Multiple sequence alignment - TraesCS1B01G304400

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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 TraesCS1B01G304400 chr1B 100.000 3223 0 0 1 3223 526433789 526430567 0.000000e+00 5952.0
1 TraesCS1B01G304400 chr1B 92.683 41 2 1 2838 2877 526380632 526380592 1.250000e-04 58.4
2 TraesCS1B01G304400 chr1A 89.109 2424 147 46 611 3006 490023922 490021588 0.000000e+00 2905.0
3 TraesCS1B01G304400 chr1A 84.530 989 87 35 2043 3006 490112592 490111645 0.000000e+00 918.0
4 TraesCS1B01G304400 chr1A 86.087 575 66 9 1 563 490024491 490023919 9.890000e-170 606.0
5 TraesCS1B01G304400 chr1A 77.042 710 77 37 2508 3165 490111259 490110584 2.400000e-86 329.0
6 TraesCS1B01G304400 chr1A 76.934 711 77 38 2508 3165 490021202 490020526 1.120000e-84 324.0
7 TraesCS1B01G304400 chr1D 87.491 1327 89 37 1687 3006 395881381 395880125 0.000000e+00 1459.0
8 TraesCS1B01G304400 chr1D 94.553 918 36 13 744 1660 395882278 395881374 0.000000e+00 1406.0
9 TraesCS1B01G304400 chr1D 84.988 806 52 17 1 777 395883044 395882279 0.000000e+00 754.0
10 TraesCS1B01G304400 chr1D 82.727 110 10 2 2505 2605 395798216 395798107 4.430000e-14 89.8
11 TraesCS1B01G304400 chr3A 80.609 361 59 8 1117 1470 599528613 599528969 5.300000e-68 268.0
12 TraesCS1B01G304400 chr3D 79.832 357 61 8 1121 1470 456641427 456641779 1.920000e-62 250.0
13 TraesCS1B01G304400 chr3B 79.552 357 62 7 1121 1470 603489684 603490036 8.930000e-61 244.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G304400 chr1B 526430567 526433789 3222 True 5952.000000 5952 100.000000 1 3223 1 chr1B.!!$R2 3222
1 TraesCS1B01G304400 chr1A 490020526 490024491 3965 True 1278.333333 2905 84.043333 1 3165 3 chr1A.!!$R1 3164
2 TraesCS1B01G304400 chr1A 490110584 490112592 2008 True 623.500000 918 80.786000 2043 3165 2 chr1A.!!$R2 1122
3 TraesCS1B01G304400 chr1D 395880125 395883044 2919 True 1206.333333 1459 89.010667 1 3006 3 chr1D.!!$R2 3005

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
273 278 0.033920 GGGGCAAACAAAGAAGCAGG 59.966 55.0 0.00 0.0 0.00 4.85 F
474 487 0.108186 ACGATCCGAGCAATTGAGCA 60.108 50.0 10.34 0.0 36.85 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2265 0.037326 TGCGAGATGTGGGTCTTGAC 60.037 55.000 0.0 0.0 32.32 3.18 R
2297 2373 4.673968 TCCGGTAGCAATCCTGTATCTAT 58.326 43.478 0.0 0.0 0.00 1.98 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
29 30 1.781786 CTACCTAGGGAGCTCAGCAA 58.218 55.000 17.19 0.00 0.00 3.91
59 60 1.885850 AGGTGTCACAAACGTCGCC 60.886 57.895 5.12 0.00 0.00 5.54
137 138 4.145876 TCAAAACTTTGTAGCTGCATCG 57.854 40.909 4.98 2.25 39.18 3.84
168 169 9.793252 CAAAACAGGTGATAAAGGATATTGAAG 57.207 33.333 0.00 0.00 0.00 3.02
175 176 8.160106 GGTGATAAAGGATATTGAAGGAGACAT 58.840 37.037 0.00 0.00 0.00 3.06
176 177 8.997323 GTGATAAAGGATATTGAAGGAGACATG 58.003 37.037 0.00 0.00 0.00 3.21
177 178 8.159447 TGATAAAGGATATTGAAGGAGACATGG 58.841 37.037 0.00 0.00 0.00 3.66
182 183 6.443206 AGGATATTGAAGGAGACATGGATAGG 59.557 42.308 0.00 0.00 0.00 2.57
184 185 7.127032 GGATATTGAAGGAGACATGGATAGGAT 59.873 40.741 0.00 0.00 0.00 3.24
229 234 1.029681 ACCGGGCAACTTTCTTCAAC 58.970 50.000 6.32 0.00 0.00 3.18
272 277 1.043022 AGGGGCAAACAAAGAAGCAG 58.957 50.000 0.00 0.00 0.00 4.24
273 278 0.033920 GGGGCAAACAAAGAAGCAGG 59.966 55.000 0.00 0.00 0.00 4.85
306 317 3.314693 AGTTACCTTTGGACCAGAGACA 58.685 45.455 13.59 0.00 0.00 3.41
315 326 0.827368 GACCAGAGACACATCCTCCC 59.173 60.000 0.00 0.00 0.00 4.30
329 340 1.227102 CTCCCCATTGATCCGGCAA 59.773 57.895 0.00 0.00 0.00 4.52
345 357 1.079127 CAACGAGATCGCCCTGGTT 60.079 57.895 1.39 0.00 44.43 3.67
353 365 1.779061 ATCGCCCTGGTTGAACCACT 61.779 55.000 14.05 0.00 44.79 4.00
363 375 0.938713 TTGAACCACTAAACCGCACG 59.061 50.000 0.00 0.00 0.00 5.34
393 406 0.108585 GTGGGAGGTGTTCAGCTTGA 59.891 55.000 5.99 0.00 0.00 3.02
397 410 2.229784 GGGAGGTGTTCAGCTTGAATTG 59.770 50.000 5.99 0.00 38.79 2.32
412 425 2.971330 TGAATTGTTGGGTGCAAAGGAT 59.029 40.909 0.00 0.00 0.00 3.24
416 429 2.950781 TGTTGGGTGCAAAGGATGTTA 58.049 42.857 0.00 0.00 0.00 2.41
474 487 0.108186 ACGATCCGAGCAATTGAGCA 60.108 50.000 10.34 0.00 36.85 4.26
498 511 5.130477 ACTCCCACATTCCGACTAATAATGT 59.870 40.000 0.00 0.00 42.91 2.71
530 544 6.922957 ACGTTTTACATTTCGTTACAGAGGTA 59.077 34.615 0.00 0.00 32.62 3.08
539 553 9.234384 CATTTCGTTACAGAGGTAGTATAGTTG 57.766 37.037 0.00 0.00 0.00 3.16
541 555 9.448438 TTTCGTTACAGAGGTAGTATAGTTGTA 57.552 33.333 0.00 0.00 0.00 2.41
560 574 5.416271 TGTATCTTAGTGGTTCCCTCAAC 57.584 43.478 0.00 0.00 0.00 3.18
590 604 4.861102 GGTATGCCGTGTAATAGTACCT 57.139 45.455 0.00 0.00 0.00 3.08
591 605 5.964958 GGTATGCCGTGTAATAGTACCTA 57.035 43.478 0.00 0.00 0.00 3.08
592 606 5.703876 GGTATGCCGTGTAATAGTACCTAC 58.296 45.833 0.00 0.00 0.00 3.18
593 607 3.969117 TGCCGTGTAATAGTACCTACG 57.031 47.619 6.31 6.31 32.31 3.51
594 608 3.278574 TGCCGTGTAATAGTACCTACGT 58.721 45.455 10.87 0.00 31.19 3.57
595 609 3.312421 TGCCGTGTAATAGTACCTACGTC 59.688 47.826 10.87 1.20 31.19 4.34
596 610 3.561725 GCCGTGTAATAGTACCTACGTCT 59.438 47.826 10.87 0.00 31.19 4.18
597 611 4.035675 GCCGTGTAATAGTACCTACGTCTT 59.964 45.833 10.87 0.00 31.19 3.01
598 612 5.505286 CCGTGTAATAGTACCTACGTCTTG 58.495 45.833 10.87 0.00 31.19 3.02
599 613 5.065218 CCGTGTAATAGTACCTACGTCTTGT 59.935 44.000 10.87 0.00 31.19 3.16
600 614 6.403636 CCGTGTAATAGTACCTACGTCTTGTT 60.404 42.308 10.87 0.00 31.19 2.83
601 615 6.467047 CGTGTAATAGTACCTACGTCTTGTTG 59.533 42.308 0.00 0.00 29.53 3.33
603 617 6.658816 TGTAATAGTACCTACGTCTTGTTGGA 59.341 38.462 0.00 0.00 45.16 3.53
604 618 3.930634 AGTACCTACGTCTTGTTGGAC 57.069 47.619 0.00 0.00 45.16 4.02
605 619 3.225104 AGTACCTACGTCTTGTTGGACA 58.775 45.455 0.00 0.00 45.16 4.02
606 620 2.814280 ACCTACGTCTTGTTGGACAG 57.186 50.000 0.00 0.00 45.16 3.51
607 621 2.313317 ACCTACGTCTTGTTGGACAGA 58.687 47.619 0.00 0.00 45.16 3.41
608 622 2.897969 ACCTACGTCTTGTTGGACAGAT 59.102 45.455 0.00 0.00 45.16 2.90
609 623 3.323979 ACCTACGTCTTGTTGGACAGATT 59.676 43.478 0.00 0.00 45.16 2.40
610 624 4.525487 ACCTACGTCTTGTTGGACAGATTA 59.475 41.667 0.00 0.00 45.16 1.75
611 625 5.103000 CCTACGTCTTGTTGGACAGATTAG 58.897 45.833 0.00 0.00 45.16 1.73
641 655 8.664211 AAGTTAAACTTAACAGGACTCTCTTG 57.336 34.615 13.38 0.00 44.14 3.02
690 726 1.570813 TGCGCGACCATATCTTCTTG 58.429 50.000 12.10 0.00 0.00 3.02
697 735 4.636206 GCGACCATATCTTCTTGGTTCTTT 59.364 41.667 0.00 0.00 46.14 2.52
698 736 5.123979 GCGACCATATCTTCTTGGTTCTTTT 59.876 40.000 0.00 0.00 46.14 2.27
699 737 6.349363 GCGACCATATCTTCTTGGTTCTTTTT 60.349 38.462 0.00 0.00 46.14 1.94
950 1022 1.340248 CCGCTATATATACCTGCCCGG 59.660 57.143 0.00 0.00 39.35 5.73
976 1050 0.680921 CGCCTCAACCACAATCCCAT 60.681 55.000 0.00 0.00 0.00 4.00
1010 1084 4.508128 ACCTACGATGGCGCCACG 62.508 66.667 34.24 34.24 42.48 4.94
1417 1491 4.656117 ACGACATCACCGCGCACA 62.656 61.111 8.75 0.00 0.00 4.57
1628 1702 2.045524 CCATGACTACCTCATCAGCCT 58.954 52.381 0.00 0.00 37.53 4.58
1678 1752 9.906660 GATCTTCAGATCGATACTTAATCTGTT 57.093 33.333 0.00 0.00 44.33 3.16
1698 1772 8.954950 TCTGTTAATCATCATCTTCTTCTTCC 57.045 34.615 0.00 0.00 0.00 3.46
1720 1794 0.309922 TCGTCCACTCAGTTCGTGTC 59.690 55.000 0.00 0.00 0.00 3.67
1726 1800 4.395542 GTCCACTCAGTTCGTGTCTATAGT 59.604 45.833 0.00 0.00 0.00 2.12
1728 1803 6.260493 GTCCACTCAGTTCGTGTCTATAGTAT 59.740 42.308 0.00 0.00 0.00 2.12
1732 1807 7.853437 CACTCAGTTCGTGTCTATAGTATTGAG 59.147 40.741 0.00 6.08 34.79 3.02
1733 1808 7.769507 ACTCAGTTCGTGTCTATAGTATTGAGA 59.230 37.037 0.00 0.00 33.35 3.27
1900 1975 2.125350 CCTGCAGAACGAGGAGGC 60.125 66.667 17.39 0.00 37.79 4.70
2205 2280 2.167281 CAGATCGTCAAGACCCACATCT 59.833 50.000 0.00 0.00 0.00 2.90
2270 2346 0.939577 CGGCTGTGCGCGTATAGATT 60.940 55.000 23.93 0.00 40.44 2.40
2283 2359 9.717892 TGCGCGTATAGATTATAGAGAAATTAG 57.282 33.333 8.43 0.00 0.00 1.73
2297 2373 6.725364 AGAGAAATTAGGCTCTTTGATGGAA 58.275 36.000 0.00 0.00 38.26 3.53
2375 2452 6.558009 GTCCTTCAGACATACACACGTTATA 58.442 40.000 0.00 0.00 45.55 0.98
2391 2485 7.527183 CACACGTTATAATTCGCTGTGATTATG 59.473 37.037 16.81 2.65 39.17 1.90
2428 2522 6.162777 AGACTTCAAATCAGCTTCTAGTCAC 58.837 40.000 0.00 0.00 34.66 3.67
2445 2539 7.568349 TCTAGTCACAATAGCAGATTGGATTT 58.432 34.615 13.93 2.73 33.56 2.17
2446 2540 6.690194 AGTCACAATAGCAGATTGGATTTC 57.310 37.500 13.93 2.94 33.56 2.17
2447 2541 6.421485 AGTCACAATAGCAGATTGGATTTCT 58.579 36.000 13.93 4.61 33.56 2.52
2457 2551 5.519206 GCAGATTGGATTTCTTTCAGATTGC 59.481 40.000 0.00 0.00 0.00 3.56
2460 2554 7.488471 CAGATTGGATTTCTTTCAGATTGCTTC 59.512 37.037 0.00 0.00 0.00 3.86
2465 2559 5.362556 TTTCTTTCAGATTGCTTCTTCCG 57.637 39.130 0.00 0.00 29.93 4.30
2467 2565 5.147330 TCTTTCAGATTGCTTCTTCCGTA 57.853 39.130 0.00 0.00 29.93 4.02
2471 2569 6.817765 TTCAGATTGCTTCTTCCGTAAATT 57.182 33.333 0.00 0.00 29.93 1.82
2472 2570 6.422776 TCAGATTGCTTCTTCCGTAAATTC 57.577 37.500 0.00 0.00 29.93 2.17
2473 2571 6.173339 TCAGATTGCTTCTTCCGTAAATTCT 58.827 36.000 0.00 0.00 29.93 2.40
2474 2572 6.655003 TCAGATTGCTTCTTCCGTAAATTCTT 59.345 34.615 0.00 0.00 29.93 2.52
2475 2573 6.744537 CAGATTGCTTCTTCCGTAAATTCTTG 59.255 38.462 0.00 0.00 29.93 3.02
2476 2574 4.419522 TGCTTCTTCCGTAAATTCTTGC 57.580 40.909 0.00 0.00 0.00 4.01
2477 2575 4.072131 TGCTTCTTCCGTAAATTCTTGCT 58.928 39.130 0.00 0.00 0.00 3.91
2478 2576 5.242434 TGCTTCTTCCGTAAATTCTTGCTA 58.758 37.500 0.00 0.00 0.00 3.49
2479 2577 5.121768 TGCTTCTTCCGTAAATTCTTGCTAC 59.878 40.000 0.00 0.00 0.00 3.58
2548 2658 2.209838 AACGCTCATCATCGATTCGT 57.790 45.000 5.89 0.00 0.00 3.85
2549 2659 1.759994 ACGCTCATCATCGATTCGTC 58.240 50.000 5.89 0.00 0.00 4.20
2550 2660 1.065551 ACGCTCATCATCGATTCGTCA 59.934 47.619 5.89 0.00 0.00 4.35
2551 2661 1.449789 CGCTCATCATCGATTCGTCAC 59.550 52.381 5.89 0.00 0.00 3.67
2552 2662 2.463876 GCTCATCATCGATTCGTCACA 58.536 47.619 5.89 0.00 0.00 3.58
2553 2663 3.055591 GCTCATCATCGATTCGTCACAT 58.944 45.455 5.89 0.00 0.00 3.21
2554 2664 3.121092 GCTCATCATCGATTCGTCACATG 60.121 47.826 5.89 2.76 0.00 3.21
2555 2665 4.045636 TCATCATCGATTCGTCACATGT 57.954 40.909 5.89 0.00 0.00 3.21
2556 2666 4.044426 TCATCATCGATTCGTCACATGTC 58.956 43.478 5.89 0.00 0.00 3.06
2557 2667 3.782889 TCATCGATTCGTCACATGTCT 57.217 42.857 5.89 0.00 0.00 3.41
2558 2668 3.695816 TCATCGATTCGTCACATGTCTC 58.304 45.455 5.89 0.00 0.00 3.36
2559 2669 3.128589 TCATCGATTCGTCACATGTCTCA 59.871 43.478 5.89 0.00 0.00 3.27
2560 2670 3.782889 TCGATTCGTCACATGTCTCAT 57.217 42.857 5.89 0.00 0.00 2.90
2561 2671 4.893424 TCGATTCGTCACATGTCTCATA 57.107 40.909 5.89 0.00 0.00 2.15
2562 2672 5.438761 TCGATTCGTCACATGTCTCATAT 57.561 39.130 5.89 0.00 0.00 1.78
2563 2673 5.452777 TCGATTCGTCACATGTCTCATATC 58.547 41.667 5.89 0.00 0.00 1.63
2564 2674 4.618912 CGATTCGTCACATGTCTCATATCC 59.381 45.833 0.00 0.00 0.00 2.59
2565 2675 5.563671 CGATTCGTCACATGTCTCATATCCT 60.564 44.000 0.00 0.00 0.00 3.24
2566 2676 4.837896 TCGTCACATGTCTCATATCCTC 57.162 45.455 0.00 0.00 0.00 3.71
2567 2677 4.207165 TCGTCACATGTCTCATATCCTCA 58.793 43.478 0.00 0.00 0.00 3.86
2568 2678 4.036852 TCGTCACATGTCTCATATCCTCAC 59.963 45.833 0.00 0.00 0.00 3.51
2569 2679 4.202050 CGTCACATGTCTCATATCCTCACA 60.202 45.833 0.00 0.00 0.00 3.58
2570 2680 5.664457 GTCACATGTCTCATATCCTCACAA 58.336 41.667 0.00 0.00 0.00 3.33
2571 2681 5.752472 GTCACATGTCTCATATCCTCACAAG 59.248 44.000 0.00 0.00 0.00 3.16
2572 2682 5.055144 CACATGTCTCATATCCTCACAAGG 58.945 45.833 0.00 0.00 44.89 3.61
2573 2683 4.102210 ACATGTCTCATATCCTCACAAGGG 59.898 45.833 0.00 0.00 43.56 3.95
2574 2684 3.994317 TGTCTCATATCCTCACAAGGGA 58.006 45.455 0.00 0.00 43.56 4.20
2575 2685 3.963374 TGTCTCATATCCTCACAAGGGAG 59.037 47.826 0.00 0.00 43.56 4.30
2576 2686 3.964031 GTCTCATATCCTCACAAGGGAGT 59.036 47.826 0.00 0.00 43.56 3.85
2577 2687 4.407296 GTCTCATATCCTCACAAGGGAGTT 59.593 45.833 0.00 0.00 43.56 3.01
2578 2688 5.598830 GTCTCATATCCTCACAAGGGAGTTA 59.401 44.000 0.00 0.00 43.56 2.24
2579 2689 6.098409 GTCTCATATCCTCACAAGGGAGTTAA 59.902 42.308 0.00 0.00 43.56 2.01
2580 2690 6.672218 TCTCATATCCTCACAAGGGAGTTAAA 59.328 38.462 0.00 0.00 43.56 1.52
2614 2724 5.592688 GCATCCACCTTTTGCCTTAGTTATA 59.407 40.000 0.00 0.00 0.00 0.98
2615 2725 6.265422 GCATCCACCTTTTGCCTTAGTTATAT 59.735 38.462 0.00 0.00 0.00 0.86
2634 2744 8.361139 AGTTATATGAGTCTGAAATAACTCCCG 58.639 37.037 11.13 0.00 38.39 5.14
2637 2747 3.835978 TGAGTCTGAAATAACTCCCGGAA 59.164 43.478 0.73 0.00 40.98 4.30
2672 2782 2.851263 ATAGTTGGTCGGCAAACTCA 57.149 45.000 14.32 0.96 39.46 3.41
2675 2785 1.676006 AGTTGGTCGGCAAACTCAAAG 59.324 47.619 3.29 0.00 33.79 2.77
2707 2817 7.816945 AACTATCCAGATTTTTCGCAAATTG 57.183 32.000 0.00 0.00 0.00 2.32
2711 2821 5.460646 TCCAGATTTTTCGCAAATTGAGAC 58.539 37.500 0.00 0.00 0.00 3.36
2722 2832 0.179073 AATTGAGACTCCCGCCATCG 60.179 55.000 0.00 0.00 0.00 3.84
2744 2854 3.274288 GCTGCTACTTCATTGTTAGCCT 58.726 45.455 0.00 0.00 33.19 4.58
2746 2856 4.156739 GCTGCTACTTCATTGTTAGCCTTT 59.843 41.667 0.00 0.00 33.19 3.11
2776 2887 9.920946 AACCTGAAGATAAGATAAAAGCCATTA 57.079 29.630 0.00 0.00 0.00 1.90
2805 2916 5.133264 GTGTGAATATAAAGAGAATGCGCG 58.867 41.667 0.00 0.00 0.00 6.86
2860 2971 0.098200 CATGCATGTCTTGACAGCGG 59.902 55.000 18.91 3.24 0.00 5.52
2863 2974 1.639298 GCATGTCTTGACAGCGGGAC 61.639 60.000 9.39 0.00 0.00 4.46
2914 3025 4.157105 TGAGCATGAATTGGTGATCAGTTG 59.843 41.667 0.00 0.00 36.00 3.16
2963 3074 6.199937 GCTTGAGATTCAGGCTTGATAAAA 57.800 37.500 0.00 0.00 44.80 1.52
2999 3982 6.566197 TTCAGGAAAAGAAGAAGAGAATGC 57.434 37.500 0.00 0.00 0.00 3.56
3009 3992 5.647225 AGAAGAAGAGAATGCTCAATTGGAC 59.353 40.000 2.79 0.00 43.81 4.02
3028 4011 5.430886 TGGACATTATGATGACACTTCAGG 58.569 41.667 4.20 0.00 36.73 3.86
3032 4015 6.715280 ACATTATGATGACACTTCAGGTTCT 58.285 36.000 4.20 0.00 36.73 3.01
3033 4016 7.170965 ACATTATGATGACACTTCAGGTTCTT 58.829 34.615 4.20 0.00 36.73 2.52
3035 4018 8.607459 CATTATGATGACACTTCAGGTTCTTAC 58.393 37.037 0.00 0.00 34.35 2.34
3036 4019 5.545063 TGATGACACTTCAGGTTCTTACA 57.455 39.130 0.00 0.00 34.35 2.41
3037 4020 5.924356 TGATGACACTTCAGGTTCTTACAA 58.076 37.500 0.00 0.00 34.35 2.41
3042 4044 6.483307 TGACACTTCAGGTTCTTACAAAGATG 59.517 38.462 0.00 0.00 37.38 2.90
3045 4047 7.441458 ACACTTCAGGTTCTTACAAAGATGTAC 59.559 37.037 0.00 0.00 41.64 2.90
3049 4051 8.185506 TCAGGTTCTTACAAAGATGTACTGTA 57.814 34.615 0.00 0.00 41.64 2.74
3051 4053 9.088512 CAGGTTCTTACAAAGATGTACTGTATC 57.911 37.037 0.00 0.00 41.64 2.24
3052 4054 8.258708 AGGTTCTTACAAAGATGTACTGTATCC 58.741 37.037 0.00 0.00 41.64 2.59
3054 4056 7.973048 TCTTACAAAGATGTACTGTATCCCT 57.027 36.000 0.00 0.00 41.64 4.20
3055 4057 9.483489 TTCTTACAAAGATGTACTGTATCCCTA 57.517 33.333 0.00 0.00 41.64 3.53
3087 4089 7.934855 AGTTCTGAAGTTAATCATGAATGCT 57.065 32.000 0.00 0.00 0.00 3.79
3104 4117 1.416030 TGCTAGTGCAGACAGAAACCA 59.584 47.619 0.00 0.00 45.31 3.67
3111 4124 3.002759 GTGCAGACAGAAACCACTTCTTC 59.997 47.826 0.00 0.00 41.97 2.87
3165 4182 4.302067 ACTCATAGATGAAGGGTCCATGT 58.698 43.478 0.00 0.00 36.18 3.21
3166 4183 4.723789 ACTCATAGATGAAGGGTCCATGTT 59.276 41.667 0.00 0.00 36.18 2.71
3167 4184 5.039920 TCATAGATGAAGGGTCCATGTTG 57.960 43.478 0.00 0.00 33.08 3.33
3168 4185 4.721274 TCATAGATGAAGGGTCCATGTTGA 59.279 41.667 0.00 0.00 33.08 3.18
3169 4186 5.370584 TCATAGATGAAGGGTCCATGTTGAT 59.629 40.000 0.00 0.00 33.08 2.57
3170 4187 6.558394 TCATAGATGAAGGGTCCATGTTGATA 59.442 38.462 0.00 0.00 33.08 2.15
3171 4188 5.301835 AGATGAAGGGTCCATGTTGATAG 57.698 43.478 0.00 0.00 0.00 2.08
3172 4189 4.723789 AGATGAAGGGTCCATGTTGATAGT 59.276 41.667 0.00 0.00 0.00 2.12
3173 4190 4.927267 TGAAGGGTCCATGTTGATAGTT 57.073 40.909 0.00 0.00 0.00 2.24
3174 4191 5.255397 TGAAGGGTCCATGTTGATAGTTT 57.745 39.130 0.00 0.00 0.00 2.66
3175 4192 5.640147 TGAAGGGTCCATGTTGATAGTTTT 58.360 37.500 0.00 0.00 0.00 2.43
3176 4193 6.074648 TGAAGGGTCCATGTTGATAGTTTTT 58.925 36.000 0.00 0.00 0.00 1.94
3177 4194 7.235079 TGAAGGGTCCATGTTGATAGTTTTTA 58.765 34.615 0.00 0.00 0.00 1.52
3178 4195 7.393234 TGAAGGGTCCATGTTGATAGTTTTTAG 59.607 37.037 0.00 0.00 0.00 1.85
3179 4196 5.652452 AGGGTCCATGTTGATAGTTTTTAGC 59.348 40.000 0.00 0.00 0.00 3.09
3180 4197 5.417580 GGGTCCATGTTGATAGTTTTTAGCA 59.582 40.000 0.00 0.00 0.00 3.49
3181 4198 6.404734 GGGTCCATGTTGATAGTTTTTAGCAG 60.405 42.308 0.00 0.00 0.00 4.24
3182 4199 6.374333 GGTCCATGTTGATAGTTTTTAGCAGA 59.626 38.462 0.00 0.00 0.00 4.26
3183 4200 7.094377 GGTCCATGTTGATAGTTTTTAGCAGAA 60.094 37.037 0.00 0.00 0.00 3.02
3184 4201 8.462016 GTCCATGTTGATAGTTTTTAGCAGAAT 58.538 33.333 0.00 0.00 0.00 2.40
3185 4202 9.679661 TCCATGTTGATAGTTTTTAGCAGAATA 57.320 29.630 0.00 0.00 0.00 1.75
3186 4203 9.722056 CCATGTTGATAGTTTTTAGCAGAATAC 57.278 33.333 0.00 0.00 0.00 1.89
3193 4210 9.278734 GATAGTTTTTAGCAGAATACAAGTTGC 57.721 33.333 1.81 0.00 36.83 4.17
3195 4212 8.391075 AGTTTTTAGCAGAATACAAGTTGCTA 57.609 30.769 1.81 1.25 44.47 3.49
3196 4213 8.290325 AGTTTTTAGCAGAATACAAGTTGCTAC 58.710 33.333 1.81 0.00 45.71 3.58
3197 4214 6.737254 TTTAGCAGAATACAAGTTGCTACC 57.263 37.500 1.81 0.00 45.71 3.18
3198 4215 4.286297 AGCAGAATACAAGTTGCTACCA 57.714 40.909 1.81 0.00 44.47 3.25
3199 4216 4.003648 AGCAGAATACAAGTTGCTACCAC 58.996 43.478 1.81 0.00 44.47 4.16
3200 4217 3.751175 GCAGAATACAAGTTGCTACCACA 59.249 43.478 1.81 0.00 33.88 4.17
3201 4218 4.215399 GCAGAATACAAGTTGCTACCACAA 59.785 41.667 1.81 0.00 33.88 3.33
3202 4219 5.106157 GCAGAATACAAGTTGCTACCACAAT 60.106 40.000 1.81 0.00 33.88 2.71
3203 4220 6.093495 GCAGAATACAAGTTGCTACCACAATA 59.907 38.462 1.81 0.00 33.88 1.90
3204 4221 7.464358 CAGAATACAAGTTGCTACCACAATAC 58.536 38.462 1.81 0.00 0.00 1.89
3205 4222 7.119116 CAGAATACAAGTTGCTACCACAATACA 59.881 37.037 1.81 0.00 0.00 2.29
3206 4223 7.829211 AGAATACAAGTTGCTACCACAATACAT 59.171 33.333 1.81 0.00 0.00 2.29
3207 4224 5.627499 ACAAGTTGCTACCACAATACATG 57.373 39.130 1.81 0.00 0.00 3.21
3208 4225 5.312895 ACAAGTTGCTACCACAATACATGA 58.687 37.500 1.81 0.00 0.00 3.07
3209 4226 5.767665 ACAAGTTGCTACCACAATACATGAA 59.232 36.000 1.81 0.00 0.00 2.57
3210 4227 5.880054 AGTTGCTACCACAATACATGAAC 57.120 39.130 0.00 0.00 0.00 3.18
3211 4228 5.312895 AGTTGCTACCACAATACATGAACA 58.687 37.500 0.00 0.00 0.00 3.18
3212 4229 5.945784 AGTTGCTACCACAATACATGAACAT 59.054 36.000 0.00 0.00 0.00 2.71
3213 4230 5.816449 TGCTACCACAATACATGAACATG 57.184 39.130 12.43 12.43 44.15 3.21
3214 4231 4.096231 TGCTACCACAATACATGAACATGC 59.904 41.667 13.71 0.00 42.39 4.06
3215 4232 4.336433 GCTACCACAATACATGAACATGCT 59.664 41.667 13.71 5.28 42.39 3.79
3216 4233 5.163622 GCTACCACAATACATGAACATGCTT 60.164 40.000 13.71 6.15 42.39 3.91
3217 4234 6.038161 GCTACCACAATACATGAACATGCTTA 59.962 38.462 13.71 1.96 42.39 3.09
3218 4235 7.255242 GCTACCACAATACATGAACATGCTTAT 60.255 37.037 13.71 4.01 42.39 1.73
3219 4236 9.271828 CTACCACAATACATGAACATGCTTATA 57.728 33.333 13.71 1.02 42.39 0.98
3220 4237 8.518430 ACCACAATACATGAACATGCTTATAA 57.482 30.769 13.71 0.00 42.39 0.98
3221 4238 9.135189 ACCACAATACATGAACATGCTTATAAT 57.865 29.630 13.71 0.00 42.39 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.757188 GCTGAGCTCCCTAGGTAGCA 60.757 60.000 26.46 7.60 41.32 3.49
29 30 1.152963 GACACCTGGCACCAACAGT 60.153 57.895 0.00 0.00 34.16 3.55
137 138 6.834168 TCCTTTATCACCTGTTTTGAATCC 57.166 37.500 0.00 0.00 0.00 3.01
168 169 4.202398 TGCAAAGATCCTATCCATGTCTCC 60.202 45.833 0.00 0.00 0.00 3.71
175 176 5.571791 TGATGATGCAAAGATCCTATCCA 57.428 39.130 0.00 0.00 0.00 3.41
176 177 5.415077 CCTTGATGATGCAAAGATCCTATCC 59.585 44.000 0.00 0.00 0.00 2.59
177 178 6.236409 TCCTTGATGATGCAAAGATCCTATC 58.764 40.000 0.00 0.00 0.00 2.08
182 183 5.763698 TGATCTCCTTGATGATGCAAAGATC 59.236 40.000 0.00 0.00 39.88 2.75
184 185 5.106876 TGATCTCCTTGATGATGCAAAGA 57.893 39.130 0.00 0.00 35.14 2.52
252 257 1.413812 CTGCTTCTTTGTTTGCCCCTT 59.586 47.619 0.00 0.00 0.00 3.95
289 294 1.507140 TGTGTCTCTGGTCCAAAGGT 58.493 50.000 0.00 0.00 0.00 3.50
290 295 2.616510 GGATGTGTCTCTGGTCCAAAGG 60.617 54.545 0.00 0.00 0.00 3.11
306 317 0.767375 CGGATCAATGGGGAGGATGT 59.233 55.000 0.00 0.00 0.00 3.06
315 326 0.461870 TCTCGTTGCCGGATCAATGG 60.462 55.000 5.05 1.22 34.58 3.16
329 340 1.541310 TTCAACCAGGGCGATCTCGT 61.541 55.000 1.14 0.00 42.22 4.18
345 357 0.179078 ACGTGCGGTTTAGTGGTTCA 60.179 50.000 0.00 0.00 0.00 3.18
371 384 1.150536 GCTGAACACCTCCCACCAA 59.849 57.895 0.00 0.00 0.00 3.67
384 397 2.224018 GCACCCAACAATTCAAGCTGAA 60.224 45.455 0.00 0.00 41.09 3.02
393 406 2.705127 ACATCCTTTGCACCCAACAATT 59.295 40.909 0.00 0.00 0.00 2.32
397 410 2.625790 TGTAACATCCTTTGCACCCAAC 59.374 45.455 0.00 0.00 0.00 3.77
412 425 0.766131 TTCCGCCTTCCCTTGTAACA 59.234 50.000 0.00 0.00 0.00 2.41
416 429 0.611896 CCATTTCCGCCTTCCCTTGT 60.612 55.000 0.00 0.00 0.00 3.16
474 487 5.130477 ACATTATTAGTCGGAATGTGGGAGT 59.870 40.000 0.00 0.00 41.17 3.85
498 511 9.121517 TGTAACGAAATGTAAAACGTTTTTCAA 57.878 25.926 28.84 17.40 44.46 2.69
518 531 9.270640 AGATACAACTATACTACCTCTGTAACG 57.729 37.037 0.00 0.00 0.00 3.18
553 567 2.373540 TACCGTTCATTCGTTGAGGG 57.626 50.000 7.95 7.95 35.27 4.30
586 600 3.489355 TCTGTCCAACAAGACGTAGGTA 58.511 45.455 0.00 0.00 39.77 3.08
589 603 5.103000 CCTAATCTGTCCAACAAGACGTAG 58.897 45.833 0.00 0.00 39.77 3.51
590 604 4.768448 TCCTAATCTGTCCAACAAGACGTA 59.232 41.667 0.00 0.00 39.77 3.57
591 605 3.576982 TCCTAATCTGTCCAACAAGACGT 59.423 43.478 0.00 0.00 39.77 4.34
592 606 4.177026 CTCCTAATCTGTCCAACAAGACG 58.823 47.826 0.00 0.00 39.77 4.18
593 607 4.223032 TCCTCCTAATCTGTCCAACAAGAC 59.777 45.833 0.00 0.00 37.28 3.01
594 608 4.425772 TCCTCCTAATCTGTCCAACAAGA 58.574 43.478 0.00 0.00 0.00 3.02
595 609 4.826274 TCCTCCTAATCTGTCCAACAAG 57.174 45.455 0.00 0.00 0.00 3.16
596 610 4.597507 ACTTCCTCCTAATCTGTCCAACAA 59.402 41.667 0.00 0.00 0.00 2.83
597 611 4.168101 ACTTCCTCCTAATCTGTCCAACA 58.832 43.478 0.00 0.00 0.00 3.33
598 612 4.828072 ACTTCCTCCTAATCTGTCCAAC 57.172 45.455 0.00 0.00 0.00 3.77
599 613 6.945636 TTAACTTCCTCCTAATCTGTCCAA 57.054 37.500 0.00 0.00 0.00 3.53
600 614 6.500751 AGTTTAACTTCCTCCTAATCTGTCCA 59.499 38.462 0.00 0.00 0.00 4.02
601 615 6.948589 AGTTTAACTTCCTCCTAATCTGTCC 58.051 40.000 0.00 0.00 0.00 4.02
602 616 9.939802 TTAAGTTTAACTTCCTCCTAATCTGTC 57.060 33.333 14.03 0.00 39.51 3.51
603 617 9.722184 GTTAAGTTTAACTTCCTCCTAATCTGT 57.278 33.333 14.03 0.00 39.51 3.41
604 618 9.720769 TGTTAAGTTTAACTTCCTCCTAATCTG 57.279 33.333 14.03 0.00 42.61 2.90
605 619 9.945904 CTGTTAAGTTTAACTTCCTCCTAATCT 57.054 33.333 14.03 0.00 42.61 2.40
606 620 9.163899 CCTGTTAAGTTTAACTTCCTCCTAATC 57.836 37.037 14.03 0.00 42.61 1.75
607 621 8.887393 TCCTGTTAAGTTTAACTTCCTCCTAAT 58.113 33.333 14.03 0.00 42.61 1.73
608 622 8.152898 GTCCTGTTAAGTTTAACTTCCTCCTAA 58.847 37.037 14.03 0.00 42.61 2.69
609 623 7.511714 AGTCCTGTTAAGTTTAACTTCCTCCTA 59.488 37.037 14.03 0.00 42.61 2.94
610 624 6.329460 AGTCCTGTTAAGTTTAACTTCCTCCT 59.671 38.462 14.03 0.50 42.61 3.69
611 625 6.531923 AGTCCTGTTAAGTTTAACTTCCTCC 58.468 40.000 14.03 1.97 42.61 4.30
641 655 3.312697 GGAAGATTGGCTTTATCGTGTCC 59.687 47.826 0.00 0.00 36.83 4.02
928 1000 2.293677 CGGGCAGGTATATATAGCGGAG 59.706 54.545 21.43 13.96 35.98 4.63
929 1001 2.304092 CGGGCAGGTATATATAGCGGA 58.696 52.381 21.43 0.00 35.98 5.54
931 1003 1.269621 GCCGGGCAGGTATATATAGCG 60.270 57.143 15.62 11.22 43.70 4.26
932 1004 1.070289 GGCCGGGCAGGTATATATAGC 59.930 57.143 25.33 13.05 43.70 2.97
933 1005 1.692519 GGGCCGGGCAGGTATATATAG 59.307 57.143 30.95 0.00 43.70 1.31
950 1022 4.329545 TGGTTGAGGCGTGAGGGC 62.330 66.667 0.00 0.00 42.69 5.19
994 1068 3.709880 TTCGTGGCGCCATCGTAGG 62.710 63.158 34.13 19.87 38.14 3.18
1263 1337 2.456119 GGTGATGAGCTTGCCGTCG 61.456 63.158 0.00 0.00 0.00 5.12
1628 1702 2.585900 ACCTGGATGTAGGACTGGTAGA 59.414 50.000 0.00 0.00 40.42 2.59
1672 1746 9.558396 GGAAGAAGAAGATGATGATTAACAGAT 57.442 33.333 0.00 0.00 0.00 2.90
1673 1747 8.766476 AGGAAGAAGAAGATGATGATTAACAGA 58.234 33.333 0.00 0.00 0.00 3.41
1674 1748 8.961294 AGGAAGAAGAAGATGATGATTAACAG 57.039 34.615 0.00 0.00 0.00 3.16
1675 1749 8.766476 AGAGGAAGAAGAAGATGATGATTAACA 58.234 33.333 0.00 0.00 0.00 2.41
1676 1750 9.260002 GAGAGGAAGAAGAAGATGATGATTAAC 57.740 37.037 0.00 0.00 0.00 2.01
1677 1751 8.140628 CGAGAGGAAGAAGAAGATGATGATTAA 58.859 37.037 0.00 0.00 0.00 1.40
1678 1752 7.286546 ACGAGAGGAAGAAGAAGATGATGATTA 59.713 37.037 0.00 0.00 0.00 1.75
1679 1753 6.098124 ACGAGAGGAAGAAGAAGATGATGATT 59.902 38.462 0.00 0.00 0.00 2.57
1680 1754 5.598005 ACGAGAGGAAGAAGAAGATGATGAT 59.402 40.000 0.00 0.00 0.00 2.45
1681 1755 4.952957 ACGAGAGGAAGAAGAAGATGATGA 59.047 41.667 0.00 0.00 0.00 2.92
1682 1756 5.261209 ACGAGAGGAAGAAGAAGATGATG 57.739 43.478 0.00 0.00 0.00 3.07
1683 1757 4.340950 GGACGAGAGGAAGAAGAAGATGAT 59.659 45.833 0.00 0.00 0.00 2.45
1684 1758 3.697045 GGACGAGAGGAAGAAGAAGATGA 59.303 47.826 0.00 0.00 0.00 2.92
1685 1759 3.445450 TGGACGAGAGGAAGAAGAAGATG 59.555 47.826 0.00 0.00 0.00 2.90
1686 1760 3.445805 GTGGACGAGAGGAAGAAGAAGAT 59.554 47.826 0.00 0.00 0.00 2.40
1687 1761 2.820787 GTGGACGAGAGGAAGAAGAAGA 59.179 50.000 0.00 0.00 0.00 2.87
1688 1762 2.823154 AGTGGACGAGAGGAAGAAGAAG 59.177 50.000 0.00 0.00 0.00 2.85
1689 1763 2.820787 GAGTGGACGAGAGGAAGAAGAA 59.179 50.000 0.00 0.00 0.00 2.52
1698 1772 0.875728 ACGAACTGAGTGGACGAGAG 59.124 55.000 12.36 0.00 0.00 3.20
1720 1794 9.755804 TTGCTTGTCAATCTCTCAATACTATAG 57.244 33.333 0.00 0.00 0.00 1.31
1726 1800 9.534565 GTATAGTTGCTTGTCAATCTCTCAATA 57.465 33.333 0.00 0.00 36.99 1.90
1728 1803 7.386059 TGTATAGTTGCTTGTCAATCTCTCAA 58.614 34.615 0.00 0.00 36.99 3.02
1732 1807 7.278646 TGTCATGTATAGTTGCTTGTCAATCTC 59.721 37.037 0.00 0.00 36.99 2.75
1733 1808 7.105588 TGTCATGTATAGTTGCTTGTCAATCT 58.894 34.615 0.00 0.00 36.99 2.40
1785 1860 2.668632 GGCCACGATGAACCTCCA 59.331 61.111 0.00 0.00 0.00 3.86
2124 2199 1.918609 GGCGTCGAAGAACATGTACTC 59.081 52.381 1.37 0.00 39.69 2.59
2190 2265 0.037326 TGCGAGATGTGGGTCTTGAC 60.037 55.000 0.00 0.00 32.32 3.18
2205 2280 8.015087 CACATCTAACTAATTTTTGAACTGCGA 58.985 33.333 0.00 0.00 0.00 5.10
2270 2346 9.159254 TCCATCAAAGAGCCTAATTTCTCTATA 57.841 33.333 5.40 0.00 38.62 1.31
2283 2359 5.936956 CCTGTATCTATTCCATCAAAGAGCC 59.063 44.000 0.00 0.00 0.00 4.70
2288 2364 7.520798 AGCAATCCTGTATCTATTCCATCAAA 58.479 34.615 0.00 0.00 0.00 2.69
2290 2366 6.692849 AGCAATCCTGTATCTATTCCATCA 57.307 37.500 0.00 0.00 0.00 3.07
2294 2370 5.411781 CGGTAGCAATCCTGTATCTATTCC 58.588 45.833 0.00 0.00 0.00 3.01
2297 2373 4.673968 TCCGGTAGCAATCCTGTATCTAT 58.326 43.478 0.00 0.00 0.00 1.98
2369 2446 6.589454 TGCATAATCACAGCGAATTATAACG 58.411 36.000 0.00 0.00 0.00 3.18
2375 2452 6.226052 TCTATCTGCATAATCACAGCGAATT 58.774 36.000 0.00 0.00 33.80 2.17
2391 2485 8.709386 TGATTTGAAGTCTAAACTCTATCTGC 57.291 34.615 0.00 0.00 33.48 4.26
2412 2506 5.982356 TGCTATTGTGACTAGAAGCTGATT 58.018 37.500 0.00 0.00 0.00 2.57
2428 2522 7.993101 TCTGAAAGAAATCCAATCTGCTATTG 58.007 34.615 5.63 5.63 42.31 1.90
2446 2540 5.862924 TTACGGAAGAAGCAATCTGAAAG 57.137 39.130 0.00 0.00 38.79 2.62
2447 2541 6.817765 ATTTACGGAAGAAGCAATCTGAAA 57.182 33.333 0.00 0.00 38.79 2.69
2457 2551 6.969828 AGTAGCAAGAATTTACGGAAGAAG 57.030 37.500 0.00 0.00 0.00 2.85
2460 2554 6.721571 TCAAGTAGCAAGAATTTACGGAAG 57.278 37.500 0.00 0.00 0.00 3.46
2475 2573 9.765795 ACCAATTTAGTGATACTATCAAGTAGC 57.234 33.333 0.01 0.00 43.49 3.58
2510 2620 9.320352 TGAGCGTTTCAGTATTATGCTTATTTA 57.680 29.630 0.00 0.00 34.46 1.40
2548 2658 5.163374 CCTTGTGAGGATATGAGACATGTGA 60.163 44.000 1.15 0.00 46.74 3.58
2549 2659 5.055144 CCTTGTGAGGATATGAGACATGTG 58.945 45.833 1.15 0.00 46.74 3.21
2550 2660 4.102210 CCCTTGTGAGGATATGAGACATGT 59.898 45.833 0.00 0.00 46.74 3.21
2551 2661 4.346127 TCCCTTGTGAGGATATGAGACATG 59.654 45.833 0.00 0.00 46.74 3.21
2552 2662 4.560739 TCCCTTGTGAGGATATGAGACAT 58.439 43.478 0.00 0.00 46.74 3.06
2553 2663 3.963374 CTCCCTTGTGAGGATATGAGACA 59.037 47.826 0.00 0.00 46.74 3.41
2554 2664 3.964031 ACTCCCTTGTGAGGATATGAGAC 59.036 47.826 0.00 0.00 46.74 3.36
2555 2665 4.271807 ACTCCCTTGTGAGGATATGAGA 57.728 45.455 0.00 0.00 46.74 3.27
2556 2666 6.485830 TTAACTCCCTTGTGAGGATATGAG 57.514 41.667 0.00 0.00 46.74 2.90
2557 2667 6.214615 TGTTTAACTCCCTTGTGAGGATATGA 59.785 38.462 0.00 0.00 46.74 2.15
2558 2668 6.414732 TGTTTAACTCCCTTGTGAGGATATG 58.585 40.000 0.00 0.00 46.74 1.78
2559 2669 6.636454 TGTTTAACTCCCTTGTGAGGATAT 57.364 37.500 0.00 0.00 46.74 1.63
2560 2670 6.012858 ACATGTTTAACTCCCTTGTGAGGATA 60.013 38.462 0.00 0.00 46.74 2.59
2561 2671 4.993705 TGTTTAACTCCCTTGTGAGGAT 57.006 40.909 0.00 0.00 46.74 3.24
2562 2672 4.104102 ACATGTTTAACTCCCTTGTGAGGA 59.896 41.667 0.00 0.00 46.74 3.71
2563 2673 4.216257 CACATGTTTAACTCCCTTGTGAGG 59.784 45.833 0.00 0.00 43.15 3.86
2564 2674 4.216257 CCACATGTTTAACTCCCTTGTGAG 59.784 45.833 0.00 0.00 36.76 3.51
2565 2675 4.141287 CCACATGTTTAACTCCCTTGTGA 58.859 43.478 0.00 0.00 36.76 3.58
2566 2676 4.141287 TCCACATGTTTAACTCCCTTGTG 58.859 43.478 0.00 3.42 35.31 3.33
2567 2677 4.447138 TCCACATGTTTAACTCCCTTGT 57.553 40.909 0.00 0.00 0.00 3.16
2568 2678 4.380867 GCATCCACATGTTTAACTCCCTTG 60.381 45.833 0.00 0.00 31.86 3.61
2569 2679 3.763897 GCATCCACATGTTTAACTCCCTT 59.236 43.478 0.00 0.00 31.86 3.95
2570 2680 3.245229 TGCATCCACATGTTTAACTCCCT 60.245 43.478 0.00 0.00 31.86 4.20
2571 2681 3.088532 TGCATCCACATGTTTAACTCCC 58.911 45.455 0.00 0.00 31.86 4.30
2572 2682 4.202050 GGATGCATCCACATGTTTAACTCC 60.202 45.833 35.93 8.44 46.38 3.85
2573 2683 4.925068 GGATGCATCCACATGTTTAACTC 58.075 43.478 35.93 7.40 46.38 3.01
2574 2684 4.989279 GGATGCATCCACATGTTTAACT 57.011 40.909 35.93 0.00 46.38 2.24
2614 2724 4.030913 TCCGGGAGTTATTTCAGACTCAT 58.969 43.478 0.00 0.00 43.14 2.90
2615 2725 3.437213 TCCGGGAGTTATTTCAGACTCA 58.563 45.455 0.00 0.00 43.14 3.41
2634 2744 7.700656 CCAACTATATCGTTTTGGTGAAATTCC 59.299 37.037 0.00 0.00 34.86 3.01
2683 2793 7.601856 TCAATTTGCGAAAAATCTGGATAGTT 58.398 30.769 0.00 0.00 0.00 2.24
2684 2794 7.121168 TCTCAATTTGCGAAAAATCTGGATAGT 59.879 33.333 0.00 0.00 0.00 2.12
2687 2797 6.071728 AGTCTCAATTTGCGAAAAATCTGGAT 60.072 34.615 0.00 0.00 0.00 3.41
2698 2808 1.019278 GCGGGAGTCTCAATTTGCGA 61.019 55.000 1.47 0.00 0.00 5.10
2722 2832 2.356069 GGCTAACAATGAAGTAGCAGCC 59.644 50.000 13.87 0.00 40.43 4.85
2746 2856 9.614792 GGCTTTTATCTTATCTTCAGGTTTCTA 57.385 33.333 0.00 0.00 0.00 2.10
2776 2887 7.255381 GCATTCTCTTTATATTCACACATGCCT 60.255 37.037 0.00 0.00 0.00 4.75
2818 2929 9.784680 CATGTCATCCTTTAATTTTTCTCTCTG 57.215 33.333 0.00 0.00 0.00 3.35
2822 2933 8.814235 CATGCATGTCATCCTTTAATTTTTCTC 58.186 33.333 18.91 0.00 31.79 2.87
2901 3012 1.695242 ACCGTACCAACTGATCACCAA 59.305 47.619 0.00 0.00 0.00 3.67
2914 3025 3.936453 TGCTGAAATATCAACACCGTACC 59.064 43.478 0.00 0.00 34.49 3.34
2960 3071 9.880157 CTTTTCCTGAAATATCATCACCATTTT 57.120 29.630 0.00 0.00 34.37 1.82
2963 3074 8.827832 TTCTTTTCCTGAAATATCATCACCAT 57.172 30.769 0.00 0.00 34.37 3.55
2994 3977 7.594015 GTCATCATAATGTCCAATTGAGCATTC 59.406 37.037 21.95 9.50 34.05 2.67
2999 3982 7.563888 AGTGTCATCATAATGTCCAATTGAG 57.436 36.000 7.12 0.00 34.32 3.02
3009 3992 7.621428 AAGAACCTGAAGTGTCATCATAATG 57.379 36.000 0.00 0.00 31.85 1.90
3028 4011 8.258708 AGGGATACAGTACATCTTTGTAAGAAC 58.741 37.037 0.00 0.00 38.11 3.01
3085 4087 1.801178 GTGGTTTCTGTCTGCACTAGC 59.199 52.381 0.00 0.00 42.57 3.42
3087 4089 3.388024 AGAAGTGGTTTCTGTCTGCACTA 59.612 43.478 0.00 0.00 44.46 2.74
3088 4090 2.171448 AGAAGTGGTTTCTGTCTGCACT 59.829 45.455 0.00 0.00 44.46 4.40
3137 4154 7.996788 TGGACCCTTCATCTATGAGTATAGTA 58.003 38.462 0.00 0.00 38.19 1.82
3146 4163 5.039920 TCAACATGGACCCTTCATCTATG 57.960 43.478 0.00 0.00 40.03 2.23
3147 4164 5.919348 ATCAACATGGACCCTTCATCTAT 57.081 39.130 0.00 0.00 0.00 1.98
3167 4184 9.278734 GCAACTTGTATTCTGCTAAAAACTATC 57.721 33.333 0.00 0.00 0.00 2.08
3168 4185 9.014297 AGCAACTTGTATTCTGCTAAAAACTAT 57.986 29.630 0.00 0.00 43.17 2.12
3169 4186 8.391075 AGCAACTTGTATTCTGCTAAAAACTA 57.609 30.769 0.00 0.00 43.17 2.24
3170 4187 7.277174 AGCAACTTGTATTCTGCTAAAAACT 57.723 32.000 0.00 0.00 43.17 2.66
3171 4188 7.537649 GGTAGCAACTTGTATTCTGCTAAAAAC 59.462 37.037 4.32 0.00 46.06 2.43
3172 4189 7.229707 TGGTAGCAACTTGTATTCTGCTAAAAA 59.770 33.333 4.32 0.00 46.06 1.94
3173 4190 6.712998 TGGTAGCAACTTGTATTCTGCTAAAA 59.287 34.615 4.32 0.00 46.06 1.52
3174 4191 6.148811 GTGGTAGCAACTTGTATTCTGCTAAA 59.851 38.462 0.00 0.00 46.06 1.85
3175 4192 5.642063 GTGGTAGCAACTTGTATTCTGCTAA 59.358 40.000 0.00 0.00 46.06 3.09
3176 4193 5.175859 GTGGTAGCAACTTGTATTCTGCTA 58.824 41.667 0.00 0.00 43.17 3.49
3177 4194 4.003648 GTGGTAGCAACTTGTATTCTGCT 58.996 43.478 0.00 0.65 46.50 4.24
3178 4195 3.751175 TGTGGTAGCAACTTGTATTCTGC 59.249 43.478 0.00 0.00 34.96 4.26
3179 4196 5.940192 TTGTGGTAGCAACTTGTATTCTG 57.060 39.130 0.00 0.00 0.00 3.02
3180 4197 7.165485 TGTATTGTGGTAGCAACTTGTATTCT 58.835 34.615 0.00 0.00 0.00 2.40
3181 4198 7.372451 TGTATTGTGGTAGCAACTTGTATTC 57.628 36.000 0.00 0.00 0.00 1.75
3182 4199 7.609918 TCATGTATTGTGGTAGCAACTTGTATT 59.390 33.333 0.00 0.00 0.00 1.89
3183 4200 7.109501 TCATGTATTGTGGTAGCAACTTGTAT 58.890 34.615 0.00 0.00 0.00 2.29
3184 4201 6.468543 TCATGTATTGTGGTAGCAACTTGTA 58.531 36.000 0.00 0.00 0.00 2.41
3185 4202 5.312895 TCATGTATTGTGGTAGCAACTTGT 58.687 37.500 0.00 0.00 0.00 3.16
3186 4203 5.878332 TCATGTATTGTGGTAGCAACTTG 57.122 39.130 0.00 0.26 0.00 3.16
3187 4204 5.767665 TGTTCATGTATTGTGGTAGCAACTT 59.232 36.000 0.00 0.00 0.00 2.66
3188 4205 5.312895 TGTTCATGTATTGTGGTAGCAACT 58.687 37.500 0.00 0.00 0.00 3.16
3189 4206 5.621197 TGTTCATGTATTGTGGTAGCAAC 57.379 39.130 0.00 0.00 0.00 4.17
3190 4207 5.392919 GCATGTTCATGTATTGTGGTAGCAA 60.393 40.000 13.24 0.00 0.00 3.91
3191 4208 4.096231 GCATGTTCATGTATTGTGGTAGCA 59.904 41.667 13.24 0.00 0.00 3.49
3192 4209 4.336433 AGCATGTTCATGTATTGTGGTAGC 59.664 41.667 13.24 0.00 0.00 3.58
3193 4210 6.441093 AAGCATGTTCATGTATTGTGGTAG 57.559 37.500 13.24 0.00 0.00 3.18
3194 4211 9.620259 TTATAAGCATGTTCATGTATTGTGGTA 57.380 29.630 13.24 0.00 0.00 3.25
3195 4212 8.518430 TTATAAGCATGTTCATGTATTGTGGT 57.482 30.769 13.24 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.