Multiple sequence alignment - TraesCS2D01G081800

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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 TraesCS2D01G081800 chr2D 100.000 3092 0 0 1 3092 35232188 35229097 0.000000e+00 5710
1 TraesCS2D01G081800 chr2D 83.333 1572 199 41 996 2551 35035165 35033641 0.000000e+00 1393
2 TraesCS2D01G081800 chr2D 88.764 267 21 5 1 258 32734885 32734619 4.980000e-83 318
3 TraesCS2D01G081800 chr2D 89.503 181 14 3 575 751 60954926 60954747 1.120000e-54 224
4 TraesCS2D01G081800 chr2B 91.223 1823 103 23 755 2553 58087190 58085401 0.000000e+00 2427
5 TraesCS2D01G081800 chr2B 90.000 1660 113 25 912 2553 58602701 58604325 0.000000e+00 2097
6 TraesCS2D01G081800 chr2B 83.955 1583 181 41 996 2551 57791199 57789663 0.000000e+00 1448
7 TraesCS2D01G081800 chr2B 92.857 840 44 4 1719 2553 58296638 58295810 0.000000e+00 1205
8 TraesCS2D01G081800 chr2B 93.020 745 40 4 964 1702 58298506 58297768 0.000000e+00 1077
9 TraesCS2D01G081800 chr2B 95.696 395 9 2 2553 2941 58085045 58084653 2.020000e-176 628
10 TraesCS2D01G081800 chr2B 92.381 420 19 2 2547 2966 58295450 58295044 1.240000e-163 586
11 TraesCS2D01G081800 chr2B 81.081 592 64 21 1 578 87182538 87181981 2.200000e-116 429
12 TraesCS2D01G081800 chr2B 92.683 205 15 0 2779 2983 58663253 58663457 2.330000e-76 296
13 TraesCS2D01G081800 chr2B 89.474 152 14 1 2557 2708 58604623 58604772 1.130000e-44 191
14 TraesCS2D01G081800 chr2B 91.262 103 9 0 2881 2983 58102293 58102191 1.160000e-29 141
15 TraesCS2D01G081800 chr2B 88.571 105 12 0 760 864 58299534 58299430 9.000000e-26 128
16 TraesCS2D01G081800 chr2B 89.899 99 7 2 2992 3088 58098858 58098761 1.160000e-24 124
17 TraesCS2D01G081800 chr2B 88.889 99 8 2 2992 3088 58293636 58293539 5.420000e-23 119
18 TraesCS2D01G081800 chr2B 89.691 97 4 4 2992 3088 58664702 58664792 5.420000e-23 119
19 TraesCS2D01G081800 chr2B 95.522 67 3 0 3022 3088 58083576 58083510 1.170000e-19 108
20 TraesCS2D01G081800 chr2A 91.074 1815 98 18 771 2553 38348717 38346935 0.000000e+00 2396
21 TraesCS2D01G081800 chr2A 90.804 1816 103 18 770 2553 38589974 38591757 0.000000e+00 2370
22 TraesCS2D01G081800 chr2A 82.569 1549 212 39 1031 2551 38341672 38340154 0.000000e+00 1312
23 TraesCS2D01G081800 chr2A 96.339 437 16 0 2547 2983 38346562 38346126 0.000000e+00 719
24 TraesCS2D01G081800 chr2A 92.195 410 26 2 2144 2553 38392633 38392230 2.670000e-160 575
25 TraesCS2D01G081800 chr2A 87.557 442 39 8 908 1344 38393060 38392630 5.950000e-137 497
26 TraesCS2D01G081800 chr2A 81.609 435 53 14 1 427 393511924 393511509 4.940000e-88 335
27 TraesCS2D01G081800 chr2A 87.189 281 28 7 303 578 580049955 580050232 2.310000e-81 313
28 TraesCS2D01G081800 chr2A 86.861 274 21 6 2651 2910 38508055 38507783 3.020000e-75 292
29 TraesCS2D01G081800 chr2A 86.916 107 10 1 776 878 38393934 38393828 1.950000e-22 117
30 TraesCS2D01G081800 chr2A 84.746 118 6 2 2547 2659 38365534 38365424 1.170000e-19 108
31 TraesCS2D01G081800 chr6D 83.276 586 61 17 1 578 362224308 362224864 3.560000e-139 505
32 TraesCS2D01G081800 chr6D 82.916 439 46 15 1 430 324812982 324813400 4.870000e-98 368
33 TraesCS2D01G081800 chr6D 88.636 176 12 5 574 743 359557945 359557772 1.120000e-49 207
34 TraesCS2D01G081800 chr5D 81.773 598 51 23 2 561 82177013 82176436 6.080000e-122 448
35 TraesCS2D01G081800 chr5D 86.833 281 29 7 303 578 426503634 426503911 1.080000e-79 307
36 TraesCS2D01G081800 chr5D 92.308 156 12 0 575 730 409439635 409439790 4.010000e-54 222
37 TraesCS2D01G081800 chr5D 89.535 172 16 2 574 743 515665601 515665430 1.870000e-52 217
38 TraesCS2D01G081800 chr5D 91.083 157 14 0 574 730 242648327 242648483 2.420000e-51 213
39 TraesCS2D01G081800 chr3D 85.057 435 50 11 1 427 16522291 16522718 2.200000e-116 429
40 TraesCS2D01G081800 chr3D 81.549 439 48 16 1 427 369417653 369418070 6.390000e-87 331
41 TraesCS2D01G081800 chr3D 86.219 283 31 7 303 578 523944892 523944611 1.800000e-77 300
42 TraesCS2D01G081800 chr3D 71.249 1193 264 61 1082 2229 9679275 9678117 2.400000e-56 230
43 TraesCS2D01G081800 chr3D 89.412 170 14 2 574 739 547518781 547518612 8.690000e-51 211
44 TraesCS2D01G081800 chr1D 84.354 441 36 17 1 427 425578729 425578308 4.800000e-108 401
45 TraesCS2D01G081800 chr1D 86.567 268 24 5 1 258 467415816 467416081 5.050000e-73 285
46 TraesCS2D01G081800 chr1D 91.720 157 13 0 574 730 403329916 403329760 5.190000e-53 219
47 TraesCS2D01G081800 chr1D 89.412 170 13 2 575 740 467037083 467036915 3.120000e-50 209
48 TraesCS2D01G081800 chr6A 89.531 277 22 5 303 578 33030367 33030097 8.210000e-91 344
49 TraesCS2D01G081800 chr5A 88.968 281 23 7 303 578 569282214 569281937 1.060000e-89 340
50 TraesCS2D01G081800 chr4D 82.439 410 51 12 1 406 419443744 419444136 3.820000e-89 339
51 TraesCS2D01G081800 chr4D 90.698 172 13 2 412 580 95529238 95529409 3.100000e-55 226
52 TraesCS2D01G081800 chr5B 74.082 926 187 38 1065 1964 57492123 57491225 6.390000e-87 331
53 TraesCS2D01G081800 chr3A 88.172 279 30 3 303 578 7122014 7122292 2.300000e-86 329
54 TraesCS2D01G081800 chr3A 71.984 1235 279 41 1000 2204 11527574 11528771 5.010000e-78 302
55 TraesCS2D01G081800 chr3A 75.340 515 101 18 1055 1547 11126820 11127330 1.120000e-54 224
56 TraesCS2D01G081800 chr3A 75.340 515 101 18 1055 1547 11135471 11135981 1.120000e-54 224
57 TraesCS2D01G081800 chr3A 75.340 515 101 18 1055 1547 11142343 11142853 1.120000e-54 224
58 TraesCS2D01G081800 chr3A 72.837 578 133 16 1067 1626 10361038 10361609 3.170000e-40 176
59 TraesCS2D01G081800 chr3A 72.609 460 91 30 1723 2172 10486587 10486153 5.420000e-23 119
60 TraesCS2D01G081800 chr1A 88.028 284 27 6 298 578 148950385 148950664 2.300000e-86 329
61 TraesCS2D01G081800 chr1A 71.550 1174 258 55 1055 2199 481628121 481629247 6.620000e-62 248
62 TraesCS2D01G081800 chrUn 73.050 846 189 24 1000 1824 290168560 290169387 2.360000e-66 263
63 TraesCS2D01G081800 chrUn 75.340 515 101 18 1055 1547 299358453 299358963 1.120000e-54 224
64 TraesCS2D01G081800 chrUn 73.043 460 89 23 1723 2172 35360183 35359749 2.500000e-26 130
65 TraesCS2D01G081800 chrUn 73.043 460 89 23 1723 2172 263318422 263317988 2.500000e-26 130
66 TraesCS2D01G081800 chrUn 88.525 61 7 0 1866 1926 43589433 43589373 1.190000e-09 75
67 TraesCS2D01G081800 chrUn 88.525 61 7 0 1866 1926 327179303 327179243 1.190000e-09 75
68 TraesCS2D01G081800 chrUn 88.525 61 7 0 1866 1926 366320995 366321055 1.190000e-09 75
69 TraesCS2D01G081800 chr7A 91.083 157 14 0 574 730 706895759 706895915 2.420000e-51 213
70 TraesCS2D01G081800 chr7A 90.588 85 8 0 236 320 602101627 602101711 2.520000e-21 113
71 TraesCS2D01G081800 chr7A 89.744 78 8 0 241 318 219846255 219846178 1.960000e-17 100
72 TraesCS2D01G081800 chr3B 80.899 178 28 5 1054 1228 13821700 13821526 5.380000e-28 135


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 TraesCS2D01G081800 chr2D 35229097 35232188 3091 True 5710.000000 5710 100.000000 1 3092 1 chr2D.!!$R3 3091
1 TraesCS2D01G081800 chr2D 35033641 35035165 1524 True 1393.000000 1393 83.333000 996 2551 1 chr2D.!!$R2 1555
2 TraesCS2D01G081800 chr2B 57789663 57791199 1536 True 1448.000000 1448 83.955000 996 2551 1 chr2B.!!$R1 1555
3 TraesCS2D01G081800 chr2B 58602701 58604772 2071 False 1144.000000 2097 89.737000 912 2708 2 chr2B.!!$F1 1796
4 TraesCS2D01G081800 chr2B 58083510 58087190 3680 True 1054.333333 2427 94.147000 755 3088 3 chr2B.!!$R3 2333
5 TraesCS2D01G081800 chr2B 58293539 58299534 5995 True 623.000000 1205 91.143600 760 3088 5 chr2B.!!$R5 2328
6 TraesCS2D01G081800 chr2B 87181981 87182538 557 True 429.000000 429 81.081000 1 578 1 chr2B.!!$R2 577
7 TraesCS2D01G081800 chr2B 58663253 58664792 1539 False 207.500000 296 91.187000 2779 3088 2 chr2B.!!$F2 309
8 TraesCS2D01G081800 chr2A 38589974 38591757 1783 False 2370.000000 2370 90.804000 770 2553 1 chr2A.!!$F1 1783
9 TraesCS2D01G081800 chr2A 38346126 38348717 2591 True 1557.500000 2396 93.706500 771 2983 2 chr2A.!!$R5 2212
10 TraesCS2D01G081800 chr2A 38340154 38341672 1518 True 1312.000000 1312 82.569000 1031 2551 1 chr2A.!!$R1 1520
11 TraesCS2D01G081800 chr2A 38392230 38393934 1704 True 396.333333 575 88.889333 776 2553 3 chr2A.!!$R6 1777
12 TraesCS2D01G081800 chr6D 362224308 362224864 556 False 505.000000 505 83.276000 1 578 1 chr6D.!!$F2 577
13 TraesCS2D01G081800 chr5D 82176436 82177013 577 True 448.000000 448 81.773000 2 561 1 chr5D.!!$R1 559
14 TraesCS2D01G081800 chr3D 9678117 9679275 1158 True 230.000000 230 71.249000 1082 2229 1 chr3D.!!$R1 1147
15 TraesCS2D01G081800 chr5B 57491225 57492123 898 True 331.000000 331 74.082000 1065 1964 1 chr5B.!!$R1 899
16 TraesCS2D01G081800 chr3A 11527574 11528771 1197 False 302.000000 302 71.984000 1000 2204 1 chr3A.!!$F6 1204
17 TraesCS2D01G081800 chr3A 11126820 11127330 510 False 224.000000 224 75.340000 1055 1547 1 chr3A.!!$F3 492
18 TraesCS2D01G081800 chr3A 11135471 11135981 510 False 224.000000 224 75.340000 1055 1547 1 chr3A.!!$F4 492
19 TraesCS2D01G081800 chr3A 11142343 11142853 510 False 224.000000 224 75.340000 1055 1547 1 chr3A.!!$F5 492
20 TraesCS2D01G081800 chr1A 481628121 481629247 1126 False 248.000000 248 71.550000 1055 2199 1 chr1A.!!$F2 1144
21 TraesCS2D01G081800 chrUn 290168560 290169387 827 False 263.000000 263 73.050000 1000 1824 1 chrUn.!!$F1 824
22 TraesCS2D01G081800 chrUn 299358453 299358963 510 False 224.000000 224 75.340000 1055 1547 1 chrUn.!!$F2 492

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
662 709 0.109597 CTCAGGTTGCGACAAATGGC 60.110 55.0 6.39 0.0 0.0 4.40 F
843 890 0.471022 AACTTTCCGGGCCCAACAAT 60.471 50.0 24.92 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2874 0.392193 TGTCGGTCTCGGAGGAGTAC 60.392 60.000 4.96 0.0 41.26 2.73 R
2599 5469 1.065199 CAGCAGCCCTTCATTCACCTA 60.065 52.381 0.00 0.0 0.00 3.08 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
66 67 2.375766 CCACTTGACGCGCTCTCAC 61.376 63.158 5.73 0.00 0.00 3.51
110 111 1.749258 GCGCTCCCTCCGGATTTTT 60.749 57.895 3.57 0.00 37.60 1.94
134 140 2.184385 TTTTTCCGCGTGCGTTTTTA 57.816 40.000 13.70 0.00 37.81 1.52
137 143 2.446753 TTCCGCGTGCGTTTTTAGCC 62.447 55.000 13.70 0.00 37.81 3.93
201 208 3.146847 CACCGGTCTTCCTTAGCTTTTT 58.853 45.455 2.59 0.00 0.00 1.94
258 275 2.430244 TTTCGCGAGAGTCACGGC 60.430 61.111 9.59 3.61 43.69 5.68
259 276 3.909258 TTTCGCGAGAGTCACGGCC 62.909 63.158 9.59 0.00 43.69 6.13
263 280 4.039357 CGAGAGTCACGGCCGTGT 62.039 66.667 46.56 34.60 45.55 4.49
267 284 1.300697 GAGTCACGGCCGTGTTTCT 60.301 57.895 46.56 39.33 45.55 2.52
268 285 0.878961 GAGTCACGGCCGTGTTTCTT 60.879 55.000 46.56 31.19 45.55 2.52
269 286 1.157870 AGTCACGGCCGTGTTTCTTG 61.158 55.000 46.56 27.39 45.55 3.02
272 289 1.153127 ACGGCCGTGTTTCTTGGAA 60.153 52.632 33.75 0.00 0.00 3.53
274 291 0.317519 CGGCCGTGTTTCTTGGAAAC 60.318 55.000 19.50 14.03 0.00 2.78
276 293 0.658897 GCCGTGTTTCTTGGAAACGA 59.341 50.000 15.34 5.41 36.38 3.85
278 295 2.478200 GCCGTGTTTCTTGGAAACGAAA 60.478 45.455 15.34 0.00 36.38 3.46
280 297 4.167268 CCGTGTTTCTTGGAAACGAAAAA 58.833 39.130 15.34 0.00 36.38 1.94
324 341 4.719369 GCGAGAGTCACGGCCGTT 62.719 66.667 32.11 15.95 0.00 4.44
451 496 2.573869 CTTCCGCGAGAGGCAAGA 59.426 61.111 8.23 0.00 43.84 3.02
463 508 1.537202 GAGGCAAGATTGTGCTTTCGT 59.463 47.619 0.00 0.00 44.31 3.85
547 594 1.597663 CGAGAGTCACGGTTTTGCTTT 59.402 47.619 1.62 0.00 0.00 3.51
561 608 2.126463 CTTTCGCGAGAGGCACGA 60.126 61.111 18.35 0.00 43.84 4.35
578 625 1.148157 CGATTGTGCTTCCGCGAGAT 61.148 55.000 8.23 0.00 39.65 2.75
579 626 1.009829 GATTGTGCTTCCGCGAGATT 58.990 50.000 8.23 0.00 39.65 2.40
580 627 1.398390 GATTGTGCTTCCGCGAGATTT 59.602 47.619 8.23 0.00 39.65 2.17
581 628 0.516877 TTGTGCTTCCGCGAGATTTG 59.483 50.000 8.23 0.00 39.65 2.32
582 629 1.298157 TGTGCTTCCGCGAGATTTGG 61.298 55.000 8.23 0.00 39.65 3.28
583 630 1.019278 GTGCTTCCGCGAGATTTGGA 61.019 55.000 8.23 0.00 39.65 3.53
584 631 1.019278 TGCTTCCGCGAGATTTGGAC 61.019 55.000 8.23 0.00 39.65 4.02
585 632 1.999051 CTTCCGCGAGATTTGGACG 59.001 57.895 8.23 0.00 0.00 4.79
590 637 3.081133 CGAGATTTGGACGCACGG 58.919 61.111 0.00 0.00 0.00 4.94
591 638 1.736645 CGAGATTTGGACGCACGGT 60.737 57.895 0.00 0.00 0.00 4.83
592 639 1.289109 CGAGATTTGGACGCACGGTT 61.289 55.000 0.00 0.00 0.00 4.44
593 640 0.872388 GAGATTTGGACGCACGGTTT 59.128 50.000 0.00 0.00 0.00 3.27
594 641 0.591170 AGATTTGGACGCACGGTTTG 59.409 50.000 0.00 0.00 0.00 2.93
595 642 0.589223 GATTTGGACGCACGGTTTGA 59.411 50.000 0.00 0.00 0.00 2.69
596 643 0.591170 ATTTGGACGCACGGTTTGAG 59.409 50.000 0.00 0.00 0.00 3.02
597 644 0.462225 TTTGGACGCACGGTTTGAGA 60.462 50.000 0.00 0.00 0.00 3.27
598 645 0.878523 TTGGACGCACGGTTTGAGAG 60.879 55.000 0.00 0.00 0.00 3.20
599 646 1.006571 GGACGCACGGTTTGAGAGA 60.007 57.895 0.00 0.00 0.00 3.10
600 647 0.389948 GGACGCACGGTTTGAGAGAT 60.390 55.000 0.00 0.00 0.00 2.75
601 648 1.135199 GGACGCACGGTTTGAGAGATA 60.135 52.381 0.00 0.00 0.00 1.98
602 649 2.602878 GACGCACGGTTTGAGAGATAA 58.397 47.619 0.00 0.00 0.00 1.75
603 650 2.991190 GACGCACGGTTTGAGAGATAAA 59.009 45.455 0.00 0.00 0.00 1.40
604 651 3.395639 ACGCACGGTTTGAGAGATAAAA 58.604 40.909 0.00 0.00 0.00 1.52
605 652 3.185797 ACGCACGGTTTGAGAGATAAAAC 59.814 43.478 0.00 0.00 0.00 2.43
613 660 8.770850 CGGTTTGAGAGATAAAACGTTTTAAA 57.229 30.769 30.92 20.07 41.77 1.52
614 661 9.389570 CGGTTTGAGAGATAAAACGTTTTAAAT 57.610 29.630 30.92 23.30 41.77 1.40
652 699 4.655762 AAAGGAAAAACTCTCAGGTTGC 57.344 40.909 0.00 0.00 0.00 4.17
653 700 2.222027 AGGAAAAACTCTCAGGTTGCG 58.778 47.619 0.00 0.00 0.00 4.85
654 701 2.158813 AGGAAAAACTCTCAGGTTGCGA 60.159 45.455 0.00 0.00 0.00 5.10
655 702 2.031944 GGAAAAACTCTCAGGTTGCGAC 60.032 50.000 0.00 0.00 0.00 5.19
656 703 2.325583 AAAACTCTCAGGTTGCGACA 57.674 45.000 6.39 0.00 0.00 4.35
657 704 2.325583 AAACTCTCAGGTTGCGACAA 57.674 45.000 6.39 0.00 0.00 3.18
658 705 2.325583 AACTCTCAGGTTGCGACAAA 57.674 45.000 6.39 0.00 0.00 2.83
659 706 2.550830 ACTCTCAGGTTGCGACAAAT 57.449 45.000 6.39 0.00 0.00 2.32
660 707 2.146342 ACTCTCAGGTTGCGACAAATG 58.854 47.619 6.39 1.71 0.00 2.32
661 708 1.466167 CTCTCAGGTTGCGACAAATGG 59.534 52.381 6.39 0.00 0.00 3.16
662 709 0.109597 CTCAGGTTGCGACAAATGGC 60.110 55.000 6.39 0.00 0.00 4.40
682 729 4.047059 GCTGCATGTGCGCCACTT 62.047 61.111 4.18 0.00 45.83 3.16
683 730 2.126618 CTGCATGTGCGCCACTTG 60.127 61.111 4.18 12.50 45.83 3.16
684 731 2.906388 TGCATGTGCGCCACTTGT 60.906 55.556 4.18 0.00 45.83 3.16
685 732 2.126734 GCATGTGCGCCACTTGTC 60.127 61.111 4.18 5.08 40.25 3.18
686 733 2.174107 CATGTGCGCCACTTGTCG 59.826 61.111 4.18 0.00 35.64 4.35
692 739 3.349006 CGCCACTTGTCGCAGCTT 61.349 61.111 0.00 0.00 0.00 3.74
693 740 2.253452 GCCACTTGTCGCAGCTTG 59.747 61.111 0.00 0.00 0.00 4.01
694 741 2.949106 CCACTTGTCGCAGCTTGG 59.051 61.111 0.00 0.00 0.00 3.61
695 742 2.620112 CCACTTGTCGCAGCTTGGG 61.620 63.158 0.00 0.00 0.00 4.12
696 743 2.980233 ACTTGTCGCAGCTTGGGC 60.980 61.111 0.00 0.00 39.06 5.36
697 744 2.979676 CTTGTCGCAGCTTGGGCA 60.980 61.111 0.00 0.00 41.70 5.36
698 745 2.974489 CTTGTCGCAGCTTGGGCAG 61.974 63.158 0.00 0.00 41.70 4.85
699 746 3.772853 TTGTCGCAGCTTGGGCAGT 62.773 57.895 0.00 0.00 41.70 4.40
700 747 2.980233 GTCGCAGCTTGGGCAGTT 60.980 61.111 0.00 0.00 41.70 3.16
701 748 2.979676 TCGCAGCTTGGGCAGTTG 60.980 61.111 0.00 0.00 41.70 3.16
702 749 4.047059 CGCAGCTTGGGCAGTTGG 62.047 66.667 0.00 0.00 41.70 3.77
703 750 2.598394 GCAGCTTGGGCAGTTGGA 60.598 61.111 0.00 0.00 41.70 3.53
704 751 2.633509 GCAGCTTGGGCAGTTGGAG 61.634 63.158 0.00 0.00 41.70 3.86
705 752 1.228367 CAGCTTGGGCAGTTGGAGT 60.228 57.895 0.00 0.00 41.70 3.85
706 753 1.228367 AGCTTGGGCAGTTGGAGTG 60.228 57.895 0.00 0.00 41.70 3.51
707 754 1.228245 GCTTGGGCAGTTGGAGTGA 60.228 57.895 0.00 0.00 38.54 3.41
708 755 0.610232 GCTTGGGCAGTTGGAGTGAT 60.610 55.000 0.00 0.00 38.54 3.06
709 756 1.457346 CTTGGGCAGTTGGAGTGATC 58.543 55.000 0.00 0.00 0.00 2.92
710 757 1.004044 CTTGGGCAGTTGGAGTGATCT 59.996 52.381 0.00 0.00 0.00 2.75
711 758 1.067295 TGGGCAGTTGGAGTGATCTT 58.933 50.000 0.00 0.00 0.00 2.40
712 759 1.425066 TGGGCAGTTGGAGTGATCTTT 59.575 47.619 0.00 0.00 0.00 2.52
713 760 1.815003 GGGCAGTTGGAGTGATCTTTG 59.185 52.381 0.00 0.00 0.00 2.77
714 761 1.200948 GGCAGTTGGAGTGATCTTTGC 59.799 52.381 0.00 0.00 0.00 3.68
715 762 1.881973 GCAGTTGGAGTGATCTTTGCA 59.118 47.619 0.00 0.00 0.00 4.08
716 763 2.294233 GCAGTTGGAGTGATCTTTGCAA 59.706 45.455 0.00 0.00 0.00 4.08
717 764 3.057033 GCAGTTGGAGTGATCTTTGCAAT 60.057 43.478 0.00 0.00 0.00 3.56
718 765 4.482386 CAGTTGGAGTGATCTTTGCAATG 58.518 43.478 0.00 2.27 0.00 2.82
719 766 4.216902 CAGTTGGAGTGATCTTTGCAATGA 59.783 41.667 16.45 16.45 0.00 2.57
720 767 4.458295 AGTTGGAGTGATCTTTGCAATGAG 59.542 41.667 18.58 6.50 0.00 2.90
721 768 4.025040 TGGAGTGATCTTTGCAATGAGT 57.975 40.909 18.58 8.54 0.00 3.41
722 769 5.164620 TGGAGTGATCTTTGCAATGAGTA 57.835 39.130 18.58 8.67 0.00 2.59
723 770 5.748402 TGGAGTGATCTTTGCAATGAGTAT 58.252 37.500 18.58 4.20 0.00 2.12
724 771 6.182627 TGGAGTGATCTTTGCAATGAGTATT 58.817 36.000 18.58 8.27 0.00 1.89
725 772 6.317140 TGGAGTGATCTTTGCAATGAGTATTC 59.683 38.462 18.58 14.68 0.00 1.75
726 773 6.238593 GGAGTGATCTTTGCAATGAGTATTCC 60.239 42.308 18.58 18.41 0.00 3.01
727 774 6.421485 AGTGATCTTTGCAATGAGTATTCCT 58.579 36.000 18.58 8.96 0.00 3.36
728 775 6.541641 AGTGATCTTTGCAATGAGTATTCCTC 59.458 38.462 18.58 10.76 40.89 3.71
739 786 4.433615 TGAGTATTCCTCAGTGATTTCGC 58.566 43.478 0.00 0.00 45.34 4.70
740 787 4.081697 TGAGTATTCCTCAGTGATTTCGCA 60.082 41.667 0.00 0.00 45.34 5.10
741 788 4.832248 AGTATTCCTCAGTGATTTCGCAA 58.168 39.130 0.00 0.00 0.00 4.85
742 789 5.245531 AGTATTCCTCAGTGATTTCGCAAA 58.754 37.500 0.00 0.00 0.00 3.68
743 790 3.896648 TTCCTCAGTGATTTCGCAAAC 57.103 42.857 0.00 0.00 0.00 2.93
744 791 3.126001 TCCTCAGTGATTTCGCAAACT 57.874 42.857 0.00 0.00 0.00 2.66
745 792 3.067106 TCCTCAGTGATTTCGCAAACTC 58.933 45.455 0.00 0.00 0.00 3.01
746 793 2.159787 CCTCAGTGATTTCGCAAACTCG 60.160 50.000 0.00 0.00 0.00 4.18
747 794 2.731451 CTCAGTGATTTCGCAAACTCGA 59.269 45.455 0.00 0.00 36.60 4.04
748 795 3.325870 TCAGTGATTTCGCAAACTCGAT 58.674 40.909 0.00 0.00 38.37 3.59
749 796 3.123453 TCAGTGATTTCGCAAACTCGATG 59.877 43.478 0.00 0.00 38.37 3.84
750 797 2.416547 AGTGATTTCGCAAACTCGATGG 59.583 45.455 0.00 0.00 38.37 3.51
751 798 2.159627 GTGATTTCGCAAACTCGATGGT 59.840 45.455 0.00 0.00 38.37 3.55
752 799 2.811431 TGATTTCGCAAACTCGATGGTT 59.189 40.909 0.00 0.00 38.37 3.67
753 800 2.961522 TTTCGCAAACTCGATGGTTC 57.038 45.000 0.00 0.00 38.37 3.62
765 812 1.740585 CGATGGTTCTCTCTCTCACGT 59.259 52.381 0.00 0.00 0.00 4.49
767 814 1.982660 TGGTTCTCTCTCTCACGTGT 58.017 50.000 16.51 0.00 0.00 4.49
783 830 2.226330 CGTGTGAATTCCCAAGTTGGA 58.774 47.619 24.06 4.42 40.96 3.53
785 832 2.031157 GTGTGAATTCCCAAGTTGGACG 60.031 50.000 24.06 7.67 40.96 4.79
842 889 1.075896 AACTTTCCGGGCCCAACAA 60.076 52.632 24.92 7.88 0.00 2.83
843 890 0.471022 AACTTTCCGGGCCCAACAAT 60.471 50.000 24.92 0.00 0.00 2.71
855 902 2.073816 CCCAACAATACGTCGCTCTTT 58.926 47.619 0.00 0.00 0.00 2.52
856 903 2.482721 CCCAACAATACGTCGCTCTTTT 59.517 45.455 0.00 0.00 0.00 2.27
1092 2352 2.027314 CTCCGCGAGATCCTGCTG 59.973 66.667 8.23 0.00 0.00 4.41
1329 2607 2.336478 CGTCACCGACTCTGAGGCT 61.336 63.158 9.20 0.00 35.63 4.58
1689 2985 0.099436 GCATCCTTGTCGGCAATGTC 59.901 55.000 1.35 0.00 33.65 3.06
1691 2987 0.327924 ATCCTTGTCGGCAATGTCCA 59.672 50.000 1.35 0.00 33.65 4.02
1725 4134 4.676444 CATGCGAAAGACGGCATG 57.324 55.556 11.05 11.05 43.54 4.06
1809 4236 0.869880 CGCGCAACCATCAGATCGTA 60.870 55.000 8.75 0.00 0.00 3.43
1965 4392 2.835895 GGGCTCTCTCCTCCGACC 60.836 72.222 0.00 0.00 0.00 4.79
2016 4461 0.689412 TGGGATACGACCAGGATGCA 60.689 55.000 0.00 0.00 32.40 3.96
2173 4632 7.437713 TGTTCATCCTTAGTCCTCATATTGT 57.562 36.000 0.00 0.00 0.00 2.71
2174 4633 7.861629 TGTTCATCCTTAGTCCTCATATTGTT 58.138 34.615 0.00 0.00 0.00 2.83
2175 4634 8.328758 TGTTCATCCTTAGTCCTCATATTGTTT 58.671 33.333 0.00 0.00 0.00 2.83
2279 4739 8.801715 TCACTAACAACTTAAACTTACCTACG 57.198 34.615 0.00 0.00 0.00 3.51
2365 4847 7.779798 TCAATATAGACAAGCTTATGGCCTTTT 59.220 33.333 3.32 0.00 43.05 2.27
2548 5033 4.593206 TCAAGATCACTTCTGGTGGTAGTT 59.407 41.667 0.00 0.00 45.38 2.24
2598 5468 6.267471 ACAGATTGGCAATTTGGTTTTCTCTA 59.733 34.615 27.92 0.00 0.00 2.43
2599 5469 7.038799 ACAGATTGGCAATTTGGTTTTCTCTAT 60.039 33.333 27.92 6.54 0.00 1.98
2620 5490 0.322816 GGTGAATGAAGGGCTGCTGA 60.323 55.000 0.00 0.00 0.00 4.26
2649 5519 9.889128 TTCTCATTGAGTTTGTCACATCATATA 57.111 29.630 13.23 0.00 33.71 0.86
2676 5546 2.545106 GGTCGACGGTGTTTACATGTTT 59.455 45.455 9.92 0.00 0.00 2.83
2689 5559 5.860941 TTACATGTTTCCTGAAAAAGGCA 57.139 34.783 2.30 0.00 46.92 4.75
2983 5859 7.309133 CCTTTCTTATGGTGCTTTCATGTAACA 60.309 37.037 0.00 0.00 0.00 2.41
2984 5860 7.517614 TTCTTATGGTGCTTTCATGTAACAA 57.482 32.000 0.00 0.00 0.00 2.83
2985 5861 7.144722 TCTTATGGTGCTTTCATGTAACAAG 57.855 36.000 0.00 0.00 0.00 3.16
2986 5862 3.641437 TGGTGCTTTCATGTAACAAGC 57.359 42.857 12.03 12.03 42.81 4.01
3006 7596 8.870075 ACAAGCATTTCTAAATCTACTCCTTT 57.130 30.769 0.00 0.00 0.00 3.11
3088 7690 4.868067 AGAGAAATGAAGTGCTGCTTTTG 58.132 39.130 0.00 0.00 37.59 2.44
3089 7691 4.581824 AGAGAAATGAAGTGCTGCTTTTGA 59.418 37.500 0.00 0.00 37.59 2.69
3090 7692 5.243283 AGAGAAATGAAGTGCTGCTTTTGAT 59.757 36.000 0.00 0.00 37.59 2.57
3091 7693 5.850614 AGAAATGAAGTGCTGCTTTTGATT 58.149 33.333 0.00 0.00 37.59 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.121030 GTGGCGCTGATCGTTGCT 61.121 61.111 7.64 0.00 41.07 3.91
110 111 2.402640 ACGCACGCGGAAAAATAAAA 57.597 40.000 16.70 0.00 44.69 1.52
120 125 2.452366 AAGGCTAAAAACGCACGCGG 62.452 55.000 16.70 0.00 44.69 6.46
124 130 4.985295 CGTTTAAAAGGCTAAAAACGCAC 58.015 39.130 20.91 0.00 44.94 5.34
179 186 1.640917 AAGCTAAGGAAGACCGGTGA 58.359 50.000 14.63 0.00 41.83 4.02
258 275 3.408288 TTTCGTTTCCAAGAAACACGG 57.592 42.857 17.62 4.67 32.15 4.94
281 298 8.580431 CGAAAGAAAAATAACAGAAAACGTGTT 58.420 29.630 0.00 0.00 41.11 3.32
282 299 7.253519 GCGAAAGAAAAATAACAGAAAACGTGT 60.254 33.333 0.00 0.00 0.00 4.49
283 300 7.049026 GCGAAAGAAAAATAACAGAAAACGTG 58.951 34.615 0.00 0.00 0.00 4.49
284 301 6.075780 CGCGAAAGAAAAATAACAGAAAACGT 60.076 34.615 0.00 0.00 0.00 3.99
285 302 6.139482 TCGCGAAAGAAAAATAACAGAAAACG 59.861 34.615 6.20 0.00 0.00 3.60
286 303 7.371338 TCGCGAAAGAAAAATAACAGAAAAC 57.629 32.000 6.20 0.00 0.00 2.43
287 304 7.411274 TCTCGCGAAAGAAAAATAACAGAAAA 58.589 30.769 11.33 0.00 0.00 2.29
288 305 6.950545 TCTCGCGAAAGAAAAATAACAGAAA 58.049 32.000 11.33 0.00 0.00 2.52
289 306 6.202188 ACTCTCGCGAAAGAAAAATAACAGAA 59.798 34.615 17.91 0.00 0.00 3.02
290 307 5.694910 ACTCTCGCGAAAGAAAAATAACAGA 59.305 36.000 17.91 0.29 0.00 3.41
291 308 5.916969 ACTCTCGCGAAAGAAAAATAACAG 58.083 37.500 17.91 0.00 0.00 3.16
292 309 5.464057 TGACTCTCGCGAAAGAAAAATAACA 59.536 36.000 17.91 0.68 0.00 2.41
293 310 5.784139 GTGACTCTCGCGAAAGAAAAATAAC 59.216 40.000 17.91 0.00 0.00 1.89
294 311 5.912528 GTGACTCTCGCGAAAGAAAAATAA 58.087 37.500 17.91 0.00 0.00 1.40
295 312 5.511088 GTGACTCTCGCGAAAGAAAAATA 57.489 39.130 17.91 0.00 0.00 1.40
296 313 4.391140 GTGACTCTCGCGAAAGAAAAAT 57.609 40.909 17.91 0.00 0.00 1.82
416 437 2.604046 AGCAAAACTGTGACTCTCGT 57.396 45.000 0.00 0.00 0.00 4.18
449 494 3.243873 TGACTCTCACGAAAGCACAATCT 60.244 43.478 0.00 0.00 0.00 2.40
451 496 2.802816 GTGACTCTCACGAAAGCACAAT 59.197 45.455 0.00 0.00 37.67 2.71
578 625 0.462225 TCTCAAACCGTGCGTCCAAA 60.462 50.000 0.00 0.00 0.00 3.28
579 626 0.878523 CTCTCAAACCGTGCGTCCAA 60.879 55.000 0.00 0.00 0.00 3.53
580 627 1.300620 CTCTCAAACCGTGCGTCCA 60.301 57.895 0.00 0.00 0.00 4.02
581 628 0.389948 ATCTCTCAAACCGTGCGTCC 60.390 55.000 0.00 0.00 0.00 4.79
582 629 2.273370 TATCTCTCAAACCGTGCGTC 57.727 50.000 0.00 0.00 0.00 5.19
583 630 2.736144 TTATCTCTCAAACCGTGCGT 57.264 45.000 0.00 0.00 0.00 5.24
584 631 3.720920 CGTTTTATCTCTCAAACCGTGCG 60.721 47.826 0.00 0.00 30.37 5.34
585 632 3.185797 ACGTTTTATCTCTCAAACCGTGC 59.814 43.478 0.00 0.00 30.37 5.34
586 633 4.985044 ACGTTTTATCTCTCAAACCGTG 57.015 40.909 0.00 0.00 30.37 4.94
587 634 5.996669 AAACGTTTTATCTCTCAAACCGT 57.003 34.783 7.96 0.00 30.37 4.83
588 635 8.770850 TTTAAAACGTTTTATCTCTCAAACCG 57.229 30.769 28.69 0.00 33.12 4.44
629 676 5.419542 GCAACCTGAGAGTTTTTCCTTTTT 58.580 37.500 0.00 0.00 0.00 1.94
630 677 4.440112 CGCAACCTGAGAGTTTTTCCTTTT 60.440 41.667 0.00 0.00 0.00 2.27
631 678 3.066760 CGCAACCTGAGAGTTTTTCCTTT 59.933 43.478 0.00 0.00 0.00 3.11
632 679 2.618709 CGCAACCTGAGAGTTTTTCCTT 59.381 45.455 0.00 0.00 0.00 3.36
633 680 2.158813 TCGCAACCTGAGAGTTTTTCCT 60.159 45.455 0.00 0.00 0.00 3.36
634 681 2.031944 GTCGCAACCTGAGAGTTTTTCC 60.032 50.000 0.00 0.00 0.00 3.13
635 682 2.612212 TGTCGCAACCTGAGAGTTTTTC 59.388 45.455 0.00 0.00 0.00 2.29
636 683 2.639065 TGTCGCAACCTGAGAGTTTTT 58.361 42.857 0.00 0.00 0.00 1.94
637 684 2.325583 TGTCGCAACCTGAGAGTTTT 57.674 45.000 0.00 0.00 0.00 2.43
638 685 2.325583 TTGTCGCAACCTGAGAGTTT 57.674 45.000 0.00 0.00 0.00 2.66
639 686 2.325583 TTTGTCGCAACCTGAGAGTT 57.674 45.000 0.00 0.00 0.00 3.01
640 687 2.146342 CATTTGTCGCAACCTGAGAGT 58.854 47.619 0.00 0.00 0.00 3.24
641 688 1.466167 CCATTTGTCGCAACCTGAGAG 59.534 52.381 0.00 0.00 0.00 3.20
642 689 1.522668 CCATTTGTCGCAACCTGAGA 58.477 50.000 0.00 0.00 0.00 3.27
643 690 0.109597 GCCATTTGTCGCAACCTGAG 60.110 55.000 0.00 0.00 0.00 3.35
644 691 1.851021 CGCCATTTGTCGCAACCTGA 61.851 55.000 0.00 0.00 0.00 3.86
645 692 1.442520 CGCCATTTGTCGCAACCTG 60.443 57.895 0.00 0.00 0.00 4.00
646 693 2.953821 CGCCATTTGTCGCAACCT 59.046 55.556 0.00 0.00 0.00 3.50
653 700 3.688475 ATGCAGCGCGCCATTTGTC 62.688 57.895 30.33 15.28 41.33 3.18
654 701 3.751246 ATGCAGCGCGCCATTTGT 61.751 55.556 30.33 4.55 41.33 2.83
655 702 3.251763 CATGCAGCGCGCCATTTG 61.252 61.111 30.33 20.85 41.33 2.32
656 703 3.751246 ACATGCAGCGCGCCATTT 61.751 55.556 30.33 15.27 41.33 2.32
657 704 4.485834 CACATGCAGCGCGCCATT 62.486 61.111 30.33 6.46 41.33 3.16
665 712 4.047059 AAGTGGCGCACATGCAGC 62.047 61.111 10.83 8.22 42.21 5.25
666 713 2.126618 CAAGTGGCGCACATGCAG 60.127 61.111 10.83 0.00 42.21 4.41
667 714 2.906388 ACAAGTGGCGCACATGCA 60.906 55.556 10.83 0.00 36.67 3.96
668 715 2.126734 GACAAGTGGCGCACATGC 60.127 61.111 10.83 0.00 36.67 4.06
669 716 2.174107 CGACAAGTGGCGCACATG 59.826 61.111 10.83 11.41 40.91 3.21
676 723 2.253452 CAAGCTGCGACAAGTGGC 59.747 61.111 0.00 0.00 34.76 5.01
677 724 2.620112 CCCAAGCTGCGACAAGTGG 61.620 63.158 0.00 0.00 0.00 4.00
678 725 2.949106 CCCAAGCTGCGACAAGTG 59.051 61.111 0.00 0.00 0.00 3.16
679 726 2.980233 GCCCAAGCTGCGACAAGT 60.980 61.111 0.00 0.00 35.50 3.16
680 727 2.974489 CTGCCCAAGCTGCGACAAG 61.974 63.158 0.00 0.00 40.80 3.16
681 728 2.979676 CTGCCCAAGCTGCGACAA 60.980 61.111 0.00 0.00 40.80 3.18
682 729 3.772853 AACTGCCCAAGCTGCGACA 62.773 57.895 0.00 0.00 41.37 4.35
683 730 2.980233 AACTGCCCAAGCTGCGAC 60.980 61.111 0.00 0.00 41.37 5.19
684 731 2.979676 CAACTGCCCAAGCTGCGA 60.980 61.111 0.00 0.00 41.37 5.10
685 732 4.047059 CCAACTGCCCAAGCTGCG 62.047 66.667 0.00 0.00 41.37 5.18
686 733 2.598394 TCCAACTGCCCAAGCTGC 60.598 61.111 0.00 0.00 41.37 5.25
687 734 1.228367 ACTCCAACTGCCCAAGCTG 60.228 57.895 0.00 0.00 43.17 4.24
688 735 1.228367 CACTCCAACTGCCCAAGCT 60.228 57.895 0.00 0.00 40.80 3.74
689 736 0.610232 ATCACTCCAACTGCCCAAGC 60.610 55.000 0.00 0.00 40.48 4.01
690 737 1.004044 AGATCACTCCAACTGCCCAAG 59.996 52.381 0.00 0.00 0.00 3.61
691 738 1.067295 AGATCACTCCAACTGCCCAA 58.933 50.000 0.00 0.00 0.00 4.12
692 739 1.067295 AAGATCACTCCAACTGCCCA 58.933 50.000 0.00 0.00 0.00 5.36
693 740 1.815003 CAAAGATCACTCCAACTGCCC 59.185 52.381 0.00 0.00 0.00 5.36
694 741 1.200948 GCAAAGATCACTCCAACTGCC 59.799 52.381 0.00 0.00 0.00 4.85
695 742 1.881973 TGCAAAGATCACTCCAACTGC 59.118 47.619 0.00 0.00 0.00 4.40
696 743 4.216902 TCATTGCAAAGATCACTCCAACTG 59.783 41.667 1.71 0.00 0.00 3.16
697 744 4.401022 TCATTGCAAAGATCACTCCAACT 58.599 39.130 1.71 0.00 0.00 3.16
698 745 4.217118 ACTCATTGCAAAGATCACTCCAAC 59.783 41.667 1.71 0.00 0.00 3.77
699 746 4.401022 ACTCATTGCAAAGATCACTCCAA 58.599 39.130 1.71 0.00 0.00 3.53
700 747 4.025040 ACTCATTGCAAAGATCACTCCA 57.975 40.909 1.71 0.00 0.00 3.86
701 748 6.238593 GGAATACTCATTGCAAAGATCACTCC 60.239 42.308 1.71 5.35 33.01 3.85
702 749 6.541641 AGGAATACTCATTGCAAAGATCACTC 59.458 38.462 1.71 0.00 35.08 3.51
703 750 6.421485 AGGAATACTCATTGCAAAGATCACT 58.579 36.000 1.71 0.00 35.08 3.41
704 751 6.690194 AGGAATACTCATTGCAAAGATCAC 57.310 37.500 1.71 0.00 35.08 3.06
705 752 6.932356 GAGGAATACTCATTGCAAAGATCA 57.068 37.500 1.71 0.00 45.85 2.92
718 765 4.433615 TGCGAAATCACTGAGGAATACTC 58.566 43.478 0.00 0.00 46.78 2.59
719 766 4.471904 TGCGAAATCACTGAGGAATACT 57.528 40.909 0.00 0.00 0.00 2.12
720 767 5.122396 AGTTTGCGAAATCACTGAGGAATAC 59.878 40.000 0.00 0.00 0.00 1.89
721 768 5.245531 AGTTTGCGAAATCACTGAGGAATA 58.754 37.500 0.00 0.00 0.00 1.75
722 769 4.074970 AGTTTGCGAAATCACTGAGGAAT 58.925 39.130 0.00 0.00 0.00 3.01
723 770 3.476552 AGTTTGCGAAATCACTGAGGAA 58.523 40.909 0.00 0.00 0.00 3.36
724 771 3.067106 GAGTTTGCGAAATCACTGAGGA 58.933 45.455 9.25 0.00 30.54 3.71
725 772 2.159787 CGAGTTTGCGAAATCACTGAGG 60.160 50.000 14.15 0.00 30.54 3.86
726 773 2.731451 TCGAGTTTGCGAAATCACTGAG 59.269 45.455 14.15 0.00 37.35 3.35
727 774 2.749776 TCGAGTTTGCGAAATCACTGA 58.250 42.857 14.15 1.08 37.35 3.41
728 775 3.410850 CATCGAGTTTGCGAAATCACTG 58.589 45.455 14.15 6.72 44.22 3.66
729 776 2.416547 CCATCGAGTTTGCGAAATCACT 59.583 45.455 14.15 0.00 44.22 3.41
730 777 2.159627 ACCATCGAGTTTGCGAAATCAC 59.840 45.455 14.15 0.00 44.22 3.06
731 778 2.422597 ACCATCGAGTTTGCGAAATCA 58.577 42.857 14.15 2.43 44.22 2.57
732 779 3.125316 AGAACCATCGAGTTTGCGAAATC 59.875 43.478 3.98 3.98 44.22 2.17
733 780 3.074412 AGAACCATCGAGTTTGCGAAAT 58.926 40.909 0.00 0.00 44.22 2.17
734 781 2.478894 GAGAACCATCGAGTTTGCGAAA 59.521 45.455 0.00 0.00 44.22 3.46
735 782 2.066262 GAGAACCATCGAGTTTGCGAA 58.934 47.619 0.00 0.00 44.22 4.70
736 783 1.272490 AGAGAACCATCGAGTTTGCGA 59.728 47.619 0.00 0.00 45.22 5.10
737 784 1.656095 GAGAGAACCATCGAGTTTGCG 59.344 52.381 0.00 0.00 0.00 4.85
738 785 2.926838 GAGAGAGAACCATCGAGTTTGC 59.073 50.000 0.00 0.00 0.00 3.68
739 786 4.082517 TGAGAGAGAGAACCATCGAGTTTG 60.083 45.833 0.00 0.00 0.00 2.93
740 787 4.082463 GTGAGAGAGAGAACCATCGAGTTT 60.082 45.833 0.00 0.00 0.00 2.66
741 788 3.442273 GTGAGAGAGAGAACCATCGAGTT 59.558 47.826 0.00 0.00 0.00 3.01
742 789 3.013921 GTGAGAGAGAGAACCATCGAGT 58.986 50.000 0.00 0.00 0.00 4.18
743 790 2.031560 CGTGAGAGAGAGAACCATCGAG 59.968 54.545 0.00 0.00 0.00 4.04
744 791 2.010497 CGTGAGAGAGAGAACCATCGA 58.990 52.381 0.00 0.00 0.00 3.59
745 792 1.740585 ACGTGAGAGAGAGAACCATCG 59.259 52.381 0.00 0.00 0.00 3.84
746 793 2.490115 ACACGTGAGAGAGAGAACCATC 59.510 50.000 25.01 0.00 0.00 3.51
747 794 2.230025 CACACGTGAGAGAGAGAACCAT 59.770 50.000 25.01 0.00 0.00 3.55
748 795 1.609072 CACACGTGAGAGAGAGAACCA 59.391 52.381 25.01 0.00 0.00 3.67
749 796 1.880675 TCACACGTGAGAGAGAGAACC 59.119 52.381 25.01 0.00 34.14 3.62
750 797 3.627732 TTCACACGTGAGAGAGAGAAC 57.372 47.619 25.01 0.00 41.13 3.01
751 798 4.321304 GGAATTCACACGTGAGAGAGAGAA 60.321 45.833 25.01 13.35 41.13 2.87
752 799 3.191581 GGAATTCACACGTGAGAGAGAGA 59.808 47.826 25.01 4.52 41.13 3.10
753 800 3.506810 GGAATTCACACGTGAGAGAGAG 58.493 50.000 25.01 2.86 41.13 3.20
765 812 2.226330 CGTCCAACTTGGGAATTCACA 58.774 47.619 6.21 6.21 39.05 3.58
767 814 1.144093 ACCGTCCAACTTGGGAATTCA 59.856 47.619 7.93 0.00 39.05 2.57
783 830 2.418334 GGGCTTTAGAAGAATCGACCGT 60.418 50.000 0.00 0.00 0.00 4.83
785 832 3.198872 CTGGGCTTTAGAAGAATCGACC 58.801 50.000 0.00 0.00 0.00 4.79
855 902 2.834549 TCTTTTGGTGCACAAGGGAAAA 59.165 40.909 20.43 12.95 40.82 2.29
856 903 2.461695 TCTTTTGGTGCACAAGGGAAA 58.538 42.857 20.43 4.24 40.82 3.13
861 947 3.118542 GCTTCTTCTTTTGGTGCACAAG 58.881 45.455 20.43 13.81 40.82 3.16
904 2124 3.187432 GGAACCGCTTCTTCTTCTTTCTG 59.813 47.826 0.00 0.00 0.00 3.02
905 2125 3.181454 TGGAACCGCTTCTTCTTCTTTCT 60.181 43.478 0.00 0.00 0.00 2.52
906 2126 3.139077 TGGAACCGCTTCTTCTTCTTTC 58.861 45.455 0.00 0.00 0.00 2.62
907 2127 3.142174 CTGGAACCGCTTCTTCTTCTTT 58.858 45.455 0.00 0.00 0.00 2.52
908 2128 2.368875 TCTGGAACCGCTTCTTCTTCTT 59.631 45.455 0.00 0.00 0.00 2.52
909 2129 1.971357 TCTGGAACCGCTTCTTCTTCT 59.029 47.619 0.00 0.00 0.00 2.85
938 2158 0.779997 ATTTGGGGAGTGGAGTGCTT 59.220 50.000 0.00 0.00 0.00 3.91
939 2159 0.329596 GATTTGGGGAGTGGAGTGCT 59.670 55.000 0.00 0.00 0.00 4.40
1584 2874 0.392193 TGTCGGTCTCGGAGGAGTAC 60.392 60.000 4.96 0.00 41.26 2.73
1689 2985 1.809207 CCTTAACGGCCAGCAATGG 59.191 57.895 2.24 0.00 0.00 3.16
1725 4134 3.858503 GCCTGTCCAAATCAAACTGAAGC 60.859 47.826 0.00 0.00 0.00 3.86
1809 4236 1.908340 GAGTGCCATCCTCTGCCTGT 61.908 60.000 0.00 0.00 0.00 4.00
1965 4392 3.855159 CCCCCTTTTCACTACCTCG 57.145 57.895 0.00 0.00 0.00 4.63
2279 4739 6.498651 TCATCTATCTAGGAAAGGGACAATCC 59.501 42.308 0.00 0.00 35.88 3.01
2365 4847 8.620416 GGCAACTACATCATATAATGACACAAA 58.380 33.333 0.00 0.00 43.01 2.83
2390 4874 2.290896 TGCTATGTCCCAAGGTTGAAGG 60.291 50.000 0.00 0.00 0.00 3.46
2548 5033 9.991906 GTTAGTAACCAGATACATATAGGCAAA 57.008 33.333 1.22 0.00 0.00 3.68
2598 5468 1.849039 AGCAGCCCTTCATTCACCTAT 59.151 47.619 0.00 0.00 0.00 2.57
2599 5469 1.065199 CAGCAGCCCTTCATTCACCTA 60.065 52.381 0.00 0.00 0.00 3.08
2620 5490 6.543465 TGATGTGACAAACTCAATGAGAACTT 59.457 34.615 18.20 4.38 33.32 2.66
2649 5519 1.670791 AAACACCGTCGACCACATTT 58.329 45.000 10.58 3.45 0.00 2.32
2689 5559 2.565834 ACTAAGGCACACACCGACTAAT 59.434 45.455 0.00 0.00 33.69 1.73
2923 5799 1.024271 ATGAGTGTGTGTGTTGGCAC 58.976 50.000 0.00 0.00 45.44 5.01
2983 5859 9.171877 CAGAAAGGAGTAGATTTAGAAATGCTT 57.828 33.333 0.00 0.00 0.00 3.91
2984 5860 7.281999 GCAGAAAGGAGTAGATTTAGAAATGCT 59.718 37.037 0.00 0.00 0.00 3.79
2985 5861 7.413644 GCAGAAAGGAGTAGATTTAGAAATGC 58.586 38.462 0.00 0.00 0.00 3.56
2986 5862 7.254590 CGGCAGAAAGGAGTAGATTTAGAAATG 60.255 40.741 0.00 0.00 0.00 2.32
2987 5863 6.763610 CGGCAGAAAGGAGTAGATTTAGAAAT 59.236 38.462 0.00 0.00 0.00 2.17
2988 5864 6.106673 CGGCAGAAAGGAGTAGATTTAGAAA 58.893 40.000 0.00 0.00 0.00 2.52
3031 7633 4.160252 AGTGGCACAAACAAAACTGAAGAT 59.840 37.500 21.41 0.00 44.16 2.40


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

AutoCloner maintained by Alex Coulton.