Multiple sequence alignment - TraesCS5A01G447200

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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 TraesCS5A01G447200 chr5A 100.000 7640 0 0 1 7640 626972834 626965195 0.000000e+00 14109.0
1 TraesCS5A01G447200 chr5A 88.262 3953 279 73 993 4909 11937472 11941275 0.000000e+00 4558.0
2 TraesCS5A01G447200 chr5A 87.187 1639 159 28 5014 6641 11941311 11942909 0.000000e+00 1816.0
3 TraesCS5A01G447200 chr5A 88.000 125 8 4 665 782 11937214 11937338 2.870000e-29 141.0
4 TraesCS5A01G447200 chr5B 95.452 6574 231 32 182 6716 621847723 621841179 0.000000e+00 10421.0
5 TraesCS5A01G447200 chr5B 83.958 1789 181 66 3198 4928 712969469 712971209 0.000000e+00 1616.0
6 TraesCS5A01G447200 chr5B 87.741 1403 128 19 1747 3135 712967699 712969071 0.000000e+00 1598.0
7 TraesCS5A01G447200 chr5B 94.249 626 26 5 7015 7640 621835203 621834588 0.000000e+00 948.0
8 TraesCS5A01G447200 chr5B 84.399 641 82 9 6006 6641 712972110 712972737 1.410000e-171 614.0
9 TraesCS5A01G447200 chr5B 82.642 530 64 14 1170 1674 712967034 712967560 1.960000e-120 444.0
10 TraesCS5A01G447200 chr5B 83.636 385 32 8 3628 4009 42460228 42460584 4.420000e-87 333.0
11 TraesCS5A01G447200 chr5B 95.349 172 8 0 5030 5201 712971214 712971385 2.720000e-69 274.0
12 TraesCS5A01G447200 chr5B 83.824 272 15 11 3296 3567 42459861 42460103 1.660000e-56 231.0
13 TraesCS5A01G447200 chr5B 87.931 116 10 3 996 1110 712966787 712966899 4.810000e-27 134.0
14 TraesCS5A01G447200 chr5D 95.749 6092 165 37 815 6840 500446540 500440477 0.000000e+00 9729.0
15 TraesCS5A01G447200 chr5D 87.023 1834 115 50 3109 4909 18173912 18175655 0.000000e+00 1954.0
16 TraesCS5A01G447200 chr5D 85.098 1993 206 57 1170 3134 562721486 562723415 0.000000e+00 1951.0
17 TraesCS5A01G447200 chr5D 86.526 1759 167 32 5014 6765 18175691 18177386 0.000000e+00 1871.0
18 TraesCS5A01G447200 chr5D 90.248 1251 92 6 1800 3050 18172691 18173911 0.000000e+00 1607.0
19 TraesCS5A01G447200 chr5D 92.795 805 29 15 6837 7638 500440448 500439670 0.000000e+00 1138.0
20 TraesCS5A01G447200 chr5D 86.271 1027 96 29 3906 4904 562724158 562725167 0.000000e+00 1074.0
21 TraesCS5A01G447200 chr5D 85.283 795 77 16 993 1773 18161678 18162446 0.000000e+00 784.0
22 TraesCS5A01G447200 chr5D 86.846 631 56 13 194 815 500447180 500446568 0.000000e+00 680.0
23 TraesCS5A01G447200 chr5D 87.523 553 62 5 5316 5864 562725427 562725976 3.890000e-177 632.0
24 TraesCS5A01G447200 chr5D 83.987 637 83 12 6006 6642 562726058 562726675 1.840000e-165 593.0
25 TraesCS5A01G447200 chr5D 84.286 630 56 9 6029 6648 562830811 562831407 6.650000e-160 575.0
26 TraesCS5A01G447200 chr5D 91.071 112 6 2 675 782 18161425 18161536 1.720000e-31 148.0
27 TraesCS5A01G447200 chr5D 93.617 94 6 0 993 1086 562721265 562721358 2.870000e-29 141.0
28 TraesCS5A01G447200 chr4A 86.544 2772 247 53 3906 6641 615696780 615694099 0.000000e+00 2937.0
29 TraesCS5A01G447200 chr4A 88.326 2133 159 34 1749 3872 615698821 615696770 0.000000e+00 2477.0
30 TraesCS5A01G447200 chr4A 85.509 697 68 14 993 1656 615699595 615698899 0.000000e+00 697.0
31 TraesCS5A01G447200 chr4A 92.222 90 7 0 693 782 615699835 615699746 2.240000e-25 128.0
32 TraesCS5A01G447200 chr7B 82.887 2688 370 49 934 3562 103896772 103894116 0.000000e+00 2333.0
33 TraesCS5A01G447200 chr7B 87.135 1508 162 17 1170 2660 49063 47571 0.000000e+00 1681.0
34 TraesCS5A01G447200 chr7B 84.010 1526 161 50 3220 4696 46942 45451 0.000000e+00 1389.0
35 TraesCS5A01G447200 chr7B 86.555 1071 119 16 3627 4682 103893991 103892931 0.000000e+00 1157.0
36 TraesCS5A01G447200 chr7B 83.316 983 136 17 4924 5897 103892498 103891535 0.000000e+00 881.0
37 TraesCS5A01G447200 chr7B 83.568 639 83 14 6006 6642 44243 43625 5.140000e-161 579.0
38 TraesCS5A01G447200 chr7B 85.366 369 25 2 3643 4009 735289196 735288855 9.430000e-94 355.0
39 TraesCS5A01G447200 chr7B 84.615 273 14 3 3296 3567 735289581 735289336 5.920000e-61 246.0
40 TraesCS5A01G447200 chr7B 87.037 162 17 2 4747 4904 45354 45193 6.090000e-41 180.0
41 TraesCS5A01G447200 chr7B 93.750 96 6 0 993 1088 49263 49168 2.220000e-30 145.0
42 TraesCS5A01G447200 chr2B 80.359 2617 431 70 991 3559 787752174 787754755 0.000000e+00 1908.0
43 TraesCS5A01G447200 chr2B 85.700 1000 120 10 3703 4696 787754945 787755927 0.000000e+00 1033.0
44 TraesCS5A01G447200 chr2B 79.464 1120 170 41 4767 5862 787756030 787757113 0.000000e+00 739.0
45 TraesCS5A01G447200 chr7A 83.836 1856 250 27 1750 3562 138509410 138507562 0.000000e+00 1720.0
46 TraesCS5A01G447200 chr7A 87.252 1059 114 13 3642 4688 138507422 138506373 0.000000e+00 1188.0
47 TraesCS5A01G447200 chr7A 83.419 977 127 20 5028 5983 138503621 138502659 0.000000e+00 874.0
48 TraesCS5A01G447200 chr7A 79.616 677 114 12 5981 6644 138502422 138501757 1.500000e-126 464.0
49 TraesCS5A01G447200 chr7D 86.053 1140 136 15 3563 4686 138424675 138423543 0.000000e+00 1203.0
50 TraesCS5A01G447200 chr7D 83.299 982 135 15 4924 5897 138423116 138422156 0.000000e+00 878.0
51 TraesCS5A01G447200 chr7D 82.087 642 97 11 2935 3562 138425355 138424718 4.060000e-147 532.0
52 TraesCS5A01G447200 chr7D 92.424 66 3 2 8 73 123494325 123494388 8.160000e-15 93.5
53 TraesCS5A01G447200 chrUn 90.667 150 11 3 8 156 24957277 24957130 6.050000e-46 196.0
54 TraesCS5A01G447200 chr4B 81.579 152 11 4 8 156 460375484 460375347 8.110000e-20 110.0
55 TraesCS5A01G447200 chr3B 83.088 136 8 4 21 156 736677926 736678046 8.110000e-20 110.0
56 TraesCS5A01G447200 chr1B 91.667 60 5 0 8 67 550913574 550913633 4.910000e-12 84.2


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 TraesCS5A01G447200 chr5A 626965195 626972834 7639 True 14109.000000 14109 100.000000 1 7640 1 chr5A.!!$R1 7639
1 TraesCS5A01G447200 chr5A 11937214 11942909 5695 False 2171.666667 4558 87.816333 665 6641 3 chr5A.!!$F1 5976
2 TraesCS5A01G447200 chr5B 621841179 621847723 6544 True 10421.000000 10421 95.452000 182 6716 1 chr5B.!!$R2 6534
3 TraesCS5A01G447200 chr5B 621834588 621835203 615 True 948.000000 948 94.249000 7015 7640 1 chr5B.!!$R1 625
4 TraesCS5A01G447200 chr5B 712966787 712972737 5950 False 780.000000 1616 87.003333 996 6641 6 chr5B.!!$F2 5645
5 TraesCS5A01G447200 chr5B 42459861 42460584 723 False 282.000000 333 83.730000 3296 4009 2 chr5B.!!$F1 713
6 TraesCS5A01G447200 chr5D 500439670 500447180 7510 True 3849.000000 9729 91.796667 194 7638 3 chr5D.!!$R1 7444
7 TraesCS5A01G447200 chr5D 18172691 18177386 4695 False 1810.666667 1954 87.932333 1800 6765 3 chr5D.!!$F3 4965
8 TraesCS5A01G447200 chr5D 562721265 562726675 5410 False 878.200000 1951 87.299200 993 6642 5 chr5D.!!$F4 5649
9 TraesCS5A01G447200 chr5D 562830811 562831407 596 False 575.000000 575 84.286000 6029 6648 1 chr5D.!!$F1 619
10 TraesCS5A01G447200 chr5D 18161425 18162446 1021 False 466.000000 784 88.177000 675 1773 2 chr5D.!!$F2 1098
11 TraesCS5A01G447200 chr4A 615694099 615699835 5736 True 1559.750000 2937 88.150250 693 6641 4 chr4A.!!$R1 5948
12 TraesCS5A01G447200 chr7B 103891535 103896772 5237 True 1457.000000 2333 84.252667 934 5897 3 chr7B.!!$R2 4963
13 TraesCS5A01G447200 chr7B 43625 49263 5638 True 794.800000 1681 87.100000 993 6642 5 chr7B.!!$R1 5649
14 TraesCS5A01G447200 chr7B 735288855 735289581 726 True 300.500000 355 84.990500 3296 4009 2 chr7B.!!$R3 713
15 TraesCS5A01G447200 chr2B 787752174 787757113 4939 False 1226.666667 1908 81.841000 991 5862 3 chr2B.!!$F1 4871
16 TraesCS5A01G447200 chr7A 138501757 138509410 7653 True 1061.500000 1720 83.530750 1750 6644 4 chr7A.!!$R1 4894
17 TraesCS5A01G447200 chr7D 138422156 138425355 3199 True 871.000000 1203 83.813000 2935 5897 3 chr7D.!!$R1 2962

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
171 172 0.032813 CTGATCCACCCAAGGCCAAT 60.033 55.000 5.01 0.00 0.00 3.16 F
573 587 0.101759 CATCCTTTCATGGCTTGCCG 59.898 55.000 7.18 0.00 0.00 5.69 F
823 916 0.107703 TTCCTGCCTGCAAGTATCCG 60.108 55.000 0.00 0.00 0.00 4.18 F
2357 2741 0.779997 AGTTGGTCATCCTTGGGCTT 59.220 50.000 0.00 0.00 34.23 4.35 F
2556 2940 1.221840 CCTCCGTGGACCATTGGAG 59.778 63.158 27.34 27.34 46.10 3.86 F
4011 5227 2.373836 TGCTTTTAGGCCTGGTGTTCTA 59.626 45.455 17.99 0.00 0.00 2.10 F
4912 8662 2.008242 TGGGGCAGCAAGTTTTGTAT 57.992 45.000 0.00 0.00 0.00 2.29 F
5219 8978 3.067106 GCCTCATTCGTTGAACTTGAGA 58.933 45.455 16.32 1.03 33.19 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 2148 0.678048 GCCCTTGCAGGTCCTGTTAG 60.678 60.000 20.24 15.97 37.47 2.34 R
2357 2741 3.008923 TGAGGAACACAGTCATGGCAATA 59.991 43.478 0.00 0.00 0.00 1.90 R
2662 3181 2.061773 CACAAGGATGATACGCGGATC 58.938 52.381 24.71 24.71 0.00 3.36 R
3158 4100 1.204941 CCCTTCACTGTCCGAGTTAGG 59.795 57.143 0.00 0.00 35.16 2.69 R
4127 5343 1.487482 GCGGGCAAAAGTTTCTTGTC 58.513 50.000 0.00 0.00 0.00 3.18 R
5920 9821 1.777272 AGGATGGGCCCTTTCATCTAC 59.223 52.381 25.70 5.70 39.57 2.59 R
6011 10154 0.897621 TCATCTCCACGCATGTCTGT 59.102 50.000 0.00 0.00 0.00 3.41 R
7095 11308 0.322008 GGAAGAAGCAGTGGGAGTGG 60.322 60.000 0.00 0.00 0.00 4.00 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
20 21 2.973945 AGGTTTAGCTGAAAGGCTACG 58.026 47.619 0.00 0.00 43.40 3.51
21 22 1.397343 GGTTTAGCTGAAAGGCTACGC 59.603 52.381 0.00 0.00 43.40 4.42
35 36 4.696899 GGCTACGCCTTTGACTATTTTT 57.303 40.909 0.00 0.00 46.69 1.94
52 53 2.507407 TTTTCTGACATGGGCCTACC 57.493 50.000 4.53 0.00 40.81 3.18
53 54 1.668826 TTTCTGACATGGGCCTACCT 58.331 50.000 4.53 0.00 41.11 3.08
54 55 2.561209 TTCTGACATGGGCCTACCTA 57.439 50.000 4.53 0.00 41.11 3.08
55 56 2.088104 TCTGACATGGGCCTACCTAG 57.912 55.000 4.53 0.00 41.11 3.02
56 57 1.291033 TCTGACATGGGCCTACCTAGT 59.709 52.381 4.53 0.00 41.11 2.57
57 58 2.516702 TCTGACATGGGCCTACCTAGTA 59.483 50.000 4.53 0.00 41.11 1.82
58 59 3.052414 TCTGACATGGGCCTACCTAGTAA 60.052 47.826 4.53 0.00 41.11 2.24
59 60 3.036091 TGACATGGGCCTACCTAGTAAC 58.964 50.000 4.53 0.00 41.11 2.50
60 61 3.306613 GACATGGGCCTACCTAGTAACT 58.693 50.000 4.53 0.00 41.11 2.24
61 62 3.710165 GACATGGGCCTACCTAGTAACTT 59.290 47.826 4.53 0.00 41.11 2.66
62 63 3.454812 ACATGGGCCTACCTAGTAACTTG 59.545 47.826 4.53 0.00 41.11 3.16
63 64 1.835531 TGGGCCTACCTAGTAACTTGC 59.164 52.381 4.53 0.00 41.11 4.01
64 65 2.117051 GGGCCTACCTAGTAACTTGCT 58.883 52.381 0.84 0.00 35.85 3.91
65 66 3.303049 GGGCCTACCTAGTAACTTGCTA 58.697 50.000 0.84 0.00 35.85 3.49
66 67 3.902467 GGGCCTACCTAGTAACTTGCTAT 59.098 47.826 0.84 0.00 35.85 2.97
67 68 5.082425 GGGCCTACCTAGTAACTTGCTATA 58.918 45.833 0.84 0.00 35.85 1.31
68 69 5.047448 GGGCCTACCTAGTAACTTGCTATAC 60.047 48.000 0.84 0.00 35.85 1.47
69 70 5.537674 GGCCTACCTAGTAACTTGCTATACA 59.462 44.000 0.00 0.00 0.00 2.29
70 71 6.210984 GGCCTACCTAGTAACTTGCTATACAT 59.789 42.308 0.00 0.00 0.00 2.29
71 72 7.395489 GGCCTACCTAGTAACTTGCTATACATA 59.605 40.741 0.00 0.00 0.00 2.29
72 73 8.460428 GCCTACCTAGTAACTTGCTATACATAG 58.540 40.741 0.00 0.00 0.00 2.23
73 74 9.517868 CCTACCTAGTAACTTGCTATACATAGT 57.482 37.037 0.00 0.00 32.96 2.12
75 76 8.179509 ACCTAGTAACTTGCTATACATAGTGG 57.820 38.462 0.00 0.00 32.96 4.00
76 77 7.091443 CCTAGTAACTTGCTATACATAGTGGC 58.909 42.308 0.00 0.00 32.96 5.01
77 78 6.732896 AGTAACTTGCTATACATAGTGGCT 57.267 37.500 0.00 0.00 32.96 4.75
78 79 7.834881 AGTAACTTGCTATACATAGTGGCTA 57.165 36.000 0.00 0.00 32.96 3.93
79 80 7.659186 AGTAACTTGCTATACATAGTGGCTAC 58.341 38.462 0.00 0.00 32.96 3.58
80 81 6.479972 AACTTGCTATACATAGTGGCTACA 57.520 37.500 2.02 0.00 32.96 2.74
81 82 6.672266 ACTTGCTATACATAGTGGCTACAT 57.328 37.500 2.02 0.00 32.96 2.29
82 83 7.776618 ACTTGCTATACATAGTGGCTACATA 57.223 36.000 2.02 0.00 32.96 2.29
83 84 7.603651 ACTTGCTATACATAGTGGCTACATAC 58.396 38.462 2.02 0.00 32.96 2.39
84 85 6.525578 TGCTATACATAGTGGCTACATACC 57.474 41.667 2.02 0.00 32.96 2.73
85 86 6.253758 TGCTATACATAGTGGCTACATACCT 58.746 40.000 2.02 0.00 32.96 3.08
86 87 6.152831 TGCTATACATAGTGGCTACATACCTG 59.847 42.308 2.02 0.00 32.96 4.00
87 88 6.405953 GCTATACATAGTGGCTACATACCTGG 60.406 46.154 2.02 0.00 32.96 4.45
88 89 2.972713 ACATAGTGGCTACATACCTGGG 59.027 50.000 2.02 0.00 0.00 4.45
89 90 2.860817 TAGTGGCTACATACCTGGGT 57.139 50.000 2.02 0.00 0.00 4.51
90 91 1.204146 AGTGGCTACATACCTGGGTG 58.796 55.000 2.02 0.00 0.00 4.61
91 92 0.180406 GTGGCTACATACCTGGGTGG 59.820 60.000 2.07 0.00 42.93 4.61
92 93 0.986019 TGGCTACATACCTGGGTGGG 60.986 60.000 2.07 0.00 41.11 4.61
93 94 1.705997 GGCTACATACCTGGGTGGGG 61.706 65.000 2.07 0.00 41.11 4.96
94 95 1.705997 GCTACATACCTGGGTGGGGG 61.706 65.000 2.07 0.00 41.11 5.40
95 96 1.694882 TACATACCTGGGTGGGGGC 60.695 63.158 2.07 0.00 41.11 5.80
96 97 3.820843 CATACCTGGGTGGGGGCC 61.821 72.222 0.00 0.00 41.11 5.80
105 106 4.129148 GTGGGGGCCCCTAGCTTG 62.129 72.222 40.43 0.00 45.70 4.01
106 107 4.693915 TGGGGGCCCCTAGCTTGT 62.694 66.667 40.43 0.00 45.70 3.16
107 108 4.129148 GGGGGCCCCTAGCTTGTG 62.129 72.222 39.92 0.00 41.34 3.33
108 109 4.129148 GGGGCCCCTAGCTTGTGG 62.129 72.222 35.49 0.00 43.05 4.17
109 110 4.129148 GGGCCCCTAGCTTGTGGG 62.129 72.222 12.23 14.45 43.05 4.61
113 114 4.129148 CCCTAGCTTGTGGGGGCC 62.129 72.222 10.31 0.00 43.67 5.80
114 115 4.129148 CCTAGCTTGTGGGGGCCC 62.129 72.222 15.76 15.76 0.00 5.80
115 116 4.489771 CTAGCTTGTGGGGGCCCG 62.490 72.222 17.79 2.72 39.42 6.13
159 160 4.414956 AGGACCGGCCCTGATCCA 62.415 66.667 9.27 0.00 37.37 3.41
160 161 4.176752 GGACCGGCCCTGATCCAC 62.177 72.222 0.00 0.00 0.00 4.02
161 162 4.176752 GACCGGCCCTGATCCACC 62.177 72.222 0.00 0.00 0.00 4.61
164 165 3.727258 CGGCCCTGATCCACCCAA 61.727 66.667 0.00 0.00 0.00 4.12
165 166 2.276740 GGCCCTGATCCACCCAAG 59.723 66.667 0.00 0.00 0.00 3.61
166 167 2.276740 GCCCTGATCCACCCAAGG 59.723 66.667 0.00 0.00 0.00 3.61
167 168 2.276740 CCCTGATCCACCCAAGGC 59.723 66.667 0.00 0.00 0.00 4.35
168 169 2.276740 CCTGATCCACCCAAGGCC 59.723 66.667 0.00 0.00 0.00 5.19
169 170 2.615465 CCTGATCCACCCAAGGCCA 61.615 63.158 5.01 0.00 0.00 5.36
170 171 1.383799 CTGATCCACCCAAGGCCAA 59.616 57.895 5.01 0.00 0.00 4.52
171 172 0.032813 CTGATCCACCCAAGGCCAAT 60.033 55.000 5.01 0.00 0.00 3.16
172 173 0.324552 TGATCCACCCAAGGCCAATG 60.325 55.000 5.01 3.01 0.00 2.82
173 174 1.679559 GATCCACCCAAGGCCAATGC 61.680 60.000 5.01 0.00 0.00 3.56
174 175 2.458969 ATCCACCCAAGGCCAATGCA 62.459 55.000 5.01 0.00 40.13 3.96
175 176 1.991167 CCACCCAAGGCCAATGCAT 60.991 57.895 5.01 0.00 40.13 3.96
176 177 0.687098 CCACCCAAGGCCAATGCATA 60.687 55.000 5.01 0.00 40.13 3.14
177 178 0.461135 CACCCAAGGCCAATGCATAC 59.539 55.000 5.01 0.00 40.13 2.39
178 179 0.687427 ACCCAAGGCCAATGCATACC 60.687 55.000 5.01 1.98 40.13 2.73
179 180 0.687098 CCCAAGGCCAATGCATACCA 60.687 55.000 5.01 0.00 40.13 3.25
180 181 0.461135 CCAAGGCCAATGCATACCAC 59.539 55.000 5.01 0.65 40.13 4.16
188 189 3.748668 GCCAATGCATACCACTACCAGAT 60.749 47.826 0.00 0.00 37.47 2.90
243 244 2.728443 GATGGGAGGGCAGCATCTCG 62.728 65.000 0.00 0.00 0.00 4.04
245 246 2.586792 GGAGGGCAGCATCTCGTT 59.413 61.111 0.00 0.00 0.00 3.85
251 252 0.881118 GGCAGCATCTCGTTTGGAAA 59.119 50.000 0.00 0.00 0.00 3.13
370 380 4.479993 AGCCTGGCTAGCCGCAAG 62.480 66.667 28.48 20.79 41.67 4.01
403 413 2.302445 CCCATCAATCAGCTCTAGAGGG 59.698 54.545 21.23 9.94 0.00 4.30
443 457 1.410882 AGGACTCTAATGGCTTCTCGC 59.589 52.381 0.00 0.00 38.13 5.03
466 480 1.670087 CGAGCGTCATTGAGGTGTTCT 60.670 52.381 8.06 0.00 0.00 3.01
475 489 4.391830 TCATTGAGGTGTTCTACGAAATGC 59.608 41.667 0.00 0.00 30.42 3.56
508 522 0.227234 CTCGCGGATTTGACGATTCG 59.773 55.000 6.13 4.14 34.94 3.34
512 526 1.267383 GCGGATTTGACGATTCGTTCC 60.267 52.381 13.72 14.35 41.37 3.62
513 527 1.326548 CGGATTTGACGATTCGTTCCC 59.673 52.381 13.72 9.12 41.37 3.97
520 534 2.101917 TGACGATTCGTTCCCTAATCCC 59.898 50.000 13.72 0.00 41.37 3.85
525 539 0.619255 TCGTTCCCTAATCCCAGCCA 60.619 55.000 0.00 0.00 0.00 4.75
526 540 0.179045 CGTTCCCTAATCCCAGCCAG 60.179 60.000 0.00 0.00 0.00 4.85
527 541 0.466372 GTTCCCTAATCCCAGCCAGC 60.466 60.000 0.00 0.00 0.00 4.85
528 542 1.645402 TTCCCTAATCCCAGCCAGCC 61.645 60.000 0.00 0.00 0.00 4.85
529 543 2.386100 CCCTAATCCCAGCCAGCCA 61.386 63.158 0.00 0.00 0.00 4.75
530 544 1.150081 CCTAATCCCAGCCAGCCAG 59.850 63.158 0.00 0.00 0.00 4.85
531 545 1.527844 CTAATCCCAGCCAGCCAGC 60.528 63.158 0.00 0.00 0.00 4.85
532 546 2.972892 CTAATCCCAGCCAGCCAGCC 62.973 65.000 0.00 0.00 0.00 4.85
548 562 2.123982 CCAGCCAGCCTCATTCCC 60.124 66.667 0.00 0.00 0.00 3.97
556 570 3.078843 GCCTCATTCCCCTGCCCAT 62.079 63.158 0.00 0.00 0.00 4.00
560 574 0.925720 TCATTCCCCTGCCCATCCTT 60.926 55.000 0.00 0.00 0.00 3.36
573 587 0.101759 CATCCTTTCATGGCTTGCCG 59.898 55.000 7.18 0.00 0.00 5.69
583 597 2.703409 GCTTGCCGTGCAGTATCG 59.297 61.111 0.00 0.00 40.61 2.92
609 623 7.337942 GGTTATTCACATTTGGTCTCTCTCATT 59.662 37.037 0.00 0.00 0.00 2.57
631 645 6.398234 TTTACTCCTGCTTTTTGTATGCAA 57.602 33.333 0.00 0.00 36.59 4.08
637 651 4.178540 CTGCTTTTTGTATGCAAGGATGG 58.821 43.478 0.00 0.00 36.59 3.51
651 665 8.641498 ATGCAAGGATGGATTTAATTAGTAGG 57.359 34.615 0.00 0.00 33.23 3.18
722 751 2.815647 GGCCGACTTGCTTCCTCG 60.816 66.667 0.00 0.00 0.00 4.63
823 916 0.107703 TTCCTGCCTGCAAGTATCCG 60.108 55.000 0.00 0.00 0.00 4.18
849 948 8.778358 GTTGTCAAGATCAGTTTTCAGTATCTT 58.222 33.333 0.00 0.00 37.37 2.40
867 966 1.203052 CTTGGCGGAATCAGCAACAAT 59.797 47.619 7.78 0.00 36.08 2.71
984 1100 8.116136 GCCAAATAAGCAAGTATTTTAACATGC 58.884 33.333 0.00 0.00 42.78 4.06
1093 1213 3.876309 AAGCCCTCAAGGTTTGAACTA 57.124 42.857 0.00 0.00 37.73 2.24
1674 1962 9.553064 CATACATAGAAAGAATAAGCTCAACCT 57.447 33.333 0.00 0.00 0.00 3.50
1729 2094 8.103305 ACTTAATTCATATTACGCCCATCTGAT 58.897 33.333 0.00 0.00 0.00 2.90
1764 2148 2.077842 ATCCATGGCAGGGGAGATGC 62.078 60.000 19.39 0.00 43.09 3.91
2118 2502 0.817654 CCAGGAGCAGTATCGTCACA 59.182 55.000 0.00 0.00 0.00 3.58
2276 2660 3.808618 GCTGGGAGTCATTCAAGACAGTT 60.809 47.826 0.00 0.00 40.98 3.16
2277 2661 4.392940 CTGGGAGTCATTCAAGACAGTTT 58.607 43.478 0.00 0.00 40.98 2.66
2357 2741 0.779997 AGTTGGTCATCCTTGGGCTT 59.220 50.000 0.00 0.00 34.23 4.35
2556 2940 1.221840 CCTCCGTGGACCATTGGAG 59.778 63.158 27.34 27.34 46.10 3.86
2957 3557 6.211184 AGCTAGGCATGATATATCAGCTATCC 59.789 42.308 24.07 17.74 40.64 2.59
3457 4463 6.980593 TCTTCTGGTTGACATTATTGTTTGG 58.019 36.000 0.00 0.00 35.79 3.28
3571 4639 7.933577 TGAGAATGAGACAAACACTTCAATACT 59.066 33.333 0.00 0.00 0.00 2.12
3612 4784 6.574350 AGTATTCATTACACTACTGCAGTCC 58.426 40.000 25.56 0.00 34.26 3.85
3820 5014 6.610020 TGCAGTAAGCCTACCTATCTTTCTAA 59.390 38.462 0.00 0.00 44.83 2.10
4011 5227 2.373836 TGCTTTTAGGCCTGGTGTTCTA 59.626 45.455 17.99 0.00 0.00 2.10
4127 5343 3.844804 ACCCTCTCTGGTTACCCTAAAAG 59.155 47.826 0.00 0.00 33.91 2.27
4912 8662 2.008242 TGGGGCAGCAAGTTTTGTAT 57.992 45.000 0.00 0.00 0.00 2.29
5219 8978 3.067106 GCCTCATTCGTTGAACTTGAGA 58.933 45.455 16.32 1.03 33.19 3.27
5377 9171 7.291566 TGACCAGGAAAAACCAAGAACTTATA 58.708 34.615 0.00 0.00 42.04 0.98
5484 9278 4.022935 TGCAAACTTCTGGAAGCAATACAG 60.023 41.667 9.91 0.00 41.87 2.74
5887 9768 7.745022 TTAGTCGGTCTTAATTTGATACACG 57.255 36.000 0.00 0.00 0.00 4.49
5920 9821 7.140705 TGTTGTTTAGATTCATTGAGCTTGTG 58.859 34.615 0.00 0.00 0.00 3.33
6373 10541 6.220201 GTTGGTTGGTTATTGTTGCAGTTAT 58.780 36.000 0.00 0.00 0.00 1.89
6595 10766 3.616956 ATGTCATCGGCTTCTTCTTGA 57.383 42.857 0.00 0.00 0.00 3.02
6682 10861 2.011046 GCAAGAGAGAAGCGGCAATCT 61.011 52.381 1.45 5.29 0.00 2.40
6683 10862 2.739932 GCAAGAGAGAAGCGGCAATCTA 60.740 50.000 1.45 0.00 0.00 1.98
6688 10867 6.202516 AGAGAGAAGCGGCAATCTATATAC 57.797 41.667 1.45 0.00 0.00 1.47
6691 10870 7.612244 AGAGAGAAGCGGCAATCTATATACTTA 59.388 37.037 1.45 0.00 0.00 2.24
6723 10902 8.880991 ATATGTGTATAGTAGAAGTGGTAGGG 57.119 38.462 0.00 0.00 0.00 3.53
6770 10949 6.491714 AAGCTCTGCTATTTAGAGGAATGA 57.508 37.500 0.00 0.00 41.52 2.57
6951 11164 1.000955 GAAGAAGCGGTGAGGTGAAGA 59.999 52.381 0.00 0.00 0.00 2.87
6952 11165 1.048601 AGAAGCGGTGAGGTGAAGAA 58.951 50.000 0.00 0.00 0.00 2.52
6953 11166 1.001406 AGAAGCGGTGAGGTGAAGAAG 59.999 52.381 0.00 0.00 0.00 2.85
6966 11179 3.558109 GGTGAAGAAGTGGAAGGAAGAGG 60.558 52.174 0.00 0.00 0.00 3.69
6971 11184 1.219393 GTGGAAGGAAGAGGAGCGG 59.781 63.158 0.00 0.00 0.00 5.52
6972 11185 2.188207 GGAAGGAAGAGGAGCGGC 59.812 66.667 0.00 0.00 0.00 6.53
6973 11186 2.202810 GAAGGAAGAGGAGCGGCG 60.203 66.667 0.51 0.51 0.00 6.46
6974 11187 4.459089 AAGGAAGAGGAGCGGCGC 62.459 66.667 26.86 26.86 0.00 6.53
6987 11200 4.521062 GGCGCGTCCTCATGCTCT 62.521 66.667 8.43 0.00 31.59 4.09
6988 11201 3.260483 GCGCGTCCTCATGCTCTG 61.260 66.667 8.43 0.00 31.59 3.35
6989 11202 2.182791 CGCGTCCTCATGCTCTGT 59.817 61.111 0.00 0.00 31.59 3.41
6990 11203 1.446792 CGCGTCCTCATGCTCTGTT 60.447 57.895 0.00 0.00 31.59 3.16
7003 11216 2.733218 CTGTTTCTCCGCGCGTCA 60.733 61.111 29.95 14.02 0.00 4.35
7034 11247 1.404851 CCTCTTCCTTCCTCTCAACGC 60.405 57.143 0.00 0.00 0.00 4.84
7035 11248 0.608640 TCTTCCTTCCTCTCAACGCC 59.391 55.000 0.00 0.00 0.00 5.68
7036 11249 0.321671 CTTCCTTCCTCTCAACGCCA 59.678 55.000 0.00 0.00 0.00 5.69
7037 11250 0.762418 TTCCTTCCTCTCAACGCCAA 59.238 50.000 0.00 0.00 0.00 4.52
7080 11293 1.548357 CCACCACTCCCACTCCTCTG 61.548 65.000 0.00 0.00 0.00 3.35
7089 11302 1.298014 CACTCCTCTGCCTTCCACC 59.702 63.158 0.00 0.00 0.00 4.61
7095 11308 4.366684 CTGCCTTCCACCCCACCC 62.367 72.222 0.00 0.00 0.00 4.61
7101 11314 4.995058 TCCACCCCACCCCACTCC 62.995 72.222 0.00 0.00 0.00 3.85
7201 11417 2.829458 GAGGTCCCCTCCGAGTCG 60.829 72.222 5.29 5.29 44.36 4.18
7468 11684 0.389166 CGCAGAACTTCGAGCTCCTT 60.389 55.000 8.47 0.00 0.00 3.36
7470 11686 1.623359 CAGAACTTCGAGCTCCTTCG 58.377 55.000 8.47 0.00 41.79 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.973945 CGTAGCCTTTCAGCTAAACCT 58.026 47.619 0.00 0.00 46.52 3.50
32 33 2.378547 AGGTAGGCCCATGTCAGAAAAA 59.621 45.455 0.00 0.00 34.66 1.94
33 34 1.992557 AGGTAGGCCCATGTCAGAAAA 59.007 47.619 0.00 0.00 34.66 2.29
34 35 1.668826 AGGTAGGCCCATGTCAGAAA 58.331 50.000 0.00 0.00 34.66 2.52
35 36 2.292918 ACTAGGTAGGCCCATGTCAGAA 60.293 50.000 0.00 0.00 34.66 3.02
36 37 1.291033 ACTAGGTAGGCCCATGTCAGA 59.709 52.381 0.00 0.00 34.66 3.27
37 38 1.794714 ACTAGGTAGGCCCATGTCAG 58.205 55.000 0.00 0.00 34.66 3.51
38 39 3.036091 GTTACTAGGTAGGCCCATGTCA 58.964 50.000 0.00 0.00 34.66 3.58
39 40 3.306613 AGTTACTAGGTAGGCCCATGTC 58.693 50.000 0.00 0.00 34.66 3.06
40 41 3.416414 AGTTACTAGGTAGGCCCATGT 57.584 47.619 0.00 0.00 34.66 3.21
41 42 3.744530 GCAAGTTACTAGGTAGGCCCATG 60.745 52.174 0.00 0.00 34.66 3.66
42 43 2.438392 GCAAGTTACTAGGTAGGCCCAT 59.562 50.000 0.00 0.00 34.66 4.00
43 44 1.835531 GCAAGTTACTAGGTAGGCCCA 59.164 52.381 0.00 0.00 34.66 5.36
44 45 2.117051 AGCAAGTTACTAGGTAGGCCC 58.883 52.381 0.00 0.00 34.57 5.80
45 46 5.537674 TGTATAGCAAGTTACTAGGTAGGCC 59.462 44.000 0.00 0.00 0.00 5.19
46 47 6.645790 TGTATAGCAAGTTACTAGGTAGGC 57.354 41.667 0.00 0.00 0.00 3.93
47 48 9.517868 ACTATGTATAGCAAGTTACTAGGTAGG 57.482 37.037 0.00 0.00 33.68 3.18
49 50 9.293404 CCACTATGTATAGCAAGTTACTAGGTA 57.707 37.037 0.00 0.00 33.68 3.08
50 51 7.255871 GCCACTATGTATAGCAAGTTACTAGGT 60.256 40.741 0.00 0.00 33.68 3.08
51 52 7.039644 AGCCACTATGTATAGCAAGTTACTAGG 60.040 40.741 0.00 0.00 33.68 3.02
52 53 7.887381 AGCCACTATGTATAGCAAGTTACTAG 58.113 38.462 0.00 0.00 33.68 2.57
53 54 7.834881 AGCCACTATGTATAGCAAGTTACTA 57.165 36.000 0.00 0.00 33.68 1.82
54 55 6.732896 AGCCACTATGTATAGCAAGTTACT 57.267 37.500 0.00 0.00 33.68 2.24
55 56 7.431249 TGTAGCCACTATGTATAGCAAGTTAC 58.569 38.462 0.00 2.58 33.68 2.50
56 57 7.591421 TGTAGCCACTATGTATAGCAAGTTA 57.409 36.000 0.00 0.00 33.68 2.24
57 58 6.479972 TGTAGCCACTATGTATAGCAAGTT 57.520 37.500 0.00 0.00 33.68 2.66
58 59 6.672266 ATGTAGCCACTATGTATAGCAAGT 57.328 37.500 0.00 0.00 33.68 3.16
59 60 7.036220 GGTATGTAGCCACTATGTATAGCAAG 58.964 42.308 0.00 0.00 33.68 4.01
60 61 6.724441 AGGTATGTAGCCACTATGTATAGCAA 59.276 38.462 0.00 0.00 33.68 3.91
61 62 6.152831 CAGGTATGTAGCCACTATGTATAGCA 59.847 42.308 0.00 0.00 33.68 3.49
62 63 6.405953 CCAGGTATGTAGCCACTATGTATAGC 60.406 46.154 0.00 0.00 33.68 2.97
63 64 6.096987 CCCAGGTATGTAGCCACTATGTATAG 59.903 46.154 0.00 0.00 36.46 1.31
64 65 5.955959 CCCAGGTATGTAGCCACTATGTATA 59.044 44.000 0.00 0.00 0.00 1.47
65 66 4.777896 CCCAGGTATGTAGCCACTATGTAT 59.222 45.833 0.00 0.00 0.00 2.29
66 67 4.157246 CCCAGGTATGTAGCCACTATGTA 58.843 47.826 0.00 0.00 0.00 2.29
67 68 2.972713 CCCAGGTATGTAGCCACTATGT 59.027 50.000 0.00 0.00 0.00 2.29
68 69 2.972713 ACCCAGGTATGTAGCCACTATG 59.027 50.000 0.00 0.00 0.00 2.23
69 70 2.972713 CACCCAGGTATGTAGCCACTAT 59.027 50.000 0.00 0.00 0.00 2.12
70 71 2.394632 CACCCAGGTATGTAGCCACTA 58.605 52.381 0.00 0.00 0.00 2.74
71 72 1.204146 CACCCAGGTATGTAGCCACT 58.796 55.000 0.00 0.00 0.00 4.00
72 73 0.180406 CCACCCAGGTATGTAGCCAC 59.820 60.000 0.00 0.00 0.00 5.01
73 74 0.986019 CCCACCCAGGTATGTAGCCA 60.986 60.000 0.00 0.00 34.66 4.75
74 75 1.705997 CCCCACCCAGGTATGTAGCC 61.706 65.000 0.00 0.00 34.66 3.93
75 76 1.705997 CCCCCACCCAGGTATGTAGC 61.706 65.000 0.00 0.00 34.66 3.58
76 77 1.705997 GCCCCCACCCAGGTATGTAG 61.706 65.000 0.00 0.00 34.66 2.74
77 78 1.694882 GCCCCCACCCAGGTATGTA 60.695 63.158 0.00 0.00 34.66 2.29
78 79 3.021263 GCCCCCACCCAGGTATGT 61.021 66.667 0.00 0.00 34.66 2.29
79 80 3.820843 GGCCCCCACCCAGGTATG 61.821 72.222 0.00 0.00 34.66 2.39
90 91 4.129148 CACAAGCTAGGGGCCCCC 62.129 72.222 38.68 22.85 45.90 5.40
91 92 4.129148 CCACAAGCTAGGGGCCCC 62.129 72.222 35.90 35.90 43.05 5.80
92 93 4.129148 CCCACAAGCTAGGGGCCC 62.129 72.222 17.12 17.12 41.58 5.80
96 97 4.129148 GGCCCCCACAAGCTAGGG 62.129 72.222 11.01 11.01 45.04 3.53
97 98 4.129148 GGGCCCCCACAAGCTAGG 62.129 72.222 12.23 0.00 35.81 3.02
98 99 4.489771 CGGGCCCCCACAAGCTAG 62.490 72.222 18.66 0.00 35.37 3.42
142 143 4.414956 TGGATCAGGGCCGGTCCT 62.415 66.667 25.80 25.80 37.71 3.85
143 144 4.176752 GTGGATCAGGGCCGGTCC 62.177 72.222 20.43 20.43 0.00 4.46
144 145 4.176752 GGTGGATCAGGGCCGGTC 62.177 72.222 1.90 0.00 0.00 4.79
147 148 3.704231 CTTGGGTGGATCAGGGCCG 62.704 68.421 0.00 0.00 0.00 6.13
148 149 2.276740 CTTGGGTGGATCAGGGCC 59.723 66.667 0.00 0.00 0.00 5.80
149 150 2.276740 CCTTGGGTGGATCAGGGC 59.723 66.667 0.00 0.00 0.00 5.19
150 151 2.276740 GCCTTGGGTGGATCAGGG 59.723 66.667 0.00 0.00 34.88 4.45
151 152 2.153898 TTGGCCTTGGGTGGATCAGG 62.154 60.000 3.32 0.00 0.00 3.86
152 153 0.032813 ATTGGCCTTGGGTGGATCAG 60.033 55.000 3.32 0.00 0.00 2.90
153 154 0.324552 CATTGGCCTTGGGTGGATCA 60.325 55.000 3.32 0.00 0.00 2.92
154 155 1.679559 GCATTGGCCTTGGGTGGATC 61.680 60.000 3.32 0.00 0.00 3.36
155 156 1.686800 GCATTGGCCTTGGGTGGAT 60.687 57.895 3.32 0.00 0.00 3.41
156 157 2.283821 GCATTGGCCTTGGGTGGA 60.284 61.111 3.32 0.00 0.00 4.02
157 158 0.687098 TATGCATTGGCCTTGGGTGG 60.687 55.000 3.54 0.00 40.13 4.61
158 159 0.461135 GTATGCATTGGCCTTGGGTG 59.539 55.000 3.54 0.00 40.13 4.61
159 160 0.687427 GGTATGCATTGGCCTTGGGT 60.687 55.000 3.54 0.00 40.13 4.51
160 161 0.687098 TGGTATGCATTGGCCTTGGG 60.687 55.000 3.54 0.00 40.13 4.12
161 162 0.461135 GTGGTATGCATTGGCCTTGG 59.539 55.000 3.54 0.00 40.13 3.61
162 163 1.477553 AGTGGTATGCATTGGCCTTG 58.522 50.000 3.54 2.66 40.13 3.61
163 164 2.654863 GTAGTGGTATGCATTGGCCTT 58.345 47.619 3.54 1.67 40.13 4.35
164 165 1.133792 GGTAGTGGTATGCATTGGCCT 60.134 52.381 3.54 0.00 40.13 5.19
165 166 1.318576 GGTAGTGGTATGCATTGGCC 58.681 55.000 3.54 6.09 40.13 5.36
166 167 1.949525 CTGGTAGTGGTATGCATTGGC 59.050 52.381 3.54 0.00 41.68 4.52
167 168 3.558931 TCTGGTAGTGGTATGCATTGG 57.441 47.619 3.54 0.00 0.00 3.16
168 169 4.707105 TGATCTGGTAGTGGTATGCATTG 58.293 43.478 3.54 0.00 0.00 2.82
169 170 4.655649 TCTGATCTGGTAGTGGTATGCATT 59.344 41.667 3.54 0.00 0.00 3.56
170 171 4.039730 GTCTGATCTGGTAGTGGTATGCAT 59.960 45.833 3.79 3.79 0.00 3.96
171 172 3.384789 GTCTGATCTGGTAGTGGTATGCA 59.615 47.826 0.00 0.00 0.00 3.96
172 173 3.243907 GGTCTGATCTGGTAGTGGTATGC 60.244 52.174 0.00 0.00 0.00 3.14
173 174 3.960755 TGGTCTGATCTGGTAGTGGTATG 59.039 47.826 0.00 0.00 0.00 2.39
174 175 4.265856 TGGTCTGATCTGGTAGTGGTAT 57.734 45.455 0.00 0.00 0.00 2.73
175 176 3.750501 TGGTCTGATCTGGTAGTGGTA 57.249 47.619 0.00 0.00 0.00 3.25
176 177 2.623418 TGGTCTGATCTGGTAGTGGT 57.377 50.000 0.00 0.00 0.00 4.16
177 178 2.103771 CCATGGTCTGATCTGGTAGTGG 59.896 54.545 2.57 1.21 0.00 4.00
178 179 3.033909 TCCATGGTCTGATCTGGTAGTG 58.966 50.000 12.58 0.00 0.00 2.74
179 180 3.052566 TCTCCATGGTCTGATCTGGTAGT 60.053 47.826 12.58 0.00 0.00 2.73
180 181 3.570540 TCTCCATGGTCTGATCTGGTAG 58.429 50.000 12.58 0.00 0.00 3.18
188 189 0.532573 GCGAGTTCTCCATGGTCTGA 59.467 55.000 12.58 6.21 0.00 3.27
243 244 2.595881 CGTCGTCGTTGACTTTCCAAAC 60.596 50.000 7.88 0.00 36.71 2.93
245 246 1.202203 CGTCGTCGTTGACTTTCCAA 58.798 50.000 7.88 0.00 36.71 3.53
270 271 0.951040 CCAGAGTTGAACGCCCTCAC 60.951 60.000 0.00 0.00 0.00 3.51
271 272 1.371183 CCAGAGTTGAACGCCCTCA 59.629 57.895 0.00 0.00 0.00 3.86
333 343 1.428912 TGAATTTTGGTCTCCCCTGCT 59.571 47.619 0.00 0.00 0.00 4.24
370 380 0.676466 TTGATGGGTGTCGTCATGGC 60.676 55.000 0.00 0.00 40.70 4.40
371 381 1.942657 GATTGATGGGTGTCGTCATGG 59.057 52.381 0.00 0.00 40.70 3.66
466 480 0.037697 ACGCTCACAGGCATTTCGTA 60.038 50.000 0.00 0.00 0.00 3.43
491 505 0.368907 AACGAATCGTCAAATCCGCG 59.631 50.000 9.32 0.00 39.99 6.46
494 508 2.629051 AGGGAACGAATCGTCAAATCC 58.371 47.619 9.32 12.17 39.99 3.01
496 510 5.986004 GATTAGGGAACGAATCGTCAAAT 57.014 39.130 9.32 4.90 41.53 2.32
508 522 0.466372 GCTGGCTGGGATTAGGGAAC 60.466 60.000 0.00 0.00 0.00 3.62
512 526 1.150081 CTGGCTGGCTGGGATTAGG 59.850 63.158 2.00 0.00 0.00 2.69
513 527 1.527844 GCTGGCTGGCTGGGATTAG 60.528 63.158 9.98 0.00 0.00 1.73
530 544 2.832201 GGAATGAGGCTGGCTGGC 60.832 66.667 9.06 10.02 42.15 4.85
531 545 2.123982 GGGAATGAGGCTGGCTGG 60.124 66.667 9.06 0.00 0.00 4.85
532 546 2.123982 GGGGAATGAGGCTGGCTG 60.124 66.667 9.06 0.00 0.00 4.85
533 547 2.286732 AGGGGAATGAGGCTGGCT 60.287 61.111 2.24 2.24 0.00 4.75
543 557 0.262876 GAAAGGATGGGCAGGGGAAT 59.737 55.000 0.00 0.00 0.00 3.01
548 562 1.397390 GCCATGAAAGGATGGGCAGG 61.397 60.000 0.00 0.00 42.96 4.85
556 570 1.074775 ACGGCAAGCCATGAAAGGA 59.925 52.632 12.19 0.00 35.37 3.36
560 574 2.596923 TGCACGGCAAGCCATGAA 60.597 55.556 11.83 0.00 34.76 2.57
573 587 5.734855 AATGTGAATAACCGATACTGCAC 57.265 39.130 0.00 0.00 0.00 4.57
583 597 6.173339 TGAGAGAGACCAAATGTGAATAACC 58.827 40.000 0.00 0.00 0.00 2.85
609 623 5.048083 CCTTGCATACAAAAAGCAGGAGTAA 60.048 40.000 0.00 0.00 39.72 2.24
651 665 6.468956 CGTTGTGTAAGCAAATCATCATTACC 59.531 38.462 0.00 0.00 0.00 2.85
722 751 5.491982 AGTATGTTGATGGTCCTCTTGTTC 58.508 41.667 0.00 0.00 0.00 3.18
783 836 6.214412 AGGAAGAGTAATGATGTCAGGACTTT 59.786 38.462 0.65 0.00 0.00 2.66
823 916 8.316640 AGATACTGAAAACTGATCTTGACAAC 57.683 34.615 0.00 0.00 0.00 3.32
849 948 0.527113 CATTGTTGCTGATTCCGCCA 59.473 50.000 0.00 0.00 0.00 5.69
867 966 5.311265 AGCAAGAAGAATGATGAGTGAACA 58.689 37.500 0.00 0.00 0.00 3.18
984 1100 2.415893 GGTCATCCTGAAAAACGCCATG 60.416 50.000 0.00 0.00 0.00 3.66
1053 1169 1.629043 TGTCGAGCTTCCCAGTAAGT 58.371 50.000 0.00 0.00 0.00 2.24
1764 2148 0.678048 GCCCTTGCAGGTCCTGTTAG 60.678 60.000 20.24 15.97 37.47 2.34
2276 2660 9.559732 TTCATCAATAACTTCTCTCTTGACAAA 57.440 29.630 0.00 0.00 0.00 2.83
2277 2661 9.212641 CTTCATCAATAACTTCTCTCTTGACAA 57.787 33.333 0.00 0.00 0.00 3.18
2357 2741 3.008923 TGAGGAACACAGTCATGGCAATA 59.991 43.478 0.00 0.00 0.00 1.90
2556 2940 6.640907 GGAACTTTTGTGATGATGTTTACCAC 59.359 38.462 0.00 0.00 0.00 4.16
2662 3181 2.061773 CACAAGGATGATACGCGGATC 58.938 52.381 24.71 24.71 0.00 3.36
2957 3557 2.292292 TCATCCATGCAAATGAGATGCG 59.708 45.455 0.00 0.00 46.76 4.73
3158 4100 1.204941 CCCTTCACTGTCCGAGTTAGG 59.795 57.143 0.00 0.00 35.16 2.69
3278 4241 2.766828 AGAATAGCCTCGCCTACTGTTT 59.233 45.455 0.00 0.00 0.00 2.83
3457 4463 2.498078 AGTACCTTGCTCACTAAGGCTC 59.502 50.000 3.80 0.00 46.89 4.70
4011 5227 3.565482 CACTCACACCAACTAATGCTGTT 59.435 43.478 0.00 0.00 0.00 3.16
4127 5343 1.487482 GCGGGCAAAAGTTTCTTGTC 58.513 50.000 0.00 0.00 0.00 3.18
4751 8445 7.418337 AAAGGAACCAACAGTGAGTTATTTT 57.582 32.000 0.00 0.23 38.74 1.82
4912 8662 7.543868 CAGGTTATCCGTTCAATTGCAAATTAA 59.456 33.333 1.71 0.00 39.05 1.40
5219 8978 6.252995 TGGATAAAAATAGTGAAGGGTTGCT 58.747 36.000 0.00 0.00 0.00 3.91
5377 9171 2.225167 TGGGGGAACGCTTAATTCCTTT 60.225 45.455 6.34 0.00 44.43 3.11
5920 9821 1.777272 AGGATGGGCCCTTTCATCTAC 59.223 52.381 25.70 5.70 39.57 2.59
6011 10154 0.897621 TCATCTCCACGCATGTCTGT 59.102 50.000 0.00 0.00 0.00 3.41
6595 10766 2.158900 CCTTGATGGAGTAGCCGAACAT 60.159 50.000 0.00 0.00 40.66 2.71
6717 10896 5.709164 ACGATGTCTATGTATGTACCCTACC 59.291 44.000 0.00 0.00 0.00 3.18
6951 11164 0.610687 CGCTCCTCTTCCTTCCACTT 59.389 55.000 0.00 0.00 0.00 3.16
6952 11165 1.261238 CCGCTCCTCTTCCTTCCACT 61.261 60.000 0.00 0.00 0.00 4.00
6953 11166 1.219393 CCGCTCCTCTTCCTTCCAC 59.781 63.158 0.00 0.00 0.00 4.02
6971 11184 3.260483 CAGAGCATGAGGACGCGC 61.260 66.667 5.73 0.00 0.00 6.86
6972 11185 1.016130 AAACAGAGCATGAGGACGCG 61.016 55.000 3.53 3.53 0.00 6.01
6973 11186 0.723981 GAAACAGAGCATGAGGACGC 59.276 55.000 0.00 0.00 0.00 5.19
6974 11187 2.266554 GAGAAACAGAGCATGAGGACG 58.733 52.381 0.00 0.00 0.00 4.79
6976 11189 1.205655 CGGAGAAACAGAGCATGAGGA 59.794 52.381 0.00 0.00 0.00 3.71
6977 11190 1.649664 CGGAGAAACAGAGCATGAGG 58.350 55.000 0.00 0.00 0.00 3.86
6978 11191 1.005340 GCGGAGAAACAGAGCATGAG 58.995 55.000 0.00 0.00 0.00 2.90
6979 11192 0.737367 CGCGGAGAAACAGAGCATGA 60.737 55.000 0.00 0.00 0.00 3.07
6980 11193 1.712081 CGCGGAGAAACAGAGCATG 59.288 57.895 0.00 0.00 0.00 4.06
6981 11194 2.103042 GCGCGGAGAAACAGAGCAT 61.103 57.895 8.83 0.00 38.95 3.79
6982 11195 2.738521 GCGCGGAGAAACAGAGCA 60.739 61.111 8.83 0.00 38.95 4.26
6983 11196 3.843240 CGCGCGGAGAAACAGAGC 61.843 66.667 24.84 0.00 36.39 4.09
6984 11197 2.430921 ACGCGCGGAGAAACAGAG 60.431 61.111 35.22 1.22 0.00 3.35
6985 11198 2.430244 GACGCGCGGAGAAACAGA 60.430 61.111 35.22 0.00 0.00 3.41
6986 11199 2.720758 CTGACGCGCGGAGAAACAG 61.721 63.158 35.22 24.72 0.00 3.16
6987 11200 2.733218 CTGACGCGCGGAGAAACA 60.733 61.111 35.22 20.33 0.00 2.83
6988 11201 2.430244 TCTGACGCGCGGAGAAAC 60.430 61.111 35.22 17.01 0.00 2.78
6989 11202 2.430244 GTCTGACGCGCGGAGAAA 60.430 61.111 35.22 12.49 30.98 2.52
6990 11203 3.610791 CTGTCTGACGCGCGGAGAA 62.611 63.158 35.22 20.54 30.98 2.87
7003 11216 2.297129 GGAAGAGGGCTGGCTGTCT 61.297 63.158 0.00 0.97 0.00 3.41
7034 11247 2.797719 GTTTTATTGGCACGTTGGTTGG 59.202 45.455 0.00 0.00 0.00 3.77
7035 11248 2.797719 GGTTTTATTGGCACGTTGGTTG 59.202 45.455 0.00 0.00 0.00 3.77
7036 11249 2.431057 TGGTTTTATTGGCACGTTGGTT 59.569 40.909 0.00 0.00 0.00 3.67
7037 11250 2.032620 TGGTTTTATTGGCACGTTGGT 58.967 42.857 0.00 0.00 0.00 3.67
7089 11302 3.650950 CAGTGGGAGTGGGGTGGG 61.651 72.222 0.00 0.00 0.00 4.61
7095 11308 0.322008 GGAAGAAGCAGTGGGAGTGG 60.322 60.000 0.00 0.00 0.00 4.00
7101 11314 0.397941 TGGACTGGAAGAAGCAGTGG 59.602 55.000 0.00 0.00 37.43 4.00
7405 11621 3.447025 GACGAGGCGGATGAAGGGG 62.447 68.421 0.00 0.00 0.00 4.79
7441 11657 1.004440 GAAGTTCTGCGGCAGGTCT 60.004 57.895 28.18 21.96 31.51 3.85


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

AutoCloner maintained by Alex Coulton.