Multiple sequence alignment - TraesCS2A01G455600

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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 TraesCS2A01G455600 chr2A 100.000 4133 0 0 1 4133 704756586 704752454 0.000000e+00 7633.0
1 TraesCS2A01G455600 chr2A 83.154 1211 170 24 1905 3110 705265526 705266707 0.000000e+00 1075.0
2 TraesCS2A01G455600 chr2A 92.407 619 44 1 2064 2682 705342857 705343472 0.000000e+00 880.0
3 TraesCS2A01G455600 chr2A 82.111 995 141 20 1100 2068 705340910 705341893 0.000000e+00 817.0
4 TraesCS2A01G455600 chr2A 90.741 108 5 4 124 230 762691328 762691431 5.570000e-29 139.0
5 TraesCS2A01G455600 chr2A 81.081 111 11 10 3375 3481 164710027 164709923 3.420000e-11 80.5
6 TraesCS2A01G455600 chr2D 93.819 3462 150 19 692 4133 564073203 564069786 0.000000e+00 5149.0
7 TraesCS2A01G455600 chr2D 88.633 1214 116 13 1902 3106 564477167 564478367 0.000000e+00 1458.0
8 TraesCS2A01G455600 chr2D 88.032 1245 123 14 1902 3133 564439307 564440538 0.000000e+00 1450.0
9 TraesCS2A01G455600 chr2D 91.980 399 16 7 274 670 564074393 564074009 2.810000e-151 545.0
10 TraesCS2A01G455600 chr2D 86.328 256 35 0 2822 3077 564424883 564425138 3.150000e-71 279.0
11 TraesCS2A01G455600 chr2D 87.879 99 11 1 1512 1610 481595364 481595461 9.390000e-22 115.0
12 TraesCS2A01G455600 chr2D 96.610 59 2 0 213 271 564076672 564076614 9.460000e-17 99.0
13 TraesCS2A01G455600 chr2D 82.653 98 13 3 3394 3489 102856173 102856078 2.650000e-12 84.2
14 TraesCS2A01G455600 chr2B 95.119 3032 113 16 741 3764 675335228 675332224 0.000000e+00 4747.0
15 TraesCS2A01G455600 chr2B 87.390 1245 128 15 1902 3133 675534974 675536202 0.000000e+00 1402.0
16 TraesCS2A01G455600 chr2B 82.329 1211 180 22 1905 3110 675525748 675526929 0.000000e+00 1020.0
17 TraesCS2A01G455600 chr2B 85.955 534 28 21 172 692 675336411 675335912 1.020000e-145 527.0
18 TraesCS2A01G455600 chr2B 99.160 119 1 0 1 119 498309503 498309621 9.000000e-52 215.0
19 TraesCS2A01G455600 chr2B 97.059 68 1 1 4067 4133 675332171 675332104 3.380000e-21 113.0
20 TraesCS2A01G455600 chr2B 80.000 145 21 6 3349 3489 154232830 154232690 2.630000e-17 100.0
21 TraesCS2A01G455600 chr2B 93.651 63 4 0 3790 3852 675332230 675332168 1.220000e-15 95.3
22 TraesCS2A01G455600 chr2B 78.231 147 20 8 3347 3489 711866131 711866269 2.650000e-12 84.2
23 TraesCS2A01G455600 chr4B 84.182 1100 134 25 1967 3054 22438650 22437579 0.000000e+00 1031.0
24 TraesCS2A01G455600 chr4B 84.399 1032 137 10 2088 3113 22488508 22487495 0.000000e+00 992.0
25 TraesCS2A01G455600 chr4B 79.851 134 21 5 3361 3489 99595868 99595736 4.400000e-15 93.5
26 TraesCS2A01G455600 chr3D 79.771 786 124 15 1900 2684 152824032 152824783 4.700000e-149 538.0
27 TraesCS2A01G455600 chr3B 79.771 786 124 15 1900 2684 223963723 223964474 4.700000e-149 538.0
28 TraesCS2A01G455600 chr3B 97.674 86 2 0 130 215 525634108 525634193 9.260000e-32 148.0
29 TraesCS2A01G455600 chr1B 95.876 97 2 2 127 222 679651585 679651490 5.530000e-34 156.0
30 TraesCS2A01G455600 chr1A 97.647 85 2 0 131 215 462746733 462746817 3.330000e-31 147.0
31 TraesCS2A01G455600 chr5B 95.556 90 4 0 127 216 532104751 532104662 1.200000e-30 145.0
32 TraesCS2A01G455600 chr5A 96.512 86 3 0 130 215 687871769 687871684 4.310000e-30 143.0
33 TraesCS2A01G455600 chr5A 92.079 101 5 3 115 215 413843520 413843423 5.570000e-29 139.0
34 TraesCS2A01G455600 chr3A 92.784 97 5 2 127 223 750297227 750297133 5.570000e-29 139.0
35 TraesCS2A01G455600 chr3A 85.714 126 14 4 94 216 736118176 736118052 3.350000e-26 130.0
36 TraesCS2A01G455600 chr6B 81.633 147 14 11 3348 3487 114938431 114938291 4.370000e-20 110.0
37 TraesCS2A01G455600 chr6B 83.333 96 10 5 3398 3489 665038318 665038225 2.650000e-12 84.2
38 TraesCS2A01G455600 chr4A 81.481 135 16 7 3361 3489 516585041 516584910 7.310000e-18 102.0


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 TraesCS2A01G455600 chr2A 704752454 704756586 4132 True 7633.000 7633 100.000000 1 4133 1 chr2A.!!$R2 4132
1 TraesCS2A01G455600 chr2A 705265526 705266707 1181 False 1075.000 1075 83.154000 1905 3110 1 chr2A.!!$F1 1205
2 TraesCS2A01G455600 chr2A 705340910 705343472 2562 False 848.500 880 87.259000 1100 2682 2 chr2A.!!$F3 1582
3 TraesCS2A01G455600 chr2D 564069786 564076672 6886 True 1931.000 5149 94.136333 213 4133 3 chr2D.!!$R2 3920
4 TraesCS2A01G455600 chr2D 564477167 564478367 1200 False 1458.000 1458 88.633000 1902 3106 1 chr2D.!!$F4 1204
5 TraesCS2A01G455600 chr2D 564439307 564440538 1231 False 1450.000 1450 88.032000 1902 3133 1 chr2D.!!$F3 1231
6 TraesCS2A01G455600 chr2B 675534974 675536202 1228 False 1402.000 1402 87.390000 1902 3133 1 chr2B.!!$F3 1231
7 TraesCS2A01G455600 chr2B 675332104 675336411 4307 True 1370.575 4747 92.946000 172 4133 4 chr2B.!!$R2 3961
8 TraesCS2A01G455600 chr2B 675525748 675526929 1181 False 1020.000 1020 82.329000 1905 3110 1 chr2B.!!$F2 1205
9 TraesCS2A01G455600 chr4B 22437579 22438650 1071 True 1031.000 1031 84.182000 1967 3054 1 chr4B.!!$R1 1087
10 TraesCS2A01G455600 chr4B 22487495 22488508 1013 True 992.000 992 84.399000 2088 3113 1 chr4B.!!$R2 1025
11 TraesCS2A01G455600 chr3D 152824032 152824783 751 False 538.000 538 79.771000 1900 2684 1 chr3D.!!$F1 784
12 TraesCS2A01G455600 chr3B 223963723 223964474 751 False 538.000 538 79.771000 1900 2684 1 chr3B.!!$F1 784

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
21 22 0.038159 GGCTGAGTCTAGTGTTGCGT 60.038 55.0 0.0 0.0 0.00 5.24 F
438 2661 0.107017 GTGGGTGATGACTGATGGGG 60.107 60.0 0.0 0.0 0.00 4.96 F
1596 5256 0.106469 TCTCCATCGTCCTCTCCAGG 60.106 60.0 0.0 0.0 42.01 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 4899 0.178921 TCCAGAGCTTGAGGGTGTCT 60.179 55.0 0.00 0.00 0.0 3.41 R
1758 5418 0.839946 ACTTGACCTGGTTCAGCTGT 59.160 50.0 14.67 0.00 0.0 4.40 R
3155 7804 1.376543 AAGACATCAATCCTGCAGCG 58.623 50.0 8.66 1.56 0.0 5.18 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 0.243907 TCGGCTGAGTCTAGTGTTGC 59.756 55.000 0.00 0.00 0.00 4.17
20 21 1.073216 CGGCTGAGTCTAGTGTTGCG 61.073 60.000 0.00 0.00 0.00 4.85
21 22 0.038159 GGCTGAGTCTAGTGTTGCGT 60.038 55.000 0.00 0.00 0.00 5.24
22 23 1.201647 GGCTGAGTCTAGTGTTGCGTA 59.798 52.381 0.00 0.00 0.00 4.42
23 24 2.520979 GCTGAGTCTAGTGTTGCGTAG 58.479 52.381 0.00 0.00 0.00 3.51
24 25 2.161808 GCTGAGTCTAGTGTTGCGTAGA 59.838 50.000 0.00 0.00 0.00 2.59
25 26 3.366070 GCTGAGTCTAGTGTTGCGTAGAA 60.366 47.826 0.00 0.00 0.00 2.10
26 27 4.795268 CTGAGTCTAGTGTTGCGTAGAAA 58.205 43.478 0.00 0.00 0.00 2.52
27 28 5.190992 TGAGTCTAGTGTTGCGTAGAAAA 57.809 39.130 0.00 0.00 0.00 2.29
28 29 4.980434 TGAGTCTAGTGTTGCGTAGAAAAC 59.020 41.667 0.00 0.00 0.00 2.43
29 30 4.940463 AGTCTAGTGTTGCGTAGAAAACA 58.060 39.130 0.00 0.00 34.15 2.83
30 31 5.353938 AGTCTAGTGTTGCGTAGAAAACAA 58.646 37.500 0.00 0.00 37.36 2.83
31 32 5.462398 AGTCTAGTGTTGCGTAGAAAACAAG 59.538 40.000 0.00 0.00 37.36 3.16
32 33 5.461078 GTCTAGTGTTGCGTAGAAAACAAGA 59.539 40.000 0.00 0.00 37.36 3.02
33 34 6.145696 GTCTAGTGTTGCGTAGAAAACAAGAT 59.854 38.462 0.00 0.00 37.36 2.40
34 35 5.095691 AGTGTTGCGTAGAAAACAAGATG 57.904 39.130 0.00 0.00 37.36 2.90
35 36 4.574828 AGTGTTGCGTAGAAAACAAGATGT 59.425 37.500 0.00 0.00 37.36 3.06
36 37 4.904154 GTGTTGCGTAGAAAACAAGATGTC 59.096 41.667 0.00 0.00 37.36 3.06
37 38 4.814234 TGTTGCGTAGAAAACAAGATGTCT 59.186 37.500 0.00 0.00 33.74 3.41
38 39 5.986741 TGTTGCGTAGAAAACAAGATGTCTA 59.013 36.000 0.00 0.00 33.74 2.59
39 40 6.649141 TGTTGCGTAGAAAACAAGATGTCTAT 59.351 34.615 0.00 0.00 33.74 1.98
40 41 6.887376 TGCGTAGAAAACAAGATGTCTATC 57.113 37.500 0.00 0.00 0.00 2.08
41 42 5.810587 TGCGTAGAAAACAAGATGTCTATCC 59.189 40.000 0.00 0.00 33.64 2.59
42 43 6.043411 GCGTAGAAAACAAGATGTCTATCCT 58.957 40.000 0.00 0.00 33.64 3.24
43 44 7.147966 TGCGTAGAAAACAAGATGTCTATCCTA 60.148 37.037 0.00 0.00 33.64 2.94
44 45 7.167801 GCGTAGAAAACAAGATGTCTATCCTAC 59.832 40.741 0.00 0.00 33.64 3.18
45 46 8.188799 CGTAGAAAACAAGATGTCTATCCTACA 58.811 37.037 0.00 0.00 33.64 2.74
46 47 9.303537 GTAGAAAACAAGATGTCTATCCTACAC 57.696 37.037 0.00 0.00 33.64 2.90
47 48 8.140112 AGAAAACAAGATGTCTATCCTACACT 57.860 34.615 0.00 0.00 33.64 3.55
48 49 8.598041 AGAAAACAAGATGTCTATCCTACACTT 58.402 33.333 0.00 0.00 33.64 3.16
49 50 9.871238 GAAAACAAGATGTCTATCCTACACTTA 57.129 33.333 0.00 0.00 33.64 2.24
50 51 9.877178 AAAACAAGATGTCTATCCTACACTTAG 57.123 33.333 0.00 0.00 33.64 2.18
51 52 8.824756 AACAAGATGTCTATCCTACACTTAGA 57.175 34.615 0.00 0.00 33.64 2.10
52 53 8.824756 ACAAGATGTCTATCCTACACTTAGAA 57.175 34.615 0.00 0.00 33.64 2.10
53 54 9.256228 ACAAGATGTCTATCCTACACTTAGAAA 57.744 33.333 0.00 0.00 33.64 2.52
62 63 7.573968 ATCCTACACTTAGAAAATCAATGGC 57.426 36.000 0.00 0.00 0.00 4.40
63 64 5.885912 TCCTACACTTAGAAAATCAATGGCC 59.114 40.000 0.00 0.00 0.00 5.36
64 65 5.652014 CCTACACTTAGAAAATCAATGGCCA 59.348 40.000 8.56 8.56 0.00 5.36
65 66 5.649782 ACACTTAGAAAATCAATGGCCAG 57.350 39.130 13.05 0.00 0.00 4.85
66 67 5.324409 ACACTTAGAAAATCAATGGCCAGA 58.676 37.500 13.05 3.90 0.00 3.86
67 68 5.954150 ACACTTAGAAAATCAATGGCCAGAT 59.046 36.000 13.05 6.63 0.00 2.90
68 69 6.438425 ACACTTAGAAAATCAATGGCCAGATT 59.562 34.615 13.05 13.12 36.09 2.40
69 70 7.038799 ACACTTAGAAAATCAATGGCCAGATTT 60.039 33.333 21.45 21.45 44.03 2.17
70 71 7.277098 CACTTAGAAAATCAATGGCCAGATTTG 59.723 37.037 25.54 19.07 42.02 2.32
71 72 7.178983 ACTTAGAAAATCAATGGCCAGATTTGA 59.821 33.333 25.54 22.90 42.02 2.69
72 73 6.363167 AGAAAATCAATGGCCAGATTTGAA 57.637 33.333 25.54 11.20 42.02 2.69
73 74 6.954232 AGAAAATCAATGGCCAGATTTGAAT 58.046 32.000 25.54 15.50 42.02 2.57
74 75 8.081517 AGAAAATCAATGGCCAGATTTGAATA 57.918 30.769 25.54 6.77 42.02 1.75
75 76 8.711170 AGAAAATCAATGGCCAGATTTGAATAT 58.289 29.630 25.54 14.37 42.02 1.28
76 77 9.985730 GAAAATCAATGGCCAGATTTGAATATA 57.014 29.630 25.54 6.15 42.02 0.86
77 78 9.768662 AAAATCAATGGCCAGATTTGAATATAC 57.231 29.630 25.54 0.00 42.02 1.47
78 79 8.716674 AATCAATGGCCAGATTTGAATATACT 57.283 30.769 21.03 4.25 33.45 2.12
79 80 7.514784 TCAATGGCCAGATTTGAATATACTG 57.485 36.000 16.20 0.00 0.00 2.74
80 81 5.972107 ATGGCCAGATTTGAATATACTGC 57.028 39.130 13.05 0.00 0.00 4.40
81 82 5.052693 TGGCCAGATTTGAATATACTGCT 57.947 39.130 0.00 0.00 0.00 4.24
82 83 5.065914 TGGCCAGATTTGAATATACTGCTC 58.934 41.667 0.00 0.00 0.00 4.26
83 84 4.457257 GGCCAGATTTGAATATACTGCTCC 59.543 45.833 0.00 0.00 0.00 4.70
84 85 4.457257 GCCAGATTTGAATATACTGCTCCC 59.543 45.833 0.00 0.00 0.00 4.30
85 86 5.747248 GCCAGATTTGAATATACTGCTCCCT 60.747 44.000 0.00 0.00 0.00 4.20
86 87 5.936956 CCAGATTTGAATATACTGCTCCCTC 59.063 44.000 0.00 0.00 0.00 4.30
87 88 6.239829 CCAGATTTGAATATACTGCTCCCTCT 60.240 42.308 0.00 0.00 0.00 3.69
88 89 6.873076 CAGATTTGAATATACTGCTCCCTCTC 59.127 42.308 0.00 0.00 0.00 3.20
89 90 6.786959 AGATTTGAATATACTGCTCCCTCTCT 59.213 38.462 0.00 0.00 0.00 3.10
90 91 6.412362 TTTGAATATACTGCTCCCTCTCTC 57.588 41.667 0.00 0.00 0.00 3.20
91 92 5.066913 TGAATATACTGCTCCCTCTCTCA 57.933 43.478 0.00 0.00 0.00 3.27
92 93 5.649265 TGAATATACTGCTCCCTCTCTCAT 58.351 41.667 0.00 0.00 0.00 2.90
93 94 5.714333 TGAATATACTGCTCCCTCTCTCATC 59.286 44.000 0.00 0.00 0.00 2.92
94 95 3.609256 ATACTGCTCCCTCTCTCATCA 57.391 47.619 0.00 0.00 0.00 3.07
95 96 1.779221 ACTGCTCCCTCTCTCATCAG 58.221 55.000 0.00 0.00 0.00 2.90
96 97 0.390124 CTGCTCCCTCTCTCATCAGC 59.610 60.000 0.00 0.00 0.00 4.26
97 98 0.325016 TGCTCCCTCTCTCATCAGCA 60.325 55.000 0.00 0.00 34.54 4.41
98 99 0.390124 GCTCCCTCTCTCATCAGCAG 59.610 60.000 0.00 0.00 0.00 4.24
99 100 1.779221 CTCCCTCTCTCATCAGCAGT 58.221 55.000 0.00 0.00 0.00 4.40
100 101 2.942804 CTCCCTCTCTCATCAGCAGTA 58.057 52.381 0.00 0.00 0.00 2.74
101 102 2.622942 CTCCCTCTCTCATCAGCAGTAC 59.377 54.545 0.00 0.00 0.00 2.73
102 103 2.024941 TCCCTCTCTCATCAGCAGTACA 60.025 50.000 0.00 0.00 0.00 2.90
103 104 2.361757 CCCTCTCTCATCAGCAGTACAG 59.638 54.545 0.00 0.00 0.00 2.74
104 105 2.361757 CCTCTCTCATCAGCAGTACAGG 59.638 54.545 0.00 0.00 0.00 4.00
105 106 2.361757 CTCTCTCATCAGCAGTACAGGG 59.638 54.545 0.00 0.00 0.00 4.45
106 107 2.106566 CTCTCATCAGCAGTACAGGGT 58.893 52.381 0.00 0.00 0.00 4.34
107 108 3.053619 TCTCTCATCAGCAGTACAGGGTA 60.054 47.826 0.00 0.00 0.00 3.69
108 109 3.024547 TCTCATCAGCAGTACAGGGTAC 58.975 50.000 0.00 0.00 0.00 3.34
126 127 6.628919 GGGTACCGTAAAAATGCTCATAAT 57.371 37.500 5.65 0.00 40.86 1.28
127 128 7.034685 GGGTACCGTAAAAATGCTCATAATT 57.965 36.000 5.65 0.00 40.86 1.40
128 129 6.915843 GGGTACCGTAAAAATGCTCATAATTG 59.084 38.462 5.65 0.00 40.86 2.32
129 130 7.201750 GGGTACCGTAAAAATGCTCATAATTGA 60.202 37.037 5.65 0.00 40.86 2.57
130 131 8.349983 GGTACCGTAAAAATGCTCATAATTGAT 58.650 33.333 0.00 0.00 0.00 2.57
133 134 9.120538 ACCGTAAAAATGCTCATAATTGATACT 57.879 29.630 0.00 0.00 0.00 2.12
134 135 9.599322 CCGTAAAAATGCTCATAATTGATACTC 57.401 33.333 0.00 0.00 0.00 2.59
135 136 9.599322 CGTAAAAATGCTCATAATTGATACTCC 57.401 33.333 0.00 0.00 0.00 3.85
136 137 9.899226 GTAAAAATGCTCATAATTGATACTCCC 57.101 33.333 0.00 0.00 0.00 4.30
137 138 8.773033 AAAAATGCTCATAATTGATACTCCCT 57.227 30.769 0.00 0.00 0.00 4.20
138 139 7.992754 AAATGCTCATAATTGATACTCCCTC 57.007 36.000 0.00 0.00 0.00 4.30
139 140 5.489792 TGCTCATAATTGATACTCCCTCC 57.510 43.478 0.00 0.00 0.00 4.30
140 141 4.021104 TGCTCATAATTGATACTCCCTCCG 60.021 45.833 0.00 0.00 0.00 4.63
141 142 4.021016 GCTCATAATTGATACTCCCTCCGT 60.021 45.833 0.00 0.00 0.00 4.69
142 143 5.185249 GCTCATAATTGATACTCCCTCCGTA 59.815 44.000 0.00 0.00 0.00 4.02
143 144 6.295123 GCTCATAATTGATACTCCCTCCGTAA 60.295 42.308 0.00 0.00 0.00 3.18
144 145 7.606135 TCATAATTGATACTCCCTCCGTAAA 57.394 36.000 0.00 0.00 0.00 2.01
145 146 7.439381 TCATAATTGATACTCCCTCCGTAAAC 58.561 38.462 0.00 0.00 0.00 2.01
146 147 5.952347 AATTGATACTCCCTCCGTAAACT 57.048 39.130 0.00 0.00 0.00 2.66
147 148 8.582437 CATAATTGATACTCCCTCCGTAAACTA 58.418 37.037 0.00 0.00 0.00 2.24
148 149 7.427989 AATTGATACTCCCTCCGTAAACTAA 57.572 36.000 0.00 0.00 0.00 2.24
149 150 7.613551 ATTGATACTCCCTCCGTAAACTAAT 57.386 36.000 0.00 0.00 0.00 1.73
150 151 6.401047 TGATACTCCCTCCGTAAACTAATG 57.599 41.667 0.00 0.00 0.00 1.90
151 152 5.895534 TGATACTCCCTCCGTAAACTAATGT 59.104 40.000 0.00 0.00 0.00 2.71
152 153 7.062322 TGATACTCCCTCCGTAAACTAATGTA 58.938 38.462 0.00 0.00 0.00 2.29
153 154 7.560991 TGATACTCCCTCCGTAAACTAATGTAA 59.439 37.037 0.00 0.00 0.00 2.41
154 155 6.218108 ACTCCCTCCGTAAACTAATGTAAG 57.782 41.667 0.00 0.00 0.00 2.34
155 156 5.954150 ACTCCCTCCGTAAACTAATGTAAGA 59.046 40.000 0.00 0.00 0.00 2.10
156 157 6.096564 ACTCCCTCCGTAAACTAATGTAAGAG 59.903 42.308 0.00 0.00 0.00 2.85
157 158 5.954150 TCCCTCCGTAAACTAATGTAAGAGT 59.046 40.000 0.00 0.00 0.00 3.24
158 159 6.040878 CCCTCCGTAAACTAATGTAAGAGTG 58.959 44.000 0.00 0.00 0.00 3.51
159 160 6.350780 CCCTCCGTAAACTAATGTAAGAGTGT 60.351 42.308 0.00 0.00 0.00 3.55
160 161 7.095270 CCTCCGTAAACTAATGTAAGAGTGTT 58.905 38.462 0.00 0.00 0.00 3.32
161 162 7.601508 CCTCCGTAAACTAATGTAAGAGTGTTT 59.398 37.037 0.00 0.00 0.00 2.83
162 163 9.630098 CTCCGTAAACTAATGTAAGAGTGTTTA 57.370 33.333 0.00 0.00 0.00 2.01
163 164 9.630098 TCCGTAAACTAATGTAAGAGTGTTTAG 57.370 33.333 0.00 0.00 32.78 1.85
164 165 9.630098 CCGTAAACTAATGTAAGAGTGTTTAGA 57.370 33.333 0.00 0.00 32.78 2.10
427 2650 2.434884 CAAGCGCTCGTGGGTGAT 60.435 61.111 12.06 0.00 0.00 3.06
428 2651 2.434884 AAGCGCTCGTGGGTGATG 60.435 61.111 12.06 0.00 0.00 3.07
429 2652 2.942796 AAGCGCTCGTGGGTGATGA 61.943 57.895 12.06 0.00 0.00 2.92
430 2653 3.188786 GCGCTCGTGGGTGATGAC 61.189 66.667 0.00 0.00 0.00 3.06
438 2661 0.107017 GTGGGTGATGACTGATGGGG 60.107 60.000 0.00 0.00 0.00 4.96
468 2691 6.211515 AGCAAATGTTTGACTTGATCACTTC 58.788 36.000 9.53 0.00 40.55 3.01
489 2712 0.528470 CGGAGAGTGACAGGAGTTCC 59.472 60.000 0.00 0.00 0.00 3.62
492 2715 2.232696 GGAGAGTGACAGGAGTTCCTTC 59.767 54.545 0.00 1.40 46.09 3.46
493 2716 2.232696 GAGAGTGACAGGAGTTCCTTCC 59.767 54.545 0.00 0.00 46.09 3.46
494 2717 2.158234 AGAGTGACAGGAGTTCCTTCCT 60.158 50.000 0.00 0.00 46.09 3.36
495 2718 2.635427 GAGTGACAGGAGTTCCTTCCTT 59.365 50.000 0.00 0.00 45.35 3.36
611 2836 5.458779 CCATTTTTCTGTCGAAACTTGGAAC 59.541 40.000 8.45 0.00 40.50 3.62
613 2838 2.589798 TCTGTCGAAACTTGGAACGT 57.410 45.000 0.00 0.00 0.00 3.99
618 2843 0.158096 CGAAACTTGGAACGTCGACG 59.842 55.000 34.58 34.58 46.33 5.12
637 2862 4.460505 GACGTTGTTAATTTCCGTCAAGG 58.539 43.478 12.18 0.00 45.23 3.61
638 2863 3.878699 ACGTTGTTAATTTCCGTCAAGGT 59.121 39.130 0.00 0.00 41.99 3.50
639 2864 4.336153 ACGTTGTTAATTTCCGTCAAGGTT 59.664 37.500 0.00 0.00 41.99 3.50
640 2865 4.907582 CGTTGTTAATTTCCGTCAAGGTTC 59.092 41.667 0.00 0.00 41.99 3.62
641 2866 5.277634 CGTTGTTAATTTCCGTCAAGGTTCT 60.278 40.000 0.00 0.00 41.99 3.01
642 2867 6.500910 GTTGTTAATTTCCGTCAAGGTTCTT 58.499 36.000 0.00 0.00 41.99 2.52
714 4133 1.593196 TTTCCGTCAAGCTTCCACTG 58.407 50.000 0.00 0.00 0.00 3.66
715 4134 0.468226 TTCCGTCAAGCTTCCACTGT 59.532 50.000 0.00 0.00 0.00 3.55
716 4135 1.334160 TCCGTCAAGCTTCCACTGTA 58.666 50.000 0.00 0.00 0.00 2.74
717 4136 1.000506 TCCGTCAAGCTTCCACTGTAC 59.999 52.381 0.00 0.00 0.00 2.90
746 4348 5.683681 TGCTTAACAAGATGATGCTCCATA 58.316 37.500 0.00 0.00 0.00 2.74
809 4445 0.109132 CAAAGTCTCATTTGGCGCCC 60.109 55.000 26.77 5.30 36.68 6.13
871 4507 1.878775 GGCAGCATTGTCACTGTCC 59.121 57.895 0.00 0.00 36.26 4.02
872 4508 0.607489 GGCAGCATTGTCACTGTCCT 60.607 55.000 0.00 0.00 36.26 3.85
909 4545 1.690633 TCCCTCCCTCATGGACAGC 60.691 63.158 0.00 0.00 38.61 4.40
1072 4714 2.262774 CTTTGCGGCCATCCTCCTCT 62.263 60.000 2.24 0.00 0.00 3.69
1087 4729 2.125552 TCTTCATCCTGTGCGGCG 60.126 61.111 0.51 0.51 0.00 6.46
1088 4730 3.197790 CTTCATCCTGTGCGGCGG 61.198 66.667 9.78 0.00 0.00 6.13
1257 4899 1.327690 GGAGGGTCATGTACGCCAGA 61.328 60.000 0.00 0.00 41.88 3.86
1260 4902 0.179108 GGGTCATGTACGCCAGAGAC 60.179 60.000 0.00 0.00 35.04 3.36
1437 5097 0.402504 TCGGCCTAACCAACAACCAT 59.597 50.000 0.00 0.00 39.03 3.55
1445 5105 0.952010 ACCAACAACCATACCGACGC 60.952 55.000 0.00 0.00 0.00 5.19
1507 5167 4.117661 GGAGCTTCGACGCCGACT 62.118 66.667 10.66 0.00 45.50 4.18
1552 5212 4.980805 TCAACAGCGTGCGGTCCC 62.981 66.667 0.00 0.00 0.00 4.46
1596 5256 0.106469 TCTCCATCGTCCTCTCCAGG 60.106 60.000 0.00 0.00 42.01 4.45
1861 5521 1.406887 GCCAGAAGGTATTTCTCGCCA 60.407 52.381 0.00 0.00 44.34 5.69
2233 6870 4.481195 GCTGGTGCCACAAGAAGA 57.519 55.556 2.60 0.00 0.00 2.87
2892 7536 4.357947 GTGGACTGCGCGGTGAGA 62.358 66.667 29.82 7.07 0.00 3.27
2944 7588 2.765807 AGAGGCCGTCCATGAGGG 60.766 66.667 0.00 0.00 40.18 4.30
2973 7617 2.951745 GTGCTGATCGACGGAGCG 60.952 66.667 7.44 0.00 35.36 5.03
2976 7620 4.933064 CTGATCGACGGAGCGCCC 62.933 72.222 2.29 3.94 0.00 6.13
3136 7785 1.630369 CCATCTCAGGGAGGTGACAAA 59.370 52.381 8.04 0.00 42.86 2.83
3155 7804 4.198530 CAAATTTGGGGCATGGAAATACC 58.801 43.478 10.49 0.00 39.54 2.73
3157 7806 1.040339 TTGGGGCATGGAAATACCGC 61.040 55.000 0.00 0.00 42.61 5.68
3171 7820 0.541392 TACCGCTGCAGGATTGATGT 59.459 50.000 17.12 0.97 34.73 3.06
3464 8114 4.016444 TCAACCTGACTTTCTTTTGCACT 58.984 39.130 0.00 0.00 0.00 4.40
3642 8295 3.756434 CCCATAGACCAAACGTTCATGTT 59.244 43.478 0.00 0.00 0.00 2.71
3772 8425 1.139734 GGAGACGAAGCTGATGCGA 59.860 57.895 0.00 0.00 45.42 5.10
3775 8428 2.507102 ACGAAGCTGATGCGACCG 60.507 61.111 0.00 0.00 45.42 4.79
3816 8469 0.030908 CGAGGCGAGTAGGGAATGAC 59.969 60.000 0.00 0.00 0.00 3.06
3881 8534 6.628398 CGAAGGGAACTCTAAAGCTTGATAGT 60.628 42.308 0.00 0.00 42.68 2.12
3885 8538 5.688176 GGAACTCTAAAGCTTGATAGTAGCG 59.312 44.000 0.00 0.00 43.37 4.26
3890 8543 0.105039 AGCTTGATAGTAGCGGGTGC 59.895 55.000 0.00 0.00 43.37 5.01
3909 8562 2.368011 GGGGGAGAGGGAAGGTTCG 61.368 68.421 0.00 0.00 0.00 3.95
3911 8564 1.199425 GGGGAGAGGGAAGGTTCGTT 61.199 60.000 0.00 0.00 0.00 3.85
3913 8566 0.036294 GGAGAGGGAAGGTTCGTTGG 60.036 60.000 0.00 0.00 0.00 3.77
3914 8567 0.685660 GAGAGGGAAGGTTCGTTGGT 59.314 55.000 0.00 0.00 0.00 3.67
3927 8580 1.291877 CGTTGGTGCCGAAGAAGGAG 61.292 60.000 0.00 0.00 0.00 3.69
3941 8594 3.111484 AGAAGGAGGGCTTAGAAGGAAG 58.889 50.000 0.00 0.00 0.00 3.46
3948 8601 1.070914 GGCTTAGAAGGAAGATCGGGG 59.929 57.143 0.00 0.00 0.00 5.73
3985 8648 2.515996 TTAGGCTAGTGGTGGCACGC 62.516 60.000 12.17 8.73 38.67 5.34
3986 8649 4.697756 GGCTAGTGGTGGCACGCA 62.698 66.667 12.17 8.11 43.02 5.24
4001 8664 1.265365 CACGCAGATCGCTGATAGAGA 59.735 52.381 0.00 0.00 45.17 3.10
4015 8678 6.019479 CGCTGATAGAGAAATAGGAACACAAC 60.019 42.308 0.00 0.00 0.00 3.32
4019 8682 8.154203 TGATAGAGAAATAGGAACACAACAACA 58.846 33.333 0.00 0.00 0.00 3.33
4020 8683 8.918202 ATAGAGAAATAGGAACACAACAACAA 57.082 30.769 0.00 0.00 0.00 2.83
4023 8686 7.990886 AGAGAAATAGGAACACAACAACAACTA 59.009 33.333 0.00 0.00 0.00 2.24
4052 8715 8.929487 ACTCTGGGAAGATAGAATAAACTAAGG 58.071 37.037 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.073216 CGCAACACTAGACTCAGCCG 61.073 60.000 0.00 0.00 0.00 5.52
2 3 0.038159 ACGCAACACTAGACTCAGCC 60.038 55.000 0.00 0.00 0.00 4.85
3 4 2.161808 TCTACGCAACACTAGACTCAGC 59.838 50.000 0.00 0.00 0.00 4.26
4 5 4.421033 TTCTACGCAACACTAGACTCAG 57.579 45.455 0.00 0.00 0.00 3.35
5 6 4.841443 TTTCTACGCAACACTAGACTCA 57.159 40.909 0.00 0.00 0.00 3.41
6 7 4.980434 TGTTTTCTACGCAACACTAGACTC 59.020 41.667 0.00 0.00 0.00 3.36
7 8 4.940463 TGTTTTCTACGCAACACTAGACT 58.060 39.130 0.00 0.00 0.00 3.24
8 9 5.461078 TCTTGTTTTCTACGCAACACTAGAC 59.539 40.000 0.00 0.00 32.57 2.59
9 10 5.593968 TCTTGTTTTCTACGCAACACTAGA 58.406 37.500 0.00 0.00 32.57 2.43
10 11 5.900339 TCTTGTTTTCTACGCAACACTAG 57.100 39.130 0.00 0.00 32.57 2.57
11 12 5.756347 ACATCTTGTTTTCTACGCAACACTA 59.244 36.000 0.00 0.00 32.57 2.74
12 13 4.574828 ACATCTTGTTTTCTACGCAACACT 59.425 37.500 0.00 0.00 32.57 3.55
13 14 4.844267 ACATCTTGTTTTCTACGCAACAC 58.156 39.130 0.00 0.00 32.57 3.32
14 15 4.814234 AGACATCTTGTTTTCTACGCAACA 59.186 37.500 0.00 0.00 0.00 3.33
15 16 5.344207 AGACATCTTGTTTTCTACGCAAC 57.656 39.130 0.00 0.00 0.00 4.17
16 17 6.312918 GGATAGACATCTTGTTTTCTACGCAA 59.687 38.462 0.00 0.00 0.00 4.85
17 18 5.810587 GGATAGACATCTTGTTTTCTACGCA 59.189 40.000 0.00 0.00 0.00 5.24
18 19 6.043411 AGGATAGACATCTTGTTTTCTACGC 58.957 40.000 0.00 0.00 0.00 4.42
19 20 8.188799 TGTAGGATAGACATCTTGTTTTCTACG 58.811 37.037 0.00 0.00 0.00 3.51
20 21 9.303537 GTGTAGGATAGACATCTTGTTTTCTAC 57.696 37.037 0.00 0.00 34.53 2.59
21 22 9.256228 AGTGTAGGATAGACATCTTGTTTTCTA 57.744 33.333 0.00 0.00 37.30 2.10
22 23 8.140112 AGTGTAGGATAGACATCTTGTTTTCT 57.860 34.615 0.00 0.00 37.30 2.52
23 24 8.779354 AAGTGTAGGATAGACATCTTGTTTTC 57.221 34.615 0.00 0.00 37.30 2.29
24 25 9.877178 CTAAGTGTAGGATAGACATCTTGTTTT 57.123 33.333 0.00 0.00 37.30 2.43
25 26 9.256228 TCTAAGTGTAGGATAGACATCTTGTTT 57.744 33.333 0.00 0.00 37.30 2.83
26 27 8.824756 TCTAAGTGTAGGATAGACATCTTGTT 57.175 34.615 0.00 0.00 37.30 2.83
27 28 8.824756 TTCTAAGTGTAGGATAGACATCTTGT 57.175 34.615 0.00 0.00 37.30 3.16
36 37 8.778358 GCCATTGATTTTCTAAGTGTAGGATAG 58.222 37.037 0.00 0.00 0.00 2.08
37 38 7.719633 GGCCATTGATTTTCTAAGTGTAGGATA 59.280 37.037 0.00 0.00 0.00 2.59
38 39 6.547510 GGCCATTGATTTTCTAAGTGTAGGAT 59.452 38.462 0.00 0.00 0.00 3.24
39 40 5.885912 GGCCATTGATTTTCTAAGTGTAGGA 59.114 40.000 0.00 0.00 0.00 2.94
40 41 5.652014 TGGCCATTGATTTTCTAAGTGTAGG 59.348 40.000 0.00 0.00 0.00 3.18
41 42 6.599244 TCTGGCCATTGATTTTCTAAGTGTAG 59.401 38.462 5.51 0.00 0.00 2.74
42 43 6.480763 TCTGGCCATTGATTTTCTAAGTGTA 58.519 36.000 5.51 0.00 0.00 2.90
43 44 5.324409 TCTGGCCATTGATTTTCTAAGTGT 58.676 37.500 5.51 0.00 0.00 3.55
44 45 5.902613 TCTGGCCATTGATTTTCTAAGTG 57.097 39.130 5.51 0.00 0.00 3.16
45 46 7.178983 TCAAATCTGGCCATTGATTTTCTAAGT 59.821 33.333 23.55 5.44 39.85 2.24
46 47 7.549839 TCAAATCTGGCCATTGATTTTCTAAG 58.450 34.615 23.55 15.17 39.85 2.18
47 48 7.479352 TCAAATCTGGCCATTGATTTTCTAA 57.521 32.000 23.55 11.47 39.85 2.10
48 49 7.479352 TTCAAATCTGGCCATTGATTTTCTA 57.521 32.000 23.55 13.30 39.85 2.10
49 50 6.363167 TTCAAATCTGGCCATTGATTTTCT 57.637 33.333 23.55 7.23 39.85 2.52
50 51 8.897872 ATATTCAAATCTGGCCATTGATTTTC 57.102 30.769 23.55 0.00 39.85 2.29
51 52 9.768662 GTATATTCAAATCTGGCCATTGATTTT 57.231 29.630 23.55 15.30 39.85 1.82
52 53 9.151177 AGTATATTCAAATCTGGCCATTGATTT 57.849 29.630 21.45 21.45 41.75 2.17
53 54 8.582437 CAGTATATTCAAATCTGGCCATTGATT 58.418 33.333 18.56 15.89 33.45 2.57
54 55 7.309621 GCAGTATATTCAAATCTGGCCATTGAT 60.310 37.037 18.56 10.93 33.45 2.57
55 56 6.016024 GCAGTATATTCAAATCTGGCCATTGA 60.016 38.462 14.87 14.87 0.00 2.57
56 57 6.015688 AGCAGTATATTCAAATCTGGCCATTG 60.016 38.462 5.51 8.82 0.00 2.82
57 58 6.073314 AGCAGTATATTCAAATCTGGCCATT 58.927 36.000 5.51 0.00 0.00 3.16
58 59 5.638133 AGCAGTATATTCAAATCTGGCCAT 58.362 37.500 5.51 0.00 0.00 4.40
59 60 5.052693 AGCAGTATATTCAAATCTGGCCA 57.947 39.130 4.71 4.71 0.00 5.36
60 61 4.457257 GGAGCAGTATATTCAAATCTGGCC 59.543 45.833 0.00 0.00 0.00 5.36
61 62 4.457257 GGGAGCAGTATATTCAAATCTGGC 59.543 45.833 0.00 0.00 0.00 4.85
62 63 5.874093 AGGGAGCAGTATATTCAAATCTGG 58.126 41.667 0.00 0.00 0.00 3.86
63 64 6.767456 AGAGGGAGCAGTATATTCAAATCTG 58.233 40.000 0.00 0.00 0.00 2.90
64 65 6.786959 AGAGAGGGAGCAGTATATTCAAATCT 59.213 38.462 0.00 0.00 0.00 2.40
65 66 7.003402 AGAGAGGGAGCAGTATATTCAAATC 57.997 40.000 0.00 0.00 0.00 2.17
66 67 6.556495 TGAGAGAGGGAGCAGTATATTCAAAT 59.444 38.462 0.00 0.00 0.00 2.32
67 68 5.899547 TGAGAGAGGGAGCAGTATATTCAAA 59.100 40.000 0.00 0.00 0.00 2.69
68 69 5.458595 TGAGAGAGGGAGCAGTATATTCAA 58.541 41.667 0.00 0.00 0.00 2.69
69 70 5.066913 TGAGAGAGGGAGCAGTATATTCA 57.933 43.478 0.00 0.00 0.00 2.57
70 71 5.714333 TGATGAGAGAGGGAGCAGTATATTC 59.286 44.000 0.00 0.00 0.00 1.75
71 72 5.649265 TGATGAGAGAGGGAGCAGTATATT 58.351 41.667 0.00 0.00 0.00 1.28
72 73 5.263599 CTGATGAGAGAGGGAGCAGTATAT 58.736 45.833 0.00 0.00 0.00 0.86
73 74 4.661222 CTGATGAGAGAGGGAGCAGTATA 58.339 47.826 0.00 0.00 0.00 1.47
74 75 3.499338 CTGATGAGAGAGGGAGCAGTAT 58.501 50.000 0.00 0.00 0.00 2.12
75 76 2.942804 CTGATGAGAGAGGGAGCAGTA 58.057 52.381 0.00 0.00 0.00 2.74
76 77 1.779221 CTGATGAGAGAGGGAGCAGT 58.221 55.000 0.00 0.00 0.00 4.40
77 78 0.390124 GCTGATGAGAGAGGGAGCAG 59.610 60.000 0.00 0.00 0.00 4.24
78 79 0.325016 TGCTGATGAGAGAGGGAGCA 60.325 55.000 0.00 0.00 34.16 4.26
79 80 0.390124 CTGCTGATGAGAGAGGGAGC 59.610 60.000 0.00 0.00 0.00 4.70
80 81 1.779221 ACTGCTGATGAGAGAGGGAG 58.221 55.000 0.00 0.00 0.00 4.30
81 82 2.024941 TGTACTGCTGATGAGAGAGGGA 60.025 50.000 0.00 0.00 0.00 4.20
82 83 2.361757 CTGTACTGCTGATGAGAGAGGG 59.638 54.545 0.00 0.00 0.00 4.30
83 84 2.361757 CCTGTACTGCTGATGAGAGAGG 59.638 54.545 0.00 0.00 0.00 3.69
84 85 2.361757 CCCTGTACTGCTGATGAGAGAG 59.638 54.545 0.00 0.00 0.00 3.20
85 86 2.291865 ACCCTGTACTGCTGATGAGAGA 60.292 50.000 0.00 0.00 0.00 3.10
86 87 2.106566 ACCCTGTACTGCTGATGAGAG 58.893 52.381 0.00 0.00 0.00 3.20
87 88 2.238084 ACCCTGTACTGCTGATGAGA 57.762 50.000 0.00 0.00 0.00 3.27
88 89 2.101582 GGTACCCTGTACTGCTGATGAG 59.898 54.545 0.00 0.00 0.00 2.90
89 90 2.108168 GGTACCCTGTACTGCTGATGA 58.892 52.381 0.00 0.00 0.00 2.92
90 91 1.202417 CGGTACCCTGTACTGCTGATG 60.202 57.143 6.25 0.00 0.00 3.07
91 92 1.112113 CGGTACCCTGTACTGCTGAT 58.888 55.000 6.25 0.00 0.00 2.90
92 93 0.251474 ACGGTACCCTGTACTGCTGA 60.251 55.000 6.25 0.00 0.00 4.26
93 94 1.466856 TACGGTACCCTGTACTGCTG 58.533 55.000 6.25 0.00 0.00 4.41
94 95 2.220653 TTACGGTACCCTGTACTGCT 57.779 50.000 6.25 4.16 0.00 4.24
95 96 3.317603 TTTTACGGTACCCTGTACTGC 57.682 47.619 6.25 0.00 0.00 4.40
96 97 4.093850 GCATTTTTACGGTACCCTGTACTG 59.906 45.833 6.25 10.82 0.00 2.74
97 98 4.019950 AGCATTTTTACGGTACCCTGTACT 60.020 41.667 6.25 0.00 0.00 2.73
98 99 4.256110 AGCATTTTTACGGTACCCTGTAC 58.744 43.478 6.25 0.00 0.00 2.90
99 100 4.020396 TGAGCATTTTTACGGTACCCTGTA 60.020 41.667 6.25 0.49 0.00 2.74
100 101 3.244630 TGAGCATTTTTACGGTACCCTGT 60.245 43.478 6.25 1.59 0.00 4.00
101 102 3.340034 TGAGCATTTTTACGGTACCCTG 58.660 45.455 6.25 0.00 0.00 4.45
102 103 3.706600 TGAGCATTTTTACGGTACCCT 57.293 42.857 6.25 0.00 0.00 4.34
103 104 6.628919 ATTATGAGCATTTTTACGGTACCC 57.371 37.500 6.25 0.00 0.00 3.69
104 105 7.699566 TCAATTATGAGCATTTTTACGGTACC 58.300 34.615 0.16 0.16 0.00 3.34
107 108 9.120538 AGTATCAATTATGAGCATTTTTACGGT 57.879 29.630 0.00 0.00 39.39 4.83
108 109 9.599322 GAGTATCAATTATGAGCATTTTTACGG 57.401 33.333 0.00 0.00 39.39 4.02
109 110 9.599322 GGAGTATCAATTATGAGCATTTTTACG 57.401 33.333 0.00 0.00 39.39 3.18
110 111 9.899226 GGGAGTATCAATTATGAGCATTTTTAC 57.101 33.333 0.00 0.00 39.39 2.01
111 112 9.866655 AGGGAGTATCAATTATGAGCATTTTTA 57.133 29.630 0.00 0.00 39.39 1.52
112 113 8.773033 AGGGAGTATCAATTATGAGCATTTTT 57.227 30.769 0.00 0.00 39.39 1.94
113 114 7.449704 GGAGGGAGTATCAATTATGAGCATTTT 59.550 37.037 0.00 0.00 39.39 1.82
114 115 6.944862 GGAGGGAGTATCAATTATGAGCATTT 59.055 38.462 0.00 0.00 39.39 2.32
115 116 6.479884 GGAGGGAGTATCAATTATGAGCATT 58.520 40.000 0.00 0.00 39.39 3.56
116 117 5.337894 CGGAGGGAGTATCAATTATGAGCAT 60.338 44.000 0.00 0.00 39.39 3.79
117 118 4.021104 CGGAGGGAGTATCAATTATGAGCA 60.021 45.833 0.00 0.00 39.39 4.26
118 119 4.021016 ACGGAGGGAGTATCAATTATGAGC 60.021 45.833 0.00 0.00 39.39 4.26
119 120 5.730296 ACGGAGGGAGTATCAATTATGAG 57.270 43.478 0.00 0.00 39.39 2.90
120 121 7.289317 AGTTTACGGAGGGAGTATCAATTATGA 59.711 37.037 0.00 0.00 40.57 2.15
121 122 7.442656 AGTTTACGGAGGGAGTATCAATTATG 58.557 38.462 0.00 0.00 36.25 1.90
122 123 7.613551 AGTTTACGGAGGGAGTATCAATTAT 57.386 36.000 0.00 0.00 36.25 1.28
123 124 8.537728 TTAGTTTACGGAGGGAGTATCAATTA 57.462 34.615 0.00 0.00 36.25 1.40
124 125 5.952347 AGTTTACGGAGGGAGTATCAATT 57.048 39.130 0.00 0.00 36.25 2.32
125 126 7.070821 ACATTAGTTTACGGAGGGAGTATCAAT 59.929 37.037 0.00 0.00 36.25 2.57
126 127 6.381994 ACATTAGTTTACGGAGGGAGTATCAA 59.618 38.462 0.00 0.00 36.25 2.57
127 128 5.895534 ACATTAGTTTACGGAGGGAGTATCA 59.104 40.000 0.00 0.00 36.25 2.15
128 129 6.402456 ACATTAGTTTACGGAGGGAGTATC 57.598 41.667 0.00 0.00 0.00 2.24
129 130 7.781693 TCTTACATTAGTTTACGGAGGGAGTAT 59.218 37.037 0.00 0.00 0.00 2.12
130 131 7.118723 TCTTACATTAGTTTACGGAGGGAGTA 58.881 38.462 0.00 0.00 0.00 2.59
131 132 5.954150 TCTTACATTAGTTTACGGAGGGAGT 59.046 40.000 0.00 0.00 0.00 3.85
132 133 6.096564 ACTCTTACATTAGTTTACGGAGGGAG 59.903 42.308 0.00 0.00 0.00 4.30
133 134 5.954150 ACTCTTACATTAGTTTACGGAGGGA 59.046 40.000 0.00 0.00 0.00 4.20
134 135 6.040878 CACTCTTACATTAGTTTACGGAGGG 58.959 44.000 0.00 0.00 0.00 4.30
135 136 6.628185 ACACTCTTACATTAGTTTACGGAGG 58.372 40.000 0.00 0.00 0.00 4.30
136 137 8.530269 AAACACTCTTACATTAGTTTACGGAG 57.470 34.615 0.00 0.00 0.00 4.63
137 138 9.630098 CTAAACACTCTTACATTAGTTTACGGA 57.370 33.333 0.00 0.00 32.23 4.69
138 139 9.630098 TCTAAACACTCTTACATTAGTTTACGG 57.370 33.333 0.00 0.00 32.23 4.02
205 206 3.454371 GTGTATGCACGTATTCCCTCT 57.546 47.619 0.00 0.00 35.75 3.69
218 219 3.496131 CCACGGGTGCGTGTATGC 61.496 66.667 0.00 0.00 38.12 3.14
230 233 0.109179 TCGATCGTAACCAACCACGG 60.109 55.000 15.94 0.00 38.66 4.94
416 2639 1.472201 CCATCAGTCATCACCCACGAG 60.472 57.143 0.00 0.00 0.00 4.18
427 2650 1.976132 GCTAGCTGCCCCATCAGTCA 61.976 60.000 7.70 0.00 36.49 3.41
428 2651 1.227793 GCTAGCTGCCCCATCAGTC 60.228 63.158 7.70 0.00 36.49 3.51
429 2652 1.565390 TTGCTAGCTGCCCCATCAGT 61.565 55.000 17.23 0.00 42.00 3.41
430 2653 0.394762 TTTGCTAGCTGCCCCATCAG 60.395 55.000 17.23 0.00 42.00 2.90
438 2661 3.565905 AGTCAAACATTTGCTAGCTGC 57.434 42.857 17.23 0.00 43.25 5.25
468 2691 0.962489 AACTCCTGTCACTCTCCGTG 59.038 55.000 0.00 0.00 45.18 4.94
493 2716 0.809385 CATGACTTCAGCCTGGCAAG 59.191 55.000 22.65 18.31 0.00 4.01
494 2717 1.246056 GCATGACTTCAGCCTGGCAA 61.246 55.000 22.65 6.35 0.00 4.52
495 2718 1.676635 GCATGACTTCAGCCTGGCA 60.677 57.895 22.65 0.00 0.00 4.92
611 2836 2.153627 ACGGAAATTAACAACGTCGACG 59.846 45.455 34.58 34.58 46.33 5.12
618 2843 6.068473 AGAACCTTGACGGAAATTAACAAC 57.932 37.500 0.00 0.00 36.31 3.32
623 2848 6.531021 AGAAGAAGAACCTTGACGGAAATTA 58.469 36.000 0.00 0.00 36.31 1.40
639 2864 8.301002 GCAAGTAGTAGAAGAAGAAGAAGAAGA 58.699 37.037 0.00 0.00 0.00 2.87
640 2865 8.303876 AGCAAGTAGTAGAAGAAGAAGAAGAAG 58.696 37.037 0.00 0.00 0.00 2.85
641 2866 8.184304 AGCAAGTAGTAGAAGAAGAAGAAGAA 57.816 34.615 0.00 0.00 0.00 2.52
642 2867 7.768807 AGCAAGTAGTAGAAGAAGAAGAAGA 57.231 36.000 0.00 0.00 0.00 2.87
716 4135 9.641770 GAGCATCATCTTGTTAAGCAAGCAAGT 62.642 40.741 12.96 2.17 44.13 3.16
717 4136 7.381225 GAGCATCATCTTGTTAAGCAAGCAAG 61.381 42.308 8.71 8.71 44.13 4.01
809 4445 3.511595 TCCGGGGATTCGACGACG 61.512 66.667 0.00 0.00 41.26 5.12
816 4452 0.466124 CCAGAGAAGTCCGGGGATTC 59.534 60.000 0.00 3.72 0.00 2.52
850 4486 0.892358 ACAGTGACAATGCTGCCCAG 60.892 55.000 2.13 0.00 36.26 4.45
871 4507 3.123804 GAGGATGTATGCCGTACACAAG 58.876 50.000 0.00 0.00 45.59 3.16
872 4508 2.159014 GGAGGATGTATGCCGTACACAA 60.159 50.000 0.00 0.00 45.59 3.33
909 4545 1.369091 GGTAGCGTTGTCAGCCATGG 61.369 60.000 7.63 7.63 34.64 3.66
1180 4822 2.266055 CAGGGAGCGGTTGGAGAC 59.734 66.667 0.00 0.00 0.00 3.36
1257 4899 0.178921 TCCAGAGCTTGAGGGTGTCT 60.179 55.000 0.00 0.00 0.00 3.41
1260 4902 2.276732 TTTTCCAGAGCTTGAGGGTG 57.723 50.000 0.00 0.00 0.00 4.61
1369 5029 1.378762 CCGGGTTGTTGGTGAGGAT 59.621 57.895 0.00 0.00 0.00 3.24
1425 5085 1.515081 CGTCGGTATGGTTGTTGGTT 58.485 50.000 0.00 0.00 0.00 3.67
1515 5175 4.377370 TCGAGTCCGACGTGGTTA 57.623 55.556 0.00 0.00 40.30 2.85
1527 5187 1.007271 CACGCTGTTGAGGTCGAGT 60.007 57.895 0.00 0.00 0.00 4.18
1758 5418 0.839946 ACTTGACCTGGTTCAGCTGT 59.160 50.000 14.67 0.00 0.00 4.40
1861 5521 4.101448 GGTGAGCGGGACCAGCAT 62.101 66.667 19.24 3.89 37.01 3.79
2514 7158 4.050934 TCGTGCTGGATGACGCGT 62.051 61.111 13.85 13.85 40.50 6.01
2770 7414 4.241999 GATGTGCATCGGCGTGGC 62.242 66.667 16.24 16.24 45.35 5.01
3136 7785 2.038659 CGGTATTTCCATGCCCCAAAT 58.961 47.619 0.00 0.00 31.41 2.32
3155 7804 1.376543 AAGACATCAATCCTGCAGCG 58.623 50.000 8.66 1.56 0.00 5.18
3157 7806 3.618351 AGGAAAGACATCAATCCTGCAG 58.382 45.455 6.78 6.78 40.73 4.41
3171 7820 8.041323 GGTCATCTAAGATAACAACAGGAAAGA 58.959 37.037 0.00 0.00 0.00 2.52
3436 8086 7.068103 TGCAAAAGAAAGTCAGGTTGATTCTAA 59.932 33.333 0.00 0.00 28.72 2.10
3437 8087 6.545666 TGCAAAAGAAAGTCAGGTTGATTCTA 59.454 34.615 0.00 0.00 28.72 2.10
3438 8088 5.360714 TGCAAAAGAAAGTCAGGTTGATTCT 59.639 36.000 0.00 0.00 29.65 2.40
3610 8263 8.654485 ACGTTTGGTCTATGGGTGTATATATA 57.346 34.615 0.00 0.00 0.00 0.86
3611 8264 7.549147 ACGTTTGGTCTATGGGTGTATATAT 57.451 36.000 0.00 0.00 0.00 0.86
3642 8295 5.407387 GGAACAATAAAGACTACAACGCAGA 59.593 40.000 0.00 0.00 0.00 4.26
3775 8428 2.508663 GTCTAAGACACCGCGGCC 60.509 66.667 28.58 15.23 32.09 6.13
3788 8441 0.393402 TACTCGCCTCGCCTTGTCTA 60.393 55.000 0.00 0.00 0.00 2.59
3852 8505 2.874457 GCTTTAGAGTTCCCTTCGCCAA 60.874 50.000 0.00 0.00 0.00 4.52
3853 8506 1.338769 GCTTTAGAGTTCCCTTCGCCA 60.339 52.381 0.00 0.00 0.00 5.69
3855 8508 2.388310 AGCTTTAGAGTTCCCTTCGC 57.612 50.000 0.00 0.00 0.00 4.70
3890 8543 2.285442 AACCTTCCCTCTCCCCCG 60.285 66.667 0.00 0.00 0.00 5.73
3903 8556 1.597027 CTTCGGCACCAACGAACCT 60.597 57.895 0.00 0.00 44.41 3.50
3909 8562 0.955919 CCTCCTTCTTCGGCACCAAC 60.956 60.000 0.00 0.00 0.00 3.77
3911 8564 2.592993 CCCTCCTTCTTCGGCACCA 61.593 63.158 0.00 0.00 0.00 4.17
3913 8566 2.436824 GCCCTCCTTCTTCGGCAC 60.437 66.667 0.00 0.00 41.25 5.01
3914 8567 0.907704 TAAGCCCTCCTTCTTCGGCA 60.908 55.000 0.00 0.00 44.18 5.69
3927 8580 1.070914 CCCGATCTTCCTTCTAAGCCC 59.929 57.143 0.00 0.00 0.00 5.19
3941 8594 0.946221 GACATGTCATCGCCCCGATC 60.946 60.000 21.07 0.00 45.19 3.69
3948 8601 1.076533 AACCGTCGACATGTCATCGC 61.077 55.000 24.93 10.53 39.46 4.58
3952 8605 0.108992 GCCTAACCGTCGACATGTCA 60.109 55.000 24.93 9.94 0.00 3.58
3985 8648 6.507958 TCCTATTTCTCTATCAGCGATCTG 57.492 41.667 0.00 0.00 41.67 2.90
3986 8649 6.491745 TGTTCCTATTTCTCTATCAGCGATCT 59.508 38.462 0.00 0.00 0.00 2.75
4001 8664 8.403236 GTTCTAGTTGTTGTTGTGTTCCTATTT 58.597 33.333 0.00 0.00 0.00 1.40
4015 8678 5.215252 TCTTCCCAGAGTTCTAGTTGTTG 57.785 43.478 0.00 0.00 0.00 3.33
4019 8682 9.716556 TTATTCTATCTTCCCAGAGTTCTAGTT 57.283 33.333 0.00 0.00 30.36 2.24
4020 8683 9.716556 TTTATTCTATCTTCCCAGAGTTCTAGT 57.283 33.333 0.00 0.00 30.36 2.57
4023 8686 8.616799 AGTTTATTCTATCTTCCCAGAGTTCT 57.383 34.615 0.00 0.00 30.36 3.01
4052 8715 3.404899 TCGTTGATTCCCACCACTTAAC 58.595 45.455 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.