4.17 0.00 0.00 2.43
6984 7249 9.575783 GAGATATTTGAAGTTCTAGTTCGTTCT 57.424 33.333 4.17 0.00 30.24 3.01
6991 7256 9.622004 TTGAAGTTCTAGTTCGTTCTAATACAG 57.378 33.333 4.17 0.00 30.24 2.74
6996 7261 9.063739 GTTCTAGTTCGTTCTAATACAGACTTG 57.936 37.037 0.00 0.00 31.12 3.16
7027 7292 7.839200 AGTTTGGCCAAGTTCATATAAATACCT 59.161 33.333 19.48 0.00 0.00 3.08
7029 7294 9.702253 TTTGGCCAAGTTCATATAAATACCTAA 57.298 29.630 19.48 0.00 0.00 2.69
7030 7295 8.685838 TGGCCAAGTTCATATAAATACCTAAC 57.314 34.615 0.61 0.00 0.00 2.34
7031 7296 8.275758 TGGCCAAGTTCATATAAATACCTAACA 58.724 33.333 0.61 0.00 0.00 2.41
7032 7297 9.297037 GGCCAAGTTCATATAAATACCTAACAT 57.703 33.333 0.00 0.00 0.00 2.71
7053 7318 8.608844 AACATCTATACAGCACTAAATTAGCC 57.391 34.615 0.00 0.00 0.00 3.93
7062 7327 7.112779 ACAGCACTAAATTAGCCTTGTTAGAT 58.887 34.615 0.00 0.00 0.00 1.98
7129 7394 2.829741 TTTCCGGAAATTGCCTTTGG 57.170 45.000 25.67 0.00 0.00 3.28
7130 7395 1.710816 TTCCGGAAATTGCCTTTGGT 58.289 45.000 16.28 0.00 0.00 3.67
7131 7396 0.965439 TCCGGAAATTGCCTTTGGTG 59.035 50.000 0.00 0.00 0.00 4.17
7132 7397 0.965439 CCGGAAATTGCCTTTGGTGA 59.035 50.000 0.00 0.00 0.00 4.02
7133 7398 1.336795 CCGGAAATTGCCTTTGGTGAC 60.337 52.381 0.00 0.00 0.00 3.67
7134 7399 1.336795 CGGAAATTGCCTTTGGTGACC 60.337 52.381 0.00 0.00 0.00 4.02
7135 7400 1.336795 GGAAATTGCCTTTGGTGACCG 60.337 52.381 0.00 0.00 0.00 4.79
7136 7401 1.611491 GAAATTGCCTTTGGTGACCGA 59.389 47.619 0.00 0.00 0.00 4.69
7137 7402 1.247567 AATTGCCTTTGGTGACCGAG 58.752 50.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.798516 GTGTGATTATGTAATGTTAATCGCTGG 59.201 37.037 13.97 0.00 42.07 4.85
108 109 3.893345 TGGATCACCCGTCGACTTATCG 61.893 54.545 14.70 0.00 43.56 2.92
120 121 2.094675 CAAATGTGGTCTGGATCACCC 58.905 52.381 10.92 0.00 41.62 4.61
121 122 1.474077 GCAAATGTGGTCTGGATCACC 59.526 52.381 10.92 0.00 41.62 4.02
178 181 7.388776 TCTCAGTTTGGCAATATGACATATAGC 59.611 37.037 8.38 0.00 33.90 2.97
181 184 7.994911 TCTTCTCAGTTTGGCAATATGACATAT 59.005 33.333 0.00 1.87 33.90 1.78
256 260 0.250295 CGAGTTCCAGCCCAACAAGA 60.250 55.000 0.00 0.00 0.00 3.02
336 340 5.442391 GGGTTTGGTTGGTGCTAATCTATA 58.558 41.667 0.00 0.00 0.00 1.31
337 341 4.278310 GGGTTTGGTTGGTGCTAATCTAT 58.722 43.478 0.00 0.00 0.00 1.98
338 342 3.692690 GGGTTTGGTTGGTGCTAATCTA 58.307 45.455 0.00 0.00 0.00 1.98
408 423 2.661537 CTCAAGTGCACCGACGCA 60.662 61.111 14.63 0.00 40.32 5.24
552 571 2.778717 CTTCCCCTCCCATCCCCC 60.779 72.222 0.00 0.00 0.00 5.40
553 572 2.778717 CCTTCCCCTCCCATCCCC 60.779 72.222 0.00 0.00 0.00 4.81
558 577 3.515383 TTGCTCCCTTCCCCTCCCA 62.515 63.158 0.00 0.00 0.00 4.37
563 582 1.465172 AAGGTTTGCTCCCTTCCCC 59.535 57.895 0.00 0.00 37.82 4.81
796 836 1.379977 CCGAGCTGGTCTAGGTGGA 60.380 63.158 5.23 0.00 37.23 4.02
811 851 1.483004 TGAGTATTTCGAATGGGCCGA 59.517 47.619 0.00 0.00 0.00 5.54
821 861 1.343821 GGTGCGCGTGAGTATTTCG 59.656 57.895 8.43 0.00 0.00 3.46
826 866 4.735132 GCCTGGTGCGCGTGAGTA 62.735 66.667 8.43 0.00 0.00 2.59
933 976 1.416401 GGATGGGATTACGGAGAGCAA 59.584 52.381 0.00 0.00 0.00 3.91
1097 1146 1.445238 GCGCACTTCTTCGAGAGCT 60.445 57.895 0.30 0.00 32.07 4.09
1133 1182 1.805120 CGCGAAACGGAGGATGGTAAT 60.805 52.381 0.00 0.00 38.44 1.89
1137 1186 3.564027 GCGCGAAACGGAGGATGG 61.564 66.667 12.10 0.00 43.93 3.51
1181 1230 2.487762 CAAGAGCCGGAGCATAACAAAA 59.512 45.455 5.05 0.00 43.56 2.44
1302 1360 1.589716 GGGTCAGCATCACACCTTGC 61.590 60.000 0.00 0.00 39.17 4.01
1325 1383 4.299155 TCAGAAAAGTAGCACGACAGAAG 58.701 43.478 0.00 0.00 0.00 2.85
1345 1404 3.269178 TGCGTCAACATTATCTGCATCA 58.731 40.909 0.00 0.00 0.00 3.07
1346 1405 3.310774 ACTGCGTCAACATTATCTGCATC 59.689 43.478 0.00 0.00 0.00 3.91
1347 1406 3.273434 ACTGCGTCAACATTATCTGCAT 58.727 40.909 0.00 0.00 0.00 3.96
1348 1407 2.698803 ACTGCGTCAACATTATCTGCA 58.301 42.857 0.00 0.00 0.00 4.41
1349 1408 3.372206 AGAACTGCGTCAACATTATCTGC 59.628 43.478 0.00 0.00 0.00 4.26
1350 1409 4.890378 CAGAACTGCGTCAACATTATCTG 58.110 43.478 0.00 0.00 0.00 2.90
1407 1466 4.095782 TGTTAGTGTTCCAGCAAACAAGAC 59.904 41.667 1.51 2.71 40.62 3.01
1420 1479 3.428870 CACACACGGAGATGTTAGTGTTC 59.571 47.826 0.00 0.00 44.32 3.18
1429 1488 5.862924 ATTAAAAGACACACACGGAGATG 57.137 39.130 0.00 0.00 0.00 2.90
1517 1588 3.056962 CAGTAGGATCCATGTCCTCATCG 60.057 52.174 15.82 0.00 45.51 3.84
1569 1640 6.486657 ACGCAATTCAGCCAGTAATAATACAT 59.513 34.615 0.00 0.00 34.29 2.29
1574 1645 4.941263 AGAACGCAATTCAGCCAGTAATAA 59.059 37.500 0.92 0.00 40.09 1.40
1580 1651 2.350522 ACTAGAACGCAATTCAGCCAG 58.649 47.619 0.00 0.00 40.09 4.85
1581 1652 2.472695 ACTAGAACGCAATTCAGCCA 57.527 45.000 0.00 0.00 40.09 4.75
1582 1653 3.003480 AGAACTAGAACGCAATTCAGCC 58.997 45.455 0.00 0.00 40.09 4.85
1604 1689 4.304110 CTGCAGCAAGAAACACATTGATT 58.696 39.130 0.00 0.00 0.00 2.57
1635 1720 3.121929 AGGGTCTTGAGCCTATTCTCA 57.878 47.619 18.49 0.00 40.99 3.27
1641 1726 0.895530 CGTCAAGGGTCTTGAGCCTA 59.104 55.000 19.95 4.70 0.00 3.93
1661 1746 3.646715 CACCCCCGGCCTTGAGAA 61.647 66.667 0.00 0.00 0.00 2.87
1680 1765 6.681729 AGAAACTTATGCGGATAGGGATTA 57.318 37.500 10.70 0.00 0.00 1.75
1683 1768 4.021368 GCTAGAAACTTATGCGGATAGGGA 60.021 45.833 10.70 0.00 0.00 4.20
1974 2060 7.103641 TCCAAACAGACACCATATTAGTCTTC 58.896 38.462 0.00 0.00 40.42 2.87
1975 2061 7.016153 TCCAAACAGACACCATATTAGTCTT 57.984 36.000 0.00 0.00 40.42 3.01
1980 2066 4.887071 GCCATCCAAACAGACACCATATTA 59.113 41.667 0.00 0.00 0.00 0.98
1981 2067 3.701040 GCCATCCAAACAGACACCATATT 59.299 43.478 0.00 0.00 0.00 1.28
2006 2092 9.209175 AGTAATAGACAAGCTAAAAAGTGACTG 57.791 33.333 0.00 0.00 31.66 3.51
2017 2103 8.152898 TCGGTACTGATAGTAATAGACAAGCTA 58.847 37.037 0.00 0.00 31.62 3.32
2021 2107 7.285566 AGGTCGGTACTGATAGTAATAGACAA 58.714 38.462 7.85 0.00 34.86 3.18
2207 2297 7.707624 ATTTGGATGTGGATGCGATAATAAT 57.292 32.000 0.00 0.00 0.00 1.28
2208 2298 7.448161 AGAATTTGGATGTGGATGCGATAATAA 59.552 33.333 0.00 0.00 0.00 1.40
2209 2299 6.942005 AGAATTTGGATGTGGATGCGATAATA 59.058 34.615 0.00 0.00 0.00 0.98
2216 2306 6.645790 AAGATAGAATTTGGATGTGGATGC 57.354 37.500 0.00 0.00 0.00 3.91
2267 2357 3.131396 AGTAGCAACCGTGAAAACTCAG 58.869 45.455 0.00 0.00 0.00 3.35
2278 2368 4.683832 AGTAGCTGATTAAGTAGCAACCG 58.316 43.478 14.07 0.00 42.29 4.44
2344 2434 5.073965 ACAAGGACCCAGTATAAAACCAGAA 59.926 40.000 0.00 0.00 0.00 3.02
2363 2453 9.594478 AATTAAAACCACTCTGTTAAAACAAGG 57.406 29.630 0.00 0.54 38.66 3.61
2409 2511 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2410 2512 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2436 2538 9.616156 TGTGGTTTATAGTGAAAACTCTACAAA 57.384 29.630 0.00 0.00 37.09 2.83
2440 2542 9.577110 CGTATGTGGTTTATAGTGAAAACTCTA 57.423 33.333 0.00 0.00 37.09 2.43
2444 2546 7.599630 TCCGTATGTGGTTTATAGTGAAAAC 57.400 36.000 0.00 0.00 36.34 2.43
2445 2547 7.825270 ACATCCGTATGTGGTTTATAGTGAAAA 59.175 33.333 0.00 0.00 44.79 2.29
2446 2548 7.332557 ACATCCGTATGTGGTTTATAGTGAAA 58.667 34.615 0.00 0.00 44.79 2.69
2447 2549 6.880484 ACATCCGTATGTGGTTTATAGTGAA 58.120 36.000 0.00 0.00 44.79 3.18
2455 2557 7.764443 GCATCTATATACATCCGTATGTGGTTT 59.236 37.037 3.56 0.00 45.99 3.27
2456 2558 7.093509 TGCATCTATATACATCCGTATGTGGTT 60.094 37.037 3.56 0.00 45.99 3.67
2459 2561 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
2464 2566 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
2485 2587 9.624697 GTGCAAAATGAATGAATCTACACTTAA 57.375 29.630 0.00 0.00 0.00 1.85
2486 2588 8.243426 GGTGCAAAATGAATGAATCTACACTTA 58.757 33.333 0.00 0.00 0.00 2.24
2487 2589 7.092716 GGTGCAAAATGAATGAATCTACACTT 58.907 34.615 0.00 0.00 0.00 3.16
2488 2590 6.623549 CGGTGCAAAATGAATGAATCTACACT 60.624 38.462 0.00 0.00 0.00 3.55
2489 2591 5.512788 CGGTGCAAAATGAATGAATCTACAC 59.487 40.000 0.00 0.00 0.00 2.90
2490 2592 5.182950 ACGGTGCAAAATGAATGAATCTACA 59.817 36.000 0.00 0.00 0.00 2.74
2491 2593 5.640732 ACGGTGCAAAATGAATGAATCTAC 58.359 37.500 0.00 0.00 0.00 2.59
2492 2594 5.895636 ACGGTGCAAAATGAATGAATCTA 57.104 34.783 0.00 0.00 0.00 1.98
2493 2595 4.789012 ACGGTGCAAAATGAATGAATCT 57.211 36.364 0.00 0.00 0.00 2.40
2494 2596 6.035843 ACATACGGTGCAAAATGAATGAATC 58.964 36.000 0.00 0.00 0.00 2.52
2495 2597 5.964758 ACATACGGTGCAAAATGAATGAAT 58.035 33.333 0.00 0.00 0.00 2.57
2496 2598 5.384063 ACATACGGTGCAAAATGAATGAA 57.616 34.783 0.00 0.00 0.00 2.57
2497 2599 5.645929 ACTACATACGGTGCAAAATGAATGA 59.354 36.000 0.00 0.00 0.00 2.57
2498 2600 5.879237 ACTACATACGGTGCAAAATGAATG 58.121 37.500 0.00 0.00 0.00 2.67
2499 2601 5.065988 GGACTACATACGGTGCAAAATGAAT 59.934 40.000 0.00 0.00 0.00 2.57
2500 2602 4.393680 GGACTACATACGGTGCAAAATGAA 59.606 41.667 0.00 0.00 0.00 2.57
2501 2603 3.936453 GGACTACATACGGTGCAAAATGA 59.064 43.478 0.00 0.00 0.00 2.57
2502 2604 3.687212 TGGACTACATACGGTGCAAAATG 59.313 43.478 0.00 0.00 31.30 2.32
2503 2605 3.687698 GTGGACTACATACGGTGCAAAAT 59.312 43.478 0.00 0.00 35.72 1.82
2504 2606 3.068560 GTGGACTACATACGGTGCAAAA 58.931 45.455 0.00 0.00 35.72 2.44
2505 2607 2.613474 GGTGGACTACATACGGTGCAAA 60.613 50.000 0.00 0.00 35.72 3.68
2506 2608 1.066716 GGTGGACTACATACGGTGCAA 60.067 52.381 0.00 0.00 35.72 4.08
2507 2609 0.533491 GGTGGACTACATACGGTGCA 59.467 55.000 0.00 0.00 0.00 4.57
2508 2610 0.822164 AGGTGGACTACATACGGTGC 59.178 55.000 0.00 0.00 0.00 5.01
2509 2611 3.066342 CACTAGGTGGACTACATACGGTG 59.934 52.174 0.00 0.00 0.00 4.94
2510 2612 3.285484 CACTAGGTGGACTACATACGGT 58.715 50.000 0.00 0.00 0.00 4.83
2511 2613 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
2523 2625 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
2524 2626 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
2525 2627 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
2541 2643 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
2544 2646 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2546 2648 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2553 2655 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2554 2656 4.591321 TTACTACTCCCTCCGTTCCTAA 57.409 45.455 0.00 0.00 0.00 2.69
2555 2657 4.591321 TTTACTACTCCCTCCGTTCCTA 57.409 45.455 0.00 0.00 0.00 2.94
2556 2658 3.463048 TTTACTACTCCCTCCGTTCCT 57.537 47.619 0.00 0.00 0.00 3.36
2557 2659 5.362143 ACTTATTTACTACTCCCTCCGTTCC 59.638 44.000 0.00 0.00 0.00 3.62
2588 2690 4.694982 GGCCCAAAATCAATCGTGAAAAAT 59.305 37.500 0.00 0.00 37.30 1.82
2593 2695 1.818060 CAGGCCCAAAATCAATCGTGA 59.182 47.619 0.00 0.00 38.41 4.35
2594 2696 1.736696 GCAGGCCCAAAATCAATCGTG 60.737 52.381 0.00 0.00 0.00 4.35
2595 2697 0.532115 GCAGGCCCAAAATCAATCGT 59.468 50.000 0.00 0.00 0.00 3.73
2596 2698 0.819582 AGCAGGCCCAAAATCAATCG 59.180 50.000 0.00 0.00 0.00 3.34
2601 2703 6.901081 ACTTATAATAGCAGGCCCAAAATC 57.099 37.500 0.00 0.00 0.00 2.17
2904 3007 2.034053 TGCATGGACGGAAAAACAGTTC 59.966 45.455 0.00 0.00 0.00 3.01
3121 3227 6.913873 TTTAGTGCGAGAAAAGTAACAGTT 57.086 33.333 0.00 0.00 0.00 3.16
3125 3231 9.104126 GAAAGAATTTAGTGCGAGAAAAGTAAC 57.896 33.333 0.00 0.00 39.27 2.50
3168 3274 6.987992 CCCTAACAGTTACTACTTGTTTGACA 59.012 38.462 0.00 0.00 32.10 3.58
3174 3280 8.702819 GGAATATCCCTAACAGTTACTACTTGT 58.297 37.037 0.00 0.00 30.26 3.16
3199 3305 7.283127 GGAACATATGCATATAACACCCTATGG 59.717 40.741 18.70 5.00 37.80 2.74
3221 3327 9.457436 TTTCCCTACATGTAAATAAGAAGGAAC 57.543 33.333 7.06 0.00 0.00 3.62
3269 3375 9.990868 ACCAAGTTAGAAATGGACCTTAATATT 57.009 29.630 0.00 0.00 37.66 1.28
3271 3377 8.387813 ACACCAAGTTAGAAATGGACCTTAATA 58.612 33.333 0.00 0.00 37.66 0.98
3326 3432 0.840722 GGGTTTCCCAGGGTCTCTCA 60.841 60.000 5.01 0.00 44.65 3.27
3351 3457 1.878211 TCTATGGTGATGGCTGGTCA 58.122 50.000 0.00 0.00 0.00 4.02
3357 3463 3.084786 GGCCTTAATCTATGGTGATGGC 58.915 50.000 0.00 0.00 34.33 4.40
3507 3613 8.190784 GCATTTTACTGCCTAAGATTATGTTGT 58.809 33.333 0.00 0.00 36.10 3.32
3508 3614 8.408601 AGCATTTTACTGCCTAAGATTATGTTG 58.591 33.333 0.00 0.00 43.33 3.33
3663 3769 5.461737 CACACCCATAACAATGTGAACAAAC 59.538 40.000 0.00 0.00 44.20 2.93
3679 3785 2.124411 GTACTACCCATCCACACCCAT 58.876 52.381 0.00 0.00 0.00 4.00
3693 3799 5.811100 GGTAGAGAAACTGGCATTGTACTAC 59.189 44.000 0.00 0.00 0.00 2.73
3713 3819 5.858581 GCAACTCAGCAAATTAAGTTGGTAG 59.141 40.000 18.68 16.97 45.48 3.18
3735 3841 5.260424 TGCAAATTAGAAATACCAGGAGCA 58.740 37.500 0.00 0.00 0.00 4.26
3769 3875 4.207891 AGGTCACATCCATCAACACTAC 57.792 45.455 0.00 0.00 0.00 2.73
3789 3895 6.090088 CCGTTGAGACAAAGAGATAACTGAAG 59.910 42.308 0.00 0.00 0.00 3.02
4068 4174 7.138692 AGCATCATCAGAAGTACAAGAAAAC 57.861 36.000 0.00 0.00 0.00 2.43
4239 4345 2.510382 TCCACCAACAACCAACTCCTTA 59.490 45.455 0.00 0.00 0.00 2.69
4245 4351 2.035632 TCCAATCCACCAACAACCAAC 58.964 47.619 0.00 0.00 0.00 3.77
4359 4465 4.571984 TCCATCAAGTCATTGTAATCTGCG 59.428 41.667 0.00 0.00 37.68 5.18
4424 4530 7.273712 AGGTACGAAGGAAGAAGGAAAATATC 58.726 38.462 0.00 0.00 0.00 1.63
4474 4580 8.593945 ACCATACCTGTCAACATCAAAATAAT 57.406 30.769 0.00 0.00 0.00 1.28
4512 4618 9.461312 GCATGATATTTTATCTTATACCCACCA 57.539 33.333 0.00 0.00 0.00 4.17
4726 4834 3.464111 ACCAAATATTACCTCCGTCCG 57.536 47.619 0.00 0.00 0.00 4.79
4874 4982 8.087982 TCAGATACTTGTTTGTTTCATCACTC 57.912 34.615 0.00 0.00 0.00 3.51
5027 5135 5.848406 CCAAAAAGTATGGCCAAAACTACA 58.152 37.500 20.95 0.00 0.00 2.74
5180 5291 4.520111 ACAAACCCAACGGTAATTTAGACC 59.480 41.667 0.00 0.00 43.71 3.85
5181 5292 5.454520 CACAAACCCAACGGTAATTTAGAC 58.545 41.667 0.00 0.00 43.71 2.59
5182 5293 4.023021 GCACAAACCCAACGGTAATTTAGA 60.023 41.667 0.00 0.00 43.71 2.10
5212 5323 9.346725 GCTAACAAATCATCAAGAAACTTAAGG 57.653 33.333 7.53 0.00 0.00 2.69
5256 5367 2.747989 GGCCCACTAGCTGTTAAAAGAC 59.252 50.000 0.00 0.00 0.00 3.01
5454 5565 3.751175 TCACAGTGTAAGCCAGCATAAAC 59.249 43.478 0.00 0.00 0.00 2.01
5578 5689 8.107095 ACAAGGTTATATTAAGTTCTCAGGCAA 58.893 33.333 0.00 0.00 0.00 4.52
5631 5742 4.470462 CAAGTTCAAAGCATACAGAGTGC 58.530 43.478 0.00 0.00 42.81 4.40
5634 5745 3.503363 TGCCAAGTTCAAAGCATACAGAG 59.497 43.478 0.00 0.00 0.00 3.35
5748 5861 6.074088 CCATAGCTTCGCTGTTCTTATAAGTG 60.074 42.308 12.19 3.47 40.10 3.16
5796 5920 4.582869 ACTCATGAAAGTAGAGCAATGCA 58.417 39.130 8.35 0.00 32.71 3.96
5811 5935 4.454678 ACTTCTCAACAAGCAACTCATGA 58.545 39.130 0.00 0.00 0.00 3.07
5854 5978 9.056005 CAGATTGACGATCCTGGAATATTTTAA 57.944 33.333 0.00 0.00 35.21 1.52
5855 5979 7.661437 CCAGATTGACGATCCTGGAATATTTTA 59.339 37.037 0.00 0.00 36.20 1.52
5856 5980 6.488006 CCAGATTGACGATCCTGGAATATTTT 59.512 38.462 0.00 0.00 36.20 1.82
6041 6168 1.583404 GTCAAAAAGTGTTGCACTGCG 59.417 47.619 2.31 0.00 44.62 5.18
6190 6317 2.353269 TGTTGCACACAAAGAGTTACGG 59.647 45.455 0.00 0.00 37.58 4.02
6192 6319 7.979115 TTTTATGTTGCACACAAAGAGTTAC 57.021 32.000 5.94 0.00 39.50 2.50
6294 6499 3.333029 TTTCATGATCCGCAAGACTCA 57.667 42.857 0.00 0.00 43.02 3.41
6318 6523 6.822676 TCTCTTTAGTTTTGTTAACACCCGAA 59.177 34.615 8.07 0.00 0.00 4.30
6477 6688 7.219322 TGTATTGTCATGTCATAATCCTCCAG 58.781 38.462 0.00 0.00 0.00 3.86
6520 6733 2.293122 GCTGCTACACATGTTTTGTCCA 59.707 45.455 0.00 0.00 36.00 4.02
6595 6808 1.561643 CTCACTGCTCCTCCCTAACA 58.438 55.000 0.00 0.00 0.00 2.41
6600 6813 1.050988 TATGCCTCACTGCTCCTCCC 61.051 60.000 0.00 0.00 0.00 4.30
6632 6845 1.699634 AGCACACTTTGGCTCCTTCTA 59.300 47.619 0.00 0.00 34.76 2.10
6681 6897 7.441017 AGCAATACCAAGCACTAAATTTTGAA 58.559 30.769 6.63 0.00 0.00 2.69
6705 6921 5.980116 CACGGAGATCCAAGAAAGTGTATAG 59.020 44.000 0.00 0.00 35.14 1.31
6716 6932 3.594603 AGTGTTACACGGAGATCCAAG 57.405 47.619 10.00 0.00 39.64 3.61
6781 6997 3.774766 TGGCTACAAGCATAAGAGGAAGA 59.225 43.478 0.78 0.00 44.75 2.87
6848 7064 7.579589 TGTAAATTTTTGATTCGAATGCCAG 57.420 32.000 16.96 0.00 0.00 4.85
6882 7099 8.793592 TGATTTTAGCTTTCTTTAAGTTCCTCC 58.206 33.333 0.00 0.00 36.19 4.30
6899 7116 7.220875 GGCAGCTTGTATTTAGTTGATTTTAGC 59.779 37.037 0.00 0.00 0.00 3.09
6907 7124 3.426159 CCACGGCAGCTTGTATTTAGTTG 60.426 47.826 0.00 0.00 0.00 3.16
6926 7143 2.225019 CAGATATGAAGATTGCGGCCAC 59.775 50.000 2.24 0.00 0.00 5.01
6932 7149 2.555757 GCCACCCAGATATGAAGATTGC 59.444 50.000 0.00 0.00 0.00 3.56
6933 7150 3.819337 CTGCCACCCAGATATGAAGATTG 59.181 47.826 0.00 0.00 44.64 2.67
6934 7151 3.461085 ACTGCCACCCAGATATGAAGATT 59.539 43.478 0.00 0.00 44.64 2.40
6936 7153 2.171237 CACTGCCACCCAGATATGAAGA 59.829 50.000 0.00 0.00 44.64 2.87
6937 7154 2.569059 CACTGCCACCCAGATATGAAG 58.431 52.381 0.00 0.00 44.64 3.02
6938 7155 1.212688 CCACTGCCACCCAGATATGAA 59.787 52.381 0.00 0.00 44.64 2.57
6939 7156 0.839277 CCACTGCCACCCAGATATGA 59.161 55.000 0.00 0.00 44.64 2.15
6940 7157 0.839277 TCCACTGCCACCCAGATATG 59.161 55.000 0.00 0.00 44.64 1.78
6941 7158 1.135094 CTCCACTGCCACCCAGATAT 58.865 55.000 0.00 0.00 44.64 1.63
6942 7159 0.042581 TCTCCACTGCCACCCAGATA 59.957 55.000 0.00 0.00 44.64 1.98
6943 7160 0.622738 ATCTCCACTGCCACCCAGAT 60.623 55.000 0.00 0.00 44.64 2.90
6944 7161 0.042581 TATCTCCACTGCCACCCAGA 59.957 55.000 0.00 0.00 44.64 3.86
6967 7232 9.276397 GTCTGTATTAGAACGAACTAGAACTTC 57.724 37.037 0.00 0.00 37.12 3.01
6976 7241 8.511465 TTACACAAGTCTGTATTAGAACGAAC 57.489 34.615 0.00 0.00 37.12 3.95
6984 7249 6.428771 GGCCAAACTTACACAAGTCTGTATTA 59.571 38.462 0.00 0.00 44.41 0.98
6987 7252 4.131596 GGCCAAACTTACACAAGTCTGTA 58.868 43.478 0.00 0.00 44.41 2.74
6991 7256 3.380320 ACTTGGCCAAACTTACACAAGTC 59.620 43.478 20.91 0.00 44.41 3.01
6996 7261 4.584327 ATGAACTTGGCCAAACTTACAC 57.416 40.909 20.91 7.46 0.00 2.90
7027 7292 9.706691 GGCTAATTTAGTGCTGTATAGATGTTA 57.293 33.333 5.38 0.00 0.00 2.41
7029 7294 7.967908 AGGCTAATTTAGTGCTGTATAGATGT 58.032 34.615 5.38 0.00 0.00 3.06
7030 7295 8.715998 CAAGGCTAATTTAGTGCTGTATAGATG 58.284 37.037 5.38 0.00 0.00 2.90
7031 7296 8.432805 ACAAGGCTAATTTAGTGCTGTATAGAT 58.567 33.333 5.38 0.00 0.00 1.98
7032 7297 7.792032 ACAAGGCTAATTTAGTGCTGTATAGA 58.208 34.615 5.38 0.00 0.00 1.98
7033 7298 8.438676 AACAAGGCTAATTTAGTGCTGTATAG 57.561 34.615 5.38 0.00 0.00 1.31
7034 7299 9.542462 CTAACAAGGCTAATTTAGTGCTGTATA 57.458 33.333 5.38 2.69 0.00 1.47
7035 7300 8.265055 TCTAACAAGGCTAATTTAGTGCTGTAT 58.735 33.333 5.38 1.92 0.00 2.29
7036 7301 7.617225 TCTAACAAGGCTAATTTAGTGCTGTA 58.383 34.615 5.38 0.00 0.00 2.74
7037 7302 6.472887 TCTAACAAGGCTAATTTAGTGCTGT 58.527 36.000 5.38 3.72 0.00 4.40
7108 7373 3.118223 ACCAAAGGCAATTTCCGGAAAAA 60.118 39.130 32.03 12.69 33.56 1.94
7109 7374 2.436173 ACCAAAGGCAATTTCCGGAAAA 59.564 40.909 32.03 16.48 33.56 2.29
7110 7375 2.043227 ACCAAAGGCAATTTCCGGAAA 58.957 42.857 30.71 30.71 34.46 3.13
7111 7376 1.342819 CACCAAAGGCAATTTCCGGAA 59.657 47.619 14.35 14.35 0.00 4.30
7112 7377 0.965439 CACCAAAGGCAATTTCCGGA 59.035 50.000 0.00 0.00 0.00 5.14
7113 7378 0.965439 TCACCAAAGGCAATTTCCGG 59.035 50.000 0.00 0.00 0.00 5.14
7114 7379 1.336795 GGTCACCAAAGGCAATTTCCG 60.337 52.381 0.00 0.00 0.00 4.30
7115 7380 1.336795 CGGTCACCAAAGGCAATTTCC 60.337 52.381 0.00 0.00 0.00 3.13
7116 7381 1.611491 TCGGTCACCAAAGGCAATTTC 59.389 47.619 0.00 0.00 0.00 2.17
7117 7382 1.613437 CTCGGTCACCAAAGGCAATTT 59.387 47.619 0.00 0.00 0.00 1.82
7118 7383 1.247567 CTCGGTCACCAAAGGCAATT 58.752 50.000 0.00 0.00 0.00 2.32
7119 7384 2.946947 CTCGGTCACCAAAGGCAAT 58.053 52.632 0.00 0.00 0.00 3.56
7120 7385 4.473643 CTCGGTCACCAAAGGCAA 57.526 55.556 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.