Multiple sequence alignment - TraesCS7B01G049400

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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 TraesCS7B01G049400 chr7B 100.000 8040 0 0 1 8040 49355855 49363894 0.000000e+00 14848.0
1 TraesCS7B01G049400 chr7B 94.829 2862 129 7 4773 7630 49613542 49610696 0.000000e+00 4447.0
2 TraesCS7B01G049400 chr7B 94.991 2196 66 18 209 2388 49620686 49618519 0.000000e+00 3406.0
3 TraesCS7B01G049400 chr7B 97.277 1726 34 5 3734 5449 49554895 49556617 0.000000e+00 2915.0
4 TraesCS7B01G049400 chr7B 94.944 1602 76 4 5670 7267 49587642 49589242 0.000000e+00 2505.0
5 TraesCS7B01G049400 chr7B 95.730 1335 44 6 451 1775 49550291 49551622 0.000000e+00 2137.0
6 TraesCS7B01G049400 chr7B 97.103 932 24 2 3809 4738 49614465 49613535 0.000000e+00 1568.0
7 TraesCS7B01G049400 chr7B 89.951 1214 86 12 1265 2465 50881836 50880646 0.000000e+00 1533.0
8 TraesCS7B01G049400 chr7B 95.146 824 37 2 6808 7630 49549779 49548958 0.000000e+00 1297.0
9 TraesCS7B01G049400 chr7B 98.263 691 12 0 2375 3065 49618211 49617521 0.000000e+00 1210.0
10 TraesCS7B01G049400 chr7B 94.347 743 35 3 1768 2507 49552780 49553518 0.000000e+00 1133.0
11 TraesCS7B01G049400 chr7B 98.443 578 9 0 2495 3072 49553533 49554110 0.000000e+00 1018.0
12 TraesCS7B01G049400 chr7B 78.585 1611 257 51 3769 5350 49181616 49183167 0.000000e+00 983.0
13 TraesCS7B01G049400 chr7B 93.761 593 20 3 3078 3654 49554307 49554898 0.000000e+00 874.0
14 TraesCS7B01G049400 chr7B 94.434 557 11 5 3114 3654 49617523 49616971 0.000000e+00 839.0
15 TraesCS7B01G049400 chr7B 98.297 411 6 1 7630 8040 352421758 352421349 0.000000e+00 719.0
16 TraesCS7B01G049400 chr7B 93.899 377 20 1 894 1270 50890007 50889634 4.210000e-157 566.0
17 TraesCS7B01G049400 chr7B 95.028 362 11 4 112 467 49549917 49550277 5.450000e-156 562.0
18 TraesCS7B01G049400 chr7B 93.767 369 22 1 7263 7630 49607628 49607996 3.280000e-153 553.0
19 TraesCS7B01G049400 chr7B 87.255 204 20 4 5352 5551 50683636 50683435 2.260000e-55 228.0
20 TraesCS7B01G049400 chr7B 87.255 204 20 4 5352 5551 50714613 50714412 2.260000e-55 228.0
21 TraesCS7B01G049400 chr7B 89.189 185 15 3 5352 5534 50717991 50717810 8.120000e-55 226.0
22 TraesCS7B01G049400 chr7B 77.056 462 57 20 332 753 49177536 49177988 3.780000e-53 220.0
23 TraesCS7B01G049400 chr7B 99.115 113 1 0 1 113 42843827 42843715 3.800000e-48 204.0
24 TraesCS7B01G049400 chr7B 99.115 113 1 0 1 113 211370808 211370696 3.800000e-48 204.0
25 TraesCS7B01G049400 chr7B 98.529 68 1 0 112 179 49620752 49620685 3.940000e-23 121.0
26 TraesCS7B01G049400 chr7B 88.525 61 7 0 2452 2512 50839397 50839337 3.110000e-09 75.0
27 TraesCS7B01G049400 chr7B 88.525 61 7 0 2452 2512 50858509 50858449 3.110000e-09 75.0
28 TraesCS7B01G049400 chr7B 100.000 29 0 0 7630 7658 605481308 605481280 4.000000e-03 54.7
29 TraesCS7B01G049400 chr7D 90.959 3451 252 23 3734 7139 95150914 95147479 0.000000e+00 4590.0
30 TraesCS7B01G049400 chr7D 87.411 3384 319 44 3791 7141 96084673 96081364 0.000000e+00 3790.0
31 TraesCS7B01G049400 chr7D 89.017 2859 198 42 737 3544 96053809 96051016 0.000000e+00 3434.0
32 TraesCS7B01G049400 chr7D 85.798 2908 265 65 4280 7141 96033178 96030373 0.000000e+00 2946.0
33 TraesCS7B01G049400 chr7D 91.343 1594 103 15 1823 3384 96086388 96084798 0.000000e+00 2146.0
34 TraesCS7B01G049400 chr7D 88.763 1673 119 33 1433 3098 95153039 95151429 0.000000e+00 1984.0
35 TraesCS7B01G049400 chr7D 86.924 1629 196 11 5522 7141 95835172 95833552 0.000000e+00 1812.0
36 TraesCS7B01G049400 chr7D 87.040 1605 192 11 5534 7129 95990552 95988955 0.000000e+00 1797.0
37 TraesCS7B01G049400 chr7D 87.074 1586 198 5 5567 7146 96017387 96015803 0.000000e+00 1786.0
38 TraesCS7B01G049400 chr7D 90.875 1348 50 19 456 1772 96087693 96086388 0.000000e+00 1740.0
39 TraesCS7B01G049400 chr7D 86.574 1579 200 6 5567 7139 95964507 95962935 0.000000e+00 1731.0
40 TraesCS7B01G049400 chr7D 85.776 1617 200 14 5534 7141 95970607 95969012 0.000000e+00 1685.0
41 TraesCS7B01G049400 chr7D 86.909 1184 147 4 5966 7141 95976277 95975094 0.000000e+00 1321.0
42 TraesCS7B01G049400 chr7D 87.238 956 119 3 5567 6521 96007050 96006097 0.000000e+00 1086.0
43 TraesCS7B01G049400 chr7D 88.286 811 36 21 356 1114 96087820 96087017 0.000000e+00 917.0
44 TraesCS7B01G049400 chr7D 85.103 725 93 9 4631 5350 95058001 95058715 0.000000e+00 726.0
45 TraesCS7B01G049400 chr7D 86.495 659 80 5 6517 7170 95997576 95996922 0.000000e+00 715.0
46 TraesCS7B01G049400 chr7D 89.104 569 38 12 356 904 95153609 95153045 0.000000e+00 686.0
47 TraesCS7B01G049400 chr7D 91.880 468 37 1 3771 4238 96048579 96048113 0.000000e+00 652.0
48 TraesCS7B01G049400 chr7D 87.218 532 44 3 3133 3652 95151434 95150915 1.160000e-162 584.0
49 TraesCS7B01G049400 chr7D 87.654 405 49 1 5567 5970 95982925 95982521 3.400000e-128 470.0
50 TraesCS7B01G049400 chr7D 93.534 232 15 0 355 586 96068210 96067979 5.970000e-91 346.0
51 TraesCS7B01G049400 chr7D 76.204 706 136 23 3770 4448 95057156 95057856 2.150000e-90 344.0
52 TraesCS7B01G049400 chr7D 84.030 263 35 7 892 1151 95053342 95053600 6.230000e-61 246.0
53 TraesCS7B01G049400 chr7D 89.691 194 14 4 5352 5543 95829308 95829119 8.060000e-60 243.0
54 TraesCS7B01G049400 chr7D 86.634 202 23 2 5352 5551 95964774 95964575 3.780000e-53 220.0
55 TraesCS7B01G049400 chr7D 87.179 195 20 3 5352 5543 95958693 95958501 4.890000e-52 217.0
56 TraesCS7B01G049400 chr7D 95.161 124 5 1 1 123 101778874 101778751 2.290000e-45 195.0
57 TraesCS7B01G049400 chr7D 83.663 202 25 4 5352 5551 95835389 95835194 4.960000e-42 183.0
58 TraesCS7B01G049400 chr7D 83.663 202 23 4 112 303 96068580 96068379 1.780000e-41 182.0
59 TraesCS7B01G049400 chr7D 97.260 73 2 0 308 380 96068291 96068219 3.050000e-24 124.0
60 TraesCS7B01G049400 chr7A 91.006 2446 182 11 4722 7131 99144675 99142232 0.000000e+00 3264.0
61 TraesCS7B01G049400 chr7A 91.255 1155 75 12 2510 3654 99146761 99145623 0.000000e+00 1550.0
62 TraesCS7B01G049400 chr7A 92.880 927 50 10 3734 4654 99145626 99144710 0.000000e+00 1332.0
63 TraesCS7B01G049400 chr7A 88.708 921 70 16 1482 2397 99147683 99146792 0.000000e+00 1094.0
64 TraesCS7B01G049400 chr7A 84.698 1026 63 14 498 1490 99148830 99147866 0.000000e+00 939.0
65 TraesCS7B01G049400 chr7A 81.608 908 128 29 4454 5350 98728958 98729837 0.000000e+00 715.0
66 TraesCS7B01G049400 chr7A 97.567 411 9 1 7630 8040 558746972 558747381 0.000000e+00 702.0
67 TraesCS7B01G049400 chr7A 85.889 574 44 11 7071 7630 98888142 98887592 1.950000e-160 577.0
68 TraesCS7B01G049400 chr7A 79.783 460 88 5 3770 4226 98728269 98728726 6.020000e-86 329.0
69 TraesCS7B01G049400 chr7A 83.984 256 35 6 892 1145 98724737 98724988 2.900000e-59 241.0
70 TraesCS7B01G049400 chr7A 92.308 117 7 2 356 471 99150537 99150422 1.800000e-36 165.0
71 TraesCS7B01G049400 chr7A 92.391 92 7 0 3655 3746 214312855 214312946 1.820000e-26 132.0
72 TraesCS7B01G049400 chr7A 96.667 60 2 0 451 510 99150414 99150355 5.130000e-17 100.0
73 TraesCS7B01G049400 chr2A 98.305 413 7 0 7628 8040 235346002 235345590 0.000000e+00 725.0
74 TraesCS7B01G049400 chr2A 97.821 413 8 1 7628 8040 235342273 235341862 0.000000e+00 712.0
75 TraesCS7B01G049400 chr2A 96.837 411 11 2 7630 8040 128695044 128695452 0.000000e+00 686.0
76 TraesCS7B01G049400 chr2A 84.921 126 12 6 3615 3736 82351034 82350912 3.940000e-23 121.0
77 TraesCS7B01G049400 chr2D 97.816 412 8 1 7630 8040 432002778 432003189 0.000000e+00 710.0
78 TraesCS7B01G049400 chr5B 97.573 412 9 1 7630 8040 147464056 147463645 0.000000e+00 704.0
79 TraesCS7B01G049400 chr5B 97.573 412 9 1 7629 8040 579598523 579598113 0.000000e+00 704.0
80 TraesCS7B01G049400 chr5B 99.115 113 1 0 1 113 141947609 141947721 3.800000e-48 204.0
81 TraesCS7B01G049400 chr5B 96.667 120 3 1 1 119 479823563 479823444 1.770000e-46 198.0
82 TraesCS7B01G049400 chr5B 95.161 124 5 1 1 123 548557018 548556895 2.290000e-45 195.0
83 TraesCS7B01G049400 chr5B 100.000 30 0 0 7630 7659 672105213 672105184 1.000000e-03 56.5
84 TraesCS7B01G049400 chr3A 97.567 411 10 0 7630 8040 83770900 83770490 0.000000e+00 704.0
85 TraesCS7B01G049400 chr3A 90.323 93 7 2 3648 3739 488042544 488042635 3.940000e-23 121.0
86 TraesCS7B01G049400 chr1B 96.875 416 11 2 7627 8040 96455578 96455993 0.000000e+00 695.0
87 TraesCS7B01G049400 chr1B 99.115 113 1 0 1 113 269218371 269218259 3.800000e-48 204.0
88 TraesCS7B01G049400 chr5D 78.884 1004 190 16 5680 6670 547237623 547236629 0.000000e+00 660.0
89 TraesCS7B01G049400 chr5D 83.810 210 30 4 6817 7024 547236457 547236250 6.370000e-46 196.0
90 TraesCS7B01G049400 chr2B 95.146 412 17 3 7630 8040 622506767 622506358 0.000000e+00 647.0
91 TraesCS7B01G049400 chr2B 86.429 420 45 7 7630 8040 774559162 774558746 4.430000e-122 449.0
92 TraesCS7B01G049400 chr2B 87.500 376 37 5 7630 7997 774486465 774486092 7.460000e-115 425.0
93 TraesCS7B01G049400 chr2B 91.667 96 7 1 3646 3740 127159438 127159533 1.820000e-26 132.0
94 TraesCS7B01G049400 chr2B 90.722 97 8 1 3651 3746 56512891 56512987 2.360000e-25 128.0
95 TraesCS7B01G049400 chr6B 97.541 122 1 1 1 122 11169429 11169548 2.940000e-49 207.0
96 TraesCS7B01G049400 chr6B 90.816 98 7 2 3649 3744 77773405 77773308 6.550000e-26 130.0
97 TraesCS7B01G049400 chr3B 97.436 117 3 0 1 117 809036999 809037115 4.920000e-47 200.0
98 TraesCS7B01G049400 chr3B 92.473 93 6 1 3647 3738 11978593 11978685 1.820000e-26 132.0
99 TraesCS7B01G049400 chr6A 89.899 99 9 1 3640 3737 249160182 249160280 8.470000e-25 126.0
100 TraesCS7B01G049400 chr4B 89.216 102 8 3 3642 3741 40169974 40170074 3.050000e-24 124.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G049400 chr7B 49355855 49363894 8039 False 14848.000000 14848 100.000000 1 8040 1 chr7B.!!$F1 8039
1 TraesCS7B01G049400 chr7B 49587642 49589242 1600 False 2505.000000 2505 94.944000 5670 7267 1 chr7B.!!$F2 1597
2 TraesCS7B01G049400 chr7B 49610696 49620752 10056 True 1931.833333 4447 96.358167 112 7630 6 chr7B.!!$R11 7518
3 TraesCS7B01G049400 chr7B 50880646 50881836 1190 True 1533.000000 1533 89.951000 1265 2465 1 chr7B.!!$R6 1200
4 TraesCS7B01G049400 chr7B 49549917 49556617 6700 False 1439.833333 2915 95.764333 112 5449 6 chr7B.!!$F5 5337
5 TraesCS7B01G049400 chr7B 49548958 49549779 821 True 1297.000000 1297 95.146000 6808 7630 1 chr7B.!!$R2 822
6 TraesCS7B01G049400 chr7B 49177536 49183167 5631 False 601.500000 983 77.820500 332 5350 2 chr7B.!!$F4 5018
7 TraesCS7B01G049400 chr7B 50714412 50717991 3579 True 227.000000 228 88.222000 5352 5551 2 chr7B.!!$R12 199
8 TraesCS7B01G049400 chr7D 96030373 96033178 2805 True 2946.000000 2946 85.798000 4280 7141 1 chr7D.!!$R10 2861
9 TraesCS7B01G049400 chr7D 96081364 96087820 6456 True 2148.250000 3790 89.478750 356 7141 4 chr7D.!!$R17 6785
10 TraesCS7B01G049400 chr7D 96048113 96053809 5696 True 2043.000000 3434 90.448500 737 4238 2 chr7D.!!$R15 3501
11 TraesCS7B01G049400 chr7D 95147479 95153609 6130 True 1961.000000 4590 89.011000 356 7139 4 chr7D.!!$R12 6783
12 TraesCS7B01G049400 chr7D 95988955 95990552 1597 True 1797.000000 1797 87.040000 5534 7129 1 chr7D.!!$R6 1595
13 TraesCS7B01G049400 chr7D 96015803 96017387 1584 True 1786.000000 1786 87.074000 5567 7146 1 chr7D.!!$R9 1579
14 TraesCS7B01G049400 chr7D 95969012 95970607 1595 True 1685.000000 1685 85.776000 5534 7141 1 chr7D.!!$R3 1607
15 TraesCS7B01G049400 chr7D 95975094 95976277 1183 True 1321.000000 1321 86.909000 5966 7141 1 chr7D.!!$R4 1175
16 TraesCS7B01G049400 chr7D 96006097 96007050 953 True 1086.000000 1086 87.238000 5567 6521 1 chr7D.!!$R8 954
17 TraesCS7B01G049400 chr7D 95833552 95835389 1837 True 997.500000 1812 85.293500 5352 7141 2 chr7D.!!$R13 1789
18 TraesCS7B01G049400 chr7D 95962935 95964774 1839 True 975.500000 1731 86.604000 5352 7139 2 chr7D.!!$R14 1787
19 TraesCS7B01G049400 chr7D 95996922 95997576 654 True 715.000000 715 86.495000 6517 7170 1 chr7D.!!$R7 653
20 TraesCS7B01G049400 chr7D 95053342 95058715 5373 False 438.666667 726 81.779000 892 5350 3 chr7D.!!$F1 4458
21 TraesCS7B01G049400 chr7D 96067979 96068580 601 True 217.333333 346 91.485667 112 586 3 chr7D.!!$R16 474
22 TraesCS7B01G049400 chr7A 99142232 99150537 8305 True 1206.285714 3264 91.074571 356 7131 7 chr7A.!!$R2 6775
23 TraesCS7B01G049400 chr7A 98887592 98888142 550 True 577.000000 577 85.889000 7071 7630 1 chr7A.!!$R1 559
24 TraesCS7B01G049400 chr7A 98724737 98729837 5100 False 428.333333 715 81.791667 892 5350 3 chr7A.!!$F3 4458
25 TraesCS7B01G049400 chr2A 235341862 235346002 4140 True 718.500000 725 98.063000 7628 8040 2 chr2A.!!$R2 412
26 TraesCS7B01G049400 chr5D 547236250 547237623 1373 True 428.000000 660 81.347000 5680 7024 2 chr5D.!!$R1 1344

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
28 29 0.036105 TGTCGCTAGGTGGTCTACGA 60.036 55.000 0.00 0.00 32.96 3.43 F
910 2677 0.988832 AAGTGTATTCCCCCGAGCAA 59.011 50.000 0.00 0.00 0.00 3.91 F
2286 5685 1.004044 CTCATGGAAGCCAACCACTCT 59.996 52.381 0.00 0.00 40.36 3.24 F
2549 6382 1.087501 TGCCGTATAAATGTGCGCAA 58.912 45.000 14.00 2.60 0.00 4.85 F
3573 10628 0.099968 CGGTCGAAGTGATTCGCCTA 59.900 55.000 16.15 0.00 43.55 3.93 F
3835 13821 2.736719 GCTATTGCTCAGCGAGTTGAGA 60.737 50.000 18.82 1.62 45.95 3.27 F
5724 17476 4.472833 AGATAAGCATCAAGGACAAGGAGT 59.527 41.667 0.00 0.00 33.21 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 2783 1.314730 AACTAACCCACTTGCCAACG 58.685 50.000 0.00 0.00 0.00 4.10 R
2405 6155 3.131577 AGGGCACATACATGCTGAAATTG 59.868 43.478 3.07 0.00 45.38 2.32 R
3234 7338 0.739462 CCGTGCAGTTGCTATCGGAA 60.739 55.000 21.30 0.00 45.16 4.30 R
3980 13967 1.208614 GCGCTTCCTTCTGTTGCAG 59.791 57.895 0.00 0.00 0.00 4.41 R
5579 17315 9.537192 TTTTCGAAGATAAAGTGTCAAGAACTA 57.463 29.630 0.00 0.00 35.04 2.24 R
5797 17549 1.686110 GCCCTCCCTTCCTCGAGAA 60.686 63.158 15.71 5.59 0.00 2.87 R
7300 19137 0.466543 CGTTTCGGGATGGGGTATGA 59.533 55.000 0.00 0.00 0.00 2.15 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.365408 GCTTGTAGTTGTCGCTAGGT 57.635 50.000 0.00 0.00 0.00 3.08
20 21 1.993370 GCTTGTAGTTGTCGCTAGGTG 59.007 52.381 0.00 0.00 0.00 4.00
21 22 2.607187 CTTGTAGTTGTCGCTAGGTGG 58.393 52.381 0.00 0.00 0.00 4.61
22 23 1.624336 TGTAGTTGTCGCTAGGTGGT 58.376 50.000 0.00 0.00 0.00 4.16
23 24 1.542915 TGTAGTTGTCGCTAGGTGGTC 59.457 52.381 0.00 0.00 0.00 4.02
24 25 1.817447 GTAGTTGTCGCTAGGTGGTCT 59.183 52.381 0.00 0.00 0.00 3.85
25 26 2.211250 AGTTGTCGCTAGGTGGTCTA 57.789 50.000 0.00 0.00 0.00 2.59
26 27 1.817447 AGTTGTCGCTAGGTGGTCTAC 59.183 52.381 0.00 0.00 0.00 2.59
27 28 0.806868 TTGTCGCTAGGTGGTCTACG 59.193 55.000 0.00 0.00 0.00 3.51
28 29 0.036105 TGTCGCTAGGTGGTCTACGA 60.036 55.000 0.00 0.00 32.96 3.43
29 30 1.089920 GTCGCTAGGTGGTCTACGAA 58.910 55.000 0.00 0.00 35.22 3.85
30 31 1.674962 GTCGCTAGGTGGTCTACGAAT 59.325 52.381 0.00 0.00 35.22 3.34
31 32 1.945394 TCGCTAGGTGGTCTACGAATC 59.055 52.381 0.00 0.00 32.69 2.52
32 33 1.948145 CGCTAGGTGGTCTACGAATCT 59.052 52.381 0.00 0.00 0.00 2.40
33 34 2.287069 CGCTAGGTGGTCTACGAATCTG 60.287 54.545 0.00 0.00 0.00 2.90
34 35 2.034812 GCTAGGTGGTCTACGAATCTGG 59.965 54.545 0.00 0.00 0.00 3.86
35 36 2.526888 AGGTGGTCTACGAATCTGGA 57.473 50.000 0.00 0.00 0.00 3.86
36 37 3.033659 AGGTGGTCTACGAATCTGGAT 57.966 47.619 0.00 0.00 0.00 3.41
37 38 2.695666 AGGTGGTCTACGAATCTGGATG 59.304 50.000 0.00 0.00 0.00 3.51
38 39 2.431057 GGTGGTCTACGAATCTGGATGT 59.569 50.000 0.00 0.00 0.00 3.06
39 40 3.635373 GGTGGTCTACGAATCTGGATGTA 59.365 47.826 0.00 0.00 0.00 2.29
40 41 4.098960 GGTGGTCTACGAATCTGGATGTAA 59.901 45.833 0.00 0.00 0.00 2.41
41 42 5.221461 GGTGGTCTACGAATCTGGATGTAAT 60.221 44.000 0.00 0.00 0.00 1.89
42 43 6.281405 GTGGTCTACGAATCTGGATGTAATT 58.719 40.000 0.00 0.00 0.00 1.40
43 44 6.761714 GTGGTCTACGAATCTGGATGTAATTT 59.238 38.462 0.00 0.00 0.00 1.82
44 45 7.280205 GTGGTCTACGAATCTGGATGTAATTTT 59.720 37.037 0.00 0.00 0.00 1.82
45 46 7.827236 TGGTCTACGAATCTGGATGTAATTTTT 59.173 33.333 0.00 0.00 0.00 1.94
46 47 9.321562 GGTCTACGAATCTGGATGTAATTTTTA 57.678 33.333 0.00 0.00 0.00 1.52
68 69 5.796350 ATTTCTGGTATTCGTTGTACTGC 57.204 39.130 0.00 0.00 0.00 4.40
69 70 3.241067 TCTGGTATTCGTTGTACTGCC 57.759 47.619 0.00 0.00 0.00 4.85
70 71 2.563620 TCTGGTATTCGTTGTACTGCCA 59.436 45.455 0.00 0.00 0.00 4.92
71 72 3.196901 TCTGGTATTCGTTGTACTGCCAT 59.803 43.478 0.00 0.00 0.00 4.40
72 73 3.266636 TGGTATTCGTTGTACTGCCATG 58.733 45.455 0.00 0.00 0.00 3.66
73 74 3.055747 TGGTATTCGTTGTACTGCCATGA 60.056 43.478 0.00 0.00 0.00 3.07
74 75 4.127171 GGTATTCGTTGTACTGCCATGAT 58.873 43.478 0.00 0.00 0.00 2.45
75 76 4.574828 GGTATTCGTTGTACTGCCATGATT 59.425 41.667 0.00 0.00 0.00 2.57
76 77 4.621068 ATTCGTTGTACTGCCATGATTG 57.379 40.909 0.00 0.00 0.00 2.67
77 78 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
78 79 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
79 80 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
80 81 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
81 82 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
82 83 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
83 84 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
84 85 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
85 86 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
86 87 7.281841 TGTACTGCCATGATTGAAGATGAATA 58.718 34.615 0.00 0.00 0.00 1.75
87 88 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
88 89 6.598503 ACTGCCATGATTGAAGATGAATAGA 58.401 36.000 0.00 0.00 0.00 1.98
89 90 7.232188 ACTGCCATGATTGAAGATGAATAGAT 58.768 34.615 0.00 0.00 0.00 1.98
90 91 7.724506 ACTGCCATGATTGAAGATGAATAGATT 59.275 33.333 0.00 0.00 0.00 2.40
91 92 7.882179 TGCCATGATTGAAGATGAATAGATTG 58.118 34.615 0.00 0.00 0.00 2.67
92 93 7.039993 TGCCATGATTGAAGATGAATAGATTGG 60.040 37.037 0.00 0.00 0.00 3.16
93 94 7.176165 GCCATGATTGAAGATGAATAGATTGGA 59.824 37.037 0.00 0.00 0.00 3.53
94 95 9.074576 CCATGATTGAAGATGAATAGATTGGAA 57.925 33.333 0.00 0.00 0.00 3.53
96 97 9.863650 ATGATTGAAGATGAATAGATTGGAAGT 57.136 29.630 0.00 0.00 0.00 3.01
97 98 9.690913 TGATTGAAGATGAATAGATTGGAAGTT 57.309 29.630 0.00 0.00 0.00 2.66
175 181 7.782168 TCTTCTCATCAGAGTATAGGTGACATT 59.218 37.037 0.00 0.00 42.66 2.71
306 400 4.723309 AGATTTCCAGCTAATGATCCACC 58.277 43.478 0.00 0.00 0.00 4.61
391 519 2.027745 TGGTTCATCTCAGCTGTCCTTC 60.028 50.000 14.67 0.06 0.00 3.46
454 614 6.600388 TGGGCTCTATATTTAGCATCAAACA 58.400 36.000 10.20 0.00 40.61 2.83
516 2215 8.417884 ACTATCTAAGACAGGAAGCTAATTGAC 58.582 37.037 0.00 0.00 0.00 3.18
910 2677 0.988832 AAGTGTATTCCCCCGAGCAA 59.011 50.000 0.00 0.00 0.00 3.91
1011 2783 3.618690 ACTTTCAGGATGGCTGTAGAC 57.381 47.619 0.00 0.00 36.16 2.59
1248 3193 4.142315 GCTTGCACATCCATAGATTTGTGT 60.142 41.667 4.11 0.00 33.49 3.72
1249 3194 4.968812 TGCACATCCATAGATTTGTGTG 57.031 40.909 4.11 0.00 33.49 3.82
1275 3220 7.537306 GCGATGTTCAAAAGCAAATCTACTAAA 59.463 33.333 0.00 0.00 0.00 1.85
1531 3684 6.357367 GGATATCTCCCATGTGTGTTTTAGT 58.643 40.000 2.05 0.00 35.28 2.24
1794 5132 9.567917 CTTCATGTCGTTGTATTAAACATATCG 57.432 33.333 0.00 0.00 38.10 2.92
1997 5339 4.208873 TGTGACGACAAATGTTACCGTTAC 59.791 41.667 11.59 11.59 39.23 2.50
2197 5596 8.561536 TTCTGTCTCCTCCCACATAAATAATA 57.438 34.615 0.00 0.00 0.00 0.98
2205 5604 3.120338 CCCACATAAATAATACCGCGCAG 60.120 47.826 8.75 0.00 0.00 5.18
2286 5685 1.004044 CTCATGGAAGCCAACCACTCT 59.996 52.381 0.00 0.00 40.36 3.24
2405 6155 5.629435 CCTTCTTCTTTTTGCAATCGTAACC 59.371 40.000 0.00 0.00 0.00 2.85
2416 6166 4.082300 TGCAATCGTAACCAATTTCAGCAT 60.082 37.500 0.00 0.00 0.00 3.79
2549 6382 1.087501 TGCCGTATAAATGTGCGCAA 58.912 45.000 14.00 2.60 0.00 4.85
2551 6384 2.098280 TGCCGTATAAATGTGCGCAATT 59.902 40.909 14.00 11.81 0.00 2.32
3036 6934 2.741092 GTGGTGGTCTTCTCCGCA 59.259 61.111 0.00 0.00 39.49 5.69
3158 7253 2.778679 GATCACCGACAAGCGCAC 59.221 61.111 11.47 0.00 39.11 5.34
3234 7338 3.499918 CGAAGCTGATGAAGACCTTGTTT 59.500 43.478 0.00 0.00 0.00 2.83
3237 7341 3.823304 AGCTGATGAAGACCTTGTTTTCC 59.177 43.478 0.00 0.00 0.00 3.13
3252 7356 1.075542 TTTCCGATAGCAACTGCACG 58.924 50.000 4.22 6.70 45.16 5.34
3466 7588 0.596082 ACGTGCATTAAGGTGGCAAC 59.404 50.000 0.00 0.00 39.57 4.17
3573 10628 0.099968 CGGTCGAAGTGATTCGCCTA 59.900 55.000 16.15 0.00 43.55 3.93
3633 11178 9.112725 CTCCATGAAAATTTTGTTTCCTTCTTT 57.887 29.630 8.47 0.00 36.80 2.52
3656 11203 4.631131 GCAGTAGCACACATATGTATCCA 58.369 43.478 8.32 0.00 36.72 3.41
3657 11204 5.240891 GCAGTAGCACACATATGTATCCAT 58.759 41.667 8.32 0.00 36.72 3.41
3658 11205 5.349817 GCAGTAGCACACATATGTATCCATC 59.650 44.000 8.32 0.00 36.72 3.51
3659 11206 5.871524 CAGTAGCACACATATGTATCCATCC 59.128 44.000 8.32 0.00 36.72 3.51
3660 11207 3.930336 AGCACACATATGTATCCATCCG 58.070 45.455 8.32 0.00 36.72 4.18
3661 11208 3.324846 AGCACACATATGTATCCATCCGT 59.675 43.478 8.32 0.00 36.72 4.69
3662 11209 4.065088 GCACACATATGTATCCATCCGTT 58.935 43.478 8.32 0.00 36.72 4.44
3663 11210 4.152402 GCACACATATGTATCCATCCGTTC 59.848 45.833 8.32 0.00 36.72 3.95
3664 11211 4.690748 CACACATATGTATCCATCCGTTCC 59.309 45.833 8.32 0.00 36.72 3.62
3665 11212 4.346709 ACACATATGTATCCATCCGTTCCA 59.653 41.667 8.32 0.00 37.26 3.53
3666 11213 5.163248 ACACATATGTATCCATCCGTTCCAA 60.163 40.000 8.32 0.00 37.26 3.53
3667 11214 5.762711 CACATATGTATCCATCCGTTCCAAA 59.237 40.000 8.32 0.00 32.29 3.28
3668 11215 6.262049 CACATATGTATCCATCCGTTCCAAAA 59.738 38.462 8.32 0.00 32.29 2.44
3669 11216 7.004086 ACATATGTATCCATCCGTTCCAAAAT 58.996 34.615 6.56 0.00 32.29 1.82
3670 11217 8.160765 ACATATGTATCCATCCGTTCCAAAATA 58.839 33.333 6.56 0.00 32.29 1.40
3671 11218 8.668353 CATATGTATCCATCCGTTCCAAAATAG 58.332 37.037 0.00 0.00 32.29 1.73
3672 11219 6.241882 TGTATCCATCCGTTCCAAAATAGA 57.758 37.500 0.00 0.00 0.00 1.98
3673 11220 6.837312 TGTATCCATCCGTTCCAAAATAGAT 58.163 36.000 0.00 0.00 0.00 1.98
3674 11221 6.710295 TGTATCCATCCGTTCCAAAATAGATG 59.290 38.462 0.00 0.00 31.49 2.90
3675 11222 5.366482 TCCATCCGTTCCAAAATAGATGA 57.634 39.130 0.00 0.00 32.55 2.92
3676 11223 5.123227 TCCATCCGTTCCAAAATAGATGAC 58.877 41.667 0.00 0.00 32.55 3.06
3677 11224 5.104527 TCCATCCGTTCCAAAATAGATGACT 60.105 40.000 0.00 0.00 32.55 3.41
3678 11225 5.237344 CCATCCGTTCCAAAATAGATGACTC 59.763 44.000 0.00 0.00 32.55 3.36
3679 11226 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3680 11227 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3681 11228 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
3682 11229 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3683 11230 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
3684 11231 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
3685 11232 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3686 11233 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3687 11234 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3688 11235 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3689 11236 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3732 11279 8.690884 TGAGTCATCTATTTTAGAACAGAGAGG 58.309 37.037 0.00 0.00 38.50 3.69
3733 11280 8.017418 AGTCATCTATTTTAGAACAGAGAGGG 57.983 38.462 0.00 0.00 38.50 4.30
3734 11281 7.621683 AGTCATCTATTTTAGAACAGAGAGGGT 59.378 37.037 0.00 0.00 38.50 4.34
3735 11282 8.915036 GTCATCTATTTTAGAACAGAGAGGGTA 58.085 37.037 0.00 0.00 38.50 3.69
3736 11283 9.661954 TCATCTATTTTAGAACAGAGAGGGTAT 57.338 33.333 0.00 0.00 38.50 2.73
3835 13821 2.736719 GCTATTGCTCAGCGAGTTGAGA 60.737 50.000 18.82 1.62 45.95 3.27
4522 14557 8.138074 GCTATCACATATGAATATCTTAGCGGA 58.862 37.037 10.38 0.00 38.69 5.54
4557 14593 9.733556 ACACCATGTTCTAATACTGTTTTATCA 57.266 29.630 0.00 0.00 0.00 2.15
5436 15521 8.378172 TCTAAATTTACACACTCCAAAGTCTG 57.622 34.615 0.00 0.00 31.71 3.51
5457 15542 9.533831 AGTCTGAAATTGTATTAATTGGAGGTT 57.466 29.630 0.00 0.00 0.00 3.50
5579 17315 4.566004 TGTAGCGCTTGACACTCTAAAAT 58.434 39.130 18.68 0.00 0.00 1.82
5590 17326 9.261180 CTTGACACTCTAAAATAGTTCTTGACA 57.739 33.333 0.00 0.00 0.00 3.58
5672 17413 7.969314 ACGATTTTGTTTGTTGCTTTTATTGT 58.031 26.923 0.00 0.00 0.00 2.71
5724 17476 4.472833 AGATAAGCATCAAGGACAAGGAGT 59.527 41.667 0.00 0.00 33.21 3.85
5797 17549 3.513515 GAGAGTCCAGAGGTTGAAGACAT 59.486 47.826 0.00 0.00 0.00 3.06
5872 17625 1.078848 GCGACACTGCATCCTCCTT 60.079 57.895 0.00 0.00 34.15 3.36
5997 17750 2.281484 GGTGTGCTCCGCCTTCAA 60.281 61.111 0.00 0.00 40.81 2.69
6071 17824 3.865745 CGATGACTTGGAAGACACCATAC 59.134 47.826 0.00 0.00 39.82 2.39
6082 17835 0.253044 ACACCATACATCGCTGCCTT 59.747 50.000 0.00 0.00 0.00 4.35
6187 17940 0.109551 TCGTAGTCGTCGACGTCTCT 60.110 55.000 34.40 29.15 41.85 3.10
6472 18235 2.731691 ATCAAACCACTGCGTCGGCT 62.732 55.000 0.00 0.00 40.82 5.52
6488 18251 1.146930 GCTTCCGAGATCATGCCCA 59.853 57.895 0.00 0.00 0.00 5.36
6771 18593 8.128582 GCATCGGTTAATTTGTTTCAGATGATA 58.871 33.333 5.88 0.00 36.13 2.15
6804 18626 1.267806 CTCTGACGTTGCTGGCAATTT 59.732 47.619 11.22 1.70 38.28 1.82
6846 18670 2.224378 CGGTGATGAATGGCTATGAGGT 60.224 50.000 0.00 0.00 0.00 3.85
6880 18704 1.872237 CGTGAGGAAGAAAGCCGACAA 60.872 52.381 0.00 0.00 0.00 3.18
6910 18734 0.392863 CCCCGATCATTGCACTGACA 60.393 55.000 9.14 0.00 0.00 3.58
6920 18744 0.250252 TGCACTGACAGCGAATTCCA 60.250 50.000 1.25 0.00 33.85 3.53
7006 18836 0.531532 AGCCGAAGATCGCAAGGATG 60.532 55.000 4.20 0.00 38.82 3.51
7106 18941 8.484641 CATGCATATGGGAATAGTGTTAGTAG 57.515 38.462 0.00 0.00 0.00 2.57
7273 19109 9.479549 AACAAAAGAATGGTCACAGGATTATAT 57.520 29.630 0.00 0.00 0.00 0.86
7321 19158 1.342672 ATACCCCATCCCGAAACGCT 61.343 55.000 0.00 0.00 0.00 5.07
7401 19238 7.336931 GCACAGAGAAAGGTTAAATCCTATTCA 59.663 37.037 0.00 0.00 36.74 2.57
7472 19309 9.811655 GTTTCTTTCTTTCTTTGGTTTTTCTTG 57.188 29.630 0.00 0.00 0.00 3.02
7796 19677 8.160521 TGGAAATACAATATGTGTTATTCCCG 57.839 34.615 18.55 0.00 44.94 5.14
8019 24030 7.495934 TCCGAGTTTGCCAAAATAAAAATTCAA 59.504 29.630 0.00 0.00 0.00 2.69
8024 24035 6.851222 TGCCAAAATAAAAATTCAAAGCGA 57.149 29.167 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.029290 ACCACCTAGCGACAACTACAAG 60.029 50.000 0.00 0.00 0.00 3.16
2 3 1.965643 ACCACCTAGCGACAACTACAA 59.034 47.619 0.00 0.00 0.00 2.41
3 4 1.542915 GACCACCTAGCGACAACTACA 59.457 52.381 0.00 0.00 0.00 2.74
5 6 2.211250 AGACCACCTAGCGACAACTA 57.789 50.000 0.00 0.00 0.00 2.24
6 7 1.817447 GTAGACCACCTAGCGACAACT 59.183 52.381 0.00 0.00 0.00 3.16
7 8 1.467035 CGTAGACCACCTAGCGACAAC 60.467 57.143 0.00 0.00 0.00 3.32
9 10 0.036105 TCGTAGACCACCTAGCGACA 60.036 55.000 0.00 0.00 31.20 4.35
10 11 1.089920 TTCGTAGACCACCTAGCGAC 58.910 55.000 0.00 0.00 34.32 5.19
12 13 1.948145 AGATTCGTAGACCACCTAGCG 59.052 52.381 0.00 0.00 34.32 4.26
13 14 2.034812 CCAGATTCGTAGACCACCTAGC 59.965 54.545 0.00 0.00 34.32 3.42
14 15 3.552875 TCCAGATTCGTAGACCACCTAG 58.447 50.000 0.00 0.00 34.32 3.02
15 16 3.657398 TCCAGATTCGTAGACCACCTA 57.343 47.619 0.00 0.00 34.32 3.08
17 18 2.431057 ACATCCAGATTCGTAGACCACC 59.569 50.000 0.00 0.00 34.32 4.61
18 19 3.802948 ACATCCAGATTCGTAGACCAC 57.197 47.619 0.00 0.00 34.32 4.16
19 20 6.479972 AATTACATCCAGATTCGTAGACCA 57.520 37.500 0.00 0.00 34.32 4.02
20 21 7.787725 AAAATTACATCCAGATTCGTAGACC 57.212 36.000 0.00 0.00 34.32 3.85
42 43 8.231837 GCAGTACAACGAATACCAGAAATAAAA 58.768 33.333 0.00 0.00 0.00 1.52
43 44 7.148373 GGCAGTACAACGAATACCAGAAATAAA 60.148 37.037 0.00 0.00 0.00 1.40
44 45 6.314400 GGCAGTACAACGAATACCAGAAATAA 59.686 38.462 0.00 0.00 0.00 1.40
45 46 5.813672 GGCAGTACAACGAATACCAGAAATA 59.186 40.000 0.00 0.00 0.00 1.40
46 47 4.634443 GGCAGTACAACGAATACCAGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
47 48 3.998341 GGCAGTACAACGAATACCAGAAA 59.002 43.478 0.00 0.00 0.00 2.52
48 49 3.007074 TGGCAGTACAACGAATACCAGAA 59.993 43.478 0.00 0.00 0.00 3.02
49 50 2.563620 TGGCAGTACAACGAATACCAGA 59.436 45.455 0.00 0.00 0.00 3.86
50 51 2.967362 TGGCAGTACAACGAATACCAG 58.033 47.619 0.00 0.00 0.00 4.00
51 52 3.055747 TCATGGCAGTACAACGAATACCA 60.056 43.478 0.00 0.00 0.00 3.25
52 53 3.527533 TCATGGCAGTACAACGAATACC 58.472 45.455 0.00 0.00 0.00 2.73
53 54 5.293324 TCAATCATGGCAGTACAACGAATAC 59.707 40.000 0.00 0.00 0.00 1.89
54 55 5.423886 TCAATCATGGCAGTACAACGAATA 58.576 37.500 0.00 0.00 0.00 1.75
55 56 4.260985 TCAATCATGGCAGTACAACGAAT 58.739 39.130 0.00 0.00 0.00 3.34
56 57 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
57 58 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
58 59 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
59 60 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
60 61 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
61 62 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
62 63 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
63 64 7.738847 TCTATTCATCTTCAATCATGGCAGTA 58.261 34.615 0.00 0.00 0.00 2.74
64 65 6.598503 TCTATTCATCTTCAATCATGGCAGT 58.401 36.000 0.00 0.00 0.00 4.40
65 66 7.689446 ATCTATTCATCTTCAATCATGGCAG 57.311 36.000 0.00 0.00 0.00 4.85
66 67 7.039993 CCAATCTATTCATCTTCAATCATGGCA 60.040 37.037 0.00 0.00 0.00 4.92
67 68 7.176165 TCCAATCTATTCATCTTCAATCATGGC 59.824 37.037 0.00 0.00 0.00 4.40
68 69 8.631480 TCCAATCTATTCATCTTCAATCATGG 57.369 34.615 0.00 0.00 0.00 3.66
70 71 9.863650 ACTTCCAATCTATTCATCTTCAATCAT 57.136 29.630 0.00 0.00 0.00 2.45
71 72 9.690913 AACTTCCAATCTATTCATCTTCAATCA 57.309 29.630 0.00 0.00 0.00 2.57
76 77 9.794685 GGAAAAACTTCCAATCTATTCATCTTC 57.205 33.333 0.00 0.00 40.79 2.87
77 78 8.462016 CGGAAAAACTTCCAATCTATTCATCTT 58.538 33.333 4.85 0.00 41.16 2.40
78 79 7.415653 GCGGAAAAACTTCCAATCTATTCATCT 60.416 37.037 4.85 0.00 41.16 2.90
79 80 6.693113 GCGGAAAAACTTCCAATCTATTCATC 59.307 38.462 4.85 0.00 41.16 2.92
80 81 6.152661 TGCGGAAAAACTTCCAATCTATTCAT 59.847 34.615 4.85 0.00 41.16 2.57
81 82 5.475220 TGCGGAAAAACTTCCAATCTATTCA 59.525 36.000 4.85 0.00 41.16 2.57
82 83 5.949735 TGCGGAAAAACTTCCAATCTATTC 58.050 37.500 4.85 0.00 41.16 1.75
83 84 5.975693 TGCGGAAAAACTTCCAATCTATT 57.024 34.783 4.85 0.00 41.16 1.73
84 85 5.975693 TTGCGGAAAAACTTCCAATCTAT 57.024 34.783 4.85 0.00 41.16 1.98
85 86 5.776173 TTTGCGGAAAAACTTCCAATCTA 57.224 34.783 0.00 0.00 41.16 1.98
86 87 4.664150 TTTGCGGAAAAACTTCCAATCT 57.336 36.364 0.00 0.00 41.16 2.40
87 88 5.726729 TTTTTGCGGAAAAACTTCCAATC 57.273 34.783 21.65 0.00 41.16 2.67
108 109 8.860088 AGTTCTTCCTTGCATATTGTAGTTTTT 58.140 29.630 0.00 0.00 0.00 1.94
109 110 8.409358 AGTTCTTCCTTGCATATTGTAGTTTT 57.591 30.769 0.00 0.00 0.00 2.43
110 111 9.686683 ATAGTTCTTCCTTGCATATTGTAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
306 400 5.968387 ACTAGTTCAAACTCAACTCGTTG 57.032 39.130 3.45 3.45 40.37 4.10
910 2677 0.179065 GGTCGGCGGCCTTTTATAGT 60.179 55.000 25.70 0.00 0.00 2.12
1011 2783 1.314730 AACTAACCCACTTGCCAACG 58.685 50.000 0.00 0.00 0.00 4.10
1248 3193 4.241590 AGATTTGCTTTTGAACATCGCA 57.758 36.364 0.00 0.00 0.00 5.10
1249 3194 5.393962 AGTAGATTTGCTTTTGAACATCGC 58.606 37.500 0.00 0.00 0.00 4.58
1342 3288 6.268825 AGATCTACTTTTCAAGTCTACGCA 57.731 37.500 0.00 0.00 41.77 5.24
1794 5132 4.944962 TTTGTCGTGACATTCCATCATC 57.055 40.909 3.14 0.00 41.52 2.92
1997 5339 4.085466 CGTTGCAACATGTTTCAACTCATG 60.085 41.667 34.91 23.21 41.99 3.07
2111 5485 3.303593 GGCAATAATCTGCGTGACATCAG 60.304 47.826 2.32 2.32 43.60 2.90
2405 6155 3.131577 AGGGCACATACATGCTGAAATTG 59.868 43.478 3.07 0.00 45.38 2.32
2631 6519 4.901197 ATGTATTGGGACGTGCCATATA 57.099 40.909 30.37 23.59 38.95 0.86
3234 7338 0.739462 CCGTGCAGTTGCTATCGGAA 60.739 55.000 21.30 0.00 45.16 4.30
3237 7341 2.703409 GCCGTGCAGTTGCTATCG 59.297 61.111 5.62 7.58 42.66 2.92
3413 7535 9.674068 TGTGGTGTCATTAGTTAATTATAAGCA 57.326 29.630 0.00 0.00 0.00 3.91
3573 10628 7.685920 TCTTCAGATCTGGGATGGGAATATATT 59.314 37.037 22.42 0.00 0.00 1.28
3633 11178 4.100808 TGGATACATATGTGTGCTACTGCA 59.899 41.667 21.43 1.38 46.17 4.41
3654 11201 5.126067 AGTCATCTATTTTGGAACGGATGG 58.874 41.667 0.00 0.00 32.58 3.51
3655 11202 5.817296 TGAGTCATCTATTTTGGAACGGATG 59.183 40.000 0.00 0.00 32.78 3.51
3656 11203 5.989477 TGAGTCATCTATTTTGGAACGGAT 58.011 37.500 0.00 0.00 0.00 4.18
3657 11204 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
3658 11205 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
3659 11206 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
3660 11207 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
3661 11208 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
3662 11209 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
3663 11210 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3706 11253 8.690884 CCTCTCTGTTCTAAAATAGATGACTCA 58.309 37.037 0.00 0.00 32.88 3.41
3707 11254 8.141268 CCCTCTCTGTTCTAAAATAGATGACTC 58.859 40.741 0.00 0.00 32.88 3.36
3708 11255 7.621683 ACCCTCTCTGTTCTAAAATAGATGACT 59.378 37.037 0.00 0.00 32.88 3.41
3709 11256 7.787028 ACCCTCTCTGTTCTAAAATAGATGAC 58.213 38.462 0.00 0.00 32.88 3.06
3710 11257 7.979786 ACCCTCTCTGTTCTAAAATAGATGA 57.020 36.000 0.00 0.00 32.88 2.92
3711 11258 9.703892 CATACCCTCTCTGTTCTAAAATAGATG 57.296 37.037 0.00 0.00 32.88 2.90
3712 11259 9.440761 ACATACCCTCTCTGTTCTAAAATAGAT 57.559 33.333 0.00 0.00 32.88 1.98
3713 11260 8.840200 ACATACCCTCTCTGTTCTAAAATAGA 57.160 34.615 0.00 0.00 32.42 1.98
3714 11261 8.919145 AGACATACCCTCTCTGTTCTAAAATAG 58.081 37.037 0.00 0.00 0.00 1.73
3715 11262 8.840200 AGACATACCCTCTCTGTTCTAAAATA 57.160 34.615 0.00 0.00 0.00 1.40
3716 11263 7.741554 AGACATACCCTCTCTGTTCTAAAAT 57.258 36.000 0.00 0.00 0.00 1.82
3717 11264 8.660295 TTAGACATACCCTCTCTGTTCTAAAA 57.340 34.615 0.00 0.00 0.00 1.52
3718 11265 8.660295 TTTAGACATACCCTCTCTGTTCTAAA 57.340 34.615 0.00 0.00 0.00 1.85
3719 11266 8.660295 TTTTAGACATACCCTCTCTGTTCTAA 57.340 34.615 0.00 0.00 0.00 2.10
3720 11267 8.660295 TTTTTAGACATACCCTCTCTGTTCTA 57.340 34.615 0.00 0.00 0.00 2.10
3721 11268 7.554959 TTTTTAGACATACCCTCTCTGTTCT 57.445 36.000 0.00 0.00 0.00 3.01
3722 11269 8.794335 AATTTTTAGACATACCCTCTCTGTTC 57.206 34.615 0.00 0.00 0.00 3.18
3723 11270 9.014297 CAAATTTTTAGACATACCCTCTCTGTT 57.986 33.333 0.00 0.00 0.00 3.16
3724 11271 8.383175 TCAAATTTTTAGACATACCCTCTCTGT 58.617 33.333 0.00 0.00 0.00 3.41
3725 11272 8.792830 TCAAATTTTTAGACATACCCTCTCTG 57.207 34.615 0.00 0.00 0.00 3.35
3726 11273 9.620259 GATCAAATTTTTAGACATACCCTCTCT 57.380 33.333 0.00 0.00 0.00 3.10
3727 11274 8.552034 CGATCAAATTTTTAGACATACCCTCTC 58.448 37.037 0.00 0.00 0.00 3.20
3728 11275 7.499232 CCGATCAAATTTTTAGACATACCCTCT 59.501 37.037 0.00 0.00 0.00 3.69
3729 11276 7.255139 CCCGATCAAATTTTTAGACATACCCTC 60.255 40.741 0.00 0.00 0.00 4.30
3730 11277 6.546034 CCCGATCAAATTTTTAGACATACCCT 59.454 38.462 0.00 0.00 0.00 4.34
3731 11278 6.734871 GCCCGATCAAATTTTTAGACATACCC 60.735 42.308 0.00 0.00 0.00 3.69
3732 11279 6.183360 TGCCCGATCAAATTTTTAGACATACC 60.183 38.462 0.00 0.00 0.00 2.73
3733 11280 6.791303 TGCCCGATCAAATTTTTAGACATAC 58.209 36.000 0.00 0.00 0.00 2.39
3734 11281 7.094162 TGTTGCCCGATCAAATTTTTAGACATA 60.094 33.333 0.00 0.00 0.00 2.29
3735 11282 5.913137 TGCCCGATCAAATTTTTAGACAT 57.087 34.783 0.00 0.00 0.00 3.06
3736 11283 5.010112 TGTTGCCCGATCAAATTTTTAGACA 59.990 36.000 0.00 0.00 0.00 3.41
3835 13821 3.966543 CGGACCTTGGTTGCCCCT 61.967 66.667 0.00 0.00 0.00 4.79
3980 13967 1.208614 GCGCTTCCTTCTGTTGCAG 59.791 57.895 0.00 0.00 0.00 4.41
5579 17315 9.537192 TTTTCGAAGATAAAGTGTCAAGAACTA 57.463 29.630 0.00 0.00 35.04 2.24
5648 17389 8.819152 AACAATAAAAGCAACAAACAAAATCG 57.181 26.923 0.00 0.00 0.00 3.34
5672 17413 7.560262 CCTCCCATCAGACGAACCTATATATAA 59.440 40.741 0.00 0.00 0.00 0.98
5724 17476 1.906824 ACGTTCCCGCTTCTCCTGA 60.907 57.895 0.00 0.00 37.70 3.86
5774 17526 2.232696 GTCTTCAACCTCTGGACTCTCC 59.767 54.545 0.00 0.00 36.96 3.71
5797 17549 1.686110 GCCCTCCCTTCCTCGAGAA 60.686 63.158 15.71 5.59 0.00 2.87
5872 17625 4.034258 GTCTCGTCGCCGTGGACA 62.034 66.667 9.02 0.00 37.61 4.02
6071 17824 1.078918 TGGAGACAAGGCAGCGATG 60.079 57.895 0.00 0.00 37.44 3.84
6082 17835 2.182827 CTGGACATCTCCTTGGAGACA 58.817 52.381 20.27 12.96 37.48 3.41
6472 18235 1.143838 CGTGGGCATGATCTCGGAA 59.856 57.895 0.00 0.00 0.00 4.30
6846 18670 4.794439 CACGGATGCGCCTCGTCA 62.794 66.667 6.51 0.00 34.73 4.35
6920 18744 3.710722 CCGCAGCCCTTCCTCTGT 61.711 66.667 0.00 0.00 33.09 3.41
7006 18836 1.949525 TGTTTGCAGAGCTCAAGAACC 59.050 47.619 17.77 0.00 0.00 3.62
7106 18941 5.799827 AATAGCAGGAGTAGGATCTTGAC 57.200 43.478 0.00 0.00 0.00 3.18
7208 19043 4.337555 GGCAGTCATCTCATAAAGTTGCAT 59.662 41.667 0.00 0.00 0.00 3.96
7300 19137 0.466543 CGTTTCGGGATGGGGTATGA 59.533 55.000 0.00 0.00 0.00 2.15
7321 19158 2.497675 GTGATGGGAGCTCACTCAGTTA 59.502 50.000 18.70 0.00 45.42 2.24
7401 19238 6.444704 TCATATAGGGGTCTCTTCTGACTTT 58.555 40.000 0.00 0.00 37.16 2.66


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

AutoCloner maintained by Alex Coulton.