Multiple sequence alignment - TraesCS3A01G081400

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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 TraesCS3A01G081400 chr3A 100.000 4863 0 0 1 4863 52560972 52556110 0.000000e+00 8981.0
1 TraesCS3A01G081400 chr3A 78.409 264 38 14 2457 2708 506914961 506914705 2.340000e-33 154.0
2 TraesCS3A01G081400 chr3D 91.131 4048 189 77 105 4050 40791563 40787584 0.000000e+00 5330.0
3 TraesCS3A01G081400 chr3D 88.694 628 41 9 4162 4784 40787468 40786866 0.000000e+00 739.0
4 TraesCS3A01G081400 chr3D 82.213 461 61 12 2263 2707 39016852 39016397 1.280000e-100 377.0
5 TraesCS3A01G081400 chr3D 95.238 105 5 0 1 105 63168696 63168800 3.010000e-37 167.0
6 TraesCS3A01G081400 chr3D 94.286 105 6 0 1 105 222821881 222821777 1.400000e-35 161.0
7 TraesCS3A01G081400 chr3D 94.521 73 4 0 4077 4149 40787583 40787511 3.980000e-21 113.0
8 TraesCS3A01G081400 chr3B 89.605 2357 153 38 2559 4860 64506537 64508856 0.000000e+00 2911.0
9 TraesCS3A01G081400 chr3B 88.838 878 69 10 1710 2567 64505436 64506304 0.000000e+00 1051.0
10 TraesCS3A01G081400 chr3B 89.205 880 41 16 812 1679 64504214 64505051 0.000000e+00 1050.0
11 TraesCS3A01G081400 chr3B 90.704 355 24 6 4510 4860 64416685 64416336 9.530000e-127 464.0
12 TraesCS3A01G081400 chr3B 83.105 219 28 9 302 516 64502002 64502215 1.790000e-44 191.0
13 TraesCS3A01G081400 chr3B 95.413 109 5 0 4406 4514 64422293 64422185 1.800000e-39 174.0
14 TraesCS3A01G081400 chr3B 93.333 105 7 0 1 105 777634247 777634351 6.520000e-34 156.0
15 TraesCS3A01G081400 chr2B 84.354 294 22 1 1211 1504 128055137 128054868 2.890000e-67 267.0
16 TraesCS3A01G081400 chr2B 93.396 106 7 0 1 106 514985822 514985717 1.810000e-34 158.0
17 TraesCS3A01G081400 chr2B 95.455 88 4 0 973 1060 128055228 128055141 1.820000e-29 141.0
18 TraesCS3A01G081400 chr2B 95.238 42 1 1 2433 2473 173443079 173443120 1.130000e-06 65.8
19 TraesCS3A01G081400 chr1D 87.500 144 17 1 1159 1302 411410270 411410412 1.080000e-36 165.0
20 TraesCS3A01G081400 chr1D 85.621 153 20 1 1152 1304 613828 613978 5.040000e-35 159.0
21 TraesCS3A01G081400 chr1D 92.647 68 5 0 1000 1067 613669 613736 1.110000e-16 99.0
22 TraesCS3A01G081400 chr1B 86.301 146 20 0 1159 1304 4476292 4476437 5.040000e-35 159.0
23 TraesCS3A01G081400 chr1B 92.647 68 5 0 1000 1067 4476114 4476181 1.110000e-16 99.0
24 TraesCS3A01G081400 chr1A 86.301 146 20 0 1159 1304 3447370 3447515 5.040000e-35 159.0
25 TraesCS3A01G081400 chr1A 90.991 111 10 0 2 112 464703121 464703011 3.030000e-32 150.0
26 TraesCS3A01G081400 chr1A 92.647 68 5 0 1000 1067 3447202 3447269 1.110000e-16 99.0
27 TraesCS3A01G081400 chr7A 94.175 103 6 0 2 104 470750572 470750470 1.810000e-34 158.0
28 TraesCS3A01G081400 chr7A 93.269 104 7 0 1 104 625597742 625597845 2.340000e-33 154.0
29 TraesCS3A01G081400 chr5D 90.083 121 12 0 1 121 201504565 201504445 1.810000e-34 158.0
30 TraesCS3A01G081400 chr6A 92.453 106 8 0 1 106 102472096 102471991 8.430000e-33 152.0
31 TraesCS3A01G081400 chr2D 88.462 78 8 1 2406 2483 120545479 120545555 5.180000e-15 93.5
32 TraesCS3A01G081400 chr6B 85.714 70 9 1 2436 2504 514285523 514285592 6.750000e-09 73.1
33 TraesCS3A01G081400 chr5A 97.619 42 1 0 2667 2708 620744996 620745037 6.750000e-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 TraesCS3A01G081400 chr3A 52556110 52560972 4862 True 8981.000000 8981 100.000000 1 4863 1 chr3A.!!$R1 4862
1 TraesCS3A01G081400 chr3D 40786866 40791563 4697 True 2060.666667 5330 91.448667 105 4784 3 chr3D.!!$R3 4679
2 TraesCS3A01G081400 chr3B 64502002 64508856 6854 False 1300.750000 2911 87.688250 302 4860 4 chr3B.!!$F2 4558

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
554 601 0.750182 CCGTGGTCCAACACAAACCT 60.750 55.0 0.0 0.0 41.38 3.50 F
2430 4560 0.388659 GTTTGGTTGCAGGCATGTGA 59.611 50.0 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 4635 0.108662 TCTGCCTATGAGTGCGTGTG 60.109 55.0 0.0 0.0 0.0 3.82 R
4258 6739 0.615850 CTCCTTCTGACCCCTGTTCC 59.384 60.0 0.0 0.0 0.0 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
23 24 6.404712 GATTAATGGTCGACCGATTAATCC 57.595 41.667 38.33 30.64 42.06 3.01
24 25 3.830744 AATGGTCGACCGATTAATCCA 57.169 42.857 28.70 9.10 39.43 3.41
25 26 2.882927 TGGTCGACCGATTAATCCAG 57.117 50.000 28.70 4.43 39.43 3.86
26 27 2.104967 TGGTCGACCGATTAATCCAGT 58.895 47.619 28.70 7.59 39.43 4.00
27 28 2.498481 TGGTCGACCGATTAATCCAGTT 59.502 45.455 28.70 0.00 39.43 3.16
28 29 3.700539 TGGTCGACCGATTAATCCAGTTA 59.299 43.478 28.70 3.66 39.43 2.24
29 30 4.160065 TGGTCGACCGATTAATCCAGTTAA 59.840 41.667 28.70 2.96 39.43 2.01
30 31 5.163385 TGGTCGACCGATTAATCCAGTTAAT 60.163 40.000 28.70 0.00 43.86 1.40
31 32 6.040729 TGGTCGACCGATTAATCCAGTTAATA 59.959 38.462 28.70 2.18 41.82 0.98
32 33 7.095270 GGTCGACCGATTAATCCAGTTAATAT 58.905 38.462 20.85 0.00 41.82 1.28
33 34 7.063074 GGTCGACCGATTAATCCAGTTAATATG 59.937 40.741 20.85 0.00 41.82 1.78
34 35 6.588756 TCGACCGATTAATCCAGTTAATATGC 59.411 38.462 9.87 0.00 41.82 3.14
35 36 6.183360 CGACCGATTAATCCAGTTAATATGCC 60.183 42.308 9.87 0.00 41.82 4.40
36 37 5.642063 ACCGATTAATCCAGTTAATATGCCG 59.358 40.000 9.87 0.00 41.82 5.69
37 38 5.872617 CCGATTAATCCAGTTAATATGCCGA 59.127 40.000 9.87 0.00 41.82 5.54
38 39 6.538742 CCGATTAATCCAGTTAATATGCCGAT 59.461 38.462 9.87 0.00 41.82 4.18
39 40 7.065803 CCGATTAATCCAGTTAATATGCCGATT 59.934 37.037 9.87 0.00 41.82 3.34
40 41 8.450964 CGATTAATCCAGTTAATATGCCGATTT 58.549 33.333 9.87 0.00 41.82 2.17
43 44 7.448748 AATCCAGTTAATATGCCGATTTACC 57.551 36.000 0.00 0.00 0.00 2.85
44 45 5.931294 TCCAGTTAATATGCCGATTTACCA 58.069 37.500 0.00 0.00 0.00 3.25
45 46 6.358178 TCCAGTTAATATGCCGATTTACCAA 58.642 36.000 0.00 0.00 0.00 3.67
46 47 7.001674 TCCAGTTAATATGCCGATTTACCAAT 58.998 34.615 0.00 0.00 0.00 3.16
47 48 7.504238 TCCAGTTAATATGCCGATTTACCAATT 59.496 33.333 0.00 0.00 0.00 2.32
48 49 8.788806 CCAGTTAATATGCCGATTTACCAATTA 58.211 33.333 0.00 0.00 0.00 1.40
59 60 6.818416 CGATTTACCAATTAATCGCTACTCC 58.182 40.000 7.84 0.00 44.24 3.85
60 61 6.645415 CGATTTACCAATTAATCGCTACTCCT 59.355 38.462 7.84 0.00 44.24 3.69
61 62 7.811236 CGATTTACCAATTAATCGCTACTCCTA 59.189 37.037 7.84 0.00 44.24 2.94
62 63 9.485206 GATTTACCAATTAATCGCTACTCCTAA 57.515 33.333 0.00 0.00 0.00 2.69
63 64 9.841295 ATTTACCAATTAATCGCTACTCCTAAA 57.159 29.630 0.00 0.00 0.00 1.85
64 65 8.652810 TTACCAATTAATCGCTACTCCTAAAC 57.347 34.615 0.00 0.00 0.00 2.01
65 66 6.885922 ACCAATTAATCGCTACTCCTAAACT 58.114 36.000 0.00 0.00 0.00 2.66
66 67 6.761714 ACCAATTAATCGCTACTCCTAAACTG 59.238 38.462 0.00 0.00 0.00 3.16
67 68 6.984474 CCAATTAATCGCTACTCCTAAACTGA 59.016 38.462 0.00 0.00 0.00 3.41
68 69 7.042658 CCAATTAATCGCTACTCCTAAACTGAC 60.043 40.741 0.00 0.00 0.00 3.51
69 70 6.770746 TTAATCGCTACTCCTAAACTGACT 57.229 37.500 0.00 0.00 0.00 3.41
70 71 4.640789 ATCGCTACTCCTAAACTGACTG 57.359 45.455 0.00 0.00 0.00 3.51
71 72 3.682696 TCGCTACTCCTAAACTGACTGA 58.317 45.455 0.00 0.00 0.00 3.41
72 73 3.690139 TCGCTACTCCTAAACTGACTGAG 59.310 47.826 0.00 0.00 0.00 3.35
73 74 3.732471 CGCTACTCCTAAACTGACTGAGC 60.732 52.174 0.00 0.00 0.00 4.26
74 75 3.193691 GCTACTCCTAAACTGACTGAGCA 59.806 47.826 0.00 0.00 0.00 4.26
75 76 3.951775 ACTCCTAAACTGACTGAGCAG 57.048 47.619 0.00 0.00 41.63 4.24
76 77 2.028567 ACTCCTAAACTGACTGAGCAGC 60.029 50.000 0.00 0.00 39.51 5.25
77 78 2.233431 CTCCTAAACTGACTGAGCAGCT 59.767 50.000 0.00 0.00 39.51 4.24
78 79 3.431415 TCCTAAACTGACTGAGCAGCTA 58.569 45.455 0.00 0.00 39.51 3.32
79 80 4.026744 TCCTAAACTGACTGAGCAGCTAT 58.973 43.478 0.00 0.00 39.51 2.97
80 81 4.098654 TCCTAAACTGACTGAGCAGCTATC 59.901 45.833 0.00 0.00 39.51 2.08
81 82 3.969287 AAACTGACTGAGCAGCTATCA 57.031 42.857 0.00 0.00 39.51 2.15
89 90 4.033990 CTGAGCAGCTATCAGTTAACGA 57.966 45.455 16.46 1.38 39.48 3.85
90 91 4.615949 CTGAGCAGCTATCAGTTAACGAT 58.384 43.478 16.46 14.38 39.48 3.73
91 92 5.011090 TGAGCAGCTATCAGTTAACGATT 57.989 39.130 14.93 1.57 0.00 3.34
92 93 5.419542 TGAGCAGCTATCAGTTAACGATTT 58.580 37.500 14.93 0.06 0.00 2.17
93 94 5.520288 TGAGCAGCTATCAGTTAACGATTTC 59.480 40.000 14.93 9.32 0.00 2.17
94 95 5.665459 AGCAGCTATCAGTTAACGATTTCT 58.335 37.500 14.93 10.79 0.00 2.52
95 96 6.109359 AGCAGCTATCAGTTAACGATTTCTT 58.891 36.000 14.93 0.00 0.00 2.52
96 97 6.036517 AGCAGCTATCAGTTAACGATTTCTTG 59.963 38.462 14.93 10.92 0.00 3.02
97 98 6.036083 GCAGCTATCAGTTAACGATTTCTTGA 59.964 38.462 14.93 6.19 0.00 3.02
98 99 7.413000 GCAGCTATCAGTTAACGATTTCTTGAA 60.413 37.037 14.93 0.00 0.00 2.69
99 100 7.900352 CAGCTATCAGTTAACGATTTCTTGAAC 59.100 37.037 14.93 1.92 0.00 3.18
100 101 7.602644 AGCTATCAGTTAACGATTTCTTGAACA 59.397 33.333 14.93 0.00 0.00 3.18
101 102 8.391106 GCTATCAGTTAACGATTTCTTGAACAT 58.609 33.333 14.93 0.00 0.00 2.71
103 104 8.955061 ATCAGTTAACGATTTCTTGAACATTG 57.045 30.769 0.00 0.00 0.00 2.82
161 162 6.921857 CCTGGCTTTTTATGTTGATGATGATC 59.078 38.462 0.00 0.00 0.00 2.92
303 305 5.885881 AGTACAACAATTTGTCTTTCGCAA 58.114 33.333 1.83 0.00 42.67 4.85
542 589 4.266976 CGAAACACATTATAGTCCGTGGTC 59.733 45.833 0.00 0.00 33.62 4.02
546 593 3.869246 CACATTATAGTCCGTGGTCCAAC 59.131 47.826 0.00 0.00 0.00 3.77
554 601 0.750182 CCGTGGTCCAACACAAACCT 60.750 55.000 0.00 0.00 41.38 3.50
799 2503 1.358759 CCGCGAGTTGCCAACTTTT 59.641 52.632 12.09 0.00 43.03 2.27
801 2505 1.002251 CCGCGAGTTGCCAACTTTTTA 60.002 47.619 12.09 0.00 43.03 1.52
857 2573 2.222027 CCGAAGCCCATTTACATCTCC 58.778 52.381 0.00 0.00 0.00 3.71
866 2582 5.645497 GCCCATTTACATCTCCATATCAGTC 59.355 44.000 0.00 0.00 0.00 3.51
878 2594 6.441924 TCTCCATATCAGTCTCAGAAAAAGGT 59.558 38.462 0.00 0.00 0.00 3.50
943 2666 3.077556 CCCAGGTCCCTCCACTCG 61.078 72.222 0.00 0.00 39.02 4.18
958 2681 2.261671 TCGAGCCGAGAAACTGCC 59.738 61.111 0.00 0.00 0.00 4.85
959 2682 3.181967 CGAGCCGAGAAACTGCCG 61.182 66.667 0.00 0.00 0.00 5.69
960 2683 3.491652 GAGCCGAGAAACTGCCGC 61.492 66.667 0.00 0.00 0.00 6.53
1126 2867 3.631952 TTCCCACGCCCGAAATCCC 62.632 63.158 0.00 0.00 0.00 3.85
1148 2889 1.064621 CAATGCCGCTCCGATTTGG 59.935 57.895 0.00 0.00 40.09 3.28
1424 3168 4.382320 GTACGCACCCGCCCTTCA 62.382 66.667 0.00 0.00 38.22 3.02
1430 3174 3.090532 ACCCGCCCTTCATCTCCC 61.091 66.667 0.00 0.00 0.00 4.30
1446 3190 2.030412 CCCGTGTGTGCTGCTGTA 59.970 61.111 0.00 0.00 0.00 2.74
1447 3191 2.029288 CCCGTGTGTGCTGCTGTAG 61.029 63.158 0.00 0.00 0.00 2.74
1594 3341 2.333926 TCGATGTACGTTTTGCTCCTG 58.666 47.619 0.00 0.00 43.13 3.86
1598 3345 0.887387 GTACGTTTTGCTCCTGCCCA 60.887 55.000 0.00 0.00 38.71 5.36
1608 3355 2.293170 GCTCCTGCCCATTCTTAGTTC 58.707 52.381 0.00 0.00 0.00 3.01
1609 3356 2.356125 GCTCCTGCCCATTCTTAGTTCA 60.356 50.000 0.00 0.00 0.00 3.18
1610 3357 3.686691 GCTCCTGCCCATTCTTAGTTCAT 60.687 47.826 0.00 0.00 0.00 2.57
1634 3381 1.490693 CGCTGCTGCCGAATTCGTAT 61.491 55.000 25.10 0.00 37.74 3.06
1664 3411 5.654650 TGTATGGTCTGTCAGGTTTTGTTTT 59.345 36.000 0.00 0.00 0.00 2.43
1691 3438 5.689819 ACAATTTGAGTATTTCAGTGTCGC 58.310 37.500 2.79 0.00 37.07 5.19
1816 3938 4.536364 ACATATGTAGTGCGCAATGAAC 57.464 40.909 22.31 12.43 0.00 3.18
1833 3955 6.507023 CAATGAACACTTTAAGCAGAAAGGT 58.493 36.000 13.15 6.87 40.17 3.50
1834 3956 6.715347 ATGAACACTTTAAGCAGAAAGGTT 57.285 33.333 13.15 12.85 40.17 3.50
1846 3968 4.777896 AGCAGAAAGGTTATACTCCACTCA 59.222 41.667 0.00 0.00 0.00 3.41
1862 3984 6.156949 ACTCCACTCATACTGTCAAATATGGT 59.843 38.462 4.65 0.80 30.98 3.55
1868 3990 7.867909 ACTCATACTGTCAAATATGGTGTATCG 59.132 37.037 4.65 0.00 30.98 2.92
1878 4000 2.596904 TGGTGTATCGGAAGCTTAGC 57.403 50.000 0.00 0.00 0.00 3.09
1891 4013 5.986135 CGGAAGCTTAGCATCATACTAACTT 59.014 40.000 11.57 0.00 0.00 2.66
1906 4028 5.388408 ACTAACTTTAGAGTCCGTCCTTG 57.612 43.478 2.95 0.00 34.21 3.61
1927 4049 2.341257 CGATTGGCTAATCTGGGATCG 58.659 52.381 19.16 3.51 40.43 3.69
1949 4071 2.734755 TTTCCCAGCAGTATCCATGG 57.265 50.000 4.97 4.97 0.00 3.66
2075 4205 7.746929 GCAATCAGCCTTACTTATCATACATC 58.253 38.462 0.00 0.00 37.23 3.06
2191 4321 4.276431 CCTCCTACTAGTGCTAGCTTACAC 59.724 50.000 17.23 5.48 36.66 2.90
2205 4335 6.018669 GCTAGCTTACACTGACATATTTGGTC 60.019 42.308 7.70 0.00 35.83 4.02
2298 4428 0.602562 TTTTTGGCCTCCTTGCATCG 59.397 50.000 3.32 0.00 0.00 3.84
2339 4469 2.751259 CTGAGCTAATGCAGGCTGAAAA 59.249 45.455 20.86 2.69 42.74 2.29
2351 4481 3.318839 CAGGCTGAAAAACCATGTTCTGA 59.681 43.478 9.42 0.00 0.00 3.27
2369 4499 4.813346 ACCTAGTTTGGTTGCCCG 57.187 55.556 0.00 0.00 36.89 6.13
2385 4515 2.912025 CGCAAAACCCCAGCCTGT 60.912 61.111 0.00 0.00 0.00 4.00
2393 4523 4.724279 AAACCCCAGCCTGTATTATAGG 57.276 45.455 2.22 2.22 38.39 2.57
2405 4535 5.634020 CCTGTATTATAGGCGAACAACTAGC 59.366 44.000 0.00 0.00 0.00 3.42
2429 4559 0.940519 CGTTTGGTTGCAGGCATGTG 60.941 55.000 0.00 0.00 0.00 3.21
2430 4560 0.388659 GTTTGGTTGCAGGCATGTGA 59.611 50.000 0.00 0.00 0.00 3.58
2432 4562 1.340088 TTGGTTGCAGGCATGTGATT 58.660 45.000 0.00 0.00 0.00 2.57
2504 4635 2.375146 ACCTTTTGTTCCAGTGGTGAC 58.625 47.619 9.54 10.03 0.00 3.67
2581 4967 5.671493 AGGTACTACATTGACAACCATAGC 58.329 41.667 0.00 0.00 36.02 2.97
2590 4976 8.710749 ACATTGACAACCATAGCCATAATAAT 57.289 30.769 0.00 0.00 0.00 1.28
2592 4978 6.573664 TGACAACCATAGCCATAATAATGC 57.426 37.500 0.00 0.00 0.00 3.56
2595 4981 5.477984 ACAACCATAGCCATAATAATGCCAG 59.522 40.000 0.00 0.00 0.00 4.85
2608 5000 2.706339 ATGCCAGAGTCTTAAGCAGG 57.294 50.000 13.15 2.20 36.80 4.85
2642 5038 9.778741 AATATAAACTTCACAGACAGACAGAAA 57.221 29.630 0.00 0.00 0.00 2.52
2663 5059 6.268847 AGAAAGACAGACAGACTAAACATCCT 59.731 38.462 0.00 0.00 0.00 3.24
2665 5061 3.929610 GACAGACAGACTAAACATCCTGC 59.070 47.826 0.00 0.00 0.00 4.85
2711 5107 1.075374 TCTTGCACTTGGCCACCTTAT 59.925 47.619 3.88 0.00 43.89 1.73
2714 5110 2.722094 TGCACTTGGCCACCTTATAAG 58.278 47.619 3.88 5.43 43.89 1.73
2740 5137 4.397919 AGTTGGTTAGGGCCTAACAAAT 57.602 40.909 41.87 31.91 45.57 2.32
2948 5352 6.360370 TCTCTTGGTAGAAGCTACAACATT 57.640 37.500 6.89 0.00 0.00 2.71
2986 5390 4.218852 CGAGGAAGATCTAATGGGAGGTAC 59.781 50.000 0.00 0.00 0.00 3.34
3045 5450 5.072741 TGATCTGGCTTTACTGCTCTTTTT 58.927 37.500 0.00 0.00 0.00 1.94
3048 5453 4.036734 TCTGGCTTTACTGCTCTTTTTGTG 59.963 41.667 0.00 0.00 0.00 3.33
3061 5466 9.515020 CTGCTCTTTTTGTGAACTGTAATTTTA 57.485 29.630 0.00 0.00 0.00 1.52
3143 5562 8.730680 GTCTAGATTTCTTTCTTTGCCATGTTA 58.269 33.333 0.00 0.00 0.00 2.41
3222 5641 7.331026 TGTCCTCTATTTACTGTCCTCATTTG 58.669 38.462 0.00 0.00 0.00 2.32
3245 5668 7.697352 TGTTTTTGTATTGAACATTGCAGAG 57.303 32.000 0.00 0.00 38.10 3.35
3405 5828 4.989279 AGTGGATTCCATGTGCATTTAC 57.011 40.909 9.01 0.00 35.28 2.01
3420 5843 4.744137 TGCATTTACATTGCACAACAGAAC 59.256 37.500 0.00 0.00 44.73 3.01
3477 5900 2.654863 ACCCTGAGTTTCTGGTGTTTG 58.345 47.619 2.04 0.00 34.10 2.93
3550 5973 5.290493 TCCAAACACTGTTCAGTATCTGT 57.710 39.130 5.11 0.00 32.61 3.41
3553 5976 6.704493 TCCAAACACTGTTCAGTATCTGTTAC 59.296 38.462 5.11 0.00 32.61 2.50
3635 6058 2.978156 ACCAATCAACCTCCACACAT 57.022 45.000 0.00 0.00 0.00 3.21
3637 6060 2.108075 ACCAATCAACCTCCACACATGA 59.892 45.455 0.00 0.00 0.00 3.07
3670 6108 6.981722 AGTTAACATGCTAGGAAAAAGTTGG 58.018 36.000 8.61 0.00 0.00 3.77
3675 6113 5.183904 ACATGCTAGGAAAAAGTTGGATGAC 59.816 40.000 0.00 0.00 0.00 3.06
3682 6120 6.314917 AGGAAAAAGTTGGATGACTTGGTAT 58.685 36.000 0.00 0.00 39.68 2.73
3764 6202 1.066430 TGACCGATGACTAAGCAACCC 60.066 52.381 0.00 0.00 0.00 4.11
3765 6203 0.252197 ACCGATGACTAAGCAACCCC 59.748 55.000 0.00 0.00 0.00 4.95
3891 6342 1.066645 AGTATTTCCCGACCGTGTTCC 60.067 52.381 0.00 0.00 0.00 3.62
3892 6343 0.975135 TATTTCCCGACCGTGTTCCA 59.025 50.000 0.00 0.00 0.00 3.53
3912 6363 5.790593 TCCAAGTGTTACTACCTCATTGTC 58.209 41.667 0.00 0.00 0.00 3.18
3946 6397 4.737054 AGAAGTCTTTGTGTTTGCACTTG 58.263 39.130 0.00 0.00 45.44 3.16
3963 6414 4.022849 GCACTTGAACAATCCTTGTAAGCT 60.023 41.667 0.00 0.00 44.59 3.74
3984 6435 4.274459 GCTATTTCTTGATGGTACTGCCTG 59.726 45.833 0.00 0.00 38.35 4.85
4050 6501 1.905215 CTCTATCCTGGCTGTATGGGG 59.095 57.143 0.00 0.00 0.00 4.96
4055 6506 0.111253 CCTGGCTGTATGGGGATTCC 59.889 60.000 0.00 0.00 0.00 3.01
4069 6520 1.395608 GGATTCCGAATTTGCGACGAA 59.604 47.619 0.00 0.00 0.00 3.85
4108 6559 4.695217 TCGTTCATTATTTTCTGGTGGC 57.305 40.909 0.00 0.00 0.00 5.01
4109 6560 4.075682 TCGTTCATTATTTTCTGGTGGCA 58.924 39.130 0.00 0.00 0.00 4.92
4128 6579 4.344865 TTCCTGTTCGGGGCAGCC 62.345 66.667 1.26 1.26 32.93 4.85
4152 6603 7.383572 GCCATGTACTCTCATCATAGTTAGTTG 59.616 40.741 0.00 0.00 0.00 3.16
4154 6605 6.806751 TGTACTCTCATCATAGTTAGTTGCC 58.193 40.000 0.00 0.00 0.00 4.52
4155 6606 5.939764 ACTCTCATCATAGTTAGTTGCCA 57.060 39.130 0.00 0.00 0.00 4.92
4157 6608 5.423610 ACTCTCATCATAGTTAGTTGCCAGT 59.576 40.000 0.00 0.00 0.00 4.00
4158 6609 5.664457 TCTCATCATAGTTAGTTGCCAGTG 58.336 41.667 0.00 0.00 0.00 3.66
4159 6610 4.191544 TCATCATAGTTAGTTGCCAGTGC 58.808 43.478 0.00 0.00 38.26 4.40
4200 6681 8.519526 CAGTAGGTTTCTTATTGGTTGCAATAA 58.480 33.333 0.59 1.59 36.14 1.40
4201 6682 9.084533 AGTAGGTTTCTTATTGGTTGCAATAAA 57.915 29.630 0.59 0.19 36.81 1.40
4207 6688 9.912634 TTTCTTATTGGTTGCAATAAAGAGAAG 57.087 29.630 0.59 6.21 36.81 2.85
4218 6699 9.448438 TTGCAATAAAGAGAAGATAAGTTGCTA 57.552 29.630 0.00 0.00 39.88 3.49
4245 6726 9.883142 AAAAACAATGGTAGATTTCTCAAACAA 57.117 25.926 0.00 0.00 0.00 2.83
4258 6739 9.617975 GATTTCTCAAACAAAAACTGGAGATAG 57.382 33.333 0.00 0.00 32.08 2.08
4259 6740 7.510549 TTCTCAAACAAAAACTGGAGATAGG 57.489 36.000 0.00 0.00 32.08 2.57
4265 6746 5.316987 ACAAAAACTGGAGATAGGAACAGG 58.683 41.667 0.00 0.00 35.34 4.00
4276 6757 0.193574 AGGAACAGGGGTCAGAAGGA 59.806 55.000 0.00 0.00 0.00 3.36
4463 6951 1.006813 ATGGCCCCACTGTTATCCAA 58.993 50.000 0.00 0.00 0.00 3.53
4479 6967 1.557371 TCCAAACAGGACACACTCACA 59.443 47.619 0.00 0.00 43.07 3.58
4480 6968 1.670811 CCAAACAGGACACACTCACAC 59.329 52.381 0.00 0.00 41.22 3.82
4481 6969 2.355197 CAAACAGGACACACTCACACA 58.645 47.619 0.00 0.00 0.00 3.72
4482 6970 2.945008 CAAACAGGACACACTCACACAT 59.055 45.455 0.00 0.00 0.00 3.21
4483 6971 2.533266 ACAGGACACACTCACACATC 57.467 50.000 0.00 0.00 0.00 3.06
4484 6972 1.070758 ACAGGACACACTCACACATCC 59.929 52.381 0.00 0.00 0.00 3.51
4485 6973 1.070601 CAGGACACACTCACACATCCA 59.929 52.381 0.00 0.00 0.00 3.41
4506 6994 3.407424 TGGCAGTATATAAGCAGGCAG 57.593 47.619 9.78 0.00 0.00 4.85
4594 7095 6.496565 AGATAGACAGGATCAGATTAACCAGG 59.503 42.308 0.00 0.00 0.00 4.45
4783 7284 2.699628 CGTCTCGTACGTTCTCTCTC 57.300 55.000 16.05 0.00 46.72 3.20
4784 7285 1.991264 CGTCTCGTACGTTCTCTCTCA 59.009 52.381 16.05 0.00 46.72 3.27
4786 7287 2.094099 GTCTCGTACGTTCTCTCTCACC 59.906 54.545 16.05 0.00 0.00 4.02
4788 7289 0.450983 CGTACGTTCTCTCTCACCCC 59.549 60.000 7.22 0.00 0.00 4.95
4790 7291 1.744522 GTACGTTCTCTCTCACCCCTC 59.255 57.143 0.00 0.00 0.00 4.30
4791 7292 0.612453 ACGTTCTCTCTCACCCCTCC 60.612 60.000 0.00 0.00 0.00 4.30
4792 7293 0.323908 CGTTCTCTCTCACCCCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
4793 7294 1.893210 CGTTCTCTCTCACCCCTCCTT 60.893 57.143 0.00 0.00 0.00 3.36
4794 7295 1.552792 GTTCTCTCTCACCCCTCCTTG 59.447 57.143 0.00 0.00 0.00 3.61
4795 7296 0.041833 TCTCTCTCACCCCTCCTTGG 59.958 60.000 0.00 0.00 0.00 3.61
4796 7297 0.252467 CTCTCTCACCCCTCCTTGGT 60.252 60.000 0.00 0.00 36.21 3.67
4797 7298 0.252284 TCTCTCACCCCTCCTTGGTC 60.252 60.000 0.00 0.00 32.46 4.02
4798 7299 0.545309 CTCTCACCCCTCCTTGGTCA 60.545 60.000 0.00 0.00 32.46 4.02
4813 7314 1.002430 TGGTCAGTCACTGATTGAGCC 59.998 52.381 23.40 17.55 43.01 4.70
4820 7321 0.035725 CACTGATTGAGCCTGAGCCA 60.036 55.000 0.00 0.00 41.25 4.75
4822 7323 1.074405 ACTGATTGAGCCTGAGCCAAA 59.926 47.619 0.00 0.00 41.25 3.28
4826 7327 2.050836 TTGAGCCTGAGCCAAACCGA 62.051 55.000 0.00 0.00 41.25 4.69
4828 7329 1.078143 AGCCTGAGCCAAACCGATC 60.078 57.895 0.00 0.00 41.25 3.69
4837 7338 1.002033 GCCAAACCGATCATCATCTGC 60.002 52.381 0.00 0.00 0.00 4.26
4860 7361 1.280710 TCTGGTGGTTGCCATATCGTT 59.719 47.619 0.00 0.00 37.96 3.85
4861 7362 1.670811 CTGGTGGTTGCCATATCGTTC 59.329 52.381 0.00 0.00 37.96 3.95
4862 7363 0.655733 GGTGGTTGCCATATCGTTCG 59.344 55.000 0.00 0.00 35.28 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.929992 TGGATTAATCGGTCGACCATTAATC 59.070 40.000 39.07 39.07 43.85 1.75
2 3 5.163385 ACTGGATTAATCGGTCGACCATTAA 60.163 40.000 31.59 31.59 35.52 1.40
3 4 4.342951 ACTGGATTAATCGGTCGACCATTA 59.657 41.667 32.80 27.43 35.14 1.90
5 6 2.698797 ACTGGATTAATCGGTCGACCAT 59.301 45.455 32.80 21.65 35.14 3.55
6 7 2.104967 ACTGGATTAATCGGTCGACCA 58.895 47.619 32.80 20.42 35.14 4.02
7 8 2.884894 ACTGGATTAATCGGTCGACC 57.115 50.000 25.28 25.28 0.00 4.79
8 9 7.411588 GCATATTAACTGGATTAATCGGTCGAC 60.412 40.741 7.13 7.13 41.66 4.20
9 10 6.588756 GCATATTAACTGGATTAATCGGTCGA 59.411 38.462 9.32 0.00 41.66 4.20
10 11 6.183360 GGCATATTAACTGGATTAATCGGTCG 60.183 42.308 9.32 0.78 41.66 4.79
11 12 6.183360 CGGCATATTAACTGGATTAATCGGTC 60.183 42.308 9.32 0.00 41.66 4.79
12 13 5.642063 CGGCATATTAACTGGATTAATCGGT 59.358 40.000 9.32 7.91 41.66 4.69
13 14 5.872617 TCGGCATATTAACTGGATTAATCGG 59.127 40.000 9.32 7.32 41.66 4.18
14 15 6.961359 TCGGCATATTAACTGGATTAATCG 57.039 37.500 9.32 0.00 41.66 3.34
17 18 9.005777 GGTAAATCGGCATATTAACTGGATTAA 57.994 33.333 0.00 0.00 37.18 1.40
18 19 8.158132 TGGTAAATCGGCATATTAACTGGATTA 58.842 33.333 0.00 0.00 0.00 1.75
19 20 7.001674 TGGTAAATCGGCATATTAACTGGATT 58.998 34.615 0.00 0.00 0.00 3.01
20 21 6.539173 TGGTAAATCGGCATATTAACTGGAT 58.461 36.000 0.00 0.00 0.00 3.41
21 22 5.931294 TGGTAAATCGGCATATTAACTGGA 58.069 37.500 0.00 0.00 0.00 3.86
22 23 6.627395 TTGGTAAATCGGCATATTAACTGG 57.373 37.500 0.00 0.00 0.00 4.00
36 37 7.964604 AGGAGTAGCGATTAATTGGTAAATC 57.035 36.000 14.74 14.61 0.00 2.17
37 38 9.841295 TTTAGGAGTAGCGATTAATTGGTAAAT 57.159 29.630 14.74 8.02 0.00 1.40
38 39 9.101655 GTTTAGGAGTAGCGATTAATTGGTAAA 57.898 33.333 14.74 5.46 0.00 2.01
39 40 8.480501 AGTTTAGGAGTAGCGATTAATTGGTAA 58.519 33.333 14.74 0.00 0.00 2.85
40 41 7.924412 CAGTTTAGGAGTAGCGATTAATTGGTA 59.076 37.037 10.03 10.03 0.00 3.25
41 42 6.761714 CAGTTTAGGAGTAGCGATTAATTGGT 59.238 38.462 11.97 11.97 0.00 3.67
42 43 6.984474 TCAGTTTAGGAGTAGCGATTAATTGG 59.016 38.462 4.84 0.00 0.00 3.16
43 44 7.707035 AGTCAGTTTAGGAGTAGCGATTAATTG 59.293 37.037 0.00 0.00 0.00 2.32
44 45 7.707035 CAGTCAGTTTAGGAGTAGCGATTAATT 59.293 37.037 0.00 0.00 0.00 1.40
45 46 7.068348 TCAGTCAGTTTAGGAGTAGCGATTAAT 59.932 37.037 0.00 0.00 0.00 1.40
46 47 6.376299 TCAGTCAGTTTAGGAGTAGCGATTAA 59.624 38.462 0.00 0.00 0.00 1.40
47 48 5.884232 TCAGTCAGTTTAGGAGTAGCGATTA 59.116 40.000 0.00 0.00 0.00 1.75
48 49 4.705507 TCAGTCAGTTTAGGAGTAGCGATT 59.294 41.667 0.00 0.00 0.00 3.34
49 50 4.270834 TCAGTCAGTTTAGGAGTAGCGAT 58.729 43.478 0.00 0.00 0.00 4.58
50 51 3.682696 TCAGTCAGTTTAGGAGTAGCGA 58.317 45.455 0.00 0.00 0.00 4.93
51 52 3.732471 GCTCAGTCAGTTTAGGAGTAGCG 60.732 52.174 0.00 0.00 0.00 4.26
52 53 3.193691 TGCTCAGTCAGTTTAGGAGTAGC 59.806 47.826 0.00 0.00 0.00 3.58
53 54 4.676723 GCTGCTCAGTCAGTTTAGGAGTAG 60.677 50.000 0.00 0.00 40.07 2.57
54 55 3.193691 GCTGCTCAGTCAGTTTAGGAGTA 59.806 47.826 0.00 0.00 36.49 2.59
55 56 2.028567 GCTGCTCAGTCAGTTTAGGAGT 60.029 50.000 0.00 0.00 36.49 3.85
56 57 2.233431 AGCTGCTCAGTCAGTTTAGGAG 59.767 50.000 0.00 0.00 36.49 3.69
57 58 2.251818 AGCTGCTCAGTCAGTTTAGGA 58.748 47.619 0.00 0.00 36.49 2.94
58 59 2.758736 AGCTGCTCAGTCAGTTTAGG 57.241 50.000 0.00 0.00 36.49 2.69
59 60 5.003692 TGATAGCTGCTCAGTCAGTTTAG 57.996 43.478 4.91 0.00 36.49 1.85
60 61 5.003692 CTGATAGCTGCTCAGTCAGTTTA 57.996 43.478 21.67 0.00 36.26 2.01
61 62 3.859443 CTGATAGCTGCTCAGTCAGTTT 58.141 45.455 21.67 0.00 36.26 2.66
62 63 3.523606 CTGATAGCTGCTCAGTCAGTT 57.476 47.619 21.67 0.00 36.26 3.16
68 69 4.033990 TCGTTAACTGATAGCTGCTCAG 57.966 45.455 20.57 20.57 44.60 3.35
69 70 4.655762 ATCGTTAACTGATAGCTGCTCA 57.344 40.909 4.91 0.00 0.00 4.26
70 71 5.751028 AGAAATCGTTAACTGATAGCTGCTC 59.249 40.000 4.91 0.00 0.00 4.26
71 72 5.665459 AGAAATCGTTAACTGATAGCTGCT 58.335 37.500 7.57 7.57 0.00 4.24
72 73 5.975410 AGAAATCGTTAACTGATAGCTGC 57.025 39.130 3.71 0.00 0.00 5.25
73 74 7.525688 TCAAGAAATCGTTAACTGATAGCTG 57.474 36.000 3.71 5.25 0.00 4.24
74 75 7.602644 TGTTCAAGAAATCGTTAACTGATAGCT 59.397 33.333 3.71 0.00 0.00 3.32
75 76 7.739295 TGTTCAAGAAATCGTTAACTGATAGC 58.261 34.615 3.71 4.75 0.00 2.97
78 79 8.023128 CCAATGTTCAAGAAATCGTTAACTGAT 58.977 33.333 3.71 5.68 0.00 2.90
79 80 7.359595 CCAATGTTCAAGAAATCGTTAACTGA 58.640 34.615 3.71 3.47 0.00 3.41
80 81 6.088085 GCCAATGTTCAAGAAATCGTTAACTG 59.912 38.462 3.71 0.00 0.00 3.16
81 82 6.149633 GCCAATGTTCAAGAAATCGTTAACT 58.850 36.000 3.71 0.00 0.00 2.24
82 83 5.918011 TGCCAATGTTCAAGAAATCGTTAAC 59.082 36.000 0.00 0.00 0.00 2.01
83 84 6.078202 TGCCAATGTTCAAGAAATCGTTAA 57.922 33.333 0.00 0.00 0.00 2.01
84 85 5.697473 TGCCAATGTTCAAGAAATCGTTA 57.303 34.783 0.00 0.00 0.00 3.18
85 86 4.582701 TGCCAATGTTCAAGAAATCGTT 57.417 36.364 0.00 0.00 0.00 3.85
86 87 4.582701 TTGCCAATGTTCAAGAAATCGT 57.417 36.364 0.00 0.00 0.00 3.73
87 88 6.034898 GGTTATTGCCAATGTTCAAGAAATCG 59.965 38.462 0.00 0.00 0.00 3.34
88 89 6.873076 TGGTTATTGCCAATGTTCAAGAAATC 59.127 34.615 0.00 0.00 35.25 2.17
89 90 6.650390 GTGGTTATTGCCAATGTTCAAGAAAT 59.350 34.615 0.00 0.00 40.68 2.17
90 91 5.988561 GTGGTTATTGCCAATGTTCAAGAAA 59.011 36.000 0.00 0.00 40.68 2.52
91 92 5.304101 AGTGGTTATTGCCAATGTTCAAGAA 59.696 36.000 0.00 0.00 40.68 2.52
92 93 4.832266 AGTGGTTATTGCCAATGTTCAAGA 59.168 37.500 0.00 0.00 40.68 3.02
93 94 5.138125 AGTGGTTATTGCCAATGTTCAAG 57.862 39.130 0.00 0.00 40.68 3.02
94 95 5.536538 TGTAGTGGTTATTGCCAATGTTCAA 59.463 36.000 0.00 0.00 40.68 2.69
95 96 5.073428 TGTAGTGGTTATTGCCAATGTTCA 58.927 37.500 0.00 0.00 40.68 3.18
96 97 5.637006 TGTAGTGGTTATTGCCAATGTTC 57.363 39.130 0.00 0.00 40.68 3.18
97 98 6.412362 TTTGTAGTGGTTATTGCCAATGTT 57.588 33.333 0.00 0.00 40.68 2.71
98 99 6.412362 TTTTGTAGTGGTTATTGCCAATGT 57.588 33.333 0.00 0.00 40.68 2.71
99 100 7.903995 ATTTTTGTAGTGGTTATTGCCAATG 57.096 32.000 0.00 0.00 40.68 2.82
100 101 8.153550 TGAATTTTTGTAGTGGTTATTGCCAAT 58.846 29.630 0.00 0.00 40.68 3.16
101 102 7.500992 TGAATTTTTGTAGTGGTTATTGCCAA 58.499 30.769 0.00 0.00 40.68 4.52
102 103 7.055667 TGAATTTTTGTAGTGGTTATTGCCA 57.944 32.000 0.00 0.00 35.93 4.92
103 104 8.546597 AATGAATTTTTGTAGTGGTTATTGCC 57.453 30.769 0.00 0.00 0.00 4.52
161 162 9.961265 AAGCATCAACTAATATGATCATTTGTG 57.039 29.630 14.65 12.40 35.38 3.33
181 182 9.585099 TTATGAAACAAATCACCAATAAGCATC 57.415 29.630 0.00 0.00 30.82 3.91
360 362 8.519526 TCGCAAAATTTCATAAAGAGTTATGGT 58.480 29.630 6.62 0.00 44.62 3.55
434 437 9.670180 GTTTTGAACTTTACGATTTTCAAACAG 57.330 29.630 7.63 0.00 43.91 3.16
542 589 6.578023 TCTTATGGAAAAAGGTTTGTGTTGG 58.422 36.000 0.00 0.00 0.00 3.77
746 2163 9.575783 GCCTAAAACGAATGGTGAAATTAATAA 57.424 29.630 0.00 0.00 0.00 1.40
799 2503 5.941647 GTGAGTAATGGGCCTACAAGTTTAA 59.058 40.000 4.53 0.00 0.00 1.52
801 2505 4.202524 TGTGAGTAATGGGCCTACAAGTTT 60.203 41.667 4.53 0.00 0.00 2.66
857 2573 7.912056 TGAACCTTTTTCTGAGACTGATATG 57.088 36.000 0.00 0.00 0.00 1.78
866 2582 7.536622 CGAAATTCAGATGAACCTTTTTCTGAG 59.463 37.037 13.40 1.22 43.82 3.35
878 2594 6.370433 TGTGTGTTTCGAAATTCAGATGAA 57.630 33.333 14.69 0.00 38.56 2.57
943 2666 3.491652 GCGGCAGTTTCTCGGCTC 61.492 66.667 0.00 0.00 37.40 4.70
1126 2867 1.168407 AATCGGAGCGGCATTGGATG 61.168 55.000 1.45 0.00 0.00 3.51
1157 2898 1.024579 CGCCCCGCTTGTTTATCTGT 61.025 55.000 0.00 0.00 0.00 3.41
1413 3154 3.090532 GGGAGATGAAGGGCGGGT 61.091 66.667 0.00 0.00 0.00 5.28
1424 3168 2.665000 CAGCACACACGGGGAGAT 59.335 61.111 0.00 0.00 0.00 2.75
1430 3174 3.554232 CTACAGCAGCACACACGG 58.446 61.111 0.00 0.00 0.00 4.94
1446 3190 2.636893 AGATGAACTGGACTGAACTGCT 59.363 45.455 0.00 0.00 0.00 4.24
1447 3191 2.740981 CAGATGAACTGGACTGAACTGC 59.259 50.000 0.00 0.00 42.39 4.40
1594 3341 3.557595 CGACAGATGAACTAAGAATGGGC 59.442 47.826 0.00 0.00 0.00 5.36
1598 3345 3.868077 GCAGCGACAGATGAACTAAGAAT 59.132 43.478 0.00 0.00 35.41 2.40
1608 3355 3.561213 CGGCAGCAGCGACAGATG 61.561 66.667 0.00 0.00 43.41 2.90
1609 3356 2.584261 ATTCGGCAGCAGCGACAGAT 62.584 55.000 0.00 0.00 43.41 2.90
1610 3357 2.786539 AATTCGGCAGCAGCGACAGA 62.787 55.000 0.00 0.00 43.41 3.41
1664 3411 7.360017 CGACACTGAAATACTCAAATTGTAGCA 60.360 37.037 0.00 0.00 32.17 3.49
1759 3881 4.588106 TCTTGGAAATTTGCAGGTGAATGA 59.412 37.500 18.88 5.94 0.00 2.57
1816 3938 7.606456 TGGAGTATAACCTTTCTGCTTAAAGTG 59.394 37.037 9.52 5.15 35.16 3.16
1846 3968 7.297936 TCCGATACACCATATTTGACAGTAT 57.702 36.000 0.00 0.00 0.00 2.12
1862 3984 4.607293 ATGATGCTAAGCTTCCGATACA 57.393 40.909 0.00 0.00 32.74 2.29
1868 3990 7.793927 AAAGTTAGTATGATGCTAAGCTTCC 57.206 36.000 0.00 0.00 32.74 3.46
1878 4000 7.013464 AGGACGGACTCTAAAGTTAGTATGATG 59.987 40.741 0.00 0.00 35.28 3.07
1891 4013 1.471119 ATCGCAAGGACGGACTCTAA 58.529 50.000 0.00 0.00 38.47 2.10
1906 4028 2.079925 GATCCCAGATTAGCCAATCGC 58.920 52.381 0.00 0.00 44.51 4.58
1927 4049 2.057137 TGGATACTGCTGGGAAATGC 57.943 50.000 0.00 0.00 37.61 3.56
2012 4142 0.178995 TCTGGCCAGATGTTGCACAA 60.179 50.000 32.00 5.23 31.41 3.33
2069 4199 8.757982 AAGAAATTGATAGTTGCAGGATGTAT 57.242 30.769 0.00 0.00 39.31 2.29
2075 4205 9.859427 TTATGAAAAGAAATTGATAGTTGCAGG 57.141 29.630 0.00 0.00 0.00 4.85
2108 4238 5.009310 GGCTCTTCAATCACATCATATGCAA 59.991 40.000 0.00 0.00 0.00 4.08
2177 4307 5.860941 ATATGTCAGTGTAAGCTAGCACT 57.139 39.130 18.83 14.94 45.69 4.40
2205 4335 6.323739 ACCACATTAATATTGTTTAGGCCCTG 59.676 38.462 0.00 0.00 0.00 4.45
2339 4469 4.827284 CCAAACTAGGTTCAGAACATGGTT 59.173 41.667 20.29 20.29 46.36 3.67
2369 4499 1.266178 AATACAGGCTGGGGTTTTGC 58.734 50.000 20.34 0.00 0.00 3.68
2385 4515 5.217393 CGTGCTAGTTGTTCGCCTATAATA 58.783 41.667 0.00 0.00 0.00 0.98
2393 4523 2.474712 GGCGTGCTAGTTGTTCGC 59.525 61.111 0.00 0.00 44.95 4.70
2399 4529 0.816421 AACCAAACGGCGTGCTAGTT 60.816 50.000 15.70 12.58 0.00 2.24
2405 4535 2.353376 CTGCAACCAAACGGCGTG 60.353 61.111 15.70 3.23 0.00 5.34
2429 4559 0.743097 GCACCTTGCATCTGGGAATC 59.257 55.000 0.00 0.00 44.26 2.52
2430 4560 2.892025 GCACCTTGCATCTGGGAAT 58.108 52.632 0.00 0.00 44.26 3.01
2504 4635 0.108662 TCTGCCTATGAGTGCGTGTG 60.109 55.000 0.00 0.00 0.00 3.82
2509 4653 2.548875 CTCTGTTCTGCCTATGAGTGC 58.451 52.381 0.00 0.00 0.00 4.40
2581 4967 6.712095 TGCTTAAGACTCTGGCATTATTATGG 59.288 38.462 6.67 0.00 32.15 2.74
2590 4976 1.352083 ACCTGCTTAAGACTCTGGCA 58.648 50.000 6.67 0.00 0.00 4.92
2592 4978 3.764434 TGACTACCTGCTTAAGACTCTGG 59.236 47.826 6.67 4.92 0.00 3.86
2625 5017 4.402474 TCTGTCTTTCTGTCTGTCTGTGAA 59.598 41.667 0.00 0.00 0.00 3.18
2641 5037 5.788450 CAGGATGTTTAGTCTGTCTGTCTT 58.212 41.667 0.00 0.00 0.00 3.01
2642 5038 4.322349 GCAGGATGTTTAGTCTGTCTGTCT 60.322 45.833 0.00 0.00 39.31 3.41
2663 5059 0.599558 GAAGCACTTGCCTTGATGCA 59.400 50.000 0.00 0.00 43.38 3.96
2665 5061 0.877071 ACGAAGCACTTGCCTTGATG 59.123 50.000 0.00 0.00 43.38 3.07
2711 5107 1.272258 GCCCTAACCAACTTGCCCTTA 60.272 52.381 0.00 0.00 0.00 2.69
2714 5110 1.982395 GGCCCTAACCAACTTGCCC 60.982 63.158 0.00 0.00 32.74 5.36
2740 5137 5.506730 TGTACATCCCACTGTGGAATAAA 57.493 39.130 27.94 7.65 40.96 1.40
2857 5261 7.019774 TCTTGCATATTCTACAAATGACAGC 57.980 36.000 0.00 0.00 0.00 4.40
2948 5352 0.459899 CCTCGTCAACATCATCGGGA 59.540 55.000 0.00 0.00 0.00 5.14
3133 5552 0.323360 GCCTGGGACTAACATGGCAA 60.323 55.000 0.00 0.00 40.04 4.52
3143 5562 1.834263 GAAGAGTACATGCCTGGGACT 59.166 52.381 0.00 0.00 0.00 3.85
3222 5641 6.421801 AGCTCTGCAATGTTCAATACAAAAAC 59.578 34.615 0.00 0.00 40.89 2.43
3405 5828 1.837648 TTGCGTTCTGTTGTGCAATG 58.162 45.000 0.00 0.00 41.95 2.82
3420 5843 6.029607 AGTTAAATATGCTGTGTGAATTGCG 58.970 36.000 0.00 0.00 0.00 4.85
3458 5881 2.654863 ACAAACACCAGAAACTCAGGG 58.345 47.619 0.00 0.00 0.00 4.45
3477 5900 2.496070 GCTAATTCACCCCCAAGGAAAC 59.504 50.000 0.00 0.00 39.89 2.78
3550 5973 5.876357 AGAAACTCAGGCATAAAGTGGTAA 58.124 37.500 0.00 0.00 0.00 2.85
3553 5976 3.372206 CGAGAAACTCAGGCATAAAGTGG 59.628 47.826 0.00 0.00 0.00 4.00
3635 6058 6.649141 CCTAGCATGTTAACTTAGTGTGTTCA 59.351 38.462 7.22 0.00 0.00 3.18
3637 6060 6.765403 TCCTAGCATGTTAACTTAGTGTGTT 58.235 36.000 7.22 0.00 0.00 3.32
3670 6108 5.163652 GGCAAACCAACTATACCAAGTCATC 60.164 44.000 0.00 0.00 35.26 2.92
3675 6113 2.758423 GGGGCAAACCAACTATACCAAG 59.242 50.000 0.00 0.00 42.91 3.61
3682 6120 2.463047 AACAAGGGGCAAACCAACTA 57.537 45.000 0.00 0.00 42.91 2.24
3885 6336 4.952460 TGAGGTAGTAACACTTGGAACAC 58.048 43.478 0.00 0.00 39.29 3.32
3891 6342 7.387673 TCATTGACAATGAGGTAGTAACACTTG 59.612 37.037 23.89 0.00 42.69 3.16
3892 6343 7.450074 TCATTGACAATGAGGTAGTAACACTT 58.550 34.615 23.89 0.00 42.69 3.16
3912 6363 4.391216 ACAAAGACTTCTCTCGCATCATTG 59.609 41.667 0.00 0.00 0.00 2.82
3963 6414 5.435686 ACAGGCAGTACCATCAAGAAATA 57.564 39.130 0.00 0.00 43.14 1.40
3984 6435 5.059404 ACATTGCACAGCTTAACCATAAC 57.941 39.130 0.00 0.00 0.00 1.89
4050 6501 2.093783 AGTTCGTCGCAAATTCGGAATC 59.906 45.455 3.28 0.00 0.00 2.52
4055 6506 2.570468 TTCAGTTCGTCGCAAATTCG 57.430 45.000 0.00 0.00 0.00 3.34
4069 6520 2.362397 ACGATATGCACGGAGATTCAGT 59.638 45.455 0.00 0.00 34.93 3.41
4109 6560 2.750350 CTGCCCCGAACAGGAACT 59.250 61.111 0.00 0.00 45.00 3.01
4128 6579 7.383572 GGCAACTAACTATGATGAGAGTACATG 59.616 40.741 0.00 0.00 0.00 3.21
4152 6603 3.057736 GGTGAATGATGATATGCACTGGC 60.058 47.826 0.00 0.00 36.90 4.85
4154 6605 4.820173 ACTGGTGAATGATGATATGCACTG 59.180 41.667 0.00 0.00 36.90 3.66
4155 6606 5.045012 ACTGGTGAATGATGATATGCACT 57.955 39.130 0.00 0.00 36.90 4.40
4157 6608 5.072193 ACCTACTGGTGAATGATGATATGCA 59.928 40.000 0.00 0.00 46.51 3.96
4158 6609 5.555017 ACCTACTGGTGAATGATGATATGC 58.445 41.667 0.00 0.00 46.51 3.14
4245 6726 3.267031 CCCCTGTTCCTATCTCCAGTTTT 59.733 47.826 0.00 0.00 0.00 2.43
4258 6739 0.615850 CTCCTTCTGACCCCTGTTCC 59.384 60.000 0.00 0.00 0.00 3.62
4259 6740 1.276705 GTCTCCTTCTGACCCCTGTTC 59.723 57.143 0.00 0.00 0.00 3.18
4265 6746 2.745968 AGAGATGTCTCCTTCTGACCC 58.254 52.381 6.41 0.00 43.88 4.46
4276 6757 7.044798 GCACAGGATAAGTAAAAGAGATGTCT 58.955 38.462 0.00 0.00 32.81 3.41
4331 6816 3.817647 CAGGCTTCATACTTATCTTGCCC 59.182 47.826 0.00 0.00 39.90 5.36
4431 6919 2.191641 GCCATGTGCTCTCCTCCC 59.808 66.667 0.00 0.00 36.87 4.30
4463 6951 2.485479 GGATGTGTGAGTGTGTCCTGTT 60.485 50.000 0.00 0.00 0.00 3.16
4479 6967 5.494724 CTGCTTATATACTGCCATGGATGT 58.505 41.667 18.40 15.28 0.00 3.06
4480 6968 4.880120 CCTGCTTATATACTGCCATGGATG 59.120 45.833 18.40 9.52 0.00 3.51
4481 6969 4.627255 GCCTGCTTATATACTGCCATGGAT 60.627 45.833 18.40 1.82 0.00 3.41
4482 6970 3.307691 GCCTGCTTATATACTGCCATGGA 60.308 47.826 18.40 0.00 0.00 3.41
4483 6971 3.012518 GCCTGCTTATATACTGCCATGG 58.987 50.000 7.63 7.63 0.00 3.66
4484 6972 3.678289 TGCCTGCTTATATACTGCCATG 58.322 45.455 4.93 0.00 0.00 3.66
4485 6973 3.328931 ACTGCCTGCTTATATACTGCCAT 59.671 43.478 4.93 0.00 0.00 4.40
4506 6994 1.135139 TCTGACGATCAGGCTAAGCAC 59.865 52.381 12.89 0.00 44.39 4.40
4594 7095 1.890979 CGGTGGCCTGCATCATCTC 60.891 63.158 3.32 0.00 0.00 2.75
4783 7284 1.127567 TGACTGACCAAGGAGGGGTG 61.128 60.000 0.00 0.00 43.89 4.61
4784 7285 1.128188 GTGACTGACCAAGGAGGGGT 61.128 60.000 0.00 0.00 43.89 4.95
4786 7287 0.322975 CAGTGACTGACCAAGGAGGG 59.677 60.000 6.79 0.00 43.89 4.30
4788 7289 3.007290 TCAATCAGTGACTGACCAAGGAG 59.993 47.826 18.72 3.26 43.63 3.69
4790 7291 3.332919 CTCAATCAGTGACTGACCAAGG 58.667 50.000 18.72 6.00 43.63 3.61
4791 7292 2.740981 GCTCAATCAGTGACTGACCAAG 59.259 50.000 18.72 15.09 43.63 3.61
4792 7293 2.550855 GGCTCAATCAGTGACTGACCAA 60.551 50.000 18.72 5.01 43.63 3.67
4793 7294 1.002430 GGCTCAATCAGTGACTGACCA 59.998 52.381 18.72 3.66 43.63 4.02
4794 7295 1.277557 AGGCTCAATCAGTGACTGACC 59.722 52.381 18.72 13.86 43.63 4.02
4795 7296 2.028658 TCAGGCTCAATCAGTGACTGAC 60.029 50.000 18.72 4.46 46.09 3.51
4797 7298 2.619147 CTCAGGCTCAATCAGTGACTG 58.381 52.381 6.18 6.18 46.05 3.51
4798 7299 1.066286 GCTCAGGCTCAATCAGTGACT 60.066 52.381 0.00 0.00 35.22 3.41
4813 7314 2.028420 TGATGATCGGTTTGGCTCAG 57.972 50.000 0.00 0.00 0.00 3.35
4820 7321 2.715749 TGGCAGATGATGATCGGTTT 57.284 45.000 0.00 0.00 33.34 3.27
4822 7323 1.976404 AGATGGCAGATGATGATCGGT 59.024 47.619 0.00 0.00 33.34 4.69
4826 7327 2.224793 CCACCAGATGGCAGATGATGAT 60.225 50.000 0.00 0.00 43.24 2.45
4828 7329 1.605753 CCACCAGATGGCAGATGATG 58.394 55.000 0.00 0.00 43.24 3.07


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

AutoCloner maintained by Alex Coulton.