Multiple sequence alignment - TraesCS3B01G226900

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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 TraesCS3B01G226900 chr3B 100.000 9630 0 0 1 9630 319822817 319832446 0.000000e+00 17784.0
1 TraesCS3B01G226900 chr3D 97.717 3198 48 5 903 4075 261735907 261739104 0.000000e+00 5478.0
2 TraesCS3B01G226900 chr3D 97.222 2088 50 6 4646 6731 261741455 261743536 0.000000e+00 3528.0
3 TraesCS3B01G226900 chr3D 94.358 1028 22 12 7077 8085 261744123 261745133 0.000000e+00 1544.0
4 TraesCS3B01G226900 chr3D 92.772 1010 55 9 8182 9188 261745130 261746124 0.000000e+00 1445.0
5 TraesCS3B01G226900 chr3D 93.788 499 19 6 9144 9630 261746122 261746620 0.000000e+00 739.0
6 TraesCS3B01G226900 chr3D 97.744 399 9 0 4076 4474 261739166 261739564 0.000000e+00 688.0
7 TraesCS3B01G226900 chr3D 93.333 255 8 1 6838 7092 261743863 261744108 1.530000e-97 368.0
8 TraesCS3B01G226900 chr3D 83.681 288 43 3 9314 9598 268955615 268955329 1.590000e-67 268.0
9 TraesCS3B01G226900 chr3D 75.658 304 70 4 9317 9618 412509235 412508934 2.170000e-31 148.0
10 TraesCS3B01G226900 chr3D 75.168 298 70 4 9317 9612 514235440 514235735 4.690000e-28 137.0
11 TraesCS3B01G226900 chr3D 88.679 106 4 6 8082 8184 349635570 349635470 1.310000e-23 122.0
12 TraesCS3B01G226900 chr3D 84.404 109 10 4 8082 8183 590847128 590847236 6.150000e-17 100.0
13 TraesCS3B01G226900 chr3A 97.618 1763 29 4 915 2668 288535826 288537584 0.000000e+00 3011.0
14 TraesCS3B01G226900 chr3A 97.480 1389 19 3 2701 4075 288537583 288538969 0.000000e+00 2357.0
15 TraesCS3B01G226900 chr3A 96.996 1165 27 6 4635 5796 288539429 288540588 0.000000e+00 1951.0
16 TraesCS3B01G226900 chr3A 95.094 1060 23 9 7049 8085 288542172 288543225 0.000000e+00 1642.0
17 TraesCS3B01G226900 chr3A 96.963 889 25 2 5723 6611 288540590 288541476 0.000000e+00 1491.0
18 TraesCS3B01G226900 chr3A 91.907 729 45 4 8566 9294 288543558 288544272 0.000000e+00 1007.0
19 TraesCS3B01G226900 chr3A 95.750 400 16 1 4076 4474 288539031 288539430 2.270000e-180 643.0
20 TraesCS3B01G226900 chr3A 93.824 340 19 2 8182 8521 288543222 288543559 2.400000e-140 510.0
21 TraesCS3B01G226900 chr3A 92.287 363 16 5 9276 9630 288544287 288544645 1.120000e-138 505.0
22 TraesCS3B01G226900 chr3A 91.798 317 9 6 6777 7092 288541882 288542182 8.940000e-115 425.0
23 TraesCS3B01G226900 chr3A 87.678 211 25 1 9389 9598 345859009 345859219 2.690000e-60 244.0
24 TraesCS3B01G226900 chr3A 77.199 307 63 6 9316 9620 387926512 387926211 1.290000e-38 172.0
25 TraesCS3B01G226900 chr1B 95.934 910 29 4 1 903 616080971 616081879 0.000000e+00 1469.0
26 TraesCS3B01G226900 chr1B 94.978 916 33 9 1 906 263932657 263931745 0.000000e+00 1424.0
27 TraesCS3B01G226900 chr1B 95.050 909 30 11 1 898 91835787 91834883 0.000000e+00 1415.0
28 TraesCS3B01G226900 chr1B 88.571 105 8 1 8082 8186 129551331 129551231 3.650000e-24 124.0
29 TraesCS3B01G226900 chr7B 95.558 923 29 7 1 912 567574164 567573243 0.000000e+00 1467.0
30 TraesCS3B01G226900 chr2B 95.738 915 24 10 1 903 646070838 646069927 0.000000e+00 1459.0
31 TraesCS3B01G226900 chr2B 95.628 915 26 8 1 903 80053207 80052295 0.000000e+00 1456.0
32 TraesCS3B01G226900 chr2B 83.117 77 10 3 7929 8004 156918878 156918952 6.240000e-07 67.6
33 TraesCS3B01G226900 chr4B 95.077 914 28 11 1 903 626636230 626637137 0.000000e+00 1423.0
34 TraesCS3B01G226900 chr5B 94.336 918 33 13 1 905 458567392 458568303 0.000000e+00 1389.0
35 TraesCS3B01G226900 chr5B 94.111 917 37 12 1 903 382698550 382699463 0.000000e+00 1378.0
36 TraesCS3B01G226900 chr5B 82.750 400 63 5 9224 9623 141446972 141447365 1.540000e-92 351.0
37 TraesCS3B01G226900 chr5B 75.333 300 69 5 9321 9618 93555006 93554710 1.300000e-28 139.0
38 TraesCS3B01G226900 chr5B 82.500 120 15 3 8070 8189 484876420 484876533 6.150000e-17 100.0
39 TraesCS3B01G226900 chr5A 80.976 410 55 13 9224 9630 144382737 144383126 4.370000e-78 303.0
40 TraesCS3B01G226900 chr5A 95.833 168 7 0 4471 4638 676319132 676319299 1.230000e-68 272.0
41 TraesCS3B01G226900 chr5A 95.266 169 8 0 4472 4640 126692563 126692731 1.590000e-67 268.0
42 TraesCS3B01G226900 chr5A 90.654 107 9 1 8082 8187 546393929 546393823 3.630000e-29 141.0
43 TraesCS3B01G226900 chr1A 98.171 164 3 0 4473 4636 185828476 185828313 4.400000e-73 287.0
44 TraesCS3B01G226900 chr1A 87.255 102 9 2 8082 8183 41366745 41366842 7.900000e-21 113.0
45 TraesCS3B01G226900 chr2D 79.551 401 76 4 9224 9622 22523464 22523860 2.050000e-71 281.0
46 TraesCS3B01G226900 chr2D 95.266 169 8 0 4473 4641 300705133 300704965 1.590000e-67 268.0
47 TraesCS3B01G226900 chr2D 87.037 108 8 3 8082 8183 32984435 32984542 6.110000e-22 117.0
48 TraesCS3B01G226900 chr2D 87.619 105 6 5 8082 8185 107564883 107564785 2.200000e-21 115.0
49 TraesCS3B01G226900 chr4A 96.386 166 6 0 4471 4636 572704512 572704677 3.430000e-69 274.0
50 TraesCS3B01G226900 chr4A 95.294 170 8 0 4469 4638 185555347 185555178 4.430000e-68 270.0
51 TraesCS3B01G226900 chr4A 96.341 164 6 0 4473 4636 560316465 560316302 4.430000e-68 270.0
52 TraesCS3B01G226900 chr4A 87.850 107 9 2 8081 8183 208037888 208037994 1.310000e-23 122.0
53 TraesCS3B01G226900 chr4D 96.364 165 6 0 4473 4637 16666599 16666763 1.230000e-68 272.0
54 TraesCS3B01G226900 chr4D 95.783 166 7 0 4471 4636 281177086 281177251 1.590000e-67 268.0
55 TraesCS3B01G226900 chr4D 75.421 297 63 8 9321 9612 361227167 361227458 1.690000e-27 135.0
56 TraesCS3B01G226900 chr4D 75.421 297 63 10 9321 9612 427660483 427660774 1.690000e-27 135.0
57 TraesCS3B01G226900 chr4D 77.727 220 43 6 9396 9612 136096557 136096341 7.850000e-26 130.0
58 TraesCS3B01G226900 chr4D 94.118 68 2 2 8070 8137 347481438 347481373 1.710000e-17 102.0
59 TraesCS3B01G226900 chr6B 76.080 301 66 6 9321 9618 266011144 266010847 1.680000e-32 152.0
60 TraesCS3B01G226900 chr6D 75.748 301 63 9 9317 9612 18070903 18071198 1.010000e-29 143.0
61 TraesCS3B01G226900 chr6D 75.667 300 61 10 9317 9612 147008713 147009004 1.300000e-28 139.0
62 TraesCS3B01G226900 chr6D 78.017 232 43 8 9396 9623 164583323 164583550 1.300000e-28 139.0
63 TraesCS3B01G226900 chr6D 89.091 110 10 2 8082 8189 50742267 50742376 1.690000e-27 135.0
64 TraesCS3B01G226900 chr6D 74.503 302 69 6 9321 9618 300223130 300222833 3.650000e-24 124.0
65 TraesCS3B01G226900 chr6D 75.889 253 54 5 9363 9612 247875005 247875253 1.310000e-23 122.0
66 TraesCS3B01G226900 chr6D 74.377 281 70 2 9318 9597 109084313 109084592 1.700000e-22 119.0
67 TraesCS3B01G226900 chr6D 74.558 283 66 6 9333 9612 111833013 111833292 1.700000e-22 119.0
68 TraesCS3B01G226900 chr6D 76.549 226 47 6 9396 9618 205501308 205501086 1.700000e-22 119.0
69 TraesCS3B01G226900 chr6D 74.000 300 74 4 9321 9618 314969715 314969418 1.700000e-22 119.0
70 TraesCS3B01G226900 chr6D 87.156 109 9 3 8082 8185 319685618 319685726 1.700000e-22 119.0
71 TraesCS3B01G226900 chr6D 74.324 296 67 7 9321 9612 379911824 379912114 6.110000e-22 117.0
72 TraesCS3B01G226900 chr6D 74.386 285 64 8 9317 9598 204256442 204256164 7.900000e-21 113.0
73 TraesCS3B01G226900 chr6D 73.770 305 70 9 9317 9618 294382554 294382257 2.840000e-20 111.0
74 TraesCS3B01G226900 chr6D 86.000 100 12 2 8082 8181 107342049 107342146 1.320000e-18 106.0
75 TraesCS3B01G226900 chr6D 89.157 83 7 2 8063 8143 30077346 30077428 1.710000e-17 102.0
76 TraesCS3B01G226900 chr6D 95.238 63 3 0 8081 8143 99730204 99730266 6.150000e-17 100.0
77 TraesCS3B01G226900 chr6D 84.466 103 15 1 8082 8183 410399843 410399945 6.150000e-17 100.0
78 TraesCS3B01G226900 chr6D 95.161 62 3 0 8082 8143 15372552 15372613 2.210000e-16 99.0
79 TraesCS3B01G226900 chr6D 92.424 66 5 0 8081 8146 57516204 57516139 2.860000e-15 95.3
80 TraesCS3B01G226900 chr6D 92.424 66 5 0 8081 8146 231497355 231497290 2.860000e-15 95.3
81 TraesCS3B01G226900 chr6D 95.000 60 3 0 8078 8137 460470342 460470401 2.860000e-15 95.3
82 TraesCS3B01G226900 chr6D 91.176 68 5 1 8071 8137 57486243 57486310 3.700000e-14 91.6
83 TraesCS3B01G226900 chr6D 82.353 102 11 3 8082 8183 26447896 26447802 2.230000e-11 82.4
84 TraesCS3B01G226900 chr6D 97.826 46 1 0 8082 8127 199144926 199144881 8.020000e-11 80.5
85 TraesCS3B01G226900 chr6D 90.741 54 3 2 8143 8194 75374035 75374088 4.830000e-08 71.3
86 TraesCS3B01G226900 chr6D 92.157 51 3 1 8138 8187 405119585 405119635 4.830000e-08 71.3
87 TraesCS3B01G226900 chr6D 95.349 43 2 0 8143 8185 316625913 316625955 1.740000e-07 69.4
88 TraesCS3B01G226900 chr6D 95.238 42 2 0 8146 8187 44495716 44495675 6.240000e-07 67.6
89 TraesCS3B01G226900 chr6D 89.286 56 3 3 8142 8194 139369292 139369347 6.240000e-07 67.6
90 TraesCS3B01G226900 chr7D 75.415 301 68 5 9321 9618 70563039 70563336 3.630000e-29 141.0
91 TraesCS3B01G226900 chr7D 87.255 102 8 2 8082 8183 604292593 604292689 2.840000e-20 111.0
92 TraesCS3B01G226900 chr5D 75.399 313 65 12 9315 9622 466201669 466201974 3.630000e-29 141.0
93 TraesCS3B01G226900 chr5D 75.850 294 57 13 9335 9622 205217843 205218128 4.690000e-28 137.0
94 TraesCS3B01G226900 chr5D 74.837 306 69 8 9317 9618 218340555 218340254 2.180000e-26 132.0
95 TraesCS3B01G226900 chr5D 87.500 112 10 2 8082 8190 481420988 481421098 1.020000e-24 126.0
96 TraesCS3B01G226900 chr5D 98.361 61 0 1 8077 8137 543829154 543829213 1.320000e-18 106.0
97 TraesCS3B01G226900 chr1D 74.671 304 73 4 9317 9618 191936140 191935839 2.180000e-26 132.0
98 TraesCS3B01G226900 chr1D 75.439 285 60 9 9333 9612 312941284 312941563 7.850000e-26 130.0
99 TraesCS3B01G226900 chr1D 74.510 306 70 8 9317 9618 79302390 79302089 1.020000e-24 126.0
100 TraesCS3B01G226900 chr1D 74.426 305 72 6 9317 9618 108125258 108124957 1.020000e-24 126.0
101 TraesCS3B01G226900 chr1D 74.914 291 65 6 9326 9612 200132771 200133057 1.020000e-24 126.0
102 TraesCS3B01G226900 chr1D 87.500 104 12 1 8082 8185 465522882 465522984 1.700000e-22 119.0
103 TraesCS3B01G226900 chr1D 95.385 65 3 0 8082 8146 340456244 340456180 4.760000e-18 104.0
104 TraesCS3B01G226900 chr1D 82.075 106 16 3 8082 8185 490375083 490374979 4.790000e-13 87.9
105 TraesCS3B01G226900 chr1D 90.164 61 6 0 4187 4247 433953316 433953256 8.020000e-11 80.5
106 TraesCS3B01G226900 chr1D 93.750 48 3 0 8146 8193 339102073 339102026 1.340000e-08 73.1
107 TraesCS3B01G226900 chr7A 88.889 108 9 3 8085 8189 16162101 16161994 7.850000e-26 130.0
108 TraesCS3B01G226900 chr6A 90.196 102 6 2 8083 8184 511531710 511531613 7.850000e-26 130.0
109 TraesCS3B01G226900 chr6A 86.486 111 10 3 8082 8191 511531614 511531720 6.110000e-22 117.0


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 TraesCS3B01G226900 chr3B 319822817 319832446 9629 False 17784.0 17784 100.000000 1 9630 1 chr3B.!!$F1 9629
1 TraesCS3B01G226900 chr3D 261735907 261746620 10713 False 1970.0 5478 95.276286 903 9630 7 chr3D.!!$F3 8727
2 TraesCS3B01G226900 chr3A 288535826 288544645 8819 False 1354.2 3011 94.971700 915 9630 10 chr3A.!!$F2 8715
3 TraesCS3B01G226900 chr1B 616080971 616081879 908 False 1469.0 1469 95.934000 1 903 1 chr1B.!!$F1 902
4 TraesCS3B01G226900 chr1B 263931745 263932657 912 True 1424.0 1424 94.978000 1 906 1 chr1B.!!$R3 905
5 TraesCS3B01G226900 chr1B 91834883 91835787 904 True 1415.0 1415 95.050000 1 898 1 chr1B.!!$R1 897
6 TraesCS3B01G226900 chr7B 567573243 567574164 921 True 1467.0 1467 95.558000 1 912 1 chr7B.!!$R1 911
7 TraesCS3B01G226900 chr2B 646069927 646070838 911 True 1459.0 1459 95.738000 1 903 1 chr2B.!!$R2 902
8 TraesCS3B01G226900 chr2B 80052295 80053207 912 True 1456.0 1456 95.628000 1 903 1 chr2B.!!$R1 902
9 TraesCS3B01G226900 chr4B 626636230 626637137 907 False 1423.0 1423 95.077000 1 903 1 chr4B.!!$F1 902
10 TraesCS3B01G226900 chr5B 458567392 458568303 911 False 1389.0 1389 94.336000 1 905 1 chr5B.!!$F3 904
11 TraesCS3B01G226900 chr5B 382698550 382699463 913 False 1378.0 1378 94.111000 1 903 1 chr5B.!!$F2 902

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
787 801 1.169034 GGAATCCAATCGGCCTGCTC 61.169 60.000 0.00 0.0 0.00 4.26 F
1849 1878 0.321564 CGATGCCACAGGGTCTTTCA 60.322 55.000 0.00 0.0 36.17 2.69 F
2611 2640 1.892474 TGGTTTCAATGTTAGCCCTGC 59.108 47.619 0.00 0.0 0.00 4.85 F
3997 4051 1.337703 CGATGCATATGTGGTTTGGGG 59.662 52.381 0.00 0.0 0.00 4.96 F
4707 6542 0.321298 TAGGAGCGTTGTTTCCTGCC 60.321 55.000 3.37 0.0 43.54 4.85 F
4810 6645 0.580104 GTCTGTTTGTCAACGTCGGG 59.420 55.000 0.00 0.0 35.40 5.14 F
6578 8491 0.615331 GGAGATGGACAGAGTTGGCA 59.385 55.000 0.00 0.0 32.23 4.92 F
6913 9132 0.692419 ATGGGGGAGGCAGTAGACAG 60.692 60.000 0.00 0.0 0.00 3.51 F
8092 10395 1.215140 AGTCTAGCTACTCCCTCCGT 58.785 55.000 0.00 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 1911 1.445582 GACGAATCCCGCGACAAGT 60.446 57.895 8.23 0.00 43.32 3.16 R
3151 3183 3.274288 GGCAGATAAGTATAGGCATGGC 58.726 50.000 12.14 12.14 0.00 4.40 R
4460 4576 2.668625 GAGGGAGTAGAAAGATCGGGT 58.331 52.381 0.00 0.00 0.00 5.28 R
5455 7292 0.827368 GTGGTGGGGCAGTTTTCAAA 59.173 50.000 0.00 0.00 0.00 2.69 R
6679 8592 0.104725 AAAGCCAACCCATCCCCAAA 60.105 50.000 0.00 0.00 0.00 3.28 R
6778 8691 0.845102 TCTTTGGTTCCCCTCCCTCC 60.845 60.000 0.00 0.00 0.00 4.30 R
7504 9785 0.605319 TGCAGCCTAAACGACCCAAG 60.605 55.000 0.00 0.00 0.00 3.61 R
8362 10665 1.420430 TTCAGACTTCCAGACCGGTT 58.580 50.000 9.42 0.00 35.57 4.44 R
8923 11229 0.597637 GTCAGTGACGGTGTCTGTGG 60.598 60.000 7.68 0.00 33.15 4.17 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
671 685 3.386078 TGCAAAAACAATTAGCCCACAGA 59.614 39.130 0.00 0.00 0.00 3.41
787 801 1.169034 GGAATCCAATCGGCCTGCTC 61.169 60.000 0.00 0.00 0.00 4.26
1005 1025 2.159382 GCGAAAGGAAAGGGAATGTCA 58.841 47.619 0.00 0.00 0.00 3.58
1556 1583 1.210478 CCCATCTGAGGTCGGTGATTT 59.790 52.381 0.00 0.00 0.00 2.17
1559 1586 3.118775 CCATCTGAGGTCGGTGATTTGTA 60.119 47.826 0.00 0.00 0.00 2.41
1849 1878 0.321564 CGATGCCACAGGGTCTTTCA 60.322 55.000 0.00 0.00 36.17 2.69
1994 2023 7.768582 ACCATAAGTTACGATGAATGTTGATGA 59.231 33.333 0.00 0.00 0.00 2.92
2325 2354 8.027189 GGGTGTTTTCCTTTCTTGTATGTATTC 58.973 37.037 0.00 0.00 0.00 1.75
2395 2424 2.325583 TATTGTGTCCTGCGGGATTC 57.674 50.000 19.55 14.21 44.33 2.52
2611 2640 1.892474 TGGTTTCAATGTTAGCCCTGC 59.108 47.619 0.00 0.00 0.00 4.85
2633 2662 9.079833 CCTGCATTGTGAAATTTCAAGTAATAG 57.920 33.333 22.07 15.33 39.21 1.73
2689 2720 6.759827 CCCAAGCACTAATACGTACAAGTAAT 59.240 38.462 10.43 1.88 0.00 1.89
2692 2723 8.653338 CAAGCACTAATACGTACAAGTAATTGT 58.347 33.333 13.70 13.70 38.85 2.71
2908 2940 9.333724 CCTATACGTATTGGTTAACTTTGGAAT 57.666 33.333 23.06 0.23 0.00 3.01
3111 3143 8.609617 TCCAACTTCTCCTCTTCAGAATATTA 57.390 34.615 0.00 0.00 0.00 0.98
3151 3183 7.961325 AAACCCATAACTTGCTGTAAAAATG 57.039 32.000 0.00 0.00 0.00 2.32
3669 3701 4.310769 TGACTAAGCAGCTTTCTTCAGTC 58.689 43.478 21.16 21.16 33.43 3.51
3997 4051 1.337703 CGATGCATATGTGGTTTGGGG 59.662 52.381 0.00 0.00 0.00 4.96
4276 4391 2.928334 CTGAGCCAGAATACTGCCATT 58.072 47.619 0.00 0.00 42.25 3.16
4306 4421 8.920174 GTGGGCCTTTAATATAGGTAATTTTGT 58.080 33.333 4.53 0.00 35.13 2.83
4352 4467 5.607119 AAACTGAATAAACCTGTACGCAG 57.393 39.130 0.00 0.00 42.22 5.18
4459 4575 1.442526 GCATAGCCGAACAGCAGCAT 61.443 55.000 0.00 0.00 34.23 3.79
4460 4576 1.869774 CATAGCCGAACAGCAGCATA 58.130 50.000 0.00 0.00 34.23 3.14
4474 4590 3.060602 GCAGCATACCCGATCTTTCTAC 58.939 50.000 0.00 0.00 0.00 2.59
4481 5801 1.964933 CCCGATCTTTCTACTCCCTCC 59.035 57.143 0.00 0.00 0.00 4.30
4502 5822 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4582 5903 7.361457 AGATTCACTCATTTTCCTCCGTATA 57.639 36.000 0.00 0.00 0.00 1.47
4591 5912 6.551975 TCATTTTCCTCCGTATATAGTCACCA 59.448 38.462 0.00 0.00 0.00 4.17
4592 5913 6.989155 TTTTCCTCCGTATATAGTCACCAT 57.011 37.500 0.00 0.00 0.00 3.55
4593 5914 6.585695 TTTCCTCCGTATATAGTCACCATC 57.414 41.667 0.00 0.00 0.00 3.51
4599 5920 6.978338 TCCGTATATAGTCACCATCTGAAAC 58.022 40.000 0.00 0.00 0.00 2.78
4605 5926 8.783660 ATATAGTCACCATCTGAAACCTCTAA 57.216 34.615 0.00 0.00 0.00 2.10
4707 6542 0.321298 TAGGAGCGTTGTTTCCTGCC 60.321 55.000 3.37 0.00 43.54 4.85
4810 6645 0.580104 GTCTGTTTGTCAACGTCGGG 59.420 55.000 0.00 0.00 35.40 5.14
4877 6713 6.787225 TGAACATTACTGTTTGTGGTGTTAC 58.213 36.000 0.00 0.00 45.57 2.50
4918 6754 9.696917 GTTAAATCTCTGTCAAAATGGTTGAAT 57.303 29.630 0.00 0.00 0.00 2.57
5000 6836 8.974060 ACAGTTAACTGAATTCTTAGTTTCCA 57.026 30.769 36.14 0.00 46.59 3.53
5100 6936 2.676076 CCCACATGTAAACAAGCTTGC 58.324 47.619 26.27 10.47 0.00 4.01
5252 7088 2.308866 ACTACCCAAAGGACCATTCTGG 59.691 50.000 0.00 0.00 39.25 3.86
5446 7283 4.078805 GGTTTTAATTCCCTATCCCACCCT 60.079 45.833 0.00 0.00 0.00 4.34
5455 7292 2.308866 CCTATCCCACCCTGTTTTCTGT 59.691 50.000 0.00 0.00 0.00 3.41
5834 7747 1.121407 TGACCAGTGTAGCCAGCAGT 61.121 55.000 0.00 0.00 0.00 4.40
6094 8007 3.514645 AGAACAATTGAATTGGCATCGC 58.485 40.909 20.69 4.80 44.42 4.58
6141 8054 7.168972 GCTCACACAACTTGTAATTAAATGCAA 59.831 33.333 0.00 0.00 35.67 4.08
6449 8362 4.092091 GGAACAATCAGTCAGCTTAACTCG 59.908 45.833 0.00 0.00 0.00 4.18
6569 8482 2.436911 CTGATGTGGATGGAGATGGACA 59.563 50.000 0.00 0.00 0.00 4.02
6578 8491 0.615331 GGAGATGGACAGAGTTGGCA 59.385 55.000 0.00 0.00 32.23 4.92
6581 8494 3.350833 GAGATGGACAGAGTTGGCAAAT 58.649 45.455 0.00 0.00 32.23 2.32
6679 8592 4.760047 GAGGTGTGCATCCGCCGT 62.760 66.667 0.00 0.00 40.04 5.68
6756 8669 1.682854 GATGGTGCAGAGAGAGAGAGG 59.317 57.143 0.00 0.00 0.00 3.69
6758 8671 1.042559 GGTGCAGAGAGAGAGAGGGG 61.043 65.000 0.00 0.00 0.00 4.79
6759 8672 1.042559 GTGCAGAGAGAGAGAGGGGG 61.043 65.000 0.00 0.00 0.00 5.40
6777 8690 4.179599 GGGGAGGGAGGGAGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
6778 8691 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
6779 8692 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
6780 8693 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
6781 8694 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
6782 8695 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
6823 9042 4.816925 CCCTCTTAATGAACCGAAGAATCC 59.183 45.833 0.00 0.00 0.00 3.01
6913 9132 0.692419 ATGGGGGAGGCAGTAGACAG 60.692 60.000 0.00 0.00 0.00 3.51
6972 9191 3.758554 AGTAGCCATGATTGGTGTTCAAC 59.241 43.478 0.00 0.00 45.57 3.18
6988 9207 2.124693 AACCCCCGTTGCAACACAG 61.125 57.895 28.01 15.89 0.00 3.66
7458 9738 6.260936 CCGCAAACTCTCACCTTATTATTCAT 59.739 38.462 0.00 0.00 0.00 2.57
7578 9863 8.410141 CAACATTGTAAGTAGAACTTGGGAAAA 58.590 33.333 2.59 0.00 39.11 2.29
7580 9865 7.230712 ACATTGTAAGTAGAACTTGGGAAAAGG 59.769 37.037 2.59 0.00 39.11 3.11
7581 9866 6.503560 TGTAAGTAGAACTTGGGAAAAGGA 57.496 37.500 2.59 0.00 39.11 3.36
7584 9869 8.002459 TGTAAGTAGAACTTGGGAAAAGGATTT 58.998 33.333 2.59 0.00 38.47 2.17
7585 9870 6.901081 AGTAGAACTTGGGAAAAGGATTTG 57.099 37.500 0.00 0.00 39.02 2.32
7586 9871 6.373759 AGTAGAACTTGGGAAAAGGATTTGT 58.626 36.000 0.00 0.00 39.02 2.83
7587 9872 5.535753 AGAACTTGGGAAAAGGATTTGTG 57.464 39.130 0.00 0.00 39.02 3.33
7669 9971 2.806608 ACTTGATGCCTTTGCTTGTG 57.193 45.000 0.00 0.00 38.71 3.33
7796 10098 7.301868 TGCAAACTCCAAAATAAAAGGATCT 57.698 32.000 0.00 0.00 0.00 2.75
7867 10169 3.323115 TGCCTGGCAATTTATGTTTGTCA 59.677 39.130 21.08 0.00 36.41 3.58
7872 10174 4.749099 TGGCAATTTATGTTTGTCAAGCAC 59.251 37.500 4.05 0.00 35.87 4.40
7874 10176 4.143347 GCAATTTATGTTTGTCAAGCACGG 60.143 41.667 4.05 0.00 0.00 4.94
7955 10257 6.621316 TTCCGTGATTGCAAACTAAAGTTA 57.379 33.333 1.71 0.00 37.25 2.24
7962 10264 8.462016 GTGATTGCAAACTAAAGTTATCATCCT 58.538 33.333 1.71 0.00 37.25 3.24
8014 10316 4.305539 TGATTTGCCATCTTCTCCAAGA 57.694 40.909 0.00 0.00 43.06 3.02
8085 10388 5.230942 TGCAAAACTCAAGTCTAGCTACTC 58.769 41.667 0.00 0.00 0.00 2.59
8086 10389 4.627900 GCAAAACTCAAGTCTAGCTACTCC 59.372 45.833 0.00 0.00 0.00 3.85
8087 10390 5.172205 CAAAACTCAAGTCTAGCTACTCCC 58.828 45.833 0.00 0.00 0.00 4.30
8088 10391 4.325084 AACTCAAGTCTAGCTACTCCCT 57.675 45.455 0.00 0.00 0.00 4.20
8089 10392 3.893521 ACTCAAGTCTAGCTACTCCCTC 58.106 50.000 0.00 0.00 0.00 4.30
8090 10393 3.219281 CTCAAGTCTAGCTACTCCCTCC 58.781 54.545 0.00 0.00 0.00 4.30
8091 10394 1.950909 CAAGTCTAGCTACTCCCTCCG 59.049 57.143 0.00 0.00 0.00 4.63
8092 10395 1.215140 AGTCTAGCTACTCCCTCCGT 58.785 55.000 0.00 0.00 0.00 4.69
8093 10396 2.406559 AGTCTAGCTACTCCCTCCGTA 58.593 52.381 0.00 0.00 0.00 4.02
8094 10397 2.776536 AGTCTAGCTACTCCCTCCGTAA 59.223 50.000 0.00 0.00 0.00 3.18
8095 10398 3.201708 AGTCTAGCTACTCCCTCCGTAAA 59.798 47.826 0.00 0.00 0.00 2.01
8096 10399 3.314913 GTCTAGCTACTCCCTCCGTAAAC 59.685 52.174 0.00 0.00 0.00 2.01
8097 10400 2.528673 AGCTACTCCCTCCGTAAACT 57.471 50.000 0.00 0.00 0.00 2.66
8098 10401 3.659183 AGCTACTCCCTCCGTAAACTA 57.341 47.619 0.00 0.00 0.00 2.24
8099 10402 3.973425 AGCTACTCCCTCCGTAAACTAA 58.027 45.455 0.00 0.00 0.00 2.24
8100 10403 4.544683 AGCTACTCCCTCCGTAAACTAAT 58.455 43.478 0.00 0.00 0.00 1.73
8101 10404 5.699143 AGCTACTCCCTCCGTAAACTAATA 58.301 41.667 0.00 0.00 0.00 0.98
8102 10405 6.313324 AGCTACTCCCTCCGTAAACTAATAT 58.687 40.000 0.00 0.00 0.00 1.28
8103 10406 7.465116 AGCTACTCCCTCCGTAAACTAATATA 58.535 38.462 0.00 0.00 0.00 0.86
8104 10407 7.946776 AGCTACTCCCTCCGTAAACTAATATAA 59.053 37.037 0.00 0.00 0.00 0.98
8105 10408 8.242739 GCTACTCCCTCCGTAAACTAATATAAG 58.757 40.741 0.00 0.00 0.00 1.73
8106 10409 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
8107 10410 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
8108 10411 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
8109 10412 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
8110 10413 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
8111 10414 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
8112 10415 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
8113 10416 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
8114 10417 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
8115 10418 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
8129 10432 8.635877 AGAGCGTTTAGATCACTACTTTAATG 57.364 34.615 0.00 0.00 37.82 1.90
8130 10433 8.467598 AGAGCGTTTAGATCACTACTTTAATGA 58.532 33.333 0.00 0.00 37.82 2.57
8131 10434 9.250624 GAGCGTTTAGATCACTACTTTAATGAT 57.749 33.333 0.00 0.00 35.77 2.45
8132 10435 9.250624 AGCGTTTAGATCACTACTTTAATGATC 57.749 33.333 7.60 7.60 46.04 2.92
8229 10532 2.301870 ACCTATCGGCTTCTTCACAACA 59.698 45.455 0.00 0.00 0.00 3.33
8293 10596 3.608796 TCCATCGCTGTTCATCAAATCA 58.391 40.909 0.00 0.00 0.00 2.57
8362 10665 6.151648 GTCTGGATTGGATCAAATTTGTCTGA 59.848 38.462 17.47 0.00 0.00 3.27
8375 10678 0.679505 TGTCTGAACCGGTCTGGAAG 59.320 55.000 8.04 1.24 42.00 3.46
8464 10767 3.134442 GGATCTCTCTGTTTCATGGCTCT 59.866 47.826 0.00 0.00 0.00 4.09
8505 10808 5.220381 CGGATCAGCGTTTCTAAATAGCTA 58.780 41.667 0.00 0.00 34.55 3.32
8511 10814 8.718102 TCAGCGTTTCTAAATAGCTAAAGATT 57.282 30.769 0.00 0.00 34.55 2.40
8536 10839 8.062065 TCATAACTTCAATTAGGCCGAAATTT 57.938 30.769 14.35 0.00 0.00 1.82
8537 10840 7.973388 TCATAACTTCAATTAGGCCGAAATTTG 59.027 33.333 14.35 10.14 0.00 2.32
8541 10844 7.213678 ACTTCAATTAGGCCGAAATTTGAAAA 58.786 30.769 20.75 7.21 0.00 2.29
8543 10846 6.754193 TCAATTAGGCCGAAATTTGAAAAGT 58.246 32.000 14.35 0.00 0.00 2.66
8545 10848 7.713073 TCAATTAGGCCGAAATTTGAAAAGTTT 59.287 29.630 14.35 0.00 38.53 2.66
8575 10881 6.161855 TGATATTGTAGGATCGTTCTTGCT 57.838 37.500 0.00 0.00 0.00 3.91
8611 10917 2.416432 GCCGACTTACCGAGCCTCT 61.416 63.158 0.00 0.00 0.00 3.69
8615 10921 1.377536 GACTTACCGAGCCTCTACGT 58.622 55.000 0.00 0.00 0.00 3.57
8616 10922 1.063764 GACTTACCGAGCCTCTACGTG 59.936 57.143 0.00 0.00 0.00 4.49
8663 10969 2.113139 CACTTGGTGCGTCCCCTT 59.887 61.111 0.00 0.00 34.77 3.95
8909 11215 0.456221 CTAGTCTCGTTGGCCATCGT 59.544 55.000 29.95 16.80 0.00 3.73
9031 11337 0.836606 TCAACACAGTCCTTGCCTCA 59.163 50.000 0.00 0.00 0.00 3.86
9084 11390 1.506493 GCGGTAGCAATCTCCATCAG 58.494 55.000 0.00 0.00 44.35 2.90
9125 11431 9.553064 AAATATCTGAGTGACCAAGCTTTATAG 57.447 33.333 0.00 0.00 0.00 1.31
9132 11438 7.665559 TGAGTGACCAAGCTTTATAGTCAAATT 59.334 33.333 15.96 8.26 39.04 1.82
9202 11542 1.140652 TGCACAGTGACATTCTCCACA 59.859 47.619 4.15 0.00 35.84 4.17
9205 11545 3.304257 GCACAGTGACATTCTCCACAAAG 60.304 47.826 4.15 0.00 35.84 2.77
9222 11562 6.091577 TCCACAAAGTTATGCAATGTAGTACG 59.908 38.462 0.00 0.00 0.00 3.67
9261 11601 1.004044 ACCCAAGATGGTGAAGAGCAG 59.996 52.381 0.00 0.00 37.20 4.24
9273 11613 3.006967 GTGAAGAGCAGGAACCTAGTCAA 59.993 47.826 0.00 0.00 0.00 3.18
9279 11619 4.833390 AGCAGGAACCTAGTCAACATAAC 58.167 43.478 0.00 0.00 0.00 1.89
9280 11620 3.617263 GCAGGAACCTAGTCAACATAACG 59.383 47.826 0.00 0.00 0.00 3.18
9369 11745 5.842328 TGAAAAGGAGGTAGAAGTAGAACCA 59.158 40.000 0.00 0.00 35.64 3.67
9379 11755 5.353394 AGAAGTAGAACCACAAGTTGACA 57.647 39.130 10.54 0.00 39.40 3.58
9398 11774 9.159254 AGTTGACATATATGATCCACCTTCTAA 57.841 33.333 19.63 0.00 0.00 2.10
9444 11820 6.799512 AGATTATGTTGCTAGAAAACATGGC 58.200 36.000 23.97 16.28 45.47 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
317 322 5.241728 GCTCTTTTTGTATGGAACTGGAACT 59.758 40.000 0.00 0.00 0.00 3.01
671 685 0.548510 GACTGGAGCTAATTGGCCCT 59.451 55.000 10.54 0.00 0.00 5.19
765 779 1.152881 AGGCCGATTGGATTCCAGC 60.153 57.895 1.98 5.83 37.49 4.85
1517 1544 4.735369 TGGGAGAAGGAAAAATACAAGCA 58.265 39.130 0.00 0.00 0.00 3.91
1529 1556 1.686428 CGACCTCAGATGGGAGAAGGA 60.686 57.143 0.00 0.00 37.05 3.36
1556 1583 9.948964 ATATATAGCTGAGCACATCAATTTACA 57.051 29.630 7.39 0.00 37.52 2.41
1559 1586 9.736414 AGAATATATAGCTGAGCACATCAATTT 57.264 29.630 7.39 0.00 37.52 1.82
1849 1878 1.779061 AATGCAACCACTCCTCCCGT 61.779 55.000 0.00 0.00 0.00 5.28
1882 1911 1.445582 GACGAATCCCGCGACAAGT 60.446 57.895 8.23 0.00 43.32 3.16
1994 2023 2.224499 ACATGGCGGCAAAAGGAAATTT 60.224 40.909 18.31 0.00 0.00 1.82
2286 2315 2.717639 AACACCCATCATGCTACTCC 57.282 50.000 0.00 0.00 0.00 3.85
2395 2424 6.292488 GCTGGACTTTCACATGAAACATTTTG 60.292 38.462 0.00 0.00 38.94 2.44
2689 2720 5.763204 GGTTAGGTGAAGTGAAGATGAACAA 59.237 40.000 0.00 0.00 0.00 2.83
2692 2723 5.560722 TGGTTAGGTGAAGTGAAGATGAA 57.439 39.130 0.00 0.00 0.00 2.57
3141 3173 6.639632 AGTATAGGCATGGCATTTTTACAG 57.360 37.500 22.64 0.00 0.00 2.74
3151 3183 3.274288 GGCAGATAAGTATAGGCATGGC 58.726 50.000 12.14 12.14 0.00 4.40
3434 3466 6.544928 TCAGAAGAGCATGTCTGGTTATTA 57.455 37.500 10.26 0.00 41.38 0.98
3435 3467 5.426689 TCAGAAGAGCATGTCTGGTTATT 57.573 39.130 10.26 0.00 41.38 1.40
3481 3513 3.685139 TGTCTTGAGTGCCTCCTAAAG 57.315 47.619 0.50 0.00 0.00 1.85
3669 3701 7.710907 TCTTCAAATATCTCTTCAACCATACCG 59.289 37.037 0.00 0.00 0.00 4.02
3840 3880 5.906113 TGTGTTTAGGACATTTGTGTGTT 57.094 34.783 0.00 0.00 41.10 3.32
4119 4234 8.581578 GGTCAATACTGGAACCTAAATTTTCAA 58.418 33.333 0.00 0.00 0.00 2.69
4276 4391 5.987019 ACCTATATTAAAGGCCCACTTGA 57.013 39.130 0.00 0.00 39.96 3.02
4352 4467 5.882557 AGCATACGAATCAATGGATTATCCC 59.117 40.000 8.98 0.00 43.69 3.85
4459 4575 3.436180 GGAGGGAGTAGAAAGATCGGGTA 60.436 52.174 0.00 0.00 0.00 3.69
4460 4576 2.668625 GAGGGAGTAGAAAGATCGGGT 58.331 52.381 0.00 0.00 0.00 5.28
4474 4590 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4502 5822 7.864108 TGTGGTGACCATTTGAAATATCTAG 57.136 36.000 7.94 0.00 35.28 2.43
4507 5827 5.355630 CCGTATGTGGTGACCATTTGAAATA 59.644 40.000 7.94 0.00 35.28 1.40
4573 5894 5.254115 TCAGATGGTGACTATATACGGAGG 58.746 45.833 0.00 0.00 0.00 4.30
4582 5903 7.496346 TTTAGAGGTTTCAGATGGTGACTAT 57.504 36.000 0.00 0.00 33.71 2.12
4605 5926 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4622 5943 5.645624 GTTTAAGTACTACTCCCTCCGTTC 58.354 45.833 0.00 0.00 0.00 3.95
4626 5947 4.676459 GCACGTTTAAGTACTACTCCCTCC 60.676 50.000 0.00 0.00 0.00 4.30
4877 6713 9.003112 CAGAGATTTAACAAAATTATGACAGCG 57.997 33.333 0.00 0.00 0.00 5.18
4918 6754 1.202867 TGTACATGCACAGGAGGCAAA 60.203 47.619 0.00 0.00 45.60 3.68
5000 6836 7.817478 GGAAACCGGAATTTACATTCAAATTCT 59.183 33.333 9.46 2.11 46.81 2.40
5064 6900 1.616865 GTGGGCCTTCAGTTTAAACCC 59.383 52.381 14.72 7.69 36.36 4.11
5100 6936 8.019669 CACAATCTGAACACTGGAAAGAAATAG 58.980 37.037 0.00 0.00 0.00 1.73
5252 7088 5.548181 AGGGCTACTAGCAGGTTAATAAC 57.452 43.478 10.27 0.00 44.75 1.89
5254 7090 7.867160 AAATAGGGCTACTAGCAGGTTAATA 57.133 36.000 10.27 0.00 44.75 0.98
5355 7192 2.224523 TGAAACGCAGGAGGAGTGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
5455 7292 0.827368 GTGGTGGGGCAGTTTTCAAA 59.173 50.000 0.00 0.00 0.00 2.69
5834 7747 0.887387 GTTTGCGCAAGGACCTGGTA 60.887 55.000 23.68 1.59 37.48 3.25
5949 7862 1.410517 TCTATCAAGAGCTGAAGCCGG 59.589 52.381 0.00 0.00 43.38 6.13
6071 7984 3.787634 CGATGCCAATTCAATTGTTCTCG 59.212 43.478 9.31 9.49 38.59 4.04
6073 7986 3.194116 AGCGATGCCAATTCAATTGTTCT 59.806 39.130 9.31 0.00 38.59 3.01
6112 8025 8.511321 CATTTAATTACAAGTTGTGTGAGCCTA 58.489 33.333 18.90 0.00 41.89 3.93
6449 8362 8.464770 TTGTAATTCAATGTGCAAATTAGCTC 57.535 30.769 0.65 0.00 34.99 4.09
6528 8441 2.024414 GCCACAAGTTCCTGTTCAAGT 58.976 47.619 0.00 0.00 0.00 3.16
6529 8442 2.033801 CAGCCACAAGTTCCTGTTCAAG 59.966 50.000 0.00 0.00 0.00 3.02
6530 8443 2.023673 CAGCCACAAGTTCCTGTTCAA 58.976 47.619 0.00 0.00 0.00 2.69
6531 8444 1.211703 TCAGCCACAAGTTCCTGTTCA 59.788 47.619 0.00 0.00 0.00 3.18
6569 8482 1.181098 AAGCGCCATTTGCCAACTCT 61.181 50.000 2.29 0.00 36.24 3.24
6578 8491 1.514087 CAGCCATCAAGCGCCATTT 59.486 52.632 2.29 0.00 38.01 2.32
6581 8494 4.032452 TCCAGCCATCAAGCGCCA 62.032 61.111 2.29 0.00 38.01 5.69
6679 8592 0.104725 AAAGCCAACCCATCCCCAAA 60.105 50.000 0.00 0.00 0.00 3.28
6686 8599 1.185315 CGAATCCAAAGCCAACCCAT 58.815 50.000 0.00 0.00 0.00 4.00
6687 8600 0.897863 CCGAATCCAAAGCCAACCCA 60.898 55.000 0.00 0.00 0.00 4.51
6742 8655 4.275781 CCCCCTCTCTCTCTCTGC 57.724 66.667 0.00 0.00 0.00 4.26
6760 8673 4.179599 CTCCCTCCCTCCCTCCCC 62.180 77.778 0.00 0.00 0.00 4.81
6761 8674 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
6762 8675 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
6763 8676 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
6764 8677 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
6765 8678 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
6766 8679 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
6767 8680 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
6768 8681 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
6769 8682 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
6770 8683 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
6771 8684 4.179599 CCCCTCCCTCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
6772 8685 4.761304 TCCCCTCCCTCCCTCCCT 62.761 72.222 0.00 0.00 0.00 4.20
6773 8686 3.707189 TTCCCCTCCCTCCCTCCC 61.707 72.222 0.00 0.00 0.00 4.30
6774 8687 2.367107 GTTCCCCTCCCTCCCTCC 60.367 72.222 0.00 0.00 0.00 4.30
6775 8688 2.367107 GGTTCCCCTCCCTCCCTC 60.367 72.222 0.00 0.00 0.00 4.30
6776 8689 2.370257 TTTGGTTCCCCTCCCTCCCT 62.370 60.000 0.00 0.00 0.00 4.20
6777 8690 1.855451 TTTGGTTCCCCTCCCTCCC 60.855 63.158 0.00 0.00 0.00 4.30
6778 8691 0.845102 TCTTTGGTTCCCCTCCCTCC 60.845 60.000 0.00 0.00 0.00 4.30
6779 8692 1.073098 TTCTTTGGTTCCCCTCCCTC 58.927 55.000 0.00 0.00 0.00 4.30
6780 8693 1.641192 GATTCTTTGGTTCCCCTCCCT 59.359 52.381 0.00 0.00 0.00 4.20
6781 8694 1.342076 GGATTCTTTGGTTCCCCTCCC 60.342 57.143 0.00 0.00 0.00 4.30
6782 8695 1.342076 GGGATTCTTTGGTTCCCCTCC 60.342 57.143 0.00 0.00 42.88 4.30
6793 9012 6.062258 TCGGTTCATTAAGAGGGATTCTTT 57.938 37.500 0.00 0.00 43.68 2.52
6823 9042 2.158900 ACACATCCGGCTCATTAAGAGG 60.159 50.000 0.00 0.00 44.86 3.69
6883 9102 1.467920 CTCCCCCATCAAAGCACTTC 58.532 55.000 0.00 0.00 0.00 3.01
6913 9132 5.359194 TCCTCATGAACATTAAGAGGGAC 57.641 43.478 15.04 0.00 44.65 4.46
6972 9191 1.603455 ATCTGTGTTGCAACGGGGG 60.603 57.895 23.79 13.73 0.00 5.40
6985 9204 9.953565 TTTAAACTACTAGGTAATTGCATCTGT 57.046 29.630 0.00 0.00 0.00 3.41
7504 9785 0.605319 TGCAGCCTAAACGACCCAAG 60.605 55.000 0.00 0.00 0.00 3.61
7578 9863 5.139727 TGTTGGTTCAAGATCACAAATCCT 58.860 37.500 0.00 0.00 0.00 3.24
7580 9865 4.919754 GCTGTTGGTTCAAGATCACAAATC 59.080 41.667 0.00 0.00 0.00 2.17
7581 9866 4.341806 TGCTGTTGGTTCAAGATCACAAAT 59.658 37.500 0.00 0.00 0.00 2.32
7584 9869 2.880268 CTGCTGTTGGTTCAAGATCACA 59.120 45.455 0.00 0.00 0.00 3.58
7585 9870 2.351157 GCTGCTGTTGGTTCAAGATCAC 60.351 50.000 0.00 0.00 0.00 3.06
7586 9871 1.881973 GCTGCTGTTGGTTCAAGATCA 59.118 47.619 0.00 0.00 0.00 2.92
7587 9872 2.157738 AGCTGCTGTTGGTTCAAGATC 58.842 47.619 0.00 0.00 0.00 2.75
7669 9971 7.332182 AGGACATAGAAAAACGTGAGAGATTTC 59.668 37.037 0.00 0.00 33.80 2.17
7796 10098 3.197766 AGCTGACATTCACCGGATAAGAA 59.802 43.478 9.46 7.18 0.00 2.52
7921 10223 1.755179 ATCACGGAAAATCCTGGCAG 58.245 50.000 7.75 7.75 33.30 4.85
7955 10257 8.597662 GCAATTTATATTGTTGCAAGGATGAT 57.402 30.769 0.00 0.00 45.57 2.45
8068 10371 3.372241 GGAGGGAGTAGCTAGACTTGAGT 60.372 52.174 0.00 0.00 0.00 3.41
8085 10388 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
8086 10389 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
8087 10390 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
8088 10391 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
8089 10392 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
8103 10406 9.088512 CATTAAAGTAGTGATCTAAACGCTCTT 57.911 33.333 0.00 0.00 0.00 2.85
8104 10407 8.467598 TCATTAAAGTAGTGATCTAAACGCTCT 58.532 33.333 0.00 0.00 0.00 4.09
8105 10408 8.630278 TCATTAAAGTAGTGATCTAAACGCTC 57.370 34.615 0.00 0.00 0.00 5.03
8106 10409 9.250624 GATCATTAAAGTAGTGATCTAAACGCT 57.749 33.333 11.46 0.00 44.08 5.07
8185 10488 2.231478 TCCCTGCGTTTTCACACAAAAA 59.769 40.909 0.00 0.00 0.00 1.94
8186 10489 1.819288 TCCCTGCGTTTTCACACAAAA 59.181 42.857 0.00 0.00 0.00 2.44
8190 10493 1.535226 GGTTTCCCTGCGTTTTCACAC 60.535 52.381 0.00 0.00 0.00 3.82
8195 10498 2.081462 CGATAGGTTTCCCTGCGTTTT 58.919 47.619 0.00 0.00 42.67 2.43
8229 10532 3.296709 GACACGTGGGTCTCCGCAT 62.297 63.158 21.57 0.00 43.53 4.73
8293 10596 4.261801 CCACGGTTTGAGACATTAAGGAT 58.738 43.478 0.00 0.00 0.00 3.24
8362 10665 1.420430 TTCAGACTTCCAGACCGGTT 58.580 50.000 9.42 0.00 35.57 4.44
8375 10678 2.933906 TCCGGTTTATGCGATTTCAGAC 59.066 45.455 0.00 0.00 0.00 3.51
8483 10786 7.438459 TCTTTAGCTATTTAGAAACGCTGATCC 59.562 37.037 0.00 0.00 32.48 3.36
8505 10808 7.556275 TCGGCCTAATTGAAGTTATGAATCTTT 59.444 33.333 0.00 0.00 0.00 2.52
8511 10814 7.639113 AATTTCGGCCTAATTGAAGTTATGA 57.361 32.000 10.80 0.00 0.00 2.15
8553 10856 5.986135 ACAGCAAGAACGATCCTACAATATC 59.014 40.000 0.00 0.00 0.00 1.63
8555 10858 5.109210 CACAGCAAGAACGATCCTACAATA 58.891 41.667 0.00 0.00 0.00 1.90
8556 10859 3.935203 CACAGCAAGAACGATCCTACAAT 59.065 43.478 0.00 0.00 0.00 2.71
8557 10860 3.325870 CACAGCAAGAACGATCCTACAA 58.674 45.455 0.00 0.00 0.00 2.41
8559 10862 2.094182 TCCACAGCAAGAACGATCCTAC 60.094 50.000 0.00 0.00 0.00 3.18
8575 10881 1.548357 GCTGAGGCTCTCCTTCCACA 61.548 60.000 16.72 0.00 44.46 4.17
8611 10917 2.217745 TCATGTGGTGGGGCACGTA 61.218 57.895 0.00 0.00 34.83 3.57
8615 10921 3.181530 TGGTCATGTGGTGGGGCA 61.182 61.111 0.00 0.00 0.00 5.36
8616 10922 2.676471 GTGGTCATGTGGTGGGGC 60.676 66.667 0.00 0.00 0.00 5.80
8738 11044 8.768955 GTTTTTGTTTTTCAGGCCAAAAATTTT 58.231 25.926 14.72 0.00 44.09 1.82
8923 11229 0.597637 GTCAGTGACGGTGTCTGTGG 60.598 60.000 7.68 0.00 33.15 4.17
8927 11233 0.603569 GGATGTCAGTGACGGTGTCT 59.396 55.000 18.17 0.00 34.95 3.41
8932 11238 2.169832 AAGTTGGATGTCAGTGACGG 57.830 50.000 18.17 0.00 34.95 4.79
9031 11337 5.510520 GGCGAAGAGGAAGATCTAATCATGT 60.511 44.000 0.00 0.00 0.00 3.21
9068 11374 2.748605 CCGACTGATGGAGATTGCTAC 58.251 52.381 0.00 0.00 0.00 3.58
9084 11390 6.285990 TCAGATATTTTTACCCTAAGCCGAC 58.714 40.000 0.00 0.00 0.00 4.79
9125 11431 6.963049 AGGTGTCAAGTATCGTAATTTGAC 57.037 37.500 15.73 15.73 45.88 3.18
9132 11438 4.021807 TCAAGCAAGGTGTCAAGTATCGTA 60.022 41.667 0.00 0.00 0.00 3.43
9202 11542 7.900782 AAGACGTACTACATTGCATAACTTT 57.099 32.000 0.00 0.00 0.00 2.66
9205 11545 7.488471 AGAGAAAGACGTACTACATTGCATAAC 59.512 37.037 0.00 0.00 0.00 1.89
9222 11562 3.438434 GGGTTTCAGCATCAGAGAAAGAC 59.562 47.826 0.00 0.00 32.48 3.01
9261 11601 9.754382 TTATTATCGTTATGTTGACTAGGTTCC 57.246 33.333 0.00 0.00 0.00 3.62
9300 11640 8.454106 GGTGGAGCATCATTGTCAATATAATAC 58.546 37.037 0.00 0.00 36.25 1.89
9301 11641 8.385491 AGGTGGAGCATCATTGTCAATATAATA 58.615 33.333 0.00 0.00 36.25 0.98
9304 11644 6.191657 AGGTGGAGCATCATTGTCAATATA 57.808 37.500 0.00 0.00 36.25 0.86
9369 11745 7.141758 AGGTGGATCATATATGTCAACTTGT 57.858 36.000 12.42 1.69 0.00 3.16
9444 11820 2.465813 ACCCATGGTTCTCTCTCTCTG 58.534 52.381 11.73 0.00 27.29 3.35
9512 11896 8.761575 TTCAACAAATTGATTAAATGCCTCTC 57.238 30.769 0.00 0.00 44.36 3.20


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

AutoCloner maintained by Alex Coulton.