Multiple sequence alignment - TraesCS5B01G072300

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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 TraesCS5B01G072300 chr5B 100.000 3493 0 0 1 3493 84625496 84628988 0.000000e+00 6451.0
1 TraesCS5B01G072300 chr5B 98.936 94 1 0 1 94 558123919 558123826 6.000000e-38 169.0
2 TraesCS5B01G072300 chr5A 94.367 2450 108 12 856 3282 71397061 71399503 0.000000e+00 3733.0
3 TraesCS5B01G072300 chr5A 87.778 270 15 8 180 436 71390858 71391122 2.040000e-77 300.0
4 TraesCS5B01G072300 chr5A 79.743 311 35 6 569 858 71396803 71397106 2.130000e-47 200.0
5 TraesCS5B01G072300 chr5A 95.604 91 4 0 91 181 331935427 331935337 2.810000e-31 147.0
6 TraesCS5B01G072300 chr5A 92.857 98 7 0 91 188 34311239 34311142 3.630000e-30 143.0
7 TraesCS5B01G072300 chr5A 92.857 98 6 1 91 187 23935675 23935578 1.310000e-29 141.0
8 TraesCS5B01G072300 chr5D 94.722 2179 84 19 883 3047 75919012 75921173 0.000000e+00 3358.0
9 TraesCS5B01G072300 chr5D 89.537 583 31 11 2937 3493 75921095 75921673 0.000000e+00 712.0
10 TraesCS5B01G072300 chr5D 93.839 211 13 0 455 665 75918532 75918742 5.630000e-83 318.0
11 TraesCS5B01G072300 chr5D 88.235 272 14 8 180 438 75918279 75918545 3.390000e-80 309.0
12 TraesCS5B01G072300 chr5D 82.704 318 51 3 3171 3488 3514818 3515131 2.650000e-71 279.0
13 TraesCS5B01G072300 chr5D 79.310 319 52 6 3170 3488 442097395 442097091 9.820000e-51 211.0
14 TraesCS5B01G072300 chr2D 89.878 1719 106 25 856 2533 22111029 22109338 0.000000e+00 2148.0
15 TraesCS5B01G072300 chr2D 85.802 1134 127 16 1388 2521 22151180 22152279 0.000000e+00 1171.0
16 TraesCS5B01G072300 chr2D 89.665 358 36 1 1259 1616 22150611 22150967 4.110000e-124 455.0
17 TraesCS5B01G072300 chr2D 83.596 317 48 4 3170 3486 334095335 334095023 9.480000e-76 294.0
18 TraesCS5B01G072300 chr2D 86.245 269 18 8 180 437 22118311 22118051 1.240000e-69 274.0
19 TraesCS5B01G072300 chr2D 82.784 273 28 9 2769 3028 22108581 22108315 3.510000e-55 226.0
20 TraesCS5B01G072300 chr2B 88.752 1547 131 26 982 2519 35124123 35125635 0.000000e+00 1853.0
21 TraesCS5B01G072300 chr2B 100.000 91 0 0 1 91 6873379 6873289 6.000000e-38 169.0
22 TraesCS5B01G072300 chr2B 100.000 91 0 0 1 91 6877332 6877242 6.000000e-38 169.0
23 TraesCS5B01G072300 chr2B 100.000 91 0 0 1 91 6959963 6959873 6.000000e-38 169.0
24 TraesCS5B01G072300 chr2B 79.339 242 31 10 180 404 35117558 35117797 6.040000e-33 152.0
25 TraesCS5B01G072300 chr7B 89.116 1176 85 22 938 2088 681580553 681579396 0.000000e+00 1423.0
26 TraesCS5B01G072300 chr7B 88.904 721 75 3 2135 2854 681579250 681578534 0.000000e+00 883.0
27 TraesCS5B01G072300 chr7B 84.543 317 45 4 3170 3485 284953359 284953672 9.410000e-81 311.0
28 TraesCS5B01G072300 chr7B 86.207 203 18 7 180 372 681616894 681616692 9.820000e-51 211.0
29 TraesCS5B01G072300 chr7B 93.684 95 5 1 91 185 128775955 128776048 1.310000e-29 141.0
30 TraesCS5B01G072300 chr7B 92.647 68 4 1 370 437 681616238 681616172 2.870000e-16 97.1
31 TraesCS5B01G072300 chr2A 90.895 626 44 1 1440 2065 23967763 23968375 0.000000e+00 828.0
32 TraesCS5B01G072300 chr2A 93.541 418 27 0 1026 1443 23966662 23967079 1.060000e-174 623.0
33 TraesCS5B01G072300 chr2A 88.192 271 19 9 180 437 23957209 23956939 9.410000e-81 311.0
34 TraesCS5B01G072300 chr2A 95.312 64 3 0 988 1051 23951326 23951263 6.170000e-18 102.0
35 TraesCS5B01G072300 chr7D 85.489 317 44 2 3170 3486 332695925 332696239 2.600000e-86 329.0
36 TraesCS5B01G072300 chr3D 84.194 310 46 3 3177 3486 266414756 266415062 7.330000e-77 298.0
37 TraesCS5B01G072300 chr3B 83.750 320 46 4 3170 3487 71401857 71401542 7.330000e-77 298.0
38 TraesCS5B01G072300 chr3B 97.917 96 2 0 1 96 17241731 17241826 2.160000e-37 167.0
39 TraesCS5B01G072300 chr3B 96.078 102 4 0 2 103 248584049 248583948 2.160000e-37 167.0
40 TraesCS5B01G072300 chr3B 93.814 97 5 1 91 186 817574774 817574678 1.010000e-30 145.0
41 TraesCS5B01G072300 chr4D 84.694 294 43 2 3194 3487 57485204 57485495 3.410000e-75 292.0
42 TraesCS5B01G072300 chr4D 80.685 321 50 10 3170 3486 206060856 206061168 4.510000e-59 239.0
43 TraesCS5B01G072300 chr3A 81.620 321 48 7 3170 3488 400099426 400099737 4.470000e-64 255.0
44 TraesCS5B01G072300 chr3A 96.078 102 4 0 1 102 588512016 588511915 2.160000e-37 167.0
45 TraesCS5B01G072300 chr3A 96.703 91 3 0 91 181 194812635 194812545 6.040000e-33 152.0
46 TraesCS5B01G072300 chr4A 81.191 319 52 7 3170 3486 240371396 240371084 2.080000e-62 250.0
47 TraesCS5B01G072300 chr6D 80.757 317 57 3 3170 3486 350345740 350346052 9.680000e-61 244.0
48 TraesCS5B01G072300 chr6A 80.126 317 57 4 3173 3488 585792851 585792540 7.540000e-57 231.0
49 TraesCS5B01G072300 chr6A 84.956 113 17 0 3170 3282 27161959 27161847 7.920000e-22 115.0
50 TraesCS5B01G072300 chr4B 83.475 236 37 2 3252 3487 86069388 86069621 5.870000e-53 219.0
51 TraesCS5B01G072300 chr4B 91.892 111 5 3 1 110 530463312 530463205 6.040000e-33 152.0
52 TraesCS5B01G072300 chr1D 77.346 309 64 6 3170 3477 469381755 469381452 9.960000e-41 178.0
53 TraesCS5B01G072300 chr6B 98.947 95 1 0 1 95 586002534 586002440 1.670000e-38 171.0
54 TraesCS5B01G072300 chr7A 95.098 102 5 0 1 102 664244982 664244881 1.000000e-35 161.0
55 TraesCS5B01G072300 chr1B 94.624 93 4 1 91 183 415759330 415759239 3.630000e-30 143.0
56 TraesCS5B01G072300 chr1B 92.784 97 7 0 91 187 573440299 573440203 1.310000e-29 141.0
57 TraesCS5B01G072300 chrUn 92.079 101 7 1 91 191 85138426 85138327 1.310000e-29 141.0
58 TraesCS5B01G072300 chrUn 85.841 113 16 0 3170 3282 96460094 96459982 1.700000e-23 121.0


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 TraesCS5B01G072300 chr5B 84625496 84628988 3492 False 6451.00 6451 100.00000 1 3493 1 chr5B.!!$F1 3492
1 TraesCS5B01G072300 chr5A 71396803 71399503 2700 False 1966.50 3733 87.05500 569 3282 2 chr5A.!!$F2 2713
2 TraesCS5B01G072300 chr5D 75918279 75921673 3394 False 1174.25 3358 91.58325 180 3493 4 chr5D.!!$F2 3313
3 TraesCS5B01G072300 chr2D 22108315 22111029 2714 True 1187.00 2148 86.33100 856 3028 2 chr2D.!!$R3 2172
4 TraesCS5B01G072300 chr2D 22150611 22152279 1668 False 813.00 1171 87.73350 1259 2521 2 chr2D.!!$F1 1262
5 TraesCS5B01G072300 chr2B 35124123 35125635 1512 False 1853.00 1853 88.75200 982 2519 1 chr2B.!!$F2 1537
6 TraesCS5B01G072300 chr7B 681578534 681580553 2019 True 1153.00 1423 89.01000 938 2854 2 chr7B.!!$R1 1916
7 TraesCS5B01G072300 chr2A 23966662 23968375 1713 False 725.50 828 92.21800 1026 2065 2 chr2A.!!$F1 1039

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
122 123 0.034186 CCAAGCATGGGTGAGGCTAA 60.034 55.0 0.0 0.0 42.15 3.09 F
800 918 0.249489 AGCGTGACAGTGACTTGGTC 60.249 55.0 0.0 0.0 0.00 4.02 F
2281 3320 0.613572 TACGTGGAGAGTGCATGGGA 60.614 55.0 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 2829 0.612732 CCCAGAGAAATGGCTTGCCA 60.613 55.0 17.19 17.19 39.17 4.92 R
2315 3354 0.547712 CCTCCTCCCTCCTCACCAAA 60.548 60.0 0.00 0.00 0.00 3.28 R
3267 4910 0.034896 ACAAGAGGGTGCGTGTAAGG 59.965 55.0 0.00 0.00 0.00 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.038033 CCTCTCTCTTCACTAAATACGTGC 58.962 45.833 0.00 0.00 32.54 5.34
24 25 4.995124 TCTCTCTTCACTAAATACGTGCC 58.005 43.478 0.00 0.00 32.54 5.01
25 26 4.461431 TCTCTCTTCACTAAATACGTGCCA 59.539 41.667 0.00 0.00 32.54 4.92
26 27 4.491676 TCTCTTCACTAAATACGTGCCAC 58.508 43.478 0.00 0.00 32.54 5.01
27 28 4.021807 TCTCTTCACTAAATACGTGCCACA 60.022 41.667 0.00 0.00 32.54 4.17
28 29 4.827692 TCTTCACTAAATACGTGCCACAT 58.172 39.130 0.00 0.00 32.54 3.21
29 30 5.968254 TCTTCACTAAATACGTGCCACATA 58.032 37.500 0.00 0.00 32.54 2.29
30 31 6.399743 TCTTCACTAAATACGTGCCACATAA 58.600 36.000 0.00 0.00 32.54 1.90
31 32 6.533723 TCTTCACTAAATACGTGCCACATAAG 59.466 38.462 0.00 0.00 32.54 1.73
32 33 4.569162 TCACTAAATACGTGCCACATAAGC 59.431 41.667 0.00 0.00 32.54 3.09
33 34 4.331443 CACTAAATACGTGCCACATAAGCA 59.669 41.667 0.00 0.00 38.08 3.91
34 35 4.938832 ACTAAATACGTGCCACATAAGCAA 59.061 37.500 0.00 0.00 43.02 3.91
35 36 4.775058 AAATACGTGCCACATAAGCAAA 57.225 36.364 0.00 0.00 43.02 3.68
36 37 4.355543 AATACGTGCCACATAAGCAAAG 57.644 40.909 0.00 0.00 43.02 2.77
37 38 1.604604 ACGTGCCACATAAGCAAAGT 58.395 45.000 0.00 0.00 43.02 2.66
38 39 1.953686 ACGTGCCACATAAGCAAAGTT 59.046 42.857 0.00 0.00 43.02 2.66
39 40 2.287547 ACGTGCCACATAAGCAAAGTTG 60.288 45.455 0.00 0.00 43.02 3.16
40 41 2.287547 CGTGCCACATAAGCAAAGTTGT 60.288 45.455 0.00 0.00 43.02 3.32
41 42 3.058570 CGTGCCACATAAGCAAAGTTGTA 60.059 43.478 0.00 0.00 43.02 2.41
42 43 4.379394 CGTGCCACATAAGCAAAGTTGTAT 60.379 41.667 0.00 0.00 43.02 2.29
43 44 5.469479 GTGCCACATAAGCAAAGTTGTATT 58.531 37.500 0.00 0.00 43.02 1.89
44 45 5.345741 GTGCCACATAAGCAAAGTTGTATTG 59.654 40.000 0.00 0.00 43.02 1.90
45 46 5.242615 TGCCACATAAGCAAAGTTGTATTGA 59.757 36.000 0.00 0.00 37.28 2.57
46 47 6.155827 GCCACATAAGCAAAGTTGTATTGAA 58.844 36.000 0.00 0.00 0.00 2.69
47 48 6.308766 GCCACATAAGCAAAGTTGTATTGAAG 59.691 38.462 0.00 0.00 0.00 3.02
48 49 7.370383 CCACATAAGCAAAGTTGTATTGAAGT 58.630 34.615 0.00 0.00 0.00 3.01
49 50 7.326789 CCACATAAGCAAAGTTGTATTGAAGTG 59.673 37.037 0.00 0.00 0.00 3.16
50 51 7.862372 CACATAAGCAAAGTTGTATTGAAGTGT 59.138 33.333 0.00 0.00 0.00 3.55
51 52 7.862372 ACATAAGCAAAGTTGTATTGAAGTGTG 59.138 33.333 0.00 0.00 0.00 3.82
52 53 5.835113 AGCAAAGTTGTATTGAAGTGTGT 57.165 34.783 0.00 0.00 0.00 3.72
53 54 5.581605 AGCAAAGTTGTATTGAAGTGTGTG 58.418 37.500 0.00 0.00 0.00 3.82
54 55 5.356751 AGCAAAGTTGTATTGAAGTGTGTGA 59.643 36.000 0.00 0.00 0.00 3.58
55 56 6.039717 AGCAAAGTTGTATTGAAGTGTGTGAT 59.960 34.615 0.00 0.00 0.00 3.06
56 57 6.142798 GCAAAGTTGTATTGAAGTGTGTGATG 59.857 38.462 0.00 0.00 0.00 3.07
57 58 6.942532 AAGTTGTATTGAAGTGTGTGATGT 57.057 33.333 0.00 0.00 0.00 3.06
58 59 6.942532 AGTTGTATTGAAGTGTGTGATGTT 57.057 33.333 0.00 0.00 0.00 2.71
59 60 8.445275 AAGTTGTATTGAAGTGTGTGATGTTA 57.555 30.769 0.00 0.00 0.00 2.41
60 61 7.861630 AGTTGTATTGAAGTGTGTGATGTTAC 58.138 34.615 0.00 0.00 0.00 2.50
61 62 7.715249 AGTTGTATTGAAGTGTGTGATGTTACT 59.285 33.333 0.00 0.00 0.00 2.24
62 63 7.652300 TGTATTGAAGTGTGTGATGTTACTC 57.348 36.000 0.00 0.00 0.00 2.59
63 64 6.649141 TGTATTGAAGTGTGTGATGTTACTCC 59.351 38.462 0.00 0.00 0.00 3.85
64 65 4.955811 TGAAGTGTGTGATGTTACTCCT 57.044 40.909 0.00 0.00 0.00 3.69
65 66 6.413783 TTGAAGTGTGTGATGTTACTCCTA 57.586 37.500 0.00 0.00 0.00 2.94
66 67 6.413783 TGAAGTGTGTGATGTTACTCCTAA 57.586 37.500 0.00 0.00 0.00 2.69
67 68 6.455647 TGAAGTGTGTGATGTTACTCCTAAG 58.544 40.000 0.00 0.00 0.00 2.18
68 69 6.041637 TGAAGTGTGTGATGTTACTCCTAAGT 59.958 38.462 0.00 0.00 39.66 2.24
69 70 6.420913 AGTGTGTGATGTTACTCCTAAGTT 57.579 37.500 0.00 0.00 36.92 2.66
70 71 6.456501 AGTGTGTGATGTTACTCCTAAGTTC 58.543 40.000 0.00 0.00 36.92 3.01
71 72 5.638234 GTGTGTGATGTTACTCCTAAGTTCC 59.362 44.000 0.00 0.00 36.92 3.62
72 73 5.542635 TGTGTGATGTTACTCCTAAGTTCCT 59.457 40.000 0.00 0.00 36.92 3.36
73 74 6.100668 GTGTGATGTTACTCCTAAGTTCCTC 58.899 44.000 0.00 0.00 36.92 3.71
74 75 5.187186 TGTGATGTTACTCCTAAGTTCCTCC 59.813 44.000 0.00 0.00 36.92 4.30
75 76 4.715297 TGATGTTACTCCTAAGTTCCTCCC 59.285 45.833 0.00 0.00 36.92 4.30
76 77 3.447950 TGTTACTCCTAAGTTCCTCCCC 58.552 50.000 0.00 0.00 36.92 4.81
77 78 3.181404 TGTTACTCCTAAGTTCCTCCCCA 60.181 47.826 0.00 0.00 36.92 4.96
78 79 1.954035 ACTCCTAAGTTCCTCCCCAC 58.046 55.000 0.00 0.00 28.74 4.61
79 80 1.437547 ACTCCTAAGTTCCTCCCCACT 59.562 52.381 0.00 0.00 28.74 4.00
80 81 1.834263 CTCCTAAGTTCCTCCCCACTG 59.166 57.143 0.00 0.00 0.00 3.66
81 82 1.151413 TCCTAAGTTCCTCCCCACTGT 59.849 52.381 0.00 0.00 0.00 3.55
82 83 1.279271 CCTAAGTTCCTCCCCACTGTG 59.721 57.143 0.00 0.00 0.00 3.66
83 84 2.257207 CTAAGTTCCTCCCCACTGTGA 58.743 52.381 9.86 0.00 0.00 3.58
84 85 0.765510 AAGTTCCTCCCCACTGTGAC 59.234 55.000 9.86 0.00 0.00 3.67
85 86 1.128188 AGTTCCTCCCCACTGTGACC 61.128 60.000 9.86 0.00 0.00 4.02
86 87 1.074090 TTCCTCCCCACTGTGACCA 60.074 57.895 9.86 0.00 0.00 4.02
87 88 1.127567 TTCCTCCCCACTGTGACCAG 61.128 60.000 9.86 1.37 44.68 4.00
88 89 2.348998 CTCCCCACTGTGACCAGC 59.651 66.667 9.86 0.00 42.81 4.85
89 90 3.249189 TCCCCACTGTGACCAGCC 61.249 66.667 9.86 0.00 42.81 4.85
90 91 3.252284 CCCCACTGTGACCAGCCT 61.252 66.667 9.86 0.00 42.81 4.58
91 92 2.833913 CCCCACTGTGACCAGCCTT 61.834 63.158 9.86 0.00 42.81 4.35
92 93 1.488705 CCCCACTGTGACCAGCCTTA 61.489 60.000 9.86 0.00 42.81 2.69
93 94 0.036010 CCCACTGTGACCAGCCTTAG 60.036 60.000 9.86 0.00 42.81 2.18
94 95 0.687354 CCACTGTGACCAGCCTTAGT 59.313 55.000 9.86 0.00 42.81 2.24
95 96 1.899814 CCACTGTGACCAGCCTTAGTA 59.100 52.381 9.86 0.00 42.81 1.82
96 97 2.501723 CCACTGTGACCAGCCTTAGTAT 59.498 50.000 9.86 0.00 42.81 2.12
97 98 3.055094 CCACTGTGACCAGCCTTAGTATT 60.055 47.826 9.86 0.00 42.81 1.89
98 99 4.565652 CCACTGTGACCAGCCTTAGTATTT 60.566 45.833 9.86 0.00 42.81 1.40
99 100 4.393062 CACTGTGACCAGCCTTAGTATTTG 59.607 45.833 0.32 0.00 42.81 2.32
100 101 4.041691 ACTGTGACCAGCCTTAGTATTTGT 59.958 41.667 0.00 0.00 42.81 2.83
101 102 5.247564 ACTGTGACCAGCCTTAGTATTTGTA 59.752 40.000 0.00 0.00 42.81 2.41
102 103 6.070194 ACTGTGACCAGCCTTAGTATTTGTAT 60.070 38.462 0.00 0.00 42.81 2.29
103 104 6.346096 TGTGACCAGCCTTAGTATTTGTATC 58.654 40.000 0.00 0.00 0.00 2.24
104 105 5.758784 GTGACCAGCCTTAGTATTTGTATCC 59.241 44.000 0.00 0.00 0.00 2.59
105 106 5.427157 TGACCAGCCTTAGTATTTGTATCCA 59.573 40.000 0.00 0.00 0.00 3.41
106 107 6.069905 TGACCAGCCTTAGTATTTGTATCCAA 60.070 38.462 0.00 0.00 0.00 3.53
107 108 6.357367 ACCAGCCTTAGTATTTGTATCCAAG 58.643 40.000 0.00 0.00 0.00 3.61
108 109 5.239525 CCAGCCTTAGTATTTGTATCCAAGC 59.760 44.000 0.00 0.00 0.00 4.01
109 110 5.822519 CAGCCTTAGTATTTGTATCCAAGCA 59.177 40.000 0.00 0.00 0.00 3.91
110 111 6.488006 CAGCCTTAGTATTTGTATCCAAGCAT 59.512 38.462 0.00 0.00 0.00 3.79
111 112 6.488006 AGCCTTAGTATTTGTATCCAAGCATG 59.512 38.462 0.00 0.00 0.00 4.06
120 121 1.578215 ATCCAAGCATGGGTGAGGCT 61.578 55.000 8.36 0.00 45.93 4.58
121 122 0.913934 TCCAAGCATGGGTGAGGCTA 60.914 55.000 8.36 0.00 42.15 3.93
122 123 0.034186 CCAAGCATGGGTGAGGCTAA 60.034 55.000 0.00 0.00 42.15 3.09
123 124 1.098050 CAAGCATGGGTGAGGCTAAC 58.902 55.000 0.00 0.00 42.15 2.34
124 125 0.698238 AAGCATGGGTGAGGCTAACA 59.302 50.000 3.97 0.00 42.15 2.41
125 126 0.698238 AGCATGGGTGAGGCTAACAA 59.302 50.000 3.97 0.00 40.84 2.83
126 127 1.098050 GCATGGGTGAGGCTAACAAG 58.902 55.000 3.97 0.00 0.00 3.16
127 128 1.614317 GCATGGGTGAGGCTAACAAGT 60.614 52.381 3.97 0.00 0.00 3.16
128 129 2.795329 CATGGGTGAGGCTAACAAGTT 58.205 47.619 3.97 0.00 0.00 2.66
129 130 3.157087 CATGGGTGAGGCTAACAAGTTT 58.843 45.455 3.97 0.00 0.00 2.66
130 131 3.306472 TGGGTGAGGCTAACAAGTTTT 57.694 42.857 3.97 0.00 0.00 2.43
131 132 4.440826 TGGGTGAGGCTAACAAGTTTTA 57.559 40.909 3.97 0.00 0.00 1.52
132 133 4.394729 TGGGTGAGGCTAACAAGTTTTAG 58.605 43.478 3.97 0.00 32.92 1.85
133 134 4.141344 TGGGTGAGGCTAACAAGTTTTAGT 60.141 41.667 3.97 0.00 32.45 2.24
134 135 4.454847 GGGTGAGGCTAACAAGTTTTAGTC 59.545 45.833 3.97 2.90 34.42 2.59
135 136 5.306394 GGTGAGGCTAACAAGTTTTAGTCT 58.694 41.667 3.97 10.01 44.91 3.24
142 143 9.740710 AGGCTAACAAGTTTTAGTCTCATTATT 57.259 29.630 6.27 0.00 39.36 1.40
157 158 9.965902 AGTCTCATTATTTTTAGTCATGGAACT 57.034 29.630 0.00 0.00 0.00 3.01
168 169 8.483307 TTTAGTCATGGAACTAAAACGTATCC 57.517 34.615 14.26 0.00 44.59 2.59
169 170 6.045072 AGTCATGGAACTAAAACGTATCCA 57.955 37.500 0.00 0.00 43.79 3.41
170 171 6.469410 AGTCATGGAACTAAAACGTATCCAA 58.531 36.000 0.00 0.00 42.97 3.53
171 172 6.594159 AGTCATGGAACTAAAACGTATCCAAG 59.406 38.462 0.00 0.00 42.97 3.61
172 173 5.353123 TCATGGAACTAAAACGTATCCAAGC 59.647 40.000 0.00 0.00 42.97 4.01
173 174 4.643463 TGGAACTAAAACGTATCCAAGCA 58.357 39.130 0.00 0.00 37.24 3.91
174 175 4.453136 TGGAACTAAAACGTATCCAAGCAC 59.547 41.667 0.00 0.00 37.24 4.40
175 176 4.142752 GGAACTAAAACGTATCCAAGCACC 60.143 45.833 0.00 0.00 0.00 5.01
176 177 3.340928 ACTAAAACGTATCCAAGCACCC 58.659 45.455 0.00 0.00 0.00 4.61
177 178 2.579410 AAAACGTATCCAAGCACCCT 57.421 45.000 0.00 0.00 0.00 4.34
178 179 2.109425 AAACGTATCCAAGCACCCTC 57.891 50.000 0.00 0.00 0.00 4.30
185 186 3.853355 ATCCAAGCACCCTCTAGATTG 57.147 47.619 0.00 0.00 0.00 2.67
198 199 9.319143 CACCCTCTAGATTGTACAAAAGATTAG 57.681 37.037 13.23 9.84 0.00 1.73
199 200 8.487028 ACCCTCTAGATTGTACAAAAGATTAGG 58.513 37.037 13.23 14.09 0.00 2.69
200 201 8.487028 CCCTCTAGATTGTACAAAAGATTAGGT 58.513 37.037 13.23 0.00 0.00 3.08
201 202 9.892130 CCTCTAGATTGTACAAAAGATTAGGTT 57.108 33.333 13.23 0.00 0.00 3.50
281 287 2.483014 ACTGACTACAGCTCGAGAGT 57.517 50.000 18.75 15.98 46.95 3.24
365 379 1.722034 TATCCCTGTCATCTCTGCCC 58.278 55.000 0.00 0.00 0.00 5.36
374 388 2.625790 GTCATCTCTGCCCGACTAGATT 59.374 50.000 0.00 0.00 0.00 2.40
420 434 6.179906 AGAGAAACATGACAAAGGAGAGAA 57.820 37.500 0.00 0.00 0.00 2.87
423 437 6.595682 AGAAACATGACAAAGGAGAGAAAGA 58.404 36.000 0.00 0.00 0.00 2.52
424 438 7.056635 AGAAACATGACAAAGGAGAGAAAGAA 58.943 34.615 0.00 0.00 0.00 2.52
425 439 7.557719 AGAAACATGACAAAGGAGAGAAAGAAA 59.442 33.333 0.00 0.00 0.00 2.52
426 440 7.645058 AACATGACAAAGGAGAGAAAGAAAA 57.355 32.000 0.00 0.00 0.00 2.29
427 441 7.645058 ACATGACAAAGGAGAGAAAGAAAAA 57.355 32.000 0.00 0.00 0.00 1.94
494 508 3.369997 GGAGAGGGAAGTCTTGGAATGTC 60.370 52.174 0.00 0.00 0.00 3.06
507 521 6.535150 GTCTTGGAATGTCGAATCTACATGAA 59.465 38.462 0.00 0.00 37.62 2.57
533 547 1.148310 CCGTGTGGCTGTCAACTAAG 58.852 55.000 0.00 0.00 0.00 2.18
537 551 1.341852 TGTGGCTGTCAACTAAGCGTA 59.658 47.619 0.00 0.00 40.46 4.42
567 581 8.457261 GTGACTTGATTATCTTCTTTGAATGCT 58.543 33.333 0.00 0.00 0.00 3.79
574 588 9.336171 GATTATCTTCTTTGAATGCTTAGTCCT 57.664 33.333 0.00 0.00 0.00 3.85
582 596 8.908903 TCTTTGAATGCTTAGTCCTTTTTGTTA 58.091 29.630 0.00 0.00 0.00 2.41
593 607 5.883673 AGTCCTTTTTGTTACTGCTGTTGTA 59.116 36.000 0.09 0.00 0.00 2.41
599 613 2.104111 TGTTACTGCTGTTGTACCTGCT 59.896 45.455 0.09 0.00 0.00 4.24
643 657 4.453136 GGCCTGAACTCGTGTTTTATGTTA 59.547 41.667 4.11 0.00 36.39 2.41
656 670 9.316730 CGTGTTTTATGTTAGCCTATAACCTTA 57.683 33.333 0.00 0.00 0.00 2.69
680 778 3.784701 ACTATGTGACTTACTCGCCTG 57.215 47.619 0.00 0.00 0.00 4.85
684 782 1.270094 TGTGACTTACTCGCCTGGTTG 60.270 52.381 0.00 0.00 0.00 3.77
695 812 4.619227 CTGGTTGTGGGCGGACGT 62.619 66.667 0.00 0.00 0.00 4.34
717 834 6.133392 CGTTTCTTGCGTCTTCATTCTAAAA 58.867 36.000 0.00 0.00 0.00 1.52
788 906 6.073980 TGTCAACTTGATTAACTAAGCGTGAC 60.074 38.462 19.00 19.00 39.84 3.67
800 918 0.249489 AGCGTGACAGTGACTTGGTC 60.249 55.000 0.00 0.00 0.00 4.02
804 922 0.828022 TGACAGTGACTTGGTCGGTT 59.172 50.000 0.00 0.00 34.95 4.44
808 926 4.171754 GACAGTGACTTGGTCGGTTATAC 58.828 47.826 0.00 0.00 34.95 1.47
829 947 1.209990 CCATGCTCAGAGAAGCTTCCT 59.790 52.381 22.81 15.99 42.94 3.36
830 948 2.553086 CATGCTCAGAGAAGCTTCCTC 58.447 52.381 22.81 17.91 42.94 3.71
831 949 1.637338 TGCTCAGAGAAGCTTCCTCA 58.363 50.000 22.81 10.76 42.94 3.86
832 950 1.274728 TGCTCAGAGAAGCTTCCTCAC 59.725 52.381 22.81 11.80 42.94 3.51
833 951 1.550072 GCTCAGAGAAGCTTCCTCACT 59.450 52.381 22.81 13.75 39.27 3.41
834 952 2.757868 GCTCAGAGAAGCTTCCTCACTA 59.242 50.000 22.81 3.51 39.27 2.74
835 953 3.428862 GCTCAGAGAAGCTTCCTCACTAC 60.429 52.174 22.81 4.14 39.27 2.73
836 954 4.016444 CTCAGAGAAGCTTCCTCACTACT 58.984 47.826 22.81 1.20 33.25 2.57
837 955 4.411927 TCAGAGAAGCTTCCTCACTACTT 58.588 43.478 22.81 0.40 33.25 2.24
838 956 5.571285 TCAGAGAAGCTTCCTCACTACTTA 58.429 41.667 22.81 1.19 33.25 2.24
839 957 6.191315 TCAGAGAAGCTTCCTCACTACTTAT 58.809 40.000 22.81 0.00 33.25 1.73
840 958 6.320164 TCAGAGAAGCTTCCTCACTACTTATC 59.680 42.308 22.81 9.08 33.25 1.75
841 959 6.321181 CAGAGAAGCTTCCTCACTACTTATCT 59.679 42.308 22.81 11.17 38.95 1.98
842 960 6.895204 AGAGAAGCTTCCTCACTACTTATCTT 59.105 38.462 22.81 0.00 35.92 2.40
843 961 8.056400 AGAGAAGCTTCCTCACTACTTATCTTA 58.944 37.037 22.81 0.00 35.92 2.10
844 962 8.002984 AGAAGCTTCCTCACTACTTATCTTAC 57.997 38.462 22.81 0.00 0.00 2.34
845 963 7.837187 AGAAGCTTCCTCACTACTTATCTTACT 59.163 37.037 22.81 0.00 0.00 2.24
846 964 7.964666 AGCTTCCTCACTACTTATCTTACTT 57.035 36.000 0.00 0.00 0.00 2.24
847 965 7.777095 AGCTTCCTCACTACTTATCTTACTTG 58.223 38.462 0.00 0.00 0.00 3.16
848 966 6.477360 GCTTCCTCACTACTTATCTTACTTGC 59.523 42.308 0.00 0.00 0.00 4.01
849 967 7.631811 GCTTCCTCACTACTTATCTTACTTGCT 60.632 40.741 0.00 0.00 0.00 3.91
850 968 7.336161 TCCTCACTACTTATCTTACTTGCTC 57.664 40.000 0.00 0.00 0.00 4.26
851 969 6.038382 TCCTCACTACTTATCTTACTTGCTCG 59.962 42.308 0.00 0.00 0.00 5.03
852 970 5.579718 TCACTACTTATCTTACTTGCTCGC 58.420 41.667 0.00 0.00 0.00 5.03
853 971 4.740695 CACTACTTATCTTACTTGCTCGCC 59.259 45.833 0.00 0.00 0.00 5.54
854 972 3.887621 ACTTATCTTACTTGCTCGCCA 57.112 42.857 0.00 0.00 0.00 5.69
858 976 0.966179 TCTTACTTGCTCGCCACTCA 59.034 50.000 0.00 0.00 0.00 3.41
896 1014 3.705072 ACTACTTATCTTACTTGCCCGCT 59.295 43.478 0.00 0.00 0.00 5.52
914 1032 2.873472 CGCTACTCTACTCGAATCCTGT 59.127 50.000 0.00 0.00 0.00 4.00
922 1040 2.016393 CTCGAATCCTGTAGCGCCCA 62.016 60.000 2.29 0.00 0.00 5.36
927 1045 3.181475 CGAATCCTGTAGCGCCCATATAT 60.181 47.826 2.29 0.00 0.00 0.86
928 1046 4.037565 CGAATCCTGTAGCGCCCATATATA 59.962 45.833 2.29 0.00 0.00 0.86
929 1047 4.939052 ATCCTGTAGCGCCCATATATAC 57.061 45.455 2.29 0.00 0.00 1.47
930 1048 3.703921 TCCTGTAGCGCCCATATATACA 58.296 45.455 2.29 3.25 0.00 2.29
931 1049 3.699538 TCCTGTAGCGCCCATATATACAG 59.300 47.826 18.63 18.63 41.82 2.74
932 1050 3.447586 CCTGTAGCGCCCATATATACAGT 59.552 47.826 21.81 0.00 41.00 3.55
933 1051 4.643334 CCTGTAGCGCCCATATATACAGTA 59.357 45.833 21.81 0.00 41.00 2.74
934 1052 5.450137 CCTGTAGCGCCCATATATACAGTAC 60.450 48.000 21.81 8.30 41.00 2.73
935 1053 5.258841 TGTAGCGCCCATATATACAGTACT 58.741 41.667 2.29 0.00 0.00 2.73
957 1084 2.791383 TTTGCCAACACTTTCATCGG 57.209 45.000 0.00 0.00 0.00 4.18
985 1122 1.532868 CTCCCTTCACTGAAACAAGCG 59.467 52.381 0.00 0.00 0.00 4.68
1224 1385 1.134901 CTCAGACGGGTTCGACGAG 59.865 63.158 0.00 0.00 40.11 4.18
1612 2473 1.810030 GTGTCGATCCGGCAGTTCC 60.810 63.158 0.00 0.00 43.72 3.62
1701 2562 1.227764 CATGGAGTCCAGATGGCGG 60.228 63.158 18.69 0.00 36.75 6.13
1747 2608 0.879765 GTCCTTCTTCCTCGACGACA 59.120 55.000 0.00 0.00 0.00 4.35
1822 2699 0.824595 GTGCATGGCATGGCTGGATA 60.825 55.000 27.48 0.00 41.91 2.59
1920 2829 1.673168 GAAATGGGCTCTGCGATTCT 58.327 50.000 0.00 0.00 0.00 2.40
2281 3320 0.613572 TACGTGGAGAGTGCATGGGA 60.614 55.000 0.00 0.00 0.00 4.37
2282 3321 1.296392 CGTGGAGAGTGCATGGGAA 59.704 57.895 0.00 0.00 0.00 3.97
2315 3354 0.976641 TGCGGACAGATGAGAAAGGT 59.023 50.000 0.00 0.00 0.00 3.50
2365 3404 3.851458 CATCAGGAAGGTGATGGATGA 57.149 47.619 6.03 0.00 46.91 2.92
2376 3415 2.774234 GTGATGGATGAGGAGGGAAAGA 59.226 50.000 0.00 0.00 0.00 2.52
2533 3653 2.209838 ACCACTCAATAGTCATCGCG 57.790 50.000 0.00 0.00 31.97 5.87
2543 3663 6.828672 TCAATAGTCATCGCGTACTATGTAG 58.171 40.000 22.59 17.55 38.58 2.74
2544 3664 3.539431 AGTCATCGCGTACTATGTAGC 57.461 47.619 5.77 0.00 0.00 3.58
2545 3665 2.876550 AGTCATCGCGTACTATGTAGCA 59.123 45.455 5.77 0.00 0.00 3.49
2656 3776 3.650942 TCTTGGGTGAGTGACCTTAACAT 59.349 43.478 0.00 0.00 45.33 2.71
2733 3853 6.761714 GTCGATGTAAGGTTGTGGAGAATTAT 59.238 38.462 0.00 0.00 0.00 1.28
2860 4435 6.320494 TGTTTTTACACCATATTCGTGCTT 57.680 33.333 0.48 0.00 34.45 3.91
2993 4572 4.576053 CACACTCATTCAGACCAGAAAACA 59.424 41.667 0.00 0.00 0.00 2.83
3196 4839 0.398381 AGCCTTCAGCCCCAAACAAA 60.398 50.000 0.00 0.00 45.47 2.83
3267 4910 0.744874 TCTGGCACGTGGATAGCTAC 59.255 55.000 18.88 0.00 0.00 3.58
3280 4923 0.819582 TAGCTACCTTACACGCACCC 59.180 55.000 0.00 0.00 0.00 4.61
3281 4924 0.903454 AGCTACCTTACACGCACCCT 60.903 55.000 0.00 0.00 0.00 4.34
3299 4942 4.161565 CACCCTCTTGTACATGGCTAGTTA 59.838 45.833 8.74 0.00 0.00 2.24
3320 4963 7.577303 AGTTATTTGGTGATATGTCAGTCCAT 58.423 34.615 3.13 0.00 32.42 3.41
3345 4988 8.458573 TCAGATATCTCTTTACAGACTCCTTC 57.541 38.462 1.03 0.00 0.00 3.46
3402 5045 6.375174 TGACATTATCAGCATGCTTTAACTGT 59.625 34.615 19.98 18.27 34.76 3.55
3403 5046 7.094248 TGACATTATCAGCATGCTTTAACTGTT 60.094 33.333 19.98 4.33 34.76 3.16
3405 5048 7.543172 ACATTATCAGCATGCTTTAACTGTTTG 59.457 33.333 19.98 14.64 34.76 2.93
3406 5049 3.641648 TCAGCATGCTTTAACTGTTTGC 58.358 40.909 19.98 1.19 34.76 3.68
3419 5062 0.032403 TGTTTGCAATGCACTGGAGC 59.968 50.000 7.72 0.00 38.71 4.70
3429 5072 0.250901 GCACTGGAGCTTTTGGAGGA 60.251 55.000 0.00 0.00 0.00 3.71
3430 5073 1.528129 CACTGGAGCTTTTGGAGGAC 58.472 55.000 0.00 0.00 0.00 3.85
3433 5076 1.349026 CTGGAGCTTTTGGAGGACTGA 59.651 52.381 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.038033 GCACGTATTTAGTGAAGAGAGAGG 58.962 45.833 0.07 0.00 41.83 3.69
1 2 5.038033 GGCACGTATTTAGTGAAGAGAGAG 58.962 45.833 0.07 0.00 41.83 3.20
2 3 4.461431 TGGCACGTATTTAGTGAAGAGAGA 59.539 41.667 0.07 0.00 41.83 3.10
3 4 4.563184 GTGGCACGTATTTAGTGAAGAGAG 59.437 45.833 0.00 0.00 41.83 3.20
4 5 4.021807 TGTGGCACGTATTTAGTGAAGAGA 60.022 41.667 13.77 0.00 41.83 3.10
5 6 4.242475 TGTGGCACGTATTTAGTGAAGAG 58.758 43.478 13.77 0.00 41.83 2.85
6 7 4.260139 TGTGGCACGTATTTAGTGAAGA 57.740 40.909 13.77 0.00 41.83 2.87
7 8 6.656314 TTATGTGGCACGTATTTAGTGAAG 57.344 37.500 19.55 0.00 41.83 3.02
8 9 5.064198 GCTTATGTGGCACGTATTTAGTGAA 59.936 40.000 19.55 4.06 41.83 3.18
9 10 4.569162 GCTTATGTGGCACGTATTTAGTGA 59.431 41.667 19.55 3.01 41.83 3.41
10 11 4.331443 TGCTTATGTGGCACGTATTTAGTG 59.669 41.667 19.55 7.87 42.15 2.74
11 12 4.509616 TGCTTATGTGGCACGTATTTAGT 58.490 39.130 19.55 0.00 34.56 2.24
12 13 5.478233 TTGCTTATGTGGCACGTATTTAG 57.522 39.130 19.55 14.85 39.55 1.85
13 14 5.413213 ACTTTGCTTATGTGGCACGTATTTA 59.587 36.000 19.55 5.10 39.55 1.40
14 15 4.217550 ACTTTGCTTATGTGGCACGTATTT 59.782 37.500 19.55 1.66 39.55 1.40
15 16 3.756434 ACTTTGCTTATGTGGCACGTATT 59.244 39.130 19.55 4.10 39.55 1.89
16 17 3.343617 ACTTTGCTTATGTGGCACGTAT 58.656 40.909 19.55 7.98 39.55 3.06
17 18 2.773487 ACTTTGCTTATGTGGCACGTA 58.227 42.857 15.38 15.38 39.55 3.57
18 19 1.604604 ACTTTGCTTATGTGGCACGT 58.395 45.000 17.65 17.65 39.55 4.49
19 20 2.287547 ACAACTTTGCTTATGTGGCACG 60.288 45.455 13.77 0.00 39.55 5.34
20 21 3.369546 ACAACTTTGCTTATGTGGCAC 57.630 42.857 11.55 11.55 39.55 5.01
21 22 5.242615 TCAATACAACTTTGCTTATGTGGCA 59.757 36.000 0.00 0.00 37.97 4.92
22 23 5.708948 TCAATACAACTTTGCTTATGTGGC 58.291 37.500 0.00 0.00 0.00 5.01
23 24 7.326789 CACTTCAATACAACTTTGCTTATGTGG 59.673 37.037 0.00 0.00 0.00 4.17
24 25 7.862372 ACACTTCAATACAACTTTGCTTATGTG 59.138 33.333 0.00 0.00 0.00 3.21
25 26 7.862372 CACACTTCAATACAACTTTGCTTATGT 59.138 33.333 0.00 0.00 0.00 2.29
26 27 7.862372 ACACACTTCAATACAACTTTGCTTATG 59.138 33.333 0.00 0.00 0.00 1.90
27 28 7.862372 CACACACTTCAATACAACTTTGCTTAT 59.138 33.333 0.00 0.00 0.00 1.73
28 29 7.066404 TCACACACTTCAATACAACTTTGCTTA 59.934 33.333 0.00 0.00 0.00 3.09
29 30 6.035843 CACACACTTCAATACAACTTTGCTT 58.964 36.000 0.00 0.00 0.00 3.91
30 31 5.356751 TCACACACTTCAATACAACTTTGCT 59.643 36.000 0.00 0.00 0.00 3.91
31 32 5.577835 TCACACACTTCAATACAACTTTGC 58.422 37.500 0.00 0.00 0.00 3.68
32 33 7.195646 ACATCACACACTTCAATACAACTTTG 58.804 34.615 0.00 0.00 0.00 2.77
33 34 7.333528 ACATCACACACTTCAATACAACTTT 57.666 32.000 0.00 0.00 0.00 2.66
34 35 6.942532 ACATCACACACTTCAATACAACTT 57.057 33.333 0.00 0.00 0.00 2.66
35 36 6.942532 AACATCACACACTTCAATACAACT 57.057 33.333 0.00 0.00 0.00 3.16
36 37 7.861630 AGTAACATCACACACTTCAATACAAC 58.138 34.615 0.00 0.00 0.00 3.32
37 38 7.172532 GGAGTAACATCACACACTTCAATACAA 59.827 37.037 0.00 0.00 0.00 2.41
38 39 6.649141 GGAGTAACATCACACACTTCAATACA 59.351 38.462 0.00 0.00 0.00 2.29
39 40 6.874134 AGGAGTAACATCACACACTTCAATAC 59.126 38.462 0.00 0.00 0.00 1.89
40 41 7.004555 AGGAGTAACATCACACACTTCAATA 57.995 36.000 0.00 0.00 0.00 1.90
41 42 5.869579 AGGAGTAACATCACACACTTCAAT 58.130 37.500 0.00 0.00 0.00 2.57
42 43 5.290493 AGGAGTAACATCACACACTTCAA 57.710 39.130 0.00 0.00 0.00 2.69
43 44 4.955811 AGGAGTAACATCACACACTTCA 57.044 40.909 0.00 0.00 0.00 3.02
44 45 6.456501 ACTTAGGAGTAACATCACACACTTC 58.543 40.000 0.00 0.00 33.32 3.01
45 46 6.420913 ACTTAGGAGTAACATCACACACTT 57.579 37.500 0.00 0.00 33.32 3.16
46 47 6.420913 AACTTAGGAGTAACATCACACACT 57.579 37.500 0.00 0.00 34.21 3.55
47 48 5.638234 GGAACTTAGGAGTAACATCACACAC 59.362 44.000 0.00 0.00 34.21 3.82
48 49 5.542635 AGGAACTTAGGAGTAACATCACACA 59.457 40.000 0.00 0.00 34.21 3.72
49 50 6.038997 AGGAACTTAGGAGTAACATCACAC 57.961 41.667 0.00 0.00 34.21 3.82
50 51 5.187186 GGAGGAACTTAGGAGTAACATCACA 59.813 44.000 0.00 0.00 41.55 3.58
51 52 5.395435 GGGAGGAACTTAGGAGTAACATCAC 60.395 48.000 0.00 0.00 41.55 3.06
52 53 4.715297 GGGAGGAACTTAGGAGTAACATCA 59.285 45.833 0.00 0.00 41.55 3.07
53 54 4.101274 GGGGAGGAACTTAGGAGTAACATC 59.899 50.000 0.00 0.00 41.55 3.06
54 55 4.038633 GGGGAGGAACTTAGGAGTAACAT 58.961 47.826 0.00 0.00 41.55 2.71
55 56 3.181404 TGGGGAGGAACTTAGGAGTAACA 60.181 47.826 0.00 0.00 41.55 2.41
56 57 3.197333 GTGGGGAGGAACTTAGGAGTAAC 59.803 52.174 0.00 0.00 41.55 2.50
57 58 3.078612 AGTGGGGAGGAACTTAGGAGTAA 59.921 47.826 0.00 0.00 41.55 2.24
58 59 2.658489 AGTGGGGAGGAACTTAGGAGTA 59.342 50.000 0.00 0.00 41.55 2.59
59 60 1.437547 AGTGGGGAGGAACTTAGGAGT 59.562 52.381 0.00 0.00 41.55 3.85
60 61 1.834263 CAGTGGGGAGGAACTTAGGAG 59.166 57.143 0.00 0.00 41.55 3.69
61 62 1.151413 ACAGTGGGGAGGAACTTAGGA 59.849 52.381 0.00 0.00 41.55 2.94
62 63 1.279271 CACAGTGGGGAGGAACTTAGG 59.721 57.143 0.00 0.00 41.55 2.69
63 64 2.028020 GTCACAGTGGGGAGGAACTTAG 60.028 54.545 0.00 0.00 41.55 2.18
64 65 1.975680 GTCACAGTGGGGAGGAACTTA 59.024 52.381 0.00 0.00 41.55 2.24
65 66 0.765510 GTCACAGTGGGGAGGAACTT 59.234 55.000 0.00 0.00 41.55 2.66
67 68 1.375326 GGTCACAGTGGGGAGGAAC 59.625 63.158 0.00 0.00 0.00 3.62
68 69 1.074090 TGGTCACAGTGGGGAGGAA 60.074 57.895 0.00 0.00 0.00 3.36
69 70 1.536418 CTGGTCACAGTGGGGAGGA 60.536 63.158 0.00 0.00 39.92 3.71
70 71 3.072476 CTGGTCACAGTGGGGAGG 58.928 66.667 0.00 0.00 39.92 4.30
71 72 2.348998 GCTGGTCACAGTGGGGAG 59.651 66.667 0.00 0.00 46.62 4.30
72 73 3.249189 GGCTGGTCACAGTGGGGA 61.249 66.667 0.00 0.00 46.62 4.81
73 74 1.488705 TAAGGCTGGTCACAGTGGGG 61.489 60.000 0.00 0.00 46.62 4.96
74 75 0.036010 CTAAGGCTGGTCACAGTGGG 60.036 60.000 0.00 0.00 46.62 4.61
75 76 0.687354 ACTAAGGCTGGTCACAGTGG 59.313 55.000 0.00 0.00 46.62 4.00
76 77 3.895232 ATACTAAGGCTGGTCACAGTG 57.105 47.619 0.00 0.00 46.62 3.66
77 78 4.041691 ACAAATACTAAGGCTGGTCACAGT 59.958 41.667 0.00 0.00 46.62 3.55
79 80 4.634012 ACAAATACTAAGGCTGGTCACA 57.366 40.909 0.00 0.00 0.00 3.58
80 81 5.758784 GGATACAAATACTAAGGCTGGTCAC 59.241 44.000 0.00 0.00 0.00 3.67
81 82 5.925509 GGATACAAATACTAAGGCTGGTCA 58.074 41.667 0.00 0.00 0.00 4.02
98 99 1.212688 CCTCACCCATGCTTGGATACA 59.787 52.381 19.85 0.49 46.92 2.29
99 100 1.972872 CCTCACCCATGCTTGGATAC 58.027 55.000 19.85 0.00 46.92 2.24
100 101 0.183492 GCCTCACCCATGCTTGGATA 59.817 55.000 19.85 4.10 46.92 2.59
101 102 1.076485 GCCTCACCCATGCTTGGAT 60.076 57.895 19.85 0.00 46.92 3.41
102 103 0.913934 TAGCCTCACCCATGCTTGGA 60.914 55.000 19.85 0.00 46.92 3.53
103 104 0.034186 TTAGCCTCACCCATGCTTGG 60.034 55.000 11.68 11.68 43.23 3.61
104 105 1.098050 GTTAGCCTCACCCATGCTTG 58.902 55.000 0.00 0.00 36.57 4.01
105 106 0.698238 TGTTAGCCTCACCCATGCTT 59.302 50.000 0.00 0.00 36.57 3.91
106 107 0.698238 TTGTTAGCCTCACCCATGCT 59.302 50.000 0.00 0.00 39.10 3.79
107 108 1.098050 CTTGTTAGCCTCACCCATGC 58.902 55.000 0.00 0.00 0.00 4.06
108 109 2.496899 ACTTGTTAGCCTCACCCATG 57.503 50.000 0.00 0.00 0.00 3.66
109 110 3.525800 AAACTTGTTAGCCTCACCCAT 57.474 42.857 0.00 0.00 0.00 4.00
110 111 3.306472 AAAACTTGTTAGCCTCACCCA 57.694 42.857 0.00 0.00 0.00 4.51
111 112 4.395625 ACTAAAACTTGTTAGCCTCACCC 58.604 43.478 0.00 0.00 34.92 4.61
112 113 5.306394 AGACTAAAACTTGTTAGCCTCACC 58.694 41.667 0.00 0.00 34.92 4.02
113 114 5.989777 TGAGACTAAAACTTGTTAGCCTCAC 59.010 40.000 6.82 0.00 42.29 3.51
114 115 6.169557 TGAGACTAAAACTTGTTAGCCTCA 57.830 37.500 6.82 6.82 43.85 3.86
115 116 7.674471 AATGAGACTAAAACTTGTTAGCCTC 57.326 36.000 2.43 2.43 39.64 4.70
116 117 9.740710 AATAATGAGACTAAAACTTGTTAGCCT 57.259 29.630 0.00 0.00 34.92 4.58
131 132 9.965902 AGTTCCATGACTAAAAATAATGAGACT 57.034 29.630 0.00 0.00 0.00 3.24
143 144 8.095792 TGGATACGTTTTAGTTCCATGACTAAA 58.904 33.333 13.13 13.13 43.56 1.85
144 145 7.613585 TGGATACGTTTTAGTTCCATGACTAA 58.386 34.615 0.00 0.00 38.78 2.24
145 146 7.172868 TGGATACGTTTTAGTTCCATGACTA 57.827 36.000 0.00 0.00 42.51 2.59
146 147 6.045072 TGGATACGTTTTAGTTCCATGACT 57.955 37.500 0.00 0.00 42.51 3.41
147 148 6.674760 GCTTGGATACGTTTTAGTTCCATGAC 60.675 42.308 0.00 0.00 42.51 3.06
148 149 5.353123 GCTTGGATACGTTTTAGTTCCATGA 59.647 40.000 0.00 0.00 42.51 3.07
149 150 5.123186 TGCTTGGATACGTTTTAGTTCCATG 59.877 40.000 0.00 1.67 42.51 3.66
150 151 5.123344 GTGCTTGGATACGTTTTAGTTCCAT 59.877 40.000 0.00 0.00 42.51 3.41
151 152 4.453136 GTGCTTGGATACGTTTTAGTTCCA 59.547 41.667 0.00 0.00 42.51 3.53
152 153 4.142752 GGTGCTTGGATACGTTTTAGTTCC 60.143 45.833 0.00 0.00 42.51 3.62
153 154 4.142752 GGGTGCTTGGATACGTTTTAGTTC 60.143 45.833 0.00 0.00 42.51 3.01
154 155 3.754850 GGGTGCTTGGATACGTTTTAGTT 59.245 43.478 0.00 0.00 42.51 2.24
155 156 3.008704 AGGGTGCTTGGATACGTTTTAGT 59.991 43.478 0.00 0.00 42.51 2.24
156 157 3.606687 AGGGTGCTTGGATACGTTTTAG 58.393 45.455 0.00 0.00 42.51 1.85
157 158 3.262405 AGAGGGTGCTTGGATACGTTTTA 59.738 43.478 0.00 0.00 42.51 1.52
158 159 2.039879 AGAGGGTGCTTGGATACGTTTT 59.960 45.455 0.00 0.00 42.51 2.43
159 160 1.628846 AGAGGGTGCTTGGATACGTTT 59.371 47.619 0.00 0.00 42.51 3.60
160 161 1.276622 AGAGGGTGCTTGGATACGTT 58.723 50.000 0.00 0.00 42.51 3.99
161 162 2.032620 CTAGAGGGTGCTTGGATACGT 58.967 52.381 0.00 0.00 42.51 3.57
162 163 2.307768 TCTAGAGGGTGCTTGGATACG 58.692 52.381 0.00 0.00 42.51 3.06
163 164 4.101741 ACAATCTAGAGGGTGCTTGGATAC 59.898 45.833 0.00 0.00 0.00 2.24
164 165 4.298626 ACAATCTAGAGGGTGCTTGGATA 58.701 43.478 0.00 0.00 0.00 2.59
165 166 3.118531 ACAATCTAGAGGGTGCTTGGAT 58.881 45.455 0.00 0.00 0.00 3.41
166 167 2.551270 ACAATCTAGAGGGTGCTTGGA 58.449 47.619 0.00 0.00 0.00 3.53
167 168 3.197766 TGTACAATCTAGAGGGTGCTTGG 59.802 47.826 13.25 0.00 0.00 3.61
168 169 4.471904 TGTACAATCTAGAGGGTGCTTG 57.528 45.455 13.25 7.74 0.00 4.01
169 170 5.499004 TTTGTACAATCTAGAGGGTGCTT 57.501 39.130 9.56 0.00 0.00 3.91
170 171 5.248477 TCTTTTGTACAATCTAGAGGGTGCT 59.752 40.000 9.56 0.00 0.00 4.40
171 172 5.488341 TCTTTTGTACAATCTAGAGGGTGC 58.512 41.667 9.56 8.11 0.00 5.01
172 173 9.319143 CTAATCTTTTGTACAATCTAGAGGGTG 57.681 37.037 9.56 4.72 0.00 4.61
173 174 8.487028 CCTAATCTTTTGTACAATCTAGAGGGT 58.513 37.037 9.56 1.33 0.00 4.34
174 175 8.487028 ACCTAATCTTTTGTACAATCTAGAGGG 58.513 37.037 9.56 15.55 0.00 4.30
175 176 9.892130 AACCTAATCTTTTGTACAATCTAGAGG 57.108 33.333 9.56 13.65 0.00 3.69
311 325 2.435059 GACTCTCCTGCCGGTTGC 60.435 66.667 1.90 0.00 41.77 4.17
365 379 6.494893 TTTTGTTGGAATGGAATCTAGTCG 57.505 37.500 0.00 0.00 0.00 4.18
374 388 8.187913 TCTTGTTGATATTTTGTTGGAATGGA 57.812 30.769 0.00 0.00 0.00 3.41
494 508 3.551890 CGGAAGGTGTTCATGTAGATTCG 59.448 47.826 0.00 0.00 33.93 3.34
533 547 7.965045 AGAAGATAATCAAGTCACTTTTACGC 58.035 34.615 0.00 0.00 0.00 4.42
560 574 7.648142 CAGTAACAAAAAGGACTAAGCATTCA 58.352 34.615 0.00 0.00 0.00 2.57
567 581 6.376018 ACAACAGCAGTAACAAAAAGGACTAA 59.624 34.615 0.00 0.00 0.00 2.24
574 588 5.677598 GCAGGTACAACAGCAGTAACAAAAA 60.678 40.000 0.00 0.00 31.60 1.94
582 596 1.597742 CAAGCAGGTACAACAGCAGT 58.402 50.000 0.00 0.00 0.00 4.40
593 607 1.211457 CATAGGAAGGAGCAAGCAGGT 59.789 52.381 0.00 0.00 0.00 4.00
599 613 4.703897 CCGAAATACATAGGAAGGAGCAA 58.296 43.478 0.00 0.00 0.00 3.91
643 657 8.368668 GTCACATAGTTCATAAGGTTATAGGCT 58.631 37.037 0.00 0.00 0.00 4.58
656 670 4.402793 AGGCGAGTAAGTCACATAGTTCAT 59.597 41.667 0.00 0.00 0.00 2.57
680 778 2.900167 GAAACGTCCGCCCACAACC 61.900 63.158 0.00 0.00 0.00 3.77
684 782 2.943653 CAAGAAACGTCCGCCCAC 59.056 61.111 0.00 0.00 0.00 4.61
717 834 4.082125 CCATGTCAGGCCTTAACTCTTTT 58.918 43.478 0.00 0.00 0.00 2.27
721 838 1.408822 CCCCATGTCAGGCCTTAACTC 60.409 57.143 0.00 0.00 0.00 3.01
722 839 0.625849 CCCCATGTCAGGCCTTAACT 59.374 55.000 0.00 0.00 0.00 2.24
723 840 0.623723 TCCCCATGTCAGGCCTTAAC 59.376 55.000 0.00 5.10 0.00 2.01
729 846 1.004277 TGTAGTTTCCCCATGTCAGGC 59.996 52.381 0.00 0.00 0.00 4.85
731 848 4.194640 CTCATGTAGTTTCCCCATGTCAG 58.805 47.826 0.00 0.00 37.73 3.51
734 851 2.308570 TGCTCATGTAGTTTCCCCATGT 59.691 45.455 0.00 0.00 37.73 3.21
788 906 3.518590 GGTATAACCGACCAAGTCACTG 58.481 50.000 0.00 0.00 36.91 3.66
800 918 2.628178 TCTCTGAGCATGGGTATAACCG 59.372 50.000 1.45 0.00 39.83 4.44
804 922 3.581101 AGCTTCTCTGAGCATGGGTATA 58.419 45.455 0.00 0.00 45.12 1.47
808 926 1.666054 GAAGCTTCTCTGAGCATGGG 58.334 55.000 19.44 0.00 45.12 4.00
829 947 5.450137 GGCGAGCAAGTAAGATAAGTAGTGA 60.450 44.000 0.00 0.00 0.00 3.41
830 948 4.740695 GGCGAGCAAGTAAGATAAGTAGTG 59.259 45.833 0.00 0.00 0.00 2.74
831 949 4.401519 TGGCGAGCAAGTAAGATAAGTAGT 59.598 41.667 0.00 0.00 0.00 2.73
832 950 4.740695 GTGGCGAGCAAGTAAGATAAGTAG 59.259 45.833 0.00 0.00 0.00 2.57
833 951 4.401519 AGTGGCGAGCAAGTAAGATAAGTA 59.598 41.667 0.00 0.00 0.00 2.24
834 952 3.195825 AGTGGCGAGCAAGTAAGATAAGT 59.804 43.478 0.00 0.00 0.00 2.24
835 953 3.786635 AGTGGCGAGCAAGTAAGATAAG 58.213 45.455 0.00 0.00 0.00 1.73
836 954 3.194755 TGAGTGGCGAGCAAGTAAGATAA 59.805 43.478 0.00 0.00 0.00 1.75
837 955 2.758423 TGAGTGGCGAGCAAGTAAGATA 59.242 45.455 0.00 0.00 0.00 1.98
838 956 1.550524 TGAGTGGCGAGCAAGTAAGAT 59.449 47.619 0.00 0.00 0.00 2.40
839 957 0.966179 TGAGTGGCGAGCAAGTAAGA 59.034 50.000 0.00 0.00 0.00 2.10
840 958 1.067565 TCTGAGTGGCGAGCAAGTAAG 60.068 52.381 0.00 0.00 0.00 2.34
841 959 0.966179 TCTGAGTGGCGAGCAAGTAA 59.034 50.000 0.00 0.00 0.00 2.24
842 960 0.528017 CTCTGAGTGGCGAGCAAGTA 59.472 55.000 0.00 0.00 0.00 2.24
843 961 1.181741 TCTCTGAGTGGCGAGCAAGT 61.182 55.000 4.32 0.00 0.00 3.16
844 962 0.037882 TTCTCTGAGTGGCGAGCAAG 60.038 55.000 4.32 0.00 0.00 4.01
845 963 0.037882 CTTCTCTGAGTGGCGAGCAA 60.038 55.000 4.32 0.00 0.00 3.91
846 964 1.588597 CTTCTCTGAGTGGCGAGCA 59.411 57.895 4.32 0.00 0.00 4.26
847 965 1.809209 GCTTCTCTGAGTGGCGAGC 60.809 63.158 4.32 4.67 0.00 5.03
848 966 0.246086 AAGCTTCTCTGAGTGGCGAG 59.754 55.000 4.32 0.00 0.00 5.03
849 967 0.244994 GAAGCTTCTCTGAGTGGCGA 59.755 55.000 19.44 0.00 0.00 5.54
850 968 0.739112 GGAAGCTTCTCTGAGTGGCG 60.739 60.000 25.05 0.00 0.00 5.69
851 969 0.392327 GGGAAGCTTCTCTGAGTGGC 60.392 60.000 25.05 9.99 0.00 5.01
852 970 0.979665 TGGGAAGCTTCTCTGAGTGG 59.020 55.000 26.24 0.38 0.00 4.00
853 971 2.235650 TGATGGGAAGCTTCTCTGAGTG 59.764 50.000 26.24 0.70 0.00 3.51
854 972 2.235898 GTGATGGGAAGCTTCTCTGAGT 59.764 50.000 26.24 10.39 0.00 3.41
858 976 3.718723 AGTAGTGATGGGAAGCTTCTCT 58.281 45.455 26.24 12.44 0.00 3.10
896 1014 4.056740 CGCTACAGGATTCGAGTAGAGTA 58.943 47.826 11.72 2.03 37.92 2.59
914 1032 8.529424 AATAAGTACTGTATATATGGGCGCTA 57.471 34.615 7.64 0.00 0.00 4.26
927 1045 7.499563 TGAAAGTGTTGGCAAATAAGTACTGTA 59.500 33.333 0.00 0.00 0.00 2.74
928 1046 6.320164 TGAAAGTGTTGGCAAATAAGTACTGT 59.680 34.615 0.00 0.00 0.00 3.55
929 1047 6.734137 TGAAAGTGTTGGCAAATAAGTACTG 58.266 36.000 0.00 0.00 0.00 2.74
930 1048 6.952773 TGAAAGTGTTGGCAAATAAGTACT 57.047 33.333 0.00 0.00 0.00 2.73
931 1049 6.523201 CGATGAAAGTGTTGGCAAATAAGTAC 59.477 38.462 0.00 0.00 0.00 2.73
932 1050 6.348950 CCGATGAAAGTGTTGGCAAATAAGTA 60.349 38.462 0.00 0.00 0.00 2.24
933 1051 5.460646 CGATGAAAGTGTTGGCAAATAAGT 58.539 37.500 0.00 0.00 0.00 2.24
934 1052 4.858692 CCGATGAAAGTGTTGGCAAATAAG 59.141 41.667 0.00 0.00 0.00 1.73
935 1053 4.520874 TCCGATGAAAGTGTTGGCAAATAA 59.479 37.500 0.00 0.00 0.00 1.40
957 1084 1.964223 TCAGTGAAGGGAGTGAGTGTC 59.036 52.381 0.00 0.00 0.00 3.67
985 1122 3.999663 CTGTCCATGTCTCTGTTTTCTCC 59.000 47.826 0.00 0.00 0.00 3.71
1545 2406 3.598715 ACCACGAACGGCGACAGA 61.599 61.111 16.62 0.00 44.57 3.41
1822 2699 2.932194 TGAGCAAGGAGGCTGCCT 60.932 61.111 23.64 23.64 45.99 4.75
1920 2829 0.612732 CCCAGAGAAATGGCTTGCCA 60.613 55.000 17.19 17.19 39.17 4.92
2103 3142 8.856153 TTGGCAAAACAATCAGATAACTACTA 57.144 30.769 0.00 0.00 0.00 1.82
2281 3320 4.398598 GCATTCGCACGCCGGTTT 62.399 61.111 1.90 0.00 38.36 3.27
2294 3333 2.026822 ACCTTTCTCATCTGTCCGCATT 60.027 45.455 0.00 0.00 0.00 3.56
2315 3354 0.547712 CCTCCTCCCTCCTCACCAAA 60.548 60.000 0.00 0.00 0.00 3.28
2365 3404 3.433740 GCGGTATTCAATCTTTCCCTCCT 60.434 47.826 0.00 0.00 0.00 3.69
2433 3473 3.318313 TCTTGTCAGAACTCCCTCCTTT 58.682 45.455 0.00 0.00 0.00 3.11
2498 3538 2.708861 AGTGGTTGTGGATACTTGGACA 59.291 45.455 0.00 0.00 37.61 4.02
2505 3545 5.730550 TGACTATTGAGTGGTTGTGGATAC 58.269 41.667 0.00 0.00 35.45 2.24
2533 3653 5.523552 TCAACATGTGCATGCTACATAGTAC 59.476 40.000 25.24 12.71 42.39 2.73
2640 3760 7.360575 ACGAATTTATGTTAAGGTCACTCAC 57.639 36.000 0.00 0.00 0.00 3.51
2700 3820 1.476891 ACCTTACATCGACGACATGCT 59.523 47.619 0.00 0.00 0.00 3.79
2733 3853 7.723616 ACCTATGTGCATAAAACCAAGCATATA 59.276 33.333 0.00 0.00 39.16 0.86
2854 4429 5.915758 GGATAGTAGTTATCACTGAAGCACG 59.084 44.000 0.00 0.00 40.02 5.34
2993 4572 9.620259 GAAGAGTTGGAGAATATAATTTCACCT 57.380 33.333 4.75 0.00 37.29 4.00
3196 4839 5.163290 GGTTTTAGCTCTAGCCTACTCCAAT 60.163 44.000 0.00 0.00 43.38 3.16
3267 4910 0.034896 ACAAGAGGGTGCGTGTAAGG 59.965 55.000 0.00 0.00 0.00 2.69
3280 4923 6.823689 ACCAAATAACTAGCCATGTACAAGAG 59.176 38.462 0.00 0.00 0.00 2.85
3281 4924 6.597672 CACCAAATAACTAGCCATGTACAAGA 59.402 38.462 0.00 0.00 0.00 3.02
3299 4942 6.005066 TGATGGACTGACATATCACCAAAT 57.995 37.500 0.00 0.00 35.29 2.32
3320 4963 7.504238 GGAAGGAGTCTGTAAAGAGATATCTGA 59.496 40.741 10.74 0.00 0.00 3.27
3345 4988 3.750371 TGGTAGACCAAACTTGACATGG 58.250 45.455 0.00 0.00 44.35 3.66
3402 5045 1.042229 AAGCTCCAGTGCATTGCAAA 58.958 45.000 13.94 0.00 41.47 3.68
3403 5046 1.042229 AAAGCTCCAGTGCATTGCAA 58.958 45.000 13.94 0.00 41.47 4.08
3405 5048 1.425412 CAAAAGCTCCAGTGCATTGC 58.575 50.000 3.19 0.46 34.99 3.56
3406 5049 1.614903 TCCAAAAGCTCCAGTGCATTG 59.385 47.619 1.49 1.49 34.24 2.82
3419 5062 8.091449 GGTATATACATCTCAGTCCTCCAAAAG 58.909 40.741 14.70 0.00 0.00 2.27
3429 5072 7.633018 ATGGTTTGGGTATATACATCTCAGT 57.367 36.000 14.70 0.00 0.00 3.41
3430 5073 9.823647 GATATGGTTTGGGTATATACATCTCAG 57.176 37.037 14.70 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.