Multiple sequence alignment - TraesCS6A01G402600

Loading Multiple Alignment...

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 TraesCS6A01G402600 chr6A 100.000 8513 0 0 1 8513 610413901 610405389 0.000000e+00 15721.0
1 TraesCS6A01G402600 chr6A 87.603 484 56 2 4140 4621 60102756 60102275 7.460000e-155 558.0
2 TraesCS6A01G402600 chr6A 86.667 390 46 4 4234 4621 52028557 52028172 2.200000e-115 427.0
3 TraesCS6A01G402600 chr6A 95.385 65 1 2 4732 4795 610409094 610409031 1.510000e-17 102.0
4 TraesCS6A01G402600 chr6A 95.385 65 1 2 4808 4871 610409170 610409107 1.510000e-17 102.0
5 TraesCS6A01G402600 chr6A 89.091 55 6 0 678 732 498957842 498957788 1.530000e-07 69.4
6 TraesCS6A01G402600 chr6D 95.268 2726 107 18 1315 4035 463873386 463870678 0.000000e+00 4300.0
7 TraesCS6A01G402600 chr6D 92.729 2723 126 38 5146 7831 463869409 463866722 0.000000e+00 3866.0
8 TraesCS6A01G402600 chr6D 97.035 742 15 3 4067 4803 463870679 463869940 0.000000e+00 1242.0
9 TraesCS6A01G402600 chr6D 96.992 532 14 2 7984 8513 463866241 463865710 0.000000e+00 893.0
10 TraesCS6A01G402600 chr6D 87.692 390 42 4 4234 4621 104073000 104072615 4.690000e-122 449.0
11 TraesCS6A01G402600 chr6D 86.923 390 45 4 4234 4621 45589910 45590295 4.720000e-117 433.0
12 TraesCS6A01G402600 chr6D 80.986 568 58 19 730 1295 463874111 463873592 1.030000e-108 405.0
13 TraesCS6A01G402600 chr6D 94.348 230 10 2 4858 5087 463869716 463869490 4.890000e-92 350.0
14 TraesCS6A01G402600 chr6D 90.476 105 8 2 7881 7984 463866712 463866609 4.140000e-28 137.0
15 TraesCS6A01G402600 chr6D 95.312 64 1 2 4809 4871 463870010 463869948 5.440000e-17 100.0
16 TraesCS6A01G402600 chr6D 85.455 55 8 0 678 732 356290207 356290153 3.320000e-04 58.4
17 TraesCS6A01G402600 chr6D 100.000 28 0 0 7695 7722 320944156 320944183 1.500000e-02 52.8
18 TraesCS6A01G402600 chr6B 92.122 1701 99 22 5148 6836 707293555 707291878 0.000000e+00 2366.0
19 TraesCS6A01G402600 chr6B 91.714 1593 102 14 3208 4784 707295685 707294107 0.000000e+00 2183.0
20 TraesCS6A01G402600 chr6B 89.323 1330 88 30 3834 5146 707319238 707320530 0.000000e+00 1620.0
21 TraesCS6A01G402600 chr6B 88.699 1345 96 19 1 1312 707299136 707297815 0.000000e+00 1591.0
22 TraesCS6A01G402600 chr6B 90.641 780 45 13 1315 2079 707297643 707296877 0.000000e+00 1011.0
23 TraesCS6A01G402600 chr6B 90.836 622 53 2 2458 3075 707296447 707295826 0.000000e+00 830.0
24 TraesCS6A01G402600 chr6B 93.164 512 27 3 5201 5708 707320682 707321189 0.000000e+00 745.0
25 TraesCS6A01G402600 chr6B 86.931 681 42 30 6876 7528 707291868 707291207 0.000000e+00 721.0
26 TraesCS6A01G402600 chr6B 89.091 440 33 4 2636 3075 707318298 707318722 4.520000e-147 532.0
27 TraesCS6A01G402600 chr6B 92.388 289 21 1 2088 2375 707296738 707296450 2.210000e-110 411.0
28 TraesCS6A01G402600 chr6B 90.066 302 18 5 4858 5152 707293977 707293681 1.730000e-101 381.0
29 TraesCS6A01G402600 chr6B 93.103 87 5 1 3075 3160 707295768 707295682 8.970000e-25 126.0
30 TraesCS6A01G402600 chr6B 92.308 52 4 0 4808 4859 707294159 707294108 3.300000e-09 75.0
31 TraesCS6A01G402600 chr6B 100.000 28 0 0 7695 7722 157797934 157797961 1.500000e-02 52.8
32 TraesCS6A01G402600 chr2A 87.692 390 42 4 4234 4621 86677472 86677087 4.690000e-122 449.0
33 TraesCS6A01G402600 chr7A 82.564 390 39 9 4234 4621 47929395 47929757 4.960000e-82 316.0
34 TraesCS6A01G402600 chr7A 86.022 93 12 1 8341 8432 634479777 634479685 1.960000e-16 99.0
35 TraesCS6A01G402600 chr7A 77.536 138 29 1 492 627 131938699 131938562 1.970000e-11 82.4
36 TraesCS6A01G402600 chr7A 87.931 58 7 0 675 732 195570112 195570055 1.530000e-07 69.4
37 TraesCS6A01G402600 chr7A 87.234 47 6 0 7695 7741 29169488 29169534 4.000000e-03 54.7
38 TraesCS6A01G402600 chr3A 85.906 149 18 1 8304 8449 743020650 743020502 1.140000e-33 156.0
39 TraesCS6A01G402600 chr3A 85.057 87 13 0 8327 8413 451771308 451771222 1.180000e-13 89.8
40 TraesCS6A01G402600 chr3A 89.706 68 6 1 477 543 723346166 723346099 1.520000e-12 86.1
41 TraesCS6A01G402600 chr3A 92.683 41 3 0 7695 7735 26476596 26476636 9.230000e-05 60.2
42 TraesCS6A01G402600 chr5D 98.810 84 1 0 2376 2459 73754896 73754813 5.320000e-32 150.0
43 TraesCS6A01G402600 chr5A 96.629 89 3 0 2371 2459 694963415 694963327 1.910000e-31 148.0
44 TraesCS6A01G402600 chr5A 96.629 89 1 2 2371 2459 318831054 318830968 6.890000e-31 147.0
45 TraesCS6A01G402600 chr5A 81.579 152 25 2 479 627 649374396 649374245 1.160000e-23 122.0
46 TraesCS6A01G402600 chr3B 98.795 83 1 0 2376 2458 495480131 495480049 1.910000e-31 148.0
47 TraesCS6A01G402600 chr3B 76.623 154 32 3 477 627 706778768 706778616 1.970000e-11 82.4
48 TraesCS6A01G402600 chr3B 88.136 59 5 2 678 734 780693667 780693609 1.530000e-07 69.4
49 TraesCS6A01G402600 chr1D 98.795 83 1 0 2377 2459 314718713 314718795 1.910000e-31 148.0
50 TraesCS6A01G402600 chr1D 90.909 55 4 1 679 732 485481451 485481505 1.190000e-08 73.1
51 TraesCS6A01G402600 chr1A 98.795 83 1 0 2376 2458 292773844 292773762 1.910000e-31 148.0
52 TraesCS6A01G402600 chr7B 95.556 90 4 0 2376 2465 291564960 291564871 2.480000e-30 145.0
53 TraesCS6A01G402600 chr7B 96.591 88 2 1 2372 2459 511302078 511301992 2.480000e-30 145.0
54 TraesCS6A01G402600 chr7D 80.769 156 23 6 476 627 548086169 548086321 1.940000e-21 115.0
55 TraesCS6A01G402600 chr7D 100.000 28 0 0 7695 7722 8481636 8481609 1.500000e-02 52.8
56 TraesCS6A01G402600 chr3D 77.333 150 28 5 478 624 580123421 580123275 5.480000e-12 84.2
57 TraesCS6A01G402600 chr3D 89.831 59 5 1 675 732 25981064 25981122 3.300000e-09 75.0
58 TraesCS6A01G402600 chrUn 88.235 68 8 0 476 543 23376247 23376180 1.970000e-11 82.4
59 TraesCS6A01G402600 chrUn 88.235 68 8 0 476 543 23379651 23379584 1.970000e-11 82.4
60 TraesCS6A01G402600 chr2B 80.180 111 17 5 8331 8438 38180926 38181034 2.550000e-10 78.7
61 TraesCS6A01G402600 chr2B 80.000 110 17 5 8332 8438 38133668 38133775 9.160000e-10 76.8
62 TraesCS6A01G402600 chr2B 89.796 49 3 2 7690 7738 37564394 37564348 2.570000e-05 62.1
63 TraesCS6A01G402600 chr2B 87.234 47 6 0 7695 7741 37717727 37717681 4.000000e-03 54.7
64 TraesCS6A01G402600 chr2B 96.774 31 1 0 7692 7722 39972479 39972509 1.500000e-02 52.8
65 TraesCS6A01G402600 chr4D 86.207 58 8 0 675 732 25461432 25461489 7.130000e-06 63.9
66 TraesCS6A01G402600 chr4A 87.037 54 7 0 675 728 703158284 703158231 2.570000e-05 62.1


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 TraesCS6A01G402600 chr6A 610405389 610413901 8512 True 15721.000000 15721 100.00000 1 8513 1 chr6A.!!$R4 8512
1 TraesCS6A01G402600 chr6D 463865710 463874111 8401 True 1411.625000 4300 92.89325 730 8513 8 chr6D.!!$R3 7783
2 TraesCS6A01G402600 chr6B 707291207 707299136 7929 True 969.500000 2366 90.88080 1 7528 10 chr6B.!!$R1 7527
3 TraesCS6A01G402600 chr6B 707318298 707321189 2891 False 965.666667 1620 90.52600 2636 5708 3 chr6B.!!$F2 3072

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
656 661 0.465460 TGAAGTGCCGGCTCAGTTTT 60.465 50.000 29.70 14.20 30.34 2.43 F
1311 1349 0.402121 GGTTCTCTCTGGCTTGGGTT 59.598 55.000 0.00 0.00 0.00 4.11 F
1592 1849 2.842457 TCTTGATGGCGAAGATGATGG 58.158 47.619 0.00 0.00 0.00 3.51 F
3061 3454 3.055385 GGAAATGTGTGGTAGCCAGTAGA 60.055 47.826 0.00 0.00 32.34 2.59 F
3439 4047 0.107017 ATCTCCAATGCCCCGAACAG 60.107 55.000 0.00 0.00 0.00 3.16 F
3930 4548 1.023513 ATTCTGTTCCTCGCAGCTGC 61.024 55.000 29.12 29.12 34.21 5.25 F
5381 6462 1.068264 GGCTTCTGCTTTACCACTTGC 60.068 52.381 0.00 0.00 39.59 4.01 F
6003 7093 0.109342 CACTGTGTTCCTTGCCCTCT 59.891 55.000 0.00 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 1717 1.672356 CCAAGCACCCAACTCCTCG 60.672 63.158 0.00 0.0 0.00 4.63 R
3178 3630 2.236766 GCTAGCCAATGGATTGCATCT 58.763 47.619 18.21 0.0 39.41 2.90 R
3439 4047 0.380378 TTCAGACCAACGCAACAAGC 59.620 50.000 0.00 0.0 40.87 4.01 R
5029 5925 1.607801 GGGAGGTTTGGGATTGCAGC 61.608 60.000 0.00 0.0 0.00 5.25 R
5381 6462 1.882912 TGTGCAAGGAACTGCTGTAG 58.117 50.000 0.00 0.0 40.86 2.74 R
5694 6775 8.161425 ACAAATGTCTTTCCTTAAACCTAGCTA 58.839 33.333 0.00 0.0 0.00 3.32 R
6940 8032 0.609662 TCCCGGCCAGTAGTTTACAC 59.390 55.000 2.24 0.0 0.00 2.90 R
7878 9001 0.179056 ATTTCCACCTATGCCGACCG 60.179 55.000 0.00 0.0 0.00 4.79 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
32 33 2.022238 GCCTTTAGGGTTTGGGGATCG 61.022 57.143 0.00 0.00 37.43 3.69
36 37 1.342672 TAGGGTTTGGGGATCGAGGC 61.343 60.000 0.00 0.00 0.00 4.70
62 63 8.698210 CAGAATGGATAAGAATGAAAATGGGAA 58.302 33.333 0.00 0.00 0.00 3.97
77 78 9.944079 TGAAAATGGGAAGATAATTATTGGGTA 57.056 29.630 0.00 0.00 0.00 3.69
105 106 4.757149 GCCACTCTAGATTGTTCTTTGTGT 59.243 41.667 9.05 0.00 33.17 3.72
109 110 6.088749 CACTCTAGATTGTTCTTTGTGTCGAG 59.911 42.308 1.99 0.00 33.17 4.04
133 134 1.898574 CCAGTGGTGTGGAAGTGGC 60.899 63.158 0.00 0.00 40.44 5.01
194 197 1.009829 GAGGTTCATCGCACATCACC 58.990 55.000 0.00 0.00 0.00 4.02
240 243 2.987149 ACAGTCTAGCAAACGTCATTCG 59.013 45.455 0.00 0.00 46.00 3.34
260 263 5.456548 TCGTATTGACAAGTTACCAGTGA 57.543 39.130 0.00 0.00 0.00 3.41
265 268 4.415881 TGACAAGTTACCAGTGACATGT 57.584 40.909 0.00 0.00 34.49 3.21
290 293 2.358247 GGTGTGCCGACCGTCAAT 60.358 61.111 0.00 0.00 0.00 2.57
295 298 1.801771 TGTGCCGACCGTCAATAAAAG 59.198 47.619 0.00 0.00 0.00 2.27
296 299 2.070783 GTGCCGACCGTCAATAAAAGA 58.929 47.619 0.00 0.00 0.00 2.52
326 329 1.850345 TGAAACCCAACCTTCTCCACT 59.150 47.619 0.00 0.00 0.00 4.00
327 330 3.050089 TGAAACCCAACCTTCTCCACTA 58.950 45.455 0.00 0.00 0.00 2.74
350 353 3.623060 CCAAACATCACCGTCTCTAATGG 59.377 47.826 0.00 0.00 40.24 3.16
359 362 3.009723 CCGTCTCTAATGGTTGTTGCAT 58.990 45.455 0.00 0.00 0.00 3.96
414 417 5.494390 AAACCTAGTCGGACCTAAAACAT 57.506 39.130 4.14 0.00 36.31 2.71
415 418 4.467198 ACCTAGTCGGACCTAAAACATG 57.533 45.455 4.14 0.00 36.31 3.21
481 484 4.339247 CCAATGGAACTTTATGGAGCGAAT 59.661 41.667 0.00 0.00 0.00 3.34
485 488 5.192927 TGGAACTTTATGGAGCGAATCAAT 58.807 37.500 0.00 0.00 0.00 2.57
487 490 5.529060 GGAACTTTATGGAGCGAATCAATCT 59.471 40.000 0.00 0.00 0.00 2.40
492 495 1.278985 TGGAGCGAATCAATCTGTGGT 59.721 47.619 0.00 0.00 0.00 4.16
499 502 3.065786 CGAATCAATCTGTGGTTGGATGG 59.934 47.826 0.00 0.00 27.56 3.51
504 507 4.288366 TCAATCTGTGGTTGGATGGTTAGA 59.712 41.667 0.00 0.00 0.00 2.10
510 513 4.141367 TGTGGTTGGATGGTTAGAAGAACA 60.141 41.667 0.00 0.00 0.00 3.18
513 516 4.455877 GGTTGGATGGTTAGAAGAACAGTG 59.544 45.833 0.00 0.00 0.00 3.66
519 522 5.068234 TGGTTAGAAGAACAGTGGTATCG 57.932 43.478 0.00 0.00 0.00 2.92
520 523 3.864003 GGTTAGAAGAACAGTGGTATCGC 59.136 47.826 0.00 0.00 0.00 4.58
522 525 3.678056 AGAAGAACAGTGGTATCGCAA 57.322 42.857 0.00 0.00 0.00 4.85
541 544 3.124976 GCAAGCTCATCAGAGTTCAAGTC 59.875 47.826 0.00 0.00 44.00 3.01
544 547 2.679349 GCTCATCAGAGTTCAAGTCCCC 60.679 54.545 0.00 0.00 44.00 4.81
563 568 1.337728 CCGACTACATTGGTGCTCACA 60.338 52.381 2.21 0.00 0.00 3.58
571 576 5.372343 ACATTGGTGCTCACATATTCCTA 57.628 39.130 2.21 0.00 0.00 2.94
591 596 5.048224 TCCTAGATTTATTCTACGCCTTCCG 60.048 44.000 0.00 0.00 38.25 4.30
613 618 2.935238 GCGATGTGCCTTAAGTGGAAGA 60.935 50.000 0.97 0.00 37.76 2.87
616 621 4.579869 GATGTGCCTTAAGTGGAAGAAGA 58.420 43.478 0.97 0.00 0.00 2.87
618 623 2.737252 GTGCCTTAAGTGGAAGAAGACG 59.263 50.000 0.97 0.00 0.00 4.18
640 645 5.929992 ACGTTTCCGTCAATCTTAAGATGAA 59.070 36.000 18.61 13.53 46.28 2.57
646 651 4.259970 CGTCAATCTTAAGATGAAGTGCCG 60.260 45.833 18.61 10.74 34.49 5.69
656 661 0.465460 TGAAGTGCCGGCTCAGTTTT 60.465 50.000 29.70 14.20 30.34 2.43
694 699 3.388024 GGATAAGGGTGAGTGTATGCTCA 59.612 47.826 0.00 0.00 42.56 4.26
717 722 2.907910 ATGTGAGCGATTTTGACTGC 57.092 45.000 0.00 0.00 0.00 4.40
835 840 2.943033 AGGACTTGAAAACGTGTGAAGG 59.057 45.455 0.00 0.00 0.00 3.46
836 841 2.681344 GGACTTGAAAACGTGTGAAGGT 59.319 45.455 0.00 0.00 0.00 3.50
847 852 4.768583 ACGTGTGAAGGTTGGTTTTACTA 58.231 39.130 0.00 0.00 0.00 1.82
961 968 1.383248 AAGTCCCATCCCCTCCTCG 60.383 63.158 0.00 0.00 0.00 4.63
973 980 1.228737 CTCCTCGGATCCTCTCCCC 60.229 68.421 10.75 0.00 41.49 4.81
974 981 2.203714 CCTCGGATCCTCTCCCCC 60.204 72.222 10.75 0.00 41.49 5.40
975 982 2.598985 CTCGGATCCTCTCCCCCG 60.599 72.222 10.75 0.00 41.49 5.73
976 983 4.916314 TCGGATCCTCTCCCCCGC 62.916 72.222 10.75 0.00 41.49 6.13
1211 1244 4.699522 GCCACCTTCGCCCTCGTT 62.700 66.667 0.00 0.00 36.96 3.85
1258 1291 1.305201 GCACAAGGTTCGTTCCTTCA 58.695 50.000 10.02 0.00 44.87 3.02
1311 1349 0.402121 GGTTCTCTCTGGCTTGGGTT 59.598 55.000 0.00 0.00 0.00 4.11
1317 1546 3.394606 TCTCTCTGGCTTGGGTTAAAACT 59.605 43.478 0.00 0.00 0.00 2.66
1408 1640 3.820467 CTGCTTGGTTGGATTACAGTGAA 59.180 43.478 0.00 0.00 0.00 3.18
1450 1701 9.095065 GTCCCCGTATATTTATTTGCTATACAG 57.905 37.037 0.00 0.00 30.96 2.74
1466 1717 8.383318 TGCTATACAGAGGCTCATTTTTAATC 57.617 34.615 18.26 0.00 0.00 1.75
1515 1766 6.330250 ACAGGAATAGGTGCTTGGATTATACT 59.670 38.462 0.00 0.00 0.00 2.12
1592 1849 2.842457 TCTTGATGGCGAAGATGATGG 58.158 47.619 0.00 0.00 0.00 3.51
1605 1862 5.186603 CGAAGATGATGGAGGGAATGATAGA 59.813 44.000 0.00 0.00 0.00 1.98
1608 1865 6.513947 AGATGATGGAGGGAATGATAGAGAT 58.486 40.000 0.00 0.00 0.00 2.75
1609 1866 7.660169 AGATGATGGAGGGAATGATAGAGATA 58.340 38.462 0.00 0.00 0.00 1.98
1610 1867 7.785985 AGATGATGGAGGGAATGATAGAGATAG 59.214 40.741 0.00 0.00 0.00 2.08
1611 1868 7.049291 TGATGGAGGGAATGATAGAGATAGA 57.951 40.000 0.00 0.00 0.00 1.98
1612 1869 7.124721 TGATGGAGGGAATGATAGAGATAGAG 58.875 42.308 0.00 0.00 0.00 2.43
1613 1870 6.726733 TGGAGGGAATGATAGAGATAGAGA 57.273 41.667 0.00 0.00 0.00 3.10
1614 1871 7.108667 TGGAGGGAATGATAGAGATAGAGAA 57.891 40.000 0.00 0.00 0.00 2.87
1615 1872 7.181361 TGGAGGGAATGATAGAGATAGAGAAG 58.819 42.308 0.00 0.00 0.00 2.85
1616 1873 7.182060 GGAGGGAATGATAGAGATAGAGAAGT 58.818 42.308 0.00 0.00 0.00 3.01
1617 1874 8.333235 GGAGGGAATGATAGAGATAGAGAAGTA 58.667 40.741 0.00 0.00 0.00 2.24
1620 1877 9.303116 GGGAATGATAGAGATAGAGAAGTAACA 57.697 37.037 0.00 0.00 0.00 2.41
1657 1914 4.383552 CCAGTATAGAAGAAACTGCTGCCT 60.384 45.833 0.00 0.00 39.42 4.75
1687 1944 3.089284 GGTTGGTACCCCATTTCTTCTG 58.911 50.000 10.07 0.00 41.49 3.02
1738 1995 4.656112 CACTAGATGGATTACTGTTCCCCT 59.344 45.833 0.00 0.00 31.87 4.79
1739 1996 4.656112 ACTAGATGGATTACTGTTCCCCTG 59.344 45.833 0.00 0.00 31.87 4.45
1972 2230 5.047377 GGCCATTCACTGTTTAATTTCCTGA 60.047 40.000 0.00 0.00 0.00 3.86
2492 2881 5.200734 CTGATCACATTTTCAGTCTGTCG 57.799 43.478 0.00 0.00 35.66 4.35
2586 2975 8.966155 TGGAGACAGGGATATACATGTTAATA 57.034 34.615 6.70 0.00 35.01 0.98
2634 3023 3.214328 CCATAGTCACTAATGGGGTTGC 58.786 50.000 0.00 0.00 0.00 4.17
3011 3403 6.240894 ACATGACCACTTACAAATCACAGAT 58.759 36.000 0.00 0.00 0.00 2.90
3061 3454 3.055385 GGAAATGTGTGGTAGCCAGTAGA 60.055 47.826 0.00 0.00 32.34 2.59
3101 3553 8.475331 AGTTCGAATCGTAATACTGAAAATGT 57.525 30.769 0.00 0.00 0.00 2.71
3178 3630 9.475620 TGTCTTCTGGTAGATTATCTTTACTCA 57.524 33.333 0.00 0.00 0.00 3.41
3248 3856 8.398743 TCTTTTATTTTGGGAAGGGTTCTCTAT 58.601 33.333 0.00 0.00 0.00 1.98
3340 3948 6.033831 GCTCATGGTGAAACAAACATATTTCG 59.966 38.462 0.00 0.00 39.98 3.46
3399 4007 5.972107 ATCTGGGATTCAACTGAACAAAG 57.028 39.130 0.00 0.00 36.80 2.77
3439 4047 0.107017 ATCTCCAATGCCCCGAACAG 60.107 55.000 0.00 0.00 0.00 3.16
3544 4152 4.941657 TCTGATGATAGTTGCTACTGCTG 58.058 43.478 11.27 0.00 40.48 4.41
3734 4348 6.070824 TCGGATATTGGAGATAGCTTGCATTA 60.071 38.462 0.00 0.00 0.00 1.90
3832 4446 4.801516 TCGTGTACAATATCATGGTGTTCG 59.198 41.667 0.00 0.00 0.00 3.95
3863 4479 4.119862 GTGCTGCTTACAGGAATATTCGA 58.880 43.478 9.32 0.00 46.73 3.71
3864 4480 4.210120 GTGCTGCTTACAGGAATATTCGAG 59.790 45.833 9.32 6.77 46.73 4.04
3865 4481 4.099419 TGCTGCTTACAGGAATATTCGAGA 59.901 41.667 9.32 0.00 41.85 4.04
3867 4483 5.050702 GCTGCTTACAGGAATATTCGAGAAC 60.051 44.000 9.32 0.00 44.63 3.01
3869 4485 5.810587 TGCTTACAGGAATATTCGAGAACAC 59.189 40.000 9.32 0.00 0.00 3.32
3930 4548 1.023513 ATTCTGTTCCTCGCAGCTGC 61.024 55.000 29.12 29.12 34.21 5.25
3954 4572 5.851177 CGTTACATAAACTGCAGTTTGGAAG 59.149 40.000 41.50 30.92 46.56 3.46
4375 5001 9.487790 AATAACATTTCTTATTGGGTGTTGTTG 57.512 29.630 0.00 0.00 32.33 3.33
4546 5177 9.988350 CAAACATGGTAATGAAGTTACAGTATC 57.012 33.333 0.00 0.00 43.65 2.24
4560 5191 6.213600 AGTTACAGTATCCACAACTGATTCCT 59.786 38.462 10.02 0.00 45.89 3.36
4621 5252 6.811170 CCTCTTGCTACTTTAGAACTCTCTTG 59.189 42.308 0.00 0.00 32.70 3.02
4644 5275 7.225784 TGGAGTGCTATTTGCTATTCAAAAA 57.774 32.000 0.00 0.00 46.60 1.94
4821 5541 3.536956 AAAACTCCGACAGTTCTGACA 57.463 42.857 6.83 0.00 45.32 3.58
4822 5542 3.753294 AAACTCCGACAGTTCTGACAT 57.247 42.857 6.83 0.00 45.32 3.06
4824 5544 2.239400 ACTCCGACAGTTCTGACATGA 58.761 47.619 0.00 0.32 26.56 3.07
4825 5545 2.828520 ACTCCGACAGTTCTGACATGAT 59.171 45.455 0.00 0.00 26.56 2.45
4828 5548 3.996363 TCCGACAGTTCTGACATGATTTG 59.004 43.478 0.00 0.00 0.00 2.32
4829 5549 3.996363 CCGACAGTTCTGACATGATTTGA 59.004 43.478 0.00 0.00 0.00 2.69
4830 5550 4.092529 CCGACAGTTCTGACATGATTTGAG 59.907 45.833 0.00 0.00 0.00 3.02
4831 5551 4.687948 CGACAGTTCTGACATGATTTGAGT 59.312 41.667 0.00 0.00 0.00 3.41
4832 5552 5.178252 CGACAGTTCTGACATGATTTGAGTT 59.822 40.000 0.00 0.00 0.00 3.01
4833 5553 6.309712 ACAGTTCTGACATGATTTGAGTTG 57.690 37.500 0.00 0.00 0.00 3.16
4834 5554 6.057533 ACAGTTCTGACATGATTTGAGTTGA 58.942 36.000 0.00 0.00 0.00 3.18
4836 5556 7.094890 ACAGTTCTGACATGATTTGAGTTGATC 60.095 37.037 0.00 0.00 0.00 2.92
4839 5559 7.933215 TCTGACATGATTTGAGTTGATCATT 57.067 32.000 0.00 0.00 40.14 2.57
4841 5561 9.623000 TCTGACATGATTTGAGTTGATCATTAT 57.377 29.630 0.00 0.00 40.14 1.28
4914 5809 6.497785 TGCCAATTGCCATTCTAATTTTTG 57.502 33.333 0.00 0.00 40.16 2.44
5050 5946 1.078347 GCAATCCCAAACCTCCCCA 59.922 57.895 0.00 0.00 0.00 4.96
5097 5994 5.592282 TGTTGCAAAAACTCTTATCTCCACA 59.408 36.000 0.00 0.00 0.00 4.17
5159 6185 4.523943 ACTCCAAAATGTATGCTTGCAAGA 59.476 37.500 30.39 15.09 0.00 3.02
5223 6300 8.576442 AGGAAAAGTAACAAACAGATTGGTATG 58.424 33.333 0.00 0.00 42.93 2.39
5274 6351 3.447229 AGCTACACCAAGTTTTGCAAGTT 59.553 39.130 0.00 0.00 0.00 2.66
5276 6353 4.032786 GCTACACCAAGTTTTGCAAGTTTG 59.967 41.667 0.00 6.01 0.00 2.93
5381 6462 1.068264 GGCTTCTGCTTTACCACTTGC 60.068 52.381 0.00 0.00 39.59 4.01
5693 6774 7.619964 TGTCACACAGATAAGAATAGTCGTA 57.380 36.000 0.00 0.00 0.00 3.43
5694 6775 8.221965 TGTCACACAGATAAGAATAGTCGTAT 57.778 34.615 0.00 0.00 31.94 3.06
5702 6783 9.386010 CAGATAAGAATAGTCGTATAGCTAGGT 57.614 37.037 0.00 0.00 29.74 3.08
5753 6834 3.403038 GCAAGACTGGTCACTGTTACAT 58.597 45.455 3.51 0.00 0.00 2.29
5754 6835 3.815401 GCAAGACTGGTCACTGTTACATT 59.185 43.478 3.51 0.00 0.00 2.71
5813 6895 3.851976 AGAACACCTGTCGATACTGAC 57.148 47.619 0.00 0.00 39.37 3.51
5983 7073 0.902516 TTTTCCAAATGCGGGGAGGG 60.903 55.000 0.00 0.00 34.02 4.30
5984 7074 3.955543 TTCCAAATGCGGGGAGGGC 62.956 63.158 0.00 0.00 34.02 5.19
5985 7075 4.757355 CCAAATGCGGGGAGGGCA 62.757 66.667 0.00 0.00 45.71 5.36
5986 7076 3.451894 CAAATGCGGGGAGGGCAC 61.452 66.667 0.00 0.00 44.23 5.01
5987 7077 3.661648 AAATGCGGGGAGGGCACT 61.662 61.111 0.00 0.00 44.23 4.40
5988 7078 3.944250 AAATGCGGGGAGGGCACTG 62.944 63.158 0.00 0.00 44.23 3.66
6003 7093 0.109342 CACTGTGTTCCTTGCCCTCT 59.891 55.000 0.00 0.00 0.00 3.69
6020 7110 2.939103 CCTCTAGGGTGAAAAATGCTCG 59.061 50.000 0.00 0.00 0.00 5.03
6034 7124 4.977741 AATGCTCGTTCAAAATTGCTTG 57.022 36.364 0.00 0.00 0.00 4.01
6054 7144 8.169977 TGCTTGGATAATGGTCTAATTCAATC 57.830 34.615 0.00 0.00 0.00 2.67
6131 7221 9.323985 AGATCAGCTCATTAAGTCAATAGAAAC 57.676 33.333 0.00 0.00 0.00 2.78
6133 7223 8.256611 TCAGCTCATTAAGTCAATAGAAACAC 57.743 34.615 0.00 0.00 0.00 3.32
6134 7224 7.877612 TCAGCTCATTAAGTCAATAGAAACACA 59.122 33.333 0.00 0.00 0.00 3.72
6135 7225 8.671921 CAGCTCATTAAGTCAATAGAAACACAT 58.328 33.333 0.00 0.00 0.00 3.21
6136 7226 9.890629 AGCTCATTAAGTCAATAGAAACACATA 57.109 29.630 0.00 0.00 0.00 2.29
6207 7297 6.422100 CAGTGCTCGATAATAGTTTGCTACAT 59.578 38.462 0.00 0.00 0.00 2.29
6224 7314 5.181748 GCTACATTGATATCCATGTCTCCC 58.818 45.833 22.04 8.69 0.00 4.30
6233 7323 3.576078 TCCATGTCTCCCGCATTTATT 57.424 42.857 0.00 0.00 0.00 1.40
6241 7331 0.248458 CCCGCATTTATTGTCGTGCC 60.248 55.000 0.00 0.00 34.20 5.01
6461 7552 2.488937 CAGTATCATGGCTTTGTGCACA 59.511 45.455 17.42 17.42 45.15 4.57
6538 7629 9.920133 TTATTATGCTTGCTTGTTGTCAATTTA 57.080 25.926 0.00 0.00 32.82 1.40
6552 7643 8.328758 TGTTGTCAATTTATTCCTGTCTATCCT 58.671 33.333 0.00 0.00 0.00 3.24
6708 7799 9.013490 GCAATATACACAATTTCAGCAGTTAAG 57.987 33.333 0.00 0.00 0.00 1.85
6777 7869 9.204570 AGTATGTTGTACATTGAGAGTTTGTAC 57.795 33.333 0.00 5.69 43.74 2.90
6940 8032 0.695347 AACTCTGAGGCCTTTCTGGG 59.305 55.000 6.77 1.29 36.00 4.45
7099 8191 2.629617 CAAGGGCAACATCTTCAAACCT 59.370 45.455 0.00 0.00 39.74 3.50
7120 8212 5.875359 ACCTCAGAAATCTAAAAAGTAGCCG 59.125 40.000 0.00 0.00 0.00 5.52
7139 8232 1.665735 CGTTTTCAAAGGCGACATGGG 60.666 52.381 0.00 0.00 0.00 4.00
7159 8252 3.117284 GGGTGGGGTGTAATGGATATGTT 60.117 47.826 0.00 0.00 0.00 2.71
7160 8253 3.888930 GGTGGGGTGTAATGGATATGTTG 59.111 47.826 0.00 0.00 0.00 3.33
7175 8268 6.316140 TGGATATGTTGCAGTAAGTTGATCAC 59.684 38.462 0.00 0.00 0.00 3.06
7185 8278 6.330278 CAGTAAGTTGATCACCGAATGAGTA 58.670 40.000 0.00 0.00 41.91 2.59
7326 8445 0.538057 CCCTGAAGCTGAAACCTGCA 60.538 55.000 0.00 0.00 0.00 4.41
7327 8446 1.321474 CCTGAAGCTGAAACCTGCAA 58.679 50.000 0.00 0.00 0.00 4.08
7378 8497 6.228273 ACTGTATCAGTGAATTGTTTCGTG 57.772 37.500 0.00 0.00 43.63 4.35
7408 8527 8.237267 ACTGAAGTATTGCAGCACTTTTTATAC 58.763 33.333 14.15 0.00 35.17 1.47
7664 8787 0.829333 ATAGCTCTGCCACAGTGAGG 59.171 55.000 0.62 1.62 32.61 3.86
7740 8863 9.884636 TTAAATAGTGTGTTGTAGCATCACTAT 57.115 29.630 9.40 9.40 46.99 2.12
7762 8885 5.392767 TCGGAATTATCCTCTATGCTGAC 57.607 43.478 0.00 0.00 44.17 3.51
7842 8965 4.598257 CCATCGGCAAGTCGAACT 57.402 55.556 0.00 0.00 42.69 3.01
7843 8966 3.733236 CCATCGGCAAGTCGAACTA 57.267 52.632 0.00 0.00 42.69 2.24
7844 8967 2.004583 CCATCGGCAAGTCGAACTAA 57.995 50.000 0.00 0.00 42.69 2.24
7845 8968 2.343101 CCATCGGCAAGTCGAACTAAA 58.657 47.619 0.00 0.00 42.69 1.85
7846 8969 2.093783 CCATCGGCAAGTCGAACTAAAC 59.906 50.000 0.00 0.00 42.69 2.01
7847 8970 1.787012 TCGGCAAGTCGAACTAAACC 58.213 50.000 0.00 0.00 36.12 3.27
7848 8971 0.437295 CGGCAAGTCGAACTAAACCG 59.563 55.000 0.00 0.00 33.74 4.44
7849 8972 1.505425 GGCAAGTCGAACTAAACCGT 58.495 50.000 0.00 0.00 0.00 4.83
7850 8973 1.458445 GGCAAGTCGAACTAAACCGTC 59.542 52.381 0.00 0.00 0.00 4.79
7851 8974 1.123756 GCAAGTCGAACTAAACCGTCG 59.876 52.381 0.00 0.00 0.00 5.12
7852 8975 1.717645 CAAGTCGAACTAAACCGTCGG 59.282 52.381 10.48 10.48 0.00 4.79
7853 8976 0.387750 AGTCGAACTAAACCGTCGGC 60.388 55.000 12.28 0.00 0.00 5.54
7854 8977 0.664166 GTCGAACTAAACCGTCGGCA 60.664 55.000 12.28 0.00 0.00 5.69
7855 8978 0.244450 TCGAACTAAACCGTCGGCAT 59.756 50.000 12.28 2.53 0.00 4.40
7856 8979 1.472082 TCGAACTAAACCGTCGGCATA 59.528 47.619 12.28 3.73 0.00 3.14
7857 8980 1.850441 CGAACTAAACCGTCGGCATAG 59.150 52.381 12.28 15.80 0.00 2.23
7858 8981 2.199236 GAACTAAACCGTCGGCATAGG 58.801 52.381 21.45 8.84 0.00 2.57
7859 8982 1.188863 ACTAAACCGTCGGCATAGGT 58.811 50.000 21.45 9.36 40.50 3.08
7862 8985 3.637184 AACCGTCGGCATAGGTTTT 57.363 47.368 12.28 0.00 45.04 2.43
7863 8986 1.900245 AACCGTCGGCATAGGTTTTT 58.100 45.000 12.28 0.00 45.04 1.94
7930 9053 2.508663 GTAGAAGTGGTCCGCCGC 60.509 66.667 0.00 0.00 45.35 6.53
7945 9068 2.190313 CGCTAAGAGGCATGCCCA 59.810 61.111 33.14 14.85 36.58 5.36
7968 9092 7.645058 CACTATTTGGAACTATGGGTCAAAT 57.355 36.000 0.00 3.57 40.03 2.32
7969 9093 7.483307 CACTATTTGGAACTATGGGTCAAATG 58.517 38.462 11.85 7.04 38.17 2.32
7972 9096 9.184523 CTATTTGGAACTATGGGTCAAATGTTA 57.815 33.333 11.85 0.00 38.17 2.41
7973 9097 7.461182 TTTGGAACTATGGGTCAAATGTTAG 57.539 36.000 0.00 0.00 0.00 2.34
7974 9098 6.381498 TGGAACTATGGGTCAAATGTTAGA 57.619 37.500 0.00 0.00 0.00 2.10
7975 9099 6.177610 TGGAACTATGGGTCAAATGTTAGAC 58.822 40.000 0.00 0.00 0.00 2.59
7976 9100 6.012858 TGGAACTATGGGTCAAATGTTAGACT 60.013 38.462 0.00 0.00 35.18 3.24
7977 9101 7.181305 TGGAACTATGGGTCAAATGTTAGACTA 59.819 37.037 0.00 0.00 35.18 2.59
7979 9103 9.614792 GAACTATGGGTCAAATGTTAGACTATT 57.385 33.333 0.00 0.00 35.18 1.73
7980 9104 8.964476 ACTATGGGTCAAATGTTAGACTATTG 57.036 34.615 0.00 0.00 35.18 1.90
8050 9542 0.674581 TGAGCGTTCCTTGGCATCTG 60.675 55.000 0.00 0.00 0.00 2.90
8060 9552 4.774124 TCCTTGGCATCTGTTCAATCTAG 58.226 43.478 0.00 0.00 0.00 2.43
8062 9554 2.923121 TGGCATCTGTTCAATCTAGCC 58.077 47.619 0.00 0.00 41.15 3.93
8192 9684 9.549078 GGGACCATTTTGTAATTTTCTTTGTTA 57.451 29.630 0.00 0.00 0.00 2.41
8204 9696 5.622770 TTTCTTTGTTAGAGCCGAAATCC 57.377 39.130 0.00 0.00 33.51 3.01
8293 9785 3.877508 AGTTTCAAATAGCGGTCTATGCC 59.122 43.478 0.00 0.00 35.75 4.40
8324 9817 4.321082 GCGGACCTCTTCTAAACGCTATAT 60.321 45.833 0.00 0.00 41.99 0.86
8371 9864 8.738554 GCGCGATATTTAAAATGTTTGTTCATA 58.261 29.630 12.10 0.00 0.00 2.15
8395 9888 4.213270 TGTTTGGATCAAAGTCACTTAGCG 59.787 41.667 0.00 0.00 33.82 4.26
8415 9908 2.701107 GCAGGACCTCTTCTAAACACC 58.299 52.381 0.00 0.00 0.00 4.16
8432 9925 3.371102 CACCATAGTGTGCTATAGCGT 57.629 47.619 19.55 6.07 38.40 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.966179 CAAACCCTAAAGGCACCACC 59.034 55.000 0.00 0.00 40.58 4.61
32 33 6.949352 TTTCATTCTTATCCATTCTGCCTC 57.051 37.500 0.00 0.00 0.00 4.70
36 37 8.241497 TCCCATTTTCATTCTTATCCATTCTG 57.759 34.615 0.00 0.00 0.00 3.02
62 63 3.308188 GGCGCCCTACCCAATAATTATCT 60.308 47.826 18.11 0.00 0.00 1.98
77 78 0.978146 ACAATCTAGAGTGGCGCCCT 60.978 55.000 26.77 20.80 0.00 5.19
105 106 3.241530 ACCACTGGCAAGGCTCGA 61.242 61.111 5.61 0.00 0.00 4.04
109 110 3.297620 CCACACCACTGGCAAGGC 61.298 66.667 5.61 0.00 0.00 4.35
149 150 8.190784 CGCATCATAGGTATGACACAGATTATA 58.809 37.037 1.72 0.00 44.66 0.98
194 197 6.823182 TGAACATCAGTGGTAATCCATTACTG 59.177 38.462 8.92 0.00 46.20 2.74
240 243 6.426937 ACATGTCACTGGTAACTTGTCAATAC 59.573 38.462 0.00 0.00 30.54 1.89
260 263 1.685224 CACACCCTAGGGCACATGT 59.315 57.895 28.88 20.98 39.32 3.21
295 298 4.645136 AGGTTGGGTTTCAAAGAGTTTCTC 59.355 41.667 0.00 0.00 37.08 2.87
296 299 4.610333 AGGTTGGGTTTCAAAGAGTTTCT 58.390 39.130 0.00 0.00 37.08 2.52
310 313 1.359168 GGTAGTGGAGAAGGTTGGGT 58.641 55.000 0.00 0.00 0.00 4.51
326 329 5.416083 CATTAGAGACGGTGATGTTTGGTA 58.584 41.667 0.00 0.00 0.00 3.25
327 330 4.253685 CATTAGAGACGGTGATGTTTGGT 58.746 43.478 0.00 0.00 0.00 3.67
414 417 6.860790 TCTTGTTGTGTATATAGTGGGTCA 57.139 37.500 0.00 0.00 0.00 4.02
415 418 8.448615 GTTTTCTTGTTGTGTATATAGTGGGTC 58.551 37.037 0.00 0.00 0.00 4.46
481 484 3.524095 AACCATCCAACCACAGATTGA 57.476 42.857 0.00 0.00 0.00 2.57
485 488 3.907474 TCTTCTAACCATCCAACCACAGA 59.093 43.478 0.00 0.00 0.00 3.41
487 490 4.141367 TGTTCTTCTAACCATCCAACCACA 60.141 41.667 0.00 0.00 0.00 4.17
492 495 4.104102 ACCACTGTTCTTCTAACCATCCAA 59.896 41.667 0.00 0.00 0.00 3.53
499 502 4.491676 TGCGATACCACTGTTCTTCTAAC 58.508 43.478 0.00 0.00 0.00 2.34
504 507 2.076863 GCTTGCGATACCACTGTTCTT 58.923 47.619 0.00 0.00 0.00 2.52
510 513 1.482182 TGATGAGCTTGCGATACCACT 59.518 47.619 0.00 0.00 0.00 4.00
513 516 2.223923 ACTCTGATGAGCTTGCGATACC 60.224 50.000 0.00 0.00 43.85 2.73
519 522 3.072944 ACTTGAACTCTGATGAGCTTGC 58.927 45.455 0.00 0.00 43.85 4.01
520 523 3.683822 GGACTTGAACTCTGATGAGCTTG 59.316 47.826 0.00 0.00 43.85 4.01
522 525 2.235898 GGGACTTGAACTCTGATGAGCT 59.764 50.000 0.00 0.00 43.85 4.09
541 544 0.462047 GAGCACCAATGTAGTCGGGG 60.462 60.000 0.00 0.00 0.00 5.73
544 547 2.078849 TGTGAGCACCAATGTAGTCG 57.921 50.000 0.00 0.00 0.00 4.18
618 623 7.237173 CACTTCATCTTAAGATTGACGGAAAC 58.763 38.462 15.49 0.00 31.21 2.78
640 645 4.579127 AAAAACTGAGCCGGCACT 57.421 50.000 31.54 9.09 0.00 4.40
656 661 8.210946 CACCCTTATCCTATGAACACATCTAAA 58.789 37.037 0.00 0.00 0.00 1.85
659 664 5.905331 TCACCCTTATCCTATGAACACATCT 59.095 40.000 0.00 0.00 0.00 2.90
666 671 6.239600 GCATACACTCACCCTTATCCTATGAA 60.240 42.308 0.00 0.00 0.00 2.57
668 673 5.247110 AGCATACACTCACCCTTATCCTATG 59.753 44.000 0.00 0.00 0.00 2.23
694 699 4.201851 GCAGTCAAAATCGCTCACATACAT 60.202 41.667 0.00 0.00 0.00 2.29
896 903 8.648097 AGCGAAACTTTTTCTTTTCTTTCTTTC 58.352 29.630 0.00 0.00 30.79 2.62
1172 1192 1.460305 GCTGGGGCAGGAGGAGATA 60.460 63.158 0.00 0.00 38.54 1.98
1195 1215 2.434359 GAACGAGGGCGAAGGTGG 60.434 66.667 0.00 0.00 41.64 4.61
1209 1242 4.144703 GGAGGTCCGCCGGAGAAC 62.145 72.222 5.82 3.06 40.50 3.01
1211 1244 4.458829 ATGGAGGTCCGCCGGAGA 62.459 66.667 5.82 0.00 40.50 3.71
1258 1291 4.546605 TCTGTTTACCCTATCCCCCAAATT 59.453 41.667 0.00 0.00 0.00 1.82
1311 1349 6.038603 GCTGATCATCTGCACCATTAGTTTTA 59.961 38.462 11.45 0.00 40.47 1.52
1317 1546 3.851458 AGCTGATCATCTGCACCATTA 57.149 42.857 17.89 0.00 42.77 1.90
1450 1701 5.119694 ACTCCTCGATTAAAAATGAGCCTC 58.880 41.667 0.00 0.00 0.00 4.70
1458 1709 3.504520 GCACCCAACTCCTCGATTAAAAA 59.495 43.478 0.00 0.00 0.00 1.94
1466 1717 1.672356 CCAAGCACCCAACTCCTCG 60.672 63.158 0.00 0.00 0.00 4.63
1515 1766 8.704849 TCATTTTTCCAATTTCCTTCTGTCTA 57.295 30.769 0.00 0.00 0.00 2.59
1533 1790 6.491403 ACATGTTCTCAGGCTTACTCATTTTT 59.509 34.615 0.00 0.00 0.00 1.94
1592 1849 9.747898 TTACTTCTCTATCTCTATCATTCCCTC 57.252 37.037 0.00 0.00 0.00 4.30
1605 1862 9.646427 GAAGATGTTTGTGTTACTTCTCTATCT 57.354 33.333 0.00 0.00 31.19 1.98
1608 1865 9.909644 GTAGAAGATGTTTGTGTTACTTCTCTA 57.090 33.333 0.00 0.00 41.61 2.43
1609 1866 7.873505 GGTAGAAGATGTTTGTGTTACTTCTCT 59.126 37.037 0.00 0.00 41.61 3.10
1610 1867 7.656137 TGGTAGAAGATGTTTGTGTTACTTCTC 59.344 37.037 0.00 0.00 41.61 2.87
1611 1868 7.506114 TGGTAGAAGATGTTTGTGTTACTTCT 58.494 34.615 0.00 0.00 43.73 2.85
1612 1869 7.441458 ACTGGTAGAAGATGTTTGTGTTACTTC 59.559 37.037 0.00 0.00 35.47 3.01
1613 1870 7.280356 ACTGGTAGAAGATGTTTGTGTTACTT 58.720 34.615 0.00 0.00 0.00 2.24
1614 1871 6.827727 ACTGGTAGAAGATGTTTGTGTTACT 58.172 36.000 0.00 0.00 0.00 2.24
1615 1872 8.773404 ATACTGGTAGAAGATGTTTGTGTTAC 57.227 34.615 0.00 0.00 0.00 2.50
1617 1874 8.812972 TCTATACTGGTAGAAGATGTTTGTGTT 58.187 33.333 0.00 0.00 0.00 3.32
1687 1944 8.870075 ATCTAATATTTTGGAAGCTACATCCC 57.130 34.615 0.40 0.00 36.04 3.85
1738 1995 6.698008 ATCGATTCTCCATGCAAAAATACA 57.302 33.333 0.00 0.00 0.00 2.29
1739 1996 6.074676 GCAATCGATTCTCCATGCAAAAATAC 60.075 38.462 7.92 0.00 34.10 1.89
1882 2140 6.061022 TCATAAGGCAGTTATGTTCTTGGA 57.939 37.500 14.46 0.00 45.84 3.53
1972 2230 8.954350 CATCTCATCTTTTCAGAATAACCACTT 58.046 33.333 0.00 0.00 30.76 3.16
2345 2734 6.919662 CAGCAAAAATGTCACACTACAATCTT 59.080 34.615 0.00 0.00 32.02 2.40
2492 2881 4.955811 AAGAAAGGGGAAAACCACATTC 57.044 40.909 0.00 0.00 42.91 2.67
3011 3403 8.815565 TCATTAGCAGGTTACAAATAATTGGA 57.184 30.769 0.00 0.00 41.01 3.53
3061 3454 5.796424 TTCGAACTTAACTTCCTACTGGT 57.204 39.130 0.00 0.00 34.23 4.00
3101 3553 9.352191 GAACTACTCTATGACTTCATACCCTTA 57.648 37.037 0.00 0.00 37.76 2.69
3178 3630 2.236766 GCTAGCCAATGGATTGCATCT 58.763 47.619 18.21 0.00 39.41 2.90
3248 3856 9.528489 ACTCCATTTTTAGCCACTAGAATTAAA 57.472 29.630 0.00 0.00 0.00 1.52
3251 3859 7.121315 GTCACTCCATTTTTAGCCACTAGAATT 59.879 37.037 0.00 0.00 0.00 2.17
3252 3860 6.599638 GTCACTCCATTTTTAGCCACTAGAAT 59.400 38.462 0.00 0.00 0.00 2.40
3411 4019 4.399303 CGGGGCATTGGAGATAAATAATCC 59.601 45.833 0.00 0.00 34.90 3.01
3439 4047 0.380378 TTCAGACCAACGCAACAAGC 59.620 50.000 0.00 0.00 40.87 4.01
3585 4198 9.434420 CCAAAACTAAATTTGATTTGCCTATCA 57.566 29.630 14.63 0.00 41.73 2.15
3832 4446 3.927142 CCTGTAAGCAGCACTAGTTACAC 59.073 47.826 0.00 0.00 41.26 2.90
3863 4479 3.910627 ACCAGAGTAATTCAGGGTGTTCT 59.089 43.478 0.00 0.00 36.81 3.01
3864 4480 4.287766 ACCAGAGTAATTCAGGGTGTTC 57.712 45.455 0.00 0.00 36.81 3.18
3865 4481 4.724279 AACCAGAGTAATTCAGGGTGTT 57.276 40.909 0.00 0.00 36.81 3.32
3867 4483 5.182001 CAGAAAACCAGAGTAATTCAGGGTG 59.818 44.000 0.00 0.00 36.81 4.61
3869 4485 5.316987 ACAGAAAACCAGAGTAATTCAGGG 58.683 41.667 0.00 0.00 36.81 4.45
3930 4548 5.351233 TCCAAACTGCAGTTTATGTAACG 57.649 39.130 37.19 24.73 45.54 3.18
4375 5001 9.770097 TTCAGGTCATCAGATTTATATTCAGAC 57.230 33.333 0.00 0.00 0.00 3.51
4510 5141 9.368674 CTTCATTACCATGTTTGCAATCAAATA 57.631 29.630 13.88 4.86 43.32 1.40
4546 5177 9.177608 TGAATAAGATTAAGGAATCAGTTGTGG 57.822 33.333 0.87 0.00 43.51 4.17
4593 5224 6.693466 AGAGTTCTAAAGTAGCAAGAGGTTC 58.307 40.000 0.00 0.00 0.00 3.62
4805 5525 3.516981 ATCATGTCAGAACTGTCGGAG 57.483 47.619 1.73 0.00 0.00 4.63
4806 5526 3.961480 AATCATGTCAGAACTGTCGGA 57.039 42.857 1.73 0.06 0.00 4.55
4807 5527 3.996363 TCAAATCATGTCAGAACTGTCGG 59.004 43.478 1.73 0.00 0.00 4.79
4808 5528 4.687948 ACTCAAATCATGTCAGAACTGTCG 59.312 41.667 1.73 0.00 0.00 4.35
4809 5529 6.203530 TCAACTCAAATCATGTCAGAACTGTC 59.796 38.462 1.73 0.00 0.00 3.51
4810 5530 6.057533 TCAACTCAAATCATGTCAGAACTGT 58.942 36.000 1.73 0.00 0.00 3.55
4812 5532 6.938596 TGATCAACTCAAATCATGTCAGAACT 59.061 34.615 0.00 0.00 0.00 3.01
4813 5533 7.137490 TGATCAACTCAAATCATGTCAGAAC 57.863 36.000 0.00 0.00 0.00 3.01
4914 5809 5.163550 GGCATCCACTGGTAATTTCCTAAAC 60.164 44.000 2.53 0.00 0.00 2.01
4944 5840 6.767524 TGAAAGGTACAACAAGTTCACAAT 57.232 33.333 0.00 0.00 0.00 2.71
5029 5925 1.607801 GGGAGGTTTGGGATTGCAGC 61.608 60.000 0.00 0.00 0.00 5.25
5106 6003 9.768662 AAAATGCATTTTGGATATAGGTGAATC 57.231 29.630 31.34 0.00 38.46 2.52
5119 6016 4.387598 TGGAGTGGAAAAATGCATTTTGG 58.612 39.130 32.23 0.00 41.27 3.28
5223 6300 9.765795 AATAGTGACTAGTATGCTATTCAAACC 57.234 33.333 11.53 1.99 38.20 3.27
5247 6324 4.099266 TGCAAAACTTGGTGTAGCTTGAAT 59.901 37.500 0.00 0.00 0.00 2.57
5274 6351 7.879160 TGATATAGATCATGCTGTAACATGCAA 59.121 33.333 0.00 0.00 45.75 4.08
5276 6353 7.548427 ACTGATATAGATCATGCTGTAACATGC 59.452 37.037 0.00 0.00 45.75 4.06
5308 6385 8.846943 ATGTGAGAACTACAATAACATTCACA 57.153 30.769 6.02 6.02 44.20 3.58
5381 6462 1.882912 TGTGCAAGGAACTGCTGTAG 58.117 50.000 0.00 0.00 40.86 2.74
5612 6693 8.722394 CCTAAAAGACATTCTTTACTGACCTTC 58.278 37.037 1.67 0.00 45.19 3.46
5682 6763 9.012161 CCTTAAACCTAGCTATACGACTATTCT 57.988 37.037 0.00 0.00 0.00 2.40
5693 6774 9.178758 CAAATGTCTTTCCTTAAACCTAGCTAT 57.821 33.333 0.00 0.00 0.00 2.97
5694 6775 8.161425 ACAAATGTCTTTCCTTAAACCTAGCTA 58.839 33.333 0.00 0.00 0.00 3.32
5702 6783 9.323985 CATGGAAAACAAATGTCTTTCCTTAAA 57.676 29.630 24.28 14.29 41.00 1.52
5797 6879 8.353684 AGAAATATAAGTCAGTATCGACAGGTG 58.646 37.037 0.00 0.00 38.43 4.00
5799 6881 9.186323 CAAGAAATATAAGTCAGTATCGACAGG 57.814 37.037 0.00 0.00 38.43 4.00
5863 6952 8.967552 TTTTACTTTACTCAAACGAAAAGCAA 57.032 26.923 0.00 0.00 33.25 3.91
5983 7073 1.518903 GAGGGCAAGGAACACAGTGC 61.519 60.000 0.00 0.00 36.24 4.40
5984 7074 0.109342 AGAGGGCAAGGAACACAGTG 59.891 55.000 0.00 0.00 0.00 3.66
5985 7075 1.625818 CTAGAGGGCAAGGAACACAGT 59.374 52.381 0.00 0.00 0.00 3.55
5986 7076 1.065854 CCTAGAGGGCAAGGAACACAG 60.066 57.143 0.00 0.00 34.58 3.66
5987 7077 0.984230 CCTAGAGGGCAAGGAACACA 59.016 55.000 0.00 0.00 34.58 3.72
5988 7078 3.863407 CCTAGAGGGCAAGGAACAC 57.137 57.895 0.00 0.00 34.58 3.32
6003 7093 3.745799 TGAACGAGCATTTTTCACCCTA 58.254 40.909 0.00 0.00 0.00 3.53
6015 7105 2.360483 TCCAAGCAATTTTGAACGAGCA 59.640 40.909 0.00 0.00 0.00 4.26
6020 7110 7.099120 AGACCATTATCCAAGCAATTTTGAAC 58.901 34.615 0.00 0.00 0.00 3.18
6034 7124 8.924511 TTCTGGATTGAATTAGACCATTATCC 57.075 34.615 0.00 0.00 0.00 2.59
6160 7250 4.220382 TGTCCCAAATAAGGCAGTTTGATG 59.780 41.667 9.78 3.18 37.48 3.07
6207 7297 2.046292 TGCGGGAGACATGGATATCAA 58.954 47.619 4.83 0.00 0.00 2.57
6224 7314 2.254918 TTGGCACGACAATAAATGCG 57.745 45.000 0.00 0.00 39.02 4.73
6233 7323 7.329717 GGAATAAACAAATTATTTGGCACGACA 59.670 33.333 20.00 1.06 42.84 4.35
6321 7412 6.093633 ACCAAAAGCTAAAGGAATACATCGTC 59.906 38.462 5.36 0.00 0.00 4.20
6670 7761 4.062293 GTGTATATTGCTTATCCACGGCA 58.938 43.478 0.00 0.00 0.00 5.69
6708 7799 5.064441 ACATCAAGAATACAAGGCTTTGC 57.936 39.130 8.71 0.00 37.85 3.68
6940 8032 0.609662 TCCCGGCCAGTAGTTTACAC 59.390 55.000 2.24 0.00 0.00 2.90
7099 8191 7.739498 AAACGGCTACTTTTTAGATTTCTGA 57.261 32.000 0.00 0.00 0.00 3.27
7120 8212 1.339929 ACCCATGTCGCCTTTGAAAAC 59.660 47.619 0.00 0.00 0.00 2.43
7139 8232 3.317993 GCAACATATCCATTACACCCCAC 59.682 47.826 0.00 0.00 0.00 4.61
7159 8252 3.394674 TTCGGTGATCAACTTACTGCA 57.605 42.857 9.52 0.00 0.00 4.41
7160 8253 3.932710 TCATTCGGTGATCAACTTACTGC 59.067 43.478 9.52 0.00 0.00 4.40
7175 8268 2.101582 ACTTGGCTAGCTACTCATTCGG 59.898 50.000 15.72 0.00 0.00 4.30
7185 8278 1.952367 GCATGGACAACTTGGCTAGCT 60.952 52.381 15.72 0.00 0.00 3.32
7235 8354 5.339008 TTGATCAACACGTTAGGAGCTAT 57.661 39.130 3.38 0.00 0.00 2.97
7282 8401 9.084533 GGGTGAGAGTGAGAAGAAAGTATATAT 57.915 37.037 0.00 0.00 0.00 0.86
7283 8402 7.506261 GGGGTGAGAGTGAGAAGAAAGTATATA 59.494 40.741 0.00 0.00 0.00 0.86
7288 8407 2.635427 GGGGTGAGAGTGAGAAGAAAGT 59.365 50.000 0.00 0.00 0.00 2.66
7292 8411 1.429299 TCAGGGGTGAGAGTGAGAAGA 59.571 52.381 0.00 0.00 0.00 2.87
7326 8445 1.686052 TGCAGATCAAACGGCCTTTTT 59.314 42.857 4.11 0.00 0.00 1.94
7327 8446 1.270550 CTGCAGATCAAACGGCCTTTT 59.729 47.619 8.42 0.42 0.00 2.27
7378 8497 5.613358 AGTGCTGCAATACTTCAGTTTAC 57.387 39.130 2.77 0.00 33.09 2.01
7465 8584 4.675976 TTTCACGGTTGGAGTCTTCTTA 57.324 40.909 0.00 0.00 0.00 2.10
7640 8763 0.254178 CTGTGGCAGAGCTATTGGGT 59.746 55.000 0.00 0.00 32.44 4.51
7688 8811 8.578308 AATGTTTGTTCATGTGTTTGTATGAG 57.422 30.769 0.00 0.00 35.01 2.90
7689 8812 8.939201 AAATGTTTGTTCATGTGTTTGTATGA 57.061 26.923 0.00 0.00 0.00 2.15
7722 8845 3.445805 TCCGATAGTGATGCTACAACACA 59.554 43.478 10.09 0.00 39.16 3.72
7726 8849 7.097192 GGATAATTCCGATAGTGATGCTACAA 58.903 38.462 0.00 0.00 29.60 2.41
7762 8885 1.509644 TATACCAGCGACTACGGCCG 61.510 60.000 26.86 26.86 40.15 6.13
7827 8950 2.344025 GGTTTAGTTCGACTTGCCGAT 58.656 47.619 0.00 0.00 38.45 4.18
7831 8954 1.123756 CGACGGTTTAGTTCGACTTGC 59.876 52.381 0.00 0.00 0.00 4.01
7832 8955 1.717645 CCGACGGTTTAGTTCGACTTG 59.282 52.381 5.48 0.00 0.00 3.16
7833 8956 1.932156 GCCGACGGTTTAGTTCGACTT 60.932 52.381 16.73 0.00 0.00 3.01
7834 8957 0.387750 GCCGACGGTTTAGTTCGACT 60.388 55.000 16.73 0.00 0.00 4.18
7835 8958 0.664166 TGCCGACGGTTTAGTTCGAC 60.664 55.000 16.73 0.00 0.00 4.20
7836 8959 0.244450 ATGCCGACGGTTTAGTTCGA 59.756 50.000 16.73 0.00 0.00 3.71
7837 8960 1.850441 CTATGCCGACGGTTTAGTTCG 59.150 52.381 16.73 0.00 0.00 3.95
7838 8961 2.199236 CCTATGCCGACGGTTTAGTTC 58.801 52.381 16.73 0.00 0.00 3.01
7839 8962 1.551883 ACCTATGCCGACGGTTTAGTT 59.448 47.619 16.73 2.75 0.00 2.24
7840 8963 1.188863 ACCTATGCCGACGGTTTAGT 58.811 50.000 16.73 4.38 0.00 2.24
7841 8964 2.304751 AACCTATGCCGACGGTTTAG 57.695 50.000 16.73 15.46 37.76 1.85
7842 8965 2.766345 AAACCTATGCCGACGGTTTA 57.234 45.000 16.73 6.75 46.15 2.01
7843 8966 3.637184 AAACCTATGCCGACGGTTT 57.363 47.368 16.73 3.85 43.98 3.27
7844 8967 1.900245 AAAAACCTATGCCGACGGTT 58.100 45.000 16.73 6.23 42.52 4.44
7845 8968 3.637184 AAAAACCTATGCCGACGGT 57.363 47.368 16.73 0.00 0.00 4.83
7865 8988 3.139850 TGCCGACCGTATTTCTCAAAAA 58.860 40.909 0.00 0.00 0.00 1.94
7866 8989 2.768698 TGCCGACCGTATTTCTCAAAA 58.231 42.857 0.00 0.00 0.00 2.44
7867 8990 2.459060 TGCCGACCGTATTTCTCAAA 57.541 45.000 0.00 0.00 0.00 2.69
7868 8991 2.684001 ATGCCGACCGTATTTCTCAA 57.316 45.000 0.00 0.00 0.00 3.02
7869 8992 2.035449 CCTATGCCGACCGTATTTCTCA 59.965 50.000 0.00 0.00 0.00 3.27
7870 8993 2.035576 ACCTATGCCGACCGTATTTCTC 59.964 50.000 0.00 0.00 0.00 2.87
7871 8994 2.037144 ACCTATGCCGACCGTATTTCT 58.963 47.619 0.00 0.00 0.00 2.52
7872 8995 2.132762 CACCTATGCCGACCGTATTTC 58.867 52.381 0.00 0.00 0.00 2.17
7873 8996 1.202604 CCACCTATGCCGACCGTATTT 60.203 52.381 0.00 0.00 0.00 1.40
7874 8997 0.391597 CCACCTATGCCGACCGTATT 59.608 55.000 0.00 0.00 0.00 1.89
7875 8998 0.468585 TCCACCTATGCCGACCGTAT 60.469 55.000 0.00 0.00 0.00 3.06
7876 8999 0.683828 TTCCACCTATGCCGACCGTA 60.684 55.000 0.00 0.00 0.00 4.02
7877 9000 1.546589 TTTCCACCTATGCCGACCGT 61.547 55.000 0.00 0.00 0.00 4.83
7878 9001 0.179056 ATTTCCACCTATGCCGACCG 60.179 55.000 0.00 0.00 0.00 4.79
7879 9002 2.876550 GTTATTTCCACCTATGCCGACC 59.123 50.000 0.00 0.00 0.00 4.79
7911 9034 1.515954 CGGCGGACCACTTCTACAT 59.484 57.895 0.00 0.00 34.57 2.29
7913 9036 1.660560 TAGCGGCGGACCACTTCTAC 61.661 60.000 9.78 0.00 34.57 2.59
7916 9039 1.810030 CTTAGCGGCGGACCACTTC 60.810 63.158 9.78 0.00 34.57 3.01
7930 9053 3.498774 AATAGTGGGCATGCCTCTTAG 57.501 47.619 34.70 0.00 36.10 2.18
7945 9068 7.182060 ACATTTGACCCATAGTTCCAAATAGT 58.818 34.615 0.00 0.00 33.43 2.12
7968 9092 8.592155 CGATCGAAATCAAACAATAGTCTAACA 58.408 33.333 10.26 0.00 31.76 2.41
7969 9093 8.804743 TCGATCGAAATCAAACAATAGTCTAAC 58.195 33.333 16.99 0.00 31.76 2.34
7972 9096 7.706607 TCATCGATCGAAATCAAACAATAGTCT 59.293 33.333 23.50 0.00 31.76 3.24
7973 9097 7.841486 TCATCGATCGAAATCAAACAATAGTC 58.159 34.615 23.50 0.00 31.76 2.59
7974 9098 7.042456 CCTCATCGATCGAAATCAAACAATAGT 60.042 37.037 23.50 0.00 31.76 2.12
7975 9099 7.169813 TCCTCATCGATCGAAATCAAACAATAG 59.830 37.037 23.50 5.78 31.76 1.73
7976 9100 6.983890 TCCTCATCGATCGAAATCAAACAATA 59.016 34.615 23.50 0.00 31.76 1.90
7977 9101 5.817296 TCCTCATCGATCGAAATCAAACAAT 59.183 36.000 23.50 0.00 31.76 2.71
7979 9103 4.754322 TCCTCATCGATCGAAATCAAACA 58.246 39.130 23.50 0.00 31.76 2.83
7980 9104 5.043903 TCTCCTCATCGATCGAAATCAAAC 58.956 41.667 23.50 0.00 31.76 2.93
8050 9542 9.722056 CACTTAAAATACATGGCTAGATTGAAC 57.278 33.333 0.00 0.00 0.00 3.18
8117 9609 6.513180 TGTAACTAATTGATCCCAGATCGTC 58.487 40.000 0.48 0.00 0.00 4.20
8188 9680 4.398044 GGATTTTGGATTTCGGCTCTAACA 59.602 41.667 0.00 0.00 0.00 2.41
8192 9684 3.085952 TGGATTTTGGATTTCGGCTCT 57.914 42.857 0.00 0.00 0.00 4.09
8204 9696 2.620242 CGAAGGGCCAATTGGATTTTG 58.380 47.619 29.02 16.54 37.39 2.44
8293 9785 0.390472 GAAGAGGTCCGCCACAAGAG 60.390 60.000 0.00 0.00 37.19 2.85
8324 9817 6.036470 GCGCTATAGCATCACTATAACATGA 58.964 40.000 23.99 0.00 42.11 3.07
8371 9864 5.106555 CGCTAAGTGACTTTGATCCAAACAT 60.107 40.000 10.85 0.00 0.00 2.71
8395 9888 2.038557 TGGTGTTTAGAAGAGGTCCTGC 59.961 50.000 0.00 0.00 0.00 4.85
8415 9908 3.018598 AGCACGCTATAGCACACTATG 57.981 47.619 23.99 12.21 39.51 2.23
8432 9925 4.348486 TGAGGCCATGGTTTTAAATAGCA 58.652 39.130 14.67 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.