Multiple sequence alignment - TraesCS6B01G106600

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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 TraesCS6B01G106600 chr6B 100.000 2738 0 0 1 2738 87331734 87328997 0.000000e+00 5057.0
1 TraesCS6B01G106600 chr6B 90.291 1030 78 10 699 1720 86647701 86648716 0.000000e+00 1328.0
2 TraesCS6B01G106600 chr6B 89.407 1029 87 9 699 1719 86446530 86445516 0.000000e+00 1277.0
3 TraesCS6B01G106600 chr6B 88.525 1037 90 10 699 1720 86672520 86671498 0.000000e+00 1229.0
4 TraesCS6B01G106600 chr6B 90.297 639 56 3 2101 2738 87206545 87205912 0.000000e+00 832.0
5 TraesCS6B01G106600 chr6B 92.410 527 36 4 149 672 86673151 86672626 0.000000e+00 749.0
6 TraesCS6B01G106600 chr6B 91.360 544 38 7 134 672 86447175 86446636 0.000000e+00 736.0
7 TraesCS6B01G106600 chr6B 93.462 413 23 4 262 672 86647185 86647595 6.480000e-171 610.0
8 TraesCS6B01G106600 chr6A 90.098 1121 83 14 699 1808 48641321 48640218 0.000000e+00 1430.0
9 TraesCS6B01G106600 chr6A 88.401 638 39 23 51 672 48642045 48641427 0.000000e+00 736.0
10 TraesCS6B01G106600 chr6A 83.607 244 30 9 1989 2224 208021166 208020925 1.280000e-53 220.0
11 TraesCS6B01G106600 chr6A 84.337 83 8 5 2438 2517 48639072 48638992 2.920000e-10 76.8
12 TraesCS6B01G106600 chr6A 97.222 36 1 0 659 694 48641377 48641342 8.190000e-06 62.1
13 TraesCS6B01G106600 chr6A 100.000 29 0 0 1836 1864 48640113 48640085 1.000000e-03 54.7
14 TraesCS6B01G106600 chr6A 100.000 29 0 0 1836 1864 48640163 48640135 1.000000e-03 54.7
15 TraesCS6B01G106600 chr6D 88.827 1083 74 23 659 1720 37117417 37116361 0.000000e+00 1286.0
16 TraesCS6B01G106600 chr6D 89.371 875 77 7 852 1716 37226543 37225675 0.000000e+00 1086.0
17 TraesCS6B01G106600 chr6D 90.240 666 41 11 22 672 37118123 37117467 0.000000e+00 848.0
18 TraesCS6B01G106600 chr6D 90.876 548 40 6 134 672 37229172 37228626 0.000000e+00 726.0
19 TraesCS6B01G106600 chr6D 88.416 423 32 6 59 479 37337803 37337396 6.810000e-136 494.0
20 TraesCS6B01G106600 chr6D 84.127 252 33 4 1978 2223 113486663 113486413 1.270000e-58 237.0
21 TraesCS6B01G106600 chr6D 89.005 191 17 4 484 672 37331078 37330890 1.640000e-57 233.0
22 TraesCS6B01G106600 chr6D 84.977 213 15 9 659 857 37228579 37228370 1.660000e-47 200.0
23 TraesCS6B01G106600 chr6D 91.379 58 3 1 1871 1926 37330829 37330772 8.130000e-11 78.7
24 TraesCS6B01G106600 chr4A 78.797 948 148 34 767 1695 626954063 626953150 3.040000e-164 588.0
25 TraesCS6B01G106600 chr5A 78.489 953 147 42 767 1702 617123152 617122241 3.060000e-159 571.0
26 TraesCS6B01G106600 chr5A 82.996 247 34 7 1988 2227 242549334 242549089 1.650000e-52 217.0
27 TraesCS6B01G106600 chr5A 82.158 241 36 5 1989 2223 689240278 689240517 1.660000e-47 200.0
28 TraesCS6B01G106600 chr5A 81.600 250 33 6 1984 2227 253612598 253612356 7.740000e-46 195.0
29 TraesCS6B01G106600 chr5D 77.836 952 159 36 767 1704 494078639 494077726 2.400000e-150 542.0
30 TraesCS6B01G106600 chr7B 76.434 959 180 30 773 1698 84324801 84325746 6.860000e-131 477.0
31 TraesCS6B01G106600 chr7B 91.204 216 16 3 2522 2735 174560042 174560256 9.590000e-75 291.0
32 TraesCS6B01G106600 chr7B 90.654 214 20 0 2525 2738 684976557 684976344 4.460000e-73 285.0
33 TraesCS6B01G106600 chr7B 88.398 181 19 1 2045 2223 423145063 423144883 1.650000e-52 217.0
34 TraesCS6B01G106600 chr7B 80.498 241 38 6 1991 2224 88278545 88278307 2.800000e-40 176.0
35 TraesCS6B01G106600 chr2D 91.324 219 16 3 2522 2738 426471992 426471775 2.060000e-76 296.0
36 TraesCS6B01G106600 chr7D 90.783 217 19 1 2523 2738 497317424 497317208 3.450000e-74 289.0
37 TraesCS6B01G106600 chr4D 90.455 220 17 4 2522 2738 284278437 284278219 1.240000e-73 287.0
38 TraesCS6B01G106600 chr4D 89.954 219 19 3 2522 2738 366006391 366006174 2.080000e-71 279.0
39 TraesCS6B01G106600 chr5B 90.411 219 18 3 2522 2738 389652867 389652650 4.460000e-73 285.0
40 TraesCS6B01G106600 chr1B 90.278 216 18 3 2522 2735 311229018 311229232 2.080000e-71 279.0
41 TraesCS6B01G106600 chr7A 83.471 242 34 4 1989 2224 125010290 125010049 1.280000e-53 220.0
42 TraesCS6B01G106600 chr2A 82.305 243 37 4 1991 2227 242371028 242370786 3.570000e-49 206.0


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 TraesCS6B01G106600 chr6B 87328997 87331734 2737 True 5057.000000 5057 100.0000 1 2738 1 chr6B.!!$R2 2737
1 TraesCS6B01G106600 chr6B 86445516 86447175 1659 True 1006.500000 1277 90.3835 134 1719 2 chr6B.!!$R3 1585
2 TraesCS6B01G106600 chr6B 86671498 86673151 1653 True 989.000000 1229 90.4675 149 1720 2 chr6B.!!$R4 1571
3 TraesCS6B01G106600 chr6B 86647185 86648716 1531 False 969.000000 1328 91.8765 262 1720 2 chr6B.!!$F1 1458
4 TraesCS6B01G106600 chr6B 87205912 87206545 633 True 832.000000 832 90.2970 2101 2738 1 chr6B.!!$R1 637
5 TraesCS6B01G106600 chr6A 48638992 48642045 3053 True 402.383333 1430 93.3430 51 2517 6 chr6A.!!$R2 2466
6 TraesCS6B01G106600 chr6D 37116361 37118123 1762 True 1067.000000 1286 89.5335 22 1720 2 chr6D.!!$R3 1698
7 TraesCS6B01G106600 chr6D 37225675 37229172 3497 True 670.666667 1086 88.4080 134 1716 3 chr6D.!!$R4 1582
8 TraesCS6B01G106600 chr4A 626953150 626954063 913 True 588.000000 588 78.7970 767 1695 1 chr4A.!!$R1 928
9 TraesCS6B01G106600 chr5A 617122241 617123152 911 True 571.000000 571 78.4890 767 1702 1 chr5A.!!$R3 935
10 TraesCS6B01G106600 chr5D 494077726 494078639 913 True 542.000000 542 77.8360 767 1704 1 chr5D.!!$R1 937
11 TraesCS6B01G106600 chr7B 84324801 84325746 945 False 477.000000 477 76.4340 773 1698 1 chr7B.!!$F1 925

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
496 524 0.465278 GAATCTCCTTCCCCTGCAGC 60.465 60.0 8.66 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 4536 0.17899 ACAAACAGGGCCTGAGTTCC 60.179 55.0 38.99 0.0 35.18 3.62 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
24 25 3.842428 CGCTGATCACAAAATGAGAAACG 59.158 43.478 0.00 0.00 41.91 3.60
28 29 6.618287 TGATCACAAAATGAGAAACGACTT 57.382 33.333 0.00 0.00 41.91 3.01
40 41 6.053005 TGAGAAACGACTTTGTCCAATAACT 58.947 36.000 0.00 0.00 30.19 2.24
46 47 6.756221 ACGACTTTGTCCAATAACTAGAGTT 58.244 36.000 0.00 0.00 41.73 3.01
74 75 5.813157 TCATTTCGACCTTATAAATGCACGA 59.187 36.000 0.00 0.00 39.39 4.35
83 84 1.948104 TAAATGCACGATTCCCTCCG 58.052 50.000 0.00 0.00 0.00 4.63
90 91 3.057734 GCACGATTCCCTCCGTAATTAG 58.942 50.000 0.00 0.00 37.23 1.73
102 103 6.231211 CCTCCGTAATTAGCAACTCCAATAT 58.769 40.000 0.00 0.00 0.00 1.28
103 104 7.383687 CCTCCGTAATTAGCAACTCCAATATA 58.616 38.462 0.00 0.00 0.00 0.86
104 105 7.876068 CCTCCGTAATTAGCAACTCCAATATAA 59.124 37.037 0.00 0.00 0.00 0.98
105 106 9.436957 CTCCGTAATTAGCAACTCCAATATAAT 57.563 33.333 0.00 0.00 0.00 1.28
126 127 2.738521 GCCATGTGAGACACGCGT 60.739 61.111 5.58 5.58 37.14 6.01
127 128 3.015293 GCCATGTGAGACACGCGTG 62.015 63.158 35.99 35.99 43.27 5.34
128 129 2.471607 CATGTGAGACACGCGTGC 59.528 61.111 37.35 28.26 38.81 5.34
209 215 0.963355 GCTCCTCCGATCCGCTCTAT 60.963 60.000 0.00 0.00 0.00 1.98
293 321 2.124983 GATGAGCAGCGGCAGGAA 60.125 61.111 12.44 0.00 44.61 3.36
311 339 1.146544 AACCCCTACCCCTGCACATT 61.147 55.000 0.00 0.00 0.00 2.71
317 345 2.771943 CCTACCCCTGCACATTCTCTTA 59.228 50.000 0.00 0.00 0.00 2.10
326 354 3.244422 TGCACATTCTCTTACTCCCGTTT 60.244 43.478 0.00 0.00 0.00 3.60
379 407 1.816863 ATGGCCGCGATATTCTCCGT 61.817 55.000 8.23 0.00 0.00 4.69
413 441 1.303948 CACCATCCTCACCATGCCA 59.696 57.895 0.00 0.00 0.00 4.92
422 450 3.049674 ACCATGCCAGTCAACGCG 61.050 61.111 3.53 3.53 0.00 6.01
427 455 3.712881 GCCAGTCAACGCGGACAC 61.713 66.667 12.47 2.88 40.29 3.67
496 524 0.465278 GAATCTCCTTCCCCTGCAGC 60.465 60.000 8.66 0.00 0.00 5.25
704 813 4.600576 TGTTCGCGAGGTGCTGCA 62.601 61.111 9.59 0.00 43.27 4.41
714 823 2.127232 GGTGCTGCACAACAACCCT 61.127 57.895 31.35 0.00 35.37 4.34
715 824 0.821711 GGTGCTGCACAACAACCCTA 60.822 55.000 31.35 0.00 35.37 3.53
875 2819 2.544359 CACAAGGACAACGACGCG 59.456 61.111 3.53 3.53 0.00 6.01
915 2859 1.324736 GCGAGGTGTTCAATAGCTTCG 59.675 52.381 0.00 0.00 0.00 3.79
929 2873 2.989253 TTCGACGAGCTGGAGCCA 60.989 61.111 1.44 0.00 43.38 4.75
950 2894 1.226323 CTACGTCGAGCACTTCCGG 60.226 63.158 0.00 0.00 0.00 5.14
1056 3014 2.031163 GTCACAGACGGCTGCCTT 59.969 61.111 20.90 7.39 46.26 4.35
1081 3046 2.992689 TAGACACGAAGCCGGCCA 60.993 61.111 26.15 0.00 40.78 5.36
1194 3159 1.000955 GACTTCGTGTGGGTCATCAGT 59.999 52.381 0.00 0.00 0.00 3.41
1199 3164 0.034896 GTGTGGGTCATCAGTTCCGT 59.965 55.000 0.00 0.00 0.00 4.69
1203 3176 2.158959 GGTCATCAGTTCCGTCGCG 61.159 63.158 0.00 0.00 0.00 5.87
1406 3386 4.760047 GGCGATGGTCACGTGGCT 62.760 66.667 21.13 0.00 37.47 4.75
1414 3394 4.367023 TCACGTGGCTGCGGTACC 62.367 66.667 17.00 0.16 35.98 3.34
1432 3412 0.036671 CCCGGACCAGTTCTACAACC 60.037 60.000 0.73 0.00 32.22 3.77
1489 3472 0.108186 CATCAGCGCCAAGGACTACA 60.108 55.000 2.29 0.00 0.00 2.74
1493 3476 2.380410 GCGCCAAGGACTACACGTG 61.380 63.158 15.48 15.48 0.00 4.49
1504 3487 0.382515 CTACACGTGGCCTCTAGAGC 59.617 60.000 21.57 9.65 0.00 4.09
1525 3511 3.469970 ATGAGGTGATCGGCGGCA 61.470 61.111 10.53 2.69 0.00 5.69
1548 3534 1.739562 GATCGCTGGATCCATCGGC 60.740 63.158 31.48 22.69 42.72 5.54
1553 3539 1.070445 CTGGATCCATCGGCAGACC 59.930 63.158 16.63 0.00 0.00 3.85
1611 3597 0.322906 GGAAGAAGGCCAAGGACCTG 60.323 60.000 5.01 0.00 37.67 4.00
1625 3611 2.092429 AGGACCTGAGTGTGAAAGCAAA 60.092 45.455 0.00 0.00 0.00 3.68
1671 3657 1.779683 GTACAGCGACGTTGGAAGC 59.220 57.895 16.27 0.00 0.00 3.86
1762 3751 5.183140 AGTTATTACAACATGAGGTGGCAAC 59.817 40.000 0.00 0.00 0.00 4.17
1780 3769 1.035932 ACGTCTGATCGGGTGGGTAG 61.036 60.000 0.62 0.00 34.94 3.18
1800 3789 3.403968 AGCCCGAACTTTCTTTCTCTTC 58.596 45.455 0.00 0.00 0.00 2.87
1813 3838 1.959747 TCTCTTCTTCGTTGTACGCG 58.040 50.000 3.53 3.53 42.21 6.01
1816 3841 1.197492 TCTTCTTCGTTGTACGCGCTA 59.803 47.619 5.73 0.00 42.21 4.26
1829 3854 2.295885 ACGCGCTACCATAAGTCTAGT 58.704 47.619 5.73 0.00 0.00 2.57
1830 3855 2.290093 ACGCGCTACCATAAGTCTAGTC 59.710 50.000 5.73 0.00 0.00 2.59
1831 3856 2.548904 CGCGCTACCATAAGTCTAGTCT 59.451 50.000 5.56 0.00 0.00 3.24
1875 3941 4.840401 CATCTTTTGCATCTTCGTACGA 57.160 40.909 15.28 15.28 0.00 3.43
1876 3942 5.395325 CATCTTTTGCATCTTCGTACGAT 57.605 39.130 20.27 0.51 0.00 3.73
1877 3943 5.799960 CATCTTTTGCATCTTCGTACGATT 58.200 37.500 20.27 4.39 0.00 3.34
1878 3944 5.203358 TCTTTTGCATCTTCGTACGATTG 57.797 39.130 20.27 17.14 0.00 2.67
1880 3946 5.407084 TCTTTTGCATCTTCGTACGATTGAA 59.593 36.000 20.27 9.23 0.00 2.69
1881 3947 5.599359 TTTGCATCTTCGTACGATTGAAA 57.401 34.783 20.27 14.54 0.00 2.69
1883 3949 5.389642 TGCATCTTCGTACGATTGAAATC 57.610 39.130 20.27 12.87 0.00 2.17
1885 3951 6.270064 TGCATCTTCGTACGATTGAAATCTA 58.730 36.000 20.27 0.00 33.24 1.98
1888 3954 7.167635 GCATCTTCGTACGATTGAAATCTAGAA 59.832 37.037 20.27 0.00 33.24 2.10
1893 4347 5.399892 CGTACGATTGAAATCTAGAAGGAGC 59.600 44.000 10.44 0.00 33.24 4.70
1923 4379 2.428902 CCGGAAACACGTCGCGTA 60.429 61.111 5.77 0.00 38.32 4.42
1926 4382 1.622269 GGAAACACGTCGCGTATCG 59.378 57.895 5.77 12.48 38.32 2.92
1952 4508 3.426615 TGTGCCCCAGTATTTAACTTGG 58.573 45.455 0.00 0.00 40.12 3.61
1953 4509 3.181427 TGTGCCCCAGTATTTAACTTGGT 60.181 43.478 0.00 0.00 39.01 3.67
1954 4510 3.442625 GTGCCCCAGTATTTAACTTGGTC 59.557 47.826 0.00 0.00 39.01 4.02
1955 4511 3.332485 TGCCCCAGTATTTAACTTGGTCT 59.668 43.478 0.00 0.00 39.01 3.85
1956 4512 4.536888 TGCCCCAGTATTTAACTTGGTCTA 59.463 41.667 0.00 0.00 39.01 2.59
1957 4513 4.880120 GCCCCAGTATTTAACTTGGTCTAC 59.120 45.833 0.00 0.00 39.01 2.59
1958 4514 5.434408 CCCCAGTATTTAACTTGGTCTACC 58.566 45.833 0.00 0.00 39.01 3.18
1959 4515 5.191124 CCCCAGTATTTAACTTGGTCTACCT 59.809 44.000 0.02 0.00 39.01 3.08
1960 4516 6.113411 CCCAGTATTTAACTTGGTCTACCTG 58.887 44.000 0.02 0.00 36.46 4.00
1961 4517 5.585047 CCAGTATTTAACTTGGTCTACCTGC 59.415 44.000 0.02 0.00 35.76 4.85
1962 4518 5.291128 CAGTATTTAACTTGGTCTACCTGCG 59.709 44.000 0.02 0.00 35.76 5.18
1963 4519 2.088950 TTAACTTGGTCTACCTGCGC 57.911 50.000 0.00 0.00 36.82 6.09
1964 4520 0.248289 TAACTTGGTCTACCTGCGCC 59.752 55.000 4.18 0.00 36.82 6.53
1965 4521 2.125106 CTTGGTCTACCTGCGCCC 60.125 66.667 4.18 0.00 36.82 6.13
1966 4522 3.682292 CTTGGTCTACCTGCGCCCC 62.682 68.421 4.18 0.00 36.82 5.80
1984 4540 2.202703 CGTCGTCGGATGGGGAAC 60.203 66.667 0.00 0.00 0.00 3.62
1985 4541 2.707849 CGTCGTCGGATGGGGAACT 61.708 63.158 0.00 0.00 0.00 3.01
1986 4542 1.141234 GTCGTCGGATGGGGAACTC 59.859 63.158 0.00 0.00 0.00 3.01
1987 4543 1.304630 TCGTCGGATGGGGAACTCA 60.305 57.895 0.00 0.00 0.00 3.41
1988 4544 1.141881 CGTCGGATGGGGAACTCAG 59.858 63.158 0.00 0.00 0.00 3.35
1989 4545 1.522569 GTCGGATGGGGAACTCAGG 59.477 63.158 0.00 0.00 0.00 3.86
1990 4546 2.190578 CGGATGGGGAACTCAGGC 59.809 66.667 0.00 0.00 0.00 4.85
1991 4547 2.597903 GGATGGGGAACTCAGGCC 59.402 66.667 0.00 0.00 0.00 5.19
1992 4548 2.597903 GATGGGGAACTCAGGCCC 59.402 66.667 0.00 0.00 43.91 5.80
1993 4549 2.003548 GATGGGGAACTCAGGCCCT 61.004 63.158 0.00 0.00 44.10 5.19
1994 4550 2.276309 GATGGGGAACTCAGGCCCTG 62.276 65.000 3.69 3.69 44.10 4.45
1995 4551 2.936032 GGGGAACTCAGGCCCTGT 60.936 66.667 11.27 0.00 44.10 4.00
1996 4552 2.539081 GGGGAACTCAGGCCCTGTT 61.539 63.158 11.27 1.52 44.10 3.16
1997 4553 1.460699 GGGAACTCAGGCCCTGTTT 59.539 57.895 11.27 5.33 41.31 2.83
1998 4554 0.895559 GGGAACTCAGGCCCTGTTTG 60.896 60.000 11.27 5.20 41.31 2.93
1999 4555 0.178990 GGAACTCAGGCCCTGTTTGT 60.179 55.000 11.27 5.85 32.61 2.83
2000 4556 1.692411 GAACTCAGGCCCTGTTTGTT 58.308 50.000 11.27 13.82 32.61 2.83
2001 4557 2.031870 GAACTCAGGCCCTGTTTGTTT 58.968 47.619 11.27 0.00 32.61 2.83
2002 4558 1.402787 ACTCAGGCCCTGTTTGTTTG 58.597 50.000 11.27 0.00 32.61 2.93
2003 4559 0.675633 CTCAGGCCCTGTTTGTTTGG 59.324 55.000 11.27 0.00 32.61 3.28
2004 4560 0.758685 TCAGGCCCTGTTTGTTTGGG 60.759 55.000 11.27 0.00 43.62 4.12
2005 4561 1.048160 CAGGCCCTGTTTGTTTGGGT 61.048 55.000 1.39 0.00 42.77 4.51
2006 4562 0.326143 AGGCCCTGTTTGTTTGGGTT 60.326 50.000 0.00 0.00 42.77 4.11
2007 4563 0.544223 GGCCCTGTTTGTTTGGGTTT 59.456 50.000 0.00 0.00 42.77 3.27
2008 4564 1.763545 GGCCCTGTTTGTTTGGGTTTA 59.236 47.619 0.00 0.00 42.77 2.01
2009 4565 2.370519 GGCCCTGTTTGTTTGGGTTTAT 59.629 45.455 0.00 0.00 42.77 1.40
2010 4566 3.556213 GGCCCTGTTTGTTTGGGTTTATC 60.556 47.826 0.00 0.00 42.77 1.75
2011 4567 3.323691 GCCCTGTTTGTTTGGGTTTATCT 59.676 43.478 0.00 0.00 42.77 1.98
2012 4568 4.202315 GCCCTGTTTGTTTGGGTTTATCTT 60.202 41.667 0.00 0.00 42.77 2.40
2013 4569 5.686387 GCCCTGTTTGTTTGGGTTTATCTTT 60.686 40.000 0.00 0.00 42.77 2.52
2014 4570 6.353323 CCCTGTTTGTTTGGGTTTATCTTTT 58.647 36.000 0.00 0.00 36.32 2.27
2015 4571 6.826231 CCCTGTTTGTTTGGGTTTATCTTTTT 59.174 34.615 0.00 0.00 36.32 1.94
2016 4572 7.011950 CCCTGTTTGTTTGGGTTTATCTTTTTC 59.988 37.037 0.00 0.00 36.32 2.29
2017 4573 7.768582 CCTGTTTGTTTGGGTTTATCTTTTTCT 59.231 33.333 0.00 0.00 0.00 2.52
2018 4574 9.161629 CTGTTTGTTTGGGTTTATCTTTTTCTT 57.838 29.630 0.00 0.00 0.00 2.52
2019 4575 9.508642 TGTTTGTTTGGGTTTATCTTTTTCTTT 57.491 25.926 0.00 0.00 0.00 2.52
2022 4578 7.980062 TGTTTGGGTTTATCTTTTTCTTTTGC 58.020 30.769 0.00 0.00 0.00 3.68
2023 4579 7.607991 TGTTTGGGTTTATCTTTTTCTTTTGCA 59.392 29.630 0.00 0.00 0.00 4.08
2024 4580 8.454894 GTTTGGGTTTATCTTTTTCTTTTGCAA 58.545 29.630 0.00 0.00 0.00 4.08
2025 4581 7.546778 TGGGTTTATCTTTTTCTTTTGCAAC 57.453 32.000 0.00 0.00 0.00 4.17
2026 4582 7.334858 TGGGTTTATCTTTTTCTTTTGCAACT 58.665 30.769 0.00 0.00 0.00 3.16
2027 4583 7.826744 TGGGTTTATCTTTTTCTTTTGCAACTT 59.173 29.630 0.00 0.00 0.00 2.66
2028 4584 8.673711 GGGTTTATCTTTTTCTTTTGCAACTTT 58.326 29.630 0.00 0.00 0.00 2.66
2038 4594 9.956720 TTTTCTTTTGCAACTTTTTCATTTTGA 57.043 22.222 0.00 0.00 0.00 2.69
2040 4596 9.771915 TTCTTTTGCAACTTTTTCATTTTGATC 57.228 25.926 0.00 0.00 0.00 2.92
2041 4597 8.944029 TCTTTTGCAACTTTTTCATTTTGATCA 58.056 25.926 0.00 0.00 0.00 2.92
2042 4598 9.557338 CTTTTGCAACTTTTTCATTTTGATCAA 57.443 25.926 3.38 3.38 0.00 2.57
2044 4600 9.719279 TTTGCAACTTTTTCATTTTGATCAATC 57.281 25.926 9.40 0.00 0.00 2.67
2045 4601 7.863666 TGCAACTTTTTCATTTTGATCAATCC 58.136 30.769 9.40 0.00 0.00 3.01
2046 4602 7.498239 TGCAACTTTTTCATTTTGATCAATCCA 59.502 29.630 9.40 0.00 0.00 3.41
2047 4603 8.508875 GCAACTTTTTCATTTTGATCAATCCAT 58.491 29.630 9.40 0.00 0.00 3.41
2054 4610 9.947433 TTTCATTTTGATCAATCCATAAAAGCT 57.053 25.926 9.40 0.00 0.00 3.74
2055 4611 9.947433 TTCATTTTGATCAATCCATAAAAGCTT 57.053 25.926 9.40 0.00 0.00 3.74
2056 4612 9.590451 TCATTTTGATCAATCCATAAAAGCTTC 57.410 29.630 9.40 0.00 0.00 3.86
2057 4613 9.595823 CATTTTGATCAATCCATAAAAGCTTCT 57.404 29.630 9.40 0.00 0.00 2.85
2065 4621 9.920946 TCAATCCATAAAAGCTTCTAAATAGGT 57.079 29.630 0.00 0.00 0.00 3.08
2066 4622 9.956720 CAATCCATAAAAGCTTCTAAATAGGTG 57.043 33.333 0.00 0.00 0.00 4.00
2067 4623 9.920946 AATCCATAAAAGCTTCTAAATAGGTGA 57.079 29.630 0.00 0.00 0.00 4.02
2069 4625 9.342308 TCCATAAAAGCTTCTAAATAGGTGATG 57.658 33.333 0.00 0.00 0.00 3.07
2070 4626 9.125026 CCATAAAAGCTTCTAAATAGGTGATGT 57.875 33.333 0.00 0.00 0.00 3.06
2073 4629 7.396540 AAAGCTTCTAAATAGGTGATGTTGG 57.603 36.000 0.00 0.00 0.00 3.77
2074 4630 6.313519 AGCTTCTAAATAGGTGATGTTGGA 57.686 37.500 0.00 0.00 0.00 3.53
2075 4631 6.352516 AGCTTCTAAATAGGTGATGTTGGAG 58.647 40.000 0.00 0.00 0.00 3.86
2076 4632 6.069963 AGCTTCTAAATAGGTGATGTTGGAGT 60.070 38.462 0.00 0.00 0.00 3.85
2077 4633 6.599638 GCTTCTAAATAGGTGATGTTGGAGTT 59.400 38.462 0.00 0.00 0.00 3.01
2078 4634 7.121315 GCTTCTAAATAGGTGATGTTGGAGTTT 59.879 37.037 0.00 0.00 0.00 2.66
2079 4635 8.934023 TTCTAAATAGGTGATGTTGGAGTTTT 57.066 30.769 0.00 0.00 0.00 2.43
2080 4636 8.934023 TCTAAATAGGTGATGTTGGAGTTTTT 57.066 30.769 0.00 0.00 0.00 1.94
2081 4637 8.792633 TCTAAATAGGTGATGTTGGAGTTTTTG 58.207 33.333 0.00 0.00 0.00 2.44
2082 4638 5.982890 ATAGGTGATGTTGGAGTTTTTGG 57.017 39.130 0.00 0.00 0.00 3.28
2083 4639 2.365293 AGGTGATGTTGGAGTTTTTGGC 59.635 45.455 0.00 0.00 0.00 4.52
2084 4640 2.365293 GGTGATGTTGGAGTTTTTGGCT 59.635 45.455 0.00 0.00 0.00 4.75
2085 4641 3.181466 GGTGATGTTGGAGTTTTTGGCTT 60.181 43.478 0.00 0.00 0.00 4.35
2086 4642 4.051237 GTGATGTTGGAGTTTTTGGCTTC 58.949 43.478 0.00 0.00 0.00 3.86
2087 4643 3.960102 TGATGTTGGAGTTTTTGGCTTCT 59.040 39.130 0.00 0.00 0.00 2.85
2088 4644 3.799281 TGTTGGAGTTTTTGGCTTCTG 57.201 42.857 0.00 0.00 0.00 3.02
2089 4645 3.360867 TGTTGGAGTTTTTGGCTTCTGA 58.639 40.909 0.00 0.00 0.00 3.27
2090 4646 3.960102 TGTTGGAGTTTTTGGCTTCTGAT 59.040 39.130 0.00 0.00 0.00 2.90
2091 4647 4.202141 TGTTGGAGTTTTTGGCTTCTGATG 60.202 41.667 0.00 0.00 0.00 3.07
2092 4648 3.831323 TGGAGTTTTTGGCTTCTGATGA 58.169 40.909 0.00 0.00 0.00 2.92
2093 4649 4.214310 TGGAGTTTTTGGCTTCTGATGAA 58.786 39.130 0.00 0.00 0.00 2.57
2094 4650 4.834496 TGGAGTTTTTGGCTTCTGATGAAT 59.166 37.500 0.00 0.00 0.00 2.57
2095 4651 5.047802 TGGAGTTTTTGGCTTCTGATGAATC 60.048 40.000 0.00 0.00 0.00 2.52
2096 4652 5.047802 GGAGTTTTTGGCTTCTGATGAATCA 60.048 40.000 0.00 0.00 35.16 2.57
2097 4653 6.409524 AGTTTTTGGCTTCTGATGAATCAA 57.590 33.333 0.00 0.00 36.18 2.57
2098 4654 7.001099 AGTTTTTGGCTTCTGATGAATCAAT 57.999 32.000 0.00 0.00 36.18 2.57
2099 4655 6.872020 AGTTTTTGGCTTCTGATGAATCAATG 59.128 34.615 0.00 0.00 36.18 2.82
2103 4659 7.649533 TTGGCTTCTGATGAATCAATGTAAT 57.350 32.000 0.00 0.00 36.18 1.89
2164 4720 6.978659 GCACCTATTTAGAAGTTTTTATGGCC 59.021 38.462 0.00 0.00 0.00 5.36
2188 4744 1.830477 TGGGCAAAGTGAAAAAGCTGT 59.170 42.857 0.00 0.00 0.00 4.40
2216 4772 5.123186 AGCAAAAGTAAAAGCCCAAACAAAC 59.877 36.000 0.00 0.00 0.00 2.93
2227 4783 2.482864 CCAAACAAACATGGCCTCAAC 58.517 47.619 3.32 0.00 0.00 3.18
2256 4965 8.909423 TGGACCATGATCCATATGTATAGTTA 57.091 34.615 4.01 0.00 44.14 2.24
2281 4990 3.947910 AGAGTTAAAATCGGACCGACA 57.052 42.857 21.02 0.00 39.18 4.35
2314 5023 4.389374 TGAGGTTGTCAGTTCAGATTTCC 58.611 43.478 0.00 0.00 0.00 3.13
2316 5025 3.139077 GGTTGTCAGTTCAGATTTCCGT 58.861 45.455 0.00 0.00 0.00 4.69
2319 5028 4.811555 TGTCAGTTCAGATTTCCGTTTG 57.188 40.909 0.00 0.00 0.00 2.93
2334 5043 1.997606 CGTTTGGCTACCCTTACGAAG 59.002 52.381 0.00 0.00 39.39 3.79
2353 5062 6.577103 ACGAAGGGGTAGCTACTTAATTTAC 58.423 40.000 22.74 4.05 0.00 2.01
2426 5181 0.820871 TTTAATTGGATGGCACGGGC 59.179 50.000 0.00 0.00 40.13 6.13
2443 5220 0.183731 GGCCCCACCCTAGAAATCAG 59.816 60.000 0.00 0.00 0.00 2.90
2444 5221 0.919710 GCCCCACCCTAGAAATCAGT 59.080 55.000 0.00 0.00 0.00 3.41
2521 5298 7.813148 ACGTACCAATTATGTAGATGTAGCATC 59.187 37.037 1.18 1.18 0.00 3.91
2546 5323 8.467598 TCTTAGAGCAACTACAATAAGGTACAG 58.532 37.037 0.00 0.00 0.00 2.74
2548 5325 7.005709 AGAGCAACTACAATAAGGTACAGTT 57.994 36.000 0.00 0.00 0.00 3.16
2554 5331 7.713734 ACTACAATAAGGTACAGTTAGCAGA 57.286 36.000 0.00 0.00 0.00 4.26
2605 5382 6.288096 ACTTAGTTGGAGGAGAGAGGATAT 57.712 41.667 0.00 0.00 0.00 1.63
2616 5393 7.092444 GGAGGAGAGAGGATATGAGAGAGAATA 60.092 44.444 0.00 0.00 0.00 1.75
2623 5400 8.271458 AGAGGATATGAGAGAGAATATAAGCGA 58.729 37.037 0.00 0.00 0.00 4.93
2652 5429 1.656095 GCAAGAGCTAGCTACAACACG 59.344 52.381 19.38 3.41 37.91 4.49
2678 5455 3.053619 TCCTAGGCACTATGTGAGAGTGA 60.054 47.826 2.96 0.00 46.01 3.41
2685 5462 5.645497 GGCACTATGTGAGAGTGAAAGATTT 59.355 40.000 6.96 0.00 46.01 2.17
2691 5468 5.559770 TGTGAGAGTGAAAGATTTGCCATA 58.440 37.500 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.634896 GTTTCTCATTTTGTGATCAGCGAT 58.365 37.500 0.00 0.00 35.97 4.58
4 5 6.233430 AGTCGTTTCTCATTTTGTGATCAG 57.767 37.500 0.00 0.00 35.97 2.90
6 7 6.912591 ACAAAGTCGTTTCTCATTTTGTGATC 59.087 34.615 0.19 0.00 37.36 2.92
7 8 6.795399 ACAAAGTCGTTTCTCATTTTGTGAT 58.205 32.000 0.19 0.00 37.36 3.06
8 9 6.189677 ACAAAGTCGTTTCTCATTTTGTGA 57.810 33.333 0.19 0.00 37.36 3.58
9 10 5.455525 GGACAAAGTCGTTTCTCATTTTGTG 59.544 40.000 5.27 0.00 38.45 3.33
10 11 5.124776 TGGACAAAGTCGTTTCTCATTTTGT 59.875 36.000 0.56 0.56 40.32 2.83
11 12 5.577835 TGGACAAAGTCGTTTCTCATTTTG 58.422 37.500 0.00 0.00 32.65 2.44
12 13 5.828299 TGGACAAAGTCGTTTCTCATTTT 57.172 34.783 0.00 0.00 32.65 1.82
13 14 5.828299 TTGGACAAAGTCGTTTCTCATTT 57.172 34.783 0.00 0.00 32.65 2.32
14 15 7.228706 AGTTATTGGACAAAGTCGTTTCTCATT 59.771 33.333 0.00 0.00 32.65 2.57
15 16 6.710744 AGTTATTGGACAAAGTCGTTTCTCAT 59.289 34.615 0.00 0.00 32.65 2.90
16 17 6.053005 AGTTATTGGACAAAGTCGTTTCTCA 58.947 36.000 0.00 0.00 32.65 3.27
17 18 6.541111 AGTTATTGGACAAAGTCGTTTCTC 57.459 37.500 0.00 0.00 32.65 2.87
18 19 7.439381 TCTAGTTATTGGACAAAGTCGTTTCT 58.561 34.615 0.00 0.00 32.65 2.52
19 20 7.384387 ACTCTAGTTATTGGACAAAGTCGTTTC 59.616 37.037 0.00 0.00 32.65 2.78
20 21 7.215085 ACTCTAGTTATTGGACAAAGTCGTTT 58.785 34.615 0.00 0.00 32.65 3.60
24 25 8.603242 TTGAACTCTAGTTATTGGACAAAGTC 57.397 34.615 0.00 0.00 38.56 3.01
28 29 9.739276 AATGATTGAACTCTAGTTATTGGACAA 57.261 29.630 0.00 0.00 38.56 3.18
46 47 8.128582 GTGCATTTATAAGGTCGAAATGATTGA 58.871 33.333 10.02 0.00 41.16 2.57
74 75 4.444449 GGAGTTGCTAATTACGGAGGGAAT 60.444 45.833 0.00 0.00 0.00 3.01
90 91 6.207417 ACATGGCAGTATTATATTGGAGTTGC 59.793 38.462 0.00 0.00 0.00 4.17
102 103 3.780902 CGTGTCTCACATGGCAGTATTA 58.219 45.455 0.00 0.00 33.40 0.98
103 104 2.621338 CGTGTCTCACATGGCAGTATT 58.379 47.619 0.00 0.00 33.40 1.89
104 105 1.740380 GCGTGTCTCACATGGCAGTAT 60.740 52.381 0.00 0.00 35.71 2.12
105 106 0.389817 GCGTGTCTCACATGGCAGTA 60.390 55.000 0.00 0.00 35.71 2.74
106 107 1.669115 GCGTGTCTCACATGGCAGT 60.669 57.895 0.00 0.00 35.71 4.40
107 108 2.733671 CGCGTGTCTCACATGGCAG 61.734 63.158 0.00 0.00 35.71 4.85
109 110 2.738521 ACGCGTGTCTCACATGGC 60.739 61.111 12.93 0.00 35.71 4.40
128 129 3.716006 CTGCTGGCCACACGAACG 61.716 66.667 0.00 0.00 0.00 3.95
131 132 3.399105 AACACTGCTGGCCACACGA 62.399 57.895 0.00 0.00 0.00 4.35
209 215 3.928005 TGGGTGGTTGTACACTTGTAA 57.072 42.857 0.00 0.00 41.09 2.41
238 261 1.132453 CGTGCTCTGTCGATGGAGTTA 59.868 52.381 15.55 6.21 32.67 2.24
291 319 1.571773 ATGTGCAGGGGTAGGGGTTC 61.572 60.000 0.00 0.00 0.00 3.62
293 321 1.543896 AATGTGCAGGGGTAGGGGT 60.544 57.895 0.00 0.00 0.00 4.95
311 339 2.611224 GGCGAAAAACGGGAGTAAGAGA 60.611 50.000 0.00 0.00 46.69 3.10
409 437 4.228567 TGTCCGCGTTGACTGGCA 62.229 61.111 15.06 0.00 36.21 4.92
413 441 1.374252 GATGGTGTCCGCGTTGACT 60.374 57.895 15.06 0.00 36.21 3.41
422 450 2.818274 GCCGAACGGATGGTGTCC 60.818 66.667 17.63 0.00 44.10 4.02
479 507 2.381941 GGCTGCAGGGGAAGGAGAT 61.382 63.158 17.12 0.00 0.00 2.75
695 788 2.127232 GGGTTGTTGTGCAGCACCT 61.127 57.895 23.06 0.00 32.73 4.00
704 813 3.751518 GTTGTCTCCATAGGGTTGTTGT 58.248 45.455 0.00 0.00 34.93 3.32
714 823 0.892755 AAGCCGTCGTTGTCTCCATA 59.107 50.000 0.00 0.00 0.00 2.74
715 824 0.389948 GAAGCCGTCGTTGTCTCCAT 60.390 55.000 0.00 0.00 0.00 3.41
875 2819 1.448717 GAAGCTCTTCTGGTCCGCC 60.449 63.158 2.55 0.00 36.69 6.13
886 2830 2.493907 GAACACCTCGCCGAAGCTCT 62.494 60.000 0.00 0.00 36.60 4.09
915 2859 1.032657 TAGTCTGGCTCCAGCTCGTC 61.033 60.000 10.99 0.33 43.31 4.20
1056 3014 1.880894 CTTCGTGTCTAGCCACCGA 59.119 57.895 0.00 0.00 31.47 4.69
1081 3046 1.584380 GAGACGTACACCACCGAGCT 61.584 60.000 0.00 0.00 0.00 4.09
1206 3179 3.041940 GAACCGTCGGTGCCACTG 61.042 66.667 19.67 0.00 35.34 3.66
1207 3180 3.515316 CTGAACCGTCGGTGCCACT 62.515 63.158 19.67 0.34 35.34 4.00
1209 3182 3.220999 CTCTGAACCGTCGGTGCCA 62.221 63.158 19.67 17.43 35.34 4.92
1347 3327 2.045926 GCCGAGTTCCAGCCACAT 60.046 61.111 0.00 0.00 0.00 3.21
1414 3394 0.682852 TGGTTGTAGAACTGGTCCGG 59.317 55.000 0.00 0.00 32.15 5.14
1432 3412 0.534412 ACCTCCACGATGAGCTTCTG 59.466 55.000 0.00 0.00 0.00 3.02
1504 3487 2.111878 GCCGATCACCTCATGGGG 59.888 66.667 11.11 11.11 40.03 4.96
1525 3511 1.071385 GATGGATCCAGCGATCACCTT 59.929 52.381 21.33 0.00 45.89 3.50
1548 3534 2.513204 CTGCTGCCCATCGGTCTG 60.513 66.667 0.00 0.00 0.00 3.51
1583 3569 2.570181 CCTTCTTCCGTACGGCGT 59.430 61.111 29.64 19.64 39.32 5.68
1584 3570 2.884207 GCCTTCTTCCGTACGGCG 60.884 66.667 29.64 21.31 40.95 6.46
1585 3571 2.510918 GGCCTTCTTCCGTACGGC 60.511 66.667 29.64 15.20 39.98 5.68
1586 3572 0.739813 CTTGGCCTTCTTCCGTACGG 60.740 60.000 28.66 28.66 0.00 4.02
1587 3573 0.739813 CCTTGGCCTTCTTCCGTACG 60.740 60.000 8.69 8.69 0.00 3.67
1588 3574 0.611714 TCCTTGGCCTTCTTCCGTAC 59.388 55.000 3.32 0.00 0.00 3.67
1611 3597 1.661460 GCGCTCTTTGCTTTCACACTC 60.661 52.381 0.00 0.00 40.11 3.51
1625 3611 2.739996 CCCTTCTCCATGGCGCTCT 61.740 63.158 6.96 0.00 0.00 4.09
1671 3657 2.228059 GCCATCAACTCATCCATCAGG 58.772 52.381 0.00 0.00 0.00 3.86
1704 3690 1.553706 TTAGTCGGGTGTCTTCTCCC 58.446 55.000 0.00 0.00 42.22 4.30
1762 3751 1.734137 CTACCCACCCGATCAGACG 59.266 63.158 0.00 0.00 0.00 4.18
1780 3769 3.403968 AGAAGAGAAAGAAAGTTCGGGC 58.596 45.455 0.00 0.00 32.50 6.13
1787 3776 6.573358 CGTACAACGAAGAAGAGAAAGAAAG 58.427 40.000 0.00 0.00 46.05 2.62
1800 3789 0.730155 TGGTAGCGCGTACAACGAAG 60.730 55.000 8.43 0.00 46.05 3.79
1813 3838 9.675464 ATCTACATAGACTAGACTTATGGTAGC 57.325 37.037 0.00 0.00 34.72 3.58
1829 3854 6.199393 CACGACGTTTCATCATCTACATAGA 58.801 40.000 0.00 0.00 36.65 1.98
1830 3855 5.108217 GCACGACGTTTCATCATCTACATAG 60.108 44.000 0.00 0.00 0.00 2.23
1831 3856 4.738252 GCACGACGTTTCATCATCTACATA 59.262 41.667 0.00 0.00 0.00 2.29
1864 3930 7.863375 CCTTCTAGATTTCAATCGTACGAAGAT 59.137 37.037 23.56 11.39 40.35 2.40
1866 3932 7.194278 TCCTTCTAGATTTCAATCGTACGAAG 58.806 38.462 23.56 17.54 40.35 3.79
1868 3934 6.688637 TCCTTCTAGATTTCAATCGTACGA 57.311 37.500 21.93 21.93 40.35 3.43
1869 3935 5.399892 GCTCCTTCTAGATTTCAATCGTACG 59.600 44.000 9.53 9.53 40.35 3.67
1870 3936 6.273825 TGCTCCTTCTAGATTTCAATCGTAC 58.726 40.000 0.00 0.00 40.35 3.67
1871 3937 6.465439 TGCTCCTTCTAGATTTCAATCGTA 57.535 37.500 0.00 0.00 40.35 3.43
1872 3938 5.344743 TGCTCCTTCTAGATTTCAATCGT 57.655 39.130 0.00 0.00 40.35 3.73
1873 3939 4.210955 GCTGCTCCTTCTAGATTTCAATCG 59.789 45.833 0.00 0.00 40.35 3.34
1874 3940 5.121811 TGCTGCTCCTTCTAGATTTCAATC 58.878 41.667 0.00 0.00 35.64 2.67
1875 3941 5.108187 TGCTGCTCCTTCTAGATTTCAAT 57.892 39.130 0.00 0.00 0.00 2.57
1876 3942 4.511527 CTGCTGCTCCTTCTAGATTTCAA 58.488 43.478 0.00 0.00 0.00 2.69
1877 3943 3.681034 GCTGCTGCTCCTTCTAGATTTCA 60.681 47.826 8.53 0.00 36.03 2.69
1878 3944 2.871633 GCTGCTGCTCCTTCTAGATTTC 59.128 50.000 8.53 0.00 36.03 2.17
1880 3946 1.836166 TGCTGCTGCTCCTTCTAGATT 59.164 47.619 17.00 0.00 40.48 2.40
1881 3947 1.413445 CTGCTGCTGCTCCTTCTAGAT 59.587 52.381 17.00 0.00 40.48 1.98
1883 3949 0.810823 GCTGCTGCTGCTCCTTCTAG 60.811 60.000 22.10 4.91 40.48 2.43
1885 3951 2.046120 GCTGCTGCTGCTCCTTCT 60.046 61.111 22.10 0.00 40.48 2.85
1923 4379 4.511246 CTGGGGCACATGGGCGAT 62.511 66.667 15.08 0.00 44.56 4.58
1926 4382 0.687427 AAATACTGGGGCACATGGGC 60.687 55.000 12.85 12.85 42.44 5.36
1928 4384 3.631250 AGTTAAATACTGGGGCACATGG 58.369 45.455 0.00 0.00 35.19 3.66
1967 4523 2.202703 GTTCCCCATCCGACGACG 60.203 66.667 0.00 0.00 39.43 5.12
1968 4524 1.141234 GAGTTCCCCATCCGACGAC 59.859 63.158 0.00 0.00 0.00 4.34
1969 4525 1.304630 TGAGTTCCCCATCCGACGA 60.305 57.895 0.00 0.00 0.00 4.20
1970 4526 1.141881 CTGAGTTCCCCATCCGACG 59.858 63.158 0.00 0.00 0.00 5.12
1971 4527 1.522569 CCTGAGTTCCCCATCCGAC 59.477 63.158 0.00 0.00 0.00 4.79
1972 4528 2.367202 GCCTGAGTTCCCCATCCGA 61.367 63.158 0.00 0.00 0.00 4.55
1973 4529 2.190578 GCCTGAGTTCCCCATCCG 59.809 66.667 0.00 0.00 0.00 4.18
1974 4530 2.597903 GGCCTGAGTTCCCCATCC 59.402 66.667 0.00 0.00 0.00 3.51
1975 4531 2.003548 AGGGCCTGAGTTCCCCATC 61.004 63.158 4.50 0.00 43.67 3.51
1976 4532 2.128226 AGGGCCTGAGTTCCCCAT 59.872 61.111 4.50 0.00 43.67 4.00
1977 4533 2.935481 CAGGGCCTGAGTTCCCCA 60.935 66.667 29.96 0.00 43.67 4.96
1978 4534 2.081585 AAACAGGGCCTGAGTTCCCC 62.082 60.000 38.99 0.00 43.67 4.81
1979 4535 0.895559 CAAACAGGGCCTGAGTTCCC 60.896 60.000 38.99 0.00 42.94 3.97
1980 4536 0.178990 ACAAACAGGGCCTGAGTTCC 60.179 55.000 38.99 0.00 35.18 3.62
1981 4537 1.692411 AACAAACAGGGCCTGAGTTC 58.308 50.000 38.99 0.00 35.18 3.01
1982 4538 1.756538 CAAACAAACAGGGCCTGAGTT 59.243 47.619 38.99 31.24 35.18 3.01
1983 4539 1.402787 CAAACAAACAGGGCCTGAGT 58.597 50.000 38.99 28.00 35.18 3.41
1984 4540 0.675633 CCAAACAAACAGGGCCTGAG 59.324 55.000 38.99 27.38 35.18 3.35
1985 4541 0.758685 CCCAAACAAACAGGGCCTGA 60.759 55.000 38.99 0.00 35.44 3.86
1986 4542 1.048160 ACCCAAACAAACAGGGCCTG 61.048 55.000 31.62 31.62 46.88 4.85
1987 4543 0.326143 AACCCAAACAAACAGGGCCT 60.326 50.000 0.00 0.00 46.88 5.19
1988 4544 0.544223 AAACCCAAACAAACAGGGCC 59.456 50.000 0.00 0.00 46.88 5.80
1989 4545 3.323691 AGATAAACCCAAACAAACAGGGC 59.676 43.478 0.00 0.00 46.88 5.19
1991 4547 7.768582 AGAAAAAGATAAACCCAAACAAACAGG 59.231 33.333 0.00 0.00 0.00 4.00
1992 4548 8.716646 AGAAAAAGATAAACCCAAACAAACAG 57.283 30.769 0.00 0.00 0.00 3.16
1993 4549 9.508642 AAAGAAAAAGATAAACCCAAACAAACA 57.491 25.926 0.00 0.00 0.00 2.83
1996 4552 8.454894 GCAAAAGAAAAAGATAAACCCAAACAA 58.545 29.630 0.00 0.00 0.00 2.83
1997 4553 7.607991 TGCAAAAGAAAAAGATAAACCCAAACA 59.392 29.630 0.00 0.00 0.00 2.83
1998 4554 7.980062 TGCAAAAGAAAAAGATAAACCCAAAC 58.020 30.769 0.00 0.00 0.00 2.93
1999 4555 8.454894 GTTGCAAAAGAAAAAGATAAACCCAAA 58.545 29.630 0.00 0.00 0.00 3.28
2000 4556 7.826744 AGTTGCAAAAGAAAAAGATAAACCCAA 59.173 29.630 0.00 0.00 0.00 4.12
2001 4557 7.334858 AGTTGCAAAAGAAAAAGATAAACCCA 58.665 30.769 0.00 0.00 0.00 4.51
2002 4558 7.786178 AGTTGCAAAAGAAAAAGATAAACCC 57.214 32.000 0.00 0.00 0.00 4.11
2012 4568 9.956720 TCAAAATGAAAAAGTTGCAAAAGAAAA 57.043 22.222 0.00 0.00 0.00 2.29
2014 4570 9.771915 GATCAAAATGAAAAAGTTGCAAAAGAA 57.228 25.926 0.00 0.00 0.00 2.52
2015 4571 8.944029 TGATCAAAATGAAAAAGTTGCAAAAGA 58.056 25.926 0.00 0.00 0.00 2.52
2016 4572 9.557338 TTGATCAAAATGAAAAAGTTGCAAAAG 57.443 25.926 5.45 0.00 0.00 2.27
2018 4574 9.719279 GATTGATCAAAATGAAAAAGTTGCAAA 57.281 25.926 13.09 0.00 0.00 3.68
2019 4575 8.344098 GGATTGATCAAAATGAAAAAGTTGCAA 58.656 29.630 13.09 0.00 0.00 4.08
2020 4576 7.498239 TGGATTGATCAAAATGAAAAAGTTGCA 59.502 29.630 13.09 0.00 0.00 4.08
2021 4577 7.863666 TGGATTGATCAAAATGAAAAAGTTGC 58.136 30.769 13.09 0.00 0.00 4.17
2028 4584 9.947433 AGCTTTTATGGATTGATCAAAATGAAA 57.053 25.926 13.09 13.40 0.00 2.69
2029 4585 9.947433 AAGCTTTTATGGATTGATCAAAATGAA 57.053 25.926 13.09 7.15 0.00 2.57
2030 4586 9.590451 GAAGCTTTTATGGATTGATCAAAATGA 57.410 29.630 13.09 1.25 0.00 2.57
2031 4587 9.595823 AGAAGCTTTTATGGATTGATCAAAATG 57.404 29.630 13.09 4.75 0.00 2.32
2039 4595 9.920946 ACCTATTTAGAAGCTTTTATGGATTGA 57.079 29.630 0.00 0.00 0.00 2.57
2040 4596 9.956720 CACCTATTTAGAAGCTTTTATGGATTG 57.043 33.333 0.00 0.00 0.00 2.67
2041 4597 9.920946 TCACCTATTTAGAAGCTTTTATGGATT 57.079 29.630 0.00 0.00 0.00 3.01
2043 4599 9.342308 CATCACCTATTTAGAAGCTTTTATGGA 57.658 33.333 0.00 0.00 0.00 3.41
2044 4600 9.125026 ACATCACCTATTTAGAAGCTTTTATGG 57.875 33.333 0.00 2.81 0.00 2.74
2047 4603 8.956426 CCAACATCACCTATTTAGAAGCTTTTA 58.044 33.333 0.00 0.00 0.00 1.52
2048 4604 7.669722 TCCAACATCACCTATTTAGAAGCTTTT 59.330 33.333 0.00 0.00 0.00 2.27
2049 4605 7.175104 TCCAACATCACCTATTTAGAAGCTTT 58.825 34.615 0.00 0.00 0.00 3.51
2050 4606 6.721318 TCCAACATCACCTATTTAGAAGCTT 58.279 36.000 0.00 0.00 0.00 3.74
2051 4607 6.069963 ACTCCAACATCACCTATTTAGAAGCT 60.070 38.462 0.00 0.00 0.00 3.74
2052 4608 6.116126 ACTCCAACATCACCTATTTAGAAGC 58.884 40.000 0.00 0.00 0.00 3.86
2053 4609 8.567285 AAACTCCAACATCACCTATTTAGAAG 57.433 34.615 0.00 0.00 0.00 2.85
2054 4610 8.934023 AAAACTCCAACATCACCTATTTAGAA 57.066 30.769 0.00 0.00 0.00 2.10
2055 4611 8.792633 CAAAAACTCCAACATCACCTATTTAGA 58.207 33.333 0.00 0.00 0.00 2.10
2056 4612 8.028938 CCAAAAACTCCAACATCACCTATTTAG 58.971 37.037 0.00 0.00 0.00 1.85
2057 4613 7.524698 GCCAAAAACTCCAACATCACCTATTTA 60.525 37.037 0.00 0.00 0.00 1.40
2058 4614 6.741240 GCCAAAAACTCCAACATCACCTATTT 60.741 38.462 0.00 0.00 0.00 1.40
2059 4615 5.279456 GCCAAAAACTCCAACATCACCTATT 60.279 40.000 0.00 0.00 0.00 1.73
2060 4616 4.220602 GCCAAAAACTCCAACATCACCTAT 59.779 41.667 0.00 0.00 0.00 2.57
2061 4617 3.572255 GCCAAAAACTCCAACATCACCTA 59.428 43.478 0.00 0.00 0.00 3.08
2062 4618 2.365293 GCCAAAAACTCCAACATCACCT 59.635 45.455 0.00 0.00 0.00 4.00
2063 4619 2.365293 AGCCAAAAACTCCAACATCACC 59.635 45.455 0.00 0.00 0.00 4.02
2064 4620 3.733443 AGCCAAAAACTCCAACATCAC 57.267 42.857 0.00 0.00 0.00 3.06
2065 4621 3.960102 AGAAGCCAAAAACTCCAACATCA 59.040 39.130 0.00 0.00 0.00 3.07
2066 4622 4.037923 TCAGAAGCCAAAAACTCCAACATC 59.962 41.667 0.00 0.00 0.00 3.06
2067 4623 3.960102 TCAGAAGCCAAAAACTCCAACAT 59.040 39.130 0.00 0.00 0.00 2.71
2068 4624 3.360867 TCAGAAGCCAAAAACTCCAACA 58.639 40.909 0.00 0.00 0.00 3.33
2069 4625 4.037923 TCATCAGAAGCCAAAAACTCCAAC 59.962 41.667 0.00 0.00 0.00 3.77
2070 4626 4.214310 TCATCAGAAGCCAAAAACTCCAA 58.786 39.130 0.00 0.00 0.00 3.53
2071 4627 3.831323 TCATCAGAAGCCAAAAACTCCA 58.169 40.909 0.00 0.00 0.00 3.86
2072 4628 4.853924 TTCATCAGAAGCCAAAAACTCC 57.146 40.909 0.00 0.00 0.00 3.85
2073 4629 6.017400 TGATTCATCAGAAGCCAAAAACTC 57.983 37.500 0.00 0.00 39.36 3.01
2074 4630 6.409524 TTGATTCATCAGAAGCCAAAAACT 57.590 33.333 0.00 0.00 39.36 2.66
2075 4631 6.647895 ACATTGATTCATCAGAAGCCAAAAAC 59.352 34.615 0.00 0.00 39.36 2.43
2076 4632 6.761312 ACATTGATTCATCAGAAGCCAAAAA 58.239 32.000 0.00 0.00 39.36 1.94
2077 4633 6.349243 ACATTGATTCATCAGAAGCCAAAA 57.651 33.333 0.00 0.00 39.36 2.44
2078 4634 5.988310 ACATTGATTCATCAGAAGCCAAA 57.012 34.783 0.00 0.00 39.36 3.28
2079 4635 7.649533 ATTACATTGATTCATCAGAAGCCAA 57.350 32.000 0.00 0.00 39.36 4.52
2080 4636 8.750515 TTATTACATTGATTCATCAGAAGCCA 57.249 30.769 0.00 0.00 39.36 4.75
2113 4669 8.816640 TTTTAGAGCTTTTATGGCTTTTGAAG 57.183 30.769 0.00 0.00 40.40 3.02
2145 4701 7.882791 CCCAAAAGGCCATAAAAACTTCTAAAT 59.117 33.333 5.01 0.00 0.00 1.40
2188 4744 6.879458 TGTTTGGGCTTTTACTTTTGCTTTTA 59.121 30.769 0.00 0.00 0.00 1.52
2200 4756 3.471680 GCCATGTTTGTTTGGGCTTTTA 58.528 40.909 0.00 0.00 41.39 1.52
2216 4772 3.803082 CCACGCGTTGAGGCCATG 61.803 66.667 10.22 0.00 0.00 3.66
2227 4783 2.186644 TGGATCATGGTCCACGCG 59.813 61.111 24.31 3.53 43.20 6.01
2256 4965 6.875195 TGTCGGTCCGATTTTAACTCTAAAAT 59.125 34.615 18.75 3.18 46.01 1.82
2262 4971 4.259690 CGATTGTCGGTCCGATTTTAACTC 60.260 45.833 18.75 2.06 38.42 3.01
2270 4979 0.179119 GGTTCGATTGTCGGTCCGAT 60.179 55.000 18.75 0.35 40.88 4.18
2272 4981 2.156446 CGGTTCGATTGTCGGTCCG 61.156 63.158 4.39 4.39 44.11 4.79
2314 5023 1.997606 CTTCGTAAGGGTAGCCAAACG 59.002 52.381 24.12 24.12 38.47 3.60
2316 5025 2.773993 CCTTCGTAAGGGTAGCCAAA 57.226 50.000 14.62 0.00 45.27 3.28
2334 5043 6.293244 CGCAATGTAAATTAAGTAGCTACCCC 60.293 42.308 20.31 0.00 0.00 4.95
2396 5151 8.027524 TGCCATCCAATTAAATAAGGCAATTA 57.972 30.769 0.00 0.00 46.76 1.40
2426 5181 1.212935 CCACTGATTTCTAGGGTGGGG 59.787 57.143 0.00 0.00 42.39 4.96
2430 5185 3.803340 TCTTCCCACTGATTTCTAGGGT 58.197 45.455 0.00 0.00 40.48 4.34
2435 5190 5.339530 CCCACTAATCTTCCCACTGATTTCT 60.340 44.000 0.00 0.00 35.01 2.52
2443 5220 3.953542 AATCCCCACTAATCTTCCCAC 57.046 47.619 0.00 0.00 0.00 4.61
2444 5221 3.980698 CCTAATCCCCACTAATCTTCCCA 59.019 47.826 0.00 0.00 0.00 4.37
2521 5298 8.251721 ACTGTACCTTATTGTAGTTGCTCTAAG 58.748 37.037 0.00 0.00 0.00 2.18
2546 5323 6.689554 ACTTTACTCCTTACAGTCTGCTAAC 58.310 40.000 0.00 0.00 0.00 2.34
2548 5325 7.449395 TGTTACTTTACTCCTTACAGTCTGCTA 59.551 37.037 0.00 0.00 0.00 3.49
2605 5382 5.312895 AGAGCTCGCTTATATTCTCTCTCA 58.687 41.667 8.37 0.00 0.00 3.27
2616 5393 2.102084 TCTTGCATGAGAGCTCGCTTAT 59.898 45.455 18.64 1.65 34.99 1.73
2640 5417 1.254026 AGGAGCACGTGTTGTAGCTA 58.746 50.000 18.38 0.00 35.84 3.32
2667 5444 4.401022 TGGCAAATCTTTCACTCTCACAT 58.599 39.130 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.