Multiple sequence alignment - TraesCS2D01G410300

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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 TraesCS2D01G410300 chr2D 100.000 3184 0 0 1 3184 524933674 524930491 0.000000e+00 5880.0
1 TraesCS2D01G410300 chr2B 88.776 1871 84 43 723 2536 620862138 620860337 0.000000e+00 2176.0
2 TraesCS2D01G410300 chr2B 88.993 745 39 18 1 726 620863134 620862414 0.000000e+00 881.0
3 TraesCS2D01G410300 chr2B 90.052 191 9 3 2676 2860 620860194 620860008 4.100000e-59 239.0
4 TraesCS2D01G410300 chr2B 97.895 95 2 0 3089 3183 620859770 620859676 7.070000e-37 165.0
5 TraesCS2D01G410300 chr2A 88.564 1644 65 37 646 2240 670315608 670314039 0.000000e+00 1881.0
6 TraesCS2D01G410300 chr2A 90.127 395 26 8 152 542 670316051 670315666 4.740000e-138 501.0
7 TraesCS2D01G410300 chr2A 80.531 226 27 11 2314 2536 670313996 670313785 1.180000e-34 158.0
8 TraesCS2D01G410300 chr6A 76.464 956 144 57 1146 2050 461644941 461645866 8.100000e-121 444.0
9 TraesCS2D01G410300 chr6D 76.151 956 150 56 1146 2050 324248449 324249377 6.310000e-117 431.0
10 TraesCS2D01G410300 chr6B 75.783 958 147 59 1146 2050 499578644 499577719 3.820000e-109 405.0
11 TraesCS2D01G410300 chr1D 89.062 64 7 0 1672 1735 300025613 300025550 2.630000e-11 80.5
12 TraesCS2D01G410300 chr1B 89.062 64 7 0 1672 1735 404897886 404897823 2.630000e-11 80.5


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 TraesCS2D01G410300 chr2D 524930491 524933674 3183 True 5880.000000 5880 100.000000 1 3184 1 chr2D.!!$R1 3183
1 TraesCS2D01G410300 chr2B 620859676 620863134 3458 True 865.250000 2176 91.429000 1 3183 4 chr2B.!!$R1 3182
2 TraesCS2D01G410300 chr2A 670313785 670316051 2266 True 846.666667 1881 86.407333 152 2536 3 chr2A.!!$R1 2384
3 TraesCS2D01G410300 chr6A 461644941 461645866 925 False 444.000000 444 76.464000 1146 2050 1 chr6A.!!$F1 904
4 TraesCS2D01G410300 chr6D 324248449 324249377 928 False 431.000000 431 76.151000 1146 2050 1 chr6D.!!$F1 904
5 TraesCS2D01G410300 chr6B 499577719 499578644 925 True 405.000000 405 75.783000 1146 2050 1 chr6B.!!$R1 904

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
40 41 0.248336 TTGATACGGCGACAGCGTAG 60.248 55.0 16.62 0.0 46.35 3.51 F
1072 1446 0.179067 TCGCACACTCCGTTTCCTTT 60.179 50.0 0.00 0.0 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1074 1448 0.464452 ATACGAGCTTTCGGGGGAAG 59.536 55.0 0.18 0.0 37.45 3.46 R
2275 2757 0.102120 CTGCTAGCTCCACGAGGAAG 59.898 60.0 17.23 0.0 45.19 3.46 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
21 22 0.320374 TCATGGGTTTCGAGCGAGTT 59.680 50.000 0.00 0.00 0.00 3.01
37 38 1.076533 AGTTTGATACGGCGACAGCG 61.077 55.000 16.62 0.00 46.35 5.18
40 41 0.248336 TTGATACGGCGACAGCGTAG 60.248 55.000 16.62 0.00 46.35 3.51
41 42 1.370172 GATACGGCGACAGCGTAGG 60.370 63.158 16.62 0.00 46.35 3.18
42 43 3.480225 ATACGGCGACAGCGTAGGC 62.480 63.158 16.62 0.00 46.35 3.93
55 56 0.510359 CGTAGGCGCCGTAGTACTAG 59.490 60.000 23.20 2.51 0.00 2.57
62 63 1.373570 GCCGTAGTACTAGGACGTGT 58.626 55.000 21.35 0.00 34.81 4.49
91 92 2.588146 ATCGTCGCCTGAACCGTACG 62.588 60.000 8.69 8.69 33.71 3.67
109 110 2.130426 GCCGAGATCTCTGGCTCCA 61.130 63.158 32.97 0.00 42.09 3.86
119 120 3.256960 TGGCTCCAACCACCTCCC 61.257 66.667 0.00 0.00 33.75 4.30
135 136 1.046472 TCCCGCTCCGGTGTAATCAT 61.046 55.000 0.00 0.00 46.80 2.45
137 138 1.336887 CCCGCTCCGGTGTAATCATAG 60.337 57.143 0.00 0.00 46.80 2.23
211 213 0.960364 CTTGCGTGCCATTACCACCT 60.960 55.000 0.00 0.00 0.00 4.00
230 232 0.472471 TGATTTAGATCCCCACCGCC 59.528 55.000 0.00 0.00 0.00 6.13
323 325 2.102420 TGTTCGCTCTCCTTCTTGTCAA 59.898 45.455 0.00 0.00 0.00 3.18
325 327 1.964223 TCGCTCTCCTTCTTGTCAACT 59.036 47.619 0.00 0.00 0.00 3.16
330 332 4.021894 GCTCTCCTTCTTGTCAACTACTCA 60.022 45.833 0.00 0.00 0.00 3.41
398 400 3.610619 CTGATCGCCTGCACCACCA 62.611 63.158 0.00 0.00 0.00 4.17
429 431 1.841556 AAGGTGGAGGACGGAAGCA 60.842 57.895 0.00 0.00 0.00 3.91
439 441 1.301677 GACGGAAGCAAAGGGAGCAG 61.302 60.000 0.00 0.00 0.00 4.24
461 463 2.102578 GTCACCCTTGATTTGGATGGG 58.897 52.381 0.00 0.00 43.26 4.00
462 464 1.006998 TCACCCTTGATTTGGATGGGG 59.993 52.381 0.00 0.00 42.00 4.96
523 534 0.455815 GCGCAAGTCCCATAAAAGGG 59.544 55.000 0.30 0.00 44.72 3.95
542 553 1.747355 GGAGAATTGACAGCCATGTGG 59.253 52.381 0.00 0.00 40.68 4.17
565 582 6.126796 TGGTGATGCTAATAGACATCTTCCAA 60.127 38.462 21.84 14.26 42.57 3.53
569 586 7.496920 TGATGCTAATAGACATCTTCCAAAGTG 59.503 37.037 18.36 0.00 42.57 3.16
579 596 7.836685 AGACATCTTCCAAAGTGTATAGAGAGA 59.163 37.037 0.00 0.00 0.00 3.10
580 597 8.006298 ACATCTTCCAAAGTGTATAGAGAGAG 57.994 38.462 0.00 0.00 0.00 3.20
581 598 7.617723 ACATCTTCCAAAGTGTATAGAGAGAGT 59.382 37.037 0.00 0.00 0.00 3.24
582 599 9.126151 CATCTTCCAAAGTGTATAGAGAGAGTA 57.874 37.037 0.00 0.00 0.00 2.59
584 601 9.702253 TCTTCCAAAGTGTATAGAGAGAGTAAT 57.298 33.333 0.00 0.00 0.00 1.89
604 621 8.358582 AGTAATAATATCCGTCCGGTATTCTT 57.641 34.615 0.00 9.90 36.47 2.52
608 625 1.153706 CCGTCCGGTATTCTTGCGT 60.154 57.895 0.00 0.00 0.00 5.24
619 636 3.678056 ATTCTTGCGTTGACAGTAGGA 57.322 42.857 0.00 0.00 0.00 2.94
620 637 2.724977 TCTTGCGTTGACAGTAGGAG 57.275 50.000 0.00 0.00 0.00 3.69
621 638 1.272490 TCTTGCGTTGACAGTAGGAGG 59.728 52.381 0.00 0.00 0.00 4.30
622 639 1.000955 CTTGCGTTGACAGTAGGAGGT 59.999 52.381 0.00 0.00 0.00 3.85
623 640 1.913778 TGCGTTGACAGTAGGAGGTA 58.086 50.000 0.00 0.00 0.00 3.08
624 641 1.816835 TGCGTTGACAGTAGGAGGTAG 59.183 52.381 0.00 0.00 0.00 3.18
625 642 1.134560 GCGTTGACAGTAGGAGGTAGG 59.865 57.143 0.00 0.00 0.00 3.18
712 759 5.104374 ACAAATAATGGCTTGATTCTTGCG 58.896 37.500 0.00 0.00 0.00 4.85
727 777 5.508200 TTCTTGCGACCAAAAGTGTAATT 57.492 34.783 0.00 0.00 0.00 1.40
775 1106 2.668212 CCATGGACCACAACGCGT 60.668 61.111 5.58 5.58 0.00 6.01
927 1280 1.002403 TGGAGAATACGGGGAGCCA 59.998 57.895 0.00 0.00 0.00 4.75
1072 1446 0.179067 TCGCACACTCCGTTTCCTTT 60.179 50.000 0.00 0.00 0.00 3.11
1074 1448 0.591659 GCACACTCCGTTTCCTTTCC 59.408 55.000 0.00 0.00 0.00 3.13
1075 1449 1.814248 GCACACTCCGTTTCCTTTCCT 60.814 52.381 0.00 0.00 0.00 3.36
1076 1450 2.572290 CACACTCCGTTTCCTTTCCTT 58.428 47.619 0.00 0.00 0.00 3.36
1078 1452 2.152016 CACTCCGTTTCCTTTCCTTCC 58.848 52.381 0.00 0.00 0.00 3.46
1079 1453 1.073444 ACTCCGTTTCCTTTCCTTCCC 59.927 52.381 0.00 0.00 0.00 3.97
1080 1454 0.402887 TCCGTTTCCTTTCCTTCCCC 59.597 55.000 0.00 0.00 0.00 4.81
1081 1455 0.611062 CCGTTTCCTTTCCTTCCCCC 60.611 60.000 0.00 0.00 0.00 5.40
1082 1456 0.958876 CGTTTCCTTTCCTTCCCCCG 60.959 60.000 0.00 0.00 0.00 5.73
1135 1509 1.498865 CGGAGCTCTCTCTCTCGCTC 61.499 65.000 14.64 0.00 46.06 5.03
1136 1510 1.934463 GAGCTCTCTCTCTCGCTCG 59.066 63.158 6.43 0.00 39.39 5.03
2128 2579 1.873698 CTTTTCCTTTCGGTCGGTCA 58.126 50.000 0.00 0.00 0.00 4.02
2137 2588 1.068417 CGGTCGGTCAGTTGGTTGA 59.932 57.895 0.00 0.00 0.00 3.18
2150 2601 2.814336 GTTGGTTGATTCCAGTGGAGAC 59.186 50.000 12.67 10.92 38.80 3.36
2168 2619 1.412710 GACAGATGATCCGGGCTTGTA 59.587 52.381 0.00 0.00 0.00 2.41
2175 2626 2.171659 TGATCCGGGCTTGTAATTGCTA 59.828 45.455 0.00 0.00 0.00 3.49
2250 2732 4.884247 AGAAAAAGAGAGACGGGTAGTTG 58.116 43.478 0.00 0.00 0.00 3.16
2259 2741 3.736720 AGACGGGTAGTTGTTTTTCCTC 58.263 45.455 0.00 0.00 0.00 3.71
2262 2744 3.072211 CGGGTAGTTGTTTTTCCTCCTC 58.928 50.000 0.00 0.00 0.00 3.71
2263 2745 3.418995 GGGTAGTTGTTTTTCCTCCTCC 58.581 50.000 0.00 0.00 0.00 4.30
2264 2746 3.074094 GGGTAGTTGTTTTTCCTCCTCCT 59.926 47.826 0.00 0.00 0.00 3.69
2265 2747 4.447325 GGGTAGTTGTTTTTCCTCCTCCTT 60.447 45.833 0.00 0.00 0.00 3.36
2268 2750 6.774170 GGTAGTTGTTTTTCCTCCTCCTTTTA 59.226 38.462 0.00 0.00 0.00 1.52
2270 2752 7.914427 AGTTGTTTTTCCTCCTCCTTTTATT 57.086 32.000 0.00 0.00 0.00 1.40
2271 2753 8.319057 AGTTGTTTTTCCTCCTCCTTTTATTT 57.681 30.769 0.00 0.00 0.00 1.40
2272 2754 8.768397 AGTTGTTTTTCCTCCTCCTTTTATTTT 58.232 29.630 0.00 0.00 0.00 1.82
2273 2755 8.826710 GTTGTTTTTCCTCCTCCTTTTATTTTG 58.173 33.333 0.00 0.00 0.00 2.44
2274 2756 6.989759 TGTTTTTCCTCCTCCTTTTATTTTGC 59.010 34.615 0.00 0.00 0.00 3.68
2275 2757 5.738619 TTTCCTCCTCCTTTTATTTTGCC 57.261 39.130 0.00 0.00 0.00 4.52
2276 2758 4.675063 TCCTCCTCCTTTTATTTTGCCT 57.325 40.909 0.00 0.00 0.00 4.75
2277 2759 5.010708 TCCTCCTCCTTTTATTTTGCCTT 57.989 39.130 0.00 0.00 0.00 4.35
2278 2760 5.016831 TCCTCCTCCTTTTATTTTGCCTTC 58.983 41.667 0.00 0.00 0.00 3.46
2279 2761 4.160439 CCTCCTCCTTTTATTTTGCCTTCC 59.840 45.833 0.00 0.00 0.00 3.46
2280 2762 5.010708 TCCTCCTTTTATTTTGCCTTCCT 57.989 39.130 0.00 0.00 0.00 3.36
2281 2763 5.016831 TCCTCCTTTTATTTTGCCTTCCTC 58.983 41.667 0.00 0.00 0.00 3.71
2282 2764 4.142381 CCTCCTTTTATTTTGCCTTCCTCG 60.142 45.833 0.00 0.00 0.00 4.63
2283 2765 4.403734 TCCTTTTATTTTGCCTTCCTCGT 58.596 39.130 0.00 0.00 0.00 4.18
2284 2766 4.217550 TCCTTTTATTTTGCCTTCCTCGTG 59.782 41.667 0.00 0.00 0.00 4.35
2285 2767 4.485163 CTTTTATTTTGCCTTCCTCGTGG 58.515 43.478 0.00 0.00 0.00 4.94
2286 2768 3.426787 TTATTTTGCCTTCCTCGTGGA 57.573 42.857 1.10 1.10 41.36 4.02
2287 2769 1.826385 ATTTTGCCTTCCTCGTGGAG 58.174 50.000 6.29 0.00 44.24 3.86
2288 2770 0.889186 TTTTGCCTTCCTCGTGGAGC 60.889 55.000 6.29 8.42 44.24 4.70
2289 2771 1.768684 TTTGCCTTCCTCGTGGAGCT 61.769 55.000 15.97 0.00 44.24 4.09
2290 2772 0.902984 TTGCCTTCCTCGTGGAGCTA 60.903 55.000 15.97 8.13 44.24 3.32
2291 2773 1.323271 TGCCTTCCTCGTGGAGCTAG 61.323 60.000 15.97 7.74 44.24 3.42
2292 2774 1.439644 CCTTCCTCGTGGAGCTAGC 59.560 63.158 6.62 6.62 44.24 3.42
2293 2775 1.323271 CCTTCCTCGTGGAGCTAGCA 61.323 60.000 18.83 0.00 44.24 3.49
2294 2776 0.102120 CTTCCTCGTGGAGCTAGCAG 59.898 60.000 18.83 3.85 44.24 4.24
2295 2777 0.323451 TTCCTCGTGGAGCTAGCAGA 60.323 55.000 18.83 7.05 44.24 4.26
2296 2778 0.323451 TCCTCGTGGAGCTAGCAGAA 60.323 55.000 18.83 0.00 37.46 3.02
2297 2779 0.532573 CCTCGTGGAGCTAGCAGAAA 59.467 55.000 18.83 0.00 34.57 2.52
2298 2780 1.066858 CCTCGTGGAGCTAGCAGAAAA 60.067 52.381 18.83 0.00 34.57 2.29
2299 2781 2.419297 CCTCGTGGAGCTAGCAGAAAAT 60.419 50.000 18.83 0.00 34.57 1.82
2300 2782 3.265791 CTCGTGGAGCTAGCAGAAAATT 58.734 45.455 18.83 0.00 0.00 1.82
2301 2783 3.002791 TCGTGGAGCTAGCAGAAAATTG 58.997 45.455 18.83 0.00 0.00 2.32
2302 2784 2.096496 CGTGGAGCTAGCAGAAAATTGG 59.904 50.000 18.83 0.00 0.00 3.16
2303 2785 3.347216 GTGGAGCTAGCAGAAAATTGGA 58.653 45.455 18.83 0.00 0.00 3.53
2304 2786 3.950395 GTGGAGCTAGCAGAAAATTGGAT 59.050 43.478 18.83 0.00 0.00 3.41
2305 2787 3.949754 TGGAGCTAGCAGAAAATTGGATG 59.050 43.478 18.83 0.00 0.00 3.51
2306 2788 3.243334 GGAGCTAGCAGAAAATTGGATGC 60.243 47.826 18.83 1.78 38.97 3.91
2311 2793 4.978083 AGCAGAAAATTGGATGCTGTAG 57.022 40.909 9.91 0.00 46.75 2.74
2401 2883 2.093764 AGCAAACAGAGCCAGCTACTAG 60.094 50.000 0.00 0.00 33.06 2.57
2403 2885 3.866449 GCAAACAGAGCCAGCTACTAGTT 60.866 47.826 0.00 0.00 0.00 2.24
2404 2886 4.620803 GCAAACAGAGCCAGCTACTAGTTA 60.621 45.833 0.00 0.00 0.00 2.24
2410 2892 5.751028 CAGAGCCAGCTACTAGTTATTGTTC 59.249 44.000 0.00 0.00 0.00 3.18
2412 2894 5.665459 AGCCAGCTACTAGTTATTGTTCTG 58.335 41.667 0.00 0.00 0.00 3.02
2431 2926 3.076621 CTGTTGCTTGATCTTGGTAGCA 58.923 45.455 0.00 0.00 41.51 3.49
2450 2945 8.257830 GGTAGCATAGCAAGAAAATACTATCC 57.742 38.462 0.00 0.00 39.30 2.59
2451 2946 8.097662 GGTAGCATAGCAAGAAAATACTATCCT 58.902 37.037 0.00 0.00 39.30 3.24
2452 2947 9.145865 GTAGCATAGCAAGAAAATACTATCCTC 57.854 37.037 0.00 0.00 0.00 3.71
2453 2948 7.739825 AGCATAGCAAGAAAATACTATCCTCA 58.260 34.615 0.00 0.00 0.00 3.86
2454 2949 7.877097 AGCATAGCAAGAAAATACTATCCTCAG 59.123 37.037 0.00 0.00 0.00 3.35
2455 2950 7.875041 GCATAGCAAGAAAATACTATCCTCAGA 59.125 37.037 0.00 0.00 0.00 3.27
2456 2951 9.421806 CATAGCAAGAAAATACTATCCTCAGAG 57.578 37.037 0.00 0.00 0.00 3.35
2457 2952 7.667575 AGCAAGAAAATACTATCCTCAGAGA 57.332 36.000 0.00 0.00 0.00 3.10
2458 2953 8.083828 AGCAAGAAAATACTATCCTCAGAGAA 57.916 34.615 0.00 0.00 0.00 2.87
2459 2954 8.713036 AGCAAGAAAATACTATCCTCAGAGAAT 58.287 33.333 0.00 0.00 0.00 2.40
2460 2955 8.772705 GCAAGAAAATACTATCCTCAGAGAATG 58.227 37.037 0.00 0.00 0.00 2.67
2461 2956 9.270640 CAAGAAAATACTATCCTCAGAGAATGG 57.729 37.037 0.00 0.00 0.00 3.16
2462 2957 8.789767 AGAAAATACTATCCTCAGAGAATGGA 57.210 34.615 0.00 0.00 0.00 3.41
2463 2958 9.218525 AGAAAATACTATCCTCAGAGAATGGAA 57.781 33.333 0.00 0.00 33.20 3.53
2464 2959 9.838339 GAAAATACTATCCTCAGAGAATGGAAA 57.162 33.333 0.00 0.00 33.20 3.13
2480 2975 4.270245 TGGAAAGGGCAAAATTTAGCTG 57.730 40.909 0.00 0.00 0.00 4.24
2524 3019 2.551459 CTCCAGCTGTTCTTGTTCCAAG 59.449 50.000 13.81 0.00 0.00 3.61
2529 3024 2.286418 GCTGTTCTTGTTCCAAGTGTCG 60.286 50.000 4.08 0.00 0.00 4.35
2537 3077 1.398390 GTTCCAAGTGTCGATGCATCC 59.602 52.381 20.87 8.49 0.00 3.51
2552 3092 1.863454 GCATCCTCGCACTCATTACTG 59.137 52.381 0.00 0.00 0.00 2.74
2553 3093 2.481969 GCATCCTCGCACTCATTACTGA 60.482 50.000 0.00 0.00 0.00 3.41
2558 3098 3.378742 CCTCGCACTCATTACTGACTAGT 59.621 47.826 0.00 0.00 40.99 2.57
2575 3130 8.272584 ACTGACTAGTAAAGCCATAAGCAACAG 61.273 40.741 0.00 0.00 38.79 3.16
2587 3142 5.801947 CCATAAGCAACAGAATAGCAACAAC 59.198 40.000 0.00 0.00 0.00 3.32
2588 3143 4.916983 AAGCAACAGAATAGCAACAACA 57.083 36.364 0.00 0.00 0.00 3.33
2589 3144 4.228912 AGCAACAGAATAGCAACAACAC 57.771 40.909 0.00 0.00 0.00 3.32
2590 3145 3.631686 AGCAACAGAATAGCAACAACACA 59.368 39.130 0.00 0.00 0.00 3.72
2591 3146 4.097741 AGCAACAGAATAGCAACAACACAA 59.902 37.500 0.00 0.00 0.00 3.33
2592 3147 4.803088 GCAACAGAATAGCAACAACACAAA 59.197 37.500 0.00 0.00 0.00 2.83
2593 3148 5.463061 GCAACAGAATAGCAACAACACAAAT 59.537 36.000 0.00 0.00 0.00 2.32
2594 3149 6.562640 GCAACAGAATAGCAACAACACAAATG 60.563 38.462 0.00 0.00 0.00 2.32
2595 3150 4.984161 ACAGAATAGCAACAACACAAATGC 59.016 37.500 0.00 0.00 39.06 3.56
2596 3151 4.983538 CAGAATAGCAACAACACAAATGCA 59.016 37.500 0.00 0.00 41.18 3.96
2597 3152 5.636121 CAGAATAGCAACAACACAAATGCAT 59.364 36.000 0.00 0.00 41.18 3.96
2598 3153 6.146510 CAGAATAGCAACAACACAAATGCATT 59.853 34.615 5.99 5.99 41.18 3.56
2599 3154 5.849357 ATAGCAACAACACAAATGCATTG 57.151 34.783 13.82 9.78 44.95 2.82
2617 3172 2.417257 GCAATGCAGGATCGGCCAA 61.417 57.895 2.24 0.00 40.02 4.52
2619 3174 0.531657 CAATGCAGGATCGGCCAAAA 59.468 50.000 2.24 0.00 40.02 2.44
2620 3175 0.819582 AATGCAGGATCGGCCAAAAG 59.180 50.000 2.24 0.00 40.02 2.27
2621 3176 1.669999 ATGCAGGATCGGCCAAAAGC 61.670 55.000 2.24 0.00 40.02 3.51
2622 3177 2.793946 CAGGATCGGCCAAAAGCG 59.206 61.111 2.24 0.00 45.17 4.68
2624 3179 1.303317 AGGATCGGCCAAAAGCGTT 60.303 52.632 2.24 0.00 45.17 4.84
2625 3180 1.154035 GGATCGGCCAAAAGCGTTG 60.154 57.895 2.24 0.00 45.17 4.10
2626 3181 1.154035 GATCGGCCAAAAGCGTTGG 60.154 57.895 15.69 15.69 45.17 3.77
2627 3182 1.862602 GATCGGCCAAAAGCGTTGGT 61.863 55.000 19.56 4.01 45.17 3.67
2628 3183 1.460273 ATCGGCCAAAAGCGTTGGTT 61.460 50.000 19.56 4.47 45.17 3.67
2630 3185 1.594021 GGCCAAAAGCGTTGGTTGG 60.594 57.895 19.56 9.94 45.17 3.77
2631 3186 1.142965 GCCAAAAGCGTTGGTTGGT 59.857 52.632 19.56 0.00 43.17 3.67
2633 3188 0.529555 CCAAAAGCGTTGGTTGGTGG 60.530 55.000 12.66 0.00 37.59 4.61
2635 3190 0.899019 AAAAGCGTTGGTTGGTGGTT 59.101 45.000 0.00 0.00 0.00 3.67
2636 3191 1.765230 AAAGCGTTGGTTGGTGGTTA 58.235 45.000 0.00 0.00 0.00 2.85
2637 3192 1.026584 AAGCGTTGGTTGGTGGTTAC 58.973 50.000 0.00 0.00 0.00 2.50
2638 3193 0.107116 AGCGTTGGTTGGTGGTTACA 60.107 50.000 0.00 0.00 0.00 2.41
2639 3194 0.955905 GCGTTGGTTGGTGGTTACAT 59.044 50.000 0.00 0.00 0.00 2.29
2640 3195 1.335506 GCGTTGGTTGGTGGTTACATG 60.336 52.381 0.00 0.00 0.00 3.21
2641 3196 2.222886 CGTTGGTTGGTGGTTACATGA 58.777 47.619 0.00 0.00 0.00 3.07
2642 3197 2.031508 CGTTGGTTGGTGGTTACATGAC 60.032 50.000 0.00 0.00 0.00 3.06
2643 3198 3.219281 GTTGGTTGGTGGTTACATGACT 58.781 45.455 0.00 0.00 0.00 3.41
2644 3199 3.586470 TGGTTGGTGGTTACATGACTT 57.414 42.857 0.00 0.00 0.00 3.01
2645 3200 4.708576 TGGTTGGTGGTTACATGACTTA 57.291 40.909 0.00 0.00 0.00 2.24
2646 3201 4.391155 TGGTTGGTGGTTACATGACTTAC 58.609 43.478 0.00 0.00 0.00 2.34
2647 3202 3.434299 GGTTGGTGGTTACATGACTTACG 59.566 47.826 0.00 0.00 0.00 3.18
2648 3203 4.060205 GTTGGTGGTTACATGACTTACGT 58.940 43.478 0.00 0.00 0.00 3.57
2649 3204 3.916761 TGGTGGTTACATGACTTACGTC 58.083 45.455 0.00 0.00 40.64 4.34
2650 3205 3.256558 GGTGGTTACATGACTTACGTCC 58.743 50.000 0.00 0.00 39.47 4.79
2651 3206 3.306225 GGTGGTTACATGACTTACGTCCA 60.306 47.826 0.00 0.00 39.47 4.02
2652 3207 3.676646 GTGGTTACATGACTTACGTCCAC 59.323 47.826 0.00 0.00 39.47 4.02
2653 3208 3.256558 GGTTACATGACTTACGTCCACC 58.743 50.000 0.00 0.00 39.47 4.61
2654 3209 3.306225 GGTTACATGACTTACGTCCACCA 60.306 47.826 0.00 0.00 39.47 4.17
2655 3210 4.501071 GTTACATGACTTACGTCCACCAT 58.499 43.478 0.00 0.00 39.47 3.55
2656 3211 2.972625 ACATGACTTACGTCCACCATG 58.027 47.619 15.02 15.02 39.47 3.66
2657 3212 1.665679 CATGACTTACGTCCACCATGC 59.334 52.381 0.00 0.00 39.47 4.06
2658 3213 0.973632 TGACTTACGTCCACCATGCT 59.026 50.000 0.00 0.00 39.47 3.79
2659 3214 1.346395 TGACTTACGTCCACCATGCTT 59.654 47.619 0.00 0.00 39.47 3.91
2660 3215 1.732259 GACTTACGTCCACCATGCTTG 59.268 52.381 0.00 0.00 33.98 4.01
2661 3216 0.447801 CTTACGTCCACCATGCTTGC 59.552 55.000 0.00 0.00 0.00 4.01
2662 3217 0.958382 TTACGTCCACCATGCTTGCC 60.958 55.000 0.00 0.00 0.00 4.52
2663 3218 2.813226 TACGTCCACCATGCTTGCCC 62.813 60.000 0.00 0.00 0.00 5.36
2664 3219 3.070576 GTCCACCATGCTTGCCCC 61.071 66.667 0.00 0.00 0.00 5.80
2665 3220 4.738998 TCCACCATGCTTGCCCCG 62.739 66.667 0.00 0.00 0.00 5.73
2698 3253 1.592939 GCGATCGCCTCCTTTCTCC 60.593 63.158 29.48 0.00 34.56 3.71
2699 3254 1.068250 CGATCGCCTCCTTTCTCCC 59.932 63.158 0.26 0.00 0.00 4.30
2706 3261 0.911525 CCTCCTTTCTCCCCTCTGCA 60.912 60.000 0.00 0.00 0.00 4.41
2707 3262 0.540923 CTCCTTTCTCCCCTCTGCAG 59.459 60.000 7.63 7.63 0.00 4.41
2749 3310 2.421399 GCCTGCCTGCATTTCTCCC 61.421 63.158 0.00 0.00 0.00 4.30
2755 3316 1.748122 CTGCATTTCTCCCGCTGCT 60.748 57.895 0.00 0.00 35.66 4.24
2756 3317 1.989966 CTGCATTTCTCCCGCTGCTG 61.990 60.000 0.00 0.00 35.66 4.41
2757 3318 2.796651 CATTTCTCCCGCTGCTGC 59.203 61.111 5.34 5.34 0.00 5.25
2838 3399 2.046285 GCTTCCCACCACATTCCCG 61.046 63.158 0.00 0.00 0.00 5.14
2840 3401 0.676782 CTTCCCACCACATTCCCGTC 60.677 60.000 0.00 0.00 0.00 4.79
2877 3477 1.550976 TGCATTGCATTGAATCCTGCA 59.449 42.857 7.38 3.86 46.08 4.41
2881 3481 1.618487 TGCATTGAATCCTGCACACA 58.382 45.000 3.86 0.00 43.11 3.72
2892 3492 1.876799 CCTGCACACAAAATGACCGTA 59.123 47.619 0.00 0.00 0.00 4.02
2894 3494 3.687212 CCTGCACACAAAATGACCGTATA 59.313 43.478 0.00 0.00 0.00 1.47
2895 3495 4.335315 CCTGCACACAAAATGACCGTATAT 59.665 41.667 0.00 0.00 0.00 0.86
2896 3496 5.525745 CCTGCACACAAAATGACCGTATATA 59.474 40.000 0.00 0.00 0.00 0.86
2897 3497 6.204688 CCTGCACACAAAATGACCGTATATAT 59.795 38.462 0.00 0.00 0.00 0.86
2898 3498 7.386573 CCTGCACACAAAATGACCGTATATATA 59.613 37.037 0.00 0.00 0.00 0.86
2899 3499 8.840833 TGCACACAAAATGACCGTATATATAT 57.159 30.769 0.00 0.00 0.00 0.86
2900 3500 9.930693 TGCACACAAAATGACCGTATATATATA 57.069 29.630 0.00 0.00 0.00 0.86
2926 3526 5.941058 TCAACAAATAAAGTGGCTCGGAATA 59.059 36.000 0.00 0.00 0.00 1.75
2927 3527 6.093495 TCAACAAATAAAGTGGCTCGGAATAG 59.907 38.462 0.00 0.00 0.00 1.73
2929 3529 5.585047 ACAAATAAAGTGGCTCGGAATAGTC 59.415 40.000 0.00 0.00 0.00 2.59
2942 3543 2.034001 GGAATAGTCGTTTCAATCGCGG 60.034 50.000 6.13 0.00 0.00 6.46
2966 3573 5.283457 ACAGCCATGAAGATTACCTACTC 57.717 43.478 0.00 0.00 0.00 2.59
2968 3575 4.101585 CAGCCATGAAGATTACCTACTCCA 59.898 45.833 0.00 0.00 0.00 3.86
2990 3597 5.295787 CCATTGTTGTTGTACACTGTACAGT 59.704 40.000 22.95 22.95 43.61 3.55
3009 3616 5.238583 ACAGTATCTGTGTAGCTTTTCACC 58.761 41.667 0.00 0.00 43.63 4.02
3014 3621 4.380531 TCTGTGTAGCTTTTCACCTTCAG 58.619 43.478 0.00 0.00 34.14 3.02
3032 3639 5.358160 CCTTCAGGTCAGATTATTTTGGGAC 59.642 44.000 0.00 0.00 0.00 4.46
3036 3643 3.954258 GGTCAGATTATTTTGGGACCTGG 59.046 47.826 0.00 0.00 41.17 4.45
3037 3644 3.954258 GTCAGATTATTTTGGGACCTGGG 59.046 47.826 0.00 0.00 0.00 4.45
3045 3652 0.397816 TTGGGACCTGGGTTTGTTGG 60.398 55.000 0.00 0.00 0.00 3.77
3054 3661 0.608130 GGGTTTGTTGGATTGGAGCC 59.392 55.000 0.00 0.00 0.00 4.70
3055 3662 1.632589 GGTTTGTTGGATTGGAGCCT 58.367 50.000 0.00 0.00 0.00 4.58
3066 3673 1.493861 TTGGAGCCTGGATCTCTCTG 58.506 55.000 12.28 0.00 0.00 3.35
3069 3676 1.688197 GGAGCCTGGATCTCTCTGAAG 59.312 57.143 12.28 0.00 0.00 3.02
3073 3680 2.954539 GCCTGGATCTCTCTGAAGAGGT 60.955 54.545 7.47 0.00 46.01 3.85
3074 3681 3.373830 CCTGGATCTCTCTGAAGAGGTT 58.626 50.000 7.47 0.00 43.28 3.50
3075 3682 3.774216 CCTGGATCTCTCTGAAGAGGTTT 59.226 47.826 7.47 0.00 43.28 3.27
3076 3683 4.224818 CCTGGATCTCTCTGAAGAGGTTTT 59.775 45.833 7.47 0.00 43.28 2.43
3077 3684 5.280419 CCTGGATCTCTCTGAAGAGGTTTTT 60.280 44.000 7.47 0.00 43.28 1.94
3103 3710 8.839310 TTTTTAAGAAGATCTCTCTCAACAGG 57.161 34.615 0.00 0.00 31.02 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.248336 CTACGCTGTCGCCGTATCAA 60.248 55.000 0.00 0.00 40.01 2.57
37 38 0.871057 CCTAGTACTACGGCGCCTAC 59.129 60.000 26.68 19.57 0.00 3.18
40 41 1.651461 GTCCTAGTACTACGGCGCC 59.349 63.158 19.07 19.07 0.00 6.53
41 42 1.278038 CGTCCTAGTACTACGGCGC 59.722 63.158 6.90 0.00 33.13 6.53
42 43 0.302890 CACGTCCTAGTACTACGGCG 59.697 60.000 19.83 19.83 40.81 6.46
43 44 1.373570 ACACGTCCTAGTACTACGGC 58.626 55.000 18.21 7.39 40.81 5.68
44 45 2.476854 GCAACACGTCCTAGTACTACGG 60.477 54.545 18.21 14.22 40.81 4.02
45 46 2.417933 AGCAACACGTCCTAGTACTACG 59.582 50.000 13.71 13.71 42.17 3.51
46 47 4.164294 CAAGCAACACGTCCTAGTACTAC 58.836 47.826 0.00 0.00 0.00 2.73
47 48 3.366679 GCAAGCAACACGTCCTAGTACTA 60.367 47.826 1.89 1.89 0.00 1.82
48 49 2.609737 GCAAGCAACACGTCCTAGTACT 60.610 50.000 0.00 0.00 0.00 2.73
55 56 0.166814 GATCAGCAAGCAACACGTCC 59.833 55.000 0.00 0.00 0.00 4.79
62 63 2.390599 GGCGACGATCAGCAAGCAA 61.391 57.895 0.00 0.00 34.54 3.91
91 92 1.680522 TTGGAGCCAGAGATCTCGGC 61.681 60.000 33.13 33.13 44.05 5.54
119 120 2.795175 ACTATGATTACACCGGAGCG 57.205 50.000 9.46 0.00 0.00 5.03
211 213 0.472471 GGCGGTGGGGATCTAAATCA 59.528 55.000 0.00 0.00 33.21 2.57
230 232 6.130298 TGGTGATAAGTGGCAAATTAATCG 57.870 37.500 0.00 0.00 0.00 3.34
398 400 2.564947 CTCCACCTTGTAGACTTGCTCT 59.435 50.000 0.00 0.00 0.00 4.09
429 431 2.032681 GGTGACGCTGCTCCCTTT 59.967 61.111 0.00 0.00 0.00 3.11
439 441 1.133025 CATCCAAATCAAGGGTGACGC 59.867 52.381 0.00 0.00 39.72 5.19
461 463 4.660938 GGCCGCCACCCCATATCC 62.661 72.222 3.91 0.00 0.00 2.59
462 464 3.553095 GAGGCCGCCACCCCATATC 62.553 68.421 13.15 0.00 0.00 1.63
523 534 2.163010 CACCACATGGCTGTCAATTCTC 59.837 50.000 0.00 0.00 39.32 2.87
542 553 7.497249 ACTTTGGAAGATGTCTATTAGCATCAC 59.503 37.037 20.42 15.75 42.72 3.06
574 591 5.647225 ACCGGACGGATATTATTACTCTCTC 59.353 44.000 18.80 0.00 38.96 3.20
579 596 7.951347 AGAATACCGGACGGATATTATTACT 57.049 36.000 18.80 8.00 38.96 2.24
580 597 7.009907 GCAAGAATACCGGACGGATATTATTAC 59.990 40.741 18.80 11.23 38.96 1.89
581 598 7.037438 GCAAGAATACCGGACGGATATTATTA 58.963 38.462 18.80 0.00 38.96 0.98
582 599 5.873164 GCAAGAATACCGGACGGATATTATT 59.127 40.000 18.80 15.85 38.96 1.40
584 601 4.616604 CGCAAGAATACCGGACGGATATTA 60.617 45.833 18.80 0.00 43.02 0.98
585 602 3.660865 GCAAGAATACCGGACGGATATT 58.339 45.455 18.80 15.86 38.96 1.28
586 603 2.352421 CGCAAGAATACCGGACGGATAT 60.352 50.000 18.80 8.63 43.02 1.63
587 604 1.001048 CGCAAGAATACCGGACGGATA 60.001 52.381 18.80 6.63 43.02 2.59
588 605 0.249322 CGCAAGAATACCGGACGGAT 60.249 55.000 18.80 3.91 43.02 4.18
589 606 1.140161 CGCAAGAATACCGGACGGA 59.860 57.895 18.80 1.45 43.02 4.69
590 607 0.738412 AACGCAAGAATACCGGACGG 60.738 55.000 9.46 9.56 43.62 4.79
591 608 0.368907 CAACGCAAGAATACCGGACG 59.631 55.000 9.46 0.74 43.62 4.79
592 609 1.392510 GTCAACGCAAGAATACCGGAC 59.607 52.381 9.46 0.00 43.62 4.79
593 610 1.001068 TGTCAACGCAAGAATACCGGA 59.999 47.619 9.46 0.00 43.62 5.14
604 621 1.816835 CTACCTCCTACTGTCAACGCA 59.183 52.381 0.00 0.00 0.00 5.24
608 625 2.176889 GTGCCTACCTCCTACTGTCAA 58.823 52.381 0.00 0.00 0.00 3.18
619 636 2.700897 GTGAGATGGTATGTGCCTACCT 59.299 50.000 8.25 0.00 41.54 3.08
620 637 2.434336 TGTGAGATGGTATGTGCCTACC 59.566 50.000 1.32 1.32 41.39 3.18
621 638 3.819564 TGTGAGATGGTATGTGCCTAC 57.180 47.619 0.00 0.00 0.00 3.18
622 639 3.071457 CCATGTGAGATGGTATGTGCCTA 59.929 47.826 0.00 0.00 34.56 3.93
623 640 2.158711 CCATGTGAGATGGTATGTGCCT 60.159 50.000 0.00 0.00 34.56 4.75
624 641 2.158769 TCCATGTGAGATGGTATGTGCC 60.159 50.000 8.59 0.00 40.06 5.01
625 642 3.198409 TCCATGTGAGATGGTATGTGC 57.802 47.619 8.59 0.00 40.06 4.57
708 755 3.304123 CGGAATTACACTTTTGGTCGCAA 60.304 43.478 0.00 0.00 0.00 4.85
712 759 3.003897 TGCACGGAATTACACTTTTGGTC 59.996 43.478 0.00 0.00 0.00 4.02
727 777 1.585517 CATGGTTGCATTGCACGGA 59.414 52.632 11.66 0.00 38.71 4.69
873 1211 8.739039 CCATTGGTATTGTTCTGTAGAAATCAA 58.261 33.333 0.00 0.00 35.58 2.57
884 1222 8.632679 CACTTATTATGCCATTGGTATTGTTCT 58.367 33.333 11.75 0.00 0.00 3.01
885 1223 7.867403 CCACTTATTATGCCATTGGTATTGTTC 59.133 37.037 11.75 0.00 0.00 3.18
886 1224 7.563188 TCCACTTATTATGCCATTGGTATTGTT 59.437 33.333 11.75 0.65 0.00 2.83
888 1226 7.448161 TCTCCACTTATTATGCCATTGGTATTG 59.552 37.037 11.75 3.11 0.00 1.90
927 1280 0.922626 GCCCCCTCTCTTTTCTGGAT 59.077 55.000 0.00 0.00 0.00 3.41
1072 1446 2.656069 CGAGCTTTCGGGGGAAGGA 61.656 63.158 0.00 0.00 0.00 3.36
1074 1448 0.464452 ATACGAGCTTTCGGGGGAAG 59.536 55.000 0.18 0.00 37.45 3.46
1075 1449 0.906775 AATACGAGCTTTCGGGGGAA 59.093 50.000 0.18 0.00 37.45 3.97
1076 1450 0.906775 AAATACGAGCTTTCGGGGGA 59.093 50.000 0.18 0.00 37.45 4.81
1078 1452 3.242641 GCTAAAAATACGAGCTTTCGGGG 60.243 47.826 0.18 0.00 37.45 5.73
1079 1453 3.242641 GGCTAAAAATACGAGCTTTCGGG 60.243 47.826 0.18 0.00 36.43 5.14
1080 1454 3.372822 TGGCTAAAAATACGAGCTTTCGG 59.627 43.478 0.18 0.00 36.43 4.30
1081 1455 4.593597 TGGCTAAAAATACGAGCTTTCG 57.406 40.909 0.00 0.00 36.43 3.46
1082 1456 6.258947 AGAGATGGCTAAAAATACGAGCTTTC 59.741 38.462 0.00 0.00 36.43 2.62
1128 1502 2.515057 GAGGGAGAGCGAGCGAGA 60.515 66.667 0.00 0.00 0.00 4.04
1129 1503 2.515991 AGAGGGAGAGCGAGCGAG 60.516 66.667 0.00 0.00 0.00 5.03
1132 1506 2.542907 CGAGAGAGGGAGAGCGAGC 61.543 68.421 0.00 0.00 0.00 5.03
1135 1509 3.591835 GGCGAGAGAGGGAGAGCG 61.592 72.222 0.00 0.00 0.00 5.03
1136 1510 1.832167 ATGGCGAGAGAGGGAGAGC 60.832 63.158 0.00 0.00 0.00 4.09
1800 2211 4.641645 TGCAGGTGGGTGGAAGCG 62.642 66.667 0.00 0.00 33.03 4.68
2128 2579 2.711009 TCTCCACTGGAATCAACCAACT 59.289 45.455 0.00 0.00 39.59 3.16
2137 2588 3.390639 GGATCATCTGTCTCCACTGGAAT 59.609 47.826 0.00 0.00 0.00 3.01
2150 2601 2.620251 TTACAAGCCCGGATCATCTG 57.380 50.000 0.73 0.00 0.00 2.90
2168 2619 4.381292 GCACCATCTTTCTTGCTAGCAATT 60.381 41.667 29.40 8.64 35.20 2.32
2250 2732 6.426937 GGCAAAATAAAAGGAGGAGGAAAAAC 59.573 38.462 0.00 0.00 0.00 2.43
2259 2741 4.142381 CGAGGAAGGCAAAATAAAAGGAGG 60.142 45.833 0.00 0.00 0.00 4.30
2262 2744 4.485163 CACGAGGAAGGCAAAATAAAAGG 58.515 43.478 0.00 0.00 0.00 3.11
2263 2745 4.217550 TCCACGAGGAAGGCAAAATAAAAG 59.782 41.667 0.00 0.00 42.23 2.27
2264 2746 4.145807 TCCACGAGGAAGGCAAAATAAAA 58.854 39.130 0.00 0.00 42.23 1.52
2265 2747 3.756434 CTCCACGAGGAAGGCAAAATAAA 59.244 43.478 2.41 0.00 45.19 1.40
2268 2750 1.826385 CTCCACGAGGAAGGCAAAAT 58.174 50.000 2.41 0.00 45.19 1.82
2270 2752 1.302511 GCTCCACGAGGAAGGCAAA 60.303 57.895 2.41 0.00 45.19 3.68
2271 2753 0.902984 TAGCTCCACGAGGAAGGCAA 60.903 55.000 14.03 0.00 45.19 4.52
2272 2754 1.304962 TAGCTCCACGAGGAAGGCA 60.305 57.895 14.03 0.21 45.19 4.75
2273 2755 1.439644 CTAGCTCCACGAGGAAGGC 59.560 63.158 2.41 3.98 45.19 4.35
2274 2756 1.323271 TGCTAGCTCCACGAGGAAGG 61.323 60.000 17.23 0.00 45.19 3.46
2275 2757 0.102120 CTGCTAGCTCCACGAGGAAG 59.898 60.000 17.23 0.00 45.19 3.46
2276 2758 0.323451 TCTGCTAGCTCCACGAGGAA 60.323 55.000 17.23 0.00 45.19 3.36
2277 2759 0.323451 TTCTGCTAGCTCCACGAGGA 60.323 55.000 17.23 0.42 43.21 3.71
2278 2760 0.532573 TTTCTGCTAGCTCCACGAGG 59.467 55.000 17.23 0.00 0.00 4.63
2279 2761 2.370281 TTTTCTGCTAGCTCCACGAG 57.630 50.000 17.23 3.56 0.00 4.18
2280 2762 3.002791 CAATTTTCTGCTAGCTCCACGA 58.997 45.455 17.23 1.95 0.00 4.35
2281 2763 2.096496 CCAATTTTCTGCTAGCTCCACG 59.904 50.000 17.23 0.00 0.00 4.94
2282 2764 3.347216 TCCAATTTTCTGCTAGCTCCAC 58.653 45.455 17.23 0.00 0.00 4.02
2283 2765 3.719268 TCCAATTTTCTGCTAGCTCCA 57.281 42.857 17.23 0.00 0.00 3.86
2284 2766 3.243334 GCATCCAATTTTCTGCTAGCTCC 60.243 47.826 17.23 0.00 0.00 4.70
2285 2767 3.631227 AGCATCCAATTTTCTGCTAGCTC 59.369 43.478 17.23 0.00 42.85 4.09
2286 2768 3.380637 CAGCATCCAATTTTCTGCTAGCT 59.619 43.478 17.23 0.00 42.79 3.32
2287 2769 3.129988 ACAGCATCCAATTTTCTGCTAGC 59.870 43.478 8.10 8.10 42.79 3.42
2288 2770 4.978083 ACAGCATCCAATTTTCTGCTAG 57.022 40.909 5.37 0.00 42.79 3.42
2289 2771 5.500234 ACTACAGCATCCAATTTTCTGCTA 58.500 37.500 5.37 0.00 42.79 3.49
2290 2772 4.338879 ACTACAGCATCCAATTTTCTGCT 58.661 39.130 0.67 0.67 45.41 4.24
2291 2773 4.708726 ACTACAGCATCCAATTTTCTGC 57.291 40.909 0.00 0.00 34.85 4.26
2292 2774 6.404074 GGAGAACTACAGCATCCAATTTTCTG 60.404 42.308 0.00 0.00 0.00 3.02
2293 2775 5.649831 GGAGAACTACAGCATCCAATTTTCT 59.350 40.000 0.00 0.00 0.00 2.52
2294 2776 5.163612 GGGAGAACTACAGCATCCAATTTTC 60.164 44.000 0.00 0.00 0.00 2.29
2295 2777 4.706962 GGGAGAACTACAGCATCCAATTTT 59.293 41.667 0.00 0.00 0.00 1.82
2296 2778 4.018050 AGGGAGAACTACAGCATCCAATTT 60.018 41.667 0.00 0.00 0.00 1.82
2297 2779 3.525199 AGGGAGAACTACAGCATCCAATT 59.475 43.478 0.00 0.00 0.00 2.32
2298 2780 3.118531 AGGGAGAACTACAGCATCCAAT 58.881 45.455 0.00 0.00 0.00 3.16
2299 2781 2.501723 GAGGGAGAACTACAGCATCCAA 59.498 50.000 0.00 0.00 0.00 3.53
2300 2782 2.111384 GAGGGAGAACTACAGCATCCA 58.889 52.381 0.00 0.00 0.00 3.41
2301 2783 2.102252 CTGAGGGAGAACTACAGCATCC 59.898 54.545 0.00 0.00 0.00 3.51
2302 2784 3.451141 CTGAGGGAGAACTACAGCATC 57.549 52.381 0.00 0.00 0.00 3.91
2305 2787 3.750828 GCTGAGGGAGAACTACAGC 57.249 57.895 0.00 0.00 44.88 4.40
2306 2788 2.426738 CAGAGCTGAGGGAGAACTACAG 59.573 54.545 0.00 0.00 0.00 2.74
2307 2789 2.451490 CAGAGCTGAGGGAGAACTACA 58.549 52.381 0.00 0.00 0.00 2.74
2308 2790 1.754226 CCAGAGCTGAGGGAGAACTAC 59.246 57.143 0.00 0.00 0.00 2.73
2309 2791 1.359474 ACCAGAGCTGAGGGAGAACTA 59.641 52.381 0.00 0.00 0.00 2.24
2310 2792 0.116143 ACCAGAGCTGAGGGAGAACT 59.884 55.000 0.00 0.00 0.00 3.01
2311 2793 0.248843 CACCAGAGCTGAGGGAGAAC 59.751 60.000 0.00 0.00 0.00 3.01
2365 2847 0.255890 TTGCTGGCCCAATCTACTCC 59.744 55.000 0.00 0.00 0.00 3.85
2366 2848 1.745653 GTTTGCTGGCCCAATCTACTC 59.254 52.381 0.00 0.00 0.00 2.59
2367 2849 1.075374 TGTTTGCTGGCCCAATCTACT 59.925 47.619 0.00 0.00 0.00 2.57
2368 2850 1.474077 CTGTTTGCTGGCCCAATCTAC 59.526 52.381 0.00 0.00 0.00 2.59
2374 2856 2.598394 GCTCTGTTTGCTGGCCCA 60.598 61.111 0.00 0.00 0.00 5.36
2401 2883 6.583806 CCAAGATCAAGCAACAGAACAATAAC 59.416 38.462 0.00 0.00 0.00 1.89
2403 2885 5.769662 ACCAAGATCAAGCAACAGAACAATA 59.230 36.000 0.00 0.00 0.00 1.90
2404 2886 4.586001 ACCAAGATCAAGCAACAGAACAAT 59.414 37.500 0.00 0.00 0.00 2.71
2410 2892 3.076621 TGCTACCAAGATCAAGCAACAG 58.923 45.455 0.00 0.00 41.74 3.16
2431 2926 9.373450 TCTCTGAGGATAGTATTTTCTTGCTAT 57.627 33.333 4.59 0.00 0.00 2.97
2445 2940 4.504689 GCCCTTTCCATTCTCTGAGGATAG 60.505 50.000 4.59 0.00 32.41 2.08
2446 2941 3.392616 GCCCTTTCCATTCTCTGAGGATA 59.607 47.826 4.59 0.00 0.00 2.59
2447 2942 2.174424 GCCCTTTCCATTCTCTGAGGAT 59.826 50.000 4.59 0.00 0.00 3.24
2448 2943 1.561542 GCCCTTTCCATTCTCTGAGGA 59.438 52.381 4.59 0.00 0.00 3.71
2449 2944 1.283029 TGCCCTTTCCATTCTCTGAGG 59.717 52.381 4.59 0.00 0.00 3.86
2450 2945 2.795231 TGCCCTTTCCATTCTCTGAG 57.205 50.000 0.00 0.00 0.00 3.35
2451 2946 3.524095 TTTGCCCTTTCCATTCTCTGA 57.476 42.857 0.00 0.00 0.00 3.27
2452 2947 4.813750 ATTTTGCCCTTTCCATTCTCTG 57.186 40.909 0.00 0.00 0.00 3.35
2453 2948 5.830799 AAATTTTGCCCTTTCCATTCTCT 57.169 34.783 0.00 0.00 0.00 3.10
2454 2949 5.582269 GCTAAATTTTGCCCTTTCCATTCTC 59.418 40.000 12.84 0.00 0.00 2.87
2455 2950 5.249163 AGCTAAATTTTGCCCTTTCCATTCT 59.751 36.000 18.94 0.00 0.00 2.40
2456 2951 5.352293 CAGCTAAATTTTGCCCTTTCCATTC 59.648 40.000 18.94 0.00 0.00 2.67
2457 2952 5.012975 TCAGCTAAATTTTGCCCTTTCCATT 59.987 36.000 18.94 0.00 0.00 3.16
2458 2953 4.531732 TCAGCTAAATTTTGCCCTTTCCAT 59.468 37.500 18.94 0.00 0.00 3.41
2459 2954 3.900601 TCAGCTAAATTTTGCCCTTTCCA 59.099 39.130 18.94 0.00 0.00 3.53
2460 2955 4.535526 TCAGCTAAATTTTGCCCTTTCC 57.464 40.909 18.94 0.00 0.00 3.13
2461 2956 5.406477 CAGTTCAGCTAAATTTTGCCCTTTC 59.594 40.000 18.94 8.15 0.00 2.62
2462 2957 5.163311 ACAGTTCAGCTAAATTTTGCCCTTT 60.163 36.000 18.94 0.15 0.00 3.11
2463 2958 4.344968 ACAGTTCAGCTAAATTTTGCCCTT 59.655 37.500 18.94 0.50 0.00 3.95
2464 2959 3.897505 ACAGTTCAGCTAAATTTTGCCCT 59.102 39.130 18.94 8.81 0.00 5.19
2480 2975 1.401552 TGCAACAGACAGCAACAGTTC 59.598 47.619 0.00 0.00 37.90 3.01
2524 3019 1.519234 TGCGAGGATGCATCGACAC 60.519 57.895 20.15 10.49 42.76 3.67
2537 3077 4.624336 ACTAGTCAGTAATGAGTGCGAG 57.376 45.455 10.71 3.09 31.45 5.03
2552 3092 6.106673 TCTGTTGCTTATGGCTTTACTAGTC 58.893 40.000 0.00 0.00 42.39 2.59
2553 3093 6.049955 TCTGTTGCTTATGGCTTTACTAGT 57.950 37.500 0.00 0.00 42.39 2.57
2558 3098 5.885352 TGCTATTCTGTTGCTTATGGCTTTA 59.115 36.000 0.00 0.00 42.39 1.85
2575 3130 6.301108 CAATGCATTTGTGTTGTTGCTATTC 58.699 36.000 9.83 0.00 36.10 1.75
2595 3150 0.596600 GCCGATCCTGCATTGCAATG 60.597 55.000 30.92 30.92 38.41 2.82
2596 3151 1.737816 GCCGATCCTGCATTGCAAT 59.262 52.632 13.18 5.99 38.41 3.56
2597 3152 2.417257 GGCCGATCCTGCATTGCAA 61.417 57.895 13.18 0.00 38.41 4.08
2598 3153 2.829914 GGCCGATCCTGCATTGCA 60.830 61.111 11.50 11.50 36.92 4.08
2599 3154 1.947597 TTTGGCCGATCCTGCATTGC 61.948 55.000 0.46 0.46 35.26 3.56
2617 3172 1.406180 GTAACCACCAACCAACGCTTT 59.594 47.619 0.00 0.00 0.00 3.51
2619 3174 0.107116 TGTAACCACCAACCAACGCT 60.107 50.000 0.00 0.00 0.00 5.07
2620 3175 0.955905 ATGTAACCACCAACCAACGC 59.044 50.000 0.00 0.00 0.00 4.84
2621 3176 2.031508 GTCATGTAACCACCAACCAACG 60.032 50.000 0.00 0.00 0.00 4.10
2622 3177 3.219281 AGTCATGTAACCACCAACCAAC 58.781 45.455 0.00 0.00 0.00 3.77
2624 3179 3.586470 AAGTCATGTAACCACCAACCA 57.414 42.857 0.00 0.00 0.00 3.67
2625 3180 3.434299 CGTAAGTCATGTAACCACCAACC 59.566 47.826 0.00 0.00 0.00 3.77
2626 3181 4.657075 CGTAAGTCATGTAACCACCAAC 57.343 45.455 0.00 0.00 0.00 3.77
2643 3198 0.958382 GGCAAGCATGGTGGACGTAA 60.958 55.000 2.68 0.00 0.00 3.18
2644 3199 1.376683 GGCAAGCATGGTGGACGTA 60.377 57.895 2.68 0.00 0.00 3.57
2645 3200 2.672996 GGCAAGCATGGTGGACGT 60.673 61.111 2.68 0.00 0.00 4.34
2646 3201 3.443045 GGGCAAGCATGGTGGACG 61.443 66.667 2.68 0.00 0.00 4.79
2647 3202 3.070576 GGGGCAAGCATGGTGGAC 61.071 66.667 2.68 0.00 0.00 4.02
2648 3203 4.738998 CGGGGCAAGCATGGTGGA 62.739 66.667 2.68 0.00 0.00 4.02
2680 3235 1.592939 GGAGAAAGGAGGCGATCGC 60.593 63.158 31.52 31.52 41.06 4.58
2681 3236 1.068250 GGGAGAAAGGAGGCGATCG 59.932 63.158 11.69 11.69 0.00 3.69
2698 3253 1.673665 GGAGCACAACTGCAGAGGG 60.674 63.158 23.35 14.74 46.97 4.30
2699 3254 0.954449 CAGGAGCACAACTGCAGAGG 60.954 60.000 23.35 14.17 46.97 3.69
2731 3292 2.421399 GGGAGAAATGCAGGCAGGC 61.421 63.158 0.00 0.00 0.00 4.85
2756 3317 2.045131 CCTTTCTGCTGCTCCAGGC 61.045 63.158 0.00 0.00 42.22 4.85
2757 3318 1.378250 CCCTTTCTGCTGCTCCAGG 60.378 63.158 0.00 1.13 33.64 4.45
2769 3330 0.803117 GAAAGTACAGCGGCCCTTTC 59.197 55.000 12.31 12.31 36.94 2.62
2846 3407 1.536940 TGCAATGCACAGCACAGTAT 58.463 45.000 2.72 0.00 43.04 2.12
2855 3416 2.675603 GCAGGATTCAATGCAATGCACA 60.676 45.455 11.23 0.00 43.04 4.57
2896 3496 8.567948 CCGAGCCACTTTATTTGTTGATTATAT 58.432 33.333 0.00 0.00 0.00 0.86
2897 3497 7.771361 TCCGAGCCACTTTATTTGTTGATTATA 59.229 33.333 0.00 0.00 0.00 0.98
2898 3498 6.601613 TCCGAGCCACTTTATTTGTTGATTAT 59.398 34.615 0.00 0.00 0.00 1.28
2899 3499 5.941058 TCCGAGCCACTTTATTTGTTGATTA 59.059 36.000 0.00 0.00 0.00 1.75
2900 3500 4.764823 TCCGAGCCACTTTATTTGTTGATT 59.235 37.500 0.00 0.00 0.00 2.57
2901 3501 4.331968 TCCGAGCCACTTTATTTGTTGAT 58.668 39.130 0.00 0.00 0.00 2.57
2902 3502 3.745799 TCCGAGCCACTTTATTTGTTGA 58.254 40.909 0.00 0.00 0.00 3.18
2917 3517 3.061139 CGATTGAAACGACTATTCCGAGC 60.061 47.826 0.00 0.00 0.00 5.03
2921 3521 2.034001 CCGCGATTGAAACGACTATTCC 60.034 50.000 8.23 0.00 0.00 3.01
2926 3526 1.336148 TGTACCGCGATTGAAACGACT 60.336 47.619 8.23 0.00 0.00 4.18
2927 3527 1.058695 CTGTACCGCGATTGAAACGAC 59.941 52.381 8.23 0.00 0.00 4.34
2929 3529 0.247145 GCTGTACCGCGATTGAAACG 60.247 55.000 8.23 0.00 0.00 3.60
2942 3543 6.163135 AGTAGGTAATCTTCATGGCTGTAC 57.837 41.667 0.00 0.00 0.00 2.90
2966 3573 5.295787 ACTGTACAGTGTACAACAACAATGG 59.704 40.000 30.53 19.91 46.77 3.16
2968 3575 8.148351 AGATACTGTACAGTGTACAACAACAAT 58.852 33.333 33.77 17.05 42.52 2.71
2990 3597 6.109156 TGAAGGTGAAAAGCTACACAGATA 57.891 37.500 16.45 2.69 38.57 1.98
3009 3616 5.358160 GGTCCCAAAATAATCTGACCTGAAG 59.642 44.000 0.00 0.00 39.30 3.02
3014 3621 3.954258 CCAGGTCCCAAAATAATCTGACC 59.046 47.826 0.00 0.00 42.00 4.02
3023 3630 2.437651 CAACAAACCCAGGTCCCAAAAT 59.562 45.455 0.00 0.00 0.00 1.82
3032 3639 1.895131 CTCCAATCCAACAAACCCAGG 59.105 52.381 0.00 0.00 0.00 4.45
3036 3643 1.273327 CAGGCTCCAATCCAACAAACC 59.727 52.381 0.00 0.00 0.00 3.27
3037 3644 1.273327 CCAGGCTCCAATCCAACAAAC 59.727 52.381 0.00 0.00 0.00 2.93
3045 3652 2.037511 CAGAGAGATCCAGGCTCCAATC 59.962 54.545 0.00 0.00 32.82 2.67
3078 3685 8.432805 ACCTGTTGAGAGAGATCTTCTTAAAAA 58.567 33.333 0.00 0.00 35.87 1.94
3079 3686 7.875041 CACCTGTTGAGAGAGATCTTCTTAAAA 59.125 37.037 0.00 0.25 35.87 1.52
3080 3687 7.382110 CACCTGTTGAGAGAGATCTTCTTAAA 58.618 38.462 0.00 0.00 35.87 1.52
3081 3688 6.071108 CCACCTGTTGAGAGAGATCTTCTTAA 60.071 42.308 0.00 2.73 35.87 1.85
3082 3689 5.420421 CCACCTGTTGAGAGAGATCTTCTTA 59.580 44.000 0.00 0.00 35.87 2.10
3083 3690 4.222588 CCACCTGTTGAGAGAGATCTTCTT 59.777 45.833 0.00 0.00 35.87 2.52
3084 3691 3.768757 CCACCTGTTGAGAGAGATCTTCT 59.231 47.826 0.00 1.78 39.43 2.85
3085 3692 3.118811 CCCACCTGTTGAGAGAGATCTTC 60.119 52.174 0.00 0.00 0.00 2.87
3086 3693 2.836981 CCCACCTGTTGAGAGAGATCTT 59.163 50.000 0.00 0.00 0.00 2.40
3087 3694 2.043664 TCCCACCTGTTGAGAGAGATCT 59.956 50.000 0.00 0.00 0.00 2.75
3088 3695 2.430332 CTCCCACCTGTTGAGAGAGATC 59.570 54.545 0.00 0.00 0.00 2.75
3089 3696 2.465813 CTCCCACCTGTTGAGAGAGAT 58.534 52.381 0.00 0.00 0.00 2.75
3090 3697 1.551099 CCTCCCACCTGTTGAGAGAGA 60.551 57.143 0.00 0.00 0.00 3.10
3091 3698 0.901124 CCTCCCACCTGTTGAGAGAG 59.099 60.000 0.00 0.00 0.00 3.20
3092 3699 1.194781 GCCTCCCACCTGTTGAGAGA 61.195 60.000 0.00 0.00 0.00 3.10
3093 3700 1.298014 GCCTCCCACCTGTTGAGAG 59.702 63.158 0.00 0.00 0.00 3.20
3094 3701 2.224159 GGCCTCCCACCTGTTGAGA 61.224 63.158 0.00 0.00 0.00 3.27
3095 3702 2.190488 GAGGCCTCCCACCTGTTGAG 62.190 65.000 23.19 0.00 37.77 3.02
3096 3703 2.121963 AGGCCTCCCACCTGTTGA 60.122 61.111 0.00 0.00 35.72 3.18
3097 3704 2.227036 AGAGGCCTCCCACCTGTTG 61.227 63.158 29.54 0.00 37.77 3.33
3098 3705 2.208349 AGAGGCCTCCCACCTGTT 59.792 61.111 29.54 4.94 37.77 3.16
3099 3706 2.608988 CAGAGGCCTCCCACCTGT 60.609 66.667 29.54 5.79 37.77 4.00
3100 3707 4.106925 GCAGAGGCCTCCCACCTG 62.107 72.222 29.54 20.65 37.77 4.00
3101 3708 4.664267 TGCAGAGGCCTCCCACCT 62.664 66.667 29.54 7.47 41.41 4.00
3102 3709 3.650950 TTGCAGAGGCCTCCCACC 61.651 66.667 29.54 14.96 40.13 4.61
3103 3710 2.360475 GTTGCAGAGGCCTCCCAC 60.360 66.667 29.54 18.71 40.13 4.61
3158 3765 2.228480 ATGCCGTAACCACCCACCT 61.228 57.895 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.