Multiple sequence alignment - TraesCS7D01G277200

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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 TraesCS7D01G277200 chr7D 100.000 4213 0 0 1 4213 265695119 265699331 0.000000e+00 7781.0
1 TraesCS7D01G277200 chr7D 93.227 812 29 4 1687 2472 534470986 534471797 0.000000e+00 1171.0
2 TraesCS7D01G277200 chr7D 92.737 179 12 1 3442 3620 312574119 312574296 1.500000e-64 257.0
3 TraesCS7D01G277200 chr5A 94.925 1005 24 5 1687 2665 483276604 483275601 0.000000e+00 1548.0
4 TraesCS7D01G277200 chr5A 92.655 177 12 1 3444 3620 367790248 367790073 1.940000e-63 254.0
5 TraesCS7D01G277200 chr6D 95.060 992 22 2 1700 2665 306494813 306495803 0.000000e+00 1535.0
6 TraesCS7D01G277200 chr6D 94.124 1004 31 3 1687 2664 396248527 396249528 0.000000e+00 1502.0
7 TraesCS7D01G277200 chr6D 91.304 184 14 2 3436 3619 458986343 458986162 2.510000e-62 250.0
8 TraesCS7D01G277200 chr6D 93.182 44 3 0 2744 2787 469794046 469794089 9.780000e-07 65.8
9 TraesCS7D01G277200 chr3D 95.040 988 22 2 1704 2665 357155625 357156611 0.000000e+00 1528.0
10 TraesCS7D01G277200 chr3D 94.538 1007 25 8 1687 2665 365531904 365530900 0.000000e+00 1528.0
11 TraesCS7D01G277200 chr3D 97.647 85 1 1 4129 4213 557724853 557724936 1.220000e-30 145.0
12 TraesCS7D01G277200 chr3D 84.127 63 5 5 2760 2820 562522875 562522934 5.880000e-04 56.5
13 TraesCS7D01G277200 chr4D 95.189 977 20 2 1715 2665 484346418 484345443 0.000000e+00 1519.0
14 TraesCS7D01G277200 chr4D 94.651 916 22 2 1775 2664 298239978 298240892 0.000000e+00 1395.0
15 TraesCS7D01G277200 chr4D 95.111 859 15 2 1833 2665 323563241 323564098 0.000000e+00 1328.0
16 TraesCS7D01G277200 chr4D 90.674 193 12 4 3451 3640 452901061 452900872 6.990000e-63 252.0
17 TraesCS7D01G277200 chr4D 92.571 175 13 0 3448 3622 457481048 457481222 6.990000e-63 252.0
18 TraesCS7D01G277200 chr1D 95.102 980 21 9 1712 2665 62127067 62126089 0.000000e+00 1519.0
19 TraesCS7D01G277200 chr1D 94.217 1003 32 5 1683 2659 105954632 105955634 0.000000e+00 1507.0
20 TraesCS7D01G277200 chr1D 89.583 192 16 3 3449 3639 1590362 1590550 1.510000e-59 241.0
21 TraesCS7D01G277200 chr1D 86.207 58 6 2 2763 2819 235570598 235570542 1.260000e-05 62.1
22 TraesCS7D01G277200 chr1D 94.872 39 2 0 2749 2787 348064348 348064386 1.260000e-05 62.1
23 TraesCS7D01G277200 chr2A 94.229 1005 31 9 1687 2665 90419670 90420673 0.000000e+00 1509.0
24 TraesCS7D01G277200 chr2A 94.643 168 9 0 3448 3615 570190646 570190479 1.160000e-65 261.0
25 TraesCS7D01G277200 chr2A 91.111 45 3 1 2747 2790 680521961 680522005 4.550000e-05 60.2
26 TraesCS7D01G277200 chr7B 93.757 913 26 6 757 1669 246001865 246002746 0.000000e+00 1341.0
27 TraesCS7D01G277200 chr7B 96.292 809 19 6 2665 3471 246002811 246003610 0.000000e+00 1317.0
28 TraesCS7D01G277200 chr7B 97.895 380 4 2 3742 4121 246004056 246004431 0.000000e+00 654.0
29 TraesCS7D01G277200 chr7B 92.814 334 22 2 220 553 246001321 246001652 2.280000e-132 483.0
30 TraesCS7D01G277200 chr7B 92.308 221 15 2 1 219 246000940 246001160 3.160000e-81 313.0
31 TraesCS7D01G277200 chr7B 94.118 85 4 1 4129 4213 107922925 107922842 1.230000e-25 128.0
32 TraesCS7D01G277200 chr7B 87.838 74 6 3 2746 2818 424155066 424154995 2.700000e-12 84.2
33 TraesCS7D01G277200 chr7A 93.122 916 23 19 754 1669 290915748 290916623 0.000000e+00 1306.0
34 TraesCS7D01G277200 chr7A 90.093 646 37 9 2814 3452 290917153 290917778 0.000000e+00 813.0
35 TraesCS7D01G277200 chr7A 92.664 259 18 1 249 507 290627779 290628036 5.140000e-99 372.0
36 TraesCS7D01G277200 chr7A 89.073 302 18 5 3830 4121 290918052 290918348 1.110000e-95 361.0
37 TraesCS7D01G277200 chr7A 88.627 255 17 5 1 251 290620350 290620596 2.460000e-77 300.0
38 TraesCS7D01G277200 chr7A 79.399 233 32 9 502 726 290629329 290629553 2.620000e-32 150.0
39 TraesCS7D01G277200 chr7A 96.471 85 2 1 4129 4213 365107601 365107684 5.680000e-29 139.0
40 TraesCS7D01G277200 chr7A 90.000 90 9 0 3615 3704 290917835 290917924 2.660000e-22 117.0
41 TraesCS7D01G277200 chr7A 87.778 90 4 5 2666 2748 290917067 290917156 9.640000e-17 99.0
42 TraesCS7D01G277200 chr7A 89.655 58 6 0 3613 3670 290917776 290917833 1.620000e-09 75.0
43 TraesCS7D01G277200 chr7A 94.286 35 2 0 2784 2818 81912875 81912909 2.000000e-03 54.7
44 TraesCS7D01G277200 chr6B 91.738 932 72 4 1736 2665 286815458 286816386 0.000000e+00 1290.0
45 TraesCS7D01G277200 chr6B 96.471 85 2 1 4129 4213 512465983 512466066 5.680000e-29 139.0
46 TraesCS7D01G277200 chr6B 89.362 47 4 1 2745 2790 514678472 514678518 1.640000e-04 58.4
47 TraesCS7D01G277200 chr6A 94.363 816 20 4 1693 2482 410901497 410902312 0.000000e+00 1229.0
48 TraesCS7D01G277200 chr2D 88.025 952 105 6 1714 2659 492575769 492574821 0.000000e+00 1118.0
49 TraesCS7D01G277200 chr2D 94.118 85 4 1 4129 4213 578202458 578202375 1.230000e-25 128.0
50 TraesCS7D01G277200 chr3B 98.162 544 10 0 1694 2237 398842370 398842913 0.000000e+00 950.0
51 TraesCS7D01G277200 chr3B 92.941 85 5 1 4129 4213 491378243 491378160 5.720000e-24 122.0
52 TraesCS7D01G277200 chr3B 100.000 29 0 0 2792 2820 310849011 310848983 2.000000e-03 54.7
53 TraesCS7D01G277200 chr3A 94.048 168 10 0 3451 3618 477708330 477708163 5.410000e-64 255.0
54 TraesCS7D01G277200 chrUn 90.761 184 16 1 3446 3629 407971352 407971170 1.170000e-60 244.0
55 TraesCS7D01G277200 chr1B 96.471 85 2 1 4129 4213 187709446 187709363 5.680000e-29 139.0
56 TraesCS7D01G277200 chr1B 93.333 45 2 1 2747 2790 662552779 662552735 9.780000e-07 65.8
57 TraesCS7D01G277200 chr4A 95.294 85 3 1 4129 4213 566298863 566298946 2.640000e-27 134.0
58 TraesCS7D01G277200 chr2B 95.294 85 3 1 4129 4213 275303494 275303577 2.640000e-27 134.0
59 TraesCS7D01G277200 chr2B 94.595 37 1 1 2792 2828 746033067 746033032 5.880000e-04 56.5
60 TraesCS7D01G277200 chr5D 100.000 29 0 0 2794 2822 330236709 330236737 2.000000e-03 54.7
61 TraesCS7D01G277200 chr5B 94.286 35 2 0 2784 2818 259544202 259544236 2.000000e-03 54.7


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 TraesCS7D01G277200 chr7D 265695119 265699331 4212 False 7781.000000 7781 100.0000 1 4213 1 chr7D.!!$F1 4212
1 TraesCS7D01G277200 chr7D 534470986 534471797 811 False 1171.000000 1171 93.2270 1687 2472 1 chr7D.!!$F3 785
2 TraesCS7D01G277200 chr5A 483275601 483276604 1003 True 1548.000000 1548 94.9250 1687 2665 1 chr5A.!!$R2 978
3 TraesCS7D01G277200 chr6D 306494813 306495803 990 False 1535.000000 1535 95.0600 1700 2665 1 chr6D.!!$F1 965
4 TraesCS7D01G277200 chr6D 396248527 396249528 1001 False 1502.000000 1502 94.1240 1687 2664 1 chr6D.!!$F2 977
5 TraesCS7D01G277200 chr3D 357155625 357156611 986 False 1528.000000 1528 95.0400 1704 2665 1 chr3D.!!$F1 961
6 TraesCS7D01G277200 chr3D 365530900 365531904 1004 True 1528.000000 1528 94.5380 1687 2665 1 chr3D.!!$R1 978
7 TraesCS7D01G277200 chr4D 484345443 484346418 975 True 1519.000000 1519 95.1890 1715 2665 1 chr4D.!!$R2 950
8 TraesCS7D01G277200 chr4D 298239978 298240892 914 False 1395.000000 1395 94.6510 1775 2664 1 chr4D.!!$F1 889
9 TraesCS7D01G277200 chr4D 323563241 323564098 857 False 1328.000000 1328 95.1110 1833 2665 1 chr4D.!!$F2 832
10 TraesCS7D01G277200 chr1D 62126089 62127067 978 True 1519.000000 1519 95.1020 1712 2665 1 chr1D.!!$R1 953
11 TraesCS7D01G277200 chr1D 105954632 105955634 1002 False 1507.000000 1507 94.2170 1683 2659 1 chr1D.!!$F2 976
12 TraesCS7D01G277200 chr2A 90419670 90420673 1003 False 1509.000000 1509 94.2290 1687 2665 1 chr2A.!!$F1 978
13 TraesCS7D01G277200 chr7B 246000940 246004431 3491 False 821.600000 1341 94.6132 1 4121 5 chr7B.!!$F1 4120
14 TraesCS7D01G277200 chr7A 290915748 290918348 2600 False 461.833333 1306 89.9535 754 4121 6 chr7A.!!$F5 3367
15 TraesCS7D01G277200 chr7A 290627779 290629553 1774 False 261.000000 372 86.0315 249 726 2 chr7A.!!$F4 477
16 TraesCS7D01G277200 chr6B 286815458 286816386 928 False 1290.000000 1290 91.7380 1736 2665 1 chr6B.!!$F1 929
17 TraesCS7D01G277200 chr6A 410901497 410902312 815 False 1229.000000 1229 94.3630 1693 2482 1 chr6A.!!$F1 789
18 TraesCS7D01G277200 chr2D 492574821 492575769 948 True 1118.000000 1118 88.0250 1714 2659 1 chr2D.!!$R1 945
19 TraesCS7D01G277200 chr3B 398842370 398842913 543 False 950.000000 950 98.1620 1694 2237 1 chr3B.!!$F1 543

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
561 724 0.034198 GAAAGCCCGGATCTCCTAGC 59.966 60.000 0.73 0.0 33.47 3.42 F
999 1227 0.247736 GCGGAGAAGAAGAAGAGGCA 59.752 55.000 0.00 0.0 0.00 4.75 F
1314 1600 1.672881 CACTCCGGAATTTCAGGCATC 59.327 52.381 5.23 0.0 31.46 3.91 F
3035 4513 1.477700 CATTTCATTGTGCCGGGTGAT 59.522 47.619 2.18 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2570 0.037303 CAGGCCTCCAGAAGCTTCAA 59.963 55.000 27.57 11.95 0.00 2.69 R
1964 2573 2.354343 GCAGGCCTCCAGAAGCTT 59.646 61.111 0.00 0.00 0.00 3.74 R
3173 4652 1.305718 AGGAGCTCCTTCGGCTTCT 60.306 57.895 30.40 4.26 46.09 2.85 R
4172 5883 0.031414 GTAACCCCAGCCTCCTAGGA 60.031 60.000 11.98 11.98 37.67 2.94 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
68 69 2.942376 TCATCATGTAATTGGACCGCAC 59.058 45.455 0.00 0.00 0.00 5.34
72 75 2.552599 TGTAATTGGACCGCACAGAA 57.447 45.000 0.00 0.00 0.00 3.02
94 97 3.584733 AAAAACCCTGCTCTCTTCACT 57.415 42.857 0.00 0.00 0.00 3.41
98 101 1.202330 CCCTGCTCTCTTCACTCCAT 58.798 55.000 0.00 0.00 0.00 3.41
99 102 1.134461 CCCTGCTCTCTTCACTCCATG 60.134 57.143 0.00 0.00 0.00 3.66
103 106 0.179936 CTCTCTTCACTCCATGCCCC 59.820 60.000 0.00 0.00 0.00 5.80
121 124 3.057245 GCCCCAAAAGTCATCAACTCTTC 60.057 47.826 0.00 0.00 37.17 2.87
123 126 4.144297 CCCAAAAGTCATCAACTCTTCCA 58.856 43.478 0.00 0.00 37.17 3.53
125 128 4.320788 CCAAAAGTCATCAACTCTTCCAGC 60.321 45.833 0.00 0.00 37.17 4.85
152 155 3.325135 ACGGGGGTCTTCAATATCTCATC 59.675 47.826 0.00 0.00 0.00 2.92
184 187 0.106268 AATGAACACCCTGCACACCA 60.106 50.000 0.00 0.00 0.00 4.17
304 467 1.609061 CGCGGGATCCAATTATGAGCT 60.609 52.381 15.23 0.00 0.00 4.09
334 497 0.463474 GCTCTCTCCTGTGCCAATCC 60.463 60.000 0.00 0.00 0.00 3.01
348 511 6.672593 TGTGCCAATCCTCCTAATAATTCTT 58.327 36.000 0.00 0.00 0.00 2.52
350 513 7.619302 TGTGCCAATCCTCCTAATAATTCTTTT 59.381 33.333 0.00 0.00 0.00 2.27
387 550 1.524355 CCATCAAGAATAGCGCGTCAG 59.476 52.381 8.43 0.00 0.00 3.51
465 628 7.621991 AGTATATCGACTTGAGAATTTTTGCG 58.378 34.615 0.00 0.00 0.00 4.85
473 636 0.321346 AGAATTTTTGCGCCAAGGGG 59.679 50.000 4.18 0.00 37.18 4.79
491 654 2.591715 AGTTGGTCCGTGCAGCAC 60.592 61.111 16.21 16.21 0.00 4.40
492 655 2.591715 GTTGGTCCGTGCAGCACT 60.592 61.111 23.15 0.00 31.34 4.40
522 685 1.613437 TGCCTAGAAAGCAAAGCCAAC 59.387 47.619 0.00 0.00 37.28 3.77
537 700 6.701400 GCAAAGCCAACTTAAAGATCTTCAAA 59.299 34.615 8.78 5.78 34.05 2.69
553 716 1.209504 TCAAATCTCGAAAGCCCGGAT 59.790 47.619 0.73 0.00 0.00 4.18
555 718 1.123928 AATCTCGAAAGCCCGGATCT 58.876 50.000 0.73 0.00 0.00 2.75
557 720 1.068250 CTCGAAAGCCCGGATCTCC 59.932 63.158 0.73 0.00 0.00 3.71
558 721 1.381327 TCGAAAGCCCGGATCTCCT 60.381 57.895 0.73 0.00 0.00 3.69
559 722 0.106369 TCGAAAGCCCGGATCTCCTA 60.106 55.000 0.73 0.00 0.00 2.94
560 723 0.315568 CGAAAGCCCGGATCTCCTAG 59.684 60.000 0.73 0.00 0.00 3.02
561 724 0.034198 GAAAGCCCGGATCTCCTAGC 59.966 60.000 0.73 0.00 33.47 3.42
562 725 0.399233 AAAGCCCGGATCTCCTAGCT 60.399 55.000 0.73 0.00 41.78 3.32
563 726 1.118356 AAGCCCGGATCTCCTAGCTG 61.118 60.000 0.73 0.00 40.47 4.24
564 727 1.834822 GCCCGGATCTCCTAGCTGT 60.835 63.158 0.73 0.00 0.00 4.40
565 728 0.539901 GCCCGGATCTCCTAGCTGTA 60.540 60.000 0.73 0.00 0.00 2.74
566 729 1.540267 CCCGGATCTCCTAGCTGTAG 58.460 60.000 0.73 0.00 0.00 2.74
567 730 1.074084 CCCGGATCTCCTAGCTGTAGA 59.926 57.143 0.73 0.00 0.00 2.59
568 731 2.489255 CCCGGATCTCCTAGCTGTAGAA 60.489 54.545 0.73 0.00 0.00 2.10
572 735 5.465935 CGGATCTCCTAGCTGTAGAAAATC 58.534 45.833 0.00 0.00 0.00 2.17
573 736 5.565834 CGGATCTCCTAGCTGTAGAAAATCC 60.566 48.000 0.00 5.23 0.00 3.01
574 737 5.542251 GGATCTCCTAGCTGTAGAAAATCCT 59.458 44.000 0.00 0.00 0.00 3.24
575 738 6.042666 GGATCTCCTAGCTGTAGAAAATCCTT 59.957 42.308 0.00 0.00 0.00 3.36
576 739 6.875972 TCTCCTAGCTGTAGAAAATCCTTT 57.124 37.500 0.00 0.00 0.00 3.11
577 740 7.973048 TCTCCTAGCTGTAGAAAATCCTTTA 57.027 36.000 0.00 0.00 0.00 1.85
578 741 7.783042 TCTCCTAGCTGTAGAAAATCCTTTAC 58.217 38.462 0.00 0.00 0.00 2.01
580 743 7.913789 TCCTAGCTGTAGAAAATCCTTTACAA 58.086 34.615 0.00 0.00 0.00 2.41
582 745 8.831550 CCTAGCTGTAGAAAATCCTTTACAATC 58.168 37.037 0.00 0.00 0.00 2.67
583 746 9.606631 CTAGCTGTAGAAAATCCTTTACAATCT 57.393 33.333 0.00 0.00 0.00 2.40
584 747 8.499403 AGCTGTAGAAAATCCTTTACAATCTC 57.501 34.615 0.00 0.00 0.00 2.75
585 748 8.325046 AGCTGTAGAAAATCCTTTACAATCTCT 58.675 33.333 0.00 0.00 0.00 3.10
586 749 9.601217 GCTGTAGAAAATCCTTTACAATCTCTA 57.399 33.333 0.00 0.00 0.00 2.43
588 751 9.601217 TGTAGAAAATCCTTTACAATCTCTAGC 57.399 33.333 0.00 0.00 0.00 3.42
589 752 9.047371 GTAGAAAATCCTTTACAATCTCTAGCC 57.953 37.037 0.00 0.00 0.00 3.93
590 753 7.633789 AGAAAATCCTTTACAATCTCTAGCCA 58.366 34.615 0.00 0.00 0.00 4.75
591 754 7.772757 AGAAAATCCTTTACAATCTCTAGCCAG 59.227 37.037 0.00 0.00 0.00 4.85
592 755 4.408182 TCCTTTACAATCTCTAGCCAGC 57.592 45.455 0.00 0.00 0.00 4.85
593 756 3.126831 CCTTTACAATCTCTAGCCAGCG 58.873 50.000 0.00 0.00 0.00 5.18
594 757 3.430929 CCTTTACAATCTCTAGCCAGCGT 60.431 47.826 0.00 0.00 0.00 5.07
595 758 3.438297 TTACAATCTCTAGCCAGCGTC 57.562 47.619 0.00 0.00 0.00 5.19
596 759 1.186200 ACAATCTCTAGCCAGCGTCA 58.814 50.000 0.00 0.00 0.00 4.35
597 760 1.134965 ACAATCTCTAGCCAGCGTCAC 60.135 52.381 0.00 0.00 0.00 3.67
598 761 0.461961 AATCTCTAGCCAGCGTCACC 59.538 55.000 0.00 0.00 0.00 4.02
599 762 1.395826 ATCTCTAGCCAGCGTCACCC 61.396 60.000 0.00 0.00 0.00 4.61
600 763 2.283604 TCTAGCCAGCGTCACCCA 60.284 61.111 0.00 0.00 0.00 4.51
601 764 2.185350 CTAGCCAGCGTCACCCAG 59.815 66.667 0.00 0.00 0.00 4.45
602 765 4.082523 TAGCCAGCGTCACCCAGC 62.083 66.667 0.00 0.00 0.00 4.85
605 768 2.594303 CCAGCGTCACCCAGCAAA 60.594 61.111 0.00 0.00 35.48 3.68
606 769 2.620112 CCAGCGTCACCCAGCAAAG 61.620 63.158 0.00 0.00 35.48 2.77
607 770 1.597854 CAGCGTCACCCAGCAAAGA 60.598 57.895 0.00 0.00 35.48 2.52
608 771 1.148273 AGCGTCACCCAGCAAAGAA 59.852 52.632 0.00 0.00 35.48 2.52
609 772 0.250901 AGCGTCACCCAGCAAAGAAT 60.251 50.000 0.00 0.00 35.48 2.40
610 773 1.003118 AGCGTCACCCAGCAAAGAATA 59.997 47.619 0.00 0.00 35.48 1.75
611 774 1.810151 GCGTCACCCAGCAAAGAATAA 59.190 47.619 0.00 0.00 0.00 1.40
612 775 2.414161 GCGTCACCCAGCAAAGAATAAC 60.414 50.000 0.00 0.00 0.00 1.89
613 776 2.811431 CGTCACCCAGCAAAGAATAACA 59.189 45.455 0.00 0.00 0.00 2.41
614 777 3.440173 CGTCACCCAGCAAAGAATAACAT 59.560 43.478 0.00 0.00 0.00 2.71
674 841 3.307480 CCCAACTGACGGTAGAAAATCCT 60.307 47.826 0.00 0.00 0.00 3.24
687 854 2.683211 AAATCCTTTGCTGGGTGACT 57.317 45.000 0.00 0.00 0.00 3.41
692 859 2.430332 TCCTTTGCTGGGTGACTTTTTG 59.570 45.455 0.00 0.00 0.00 2.44
693 860 2.483538 CCTTTGCTGGGTGACTTTTTGG 60.484 50.000 0.00 0.00 0.00 3.28
696 864 2.183679 TGCTGGGTGACTTTTTGGTTT 58.816 42.857 0.00 0.00 0.00 3.27
729 899 3.375647 TTTTTAGGGGATGCTGGGTAC 57.624 47.619 0.00 0.00 0.00 3.34
731 901 2.280308 TTAGGGGATGCTGGGTACTT 57.720 50.000 0.00 0.00 0.00 2.24
732 902 1.507140 TAGGGGATGCTGGGTACTTG 58.493 55.000 0.00 0.00 0.00 3.16
733 903 1.227383 GGGGATGCTGGGTACTTGG 59.773 63.158 0.00 0.00 0.00 3.61
735 905 0.623723 GGGATGCTGGGTACTTGGAA 59.376 55.000 0.00 0.00 0.00 3.53
737 907 2.358195 GGGATGCTGGGTACTTGGAATT 60.358 50.000 0.00 0.00 0.00 2.17
742 912 1.638589 CTGGGTACTTGGAATTGGGGA 59.361 52.381 0.00 0.00 0.00 4.81
743 913 2.042433 CTGGGTACTTGGAATTGGGGAA 59.958 50.000 0.00 0.00 0.00 3.97
744 914 2.225167 TGGGTACTTGGAATTGGGGAAC 60.225 50.000 0.00 0.00 0.00 3.62
745 915 2.089201 GGTACTTGGAATTGGGGAACG 58.911 52.381 0.00 0.00 0.00 3.95
746 916 1.471287 GTACTTGGAATTGGGGAACGC 59.529 52.381 0.00 0.00 43.69 4.84
811 1039 1.797211 CGAGGCCCGGTAGAGACATC 61.797 65.000 0.00 0.00 33.91 3.06
820 1048 2.366533 GGTAGAGACATCGTGACTCCA 58.633 52.381 11.46 0.06 39.41 3.86
821 1049 2.952978 GGTAGAGACATCGTGACTCCAT 59.047 50.000 11.46 1.61 39.41 3.41
822 1050 3.243234 GGTAGAGACATCGTGACTCCATG 60.243 52.174 11.46 0.00 39.41 3.66
824 1052 2.687425 AGAGACATCGTGACTCCATGAG 59.313 50.000 0.00 0.00 41.22 2.90
825 1053 2.685388 GAGACATCGTGACTCCATGAGA 59.315 50.000 0.00 0.00 41.22 3.27
901 1129 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
902 1130 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
903 1131 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
904 1132 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
905 1133 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
906 1134 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
907 1135 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
908 1136 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
909 1137 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
910 1138 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
911 1139 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
912 1140 3.312890 AGAGAGAGAGAGAGAGAGGGAG 58.687 54.545 0.00 0.00 0.00 4.30
913 1141 3.051803 AGAGAGAGAGAGAGAGAGGGAGA 60.052 52.174 0.00 0.00 0.00 3.71
914 1142 3.312890 AGAGAGAGAGAGAGAGGGAGAG 58.687 54.545 0.00 0.00 0.00 3.20
926 1154 0.413832 AGGGAGAGCAGTGTAGGGAA 59.586 55.000 0.00 0.00 0.00 3.97
999 1227 0.247736 GCGGAGAAGAAGAAGAGGCA 59.752 55.000 0.00 0.00 0.00 4.75
1035 1263 1.883021 CATCAACGGGAACAAGGGC 59.117 57.895 0.00 0.00 0.00 5.19
1314 1600 1.672881 CACTCCGGAATTTCAGGCATC 59.327 52.381 5.23 0.00 31.46 3.91
1460 1746 2.611971 GCCTACTTGTGAACCATCGACA 60.612 50.000 0.00 0.00 0.00 4.35
1613 1899 7.259290 ACATTGATAAGCGTATTGTAAAGGG 57.741 36.000 0.00 0.00 0.00 3.95
1615 1901 7.338449 ACATTGATAAGCGTATTGTAAAGGGTT 59.662 33.333 0.00 0.00 0.00 4.11
1743 2351 4.653801 ACAACAAAGCCTTTAGTCCCAAAT 59.346 37.500 0.00 0.00 0.00 2.32
1746 2354 6.987403 ACAAAGCCTTTAGTCCCAAATAAA 57.013 33.333 0.00 0.00 0.00 1.40
1817 2426 2.860009 CTCTGGCACATGGATAGCAAT 58.140 47.619 0.00 0.00 38.20 3.56
1915 2524 3.370527 CCATGTCAAATTCGGTCTACCCT 60.371 47.826 0.00 0.00 0.00 4.34
1964 2573 1.887242 GCCGTCCGCTATGCATTGA 60.887 57.895 12.54 0.00 0.00 2.57
2571 3762 7.130681 GGATATCTCCTTGTATATCCCTTGG 57.869 44.000 2.05 0.00 44.42 3.61
2718 4182 6.488344 TGCTGATTCTAGGATGTGACTAGTAG 59.512 42.308 0.00 0.00 39.13 2.57
2847 4318 1.687054 CCTGCCATGTGTGATGGGATT 60.687 52.381 0.00 0.00 38.84 3.01
2941 4418 3.821421 ATACCTTAGAACCAGCTTCGG 57.179 47.619 0.00 0.00 33.60 4.30
2963 4441 5.856455 CGGTCCATTCATTGTTTTGAAGTAC 59.144 40.000 0.00 0.00 38.90 2.73
3035 4513 1.477700 CATTTCATTGTGCCGGGTGAT 59.522 47.619 2.18 0.00 0.00 3.06
3048 4527 4.648762 TGCCGGGTGATTTTATGAATCATT 59.351 37.500 2.18 0.00 38.71 2.57
3173 4652 2.672996 GCTCGCAAGGCCAAGGAA 60.673 61.111 5.01 0.00 38.47 3.36
3311 4791 3.810623 ACCTAAACATTCTACCCTCCCA 58.189 45.455 0.00 0.00 0.00 4.37
3329 4810 2.816087 CCCAACTCCATGACTTGTTCTG 59.184 50.000 0.00 0.00 0.00 3.02
3331 4812 3.750130 CCAACTCCATGACTTGTTCTGAG 59.250 47.826 0.00 0.00 0.00 3.35
3507 5087 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
3548 5211 6.458232 ACTTTAGAGTGTAGATTCGCTCAT 57.542 37.500 9.37 0.00 44.43 2.90
3559 5222 0.516877 TTCGCTCATTTTGCTCCGTG 59.483 50.000 0.00 0.00 0.00 4.94
3579 5242 4.986034 CGTGTGTAGTCACTTGTTGGAATA 59.014 41.667 0.00 0.00 44.14 1.75
3580 5243 5.637810 CGTGTGTAGTCACTTGTTGGAATAT 59.362 40.000 0.00 0.00 44.14 1.28
3581 5244 6.183360 CGTGTGTAGTCACTTGTTGGAATATC 60.183 42.308 0.00 0.00 44.14 1.63
3582 5245 6.874134 GTGTGTAGTCACTTGTTGGAATATCT 59.126 38.462 0.00 0.00 44.14 1.98
3583 5246 6.873605 TGTGTAGTCACTTGTTGGAATATCTG 59.126 38.462 0.00 0.00 44.14 2.90
3584 5247 7.097192 GTGTAGTCACTTGTTGGAATATCTGA 58.903 38.462 0.00 0.00 40.98 3.27
3585 5248 7.602644 GTGTAGTCACTTGTTGGAATATCTGAA 59.397 37.037 0.00 0.00 40.98 3.02
3586 5249 8.154203 TGTAGTCACTTGTTGGAATATCTGAAA 58.846 33.333 0.00 0.00 0.00 2.69
3587 5250 8.999431 GTAGTCACTTGTTGGAATATCTGAAAA 58.001 33.333 0.00 0.00 0.00 2.29
3619 5282 7.912056 ATTTAAAAACGGAGGGAGTAGTAAC 57.088 36.000 0.00 0.00 0.00 2.50
3631 5294 4.816925 GGGAGTAGTAACTTCATGGCATTC 59.183 45.833 0.00 0.00 35.56 2.67
3638 5301 3.083122 ACTTCATGGCATTCTTCTGCT 57.917 42.857 0.00 0.00 41.95 4.24
3639 5302 3.015327 ACTTCATGGCATTCTTCTGCTC 58.985 45.455 0.00 0.00 41.95 4.26
3640 5303 2.793288 TCATGGCATTCTTCTGCTCA 57.207 45.000 0.00 0.00 41.95 4.26
3645 5308 3.489355 TGGCATTCTTCTGCTCAAGAAA 58.511 40.909 12.76 0.00 44.38 2.52
3676 5339 6.016693 ACACGATGGTTCAATACAATTCACAA 60.017 34.615 0.00 0.00 0.00 3.33
3704 5367 6.298853 CGCTTTTCTTTTAATTGATTGGCAC 58.701 36.000 0.00 0.00 0.00 5.01
3762 5463 2.385803 TGTTCGGATTCTACCTCCTCC 58.614 52.381 0.00 0.00 0.00 4.30
3763 5464 2.024273 TGTTCGGATTCTACCTCCTCCT 60.024 50.000 0.00 0.00 0.00 3.69
3764 5465 2.624364 GTTCGGATTCTACCTCCTCCTC 59.376 54.545 0.00 0.00 0.00 3.71
3765 5466 1.850998 TCGGATTCTACCTCCTCCTCA 59.149 52.381 0.00 0.00 0.00 3.86
3766 5467 1.957877 CGGATTCTACCTCCTCCTCAC 59.042 57.143 0.00 0.00 0.00 3.51
3770 5471 2.125773 TCTACCTCCTCCTCACGAAC 57.874 55.000 0.00 0.00 0.00 3.95
4145 5856 9.804547 TTTTATTTTATCTTTGCGTTTCATTGC 57.195 25.926 0.00 0.00 0.00 3.56
4146 5857 8.526218 TTATTTTATCTTTGCGTTTCATTGCA 57.474 26.923 0.00 0.00 39.81 4.08
4147 5858 7.599630 ATTTTATCTTTGCGTTTCATTGCAT 57.400 28.000 0.00 0.00 41.42 3.96
4148 5859 7.418840 TTTTATCTTTGCGTTTCATTGCATT 57.581 28.000 0.00 0.00 41.42 3.56
4149 5860 4.914312 ATCTTTGCGTTTCATTGCATTG 57.086 36.364 2.08 2.08 41.42 2.82
4150 5861 3.974912 TCTTTGCGTTTCATTGCATTGA 58.025 36.364 7.19 7.19 41.42 2.57
4151 5862 4.366586 TCTTTGCGTTTCATTGCATTGAA 58.633 34.783 17.74 17.74 41.42 2.69
4152 5863 4.445052 TCTTTGCGTTTCATTGCATTGAAG 59.555 37.500 19.96 12.92 41.42 3.02
4153 5864 3.639716 TGCGTTTCATTGCATTGAAGA 57.360 38.095 19.96 11.24 36.97 2.87
4154 5865 3.567530 TGCGTTTCATTGCATTGAAGAG 58.432 40.909 19.96 18.18 36.97 2.85
4155 5866 3.252944 TGCGTTTCATTGCATTGAAGAGA 59.747 39.130 19.96 7.02 36.97 3.10
4156 5867 4.229096 GCGTTTCATTGCATTGAAGAGAA 58.771 39.130 19.96 6.71 36.97 2.87
4157 5868 4.322804 GCGTTTCATTGCATTGAAGAGAAG 59.677 41.667 19.96 11.61 36.97 2.85
4158 5869 4.855388 CGTTTCATTGCATTGAAGAGAAGG 59.145 41.667 19.96 10.22 36.97 3.46
4159 5870 5.166398 GTTTCATTGCATTGAAGAGAAGGG 58.834 41.667 19.96 0.00 36.97 3.95
4160 5871 4.305539 TCATTGCATTGAAGAGAAGGGA 57.694 40.909 8.80 0.00 0.00 4.20
4161 5872 4.863548 TCATTGCATTGAAGAGAAGGGAT 58.136 39.130 8.80 0.00 0.00 3.85
4162 5873 6.005066 TCATTGCATTGAAGAGAAGGGATA 57.995 37.500 8.80 0.00 0.00 2.59
4163 5874 6.060136 TCATTGCATTGAAGAGAAGGGATAG 58.940 40.000 8.80 0.00 0.00 2.08
4164 5875 5.441718 TTGCATTGAAGAGAAGGGATAGT 57.558 39.130 0.00 0.00 0.00 2.12
4165 5876 6.560003 TTGCATTGAAGAGAAGGGATAGTA 57.440 37.500 0.00 0.00 0.00 1.82
4166 5877 5.918608 TGCATTGAAGAGAAGGGATAGTAC 58.081 41.667 0.00 0.00 0.00 2.73
4167 5878 5.425217 TGCATTGAAGAGAAGGGATAGTACA 59.575 40.000 0.00 0.00 0.00 2.90
4168 5879 6.100279 TGCATTGAAGAGAAGGGATAGTACAT 59.900 38.462 0.00 0.00 0.00 2.29
4169 5880 6.995091 GCATTGAAGAGAAGGGATAGTACATT 59.005 38.462 0.00 0.00 0.00 2.71
4170 5881 7.172361 GCATTGAAGAGAAGGGATAGTACATTC 59.828 40.741 0.00 0.00 0.00 2.67
4171 5882 6.732896 TGAAGAGAAGGGATAGTACATTCC 57.267 41.667 5.72 5.72 0.00 3.01
4172 5883 6.444704 TGAAGAGAAGGGATAGTACATTCCT 58.555 40.000 12.33 6.67 32.34 3.36
4173 5884 6.551601 TGAAGAGAAGGGATAGTACATTCCTC 59.448 42.308 12.33 5.16 32.34 3.71
4174 5885 5.399113 AGAGAAGGGATAGTACATTCCTCC 58.601 45.833 12.33 0.00 32.34 4.30
4175 5886 5.137082 AGAGAAGGGATAGTACATTCCTCCT 59.863 44.000 12.33 3.28 32.34 3.69
4176 5887 6.335850 AGAGAAGGGATAGTACATTCCTCCTA 59.664 42.308 12.33 0.00 32.34 2.94
4177 5888 6.557568 AGAAGGGATAGTACATTCCTCCTAG 58.442 44.000 12.33 0.00 32.34 3.02
4178 5889 5.278127 AGGGATAGTACATTCCTCCTAGG 57.722 47.826 0.82 0.82 36.46 3.02
4179 5890 4.926987 AGGGATAGTACATTCCTCCTAGGA 59.073 45.833 11.98 11.98 44.10 2.94
4180 5891 5.015817 AGGGATAGTACATTCCTCCTAGGAG 59.984 48.000 29.27 29.27 46.73 3.69
4188 5899 2.699496 CTCCTAGGAGGCTGGGGT 59.301 66.667 28.68 0.00 38.51 4.95
4189 5900 1.003573 CTCCTAGGAGGCTGGGGTT 59.996 63.158 28.68 0.00 38.51 4.11
4190 5901 0.264955 CTCCTAGGAGGCTGGGGTTA 59.735 60.000 28.68 0.00 38.51 2.85
4191 5902 0.031414 TCCTAGGAGGCTGGGGTTAC 60.031 60.000 7.62 0.00 34.61 2.50
4192 5903 0.326238 CCTAGGAGGCTGGGGTTACA 60.326 60.000 1.05 0.00 0.00 2.41
4193 5904 1.580059 CTAGGAGGCTGGGGTTACAA 58.420 55.000 0.00 0.00 0.00 2.41
4194 5905 1.913419 CTAGGAGGCTGGGGTTACAAA 59.087 52.381 0.00 0.00 0.00 2.83
4195 5906 1.154430 AGGAGGCTGGGGTTACAAAA 58.846 50.000 0.00 0.00 0.00 2.44
4196 5907 1.075536 AGGAGGCTGGGGTTACAAAAG 59.924 52.381 0.00 0.00 0.00 2.27
4197 5908 1.074889 GGAGGCTGGGGTTACAAAAGA 59.925 52.381 0.00 0.00 0.00 2.52
4198 5909 2.291605 GGAGGCTGGGGTTACAAAAGAT 60.292 50.000 0.00 0.00 0.00 2.40
4199 5910 3.431415 GAGGCTGGGGTTACAAAAGATT 58.569 45.455 0.00 0.00 0.00 2.40
4200 5911 3.165071 AGGCTGGGGTTACAAAAGATTG 58.835 45.455 0.00 0.00 42.46 2.67
4212 5923 4.934075 CAAAAGATTGTGCTCTCGATCA 57.066 40.909 0.00 0.00 32.34 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.942376 GTGCGGTCCAATTACATGATGA 59.058 45.455 0.00 0.00 0.00 2.92
51 52 2.355197 TCTGTGCGGTCCAATTACATG 58.645 47.619 0.00 0.00 0.00 3.21
82 85 0.251354 GGCATGGAGTGAAGAGAGCA 59.749 55.000 0.00 0.00 0.00 4.26
94 97 1.076841 TGATGACTTTTGGGGCATGGA 59.923 47.619 0.00 0.00 0.00 3.41
98 101 2.158475 AGAGTTGATGACTTTTGGGGCA 60.158 45.455 0.00 0.00 39.19 5.36
99 102 2.519013 AGAGTTGATGACTTTTGGGGC 58.481 47.619 0.00 0.00 39.19 5.80
103 106 4.612259 CGCTGGAAGAGTTGATGACTTTTG 60.612 45.833 0.00 0.00 39.19 2.44
125 128 3.702284 TATTGAAGACCCCCGTGTGCG 62.702 57.143 0.00 0.00 37.95 5.34
152 155 3.367703 GGTGTTCATTCCCTTTGATGCTG 60.368 47.826 0.00 0.00 0.00 4.41
184 187 4.898607 TTTTTGGCGTGAGGAGCT 57.101 50.000 0.00 0.00 34.52 4.09
304 467 6.095440 GGCACAGGAGAGAGCAAAAATATTTA 59.905 38.462 0.01 0.00 0.00 1.40
348 511 6.764379 TGATGGACGTGATATTATGGCTAAA 58.236 36.000 0.00 0.00 0.00 1.85
350 513 5.993748 TGATGGACGTGATATTATGGCTA 57.006 39.130 0.00 0.00 0.00 3.93
387 550 1.271271 GGGCCTCATCCATCACAGATC 60.271 57.143 0.84 0.00 0.00 2.75
465 628 2.035783 GGACCAACTCCCCTTGGC 59.964 66.667 0.00 0.00 44.19 4.52
473 636 2.280797 TGCTGCACGGACCAACTC 60.281 61.111 0.00 0.00 0.00 3.01
491 654 5.431765 TGCTTTCTAGGCAATCCTTAAGAG 58.568 41.667 3.36 0.00 40.66 2.85
492 655 5.435686 TGCTTTCTAGGCAATCCTTAAGA 57.564 39.130 3.36 0.00 40.66 2.10
507 670 5.852282 TCTTTAAGTTGGCTTTGCTTTCT 57.148 34.783 0.00 0.00 36.22 2.52
522 685 7.907563 GGCTTTCGAGATTTGAAGATCTTTAAG 59.092 37.037 9.87 0.00 36.54 1.85
537 700 0.676736 GAGATCCGGGCTTTCGAGAT 59.323 55.000 0.00 0.00 0.00 2.75
553 716 6.875972 AAAGGATTTTCTACAGCTAGGAGA 57.124 37.500 0.00 0.00 31.62 3.71
555 718 7.490657 TGTAAAGGATTTTCTACAGCTAGGA 57.509 36.000 0.00 0.00 40.09 2.94
557 720 9.606631 AGATTGTAAAGGATTTTCTACAGCTAG 57.393 33.333 0.00 0.00 40.09 3.42
558 721 9.601217 GAGATTGTAAAGGATTTTCTACAGCTA 57.399 33.333 0.00 0.00 40.09 3.32
559 722 8.325046 AGAGATTGTAAAGGATTTTCTACAGCT 58.675 33.333 0.00 0.00 40.09 4.24
560 723 8.499403 AGAGATTGTAAAGGATTTTCTACAGC 57.501 34.615 0.00 0.00 40.09 4.40
562 725 9.601217 GCTAGAGATTGTAAAGGATTTTCTACA 57.399 33.333 0.00 0.00 40.09 2.74
563 726 9.047371 GGCTAGAGATTGTAAAGGATTTTCTAC 57.953 37.037 0.00 0.00 40.09 2.59
564 727 8.768397 TGGCTAGAGATTGTAAAGGATTTTCTA 58.232 33.333 0.00 0.00 40.09 2.10
565 728 7.633789 TGGCTAGAGATTGTAAAGGATTTTCT 58.366 34.615 0.00 0.00 40.09 2.52
566 729 7.467947 GCTGGCTAGAGATTGTAAAGGATTTTC 60.468 40.741 0.00 0.00 40.09 2.29
567 730 6.319911 GCTGGCTAGAGATTGTAAAGGATTTT 59.680 38.462 0.00 0.00 40.09 1.82
568 731 5.825151 GCTGGCTAGAGATTGTAAAGGATTT 59.175 40.000 0.00 0.00 43.42 2.17
572 735 3.126831 CGCTGGCTAGAGATTGTAAAGG 58.873 50.000 0.00 0.00 0.00 3.11
573 736 3.786635 ACGCTGGCTAGAGATTGTAAAG 58.213 45.455 8.02 0.00 0.00 1.85
574 737 3.194755 TGACGCTGGCTAGAGATTGTAAA 59.805 43.478 8.02 0.00 0.00 2.01
575 738 2.758423 TGACGCTGGCTAGAGATTGTAA 59.242 45.455 8.02 0.00 0.00 2.41
576 739 2.099263 GTGACGCTGGCTAGAGATTGTA 59.901 50.000 8.02 0.00 0.00 2.41
577 740 1.134965 GTGACGCTGGCTAGAGATTGT 60.135 52.381 8.02 0.00 0.00 2.71
578 741 1.565305 GTGACGCTGGCTAGAGATTG 58.435 55.000 8.02 0.00 0.00 2.67
580 743 1.395826 GGGTGACGCTGGCTAGAGAT 61.396 60.000 8.02 0.00 0.00 2.75
582 745 2.290122 CTGGGTGACGCTGGCTAGAG 62.290 65.000 0.00 0.00 0.00 2.43
583 746 2.283604 TGGGTGACGCTGGCTAGA 60.284 61.111 0.00 0.00 0.00 2.43
584 747 2.185350 CTGGGTGACGCTGGCTAG 59.815 66.667 0.31 0.00 0.00 3.42
585 748 4.082523 GCTGGGTGACGCTGGCTA 62.083 66.667 8.47 0.00 0.00 3.93
588 751 2.594303 TTTGCTGGGTGACGCTGG 60.594 61.111 8.47 0.00 0.00 4.85
589 752 1.165907 TTCTTTGCTGGGTGACGCTG 61.166 55.000 0.31 1.33 0.00 5.18
590 753 0.250901 ATTCTTTGCTGGGTGACGCT 60.251 50.000 0.31 0.00 0.00 5.07
591 754 1.448985 TATTCTTTGCTGGGTGACGC 58.551 50.000 0.00 0.00 0.00 5.19
592 755 2.811431 TGTTATTCTTTGCTGGGTGACG 59.189 45.455 0.00 0.00 0.00 4.35
593 756 4.702131 AGATGTTATTCTTTGCTGGGTGAC 59.298 41.667 0.00 0.00 0.00 3.67
594 757 4.922206 AGATGTTATTCTTTGCTGGGTGA 58.078 39.130 0.00 0.00 0.00 4.02
595 758 4.701651 TGAGATGTTATTCTTTGCTGGGTG 59.298 41.667 0.00 0.00 0.00 4.61
596 759 4.922206 TGAGATGTTATTCTTTGCTGGGT 58.078 39.130 0.00 0.00 0.00 4.51
597 760 5.649395 TCTTGAGATGTTATTCTTTGCTGGG 59.351 40.000 0.00 0.00 0.00 4.45
598 761 6.149973 TGTCTTGAGATGTTATTCTTTGCTGG 59.850 38.462 0.00 0.00 0.00 4.85
599 762 7.020010 GTGTCTTGAGATGTTATTCTTTGCTG 58.980 38.462 0.00 0.00 0.00 4.41
600 763 6.150140 GGTGTCTTGAGATGTTATTCTTTGCT 59.850 38.462 0.00 0.00 0.00 3.91
601 764 6.150140 AGGTGTCTTGAGATGTTATTCTTTGC 59.850 38.462 0.00 0.00 0.00 3.68
602 765 7.678947 AGGTGTCTTGAGATGTTATTCTTTG 57.321 36.000 0.00 0.00 0.00 2.77
603 766 8.697507 AAAGGTGTCTTGAGATGTTATTCTTT 57.302 30.769 0.00 0.00 32.75 2.52
604 767 8.697507 AAAAGGTGTCTTGAGATGTTATTCTT 57.302 30.769 0.00 0.00 32.75 2.52
605 768 8.697507 AAAAAGGTGTCTTGAGATGTTATTCT 57.302 30.769 0.00 0.00 32.75 2.40
632 795 5.305585 TGGGTGTCTTGAGAGATTGTAAAC 58.694 41.667 0.00 0.00 33.70 2.01
635 798 4.593206 AGTTGGGTGTCTTGAGAGATTGTA 59.407 41.667 0.00 0.00 33.70 2.41
645 808 0.179056 ACCGTCAGTTGGGTGTCTTG 60.179 55.000 0.00 0.00 34.58 3.02
674 841 2.183679 ACCAAAAAGTCACCCAGCAAA 58.816 42.857 0.00 0.00 0.00 3.68
687 854 4.846168 AAAGCAACCCCTAAACCAAAAA 57.154 36.364 0.00 0.00 0.00 1.94
716 886 0.623723 TTCCAAGTACCCAGCATCCC 59.376 55.000 0.00 0.00 0.00 3.85
728 898 1.241315 CGCGTTCCCCAATTCCAAGT 61.241 55.000 0.00 0.00 0.00 3.16
729 899 0.958382 TCGCGTTCCCCAATTCCAAG 60.958 55.000 5.77 0.00 0.00 3.61
731 901 1.376683 CTCGCGTTCCCCAATTCCA 60.377 57.895 5.77 0.00 0.00 3.53
732 902 2.112815 CCTCGCGTTCCCCAATTCC 61.113 63.158 5.77 0.00 0.00 3.01
733 903 2.761195 GCCTCGCGTTCCCCAATTC 61.761 63.158 5.77 0.00 0.00 2.17
735 905 4.796495 GGCCTCGCGTTCCCCAAT 62.796 66.667 5.77 0.00 0.00 3.16
744 914 3.177194 TATCCCCAATGGCCTCGCG 62.177 63.158 3.32 0.00 0.00 5.87
745 915 1.600916 GTATCCCCAATGGCCTCGC 60.601 63.158 3.32 0.00 0.00 5.03
746 916 1.073199 GGTATCCCCAATGGCCTCG 59.927 63.158 3.32 0.00 0.00 4.63
811 1039 1.680522 CCCCCTCTCATGGAGTCACG 61.681 65.000 9.47 0.00 40.30 4.35
827 1055 2.593420 CCCACGTACCATTCCCCC 59.407 66.667 0.00 0.00 0.00 5.40
901 1129 0.704076 ACACTGCTCTCCCTCTCTCT 59.296 55.000 0.00 0.00 0.00 3.10
902 1130 2.297701 CTACACTGCTCTCCCTCTCTC 58.702 57.143 0.00 0.00 0.00 3.20
903 1131 1.064017 CCTACACTGCTCTCCCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
904 1132 1.398692 CCTACACTGCTCTCCCTCTC 58.601 60.000 0.00 0.00 0.00 3.20
905 1133 0.032615 CCCTACACTGCTCTCCCTCT 60.033 60.000 0.00 0.00 0.00 3.69
906 1134 0.033011 TCCCTACACTGCTCTCCCTC 60.033 60.000 0.00 0.00 0.00 4.30
907 1135 0.413832 TTCCCTACACTGCTCTCCCT 59.586 55.000 0.00 0.00 0.00 4.20
908 1136 1.276622 TTTCCCTACACTGCTCTCCC 58.723 55.000 0.00 0.00 0.00 4.30
909 1137 2.482142 CGATTTCCCTACACTGCTCTCC 60.482 54.545 0.00 0.00 0.00 3.71
910 1138 2.166664 ACGATTTCCCTACACTGCTCTC 59.833 50.000 0.00 0.00 0.00 3.20
911 1139 2.093973 CACGATTTCCCTACACTGCTCT 60.094 50.000 0.00 0.00 0.00 4.09
912 1140 2.094182 TCACGATTTCCCTACACTGCTC 60.094 50.000 0.00 0.00 0.00 4.26
913 1141 1.899814 TCACGATTTCCCTACACTGCT 59.100 47.619 0.00 0.00 0.00 4.24
914 1142 2.000447 GTCACGATTTCCCTACACTGC 59.000 52.381 0.00 0.00 0.00 4.40
926 1154 1.183030 TCCGGTGGTCAGTCACGATT 61.183 55.000 0.00 0.00 38.46 3.34
1035 1263 1.153823 CCAGAAGTCGTAGCACCGG 60.154 63.158 0.00 0.00 0.00 5.28
1314 1600 1.738099 CTGCCACGAAAGACCGGAG 60.738 63.158 9.46 0.00 0.00 4.63
1460 1746 4.926238 GGCTACATCGAATCGATTCAGAAT 59.074 41.667 31.57 22.57 44.59 2.40
1591 1877 7.338449 ACAACCCTTTACAATACGCTTATCAAT 59.662 33.333 0.00 0.00 0.00 2.57
1613 1899 4.610680 GCACAAAAGACTCCGATACACAAC 60.611 45.833 0.00 0.00 0.00 3.32
1615 1901 3.064207 GCACAAAAGACTCCGATACACA 58.936 45.455 0.00 0.00 0.00 3.72
1743 2351 3.714798 CACCTCTAGCCTACCCCAATTTA 59.285 47.826 0.00 0.00 0.00 1.40
1746 2354 1.294068 TCACCTCTAGCCTACCCCAAT 59.706 52.381 0.00 0.00 0.00 3.16
1817 2426 1.685224 GACAGGGGTGCATGGAAGA 59.315 57.895 0.00 0.00 0.00 2.87
1915 2524 1.556911 GGAGAATGTCAAGAGAGGGCA 59.443 52.381 0.00 0.00 0.00 5.36
1961 2570 0.037303 CAGGCCTCCAGAAGCTTCAA 59.963 55.000 27.57 11.95 0.00 2.69
1964 2573 2.354343 GCAGGCCTCCAGAAGCTT 59.646 61.111 0.00 0.00 0.00 3.74
2868 4345 7.230712 GGAATCGGTGTATTATCCCTTTGAAAT 59.769 37.037 0.00 0.00 0.00 2.17
2941 4418 8.871686 AAAGTACTTCAAAACAATGAATGGAC 57.128 30.769 8.95 0.00 38.55 4.02
2963 4441 4.985409 GTCATCTTATCTAGCACCCGAAAG 59.015 45.833 0.00 0.00 0.00 2.62
3048 4527 5.961272 TCACGATTTCACTATCAGCTTACA 58.039 37.500 0.00 0.00 0.00 2.41
3173 4652 1.305718 AGGAGCTCCTTCGGCTTCT 60.306 57.895 30.40 4.26 46.09 2.85
3311 4791 4.802248 GCTCTCAGAACAAGTCATGGAGTT 60.802 45.833 0.00 0.00 0.00 3.01
3329 4810 5.688176 GGTAGTTTATCGAACTCATGCTCTC 59.312 44.000 0.00 0.00 45.40 3.20
3331 4812 5.593010 AGGTAGTTTATCGAACTCATGCTC 58.407 41.667 0.00 0.00 45.40 4.26
3490 5070 5.584649 ACATCCGTATGTTGTAGTCCATTTG 59.415 40.000 0.00 0.00 44.07 2.32
3548 5211 2.206750 GTGACTACACACGGAGCAAAA 58.793 47.619 0.00 0.00 45.32 2.44
3559 5222 7.097192 TCAGATATTCCAACAAGTGACTACAC 58.903 38.462 0.00 0.00 46.24 2.90
3585 5248 9.743581 TCCCTCCGTTTTTAAATATAAGTCTTT 57.256 29.630 0.00 0.00 0.00 2.52
3586 5249 9.392259 CTCCCTCCGTTTTTAAATATAAGTCTT 57.608 33.333 0.00 0.00 0.00 3.01
3587 5250 8.546322 ACTCCCTCCGTTTTTAAATATAAGTCT 58.454 33.333 0.00 0.00 0.00 3.24
3596 5259 7.066307 AGTTACTACTCCCTCCGTTTTTAAA 57.934 36.000 0.00 0.00 0.00 1.52
3600 5263 4.590222 TGAAGTTACTACTCCCTCCGTTTT 59.410 41.667 0.00 0.00 31.99 2.43
3610 5273 7.010923 CAGAAGAATGCCATGAAGTTACTACTC 59.989 40.741 0.00 0.00 31.99 2.59
3638 5301 2.807967 CCATCGTGTTGCTCTTTCTTGA 59.192 45.455 0.00 0.00 0.00 3.02
3639 5302 2.549754 ACCATCGTGTTGCTCTTTCTTG 59.450 45.455 0.00 0.00 0.00 3.02
3640 5303 2.851195 ACCATCGTGTTGCTCTTTCTT 58.149 42.857 0.00 0.00 0.00 2.52
3645 5308 2.254546 TTGAACCATCGTGTTGCTCT 57.745 45.000 0.00 0.00 0.00 4.09
3676 5339 7.010460 GCCAATCAATTAAAAGAAAAGCGCTAT 59.990 33.333 12.05 1.76 0.00 2.97
3725 5388 2.664402 ACAACTGAAGACAAGCCCAT 57.336 45.000 0.00 0.00 0.00 4.00
3788 5489 9.794685 GAAATCTTCCATTTTCCAATCTTAGTC 57.205 33.333 0.00 0.00 0.00 2.59
4121 5832 8.526218 TGCAATGAAACGCAAAGATAAAATAA 57.474 26.923 0.00 0.00 34.59 1.40
4122 5833 8.700722 ATGCAATGAAACGCAAAGATAAAATA 57.299 26.923 0.00 0.00 42.37 1.40
4123 5834 7.599630 ATGCAATGAAACGCAAAGATAAAAT 57.400 28.000 0.00 0.00 42.37 1.82
4124 5835 7.170489 TCAATGCAATGAAACGCAAAGATAAAA 59.830 29.630 0.85 0.00 42.37 1.52
4125 5836 6.644181 TCAATGCAATGAAACGCAAAGATAAA 59.356 30.769 0.85 0.00 42.37 1.40
4126 5837 6.155136 TCAATGCAATGAAACGCAAAGATAA 58.845 32.000 0.85 0.00 42.37 1.75
4127 5838 5.707931 TCAATGCAATGAAACGCAAAGATA 58.292 33.333 0.85 0.00 42.37 1.98
4128 5839 4.558178 TCAATGCAATGAAACGCAAAGAT 58.442 34.783 0.85 0.00 42.37 2.40
4129 5840 3.974912 TCAATGCAATGAAACGCAAAGA 58.025 36.364 0.85 0.00 42.37 2.52
4130 5841 4.445052 TCTTCAATGCAATGAAACGCAAAG 59.555 37.500 17.51 5.02 42.37 2.77
4131 5842 4.366586 TCTTCAATGCAATGAAACGCAAA 58.633 34.783 17.51 0.00 42.37 3.68
4132 5843 3.974912 TCTTCAATGCAATGAAACGCAA 58.025 36.364 17.51 0.00 42.37 4.85
4133 5844 3.252944 TCTCTTCAATGCAATGAAACGCA 59.747 39.130 17.51 2.57 43.45 5.24
4134 5845 3.825308 TCTCTTCAATGCAATGAAACGC 58.175 40.909 17.51 0.00 38.75 4.84
4135 5846 4.855388 CCTTCTCTTCAATGCAATGAAACG 59.145 41.667 17.51 11.39 38.75 3.60
4136 5847 5.047802 TCCCTTCTCTTCAATGCAATGAAAC 60.048 40.000 17.51 0.00 38.75 2.78
4137 5848 5.078949 TCCCTTCTCTTCAATGCAATGAAA 58.921 37.500 17.51 8.46 38.75 2.69
4138 5849 4.665451 TCCCTTCTCTTCAATGCAATGAA 58.335 39.130 16.12 16.12 37.70 2.57
4139 5850 4.305539 TCCCTTCTCTTCAATGCAATGA 57.694 40.909 0.00 0.00 0.00 2.57
4140 5851 5.826737 ACTATCCCTTCTCTTCAATGCAATG 59.173 40.000 0.00 0.00 0.00 2.82
4141 5852 6.011122 ACTATCCCTTCTCTTCAATGCAAT 57.989 37.500 0.00 0.00 0.00 3.56
4142 5853 5.441718 ACTATCCCTTCTCTTCAATGCAA 57.558 39.130 0.00 0.00 0.00 4.08
4143 5854 5.425217 TGTACTATCCCTTCTCTTCAATGCA 59.575 40.000 0.00 0.00 0.00 3.96
4144 5855 5.918608 TGTACTATCCCTTCTCTTCAATGC 58.081 41.667 0.00 0.00 0.00 3.56
4145 5856 7.659390 GGAATGTACTATCCCTTCTCTTCAATG 59.341 40.741 6.31 0.00 0.00 2.82
4146 5857 7.570607 AGGAATGTACTATCCCTTCTCTTCAAT 59.429 37.037 12.23 0.00 36.31 2.57
4147 5858 6.903534 AGGAATGTACTATCCCTTCTCTTCAA 59.096 38.462 12.23 0.00 36.31 2.69
4148 5859 6.444704 AGGAATGTACTATCCCTTCTCTTCA 58.555 40.000 12.23 0.00 36.31 3.02
4149 5860 6.014925 GGAGGAATGTACTATCCCTTCTCTTC 60.015 46.154 12.23 4.01 36.31 2.87
4150 5861 5.841783 GGAGGAATGTACTATCCCTTCTCTT 59.158 44.000 12.23 0.00 36.31 2.85
4151 5862 5.137082 AGGAGGAATGTACTATCCCTTCTCT 59.863 44.000 12.23 4.20 36.31 3.10
4152 5863 5.399113 AGGAGGAATGTACTATCCCTTCTC 58.601 45.833 12.23 5.38 36.31 2.87
4153 5864 5.426325 AGGAGGAATGTACTATCCCTTCT 57.574 43.478 12.23 6.54 36.31 2.85
4154 5865 5.717654 CCTAGGAGGAATGTACTATCCCTTC 59.282 48.000 1.05 4.67 37.67 3.46
4155 5866 5.378985 TCCTAGGAGGAATGTACTATCCCTT 59.621 44.000 7.62 5.41 42.51 3.95
4156 5867 4.926987 TCCTAGGAGGAATGTACTATCCCT 59.073 45.833 7.62 5.42 42.51 4.20
4157 5868 5.265989 CTCCTAGGAGGAATGTACTATCCC 58.734 50.000 28.68 5.94 45.28 3.85
4171 5882 0.264955 TAACCCCAGCCTCCTAGGAG 59.735 60.000 29.27 29.27 37.67 3.69
4172 5883 0.031414 GTAACCCCAGCCTCCTAGGA 60.031 60.000 11.98 11.98 37.67 2.94
4173 5884 0.326238 TGTAACCCCAGCCTCCTAGG 60.326 60.000 0.82 0.82 38.80 3.02
4174 5885 1.580059 TTGTAACCCCAGCCTCCTAG 58.420 55.000 0.00 0.00 0.00 3.02
4175 5886 2.047769 TTTGTAACCCCAGCCTCCTA 57.952 50.000 0.00 0.00 0.00 2.94
4176 5887 1.075536 CTTTTGTAACCCCAGCCTCCT 59.924 52.381 0.00 0.00 0.00 3.69
4177 5888 1.074889 TCTTTTGTAACCCCAGCCTCC 59.925 52.381 0.00 0.00 0.00 4.30
4178 5889 2.579410 TCTTTTGTAACCCCAGCCTC 57.421 50.000 0.00 0.00 0.00 4.70
4179 5890 3.165071 CAATCTTTTGTAACCCCAGCCT 58.835 45.455 0.00 0.00 0.00 4.58
4180 5891 2.897326 ACAATCTTTTGTAACCCCAGCC 59.103 45.455 0.00 0.00 44.22 4.85
4181 5892 3.860754 GCACAATCTTTTGTAACCCCAGC 60.861 47.826 0.00 0.00 44.24 4.85
4182 5893 3.573967 AGCACAATCTTTTGTAACCCCAG 59.426 43.478 0.00 0.00 44.24 4.45
4183 5894 3.571590 AGCACAATCTTTTGTAACCCCA 58.428 40.909 0.00 0.00 44.24 4.96
4184 5895 3.826729 AGAGCACAATCTTTTGTAACCCC 59.173 43.478 0.00 0.00 44.24 4.95
4185 5896 4.378459 CGAGAGCACAATCTTTTGTAACCC 60.378 45.833 0.00 0.00 44.24 4.11
4186 5897 4.451096 TCGAGAGCACAATCTTTTGTAACC 59.549 41.667 0.00 0.00 44.24 2.85
4187 5898 5.591643 TCGAGAGCACAATCTTTTGTAAC 57.408 39.130 0.00 0.00 44.24 2.50
4188 5899 5.931724 TGATCGAGAGCACAATCTTTTGTAA 59.068 36.000 0.00 0.00 44.24 2.41
4189 5900 5.478407 TGATCGAGAGCACAATCTTTTGTA 58.522 37.500 0.00 0.00 44.24 2.41
4191 5902 4.934075 TGATCGAGAGCACAATCTTTTG 57.066 40.909 0.00 0.00 38.86 2.44


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

AutoCloner maintained by Alex Coulton.