Multiple sequence alignment - TraesCS5A01G159600

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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 TraesCS5A01G159600 chr5A 100.000 3316 0 0 1 3316 340271322 340268007 0.000000e+00 6124.0
1 TraesCS5A01G159600 chr5D 83.664 3275 270 125 5 3112 255990790 255987614 0.000000e+00 2839.0
2 TraesCS5A01G159600 chr5D 79.891 552 83 18 18 549 464702161 464702704 2.410000e-101 379.0
3 TraesCS5A01G159600 chr5D 91.892 74 6 0 3243 3316 255987445 255987372 1.630000e-18 104.0
4 TraesCS5A01G159600 chr5B 87.429 2124 129 69 1066 3112 289797945 289795883 0.000000e+00 2316.0
5 TraesCS5A01G159600 chr5B 78.710 620 97 22 5 600 538571626 538572234 6.710000e-102 381.0
6 TraesCS5A01G159600 chr5B 78.571 602 96 23 18 596 545811558 545812149 1.880000e-97 366.0
7 TraesCS5A01G159600 chr5B 84.890 364 34 13 706 1060 289798334 289797983 6.810000e-92 348.0
8 TraesCS5A01G159600 chr7B 80.033 601 88 19 18 596 498599179 498599769 1.840000e-112 416.0
9 TraesCS5A01G159600 chr1B 79.867 601 91 17 18 597 94009724 94009133 2.380000e-111 412.0
10 TraesCS5A01G159600 chr3B 79.368 601 93 20 18 596 708392171 708392762 8.620000e-106 394.0
11 TraesCS5A01G159600 chr3B 79.200 625 83 32 5 596 746797382 746796772 1.120000e-104 390.0
12 TraesCS5A01G159600 chr3B 94.118 51 3 0 1263 1313 627613306 627613256 9.860000e-11 78.7
13 TraesCS5A01G159600 chr2B 80.035 571 83 21 49 597 666052978 666052417 8.620000e-106 394.0
14 TraesCS5A01G159600 chr2B 77.949 195 25 13 426 604 57887619 57887811 4.520000e-19 106.0
15 TraesCS5A01G159600 chr6A 77.996 559 105 13 50 599 453125553 453125004 5.300000e-88 335.0
16 TraesCS5A01G159600 chr6A 82.229 332 56 3 1146 1475 187272319 187271989 1.950000e-72 283.0
17 TraesCS5A01G159600 chr4D 81.671 371 51 11 240 596 360491893 360491526 3.240000e-75 292.0
18 TraesCS5A01G159600 chr6B 82.866 321 51 4 1157 1475 245985742 245985424 5.410000e-73 285.0
19 TraesCS5A01G159600 chr7A 74.870 577 117 19 2 560 707993773 707994339 1.540000e-58 237.0
20 TraesCS5A01G159600 chr7A 75.870 460 98 10 145 595 641948254 641947799 4.310000e-54 222.0
21 TraesCS5A01G159600 chr4B 80.526 190 29 7 1280 1465 522432038 522432223 4.460000e-29 139.0
22 TraesCS5A01G159600 chr3D 94.118 51 3 0 1263 1313 471970283 471970233 9.860000e-11 78.7
23 TraesCS5A01G159600 chr4A 80.412 97 19 0 500 596 168734043 168734139 1.280000e-09 75.0
24 TraesCS5A01G159600 chr3A 100.000 39 0 0 1275 1313 614574203 614574165 4.590000e-09 73.1


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 TraesCS5A01G159600 chr5A 340268007 340271322 3315 True 6124.0 6124 100.0000 1 3316 1 chr5A.!!$R1 3315
1 TraesCS5A01G159600 chr5D 255987372 255990790 3418 True 1471.5 2839 87.7780 5 3316 2 chr5D.!!$R1 3311
2 TraesCS5A01G159600 chr5D 464702161 464702704 543 False 379.0 379 79.8910 18 549 1 chr5D.!!$F1 531
3 TraesCS5A01G159600 chr5B 289795883 289798334 2451 True 1332.0 2316 86.1595 706 3112 2 chr5B.!!$R1 2406
4 TraesCS5A01G159600 chr5B 538571626 538572234 608 False 381.0 381 78.7100 5 600 1 chr5B.!!$F1 595
5 TraesCS5A01G159600 chr5B 545811558 545812149 591 False 366.0 366 78.5710 18 596 1 chr5B.!!$F2 578
6 TraesCS5A01G159600 chr7B 498599179 498599769 590 False 416.0 416 80.0330 18 596 1 chr7B.!!$F1 578
7 TraesCS5A01G159600 chr1B 94009133 94009724 591 True 412.0 412 79.8670 18 597 1 chr1B.!!$R1 579
8 TraesCS5A01G159600 chr3B 708392171 708392762 591 False 394.0 394 79.3680 18 596 1 chr3B.!!$F1 578
9 TraesCS5A01G159600 chr3B 746796772 746797382 610 True 390.0 390 79.2000 5 596 1 chr3B.!!$R2 591
10 TraesCS5A01G159600 chr2B 666052417 666052978 561 True 394.0 394 80.0350 49 597 1 chr2B.!!$R1 548
11 TraesCS5A01G159600 chr6A 453125004 453125553 549 True 335.0 335 77.9960 50 599 1 chr6A.!!$R2 549
12 TraesCS5A01G159600 chr7A 707993773 707994339 566 False 237.0 237 74.8700 2 560 1 chr7A.!!$F1 558

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
780 823 0.121197 TCCCCATCCCTATCCATCCC 59.879 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2336 2517 0.247736 GAGCTTCGAGCAAGGAAGGA 59.752 55.0 11.7 0.0 45.56 3.36 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 2.224314 GCTAGGCGATTGTCTTTATGGC 59.776 50.000 0.00 0.00 0.00 4.40
31 32 1.557371 TGTCTTTATGGCCGGTGATGA 59.443 47.619 1.90 0.00 0.00 2.92
41 42 1.548269 GCCGGTGATGAATTTGGGAAA 59.452 47.619 1.90 0.00 0.00 3.13
43 44 2.415357 CCGGTGATGAATTTGGGAAACG 60.415 50.000 0.00 0.00 0.00 3.60
53 54 0.533308 TTGGGAAACGGTCGGTTCAG 60.533 55.000 20.46 0.00 43.15 3.02
83 84 4.634703 TGGCGGCGGTGACAACAT 62.635 61.111 9.78 0.00 0.00 2.71
105 114 1.538512 CTTGTGATGGACTTGTGGCTG 59.461 52.381 0.00 0.00 0.00 4.85
109 118 3.557903 ATGGACTTGTGGCTGCGCT 62.558 57.895 9.73 0.00 0.00 5.92
114 123 2.828095 TTGTGGCTGCGCTGTTGT 60.828 55.556 16.05 0.00 0.00 3.32
129 138 4.927782 TGTGCCGGCGTTTGCTCT 62.928 61.111 23.90 0.00 42.25 4.09
140 149 1.415374 GTTTGCTCTAGCGTCGACAA 58.585 50.000 17.16 0.00 45.83 3.18
143 152 1.874466 GCTCTAGCGTCGACAAGGC 60.874 63.158 17.16 11.10 39.09 4.35
150 159 4.090057 GTCGACAAGGCGCTTGGC 62.090 66.667 11.55 16.45 45.27 4.52
224 241 2.420722 GACGAAACTTGTGTTGGGTTCA 59.579 45.455 0.00 0.00 36.39 3.18
236 253 2.214376 TGGGTTCATGGTTGATGGAC 57.786 50.000 0.00 0.00 39.65 4.02
257 275 5.012328 ACGACAGGTATGATTTTCTCCTC 57.988 43.478 0.00 0.00 0.00 3.71
275 293 1.883084 CCGGCGTCTTAGTCATGGC 60.883 63.158 6.01 0.00 0.00 4.40
277 295 1.141019 GGCGTCTTAGTCATGGCGA 59.859 57.895 0.00 0.00 0.00 5.54
291 309 2.581354 GCGAGGTGCCAGATCTGT 59.419 61.111 21.11 1.98 37.76 3.41
300 318 4.716784 AGGTGCCAGATCTGTAGTTTGATA 59.283 41.667 21.11 0.00 0.00 2.15
346 364 5.065859 TGTCTGATTTGTTCAACGACAATGT 59.934 36.000 0.00 0.00 36.89 2.71
415 433 3.612247 ATGGAGCCGCGTCAAGCTT 62.612 57.895 4.92 0.00 45.59 3.74
420 438 2.978010 CCGCGTCAAGCTTGGGTT 60.978 61.111 25.73 0.00 45.59 4.11
491 521 0.984995 GGAGGTAGGGTGTCAAGCTT 59.015 55.000 0.00 0.00 0.00 3.74
494 524 2.832733 GAGGTAGGGTGTCAAGCTTAGT 59.167 50.000 0.00 0.00 0.00 2.24
497 527 2.841442 AGGGTGTCAAGCTTAGTGAC 57.159 50.000 9.64 9.64 44.67 3.67
498 528 1.000955 AGGGTGTCAAGCTTAGTGACG 59.999 52.381 11.42 0.00 46.89 4.35
533 563 6.540914 TCTTTTTAGTTTTGTCATGTCGGTCT 59.459 34.615 0.00 0.00 0.00 3.85
535 565 7.789273 TTTTAGTTTTGTCATGTCGGTCTTA 57.211 32.000 0.00 0.00 0.00 2.10
537 567 5.924475 AGTTTTGTCATGTCGGTCTTAAG 57.076 39.130 0.00 0.00 0.00 1.85
539 569 4.610605 TTTGTCATGTCGGTCTTAAGGA 57.389 40.909 1.85 0.00 0.00 3.36
564 594 9.530129 GAAACTTGTACTTTGATCTTTACGATG 57.470 33.333 0.00 0.00 30.84 3.84
569 599 8.014322 TGTACTTTGATCTTTACGATGTGAAC 57.986 34.615 0.00 0.00 30.84 3.18
572 602 6.422701 ACTTTGATCTTTACGATGTGAACGAA 59.577 34.615 0.00 0.00 30.84 3.85
641 671 1.098050 ATCAGCTGGGCGAAACAATC 58.902 50.000 15.13 0.00 0.00 2.67
648 678 0.454452 GGGCGAAACAATCTTCACGC 60.454 55.000 0.00 0.00 44.18 5.34
666 697 1.465020 CGCCGTCGTACATGCATTTTT 60.465 47.619 0.00 0.00 0.00 1.94
715 758 7.445402 CCGAATAATCAGGTATTGGTCATTTCT 59.555 37.037 0.00 0.00 0.00 2.52
723 766 6.015519 CAGGTATTGGTCATTTCTGTTGGAAA 60.016 38.462 0.00 0.00 46.33 3.13
724 767 6.553100 AGGTATTGGTCATTTCTGTTGGAAAA 59.447 34.615 0.00 0.00 45.56 2.29
728 771 6.088016 TGGTCATTTCTGTTGGAAAAGATG 57.912 37.500 0.00 0.00 45.56 2.90
730 773 5.473039 GTCATTTCTGTTGGAAAAGATGGG 58.527 41.667 0.00 0.00 45.56 4.00
731 774 4.021192 TCATTTCTGTTGGAAAAGATGGGC 60.021 41.667 0.00 0.00 45.56 5.36
732 775 1.533625 TCTGTTGGAAAAGATGGGCG 58.466 50.000 0.00 0.00 0.00 6.13
733 776 1.073125 TCTGTTGGAAAAGATGGGCGA 59.927 47.619 0.00 0.00 0.00 5.54
734 777 1.470098 CTGTTGGAAAAGATGGGCGAG 59.530 52.381 0.00 0.00 0.00 5.03
735 778 1.073125 TGTTGGAAAAGATGGGCGAGA 59.927 47.619 0.00 0.00 0.00 4.04
752 795 4.867608 GGCGAGAGAGAGATATTATTTGCC 59.132 45.833 0.00 0.00 0.00 4.52
754 797 5.804979 GCGAGAGAGAGATATTATTTGCCTC 59.195 44.000 0.00 0.00 0.00 4.70
780 823 0.121197 TCCCCATCCCTATCCATCCC 59.879 60.000 0.00 0.00 0.00 3.85
781 824 0.921256 CCCCATCCCTATCCATCCCC 60.921 65.000 0.00 0.00 0.00 4.81
782 825 1.274703 CCCATCCCTATCCATCCCCG 61.275 65.000 0.00 0.00 0.00 5.73
783 826 0.547712 CCATCCCTATCCATCCCCGT 60.548 60.000 0.00 0.00 0.00 5.28
784 827 0.905357 CATCCCTATCCATCCCCGTC 59.095 60.000 0.00 0.00 0.00 4.79
785 828 0.252742 ATCCCTATCCATCCCCGTCC 60.253 60.000 0.00 0.00 0.00 4.79
787 830 0.547712 CCCTATCCATCCCCGTCCAT 60.548 60.000 0.00 0.00 0.00 3.41
788 831 1.273609 CCCTATCCATCCCCGTCCATA 60.274 57.143 0.00 0.00 0.00 2.74
796 843 2.510691 CCCGTCCATACCACACGC 60.511 66.667 0.00 0.00 32.03 5.34
872 928 1.894756 GCTGTACCCACGCCACAAA 60.895 57.895 0.00 0.00 0.00 2.83
873 929 1.241315 GCTGTACCCACGCCACAAAT 61.241 55.000 0.00 0.00 0.00 2.32
874 930 1.946747 GCTGTACCCACGCCACAAATA 60.947 52.381 0.00 0.00 0.00 1.40
875 931 1.735571 CTGTACCCACGCCACAAATAC 59.264 52.381 0.00 0.00 0.00 1.89
876 932 1.348366 TGTACCCACGCCACAAATACT 59.652 47.619 0.00 0.00 0.00 2.12
877 933 2.566279 TGTACCCACGCCACAAATACTA 59.434 45.455 0.00 0.00 0.00 1.82
878 934 2.396590 ACCCACGCCACAAATACTAG 57.603 50.000 0.00 0.00 0.00 2.57
881 937 3.118884 ACCCACGCCACAAATACTAGTAG 60.119 47.826 8.85 0.00 0.00 2.57
885 941 4.025730 CACGCCACAAATACTAGTAGCATG 60.026 45.833 8.85 9.29 0.00 4.06
911 967 3.787001 CGTCCCCTTCCCCTGCTC 61.787 72.222 0.00 0.00 0.00 4.26
935 991 1.301953 GAACCCGTTACAACCGGCT 60.302 57.895 0.00 0.00 44.13 5.52
936 992 1.293963 GAACCCGTTACAACCGGCTC 61.294 60.000 0.00 0.00 44.13 4.70
937 993 2.812178 CCCGTTACAACCGGCTCG 60.812 66.667 0.00 0.00 44.13 5.03
938 994 3.484547 CCGTTACAACCGGCTCGC 61.485 66.667 0.00 0.00 38.85 5.03
939 995 2.431942 CGTTACAACCGGCTCGCT 60.432 61.111 0.00 0.00 0.00 4.93
1050 1128 1.065418 CACACCCCATCCCAAGTAGAC 60.065 57.143 0.00 0.00 0.00 2.59
1071 1181 2.910579 CCAGATCGGTAACCTCCCA 58.089 57.895 0.00 0.00 0.00 4.37
1073 1183 1.557832 CCAGATCGGTAACCTCCCAAA 59.442 52.381 0.00 0.00 0.00 3.28
1075 1185 3.467803 CAGATCGGTAACCTCCCAAATC 58.532 50.000 0.00 0.00 0.00 2.17
1080 1190 2.629051 GGTAACCTCCCAAATCACTCG 58.371 52.381 0.00 0.00 0.00 4.18
1094 1204 2.902523 TCACTCGCTCACTACTCGTAT 58.097 47.619 0.00 0.00 0.00 3.06
1096 1206 2.608090 CACTCGCTCACTACTCGTATCA 59.392 50.000 0.00 0.00 0.00 2.15
1097 1207 2.608546 ACTCGCTCACTACTCGTATCAC 59.391 50.000 0.00 0.00 0.00 3.06
1272 1400 3.727258 CAAGTCCATCCCGGGGCA 61.727 66.667 23.50 1.15 34.02 5.36
1486 1614 0.323908 AGCGCAAGTACTCCTCCTCT 60.324 55.000 11.47 0.00 41.68 3.69
1492 1620 3.880117 GCAAGTACTCCTCCTCTTCCTCT 60.880 52.174 0.00 0.00 0.00 3.69
1534 1677 2.749865 CGCCATGGCAAACGACGAT 61.750 57.895 34.93 0.00 42.06 3.73
1633 1776 1.979693 GGACCTCAGCGACTCCAGT 60.980 63.158 0.00 0.00 0.00 4.00
1883 2041 2.361610 CCATGCCACCACCACCTC 60.362 66.667 0.00 0.00 0.00 3.85
1947 2105 2.755469 GCCACCCATGCCGTTCAT 60.755 61.111 0.00 0.00 35.31 2.57
2020 2178 2.621338 GAGTTCCTGTCGATGATGCAA 58.379 47.619 0.00 0.00 0.00 4.08
2135 2293 1.875576 GCATGGCCAAGATCGAGTAGG 60.876 57.143 10.96 0.00 0.00 3.18
2136 2294 1.688735 CATGGCCAAGATCGAGTAGGA 59.311 52.381 10.96 0.00 0.00 2.94
2137 2295 1.860641 TGGCCAAGATCGAGTAGGAA 58.139 50.000 0.61 0.00 0.00 3.36
2138 2296 1.757118 TGGCCAAGATCGAGTAGGAAG 59.243 52.381 0.61 0.00 0.00 3.46
2141 2299 2.801342 GCCAAGATCGAGTAGGAAGCAG 60.801 54.545 0.00 0.00 0.00 4.24
2143 2301 2.428890 CAAGATCGAGTAGGAAGCAGGT 59.571 50.000 0.00 0.00 0.00 4.00
2150 2308 3.616560 CGAGTAGGAAGCAGGTAAGCAAA 60.617 47.826 0.00 0.00 36.85 3.68
2173 2331 1.267832 GCAGCTCGACAACAAACGAAA 60.268 47.619 0.00 0.00 38.05 3.46
2179 2337 3.613563 TCGACAACAAACGAAAATGAGC 58.386 40.909 0.00 0.00 35.62 4.26
2182 2340 3.964909 ACAACAAACGAAAATGAGCCTC 58.035 40.909 0.00 0.00 0.00 4.70
2197 2355 0.108233 GCCTCTCTGCTCCACTCAAG 60.108 60.000 0.00 0.00 0.00 3.02
2198 2356 1.554836 CCTCTCTGCTCCACTCAAGA 58.445 55.000 0.00 0.00 0.00 3.02
2224 2405 0.668535 AAACAAACGGAAGGCAGAGC 59.331 50.000 0.00 0.00 0.00 4.09
2225 2406 0.465460 AACAAACGGAAGGCAGAGCA 60.465 50.000 0.00 0.00 0.00 4.26
2226 2407 0.886490 ACAAACGGAAGGCAGAGCAG 60.886 55.000 0.00 0.00 0.00 4.24
2227 2408 0.603707 CAAACGGAAGGCAGAGCAGA 60.604 55.000 0.00 0.00 0.00 4.26
2228 2409 0.321122 AAACGGAAGGCAGAGCAGAG 60.321 55.000 0.00 0.00 0.00 3.35
2254 2435 4.503991 GGCAAGTGAAGAGGAGAAGAAGAA 60.504 45.833 0.00 0.00 0.00 2.52
2256 2437 4.535526 AGTGAAGAGGAGAAGAAGAAGC 57.464 45.455 0.00 0.00 0.00 3.86
2286 2467 1.017387 GGCGGCCTGTTTAGATCTTG 58.983 55.000 12.87 0.00 0.00 3.02
2311 2492 3.813724 GCCCGACAATAATTCCCTAGTTC 59.186 47.826 0.00 0.00 0.00 3.01
2313 2494 4.056050 CCGACAATAATTCCCTAGTTCCG 58.944 47.826 0.00 0.00 0.00 4.30
2329 2510 4.235360 AGTTCCGTGTCTCGATTAGTTTG 58.765 43.478 0.00 0.00 42.86 2.93
2336 2517 6.292703 CCGTGTCTCGATTAGTTTGTTTCTTT 60.293 38.462 0.00 0.00 42.86 2.52
2353 2538 1.466558 CTTTCCTTCCTTGCTCGAAGC 59.533 52.381 0.00 0.00 42.82 3.86
2366 2551 2.568696 TCGAAGCTCCATCGAAGAAG 57.431 50.000 6.52 0.00 45.46 2.85
2367 2552 2.092323 TCGAAGCTCCATCGAAGAAGA 58.908 47.619 6.52 0.00 45.46 2.87
2368 2553 2.690497 TCGAAGCTCCATCGAAGAAGAT 59.310 45.455 6.52 0.00 45.46 2.40
2369 2554 3.883489 TCGAAGCTCCATCGAAGAAGATA 59.117 43.478 6.52 0.00 45.46 1.98
2396 2589 6.867519 TCATGTTCATGGTAGTTCCTTCTA 57.132 37.500 12.02 0.00 37.07 2.10
2399 2592 6.620877 TGTTCATGGTAGTTCCTTCTACAT 57.379 37.500 0.00 0.00 41.20 2.29
2400 2593 6.640518 TGTTCATGGTAGTTCCTTCTACATC 58.359 40.000 0.00 0.00 41.20 3.06
2401 2594 6.212589 TGTTCATGGTAGTTCCTTCTACATCA 59.787 38.462 0.00 0.00 41.20 3.07
2478 2683 2.144482 GCAAACATGTTGCTTGCTCT 57.856 45.000 21.17 0.00 43.77 4.09
2528 2741 7.024171 GGGAAAAGAAGAAATGAAACGAGATC 58.976 38.462 0.00 0.00 0.00 2.75
2536 2754 4.946784 AATGAAACGAGATCGGGAAAAG 57.053 40.909 7.22 0.00 44.95 2.27
2552 2770 1.554583 AAAGGAGAGGCCGAGTTCCC 61.555 60.000 12.40 3.58 43.43 3.97
2586 2805 7.931407 TCACATCTGCTTCTTCAGTTTTACTAA 59.069 33.333 0.00 0.00 35.63 2.24
2622 2842 1.206115 GGCGTTTCGTTTTGGTGCTG 61.206 55.000 0.00 0.00 0.00 4.41
2661 2881 3.119459 TCTGTTTTGCGTTGGCTGTTTTA 60.119 39.130 0.00 0.00 40.82 1.52
2731 2962 2.765807 AGGGATCGGCAGTGGAGG 60.766 66.667 0.00 0.00 0.00 4.30
2788 3031 0.933700 CCCCCTCTCTCTCTCTCCTT 59.066 60.000 0.00 0.00 0.00 3.36
2789 3032 1.290732 CCCCCTCTCTCTCTCTCCTTT 59.709 57.143 0.00 0.00 0.00 3.11
2791 3034 3.052490 CCCCCTCTCTCTCTCTCCTTTTA 60.052 52.174 0.00 0.00 0.00 1.52
2792 3035 3.958147 CCCCTCTCTCTCTCTCCTTTTAC 59.042 52.174 0.00 0.00 0.00 2.01
2793 3036 4.325816 CCCCTCTCTCTCTCTCCTTTTACT 60.326 50.000 0.00 0.00 0.00 2.24
2795 3038 6.062095 CCCTCTCTCTCTCTCCTTTTACTAG 58.938 48.000 0.00 0.00 0.00 2.57
2796 3039 6.353602 CCCTCTCTCTCTCTCCTTTTACTAGT 60.354 46.154 0.00 0.00 0.00 2.57
2800 3043 9.369672 TCTCTCTCTCTCCTTTTACTAGTTTTT 57.630 33.333 0.00 0.00 0.00 1.94
2822 3065 8.411991 TTTTTGGTTTTACTGACTTATAGGGG 57.588 34.615 0.00 0.00 0.00 4.79
2823 3066 5.703730 TGGTTTTACTGACTTATAGGGGG 57.296 43.478 0.00 0.00 0.00 5.40
2824 3067 5.352264 TGGTTTTACTGACTTATAGGGGGA 58.648 41.667 0.00 0.00 0.00 4.81
2825 3068 5.427481 TGGTTTTACTGACTTATAGGGGGAG 59.573 44.000 0.00 0.00 0.00 4.30
2826 3069 5.664457 GGTTTTACTGACTTATAGGGGGAGA 59.336 44.000 0.00 0.00 0.00 3.71
2827 3070 6.157471 GGTTTTACTGACTTATAGGGGGAGAA 59.843 42.308 0.00 0.00 0.00 2.87
2828 3071 7.273712 GTTTTACTGACTTATAGGGGGAGAAG 58.726 42.308 0.00 0.00 0.00 2.85
2829 3072 4.628661 ACTGACTTATAGGGGGAGAAGT 57.371 45.455 0.00 0.00 33.65 3.01
2830 3073 5.745988 ACTGACTTATAGGGGGAGAAGTA 57.254 43.478 0.00 0.00 31.16 2.24
2831 3074 5.707495 ACTGACTTATAGGGGGAGAAGTAG 58.293 45.833 0.00 0.00 31.16 2.57
2832 3075 5.196165 ACTGACTTATAGGGGGAGAAGTAGT 59.804 44.000 0.00 0.00 31.16 2.73
2833 3076 6.392245 ACTGACTTATAGGGGGAGAAGTAGTA 59.608 42.308 0.00 0.00 31.16 1.82
2834 3077 6.850234 TGACTTATAGGGGGAGAAGTAGTAG 58.150 44.000 0.00 0.00 31.16 2.57
2835 3078 6.183361 TGACTTATAGGGGGAGAAGTAGTAGG 60.183 46.154 0.00 0.00 31.16 3.18
2836 3079 5.921861 ACTTATAGGGGGAGAAGTAGTAGGA 59.078 44.000 0.00 0.00 29.24 2.94
2837 3080 6.045813 ACTTATAGGGGGAGAAGTAGTAGGAG 59.954 46.154 0.00 0.00 29.24 3.69
2838 3081 2.587053 AGGGGGAGAAGTAGTAGGAGT 58.413 52.381 0.00 0.00 0.00 3.85
2839 3082 3.757362 AGGGGGAGAAGTAGTAGGAGTA 58.243 50.000 0.00 0.00 0.00 2.59
2840 3083 3.462954 AGGGGGAGAAGTAGTAGGAGTAC 59.537 52.174 0.00 0.00 0.00 2.73
2841 3084 3.203934 GGGGGAGAAGTAGTAGGAGTACA 59.796 52.174 0.00 0.00 0.00 2.90
2842 3085 4.325658 GGGGGAGAAGTAGTAGGAGTACAA 60.326 50.000 0.00 0.00 0.00 2.41
2843 3086 5.456779 GGGGAGAAGTAGTAGGAGTACAAT 58.543 45.833 0.00 0.00 0.00 2.71
2844 3087 6.411320 GGGGGAGAAGTAGTAGGAGTACAATA 60.411 46.154 0.00 0.00 0.00 1.90
2845 3088 6.489700 GGGGAGAAGTAGTAGGAGTACAATAC 59.510 46.154 0.00 0.00 0.00 1.89
2846 3089 7.289310 GGGAGAAGTAGTAGGAGTACAATACT 58.711 42.308 0.00 2.94 42.86 2.12
2868 3111 1.902938 TTGACATGTGGGCGATTGAA 58.097 45.000 1.15 0.00 0.00 2.69
2869 3112 2.127271 TGACATGTGGGCGATTGAAT 57.873 45.000 1.15 0.00 0.00 2.57
2870 3113 1.744522 TGACATGTGGGCGATTGAATG 59.255 47.619 1.15 0.00 0.00 2.67
2871 3114 2.016318 GACATGTGGGCGATTGAATGA 58.984 47.619 1.15 0.00 0.00 2.57
2879 3122 0.040958 GCGATTGAATGATGGACGGC 60.041 55.000 0.00 0.00 0.00 5.68
2881 3124 0.588252 GATTGAATGATGGACGGCCG 59.412 55.000 26.86 26.86 36.79 6.13
2906 3149 1.453745 CGTGTGGGGATGGGAATGG 60.454 63.158 0.00 0.00 0.00 3.16
2907 3150 1.758122 GTGTGGGGATGGGAATGGC 60.758 63.158 0.00 0.00 0.00 4.40
2985 3232 0.657368 CCGCAACGCAAAGTGAAGTC 60.657 55.000 0.00 0.00 0.00 3.01
2987 3234 1.466855 GCAACGCAAAGTGAAGTCAC 58.533 50.000 3.12 3.12 46.77 3.67
3008 3285 1.438651 TGACTGACCGCTTGCATTAC 58.561 50.000 0.00 0.00 0.00 1.89
3016 3293 0.447801 CGCTTGCATTACTGTCCCAC 59.552 55.000 0.00 0.00 0.00 4.61
3052 3338 2.801483 AGTAAGCTCTCTCTGACTGCA 58.199 47.619 0.00 0.00 0.00 4.41
3053 3339 2.754552 AGTAAGCTCTCTCTGACTGCAG 59.245 50.000 13.48 13.48 43.67 4.41
3054 3340 0.247185 AAGCTCTCTCTGACTGCAGC 59.753 55.000 15.27 7.45 42.01 5.25
3055 3341 1.153588 GCTCTCTCTGACTGCAGCC 60.154 63.158 15.27 2.30 42.01 4.85
3056 3342 1.139308 CTCTCTCTGACTGCAGCCG 59.861 63.158 15.27 2.03 42.01 5.52
3057 3343 2.508887 CTCTCTGACTGCAGCCGC 60.509 66.667 15.27 4.09 42.01 6.53
3058 3344 2.993840 TCTCTGACTGCAGCCGCT 60.994 61.111 15.27 0.00 42.01 5.52
3059 3345 2.814341 CTCTGACTGCAGCCGCTG 60.814 66.667 15.27 16.47 42.01 5.18
3119 3489 2.404923 TCAAACCGTGTCAAGACCAA 57.595 45.000 0.00 0.00 0.00 3.67
3125 3495 2.616842 ACCGTGTCAAGACCAAATGAAC 59.383 45.455 0.00 0.00 0.00 3.18
3134 3504 5.465390 TCAAGACCAAATGAACTTGACGTAG 59.535 40.000 13.75 0.00 42.05 3.51
3153 3523 7.931578 ACGTAGTAATTCCATTTCCATCAAA 57.068 32.000 0.00 0.00 41.94 2.69
3154 3524 7.758495 ACGTAGTAATTCCATTTCCATCAAAC 58.242 34.615 0.00 0.00 41.94 2.93
3155 3525 7.610305 ACGTAGTAATTCCATTTCCATCAAACT 59.390 33.333 0.00 0.00 41.94 2.66
3156 3526 9.104965 CGTAGTAATTCCATTTCCATCAAACTA 57.895 33.333 0.00 0.00 0.00 2.24
3168 3538 9.911788 ATTTCCATCAAACTATGTATCTGAACT 57.088 29.630 0.00 0.00 0.00 3.01
3195 3565 3.784338 ACAGAGGCACAACAAACATTTG 58.216 40.909 2.77 2.77 43.62 2.32
3196 3566 3.446873 ACAGAGGCACAACAAACATTTGA 59.553 39.130 11.24 0.00 40.55 2.69
3198 3568 4.446385 CAGAGGCACAACAAACATTTGATG 59.554 41.667 11.24 11.50 43.80 3.07
3199 3569 4.341806 AGAGGCACAACAAACATTTGATGA 59.658 37.500 18.18 0.00 41.68 2.92
3200 3570 4.370917 AGGCACAACAAACATTTGATGAC 58.629 39.130 18.18 11.74 41.68 3.06
3201 3571 4.099881 AGGCACAACAAACATTTGATGACT 59.900 37.500 18.18 13.39 41.68 3.41
3202 3572 4.445385 GGCACAACAAACATTTGATGACTC 59.555 41.667 18.18 8.44 41.68 3.36
3203 3573 5.284079 GCACAACAAACATTTGATGACTCT 58.716 37.500 18.18 0.00 41.68 3.24
3204 3574 5.750067 GCACAACAAACATTTGATGACTCTT 59.250 36.000 18.18 0.00 41.68 2.85
3205 3575 6.256321 GCACAACAAACATTTGATGACTCTTT 59.744 34.615 18.18 0.00 41.68 2.52
3206 3576 7.201548 GCACAACAAACATTTGATGACTCTTTT 60.202 33.333 18.18 0.00 41.68 2.27
3207 3577 8.658609 CACAACAAACATTTGATGACTCTTTTT 58.341 29.630 18.18 0.00 41.68 1.94
3241 3611 8.665685 ACAGCAACTATGTATTTTAACTACTGC 58.334 33.333 0.00 0.00 0.00 4.40
3246 3616 8.154649 ACTATGTATTTTAACTACTGCATGCC 57.845 34.615 16.68 0.00 0.00 4.40
3248 3618 6.677781 TGTATTTTAACTACTGCATGCCTC 57.322 37.500 16.68 0.00 0.00 4.70
3254 3624 0.602106 CTACTGCATGCCTCGGATGG 60.602 60.000 16.68 0.00 0.00 3.51
3261 3631 0.399454 ATGCCTCGGATGGATTCAGG 59.601 55.000 0.00 0.00 0.00 3.86
3302 3672 2.954868 GCCGGTGTCGCGTCTATG 60.955 66.667 5.77 0.00 34.56 2.23
3303 3673 2.954868 CCGGTGTCGCGTCTATGC 60.955 66.667 5.77 0.00 34.56 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.805295 CGGCCATAAAGACAATCGCCTA 60.805 50.000 2.24 0.00 32.64 3.93
22 23 2.415357 CGTTTCCCAAATTCATCACCGG 60.415 50.000 0.00 0.00 0.00 5.28
31 32 1.610038 GAACCGACCGTTTCCCAAATT 59.390 47.619 0.00 0.00 33.74 1.82
41 42 4.052229 CTCGCCTGAACCGACCGT 62.052 66.667 0.00 0.00 0.00 4.83
43 44 2.722201 ATCCTCGCCTGAACCGACC 61.722 63.158 0.00 0.00 0.00 4.79
75 76 4.717877 AGTCCATCACAAGAATGTTGTCA 58.282 39.130 0.00 0.00 37.82 3.58
80 81 3.822735 CCACAAGTCCATCACAAGAATGT 59.177 43.478 0.00 0.00 41.61 2.71
81 82 3.366679 GCCACAAGTCCATCACAAGAATG 60.367 47.826 0.00 0.00 0.00 2.67
82 83 2.821969 GCCACAAGTCCATCACAAGAAT 59.178 45.455 0.00 0.00 0.00 2.40
83 84 2.158623 AGCCACAAGTCCATCACAAGAA 60.159 45.455 0.00 0.00 0.00 2.52
109 118 4.560856 GCAAACGCCGGCACAACA 62.561 61.111 28.98 0.00 0.00 3.33
114 123 2.434185 CTAGAGCAAACGCCGGCA 60.434 61.111 28.98 1.46 0.00 5.69
116 125 3.554692 CGCTAGAGCAAACGCCGG 61.555 66.667 0.00 0.00 42.21 6.13
140 149 1.144936 GACTATCTGCCAAGCGCCT 59.855 57.895 2.29 0.00 36.24 5.52
143 152 1.957177 TCTAGGACTATCTGCCAAGCG 59.043 52.381 0.00 0.00 0.00 4.68
150 159 3.825585 TGCATCTGCTCTAGGACTATCTG 59.174 47.826 3.53 0.00 42.66 2.90
153 162 4.111255 TCTGCATCTGCTCTAGGACTAT 57.889 45.455 3.53 0.00 42.66 2.12
224 241 0.984230 ACCTGTCGTCCATCAACCAT 59.016 50.000 0.00 0.00 0.00 3.55
236 253 4.372656 GGAGGAGAAAATCATACCTGTCG 58.627 47.826 0.00 0.00 0.00 4.35
257 275 1.883084 GCCATGACTAAGACGCCGG 60.883 63.158 0.00 0.00 0.00 6.13
275 293 1.107114 ACTACAGATCTGGCACCTCG 58.893 55.000 26.08 8.67 34.19 4.63
277 295 2.906389 TCAAACTACAGATCTGGCACCT 59.094 45.455 26.08 7.80 34.19 4.00
291 309 2.094078 CCCCGGACACGTTATCAAACTA 60.094 50.000 0.73 0.00 38.78 2.24
300 318 2.203098 CAACACCCCGGACACGTT 60.203 61.111 0.73 0.00 38.78 3.99
320 338 3.002246 TGTCGTTGAACAAATCAGACAGC 59.998 43.478 0.00 0.00 37.95 4.40
322 340 5.065859 ACATTGTCGTTGAACAAATCAGACA 59.934 36.000 0.00 0.00 42.10 3.41
389 407 3.032609 GCGGCTCCATCGTCGATG 61.033 66.667 25.19 25.19 39.52 3.84
394 412 3.989698 CTTGACGCGGCTCCATCGT 62.990 63.158 15.80 3.45 39.33 3.73
410 428 1.742308 TCACCTCCTAACCCAAGCTT 58.258 50.000 0.00 0.00 0.00 3.74
415 433 2.293519 TGATGGATCACCTCCTAACCCA 60.294 50.000 0.00 0.00 45.21 4.51
446 464 3.056393 ACCACCACAGCAATCATCAAATG 60.056 43.478 0.00 0.00 0.00 2.32
447 465 3.056393 CACCACCACAGCAATCATCAAAT 60.056 43.478 0.00 0.00 0.00 2.32
448 466 2.296752 CACCACCACAGCAATCATCAAA 59.703 45.455 0.00 0.00 0.00 2.69
450 468 1.536940 CACCACCACAGCAATCATCA 58.463 50.000 0.00 0.00 0.00 3.07
452 470 1.252904 GGCACCACCACAGCAATCAT 61.253 55.000 0.00 0.00 38.86 2.45
477 495 2.230508 CGTCACTAAGCTTGACACCCTA 59.769 50.000 9.86 0.00 43.09 3.53
491 521 4.395959 AAAGACAACAGAACCGTCACTA 57.604 40.909 0.00 0.00 31.92 2.74
494 524 5.180271 ACTAAAAAGACAACAGAACCGTCA 58.820 37.500 0.00 0.00 31.92 4.35
497 527 6.804783 ACAAAACTAAAAAGACAACAGAACCG 59.195 34.615 0.00 0.00 0.00 4.44
498 528 7.810759 TGACAAAACTAAAAAGACAACAGAACC 59.189 33.333 0.00 0.00 0.00 3.62
535 565 8.557029 CGTAAAGATCAAAGTACAAGTTTCCTT 58.443 33.333 0.00 0.00 0.00 3.36
537 567 8.080083 TCGTAAAGATCAAAGTACAAGTTTCC 57.920 34.615 0.00 0.00 0.00 3.13
539 569 9.052759 ACATCGTAAAGATCAAAGTACAAGTTT 57.947 29.630 0.00 0.00 37.52 2.66
564 594 7.003939 TCATGATGATATGTGTTTCGTTCAC 57.996 36.000 0.00 0.00 36.48 3.18
666 697 8.470805 TCGGCTTTTCAATAATAATAGGCAAAA 58.529 29.630 0.00 0.00 32.47 2.44
667 698 8.001881 TCGGCTTTTCAATAATAATAGGCAAA 57.998 30.769 0.00 0.00 32.47 3.68
668 699 7.575414 TCGGCTTTTCAATAATAATAGGCAA 57.425 32.000 0.00 0.00 32.47 4.52
669 700 7.575414 TTCGGCTTTTCAATAATAATAGGCA 57.425 32.000 0.00 0.00 32.47 4.75
676 707 9.349713 ACCTGATTATTCGGCTTTTCAATAATA 57.650 29.630 0.00 0.00 34.34 0.98
677 708 8.237811 ACCTGATTATTCGGCTTTTCAATAAT 57.762 30.769 0.00 0.00 36.05 1.28
678 709 7.639113 ACCTGATTATTCGGCTTTTCAATAA 57.361 32.000 0.00 0.00 0.00 1.40
679 710 8.918202 ATACCTGATTATTCGGCTTTTCAATA 57.082 30.769 0.00 0.00 0.00 1.90
680 711 7.823745 ATACCTGATTATTCGGCTTTTCAAT 57.176 32.000 0.00 0.00 0.00 2.57
681 712 7.416213 CCAATACCTGATTATTCGGCTTTTCAA 60.416 37.037 0.00 0.00 0.00 2.69
682 713 6.039270 CCAATACCTGATTATTCGGCTTTTCA 59.961 38.462 0.00 0.00 0.00 2.69
683 714 6.039382 ACCAATACCTGATTATTCGGCTTTTC 59.961 38.462 0.00 0.00 0.00 2.29
688 719 4.385825 TGACCAATACCTGATTATTCGGC 58.614 43.478 0.00 0.00 0.00 5.54
696 727 5.653769 CCAACAGAAATGACCAATACCTGAT 59.346 40.000 0.00 0.00 0.00 2.90
715 758 1.073125 TCTCGCCCATCTTTTCCAACA 59.927 47.619 0.00 0.00 0.00 3.33
723 766 2.380064 ATCTCTCTCTCGCCCATCTT 57.620 50.000 0.00 0.00 0.00 2.40
724 767 3.737559 ATATCTCTCTCTCGCCCATCT 57.262 47.619 0.00 0.00 0.00 2.90
728 771 4.867608 GCAAATAATATCTCTCTCTCGCCC 59.132 45.833 0.00 0.00 0.00 6.13
730 773 5.719173 AGGCAAATAATATCTCTCTCTCGC 58.281 41.667 0.00 0.00 0.00 5.03
731 774 6.329496 GGAGGCAAATAATATCTCTCTCTCG 58.671 44.000 0.00 0.00 0.00 4.04
732 775 6.440328 AGGGAGGCAAATAATATCTCTCTCTC 59.560 42.308 0.00 0.00 30.16 3.20
733 776 6.330218 AGGGAGGCAAATAATATCTCTCTCT 58.670 40.000 0.00 0.00 30.16 3.10
734 777 6.351796 GGAGGGAGGCAAATAATATCTCTCTC 60.352 46.154 9.35 9.35 46.07 3.20
735 778 5.487131 GGAGGGAGGCAAATAATATCTCTCT 59.513 44.000 0.85 0.00 37.60 3.10
752 795 1.772156 GGGATGGGGAAGGAGGGAG 60.772 68.421 0.00 0.00 0.00 4.30
754 797 0.197145 ATAGGGATGGGGAAGGAGGG 59.803 60.000 0.00 0.00 0.00 4.30
780 823 1.809619 CTGCGTGTGGTATGGACGG 60.810 63.158 0.00 0.00 33.68 4.79
781 824 1.809619 CCTGCGTGTGGTATGGACG 60.810 63.158 0.00 0.00 36.18 4.79
782 825 0.460284 CTCCTGCGTGTGGTATGGAC 60.460 60.000 0.00 0.00 0.00 4.02
783 826 1.897423 CTCCTGCGTGTGGTATGGA 59.103 57.895 0.00 0.00 0.00 3.41
784 827 1.815421 GCTCCTGCGTGTGGTATGG 60.815 63.158 0.00 0.00 0.00 2.74
785 828 1.079197 TGCTCCTGCGTGTGGTATG 60.079 57.895 0.00 0.00 43.34 2.39
787 830 2.656646 CTGCTCCTGCGTGTGGTA 59.343 61.111 0.00 0.00 43.34 3.25
788 831 4.320456 CCTGCTCCTGCGTGTGGT 62.320 66.667 0.00 0.00 43.34 4.16
796 843 2.630158 CAAATGACTCTCCTGCTCCTG 58.370 52.381 0.00 0.00 0.00 3.86
872 928 2.299297 GGGCGGTTCATGCTACTAGTAT 59.701 50.000 2.33 0.00 0.00 2.12
873 929 1.684983 GGGCGGTTCATGCTACTAGTA 59.315 52.381 1.89 1.89 0.00 1.82
874 930 0.464452 GGGCGGTTCATGCTACTAGT 59.536 55.000 0.00 0.00 0.00 2.57
875 931 0.249911 GGGGCGGTTCATGCTACTAG 60.250 60.000 0.00 0.00 0.00 2.57
876 932 1.827394 GGGGCGGTTCATGCTACTA 59.173 57.895 0.00 0.00 0.00 1.82
877 933 2.590092 GGGGCGGTTCATGCTACT 59.410 61.111 0.00 0.00 0.00 2.57
878 934 2.895372 CGGGGCGGTTCATGCTAC 60.895 66.667 0.00 0.00 0.00 3.58
1000 1056 1.904990 GAGACAGAGGGGAAGGGTGC 61.905 65.000 0.00 0.00 0.00 5.01
1004 1060 1.199615 GAAGGAGACAGAGGGGAAGG 58.800 60.000 0.00 0.00 0.00 3.46
1071 1181 2.488545 ACGAGTAGTGAGCGAGTGATTT 59.511 45.455 0.00 0.00 0.00 2.17
1073 1183 1.740297 ACGAGTAGTGAGCGAGTGAT 58.260 50.000 0.00 0.00 0.00 3.06
1075 1185 2.608090 TGATACGAGTAGTGAGCGAGTG 59.392 50.000 0.00 0.00 0.00 3.51
1094 1204 4.063689 GGTAGATCCTCGATCGTAAGTGA 58.936 47.826 15.94 6.28 43.17 3.41
1096 1206 3.065655 CGGTAGATCCTCGATCGTAAGT 58.934 50.000 15.94 0.10 43.17 2.24
1097 1207 2.415857 CCGGTAGATCCTCGATCGTAAG 59.584 54.545 15.94 5.89 43.17 2.34
1429 1557 1.234821 GGTTCTTGATGGCGTTGTCA 58.765 50.000 0.00 0.00 0.00 3.58
1513 1653 2.281139 TCGTTTGCCATGGCGTCA 60.281 55.556 30.87 15.36 45.51 4.35
1633 1776 2.039624 GAGGGGAGGCTCTGGTGA 59.960 66.667 15.23 0.00 0.00 4.02
1883 2041 1.519719 GCTGTACAGGAGCAGGAGG 59.480 63.158 23.95 0.00 36.40 4.30
1990 2148 0.841289 ACAGGAACTCCCCGTTGAAA 59.159 50.000 0.00 0.00 34.60 2.69
2020 2178 1.074727 ACCTCGATCCGGATCATCTCT 59.925 52.381 36.89 16.73 37.69 3.10
2135 2293 3.311966 CTGCTTTTTGCTTACCTGCTTC 58.688 45.455 0.00 0.00 43.37 3.86
2136 2294 2.546584 GCTGCTTTTTGCTTACCTGCTT 60.547 45.455 0.00 0.00 43.37 3.91
2137 2295 1.000171 GCTGCTTTTTGCTTACCTGCT 60.000 47.619 0.00 0.00 43.37 4.24
2138 2296 1.000171 AGCTGCTTTTTGCTTACCTGC 60.000 47.619 0.00 0.00 43.37 4.85
2141 2299 1.535462 TCGAGCTGCTTTTTGCTTACC 59.465 47.619 2.53 0.00 43.37 2.85
2143 2301 2.217750 TGTCGAGCTGCTTTTTGCTTA 58.782 42.857 2.53 0.00 43.37 3.09
2150 2308 1.268032 CGTTTGTTGTCGAGCTGCTTT 60.268 47.619 2.53 0.00 0.00 3.51
2162 2320 4.023707 AGAGAGGCTCATTTTCGTTTGTTG 60.024 41.667 18.26 0.00 32.06 3.33
2179 2337 1.477700 CTCTTGAGTGGAGCAGAGAGG 59.522 57.143 0.00 0.00 0.00 3.69
2197 2355 2.287608 CCTTCCGTTTGTTTCTTGGCTC 60.288 50.000 0.00 0.00 0.00 4.70
2198 2356 1.681264 CCTTCCGTTTGTTTCTTGGCT 59.319 47.619 0.00 0.00 0.00 4.75
2224 2405 1.004560 TCTTCACTTGCCGCCTCTG 60.005 57.895 0.00 0.00 0.00 3.35
2225 2406 1.294780 CTCTTCACTTGCCGCCTCT 59.705 57.895 0.00 0.00 0.00 3.69
2226 2407 1.743252 CCTCTTCACTTGCCGCCTC 60.743 63.158 0.00 0.00 0.00 4.70
2227 2408 2.177594 CTCCTCTTCACTTGCCGCCT 62.178 60.000 0.00 0.00 0.00 5.52
2228 2409 1.743252 CTCCTCTTCACTTGCCGCC 60.743 63.158 0.00 0.00 0.00 6.13
2286 2467 2.375146 AGGGAATTATTGTCGGGCAAC 58.625 47.619 0.00 0.00 40.28 4.17
2311 2492 4.684703 AGAAACAAACTAATCGAGACACGG 59.315 41.667 0.00 0.00 42.82 4.94
2313 2494 7.041984 AGGAAAGAAACAAACTAATCGAGACAC 60.042 37.037 0.00 0.00 0.00 3.67
2329 2510 3.139077 TCGAGCAAGGAAGGAAAGAAAC 58.861 45.455 0.00 0.00 0.00 2.78
2336 2517 0.247736 GAGCTTCGAGCAAGGAAGGA 59.752 55.000 11.70 0.00 45.56 3.36
2353 2538 7.377398 ACATGAATCTATCTTCTTCGATGGAG 58.623 38.462 0.00 0.00 34.92 3.86
2365 2550 8.153550 GGAACTACCATGAACATGAATCTATCT 58.846 37.037 15.21 0.00 41.20 1.98
2366 2551 8.153550 AGGAACTACCATGAACATGAATCTATC 58.846 37.037 15.21 6.99 37.83 2.08
2367 2552 8.038862 AGGAACTACCATGAACATGAATCTAT 57.961 34.615 15.21 0.00 37.83 1.98
2368 2553 7.437713 AGGAACTACCATGAACATGAATCTA 57.562 36.000 15.21 0.68 37.83 1.98
2369 2554 6.319048 AGGAACTACCATGAACATGAATCT 57.681 37.500 15.21 2.16 37.83 2.40
2396 2589 2.701107 TCTTCGTCTCGTCTCTGATGT 58.299 47.619 0.00 0.00 0.00 3.06
2399 2592 3.564644 AGTTTTCTTCGTCTCGTCTCTGA 59.435 43.478 0.00 0.00 0.00 3.27
2400 2593 3.891324 AGTTTTCTTCGTCTCGTCTCTG 58.109 45.455 0.00 0.00 0.00 3.35
2401 2594 4.538917 GAAGTTTTCTTCGTCTCGTCTCT 58.461 43.478 0.00 0.00 45.24 3.10
2427 2622 4.189231 CCTAGTTTATTTGCCACGCTAGT 58.811 43.478 0.00 0.00 0.00 2.57
2528 2741 2.125106 CGGCCTCTCCTTTTCCCG 60.125 66.667 0.00 0.00 0.00 5.14
2536 2754 3.839432 CGGGAACTCGGCCTCTCC 61.839 72.222 0.00 0.56 0.00 3.71
2552 2770 2.057316 GAAGCAGATGTGATCGATCCG 58.943 52.381 22.31 5.49 0.00 4.18
2586 2805 5.656213 AACGCCTATGTTAGAGTAGTTGT 57.344 39.130 0.00 0.00 0.00 3.32
2598 2817 2.031508 CACCAAAACGAAACGCCTATGT 60.032 45.455 0.00 0.00 0.00 2.29
2604 2823 1.206115 CCAGCACCAAAACGAAACGC 61.206 55.000 0.00 0.00 0.00 4.84
2622 2842 3.939066 ACAGAAATGTGCACCTACTACC 58.061 45.455 15.69 0.00 0.00 3.18
2661 2881 2.586425 CAAACCAGACACTCCAACCAT 58.414 47.619 0.00 0.00 0.00 3.55
2731 2962 2.629050 TTAGCTGTCGCTCGCCCATC 62.629 60.000 0.00 0.00 45.15 3.51
2770 3002 2.846665 AAAGGAGAGAGAGAGAGGGG 57.153 55.000 0.00 0.00 0.00 4.79
2774 3006 8.943594 AAAACTAGTAAAAGGAGAGAGAGAGA 57.056 34.615 0.00 0.00 0.00 3.10
2800 3043 5.791664 TCCCCCTATAAGTCAGTAAAACCAA 59.208 40.000 0.00 0.00 0.00 3.67
2802 3045 5.664457 TCTCCCCCTATAAGTCAGTAAAACC 59.336 44.000 0.00 0.00 0.00 3.27
2803 3046 6.803366 TCTCCCCCTATAAGTCAGTAAAAC 57.197 41.667 0.00 0.00 0.00 2.43
2804 3047 6.964086 ACTTCTCCCCCTATAAGTCAGTAAAA 59.036 38.462 0.00 0.00 0.00 1.52
2805 3048 6.509386 ACTTCTCCCCCTATAAGTCAGTAAA 58.491 40.000 0.00 0.00 0.00 2.01
2807 3050 5.745988 ACTTCTCCCCCTATAAGTCAGTA 57.254 43.478 0.00 0.00 0.00 2.74
2809 3052 5.707495 ACTACTTCTCCCCCTATAAGTCAG 58.293 45.833 0.00 0.00 34.23 3.51
2810 3053 5.745988 ACTACTTCTCCCCCTATAAGTCA 57.254 43.478 0.00 0.00 34.23 3.41
2811 3054 6.045341 TCCTACTACTTCTCCCCCTATAAGTC 59.955 46.154 0.00 0.00 34.23 3.01
2812 3055 5.921861 TCCTACTACTTCTCCCCCTATAAGT 59.078 44.000 0.00 0.00 36.26 2.24
2813 3056 6.045813 ACTCCTACTACTTCTCCCCCTATAAG 59.954 46.154 0.00 0.00 0.00 1.73
2814 3057 5.921861 ACTCCTACTACTTCTCCCCCTATAA 59.078 44.000 0.00 0.00 0.00 0.98
2816 3059 4.326610 ACTCCTACTACTTCTCCCCCTAT 58.673 47.826 0.00 0.00 0.00 2.57
2817 3060 3.757362 ACTCCTACTACTTCTCCCCCTA 58.243 50.000 0.00 0.00 0.00 3.53
2819 3062 3.203934 TGTACTCCTACTACTTCTCCCCC 59.796 52.174 0.00 0.00 0.00 5.40
2820 3063 4.516652 TGTACTCCTACTACTTCTCCCC 57.483 50.000 0.00 0.00 0.00 4.81
2821 3064 7.289310 AGTATTGTACTCCTACTACTTCTCCC 58.711 42.308 0.00 0.00 32.47 4.30
2822 3065 8.750515 AAGTATTGTACTCCTACTACTTCTCC 57.249 38.462 0.00 0.00 38.26 3.71
2828 3071 9.918630 TGTCAAAAAGTATTGTACTCCTACTAC 57.081 33.333 0.00 0.00 38.26 2.73
2830 3073 9.436957 CATGTCAAAAAGTATTGTACTCCTACT 57.563 33.333 0.00 0.00 38.26 2.57
2831 3074 9.216117 ACATGTCAAAAAGTATTGTACTCCTAC 57.784 33.333 0.00 0.00 38.26 3.18
2832 3075 9.214957 CACATGTCAAAAAGTATTGTACTCCTA 57.785 33.333 0.00 0.00 38.26 2.94
2833 3076 7.174946 CCACATGTCAAAAAGTATTGTACTCCT 59.825 37.037 0.00 0.00 38.26 3.69
2834 3077 7.305474 CCACATGTCAAAAAGTATTGTACTCC 58.695 38.462 0.00 0.00 38.26 3.85
2835 3078 7.305474 CCCACATGTCAAAAAGTATTGTACTC 58.695 38.462 0.00 0.00 38.26 2.59
2836 3079 6.294508 GCCCACATGTCAAAAAGTATTGTACT 60.295 38.462 0.00 0.00 41.73 2.73
2837 3080 5.861787 GCCCACATGTCAAAAAGTATTGTAC 59.138 40.000 0.00 0.00 0.00 2.90
2838 3081 5.335269 CGCCCACATGTCAAAAAGTATTGTA 60.335 40.000 0.00 0.00 0.00 2.41
2839 3082 4.558496 CGCCCACATGTCAAAAAGTATTGT 60.558 41.667 0.00 0.00 0.00 2.71
2840 3083 3.919804 CGCCCACATGTCAAAAAGTATTG 59.080 43.478 0.00 0.00 0.00 1.90
2841 3084 3.823873 TCGCCCACATGTCAAAAAGTATT 59.176 39.130 0.00 0.00 0.00 1.89
2842 3085 3.417101 TCGCCCACATGTCAAAAAGTAT 58.583 40.909 0.00 0.00 0.00 2.12
2843 3086 2.852449 TCGCCCACATGTCAAAAAGTA 58.148 42.857 0.00 0.00 0.00 2.24
2844 3087 1.686355 TCGCCCACATGTCAAAAAGT 58.314 45.000 0.00 0.00 0.00 2.66
2845 3088 2.988493 CAATCGCCCACATGTCAAAAAG 59.012 45.455 0.00 0.00 0.00 2.27
2846 3089 2.625314 TCAATCGCCCACATGTCAAAAA 59.375 40.909 0.00 0.00 0.00 1.94
2850 3093 1.744522 CATTCAATCGCCCACATGTCA 59.255 47.619 0.00 0.00 0.00 3.58
2868 3111 3.550431 CTCCCGGCCGTCCATCAT 61.550 66.667 26.12 0.00 0.00 2.45
2906 3149 1.598701 AAAGCTCCTTTCCGCCATGC 61.599 55.000 0.00 0.00 0.00 4.06
2907 3150 0.171903 CAAAGCTCCTTTCCGCCATG 59.828 55.000 0.00 0.00 30.60 3.66
2956 3203 2.710698 CGTTGCGGTCCGTTGTTT 59.289 55.556 13.94 0.00 0.00 2.83
2959 3206 3.456431 TTTGCGTTGCGGTCCGTTG 62.456 57.895 13.94 1.55 0.00 4.10
2960 3207 3.175976 CTTTGCGTTGCGGTCCGTT 62.176 57.895 13.94 0.00 0.00 4.44
2961 3208 3.645975 CTTTGCGTTGCGGTCCGT 61.646 61.111 13.94 0.00 0.00 4.69
2962 3209 3.645975 ACTTTGCGTTGCGGTCCG 61.646 61.111 6.99 6.99 0.00 4.79
2963 3210 2.051345 CACTTTGCGTTGCGGTCC 60.051 61.111 0.00 0.00 0.00 4.46
2964 3211 0.657368 CTTCACTTTGCGTTGCGGTC 60.657 55.000 0.00 0.00 0.00 4.79
2965 3212 1.355210 CTTCACTTTGCGTTGCGGT 59.645 52.632 0.00 0.00 0.00 5.68
2966 3213 0.657368 GACTTCACTTTGCGTTGCGG 60.657 55.000 0.00 0.00 0.00 5.69
2985 3232 1.229975 TGCAAGCGGTCAGTCATGTG 61.230 55.000 0.00 0.00 0.00 3.21
2987 3234 0.806868 AATGCAAGCGGTCAGTCATG 59.193 50.000 0.00 0.00 0.00 3.07
2988 3235 2.009774 GTAATGCAAGCGGTCAGTCAT 58.990 47.619 0.00 0.00 0.00 3.06
3008 3285 0.320771 CCTCCGTCTTTGTGGGACAG 60.321 60.000 0.00 0.00 41.80 3.51
3016 3293 3.186613 GCTTACTTGTTCCTCCGTCTTTG 59.813 47.826 0.00 0.00 0.00 2.77
3053 3339 1.442688 GTTTTAGCACAGCAGCGGC 60.443 57.895 0.00 0.00 40.15 6.53
3054 3340 1.394917 CTAGTTTTAGCACAGCAGCGG 59.605 52.381 0.00 0.00 40.15 5.52
3055 3341 2.069273 ACTAGTTTTAGCACAGCAGCG 58.931 47.619 0.00 0.00 40.15 5.18
3056 3342 3.067106 TGACTAGTTTTAGCACAGCAGC 58.933 45.455 0.00 0.00 0.00 5.25
3057 3343 4.752101 ACTTGACTAGTTTTAGCACAGCAG 59.248 41.667 0.00 0.00 31.29 4.24
3058 3344 4.703897 ACTTGACTAGTTTTAGCACAGCA 58.296 39.130 0.00 0.00 31.29 4.41
3059 3345 5.444122 CAACTTGACTAGTTTTAGCACAGC 58.556 41.667 0.00 0.00 44.73 4.40
3060 3346 5.237344 AGCAACTTGACTAGTTTTAGCACAG 59.763 40.000 0.00 0.00 44.73 3.66
3113 3483 4.957296 ACTACGTCAAGTTCATTTGGTCT 58.043 39.130 0.00 0.00 0.00 3.85
3119 3489 8.561738 AATGGAATTACTACGTCAAGTTCATT 57.438 30.769 0.00 0.00 32.46 2.57
3125 3495 6.978343 TGGAAATGGAATTACTACGTCAAG 57.022 37.500 0.00 0.00 33.67 3.02
3130 3500 7.985476 AGTTTGATGGAAATGGAATTACTACG 58.015 34.615 0.00 0.00 33.67 3.51
3137 3507 9.872684 AGATACATAGTTTGATGGAAATGGAAT 57.127 29.630 0.00 0.00 0.00 3.01
3138 3508 9.123902 CAGATACATAGTTTGATGGAAATGGAA 57.876 33.333 0.00 0.00 0.00 3.53
3139 3509 8.493607 TCAGATACATAGTTTGATGGAAATGGA 58.506 33.333 0.00 0.00 0.00 3.41
3140 3510 8.681486 TCAGATACATAGTTTGATGGAAATGG 57.319 34.615 0.00 0.00 0.00 3.16
3141 3511 9.941664 GTTCAGATACATAGTTTGATGGAAATG 57.058 33.333 0.00 0.00 0.00 2.32
3142 3512 9.911788 AGTTCAGATACATAGTTTGATGGAAAT 57.088 29.630 0.00 0.00 0.00 2.17
3144 3514 8.762645 AGAGTTCAGATACATAGTTTGATGGAA 58.237 33.333 0.00 0.00 0.00 3.53
3145 3515 8.311395 AGAGTTCAGATACATAGTTTGATGGA 57.689 34.615 0.00 0.00 0.00 3.41
3146 3516 9.689976 CTAGAGTTCAGATACATAGTTTGATGG 57.310 37.037 0.00 0.00 0.00 3.51
3153 3523 9.772973 CTCTGTACTAGAGTTCAGATACATAGT 57.227 37.037 16.44 0.00 46.39 2.12
3168 3538 4.100344 TGTTTGTTGTGCCTCTGTACTAGA 59.900 41.667 0.00 0.00 0.00 2.43
3173 3543 4.642437 TCAAATGTTTGTTGTGCCTCTGTA 59.358 37.500 5.48 0.00 39.18 2.74
3176 3546 4.341806 TCATCAAATGTTTGTTGTGCCTCT 59.658 37.500 13.32 0.00 38.42 3.69
3215 3585 8.665685 GCAGTAGTTAAAATACATAGTTGCTGT 58.334 33.333 0.00 0.00 0.00 4.40
3216 3586 8.664798 TGCAGTAGTTAAAATACATAGTTGCTG 58.335 33.333 9.63 0.00 0.00 4.41
3217 3587 8.786826 TGCAGTAGTTAAAATACATAGTTGCT 57.213 30.769 9.63 0.00 0.00 3.91
3218 3588 9.438291 CATGCAGTAGTTAAAATACATAGTTGC 57.562 33.333 0.00 3.80 0.00 4.17
3219 3589 9.438291 GCATGCAGTAGTTAAAATACATAGTTG 57.562 33.333 14.21 0.00 0.00 3.16
3220 3590 8.621286 GGCATGCAGTAGTTAAAATACATAGTT 58.379 33.333 21.36 0.00 0.00 2.24
3221 3591 7.993183 AGGCATGCAGTAGTTAAAATACATAGT 59.007 33.333 21.36 0.00 0.00 2.12
3222 3592 8.383318 AGGCATGCAGTAGTTAAAATACATAG 57.617 34.615 21.36 0.00 0.00 2.23
3223 3593 7.170828 CGAGGCATGCAGTAGTTAAAATACATA 59.829 37.037 21.36 0.00 0.00 2.29
3224 3594 6.017934 CGAGGCATGCAGTAGTTAAAATACAT 60.018 38.462 21.36 0.00 0.00 2.29
3225 3595 5.293324 CGAGGCATGCAGTAGTTAAAATACA 59.707 40.000 21.36 0.00 0.00 2.29
3226 3596 5.277345 CCGAGGCATGCAGTAGTTAAAATAC 60.277 44.000 21.36 0.00 0.00 1.89
3227 3597 4.814234 CCGAGGCATGCAGTAGTTAAAATA 59.186 41.667 21.36 0.00 0.00 1.40
3228 3598 3.627577 CCGAGGCATGCAGTAGTTAAAAT 59.372 43.478 21.36 0.00 0.00 1.82
3229 3599 3.006940 CCGAGGCATGCAGTAGTTAAAA 58.993 45.455 21.36 0.00 0.00 1.52
3230 3600 2.235155 TCCGAGGCATGCAGTAGTTAAA 59.765 45.455 21.36 0.00 0.00 1.52
3231 3601 1.828595 TCCGAGGCATGCAGTAGTTAA 59.171 47.619 21.36 0.00 0.00 2.01
3232 3602 1.480789 TCCGAGGCATGCAGTAGTTA 58.519 50.000 21.36 0.00 0.00 2.24
3233 3603 0.833287 ATCCGAGGCATGCAGTAGTT 59.167 50.000 21.36 0.00 0.00 2.24
3234 3604 0.105593 CATCCGAGGCATGCAGTAGT 59.894 55.000 21.36 0.00 0.00 2.73
3235 3605 0.602106 CCATCCGAGGCATGCAGTAG 60.602 60.000 21.36 6.23 0.00 2.57
3239 3609 0.535780 GAATCCATCCGAGGCATGCA 60.536 55.000 21.36 0.00 0.00 3.96
3241 3611 1.520494 CTGAATCCATCCGAGGCATG 58.480 55.000 0.00 0.00 0.00 4.06
3246 3616 1.069823 CCTCACCTGAATCCATCCGAG 59.930 57.143 0.00 0.00 0.00 4.63
3248 3618 1.069823 CTCCTCACCTGAATCCATCCG 59.930 57.143 0.00 0.00 0.00 4.18
3254 3624 1.134551 GTGGCTCTCCTCACCTGAATC 60.135 57.143 0.00 0.00 0.00 2.52
3261 3631 3.386237 AGGCGTGGCTCTCCTCAC 61.386 66.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.