Multiple sequence alignment - TraesCS3A01G462700

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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 TraesCS3A01G462700 chr3A 100.000 5315 0 0 1 5315 697614714 697620028 0.000000e+00 9816.0
1 TraesCS3A01G462700 chr3A 95.183 1308 54 6 1062 2362 646405527 646406832 0.000000e+00 2058.0
2 TraesCS3A01G462700 chr3A 95.015 1304 57 6 1063 2362 414209374 414210673 0.000000e+00 2041.0
3 TraesCS3A01G462700 chr3A 85.666 1486 139 25 3004 4446 697673670 697675124 0.000000e+00 1496.0
4 TraesCS3A01G462700 chr3A 79.533 943 170 17 3004 3936 697680126 697681055 0.000000e+00 651.0
5 TraesCS3A01G462700 chr3A 78.689 427 47 13 4605 5016 697675209 697675606 1.480000e-60 244.0
6 TraesCS3A01G462700 chr3A 100.000 85 0 0 4522 4606 660055876 660055960 1.980000e-34 158.0
7 TraesCS3A01G462700 chr3A 96.774 93 2 1 4517 4609 727583900 727583991 2.560000e-33 154.0
8 TraesCS3A01G462700 chr3A 75.945 291 32 19 4264 4523 697681656 697681939 1.210000e-21 115.0
9 TraesCS3A01G462700 chr3D 93.092 1549 77 10 3004 4523 562504380 562505927 0.000000e+00 2241.0
10 TraesCS3A01G462700 chr3D 86.474 1486 144 24 3004 4446 562538443 562539914 0.000000e+00 1578.0
11 TraesCS3A01G462700 chr3D 93.681 728 28 9 4605 5315 562505926 562506652 0.000000e+00 1074.0
12 TraesCS3A01G462700 chr3D 80.000 940 151 27 3004 3929 562545344 562546260 0.000000e+00 660.0
13 TraesCS3A01G462700 chr3D 76.635 1040 174 41 3004 4007 561462385 561461379 1.320000e-140 510.0
14 TraesCS3A01G462700 chr3D 77.403 770 132 29 3004 3744 562348276 562349032 2.290000e-113 420.0
15 TraesCS3A01G462700 chr3D 83.333 432 46 12 4605 5016 562539997 562540422 5.030000e-100 375.0
16 TraesCS3A01G462700 chr3D 74.190 957 188 39 3004 3921 561711471 561710535 1.420000e-90 344.0
17 TraesCS3A01G462700 chr3D 90.496 242 23 0 2483 2724 562503658 562503899 2.390000e-83 320.0
18 TraesCS3A01G462700 chr3D 87.624 202 22 2 2731 2930 562347782 562347982 1.150000e-56 231.0
19 TraesCS3A01G462700 chr3D 87.562 201 22 2 2731 2929 562432891 562433090 4.140000e-56 230.0
20 TraesCS3A01G462700 chr3D 88.462 130 12 2 2362 2488 562503492 562503621 2.560000e-33 154.0
21 TraesCS3A01G462700 chr3D 87.402 127 15 1 2845 2971 562503966 562504091 1.540000e-30 145.0
22 TraesCS3A01G462700 chr3D 76.125 289 31 19 4266 4523 562565293 562565574 3.360000e-22 117.0
23 TraesCS3A01G462700 chr3B 92.308 1560 78 18 3004 4523 749725965 749727522 0.000000e+00 2178.0
24 TraesCS3A01G462700 chr3B 86.219 1386 125 25 3004 4346 749860117 749861479 0.000000e+00 1441.0
25 TraesCS3A01G462700 chr3B 94.611 501 19 7 4822 5315 749727812 749728311 0.000000e+00 769.0
26 TraesCS3A01G462700 chr3B 80.407 934 161 13 3004 3929 749979539 749980458 0.000000e+00 691.0
27 TraesCS3A01G462700 chr3B 85.523 449 36 10 14 444 775312523 775312960 4.890000e-120 442.0
28 TraesCS3A01G462700 chr3B 82.944 428 53 10 4605 5016 749861585 749862008 8.410000e-98 368.0
29 TraesCS3A01G462700 chr3B 89.153 295 27 2 711 1001 775313034 775313327 3.910000e-96 363.0
30 TraesCS3A01G462700 chr3B 82.552 384 41 18 2363 2728 749720280 749720655 1.110000e-81 315.0
31 TraesCS3A01G462700 chr3B 89.806 206 11 2 4605 4800 749727521 749727726 6.830000e-64 255.0
32 TraesCS3A01G462700 chr3B 83.065 248 22 12 2743 2985 749725408 749725640 1.940000e-49 207.0
33 TraesCS3A01G462700 chr3B 84.699 183 20 2 2731 2912 749647925 749648100 5.470000e-40 176.0
34 TraesCS3A01G462700 chr3B 94.203 69 2 2 4457 4523 749981572 749981640 2.620000e-18 104.0
35 TraesCS3A01G462700 chr2A 95.402 1305 51 6 1063 2361 699995574 699994273 0.000000e+00 2069.0
36 TraesCS3A01G462700 chr2A 95.745 94 4 0 4522 4615 750532392 750532485 9.220000e-33 152.0
37 TraesCS3A01G462700 chr2A 97.561 41 1 0 646 686 483623112 483623072 2.660000e-08 71.3
38 TraesCS3A01G462700 chr6A 95.326 1305 52 6 1063 2361 519184636 519185937 0.000000e+00 2063.0
39 TraesCS3A01G462700 chr6A 95.012 1303 59 6 1063 2362 98288504 98287205 0.000000e+00 2041.0
40 TraesCS3A01G462700 chr1A 95.176 1306 54 5 1063 2362 534431533 534430231 0.000000e+00 2054.0
41 TraesCS3A01G462700 chr1A 95.092 1304 58 5 1063 2362 36808609 36809910 0.000000e+00 2049.0
42 TraesCS3A01G462700 chr1A 94.889 1311 57 8 1062 2362 380984378 380985688 0.000000e+00 2041.0
43 TraesCS3A01G462700 chr1A 80.762 499 67 14 5 486 13776003 13776489 3.910000e-96 363.0
44 TraesCS3A01G462700 chr1A 82.168 286 42 5 784 1064 328081856 328081575 2.470000e-58 237.0
45 TraesCS3A01G462700 chr7A 95.161 1302 58 5 1063 2362 251941463 251940165 0.000000e+00 2050.0
46 TraesCS3A01G462700 chr7A 75.333 750 126 27 4 735 27880039 27880747 6.690000e-79 305.0
47 TraesCS3A01G462700 chr7A 81.053 285 40 7 778 1058 27880833 27881107 1.160000e-51 215.0
48 TraesCS3A01G462700 chr7D 88.998 509 42 6 562 1059 564627826 564628331 7.560000e-173 617.0
49 TraesCS3A01G462700 chr7D 86.162 383 38 8 317 694 564627449 564627821 2.980000e-107 399.0
50 TraesCS3A01G462700 chr7D 90.074 272 22 2 3 274 564627180 564627446 1.100000e-91 348.0
51 TraesCS3A01G462700 chr6D 77.285 744 91 44 1 735 269120903 269121577 3.020000e-97 366.0
52 TraesCS3A01G462700 chr6D 82.160 213 31 6 20 231 2733316 2733110 5.470000e-40 176.0
53 TraesCS3A01G462700 chr6D 98.889 90 1 0 4517 4606 15372641 15372552 1.530000e-35 161.0
54 TraesCS3A01G462700 chr5A 81.788 302 44 8 765 1058 618868401 618868103 5.320000e-60 243.0
55 TraesCS3A01G462700 chrUn 89.941 169 12 2 888 1052 313257250 313257083 4.170000e-51 213.0
56 TraesCS3A01G462700 chrUn 85.034 147 14 4 918 1056 77527612 77527466 5.550000e-30 143.0
57 TraesCS3A01G462700 chr7B 96.842 95 2 1 4513 4606 622831029 622831123 1.980000e-34 158.0
58 TraesCS3A01G462700 chr7B 95.745 94 4 0 4514 4607 427291862 427291955 9.220000e-33 152.0
59 TraesCS3A01G462700 chr6B 97.753 89 2 0 4522 4610 718478685 718478773 2.560000e-33 154.0
60 TraesCS3A01G462700 chr4A 95.789 95 2 2 4513 4607 413301318 413301410 9.220000e-33 152.0
61 TraesCS3A01G462700 chr1D 93.939 99 4 2 4522 4619 415055221 415055124 1.190000e-31 148.0
62 TraesCS3A01G462700 chr1B 85.106 94 12 2 976 1068 139669920 139670012 1.580000e-15 95.3


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 TraesCS3A01G462700 chr3A 697614714 697620028 5314 False 9816.000000 9816 100.000000 1 5315 1 chr3A.!!$F4 5314
1 TraesCS3A01G462700 chr3A 646405527 646406832 1305 False 2058.000000 2058 95.183000 1062 2362 1 chr3A.!!$F2 1300
2 TraesCS3A01G462700 chr3A 414209374 414210673 1299 False 2041.000000 2041 95.015000 1063 2362 1 chr3A.!!$F1 1299
3 TraesCS3A01G462700 chr3A 697673670 697675606 1936 False 870.000000 1496 82.177500 3004 5016 2 chr3A.!!$F6 2012
4 TraesCS3A01G462700 chr3A 697680126 697681939 1813 False 383.000000 651 77.739000 3004 4523 2 chr3A.!!$F7 1519
5 TraesCS3A01G462700 chr3D 562538443 562540422 1979 False 976.500000 1578 84.903500 3004 5016 2 chr3D.!!$F6 2012
6 TraesCS3A01G462700 chr3D 562503492 562506652 3160 False 786.800000 2241 90.626600 2362 5315 5 chr3D.!!$F5 2953
7 TraesCS3A01G462700 chr3D 562545344 562546260 916 False 660.000000 660 80.000000 3004 3929 1 chr3D.!!$F2 925
8 TraesCS3A01G462700 chr3D 561461379 561462385 1006 True 510.000000 510 76.635000 3004 4007 1 chr3D.!!$R1 1003
9 TraesCS3A01G462700 chr3D 561710535 561711471 936 True 344.000000 344 74.190000 3004 3921 1 chr3D.!!$R2 917
10 TraesCS3A01G462700 chr3D 562347782 562349032 1250 False 325.500000 420 82.513500 2731 3744 2 chr3D.!!$F4 1013
11 TraesCS3A01G462700 chr3B 749860117 749862008 1891 False 904.500000 1441 84.581500 3004 5016 2 chr3B.!!$F4 2012
12 TraesCS3A01G462700 chr3B 749725408 749728311 2903 False 852.250000 2178 89.947500 2743 5315 4 chr3B.!!$F3 2572
13 TraesCS3A01G462700 chr3B 775312523 775313327 804 False 402.500000 442 87.338000 14 1001 2 chr3B.!!$F6 987
14 TraesCS3A01G462700 chr3B 749979539 749981640 2101 False 397.500000 691 87.305000 3004 4523 2 chr3B.!!$F5 1519
15 TraesCS3A01G462700 chr2A 699994273 699995574 1301 True 2069.000000 2069 95.402000 1063 2361 1 chr2A.!!$R2 1298
16 TraesCS3A01G462700 chr6A 519184636 519185937 1301 False 2063.000000 2063 95.326000 1063 2361 1 chr6A.!!$F1 1298
17 TraesCS3A01G462700 chr6A 98287205 98288504 1299 True 2041.000000 2041 95.012000 1063 2362 1 chr6A.!!$R1 1299
18 TraesCS3A01G462700 chr1A 534430231 534431533 1302 True 2054.000000 2054 95.176000 1063 2362 1 chr1A.!!$R2 1299
19 TraesCS3A01G462700 chr1A 36808609 36809910 1301 False 2049.000000 2049 95.092000 1063 2362 1 chr1A.!!$F2 1299
20 TraesCS3A01G462700 chr1A 380984378 380985688 1310 False 2041.000000 2041 94.889000 1062 2362 1 chr1A.!!$F3 1300
21 TraesCS3A01G462700 chr7A 251940165 251941463 1298 True 2050.000000 2050 95.161000 1063 2362 1 chr7A.!!$R1 1299
22 TraesCS3A01G462700 chr7A 27880039 27881107 1068 False 260.000000 305 78.193000 4 1058 2 chr7A.!!$F1 1054
23 TraesCS3A01G462700 chr7D 564627180 564628331 1151 False 454.666667 617 88.411333 3 1059 3 chr7D.!!$F1 1056
24 TraesCS3A01G462700 chr6D 269120903 269121577 674 False 366.000000 366 77.285000 1 735 1 chr6D.!!$F1 734

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
557 575 0.109086 CTGCGTCGATGAGGTTCACT 60.109 55.0 9.31 0.0 0.00 3.41 F
590 744 0.177836 CCGCCCACATGTATGAGACA 59.822 55.0 0.00 0.0 43.97 3.41 F
1118 1328 0.178978 GGCCCCTTCAGATCCAATCC 60.179 60.0 0.00 0.0 0.00 3.01 F
2486 2807 0.451628 CTGCGACGACAGCAACAATG 60.452 55.0 0.00 0.0 44.67 2.82 F
3176 3894 0.400213 TCAAGAACTGCCGGAATGGT 59.600 50.0 5.05 0.0 41.21 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2404 2723 0.242017 GCCACAGGTTGCAGCTTTAG 59.758 55.0 0.00 0.0 0.0 1.85 R
2576 2940 0.038166 GCACAAGGTCTTCCCCATCA 59.962 55.0 0.00 0.0 0.0 3.07 R
2734 3098 0.237761 GTCTCACACGTGCGTCTAGT 59.762 55.0 17.22 0.0 0.0 2.57 R
3600 4363 0.182537 AGCATATAGTTGCCCCGCAA 59.817 50.0 0.00 0.0 46.8 4.85 R
4594 6024 0.105453 ATGGCATCTACTCCCTCCGT 60.105 55.0 0.00 0.0 0.0 4.69 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
32 33 6.322201 CAGATTGAAACTAGCCCAAACCATAT 59.678 38.462 0.00 0.00 0.00 1.78
33 34 7.502226 CAGATTGAAACTAGCCCAAACCATATA 59.498 37.037 0.00 0.00 0.00 0.86
34 35 8.227507 AGATTGAAACTAGCCCAAACCATATAT 58.772 33.333 0.00 0.00 0.00 0.86
35 36 9.515226 GATTGAAACTAGCCCAAACCATATATA 57.485 33.333 0.00 0.00 0.00 0.86
42 43 4.663120 AGCCCAAACCATATATACCACTCA 59.337 41.667 0.00 0.00 0.00 3.41
67 68 4.639310 CCTCTTTCATTCAGACCAATCCAG 59.361 45.833 0.00 0.00 0.00 3.86
113 114 1.671845 GACCAAACCAAACTACGTGCA 59.328 47.619 0.00 0.00 0.00 4.57
131 132 0.835543 CATTTTCCACCCAGCCCCAA 60.836 55.000 0.00 0.00 0.00 4.12
144 145 1.419762 AGCCCCAACCAAACCATTTTC 59.580 47.619 0.00 0.00 0.00 2.29
150 151 3.311048 CCAACCAAACCATTTTCCGTTTG 59.689 43.478 5.83 5.83 45.40 2.93
152 153 5.109903 CAACCAAACCATTTTCCGTTTGTA 58.890 37.500 10.70 0.00 44.70 2.41
170 171 6.293190 CGTTTGTAGGTTGAAACTGCAATCTA 60.293 38.462 14.30 0.00 39.73 1.98
200 204 0.950555 CACAAGAAGCTGGCGTGCTA 60.951 55.000 5.27 0.00 43.24 3.49
416 431 1.499438 AGTCCGAGGGATAGGATGTCA 59.501 52.381 0.00 0.00 38.97 3.58
447 465 2.745100 AGCAGCTGACATGCACCG 60.745 61.111 20.43 0.00 46.31 4.94
448 466 4.471726 GCAGCTGACATGCACCGC 62.472 66.667 20.43 0.00 43.31 5.68
555 573 0.388520 CACTGCGTCGATGAGGTTCA 60.389 55.000 9.31 0.00 0.00 3.18
557 575 0.109086 CTGCGTCGATGAGGTTCACT 60.109 55.000 9.31 0.00 0.00 3.41
559 577 0.388649 GCGTCGATGAGGTTCACTGT 60.389 55.000 9.31 0.00 0.00 3.55
560 578 1.618861 CGTCGATGAGGTTCACTGTC 58.381 55.000 0.00 0.00 0.00 3.51
569 723 1.003580 AGGTTCACTGTCGATGCCATT 59.996 47.619 0.00 0.00 0.00 3.16
587 741 0.747644 TTGCCGCCCACATGTATGAG 60.748 55.000 0.00 0.00 0.00 2.90
590 744 0.177836 CCGCCCACATGTATGAGACA 59.822 55.000 0.00 0.00 43.97 3.41
592 746 1.134699 CGCCCACATGTATGAGACACT 60.135 52.381 0.00 0.00 42.17 3.55
593 747 2.555199 GCCCACATGTATGAGACACTC 58.445 52.381 0.00 0.00 42.17 3.51
594 748 2.743183 GCCCACATGTATGAGACACTCC 60.743 54.545 0.00 0.00 42.17 3.85
595 749 2.501316 CCCACATGTATGAGACACTCCA 59.499 50.000 0.00 0.00 42.17 3.86
597 751 3.196469 CCACATGTATGAGACACTCCAGT 59.804 47.826 0.00 0.00 42.17 4.00
598 752 4.428209 CACATGTATGAGACACTCCAGTC 58.572 47.826 0.00 0.00 42.17 3.51
608 762 4.079850 CTCCAGTCTGCAGCGGCT 62.080 66.667 9.47 0.00 41.91 5.52
625 781 2.050077 TGTGCGCTCGTCAGACAG 60.050 61.111 9.73 0.00 0.00 3.51
690 847 2.506217 CCACGTCGACGACCATGG 60.506 66.667 41.52 32.44 43.02 3.66
752 912 2.439104 GCCTTGGCGATCCTCCTCT 61.439 63.158 0.00 0.00 0.00 3.69
755 915 1.306141 TTGGCGATCCTCCTCTGGT 60.306 57.895 0.00 0.00 0.00 4.00
759 919 1.965754 GCGATCCTCCTCTGGTTGCT 61.966 60.000 0.00 0.00 0.00 3.91
760 920 0.539051 CGATCCTCCTCTGGTTGCTT 59.461 55.000 0.00 0.00 0.00 3.91
779 979 4.469586 TGCTTGTACTCCATCAGGACATTA 59.530 41.667 0.00 0.00 46.21 1.90
791 991 8.447200 TCCATCAGGACATTAATGAATGGAATA 58.553 33.333 22.16 7.89 45.83 1.75
847 1047 1.758440 AACTGAAGCTGGCCGTCTCA 61.758 55.000 0.00 0.00 0.00 3.27
882 1088 3.248024 AGAGACTGGGTTATGTCCACAA 58.752 45.455 0.00 0.00 34.02 3.33
900 1106 5.068460 TCCACAAATTGAAACGGTTTGAGAT 59.932 36.000 11.43 0.00 36.58 2.75
935 1141 6.998074 TGTGTCTAGATCAAACCAGTCAAATT 59.002 34.615 0.00 0.00 0.00 1.82
950 1156 8.641541 ACCAGTCAAATTCAGTGTTTGATAAAT 58.358 29.630 10.95 0.00 44.56 1.40
971 1181 5.941555 ATTCCAAACCACACCTGTTTTAA 57.058 34.783 0.00 0.00 33.82 1.52
1004 1214 4.568760 CCATTTACACCAACCAAACACAAC 59.431 41.667 0.00 0.00 0.00 3.32
1059 1269 4.010349 CAAGTCCAAACTATTCCCAGGTC 58.990 47.826 0.00 0.00 33.48 3.85
1060 1270 3.532102 AGTCCAAACTATTCCCAGGTCT 58.468 45.455 0.00 0.00 32.59 3.85
1094 1304 1.613284 ATAGGGGCAAGGGAGAGGGA 61.613 60.000 0.00 0.00 0.00 4.20
1098 1308 2.690510 GCAAGGGAGAGGGAGGCT 60.691 66.667 0.00 0.00 0.00 4.58
1118 1328 0.178978 GGCCCCTTCAGATCCAATCC 60.179 60.000 0.00 0.00 0.00 3.01
1122 1332 2.042464 CCCTTCAGATCCAATCCGAGA 58.958 52.381 0.00 0.00 0.00 4.04
1205 1422 4.815108 CCCCAAACCCTAGGCGCC 62.815 72.222 21.89 21.89 0.00 6.53
1281 1498 4.574614 CCCATAGGGCCCTCCGGA 62.575 72.222 32.32 17.01 41.52 5.14
1380 1599 2.418197 CCGGTGACCGTATGATGACTTT 60.418 50.000 23.73 0.00 46.80 2.66
1420 1639 3.834732 CGAACCATTCCGGAACTCT 57.165 52.632 21.56 0.00 38.63 3.24
1543 1792 0.536687 CTACGGGCTCGGGAGTCATA 60.537 60.000 12.42 0.00 41.39 2.15
1548 1797 1.333177 GGCTCGGGAGTCATACAGAT 58.667 55.000 0.00 0.00 32.23 2.90
1564 1813 2.501723 ACAGATATGCCCGAGACAACTT 59.498 45.455 0.00 0.00 0.00 2.66
1667 1972 6.405065 CCACGATGTCAAGGATTCAATCAATT 60.405 38.462 0.00 0.00 0.00 2.32
1731 2036 0.886563 ATTCGATCGTCGGTATCCCC 59.113 55.000 15.94 0.00 40.88 4.81
1854 2159 3.233919 TACCGAGTGGGCCCAGAGT 62.234 63.158 29.55 21.89 40.62 3.24
1915 2220 1.172180 CGTGCCAACCCAACAGACAT 61.172 55.000 0.00 0.00 0.00 3.06
1966 2271 1.880646 GCCACCCAGTTACGTTGTGAT 60.881 52.381 0.00 0.00 0.00 3.06
2166 2472 3.675348 ACATCCAATGTCCATGGTCAT 57.325 42.857 17.51 17.51 39.92 3.06
2266 2572 6.481313 CCACACATGTATCTGAGTTTCCTATG 59.519 42.308 0.00 0.00 0.00 2.23
2314 2620 6.757897 AACGATTATCATGAGCAAGGAAAA 57.242 33.333 0.09 0.00 0.00 2.29
2362 2681 5.885912 GTCTTTAGGGCATATTTCCAACAGA 59.114 40.000 0.00 0.00 0.00 3.41
2363 2682 6.377146 GTCTTTAGGGCATATTTCCAACAGAA 59.623 38.462 0.00 0.00 0.00 3.02
2384 2703 4.395959 AAAAGCTATAATCGGTGTCGGA 57.604 40.909 0.00 0.00 36.95 4.55
2418 2739 1.142870 TGTGTCCTAAAGCTGCAACCT 59.857 47.619 1.02 0.00 0.00 3.50
2420 2741 1.142870 TGTCCTAAAGCTGCAACCTGT 59.857 47.619 1.02 0.00 0.00 4.00
2478 2799 3.108289 CCTGTGCTGCGACGACAG 61.108 66.667 10.03 10.03 40.80 3.51
2485 2806 1.862123 CTGCGACGACAGCAACAAT 59.138 52.632 0.00 0.00 44.67 2.71
2486 2807 0.451628 CTGCGACGACAGCAACAATG 60.452 55.000 0.00 0.00 44.67 2.82
2539 2903 1.612442 TAGAGGTGGACTGGTGGCC 60.612 63.158 0.00 0.00 0.00 5.36
2541 2905 2.776526 AGGTGGACTGGTGGCCAA 60.777 61.111 7.24 0.00 35.63 4.52
2576 2940 0.457035 GGTGATGCAAACATGGCGAT 59.543 50.000 0.00 0.00 36.35 4.58
2577 2941 1.552226 GTGATGCAAACATGGCGATG 58.448 50.000 7.21 7.21 36.35 3.84
2592 2956 1.959042 CGATGATGGGGAAGACCTTG 58.041 55.000 0.00 0.00 40.03 3.61
2617 2981 4.530857 CGGCGCCCTAAGGTCCTG 62.531 72.222 23.46 0.00 34.57 3.86
2621 2985 1.972660 GCGCCCTAAGGTCCTGATGT 61.973 60.000 0.00 0.00 34.57 3.06
2630 2994 1.080772 GTCCTGATGTGCGACGACA 60.081 57.895 0.00 0.35 0.00 4.35
2635 2999 3.767301 ATGTGCGACGACATCACG 58.233 55.556 0.00 0.00 30.34 4.35
2642 3006 2.602267 ACGACATCACGGGGTCCA 60.602 61.111 0.00 0.00 37.61 4.02
2647 3011 1.374947 CATCACGGGGTCCAACTGT 59.625 57.895 0.00 0.00 0.00 3.55
2655 3019 4.876701 GTCCAACTGTGACCTGCA 57.123 55.556 0.00 0.00 0.00 4.41
2690 3054 3.257933 GCTCGTGCAAGAGGTTGG 58.742 61.111 27.42 6.62 38.63 3.77
2691 3055 2.970974 GCTCGTGCAAGAGGTTGGC 61.971 63.158 27.42 12.61 38.63 4.52
2698 3062 1.032014 GCAAGAGGTTGGCAACTTGA 58.968 50.000 27.77 0.00 41.16 3.02
2711 3075 1.599071 CAACTTGAGATGTGCGTGTGT 59.401 47.619 0.00 0.00 0.00 3.72
2720 3084 1.587876 GTGCGTGTGTCGTGTGAGA 60.588 57.895 0.00 0.00 42.13 3.27
2721 3085 1.587876 TGCGTGTGTCGTGTGAGAC 60.588 57.895 0.00 0.00 42.13 3.36
2733 3097 1.728971 GTGTGAGACGATGCAAAGAGG 59.271 52.381 0.00 0.00 0.00 3.69
2734 3098 1.618343 TGTGAGACGATGCAAAGAGGA 59.382 47.619 0.00 0.00 0.00 3.71
2735 3099 1.996191 GTGAGACGATGCAAAGAGGAC 59.004 52.381 0.00 0.00 0.00 3.85
2736 3100 1.895798 TGAGACGATGCAAAGAGGACT 59.104 47.619 0.00 0.00 0.00 3.85
2740 3104 3.129638 AGACGATGCAAAGAGGACTAGAC 59.870 47.826 0.00 0.00 0.00 2.59
2774 3138 3.637229 ACGAAGATGACGTAAGGGATGAT 59.363 43.478 0.00 0.00 42.17 2.45
2815 3179 8.836413 CAACCATTATTAGTGTCGTAATCCAAT 58.164 33.333 0.00 0.00 0.00 3.16
2835 3199 1.211709 GTGAAAAATGGACCGGCGG 59.788 57.895 27.06 27.06 0.00 6.13
2875 3241 1.135315 CATCGTGTGAGGCCAAAATGG 60.135 52.381 5.01 0.00 41.55 3.16
2889 3255 2.752354 CAAAATGGCGTAAGGGATGACA 59.248 45.455 0.00 0.00 36.16 3.58
2905 3273 1.077357 ACACGAGGGCACAAACCAA 60.077 52.632 0.00 0.00 0.00 3.67
2934 3304 8.472413 GTTACTAGTGTCCTGTATAATCCAACA 58.528 37.037 5.39 0.00 0.00 3.33
2943 3313 5.592688 CCTGTATAATCCAACACCGGAAAAT 59.407 40.000 9.46 0.00 38.95 1.82
3162 3880 0.811219 CAGATGCCCGCGAATCAAGA 60.811 55.000 8.23 0.00 0.00 3.02
3176 3894 0.400213 TCAAGAACTGCCGGAATGGT 59.600 50.000 5.05 0.00 41.21 3.55
3428 4176 1.817099 CGTCCTTGGATCTGGCAGC 60.817 63.158 10.34 0.00 0.00 5.25
3470 4221 0.539438 CGGCAGAGATAGAGCTCCCT 60.539 60.000 10.93 5.28 35.49 4.20
3571 4334 3.648545 GGTCTAGATTTAGCCACCAGGAT 59.351 47.826 0.00 0.00 36.89 3.24
3584 4347 1.355720 ACCAGGATCCTTTTCACCCTG 59.644 52.381 13.00 0.00 42.92 4.45
3816 4603 3.304592 CGATGTTTGCCTTGATGTTGTCA 60.305 43.478 0.00 0.00 34.25 3.58
3840 4627 0.804989 CGGGGACAATGCTGACTTTC 59.195 55.000 0.00 0.00 0.00 2.62
3854 4641 5.928839 TGCTGACTTTCTGTTCTTAGATCAC 59.071 40.000 0.00 0.00 0.00 3.06
4026 4844 0.881118 AGCGCGGAATGTGTTTGATT 59.119 45.000 8.83 0.00 0.00 2.57
4079 4897 8.079211 TCTGCAATAGAGAGGTATGTACTTTT 57.921 34.615 0.00 0.00 0.00 2.27
4284 5517 2.325583 TCTGGTAATGATCGGTTGCC 57.674 50.000 9.79 9.79 32.68 4.52
4288 5521 2.104111 TGGTAATGATCGGTTGCCTAGG 59.896 50.000 3.67 3.67 33.17 3.02
4298 5531 2.030274 CGGTTGCCTAGGAAAACTTTGG 60.030 50.000 15.97 0.00 0.00 3.28
4319 5552 6.047511 TGGATGGTGACCAAATAAAAATGG 57.952 37.500 9.06 0.00 42.60 3.16
4398 5631 6.542821 TCTTTTGTATTCTTGACAGGGATGT 58.457 36.000 0.00 0.00 0.00 3.06
4499 5928 5.721960 ACCCATCATCACTAGTTCACTACTT 59.278 40.000 0.00 0.00 38.33 2.24
4500 5929 6.127310 ACCCATCATCACTAGTTCACTACTTC 60.127 42.308 0.00 0.00 38.33 3.01
4524 5954 9.807921 TTCAGTTCTAAGGGAAAATTTGATACT 57.192 29.630 0.00 0.00 35.51 2.12
4525 5955 9.449719 TCAGTTCTAAGGGAAAATTTGATACTC 57.550 33.333 0.00 0.00 35.51 2.59
4526 5956 8.678199 CAGTTCTAAGGGAAAATTTGATACTCC 58.322 37.037 0.00 0.00 35.51 3.85
4527 5957 7.834681 AGTTCTAAGGGAAAATTTGATACTCCC 59.165 37.037 14.68 14.68 45.35 4.30
4532 5962 5.510430 GGGAAAATTTGATACTCCCTCTGT 58.490 41.667 15.08 0.00 42.25 3.41
4533 5963 6.659824 GGGAAAATTTGATACTCCCTCTGTA 58.340 40.000 15.08 0.00 42.25 2.74
4534 5964 7.116736 GGGAAAATTTGATACTCCCTCTGTAA 58.883 38.462 15.08 0.00 42.25 2.41
4535 5965 7.614192 GGGAAAATTTGATACTCCCTCTGTAAA 59.386 37.037 15.08 0.00 42.25 2.01
4536 5966 9.190317 GGAAAATTTGATACTCCCTCTGTAAAT 57.810 33.333 0.00 0.00 0.00 1.40
4597 6027 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
4598 6028 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
4599 6029 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
4600 6030 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
4601 6031 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
4602 6032 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
4603 6033 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
4604 6034 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4605 6035 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4646 6076 0.685458 ATCCCAATGGCAGCCAGAAC 60.685 55.000 21.51 0.00 36.75 3.01
4649 6079 0.245539 CCAATGGCAGCCAGAACAAG 59.754 55.000 21.51 5.50 36.75 3.16
4665 6097 1.610522 ACAAGAAGTGATGCTTGGTGC 59.389 47.619 0.00 0.00 44.33 5.01
4695 6127 4.042809 ACTCCACAACAATGGTATTCCTCA 59.957 41.667 0.00 0.00 40.95 3.86
4708 6144 5.129650 TGGTATTCCTCATCACGGACAAATA 59.870 40.000 0.00 0.00 34.23 1.40
4746 6191 9.844257 AAATTAGAGTGCTAGCTTATCAGAAAT 57.156 29.630 17.23 9.19 0.00 2.17
4779 6224 6.983984 TCATCAACTGAAGCATTGATTTGAA 58.016 32.000 0.00 0.00 41.69 2.69
4920 6439 4.868268 ACACTCCTGACCATAGCTAACTA 58.132 43.478 0.00 0.00 0.00 2.24
4951 6470 2.030451 GCTCCCTCACAAAAGCAAAGAG 60.030 50.000 0.00 0.00 34.86 2.85
5068 6587 3.345508 TGAATCATCAGCTGAAGCAGT 57.654 42.857 22.50 6.54 45.16 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.847265 TGAGTGGTATATATGGTTTGGGCTA 59.153 40.000 0.00 0.00 0.00 3.93
32 33 5.425217 TGAATGAAAGAGGCTGAGTGGTATA 59.575 40.000 0.00 0.00 0.00 1.47
33 34 4.225942 TGAATGAAAGAGGCTGAGTGGTAT 59.774 41.667 0.00 0.00 0.00 2.73
34 35 3.582647 TGAATGAAAGAGGCTGAGTGGTA 59.417 43.478 0.00 0.00 0.00 3.25
35 36 2.373169 TGAATGAAAGAGGCTGAGTGGT 59.627 45.455 0.00 0.00 0.00 4.16
42 43 3.795688 TTGGTCTGAATGAAAGAGGCT 57.204 42.857 0.00 0.00 0.00 4.58
67 68 6.209788 TGGATTATGGTGGTTAAAGTTTGGAC 59.790 38.462 0.00 0.00 0.00 4.02
113 114 0.835971 GTTGGGGCTGGGTGGAAAAT 60.836 55.000 0.00 0.00 0.00 1.82
144 145 2.356382 TGCAGTTTCAACCTACAAACGG 59.644 45.455 0.00 0.00 37.54 4.44
150 151 6.861572 GGTTTTAGATTGCAGTTTCAACCTAC 59.138 38.462 6.54 0.00 0.00 3.18
152 153 5.362430 TGGTTTTAGATTGCAGTTTCAACCT 59.638 36.000 12.18 0.00 33.66 3.50
170 171 3.068590 CAGCTTCTTGTGTCCATGGTTTT 59.931 43.478 12.58 0.00 0.00 2.43
200 204 2.847234 TCACGGGCCTGGTTGACT 60.847 61.111 18.00 0.00 0.00 3.41
284 296 0.784778 GATCAACTACTATGCGCGGC 59.215 55.000 8.83 0.00 0.00 6.53
285 297 2.423926 AGATCAACTACTATGCGCGG 57.576 50.000 8.83 0.00 0.00 6.46
286 298 3.372060 TGAAGATCAACTACTATGCGCG 58.628 45.455 0.00 0.00 0.00 6.86
287 299 3.183373 GCTGAAGATCAACTACTATGCGC 59.817 47.826 0.00 0.00 0.00 6.09
290 302 7.763528 ACTTGAAGCTGAAGATCAACTACTATG 59.236 37.037 11.75 0.00 0.00 2.23
291 303 7.846066 ACTTGAAGCTGAAGATCAACTACTAT 58.154 34.615 11.75 0.00 0.00 2.12
336 348 1.734137 CACCTCACGGCGCTACTAT 59.266 57.895 6.90 0.00 0.00 2.12
379 392 0.766674 ACTAGGTGTTCTGGTGCCCA 60.767 55.000 0.00 0.00 35.77 5.36
380 393 0.036294 GACTAGGTGTTCTGGTGCCC 60.036 60.000 0.00 0.00 37.32 5.36
447 465 1.333619 TCTTGTCACCAAAAGCTTCGC 59.666 47.619 0.00 0.00 0.00 4.70
448 466 3.691049 TTCTTGTCACCAAAAGCTTCG 57.309 42.857 0.00 0.00 0.00 3.79
465 483 1.515954 CCTCGCCCGTGTACATTCT 59.484 57.895 0.00 0.00 0.00 2.40
555 573 2.108514 CGGCAATGGCATCGACAGT 61.109 57.895 7.75 0.00 43.71 3.55
557 575 3.507924 GCGGCAATGGCATCGACA 61.508 61.111 10.78 0.00 43.71 4.35
569 723 1.153188 CTCATACATGTGGGCGGCA 60.153 57.895 12.47 0.00 0.00 5.69
587 741 1.735920 CGCTGCAGACTGGAGTGTC 60.736 63.158 24.71 9.19 40.72 3.67
590 744 4.385405 GCCGCTGCAGACTGGAGT 62.385 66.667 23.09 0.00 38.17 3.85
592 746 4.383861 CAGCCGCTGCAGACTGGA 62.384 66.667 20.43 0.00 41.13 3.86
593 747 4.694233 ACAGCCGCTGCAGACTGG 62.694 66.667 25.94 20.59 41.13 4.00
594 748 3.420606 CACAGCCGCTGCAGACTG 61.421 66.667 20.43 21.93 41.13 3.51
608 762 2.050077 CTGTCTGACGAGCGCACA 60.050 61.111 11.47 1.56 0.00 4.57
642 798 2.360980 CTCCGACCCAGACTCCCT 59.639 66.667 0.00 0.00 0.00 4.20
724 881 2.820037 GCCAAGGCTACGACCAGC 60.820 66.667 3.29 0.00 41.02 4.85
752 912 2.290260 CCTGATGGAGTACAAGCAACCA 60.290 50.000 0.00 0.00 34.57 3.67
755 915 2.637382 TGTCCTGATGGAGTACAAGCAA 59.363 45.455 0.00 0.00 44.16 3.91
759 919 7.194112 TCATTAATGTCCTGATGGAGTACAA 57.806 36.000 14.97 0.00 44.16 2.41
760 920 6.806668 TCATTAATGTCCTGATGGAGTACA 57.193 37.500 14.97 0.00 44.16 2.90
791 991 8.129840 CAGCTTACGTACTACATAGTTCAATCT 58.870 37.037 0.00 0.00 37.73 2.40
798 998 5.296283 CACTCCAGCTTACGTACTACATAGT 59.704 44.000 0.00 0.00 40.24 2.12
802 1002 2.163010 GCACTCCAGCTTACGTACTACA 59.837 50.000 0.00 0.00 0.00 2.74
803 1003 2.163010 TGCACTCCAGCTTACGTACTAC 59.837 50.000 0.00 0.00 34.99 2.73
882 1088 6.391227 AGTTGATCTCAAACCGTTTCAATT 57.609 33.333 0.00 0.00 37.63 2.32
900 1106 5.447624 TGATCTAGACACAAACGAGTTGA 57.552 39.130 9.95 0.00 39.87 3.18
950 1156 5.740290 TTTAAAACAGGTGTGGTTTGGAA 57.260 34.783 0.00 0.00 43.71 3.53
971 1181 4.046286 TGGTGTAAATGGGCTGAGAATT 57.954 40.909 0.00 0.00 0.00 2.17
1004 1214 5.799827 TTCAGTTTGGTTTTCCTATTGGG 57.200 39.130 0.00 0.00 41.38 4.12
1039 1249 3.532102 AGACCTGGGAATAGTTTGGACT 58.468 45.455 0.00 0.00 39.97 3.85
1094 1304 2.286732 ATCTGAAGGGGCCAGCCT 60.287 61.111 4.39 0.00 36.10 4.58
1098 1308 0.552848 GATTGGATCTGAAGGGGCCA 59.447 55.000 4.39 0.00 0.00 5.36
1105 1315 2.435805 CCCTTCTCGGATTGGATCTGAA 59.564 50.000 1.53 0.00 43.65 3.02
1254 1471 1.990424 CCCTATGGGCTGTGTGTGA 59.010 57.895 0.00 0.00 35.35 3.58
1420 1639 1.651240 GAGATCCCGGACGTCACGAA 61.651 60.000 22.53 13.23 0.00 3.85
1458 1677 6.882610 ATAGATGTACGTGGTTACCGAATA 57.117 37.500 0.00 0.00 0.00 1.75
1543 1792 2.111384 AGTTGTCTCGGGCATATCTGT 58.889 47.619 0.00 0.00 0.00 3.41
1548 1797 1.404986 CGGAAAGTTGTCTCGGGCATA 60.405 52.381 0.00 0.00 0.00 3.14
1667 1972 3.071892 AGACAAAGGGAATTGTGTACGGA 59.928 43.478 0.00 0.00 43.31 4.69
1702 2007 0.389391 ACGATCGAATCTCGGGCAAT 59.611 50.000 24.34 0.00 40.88 3.56
1731 2036 5.872617 TGGTAACGAGATTGAACAAGGTATG 59.127 40.000 0.00 0.00 42.51 2.39
1966 2271 1.260538 TGCTTTGGGTGTGCCAAACA 61.261 50.000 0.00 0.00 34.15 2.83
2052 2357 6.558009 AGATCGTGTAGTTCGTATGCTAAAA 58.442 36.000 0.00 0.00 0.00 1.52
2081 2387 5.497474 GACAAGACCCAATCTTAAGCCTAA 58.503 41.667 0.00 0.00 46.52 2.69
2090 2396 2.644299 TGTGATGGACAAGACCCAATCT 59.356 45.455 0.00 0.00 40.46 2.40
2166 2472 6.645306 TGATCAATAGATGGTTACGGTTTCA 58.355 36.000 0.00 0.00 33.72 2.69
2339 2658 6.073447 TCTGTTGGAAATATGCCCTAAAGA 57.927 37.500 0.00 0.00 0.00 2.52
2342 2661 7.546250 TTTTTCTGTTGGAAATATGCCCTAA 57.454 32.000 0.00 0.00 42.63 2.69
2362 2681 4.569564 GTCCGACACCGATTATAGCTTTTT 59.430 41.667 0.00 0.00 38.22 1.94
2363 2682 4.117685 GTCCGACACCGATTATAGCTTTT 58.882 43.478 0.00 0.00 38.22 2.27
2364 2683 3.492137 GGTCCGACACCGATTATAGCTTT 60.492 47.826 0.00 0.00 34.56 3.51
2365 2684 2.035576 GGTCCGACACCGATTATAGCTT 59.964 50.000 0.00 0.00 34.56 3.74
2366 2685 1.612463 GGTCCGACACCGATTATAGCT 59.388 52.381 0.00 0.00 34.56 3.32
2367 2686 2.061740 GGTCCGACACCGATTATAGC 57.938 55.000 0.00 0.00 34.56 2.97
2384 2703 2.664851 CACATGTCGTGGCACGGT 60.665 61.111 36.30 24.32 42.81 4.83
2404 2723 0.242017 GCCACAGGTTGCAGCTTTAG 59.758 55.000 0.00 0.00 0.00 1.85
2405 2724 1.514678 CGCCACAGGTTGCAGCTTTA 61.515 55.000 0.00 0.00 0.00 1.85
2406 2725 2.848858 CGCCACAGGTTGCAGCTTT 61.849 57.895 0.00 0.00 0.00 3.51
2418 2739 3.705934 TTGTTGCAGGGTCGCCACA 62.706 57.895 0.00 0.00 35.90 4.17
2420 2741 2.904866 GTTGTTGCAGGGTCGCCA 60.905 61.111 0.00 0.00 0.00 5.69
2506 2870 1.403493 CTCTACAGTCGCATCATCGC 58.597 55.000 0.00 0.00 0.00 4.58
2539 2903 3.499157 TCACCGTAAAAAGGGAATCGTTG 59.501 43.478 0.00 0.00 0.00 4.10
2541 2905 3.405823 TCACCGTAAAAAGGGAATCGT 57.594 42.857 0.00 0.00 0.00 3.73
2576 2940 0.038166 GCACAAGGTCTTCCCCATCA 59.962 55.000 0.00 0.00 0.00 3.07
2577 2941 1.026718 CGCACAAGGTCTTCCCCATC 61.027 60.000 0.00 0.00 0.00 3.51
2604 2968 0.464554 GCACATCAGGACCTTAGGGC 60.465 60.000 2.32 0.00 35.63 5.19
2621 2985 4.429212 CCCCGTGATGTCGTCGCA 62.429 66.667 6.43 0.00 37.18 5.10
2630 2994 1.125093 TCACAGTTGGACCCCGTGAT 61.125 55.000 0.00 0.00 31.92 3.06
2642 3006 1.069765 CCTCGTGCAGGTCACAGTT 59.930 57.895 6.26 0.00 45.92 3.16
2662 3026 2.249309 CACGAGCAAGCACCAACG 59.751 61.111 0.00 0.00 0.00 4.10
2690 3054 0.588252 ACACGCACATCTCAAGTTGC 59.412 50.000 0.00 0.00 0.00 4.17
2691 3055 1.599071 ACACACGCACATCTCAAGTTG 59.401 47.619 0.00 0.00 0.00 3.16
2698 3062 1.067416 ACACGACACACGCACATCT 59.933 52.632 0.00 0.00 46.94 2.90
2720 3084 2.159366 CGTCTAGTCCTCTTTGCATCGT 60.159 50.000 0.00 0.00 0.00 3.73
2721 3085 2.455032 CGTCTAGTCCTCTTTGCATCG 58.545 52.381 0.00 0.00 0.00 3.84
2722 3086 2.197577 GCGTCTAGTCCTCTTTGCATC 58.802 52.381 0.00 0.00 0.00 3.91
2723 3087 1.550524 TGCGTCTAGTCCTCTTTGCAT 59.449 47.619 0.00 0.00 0.00 3.96
2724 3088 0.966179 TGCGTCTAGTCCTCTTTGCA 59.034 50.000 0.00 0.00 0.00 4.08
2725 3089 1.351153 GTGCGTCTAGTCCTCTTTGC 58.649 55.000 0.00 0.00 0.00 3.68
2726 3090 1.068472 ACGTGCGTCTAGTCCTCTTTG 60.068 52.381 0.00 0.00 0.00 2.77
2727 3091 1.068472 CACGTGCGTCTAGTCCTCTTT 60.068 52.381 0.82 0.00 0.00 2.52
2728 3092 0.522180 CACGTGCGTCTAGTCCTCTT 59.478 55.000 0.82 0.00 0.00 2.85
2729 3093 0.605860 ACACGTGCGTCTAGTCCTCT 60.606 55.000 17.22 0.00 0.00 3.69
2730 3094 0.454620 CACACGTGCGTCTAGTCCTC 60.455 60.000 17.22 0.00 0.00 3.71
2731 3095 0.887836 TCACACGTGCGTCTAGTCCT 60.888 55.000 17.22 0.00 0.00 3.85
2732 3096 0.454620 CTCACACGTGCGTCTAGTCC 60.455 60.000 17.22 0.00 0.00 3.85
2733 3097 0.516001 TCTCACACGTGCGTCTAGTC 59.484 55.000 17.22 0.00 0.00 2.59
2734 3098 0.237761 GTCTCACACGTGCGTCTAGT 59.762 55.000 17.22 0.00 0.00 2.57
2735 3099 0.789753 CGTCTCACACGTGCGTCTAG 60.790 60.000 17.22 6.18 44.07 2.43
2736 3100 1.205820 CGTCTCACACGTGCGTCTA 59.794 57.895 17.22 0.00 44.07 2.59
2774 3138 4.292145 TTGGATTGTGCCCCCGCA 62.292 61.111 0.00 0.00 44.78 5.69
2815 3179 1.519751 CGCCGGTCCATTTTTCACCA 61.520 55.000 1.90 0.00 0.00 4.17
2835 3199 4.511617 TGCATCTCATCCTCGAGTATTC 57.488 45.455 12.31 0.00 34.46 1.75
2868 3234 2.752354 TGTCATCCCTTACGCCATTTTG 59.248 45.455 0.00 0.00 0.00 2.44
2875 3241 0.527817 CCTCGTGTCATCCCTTACGC 60.528 60.000 0.00 0.00 36.56 4.42
2889 3255 1.826487 GGTTGGTTTGTGCCCTCGT 60.826 57.895 0.00 0.00 0.00 4.18
2905 3273 6.264067 GGATTATACAGGACACTAGTAACGGT 59.736 42.308 0.00 0.00 0.00 4.83
2934 3304 4.301072 TCTTCTTGATCCATTTTCCGGT 57.699 40.909 0.00 0.00 0.00 5.28
2943 3313 4.846367 TCCTTCCTCTTTCTTCTTGATCCA 59.154 41.667 0.00 0.00 0.00 3.41
2985 3388 4.142513 GCGCTCTTTCTTCTTGATCCATTT 60.143 41.667 0.00 0.00 0.00 2.32
2988 3391 2.289631 TGCGCTCTTTCTTCTTGATCCA 60.290 45.455 9.73 0.00 0.00 3.41
2989 3392 2.350522 TGCGCTCTTTCTTCTTGATCC 58.649 47.619 9.73 0.00 0.00 3.36
2990 3393 3.425492 GGTTGCGCTCTTTCTTCTTGATC 60.425 47.826 9.73 0.00 0.00 2.92
2992 3395 1.873591 GGTTGCGCTCTTTCTTCTTGA 59.126 47.619 9.73 0.00 0.00 3.02
2993 3396 1.068954 GGGTTGCGCTCTTTCTTCTTG 60.069 52.381 9.73 0.00 0.00 3.02
2994 3397 1.239347 GGGTTGCGCTCTTTCTTCTT 58.761 50.000 9.73 0.00 0.00 2.52
2996 3399 1.497722 CGGGTTGCGCTCTTTCTTC 59.502 57.895 9.73 0.00 0.00 2.87
2998 3401 3.050275 GCGGGTTGCGCTCTTTCT 61.050 61.111 9.73 0.00 0.00 2.52
3162 3880 2.746277 GCGACCATTCCGGCAGTT 60.746 61.111 0.00 0.00 39.03 3.16
3453 4201 1.993956 TCAGGGAGCTCTATCTCTGC 58.006 55.000 14.64 0.00 45.79 4.26
3470 4221 4.470334 TTCATGGAAGACGATGTCATCA 57.530 40.909 13.22 0.00 32.74 3.07
3571 4334 1.628846 GTAGCTCCAGGGTGAAAAGGA 59.371 52.381 0.00 0.00 0.00 3.36
3584 4347 1.383523 GCAATCCAACTGGTAGCTCC 58.616 55.000 0.00 0.00 36.34 4.70
3600 4363 0.182537 AGCATATAGTTGCCCCGCAA 59.817 50.000 0.00 0.00 46.80 4.85
3641 4404 2.939756 GTCTGCACTGACGAGATAGAGA 59.060 50.000 0.00 0.00 0.00 3.10
3744 4519 2.034687 GCATGCCTGACCCACACT 59.965 61.111 6.36 0.00 0.00 3.55
3816 4603 3.319198 AGCATTGTCCCCGACCGT 61.319 61.111 0.00 0.00 0.00 4.83
3840 4627 3.616956 TGCTGGGTGATCTAAGAACAG 57.383 47.619 0.00 0.00 0.00 3.16
4284 5517 4.459337 GGTCACCATCCAAAGTTTTCCTAG 59.541 45.833 0.00 0.00 0.00 3.02
4288 5521 4.664150 TTGGTCACCATCCAAAGTTTTC 57.336 40.909 0.00 0.00 41.25 2.29
4298 5531 5.486526 TGCCATTTTTATTTGGTCACCATC 58.513 37.500 0.00 0.00 35.34 3.51
4319 5552 1.542915 TCTCTTCCATTTGCTGCTTGC 59.457 47.619 0.00 0.00 43.25 4.01
4398 5631 3.550233 GCATACCGTCTTATCGCTTGAGA 60.550 47.826 0.00 0.00 0.00 3.27
4499 5928 9.449719 GAGTATCAAATTTTCCCTTAGAACTGA 57.550 33.333 0.00 0.00 31.04 3.41
4500 5929 8.678199 GGAGTATCAAATTTTCCCTTAGAACTG 58.322 37.037 0.00 0.00 36.25 3.16
4571 6001 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
4572 6002 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
4573 6003 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
4574 6004 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
4575 6005 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
4576 6006 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
4577 6007 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
4578 6008 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4579 6009 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4580 6010 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
4581 6011 9.512588 TCTACTCCCTCCGTAAACTAATATAAG 57.487 37.037 0.00 0.00 0.00 1.73
4583 6013 9.458727 CATCTACTCCCTCCGTAAACTAATATA 57.541 37.037 0.00 0.00 0.00 0.86
4584 6014 7.093858 GCATCTACTCCCTCCGTAAACTAATAT 60.094 40.741 0.00 0.00 0.00 1.28
4585 6015 6.208204 GCATCTACTCCCTCCGTAAACTAATA 59.792 42.308 0.00 0.00 0.00 0.98
4586 6016 5.010820 GCATCTACTCCCTCCGTAAACTAAT 59.989 44.000 0.00 0.00 0.00 1.73
4587 6017 4.340381 GCATCTACTCCCTCCGTAAACTAA 59.660 45.833 0.00 0.00 0.00 2.24
4588 6018 3.887716 GCATCTACTCCCTCCGTAAACTA 59.112 47.826 0.00 0.00 0.00 2.24
4589 6019 2.694109 GCATCTACTCCCTCCGTAAACT 59.306 50.000 0.00 0.00 0.00 2.66
4590 6020 2.223994 GGCATCTACTCCCTCCGTAAAC 60.224 54.545 0.00 0.00 0.00 2.01
4591 6021 2.037144 GGCATCTACTCCCTCCGTAAA 58.963 52.381 0.00 0.00 0.00 2.01
4592 6022 1.063492 TGGCATCTACTCCCTCCGTAA 60.063 52.381 0.00 0.00 0.00 3.18
4593 6023 0.554305 TGGCATCTACTCCCTCCGTA 59.446 55.000 0.00 0.00 0.00 4.02
4594 6024 0.105453 ATGGCATCTACTCCCTCCGT 60.105 55.000 0.00 0.00 0.00 4.69
4595 6025 1.051812 AATGGCATCTACTCCCTCCG 58.948 55.000 0.00 0.00 0.00 4.63
4596 6026 3.511477 TCTAATGGCATCTACTCCCTCC 58.489 50.000 0.00 0.00 0.00 4.30
4597 6027 4.774726 TCATCTAATGGCATCTACTCCCTC 59.225 45.833 0.00 0.00 0.00 4.30
4598 6028 4.756564 TCATCTAATGGCATCTACTCCCT 58.243 43.478 0.00 0.00 0.00 4.20
4599 6029 5.012561 ACTTCATCTAATGGCATCTACTCCC 59.987 44.000 0.00 0.00 0.00 4.30
4600 6030 6.107901 ACTTCATCTAATGGCATCTACTCC 57.892 41.667 0.00 0.00 0.00 3.85
4601 6031 8.443953 AAAACTTCATCTAATGGCATCTACTC 57.556 34.615 0.00 0.00 0.00 2.59
4604 6034 9.507329 GGATAAAACTTCATCTAATGGCATCTA 57.493 33.333 0.00 0.00 0.00 1.98
4605 6035 7.449704 GGGATAAAACTTCATCTAATGGCATCT 59.550 37.037 0.00 0.00 0.00 2.90
4646 6076 2.342910 GCACCAAGCATCACTTCTTG 57.657 50.000 0.00 0.00 44.79 3.02
4665 6097 2.224018 CCATTGTTGTGGAGTTTGTGGG 60.224 50.000 0.00 0.00 42.02 4.61
4716 6152 9.757227 CTGATAAGCTAGCACTCTAATTTACTT 57.243 33.333 18.83 0.00 0.00 2.24
4746 6191 8.403236 CAATGCTTCAGTTGATGATTAATCAGA 58.597 33.333 21.97 10.76 46.01 3.27
4881 6400 8.928448 TCAGGAGTGTAGCTAATCTTTGATATT 58.072 33.333 0.00 0.00 0.00 1.28
4882 6401 8.364142 GTCAGGAGTGTAGCTAATCTTTGATAT 58.636 37.037 0.00 0.00 0.00 1.63
4897 6416 4.868268 AGTTAGCTATGGTCAGGAGTGTA 58.132 43.478 0.00 0.00 0.00 2.90
4920 6439 4.574674 TTGTGAGGGAGCAAAGTGATAT 57.425 40.909 0.00 0.00 0.00 1.63
4951 6470 4.106029 TGAATTCTAGCACCTCGTGTAC 57.894 45.455 7.05 0.00 35.75 2.90
5068 6587 1.343789 TGGTGGTACCGAACGAAATCA 59.656 47.619 7.57 0.00 42.58 2.57
5115 6635 5.046304 TCAAGACAGGCAGAAGTTTAGCTAT 60.046 40.000 0.00 0.00 0.00 2.97
5230 6750 0.396435 CTTTTGGGAGGGGCCAAAAC 59.604 55.000 4.39 0.00 39.34 2.43


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

AutoCloner maintained by Alex Coulton.