Multiple sequence alignment - TraesCS2D01G594400

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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 TraesCS2D01G594400 chr2D 100.000 6141 0 0 1 6141 648243749 648237609 0.000000e+00 11341
1 TraesCS2D01G594400 chr2B 91.540 2376 117 24 2832 5166 783229512 783227180 0.000000e+00 3197
2 TraesCS2D01G594400 chr2B 93.815 1439 71 7 2827 4258 782536379 782534952 0.000000e+00 2148
3 TraesCS2D01G594400 chr2B 93.264 1440 78 7 2827 4258 782686840 782685412 0.000000e+00 2104
4 TraesCS2D01G594400 chr2B 91.409 1490 75 13 2918 4385 782835455 782833997 0.000000e+00 1993
5 TraesCS2D01G594400 chr2B 90.206 1552 114 17 33 1568 783231969 783230440 0.000000e+00 1989
6 TraesCS2D01G594400 chr2B 94.444 1260 56 6 2918 4176 782960577 782959331 0.000000e+00 1927
7 TraesCS2D01G594400 chr2B 92.546 1033 59 14 545 1568 782538383 782537360 0.000000e+00 1465
8 TraesCS2D01G594400 chr2B 92.159 1033 65 14 544 1568 782688843 782687819 0.000000e+00 1445
9 TraesCS2D01G594400 chr2B 89.061 1161 87 20 33 1177 782972146 782971010 0.000000e+00 1404
10 TraesCS2D01G594400 chr2B 89.052 1160 88 20 33 1177 782847681 782846546 0.000000e+00 1402
11 TraesCS2D01G594400 chr2B 88.249 851 75 12 33 874 782987115 782986281 0.000000e+00 994
12 TraesCS2D01G594400 chr2B 89.364 818 44 20 4350 5166 782959016 782958241 0.000000e+00 989
13 TraesCS2D01G594400 chr2B 85.613 987 90 27 5166 6141 783226985 783226040 0.000000e+00 989
14 TraesCS2D01G594400 chr2B 89.242 818 45 20 4350 5166 782833979 782833204 0.000000e+00 983
15 TraesCS2D01G594400 chr2B 87.910 670 55 13 2180 2827 782961539 782960874 0.000000e+00 765
16 TraesCS2D01G594400 chr2B 87.892 669 55 11 2180 2827 783230261 783229598 0.000000e+00 763
17 TraesCS2D01G594400 chr2B 87.761 670 56 13 2180 2827 782836417 782835752 0.000000e+00 760
18 TraesCS2D01G594400 chr2B 87.141 661 56 14 2189 2826 782537163 782536509 0.000000e+00 723
19 TraesCS2D01G594400 chr2B 86.275 663 58 17 2189 2827 782687622 782686969 0.000000e+00 689
20 TraesCS2D01G594400 chr2B 91.721 459 30 4 4328 4782 782685410 782684956 1.120000e-176 630
21 TraesCS2D01G594400 chr2B 94.710 397 19 2 1174 1568 782962119 782961723 3.150000e-172 616
22 TraesCS2D01G594400 chr2B 90.870 460 33 5 4328 4782 782534950 782534495 5.260000e-170 608
23 TraesCS2D01G594400 chr2B 94.444 396 20 2 1175 1568 782836996 782836601 5.260000e-170 608
24 TraesCS2D01G594400 chr2B 87.321 489 43 9 5166 5646 782958018 782957541 5.410000e-150 542
25 TraesCS2D01G594400 chr2B 86.503 489 43 10 5166 5646 782832981 782832508 3.280000e-142 516
26 TraesCS2D01G594400 chr2B 88.432 389 25 7 4778 5166 782681665 782681297 9.390000e-123 451
27 TraesCS2D01G594400 chr2B 88.402 388 25 8 4778 5165 782531213 782530846 3.380000e-122 449
28 TraesCS2D01G594400 chr2B 90.735 313 21 7 4856 5166 782534502 782534196 1.590000e-110 411
29 TraesCS2D01G594400 chr2B 90.415 313 22 7 4856 5166 782684963 782684657 7.410000e-109 405
30 TraesCS2D01G594400 chr2B 81.020 490 70 14 31 513 782689924 782689451 9.720000e-98 368
31 TraesCS2D01G594400 chr2B 81.159 483 66 17 38 513 782539459 782538995 1.260000e-96 364
32 TraesCS2D01G594400 chr2B 80.568 458 66 15 5691 6131 583535766 583536217 1.280000e-86 331
33 TraesCS2D01G594400 chr2B 85.284 299 28 7 5404 5690 782680784 782680490 1.670000e-75 294
34 TraesCS2D01G594400 chr2B 94.805 154 7 1 5170 5323 782684429 782684277 7.960000e-59 239
35 TraesCS2D01G594400 chr2B 91.176 170 14 1 4564 4732 782531652 782531483 4.790000e-56 230
36 TraesCS2D01G594400 chr2B 91.176 170 14 1 4564 4732 782682104 782681935 4.790000e-56 230
37 TraesCS2D01G594400 chr2B 92.857 154 10 1 5170 5323 782533968 782533816 8.010000e-54 222
38 TraesCS2D01G594400 chr2B 91.447 152 7 3 1645 1792 782687819 782687670 2.900000e-48 204
39 TraesCS2D01G594400 chr2B 91.946 149 7 2 1645 1792 783230440 783230296 2.900000e-48 204
40 TraesCS2D01G594400 chr2B 88.439 173 11 4 5522 5690 782533805 782533638 3.750000e-47 200
41 TraesCS2D01G594400 chr2B 88.439 173 11 4 5522 5690 782684266 782684099 3.750000e-47 200
42 TraesCS2D01G594400 chr2B 93.600 125 6 1 1668 1792 782961696 782961574 1.050000e-42 185
43 TraesCS2D01G594400 chr2B 92.800 125 7 1 1668 1792 782836574 782836452 4.890000e-41 180
44 TraesCS2D01G594400 chr2B 81.773 203 18 7 4183 4385 782959217 782959034 1.070000e-32 152
45 TraesCS2D01G594400 chrUn 89.042 2254 156 40 2827 5054 31206709 31208897 0.000000e+00 2710
46 TraesCS2D01G594400 chrUn 89.390 1442 90 27 1405 2827 31205162 31206559 0.000000e+00 1757
47 TraesCS2D01G594400 chrUn 91.964 1120 72 11 289 1400 31203928 31205037 0.000000e+00 1554
48 TraesCS2D01G594400 chrUn 93.527 448 19 5 3699 4146 476027389 476027826 0.000000e+00 658
49 TraesCS2D01G594400 chrUn 78.488 516 93 16 78 583 99118201 99117694 7.680000e-84 322
50 TraesCS2D01G594400 chr5B 87.610 1251 107 31 2946 4187 593211126 593209915 0.000000e+00 1408
51 TraesCS2D01G594400 chr5B 86.442 1040 110 19 1805 2827 593212362 593211337 0.000000e+00 1110
52 TraesCS2D01G594400 chr5B 79.383 810 103 37 1020 1807 593213155 593212388 4.250000e-141 512
53 TraesCS2D01G594400 chr5B 82.214 551 56 21 4226 4771 593209904 593209391 2.630000e-118 436
54 TraesCS2D01G594400 chr5B 84.127 252 34 2 4803 5054 593209183 593208938 7.960000e-59 239
55 TraesCS2D01G594400 chr7D 81.996 511 82 9 77 583 159068276 159068780 5.690000e-115 425
56 TraesCS2D01G594400 chr5D 83.585 463 58 10 5691 6140 417598386 417597929 9.520000e-113 418
57 TraesCS2D01G594400 chr1D 81.410 468 58 14 5691 6135 28652349 28652810 7.570000e-94 355
58 TraesCS2D01G594400 chr4D 82.952 393 58 5 5691 6075 213301917 213301526 4.560000e-91 346
59 TraesCS2D01G594400 chr6A 81.519 395 54 13 5691 6075 492099096 492099481 2.150000e-79 307
60 TraesCS2D01G594400 chr2A 81.266 395 59 9 5690 6075 73940065 73940453 7.730000e-79 305
61 TraesCS2D01G594400 chr2A 83.234 334 46 3 5818 6141 126620095 126619762 1.290000e-76 298
62 TraesCS2D01G594400 chr4A 81.421 366 50 15 5691 6041 714383790 714384152 3.620000e-72 283
63 TraesCS2D01G594400 chr4A 79.949 394 63 10 5691 6075 502604431 502604045 6.060000e-70 276
64 TraesCS2D01G594400 chr4A 81.232 357 48 6 5800 6141 83431058 83430706 2.820000e-68 270
65 TraesCS2D01G594400 chr3D 78.316 475 65 19 5690 6141 342696492 342696033 7.840000e-69 272


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 TraesCS2D01G594400 chr2D 648237609 648243749 6140 True 11341.000000 11341 100.000000 1 6141 1 chr2D.!!$R1 6140
1 TraesCS2D01G594400 chr2B 783226040 783231969 5929 True 1428.400000 3197 89.439400 33 6141 5 chr2B.!!$R8 6108
2 TraesCS2D01G594400 chr2B 782971010 782972146 1136 True 1404.000000 1404 89.061000 33 1177 1 chr2B.!!$R2 1144
3 TraesCS2D01G594400 chr2B 782846546 782847681 1135 True 1402.000000 1402 89.052000 33 1177 1 chr2B.!!$R1 1144
4 TraesCS2D01G594400 chr2B 782986281 782987115 834 True 994.000000 994 88.249000 33 874 1 chr2B.!!$R3 841
5 TraesCS2D01G594400 chr2B 782832508 782836996 4488 True 840.000000 1993 90.359833 1175 5646 6 chr2B.!!$R6 4471
6 TraesCS2D01G594400 chr2B 782957541 782962119 4578 True 739.428571 1927 89.874571 1174 5646 7 chr2B.!!$R7 4472
7 TraesCS2D01G594400 chr2B 782530846 782539459 8613 True 682.000000 2148 89.714000 38 5690 10 chr2B.!!$R4 5652
8 TraesCS2D01G594400 chr2B 782680490 782689924 9434 True 604.916667 2104 89.536417 31 5690 12 chr2B.!!$R5 5659
9 TraesCS2D01G594400 chrUn 31203928 31208897 4969 False 2007.000000 2710 90.132000 289 5054 3 chrUn.!!$F2 4765
10 TraesCS2D01G594400 chrUn 99117694 99118201 507 True 322.000000 322 78.488000 78 583 1 chrUn.!!$R1 505
11 TraesCS2D01G594400 chr5B 593208938 593213155 4217 True 741.000000 1408 83.955200 1020 5054 5 chr5B.!!$R1 4034
12 TraesCS2D01G594400 chr7D 159068276 159068780 504 False 425.000000 425 81.996000 77 583 1 chr7D.!!$F1 506

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
322 325 0.034380 TGCTCTAGCCAGGTAGACGT 60.034 55.000 2.51 0.00 41.18 4.34 F
809 1441 0.036022 GGGATATGCTCCTCTGCCAC 59.964 60.000 0.00 0.00 44.28 5.01 F
888 1527 1.072331 CTAGCCAACTGGTGTCCTTGT 59.928 52.381 0.00 0.00 37.57 3.16 F
2085 2920 1.544759 GGGGAAGCTGGTCGAAAAAGA 60.545 52.381 0.00 0.00 0.00 2.52 F
2756 3618 1.291272 GGAAGACAAGTACGGCGGT 59.709 57.895 13.24 1.39 0.00 5.68 F
3477 4621 2.046892 CTGGAGCCAGTGGTTCGG 60.047 66.667 18.62 10.79 39.10 4.30 F
4831 6422 1.327460 CACACAGACACGTGGTTGAAG 59.673 52.381 21.57 15.97 41.38 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2900 0.881796 CTTTTTCGACCAGCTTCCCC 59.118 55.000 0.00 0.00 0.00 4.81 R
2308 3170 1.221466 TGTCCTTCAGCGCTTTGACG 61.221 55.000 7.50 0.91 0.00 4.35 R
2538 3400 1.344114 TCAATGCCTTTCTGGTTTGGC 59.656 47.619 0.00 0.00 45.10 4.52 R
3384 4528 2.034812 GGAGTCTTGGTATGGCTCGTAG 59.965 54.545 0.00 0.00 0.00 3.51 R
4441 5788 1.747924 GGGAACTAGTACCACTCGACC 59.252 57.143 10.76 0.00 0.00 4.79 R
5067 6658 0.171007 CACGGCTGGCTTGTTATTGG 59.829 55.000 0.00 0.00 0.00 3.16 R
5852 11302 0.027586 GAAATTGGTTCGCGGGATCG 59.972 55.000 6.13 0.00 39.81 3.69 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.470888 CCGGCGGTCATCCTCCTT 61.471 66.667 19.97 0.00 36.51 3.36
18 19 2.584608 CGGCGGTCATCCTCCTTT 59.415 61.111 0.00 0.00 36.51 3.11
19 20 1.078426 CGGCGGTCATCCTCCTTTT 60.078 57.895 0.00 0.00 36.51 2.27
20 21 1.090052 CGGCGGTCATCCTCCTTTTC 61.090 60.000 0.00 0.00 36.51 2.29
21 22 0.253327 GGCGGTCATCCTCCTTTTCT 59.747 55.000 0.00 0.00 35.82 2.52
22 23 1.485066 GGCGGTCATCCTCCTTTTCTA 59.515 52.381 0.00 0.00 35.82 2.10
23 24 2.093128 GGCGGTCATCCTCCTTTTCTAA 60.093 50.000 0.00 0.00 35.82 2.10
24 25 3.606687 GCGGTCATCCTCCTTTTCTAAA 58.393 45.455 0.00 0.00 0.00 1.85
25 26 4.007659 GCGGTCATCCTCCTTTTCTAAAA 58.992 43.478 0.00 0.00 0.00 1.52
26 27 4.457949 GCGGTCATCCTCCTTTTCTAAAAA 59.542 41.667 0.00 0.00 0.00 1.94
74 75 5.353400 GCCTTTTGTCTACCGTTAATTAGCT 59.647 40.000 0.00 0.00 0.00 3.32
162 163 1.748244 GCCCATCTTCAGCATAGCACA 60.748 52.381 0.00 0.00 0.00 4.57
322 325 0.034380 TGCTCTAGCCAGGTAGACGT 60.034 55.000 2.51 0.00 41.18 4.34
329 332 2.945456 AGCCAGGTAGACGTCATCATA 58.055 47.619 19.50 0.00 0.00 2.15
334 337 5.527582 GCCAGGTAGACGTCATCATAAAAAT 59.472 40.000 19.50 0.00 0.00 1.82
364 368 1.126488 CTCTGGCCTCTGCAGGATAA 58.874 55.000 15.13 0.00 43.65 1.75
522 539 8.035984 TGTGTAGATAATTGTTTGTCGATACCA 58.964 33.333 0.00 0.00 0.00 3.25
536 553 2.418628 CGATACCACGCAACCAATTTCT 59.581 45.455 0.00 0.00 0.00 2.52
546 563 6.365789 CACGCAACCAATTTCTGAACATATTT 59.634 34.615 0.00 0.00 0.00 1.40
587 1212 9.110502 GGGGTAAAGATTTGAATCTACTGTTAG 57.889 37.037 6.66 0.00 44.67 2.34
630 1256 6.469410 AGTTTCAACATGTCGATTAGGGTAA 58.531 36.000 0.00 0.00 0.00 2.85
638 1264 8.246430 ACATGTCGATTAGGGTAAAGAGATTA 57.754 34.615 0.00 0.00 0.00 1.75
662 1288 6.840780 ATATTTAAAGAGCACAGTTTGGCT 57.159 33.333 0.00 0.00 44.48 4.75
743 1369 6.539103 AGGTACAACTTTTCACTGTTCTCTTC 59.461 38.462 0.00 0.00 0.00 2.87
747 1373 7.253422 ACAACTTTTCACTGTTCTCTTCAATG 58.747 34.615 0.00 0.00 0.00 2.82
764 1390 9.467258 CTCTTCAATGAATGTACAAAACACATT 57.533 29.630 0.00 5.27 46.58 2.71
809 1441 0.036022 GGGATATGCTCCTCTGCCAC 59.964 60.000 0.00 0.00 44.28 5.01
812 1447 2.549778 GGATATGCTCCTCTGCCACTTC 60.550 54.545 0.00 0.00 41.29 3.01
818 1453 1.072965 CTCCTCTGCCACTTCTTTGGT 59.927 52.381 0.00 0.00 39.09 3.67
857 1492 4.213482 GCACAGTGGTAAGTTACAAAGAGG 59.787 45.833 14.81 1.78 0.00 3.69
868 1503 1.303643 CAAAGAGGTCCCACCAGGC 60.304 63.158 0.00 0.00 41.95 4.85
880 1519 3.081554 CCAGGCTAGCCAACTGGT 58.918 61.111 34.70 11.07 45.21 4.00
885 1524 1.679898 GCTAGCCAACTGGTGTCCT 59.320 57.895 2.29 0.00 37.57 3.85
888 1527 1.072331 CTAGCCAACTGGTGTCCTTGT 59.928 52.381 0.00 0.00 37.57 3.16
934 1577 2.512896 AGCTTCATTCTCATCCCACCAT 59.487 45.455 0.00 0.00 0.00 3.55
1093 1737 2.534396 CCCACCACCCACCTTAGCA 61.534 63.158 0.00 0.00 0.00 3.49
1356 2008 7.709269 TTTCTAGCACAAATGTATATCCGTC 57.291 36.000 0.00 0.00 0.00 4.79
1376 2029 8.696410 TCCGTCAATTTAAAAGAAATAATGGC 57.304 30.769 0.00 0.00 0.00 4.40
1377 2030 8.307483 TCCGTCAATTTAAAAGAAATAATGGCA 58.693 29.630 0.00 0.00 0.00 4.92
1481 2270 9.554395 ACAAAATGTTATATATGTCGTCATCCA 57.446 29.630 0.00 0.00 35.70 3.41
1592 2384 8.406297 CCCTGCCTTAATTTTTGTTCTATCTAC 58.594 37.037 0.00 0.00 0.00 2.59
1664 2466 9.599322 GATCTACTTTTCAGTGTTACAAACATG 57.401 33.333 0.00 0.00 44.35 3.21
1707 2513 6.784031 AGTCCTTCTCCTTAATTTCATGTGT 58.216 36.000 0.00 0.00 0.00 3.72
1708 2514 6.656693 AGTCCTTCTCCTTAATTTCATGTGTG 59.343 38.462 0.00 0.00 0.00 3.82
1793 2599 7.113658 ACCATCTGTATGAAGTAAGTACTGG 57.886 40.000 0.00 0.00 36.50 4.00
1866 2700 2.051334 TTGGGAATATCCAAGGCACG 57.949 50.000 0.00 0.00 41.44 5.34
1868 2702 1.774254 TGGGAATATCCAAGGCACGAT 59.226 47.619 0.00 0.00 38.64 3.73
1880 2714 5.295787 TCCAAGGCACGATTACAATAATCAC 59.704 40.000 8.80 0.00 0.00 3.06
1913 2747 9.853555 GGAACAGGAAATTTTTGAACAATTTTT 57.146 25.926 3.84 0.00 34.61 1.94
2040 2875 4.402155 ACTGCTTGAATTGTGTTTTCTGGA 59.598 37.500 0.00 0.00 0.00 3.86
2085 2920 1.544759 GGGGAAGCTGGTCGAAAAAGA 60.545 52.381 0.00 0.00 0.00 2.52
2259 3100 9.590451 AACCATTTTGAATATGCACTTCTAATG 57.410 29.630 19.12 19.12 31.98 1.90
2308 3170 3.118261 TCATTTATGACTGGCAGGAGGAC 60.118 47.826 20.34 5.33 0.00 3.85
2365 3227 2.907892 AGGTTCTCCATCTCTTGGTCA 58.092 47.619 0.00 0.00 46.52 4.02
2384 3246 6.245408 TGGTCAAGAATACTGCCAAGTAAAT 58.755 36.000 0.00 0.00 42.17 1.40
2385 3247 7.398829 TGGTCAAGAATACTGCCAAGTAAATA 58.601 34.615 0.00 0.00 42.17 1.40
2386 3248 7.335924 TGGTCAAGAATACTGCCAAGTAAATAC 59.664 37.037 0.00 0.00 42.17 1.89
2500 3362 7.283580 TGTTATATTGTTGGGGTCCTAATTTCG 59.716 37.037 0.00 0.00 0.00 3.46
2538 3400 2.359900 CTTTCAGATGGGACGGGAAAG 58.640 52.381 0.00 0.00 38.68 2.62
2568 3430 5.122396 CCAGAAAGGCATTGACTACTACAAC 59.878 44.000 0.00 0.00 0.00 3.32
2571 3433 5.941948 AAGGCATTGACTACTACAACAAC 57.058 39.130 0.00 0.00 0.00 3.32
2574 3436 4.392138 GGCATTGACTACTACAACAACCTC 59.608 45.833 0.00 0.00 0.00 3.85
2615 3477 5.587289 TCATGGTGAAAACCTTTTTCTTCG 58.413 37.500 11.58 0.00 0.00 3.79
2646 3508 7.615403 TGATTAGTGCTTAATGAGTCAGACTT 58.385 34.615 4.05 0.00 32.09 3.01
2756 3618 1.291272 GGAAGACAAGTACGGCGGT 59.709 57.895 13.24 1.39 0.00 5.68
2852 3865 3.435671 GTGGACCATGAGTAGAAAAACGG 59.564 47.826 0.00 0.00 0.00 4.44
2867 3880 6.729187 AGAAAAACGGTTCTTTTCAGATCAG 58.271 36.000 16.25 0.00 42.63 2.90
2899 3912 5.408204 TGTATTGTCATTCGATGATGCAC 57.592 39.130 0.00 0.00 42.04 4.57
2922 4061 8.440833 GCACCAGTAAACTAACATAACTACTTG 58.559 37.037 0.00 0.00 0.00 3.16
3075 4219 3.312421 ACGAGCCACATACATATTGTTGC 59.688 43.478 0.00 0.00 36.33 4.17
3235 4379 2.645163 TGTTCAAAGCGCATTACAACG 58.355 42.857 11.47 0.00 0.00 4.10
3301 4445 7.541162 ACAAGCAACAACTAGTCGTATGTATA 58.459 34.615 0.00 0.00 0.00 1.47
3477 4621 2.046892 CTGGAGCCAGTGGTTCGG 60.047 66.667 18.62 10.79 39.10 4.30
3704 4848 5.183140 AGAAAATATGGTTGAGGACAAACCG 59.817 40.000 0.00 0.00 42.42 4.44
3824 4974 6.492087 TGACATCGGTCCTATTGTATGTATCA 59.508 38.462 0.00 0.00 43.65 2.15
3942 5092 5.153950 AGTCAGCCAGGACTTTAGTTAAG 57.846 43.478 0.00 0.00 45.59 1.85
4284 5577 6.425504 CCATTATCTTTTCAGTTCTCATCGC 58.574 40.000 0.00 0.00 0.00 4.58
4320 5616 5.987953 GTCGAGGGGTTGATTAATTAGGTAC 59.012 44.000 0.00 0.00 0.00 3.34
4442 5789 8.506140 CACTAATGTGTAAACAATCTTTGTGG 57.494 34.615 0.00 0.00 40.44 4.17
4443 5790 8.134895 CACTAATGTGTAAACAATCTTTGTGGT 58.865 33.333 0.00 0.00 40.44 4.16
4444 5791 8.349983 ACTAATGTGTAAACAATCTTTGTGGTC 58.650 33.333 0.00 0.00 44.59 4.02
4445 5792 5.163302 TGTGTAAACAATCTTTGTGGTCG 57.837 39.130 0.00 0.00 44.59 4.79
4446 5793 4.876679 TGTGTAAACAATCTTTGTGGTCGA 59.123 37.500 0.00 0.00 44.59 4.20
4447 5794 5.007234 TGTGTAAACAATCTTTGTGGTCGAG 59.993 40.000 0.00 0.00 44.59 4.04
4771 6159 8.939929 CATACCCTAATAGCACATTGATTACTG 58.060 37.037 0.00 0.00 0.00 2.74
4772 6160 6.900194 ACCCTAATAGCACATTGATTACTGT 58.100 36.000 0.00 0.00 0.00 3.55
4822 6413 6.020678 CACATGTATACATACACACAGACACG 60.021 42.308 17.86 4.07 45.11 4.49
4831 6422 1.327460 CACACAGACACGTGGTTGAAG 59.673 52.381 21.57 15.97 41.38 3.02
5045 6636 2.572290 AGTTCAACTCCGTCCCAAAAG 58.428 47.619 0.00 0.00 0.00 2.27
5067 6658 3.128764 GCCTTGCTTAAGACCACCAATAC 59.871 47.826 6.67 0.00 0.00 1.89
5071 6662 4.929479 TGCTTAAGACCACCAATACCAAT 58.071 39.130 6.67 0.00 0.00 3.16
5072 6663 6.068461 TGCTTAAGACCACCAATACCAATA 57.932 37.500 6.67 0.00 0.00 1.90
5073 6664 6.486056 TGCTTAAGACCACCAATACCAATAA 58.514 36.000 6.67 0.00 0.00 1.40
5074 6665 6.376018 TGCTTAAGACCACCAATACCAATAAC 59.624 38.462 6.67 0.00 0.00 1.89
5076 6667 7.094118 GCTTAAGACCACCAATACCAATAACAA 60.094 37.037 6.67 0.00 0.00 2.83
5077 6668 6.834168 AAGACCACCAATACCAATAACAAG 57.166 37.500 0.00 0.00 0.00 3.16
5078 6669 4.705023 AGACCACCAATACCAATAACAAGC 59.295 41.667 0.00 0.00 0.00 4.01
5079 6670 3.767131 ACCACCAATACCAATAACAAGCC 59.233 43.478 0.00 0.00 0.00 4.35
5080 6671 3.766591 CCACCAATACCAATAACAAGCCA 59.233 43.478 0.00 0.00 0.00 4.75
5081 6672 4.142182 CCACCAATACCAATAACAAGCCAG 60.142 45.833 0.00 0.00 0.00 4.85
5102 6696 1.566018 CGTGACTGCTTCCGTTTCCC 61.566 60.000 0.00 0.00 0.00 3.97
5114 6712 2.965831 TCCGTTTCCCTATGATGGAGAG 59.034 50.000 0.00 0.00 32.37 3.20
5122 6720 2.045524 CTATGATGGAGAGGTGGTGCT 58.954 52.381 0.00 0.00 0.00 4.40
5123 6721 0.835941 ATGATGGAGAGGTGGTGCTC 59.164 55.000 0.00 0.00 0.00 4.26
5124 6722 0.252421 TGATGGAGAGGTGGTGCTCT 60.252 55.000 0.00 0.00 0.00 4.09
5125 6723 0.177604 GATGGAGAGGTGGTGCTCTG 59.822 60.000 0.00 0.00 0.00 3.35
5126 6724 1.908340 ATGGAGAGGTGGTGCTCTGC 61.908 60.000 0.00 0.00 38.32 4.26
5137 6735 2.093500 TGGTGCTCTGCTATGTTCGAAT 60.093 45.455 0.00 0.00 0.00 3.34
5147 6745 8.239681 TCTGCTATGTTCGAATAAATAATCCG 57.760 34.615 0.00 0.00 0.00 4.18
5154 6752 6.704050 TGTTCGAATAAATAATCCGATGCTGA 59.296 34.615 0.00 0.00 0.00 4.26
5191 7018 5.411669 TCTCTTTTTCTTTATGTCGGGCTTC 59.588 40.000 0.00 0.00 0.00 3.86
5235 7065 4.022329 CCGAACTATTTCCCTTTTGCTTGT 60.022 41.667 0.00 0.00 0.00 3.16
5264 7094 7.758495 ACCTTTGTATTCAATAATCGTGTTCC 58.242 34.615 0.00 0.00 33.32 3.62
5268 7098 7.915293 TGTATTCAATAATCGTGTTCCTGTT 57.085 32.000 0.00 0.00 0.00 3.16
5309 7139 1.896220 TAAAGTGAGGCCTTGTGCTG 58.104 50.000 6.77 0.00 40.92 4.41
5372 7202 0.182061 TCATTCTGATGCAGAGGCCC 59.818 55.000 0.00 0.00 41.75 5.80
5373 7203 0.183014 CATTCTGATGCAGAGGCCCT 59.817 55.000 0.00 0.00 41.75 5.19
5389 7219 2.986728 GGCCCTGGATAATCCTCCTTTA 59.013 50.000 0.00 0.00 37.46 1.85
5390 7220 3.397955 GGCCCTGGATAATCCTCCTTTAA 59.602 47.826 0.00 0.00 37.46 1.52
5391 7221 4.141018 GGCCCTGGATAATCCTCCTTTAAA 60.141 45.833 0.00 0.00 37.46 1.52
5421 7256 1.648116 ATGTGAGGGGCAAAAGCAAT 58.352 45.000 0.00 0.00 0.00 3.56
5443 7278 7.307337 GCAATTGTCAAGGGAAAACTTATGTTG 60.307 37.037 7.40 0.00 36.39 3.33
5450 7285 8.750298 TCAAGGGAAAACTTATGTTGTTTGTTA 58.250 29.630 0.00 0.00 37.64 2.41
5490 7325 4.467769 AGGCTCAACCATCCATAAATCTG 58.532 43.478 0.00 0.00 43.14 2.90
5491 7326 4.079558 AGGCTCAACCATCCATAAATCTGT 60.080 41.667 0.00 0.00 43.14 3.41
5492 7327 4.646492 GGCTCAACCATCCATAAATCTGTT 59.354 41.667 0.00 0.00 38.86 3.16
5493 7328 5.127682 GGCTCAACCATCCATAAATCTGTTT 59.872 40.000 0.00 0.00 38.86 2.83
5496 7331 7.917505 GCTCAACCATCCATAAATCTGTTTTAG 59.082 37.037 0.00 0.00 33.40 1.85
5512 7347 6.874664 TCTGTTTTAGTGATGGCGTGTATTTA 59.125 34.615 0.00 0.00 0.00 1.40
5517 7352 7.956420 TTAGTGATGGCGTGTATTTATAAGG 57.044 36.000 0.00 0.00 0.00 2.69
5520 7355 6.260050 AGTGATGGCGTGTATTTATAAGGTTG 59.740 38.462 0.00 0.00 0.00 3.77
5536 7371 3.365472 AGGTTGGAATATTGGCAAGGAC 58.635 45.455 5.96 0.00 0.00 3.85
5568 7403 3.512724 CCATTGGAGGCATGTTCTCTTTT 59.487 43.478 14.67 1.98 0.00 2.27
5575 7410 4.322567 AGGCATGTTCTCTTTTCTCACTC 58.677 43.478 0.00 0.00 0.00 3.51
5577 7412 4.067896 GCATGTTCTCTTTTCTCACTCCA 58.932 43.478 0.00 0.00 0.00 3.86
5599 7434 4.454728 TCTTTGAGCAATAAACCCATGC 57.545 40.909 0.00 0.00 40.34 4.06
5633 7468 5.332743 ACAGACTTCATCTCTTCTTCTCCT 58.667 41.667 0.00 0.00 34.41 3.69
5741 11191 1.760875 GCCCTACGATCACCCAGGA 60.761 63.158 0.00 0.00 0.00 3.86
5751 11201 4.164221 ACGATCACCCAGGAACAATAAGAT 59.836 41.667 0.00 0.00 0.00 2.40
5758 11208 4.646040 CCCAGGAACAATAAGATGCATTGA 59.354 41.667 0.00 0.00 36.95 2.57
5793 11243 1.069378 CGTTACCGACTCCGAGTTGC 61.069 60.000 10.02 0.00 38.22 4.17
5798 11248 3.482783 GACTCCGAGTTGCAGCGC 61.483 66.667 0.00 0.00 0.00 5.92
5815 11265 0.167470 CGCAAGAAGACGAGTCGGTA 59.833 55.000 18.30 0.00 43.02 4.02
5827 11277 4.626042 ACGAGTCGGTATAGATCGTACTT 58.374 43.478 18.30 0.00 44.11 2.24
5833 11283 4.753610 TCGGTATAGATCGTACTTGGAGTG 59.246 45.833 10.00 0.00 0.00 3.51
5838 11288 1.476891 GATCGTACTTGGAGTGCCTCA 59.523 52.381 4.85 0.00 34.31 3.86
5843 11293 1.972872 ACTTGGAGTGCCTCAAACTG 58.027 50.000 4.85 0.00 34.31 3.16
5852 11302 4.319177 AGTGCCTCAAACTGTAGATGAAC 58.681 43.478 0.00 0.00 0.00 3.18
5860 11310 1.067212 ACTGTAGATGAACGATCCCGC 59.933 52.381 0.00 0.00 39.95 6.13
5866 11316 2.125832 GAACGATCCCGCGAACCA 60.126 61.111 8.23 0.00 39.95 3.67
5867 11317 1.738830 GAACGATCCCGCGAACCAA 60.739 57.895 8.23 0.00 39.95 3.67
5868 11318 1.078708 AACGATCCCGCGAACCAAT 60.079 52.632 8.23 0.00 39.95 3.16
5869 11319 0.675522 AACGATCCCGCGAACCAATT 60.676 50.000 8.23 0.00 39.95 2.32
5870 11320 0.675522 ACGATCCCGCGAACCAATTT 60.676 50.000 8.23 0.00 39.95 1.82
5872 11322 0.380733 GATCCCGCGAACCAATTTCC 59.619 55.000 8.23 0.00 0.00 3.13
5873 11323 0.034477 ATCCCGCGAACCAATTTCCT 60.034 50.000 8.23 0.00 0.00 3.36
5874 11324 0.675522 TCCCGCGAACCAATTTCCTC 60.676 55.000 8.23 0.00 0.00 3.71
5875 11325 1.423845 CCGCGAACCAATTTCCTCG 59.576 57.895 8.23 0.00 0.00 4.63
5878 11328 3.676091 CGAACCAATTTCCTCGCAC 57.324 52.632 0.00 0.00 0.00 5.34
5879 11329 0.179225 CGAACCAATTTCCTCGCACG 60.179 55.000 0.00 0.00 0.00 5.34
5897 11355 3.249687 GGAAGACCGAAAGCATGGT 57.750 52.632 0.00 0.00 42.42 3.55
5905 11363 3.034635 ACCGAAAGCATGGTCTCTCTAT 58.965 45.455 0.00 0.00 31.16 1.98
5917 11375 5.265191 TGGTCTCTCTATGAGTTACAAGCT 58.735 41.667 0.00 0.00 43.13 3.74
5923 11381 7.561722 TCTCTCTATGAGTTACAAGCTTATGGT 59.438 37.037 0.00 0.00 43.13 3.55
5934 11392 3.460857 AGCTTATGGTCTTCACGATCC 57.539 47.619 0.00 0.00 0.00 3.36
5936 11394 2.743938 CTTATGGTCTTCACGATCCGG 58.256 52.381 0.00 0.00 0.00 5.14
5956 11414 2.819595 GCGCTTCGGCATCCAGAA 60.820 61.111 0.00 0.00 41.88 3.02
5962 11420 2.545946 GCTTCGGCATCCAGAACTAATC 59.454 50.000 0.00 0.00 41.33 1.75
5963 11421 3.797039 CTTCGGCATCCAGAACTAATCA 58.203 45.455 0.00 0.00 0.00 2.57
5970 11428 1.068588 TCCAGAACTAATCATCGCCGG 59.931 52.381 0.00 0.00 0.00 6.13
5990 11448 3.761752 CGGAGAATTAGAGGGAGGAGATC 59.238 52.174 0.00 0.00 0.00 2.75
5994 11452 3.905493 ATTAGAGGGAGGAGATCGGAA 57.095 47.619 0.00 0.00 0.00 4.30
6001 11459 1.187087 GAGGAGATCGGAACCACACT 58.813 55.000 0.00 0.00 0.00 3.55
6007 11465 2.185310 ATCGGAACCACACTGGGCTC 62.185 60.000 0.00 0.00 43.37 4.70
6009 11467 2.034221 GAACCACACTGGGCTCCC 59.966 66.667 0.00 0.00 43.37 4.30
6064 11522 6.258947 GCTCTTATTGATCAACTAGGACCAAC 59.741 42.308 11.07 0.00 0.00 3.77
6067 11525 8.696374 TCTTATTGATCAACTAGGACCAACTAG 58.304 37.037 11.07 0.00 44.71 2.57
6077 11535 4.949966 AGGACCAACTAGAACTAGAGGA 57.050 45.455 21.54 0.00 36.30 3.71
6079 11537 4.292836 AGGACCAACTAGAACTAGAGGAGT 59.707 45.833 21.54 11.95 41.56 3.85
6135 11594 8.528044 AGCCTCTAGTATATATAGGTTTGAGC 57.472 38.462 0.00 0.00 0.00 4.26
6138 11597 7.774157 CCTCTAGTATATATAGGTTTGAGCGGA 59.226 40.741 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.981859 TAGAAAAGGAGGATGACCGC 57.018 50.000 0.00 0.00 41.83 5.68
27 28 4.156455 TGACTTGACTCTGCCTCTTTTT 57.844 40.909 0.00 0.00 0.00 1.94
28 29 3.845781 TGACTTGACTCTGCCTCTTTT 57.154 42.857 0.00 0.00 0.00 2.27
29 30 3.672808 CATGACTTGACTCTGCCTCTTT 58.327 45.455 0.00 0.00 0.00 2.52
113 114 7.942341 TCTTTTTAATGTGGTTGTATCACCTCT 59.058 33.333 0.00 0.00 37.75 3.69
162 163 0.814457 ACGTGTTGGTTGTGTGCATT 59.186 45.000 0.00 0.00 0.00 3.56
286 289 1.146263 CATACGGCCAGGGAGGTTC 59.854 63.158 2.24 0.00 40.61 3.62
329 332 6.915786 AGGCCAGAGGACAGATATAATTTTT 58.084 36.000 5.01 0.00 29.21 1.94
334 337 4.155709 CAGAGGCCAGAGGACAGATATAA 58.844 47.826 5.01 0.00 29.21 0.98
364 368 1.139058 GAGATGGCTCCGTACATGGTT 59.861 52.381 0.00 0.00 35.01 3.67
504 521 3.995048 TGCGTGGTATCGACAAACAATTA 59.005 39.130 0.00 0.00 0.00 1.40
522 539 5.643379 ATATGTTCAGAAATTGGTTGCGT 57.357 34.783 0.00 0.00 0.00 5.24
587 1212 9.654663 TTGAAACTCTTCTTATCCTAAGCTAAC 57.345 33.333 0.00 0.00 32.33 2.34
596 1221 6.590292 TCGACATGTTGAAACTCTTCTTATCC 59.410 38.462 13.64 0.00 32.33 2.59
638 1264 7.232118 AGCCAAACTGTGCTCTTTAAATATT 57.768 32.000 0.00 0.00 30.33 1.28
743 1369 9.985318 ACAAAAATGTGTTTTGTACATTCATTG 57.015 25.926 13.89 17.92 46.91 2.82
764 1390 5.560724 TGGGTCAAATCCAACAAAACAAAA 58.439 33.333 0.00 0.00 0.00 2.44
768 1397 4.501400 CCTCTGGGTCAAATCCAACAAAAC 60.501 45.833 0.00 0.00 33.36 2.43
777 1406 3.073650 AGCATATCCCTCTGGGTCAAATC 59.926 47.826 2.25 0.00 44.74 2.17
809 1441 1.108727 TGCAGCCCACACCAAAGAAG 61.109 55.000 0.00 0.00 0.00 2.85
812 1447 2.567497 CCTGCAGCCCACACCAAAG 61.567 63.158 8.66 0.00 0.00 2.77
857 1492 2.602676 TTGGCTAGCCTGGTGGGAC 61.603 63.158 33.07 5.09 37.23 4.46
868 1503 1.072331 ACAAGGACACCAGTTGGCTAG 59.928 52.381 0.00 0.00 39.32 3.42
880 1519 3.071023 CCCTAAGACACAAGACAAGGACA 59.929 47.826 0.00 0.00 0.00 4.02
885 1524 3.456644 TGGAACCCTAAGACACAAGACAA 59.543 43.478 0.00 0.00 0.00 3.18
888 1527 2.038557 GCTGGAACCCTAAGACACAAGA 59.961 50.000 0.00 0.00 0.00 3.02
934 1577 1.351017 GAATCTGTCAAGTGGGGGTGA 59.649 52.381 0.00 0.00 0.00 4.02
986 1629 2.897969 TGAGGAGTGAGTTCCCTTGTAC 59.102 50.000 0.00 0.00 38.02 2.90
1093 1737 0.613260 TGTCCTGCACGGCTTCTAAT 59.387 50.000 0.00 0.00 0.00 1.73
1402 2175 8.698973 TTTTGACATCATGTTTTCCCTTAGTA 57.301 30.769 0.00 0.00 0.00 1.82
1403 2176 7.595819 TTTTGACATCATGTTTTCCCTTAGT 57.404 32.000 0.00 0.00 0.00 2.24
1481 2270 4.574674 TCCAAGCACCTTCAATCTACAT 57.425 40.909 0.00 0.00 0.00 2.29
1565 2354 6.954102 AGATAGAACAAAAATTAAGGCAGGGT 59.046 34.615 0.00 0.00 0.00 4.34
1566 2355 7.410120 AGATAGAACAAAAATTAAGGCAGGG 57.590 36.000 0.00 0.00 0.00 4.45
1569 2358 8.556213 ACGTAGATAGAACAAAAATTAAGGCA 57.444 30.769 0.00 0.00 0.00 4.75
1664 2466 9.267084 GAAGGACTCAGGAAAGAATAATATCAC 57.733 37.037 0.00 0.00 0.00 3.06
1683 2489 6.656693 CACACATGAAATTAAGGAGAAGGACT 59.343 38.462 0.00 0.00 0.00 3.85
1707 2513 9.899226 GATATGCGCTCTGTTCATATATATACA 57.101 33.333 9.73 0.00 34.58 2.29
1708 2514 9.347934 GGATATGCGCTCTGTTCATATATATAC 57.652 37.037 9.73 0.00 34.58 1.47
1793 2599 2.369394 CCTCCAAAGTTACTGGCATCC 58.631 52.381 0.00 0.00 33.63 3.51
1808 2642 2.757894 TTTTAACAAGTGGCCCTCCA 57.242 45.000 0.00 0.00 40.85 3.86
1866 2700 8.556194 TGTTCCATTAGCGTGATTATTGTAATC 58.444 33.333 3.37 3.37 0.00 1.75
1868 2702 7.011950 CCTGTTCCATTAGCGTGATTATTGTAA 59.988 37.037 0.00 0.00 0.00 2.41
1880 2714 6.155827 TCAAAAATTTCCTGTTCCATTAGCG 58.844 36.000 0.00 0.00 0.00 4.26
1913 2747 9.739276 AAAGATAACATATCCAGTTTCTGTGAA 57.261 29.630 0.00 0.00 0.00 3.18
1943 2777 9.626045 GTGATTTCCTTCGTATTTTCATTCTTT 57.374 29.630 0.00 0.00 0.00 2.52
1946 2780 8.964420 TTGTGATTTCCTTCGTATTTTCATTC 57.036 30.769 0.00 0.00 0.00 2.67
2022 2857 6.462552 TCATGTCCAGAAAACACAATTCAA 57.537 33.333 0.00 0.00 0.00 2.69
2040 2875 9.874205 CCATTTTTGACTTTGGTATAATCATGT 57.126 29.630 0.00 0.00 0.00 3.21
2065 2900 0.881796 CTTTTTCGACCAGCTTCCCC 59.118 55.000 0.00 0.00 0.00 4.81
2085 2920 3.845781 ATATGAAAGGACCACTCGCAT 57.154 42.857 0.00 0.00 0.00 4.73
2308 3170 1.221466 TGTCCTTCAGCGCTTTGACG 61.221 55.000 7.50 0.91 0.00 4.35
2365 3227 9.953565 TTGTAGTATTTACTTGGCAGTATTCTT 57.046 29.630 0.00 0.00 35.32 2.52
2455 3317 3.331150 ACAATTCTTATCGGTTGCGTCA 58.669 40.909 0.00 0.00 0.00 4.35
2500 3362 4.202141 TGAAAGCCATAATAAGCATGTGCC 60.202 41.667 0.57 0.00 43.38 5.01
2538 3400 1.344114 TCAATGCCTTTCTGGTTTGGC 59.656 47.619 0.00 0.00 45.10 4.52
2615 3477 7.094805 TGACTCATTAAGCACTAATCAAACCAC 60.095 37.037 0.00 0.00 0.00 4.16
2756 3618 5.957842 ACACAATCTGCCGATTTAAGAAA 57.042 34.783 0.00 0.00 37.77 2.52
2852 3865 8.749499 CAACATTGTTTCTGATCTGAAAAGAAC 58.251 33.333 24.18 15.51 37.63 3.01
2867 3880 8.577939 CATCGAATGACAATACAACATTGTTTC 58.422 33.333 1.98 4.82 41.76 2.78
3235 4379 6.761099 TCTCTCTCTTTGTGTATGTACCTC 57.239 41.667 0.00 0.00 0.00 3.85
3330 4474 2.693762 CCCATGCTGCAGTTGGTCG 61.694 63.158 26.30 14.56 0.00 4.79
3384 4528 2.034812 GGAGTCTTGGTATGGCTCGTAG 59.965 54.545 0.00 0.00 0.00 3.51
3704 4848 9.924650 TTTCTCAAAGGATCTGTAAAGTACTAC 57.075 33.333 0.00 0.00 0.00 2.73
3824 4974 7.932683 AAATTAACCAGGTAGCTAGTAGGAT 57.067 36.000 11.18 3.53 0.00 3.24
4284 5577 2.325082 CCTCGACAAAAGGCCCACG 61.325 63.158 0.00 0.00 0.00 4.94
4437 5784 2.867624 ACTAGTACCACTCGACCACAA 58.132 47.619 0.00 0.00 0.00 3.33
4438 5785 2.574006 ACTAGTACCACTCGACCACA 57.426 50.000 0.00 0.00 0.00 4.17
4439 5786 2.163211 GGAACTAGTACCACTCGACCAC 59.837 54.545 0.00 0.00 0.00 4.16
4440 5787 2.440409 GGAACTAGTACCACTCGACCA 58.560 52.381 0.00 0.00 0.00 4.02
4441 5788 1.747924 GGGAACTAGTACCACTCGACC 59.252 57.143 10.76 0.00 0.00 4.79
4442 5789 2.682352 GAGGGAACTAGTACCACTCGAC 59.318 54.545 16.38 0.00 44.43 4.20
4443 5790 2.306805 TGAGGGAACTAGTACCACTCGA 59.693 50.000 17.51 8.33 44.43 4.04
4444 5791 2.719739 TGAGGGAACTAGTACCACTCG 58.280 52.381 17.51 0.00 44.43 4.18
4445 5792 5.187186 TGATTTGAGGGAACTAGTACCACTC 59.813 44.000 16.44 16.44 44.43 3.51
4446 5793 5.091552 TGATTTGAGGGAACTAGTACCACT 58.908 41.667 16.38 9.05 44.43 4.00
4447 5794 5.187186 TCTGATTTGAGGGAACTAGTACCAC 59.813 44.000 16.38 11.62 44.43 4.16
4529 5894 6.013725 ACAAGTTAGAGGTAATCCATCACACA 60.014 38.462 0.00 0.00 35.89 3.72
4705 6073 6.653320 TGTAGGTAAGAGTGCAAAATAAGTGG 59.347 38.462 0.00 0.00 0.00 4.00
4746 6132 8.660435 ACAGTAATCAATGTGCTATTAGGGTAT 58.340 33.333 0.00 0.00 0.00 2.73
4747 6133 8.029782 ACAGTAATCAATGTGCTATTAGGGTA 57.970 34.615 0.00 0.00 0.00 3.69
4748 6134 6.900194 ACAGTAATCAATGTGCTATTAGGGT 58.100 36.000 0.00 0.00 0.00 4.34
4749 6135 8.902540 TTACAGTAATCAATGTGCTATTAGGG 57.097 34.615 0.00 0.00 0.00 3.53
4771 6159 4.797868 TGCATGGTAACGTACGTACATTAC 59.202 41.667 27.84 27.84 34.99 1.89
4772 6160 4.991472 TGCATGGTAACGTACGTACATTA 58.009 39.130 23.12 17.48 42.51 1.90
4822 6413 2.924290 CGCTTAGCTAGACTTCAACCAC 59.076 50.000 1.76 0.00 0.00 4.16
4831 6422 0.573055 GAAAGCGCGCTTAGCTAGAC 59.427 55.000 42.98 23.65 45.31 2.59
5045 6636 1.616159 TTGGTGGTCTTAAGCAAGGC 58.384 50.000 0.00 0.00 35.53 4.35
5067 6658 0.171007 CACGGCTGGCTTGTTATTGG 59.829 55.000 0.00 0.00 0.00 3.16
5071 6662 0.602638 CAGTCACGGCTGGCTTGTTA 60.603 55.000 7.56 0.00 25.77 2.41
5072 6663 1.893808 CAGTCACGGCTGGCTTGTT 60.894 57.895 7.56 0.00 25.77 2.83
5073 6664 2.281070 CAGTCACGGCTGGCTTGT 60.281 61.111 7.56 0.00 25.77 3.16
5074 6665 3.730761 GCAGTCACGGCTGGCTTG 61.731 66.667 0.11 0.99 37.00 4.01
5076 6667 3.890936 GAAGCAGTCACGGCTGGCT 62.891 63.158 2.13 0.00 41.66 4.75
5077 6668 3.426568 GAAGCAGTCACGGCTGGC 61.427 66.667 2.13 0.00 41.66 4.85
5078 6669 2.743928 GGAAGCAGTCACGGCTGG 60.744 66.667 2.13 0.00 41.66 4.85
5079 6670 3.114616 CGGAAGCAGTCACGGCTG 61.115 66.667 2.13 0.00 41.66 4.85
5080 6671 2.660258 AAACGGAAGCAGTCACGGCT 62.660 55.000 0.00 0.00 45.15 5.52
5081 6672 2.171489 GAAACGGAAGCAGTCACGGC 62.171 60.000 0.00 0.00 0.00 5.68
5102 6696 2.036992 GAGCACCACCTCTCCATCATAG 59.963 54.545 0.00 0.00 0.00 2.23
5114 6712 1.373570 GAACATAGCAGAGCACCACC 58.626 55.000 0.00 0.00 0.00 4.61
5122 6720 8.085909 TCGGATTATTTATTCGAACATAGCAGA 58.914 33.333 0.00 0.00 41.27 4.26
5123 6721 8.239681 TCGGATTATTTATTCGAACATAGCAG 57.760 34.615 0.00 0.00 41.27 4.24
5124 6722 8.655970 CATCGGATTATTTATTCGAACATAGCA 58.344 33.333 0.00 0.00 46.89 3.49
5125 6723 7.636359 GCATCGGATTATTTATTCGAACATAGC 59.364 37.037 0.00 0.00 46.89 2.97
5126 6724 8.873830 AGCATCGGATTATTTATTCGAACATAG 58.126 33.333 0.00 0.00 46.89 2.23
5168 6995 5.181245 TGAAGCCCGACATAAAGAAAAAGAG 59.819 40.000 0.00 0.00 0.00 2.85
5235 7065 8.788806 ACACGATTATTGAATACAAAGGTTCAA 58.211 29.630 3.39 3.39 45.27 2.69
5264 7094 7.916128 ATAGATAAATCGACGAGTTCAACAG 57.084 36.000 14.48 0.00 0.00 3.16
5399 7229 1.344114 TGCTTTTGCCCCTCACATTTC 59.656 47.619 0.00 0.00 46.87 2.17
5403 7233 1.070445 CAATTGCTTTTGCCCCTCACA 59.930 47.619 0.00 0.00 46.87 3.58
5404 7234 1.070601 ACAATTGCTTTTGCCCCTCAC 59.929 47.619 5.05 0.00 46.87 3.51
5421 7256 6.783708 ACAACATAAGTTTTCCCTTGACAA 57.216 33.333 0.00 0.00 35.28 3.18
5443 7278 6.024552 TGAAGGCAGAATCCAATAACAAAC 57.975 37.500 0.00 0.00 0.00 2.93
5490 7325 9.646336 CTTATAAATACACGCCATCACTAAAAC 57.354 33.333 0.00 0.00 0.00 2.43
5491 7326 8.832521 CCTTATAAATACACGCCATCACTAAAA 58.167 33.333 0.00 0.00 0.00 1.52
5492 7327 7.988599 ACCTTATAAATACACGCCATCACTAAA 59.011 33.333 0.00 0.00 0.00 1.85
5493 7328 7.502696 ACCTTATAAATACACGCCATCACTAA 58.497 34.615 0.00 0.00 0.00 2.24
5496 7331 6.427150 CAACCTTATAAATACACGCCATCAC 58.573 40.000 0.00 0.00 0.00 3.06
5512 7347 5.598417 GTCCTTGCCAATATTCCAACCTTAT 59.402 40.000 0.00 0.00 0.00 1.73
5517 7352 5.343307 AATGTCCTTGCCAATATTCCAAC 57.657 39.130 0.00 0.00 0.00 3.77
5520 7355 6.715347 ACTAAATGTCCTTGCCAATATTCC 57.285 37.500 0.00 0.00 0.00 3.01
5536 7371 5.771666 ACATGCCTCCAATGGATACTAAATG 59.228 40.000 0.87 4.47 37.61 2.32
5568 7403 4.564782 ATTGCTCAAAGATGGAGTGAGA 57.435 40.909 4.14 0.00 41.08 3.27
5575 7410 5.353938 CATGGGTTTATTGCTCAAAGATGG 58.646 41.667 0.00 0.00 0.00 3.51
5577 7412 4.440525 CGCATGGGTTTATTGCTCAAAGAT 60.441 41.667 0.68 0.00 34.23 2.40
5599 7434 7.030165 AGAGATGAAGTCTGTAACACATTACG 58.970 38.462 0.00 0.00 43.23 3.18
5722 11172 2.417516 CTGGGTGATCGTAGGGCG 59.582 66.667 0.00 0.00 43.01 6.13
5724 11174 0.464452 GTTCCTGGGTGATCGTAGGG 59.536 60.000 0.00 0.00 0.00 3.53
5729 11179 4.137116 TCTTATTGTTCCTGGGTGATCG 57.863 45.455 0.00 0.00 0.00 3.69
5734 11184 3.737559 TGCATCTTATTGTTCCTGGGT 57.262 42.857 0.00 0.00 0.00 4.51
5737 11187 6.183360 ACCATCAATGCATCTTATTGTTCCTG 60.183 38.462 0.00 0.00 36.97 3.86
5741 11191 6.819649 CCAAACCATCAATGCATCTTATTGTT 59.180 34.615 0.00 0.00 36.97 2.83
5751 11201 4.886496 TCAAATCCAAACCATCAATGCA 57.114 36.364 0.00 0.00 0.00 3.96
5758 11208 5.576447 GGTAACGATCAAATCCAAACCAT 57.424 39.130 0.00 0.00 0.00 3.55
5789 11239 1.439365 CGTCTTCTTGCGCTGCAAC 60.439 57.895 9.73 0.00 43.99 4.17
5793 11243 1.669158 CGACTCGTCTTCTTGCGCTG 61.669 60.000 9.73 1.08 0.00 5.18
5798 11248 5.612925 CGATCTATACCGACTCGTCTTCTTG 60.613 48.000 0.00 0.00 0.00 3.02
5815 11265 3.567397 AGGCACTCCAAGTACGATCTAT 58.433 45.455 0.00 0.00 33.74 1.98
5833 11283 3.585862 TCGTTCATCTACAGTTTGAGGC 58.414 45.455 0.00 0.00 0.00 4.70
5838 11288 3.782046 CGGGATCGTTCATCTACAGTTT 58.218 45.455 0.00 0.00 0.00 2.66
5843 11293 0.309922 TCGCGGGATCGTTCATCTAC 59.690 55.000 6.13 0.00 38.89 2.59
5852 11302 0.027586 GAAATTGGTTCGCGGGATCG 59.972 55.000 6.13 0.00 39.81 3.69
5860 11310 0.179225 CGTGCGAGGAAATTGGTTCG 60.179 55.000 0.00 2.44 37.08 3.95
5879 11329 1.087501 GACCATGCTTTCGGTCTTCC 58.912 55.000 0.00 0.00 46.83 3.46
5905 11363 5.932303 GTGAAGACCATAAGCTTGTAACTCA 59.068 40.000 9.86 0.56 0.00 3.41
5917 11375 1.202486 GCCGGATCGTGAAGACCATAA 60.202 52.381 5.05 0.00 0.00 1.90
5923 11381 2.184322 GCTGCCGGATCGTGAAGA 59.816 61.111 5.05 0.00 0.00 2.87
5946 11404 2.481952 GCGATGATTAGTTCTGGATGCC 59.518 50.000 0.00 0.00 0.00 4.40
5947 11405 2.481952 GGCGATGATTAGTTCTGGATGC 59.518 50.000 0.00 0.00 0.00 3.91
5949 11407 2.289072 CCGGCGATGATTAGTTCTGGAT 60.289 50.000 9.30 0.00 0.00 3.41
5952 11410 2.034685 TCTCCGGCGATGATTAGTTCTG 59.965 50.000 9.30 0.00 0.00 3.02
5956 11414 3.753294 AATTCTCCGGCGATGATTAGT 57.247 42.857 9.30 0.00 0.00 2.24
5962 11420 1.337260 CCCTCTAATTCTCCGGCGATG 60.337 57.143 9.30 0.00 0.00 3.84
5963 11421 0.969894 CCCTCTAATTCTCCGGCGAT 59.030 55.000 9.30 0.00 0.00 4.58
5970 11428 3.761752 CCGATCTCCTCCCTCTAATTCTC 59.238 52.174 0.00 0.00 0.00 2.87
5990 11448 2.358737 GAGCCCAGTGTGGTTCCG 60.359 66.667 3.96 0.00 35.17 4.30
6001 11459 1.905839 TCCTCATAATTGGGAGCCCA 58.094 50.000 3.58 3.58 45.63 5.36
6007 11465 7.507797 AGATCCTCTAATCCTCATAATTGGG 57.492 40.000 0.00 0.00 0.00 4.12
6033 11491 9.019656 TCCTAGTTGATCAATAAGAGCTAGATC 57.980 37.037 21.40 0.00 36.51 2.75
6056 11514 4.292836 ACTCCTCTAGTTCTAGTTGGTCCT 59.707 45.833 15.08 0.00 33.35 3.85
6064 11522 7.696992 AGTTTTGAGACTCCTCTAGTTCTAG 57.303 40.000 0.00 0.83 39.07 2.43
6067 11525 6.422400 CACAAGTTTTGAGACTCCTCTAGTTC 59.578 42.308 0.00 0.00 39.07 3.01
6077 11535 6.811253 TTTGTACACACAAGTTTTGAGACT 57.189 33.333 0.00 0.00 45.17 3.24
6079 11537 6.207810 ACCTTTTGTACACACAAGTTTTGAGA 59.792 34.615 0.00 0.00 45.17 3.27


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

AutoCloner maintained by Alex Coulton.