Multiple sequence alignment - TraesCS7A01G329000

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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 TraesCS7A01G329000 chr7A 100.000 6646 0 0 1 6646 478581343 478574698 0.000000e+00 12273.0
1 TraesCS7A01G329000 chr7A 94.444 54 3 0 3248 3301 125264716 125264769 4.270000e-12 84.2
2 TraesCS7A01G329000 chr7B 95.461 2115 81 6 2006 4115 431682587 431680483 0.000000e+00 3360.0
3 TraesCS7A01G329000 chr7B 92.467 1500 79 18 85 1574 431686113 431684638 0.000000e+00 2113.0
4 TraesCS7A01G329000 chr7B 91.732 1270 75 15 4865 6120 431679617 431678364 0.000000e+00 1736.0
5 TraesCS7A01G329000 chr7B 92.500 520 32 4 4204 4716 431680129 431679610 0.000000e+00 737.0
6 TraesCS7A01G329000 chr7B 93.056 432 23 2 1580 2011 431684593 431684169 5.660000e-175 625.0
7 TraesCS7A01G329000 chr7B 88.646 229 25 1 6154 6381 637332182 637331954 1.830000e-70 278.0
8 TraesCS7A01G329000 chr7B 95.349 86 4 0 1 86 431686227 431686142 3.230000e-28 137.0
9 TraesCS7A01G329000 chr7D 96.504 1945 59 8 2795 4734 416244108 416242168 0.000000e+00 3206.0
10 TraesCS7A01G329000 chr7D 92.663 1472 75 17 85 1546 416248556 416247108 0.000000e+00 2089.0
11 TraesCS7A01G329000 chr7D 95.697 976 40 2 1999 2972 416245075 416244100 0.000000e+00 1568.0
12 TraesCS7A01G329000 chr7D 88.310 1343 95 28 4782 6074 416242162 416240832 0.000000e+00 1554.0
13 TraesCS7A01G329000 chr7D 91.770 486 38 2 6157 6641 503740569 503741053 0.000000e+00 675.0
14 TraesCS7A01G329000 chr7D 89.744 507 35 5 6156 6646 118350381 118349876 3.380000e-177 632.0
15 TraesCS7A01G329000 chr7D 92.824 432 24 2 1580 2011 416247026 416246602 2.630000e-173 619.0
16 TraesCS7A01G329000 chr7D 88.421 475 37 6 6183 6641 169456187 169455715 2.090000e-154 556.0
17 TraesCS7A01G329000 chr7D 98.780 82 1 0 1 82 416248671 416248590 5.370000e-31 147.0
18 TraesCS7A01G329000 chr7D 95.082 61 2 1 4728 4787 463883561 463883621 1.970000e-15 95.3
19 TraesCS7A01G329000 chr7D 92.593 54 4 0 3248 3301 81915487 81915540 1.990000e-10 78.7
20 TraesCS7A01G329000 chr3D 90.965 487 42 2 6156 6641 39996951 39997436 0.000000e+00 654.0
21 TraesCS7A01G329000 chr3D 92.273 440 31 3 6148 6586 35814624 35814187 7.320000e-174 621.0
22 TraesCS7A01G329000 chr6B 89.837 492 47 3 6157 6646 545589327 545588837 4.370000e-176 628.0
23 TraesCS7A01G329000 chr6B 91.429 70 5 1 4728 4797 487538481 487538549 1.970000e-15 95.3
24 TraesCS7A01G329000 chr3B 89.820 501 34 6 6157 6641 723620996 723620497 1.570000e-175 627.0
25 TraesCS7A01G329000 chr3B 92.958 71 2 3 4728 4797 620673533 620673465 4.240000e-17 100.0
26 TraesCS7A01G329000 chr1D 89.421 501 36 5 6157 6641 65881653 65882152 3.410000e-172 616.0
27 TraesCS7A01G329000 chr1D 89.264 503 36 4 6156 6641 205097710 205097209 1.220000e-171 614.0
28 TraesCS7A01G329000 chr1D 98.148 54 1 0 4728 4781 105351617 105351670 1.970000e-15 95.3
29 TraesCS7A01G329000 chr1D 98.148 54 1 0 4728 4781 127930310 127930363 1.970000e-15 95.3
30 TraesCS7A01G329000 chr1D 92.593 54 4 0 3248 3301 96067124 96067177 1.990000e-10 78.7
31 TraesCS7A01G329000 chr5D 88.560 507 41 8 6157 6646 482380378 482379872 3.430000e-167 599.0
32 TraesCS7A01G329000 chr4D 88.623 501 39 6 6157 6641 434151069 434151567 1.600000e-165 593.0
33 TraesCS7A01G329000 chr4D 96.610 59 2 0 4728 4786 320108377 320108435 1.530000e-16 99.0
34 TraesCS7A01G329000 chr5A 87.743 514 45 7 6143 6639 277969681 277970193 9.600000e-163 584.0
35 TraesCS7A01G329000 chr2D 90.164 122 12 0 511 632 651319276 651319397 6.900000e-35 159.0
36 TraesCS7A01G329000 chr2B 88.525 122 14 0 511 632 780789477 780789598 1.490000e-31 148.0
37 TraesCS7A01G329000 chr2B 90.000 60 5 1 3248 3307 373982517 373982459 7.150000e-10 76.8
38 TraesCS7A01G329000 chr2A 87.597 129 14 1 511 637 776286846 776286718 1.490000e-31 148.0
39 TraesCS7A01G329000 chr6A 98.246 57 1 0 4728 4784 255217511 255217455 4.240000e-17 100.0
40 TraesCS7A01G329000 chr6A 90.164 61 5 1 3248 3307 269000928 269000868 1.990000e-10 78.7
41 TraesCS7A01G329000 chr6D 95.238 63 1 2 4728 4788 296696732 296696794 1.530000e-16 99.0
42 TraesCS7A01G329000 chr6D 90.164 61 5 1 3248 3307 194260454 194260394 1.990000e-10 78.7
43 TraesCS7A01G329000 chr6D 92.727 55 3 1 3248 3302 348280415 348280468 1.990000e-10 78.7
44 TraesCS7A01G329000 chr3A 95.238 63 2 1 4728 4790 264038373 264038434 1.530000e-16 99.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G329000 chr7A 478574698 478581343 6645 True 12273.000000 12273 100.000000 1 6646 1 chr7A.!!$R1 6645
1 TraesCS7A01G329000 chr7B 431678364 431686227 7863 True 1451.333333 3360 93.427500 1 6120 6 chr7B.!!$R2 6119
2 TraesCS7A01G329000 chr7D 416240832 416248671 7839 True 1530.500000 3206 94.129667 1 6074 6 chr7D.!!$R3 6073
3 TraesCS7A01G329000 chr7D 118349876 118350381 505 True 632.000000 632 89.744000 6156 6646 1 chr7D.!!$R1 490
4 TraesCS7A01G329000 chr1D 205097209 205097710 501 True 614.000000 614 89.264000 6156 6641 1 chr1D.!!$R1 485
5 TraesCS7A01G329000 chr5D 482379872 482380378 506 True 599.000000 599 88.560000 6157 6646 1 chr5D.!!$R1 489
6 TraesCS7A01G329000 chr5A 277969681 277970193 512 False 584.000000 584 87.743000 6143 6639 1 chr5A.!!$F1 496

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
479 513 1.203523 AGCGGCGGAAAAATAAATGCA 59.796 42.857 9.78 0.0 0.0 3.96 F
1660 1760 0.106708 TCCAGTTCGAGTTGCTTGCT 59.893 50.000 0.00 0.0 0.0 3.91 F
2700 4403 0.034896 CCTGGTACGGCAGTGACTTT 59.965 55.000 0.00 0.0 0.0 2.66 F
2842 4716 0.036732 TTGATCACACTGGACCTGCC 59.963 55.000 0.00 0.0 37.1 4.85 F
3301 5175 0.319405 CTCCAAGCTGCCCCTTTTTG 59.681 55.000 0.00 0.0 0.0 2.44 F
4750 6899 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2070 0.036164 AGCAAACCCGTGTATGAGCA 59.964 50.0 0.00 0.0 0.00 4.26 R
3283 5157 0.398381 ACAAAAAGGGGCAGCTTGGA 60.398 50.0 0.00 0.0 0.00 3.53 R
3869 5743 0.538287 AGAGAAGCAACCCAGCAACC 60.538 55.0 0.00 0.0 36.85 3.77 R
4737 6886 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.0 7.96 0.0 33.18 4.58 R
5128 7283 0.536233 AACGTGCACATACAAGGGCA 60.536 50.0 18.64 0.0 0.00 5.36 R
6138 8341 0.033504 TCCTGCCAGAGTCAAACGTC 59.966 55.0 0.00 0.0 0.00 4.34 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
82 83 6.449698 CAACAGACCATTTTAAGCATCACTT 58.550 36.000 0.00 0.00 42.76 3.16
100 132 7.278646 GCATCACTTATTACTTGATGAGTGTCA 59.721 37.037 13.63 0.00 46.45 3.58
154 186 4.638421 TCATCACCTTATTTGGCTAAACCG 59.362 41.667 0.00 0.00 43.94 4.44
266 299 5.294552 CCCACAAGCTATTTCTACTGTTAGC 59.705 44.000 0.00 1.18 37.84 3.09
353 386 1.343069 CCTAGGCTGTACCCATCCTC 58.657 60.000 0.00 0.00 38.21 3.71
476 510 2.477189 CGACAGCGGCGGAAAAATAAAT 60.477 45.455 9.78 0.00 0.00 1.40
477 511 2.851824 GACAGCGGCGGAAAAATAAATG 59.148 45.455 9.78 0.00 0.00 2.32
478 512 1.587946 CAGCGGCGGAAAAATAAATGC 59.412 47.619 9.78 0.00 0.00 3.56
479 513 1.203523 AGCGGCGGAAAAATAAATGCA 59.796 42.857 9.78 0.00 0.00 3.96
481 515 2.733858 GCGGCGGAAAAATAAATGCAGA 60.734 45.455 9.78 0.00 0.00 4.26
483 517 4.111916 CGGCGGAAAAATAAATGCAGAAT 58.888 39.130 0.00 0.00 0.00 2.40
719 755 2.332514 CGCATTATGCCCTTGCCG 59.667 61.111 11.90 0.00 41.12 5.69
731 774 3.954465 CTTGCCGCAGCTCAGCTCT 62.954 63.158 0.00 0.00 36.40 4.09
780 823 1.456705 CCTCCTCCTTCCTCCTCGG 60.457 68.421 0.00 0.00 0.00 4.63
781 824 1.456705 CTCCTCCTTCCTCCTCGGG 60.457 68.421 0.00 0.00 0.00 5.14
782 825 2.231540 CTCCTCCTTCCTCCTCGGGT 62.232 65.000 0.00 0.00 0.00 5.28
1011 1062 2.126031 GAAGTCGTGACGGCTCCC 60.126 66.667 14.17 4.20 42.48 4.30
1150 1201 1.874019 CGTCCTTCGATCGCAGGTG 60.874 63.158 28.96 20.15 42.86 4.00
1151 1202 1.519455 GTCCTTCGATCGCAGGTGG 60.519 63.158 28.96 16.59 30.54 4.61
1173 1224 2.202492 CCTTCCTCGTCGTGCTCG 60.202 66.667 0.81 0.81 38.55 5.03
1180 1231 0.316278 CTCGTCGTGCTCGTCCTATG 60.316 60.000 8.17 0.00 38.33 2.23
1233 1284 1.104577 GCCGTGGAGGTTTGGTTTGA 61.105 55.000 0.00 0.00 43.70 2.69
1421 1472 3.182996 AAGGGCGGGAAAGGTGGT 61.183 61.111 0.00 0.00 0.00 4.16
1424 1475 4.966787 GGCGGGAAAGGTGGTGCA 62.967 66.667 0.00 0.00 0.00 4.57
1496 1547 2.737376 GAACACGCCCGACAGGTC 60.737 66.667 0.00 0.00 38.26 3.85
1499 1550 4.308458 CACGCCCGACAGGTCCAA 62.308 66.667 0.00 0.00 38.26 3.53
1511 1563 1.077429 GGTCCAATGTCCAGCCCTC 60.077 63.158 0.00 0.00 0.00 4.30
1521 1573 1.071699 GTCCAGCCCTCACTTGTTACA 59.928 52.381 0.00 0.00 0.00 2.41
1525 1577 1.000955 AGCCCTCACTTGTTACAGTCG 59.999 52.381 0.00 0.00 0.00 4.18
1535 1587 2.734670 TGTTACAGTCGACAAACCTCG 58.265 47.619 19.50 0.00 34.83 4.63
1549 1609 6.567321 CGACAAACCTCGGACGATACTAATAT 60.567 42.308 0.00 0.00 0.00 1.28
1552 1612 7.014038 ACAAACCTCGGACGATACTAATATCTT 59.986 37.037 0.00 0.00 35.88 2.40
1562 1622 8.850007 ACGATACTAATATCTTCAGCTGTAGA 57.150 34.615 23.22 23.22 35.88 2.59
1563 1623 9.456147 ACGATACTAATATCTTCAGCTGTAGAT 57.544 33.333 30.86 30.86 35.88 1.98
1660 1760 0.106708 TCCAGTTCGAGTTGCTTGCT 59.893 50.000 0.00 0.00 0.00 3.91
1664 1764 2.225019 CAGTTCGAGTTGCTTGCTCAAT 59.775 45.455 0.00 0.00 33.45 2.57
1687 1787 9.044150 CAATTACATTGAAAATTCGGCCATATT 57.956 29.630 2.24 0.00 42.83 1.28
1688 1788 9.612066 AATTACATTGAAAATTCGGCCATATTT 57.388 25.926 2.24 4.80 0.00 1.40
1689 1789 6.907206 ACATTGAAAATTCGGCCATATTTG 57.093 33.333 2.24 0.00 0.00 2.32
1690 1790 6.638610 ACATTGAAAATTCGGCCATATTTGA 58.361 32.000 2.24 0.00 0.00 2.69
1691 1791 7.274447 ACATTGAAAATTCGGCCATATTTGAT 58.726 30.769 2.24 1.38 0.00 2.57
1692 1792 7.769970 ACATTGAAAATTCGGCCATATTTGATT 59.230 29.630 2.24 0.00 0.00 2.57
1693 1793 7.769272 TTGAAAATTCGGCCATATTTGATTC 57.231 32.000 2.24 3.53 0.00 2.52
1694 1794 7.111247 TGAAAATTCGGCCATATTTGATTCT 57.889 32.000 2.24 0.00 0.00 2.40
1702 1802 5.663456 GGCCATATTTGATTCTTTTGCTCA 58.337 37.500 0.00 0.00 0.00 4.26
1727 1827 4.365899 TCATACTACGGTAGCACAACTG 57.634 45.455 14.91 4.48 0.00 3.16
1742 1842 4.023279 GCACAACTGTATTTGGTCATGTCA 60.023 41.667 0.00 0.00 0.00 3.58
1799 1899 1.272490 TCTTCTTACGGTCTGCAGGTG 59.728 52.381 15.13 6.55 0.00 4.00
1802 1902 0.732880 CTTACGGTCTGCAGGTGTCG 60.733 60.000 15.13 14.41 0.00 4.35
1832 1932 3.054875 TCCTTGGAGGAATGAGTGTCATG 60.055 47.826 0.00 0.00 42.51 3.07
1908 2008 7.429633 TGTTTTATCACAGGTACCAACATTTG 58.570 34.615 15.94 4.75 0.00 2.32
1935 2035 2.559668 CTGTTTCATCACAGGTGCCAAT 59.440 45.455 0.00 0.00 40.60 3.16
1947 2047 3.379372 CAGGTGCCAATAATGTCCTGAAG 59.621 47.826 0.00 0.00 38.82 3.02
2004 2104 4.466015 GGGTTTGCTATTTGGAATTGAGGA 59.534 41.667 0.00 0.00 0.00 3.71
2156 3856 6.591935 ACGTATTAGATGTTCCATTCCATGT 58.408 36.000 0.00 0.00 0.00 3.21
2220 3920 6.325919 AGAAAATGATCAACGCCTGTTTAA 57.674 33.333 0.00 0.00 35.72 1.52
2267 3968 8.469200 TGGCCTATCACTTTTATCTTTCAAATG 58.531 33.333 3.32 0.00 0.00 2.32
2293 3994 3.182887 TGGCCATTAACCAACCTGATT 57.817 42.857 0.00 0.00 33.12 2.57
2305 4006 4.226620 ACCAACCTGATTTACCGACCTATT 59.773 41.667 0.00 0.00 0.00 1.73
2306 4007 5.190677 CCAACCTGATTTACCGACCTATTT 58.809 41.667 0.00 0.00 0.00 1.40
2365 4066 5.660460 AGGTTTTGTGGTCTTTGCTTAAAG 58.340 37.500 0.00 0.00 0.00 1.85
2399 4100 7.627513 GCATAATATCAACTTGAACAAACGGGA 60.628 37.037 0.00 0.00 0.00 5.14
2407 4108 1.162698 GAACAAACGGGAAGGCTACC 58.837 55.000 0.00 0.00 0.00 3.18
2441 4144 2.756760 ACTGCCTTTCACAATGCCATAG 59.243 45.455 0.00 0.00 0.00 2.23
2466 4169 9.877178 AGTGACCTTATTATTTAGAACACTGAG 57.123 33.333 0.00 0.00 34.39 3.35
2546 4249 5.700373 TGGCATTTGTTTTAGGATCTTTTGC 59.300 36.000 0.00 0.00 0.00 3.68
2570 4273 6.072508 GCCATTGTTGTCTGATCTTTTAGTGA 60.073 38.462 0.00 0.00 0.00 3.41
2575 4278 6.650807 TGTTGTCTGATCTTTTAGTGATGACC 59.349 38.462 0.00 0.00 0.00 4.02
2634 4337 8.830580 AGGACATTTTCATTGTACAGATTATCG 58.169 33.333 0.00 0.00 29.81 2.92
2700 4403 0.034896 CCTGGTACGGCAGTGACTTT 59.965 55.000 0.00 0.00 0.00 2.66
2751 4454 1.557832 AGCCCAAGAAGGTGCGTATTA 59.442 47.619 0.00 0.00 38.25 0.98
2757 4460 6.404954 GCCCAAGAAGGTGCGTATTATTTTTA 60.405 38.462 0.00 0.00 34.66 1.52
2830 4704 9.049523 TCATAATCTTCTTAGCACATTGATCAC 57.950 33.333 0.00 0.00 0.00 3.06
2831 4705 8.833493 CATAATCTTCTTAGCACATTGATCACA 58.167 33.333 0.00 0.00 0.00 3.58
2842 4716 0.036732 TTGATCACACTGGACCTGCC 59.963 55.000 0.00 0.00 37.10 4.85
2948 4822 0.400213 TGCCCTTGGAAATCTGTCGT 59.600 50.000 0.00 0.00 0.00 4.34
2971 4845 6.197282 CGTGCTCAGATACTGTTAATACACTG 59.803 42.308 0.00 0.00 32.61 3.66
3301 5175 0.319405 CTCCAAGCTGCCCCTTTTTG 59.681 55.000 0.00 0.00 0.00 2.44
3395 5269 4.284178 AGGCTGTAGCAAATCCATGAATT 58.716 39.130 6.18 0.00 44.36 2.17
3431 5305 8.552034 GCATTCTGGACTGATTACTTACAATAC 58.448 37.037 0.00 0.00 0.00 1.89
3563 5437 6.884472 TGGAGATCTGGTAAATTAGAACCA 57.116 37.500 0.00 6.96 43.47 3.67
3586 5460 7.093509 ACCACTTAACCTTTGTTTCAGTTGAAT 60.094 33.333 0.00 0.00 35.87 2.57
3663 5537 9.492973 GTGTTTAACACCCACTTATTACTCTTA 57.507 33.333 16.58 0.00 43.05 2.10
3869 5743 3.445096 CCAAAGAATGCAGTTTAGAGGGG 59.555 47.826 0.00 0.00 0.00 4.79
3941 5815 6.318900 ACTTAGGCCCAAAAGAATCTATTTCG 59.681 38.462 15.09 0.00 39.46 3.46
4017 5891 5.130311 TGGCTTATCTCTGTGCCTTGTATTA 59.870 40.000 0.00 0.00 45.11 0.98
4096 5970 4.704833 GCCACGAGCTTGGAGCCA 62.705 66.667 8.71 0.00 43.77 4.75
4114 6228 5.186992 GGAGCCAAACCACCAATTTTATACT 59.813 40.000 0.00 0.00 0.00 2.12
4305 6448 6.899393 TTCTAGTGATGGTGCTTTTCATTT 57.101 33.333 0.00 0.00 0.00 2.32
4336 6479 8.405531 TGAATTTATTAGCAAGTTGGCACTATC 58.594 33.333 4.75 0.00 35.83 2.08
4338 6481 1.651987 TAGCAAGTTGGCACTATCGC 58.348 50.000 4.75 0.00 35.83 4.58
4420 6565 7.673641 TCCTGAATGGTTTATTTATTGCCAT 57.326 32.000 0.00 0.00 41.22 4.40
4734 6883 6.397217 AAGTACACCCACCATATTTTACCT 57.603 37.500 0.00 0.00 0.00 3.08
4735 6884 5.997843 AGTACACCCACCATATTTTACCTC 58.002 41.667 0.00 0.00 0.00 3.85
4737 6886 6.904654 AGTACACCCACCATATTTTACCTCTA 59.095 38.462 0.00 0.00 0.00 2.43
4738 6887 6.248569 ACACCCACCATATTTTACCTCTAG 57.751 41.667 0.00 0.00 0.00 2.43
4739 6888 5.063880 CACCCACCATATTTTACCTCTAGC 58.936 45.833 0.00 0.00 0.00 3.42
4740 6889 4.104261 ACCCACCATATTTTACCTCTAGCC 59.896 45.833 0.00 0.00 0.00 3.93
4741 6890 4.351111 CCCACCATATTTTACCTCTAGCCT 59.649 45.833 0.00 0.00 0.00 4.58
4742 6891 5.546499 CCCACCATATTTTACCTCTAGCCTA 59.454 44.000 0.00 0.00 0.00 3.93
4743 6892 6.465084 CCACCATATTTTACCTCTAGCCTAC 58.535 44.000 0.00 0.00 0.00 3.18
4744 6893 6.465084 CACCATATTTTACCTCTAGCCTACC 58.535 44.000 0.00 0.00 0.00 3.18
4745 6894 5.546887 ACCATATTTTACCTCTAGCCTACCC 59.453 44.000 0.00 0.00 0.00 3.69
4746 6895 5.045797 CCATATTTTACCTCTAGCCTACCCC 60.046 48.000 0.00 0.00 0.00 4.95
4747 6896 3.495186 TTTTACCTCTAGCCTACCCCA 57.505 47.619 0.00 0.00 0.00 4.96
4748 6897 3.495186 TTTACCTCTAGCCTACCCCAA 57.505 47.619 0.00 0.00 0.00 4.12
4749 6898 2.466547 TACCTCTAGCCTACCCCAAC 57.533 55.000 0.00 0.00 0.00 3.77
4750 6899 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
4751 6900 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
4752 6901 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
4753 6902 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
4754 6903 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
4755 6904 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
4756 6905 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
4767 6916 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
4768 6917 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
4769 6918 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
4770 6919 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
4771 6920 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
4772 6921 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
4773 6922 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
4774 6923 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
4775 6924 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
4776 6925 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
4777 6926 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
4778 6927 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
4779 6928 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
4780 6929 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
4781 6930 5.393678 GGACTAAAGGCTTTGTTGTTGTTGA 60.394 40.000 22.32 0.00 0.00 3.18
4782 6931 6.220726 ACTAAAGGCTTTGTTGTTGTTGAT 57.779 33.333 22.32 0.00 0.00 2.57
4783 6932 7.341445 ACTAAAGGCTTTGTTGTTGTTGATA 57.659 32.000 22.32 0.00 0.00 2.15
4784 6933 7.777095 ACTAAAGGCTTTGTTGTTGTTGATAA 58.223 30.769 22.32 0.00 0.00 1.75
5053 7206 5.095691 ACTACTTGCAACAATCAGAAACG 57.904 39.130 0.00 0.00 0.00 3.60
5110 7265 2.496871 CTGGATGCAAGCCCAAAATACA 59.503 45.455 6.52 0.00 46.54 2.29
5119 7274 6.370994 TGCAAGCCCAAAATACAATATGTTTG 59.629 34.615 0.00 0.00 0.00 2.93
5128 7283 9.393249 CAAAATACAATATGTTTGACTTGACGT 57.607 29.630 0.00 0.00 33.70 4.34
5129 7284 8.948853 AAATACAATATGTTTGACTTGACGTG 57.051 30.769 0.00 0.00 0.00 4.49
5137 7296 0.753867 TGACTTGACGTGCCCTTGTA 59.246 50.000 0.00 0.00 0.00 2.41
5146 7305 1.072332 TGCCCTTGTATGTGCACGT 59.928 52.632 17.19 17.19 0.00 4.49
5170 7329 4.230603 CAGGATGCAATGGAGCGT 57.769 55.556 0.00 0.00 37.31 5.07
5242 7401 1.406069 CCAGAAACCGCAGCATCTACT 60.406 52.381 0.00 0.00 0.00 2.57
5284 7443 1.782201 ATGTGGTGCCTGGAGCTTCA 61.782 55.000 0.00 0.00 44.23 3.02
5293 7452 0.390866 CTGGAGCTTCATCACGTGCT 60.391 55.000 11.67 2.45 38.59 4.40
5319 7478 1.602237 GGCCTGGTCCGAAAGATGA 59.398 57.895 0.00 0.00 0.00 2.92
5401 7560 1.402787 CCTTGTTTGTGCTCCTGGTT 58.597 50.000 0.00 0.00 0.00 3.67
5440 7599 1.112315 TGTTTGCGTTCCCTGCCAAT 61.112 50.000 0.00 0.00 0.00 3.16
5533 7694 1.067295 TCCAAACCTCAGCTGTGGAT 58.933 50.000 35.28 24.21 33.43 3.41
5612 7773 5.439721 TGAACATGATCCATCCTTTTCGAT 58.560 37.500 0.00 0.00 0.00 3.59
5615 7776 4.818546 ACATGATCCATCCTTTTCGATGAC 59.181 41.667 0.00 0.00 41.92 3.06
5627 7788 3.417069 TTCGATGACAGGGACAATTGT 57.583 42.857 11.78 11.78 0.00 2.71
5628 7789 2.698803 TCGATGACAGGGACAATTGTG 58.301 47.619 17.58 3.85 0.00 3.33
5649 7810 5.048782 TGTGTGGAGTATTTTTGAGTGATGC 60.049 40.000 0.00 0.00 0.00 3.91
5697 7858 3.276857 GGTCATTGAGATGTGTGATGCT 58.723 45.455 0.00 0.00 34.77 3.79
5698 7859 4.080975 TGGTCATTGAGATGTGTGATGCTA 60.081 41.667 0.00 0.00 34.77 3.49
5710 7877 1.043816 TGATGCTAGGCTAGGCTCAC 58.956 55.000 23.89 16.14 0.00 3.51
5717 7884 2.124942 GCTAGGCTCACCCACAGC 60.125 66.667 0.00 0.00 36.95 4.40
5767 7934 2.872245 TCACTCTCTTTTCCAGTTTGCG 59.128 45.455 0.00 0.00 0.00 4.85
5888 8069 6.127281 TGGATTAATCATTTGTGCTGATGCTT 60.127 34.615 17.07 0.00 40.48 3.91
5894 8075 6.426980 TCATTTGTGCTGATGCTTTACTAG 57.573 37.500 0.00 0.00 40.48 2.57
6001 8194 2.547855 GGTTGGGCTTGATTTTGACACC 60.548 50.000 0.00 0.00 0.00 4.16
6036 8239 6.052360 TCTGTCCGCAGCATACAAATTTATA 58.948 36.000 0.00 0.00 42.29 0.98
6063 8266 1.414181 CTACCATGAGGAAGACGCCAT 59.586 52.381 0.00 0.00 38.69 4.40
6064 8267 0.620556 ACCATGAGGAAGACGCCATT 59.379 50.000 0.00 0.00 38.69 3.16
6105 8308 5.965334 GCAGTATTTTGTGATACATCAACCG 59.035 40.000 0.00 0.00 38.75 4.44
6120 8323 4.054780 TCAACCGGTAGCTTGCTTATAG 57.945 45.455 8.00 0.00 0.00 1.31
6121 8324 3.702548 TCAACCGGTAGCTTGCTTATAGA 59.297 43.478 8.00 0.00 0.00 1.98
6122 8325 4.344102 TCAACCGGTAGCTTGCTTATAGAT 59.656 41.667 8.00 0.00 0.00 1.98
6123 8326 4.258702 ACCGGTAGCTTGCTTATAGATG 57.741 45.455 4.49 0.00 0.00 2.90
6124 8327 2.996621 CCGGTAGCTTGCTTATAGATGC 59.003 50.000 0.00 0.00 0.00 3.91
6125 8328 3.554960 CCGGTAGCTTGCTTATAGATGCA 60.555 47.826 0.00 0.00 37.42 3.96
6126 8329 4.248859 CGGTAGCTTGCTTATAGATGCAT 58.751 43.478 0.00 0.00 39.07 3.96
6127 8330 4.092529 CGGTAGCTTGCTTATAGATGCATG 59.907 45.833 2.46 3.12 39.07 4.06
6131 8334 4.421033 CTTGCTTATAGATGCATGCAGG 57.579 45.455 26.69 2.70 39.07 4.85
6132 8335 2.156917 TGCTTATAGATGCATGCAGGC 58.843 47.619 26.69 18.05 33.94 4.85
6139 8342 4.354162 TGCATGCAGGCAGCCAGA 62.354 61.111 24.07 0.00 44.83 3.86
6140 8343 3.823330 GCATGCAGGCAGCCAGAC 61.823 66.667 20.11 2.44 44.83 3.51
6141 8344 3.506096 CATGCAGGCAGCCAGACG 61.506 66.667 15.80 0.00 44.83 4.18
6142 8345 4.025858 ATGCAGGCAGCCAGACGT 62.026 61.111 15.80 0.15 44.83 4.34
6143 8346 3.557903 ATGCAGGCAGCCAGACGTT 62.558 57.895 15.80 0.00 44.83 3.99
6144 8347 2.980233 GCAGGCAGCCAGACGTTT 60.980 61.111 15.80 0.00 37.23 3.60
6145 8348 2.949106 CAGGCAGCCAGACGTTTG 59.051 61.111 15.80 0.00 0.00 2.93
6146 8349 1.597854 CAGGCAGCCAGACGTTTGA 60.598 57.895 15.80 0.00 0.00 2.69
6147 8350 1.598130 AGGCAGCCAGACGTTTGAC 60.598 57.895 15.80 0.00 0.00 3.18
6148 8351 1.598130 GGCAGCCAGACGTTTGACT 60.598 57.895 6.55 0.00 0.00 3.41
6149 8352 1.569479 GGCAGCCAGACGTTTGACTC 61.569 60.000 6.55 0.00 0.00 3.36
6150 8353 0.601311 GCAGCCAGACGTTTGACTCT 60.601 55.000 7.81 0.00 0.00 3.24
6151 8354 1.143305 CAGCCAGACGTTTGACTCTG 58.857 55.000 7.81 7.90 34.73 3.35
6153 8356 2.533318 CCAGACGTTTGACTCTGGC 58.467 57.895 7.81 0.00 45.54 4.85
6154 8357 0.249868 CCAGACGTTTGACTCTGGCA 60.250 55.000 7.81 0.00 45.54 4.92
6160 8363 1.272490 CGTTTGACTCTGGCAGGAGTA 59.728 52.381 15.73 0.58 45.32 2.59
6215 8418 7.340232 AGTTGTAACGGGTCAGTATCACTATTA 59.660 37.037 0.00 0.00 0.00 0.98
6272 8475 1.066716 TCGTTGCAATACGGGCTAAGT 60.067 47.619 10.80 0.00 41.67 2.24
6282 8485 1.690352 ACGGGCTAAGTGGCGTATAAT 59.310 47.619 0.00 0.00 42.84 1.28
6284 8487 2.547218 CGGGCTAAGTGGCGTATAATGT 60.547 50.000 0.00 0.00 42.84 2.71
6291 8494 7.385752 GGCTAAGTGGCGTATAATGTTGTATTA 59.614 37.037 0.00 0.00 0.00 0.98
6295 8498 6.757947 AGTGGCGTATAATGTTGTATTAACGT 59.242 34.615 0.00 0.00 0.00 3.99
6385 8604 1.784525 GAACCCAACTCACTCACTCG 58.215 55.000 0.00 0.00 0.00 4.18
6407 8626 2.764547 GAACCCTAGCCCTCGCCT 60.765 66.667 0.00 0.00 34.57 5.52
6432 8651 2.512515 GCTCTCGCCCGCTGATTT 60.513 61.111 0.00 0.00 0.00 2.17
6499 8718 1.812525 GAGGATGAGAGCAGCGACA 59.187 57.895 0.00 0.00 0.00 4.35
6534 8754 5.125367 TGCAGTACATAACTCCTCCTCTA 57.875 43.478 0.00 0.00 35.76 2.43
6619 8840 4.716287 GGGGATTTGATCTTTGATTTGGGA 59.284 41.667 0.00 0.00 0.00 4.37
6622 8843 5.163374 GGATTTGATCTTTGATTTGGGAGGG 60.163 44.000 0.00 0.00 0.00 4.30
6643 8864 3.181466 GGTTTGGTTCATTTTGCTCCTGT 60.181 43.478 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 8.729756 CCAATTGTTGACACTCATCAAGTAATA 58.270 33.333 4.43 0.00 38.84 0.98
100 132 6.267471 TGCTTACATTTTCTCCTCCAATTGTT 59.733 34.615 4.43 0.00 0.00 2.83
154 186 6.518208 AGTCTCACTAACTGTAGGATTGTC 57.482 41.667 0.00 0.00 0.00 3.18
266 299 6.934645 TCACTTTTGATGTTTACTACCTCCAG 59.065 38.462 0.00 0.00 0.00 3.86
353 386 9.561270 TCTCGCATATTTAGATTAGATCTTTCG 57.439 33.333 0.00 0.00 40.76 3.46
731 774 2.093658 GGCGACCTACTCCAATTCAGAA 60.094 50.000 0.00 0.00 0.00 3.02
780 823 0.472471 TCCTTTCACCTGTGACCACC 59.528 55.000 0.00 0.00 39.66 4.61
781 824 1.884235 CTCCTTTCACCTGTGACCAC 58.116 55.000 0.00 0.00 39.66 4.16
782 825 0.108585 GCTCCTTTCACCTGTGACCA 59.891 55.000 0.00 0.00 39.66 4.02
983 1031 1.657487 ACGACTTCACGTGACGCAG 60.657 57.895 19.90 15.86 44.84 5.18
1026 1077 1.189752 GATCTGGTCTGGACTGCAGA 58.810 55.000 23.35 10.45 35.28 4.26
1029 1080 1.520342 GCGATCTGGTCTGGACTGC 60.520 63.158 0.67 0.00 0.00 4.40
1150 1201 2.184579 CGACGAGGAAGGGAAGCC 59.815 66.667 0.00 0.00 0.00 4.35
1151 1202 1.446272 CACGACGAGGAAGGGAAGC 60.446 63.158 0.00 0.00 0.00 3.86
1173 1224 0.761187 TGCCTGAGATGCCATAGGAC 59.239 55.000 0.00 0.00 31.91 3.85
1180 1231 2.203181 GCCTCTGCCTGAGATGCC 60.203 66.667 0.00 0.00 45.39 4.40
1221 1272 5.428184 TGAAACCAAATCAAACCAAACCT 57.572 34.783 0.00 0.00 0.00 3.50
1225 1276 4.100189 ACCGATGAAACCAAATCAAACCAA 59.900 37.500 0.00 0.00 0.00 3.67
1233 1284 4.783764 GGAAGAACCGATGAAACCAAAT 57.216 40.909 0.00 0.00 0.00 2.32
1307 1358 0.394625 GGAGCAGGGAGTAGACGAGT 60.395 60.000 0.00 0.00 0.00 4.18
1421 1472 1.295423 GTCGTTAGAAGCCCCTGCA 59.705 57.895 0.00 0.00 41.13 4.41
1424 1475 2.577593 GCGTCGTTAGAAGCCCCT 59.422 61.111 0.00 0.00 44.32 4.79
1496 1547 0.038744 AAGTGAGGGCTGGACATTGG 59.961 55.000 0.00 0.00 0.00 3.16
1499 1550 0.773644 AACAAGTGAGGGCTGGACAT 59.226 50.000 0.00 0.00 0.00 3.06
1511 1563 3.869246 AGGTTTGTCGACTGTAACAAGTG 59.131 43.478 17.92 0.00 36.78 3.16
1521 1573 1.168407 TCGTCCGAGGTTTGTCGACT 61.168 55.000 17.92 0.00 42.85 4.18
1525 1577 2.935481 AGTATCGTCCGAGGTTTGTC 57.065 50.000 0.00 0.00 0.00 3.18
1535 1587 6.915349 ACAGCTGAAGATATTAGTATCGTCC 58.085 40.000 23.35 4.77 41.95 4.79
1586 1686 7.339976 GTCTGAAACCTACAGGAGAGTACTAAT 59.660 40.741 1.29 0.00 38.94 1.73
1613 1713 2.513753 TGTTGGGACTGCCACATTAAG 58.486 47.619 0.00 0.00 35.15 1.85
1614 1714 2.666272 TGTTGGGACTGCCACATTAA 57.334 45.000 0.00 0.00 35.15 1.40
1617 1717 2.014010 AATTGTTGGGACTGCCACAT 57.986 45.000 0.00 0.00 35.15 3.21
1664 1764 8.253810 TCAAATATGGCCGAATTTTCAATGTAA 58.746 29.630 11.38 0.00 0.00 2.41
1687 1787 8.571461 AGTATGATCTTGAGCAAAAGAATCAA 57.429 30.769 5.33 0.00 39.54 2.57
1688 1788 9.102757 GTAGTATGATCTTGAGCAAAAGAATCA 57.897 33.333 5.33 9.36 39.54 2.57
1689 1789 8.272176 CGTAGTATGATCTTGAGCAAAAGAATC 58.728 37.037 5.33 5.13 39.54 2.52
1690 1790 7.225538 CCGTAGTATGATCTTGAGCAAAAGAAT 59.774 37.037 5.33 0.00 39.54 2.40
1691 1791 6.535150 CCGTAGTATGATCTTGAGCAAAAGAA 59.465 38.462 5.33 0.00 39.54 2.52
1692 1792 6.042777 CCGTAGTATGATCTTGAGCAAAAGA 58.957 40.000 3.85 3.85 40.36 2.52
1693 1793 5.812642 ACCGTAGTATGATCTTGAGCAAAAG 59.187 40.000 0.00 0.00 0.00 2.27
1694 1794 5.730550 ACCGTAGTATGATCTTGAGCAAAA 58.269 37.500 0.00 0.00 0.00 2.44
1702 1802 5.360144 AGTTGTGCTACCGTAGTATGATCTT 59.640 40.000 7.40 0.00 0.00 2.40
1727 1827 4.250464 TCCGAGTTGACATGACCAAATAC 58.750 43.478 0.00 0.00 0.00 1.89
1832 1932 8.919145 CCTTCAGAAGACCATATATAGATACCC 58.081 40.741 12.14 0.00 0.00 3.69
1908 2008 0.524862 CTGTGATGAAACAGCAGGCC 59.475 55.000 0.00 0.00 41.05 5.19
1914 2014 1.608055 TGGCACCTGTGATGAAACAG 58.392 50.000 0.51 0.00 45.93 3.16
1935 2035 2.906389 AGTGCCACTCTTCAGGACATTA 59.094 45.455 0.00 0.00 0.00 1.90
1947 2047 4.377897 AGTTTACAACACTAGTGCCACTC 58.622 43.478 22.90 7.70 0.00 3.51
1970 2070 0.036164 AGCAAACCCGTGTATGAGCA 59.964 50.000 0.00 0.00 0.00 4.26
1975 2075 3.958018 TCCAAATAGCAAACCCGTGTAT 58.042 40.909 0.00 0.00 0.00 2.29
2042 3742 9.823647 GAACTTGAGTTCCATTATATCTTCTCA 57.176 33.333 11.87 0.00 46.42 3.27
2202 3902 9.950680 CTATTTTATTAAACAGGCGTTGATCAT 57.049 29.630 0.00 0.00 34.86 2.45
2220 3920 9.066842 AGGCCAAGATGAGGATATCTATTTTAT 57.933 33.333 5.01 0.00 36.42 1.40
2239 3939 7.630242 TGAAAGATAAAAGTGATAGGCCAAG 57.370 36.000 5.01 0.00 0.00 3.61
2267 3968 2.959516 GTTGGTTAATGGCCAAGCTTC 58.040 47.619 10.96 0.00 45.50 3.86
2273 3974 2.917713 ATCAGGTTGGTTAATGGCCA 57.082 45.000 8.56 8.56 0.00 5.36
2293 3994 8.755977 AGAAAGATAACAGAAATAGGTCGGTAA 58.244 33.333 0.00 0.00 0.00 2.85
2305 4006 5.488341 GCCAGGTACAGAAAGATAACAGAA 58.512 41.667 0.00 0.00 0.00 3.02
2306 4007 4.081087 GGCCAGGTACAGAAAGATAACAGA 60.081 45.833 0.00 0.00 0.00 3.41
2407 4108 6.183360 TGTGAAAGGCAGTTTACAAGGTAAAG 60.183 38.462 2.04 0.00 0.00 1.85
2441 4144 9.654663 ACTCAGTGTTCTAAATAATAAGGTCAC 57.345 33.333 0.00 0.00 0.00 3.67
2487 4190 3.306919 CCCACCCCAGAATTCAACAAATG 60.307 47.826 8.44 0.00 0.00 2.32
2546 4249 7.439157 TCACTAAAAGATCAGACAACAATGG 57.561 36.000 0.00 0.00 0.00 3.16
2634 4337 7.054124 TGATAACCTGGGAAATAACATCAGTC 58.946 38.462 0.00 0.00 0.00 3.51
2700 4403 4.802947 AGGAGCAGCCTCTCATCA 57.197 55.556 5.36 0.00 46.97 3.07
2757 4460 5.012871 GGGAAGGAAACCAAAGTACTAGAGT 59.987 44.000 0.00 0.00 0.00 3.24
2830 4704 1.071471 AAGTTCGGCAGGTCCAGTG 59.929 57.895 0.00 0.00 34.01 3.66
2831 4705 1.071471 CAAGTTCGGCAGGTCCAGT 59.929 57.895 0.00 0.00 34.01 4.00
2948 4822 7.404671 TCAGTGTATTAACAGTATCTGAGCA 57.595 36.000 3.70 0.00 37.15 4.26
2984 4858 6.386654 CCCACCTGTAACACATCAAAATTAC 58.613 40.000 0.00 0.00 0.00 1.89
3244 5118 4.677151 AGGGTCCGGGGAAGGCTT 62.677 66.667 0.00 0.00 0.00 4.35
3283 5157 0.398381 ACAAAAAGGGGCAGCTTGGA 60.398 50.000 0.00 0.00 0.00 3.53
3287 5161 5.816955 TTTAATAACAAAAAGGGGCAGCT 57.183 34.783 0.00 0.00 0.00 4.24
3350 5224 0.933097 GCACATGCGACTATGACTGG 59.067 55.000 0.00 0.00 0.00 4.00
3395 5269 2.083774 GTCCAGAATGCGGAACATGAA 58.916 47.619 0.00 0.00 39.60 2.57
3431 5305 6.100004 ACAACTGTCAATCTATGGAAGTACG 58.900 40.000 0.00 0.00 0.00 3.67
3558 5432 6.203808 ACTGAAACAAAGGTTAAGTGGTTC 57.796 37.500 0.00 0.00 39.05 3.62
3586 5460 3.146066 AGCTTGGAATTCGTTGTGCTTA 58.854 40.909 0.00 0.00 0.00 3.09
3848 5722 3.445096 CCCCCTCTAAACTGCATTCTTTG 59.555 47.826 0.00 0.00 0.00 2.77
3869 5743 0.538287 AGAGAAGCAACCCAGCAACC 60.538 55.000 0.00 0.00 36.85 3.77
3941 5815 6.603940 ACCTTCAGATCAGATATAGCTTCC 57.396 41.667 0.00 0.00 0.00 3.46
4017 5891 8.265764 GGAGACTACATAGGTAACAAGGAAAAT 58.734 37.037 0.00 0.00 41.41 1.82
4143 6257 7.837202 ATGCCTGTTCACATTTTCAATATTG 57.163 32.000 9.29 9.29 0.00 1.90
4144 6258 8.851541 AAATGCCTGTTCACATTTTCAATATT 57.148 26.923 0.00 0.00 42.34 1.28
4305 6448 7.175816 TGCCAACTTGCTAATAAATTCAGTACA 59.824 33.333 0.00 0.00 0.00 2.90
4336 6479 2.154462 CTAATGAGGGGCAATAAGGCG 58.846 52.381 0.00 0.00 45.36 5.52
4338 6481 4.792068 TCAACTAATGAGGGGCAATAAGG 58.208 43.478 0.00 0.00 33.04 2.69
4339 6482 6.966534 ATTCAACTAATGAGGGGCAATAAG 57.033 37.500 0.00 0.00 39.77 1.73
4734 6883 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
4735 6884 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
4737 6886 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
4746 6895 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
4747 6896 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
4748 6897 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
4749 6898 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
4750 6899 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
4751 6900 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
4752 6901 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
4753 6902 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
4754 6903 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
4755 6904 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
4756 6905 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
4757 6906 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
4758 6907 5.646606 TCAACAACAACAAAGCCTTTAGTC 58.353 37.500 0.00 0.00 0.00 2.59
4759 6908 5.652994 TCAACAACAACAAAGCCTTTAGT 57.347 34.783 0.00 0.00 0.00 2.24
4760 6909 8.641499 TTTATCAACAACAACAAAGCCTTTAG 57.359 30.769 0.00 0.00 0.00 1.85
4761 6910 9.092876 CTTTTATCAACAACAACAAAGCCTTTA 57.907 29.630 0.00 0.00 0.00 1.85
4762 6911 7.821846 TCTTTTATCAACAACAACAAAGCCTTT 59.178 29.630 0.00 0.00 0.00 3.11
4763 6912 7.327214 TCTTTTATCAACAACAACAAAGCCTT 58.673 30.769 0.00 0.00 0.00 4.35
4764 6913 6.872920 TCTTTTATCAACAACAACAAAGCCT 58.127 32.000 0.00 0.00 0.00 4.58
4765 6914 7.398746 GTTCTTTTATCAACAACAACAAAGCC 58.601 34.615 0.00 0.00 0.00 4.35
4766 6915 7.398746 GGTTCTTTTATCAACAACAACAAAGC 58.601 34.615 0.00 0.00 0.00 3.51
4767 6916 7.763985 AGGGTTCTTTTATCAACAACAACAAAG 59.236 33.333 0.00 0.00 0.00 2.77
4768 6917 7.616313 AGGGTTCTTTTATCAACAACAACAAA 58.384 30.769 0.00 0.00 0.00 2.83
4769 6918 7.176589 AGGGTTCTTTTATCAACAACAACAA 57.823 32.000 0.00 0.00 0.00 2.83
4770 6919 6.783708 AGGGTTCTTTTATCAACAACAACA 57.216 33.333 0.00 0.00 0.00 3.33
4771 6920 9.027129 GTTTAGGGTTCTTTTATCAACAACAAC 57.973 33.333 0.00 0.00 0.00 3.32
4772 6921 8.198778 GGTTTAGGGTTCTTTTATCAACAACAA 58.801 33.333 0.00 0.00 0.00 2.83
4773 6922 7.201929 GGGTTTAGGGTTCTTTTATCAACAACA 60.202 37.037 0.00 0.00 0.00 3.33
4774 6923 7.014905 AGGGTTTAGGGTTCTTTTATCAACAAC 59.985 37.037 0.00 0.00 0.00 3.32
4775 6924 7.070629 AGGGTTTAGGGTTCTTTTATCAACAA 58.929 34.615 0.00 0.00 0.00 2.83
4776 6925 6.616577 AGGGTTTAGGGTTCTTTTATCAACA 58.383 36.000 0.00 0.00 0.00 3.33
4777 6926 6.152323 GGAGGGTTTAGGGTTCTTTTATCAAC 59.848 42.308 0.00 0.00 0.00 3.18
4778 6927 6.046286 AGGAGGGTTTAGGGTTCTTTTATCAA 59.954 38.462 0.00 0.00 0.00 2.57
4779 6928 5.554350 AGGAGGGTTTAGGGTTCTTTTATCA 59.446 40.000 0.00 0.00 0.00 2.15
4780 6929 6.075949 AGGAGGGTTTAGGGTTCTTTTATC 57.924 41.667 0.00 0.00 0.00 1.75
4781 6930 6.479395 AAGGAGGGTTTAGGGTTCTTTTAT 57.521 37.500 0.00 0.00 0.00 1.40
4782 6931 5.935668 AAGGAGGGTTTAGGGTTCTTTTA 57.064 39.130 0.00 0.00 0.00 1.52
4783 6932 4.827036 AAGGAGGGTTTAGGGTTCTTTT 57.173 40.909 0.00 0.00 0.00 2.27
4784 6933 4.480115 CAAAGGAGGGTTTAGGGTTCTTT 58.520 43.478 0.00 0.00 0.00 2.52
4840 6989 6.510879 CCCTTACAATCAGAGGGTAAAAAC 57.489 41.667 0.00 0.00 44.22 2.43
4849 6998 6.648879 TTTGTTTTCCCCTTACAATCAGAG 57.351 37.500 0.00 0.00 32.39 3.35
4928 7081 3.438087 AGAAAAGGATGTGATCAGTTGCG 59.562 43.478 0.00 0.00 0.00 4.85
5053 7206 4.393371 GGAGAGAACATAAGCACCTTTGTC 59.607 45.833 0.00 0.00 0.00 3.18
5110 7265 3.190535 GGGCACGTCAAGTCAAACATATT 59.809 43.478 0.00 0.00 0.00 1.28
5119 7274 1.732259 CATACAAGGGCACGTCAAGTC 59.268 52.381 0.00 0.00 0.00 3.01
5128 7283 0.536233 AACGTGCACATACAAGGGCA 60.536 50.000 18.64 0.00 0.00 5.36
5129 7284 1.129811 GTAACGTGCACATACAAGGGC 59.870 52.381 18.64 0.00 0.00 5.19
5137 7296 0.955428 CCTGCAGGTAACGTGCACAT 60.955 55.000 25.53 7.55 42.90 3.21
5242 7401 2.811431 CCAAAACGATTCTAGTGTGGCA 59.189 45.455 0.00 0.00 0.00 4.92
5299 7458 1.616628 ATCTTTCGGACCAGGCCCT 60.617 57.895 0.00 0.00 0.00 5.19
5305 7464 1.447838 GCGCTCATCTTTCGGACCA 60.448 57.895 0.00 0.00 0.00 4.02
5306 7465 2.174319 GGCGCTCATCTTTCGGACC 61.174 63.158 7.64 0.00 0.00 4.46
5310 7469 0.740868 TTCAGGGCGCTCATCTTTCG 60.741 55.000 11.40 0.00 0.00 3.46
5344 7503 2.222027 CTGTTGTCTTGTGTTCTCCCC 58.778 52.381 0.00 0.00 0.00 4.81
5358 7517 3.077359 GCTAGGATGCTGAAACTGTTGT 58.923 45.455 0.00 0.00 0.00 3.32
5401 7560 7.362056 GCAAACATAAATCCAACTAGAAGAGCA 60.362 37.037 0.00 0.00 0.00 4.26
5440 7599 5.705441 AGCATGAATTACTCAGGTTTTCGAA 59.295 36.000 0.00 0.00 38.15 3.71
5533 7694 6.592607 ACGAAAGAAACTCTACACTTTTCACA 59.407 34.615 0.00 0.00 33.61 3.58
5612 7773 1.492599 TCCACACAATTGTCCCTGTCA 59.507 47.619 8.48 0.00 31.66 3.58
5615 7776 2.276732 ACTCCACACAATTGTCCCTG 57.723 50.000 8.48 4.40 31.66 4.45
5627 7788 5.069318 TGCATCACTCAAAAATACTCCACA 58.931 37.500 0.00 0.00 0.00 4.17
5628 7789 5.627499 TGCATCACTCAAAAATACTCCAC 57.373 39.130 0.00 0.00 0.00 4.02
5649 7810 3.883744 AAGACGACGGCAGGGCTTG 62.884 63.158 2.19 0.00 0.00 4.01
5665 7826 6.584942 CACATCTCAATGACCAAACAATGAAG 59.415 38.462 0.00 0.00 36.67 3.02
5697 7858 0.687757 CTGTGGGTGAGCCTAGCCTA 60.688 60.000 1.06 0.00 38.99 3.93
5698 7859 1.992277 CTGTGGGTGAGCCTAGCCT 60.992 63.158 1.06 0.00 38.99 4.58
5710 7877 2.019249 ACGATCATCAAATGCTGTGGG 58.981 47.619 0.00 0.00 0.00 4.61
5717 7884 3.302286 CGTCTCTGCACGATCATCAAATG 60.302 47.826 0.00 0.00 42.69 2.32
5767 7934 5.127031 TGCCTTTTCTCATAATTTAGTGGGC 59.873 40.000 0.00 0.00 0.00 5.36
5888 8069 4.502604 GGCCAACACTCACTTGTCTAGTAA 60.503 45.833 0.00 0.00 34.56 2.24
5894 8075 1.334869 CAAGGCCAACACTCACTTGTC 59.665 52.381 5.01 0.00 35.15 3.18
6036 8239 4.265073 GTCTTCCTCATGGTAGCAAATGT 58.735 43.478 0.00 0.00 31.69 2.71
6063 8266 4.389374 ACTGCTTGCTTGCTCTAGTTTAA 58.611 39.130 3.47 0.00 0.00 1.52
6064 8267 4.008074 ACTGCTTGCTTGCTCTAGTTTA 57.992 40.909 3.47 0.00 0.00 2.01
6105 8308 5.542616 CATGCATCTATAAGCAAGCTACC 57.457 43.478 0.00 0.00 44.88 3.18
6120 8323 3.138930 CTGGCTGCCTGCATGCATC 62.139 63.158 22.97 16.35 45.15 3.91
6121 8324 3.147595 CTGGCTGCCTGCATGCAT 61.148 61.111 22.97 0.00 45.15 3.96
6122 8325 4.354162 TCTGGCTGCCTGCATGCA 62.354 61.111 21.29 21.29 45.15 3.96
6123 8326 3.823330 GTCTGGCTGCCTGCATGC 61.823 66.667 21.03 11.82 45.15 4.06
6124 8327 3.506096 CGTCTGGCTGCCTGCATG 61.506 66.667 21.03 10.72 45.15 4.06
6125 8328 3.557903 AACGTCTGGCTGCCTGCAT 62.558 57.895 21.03 5.31 45.15 3.96
6126 8329 3.772853 AAACGTCTGGCTGCCTGCA 62.773 57.895 21.03 6.90 45.15 4.41
6127 8330 2.980233 AAACGTCTGGCTGCCTGC 60.980 61.111 21.03 13.84 41.94 4.85
6128 8331 1.597854 TCAAACGTCTGGCTGCCTG 60.598 57.895 21.03 19.66 0.00 4.85
6129 8332 1.598130 GTCAAACGTCTGGCTGCCT 60.598 57.895 21.03 0.00 0.00 4.75
6130 8333 1.569479 GAGTCAAACGTCTGGCTGCC 61.569 60.000 12.87 12.87 29.28 4.85
6131 8334 0.601311 AGAGTCAAACGTCTGGCTGC 60.601 55.000 0.00 0.00 29.28 5.25
6132 8335 1.143305 CAGAGTCAAACGTCTGGCTG 58.857 55.000 0.00 0.00 37.19 4.85
6133 8336 3.595691 CAGAGTCAAACGTCTGGCT 57.404 52.632 0.00 0.00 37.19 4.75
6136 8339 1.143305 CTGCCAGAGTCAAACGTCTG 58.857 55.000 0.00 0.00 40.03 3.51
6137 8340 0.034059 CCTGCCAGAGTCAAACGTCT 59.966 55.000 0.00 0.00 0.00 4.18
6138 8341 0.033504 TCCTGCCAGAGTCAAACGTC 59.966 55.000 0.00 0.00 0.00 4.34
6139 8342 0.034059 CTCCTGCCAGAGTCAAACGT 59.966 55.000 0.00 0.00 0.00 3.99
6140 8343 0.034059 ACTCCTGCCAGAGTCAAACG 59.966 55.000 0.00 0.00 43.76 3.60
6141 8344 3.402628 TTACTCCTGCCAGAGTCAAAC 57.597 47.619 8.86 0.00 43.76 2.93
6142 8345 4.640771 ATTTACTCCTGCCAGAGTCAAA 57.359 40.909 8.86 8.77 43.76 2.69
6143 8346 4.326826 CAATTTACTCCTGCCAGAGTCAA 58.673 43.478 8.86 5.79 43.76 3.18
6144 8347 3.869912 GCAATTTACTCCTGCCAGAGTCA 60.870 47.826 8.86 0.00 43.76 3.41
6145 8348 2.680339 GCAATTTACTCCTGCCAGAGTC 59.320 50.000 8.86 0.00 43.76 3.36
6147 8350 2.681848 CTGCAATTTACTCCTGCCAGAG 59.318 50.000 0.00 0.00 39.91 3.35
6148 8351 2.618816 CCTGCAATTTACTCCTGCCAGA 60.619 50.000 0.00 0.00 35.13 3.86
6149 8352 1.747355 CCTGCAATTTACTCCTGCCAG 59.253 52.381 0.00 0.00 35.13 4.85
6150 8353 1.616725 CCCTGCAATTTACTCCTGCCA 60.617 52.381 0.00 0.00 35.13 4.92
6151 8354 1.106285 CCCTGCAATTTACTCCTGCC 58.894 55.000 0.00 0.00 35.13 4.85
6152 8355 2.128771 TCCCTGCAATTTACTCCTGC 57.871 50.000 0.00 0.00 36.60 4.85
6153 8356 3.690460 ACTTCCCTGCAATTTACTCCTG 58.310 45.455 0.00 0.00 0.00 3.86
6154 8357 5.191722 TGATACTTCCCTGCAATTTACTCCT 59.808 40.000 0.00 0.00 0.00 3.69
6160 8363 4.666512 AGTGTGATACTTCCCTGCAATTT 58.333 39.130 0.00 0.00 35.67 1.82
6187 8390 3.575256 TGATACTGACCCGTTACAACTGT 59.425 43.478 0.00 0.00 0.00 3.55
6272 8475 7.064371 ACAACGTTAATACAACATTATACGCCA 59.936 33.333 0.00 0.00 0.00 5.69
6282 8485 8.590719 TTGTCAGATACAACGTTAATACAACA 57.409 30.769 0.00 0.00 43.22 3.33
6295 8498 0.035820 GGCCGGGTTGTCAGATACAA 60.036 55.000 2.18 0.00 45.90 2.41
6358 8561 0.761323 TGAGTTGGGTTCGACCAGGA 60.761 55.000 0.00 0.00 42.47 3.86
6385 8604 3.387225 GAGGGCTAGGGTTCGTGGC 62.387 68.421 0.00 0.00 0.00 5.01
6534 8754 2.343101 CCGGTACAACATGATGTCGTT 58.657 47.619 12.36 0.00 34.75 3.85
6619 8840 2.368548 GGAGCAAAATGAACCAAACCCT 59.631 45.455 0.00 0.00 0.00 4.34
6622 8843 4.058721 ACAGGAGCAAAATGAACCAAAC 57.941 40.909 0.00 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.