Multiple sequence alignment - TraesCS5D01G479400

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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 TraesCS5D01G479400 chr5D 100.000 2504 0 0 1 2504 517601481 517598978 0.000000e+00 4625.0
1 TraesCS5D01G479400 chr5D 88.517 418 38 7 210 623 517591977 517591566 4.810000e-137 497.0
2 TraesCS5D01G479400 chr5D 79.740 538 62 20 1730 2227 517590514 517589984 1.840000e-91 346.0
3 TraesCS5D01G479400 chr5D 87.413 286 15 11 915 1189 517591356 517591081 2.420000e-80 309.0
4 TraesCS5D01G479400 chr5D 92.381 210 16 0 1301 1510 517521473 517521264 1.460000e-77 300.0
5 TraesCS5D01G479400 chr5D 83.154 279 28 11 1302 1563 517590902 517590626 1.160000e-58 237.0
6 TraesCS5D01G479400 chr5D 100.000 99 0 0 2406 2504 6250660 6250562 1.530000e-42 183.0
7 TraesCS5D01G479400 chr5D 80.583 206 17 12 479 672 517591597 517591403 1.210000e-28 137.0
8 TraesCS5D01G479400 chr5D 79.630 162 25 8 2181 2338 425810372 425810529 2.630000e-20 110.0
9 TraesCS5D01G479400 chr5D 95.918 49 1 1 830 877 517521927 517521879 7.430000e-11 78.7
10 TraesCS5D01G479400 chr5A 92.974 854 45 8 1561 2405 644922542 644921695 0.000000e+00 1230.0
11 TraesCS5D01G479400 chr5A 90.208 674 31 14 901 1551 644923443 644922782 0.000000e+00 846.0
12 TraesCS5D01G479400 chr5A 89.006 473 36 8 210 672 644921160 644920694 2.790000e-159 571.0
13 TraesCS5D01G479400 chr5A 91.687 409 24 7 1 399 645001729 645001321 2.180000e-155 558.0
14 TraesCS5D01G479400 chr5A 86.236 356 23 10 552 882 644923785 644923431 1.830000e-96 363.0
15 TraesCS5D01G479400 chr5A 91.892 259 19 1 163 419 644927582 644927324 6.580000e-96 361.0
16 TraesCS5D01G479400 chr5A 92.891 211 13 1 1302 1510 644910778 644910568 3.130000e-79 305.0
17 TraesCS5D01G479400 chr5A 84.364 275 23 6 915 1189 644920676 644920422 4.130000e-63 252.0
18 TraesCS5D01G479400 chr5A 81.295 278 35 8 1302 1563 644920132 644919856 2.520000e-50 209.0
19 TraesCS5D01G479400 chr5A 81.250 112 13 4 552 663 644920892 644920789 1.600000e-12 84.2
20 TraesCS5D01G479400 chr5A 82.796 93 14 2 1478 1569 644998570 644998479 5.740000e-12 82.4
21 TraesCS5D01G479400 chr5A 93.878 49 2 1 830 877 644911284 644911236 3.450000e-09 73.1
22 TraesCS5D01G479400 chr5A 97.143 35 1 0 462 496 644920740 644920706 2.690000e-05 60.2
23 TraesCS5D01G479400 chr5B 91.321 795 53 9 1 781 650133665 650132873 0.000000e+00 1072.0
24 TraesCS5D01G479400 chr5B 93.902 574 33 2 979 1551 650132865 650132293 0.000000e+00 865.0
25 TraesCS5D01G479400 chr5B 94.141 495 23 5 1915 2405 650127536 650127044 0.000000e+00 749.0
26 TraesCS5D01G479400 chr5B 87.277 448 28 16 255 677 650125227 650124784 3.740000e-133 484.0
27 TraesCS5D01G479400 chr5B 80.531 678 75 28 915 1560 650046366 650045714 3.770000e-128 468.0
28 TraesCS5D01G479400 chr5B 87.052 363 17 13 1561 1923 650132211 650131879 1.410000e-102 383.0
29 TraesCS5D01G479400 chr5B 84.783 276 16 11 931 1189 650124777 650124511 1.150000e-63 254.0
30 TraesCS5D01G479400 chr5B 87.037 216 20 7 1255 1463 650053461 650053247 1.160000e-58 237.0
31 TraesCS5D01G479400 chr5B 79.649 285 37 13 918 1190 650053760 650053485 4.250000e-43 185.0
32 TraesCS5D01G479400 chr5B 86.047 86 8 2 552 633 650124997 650124912 3.430000e-14 89.8
33 TraesCS5D01G479400 chr5B 88.060 67 6 2 2273 2338 515110501 515110566 7.430000e-11 78.7
34 TraesCS5D01G479400 chr5B 95.918 49 1 1 830 877 650046416 650046368 7.430000e-11 78.7
35 TraesCS5D01G479400 chr5B 94.286 35 2 0 924 958 650046965 650046931 1.000000e-03 54.7
36 TraesCS5D01G479400 chr5B 94.286 35 2 0 924 958 650054381 650054347 1.000000e-03 54.7
37 TraesCS5D01G479400 chr7A 76.139 373 78 8 1974 2338 177211879 177211510 4.250000e-43 185.0
38 TraesCS5D01G479400 chrUn 100.000 99 0 0 2406 2504 189403144 189403242 1.530000e-42 183.0
39 TraesCS5D01G479400 chrUn 100.000 99 0 0 2406 2504 251413408 251413310 1.530000e-42 183.0
40 TraesCS5D01G479400 chrUn 100.000 99 0 0 2406 2504 345936615 345936517 1.530000e-42 183.0
41 TraesCS5D01G479400 chr6D 100.000 99 0 0 2406 2504 124528185 124528283 1.530000e-42 183.0
42 TraesCS5D01G479400 chr6D 100.000 99 0 0 2406 2504 283217802 283217900 1.530000e-42 183.0
43 TraesCS5D01G479400 chr4D 100.000 99 0 0 2406 2504 30403892 30403990 1.530000e-42 183.0
44 TraesCS5D01G479400 chr1D 100.000 99 0 0 2406 2504 269417409 269417507 1.530000e-42 183.0
45 TraesCS5D01G479400 chr1A 100.000 99 0 0 2406 2504 554484637 554484735 1.530000e-42 183.0
46 TraesCS5D01G479400 chr7D 78.750 240 47 4 2102 2339 175567511 175567274 9.270000e-35 158.0
47 TraesCS5D01G479400 chr7B 74.734 376 84 7 1972 2339 140853122 140852750 9.270000e-35 158.0
48 TraesCS5D01G479400 chr4B 80.537 149 28 1 2192 2339 108184769 108184621 2.040000e-21 113.0
49 TraesCS5D01G479400 chr4A 80.000 140 22 4 2202 2339 461627969 461628104 5.700000e-17 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 TraesCS5D01G479400 chr5D 517598978 517601481 2503 True 4625.000000 4625 100.000000 1 2504 1 chr5D.!!$R2 2503
1 TraesCS5D01G479400 chr5D 517589984 517591977 1993 True 305.200000 497 83.881400 210 2227 5 chr5D.!!$R4 2017
2 TraesCS5D01G479400 chr5A 644919856 644927582 7726 True 441.822222 1230 88.263111 163 2405 9 chr5A.!!$R2 2242
3 TraesCS5D01G479400 chr5A 644998479 645001729 3250 True 320.200000 558 87.241500 1 1569 2 chr5A.!!$R3 1568
4 TraesCS5D01G479400 chr5B 650131879 650133665 1786 True 773.333333 1072 90.758333 1 1923 3 chr5B.!!$R4 1922
5 TraesCS5D01G479400 chr5B 650124511 650127536 3025 True 394.200000 749 88.062000 255 2405 4 chr5B.!!$R3 2150
6 TraesCS5D01G479400 chr5B 650045714 650046965 1251 True 200.466667 468 90.245000 830 1560 3 chr5B.!!$R1 730

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
891 6998 0.104304 GGACACTACATGCTACCCCG 59.896 60.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 13166 0.036765 TTCGCACGGGATTAAGCTGT 60.037 50.0 0.0 0.0 0.0 4.4 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
90 91 3.637432 CTGATTCTACAGAGTCGATGGC 58.363 50.000 0.00 0.00 39.94 4.40
243 245 3.855503 TTGAGGTGCCTGCTGCTGG 62.856 63.158 19.96 19.96 42.00 4.85
404 2495 5.822519 GCCATGATGGTATGAGTTGAGTTAA 59.177 40.000 13.84 0.00 40.46 2.01
499 6089 2.612285 TCCATCTCTGTGGACTGTCT 57.388 50.000 7.85 0.00 43.20 3.41
500 6090 2.174360 TCCATCTCTGTGGACTGTCTG 58.826 52.381 7.85 0.00 43.20 3.51
501 6091 1.405256 CCATCTCTGTGGACTGTCTGC 60.405 57.143 7.85 1.82 42.02 4.26
515 6175 1.217882 GTCTGCGATAATTCACCGGG 58.782 55.000 6.32 0.00 0.00 5.73
585 6289 1.940613 GTGGGCTGTCGTGATAATTCC 59.059 52.381 0.00 0.00 0.00 3.01
590 6298 2.420129 GCTGTCGTGATAATTCCCTGGT 60.420 50.000 0.00 0.00 0.00 4.00
594 6302 4.468510 TGTCGTGATAATTCCCTGGTAGTT 59.531 41.667 0.00 0.00 0.00 2.24
606 6314 2.169352 CCTGGTAGTTCATCTCTGTGGG 59.831 54.545 0.00 0.00 0.00 4.61
612 6320 1.002430 GTTCATCTCTGTGGGCTGTCA 59.998 52.381 0.00 0.00 0.00 3.58
614 6322 2.750814 TCATCTCTGTGGGCTGTCATA 58.249 47.619 0.00 0.00 0.00 2.15
621 6329 6.291377 TCTCTGTGGGCTGTCATAATAATTC 58.709 40.000 0.00 0.00 0.00 2.17
622 6330 6.000246 TCTGTGGGCTGTCATAATAATTCA 58.000 37.500 0.00 0.00 0.00 2.57
623 6331 5.822519 TCTGTGGGCTGTCATAATAATTCAC 59.177 40.000 0.00 0.00 0.00 3.18
633 6344 7.112122 TGTCATAATAATTCACTGGAAGCAGT 58.888 34.615 0.00 0.00 37.60 4.40
698 6409 2.337532 GGTTGTGCTGCAGCCTTG 59.662 61.111 34.64 0.00 44.03 3.61
703 6419 0.603707 TGTGCTGCAGCCTTGTAGAC 60.604 55.000 34.64 23.67 39.14 2.59
726 6442 2.969821 TTGTGCTGGAACCTGGTAAT 57.030 45.000 0.00 0.00 0.00 1.89
744 6460 0.468226 ATGATAATGACCACGGGCGT 59.532 50.000 0.00 0.00 0.00 5.68
750 6466 2.813908 GACCACGGGCGTCATGTC 60.814 66.667 1.91 0.00 0.00 3.06
752 6468 2.815211 CCACGGGCGTCATGTCAG 60.815 66.667 0.00 0.00 0.00 3.51
758 6474 1.503542 GGCGTCATGTCAGCTTTGG 59.496 57.895 8.98 0.00 0.00 3.28
762 6478 2.225491 GCGTCATGTCAGCTTTGGTTTA 59.775 45.455 0.00 0.00 0.00 2.01
826 6566 2.017049 ACGGAGAAAATAGGTGCATGC 58.983 47.619 11.82 11.82 0.00 4.06
882 6989 1.282157 GCCAGGGAAAGGACACTACAT 59.718 52.381 0.00 0.00 0.00 2.29
884 6991 2.359900 CAGGGAAAGGACACTACATGC 58.640 52.381 0.00 0.00 0.00 4.06
885 6992 2.026822 CAGGGAAAGGACACTACATGCT 60.027 50.000 0.00 0.00 0.00 3.79
888 6995 3.532542 GGAAAGGACACTACATGCTACC 58.467 50.000 0.00 0.00 0.00 3.18
889 6996 3.532542 GAAAGGACACTACATGCTACCC 58.467 50.000 0.00 0.00 0.00 3.69
890 6997 1.497161 AGGACACTACATGCTACCCC 58.503 55.000 0.00 0.00 0.00 4.95
891 6998 0.104304 GGACACTACATGCTACCCCG 59.896 60.000 0.00 0.00 0.00 5.73
892 6999 0.529992 GACACTACATGCTACCCCGC 60.530 60.000 0.00 0.00 0.00 6.13
893 7000 1.261938 ACACTACATGCTACCCCGCA 61.262 55.000 0.00 0.00 45.10 5.69
894 7001 0.107897 CACTACATGCTACCCCGCAA 60.108 55.000 0.00 0.00 44.06 4.85
895 7002 0.616371 ACTACATGCTACCCCGCAAA 59.384 50.000 0.00 0.00 44.06 3.68
896 7003 1.003812 ACTACATGCTACCCCGCAAAA 59.996 47.619 0.00 0.00 44.06 2.44
897 7004 2.088423 CTACATGCTACCCCGCAAAAA 58.912 47.619 0.00 0.00 44.06 1.94
955 7065 6.548321 ACAAGTTTATCCCAAACACCTATCA 58.452 36.000 3.02 0.00 32.81 2.15
958 7068 6.790319 AGTTTATCCCAAACACCTATCAACT 58.210 36.000 3.02 0.00 32.81 3.16
961 7071 8.674607 GTTTATCCCAAACACCTATCAACTTAG 58.325 37.037 0.00 0.00 0.00 2.18
1026 7160 7.542890 TGCTATATATAGAGAGAGTTGCTTGC 58.457 38.462 21.65 4.34 32.05 4.01
1116 7272 1.459592 CAAGTTTAGGAGCGACCAACG 59.540 52.381 5.84 0.00 45.66 4.10
1196 7352 1.079543 ATCCTCGCACACTCACAGC 60.080 57.895 0.00 0.00 0.00 4.40
1473 10636 1.520666 CTCCGCCTTCCCGTACATT 59.479 57.895 0.00 0.00 0.00 2.71
1528 12541 1.344438 TCCACCTCATCACACAGTGAC 59.656 52.381 7.81 0.00 45.65 3.67
1670 12755 3.142951 TGTAAAACCTGGTTCCATGTCG 58.857 45.455 13.36 0.00 0.00 4.35
1682 12767 3.461773 ATGTCGCGCTGGTAGGCT 61.462 61.111 5.56 0.00 0.00 4.58
1683 12768 3.432051 ATGTCGCGCTGGTAGGCTC 62.432 63.158 5.56 0.00 0.00 4.70
1687 12772 4.577246 GCGCTGGTAGGCTCGGAG 62.577 72.222 0.00 0.00 0.00 4.63
1688 12773 3.141488 CGCTGGTAGGCTCGGAGT 61.141 66.667 6.90 0.00 0.00 3.85
1689 12774 2.711922 CGCTGGTAGGCTCGGAGTT 61.712 63.158 6.90 0.00 0.00 3.01
1690 12775 1.381928 CGCTGGTAGGCTCGGAGTTA 61.382 60.000 6.90 0.00 0.00 2.24
1691 12776 0.386113 GCTGGTAGGCTCGGAGTTAG 59.614 60.000 6.90 0.00 0.00 2.34
1692 12777 1.765230 CTGGTAGGCTCGGAGTTAGT 58.235 55.000 6.90 0.00 0.00 2.24
1693 12778 2.100989 CTGGTAGGCTCGGAGTTAGTT 58.899 52.381 6.90 0.00 0.00 2.24
1694 12779 1.822990 TGGTAGGCTCGGAGTTAGTTG 59.177 52.381 6.90 0.00 0.00 3.16
1695 12780 2.097825 GGTAGGCTCGGAGTTAGTTGA 58.902 52.381 6.90 0.00 0.00 3.18
1696 12781 2.099427 GGTAGGCTCGGAGTTAGTTGAG 59.901 54.545 6.90 0.00 0.00 3.02
1697 12782 2.217510 AGGCTCGGAGTTAGTTGAGA 57.782 50.000 6.90 0.00 0.00 3.27
1698 12783 1.819903 AGGCTCGGAGTTAGTTGAGAC 59.180 52.381 6.90 0.00 36.72 3.36
1699 12784 1.819903 GGCTCGGAGTTAGTTGAGACT 59.180 52.381 6.90 0.00 39.97 3.24
1700 12785 2.416162 GGCTCGGAGTTAGTTGAGACTG 60.416 54.545 6.90 0.00 36.60 3.51
1701 12786 2.229302 GCTCGGAGTTAGTTGAGACTGT 59.771 50.000 6.90 0.00 36.60 3.55
1702 12787 3.305471 GCTCGGAGTTAGTTGAGACTGTT 60.305 47.826 6.90 0.00 36.60 3.16
1703 12788 4.796618 GCTCGGAGTTAGTTGAGACTGTTT 60.797 45.833 6.90 0.00 36.60 2.83
1704 12789 5.564259 GCTCGGAGTTAGTTGAGACTGTTTA 60.564 44.000 6.90 0.00 36.60 2.01
1705 12790 6.395426 TCGGAGTTAGTTGAGACTGTTTAA 57.605 37.500 0.00 0.00 36.60 1.52
1706 12791 6.989659 TCGGAGTTAGTTGAGACTGTTTAAT 58.010 36.000 0.00 0.00 36.60 1.40
1707 12792 8.114331 TCGGAGTTAGTTGAGACTGTTTAATA 57.886 34.615 0.00 0.00 36.60 0.98
1708 12793 8.579006 TCGGAGTTAGTTGAGACTGTTTAATAA 58.421 33.333 0.00 0.00 36.60 1.40
1755 12842 3.443099 TGTATGGTCTCTGCTCAATCG 57.557 47.619 0.00 0.00 0.00 3.34
1822 12911 3.050703 CGGTGAACGGATCCTTCTG 57.949 57.895 10.75 0.00 39.42 3.02
1857 12946 6.980978 GCATATATGTACAGTTGTCACACTCT 59.019 38.462 14.14 0.00 0.00 3.24
1927 13026 3.745332 TTGCATCAAAGATACACAGCG 57.255 42.857 0.00 0.00 0.00 5.18
1931 13030 3.261580 CATCAAAGATACACAGCGGACA 58.738 45.455 0.00 0.00 0.00 4.02
1952 13053 1.153823 GTACTGTCCGTGCAGCGAT 60.154 57.895 9.75 0.00 44.77 4.58
1955 13056 2.125952 TGTCCGTGCAGCGATGAG 60.126 61.111 4.02 0.00 44.77 2.90
1968 13069 0.958091 CGATGAGCGGATCCTTCTCT 59.042 55.000 23.16 13.58 36.03 3.10
1975 13076 0.101399 CGGATCCTTCTCTGTGGACG 59.899 60.000 10.75 0.00 34.90 4.79
1978 13079 0.811915 ATCCTTCTCTGTGGACGACG 59.188 55.000 0.00 0.00 34.90 5.12
1979 13080 1.213013 CCTTCTCTGTGGACGACGG 59.787 63.158 0.00 0.00 0.00 4.79
1983 13084 0.820482 TCTCTGTGGACGACGGTTCA 60.820 55.000 0.00 0.00 32.09 3.18
1990 13091 2.726691 GACGACGGTTCATGGCACG 61.727 63.158 0.00 0.00 0.00 5.34
1995 13096 2.324330 CGGTTCATGGCACGCAAGA 61.324 57.895 0.00 0.00 43.62 3.02
2007 13108 2.161486 CGCAAGAGCTAGGACACGC 61.161 63.158 0.00 0.00 43.02 5.34
2030 13131 1.054231 TTTTGGGCCACATGATTGCA 58.946 45.000 5.23 0.00 0.00 4.08
2031 13132 1.277579 TTTGGGCCACATGATTGCAT 58.722 45.000 5.23 0.00 34.29 3.96
2033 13134 1.361271 GGGCCACATGATTGCATCG 59.639 57.895 4.39 0.00 30.68 3.84
2039 13141 2.031420 CCACATGATTGCATCGTGATCC 60.031 50.000 18.99 0.00 46.73 3.36
2051 13153 4.794981 GCATCGTGATCCGTAAAGTGGATA 60.795 45.833 0.00 0.00 46.17 2.59
2052 13154 4.563337 TCGTGATCCGTAAAGTGGATAG 57.437 45.455 0.00 0.00 46.17 2.08
2057 13159 4.899457 TGATCCGTAAAGTGGATAGGTCAT 59.101 41.667 0.00 0.00 46.17 3.06
2058 13160 4.665833 TCCGTAAAGTGGATAGGTCATG 57.334 45.455 0.00 0.00 0.00 3.07
2062 13164 4.680708 CGTAAAGTGGATAGGTCATGTGCT 60.681 45.833 0.00 0.00 0.00 4.40
2064 13166 5.435686 AAAGTGGATAGGTCATGTGCTTA 57.564 39.130 0.00 0.00 0.00 3.09
2065 13167 4.408182 AGTGGATAGGTCATGTGCTTAC 57.592 45.455 0.00 0.00 0.00 2.34
2077 13203 2.627945 TGTGCTTACAGCTTAATCCCG 58.372 47.619 0.00 0.00 42.97 5.14
2080 13206 1.330829 GCTTACAGCTTAATCCCGTGC 59.669 52.381 0.00 0.00 38.45 5.34
2113 13239 4.365514 TGATACAGGTTTTGGCAGAGAA 57.634 40.909 0.00 0.00 0.00 2.87
2115 13241 5.324409 TGATACAGGTTTTGGCAGAGAAAT 58.676 37.500 0.00 0.00 0.00 2.17
2130 13256 0.879090 GAAATCACGGTTCACCCACC 59.121 55.000 0.00 0.00 0.00 4.61
2138 13264 1.705997 GGTTCACCCACCACACCTCT 61.706 60.000 0.00 0.00 36.73 3.69
2143 13269 0.768221 ACCCACCACACCTCTCATGT 60.768 55.000 0.00 0.00 0.00 3.21
2144 13270 0.401738 CCCACCACACCTCTCATGTT 59.598 55.000 0.00 0.00 0.00 2.71
2174 13300 8.325787 TCTCCTAACTTCACAATTATAAGCCAA 58.674 33.333 0.00 0.00 0.00 4.52
2177 13303 8.686334 CCTAACTTCACAATTATAAGCCAATGT 58.314 33.333 0.00 0.00 0.00 2.71
2221 13347 7.008859 CCAATTTGTATTTCGTTTGCACATTC 58.991 34.615 0.00 0.00 0.00 2.67
2227 13353 3.946308 TTCGTTTGCACATTCGTGTTA 57.054 38.095 0.00 0.00 45.50 2.41
2228 13354 3.513462 TCGTTTGCACATTCGTGTTAG 57.487 42.857 0.00 0.00 45.50 2.34
2229 13355 2.867368 TCGTTTGCACATTCGTGTTAGT 59.133 40.909 0.00 0.00 45.50 2.24
2230 13356 3.310227 TCGTTTGCACATTCGTGTTAGTT 59.690 39.130 0.00 0.00 45.50 2.24
2231 13357 3.417321 CGTTTGCACATTCGTGTTAGTTG 59.583 43.478 0.00 0.00 45.50 3.16
2232 13358 4.347813 GTTTGCACATTCGTGTTAGTTGT 58.652 39.130 0.00 0.00 45.50 3.32
2233 13359 3.600717 TGCACATTCGTGTTAGTTGTG 57.399 42.857 0.00 0.00 45.50 3.33
2234 13360 3.198872 TGCACATTCGTGTTAGTTGTGA 58.801 40.909 5.60 0.00 45.50 3.58
2235 13361 3.001838 TGCACATTCGTGTTAGTTGTGAC 59.998 43.478 5.60 0.00 45.50 3.67
2236 13362 3.783377 CACATTCGTGTTAGTTGTGACG 58.217 45.455 0.00 0.00 39.98 4.35
2237 13363 2.798283 ACATTCGTGTTAGTTGTGACGG 59.202 45.455 0.00 0.00 32.68 4.79
2238 13364 1.855513 TTCGTGTTAGTTGTGACGGG 58.144 50.000 0.00 0.00 32.68 5.28
2239 13365 0.032403 TCGTGTTAGTTGTGACGGGG 59.968 55.000 0.00 0.00 32.68 5.73
2240 13366 0.947180 CGTGTTAGTTGTGACGGGGG 60.947 60.000 0.00 0.00 0.00 5.40
2241 13367 1.071814 TGTTAGTTGTGACGGGGGC 59.928 57.895 0.00 0.00 0.00 5.80
2242 13368 1.373812 GTTAGTTGTGACGGGGGCT 59.626 57.895 0.00 0.00 0.00 5.19
2243 13369 0.250597 GTTAGTTGTGACGGGGGCTT 60.251 55.000 0.00 0.00 0.00 4.35
2244 13370 0.475044 TTAGTTGTGACGGGGGCTTT 59.525 50.000 0.00 0.00 0.00 3.51
2245 13371 0.250553 TAGTTGTGACGGGGGCTTTG 60.251 55.000 0.00 0.00 0.00 2.77
2246 13372 2.203422 TTGTGACGGGGGCTTTGG 60.203 61.111 0.00 0.00 0.00 3.28
2247 13373 2.758207 TTGTGACGGGGGCTTTGGA 61.758 57.895 0.00 0.00 0.00 3.53
2248 13374 2.359975 GTGACGGGGGCTTTGGAG 60.360 66.667 0.00 0.00 0.00 3.86
2249 13375 2.528127 TGACGGGGGCTTTGGAGA 60.528 61.111 0.00 0.00 0.00 3.71
2250 13376 2.150719 TGACGGGGGCTTTGGAGAA 61.151 57.895 0.00 0.00 0.00 2.87
2251 13377 1.377333 GACGGGGGCTTTGGAGAAG 60.377 63.158 0.00 0.00 0.00 2.85
2252 13378 2.044946 CGGGGGCTTTGGAGAAGG 60.045 66.667 0.00 0.00 0.00 3.46
2253 13379 2.363018 GGGGGCTTTGGAGAAGGC 60.363 66.667 3.98 3.98 41.52 4.35
2257 13383 4.830573 GCTTTGGAGAAGGCCACT 57.169 55.556 5.01 3.29 37.75 4.00
2258 13384 2.560954 GCTTTGGAGAAGGCCACTC 58.439 57.895 17.92 17.92 37.75 3.51
2259 13385 0.037447 GCTTTGGAGAAGGCCACTCT 59.963 55.000 22.83 16.31 37.75 3.24
2260 13386 1.546548 GCTTTGGAGAAGGCCACTCTT 60.547 52.381 22.83 2.46 37.75 2.85
2261 13387 2.431454 CTTTGGAGAAGGCCACTCTTC 58.569 52.381 22.83 15.50 42.43 2.87
2262 13388 1.434188 TTGGAGAAGGCCACTCTTCA 58.566 50.000 22.83 17.56 44.01 3.02
2263 13389 1.434188 TGGAGAAGGCCACTCTTCAA 58.566 50.000 22.83 9.26 44.01 2.69
2264 13390 1.072331 TGGAGAAGGCCACTCTTCAAC 59.928 52.381 22.83 11.12 44.01 3.18
2265 13391 1.072331 GGAGAAGGCCACTCTTCAACA 59.928 52.381 22.83 0.00 44.01 3.33
2266 13392 2.290577 GGAGAAGGCCACTCTTCAACAT 60.291 50.000 22.83 0.00 44.01 2.71
2267 13393 2.746362 GAGAAGGCCACTCTTCAACATG 59.254 50.000 18.59 0.00 44.01 3.21
2268 13394 2.107204 AGAAGGCCACTCTTCAACATGT 59.893 45.455 5.01 0.00 44.01 3.21
2269 13395 2.664402 AGGCCACTCTTCAACATGTT 57.336 45.000 5.01 4.92 0.00 2.71
2270 13396 2.949447 AGGCCACTCTTCAACATGTTT 58.051 42.857 8.77 0.00 0.00 2.83
2271 13397 2.624838 AGGCCACTCTTCAACATGTTTG 59.375 45.455 8.77 3.45 0.00 2.93
2272 13398 2.288395 GGCCACTCTTCAACATGTTTGG 60.288 50.000 16.96 16.96 0.00 3.28
2273 13399 2.622942 GCCACTCTTCAACATGTTTGGA 59.377 45.455 22.98 10.90 0.00 3.53
2274 13400 3.550842 GCCACTCTTCAACATGTTTGGAC 60.551 47.826 22.98 13.21 0.00 4.02
2275 13401 3.631686 CCACTCTTCAACATGTTTGGACA 59.368 43.478 16.48 0.00 40.71 4.02
2276 13402 4.097741 CCACTCTTCAACATGTTTGGACAA 59.902 41.667 16.48 2.31 39.66 3.18
2277 13403 5.276270 CACTCTTCAACATGTTTGGACAAG 58.724 41.667 8.77 6.52 39.66 3.16
2278 13404 4.949856 ACTCTTCAACATGTTTGGACAAGT 59.050 37.500 8.77 7.32 39.21 3.16
2279 13405 5.418840 ACTCTTCAACATGTTTGGACAAGTT 59.581 36.000 8.77 0.00 45.55 2.66
2280 13406 6.071391 ACTCTTCAACATGTTTGGACAAGTTT 60.071 34.615 8.77 0.00 43.04 2.66
2281 13407 6.696411 TCTTCAACATGTTTGGACAAGTTTT 58.304 32.000 8.77 0.00 43.04 2.43
2282 13408 7.158021 TCTTCAACATGTTTGGACAAGTTTTT 58.842 30.769 8.77 0.00 43.04 1.94
2283 13409 6.718454 TCAACATGTTTGGACAAGTTTTTG 57.282 33.333 8.77 0.00 43.04 2.44
2284 13410 6.459066 TCAACATGTTTGGACAAGTTTTTGA 58.541 32.000 8.77 0.00 43.04 2.69
2285 13411 6.931281 TCAACATGTTTGGACAAGTTTTTGAA 59.069 30.769 8.77 0.00 43.04 2.69
2286 13412 7.442364 TCAACATGTTTGGACAAGTTTTTGAAA 59.558 29.630 8.77 0.00 43.04 2.69
2287 13413 7.127917 ACATGTTTGGACAAGTTTTTGAAAC 57.872 32.000 0.00 0.00 39.66 2.78
2288 13414 6.934083 ACATGTTTGGACAAGTTTTTGAAACT 59.066 30.769 0.00 0.44 39.66 2.66
2289 13415 7.443879 ACATGTTTGGACAAGTTTTTGAAACTT 59.556 29.630 11.81 11.81 39.66 2.66
2290 13416 7.414814 TGTTTGGACAAGTTTTTGAAACTTC 57.585 32.000 14.07 6.34 38.32 3.01
2291 13417 6.986817 TGTTTGGACAAGTTTTTGAAACTTCA 59.013 30.769 14.07 8.35 38.32 3.02
2292 13418 7.042389 TGTTTGGACAAGTTTTTGAAACTTCAC 60.042 33.333 14.07 11.17 38.32 3.18
2293 13419 5.474825 TGGACAAGTTTTTGAAACTTCACC 58.525 37.500 14.07 17.50 38.32 4.02
2294 13420 5.011125 TGGACAAGTTTTTGAAACTTCACCA 59.989 36.000 22.51 22.51 38.32 4.17
2295 13421 5.929415 GGACAAGTTTTTGAAACTTCACCAA 59.071 36.000 20.69 0.00 38.32 3.67
2296 13422 6.090763 GGACAAGTTTTTGAAACTTCACCAAG 59.909 38.462 20.69 11.85 38.32 3.61
2297 13423 6.521162 ACAAGTTTTTGAAACTTCACCAAGT 58.479 32.000 14.07 7.16 39.90 3.16
2298 13424 6.989759 ACAAGTTTTTGAAACTTCACCAAGTT 59.010 30.769 14.07 0.00 44.09 2.66
2310 13436 7.639113 ACTTCACCAAGTTTCAACTATTGAA 57.361 32.000 0.00 0.00 40.16 2.69
2311 13437 8.062065 ACTTCACCAAGTTTCAACTATTGAAA 57.938 30.769 11.68 11.68 46.59 2.69
2350 13476 8.812513 AATGATAAATTCACTCTCATTCACCA 57.187 30.769 0.00 0.00 37.11 4.17
2351 13477 8.812513 ATGATAAATTCACTCTCATTCACCAA 57.187 30.769 0.00 0.00 37.11 3.67
2352 13478 8.272545 TGATAAATTCACTCTCATTCACCAAG 57.727 34.615 0.00 0.00 0.00 3.61
2353 13479 7.884877 TGATAAATTCACTCTCATTCACCAAGT 59.115 33.333 0.00 0.00 0.00 3.16
2354 13480 6.966534 AAATTCACTCTCATTCACCAAGTT 57.033 33.333 0.00 0.00 0.00 2.66
2355 13481 6.966534 AATTCACTCTCATTCACCAAGTTT 57.033 33.333 0.00 0.00 0.00 2.66
2356 13482 6.566197 ATTCACTCTCATTCACCAAGTTTC 57.434 37.500 0.00 0.00 0.00 2.78
2357 13483 5.034852 TCACTCTCATTCACCAAGTTTCA 57.965 39.130 0.00 0.00 0.00 2.69
2358 13484 5.436175 TCACTCTCATTCACCAAGTTTCAA 58.564 37.500 0.00 0.00 0.00 2.69
2359 13485 5.885352 TCACTCTCATTCACCAAGTTTCAAA 59.115 36.000 0.00 0.00 0.00 2.69
2360 13486 6.376864 TCACTCTCATTCACCAAGTTTCAAAA 59.623 34.615 0.00 0.00 0.00 2.44
2361 13487 6.473455 CACTCTCATTCACCAAGTTTCAAAAC 59.527 38.462 0.00 0.00 39.17 2.43
2378 13504 8.425577 TTTCAAAACTTCAACTGAAACACAAA 57.574 26.923 0.00 0.00 33.90 2.83
2379 13505 8.600449 TTCAAAACTTCAACTGAAACACAAAT 57.400 26.923 0.00 0.00 33.07 2.32
2380 13506 8.600449 TCAAAACTTCAACTGAAACACAAATT 57.400 26.923 0.00 0.00 33.07 1.82
2381 13507 9.050601 TCAAAACTTCAACTGAAACACAAATTT 57.949 25.926 0.00 0.00 33.07 1.82
2386 13512 8.931775 ACTTCAACTGAAACACAAATTTAAACC 58.068 29.630 0.00 0.00 33.07 3.27
2387 13513 7.835634 TCAACTGAAACACAAATTTAAACCC 57.164 32.000 0.00 0.00 0.00 4.11
2388 13514 7.616313 TCAACTGAAACACAAATTTAAACCCT 58.384 30.769 0.00 0.00 0.00 4.34
2389 13515 8.750298 TCAACTGAAACACAAATTTAAACCCTA 58.250 29.630 0.00 0.00 0.00 3.53
2390 13516 9.372369 CAACTGAAACACAAATTTAAACCCTAA 57.628 29.630 0.00 0.00 0.00 2.69
2391 13517 9.594478 AACTGAAACACAAATTTAAACCCTAAG 57.406 29.630 0.00 0.00 0.00 2.18
2392 13518 8.201464 ACTGAAACACAAATTTAAACCCTAAGG 58.799 33.333 0.00 0.00 40.04 2.69
2393 13519 6.987404 TGAAACACAAATTTAAACCCTAAGGC 59.013 34.615 0.00 0.00 36.11 4.35
2394 13520 5.477607 ACACAAATTTAAACCCTAAGGCC 57.522 39.130 0.00 0.00 36.11 5.19
2395 13521 5.152193 ACACAAATTTAAACCCTAAGGCCT 58.848 37.500 0.00 0.00 36.11 5.19
2396 13522 6.316513 ACACAAATTTAAACCCTAAGGCCTA 58.683 36.000 5.16 0.00 36.11 3.93
2397 13523 6.436218 ACACAAATTTAAACCCTAAGGCCTAG 59.564 38.462 5.16 3.78 36.11 3.02
2398 13524 6.436218 CACAAATTTAAACCCTAAGGCCTAGT 59.564 38.462 5.16 0.00 36.11 2.57
2399 13525 7.014449 ACAAATTTAAACCCTAAGGCCTAGTT 58.986 34.615 5.16 5.01 36.11 2.24
2400 13526 7.511371 ACAAATTTAAACCCTAAGGCCTAGTTT 59.489 33.333 20.38 20.38 36.11 2.66
2401 13527 7.476540 AATTTAAACCCTAAGGCCTAGTTTG 57.523 36.000 23.24 9.55 36.11 2.93
2402 13528 3.451402 AAACCCTAAGGCCTAGTTTGG 57.549 47.619 5.16 5.35 36.11 3.28
2413 13539 1.956477 CCTAGTTTGGCACACAAGCTT 59.044 47.619 6.55 0.00 46.79 3.74
2414 13540 3.146066 CCTAGTTTGGCACACAAGCTTA 58.854 45.455 6.55 0.00 46.79 3.09
2415 13541 3.758554 CCTAGTTTGGCACACAAGCTTAT 59.241 43.478 6.55 0.00 46.79 1.73
2416 13542 3.923017 AGTTTGGCACACAAGCTTATC 57.077 42.857 6.55 0.00 46.79 1.75
2417 13543 2.226437 AGTTTGGCACACAAGCTTATCG 59.774 45.455 6.55 0.00 46.79 2.92
2418 13544 0.521291 TTGGCACACAAGCTTATCGC 59.479 50.000 0.00 0.00 39.29 4.58
2419 13545 1.305219 TGGCACACAAGCTTATCGCC 61.305 55.000 17.15 17.15 40.39 5.54
2420 13546 1.305219 GGCACACAAGCTTATCGCCA 61.305 55.000 18.44 0.00 40.39 5.69
2421 13547 0.521291 GCACACAAGCTTATCGCCAA 59.479 50.000 0.00 0.00 40.39 4.52
2422 13548 1.068610 GCACACAAGCTTATCGCCAAA 60.069 47.619 0.00 0.00 40.39 3.28
2423 13549 2.415893 GCACACAAGCTTATCGCCAAAT 60.416 45.455 0.00 0.00 40.39 2.32
2424 13550 3.173599 CACACAAGCTTATCGCCAAATG 58.826 45.455 0.00 0.00 40.39 2.32
2425 13551 2.819608 ACACAAGCTTATCGCCAAATGT 59.180 40.909 0.00 0.00 40.39 2.71
2426 13552 3.119849 ACACAAGCTTATCGCCAAATGTC 60.120 43.478 0.00 0.00 40.39 3.06
2427 13553 2.423538 ACAAGCTTATCGCCAAATGTCC 59.576 45.455 0.00 0.00 40.39 4.02
2428 13554 1.680338 AGCTTATCGCCAAATGTCCC 58.320 50.000 0.00 0.00 40.39 4.46
2429 13555 1.212935 AGCTTATCGCCAAATGTCCCT 59.787 47.619 0.00 0.00 40.39 4.20
2430 13556 2.024414 GCTTATCGCCAAATGTCCCTT 58.976 47.619 0.00 0.00 0.00 3.95
2431 13557 2.033424 GCTTATCGCCAAATGTCCCTTC 59.967 50.000 0.00 0.00 0.00 3.46
2432 13558 3.545703 CTTATCGCCAAATGTCCCTTCT 58.454 45.455 0.00 0.00 0.00 2.85
2433 13559 4.703897 CTTATCGCCAAATGTCCCTTCTA 58.296 43.478 0.00 0.00 0.00 2.10
2434 13560 3.864789 ATCGCCAAATGTCCCTTCTAT 57.135 42.857 0.00 0.00 0.00 1.98
2435 13561 3.644966 TCGCCAAATGTCCCTTCTATT 57.355 42.857 0.00 0.00 0.00 1.73
2436 13562 4.764050 TCGCCAAATGTCCCTTCTATTA 57.236 40.909 0.00 0.00 0.00 0.98
2437 13563 5.105567 TCGCCAAATGTCCCTTCTATTAA 57.894 39.130 0.00 0.00 0.00 1.40
2438 13564 5.123227 TCGCCAAATGTCCCTTCTATTAAG 58.877 41.667 0.00 0.00 0.00 1.85
2439 13565 5.104693 TCGCCAAATGTCCCTTCTATTAAGA 60.105 40.000 0.00 0.00 0.00 2.10
2440 13566 5.588648 CGCCAAATGTCCCTTCTATTAAGAA 59.411 40.000 0.00 0.00 39.47 2.52
2451 13577 2.963782 TCTATTAAGAAGACCTCCCGGC 59.036 50.000 0.00 0.00 0.00 6.13
2452 13578 0.837940 ATTAAGAAGACCTCCCGGCC 59.162 55.000 0.00 0.00 0.00 6.13
2453 13579 1.610554 TTAAGAAGACCTCCCGGCCG 61.611 60.000 21.04 21.04 0.00 6.13
2454 13580 2.793317 TAAGAAGACCTCCCGGCCGT 62.793 60.000 26.12 4.16 0.00 5.68
2455 13581 4.452733 GAAGACCTCCCGGCCGTG 62.453 72.222 26.12 14.27 0.00 4.94
2470 13596 1.447643 CGTGAGGCTTATCCAGGGG 59.552 63.158 0.00 0.00 37.29 4.79
2471 13597 1.048724 CGTGAGGCTTATCCAGGGGA 61.049 60.000 0.00 0.00 37.29 4.81
2472 13598 1.439543 GTGAGGCTTATCCAGGGGAT 58.560 55.000 2.92 2.92 45.40 3.85
2473 13599 1.072965 GTGAGGCTTATCCAGGGGATG 59.927 57.143 8.01 0.00 43.06 3.51
2474 13600 1.345422 TGAGGCTTATCCAGGGGATGT 60.345 52.381 8.01 0.00 43.06 3.06
2475 13601 1.777272 GAGGCTTATCCAGGGGATGTT 59.223 52.381 8.01 0.00 43.06 2.71
2476 13602 2.175715 GAGGCTTATCCAGGGGATGTTT 59.824 50.000 8.01 0.00 43.06 2.83
2477 13603 2.587307 AGGCTTATCCAGGGGATGTTTT 59.413 45.455 8.01 0.00 43.06 2.43
2478 13604 3.012844 AGGCTTATCCAGGGGATGTTTTT 59.987 43.478 8.01 0.00 43.06 1.94
2498 13624 6.610741 TTTTTATTTGCATTCACGCCTTTT 57.389 29.167 0.00 0.00 0.00 2.27
2499 13625 7.715265 TTTTTATTTGCATTCACGCCTTTTA 57.285 28.000 0.00 0.00 0.00 1.52
2500 13626 6.942886 TTTATTTGCATTCACGCCTTTTAG 57.057 33.333 0.00 0.00 0.00 1.85
2501 13627 4.782019 ATTTGCATTCACGCCTTTTAGA 57.218 36.364 0.00 0.00 0.00 2.10
2502 13628 4.576216 TTTGCATTCACGCCTTTTAGAA 57.424 36.364 0.00 0.00 0.00 2.10
2503 13629 4.576216 TTGCATTCACGCCTTTTAGAAA 57.424 36.364 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.029947 TGCGCCATCGACTCTGTAGA 61.030 55.000 4.18 0.00 38.10 2.59
243 245 2.032924 CACGAGGACCAACAAAGGAAAC 59.967 50.000 0.00 0.00 0.00 2.78
404 2495 5.520288 CGAGAAACAATGATGGATAACGAGT 59.480 40.000 0.00 0.00 0.00 4.18
499 6089 0.828022 ACTCCCGGTGAATTATCGCA 59.172 50.000 0.00 0.00 37.83 5.10
500 6090 1.499049 GACTCCCGGTGAATTATCGC 58.501 55.000 0.00 0.00 35.26 4.58
501 6091 1.270147 GGGACTCCCGGTGAATTATCG 60.270 57.143 0.00 0.00 32.13 2.92
550 6250 1.680522 CCCACAGAGATGGACTCCCG 61.681 65.000 0.00 0.00 45.96 5.14
553 6253 0.177604 CAGCCCACAGAGATGGACTC 59.822 60.000 0.00 0.00 43.02 3.36
585 6289 2.169352 CCCACAGAGATGAACTACCAGG 59.831 54.545 0.00 0.00 0.00 4.45
590 6298 2.497675 GACAGCCCACAGAGATGAACTA 59.502 50.000 0.00 0.00 0.00 2.24
594 6302 1.576577 ATGACAGCCCACAGAGATGA 58.423 50.000 0.00 0.00 0.00 2.92
606 6314 6.038603 TGCTTCCAGTGAATTATTATGACAGC 59.961 38.462 0.00 0.00 0.00 4.40
698 6409 2.415512 GGTTCCAGCACAATTCGTCTAC 59.584 50.000 0.00 0.00 0.00 2.59
703 6419 0.523072 CCAGGTTCCAGCACAATTCG 59.477 55.000 0.00 0.00 0.00 3.34
726 6442 0.179094 GACGCCCGTGGTCATTATCA 60.179 55.000 0.00 0.00 34.56 2.15
788 6508 6.002082 TCTCCGTCTTCCGATTCTTATATCA 58.998 40.000 0.00 0.00 39.56 2.15
794 6514 3.955650 TTTCTCCGTCTTCCGATTCTT 57.044 42.857 0.00 0.00 39.56 2.52
807 6527 2.016318 TGCATGCACCTATTTTCTCCG 58.984 47.619 18.46 0.00 0.00 4.63
826 6566 3.567164 GCATACATCTCCAATTCCCAGTG 59.433 47.826 0.00 0.00 0.00 3.66
898 7005 4.459337 GGCTTAGCATGTAGTGTCCTTTTT 59.541 41.667 6.53 0.00 0.00 1.94
899 7006 4.010349 GGCTTAGCATGTAGTGTCCTTTT 58.990 43.478 6.53 0.00 0.00 2.27
900 7007 3.610911 GGCTTAGCATGTAGTGTCCTTT 58.389 45.455 6.53 0.00 0.00 3.11
901 7008 2.418746 CGGCTTAGCATGTAGTGTCCTT 60.419 50.000 6.53 0.00 0.00 3.36
902 7009 1.137086 CGGCTTAGCATGTAGTGTCCT 59.863 52.381 6.53 0.00 0.00 3.85
903 7010 1.571919 CGGCTTAGCATGTAGTGTCC 58.428 55.000 6.53 0.00 0.00 4.02
904 7011 1.571919 CCGGCTTAGCATGTAGTGTC 58.428 55.000 6.53 0.00 0.00 3.67
905 7012 0.178068 CCCGGCTTAGCATGTAGTGT 59.822 55.000 6.53 0.00 0.00 3.55
906 7013 0.464036 TCCCGGCTTAGCATGTAGTG 59.536 55.000 6.53 0.00 0.00 2.74
907 7014 0.753262 CTCCCGGCTTAGCATGTAGT 59.247 55.000 6.53 0.00 0.00 2.73
908 7015 0.753262 ACTCCCGGCTTAGCATGTAG 59.247 55.000 6.53 0.47 0.00 2.74
909 7016 0.750850 GACTCCCGGCTTAGCATGTA 59.249 55.000 6.53 0.00 0.00 2.29
910 7017 1.264749 TGACTCCCGGCTTAGCATGT 61.265 55.000 6.53 0.00 0.00 3.21
913 7020 0.321298 GTTTGACTCCCGGCTTAGCA 60.321 55.000 6.53 0.00 0.00 3.49
978 7101 1.062587 CCAGTTTTCGGCGTCATCATC 59.937 52.381 6.85 0.00 0.00 2.92
979 7102 1.086696 CCAGTTTTCGGCGTCATCAT 58.913 50.000 6.85 0.00 0.00 2.45
980 7103 1.573829 GCCAGTTTTCGGCGTCATCA 61.574 55.000 6.85 0.00 40.35 3.07
1026 7160 0.313043 CTTGTGTCTGCCCAAAGCTG 59.687 55.000 0.00 0.00 44.23 4.24
1116 7272 1.584308 GCGTGCTACTCTTCATCGTTC 59.416 52.381 0.00 0.00 0.00 3.95
1145 7301 1.744522 GACGGTCTGGAGAAGTAGGAC 59.255 57.143 0.00 0.00 0.00 3.85
1467 10629 2.516225 GGCGGGCAGGGAATGTAC 60.516 66.667 0.00 0.00 0.00 2.90
1528 12541 2.916502 TTTCCGGCCGGACATCGATG 62.917 60.000 45.68 23.68 45.11 3.84
1538 12551 6.143278 GCTGTTTATTTTATATTTTCCGGCCG 59.857 38.462 21.04 21.04 0.00 6.13
1601 12686 7.013942 ACGGAGCAACATCAACTATATACTGTA 59.986 37.037 0.00 0.00 0.00 2.74
1603 12688 6.216569 ACGGAGCAACATCAACTATATACTG 58.783 40.000 0.00 0.00 0.00 2.74
1605 12690 8.758633 ATTACGGAGCAACATCAACTATATAC 57.241 34.615 0.00 0.00 0.00 1.47
1670 12755 4.577246 CTCCGAGCCTACCAGCGC 62.577 72.222 0.00 0.00 38.01 5.92
1682 12767 4.931661 AAACAGTCTCAACTAACTCCGA 57.068 40.909 0.00 0.00 33.25 4.55
1683 12768 8.752766 TTATTAAACAGTCTCAACTAACTCCG 57.247 34.615 0.00 0.00 33.25 4.63
1736 12822 3.717400 TCGATTGAGCAGAGACCATAC 57.283 47.619 0.00 0.00 0.00 2.39
1755 12842 8.226543 TCGCACAAATAAACTGATTTTCATTC 57.773 30.769 0.00 0.00 0.00 2.67
1822 12911 4.968259 TGTACATATATGCTTGACCACCC 58.032 43.478 12.79 0.00 0.00 4.61
1857 12946 4.689071 ACATAATTATTCCGACTCGCACA 58.311 39.130 0.00 0.00 0.00 4.57
1931 13030 1.014044 CGCTGCACGGACAGTACAAT 61.014 55.000 0.00 0.00 39.96 2.71
1952 13053 0.820226 CACAGAGAAGGATCCGCTCA 59.180 55.000 28.25 0.00 0.00 4.26
1955 13056 0.179097 GTCCACAGAGAAGGATCCGC 60.179 60.000 5.98 2.53 36.11 5.54
1968 13069 1.005512 CCATGAACCGTCGTCCACA 60.006 57.895 0.00 0.00 0.00 4.17
1975 13076 2.513065 CTTGCGTGCCATGAACCGTC 62.513 60.000 0.00 0.00 0.00 4.79
1978 13079 1.503542 CTCTTGCGTGCCATGAACC 59.496 57.895 0.00 0.00 0.00 3.62
1979 13080 1.154150 GCTCTTGCGTGCCATGAAC 60.154 57.895 0.00 0.00 0.00 3.18
1983 13084 1.153289 CCTAGCTCTTGCGTGCCAT 60.153 57.895 0.00 0.00 45.42 4.40
1990 13091 2.161486 CGCGTGTCCTAGCTCTTGC 61.161 63.158 0.00 0.00 40.05 4.01
1995 13096 0.249398 AAAATCCGCGTGTCCTAGCT 59.751 50.000 4.92 0.00 0.00 3.32
1998 13099 0.391927 CCCAAAATCCGCGTGTCCTA 60.392 55.000 4.92 0.00 0.00 2.94
2007 13108 1.113788 ATCATGTGGCCCAAAATCCG 58.886 50.000 0.00 0.00 0.00 4.18
2033 13134 4.098960 TGACCTATCCACTTTACGGATCAC 59.901 45.833 0.00 0.00 42.44 3.06
2039 13141 3.555956 GCACATGACCTATCCACTTTACG 59.444 47.826 0.00 0.00 0.00 3.18
2062 13164 1.205179 TCGCACGGGATTAAGCTGTAA 59.795 47.619 0.00 0.00 0.00 2.41
2064 13166 0.036765 TTCGCACGGGATTAAGCTGT 60.037 50.000 0.00 0.00 0.00 4.40
2065 13167 1.299541 ATTCGCACGGGATTAAGCTG 58.700 50.000 0.00 0.00 0.00 4.24
2077 13203 2.613595 TGTATCATGCAGGAATTCGCAC 59.386 45.455 4.62 0.00 41.79 5.34
2095 13221 4.518970 GTGATTTCTCTGCCAAAACCTGTA 59.481 41.667 0.00 0.00 0.00 2.74
2101 13227 2.582052 ACCGTGATTTCTCTGCCAAAA 58.418 42.857 0.00 0.00 0.00 2.44
2102 13228 2.270352 ACCGTGATTTCTCTGCCAAA 57.730 45.000 0.00 0.00 0.00 3.28
2103 13229 2.151202 GAACCGTGATTTCTCTGCCAA 58.849 47.619 0.00 0.00 0.00 4.52
2104 13230 1.071542 TGAACCGTGATTTCTCTGCCA 59.928 47.619 0.00 0.00 0.00 4.92
2105 13231 1.464997 GTGAACCGTGATTTCTCTGCC 59.535 52.381 0.00 0.00 0.00 4.85
2106 13232 1.464997 GGTGAACCGTGATTTCTCTGC 59.535 52.381 0.00 0.00 0.00 4.26
2113 13239 0.536460 GTGGTGGGTGAACCGTGATT 60.536 55.000 0.00 0.00 43.73 2.57
2115 13241 2.368011 TGTGGTGGGTGAACCGTGA 61.368 57.895 0.00 0.00 43.73 4.35
2190 13316 8.616076 TGCAAACGAAATACAAATTGGATTTTT 58.384 25.926 16.44 6.25 40.77 1.94
2221 13347 0.947180 CCCCCGTCACAACTAACACG 60.947 60.000 0.00 0.00 0.00 4.49
2227 13353 1.528309 CAAAGCCCCCGTCACAACT 60.528 57.895 0.00 0.00 0.00 3.16
2228 13354 2.561037 CCAAAGCCCCCGTCACAAC 61.561 63.158 0.00 0.00 0.00 3.32
2229 13355 2.203422 CCAAAGCCCCCGTCACAA 60.203 61.111 0.00 0.00 0.00 3.33
2230 13356 3.172106 TCCAAAGCCCCCGTCACA 61.172 61.111 0.00 0.00 0.00 3.58
2231 13357 2.359975 CTCCAAAGCCCCCGTCAC 60.360 66.667 0.00 0.00 0.00 3.67
2232 13358 2.124507 CTTCTCCAAAGCCCCCGTCA 62.125 60.000 0.00 0.00 0.00 4.35
2233 13359 1.377333 CTTCTCCAAAGCCCCCGTC 60.377 63.158 0.00 0.00 0.00 4.79
2234 13360 2.757077 CTTCTCCAAAGCCCCCGT 59.243 61.111 0.00 0.00 0.00 5.28
2235 13361 2.044946 CCTTCTCCAAAGCCCCCG 60.045 66.667 0.00 0.00 0.00 5.73
2236 13362 2.363018 GCCTTCTCCAAAGCCCCC 60.363 66.667 0.00 0.00 0.00 5.40
2237 13363 2.363018 GGCCTTCTCCAAAGCCCC 60.363 66.667 0.00 0.00 39.60 5.80
2238 13364 1.979155 GTGGCCTTCTCCAAAGCCC 60.979 63.158 3.32 0.00 45.14 5.19
2239 13365 0.962855 GAGTGGCCTTCTCCAAAGCC 60.963 60.000 3.32 0.00 45.96 4.35
2240 13366 0.037447 AGAGTGGCCTTCTCCAAAGC 59.963 55.000 19.61 1.31 37.96 3.51
2241 13367 2.224621 TGAAGAGTGGCCTTCTCCAAAG 60.225 50.000 19.61 0.00 42.20 2.77
2242 13368 1.774254 TGAAGAGTGGCCTTCTCCAAA 59.226 47.619 19.61 7.39 42.20 3.28
2243 13369 1.434188 TGAAGAGTGGCCTTCTCCAA 58.566 50.000 19.61 7.66 42.20 3.53
2244 13370 1.072331 GTTGAAGAGTGGCCTTCTCCA 59.928 52.381 19.61 8.41 42.20 3.86
2245 13371 1.072331 TGTTGAAGAGTGGCCTTCTCC 59.928 52.381 19.61 6.11 42.20 3.71
2246 13372 2.550830 TGTTGAAGAGTGGCCTTCTC 57.449 50.000 16.88 16.88 42.20 2.87
2247 13373 2.107204 ACATGTTGAAGAGTGGCCTTCT 59.893 45.455 3.32 4.16 42.20 2.85
2248 13374 2.508526 ACATGTTGAAGAGTGGCCTTC 58.491 47.619 3.32 1.37 42.09 3.46
2249 13375 2.664402 ACATGTTGAAGAGTGGCCTT 57.336 45.000 3.32 0.00 0.00 4.35
2250 13376 2.624838 CAAACATGTTGAAGAGTGGCCT 59.375 45.455 12.82 0.00 0.00 5.19
2251 13377 2.288395 CCAAACATGTTGAAGAGTGGCC 60.288 50.000 12.82 0.00 0.00 5.36
2252 13378 2.622942 TCCAAACATGTTGAAGAGTGGC 59.377 45.455 12.82 0.00 0.00 5.01
2253 13379 3.631686 TGTCCAAACATGTTGAAGAGTGG 59.368 43.478 12.82 14.54 0.00 4.00
2254 13380 4.898829 TGTCCAAACATGTTGAAGAGTG 57.101 40.909 12.82 5.28 0.00 3.51
2255 13381 4.949856 ACTTGTCCAAACATGTTGAAGAGT 59.050 37.500 12.82 9.96 39.92 3.24
2256 13382 5.505173 ACTTGTCCAAACATGTTGAAGAG 57.495 39.130 12.82 9.40 39.92 2.85
2257 13383 5.913137 AACTTGTCCAAACATGTTGAAGA 57.087 34.783 12.82 6.61 46.30 2.87
2258 13384 6.966435 AAAACTTGTCCAAACATGTTGAAG 57.034 33.333 12.82 11.36 46.95 3.02
2259 13385 6.931281 TCAAAAACTTGTCCAAACATGTTGAA 59.069 30.769 12.82 0.00 46.95 2.69
2260 13386 6.459066 TCAAAAACTTGTCCAAACATGTTGA 58.541 32.000 12.82 2.93 46.95 3.18
2261 13387 6.718454 TCAAAAACTTGTCCAAACATGTTG 57.282 33.333 12.82 6.46 46.95 3.33
2263 13389 6.934083 AGTTTCAAAAACTTGTCCAAACATGT 59.066 30.769 0.00 0.00 43.46 3.21
2264 13390 7.363205 AGTTTCAAAAACTTGTCCAAACATG 57.637 32.000 0.00 0.00 34.73 3.21
2265 13391 7.659390 TGAAGTTTCAAAAACTTGTCCAAACAT 59.341 29.630 19.40 0.00 40.27 2.71
2266 13392 6.986817 TGAAGTTTCAAAAACTTGTCCAAACA 59.013 30.769 19.40 8.77 40.27 2.83
2267 13393 7.287950 GTGAAGTTTCAAAAACTTGTCCAAAC 58.712 34.615 19.40 4.01 40.27 2.93
2268 13394 6.425417 GGTGAAGTTTCAAAAACTTGTCCAAA 59.575 34.615 19.40 0.00 40.27 3.28
2269 13395 5.929415 GGTGAAGTTTCAAAAACTTGTCCAA 59.071 36.000 19.40 1.55 40.27 3.53
2270 13396 5.011125 TGGTGAAGTTTCAAAAACTTGTCCA 59.989 36.000 19.40 20.46 40.27 4.02
2271 13397 5.474825 TGGTGAAGTTTCAAAAACTTGTCC 58.525 37.500 19.40 18.77 40.27 4.02
2272 13398 6.645003 ACTTGGTGAAGTTTCAAAAACTTGTC 59.355 34.615 19.40 12.50 39.56 3.18
2273 13399 6.521162 ACTTGGTGAAGTTTCAAAAACTTGT 58.479 32.000 19.40 9.30 39.56 3.16
2286 13412 7.639113 TTCAATAGTTGAAACTTGGTGAAGT 57.361 32.000 0.21 0.00 45.94 3.01
2325 13451 8.812513 TGGTGAATGAGAGTGAATTTATCATT 57.187 30.769 0.00 0.00 41.88 2.57
2326 13452 8.812513 TTGGTGAATGAGAGTGAATTTATCAT 57.187 30.769 0.00 0.00 40.97 2.45
2327 13453 7.884877 ACTTGGTGAATGAGAGTGAATTTATCA 59.115 33.333 0.00 0.00 35.05 2.15
2328 13454 8.273780 ACTTGGTGAATGAGAGTGAATTTATC 57.726 34.615 0.00 0.00 0.00 1.75
2329 13455 8.641498 AACTTGGTGAATGAGAGTGAATTTAT 57.359 30.769 0.00 0.00 0.00 1.40
2330 13456 8.463930 AAACTTGGTGAATGAGAGTGAATTTA 57.536 30.769 0.00 0.00 0.00 1.40
2331 13457 6.966534 AACTTGGTGAATGAGAGTGAATTT 57.033 33.333 0.00 0.00 0.00 1.82
2332 13458 6.547141 TGAAACTTGGTGAATGAGAGTGAATT 59.453 34.615 0.00 0.00 0.00 2.17
2333 13459 6.064060 TGAAACTTGGTGAATGAGAGTGAAT 58.936 36.000 0.00 0.00 0.00 2.57
2334 13460 5.436175 TGAAACTTGGTGAATGAGAGTGAA 58.564 37.500 0.00 0.00 0.00 3.18
2335 13461 5.034852 TGAAACTTGGTGAATGAGAGTGA 57.965 39.130 0.00 0.00 0.00 3.41
2336 13462 5.756195 TTGAAACTTGGTGAATGAGAGTG 57.244 39.130 0.00 0.00 0.00 3.51
2337 13463 6.378280 AGTTTTGAAACTTGGTGAATGAGAGT 59.622 34.615 3.37 0.00 46.52 3.24
2338 13464 6.799512 AGTTTTGAAACTTGGTGAATGAGAG 58.200 36.000 3.37 0.00 46.52 3.20
2339 13465 6.773976 AGTTTTGAAACTTGGTGAATGAGA 57.226 33.333 3.37 0.00 46.52 3.27
2353 13479 8.425577 TTTGTGTTTCAGTTGAAGTTTTGAAA 57.574 26.923 0.00 0.00 37.25 2.69
2354 13480 8.600449 ATTTGTGTTTCAGTTGAAGTTTTGAA 57.400 26.923 0.00 0.00 35.21 2.69
2355 13481 8.600449 AATTTGTGTTTCAGTTGAAGTTTTGA 57.400 26.923 0.00 0.00 35.21 2.69
2360 13486 8.931775 GGTTTAAATTTGTGTTTCAGTTGAAGT 58.068 29.630 0.00 0.00 35.21 3.01
2361 13487 8.387354 GGGTTTAAATTTGTGTTTCAGTTGAAG 58.613 33.333 0.00 0.00 35.21 3.02
2362 13488 8.097662 AGGGTTTAAATTTGTGTTTCAGTTGAA 58.902 29.630 0.00 0.00 0.00 2.69
2363 13489 7.616313 AGGGTTTAAATTTGTGTTTCAGTTGA 58.384 30.769 0.00 0.00 0.00 3.18
2364 13490 7.841915 AGGGTTTAAATTTGTGTTTCAGTTG 57.158 32.000 0.00 0.00 0.00 3.16
2365 13491 9.594478 CTTAGGGTTTAAATTTGTGTTTCAGTT 57.406 29.630 0.00 0.00 0.00 3.16
2366 13492 8.201464 CCTTAGGGTTTAAATTTGTGTTTCAGT 58.799 33.333 0.00 0.00 0.00 3.41
2367 13493 7.170828 GCCTTAGGGTTTAAATTTGTGTTTCAG 59.829 37.037 0.00 0.00 34.45 3.02
2368 13494 6.987404 GCCTTAGGGTTTAAATTTGTGTTTCA 59.013 34.615 0.00 0.00 34.45 2.69
2369 13495 6.425721 GGCCTTAGGGTTTAAATTTGTGTTTC 59.574 38.462 0.00 0.00 34.45 2.78
2370 13496 6.100569 AGGCCTTAGGGTTTAAATTTGTGTTT 59.899 34.615 0.00 0.00 34.45 2.83
2371 13497 5.605069 AGGCCTTAGGGTTTAAATTTGTGTT 59.395 36.000 0.00 0.00 34.45 3.32
2372 13498 5.152193 AGGCCTTAGGGTTTAAATTTGTGT 58.848 37.500 0.00 0.00 34.45 3.72
2373 13499 5.738619 AGGCCTTAGGGTTTAAATTTGTG 57.261 39.130 0.00 0.00 34.45 3.33
2374 13500 6.558498 ACTAGGCCTTAGGGTTTAAATTTGT 58.442 36.000 12.58 0.00 33.42 2.83
2375 13501 7.476540 AACTAGGCCTTAGGGTTTAAATTTG 57.523 36.000 12.58 0.00 33.42 2.32
2376 13502 7.038587 CCAAACTAGGCCTTAGGGTTTAAATTT 60.039 37.037 12.58 0.00 33.42 1.82
2377 13503 6.439375 CCAAACTAGGCCTTAGGGTTTAAATT 59.561 38.462 12.58 0.00 33.42 1.82
2378 13504 5.955959 CCAAACTAGGCCTTAGGGTTTAAAT 59.044 40.000 12.58 0.00 33.42 1.40
2379 13505 5.326900 CCAAACTAGGCCTTAGGGTTTAAA 58.673 41.667 12.58 0.00 33.42 1.52
2380 13506 4.925836 CCAAACTAGGCCTTAGGGTTTAA 58.074 43.478 12.58 0.00 33.42 1.52
2381 13507 4.579647 CCAAACTAGGCCTTAGGGTTTA 57.420 45.455 12.58 0.00 33.42 2.01
2382 13508 3.451402 CCAAACTAGGCCTTAGGGTTT 57.549 47.619 12.58 14.49 33.42 3.27
2393 13519 1.609208 AGCTTGTGTGCCAAACTAGG 58.391 50.000 0.00 0.00 27.71 3.02
2394 13520 4.436050 CGATAAGCTTGTGTGCCAAACTAG 60.436 45.833 9.86 0.00 29.41 2.57
2395 13521 3.435327 CGATAAGCTTGTGTGCCAAACTA 59.565 43.478 9.86 0.00 29.41 2.24
2396 13522 2.226437 CGATAAGCTTGTGTGCCAAACT 59.774 45.455 9.86 0.00 30.77 2.66
2397 13523 2.584791 CGATAAGCTTGTGTGCCAAAC 58.415 47.619 9.86 0.00 31.20 2.93
2398 13524 1.068610 GCGATAAGCTTGTGTGCCAAA 60.069 47.619 9.86 0.00 44.04 3.28
2399 13525 0.521291 GCGATAAGCTTGTGTGCCAA 59.479 50.000 9.86 0.00 44.04 4.52
2400 13526 2.170738 GCGATAAGCTTGTGTGCCA 58.829 52.632 9.86 0.00 44.04 4.92
2411 13537 3.545703 AGAAGGGACATTTGGCGATAAG 58.454 45.455 0.00 0.00 0.00 1.73
2412 13538 3.644966 AGAAGGGACATTTGGCGATAA 57.355 42.857 0.00 0.00 0.00 1.75
2413 13539 4.974645 ATAGAAGGGACATTTGGCGATA 57.025 40.909 0.00 0.00 0.00 2.92
2414 13540 3.864789 ATAGAAGGGACATTTGGCGAT 57.135 42.857 0.00 0.00 0.00 4.58
2415 13541 3.644966 AATAGAAGGGACATTTGGCGA 57.355 42.857 0.00 0.00 0.00 5.54
2416 13542 5.123227 TCTTAATAGAAGGGACATTTGGCG 58.877 41.667 0.00 0.00 0.00 5.69
2451 13577 1.447643 CCCTGGATAAGCCTCACGG 59.552 63.158 0.00 0.00 37.63 4.94
2452 13578 1.048724 TCCCCTGGATAAGCCTCACG 61.049 60.000 0.00 0.00 37.63 4.35
2453 13579 1.072965 CATCCCCTGGATAAGCCTCAC 59.927 57.143 0.00 0.00 40.98 3.51
2454 13580 1.345422 ACATCCCCTGGATAAGCCTCA 60.345 52.381 0.00 0.00 40.98 3.86
2455 13581 1.439543 ACATCCCCTGGATAAGCCTC 58.560 55.000 0.00 0.00 40.98 4.70
2456 13582 1.912862 AACATCCCCTGGATAAGCCT 58.087 50.000 0.00 0.00 40.98 4.58
2457 13583 2.755952 AAACATCCCCTGGATAAGCC 57.244 50.000 0.00 0.00 40.98 4.35
2475 13601 6.610741 AAAAGGCGTGAATGCAAATAAAAA 57.389 29.167 0.00 0.00 36.28 1.94
2476 13602 7.148641 TCTAAAAGGCGTGAATGCAAATAAAA 58.851 30.769 0.00 0.00 36.28 1.52
2477 13603 6.682746 TCTAAAAGGCGTGAATGCAAATAAA 58.317 32.000 0.00 0.00 36.28 1.40
2478 13604 6.260870 TCTAAAAGGCGTGAATGCAAATAA 57.739 33.333 0.00 0.00 36.28 1.40
2479 13605 5.888691 TCTAAAAGGCGTGAATGCAAATA 57.111 34.783 0.00 0.00 36.28 1.40
2480 13606 4.782019 TCTAAAAGGCGTGAATGCAAAT 57.218 36.364 0.00 0.00 36.28 2.32
2481 13607 4.576216 TTCTAAAAGGCGTGAATGCAAA 57.424 36.364 0.00 0.00 36.28 3.68
2482 13608 4.576216 TTTCTAAAAGGCGTGAATGCAA 57.424 36.364 0.00 0.00 36.28 4.08


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

AutoCloner maintained by Alex Coulton.