Multiple sequence alignment - TraesCS2A01G435900

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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 TraesCS2A01G435900 chr2A 100.000 4685 0 0 1 4685 688236878 688232194 0.000000e+00 8652.0
1 TraesCS2A01G435900 chr2B 89.317 1844 122 43 2503 4280 651931317 651933151 0.000000e+00 2244.0
2 TraesCS2A01G435900 chr2B 93.044 877 60 1 1582 2457 651930442 651931318 0.000000e+00 1280.0
3 TraesCS2A01G435900 chr2B 90.936 673 37 14 851 1522 651929794 651930443 0.000000e+00 883.0
4 TraesCS2A01G435900 chr2B 92.222 270 17 3 4416 4685 651933271 651933536 3.420000e-101 379.0
5 TraesCS2A01G435900 chr2B 93.814 194 12 0 7 200 651928657 651928850 4.590000e-75 292.0
6 TraesCS2A01G435900 chr2B 90.323 186 17 1 197 382 651929083 651929267 4.680000e-60 243.0
7 TraesCS2A01G435900 chr2B 79.228 337 34 15 430 733 651929270 651929603 7.950000e-48 202.0
8 TraesCS2A01G435900 chr2D 94.127 1277 59 11 2960 4227 545039511 545040780 0.000000e+00 1929.0
9 TraesCS2A01G435900 chr2D 90.544 1396 107 13 1579 2956 545038089 545039477 0.000000e+00 1823.0
10 TraesCS2A01G435900 chr2D 88.962 761 45 19 758 1511 545037360 545038088 0.000000e+00 904.0
11 TraesCS2A01G435900 chr2D 87.685 406 32 6 1 406 545036372 545036759 1.540000e-124 457.0
12 TraesCS2A01G435900 chr2D 92.021 188 13 2 554 740 545036906 545037092 3.600000e-66 263.0
13 TraesCS2A01G435900 chr2D 90.299 134 12 1 422 554 545036745 545036878 1.730000e-39 174.0
14 TraesCS2A01G435900 chr2D 98.214 56 1 0 4630 4685 545041568 545041623 1.070000e-16 99.0
15 TraesCS2A01G435900 chr4A 96.774 31 1 0 4400 4430 724580673 724580703 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 TraesCS2A01G435900 chr2A 688232194 688236878 4684 True 8652 8652 100.000000 1 4685 1 chr2A.!!$R1 4684
1 TraesCS2A01G435900 chr2B 651928657 651933536 4879 False 789 2244 89.840571 7 4685 7 chr2B.!!$F1 4678
2 TraesCS2A01G435900 chr2D 545036372 545041623 5251 False 807 1929 91.693143 1 4685 7 chr2D.!!$F1 4684

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
335 577 0.108186 ATGAGAGCCGTTCAATCGCA 60.108 50.0 0.00 0.0 0.0 5.10 F
336 578 0.108186 TGAGAGCCGTTCAATCGCAT 60.108 50.0 0.00 0.0 0.0 4.73 F
1673 2222 0.529992 GCCCTAGTATTGACGCGCTT 60.530 55.0 5.73 0.0 0.0 4.68 F
3415 4050 0.447801 CTTTCGCCAGGAAATCACCG 59.552 55.0 0.00 0.0 43.4 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 2213 0.032130 ACTCAGAGAAAAGCGCGTCA 59.968 50.0 8.43 0.0 0.00 4.35 R
1823 2372 0.387202 CACTCAGGCTCCGATACCAG 59.613 60.0 0.00 0.0 0.00 4.00 R
3441 4076 0.402121 GAACCTCTGGAGCTGGGTTT 59.598 55.0 0.00 0.0 41.44 3.27 R
4285 4984 0.249120 TCATCCCACACATGTCGTCC 59.751 55.0 0.00 0.0 0.00 4.79 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
79 80 1.457455 CCCAAAACCAGGGCACTGT 60.457 57.895 16.38 0.00 43.36 3.55
92 93 0.110056 GCACTGTCAAGATTGTGGCG 60.110 55.000 0.00 0.00 0.00 5.69
150 151 0.957888 GGCACTCCCTTTCAGCAGAC 60.958 60.000 0.00 0.00 0.00 3.51
257 494 6.923199 ATTTCAAATGAAGGATGGTTCAGT 57.077 33.333 0.00 0.00 39.78 3.41
334 576 1.009829 AATGAGAGCCGTTCAATCGC 58.990 50.000 0.00 0.00 0.00 4.58
335 577 0.108186 ATGAGAGCCGTTCAATCGCA 60.108 50.000 0.00 0.00 0.00 5.10
336 578 0.108186 TGAGAGCCGTTCAATCGCAT 60.108 50.000 0.00 0.00 0.00 4.73
337 579 0.579156 GAGAGCCGTTCAATCGCATC 59.421 55.000 0.00 0.00 0.00 3.91
338 580 1.148157 AGAGCCGTTCAATCGCATCG 61.148 55.000 0.00 0.00 0.00 3.84
354 596 2.671070 GCATCGTGGTTGTCAAATTCCC 60.671 50.000 0.00 0.00 0.00 3.97
363 605 8.792633 CGTGGTTGTCAAATTCCCATATAATAT 58.207 33.333 0.00 0.00 0.00 1.28
364 606 9.912634 GTGGTTGTCAAATTCCCATATAATATG 57.087 33.333 0.00 0.00 0.00 1.78
385 641 5.041951 TGTTCCTTTGATTTCGATTTCCG 57.958 39.130 0.00 0.00 40.25 4.30
387 643 5.701750 TGTTCCTTTGATTTCGATTTCCGTA 59.298 36.000 0.00 0.00 39.75 4.02
391 647 8.495361 TCCTTTGATTTCGATTTCCGTATTTA 57.505 30.769 0.00 0.00 39.75 1.40
392 648 8.392612 TCCTTTGATTTCGATTTCCGTATTTAC 58.607 33.333 0.00 0.00 39.75 2.01
395 651 8.945481 TTGATTTCGATTTCCGTATTTACCTA 57.055 30.769 0.00 0.00 39.75 3.08
397 653 8.415553 TGATTTCGATTTCCGTATTTACCTAGA 58.584 33.333 0.00 0.00 39.75 2.43
398 654 9.420551 GATTTCGATTTCCGTATTTACCTAGAT 57.579 33.333 0.00 0.00 39.75 1.98
399 655 8.807667 TTTCGATTTCCGTATTTACCTAGATC 57.192 34.615 0.00 0.00 39.75 2.75
400 656 6.917533 TCGATTTCCGTATTTACCTAGATCC 58.082 40.000 0.00 0.00 39.75 3.36
401 657 6.718454 TCGATTTCCGTATTTACCTAGATCCT 59.282 38.462 0.00 0.00 39.75 3.24
402 658 7.028361 CGATTTCCGTATTTACCTAGATCCTC 58.972 42.308 0.00 0.00 0.00 3.71
403 659 7.094291 CGATTTCCGTATTTACCTAGATCCTCT 60.094 40.741 0.00 0.00 0.00 3.69
404 660 7.909485 TTTCCGTATTTACCTAGATCCTCTT 57.091 36.000 0.00 0.00 0.00 2.85
405 661 7.909485 TTCCGTATTTACCTAGATCCTCTTT 57.091 36.000 0.00 0.00 0.00 2.52
406 662 7.909485 TCCGTATTTACCTAGATCCTCTTTT 57.091 36.000 0.00 0.00 0.00 2.27
407 663 8.315220 TCCGTATTTACCTAGATCCTCTTTTT 57.685 34.615 0.00 0.00 0.00 1.94
439 695 3.648739 GGGACCTAGATCCTCTTTGACT 58.351 50.000 2.23 0.00 38.95 3.41
440 696 4.034410 GGGACCTAGATCCTCTTTGACTT 58.966 47.826 2.23 0.00 38.95 3.01
458 714 7.692460 TTGACTTAAAGATCATCACAATGCT 57.308 32.000 0.00 0.00 32.58 3.79
474 730 5.694910 CACAATGCTCTGAAAGAAAGCAAAT 59.305 36.000 0.00 0.00 45.52 2.32
497 753 2.660552 AAGTGGCACGTCCGTTCG 60.661 61.111 12.71 0.00 37.80 3.95
504 760 1.082117 GCACGTCCGTTCGAATCCAT 61.082 55.000 0.00 0.00 34.70 3.41
507 763 2.280708 CACGTCCGTTCGAATCCATTAC 59.719 50.000 0.00 0.00 34.70 1.89
565 849 2.411748 TGTAGCAAGAAAATCGAGTGCG 59.588 45.455 0.00 0.00 40.17 5.34
636 921 3.950397 TCAGACGGCCTATGTTCATTTT 58.050 40.909 0.00 0.00 0.00 1.82
666 952 8.343787 TCTATCTAAGGTTCAAAATCCCCAAAT 58.656 33.333 0.00 0.00 0.00 2.32
672 958 7.186570 AGGTTCAAAATCCCCAAATAATCTG 57.813 36.000 0.00 0.00 0.00 2.90
700 986 0.540365 CCTTGGAAGCAAAGGAGCCA 60.540 55.000 0.00 0.00 46.08 4.75
725 1011 9.415544 CATTATTTCCTTCCTTTTTGAGAAGTG 57.584 33.333 0.00 0.00 38.24 3.16
743 1249 8.330247 TGAGAAGTGTAATACTCCTACTCTCTT 58.670 37.037 0.00 0.00 38.35 2.85
753 1259 6.388619 ACTCCTACTCTCTTTCTCTCTCTT 57.611 41.667 0.00 0.00 0.00 2.85
754 1260 6.415573 ACTCCTACTCTCTTTCTCTCTCTTC 58.584 44.000 0.00 0.00 0.00 2.87
756 1262 4.887655 CCTACTCTCTTTCTCTCTCTTCCC 59.112 50.000 0.00 0.00 0.00 3.97
770 1276 4.444611 TCTCTTCCCCCTAATTTCTCCAA 58.555 43.478 0.00 0.00 0.00 3.53
771 1277 4.855599 TCTCTTCCCCCTAATTTCTCCAAA 59.144 41.667 0.00 0.00 0.00 3.28
774 1280 6.570680 TCTTCCCCCTAATTTCTCCAAATTT 58.429 36.000 0.00 0.00 41.56 1.82
775 1281 7.022496 TCTTCCCCCTAATTTCTCCAAATTTT 58.978 34.615 0.00 0.00 41.56 1.82
776 1282 7.515861 TCTTCCCCCTAATTTCTCCAAATTTTT 59.484 33.333 0.00 0.00 41.56 1.94
824 1360 4.208873 TCAAAAGCATTCGTGCACAAAATC 59.791 37.500 18.64 9.62 37.25 2.17
886 1423 2.096248 TGTGGACACAAGTTTGGTTCC 58.904 47.619 2.08 6.94 38.56 3.62
887 1424 2.291282 TGTGGACACAAGTTTGGTTCCT 60.291 45.455 2.08 0.00 38.56 3.36
891 1428 3.013921 GACACAAGTTTGGTTCCTGTCA 58.986 45.455 7.34 0.00 32.60 3.58
905 1442 1.512996 CTGTCAGGGTTGCAGTGCTG 61.513 60.000 17.60 5.78 0.00 4.41
908 1445 2.113986 AGGGTTGCAGTGCTGGTC 59.886 61.111 17.60 3.94 0.00 4.02
910 1447 1.529244 GGGTTGCAGTGCTGGTCTT 60.529 57.895 17.60 0.00 0.00 3.01
934 1471 1.337823 CCTTGACACGTTCCAGTAGGG 60.338 57.143 0.00 0.00 34.83 3.53
1038 1575 3.700350 CTCCTCCTCCCCCACCCT 61.700 72.222 0.00 0.00 0.00 4.34
1075 1624 4.798682 CCCTCCCTACCCACCGCT 62.799 72.222 0.00 0.00 0.00 5.52
1345 1894 4.443266 AGGCGAACGAGCAGGAGC 62.443 66.667 0.00 0.00 39.27 4.70
1513 2062 3.569701 ACACCATTTGCTTTGACTACTGG 59.430 43.478 0.00 0.00 0.00 4.00
1514 2063 3.057315 CACCATTTGCTTTGACTACTGGG 60.057 47.826 0.00 0.00 0.00 4.45
1522 2071 4.100344 TGCTTTGACTACTGGGCGATTATA 59.900 41.667 0.00 0.00 0.00 0.98
1524 2073 5.177696 GCTTTGACTACTGGGCGATTATAAG 59.822 44.000 0.00 0.00 0.00 1.73
1527 2076 5.597806 TGACTACTGGGCGATTATAAGTTG 58.402 41.667 0.00 0.00 0.00 3.16
1529 2078 4.652421 ACTACTGGGCGATTATAAGTTGGA 59.348 41.667 0.00 0.00 0.00 3.53
1530 2079 3.805207 ACTGGGCGATTATAAGTTGGAC 58.195 45.455 0.00 0.00 0.00 4.02
1531 2080 3.139077 CTGGGCGATTATAAGTTGGACC 58.861 50.000 0.00 0.00 0.00 4.46
1532 2081 2.506231 TGGGCGATTATAAGTTGGACCA 59.494 45.455 0.00 0.00 0.00 4.02
1533 2082 2.876550 GGGCGATTATAAGTTGGACCAC 59.123 50.000 0.00 0.00 0.00 4.16
1534 2083 2.542595 GGCGATTATAAGTTGGACCACG 59.457 50.000 0.00 0.00 0.00 4.94
1535 2084 3.450578 GCGATTATAAGTTGGACCACGA 58.549 45.455 0.00 0.00 0.00 4.35
1536 2085 3.489785 GCGATTATAAGTTGGACCACGAG 59.510 47.826 0.00 0.00 0.00 4.18
1537 2086 4.735578 GCGATTATAAGTTGGACCACGAGA 60.736 45.833 0.00 0.00 0.00 4.04
1538 2087 5.529791 CGATTATAAGTTGGACCACGAGAT 58.470 41.667 0.00 0.00 0.00 2.75
1539 2088 6.675026 CGATTATAAGTTGGACCACGAGATA 58.325 40.000 0.00 0.00 0.00 1.98
1540 2089 7.313646 CGATTATAAGTTGGACCACGAGATAT 58.686 38.462 0.00 0.00 0.00 1.63
1541 2090 7.273598 CGATTATAAGTTGGACCACGAGATATG 59.726 40.741 0.00 0.00 0.00 1.78
1542 2091 7.591421 TTATAAGTTGGACCACGAGATATGA 57.409 36.000 0.00 0.00 0.00 2.15
1543 2092 4.819105 AAGTTGGACCACGAGATATGAA 57.181 40.909 0.00 0.00 0.00 2.57
1544 2093 4.819105 AGTTGGACCACGAGATATGAAA 57.181 40.909 0.00 0.00 0.00 2.69
1545 2094 4.759782 AGTTGGACCACGAGATATGAAAG 58.240 43.478 0.00 0.00 0.00 2.62
1546 2095 4.466370 AGTTGGACCACGAGATATGAAAGA 59.534 41.667 0.00 0.00 0.00 2.52
1547 2096 5.129485 AGTTGGACCACGAGATATGAAAGAT 59.871 40.000 0.00 0.00 0.00 2.40
1548 2097 6.323996 AGTTGGACCACGAGATATGAAAGATA 59.676 38.462 0.00 0.00 0.00 1.98
1549 2098 6.332735 TGGACCACGAGATATGAAAGATAG 57.667 41.667 0.00 0.00 0.00 2.08
1550 2099 5.243954 TGGACCACGAGATATGAAAGATAGG 59.756 44.000 0.00 0.00 0.00 2.57
1551 2100 5.477291 GGACCACGAGATATGAAAGATAGGA 59.523 44.000 0.00 0.00 0.00 2.94
1552 2101 6.153680 GGACCACGAGATATGAAAGATAGGAT 59.846 42.308 0.00 0.00 0.00 3.24
1553 2102 6.929625 ACCACGAGATATGAAAGATAGGATG 58.070 40.000 0.00 0.00 0.00 3.51
1554 2103 6.071108 ACCACGAGATATGAAAGATAGGATGG 60.071 42.308 0.00 0.00 0.00 3.51
1555 2104 6.153510 CCACGAGATATGAAAGATAGGATGGA 59.846 42.308 0.00 0.00 0.00 3.41
1556 2105 7.310052 CCACGAGATATGAAAGATAGGATGGAA 60.310 40.741 0.00 0.00 0.00 3.53
1557 2106 7.543868 CACGAGATATGAAAGATAGGATGGAAC 59.456 40.741 0.00 0.00 0.00 3.62
1558 2107 6.749578 CGAGATATGAAAGATAGGATGGAACG 59.250 42.308 0.00 0.00 0.00 3.95
1559 2108 7.362142 CGAGATATGAAAGATAGGATGGAACGA 60.362 40.741 0.00 0.00 0.00 3.85
1560 2109 8.372877 AGATATGAAAGATAGGATGGAACGAT 57.627 34.615 0.00 0.00 0.00 3.73
1561 2110 8.256605 AGATATGAAAGATAGGATGGAACGATG 58.743 37.037 0.00 0.00 0.00 3.84
1562 2111 5.869649 TGAAAGATAGGATGGAACGATGA 57.130 39.130 0.00 0.00 0.00 2.92
1563 2112 5.847304 TGAAAGATAGGATGGAACGATGAG 58.153 41.667 0.00 0.00 0.00 2.90
1564 2113 5.363868 TGAAAGATAGGATGGAACGATGAGT 59.636 40.000 0.00 0.00 0.00 3.41
1566 2115 5.878406 AGATAGGATGGAACGATGAGTTT 57.122 39.130 0.00 0.00 44.35 2.66
1567 2116 6.240549 AGATAGGATGGAACGATGAGTTTT 57.759 37.500 0.00 0.00 44.35 2.43
1568 2117 6.653989 AGATAGGATGGAACGATGAGTTTTT 58.346 36.000 0.00 0.00 44.35 1.94
1613 2162 7.136119 TGATTTGTTGTTTGTAGGATTTCGTC 58.864 34.615 0.00 0.00 0.00 4.20
1631 2180 0.541998 TCGAAGCACAGGGGAAGAGA 60.542 55.000 0.00 0.00 0.00 3.10
1664 2213 2.040178 CCTGAGTTCCGCCCTAGTATT 58.960 52.381 0.00 0.00 0.00 1.89
1673 2222 0.529992 GCCCTAGTATTGACGCGCTT 60.530 55.000 5.73 0.00 0.00 4.68
1751 2300 2.545113 GGCGGCTGATGTCGTTTCTATA 60.545 50.000 0.00 0.00 44.07 1.31
1804 2353 3.917300 AGGGACTGGTAGAACCTATCAG 58.083 50.000 11.53 11.53 39.58 2.90
1838 2387 0.757188 AGGACTGGTATCGGAGCCTG 60.757 60.000 1.02 6.70 0.00 4.85
1943 2493 6.442952 TGTTAATGTTGTGTTGCCTTGTATC 58.557 36.000 0.00 0.00 0.00 2.24
1946 2496 3.561143 TGTTGTGTTGCCTTGTATCCTT 58.439 40.909 0.00 0.00 0.00 3.36
1997 2547 8.574196 AAGTGTTGTTTAATTTGTGTAGATGC 57.426 30.769 0.00 0.00 0.00 3.91
2044 2594 4.541085 TCATGTGAATCGCAATGACATC 57.459 40.909 0.00 0.00 0.00 3.06
2123 2673 6.866480 TGCTTCAGTCAAACTCATTTTCTTT 58.134 32.000 0.00 0.00 0.00 2.52
2181 2740 6.057321 TGTACTCCCGGAAATGAATTAGTT 57.943 37.500 0.73 0.00 0.00 2.24
2376 2935 7.679638 GCATAACTTGAAGCCAATACAGGTAAG 60.680 40.741 0.00 0.00 0.00 2.34
2377 2936 4.010349 ACTTGAAGCCAATACAGGTAAGC 58.990 43.478 0.00 0.00 0.00 3.09
2381 2941 4.830046 TGAAGCCAATACAGGTAAGCAAAA 59.170 37.500 0.00 0.00 0.00 2.44
2404 2964 3.439129 TCTTCAGAGAACATGCAGCATTG 59.561 43.478 4.69 0.12 0.00 2.82
2405 2965 2.089201 TCAGAGAACATGCAGCATTGG 58.911 47.619 4.69 0.00 0.00 3.16
2407 2967 1.180029 GAGAACATGCAGCATTGGGT 58.820 50.000 4.69 0.00 0.00 4.51
2409 2969 1.972795 AGAACATGCAGCATTGGGTTT 59.027 42.857 4.69 0.00 0.00 3.27
2464 3024 7.696017 ACTTATCCTTAAAAGCTTACCTTGGA 58.304 34.615 0.00 5.02 33.01 3.53
2466 3026 5.578157 TCCTTAAAAGCTTACCTTGGAGT 57.422 39.130 0.00 0.00 33.01 3.85
2478 3039 9.755122 AGCTTACCTTGGAGTTAAATAAAAGAT 57.245 29.630 0.00 0.00 0.00 2.40
2498 3059 9.502091 AAAAGATGTAGCATAGTACTGAAACAA 57.498 29.630 5.39 0.00 0.00 2.83
2499 3060 9.502091 AAAGATGTAGCATAGTACTGAAACAAA 57.498 29.630 5.39 0.00 0.00 2.83
2501 3062 8.094548 AGATGTAGCATAGTACTGAAACAAACA 58.905 33.333 5.39 2.04 0.00 2.83
2516 3077 7.199766 TGAAACAAACATTTTGCTAGTACTGG 58.800 34.615 5.39 3.15 0.00 4.00
2518 3079 6.313744 ACAAACATTTTGCTAGTACTGGTC 57.686 37.500 5.39 0.00 0.00 4.02
2589 3159 9.158233 CATATATAGATGATGACATTGTGCACA 57.842 33.333 17.42 17.42 36.82 4.57
2603 3173 1.330521 GTGCACACAGACATCAACGTT 59.669 47.619 13.17 0.00 0.00 3.99
2605 3175 1.921573 GCACACAGACATCAACGTTGC 60.922 52.381 23.47 9.39 0.00 4.17
2664 3234 2.026262 GGATTTGTGGAGGCCTGAACTA 60.026 50.000 12.00 1.55 0.00 2.24
2887 3460 3.126001 ACTTTGTTCGATCTGGCAAGA 57.874 42.857 0.00 0.00 36.69 3.02
2895 3468 2.165234 TCGATCTGGCAAGAGAAGTGAG 59.835 50.000 0.00 0.00 35.37 3.51
2897 3470 2.015456 TCTGGCAAGAGAAGTGAGGA 57.985 50.000 0.00 0.00 0.00 3.71
2898 3471 1.620819 TCTGGCAAGAGAAGTGAGGAC 59.379 52.381 0.00 0.00 0.00 3.85
3018 3621 5.521372 TGACAGCATGAACTATCTGAAATCG 59.479 40.000 0.00 0.00 39.69 3.34
3096 3699 2.035704 TGCAAAGCGAATGTCCAATGTT 59.964 40.909 0.00 0.00 0.00 2.71
3158 3763 7.439056 GGCTGATTTATGGGTATGTTTGATTTG 59.561 37.037 0.00 0.00 0.00 2.32
3179 3784 3.759086 TGCCCACGCTTAATTTCATTACA 59.241 39.130 0.00 0.00 35.36 2.41
3180 3785 4.400884 TGCCCACGCTTAATTTCATTACAT 59.599 37.500 0.00 0.00 35.36 2.29
3195 3800 6.407475 TCATTACATTGTGACTGTCAATCG 57.593 37.500 12.81 4.32 33.92 3.34
3196 3801 5.351189 TCATTACATTGTGACTGTCAATCGG 59.649 40.000 12.81 5.73 33.92 4.18
3200 3805 3.676291 TTGTGACTGTCAATCGGATGA 57.324 42.857 12.81 0.00 0.00 2.92
3202 3807 2.562738 TGTGACTGTCAATCGGATGAGT 59.437 45.455 12.81 0.00 0.00 3.41
3221 3826 4.334203 TGAGTTATGTCGCTGTTGTTGTTT 59.666 37.500 0.00 0.00 0.00 2.83
3229 3864 4.437820 GTCGCTGTTGTTGTTTCTTCATTC 59.562 41.667 0.00 0.00 0.00 2.67
3233 3868 5.005682 GCTGTTGTTGTTTCTTCATTCCAAC 59.994 40.000 0.00 0.00 36.74 3.77
3236 3871 4.681744 TGTTGTTTCTTCATTCCAACAGC 58.318 39.130 0.00 0.00 40.12 4.40
3313 3948 5.011635 TGTGCTACAAGGTTTCAGACTGATA 59.988 40.000 5.87 0.00 0.00 2.15
3314 3949 5.932303 GTGCTACAAGGTTTCAGACTGATAA 59.068 40.000 5.87 1.28 0.00 1.75
3411 4046 0.965363 TGCCCTTTCGCCAGGAAATC 60.965 55.000 0.00 0.00 43.40 2.17
3413 4048 0.811281 CCCTTTCGCCAGGAAATCAC 59.189 55.000 0.00 0.00 43.40 3.06
3415 4050 0.447801 CTTTCGCCAGGAAATCACCG 59.552 55.000 0.00 0.00 43.40 4.94
3438 4073 3.567797 GCATCGCCGCTGTTCCTC 61.568 66.667 0.00 0.00 0.00 3.71
3441 4076 3.001902 ATCGCCGCTGTTCCTCGAA 62.002 57.895 0.00 0.00 32.74 3.71
3516 4151 3.077088 AGAGTAACCTTGTCAGGGGAGTA 59.923 47.826 5.89 0.00 46.01 2.59
3564 4199 7.962995 ATGTGAGTTCTTAGAACCTCTATCA 57.037 36.000 20.05 14.06 0.00 2.15
3700 4335 2.579207 TTAGAGCACACACCTATCGC 57.421 50.000 0.00 0.00 0.00 4.58
3710 4345 1.278238 CACCTATCGCCACGAAGTTC 58.722 55.000 0.00 0.00 41.61 3.01
3786 4428 4.999950 CCATGCATAGGATCCACTTCTTAC 59.000 45.833 15.82 0.00 0.00 2.34
3787 4429 5.455183 CCATGCATAGGATCCACTTCTTACA 60.455 44.000 15.82 1.23 0.00 2.41
3788 4430 5.282055 TGCATAGGATCCACTTCTTACAG 57.718 43.478 15.82 0.00 0.00 2.74
3811 4453 4.454847 GCAGTACCACTTCTAAAAACCTCC 59.545 45.833 0.00 0.00 0.00 4.30
3889 4531 3.022607 TCTCGGAAACTTTCTCGGTTC 57.977 47.619 1.57 0.00 0.00 3.62
4068 4710 1.810030 GTAACTCTCCGGCAAGCGG 60.810 63.158 0.00 0.00 0.00 5.52
4185 4831 4.764172 ACATTAGGCAAAGAGCTAGAGTG 58.236 43.478 0.00 0.00 44.79 3.51
4227 4873 4.367039 ACTATATGATTTTGGACCCCCG 57.633 45.455 0.00 0.00 34.29 5.73
4234 4923 1.333177 TTTTGGACCCCCGTTTGATG 58.667 50.000 0.00 0.00 34.29 3.07
4245 4934 3.194542 CCCCGTTTGATGGCATTTTTAGA 59.805 43.478 0.00 0.00 0.00 2.10
4247 4936 5.068460 CCCCGTTTGATGGCATTTTTAGATA 59.932 40.000 0.00 0.00 0.00 1.98
4250 4949 6.144402 CCGTTTGATGGCATTTTTAGATATGC 59.856 38.462 0.00 0.00 44.93 3.14
4264 4963 8.498054 TTTTAGATATGCCAGTTTCTTCAGAG 57.502 34.615 0.00 0.00 0.00 3.35
4266 4965 1.446907 ATGCCAGTTTCTTCAGAGCG 58.553 50.000 0.00 0.00 0.00 5.03
4271 4970 1.808945 CAGTTTCTTCAGAGCGGCATT 59.191 47.619 1.45 0.00 0.00 3.56
4273 4972 3.003480 AGTTTCTTCAGAGCGGCATTAC 58.997 45.455 1.45 0.00 0.00 1.89
4285 4984 2.223572 GCGGCATTACATTTTCTGGGAG 60.224 50.000 0.00 0.00 0.00 4.30
4288 4987 3.381590 GGCATTACATTTTCTGGGAGGAC 59.618 47.826 0.00 0.00 0.00 3.85
4290 4989 4.513442 CATTACATTTTCTGGGAGGACGA 58.487 43.478 0.00 0.00 0.00 4.20
4292 4991 1.697432 ACATTTTCTGGGAGGACGACA 59.303 47.619 0.00 0.00 0.00 4.35
4293 4992 2.305927 ACATTTTCTGGGAGGACGACAT 59.694 45.455 0.00 0.00 0.00 3.06
4294 4993 2.472695 TTTTCTGGGAGGACGACATG 57.527 50.000 0.00 0.00 0.00 3.21
4295 4994 1.348064 TTTCTGGGAGGACGACATGT 58.652 50.000 0.00 0.00 0.00 3.21
4296 4995 0.608130 TTCTGGGAGGACGACATGTG 59.392 55.000 1.15 0.00 0.00 3.21
4297 4996 0.541998 TCTGGGAGGACGACATGTGT 60.542 55.000 1.15 1.22 0.00 3.72
4298 4997 0.390340 CTGGGAGGACGACATGTGTG 60.390 60.000 1.15 0.00 0.00 3.82
4299 4998 1.079127 GGGAGGACGACATGTGTGG 60.079 63.158 1.15 0.00 0.00 4.17
4314 5013 3.476552 TGTGTGGGATGACAGTTTCTTC 58.523 45.455 0.00 0.00 0.00 2.87
4349 5052 0.250467 GATGTGTGTGAGGTGGCAGT 60.250 55.000 0.00 0.00 0.00 4.40
4354 5057 1.064758 TGTGTGAGGTGGCAGTTTCTT 60.065 47.619 0.00 0.00 0.00 2.52
4355 5058 2.024414 GTGTGAGGTGGCAGTTTCTTT 58.976 47.619 0.00 0.00 0.00 2.52
4363 5066 3.317993 GGTGGCAGTTTCTTTAGAGCAAA 59.682 43.478 0.00 0.00 0.00 3.68
4376 5079 9.467258 TTCTTTAGAGCAAAATGACATTTTCTG 57.533 29.630 20.73 13.93 40.27 3.02
4377 5080 8.849168 TCTTTAGAGCAAAATGACATTTTCTGA 58.151 29.630 20.73 11.08 40.27 3.27
4378 5081 9.467258 CTTTAGAGCAAAATGACATTTTCTGAA 57.533 29.630 20.73 16.42 40.27 3.02
4384 5087 6.703165 GCAAAATGACATTTTCTGAAAGGACT 59.297 34.615 20.73 0.00 40.27 3.85
4397 5165 6.049149 TCTGAAAGGACTGACACAACTAAAG 58.951 40.000 0.00 0.00 0.00 1.85
4401 5169 3.134804 AGGACTGACACAACTAAAGCTGT 59.865 43.478 0.00 0.00 0.00 4.40
4411 5179 5.004726 CACAACTAAAGCTGTCAGCAAAAAC 59.995 40.000 26.23 0.00 45.56 2.43
4450 5218 3.123620 GCGGACTTCAGCAGCCAG 61.124 66.667 0.00 0.00 37.03 4.85
4454 5222 1.134699 CGGACTTCAGCAGCCAGATAA 60.135 52.381 0.00 0.00 0.00 1.75
4455 5223 2.284190 GGACTTCAGCAGCCAGATAAC 58.716 52.381 0.00 0.00 0.00 1.89
4456 5224 2.355108 GGACTTCAGCAGCCAGATAACA 60.355 50.000 0.00 0.00 0.00 2.41
4457 5225 3.539604 GACTTCAGCAGCCAGATAACAT 58.460 45.455 0.00 0.00 0.00 2.71
4480 5248 3.364549 TCCGATGATTTTTCAATGGGCT 58.635 40.909 0.00 0.00 0.00 5.19
4493 5261 6.617782 TTCAATGGGCTTCCAAATCATAAA 57.382 33.333 0.00 0.00 44.86 1.40
4494 5262 6.224665 TCAATGGGCTTCCAAATCATAAAG 57.775 37.500 0.00 0.00 44.86 1.85
4519 5287 8.312564 AGTACTACTCCTAAACATGTTTCCTTC 58.687 37.037 26.46 8.11 34.23 3.46
4553 5321 6.266323 TCGTGAATATTTGAGCTACAGTCTC 58.734 40.000 0.00 0.00 0.00 3.36
4566 5334 4.862018 GCTACAGTCTCTGAATGAACTGAC 59.138 45.833 8.24 0.00 35.18 3.51
4578 5346 5.598005 TGAATGAACTGACAAAATGAACCCT 59.402 36.000 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.552337 TGTGGGCTCAAAGCAAACAAA 59.448 42.857 0.00 0.00 44.75 2.83
22 23 1.072965 AGGTCTCTTGTGGGCTCAAAG 59.927 52.381 0.00 0.00 0.00 2.77
107 108 7.875554 GCCCAGACCAATGAATTTAACTTTTTA 59.124 33.333 0.00 0.00 0.00 1.52
175 176 6.959361 AGTAATGTGTTTCAACAGTCACATC 58.041 36.000 9.49 0.53 46.33 3.06
242 479 2.026262 GCCCTAACTGAACCATCCTTCA 60.026 50.000 0.00 0.00 0.00 3.02
250 487 0.542333 GAGGAGGCCCTAACTGAACC 59.458 60.000 0.00 0.00 44.53 3.62
257 494 2.270434 ACATCAAGAGGAGGCCCTAA 57.730 50.000 0.00 0.00 44.53 2.69
314 551 1.267732 GCGATTGAACGGCTCTCATTG 60.268 52.381 0.00 0.00 0.00 2.82
315 552 1.009829 GCGATTGAACGGCTCTCATT 58.990 50.000 0.00 0.00 0.00 2.57
334 576 2.556189 TGGGAATTTGACAACCACGATG 59.444 45.455 0.00 0.00 0.00 3.84
335 577 2.870175 TGGGAATTTGACAACCACGAT 58.130 42.857 0.00 0.00 0.00 3.73
336 578 2.350057 TGGGAATTTGACAACCACGA 57.650 45.000 0.00 0.00 0.00 4.35
337 579 4.981806 ATATGGGAATTTGACAACCACG 57.018 40.909 0.00 0.00 33.42 4.94
338 580 9.912634 CATATTATATGGGAATTTGACAACCAC 57.087 33.333 4.38 0.00 33.42 4.16
363 605 4.517453 ACGGAAATCGAAATCAAAGGAACA 59.483 37.500 0.00 0.00 42.43 3.18
364 606 5.043189 ACGGAAATCGAAATCAAAGGAAC 57.957 39.130 0.00 0.00 42.43 3.62
375 617 7.232127 AGGATCTAGGTAAATACGGAAATCGAA 59.768 37.037 0.00 0.00 42.43 3.71
409 665 0.996583 ATCTAGGTCCCCCGCAAAAA 59.003 50.000 0.00 0.00 35.12 1.94
410 666 0.544697 GATCTAGGTCCCCCGCAAAA 59.455 55.000 0.00 0.00 35.12 2.44
411 667 1.342672 GGATCTAGGTCCCCCGCAAA 61.343 60.000 11.38 0.00 35.12 3.68
412 668 1.764854 GGATCTAGGTCCCCCGCAA 60.765 63.158 11.38 0.00 35.12 4.85
413 669 2.122989 GGATCTAGGTCCCCCGCA 60.123 66.667 11.38 0.00 35.12 5.69
414 670 1.909287 GAGGATCTAGGTCCCCCGC 60.909 68.421 18.95 2.34 39.17 6.13
415 671 4.523512 GAGGATCTAGGTCCCCCG 57.476 66.667 18.95 0.00 39.17 5.73
431 687 8.239314 GCATTGTGATGATCTTTAAGTCAAAGA 58.761 33.333 2.20 2.20 43.40 2.52
432 688 8.242053 AGCATTGTGATGATCTTTAAGTCAAAG 58.758 33.333 0.00 0.00 39.18 2.77
433 689 8.114331 AGCATTGTGATGATCTTTAAGTCAAA 57.886 30.769 0.00 0.00 35.16 2.69
434 690 7.692460 AGCATTGTGATGATCTTTAAGTCAA 57.308 32.000 0.00 0.00 35.16 3.18
435 691 7.312657 GAGCATTGTGATGATCTTTAAGTCA 57.687 36.000 0.00 0.00 43.59 3.41
447 703 4.857588 GCTTTCTTTCAGAGCATTGTGATG 59.142 41.667 0.00 0.00 36.45 3.07
457 713 7.866393 ACTTGATTCATTTGCTTTCTTTCAGAG 59.134 33.333 0.00 0.00 0.00 3.35
458 714 7.650504 CACTTGATTCATTTGCTTTCTTTCAGA 59.349 33.333 0.00 0.00 0.00 3.27
474 730 0.948623 CGGACGTGCCACTTGATTCA 60.949 55.000 0.00 0.00 35.94 2.57
636 921 9.031537 GGGGATTTTGAACCTTAGATAGAAAAA 57.968 33.333 0.00 0.00 0.00 1.94
643 928 8.909423 TTATTTGGGGATTTTGAACCTTAGAT 57.091 30.769 0.00 0.00 0.00 1.98
666 952 8.821686 TGCTTCCAAGGAATTTTATCAGATTA 57.178 30.769 1.35 0.00 33.28 1.75
672 958 6.935167 TCCTTTGCTTCCAAGGAATTTTATC 58.065 36.000 1.35 0.00 36.23 1.75
700 986 9.147732 ACACTTCTCAAAAAGGAAGGAAATAAT 57.852 29.630 0.00 0.00 42.05 1.28
711 997 9.152595 GTAGGAGTATTACACTTCTCAAAAAGG 57.847 37.037 0.00 0.00 39.00 3.11
725 1011 9.269453 GAGAGAGAAAGAGAGTAGGAGTATTAC 57.731 40.741 0.00 0.00 0.00 1.89
743 1249 5.604752 AGAAATTAGGGGGAAGAGAGAGAA 58.395 41.667 0.00 0.00 0.00 2.87
824 1360 1.224069 CTTCTGGGTCAGCACACACG 61.224 60.000 0.00 0.00 30.50 4.49
833 1369 0.178992 CCAGCCAAACTTCTGGGTCA 60.179 55.000 0.51 0.00 45.44 4.02
886 1423 1.228063 AGCACTGCAACCCTGACAG 60.228 57.895 3.30 0.00 34.67 3.51
887 1424 1.526686 CAGCACTGCAACCCTGACA 60.527 57.895 3.30 0.00 0.00 3.58
891 1428 1.999634 AAGACCAGCACTGCAACCCT 62.000 55.000 3.30 0.00 0.00 4.34
905 1442 1.963172 ACGTGTCAAGGGAAAAGACC 58.037 50.000 0.00 0.00 0.00 3.85
908 1445 2.290641 CTGGAACGTGTCAAGGGAAAAG 59.709 50.000 0.00 0.00 0.00 2.27
910 1447 1.210967 ACTGGAACGTGTCAAGGGAAA 59.789 47.619 0.00 0.00 30.44 3.13
934 1471 3.272334 CCGCGGCTTATCCAGTGC 61.272 66.667 14.67 0.00 34.01 4.40
1332 1881 2.125350 CCCTGCTCCTGCTCGTTC 60.125 66.667 0.00 0.00 40.48 3.95
1345 1894 4.135153 CCACTCCTCGTCGCCCTG 62.135 72.222 0.00 0.00 0.00 4.45
1513 2062 2.542595 CGTGGTCCAACTTATAATCGCC 59.457 50.000 0.00 0.00 0.00 5.54
1514 2063 3.450578 TCGTGGTCCAACTTATAATCGC 58.549 45.455 0.00 0.00 0.00 4.58
1522 2071 4.819105 TTCATATCTCGTGGTCCAACTT 57.181 40.909 0.00 0.00 0.00 2.66
1524 2073 4.755411 TCTTTCATATCTCGTGGTCCAAC 58.245 43.478 0.00 0.00 0.00 3.77
1527 2076 5.477291 TCCTATCTTTCATATCTCGTGGTCC 59.523 44.000 0.00 0.00 0.00 4.46
1529 2078 6.071108 CCATCCTATCTTTCATATCTCGTGGT 60.071 42.308 0.00 0.00 0.00 4.16
1530 2079 6.153510 TCCATCCTATCTTTCATATCTCGTGG 59.846 42.308 0.00 0.00 0.00 4.94
1531 2080 7.163001 TCCATCCTATCTTTCATATCTCGTG 57.837 40.000 0.00 0.00 0.00 4.35
1532 2081 7.575909 CGTTCCATCCTATCTTTCATATCTCGT 60.576 40.741 0.00 0.00 0.00 4.18
1533 2082 6.749578 CGTTCCATCCTATCTTTCATATCTCG 59.250 42.308 0.00 0.00 0.00 4.04
1534 2083 7.831753 TCGTTCCATCCTATCTTTCATATCTC 58.168 38.462 0.00 0.00 0.00 2.75
1535 2084 7.782897 TCGTTCCATCCTATCTTTCATATCT 57.217 36.000 0.00 0.00 0.00 1.98
1536 2085 8.253810 TCATCGTTCCATCCTATCTTTCATATC 58.746 37.037 0.00 0.00 0.00 1.63
1537 2086 8.138928 TCATCGTTCCATCCTATCTTTCATAT 57.861 34.615 0.00 0.00 0.00 1.78
1538 2087 7.233553 ACTCATCGTTCCATCCTATCTTTCATA 59.766 37.037 0.00 0.00 0.00 2.15
1539 2088 6.042552 ACTCATCGTTCCATCCTATCTTTCAT 59.957 38.462 0.00 0.00 0.00 2.57
1540 2089 5.363868 ACTCATCGTTCCATCCTATCTTTCA 59.636 40.000 0.00 0.00 0.00 2.69
1541 2090 5.848406 ACTCATCGTTCCATCCTATCTTTC 58.152 41.667 0.00 0.00 0.00 2.62
1542 2091 5.878406 ACTCATCGTTCCATCCTATCTTT 57.122 39.130 0.00 0.00 0.00 2.52
1543 2092 5.878406 AACTCATCGTTCCATCCTATCTT 57.122 39.130 0.00 0.00 0.00 2.40
1544 2093 5.878406 AAACTCATCGTTCCATCCTATCT 57.122 39.130 0.00 0.00 33.90 1.98
1545 2094 6.927294 AAAAACTCATCGTTCCATCCTATC 57.073 37.500 0.00 0.00 33.90 2.08
1585 2134 8.812329 CGAAATCCTACAAACAACAAATCAAAA 58.188 29.630 0.00 0.00 0.00 2.44
1586 2135 7.976734 ACGAAATCCTACAAACAACAAATCAAA 59.023 29.630 0.00 0.00 0.00 2.69
1587 2136 7.484975 ACGAAATCCTACAAACAACAAATCAA 58.515 30.769 0.00 0.00 0.00 2.57
1588 2137 7.033530 ACGAAATCCTACAAACAACAAATCA 57.966 32.000 0.00 0.00 0.00 2.57
1589 2138 6.302313 CGACGAAATCCTACAAACAACAAATC 59.698 38.462 0.00 0.00 0.00 2.17
1590 2139 6.017770 TCGACGAAATCCTACAAACAACAAAT 60.018 34.615 0.00 0.00 0.00 2.32
1601 2150 2.599082 CTGTGCTTCGACGAAATCCTAC 59.401 50.000 12.03 6.99 0.00 3.18
1613 2162 0.390472 GTCTCTTCCCCTGTGCTTCG 60.390 60.000 0.00 0.00 0.00 3.79
1664 2213 0.032130 ACTCAGAGAAAAGCGCGTCA 59.968 50.000 8.43 0.00 0.00 4.35
1673 2222 6.404623 CCACACATTTTGACAACTCAGAGAAA 60.405 38.462 3.79 0.00 0.00 2.52
1733 2282 3.555168 CCCCTATAGAAACGACATCAGCC 60.555 52.174 0.00 0.00 0.00 4.85
1751 2300 2.685380 CCGAGCCAAGAGTCCCCT 60.685 66.667 0.00 0.00 0.00 4.79
1823 2372 0.387202 CACTCAGGCTCCGATACCAG 59.613 60.000 0.00 0.00 0.00 4.00
1838 2387 2.828520 TCTCACCTTCCATCTGTCACTC 59.171 50.000 0.00 0.00 0.00 3.51
1943 2493 3.303990 CCATCCGCATTCGTTATCAAAGG 60.304 47.826 0.00 0.00 0.00 3.11
1946 2496 1.601903 GCCATCCGCATTCGTTATCAA 59.398 47.619 0.00 0.00 37.47 2.57
2044 2594 5.344743 TGGAGATTGTGCTAGAAACCTAG 57.655 43.478 0.00 0.00 37.33 3.02
2181 2740 5.302059 CCTCGGGACATCTTCACTAGAATTA 59.698 44.000 0.00 0.00 36.22 1.40
2187 2746 2.100197 CACCTCGGGACATCTTCACTA 58.900 52.381 0.00 0.00 0.00 2.74
2302 2861 0.546507 TGACCACAGTGCCCCATCTA 60.547 55.000 0.00 0.00 0.00 1.98
2314 2873 2.535012 TCTTGTACGCAATGACCACA 57.465 45.000 0.00 0.00 33.65 4.17
2376 2935 4.801891 TGCATGTTCTCTGAAGATTTTGC 58.198 39.130 0.00 0.00 33.64 3.68
2377 2936 4.857588 GCTGCATGTTCTCTGAAGATTTTG 59.142 41.667 0.00 0.00 0.00 2.44
2381 2941 3.345508 TGCTGCATGTTCTCTGAAGAT 57.654 42.857 0.00 0.00 0.00 2.40
2478 3039 8.615878 AATGTTTGTTTCAGTACTATGCTACA 57.384 30.769 0.00 0.00 0.00 2.74
2482 3043 7.382218 AGCAAAATGTTTGTTTCAGTACTATGC 59.618 33.333 0.00 0.00 0.00 3.14
2488 3049 9.116067 AGTACTAGCAAAATGTTTGTTTCAGTA 57.884 29.630 0.00 0.87 0.00 2.74
2498 3059 4.890088 TCGACCAGTACTAGCAAAATGTT 58.110 39.130 0.00 0.00 0.00 2.71
2499 3060 4.495422 CTCGACCAGTACTAGCAAAATGT 58.505 43.478 0.00 0.00 0.00 2.71
2501 3062 3.514309 ACCTCGACCAGTACTAGCAAAAT 59.486 43.478 0.00 0.00 0.00 1.82
2516 3077 6.663944 AATAGCAAAATAGTCAACCTCGAC 57.336 37.500 0.00 0.00 36.08 4.20
2578 3148 2.574450 TGATGTCTGTGTGCACAATGT 58.426 42.857 23.59 4.58 41.33 2.71
2589 3159 2.288666 AGTTGCAACGTTGATGTCTGT 58.711 42.857 31.62 5.83 0.00 3.41
2664 3234 2.806945 TCATTGAAATCTTCCCGGCT 57.193 45.000 0.00 0.00 0.00 5.52
2667 3237 7.035840 AGAATCAATCATTGAAATCTTCCCG 57.964 36.000 3.63 0.00 43.95 5.14
2766 3336 0.911769 CTGCTTCCCTACCACCATCA 59.088 55.000 0.00 0.00 0.00 3.07
2767 3337 0.912486 ACTGCTTCCCTACCACCATC 59.088 55.000 0.00 0.00 0.00 3.51
2856 3429 6.591834 CAGATCGAACAAAGTAGATGGAAAGT 59.408 38.462 0.00 0.00 0.00 2.66
2870 3443 3.244215 ACTTCTCTTGCCAGATCGAACAA 60.244 43.478 0.00 0.00 0.00 2.83
2887 3460 7.670364 CAAAATTATTTTGGGTCCTCACTTCT 58.330 34.615 19.38 0.00 44.75 2.85
3018 3621 2.037121 CCAAACATCCCCAACTCCAAAC 59.963 50.000 0.00 0.00 0.00 2.93
3158 3763 4.364415 TGTAATGAAATTAAGCGTGGGC 57.636 40.909 0.00 0.00 41.12 5.36
3179 3784 4.186926 CTCATCCGATTGACAGTCACAAT 58.813 43.478 1.52 0.00 40.08 2.71
3180 3785 3.006859 ACTCATCCGATTGACAGTCACAA 59.993 43.478 1.52 0.00 0.00 3.33
3195 3800 3.262420 ACAACAGCGACATAACTCATCC 58.738 45.455 0.00 0.00 0.00 3.51
3196 3801 4.152402 ACAACAACAGCGACATAACTCATC 59.848 41.667 0.00 0.00 0.00 2.92
3200 3805 4.574828 AGAAACAACAACAGCGACATAACT 59.425 37.500 0.00 0.00 0.00 2.24
3202 3807 5.065346 TGAAGAAACAACAACAGCGACATAA 59.935 36.000 0.00 0.00 0.00 1.90
3221 3826 1.442769 GCTCGCTGTTGGAATGAAGA 58.557 50.000 0.00 0.00 0.00 2.87
3229 3864 0.737715 GACAGTAGGCTCGCTGTTGG 60.738 60.000 20.63 0.87 44.89 3.77
3233 3868 3.119291 CAATAAGACAGTAGGCTCGCTG 58.881 50.000 14.86 14.86 38.58 5.18
3236 3871 3.802948 ACCAATAAGACAGTAGGCTCG 57.197 47.619 0.00 0.00 0.00 5.03
3294 3929 7.333423 CCGATTTTATCAGTCTGAAACCTTGTA 59.667 37.037 6.64 0.00 0.00 2.41
3313 3948 1.913419 TCTAGTTCTGCCCCCGATTTT 59.087 47.619 0.00 0.00 0.00 1.82
3314 3949 1.486726 CTCTAGTTCTGCCCCCGATTT 59.513 52.381 0.00 0.00 0.00 2.17
3438 4073 0.674895 CCTCTGGAGCTGGGTTTTCG 60.675 60.000 0.00 0.00 0.00 3.46
3441 4076 0.402121 GAACCTCTGGAGCTGGGTTT 59.598 55.000 0.00 0.00 41.44 3.27
3516 4151 0.921256 CCAGGATTTCAGGGGGAGGT 60.921 60.000 0.00 0.00 0.00 3.85
3564 4199 1.227853 GTCACCCACCGCTTTGTCT 60.228 57.895 0.00 0.00 0.00 3.41
3700 4335 5.171476 ACTTATGACTGATGAACTTCGTGG 58.829 41.667 0.00 0.00 0.00 4.94
3710 4345 7.848051 GTCTCGCAAAAATACTTATGACTGATG 59.152 37.037 0.00 0.00 0.00 3.07
3730 4365 1.454653 GTTTGTTAGTGGTCGTCTCGC 59.545 52.381 0.00 0.00 0.00 5.03
3786 4428 5.063880 AGGTTTTTAGAAGTGGTACTGCTG 58.936 41.667 0.00 0.00 34.24 4.41
3787 4429 5.306114 AGGTTTTTAGAAGTGGTACTGCT 57.694 39.130 0.00 0.00 37.91 4.24
3788 4430 4.454847 GGAGGTTTTTAGAAGTGGTACTGC 59.545 45.833 0.00 0.00 0.00 4.40
3811 4453 5.756347 TCGGATTACATTAAATCTCCAACGG 59.244 40.000 0.00 0.00 36.34 4.44
3889 4531 3.905784 AGTCGTACCTTGTTCCTTTACG 58.094 45.455 0.00 0.00 37.47 3.18
4068 4710 2.434185 TCGACGGCTTGTCCATGC 60.434 61.111 0.00 0.00 45.23 4.06
4245 4934 3.201290 CGCTCTGAAGAAACTGGCATAT 58.799 45.455 0.00 0.00 0.00 1.78
4247 4936 1.446907 CGCTCTGAAGAAACTGGCAT 58.553 50.000 0.00 0.00 0.00 4.40
4250 4949 0.603707 TGCCGCTCTGAAGAAACTGG 60.604 55.000 0.00 0.00 0.00 4.00
4257 4956 4.095483 AGAAAATGTAATGCCGCTCTGAAG 59.905 41.667 0.00 0.00 0.00 3.02
4264 4963 1.748493 TCCCAGAAAATGTAATGCCGC 59.252 47.619 0.00 0.00 0.00 6.53
4266 4965 3.381590 GTCCTCCCAGAAAATGTAATGCC 59.618 47.826 0.00 0.00 0.00 4.40
4271 4970 2.901192 TGTCGTCCTCCCAGAAAATGTA 59.099 45.455 0.00 0.00 0.00 2.29
4273 4972 2.472695 TGTCGTCCTCCCAGAAAATG 57.527 50.000 0.00 0.00 0.00 2.32
4285 4984 0.249120 TCATCCCACACATGTCGTCC 59.751 55.000 0.00 0.00 0.00 4.79
4288 4987 1.338105 ACTGTCATCCCACACATGTCG 60.338 52.381 0.00 0.00 0.00 4.35
4290 4989 2.957402 AACTGTCATCCCACACATGT 57.043 45.000 0.00 0.00 0.00 3.21
4292 4991 3.795688 AGAAACTGTCATCCCACACAT 57.204 42.857 0.00 0.00 0.00 3.21
4293 4992 3.118075 TGAAGAAACTGTCATCCCACACA 60.118 43.478 0.00 0.00 0.00 3.72
4294 4993 3.476552 TGAAGAAACTGTCATCCCACAC 58.523 45.455 0.00 0.00 0.00 3.82
4295 4994 3.855255 TGAAGAAACTGTCATCCCACA 57.145 42.857 0.00 0.00 0.00 4.17
4296 4995 4.557496 GCTTTGAAGAAACTGTCATCCCAC 60.557 45.833 0.00 0.00 0.00 4.61
4297 4996 3.569701 GCTTTGAAGAAACTGTCATCCCA 59.430 43.478 0.00 0.00 0.00 4.37
4298 4997 3.365364 CGCTTTGAAGAAACTGTCATCCC 60.365 47.826 0.00 0.00 0.00 3.85
4299 4998 3.498397 TCGCTTTGAAGAAACTGTCATCC 59.502 43.478 0.00 0.00 0.00 3.51
4314 5013 0.521867 CATCGTGCCATGTCGCTTTG 60.522 55.000 0.00 0.00 0.00 2.77
4340 5043 2.106511 TGCTCTAAAGAAACTGCCACCT 59.893 45.455 0.00 0.00 0.00 4.00
4342 5045 4.568152 TTTGCTCTAAAGAAACTGCCAC 57.432 40.909 0.00 0.00 0.00 5.01
4354 5057 9.467258 CTTTCAGAAAATGTCATTTTGCTCTAA 57.533 29.630 24.74 14.68 42.15 2.10
4355 5058 8.084073 CCTTTCAGAAAATGTCATTTTGCTCTA 58.916 33.333 24.74 10.95 42.15 2.43
4363 5066 6.547141 TGTCAGTCCTTTCAGAAAATGTCATT 59.453 34.615 0.00 0.00 0.00 2.57
4376 5079 4.816925 AGCTTTAGTTGTGTCAGTCCTTTC 59.183 41.667 0.00 0.00 0.00 2.62
4377 5080 4.576463 CAGCTTTAGTTGTGTCAGTCCTTT 59.424 41.667 0.00 0.00 0.00 3.11
4378 5081 4.130118 CAGCTTTAGTTGTGTCAGTCCTT 58.870 43.478 0.00 0.00 0.00 3.36
4384 5087 2.872245 GCTGACAGCTTTAGTTGTGTCA 59.128 45.455 20.41 7.51 45.39 3.58
4397 5165 1.112459 CGAACGTTTTTGCTGACAGC 58.888 50.000 20.86 20.86 42.82 4.40
4401 5169 2.786578 GCATTTCGAACGTTTTTGCTGA 59.213 40.909 0.46 0.00 0.00 4.26
4411 5179 1.644786 GGAGGGTGGCATTTCGAACG 61.645 60.000 0.00 0.00 0.00 3.95
4436 5204 2.977914 TGTTATCTGGCTGCTGAAGTC 58.022 47.619 0.00 0.00 0.00 3.01
4445 5213 4.422073 TCATCGGAAATGTTATCTGGCT 57.578 40.909 0.00 0.00 0.00 4.75
4448 5216 9.571810 TTGAAAAATCATCGGAAATGTTATCTG 57.428 29.630 0.00 0.00 0.00 2.90
4454 5222 6.108015 CCCATTGAAAAATCATCGGAAATGT 58.892 36.000 0.00 0.00 0.00 2.71
4455 5223 5.006941 GCCCATTGAAAAATCATCGGAAATG 59.993 40.000 0.00 0.00 0.00 2.32
4456 5224 5.104817 AGCCCATTGAAAAATCATCGGAAAT 60.105 36.000 0.00 0.00 0.00 2.17
4457 5225 4.222588 AGCCCATTGAAAAATCATCGGAAA 59.777 37.500 0.00 0.00 0.00 3.13
4493 5261 7.793948 AGGAAACATGTTTAGGAGTAGTACT 57.206 36.000 23.33 1.37 32.11 2.73
4494 5262 8.092687 TGAAGGAAACATGTTTAGGAGTAGTAC 58.907 37.037 23.33 7.22 32.11 2.73
4519 5287 9.079833 AGCTCAAATATTCACGATTTTGAAATG 57.920 29.630 0.00 0.00 38.95 2.32
4542 5310 4.769488 TCAGTTCATTCAGAGACTGTAGCT 59.231 41.667 0.00 0.00 37.03 3.32
4553 5321 5.922544 GGGTTCATTTTGTCAGTTCATTCAG 59.077 40.000 0.00 0.00 0.00 3.02
4566 5334 8.179615 GGTACGTAATTTCTAGGGTTCATTTTG 58.820 37.037 0.00 0.00 0.00 2.44
4620 5388 4.870426 CAGGAGAAGCAACGCTATAAAGAA 59.130 41.667 0.00 0.00 38.25 2.52
4623 5391 4.433615 CTCAGGAGAAGCAACGCTATAAA 58.566 43.478 0.00 0.00 38.25 1.40


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

AutoCloner maintained by Alex Coulton.