Multiple sequence alignment - TraesCS3A01G481900

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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 TraesCS3A01G481900 chr3A 100.000 2915 0 0 1 2915 712620085 712622999 0.000000e+00 5384.0
1 TraesCS3A01G481900 chr3A 83.230 972 105 27 1839 2761 108025714 108026676 0.000000e+00 839.0
2 TraesCS3A01G481900 chr3A 84.810 158 17 4 2762 2913 108029255 108029411 5.030000e-33 152.0
3 TraesCS3A01G481900 chr7A 98.110 2169 33 6 748 2915 134549240 134551401 0.000000e+00 3771.0
4 TraesCS3A01G481900 chr1A 88.915 866 69 10 726 1565 485565910 485565046 0.000000e+00 1042.0
5 TraesCS3A01G481900 chr1A 82.819 972 108 26 1839 2761 537066264 537065303 0.000000e+00 815.0
6 TraesCS3A01G481900 chr1A 84.810 158 17 4 2762 2913 537062633 537062477 5.030000e-33 152.0
7 TraesCS3A01G481900 chr1D 88.515 862 76 9 726 1565 386127377 386126517 0.000000e+00 1022.0
8 TraesCS3A01G481900 chr1B 88.515 862 76 7 726 1565 518266363 518265503 0.000000e+00 1022.0
9 TraesCS3A01G481900 chr6B 83.659 1126 120 30 1840 2910 659638284 659637168 0.000000e+00 1002.0
10 TraesCS3A01G481900 chr7B 83.585 1127 124 28 1839 2912 51622570 51621452 0.000000e+00 1000.0
11 TraesCS3A01G481900 chr5B 83.260 1129 124 31 1840 2912 505692851 505691732 0.000000e+00 977.0
12 TraesCS3A01G481900 chr5B 88.732 71 7 1 258 328 655716193 655716124 5.180000e-13 86.1
13 TraesCS3A01G481900 chr4B 83.245 1128 124 31 1840 2912 395822607 395823724 0.000000e+00 976.0
14 TraesCS3A01G481900 chr5D 83.801 1068 102 28 1839 2856 505889097 505890143 0.000000e+00 948.0
15 TraesCS3A01G481900 chr5D 87.400 500 35 11 259 735 435120707 435121201 1.530000e-152 549.0
16 TraesCS3A01G481900 chr6D 84.115 768 51 38 256 986 161148017 161148750 0.000000e+00 676.0
17 TraesCS3A01G481900 chr6A 84.540 718 56 32 259 950 77889171 77889859 0.000000e+00 660.0
18 TraesCS3A01G481900 chr6A 83.906 727 62 24 259 958 78018689 78019387 0.000000e+00 643.0
19 TraesCS3A01G481900 chr6A 88.571 70 5 3 260 328 65566474 65566407 6.700000e-12 82.4
20 TraesCS3A01G481900 chr6A 100.000 32 0 0 955 986 77889884 77889915 3.140000e-05 60.2
21 TraesCS3A01G481900 chr6A 100.000 32 0 0 955 986 78019402 78019433 3.140000e-05 60.2
22 TraesCS3A01G481900 chr4A 82.744 707 53 25 258 938 94762237 94762900 1.520000e-157 566.0
23 TraesCS3A01G481900 chr2A 88.235 391 27 7 347 724 579837220 579836836 1.590000e-122 449.0
24 TraesCS3A01G481900 chr2A 89.506 162 15 2 1572 1732 579836729 579836569 1.370000e-48 204.0
25 TraesCS3A01G481900 chr3D 93.091 275 4 3 1 260 577339982 577340256 3.520000e-104 388.0
26 TraesCS3A01G481900 chr3B 91.273 275 9 3 1 260 769631885 769632159 7.680000e-96 361.0
27 TraesCS3A01G481900 chr3B 91.273 275 9 3 1 260 769813102 769813376 7.680000e-96 361.0
28 TraesCS3A01G481900 chr3B 87.234 282 14 6 1 260 770116502 770116783 4.720000e-78 302.0


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 TraesCS3A01G481900 chr3A 712620085 712622999 2914 False 5384.0 5384 100.0000 1 2915 1 chr3A.!!$F1 2914
1 TraesCS3A01G481900 chr3A 108025714 108029411 3697 False 495.5 839 84.0200 1839 2913 2 chr3A.!!$F2 1074
2 TraesCS3A01G481900 chr7A 134549240 134551401 2161 False 3771.0 3771 98.1100 748 2915 1 chr7A.!!$F1 2167
3 TraesCS3A01G481900 chr1A 485565046 485565910 864 True 1042.0 1042 88.9150 726 1565 1 chr1A.!!$R1 839
4 TraesCS3A01G481900 chr1A 537062477 537066264 3787 True 483.5 815 83.8145 1839 2913 2 chr1A.!!$R2 1074
5 TraesCS3A01G481900 chr1D 386126517 386127377 860 True 1022.0 1022 88.5150 726 1565 1 chr1D.!!$R1 839
6 TraesCS3A01G481900 chr1B 518265503 518266363 860 True 1022.0 1022 88.5150 726 1565 1 chr1B.!!$R1 839
7 TraesCS3A01G481900 chr6B 659637168 659638284 1116 True 1002.0 1002 83.6590 1840 2910 1 chr6B.!!$R1 1070
8 TraesCS3A01G481900 chr7B 51621452 51622570 1118 True 1000.0 1000 83.5850 1839 2912 1 chr7B.!!$R1 1073
9 TraesCS3A01G481900 chr5B 505691732 505692851 1119 True 977.0 977 83.2600 1840 2912 1 chr5B.!!$R1 1072
10 TraesCS3A01G481900 chr4B 395822607 395823724 1117 False 976.0 976 83.2450 1840 2912 1 chr4B.!!$F1 1072
11 TraesCS3A01G481900 chr5D 505889097 505890143 1046 False 948.0 948 83.8010 1839 2856 1 chr5D.!!$F2 1017
12 TraesCS3A01G481900 chr6D 161148017 161148750 733 False 676.0 676 84.1150 256 986 1 chr6D.!!$F1 730
13 TraesCS3A01G481900 chr6A 77889171 77889915 744 False 360.1 660 92.2700 259 986 2 chr6A.!!$F1 727
14 TraesCS3A01G481900 chr6A 78018689 78019433 744 False 351.6 643 91.9530 259 986 2 chr6A.!!$F2 727
15 TraesCS3A01G481900 chr4A 94762237 94762900 663 False 566.0 566 82.7440 258 938 1 chr4A.!!$F1 680
16 TraesCS3A01G481900 chr2A 579836569 579837220 651 True 326.5 449 88.8705 347 1732 2 chr2A.!!$R1 1385

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
120 121 0.036875 GTGGACTTGGGGTTCTCCAG 59.963 60.0 0.0 0.0 38.17 3.86 F
121 122 0.104672 TGGACTTGGGGTTCTCCAGA 60.105 55.0 0.0 0.0 38.17 3.86 F
734 811 0.323087 CCTTTTTGTAGGGACGGGGG 60.323 60.0 0.0 0.0 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1080 1201 1.264749 TTACCTGCTCGGCCACATCT 61.265 55.000 2.24 0.0 35.61 2.90 R
1717 1843 2.104622 TGCGATCTTTGCAGATATGGGA 59.895 45.455 0.00 0.0 40.14 4.37 R
2057 2184 4.097892 TGCCTTTTTCTCTCTTTCCACAAC 59.902 41.667 0.00 0.0 0.00 3.32 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
19 20 2.353357 CCTTGGGCAGCAATATCTCA 57.647 50.000 0.00 0.00 0.00 3.27
20 21 2.872732 CCTTGGGCAGCAATATCTCAT 58.127 47.619 0.00 0.00 0.00 2.90
21 22 2.818432 CCTTGGGCAGCAATATCTCATC 59.182 50.000 0.00 0.00 0.00 2.92
22 23 3.483421 CTTGGGCAGCAATATCTCATCA 58.517 45.455 0.00 0.00 0.00 3.07
23 24 3.581265 TGGGCAGCAATATCTCATCAA 57.419 42.857 0.00 0.00 0.00 2.57
24 25 3.483421 TGGGCAGCAATATCTCATCAAG 58.517 45.455 0.00 0.00 0.00 3.02
25 26 3.117776 TGGGCAGCAATATCTCATCAAGT 60.118 43.478 0.00 0.00 0.00 3.16
26 27 3.887716 GGGCAGCAATATCTCATCAAGTT 59.112 43.478 0.00 0.00 0.00 2.66
27 28 4.261489 GGGCAGCAATATCTCATCAAGTTG 60.261 45.833 0.00 0.00 0.00 3.16
28 29 4.261489 GGCAGCAATATCTCATCAAGTTGG 60.261 45.833 2.34 0.00 0.00 3.77
29 30 4.337555 GCAGCAATATCTCATCAAGTTGGT 59.662 41.667 2.34 0.00 0.00 3.67
30 31 5.732528 GCAGCAATATCTCATCAAGTTGGTG 60.733 44.000 10.02 10.02 43.77 4.17
31 32 4.337555 AGCAATATCTCATCAAGTTGGTGC 59.662 41.667 11.48 0.00 0.00 5.01
32 33 4.787563 GCAATATCTCATCAAGTTGGTGCG 60.788 45.833 11.48 5.45 0.00 5.34
33 34 1.742761 ATCTCATCAAGTTGGTGCGG 58.257 50.000 11.48 6.88 0.00 5.69
34 35 0.684535 TCTCATCAAGTTGGTGCGGA 59.315 50.000 11.48 9.03 0.00 5.54
35 36 1.278985 TCTCATCAAGTTGGTGCGGAT 59.721 47.619 11.48 0.00 0.00 4.18
36 37 1.399440 CTCATCAAGTTGGTGCGGATG 59.601 52.381 11.48 2.67 37.33 3.51
37 38 1.003003 TCATCAAGTTGGTGCGGATGA 59.997 47.619 11.48 5.04 41.31 2.92
38 39 1.811965 CATCAAGTTGGTGCGGATGAA 59.188 47.619 2.53 0.00 38.03 2.57
39 40 1.234821 TCAAGTTGGTGCGGATGAAC 58.765 50.000 2.34 0.00 0.00 3.18
40 41 0.950836 CAAGTTGGTGCGGATGAACA 59.049 50.000 0.00 0.00 0.00 3.18
41 42 1.541147 CAAGTTGGTGCGGATGAACAT 59.459 47.619 0.00 0.00 0.00 2.71
42 43 1.909700 AGTTGGTGCGGATGAACATT 58.090 45.000 4.31 0.00 0.00 2.71
43 44 2.238521 AGTTGGTGCGGATGAACATTT 58.761 42.857 4.31 0.00 0.00 2.32
44 45 2.030007 AGTTGGTGCGGATGAACATTTG 60.030 45.455 4.31 0.00 0.00 2.32
45 46 0.243365 TGGTGCGGATGAACATTTGC 59.757 50.000 0.00 0.00 0.00 3.68
46 47 0.243365 GGTGCGGATGAACATTTGCA 59.757 50.000 9.58 9.58 0.00 4.08
47 48 1.135024 GGTGCGGATGAACATTTGCAT 60.135 47.619 14.36 0.00 35.03 3.96
48 49 1.921887 GTGCGGATGAACATTTGCATG 59.078 47.619 14.36 0.00 35.03 4.06
49 50 1.545136 TGCGGATGAACATTTGCATGT 59.455 42.857 9.58 0.00 46.34 3.21
50 51 1.921887 GCGGATGAACATTTGCATGTG 59.078 47.619 0.00 0.00 43.34 3.21
51 52 2.671914 GCGGATGAACATTTGCATGTGT 60.672 45.455 0.00 0.00 43.34 3.72
52 53 2.918600 CGGATGAACATTTGCATGTGTG 59.081 45.455 5.38 0.00 43.34 3.82
53 54 3.366171 CGGATGAACATTTGCATGTGTGA 60.366 43.478 5.38 0.00 43.34 3.58
54 55 4.171005 GGATGAACATTTGCATGTGTGAG 58.829 43.478 5.38 0.00 43.34 3.51
55 56 4.082625 GGATGAACATTTGCATGTGTGAGA 60.083 41.667 5.38 0.00 43.34 3.27
56 57 5.393787 GGATGAACATTTGCATGTGTGAGAT 60.394 40.000 5.38 0.00 43.34 2.75
57 58 4.800784 TGAACATTTGCATGTGTGAGATG 58.199 39.130 5.38 0.00 43.34 2.90
58 59 4.278919 TGAACATTTGCATGTGTGAGATGT 59.721 37.500 5.38 0.00 43.34 3.06
59 60 4.859304 ACATTTGCATGTGTGAGATGTT 57.141 36.364 3.92 0.00 42.46 2.71
60 61 4.552355 ACATTTGCATGTGTGAGATGTTG 58.448 39.130 3.92 0.00 42.46 3.33
61 62 2.710220 TTGCATGTGTGAGATGTTGC 57.290 45.000 0.00 0.00 0.00 4.17
62 63 1.900245 TGCATGTGTGAGATGTTGCT 58.100 45.000 0.00 0.00 0.00 3.91
63 64 2.232399 TGCATGTGTGAGATGTTGCTT 58.768 42.857 0.00 0.00 0.00 3.91
64 65 2.227149 TGCATGTGTGAGATGTTGCTTC 59.773 45.455 0.00 0.00 0.00 3.86
65 66 2.486982 GCATGTGTGAGATGTTGCTTCT 59.513 45.455 0.00 0.00 0.00 2.85
66 67 3.425892 GCATGTGTGAGATGTTGCTTCTC 60.426 47.826 0.00 5.43 40.06 2.87
67 68 3.758755 TGTGTGAGATGTTGCTTCTCT 57.241 42.857 11.52 0.00 40.26 3.10
68 69 3.657634 TGTGTGAGATGTTGCTTCTCTC 58.342 45.455 11.52 9.18 40.26 3.20
69 70 2.999355 GTGTGAGATGTTGCTTCTCTCC 59.001 50.000 11.52 5.19 40.26 3.71
70 71 2.634453 TGTGAGATGTTGCTTCTCTCCA 59.366 45.455 11.52 7.02 40.26 3.86
71 72 3.262660 TGTGAGATGTTGCTTCTCTCCAT 59.737 43.478 11.52 0.00 40.26 3.41
72 73 3.870419 GTGAGATGTTGCTTCTCTCCATC 59.130 47.826 11.52 0.00 40.26 3.51
73 74 3.516700 TGAGATGTTGCTTCTCTCCATCA 59.483 43.478 11.52 0.00 40.26 3.07
74 75 4.019950 TGAGATGTTGCTTCTCTCCATCAA 60.020 41.667 11.52 0.00 40.26 2.57
75 76 5.113446 AGATGTTGCTTCTCTCCATCAAT 57.887 39.130 0.00 0.00 35.50 2.57
76 77 5.124645 AGATGTTGCTTCTCTCCATCAATC 58.875 41.667 0.00 0.00 35.50 2.67
77 78 4.290711 TGTTGCTTCTCTCCATCAATCA 57.709 40.909 0.00 0.00 0.00 2.57
78 79 4.005650 TGTTGCTTCTCTCCATCAATCAC 58.994 43.478 0.00 0.00 0.00 3.06
79 80 3.272574 TGCTTCTCTCCATCAATCACC 57.727 47.619 0.00 0.00 0.00 4.02
80 81 2.842496 TGCTTCTCTCCATCAATCACCT 59.158 45.455 0.00 0.00 0.00 4.00
81 82 3.118482 TGCTTCTCTCCATCAATCACCTC 60.118 47.826 0.00 0.00 0.00 3.85
82 83 3.134442 GCTTCTCTCCATCAATCACCTCT 59.866 47.826 0.00 0.00 0.00 3.69
83 84 4.343526 GCTTCTCTCCATCAATCACCTCTA 59.656 45.833 0.00 0.00 0.00 2.43
84 85 5.011943 GCTTCTCTCCATCAATCACCTCTAT 59.988 44.000 0.00 0.00 0.00 1.98
85 86 6.662865 TTCTCTCCATCAATCACCTCTATC 57.337 41.667 0.00 0.00 0.00 2.08
86 87 4.764308 TCTCTCCATCAATCACCTCTATCG 59.236 45.833 0.00 0.00 0.00 2.92
87 88 3.256879 TCTCCATCAATCACCTCTATCGC 59.743 47.826 0.00 0.00 0.00 4.58
88 89 2.965147 TCCATCAATCACCTCTATCGCA 59.035 45.455 0.00 0.00 0.00 5.10
89 90 3.006217 TCCATCAATCACCTCTATCGCAG 59.994 47.826 0.00 0.00 0.00 5.18
90 91 3.006217 CCATCAATCACCTCTATCGCAGA 59.994 47.826 0.00 0.00 45.75 4.26
97 98 1.578926 CTCTATCGCAGAGCCCTCG 59.421 63.158 1.56 0.00 44.34 4.63
98 99 2.049618 CTATCGCAGAGCCCTCGC 60.050 66.667 0.00 3.24 43.63 5.03
99 100 3.565910 CTATCGCAGAGCCCTCGCC 62.566 68.421 6.56 0.00 43.63 5.54
109 110 4.760047 CCCTCGCCGGTGGACTTG 62.760 72.222 16.49 0.79 0.00 3.16
110 111 4.760047 CCTCGCCGGTGGACTTGG 62.760 72.222 16.49 6.36 0.00 3.61
111 112 4.760047 CTCGCCGGTGGACTTGGG 62.760 72.222 16.49 0.00 0.00 4.12
114 115 4.280019 GCCGGTGGACTTGGGGTT 62.280 66.667 1.90 0.00 0.00 4.11
115 116 2.033602 CCGGTGGACTTGGGGTTC 59.966 66.667 0.00 0.00 0.00 3.62
116 117 2.526046 CCGGTGGACTTGGGGTTCT 61.526 63.158 0.00 0.00 0.00 3.01
117 118 1.003718 CGGTGGACTTGGGGTTCTC 60.004 63.158 0.00 0.00 0.00 2.87
118 119 1.379146 GGTGGACTTGGGGTTCTCC 59.621 63.158 0.00 0.00 30.94 3.71
119 120 1.423794 GGTGGACTTGGGGTTCTCCA 61.424 60.000 0.00 0.00 37.12 3.86
120 121 0.036875 GTGGACTTGGGGTTCTCCAG 59.963 60.000 0.00 0.00 38.17 3.86
121 122 0.104672 TGGACTTGGGGTTCTCCAGA 60.105 55.000 0.00 0.00 38.17 3.86
122 123 0.615850 GGACTTGGGGTTCTCCAGAG 59.384 60.000 0.00 0.00 38.17 3.35
123 124 1.645710 GACTTGGGGTTCTCCAGAGA 58.354 55.000 0.00 0.00 38.17 3.10
124 125 1.978580 GACTTGGGGTTCTCCAGAGAA 59.021 52.381 6.00 6.00 44.47 2.87
133 134 3.834489 TTCTCCAGAGAATCATGAGGC 57.166 47.619 6.00 0.00 42.06 4.70
134 135 2.755686 TCTCCAGAGAATCATGAGGCA 58.244 47.619 0.09 0.00 37.82 4.75
135 136 3.315596 TCTCCAGAGAATCATGAGGCAT 58.684 45.455 0.09 0.00 37.82 4.40
136 137 3.071167 TCTCCAGAGAATCATGAGGCATG 59.929 47.826 0.09 1.08 37.57 4.06
137 138 5.183369 TCTCCAGAGAATCATGAGGCATGA 61.183 45.833 11.98 11.98 42.38 3.07
138 139 6.633832 TCTCCAGAGAATCATGAGGCATGAA 61.634 44.000 13.39 0.00 41.95 2.57
139 140 8.585864 TCTCCAGAGAATCATGAGGCATGAAC 62.586 46.154 13.39 10.68 41.95 3.18
146 147 4.976224 TCATGAGGCATGAACAGAATTG 57.024 40.909 7.58 0.00 46.17 2.32
147 148 3.697542 TCATGAGGCATGAACAGAATTGG 59.302 43.478 7.58 0.00 46.17 3.16
148 149 3.438216 TGAGGCATGAACAGAATTGGA 57.562 42.857 0.00 0.00 0.00 3.53
149 150 3.349927 TGAGGCATGAACAGAATTGGAG 58.650 45.455 0.00 0.00 0.00 3.86
150 151 3.245016 TGAGGCATGAACAGAATTGGAGT 60.245 43.478 0.00 0.00 0.00 3.85
151 152 4.019411 TGAGGCATGAACAGAATTGGAGTA 60.019 41.667 0.00 0.00 0.00 2.59
152 153 5.121380 AGGCATGAACAGAATTGGAGTAT 57.879 39.130 0.00 0.00 0.00 2.12
153 154 5.513233 AGGCATGAACAGAATTGGAGTATT 58.487 37.500 0.00 0.00 0.00 1.89
154 155 5.591877 AGGCATGAACAGAATTGGAGTATTC 59.408 40.000 0.00 0.00 35.26 1.75
155 156 5.591877 GGCATGAACAGAATTGGAGTATTCT 59.408 40.000 0.00 0.00 43.79 2.40
156 157 6.238593 GGCATGAACAGAATTGGAGTATTCTC 60.239 42.308 0.00 0.00 41.68 2.87
177 178 7.060383 TCTCCAGAGAAGAAACATCATATCC 57.940 40.000 0.00 0.00 33.91 2.59
178 179 6.042552 TCTCCAGAGAAGAAACATCATATCCC 59.957 42.308 0.00 0.00 33.91 3.85
179 180 4.993584 CCAGAGAAGAAACATCATATCCCG 59.006 45.833 0.00 0.00 0.00 5.14
180 181 4.450419 CAGAGAAGAAACATCATATCCCGC 59.550 45.833 0.00 0.00 0.00 6.13
181 182 4.101585 AGAGAAGAAACATCATATCCCGCA 59.898 41.667 0.00 0.00 0.00 5.69
182 183 4.384056 AGAAGAAACATCATATCCCGCAG 58.616 43.478 0.00 0.00 0.00 5.18
183 184 3.845781 AGAAACATCATATCCCGCAGT 57.154 42.857 0.00 0.00 0.00 4.40
184 185 4.156455 AGAAACATCATATCCCGCAGTT 57.844 40.909 0.00 0.00 0.00 3.16
185 186 3.879295 AGAAACATCATATCCCGCAGTTG 59.121 43.478 0.00 0.00 0.00 3.16
186 187 3.558931 AACATCATATCCCGCAGTTGA 57.441 42.857 0.00 0.00 0.00 3.18
187 188 3.777106 ACATCATATCCCGCAGTTGAT 57.223 42.857 0.00 0.00 0.00 2.57
188 189 3.668447 ACATCATATCCCGCAGTTGATC 58.332 45.455 0.00 0.00 0.00 2.92
189 190 3.326006 ACATCATATCCCGCAGTTGATCT 59.674 43.478 0.00 0.00 0.00 2.75
190 191 3.667497 TCATATCCCGCAGTTGATCTC 57.333 47.619 0.00 0.00 0.00 2.75
191 192 3.234353 TCATATCCCGCAGTTGATCTCT 58.766 45.455 0.00 0.00 0.00 3.10
192 193 3.006217 TCATATCCCGCAGTTGATCTCTG 59.994 47.826 12.03 12.03 36.18 3.35
193 194 1.198713 ATCCCGCAGTTGATCTCTGT 58.801 50.000 15.80 0.00 35.60 3.41
194 195 1.847328 TCCCGCAGTTGATCTCTGTA 58.153 50.000 15.80 2.65 35.60 2.74
195 196 1.751351 TCCCGCAGTTGATCTCTGTAG 59.249 52.381 15.80 11.63 35.60 2.74
196 197 1.202463 CCCGCAGTTGATCTCTGTAGG 60.202 57.143 15.80 16.95 35.60 3.18
197 198 1.478510 CCGCAGTTGATCTCTGTAGGT 59.521 52.381 15.80 0.00 35.60 3.08
198 199 2.093973 CCGCAGTTGATCTCTGTAGGTT 60.094 50.000 15.80 0.00 35.60 3.50
199 200 3.182967 CGCAGTTGATCTCTGTAGGTTC 58.817 50.000 15.80 2.76 35.60 3.62
200 201 3.119316 CGCAGTTGATCTCTGTAGGTTCT 60.119 47.826 15.80 0.00 35.60 3.01
201 202 4.619394 CGCAGTTGATCTCTGTAGGTTCTT 60.619 45.833 15.80 0.00 35.60 2.52
202 203 5.393135 CGCAGTTGATCTCTGTAGGTTCTTA 60.393 44.000 15.80 0.00 35.60 2.10
203 204 6.578023 GCAGTTGATCTCTGTAGGTTCTTAT 58.422 40.000 15.80 0.00 35.60 1.73
204 205 7.468768 CGCAGTTGATCTCTGTAGGTTCTTATA 60.469 40.741 15.80 0.00 35.60 0.98
205 206 8.198109 GCAGTTGATCTCTGTAGGTTCTTATAA 58.802 37.037 15.80 0.00 35.60 0.98
208 209 9.400638 GTTGATCTCTGTAGGTTCTTATAATCG 57.599 37.037 0.00 0.00 0.00 3.34
209 210 8.919777 TGATCTCTGTAGGTTCTTATAATCGA 57.080 34.615 0.00 0.00 0.00 3.59
210 211 9.004717 TGATCTCTGTAGGTTCTTATAATCGAG 57.995 37.037 0.00 0.00 0.00 4.04
211 212 8.927675 ATCTCTGTAGGTTCTTATAATCGAGT 57.072 34.615 0.00 0.00 0.00 4.18
213 214 9.491675 TCTCTGTAGGTTCTTATAATCGAGTAG 57.508 37.037 0.00 0.00 0.00 2.57
214 215 9.491675 CTCTGTAGGTTCTTATAATCGAGTAGA 57.508 37.037 0.00 0.00 0.00 2.59
215 216 9.491675 TCTGTAGGTTCTTATAATCGAGTAGAG 57.508 37.037 0.00 0.00 0.00 2.43
216 217 9.491675 CTGTAGGTTCTTATAATCGAGTAGAGA 57.508 37.037 0.00 1.95 0.00 3.10
226 227 9.770503 TTATAATCGAGTAGAGATATTTGACGC 57.229 33.333 0.00 0.00 0.00 5.19
227 228 5.950758 ATCGAGTAGAGATATTTGACGCT 57.049 39.130 0.00 0.00 0.00 5.07
228 229 5.096954 TCGAGTAGAGATATTTGACGCTG 57.903 43.478 0.00 0.00 0.00 5.18
229 230 3.666334 CGAGTAGAGATATTTGACGCTGC 59.334 47.826 0.00 0.00 0.00 5.25
230 231 4.611943 GAGTAGAGATATTTGACGCTGCA 58.388 43.478 0.00 0.00 0.00 4.41
231 232 5.011090 AGTAGAGATATTTGACGCTGCAA 57.989 39.130 0.00 0.00 0.00 4.08
232 233 5.419542 AGTAGAGATATTTGACGCTGCAAA 58.580 37.500 0.00 3.76 41.49 3.68
233 234 5.874810 AGTAGAGATATTTGACGCTGCAAAA 59.125 36.000 0.00 0.00 40.72 2.44
234 235 5.627499 AGAGATATTTGACGCTGCAAAAA 57.373 34.783 0.00 0.00 40.72 1.94
235 236 5.393962 AGAGATATTTGACGCTGCAAAAAC 58.606 37.500 0.00 1.67 40.72 2.43
236 237 5.048782 AGAGATATTTGACGCTGCAAAAACA 60.049 36.000 0.00 0.00 40.72 2.83
237 238 4.917415 AGATATTTGACGCTGCAAAAACAC 59.083 37.500 0.00 0.06 40.72 3.32
238 239 2.645730 TTTGACGCTGCAAAAACACT 57.354 40.000 0.00 0.00 35.03 3.55
239 240 2.645730 TTGACGCTGCAAAAACACTT 57.354 40.000 0.00 0.00 0.00 3.16
240 241 2.187351 TGACGCTGCAAAAACACTTC 57.813 45.000 0.00 0.00 0.00 3.01
241 242 1.470494 TGACGCTGCAAAAACACTTCA 59.530 42.857 0.00 0.00 0.00 3.02
242 243 1.846175 GACGCTGCAAAAACACTTCAC 59.154 47.619 0.00 0.00 0.00 3.18
243 244 1.201181 ACGCTGCAAAAACACTTCACA 59.799 42.857 0.00 0.00 0.00 3.58
244 245 1.583404 CGCTGCAAAAACACTTCACAC 59.417 47.619 0.00 0.00 0.00 3.82
245 246 2.605030 GCTGCAAAAACACTTCACACA 58.395 42.857 0.00 0.00 0.00 3.72
246 247 2.345341 GCTGCAAAAACACTTCACACAC 59.655 45.455 0.00 0.00 0.00 3.82
247 248 3.836949 CTGCAAAAACACTTCACACACT 58.163 40.909 0.00 0.00 0.00 3.55
248 249 3.573598 TGCAAAAACACTTCACACACTG 58.426 40.909 0.00 0.00 0.00 3.66
249 250 2.923020 GCAAAAACACTTCACACACTGG 59.077 45.455 0.00 0.00 0.00 4.00
250 251 3.613910 GCAAAAACACTTCACACACTGGT 60.614 43.478 0.00 0.00 0.00 4.00
251 252 4.555262 CAAAAACACTTCACACACTGGTT 58.445 39.130 0.00 0.00 0.00 3.67
252 253 4.434713 AAAACACTTCACACACTGGTTC 57.565 40.909 0.00 0.00 0.00 3.62
253 254 3.350219 AACACTTCACACACTGGTTCT 57.650 42.857 0.00 0.00 0.00 3.01
254 255 2.632377 ACACTTCACACACTGGTTCTG 58.368 47.619 0.00 0.00 0.00 3.02
275 276 6.690530 TCTGGAAATTAAAACCATTCAGCTG 58.309 36.000 7.63 7.63 33.08 4.24
316 317 1.666553 GATGTCCACGTCGGCAACA 60.667 57.895 0.00 0.00 33.14 3.33
426 443 2.756283 CCGCCTCGTCCTCCTCTT 60.756 66.667 0.00 0.00 0.00 2.85
511 537 3.773154 GCCCCTCCTCCTCCTCCT 61.773 72.222 0.00 0.00 0.00 3.69
587 613 2.092323 GGGTTCATCGGAAAGAAAGGG 58.908 52.381 0.00 0.00 34.13 3.95
625 653 3.227276 CGCCGTCTCCTATGCCCT 61.227 66.667 0.00 0.00 0.00 5.19
649 677 1.110518 CCCGCCTACTCTTCCTCTCC 61.111 65.000 0.00 0.00 0.00 3.71
650 678 0.395862 CCGCCTACTCTTCCTCTCCA 60.396 60.000 0.00 0.00 0.00 3.86
682 710 1.022735 TATCCTCGACGCAGAAGGAC 58.977 55.000 5.25 0.00 0.00 3.85
685 713 1.581954 CTCGACGCAGAAGGACAGT 59.418 57.895 0.00 0.00 0.00 3.55
734 811 0.323087 CCTTTTTGTAGGGACGGGGG 60.323 60.000 0.00 0.00 0.00 5.40
771 872 1.884075 CGTGTGAGTCGGATGGGGAA 61.884 60.000 0.00 0.00 0.00 3.97
880 981 1.027255 AGCTCTACGAAGCGCTCTCA 61.027 55.000 12.06 0.00 39.62 3.27
896 997 0.460987 CTCATTCTGCACGGAGGACC 60.461 60.000 0.00 0.00 0.00 4.46
1056 1177 3.385384 CTCCCCGTGCTCTGCTCA 61.385 66.667 0.00 0.00 0.00 4.26
1219 1344 4.252878 TGCAAGCGTTTGAGAAGATATCA 58.747 39.130 16.78 0.00 36.36 2.15
1283 1408 2.943033 GTTGTGCTGGTATACATGGACC 59.057 50.000 5.01 2.01 36.17 4.46
1506 1631 5.396213 GCAGTCTGAGGAGAAGATGGTATTT 60.396 44.000 3.32 0.00 0.00 1.40
1666 1792 1.269778 TGTCAAGGTGAGCTTCTGTCG 60.270 52.381 0.00 0.00 0.00 4.35
1711 1837 2.521547 TCTGCATCACTCTCTCTCCA 57.478 50.000 0.00 0.00 0.00 3.86
1717 1843 6.099413 TCTGCATCACTCTCTCTCCATTTATT 59.901 38.462 0.00 0.00 0.00 1.40
1795 1921 6.119536 TCCCACTATTGTTACCATGTTGATC 58.880 40.000 0.00 0.00 0.00 2.92
1859 1985 7.170998 AGCGTATAAATGGTTTTTCTCCTATCG 59.829 37.037 0.00 0.00 0.00 2.92
1970 2096 8.389779 TGCTGATTGTTTTCTGTCATTAGTAA 57.610 30.769 0.00 0.00 0.00 2.24
2057 2184 0.798776 GTTCATCGTCCAAGCACCTG 59.201 55.000 0.00 0.00 0.00 4.00
2377 2520 3.127895 TGTTCGGCTGCAATAATTACCAC 59.872 43.478 0.50 0.00 0.00 4.16
2504 2647 7.854557 TTCATACTAACTACGAGCTTCACTA 57.145 36.000 0.00 0.00 0.00 2.74
2683 2850 5.707298 GCACCTATACTAATTGGCATCACAT 59.293 40.000 0.00 0.00 31.80 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.353357 TGAGATATTGCTGCCCAAGG 57.647 50.000 0.00 0.00 36.76 3.61
1 2 3.483421 TGATGAGATATTGCTGCCCAAG 58.517 45.455 0.00 0.00 36.76 3.61
2 3 3.581265 TGATGAGATATTGCTGCCCAA 57.419 42.857 0.00 0.00 37.94 4.12
3 4 3.117776 ACTTGATGAGATATTGCTGCCCA 60.118 43.478 0.00 0.00 0.00 5.36
4 5 3.484407 ACTTGATGAGATATTGCTGCCC 58.516 45.455 0.00 0.00 0.00 5.36
5 6 4.261489 CCAACTTGATGAGATATTGCTGCC 60.261 45.833 0.00 0.00 0.00 4.85
6 7 4.337555 ACCAACTTGATGAGATATTGCTGC 59.662 41.667 0.00 0.00 0.00 5.25
7 8 5.732528 GCACCAACTTGATGAGATATTGCTG 60.733 44.000 0.00 0.00 0.00 4.41
8 9 4.337555 GCACCAACTTGATGAGATATTGCT 59.662 41.667 0.00 0.00 0.00 3.91
9 10 4.604976 GCACCAACTTGATGAGATATTGC 58.395 43.478 0.00 0.00 0.00 3.56
10 11 4.260907 CCGCACCAACTTGATGAGATATTG 60.261 45.833 0.00 0.00 0.00 1.90
11 12 3.879295 CCGCACCAACTTGATGAGATATT 59.121 43.478 0.00 0.00 0.00 1.28
12 13 3.134623 TCCGCACCAACTTGATGAGATAT 59.865 43.478 0.00 0.00 0.00 1.63
13 14 2.499693 TCCGCACCAACTTGATGAGATA 59.500 45.455 0.00 0.00 0.00 1.98
14 15 1.278985 TCCGCACCAACTTGATGAGAT 59.721 47.619 0.00 0.00 0.00 2.75
15 16 0.684535 TCCGCACCAACTTGATGAGA 59.315 50.000 0.00 0.00 0.00 3.27
16 17 1.399440 CATCCGCACCAACTTGATGAG 59.601 52.381 0.00 0.00 35.89 2.90
17 18 1.003003 TCATCCGCACCAACTTGATGA 59.997 47.619 0.00 0.00 39.45 2.92
18 19 1.452110 TCATCCGCACCAACTTGATG 58.548 50.000 0.00 0.00 35.32 3.07
19 20 1.812571 GTTCATCCGCACCAACTTGAT 59.187 47.619 0.00 0.00 0.00 2.57
20 21 1.234821 GTTCATCCGCACCAACTTGA 58.765 50.000 0.00 0.00 0.00 3.02
21 22 0.950836 TGTTCATCCGCACCAACTTG 59.049 50.000 0.00 0.00 0.00 3.16
22 23 1.909700 ATGTTCATCCGCACCAACTT 58.090 45.000 0.00 0.00 0.00 2.66
23 24 1.909700 AATGTTCATCCGCACCAACT 58.090 45.000 0.00 0.00 0.00 3.16
24 25 2.327568 CAAATGTTCATCCGCACCAAC 58.672 47.619 0.00 0.00 0.00 3.77
25 26 1.336702 GCAAATGTTCATCCGCACCAA 60.337 47.619 0.00 0.00 0.00 3.67
26 27 0.243365 GCAAATGTTCATCCGCACCA 59.757 50.000 0.00 0.00 0.00 4.17
27 28 0.243365 TGCAAATGTTCATCCGCACC 59.757 50.000 5.41 0.00 0.00 5.01
28 29 1.921887 CATGCAAATGTTCATCCGCAC 59.078 47.619 9.95 0.00 31.22 5.34
29 30 1.545136 ACATGCAAATGTTCATCCGCA 59.455 42.857 10.10 10.10 0.00 5.69
30 31 1.921887 CACATGCAAATGTTCATCCGC 59.078 47.619 0.00 0.00 31.37 5.54
31 32 2.918600 CACACATGCAAATGTTCATCCG 59.081 45.455 3.56 0.00 31.37 4.18
32 33 4.082625 TCTCACACATGCAAATGTTCATCC 60.083 41.667 3.56 0.00 31.37 3.51
33 34 5.050644 TCTCACACATGCAAATGTTCATC 57.949 39.130 3.56 0.00 31.37 2.92
34 35 5.047590 ACATCTCACACATGCAAATGTTCAT 60.048 36.000 3.56 0.00 31.37 2.57
35 36 4.278919 ACATCTCACACATGCAAATGTTCA 59.721 37.500 3.56 0.00 31.37 3.18
36 37 4.801891 ACATCTCACACATGCAAATGTTC 58.198 39.130 3.56 0.00 31.37 3.18
37 38 4.859304 ACATCTCACACATGCAAATGTT 57.141 36.364 3.56 0.00 31.37 2.71
38 39 4.552355 CAACATCTCACACATGCAAATGT 58.448 39.130 0.00 0.00 34.64 2.71
39 40 3.366724 GCAACATCTCACACATGCAAATG 59.633 43.478 0.00 0.00 34.10 2.32
40 41 3.257375 AGCAACATCTCACACATGCAAAT 59.743 39.130 0.00 0.00 36.30 2.32
41 42 2.624364 AGCAACATCTCACACATGCAAA 59.376 40.909 0.00 0.00 36.30 3.68
42 43 2.232399 AGCAACATCTCACACATGCAA 58.768 42.857 0.00 0.00 36.30 4.08
43 44 1.900245 AGCAACATCTCACACATGCA 58.100 45.000 0.00 0.00 36.30 3.96
44 45 2.486982 AGAAGCAACATCTCACACATGC 59.513 45.455 0.00 0.00 0.00 4.06
45 46 4.001652 AGAGAAGCAACATCTCACACATG 58.998 43.478 6.35 0.00 44.64 3.21
46 47 4.252073 GAGAGAAGCAACATCTCACACAT 58.748 43.478 6.35 0.00 44.64 3.21
47 48 3.555795 GGAGAGAAGCAACATCTCACACA 60.556 47.826 6.35 0.00 44.64 3.72
48 49 2.999355 GGAGAGAAGCAACATCTCACAC 59.001 50.000 6.35 0.00 44.64 3.82
49 50 2.634453 TGGAGAGAAGCAACATCTCACA 59.366 45.455 6.35 2.48 44.64 3.58
50 51 3.325293 TGGAGAGAAGCAACATCTCAC 57.675 47.619 6.35 0.10 44.64 3.51
51 52 3.516700 TGATGGAGAGAAGCAACATCTCA 59.483 43.478 6.35 0.00 44.64 3.27
52 53 4.134379 TGATGGAGAGAAGCAACATCTC 57.866 45.455 0.00 0.00 42.95 2.75
53 54 4.564782 TTGATGGAGAGAAGCAACATCT 57.435 40.909 0.00 0.00 38.88 2.90
54 55 4.880120 TGATTGATGGAGAGAAGCAACATC 59.120 41.667 0.00 0.00 38.65 3.06
55 56 4.639310 GTGATTGATGGAGAGAAGCAACAT 59.361 41.667 0.00 0.00 0.00 2.71
56 57 4.005650 GTGATTGATGGAGAGAAGCAACA 58.994 43.478 0.00 0.00 0.00 3.33
57 58 3.376546 GGTGATTGATGGAGAGAAGCAAC 59.623 47.826 0.00 0.00 0.00 4.17
58 59 3.265221 AGGTGATTGATGGAGAGAAGCAA 59.735 43.478 0.00 0.00 0.00 3.91
59 60 2.842496 AGGTGATTGATGGAGAGAAGCA 59.158 45.455 0.00 0.00 0.00 3.91
60 61 3.134442 AGAGGTGATTGATGGAGAGAAGC 59.866 47.826 0.00 0.00 0.00 3.86
61 62 6.570186 CGATAGAGGTGATTGATGGAGAGAAG 60.570 46.154 0.00 0.00 39.76 2.85
62 63 5.242615 CGATAGAGGTGATTGATGGAGAGAA 59.757 44.000 0.00 0.00 39.76 2.87
63 64 4.764308 CGATAGAGGTGATTGATGGAGAGA 59.236 45.833 0.00 0.00 39.76 3.10
64 65 4.617995 GCGATAGAGGTGATTGATGGAGAG 60.618 50.000 0.00 0.00 39.76 3.20
65 66 3.256879 GCGATAGAGGTGATTGATGGAGA 59.743 47.826 0.00 0.00 39.76 3.71
66 67 3.006217 TGCGATAGAGGTGATTGATGGAG 59.994 47.826 0.00 0.00 39.76 3.86
67 68 2.965147 TGCGATAGAGGTGATTGATGGA 59.035 45.455 0.00 0.00 39.76 3.41
68 69 3.006217 TCTGCGATAGAGGTGATTGATGG 59.994 47.826 0.00 0.00 39.76 3.51
69 70 4.248691 TCTGCGATAGAGGTGATTGATG 57.751 45.455 0.00 0.00 39.76 3.07
80 81 2.556459 GCGAGGGCTCTGCGATAGA 61.556 63.158 9.25 0.00 34.91 1.98
81 82 2.049618 GCGAGGGCTCTGCGATAG 60.050 66.667 9.25 0.00 35.83 2.08
82 83 3.606662 GGCGAGGGCTCTGCGATA 61.607 66.667 9.25 0.00 39.81 2.92
92 93 4.760047 CAAGTCCACCGGCGAGGG 62.760 72.222 9.30 9.77 46.96 4.30
94 95 4.760047 CCCAAGTCCACCGGCGAG 62.760 72.222 9.30 0.06 0.00 5.03
97 98 4.280019 AACCCCAAGTCCACCGGC 62.280 66.667 0.00 0.00 0.00 6.13
98 99 2.033602 GAACCCCAAGTCCACCGG 59.966 66.667 0.00 0.00 0.00 5.28
99 100 1.003718 GAGAACCCCAAGTCCACCG 60.004 63.158 0.00 0.00 0.00 4.94
100 101 1.379146 GGAGAACCCCAAGTCCACC 59.621 63.158 0.00 0.00 0.00 4.61
101 102 0.036875 CTGGAGAACCCCAAGTCCAC 59.963 60.000 0.00 0.00 35.22 4.02
102 103 0.104672 TCTGGAGAACCCCAAGTCCA 60.105 55.000 0.00 0.00 37.52 4.02
103 104 0.615850 CTCTGGAGAACCCCAAGTCC 59.384 60.000 0.00 0.00 35.47 3.85
104 105 1.645710 TCTCTGGAGAACCCCAAGTC 58.354 55.000 0.00 0.00 35.47 3.01
105 106 2.118403 TTCTCTGGAGAACCCCAAGT 57.882 50.000 8.74 0.00 42.06 3.16
112 113 6.484041 CATGCCTCATGATTCTCTGGAGAAC 61.484 48.000 14.23 9.55 43.81 3.01
113 114 4.444449 CATGCCTCATGATTCTCTGGAGAA 60.444 45.833 14.29 14.29 43.81 2.87
114 115 2.755686 TGCCTCATGATTCTCTGGAGA 58.244 47.619 0.00 0.00 35.27 3.71
115 116 3.071167 TCATGCCTCATGATTCTCTGGAG 59.929 47.826 5.48 0.00 44.60 3.86
116 117 3.043418 TCATGCCTCATGATTCTCTGGA 58.957 45.455 5.48 0.00 44.60 3.86
117 118 3.487120 TCATGCCTCATGATTCTCTGG 57.513 47.619 5.48 0.00 44.60 3.86
126 127 3.697542 TCCAATTCTGTTCATGCCTCATG 59.302 43.478 0.59 0.59 42.60 3.07
127 128 3.952323 CTCCAATTCTGTTCATGCCTCAT 59.048 43.478 0.00 0.00 0.00 2.90
128 129 3.245016 ACTCCAATTCTGTTCATGCCTCA 60.245 43.478 0.00 0.00 0.00 3.86
129 130 3.350833 ACTCCAATTCTGTTCATGCCTC 58.649 45.455 0.00 0.00 0.00 4.70
130 131 3.446442 ACTCCAATTCTGTTCATGCCT 57.554 42.857 0.00 0.00 0.00 4.75
131 132 5.591877 AGAATACTCCAATTCTGTTCATGCC 59.408 40.000 0.00 0.00 43.09 4.40
132 133 6.690194 AGAATACTCCAATTCTGTTCATGC 57.310 37.500 0.00 0.00 43.09 4.06
147 148 7.551585 TGATGTTTCTTCTCTGGAGAATACTC 58.448 38.462 12.61 10.55 45.40 2.59
148 149 7.487822 TGATGTTTCTTCTCTGGAGAATACT 57.512 36.000 12.61 4.05 45.40 2.12
149 150 9.995003 ATATGATGTTTCTTCTCTGGAGAATAC 57.005 33.333 12.61 11.41 45.40 1.89
151 152 8.156165 GGATATGATGTTTCTTCTCTGGAGAAT 58.844 37.037 12.61 0.00 45.40 2.40
152 153 7.419518 GGGATATGATGTTTCTTCTCTGGAGAA 60.420 40.741 11.81 11.81 44.47 2.87
153 154 6.042552 GGGATATGATGTTTCTTCTCTGGAGA 59.957 42.308 0.00 0.00 35.27 3.71
154 155 6.229733 GGGATATGATGTTTCTTCTCTGGAG 58.770 44.000 0.00 0.00 0.00 3.86
155 156 5.221521 CGGGATATGATGTTTCTTCTCTGGA 60.222 44.000 0.00 0.00 0.00 3.86
156 157 4.993584 CGGGATATGATGTTTCTTCTCTGG 59.006 45.833 0.00 0.00 0.00 3.86
157 158 4.450419 GCGGGATATGATGTTTCTTCTCTG 59.550 45.833 0.00 0.00 0.00 3.35
158 159 4.101585 TGCGGGATATGATGTTTCTTCTCT 59.898 41.667 0.00 0.00 0.00 3.10
159 160 4.380531 TGCGGGATATGATGTTTCTTCTC 58.619 43.478 0.00 0.00 0.00 2.87
160 161 4.141620 ACTGCGGGATATGATGTTTCTTCT 60.142 41.667 0.00 0.00 0.00 2.85
161 162 4.130118 ACTGCGGGATATGATGTTTCTTC 58.870 43.478 0.00 0.00 0.00 2.87
162 163 4.156455 ACTGCGGGATATGATGTTTCTT 57.844 40.909 0.00 0.00 0.00 2.52
163 164 3.845781 ACTGCGGGATATGATGTTTCT 57.154 42.857 0.00 0.00 0.00 2.52
164 165 3.876914 TCAACTGCGGGATATGATGTTTC 59.123 43.478 0.00 0.00 0.00 2.78
165 166 3.884895 TCAACTGCGGGATATGATGTTT 58.115 40.909 0.00 0.00 0.00 2.83
166 167 3.558931 TCAACTGCGGGATATGATGTT 57.441 42.857 0.00 0.00 0.00 2.71
167 168 3.326006 AGATCAACTGCGGGATATGATGT 59.674 43.478 9.28 4.19 31.24 3.06
168 169 3.931468 GAGATCAACTGCGGGATATGATG 59.069 47.826 9.28 0.00 31.24 3.07
169 170 3.837146 AGAGATCAACTGCGGGATATGAT 59.163 43.478 0.00 1.23 33.64 2.45
170 171 3.006217 CAGAGATCAACTGCGGGATATGA 59.994 47.826 0.00 0.00 0.00 2.15
171 172 3.244009 ACAGAGATCAACTGCGGGATATG 60.244 47.826 16.27 0.00 38.74 1.78
172 173 2.968574 ACAGAGATCAACTGCGGGATAT 59.031 45.455 16.27 0.00 38.74 1.63
173 174 2.388735 ACAGAGATCAACTGCGGGATA 58.611 47.619 16.27 0.00 38.74 2.59
174 175 1.198713 ACAGAGATCAACTGCGGGAT 58.801 50.000 16.27 0.00 38.74 3.85
175 176 1.751351 CTACAGAGATCAACTGCGGGA 59.249 52.381 16.27 0.00 38.74 5.14
176 177 1.202463 CCTACAGAGATCAACTGCGGG 60.202 57.143 16.27 14.37 38.74 6.13
177 178 1.478510 ACCTACAGAGATCAACTGCGG 59.521 52.381 16.27 17.33 38.74 5.69
178 179 2.949451 ACCTACAGAGATCAACTGCG 57.051 50.000 16.27 9.82 38.74 5.18
179 180 4.464069 AGAACCTACAGAGATCAACTGC 57.536 45.455 16.27 3.55 38.74 4.40
182 183 9.400638 CGATTATAAGAACCTACAGAGATCAAC 57.599 37.037 0.00 0.00 0.00 3.18
183 184 9.350951 TCGATTATAAGAACCTACAGAGATCAA 57.649 33.333 0.00 0.00 0.00 2.57
184 185 8.919777 TCGATTATAAGAACCTACAGAGATCA 57.080 34.615 0.00 0.00 0.00 2.92
185 186 9.005777 ACTCGATTATAAGAACCTACAGAGATC 57.994 37.037 0.00 0.00 0.00 2.75
186 187 8.927675 ACTCGATTATAAGAACCTACAGAGAT 57.072 34.615 0.00 0.00 0.00 2.75
187 188 9.491675 CTACTCGATTATAAGAACCTACAGAGA 57.508 37.037 0.00 0.00 0.00 3.10
188 189 9.491675 TCTACTCGATTATAAGAACCTACAGAG 57.508 37.037 0.00 0.00 0.00 3.35
189 190 9.491675 CTCTACTCGATTATAAGAACCTACAGA 57.508 37.037 0.00 0.00 0.00 3.41
190 191 9.491675 TCTCTACTCGATTATAAGAACCTACAG 57.508 37.037 0.00 0.00 0.00 2.74
200 201 9.770503 GCGTCAAATATCTCTACTCGATTATAA 57.229 33.333 0.00 0.00 0.00 0.98
201 202 9.163899 AGCGTCAAATATCTCTACTCGATTATA 57.836 33.333 0.00 0.00 0.00 0.98
202 203 7.965655 CAGCGTCAAATATCTCTACTCGATTAT 59.034 37.037 0.00 0.00 0.00 1.28
203 204 7.298854 CAGCGTCAAATATCTCTACTCGATTA 58.701 38.462 0.00 0.00 0.00 1.75
204 205 6.146216 CAGCGTCAAATATCTCTACTCGATT 58.854 40.000 0.00 0.00 0.00 3.34
205 206 5.694816 CAGCGTCAAATATCTCTACTCGAT 58.305 41.667 0.00 0.00 0.00 3.59
206 207 4.554919 GCAGCGTCAAATATCTCTACTCGA 60.555 45.833 0.00 0.00 0.00 4.04
207 208 3.666334 GCAGCGTCAAATATCTCTACTCG 59.334 47.826 0.00 0.00 0.00 4.18
208 209 4.611943 TGCAGCGTCAAATATCTCTACTC 58.388 43.478 0.00 0.00 0.00 2.59
209 210 4.655762 TGCAGCGTCAAATATCTCTACT 57.344 40.909 0.00 0.00 0.00 2.57
210 211 5.718649 TTTGCAGCGTCAAATATCTCTAC 57.281 39.130 2.91 0.00 31.64 2.59
211 212 6.148645 TGTTTTTGCAGCGTCAAATATCTCTA 59.851 34.615 7.13 0.00 36.04 2.43
212 213 5.048782 TGTTTTTGCAGCGTCAAATATCTCT 60.049 36.000 7.13 0.00 36.04 3.10
213 214 5.059710 GTGTTTTTGCAGCGTCAAATATCTC 59.940 40.000 7.13 1.16 36.04 2.75
214 215 4.917415 GTGTTTTTGCAGCGTCAAATATCT 59.083 37.500 7.13 0.00 36.04 1.98
215 216 4.917415 AGTGTTTTTGCAGCGTCAAATATC 59.083 37.500 7.13 3.30 36.04 1.63
216 217 4.870363 AGTGTTTTTGCAGCGTCAAATAT 58.130 34.783 7.13 0.00 36.04 1.28
217 218 4.300189 AGTGTTTTTGCAGCGTCAAATA 57.700 36.364 7.13 1.30 36.04 1.40
218 219 3.163630 AGTGTTTTTGCAGCGTCAAAT 57.836 38.095 7.13 0.00 36.04 2.32
219 220 2.645730 AGTGTTTTTGCAGCGTCAAA 57.354 40.000 2.91 2.91 34.47 2.69
220 221 2.095008 TGAAGTGTTTTTGCAGCGTCAA 60.095 40.909 0.00 0.00 0.00 3.18
221 222 1.470494 TGAAGTGTTTTTGCAGCGTCA 59.530 42.857 0.00 0.00 0.00 4.35
222 223 1.846175 GTGAAGTGTTTTTGCAGCGTC 59.154 47.619 0.00 0.00 0.00 5.19
223 224 1.201181 TGTGAAGTGTTTTTGCAGCGT 59.799 42.857 0.00 0.00 0.00 5.07
224 225 1.583404 GTGTGAAGTGTTTTTGCAGCG 59.417 47.619 0.00 0.00 0.00 5.18
225 226 2.345341 GTGTGTGAAGTGTTTTTGCAGC 59.655 45.455 0.00 0.00 0.00 5.25
226 227 3.609373 CAGTGTGTGAAGTGTTTTTGCAG 59.391 43.478 0.00 0.00 0.00 4.41
227 228 3.573598 CAGTGTGTGAAGTGTTTTTGCA 58.426 40.909 0.00 0.00 0.00 4.08
228 229 2.923020 CCAGTGTGTGAAGTGTTTTTGC 59.077 45.455 0.00 0.00 0.00 3.68
229 230 4.173036 ACCAGTGTGTGAAGTGTTTTTG 57.827 40.909 0.00 0.00 0.00 2.44
230 231 4.522789 AGAACCAGTGTGTGAAGTGTTTTT 59.477 37.500 0.00 0.00 0.00 1.94
231 232 4.079253 AGAACCAGTGTGTGAAGTGTTTT 58.921 39.130 0.00 0.00 0.00 2.43
232 233 3.440173 CAGAACCAGTGTGTGAAGTGTTT 59.560 43.478 0.00 0.00 0.00 2.83
233 234 3.009723 CAGAACCAGTGTGTGAAGTGTT 58.990 45.455 0.00 0.00 0.00 3.32
234 235 2.632377 CAGAACCAGTGTGTGAAGTGT 58.368 47.619 0.00 0.00 0.00 3.55
235 236 1.942657 CCAGAACCAGTGTGTGAAGTG 59.057 52.381 0.00 0.00 0.00 3.16
236 237 1.837439 TCCAGAACCAGTGTGTGAAGT 59.163 47.619 0.00 0.00 0.00 3.01
237 238 2.620251 TCCAGAACCAGTGTGTGAAG 57.380 50.000 0.00 0.00 0.00 3.02
238 239 3.358111 TTTCCAGAACCAGTGTGTGAA 57.642 42.857 0.00 0.00 0.00 3.18
239 240 3.576078 ATTTCCAGAACCAGTGTGTGA 57.424 42.857 0.00 0.00 0.00 3.58
240 241 5.766150 TTAATTTCCAGAACCAGTGTGTG 57.234 39.130 0.00 0.00 0.00 3.82
241 242 6.406512 GGTTTTAATTTCCAGAACCAGTGTGT 60.407 38.462 0.00 0.00 39.56 3.72
242 243 5.983118 GGTTTTAATTTCCAGAACCAGTGTG 59.017 40.000 0.00 0.00 39.56 3.82
243 244 5.659079 TGGTTTTAATTTCCAGAACCAGTGT 59.341 36.000 2.37 0.00 43.36 3.55
244 245 6.155475 TGGTTTTAATTTCCAGAACCAGTG 57.845 37.500 2.37 0.00 43.36 3.66
248 249 6.368791 GCTGAATGGTTTTAATTTCCAGAACC 59.631 38.462 0.00 0.00 40.06 3.62
249 250 7.116805 CAGCTGAATGGTTTTAATTTCCAGAAC 59.883 37.037 8.42 0.00 34.62 3.01
250 251 7.153985 CAGCTGAATGGTTTTAATTTCCAGAA 58.846 34.615 8.42 0.00 34.62 3.02
251 252 6.690530 CAGCTGAATGGTTTTAATTTCCAGA 58.309 36.000 8.42 0.00 34.62 3.86
252 253 5.349543 GCAGCTGAATGGTTTTAATTTCCAG 59.650 40.000 20.43 0.00 34.62 3.86
253 254 5.237048 GCAGCTGAATGGTTTTAATTTCCA 58.763 37.500 20.43 0.00 35.64 3.53
254 255 4.327087 CGCAGCTGAATGGTTTTAATTTCC 59.673 41.667 20.43 0.00 0.00 3.13
301 302 1.007038 TACTGTTGCCGACGTGGAC 60.007 57.895 0.00 0.00 42.00 4.02
333 334 3.953542 AAAGCGAAGGGGATAAATCCT 57.046 42.857 8.85 0.00 46.35 3.24
343 344 9.129209 CTTTTTCTTAGAATAAAAAGCGAAGGG 57.871 33.333 10.72 0.00 42.47 3.95
344 345 9.893305 TCTTTTTCTTAGAATAAAAAGCGAAGG 57.107 29.630 15.50 0.00 45.68 3.46
371 386 3.600388 TGAAGGCGATTTTCTCCTCTTC 58.400 45.455 0.00 0.00 28.59 2.87
373 388 2.679349 GCTGAAGGCGATTTTCTCCTCT 60.679 50.000 0.00 0.00 28.59 3.69
511 537 1.065273 GCGAGACGGCGGAAGATAA 59.935 57.895 13.24 0.00 0.00 1.75
546 572 3.193267 CCTAGCCTAGATAGCTTGCTCAG 59.807 52.174 7.84 5.36 41.83 3.35
649 677 2.282555 CGAGGATAAACACGATGCTGTG 59.717 50.000 0.00 3.30 45.41 3.66
650 678 2.165641 TCGAGGATAAACACGATGCTGT 59.834 45.455 0.00 0.00 0.00 4.40
750 851 1.676678 CCCCATCCGACTCACACGAT 61.677 60.000 0.00 0.00 0.00 3.73
880 981 2.670148 GGGGTCCTCCGTGCAGAAT 61.670 63.158 0.00 0.00 36.01 2.40
1080 1201 1.264749 TTACCTGCTCGGCCACATCT 61.265 55.000 2.24 0.00 35.61 2.90
1506 1631 5.807909 AGCTCGGTTAAATTAGTGGGTAAA 58.192 37.500 0.00 0.00 0.00 2.01
1711 1837 7.362401 GCGATCTTTGCAGATATGGGAATAAAT 60.362 37.037 0.00 0.00 40.14 1.40
1717 1843 2.104622 TGCGATCTTTGCAGATATGGGA 59.895 45.455 0.00 0.00 40.14 4.37
1970 2096 9.436957 CTAATTCTCAGTTTGTACAACTATGGT 57.563 33.333 8.07 0.00 0.00 3.55
2057 2184 4.097892 TGCCTTTTTCTCTCTTTCCACAAC 59.902 41.667 0.00 0.00 0.00 3.32
2377 2520 5.861251 TCATATTTGTTTAGCAAGCAAACCG 59.139 36.000 11.06 5.62 38.47 4.44
2504 2647 8.204903 AGCCTGAATACTTGATCTCTTATCAT 57.795 34.615 0.00 0.00 0.00 2.45
2842 5706 6.863126 GGACCAACAACTTTGAATCTGTAATG 59.137 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.