Multiple sequence alignment - TraesCS3B01G298700

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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 TraesCS3B01G298700 chr3B 100.000 4597 0 0 1 4597 479493780 479498376 0.000000e+00 8490.0
1 TraesCS3B01G298700 chr3B 86.092 1891 126 45 1906 3729 411506645 411504825 0.000000e+00 1908.0
2 TraesCS3B01G298700 chr3B 89.243 753 62 9 3861 4595 27047806 27047055 0.000000e+00 924.0
3 TraesCS3B01G298700 chr3B 88.518 749 63 11 3865 4595 92668188 92667445 0.000000e+00 885.0
4 TraesCS3B01G298700 chr3B 95.652 299 10 2 54 352 127361285 127361580 1.160000e-130 477.0
5 TraesCS3B01G298700 chr3B 94.667 300 12 3 53 352 127358673 127358968 3.240000e-126 462.0
6 TraesCS3B01G298700 chr3B 87.593 403 44 4 7 409 644925646 644925250 3.240000e-126 462.0
7 TraesCS3B01G298700 chr3B 94.352 301 14 1 52 352 98803388 98803091 4.190000e-125 459.0
8 TraesCS3B01G298700 chr3B 89.971 349 29 4 47 395 823180280 823179938 3.260000e-121 446.0
9 TraesCS3B01G298700 chr3B 84.581 454 28 16 970 1416 411507836 411507418 3.310000e-111 412.0
10 TraesCS3B01G298700 chr3B 90.148 203 12 5 541 741 411510280 411510084 1.640000e-64 257.0
11 TraesCS3B01G298700 chr3B 81.863 204 16 8 351 536 783452907 783452707 7.970000e-33 152.0
12 TraesCS3B01G298700 chr3B 81.500 200 18 9 1605 1791 411506993 411506800 3.710000e-31 147.0
13 TraesCS3B01G298700 chr3B 82.857 140 19 4 403 541 733115278 733115413 2.250000e-23 121.0
14 TraesCS3B01G298700 chr3B 95.122 41 1 1 502 542 818291249 818291210 3.840000e-06 63.9
15 TraesCS3B01G298700 chr3A 91.783 2714 131 31 541 3192 489565371 489568054 0.000000e+00 3692.0
16 TraesCS3B01G298700 chr3A 85.960 2037 136 51 1906 3866 429462793 429464755 0.000000e+00 2039.0
17 TraesCS3B01G298700 chr3A 89.405 689 27 5 3194 3868 489568085 489568741 0.000000e+00 826.0
18 TraesCS3B01G298700 chr3A 86.159 289 17 10 918 1200 429461628 429461899 1.620000e-74 291.0
19 TraesCS3B01G298700 chr3A 91.398 186 13 2 611 795 429461048 429461231 7.630000e-63 252.0
20 TraesCS3B01G298700 chr3A 85.321 109 7 4 803 910 429461493 429461593 2.260000e-18 104.0
21 TraesCS3B01G298700 chr3D 91.171 2050 96 27 1597 3599 367358244 367360255 0.000000e+00 2704.0
22 TraesCS3B01G298700 chr3D 87.139 1765 112 34 1906 3599 309689331 309691051 0.000000e+00 1895.0
23 TraesCS3B01G298700 chr3D 89.780 910 33 18 720 1601 367356862 367357739 0.000000e+00 1110.0
24 TraesCS3B01G298700 chr3D 83.186 565 38 21 801 1353 309688147 309688666 9.010000e-127 464.0
25 TraesCS3B01G298700 chr3D 93.204 206 13 1 3663 3867 367360324 367360529 7.470000e-78 302.0
26 TraesCS3B01G298700 chr3D 77.895 475 54 33 1363 1825 309688766 309689201 9.880000e-62 248.0
27 TraesCS3B01G298700 chr3D 90.000 190 4 4 543 730 367347385 367347561 9.950000e-57 231.0
28 TraesCS3B01G298700 chr3D 94.231 104 4 2 640 741 309677730 309677833 1.710000e-34 158.0
29 TraesCS3B01G298700 chr3D 95.890 73 2 1 3632 3703 309691055 309691127 2.910000e-22 117.0
30 TraesCS3B01G298700 chr3D 100.000 54 0 0 3625 3678 367360252 367360305 2.930000e-17 100.0
31 TraesCS3B01G298700 chrUn 89.200 750 65 8 3864 4597 8848241 8848990 0.000000e+00 922.0
32 TraesCS3B01G298700 chrUn 85.500 200 23 4 1055 1251 8110892 8111088 2.170000e-48 204.0
33 TraesCS3B01G298700 chr7B 88.933 750 60 11 3867 4597 679571457 679572202 0.000000e+00 904.0
34 TraesCS3B01G298700 chr7B 88.462 52 3 3 491 541 196707665 196707714 4.970000e-05 60.2
35 TraesCS3B01G298700 chr2B 88.360 756 61 9 3868 4597 47645250 47646004 0.000000e+00 883.0
36 TraesCS3B01G298700 chr2B 86.684 751 65 22 3867 4597 728929643 728930378 0.000000e+00 800.0
37 TraesCS3B01G298700 chr2B 95.318 299 11 1 54 352 593792211 593791916 5.380000e-129 472.0
38 TraesCS3B01G298700 chr4A 88.766 721 58 18 3896 4597 649837871 649838587 0.000000e+00 861.0
39 TraesCS3B01G298700 chr4A 93.023 43 3 0 505 547 5117982 5117940 3.840000e-06 63.9
40 TraesCS3B01G298700 chr5B 87.968 748 63 12 3866 4596 678098642 678097905 0.000000e+00 857.0
41 TraesCS3B01G298700 chr5B 87.318 757 65 4 3867 4597 653306596 653305845 0.000000e+00 837.0
42 TraesCS3B01G298700 chr5B 84.768 151 18 1 355 500 538593667 538593817 3.710000e-31 147.0
43 TraesCS3B01G298700 chr5B 98.276 58 1 0 354 411 353210538 353210481 8.140000e-18 102.0
44 TraesCS3B01G298700 chr6B 87.251 753 63 15 3865 4597 35073224 35072485 0.000000e+00 828.0
45 TraesCS3B01G298700 chr6B 87.118 753 64 15 3865 4597 35102519 35101780 0.000000e+00 822.0
46 TraesCS3B01G298700 chr6B 86.447 760 75 11 3864 4597 1975154 1975911 0.000000e+00 808.0
47 TraesCS3B01G298700 chr6B 94.333 300 14 1 53 352 479295957 479296253 1.510000e-124 457.0
48 TraesCS3B01G298700 chr4B 93.090 521 34 1 4077 4597 562348484 562347966 0.000000e+00 761.0
49 TraesCS3B01G298700 chr4B 85.827 381 42 7 3865 4238 34442957 34442582 1.200000e-105 394.0
50 TraesCS3B01G298700 chr4B 98.077 52 1 0 4 55 652975081 652975132 1.760000e-14 91.6
51 TraesCS3B01G298700 chr1B 84.923 776 72 21 3864 4597 29920989 29921761 0.000000e+00 743.0
52 TraesCS3B01G298700 chr1B 95.652 299 9 2 54 352 657044585 657044879 1.160000e-130 477.0
53 TraesCS3B01G298700 chr1B 86.352 381 45 5 3861 4238 561620778 561621154 4.280000e-110 409.0
54 TraesCS3B01G298700 chr1B 87.640 356 34 7 3863 4214 279534161 279534510 5.540000e-109 405.0
55 TraesCS3B01G298700 chr1B 89.899 99 7 1 1156 1251 105092976 105093074 1.740000e-24 124.0
56 TraesCS3B01G298700 chr1B 79.042 167 17 6 352 500 46871816 46871982 1.050000e-16 99.0
57 TraesCS3B01G298700 chr2D 94.040 302 15 1 51 352 628034735 628034437 5.420000e-124 455.0
58 TraesCS3B01G298700 chr2D 82.738 168 10 7 351 500 299555132 299554966 1.040000e-26 132.0
59 TraesCS3B01G298700 chr2D 90.625 64 5 1 3 66 362931019 362930957 2.950000e-12 84.2
60 TraesCS3B01G298700 chr7D 88.102 353 37 3 3865 4214 628443205 628443555 9.200000e-112 414.0
61 TraesCS3B01G298700 chr1D 86.500 200 21 4 1055 1251 460789464 460789660 1.000000e-51 215.0
62 TraesCS3B01G298700 chr1D 91.935 62 5 0 5 66 57422845 57422784 2.280000e-13 87.9
63 TraesCS3B01G298700 chr1A 84.545 220 26 6 1059 1273 551875137 551875353 1.300000e-50 211.0
64 TraesCS3B01G298700 chr1A 85.119 168 7 5 351 500 15510412 15510579 6.160000e-34 156.0
65 TraesCS3B01G298700 chr6A 83.069 189 21 3 351 533 29780279 29780096 1.320000e-35 161.0
66 TraesCS3B01G298700 chr2A 83.626 171 10 6 351 503 75607274 75607104 1.330000e-30 145.0
67 TraesCS3B01G298700 chr2A 97.561 41 0 1 502 541 41029260 41029220 8.250000e-08 69.4
68 TraesCS3B01G298700 chr4D 83.333 168 10 6 351 500 332376511 332376344 6.200000e-29 139.0
69 TraesCS3B01G298700 chr5A 81.977 172 12 7 351 504 304124330 304124160 1.340000e-25 128.0
70 TraesCS3B01G298700 chr5A 92.500 80 6 0 404 483 211607850 211607929 1.050000e-21 115.0
71 TraesCS3B01G298700 chr5A 89.796 49 2 3 506 554 538851176 538851131 4.970000e-05 60.2
72 TraesCS3B01G298700 chr6D 82.963 135 18 4 351 480 183016697 183016831 2.910000e-22 117.0
73 TraesCS3B01G298700 chr6D 91.803 61 5 0 6 66 54121217 54121157 8.190000e-13 86.1
74 TraesCS3B01G298700 chr6D 91.803 61 5 0 6 66 70376601 70376661 8.190000e-13 86.1
75 TraesCS3B01G298700 chr6D 91.803 61 5 0 6 66 296961661 296961601 8.190000e-13 86.1
76 TraesCS3B01G298700 chr7A 98.276 58 1 0 354 411 659640988 659640931 8.140000e-18 102.0
77 TraesCS3B01G298700 chr5D 93.443 61 4 0 6 66 147361922 147361982 1.760000e-14 91.6


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 TraesCS3B01G298700 chr3B 479493780 479498376 4596 False 8490.0 8490 100.00000 1 4597 1 chr3B.!!$F1 4596
1 TraesCS3B01G298700 chr3B 27047055 27047806 751 True 924.0 924 89.24300 3861 4595 1 chr3B.!!$R1 734
2 TraesCS3B01G298700 chr3B 92667445 92668188 743 True 885.0 885 88.51800 3865 4595 1 chr3B.!!$R2 730
3 TraesCS3B01G298700 chr3B 411504825 411510280 5455 True 681.0 1908 85.58025 541 3729 4 chr3B.!!$R8 3188
4 TraesCS3B01G298700 chr3B 127358673 127361580 2907 False 469.5 477 95.15950 53 352 2 chr3B.!!$F3 299
5 TraesCS3B01G298700 chr3A 489565371 489568741 3370 False 2259.0 3692 90.59400 541 3868 2 chr3A.!!$F2 3327
6 TraesCS3B01G298700 chr3A 429461048 429464755 3707 False 671.5 2039 87.20950 611 3866 4 chr3A.!!$F1 3255
7 TraesCS3B01G298700 chr3D 367356862 367360529 3667 False 1054.0 2704 93.53875 720 3867 4 chr3D.!!$F4 3147
8 TraesCS3B01G298700 chr3D 309688147 309691127 2980 False 681.0 1895 86.02750 801 3703 4 chr3D.!!$F3 2902
9 TraesCS3B01G298700 chrUn 8848241 8848990 749 False 922.0 922 89.20000 3864 4597 1 chrUn.!!$F2 733
10 TraesCS3B01G298700 chr7B 679571457 679572202 745 False 904.0 904 88.93300 3867 4597 1 chr7B.!!$F2 730
11 TraesCS3B01G298700 chr2B 47645250 47646004 754 False 883.0 883 88.36000 3868 4597 1 chr2B.!!$F1 729
12 TraesCS3B01G298700 chr2B 728929643 728930378 735 False 800.0 800 86.68400 3867 4597 1 chr2B.!!$F2 730
13 TraesCS3B01G298700 chr4A 649837871 649838587 716 False 861.0 861 88.76600 3896 4597 1 chr4A.!!$F1 701
14 TraesCS3B01G298700 chr5B 678097905 678098642 737 True 857.0 857 87.96800 3866 4596 1 chr5B.!!$R3 730
15 TraesCS3B01G298700 chr5B 653305845 653306596 751 True 837.0 837 87.31800 3867 4597 1 chr5B.!!$R2 730
16 TraesCS3B01G298700 chr6B 35072485 35073224 739 True 828.0 828 87.25100 3865 4597 1 chr6B.!!$R1 732
17 TraesCS3B01G298700 chr6B 35101780 35102519 739 True 822.0 822 87.11800 3865 4597 1 chr6B.!!$R2 732
18 TraesCS3B01G298700 chr6B 1975154 1975911 757 False 808.0 808 86.44700 3864 4597 1 chr6B.!!$F1 733
19 TraesCS3B01G298700 chr4B 562347966 562348484 518 True 761.0 761 93.09000 4077 4597 1 chr4B.!!$R2 520
20 TraesCS3B01G298700 chr1B 29920989 29921761 772 False 743.0 743 84.92300 3864 4597 1 chr1B.!!$F1 733

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
534 3146 0.331278 CCCCATTACAACCAGCCTCA 59.669 55.000 0.0 0.0 0.00 3.86 F
1474 6584 1.270732 GGCTCATCGAGATTGCTCCAT 60.271 52.381 0.0 0.0 37.91 3.41 F
2313 8107 0.760567 TGGCCATCAGCGTCTCCTAT 60.761 55.000 0.0 0.0 45.17 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 7554 1.340697 ACCGTGGAGGAAATTTAGGCC 60.341 52.381 0.00 0.0 45.0 5.19 R
2585 8391 0.759346 GCCCCGACATGAGGATAAGT 59.241 55.000 12.39 0.0 0.0 2.24 R
3743 9715 0.464013 TTTCGCCTCGGACACCAAAA 60.464 50.000 0.00 0.0 0.0 2.44 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
17 18 4.096003 GGCTTCAGGCTGCCCGTA 62.096 66.667 16.57 0.00 43.11 4.02
18 19 2.046314 GCTTCAGGCTGCCCGTAA 60.046 61.111 16.57 6.42 38.06 3.18
19 20 1.452108 GCTTCAGGCTGCCCGTAAT 60.452 57.895 16.57 0.00 38.06 1.89
20 21 1.718757 GCTTCAGGCTGCCCGTAATG 61.719 60.000 16.57 6.81 38.06 1.90
21 22 1.077787 TTCAGGCTGCCCGTAATGG 60.078 57.895 16.57 0.00 35.76 3.16
22 23 1.847798 TTCAGGCTGCCCGTAATGGT 61.848 55.000 16.57 0.00 35.15 3.55
23 24 0.978667 TCAGGCTGCCCGTAATGGTA 60.979 55.000 16.57 0.00 35.15 3.25
24 25 0.532862 CAGGCTGCCCGTAATGGTAG 60.533 60.000 16.57 0.00 40.72 3.18
25 26 0.981277 AGGCTGCCCGTAATGGTAGT 60.981 55.000 16.57 0.00 39.99 2.73
26 27 0.754472 GGCTGCCCGTAATGGTAGTA 59.246 55.000 7.66 0.00 39.99 1.82
27 28 1.346722 GGCTGCCCGTAATGGTAGTAT 59.653 52.381 7.66 0.00 39.99 2.12
28 29 2.612221 GGCTGCCCGTAATGGTAGTATC 60.612 54.545 7.66 0.00 39.99 2.24
29 30 2.036733 GCTGCCCGTAATGGTAGTATCA 59.963 50.000 0.00 0.00 39.99 2.15
30 31 3.306780 GCTGCCCGTAATGGTAGTATCAT 60.307 47.826 0.00 0.00 39.99 2.45
31 32 4.081862 GCTGCCCGTAATGGTAGTATCATA 60.082 45.833 0.00 0.00 39.99 2.15
32 33 5.651530 CTGCCCGTAATGGTAGTATCATAG 58.348 45.833 0.00 0.00 33.82 2.23
33 34 4.464951 TGCCCGTAATGGTAGTATCATAGG 59.535 45.833 0.00 1.45 35.15 2.57
34 35 4.465305 GCCCGTAATGGTAGTATCATAGGT 59.535 45.833 0.00 0.00 35.15 3.08
35 36 5.653769 GCCCGTAATGGTAGTATCATAGGTA 59.346 44.000 0.00 0.00 35.15 3.08
36 37 6.183360 GCCCGTAATGGTAGTATCATAGGTAG 60.183 46.154 0.00 0.00 35.15 3.18
37 38 6.888632 CCCGTAATGGTAGTATCATAGGTAGT 59.111 42.308 0.00 0.00 35.15 2.73
38 39 8.049117 CCCGTAATGGTAGTATCATAGGTAGTA 58.951 40.741 0.00 0.00 35.15 1.82
39 40 9.624373 CCGTAATGGTAGTATCATAGGTAGTAT 57.376 37.037 0.00 0.00 0.00 2.12
44 45 8.521170 TGGTAGTATCATAGGTAGTATCATGC 57.479 38.462 0.00 0.00 0.00 4.06
45 46 8.113462 TGGTAGTATCATAGGTAGTATCATGCA 58.887 37.037 0.00 0.00 0.00 3.96
46 47 9.137459 GGTAGTATCATAGGTAGTATCATGCAT 57.863 37.037 0.00 0.00 0.00 3.96
47 48 9.958234 GTAGTATCATAGGTAGTATCATGCATG 57.042 37.037 21.07 21.07 0.00 4.06
48 49 7.495901 AGTATCATAGGTAGTATCATGCATGC 58.504 38.462 22.25 11.82 0.00 4.06
49 50 5.089970 TCATAGGTAGTATCATGCATGCC 57.910 43.478 22.25 15.40 0.00 4.40
50 51 4.531732 TCATAGGTAGTATCATGCATGCCA 59.468 41.667 22.25 8.84 0.00 4.92
51 52 3.862877 AGGTAGTATCATGCATGCCAA 57.137 42.857 22.25 5.34 0.00 4.52
65 66 0.834687 TGCCAACTACTCCCTCCGTT 60.835 55.000 0.00 0.00 0.00 4.44
114 2726 1.609501 CGTGACCAAGGAGGAGGGA 60.610 63.158 0.00 0.00 41.22 4.20
120 2732 1.856920 ACCAAGGAGGAGGGAAAAACA 59.143 47.619 0.00 0.00 41.22 2.83
192 2804 0.661187 CCACTGCATGTCGTGTTTGC 60.661 55.000 13.12 0.00 36.91 3.68
283 2895 5.240713 ACGAGGTAGAAGTTAATGTACCG 57.759 43.478 0.00 0.00 42.49 4.02
341 2953 7.393841 AAGATGACTTACACACCTACTAGAC 57.606 40.000 0.00 0.00 34.28 2.59
342 2954 5.585445 AGATGACTTACACACCTACTAGACG 59.415 44.000 0.00 0.00 0.00 4.18
343 2955 4.005650 TGACTTACACACCTACTAGACGG 58.994 47.826 0.00 0.00 0.00 4.79
344 2956 4.256920 GACTTACACACCTACTAGACGGA 58.743 47.826 0.00 0.00 0.00 4.69
345 2957 4.260170 ACTTACACACCTACTAGACGGAG 58.740 47.826 0.00 0.00 0.00 4.63
346 2958 2.125773 ACACACCTACTAGACGGAGG 57.874 55.000 0.00 0.00 36.36 4.30
347 2959 1.340795 ACACACCTACTAGACGGAGGG 60.341 57.143 0.00 0.00 34.41 4.30
348 2960 1.064906 CACACCTACTAGACGGAGGGA 60.065 57.143 0.00 0.00 34.41 4.20
349 2961 1.212441 ACACCTACTAGACGGAGGGAG 59.788 57.143 0.00 0.00 34.41 4.30
350 2962 1.212441 CACCTACTAGACGGAGGGAGT 59.788 57.143 0.00 0.00 34.41 3.85
351 2963 2.437281 CACCTACTAGACGGAGGGAGTA 59.563 54.545 0.00 0.00 34.41 2.59
352 2964 3.118112 CACCTACTAGACGGAGGGAGTAA 60.118 52.174 0.00 0.00 34.41 2.24
353 2965 3.136260 ACCTACTAGACGGAGGGAGTAAG 59.864 52.174 0.00 0.00 34.41 2.34
354 2966 2.055684 ACTAGACGGAGGGAGTAAGC 57.944 55.000 0.00 0.00 0.00 3.09
355 2967 1.284198 ACTAGACGGAGGGAGTAAGCA 59.716 52.381 0.00 0.00 0.00 3.91
356 2968 2.291411 ACTAGACGGAGGGAGTAAGCAA 60.291 50.000 0.00 0.00 0.00 3.91
357 2969 1.867363 AGACGGAGGGAGTAAGCAAT 58.133 50.000 0.00 0.00 0.00 3.56
358 2970 2.188817 AGACGGAGGGAGTAAGCAATT 58.811 47.619 0.00 0.00 0.00 2.32
359 2971 2.572104 AGACGGAGGGAGTAAGCAATTT 59.428 45.455 0.00 0.00 0.00 1.82
360 2972 3.009143 AGACGGAGGGAGTAAGCAATTTT 59.991 43.478 0.00 0.00 0.00 1.82
361 2973 3.081804 ACGGAGGGAGTAAGCAATTTTG 58.918 45.455 0.00 0.00 0.00 2.44
362 2974 3.244770 ACGGAGGGAGTAAGCAATTTTGA 60.245 43.478 0.00 0.00 0.00 2.69
363 2975 3.947834 CGGAGGGAGTAAGCAATTTTGAT 59.052 43.478 0.00 0.00 0.00 2.57
364 2976 4.201950 CGGAGGGAGTAAGCAATTTTGATG 60.202 45.833 0.00 0.00 0.00 3.07
365 2977 4.949856 GGAGGGAGTAAGCAATTTTGATGA 59.050 41.667 0.00 0.00 0.00 2.92
366 2978 5.067023 GGAGGGAGTAAGCAATTTTGATGAG 59.933 44.000 0.00 0.00 0.00 2.90
367 2979 5.819991 AGGGAGTAAGCAATTTTGATGAGA 58.180 37.500 0.00 0.00 0.00 3.27
368 2980 6.430007 AGGGAGTAAGCAATTTTGATGAGAT 58.570 36.000 0.00 0.00 0.00 2.75
369 2981 6.320672 AGGGAGTAAGCAATTTTGATGAGATG 59.679 38.462 0.00 0.00 0.00 2.90
370 2982 6.096001 GGGAGTAAGCAATTTTGATGAGATGT 59.904 38.462 0.00 0.00 0.00 3.06
371 2983 7.192232 GGAGTAAGCAATTTTGATGAGATGTC 58.808 38.462 0.00 0.00 0.00 3.06
372 2984 7.148188 GGAGTAAGCAATTTTGATGAGATGTCA 60.148 37.037 0.00 0.00 37.02 3.58
373 2985 8.289939 AGTAAGCAATTTTGATGAGATGTCAT 57.710 30.769 4.78 4.78 46.75 3.06
374 2986 9.399797 AGTAAGCAATTTTGATGAGATGTCATA 57.600 29.630 5.15 0.00 43.92 2.15
375 2987 9.661187 GTAAGCAATTTTGATGAGATGTCATAG 57.339 33.333 5.15 0.00 43.92 2.23
376 2988 8.515695 AAGCAATTTTGATGAGATGTCATAGA 57.484 30.769 5.15 0.00 43.92 1.98
377 2989 8.515695 AGCAATTTTGATGAGATGTCATAGAA 57.484 30.769 5.15 1.15 43.92 2.10
378 2990 9.132923 AGCAATTTTGATGAGATGTCATAGAAT 57.867 29.630 5.15 4.07 43.92 2.40
379 2991 9.745880 GCAATTTTGATGAGATGTCATAGAATT 57.254 29.630 5.15 9.32 43.92 2.17
403 3015 8.924511 TTAAATGAAGAAAGAGATGGTTGAGT 57.075 30.769 0.00 0.00 0.00 3.41
406 3018 8.729805 AATGAAGAAAGAGATGGTTGAGTATC 57.270 34.615 0.00 0.00 0.00 2.24
437 3049 6.668541 ATGATGTACTACTTTGTGTCATGC 57.331 37.500 0.00 0.00 0.00 4.06
438 3050 5.546526 TGATGTACTACTTTGTGTCATGCA 58.453 37.500 0.00 0.00 0.00 3.96
439 3051 6.172630 TGATGTACTACTTTGTGTCATGCAT 58.827 36.000 0.00 0.00 0.00 3.96
440 3052 7.327214 TGATGTACTACTTTGTGTCATGCATA 58.673 34.615 0.00 0.00 0.00 3.14
441 3053 7.821846 TGATGTACTACTTTGTGTCATGCATAA 59.178 33.333 0.00 0.00 0.00 1.90
442 3054 8.737168 ATGTACTACTTTGTGTCATGCATAAT 57.263 30.769 0.00 0.00 0.00 1.28
443 3055 9.830975 ATGTACTACTTTGTGTCATGCATAATA 57.169 29.630 0.00 0.00 0.00 0.98
444 3056 9.660180 TGTACTACTTTGTGTCATGCATAATAA 57.340 29.630 0.00 0.00 0.00 1.40
490 3102 7.639039 ACCAACATATGATACTTTACATTGCG 58.361 34.615 10.38 0.00 0.00 4.85
491 3103 7.077605 CCAACATATGATACTTTACATTGCGG 58.922 38.462 10.38 0.00 0.00 5.69
492 3104 7.041440 CCAACATATGATACTTTACATTGCGGA 60.041 37.037 10.38 0.00 0.00 5.54
493 3105 8.506437 CAACATATGATACTTTACATTGCGGAT 58.494 33.333 10.38 0.00 0.00 4.18
494 3106 8.032952 ACATATGATACTTTACATTGCGGATG 57.967 34.615 10.38 0.00 41.71 3.51
496 3108 9.150348 CATATGATACTTTACATTGCGGATGTA 57.850 33.333 0.00 8.24 47.00 2.29
528 3140 8.694171 ATATATGATACTCCCCATTACAACCA 57.306 34.615 0.00 0.00 0.00 3.67
529 3141 4.771114 TGATACTCCCCATTACAACCAG 57.229 45.455 0.00 0.00 0.00 4.00
530 3142 3.118038 TGATACTCCCCATTACAACCAGC 60.118 47.826 0.00 0.00 0.00 4.85
531 3143 0.331616 ACTCCCCATTACAACCAGCC 59.668 55.000 0.00 0.00 0.00 4.85
532 3144 0.625849 CTCCCCATTACAACCAGCCT 59.374 55.000 0.00 0.00 0.00 4.58
533 3145 0.623723 TCCCCATTACAACCAGCCTC 59.376 55.000 0.00 0.00 0.00 4.70
534 3146 0.331278 CCCCATTACAACCAGCCTCA 59.669 55.000 0.00 0.00 0.00 3.86
535 3147 1.683011 CCCCATTACAACCAGCCTCAG 60.683 57.143 0.00 0.00 0.00 3.35
536 3148 1.281867 CCCATTACAACCAGCCTCAGA 59.718 52.381 0.00 0.00 0.00 3.27
537 3149 2.636830 CCATTACAACCAGCCTCAGAG 58.363 52.381 0.00 0.00 0.00 3.35
538 3150 2.237143 CCATTACAACCAGCCTCAGAGA 59.763 50.000 0.00 0.00 0.00 3.10
539 3151 3.307691 CCATTACAACCAGCCTCAGAGAA 60.308 47.826 0.00 0.00 0.00 2.87
540 3152 4.326826 CATTACAACCAGCCTCAGAGAAA 58.673 43.478 0.00 0.00 0.00 2.52
541 3153 2.557920 ACAACCAGCCTCAGAGAAAG 57.442 50.000 0.00 0.00 0.00 2.62
542 3154 2.050144 ACAACCAGCCTCAGAGAAAGA 58.950 47.619 0.00 0.00 0.00 2.52
543 3155 2.439507 ACAACCAGCCTCAGAGAAAGAA 59.560 45.455 0.00 0.00 0.00 2.52
544 3156 3.117888 ACAACCAGCCTCAGAGAAAGAAA 60.118 43.478 0.00 0.00 0.00 2.52
569 3181 6.402981 AGAGGAAAGGAATTTAAGGCCTTA 57.597 37.500 21.68 21.68 40.97 2.69
572 3184 7.901322 AGAGGAAAGGAATTTAAGGCCTTATTT 59.099 33.333 25.70 20.16 40.97 1.40
649 3265 4.436847 CGTTCTATCCTCAACATCGTTACG 59.563 45.833 0.00 0.00 0.00 3.18
651 3267 6.489675 GTTCTATCCTCAACATCGTTACGTA 58.510 40.000 4.24 0.00 0.00 3.57
652 3268 6.052840 TCTATCCTCAACATCGTTACGTAC 57.947 41.667 4.24 0.00 0.00 3.67
653 3269 4.707030 ATCCTCAACATCGTTACGTACA 57.293 40.909 4.24 0.00 0.00 2.90
654 3270 4.707030 TCCTCAACATCGTTACGTACAT 57.293 40.909 4.24 0.00 0.00 2.29
767 3644 6.109156 TGCACAGGATCCACGTTATATATT 57.891 37.500 15.82 0.00 0.00 1.28
777 3654 5.704053 TCCACGTTATATATTCTCAGAGCGA 59.296 40.000 0.00 0.00 0.00 4.93
985 5724 1.405821 GTTCGATCATCCACCTCGAGT 59.594 52.381 12.31 0.00 41.83 4.18
1040 5809 2.683933 GCGGAAGGACCAGGAGGA 60.684 66.667 0.00 0.00 38.90 3.71
1041 5810 3.020237 GCGGAAGGACCAGGAGGAC 62.020 68.421 0.00 0.00 38.90 3.85
1042 5811 2.711922 CGGAAGGACCAGGAGGACG 61.712 68.421 0.00 0.00 38.90 4.79
1043 5812 2.579738 GAAGGACCAGGAGGACGC 59.420 66.667 0.00 0.00 38.69 5.19
1044 5813 3.003763 AAGGACCAGGAGGACGCC 61.004 66.667 0.00 0.00 38.69 5.68
1360 6379 1.687563 TCCATTCGCCTCGTGATAGA 58.312 50.000 0.00 0.00 0.00 1.98
1428 6538 1.416813 CTCTGCTCGTCCATTGCGAC 61.417 60.000 0.00 0.00 34.47 5.19
1474 6584 1.270732 GGCTCATCGAGATTGCTCCAT 60.271 52.381 0.00 0.00 37.91 3.41
1475 6585 2.067766 GCTCATCGAGATTGCTCCATC 58.932 52.381 0.00 0.00 37.91 3.51
1587 6723 2.418976 CAGTTGGATGAGCATGTGACTG 59.581 50.000 0.00 0.00 0.00 3.51
1618 7319 8.575649 TTTTCTAACTGGGAATTATTGAGACC 57.424 34.615 0.00 0.00 0.00 3.85
1707 7417 6.879276 TCCTTGTATCAACTAGTCCGATAG 57.121 41.667 12.85 6.10 0.00 2.08
1828 7554 3.388308 TGGATTTTGCACCATTTTGTCG 58.612 40.909 0.00 0.00 0.00 4.35
2283 8077 1.688187 GACGGGGATGGGGTACACT 60.688 63.158 0.00 0.00 0.00 3.55
2310 8104 2.202987 CTGGCCATCAGCGTCTCC 60.203 66.667 5.51 0.00 45.17 3.71
2313 8107 0.760567 TGGCCATCAGCGTCTCCTAT 60.761 55.000 0.00 0.00 45.17 2.57
2477 8277 8.204903 TGGTAACCACTTGAACCTAGTAATTA 57.795 34.615 0.00 0.00 32.99 1.40
2502 8303 7.605410 AAAATGAAATTAGCTCTGCATTTGG 57.395 32.000 9.13 0.00 33.67 3.28
2503 8304 6.534475 AATGAAATTAGCTCTGCATTTGGA 57.466 33.333 0.00 0.00 32.46 3.53
2504 8305 6.726490 ATGAAATTAGCTCTGCATTTGGAT 57.274 33.333 0.00 0.00 0.00 3.41
2505 8306 6.534475 TGAAATTAGCTCTGCATTTGGATT 57.466 33.333 0.00 0.00 0.00 3.01
2513 8314 5.477984 AGCTCTGCATTTGGATTTTCAGTTA 59.522 36.000 0.00 0.00 0.00 2.24
2514 8320 6.015180 AGCTCTGCATTTGGATTTTCAGTTAA 60.015 34.615 0.00 0.00 0.00 2.01
2515 8321 6.089954 GCTCTGCATTTGGATTTTCAGTTAAC 59.910 38.462 0.00 0.00 0.00 2.01
2520 8326 6.701400 GCATTTGGATTTTCAGTTAACTGTGT 59.299 34.615 29.83 16.75 44.12 3.72
2549 8355 9.558396 AATCATGTAATGTTTCCATTTGTTGTT 57.442 25.926 0.00 0.00 46.80 2.83
2550 8356 8.362860 TCATGTAATGTTTCCATTTGTTGTTG 57.637 30.769 0.00 0.00 46.80 3.33
2551 8357 7.440556 TCATGTAATGTTTCCATTTGTTGTTGG 59.559 33.333 0.00 0.00 46.80 3.77
2552 8358 6.051717 TGTAATGTTTCCATTTGTTGTTGGG 58.948 36.000 0.00 0.00 41.50 4.12
2553 8359 4.769345 ATGTTTCCATTTGTTGTTGGGT 57.231 36.364 0.00 0.00 33.62 4.51
2561 8367 4.201901 CCATTTGTTGTTGGGTTTTTCAGC 60.202 41.667 0.00 0.00 0.00 4.26
2585 8391 2.637382 TGAGTGGTGGTCATTTGAGCTA 59.363 45.455 10.74 0.00 42.60 3.32
2591 8397 5.294552 GTGGTGGTCATTTGAGCTACTTATC 59.705 44.000 10.74 0.00 42.60 1.75
2663 8486 7.335627 TCTCAATATGGTACCCACTGTTTTAG 58.664 38.462 10.07 0.00 35.80 1.85
2739 8567 0.894835 TTCACAGCCTCACGAGCATA 59.105 50.000 0.00 0.00 0.00 3.14
2742 8570 0.458543 ACAGCCTCACGAGCATAACG 60.459 55.000 0.00 0.00 0.00 3.18
2795 8623 1.751351 TGCTGGAAGGTACGATCTCTG 59.249 52.381 0.00 0.00 0.00 3.35
2807 8635 3.851098 ACGATCTCTGAAGGCAGTTAAC 58.149 45.455 0.00 0.00 42.84 2.01
2822 8650 0.533491 TTAACTACACGGCCGATGCT 59.467 50.000 35.90 17.47 37.74 3.79
2912 8746 2.812011 GAGTAGCAAACGAATTGGGTGT 59.188 45.455 0.00 0.00 39.54 4.16
3057 8891 3.532155 GAGGAGGTCGCATCCGCT 61.532 66.667 6.94 0.00 42.02 5.52
3150 9008 7.307694 GTCACATTCATTTCTTCTGCATAACA 58.692 34.615 0.00 0.00 0.00 2.41
3437 9338 3.299503 ACTGGCAGAAGATGGTTTGTTT 58.700 40.909 23.66 0.00 0.00 2.83
3599 9531 4.646945 TCGAGATCTCTGCTGGAATAGTTT 59.353 41.667 20.26 0.00 0.00 2.66
3600 9532 5.127845 TCGAGATCTCTGCTGGAATAGTTTT 59.872 40.000 20.26 0.00 0.00 2.43
3601 9533 5.814705 CGAGATCTCTGCTGGAATAGTTTTT 59.185 40.000 20.26 0.00 0.00 1.94
3602 9534 6.019156 CGAGATCTCTGCTGGAATAGTTTTTC 60.019 42.308 20.26 0.00 0.00 2.29
3603 9535 6.956497 AGATCTCTGCTGGAATAGTTTTTCT 58.044 36.000 0.00 0.00 0.00 2.52
3604 9536 6.822676 AGATCTCTGCTGGAATAGTTTTTCTG 59.177 38.462 0.00 0.00 0.00 3.02
3605 9537 6.114187 TCTCTGCTGGAATAGTTTTTCTGA 57.886 37.500 0.00 0.00 0.00 3.27
3606 9538 6.169094 TCTCTGCTGGAATAGTTTTTCTGAG 58.831 40.000 0.00 0.00 0.00 3.35
3607 9539 6.014242 TCTCTGCTGGAATAGTTTTTCTGAGA 60.014 38.462 0.00 0.00 0.00 3.27
3608 9540 5.934625 TCTGCTGGAATAGTTTTTCTGAGAC 59.065 40.000 0.00 0.00 0.00 3.36
3609 9541 5.869579 TGCTGGAATAGTTTTTCTGAGACT 58.130 37.500 0.00 0.00 0.00 3.24
3610 9542 7.004555 TGCTGGAATAGTTTTTCTGAGACTA 57.995 36.000 0.00 0.00 0.00 2.59
3611 9543 7.624549 TGCTGGAATAGTTTTTCTGAGACTAT 58.375 34.615 0.00 5.25 38.01 2.12
3612 9544 8.758829 TGCTGGAATAGTTTTTCTGAGACTATA 58.241 33.333 9.40 0.00 36.00 1.31
3613 9545 9.601217 GCTGGAATAGTTTTTCTGAGACTATAA 57.399 33.333 9.40 2.20 36.00 0.98
3619 9551 9.810545 ATAGTTTTTCTGAGACTATAACTGCTC 57.189 33.333 0.00 0.00 35.45 4.26
3620 9552 6.809196 AGTTTTTCTGAGACTATAACTGCTCG 59.191 38.462 0.00 0.00 0.00 5.03
3621 9553 6.510879 TTTTCTGAGACTATAACTGCTCGA 57.489 37.500 0.00 0.00 0.00 4.04
3622 9554 6.510879 TTTCTGAGACTATAACTGCTCGAA 57.489 37.500 0.00 0.00 0.00 3.71
3623 9555 5.743026 TCTGAGACTATAACTGCTCGAAG 57.257 43.478 0.00 0.00 0.00 3.79
3624 9556 5.429130 TCTGAGACTATAACTGCTCGAAGA 58.571 41.667 0.00 0.00 0.00 2.87
3743 9715 6.773200 CCACTCTTTTTCTCCCTCTTTACTTT 59.227 38.462 0.00 0.00 0.00 2.66
3794 9766 4.503714 AGCTCGATTTTGAAATCCCCTA 57.496 40.909 10.06 0.00 41.30 3.53
3824 9796 0.442699 CCGCTTAGTTTTGCTCGACC 59.557 55.000 0.00 0.00 0.00 4.79
3841 9813 1.000771 CCCGGACAGACAGAGAGGA 60.001 63.158 0.73 0.00 0.00 3.71
3850 9822 0.396060 GACAGAGAGGATCCATGCCC 59.604 60.000 15.82 0.00 33.66 5.36
3915 9887 0.882927 CGCCCCAGACAACTTTTCGA 60.883 55.000 0.00 0.00 0.00 3.71
3923 9895 0.463116 ACAACTTTTCGACCGCCAGT 60.463 50.000 0.00 0.00 0.00 4.00
3955 9928 2.131709 CCTAATCGCGTCCCAGGGA 61.132 63.158 3.01 3.01 37.49 4.20
3991 9964 3.059386 GGGTCGAAATTGGCGCCA 61.059 61.111 29.03 29.03 0.00 5.69
3997 9970 2.755469 AAATTGGCGCCAGCGGAT 60.755 55.556 30.75 17.86 46.35 4.18
4119 10127 3.437795 GTCTTCCCGACGCCTCGA 61.438 66.667 6.68 0.00 43.06 4.04
4275 10333 2.281070 CTGCGTTGGAGTGCCACT 60.281 61.111 0.00 0.00 45.94 4.00
4276 10335 1.893808 CTGCGTTGGAGTGCCACTT 60.894 57.895 0.00 0.00 45.94 3.16
4304 10396 0.537600 CCTCTCCCGCCGATCTCTTA 60.538 60.000 0.00 0.00 0.00 2.10
4309 10401 1.213013 CCGCCGATCTCTTATCCCG 59.787 63.158 0.00 0.00 0.00 5.14
4480 10572 1.605992 CTGGAGGCTCAGCAATGGA 59.394 57.895 17.69 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.097547 CCATTACGGGCAGCCTGAAG 61.098 60.000 28.29 12.40 33.36 3.02
5 6 0.532862 CTACCATTACGGGCAGCCTG 60.533 60.000 19.77 19.77 40.22 4.85
6 7 0.981277 ACTACCATTACGGGCAGCCT 60.981 55.000 12.43 0.00 40.22 4.58
7 8 0.754472 TACTACCATTACGGGCAGCC 59.246 55.000 1.26 1.26 40.22 4.85
8 9 2.036733 TGATACTACCATTACGGGCAGC 59.963 50.000 0.00 0.00 40.22 5.25
9 10 4.537135 ATGATACTACCATTACGGGCAG 57.463 45.455 0.00 0.00 40.22 4.85
10 11 4.464951 CCTATGATACTACCATTACGGGCA 59.535 45.833 0.00 0.00 40.22 5.36
11 12 4.465305 ACCTATGATACTACCATTACGGGC 59.535 45.833 0.00 0.00 40.22 6.13
12 13 6.888632 ACTACCTATGATACTACCATTACGGG 59.111 42.308 0.00 0.00 40.22 5.28
13 14 7.934855 ACTACCTATGATACTACCATTACGG 57.065 40.000 0.00 0.00 42.50 4.02
18 19 9.137459 GCATGATACTACCTATGATACTACCAT 57.863 37.037 0.00 0.00 0.00 3.55
19 20 8.113462 TGCATGATACTACCTATGATACTACCA 58.887 37.037 0.00 0.00 0.00 3.25
20 21 8.521170 TGCATGATACTACCTATGATACTACC 57.479 38.462 0.00 0.00 0.00 3.18
21 22 9.958234 CATGCATGATACTACCTATGATACTAC 57.042 37.037 22.59 0.00 0.00 2.73
22 23 8.633561 GCATGCATGATACTACCTATGATACTA 58.366 37.037 30.64 0.00 0.00 1.82
23 24 7.418368 GGCATGCATGATACTACCTATGATACT 60.418 40.741 30.64 0.00 0.00 2.12
24 25 6.703607 GGCATGCATGATACTACCTATGATAC 59.296 42.308 30.64 5.71 0.00 2.24
25 26 6.383726 TGGCATGCATGATACTACCTATGATA 59.616 38.462 30.64 0.87 0.00 2.15
26 27 5.190330 TGGCATGCATGATACTACCTATGAT 59.810 40.000 30.64 0.00 0.00 2.45
27 28 4.531732 TGGCATGCATGATACTACCTATGA 59.468 41.667 30.64 1.93 0.00 2.15
28 29 4.835678 TGGCATGCATGATACTACCTATG 58.164 43.478 30.64 0.23 0.00 2.23
29 30 5.013495 AGTTGGCATGCATGATACTACCTAT 59.987 40.000 30.64 7.77 0.00 2.57
30 31 4.347876 AGTTGGCATGCATGATACTACCTA 59.652 41.667 30.64 13.97 0.00 3.08
31 32 3.137176 AGTTGGCATGCATGATACTACCT 59.863 43.478 30.64 11.98 0.00 3.08
32 33 3.480470 AGTTGGCATGCATGATACTACC 58.520 45.455 30.64 19.65 0.00 3.18
33 34 5.300752 AGTAGTTGGCATGCATGATACTAC 58.699 41.667 32.52 32.52 37.52 2.73
34 35 5.511373 GGAGTAGTTGGCATGCATGATACTA 60.511 44.000 30.64 25.19 0.00 1.82
35 36 4.384056 GAGTAGTTGGCATGCATGATACT 58.616 43.478 30.64 26.11 0.00 2.12
36 37 3.499918 GGAGTAGTTGGCATGCATGATAC 59.500 47.826 30.64 21.28 0.00 2.24
37 38 3.496692 GGGAGTAGTTGGCATGCATGATA 60.497 47.826 30.64 14.66 0.00 2.15
38 39 2.579873 GGAGTAGTTGGCATGCATGAT 58.420 47.619 30.64 11.73 0.00 2.45
39 40 1.408683 GGGAGTAGTTGGCATGCATGA 60.409 52.381 30.64 7.50 0.00 3.07
40 41 1.027357 GGGAGTAGTTGGCATGCATG 58.973 55.000 22.70 22.70 0.00 4.06
41 42 0.921896 AGGGAGTAGTTGGCATGCAT 59.078 50.000 21.36 4.57 0.00 3.96
42 43 0.253044 GAGGGAGTAGTTGGCATGCA 59.747 55.000 21.36 2.54 0.00 3.96
43 44 0.464554 GGAGGGAGTAGTTGGCATGC 60.465 60.000 9.90 9.90 0.00 4.06
44 45 0.179073 CGGAGGGAGTAGTTGGCATG 60.179 60.000 0.00 0.00 0.00 4.06
45 46 0.617820 ACGGAGGGAGTAGTTGGCAT 60.618 55.000 0.00 0.00 0.00 4.40
46 47 0.834687 AACGGAGGGAGTAGTTGGCA 60.835 55.000 0.00 0.00 0.00 4.92
47 48 0.323957 AAACGGAGGGAGTAGTTGGC 59.676 55.000 0.00 0.00 0.00 4.52
48 49 2.167900 CCTAAACGGAGGGAGTAGTTGG 59.832 54.545 0.00 0.00 32.39 3.77
49 50 2.830321 ACCTAAACGGAGGGAGTAGTTG 59.170 50.000 5.42 0.00 41.36 3.16
50 51 2.830321 CACCTAAACGGAGGGAGTAGTT 59.170 50.000 5.42 0.00 41.36 2.24
51 52 2.042162 TCACCTAAACGGAGGGAGTAGT 59.958 50.000 5.42 0.00 41.36 2.73
81 82 2.095853 GGTCACGGTGCTCAACATAATG 59.904 50.000 2.51 0.00 0.00 1.90
82 83 2.290008 TGGTCACGGTGCTCAACATAAT 60.290 45.455 2.51 0.00 0.00 1.28
86 2698 0.813610 CTTGGTCACGGTGCTCAACA 60.814 55.000 2.51 0.00 0.00 3.33
91 2703 2.743718 CTCCTTGGTCACGGTGCT 59.256 61.111 2.51 0.00 0.00 4.40
192 2804 8.506437 TGCATGTTTTTAATGACTTGAGACTAG 58.494 33.333 0.00 0.00 0.00 2.57
283 2895 1.173913 ATCCCAAAACACTTAGGCGC 58.826 50.000 0.00 0.00 0.00 6.53
336 2948 2.054232 TGCTTACTCCCTCCGTCTAG 57.946 55.000 0.00 0.00 0.00 2.43
337 2949 2.519771 TTGCTTACTCCCTCCGTCTA 57.480 50.000 0.00 0.00 0.00 2.59
338 2950 1.867363 ATTGCTTACTCCCTCCGTCT 58.133 50.000 0.00 0.00 0.00 4.18
339 2951 2.693267 AATTGCTTACTCCCTCCGTC 57.307 50.000 0.00 0.00 0.00 4.79
340 2952 3.081804 CAAAATTGCTTACTCCCTCCGT 58.918 45.455 0.00 0.00 0.00 4.69
341 2953 3.343617 TCAAAATTGCTTACTCCCTCCG 58.656 45.455 0.00 0.00 0.00 4.63
342 2954 4.949856 TCATCAAAATTGCTTACTCCCTCC 59.050 41.667 0.00 0.00 0.00 4.30
343 2955 5.882557 TCTCATCAAAATTGCTTACTCCCTC 59.117 40.000 0.00 0.00 0.00 4.30
344 2956 5.819991 TCTCATCAAAATTGCTTACTCCCT 58.180 37.500 0.00 0.00 0.00 4.20
345 2957 6.096001 ACATCTCATCAAAATTGCTTACTCCC 59.904 38.462 0.00 0.00 0.00 4.30
346 2958 7.093322 ACATCTCATCAAAATTGCTTACTCC 57.907 36.000 0.00 0.00 0.00 3.85
347 2959 7.755591 TGACATCTCATCAAAATTGCTTACTC 58.244 34.615 0.00 0.00 0.00 2.59
348 2960 7.692460 TGACATCTCATCAAAATTGCTTACT 57.308 32.000 0.00 0.00 0.00 2.24
349 2961 9.661187 CTATGACATCTCATCAAAATTGCTTAC 57.339 33.333 0.00 0.00 38.21 2.34
350 2962 9.617523 TCTATGACATCTCATCAAAATTGCTTA 57.382 29.630 0.00 0.00 38.21 3.09
351 2963 8.515695 TCTATGACATCTCATCAAAATTGCTT 57.484 30.769 0.00 0.00 38.21 3.91
352 2964 8.515695 TTCTATGACATCTCATCAAAATTGCT 57.484 30.769 0.00 0.00 38.21 3.91
353 2965 9.745880 AATTCTATGACATCTCATCAAAATTGC 57.254 29.630 0.00 0.00 38.21 3.56
377 2989 9.525826 ACTCAACCATCTCTTTCTTCATTTAAT 57.474 29.630 0.00 0.00 0.00 1.40
378 2990 8.924511 ACTCAACCATCTCTTTCTTCATTTAA 57.075 30.769 0.00 0.00 0.00 1.52
380 2992 9.171877 GATACTCAACCATCTCTTTCTTCATTT 57.828 33.333 0.00 0.00 0.00 2.32
381 2993 8.324306 TGATACTCAACCATCTCTTTCTTCATT 58.676 33.333 0.00 0.00 0.00 2.57
382 2994 7.855375 TGATACTCAACCATCTCTTTCTTCAT 58.145 34.615 0.00 0.00 0.00 2.57
383 2995 7.244886 TGATACTCAACCATCTCTTTCTTCA 57.755 36.000 0.00 0.00 0.00 3.02
384 2996 9.995003 ATATGATACTCAACCATCTCTTTCTTC 57.005 33.333 0.00 0.00 0.00 2.87
411 3023 8.664798 GCATGACACAAAGTAGTACATCATTTA 58.335 33.333 2.52 0.00 0.00 1.40
412 3024 7.174772 TGCATGACACAAAGTAGTACATCATTT 59.825 33.333 2.52 0.00 0.00 2.32
413 3025 6.654582 TGCATGACACAAAGTAGTACATCATT 59.345 34.615 2.52 0.00 0.00 2.57
414 3026 6.172630 TGCATGACACAAAGTAGTACATCAT 58.827 36.000 2.52 0.00 0.00 2.45
415 3027 5.546526 TGCATGACACAAAGTAGTACATCA 58.453 37.500 2.52 0.00 0.00 3.07
416 3028 6.668541 ATGCATGACACAAAGTAGTACATC 57.331 37.500 0.00 0.00 0.00 3.06
417 3029 8.737168 ATTATGCATGACACAAAGTAGTACAT 57.263 30.769 10.16 0.00 0.00 2.29
418 3030 9.660180 TTATTATGCATGACACAAAGTAGTACA 57.340 29.630 10.16 0.00 0.00 2.90
464 3076 8.769891 CGCAATGTAAAGTATCATATGTTGGTA 58.230 33.333 1.90 0.00 0.00 3.25
465 3077 7.255104 CCGCAATGTAAAGTATCATATGTTGGT 60.255 37.037 1.90 0.00 0.00 3.67
466 3078 7.041440 TCCGCAATGTAAAGTATCATATGTTGG 60.041 37.037 1.90 0.00 0.00 3.77
467 3079 7.860613 TCCGCAATGTAAAGTATCATATGTTG 58.139 34.615 1.90 0.00 0.00 3.33
468 3080 8.506437 CATCCGCAATGTAAAGTATCATATGTT 58.494 33.333 1.90 0.00 0.00 2.71
469 3081 7.661437 ACATCCGCAATGTAAAGTATCATATGT 59.339 33.333 1.90 0.00 46.95 2.29
470 3082 8.032952 ACATCCGCAATGTAAAGTATCATATG 57.967 34.615 0.00 0.00 46.95 1.78
502 3114 9.122954 TGGTTGTAATGGGGAGTATCATATATT 57.877 33.333 0.00 0.00 36.25 1.28
503 3115 8.694171 TGGTTGTAATGGGGAGTATCATATAT 57.306 34.615 0.00 0.00 36.25 0.86
504 3116 7.311046 GCTGGTTGTAATGGGGAGTATCATATA 60.311 40.741 0.00 0.00 36.25 0.86
505 3117 6.522459 GCTGGTTGTAATGGGGAGTATCATAT 60.522 42.308 0.00 0.00 36.25 1.78
506 3118 5.221843 GCTGGTTGTAATGGGGAGTATCATA 60.222 44.000 0.00 0.00 36.25 2.15
507 3119 4.446311 GCTGGTTGTAATGGGGAGTATCAT 60.446 45.833 0.00 0.00 36.25 2.45
508 3120 3.118038 GCTGGTTGTAATGGGGAGTATCA 60.118 47.826 0.00 0.00 36.25 2.15
509 3121 3.477530 GCTGGTTGTAATGGGGAGTATC 58.522 50.000 0.00 0.00 0.00 2.24
510 3122 2.174854 GGCTGGTTGTAATGGGGAGTAT 59.825 50.000 0.00 0.00 0.00 2.12
511 3123 1.562475 GGCTGGTTGTAATGGGGAGTA 59.438 52.381 0.00 0.00 0.00 2.59
512 3124 0.331616 GGCTGGTTGTAATGGGGAGT 59.668 55.000 0.00 0.00 0.00 3.85
513 3125 0.625849 AGGCTGGTTGTAATGGGGAG 59.374 55.000 0.00 0.00 0.00 4.30
514 3126 0.623723 GAGGCTGGTTGTAATGGGGA 59.376 55.000 0.00 0.00 0.00 4.81
515 3127 0.331278 TGAGGCTGGTTGTAATGGGG 59.669 55.000 0.00 0.00 0.00 4.96
516 3128 1.281867 TCTGAGGCTGGTTGTAATGGG 59.718 52.381 0.00 0.00 0.00 4.00
517 3129 2.237143 TCTCTGAGGCTGGTTGTAATGG 59.763 50.000 4.59 0.00 0.00 3.16
518 3130 3.616956 TCTCTGAGGCTGGTTGTAATG 57.383 47.619 4.59 0.00 0.00 1.90
519 3131 4.287067 TCTTTCTCTGAGGCTGGTTGTAAT 59.713 41.667 4.59 0.00 0.00 1.89
520 3132 3.646162 TCTTTCTCTGAGGCTGGTTGTAA 59.354 43.478 4.59 0.00 0.00 2.41
521 3133 3.239449 TCTTTCTCTGAGGCTGGTTGTA 58.761 45.455 4.59 0.00 0.00 2.41
522 3134 2.050144 TCTTTCTCTGAGGCTGGTTGT 58.950 47.619 4.59 0.00 0.00 3.32
523 3135 2.847327 TCTTTCTCTGAGGCTGGTTG 57.153 50.000 4.59 0.00 0.00 3.77
524 3136 3.864789 TTTCTTTCTCTGAGGCTGGTT 57.135 42.857 4.59 0.00 0.00 3.67
525 3137 3.864789 TTTTCTTTCTCTGAGGCTGGT 57.135 42.857 4.59 0.00 0.00 4.00
526 3138 4.392940 TCTTTTTCTTTCTCTGAGGCTGG 58.607 43.478 4.59 0.00 0.00 4.85
527 3139 4.455190 CCTCTTTTTCTTTCTCTGAGGCTG 59.545 45.833 4.59 0.00 34.16 4.85
528 3140 4.349342 TCCTCTTTTTCTTTCTCTGAGGCT 59.651 41.667 4.59 0.00 39.36 4.58
529 3141 4.646572 TCCTCTTTTTCTTTCTCTGAGGC 58.353 43.478 4.59 0.00 39.36 4.70
530 3142 6.206438 CCTTTCCTCTTTTTCTTTCTCTGAGG 59.794 42.308 4.59 0.00 40.47 3.86
531 3143 6.995091 TCCTTTCCTCTTTTTCTTTCTCTGAG 59.005 38.462 0.00 0.00 0.00 3.35
532 3144 6.900194 TCCTTTCCTCTTTTTCTTTCTCTGA 58.100 36.000 0.00 0.00 0.00 3.27
533 3145 7.573968 TTCCTTTCCTCTTTTTCTTTCTCTG 57.426 36.000 0.00 0.00 0.00 3.35
534 3146 8.774546 AATTCCTTTCCTCTTTTTCTTTCTCT 57.225 30.769 0.00 0.00 0.00 3.10
539 3151 8.150945 GCCTTAAATTCCTTTCCTCTTTTTCTT 58.849 33.333 0.00 0.00 0.00 2.52
540 3152 7.256332 GGCCTTAAATTCCTTTCCTCTTTTTCT 60.256 37.037 0.00 0.00 0.00 2.52
541 3153 6.874134 GGCCTTAAATTCCTTTCCTCTTTTTC 59.126 38.462 0.00 0.00 0.00 2.29
542 3154 6.558775 AGGCCTTAAATTCCTTTCCTCTTTTT 59.441 34.615 0.00 0.00 0.00 1.94
543 3155 6.084738 AGGCCTTAAATTCCTTTCCTCTTTT 58.915 36.000 0.00 0.00 0.00 2.27
544 3156 5.655394 AGGCCTTAAATTCCTTTCCTCTTT 58.345 37.500 0.00 0.00 0.00 2.52
569 3181 2.539302 CCCACTTCAATCCCCACAAAT 58.461 47.619 0.00 0.00 0.00 2.32
572 3184 1.076549 GCCCACTTCAATCCCCACA 59.923 57.895 0.00 0.00 0.00 4.17
600 3212 6.015010 AGTCTTCTACCAATCGCTATGCTAAT 60.015 38.462 0.00 0.00 0.00 1.73
649 3265 1.267732 GCATTCAGCACTGCGATGTAC 60.268 52.381 13.19 0.00 44.79 2.90
651 3267 1.798735 GCATTCAGCACTGCGATGT 59.201 52.632 13.19 0.00 44.79 3.06
652 3268 4.684265 GCATTCAGCACTGCGATG 57.316 55.556 9.42 9.42 44.79 3.84
795 3679 3.335534 GTGGTCGTGACGGCACAC 61.336 66.667 23.63 17.77 45.41 3.82
1254 6023 3.477578 GAGGGTGGGGATAAGCGGC 62.478 68.421 0.00 0.00 0.00 6.53
1428 6538 2.047274 ACCATGACCGTCGCCAAG 60.047 61.111 0.00 0.00 0.00 3.61
1474 6584 5.935945 TCCCTTGTCTGTATTTCAACAAGA 58.064 37.500 13.97 0.00 41.66 3.02
1475 6585 6.633500 TTCCCTTGTCTGTATTTCAACAAG 57.367 37.500 7.03 7.03 40.48 3.16
1565 6701 2.039480 AGTCACATGCTCATCCAACTGT 59.961 45.455 0.00 0.00 0.00 3.55
1587 6723 9.191995 CAATAATTCCCAGTTAGAAAAACACAC 57.808 33.333 0.00 0.00 0.00 3.82
1618 7319 2.057316 CACAAGTTCAGTCTCTCGCTG 58.943 52.381 0.00 0.00 35.43 5.18
1707 7417 3.702555 GCGGTGTCACACTGTCGC 61.703 66.667 18.25 15.56 42.21 5.19
1828 7554 1.340697 ACCGTGGAGGAAATTTAGGCC 60.341 52.381 0.00 0.00 45.00 5.19
1890 7684 5.677178 GCCGATCTGTTTCACGAATTAATTC 59.323 40.000 16.79 16.79 0.00 2.17
1891 7685 5.123186 TGCCGATCTGTTTCACGAATTAATT 59.877 36.000 0.00 0.00 0.00 1.40
1892 7686 4.634004 TGCCGATCTGTTTCACGAATTAAT 59.366 37.500 0.00 0.00 0.00 1.40
1893 7687 3.997681 TGCCGATCTGTTTCACGAATTAA 59.002 39.130 0.00 0.00 0.00 1.40
1894 7688 3.591023 TGCCGATCTGTTTCACGAATTA 58.409 40.909 0.00 0.00 0.00 1.40
2268 8062 3.056754 GCCAGTGTACCCCATCCCC 62.057 68.421 0.00 0.00 0.00 4.81
2477 8277 7.879160 TCCAAATGCAGAGCTAATTTCATTTTT 59.121 29.630 0.00 0.00 33.47 1.94
2490 8291 4.184079 ACTGAAAATCCAAATGCAGAGC 57.816 40.909 0.00 0.00 0.00 4.09
2493 8294 6.925165 ACAGTTAACTGAAAATCCAAATGCAG 59.075 34.615 36.14 9.01 46.59 4.41
2501 8302 8.999431 TGATTAGACACAGTTAACTGAAAATCC 58.001 33.333 36.14 19.56 46.59 3.01
2504 8305 9.337396 ACATGATTAGACACAGTTAACTGAAAA 57.663 29.630 36.14 22.24 46.59 2.29
2505 8306 8.902540 ACATGATTAGACACAGTTAACTGAAA 57.097 30.769 36.14 21.97 46.59 2.69
2513 8314 8.730680 GGAAACATTACATGATTAGACACAGTT 58.269 33.333 0.00 0.00 0.00 3.16
2514 8320 7.882791 TGGAAACATTACATGATTAGACACAGT 59.117 33.333 0.00 0.00 33.40 3.55
2515 8321 8.267620 TGGAAACATTACATGATTAGACACAG 57.732 34.615 0.00 0.00 33.40 3.66
2538 8344 4.201901 GCTGAAAAACCCAACAACAAATGG 60.202 41.667 0.00 0.00 36.42 3.16
2545 8351 2.834549 TCAAGGCTGAAAAACCCAACAA 59.165 40.909 0.00 0.00 0.00 2.83
2546 8352 2.430332 CTCAAGGCTGAAAAACCCAACA 59.570 45.455 0.00 0.00 0.00 3.33
2547 8353 2.430694 ACTCAAGGCTGAAAAACCCAAC 59.569 45.455 0.00 0.00 0.00 3.77
2548 8354 2.430332 CACTCAAGGCTGAAAAACCCAA 59.570 45.455 0.00 0.00 0.00 4.12
2549 8355 2.031120 CACTCAAGGCTGAAAAACCCA 58.969 47.619 0.00 0.00 0.00 4.51
2550 8356 1.341209 CCACTCAAGGCTGAAAAACCC 59.659 52.381 0.00 0.00 0.00 4.11
2551 8357 2.031870 ACCACTCAAGGCTGAAAAACC 58.968 47.619 0.00 0.00 0.00 3.27
2552 8358 2.223805 CCACCACTCAAGGCTGAAAAAC 60.224 50.000 0.00 0.00 0.00 2.43
2553 8359 2.031120 CCACCACTCAAGGCTGAAAAA 58.969 47.619 0.00 0.00 0.00 1.94
2561 8367 2.816087 CTCAAATGACCACCACTCAAGG 59.184 50.000 0.00 0.00 0.00 3.61
2585 8391 0.759346 GCCCCGACATGAGGATAAGT 59.241 55.000 12.39 0.00 0.00 2.24
2591 8397 1.153289 CAGAAGCCCCGACATGAGG 60.153 63.158 0.00 1.91 0.00 3.86
2739 8567 7.709613 CCATAAGGTATAGTAAAGAGCAACGTT 59.290 37.037 0.00 0.00 0.00 3.99
2742 8570 8.422566 AGTCCATAAGGTATAGTAAAGAGCAAC 58.577 37.037 0.00 0.00 35.89 4.17
2795 8623 1.730612 GCCGTGTAGTTAACTGCCTTC 59.269 52.381 18.56 8.98 0.00 3.46
2807 8635 0.802494 AAAAAGCATCGGCCGTGTAG 59.198 50.000 27.15 14.31 42.56 2.74
2871 8704 2.803386 TCGCGTGCTGTTCATTAAGAAA 59.197 40.909 5.77 0.00 38.13 2.52
2912 8746 2.902457 GCTCCTTCGGGGTTCCCAA 61.902 63.158 10.25 0.00 45.83 4.12
3108 8942 1.132849 TGACCTGAGAGAACCCCTTGA 60.133 52.381 0.00 0.00 0.00 3.02
3150 9008 4.582656 TGGAAACGATGGACAACTTGAAAT 59.417 37.500 0.00 0.00 0.00 2.17
3437 9338 5.560722 TGATTTGTAAGTGGGTTCAGAGA 57.439 39.130 0.00 0.00 0.00 3.10
3599 9531 6.374613 TCTTCGAGCAGTTATAGTCTCAGAAA 59.625 38.462 0.00 0.00 0.00 2.52
3600 9532 5.880887 TCTTCGAGCAGTTATAGTCTCAGAA 59.119 40.000 0.00 0.00 0.00 3.02
3601 9533 5.429130 TCTTCGAGCAGTTATAGTCTCAGA 58.571 41.667 0.00 0.00 0.00 3.27
3602 9534 5.295787 ACTCTTCGAGCAGTTATAGTCTCAG 59.704 44.000 0.00 0.00 32.04 3.35
3603 9535 5.186942 ACTCTTCGAGCAGTTATAGTCTCA 58.813 41.667 0.00 0.00 32.04 3.27
3604 9536 5.744666 ACTCTTCGAGCAGTTATAGTCTC 57.255 43.478 0.00 0.00 32.04 3.36
3605 9537 6.238157 CGTAACTCTTCGAGCAGTTATAGTCT 60.238 42.308 16.87 0.00 37.42 3.24
3606 9538 5.902981 CGTAACTCTTCGAGCAGTTATAGTC 59.097 44.000 16.87 7.34 37.42 2.59
3607 9539 5.730010 GCGTAACTCTTCGAGCAGTTATAGT 60.730 44.000 16.87 0.00 37.42 2.12
3608 9540 4.671516 GCGTAACTCTTCGAGCAGTTATAG 59.328 45.833 16.87 15.03 37.42 1.31
3609 9541 4.334759 AGCGTAACTCTTCGAGCAGTTATA 59.665 41.667 16.87 0.99 37.42 0.98
3610 9542 3.128938 AGCGTAACTCTTCGAGCAGTTAT 59.871 43.478 16.87 4.02 37.42 1.89
3611 9543 2.486982 AGCGTAACTCTTCGAGCAGTTA 59.513 45.455 12.11 12.11 34.60 2.24
3612 9544 1.269998 AGCGTAACTCTTCGAGCAGTT 59.730 47.619 13.73 13.73 36.75 3.16
3613 9545 0.882474 AGCGTAACTCTTCGAGCAGT 59.118 50.000 0.00 0.00 32.04 4.40
3614 9546 1.263776 CAGCGTAACTCTTCGAGCAG 58.736 55.000 0.00 0.00 32.04 4.24
3615 9547 0.732880 GCAGCGTAACTCTTCGAGCA 60.733 55.000 0.00 0.00 32.04 4.26
3616 9548 0.732880 TGCAGCGTAACTCTTCGAGC 60.733 55.000 0.00 0.00 32.04 5.03
3617 9549 1.698165 TTGCAGCGTAACTCTTCGAG 58.302 50.000 0.00 0.00 35.52 4.04
3618 9550 2.363788 ATTGCAGCGTAACTCTTCGA 57.636 45.000 0.00 0.00 0.00 3.71
3619 9551 3.455619 AAATTGCAGCGTAACTCTTCG 57.544 42.857 0.00 0.00 0.00 3.79
3620 9552 4.537015 ACAAAATTGCAGCGTAACTCTTC 58.463 39.130 0.00 0.00 0.00 2.87
3621 9553 4.568152 ACAAAATTGCAGCGTAACTCTT 57.432 36.364 0.00 0.00 0.00 2.85
3622 9554 4.154195 CCTACAAAATTGCAGCGTAACTCT 59.846 41.667 0.00 0.00 0.00 3.24
3623 9555 4.403453 CCTACAAAATTGCAGCGTAACTC 58.597 43.478 0.00 0.00 0.00 3.01
3624 9556 3.190535 CCCTACAAAATTGCAGCGTAACT 59.809 43.478 0.00 0.00 0.00 2.24
3625 9557 3.498082 CCCTACAAAATTGCAGCGTAAC 58.502 45.455 0.00 0.00 0.00 2.50
3626 9558 2.490115 CCCCTACAAAATTGCAGCGTAA 59.510 45.455 0.00 0.00 0.00 3.18
3627 9559 2.088423 CCCCTACAAAATTGCAGCGTA 58.912 47.619 0.00 0.00 0.00 4.42
3699 9665 1.206610 GGTTTACGTCCTCTTCCTCCC 59.793 57.143 0.00 0.00 0.00 4.30
3743 9715 0.464013 TTTCGCCTCGGACACCAAAA 60.464 50.000 0.00 0.00 0.00 2.44
3755 9727 1.000274 GCTTCACCAAACATTTCGCCT 60.000 47.619 0.00 0.00 0.00 5.52
3824 9796 1.028905 GATCCTCTCTGTCTGTCCGG 58.971 60.000 0.00 0.00 0.00 5.14
3841 9813 2.507944 GAGCTGTCGGGCATGGAT 59.492 61.111 0.00 0.00 34.17 3.41
3850 9822 1.267832 GCTCTAAGTCTCGAGCTGTCG 60.268 57.143 7.81 0.00 46.87 4.35
3897 9869 0.591659 GTCGAAAAGTTGTCTGGGGC 59.408 55.000 0.00 0.00 0.00 5.80
3939 9911 3.213264 GTCCCTGGGACGCGATTA 58.787 61.111 28.96 0.00 43.14 1.75
3965 9938 2.734948 AATTTCGACCCGAACCGGCA 62.735 55.000 0.00 0.00 45.64 5.69
3991 9964 1.146263 GATTCGGGTTGGATCCGCT 59.854 57.895 7.39 0.00 46.43 5.52
4229 10262 3.633065 GAGACCATATATAGCCGAGGGAC 59.367 52.174 0.00 0.00 0.00 4.46
4275 10333 2.041265 GGGAGAGGGAGGGCTGAA 59.959 66.667 0.00 0.00 0.00 3.02
4276 10335 4.465446 CGGGAGAGGGAGGGCTGA 62.465 72.222 0.00 0.00 0.00 4.26
4304 10396 2.444895 GAGGGAGTGGCTCGGGAT 60.445 66.667 0.00 0.00 0.00 3.85
4309 10401 2.766229 GGGGAGAGGGAGTGGCTC 60.766 72.222 0.00 0.00 0.00 4.70
4480 10572 3.023735 GGGGGAATGGGCACTCCT 61.024 66.667 0.00 0.00 36.20 3.69
4557 10649 3.125573 CGGCGTCGGTGAGAGAGA 61.126 66.667 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.