Multiple sequence alignment - TraesCS7B01G122700

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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 TraesCS7B01G122700 chr7B 100.000 2357 0 0 1 2357 144085904 144083548 0.000000e+00 4353.0
1 TraesCS7B01G122700 chr7B 94.303 983 52 4 1378 2357 411920354 411921335 0.000000e+00 1502.0
2 TraesCS7B01G122700 chr7B 94.297 982 53 3 1379 2357 277647907 277648888 0.000000e+00 1500.0
3 TraesCS7B01G122700 chr7B 94.954 753 29 3 635 1379 720163389 720162638 0.000000e+00 1171.0
4 TraesCS7B01G122700 chr4B 95.422 983 40 5 1379 2357 445246263 445247244 0.000000e+00 1561.0
5 TraesCS7B01G122700 chr4B 95.080 752 29 2 636 1379 417552462 417551711 0.000000e+00 1177.0
6 TraesCS7B01G122700 chr3B 95.107 981 45 3 1380 2357 731093706 731092726 0.000000e+00 1543.0
7 TraesCS7B01G122700 chr3B 94.807 982 48 3 1379 2357 486763913 486762932 0.000000e+00 1528.0
8 TraesCS7B01G122700 chr3B 94.490 980 52 2 1380 2357 611104182 611105161 0.000000e+00 1509.0
9 TraesCS7B01G122700 chr3B 94.196 982 54 3 1378 2357 486757336 486756356 0.000000e+00 1495.0
10 TraesCS7B01G122700 chr4A 94.399 982 51 4 1378 2355 741083239 741082258 0.000000e+00 1506.0
11 TraesCS7B01G122700 chr4A 94.312 756 34 3 632 1379 736237397 736238151 0.000000e+00 1149.0
12 TraesCS7B01G122700 chr2B 94.292 981 51 4 1380 2357 325170464 325169486 0.000000e+00 1496.0
13 TraesCS7B01G122700 chr1D 95.750 753 24 2 635 1379 205134697 205133945 0.000000e+00 1206.0
14 TraesCS7B01G122700 chr1D 95.623 754 23 4 635 1379 60171816 60171064 0.000000e+00 1201.0
15 TraesCS7B01G122700 chr1D 95.485 753 26 2 635 1379 247505758 247505006 0.000000e+00 1195.0
16 TraesCS7B01G122700 chr1D 94.612 761 24 4 633 1379 451393400 451392643 0.000000e+00 1162.0
17 TraesCS7B01G122700 chr1D 94.415 752 32 4 636 1379 411532273 411531524 0.000000e+00 1147.0
18 TraesCS7B01G122700 chr1D 92.784 97 7 0 1 97 51916229 51916325 8.780000e-30 141.0
19 TraesCS7B01G122700 chr1D 91.579 95 8 0 3 97 254383964 254384058 5.290000e-27 132.0
20 TraesCS7B01G122700 chr1D 89.691 97 10 0 1 97 176207800 176207704 8.840000e-25 124.0
21 TraesCS7B01G122700 chr2D 95.618 753 25 2 635 1379 73126872 73126120 0.000000e+00 1201.0
22 TraesCS7B01G122700 chr2D 95.352 753 26 3 636 1379 621748803 621749555 0.000000e+00 1188.0
23 TraesCS7B01G122700 chr2D 94.600 463 15 4 635 1087 22824365 22823903 0.000000e+00 708.0
24 TraesCS7B01G122700 chr7D 95.352 753 25 4 635 1379 497560907 497561657 0.000000e+00 1188.0
25 TraesCS7B01G122700 chr7D 88.219 365 35 3 229 592 178013510 178013153 1.670000e-116 429.0
26 TraesCS7B01G122700 chr3D 95.219 753 28 2 635 1379 584701392 584700640 0.000000e+00 1184.0
27 TraesCS7B01G122700 chr3D 94.814 752 29 4 636 1379 587420226 587419477 0.000000e+00 1164.0
28 TraesCS7B01G122700 chr5D 95.219 753 27 3 635 1379 275171748 275170997 0.000000e+00 1182.0
29 TraesCS7B01G122700 chr5D 91.591 440 21 4 635 1066 417759727 417760158 5.610000e-166 593.0
30 TraesCS7B01G122700 chr5D 92.784 97 7 0 1 97 143232764 143232668 8.780000e-30 141.0
31 TraesCS7B01G122700 chr5D 92.000 100 8 0 1 100 503229305 503229206 8.780000e-30 141.0
32 TraesCS7B01G122700 chr5D 92.000 100 8 0 1 100 503239086 503238987 8.780000e-30 141.0
33 TraesCS7B01G122700 chr5D 92.000 100 8 0 1 100 503243332 503243233 8.780000e-30 141.0
34 TraesCS7B01G122700 chr6D 94.841 756 30 3 632 1379 57791145 57790391 0.000000e+00 1171.0
35 TraesCS7B01G122700 chr6D 94.688 753 32 2 635 1379 142136692 142135940 0.000000e+00 1162.0
36 TraesCS7B01G122700 chr6D 94.555 753 33 2 635 1379 28035042 28034290 0.000000e+00 1157.0
37 TraesCS7B01G122700 chr6D 94.698 679 27 3 636 1306 89225602 89226279 0.000000e+00 1046.0
38 TraesCS7B01G122700 chr6D 92.784 97 7 0 1 97 389250434 389250338 8.780000e-30 141.0
39 TraesCS7B01G122700 chr6D 92.000 100 8 0 1 100 389250979 389250880 8.780000e-30 141.0
40 TraesCS7B01G122700 chr6D 92.784 97 7 0 1 97 389255229 389255133 8.780000e-30 141.0
41 TraesCS7B01G122700 chr6D 90.722 97 9 0 1 97 14943967 14944063 1.900000e-26 130.0
42 TraesCS7B01G122700 chr6D 91.011 89 8 0 1 89 168264799 168264711 1.140000e-23 121.0
43 TraesCS7B01G122700 chr3A 94.320 757 32 5 632 1379 623352673 623353427 0.000000e+00 1149.0
44 TraesCS7B01G122700 chr3A 93.676 759 33 5 635 1379 727256294 727257051 0.000000e+00 1122.0
45 TraesCS7B01G122700 chr4D 94.164 754 35 3 635 1379 23004046 23003293 0.000000e+00 1140.0
46 TraesCS7B01G122700 chr4D 94.164 754 35 3 635 1379 434352836 434352083 0.000000e+00 1140.0
47 TraesCS7B01G122700 chr4D 92.784 97 7 0 1 97 415546444 415546540 8.780000e-30 141.0
48 TraesCS7B01G122700 chr4D 92.500 80 6 0 18 97 404463777 404463856 5.320000e-22 115.0
49 TraesCS7B01G122700 chr1B 94.079 760 30 7 634 1379 14562396 14561638 0.000000e+00 1140.0
50 TraesCS7B01G122700 chrUn 94.149 752 35 3 636 1379 347669028 347669778 0.000000e+00 1136.0
51 TraesCS7B01G122700 chrUn 94.024 753 35 4 636 1379 83676865 83677616 0.000000e+00 1133.0
52 TraesCS7B01G122700 chrUn 93.883 752 37 3 636 1379 417468519 417469269 0.000000e+00 1125.0
53 TraesCS7B01G122700 chrUn 93.386 756 42 2 632 1379 63293172 63293927 0.000000e+00 1112.0
54 TraesCS7B01G122700 chrUn 93.484 752 40 3 636 1379 33415202 33414452 0.000000e+00 1109.0
55 TraesCS7B01G122700 chrUn 93.484 752 40 3 636 1379 33449105 33448355 0.000000e+00 1109.0
56 TraesCS7B01G122700 chrUn 93.254 756 43 2 632 1379 63399027 63398272 0.000000e+00 1107.0
57 TraesCS7B01G122700 chrUn 93.720 621 30 3 636 1248 387205049 387204430 0.000000e+00 922.0
58 TraesCS7B01G122700 chr5B 93.600 750 40 7 632 1379 689102211 689101468 0.000000e+00 1112.0
59 TraesCS7B01G122700 chr6A 94.627 335 9 3 635 961 39449470 39449803 5.810000e-141 510.0
60 TraesCS7B01G122700 chr7A 86.027 365 43 4 229 592 182024976 182024619 3.670000e-103 385.0
61 TraesCS7B01G122700 chr7A 96.226 53 1 1 103 154 182025296 182025244 4.170000e-13 86.1


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 TraesCS7B01G122700 chr7B 144083548 144085904 2356 True 4353.00 4353 100.0000 1 2357 1 chr7B.!!$R1 2356
1 TraesCS7B01G122700 chr7B 411920354 411921335 981 False 1502.00 1502 94.3030 1378 2357 1 chr7B.!!$F2 979
2 TraesCS7B01G122700 chr7B 277647907 277648888 981 False 1500.00 1500 94.2970 1379 2357 1 chr7B.!!$F1 978
3 TraesCS7B01G122700 chr7B 720162638 720163389 751 True 1171.00 1171 94.9540 635 1379 1 chr7B.!!$R2 744
4 TraesCS7B01G122700 chr4B 445246263 445247244 981 False 1561.00 1561 95.4220 1379 2357 1 chr4B.!!$F1 978
5 TraesCS7B01G122700 chr4B 417551711 417552462 751 True 1177.00 1177 95.0800 636 1379 1 chr4B.!!$R1 743
6 TraesCS7B01G122700 chr3B 731092726 731093706 980 True 1543.00 1543 95.1070 1380 2357 1 chr3B.!!$R3 977
7 TraesCS7B01G122700 chr3B 486762932 486763913 981 True 1528.00 1528 94.8070 1379 2357 1 chr3B.!!$R2 978
8 TraesCS7B01G122700 chr3B 611104182 611105161 979 False 1509.00 1509 94.4900 1380 2357 1 chr3B.!!$F1 977
9 TraesCS7B01G122700 chr3B 486756356 486757336 980 True 1495.00 1495 94.1960 1378 2357 1 chr3B.!!$R1 979
10 TraesCS7B01G122700 chr4A 741082258 741083239 981 True 1506.00 1506 94.3990 1378 2355 1 chr4A.!!$R1 977
11 TraesCS7B01G122700 chr4A 736237397 736238151 754 False 1149.00 1149 94.3120 632 1379 1 chr4A.!!$F1 747
12 TraesCS7B01G122700 chr2B 325169486 325170464 978 True 1496.00 1496 94.2920 1380 2357 1 chr2B.!!$R1 977
13 TraesCS7B01G122700 chr1D 205133945 205134697 752 True 1206.00 1206 95.7500 635 1379 1 chr1D.!!$R3 744
14 TraesCS7B01G122700 chr1D 60171064 60171816 752 True 1201.00 1201 95.6230 635 1379 1 chr1D.!!$R1 744
15 TraesCS7B01G122700 chr1D 247505006 247505758 752 True 1195.00 1195 95.4850 635 1379 1 chr1D.!!$R4 744
16 TraesCS7B01G122700 chr1D 451392643 451393400 757 True 1162.00 1162 94.6120 633 1379 1 chr1D.!!$R6 746
17 TraesCS7B01G122700 chr1D 411531524 411532273 749 True 1147.00 1147 94.4150 636 1379 1 chr1D.!!$R5 743
18 TraesCS7B01G122700 chr2D 73126120 73126872 752 True 1201.00 1201 95.6180 635 1379 1 chr2D.!!$R2 744
19 TraesCS7B01G122700 chr2D 621748803 621749555 752 False 1188.00 1188 95.3520 636 1379 1 chr2D.!!$F1 743
20 TraesCS7B01G122700 chr7D 497560907 497561657 750 False 1188.00 1188 95.3520 635 1379 1 chr7D.!!$F1 744
21 TraesCS7B01G122700 chr3D 584700640 584701392 752 True 1184.00 1184 95.2190 635 1379 1 chr3D.!!$R1 744
22 TraesCS7B01G122700 chr3D 587419477 587420226 749 True 1164.00 1164 94.8140 636 1379 1 chr3D.!!$R2 743
23 TraesCS7B01G122700 chr5D 275170997 275171748 751 True 1182.00 1182 95.2190 635 1379 1 chr5D.!!$R2 744
24 TraesCS7B01G122700 chr6D 57790391 57791145 754 True 1171.00 1171 94.8410 632 1379 1 chr6D.!!$R2 747
25 TraesCS7B01G122700 chr6D 142135940 142136692 752 True 1162.00 1162 94.6880 635 1379 1 chr6D.!!$R3 744
26 TraesCS7B01G122700 chr6D 28034290 28035042 752 True 1157.00 1157 94.5550 635 1379 1 chr6D.!!$R1 744
27 TraesCS7B01G122700 chr6D 89225602 89226279 677 False 1046.00 1046 94.6980 636 1306 1 chr6D.!!$F2 670
28 TraesCS7B01G122700 chr3A 623352673 623353427 754 False 1149.00 1149 94.3200 632 1379 1 chr3A.!!$F1 747
29 TraesCS7B01G122700 chr3A 727256294 727257051 757 False 1122.00 1122 93.6760 635 1379 1 chr3A.!!$F2 744
30 TraesCS7B01G122700 chr4D 23003293 23004046 753 True 1140.00 1140 94.1640 635 1379 1 chr4D.!!$R1 744
31 TraesCS7B01G122700 chr4D 434352083 434352836 753 True 1140.00 1140 94.1640 635 1379 1 chr4D.!!$R2 744
32 TraesCS7B01G122700 chr1B 14561638 14562396 758 True 1140.00 1140 94.0790 634 1379 1 chr1B.!!$R1 745
33 TraesCS7B01G122700 chrUn 347669028 347669778 750 False 1136.00 1136 94.1490 636 1379 1 chrUn.!!$F3 743
34 TraesCS7B01G122700 chrUn 83676865 83677616 751 False 1133.00 1133 94.0240 636 1379 1 chrUn.!!$F2 743
35 TraesCS7B01G122700 chrUn 417468519 417469269 750 False 1125.00 1125 93.8830 636 1379 1 chrUn.!!$F4 743
36 TraesCS7B01G122700 chrUn 63293172 63293927 755 False 1112.00 1112 93.3860 632 1379 1 chrUn.!!$F1 747
37 TraesCS7B01G122700 chrUn 33414452 33415202 750 True 1109.00 1109 93.4840 636 1379 1 chrUn.!!$R1 743
38 TraesCS7B01G122700 chrUn 33448355 33449105 750 True 1109.00 1109 93.4840 636 1379 1 chrUn.!!$R2 743
39 TraesCS7B01G122700 chrUn 63398272 63399027 755 True 1107.00 1107 93.2540 632 1379 1 chrUn.!!$R3 747
40 TraesCS7B01G122700 chrUn 387204430 387205049 619 True 922.00 922 93.7200 636 1248 1 chrUn.!!$R4 612
41 TraesCS7B01G122700 chr5B 689101468 689102211 743 True 1112.00 1112 93.6000 632 1379 1 chr5B.!!$R1 747
42 TraesCS7B01G122700 chr7A 182024619 182025296 677 True 235.55 385 91.1265 103 592 2 chr7A.!!$R1 489

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
246 441 0.035056 ACTGGCCACACCTAAGATGC 60.035 55.0 0.0 0.0 40.22 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1722 0.321122 CCAACTCTTCTTCCGCTGCT 60.321 55.0 0.0 0.0 0.0 4.24 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
22 23 5.269459 CGATGCTTATTCCTCAAATACCG 57.731 43.478 0.00 0.00 29.39 4.02
23 24 4.750098 CGATGCTTATTCCTCAAATACCGT 59.250 41.667 0.00 0.00 29.39 4.83
24 25 5.236478 CGATGCTTATTCCTCAAATACCGTT 59.764 40.000 0.00 0.00 29.39 4.44
25 26 6.422701 CGATGCTTATTCCTCAAATACCGTTA 59.577 38.462 0.00 0.00 29.39 3.18
26 27 7.117812 CGATGCTTATTCCTCAAATACCGTTAT 59.882 37.037 0.00 0.00 29.39 1.89
27 28 8.691661 ATGCTTATTCCTCAAATACCGTTATT 57.308 30.769 0.00 0.00 29.39 1.40
28 29 7.925993 TGCTTATTCCTCAAATACCGTTATTG 58.074 34.615 0.00 0.00 29.39 1.90
29 30 7.554835 TGCTTATTCCTCAAATACCGTTATTGT 59.445 33.333 0.00 0.00 29.39 2.71
30 31 8.403236 GCTTATTCCTCAAATACCGTTATTGTT 58.597 33.333 0.00 0.00 29.39 2.83
33 34 7.989416 TTCCTCAAATACCGTTATTGTTTCT 57.011 32.000 0.00 0.00 0.00 2.52
34 35 7.989416 TCCTCAAATACCGTTATTGTTTCTT 57.011 32.000 0.00 0.00 0.00 2.52
35 36 8.036273 TCCTCAAATACCGTTATTGTTTCTTC 57.964 34.615 0.00 0.00 0.00 2.87
36 37 7.881232 TCCTCAAATACCGTTATTGTTTCTTCT 59.119 33.333 0.00 0.00 0.00 2.85
37 38 8.175716 CCTCAAATACCGTTATTGTTTCTTCTC 58.824 37.037 0.00 0.00 0.00 2.87
38 39 8.036273 TCAAATACCGTTATTGTTTCTTCTCC 57.964 34.615 0.00 0.00 0.00 3.71
39 40 6.657836 AATACCGTTATTGTTTCTTCTCCG 57.342 37.500 0.00 0.00 0.00 4.63
40 41 4.261578 ACCGTTATTGTTTCTTCTCCGA 57.738 40.909 0.00 0.00 0.00 4.55
41 42 4.243270 ACCGTTATTGTTTCTTCTCCGAG 58.757 43.478 0.00 0.00 0.00 4.63
42 43 4.021719 ACCGTTATTGTTTCTTCTCCGAGA 60.022 41.667 0.00 0.00 0.00 4.04
43 44 4.927425 CCGTTATTGTTTCTTCTCCGAGAA 59.073 41.667 10.44 10.44 34.00 2.87
44 45 5.407387 CCGTTATTGTTTCTTCTCCGAGAAA 59.593 40.000 11.94 1.43 41.88 2.52
45 46 6.073440 CCGTTATTGTTTCTTCTCCGAGAAAA 60.073 38.462 11.94 3.83 44.63 2.29
46 47 7.010023 CGTTATTGTTTCTTCTCCGAGAAAAG 58.990 38.462 11.94 1.82 44.63 2.27
47 48 7.095774 CGTTATTGTTTCTTCTCCGAGAAAAGA 60.096 37.037 11.94 4.20 44.63 2.52
48 49 8.557029 GTTATTGTTTCTTCTCCGAGAAAAGAA 58.443 33.333 11.94 9.79 44.63 2.52
49 50 6.604735 TTGTTTCTTCTCCGAGAAAAGAAG 57.395 37.500 11.94 5.90 44.63 2.85
50 51 5.671493 TGTTTCTTCTCCGAGAAAAGAAGT 58.329 37.500 11.94 0.00 44.63 3.01
51 52 6.113411 TGTTTCTTCTCCGAGAAAAGAAGTT 58.887 36.000 11.94 0.00 44.63 2.66
52 53 6.037172 TGTTTCTTCTCCGAGAAAAGAAGTTG 59.963 38.462 11.94 0.00 44.63 3.16
53 54 5.531122 TCTTCTCCGAGAAAAGAAGTTGA 57.469 39.130 11.94 1.05 45.64 3.18
54 55 5.290386 TCTTCTCCGAGAAAAGAAGTTGAC 58.710 41.667 11.94 0.00 45.64 3.18
55 56 4.665833 TCTCCGAGAAAAGAAGTTGACA 57.334 40.909 0.00 0.00 0.00 3.58
56 57 5.018539 TCTCCGAGAAAAGAAGTTGACAA 57.981 39.130 0.00 0.00 0.00 3.18
57 58 5.611374 TCTCCGAGAAAAGAAGTTGACAAT 58.389 37.500 0.00 0.00 0.00 2.71
58 59 5.696724 TCTCCGAGAAAAGAAGTTGACAATC 59.303 40.000 0.00 0.00 0.00 2.67
59 60 4.755123 TCCGAGAAAAGAAGTTGACAATCC 59.245 41.667 0.00 0.00 0.00 3.01
60 61 4.377431 CCGAGAAAAGAAGTTGACAATCCG 60.377 45.833 0.00 0.00 0.00 4.18
61 62 4.211374 CGAGAAAAGAAGTTGACAATCCGT 59.789 41.667 0.00 0.00 0.00 4.69
62 63 5.404366 CGAGAAAAGAAGTTGACAATCCGTA 59.596 40.000 0.00 0.00 0.00 4.02
63 64 6.400091 CGAGAAAAGAAGTTGACAATCCGTAG 60.400 42.308 0.00 0.00 0.00 3.51
76 77 1.749033 CCGTAGGCCTTCCATCTCC 59.251 63.158 12.58 0.00 46.14 3.71
77 78 1.048724 CCGTAGGCCTTCCATCTCCA 61.049 60.000 12.58 0.00 46.14 3.86
78 79 0.105039 CGTAGGCCTTCCATCTCCAC 59.895 60.000 12.58 0.00 33.74 4.02
79 80 0.105039 GTAGGCCTTCCATCTCCACG 59.895 60.000 12.58 0.00 33.74 4.94
80 81 0.325296 TAGGCCTTCCATCTCCACGT 60.325 55.000 12.58 0.00 33.74 4.49
81 82 1.450312 GGCCTTCCATCTCCACGTG 60.450 63.158 9.08 9.08 0.00 4.49
82 83 1.450312 GCCTTCCATCTCCACGTGG 60.450 63.158 29.26 29.26 36.82 4.94
83 84 1.983224 CCTTCCATCTCCACGTGGT 59.017 57.895 32.74 12.72 36.84 4.16
84 85 1.191535 CCTTCCATCTCCACGTGGTA 58.808 55.000 32.74 22.52 36.84 3.25
85 86 1.762957 CCTTCCATCTCCACGTGGTAT 59.237 52.381 32.74 23.65 36.84 2.73
86 87 2.170607 CCTTCCATCTCCACGTGGTATT 59.829 50.000 32.74 16.18 36.84 1.89
87 88 2.979814 TCCATCTCCACGTGGTATTG 57.020 50.000 32.74 24.99 36.84 1.90
88 89 1.134521 TCCATCTCCACGTGGTATTGC 60.135 52.381 32.74 0.00 36.84 3.56
89 90 1.134401 CCATCTCCACGTGGTATTGCT 60.134 52.381 32.74 11.49 36.34 3.91
90 91 2.205074 CATCTCCACGTGGTATTGCTC 58.795 52.381 32.74 0.00 36.34 4.26
91 92 0.535335 TCTCCACGTGGTATTGCTCC 59.465 55.000 32.74 0.00 36.34 4.70
92 93 0.806102 CTCCACGTGGTATTGCTCCG 60.806 60.000 32.74 4.60 36.34 4.63
93 94 1.079405 CCACGTGGTATTGCTCCGT 60.079 57.895 26.95 0.00 0.00 4.69
94 95 1.082117 CCACGTGGTATTGCTCCGTC 61.082 60.000 26.95 0.00 0.00 4.79
95 96 0.389296 CACGTGGTATTGCTCCGTCA 60.389 55.000 7.95 0.00 0.00 4.35
96 97 0.108804 ACGTGGTATTGCTCCGTCAG 60.109 55.000 0.00 0.00 0.00 3.51
97 98 0.108804 CGTGGTATTGCTCCGTCAGT 60.109 55.000 0.00 0.00 0.00 3.41
98 99 1.133598 CGTGGTATTGCTCCGTCAGTA 59.866 52.381 0.00 0.00 0.00 2.74
99 100 2.223735 CGTGGTATTGCTCCGTCAGTAT 60.224 50.000 0.00 0.00 0.00 2.12
100 101 3.123804 GTGGTATTGCTCCGTCAGTATG 58.876 50.000 0.00 0.00 37.54 2.39
101 102 2.135933 GGTATTGCTCCGTCAGTATGC 58.864 52.381 0.00 0.00 34.76 3.14
117 118 0.544833 ATGCCAAGACAATTGGGCCA 60.545 50.000 17.52 0.00 45.83 5.36
157 158 9.856488 GTCTCTTAATTTTCCCTAATTTTCACC 57.144 33.333 0.00 0.00 0.00 4.02
158 159 8.736244 TCTCTTAATTTTCCCTAATTTTCACCG 58.264 33.333 0.00 0.00 0.00 4.94
159 160 7.832769 TCTTAATTTTCCCTAATTTTCACCGG 58.167 34.615 0.00 0.00 0.00 5.28
161 162 1.842052 TTCCCTAATTTTCACCGGGC 58.158 50.000 6.32 0.00 34.84 6.13
162 163 0.996583 TCCCTAATTTTCACCGGGCT 59.003 50.000 6.32 0.00 34.84 5.19
163 164 2.198336 TCCCTAATTTTCACCGGGCTA 58.802 47.619 6.32 0.00 34.84 3.93
166 167 4.070009 CCCTAATTTTCACCGGGCTATAC 58.930 47.826 6.32 0.00 0.00 1.47
169 170 5.826208 CCTAATTTTCACCGGGCTATACTTT 59.174 40.000 6.32 0.00 0.00 2.66
246 441 0.035056 ACTGGCCACACCTAAGATGC 60.035 55.000 0.00 0.00 40.22 3.91
276 471 0.753262 GCATGACCCTGGACGACTAT 59.247 55.000 0.00 0.00 0.00 2.12
277 472 1.539065 GCATGACCCTGGACGACTATG 60.539 57.143 0.00 0.00 0.00 2.23
278 473 2.031870 CATGACCCTGGACGACTATGA 58.968 52.381 0.00 0.00 0.00 2.15
285 480 3.133003 CCCTGGACGACTATGAGTTTGAT 59.867 47.826 0.00 0.00 0.00 2.57
295 490 6.083098 ACTATGAGTTTGATCTCAGATCCG 57.917 41.667 12.37 0.00 45.70 4.18
310 505 2.093658 AGATCCGAACTTGGCGTACAAT 60.094 45.455 0.00 0.00 38.65 2.71
311 506 3.131577 AGATCCGAACTTGGCGTACAATA 59.868 43.478 0.00 0.00 38.65 1.90
319 514 2.531376 GGCGTACAATAGCGTGGCC 61.531 63.158 0.00 0.00 34.18 5.36
343 538 7.355778 CCAATTTATCTCGGATGTTCTTTAGC 58.644 38.462 0.00 0.00 0.00 3.09
346 541 4.913335 ATCTCGGATGTTCTTTAGCGTA 57.087 40.909 0.00 0.00 0.00 4.42
370 565 2.563702 TCGTGTTTGGTTAGGGACAAC 58.436 47.619 0.00 0.00 0.00 3.32
371 566 2.093075 TCGTGTTTGGTTAGGGACAACA 60.093 45.455 0.00 0.00 0.00 3.33
373 568 3.304391 CGTGTTTGGTTAGGGACAACATG 60.304 47.826 0.00 0.00 30.01 3.21
375 570 1.917872 TTGGTTAGGGACAACATGGC 58.082 50.000 0.00 0.00 0.00 4.40
381 576 3.747976 GGACAACATGGCGGTGGC 61.748 66.667 0.00 0.00 38.90 5.01
407 602 4.641868 TCCCAGGGTTAGGAATAATGTCT 58.358 43.478 5.01 0.00 0.00 3.41
414 609 5.434408 GGTTAGGAATAATGTCTTTCCCGT 58.566 41.667 0.00 0.00 41.99 5.28
416 611 6.346896 GTTAGGAATAATGTCTTTCCCGTCT 58.653 40.000 0.00 0.00 41.99 4.18
418 613 5.816682 AGGAATAATGTCTTTCCCGTCTTT 58.183 37.500 0.00 0.00 41.99 2.52
443 638 8.993404 TTCCATATTCCATTGATGTATTGTCA 57.007 30.769 0.00 0.00 0.00 3.58
447 642 5.559427 TTCCATTGATGTATTGTCAACGG 57.441 39.130 0.00 0.00 39.58 4.44
454 649 1.338674 TGTATTGTCAACGGCAGAGGG 60.339 52.381 0.00 0.00 0.00 4.30
467 663 1.528309 AGAGGGCGTGGGTTTTGTG 60.528 57.895 0.00 0.00 0.00 3.33
469 665 1.792118 GAGGGCGTGGGTTTTGTGTC 61.792 60.000 0.00 0.00 0.00 3.67
475 671 1.745827 CGTGGGTTTTGTGTCTCTGGT 60.746 52.381 0.00 0.00 0.00 4.00
482 678 1.048601 TTGTGTCTCTGGTGGGTCTC 58.951 55.000 0.00 0.00 0.00 3.36
483 679 0.832135 TGTGTCTCTGGTGGGTCTCC 60.832 60.000 0.00 0.00 0.00 3.71
485 681 2.037367 TCTCTGGTGGGTCTCCGG 59.963 66.667 0.00 0.00 35.24 5.14
494 690 3.133946 GGTCTCCGGAGATCCAGC 58.866 66.667 35.64 22.15 39.97 4.85
497 693 1.456518 TCTCCGGAGATCCAGCCTG 60.457 63.158 30.49 1.35 35.14 4.85
501 697 0.462759 CCGGAGATCCAGCCTGTTTC 60.463 60.000 0.00 0.00 35.14 2.78
504 700 0.250513 GAGATCCAGCCTGTTTCGGT 59.749 55.000 0.00 0.00 0.00 4.69
505 701 0.693049 AGATCCAGCCTGTTTCGGTT 59.307 50.000 0.00 0.00 0.00 4.44
506 702 1.073923 AGATCCAGCCTGTTTCGGTTT 59.926 47.619 0.00 0.00 0.00 3.27
507 703 1.468914 GATCCAGCCTGTTTCGGTTTC 59.531 52.381 0.00 0.00 0.00 2.78
508 704 0.536460 TCCAGCCTGTTTCGGTTTCC 60.536 55.000 0.00 0.00 0.00 3.13
532 728 5.688621 CGATGGTTTCGTCTAAATTCGGATA 59.311 40.000 0.00 0.00 43.01 2.59
549 745 5.800296 TCGGATAACTTTCATGGTCTTTGA 58.200 37.500 0.00 0.00 0.00 2.69
551 747 6.148811 TCGGATAACTTTCATGGTCTTTGAAC 59.851 38.462 0.00 0.00 33.03 3.18
569 765 9.930693 TCTTTGAACTTTCTAGAAGTCCTTATC 57.069 33.333 5.12 2.16 0.00 1.75
571 767 7.698506 TGAACTTTCTAGAAGTCCTTATCGA 57.301 36.000 5.12 0.00 0.00 3.59
585 781 6.605594 AGTCCTTATCGATGTTCTCTTCTCTT 59.394 38.462 8.54 0.00 0.00 2.85
592 788 1.072331 TGTTCTCTTCTCTTGGGTGCC 59.928 52.381 0.00 0.00 0.00 5.01
593 789 1.349357 GTTCTCTTCTCTTGGGTGCCT 59.651 52.381 0.00 0.00 0.00 4.75
594 790 2.567615 GTTCTCTTCTCTTGGGTGCCTA 59.432 50.000 0.00 0.00 0.00 3.93
595 791 2.180276 TCTCTTCTCTTGGGTGCCTAC 58.820 52.381 0.00 0.00 0.00 3.18
596 792 1.902508 CTCTTCTCTTGGGTGCCTACA 59.097 52.381 0.00 0.00 0.00 2.74
597 793 1.902508 TCTTCTCTTGGGTGCCTACAG 59.097 52.381 0.00 0.00 0.00 2.74
598 794 1.625818 CTTCTCTTGGGTGCCTACAGT 59.374 52.381 0.00 0.00 0.00 3.55
599 795 0.976641 TCTCTTGGGTGCCTACAGTG 59.023 55.000 0.00 0.00 0.00 3.66
600 796 0.674895 CTCTTGGGTGCCTACAGTGC 60.675 60.000 0.00 0.00 0.00 4.40
601 797 1.675641 CTTGGGTGCCTACAGTGCC 60.676 63.158 0.00 0.00 0.00 5.01
602 798 3.545124 TTGGGTGCCTACAGTGCCG 62.545 63.158 0.00 0.00 0.00 5.69
603 799 3.702048 GGGTGCCTACAGTGCCGA 61.702 66.667 0.00 0.00 0.00 5.54
604 800 2.345991 GGTGCCTACAGTGCCGAA 59.654 61.111 0.00 0.00 0.00 4.30
605 801 1.078426 GGTGCCTACAGTGCCGAAT 60.078 57.895 0.00 0.00 0.00 3.34
606 802 1.090052 GGTGCCTACAGTGCCGAATC 61.090 60.000 0.00 0.00 0.00 2.52
607 803 1.153647 TGCCTACAGTGCCGAATCG 60.154 57.895 0.00 0.00 0.00 3.34
608 804 2.526120 GCCTACAGTGCCGAATCGC 61.526 63.158 0.00 0.00 0.00 4.58
609 805 1.153647 CCTACAGTGCCGAATCGCA 60.154 57.895 0.00 0.00 36.08 5.10
610 806 0.530650 CCTACAGTGCCGAATCGCAT 60.531 55.000 0.00 0.00 41.70 4.73
611 807 1.290203 CTACAGTGCCGAATCGCATT 58.710 50.000 0.00 0.00 41.70 3.56
612 808 4.676444 CAGTGCCGAATCGCATTG 57.324 55.556 0.00 2.82 41.70 2.82
613 809 1.584483 CAGTGCCGAATCGCATTGC 60.584 57.895 0.00 0.00 39.25 3.56
614 810 2.039974 AGTGCCGAATCGCATTGCA 61.040 52.632 9.69 0.00 41.70 4.08
615 811 1.584483 GTGCCGAATCGCATTGCAG 60.584 57.895 9.69 1.90 41.70 4.41
616 812 2.653130 GCCGAATCGCATTGCAGC 60.653 61.111 9.69 0.00 0.00 5.25
617 813 3.104766 CCGAATCGCATTGCAGCT 58.895 55.556 9.69 0.00 0.00 4.24
618 814 1.010350 CCGAATCGCATTGCAGCTC 60.010 57.895 9.69 0.45 0.00 4.09
619 815 1.010350 CGAATCGCATTGCAGCTCC 60.010 57.895 9.69 0.00 0.00 4.70
620 816 1.708193 CGAATCGCATTGCAGCTCCA 61.708 55.000 9.69 0.00 0.00 3.86
621 817 0.666913 GAATCGCATTGCAGCTCCAT 59.333 50.000 9.69 0.00 0.00 3.41
622 818 1.875514 GAATCGCATTGCAGCTCCATA 59.124 47.619 9.69 0.00 0.00 2.74
623 819 1.520494 ATCGCATTGCAGCTCCATAG 58.480 50.000 9.69 0.00 0.00 2.23
624 820 0.533531 TCGCATTGCAGCTCCATAGG 60.534 55.000 9.69 0.00 0.00 2.57
625 821 1.658673 GCATTGCAGCTCCATAGGC 59.341 57.895 3.15 0.00 0.00 3.93
626 822 1.803366 GCATTGCAGCTCCATAGGCC 61.803 60.000 3.15 0.00 0.00 5.19
627 823 0.178998 CATTGCAGCTCCATAGGCCT 60.179 55.000 11.78 11.78 0.00 5.19
628 824 0.178998 ATTGCAGCTCCATAGGCCTG 60.179 55.000 17.99 0.00 0.00 4.85
629 825 2.594013 GCAGCTCCATAGGCCTGC 60.594 66.667 17.99 10.14 39.26 4.85
630 826 2.112718 CAGCTCCATAGGCCTGCC 59.887 66.667 17.99 0.00 0.00 4.85
788 985 0.622136 TCTGTCGCTACTCCTACCCA 59.378 55.000 0.00 0.00 0.00 4.51
863 1060 5.063204 CCAAATCCTAACATCTAATGCCGA 58.937 41.667 0.00 0.00 0.00 5.54
962 1167 2.514160 TCCATCTCCAGAGCAGGTACTA 59.486 50.000 0.00 0.00 36.02 1.82
976 1181 3.192001 CAGGTACTAACGCACAGACCTTA 59.808 47.826 0.00 0.00 36.02 2.69
995 1200 4.039357 CAGGCCTGTCGTCGACGT 62.039 66.667 34.40 13.39 40.80 4.34
1214 1427 0.397941 CAGCAGTTCCTCCCAAGACA 59.602 55.000 0.00 0.00 0.00 3.41
1497 1722 4.476410 CTAGACGCGCAGTGCCGA 62.476 66.667 25.89 8.68 45.12 5.54
1734 1960 1.071699 ACACATGCAAACCCTAGTCGT 59.928 47.619 0.00 0.00 0.00 4.34
1755 1981 2.813908 GCCGAAGCGATCAACCGT 60.814 61.111 0.00 0.00 0.00 4.83
1809 2035 0.456312 CCGTCGTAGGCTCAACACTC 60.456 60.000 0.00 0.00 0.00 3.51
1929 2155 2.399611 CTTCCTTTAAGCGCGCGG 59.600 61.111 33.06 20.54 0.00 6.46
2022 2249 2.902423 AAGGCGTGCTGACCACCAAA 62.902 55.000 0.00 0.00 41.53 3.28
2081 2308 5.063880 GTGTCATACTTCTGTTCCCTTTGT 58.936 41.667 0.00 0.00 0.00 2.83
2172 2400 0.179004 AGTGATGCCGACCAAAACCA 60.179 50.000 0.00 0.00 0.00 3.67
2185 2413 6.425114 CCGACCAAAACCAGATTATCTCATAG 59.575 42.308 0.00 0.00 0.00 2.23
2321 2550 2.374170 ACTGGACAAACCCGAAACCTAT 59.626 45.455 0.00 0.00 38.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.750098 ACGGTATTTGAGGAATAAGCATCG 59.250 41.667 0.00 0.00 32.20 3.84
1 2 6.619801 AACGGTATTTGAGGAATAAGCATC 57.380 37.500 0.00 0.00 32.20 3.91
4 5 7.927048 ACAATAACGGTATTTGAGGAATAAGC 58.073 34.615 2.09 0.00 32.20 3.09
7 8 9.675464 AGAAACAATAACGGTATTTGAGGAATA 57.325 29.630 2.09 0.00 0.00 1.75
8 9 8.575649 AGAAACAATAACGGTATTTGAGGAAT 57.424 30.769 2.09 0.00 0.00 3.01
9 10 7.989416 AGAAACAATAACGGTATTTGAGGAA 57.011 32.000 2.09 0.00 0.00 3.36
10 11 7.881232 AGAAGAAACAATAACGGTATTTGAGGA 59.119 33.333 2.09 0.00 0.00 3.71
11 12 8.040716 AGAAGAAACAATAACGGTATTTGAGG 57.959 34.615 2.09 0.00 0.00 3.86
12 13 8.175716 GGAGAAGAAACAATAACGGTATTTGAG 58.824 37.037 2.09 0.00 0.00 3.02
13 14 7.148540 CGGAGAAGAAACAATAACGGTATTTGA 60.149 37.037 2.09 0.00 0.00 2.69
14 15 6.959311 CGGAGAAGAAACAATAACGGTATTTG 59.041 38.462 2.09 2.27 0.00 2.32
15 16 6.875195 TCGGAGAAGAAACAATAACGGTATTT 59.125 34.615 2.09 0.00 0.00 1.40
16 17 6.400568 TCGGAGAAGAAACAATAACGGTATT 58.599 36.000 0.00 0.00 0.00 1.89
17 18 5.969423 TCGGAGAAGAAACAATAACGGTAT 58.031 37.500 0.00 0.00 0.00 2.73
18 19 5.183713 TCTCGGAGAAGAAACAATAACGGTA 59.816 40.000 4.96 0.00 34.09 4.02
19 20 4.021719 TCTCGGAGAAGAAACAATAACGGT 60.022 41.667 4.96 0.00 34.09 4.83
20 21 4.491676 TCTCGGAGAAGAAACAATAACGG 58.508 43.478 4.96 0.00 34.09 4.44
21 22 6.462073 TTTCTCGGAGAAGAAACAATAACG 57.538 37.500 18.93 0.00 35.37 3.18
22 23 8.084590 TCTTTTCTCGGAGAAGAAACAATAAC 57.915 34.615 18.93 0.00 35.37 1.89
23 24 8.671384 TTCTTTTCTCGGAGAAGAAACAATAA 57.329 30.769 18.93 8.40 38.96 1.40
33 34 5.018539 TGTCAACTTCTTTTCTCGGAGAA 57.981 39.130 16.19 16.19 34.09 2.87
34 35 4.665833 TGTCAACTTCTTTTCTCGGAGA 57.334 40.909 2.97 2.97 0.00 3.71
35 36 5.106908 GGATTGTCAACTTCTTTTCTCGGAG 60.107 44.000 0.00 0.00 0.00 4.63
36 37 4.755123 GGATTGTCAACTTCTTTTCTCGGA 59.245 41.667 0.00 0.00 0.00 4.55
37 38 4.377431 CGGATTGTCAACTTCTTTTCTCGG 60.377 45.833 0.00 0.00 0.00 4.63
38 39 4.211374 ACGGATTGTCAACTTCTTTTCTCG 59.789 41.667 0.00 0.00 0.00 4.04
39 40 5.674933 ACGGATTGTCAACTTCTTTTCTC 57.325 39.130 0.00 0.00 0.00 2.87
40 41 5.701290 CCTACGGATTGTCAACTTCTTTTCT 59.299 40.000 0.00 0.00 0.00 2.52
41 42 5.617087 GCCTACGGATTGTCAACTTCTTTTC 60.617 44.000 0.00 0.00 0.00 2.29
42 43 4.215613 GCCTACGGATTGTCAACTTCTTTT 59.784 41.667 0.00 0.00 0.00 2.27
43 44 3.751698 GCCTACGGATTGTCAACTTCTTT 59.248 43.478 0.00 0.00 0.00 2.52
44 45 3.335579 GCCTACGGATTGTCAACTTCTT 58.664 45.455 0.00 0.00 0.00 2.52
45 46 2.354805 GGCCTACGGATTGTCAACTTCT 60.355 50.000 0.00 0.00 0.00 2.85
46 47 2.007608 GGCCTACGGATTGTCAACTTC 58.992 52.381 0.00 0.00 0.00 3.01
47 48 1.628846 AGGCCTACGGATTGTCAACTT 59.371 47.619 1.29 0.00 0.00 2.66
48 49 1.276622 AGGCCTACGGATTGTCAACT 58.723 50.000 1.29 0.00 0.00 3.16
49 50 2.007608 GAAGGCCTACGGATTGTCAAC 58.992 52.381 5.16 0.00 0.00 3.18
50 51 1.065709 GGAAGGCCTACGGATTGTCAA 60.066 52.381 5.16 0.00 0.00 3.18
51 52 0.539986 GGAAGGCCTACGGATTGTCA 59.460 55.000 5.16 0.00 0.00 3.58
52 53 0.539986 TGGAAGGCCTACGGATTGTC 59.460 55.000 5.16 0.00 34.31 3.18
53 54 1.141053 GATGGAAGGCCTACGGATTGT 59.859 52.381 5.16 0.00 34.31 2.71
54 55 1.417890 AGATGGAAGGCCTACGGATTG 59.582 52.381 5.16 0.00 34.31 2.67
55 56 1.694696 GAGATGGAAGGCCTACGGATT 59.305 52.381 5.16 0.00 34.31 3.01
56 57 1.343069 GAGATGGAAGGCCTACGGAT 58.657 55.000 5.16 0.00 34.31 4.18
57 58 0.759436 GGAGATGGAAGGCCTACGGA 60.759 60.000 5.16 0.00 34.31 4.69
58 59 1.048724 TGGAGATGGAAGGCCTACGG 61.049 60.000 5.16 0.00 34.31 4.02
59 60 0.105039 GTGGAGATGGAAGGCCTACG 59.895 60.000 5.16 0.00 34.31 3.51
60 61 0.105039 CGTGGAGATGGAAGGCCTAC 59.895 60.000 5.16 2.29 34.31 3.18
61 62 0.325296 ACGTGGAGATGGAAGGCCTA 60.325 55.000 5.16 0.00 34.31 3.93
62 63 1.613630 ACGTGGAGATGGAAGGCCT 60.614 57.895 0.00 0.00 34.31 5.19
63 64 1.450312 CACGTGGAGATGGAAGGCC 60.450 63.158 7.95 0.00 0.00 5.19
64 65 1.450312 CCACGTGGAGATGGAAGGC 60.450 63.158 31.31 0.00 38.34 4.35
65 66 1.191535 TACCACGTGGAGATGGAAGG 58.808 55.000 40.21 10.82 39.46 3.46
66 67 3.198068 CAATACCACGTGGAGATGGAAG 58.802 50.000 40.21 17.83 39.46 3.46
67 68 2.679639 GCAATACCACGTGGAGATGGAA 60.680 50.000 40.21 15.81 39.46 3.53
68 69 1.134521 GCAATACCACGTGGAGATGGA 60.135 52.381 40.21 17.38 39.46 3.41
69 70 1.134401 AGCAATACCACGTGGAGATGG 60.134 52.381 40.21 27.70 42.13 3.51
70 71 2.205074 GAGCAATACCACGTGGAGATG 58.795 52.381 40.21 30.53 38.94 2.90
71 72 1.139058 GGAGCAATACCACGTGGAGAT 59.861 52.381 40.21 27.54 38.94 2.75
72 73 0.535335 GGAGCAATACCACGTGGAGA 59.465 55.000 40.21 26.59 38.94 3.71
73 74 0.806102 CGGAGCAATACCACGTGGAG 60.806 60.000 40.21 25.07 38.94 3.86
74 75 1.216977 CGGAGCAATACCACGTGGA 59.783 57.895 40.21 23.58 38.94 4.02
75 76 1.079405 ACGGAGCAATACCACGTGG 60.079 57.895 32.83 32.83 42.17 4.94
76 77 0.389296 TGACGGAGCAATACCACGTG 60.389 55.000 9.08 9.08 37.96 4.49
77 78 0.108804 CTGACGGAGCAATACCACGT 60.109 55.000 0.00 0.00 40.85 4.49
78 79 0.108804 ACTGACGGAGCAATACCACG 60.109 55.000 0.00 0.00 0.00 4.94
79 80 2.953466 TACTGACGGAGCAATACCAC 57.047 50.000 0.00 0.00 0.00 4.16
80 81 2.483013 GCATACTGACGGAGCAATACCA 60.483 50.000 0.00 0.00 0.00 3.25
81 82 2.135933 GCATACTGACGGAGCAATACC 58.864 52.381 0.00 0.00 0.00 2.73
82 83 2.135933 GGCATACTGACGGAGCAATAC 58.864 52.381 0.00 0.00 0.00 1.89
83 84 1.760029 TGGCATACTGACGGAGCAATA 59.240 47.619 0.00 0.00 0.00 1.90
84 85 0.541392 TGGCATACTGACGGAGCAAT 59.459 50.000 0.00 0.00 0.00 3.56
85 86 0.323302 TTGGCATACTGACGGAGCAA 59.677 50.000 0.00 0.00 0.00 3.91
86 87 0.108186 CTTGGCATACTGACGGAGCA 60.108 55.000 0.00 0.00 0.00 4.26
87 88 0.175760 TCTTGGCATACTGACGGAGC 59.824 55.000 0.00 0.00 0.00 4.70
88 89 1.204704 TGTCTTGGCATACTGACGGAG 59.795 52.381 0.00 0.00 32.64 4.63
89 90 1.262417 TGTCTTGGCATACTGACGGA 58.738 50.000 0.00 0.00 32.64 4.69
90 91 2.093306 TTGTCTTGGCATACTGACGG 57.907 50.000 0.00 0.00 32.64 4.79
91 92 3.181507 CCAATTGTCTTGGCATACTGACG 60.182 47.826 4.43 0.00 32.18 4.35
92 93 3.129287 CCCAATTGTCTTGGCATACTGAC 59.871 47.826 4.43 0.00 38.23 3.51
93 94 3.355378 CCCAATTGTCTTGGCATACTGA 58.645 45.455 4.43 0.00 38.23 3.41
94 95 2.159198 GCCCAATTGTCTTGGCATACTG 60.159 50.000 15.97 0.00 43.46 2.74
95 96 2.102578 GCCCAATTGTCTTGGCATACT 58.897 47.619 15.97 0.00 43.46 2.12
96 97 1.136891 GGCCCAATTGTCTTGGCATAC 59.863 52.381 20.60 4.68 45.83 2.39
97 98 1.272928 TGGCCCAATTGTCTTGGCATA 60.273 47.619 20.60 9.59 45.83 3.14
98 99 0.544833 TGGCCCAATTGTCTTGGCAT 60.545 50.000 20.60 0.00 45.83 4.40
99 100 0.544833 ATGGCCCAATTGTCTTGGCA 60.545 50.000 20.60 15.89 45.83 4.92
100 101 0.176449 GATGGCCCAATTGTCTTGGC 59.824 55.000 13.35 13.35 43.26 4.52
101 102 1.753073 GAGATGGCCCAATTGTCTTGG 59.247 52.381 0.00 0.00 39.25 3.61
150 151 4.023726 ACAAAGTATAGCCCGGTGAAAA 57.976 40.909 0.00 0.00 0.00 2.29
154 155 3.530265 TGTACAAAGTATAGCCCGGTG 57.470 47.619 0.00 0.00 0.00 4.94
155 156 3.453353 ACATGTACAAAGTATAGCCCGGT 59.547 43.478 0.00 0.00 0.00 5.28
156 157 3.807622 CACATGTACAAAGTATAGCCCGG 59.192 47.826 0.00 0.00 0.00 5.73
157 158 4.439057 ACACATGTACAAAGTATAGCCCG 58.561 43.478 0.00 0.00 0.00 6.13
239 434 0.744414 GCGCCAACCTCAGCATCTTA 60.744 55.000 0.00 0.00 0.00 2.10
246 441 2.401766 GGTCATGCGCCAACCTCAG 61.402 63.158 4.18 0.00 0.00 3.35
276 471 4.464244 AGTTCGGATCTGAGATCAAACTCA 59.536 41.667 24.75 0.00 43.39 3.41
277 472 5.004922 AGTTCGGATCTGAGATCAAACTC 57.995 43.478 24.75 12.91 37.42 3.01
278 473 5.174395 CAAGTTCGGATCTGAGATCAAACT 58.826 41.667 24.75 24.75 31.37 2.66
285 480 0.173481 CGCCAAGTTCGGATCTGAGA 59.827 55.000 4.04 0.00 0.00 3.27
295 490 1.997606 ACGCTATTGTACGCCAAGTTC 59.002 47.619 0.00 0.00 36.25 3.01
310 505 2.479837 CGAGATAAATTGGCCACGCTA 58.520 47.619 3.88 0.00 0.00 4.26
311 506 1.299541 CGAGATAAATTGGCCACGCT 58.700 50.000 3.88 0.00 0.00 5.07
319 514 7.065894 CGCTAAAGAACATCCGAGATAAATTG 58.934 38.462 0.00 0.00 0.00 2.32
343 538 4.451774 TCCCTAACCAAACACGAAAATACG 59.548 41.667 0.00 0.00 39.31 3.06
346 541 4.208746 TGTCCCTAACCAAACACGAAAAT 58.791 39.130 0.00 0.00 0.00 1.82
381 576 0.546598 ATTCCTAACCCTGGGAAGCG 59.453 55.000 22.23 10.15 44.63 4.68
387 582 5.828328 GGAAAGACATTATTCCTAACCCTGG 59.172 44.000 0.00 0.00 41.54 4.45
388 583 5.828328 GGGAAAGACATTATTCCTAACCCTG 59.172 44.000 4.70 0.00 43.75 4.45
407 602 4.924625 TGGAATATGGAAAAGACGGGAAA 58.075 39.130 0.00 0.00 0.00 3.13
418 613 8.993404 TGACAATACATCAATGGAATATGGAA 57.007 30.769 0.00 0.00 0.00 3.53
447 642 2.597510 AAAACCCACGCCCTCTGC 60.598 61.111 0.00 0.00 0.00 4.26
454 649 0.307760 CAGAGACACAAAACCCACGC 59.692 55.000 0.00 0.00 0.00 5.34
467 663 2.352032 CCGGAGACCCACCAGAGAC 61.352 68.421 0.00 0.00 0.00 3.36
469 665 2.037367 TCCGGAGACCCACCAGAG 59.963 66.667 0.00 0.00 0.00 3.35
482 678 0.462759 GAAACAGGCTGGATCTCCGG 60.463 60.000 20.34 0.00 45.30 5.14
483 679 0.807667 CGAAACAGGCTGGATCTCCG 60.808 60.000 20.34 9.21 39.43 4.63
485 681 0.250513 ACCGAAACAGGCTGGATCTC 59.749 55.000 20.34 8.23 33.69 2.75
509 705 5.986004 ATCCGAATTTAGACGAAACCATC 57.014 39.130 0.00 0.00 0.00 3.51
510 706 7.046033 AGTTATCCGAATTTAGACGAAACCAT 58.954 34.615 0.00 0.00 0.00 3.55
513 709 8.437742 TGAAAGTTATCCGAATTTAGACGAAAC 58.562 33.333 0.00 0.00 0.00 2.78
516 712 7.223971 CCATGAAAGTTATCCGAATTTAGACGA 59.776 37.037 0.00 0.00 0.00 4.20
532 728 7.410120 AGAAAGTTCAAAGACCATGAAAGTT 57.590 32.000 0.00 0.00 38.44 2.66
549 745 8.068892 ACATCGATAAGGACTTCTAGAAAGTT 57.931 34.615 6.63 0.78 0.00 2.66
551 747 8.410141 AGAACATCGATAAGGACTTCTAGAAAG 58.590 37.037 6.63 3.77 0.00 2.62
569 765 3.257393 CACCCAAGAGAAGAGAACATCG 58.743 50.000 0.00 0.00 0.00 3.84
571 767 2.290577 GGCACCCAAGAGAAGAGAACAT 60.291 50.000 0.00 0.00 0.00 2.71
585 781 4.015406 CGGCACTGTAGGCACCCA 62.015 66.667 0.00 0.00 0.00 4.51
592 788 4.494811 TGCGATTCGGCACTGTAG 57.505 55.556 8.34 0.00 38.17 2.74
599 795 2.653130 GCTGCAATGCGATTCGGC 60.653 61.111 8.34 3.21 0.00 5.54
600 796 1.010350 GAGCTGCAATGCGATTCGG 60.010 57.895 8.34 0.00 38.13 4.30
601 797 1.010350 GGAGCTGCAATGCGATTCG 60.010 57.895 0.00 0.62 38.13 3.34
602 798 0.666913 ATGGAGCTGCAATGCGATTC 59.333 50.000 13.45 0.00 38.13 2.52
603 799 1.878088 CTATGGAGCTGCAATGCGATT 59.122 47.619 13.45 0.00 38.13 3.34
604 800 1.520494 CTATGGAGCTGCAATGCGAT 58.480 50.000 13.45 0.00 38.13 4.58
605 801 0.533531 CCTATGGAGCTGCAATGCGA 60.534 55.000 13.45 0.00 38.13 5.10
606 802 1.947013 CCTATGGAGCTGCAATGCG 59.053 57.895 13.45 0.63 38.13 4.73
607 803 1.658673 GCCTATGGAGCTGCAATGC 59.341 57.895 13.45 11.54 0.00 3.56
608 804 0.178998 AGGCCTATGGAGCTGCAATG 60.179 55.000 13.45 7.94 0.00 2.82
609 805 0.178998 CAGGCCTATGGAGCTGCAAT 60.179 55.000 13.45 3.65 0.00 3.56
610 806 1.225426 CAGGCCTATGGAGCTGCAA 59.775 57.895 13.45 0.73 0.00 4.08
611 807 2.913501 CAGGCCTATGGAGCTGCA 59.086 61.111 11.44 11.44 0.00 4.41
612 808 2.594013 GCAGGCCTATGGAGCTGC 60.594 66.667 3.98 0.00 0.00 5.25
613 809 1.123861 TAGGCAGGCCTATGGAGCTG 61.124 60.000 15.86 0.00 46.14 4.24
614 810 0.835543 CTAGGCAGGCCTATGGAGCT 60.836 60.000 19.69 0.00 46.46 4.09
615 811 1.124477 ACTAGGCAGGCCTATGGAGC 61.124 60.000 19.69 3.64 46.46 4.70
616 812 1.428869 AACTAGGCAGGCCTATGGAG 58.571 55.000 19.69 12.64 46.46 3.86
617 813 1.893315 AAACTAGGCAGGCCTATGGA 58.107 50.000 19.69 0.32 46.46 3.41
618 814 2.736670 AAAACTAGGCAGGCCTATGG 57.263 50.000 19.69 11.97 46.46 2.74
788 985 0.392706 TCGACACCACTGCATCAAGT 59.607 50.000 0.00 0.00 0.00 3.16
863 1060 0.698886 TCCTGCTAGGATGGGGCATT 60.699 55.000 1.25 0.00 40.06 3.56
962 1167 0.034896 CCTGGTAAGGTCTGTGCGTT 59.965 55.000 0.00 0.00 38.96 4.84
976 1181 3.681835 GTCGACGACAGGCCTGGT 61.682 66.667 35.42 24.64 32.09 4.00
995 1200 3.610619 CTGTCTGGCGCCATGGTGA 62.611 63.158 32.87 21.35 0.00 4.02
1157 1370 2.670148 GGATGGTGGGCTCCGAGTT 61.670 63.158 0.00 0.00 0.00 3.01
1289 1502 2.747514 ATCCACCCCCAAACCCCTCT 62.748 60.000 0.00 0.00 0.00 3.69
1497 1722 0.321122 CCAACTCTTCTTCCGCTGCT 60.321 55.000 0.00 0.00 0.00 4.24
1533 1758 1.380524 GAACGAGGAGGAGACGATCA 58.619 55.000 0.00 0.00 0.00 2.92
1582 1807 1.662446 CGGCGAACTTGTACGTGGT 60.662 57.895 0.00 0.00 0.00 4.16
1637 1862 2.426023 GGTGTTCCTCCTGCACGT 59.574 61.111 0.00 0.00 34.25 4.49
1826 2052 3.325716 ACCGAGTAGACTTTGGGCTTTAA 59.674 43.478 6.79 0.00 0.00 1.52
1929 2155 1.017701 CCGACTTGAACCTAACGGGC 61.018 60.000 0.00 0.00 39.10 6.13
1989 2216 1.520342 GCCTTGCTAGAGACCGCTG 60.520 63.158 0.00 0.00 0.00 5.18
2012 2239 4.641396 CTTCATAGTCTGTTTGGTGGTCA 58.359 43.478 0.00 0.00 0.00 4.02
2022 2249 3.118592 GCCTAACCAGCTTCATAGTCTGT 60.119 47.826 0.00 0.00 0.00 3.41
2081 2308 3.797524 GCCCGACAACATATATCGTGTGA 60.798 47.826 3.10 0.00 34.02 3.58
2172 2400 4.461081 GCGACAGGGACTATGAGATAATCT 59.539 45.833 0.00 0.00 36.02 2.40
2185 2413 3.704231 ATGGCCATGCGACAGGGAC 62.704 63.158 20.04 11.32 44.57 4.46
2321 2550 3.006110 CCGTGACTGGGTAGTTACAAAGA 59.994 47.826 0.00 0.00 41.95 2.52


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

AutoCloner maintained by Alex Coulton.