Multiple sequence alignment - TraesCS7A01G080300

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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 TraesCS7A01G080300 chr7A 100.000 5581 0 0 1 5581 46101588 46096008 0.000000e+00 10307.0
1 TraesCS7A01G080300 chr7A 94.769 2638 113 12 980 3607 44821867 44824489 0.000000e+00 4084.0
2 TraesCS7A01G080300 chr7A 94.499 2636 134 10 980 3609 46062017 46059387 0.000000e+00 4054.0
3 TraesCS7A01G080300 chr7A 91.195 2578 188 18 1036 3606 44448267 44445722 0.000000e+00 3467.0
4 TraesCS7A01G080300 chr7A 86.979 2665 250 44 980 3606 45982455 45979850 0.000000e+00 2909.0
5 TraesCS7A01G080300 chr7A 85.417 2599 297 47 1050 3601 45857676 45855113 0.000000e+00 2625.0
6 TraesCS7A01G080300 chr7A 94.989 938 25 6 4020 4939 44824869 44825802 0.000000e+00 1452.0
7 TraesCS7A01G080300 chr7A 94.613 891 24 8 4023 4894 46059108 46058223 0.000000e+00 1358.0
8 TraesCS7A01G080300 chr7A 92.424 528 27 3 4934 5449 44826496 44827022 0.000000e+00 741.0
9 TraesCS7A01G080300 chr7A 90.361 415 29 2 5044 5449 46081230 46080818 8.230000e-148 534.0
10 TraesCS7A01G080300 chr7A 84.986 353 42 9 4895 5245 107018977 107019320 1.150000e-91 348.0
11 TraesCS7A01G080300 chr7A 85.563 284 12 16 3731 3985 46059390 46059107 2.560000e-68 270.0
12 TraesCS7A01G080300 chr7A 99.254 134 1 0 5448 5581 74822819 74822686 5.590000e-60 243.0
13 TraesCS7A01G080300 chr7A 95.683 139 5 1 3731 3869 44824488 44824625 7.280000e-54 222.0
14 TraesCS7A01G080300 chr7A 89.744 78 5 3 4543 4617 706025525 706025448 4.600000e-16 97.1
15 TraesCS7A01G080300 chr7A 94.915 59 3 0 3874 3932 44824789 44824847 5.950000e-15 93.5
16 TraesCS7A01G080300 chr7A 92.063 63 5 0 4481 4543 31695803 31695741 7.700000e-14 89.8
17 TraesCS7A01G080300 chr7A 90.476 63 6 0 4481 4543 36365794 36365856 3.580000e-12 84.2
18 TraesCS7A01G080300 chr7A 94.444 54 3 0 3502 3555 45979372 45979319 3.580000e-12 84.2
19 TraesCS7A01G080300 chr7A 90.476 63 6 0 4481 4543 736411279 736411217 3.580000e-12 84.2
20 TraesCS7A01G080300 chr4A 87.687 2680 264 28 980 3606 654059729 654057063 0.000000e+00 3061.0
21 TraesCS7A01G080300 chr4A 90.530 2302 191 19 977 3260 652815048 652817340 0.000000e+00 3018.0
22 TraesCS7A01G080300 chr4A 85.753 2576 292 47 1057 3601 653074415 653076946 0.000000e+00 2654.0
23 TraesCS7A01G080300 chr4A 88.357 1735 156 17 1895 3590 653410942 653412669 0.000000e+00 2043.0
24 TraesCS7A01G080300 chr4A 87.694 902 88 14 977 1860 653410048 653410944 0.000000e+00 1029.0
25 TraesCS7A01G080300 chr4A 86.285 576 52 8 4895 5448 590940661 590941231 8.000000e-168 601.0
26 TraesCS7A01G080300 chr4A 97.794 136 3 0 5445 5580 11608996 11608861 9.350000e-58 235.0
27 TraesCS7A01G080300 chr7D 86.592 2506 279 34 1050 3528 43634554 43632079 0.000000e+00 2713.0
28 TraesCS7A01G080300 chr7D 90.696 1494 130 6 1886 3375 43637647 43636159 0.000000e+00 1980.0
29 TraesCS7A01G080300 chr3A 97.352 982 24 1 1 980 708506011 708505030 0.000000e+00 1668.0
30 TraesCS7A01G080300 chr3A 96.846 983 28 2 1 981 742895276 742894295 0.000000e+00 1640.0
31 TraesCS7A01G080300 chr3A 96.443 984 31 3 1 981 647220891 647219909 0.000000e+00 1620.0
32 TraesCS7A01G080300 chr3A 99.242 132 1 0 5450 5581 703367127 703367258 7.230000e-59 239.0
33 TraesCS7A01G080300 chr3A 93.893 131 8 0 3603 3733 511600130 511600000 1.230000e-46 198.0
34 TraesCS7A01G080300 chr3A 90.476 63 6 0 4481 4543 731556674 731556612 3.580000e-12 84.2
35 TraesCS7A01G080300 chr6A 97.053 984 27 1 1 982 41492480 41493463 0.000000e+00 1655.0
36 TraesCS7A01G080300 chr6A 96.548 985 31 2 1 982 575463529 575464513 0.000000e+00 1628.0
37 TraesCS7A01G080300 chr6A 97.122 139 4 0 5443 5581 472903577 472903715 9.350000e-58 235.0
38 TraesCS7A01G080300 chr6A 80.537 149 18 4 4481 4618 552936873 552936725 2.750000e-18 104.0
39 TraesCS7A01G080300 chr2A 96.748 984 28 3 1 982 111909523 111908542 0.000000e+00 1637.0
40 TraesCS7A01G080300 chr2A 95.337 1008 41 5 1 1004 605190245 605189240 0.000000e+00 1596.0
41 TraesCS7A01G080300 chr5A 96.033 983 37 1 1 981 580209409 580210391 0.000000e+00 1598.0
42 TraesCS7A01G080300 chr5A 88.811 572 43 4 4895 5449 474251857 474251290 0.000000e+00 682.0
43 TraesCS7A01G080300 chr5A 87.197 578 48 7 4895 5449 582129527 582128953 7.890000e-178 634.0
44 TraesCS7A01G080300 chr5A 86.851 578 50 7 4895 5449 582124902 582124328 1.710000e-174 623.0
45 TraesCS7A01G080300 chr5A 85.540 574 59 5 4895 5449 692378715 692379283 3.750000e-161 579.0
46 TraesCS7A01G080300 chr5A 81.553 412 66 7 5042 5449 212223641 212224046 1.160000e-86 331.0
47 TraesCS7A01G080300 chr2D 95.838 985 36 4 1 982 484887419 484886437 0.000000e+00 1587.0
48 TraesCS7A01G080300 chr1B 88.986 572 41 5 4895 5449 627701682 627702248 0.000000e+00 688.0
49 TraesCS7A01G080300 chr1D 88.225 569 48 6 4895 5449 3299431 3298868 0.000000e+00 662.0
50 TraesCS7A01G080300 chr7B 87.500 576 48 7 4895 5449 677230862 677230290 1.310000e-180 643.0
51 TraesCS7A01G080300 chr7B 87.500 576 47 8 4895 5449 677235497 677234926 4.710000e-180 641.0
52 TraesCS7A01G080300 chr7B 93.284 134 8 1 3602 3734 699930307 699930440 4.410000e-46 196.0
53 TraesCS7A01G080300 chrUn 87.391 571 51 5 4895 5448 306692639 306692073 2.190000e-178 636.0
54 TraesCS7A01G080300 chrUn 87.611 565 49 5 4895 5442 375856185 375856745 2.190000e-178 636.0
55 TraesCS7A01G080300 chrUn 88.438 320 26 3 4895 5206 459827644 459827960 5.280000e-100 375.0
56 TraesCS7A01G080300 chr2B 85.069 576 59 14 4895 5449 12212561 12211992 3.780000e-156 562.0
57 TraesCS7A01G080300 chr2B 84.722 576 61 14 4895 5449 12198834 12198265 8.170000e-153 551.0
58 TraesCS7A01G080300 chr2B 99.242 132 1 0 5450 5581 577638431 577638562 7.230000e-59 239.0
59 TraesCS7A01G080300 chr3B 84.477 554 67 5 4897 5449 222178546 222179081 3.830000e-146 529.0
60 TraesCS7A01G080300 chr3B 93.846 130 8 0 3603 3732 741865847 741865976 4.410000e-46 196.0
61 TraesCS7A01G080300 chr5D 98.529 136 2 0 5446 5581 2466351 2466216 2.010000e-59 241.0
62 TraesCS7A01G080300 chr5D 92.701 137 10 0 3598 3734 538352115 538352251 1.230000e-46 198.0
63 TraesCS7A01G080300 chr1A 99.242 132 1 0 5450 5581 17101885 17102016 7.230000e-59 239.0
64 TraesCS7A01G080300 chr1A 98.507 134 2 0 5448 5581 479251382 479251249 2.600000e-58 237.0
65 TraesCS7A01G080300 chr1A 98.496 133 2 0 5449 5581 253786527 253786659 9.350000e-58 235.0
66 TraesCS7A01G080300 chr1A 94.574 129 7 0 3604 3732 287275009 287275137 3.410000e-47 200.0
67 TraesCS7A01G080300 chr6B 92.647 136 10 0 3598 3733 346808636 346808771 4.410000e-46 196.0
68 TraesCS7A01G080300 chr6B 93.846 130 8 0 3603 3732 659825854 659825983 4.410000e-46 196.0
69 TraesCS7A01G080300 chr6B 90.411 146 14 0 3590 3735 642870571 642870426 5.710000e-45 193.0
70 TraesCS7A01G080300 chr6B 100.000 36 0 0 4544 4579 644759832 644759797 3.610000e-07 67.6
71 TraesCS7A01G080300 chr3D 93.130 131 9 0 3604 3734 161496029 161495899 5.710000e-45 193.0
72 TraesCS7A01G080300 chr3D 78.378 148 23 7 4481 4627 538606966 538606827 2.770000e-13 87.9
73 TraesCS7A01G080300 chr6D 82.162 185 22 6 4477 4651 7439129 7439312 1.250000e-31 148.0
74 TraesCS7A01G080300 chr5B 92.593 54 3 1 4543 4595 46766707 46766760 6.000000e-10 76.8


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 TraesCS7A01G080300 chr7A 46096008 46101588 5580 True 10307.0 10307 100.000000 1 5581 1 chr7A.!!$R5 5580
1 TraesCS7A01G080300 chr7A 44445722 44448267 2545 True 3467.0 3467 91.195000 1036 3606 1 chr7A.!!$R2 2570
2 TraesCS7A01G080300 chr7A 45855113 45857676 2563 True 2625.0 2625 85.417000 1050 3601 1 chr7A.!!$R3 2551
3 TraesCS7A01G080300 chr7A 46058223 46062017 3794 True 1894.0 4054 91.558333 980 4894 3 chr7A.!!$R10 3914
4 TraesCS7A01G080300 chr7A 45979319 45982455 3136 True 1496.6 2909 90.711500 980 3606 2 chr7A.!!$R9 2626
5 TraesCS7A01G080300 chr7A 44821867 44827022 5155 False 1318.5 4084 94.556000 980 5449 5 chr7A.!!$F3 4469
6 TraesCS7A01G080300 chr4A 654057063 654059729 2666 True 3061.0 3061 87.687000 980 3606 1 chr4A.!!$R2 2626
7 TraesCS7A01G080300 chr4A 652815048 652817340 2292 False 3018.0 3018 90.530000 977 3260 1 chr4A.!!$F2 2283
8 TraesCS7A01G080300 chr4A 653074415 653076946 2531 False 2654.0 2654 85.753000 1057 3601 1 chr4A.!!$F3 2544
9 TraesCS7A01G080300 chr4A 653410048 653412669 2621 False 1536.0 2043 88.025500 977 3590 2 chr4A.!!$F4 2613
10 TraesCS7A01G080300 chr4A 590940661 590941231 570 False 601.0 601 86.285000 4895 5448 1 chr4A.!!$F1 553
11 TraesCS7A01G080300 chr7D 43632079 43637647 5568 True 2346.5 2713 88.644000 1050 3528 2 chr7D.!!$R1 2478
12 TraesCS7A01G080300 chr3A 708505030 708506011 981 True 1668.0 1668 97.352000 1 980 1 chr3A.!!$R3 979
13 TraesCS7A01G080300 chr3A 742894295 742895276 981 True 1640.0 1640 96.846000 1 981 1 chr3A.!!$R5 980
14 TraesCS7A01G080300 chr3A 647219909 647220891 982 True 1620.0 1620 96.443000 1 981 1 chr3A.!!$R2 980
15 TraesCS7A01G080300 chr6A 41492480 41493463 983 False 1655.0 1655 97.053000 1 982 1 chr6A.!!$F1 981
16 TraesCS7A01G080300 chr6A 575463529 575464513 984 False 1628.0 1628 96.548000 1 982 1 chr6A.!!$F3 981
17 TraesCS7A01G080300 chr2A 111908542 111909523 981 True 1637.0 1637 96.748000 1 982 1 chr2A.!!$R1 981
18 TraesCS7A01G080300 chr2A 605189240 605190245 1005 True 1596.0 1596 95.337000 1 1004 1 chr2A.!!$R2 1003
19 TraesCS7A01G080300 chr5A 580209409 580210391 982 False 1598.0 1598 96.033000 1 981 1 chr5A.!!$F2 980
20 TraesCS7A01G080300 chr5A 474251290 474251857 567 True 682.0 682 88.811000 4895 5449 1 chr5A.!!$R1 554
21 TraesCS7A01G080300 chr5A 582128953 582129527 574 True 634.0 634 87.197000 4895 5449 1 chr5A.!!$R3 554
22 TraesCS7A01G080300 chr5A 582124328 582124902 574 True 623.0 623 86.851000 4895 5449 1 chr5A.!!$R2 554
23 TraesCS7A01G080300 chr5A 692378715 692379283 568 False 579.0 579 85.540000 4895 5449 1 chr5A.!!$F3 554
24 TraesCS7A01G080300 chr2D 484886437 484887419 982 True 1587.0 1587 95.838000 1 982 1 chr2D.!!$R1 981
25 TraesCS7A01G080300 chr1B 627701682 627702248 566 False 688.0 688 88.986000 4895 5449 1 chr1B.!!$F1 554
26 TraesCS7A01G080300 chr1D 3298868 3299431 563 True 662.0 662 88.225000 4895 5449 1 chr1D.!!$R1 554
27 TraesCS7A01G080300 chr7B 677230290 677230862 572 True 643.0 643 87.500000 4895 5449 1 chr7B.!!$R1 554
28 TraesCS7A01G080300 chr7B 677234926 677235497 571 True 641.0 641 87.500000 4895 5449 1 chr7B.!!$R2 554
29 TraesCS7A01G080300 chrUn 306692073 306692639 566 True 636.0 636 87.391000 4895 5448 1 chrUn.!!$R1 553
30 TraesCS7A01G080300 chrUn 375856185 375856745 560 False 636.0 636 87.611000 4895 5442 1 chrUn.!!$F1 547
31 TraesCS7A01G080300 chr2B 12211992 12212561 569 True 562.0 562 85.069000 4895 5449 1 chr2B.!!$R2 554
32 TraesCS7A01G080300 chr2B 12198265 12198834 569 True 551.0 551 84.722000 4895 5449 1 chr2B.!!$R1 554
33 TraesCS7A01G080300 chr3B 222178546 222179081 535 False 529.0 529 84.477000 4897 5449 1 chr3B.!!$F1 552

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
710 715 0.389817 CACCGAGAACGCAAGATCCA 60.390 55.000 0.00 0.0 40.46 3.41 F
1176 3230 0.458025 CTTCTACGACCAGGCGTTCC 60.458 60.000 2.80 0.0 42.71 3.62 F
2381 4460 0.034616 GTGCTCTGGAGTTGCTCTGT 59.965 55.000 0.00 0.0 0.00 3.41 F
2592 4674 1.663702 GGACGTACTGTGTTGCGCT 60.664 57.895 9.73 0.0 0.00 5.92 F
2891 4977 2.229792 TGCTTGCTTCTTGTTGTAGGG 58.770 47.619 0.00 0.0 0.00 3.53 F
3115 5203 2.260822 AGCCCTTCTAGTTTCTCTGCA 58.739 47.619 0.00 0.0 0.00 4.41 F
3733 5871 0.116940 TTTGGTACGGAGGGGGTACT 59.883 55.000 0.00 0.0 40.04 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 3998 0.321671 GCAGCTTGTCAGGTAGTCCA 59.678 55.0 0.0 0.0 35.89 4.02 R
2916 5002 0.327924 TGATTTCCTCCACGCCACAT 59.672 50.0 0.0 0.0 0.00 3.21 R
3714 5852 0.116940 AGTACCCCCTCCGTACCAAA 59.883 55.0 0.0 0.0 37.41 3.28 R
3715 5853 0.324645 GAGTACCCCCTCCGTACCAA 60.325 60.0 0.0 0.0 37.41 3.67 R
3717 5855 0.467106 GAGAGTACCCCCTCCGTACC 60.467 65.0 0.0 0.0 37.41 3.34 R
4418 6746 0.546507 TGACACCCATCTACTGCCCA 60.547 55.0 0.0 0.0 0.00 5.36 R
5558 8771 0.030101 TTTTCGGGTCTGCAAAAGCG 59.970 50.0 0.0 0.0 0.00 4.68 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
201 205 5.043248 CCCAAACAATATTCTCGCCAATTC 58.957 41.667 0.00 0.00 0.00 2.17
431 435 1.168714 GCCCGTGAGAAAAAGCAGAT 58.831 50.000 0.00 0.00 0.00 2.90
487 491 3.090037 GGAGAGAGGCGCATTACCTATA 58.910 50.000 10.83 0.00 37.77 1.31
573 578 3.441572 CCACAAGCGAAATCAGAGGAAAT 59.558 43.478 0.00 0.00 0.00 2.17
650 655 3.390967 TCACTCACCATTTTCTGAGGACA 59.609 43.478 0.00 0.00 38.63 4.02
710 715 0.389817 CACCGAGAACGCAAGATCCA 60.390 55.000 0.00 0.00 40.46 3.41
913 918 2.797792 GCTCAAAATTGTCGCACCACAA 60.798 45.455 0.00 0.00 40.54 3.33
1012 1019 1.706287 CGTCTCCGCTCACAGATCGA 61.706 60.000 0.00 0.00 0.00 3.59
1094 3145 2.031012 CACAGCCTCAACTGCCGA 59.969 61.111 0.00 0.00 41.60 5.54
1176 3230 0.458025 CTTCTACGACCAGGCGTTCC 60.458 60.000 2.80 0.00 42.71 3.62
1277 3331 2.363038 CGACCCCGTCTCCAACATTATA 59.637 50.000 0.00 0.00 0.00 0.98
1285 3339 6.049149 CCGTCTCCAACATTATACTCAACAT 58.951 40.000 0.00 0.00 0.00 2.71
1301 3355 3.443479 ATCCTCGCCCTCCTCCCT 61.443 66.667 0.00 0.00 0.00 4.20
1302 3356 2.091924 ATCCTCGCCCTCCTCCCTA 61.092 63.158 0.00 0.00 0.00 3.53
1337 3391 4.021925 GCCTCCACCGCTTCACCT 62.022 66.667 0.00 0.00 0.00 4.00
1342 3396 3.052082 CACCGCTTCACCTGCCAG 61.052 66.667 0.00 0.00 0.00 4.85
1415 3469 0.846693 ACAGGTCCTGCCAAAGTCTT 59.153 50.000 19.40 0.00 40.61 3.01
1425 3479 2.575805 CCAAAGTCTTCTGGCCTTCT 57.424 50.000 3.32 0.00 0.00 2.85
1556 3613 1.848652 AGGGTGAAGAAGCGCTACTA 58.151 50.000 12.05 0.00 0.00 1.82
1680 3740 2.821991 AGAGGACGACTTTCACCTTG 57.178 50.000 0.00 0.00 32.53 3.61
1771 3831 4.060372 GCGCATGATGATGAGCCT 57.940 55.556 9.65 0.00 46.49 4.58
1808 3868 6.461509 CCACCATAATCAATACCAGAAAAGGC 60.462 42.308 0.00 0.00 0.00 4.35
1835 3895 3.170717 TCTCCATGTCCGTAAGAACCTT 58.829 45.455 0.00 0.00 43.02 3.50
1853 3913 4.702081 GACGCCGTGTGCTCGACT 62.702 66.667 0.00 0.00 38.05 4.18
1896 3959 2.187946 GGATCACCTCCACAGCCG 59.812 66.667 0.00 0.00 44.26 5.52
1934 3998 1.445066 CATCTCGTCGCTGCAGTGT 60.445 57.895 25.68 3.48 0.00 3.55
1940 4004 1.289066 GTCGCTGCAGTGTGGACTA 59.711 57.895 25.68 3.48 0.00 2.59
1972 4036 0.535102 CAACGTTGCCTGGGAAGAGT 60.535 55.000 16.51 1.86 0.00 3.24
2177 4241 0.921896 CCATGGACCCTGTCTCCAAT 59.078 55.000 5.56 0.00 41.27 3.16
2333 4397 0.463654 TTATGGAGCTCGCCGCATTT 60.464 50.000 7.83 0.00 42.61 2.32
2355 4434 1.152830 GGCCCCCAGTTCTCAACAA 59.847 57.895 0.00 0.00 0.00 2.83
2381 4460 0.034616 GTGCTCTGGAGTTGCTCTGT 59.965 55.000 0.00 0.00 0.00 3.41
2592 4674 1.663702 GGACGTACTGTGTTGCGCT 60.664 57.895 9.73 0.00 0.00 5.92
2605 4687 2.488937 TGTTGCGCTTTGATGACATGAT 59.511 40.909 9.73 0.00 0.00 2.45
2891 4977 2.229792 TGCTTGCTTCTTGTTGTAGGG 58.770 47.619 0.00 0.00 0.00 3.53
2993 5079 2.544267 GCGTGAACTTCACTGCTACTTT 59.456 45.455 21.39 0.00 44.85 2.66
3115 5203 2.260822 AGCCCTTCTAGTTTCTCTGCA 58.739 47.619 0.00 0.00 0.00 4.41
3320 5408 3.323115 GGATGACATGCTAGAGATGGACA 59.677 47.826 0.00 1.04 0.00 4.02
3445 5557 4.286032 AGCTGTGAAGTTGGACCATAGTAA 59.714 41.667 0.00 0.00 0.00 2.24
3481 5601 4.758688 TGCTGTGTGTTATGATGTCCTAG 58.241 43.478 0.00 0.00 0.00 3.02
3508 5632 2.884639 GGGCATCCTGCGTTGTATTATT 59.115 45.455 0.00 0.00 46.21 1.40
3513 5637 5.180117 GCATCCTGCGTTGTATTATTGAGAT 59.820 40.000 0.00 0.00 31.71 2.75
3609 5747 5.385509 TTGCTTGGCCTTGTTAAATACTC 57.614 39.130 3.32 0.00 0.00 2.59
3610 5748 3.761752 TGCTTGGCCTTGTTAAATACTCC 59.238 43.478 3.32 0.00 0.00 3.85
3611 5749 3.130516 GCTTGGCCTTGTTAAATACTCCC 59.869 47.826 3.32 0.00 0.00 4.30
3612 5750 4.600062 CTTGGCCTTGTTAAATACTCCCT 58.400 43.478 3.32 0.00 0.00 4.20
3613 5751 4.230745 TGGCCTTGTTAAATACTCCCTC 57.769 45.455 3.32 0.00 0.00 4.30
3614 5752 3.850173 TGGCCTTGTTAAATACTCCCTCT 59.150 43.478 3.32 0.00 0.00 3.69
3615 5753 4.200092 GGCCTTGTTAAATACTCCCTCTG 58.800 47.826 0.00 0.00 0.00 3.35
3616 5754 4.324331 GGCCTTGTTAAATACTCCCTCTGT 60.324 45.833 0.00 0.00 0.00 3.41
3618 5756 5.354513 GCCTTGTTAAATACTCCCTCTGTTC 59.645 44.000 0.00 0.00 0.00 3.18
3619 5757 5.880887 CCTTGTTAAATACTCCCTCTGTTCC 59.119 44.000 0.00 0.00 0.00 3.62
3620 5758 6.442541 TTGTTAAATACTCCCTCTGTTCCA 57.557 37.500 0.00 0.00 0.00 3.53
3621 5759 6.442541 TGTTAAATACTCCCTCTGTTCCAA 57.557 37.500 0.00 0.00 0.00 3.53
3622 5760 6.843752 TGTTAAATACTCCCTCTGTTCCAAA 58.156 36.000 0.00 0.00 0.00 3.28
3623 5761 7.291566 TGTTAAATACTCCCTCTGTTCCAAAA 58.708 34.615 0.00 0.00 0.00 2.44
3624 5762 7.947890 TGTTAAATACTCCCTCTGTTCCAAAAT 59.052 33.333 0.00 0.00 0.00 1.82
3625 5763 8.803235 GTTAAATACTCCCTCTGTTCCAAAATT 58.197 33.333 0.00 0.00 0.00 1.82
3627 5765 7.855784 AATACTCCCTCTGTTCCAAAATTTT 57.144 32.000 0.00 0.00 0.00 1.82
3630 5768 5.425217 ACTCCCTCTGTTCCAAAATTTTTGT 59.575 36.000 18.05 0.00 0.00 2.83
3631 5769 5.912892 TCCCTCTGTTCCAAAATTTTTGTC 58.087 37.500 18.05 10.14 0.00 3.18
3633 5771 6.156083 TCCCTCTGTTCCAAAATTTTTGTCTT 59.844 34.615 18.05 0.00 0.00 3.01
3634 5772 7.343316 TCCCTCTGTTCCAAAATTTTTGTCTTA 59.657 33.333 18.05 4.30 0.00 2.10
3666 5804 8.002984 TCTAAATACGGATGTATCAAGTCACA 57.997 34.615 0.00 0.00 40.42 3.58
3668 5806 9.261180 CTAAATACGGATGTATCAAGTCACATT 57.739 33.333 0.00 0.00 40.42 2.71
3671 5809 9.607988 AATACGGATGTATCAAGTCACATTTTA 57.392 29.630 0.00 0.00 40.42 1.52
3672 5810 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
3674 5812 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
3675 5813 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
3706 5844 8.162878 ACATCCGTATCTAGACGAATTTAAGA 57.837 34.615 5.60 0.00 45.82 2.10
3707 5845 8.074972 ACATCCGTATCTAGACGAATTTAAGAC 58.925 37.037 5.60 0.00 45.82 3.01
3708 5846 7.558161 TCCGTATCTAGACGAATTTAAGACA 57.442 36.000 5.60 0.00 45.82 3.41
3709 5847 7.988737 TCCGTATCTAGACGAATTTAAGACAA 58.011 34.615 5.60 0.00 45.82 3.18
3710 5848 8.127327 TCCGTATCTAGACGAATTTAAGACAAG 58.873 37.037 5.60 0.00 45.82 3.16
3711 5849 8.127327 CCGTATCTAGACGAATTTAAGACAAGA 58.873 37.037 5.60 0.00 45.82 3.02
3712 5850 9.499585 CGTATCTAGACGAATTTAAGACAAGAA 57.500 33.333 0.00 0.00 45.82 2.52
3719 5857 8.630037 AGACGAATTTAAGACAAGAATTTTGGT 58.370 29.630 0.00 0.00 0.00 3.67
3720 5858 9.887406 GACGAATTTAAGACAAGAATTTTGGTA 57.113 29.630 0.00 0.00 0.00 3.25
3721 5859 9.673454 ACGAATTTAAGACAAGAATTTTGGTAC 57.327 29.630 0.00 0.00 0.00 3.34
3722 5860 8.837059 CGAATTTAAGACAAGAATTTTGGTACG 58.163 33.333 5.68 0.00 0.00 3.67
3723 5861 9.124807 GAATTTAAGACAAGAATTTTGGTACGG 57.875 33.333 0.00 0.00 0.00 4.02
3724 5862 7.804843 TTTAAGACAAGAATTTTGGTACGGA 57.195 32.000 0.00 0.00 0.00 4.69
3725 5863 5.941948 AAGACAAGAATTTTGGTACGGAG 57.058 39.130 0.00 0.00 0.00 4.63
3726 5864 4.324267 AGACAAGAATTTTGGTACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
3727 5865 3.418047 ACAAGAATTTTGGTACGGAGGG 58.582 45.455 0.00 0.00 0.00 4.30
3728 5866 2.752903 CAAGAATTTTGGTACGGAGGGG 59.247 50.000 0.00 0.00 0.00 4.79
3729 5867 1.283905 AGAATTTTGGTACGGAGGGGG 59.716 52.381 0.00 0.00 0.00 5.40
3730 5868 1.005097 GAATTTTGGTACGGAGGGGGT 59.995 52.381 0.00 0.00 0.00 4.95
3731 5869 1.969713 ATTTTGGTACGGAGGGGGTA 58.030 50.000 0.00 0.00 0.00 3.69
3732 5870 0.983467 TTTTGGTACGGAGGGGGTAC 59.017 55.000 0.00 0.00 39.56 3.34
3733 5871 0.116940 TTTGGTACGGAGGGGGTACT 59.883 55.000 0.00 0.00 40.04 2.73
3759 5897 0.953471 GTGAAGCCCGTGCATGTACA 60.953 55.000 14.55 0.00 41.13 2.90
3837 6005 6.696148 CGATGGTGAGGTAGTTATGTTTACTC 59.304 42.308 0.00 0.00 0.00 2.59
3864 6032 5.121768 CGGGTTCTTGTAACTCCTTGTATTG 59.878 44.000 0.00 0.00 0.00 1.90
3869 6037 9.797556 GTTCTTGTAACTCCTTGTATTGTTTTT 57.202 29.630 0.00 0.00 0.00 1.94
3922 6249 7.755582 TGCTTCTTTTTCTTAGTTTTCTTGC 57.244 32.000 0.00 0.00 0.00 4.01
3987 6314 2.032981 GCTTAACGATGGCCCATGG 58.967 57.895 0.00 4.14 0.00 3.66
3988 6315 0.751643 GCTTAACGATGGCCCATGGT 60.752 55.000 11.73 5.44 34.44 3.55
3989 6316 1.762708 CTTAACGATGGCCCATGGTT 58.237 50.000 24.65 24.65 43.20 3.67
3990 6317 2.925724 CTTAACGATGGCCCATGGTTA 58.074 47.619 22.76 22.76 40.08 2.85
3991 6318 2.335316 TAACGATGGCCCATGGTTAC 57.665 50.000 22.76 0.00 40.08 2.50
3992 6319 0.329931 AACGATGGCCCATGGTTACA 59.670 50.000 20.93 6.86 40.08 2.41
3993 6320 0.550914 ACGATGGCCCATGGTTACAT 59.449 50.000 11.73 11.60 37.99 2.29
3994 6321 1.771854 ACGATGGCCCATGGTTACATA 59.228 47.619 11.73 0.00 34.99 2.29
3995 6322 2.173782 ACGATGGCCCATGGTTACATAA 59.826 45.455 11.73 0.00 34.99 1.90
3996 6323 3.218453 CGATGGCCCATGGTTACATAAA 58.782 45.455 11.73 0.00 34.99 1.40
3997 6324 3.634448 CGATGGCCCATGGTTACATAAAA 59.366 43.478 11.73 0.00 34.99 1.52
3998 6325 4.098654 CGATGGCCCATGGTTACATAAAAA 59.901 41.667 11.73 0.00 34.99 1.94
3999 6326 5.600696 GATGGCCCATGGTTACATAAAAAG 58.399 41.667 11.73 0.00 34.99 2.27
4004 6331 6.099341 GCCCATGGTTACATAAAAAGAAGTG 58.901 40.000 11.73 0.00 34.99 3.16
4007 6334 7.394923 CCCATGGTTACATAAAAAGAAGTGGTA 59.605 37.037 11.73 0.00 34.99 3.25
4022 6349 5.239525 AGAAGTGGTACAGAAAATCAAGCAC 59.760 40.000 0.00 0.00 41.80 4.40
4023 6350 4.460263 AGTGGTACAGAAAATCAAGCACA 58.540 39.130 5.85 0.00 41.80 4.57
4043 6370 8.097791 AGCACAAAATATAGTTAAGGGAGGTA 57.902 34.615 0.00 0.00 0.00 3.08
4044 6371 8.724310 AGCACAAAATATAGTTAAGGGAGGTAT 58.276 33.333 0.00 0.00 0.00 2.73
4086 6413 5.211174 TGCATGAGAGAATACAGGATCAG 57.789 43.478 0.00 0.00 0.00 2.90
4266 6594 8.397906 CCATGTGAACATAATTTACTGGTGTAG 58.602 37.037 0.00 0.00 34.26 2.74
4285 6613 4.759693 TGTAGTTCATGGTGTCATTGGAAC 59.240 41.667 0.00 0.00 36.94 3.62
4418 6746 2.086869 CGAATGACCTTGCTGTCCATT 58.913 47.619 0.00 0.00 34.25 3.16
4694 7041 8.554835 TCATTGACATCCGTATAAAAGAAACA 57.445 30.769 0.00 0.00 0.00 2.83
4711 7058 0.478072 ACAAGTGAAGTGGGATGGCA 59.522 50.000 0.00 0.00 0.00 4.92
5074 8134 5.604565 AGAAAGCTGGCCAATTATTAATGC 58.395 37.500 7.01 2.79 0.00 3.56
5286 8494 4.764823 GTGGTTGGTAATTTGATCTGGACA 59.235 41.667 0.00 0.00 0.00 4.02
5370 8583 4.870991 GGAAAGACAAGATAAGAAGGTCCG 59.129 45.833 0.00 0.00 0.00 4.79
5374 8587 5.014858 AGACAAGATAAGAAGGTCCGTACA 58.985 41.667 0.00 0.00 0.00 2.90
5442 8655 3.930035 CAGAGGAATTAGGGGGTAGACT 58.070 50.000 0.00 0.00 0.00 3.24
5449 8662 2.337359 TAGGGGGTAGACTGCAAACT 57.663 50.000 0.00 0.00 0.00 2.66
5450 8663 0.693049 AGGGGGTAGACTGCAAACTG 59.307 55.000 3.05 0.00 0.00 3.16
5451 8664 0.400594 GGGGGTAGACTGCAAACTGT 59.599 55.000 3.05 0.00 0.00 3.55
5452 8665 1.202891 GGGGGTAGACTGCAAACTGTT 60.203 52.381 3.05 0.00 0.00 3.16
5453 8666 1.880027 GGGGTAGACTGCAAACTGTTG 59.120 52.381 0.00 0.00 37.83 3.33
5454 8667 2.486548 GGGGTAGACTGCAAACTGTTGA 60.487 50.000 0.00 0.00 36.83 3.18
5455 8668 2.548480 GGGTAGACTGCAAACTGTTGAC 59.452 50.000 0.00 0.00 36.83 3.18
5456 8669 3.202906 GGTAGACTGCAAACTGTTGACA 58.797 45.455 0.00 0.00 36.83 3.58
5457 8670 3.002348 GGTAGACTGCAAACTGTTGACAC 59.998 47.826 0.00 0.00 36.83 3.67
5458 8671 2.710377 AGACTGCAAACTGTTGACACA 58.290 42.857 0.00 0.00 36.83 3.72
5459 8672 2.420022 AGACTGCAAACTGTTGACACAC 59.580 45.455 0.00 0.00 36.83 3.82
5460 8673 1.130373 ACTGCAAACTGTTGACACACG 59.870 47.619 0.00 0.00 36.83 4.49
5461 8674 1.396648 CTGCAAACTGTTGACACACGA 59.603 47.619 0.00 0.00 36.83 4.35
5462 8675 1.807142 TGCAAACTGTTGACACACGAA 59.193 42.857 0.00 0.00 36.83 3.85
5463 8676 2.173964 GCAAACTGTTGACACACGAAC 58.826 47.619 0.00 0.00 36.83 3.95
5464 8677 2.413502 GCAAACTGTTGACACACGAACA 60.414 45.455 0.00 0.00 36.83 3.18
5465 8678 3.160545 CAAACTGTTGACACACGAACAC 58.839 45.455 0.00 0.00 36.83 3.32
5466 8679 0.996462 ACTGTTGACACACGAACACG 59.004 50.000 0.00 0.00 0.00 4.49
5467 8680 0.996462 CTGTTGACACACGAACACGT 59.004 50.000 0.00 0.00 41.02 4.49
5468 8681 0.993532 TGTTGACACACGAACACGTC 59.006 50.000 0.00 0.00 38.21 4.34
5469 8682 0.993532 GTTGACACACGAACACGTCA 59.006 50.000 0.00 0.00 38.21 4.35
5470 8683 0.993532 TTGACACACGAACACGTCAC 59.006 50.000 0.00 0.00 38.07 3.67
5471 8684 1.135114 TGACACACGAACACGTCACG 61.135 55.000 0.00 0.00 38.21 4.35
5472 8685 1.135699 GACACACGAACACGTCACGT 61.136 55.000 0.00 0.00 42.36 4.49
5481 8694 2.949106 ACGTCACGTGTACCCTCG 59.051 61.111 16.51 13.30 39.18 4.63
5482 8695 1.597854 ACGTCACGTGTACCCTCGA 60.598 57.895 16.51 0.00 39.18 4.04
5483 8696 1.154338 CGTCACGTGTACCCTCGAC 60.154 63.158 16.51 2.42 0.00 4.20
5484 8697 1.154338 GTCACGTGTACCCTCGACG 60.154 63.158 16.51 5.37 39.03 5.12
5485 8698 2.503375 CACGTGTACCCTCGACGC 60.503 66.667 7.58 0.00 36.56 5.19
5486 8699 3.741476 ACGTGTACCCTCGACGCC 61.741 66.667 2.89 0.00 36.56 5.68
5487 8700 4.824166 CGTGTACCCTCGACGCCG 62.824 72.222 0.00 0.00 37.07 6.46
5488 8701 4.487412 GTGTACCCTCGACGCCGG 62.487 72.222 0.00 0.00 36.24 6.13
5507 8720 3.414272 GGTGATGCACCGCAGATC 58.586 61.111 0.22 0.00 44.95 2.75
5508 8721 1.450134 GGTGATGCACCGCAGATCA 60.450 57.895 0.22 0.00 44.95 2.92
5509 8722 1.709147 GGTGATGCACCGCAGATCAC 61.709 60.000 12.21 12.21 44.95 3.06
5510 8723 1.810853 TGATGCACCGCAGATCACG 60.811 57.895 0.00 0.00 43.65 4.35
5511 8724 1.811266 GATGCACCGCAGATCACGT 60.811 57.895 7.30 0.00 43.65 4.49
5512 8725 1.756375 GATGCACCGCAGATCACGTC 61.756 60.000 7.30 0.00 43.65 4.34
5513 8726 3.545481 GCACCGCAGATCACGTCG 61.545 66.667 7.30 0.00 0.00 5.12
5514 8727 2.178273 CACCGCAGATCACGTCGA 59.822 61.111 0.00 0.00 0.00 4.20
5515 8728 1.443702 CACCGCAGATCACGTCGAA 60.444 57.895 0.00 0.00 0.00 3.71
5516 8729 1.154016 ACCGCAGATCACGTCGAAG 60.154 57.895 0.00 0.00 0.00 3.79
5517 8730 1.874019 CCGCAGATCACGTCGAAGG 60.874 63.158 0.00 0.00 0.00 3.46
5518 8731 1.136774 CGCAGATCACGTCGAAGGA 59.863 57.895 0.00 0.00 0.00 3.36
5519 8732 0.863538 CGCAGATCACGTCGAAGGAG 60.864 60.000 0.00 0.00 0.00 3.69
5520 8733 0.452184 GCAGATCACGTCGAAGGAGA 59.548 55.000 0.00 0.71 0.00 3.71
5521 8734 1.795889 GCAGATCACGTCGAAGGAGAC 60.796 57.143 0.00 0.00 37.76 3.36
5522 8735 1.096416 AGATCACGTCGAAGGAGACC 58.904 55.000 0.00 0.00 37.85 3.85
5523 8736 0.100861 GATCACGTCGAAGGAGACCC 59.899 60.000 0.00 0.00 37.85 4.46
5524 8737 1.654954 ATCACGTCGAAGGAGACCCG 61.655 60.000 0.00 0.00 37.85 5.28
5525 8738 3.060615 ACGTCGAAGGAGACCCGG 61.061 66.667 0.00 0.00 37.85 5.73
5526 8739 4.493747 CGTCGAAGGAGACCCGGC 62.494 72.222 0.00 0.00 37.85 6.13
5527 8740 4.144703 GTCGAAGGAGACCCGGCC 62.145 72.222 0.00 0.00 37.58 6.13
5530 8743 4.144703 GAAGGAGACCCGGCCGAC 62.145 72.222 30.73 17.56 37.58 4.79
5553 8766 3.598678 CGATACGCAAGACAGTCGA 57.401 52.632 0.00 0.00 43.62 4.20
5554 8767 1.181001 CGATACGCAAGACAGTCGAC 58.819 55.000 7.70 7.70 43.62 4.20
5555 8768 1.181001 GATACGCAAGACAGTCGACG 58.819 55.000 10.46 7.86 43.62 5.12
5556 8769 0.179171 ATACGCAAGACAGTCGACGG 60.179 55.000 14.42 14.42 43.62 4.79
5557 8770 2.191354 TACGCAAGACAGTCGACGGG 62.191 60.000 19.84 13.94 43.62 5.28
5558 8771 3.112709 GCAAGACAGTCGACGGGC 61.113 66.667 19.84 17.29 0.00 6.13
5559 8772 2.805353 CAAGACAGTCGACGGGCG 60.805 66.667 19.84 0.00 42.69 6.13
5560 8773 4.719369 AAGACAGTCGACGGGCGC 62.719 66.667 19.84 0.00 40.61 6.53
5562 8775 4.719369 GACAGTCGACGGGCGCTT 62.719 66.667 19.84 0.00 40.61 4.68
5563 8776 4.295119 ACAGTCGACGGGCGCTTT 62.295 61.111 19.84 0.00 40.61 3.51
5564 8777 3.041940 CAGTCGACGGGCGCTTTT 61.042 61.111 10.46 0.00 40.61 2.27
5565 8778 3.041940 AGTCGACGGGCGCTTTTG 61.042 61.111 10.46 0.00 40.61 2.44
5566 8779 4.736631 GTCGACGGGCGCTTTTGC 62.737 66.667 7.64 0.00 40.61 3.68
5577 8790 3.957383 GCTTTTGCAGACCCGAAAA 57.043 47.368 0.00 0.00 46.58 2.29
5578 8791 1.487482 GCTTTTGCAGACCCGAAAAC 58.513 50.000 0.00 0.00 46.58 2.43
5579 8792 1.868109 GCTTTTGCAGACCCGAAAACC 60.868 52.381 0.00 0.00 46.58 3.27
5580 8793 0.747852 TTTTGCAGACCCGAAAACCC 59.252 50.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
201 205 3.305608 GCAGTGAAGAAATGGGTGGAAAG 60.306 47.826 0.00 0.00 0.00 2.62
389 393 1.552337 ACACTGTCTGCCACTGATAGG 59.448 52.381 3.94 0.00 0.00 2.57
431 435 2.006748 CAATTAGGGGGTGGCCTCA 58.993 57.895 3.32 0.00 0.00 3.86
487 491 1.298859 GCCGCCAGATTCAACTTCGT 61.299 55.000 0.00 0.00 0.00 3.85
563 567 4.288398 AGATCTCAGCTCATTTCCTCTGA 58.712 43.478 0.00 0.00 34.74 3.27
573 578 1.109920 GGCCCGTAGATCTCAGCTCA 61.110 60.000 0.00 0.00 0.00 4.26
710 715 2.920912 TTCTTCTCCGGTGGCGGT 60.921 61.111 0.00 0.00 0.00 5.68
913 918 1.263217 GACGTTGTTCGAGCAAATGGT 59.737 47.619 16.65 14.05 42.86 3.55
1012 1019 3.008375 AGACGCCATATTATCAGCCACAT 59.992 43.478 0.00 0.00 0.00 3.21
1119 3173 3.733960 GGCGTTTTCCAGGTCGGC 61.734 66.667 0.00 0.00 41.00 5.54
1176 3230 4.473520 CCTACAGGGCAGCCGGTG 62.474 72.222 15.78 13.12 0.00 4.94
1190 3244 2.523412 CGGCCCGGAATCCTCCTA 60.523 66.667 0.73 0.00 39.93 2.94
1207 3261 1.079750 GTTGTGAGGAGGTCGAGGC 60.080 63.158 0.00 0.00 0.00 4.70
1277 3331 1.617947 GGAGGGCGAGGATGTTGAGT 61.618 60.000 0.00 0.00 0.00 3.41
1285 3339 1.882189 TTTAGGGAGGAGGGCGAGGA 61.882 60.000 0.00 0.00 0.00 3.71
1332 3386 1.072331 GGACTTCTTTCTGGCAGGTGA 59.928 52.381 15.73 7.72 0.00 4.02
1337 3391 3.632145 GTCTTTTGGACTTCTTTCTGGCA 59.368 43.478 0.00 0.00 41.46 4.92
1415 3469 4.298626 AGTATACCATGAAGAAGGCCAGA 58.701 43.478 5.01 0.00 0.00 3.86
1425 3479 3.646162 AGGCATCCGAAGTATACCATGAA 59.354 43.478 0.00 0.00 0.00 2.57
1556 3613 2.599677 GTCCTATCGGATTCAGGGTCT 58.400 52.381 6.91 0.00 42.43 3.85
1680 3740 3.682377 GCTGAAAAGAGTAGCTTCTCCAC 59.318 47.826 15.97 6.71 35.24 4.02
1808 3868 1.037493 TACGGACATGGAGAATCGGG 58.963 55.000 0.00 0.00 34.37 5.14
1853 3913 1.837051 CTCTATAGTGGCGGGGGCA 60.837 63.158 0.00 0.00 35.21 5.36
1896 3959 0.591659 GGTTTTCGGTCCAAGCAGAC 59.408 55.000 0.00 0.00 35.95 3.51
1908 3972 0.736325 AGCGACGAGATGGGTTTTCG 60.736 55.000 0.00 0.00 40.02 3.46
1934 3998 0.321671 GCAGCTTGTCAGGTAGTCCA 59.678 55.000 0.00 0.00 35.89 4.02
1940 4004 0.748005 AACGTTGCAGCTTGTCAGGT 60.748 50.000 0.00 0.00 0.00 4.00
1972 4036 8.548025 TCTTCAAATATTGTTCCAGACCATCTA 58.452 33.333 0.00 0.00 0.00 1.98
2177 4241 6.548251 TGTACCAGATGGAGTTGACGATAATA 59.452 38.462 5.72 0.00 38.94 0.98
2355 4434 0.475906 AACTCCAGAGCACAAGCCTT 59.524 50.000 0.00 0.00 43.56 4.35
2381 4460 1.270785 ACGATGTCACATCTTGCACCA 60.271 47.619 15.89 0.00 0.00 4.17
2592 4674 9.605275 CCTAAGAAGAACTATCATGTCATCAAA 57.395 33.333 0.00 0.00 0.00 2.69
2605 4687 3.305813 CCACACACGCCTAAGAAGAACTA 60.306 47.826 0.00 0.00 0.00 2.24
2916 5002 0.327924 TGATTTCCTCCACGCCACAT 59.672 50.000 0.00 0.00 0.00 3.21
2993 5079 2.816087 GTCCTCTGAAGCTGCAAATCAA 59.184 45.455 1.02 0.00 0.00 2.57
3115 5203 1.181098 AAAAGCCAATCAGCCGTGCT 61.181 50.000 0.00 0.00 40.77 4.40
3320 5408 1.678627 CATCTCCGAACTGAGGACGAT 59.321 52.381 0.00 0.00 33.58 3.73
3508 5632 4.880120 GCTGAAGAATGTCATCCAATCTCA 59.120 41.667 0.00 0.00 31.95 3.27
3513 5637 3.129813 GCATGCTGAAGAATGTCATCCAA 59.870 43.478 11.37 0.00 33.51 3.53
3609 5747 5.917462 AGACAAAAATTTTGGAACAGAGGG 58.083 37.500 20.79 0.00 42.39 4.30
3610 5748 8.413229 TCTAAGACAAAAATTTTGGAACAGAGG 58.587 33.333 20.79 5.38 42.39 3.69
3611 5749 9.971922 ATCTAAGACAAAAATTTTGGAACAGAG 57.028 29.630 20.79 10.76 42.39 3.35
3641 5779 8.002984 TGTGACTTGATACATCCGTATTTAGA 57.997 34.615 0.00 0.00 38.48 2.10
3642 5780 8.818141 ATGTGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
3643 5781 9.607988 AAATGTGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
3644 5782 8.506168 AAATGTGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
3646 5784 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
3647 5785 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
3648 5786 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
3649 5787 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
3681 5819 8.074972 GTCTTAAATTCGTCTAGATACGGATGT 58.925 37.037 0.00 0.00 40.19 3.06
3682 5820 8.074370 TGTCTTAAATTCGTCTAGATACGGATG 58.926 37.037 0.00 0.00 40.19 3.51
3683 5821 8.162878 TGTCTTAAATTCGTCTAGATACGGAT 57.837 34.615 0.00 0.00 42.90 4.18
3684 5822 7.558161 TGTCTTAAATTCGTCTAGATACGGA 57.442 36.000 0.00 0.00 43.05 4.69
3686 5824 9.499585 TTCTTGTCTTAAATTCGTCTAGATACG 57.500 33.333 0.00 0.00 44.19 3.06
3693 5831 8.630037 ACCAAAATTCTTGTCTTAAATTCGTCT 58.370 29.630 0.00 0.00 0.00 4.18
3694 5832 8.797266 ACCAAAATTCTTGTCTTAAATTCGTC 57.203 30.769 0.00 0.00 0.00 4.20
3695 5833 9.673454 GTACCAAAATTCTTGTCTTAAATTCGT 57.327 29.630 0.00 0.00 0.00 3.85
3696 5834 8.837059 CGTACCAAAATTCTTGTCTTAAATTCG 58.163 33.333 0.00 0.00 0.00 3.34
3697 5835 9.124807 CCGTACCAAAATTCTTGTCTTAAATTC 57.875 33.333 0.00 0.00 0.00 2.17
3698 5836 8.852135 TCCGTACCAAAATTCTTGTCTTAAATT 58.148 29.630 0.00 0.00 0.00 1.82
3699 5837 8.398878 TCCGTACCAAAATTCTTGTCTTAAAT 57.601 30.769 0.00 0.00 0.00 1.40
3700 5838 7.040961 CCTCCGTACCAAAATTCTTGTCTTAAA 60.041 37.037 0.00 0.00 0.00 1.52
3701 5839 6.428771 CCTCCGTACCAAAATTCTTGTCTTAA 59.571 38.462 0.00 0.00 0.00 1.85
3702 5840 5.935789 CCTCCGTACCAAAATTCTTGTCTTA 59.064 40.000 0.00 0.00 0.00 2.10
3703 5841 4.760204 CCTCCGTACCAAAATTCTTGTCTT 59.240 41.667 0.00 0.00 0.00 3.01
3704 5842 4.324267 CCTCCGTACCAAAATTCTTGTCT 58.676 43.478 0.00 0.00 0.00 3.41
3705 5843 3.439129 CCCTCCGTACCAAAATTCTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
3706 5844 3.418047 CCCTCCGTACCAAAATTCTTGT 58.582 45.455 0.00 0.00 0.00 3.16
3707 5845 2.752903 CCCCTCCGTACCAAAATTCTTG 59.247 50.000 0.00 0.00 0.00 3.02
3708 5846 2.291346 CCCCCTCCGTACCAAAATTCTT 60.291 50.000 0.00 0.00 0.00 2.52
3709 5847 1.283905 CCCCCTCCGTACCAAAATTCT 59.716 52.381 0.00 0.00 0.00 2.40
3710 5848 1.005097 ACCCCCTCCGTACCAAAATTC 59.995 52.381 0.00 0.00 0.00 2.17
3711 5849 1.078115 ACCCCCTCCGTACCAAAATT 58.922 50.000 0.00 0.00 0.00 1.82
3712 5850 1.561076 GTACCCCCTCCGTACCAAAAT 59.439 52.381 0.00 0.00 31.72 1.82
3713 5851 0.983467 GTACCCCCTCCGTACCAAAA 59.017 55.000 0.00 0.00 31.72 2.44
3714 5852 0.116940 AGTACCCCCTCCGTACCAAA 59.883 55.000 0.00 0.00 37.41 3.28
3715 5853 0.324645 GAGTACCCCCTCCGTACCAA 60.325 60.000 0.00 0.00 37.41 3.67
3716 5854 1.217057 AGAGTACCCCCTCCGTACCA 61.217 60.000 0.00 0.00 37.41 3.25
3717 5855 0.467106 GAGAGTACCCCCTCCGTACC 60.467 65.000 0.00 0.00 37.41 3.34
3718 5856 0.817229 CGAGAGTACCCCCTCCGTAC 60.817 65.000 0.00 0.00 37.04 3.67
3719 5857 1.274703 ACGAGAGTACCCCCTCCGTA 61.275 60.000 0.00 0.00 46.88 4.02
3720 5858 2.274760 CGAGAGTACCCCCTCCGT 59.725 66.667 0.00 0.00 31.53 4.69
3721 5859 2.274760 ACGAGAGTACCCCCTCCG 59.725 66.667 0.00 0.00 46.88 4.63
3732 5870 2.202492 CGGGCTTCACGACGAGAG 60.202 66.667 0.00 0.00 0.00 3.20
3733 5871 2.981909 ACGGGCTTCACGACGAGA 60.982 61.111 0.00 0.00 34.93 4.04
3837 6005 1.271656 AGGAGTTACAAGAACCCGTCG 59.728 52.381 0.00 0.00 0.00 5.12
3875 6202 6.813152 GCAATAAAGACTGGCATGTAACAAAT 59.187 34.615 0.00 0.00 0.00 2.32
3985 6312 8.212312 TCTGTACCACTTCTTTTTATGTAACCA 58.788 33.333 0.00 0.00 0.00 3.67
3986 6313 8.611654 TCTGTACCACTTCTTTTTATGTAACC 57.388 34.615 0.00 0.00 0.00 2.85
3994 6321 7.706607 GCTTGATTTTCTGTACCACTTCTTTTT 59.293 33.333 0.00 0.00 0.00 1.94
3995 6322 7.147915 TGCTTGATTTTCTGTACCACTTCTTTT 60.148 33.333 0.00 0.00 0.00 2.27
3996 6323 6.321181 TGCTTGATTTTCTGTACCACTTCTTT 59.679 34.615 0.00 0.00 0.00 2.52
3997 6324 5.827797 TGCTTGATTTTCTGTACCACTTCTT 59.172 36.000 0.00 0.00 0.00 2.52
3998 6325 5.239525 GTGCTTGATTTTCTGTACCACTTCT 59.760 40.000 0.00 0.00 0.00 2.85
3999 6326 5.008613 TGTGCTTGATTTTCTGTACCACTTC 59.991 40.000 0.00 0.00 0.00 3.01
4004 6331 8.986477 ATATTTTGTGCTTGATTTTCTGTACC 57.014 30.769 0.00 0.00 0.00 3.34
4016 6343 7.339466 ACCTCCCTTAACTATATTTTGTGCTTG 59.661 37.037 0.00 0.00 0.00 4.01
4017 6344 7.410991 ACCTCCCTTAACTATATTTTGTGCTT 58.589 34.615 0.00 0.00 0.00 3.91
4018 6345 6.970191 ACCTCCCTTAACTATATTTTGTGCT 58.030 36.000 0.00 0.00 0.00 4.40
4019 6346 8.919777 ATACCTCCCTTAACTATATTTTGTGC 57.080 34.615 0.00 0.00 0.00 4.57
4043 6370 9.597170 CATGCATGAACAACTAGCTCTATATAT 57.403 33.333 22.59 0.00 0.00 0.86
4044 6371 8.806146 TCATGCATGAACAACTAGCTCTATATA 58.194 33.333 26.87 0.00 33.08 0.86
4086 6413 1.135333 CTGCTCTACCGGTTTCTCTCC 59.865 57.143 15.04 0.00 0.00 3.71
4244 6572 8.995220 TGAACTACACCAGTAAATTATGTTCAC 58.005 33.333 0.00 0.00 35.14 3.18
4266 6594 4.613622 CGAAGTTCCAATGACACCATGAAC 60.614 45.833 0.00 0.00 36.62 3.18
4418 6746 0.546507 TGACACCCATCTACTGCCCA 60.547 55.000 0.00 0.00 0.00 5.36
4694 7041 0.773644 AGTGCCATCCCACTTCACTT 59.226 50.000 0.00 0.00 43.19 3.16
4711 7058 6.012858 TGGTTCACCATAATCTCCAGTAAAGT 60.013 38.462 0.00 0.00 42.01 2.66
4990 8037 8.296713 AGTACGAATTCACATGTAAAGCAATTT 58.703 29.630 6.22 0.00 0.00 1.82
5053 8113 5.356291 TGCATTAATAATTGGCCAGCTTT 57.644 34.783 5.11 4.12 0.00 3.51
5286 8494 5.393461 CGTTACAACTAGTTTCCGGGATAGT 60.393 44.000 5.07 0.00 0.00 2.12
5336 8549 1.325355 TGTCTTTCCGAAGAGTCCGT 58.675 50.000 0.00 0.00 42.35 4.69
5346 8559 4.870991 GGACCTTCTTATCTTGTCTTTCCG 59.129 45.833 0.00 0.00 0.00 4.30
5370 8583 3.798202 CATCTTTGAGGCTAGGGTGTAC 58.202 50.000 0.00 0.00 0.00 2.90
5374 8587 0.179000 CGCATCTTTGAGGCTAGGGT 59.821 55.000 2.88 0.00 37.20 4.34
5442 8655 1.443802 TCGTGTGTCAACAGTTTGCA 58.556 45.000 0.00 0.00 36.84 4.08
5464 8677 1.597854 TCGAGGGTACACGTGACGT 60.598 57.895 25.01 4.10 42.36 4.34
5465 8678 1.154338 GTCGAGGGTACACGTGACG 60.154 63.158 25.01 16.05 0.00 4.35
5466 8679 1.154338 CGTCGAGGGTACACGTGAC 60.154 63.158 25.01 15.43 0.00 3.67
5467 8680 2.969806 GCGTCGAGGGTACACGTGA 61.970 63.158 25.01 2.68 35.91 4.35
5468 8681 2.503375 GCGTCGAGGGTACACGTG 60.503 66.667 15.48 15.48 35.91 4.49
5469 8682 3.741476 GGCGTCGAGGGTACACGT 61.741 66.667 7.31 0.00 35.91 4.49
5470 8683 4.824166 CGGCGTCGAGGGTACACG 62.824 72.222 1.44 0.00 39.00 4.49
5471 8684 4.487412 CCGGCGTCGAGGGTACAC 62.487 72.222 12.93 0.00 39.00 2.90
5491 8704 1.717937 GTGATCTGCGGTGCATCAC 59.282 57.895 9.38 9.38 39.96 3.06
5492 8705 1.810853 CGTGATCTGCGGTGCATCA 60.811 57.895 0.00 0.00 38.13 3.07
5493 8706 1.756375 GACGTGATCTGCGGTGCATC 61.756 60.000 13.14 0.00 38.13 3.91
5494 8707 1.811266 GACGTGATCTGCGGTGCAT 60.811 57.895 13.14 0.00 38.13 3.96
5495 8708 2.432456 GACGTGATCTGCGGTGCA 60.432 61.111 13.14 0.00 36.92 4.57
5496 8709 3.545481 CGACGTGATCTGCGGTGC 61.545 66.667 13.14 3.74 0.00 5.01
5497 8710 1.406219 CTTCGACGTGATCTGCGGTG 61.406 60.000 13.14 6.48 0.00 4.94
5498 8711 1.154016 CTTCGACGTGATCTGCGGT 60.154 57.895 13.14 0.00 0.00 5.68
5499 8712 1.874019 CCTTCGACGTGATCTGCGG 60.874 63.158 13.14 0.00 0.00 5.69
5500 8713 0.863538 CTCCTTCGACGTGATCTGCG 60.864 60.000 0.00 8.33 0.00 5.18
5501 8714 0.452184 TCTCCTTCGACGTGATCTGC 59.548 55.000 0.00 0.00 0.00 4.26
5502 8715 1.202200 GGTCTCCTTCGACGTGATCTG 60.202 57.143 0.00 0.00 34.75 2.90
5503 8716 1.096416 GGTCTCCTTCGACGTGATCT 58.904 55.000 0.00 0.00 34.75 2.75
5504 8717 0.100861 GGGTCTCCTTCGACGTGATC 59.899 60.000 0.00 0.00 34.75 2.92
5505 8718 1.654954 CGGGTCTCCTTCGACGTGAT 61.655 60.000 0.00 0.00 34.75 3.06
5506 8719 2.330372 CGGGTCTCCTTCGACGTGA 61.330 63.158 0.00 0.00 34.75 4.35
5507 8720 2.178521 CGGGTCTCCTTCGACGTG 59.821 66.667 0.00 0.00 34.75 4.49
5508 8721 3.060615 CCGGGTCTCCTTCGACGT 61.061 66.667 0.00 0.00 34.75 4.34
5509 8722 4.493747 GCCGGGTCTCCTTCGACG 62.494 72.222 2.18 0.00 34.75 5.12
5510 8723 4.144703 GGCCGGGTCTCCTTCGAC 62.145 72.222 2.18 0.00 0.00 4.20
5513 8726 4.144703 GTCGGCCGGGTCTCCTTC 62.145 72.222 27.83 1.14 0.00 3.46
5535 8748 1.181001 GTCGACTGTCTTGCGTATCG 58.819 55.000 8.70 0.00 0.00 2.92
5536 8749 1.181001 CGTCGACTGTCTTGCGTATC 58.819 55.000 14.70 0.00 0.00 2.24
5537 8750 0.179171 CCGTCGACTGTCTTGCGTAT 60.179 55.000 14.70 0.00 0.00 3.06
5538 8751 1.208358 CCGTCGACTGTCTTGCGTA 59.792 57.895 14.70 0.00 0.00 4.42
5539 8752 2.050351 CCGTCGACTGTCTTGCGT 60.050 61.111 14.70 0.00 0.00 5.24
5540 8753 2.805353 CCCGTCGACTGTCTTGCG 60.805 66.667 14.70 7.28 0.00 4.85
5541 8754 3.112709 GCCCGTCGACTGTCTTGC 61.113 66.667 14.70 2.09 0.00 4.01
5542 8755 2.805353 CGCCCGTCGACTGTCTTG 60.805 66.667 14.70 0.00 41.67 3.02
5543 8756 4.719369 GCGCCCGTCGACTGTCTT 62.719 66.667 14.70 0.00 41.67 3.01
5545 8758 4.719369 AAGCGCCCGTCGACTGTC 62.719 66.667 14.70 0.00 41.67 3.51
5546 8759 3.802418 AAAAGCGCCCGTCGACTGT 62.802 57.895 14.70 0.00 41.67 3.55
5547 8760 3.041940 AAAAGCGCCCGTCGACTG 61.042 61.111 14.70 7.04 41.67 3.51
5548 8761 3.041940 CAAAAGCGCCCGTCGACT 61.042 61.111 14.70 0.00 41.67 4.18
5549 8762 4.736631 GCAAAAGCGCCCGTCGAC 62.737 66.667 2.29 5.18 41.67 4.20
5551 8764 4.741781 CTGCAAAAGCGCCCGTCG 62.742 66.667 2.29 0.00 42.12 5.12
5552 8765 3.353836 TCTGCAAAAGCGCCCGTC 61.354 61.111 2.29 0.00 0.00 4.79
5553 8766 3.660111 GTCTGCAAAAGCGCCCGT 61.660 61.111 2.29 0.00 0.00 5.28
5554 8767 4.404654 GGTCTGCAAAAGCGCCCG 62.405 66.667 2.29 0.00 0.00 6.13
5555 8768 4.056125 GGGTCTGCAAAAGCGCCC 62.056 66.667 2.29 0.00 34.89 6.13
5556 8769 4.404654 CGGGTCTGCAAAAGCGCC 62.405 66.667 2.29 0.00 0.00 6.53
5557 8770 2.400896 TTTCGGGTCTGCAAAAGCGC 62.401 55.000 0.00 0.00 0.00 5.92
5558 8771 0.030101 TTTTCGGGTCTGCAAAAGCG 59.970 50.000 0.00 0.00 0.00 4.68
5559 8772 1.487482 GTTTTCGGGTCTGCAAAAGC 58.513 50.000 0.00 0.00 0.00 3.51
5560 8773 1.269569 GGGTTTTCGGGTCTGCAAAAG 60.270 52.381 0.00 0.00 0.00 2.27
5561 8774 0.747852 GGGTTTTCGGGTCTGCAAAA 59.252 50.000 0.00 0.00 0.00 2.44
5562 8775 2.421220 GGGTTTTCGGGTCTGCAAA 58.579 52.632 0.00 0.00 0.00 3.68
5563 8776 4.167597 GGGTTTTCGGGTCTGCAA 57.832 55.556 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.