Multiple sequence alignment - TraesCS4D01G118800

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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 TraesCS4D01G118800 chr4D 100.000 7447 0 0 1 7447 100225466 100232912 0.000000e+00 13753
1 TraesCS4D01G118800 chr4D 95.372 605 27 1 1 604 100204152 100204756 0.000000e+00 961
2 TraesCS4D01G118800 chr4D 92.405 158 11 1 4029 4185 75266747 75266904 2.700000e-54 224
3 TraesCS4D01G118800 chr4D 91.411 163 13 1 4030 4191 21147732 21147894 9.730000e-54 222
4 TraesCS4D01G118800 chr4D 90.854 164 11 2 4028 4190 25439794 25439954 4.520000e-52 217
5 TraesCS4D01G118800 chr4D 90.419 167 10 4 4029 4190 363677554 363677389 1.630000e-51 215
6 TraesCS4D01G118800 chr4D 89.412 170 17 1 4029 4197 334164553 334164384 5.850000e-51 213
7 TraesCS4D01G118800 chr4B 94.125 4562 155 42 2572 7084 142519449 142523946 0.000000e+00 6835
8 TraesCS4D01G118800 chr4B 95.619 525 14 5 894 1413 142518144 142518664 0.000000e+00 833
9 TraesCS4D01G118800 chr4B 93.386 378 24 1 7070 7447 142532448 142532824 6.530000e-155 558
10 TraesCS4D01G118800 chr4B 88.710 310 9 14 605 898 142517771 142518070 9.190000e-94 355
11 TraesCS4D01G118800 chr4B 90.000 170 15 2 4022 4190 28724311 28724143 1.260000e-52 219
12 TraesCS4D01G118800 chr4B 87.047 193 23 2 2374 2565 142518857 142519048 4.520000e-52 217
13 TraesCS4D01G118800 chr4A 94.123 3148 98 47 4155 7283 476339897 476336818 0.000000e+00 4708
14 TraesCS4D01G118800 chr4A 97.552 2328 49 5 1802 4124 476342218 476339894 0.000000e+00 3976
15 TraesCS4D01G118800 chr4A 94.463 1192 46 11 605 1792 476343681 476342506 0.000000e+00 1818
16 TraesCS4D01G118800 chr4A 91.716 169 14 0 7279 7447 476335059 476334891 1.250000e-57 235
17 TraesCS4D01G118800 chr7D 94.884 606 29 2 1 604 66746200 66745595 0.000000e+00 946
18 TraesCS4D01G118800 chr7D 94.884 606 29 2 1 604 572498593 572499198 0.000000e+00 946
19 TraesCS4D01G118800 chr7D 94.693 603 31 1 3 604 572486895 572487497 0.000000e+00 935
20 TraesCS4D01G118800 chr7D 96.220 291 10 1 2079 2368 381969533 381969243 6.760000e-130 475
21 TraesCS4D01G118800 chr7D 93.485 307 15 1 1447 1753 579041937 579041636 1.140000e-122 451
22 TraesCS4D01G118800 chr7D 93.972 282 12 2 1804 2080 381942664 381942383 8.930000e-114 422
23 TraesCS4D01G118800 chr7D 90.533 169 15 1 4023 4190 566026568 566026736 9.730000e-54 222
24 TraesCS4D01G118800 chr2D 94.719 606 28 4 1 604 94434893 94435496 0.000000e+00 939
25 TraesCS4D01G118800 chr2D 93.972 282 12 2 1804 2080 200945877 200945596 8.930000e-114 422
26 TraesCS4D01G118800 chr3D 94.554 606 31 2 1 604 588701535 588700930 0.000000e+00 935
27 TraesCS4D01G118800 chr3D 93.972 282 12 2 1804 2080 602850051 602849770 8.930000e-114 422
28 TraesCS4D01G118800 chr3D 91.018 167 14 1 4030 4195 187836469 187836303 2.700000e-54 224
29 TraesCS4D01G118800 chr3D 88.276 145 15 2 2366 2509 107670910 107670767 9.930000e-39 172
30 TraesCS4D01G118800 chr5D 94.545 605 32 1 1 604 372068133 372067529 0.000000e+00 933
31 TraesCS4D01G118800 chr5D 94.389 606 32 2 1 604 298583440 298584045 0.000000e+00 929
32 TraesCS4D01G118800 chr5D 96.220 291 10 1 2079 2368 301070185 301069895 6.760000e-130 475
33 TraesCS4D01G118800 chr5D 90.909 165 14 1 4027 4190 234845619 234845455 3.500000e-53 220
34 TraesCS4D01G118800 chr5D 90.798 163 14 1 4029 4190 461072764 461072602 4.520000e-52 217
35 TraesCS4D01G118800 chr6D 94.389 606 32 2 1 604 70841983 70842588 0.000000e+00 929
36 TraesCS4D01G118800 chr6D 96.220 291 10 1 2079 2368 458902416 458902706 6.760000e-130 475
37 TraesCS4D01G118800 chr6D 95.876 291 11 1 2079 2368 124521755 124522045 3.150000e-128 470
38 TraesCS4D01G118800 chr6D 93.038 158 10 1 4030 4186 335991173 335991016 5.810000e-56 230
39 TraesCS4D01G118800 chr6D 89.412 170 17 1 4026 4194 338408400 338408569 5.850000e-51 213
40 TraesCS4D01G118800 chr6D 89.759 166 16 1 4029 4193 90112237 90112402 2.110000e-50 211
41 TraesCS4D01G118800 chr6D 90.184 163 15 1 4030 4191 93646387 93646225 2.110000e-50 211
42 TraesCS4D01G118800 chr6D 90.566 159 14 1 4033 4190 152257950 152257792 7.570000e-50 209
43 TraesCS4D01G118800 chr6D 89.634 164 16 1 4030 4192 256724322 256724159 2.720000e-49 207
44 TraesCS4D01G118800 chr6D 89.222 167 16 2 4026 4190 467802437 467802271 2.720000e-49 207
45 TraesCS4D01G118800 chr3B 96.233 292 10 1 2078 2368 381837647 381837356 1.880000e-130 477
46 TraesCS4D01G118800 chr3B 91.018 167 13 2 4030 4195 269252150 269251985 2.700000e-54 224
47 TraesCS4D01G118800 chr3B 88.000 150 18 0 2366 2515 245935484 245935633 2.140000e-40 178
48 TraesCS4D01G118800 chr3B 86.624 157 20 1 2353 2509 158707640 158707485 9.930000e-39 172
49 TraesCS4D01G118800 chrUn 96.220 291 10 1 2079 2368 399419304 399419014 6.760000e-130 475
50 TraesCS4D01G118800 chrUn 95.876 291 11 1 2079 2368 189396715 189397005 3.150000e-128 470
51 TraesCS4D01G118800 chrUn 93.750 304 14 1 1447 1750 281713643 281713941 1.140000e-122 451
52 TraesCS4D01G118800 chrUn 93.485 307 15 1 1447 1753 378556742 378556441 1.140000e-122 451
53 TraesCS4D01G118800 chrUn 93.750 304 14 1 1447 1750 430365927 430366225 1.140000e-122 451
54 TraesCS4D01G118800 chrUn 93.160 307 16 1 1447 1753 424119099 424118798 5.300000e-121 446
55 TraesCS4D01G118800 chrUn 93.972 282 12 2 1804 2080 45088323 45088604 8.930000e-114 422
56 TraesCS4D01G118800 chrUn 93.972 282 12 2 1804 2080 414975761 414976042 8.930000e-114 422
57 TraesCS4D01G118800 chrUn 88.571 175 17 2 4030 4201 27078675 27078501 7.570000e-50 209
58 TraesCS4D01G118800 chrUn 89.634 164 15 2 4028 4190 96280160 96280322 2.720000e-49 207
59 TraesCS4D01G118800 chrUn 90.446 157 14 1 4030 4185 96473984 96474140 9.790000e-49 206
60 TraesCS4D01G118800 chrUn 90.850 153 13 1 4030 4181 11760634 11760482 3.520000e-48 204
61 TraesCS4D01G118800 chrUn 89.506 162 16 1 4030 4190 451646483 451646644 3.520000e-48 204
62 TraesCS4D01G118800 chrUn 88.957 163 16 2 4030 4191 122428755 122428916 4.560000e-47 200
63 TraesCS4D01G118800 chrUn 88.485 165 18 1 4030 4193 95767450 95767614 1.640000e-46 198
64 TraesCS4D01G118800 chrUn 88.415 164 18 1 4029 4191 93728817 93728654 5.890000e-46 196
65 TraesCS4D01G118800 chrUn 88.272 162 17 2 4030 4190 81477639 81477799 7.630000e-45 193
66 TraesCS4D01G118800 chr1D 96.220 291 10 1 2079 2368 269411031 269411321 6.760000e-130 475
67 TraesCS4D01G118800 chr1D 90.909 165 13 2 4027 4190 418198367 418198530 3.500000e-53 220
68 TraesCS4D01G118800 chr1D 89.080 174 16 3 4030 4202 463382066 463381895 5.850000e-51 213
69 TraesCS4D01G118800 chr7B 93.750 304 14 1 1447 1750 742948535 742948833 1.140000e-122 451
70 TraesCS4D01G118800 chr5A 93.485 307 15 1 1447 1753 16544757 16544456 1.140000e-122 451
71 TraesCS4D01G118800 chr5A 93.485 307 15 1 1447 1753 420185905 420185604 1.140000e-122 451
72 TraesCS4D01G118800 chr7A 93.972 282 12 2 1804 2080 60294813 60295094 8.930000e-114 422
73 TraesCS4D01G118800 chr7A 93.972 282 12 2 1804 2080 708259583 708259302 8.930000e-114 422
74 TraesCS4D01G118800 chr7A 89.437 142 13 2 2366 2506 543778275 543778135 2.140000e-40 178
75 TraesCS4D01G118800 chr2A 93.972 282 12 2 1804 2080 735235897 735235616 8.930000e-114 422
76 TraesCS4D01G118800 chr2A 90.370 135 12 1 2366 2500 678362893 678363026 7.680000e-40 176
77 TraesCS4D01G118800 chr3A 91.176 170 13 2 4023 4190 500524972 500525141 5.810000e-56 230
78 TraesCS4D01G118800 chr3A 91.071 168 14 1 4029 4195 607058573 607058406 7.520000e-55 226
79 TraesCS4D01G118800 chr3A 91.018 167 14 1 4030 4195 238686210 238686376 2.700000e-54 224
80 TraesCS4D01G118800 chr3A 89.781 137 14 0 2366 2502 251035891 251035755 7.680000e-40 176
81 TraesCS4D01G118800 chr2B 91.515 165 13 1 4027 4190 585712491 585712655 7.520000e-55 226
82 TraesCS4D01G118800 chr5B 91.411 163 12 2 4029 4190 577082582 577082743 9.730000e-54 222
83 TraesCS4D01G118800 chr6B 90.000 170 16 1 4026 4194 481858016 481857847 1.260000e-52 219
84 TraesCS4D01G118800 chr1A 88.701 177 17 2 4029 4204 181769589 181769415 5.850000e-51 213
85 TraesCS4D01G118800 chr6A 92.308 130 10 0 2366 2495 538097702 538097831 1.280000e-42 185


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 TraesCS4D01G118800 chr4D 100225466 100232912 7446 False 13753.00 13753 100.00000 1 7447 1 chr4D.!!$F5 7446
1 TraesCS4D01G118800 chr4D 100204152 100204756 604 False 961.00 961 95.37200 1 604 1 chr4D.!!$F4 603
2 TraesCS4D01G118800 chr4B 142517771 142523946 6175 False 2060.00 6835 91.37525 605 7084 4 chr4B.!!$F2 6479
3 TraesCS4D01G118800 chr4A 476334891 476343681 8790 True 2684.25 4708 94.46350 605 7447 4 chr4A.!!$R1 6842
4 TraesCS4D01G118800 chr7D 66745595 66746200 605 True 946.00 946 94.88400 1 604 1 chr7D.!!$R1 603
5 TraesCS4D01G118800 chr7D 572498593 572499198 605 False 946.00 946 94.88400 1 604 1 chr7D.!!$F3 603
6 TraesCS4D01G118800 chr7D 572486895 572487497 602 False 935.00 935 94.69300 3 604 1 chr7D.!!$F2 601
7 TraesCS4D01G118800 chr2D 94434893 94435496 603 False 939.00 939 94.71900 1 604 1 chr2D.!!$F1 603
8 TraesCS4D01G118800 chr3D 588700930 588701535 605 True 935.00 935 94.55400 1 604 1 chr3D.!!$R3 603
9 TraesCS4D01G118800 chr5D 372067529 372068133 604 True 933.00 933 94.54500 1 604 1 chr5D.!!$R3 603
10 TraesCS4D01G118800 chr5D 298583440 298584045 605 False 929.00 929 94.38900 1 604 1 chr5D.!!$F1 603
11 TraesCS4D01G118800 chr6D 70841983 70842588 605 False 929.00 929 94.38900 1 604 1 chr6D.!!$F1 603

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
616 620 0.721718 GTCGCACAACCATAGCAGAC 59.278 55.000 0.00 0.0 0.00 3.51 F
1413 1520 0.179084 AGGACATAACCGGATGCACG 60.179 55.000 9.46 0.0 34.73 5.34 F
1930 2323 0.666274 TAAGCAGTGTGGTTCGAGCG 60.666 55.000 0.00 0.0 39.08 5.03 F
2821 3616 1.702957 ACCAAAAGTCTCGGGATGGAA 59.297 47.619 9.66 0.0 0.00 3.53 F
4586 5383 2.611971 CCTGCTTGCATGCATGAACTTT 60.612 45.455 31.38 0.0 42.48 2.66 F
5028 5825 2.393271 ACTTGGCTAGCACTGTGATC 57.607 50.000 18.24 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 2441 0.251787 AGGGTGGATCAAAAGGCACC 60.252 55.000 7.76 7.76 0.00 5.01 R
2641 3434 1.797933 CGCGTGAGACTGAAGACCG 60.798 63.158 0.00 0.00 0.00 4.79 R
3054 3849 2.006888 ACATGCGTTCCGTAATTCTGG 58.993 47.619 0.00 0.00 0.00 3.86 R
4651 5448 0.832626 ATGCAGTCGATGGACCATCA 59.167 50.000 29.58 16.42 44.54 3.07 R
5390 6205 1.123756 GTAAAACGGCGTTGTCTCTCG 59.876 52.381 27.50 0.00 0.00 4.04 R
6992 7838 0.035152 ATCCATTCGCACCTTGCTCA 60.035 50.000 0.00 0.00 42.25 4.26 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
21 22 3.477210 AAGGAGACAAGACAAGGTGAC 57.523 47.619 0.00 0.00 0.00 3.67
214 215 4.514577 ATGACCGGCGGAGAAGCG 62.515 66.667 35.78 3.81 38.18 4.68
364 368 3.383185 ACATAGAGAGAAAAGGAGAGCCG 59.617 47.826 0.00 0.00 39.96 5.52
368 372 2.185310 GAGAAAAGGAGAGCCGGCCA 62.185 60.000 26.15 0.00 39.96 5.36
403 407 1.003580 CCCTAGCCAAACAGCTCAAGA 59.996 52.381 0.00 0.00 43.67 3.02
512 516 2.131709 CCTGGGTAAGATCCGCCGA 61.132 63.158 0.00 0.00 0.00 5.54
526 530 2.027073 GCCGACGTGCATGTCTTCA 61.027 57.895 30.85 0.00 36.71 3.02
533 537 3.674997 ACGTGCATGTCTTCACCTTATT 58.325 40.909 5.51 0.00 0.00 1.40
540 544 5.335661 GCATGTCTTCACCTTATTCCGTTTT 60.336 40.000 0.00 0.00 0.00 2.43
544 548 5.699458 GTCTTCACCTTATTCCGTTTTCAGA 59.301 40.000 0.00 0.00 0.00 3.27
550 554 2.536761 ATTCCGTTTTCAGACACCGA 57.463 45.000 0.00 0.00 0.00 4.69
552 556 3.663995 TTCCGTTTTCAGACACCGATA 57.336 42.857 0.00 0.00 0.00 2.92
580 584 3.737559 ACTGGCTCCCACAATGATAAA 57.262 42.857 0.00 0.00 0.00 1.40
584 588 3.299503 GGCTCCCACAATGATAAACCAT 58.700 45.455 0.00 0.00 0.00 3.55
587 591 3.891366 CTCCCACAATGATAAACCATCCC 59.109 47.826 0.00 0.00 32.09 3.85
610 614 2.436173 TGGGATATGTCGCACAACCATA 59.564 45.455 5.05 0.00 41.74 2.74
614 618 1.372582 ATGTCGCACAACCATAGCAG 58.627 50.000 0.00 0.00 0.00 4.24
616 620 0.721718 GTCGCACAACCATAGCAGAC 59.278 55.000 0.00 0.00 0.00 3.51
685 690 2.016318 CAACATCCACTGTGTGTGTGT 58.984 47.619 13.66 7.22 44.81 3.72
686 691 1.667236 ACATCCACTGTGTGTGTGTG 58.333 50.000 12.58 0.00 44.81 3.82
713 718 2.882742 GCGACAAAGTTGCTAGGAAG 57.117 50.000 0.00 0.00 39.63 3.46
714 719 2.413837 GCGACAAAGTTGCTAGGAAGA 58.586 47.619 0.00 0.00 39.63 2.87
716 721 2.737252 CGACAAAGTTGCTAGGAAGACC 59.263 50.000 0.00 0.00 0.00 3.85
717 722 3.075148 GACAAAGTTGCTAGGAAGACCC 58.925 50.000 0.00 0.00 36.73 4.46
718 723 2.076863 CAAAGTTGCTAGGAAGACCCG 58.923 52.381 0.00 0.00 40.87 5.28
733 738 1.805945 CCCGGCGAGTCTTTCTTCG 60.806 63.158 9.30 0.00 0.00 3.79
937 1036 4.409342 CGAGATGGGTTCTGCTCG 57.591 61.111 0.00 0.00 43.25 5.03
952 1051 3.792053 CTCGCCCCGGAATTCTCGG 62.792 68.421 21.58 21.58 46.43 4.63
991 1090 4.966787 GTTCTTGGGCCGCCACCA 62.967 66.667 12.58 0.00 35.88 4.17
1200 1299 2.040544 CGGTGTGCCCAAGGATGTC 61.041 63.158 0.00 0.00 0.00 3.06
1285 1384 1.276145 GCCGACGACTGACACTGTTC 61.276 60.000 0.00 0.00 0.00 3.18
1320 1427 5.007724 GTCTCTGAATTTGGTCGTTTGTCTT 59.992 40.000 0.00 0.00 0.00 3.01
1321 1428 5.588648 TCTCTGAATTTGGTCGTTTGTCTTT 59.411 36.000 0.00 0.00 0.00 2.52
1322 1429 6.094881 TCTCTGAATTTGGTCGTTTGTCTTTT 59.905 34.615 0.00 0.00 0.00 2.27
1351 1458 3.804325 TCATCGCTAGCTGCTTGATTAAC 59.196 43.478 15.16 0.00 40.11 2.01
1366 1473 6.623549 GCTTGATTAACTGCATGCTGTTTCTA 60.624 38.462 37.19 26.55 38.64 2.10
1413 1520 0.179084 AGGACATAACCGGATGCACG 60.179 55.000 9.46 0.00 34.73 5.34
1416 1529 1.351707 CATAACCGGATGCACGCAC 59.648 57.895 9.46 0.00 0.00 5.34
1431 1544 1.757118 ACGCACATGCTATGTAGGAGT 59.243 47.619 1.82 0.00 42.70 3.85
1432 1545 2.956333 ACGCACATGCTATGTAGGAGTA 59.044 45.455 1.82 0.00 42.70 2.59
1433 1546 3.243434 ACGCACATGCTATGTAGGAGTAC 60.243 47.826 1.82 0.00 42.70 2.73
1434 1547 3.243401 CGCACATGCTATGTAGGAGTACA 60.243 47.826 1.82 0.00 42.70 2.90
1435 1548 4.693283 GCACATGCTATGTAGGAGTACAA 58.307 43.478 0.00 0.00 42.70 2.41
1436 1549 4.508124 GCACATGCTATGTAGGAGTACAAC 59.492 45.833 0.00 0.00 42.70 3.32
1437 1550 5.682471 GCACATGCTATGTAGGAGTACAACT 60.682 44.000 0.00 0.00 42.70 3.16
1438 1551 5.750547 CACATGCTATGTAGGAGTACAACTG 59.249 44.000 0.00 0.00 42.54 3.16
1470 1583 4.982295 GTGCCAATTCCAGTTTTGAACTAC 59.018 41.667 0.00 0.00 40.46 2.73
1475 1588 3.134574 TCCAGTTTTGAACTACCGCAT 57.865 42.857 0.00 0.00 40.46 4.73
1534 1647 2.474816 GCTACTGACGGATAAGCCAAG 58.525 52.381 0.00 0.00 35.94 3.61
1570 1683 5.234543 GTCTAATTCCGCGATAAAAGAGCTT 59.765 40.000 8.23 0.00 0.00 3.74
1647 1760 2.477825 CCGATACATCTCCAGCTTGTG 58.522 52.381 0.00 0.00 0.00 3.33
1707 1820 3.126831 GTCTGGTCTGATCATTTAGCGG 58.873 50.000 0.00 0.28 0.00 5.52
1708 1821 1.869767 CTGGTCTGATCATTTAGCGGC 59.130 52.381 0.00 0.00 0.00 6.53
1709 1822 1.486310 TGGTCTGATCATTTAGCGGCT 59.514 47.619 7.98 7.98 0.00 5.52
1710 1823 2.139118 GGTCTGATCATTTAGCGGCTC 58.861 52.381 5.39 0.00 0.00 4.70
1711 1824 2.483714 GGTCTGATCATTTAGCGGCTCA 60.484 50.000 5.39 0.00 0.00 4.26
1728 1841 2.520979 CTCAGCTCTTTCTAACCGACG 58.479 52.381 0.00 0.00 0.00 5.12
1792 1905 6.237490 CGCATGAAGTTCCGTTAGTAGTTTAG 60.237 42.308 0.00 0.00 0.00 1.85
1793 1906 6.035758 GCATGAAGTTCCGTTAGTAGTTTAGG 59.964 42.308 0.00 0.00 0.00 2.69
1795 1908 6.681777 TGAAGTTCCGTTAGTAGTTTAGGTC 58.318 40.000 0.00 0.00 0.00 3.85
1796 1909 5.302357 AGTTCCGTTAGTAGTTTAGGTCG 57.698 43.478 0.00 0.00 0.00 4.79
1797 1910 4.156739 AGTTCCGTTAGTAGTTTAGGTCGG 59.843 45.833 0.00 0.00 38.36 4.79
1800 1913 3.633986 CCGTTAGTAGTTTAGGTCGGGAT 59.366 47.826 0.00 0.00 34.24 3.85
1801 1914 4.498682 CCGTTAGTAGTTTAGGTCGGGATG 60.499 50.000 0.00 0.00 34.24 3.51
1802 1915 4.336433 CGTTAGTAGTTTAGGTCGGGATGA 59.664 45.833 0.00 0.00 0.00 2.92
1803 1916 5.163622 CGTTAGTAGTTTAGGTCGGGATGAA 60.164 44.000 0.00 0.00 0.00 2.57
1890 2281 3.205056 AGATCAGAGATCAGAGTCAGGGT 59.795 47.826 9.43 0.00 0.00 4.34
1930 2323 0.666274 TAAGCAGTGTGGTTCGAGCG 60.666 55.000 0.00 0.00 39.08 5.03
2047 2440 8.880991 TCTGACAAGTTAGGTTAGAGAATACT 57.119 34.615 0.00 0.00 0.00 2.12
2048 2441 8.740906 TCTGACAAGTTAGGTTAGAGAATACTG 58.259 37.037 0.00 0.00 0.00 2.74
2102 2496 5.495926 ACAAGACAGACCTTCATGAAGAT 57.504 39.130 32.49 20.01 40.79 2.40
2146 2540 6.339587 GGACATTTCCACATTAAGGTGAAA 57.660 37.500 21.22 17.57 42.30 2.69
2331 2725 5.116180 TGCTATCAATCACTTCGGTTAAGG 58.884 41.667 0.00 0.00 39.73 2.69
2533 2927 8.515414 ACATATTTCTTTGAGGCTGTTTACTTC 58.485 33.333 0.00 0.00 0.00 3.01
2569 2963 9.729023 CATCGGCACTTGTTTGATTATAAATTA 57.271 29.630 0.00 0.00 0.00 1.40
2641 3434 8.347771 TCAGTTAATTATCATCTTGCTTCATGC 58.652 33.333 0.00 0.00 43.25 4.06
2709 3504 4.141620 ACTGTAGATGGCTGGGTATTTCAG 60.142 45.833 0.00 0.00 35.49 3.02
2821 3616 1.702957 ACCAAAAGTCTCGGGATGGAA 59.297 47.619 9.66 0.00 0.00 3.53
2987 3782 3.243737 GGAAGGCCCTTAACAGTGTTTTG 60.244 47.826 14.90 7.34 0.00 2.44
3054 3849 5.915196 GTGTTGAGCTTTTAACAGGTTCATC 59.085 40.000 11.03 0.00 37.46 2.92
3063 3858 7.755373 GCTTTTAACAGGTTCATCCAGAATTAC 59.245 37.037 0.00 0.00 38.76 1.89
3569 4365 4.770795 CCCAACTTCCTCTGGTTATACAG 58.229 47.826 0.00 0.00 39.84 2.74
3643 4439 7.225341 GCCATTGAAATTGTGAATATCCTTTCC 59.775 37.037 0.00 0.00 0.00 3.13
3763 4559 3.190744 CCCAGTCATCATCAATATGCTGC 59.809 47.826 0.00 0.00 30.81 5.25
3780 4576 4.141287 TGCTGCTACCATTGTTTTGTAGT 58.859 39.130 0.00 0.00 35.50 2.73
3978 4774 4.021280 TGATGTGCACTGCAATTTTATGGT 60.021 37.500 19.41 0.00 41.47 3.55
4050 4847 8.631797 CCTAGTACTCCCTCTGTTTCTAAATAC 58.368 40.741 0.00 0.00 0.00 1.89
4186 4983 6.842676 AGGCTTATATTTAGAAACAGAGGGG 58.157 40.000 0.00 0.00 0.00 4.79
4193 4990 4.837093 TTAGAAACAGAGGGGGTACATG 57.163 45.455 0.00 0.00 0.00 3.21
4586 5383 2.611971 CCTGCTTGCATGCATGAACTTT 60.612 45.455 31.38 0.00 42.48 2.66
4706 5503 3.099141 ACCAATCCGCCATTCTTTTGAT 58.901 40.909 0.00 0.00 0.00 2.57
4943 5740 3.657727 ACCCTCTCCATCAAAGGAAAGAA 59.342 43.478 0.00 0.00 37.20 2.52
5028 5825 2.393271 ACTTGGCTAGCACTGTGATC 57.607 50.000 18.24 0.00 0.00 2.92
5089 5898 9.888878 CATGCCATTGTTATCTTAGTCAATTAG 57.111 33.333 0.00 0.00 0.00 1.73
5259 6072 9.747898 AATTTATCCACCAGAAAATACAGTGTA 57.252 29.630 5.24 5.24 0.00 2.90
5374 6189 3.493334 CTCTCTCTCTCTCTCCATGCAT 58.507 50.000 0.00 0.00 0.00 3.96
5376 6191 3.117587 TCTCTCTCTCTCTCCATGCATGA 60.118 47.826 28.31 12.81 0.00 3.07
6125 6940 2.663196 CTCGGGGTGTGGGACTTC 59.337 66.667 0.00 0.00 0.00 3.01
6197 7012 3.148279 ACCACCCGGAGATCGCTC 61.148 66.667 0.73 0.00 40.54 5.03
6308 7123 1.021390 CGAGCGATGCAGGGAAGTTT 61.021 55.000 0.00 0.00 0.00 2.66
6309 7124 1.739035 CGAGCGATGCAGGGAAGTTTA 60.739 52.381 0.00 0.00 0.00 2.01
6505 7320 3.731867 GCATATGGTGTTGTAAGTGCAGC 60.732 47.826 4.56 0.00 0.00 5.25
6519 7334 3.396491 GCAGCTGCAGTTGTGATTC 57.604 52.632 33.36 10.41 41.59 2.52
6534 7349 6.818142 AGTTGTGATTCCCTTTTCTTGTTTTG 59.182 34.615 0.00 0.00 0.00 2.44
6553 7369 8.918202 TGTTTTGGTAGTCAAGTGATAGATTT 57.082 30.769 0.00 0.00 36.62 2.17
6648 7465 4.568152 ACAATTTTGGTGGAGTTCTTCG 57.432 40.909 0.00 0.00 0.00 3.79
6687 7504 5.390991 GGCTTCAGTCTTGTAAAGTGCATAC 60.391 44.000 0.00 0.00 46.34 2.39
6734 7551 2.165167 CCTTTCCCGTCCCCTTTAAAC 58.835 52.381 0.00 0.00 0.00 2.01
6787 7604 4.055094 AGTAATGGAAAGGGGATTAGCCT 58.945 43.478 0.00 0.00 36.66 4.58
6795 7612 2.217776 AGGGGATTAGCCTGGTTCAAT 58.782 47.619 0.00 0.00 36.66 2.57
6823 7640 1.082679 TACCAGAGCGTCGTCTCTCG 61.083 60.000 13.88 11.22 41.22 4.04
6862 7697 1.371558 GGGTGTCTGCGAGGAAAGT 59.628 57.895 0.00 0.00 0.00 2.66
6867 7702 0.318762 GTCTGCGAGGAAAGTGACCT 59.681 55.000 0.00 0.00 40.80 3.85
6870 7705 2.035442 GCGAGGAAAGTGACCTGCC 61.035 63.158 0.00 0.00 37.93 4.85
6951 7797 2.268730 CGAAAGCAAAGGATTCTGCC 57.731 50.000 0.00 0.00 39.47 4.85
6957 7803 1.101331 CAAAGGATTCTGCCTCTGCC 58.899 55.000 0.00 0.00 37.26 4.85
6959 7805 1.557269 AAGGATTCTGCCTCTGCCGT 61.557 55.000 0.00 0.00 37.26 5.68
6972 7818 2.684881 CTCTGCCGTATCCAGCAAAAAT 59.315 45.455 0.00 0.00 38.82 1.82
6986 7832 5.039333 CAGCAAAAATCCTCGAATTCATCC 58.961 41.667 6.22 0.00 0.00 3.51
6987 7833 4.952335 AGCAAAAATCCTCGAATTCATCCT 59.048 37.500 6.22 0.00 0.00 3.24
6988 7834 5.039333 GCAAAAATCCTCGAATTCATCCTG 58.961 41.667 6.22 0.00 0.00 3.86
6989 7835 5.163622 GCAAAAATCCTCGAATTCATCCTGA 60.164 40.000 6.22 0.00 0.00 3.86
6990 7836 6.460676 GCAAAAATCCTCGAATTCATCCTGAT 60.461 38.462 6.22 0.00 0.00 2.90
6991 7837 6.874288 AAAATCCTCGAATTCATCCTGATC 57.126 37.500 6.22 0.00 0.00 2.92
6992 7838 5.822132 AATCCTCGAATTCATCCTGATCT 57.178 39.130 6.22 0.00 0.00 2.75
6993 7839 4.597404 TCCTCGAATTCATCCTGATCTG 57.403 45.455 6.22 0.00 0.00 2.90
6994 7840 4.218312 TCCTCGAATTCATCCTGATCTGA 58.782 43.478 6.22 0.00 0.00 3.27
6995 7841 4.280425 TCCTCGAATTCATCCTGATCTGAG 59.720 45.833 6.22 0.00 0.00 3.35
6996 7842 3.987547 TCGAATTCATCCTGATCTGAGC 58.012 45.455 6.22 0.00 0.00 4.26
6997 7843 3.385755 TCGAATTCATCCTGATCTGAGCA 59.614 43.478 6.22 0.00 0.00 4.26
6998 7844 4.124970 CGAATTCATCCTGATCTGAGCAA 58.875 43.478 6.22 0.00 0.00 3.91
6999 7845 4.211584 CGAATTCATCCTGATCTGAGCAAG 59.788 45.833 6.22 0.00 0.00 4.01
7000 7846 3.555527 TTCATCCTGATCTGAGCAAGG 57.444 47.619 0.38 1.33 0.00 3.61
7001 7847 2.475155 TCATCCTGATCTGAGCAAGGT 58.525 47.619 0.38 0.00 0.00 3.50
7002 7848 2.169978 TCATCCTGATCTGAGCAAGGTG 59.830 50.000 0.00 0.00 0.00 4.00
7003 7849 0.251354 TCCTGATCTGAGCAAGGTGC 59.749 55.000 0.38 0.00 45.46 5.01
7061 7908 4.473520 ACATTCCGCCTGCCCTCG 62.474 66.667 0.00 0.00 0.00 4.63
7099 7946 5.478679 TCAAATATTGGCGGGAAAAAGAGAA 59.521 36.000 0.00 0.00 0.00 2.87
7126 7973 5.987347 ACAAGCAGGTGATGAAATTGAAAAG 59.013 36.000 0.00 0.00 0.00 2.27
7130 7977 5.544650 CAGGTGATGAAATTGAAAAGGCTT 58.455 37.500 0.00 0.00 0.00 4.35
7131 7978 6.690530 CAGGTGATGAAATTGAAAAGGCTTA 58.309 36.000 0.00 0.00 0.00 3.09
7132 7979 7.325694 CAGGTGATGAAATTGAAAAGGCTTAT 58.674 34.615 0.00 0.00 0.00 1.73
7133 7980 7.820872 CAGGTGATGAAATTGAAAAGGCTTATT 59.179 33.333 0.00 0.00 0.00 1.40
7134 7981 8.037166 AGGTGATGAAATTGAAAAGGCTTATTC 58.963 33.333 0.00 7.60 0.00 1.75
7135 7982 7.009540 GGTGATGAAATTGAAAAGGCTTATTCG 59.990 37.037 0.00 0.00 0.00 3.34
7136 7983 6.531240 TGATGAAATTGAAAAGGCTTATTCGC 59.469 34.615 0.00 0.00 0.00 4.70
7137 7984 5.777802 TGAAATTGAAAAGGCTTATTCGCA 58.222 33.333 0.00 0.00 0.00 5.10
7158 8005 1.040339 AACTAGAGAGCGCCTGGAGG 61.040 60.000 2.29 0.00 38.53 4.30
7180 8035 4.702131 GGGCAATACTCACAAGATGACTTT 59.298 41.667 0.00 0.00 33.70 2.66
7239 8094 0.179215 GCAAGAACAACTCGATGCCG 60.179 55.000 0.00 0.00 36.39 5.69
7296 9914 6.541641 GCTGAATTCTAACACAATGAGGATCT 59.458 38.462 7.05 0.00 34.92 2.75
7331 9949 1.653151 GTAGGATGCCGAAACCAGTC 58.347 55.000 0.00 0.00 0.00 3.51
7332 9950 0.174845 TAGGATGCCGAAACCAGTCG 59.825 55.000 0.00 0.00 40.77 4.18
7337 9955 3.423154 CCGAAACCAGTCGCAGCC 61.423 66.667 0.00 0.00 39.74 4.85
7347 9965 4.804420 TCGCAGCCCCCTCCTCAT 62.804 66.667 0.00 0.00 0.00 2.90
7356 9974 2.509964 GCCCCCTCCTCATAGAAGAAAA 59.490 50.000 0.00 0.00 0.00 2.29
7400 10018 6.889301 TCTACTCTTTCTACACCGAAGAAA 57.111 37.500 0.00 0.00 39.91 2.52
7413 10031 2.874701 CCGAAGAAAGTGCCATATCCAG 59.125 50.000 0.00 0.00 0.00 3.86
7432 10050 7.856145 ATCCAGTGAAGAAAATGACACTATC 57.144 36.000 0.00 0.00 40.84 2.08
7436 10054 8.660373 CCAGTGAAGAAAATGACACTATCTTAC 58.340 37.037 0.00 0.00 40.84 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.542030 CTCTCACTGTAGCGTCACCTT 59.458 52.381 0.00 0.00 0.00 3.50
21 22 2.103143 CGGGCTCTCACTGTAGCG 59.897 66.667 0.00 0.00 39.71 4.26
214 215 1.004440 GTCAGTGTCTGTGCTCCCC 60.004 63.158 0.00 0.00 32.61 4.81
368 372 2.131023 CTAGGGGAAGAAGAAGGGCAT 58.869 52.381 0.00 0.00 0.00 4.40
403 407 6.464222 TCAATACAAGTAGCTACAAGTGCTT 58.536 36.000 25.28 15.95 41.46 3.91
488 492 1.492764 GGATCTTACCCAGGTTCGGA 58.507 55.000 0.00 0.00 0.00 4.55
512 516 2.831685 TAAGGTGAAGACATGCACGT 57.168 45.000 0.00 0.00 35.91 4.49
526 530 4.070009 GGTGTCTGAAAACGGAATAAGGT 58.930 43.478 0.00 0.00 0.00 3.50
533 537 3.663995 TTATCGGTGTCTGAAAACGGA 57.336 42.857 5.30 5.13 0.00 4.69
540 544 5.872617 CCAGTAAAACATTATCGGTGTCTGA 59.127 40.000 0.00 0.00 0.00 3.27
544 548 4.585879 AGCCAGTAAAACATTATCGGTGT 58.414 39.130 0.00 0.00 0.00 4.16
550 554 4.929479 TGTGGGAGCCAGTAAAACATTAT 58.071 39.130 0.00 0.00 32.34 1.28
552 556 3.237268 TGTGGGAGCCAGTAAAACATT 57.763 42.857 0.00 0.00 32.34 2.71
587 591 1.670811 GGTTGTGCGACATATCCCAAG 59.329 52.381 0.00 0.00 0.00 3.61
592 596 3.130633 TGCTATGGTTGTGCGACATATC 58.869 45.455 0.00 0.00 0.00 1.63
610 614 3.242903 CGTCTATCGAATGTGAGTCTGCT 60.243 47.826 0.00 0.00 42.86 4.24
614 618 3.548415 GGGACGTCTATCGAATGTGAGTC 60.548 52.174 16.46 0.00 42.86 3.36
616 620 2.619177 AGGGACGTCTATCGAATGTGAG 59.381 50.000 16.46 0.00 42.86 3.51
685 690 0.814457 AACTTTGTCGCTGGCAAACA 59.186 45.000 4.58 0.00 33.04 2.83
686 691 1.199624 CAACTTTGTCGCTGGCAAAC 58.800 50.000 4.58 0.00 33.04 2.93
707 712 1.751927 GACTCGCCGGGTCTTCCTA 60.752 63.158 10.48 0.00 0.00 2.94
708 713 3.069318 GACTCGCCGGGTCTTCCT 61.069 66.667 10.48 0.00 0.00 3.36
710 715 2.971452 AAGACTCGCCGGGTCTTC 59.029 61.111 25.89 0.00 46.96 2.87
712 717 1.186267 AAGAAAGACTCGCCGGGTCT 61.186 55.000 15.18 15.18 44.73 3.85
713 718 0.736672 GAAGAAAGACTCGCCGGGTC 60.737 60.000 9.61 9.61 0.00 4.46
714 719 1.292541 GAAGAAAGACTCGCCGGGT 59.707 57.895 2.18 0.00 0.00 5.28
716 721 1.805945 CCGAAGAAAGACTCGCCGG 60.806 63.158 0.00 0.00 37.48 6.13
717 722 1.071567 GACCGAAGAAAGACTCGCCG 61.072 60.000 0.00 0.00 0.00 6.46
718 723 0.736672 GGACCGAAGAAAGACTCGCC 60.737 60.000 0.00 0.00 0.00 5.54
733 738 1.653151 GATAAAGGCTCGTGTGGACC 58.347 55.000 0.00 0.00 0.00 4.46
952 1051 3.627218 GCGGGTTCTACGATGCGC 61.627 66.667 0.00 0.00 0.00 6.09
991 1090 2.843113 CCTCTTCCTCCATTTCAGGACT 59.157 50.000 0.00 0.00 39.95 3.85
1200 1299 2.336478 ACTCTCACCGGAGCAGTCG 61.336 63.158 9.46 0.00 41.13 4.18
1285 1384 6.757947 ACCAAATTCAGAGACAAAACACAATG 59.242 34.615 0.00 0.00 0.00 2.82
1320 1427 4.908736 GCAGCTAGCGATGAATTAACAAA 58.091 39.130 9.55 0.00 0.00 2.83
1321 1428 4.536364 GCAGCTAGCGATGAATTAACAA 57.464 40.909 9.55 0.00 0.00 2.83
1351 1458 4.494350 ACAGTTTAGAAACAGCATGCAG 57.506 40.909 21.98 15.38 42.53 4.41
1366 1473 4.618920 ACCAGGATACGAAGAACAGTTT 57.381 40.909 0.00 0.00 46.39 2.66
1413 1520 4.322080 TGTACTCCTACATAGCATGTGC 57.678 45.455 10.77 0.00 44.60 4.57
1416 1529 5.907207 ACAGTTGTACTCCTACATAGCATG 58.093 41.667 0.00 0.00 32.70 4.06
1431 1544 2.158885 TGGCACAGCTTGTACAGTTGTA 60.159 45.455 12.06 0.00 44.69 2.41
1433 1546 1.308047 TGGCACAGCTTGTACAGTTG 58.692 50.000 0.00 1.92 39.60 3.16
1434 1547 2.051334 TTGGCACAGCTTGTACAGTT 57.949 45.000 0.00 0.00 42.39 3.16
1435 1548 2.276732 ATTGGCACAGCTTGTACAGT 57.723 45.000 0.00 0.00 42.39 3.55
1436 1549 2.095059 GGAATTGGCACAGCTTGTACAG 60.095 50.000 0.00 0.00 42.39 2.74
1437 1550 1.885887 GGAATTGGCACAGCTTGTACA 59.114 47.619 0.00 0.00 42.39 2.90
1438 1551 1.885887 TGGAATTGGCACAGCTTGTAC 59.114 47.619 0.00 0.00 42.39 2.90
1470 1583 4.882671 AAGCTATGAAACAAGTATGCGG 57.117 40.909 0.00 0.00 0.00 5.69
1534 1647 5.050567 CGCGGAATTAGACCAACTATTAACC 60.051 44.000 0.00 0.00 0.00 2.85
1598 1711 2.358510 CCCCACCAATGTGATCTCCATT 60.359 50.000 5.64 5.64 45.76 3.16
1647 1760 1.532007 TGCGTTACCCGTGATTGAAAC 59.468 47.619 0.00 0.00 39.32 2.78
1694 1807 1.139654 AGCTGAGCCGCTAAATGATCA 59.860 47.619 0.00 0.00 38.76 2.92
1707 1820 2.263945 GTCGGTTAGAAAGAGCTGAGC 58.736 52.381 0.00 0.00 0.00 4.26
1708 1821 2.520979 CGTCGGTTAGAAAGAGCTGAG 58.479 52.381 0.00 0.00 0.00 3.35
1709 1822 1.201647 CCGTCGGTTAGAAAGAGCTGA 59.798 52.381 2.08 0.00 0.00 4.26
1710 1823 1.630148 CCGTCGGTTAGAAAGAGCTG 58.370 55.000 2.08 0.00 0.00 4.24
1711 1824 0.531200 CCCGTCGGTTAGAAAGAGCT 59.469 55.000 11.06 0.00 0.00 4.09
1758 1871 3.243877 CGGAACTTCATGCGAATCTACAG 59.756 47.826 0.00 0.00 36.09 2.74
1801 1914 8.955252 GATCTTTGCAGAGGACAAAGGTACTTC 61.955 44.444 14.31 3.67 45.95 3.01
1802 1915 7.243332 GATCTTTGCAGAGGACAAAGGTACTT 61.243 42.308 14.31 0.00 45.95 2.24
1803 1916 3.744660 CTTTGCAGAGGACAAAGGTACT 58.255 45.455 8.08 0.00 46.58 2.73
1853 2244 9.283768 GATCTCTGATCTAGTAGATGTGAGAAA 57.716 37.037 27.69 16.61 40.12 2.52
1930 2323 2.233431 AGAACTCAGCAGTGACTGATCC 59.767 50.000 18.18 0.00 45.34 3.36
1985 2378 1.202698 ACAAGAAGAAGGCAAGAGCGT 60.203 47.619 0.00 0.00 43.41 5.07
2047 2440 0.541764 GGGTGGATCAAAAGGCACCA 60.542 55.000 15.64 0.00 34.63 4.17
2048 2441 0.251787 AGGGTGGATCAAAAGGCACC 60.252 55.000 7.76 7.76 0.00 5.01
2225 2619 3.041946 AGATAGGGGCTTCAGTACTTGG 58.958 50.000 0.00 0.00 0.00 3.61
2269 2663 8.562892 CATAGGGCATCTTCTATTTTTAGTGTG 58.437 37.037 0.00 0.00 0.00 3.82
2314 2708 3.555956 CGATCCCTTAACCGAAGTGATTG 59.444 47.826 0.00 0.00 32.94 2.67
2412 2806 4.398988 ACTGAAATGAGTGAACAAGCACAA 59.601 37.500 0.00 0.00 41.19 3.33
2569 2963 9.638239 CAATTTGTTAGTGCCACAATTAATAGT 57.362 29.630 0.00 0.00 34.13 2.12
2594 3382 4.946772 TGAGTTGATGTCAGACCAAAAACA 59.053 37.500 0.00 0.00 0.00 2.83
2641 3434 1.797933 CGCGTGAGACTGAAGACCG 60.798 63.158 0.00 0.00 0.00 4.79
2821 3616 7.147123 ACCTTATATAAAGGAATGGTCTTGCCT 60.147 37.037 10.67 0.00 39.81 4.75
3021 3816 6.600032 TGTTAAAAGCTCAACACTGTTAAGGA 59.400 34.615 4.81 0.00 29.52 3.36
3054 3849 2.006888 ACATGCGTTCCGTAATTCTGG 58.993 47.619 0.00 0.00 0.00 3.86
3063 3858 2.032894 GGATGTTATGACATGCGTTCCG 60.033 50.000 8.00 0.00 46.27 4.30
3569 4365 9.797556 AACAAAAATTAAACTCTTACAGGACAC 57.202 29.630 0.00 0.00 0.00 3.67
3668 4464 2.832129 ACCATGATACCGAGTGAACTGT 59.168 45.455 0.00 0.00 0.00 3.55
3763 4559 9.052759 AGTCAAGTAACTACAAAACAATGGTAG 57.947 33.333 0.00 0.00 40.19 3.18
3978 4774 7.362056 GCAGGCATAGTTTGTTCTAGAAAATGA 60.362 37.037 6.78 0.00 0.00 2.57
4050 4847 7.710907 TCCGTATTGGAATCTCTAAATGTCTTG 59.289 37.037 0.00 0.00 46.38 3.02
4186 4983 4.134563 ACTGGTTTGTTCACTCATGTACC 58.865 43.478 0.00 0.00 0.00 3.34
4193 4990 3.279434 AGGTCAACTGGTTTGTTCACTC 58.721 45.455 0.00 0.00 36.49 3.51
4550 5347 5.887598 TGCAAGCAGGACATCTAAACAATAT 59.112 36.000 0.00 0.00 0.00 1.28
4651 5448 0.832626 ATGCAGTCGATGGACCATCA 59.167 50.000 29.58 16.42 44.54 3.07
4706 5503 7.598493 GCTTCATTACAATAGCAAACTTTTGGA 59.402 33.333 3.95 0.00 38.66 3.53
4943 5740 1.075482 CAAGGATGGGCACACAGGT 59.925 57.895 0.00 0.00 0.00 4.00
5018 5815 5.414360 TGAAGTCAATAGAGATCACAGTGC 58.586 41.667 0.00 0.00 0.00 4.40
5089 5898 9.944663 TTGTTACTCACTTGTTAATTTGATGTC 57.055 29.630 0.00 0.00 0.00 3.06
5120 5932 9.498176 ACAAAGGACAAAGTTTATCGTAATAGT 57.502 29.630 0.00 0.00 0.00 2.12
5390 6205 1.123756 GTAAAACGGCGTTGTCTCTCG 59.876 52.381 27.50 0.00 0.00 4.04
5576 6391 9.846248 AGCAACATTCTAAATCACTCATAAAAC 57.154 29.630 0.00 0.00 0.00 2.43
5577 6392 9.844790 CAGCAACATTCTAAATCACTCATAAAA 57.155 29.630 0.00 0.00 0.00 1.52
5704 6519 4.515567 TGGAGACTAGTATGCAGATACGTG 59.484 45.833 7.70 0.00 39.69 4.49
6054 6869 2.125326 CCCCGATGAGCACCTCGTA 61.125 63.158 7.88 0.00 33.57 3.43
6125 6940 1.578583 ACAGGACGTTCTTCAAACCG 58.421 50.000 0.00 0.00 0.00 4.44
6197 7012 2.124403 GCAGGGCTGTGATCCCAG 60.124 66.667 0.11 0.11 46.36 4.45
6236 7051 3.000727 CGTGATGTTAGAAGGACCAACC 58.999 50.000 0.00 0.00 39.35 3.77
6308 7123 2.357952 CGACCTGTCCACGATCTTCATA 59.642 50.000 0.00 0.00 0.00 2.15
6309 7124 1.135139 CGACCTGTCCACGATCTTCAT 59.865 52.381 0.00 0.00 0.00 2.57
6505 7320 3.571401 AGAAAAGGGAATCACAACTGCAG 59.429 43.478 13.48 13.48 0.00 4.41
6519 7334 5.845391 TGACTACCAAAACAAGAAAAGGG 57.155 39.130 0.00 0.00 0.00 3.95
6534 7349 8.643324 ACCAGATAAATCTATCACTTGACTACC 58.357 37.037 0.00 0.00 37.05 3.18
6553 7369 3.193903 TGCAAACAGCTACGTACCAGATA 59.806 43.478 0.00 0.00 45.94 1.98
6648 7465 1.170290 AAGCCCTGTACAAACACCGC 61.170 55.000 0.00 0.00 0.00 5.68
6734 7551 6.507900 ACCGAAATACATCAGTCACATAGAG 58.492 40.000 0.00 0.00 0.00 2.43
6823 7640 4.035675 CCCGAGCCAGATTATTCTTTTCAC 59.964 45.833 0.00 0.00 0.00 3.18
6862 7697 0.116342 TCTTCAGTAGGGGCAGGTCA 59.884 55.000 0.00 0.00 0.00 4.02
6867 7702 2.501723 GTCAGATTCTTCAGTAGGGGCA 59.498 50.000 0.00 0.00 0.00 5.36
6870 7705 3.107601 TGGGTCAGATTCTTCAGTAGGG 58.892 50.000 0.00 0.00 0.00 3.53
6930 7768 1.068333 GCAGAATCCTTTGCTTTCGCA 60.068 47.619 0.00 0.00 46.24 5.10
6935 7773 2.444421 CAGAGGCAGAATCCTTTGCTT 58.556 47.619 0.00 0.00 40.15 3.91
6957 7803 3.194861 TCGAGGATTTTTGCTGGATACG 58.805 45.455 0.00 0.00 42.51 3.06
6959 7805 5.885352 TGAATTCGAGGATTTTTGCTGGATA 59.115 36.000 0.04 0.00 0.00 2.59
6986 7832 0.108472 TCGCACCTTGCTCAGATCAG 60.108 55.000 0.00 0.00 42.25 2.90
6987 7833 0.321346 TTCGCACCTTGCTCAGATCA 59.679 50.000 0.00 0.00 42.25 2.92
6988 7834 1.329906 CATTCGCACCTTGCTCAGATC 59.670 52.381 0.00 0.00 42.25 2.75
6989 7835 1.376543 CATTCGCACCTTGCTCAGAT 58.623 50.000 0.00 0.00 42.25 2.90
6990 7836 0.674581 CCATTCGCACCTTGCTCAGA 60.675 55.000 0.00 0.00 42.25 3.27
6991 7837 0.674581 TCCATTCGCACCTTGCTCAG 60.675 55.000 0.00 0.00 42.25 3.35
6992 7838 0.035152 ATCCATTCGCACCTTGCTCA 60.035 50.000 0.00 0.00 42.25 4.26
6993 7839 0.379669 CATCCATTCGCACCTTGCTC 59.620 55.000 0.00 0.00 42.25 4.26
6994 7840 1.660560 GCATCCATTCGCACCTTGCT 61.661 55.000 0.00 0.00 42.25 3.91
6995 7841 1.226773 GCATCCATTCGCACCTTGC 60.227 57.895 0.00 0.00 40.69 4.01
6996 7842 1.063006 CGCATCCATTCGCACCTTG 59.937 57.895 0.00 0.00 0.00 3.61
6997 7843 1.377202 ACGCATCCATTCGCACCTT 60.377 52.632 0.00 0.00 0.00 3.50
6998 7844 2.108514 CACGCATCCATTCGCACCT 61.109 57.895 0.00 0.00 0.00 4.00
6999 7845 1.439353 ATCACGCATCCATTCGCACC 61.439 55.000 0.00 0.00 0.00 5.01
7000 7846 0.041839 GATCACGCATCCATTCGCAC 60.042 55.000 0.00 0.00 0.00 5.34
7001 7847 0.179076 AGATCACGCATCCATTCGCA 60.179 50.000 0.00 0.00 30.71 5.10
7002 7848 0.234106 CAGATCACGCATCCATTCGC 59.766 55.000 0.00 0.00 30.71 4.70
7003 7849 1.791204 CTCAGATCACGCATCCATTCG 59.209 52.381 0.00 0.00 30.71 3.34
7061 7908 7.485913 CGCCAATATTTGAACTTATCATATGCC 59.514 37.037 0.00 0.00 38.03 4.40
7099 7946 4.828939 TCAATTTCATCACCTGCTTGTTCT 59.171 37.500 0.00 0.00 0.00 3.01
7126 7973 4.260415 GCTCTCTAGTTTTGCGAATAAGCC 60.260 45.833 0.00 0.00 36.02 4.35
7135 7982 0.723981 CAGGCGCTCTCTAGTTTTGC 59.276 55.000 7.64 0.00 0.00 3.68
7136 7983 1.066858 TCCAGGCGCTCTCTAGTTTTG 60.067 52.381 7.64 0.00 0.00 2.44
7137 7984 1.205893 CTCCAGGCGCTCTCTAGTTTT 59.794 52.381 7.64 0.00 0.00 2.43
7158 8005 5.886960 AAAGTCATCTTGTGAGTATTGCC 57.113 39.130 0.00 0.00 39.61 4.52
7164 8019 9.512588 AATTGATTCTAAAGTCATCTTGTGAGT 57.487 29.630 0.00 0.00 42.34 3.41
7180 8035 4.191544 CTCCTTGGTGCGAATTGATTCTA 58.808 43.478 2.58 0.00 34.69 2.10
7254 8109 2.266055 CCTCTGGCGAGTTCCACC 59.734 66.667 0.00 0.00 35.43 4.61
7265 8120 3.942829 TGTGTTAGAATTCAGCCTCTGG 58.057 45.455 8.44 0.00 31.51 3.86
7296 9914 4.794278 TCCTACGATTGTAGTCTTTGCA 57.206 40.909 17.25 0.00 45.49 4.08
7331 9949 2.844362 TATGAGGAGGGGGCTGCG 60.844 66.667 0.00 0.00 0.00 5.18
7332 9950 1.056700 TTCTATGAGGAGGGGGCTGC 61.057 60.000 0.00 0.00 0.00 5.25
7337 9955 6.667661 AGAAATTTTCTTCTATGAGGAGGGG 58.332 40.000 5.82 0.00 36.36 4.79
7368 9986 6.253942 GGTGTAGAAAGAGTAGATTTCTTCGC 59.746 42.308 6.28 7.83 42.86 4.70
7369 9987 6.469595 CGGTGTAGAAAGAGTAGATTTCTTCG 59.530 42.308 6.28 3.63 42.86 3.79
7400 10018 4.574674 TTTCTTCACTGGATATGGCACT 57.425 40.909 0.00 0.00 0.00 4.40
7413 10031 7.063544 AGCGTAAGATAGTGTCATTTTCTTCAC 59.936 37.037 4.67 0.00 43.02 3.18


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

AutoCloner maintained by Alex Coulton.