Multiple sequence alignment - TraesCS7D01G244100

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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 TraesCS7D01G244100 chr7D 100.000 9128 0 0 1 9128 211644251 211635124 0.000000e+00 16857.0
1 TraesCS7D01G244100 chr7D 91.156 147 13 0 387 533 429280749 429280603 5.590000e-47 200.0
2 TraesCS7D01G244100 chr7D 97.500 40 1 0 7313 7352 40415896 40415935 1.640000e-07 69.4
3 TraesCS7D01G244100 chr7D 96.970 33 0 1 6708 6740 513097752 513097783 5.000000e-03 54.7
4 TraesCS7D01G244100 chr7A 97.567 3823 70 11 3122 6938 223530936 223527131 0.000000e+00 6523.0
5 TraesCS7D01G244100 chr7A 95.622 1576 37 8 1521 3095 223532899 223531355 0.000000e+00 2499.0
6 TraesCS7D01G244100 chr7A 87.476 1581 90 49 14 1522 223534526 223532982 0.000000e+00 1724.0
7 TraesCS7D01G244100 chr7A 95.035 705 23 3 6994 7697 223527128 223526435 0.000000e+00 1098.0
8 TraesCS7D01G244100 chr7A 90.299 835 32 20 8254 9073 223525931 223525131 0.000000e+00 1048.0
9 TraesCS7D01G244100 chr7A 92.276 492 17 6 7766 8257 223526432 223525962 0.000000e+00 678.0
10 TraesCS7D01G244100 chr7A 100.000 28 0 0 3579 3606 32942241 32942268 1.700000e-02 52.8
11 TraesCS7D01G244100 chr7B 95.896 2388 51 11 806 3160 189893676 189896049 0.000000e+00 3823.0
12 TraesCS7D01G244100 chr7B 96.567 2243 51 10 4748 6989 189898418 189900635 0.000000e+00 3692.0
13 TraesCS7D01G244100 chr7B 96.301 1757 50 9 7300 9046 189900767 189902518 0.000000e+00 2870.0
14 TraesCS7D01G244100 chr7B 97.107 968 19 3 3758 4723 189896639 189897599 0.000000e+00 1624.0
15 TraesCS7D01G244100 chr7B 94.393 321 14 1 3211 3531 189896322 189896638 2.960000e-134 490.0
16 TraesCS7D01G244100 chr7B 95.364 151 6 1 7135 7285 189900636 189900785 1.180000e-58 239.0
17 TraesCS7D01G244100 chr4B 81.560 2782 473 31 3628 6384 187359285 187362051 0.000000e+00 2259.0
18 TraesCS7D01G244100 chr4B 88.462 208 18 5 585 791 377733285 377733083 7.080000e-61 246.0
19 TraesCS7D01G244100 chr6B 81.252 2779 469 38 3629 6384 62113947 62116696 0.000000e+00 2198.0
20 TraesCS7D01G244100 chr6B 81.707 328 53 6 6386 6707 62117225 62117551 5.430000e-67 267.0
21 TraesCS7D01G244100 chr6B 89.151 212 20 3 585 795 98990846 98990637 2.530000e-65 261.0
22 TraesCS7D01G244100 chr6B 87.037 162 20 1 369 530 6833042 6832882 2.020000e-41 182.0
23 TraesCS7D01G244100 chr6B 88.889 144 16 0 387 530 492049132 492048989 2.620000e-40 178.0
24 TraesCS7D01G244100 chr6B 92.683 123 7 2 673 795 369283472 369283352 9.420000e-40 176.0
25 TraesCS7D01G244100 chr4A 79.240 2789 530 42 3622 6382 475390609 475387842 0.000000e+00 1897.0
26 TraesCS7D01G244100 chr4A 87.124 233 22 7 570 795 673797555 673797324 3.270000e-64 257.0
27 TraesCS7D01G244100 chr5A 79.322 2742 521 39 3630 6344 473243017 473245739 0.000000e+00 1881.0
28 TraesCS7D01G244100 chr5A 79.006 2777 515 48 3630 6377 685967522 685964785 0.000000e+00 1836.0
29 TraesCS7D01G244100 chr5A 84.211 209 28 5 589 795 708315494 708315289 2.010000e-46 198.0
30 TraesCS7D01G244100 chr1B 86.005 1672 211 14 4728 6384 570856042 570854379 0.000000e+00 1770.0
31 TraesCS7D01G244100 chr1B 82.010 1751 268 24 4655 6384 6854478 6852754 0.000000e+00 1445.0
32 TraesCS7D01G244100 chr1B 88.889 144 16 0 387 530 554000404 554000547 2.620000e-40 178.0
33 TraesCS7D01G244100 chr6A 85.316 1471 202 8 4927 6384 573847504 573846035 0.000000e+00 1507.0
34 TraesCS7D01G244100 chr6A 82.780 1266 205 9 3635 4897 573848761 573847506 0.000000e+00 1118.0
35 TraesCS7D01G244100 chr6A 91.473 129 9 2 668 795 266988419 266988292 9.420000e-40 176.0
36 TraesCS7D01G244100 chr6A 85.185 162 23 1 369 530 127604206 127604046 2.040000e-36 165.0
37 TraesCS7D01G244100 chr6A 87.879 99 9 3 583 679 26424652 26424555 7.490000e-21 113.0
38 TraesCS7D01G244100 chr1A 79.285 2153 419 24 3626 5766 457821975 457824112 0.000000e+00 1480.0
39 TraesCS7D01G244100 chr1A 90.521 211 17 3 583 791 14470176 14469967 9.030000e-70 276.0
40 TraesCS7D01G244100 chr6D 81.314 1279 213 23 5122 6384 19523141 19524409 0.000000e+00 1014.0
41 TraesCS7D01G244100 chr6D 90.071 141 10 4 392 530 428890538 428890676 7.280000e-41 180.0
42 TraesCS7D01G244100 chr6D 96.970 33 1 0 6703 6735 464120142 464120174 1.000000e-03 56.5
43 TraesCS7D01G244100 chr3B 77.672 1469 251 48 3960 5384 235888690 235890125 0.000000e+00 824.0
44 TraesCS7D01G244100 chr3B 78.710 977 197 9 5390 6358 235900343 235901316 7.730000e-180 641.0
45 TraesCS7D01G244100 chr2B 88.372 215 19 5 582 795 161202138 161202347 4.230000e-63 254.0
46 TraesCS7D01G244100 chr2B 96.875 32 1 0 2 33 585716626 585716657 5.000000e-03 54.7
47 TraesCS7D01G244100 chr2D 84.810 237 14 3 579 795 120561222 120561456 1.540000e-52 219.0
48 TraesCS7D01G244100 chr2D 85.455 165 16 7 355 517 427324270 427324112 2.040000e-36 165.0
49 TraesCS7D01G244100 chr3A 84.018 219 28 7 579 795 162223002 162223215 4.320000e-48 204.0
50 TraesCS7D01G244100 chrUn 83.857 223 25 10 580 795 45399692 45399910 1.550000e-47 202.0
51 TraesCS7D01G244100 chr2A 90.141 142 14 0 392 533 718971871 718971730 1.570000e-42 185.0
52 TraesCS7D01G244100 chr2A 91.489 47 4 0 7307 7353 750176182 750176228 2.130000e-06 65.8
53 TraesCS7D01G244100 chr2A 90.909 44 3 1 2 45 150120418 150120376 3.560000e-04 58.4
54 TraesCS7D01G244100 chr5D 88.591 149 13 3 355 502 312383728 312383873 2.620000e-40 178.0
55 TraesCS7D01G244100 chr5D 100.000 30 0 0 3579 3608 288324729 288324700 1.000000e-03 56.5
56 TraesCS7D01G244100 chr5B 93.458 107 3 4 575 679 111623513 111623617 1.230000e-33 156.0


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 TraesCS7D01G244100 chr7D 211635124 211644251 9127 True 16857.000000 16857 100.000000 1 9128 1 chr7D.!!$R1 9127
1 TraesCS7D01G244100 chr7A 223525131 223534526 9395 True 2261.666667 6523 93.045833 14 9073 6 chr7A.!!$R1 9059
2 TraesCS7D01G244100 chr7B 189893676 189902518 8842 False 2123.000000 3823 95.938000 806 9046 6 chr7B.!!$F1 8240
3 TraesCS7D01G244100 chr4B 187359285 187362051 2766 False 2259.000000 2259 81.560000 3628 6384 1 chr4B.!!$F1 2756
4 TraesCS7D01G244100 chr6B 62113947 62117551 3604 False 1232.500000 2198 81.479500 3629 6707 2 chr6B.!!$F1 3078
5 TraesCS7D01G244100 chr4A 475387842 475390609 2767 True 1897.000000 1897 79.240000 3622 6382 1 chr4A.!!$R1 2760
6 TraesCS7D01G244100 chr5A 473243017 473245739 2722 False 1881.000000 1881 79.322000 3630 6344 1 chr5A.!!$F1 2714
7 TraesCS7D01G244100 chr5A 685964785 685967522 2737 True 1836.000000 1836 79.006000 3630 6377 1 chr5A.!!$R1 2747
8 TraesCS7D01G244100 chr1B 570854379 570856042 1663 True 1770.000000 1770 86.005000 4728 6384 1 chr1B.!!$R2 1656
9 TraesCS7D01G244100 chr1B 6852754 6854478 1724 True 1445.000000 1445 82.010000 4655 6384 1 chr1B.!!$R1 1729
10 TraesCS7D01G244100 chr6A 573846035 573848761 2726 True 1312.500000 1507 84.048000 3635 6384 2 chr6A.!!$R4 2749
11 TraesCS7D01G244100 chr1A 457821975 457824112 2137 False 1480.000000 1480 79.285000 3626 5766 1 chr1A.!!$F1 2140
12 TraesCS7D01G244100 chr6D 19523141 19524409 1268 False 1014.000000 1014 81.314000 5122 6384 1 chr6D.!!$F1 1262
13 TraesCS7D01G244100 chr3B 235888690 235890125 1435 False 824.000000 824 77.672000 3960 5384 1 chr3B.!!$F1 1424
14 TraesCS7D01G244100 chr3B 235900343 235901316 973 False 641.000000 641 78.710000 5390 6358 1 chr3B.!!$F2 968

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
19 20 0.815095 TAAATCTGTGCCTCTCGCGA 59.185 50.000 9.26 9.26 42.08 5.87 F
1324 1405 0.909610 CCCCTCTGGTAACTGCTCCA 60.910 60.000 0.00 0.00 35.12 3.86 F
1413 1494 0.951558 CAACTGTTGTAGGTGGTGGC 59.048 55.000 12.30 0.00 40.58 5.01 F
2727 2928 1.603455 TTTTTGGAGGCTGCGGAGG 60.603 57.895 5.93 0.00 0.00 4.30 F
4024 4840 0.313672 AGCGCATCCGAGAATCTCTC 59.686 55.000 11.47 0.61 40.06 3.20 F
4699 5556 0.540365 CCCTGCAGTGGGTTCACAAT 60.540 55.000 13.81 0.00 45.91 2.71 F
6235 7915 1.344763 GGAGACCAGCTTATACGCCAT 59.655 52.381 0.00 0.00 0.00 4.40 F
6765 8983 0.107214 AACGGATGGGGCACATACTG 60.107 55.000 10.86 6.32 40.72 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1715 1880 1.001641 ATGGAGGCCAACTGCTGAC 60.002 57.895 5.01 0.0 36.95 3.51 R
2729 2930 0.805711 CGACTCCGTGCATGCATACA 60.806 55.000 25.64 9.4 0.00 2.29 R
3265 4078 0.916358 CTCCACTCCCCCTCCACATT 60.916 60.000 0.00 0.0 0.00 2.71 R
4567 5424 0.387929 ATATGGCGTCTGTGTACGGG 59.612 55.000 0.00 0.0 43.06 5.28 R
5853 7519 0.325203 GCCAAGGAGACCCTCTCTCT 60.325 60.000 0.00 0.0 44.63 3.10 R
6257 7937 2.420687 CCCAGTGAGCATAAAGGACCTC 60.421 54.545 0.00 0.0 0.00 3.85 R
7908 10128 1.079057 GTCTTTCAGGGCGGACTCC 60.079 63.158 0.00 0.0 0.00 3.85 R
8588 10842 0.321653 AATCCTGCAGACCAACCGAC 60.322 55.000 17.39 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
19 20 0.815095 TAAATCTGTGCCTCTCGCGA 59.185 50.000 9.26 9.26 42.08 5.87
35 36 2.349275 TCGCGAAAGAAAGAAAACACGT 59.651 40.909 6.20 0.00 0.00 4.49
40 41 6.236993 CGCGAAAGAAAGAAAACACGTTTTTA 60.237 34.615 0.00 0.00 42.26 1.52
78 84 4.559153 ACTTATGAAAGCAAACATGTGCC 58.441 39.130 0.00 0.00 46.14 5.01
84 96 1.443194 GCAAACATGTGCCTGCGAG 60.443 57.895 0.00 0.00 38.66 5.03
106 118 4.450419 AGAGAAGCAAATTTGTGTCTCTCG 59.550 41.667 30.35 6.13 42.02 4.04
109 121 1.194547 GCAAATTTGTGTCTCTCGCGA 59.805 47.619 19.03 9.26 0.00 5.87
112 124 4.278858 CAAATTTGTGTCTCTCGCGAAAA 58.721 39.130 11.33 6.28 34.19 2.29
159 172 1.066430 TGGCTCTCGCGGAAGTTAATT 60.066 47.619 6.13 0.00 36.88 1.40
160 173 1.593469 GGCTCTCGCGGAAGTTAATTC 59.407 52.381 6.13 0.00 36.88 2.17
182 195 1.673920 TGCCTCCACGAGAAACAAAAC 59.326 47.619 0.00 0.00 0.00 2.43
184 197 3.135994 GCCTCCACGAGAAACAAAACTA 58.864 45.455 0.00 0.00 0.00 2.24
193 206 5.179555 ACGAGAAACAAAACTATGCCTCTTC 59.820 40.000 0.00 0.00 0.00 2.87
259 272 3.198872 CAGAATCTAGAGAAAACCGGGC 58.801 50.000 6.32 0.00 0.00 6.13
299 313 9.353999 CCAGGAAAAATATTCTAAAAACCGAAG 57.646 33.333 0.00 0.00 0.00 3.79
337 351 7.454260 AAAAATACAAAATCTCGAGGAAGCT 57.546 32.000 13.56 0.00 0.00 3.74
346 360 2.097038 CGAGGAAGCTCCAAGCACG 61.097 63.158 1.29 0.00 45.56 5.34
348 362 3.435186 GGAAGCTCCAAGCACGGC 61.435 66.667 1.29 0.00 45.56 5.68
349 363 2.359230 GAAGCTCCAAGCACGGCT 60.359 61.111 1.29 0.00 45.56 5.52
351 365 4.749310 AGCTCCAAGCACGGCTCG 62.749 66.667 1.29 0.00 45.56 5.03
372 386 4.095782 TCGTAAGCTAATTGGTTTGATGCC 59.904 41.667 1.08 0.00 37.56 4.40
390 404 2.243602 CCAAAAATTGGTGTGCTGCT 57.756 45.000 0.00 0.00 45.93 4.24
406 434 3.055167 TGCTGCTAAATGTTGGCTAGAGA 60.055 43.478 0.00 0.00 38.08 3.10
409 437 5.505324 GCTGCTAAATGTTGGCTAGAGATTG 60.505 44.000 0.00 0.00 38.08 2.67
410 438 4.883585 TGCTAAATGTTGGCTAGAGATTGG 59.116 41.667 0.00 0.00 38.08 3.16
444 472 7.441760 CCAATTTTCATTGTCAATCTCACCAAA 59.558 33.333 0.00 0.00 38.58 3.28
445 473 8.828644 CAATTTTCATTGTCAATCTCACCAAAA 58.171 29.630 0.00 0.00 35.86 2.44
450 478 4.305989 TGTCAATCTCACCAAAAGTTGC 57.694 40.909 0.00 0.00 0.00 4.17
475 503 8.730970 CCAAATATTGGCAACTTTTGATTTTG 57.269 30.769 26.13 16.05 45.17 2.44
476 504 7.326547 CCAAATATTGGCAACTTTTGATTTTGC 59.673 33.333 26.13 0.00 45.17 3.68
481 509 4.880886 GCAACTTTTGATTTTGCCAAGT 57.119 36.364 0.00 0.00 39.82 3.16
482 510 4.590226 GCAACTTTTGATTTTGCCAAGTG 58.410 39.130 0.00 0.00 39.82 3.16
483 511 4.094739 GCAACTTTTGATTTTGCCAAGTGT 59.905 37.500 0.00 0.00 39.82 3.55
484 512 5.391843 GCAACTTTTGATTTTGCCAAGTGTT 60.392 36.000 0.00 0.00 39.82 3.32
485 513 5.799681 ACTTTTGATTTTGCCAAGTGTTG 57.200 34.783 0.00 0.00 0.00 3.33
497 525 2.036992 CCAAGTGTTGGCTTGCCAAATA 59.963 45.455 26.12 16.37 45.17 1.40
517 545 7.306213 CAAATATTGGCAATGCAAAATGTTGA 58.694 30.769 22.57 0.00 36.83 3.18
532 560 7.622672 GCAAAATGTTGATAGCAAACCAATCAG 60.623 37.037 0.00 0.00 36.83 2.90
558 586 1.978455 TTGTGGACTCACGCAAGGGT 61.978 55.000 0.00 0.00 46.42 4.34
559 587 1.227853 GTGGACTCACGCAAGGGTT 60.228 57.895 0.00 0.00 45.20 4.11
560 588 1.070786 TGGACTCACGCAAGGGTTC 59.929 57.895 0.00 0.00 45.20 3.62
561 589 1.671379 GGACTCACGCAAGGGTTCC 60.671 63.158 0.00 0.00 45.20 3.62
606 634 5.129368 AGGGCATGTACAATGGTTCTATT 57.871 39.130 0.00 0.00 0.00 1.73
611 639 7.425606 GGCATGTACAATGGTTCTATTTTAGG 58.574 38.462 0.00 0.00 0.00 2.69
619 647 6.715347 ATGGTTCTATTTTAGGAATGCCAC 57.285 37.500 0.00 0.00 36.29 5.01
620 648 4.638421 TGGTTCTATTTTAGGAATGCCACG 59.362 41.667 0.00 0.00 36.29 4.94
624 652 5.607477 TCTATTTTAGGAATGCCACGTAGG 58.393 41.667 0.00 0.00 41.84 3.18
631 659 4.389374 AGGAATGCCACGTAGGATAAATG 58.611 43.478 8.04 0.00 41.22 2.32
632 660 4.102524 AGGAATGCCACGTAGGATAAATGA 59.897 41.667 8.04 0.00 41.22 2.57
637 665 3.997021 GCCACGTAGGATAAATGATGAGG 59.003 47.826 8.04 0.00 41.22 3.86
649 677 2.928036 TGATGAGGTGGAGGAGAGAA 57.072 50.000 0.00 0.00 0.00 2.87
651 679 2.834549 TGATGAGGTGGAGGAGAGAAAC 59.165 50.000 0.00 0.00 0.00 2.78
663 691 7.607991 GTGGAGGAGAGAAACATCATAAGAAAA 59.392 37.037 0.00 0.00 0.00 2.29
664 692 7.826252 TGGAGGAGAGAAACATCATAAGAAAAG 59.174 37.037 0.00 0.00 0.00 2.27
665 693 7.281999 GGAGGAGAGAAACATCATAAGAAAAGG 59.718 40.741 0.00 0.00 0.00 3.11
666 694 6.601217 AGGAGAGAAACATCATAAGAAAAGGC 59.399 38.462 0.00 0.00 0.00 4.35
668 696 7.121907 GGAGAGAAACATCATAAGAAAAGGCTT 59.878 37.037 0.00 0.00 0.00 4.35
669 697 7.824672 AGAGAAACATCATAAGAAAAGGCTTG 58.175 34.615 0.00 0.00 0.00 4.01
670 698 7.449704 AGAGAAACATCATAAGAAAAGGCTTGT 59.550 33.333 0.00 0.00 0.00 3.16
671 699 7.597386 AGAAACATCATAAGAAAAGGCTTGTC 58.403 34.615 9.51 9.51 0.00 3.18
673 701 7.530426 AACATCATAAGAAAAGGCTTGTCTT 57.470 32.000 30.04 30.04 35.77 3.01
688 744 7.338710 AGGCTTGTCTTTCTTAGCACAATATA 58.661 34.615 0.00 0.00 35.36 0.86
756 812 8.333908 GCTAAAAGATGACTCATTGTAGACATG 58.666 37.037 0.00 0.00 33.08 3.21
757 813 9.376075 CTAAAAGATGACTCATTGTAGACATGT 57.624 33.333 0.00 0.00 33.08 3.21
788 844 7.549615 TTCATCTCTAAATCACATGCAAGAG 57.450 36.000 0.00 0.00 33.37 2.85
793 849 8.846943 TCTCTAAATCACATGCAAGAGTTTAA 57.153 30.769 7.47 0.00 33.72 1.52
794 850 8.939929 TCTCTAAATCACATGCAAGAGTTTAAG 58.060 33.333 7.47 5.52 33.72 1.85
795 851 8.621532 TCTAAATCACATGCAAGAGTTTAAGT 57.378 30.769 0.00 0.00 0.00 2.24
797 853 9.760660 CTAAATCACATGCAAGAGTTTAAGTAC 57.239 33.333 0.00 0.00 0.00 2.73
798 854 7.744087 AATCACATGCAAGAGTTTAAGTACA 57.256 32.000 0.00 0.00 0.00 2.90
801 857 7.584108 TCACATGCAAGAGTTTAAGTACAATG 58.416 34.615 0.00 0.00 0.00 2.82
802 858 6.306356 CACATGCAAGAGTTTAAGTACAATGC 59.694 38.462 0.00 0.00 0.00 3.56
803 859 5.371115 TGCAAGAGTTTAAGTACAATGCC 57.629 39.130 0.00 0.00 0.00 4.40
804 860 4.217550 TGCAAGAGTTTAAGTACAATGCCC 59.782 41.667 0.00 0.00 0.00 5.36
805 861 4.459337 GCAAGAGTTTAAGTACAATGCCCT 59.541 41.667 0.00 0.00 0.00 5.19
806 862 5.048013 GCAAGAGTTTAAGTACAATGCCCTT 60.048 40.000 0.00 0.00 0.00 3.95
807 863 6.150474 GCAAGAGTTTAAGTACAATGCCCTTA 59.850 38.462 0.00 0.00 0.00 2.69
809 865 7.253905 AGAGTTTAAGTACAATGCCCTTAGA 57.746 36.000 0.00 0.00 0.00 2.10
810 866 7.686434 AGAGTTTAAGTACAATGCCCTTAGAA 58.314 34.615 0.00 0.00 0.00 2.10
967 1036 4.135153 TGAGCGCTCGGAGGAAGC 62.135 66.667 30.75 6.47 0.00 3.86
968 1037 4.882396 GAGCGCTCGGAGGAAGCC 62.882 72.222 23.61 0.00 0.00 4.35
1324 1405 0.909610 CCCCTCTGGTAACTGCTCCA 60.910 60.000 0.00 0.00 35.12 3.86
1353 1434 2.702592 TATTTTCTCGGCCGATTGGT 57.297 45.000 31.19 16.10 37.67 3.67
1355 1436 1.729284 TTTTCTCGGCCGATTGGTAC 58.271 50.000 31.19 0.00 37.67 3.34
1365 1446 2.416431 GCCGATTGGTACTGACGTACTT 60.416 50.000 0.00 0.00 44.30 2.24
1366 1447 3.432782 CCGATTGGTACTGACGTACTTC 58.567 50.000 0.00 0.00 44.30 3.01
1367 1448 3.119743 CCGATTGGTACTGACGTACTTCA 60.120 47.826 1.71 1.71 44.30 3.02
1368 1449 4.439700 CCGATTGGTACTGACGTACTTCAT 60.440 45.833 2.10 0.00 44.30 2.57
1369 1450 4.499399 CGATTGGTACTGACGTACTTCATG 59.501 45.833 2.10 0.66 44.30 3.07
1370 1451 4.859304 TTGGTACTGACGTACTTCATGT 57.141 40.909 2.10 6.19 44.30 3.21
1374 1455 5.047590 TGGTACTGACGTACTTCATGTTCAT 60.048 40.000 2.10 0.00 44.30 2.57
1389 1470 4.220693 TGTTCATGGATGAAGGTGTAGG 57.779 45.455 2.20 0.00 46.44 3.18
1413 1494 0.951558 CAACTGTTGTAGGTGGTGGC 59.048 55.000 12.30 0.00 40.58 5.01
1536 1701 9.924650 AACTTAGTACTAGTATGTTGGTTTGAG 57.075 33.333 5.75 0.00 0.00 3.02
1546 1711 8.324163 AGTATGTTGGTTTGAGTTAGTGAATC 57.676 34.615 0.00 0.00 0.00 2.52
1715 1880 2.253452 GCAAGGACTTGTGCAGCG 59.747 61.111 13.08 0.00 42.31 5.18
1982 2173 2.360100 CTGCTGGCTGCTGCTCTT 60.360 61.111 17.45 0.00 43.37 2.85
2029 2220 4.642445 TGTCGAGTGTGTCTTTGAAGTA 57.358 40.909 0.00 0.00 0.00 2.24
2500 2692 6.152661 TCTGTGTCCAAAATGACAACTTTTCT 59.847 34.615 0.00 0.00 46.17 2.52
2507 2699 6.593382 CCAAAATGACAACTTTTCTTGAACCA 59.407 34.615 0.00 0.00 0.00 3.67
2608 2800 7.936847 ACTTTGTATCATTTGGTCAACAGTCTA 59.063 33.333 0.00 0.00 0.00 2.59
2662 2854 9.898152 ATTTTTAAGAGCAGCTCTAGTAGAATT 57.102 29.630 25.66 9.67 40.28 2.17
2726 2927 4.079446 TTTTTGGAGGCTGCGGAG 57.921 55.556 0.00 0.00 0.00 4.63
2727 2928 1.603455 TTTTTGGAGGCTGCGGAGG 60.603 57.895 5.93 0.00 0.00 4.30
2728 2929 4.722700 TTTGGAGGCTGCGGAGGC 62.723 66.667 23.28 23.28 45.31 4.70
2742 2943 1.645455 GAGGCTGTATGCATGCACG 59.355 57.895 25.37 12.82 45.15 5.34
2895 3096 7.050377 AGTCACACTGCAGCTTAATACATATT 58.950 34.615 15.27 0.00 0.00 1.28
3452 4265 1.094785 GCTGCGACATTGGTATTGGT 58.905 50.000 0.00 0.00 0.00 3.67
3475 4288 3.023832 CAGAAGAGAGGGGAAGAGAGAC 58.976 54.545 0.00 0.00 0.00 3.36
3569 4382 8.846211 GGTATTTTAGCAGTTATTTGCCTATCA 58.154 33.333 0.00 0.00 45.18 2.15
3694 4508 0.754472 ACAAATTGCCAGCAACAGCT 59.246 45.000 7.31 0.00 38.88 4.24
3800 4614 4.791411 GCGCAACTCCATTACAAGTTTGAA 60.791 41.667 0.30 0.00 33.53 2.69
3830 4644 4.398988 ACGCCACACATACATCATTGAAAT 59.601 37.500 0.00 0.00 0.00 2.17
3936 4750 5.466728 TCAGTTGCACAGAATCTGTTTCTAC 59.533 40.000 13.99 14.20 42.59 2.59
4023 4839 0.749649 AAGCGCATCCGAGAATCTCT 59.250 50.000 11.47 0.00 36.29 3.10
4024 4840 0.313672 AGCGCATCCGAGAATCTCTC 59.686 55.000 11.47 0.61 40.06 3.20
4025 4841 0.665972 GCGCATCCGAGAATCTCTCC 60.666 60.000 8.77 0.00 40.34 3.71
4026 4842 0.670706 CGCATCCGAGAATCTCTCCA 59.329 55.000 8.77 0.00 40.34 3.86
4027 4843 1.335780 CGCATCCGAGAATCTCTCCAG 60.336 57.143 8.77 0.00 40.34 3.86
4028 4844 1.959985 GCATCCGAGAATCTCTCCAGA 59.040 52.381 8.77 0.70 40.34 3.86
4029 4845 2.363680 GCATCCGAGAATCTCTCCAGAA 59.636 50.000 8.77 0.00 40.34 3.02
4075 4898 1.174078 TGCCACACCACAAGCATCTG 61.174 55.000 0.00 0.00 0.00 2.90
4567 5424 1.209504 TCATGCACAGGGGTAAGCTAC 59.790 52.381 0.00 0.00 0.00 3.58
4699 5556 0.540365 CCCTGCAGTGGGTTCACAAT 60.540 55.000 13.81 0.00 45.91 2.71
5475 7136 9.444600 TTTTCCACACACTCTCTTTAATATACC 57.555 33.333 0.00 0.00 0.00 2.73
5748 7409 8.235226 TCATCTACAAAGAGTAACTGACTTACG 58.765 37.037 0.00 0.00 39.06 3.18
5850 7516 6.820656 CCTCTGCACAGATAAGAAACAAGTAT 59.179 38.462 0.00 0.00 36.76 2.12
5851 7517 7.201591 CCTCTGCACAGATAAGAAACAAGTATG 60.202 40.741 0.00 0.00 36.76 2.39
5852 7518 6.595326 TCTGCACAGATAAGAAACAAGTATGG 59.405 38.462 0.00 0.00 31.41 2.74
5853 7519 6.472016 TGCACAGATAAGAAACAAGTATGGA 58.528 36.000 0.00 0.00 0.00 3.41
6144 7824 8.846423 AATATTATCCGAGATTAGTCTCCCAT 57.154 34.615 9.46 4.66 46.67 4.00
6235 7915 1.344763 GGAGACCAGCTTATACGCCAT 59.655 52.381 0.00 0.00 0.00 4.40
6257 7937 4.323417 TGTTACACAGGCTTATTGGTCTG 58.677 43.478 0.00 0.00 43.72 3.51
6545 8761 0.179189 CGCGCCATTCTCCTGAAAAC 60.179 55.000 0.00 0.00 35.63 2.43
6753 8971 3.536956 TTGAGGCTAGGTTAACGGATG 57.463 47.619 0.00 0.00 0.00 3.51
6754 8972 1.760613 TGAGGCTAGGTTAACGGATGG 59.239 52.381 0.00 0.00 0.00 3.51
6756 8974 0.108019 GGCTAGGTTAACGGATGGGG 59.892 60.000 0.00 0.00 0.00 4.96
6757 8975 0.534427 GCTAGGTTAACGGATGGGGC 60.534 60.000 0.00 0.00 0.00 5.80
6758 8976 0.834612 CTAGGTTAACGGATGGGGCA 59.165 55.000 0.00 0.00 0.00 5.36
6761 8979 0.395173 GGTTAACGGATGGGGCACAT 60.395 55.000 0.00 0.00 44.18 3.21
6762 8980 1.134037 GGTTAACGGATGGGGCACATA 60.134 52.381 0.06 0.00 40.72 2.29
6763 8981 1.944709 GTTAACGGATGGGGCACATAC 59.055 52.381 0.06 0.24 40.72 2.39
6764 8982 1.502690 TAACGGATGGGGCACATACT 58.497 50.000 10.86 0.00 40.72 2.12
6765 8983 0.107214 AACGGATGGGGCACATACTG 60.107 55.000 10.86 6.32 40.72 2.74
6766 8984 1.227943 CGGATGGGGCACATACTGG 60.228 63.158 10.86 0.00 40.72 4.00
6810 9028 0.634465 ACTGGTTTTGGGGTGAGGTT 59.366 50.000 0.00 0.00 0.00 3.50
6878 9096 2.236146 TGAACAACCCGCTGAGTCATAT 59.764 45.455 0.00 0.00 0.00 1.78
6886 9104 2.416027 CCGCTGAGTCATATATGGACCG 60.416 54.545 12.78 7.31 35.89 4.79
6938 9156 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
6940 9158 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
6941 9159 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
6942 9160 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
6943 9161 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
6944 9162 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
6945 9163 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
6956 9174 0.172352 CTCTCTCTCCTGTGCCGAAC 59.828 60.000 0.00 0.00 0.00 3.95
6984 9202 2.575921 AATCTCCTCCATCTCCACCA 57.424 50.000 0.00 0.00 0.00 4.17
6987 9205 1.306997 TCCTCCATCTCCACCACCC 60.307 63.158 0.00 0.00 0.00 4.61
6988 9206 2.378634 CCTCCATCTCCACCACCCC 61.379 68.421 0.00 0.00 0.00 4.95
6989 9207 2.687200 TCCATCTCCACCACCCCG 60.687 66.667 0.00 0.00 0.00 5.73
6990 9208 4.489771 CCATCTCCACCACCCCGC 62.490 72.222 0.00 0.00 0.00 6.13
6991 9209 4.489771 CATCTCCACCACCCCGCC 62.490 72.222 0.00 0.00 0.00 6.13
7083 9301 3.138798 GCCTCCAGCATGCCACTG 61.139 66.667 15.66 6.23 42.97 3.66
7165 9383 0.726827 CTCACGCCAATTGCACGTAT 59.273 50.000 19.98 1.54 41.33 3.06
7582 9802 9.314321 ACACTTCGACACCTAATTATTCATAAG 57.686 33.333 0.00 0.00 0.00 1.73
7685 9905 0.401738 ATCAGCCATCCCATAACCGG 59.598 55.000 0.00 0.00 0.00 5.28
7739 9959 1.168714 GGCCCGAATATCCTCATTGC 58.831 55.000 0.00 0.00 0.00 3.56
7741 9961 1.442769 CCCGAATATCCTCATTGCCG 58.557 55.000 0.00 0.00 0.00 5.69
7908 10128 0.739813 CCGAGACAAAAGGGCTACCG 60.740 60.000 0.00 0.00 43.47 4.02
7921 10141 4.051167 TACCGGAGTCCGCCCTGA 62.051 66.667 26.60 5.56 46.86 3.86
7935 10155 1.078848 CCTGAAAGACTGCTCCGGG 60.079 63.158 0.00 0.00 34.07 5.73
7944 10164 4.408396 TGCTCCGGGGAAGCCCTA 62.408 66.667 4.80 0.00 44.66 3.53
8022 10242 1.292223 GGTGAGCGTTGGAGTAGCA 59.708 57.895 0.00 0.00 0.00 3.49
8082 10302 1.137086 CAGTACCAACCTGATCTCCCG 59.863 57.143 0.00 0.00 31.38 5.14
8164 10384 3.614616 AGAATCAATCGACGAAACTCTGC 59.385 43.478 0.00 0.00 0.00 4.26
8244 10496 4.448537 TTTTGTTAGCATTTGATCCGGG 57.551 40.909 0.00 0.00 0.00 5.73
8321 10573 8.055279 AGACCAATTGGATGTATACACTTTTG 57.945 34.615 31.22 8.01 38.94 2.44
8323 10575 6.154363 ACCAATTGGATGTATACACTTTTGGG 59.846 38.462 31.22 16.90 38.94 4.12
8462 10716 7.269937 CAGATGCTTTATCACTTTCTTTTCGTG 59.730 37.037 0.00 0.00 38.31 4.35
8477 10731 1.875009 TCGTGAGATATACGGCGAGT 58.125 50.000 16.62 3.61 41.58 4.18
8521 10775 5.412904 ACTGCTATTTAAAACCTCTGTCAGC 59.587 40.000 0.00 0.00 0.00 4.26
8588 10842 5.065914 AGTGGTGAATTATTGGATCATCCG 58.934 41.667 0.00 0.00 40.17 4.18
8608 10862 0.321564 TCGGTTGGTCTGCAGGATTG 60.322 55.000 15.13 0.00 0.00 2.67
8726 10980 2.693762 CCTTCCATGTGCTGCCACG 61.694 63.158 0.00 0.00 45.04 4.94
8926 11194 3.284711 TGCATGATGGCACCAATGA 57.715 47.368 0.00 0.00 39.25 2.57
8927 11195 1.783071 TGCATGATGGCACCAATGAT 58.217 45.000 0.00 0.00 39.25 2.45
8928 11196 2.946785 TGCATGATGGCACCAATGATA 58.053 42.857 0.00 0.00 39.25 2.15
8929 11197 2.624364 TGCATGATGGCACCAATGATAC 59.376 45.455 0.00 0.00 39.25 2.24
8930 11198 2.351060 GCATGATGGCACCAATGATACG 60.351 50.000 0.00 0.00 0.00 3.06
9007 11276 4.457257 AGAAACTCAGGCTGTCATTAAAGC 59.543 41.667 15.27 0.00 38.76 3.51
9011 11285 3.609853 TCAGGCTGTCATTAAAGCGAAT 58.390 40.909 15.27 0.00 40.46 3.34
9036 11310 0.306533 TCGCTTCAACAAGAAACCGC 59.693 50.000 0.00 0.00 35.40 5.68
9069 11348 3.469863 GACACGGGCCACTGAACCA 62.470 63.158 4.39 0.00 0.00 3.67
9073 11352 2.520968 GGGCCACTGAACCAACCT 59.479 61.111 4.39 0.00 0.00 3.50
9074 11353 1.765074 GGGCCACTGAACCAACCTA 59.235 57.895 4.39 0.00 0.00 3.08
9075 11354 0.608308 GGGCCACTGAACCAACCTAC 60.608 60.000 4.39 0.00 0.00 3.18
9076 11355 0.400594 GGCCACTGAACCAACCTACT 59.599 55.000 0.00 0.00 0.00 2.57
9077 11356 1.626825 GGCCACTGAACCAACCTACTA 59.373 52.381 0.00 0.00 0.00 1.82
9078 11357 2.614734 GGCCACTGAACCAACCTACTAC 60.615 54.545 0.00 0.00 0.00 2.73
9079 11358 2.614734 GCCACTGAACCAACCTACTACC 60.615 54.545 0.00 0.00 0.00 3.18
9080 11359 2.027469 CCACTGAACCAACCTACTACCC 60.027 54.545 0.00 0.00 0.00 3.69
9081 11360 1.897802 ACTGAACCAACCTACTACCCG 59.102 52.381 0.00 0.00 0.00 5.28
9082 11361 0.609662 TGAACCAACCTACTACCCGC 59.390 55.000 0.00 0.00 0.00 6.13
9083 11362 0.459063 GAACCAACCTACTACCCGCG 60.459 60.000 0.00 0.00 0.00 6.46
9084 11363 1.187567 AACCAACCTACTACCCGCGT 61.188 55.000 4.92 0.00 0.00 6.01
9085 11364 1.153706 CCAACCTACTACCCGCGTG 60.154 63.158 4.92 0.00 0.00 5.34
9086 11365 1.588082 CAACCTACTACCCGCGTGT 59.412 57.895 4.92 0.99 0.00 4.49
9087 11366 0.037975 CAACCTACTACCCGCGTGTT 60.038 55.000 4.92 0.00 0.00 3.32
9088 11367 0.037975 AACCTACTACCCGCGTGTTG 60.038 55.000 4.92 2.90 0.00 3.33
9089 11368 1.808390 CCTACTACCCGCGTGTTGC 60.808 63.158 4.92 0.00 41.47 4.17
9090 11369 1.808390 CTACTACCCGCGTGTTGCC 60.808 63.158 4.92 0.00 42.08 4.52
9091 11370 3.299524 TACTACCCGCGTGTTGCCC 62.300 63.158 4.92 0.00 42.08 5.36
9097 11376 4.988598 CGCGTGTTGCCCCAGTCT 62.989 66.667 0.00 0.00 42.08 3.24
9098 11377 2.594592 GCGTGTTGCCCCAGTCTT 60.595 61.111 0.00 0.00 37.76 3.01
9099 11378 2.617274 GCGTGTTGCCCCAGTCTTC 61.617 63.158 0.00 0.00 37.76 2.87
9100 11379 1.071471 CGTGTTGCCCCAGTCTTCT 59.929 57.895 0.00 0.00 0.00 2.85
9101 11380 1.230635 CGTGTTGCCCCAGTCTTCTG 61.231 60.000 0.00 0.00 41.01 3.02
9102 11381 1.228245 TGTTGCCCCAGTCTTCTGC 60.228 57.895 0.00 0.00 40.09 4.26
9103 11382 2.032528 TTGCCCCAGTCTTCTGCG 59.967 61.111 0.00 0.00 40.09 5.18
9104 11383 4.704833 TGCCCCAGTCTTCTGCGC 62.705 66.667 0.00 0.00 40.09 6.09
9106 11385 4.785453 CCCCAGTCTTCTGCGCCC 62.785 72.222 4.18 0.00 40.09 6.13
9107 11386 4.020617 CCCAGTCTTCTGCGCCCA 62.021 66.667 4.18 0.00 40.09 5.36
9108 11387 2.270205 CCAGTCTTCTGCGCCCAT 59.730 61.111 4.18 0.00 40.09 4.00
9109 11388 1.817099 CCAGTCTTCTGCGCCCATC 60.817 63.158 4.18 0.00 40.09 3.51
9110 11389 1.220206 CAGTCTTCTGCGCCCATCT 59.780 57.895 4.18 0.00 34.79 2.90
9111 11390 1.088340 CAGTCTTCTGCGCCCATCTG 61.088 60.000 4.18 2.44 34.79 2.90
9112 11391 2.124983 TCTTCTGCGCCCATCTGC 60.125 61.111 4.18 0.00 0.00 4.26
9113 11392 3.207669 CTTCTGCGCCCATCTGCC 61.208 66.667 4.18 0.00 0.00 4.85
9114 11393 3.982316 CTTCTGCGCCCATCTGCCA 62.982 63.158 4.18 0.00 0.00 4.92
9115 11394 3.348554 TTCTGCGCCCATCTGCCAT 62.349 57.895 4.18 0.00 0.00 4.40
9116 11395 2.831742 CTGCGCCCATCTGCCATT 60.832 61.111 4.18 0.00 0.00 3.16
9117 11396 3.133767 CTGCGCCCATCTGCCATTG 62.134 63.158 4.18 0.00 0.00 2.82
9118 11397 4.580551 GCGCCCATCTGCCATTGC 62.581 66.667 0.00 0.00 38.26 3.56
9119 11398 4.260355 CGCCCATCTGCCATTGCG 62.260 66.667 0.00 0.00 41.78 4.85
9120 11399 3.142838 GCCCATCTGCCATTGCGT 61.143 61.111 0.00 0.00 41.78 5.24
9121 11400 2.802792 CCCATCTGCCATTGCGTG 59.197 61.111 0.00 0.00 41.78 5.34
9122 11401 2.048023 CCCATCTGCCATTGCGTGT 61.048 57.895 0.00 0.00 41.78 4.49
9123 11402 1.138036 CCATCTGCCATTGCGTGTG 59.862 57.895 0.00 0.00 41.78 3.82
9124 11403 1.138036 CATCTGCCATTGCGTGTGG 59.862 57.895 0.00 0.00 41.78 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.037326 TTCGCGAGAGGCACAGATTT 60.037 50.000 9.59 0.00 43.84 2.17
2 3 0.037326 TTTCGCGAGAGGCACAGATT 60.037 50.000 9.59 0.00 43.84 2.40
3 4 0.459237 CTTTCGCGAGAGGCACAGAT 60.459 55.000 18.35 0.00 43.84 2.90
5 6 0.667487 TTCTTTCGCGAGAGGCACAG 60.667 55.000 24.53 7.01 43.84 3.66
7 8 0.440371 CTTTCTTTCGCGAGAGGCAC 59.560 55.000 24.53 0.00 43.84 5.01
8 9 0.317160 TCTTTCTTTCGCGAGAGGCA 59.683 50.000 24.53 10.58 43.84 4.75
9 10 1.429463 TTCTTTCTTTCGCGAGAGGC 58.571 50.000 24.53 0.00 43.69 4.70
10 11 3.247648 TGTTTTCTTTCTTTCGCGAGAGG 59.752 43.478 24.53 10.46 43.69 3.69
11 12 4.204581 GTGTTTTCTTTCTTTCGCGAGAG 58.795 43.478 19.89 19.89 43.69 3.20
12 13 3.302221 CGTGTTTTCTTTCTTTCGCGAGA 60.302 43.478 9.59 3.35 39.20 4.04
35 36 6.385649 AGTTGTGCCTCTCGAAAATAAAAA 57.614 33.333 0.00 0.00 0.00 1.94
40 41 5.245531 TCATAAGTTGTGCCTCTCGAAAAT 58.754 37.500 0.00 0.00 0.00 1.82
44 45 3.953712 TTCATAAGTTGTGCCTCTCGA 57.046 42.857 0.00 0.00 0.00 4.04
78 84 3.231965 CACAAATTTGCTTCTCTCGCAG 58.768 45.455 18.12 0.00 38.80 5.18
84 96 4.706527 CGAGAGACACAAATTTGCTTCTC 58.293 43.478 27.32 27.32 38.62 2.87
150 163 3.741805 GTGGAGGCACGAATTAACTTC 57.258 47.619 0.00 0.00 0.00 3.01
177 190 2.985896 TCCGGAAGAGGCATAGTTTTG 58.014 47.619 0.00 0.00 0.00 2.44
247 260 1.137282 TGGTTTTTGCCCGGTTTTCTC 59.863 47.619 0.00 0.00 0.00 2.87
249 262 2.025589 TTGGTTTTTGCCCGGTTTTC 57.974 45.000 0.00 0.00 0.00 2.29
276 289 9.058424 CGTCTTCGGTTTTTAGAATATTTTTCC 57.942 33.333 0.00 0.00 0.00 3.13
277 290 8.572976 GCGTCTTCGGTTTTTAGAATATTTTTC 58.427 33.333 0.00 0.00 37.56 2.29
283 297 4.236935 ACGCGTCTTCGGTTTTTAGAATA 58.763 39.130 5.58 0.00 37.56 1.75
284 298 3.062042 ACGCGTCTTCGGTTTTTAGAAT 58.938 40.909 5.58 0.00 37.56 2.40
337 351 1.080093 CTTACGAGCCGTGCTTGGA 60.080 57.895 15.02 6.12 43.81 3.53
348 362 5.266242 GCATCAAACCAATTAGCTTACGAG 58.734 41.667 0.00 0.00 0.00 4.18
349 363 4.095782 GGCATCAAACCAATTAGCTTACGA 59.904 41.667 0.00 0.00 0.00 3.43
351 365 5.323371 TGGCATCAAACCAATTAGCTTAC 57.677 39.130 0.00 0.00 33.12 2.34
356 370 7.306953 CCAATTTTTGGCATCAAACCAATTAG 58.693 34.615 0.00 0.00 46.25 1.73
372 386 5.236911 ACATTTAGCAGCACACCAATTTTTG 59.763 36.000 0.00 0.00 0.00 2.44
377 391 3.306225 CCAACATTTAGCAGCACACCAAT 60.306 43.478 0.00 0.00 0.00 3.16
380 394 1.669795 GCCAACATTTAGCAGCACACC 60.670 52.381 0.00 0.00 0.00 4.16
382 396 1.619654 AGCCAACATTTAGCAGCACA 58.380 45.000 0.00 0.00 0.00 4.57
387 401 4.883585 CCAATCTCTAGCCAACATTTAGCA 59.116 41.667 0.00 0.00 0.00 3.49
388 402 4.884164 ACCAATCTCTAGCCAACATTTAGC 59.116 41.667 0.00 0.00 0.00 3.09
389 403 6.678900 GCAACCAATCTCTAGCCAACATTTAG 60.679 42.308 0.00 0.00 0.00 1.85
390 404 5.125417 GCAACCAATCTCTAGCCAACATTTA 59.875 40.000 0.00 0.00 0.00 1.40
410 438 7.418840 TTGACAATGAAAATTGGTATGCAAC 57.581 32.000 0.00 0.00 35.93 4.17
431 459 3.295093 TGGCAACTTTTGGTGAGATTGA 58.705 40.909 0.00 0.00 40.19 2.57
460 488 4.094739 ACACTTGGCAAAATCAAAAGTTGC 59.905 37.500 0.00 0.00 45.48 4.17
497 525 5.065474 GCTATCAACATTTTGCATTGCCAAT 59.935 36.000 6.12 1.85 32.17 3.16
502 530 6.073167 TGGTTTGCTATCAACATTTTGCATTG 60.073 34.615 0.00 0.00 32.17 2.82
513 541 5.393962 GTCACTGATTGGTTTGCTATCAAC 58.606 41.667 0.00 0.00 30.75 3.18
517 545 3.010584 AGGGTCACTGATTGGTTTGCTAT 59.989 43.478 0.00 0.00 0.00 2.97
532 560 0.600255 CGTGAGTCCACAAGGGTCAC 60.600 60.000 0.00 0.00 43.34 3.67
561 589 3.708451 AGTAAGCAATTAACCAAGGGGG 58.292 45.455 0.00 0.00 44.81 5.40
573 601 5.110814 TGTACATGCCCTAAGTAAGCAAT 57.889 39.130 0.00 0.00 40.46 3.56
577 605 5.437060 ACCATTGTACATGCCCTAAGTAAG 58.563 41.667 0.00 0.00 0.00 2.34
579 607 5.190925 AGAACCATTGTACATGCCCTAAGTA 59.809 40.000 0.00 0.00 0.00 2.24
580 608 4.018415 AGAACCATTGTACATGCCCTAAGT 60.018 41.667 0.00 0.00 0.00 2.24
581 609 4.526970 AGAACCATTGTACATGCCCTAAG 58.473 43.478 0.00 0.00 0.00 2.18
606 634 5.617528 TTATCCTACGTGGCATTCCTAAA 57.382 39.130 0.00 0.00 35.26 1.85
611 639 5.700832 TCATCATTTATCCTACGTGGCATTC 59.299 40.000 0.00 0.00 35.26 2.67
619 647 5.468540 TCCACCTCATCATTTATCCTACG 57.531 43.478 0.00 0.00 0.00 3.51
620 648 5.544176 TCCTCCACCTCATCATTTATCCTAC 59.456 44.000 0.00 0.00 0.00 3.18
624 652 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
631 659 2.834549 TGTTTCTCTCCTCCACCTCATC 59.165 50.000 0.00 0.00 0.00 2.92
632 660 2.907892 TGTTTCTCTCCTCCACCTCAT 58.092 47.619 0.00 0.00 0.00 2.90
637 665 6.227298 TCTTATGATGTTTCTCTCCTCCAC 57.773 41.667 0.00 0.00 0.00 4.02
649 677 7.530426 AAGACAAGCCTTTTCTTATGATGTT 57.470 32.000 4.07 0.00 0.00 2.71
651 679 7.824672 AGAAAGACAAGCCTTTTCTTATGATG 58.175 34.615 6.30 0.00 36.58 3.07
663 691 3.492102 TGTGCTAAGAAAGACAAGCCT 57.508 42.857 0.00 0.00 33.99 4.58
664 692 4.773323 ATTGTGCTAAGAAAGACAAGCC 57.227 40.909 0.00 0.00 32.48 4.35
665 693 9.050601 AGATATATTGTGCTAAGAAAGACAAGC 57.949 33.333 0.00 0.00 32.48 4.01
668 696 9.534565 GTGAGATATATTGTGCTAAGAAAGACA 57.465 33.333 0.00 0.00 0.00 3.41
669 697 8.983724 GGTGAGATATATTGTGCTAAGAAAGAC 58.016 37.037 0.00 0.00 0.00 3.01
670 698 8.704668 TGGTGAGATATATTGTGCTAAGAAAGA 58.295 33.333 0.00 0.00 0.00 2.52
671 699 8.893219 TGGTGAGATATATTGTGCTAAGAAAG 57.107 34.615 0.00 0.00 0.00 2.62
706 762 9.936759 AGCCTTATCTTCAATAACTAGCTATTC 57.063 33.333 0.00 0.00 0.00 1.75
735 791 8.627208 AAAACATGTCTACAATGAGTCATCTT 57.373 30.769 5.98 0.00 0.00 2.40
777 833 6.306356 GCATTGTACTTAAACTCTTGCATGTG 59.694 38.462 0.00 0.00 0.00 3.21
810 866 8.710835 TCCGTTTGCTAAATCTTTTTCTTTTT 57.289 26.923 0.00 0.00 0.00 1.94
833 902 4.526650 TCCTAGGAATTTGCAAAAACCTCC 59.473 41.667 30.26 24.30 32.60 4.30
1324 1405 4.494484 GGCCGAGAAAATAAGTTGCAAAT 58.506 39.130 0.00 0.00 0.00 2.32
1353 1434 5.184287 TCCATGAACATGAAGTACGTCAGTA 59.816 40.000 16.54 2.51 41.20 2.74
1355 1436 4.494484 TCCATGAACATGAAGTACGTCAG 58.506 43.478 16.54 10.99 41.20 3.51
1365 1446 4.305539 ACACCTTCATCCATGAACATGA 57.694 40.909 15.21 0.00 41.51 3.07
1366 1447 4.577693 CCTACACCTTCATCCATGAACATG 59.422 45.833 7.70 7.70 41.51 3.21
1367 1448 4.385643 CCCTACACCTTCATCCATGAACAT 60.386 45.833 0.00 0.00 41.51 2.71
1368 1449 3.054434 CCCTACACCTTCATCCATGAACA 60.054 47.826 0.00 0.00 41.51 3.18
1369 1450 3.054361 ACCCTACACCTTCATCCATGAAC 60.054 47.826 0.00 0.00 41.51 3.18
1370 1451 3.054434 CACCCTACACCTTCATCCATGAA 60.054 47.826 0.00 2.07 43.94 2.57
1374 1455 1.906574 GACACCCTACACCTTCATCCA 59.093 52.381 0.00 0.00 0.00 3.41
1389 1470 2.218603 CCACCTACAACAGTTGACACC 58.781 52.381 20.56 0.00 0.00 4.16
1413 1494 3.820467 TGCCTGTAATTTTGGACTCACAG 59.180 43.478 0.00 0.00 34.54 3.66
1715 1880 1.001641 ATGGAGGCCAACTGCTGAC 60.002 57.895 5.01 0.00 36.95 3.51
1982 2173 2.883730 GTCATGAACGCGCCGCTA 60.884 61.111 5.73 0.00 0.00 4.26
1988 2179 3.309682 ACAATAGATTGGTCATGAACGCG 59.690 43.478 3.53 3.53 41.96 6.01
2029 2220 6.963083 ATAGTTAAGGTCGAGACTTGCTAT 57.037 37.500 11.47 13.73 0.00 2.97
2586 2778 7.394016 ACATAGACTGTTGACCAAATGATACA 58.606 34.615 0.00 0.00 32.90 2.29
2608 2800 6.919158 TCACTAACTACTACCATCCCTACAT 58.081 40.000 0.00 0.00 0.00 2.29
2722 2923 1.524393 TGCATGCATACAGCCTCCG 60.524 57.895 18.46 0.00 44.83 4.63
2724 2925 1.645455 CGTGCATGCATACAGCCTC 59.355 57.895 25.64 7.15 44.83 4.70
2725 2926 1.820906 CCGTGCATGCATACAGCCT 60.821 57.895 25.64 0.00 44.83 4.58
2726 2927 1.779025 CTCCGTGCATGCATACAGCC 61.779 60.000 25.64 8.75 44.83 4.85
2727 2928 1.091771 ACTCCGTGCATGCATACAGC 61.092 55.000 25.64 9.55 45.96 4.40
2728 2929 0.933097 GACTCCGTGCATGCATACAG 59.067 55.000 25.64 20.26 0.00 2.74
2729 2930 0.805711 CGACTCCGTGCATGCATACA 60.806 55.000 25.64 9.40 0.00 2.29
2730 2931 1.927210 CGACTCCGTGCATGCATAC 59.073 57.895 25.64 11.18 0.00 2.39
2731 2932 1.882625 GCGACTCCGTGCATGCATA 60.883 57.895 25.64 11.72 38.24 3.14
2732 2933 3.197790 GCGACTCCGTGCATGCAT 61.198 61.111 25.64 7.13 38.24 3.96
2785 2986 1.467920 CTTGAGGTTGATCTTGCCCC 58.532 55.000 0.00 0.00 0.00 5.80
2841 3042 9.653516 TTTTCTGCCCCTATATATGAATGAAAA 57.346 29.630 0.00 0.00 0.00 2.29
2895 3096 9.347934 CGCCACATTTACATTAGTTAATTTTCA 57.652 29.630 0.00 0.00 0.00 2.69
2909 3110 2.748251 CCGCCCGCCACATTTACA 60.748 61.111 0.00 0.00 0.00 2.41
3265 4078 0.916358 CTCCACTCCCCCTCCACATT 60.916 60.000 0.00 0.00 0.00 2.71
3452 4265 1.077828 TCTCTTCCCCTCTCTTCTGCA 59.922 52.381 0.00 0.00 0.00 4.41
3475 4288 3.134804 AGGACACTCCATATTTCCCTTCG 59.865 47.826 0.00 0.00 39.61 3.79
3569 4382 2.014068 GCAGAGTCGCCAATAAAGCCT 61.014 52.381 0.00 0.00 0.00 4.58
3637 4450 7.716799 ATAATGGAATGCTTTGTGTTCCTTA 57.283 32.000 5.14 2.74 41.52 2.69
3694 4508 6.323739 ACCAGCTTCCAGATTTTGTAAAAGAA 59.676 34.615 0.00 0.00 0.00 2.52
3800 4614 1.343142 TGTATGTGTGGCGTCTTGTCT 59.657 47.619 0.00 0.00 0.00 3.41
3830 4644 9.905713 AAAAATTAGAGTATAGATGCCTGTGAA 57.094 29.630 0.00 0.00 0.00 3.18
3936 4750 2.887568 GCTGCGACCGAGTGATGG 60.888 66.667 0.00 0.00 0.00 3.51
4023 4839 1.416401 GCGGGTAATCTGGATTCTGGA 59.584 52.381 0.00 0.00 32.50 3.86
4024 4840 1.140852 TGCGGGTAATCTGGATTCTGG 59.859 52.381 0.00 0.00 32.50 3.86
4025 4841 2.213499 GTGCGGGTAATCTGGATTCTG 58.787 52.381 0.00 0.00 32.50 3.02
4026 4842 1.141053 GGTGCGGGTAATCTGGATTCT 59.859 52.381 0.00 0.00 32.50 2.40
4027 4843 1.134220 TGGTGCGGGTAATCTGGATTC 60.134 52.381 0.00 0.00 32.50 2.52
4028 4844 0.916086 TGGTGCGGGTAATCTGGATT 59.084 50.000 1.40 1.40 34.93 3.01
4029 4845 0.469917 CTGGTGCGGGTAATCTGGAT 59.530 55.000 0.00 0.00 0.00 3.41
4075 4898 3.079578 GAGGTTGGGGCTTTGTTAGTAC 58.920 50.000 0.00 0.00 0.00 2.73
4567 5424 0.387929 ATATGGCGTCTGTGTACGGG 59.612 55.000 0.00 0.00 43.06 5.28
4699 5556 0.740868 GTTGCGATGGCTACTGCAGA 60.741 55.000 23.35 2.95 40.95 4.26
5475 7136 2.041755 AGGCCAGGAAAAGGACCTTTAG 59.958 50.000 19.86 10.08 33.32 1.85
5573 7234 1.359130 ACAAGGCAAGGGCTAAAGGAT 59.641 47.619 0.00 0.00 37.50 3.24
5748 7409 1.479709 TCTGTAGAGAAGCTCCCAGC 58.520 55.000 0.00 0.00 42.84 4.85
5852 7518 1.775385 CCAAGGAGACCCTCTCTCTC 58.225 60.000 0.00 0.00 44.63 3.20
5853 7519 0.325203 GCCAAGGAGACCCTCTCTCT 60.325 60.000 0.00 0.00 44.63 3.10
6144 7824 2.571212 CAACCAGAGTACCTTTGTGCA 58.429 47.619 0.00 0.00 0.00 4.57
6257 7937 2.420687 CCCAGTGAGCATAAAGGACCTC 60.421 54.545 0.00 0.00 0.00 3.85
6545 8761 3.839490 AGAGGAAGCTGGGAGATCATATG 59.161 47.826 0.00 0.00 0.00 1.78
6753 8971 1.917872 TGAAAACCAGTATGTGCCCC 58.082 50.000 0.00 0.00 0.00 5.80
6754 8972 4.535526 AATTGAAAACCAGTATGTGCCC 57.464 40.909 0.00 0.00 0.00 5.36
6810 9028 6.264292 ACACTATCAAAACCAGTATGTGCAAA 59.736 34.615 0.00 0.00 0.00 3.68
6886 9104 4.693095 GGAAGAAGATGGAACTGACAAGTC 59.307 45.833 0.00 0.00 34.77 3.01
6938 9156 1.587043 CGTTCGGCACAGGAGAGAGA 61.587 60.000 0.00 0.00 0.00 3.10
6940 9158 1.863662 GACGTTCGGCACAGGAGAGA 61.864 60.000 0.00 0.00 0.00 3.10
6941 9159 1.444553 GACGTTCGGCACAGGAGAG 60.445 63.158 0.00 0.00 0.00 3.20
6942 9160 2.649034 GACGTTCGGCACAGGAGA 59.351 61.111 0.00 0.00 0.00 3.71
6943 9161 2.805353 CGACGTTCGGCACAGGAG 60.805 66.667 0.00 0.00 36.00 3.69
6989 9207 4.035102 GAGGTGGGGGACTGTGGC 62.035 72.222 0.00 0.00 0.00 5.01
6990 9208 2.203998 AGAGGTGGGGGACTGTGG 60.204 66.667 0.00 0.00 0.00 4.17
6991 9209 2.650116 CGAGAGGTGGGGGACTGTG 61.650 68.421 0.00 0.00 0.00 3.66
6992 9210 2.283966 CGAGAGGTGGGGGACTGT 60.284 66.667 0.00 0.00 0.00 3.55
7021 9239 0.972471 TCGAGAAGGGATGCTGCAGA 60.972 55.000 20.43 2.70 0.00 4.26
7033 9251 1.807573 GGAGCTTGGCGTCGAGAAG 60.808 63.158 8.91 0.00 0.00 2.85
7083 9301 1.293963 TGAATCGCTGCACTGCTGTC 61.294 55.000 9.40 0.66 0.00 3.51
7133 9351 2.954684 CGTGAGGCCTGGGTGCTTA 61.955 63.158 12.00 0.00 0.00 3.09
7165 9383 2.978824 GACCCGGAGCTTGCTACA 59.021 61.111 0.73 0.00 0.00 2.74
7222 9440 2.016961 CGTGCATCCCATGTGCTAC 58.983 57.895 8.11 4.51 42.92 3.58
7290 9508 1.804151 CGGATCAGAACCTCGCAAAAA 59.196 47.619 0.00 0.00 0.00 1.94
7304 9522 2.549082 TGGGGTTAGGTTAACGGATCA 58.451 47.619 0.00 0.00 39.54 2.92
7495 9715 3.609853 TGAACGAATGAAGGATGAAGGG 58.390 45.455 0.00 0.00 0.00 3.95
7685 9905 3.062639 CAGATATTCAAGTCCGCACACAC 59.937 47.826 0.00 0.00 0.00 3.82
7739 9959 5.063312 TGCATTCACGCATATATCAATACGG 59.937 40.000 0.00 0.00 36.86 4.02
7741 9961 8.900511 ATTTGCATTCACGCATATATCAATAC 57.099 30.769 0.00 0.00 42.62 1.89
7908 10128 1.079057 GTCTTTCAGGGCGGACTCC 60.079 63.158 0.00 0.00 0.00 3.85
7921 10141 1.679898 CTTCCCCGGAGCAGTCTTT 59.320 57.895 0.73 0.00 0.00 2.52
7935 10155 1.205460 TTCCACCACCTAGGGCTTCC 61.205 60.000 14.81 0.00 43.89 3.46
8022 10242 1.084370 GCCTCGCTGCTTCGTACAAT 61.084 55.000 0.00 0.00 0.00 2.71
8082 10302 1.743252 CAGTCCTTGCGCTTCCTCC 60.743 63.158 9.73 0.00 0.00 4.30
8164 10384 5.342433 TGATGTGTTTCAGTTTGAAAGCAG 58.658 37.500 4.59 0.00 45.83 4.24
8244 10496 5.045872 AGAATGCAAGCAAAAAGAGAACAC 58.954 37.500 0.00 0.00 0.00 3.32
8321 10573 2.704596 GTCTAATTACCTCCTGACCCCC 59.295 54.545 0.00 0.00 0.00 5.40
8323 10575 4.654262 TCATGTCTAATTACCTCCTGACCC 59.346 45.833 0.00 0.00 0.00 4.46
8383 10637 1.404851 GGACAAGTAGGCAGCTCACTC 60.405 57.143 0.00 0.00 0.00 3.51
8385 10639 0.610687 AGGACAAGTAGGCAGCTCAC 59.389 55.000 0.00 0.00 0.00 3.51
8454 10708 3.624900 TCGCCGTATATCTCACGAAAAG 58.375 45.455 0.00 0.00 41.91 2.27
8462 10716 4.474113 CAACCTTACTCGCCGTATATCTC 58.526 47.826 0.00 0.00 0.00 2.75
8477 10731 5.529800 GCAGTAAAGTTCTTCACCAACCTTA 59.470 40.000 0.00 0.00 0.00 2.69
8521 10775 2.823829 GCGCTATTTGGCCCGTGAG 61.824 63.158 0.00 0.00 0.00 3.51
8588 10842 0.321653 AATCCTGCAGACCAACCGAC 60.322 55.000 17.39 0.00 0.00 4.79
8608 10862 4.333926 GCTCCTGATGACCTTGACATTTAC 59.666 45.833 0.00 0.00 0.00 2.01
8726 10980 7.548097 AGAGAAGTTTTTCTTTTCCTTTCACC 58.452 34.615 0.00 0.00 43.63 4.02
8920 11188 1.238439 GGTCATGGGCGTATCATTGG 58.762 55.000 0.00 0.00 0.00 3.16
8921 11189 1.965935 TGGTCATGGGCGTATCATTG 58.034 50.000 0.00 0.00 0.00 2.82
8922 11190 2.727123 TTGGTCATGGGCGTATCATT 57.273 45.000 0.00 0.00 0.00 2.57
8923 11191 2.373169 AGATTGGTCATGGGCGTATCAT 59.627 45.455 0.00 0.00 0.00 2.45
8924 11192 1.768275 AGATTGGTCATGGGCGTATCA 59.232 47.619 0.00 0.00 0.00 2.15
8925 11193 2.549754 CAAGATTGGTCATGGGCGTATC 59.450 50.000 0.00 0.00 0.00 2.24
8926 11194 2.575532 CAAGATTGGTCATGGGCGTAT 58.424 47.619 0.00 0.00 0.00 3.06
8927 11195 2.016604 GCAAGATTGGTCATGGGCGTA 61.017 52.381 0.00 0.00 0.00 4.42
8928 11196 1.315257 GCAAGATTGGTCATGGGCGT 61.315 55.000 0.00 0.00 0.00 5.68
8929 11197 1.314534 TGCAAGATTGGTCATGGGCG 61.315 55.000 0.00 0.00 0.00 6.13
8930 11198 0.174162 GTGCAAGATTGGTCATGGGC 59.826 55.000 0.00 0.00 0.00 5.36
8988 11257 2.028112 TCGCTTTAATGACAGCCTGAGT 60.028 45.455 0.00 0.00 31.82 3.41
9011 11285 4.499019 GGTTTCTTGTTGAAGCGAAATGGA 60.499 41.667 0.00 0.00 36.86 3.41
9069 11348 0.037975 CAACACGCGGGTAGTAGGTT 60.038 55.000 17.66 1.84 0.00 3.50
9073 11352 2.262292 GGCAACACGCGGGTAGTA 59.738 61.111 17.66 0.00 43.84 1.82
9074 11353 4.692475 GGGCAACACGCGGGTAGT 62.692 66.667 17.66 0.00 43.84 2.73
9083 11362 1.518903 GCAGAAGACTGGGGCAACAC 61.519 60.000 0.00 0.00 43.62 3.32
9084 11363 1.228245 GCAGAAGACTGGGGCAACA 60.228 57.895 0.00 0.00 43.62 3.33
9085 11364 3.673599 GCAGAAGACTGGGGCAAC 58.326 61.111 0.00 0.00 43.62 4.17
9091 11370 1.817099 GATGGGCGCAGAAGACTGG 60.817 63.158 10.83 0.00 43.62 4.00
9092 11371 1.088340 CAGATGGGCGCAGAAGACTG 61.088 60.000 10.83 6.94 45.91 3.51
9093 11372 1.220206 CAGATGGGCGCAGAAGACT 59.780 57.895 10.83 0.00 0.00 3.24
9094 11373 2.467826 GCAGATGGGCGCAGAAGAC 61.468 63.158 10.83 0.00 0.00 3.01
9095 11374 2.124983 GCAGATGGGCGCAGAAGA 60.125 61.111 10.83 0.00 0.00 2.87
9096 11375 3.207669 GGCAGATGGGCGCAGAAG 61.208 66.667 10.83 2.19 33.57 2.85
9103 11382 3.142838 ACGCAATGGCAGATGGGC 61.143 61.111 16.62 4.73 41.24 5.36
9104 11383 2.048023 ACACGCAATGGCAGATGGG 61.048 57.895 15.54 15.54 41.24 4.00
9105 11384 1.138036 CACACGCAATGGCAGATGG 59.862 57.895 0.00 0.00 41.24 3.51
9106 11385 1.138036 CCACACGCAATGGCAGATG 59.862 57.895 0.00 0.00 41.24 2.90
9107 11386 3.594568 CCACACGCAATGGCAGAT 58.405 55.556 0.00 0.00 41.24 2.90


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

AutoCloner maintained by Alex Coulton.