Multiple sequence alignment - TraesCS3A01G511200

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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 TraesCS3A01G511200 chr3A 100.000 4198 0 0 1 4198 730885929 730890126 0.000000e+00 7753.0
1 TraesCS3A01G511200 chr3A 80.657 1370 234 26 2064 3415 732043537 732042181 0.000000e+00 1033.0
2 TraesCS3A01G511200 chr3A 84.196 367 52 2 1 361 405792979 405792613 6.680000e-93 351.0
3 TraesCS3A01G511200 chr3A 82.192 365 61 2 1 361 743484892 743485256 1.130000e-80 311.0
4 TraesCS3A01G511200 chr3A 88.163 245 25 3 1285 1528 576278500 576278259 5.310000e-74 289.0
5 TraesCS3A01G511200 chr3A 83.333 252 40 1 1674 1925 730952478 730952229 9.080000e-57 231.0
6 TraesCS3A01G511200 chr3A 93.684 95 6 0 508 602 730880082 730880176 4.380000e-30 143.0
7 TraesCS3A01G511200 chr3A 83.333 156 12 7 342 486 730877630 730877782 9.470000e-27 132.0
8 TraesCS3A01G511200 chr3A 79.710 207 22 12 2428 2622 731836222 731836024 9.470000e-27 132.0
9 TraesCS3A01G511200 chr3D 93.221 2552 141 14 1649 4196 602216318 602213795 0.000000e+00 3725.0
10 TraesCS3A01G511200 chr3D 81.787 1455 196 30 2085 3519 602241196 602239791 0.000000e+00 1155.0
11 TraesCS3A01G511200 chr3D 81.428 1373 232 19 2057 3415 602275336 602273973 0.000000e+00 1101.0
12 TraesCS3A01G511200 chr3D 87.696 382 38 5 1 375 602219894 602219515 1.790000e-118 436.0
13 TraesCS3A01G511200 chr3D 86.216 399 52 3 1632 2029 602248860 602248464 3.000000e-116 429.0
14 TraesCS3A01G511200 chr3D 93.750 256 14 2 1043 1297 602217605 602217351 2.370000e-102 383.0
15 TraesCS3A01G511200 chr3D 88.358 335 16 12 716 1050 602219113 602218802 8.520000e-102 381.0
16 TraesCS3A01G511200 chr3D 92.827 237 14 3 407 642 602219339 602219105 1.450000e-89 340.0
17 TraesCS3A01G511200 chr3D 87.843 255 26 4 1285 1538 346851198 346851448 1.140000e-75 294.0
18 TraesCS3A01G511200 chr3D 90.845 142 10 2 1519 1657 602217265 602217124 1.990000e-43 187.0
19 TraesCS3A01G511200 chr3D 82.857 175 12 7 717 891 602221328 602221172 1.570000e-29 141.0
20 TraesCS3A01G511200 chr3D 76.289 194 44 2 158 350 19054187 19054379 7.430000e-18 102.0
21 TraesCS3A01G511200 chr3D 77.397 146 10 10 892 1036 602249339 602249216 9.740000e-07 65.8
22 TraesCS3A01G511200 chr3B 92.228 2496 154 11 1712 4198 809233431 809235895 0.000000e+00 3498.0
23 TraesCS3A01G511200 chr3B 93.879 2173 122 5 1553 3720 809363400 809361234 0.000000e+00 3265.0
24 TraesCS3A01G511200 chr3B 82.955 1936 252 38 1632 3520 809452658 809450754 0.000000e+00 1676.0
25 TraesCS3A01G511200 chr3B 81.046 1377 230 25 2057 3415 809540452 809539089 0.000000e+00 1068.0
26 TraesCS3A01G511200 chr3B 86.387 573 61 9 719 1277 809363971 809363402 9.980000e-171 610.0
27 TraesCS3A01G511200 chr3B 84.235 425 36 8 3714 4136 809351191 809350796 6.580000e-103 385.0
28 TraesCS3A01G511200 chr3B 89.431 246 23 3 1285 1529 793387695 793387452 1.470000e-79 307.0
29 TraesCS3A01G511200 chr3B 81.868 364 60 4 1 359 3023521 3023159 6.820000e-78 302.0
30 TraesCS3A01G511200 chr3B 94.505 182 9 1 1097 1278 809233233 809233413 3.200000e-71 279.0
31 TraesCS3A01G511200 chr3B 74.606 508 97 20 2588 3079 809457841 809457350 1.190000e-45 195.0
32 TraesCS3A01G511200 chr1B 85.054 368 48 3 1 361 584756356 584756723 6.630000e-98 368.0
33 TraesCS3A01G511200 chr1B 83.420 386 57 3 1 379 16918304 16918689 6.680000e-93 351.0
34 TraesCS3A01G511200 chr1B 83.967 368 52 3 1 361 3287484 3287851 3.110000e-91 346.0
35 TraesCS3A01G511200 chr6B 88.980 245 23 3 1285 1528 523343637 523343878 2.450000e-77 300.0
36 TraesCS3A01G511200 chr6B 87.854 247 26 3 1284 1529 98854534 98854291 1.910000e-73 287.0
37 TraesCS3A01G511200 chr5A 90.393 229 20 2 1285 1513 649599108 649598882 2.450000e-77 300.0
38 TraesCS3A01G511200 chr5A 79.019 367 65 9 1 359 516673067 516672705 1.510000e-59 241.0
39 TraesCS3A01G511200 chr7D 88.306 248 25 3 1285 1531 34602919 34602675 1.140000e-75 294.0
40 TraesCS3A01G511200 chr5B 88.048 251 24 5 1285 1533 347274287 347274041 4.110000e-75 292.0
41 TraesCS3A01G511200 chr1A 87.649 251 26 4 1283 1531 262937742 262937495 1.910000e-73 287.0
42 TraesCS3A01G511200 chr6A 95.455 44 2 0 676 719 572335410 572335367 2.090000e-08 71.3


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 TraesCS3A01G511200 chr3A 730885929 730890126 4197 False 7753.0 7753 100.000000 1 4198 1 chr3A.!!$F1 4197
1 TraesCS3A01G511200 chr3A 732042181 732043537 1356 True 1033.0 1033 80.657000 2064 3415 1 chr3A.!!$R5 1351
2 TraesCS3A01G511200 chr3D 602239791 602241196 1405 True 1155.0 1155 81.787000 2085 3519 1 chr3D.!!$R1 1434
3 TraesCS3A01G511200 chr3D 602273973 602275336 1363 True 1101.0 1101 81.428000 2057 3415 1 chr3D.!!$R2 1358
4 TraesCS3A01G511200 chr3D 602213795 602221328 7533 True 799.0 3725 89.936286 1 4196 7 chr3D.!!$R3 4195
5 TraesCS3A01G511200 chr3D 602248464 602249339 875 True 247.4 429 81.806500 892 2029 2 chr3D.!!$R4 1137
6 TraesCS3A01G511200 chr3B 809361234 809363971 2737 True 1937.5 3265 90.133000 719 3720 2 chr3B.!!$R7 3001
7 TraesCS3A01G511200 chr3B 809233233 809235895 2662 False 1888.5 3498 93.366500 1097 4198 2 chr3B.!!$F1 3101
8 TraesCS3A01G511200 chr3B 809450754 809452658 1904 True 1676.0 1676 82.955000 1632 3520 1 chr3B.!!$R4 1888
9 TraesCS3A01G511200 chr3B 809539089 809540452 1363 True 1068.0 1068 81.046000 2057 3415 1 chr3B.!!$R6 1358

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
199 1637 0.106708 AGAGTGCGTGGAAGAAAGCA 59.893 50.0 0.0 0.0 37.26 3.91 F
1445 4271 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.0 0.0 0.0 34.43 6.53 F
2166 5830 0.716108 GTCGAGTGCGTCAAGATTGG 59.284 55.0 0.0 0.0 38.98 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 5303 0.177141 CCCTGCCAATGCCAAATCAG 59.823 55.0 0.0 0.0 36.33 2.90 R
2311 5978 0.472471 TGAACCACCAAGGGACACTC 59.528 55.0 0.0 0.0 43.89 3.51 R
3462 7170 0.320683 GAAACATTTGCACTGGGGGC 60.321 55.0 0.0 0.0 0.00 5.80 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 1458 1.003851 GCAGCTTAAATCGCGGTGTA 58.996 50.000 6.13 0.00 0.00 2.90
30 1465 2.396590 AAATCGCGGTGTATCAAGGT 57.603 45.000 6.13 0.00 0.00 3.50
33 1468 1.175654 TCGCGGTGTATCAAGGTGTA 58.824 50.000 6.13 0.00 0.00 2.90
43 1478 4.344102 TGTATCAAGGTGTATGCCTAGGAC 59.656 45.833 14.75 1.98 38.03 3.85
95 1533 1.151777 CGAGTGGTGCTCAACGTTGT 61.152 55.000 26.47 5.82 44.33 3.32
115 1553 5.707242 TGTCGACAAGTCTACAATCTCTT 57.293 39.130 17.62 0.00 33.22 2.85
120 1558 7.594015 GTCGACAAGTCTACAATCTCTTTGTTA 59.406 37.037 11.55 0.00 46.51 2.41
174 1612 7.963532 AGAACACCGATACAAGGTATCATTAT 58.036 34.615 14.65 1.17 40.59 1.28
176 1614 6.387465 ACACCGATACAAGGTATCATTATCG 58.613 40.000 14.65 0.00 40.59 2.92
178 1616 7.093902 ACACCGATACAAGGTATCATTATCGAT 60.094 37.037 14.65 2.16 42.59 3.59
180 1618 7.122204 ACCGATACAAGGTATCATTATCGATGA 59.878 37.037 8.54 0.00 42.59 2.92
189 1627 3.632189 TCATTATCGATGAGAGTGCGTG 58.368 45.455 8.54 0.00 39.83 5.34
194 1632 0.171231 CGATGAGAGTGCGTGGAAGA 59.829 55.000 0.00 0.00 0.00 2.87
195 1633 1.402852 CGATGAGAGTGCGTGGAAGAA 60.403 52.381 0.00 0.00 0.00 2.52
196 1634 2.688507 GATGAGAGTGCGTGGAAGAAA 58.311 47.619 0.00 0.00 0.00 2.52
197 1635 2.154854 TGAGAGTGCGTGGAAGAAAG 57.845 50.000 0.00 0.00 0.00 2.62
198 1636 0.793250 GAGAGTGCGTGGAAGAAAGC 59.207 55.000 0.00 0.00 0.00 3.51
199 1637 0.106708 AGAGTGCGTGGAAGAAAGCA 59.893 50.000 0.00 0.00 37.26 3.91
202 1640 1.748493 AGTGCGTGGAAGAAAGCAAAA 59.252 42.857 0.00 0.00 41.56 2.44
203 1641 2.362077 AGTGCGTGGAAGAAAGCAAAAT 59.638 40.909 0.00 0.00 41.56 1.82
204 1642 3.123050 GTGCGTGGAAGAAAGCAAAATT 58.877 40.909 0.00 0.00 41.56 1.82
205 1643 3.060339 GTGCGTGGAAGAAAGCAAAATTG 60.060 43.478 0.00 0.00 41.56 2.32
207 1645 3.182372 GCGTGGAAGAAAGCAAAATTGAC 59.818 43.478 0.00 0.00 0.00 3.18
232 1672 5.062528 TCAACTATGTTTGCACTGATGACA 58.937 37.500 0.00 0.00 0.00 3.58
239 1679 0.594602 TGCACTGATGACAAGCTTGC 59.405 50.000 26.27 18.37 0.00 4.01
240 1680 0.594602 GCACTGATGACAAGCTTGCA 59.405 50.000 26.27 23.01 0.00 4.08
247 1687 5.032327 TGATGACAAGCTTGCAGATATCT 57.968 39.130 26.27 8.88 0.00 1.98
251 1691 6.668541 TGACAAGCTTGCAGATATCTTAAC 57.331 37.500 26.27 0.00 0.00 2.01
252 1692 6.409704 TGACAAGCTTGCAGATATCTTAACT 58.590 36.000 26.27 0.95 0.00 2.24
270 1710 1.617357 ACTAGGTCTTTGGGACGACAC 59.383 52.381 0.00 0.00 45.35 3.67
271 1711 1.893801 CTAGGTCTTTGGGACGACACT 59.106 52.381 0.00 0.00 45.35 3.55
290 1730 3.308053 CACTAGTTCATGAAGATGTGGCG 59.692 47.826 8.80 0.00 0.00 5.69
306 1746 0.672401 GGCGAAGGATTGACGTCCAA 60.672 55.000 14.12 7.96 40.90 3.53
308 1748 1.939838 GCGAAGGATTGACGTCCAAGT 60.940 52.381 14.12 0.00 40.90 3.16
331 1771 3.824443 TGTGAAGTGAGGACATCGTCTTA 59.176 43.478 3.48 0.00 32.47 2.10
347 1787 3.558321 CGTCTTAAGGGGGTGATTGTTGA 60.558 47.826 1.85 0.00 0.00 3.18
358 1798 4.920927 GGGTGATTGTTGAAATTAACCACG 59.079 41.667 0.00 0.00 0.00 4.94
368 1808 9.275398 TGTTGAAATTAACCACGATTAGTAGTT 57.725 29.630 0.00 0.00 38.24 2.24
375 1815 8.931385 TTAACCACGATTAGTAGTTTATGTCC 57.069 34.615 0.00 0.00 36.20 4.02
376 1816 5.585390 ACCACGATTAGTAGTTTATGTCCG 58.415 41.667 0.00 0.00 0.00 4.79
379 1819 4.098349 ACGATTAGTAGTTTATGTCCGGCA 59.902 41.667 0.00 0.00 0.00 5.69
394 1844 1.067974 CCGGCATCAGTCACCGTATAA 59.932 52.381 0.00 0.00 45.49 0.98
400 1850 4.686554 GCATCAGTCACCGTATAAGATTCC 59.313 45.833 0.00 0.00 0.00 3.01
404 1854 7.450124 TCAGTCACCGTATAAGATTCCTATC 57.550 40.000 0.00 0.00 0.00 2.08
405 1855 7.002276 TCAGTCACCGTATAAGATTCCTATCA 58.998 38.462 0.00 0.00 32.95 2.15
469 2053 6.894735 TGTATCCCCTTGTAAGATTAACCA 57.105 37.500 0.00 0.00 0.00 3.67
476 2060 6.318900 CCCCTTGTAAGATTAACCAAGATCAC 59.681 42.308 0.00 0.00 37.14 3.06
483 2067 9.994432 GTAAGATTAACCAAGATCACATCAAAG 57.006 33.333 0.00 0.00 0.00 2.77
527 2111 2.213499 GGTCCTGTAGCCATCAAATCG 58.787 52.381 0.00 0.00 0.00 3.34
566 2150 1.077930 TGAGTAGCCGGCGACTAGT 60.078 57.895 37.44 20.49 32.22 2.57
593 2177 0.606096 TGGTACGTGCATGTGCTAGT 59.394 50.000 23.75 8.50 42.66 2.57
597 2181 3.243434 GGTACGTGCATGTGCTAGTATCT 60.243 47.826 23.75 0.00 42.66 1.98
603 2187 4.804139 GTGCATGTGCTAGTATCTTACGTT 59.196 41.667 6.55 0.00 42.66 3.99
606 2190 3.688272 TGTGCTAGTATCTTACGTTCGC 58.312 45.455 0.00 0.00 0.00 4.70
612 2196 4.346734 AGTATCTTACGTTCGCGAAGAA 57.653 40.909 24.13 15.33 44.71 2.52
645 2229 4.394439 GCTAGCTAGCTACTTCCTTTGT 57.606 45.455 33.71 0.00 45.62 2.83
646 2230 4.760878 GCTAGCTAGCTACTTCCTTTGTT 58.239 43.478 33.71 0.00 45.62 2.83
647 2231 5.179533 GCTAGCTAGCTACTTCCTTTGTTT 58.820 41.667 33.71 0.00 45.62 2.83
648 2232 5.292345 GCTAGCTAGCTACTTCCTTTGTTTC 59.708 44.000 33.71 3.16 45.62 2.78
649 2233 4.580868 AGCTAGCTACTTCCTTTGTTTCC 58.419 43.478 17.69 0.00 0.00 3.13
650 2234 4.287326 AGCTAGCTACTTCCTTTGTTTCCT 59.713 41.667 17.69 0.00 0.00 3.36
651 2235 5.004448 GCTAGCTACTTCCTTTGTTTCCTT 58.996 41.667 7.70 0.00 0.00 3.36
652 2236 5.473846 GCTAGCTACTTCCTTTGTTTCCTTT 59.526 40.000 7.70 0.00 0.00 3.11
653 2237 5.774498 AGCTACTTCCTTTGTTTCCTTTG 57.226 39.130 0.00 0.00 0.00 2.77
654 2238 5.201243 AGCTACTTCCTTTGTTTCCTTTGT 58.799 37.500 0.00 0.00 0.00 2.83
655 2239 5.656859 AGCTACTTCCTTTGTTTCCTTTGTT 59.343 36.000 0.00 0.00 0.00 2.83
656 2240 6.154534 AGCTACTTCCTTTGTTTCCTTTGTTT 59.845 34.615 0.00 0.00 0.00 2.83
657 2241 6.475727 GCTACTTCCTTTGTTTCCTTTGTTTC 59.524 38.462 0.00 0.00 0.00 2.78
658 2242 6.353404 ACTTCCTTTGTTTCCTTTGTTTCA 57.647 33.333 0.00 0.00 0.00 2.69
659 2243 6.764379 ACTTCCTTTGTTTCCTTTGTTTCAA 58.236 32.000 0.00 0.00 0.00 2.69
660 2244 7.220740 ACTTCCTTTGTTTCCTTTGTTTCAAA 58.779 30.769 0.00 0.00 0.00 2.69
661 2245 7.717436 ACTTCCTTTGTTTCCTTTGTTTCAAAA 59.283 29.630 0.00 0.00 0.00 2.44
662 2246 8.628630 TTCCTTTGTTTCCTTTGTTTCAAAAT 57.371 26.923 0.00 0.00 0.00 1.82
663 2247 9.726438 TTCCTTTGTTTCCTTTGTTTCAAAATA 57.274 25.926 0.00 0.00 0.00 1.40
664 2248 9.726438 TCCTTTGTTTCCTTTGTTTCAAAATAA 57.274 25.926 0.00 0.00 0.00 1.40
728 2312 3.219281 GGAGAGAGTAGCTTCCTGGTAG 58.781 54.545 0.00 0.00 0.00 3.18
737 2321 0.892755 CTTCCTGGTAGGTGCGTGTA 59.107 55.000 0.00 0.00 36.53 2.90
768 2352 6.701145 AGATTCGATCAGCTACTGAGTTAA 57.299 37.500 3.42 0.00 44.08 2.01
833 2417 1.375908 GGCCAGATCAACGACTGCA 60.376 57.895 0.00 0.00 33.40 4.41
836 2420 0.376152 CCAGATCAACGACTGCATGC 59.624 55.000 11.82 11.82 33.40 4.06
927 2537 0.769873 TAAACCCCACGCCCTTTACA 59.230 50.000 0.00 0.00 0.00 2.41
981 2601 9.377312 CTCTCTCGTATCTGATAATCATAGTCA 57.623 37.037 0.00 0.00 0.00 3.41
1212 4036 4.035102 GCCCACCACCTCCAGGAC 62.035 72.222 0.00 0.00 38.94 3.85
1280 4106 2.667481 CAGGCCACATGCAAATTTTACG 59.333 45.455 5.01 0.00 43.89 3.18
1281 4107 1.393196 GGCCACATGCAAATTTTACGC 59.607 47.619 0.00 0.00 43.89 4.42
1294 4120 1.927487 TTTACGCACTACTCCCTCCA 58.073 50.000 0.00 0.00 0.00 3.86
1297 4123 1.276622 ACGCACTACTCCCTCCATTT 58.723 50.000 0.00 0.00 0.00 2.32
1298 4124 1.628846 ACGCACTACTCCCTCCATTTT 59.371 47.619 0.00 0.00 0.00 1.82
1299 4125 2.280628 CGCACTACTCCCTCCATTTTC 58.719 52.381 0.00 0.00 0.00 2.29
1302 4128 4.079253 GCACTACTCCCTCCATTTTCAAA 58.921 43.478 0.00 0.00 0.00 2.69
1303 4129 4.522789 GCACTACTCCCTCCATTTTCAAAA 59.477 41.667 0.00 0.00 0.00 2.44
1304 4130 5.185828 GCACTACTCCCTCCATTTTCAAAAT 59.814 40.000 0.00 0.00 0.00 1.82
1305 4131 6.377146 GCACTACTCCCTCCATTTTCAAAATA 59.623 38.462 0.00 0.00 0.00 1.40
1307 4133 9.627123 CACTACTCCCTCCATTTTCAAAATATA 57.373 33.333 0.00 0.00 0.00 0.86
1311 4137 9.628500 ACTCCCTCCATTTTCAAAATATAGTAC 57.372 33.333 0.00 0.00 0.00 2.73
1312 4138 8.671384 TCCCTCCATTTTCAAAATATAGTACG 57.329 34.615 0.00 0.00 0.00 3.67
1313 4139 7.227910 TCCCTCCATTTTCAAAATATAGTACGC 59.772 37.037 0.00 0.00 0.00 4.42
1314 4140 7.228706 CCCTCCATTTTCAAAATATAGTACGCT 59.771 37.037 0.00 0.00 0.00 5.07
1315 4141 8.283291 CCTCCATTTTCAAAATATAGTACGCTC 58.717 37.037 0.00 0.00 0.00 5.03
1316 4142 7.847487 TCCATTTTCAAAATATAGTACGCTCG 58.153 34.615 0.00 0.00 0.00 5.03
1317 4143 6.573725 CCATTTTCAAAATATAGTACGCTCGC 59.426 38.462 0.00 0.00 0.00 5.03
1318 4144 4.941727 TTCAAAATATAGTACGCTCGCG 57.058 40.909 10.06 10.06 46.03 5.87
1342 4168 3.374042 TTTGAGGTCCAACTTTGACCA 57.626 42.857 13.24 0.00 41.22 4.02
1344 4170 4.715534 TTGAGGTCCAACTTTGACCATA 57.284 40.909 13.24 0.84 41.22 2.74
1345 4171 4.715534 TGAGGTCCAACTTTGACCATAA 57.284 40.909 13.24 0.00 41.22 1.90
1359 4185 9.840427 ACTTTGACCATAAATTTAATCAACGAG 57.160 29.630 21.04 17.31 0.00 4.18
1363 4189 7.011828 ACCATAAATTTAATCAACGAGACCG 57.988 36.000 1.21 0.00 42.50 4.79
1366 4192 7.011109 CCATAAATTTAATCAACGAGACCGACT 59.989 37.037 1.21 0.00 39.50 4.18
1367 4193 5.779806 AATTTAATCAACGAGACCGACTG 57.220 39.130 0.00 0.00 39.50 3.51
1368 4194 2.273370 TAATCAACGAGACCGACTGC 57.727 50.000 0.00 0.00 39.50 4.40
1370 4196 1.583495 ATCAACGAGACCGACTGCGA 61.583 55.000 0.00 0.00 40.82 5.10
1371 4197 2.081212 CAACGAGACCGACTGCGAC 61.081 63.158 0.00 0.00 40.82 5.19
1372 4198 3.590443 AACGAGACCGACTGCGACG 62.590 63.158 0.00 0.00 40.82 5.12
1380 4206 2.513159 CGACTGCGACGGAAGAAAA 58.487 52.632 0.00 0.00 40.82 2.29
1381 4207 0.856641 CGACTGCGACGGAAGAAAAA 59.143 50.000 0.00 0.00 40.82 1.94
1436 4262 7.566858 ACGAATTCACTGACATAATTTTTGC 57.433 32.000 6.22 0.00 0.00 3.68
1437 4263 7.370383 ACGAATTCACTGACATAATTTTTGCT 58.630 30.769 6.22 0.00 0.00 3.91
1438 4264 7.538678 ACGAATTCACTGACATAATTTTTGCTC 59.461 33.333 6.22 0.00 0.00 4.26
1439 4265 7.008628 CGAATTCACTGACATAATTTTTGCTCC 59.991 37.037 6.22 0.00 0.00 4.70
1440 4266 5.643379 TCACTGACATAATTTTTGCTCCC 57.357 39.130 0.00 0.00 0.00 4.30
1441 4267 4.155826 TCACTGACATAATTTTTGCTCCCG 59.844 41.667 0.00 0.00 0.00 5.14
1442 4268 3.119495 ACTGACATAATTTTTGCTCCCGC 60.119 43.478 0.00 0.00 0.00 6.13
1443 4269 2.165437 TGACATAATTTTTGCTCCCGCC 59.835 45.455 0.00 0.00 34.43 6.13
1444 4270 1.134175 ACATAATTTTTGCTCCCGCCG 59.866 47.619 0.00 0.00 34.43 6.46
1445 4271 0.102300 ATAATTTTTGCTCCCGCCGC 59.898 50.000 0.00 0.00 34.43 6.53
1446 4272 1.244697 TAATTTTTGCTCCCGCCGCA 61.245 50.000 0.00 0.00 35.22 5.69
1447 4273 2.490993 AATTTTTGCTCCCGCCGCAG 62.491 55.000 0.00 0.00 38.80 5.18
1448 4274 4.947147 TTTTGCTCCCGCCGCAGT 62.947 61.111 0.00 0.00 38.80 4.40
1460 4286 3.244105 CGCAGTCGGTCTTGTTGG 58.756 61.111 0.00 0.00 0.00 3.77
1461 4287 1.594293 CGCAGTCGGTCTTGTTGGT 60.594 57.895 0.00 0.00 0.00 3.67
1462 4288 1.157870 CGCAGTCGGTCTTGTTGGTT 61.158 55.000 0.00 0.00 0.00 3.67
1463 4289 1.870580 CGCAGTCGGTCTTGTTGGTTA 60.871 52.381 0.00 0.00 0.00 2.85
1464 4290 2.215196 GCAGTCGGTCTTGTTGGTTAA 58.785 47.619 0.00 0.00 0.00 2.01
1465 4291 2.614983 GCAGTCGGTCTTGTTGGTTAAA 59.385 45.455 0.00 0.00 0.00 1.52
1466 4292 3.252458 GCAGTCGGTCTTGTTGGTTAAAT 59.748 43.478 0.00 0.00 0.00 1.40
1467 4293 4.261447 GCAGTCGGTCTTGTTGGTTAAATT 60.261 41.667 0.00 0.00 0.00 1.82
1468 4294 5.735070 GCAGTCGGTCTTGTTGGTTAAATTT 60.735 40.000 0.00 0.00 0.00 1.82
1469 4295 6.513720 GCAGTCGGTCTTGTTGGTTAAATTTA 60.514 38.462 0.00 0.00 0.00 1.40
1470 4296 7.590279 CAGTCGGTCTTGTTGGTTAAATTTAT 58.410 34.615 0.00 0.00 0.00 1.40
1471 4297 8.079809 CAGTCGGTCTTGTTGGTTAAATTTATT 58.920 33.333 0.00 0.00 0.00 1.40
1472 4298 9.287373 AGTCGGTCTTGTTGGTTAAATTTATTA 57.713 29.630 0.00 0.00 0.00 0.98
1496 4322 9.671279 TTATCAAAGTTGAAGCATGAGAATAGA 57.329 29.630 0.00 0.00 41.13 1.98
1497 4323 7.606858 TCAAAGTTGAAGCATGAGAATAGAG 57.393 36.000 0.00 0.00 33.55 2.43
1498 4324 6.596888 TCAAAGTTGAAGCATGAGAATAGAGG 59.403 38.462 0.00 0.00 33.55 3.69
1499 4325 5.946942 AGTTGAAGCATGAGAATAGAGGA 57.053 39.130 0.00 0.00 0.00 3.71
1500 4326 6.305272 AGTTGAAGCATGAGAATAGAGGAA 57.695 37.500 0.00 0.00 0.00 3.36
1501 4327 6.347696 AGTTGAAGCATGAGAATAGAGGAAG 58.652 40.000 0.00 0.00 0.00 3.46
1502 4328 4.701765 TGAAGCATGAGAATAGAGGAAGC 58.298 43.478 0.00 0.00 0.00 3.86
1503 4329 4.162888 TGAAGCATGAGAATAGAGGAAGCA 59.837 41.667 0.00 0.00 0.00 3.91
1504 4330 4.070630 AGCATGAGAATAGAGGAAGCAC 57.929 45.455 0.00 0.00 0.00 4.40
1505 4331 3.710677 AGCATGAGAATAGAGGAAGCACT 59.289 43.478 0.00 0.00 0.00 4.40
1506 4332 4.898265 AGCATGAGAATAGAGGAAGCACTA 59.102 41.667 0.00 0.00 0.00 2.74
1507 4333 5.543405 AGCATGAGAATAGAGGAAGCACTAT 59.457 40.000 0.00 0.00 0.00 2.12
1508 4334 6.723515 AGCATGAGAATAGAGGAAGCACTATA 59.276 38.462 0.00 0.00 0.00 1.31
1509 4335 7.399765 AGCATGAGAATAGAGGAAGCACTATAT 59.600 37.037 0.00 0.00 0.00 0.86
1510 4336 8.040132 GCATGAGAATAGAGGAAGCACTATATT 58.960 37.037 0.00 3.60 37.52 1.28
1511 4337 9.941325 CATGAGAATAGAGGAAGCACTATATTT 57.059 33.333 0.00 0.00 35.62 1.40
1599 4428 3.947910 ATCCAAAATCACAGCAACCAG 57.052 42.857 0.00 0.00 0.00 4.00
1659 5303 7.342318 TGAGTACAATTTTCTAACGTGCTAC 57.658 36.000 0.00 0.00 0.00 3.58
1747 5394 3.073650 AGAGCTTCTCCATCAACAACCTT 59.926 43.478 0.00 0.00 0.00 3.50
1771 5418 2.739932 CGACCCTTTCATCGAGAGCAAT 60.740 50.000 0.00 0.00 40.86 3.56
1876 5523 3.460672 ATACATCACCAGCGGCGGG 62.461 63.158 17.86 17.86 0.00 6.13
1942 5603 1.634757 TTGTGTGCACGCGGATCATC 61.635 55.000 24.30 3.79 0.00 2.92
2019 5681 7.121611 TCTGGACACGTATAGTTATTTCACTCA 59.878 37.037 0.00 0.00 0.00 3.41
2092 5754 6.265422 GGGAGATTTTTCGTGATGGGATTATT 59.735 38.462 0.00 0.00 0.00 1.40
2119 5781 3.898517 TCTTGTGACTCACACTACTCG 57.101 47.619 11.58 0.00 44.47 4.18
2166 5830 0.716108 GTCGAGTGCGTCAAGATTGG 59.284 55.000 0.00 0.00 38.98 3.16
2188 5852 2.996621 CACACTTGTTTCCGGAGAGATC 59.003 50.000 3.34 0.00 0.00 2.75
2311 5978 5.922544 CAGATGGTTAAAACTGGCTTTCTTG 59.077 40.000 0.00 0.00 0.00 3.02
2417 6090 7.765819 TGACGATCTTGACAACATCATAAGAAT 59.234 33.333 4.60 0.00 37.11 2.40
2488 6161 1.142465 CTCTGGCTGGCCTTATGATGT 59.858 52.381 13.05 0.00 36.94 3.06
2502 6175 7.649306 GGCCTTATGATGTCATTTATCAAACAC 59.351 37.037 0.00 0.00 38.01 3.32
2543 6234 6.450845 TCGTAATTACCACTTGTTGTAACG 57.549 37.500 10.01 0.00 30.35 3.18
2552 6243 6.031471 ACCACTTGTTGTAACGAATTTGAAC 58.969 36.000 0.00 0.00 0.00 3.18
2557 6248 8.856247 ACTTGTTGTAACGAATTTGAACTTTTC 58.144 29.630 0.00 0.00 0.00 2.29
2859 6551 2.909006 AGAGGCATCCAGAAAGAAGTCA 59.091 45.455 0.00 0.00 0.00 3.41
2915 6607 0.978667 GTCTCAGGGAGAAGGGGGTC 60.979 65.000 0.00 0.00 40.59 4.46
3186 6878 4.340263 CGATGTGCATGACAAGAATTCAG 58.660 43.478 8.44 2.21 38.36 3.02
3273 6967 4.161333 CGTTTGATTGATCTGGCTTTCAC 58.839 43.478 0.00 0.00 0.00 3.18
3289 6983 6.495181 TGGCTTTCACAATTTGGACCTAAATA 59.505 34.615 0.78 0.00 30.47 1.40
3462 7170 0.898326 GGGGTAGCAACTTGTTGGGG 60.898 60.000 14.30 0.00 0.00 4.96
3467 7175 2.922503 CAACTTGTTGGGGCCCCC 60.923 66.667 38.81 24.30 45.71 5.40
3488 7196 3.005684 CCAGTGCAAATGTTTCCAGCTAA 59.994 43.478 0.00 0.00 0.00 3.09
3514 7222 6.770542 ACCTAGTTTCCCTCTGTTAAGAAAG 58.229 40.000 0.00 0.00 30.03 2.62
3521 7229 3.503748 CCCTCTGTTAAGAAAGCAAGGTG 59.496 47.826 0.00 0.00 30.03 4.00
3616 7324 5.067273 TGTAACAATTCTAGTGGGGTTGTG 58.933 41.667 0.00 0.00 33.67 3.33
3662 7370 8.466798 GTTGTAACAATTATATTGCTCCCAGTT 58.533 33.333 0.00 0.00 0.00 3.16
3842 7550 3.492353 GGGAGCCATGGCCTGCTA 61.492 66.667 33.14 0.00 43.17 3.49
3900 7608 3.276091 CGACGGTGCTGCAACCAA 61.276 61.111 12.81 0.00 40.53 3.67
3913 7621 3.023119 TGCAACCAATGTCAGTTCTTGT 58.977 40.909 0.00 0.00 0.00 3.16
3938 7646 0.039617 CCGGCGACAAAATTTGCTGA 60.040 50.000 9.30 0.00 35.76 4.26
3942 7650 2.220824 GGCGACAAAATTTGCTGAAACC 59.779 45.455 5.52 0.00 0.00 3.27
3943 7651 2.863137 GCGACAAAATTTGCTGAAACCA 59.137 40.909 5.52 0.00 0.00 3.67
3972 7680 1.152333 ATGCTGGGATGGCATGCAT 60.152 52.632 21.36 17.67 46.85 3.96
3991 7699 4.078516 GCGAGCTACAACCGGGGT 62.079 66.667 6.32 6.30 0.00 4.95
3998 7706 2.886730 CTACAACCGGGGTGATGGCC 62.887 65.000 21.14 0.00 0.00 5.36
3999 7707 4.047125 CAACCGGGGTGATGGCCT 62.047 66.667 6.08 0.00 0.00 5.19
4000 7708 3.264845 AACCGGGGTGATGGCCTT 61.265 61.111 6.32 0.00 0.00 4.35
4004 7712 1.604147 CCGGGGTGATGGCCTTTTTC 61.604 60.000 3.32 0.00 0.00 2.29
4020 7728 5.527214 GCCTTTTTCTTTTGCTACCATTGTT 59.473 36.000 0.00 0.00 0.00 2.83
4085 7793 0.963962 CCATGCTTTTGTGACCAGCT 59.036 50.000 0.00 0.00 34.42 4.24
4090 7798 1.896220 CTTTTGTGACCAGCTAGGCA 58.104 50.000 0.00 0.00 43.14 4.75
4102 7810 0.467384 GCTAGGCATCTTCCTCAGCA 59.533 55.000 0.00 0.00 37.66 4.41
4104 7812 1.070445 CTAGGCATCTTCCTCAGCAGG 59.930 57.143 0.00 0.00 42.01 4.85
4114 7822 1.333636 CCTCAGCAGGGACGGAAGAT 61.334 60.000 0.00 0.00 35.89 2.40
4159 7867 4.410400 GCAGGGTAGCCGGCAAGT 62.410 66.667 31.54 11.17 0.00 3.16
4175 7883 3.009115 GTGCAGGTGGCCTAGGGA 61.009 66.667 11.72 0.00 43.89 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.094785 ACCGCGATTTAAGCTGCAAT 58.905 45.000 8.23 0.00 0.00 3.56
4 5 1.003851 TACACCGCGATTTAAGCTGC 58.996 50.000 8.23 0.00 0.00 5.25
6 7 3.173668 TGATACACCGCGATTTAAGCT 57.826 42.857 8.23 0.00 0.00 3.74
7 8 3.303132 CCTTGATACACCGCGATTTAAGC 60.303 47.826 8.23 0.00 0.00 3.09
8 9 3.869246 ACCTTGATACACCGCGATTTAAG 59.131 43.478 8.23 2.62 0.00 1.85
9 10 3.619483 CACCTTGATACACCGCGATTTAA 59.381 43.478 8.23 0.00 0.00 1.52
23 1458 2.365617 CGTCCTAGGCATACACCTTGAT 59.634 50.000 2.96 0.00 41.50 2.57
43 1478 0.453793 CCTGTGAGCTCACCTAGTCG 59.546 60.000 37.23 20.40 45.88 4.18
49 1484 1.215647 CCGTACCTGTGAGCTCACC 59.784 63.158 37.23 23.18 45.88 4.02
50 1485 0.601558 TTCCGTACCTGTGAGCTCAC 59.398 55.000 35.04 35.04 46.59 3.51
51 1486 0.601558 GTTCCGTACCTGTGAGCTCA 59.398 55.000 13.74 13.74 0.00 4.26
52 1487 0.108756 GGTTCCGTACCTGTGAGCTC 60.109 60.000 6.82 6.82 44.10 4.09
53 1488 1.972978 GGTTCCGTACCTGTGAGCT 59.027 57.895 0.00 0.00 44.10 4.09
54 1489 4.592426 GGTTCCGTACCTGTGAGC 57.408 61.111 0.00 0.00 44.10 4.26
62 1500 1.668047 CCACTCGTTCTGGTTCCGTAC 60.668 57.143 0.00 0.00 0.00 3.67
115 1553 5.843673 TGATGCACTGGTTTCTTTAACAA 57.156 34.783 0.00 0.00 38.55 2.83
120 1558 3.233507 ACCATGATGCACTGGTTTCTTT 58.766 40.909 10.79 0.00 43.21 2.52
174 1612 0.171231 CTTCCACGCACTCTCATCGA 59.829 55.000 0.00 0.00 0.00 3.59
176 1614 2.370281 TTCTTCCACGCACTCTCATC 57.630 50.000 0.00 0.00 0.00 2.92
178 1616 1.873903 GCTTTCTTCCACGCACTCTCA 60.874 52.381 0.00 0.00 0.00 3.27
180 1618 0.106708 TGCTTTCTTCCACGCACTCT 59.893 50.000 0.00 0.00 0.00 3.24
189 1627 6.703165 AGTTGATGTCAATTTTGCTTTCTTCC 59.297 34.615 0.00 0.00 38.24 3.46
207 1645 6.025896 GTCATCAGTGCAAACATAGTTGATG 58.974 40.000 0.00 5.46 40.89 3.07
225 1665 5.032327 AGATATCTGCAAGCTTGTCATCA 57.968 39.130 26.55 15.09 0.00 3.07
232 1672 7.070571 AGACCTAGTTAAGATATCTGCAAGCTT 59.929 37.037 5.86 0.00 0.00 3.74
239 1679 8.145122 GTCCCAAAGACCTAGTTAAGATATCTG 58.855 40.741 5.86 0.00 39.84 2.90
240 1680 7.014422 CGTCCCAAAGACCTAGTTAAGATATCT 59.986 40.741 0.00 0.00 43.08 1.98
247 1687 3.896888 TGTCGTCCCAAAGACCTAGTTAA 59.103 43.478 0.00 0.00 43.08 2.01
251 1691 1.893801 AGTGTCGTCCCAAAGACCTAG 59.106 52.381 0.00 0.00 43.08 3.02
252 1692 2.005370 AGTGTCGTCCCAAAGACCTA 57.995 50.000 0.00 0.00 43.08 3.08
270 1710 3.785486 TCGCCACATCTTCATGAACTAG 58.215 45.455 3.38 0.00 33.72 2.57
271 1711 3.885724 TCGCCACATCTTCATGAACTA 57.114 42.857 3.38 0.00 33.72 2.24
290 1730 3.058914 CACAACTTGGACGTCAATCCTTC 60.059 47.826 18.91 0.00 39.75 3.46
306 1746 2.365617 ACGATGTCCTCACTTCACAACT 59.634 45.455 0.00 0.00 0.00 3.16
308 1748 2.628178 AGACGATGTCCTCACTTCACAA 59.372 45.455 0.00 0.00 32.18 3.33
331 1771 5.012664 GGTTAATTTCAACAATCACCCCCTT 59.987 40.000 0.00 0.00 0.00 3.95
358 1798 6.220930 TGATGCCGGACATAAACTACTAATC 58.779 40.000 5.05 0.00 39.84 1.75
368 1808 1.134521 GGTGACTGATGCCGGACATAA 60.135 52.381 5.05 0.00 39.84 1.90
376 1816 3.728076 TCTTATACGGTGACTGATGCC 57.272 47.619 0.00 0.00 0.00 4.40
379 1819 7.670140 TGATAGGAATCTTATACGGTGACTGAT 59.330 37.037 0.00 0.00 32.93 2.90
442 2026 9.449719 GGTTAATCTTACAAGGGGATACATATG 57.550 37.037 0.00 0.00 39.74 1.78
443 2027 9.177927 TGGTTAATCTTACAAGGGGATACATAT 57.822 33.333 0.00 0.00 39.74 1.78
476 2060 8.905702 CGGTCTTGTTTCTTTATTTCTTTGATG 58.094 33.333 0.00 0.00 0.00 3.07
483 2067 7.178074 CCGTATCGGTCTTGTTTCTTTATTTC 58.822 38.462 0.00 0.00 42.73 2.17
509 2093 1.475034 GGCGATTTGATGGCTACAGGA 60.475 52.381 0.00 0.00 34.17 3.86
527 2111 2.089349 GCACGAGAGAACACGAGGC 61.089 63.158 0.00 0.00 34.51 4.70
593 2177 3.964347 CGATTCTTCGCGAACGTAAGATA 59.036 43.478 19.38 4.96 38.75 1.98
597 2181 2.245795 TCGATTCTTCGCGAACGTAA 57.754 45.000 19.38 12.81 45.10 3.18
603 2187 1.404035 TCCTTGATCGATTCTTCGCGA 59.596 47.619 3.71 3.71 45.10 5.87
606 2190 3.090952 AGCTCCTTGATCGATTCTTCG 57.909 47.619 0.00 0.00 46.87 3.79
612 2196 2.491693 GCTAGCTAGCTCCTTGATCGAT 59.508 50.000 33.71 0.00 45.62 3.59
634 2218 7.469537 TGAAACAAAGGAAACAAAGGAAGTA 57.530 32.000 0.00 0.00 0.00 2.24
635 2219 6.353404 TGAAACAAAGGAAACAAAGGAAGT 57.647 33.333 0.00 0.00 0.00 3.01
636 2220 7.665561 TTTGAAACAAAGGAAACAAAGGAAG 57.334 32.000 0.00 0.00 0.00 3.46
637 2221 8.628630 ATTTTGAAACAAAGGAAACAAAGGAA 57.371 26.923 0.00 0.00 0.00 3.36
638 2222 9.726438 TTATTTTGAAACAAAGGAAACAAAGGA 57.274 25.926 0.00 0.00 0.00 3.36
692 2276 9.962783 GCTACTCTCTCCGTTCTAAAATAAATA 57.037 33.333 0.00 0.00 0.00 1.40
693 2277 8.697292 AGCTACTCTCTCCGTTCTAAAATAAAT 58.303 33.333 0.00 0.00 0.00 1.40
694 2278 8.064336 AGCTACTCTCTCCGTTCTAAAATAAA 57.936 34.615 0.00 0.00 0.00 1.40
695 2279 7.642082 AGCTACTCTCTCCGTTCTAAAATAA 57.358 36.000 0.00 0.00 0.00 1.40
696 2280 7.201803 GGAAGCTACTCTCTCCGTTCTAAAATA 60.202 40.741 0.00 0.00 0.00 1.40
697 2281 6.406065 GGAAGCTACTCTCTCCGTTCTAAAAT 60.406 42.308 0.00 0.00 0.00 1.82
698 2282 5.105837 GGAAGCTACTCTCTCCGTTCTAAAA 60.106 44.000 0.00 0.00 0.00 1.52
699 2283 4.398673 GGAAGCTACTCTCTCCGTTCTAAA 59.601 45.833 0.00 0.00 0.00 1.85
700 2284 3.946558 GGAAGCTACTCTCTCCGTTCTAA 59.053 47.826 0.00 0.00 0.00 2.10
701 2285 3.200385 AGGAAGCTACTCTCTCCGTTCTA 59.800 47.826 0.00 0.00 0.00 2.10
702 2286 2.025699 AGGAAGCTACTCTCTCCGTTCT 60.026 50.000 0.00 0.00 0.00 3.01
703 2287 2.098443 CAGGAAGCTACTCTCTCCGTTC 59.902 54.545 0.00 0.00 0.00 3.95
704 2288 2.096248 CAGGAAGCTACTCTCTCCGTT 58.904 52.381 0.00 0.00 0.00 4.44
705 2289 1.683629 CCAGGAAGCTACTCTCTCCGT 60.684 57.143 0.00 0.00 0.00 4.69
706 2290 1.028905 CCAGGAAGCTACTCTCTCCG 58.971 60.000 0.00 0.00 0.00 4.63
707 2291 2.153034 ACCAGGAAGCTACTCTCTCC 57.847 55.000 0.00 0.00 0.00 3.71
708 2292 3.219281 CCTACCAGGAAGCTACTCTCTC 58.781 54.545 0.00 0.00 37.67 3.20
709 2293 2.583566 ACCTACCAGGAAGCTACTCTCT 59.416 50.000 0.00 0.00 37.67 3.10
710 2294 2.691011 CACCTACCAGGAAGCTACTCTC 59.309 54.545 0.00 0.00 37.67 3.20
711 2295 2.741145 CACCTACCAGGAAGCTACTCT 58.259 52.381 0.00 0.00 37.67 3.24
712 2296 1.137282 GCACCTACCAGGAAGCTACTC 59.863 57.143 0.00 0.00 37.67 2.59
713 2297 1.196012 GCACCTACCAGGAAGCTACT 58.804 55.000 0.00 0.00 37.67 2.57
714 2298 0.179108 CGCACCTACCAGGAAGCTAC 60.179 60.000 0.00 0.00 37.67 3.58
737 2321 4.620589 AGCTGATCGAATCTTGATGGAT 57.379 40.909 0.00 0.00 0.00 3.41
768 2352 5.850614 ACTCCACGTACATAGTTTGAAAGT 58.149 37.500 0.00 0.00 0.00 2.66
833 2417 2.289694 ACTTTCCGTCAAGTGCTAGCAT 60.290 45.455 22.51 2.08 35.57 3.79
836 2420 4.265556 CGATTACTTTCCGTCAAGTGCTAG 59.734 45.833 6.71 0.00 37.57 3.42
868 2452 3.244630 TGTTGGCCTAATCCTTGTACGTT 60.245 43.478 3.32 0.00 0.00 3.99
882 2466 2.613977 CGAAGAACAGAGATGTTGGCCT 60.614 50.000 3.32 0.00 31.35 5.19
927 2537 0.698818 GTGGGTGTGGGAGAAGGATT 59.301 55.000 0.00 0.00 0.00 3.01
981 2601 1.489481 TCTTCAGATCACCGCCTCAT 58.511 50.000 0.00 0.00 0.00 2.90
1050 3874 3.622163 CAGCTTTCAGGTGATCATCAGTC 59.378 47.826 9.06 0.00 45.98 3.51
1191 4015 3.172106 TGGAGGTGGTGGGCGAAA 61.172 61.111 0.00 0.00 0.00 3.46
1212 4036 1.820906 CATGTGATGGGCGGTCCTG 60.821 63.158 0.00 0.00 36.20 3.86
1260 4084 2.930455 GCGTAAAATTTGCATGTGGCCT 60.930 45.455 3.32 0.00 43.89 5.19
1280 4106 3.350219 TGAAAATGGAGGGAGTAGTGC 57.650 47.619 0.00 0.00 0.00 4.40
1281 4107 6.840780 ATTTTGAAAATGGAGGGAGTAGTG 57.159 37.500 1.78 0.00 0.00 2.74
1294 4120 6.352526 CGCGAGCGTACTATATTTTGAAAAT 58.647 36.000 0.00 8.35 34.35 1.82
1297 4123 4.941727 CGCGAGCGTACTATATTTTGAA 57.058 40.909 0.00 0.00 34.35 2.69
1328 4154 9.921637 TGATTAAATTTATGGTCAAAGTTGGAC 57.078 29.630 1.31 1.31 29.44 4.02
1333 4159 9.840427 CTCGTTGATTAAATTTATGGTCAAAGT 57.160 29.630 20.32 0.00 0.00 2.66
1335 4161 9.834628 GTCTCGTTGATTAAATTTATGGTCAAA 57.165 29.630 16.35 7.28 0.00 2.69
1336 4162 8.455682 GGTCTCGTTGATTAAATTTATGGTCAA 58.544 33.333 13.07 13.07 0.00 3.18
1337 4163 7.201574 CGGTCTCGTTGATTAAATTTATGGTCA 60.202 37.037 0.00 2.14 0.00 4.02
1338 4164 7.010738 TCGGTCTCGTTGATTAAATTTATGGTC 59.989 37.037 0.00 0.00 37.69 4.02
1342 4168 7.465513 GCAGTCGGTCTCGTTGATTAAATTTAT 60.466 37.037 0.00 0.00 37.69 1.40
1344 4170 5.390567 GCAGTCGGTCTCGTTGATTAAATTT 60.391 40.000 0.00 0.00 37.69 1.82
1345 4171 4.092968 GCAGTCGGTCTCGTTGATTAAATT 59.907 41.667 0.00 0.00 37.69 1.82
1355 4181 4.086178 CGTCGCAGTCGGTCTCGT 62.086 66.667 0.00 0.00 35.06 4.18
1410 4236 9.289303 GCAAAAATTATGTCAGTGAATTCGTAT 57.711 29.630 0.00 0.00 0.00 3.06
1411 4237 8.511321 AGCAAAAATTATGTCAGTGAATTCGTA 58.489 29.630 0.00 0.00 0.00 3.43
1412 4238 7.370383 AGCAAAAATTATGTCAGTGAATTCGT 58.630 30.769 0.00 0.00 0.00 3.85
1413 4239 7.008628 GGAGCAAAAATTATGTCAGTGAATTCG 59.991 37.037 0.00 0.00 0.00 3.34
1414 4240 7.276438 GGGAGCAAAAATTATGTCAGTGAATTC 59.724 37.037 0.00 0.00 0.00 2.17
1415 4241 7.099120 GGGAGCAAAAATTATGTCAGTGAATT 58.901 34.615 0.00 0.00 0.00 2.17
1416 4242 6.625740 CGGGAGCAAAAATTATGTCAGTGAAT 60.626 38.462 0.00 0.00 0.00 2.57
1417 4243 5.335583 CGGGAGCAAAAATTATGTCAGTGAA 60.336 40.000 0.00 0.00 0.00 3.18
1418 4244 4.155826 CGGGAGCAAAAATTATGTCAGTGA 59.844 41.667 0.00 0.00 0.00 3.41
1419 4245 4.414852 CGGGAGCAAAAATTATGTCAGTG 58.585 43.478 0.00 0.00 0.00 3.66
1420 4246 4.701956 CGGGAGCAAAAATTATGTCAGT 57.298 40.909 0.00 0.00 0.00 3.41
1443 4269 1.157870 AACCAACAAGACCGACTGCG 61.158 55.000 0.00 0.00 37.24 5.18
1444 4270 1.873698 TAACCAACAAGACCGACTGC 58.126 50.000 0.00 0.00 0.00 4.40
1445 4271 5.432885 AATTTAACCAACAAGACCGACTG 57.567 39.130 0.00 0.00 0.00 3.51
1446 4272 7.754851 ATAAATTTAACCAACAAGACCGACT 57.245 32.000 1.21 0.00 0.00 4.18
1470 4296 9.671279 TCTATTCTCATGCTTCAACTTTGATAA 57.329 29.630 0.00 0.00 37.00 1.75
1471 4297 9.322773 CTCTATTCTCATGCTTCAACTTTGATA 57.677 33.333 0.00 0.00 37.00 2.15
1472 4298 7.282675 CCTCTATTCTCATGCTTCAACTTTGAT 59.717 37.037 0.00 0.00 37.00 2.57
1473 4299 6.596888 CCTCTATTCTCATGCTTCAACTTTGA 59.403 38.462 0.00 0.00 34.92 2.69
1474 4300 6.596888 TCCTCTATTCTCATGCTTCAACTTTG 59.403 38.462 0.00 0.00 0.00 2.77
1475 4301 6.715280 TCCTCTATTCTCATGCTTCAACTTT 58.285 36.000 0.00 0.00 0.00 2.66
1476 4302 6.305272 TCCTCTATTCTCATGCTTCAACTT 57.695 37.500 0.00 0.00 0.00 2.66
1477 4303 5.946942 TCCTCTATTCTCATGCTTCAACT 57.053 39.130 0.00 0.00 0.00 3.16
1478 4304 5.007528 GCTTCCTCTATTCTCATGCTTCAAC 59.992 44.000 0.00 0.00 0.00 3.18
1479 4305 5.121811 GCTTCCTCTATTCTCATGCTTCAA 58.878 41.667 0.00 0.00 0.00 2.69
1480 4306 4.162888 TGCTTCCTCTATTCTCATGCTTCA 59.837 41.667 0.00 0.00 0.00 3.02
1481 4307 4.511082 GTGCTTCCTCTATTCTCATGCTTC 59.489 45.833 0.00 0.00 0.00 3.86
1482 4308 4.163839 AGTGCTTCCTCTATTCTCATGCTT 59.836 41.667 0.00 0.00 0.00 3.91
1483 4309 3.710677 AGTGCTTCCTCTATTCTCATGCT 59.289 43.478 0.00 0.00 0.00 3.79
1484 4310 4.070630 AGTGCTTCCTCTATTCTCATGC 57.929 45.455 0.00 0.00 0.00 4.06
1485 4311 9.941325 AAATATAGTGCTTCCTCTATTCTCATG 57.059 33.333 0.00 0.00 31.97 3.07
1496 4322 9.136323 CCCTCATTTTAAAATATAGTGCTTCCT 57.864 33.333 12.98 0.00 0.00 3.36
1497 4323 9.131791 TCCCTCATTTTAAAATATAGTGCTTCC 57.868 33.333 12.98 0.00 0.00 3.46
1628 4457 9.063615 ACGTTAGAAAATTGTACTCATTTTCCT 57.936 29.630 25.06 18.92 42.23 3.36
1659 5303 0.177141 CCCTGCCAATGCCAAATCAG 59.823 55.000 0.00 0.00 36.33 2.90
1696 5343 1.266175 TCGAGGACACTGAAGTCGAAC 59.734 52.381 0.00 0.00 39.42 3.95
1747 5394 1.218047 CTCGATGAAAGGGTCGCCA 59.782 57.895 0.00 0.00 37.74 5.69
1771 5418 1.509463 CCTAGAGTGCACGCCGTAA 59.491 57.895 17.50 0.00 0.00 3.18
1844 5491 5.221904 TGGTGATGTATCCCCAATACTCATG 60.222 44.000 0.00 0.00 40.85 3.07
1876 5523 0.971386 TGTGTAGGTTCCCTTCGGTC 59.029 55.000 0.00 0.00 34.61 4.79
1895 5542 2.625282 ACTGACCCAACTAGTAGGCT 57.375 50.000 11.01 0.00 0.00 4.58
2092 5754 3.057019 GTGTGAGTCACAAGATGCGTAA 58.943 45.455 27.03 0.00 46.28 3.18
2119 5781 1.153349 CCTAGCCGCCTTGAAGACC 60.153 63.158 0.00 0.00 0.00 3.85
2166 5830 0.868406 CTCTCCGGAAACAAGTGTGC 59.132 55.000 5.23 0.00 0.00 4.57
2188 5852 2.505866 GACTTAAAATCCGCGCAGTTG 58.494 47.619 8.75 0.00 0.00 3.16
2311 5978 0.472471 TGAACCACCAAGGGACACTC 59.528 55.000 0.00 0.00 43.89 3.51
2417 6090 4.346730 TCGGAACCCACATTTCTCTAGTA 58.653 43.478 0.00 0.00 0.00 1.82
2488 6161 4.390264 TCACCCACGTGTTTGATAAATGA 58.610 39.130 15.65 1.84 41.09 2.57
2502 6175 3.259064 ACGAATCTTAACATCACCCACG 58.741 45.455 0.00 0.00 0.00 4.94
2520 6209 6.212235 TCGTTACAACAAGTGGTAATTACGA 58.788 36.000 9.46 8.36 32.63 3.43
2792 6484 2.421388 CCACAAGAACAAGGGTGAGTGA 60.421 50.000 0.00 0.00 33.16 3.41
2834 6526 3.895232 TCTTTCTGGATGCCTCTGTAC 57.105 47.619 0.00 0.00 0.00 2.90
2859 6551 2.481952 GAGCGTTTCTCATGCACTTCTT 59.518 45.455 0.00 0.00 40.31 2.52
2882 6574 1.367840 GAGACGGCTTGTGAGGTGT 59.632 57.895 0.00 0.00 0.00 4.16
2915 6607 2.094894 CAGCTCATTTAGGAACGCACTG 59.905 50.000 0.00 0.00 0.00 3.66
3186 6878 2.555199 ACAACGATCTTATGCAGCTCC 58.445 47.619 0.00 0.00 0.00 4.70
3359 7061 8.546597 AGTAAACACCAAATAAATCAATTGGC 57.453 30.769 5.42 0.00 45.99 4.52
3370 7072 7.177568 ACCATGCACAATAGTAAACACCAAATA 59.822 33.333 0.00 0.00 0.00 1.40
3382 7084 9.723601 AAATAATTTGAAACCATGCACAATAGT 57.276 25.926 0.00 0.00 0.00 2.12
3462 7170 0.320683 GAAACATTTGCACTGGGGGC 60.321 55.000 0.00 0.00 0.00 5.80
3467 7175 2.806608 AGCTGGAAACATTTGCACTG 57.193 45.000 0.00 0.00 41.51 3.66
3488 7196 6.758806 TCTTAACAGAGGGAAACTAGGTTT 57.241 37.500 0.00 0.00 38.54 3.27
3514 7222 1.838112 TCATGGATTGGTCACCTTGC 58.162 50.000 0.00 0.00 33.32 4.01
3521 7229 6.323225 AGGAATCTTTGATTCATGGATTGGTC 59.677 38.462 18.26 5.70 0.00 4.02
3616 7324 6.388278 ACAACTAGGAACGTTAGTGAGATTC 58.612 40.000 0.00 0.00 31.96 2.52
3653 7361 3.057245 GGTTGAAGAATGAAACTGGGAGC 60.057 47.826 0.00 0.00 0.00 4.70
3662 7370 3.329386 CAGCGAGAGGTTGAAGAATGAA 58.671 45.455 0.00 0.00 41.81 2.57
3800 7508 4.066139 AACAGGCCATGGCTCCCC 62.066 66.667 34.70 19.02 41.60 4.81
3801 7509 2.757099 CAACAGGCCATGGCTCCC 60.757 66.667 34.70 19.40 41.60 4.30
3802 7510 3.455469 GCAACAGGCCATGGCTCC 61.455 66.667 34.70 20.16 41.60 4.70
3803 7511 3.818787 CGCAACAGGCCATGGCTC 61.819 66.667 34.70 24.32 40.31 4.70
3804 7512 4.349503 TCGCAACAGGCCATGGCT 62.350 61.111 34.70 18.82 40.31 4.75
3805 7513 3.818787 CTCGCAACAGGCCATGGC 61.819 66.667 29.47 29.47 40.31 4.40
3806 7514 3.818787 GCTCGCAACAGGCCATGG 61.819 66.667 7.63 7.63 40.31 3.66
3807 7515 4.170062 CGCTCGCAACAGGCCATG 62.170 66.667 5.01 2.64 40.31 3.66
3842 7550 4.212636 CGTCAATAAAAGGAACCGACTTGT 59.787 41.667 0.00 0.00 0.00 3.16
3900 7608 3.314553 CGGTCGTAACAAGAACTGACAT 58.685 45.455 0.00 0.00 0.00 3.06
3913 7621 1.510776 AATTTTGTCGCCGGTCGTAA 58.489 45.000 16.00 10.80 39.67 3.18
3950 7658 3.022497 TGCCATCCCAGCATCCCA 61.022 61.111 0.00 0.00 34.69 4.37
3972 7680 4.077184 CCCGGTTGTAGCTCGCCA 62.077 66.667 0.00 0.00 0.00 5.69
3991 7699 4.262420 GGTAGCAAAAGAAAAAGGCCATCA 60.262 41.667 5.01 0.00 0.00 3.07
3998 7706 7.358352 CGCTAACAATGGTAGCAAAAGAAAAAG 60.358 37.037 27.30 5.73 36.69 2.27
3999 7707 6.419413 CGCTAACAATGGTAGCAAAAGAAAAA 59.581 34.615 27.30 0.00 36.69 1.94
4000 7708 5.918011 CGCTAACAATGGTAGCAAAAGAAAA 59.082 36.000 27.30 0.00 36.69 2.29
4004 7712 4.419522 ACGCTAACAATGGTAGCAAAAG 57.580 40.909 27.30 14.75 36.69 2.27
4037 7745 6.200808 TGTTGTCGCAGCAATTTATATCATG 58.799 36.000 0.00 0.00 0.00 3.07
4038 7746 6.375945 TGTTGTCGCAGCAATTTATATCAT 57.624 33.333 0.00 0.00 0.00 2.45
4042 7750 5.398169 CCTTTGTTGTCGCAGCAATTTATA 58.602 37.500 9.17 0.00 34.82 0.98
4044 7752 3.637432 CCTTTGTTGTCGCAGCAATTTA 58.363 40.909 9.17 0.00 34.82 1.40
4085 7793 1.126488 CCTGCTGAGGAAGATGCCTA 58.874 55.000 0.00 0.00 42.93 3.93
4090 7798 1.333636 CCGTCCCTGCTGAGGAAGAT 61.334 60.000 12.67 0.00 42.93 2.40
4102 7810 2.363795 TCGCCATCTTCCGTCCCT 60.364 61.111 0.00 0.00 0.00 4.20
4104 7812 2.586357 GCTCGCCATCTTCCGTCC 60.586 66.667 0.00 0.00 0.00 4.79
4144 7852 4.410400 GCACTTGCCGGCTACCCT 62.410 66.667 29.70 2.08 34.31 4.34
4159 7867 2.688666 CTCCCTAGGCCACCTGCA 60.689 66.667 5.01 0.00 43.89 4.41


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

AutoCloner maintained by Alex Coulton.