Multiple sequence alignment - TraesCS4A01G038700

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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 TraesCS4A01G038700 chr4A 100.000 5008 0 0 1 5008 30774837 30779844 0.000000e+00 9249.0
1 TraesCS4A01G038700 chr4A 91.509 106 7 2 2392 2496 452252050 452252154 1.450000e-30 145.0
2 TraesCS4A01G038700 chr3D 93.212 2961 114 20 1 2925 482838223 482835314 0.000000e+00 4274.0
3 TraesCS4A01G038700 chr3D 97.059 1904 43 5 3107 5008 482835331 482833439 0.000000e+00 3193.0
4 TraesCS4A01G038700 chr3D 82.614 765 58 32 4244 4987 339862995 339862285 1.540000e-169 606.0
5 TraesCS4A01G038700 chr3D 92.029 138 11 0 2704 2841 590202087 590202224 1.420000e-45 195.0
6 TraesCS4A01G038700 chr3D 92.381 105 6 2 2394 2496 135533996 135534100 1.120000e-31 148.0
7 TraesCS4A01G038700 chr2B 95.903 1904 73 5 3107 5008 675713873 675715773 0.000000e+00 3079.0
8 TraesCS4A01G038700 chr2B 94.489 1506 56 10 3107 4608 601733709 601735191 0.000000e+00 2296.0
9 TraesCS4A01G038700 chr2B 92.418 976 59 3 965 1936 601730458 601731422 0.000000e+00 1378.0
10 TraesCS4A01G038700 chr2B 90.685 934 85 2 963 1895 663335699 663334767 0.000000e+00 1242.0
11 TraesCS4A01G038700 chr2B 94.560 625 20 5 2105 2716 601732563 601733186 0.000000e+00 953.0
12 TraesCS4A01G038700 chr2B 88.296 769 73 5 1 765 663336705 663335950 0.000000e+00 905.0
13 TraesCS4A01G038700 chr2B 86.331 695 49 7 295 966 601729757 601730428 0.000000e+00 715.0
14 TraesCS4A01G038700 chr2B 98.289 409 5 2 4600 5008 601737439 601737845 0.000000e+00 715.0
15 TraesCS4A01G038700 chr2B 85.605 521 46 12 1895 2405 663333944 663333443 2.070000e-143 520.0
16 TraesCS4A01G038700 chr2B 94.983 299 15 0 1 299 601720822 601721120 2.110000e-128 470.0
17 TraesCS4A01G038700 chr2B 98.942 189 2 0 2925 3113 368306164 368306352 6.210000e-89 339.0
18 TraesCS4A01G038700 chr2B 97.949 195 4 0 2925 3119 380067775 380067969 6.210000e-89 339.0
19 TraesCS4A01G038700 chr2B 97.938 194 2 1 2922 3115 599279024 599279215 8.030000e-88 335.0
20 TraesCS4A01G038700 chr2B 89.286 196 19 2 771 965 663335922 663335728 1.390000e-60 244.0
21 TraesCS4A01G038700 chr2B 98.765 81 0 1 2028 2107 601732056 601732136 5.230000e-30 143.0
22 TraesCS4A01G038700 chr2B 93.182 88 5 1 1930 2016 601731983 601732070 1.460000e-25 128.0
23 TraesCS4A01G038700 chr2B 93.243 74 5 0 2852 2925 601733653 601733726 5.300000e-20 110.0
24 TraesCS4A01G038700 chr4B 94.280 1923 73 15 3107 5008 22447480 22445574 0.000000e+00 2907.0
25 TraesCS4A01G038700 chr4B 93.792 451 14 5 2236 2674 22448065 22447617 0.000000e+00 665.0
26 TraesCS4A01G038700 chr4B 95.775 71 3 0 2855 2925 22447533 22447463 1.140000e-21 115.0
27 TraesCS4A01G038700 chr6A 93.364 1763 82 14 963 2716 561590949 561589213 0.000000e+00 2575.0
28 TraesCS4A01G038700 chr6A 93.193 1763 85 14 963 2716 561449689 561451425 0.000000e+00 2558.0
29 TraesCS4A01G038700 chr6A 92.626 1763 95 5 963 2716 561604206 561602470 0.000000e+00 2503.0
30 TraesCS4A01G038700 chr6A 90.264 832 60 2 152 962 561448826 561449657 0.000000e+00 1068.0
31 TraesCS4A01G038700 chr6A 90.048 834 63 2 152 965 561605068 561604235 0.000000e+00 1062.0
32 TraesCS4A01G038700 chr6A 97.190 605 15 2 3107 3709 561602084 561601480 0.000000e+00 1022.0
33 TraesCS4A01G038700 chr6A 97.025 605 16 2 3107 3709 561588828 561588224 0.000000e+00 1016.0
34 TraesCS4A01G038700 chr6A 96.860 605 17 2 3107 3709 561451810 561452414 0.000000e+00 1011.0
35 TraesCS4A01G038700 chr6A 87.062 371 27 2 616 965 561591348 561590978 2.810000e-107 399.0
36 TraesCS4A01G038700 chr6A 97.959 196 2 2 2925 3120 233342580 233342387 6.210000e-89 339.0
37 TraesCS4A01G038700 chr6A 93.711 159 10 0 1 159 561605404 561605246 6.480000e-59 239.0
38 TraesCS4A01G038700 chr6A 92.500 160 10 2 1 159 561448490 561448648 1.400000e-55 228.0
39 TraesCS4A01G038700 chr6A 91.791 134 11 0 2708 2841 7971128 7970995 2.380000e-43 187.0
40 TraesCS4A01G038700 chr6A 90.977 133 10 1 2709 2841 9580525 9580655 1.430000e-40 178.0
41 TraesCS4A01G038700 chr6A 95.946 74 3 0 2852 2925 561451754 561451827 2.450000e-23 121.0
42 TraesCS4A01G038700 chr6A 97.183 71 2 0 2855 2925 561588881 561588811 2.450000e-23 121.0
43 TraesCS4A01G038700 chr6A 95.775 71 3 0 2855 2925 561602137 561602067 1.140000e-21 115.0
44 TraesCS4A01G038700 chr2D 93.382 1632 82 8 3397 5008 564470776 564472401 0.000000e+00 2392.0
45 TraesCS4A01G038700 chr2D 90.285 1791 83 16 963 2716 564468398 564470134 0.000000e+00 2259.0
46 TraesCS4A01G038700 chr2D 95.068 1318 43 9 3548 4855 601807189 601805884 0.000000e+00 2054.0
47 TraesCS4A01G038700 chr2D 91.565 984 61 3 1 962 564467383 564468366 0.000000e+00 1338.0
48 TraesCS4A01G038700 chr2D 89.113 992 73 12 1 962 556220654 556221640 0.000000e+00 1201.0
49 TraesCS4A01G038700 chr2D 89.373 941 83 5 963 1895 556221672 556222603 0.000000e+00 1168.0
50 TraesCS4A01G038700 chr2D 97.105 449 11 2 3141 3588 601807632 601807185 0.000000e+00 756.0
51 TraesCS4A01G038700 chr2D 89.060 521 42 7 1895 2405 556223391 556223906 2.540000e-177 632.0
52 TraesCS4A01G038700 chr2D 96.350 274 9 1 3109 3381 564470521 564470794 2.750000e-122 449.0
53 TraesCS4A01G038700 chr2D 98.065 155 3 0 4854 5008 601805782 601805628 2.300000e-68 270.0
54 TraesCS4A01G038700 chr2D 87.805 205 13 5 4800 4996 43956766 43956566 3.900000e-56 230.0
55 TraesCS4A01G038700 chr2D 91.892 74 6 0 2852 2925 564470463 564470536 2.470000e-18 104.0
56 TraesCS4A01G038700 chr2A 89.925 933 83 4 963 1895 695817457 695818378 0.000000e+00 1192.0
57 TraesCS4A01G038700 chr2A 87.867 989 85 12 1 961 695816443 695817424 0.000000e+00 1129.0
58 TraesCS4A01G038700 chr2A 90.289 762 65 4 1 758 695973842 695974598 0.000000e+00 989.0
59 TraesCS4A01G038700 chr2A 90.831 698 56 4 963 1660 695974864 695975553 0.000000e+00 928.0
60 TraesCS4A01G038700 chr2A 88.868 521 43 7 1895 2405 695977128 695977643 1.180000e-175 627.0
61 TraesCS4A01G038700 chr2A 88.676 521 44 7 1895 2405 695819148 695819663 5.510000e-174 621.0
62 TraesCS4A01G038700 chr2A 90.104 192 18 1 771 961 695974643 695974834 1.080000e-61 248.0
63 TraesCS4A01G038700 chr2A 95.302 149 6 1 4860 5008 46318502 46318355 8.380000e-58 235.0
64 TraesCS4A01G038700 chr2A 91.045 134 10 1 2708 2841 545064927 545064796 3.980000e-41 180.0
65 TraesCS4A01G038700 chr2A 76.638 351 44 27 3280 3614 79344248 79344576 5.190000e-35 159.0
66 TraesCS4A01G038700 chr3B 84.615 780 72 30 4247 5004 438581756 438581003 0.000000e+00 732.0
67 TraesCS4A01G038700 chr3B 98.438 192 3 0 2917 3108 393642547 393642738 6.210000e-89 339.0
68 TraesCS4A01G038700 chr3B 94.815 135 6 1 2707 2841 2021646 2021779 5.080000e-50 209.0
69 TraesCS4A01G038700 chr3A 82.835 769 64 29 4254 5005 464895710 464896427 1.180000e-175 627.0
70 TraesCS4A01G038700 chr3A 91.089 101 7 2 2403 2501 516801727 516801827 8.750000e-28 135.0
71 TraesCS4A01G038700 chr1A 98.958 192 1 1 2925 3116 3675288 3675098 4.800000e-90 342.0
72 TraesCS4A01G038700 chr7B 98.947 190 1 1 2922 3111 619432577 619432389 6.210000e-89 339.0
73 TraesCS4A01G038700 chr7B 91.791 134 11 0 2708 2841 152051179 152051046 2.380000e-43 187.0
74 TraesCS4A01G038700 chr7B 89.720 107 7 4 2403 2507 33806926 33807030 3.150000e-27 134.0
75 TraesCS4A01G038700 chr5A 97.938 194 3 1 2925 3118 464473865 464473673 8.030000e-88 335.0
76 TraesCS4A01G038700 chr1B 97.927 193 4 0 2925 3117 166589488 166589296 8.030000e-88 335.0
77 TraesCS4A01G038700 chr1B 91.111 135 12 0 2707 2841 285341086 285341220 3.080000e-42 183.0
78 TraesCS4A01G038700 chr6B 81.459 329 47 12 1436 1754 415777383 415777707 1.790000e-64 257.0
79 TraesCS4A01G038700 chr6B 91.791 134 11 0 2708 2841 415877818 415877685 2.380000e-43 187.0
80 TraesCS4A01G038700 chr5B 87.500 96 9 3 3043 3136 577021702 577021796 1.910000e-19 108.0
81 TraesCS4A01G038700 chr6D 97.619 42 1 0 4608 4649 428290165 428290206 6.950000e-09 73.1


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 TraesCS4A01G038700 chr4A 30774837 30779844 5007 False 9249.000000 9249 100.000000 1 5008 1 chr4A.!!$F1 5007
1 TraesCS4A01G038700 chr3D 482833439 482838223 4784 True 3733.500000 4274 95.135500 1 5008 2 chr3D.!!$R2 5007
2 TraesCS4A01G038700 chr3D 339862285 339862995 710 True 606.000000 606 82.614000 4244 4987 1 chr3D.!!$R1 743
3 TraesCS4A01G038700 chr2B 675713873 675715773 1900 False 3079.000000 3079 95.903000 3107 5008 1 chr2B.!!$F5 1901
4 TraesCS4A01G038700 chr2B 601729757 601737845 8088 False 804.750000 2296 93.909625 295 5008 8 chr2B.!!$F6 4713
5 TraesCS4A01G038700 chr2B 663333443 663336705 3262 True 727.750000 1242 88.468000 1 2405 4 chr2B.!!$R1 2404
6 TraesCS4A01G038700 chr4B 22445574 22448065 2491 True 1229.000000 2907 94.615667 2236 5008 3 chr4B.!!$R1 2772
7 TraesCS4A01G038700 chr6A 561588224 561591348 3124 True 1027.750000 2575 93.658500 616 3709 4 chr6A.!!$R3 3093
8 TraesCS4A01G038700 chr6A 561448490 561452414 3924 False 997.200000 2558 93.752600 1 3709 5 chr6A.!!$F2 3708
9 TraesCS4A01G038700 chr6A 561601480 561605404 3924 True 988.200000 2503 93.870000 1 3709 5 chr6A.!!$R4 3708
10 TraesCS4A01G038700 chr2D 564467383 564472401 5018 False 1308.400000 2392 92.694800 1 5008 5 chr2D.!!$F2 5007
11 TraesCS4A01G038700 chr2D 601805628 601807632 2004 True 1026.666667 2054 96.746000 3141 5008 3 chr2D.!!$R2 1867
12 TraesCS4A01G038700 chr2D 556220654 556223906 3252 False 1000.333333 1201 89.182000 1 2405 3 chr2D.!!$F1 2404
13 TraesCS4A01G038700 chr2A 695816443 695819663 3220 False 980.666667 1192 88.822667 1 2405 3 chr2A.!!$F2 2404
14 TraesCS4A01G038700 chr2A 695973842 695977643 3801 False 698.000000 989 90.023000 1 2405 4 chr2A.!!$F3 2404
15 TraesCS4A01G038700 chr3B 438581003 438581756 753 True 732.000000 732 84.615000 4247 5004 1 chr3B.!!$R1 757
16 TraesCS4A01G038700 chr3A 464895710 464896427 717 False 627.000000 627 82.835000 4254 5005 1 chr3A.!!$F1 751

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
817 1056 0.464036 GATAGGTCGACATGTGCCCA 59.536 55.0 18.91 0.0 0.00 5.36 F
2007 4292 0.798776 GGTTGCACGACTGAATCTGG 59.201 55.0 0.00 0.0 0.00 3.86 F
2736 5520 1.012486 AAAGCGTCCCTAAAGCGTCG 61.012 55.0 0.00 0.0 37.45 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2754 5538 1.153349 GACGCCTTAAGCCTGGAGG 60.153 63.158 0.00 0.0 38.78 4.30 R
2923 6040 0.105964 TGCACCAGGTTGCCCTTTTA 60.106 50.000 10.46 0.0 42.25 1.52 R
4442 7622 0.536260 AAGGCACAAACAAAGCTGCA 59.464 45.000 1.02 0.0 0.00 4.41 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
25 26 2.765699 GGCTTCCAAGATCTCTCAGACT 59.234 50.000 0.00 0.00 0.00 3.24
58 60 0.749091 TTGATGAAGGGCGGCAGATG 60.749 55.000 12.47 0.00 0.00 2.90
137 139 4.457257 GCCAAAGCAATCTTGAAGTAGTCT 59.543 41.667 0.00 0.00 39.53 3.24
163 350 3.322466 CCGGAGCTGGAGGTTGGT 61.322 66.667 0.00 0.00 0.00 3.67
242 431 5.576447 ATCAAAACAACTCGAAGTTTGGT 57.424 34.783 10.02 0.00 36.03 3.67
299 490 1.451927 GGCGATGTGGAGAATGGCA 60.452 57.895 0.00 0.00 31.07 4.92
472 663 2.171448 CCTCCATTGAAGTACCTCCCAG 59.829 54.545 0.00 0.00 0.00 4.45
657 854 4.473520 CGGCTCGCTTGGGTGGAT 62.474 66.667 0.00 0.00 0.00 3.41
729 935 2.285743 ACAGGGGAGGGAGAAGCC 60.286 66.667 0.00 0.00 0.00 4.35
734 940 1.076192 GGGAGGGAGAAGCCGTAGA 60.076 63.158 0.00 0.00 37.63 2.59
766 981 0.842467 AGGAACAGAGGAAGTGGGGG 60.842 60.000 0.00 0.00 0.00 5.40
769 984 1.423921 GAACAGAGGAAGTGGGGGAAA 59.576 52.381 0.00 0.00 0.00 3.13
817 1056 0.464036 GATAGGTCGACATGTGCCCA 59.536 55.000 18.91 0.00 0.00 5.36
827 1066 2.562298 GACATGTGCCCAATTTCCTTCA 59.438 45.455 1.15 0.00 0.00 3.02
925 1166 2.708325 ACTGGCCATCTCCCTATCTTTC 59.292 50.000 5.51 0.00 0.00 2.62
936 1177 3.384789 TCCCTATCTTTCGACAGTGATGG 59.615 47.826 0.00 0.00 0.00 3.51
1108 1380 2.338577 AGATGCAAAGCCGCTAGATT 57.661 45.000 0.00 0.00 0.00 2.40
1195 1467 5.681437 GCCAAGTACATAGATTTCGAGGTCA 60.681 44.000 0.00 0.00 0.00 4.02
1226 1498 2.360801 GAGCTAGACTGTCTCCATCACC 59.639 54.545 14.62 0.00 0.00 4.02
1440 1712 7.417797 GCTTGGAGATAAAATTTATCCTTGGCA 60.418 37.037 18.92 5.12 0.00 4.92
1461 1733 1.271762 TGCAAGCCAAGAAGCTCTCAT 60.272 47.619 0.00 0.00 44.11 2.90
1629 1902 5.307716 ACTCCCACATCAATCCAAAACAAAT 59.692 36.000 0.00 0.00 0.00 2.32
1745 2603 2.036733 CTGGGTCACTGACGGTTTTCTA 59.963 50.000 3.04 0.00 32.65 2.10
1780 2655 6.670464 TGGTACTCTGGTAATGAGTTGGAATA 59.330 38.462 1.67 0.00 41.45 1.75
1843 2730 5.603395 TCGGTCCATTATATGTACCCTTGAA 59.397 40.000 0.00 0.00 36.02 2.69
1846 2733 6.409925 GGTCCATTATATGTACCCTTGAACCA 60.410 42.308 0.00 0.00 33.54 3.67
1901 3618 9.799106 CATGATATATTTAGGAGGTTTGGTCTT 57.201 33.333 0.00 0.00 0.00 3.01
1995 4280 1.081242 CTCCATGCGTTGGTTGCAC 60.081 57.895 5.49 0.00 46.57 4.57
2005 4290 1.873591 GTTGGTTGCACGACTGAATCT 59.126 47.619 0.00 0.00 0.00 2.40
2006 4291 1.511850 TGGTTGCACGACTGAATCTG 58.488 50.000 0.00 0.00 0.00 2.90
2007 4292 0.798776 GGTTGCACGACTGAATCTGG 59.201 55.000 0.00 0.00 0.00 3.86
2008 4293 1.512926 GTTGCACGACTGAATCTGGT 58.487 50.000 0.00 0.00 0.00 4.00
2009 4294 2.611971 GGTTGCACGACTGAATCTGGTA 60.612 50.000 0.00 0.00 0.00 3.25
2010 4295 3.262420 GTTGCACGACTGAATCTGGTAT 58.738 45.455 0.00 0.00 0.00 2.73
2011 4296 4.430007 GTTGCACGACTGAATCTGGTATA 58.570 43.478 0.00 0.00 0.00 1.47
2012 4297 4.937201 TGCACGACTGAATCTGGTATAT 57.063 40.909 0.00 0.00 0.00 0.86
2013 4298 4.620982 TGCACGACTGAATCTGGTATATG 58.379 43.478 0.00 0.00 0.00 1.78
2014 4299 3.990469 GCACGACTGAATCTGGTATATGG 59.010 47.826 0.00 0.00 0.00 2.74
2015 4300 4.262036 GCACGACTGAATCTGGTATATGGA 60.262 45.833 0.00 0.00 0.00 3.41
2016 4301 5.567623 GCACGACTGAATCTGGTATATGGAT 60.568 44.000 0.00 0.00 0.00 3.41
2017 4302 6.350194 GCACGACTGAATCTGGTATATGGATA 60.350 42.308 0.00 0.00 0.00 2.59
2018 4303 7.631594 GCACGACTGAATCTGGTATATGGATAT 60.632 40.741 0.00 0.00 0.00 1.63
2019 4304 8.903820 CACGACTGAATCTGGTATATGGATATA 58.096 37.037 0.00 0.00 0.00 0.86
2020 4305 9.126151 ACGACTGAATCTGGTATATGGATATAG 57.874 37.037 0.00 0.00 0.00 1.31
2021 4306 9.126151 CGACTGAATCTGGTATATGGATATAGT 57.874 37.037 0.00 0.00 0.00 2.12
2160 4898 9.102757 GATTCTTATTGTAGCAGTTGATCTTGA 57.897 33.333 0.00 0.00 0.00 3.02
2347 5091 7.963532 TGAACTACTCATCAACCTAGAACTTT 58.036 34.615 0.00 0.00 0.00 2.66
2396 5140 6.128063 CCTTCTCGATTCAGCTTCTTCATTTT 60.128 38.462 0.00 0.00 0.00 1.82
2401 5145 6.149973 TCGATTCAGCTTCTTCATTTTCACAT 59.850 34.615 0.00 0.00 0.00 3.21
2503 5269 7.643123 AGGGAGTACAATTTAGTCCATGATTT 58.357 34.615 16.66 0.00 38.49 2.17
2666 5443 9.003658 CACTCAACCTTGATATAAGAAGTGTTT 57.996 33.333 0.00 0.00 36.46 2.83
2735 5519 1.657594 GTAAAGCGTCCCTAAAGCGTC 59.342 52.381 0.00 0.00 37.45 5.19
2736 5520 1.012486 AAAGCGTCCCTAAAGCGTCG 61.012 55.000 0.00 0.00 37.45 5.12
2754 5538 2.082354 GCTTAAGTGTCAGAGCGCC 58.918 57.895 2.29 0.00 0.00 6.53
2916 6033 9.798994 ATGCAAATCAGTTGATAAATCTCTTTC 57.201 29.630 0.00 0.00 39.87 2.62
2917 6034 8.795513 TGCAAATCAGTTGATAAATCTCTTTCA 58.204 29.630 0.00 0.00 39.87 2.69
2918 6035 9.630098 GCAAATCAGTTGATAAATCTCTTTCAA 57.370 29.630 0.00 0.00 39.87 2.69
2922 6039 8.924511 TCAGTTGATAAATCTCTTTCAAACCT 57.075 30.769 0.00 0.00 0.00 3.50
2923 6040 9.354673 TCAGTTGATAAATCTCTTTCAAACCTT 57.645 29.630 0.00 0.00 0.00 3.50
2946 6063 4.413928 GGCAACCTGGTGCATGTA 57.586 55.556 18.44 0.00 46.81 2.29
2947 6064 2.183409 GGCAACCTGGTGCATGTAG 58.817 57.895 18.44 0.00 46.81 2.74
2948 6065 1.508088 GCAACCTGGTGCATGTAGC 59.492 57.895 6.00 6.00 44.29 3.58
2949 6066 0.962356 GCAACCTGGTGCATGTAGCT 60.962 55.000 14.15 0.00 44.29 3.32
2950 6067 1.089920 CAACCTGGTGCATGTAGCTC 58.910 55.000 14.15 0.00 45.94 4.09
2956 6073 1.450312 GTGCATGTAGCTCCCGCTT 60.450 57.895 0.00 0.00 46.47 4.68
2957 6074 1.450134 TGCATGTAGCTCCCGCTTG 60.450 57.895 0.00 0.00 46.47 4.01
2958 6075 2.828128 GCATGTAGCTCCCGCTTGC 61.828 63.158 0.00 0.00 46.47 4.01
2959 6076 2.202932 ATGTAGCTCCCGCTTGCG 60.203 61.111 8.14 8.14 46.47 4.85
2962 6079 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
2974 6091 4.785453 GCGCAGGGTCCAGGGAAG 62.785 72.222 0.30 0.00 0.00 3.46
2975 6092 4.101448 CGCAGGGTCCAGGGAAGG 62.101 72.222 0.00 0.00 0.00 3.46
2976 6093 3.732849 GCAGGGTCCAGGGAAGGG 61.733 72.222 0.00 0.00 0.00 3.95
2977 6094 2.204151 CAGGGTCCAGGGAAGGGT 60.204 66.667 0.00 0.00 0.00 4.34
2978 6095 2.125225 AGGGTCCAGGGAAGGGTC 59.875 66.667 0.00 0.00 0.00 4.46
2979 6096 3.015753 GGGTCCAGGGAAGGGTCC 61.016 72.222 0.00 0.00 44.10 4.46
2980 6097 3.400054 GGTCCAGGGAAGGGTCCG 61.400 72.222 0.00 0.00 46.04 4.79
2981 6098 2.284405 GTCCAGGGAAGGGTCCGA 60.284 66.667 0.00 0.00 46.04 4.55
2982 6099 2.284405 TCCAGGGAAGGGTCCGAC 60.284 66.667 0.00 0.00 46.04 4.79
2983 6100 3.400054 CCAGGGAAGGGTCCGACC 61.400 72.222 9.30 9.30 46.04 4.79
2984 6101 2.606519 CAGGGAAGGGTCCGACCA 60.607 66.667 19.43 0.00 46.04 4.02
2985 6102 2.606826 AGGGAAGGGTCCGACCAC 60.607 66.667 19.43 8.70 46.04 4.16
2986 6103 2.606826 GGGAAGGGTCCGACCACT 60.607 66.667 19.43 10.80 46.04 4.00
2987 6104 2.222013 GGGAAGGGTCCGACCACTT 61.222 63.158 19.43 17.88 46.04 3.16
2988 6105 1.759236 GGAAGGGTCCGACCACTTT 59.241 57.895 19.43 9.96 41.02 2.66
2989 6106 0.605589 GGAAGGGTCCGACCACTTTG 60.606 60.000 19.43 0.00 41.02 2.77
2990 6107 0.605589 GAAGGGTCCGACCACTTTGG 60.606 60.000 19.43 0.00 41.02 3.28
2991 6108 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
2992 6109 2.826003 GGGTCCGACCACTTTGGGT 61.826 63.158 19.43 0.00 43.37 4.51
3003 6120 4.700700 ACCACTTTGGGTCTATATTACGC 58.299 43.478 0.00 0.00 43.37 4.42
3004 6121 4.162698 ACCACTTTGGGTCTATATTACGCA 59.837 41.667 0.00 4.23 43.37 5.24
3005 6122 4.750098 CCACTTTGGGTCTATATTACGCAG 59.250 45.833 7.42 2.21 40.36 5.18
3006 6123 4.211374 CACTTTGGGTCTATATTACGCAGC 59.789 45.833 7.42 0.00 40.36 5.25
3007 6124 3.396260 TTGGGTCTATATTACGCAGCC 57.604 47.619 7.42 0.00 40.36 4.85
3008 6125 2.605257 TGGGTCTATATTACGCAGCCT 58.395 47.619 4.23 0.00 35.18 4.58
3009 6126 2.969950 TGGGTCTATATTACGCAGCCTT 59.030 45.455 4.23 0.00 35.18 4.35
3010 6127 3.389983 TGGGTCTATATTACGCAGCCTTT 59.610 43.478 4.23 0.00 35.18 3.11
3011 6128 3.995048 GGGTCTATATTACGCAGCCTTTC 59.005 47.826 0.00 0.00 0.00 2.62
3012 6129 3.995048 GGTCTATATTACGCAGCCTTTCC 59.005 47.826 0.00 0.00 0.00 3.13
3013 6130 3.995048 GTCTATATTACGCAGCCTTTCCC 59.005 47.826 0.00 0.00 0.00 3.97
3014 6131 3.901844 TCTATATTACGCAGCCTTTCCCT 59.098 43.478 0.00 0.00 0.00 4.20
3015 6132 5.047519 GTCTATATTACGCAGCCTTTCCCTA 60.048 44.000 0.00 0.00 0.00 3.53
3016 6133 2.327200 ATTACGCAGCCTTTCCCTAC 57.673 50.000 0.00 0.00 0.00 3.18
3017 6134 0.978151 TTACGCAGCCTTTCCCTACA 59.022 50.000 0.00 0.00 0.00 2.74
3018 6135 1.200519 TACGCAGCCTTTCCCTACAT 58.799 50.000 0.00 0.00 0.00 2.29
3019 6136 0.328258 ACGCAGCCTTTCCCTACATT 59.672 50.000 0.00 0.00 0.00 2.71
3020 6137 1.271926 ACGCAGCCTTTCCCTACATTT 60.272 47.619 0.00 0.00 0.00 2.32
3021 6138 1.401905 CGCAGCCTTTCCCTACATTTC 59.598 52.381 0.00 0.00 0.00 2.17
3022 6139 2.728007 GCAGCCTTTCCCTACATTTCT 58.272 47.619 0.00 0.00 0.00 2.52
3023 6140 2.424956 GCAGCCTTTCCCTACATTTCTG 59.575 50.000 0.00 0.00 0.00 3.02
3024 6141 3.690460 CAGCCTTTCCCTACATTTCTGT 58.310 45.455 0.00 0.00 39.49 3.41
3025 6142 4.843728 CAGCCTTTCCCTACATTTCTGTA 58.156 43.478 0.00 0.00 36.79 2.74
3026 6143 5.253330 CAGCCTTTCCCTACATTTCTGTAA 58.747 41.667 0.00 0.00 37.41 2.41
3027 6144 5.355350 CAGCCTTTCCCTACATTTCTGTAAG 59.645 44.000 0.00 0.00 37.41 2.34
3028 6145 5.250774 AGCCTTTCCCTACATTTCTGTAAGA 59.749 40.000 0.00 0.00 44.68 2.10
3040 6157 3.685139 TCTGTAAGAGGCTGTTTCCAG 57.315 47.619 0.90 9.48 38.67 3.86
3041 6158 2.303022 TCTGTAAGAGGCTGTTTCCAGG 59.697 50.000 17.71 5.83 38.67 4.45
3042 6159 2.303022 CTGTAAGAGGCTGTTTCCAGGA 59.697 50.000 0.90 0.00 35.89 3.86
3043 6160 2.038557 TGTAAGAGGCTGTTTCCAGGAC 59.961 50.000 0.90 0.00 39.22 3.85
3044 6161 1.439543 AAGAGGCTGTTTCCAGGACT 58.560 50.000 0.00 0.00 39.22 3.85
3045 6162 1.439543 AGAGGCTGTTTCCAGGACTT 58.560 50.000 0.00 0.00 39.22 3.01
3046 6163 1.072965 AGAGGCTGTTTCCAGGACTTG 59.927 52.381 0.00 0.00 39.22 3.16
3047 6164 1.072331 GAGGCTGTTTCCAGGACTTGA 59.928 52.381 0.00 0.00 39.22 3.02
3048 6165 1.494721 AGGCTGTTTCCAGGACTTGAA 59.505 47.619 0.00 0.00 39.22 2.69
3049 6166 1.609072 GGCTGTTTCCAGGACTTGAAC 59.391 52.381 0.00 0.00 39.22 3.18
3050 6167 1.609072 GCTGTTTCCAGGACTTGAACC 59.391 52.381 0.00 0.00 39.22 3.62
3051 6168 2.230660 CTGTTTCCAGGACTTGAACCC 58.769 52.381 0.00 0.00 34.90 4.11
3052 6169 1.566703 TGTTTCCAGGACTTGAACCCA 59.433 47.619 0.00 0.00 0.00 4.51
3053 6170 2.176798 TGTTTCCAGGACTTGAACCCAT 59.823 45.455 0.00 0.00 0.00 4.00
3054 6171 2.558359 GTTTCCAGGACTTGAACCCATG 59.442 50.000 0.00 0.00 0.00 3.66
3055 6172 1.741028 TCCAGGACTTGAACCCATGA 58.259 50.000 0.00 0.00 0.00 3.07
3056 6173 1.351017 TCCAGGACTTGAACCCATGAC 59.649 52.381 0.00 0.00 0.00 3.06
3057 6174 1.614317 CCAGGACTTGAACCCATGACC 60.614 57.143 0.00 0.00 34.29 4.02
3058 6175 1.352352 CAGGACTTGAACCCATGACCT 59.648 52.381 0.00 0.00 40.96 3.85
3059 6176 1.630878 AGGACTTGAACCCATGACCTC 59.369 52.381 0.00 0.00 37.82 3.85
3060 6177 1.351017 GGACTTGAACCCATGACCTCA 59.649 52.381 0.00 0.00 32.45 3.86
3061 6178 2.025887 GGACTTGAACCCATGACCTCAT 60.026 50.000 0.00 0.00 36.96 2.90
3073 6190 2.154139 ACCTCATGGTCACAAGGCA 58.846 52.632 0.00 0.00 44.78 4.75
3074 6191 0.037303 ACCTCATGGTCACAAGGCAG 59.963 55.000 0.00 0.00 44.78 4.85
3075 6192 1.310933 CCTCATGGTCACAAGGCAGC 61.311 60.000 0.00 0.00 0.00 5.25
3076 6193 0.607217 CTCATGGTCACAAGGCAGCA 60.607 55.000 0.00 0.00 0.00 4.41
3077 6194 0.607217 TCATGGTCACAAGGCAGCAG 60.607 55.000 0.00 0.00 0.00 4.24
3078 6195 1.975407 ATGGTCACAAGGCAGCAGC 60.975 57.895 0.00 0.00 41.10 5.25
3079 6196 2.282040 GGTCACAAGGCAGCAGCT 60.282 61.111 0.00 0.00 41.70 4.24
3080 6197 1.900498 GGTCACAAGGCAGCAGCTT 60.900 57.895 0.00 0.00 41.70 3.74
3081 6198 1.458639 GGTCACAAGGCAGCAGCTTT 61.459 55.000 0.00 0.00 41.17 3.51
3082 6199 1.238439 GTCACAAGGCAGCAGCTTTA 58.762 50.000 0.00 0.00 38.07 1.85
3083 6200 1.068954 GTCACAAGGCAGCAGCTTTAC 60.069 52.381 0.00 0.00 38.07 2.01
3084 6201 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
3085 6202 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
3086 6203 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
3087 6204 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
3088 6205 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
3092 6209 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
3093 6210 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
3094 6211 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
3095 6212 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
3096 6213 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
3097 6214 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
3098 6215 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
3099 6216 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
3326 6447 4.100808 GCCTCCTACAGATCTCTTTGTCAT 59.899 45.833 0.00 0.00 0.00 3.06
3353 6474 4.575885 TGTACTGGTGGTCTTTAATCTGC 58.424 43.478 0.00 0.00 0.00 4.26
3567 6725 7.363530 GGAACAGTAGTAGGTGTCATTGTCATA 60.364 40.741 0.00 0.00 0.00 2.15
3617 6783 4.906618 TGGTAAAAGATGGTCTGAACTCC 58.093 43.478 0.00 0.00 0.00 3.85
3685 6851 8.546597 TCAGATAATTCAGTTCGTTCATTTCA 57.453 30.769 0.00 0.00 0.00 2.69
3763 6929 4.083862 GCCCGCCTCTTCCGACTT 62.084 66.667 0.00 0.00 0.00 3.01
3819 6985 1.126113 CCACGACAGTAACAACGATGC 59.874 52.381 0.00 0.00 0.00 3.91
3875 7041 1.339727 CGACTCCCCTCCCGAAATTTT 60.340 52.381 0.00 0.00 0.00 1.82
3905 7071 9.904198 TGTTACTTTCTTGATCATGGATTCATA 57.096 29.630 8.60 0.00 31.33 2.15
3918 7084 6.214005 TCATGGATTCATAGTGCTGATATCCA 59.786 38.462 14.23 14.23 41.54 3.41
3919 7085 6.438186 TGGATTCATAGTGCTGATATCCAA 57.562 37.500 0.00 0.00 38.46 3.53
3963 7129 7.233348 AGCAAATATGGTCAATGGGTAATAAGG 59.767 37.037 0.00 0.00 29.35 2.69
3991 7158 2.282745 GCCTTCCTGTTGGCTGCT 60.283 61.111 0.00 0.00 45.26 4.24
4036 7203 3.002246 TCAGCACGTGAACTTTGAATCAC 59.998 43.478 22.23 0.00 41.95 3.06
4122 7289 2.668457 GACCATATATGCACGCAGCTAC 59.332 50.000 7.24 0.00 45.94 3.58
4541 7721 9.243637 GTCTAAAAATGTATCTTGTTTGTGCAA 57.756 29.630 0.00 0.00 0.00 4.08
4784 10243 1.614824 AGGCCCTAGTTGCTGCTCT 60.615 57.895 0.00 2.21 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.634973 TCATCAATGAGCCACCCAAGA 59.365 47.619 0.00 0.00 32.11 3.02
58 60 2.190578 CTTCGGGGCTCATGGGAC 59.809 66.667 0.00 0.00 0.00 4.46
163 350 1.609635 TATCCGCGACCTTGAAGGCA 61.610 55.000 11.96 0.00 39.63 4.75
242 431 2.159382 GAATGCTTCCTTGGGACGAAA 58.841 47.619 0.00 0.00 0.00 3.46
263 454 1.963515 GCCAACTTCATCACCCTTTGT 59.036 47.619 0.00 0.00 0.00 2.83
299 490 3.579586 AGTTGCATCATTTGACACCCAAT 59.420 39.130 0.00 0.00 34.23 3.16
346 537 1.229428 GCTAGACAGCTTTGTGTGCA 58.771 50.000 0.00 0.00 44.93 4.57
472 663 0.603975 AAGACGACTTTCTGCTGCCC 60.604 55.000 0.00 0.00 31.71 5.36
542 739 3.423154 GGACAACGCTTCCGCCAG 61.423 66.667 0.00 0.00 38.22 4.85
657 854 2.576648 GAGCCCTCCCTTTCTTTCCTTA 59.423 50.000 0.00 0.00 0.00 2.69
688 894 1.743623 CCGCCATTGTCGCAACCTA 60.744 57.895 0.00 0.00 0.00 3.08
691 897 1.442017 GAACCGCCATTGTCGCAAC 60.442 57.895 0.00 0.00 0.00 4.17
729 935 2.049475 CTCTCGCGGAACCCTCTACG 62.049 65.000 6.13 0.00 0.00 3.51
734 940 2.283676 TTCCTCTCGCGGAACCCT 60.284 61.111 6.13 0.00 38.12 4.34
738 944 1.595993 CCTCTGTTCCTCTCGCGGAA 61.596 60.000 6.13 0.00 40.64 4.30
741 947 0.179150 CTTCCTCTGTTCCTCTCGCG 60.179 60.000 0.00 0.00 0.00 5.87
766 981 0.179012 TGGGTTTCTCGGTGGGTTTC 60.179 55.000 0.00 0.00 0.00 2.78
769 984 1.454539 CTTGGGTTTCTCGGTGGGT 59.545 57.895 0.00 0.00 0.00 4.51
777 1016 3.443588 GCCGTTGCTTGGGTTTCT 58.556 55.556 0.00 0.00 33.53 2.52
799 1038 0.908910 TTGGGCACATGTCGACCTAT 59.091 50.000 14.12 0.00 0.00 2.57
888 1127 0.934496 CAGTCGGTTTCGCTTTGACA 59.066 50.000 0.00 0.00 36.13 3.58
925 1166 1.884464 CATCCCGCCATCACTGTCG 60.884 63.158 0.00 0.00 0.00 4.35
936 1177 1.970917 CTCGCTTTGTCACATCCCGC 61.971 60.000 0.00 0.00 0.00 6.13
1080 1352 2.680577 GGCTTTGCATCTTTCACCTTG 58.319 47.619 0.00 0.00 0.00 3.61
1108 1380 1.659233 CTGATTTTGTGGTGCCGCA 59.341 52.632 0.00 0.00 34.35 5.69
1162 1434 2.979814 ATGTACTTGGCTATCACGCA 57.020 45.000 0.00 0.00 0.00 5.24
1195 1467 0.841289 AGTCTAGCTCTCGGTAGCCT 59.159 55.000 0.00 0.00 43.86 4.58
1226 1498 0.606401 TCCAGGCAGGCTCTTTTTCG 60.606 55.000 0.00 0.00 37.29 3.46
1379 1651 0.394565 GATCGCTGGGTAAGGATGCT 59.605 55.000 0.00 0.00 0.00 3.79
1440 1712 1.271762 TGAGAGCTTCTTGGCTTGCAT 60.272 47.619 0.00 0.00 43.20 3.96
1461 1733 5.745988 AGGGATCCTAACTAACCTCACTA 57.254 43.478 12.58 0.00 28.47 2.74
1605 1878 3.843422 TGTTTTGGATTGATGTGGGAGT 58.157 40.909 0.00 0.00 0.00 3.85
1629 1902 5.476950 TTGAGGTAATACCCTACTCCTGA 57.523 43.478 5.71 0.00 39.75 3.86
1745 2603 1.902508 CCAGAGTACCAGTGATGGTGT 59.097 52.381 10.17 0.00 43.03 4.16
1780 2655 7.818930 AGATCGCAAACCAATTGATTTAAACAT 59.181 29.630 7.12 0.00 41.85 2.71
1846 2733 2.244651 GCGCAGAAGACCAACACGT 61.245 57.895 0.30 0.00 0.00 4.49
1995 4280 9.126151 ACTATATCCATATACCAGATTCAGTCG 57.874 37.037 0.00 0.00 0.00 4.18
2024 4309 7.415541 CGACATGATCTCCACATACCAATTTTT 60.416 37.037 0.00 0.00 0.00 1.94
2025 4310 6.038603 CGACATGATCTCCACATACCAATTTT 59.961 38.462 0.00 0.00 0.00 1.82
2026 4311 5.528690 CGACATGATCTCCACATACCAATTT 59.471 40.000 0.00 0.00 0.00 1.82
2027 4312 5.059161 CGACATGATCTCCACATACCAATT 58.941 41.667 0.00 0.00 0.00 2.32
2028 4313 4.344968 TCGACATGATCTCCACATACCAAT 59.655 41.667 0.00 0.00 0.00 3.16
2160 4898 7.175104 AGGAGAACATACACACATACCAAAAT 58.825 34.615 0.00 0.00 0.00 1.82
2347 5091 8.226810 AGGGATTATATCATCCAAACAATCACA 58.773 33.333 16.15 0.00 44.36 3.58
2396 5140 7.786046 TTAGTTTACAGAGGGAGTAATGTGA 57.214 36.000 0.00 0.00 32.07 3.58
2503 5269 5.009631 CCACCAACAATCCAAGTGAGAATA 58.990 41.667 0.00 0.00 0.00 1.75
2509 5275 1.270550 GAGCCACCAACAATCCAAGTG 59.729 52.381 0.00 0.00 0.00 3.16
2598 5367 6.423604 GTGAAATTTGTTCACCCAATAACCAG 59.576 38.462 7.80 0.00 42.07 4.00
2656 5433 8.732746 ACAGTAGTATGAAACAAACACTTCTT 57.267 30.769 0.00 0.00 0.00 2.52
2666 5443 7.833786 ACGAAATAGGACAGTAGTATGAAACA 58.166 34.615 0.00 0.00 0.00 2.83
2689 5473 9.746711 CAAACAGAGAACTGAATTATCTAAACG 57.253 33.333 0.00 0.00 46.03 3.60
2736 5520 1.362406 GGGCGCTCTGACACTTAAGC 61.362 60.000 7.64 0.00 0.00 3.09
2753 5537 2.190578 CGCCTTAAGCCTGGAGGG 59.809 66.667 0.00 0.00 38.78 4.30
2754 5538 1.153349 GACGCCTTAAGCCTGGAGG 60.153 63.158 0.00 0.00 38.78 4.30
2853 5970 9.599322 CATAGTTTTAACTAGCTTTGAACACAG 57.401 33.333 8.20 0.00 44.06 3.66
2892 6009 9.630098 TTGAAAGAGATTTATCAACTGATTTGC 57.370 29.630 0.00 0.00 36.05 3.68
2907 6024 6.326323 TGCCCTTTTAAGGTTTGAAAGAGATT 59.674 34.615 7.69 0.00 44.98 2.40
2908 6025 5.838521 TGCCCTTTTAAGGTTTGAAAGAGAT 59.161 36.000 7.69 0.00 44.98 2.75
2909 6026 5.205056 TGCCCTTTTAAGGTTTGAAAGAGA 58.795 37.500 7.69 0.00 44.98 3.10
2910 6027 5.529581 TGCCCTTTTAAGGTTTGAAAGAG 57.470 39.130 7.69 0.00 44.98 2.85
2911 6028 5.395879 GGTTGCCCTTTTAAGGTTTGAAAGA 60.396 40.000 7.69 0.00 44.98 2.52
2912 6029 4.814234 GGTTGCCCTTTTAAGGTTTGAAAG 59.186 41.667 7.69 0.60 44.98 2.62
2913 6030 4.471747 AGGTTGCCCTTTTAAGGTTTGAAA 59.528 37.500 7.69 0.00 44.98 2.69
2914 6031 4.034410 AGGTTGCCCTTTTAAGGTTTGAA 58.966 39.130 7.69 0.00 44.98 2.69
2915 6032 3.386402 CAGGTTGCCCTTTTAAGGTTTGA 59.614 43.478 7.69 0.00 44.98 2.69
2916 6033 3.494223 CCAGGTTGCCCTTTTAAGGTTTG 60.494 47.826 7.69 0.00 44.98 2.93
2917 6034 2.703536 CCAGGTTGCCCTTTTAAGGTTT 59.296 45.455 7.69 0.00 44.98 3.27
2918 6035 2.325484 CCAGGTTGCCCTTTTAAGGTT 58.675 47.619 7.69 0.00 44.98 3.50
2919 6036 1.219469 ACCAGGTTGCCCTTTTAAGGT 59.781 47.619 7.69 0.00 44.98 3.50
2920 6037 1.618343 CACCAGGTTGCCCTTTTAAGG 59.382 52.381 1.35 1.35 46.06 2.69
2921 6038 1.000843 GCACCAGGTTGCCCTTTTAAG 59.999 52.381 0.00 0.00 39.89 1.85
2922 6039 1.044611 GCACCAGGTTGCCCTTTTAA 58.955 50.000 0.00 0.00 39.89 1.52
2923 6040 0.105964 TGCACCAGGTTGCCCTTTTA 60.106 50.000 10.46 0.00 42.25 1.52
2924 6041 0.763986 ATGCACCAGGTTGCCCTTTT 60.764 50.000 10.46 0.00 42.25 2.27
2925 6042 1.152269 ATGCACCAGGTTGCCCTTT 60.152 52.632 10.46 0.00 42.25 3.11
2926 6043 1.909781 CATGCACCAGGTTGCCCTT 60.910 57.895 10.46 0.00 42.25 3.95
2927 6044 1.788518 TACATGCACCAGGTTGCCCT 61.789 55.000 10.46 0.00 42.25 5.19
2928 6045 1.304052 TACATGCACCAGGTTGCCC 60.304 57.895 10.46 0.00 42.25 5.36
2929 6046 1.937546 GCTACATGCACCAGGTTGCC 61.938 60.000 10.46 0.00 39.88 4.52
2930 6047 0.962356 AGCTACATGCACCAGGTTGC 60.962 55.000 8.03 8.03 44.17 4.17
2931 6048 1.089920 GAGCTACATGCACCAGGTTG 58.910 55.000 0.00 0.00 45.94 3.77
2932 6049 3.558674 GAGCTACATGCACCAGGTT 57.441 52.632 0.00 0.00 45.94 3.50
2957 6074 4.785453 CTTCCCTGGACCCTGCGC 62.785 72.222 0.00 0.00 0.00 6.09
2958 6075 4.101448 CCTTCCCTGGACCCTGCG 62.101 72.222 0.00 0.00 0.00 5.18
2959 6076 3.732849 CCCTTCCCTGGACCCTGC 61.733 72.222 0.00 0.00 0.00 4.85
2960 6077 2.204151 ACCCTTCCCTGGACCCTG 60.204 66.667 0.00 0.00 0.00 4.45
2961 6078 2.125225 GACCCTTCCCTGGACCCT 59.875 66.667 0.00 0.00 0.00 4.34
2962 6079 3.015753 GGACCCTTCCCTGGACCC 61.016 72.222 0.00 0.00 35.57 4.46
2963 6080 3.400054 CGGACCCTTCCCTGGACC 61.400 72.222 0.00 0.00 38.99 4.46
2964 6081 2.284405 TCGGACCCTTCCCTGGAC 60.284 66.667 0.00 0.00 38.99 4.02
2965 6082 2.284405 GTCGGACCCTTCCCTGGA 60.284 66.667 0.00 0.00 38.99 3.86
2966 6083 3.400054 GGTCGGACCCTTCCCTGG 61.400 72.222 16.55 0.00 38.99 4.45
2967 6084 2.606519 TGGTCGGACCCTTCCCTG 60.607 66.667 23.81 0.00 38.99 4.45
2968 6085 2.606826 GTGGTCGGACCCTTCCCT 60.607 66.667 23.81 0.00 38.99 4.20
2969 6086 1.775934 AAAGTGGTCGGACCCTTCCC 61.776 60.000 23.81 7.17 38.99 3.97
2970 6087 0.605589 CAAAGTGGTCGGACCCTTCC 60.606 60.000 23.81 9.51 37.50 3.46
2971 6088 0.605589 CCAAAGTGGTCGGACCCTTC 60.606 60.000 23.81 13.97 37.50 3.46
2972 6089 1.454539 CCAAAGTGGTCGGACCCTT 59.545 57.895 23.81 21.08 37.50 3.95
2973 6090 2.526046 CCCAAAGTGGTCGGACCCT 61.526 63.158 23.81 16.82 37.50 4.34
2974 6091 2.033602 CCCAAAGTGGTCGGACCC 59.966 66.667 23.81 14.91 37.50 4.46
2975 6092 1.302271 GACCCAAAGTGGTCGGACC 60.302 63.158 20.36 20.36 44.98 4.46
2976 6093 4.373771 GACCCAAAGTGGTCGGAC 57.626 61.111 0.00 0.00 44.98 4.79
2981 6098 4.162698 TGCGTAATATAGACCCAAAGTGGT 59.837 41.667 0.00 0.00 42.79 4.16
2982 6099 4.699637 TGCGTAATATAGACCCAAAGTGG 58.300 43.478 0.00 0.00 37.25 4.00
2983 6100 4.211374 GCTGCGTAATATAGACCCAAAGTG 59.789 45.833 0.00 0.00 0.00 3.16
2984 6101 4.377897 GCTGCGTAATATAGACCCAAAGT 58.622 43.478 0.00 0.00 0.00 2.66
2985 6102 3.746492 GGCTGCGTAATATAGACCCAAAG 59.254 47.826 0.00 0.00 0.00 2.77
2986 6103 3.389983 AGGCTGCGTAATATAGACCCAAA 59.610 43.478 0.00 0.00 0.00 3.28
2987 6104 2.969950 AGGCTGCGTAATATAGACCCAA 59.030 45.455 0.00 0.00 0.00 4.12
2988 6105 2.605257 AGGCTGCGTAATATAGACCCA 58.395 47.619 0.00 0.00 0.00 4.51
2989 6106 3.679824 AAGGCTGCGTAATATAGACCC 57.320 47.619 0.00 0.00 0.00 4.46
2990 6107 3.995048 GGAAAGGCTGCGTAATATAGACC 59.005 47.826 0.00 0.00 0.00 3.85
2991 6108 3.995048 GGGAAAGGCTGCGTAATATAGAC 59.005 47.826 0.00 0.00 0.00 2.59
2992 6109 3.901844 AGGGAAAGGCTGCGTAATATAGA 59.098 43.478 0.00 0.00 0.00 1.98
2993 6110 4.273148 AGGGAAAGGCTGCGTAATATAG 57.727 45.455 0.00 0.00 0.00 1.31
2994 6111 4.589798 TGTAGGGAAAGGCTGCGTAATATA 59.410 41.667 0.00 0.00 0.00 0.86
2995 6112 3.389983 TGTAGGGAAAGGCTGCGTAATAT 59.610 43.478 0.00 0.00 0.00 1.28
2996 6113 2.767394 TGTAGGGAAAGGCTGCGTAATA 59.233 45.455 0.00 0.00 0.00 0.98
2997 6114 1.557832 TGTAGGGAAAGGCTGCGTAAT 59.442 47.619 0.00 0.00 0.00 1.89
2998 6115 0.978151 TGTAGGGAAAGGCTGCGTAA 59.022 50.000 0.00 0.00 0.00 3.18
2999 6116 1.200519 ATGTAGGGAAAGGCTGCGTA 58.799 50.000 0.00 0.00 0.00 4.42
3000 6117 0.328258 AATGTAGGGAAAGGCTGCGT 59.672 50.000 0.00 0.00 0.00 5.24
3001 6118 1.401905 GAAATGTAGGGAAAGGCTGCG 59.598 52.381 0.00 0.00 0.00 5.18
3002 6119 2.424956 CAGAAATGTAGGGAAAGGCTGC 59.575 50.000 0.00 0.00 0.00 5.25
3003 6120 3.690460 ACAGAAATGTAGGGAAAGGCTG 58.310 45.455 0.00 0.00 0.00 4.85
3004 6121 5.250774 TCTTACAGAAATGTAGGGAAAGGCT 59.749 40.000 0.00 0.00 0.00 4.58
3005 6122 5.497474 TCTTACAGAAATGTAGGGAAAGGC 58.503 41.667 0.00 0.00 0.00 4.35
3006 6123 6.116126 CCTCTTACAGAAATGTAGGGAAAGG 58.884 44.000 0.00 0.00 0.00 3.11
3007 6124 5.586643 GCCTCTTACAGAAATGTAGGGAAAG 59.413 44.000 0.00 0.00 0.00 2.62
3008 6125 5.250774 AGCCTCTTACAGAAATGTAGGGAAA 59.749 40.000 0.00 0.00 0.00 3.13
3009 6126 4.783227 AGCCTCTTACAGAAATGTAGGGAA 59.217 41.667 0.00 0.00 0.00 3.97
3010 6127 4.162320 CAGCCTCTTACAGAAATGTAGGGA 59.838 45.833 0.00 0.00 0.00 4.20
3011 6128 4.080863 ACAGCCTCTTACAGAAATGTAGGG 60.081 45.833 0.00 0.66 0.00 3.53
3012 6129 5.091261 ACAGCCTCTTACAGAAATGTAGG 57.909 43.478 0.00 0.00 0.00 3.18
3013 6130 6.092807 GGAAACAGCCTCTTACAGAAATGTAG 59.907 42.308 0.00 0.00 0.00 2.74
3014 6131 5.938125 GGAAACAGCCTCTTACAGAAATGTA 59.062 40.000 0.00 0.00 0.00 2.29
3015 6132 4.762251 GGAAACAGCCTCTTACAGAAATGT 59.238 41.667 0.00 0.00 0.00 2.71
3016 6133 4.761739 TGGAAACAGCCTCTTACAGAAATG 59.238 41.667 0.00 0.00 35.01 2.32
3017 6134 4.985538 TGGAAACAGCCTCTTACAGAAAT 58.014 39.130 0.00 0.00 35.01 2.17
3018 6135 4.431416 TGGAAACAGCCTCTTACAGAAA 57.569 40.909 0.00 0.00 35.01 2.52
3032 6149 1.566703 TGGGTTCAAGTCCTGGAAACA 59.433 47.619 0.00 0.00 32.36 2.83
3033 6150 2.358322 TGGGTTCAAGTCCTGGAAAC 57.642 50.000 0.00 0.00 0.00 2.78
3034 6151 2.445145 TCATGGGTTCAAGTCCTGGAAA 59.555 45.455 0.00 0.00 0.00 3.13
3035 6152 2.061848 TCATGGGTTCAAGTCCTGGAA 58.938 47.619 0.00 0.00 0.00 3.53
3036 6153 1.351017 GTCATGGGTTCAAGTCCTGGA 59.649 52.381 0.00 0.00 0.00 3.86
3037 6154 1.614317 GGTCATGGGTTCAAGTCCTGG 60.614 57.143 0.00 0.00 0.00 4.45
3038 6155 1.352352 AGGTCATGGGTTCAAGTCCTG 59.648 52.381 0.00 0.00 0.00 3.86
3039 6156 1.630878 GAGGTCATGGGTTCAAGTCCT 59.369 52.381 0.00 0.00 0.00 3.85
3040 6157 1.351017 TGAGGTCATGGGTTCAAGTCC 59.649 52.381 0.00 0.00 0.00 3.85
3041 6158 2.859165 TGAGGTCATGGGTTCAAGTC 57.141 50.000 0.00 0.00 0.00 3.01
3056 6173 1.310933 GCTGCCTTGTGACCATGAGG 61.311 60.000 0.00 0.00 42.21 3.86
3057 6174 0.607217 TGCTGCCTTGTGACCATGAG 60.607 55.000 0.00 0.00 0.00 2.90
3058 6175 0.607217 CTGCTGCCTTGTGACCATGA 60.607 55.000 0.00 0.00 0.00 3.07
3059 6176 1.880894 CTGCTGCCTTGTGACCATG 59.119 57.895 0.00 0.00 0.00 3.66
3060 6177 1.975407 GCTGCTGCCTTGTGACCAT 60.975 57.895 3.85 0.00 0.00 3.55
3061 6178 2.595463 GCTGCTGCCTTGTGACCA 60.595 61.111 3.85 0.00 0.00 4.02
3062 6179 1.458639 AAAGCTGCTGCCTTGTGACC 61.459 55.000 12.44 0.00 40.80 4.02
3063 6180 1.068954 GTAAAGCTGCTGCCTTGTGAC 60.069 52.381 12.44 0.00 40.80 3.67
3064 6181 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
3065 6182 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
3066 6183 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
3067 6184 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
3068 6185 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
3069 6186 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
3070 6187 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
3075 6192 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
3076 6193 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
3077 6194 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
3078 6195 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
3079 6196 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
3080 6197 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
3081 6198 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
3089 6206 2.843912 ATTGAAGGGGAGCCTTGGCG 62.844 60.000 5.95 0.00 0.00 5.69
3090 6207 1.000866 ATTGAAGGGGAGCCTTGGC 59.999 57.895 2.97 2.97 0.00 4.52
3091 6208 0.627986 AGATTGAAGGGGAGCCTTGG 59.372 55.000 0.00 0.00 0.00 3.61
3092 6209 1.563410 AGAGATTGAAGGGGAGCCTTG 59.437 52.381 0.00 0.00 0.00 3.61
3093 6210 1.978361 AGAGATTGAAGGGGAGCCTT 58.022 50.000 0.00 0.00 0.00 4.35
3094 6211 1.978361 AAGAGATTGAAGGGGAGCCT 58.022 50.000 0.00 0.00 0.00 4.58
3095 6212 2.025887 TGAAAGAGATTGAAGGGGAGCC 60.026 50.000 0.00 0.00 0.00 4.70
3096 6213 3.356529 TGAAAGAGATTGAAGGGGAGC 57.643 47.619 0.00 0.00 0.00 4.70
3097 6214 4.460731 GGTTTGAAAGAGATTGAAGGGGAG 59.539 45.833 0.00 0.00 0.00 4.30
3098 6215 4.106341 AGGTTTGAAAGAGATTGAAGGGGA 59.894 41.667 0.00 0.00 0.00 4.81
3099 6216 4.411013 AGGTTTGAAAGAGATTGAAGGGG 58.589 43.478 0.00 0.00 0.00 4.79
3100 6217 6.071896 GGTAAGGTTTGAAAGAGATTGAAGGG 60.072 42.308 0.00 0.00 0.00 3.95
3101 6218 6.717084 AGGTAAGGTTTGAAAGAGATTGAAGG 59.283 38.462 0.00 0.00 0.00 3.46
3102 6219 7.445402 TCAGGTAAGGTTTGAAAGAGATTGAAG 59.555 37.037 0.00 0.00 0.00 3.02
3103 6220 7.287061 TCAGGTAAGGTTTGAAAGAGATTGAA 58.713 34.615 0.00 0.00 0.00 2.69
3104 6221 6.837312 TCAGGTAAGGTTTGAAAGAGATTGA 58.163 36.000 0.00 0.00 0.00 2.57
3105 6222 6.936900 TCTCAGGTAAGGTTTGAAAGAGATTG 59.063 38.462 0.00 0.00 0.00 2.67
3269 6390 8.954350 CAATCTAAATCTCAGACTTTCCAACAT 58.046 33.333 0.00 0.00 0.00 2.71
3270 6391 7.939039 ACAATCTAAATCTCAGACTTTCCAACA 59.061 33.333 0.00 0.00 0.00 3.33
3271 6392 8.329203 ACAATCTAAATCTCAGACTTTCCAAC 57.671 34.615 0.00 0.00 0.00 3.77
3273 6394 8.156820 TCAACAATCTAAATCTCAGACTTTCCA 58.843 33.333 0.00 0.00 0.00 3.53
3326 6447 7.390440 CAGATTAAAGACCACCAGTACATTTCA 59.610 37.037 0.00 0.00 0.00 2.69
3567 6725 8.198109 GTGTACACTACAGACTGATAAATCCAT 58.802 37.037 18.92 0.00 39.77 3.41
3617 6783 5.564048 ACCAGTAGTTTCTACTAGCTTCG 57.436 43.478 8.77 0.00 37.53 3.79
3685 6851 6.150474 AGTTTGTACTAGCGGCAAAATGTTAT 59.850 34.615 1.45 0.00 34.47 1.89
3746 6912 4.083862 AAGTCGGAAGAGGCGGGC 62.084 66.667 0.00 0.00 43.49 6.13
3786 6952 3.374402 CGTGGTCAGACCTCCGCT 61.374 66.667 20.82 0.00 39.58 5.52
3819 6985 5.117355 ACATTCTGAGATTGTGCAGTTTG 57.883 39.130 9.00 0.00 33.90 2.93
3875 7041 5.945191 TCCATGATCAAGAAAGTAACATGCA 59.055 36.000 0.00 0.00 34.35 3.96
3905 7071 6.737720 TCTCTGTATTTGGATATCAGCACT 57.262 37.500 4.83 0.00 0.00 4.40
3918 7084 4.645535 TGCTGTTGAGCTTCTCTGTATTT 58.354 39.130 0.00 0.00 46.39 1.40
3919 7085 4.277515 TGCTGTTGAGCTTCTCTGTATT 57.722 40.909 0.00 0.00 46.39 1.89
4036 7203 5.649395 TCATTTCAACTCCAATCAGCCTTAG 59.351 40.000 0.00 0.00 0.00 2.18
4100 7267 1.345741 AGCTGCGTGCATATATGGTCT 59.654 47.619 14.51 0.00 45.94 3.85
4122 7289 4.111375 AGGACTACGTGTAGAAATGCAG 57.889 45.455 13.69 0.00 36.97 4.41
4202 7369 2.211250 AGTAGGCAGACGAGTTACCA 57.789 50.000 0.00 0.00 0.00 3.25
4433 7613 4.937015 ACAAACAAAGCTGCATTTTCTGTT 59.063 33.333 1.02 0.00 0.00 3.16
4442 7622 0.536260 AAGGCACAAACAAAGCTGCA 59.464 45.000 1.02 0.00 0.00 4.41
4445 7625 2.027285 ACCAAAAGGCACAAACAAAGCT 60.027 40.909 0.00 0.00 0.00 3.74
4496 7676 3.386402 AGACTAAGATGCTTAGTGCCTCC 59.614 47.826 20.84 8.95 42.00 4.30
4541 7721 4.442706 CGTTCAGATAGTTACCCTGCAAT 58.557 43.478 0.00 0.00 0.00 3.56
4571 7768 9.496873 CATACGGGTGATATTTGACCTAAAATA 57.503 33.333 0.00 0.00 36.65 1.40
4921 10485 6.903883 AAACAGGTGCTATACTATTTGACG 57.096 37.500 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.