Multiple sequence alignment - TraesCS1A01G126700

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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 TraesCS1A01G126700 chr1A 100.000 2411 0 0 1 2411 152715301 152712891 0.000000e+00 4453
1 TraesCS1A01G126700 chr1A 90.698 1118 96 4 677 1792 494701694 494700583 0.000000e+00 1482
2 TraesCS1A01G126700 chr1A 91.429 350 10 3 1891 2224 494700593 494700248 1.690000e-126 462
3 TraesCS1A01G126700 chr1A 99.468 188 1 0 2224 2411 71671885 71672072 2.300000e-90 342
4 TraesCS1A01G126700 chr1A 99.468 188 1 0 2224 2411 321423473 321423660 2.300000e-90 342
5 TraesCS1A01G126700 chr3B 90.868 1566 115 8 677 2224 499928302 499926747 0.000000e+00 2074
6 TraesCS1A01G126700 chr3B 86.196 623 61 17 3 602 675857968 675857348 0.000000e+00 651
7 TraesCS1A01G126700 chr3B 83.146 712 116 2 677 1386 815401222 815401931 0.000000e+00 647
8 TraesCS1A01G126700 chr3B 85.484 620 66 11 2 599 192369362 192368745 2.040000e-175 625
9 TraesCS1A01G126700 chr3B 92.248 258 20 0 1967 2224 815429822 815430079 1.360000e-97 366
10 TraesCS1A01G126700 chr3B 89.431 123 10 3 1799 1920 815429462 815429582 4.150000e-33 152
11 TraesCS1A01G126700 chr3A 91.882 1121 84 5 674 1792 340259196 340260311 0.000000e+00 1559
12 TraesCS1A01G126700 chr3A 92.170 894 64 4 900 1792 599892294 599891406 0.000000e+00 1258
13 TraesCS1A01G126700 chr3A 91.601 893 70 3 900 1792 17494222 17493335 0.000000e+00 1229
14 TraesCS1A01G126700 chr3A 84.776 624 70 12 2 602 585290620 585289999 9.540000e-169 603
15 TraesCS1A01G126700 chr6A 92.092 999 75 2 794 1792 60606806 60605812 0.000000e+00 1404
16 TraesCS1A01G126700 chr6A 85.133 565 45 16 154 680 294612888 294613451 2.110000e-150 542
17 TraesCS1A01G126700 chr6A 92.286 350 11 6 1891 2224 60605822 60605473 1.300000e-132 483
18 TraesCS1A01G126700 chr6A 92.953 298 21 0 1927 2224 195277384 195277087 3.680000e-118 435
19 TraesCS1A01G126700 chr6A 99.468 188 1 0 2224 2411 17626107 17625920 2.300000e-90 342
20 TraesCS1A01G126700 chr6A 99.468 188 1 0 2224 2411 560253973 560253786 2.300000e-90 342
21 TraesCS1A01G126700 chr6A 80.870 345 47 11 677 1020 195290446 195290120 1.110000e-63 254
22 TraesCS1A01G126700 chr6A 93.600 125 5 2 677 800 60616430 60616308 1.470000e-42 183
23 TraesCS1A01G126700 chr5A 90.361 747 69 2 677 1421 536904941 536905686 0.000000e+00 977
24 TraesCS1A01G126700 chr5A 99.468 188 1 0 2224 2411 108822243 108822430 2.300000e-90 342
25 TraesCS1A01G126700 chr5A 99.468 188 1 0 2224 2411 560392243 560392056 2.300000e-90 342
26 TraesCS1A01G126700 chr5A 93.069 101 6 1 1821 1920 508535480 508535380 1.930000e-31 147
27 TraesCS1A01G126700 chr5A 93.069 101 6 1 1821 1920 508560368 508560268 1.930000e-31 147
28 TraesCS1A01G126700 chr3D 87.500 720 49 16 1 680 418808290 418809008 0.000000e+00 793
29 TraesCS1A01G126700 chr2D 87.500 720 48 19 1 680 197218295 197219012 0.000000e+00 793
30 TraesCS1A01G126700 chr2D 84.840 719 69 22 1 680 550800358 550801075 0.000000e+00 688
31 TraesCS1A01G126700 chr1D 87.465 718 50 17 1 680 223145710 223144995 0.000000e+00 791
32 TraesCS1A01G126700 chr1D 87.291 716 49 23 6 680 79605212 79605926 0.000000e+00 780
33 TraesCS1A01G126700 chr1D 90.335 269 22 4 383 648 109063548 109063281 1.370000e-92 350
34 TraesCS1A01G126700 chr2A 86.536 713 56 17 7 680 521725744 521725033 0.000000e+00 749
35 TraesCS1A01G126700 chr4D 87.406 667 56 16 3 648 385820472 385821131 0.000000e+00 741
36 TraesCS1A01G126700 chr4D 83.582 670 82 16 2 648 255197936 255197272 9.540000e-169 603
37 TraesCS1A01G126700 chr4D 90.604 298 21 1 1934 2224 55490972 55491269 2.910000e-104 388
38 TraesCS1A01G126700 chr6B 82.577 815 95 21 677 1460 274388529 274389327 0.000000e+00 675
39 TraesCS1A01G126700 chr6B 86.893 618 55 11 2 596 612595941 612596555 0.000000e+00 669
40 TraesCS1A01G126700 chr6B 93.857 293 17 1 1932 2224 274389329 274389620 7.910000e-120 440
41 TraesCS1A01G126700 chr7A 86.201 616 63 10 2 596 518334826 518335440 0.000000e+00 647
42 TraesCS1A01G126700 chr7A 99.468 188 1 0 2224 2411 276273164 276272977 2.300000e-90 342
43 TraesCS1A01G126700 chr7A 99.468 188 1 0 2224 2411 549575673 549575486 2.300000e-90 342
44 TraesCS1A01G126700 chr7A 99.468 188 1 0 2224 2411 619351636 619351449 2.300000e-90 342
45 TraesCS1A01G126700 chr2B 86.224 617 61 12 2 596 500216863 500217477 0.000000e+00 647
46 TraesCS1A01G126700 chr2B 84.226 672 78 16 1 648 799660728 799661395 1.570000e-176 628
47 TraesCS1A01G126700 chr2B 87.213 305 35 3 677 980 381382909 381383210 6.380000e-91 344
48 TraesCS1A01G126700 chr1B 85.622 619 64 11 2 596 233637401 233638018 5.660000e-176 627
49 TraesCS1A01G126700 chr4B 85.684 468 58 9 2 463 371280970 371280506 3.600000e-133 484
50 TraesCS1A01G126700 chr6D 92.424 264 16 2 1928 2191 149886039 149886298 8.140000e-100 374
51 TraesCS1A01G126700 chr6D 81.236 453 71 7 1014 1466 149885609 149886047 1.060000e-93 353
52 TraesCS1A01G126700 chr4A 89.597 298 24 1 1934 2224 541425872 541425575 2.930000e-99 372


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 TraesCS1A01G126700 chr1A 152712891 152715301 2410 True 4453.0 4453 100.0000 1 2411 1 chr1A.!!$R1 2410
1 TraesCS1A01G126700 chr1A 494700248 494701694 1446 True 972.0 1482 91.0635 677 2224 2 chr1A.!!$R2 1547
2 TraesCS1A01G126700 chr3B 499926747 499928302 1555 True 2074.0 2074 90.8680 677 2224 1 chr3B.!!$R2 1547
3 TraesCS1A01G126700 chr3B 675857348 675857968 620 True 651.0 651 86.1960 3 602 1 chr3B.!!$R3 599
4 TraesCS1A01G126700 chr3B 815401222 815401931 709 False 647.0 647 83.1460 677 1386 1 chr3B.!!$F1 709
5 TraesCS1A01G126700 chr3B 192368745 192369362 617 True 625.0 625 85.4840 2 599 1 chr3B.!!$R1 597
6 TraesCS1A01G126700 chr3B 815429462 815430079 617 False 259.0 366 90.8395 1799 2224 2 chr3B.!!$F2 425
7 TraesCS1A01G126700 chr3A 340259196 340260311 1115 False 1559.0 1559 91.8820 674 1792 1 chr3A.!!$F1 1118
8 TraesCS1A01G126700 chr3A 599891406 599892294 888 True 1258.0 1258 92.1700 900 1792 1 chr3A.!!$R3 892
9 TraesCS1A01G126700 chr3A 17493335 17494222 887 True 1229.0 1229 91.6010 900 1792 1 chr3A.!!$R1 892
10 TraesCS1A01G126700 chr3A 585289999 585290620 621 True 603.0 603 84.7760 2 602 1 chr3A.!!$R2 600
11 TraesCS1A01G126700 chr6A 60605473 60606806 1333 True 943.5 1404 92.1890 794 2224 2 chr6A.!!$R6 1430
12 TraesCS1A01G126700 chr6A 294612888 294613451 563 False 542.0 542 85.1330 154 680 1 chr6A.!!$F1 526
13 TraesCS1A01G126700 chr5A 536904941 536905686 745 False 977.0 977 90.3610 677 1421 1 chr5A.!!$F2 744
14 TraesCS1A01G126700 chr3D 418808290 418809008 718 False 793.0 793 87.5000 1 680 1 chr3D.!!$F1 679
15 TraesCS1A01G126700 chr2D 197218295 197219012 717 False 793.0 793 87.5000 1 680 1 chr2D.!!$F1 679
16 TraesCS1A01G126700 chr2D 550800358 550801075 717 False 688.0 688 84.8400 1 680 1 chr2D.!!$F2 679
17 TraesCS1A01G126700 chr1D 223144995 223145710 715 True 791.0 791 87.4650 1 680 1 chr1D.!!$R2 679
18 TraesCS1A01G126700 chr1D 79605212 79605926 714 False 780.0 780 87.2910 6 680 1 chr1D.!!$F1 674
19 TraesCS1A01G126700 chr2A 521725033 521725744 711 True 749.0 749 86.5360 7 680 1 chr2A.!!$R1 673
20 TraesCS1A01G126700 chr4D 385820472 385821131 659 False 741.0 741 87.4060 3 648 1 chr4D.!!$F2 645
21 TraesCS1A01G126700 chr4D 255197272 255197936 664 True 603.0 603 83.5820 2 648 1 chr4D.!!$R1 646
22 TraesCS1A01G126700 chr6B 612595941 612596555 614 False 669.0 669 86.8930 2 596 1 chr6B.!!$F1 594
23 TraesCS1A01G126700 chr6B 274388529 274389620 1091 False 557.5 675 88.2170 677 2224 2 chr6B.!!$F2 1547
24 TraesCS1A01G126700 chr7A 518334826 518335440 614 False 647.0 647 86.2010 2 596 1 chr7A.!!$F1 594
25 TraesCS1A01G126700 chr2B 500216863 500217477 614 False 647.0 647 86.2240 2 596 1 chr2B.!!$F2 594
26 TraesCS1A01G126700 chr2B 799660728 799661395 667 False 628.0 628 84.2260 1 648 1 chr2B.!!$F3 647
27 TraesCS1A01G126700 chr1B 233637401 233638018 617 False 627.0 627 85.6220 2 596 1 chr1B.!!$F1 594
28 TraesCS1A01G126700 chr6D 149885609 149886298 689 False 363.5 374 86.8300 1014 2191 2 chr6D.!!$F1 1177

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
858 927 0.674895 CAAAGCCGGTCTTCCTCCTG 60.675 60.0 1.9 0.0 32.88 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 2667 0.023732 CGAACGTCAAGCATGCGTAG 59.976 55.0 13.01 6.39 37.99 3.51 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
88 89 3.056313 CTTAGCCCTTGCCGCAAGC 62.056 63.158 25.08 16.85 39.85 4.01
133 135 4.963318 ACATCTTTTGTGAGTCTCTGGA 57.037 40.909 0.65 0.00 37.11 3.86
158 160 1.413445 ACCGCACTACCAACACACTAA 59.587 47.619 0.00 0.00 0.00 2.24
176 179 9.034800 ACACACTAATGGTTTGGATATTTGATT 57.965 29.630 0.00 0.00 30.52 2.57
274 278 2.128035 AGCTTAATAGACATCGTGCGC 58.872 47.619 0.00 0.00 0.00 6.09
276 280 1.452025 CTTAATAGACATCGTGCGCCG 59.548 52.381 4.18 8.64 38.13 6.46
277 281 0.937699 TAATAGACATCGTGCGCCGC 60.938 55.000 4.18 0.00 36.19 6.53
330 372 2.573369 GTAGATAGGTCTGCTCACCGA 58.427 52.381 0.00 0.00 41.90 4.69
363 405 1.792757 ATGCAGGAGTTCTTGGGGCA 61.793 55.000 0.00 0.00 0.00 5.36
364 406 1.973812 GCAGGAGTTCTTGGGGCAC 60.974 63.158 0.00 0.00 0.00 5.01
508 569 1.458927 GGGTAAGTTGGTGCACCCT 59.541 57.895 32.62 20.49 46.08 4.34
552 613 1.767759 TAGCCTGTCCTACGGTAACC 58.232 55.000 0.00 0.00 0.00 2.85
580 641 2.296190 TGGAGTTGTATCCCGATCGATG 59.704 50.000 18.66 7.52 38.72 3.84
644 706 2.564062 TCCGGGATTGTTTTCTCGTAGT 59.436 45.455 0.00 0.00 37.93 2.73
717 784 2.870175 AGCGTACATCTAGCTCCTGAT 58.130 47.619 0.00 0.00 36.33 2.90
789 858 2.122056 ACCCCTGGTCTACGCCTT 59.878 61.111 0.00 0.00 0.00 4.35
798 867 0.889306 GTCTACGCCTTGAGGTCACT 59.111 55.000 0.00 0.00 37.57 3.41
802 871 1.376424 CGCCTTGAGGTCACTGCAT 60.376 57.895 0.00 0.00 37.57 3.96
858 927 0.674895 CAAAGCCGGTCTTCCTCCTG 60.675 60.000 1.90 0.00 32.88 3.86
874 943 1.068121 CCTGTCCCCCAAACTCTCTT 58.932 55.000 0.00 0.00 0.00 2.85
930 999 2.112998 CATCCAATCCAAGGCCATTGT 58.887 47.619 5.01 0.00 37.17 2.71
957 1026 1.064537 TGCAGAGATTAATGGCAGCCA 60.065 47.619 18.99 18.99 38.19 4.75
985 1054 4.016706 GCTGCCGGTAGGGTGTGT 62.017 66.667 21.82 0.00 38.44 3.72
1011 1107 0.536687 CTGCATCCATGGAAGGCGAT 60.537 55.000 27.07 7.28 33.21 4.58
1012 1108 0.764271 TGCATCCATGGAAGGCGATA 59.236 50.000 27.07 13.93 33.21 2.92
1019 1115 1.967066 CATGGAAGGCGATAGAGGAGT 59.033 52.381 0.00 0.00 39.76 3.85
1034 1130 1.437986 GAGTAGAAGCCGGCGATGT 59.562 57.895 23.20 15.47 0.00 3.06
1049 1145 0.322816 GATGTCCAGCAAGGCAAGGA 60.323 55.000 0.00 0.00 37.29 3.36
1087 1183 3.047280 GAACACGCGACCATGGCA 61.047 61.111 15.93 0.00 0.00 4.92
1090 1186 3.490759 CACGCGACCATGGCAGAC 61.491 66.667 15.93 0.00 0.00 3.51
1137 1233 3.640407 GCAGCCAGGGTCTGTCCA 61.640 66.667 10.15 0.00 38.11 4.02
1138 1234 3.160585 CAGCCAGGGTCTGTCCAA 58.839 61.111 0.00 0.00 38.11 3.53
1139 1235 1.455849 CAGCCAGGGTCTGTCCAAA 59.544 57.895 0.00 0.00 38.11 3.28
1152 1248 1.272425 TGTCCAAATCCGCCCTCAAAT 60.272 47.619 0.00 0.00 0.00 2.32
1162 1258 1.463674 GCCCTCAAATGTCAATCGGT 58.536 50.000 0.00 0.00 0.00 4.69
1194 1290 0.521735 GCGTCGGAGCCAAAATTTCT 59.478 50.000 0.00 0.00 0.00 2.52
1215 1311 3.581265 AGGTACCTAGAGCTGGTAGAC 57.419 52.381 14.41 0.00 40.32 2.59
1216 1312 2.851194 AGGTACCTAGAGCTGGTAGACA 59.149 50.000 14.41 0.00 40.32 3.41
1325 1421 1.973281 CGACAGGTGCTGGGCAAAT 60.973 57.895 0.00 0.00 41.47 2.32
1333 1429 2.713967 GCTGGGCAAATCGGTGCAT 61.714 57.895 8.54 0.00 46.81 3.96
1480 1576 8.324306 TGAATGAATAATCAAGTCTTGGTCTCT 58.676 33.333 12.66 0.00 39.49 3.10
1503 1599 1.339438 ACGTTGAGGCTTGCATGATCT 60.339 47.619 3.33 0.00 0.00 2.75
1515 1611 4.625972 TGCATGATCTGTTGCAATACAG 57.374 40.909 11.61 11.61 45.30 2.74
1614 1710 4.080356 AGTTGGCTGGATGCAATCTAAGTA 60.080 41.667 0.00 0.00 44.71 2.24
1651 1747 7.431960 TCATTGCAATCTTATCAAATACGTTGC 59.568 33.333 9.53 0.00 40.62 4.17
1698 1794 2.969262 TGGTTGGTAGATGACAGTGTCA 59.031 45.455 27.35 27.35 46.90 3.58
1717 1813 5.910723 GTGTCATCGTTACAATTTTCGGTTT 59.089 36.000 0.00 0.00 0.00 3.27
1725 1821 9.119329 TCGTTACAATTTTCGGTTTCATAATTG 57.881 29.630 0.00 0.00 40.34 2.32
1772 1868 3.991367 AGTCCTGGTCTTTGAAGTTACG 58.009 45.455 0.00 0.00 0.00 3.18
1773 1869 3.640029 AGTCCTGGTCTTTGAAGTTACGA 59.360 43.478 0.00 0.00 0.00 3.43
2034 2355 1.535896 GACGCTCTCATATAGTCCGCA 59.464 52.381 0.00 0.00 0.00 5.69
2225 2546 9.740239 ATTCATGATGCACATTGTTTATTAGTC 57.260 29.630 0.00 0.00 37.07 2.59
2226 2547 8.510243 TCATGATGCACATTGTTTATTAGTCT 57.490 30.769 0.00 0.00 37.07 3.24
2227 2548 8.959548 TCATGATGCACATTGTTTATTAGTCTT 58.040 29.630 0.00 0.00 37.07 3.01
2228 2549 9.016623 CATGATGCACATTGTTTATTAGTCTTG 57.983 33.333 0.00 0.00 37.07 3.02
2229 2550 8.334263 TGATGCACATTGTTTATTAGTCTTGA 57.666 30.769 0.00 0.00 0.00 3.02
2230 2551 8.959548 TGATGCACATTGTTTATTAGTCTTGAT 58.040 29.630 0.00 0.00 0.00 2.57
2234 2555 9.503427 GCACATTGTTTATTAGTCTTGATAACC 57.497 33.333 0.00 0.00 0.00 2.85
2236 2557 9.747898 ACATTGTTTATTAGTCTTGATAACCCA 57.252 29.630 0.00 0.00 0.00 4.51
2238 2559 9.747898 ATTGTTTATTAGTCTTGATAACCCACA 57.252 29.630 0.00 0.00 0.00 4.17
2239 2560 9.575868 TTGTTTATTAGTCTTGATAACCCACAA 57.424 29.630 0.00 0.00 0.00 3.33
2240 2561 9.226606 TGTTTATTAGTCTTGATAACCCACAAG 57.773 33.333 0.00 0.00 43.03 3.16
2241 2562 9.227777 GTTTATTAGTCTTGATAACCCACAAGT 57.772 33.333 0.00 0.00 42.50 3.16
2246 2567 7.125792 AGTCTTGATAACCCACAAGTATAGG 57.874 40.000 0.00 0.00 42.50 2.57
2253 2574 1.002087 CCCACAAGTATAGGGGATCGC 59.998 57.143 0.06 0.06 43.57 4.58
2254 2575 1.691976 CCACAAGTATAGGGGATCGCA 59.308 52.381 12.32 0.00 0.00 5.10
2255 2576 2.104111 CCACAAGTATAGGGGATCGCAA 59.896 50.000 12.32 0.00 0.00 4.85
2256 2577 3.131396 CACAAGTATAGGGGATCGCAAC 58.869 50.000 12.32 4.19 0.00 4.17
2257 2578 2.769663 ACAAGTATAGGGGATCGCAACA 59.230 45.455 12.32 0.00 0.00 3.33
2258 2579 3.181465 ACAAGTATAGGGGATCGCAACAG 60.181 47.826 12.32 4.14 0.00 3.16
2259 2580 2.679082 AGTATAGGGGATCGCAACAGT 58.321 47.619 12.32 0.00 0.00 3.55
2260 2581 3.039011 AGTATAGGGGATCGCAACAGTT 58.961 45.455 12.32 0.00 0.00 3.16
2261 2582 3.454812 AGTATAGGGGATCGCAACAGTTT 59.545 43.478 12.32 0.00 0.00 2.66
2262 2583 2.871096 TAGGGGATCGCAACAGTTTT 57.129 45.000 12.32 0.00 0.00 2.43
2263 2584 1.995376 AGGGGATCGCAACAGTTTTT 58.005 45.000 12.32 0.00 0.00 1.94
2264 2585 1.613437 AGGGGATCGCAACAGTTTTTG 59.387 47.619 12.32 0.00 0.00 2.44
2265 2586 1.611491 GGGGATCGCAACAGTTTTTGA 59.389 47.619 12.32 0.00 0.00 2.69
2266 2587 2.231235 GGGGATCGCAACAGTTTTTGAT 59.769 45.455 12.32 0.00 0.00 2.57
2267 2588 3.442273 GGGGATCGCAACAGTTTTTGATA 59.558 43.478 12.32 0.00 0.00 2.15
2268 2589 4.082463 GGGGATCGCAACAGTTTTTGATAA 60.082 41.667 12.32 0.00 0.00 1.75
2269 2590 5.095490 GGGATCGCAACAGTTTTTGATAAG 58.905 41.667 4.64 0.00 0.00 1.73
2270 2591 5.335661 GGGATCGCAACAGTTTTTGATAAGT 60.336 40.000 4.64 0.00 0.00 2.24
2271 2592 6.128117 GGGATCGCAACAGTTTTTGATAAGTA 60.128 38.462 4.64 0.00 0.00 2.24
2272 2593 7.302524 GGATCGCAACAGTTTTTGATAAGTAA 58.697 34.615 0.00 0.00 0.00 2.24
2273 2594 7.481798 GGATCGCAACAGTTTTTGATAAGTAAG 59.518 37.037 0.00 0.00 0.00 2.34
2274 2595 7.485418 TCGCAACAGTTTTTGATAAGTAAGA 57.515 32.000 0.00 0.00 0.00 2.10
2275 2596 7.572759 TCGCAACAGTTTTTGATAAGTAAGAG 58.427 34.615 0.00 0.00 0.00 2.85
2276 2597 7.225931 TCGCAACAGTTTTTGATAAGTAAGAGT 59.774 33.333 0.00 0.00 0.00 3.24
2277 2598 7.321271 CGCAACAGTTTTTGATAAGTAAGAGTG 59.679 37.037 0.00 0.00 0.00 3.51
2278 2599 8.129211 GCAACAGTTTTTGATAAGTAAGAGTGT 58.871 33.333 0.00 0.00 0.00 3.55
2279 2600 9.651718 CAACAGTTTTTGATAAGTAAGAGTGTC 57.348 33.333 0.00 0.00 0.00 3.67
2280 2601 8.073355 ACAGTTTTTGATAAGTAAGAGTGTCG 57.927 34.615 0.00 0.00 0.00 4.35
2281 2602 7.924412 ACAGTTTTTGATAAGTAAGAGTGTCGA 59.076 33.333 0.00 0.00 0.00 4.20
2282 2603 8.761497 CAGTTTTTGATAAGTAAGAGTGTCGAA 58.239 33.333 0.00 0.00 0.00 3.71
2283 2604 8.762426 AGTTTTTGATAAGTAAGAGTGTCGAAC 58.238 33.333 0.00 0.00 0.00 3.95
2284 2605 7.647907 TTTTGATAAGTAAGAGTGTCGAACC 57.352 36.000 0.00 0.00 0.00 3.62
2285 2606 5.320549 TGATAAGTAAGAGTGTCGAACCC 57.679 43.478 0.00 0.00 0.00 4.11
2286 2607 4.768448 TGATAAGTAAGAGTGTCGAACCCA 59.232 41.667 0.00 0.00 0.00 4.51
2287 2608 5.244402 TGATAAGTAAGAGTGTCGAACCCAA 59.756 40.000 0.00 0.00 0.00 4.12
2288 2609 3.382048 AGTAAGAGTGTCGAACCCAAC 57.618 47.619 0.00 0.00 0.00 3.77
2289 2610 2.056577 GTAAGAGTGTCGAACCCAACG 58.943 52.381 0.00 0.00 0.00 4.10
2290 2611 0.748450 AAGAGTGTCGAACCCAACGA 59.252 50.000 0.00 0.00 37.43 3.85
2291 2612 0.314302 AGAGTGTCGAACCCAACGAG 59.686 55.000 0.00 0.00 40.37 4.18
2292 2613 0.666577 GAGTGTCGAACCCAACGAGG 60.667 60.000 0.00 0.00 40.37 4.63
2293 2614 1.111116 AGTGTCGAACCCAACGAGGA 61.111 55.000 0.00 0.00 41.22 3.71
2294 2615 0.666577 GTGTCGAACCCAACGAGGAG 60.667 60.000 0.00 0.00 41.22 3.69
2295 2616 1.737008 GTCGAACCCAACGAGGAGC 60.737 63.158 0.00 0.00 41.22 4.70
2296 2617 1.906824 TCGAACCCAACGAGGAGCT 60.907 57.895 0.00 0.00 41.22 4.09
2297 2618 0.609957 TCGAACCCAACGAGGAGCTA 60.610 55.000 0.00 0.00 41.22 3.32
2298 2619 0.245539 CGAACCCAACGAGGAGCTAA 59.754 55.000 0.00 0.00 41.22 3.09
2299 2620 1.337447 CGAACCCAACGAGGAGCTAAA 60.337 52.381 0.00 0.00 41.22 1.85
2300 2621 2.347731 GAACCCAACGAGGAGCTAAAG 58.652 52.381 0.00 0.00 41.22 1.85
2301 2622 0.613777 ACCCAACGAGGAGCTAAAGG 59.386 55.000 0.00 0.00 41.22 3.11
2302 2623 0.613777 CCCAACGAGGAGCTAAAGGT 59.386 55.000 0.00 0.00 41.22 3.50
2303 2624 1.829222 CCCAACGAGGAGCTAAAGGTA 59.171 52.381 0.00 0.00 41.22 3.08
2304 2625 2.159085 CCCAACGAGGAGCTAAAGGTAG 60.159 54.545 0.00 0.00 41.22 3.18
2305 2626 2.758979 CCAACGAGGAGCTAAAGGTAGA 59.241 50.000 0.00 0.00 41.22 2.59
2306 2627 3.194968 CCAACGAGGAGCTAAAGGTAGAA 59.805 47.826 0.00 0.00 41.22 2.10
2307 2628 4.174762 CAACGAGGAGCTAAAGGTAGAAC 58.825 47.826 0.00 0.00 0.00 3.01
2308 2629 3.428532 ACGAGGAGCTAAAGGTAGAACA 58.571 45.455 0.00 0.00 0.00 3.18
2309 2630 3.830755 ACGAGGAGCTAAAGGTAGAACAA 59.169 43.478 0.00 0.00 0.00 2.83
2310 2631 4.282703 ACGAGGAGCTAAAGGTAGAACAAA 59.717 41.667 0.00 0.00 0.00 2.83
2311 2632 5.046520 ACGAGGAGCTAAAGGTAGAACAAAT 60.047 40.000 0.00 0.00 0.00 2.32
2312 2633 6.154021 ACGAGGAGCTAAAGGTAGAACAAATA 59.846 38.462 0.00 0.00 0.00 1.40
2313 2634 7.147707 ACGAGGAGCTAAAGGTAGAACAAATAT 60.148 37.037 0.00 0.00 0.00 1.28
2314 2635 7.711339 CGAGGAGCTAAAGGTAGAACAAATATT 59.289 37.037 0.00 0.00 0.00 1.28
2315 2636 8.966069 AGGAGCTAAAGGTAGAACAAATATTC 57.034 34.615 0.00 0.00 0.00 1.75
2316 2637 7.993758 AGGAGCTAAAGGTAGAACAAATATTCC 59.006 37.037 0.00 0.00 0.00 3.01
2317 2638 7.228906 GGAGCTAAAGGTAGAACAAATATTCCC 59.771 40.741 0.00 0.00 0.00 3.97
2318 2639 7.873195 AGCTAAAGGTAGAACAAATATTCCCT 58.127 34.615 0.00 0.00 0.00 4.20
2319 2640 7.993758 AGCTAAAGGTAGAACAAATATTCCCTC 59.006 37.037 0.00 0.00 0.00 4.30
2320 2641 7.773690 GCTAAAGGTAGAACAAATATTCCCTCA 59.226 37.037 0.00 0.00 0.00 3.86
2321 2642 9.681062 CTAAAGGTAGAACAAATATTCCCTCAA 57.319 33.333 0.00 0.00 0.00 3.02
2322 2643 8.581253 AAAGGTAGAACAAATATTCCCTCAAG 57.419 34.615 0.00 0.00 0.00 3.02
2323 2644 7.272144 AGGTAGAACAAATATTCCCTCAAGT 57.728 36.000 0.00 0.00 0.00 3.16
2324 2645 7.699878 AGGTAGAACAAATATTCCCTCAAGTT 58.300 34.615 0.00 0.00 0.00 2.66
2325 2646 7.829706 AGGTAGAACAAATATTCCCTCAAGTTC 59.170 37.037 0.00 0.00 35.58 3.01
2326 2647 7.829706 GGTAGAACAAATATTCCCTCAAGTTCT 59.170 37.037 0.00 0.00 44.45 3.01
2327 2648 9.886132 GTAGAACAAATATTCCCTCAAGTTCTA 57.114 33.333 0.00 0.00 42.83 2.10
2329 2650 9.620259 AGAACAAATATTCCCTCAAGTTCTATC 57.380 33.333 0.00 0.00 41.64 2.08
2330 2651 8.438676 AACAAATATTCCCTCAAGTTCTATCG 57.561 34.615 0.00 0.00 0.00 2.92
2331 2652 7.792032 ACAAATATTCCCTCAAGTTCTATCGA 58.208 34.615 0.00 0.00 0.00 3.59
2332 2653 7.711339 ACAAATATTCCCTCAAGTTCTATCGAC 59.289 37.037 0.00 0.00 0.00 4.20
2333 2654 4.674281 ATTCCCTCAAGTTCTATCGACC 57.326 45.455 0.00 0.00 0.00 4.79
2334 2655 3.095912 TCCCTCAAGTTCTATCGACCA 57.904 47.619 0.00 0.00 0.00 4.02
2335 2656 2.758979 TCCCTCAAGTTCTATCGACCAC 59.241 50.000 0.00 0.00 0.00 4.16
2336 2657 2.159085 CCCTCAAGTTCTATCGACCACC 60.159 54.545 0.00 0.00 0.00 4.61
2337 2658 2.479730 CCTCAAGTTCTATCGACCACCG 60.480 54.545 0.00 0.00 40.25 4.94
2347 2668 1.830279 TCGACCACCGATACAACTCT 58.170 50.000 0.00 0.00 43.23 3.24
2348 2669 2.989909 TCGACCACCGATACAACTCTA 58.010 47.619 0.00 0.00 43.23 2.43
2349 2670 2.679837 TCGACCACCGATACAACTCTAC 59.320 50.000 0.00 0.00 43.23 2.59
2350 2671 2.538333 CGACCACCGATACAACTCTACG 60.538 54.545 0.00 0.00 41.76 3.51
2351 2672 1.133790 ACCACCGATACAACTCTACGC 59.866 52.381 0.00 0.00 0.00 4.42
2352 2673 1.133598 CCACCGATACAACTCTACGCA 59.866 52.381 0.00 0.00 0.00 5.24
2353 2674 2.223735 CCACCGATACAACTCTACGCAT 60.224 50.000 0.00 0.00 0.00 4.73
2354 2675 2.789339 CACCGATACAACTCTACGCATG 59.211 50.000 0.00 0.00 0.00 4.06
2355 2676 1.787155 CCGATACAACTCTACGCATGC 59.213 52.381 7.91 7.91 0.00 4.06
2356 2677 2.543861 CCGATACAACTCTACGCATGCT 60.544 50.000 17.13 5.50 0.00 3.79
2357 2678 3.116300 CGATACAACTCTACGCATGCTT 58.884 45.455 17.13 9.37 0.00 3.91
2358 2679 3.060940 CGATACAACTCTACGCATGCTTG 60.061 47.826 17.13 14.23 0.00 4.01
2359 2680 2.455674 ACAACTCTACGCATGCTTGA 57.544 45.000 17.13 9.76 0.00 3.02
2360 2681 2.069273 ACAACTCTACGCATGCTTGAC 58.931 47.619 17.13 0.00 0.00 3.18
2361 2682 1.059692 CAACTCTACGCATGCTTGACG 59.940 52.381 17.13 8.99 0.00 4.35
2362 2683 0.243907 ACTCTACGCATGCTTGACGT 59.756 50.000 17.13 19.73 38.50 4.34
2363 2684 1.336887 ACTCTACGCATGCTTGACGTT 60.337 47.619 17.13 10.04 37.05 3.99
2364 2685 1.321743 CTCTACGCATGCTTGACGTTC 59.678 52.381 17.13 0.00 37.05 3.95
2365 2686 0.023732 CTACGCATGCTTGACGTTCG 59.976 55.000 17.13 10.03 37.05 3.95
2366 2687 1.951181 TACGCATGCTTGACGTTCGC 61.951 55.000 17.13 0.00 37.05 4.70
2367 2688 2.863153 GCATGCTTGACGTTCGCT 59.137 55.556 11.37 0.00 0.00 4.93
2368 2689 1.207593 GCATGCTTGACGTTCGCTT 59.792 52.632 11.37 0.00 0.00 4.68
2369 2690 0.385974 GCATGCTTGACGTTCGCTTT 60.386 50.000 11.37 0.00 0.00 3.51
2370 2691 1.136085 GCATGCTTGACGTTCGCTTTA 60.136 47.619 11.37 0.00 0.00 1.85
2371 2692 2.495939 CATGCTTGACGTTCGCTTTAC 58.504 47.619 0.00 0.00 0.00 2.01
2372 2693 0.863144 TGCTTGACGTTCGCTTTACC 59.137 50.000 0.00 0.00 0.00 2.85
2373 2694 1.145803 GCTTGACGTTCGCTTTACCT 58.854 50.000 0.00 0.00 0.00 3.08
2374 2695 2.288334 TGCTTGACGTTCGCTTTACCTA 60.288 45.455 0.00 0.00 0.00 3.08
2375 2696 2.344741 GCTTGACGTTCGCTTTACCTAG 59.655 50.000 0.00 0.00 0.00 3.02
2376 2697 3.829948 CTTGACGTTCGCTTTACCTAGA 58.170 45.455 0.00 0.00 0.00 2.43
2377 2698 3.921119 TGACGTTCGCTTTACCTAGAA 57.079 42.857 0.00 0.00 0.00 2.10
2378 2699 3.568538 TGACGTTCGCTTTACCTAGAAC 58.431 45.455 0.00 0.00 39.46 3.01
2379 2700 3.004629 TGACGTTCGCTTTACCTAGAACA 59.995 43.478 7.74 0.00 42.01 3.18
2380 2701 3.981211 ACGTTCGCTTTACCTAGAACAA 58.019 40.909 7.74 0.00 42.01 2.83
2381 2702 3.985925 ACGTTCGCTTTACCTAGAACAAG 59.014 43.478 7.74 0.00 42.01 3.16
2382 2703 3.985925 CGTTCGCTTTACCTAGAACAAGT 59.014 43.478 7.74 0.00 42.01 3.16
2383 2704 5.156355 CGTTCGCTTTACCTAGAACAAGTA 58.844 41.667 7.74 0.00 42.01 2.24
2384 2705 5.803967 CGTTCGCTTTACCTAGAACAAGTAT 59.196 40.000 7.74 0.00 42.01 2.12
2385 2706 6.237490 CGTTCGCTTTACCTAGAACAAGTATG 60.237 42.308 7.74 0.00 42.01 2.39
2386 2707 6.519679 TCGCTTTACCTAGAACAAGTATGA 57.480 37.500 0.00 0.00 0.00 2.15
2387 2708 6.927416 TCGCTTTACCTAGAACAAGTATGAA 58.073 36.000 0.00 0.00 0.00 2.57
2388 2709 7.380536 TCGCTTTACCTAGAACAAGTATGAAA 58.619 34.615 0.00 0.00 0.00 2.69
2389 2710 7.330208 TCGCTTTACCTAGAACAAGTATGAAAC 59.670 37.037 0.00 0.00 0.00 2.78
2390 2711 7.331193 CGCTTTACCTAGAACAAGTATGAAACT 59.669 37.037 0.00 0.00 41.49 2.66
2391 2712 9.649167 GCTTTACCTAGAACAAGTATGAAACTA 57.351 33.333 0.00 0.00 37.50 2.24
2396 2717 9.091220 ACCTAGAACAAGTATGAAACTAGAAGT 57.909 33.333 0.00 0.00 37.50 3.01
2409 2730 8.015185 TGAAACTAGAAGTACTTTGTAGGTGT 57.985 34.615 21.29 11.44 37.05 4.16
2410 2731 8.480501 TGAAACTAGAAGTACTTTGTAGGTGTT 58.519 33.333 21.29 15.01 37.05 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 134 1.076332 GTTGGTAGTGCGGTCACATC 58.924 55.000 5.59 0.00 45.49 3.06
133 135 0.394938 TGTTGGTAGTGCGGTCACAT 59.605 50.000 5.59 0.00 45.49 3.21
158 160 5.536161 CCCTCGAATCAAATATCCAAACCAT 59.464 40.000 0.00 0.00 0.00 3.55
274 278 3.890674 GCTTACCAGTCCAAGCGG 58.109 61.111 0.00 0.00 37.96 5.52
276 280 0.036875 AGGTGCTTACCAGTCCAAGC 59.963 55.000 0.00 0.00 45.90 4.01
277 281 2.427506 GAAGGTGCTTACCAGTCCAAG 58.572 52.381 0.00 0.00 0.00 3.61
330 372 4.341502 GCATGTTGCGTTGGCGGT 62.342 61.111 0.00 0.00 44.10 5.68
363 405 2.227036 CCCAGGGTCTTGAGCCAGT 61.227 63.158 19.28 0.00 0.00 4.00
364 406 2.673523 CCCAGGGTCTTGAGCCAG 59.326 66.667 19.28 12.06 0.00 4.85
463 508 2.605097 GCTCGATTAACTCCGGCTAGAC 60.605 54.545 0.00 0.00 0.00 2.59
464 509 1.607628 GCTCGATTAACTCCGGCTAGA 59.392 52.381 0.00 0.00 0.00 2.43
465 510 1.663445 CGCTCGATTAACTCCGGCTAG 60.663 57.143 0.00 0.00 0.00 3.42
466 511 0.309922 CGCTCGATTAACTCCGGCTA 59.690 55.000 0.00 0.00 0.00 3.93
508 569 4.635765 CGATAGATGTTTTCTTCCCTGCAA 59.364 41.667 0.00 0.00 35.79 4.08
552 613 2.618053 GGGATACAACTCCAAGTGTCG 58.382 52.381 0.00 0.00 37.01 4.35
580 641 3.373439 CCTCAGCATCAAGTTCTAGTTGC 59.627 47.826 0.00 0.00 0.00 4.17
608 670 1.824230 CCCGGAGCCATCATTTTCAAA 59.176 47.619 0.73 0.00 0.00 2.69
644 706 1.198713 GCCCAGAGATCACTTCCTCA 58.801 55.000 0.00 0.00 32.07 3.86
743 810 4.815973 TACCAGCGGGGGAGCCAT 62.816 66.667 8.08 0.00 42.91 4.40
789 858 1.216444 GCTCGATGCAGTGACCTCA 59.784 57.895 0.00 0.00 42.31 3.86
802 871 2.488355 GATTGGGTCGTCGCTCGA 59.512 61.111 0.00 0.00 46.83 4.04
858 927 1.279558 GAGGAAGAGAGTTTGGGGGAC 59.720 57.143 0.00 0.00 0.00 4.46
874 943 1.054406 GTGGGATTGGATCGGGAGGA 61.054 60.000 0.00 0.00 0.00 3.71
930 999 3.633525 GCCATTAATCTCTGCATGACCAA 59.366 43.478 0.00 0.00 0.00 3.67
957 1026 1.424638 ACCGGCAGCTTATATGGACT 58.575 50.000 0.00 0.00 0.00 3.85
985 1054 0.758123 TCCATGGATGCAGTGCGATA 59.242 50.000 11.44 0.00 0.00 2.92
1011 1107 0.818445 CGCCGGCTTCTACTCCTCTA 60.818 60.000 26.68 0.00 0.00 2.43
1012 1108 2.122167 CGCCGGCTTCTACTCCTCT 61.122 63.158 26.68 0.00 0.00 3.69
1019 1115 2.016393 CTGGACATCGCCGGCTTCTA 62.016 60.000 26.68 12.03 0.00 2.10
1034 1130 2.032528 CGTCCTTGCCTTGCTGGA 59.967 61.111 0.49 0.00 38.35 3.86
1087 1183 0.399233 GGGCCTACAGATCCAGGTCT 60.399 60.000 0.84 0.00 36.73 3.85
1090 1186 1.467678 CGAGGGCCTACAGATCCAGG 61.468 65.000 5.73 1.98 34.85 4.45
1129 1225 0.744771 GAGGGCGGATTTGGACAGAC 60.745 60.000 0.00 0.00 0.00 3.51
1132 1228 0.111446 TTTGAGGGCGGATTTGGACA 59.889 50.000 0.00 0.00 0.00 4.02
1137 1233 2.214376 TGACATTTGAGGGCGGATTT 57.786 45.000 0.00 0.00 0.00 2.17
1138 1234 2.214376 TTGACATTTGAGGGCGGATT 57.786 45.000 0.00 0.00 0.00 3.01
1139 1235 2.301346 GATTGACATTTGAGGGCGGAT 58.699 47.619 0.00 0.00 0.00 4.18
1152 1248 2.431771 CGCCGACACCGATTGACA 60.432 61.111 0.00 0.00 38.22 3.58
1194 1290 4.042884 TGTCTACCAGCTCTAGGTACCTA 58.957 47.826 20.60 20.60 40.54 3.08
1309 1405 1.973281 CGATTTGCCCAGCACCTGT 60.973 57.895 0.00 0.00 38.71 4.00
1325 1421 4.758251 CACCTGCCGATGCACCGA 62.758 66.667 0.00 0.00 44.23 4.69
1480 1576 2.499197 TCATGCAAGCCTCAACGTTAA 58.501 42.857 0.00 0.00 0.00 2.01
1503 1599 3.605634 AGATAACCGCTGTATTGCAACA 58.394 40.909 0.00 0.00 0.00 3.33
1515 1611 4.025979 CGGACTAATTGACAAGATAACCGC 60.026 45.833 11.00 0.00 0.00 5.68
1553 1649 8.746922 TGACAAGATTAAACTGATTTGCATTC 57.253 30.769 0.00 0.00 0.00 2.67
1554 1650 9.199982 CTTGACAAGATTAAACTGATTTGCATT 57.800 29.630 9.76 0.00 0.00 3.56
1589 1685 3.370840 AGATTGCATCCAGCCAACTAA 57.629 42.857 0.00 0.00 44.83 2.24
1651 1747 4.627611 ACGAATCAAAGATTGCATCAGG 57.372 40.909 0.00 0.00 0.00 3.86
1698 1794 9.849166 AATTATGAAACCGAAAATTGTAACGAT 57.151 25.926 0.00 0.00 0.00 3.73
1699 1795 9.119329 CAATTATGAAACCGAAAATTGTAACGA 57.881 29.630 0.00 0.00 34.41 3.85
1700 1796 8.369588 CCAATTATGAAACCGAAAATTGTAACG 58.630 33.333 0.00 0.00 36.34 3.18
1738 1834 4.039973 AGACCAGGACTTATTGTTCGTTCA 59.960 41.667 0.00 0.00 0.00 3.18
1962 2235 7.936301 TGTAATATTAGATGTGGTGCAATGCTA 59.064 33.333 6.82 0.00 0.00 3.49
2030 2351 8.834444 CCTAATGTTTTAGACTGCGATTGCGG 62.834 46.154 12.54 12.54 41.28 5.69
2034 2355 7.103641 TCTTCCTAATGTTTTAGACTGCGATT 58.896 34.615 0.00 0.00 37.59 3.34
2224 2545 5.368523 CCCCTATACTTGTGGGTTATCAAGA 59.631 44.000 11.07 0.00 42.22 3.02
2225 2546 5.368523 TCCCCTATACTTGTGGGTTATCAAG 59.631 44.000 0.00 0.00 44.29 3.02
2226 2547 5.290335 TCCCCTATACTTGTGGGTTATCAA 58.710 41.667 0.00 0.00 39.31 2.57
2227 2548 4.898268 TCCCCTATACTTGTGGGTTATCA 58.102 43.478 0.00 0.00 39.31 2.15
2228 2549 5.337330 CGATCCCCTATACTTGTGGGTTATC 60.337 48.000 0.00 0.00 39.31 1.75
2229 2550 4.530946 CGATCCCCTATACTTGTGGGTTAT 59.469 45.833 0.00 0.00 39.31 1.89
2230 2551 3.899360 CGATCCCCTATACTTGTGGGTTA 59.101 47.826 0.00 0.00 39.31 2.85
2231 2552 2.704065 CGATCCCCTATACTTGTGGGTT 59.296 50.000 0.00 0.00 39.31 4.11
2232 2553 2.326428 CGATCCCCTATACTTGTGGGT 58.674 52.381 0.00 0.00 39.31 4.51
2233 2554 1.002087 GCGATCCCCTATACTTGTGGG 59.998 57.143 0.00 0.00 40.59 4.61
2234 2555 1.691976 TGCGATCCCCTATACTTGTGG 59.308 52.381 0.00 0.00 0.00 4.17
2235 2556 3.131396 GTTGCGATCCCCTATACTTGTG 58.869 50.000 0.00 0.00 0.00 3.33
2236 2557 2.769663 TGTTGCGATCCCCTATACTTGT 59.230 45.455 0.00 0.00 0.00 3.16
2237 2558 3.181465 ACTGTTGCGATCCCCTATACTTG 60.181 47.826 0.00 0.00 0.00 3.16
2238 2559 3.039011 ACTGTTGCGATCCCCTATACTT 58.961 45.455 0.00 0.00 0.00 2.24
2239 2560 2.679082 ACTGTTGCGATCCCCTATACT 58.321 47.619 0.00 0.00 0.00 2.12
2240 2561 3.470645 AACTGTTGCGATCCCCTATAC 57.529 47.619 0.00 0.00 0.00 1.47
2241 2562 4.497291 AAAACTGTTGCGATCCCCTATA 57.503 40.909 0.00 0.00 0.00 1.31
2242 2563 3.366052 AAAACTGTTGCGATCCCCTAT 57.634 42.857 0.00 0.00 0.00 2.57
2243 2564 2.817258 CAAAAACTGTTGCGATCCCCTA 59.183 45.455 0.00 0.00 0.00 3.53
2244 2565 1.613437 CAAAAACTGTTGCGATCCCCT 59.387 47.619 0.00 0.00 0.00 4.79
2245 2566 1.611491 TCAAAAACTGTTGCGATCCCC 59.389 47.619 0.00 0.00 0.00 4.81
2246 2567 3.575965 ATCAAAAACTGTTGCGATCCC 57.424 42.857 0.00 0.00 0.00 3.85
2247 2568 5.699839 ACTTATCAAAAACTGTTGCGATCC 58.300 37.500 0.00 0.00 0.00 3.36
2248 2569 8.227791 TCTTACTTATCAAAAACTGTTGCGATC 58.772 33.333 0.00 0.00 0.00 3.69
2249 2570 8.094798 TCTTACTTATCAAAAACTGTTGCGAT 57.905 30.769 0.00 0.00 0.00 4.58
2250 2571 7.225931 ACTCTTACTTATCAAAAACTGTTGCGA 59.774 33.333 0.00 0.00 0.00 5.10
2251 2572 7.321271 CACTCTTACTTATCAAAAACTGTTGCG 59.679 37.037 0.00 0.00 0.00 4.85
2252 2573 8.129211 ACACTCTTACTTATCAAAAACTGTTGC 58.871 33.333 0.00 0.00 0.00 4.17
2253 2574 9.651718 GACACTCTTACTTATCAAAAACTGTTG 57.348 33.333 0.00 0.00 0.00 3.33
2254 2575 8.548721 CGACACTCTTACTTATCAAAAACTGTT 58.451 33.333 0.00 0.00 0.00 3.16
2255 2576 7.924412 TCGACACTCTTACTTATCAAAAACTGT 59.076 33.333 0.00 0.00 0.00 3.55
2256 2577 8.294341 TCGACACTCTTACTTATCAAAAACTG 57.706 34.615 0.00 0.00 0.00 3.16
2257 2578 8.762426 GTTCGACACTCTTACTTATCAAAAACT 58.238 33.333 0.00 0.00 0.00 2.66
2258 2579 8.008279 GGTTCGACACTCTTACTTATCAAAAAC 58.992 37.037 0.00 0.00 0.00 2.43
2259 2580 7.172019 GGGTTCGACACTCTTACTTATCAAAAA 59.828 37.037 0.00 0.00 0.00 1.94
2260 2581 6.647895 GGGTTCGACACTCTTACTTATCAAAA 59.352 38.462 0.00 0.00 0.00 2.44
2261 2582 6.161381 GGGTTCGACACTCTTACTTATCAAA 58.839 40.000 0.00 0.00 0.00 2.69
2262 2583 5.244402 TGGGTTCGACACTCTTACTTATCAA 59.756 40.000 0.00 0.00 0.00 2.57
2263 2584 4.768448 TGGGTTCGACACTCTTACTTATCA 59.232 41.667 0.00 0.00 0.00 2.15
2264 2585 5.320549 TGGGTTCGACACTCTTACTTATC 57.679 43.478 0.00 0.00 0.00 1.75
2265 2586 5.476614 GTTGGGTTCGACACTCTTACTTAT 58.523 41.667 0.00 0.00 0.00 1.73
2266 2587 4.557296 CGTTGGGTTCGACACTCTTACTTA 60.557 45.833 0.00 0.00 0.00 2.24
2267 2588 3.725490 GTTGGGTTCGACACTCTTACTT 58.275 45.455 0.00 0.00 0.00 2.24
2268 2589 2.288030 CGTTGGGTTCGACACTCTTACT 60.288 50.000 0.00 0.00 0.00 2.24
2269 2590 2.056577 CGTTGGGTTCGACACTCTTAC 58.943 52.381 0.00 0.00 0.00 2.34
2270 2591 1.955778 TCGTTGGGTTCGACACTCTTA 59.044 47.619 0.00 0.00 32.30 2.10
2271 2592 0.748450 TCGTTGGGTTCGACACTCTT 59.252 50.000 0.00 0.00 32.30 2.85
2272 2593 0.314302 CTCGTTGGGTTCGACACTCT 59.686 55.000 0.00 0.00 33.71 3.24
2273 2594 0.666577 CCTCGTTGGGTTCGACACTC 60.667 60.000 0.00 0.00 33.71 3.51
2274 2595 1.111116 TCCTCGTTGGGTTCGACACT 61.111 55.000 0.00 0.00 36.20 3.55
2275 2596 0.666577 CTCCTCGTTGGGTTCGACAC 60.667 60.000 0.00 0.00 36.20 3.67
2276 2597 1.663739 CTCCTCGTTGGGTTCGACA 59.336 57.895 0.00 0.00 36.20 4.35
2277 2598 1.737008 GCTCCTCGTTGGGTTCGAC 60.737 63.158 0.00 0.00 36.20 4.20
2278 2599 0.609957 TAGCTCCTCGTTGGGTTCGA 60.610 55.000 0.00 0.00 36.20 3.71
2279 2600 0.245539 TTAGCTCCTCGTTGGGTTCG 59.754 55.000 0.00 0.00 36.20 3.95
2280 2601 2.347731 CTTTAGCTCCTCGTTGGGTTC 58.652 52.381 0.00 0.00 36.20 3.62
2281 2602 1.003233 CCTTTAGCTCCTCGTTGGGTT 59.997 52.381 0.00 0.00 36.20 4.11
2282 2603 0.613777 CCTTTAGCTCCTCGTTGGGT 59.386 55.000 0.00 0.00 36.20 4.51
2283 2604 0.613777 ACCTTTAGCTCCTCGTTGGG 59.386 55.000 0.00 0.00 36.20 4.12
2284 2605 2.758979 TCTACCTTTAGCTCCTCGTTGG 59.241 50.000 0.00 0.00 37.10 3.77
2285 2606 4.174762 GTTCTACCTTTAGCTCCTCGTTG 58.825 47.826 0.00 0.00 0.00 4.10
2286 2607 3.830755 TGTTCTACCTTTAGCTCCTCGTT 59.169 43.478 0.00 0.00 0.00 3.85
2287 2608 3.428532 TGTTCTACCTTTAGCTCCTCGT 58.571 45.455 0.00 0.00 0.00 4.18
2288 2609 4.451629 TTGTTCTACCTTTAGCTCCTCG 57.548 45.455 0.00 0.00 0.00 4.63
2289 2610 8.966069 AATATTTGTTCTACCTTTAGCTCCTC 57.034 34.615 0.00 0.00 0.00 3.71
2290 2611 7.993758 GGAATATTTGTTCTACCTTTAGCTCCT 59.006 37.037 0.00 0.00 0.00 3.69
2291 2612 7.228906 GGGAATATTTGTTCTACCTTTAGCTCC 59.771 40.741 0.00 0.00 0.00 4.70
2292 2613 7.993758 AGGGAATATTTGTTCTACCTTTAGCTC 59.006 37.037 0.00 0.00 0.00 4.09
2293 2614 7.873195 AGGGAATATTTGTTCTACCTTTAGCT 58.127 34.615 0.00 0.00 0.00 3.32
2294 2615 7.773690 TGAGGGAATATTTGTTCTACCTTTAGC 59.226 37.037 0.00 0.00 0.00 3.09
2295 2616 9.681062 TTGAGGGAATATTTGTTCTACCTTTAG 57.319 33.333 0.00 0.00 0.00 1.85
2296 2617 9.681062 CTTGAGGGAATATTTGTTCTACCTTTA 57.319 33.333 0.00 0.00 0.00 1.85
2297 2618 8.170730 ACTTGAGGGAATATTTGTTCTACCTTT 58.829 33.333 0.00 0.00 0.00 3.11
2298 2619 7.699878 ACTTGAGGGAATATTTGTTCTACCTT 58.300 34.615 0.00 0.00 0.00 3.50
2299 2620 7.272144 ACTTGAGGGAATATTTGTTCTACCT 57.728 36.000 0.00 0.00 0.00 3.08
2300 2621 7.829706 AGAACTTGAGGGAATATTTGTTCTACC 59.170 37.037 0.00 0.00 40.35 3.18
2301 2622 8.794335 AGAACTTGAGGGAATATTTGTTCTAC 57.206 34.615 0.00 0.00 40.35 2.59
2303 2624 9.620259 GATAGAACTTGAGGGAATATTTGTTCT 57.380 33.333 0.00 0.00 43.21 3.01
2304 2625 8.552034 CGATAGAACTTGAGGGAATATTTGTTC 58.448 37.037 0.00 0.00 39.76 3.18
2305 2626 8.265055 TCGATAGAACTTGAGGGAATATTTGTT 58.735 33.333 0.00 0.00 46.15 2.83
2306 2627 7.792032 TCGATAGAACTTGAGGGAATATTTGT 58.208 34.615 0.00 0.00 46.15 2.83
2329 2650 2.538333 CGTAGAGTTGTATCGGTGGTCG 60.538 54.545 0.00 0.00 40.90 4.79
2330 2651 2.793933 GCGTAGAGTTGTATCGGTGGTC 60.794 54.545 0.00 0.00 0.00 4.02
2331 2652 1.133790 GCGTAGAGTTGTATCGGTGGT 59.866 52.381 0.00 0.00 0.00 4.16
2332 2653 1.133598 TGCGTAGAGTTGTATCGGTGG 59.866 52.381 0.00 0.00 0.00 4.61
2333 2654 2.554806 TGCGTAGAGTTGTATCGGTG 57.445 50.000 0.00 0.00 0.00 4.94
2334 2655 2.798499 GCATGCGTAGAGTTGTATCGGT 60.798 50.000 0.00 0.00 0.00 4.69
2335 2656 1.787155 GCATGCGTAGAGTTGTATCGG 59.213 52.381 0.00 0.00 0.00 4.18
2336 2657 2.732366 AGCATGCGTAGAGTTGTATCG 58.268 47.619 13.01 0.00 0.00 2.92
2337 2658 4.026475 GTCAAGCATGCGTAGAGTTGTATC 60.026 45.833 13.01 2.83 0.00 2.24
2338 2659 3.865745 GTCAAGCATGCGTAGAGTTGTAT 59.134 43.478 13.01 0.00 0.00 2.29
2339 2660 3.250744 GTCAAGCATGCGTAGAGTTGTA 58.749 45.455 13.01 0.00 0.00 2.41
2340 2661 2.069273 GTCAAGCATGCGTAGAGTTGT 58.931 47.619 13.01 0.00 0.00 3.32
2341 2662 1.059692 CGTCAAGCATGCGTAGAGTTG 59.940 52.381 13.01 10.30 0.00 3.16
2342 2663 1.336887 ACGTCAAGCATGCGTAGAGTT 60.337 47.619 13.01 0.00 37.47 3.01
2343 2664 0.243907 ACGTCAAGCATGCGTAGAGT 59.756 50.000 13.01 8.62 37.47 3.24
2344 2665 1.321743 GAACGTCAAGCATGCGTAGAG 59.678 52.381 13.01 7.96 37.99 2.43
2345 2666 1.346365 GAACGTCAAGCATGCGTAGA 58.654 50.000 13.01 8.85 37.99 2.59
2346 2667 0.023732 CGAACGTCAAGCATGCGTAG 59.976 55.000 13.01 6.39 37.99 3.51
2347 2668 1.951181 GCGAACGTCAAGCATGCGTA 61.951 55.000 13.01 0.00 37.99 4.42
2348 2669 2.853210 CGAACGTCAAGCATGCGT 59.147 55.556 13.01 6.07 39.69 5.24
2349 2670 2.498761 AAGCGAACGTCAAGCATGCG 62.499 55.000 13.01 0.00 33.98 4.73
2350 2671 0.385974 AAAGCGAACGTCAAGCATGC 60.386 50.000 10.51 10.51 0.00 4.06
2351 2672 2.495939 GTAAAGCGAACGTCAAGCATG 58.504 47.619 11.46 0.00 0.00 4.06
2352 2673 1.463444 GGTAAAGCGAACGTCAAGCAT 59.537 47.619 11.46 0.00 0.00 3.79
2353 2674 0.863144 GGTAAAGCGAACGTCAAGCA 59.137 50.000 11.46 0.00 0.00 3.91
2354 2675 1.145803 AGGTAAAGCGAACGTCAAGC 58.854 50.000 0.00 0.00 0.00 4.01
2355 2676 3.829948 TCTAGGTAAAGCGAACGTCAAG 58.170 45.455 0.00 0.00 0.00 3.02
2356 2677 3.921119 TCTAGGTAAAGCGAACGTCAA 57.079 42.857 0.00 0.00 0.00 3.18
2357 2678 3.004629 TGTTCTAGGTAAAGCGAACGTCA 59.995 43.478 0.00 0.00 38.78 4.35
2358 2679 3.568538 TGTTCTAGGTAAAGCGAACGTC 58.431 45.455 0.00 0.00 38.78 4.34
2359 2680 3.648339 TGTTCTAGGTAAAGCGAACGT 57.352 42.857 0.00 0.00 38.78 3.99
2360 2681 3.985925 ACTTGTTCTAGGTAAAGCGAACG 59.014 43.478 0.00 0.00 38.78 3.95
2361 2682 6.810182 TCATACTTGTTCTAGGTAAAGCGAAC 59.190 38.462 0.00 0.00 37.02 3.95
2362 2683 6.927416 TCATACTTGTTCTAGGTAAAGCGAA 58.073 36.000 0.00 0.00 0.00 4.70
2363 2684 6.519679 TCATACTTGTTCTAGGTAAAGCGA 57.480 37.500 0.00 0.00 0.00 4.93
2364 2685 7.331193 AGTTTCATACTTGTTCTAGGTAAAGCG 59.669 37.037 0.00 0.00 31.29 4.68
2365 2686 8.549338 AGTTTCATACTTGTTCTAGGTAAAGC 57.451 34.615 0.00 0.00 31.29 3.51
2370 2691 9.091220 ACTTCTAGTTTCATACTTGTTCTAGGT 57.909 33.333 0.00 0.00 38.33 3.08
2383 2704 8.648693 ACACCTACAAAGTACTTCTAGTTTCAT 58.351 33.333 8.95 0.00 0.00 2.57
2384 2705 8.015185 ACACCTACAAAGTACTTCTAGTTTCA 57.985 34.615 8.95 0.00 0.00 2.69
2385 2706 8.883954 AACACCTACAAAGTACTTCTAGTTTC 57.116 34.615 8.95 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.