Multiple sequence alignment - TraesCS7A01G175000

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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 TraesCS7A01G175000 chr7A 100.000 4142 0 0 1 4142 128777637 128773496 0.000000e+00 7649.0
1 TraesCS7A01G175000 chr7A 87.500 392 36 6 3493 3874 152356236 152356624 1.370000e-119 440.0
2 TraesCS7A01G175000 chr7A 89.011 273 30 0 3870 4142 152356651 152356923 5.130000e-89 339.0
3 TraesCS7A01G175000 chr7D 89.149 2866 201 55 637 3434 128748986 128746163 0.000000e+00 3469.0
4 TraesCS7A01G175000 chr7D 88.263 2769 220 62 718 3434 128481078 128478363 0.000000e+00 3216.0
5 TraesCS7A01G175000 chr7D 91.266 1683 115 21 1761 3434 128143337 128141678 0.000000e+00 2265.0
6 TraesCS7A01G175000 chr7D 86.720 753 51 25 718 1438 128144946 128144211 0.000000e+00 791.0
7 TraesCS7A01G175000 chr7D 84.719 445 53 10 2934 3374 128472151 128471718 8.230000e-117 431.0
8 TraesCS7A01G175000 chr7D 92.527 281 19 1 1453 1733 128143797 128143519 6.450000e-108 401.0
9 TraesCS7A01G175000 chr7D 82.692 468 60 13 2917 3374 128745613 128745157 3.000000e-106 396.0
10 TraesCS7A01G175000 chr7D 83.803 284 14 13 189 457 128749248 128748982 1.490000e-59 241.0
11 TraesCS7A01G175000 chr7D 88.770 187 9 5 1 180 128749404 128749223 6.970000e-53 219.0
12 TraesCS7A01G175000 chr7B 88.432 2844 215 55 637 3414 89920622 89917827 0.000000e+00 3325.0
13 TraesCS7A01G175000 chr7B 89.102 2560 198 54 718 3254 89789465 89786964 0.000000e+00 3107.0
14 TraesCS7A01G175000 chr7B 89.463 2031 160 29 1404 3414 89885686 89883690 0.000000e+00 2516.0
15 TraesCS7A01G175000 chr7B 92.994 785 49 6 2379 3160 89912293 89911512 0.000000e+00 1140.0
16 TraesCS7A01G175000 chr7B 85.921 483 30 12 1 457 89921088 89920618 8.050000e-132 481.0
17 TraesCS7A01G175000 chr7B 88.235 391 35 5 3494 3874 362387031 362386642 1.360000e-124 457.0
18 TraesCS7A01G175000 chr7B 83.830 470 41 18 677 1130 89891883 89891433 8.280000e-112 414.0
19 TraesCS7A01G175000 chr7B 87.903 248 11 11 1171 1415 89891435 89891204 1.470000e-69 274.0
20 TraesCS7A01G175000 chr7B 90.741 54 0 2 397 446 89789600 89789548 2.670000e-07 67.6
21 TraesCS7A01G175000 chr6B 80.711 1462 227 31 1481 2912 585327725 585329161 0.000000e+00 1086.0
22 TraesCS7A01G175000 chr6B 89.855 69 5 2 3493 3561 193182117 193182051 2.050000e-13 87.9
23 TraesCS7A01G175000 chr6B 89.706 68 5 2 3494 3561 459262355 459262290 7.380000e-13 86.1
24 TraesCS7A01G175000 chr6A 79.087 1358 230 31 1817 3142 537874866 537876201 0.000000e+00 885.0
25 TraesCS7A01G175000 chr6A 89.899 198 16 4 451 647 233960068 233959874 6.870000e-63 252.0
26 TraesCS7A01G175000 chr6A 86.000 200 21 6 452 644 37811587 37811786 1.510000e-49 207.0
27 TraesCS7A01G175000 chr6D 80.717 1115 189 12 1817 2912 391694491 391695598 0.000000e+00 845.0
28 TraesCS7A01G175000 chr6D 90.040 251 22 1 1481 1731 391694136 391694383 5.170000e-84 322.0
29 TraesCS7A01G175000 chr6D 82.937 252 43 0 1480 1731 391687690 391687941 1.160000e-55 228.0
30 TraesCS7A01G175000 chr3B 85.204 392 47 5 3493 3874 408589171 408589561 3.880000e-105 392.0
31 TraesCS7A01G175000 chr4D 91.941 273 22 0 3870 4142 389338283 389338011 2.340000e-102 383.0
32 TraesCS7A01G175000 chr5D 89.377 273 29 0 3870 4142 409021234 409021506 1.100000e-90 344.0
33 TraesCS7A01G175000 chr5D 81.765 170 26 4 1236 1403 544879549 544879715 2.010000e-28 137.0
34 TraesCS7A01G175000 chr5A 91.099 191 15 2 452 640 341143405 341143595 1.480000e-64 257.0
35 TraesCS7A01G175000 chr5A 87.283 173 16 4 458 630 98434069 98434235 4.230000e-45 193.0
36 TraesCS7A01G175000 chr2A 88.235 187 19 3 460 644 748960965 748960780 1.940000e-53 220.0
37 TraesCS7A01G175000 chr2A 85.204 196 23 5 453 642 25378816 25379011 3.270000e-46 196.0
38 TraesCS7A01G175000 chr3A 87.701 187 21 2 458 642 698147018 698147204 2.510000e-52 217.0
39 TraesCS7A01G175000 chr3A 87.027 185 18 6 459 637 234224608 234224424 1.950000e-48 204.0
40 TraesCS7A01G175000 chr1D 86.486 185 17 4 460 636 468861456 468861640 3.270000e-46 196.0
41 TraesCS7A01G175000 chr1D 94.286 35 2 0 1980 2014 23247993 23248027 2.000000e-03 54.7
42 TraesCS7A01G175000 chr5B 82.456 171 24 5 1236 1403 687459088 687459255 1.200000e-30 145.0
43 TraesCS7A01G175000 chr1A 79.762 168 33 1 1236 1403 569341496 569341330 2.020000e-23 121.0
44 TraesCS7A01G175000 chr1A 94.286 35 2 0 1980 2014 24339349 24339383 2.000000e-03 54.7
45 TraesCS7A01G175000 chr2B 91.429 70 4 2 3492 3561 443792133 443792200 1.230000e-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 TraesCS7A01G175000 chr7A 128773496 128777637 4141 True 7649.000000 7649 100.0000 1 4142 1 chr7A.!!$R1 4141
1 TraesCS7A01G175000 chr7A 152356236 152356923 687 False 389.500000 440 88.2555 3493 4142 2 chr7A.!!$F1 649
2 TraesCS7A01G175000 chr7D 128478363 128481078 2715 True 3216.000000 3216 88.2630 718 3434 1 chr7D.!!$R2 2716
3 TraesCS7A01G175000 chr7D 128141678 128144946 3268 True 1152.333333 2265 90.1710 718 3434 3 chr7D.!!$R3 2716
4 TraesCS7A01G175000 chr7D 128745157 128749404 4247 True 1081.250000 3469 86.1035 1 3434 4 chr7D.!!$R4 3433
5 TraesCS7A01G175000 chr7B 89883690 89885686 1996 True 2516.000000 2516 89.4630 1404 3414 1 chr7B.!!$R1 2010
6 TraesCS7A01G175000 chr7B 89917827 89921088 3261 True 1903.000000 3325 87.1765 1 3414 2 chr7B.!!$R6 3413
7 TraesCS7A01G175000 chr7B 89786964 89789600 2636 True 1587.300000 3107 89.9215 397 3254 2 chr7B.!!$R4 2857
8 TraesCS7A01G175000 chr7B 89911512 89912293 781 True 1140.000000 1140 92.9940 2379 3160 1 chr7B.!!$R2 781
9 TraesCS7A01G175000 chr7B 89891204 89891883 679 True 344.000000 414 85.8665 677 1415 2 chr7B.!!$R5 738
10 TraesCS7A01G175000 chr6B 585327725 585329161 1436 False 1086.000000 1086 80.7110 1481 2912 1 chr6B.!!$F1 1431
11 TraesCS7A01G175000 chr6A 537874866 537876201 1335 False 885.000000 885 79.0870 1817 3142 1 chr6A.!!$F2 1325
12 TraesCS7A01G175000 chr6D 391694136 391695598 1462 False 583.500000 845 85.3785 1481 2912 2 chr6D.!!$F2 1431

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
347 374 0.108992 TCGTACGTGCTTGGATGGAC 60.109 55.000 16.05 0.00 0.00 4.02 F
1238 1395 0.725784 GCGTTCGTGCATCCTGTTTG 60.726 55.000 0.00 0.00 34.15 2.93 F
1491 2060 1.133945 TGTGTACACAGGCATGGTGTT 60.134 47.619 24.62 1.29 46.75 3.32 F
2145 2881 1.296392 CATGGACGCACTCCTCCAA 59.704 57.895 0.00 0.00 40.05 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 2478 0.663153 AGCAACGACAACTTGGCTTC 59.337 50.000 0.0 0.0 0.00 3.86 R
2569 3329 0.178990 GGCTTGTTGGGGAAGTCTGT 60.179 55.000 0.0 0.0 0.00 3.41 R
2932 3693 1.000506 GAATGCATAGCCATTGCCCAG 59.999 52.381 0.0 0.0 39.39 4.45 R
3988 5095 0.037790 GACATCAGATAGGAGGGCGC 60.038 60.000 0.0 0.0 0.00 6.53 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.690786 CATGCATGGTTGTTTCCCTTG 58.309 47.619 19.40 0.00 0.00 3.61
28 29 3.617288 GCATGGTTGTTTCCCTTGGAATC 60.617 47.826 0.00 0.00 41.71 2.52
37 38 0.657840 CCCTTGGAATCGATTGCGTC 59.342 55.000 22.40 5.76 38.98 5.19
99 119 1.144969 TCATTTCCTCACGCGTTGAC 58.855 50.000 10.22 0.00 0.00 3.18
100 120 0.179250 CATTTCCTCACGCGTTGACG 60.179 55.000 10.22 0.00 43.27 4.35
121 142 0.444260 GCTTTGCTCGTTCCTGCTAC 59.556 55.000 0.00 0.00 0.00 3.58
126 147 2.566913 TGCTCGTTCCTGCTACAAAAA 58.433 42.857 0.00 0.00 0.00 1.94
127 148 2.289547 TGCTCGTTCCTGCTACAAAAAC 59.710 45.455 0.00 0.00 0.00 2.43
128 149 2.661979 GCTCGTTCCTGCTACAAAAACG 60.662 50.000 0.00 0.00 42.87 3.60
129 150 2.798283 CTCGTTCCTGCTACAAAAACGA 59.202 45.455 13.03 13.03 46.46 3.85
130 151 2.798283 TCGTTCCTGCTACAAAAACGAG 59.202 45.455 10.82 0.00 44.56 4.18
132 153 1.519408 TCCTGCTACAAAAACGAGCC 58.481 50.000 0.00 0.00 35.24 4.70
133 154 1.202710 TCCTGCTACAAAAACGAGCCA 60.203 47.619 0.00 0.00 35.24 4.75
135 156 1.873591 CTGCTACAAAAACGAGCCACT 59.126 47.619 0.00 0.00 35.24 4.00
136 157 3.064207 CTGCTACAAAAACGAGCCACTA 58.936 45.455 0.00 0.00 35.24 2.74
137 158 2.803956 TGCTACAAAAACGAGCCACTAC 59.196 45.455 0.00 0.00 35.24 2.73
138 159 3.064931 GCTACAAAAACGAGCCACTACT 58.935 45.455 0.00 0.00 0.00 2.57
183 205 8.915654 GTCAAAATAGAACTAACATGGCAAAAG 58.084 33.333 0.00 0.00 0.00 2.27
188 210 6.478512 AGAACTAACATGGCAAAAGGAAAA 57.521 33.333 0.00 0.00 0.00 2.29
189 211 6.883744 AGAACTAACATGGCAAAAGGAAAAA 58.116 32.000 0.00 0.00 0.00 1.94
190 212 6.761242 AGAACTAACATGGCAAAAGGAAAAAC 59.239 34.615 0.00 0.00 0.00 2.43
204 226 7.997107 AAAGGAAAAACGTCAAAATAGAACC 57.003 32.000 0.00 0.00 0.00 3.62
207 229 6.976349 AGGAAAAACGTCAAAATAGAACCAAC 59.024 34.615 0.00 0.00 0.00 3.77
240 262 1.382522 GCATCCAGATGAGGCGAAAA 58.617 50.000 11.81 0.00 41.45 2.29
284 310 0.248866 CACCACACGTTCCAAAAGCC 60.249 55.000 0.00 0.00 0.00 4.35
286 312 1.362355 CACACGTTCCAAAAGCCCC 59.638 57.895 0.00 0.00 0.00 5.80
310 337 6.360681 CCTCGTGTGTTTTCTGATTGATTTTC 59.639 38.462 0.00 0.00 0.00 2.29
344 371 1.988409 CGTCGTACGTGCTTGGATG 59.012 57.895 16.05 0.00 36.74 3.51
347 374 0.108992 TCGTACGTGCTTGGATGGAC 60.109 55.000 16.05 0.00 0.00 4.02
354 381 5.036117 ACGTGCTTGGATGGACTAATTAT 57.964 39.130 0.00 0.00 0.00 1.28
355 382 5.437060 ACGTGCTTGGATGGACTAATTATT 58.563 37.500 0.00 0.00 0.00 1.40
396 436 2.546584 GCAAAGGGTTCAAGGCTTTGAG 60.547 50.000 11.40 0.00 43.76 3.02
397 437 1.332195 AAGGGTTCAAGGCTTTGAGC 58.668 50.000 15.69 15.69 43.76 4.26
453 501 2.483491 GCGACCAACCAACGGTTAATAA 59.517 45.455 0.00 0.00 45.01 1.40
454 502 3.667695 GCGACCAACCAACGGTTAATAAC 60.668 47.826 0.00 0.00 45.01 1.89
455 503 3.497640 CGACCAACCAACGGTTAATAACA 59.502 43.478 5.45 0.00 45.01 2.41
456 504 4.024218 CGACCAACCAACGGTTAATAACAA 60.024 41.667 5.45 0.00 45.01 2.83
457 505 5.505324 CGACCAACCAACGGTTAATAACAAA 60.505 40.000 5.45 0.00 45.01 2.83
458 506 6.218108 ACCAACCAACGGTTAATAACAAAA 57.782 33.333 5.45 0.00 45.01 2.44
459 507 6.637657 ACCAACCAACGGTTAATAACAAAAA 58.362 32.000 5.45 0.00 45.01 1.94
460 508 6.534436 ACCAACCAACGGTTAATAACAAAAAC 59.466 34.615 5.45 0.00 45.01 2.43
461 509 6.534079 CCAACCAACGGTTAATAACAAAAACA 59.466 34.615 5.45 0.00 45.01 2.83
462 510 7.254151 CCAACCAACGGTTAATAACAAAAACAG 60.254 37.037 5.45 0.00 45.01 3.16
463 511 6.865411 ACCAACGGTTAATAACAAAAACAGT 58.135 32.000 5.45 0.00 33.83 3.55
464 512 7.321908 ACCAACGGTTAATAACAAAAACAGTT 58.678 30.769 5.45 0.00 40.51 3.16
465 513 7.818446 ACCAACGGTTAATAACAAAAACAGTTT 59.182 29.630 5.45 0.00 38.75 2.66
466 514 8.657729 CCAACGGTTAATAACAAAAACAGTTTT 58.342 29.630 5.37 5.37 38.75 2.43
500 548 7.651808 ACATCTAAATGTGCCATAAGTATTGC 58.348 34.615 0.00 0.00 44.51 3.56
501 549 7.285172 ACATCTAAATGTGCCATAAGTATTGCA 59.715 33.333 0.00 0.00 44.51 4.08
510 558 7.822161 TGCCATAAGTATTGCACATCTAAAT 57.178 32.000 0.00 0.00 30.49 1.40
511 559 7.874940 TGCCATAAGTATTGCACATCTAAATC 58.125 34.615 0.00 0.00 30.49 2.17
512 560 7.501892 TGCCATAAGTATTGCACATCTAAATCA 59.498 33.333 0.00 0.00 30.49 2.57
513 561 8.517878 GCCATAAGTATTGCACATCTAAATCAT 58.482 33.333 0.00 0.00 0.00 2.45
543 591 9.599866 TCATTGATCTTACGTTGAGATTTATGT 57.400 29.630 20.66 4.57 34.13 2.29
585 633 7.985634 TTTTCTTTGTGCTTGATTCACTTAC 57.014 32.000 0.00 0.00 35.58 2.34
586 634 6.942532 TTCTTTGTGCTTGATTCACTTACT 57.057 33.333 0.00 0.00 35.58 2.24
587 635 6.942532 TCTTTGTGCTTGATTCACTTACTT 57.057 33.333 0.00 0.00 35.58 2.24
588 636 8.445275 TTCTTTGTGCTTGATTCACTTACTTA 57.555 30.769 0.00 0.00 35.58 2.24
589 637 8.445275 TCTTTGTGCTTGATTCACTTACTTAA 57.555 30.769 0.00 0.00 35.58 1.85
590 638 8.898761 TCTTTGTGCTTGATTCACTTACTTAAA 58.101 29.630 0.00 0.00 35.58 1.52
591 639 9.683069 CTTTGTGCTTGATTCACTTACTTAAAT 57.317 29.630 0.00 0.00 35.58 1.40
592 640 9.462174 TTTGTGCTTGATTCACTTACTTAAATG 57.538 29.630 0.00 0.00 35.58 2.32
593 641 8.165239 TGTGCTTGATTCACTTACTTAAATGT 57.835 30.769 0.00 0.00 35.58 2.71
594 642 8.075574 TGTGCTTGATTCACTTACTTAAATGTG 58.924 33.333 0.00 0.00 35.58 3.21
595 643 7.061094 GTGCTTGATTCACTTACTTAAATGTGC 59.939 37.037 0.00 0.00 0.00 4.57
596 644 7.083858 GCTTGATTCACTTACTTAAATGTGCA 58.916 34.615 0.00 0.00 0.00 4.57
597 645 7.594758 GCTTGATTCACTTACTTAAATGTGCAA 59.405 33.333 0.00 0.00 0.00 4.08
598 646 9.630098 CTTGATTCACTTACTTAAATGTGCAAT 57.370 29.630 0.00 0.00 0.00 3.56
608 656 9.920133 TTACTTAAATGTGCAATAATCAAAGCA 57.080 25.926 0.00 0.00 34.10 3.91
617 665 7.812690 TGCAATAATCAAAGCACATCTAGAT 57.187 32.000 0.00 0.00 31.05 1.98
618 666 7.645402 TGCAATAATCAAAGCACATCTAGATG 58.355 34.615 27.63 27.63 44.15 2.90
634 682 2.383855 AGATGTGCTCTAGACACTCCC 58.616 52.381 19.44 11.90 38.86 4.30
635 683 2.103373 GATGTGCTCTAGACACTCCCA 58.897 52.381 19.44 6.48 38.86 4.37
636 684 2.009681 TGTGCTCTAGACACTCCCAA 57.990 50.000 19.44 3.91 38.86 4.12
641 689 3.135712 TGCTCTAGACACTCCCAAACAAA 59.864 43.478 0.00 0.00 0.00 2.83
652 700 8.980143 ACACTCCCAAACAAATAAATTAATCG 57.020 30.769 0.00 0.00 0.00 3.34
662 710 8.336801 ACAAATAAATTAATCGATCTAGGGGC 57.663 34.615 0.00 0.00 0.00 5.80
714 782 1.202698 GCCTCCACTTTCCATAGCGAT 60.203 52.381 0.00 0.00 0.00 4.58
722 790 2.254546 TTCCATAGCGATTGCCGATT 57.745 45.000 0.00 0.00 44.31 3.34
723 791 3.394674 TTCCATAGCGATTGCCGATTA 57.605 42.857 0.00 0.00 44.31 1.75
727 795 4.868171 TCCATAGCGATTGCCGATTATAAC 59.132 41.667 0.00 0.00 44.31 1.89
752 825 9.890629 ACTTTGACAAGAAGCTAATCATATGTA 57.109 29.630 1.90 0.00 33.72 2.29
755 828 8.837788 TGACAAGAAGCTAATCATATGTATGG 57.162 34.615 1.90 0.00 34.50 2.74
811 901 2.506544 CGATCTTGTCGCCCATACG 58.493 57.895 0.00 0.00 44.33 3.06
923 1033 2.159462 GCAGCTTCATAACTTGTGGCTC 60.159 50.000 0.00 0.00 34.12 4.70
932 1046 2.543777 ACTTGTGGCTCGCTTCTTAA 57.456 45.000 0.00 0.00 0.00 1.85
1022 1136 2.254508 GGGTATGGCTAAGATACCGGT 58.745 52.381 13.98 13.98 44.46 5.28
1133 1247 5.868257 TGTAAGTCTGCTTGCATTTATTCG 58.132 37.500 0.00 0.00 41.28 3.34
1147 1262 8.732413 TGCATTTATTCGCATTCATTTCTATC 57.268 30.769 0.00 0.00 31.95 2.08
1227 1384 1.214367 ACTTACTTGTGGCGTTCGTG 58.786 50.000 0.00 0.00 0.00 4.35
1232 1389 2.513065 CTTGTGGCGTTCGTGCATCC 62.513 60.000 0.00 0.00 36.28 3.51
1234 1391 2.741985 TGGCGTTCGTGCATCCTG 60.742 61.111 0.00 0.00 36.28 3.86
1238 1395 0.725784 GCGTTCGTGCATCCTGTTTG 60.726 55.000 0.00 0.00 34.15 2.93
1258 1415 3.347216 TGGCAGATTAAAGAGAGCAACC 58.653 45.455 0.00 0.00 0.00 3.77
1296 1456 2.989824 AGGACCGTCCTCACCGTG 60.990 66.667 14.84 0.00 45.66 4.94
1416 1578 4.966805 TGGTAAGTTATAGTTAGCCTGGCT 59.033 41.667 26.52 26.52 43.41 4.75
1446 1614 5.469760 CCGTTCATTGCATATAACCATCAGA 59.530 40.000 0.00 0.00 0.00 3.27
1467 1636 5.471257 AGAAAACCTATCTTCTGACGTGAC 58.529 41.667 0.00 0.00 30.67 3.67
1491 2060 1.133945 TGTGTACACAGGCATGGTGTT 60.134 47.619 24.62 1.29 46.75 3.32
1550 2119 1.846439 CATTACCCAGTGTCCCATCCT 59.154 52.381 0.00 0.00 0.00 3.24
1689 2258 2.593956 GCTCGGAACCACCTTCCCT 61.594 63.158 0.00 0.00 45.50 4.20
1707 2276 2.430332 CCCTTTCAAGAAGCCACACAAA 59.570 45.455 0.00 0.00 0.00 2.83
1725 2294 3.775316 ACAAAGAGATACCCGTCATCCTT 59.225 43.478 0.00 0.00 0.00 3.36
1733 2302 6.023603 AGATACCCGTCATCCTTGGTATATT 58.976 40.000 0.00 0.00 42.61 1.28
1756 2475 7.750229 TTCATTACTTCCATCCATGCTTATC 57.250 36.000 0.00 0.00 0.00 1.75
1757 2476 7.083062 TCATTACTTCCATCCATGCTTATCT 57.917 36.000 0.00 0.00 0.00 1.98
1759 2478 7.446319 TCATTACTTCCATCCATGCTTATCTTG 59.554 37.037 0.00 0.00 0.00 3.02
1804 2540 7.970384 TGAATGTCGTTAACTTGATATGTTCC 58.030 34.615 3.71 0.00 0.00 3.62
1864 2600 3.910490 ATCTGCTCGAGGAGGCGC 61.910 66.667 30.47 9.60 34.00 6.53
1914 2650 2.024868 CGCGAACACCATCAACGGA 61.025 57.895 0.00 0.00 0.00 4.69
2112 2848 1.402968 GCCGTCAAGCACATCATGATT 59.597 47.619 5.16 0.00 37.42 2.57
2143 2879 2.187946 CCATGGACGCACTCCTCC 59.812 66.667 5.56 0.00 40.26 4.30
2145 2881 1.296392 CATGGACGCACTCCTCCAA 59.704 57.895 0.00 0.00 40.05 3.53
2535 3295 3.515286 GCCGTCGACATCCTCGGA 61.515 66.667 17.16 0.00 44.86 4.55
2917 3678 4.974645 ACAAATCCTGGTGAGTCAACTA 57.025 40.909 10.10 0.00 0.00 2.24
2918 3679 5.505181 ACAAATCCTGGTGAGTCAACTAT 57.495 39.130 10.10 0.00 0.00 2.12
2919 3680 6.620877 ACAAATCCTGGTGAGTCAACTATA 57.379 37.500 10.10 0.00 0.00 1.31
2942 3703 1.856629 ATTCAGGTTCTGGGCAATGG 58.143 50.000 0.00 0.00 31.51 3.16
2945 3706 0.034186 CAGGTTCTGGGCAATGGCTA 60.034 55.000 6.78 0.00 40.87 3.93
2948 3709 0.386838 GTTCTGGGCAATGGCTATGC 59.613 55.000 6.78 6.54 43.08 3.14
3049 3813 1.563111 CCATTTTGATCGCCATGTGC 58.437 50.000 0.00 0.00 0.00 4.57
3143 3907 2.423538 CCAACATGCCTACCTGCTAAAC 59.576 50.000 0.00 0.00 0.00 2.01
3155 3919 2.428171 CCTGCTAAACAATCCACATGGG 59.572 50.000 0.00 0.00 35.41 4.00
3175 3939 0.963962 AAAAGGCAGACATGTGCAGG 59.036 50.000 1.15 0.00 45.93 4.85
3279 4048 3.141272 AGGTTTGTGTGGAATAAAGGGGA 59.859 43.478 0.00 0.00 0.00 4.81
3280 4049 4.093743 GGTTTGTGTGGAATAAAGGGGAT 58.906 43.478 0.00 0.00 0.00 3.85
3298 4067 4.696479 GGATAGTTGACTCCCATGTGAT 57.304 45.455 0.00 0.00 0.00 3.06
3299 4068 4.636249 GGATAGTTGACTCCCATGTGATC 58.364 47.826 0.00 0.00 0.00 2.92
3302 4071 2.012673 GTTGACTCCCATGTGATCAGC 58.987 52.381 0.00 0.00 0.00 4.26
3305 4074 1.209019 GACTCCCATGTGATCAGCAGT 59.791 52.381 0.00 0.00 0.00 4.40
3306 4075 1.209019 ACTCCCATGTGATCAGCAGTC 59.791 52.381 0.00 0.00 0.00 3.51
3381 4154 9.525007 GTGTAAATGTGTTTCTTGTACTATTCG 57.475 33.333 0.00 0.00 0.00 3.34
3434 4212 5.910637 TTACGAATTCCGGTTATATGCAC 57.089 39.130 0.00 0.00 43.93 4.57
3435 4213 3.799366 ACGAATTCCGGTTATATGCACA 58.201 40.909 0.00 0.00 43.93 4.57
3436 4214 4.385825 ACGAATTCCGGTTATATGCACAT 58.614 39.130 0.00 0.00 43.93 3.21
3438 4216 5.298276 ACGAATTCCGGTTATATGCACATTT 59.702 36.000 0.00 0.00 43.93 2.32
3439 4217 5.851177 CGAATTCCGGTTATATGCACATTTC 59.149 40.000 0.00 0.00 33.91 2.17
3440 4218 5.705609 ATTCCGGTTATATGCACATTTCC 57.294 39.130 0.00 0.00 0.00 3.13
3442 4220 4.724399 TCCGGTTATATGCACATTTCCAT 58.276 39.130 0.00 0.00 0.00 3.41
3452 4268 3.808726 TGCACATTTCCATTTCAAGCAAC 59.191 39.130 0.00 0.00 0.00 4.17
3465 4281 6.767524 TTTCAAGCAACAGTTCTAAAAGGA 57.232 33.333 0.00 0.00 0.00 3.36
3469 4285 4.390264 AGCAACAGTTCTAAAAGGACTCC 58.610 43.478 0.00 0.00 0.00 3.85
3472 4288 4.522722 ACAGTTCTAAAAGGACTCCTCG 57.477 45.455 0.00 0.00 30.89 4.63
3474 4290 4.022155 ACAGTTCTAAAAGGACTCCTCGTC 60.022 45.833 0.00 0.00 42.07 4.20
3487 4303 6.796705 GACTCCTCGTCCTTTCAATAAAAA 57.203 37.500 0.00 0.00 36.62 1.94
3488 4304 6.555812 ACTCCTCGTCCTTTCAATAAAAAC 57.444 37.500 0.00 0.00 0.00 2.43
3489 4305 6.059484 ACTCCTCGTCCTTTCAATAAAAACA 58.941 36.000 0.00 0.00 0.00 2.83
3490 4306 6.204882 ACTCCTCGTCCTTTCAATAAAAACAG 59.795 38.462 0.00 0.00 0.00 3.16
3491 4307 6.059484 TCCTCGTCCTTTCAATAAAAACAGT 58.941 36.000 0.00 0.00 0.00 3.55
3492 4308 6.544564 TCCTCGTCCTTTCAATAAAAACAGTT 59.455 34.615 0.00 0.00 0.00 3.16
3493 4309 7.067737 TCCTCGTCCTTTCAATAAAAACAGTTT 59.932 33.333 0.00 0.00 0.00 2.66
3494 4310 7.704899 CCTCGTCCTTTCAATAAAAACAGTTTT 59.295 33.333 5.37 5.37 40.15 2.43
3495 4311 8.989653 TCGTCCTTTCAATAAAAACAGTTTTT 57.010 26.923 24.06 24.06 44.43 1.94
3515 4331 3.374220 TTTTCTCAAGAGTACGCCGAA 57.626 42.857 0.00 0.00 0.00 4.30
3542 4358 7.176340 GGCGTACCTTATCTTTATAGAAGAGGA 59.824 40.741 16.70 4.16 38.13 3.71
3543 4359 8.238631 GCGTACCTTATCTTTATAGAAGAGGAG 58.761 40.741 16.70 10.85 38.13 3.69
3566 4382 5.416952 AGGAAAATCATGTACAAGAAGCCAG 59.583 40.000 4.69 0.00 0.00 4.85
3589 4406 1.217916 TGGAACAAACCTCCACCTCA 58.782 50.000 0.00 0.00 38.07 3.86
3590 4407 1.133915 TGGAACAAACCTCCACCTCAC 60.134 52.381 0.00 0.00 38.07 3.51
3595 4412 1.696097 AAACCTCCACCTCACGCACT 61.696 55.000 0.00 0.00 0.00 4.40
3605 4422 0.389948 CTCACGCACTCACCCTTACC 60.390 60.000 0.00 0.00 0.00 2.85
3608 4425 2.675371 GCACTCACCCTTACCCCC 59.325 66.667 0.00 0.00 0.00 5.40
3609 4426 2.228480 GCACTCACCCTTACCCCCA 61.228 63.158 0.00 0.00 0.00 4.96
3610 4427 1.683441 CACTCACCCTTACCCCCAC 59.317 63.158 0.00 0.00 0.00 4.61
3611 4428 1.131303 CACTCACCCTTACCCCCACA 61.131 60.000 0.00 0.00 0.00 4.17
3612 4429 1.131928 ACTCACCCTTACCCCCACAC 61.132 60.000 0.00 0.00 0.00 3.82
3629 4448 4.510571 CCACACTTACCCTATACCAACAC 58.489 47.826 0.00 0.00 0.00 3.32
3662 4488 3.075005 TGCTCCACCTAGACCCGC 61.075 66.667 0.00 0.00 0.00 6.13
3683 4509 1.092345 GCCTTCCACGCCTTGATCTC 61.092 60.000 0.00 0.00 0.00 2.75
3690 4516 2.358957 CACGCCTTGATCTCATCCAAA 58.641 47.619 0.00 0.00 0.00 3.28
3696 4522 3.069158 CCTTGATCTCATCCAAAATGGCC 59.931 47.826 0.00 0.00 37.47 5.36
3767 4593 1.665679 CGCGTTCTGTTGCTTCCATAT 59.334 47.619 0.00 0.00 0.00 1.78
3777 4691 1.421268 TGCTTCCATATCGCCCAGATT 59.579 47.619 0.00 0.00 40.66 2.40
3789 4703 1.843368 CCCAGATTGTGGCAATGACT 58.157 50.000 0.00 0.00 46.45 3.41
3820 4734 0.249741 ACCACGTTTCCCACTCTTCG 60.250 55.000 0.00 0.00 0.00 3.79
3825 4739 3.744426 CACGTTTCCCACTCTTCGTAAAT 59.256 43.478 0.00 0.00 0.00 1.40
3835 4749 6.239345 CCCACTCTTCGTAAATAAGCTCCTAT 60.239 42.308 0.00 0.00 0.00 2.57
3848 4842 1.500474 CTCCTATCCTCAAGCCACCA 58.500 55.000 0.00 0.00 0.00 4.17
3870 4864 1.843851 TCCAACAAAGTGTCCTGAGGT 59.156 47.619 0.00 0.00 0.00 3.85
3887 4912 4.234550 TGAGGTTCCAGATATAGTGCCAT 58.765 43.478 0.00 0.00 0.00 4.40
3894 4919 6.842437 TCCAGATATAGTGCCATACTTCTC 57.158 41.667 0.00 0.00 40.89 2.87
3896 4921 7.699878 TCCAGATATAGTGCCATACTTCTCTA 58.300 38.462 0.00 0.00 40.89 2.43
3899 4924 4.775058 ATAGTGCCATACTTCTCTAGCG 57.225 45.455 0.00 0.00 40.89 4.26
3915 4940 3.625232 CGTACACGCACTGCACTT 58.375 55.556 1.11 0.00 0.00 3.16
3917 4942 1.346365 CGTACACGCACTGCACTTAT 58.654 50.000 1.11 0.00 0.00 1.73
3927 5034 3.242413 GCACTGCACTTATATGTGTTCCG 60.242 47.826 17.33 7.82 39.89 4.30
3929 5036 1.930503 TGCACTTATATGTGTTCCGCG 59.069 47.619 17.33 0.00 39.89 6.46
3938 5045 1.717194 TGTGTTCCGCGTTATCTTCC 58.283 50.000 4.92 0.00 0.00 3.46
3986 5093 1.908340 GCTCCTCCTGCAGACCATGT 61.908 60.000 17.39 0.00 0.00 3.21
3988 5095 1.153489 CCTCCTGCAGACCATGTCG 60.153 63.158 17.39 0.00 37.67 4.35
4013 5120 4.649692 CCCTCCTATCTGATGTCCAAATG 58.350 47.826 0.00 0.00 0.00 2.32
4031 5138 3.367743 CGGTGCTGCACTGCCATT 61.368 61.111 29.54 0.00 33.85 3.16
4073 5180 0.039165 GAAGCGCCCAACTTTTCCAG 60.039 55.000 2.29 0.00 0.00 3.86
4100 5207 4.751431 GCAAATGGCACCCTCTCT 57.249 55.556 0.00 0.00 43.97 3.10
4108 5215 2.988839 GCACCCTCTCTGCCCCAAT 61.989 63.158 0.00 0.00 0.00 3.16
4109 5216 1.635817 GCACCCTCTCTGCCCCAATA 61.636 60.000 0.00 0.00 0.00 1.90
4112 5219 0.181350 CCCTCTCTGCCCCAATACAC 59.819 60.000 0.00 0.00 0.00 2.90
4131 5238 3.914426 ACAATCTGTGATAGGTGGACC 57.086 47.619 0.00 0.00 0.00 4.46
4136 5243 1.327690 TGTGATAGGTGGACCGAGCC 61.328 60.000 0.00 0.00 42.08 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 136 1.961793 AGTGGCTCGTTTTTGTAGCA 58.038 45.000 0.00 0.00 38.01 3.49
121 142 3.241995 GCGATAGTAGTGGCTCGTTTTTG 60.242 47.826 0.00 0.00 39.35 2.44
126 147 0.945813 GAGCGATAGTAGTGGCTCGT 59.054 55.000 4.68 0.00 39.55 4.18
127 148 3.757623 GAGCGATAGTAGTGGCTCG 57.242 57.895 4.68 0.00 39.55 5.03
128 149 1.676529 TGTGAGCGATAGTAGTGGCTC 59.323 52.381 11.10 11.10 46.31 4.70
129 150 1.763968 TGTGAGCGATAGTAGTGGCT 58.236 50.000 0.00 0.00 35.78 4.75
130 151 2.194271 GTTGTGAGCGATAGTAGTGGC 58.806 52.381 0.00 0.00 39.35 5.01
132 153 6.291112 CGTTATTGTTGTGAGCGATAGTAGTG 60.291 42.308 0.00 0.00 39.35 2.74
133 154 5.742453 CGTTATTGTTGTGAGCGATAGTAGT 59.258 40.000 0.00 0.00 39.35 2.73
135 156 5.643664 ACGTTATTGTTGTGAGCGATAGTA 58.356 37.500 0.00 0.00 39.35 1.82
136 157 4.491676 ACGTTATTGTTGTGAGCGATAGT 58.508 39.130 0.00 0.00 39.35 2.12
137 158 4.561213 TGACGTTATTGTTGTGAGCGATAG 59.439 41.667 0.00 0.00 0.00 2.08
138 159 4.487019 TGACGTTATTGTTGTGAGCGATA 58.513 39.130 0.00 0.00 0.00 2.92
183 205 6.752815 TGTTGGTTCTATTTTGACGTTTTTCC 59.247 34.615 0.00 0.00 0.00 3.13
188 210 5.768317 CCATGTTGGTTCTATTTTGACGTT 58.232 37.500 0.00 0.00 31.35 3.99
189 211 4.320935 GCCATGTTGGTTCTATTTTGACGT 60.321 41.667 0.00 0.00 40.46 4.34
190 212 4.165779 GCCATGTTGGTTCTATTTTGACG 58.834 43.478 0.00 0.00 40.46 4.35
220 242 0.252761 TTTCGCCTCATCTGGATGCA 59.747 50.000 5.77 0.00 37.02 3.96
221 243 1.064654 GTTTTCGCCTCATCTGGATGC 59.935 52.381 5.77 0.00 38.65 3.91
236 258 3.192466 GCATGCATCCATTCCTGTTTTC 58.808 45.455 14.21 0.00 0.00 2.29
240 262 1.961394 GATGCATGCATCCATTCCTGT 59.039 47.619 39.28 15.46 45.06 4.00
260 282 2.663852 GGAACGTGTGGTGGGTCG 60.664 66.667 0.00 0.00 0.00 4.79
261 283 0.748729 TTTGGAACGTGTGGTGGGTC 60.749 55.000 0.00 0.00 0.00 4.46
262 284 0.323542 TTTTGGAACGTGTGGTGGGT 60.324 50.000 0.00 0.00 0.00 4.51
263 285 0.383949 CTTTTGGAACGTGTGGTGGG 59.616 55.000 0.00 0.00 0.00 4.61
284 310 3.138304 TCAATCAGAAAACACACGAGGG 58.862 45.455 0.00 0.00 0.00 4.30
286 312 6.360681 GGAAAATCAATCAGAAAACACACGAG 59.639 38.462 0.00 0.00 0.00 4.18
310 337 1.429463 GACGTAGGTGCAACTTCTGG 58.571 55.000 10.94 0.00 36.74 3.86
344 371 4.698780 GCCCACGGGATTAATAATTAGTCC 59.301 45.833 6.21 0.00 40.29 3.85
347 374 4.939509 CGCCCACGGGATTAATAATTAG 57.060 45.455 6.21 0.00 37.50 1.73
377 417 1.688735 GCTCAAAGCCTTGAACCCTTT 59.311 47.619 0.00 0.00 41.05 3.11
486 534 7.501892 TGATTTAGATGTGCAATACTTATGGCA 59.498 33.333 0.00 0.00 40.19 4.92
487 535 7.874940 TGATTTAGATGTGCAATACTTATGGC 58.125 34.615 0.00 0.00 33.16 4.40
517 565 9.599866 ACATAAATCTCAACGTAAGATCAATGA 57.400 29.630 24.22 10.43 43.62 2.57
560 608 8.250332 AGTAAGTGAATCAAGCACAAAGAAAAA 58.750 29.630 0.00 0.00 38.70 1.94
561 609 7.771183 AGTAAGTGAATCAAGCACAAAGAAAA 58.229 30.769 0.00 0.00 38.70 2.29
562 610 7.333528 AGTAAGTGAATCAAGCACAAAGAAA 57.666 32.000 0.00 0.00 38.70 2.52
563 611 6.942532 AGTAAGTGAATCAAGCACAAAGAA 57.057 33.333 0.00 0.00 38.70 2.52
564 612 6.942532 AAGTAAGTGAATCAAGCACAAAGA 57.057 33.333 0.00 0.00 38.70 2.52
565 613 9.683069 ATTTAAGTAAGTGAATCAAGCACAAAG 57.317 29.630 0.00 0.00 38.70 2.77
566 614 9.462174 CATTTAAGTAAGTGAATCAAGCACAAA 57.538 29.630 0.00 0.00 38.70 2.83
567 615 8.629158 ACATTTAAGTAAGTGAATCAAGCACAA 58.371 29.630 0.00 0.00 38.70 3.33
568 616 8.075574 CACATTTAAGTAAGTGAATCAAGCACA 58.924 33.333 0.00 0.00 38.70 4.57
569 617 7.061094 GCACATTTAAGTAAGTGAATCAAGCAC 59.939 37.037 0.00 0.00 33.99 4.40
570 618 7.083858 GCACATTTAAGTAAGTGAATCAAGCA 58.916 34.615 0.00 0.00 33.99 3.91
571 619 7.083858 TGCACATTTAAGTAAGTGAATCAAGC 58.916 34.615 0.00 0.00 33.99 4.01
572 620 9.630098 ATTGCACATTTAAGTAAGTGAATCAAG 57.370 29.630 0.00 0.00 33.99 3.02
582 630 9.920133 TGCTTTGATTATTGCACATTTAAGTAA 57.080 25.926 0.00 0.00 0.00 2.24
593 641 7.645402 CATCTAGATGTGCTTTGATTATTGCA 58.355 34.615 22.42 0.00 34.23 4.08
613 661 3.053619 TGGGAGTGTCTAGAGCACATCTA 60.054 47.826 20.38 11.20 39.64 1.98
614 662 2.291865 TGGGAGTGTCTAGAGCACATCT 60.292 50.000 20.38 6.75 42.47 2.90
615 663 2.103373 TGGGAGTGTCTAGAGCACATC 58.897 52.381 20.38 15.59 39.17 3.06
616 664 2.238084 TGGGAGTGTCTAGAGCACAT 57.762 50.000 20.38 10.44 39.17 3.21
617 665 2.009681 TTGGGAGTGTCTAGAGCACA 57.990 50.000 20.38 3.96 39.17 4.57
618 666 2.037251 TGTTTGGGAGTGTCTAGAGCAC 59.963 50.000 14.12 14.12 37.13 4.40
619 667 2.325484 TGTTTGGGAGTGTCTAGAGCA 58.675 47.619 0.00 0.00 0.00 4.26
620 668 3.402628 TTGTTTGGGAGTGTCTAGAGC 57.597 47.619 0.00 0.00 0.00 4.09
621 669 7.979444 TTTATTTGTTTGGGAGTGTCTAGAG 57.021 36.000 0.00 0.00 0.00 2.43
622 670 8.934023 AATTTATTTGTTTGGGAGTGTCTAGA 57.066 30.769 0.00 0.00 0.00 2.43
626 674 9.072294 CGATTAATTTATTTGTTTGGGAGTGTC 57.928 33.333 0.00 0.00 0.00 3.67
627 675 8.798402 TCGATTAATTTATTTGTTTGGGAGTGT 58.202 29.630 0.00 0.00 0.00 3.55
628 676 9.801873 ATCGATTAATTTATTTGTTTGGGAGTG 57.198 29.630 0.00 0.00 0.00 3.51
636 684 8.793592 GCCCCTAGATCGATTAATTTATTTGTT 58.206 33.333 0.00 0.00 0.00 2.83
641 689 7.607991 CAGTTGCCCCTAGATCGATTAATTTAT 59.392 37.037 0.00 0.00 0.00 1.40
652 700 1.133976 ACATGCAGTTGCCCCTAGATC 60.134 52.381 1.06 0.00 41.18 2.75
656 704 1.678635 GCACATGCAGTTGCCCCTA 60.679 57.895 10.57 0.00 41.18 3.53
714 782 7.441890 TTCTTGTCAAAGTTATAATCGGCAA 57.558 32.000 0.00 0.00 34.78 4.52
752 825 1.108776 GCTGATGTGCATGGTTCCAT 58.891 50.000 0.00 0.00 0.00 3.41
753 826 0.251253 TGCTGATGTGCATGGTTCCA 60.251 50.000 0.00 0.00 38.12 3.53
754 827 0.171903 GTGCTGATGTGCATGGTTCC 59.828 55.000 0.00 0.00 45.23 3.62
755 828 0.883153 TGTGCTGATGTGCATGGTTC 59.117 50.000 0.00 0.00 45.23 3.62
807 897 8.598924 CACGAGGTATTTATAGATCGTACGTAT 58.401 37.037 16.05 8.53 41.04 3.06
808 898 7.411912 GCACGAGGTATTTATAGATCGTACGTA 60.412 40.741 16.05 0.32 41.04 3.57
809 899 6.619446 GCACGAGGTATTTATAGATCGTACGT 60.619 42.308 16.05 2.33 41.04 3.57
811 901 5.731723 CGCACGAGGTATTTATAGATCGTAC 59.268 44.000 8.15 4.09 41.04 3.67
858 951 0.331278 TGTGTGGGATGGAATGGACC 59.669 55.000 0.00 0.00 0.00 4.46
905 998 1.202076 GCGAGCCACAAGTTATGAAGC 60.202 52.381 0.00 0.00 0.00 3.86
906 999 2.350522 AGCGAGCCACAAGTTATGAAG 58.649 47.619 0.00 0.00 0.00 3.02
907 1000 2.472695 AGCGAGCCACAAGTTATGAA 57.527 45.000 0.00 0.00 0.00 2.57
923 1033 3.724751 CGTCGGAGATTAGTTAAGAAGCG 59.275 47.826 0.00 0.00 40.67 4.68
932 1046 1.131883 CGTGAACCGTCGGAGATTAGT 59.868 52.381 20.51 0.00 40.67 2.24
1008 1122 0.532196 GCACCACCGGTATCTTAGCC 60.532 60.000 6.87 0.00 32.11 3.93
1022 1136 1.698506 CCCAAGTAACCAAAGCACCA 58.301 50.000 0.00 0.00 0.00 4.17
1056 1170 1.896122 CGGGGCTAACGGAAACTCCT 61.896 60.000 0.00 0.00 33.30 3.69
1198 1355 5.880332 ACGCCACAAGTAAGTTTATGATCAT 59.120 36.000 13.81 13.81 0.00 2.45
1199 1356 5.242434 ACGCCACAAGTAAGTTTATGATCA 58.758 37.500 0.00 0.00 0.00 2.92
1200 1357 5.796350 ACGCCACAAGTAAGTTTATGATC 57.204 39.130 0.00 0.00 0.00 2.92
1234 1391 5.157067 GTTGCTCTCTTTAATCTGCCAAAC 58.843 41.667 0.00 0.00 0.00 2.93
1238 1395 3.127721 GTGGTTGCTCTCTTTAATCTGCC 59.872 47.826 0.00 0.00 0.00 4.85
1248 1405 1.668294 CCTCGTGTGGTTGCTCTCT 59.332 57.895 0.00 0.00 0.00 3.10
1258 1415 2.031516 CCTTGCAGAGCCTCGTGTG 61.032 63.158 0.00 0.00 0.00 3.82
1318 1478 4.285149 CTTGCGCGCGTAGATGGC 62.285 66.667 32.35 13.23 0.00 4.40
1429 1591 8.995027 ATAGGTTTTCTGATGGTTATATGCAA 57.005 30.769 0.00 0.00 0.00 4.08
1446 1614 5.209818 TGTCACGTCAGAAGATAGGTTTT 57.790 39.130 0.00 0.00 0.00 2.43
1467 1636 3.313249 CACCATGCCTGTGTACACATATG 59.687 47.826 28.03 26.57 41.01 1.78
1491 2060 4.947147 GGGTTGCGTGGCTGGTCA 62.947 66.667 0.00 0.00 0.00 4.02
1584 2153 1.108132 GCGTACCCTCTTCCTCGGAT 61.108 60.000 0.00 0.00 0.00 4.18
1689 2258 4.269183 TCTCTTTGTGTGGCTTCTTGAAA 58.731 39.130 0.00 0.00 0.00 2.69
1707 2276 2.320781 CCAAGGATGACGGGTATCTCT 58.679 52.381 0.00 0.00 0.00 3.10
1725 2294 7.611467 GCATGGATGGAAGTAATGAATATACCA 59.389 37.037 0.00 0.00 0.00 3.25
1733 2302 7.083062 AGATAAGCATGGATGGAAGTAATGA 57.917 36.000 0.00 0.00 0.00 2.57
1757 2476 1.202245 GCAACGACAACTTGGCTTCAA 60.202 47.619 0.00 0.00 0.00 2.69
1759 2478 0.663153 AGCAACGACAACTTGGCTTC 59.337 50.000 0.00 0.00 0.00 3.86
1769 2488 1.577468 ACGACATTCAAGCAACGACA 58.423 45.000 0.00 0.00 0.00 4.35
1772 2494 4.128554 AGTTAACGACATTCAAGCAACG 57.871 40.909 0.00 0.00 0.00 4.10
1804 2540 1.604278 CTCACCTGCATGCATGAGATG 59.396 52.381 33.38 20.44 40.92 2.90
2143 2879 4.389576 GTCAGCGCGGTTGGCTTG 62.390 66.667 8.73 0.00 39.08 4.01
2157 2893 3.146231 TAATACCGGCCGCCGTCA 61.146 61.111 29.21 17.15 46.80 4.35
2172 2920 2.185867 GTCCTCGCGGCCATGTAA 59.814 61.111 6.13 0.00 0.00 2.41
2389 3143 2.176273 GCATGCGCTCATCGACCTT 61.176 57.895 9.73 0.00 41.67 3.50
2535 3295 1.823041 GACGGAGCGGTAGTAGGCT 60.823 63.158 0.00 0.00 43.42 4.58
2569 3329 0.178990 GGCTTGTTGGGGAAGTCTGT 60.179 55.000 0.00 0.00 0.00 3.41
2917 3678 7.121382 CCATTGCCCAGAACCTGAATATATAT 58.879 38.462 0.00 0.00 32.44 0.86
2918 3679 6.484288 CCATTGCCCAGAACCTGAATATATA 58.516 40.000 0.00 0.00 32.44 0.86
2919 3680 5.327732 CCATTGCCCAGAACCTGAATATAT 58.672 41.667 0.00 0.00 32.44 0.86
2932 3693 1.000506 GAATGCATAGCCATTGCCCAG 59.999 52.381 0.00 0.00 39.39 4.45
2942 3703 4.355543 TTCGTTCCAAAGAATGCATAGC 57.644 40.909 0.00 0.00 38.65 2.97
2945 3706 7.546358 TGATTAATTCGTTCCAAAGAATGCAT 58.454 30.769 0.00 0.00 38.65 3.96
2948 3709 8.853345 CACTTGATTAATTCGTTCCAAAGAATG 58.147 33.333 1.85 0.00 37.23 2.67
3049 3813 2.154462 GACAGTGTTCATTCCCCACAG 58.846 52.381 0.00 0.00 0.00 3.66
3143 3907 1.901159 TGCCTTTTCCCATGTGGATTG 59.099 47.619 0.00 0.00 44.66 2.67
3155 3919 1.068055 CCTGCACATGTCTGCCTTTTC 60.068 52.381 0.00 0.00 36.21 2.29
3175 3939 4.766404 ACAATTTTCCGGTCTGATTGTC 57.234 40.909 16.62 0.00 36.50 3.18
3258 4027 3.502356 TCCCCTTTATTCCACACAAACC 58.498 45.455 0.00 0.00 0.00 3.27
3260 4029 6.147437 ACTATCCCCTTTATTCCACACAAA 57.853 37.500 0.00 0.00 0.00 2.83
3279 4048 4.444022 GCTGATCACATGGGAGTCAACTAT 60.444 45.833 2.98 0.00 0.00 2.12
3280 4049 3.118629 GCTGATCACATGGGAGTCAACTA 60.119 47.826 2.98 0.00 0.00 2.24
3434 4212 5.987347 AGAACTGTTGCTTGAAATGGAAATG 59.013 36.000 0.00 0.00 0.00 2.32
3435 4213 6.165700 AGAACTGTTGCTTGAAATGGAAAT 57.834 33.333 0.00 0.00 0.00 2.17
3436 4214 5.596836 AGAACTGTTGCTTGAAATGGAAA 57.403 34.783 0.00 0.00 0.00 3.13
3438 4216 6.707440 TTTAGAACTGTTGCTTGAAATGGA 57.293 33.333 0.00 0.00 0.00 3.41
3439 4217 6.421801 CCTTTTAGAACTGTTGCTTGAAATGG 59.578 38.462 0.00 2.94 0.00 3.16
3440 4218 7.168135 GTCCTTTTAGAACTGTTGCTTGAAATG 59.832 37.037 0.00 0.00 0.00 2.32
3442 4220 6.377146 AGTCCTTTTAGAACTGTTGCTTGAAA 59.623 34.615 0.00 1.02 0.00 2.69
3452 4268 4.487019 GACGAGGAGTCCTTTTAGAACTG 58.513 47.826 14.41 0.00 43.95 3.16
3465 4281 6.059484 TGTTTTTATTGAAAGGACGAGGAGT 58.941 36.000 0.00 0.00 0.00 3.85
3469 4285 8.628882 AAAACTGTTTTTATTGAAAGGACGAG 57.371 30.769 12.50 0.00 32.90 4.18
3494 4310 3.374220 TCGGCGTACTCTTGAGAAAAA 57.626 42.857 6.85 0.00 0.00 1.94
3495 4311 3.314553 CTTCGGCGTACTCTTGAGAAAA 58.685 45.455 6.85 0.00 0.00 2.29
3496 4312 2.352421 CCTTCGGCGTACTCTTGAGAAA 60.352 50.000 6.85 0.00 0.00 2.52
3497 4313 1.201647 CCTTCGGCGTACTCTTGAGAA 59.798 52.381 6.85 0.00 0.00 2.87
3498 4314 0.809385 CCTTCGGCGTACTCTTGAGA 59.191 55.000 6.85 0.00 0.00 3.27
3499 4315 0.802607 GCCTTCGGCGTACTCTTGAG 60.803 60.000 6.85 0.00 39.62 3.02
3500 4316 1.214589 GCCTTCGGCGTACTCTTGA 59.785 57.895 6.85 0.00 39.62 3.02
3501 4317 3.782042 GCCTTCGGCGTACTCTTG 58.218 61.111 6.85 0.00 39.62 3.02
3518 4334 8.732531 CCTCCTCTTCTATAAAGATAAGGTACG 58.267 40.741 7.14 0.00 36.15 3.67
3534 4350 6.627087 TGTACATGATTTTCCTCCTCTTCT 57.373 37.500 0.00 0.00 0.00 2.85
3542 4358 5.324409 TGGCTTCTTGTACATGATTTTCCT 58.676 37.500 11.84 0.00 0.00 3.36
3543 4359 5.415701 TCTGGCTTCTTGTACATGATTTTCC 59.584 40.000 11.84 10.65 0.00 3.13
3549 4365 4.383444 CCATCTCTGGCTTCTTGTACATGA 60.383 45.833 7.33 7.33 35.23 3.07
3566 4382 2.437413 GGTGGAGGTTTGTTCCATCTC 58.563 52.381 0.00 0.00 45.85 2.75
3589 4406 2.590114 GGGGTAAGGGTGAGTGCGT 61.590 63.158 0.00 0.00 0.00 5.24
3590 4407 2.267961 GGGGTAAGGGTGAGTGCG 59.732 66.667 0.00 0.00 0.00 5.34
3595 4412 0.402272 AAGTGTGGGGGTAAGGGTGA 60.402 55.000 0.00 0.00 0.00 4.02
3605 4422 2.766736 TGGTATAGGGTAAGTGTGGGG 58.233 52.381 0.00 0.00 0.00 4.96
3608 4425 5.187186 AGAGTGTTGGTATAGGGTAAGTGTG 59.813 44.000 0.00 0.00 0.00 3.82
3609 4426 5.339477 AGAGTGTTGGTATAGGGTAAGTGT 58.661 41.667 0.00 0.00 0.00 3.55
3610 4427 5.421056 TGAGAGTGTTGGTATAGGGTAAGTG 59.579 44.000 0.00 0.00 0.00 3.16
3611 4428 5.421374 GTGAGAGTGTTGGTATAGGGTAAGT 59.579 44.000 0.00 0.00 0.00 2.24
3612 4429 5.421056 TGTGAGAGTGTTGGTATAGGGTAAG 59.579 44.000 0.00 0.00 0.00 2.34
3629 4448 2.731976 GGAGCACTACGTTTTGTGAGAG 59.268 50.000 16.51 0.00 36.38 3.20
3673 4499 3.492137 GCCATTTTGGATGAGATCAAGGC 60.492 47.826 0.00 0.00 40.96 4.35
3683 4509 1.153588 GCCACGGCCATTTTGGATG 60.154 57.895 12.73 0.00 40.96 3.51
3714 4540 1.571460 GACTCGCCAACAACTGCAG 59.429 57.895 13.48 13.48 0.00 4.41
3754 4580 0.254462 TGGGCGATATGGAAGCAACA 59.746 50.000 0.00 0.00 0.00 3.33
3777 4691 2.632512 TGACACTCTAGTCATTGCCACA 59.367 45.455 0.00 0.00 43.18 4.17
3786 4700 3.714391 ACGTGGTTTTGACACTCTAGTC 58.286 45.455 0.00 0.00 36.71 2.59
3789 4703 3.872771 GGAAACGTGGTTTTGACACTCTA 59.127 43.478 0.00 0.00 35.77 2.43
3820 4734 5.935206 GGCTTGAGGATAGGAGCTTATTTAC 59.065 44.000 0.00 0.00 35.53 2.01
3825 4739 2.700897 GTGGCTTGAGGATAGGAGCTTA 59.299 50.000 0.00 0.00 35.53 3.09
3835 4749 0.776810 TTGGAATGGTGGCTTGAGGA 59.223 50.000 0.00 0.00 0.00 3.71
3848 4842 3.117512 ACCTCAGGACACTTTGTTGGAAT 60.118 43.478 0.00 0.00 0.00 3.01
3870 4864 7.013220 AGAGAAGTATGGCACTATATCTGGAA 58.987 38.462 0.00 0.00 36.04 3.53
3899 4924 3.863424 ACATATAAGTGCAGTGCGTGTAC 59.137 43.478 11.20 2.64 41.86 2.90
3914 4939 5.693104 GGAAGATAACGCGGAACACATATAA 59.307 40.000 12.47 0.00 0.00 0.98
3915 4940 5.010314 AGGAAGATAACGCGGAACACATATA 59.990 40.000 12.47 0.00 0.00 0.86
3917 4942 3.131577 AGGAAGATAACGCGGAACACATA 59.868 43.478 12.47 0.00 0.00 2.29
3938 5045 3.993081 CCTGCTACTTGTGTCTTCAAGAG 59.007 47.826 12.38 7.24 45.11 2.85
3950 5057 2.187946 CCCTCGGCCTGCTACTTG 59.812 66.667 0.00 0.00 0.00 3.16
3986 5093 1.228583 ATCAGATAGGAGGGCGCGA 60.229 57.895 12.10 0.00 0.00 5.87
3988 5095 0.037790 GACATCAGATAGGAGGGCGC 60.038 60.000 0.00 0.00 0.00 6.53
4030 5137 5.189928 TCAAGTGTAAACTCTTTGCCTGAA 58.810 37.500 0.00 0.00 0.00 3.02
4031 5138 4.776349 TCAAGTGTAAACTCTTTGCCTGA 58.224 39.130 0.00 0.00 0.00 3.86
4100 5207 2.445427 CACAGATTGTGTATTGGGGCA 58.555 47.619 1.13 0.00 43.08 5.36
4112 5219 2.430694 TCGGTCCACCTATCACAGATTG 59.569 50.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.