Multiple sequence alignment - TraesCS2B01G276900

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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 TraesCS2B01G276900 chr2B 100.000 9572 0 0 1 9572 382588832 382598403 0.000000e+00 17677.0
1 TraesCS2B01G276900 chr2B 95.357 2154 76 5 4553 6683 383374862 383377014 0.000000e+00 3402.0
2 TraesCS2B01G276900 chr2B 87.967 482 47 9 8254 8733 733898096 733898568 8.400000e-155 558.0
3 TraesCS2B01G276900 chr2B 95.238 294 13 1 6390 6683 331152695 331152403 1.880000e-126 464.0
4 TraesCS2B01G276900 chr2B 92.749 331 7 1 6370 6683 382593185 382593515 6.770000e-126 462.0
5 TraesCS2B01G276900 chr2B 89.189 111 7 5 9403 9511 382733964 382734071 6.030000e-27 134.0
6 TraesCS2B01G276900 chr2D 94.221 2959 90 24 6678 9572 314496172 314499113 0.000000e+00 4442.0
7 TraesCS2B01G276900 chr2D 96.455 2285 74 5 2071 4351 314493899 314496180 0.000000e+00 3764.0
8 TraesCS2B01G276900 chr2D 94.048 1008 36 8 991 1994 314492431 314493418 0.000000e+00 1507.0
9 TraesCS2B01G276900 chr2D 91.450 538 32 9 335 861 314368890 314369424 0.000000e+00 726.0
10 TraesCS2B01G276900 chr2D 87.213 305 31 4 1 297 314368591 314368895 3.310000e-89 340.0
11 TraesCS2B01G276900 chr2D 90.541 74 7 0 922 995 314369421 314369494 2.200000e-16 99.0
12 TraesCS2B01G276900 chr2D 87.931 58 4 1 9362 9416 314796135 314796192 2.230000e-06 65.8
13 TraesCS2B01G276900 chr2A 96.206 2293 78 6 2069 4357 421067859 421065572 0.000000e+00 3744.0
14 TraesCS2B01G276900 chr2A 95.311 1834 54 6 6676 8495 421065588 421063773 0.000000e+00 2881.0
15 TraesCS2B01G276900 chr2A 89.346 1605 100 30 1 1567 421078285 421076714 0.000000e+00 1951.0
16 TraesCS2B01G276900 chr2A 93.345 1112 42 14 8493 9572 421063712 421062601 0.000000e+00 1615.0
17 TraesCS2B01G276900 chr2A 91.219 1173 71 5 7904 9071 422127682 422128827 0.000000e+00 1567.0
18 TraesCS2B01G276900 chr2A 96.215 687 18 3 7074 7759 422111211 422111890 0.000000e+00 1118.0
19 TraesCS2B01G276900 chr2A 95.565 451 18 2 1566 2014 421068530 421068080 0.000000e+00 721.0
20 TraesCS2B01G276900 chr2A 96.226 159 5 1 7751 7909 422113768 422113925 9.540000e-65 259.0
21 TraesCS2B01G276900 chr2A 94.631 149 8 0 6935 7083 422110649 422110797 2.080000e-56 231.0
22 TraesCS2B01G276900 chr2A 95.082 122 3 1 6822 6940 422104348 422104469 1.270000e-43 189.0
23 TraesCS2B01G276900 chr2A 82.383 193 13 8 9362 9533 422222876 422223068 2.150000e-31 148.0
24 TraesCS2B01G276900 chr2A 92.000 100 6 2 9422 9520 421059324 421059226 1.300000e-28 139.0
25 TraesCS2B01G276900 chr7D 94.706 2361 80 15 4354 6683 545396424 545394078 0.000000e+00 3626.0
26 TraesCS2B01G276900 chr6B 91.152 2396 142 31 4340 6686 88754972 88752598 0.000000e+00 3186.0
27 TraesCS2B01G276900 chr6B 93.645 1904 106 9 4354 6248 312248416 312246519 0.000000e+00 2832.0
28 TraesCS2B01G276900 chr6B 88.643 361 33 7 8368 8728 433067884 433067532 5.310000e-117 433.0
29 TraesCS2B01G276900 chr6A 89.516 2356 190 20 4354 6685 493730390 493732712 0.000000e+00 2929.0
30 TraesCS2B01G276900 chr3B 92.429 2021 91 15 4723 6683 823254897 823256915 0.000000e+00 2828.0
31 TraesCS2B01G276900 chr3B 81.880 1915 259 60 4807 6686 299781593 299779732 0.000000e+00 1533.0
32 TraesCS2B01G276900 chr3B 90.476 483 36 8 6209 6684 225354717 225354238 6.310000e-176 628.0
33 TraesCS2B01G276900 chr3B 88.095 420 26 7 6287 6683 322288199 322287781 2.420000e-130 477.0
34 TraesCS2B01G276900 chr3B 85.677 384 30 13 4354 4725 256726752 256726382 1.950000e-101 381.0
35 TraesCS2B01G276900 chr3B 85.677 384 29 13 4354 4725 299785255 299784886 1.950000e-101 381.0
36 TraesCS2B01G276900 chr3B 80.562 427 56 20 6207 6627 322297409 322297814 4.340000e-78 303.0
37 TraesCS2B01G276900 chr7A 88.599 2342 216 23 4354 6683 314427390 314425088 0.000000e+00 2798.0
38 TraesCS2B01G276900 chr7A 88.497 2356 211 29 4354 6694 314423428 314421118 0.000000e+00 2795.0
39 TraesCS2B01G276900 chr7A 90.593 1871 145 12 4354 6216 314425402 314423555 0.000000e+00 2451.0
40 TraesCS2B01G276900 chr7A 88.170 1268 112 12 4354 5602 245982103 245980855 0.000000e+00 1476.0
41 TraesCS2B01G276900 chr7A 81.984 383 43 15 4354 4726 431925217 431924851 1.560000e-77 302.0
42 TraesCS2B01G276900 chr7A 93.532 201 13 0 4354 4554 680330826 680331026 5.620000e-77 300.0
43 TraesCS2B01G276900 chr4B 93.397 1878 113 4 4354 6225 392845750 392847622 0.000000e+00 2771.0
44 TraesCS2B01G276900 chr4B 87.812 361 36 6 8368 8728 301702778 301702426 5.350000e-112 416.0
45 TraesCS2B01G276900 chr4B 87.812 361 36 6 8368 8728 301757041 301756689 5.350000e-112 416.0
46 TraesCS2B01G276900 chr4B 87.812 361 36 6 8368 8728 301864571 301864219 5.350000e-112 416.0
47 TraesCS2B01G276900 chr4A 87.997 2341 205 27 4354 6683 583754117 583751842 0.000000e+00 2697.0
48 TraesCS2B01G276900 chr4A 86.424 1893 217 17 6793 8683 722099213 722101067 0.000000e+00 2036.0
49 TraesCS2B01G276900 chr4A 86.371 1893 218 17 6793 8683 722081827 722083681 0.000000e+00 2030.0
50 TraesCS2B01G276900 chr1B 90.950 1978 161 15 4354 6316 116527736 116525762 0.000000e+00 2645.0
51 TraesCS2B01G276900 chr1B 80.955 1654 241 56 4807 6426 421462155 421460542 0.000000e+00 1242.0
52 TraesCS2B01G276900 chrUn 88.369 1943 188 16 6793 8733 2105270 2103364 0.000000e+00 2302.0
53 TraesCS2B01G276900 chrUn 80.000 605 85 23 6113 6684 26910664 26911265 1.920000e-111 414.0
54 TraesCS2B01G276900 chrUn 75.943 212 36 11 8905 9106 341241509 341241303 2.850000e-15 95.3
55 TraesCS2B01G276900 chr3A 88.477 1267 122 13 4354 5602 746139829 746138569 0.000000e+00 1509.0
56 TraesCS2B01G276900 chr3A 88.379 1265 126 8 4354 5602 698027293 698028552 0.000000e+00 1502.0
57 TraesCS2B01G276900 chr3A 82.373 590 74 12 6117 6683 251346610 251347192 4.020000e-133 486.0
58 TraesCS2B01G276900 chr3A 92.727 275 20 0 4354 4628 675347675 675347949 1.940000e-106 398.0
59 TraesCS2B01G276900 chr3A 94.175 206 12 0 4354 4559 251341233 251341438 2.010000e-81 315.0
60 TraesCS2B01G276900 chr5B 79.345 1801 281 52 4841 6590 291801444 291799684 0.000000e+00 1181.0
61 TraesCS2B01G276900 chr5B 77.358 212 35 10 8907 9109 245555812 245555605 7.860000e-21 113.0
62 TraesCS2B01G276900 chr5D 82.577 683 82 17 5952 6627 157076349 157077001 1.400000e-157 568.0
63 TraesCS2B01G276900 chr1D 87.500 480 53 5 8254 8733 365917316 365916844 1.820000e-151 547.0
64 TraesCS2B01G276900 chr1D 84.392 378 52 5 8737 9109 203870338 203869963 1.960000e-96 364.0
65 TraesCS2B01G276900 chr3D 90.305 361 34 1 6293 6652 121729686 121729326 1.130000e-128 472.0
66 TraesCS2B01G276900 chr7B 74.434 309 56 16 8815 9109 158933967 158933668 2.830000e-20 111.0
67 TraesCS2B01G276900 chr6D 74.267 307 60 15 8815 9109 460366800 460367099 2.830000e-20 111.0
68 TraesCS2B01G276900 chr1A 75.688 218 38 11 8899 9106 569489118 569489330 2.850000e-15 95.3
69 TraesCS2B01G276900 chr1A 75.688 218 38 11 8899 9106 569512127 569512339 2.850000e-15 95.3


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 TraesCS2B01G276900 chr2B 382588832 382598403 9571 False 17677.000000 17677 100.000000 1 9572 1 chr2B.!!$F1 9571
1 TraesCS2B01G276900 chr2B 383374862 383377014 2152 False 3402.000000 3402 95.357000 4553 6683 1 chr2B.!!$F4 2130
2 TraesCS2B01G276900 chr2D 314492431 314499113 6682 False 3237.666667 4442 94.908000 991 9572 3 chr2D.!!$F3 8581
3 TraesCS2B01G276900 chr2D 314368591 314369494 903 False 388.333333 726 89.734667 1 995 3 chr2D.!!$F2 994
4 TraesCS2B01G276900 chr2A 421076714 421078285 1571 True 1951.000000 1951 89.346000 1 1567 1 chr2A.!!$R1 1566
5 TraesCS2B01G276900 chr2A 421059226 421068530 9304 True 1820.000000 3744 94.485400 1566 9572 5 chr2A.!!$R2 8006
6 TraesCS2B01G276900 chr2A 422127682 422128827 1145 False 1567.000000 1567 91.219000 7904 9071 1 chr2A.!!$F2 1167
7 TraesCS2B01G276900 chr2A 422110649 422113925 3276 False 536.000000 1118 95.690667 6935 7909 3 chr2A.!!$F4 974
8 TraesCS2B01G276900 chr7D 545394078 545396424 2346 True 3626.000000 3626 94.706000 4354 6683 1 chr7D.!!$R1 2329
9 TraesCS2B01G276900 chr6B 88752598 88754972 2374 True 3186.000000 3186 91.152000 4340 6686 1 chr6B.!!$R1 2346
10 TraesCS2B01G276900 chr6B 312246519 312248416 1897 True 2832.000000 2832 93.645000 4354 6248 1 chr6B.!!$R2 1894
11 TraesCS2B01G276900 chr6A 493730390 493732712 2322 False 2929.000000 2929 89.516000 4354 6685 1 chr6A.!!$F1 2331
12 TraesCS2B01G276900 chr3B 823254897 823256915 2018 False 2828.000000 2828 92.429000 4723 6683 1 chr3B.!!$F2 1960
13 TraesCS2B01G276900 chr3B 299779732 299785255 5523 True 957.000000 1533 83.778500 4354 6686 2 chr3B.!!$R4 2332
14 TraesCS2B01G276900 chr7A 314421118 314427390 6272 True 2681.333333 2798 89.229667 4354 6694 3 chr7A.!!$R3 2340
15 TraesCS2B01G276900 chr7A 245980855 245982103 1248 True 1476.000000 1476 88.170000 4354 5602 1 chr7A.!!$R1 1248
16 TraesCS2B01G276900 chr4B 392845750 392847622 1872 False 2771.000000 2771 93.397000 4354 6225 1 chr4B.!!$F1 1871
17 TraesCS2B01G276900 chr4A 583751842 583754117 2275 True 2697.000000 2697 87.997000 4354 6683 1 chr4A.!!$R1 2329
18 TraesCS2B01G276900 chr4A 722099213 722101067 1854 False 2036.000000 2036 86.424000 6793 8683 1 chr4A.!!$F2 1890
19 TraesCS2B01G276900 chr4A 722081827 722083681 1854 False 2030.000000 2030 86.371000 6793 8683 1 chr4A.!!$F1 1890
20 TraesCS2B01G276900 chr1B 116525762 116527736 1974 True 2645.000000 2645 90.950000 4354 6316 1 chr1B.!!$R1 1962
21 TraesCS2B01G276900 chr1B 421460542 421462155 1613 True 1242.000000 1242 80.955000 4807 6426 1 chr1B.!!$R2 1619
22 TraesCS2B01G276900 chrUn 2103364 2105270 1906 True 2302.000000 2302 88.369000 6793 8733 1 chrUn.!!$R1 1940
23 TraesCS2B01G276900 chrUn 26910664 26911265 601 False 414.000000 414 80.000000 6113 6684 1 chrUn.!!$F1 571
24 TraesCS2B01G276900 chr3A 746138569 746139829 1260 True 1509.000000 1509 88.477000 4354 5602 1 chr3A.!!$R1 1248
25 TraesCS2B01G276900 chr3A 698027293 698028552 1259 False 1502.000000 1502 88.379000 4354 5602 1 chr3A.!!$F4 1248
26 TraesCS2B01G276900 chr3A 251346610 251347192 582 False 486.000000 486 82.373000 6117 6683 1 chr3A.!!$F2 566
27 TraesCS2B01G276900 chr5B 291799684 291801444 1760 True 1181.000000 1181 79.345000 4841 6590 1 chr5B.!!$R2 1749
28 TraesCS2B01G276900 chr5D 157076349 157077001 652 False 568.000000 568 82.577000 5952 6627 1 chr5D.!!$F1 675

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
951 984 0.036010 ATTTCAGCTGGTGGAGACGG 60.036 55.000 15.13 0.00 0.00 4.79 F
1947 1986 0.395586 TTGCTGTTTGCCACCTGACT 60.396 50.000 0.00 0.00 42.00 3.41 F
2795 3243 0.034574 ATTGCAGCCCGGTGTATCAA 60.035 50.000 0.00 0.00 0.00 2.57 F
3592 4041 0.919710 AAGAGCAACAGGATACCCCC 59.080 55.000 0.00 0.00 34.66 5.40 F
5125 10786 1.145819 GGCTGACTGGAGATCCTGC 59.854 63.158 5.73 0.71 38.38 4.85 F
6172 14016 1.048601 TCTCCTCCGGCATGAATACC 58.951 55.000 0.00 0.00 0.00 2.73 F
6997 15068 0.402887 TGGGCATATGCTCCTCCATG 59.597 55.000 24.67 0.00 41.95 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2662 3110 1.001860 GCAAAAGGTTATGCCAAGCCA 59.998 47.619 0.00 0.0 40.61 4.75 R
3448 3897 0.902516 GGAGGAGACTGCCTGACACT 60.903 60.000 0.00 0.0 44.13 3.55 R
4385 4834 0.494551 TCCTTCCCCTACAACCTCCA 59.505 55.000 0.00 0.0 0.00 3.86 R
5482 11143 0.253327 CCCTCAACTAGCTCAACCCC 59.747 60.000 0.00 0.0 0.00 4.95 R
6883 14909 1.538047 TCAGCATTTGGCCTGAAGTC 58.462 50.000 3.32 0.0 46.50 3.01 R
7770 18152 2.549754 GCCGAACACTCCATATGATTGG 59.450 50.000 3.65 0.0 38.18 3.16 R
8980 19518 0.979709 CAGAGGACAGAGGGGATGCA 60.980 60.000 0.00 0.0 0.00 3.96 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
35 36 8.034215 TCCTTTTGATGATTATGTGCGAAAAAT 58.966 29.630 0.00 0.00 0.00 1.82
40 41 7.195646 TGATGATTATGTGCGAAAAATTCTCC 58.804 34.615 0.00 0.00 0.00 3.71
42 43 7.099266 TGATTATGTGCGAAAAATTCTCCAT 57.901 32.000 0.00 0.00 0.00 3.41
46 47 4.797471 TGTGCGAAAAATTCTCCATTGAG 58.203 39.130 0.00 0.00 40.17 3.02
53 54 7.754924 GCGAAAAATTCTCCATTGAGTATTCAA 59.245 33.333 2.87 2.87 46.67 2.69
92 99 7.756395 ATTGGTTATCTAGATTGATGCCTTG 57.244 36.000 11.25 0.00 0.00 3.61
130 137 2.550830 ACTCACAAGTCACATCCCAC 57.449 50.000 0.00 0.00 0.00 4.61
142 149 0.890683 CATCCCACCTTCCTTTGCAC 59.109 55.000 0.00 0.00 0.00 4.57
147 154 1.548582 CCACCTTCCTTTGCACTGGAT 60.549 52.381 7.59 0.00 31.76 3.41
169 176 5.052693 TCACATCTTTATAGGGCATGCTT 57.947 39.130 18.92 9.04 0.00 3.91
171 178 6.600388 TCACATCTTTATAGGGCATGCTTTA 58.400 36.000 18.92 10.70 0.00 1.85
172 179 7.233632 TCACATCTTTATAGGGCATGCTTTAT 58.766 34.615 18.92 16.74 0.00 1.40
184 191 8.482852 AGGGCATGCTTTATAATTTTACAGAT 57.517 30.769 18.92 0.00 0.00 2.90
185 192 8.362639 AGGGCATGCTTTATAATTTTACAGATG 58.637 33.333 18.92 0.00 0.00 2.90
249 257 5.621228 CACGAACTTTTACATCAGCAAGTTC 59.379 40.000 11.83 11.83 46.21 3.01
264 272 5.754890 CAGCAAGTTCCAAGCTTACATTTTT 59.245 36.000 0.00 0.00 36.26 1.94
277 285 9.768662 AAGCTTACATTTTTCTGTCAATTGATT 57.231 25.926 12.12 0.00 0.00 2.57
322 331 7.716123 TGTTTTCTTTGATGCTCAATCCATTTT 59.284 29.630 0.41 0.00 36.11 1.82
355 364 9.630098 ATGTAGCATTTTTCTTTGTTACTGATG 57.370 29.630 0.00 0.00 32.65 3.07
356 365 8.845227 TGTAGCATTTTTCTTTGTTACTGATGA 58.155 29.630 0.00 0.00 32.65 2.92
357 366 9.677567 GTAGCATTTTTCTTTGTTACTGATGAA 57.322 29.630 0.00 0.00 29.90 2.57
358 367 8.579682 AGCATTTTTCTTTGTTACTGATGAAC 57.420 30.769 0.00 0.00 0.00 3.18
359 368 7.653311 AGCATTTTTCTTTGTTACTGATGAACC 59.347 33.333 0.00 0.00 0.00 3.62
362 371 6.385649 TTTCTTTGTTACTGATGAACCACC 57.614 37.500 0.00 0.00 0.00 4.61
363 372 5.304686 TCTTTGTTACTGATGAACCACCT 57.695 39.130 0.00 0.00 0.00 4.00
364 373 6.428083 TCTTTGTTACTGATGAACCACCTA 57.572 37.500 0.00 0.00 0.00 3.08
365 374 6.228258 TCTTTGTTACTGATGAACCACCTAC 58.772 40.000 0.00 0.00 0.00 3.18
366 375 4.182693 TGTTACTGATGAACCACCTACG 57.817 45.455 0.00 0.00 0.00 3.51
369 378 2.244695 ACTGATGAACCACCTACGACA 58.755 47.619 0.00 0.00 0.00 4.35
370 379 2.631062 ACTGATGAACCACCTACGACAA 59.369 45.455 0.00 0.00 0.00 3.18
371 380 2.993899 CTGATGAACCACCTACGACAAC 59.006 50.000 0.00 0.00 0.00 3.32
372 381 1.990563 GATGAACCACCTACGACAACG 59.009 52.381 0.00 0.00 45.75 4.10
373 382 0.598158 TGAACCACCTACGACAACGC 60.598 55.000 0.00 0.00 43.96 4.84
376 385 2.369629 CCACCTACGACAACGCGTG 61.370 63.158 14.98 10.05 45.23 5.34
377 386 2.049802 ACCTACGACAACGCGTGG 60.050 61.111 14.98 14.06 45.23 4.94
379 388 3.475774 CTACGACAACGCGTGGGC 61.476 66.667 19.66 15.39 45.23 5.36
419 438 8.458843 AGTAATATGTAAATCCAGTGTTGTTGC 58.541 33.333 0.00 0.00 0.00 4.17
455 474 9.961264 ATATATGGAGTGAGTATAGACGAAGAA 57.039 33.333 0.00 0.00 0.00 2.52
460 479 5.498393 AGTGAGTATAGACGAAGAACCTGA 58.502 41.667 0.00 0.00 0.00 3.86
611 634 7.913674 AAGAAGAGAATTTGTAGACCATGTC 57.086 36.000 0.00 0.00 0.00 3.06
744 771 9.126151 AGAGTGGATATGGTAATGATATAGTCG 57.874 37.037 0.00 0.00 0.00 4.18
766 793 8.709646 AGTCGTAGTTGTAATCTGTCATTTTTC 58.290 33.333 0.00 0.00 0.00 2.29
768 795 9.917129 TCGTAGTTGTAATCTGTCATTTTTCTA 57.083 29.630 0.00 0.00 0.00 2.10
778 810 4.326826 TGTCATTTTTCTAGAGTGGCCTG 58.673 43.478 3.32 0.00 0.00 4.85
781 813 5.241728 GTCATTTTTCTAGAGTGGCCTGTTT 59.758 40.000 3.32 0.00 0.00 2.83
787 819 1.109323 AGAGTGGCCTGTTTTGTGCC 61.109 55.000 3.32 0.00 45.56 5.01
818 851 8.084684 GGTTCAATTATCCTATGGCATTTTCTC 58.915 37.037 4.78 0.00 0.00 2.87
923 956 2.217510 TCTCCTCAAAGCGGTAGACT 57.782 50.000 0.00 0.00 0.00 3.24
925 958 1.819288 CTCCTCAAAGCGGTAGACTGA 59.181 52.381 0.00 0.00 0.00 3.41
926 959 1.544691 TCCTCAAAGCGGTAGACTGAC 59.455 52.381 0.00 0.00 0.00 3.51
927 960 1.404315 CCTCAAAGCGGTAGACTGACC 60.404 57.143 0.00 0.00 36.00 4.02
928 961 1.546476 CTCAAAGCGGTAGACTGACCT 59.454 52.381 0.00 0.00 37.34 3.85
929 962 2.753452 CTCAAAGCGGTAGACTGACCTA 59.247 50.000 0.00 0.00 37.34 3.08
930 963 2.753452 TCAAAGCGGTAGACTGACCTAG 59.247 50.000 0.00 0.00 37.34 3.02
931 964 1.765230 AAGCGGTAGACTGACCTAGG 58.235 55.000 7.41 7.41 37.34 3.02
932 965 0.917533 AGCGGTAGACTGACCTAGGA 59.082 55.000 17.98 0.00 37.34 2.94
933 966 1.495574 AGCGGTAGACTGACCTAGGAT 59.504 52.381 17.98 0.00 37.34 3.24
934 967 2.091775 AGCGGTAGACTGACCTAGGATT 60.092 50.000 17.98 0.00 37.34 3.01
935 968 2.694109 GCGGTAGACTGACCTAGGATTT 59.306 50.000 17.98 0.00 37.34 2.17
936 969 3.243468 GCGGTAGACTGACCTAGGATTTC 60.243 52.174 17.98 2.94 37.34 2.17
937 970 3.952323 CGGTAGACTGACCTAGGATTTCA 59.048 47.826 17.98 8.16 37.34 2.69
938 971 4.036971 CGGTAGACTGACCTAGGATTTCAG 59.963 50.000 20.90 20.90 42.17 3.02
939 972 4.202172 GGTAGACTGACCTAGGATTTCAGC 60.202 50.000 21.95 16.13 40.46 4.26
940 973 3.718723 AGACTGACCTAGGATTTCAGCT 58.281 45.455 21.95 17.57 40.46 4.24
941 974 3.450457 AGACTGACCTAGGATTTCAGCTG 59.550 47.826 21.95 7.63 40.46 4.24
942 975 2.503356 ACTGACCTAGGATTTCAGCTGG 59.497 50.000 21.95 5.79 40.46 4.85
943 976 2.503356 CTGACCTAGGATTTCAGCTGGT 59.497 50.000 17.98 0.00 30.90 4.00
944 977 2.237143 TGACCTAGGATTTCAGCTGGTG 59.763 50.000 17.98 0.00 0.00 4.17
945 978 1.561542 ACCTAGGATTTCAGCTGGTGG 59.438 52.381 17.98 7.19 0.00 4.61
946 979 1.839994 CCTAGGATTTCAGCTGGTGGA 59.160 52.381 15.13 0.00 0.00 4.02
947 980 2.158842 CCTAGGATTTCAGCTGGTGGAG 60.159 54.545 15.13 2.68 0.00 3.86
948 981 1.661463 AGGATTTCAGCTGGTGGAGA 58.339 50.000 15.13 0.00 0.00 3.71
949 982 1.280421 AGGATTTCAGCTGGTGGAGAC 59.720 52.381 15.13 0.00 0.00 3.36
950 983 1.363744 GATTTCAGCTGGTGGAGACG 58.636 55.000 15.13 0.00 0.00 4.18
951 984 0.036010 ATTTCAGCTGGTGGAGACGG 60.036 55.000 15.13 0.00 0.00 4.79
952 985 1.407656 TTTCAGCTGGTGGAGACGGT 61.408 55.000 15.13 0.00 0.00 4.83
1006 1039 2.746277 ACGGCGAGGAAATGGCAC 60.746 61.111 16.62 0.00 33.59 5.01
1074 1107 3.069318 GTCGCCGACTCCCTCCTT 61.069 66.667 10.56 0.00 0.00 3.36
1150 1183 4.749310 CCTCTCACGCCGCTTGCT 62.749 66.667 0.00 0.00 38.05 3.91
1343 1377 7.983307 TGATTGTTTTGAGGATTTTTGTTTGG 58.017 30.769 0.00 0.00 0.00 3.28
1407 1441 1.530183 GATGATGGGGAGCAAGGGC 60.530 63.158 0.00 0.00 41.61 5.19
1552 1586 6.265876 TCTGATGTTTGGTTTTAGGGTTTACC 59.734 38.462 0.00 0.00 40.67 2.85
1568 1605 5.277490 GGGTTTACCGGATTAGAATTAACGC 60.277 44.000 9.46 0.00 36.71 4.84
1629 1666 4.397103 TCCGTATTGTAAGATGTCTCGTGT 59.603 41.667 0.00 0.00 0.00 4.49
1655 1692 1.061411 CGAGTGTGCCAATCATGCG 59.939 57.895 4.07 0.00 0.00 4.73
1659 1696 1.303155 TGTGCCAATCATGCGACCA 60.303 52.632 0.00 0.00 0.00 4.02
1947 1986 0.395586 TTGCTGTTTGCCACCTGACT 60.396 50.000 0.00 0.00 42.00 3.41
1977 2016 0.991146 TGATGGGTTTAGCTGCCTGA 59.009 50.000 0.00 0.00 0.00 3.86
2014 2053 6.440647 TCCATAGTGGTAAGAACTTCTCATGT 59.559 38.462 0.00 0.00 39.03 3.21
2015 2054 6.536582 CCATAGTGGTAAGAACTTCTCATGTG 59.463 42.308 0.00 0.00 31.35 3.21
2016 2055 5.808366 AGTGGTAAGAACTTCTCATGTGA 57.192 39.130 0.00 0.00 0.00 3.58
2017 2056 6.365970 AGTGGTAAGAACTTCTCATGTGAT 57.634 37.500 0.00 0.00 0.00 3.06
2018 2057 6.169094 AGTGGTAAGAACTTCTCATGTGATG 58.831 40.000 8.62 8.62 0.00 3.07
2019 2058 5.934625 GTGGTAAGAACTTCTCATGTGATGT 59.065 40.000 9.74 9.74 0.00 3.06
2020 2059 6.091441 GTGGTAAGAACTTCTCATGTGATGTC 59.909 42.308 14.45 9.53 0.00 3.06
2021 2060 5.582665 GGTAAGAACTTCTCATGTGATGTCC 59.417 44.000 14.45 8.85 0.00 4.02
2022 2061 5.495926 AAGAACTTCTCATGTGATGTCCT 57.504 39.130 14.45 6.72 0.00 3.85
2023 2062 5.083533 AGAACTTCTCATGTGATGTCCTC 57.916 43.478 14.45 10.46 0.00 3.71
2024 2063 3.902881 ACTTCTCATGTGATGTCCTCC 57.097 47.619 9.74 0.00 0.00 4.30
2025 2064 3.176411 ACTTCTCATGTGATGTCCTCCA 58.824 45.455 9.74 0.00 0.00 3.86
2026 2065 3.779183 ACTTCTCATGTGATGTCCTCCAT 59.221 43.478 9.74 0.00 36.13 3.41
2027 2066 3.832615 TCTCATGTGATGTCCTCCATG 57.167 47.619 0.00 0.00 35.52 3.66
2028 2067 3.109928 TCTCATGTGATGTCCTCCATGT 58.890 45.455 0.00 0.00 35.62 3.21
2029 2068 3.520721 TCTCATGTGATGTCCTCCATGTT 59.479 43.478 0.00 0.00 35.62 2.71
2030 2069 4.019051 TCTCATGTGATGTCCTCCATGTTT 60.019 41.667 0.00 0.00 35.62 2.83
2031 2070 4.264253 TCATGTGATGTCCTCCATGTTTC 58.736 43.478 0.00 0.00 35.62 2.78
2032 2071 3.786368 TGTGATGTCCTCCATGTTTCA 57.214 42.857 0.00 0.00 32.56 2.69
2033 2072 4.305539 TGTGATGTCCTCCATGTTTCAT 57.694 40.909 0.00 0.00 32.56 2.57
2034 2073 4.011698 TGTGATGTCCTCCATGTTTCATG 58.988 43.478 3.11 3.11 32.56 3.07
2035 2074 4.012374 GTGATGTCCTCCATGTTTCATGT 58.988 43.478 8.57 0.00 32.56 3.21
2036 2075 4.460382 GTGATGTCCTCCATGTTTCATGTT 59.540 41.667 8.57 0.00 32.56 2.71
2037 2076 4.701651 TGATGTCCTCCATGTTTCATGTTC 59.298 41.667 8.57 0.00 32.56 3.18
2038 2077 4.371624 TGTCCTCCATGTTTCATGTTCT 57.628 40.909 8.57 0.00 0.00 3.01
2039 2078 4.326826 TGTCCTCCATGTTTCATGTTCTC 58.673 43.478 8.57 0.00 0.00 2.87
2040 2079 3.691609 GTCCTCCATGTTTCATGTTCTCC 59.308 47.826 8.57 0.00 0.00 3.71
2041 2080 3.019564 CCTCCATGTTTCATGTTCTCCC 58.980 50.000 8.57 0.00 0.00 4.30
2042 2081 3.019564 CTCCATGTTTCATGTTCTCCCC 58.980 50.000 8.57 0.00 0.00 4.81
2043 2082 2.102578 CCATGTTTCATGTTCTCCCCC 58.897 52.381 8.57 0.00 0.00 5.40
2078 2117 2.981909 TGCCAAGCTGCTGCAGAC 60.982 61.111 32.30 22.02 42.74 3.51
2079 2118 3.745803 GCCAAGCTGCTGCAGACC 61.746 66.667 32.30 15.86 42.74 3.85
2080 2119 3.060615 CCAAGCTGCTGCAGACCC 61.061 66.667 32.30 15.13 42.74 4.46
2081 2120 3.429141 CAAGCTGCTGCAGACCCG 61.429 66.667 32.30 13.28 42.74 5.28
2082 2121 4.711949 AAGCTGCTGCAGACCCGG 62.712 66.667 32.30 6.05 42.74 5.73
2175 2620 9.508567 GAAAGTTATTTTTCTATCAGGCATCAC 57.491 33.333 0.00 0.00 34.87 3.06
2194 2639 6.470235 GCATCACAAACTAATAACACTCATGC 59.530 38.462 0.00 0.00 0.00 4.06
2246 2692 6.014669 TGGCTACATTTTATTTTGCAACCTCT 60.015 34.615 0.00 0.00 0.00 3.69
2319 2765 4.936891 GTGAAGCTCACAGTTTTGGAATT 58.063 39.130 10.30 0.00 46.22 2.17
2355 2801 2.492881 TCGTTTGGTCCATAAGTAGCGA 59.507 45.455 0.00 0.00 0.00 4.93
2358 2804 2.526304 TGGTCCATAAGTAGCGATGC 57.474 50.000 0.00 0.00 0.00 3.91
2453 2899 5.589050 ACTTGTGGAACTTTGAGTCCTTTAC 59.411 40.000 0.00 0.00 38.04 2.01
2485 2931 9.669353 CAGTATTAGATTGATAATTTGTGGTGC 57.331 33.333 0.00 0.00 0.00 5.01
2581 3027 4.674885 GCAATTTGGCATAATGTTTTGGGC 60.675 41.667 0.00 0.00 0.00 5.36
2615 3063 2.500646 CCAATTTGCCGCCCCATC 59.499 61.111 0.00 0.00 0.00 3.51
2616 3064 2.059786 CCAATTTGCCGCCCCATCT 61.060 57.895 0.00 0.00 0.00 2.90
2659 3107 4.580167 ACTGTGTGTGCTGTTGTCAATATT 59.420 37.500 0.00 0.00 0.00 1.28
2662 3110 5.299028 TGTGTGTGCTGTTGTCAATATTCTT 59.701 36.000 0.00 0.00 0.00 2.52
2709 3157 7.548196 TGGTGATTTTCATCGTTCTTATACC 57.452 36.000 0.00 0.00 27.66 2.73
2726 3174 7.221450 TCTTATACCCCATCCACTTAAATTCG 58.779 38.462 0.00 0.00 0.00 3.34
2728 3176 3.352648 ACCCCATCCACTTAAATTCGTG 58.647 45.455 0.00 0.00 0.00 4.35
2795 3243 0.034574 ATTGCAGCCCGGTGTATCAA 60.035 50.000 0.00 0.00 0.00 2.57
2800 3248 1.077716 GCCCGGTGTATCAAGGCTT 60.078 57.895 0.00 0.00 40.57 4.35
2805 3253 4.710324 CCCGGTGTATCAAGGCTTATAAA 58.290 43.478 0.00 0.00 0.00 1.40
3120 3569 4.640364 ACAATTAATGCCACCAAAGGTTG 58.360 39.130 0.00 0.00 31.02 3.77
3165 3614 5.755375 CGGAAAGCATAAGTCATGACACTAT 59.245 40.000 27.02 18.81 36.69 2.12
3181 3630 5.932303 TGACACTATGACTAAAAGAACCAGC 59.068 40.000 0.00 0.00 0.00 4.85
3258 3707 1.731720 ATGACTTGCCTCTTTCGAGC 58.268 50.000 0.00 0.00 35.90 5.03
3391 3840 1.200020 CTCAATGCCGGGAAAGTTGTC 59.800 52.381 0.00 0.00 0.00 3.18
3425 3874 3.865745 GGATGACCGACATAGTTTGAGTG 59.134 47.826 0.00 0.00 39.56 3.51
3448 3897 6.003326 TGAAGATTCTGCACAGTTTGGAATA 58.997 36.000 0.00 0.00 0.00 1.75
3514 3963 4.679373 AAGTGACACAGAAGACACAGAT 57.321 40.909 8.59 0.00 35.97 2.90
3588 4037 6.651225 ACTTTCTTACAAGAGCAACAGGATAC 59.349 38.462 0.00 0.00 36.22 2.24
3592 4041 0.919710 AAGAGCAACAGGATACCCCC 59.080 55.000 0.00 0.00 34.66 5.40
3680 4129 6.943981 TCTTACGAAGTTGAAACAATCTGTG 58.056 36.000 0.00 0.00 37.78 3.66
3710 4159 7.108194 AGTACTCATCAATCATTGCTTTCTCA 58.892 34.615 0.00 0.00 0.00 3.27
3807 4256 3.825014 ACTTAGACGCCACTTTCAGAGTA 59.175 43.478 0.00 0.00 36.65 2.59
3918 4367 5.293560 GCGAGCTTCAGGATAAATCTACTT 58.706 41.667 0.00 0.00 0.00 2.24
4206 4655 4.438472 GCTTCTGCTCTAAATGCCAGAAAG 60.438 45.833 0.00 0.00 36.03 2.62
4385 4834 3.097293 TCCTACCGGACCTGCTCT 58.903 61.111 9.46 0.00 33.30 4.09
5021 10682 2.124695 GACCCTGCACGGAATCCC 60.125 66.667 8.88 0.00 33.16 3.85
5110 10771 2.812499 CGGGCGTAGTACATGGCT 59.188 61.111 0.00 0.00 38.74 4.75
5125 10786 1.145819 GGCTGACTGGAGATCCTGC 59.854 63.158 5.73 0.71 38.38 4.85
5483 11144 2.153913 CGAAAGAACTGGTCGCAGG 58.846 57.895 0.00 0.00 0.00 4.85
5492 11153 4.021925 GGTCGCAGGGGTTGAGCT 62.022 66.667 0.00 0.00 0.00 4.09
5541 11202 1.153353 GTGGCGAAGTCGATTTTGGA 58.847 50.000 9.68 0.00 43.02 3.53
5542 11203 1.533731 GTGGCGAAGTCGATTTTGGAA 59.466 47.619 9.68 0.00 43.02 3.53
5626 11287 3.319198 GGTGGAGCCTGGTCGGAA 61.319 66.667 0.00 0.00 33.16 4.30
5749 11410 2.270850 GCCCACGCTGGTATTGGA 59.729 61.111 3.82 0.00 35.17 3.53
5956 11623 2.930562 GGGGACTGCTGGAGGTGT 60.931 66.667 0.14 0.00 0.00 4.16
6172 14016 1.048601 TCTCCTCCGGCATGAATACC 58.951 55.000 0.00 0.00 0.00 2.73
6344 14306 3.176411 AGTGATGGAGAAGACATGGTCA 58.824 45.455 0.00 0.00 34.60 4.02
6687 14702 4.035208 GGCTAAACCGGTCATAACAGATTG 59.965 45.833 8.04 0.00 0.00 2.67
6863 14889 1.454847 CCTCTCCTCTCCTGTCCCG 60.455 68.421 0.00 0.00 0.00 5.14
6993 15064 1.133976 AGTGTTGGGCATATGCTCCTC 60.134 52.381 24.67 16.90 41.95 3.71
6997 15068 0.402887 TGGGCATATGCTCCTCCATG 59.597 55.000 24.67 0.00 41.95 3.66
7121 15615 9.060347 CATAATGGAAAGTTATGCAGACTGTAT 57.940 33.333 11.02 11.02 34.06 2.29
7175 15669 7.562454 TCCAAATTTGCAGAGATAAGATGGAAT 59.438 33.333 12.92 0.00 0.00 3.01
7384 15879 2.945447 TGTGCAAATAGCTTCATGCC 57.055 45.000 12.83 6.77 45.94 4.40
7486 15982 7.466746 TGCCATCCTATAATGATTTTTAGCC 57.533 36.000 0.00 0.00 0.00 3.93
8085 18471 3.057019 TCAAATGACAGACACGTGTAGC 58.943 45.455 23.44 10.50 0.00 3.58
8086 18472 2.799978 CAAATGACAGACACGTGTAGCA 59.200 45.455 23.44 16.78 0.00 3.49
8087 18473 2.812358 ATGACAGACACGTGTAGCAA 57.188 45.000 23.44 9.45 0.00 3.91
8089 18475 1.135333 TGACAGACACGTGTAGCAACA 59.865 47.619 23.44 14.96 0.00 3.33
8090 18476 2.223947 TGACAGACACGTGTAGCAACAT 60.224 45.455 23.44 2.88 38.08 2.71
8091 18477 2.135139 ACAGACACGTGTAGCAACATG 58.865 47.619 23.44 13.41 46.30 3.21
8092 18478 1.460743 CAGACACGTGTAGCAACATGG 59.539 52.381 23.44 0.00 45.34 3.66
8094 18480 1.726791 GACACGTGTAGCAACATGGAG 59.273 52.381 23.44 0.00 45.34 3.86
8184 18570 3.325870 TGATTCAGTTTACGAGGCACAG 58.674 45.455 0.00 0.00 0.00 3.66
8328 18714 4.276926 CAGCTTTTCCTGAGTGCTAAAGTT 59.723 41.667 0.00 0.00 34.77 2.66
8348 18734 4.879545 AGTTTGTCTCCTTTCGTTAAAGCA 59.120 37.500 0.00 0.00 40.73 3.91
8662 19197 3.658757 TTTCCTTTGCTGGTTACATGC 57.341 42.857 0.00 0.00 0.00 4.06
8760 19295 0.542333 TTGGTTGTCCACGGTCTTGA 59.458 50.000 0.00 0.00 44.22 3.02
8762 19297 1.142060 TGGTTGTCCACGGTCTTGAAT 59.858 47.619 0.00 0.00 39.03 2.57
8840 19375 0.664761 CACTCTGGCAACACCACAAG 59.335 55.000 0.00 0.00 46.36 3.16
8870 19405 1.194218 TCGACAAGATCATGCCCTCA 58.806 50.000 0.00 0.00 0.00 3.86
8949 19487 4.347607 AGCCAAAGGAGTTGCATTAATCT 58.652 39.130 0.00 0.00 35.74 2.40
8980 19518 2.086610 ACTGATGTTTTTGGGGCTGT 57.913 45.000 0.00 0.00 0.00 4.40
9423 19991 4.793678 GCACAAATGATTCAGTCAGCAACA 60.794 41.667 0.00 0.00 40.92 3.33
9425 19993 5.174398 CACAAATGATTCAGTCAGCAACAAC 59.826 40.000 0.00 0.00 40.92 3.32
9426 19994 5.163530 ACAAATGATTCAGTCAGCAACAACA 60.164 36.000 0.00 0.00 40.92 3.33
9427 19995 5.518848 AATGATTCAGTCAGCAACAACAA 57.481 34.783 0.00 0.00 40.92 2.83
9482 20067 8.528643 AGGTACTTAATTGGAAATTTAGGTTGC 58.471 33.333 0.00 0.00 27.25 4.17
9505 20090 7.860613 TGCCATACGAAATGTAAGATGTATTG 58.139 34.615 0.00 0.00 36.44 1.90
9544 20129 5.648960 TCCGATGAATGCATGCATATTACAT 59.351 36.000 32.36 28.86 35.31 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.195646 TGGAGAATTTTTCGCACATAATCATC 58.804 34.615 0.00 0.00 34.02 2.92
20 21 7.546358 TCAATGGAGAATTTTTCGCACATAAT 58.454 30.769 0.00 0.00 34.02 1.28
63 70 9.899226 GGCATCAATCTAGATAACCAATTAAAC 57.101 33.333 5.46 0.00 0.00 2.01
66 73 9.288576 CAAGGCATCAATCTAGATAACCAATTA 57.711 33.333 5.46 0.00 0.00 1.40
71 78 6.291377 TCACAAGGCATCAATCTAGATAACC 58.709 40.000 5.46 3.74 0.00 2.85
92 99 7.192913 TGTGAGTCATTACAATTGTGTTTCAC 58.807 34.615 21.42 21.07 39.30 3.18
111 118 1.072331 GGTGGGATGTGACTTGTGAGT 59.928 52.381 0.00 0.00 39.32 3.41
130 137 1.815003 GTGATCCAGTGCAAAGGAAGG 59.185 52.381 11.95 0.00 37.48 3.46
142 149 5.233083 TGCCCTATAAAGATGTGATCCAG 57.767 43.478 0.00 0.00 0.00 3.86
147 154 4.712051 AGCATGCCCTATAAAGATGTGA 57.288 40.909 15.66 0.00 0.00 3.58
169 176 9.729023 CGAAATGCCACATCTGTAAAATTATAA 57.271 29.630 0.00 0.00 0.00 0.98
171 178 7.995289 TCGAAATGCCACATCTGTAAAATTAT 58.005 30.769 0.00 0.00 0.00 1.28
172 179 7.384439 TCGAAATGCCACATCTGTAAAATTA 57.616 32.000 0.00 0.00 0.00 1.40
184 191 4.533919 ATTTTGGATTCGAAATGCCACA 57.466 36.364 14.86 8.11 36.05 4.17
185 192 5.650543 AGTATTTTGGATTCGAAATGCCAC 58.349 37.500 14.86 0.58 39.00 5.01
217 225 7.960738 GCTGATGTAAAAGTTCGTGCTTAATAA 59.039 33.333 0.00 0.00 0.00 1.40
224 232 3.536158 TGCTGATGTAAAAGTTCGTGC 57.464 42.857 0.00 0.00 0.00 5.34
249 257 7.652909 TCAATTGACAGAAAAATGTAAGCTTGG 59.347 33.333 9.86 0.00 32.25 3.61
329 338 9.630098 CATCAGTAACAAAGAAAAATGCTACAT 57.370 29.630 0.00 0.00 0.00 2.29
348 357 3.423749 TGTCGTAGGTGGTTCATCAGTA 58.576 45.455 0.00 0.00 0.00 2.74
349 358 2.244695 TGTCGTAGGTGGTTCATCAGT 58.755 47.619 0.00 0.00 0.00 3.41
350 359 2.993899 GTTGTCGTAGGTGGTTCATCAG 59.006 50.000 0.00 0.00 0.00 2.90
351 360 2.608506 CGTTGTCGTAGGTGGTTCATCA 60.609 50.000 0.00 0.00 0.00 3.07
352 361 1.990563 CGTTGTCGTAGGTGGTTCATC 59.009 52.381 0.00 0.00 0.00 2.92
353 362 1.938016 GCGTTGTCGTAGGTGGTTCAT 60.938 52.381 0.00 0.00 39.49 2.57
354 363 0.598158 GCGTTGTCGTAGGTGGTTCA 60.598 55.000 0.00 0.00 39.49 3.18
355 364 1.611592 CGCGTTGTCGTAGGTGGTTC 61.612 60.000 0.00 0.00 39.49 3.62
356 365 1.662446 CGCGTTGTCGTAGGTGGTT 60.662 57.895 0.00 0.00 39.49 3.67
357 366 2.049802 CGCGTTGTCGTAGGTGGT 60.050 61.111 0.00 0.00 39.49 4.16
358 367 2.049802 ACGCGTTGTCGTAGGTGG 60.050 61.111 5.58 0.00 41.36 4.61
359 368 2.369629 CCACGCGTTGTCGTAGGTG 61.370 63.158 10.22 0.00 41.21 4.00
362 371 3.475774 GCCCACGCGTTGTCGTAG 61.476 66.667 10.22 0.00 41.21 3.51
363 372 4.281947 TGCCCACGCGTTGTCGTA 62.282 61.111 10.22 0.00 41.21 3.43
369 378 3.463728 TAGTTGGTGCCCACGCGTT 62.464 57.895 10.22 0.00 38.08 4.84
370 379 3.876589 CTAGTTGGTGCCCACGCGT 62.877 63.158 5.58 5.58 38.08 6.01
371 380 3.118454 CTAGTTGGTGCCCACGCG 61.118 66.667 3.53 3.53 38.08 6.01
372 381 1.170290 AAACTAGTTGGTGCCCACGC 61.170 55.000 9.34 0.00 30.78 5.34
373 382 0.872388 GAAACTAGTTGGTGCCCACG 59.128 55.000 9.34 0.00 30.78 4.94
375 384 1.493022 ACTGAAACTAGTTGGTGCCCA 59.507 47.619 9.34 0.68 0.00 5.36
376 385 2.271944 ACTGAAACTAGTTGGTGCCC 57.728 50.000 9.34 0.00 0.00 5.36
377 386 6.598064 ACATATTACTGAAACTAGTTGGTGCC 59.402 38.462 9.34 0.00 32.19 5.01
378 387 7.611213 ACATATTACTGAAACTAGTTGGTGC 57.389 36.000 9.34 0.23 32.19 5.01
391 400 9.733556 AACAACACTGGATTTACATATTACTGA 57.266 29.630 0.00 0.00 0.00 3.41
392 401 9.773328 CAACAACACTGGATTTACATATTACTG 57.227 33.333 0.00 0.00 0.00 2.74
393 402 8.458843 GCAACAACACTGGATTTACATATTACT 58.541 33.333 0.00 0.00 0.00 2.24
394 403 8.458843 AGCAACAACACTGGATTTACATATTAC 58.541 33.333 0.00 0.00 0.00 1.89
395 404 8.574251 AGCAACAACACTGGATTTACATATTA 57.426 30.769 0.00 0.00 0.00 0.98
433 452 5.299782 GGTTCTTCGTCTATACTCACTCCAT 59.700 44.000 0.00 0.00 0.00 3.41
434 453 4.639310 GGTTCTTCGTCTATACTCACTCCA 59.361 45.833 0.00 0.00 0.00 3.86
438 457 5.814764 TCAGGTTCTTCGTCTATACTCAC 57.185 43.478 0.00 0.00 0.00 3.51
445 464 4.081697 TGCATCATTCAGGTTCTTCGTCTA 60.082 41.667 0.00 0.00 0.00 2.59
449 468 3.005554 AGTGCATCATTCAGGTTCTTCG 58.994 45.455 0.00 0.00 0.00 3.79
586 609 8.041323 GGACATGGTCTACAAATTCTCTTCTTA 58.959 37.037 0.00 0.00 32.47 2.10
611 634 7.449395 TCATTCTTTTGCTATTATCCCATGAGG 59.551 37.037 0.00 0.00 0.00 3.86
676 702 7.392953 TGCAAACTGATTGAAATGGATACACTA 59.607 33.333 1.49 0.00 46.86 2.74
766 793 1.537202 GCACAAAACAGGCCACTCTAG 59.463 52.381 5.01 0.00 0.00 2.43
768 795 1.109323 GGCACAAAACAGGCCACTCT 61.109 55.000 5.01 0.00 46.92 3.24
769 796 1.363807 GGCACAAAACAGGCCACTC 59.636 57.895 5.01 0.00 46.92 3.51
787 819 4.935808 GCCATAGGATAATTGAACCCGTAG 59.064 45.833 0.00 0.00 0.00 3.51
855 888 1.402107 CCTGCTTTGTGGGCCAGTTT 61.402 55.000 6.40 0.00 0.00 2.66
857 890 2.203538 CCTGCTTTGTGGGCCAGT 60.204 61.111 6.40 0.00 0.00 4.00
896 929 2.271800 CGCTTTGAGGAGAATAGCGTT 58.728 47.619 0.00 0.00 46.82 4.84
897 930 1.927895 CGCTTTGAGGAGAATAGCGT 58.072 50.000 0.00 0.00 46.82 5.07
923 956 2.237143 CACCAGCTGAAATCCTAGGTCA 59.763 50.000 17.39 4.46 0.00 4.02
925 958 1.561542 CCACCAGCTGAAATCCTAGGT 59.438 52.381 17.39 0.00 0.00 3.08
926 959 1.839994 TCCACCAGCTGAAATCCTAGG 59.160 52.381 17.39 0.82 0.00 3.02
927 960 2.768527 TCTCCACCAGCTGAAATCCTAG 59.231 50.000 17.39 3.29 0.00 3.02
928 961 2.501723 GTCTCCACCAGCTGAAATCCTA 59.498 50.000 17.39 0.00 0.00 2.94
929 962 1.280421 GTCTCCACCAGCTGAAATCCT 59.720 52.381 17.39 0.00 0.00 3.24
930 963 1.743996 GTCTCCACCAGCTGAAATCC 58.256 55.000 17.39 0.00 0.00 3.01
931 964 1.363744 CGTCTCCACCAGCTGAAATC 58.636 55.000 17.39 0.00 0.00 2.17
932 965 0.036010 CCGTCTCCACCAGCTGAAAT 60.036 55.000 17.39 0.00 0.00 2.17
933 966 1.371183 CCGTCTCCACCAGCTGAAA 59.629 57.895 17.39 0.00 0.00 2.69
934 967 0.541063 TACCGTCTCCACCAGCTGAA 60.541 55.000 17.39 0.00 0.00 3.02
935 968 0.324368 ATACCGTCTCCACCAGCTGA 60.324 55.000 17.39 0.00 0.00 4.26
936 969 0.103208 GATACCGTCTCCACCAGCTG 59.897 60.000 6.78 6.78 0.00 4.24
937 970 1.043673 GGATACCGTCTCCACCAGCT 61.044 60.000 0.00 0.00 32.72 4.24
938 971 1.442148 GGATACCGTCTCCACCAGC 59.558 63.158 0.00 0.00 32.72 4.85
951 984 1.640917 TGGCTTCGATAGGGGGATAC 58.359 55.000 0.00 0.00 0.00 2.24
952 985 2.467880 GATGGCTTCGATAGGGGGATA 58.532 52.381 0.00 0.00 0.00 2.59
1074 1107 1.675219 GTTGCTTACGAGGTGGGGA 59.325 57.895 0.00 0.00 0.00 4.81
1150 1183 1.000993 GCAGAGGAGGGAGGACAGA 59.999 63.158 0.00 0.00 0.00 3.41
1343 1377 7.311364 TCGAATTGCCTTGTTTACCTAATAC 57.689 36.000 0.00 0.00 0.00 1.89
1407 1441 0.603707 AATACCTGATCCCATGCGCG 60.604 55.000 0.00 0.00 0.00 6.86
1414 1448 3.135530 AGTCTGAAGCAATACCTGATCCC 59.864 47.826 0.00 0.00 0.00 3.85
1552 1586 4.868450 TTGGTGCGTTAATTCTAATCCG 57.132 40.909 0.00 0.00 0.00 4.18
1568 1605 3.130340 ACTGGTTACTTGCAAGTTTGGTG 59.870 43.478 35.20 23.40 40.37 4.17
1629 1666 1.815817 TTGGCACACTCGAGCTGCTA 61.816 55.000 26.38 21.20 39.29 3.49
1655 1692 3.798202 ACTGAAACTCACTCTGTTGGTC 58.202 45.455 0.00 0.00 0.00 4.02
1659 1696 4.744795 ACTGACTGAAACTCACTCTGTT 57.255 40.909 0.00 0.00 0.00 3.16
1862 1901 6.590656 AGGGGATGAAACAGGTAAATATGA 57.409 37.500 0.00 0.00 0.00 2.15
1947 1986 6.096705 CAGCTAAACCCATCATCAAAATGGTA 59.903 38.462 1.79 0.00 41.84 3.25
1977 2016 9.615660 TCTTACCACTATGGAGATAATATTGGT 57.384 33.333 0.84 9.52 42.74 3.67
2005 2044 3.900966 TGGAGGACATCACATGAGAAG 57.099 47.619 0.00 0.00 0.00 2.85
2014 2053 4.305539 ACATGAAACATGGAGGACATCA 57.694 40.909 14.70 0.00 37.84 3.07
2015 2054 4.946157 AGAACATGAAACATGGAGGACATC 59.054 41.667 14.70 3.64 37.84 3.06
2016 2055 4.927049 AGAACATGAAACATGGAGGACAT 58.073 39.130 14.70 0.00 41.57 3.06
2017 2056 4.326826 GAGAACATGAAACATGGAGGACA 58.673 43.478 14.70 0.00 0.00 4.02
2018 2057 3.691609 GGAGAACATGAAACATGGAGGAC 59.308 47.826 14.70 4.13 0.00 3.85
2019 2058 3.308402 GGGAGAACATGAAACATGGAGGA 60.308 47.826 14.70 0.00 0.00 3.71
2020 2059 3.019564 GGGAGAACATGAAACATGGAGG 58.980 50.000 14.70 0.00 0.00 4.30
2021 2060 3.019564 GGGGAGAACATGAAACATGGAG 58.980 50.000 14.70 0.00 0.00 3.86
2022 2061 2.291540 GGGGGAGAACATGAAACATGGA 60.292 50.000 14.70 0.00 0.00 3.41
2023 2062 2.102578 GGGGGAGAACATGAAACATGG 58.897 52.381 14.70 0.00 0.00 3.66
2061 2100 2.981909 GTCTGCAGCAGCTTGGCA 60.982 61.111 18.43 7.19 42.74 4.92
2062 2101 3.745803 GGTCTGCAGCAGCTTGGC 61.746 66.667 18.43 5.05 42.74 4.52
2063 2102 3.060615 GGGTCTGCAGCAGCTTGG 61.061 66.667 18.43 0.00 42.74 3.61
2064 2103 3.429141 CGGGTCTGCAGCAGCTTG 61.429 66.667 18.43 3.55 42.74 4.01
2065 2104 4.711949 CCGGGTCTGCAGCAGCTT 62.712 66.667 18.43 0.00 42.74 3.74
2068 2107 4.007644 TGTCCGGGTCTGCAGCAG 62.008 66.667 17.10 17.10 0.00 4.24
2069 2108 4.314440 GTGTCCGGGTCTGCAGCA 62.314 66.667 9.47 0.00 0.00 4.41
2071 2110 3.314331 AGGTGTCCGGGTCTGCAG 61.314 66.667 7.63 7.63 0.00 4.41
2072 2111 3.625897 CAGGTGTCCGGGTCTGCA 61.626 66.667 0.00 0.00 0.00 4.41
2074 2113 4.394712 GGCAGGTGTCCGGGTCTG 62.395 72.222 0.00 5.77 0.00 3.51
2079 2118 3.402681 ATGAGGGCAGGTGTCCGG 61.403 66.667 0.00 0.00 46.49 5.14
2080 2119 2.124983 CATGAGGGCAGGTGTCCG 60.125 66.667 0.00 0.00 46.49 4.79
2081 2120 2.439156 GCATGAGGGCAGGTGTCC 60.439 66.667 0.00 0.00 40.99 4.02
2082 2121 2.042831 GTGCATGAGGGCAGGTGTC 61.043 63.158 0.00 0.00 45.96 3.67
2083 2122 2.034687 GTGCATGAGGGCAGGTGT 59.965 61.111 0.00 0.00 45.96 4.16
2084 2123 1.592400 CTTGTGCATGAGGGCAGGTG 61.592 60.000 0.00 0.00 45.96 4.00
2106 2551 6.530019 AAAACCTTGATGGCTAAAGTATGG 57.470 37.500 0.00 0.00 40.22 2.74
2355 2801 1.883926 GGTTTAGTTTGGACACGGCAT 59.116 47.619 0.00 0.00 0.00 4.40
2358 2804 3.069289 GGTAGGTTTAGTTTGGACACGG 58.931 50.000 0.00 0.00 0.00 4.94
2485 2931 6.005823 TCCAATAAATAGCCTGATGTGATGG 58.994 40.000 0.00 0.00 0.00 3.51
2542 2988 7.118971 TGCCAAATTGCCACTTCAATAATAAAC 59.881 33.333 0.00 0.00 35.77 2.01
2581 3027 1.596603 TGGCATGAATAGGATGCACG 58.403 50.000 0.00 0.00 46.77 5.34
2615 3063 5.006455 CAGTTCTGCACATGCTAGATGTTAG 59.994 44.000 5.31 2.75 42.66 2.34
2616 3064 4.872124 CAGTTCTGCACATGCTAGATGTTA 59.128 41.667 5.31 0.00 42.66 2.41
2659 3107 2.603075 AAGGTTATGCCAAGCCAAGA 57.397 45.000 0.00 0.00 40.61 3.02
2662 3110 1.001860 GCAAAAGGTTATGCCAAGCCA 59.998 47.619 0.00 0.00 40.61 4.75
2709 3157 6.317642 TCATAACACGAATTTAAGTGGATGGG 59.682 38.462 16.84 6.05 42.25 4.00
2726 3174 7.553881 ACACACTAGCCAATATTCATAACAC 57.446 36.000 0.00 0.00 0.00 3.32
2728 3176 7.985476 ACAACACACTAGCCAATATTCATAAC 58.015 34.615 0.00 0.00 0.00 1.89
2805 3253 6.021030 TGGGGTAACATAGAAGTTCAGTAGT 58.979 40.000 5.50 0.00 39.74 2.73
2878 3326 5.061853 GCCATCAAGATATTCTCAGCTGAA 58.938 41.667 18.85 3.88 0.00 3.02
2886 3334 7.565190 TTAGAGATGGCCATCAAGATATTCT 57.435 36.000 40.05 32.14 40.22 2.40
3120 3569 2.859806 GCAGCAGATGAACAACCAACAC 60.860 50.000 0.00 0.00 0.00 3.32
3157 3606 5.932303 GCTGGTTCTTTTAGTCATAGTGTCA 59.068 40.000 0.00 0.00 0.00 3.58
3165 3614 6.293955 GCTTGTAATGCTGGTTCTTTTAGTCA 60.294 38.462 0.00 0.00 33.64 3.41
3258 3707 7.547019 TCAGAAGCTTCAGAATAATGTGTAGTG 59.453 37.037 27.57 11.33 0.00 2.74
3425 3874 4.836125 TTCCAAACTGTGCAGAATCTTC 57.164 40.909 6.17 0.00 0.00 2.87
3448 3897 0.902516 GGAGGAGACTGCCTGACACT 60.903 60.000 0.00 0.00 44.13 3.55
3514 3963 7.253983 GCAAGTTTCACAAATATATCTCGTCGA 60.254 37.037 0.00 0.00 0.00 4.20
3561 4010 5.527582 TCCTGTTGCTCTTGTAAGAAAGTTC 59.472 40.000 0.00 0.00 34.03 3.01
3588 4037 1.981495 ACTGAGAGAGACTTTTGGGGG 59.019 52.381 0.00 0.00 0.00 5.40
3592 4041 7.172190 TGCTTTGAATACTGAGAGAGACTTTTG 59.828 37.037 0.00 0.00 0.00 2.44
3680 4129 5.587844 AGCAATGATTGATGAGTACTTGGTC 59.412 40.000 9.76 0.00 0.00 4.02
3710 4159 7.592885 AAGCCTTATCATTAACATCTGCATT 57.407 32.000 0.00 0.00 0.00 3.56
3768 4217 7.326063 GCGTCTAAGTAATTTCAGCAAACAAAT 59.674 33.333 0.00 0.00 0.00 2.32
3789 4238 1.961394 TGTACTCTGAAAGTGGCGTCT 59.039 47.619 0.00 0.00 39.11 4.18
3918 4367 1.178534 GCCTGCCTTTGTAAGTGCCA 61.179 55.000 0.00 0.00 0.00 4.92
4206 4655 7.928908 TGAACAATGAACAAAGTTAATGAGC 57.071 32.000 0.00 0.00 0.00 4.26
4385 4834 0.494551 TCCTTCCCCTACAACCTCCA 59.505 55.000 0.00 0.00 0.00 3.86
5386 11047 2.494059 GCGGCACAGACATGGTATTAT 58.506 47.619 0.00 0.00 0.00 1.28
5482 11143 0.253327 CCCTCAACTAGCTCAACCCC 59.747 60.000 0.00 0.00 0.00 4.95
5483 11144 0.253327 CCCCTCAACTAGCTCAACCC 59.747 60.000 0.00 0.00 0.00 4.11
5614 11275 2.517609 GGAGTATTCCGACCAGGCT 58.482 57.895 0.00 0.00 40.77 4.58
5626 11287 2.288642 TAGGTCGCCACCCGGAGTAT 62.289 60.000 0.73 0.00 45.12 2.12
5749 11410 2.066999 GTTCCCGCCCTCTCCATCT 61.067 63.158 0.00 0.00 0.00 2.90
6323 14285 3.176411 TGACCATGTCTTCTCCATCACT 58.824 45.455 0.00 0.00 33.15 3.41
6344 14306 2.108970 GGTATCCAGAGACTCGGGTTT 58.891 52.381 19.53 11.86 33.27 3.27
6687 14702 2.112029 ACCCGCAAAAGGTGACAAC 58.888 52.632 0.00 0.00 35.85 3.32
6806 14832 9.612066 AAAGAAAAACATTAGCAAAATTGAGGA 57.388 25.926 0.00 0.00 0.00 3.71
6883 14909 1.538047 TCAGCATTTGGCCTGAAGTC 58.462 50.000 3.32 0.00 46.50 3.01
6943 15014 7.442969 ACATTTACTCAAACACGAGGAATACAA 59.557 33.333 0.00 0.00 35.74 2.41
6993 15064 2.564771 ACATATCGTCCTGCAACATGG 58.435 47.619 0.00 0.00 0.00 3.66
6997 15068 5.984233 TGAATAACATATCGTCCTGCAAC 57.016 39.130 0.00 0.00 0.00 4.17
7048 15119 4.265320 GCTTACATTGCCAACGAAATAAGC 59.735 41.667 0.00 0.00 0.00 3.09
7175 15669 5.661056 ATCAGTTCAGACGTCCATTTAGA 57.339 39.130 13.01 4.86 0.00 2.10
7384 15879 2.969443 GTCACCAAGAAACCATGACG 57.031 50.000 0.00 0.00 31.19 4.35
7486 15982 2.673368 GTGCAGTAACCAGAATTCCTCG 59.327 50.000 0.65 0.00 0.00 4.63
7770 18152 2.549754 GCCGAACACTCCATATGATTGG 59.450 50.000 3.65 0.00 38.18 3.16
7774 18156 3.558931 ATTGCCGAACACTCCATATGA 57.441 42.857 3.65 0.00 0.00 2.15
8061 18447 4.316205 ACACGTGTCTGTCATTTGACTA 57.684 40.909 17.22 0.00 44.99 2.59
8085 18471 5.181009 ACATAGACATCACACTCCATGTTG 58.819 41.667 0.00 0.00 40.64 3.33
8086 18472 5.188555 AGACATAGACATCACACTCCATGTT 59.811 40.000 0.00 0.00 40.64 2.71
8087 18473 4.713814 AGACATAGACATCACACTCCATGT 59.286 41.667 0.00 0.00 44.81 3.21
8089 18475 5.068855 CAGAGACATAGACATCACACTCCAT 59.931 44.000 0.00 0.00 0.00 3.41
8090 18476 4.400567 CAGAGACATAGACATCACACTCCA 59.599 45.833 0.00 0.00 0.00 3.86
8091 18477 4.400884 ACAGAGACATAGACATCACACTCC 59.599 45.833 0.00 0.00 0.00 3.85
8092 18478 5.574891 ACAGAGACATAGACATCACACTC 57.425 43.478 0.00 0.00 0.00 3.51
8094 18480 5.960113 AGAACAGAGACATAGACATCACAC 58.040 41.667 0.00 0.00 0.00 3.82
8184 18570 9.255304 TGCCTTTTACAGTTGAATTTTTGTATC 57.745 29.630 0.00 0.00 0.00 2.24
8328 18714 5.355910 AGTTTGCTTTAACGAAAGGAGACAA 59.644 36.000 12.75 1.54 45.19 3.18
8385 18771 3.922171 AGGAGAGGCTTTGGATTGTAG 57.078 47.619 0.00 0.00 0.00 2.74
8604 19139 9.788960 GATTACCAAATATTCAACCTCAGAAAC 57.211 33.333 0.00 0.00 0.00 2.78
8662 19197 5.120053 TGAATTGTGCGAGCCAATATATACG 59.880 40.000 10.55 0.00 32.40 3.06
8760 19295 0.980231 AGAGAGGCCGGAGAAGCATT 60.980 55.000 5.05 0.00 0.00 3.56
8762 19297 2.038007 AGAGAGGCCGGAGAAGCA 59.962 61.111 5.05 0.00 0.00 3.91
8870 19405 1.301479 GCGAACAAGGTCCGAGGTT 60.301 57.895 0.00 0.00 0.00 3.50
8949 19487 7.416213 CCCAAAAACATCAGTTCAAGTTACAGA 60.416 37.037 0.00 0.00 36.84 3.41
8980 19518 0.979709 CAGAGGACAGAGGGGATGCA 60.980 60.000 0.00 0.00 0.00 3.96
9015 19553 3.177194 TACACAAGCTGGCGTGGCT 62.177 57.895 13.83 0.00 42.31 4.75
9321 19889 3.006752 TGCCCAATGGAAGCTTTTAACTG 59.993 43.478 0.00 0.00 0.00 3.16
9482 20067 7.860613 TGCAATACATCTTACATTTCGTATGG 58.139 34.615 0.00 0.00 0.00 2.74
9505 20090 7.746475 GCATTCATCGGAGTATTTATAAACTGC 59.254 37.037 0.00 0.00 0.00 4.40
9544 20129 2.629617 TCAGGCGAGATGAATCATAGCA 59.370 45.455 15.81 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.