Multiple sequence alignment - TraesCS2D01G423700

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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 TraesCS2D01G423700 chr2D 100.000 4461 0 0 1 4461 536923058 536918598 0.000000e+00 8239.0
1 TraesCS2D01G423700 chr2D 79.790 381 63 14 1805 2178 87981999 87981626 9.510000e-67 265.0
2 TraesCS2D01G423700 chr2A 88.169 4277 285 122 319 4461 679513437 679509248 0.000000e+00 4891.0
3 TraesCS2D01G423700 chr2A 92.647 68 4 1 141 208 679513560 679513494 3.670000e-16 97.1
4 TraesCS2D01G423700 chr2B 90.688 2019 122 34 590 2564 638971946 638969950 0.000000e+00 2627.0
5 TraesCS2D01G423700 chr2B 89.226 594 53 9 3874 4460 638968517 638967928 0.000000e+00 732.0
6 TraesCS2D01G423700 chr2B 90.189 581 22 12 19 567 638972581 638972004 0.000000e+00 725.0
7 TraesCS2D01G423700 chr2B 82.719 868 90 30 2993 3825 638969558 638968716 0.000000e+00 717.0
8 TraesCS2D01G423700 chr2B 94.694 245 13 0 2657 2901 638969877 638969633 9.050000e-102 381.0
9 TraesCS2D01G423700 chr5B 88.636 396 42 2 1317 1709 246223012 246222617 3.120000e-131 479.0
10 TraesCS2D01G423700 chr5B 94.388 196 10 1 1318 1512 246180325 246180130 2.610000e-77 300.0
11 TraesCS2D01G423700 chr5B 96.364 110 4 0 1548 1657 246152451 246152342 9.860000e-42 182.0
12 TraesCS2D01G423700 chr3A 90.169 356 31 3 1317 1668 272768192 272767837 1.130000e-125 460.0
13 TraesCS2D01G423700 chr7D 80.652 491 79 12 1325 1807 584855742 584855260 2.540000e-97 366.0
14 TraesCS2D01G423700 chr7D 81.510 384 59 11 1805 2182 584855168 584854791 5.610000e-79 305.0
15 TraesCS2D01G423700 chr7D 80.679 383 66 8 1805 2183 92809553 92809175 1.570000e-74 291.0
16 TraesCS2D01G423700 chr7A 79.588 485 83 12 1325 1801 675229850 675230326 2.570000e-87 333.0
17 TraesCS2D01G423700 chr7A 81.250 384 60 11 1805 2182 675230415 675230792 2.610000e-77 300.0
18 TraesCS2D01G423700 chr7A 79.534 386 64 15 1805 2182 630247517 630247139 1.230000e-65 261.0
19 TraesCS2D01G423700 chr7B 79.016 386 67 14 1805 2183 653019045 653018667 7.410000e-63 252.0
20 TraesCS2D01G423700 chr7B 79.016 386 64 13 1805 2182 660062140 660062516 9.580000e-62 248.0
21 TraesCS2D01G423700 chr6B 95.833 144 5 1 1566 1709 32658247 32658389 9.650000e-57 231.0
22 TraesCS2D01G423700 chr4D 96.875 64 2 0 1445 1508 344366557 344366620 1.700000e-19 108.0


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 TraesCS2D01G423700 chr2D 536918598 536923058 4460 True 8239.00 8239 100.0000 1 4461 1 chr2D.!!$R2 4460
1 TraesCS2D01G423700 chr2A 679509248 679513560 4312 True 2494.05 4891 90.4080 141 4461 2 chr2A.!!$R1 4320
2 TraesCS2D01G423700 chr2B 638967928 638972581 4653 True 1036.40 2627 89.5032 19 4460 5 chr2B.!!$R1 4441
3 TraesCS2D01G423700 chr7D 584854791 584855742 951 True 335.50 366 81.0810 1325 2182 2 chr7D.!!$R2 857
4 TraesCS2D01G423700 chr7A 675229850 675230792 942 False 316.50 333 80.4190 1325 2182 2 chr7A.!!$F1 857

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
42 43 0.532573 CGCTCTAGTTCCAGCCTTGA 59.467 55.0 0.00 0.0 31.37 3.02 F
375 392 1.667236 TAAGCATCCACCAGAATGCG 58.333 50.0 2.04 0.0 44.08 4.73 F
2217 2425 0.169009 GCTCCAAGTTTCATGGCGAC 59.831 55.0 0.00 0.0 37.88 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2239 1.375908 GTCGCCCATGCACTTCTCA 60.376 57.895 0.00 0.0 37.32 3.27 R
2226 2434 0.111061 AGGCAAATCCAGCAGTGTCA 59.889 50.000 0.00 0.0 37.29 3.58 R
3874 4321 0.036875 GGCCAAGTAGTTCTGCCTGT 59.963 55.000 11.52 0.0 39.05 4.00 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 3.102097 GCCATTTCTCCGGCGAAG 58.898 61.111 9.30 0.00 38.82 3.79
42 43 0.532573 CGCTCTAGTTCCAGCCTTGA 59.467 55.000 0.00 0.00 31.37 3.02
71 72 4.036734 GCCTGCGGATCATAAAGAATTTCA 59.963 41.667 0.00 0.00 40.09 2.69
117 118 6.346096 TGTTAGGTAGCATATGGAAACTGTC 58.654 40.000 4.56 0.00 0.00 3.51
137 138 1.880675 CTGATGCAGATCCTGGAATGC 59.119 52.381 23.22 23.22 35.08 3.56
263 264 2.046313 CACTGACACTGAATTTTGCGC 58.954 47.619 0.00 0.00 0.00 6.09
270 271 3.067461 ACACTGAATTTTGCGCAACCTAA 59.933 39.130 24.99 15.59 0.00 2.69
277 278 3.717400 TTTGCGCAACCTAATTGAACA 57.283 38.095 24.99 0.00 41.23 3.18
316 333 3.165058 TGCCAGATGATGTACTCGAAC 57.835 47.619 0.00 0.00 0.00 3.95
362 379 7.524367 GCATCAATTAGTGGCCTTATTAAGCAT 60.524 37.037 3.32 0.00 0.00 3.79
375 392 1.667236 TAAGCATCCACCAGAATGCG 58.333 50.000 2.04 0.00 44.08 4.73
583 633 3.408634 TGTCAGTGTCACGACTCTCATA 58.591 45.455 20.72 5.14 33.38 2.15
584 634 4.010349 TGTCAGTGTCACGACTCTCATAT 58.990 43.478 20.72 0.00 33.38 1.78
585 635 4.142600 TGTCAGTGTCACGACTCTCATATG 60.143 45.833 20.72 0.00 33.38 1.78
588 638 3.629855 AGTGTCACGACTCTCATATGGAG 59.370 47.826 15.59 15.59 45.49 3.86
605 676 3.609853 TGGAGAAGAATGGAATTGGTCG 58.390 45.455 0.00 0.00 36.07 4.79
622 693 2.295349 GGTCGGAGCCTAATTATCACGA 59.705 50.000 0.00 0.00 0.00 4.35
625 696 3.572682 TCGGAGCCTAATTATCACGACAT 59.427 43.478 0.00 0.00 0.00 3.06
666 737 2.998670 CAAGCATTGTCACATCTCTCGT 59.001 45.455 0.00 0.00 42.34 4.18
667 738 4.176271 CAAGCATTGTCACATCTCTCGTA 58.824 43.478 0.00 0.00 42.34 3.43
668 739 3.775202 AGCATTGTCACATCTCTCGTAC 58.225 45.455 0.00 0.00 0.00 3.67
682 753 7.281324 ACATCTCTCGTACTATCATATAGTGCC 59.719 40.741 9.35 0.83 0.00 5.01
687 758 5.651139 TCGTACTATCATATAGTGCCCCTTC 59.349 44.000 9.35 0.00 0.00 3.46
780 852 4.655027 TGTACAGCGACATAACGTAGAAG 58.345 43.478 0.00 0.00 35.59 2.85
858 930 6.031751 TCCCCCAAAATGTTTTTATTCTCG 57.968 37.500 0.00 0.00 0.00 4.04
860 932 5.867174 CCCCCAAAATGTTTTTATTCTCGTC 59.133 40.000 0.00 0.00 0.00 4.20
865 938 9.113876 CCAAAATGTTTTTATTCTCGTCTACAC 57.886 33.333 0.00 0.00 0.00 2.90
866 939 9.658475 CAAAATGTTTTTATTCTCGTCTACACA 57.342 29.630 0.00 0.00 0.00 3.72
880 953 7.544566 TCTCGTCTACACATTTCCTATGAAAAC 59.455 37.037 0.00 0.00 43.37 2.43
881 954 7.383687 TCGTCTACACATTTCCTATGAAAACT 58.616 34.615 0.00 0.00 43.37 2.66
882 955 7.544566 TCGTCTACACATTTCCTATGAAAACTC 59.455 37.037 0.00 0.00 43.37 3.01
883 956 7.462856 CGTCTACACATTTCCTATGAAAACTCG 60.463 40.741 0.00 0.00 43.37 4.18
884 957 7.331193 GTCTACACATTTCCTATGAAAACTCGT 59.669 37.037 0.00 0.00 43.37 4.18
885 958 8.525316 TCTACACATTTCCTATGAAAACTCGTA 58.475 33.333 0.00 0.00 43.37 3.43
891 982 4.346730 TCCTATGAAAACTCGTACCTGGA 58.653 43.478 0.00 0.00 0.00 3.86
956 1047 2.316108 ACCCAGCCACGAAATTTTCTT 58.684 42.857 7.50 0.00 0.00 2.52
957 1048 2.296190 ACCCAGCCACGAAATTTTCTTC 59.704 45.455 7.50 0.00 0.00 2.87
958 1049 2.352715 CCCAGCCACGAAATTTTCTTCC 60.353 50.000 7.50 0.00 0.00 3.46
1288 1385 2.355363 CGTTCAAGTCGCGGTCCA 60.355 61.111 6.13 0.00 0.00 4.02
1608 1708 2.490217 CGGGTGGAGTACGAGCTG 59.510 66.667 0.00 0.00 0.00 4.24
2040 2239 2.109799 CTGCCGGCGGAGATGATT 59.890 61.111 32.31 0.00 0.00 2.57
2191 2390 0.753111 GTACAGGGGTACGATCGGGT 60.753 60.000 20.98 1.14 40.41 5.28
2196 2404 2.418083 GGGTACGATCGGGTTCGGT 61.418 63.158 20.98 0.00 43.33 4.69
2198 2406 0.803380 GGTACGATCGGGTTCGGTTG 60.803 60.000 20.98 0.00 43.33 3.77
2203 2411 2.515996 GATCGGGTTCGGTTGCTCCA 62.516 60.000 0.00 0.00 36.95 3.86
2204 2412 2.119484 ATCGGGTTCGGTTGCTCCAA 62.119 55.000 0.00 0.00 36.95 3.53
2205 2413 2.325082 CGGGTTCGGTTGCTCCAAG 61.325 63.158 0.00 0.00 35.57 3.61
2217 2425 0.169009 GCTCCAAGTTTCATGGCGAC 59.831 55.000 0.00 0.00 37.88 5.19
2228 2436 9.582613 CAAGTTTCATGGCGACAAGAGAATTGA 62.583 40.741 18.77 2.90 45.25 2.57
2230 2438 2.542020 TGGCGACAAGAGAATTGACA 57.458 45.000 0.00 0.00 37.44 3.58
2231 2439 2.143122 TGGCGACAAGAGAATTGACAC 58.857 47.619 0.00 0.00 37.44 3.67
2237 2445 3.144506 ACAAGAGAATTGACACTGCTGG 58.855 45.455 0.00 0.00 0.00 4.85
2243 2451 3.057033 AGAATTGACACTGCTGGATTTGC 60.057 43.478 0.00 0.00 0.00 3.68
2267 2475 5.221048 CCTGAAAGAAACTGATCGTGGTTTT 60.221 40.000 10.90 4.21 36.04 2.43
2388 2597 8.141268 ACAAGGTTTACATTTTACAACCTGATG 58.859 33.333 3.24 2.36 46.87 3.07
2389 2598 8.356657 CAAGGTTTACATTTTACAACCTGATGA 58.643 33.333 3.24 0.00 46.87 2.92
2390 2599 8.650143 AGGTTTACATTTTACAACCTGATGAT 57.350 30.769 1.59 0.00 46.00 2.45
2391 2600 9.747898 AGGTTTACATTTTACAACCTGATGATA 57.252 29.630 1.59 0.00 46.00 2.15
2396 2605 8.635765 ACATTTTACAACCTGATGATAACAGT 57.364 30.769 0.00 0.00 34.04 3.55
2397 2606 9.077885 ACATTTTACAACCTGATGATAACAGTT 57.922 29.630 0.00 0.00 34.04 3.16
2398 2607 9.345517 CATTTTACAACCTGATGATAACAGTTG 57.654 33.333 0.00 0.00 35.15 3.16
2399 2608 6.494893 TTACAACCTGATGATAACAGTTGC 57.505 37.500 0.00 0.00 33.85 4.17
2400 2609 3.758554 ACAACCTGATGATAACAGTTGCC 59.241 43.478 0.00 0.00 33.85 4.52
2401 2610 2.632377 ACCTGATGATAACAGTTGCCG 58.368 47.619 0.00 0.00 34.04 5.69
2432 2644 2.868583 CTGGTCGATCGCTTCATTTCAT 59.131 45.455 11.09 0.00 0.00 2.57
2456 2668 5.413309 AGTTCTGCTCACTGCTAATTACT 57.587 39.130 0.00 0.00 43.37 2.24
2458 2670 5.047021 AGTTCTGCTCACTGCTAATTACTGA 60.047 40.000 0.00 0.00 43.37 3.41
2459 2671 5.003692 TCTGCTCACTGCTAATTACTGAG 57.996 43.478 0.00 0.00 43.37 3.35
2460 2672 4.464244 TCTGCTCACTGCTAATTACTGAGT 59.536 41.667 0.00 0.00 43.37 3.41
2469 2689 9.973450 CACTGCTAATTACTGAGTAATCTGTAT 57.027 33.333 17.37 5.20 37.69 2.29
2479 2699 8.394971 ACTGAGTAATCTGTATGATCTCTCTG 57.605 38.462 0.47 0.00 38.30 3.35
2504 2724 1.977009 ATGGAGACGGACGAGTGCA 60.977 57.895 0.00 0.00 0.00 4.57
2554 2774 1.227999 ACAAGACCAACATCACCGCG 61.228 55.000 0.00 0.00 0.00 6.46
2559 2779 2.174107 CAACATCACCGCGTGCAG 59.826 61.111 4.92 2.45 32.98 4.41
2566 2786 4.675029 ACCGCGTGCAGGGTACAC 62.675 66.667 4.92 0.00 33.95 2.90
2569 2789 1.804326 CGCGTGCAGGGTACACTAC 60.804 63.158 8.72 0.00 35.84 2.73
2570 2790 1.290955 GCGTGCAGGGTACACTACA 59.709 57.895 8.72 0.00 35.84 2.74
2571 2791 0.736325 GCGTGCAGGGTACACTACAG 60.736 60.000 8.72 0.00 35.84 2.74
2575 2795 2.167693 GTGCAGGGTACACTACAGCATA 59.832 50.000 11.37 0.00 35.84 3.14
2577 2797 2.483188 GCAGGGTACACTACAGCATACC 60.483 54.545 0.00 0.00 37.03 2.73
2578 2798 3.031736 CAGGGTACACTACAGCATACCT 58.968 50.000 0.00 0.00 37.75 3.08
2592 2812 3.950395 AGCATACCTCATTCCTTTTCTGC 59.050 43.478 0.00 0.00 0.00 4.26
2593 2813 3.950395 GCATACCTCATTCCTTTTCTGCT 59.050 43.478 0.00 0.00 0.00 4.24
2594 2814 4.400567 GCATACCTCATTCCTTTTCTGCTT 59.599 41.667 0.00 0.00 0.00 3.91
2595 2815 5.105595 GCATACCTCATTCCTTTTCTGCTTT 60.106 40.000 0.00 0.00 0.00 3.51
2596 2816 6.573094 GCATACCTCATTCCTTTTCTGCTTTT 60.573 38.462 0.00 0.00 0.00 2.27
2599 2819 5.221322 ACCTCATTCCTTTTCTGCTTTTCAC 60.221 40.000 0.00 0.00 0.00 3.18
2600 2820 5.221303 CCTCATTCCTTTTCTGCTTTTCACA 60.221 40.000 0.00 0.00 0.00 3.58
2601 2821 6.219417 TCATTCCTTTTCTGCTTTTCACAA 57.781 33.333 0.00 0.00 0.00 3.33
2602 2822 6.042143 TCATTCCTTTTCTGCTTTTCACAAC 58.958 36.000 0.00 0.00 0.00 3.32
2603 2823 5.398603 TTCCTTTTCTGCTTTTCACAACA 57.601 34.783 0.00 0.00 0.00 3.33
2604 2824 4.743493 TCCTTTTCTGCTTTTCACAACAC 58.257 39.130 0.00 0.00 0.00 3.32
2605 2825 4.462483 TCCTTTTCTGCTTTTCACAACACT 59.538 37.500 0.00 0.00 0.00 3.55
2606 2826 5.047377 TCCTTTTCTGCTTTTCACAACACTT 60.047 36.000 0.00 0.00 0.00 3.16
2608 2828 5.384063 TTTCTGCTTTTCACAACACTTGA 57.616 34.783 0.00 0.00 0.00 3.02
2609 2829 4.621068 TCTGCTTTTCACAACACTTGAG 57.379 40.909 0.00 0.00 0.00 3.02
2610 2830 4.260985 TCTGCTTTTCACAACACTTGAGA 58.739 39.130 0.00 0.00 0.00 3.27
2611 2831 4.333649 TCTGCTTTTCACAACACTTGAGAG 59.666 41.667 0.00 0.00 32.02 3.20
2612 2832 4.009675 TGCTTTTCACAACACTTGAGAGT 58.990 39.130 0.00 0.00 36.25 3.24
2613 2833 4.458989 TGCTTTTCACAACACTTGAGAGTT 59.541 37.500 0.00 0.00 32.54 3.01
2614 2834 4.795278 GCTTTTCACAACACTTGAGAGTTG 59.205 41.667 16.34 16.34 46.94 3.16
2615 2835 5.391950 GCTTTTCACAACACTTGAGAGTTGA 60.392 40.000 22.28 4.20 45.31 3.18
2617 2837 4.736126 TCACAACACTTGAGAGTTGAGA 57.264 40.909 22.28 17.98 45.31 3.27
2618 2838 4.433615 TCACAACACTTGAGAGTTGAGAC 58.566 43.478 22.28 0.00 45.31 3.36
2620 2840 4.872691 CACAACACTTGAGAGTTGAGACTT 59.127 41.667 22.28 2.97 45.31 3.01
2621 2841 6.042777 CACAACACTTGAGAGTTGAGACTTA 58.957 40.000 22.28 0.00 45.31 2.24
2622 2842 6.019479 CACAACACTTGAGAGTTGAGACTTAC 60.019 42.308 22.28 0.00 45.31 2.34
2626 2846 4.525100 ACTTGAGAGTTGAGACTTACTCCC 59.475 45.833 12.53 4.80 44.34 4.30
2627 2847 4.114015 TGAGAGTTGAGACTTACTCCCA 57.886 45.455 12.53 6.84 44.34 4.37
2629 2849 3.827302 GAGAGTTGAGACTTACTCCCACA 59.173 47.826 12.53 0.00 44.34 4.17
2631 2851 3.574826 GAGTTGAGACTTACTCCCACAGT 59.425 47.826 7.21 0.00 44.34 3.55
2645 2887 1.202604 CCACAGTAAACTGACCGGTGT 60.203 52.381 14.63 0.09 46.59 4.16
2692 2944 3.626924 GGGAGGGTGTGCGAGTGT 61.627 66.667 0.00 0.00 0.00 3.55
2882 3134 2.747686 GGTTCAAGGGAGACGGCA 59.252 61.111 0.00 0.00 0.00 5.69
2904 3160 2.551270 CTGCGAAGGTGCGTTCAC 59.449 61.111 5.64 0.00 42.40 3.18
2917 3173 1.606350 CGTTCACCTCGTTCAGTCGC 61.606 60.000 0.00 0.00 0.00 5.19
2940 3196 1.215423 ACCTTCCTTCCACTTGCAGTT 59.785 47.619 0.00 0.00 0.00 3.16
2945 3201 1.882623 CCTTCCACTTGCAGTTTCTCC 59.117 52.381 0.00 0.00 0.00 3.71
2979 3242 1.482593 GTGGGTGGTAGGAGACTGATG 59.517 57.143 0.00 0.00 43.88 3.07
3169 3432 4.802051 CGATGGGGTGGCTGGTGG 62.802 72.222 0.00 0.00 0.00 4.61
3259 3528 2.388310 GGTAAGGACCAGAGTTCAGC 57.612 55.000 0.00 0.00 46.12 4.26
3285 3562 2.573369 CCTCCTCCGTCTCGAAATCTA 58.427 52.381 0.00 0.00 0.00 1.98
3290 3567 3.367607 CTCCGTCTCGAAATCTAGCAAG 58.632 50.000 0.00 0.00 0.00 4.01
3291 3569 1.855360 CCGTCTCGAAATCTAGCAAGC 59.145 52.381 0.00 0.00 0.00 4.01
3293 3571 2.923655 CGTCTCGAAATCTAGCAAGCAA 59.076 45.455 0.00 0.00 0.00 3.91
3298 3576 3.691118 TCGAAATCTAGCAAGCAAGCAAT 59.309 39.130 3.19 0.00 36.85 3.56
3304 3582 1.612676 AGCAAGCAAGCAATCACTGA 58.387 45.000 3.19 0.00 36.85 3.41
3311 3589 4.806330 AGCAAGCAATCACTGAATCTTTG 58.194 39.130 0.00 0.00 0.00 2.77
3321 3600 2.549754 ACTGAATCTTTGTTGCTGACGG 59.450 45.455 0.00 0.00 0.00 4.79
3322 3601 2.807967 CTGAATCTTTGTTGCTGACGGA 59.192 45.455 0.00 0.00 0.00 4.69
3326 3605 4.647424 ATCTTTGTTGCTGACGGAAAAA 57.353 36.364 0.00 0.00 0.00 1.94
3401 3681 1.528824 CAGTACATGCCCCTGGAGG 59.471 63.158 0.00 0.00 0.00 4.30
3463 3743 0.464036 CCGTGGAAGCAGCATAGGTA 59.536 55.000 0.00 0.00 0.00 3.08
3464 3744 1.539065 CCGTGGAAGCAGCATAGGTAG 60.539 57.143 0.00 0.00 0.00 3.18
3465 3745 1.587547 GTGGAAGCAGCATAGGTAGC 58.412 55.000 0.00 0.00 0.00 3.58
3466 3746 0.469917 TGGAAGCAGCATAGGTAGCC 59.530 55.000 0.00 0.00 0.00 3.93
3467 3747 0.250510 GGAAGCAGCATAGGTAGCCC 60.251 60.000 0.00 0.00 0.00 5.19
3468 3748 0.601311 GAAGCAGCATAGGTAGCCCG 60.601 60.000 0.00 0.00 35.12 6.13
3469 3749 1.338136 AAGCAGCATAGGTAGCCCGT 61.338 55.000 0.00 0.00 35.12 5.28
3483 3763 0.249911 GCCCGTAGCCAGGTAATGAG 60.250 60.000 0.00 0.00 34.35 2.90
3489 3769 4.442706 CGTAGCCAGGTAATGAGTGAATT 58.557 43.478 0.00 0.00 0.00 2.17
3491 3771 4.574674 AGCCAGGTAATGAGTGAATTGA 57.425 40.909 0.00 0.00 0.00 2.57
3492 3772 4.922206 AGCCAGGTAATGAGTGAATTGAA 58.078 39.130 0.00 0.00 0.00 2.69
3493 3773 5.513233 AGCCAGGTAATGAGTGAATTGAAT 58.487 37.500 0.00 0.00 0.00 2.57
3494 3774 5.359009 AGCCAGGTAATGAGTGAATTGAATG 59.641 40.000 0.00 0.00 0.00 2.67
3495 3775 5.450965 GCCAGGTAATGAGTGAATTGAATGG 60.451 44.000 0.00 0.00 0.00 3.16
3499 3779 5.981315 GGTAATGAGTGAATTGAATGGCATG 59.019 40.000 0.00 0.00 0.00 4.06
3500 3780 5.925506 AATGAGTGAATTGAATGGCATGA 57.074 34.783 0.00 0.00 0.00 3.07
3514 3803 1.824230 GGCATGACTGGTTTTGGCATA 59.176 47.619 0.00 0.00 35.00 3.14
3522 3811 6.872920 TGACTGGTTTTGGCATAATAAATCC 58.127 36.000 0.00 0.00 0.00 3.01
3526 3815 6.648192 TGGTTTTGGCATAATAAATCCCTTG 58.352 36.000 0.00 0.00 0.00 3.61
3528 3817 4.953940 TTGGCATAATAAATCCCTTGGC 57.046 40.909 0.00 0.00 0.00 4.52
3535 3824 2.507407 TAAATCCCTTGGCTGGTGAC 57.493 50.000 0.00 0.00 0.00 3.67
3537 3826 0.329596 AATCCCTTGGCTGGTGACTC 59.670 55.000 0.00 0.00 0.00 3.36
3553 3844 4.636206 GGTGACTCCAGGTGTTGATTATTC 59.364 45.833 0.00 0.00 35.97 1.75
3554 3845 4.636206 GTGACTCCAGGTGTTGATTATTCC 59.364 45.833 0.00 0.00 0.00 3.01
3556 3847 5.724370 TGACTCCAGGTGTTGATTATTCCTA 59.276 40.000 0.00 0.00 0.00 2.94
3560 3851 4.576463 CCAGGTGTTGATTATTCCTACTGC 59.424 45.833 0.00 0.00 0.00 4.40
3569 3860 5.586243 TGATTATTCCTACTGCTTGCTTGAC 59.414 40.000 0.00 0.00 0.00 3.18
3573 3864 3.926616 TCCTACTGCTTGCTTGACTTAC 58.073 45.455 0.00 0.00 0.00 2.34
3579 3870 4.453819 ACTGCTTGCTTGACTTACTTGATC 59.546 41.667 0.00 0.00 0.00 2.92
3580 3871 3.433274 TGCTTGCTTGACTTACTTGATCG 59.567 43.478 0.00 0.00 0.00 3.69
3627 3921 9.111613 CAGCTCTGAGATTTCAAGATAGATTTT 57.888 33.333 9.28 0.00 31.69 1.82
3715 4013 2.230750 GCAGGAGCTCTTGCATTTTCTT 59.769 45.455 37.42 0.00 46.60 2.52
3721 4019 6.266330 AGGAGCTCTTGCATTTTCTTTACTTT 59.734 34.615 14.64 0.00 42.74 2.66
3722 4020 6.364435 GGAGCTCTTGCATTTTCTTTACTTTG 59.636 38.462 14.64 0.00 42.74 2.77
3735 4033 9.567848 TTTTCTTTACTTTGTGCTTTTGTAGAG 57.432 29.630 0.00 0.00 0.00 2.43
3737 4038 8.142994 TCTTTACTTTGTGCTTTTGTAGAGAG 57.857 34.615 0.00 0.00 0.00 3.20
3738 4039 7.985184 TCTTTACTTTGTGCTTTTGTAGAGAGA 59.015 33.333 0.00 0.00 0.00 3.10
3739 4040 7.715265 TTACTTTGTGCTTTTGTAGAGAGAG 57.285 36.000 0.00 0.00 0.00 3.20
3740 4041 4.513318 ACTTTGTGCTTTTGTAGAGAGAGC 59.487 41.667 0.00 0.00 0.00 4.09
3755 4056 4.655186 AGAGAGAGCTGCCAGATAGATTTT 59.345 41.667 0.00 0.00 0.00 1.82
3758 4059 5.104610 AGAGAGCTGCCAGATAGATTTTGAA 60.105 40.000 0.00 0.00 0.00 2.69
3761 4062 5.012239 AGCTGCCAGATAGATTTTGAAACA 58.988 37.500 0.00 0.00 0.00 2.83
3762 4063 5.098211 GCTGCCAGATAGATTTTGAAACAC 58.902 41.667 0.00 0.00 0.00 3.32
3764 4065 6.626623 GCTGCCAGATAGATTTTGAAACACAT 60.627 38.462 0.00 0.00 0.00 3.21
3765 4066 7.230849 TGCCAGATAGATTTTGAAACACATT 57.769 32.000 0.00 0.00 0.00 2.71
3766 4067 7.669427 TGCCAGATAGATTTTGAAACACATTT 58.331 30.769 0.00 0.00 0.00 2.32
3767 4068 7.599621 TGCCAGATAGATTTTGAAACACATTTG 59.400 33.333 0.00 0.00 0.00 2.32
3790 4098 6.519382 TGAGATGTGAAATAGGATAGCAGTG 58.481 40.000 0.00 0.00 0.00 3.66
3807 4115 3.284617 CAGTGATGAATCTGCCCATTGA 58.715 45.455 0.00 0.00 0.00 2.57
3839 4286 6.690194 ATTTGAGATAAAGATGTCCAGTGC 57.310 37.500 0.00 0.00 0.00 4.40
3841 4288 4.763073 TGAGATAAAGATGTCCAGTGCAG 58.237 43.478 0.00 0.00 0.00 4.41
3844 4291 5.181748 AGATAAAGATGTCCAGTGCAGAAC 58.818 41.667 0.00 0.00 0.00 3.01
3845 4292 2.191128 AAGATGTCCAGTGCAGAACC 57.809 50.000 0.00 0.00 0.00 3.62
3846 4293 0.036952 AGATGTCCAGTGCAGAACCG 60.037 55.000 0.00 0.00 0.00 4.44
3847 4294 1.003355 ATGTCCAGTGCAGAACCGG 60.003 57.895 0.00 0.00 0.00 5.28
3849 4296 1.668151 GTCCAGTGCAGAACCGGAC 60.668 63.158 9.46 0.00 46.57 4.79
3850 4297 2.137528 TCCAGTGCAGAACCGGACA 61.138 57.895 9.46 0.00 29.83 4.02
3851 4298 1.227823 CCAGTGCAGAACCGGACAA 60.228 57.895 9.46 0.00 0.00 3.18
3861 4308 2.432628 CCGGACAAGCTGGTCGTC 60.433 66.667 15.17 6.26 38.70 4.20
3873 4320 3.195610 AGCTGGTCGTCATACAGATTTGA 59.804 43.478 0.00 0.00 34.21 2.69
3874 4321 3.932710 GCTGGTCGTCATACAGATTTGAA 59.067 43.478 0.00 0.00 34.21 2.69
3875 4322 4.201724 GCTGGTCGTCATACAGATTTGAAC 60.202 45.833 0.00 0.00 34.21 3.18
3876 4323 4.888917 TGGTCGTCATACAGATTTGAACA 58.111 39.130 0.00 0.00 0.00 3.18
3877 4324 4.929211 TGGTCGTCATACAGATTTGAACAG 59.071 41.667 0.00 0.00 0.00 3.16
3879 4326 3.932710 TCGTCATACAGATTTGAACAGGC 59.067 43.478 0.00 0.00 0.00 4.85
3880 4327 3.684305 CGTCATACAGATTTGAACAGGCA 59.316 43.478 0.00 0.00 0.00 4.75
3881 4328 4.201753 CGTCATACAGATTTGAACAGGCAG 60.202 45.833 0.00 0.00 0.00 4.85
3882 4329 4.937620 GTCATACAGATTTGAACAGGCAGA 59.062 41.667 0.00 0.00 0.00 4.26
3884 4341 5.412594 TCATACAGATTTGAACAGGCAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
3889 4346 5.471456 CAGATTTGAACAGGCAGAACTACTT 59.529 40.000 0.00 0.00 0.00 2.24
3906 4364 6.731292 ACTACTTGGCCTTTTCTGATTTTT 57.269 33.333 3.32 0.00 0.00 1.94
3930 4388 5.296748 TGTCATCAATTTGTCTCGAACTGA 58.703 37.500 0.00 0.00 0.00 3.41
3931 4389 5.406477 TGTCATCAATTTGTCTCGAACTGAG 59.594 40.000 0.00 0.00 46.72 3.35
3932 4390 5.406780 GTCATCAATTTGTCTCGAACTGAGT 59.593 40.000 0.00 0.00 45.46 3.41
3933 4391 6.586463 GTCATCAATTTGTCTCGAACTGAGTA 59.414 38.462 0.00 0.00 45.46 2.59
3947 4408 8.433421 TCGAACTGAGTAATTTTGACTTCTTT 57.567 30.769 0.00 0.00 0.00 2.52
3968 4429 2.003196 AAATACCATTTTTGGGCGCG 57.997 45.000 0.00 0.00 0.00 6.86
3969 4430 1.178276 AATACCATTTTTGGGCGCGA 58.822 45.000 12.10 0.00 0.00 5.87
3974 4437 1.533756 CCATTTTTGGGCGCGATGTAG 60.534 52.381 12.10 0.00 0.00 2.74
3977 4440 1.240256 TTTTGGGCGCGATGTAGTTT 58.760 45.000 12.10 0.00 0.00 2.66
3979 4442 1.647346 TTGGGCGCGATGTAGTTTAG 58.353 50.000 12.10 0.00 0.00 1.85
3983 4446 2.222953 GGGCGCGATGTAGTTTAGTTTG 60.223 50.000 12.10 0.00 0.00 2.93
3989 4452 5.390613 GCGATGTAGTTTAGTTTGCACATT 58.609 37.500 0.00 0.00 0.00 2.71
3991 4454 6.598525 CGATGTAGTTTAGTTTGCACATTCA 58.401 36.000 0.00 0.00 0.00 2.57
3996 4459 8.247562 TGTAGTTTAGTTTGCACATTCAAGTTT 58.752 29.630 0.00 0.00 0.00 2.66
4000 4463 5.329035 AGTTTGCACATTCAAGTTTCTGT 57.671 34.783 0.00 0.00 0.00 3.41
4004 4467 7.981225 AGTTTGCACATTCAAGTTTCTGTATTT 59.019 29.630 0.00 0.00 0.00 1.40
4015 4478 9.184523 TCAAGTTTCTGTATTTTCTTTTCTCCA 57.815 29.630 0.00 0.00 0.00 3.86
4016 4479 9.455847 CAAGTTTCTGTATTTTCTTTTCTCCAG 57.544 33.333 0.00 0.00 0.00 3.86
4017 4480 7.652727 AGTTTCTGTATTTTCTTTTCTCCAGC 58.347 34.615 0.00 0.00 0.00 4.85
4018 4481 7.285401 AGTTTCTGTATTTTCTTTTCTCCAGCA 59.715 33.333 0.00 0.00 0.00 4.41
4019 4482 6.560253 TCTGTATTTTCTTTTCTCCAGCAC 57.440 37.500 0.00 0.00 0.00 4.40
4020 4483 6.299141 TCTGTATTTTCTTTTCTCCAGCACT 58.701 36.000 0.00 0.00 0.00 4.40
4021 4484 7.450074 TCTGTATTTTCTTTTCTCCAGCACTA 58.550 34.615 0.00 0.00 0.00 2.74
4032 4497 1.134250 TCCAGCACTAAACACAGCACA 60.134 47.619 0.00 0.00 0.00 4.57
4033 4498 1.675483 CCAGCACTAAACACAGCACAA 59.325 47.619 0.00 0.00 0.00 3.33
4075 4541 3.816523 TGGACAACCCGAAAATACAAGAC 59.183 43.478 0.00 0.00 37.93 3.01
4114 4580 4.172505 GCCTTAGATGAGTGATGCTATCG 58.827 47.826 0.00 0.00 0.00 2.92
4360 4826 9.134734 TGAAAGTGAAAACAACAAAGTCAATAC 57.865 29.630 0.00 0.00 0.00 1.89
4366 4832 4.209452 ACAACAAAGTCAATACACTGCG 57.791 40.909 0.00 0.00 0.00 5.18
4392 4858 0.846015 TCATGAAGCATAGGGGGTGG 59.154 55.000 0.00 0.00 0.00 4.61
4411 4877 3.454082 GTGGGATCTTGAATGAGAGAGGT 59.546 47.826 0.00 0.00 0.00 3.85
4414 4880 4.367450 GGATCTTGAATGAGAGAGGTTCG 58.633 47.826 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.813179 CGCTTCGCCGGAGAAATGG 61.813 63.158 21.43 11.28 0.00 3.16
7 8 2.703409 CGCTTCGCCGGAGAAATG 59.297 61.111 21.43 11.99 0.00 2.32
18 19 1.142778 GCTGGAACTAGAGCGCTTCG 61.143 60.000 13.26 5.60 0.00 3.79
19 20 0.808060 GGCTGGAACTAGAGCGCTTC 60.808 60.000 13.26 4.01 35.95 3.86
20 21 1.219393 GGCTGGAACTAGAGCGCTT 59.781 57.895 13.26 4.13 35.95 4.68
21 22 1.261238 AAGGCTGGAACTAGAGCGCT 61.261 55.000 11.27 11.27 35.95 5.92
22 23 1.086634 CAAGGCTGGAACTAGAGCGC 61.087 60.000 0.00 0.00 35.95 5.92
23 24 0.532573 TCAAGGCTGGAACTAGAGCG 59.467 55.000 0.00 0.00 35.95 5.03
117 118 1.880675 GCATTCCAGGATCTGCATCAG 59.119 52.381 16.31 0.00 34.77 2.90
137 138 7.935755 AGTAGATGATGGTGAACTGGATTTATG 59.064 37.037 0.00 0.00 0.00 1.90
140 141 6.070021 TGAGTAGATGATGGTGAACTGGATTT 60.070 38.462 0.00 0.00 0.00 2.17
147 148 4.272018 GCACATGAGTAGATGATGGTGAAC 59.728 45.833 0.00 0.00 0.00 3.18
226 227 6.649141 GTGTCAGTGTGTTTGGATAGTATTCA 59.351 38.462 0.00 0.00 0.00 2.57
232 233 4.631131 TCAGTGTCAGTGTGTTTGGATAG 58.369 43.478 7.54 0.00 0.00 2.08
263 264 8.606040 AAACCATGAAATGTTCAATTAGGTTG 57.394 30.769 15.17 1.93 44.81 3.77
298 315 4.936891 TCATGTTCGAGTACATCATCTGG 58.063 43.478 0.00 0.00 36.64 3.86
329 346 5.368989 AGGCCACTAATTGATGCTTACTAC 58.631 41.667 5.01 0.00 0.00 2.73
330 347 5.630415 AGGCCACTAATTGATGCTTACTA 57.370 39.130 5.01 0.00 0.00 1.82
331 348 4.510167 AGGCCACTAATTGATGCTTACT 57.490 40.909 5.01 0.00 0.00 2.24
362 379 5.883115 TGATAATTAAACGCATTCTGGTGGA 59.117 36.000 0.00 0.00 0.00 4.02
375 392 7.582667 ACTACCCAAGCCATGATAATTAAAC 57.417 36.000 0.00 0.00 0.00 2.01
583 633 4.202441 CGACCAATTCCATTCTTCTCCAT 58.798 43.478 0.00 0.00 0.00 3.41
584 634 3.609853 CGACCAATTCCATTCTTCTCCA 58.390 45.455 0.00 0.00 0.00 3.86
585 635 2.945668 CCGACCAATTCCATTCTTCTCC 59.054 50.000 0.00 0.00 0.00 3.71
588 638 2.356069 GCTCCGACCAATTCCATTCTTC 59.644 50.000 0.00 0.00 0.00 2.87
605 676 3.997021 CCATGTCGTGATAATTAGGCTCC 59.003 47.826 0.00 0.00 0.00 4.70
622 693 1.735360 GCACAGCAACACACCATGT 59.265 52.632 0.00 0.00 46.42 3.21
625 696 1.713937 CTTCGCACAGCAACACACCA 61.714 55.000 0.00 0.00 0.00 4.17
651 722 6.944234 ATGATAGTACGAGAGATGTGACAA 57.056 37.500 0.00 0.00 0.00 3.18
664 735 5.163540 GGAAGGGGCACTATATGATAGTACG 60.164 48.000 0.00 0.00 0.00 3.67
666 737 5.910931 TGGAAGGGGCACTATATGATAGTA 58.089 41.667 0.00 0.00 0.00 1.82
667 738 4.763355 TGGAAGGGGCACTATATGATAGT 58.237 43.478 0.00 0.00 0.00 2.12
668 739 5.762179 TTGGAAGGGGCACTATATGATAG 57.238 43.478 0.00 0.00 0.00 2.08
858 930 7.331193 ACGAGTTTTCATAGGAAATGTGTAGAC 59.669 37.037 3.00 0.00 42.31 2.59
860 932 7.596749 ACGAGTTTTCATAGGAAATGTGTAG 57.403 36.000 3.00 0.00 42.31 2.74
865 938 6.037172 CCAGGTACGAGTTTTCATAGGAAATG 59.963 42.308 3.00 0.00 42.31 2.32
866 939 6.070424 TCCAGGTACGAGTTTTCATAGGAAAT 60.070 38.462 3.00 0.00 42.31 2.17
891 982 3.139077 GTGGAGACGACATGGAAGTTTT 58.861 45.455 0.00 0.00 0.00 2.43
925 1016 1.757699 GTGGCTGGGTTGGTTAAAACA 59.242 47.619 0.00 0.00 0.00 2.83
956 1047 0.321671 CTTCCTCTGCGTTCTTGGGA 59.678 55.000 0.00 0.00 0.00 4.37
957 1048 1.301677 GCTTCCTCTGCGTTCTTGGG 61.302 60.000 0.00 0.00 0.00 4.12
958 1049 0.603707 TGCTTCCTCTGCGTTCTTGG 60.604 55.000 0.00 0.00 0.00 3.61
1608 1708 1.647084 GTCGTTGCTGTTGGTCCAC 59.353 57.895 0.00 0.00 0.00 4.02
2040 2239 1.375908 GTCGCCCATGCACTTCTCA 60.376 57.895 0.00 0.00 37.32 3.27
2186 2385 2.725203 CTTGGAGCAACCGAACCCGA 62.725 60.000 0.00 0.00 42.61 5.14
2187 2386 2.281208 TTGGAGCAACCGAACCCG 60.281 61.111 0.00 0.00 42.61 5.28
2189 2388 1.001706 GAAACTTGGAGCAACCGAACC 60.002 52.381 0.00 0.00 42.61 3.62
2191 2390 2.045561 TGAAACTTGGAGCAACCGAA 57.954 45.000 0.00 0.00 42.61 4.30
2196 2404 0.597568 CGCCATGAAACTTGGAGCAA 59.402 50.000 0.00 0.00 36.26 3.91
2198 2406 0.169009 GTCGCCATGAAACTTGGAGC 59.831 55.000 0.00 0.00 36.26 4.70
2203 2411 3.126001 TCTCTTGTCGCCATGAAACTT 57.874 42.857 0.00 0.00 0.00 2.66
2204 2412 2.839486 TCTCTTGTCGCCATGAAACT 57.161 45.000 0.00 0.00 0.00 2.66
2205 2413 4.083324 TCAATTCTCTTGTCGCCATGAAAC 60.083 41.667 0.00 0.00 0.00 2.78
2217 2425 3.405831 TCCAGCAGTGTCAATTCTCTTG 58.594 45.455 0.00 0.00 0.00 3.02
2218 2426 3.777106 TCCAGCAGTGTCAATTCTCTT 57.223 42.857 0.00 0.00 0.00 2.85
2219 2427 3.996921 ATCCAGCAGTGTCAATTCTCT 57.003 42.857 0.00 0.00 0.00 3.10
2220 2428 4.730657 CAAATCCAGCAGTGTCAATTCTC 58.269 43.478 0.00 0.00 0.00 2.87
2221 2429 3.057033 GCAAATCCAGCAGTGTCAATTCT 60.057 43.478 0.00 0.00 0.00 2.40
2222 2430 3.248266 GCAAATCCAGCAGTGTCAATTC 58.752 45.455 0.00 0.00 0.00 2.17
2223 2431 2.028748 GGCAAATCCAGCAGTGTCAATT 60.029 45.455 0.00 0.00 34.01 2.32
2224 2432 1.547372 GGCAAATCCAGCAGTGTCAAT 59.453 47.619 0.00 0.00 34.01 2.57
2225 2433 0.961019 GGCAAATCCAGCAGTGTCAA 59.039 50.000 0.00 0.00 34.01 3.18
2226 2434 0.111061 AGGCAAATCCAGCAGTGTCA 59.889 50.000 0.00 0.00 37.29 3.58
2227 2435 0.524862 CAGGCAAATCCAGCAGTGTC 59.475 55.000 0.00 0.00 37.29 3.67
2228 2436 0.111061 TCAGGCAAATCCAGCAGTGT 59.889 50.000 0.00 0.00 37.29 3.55
2229 2437 1.250328 TTCAGGCAAATCCAGCAGTG 58.750 50.000 0.00 0.00 37.29 3.66
2230 2438 1.891150 CTTTCAGGCAAATCCAGCAGT 59.109 47.619 0.00 0.00 37.29 4.40
2231 2439 2.165167 TCTTTCAGGCAAATCCAGCAG 58.835 47.619 0.00 0.00 37.29 4.24
2237 2445 5.091431 CGATCAGTTTCTTTCAGGCAAATC 58.909 41.667 0.00 0.00 0.00 2.17
2243 2451 3.403038 ACCACGATCAGTTTCTTTCAGG 58.597 45.455 0.00 0.00 0.00 3.86
2388 2597 2.854522 ACAGCCGGCAACTGTTATC 58.145 52.632 31.54 0.00 46.01 1.75
2393 2602 1.007387 GGAAAACAGCCGGCAACTG 60.007 57.895 31.54 21.18 41.08 3.16
2394 2603 1.152756 AGGAAAACAGCCGGCAACT 60.153 52.632 31.54 9.05 0.00 3.16
2395 2604 1.007387 CAGGAAAACAGCCGGCAAC 60.007 57.895 31.54 12.23 0.00 4.17
2396 2605 2.199652 CCAGGAAAACAGCCGGCAA 61.200 57.895 31.54 0.00 0.00 4.52
2397 2606 2.597217 CCAGGAAAACAGCCGGCA 60.597 61.111 31.54 0.00 0.00 5.69
2398 2607 2.597510 ACCAGGAAAACAGCCGGC 60.598 61.111 21.89 21.89 0.00 6.13
2399 2608 2.325082 CGACCAGGAAAACAGCCGG 61.325 63.158 0.00 0.00 0.00 6.13
2400 2609 0.673644 ATCGACCAGGAAAACAGCCG 60.674 55.000 0.00 0.00 0.00 5.52
2401 2610 1.087501 GATCGACCAGGAAAACAGCC 58.912 55.000 0.00 0.00 0.00 4.85
2456 2668 6.208402 GCCAGAGAGATCATACAGATTACTCA 59.792 42.308 0.00 0.00 39.45 3.41
2458 2670 6.073981 TGCCAGAGAGATCATACAGATTACT 58.926 40.000 0.00 0.00 37.00 2.24
2459 2671 6.208402 TCTGCCAGAGAGATCATACAGATTAC 59.792 42.308 0.00 0.00 37.00 1.89
2460 2672 6.208402 GTCTGCCAGAGAGATCATACAGATTA 59.792 42.308 0.00 0.00 37.00 1.75
2469 2689 1.761198 CCATGTCTGCCAGAGAGATCA 59.239 52.381 0.00 0.00 32.28 2.92
2475 2695 0.179116 CGTCTCCATGTCTGCCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
2476 2696 1.607801 CCGTCTCCATGTCTGCCAGA 61.608 60.000 0.00 0.00 0.00 3.86
2477 2697 1.153489 CCGTCTCCATGTCTGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
2479 2699 1.153549 GTCCGTCTCCATGTCTGCC 60.154 63.158 0.00 0.00 0.00 4.85
2504 2724 4.341502 GCCGCCGTTGTTGTGCAT 62.342 61.111 0.00 0.00 0.00 3.96
2554 2774 0.320374 TGCTGTAGTGTACCCTGCAC 59.680 55.000 0.00 0.00 37.13 4.57
2559 2779 3.028850 TGAGGTATGCTGTAGTGTACCC 58.971 50.000 9.64 0.00 37.83 3.69
2566 2786 6.259608 CAGAAAAGGAATGAGGTATGCTGTAG 59.740 42.308 0.00 0.00 0.00 2.74
2569 2789 4.201990 GCAGAAAAGGAATGAGGTATGCTG 60.202 45.833 0.00 0.00 0.00 4.41
2570 2790 3.950395 GCAGAAAAGGAATGAGGTATGCT 59.050 43.478 0.00 0.00 0.00 3.79
2571 2791 3.950395 AGCAGAAAAGGAATGAGGTATGC 59.050 43.478 0.00 0.00 0.00 3.14
2575 2795 4.895297 TGAAAAGCAGAAAAGGAATGAGGT 59.105 37.500 0.00 0.00 0.00 3.85
2577 2797 5.835257 TGTGAAAAGCAGAAAAGGAATGAG 58.165 37.500 0.00 0.00 0.00 2.90
2578 2798 5.850557 TGTGAAAAGCAGAAAAGGAATGA 57.149 34.783 0.00 0.00 0.00 2.57
2592 2812 6.092670 TCTCAACTCTCAAGTGTTGTGAAAAG 59.907 38.462 19.31 12.31 43.11 2.27
2593 2813 5.937540 TCTCAACTCTCAAGTGTTGTGAAAA 59.062 36.000 19.31 5.65 43.11 2.29
2594 2814 5.351465 GTCTCAACTCTCAAGTGTTGTGAAA 59.649 40.000 21.54 7.26 45.25 2.69
2595 2815 4.870426 GTCTCAACTCTCAAGTGTTGTGAA 59.130 41.667 21.54 9.91 45.25 3.18
2596 2816 4.160439 AGTCTCAACTCTCAAGTGTTGTGA 59.840 41.667 18.99 18.66 44.90 3.58
2599 2819 6.276847 AGTAAGTCTCAACTCTCAAGTGTTG 58.723 40.000 15.42 15.42 45.57 3.33
2600 2820 6.461788 GGAGTAAGTCTCAACTCTCAAGTGTT 60.462 42.308 12.62 0.00 44.40 3.32
2601 2821 5.010213 GGAGTAAGTCTCAACTCTCAAGTGT 59.990 44.000 12.62 0.00 44.40 3.55
2602 2822 5.465935 GGAGTAAGTCTCAACTCTCAAGTG 58.534 45.833 12.62 0.00 44.40 3.16
2603 2823 4.525100 GGGAGTAAGTCTCAACTCTCAAGT 59.475 45.833 12.62 0.00 41.90 3.16
2604 2824 5.066968 GGGAGTAAGTCTCAACTCTCAAG 57.933 47.826 12.62 0.00 41.90 3.02
2608 2828 3.829601 CTGTGGGAGTAAGTCTCAACTCT 59.170 47.826 12.62 0.00 44.40 3.24
2609 2829 3.574826 ACTGTGGGAGTAAGTCTCAACTC 59.425 47.826 6.72 6.72 44.40 3.01
2610 2830 3.577919 ACTGTGGGAGTAAGTCTCAACT 58.422 45.455 0.00 0.00 44.40 3.16
2611 2831 5.464030 TTACTGTGGGAGTAAGTCTCAAC 57.536 43.478 0.00 0.00 41.42 3.18
2612 2832 5.601313 AGTTTACTGTGGGAGTAAGTCTCAA 59.399 40.000 0.00 0.00 45.85 3.02
2613 2833 5.010719 CAGTTTACTGTGGGAGTAAGTCTCA 59.989 44.000 1.69 0.00 45.85 3.27
2614 2834 5.243283 TCAGTTTACTGTGGGAGTAAGTCTC 59.757 44.000 9.53 0.00 45.85 3.36
2615 2835 5.010820 GTCAGTTTACTGTGGGAGTAAGTCT 59.989 44.000 9.53 0.00 45.85 3.24
2617 2837 4.040095 GGTCAGTTTACTGTGGGAGTAAGT 59.960 45.833 9.53 0.00 45.85 2.24
2618 2838 4.566987 GGTCAGTTTACTGTGGGAGTAAG 58.433 47.826 9.53 0.00 45.85 2.34
2620 2840 2.559668 CGGTCAGTTTACTGTGGGAGTA 59.440 50.000 9.53 0.00 44.12 2.59
2621 2841 1.343465 CGGTCAGTTTACTGTGGGAGT 59.657 52.381 9.53 0.00 44.12 3.85
2622 2842 1.337823 CCGGTCAGTTTACTGTGGGAG 60.338 57.143 9.53 0.00 44.12 4.30
2626 2846 1.864711 CACACCGGTCAGTTTACTGTG 59.135 52.381 2.59 2.33 44.12 3.66
2627 2847 1.808891 GCACACCGGTCAGTTTACTGT 60.809 52.381 2.59 0.00 44.12 3.55
2629 2849 0.599204 CGCACACCGGTCAGTTTACT 60.599 55.000 2.59 0.00 0.00 2.24
2631 2851 1.957186 GCGCACACCGGTCAGTTTA 60.957 57.895 2.59 0.00 37.44 2.01
2722 2974 0.470766 TGCACTCCTTGTACCCGTTT 59.529 50.000 0.00 0.00 0.00 3.60
2904 3160 1.444553 GGTGAGCGACTGAACGAGG 60.445 63.158 0.00 0.00 35.09 4.63
2909 3165 1.000955 GAAGGAAGGTGAGCGACTGAA 59.999 52.381 0.00 0.00 0.00 3.02
2917 3173 1.202806 TGCAAGTGGAAGGAAGGTGAG 60.203 52.381 0.00 0.00 0.00 3.51
2940 3196 4.329545 GCCACAGGCCACGGAGAA 62.330 66.667 5.01 0.00 44.06 2.87
2979 3242 0.600255 CAATGGCGGTCCGGAGTATC 60.600 60.000 14.38 0.00 34.14 2.24
2988 3251 2.742372 ACGTCTGCAATGGCGGTC 60.742 61.111 4.92 0.00 46.81 4.79
3285 3562 1.612676 TCAGTGATTGCTTGCTTGCT 58.387 45.000 0.00 0.00 0.00 3.91
3290 3567 4.553323 ACAAAGATTCAGTGATTGCTTGC 58.447 39.130 0.00 0.00 0.00 4.01
3291 3569 5.107607 GCAACAAAGATTCAGTGATTGCTTG 60.108 40.000 14.98 12.85 38.48 4.01
3293 3571 4.280174 AGCAACAAAGATTCAGTGATTGCT 59.720 37.500 17.87 17.87 44.92 3.91
3298 3576 3.248363 CGTCAGCAACAAAGATTCAGTGA 59.752 43.478 0.00 0.00 0.00 3.41
3304 3582 4.647424 TTTTCCGTCAGCAACAAAGATT 57.353 36.364 0.00 0.00 0.00 2.40
3326 3605 4.690280 CCGCTGCACCAGATTTTAATTTTT 59.310 37.500 0.00 0.00 32.44 1.94
3332 3611 2.289756 TGTACCGCTGCACCAGATTTTA 60.290 45.455 0.00 0.00 32.44 1.52
3466 3746 1.754803 TCACTCATTACCTGGCTACGG 59.245 52.381 0.00 0.00 0.00 4.02
3467 3747 3.520290 TTCACTCATTACCTGGCTACG 57.480 47.619 0.00 0.00 0.00 3.51
3468 3748 5.428253 TCAATTCACTCATTACCTGGCTAC 58.572 41.667 0.00 0.00 0.00 3.58
3469 3749 5.692115 TCAATTCACTCATTACCTGGCTA 57.308 39.130 0.00 0.00 0.00 3.93
3483 3763 3.194116 ACCAGTCATGCCATTCAATTCAC 59.806 43.478 0.00 0.00 0.00 3.18
3489 3769 2.299582 CCAAAACCAGTCATGCCATTCA 59.700 45.455 0.00 0.00 0.00 2.57
3491 3771 1.002315 GCCAAAACCAGTCATGCCATT 59.998 47.619 0.00 0.00 0.00 3.16
3492 3772 0.609662 GCCAAAACCAGTCATGCCAT 59.390 50.000 0.00 0.00 0.00 4.40
3493 3773 0.758310 TGCCAAAACCAGTCATGCCA 60.758 50.000 0.00 0.00 0.00 4.92
3494 3774 0.609662 ATGCCAAAACCAGTCATGCC 59.390 50.000 0.00 0.00 0.00 4.40
3495 3775 3.591196 TTATGCCAAAACCAGTCATGC 57.409 42.857 0.00 0.00 0.00 4.06
3499 3779 6.098266 AGGGATTTATTATGCCAAAACCAGTC 59.902 38.462 0.00 0.00 30.42 3.51
3500 3780 5.963865 AGGGATTTATTATGCCAAAACCAGT 59.036 36.000 0.00 0.00 30.42 4.00
3514 3803 3.011708 AGTCACCAGCCAAGGGATTTATT 59.988 43.478 0.00 0.00 0.00 1.40
3522 3811 3.160585 TGGAGTCACCAGCCAAGG 58.839 61.111 0.00 0.00 44.64 3.61
3535 3824 6.051717 CAGTAGGAATAATCAACACCTGGAG 58.948 44.000 0.00 0.00 32.90 3.86
3537 3826 4.576463 GCAGTAGGAATAATCAACACCTGG 59.424 45.833 0.00 0.00 32.90 4.45
3553 3844 3.931578 AGTAAGTCAAGCAAGCAGTAGG 58.068 45.455 0.00 0.00 0.00 3.18
3554 3845 4.991056 TCAAGTAAGTCAAGCAAGCAGTAG 59.009 41.667 0.00 0.00 0.00 2.57
3556 3847 3.808728 TCAAGTAAGTCAAGCAAGCAGT 58.191 40.909 0.00 0.00 0.00 4.40
3560 3851 5.597813 AACGATCAAGTAAGTCAAGCAAG 57.402 39.130 0.00 0.00 0.00 4.01
3579 3870 7.915397 AGCTGGCTGTAAATATGAAAAATAACG 59.085 33.333 0.00 0.00 0.00 3.18
3580 3871 9.237846 GAGCTGGCTGTAAATATGAAAAATAAC 57.762 33.333 0.00 0.00 0.00 1.89
3600 3894 6.159299 TCTATCTTGAAATCTCAGAGCTGG 57.841 41.667 0.00 0.00 31.69 4.85
3627 3921 3.816398 TGGTATTCACCCATTTGTGGA 57.184 42.857 0.00 0.00 45.11 4.02
3651 3947 7.824289 AGCTATAAGCAACTTCTTTCATGTACA 59.176 33.333 0.00 0.00 45.56 2.90
3653 3949 8.792830 AAGCTATAAGCAACTTCTTTCATGTA 57.207 30.769 1.22 0.00 45.56 2.29
3715 4013 6.202954 GCTCTCTCTACAAAAGCACAAAGTAA 59.797 38.462 0.00 0.00 33.21 2.24
3721 4019 3.657634 CAGCTCTCTCTACAAAAGCACA 58.342 45.455 0.00 0.00 35.42 4.57
3722 4020 2.414825 GCAGCTCTCTCTACAAAAGCAC 59.585 50.000 0.00 0.00 35.42 4.40
3735 4033 4.701765 TCAAAATCTATCTGGCAGCTCTC 58.298 43.478 10.34 0.00 0.00 3.20
3737 4038 5.124457 TGTTTCAAAATCTATCTGGCAGCTC 59.876 40.000 10.34 0.00 0.00 4.09
3738 4039 5.012239 TGTTTCAAAATCTATCTGGCAGCT 58.988 37.500 10.34 2.00 0.00 4.24
3739 4040 5.098211 GTGTTTCAAAATCTATCTGGCAGC 58.902 41.667 10.34 0.00 0.00 5.25
3740 4041 6.258230 TGTGTTTCAAAATCTATCTGGCAG 57.742 37.500 8.58 8.58 0.00 4.85
3755 4056 8.298854 CCTATTTCACATCTCAAATGTGTTTCA 58.701 33.333 15.55 0.00 46.82 2.69
3758 4059 8.585471 ATCCTATTTCACATCTCAAATGTGTT 57.415 30.769 15.55 6.99 46.82 3.32
3761 4062 7.994911 TGCTATCCTATTTCACATCTCAAATGT 59.005 33.333 0.00 0.00 0.00 2.71
3762 4063 8.387190 TGCTATCCTATTTCACATCTCAAATG 57.613 34.615 0.00 0.00 0.00 2.32
3764 4065 7.496920 CACTGCTATCCTATTTCACATCTCAAA 59.503 37.037 0.00 0.00 0.00 2.69
3765 4066 6.988580 CACTGCTATCCTATTTCACATCTCAA 59.011 38.462 0.00 0.00 0.00 3.02
3766 4067 6.324770 TCACTGCTATCCTATTTCACATCTCA 59.675 38.462 0.00 0.00 0.00 3.27
3767 4068 6.753180 TCACTGCTATCCTATTTCACATCTC 58.247 40.000 0.00 0.00 0.00 2.75
3771 4072 6.484364 TCATCACTGCTATCCTATTTCACA 57.516 37.500 0.00 0.00 0.00 3.58
3772 4073 7.877097 AGATTCATCACTGCTATCCTATTTCAC 59.123 37.037 0.00 0.00 0.00 3.18
3773 4074 7.876582 CAGATTCATCACTGCTATCCTATTTCA 59.123 37.037 0.00 0.00 0.00 2.69
3790 4098 4.823442 TGTACATCAATGGGCAGATTCATC 59.177 41.667 0.00 0.00 0.00 2.92
3839 4286 0.951040 GACCAGCTTGTCCGGTTCTG 60.951 60.000 6.68 2.92 31.63 3.02
3841 4288 2.027625 CGACCAGCTTGTCCGGTTC 61.028 63.158 12.05 0.00 31.63 3.62
3844 4291 2.432628 GACGACCAGCTTGTCCGG 60.433 66.667 12.05 0.00 31.35 5.14
3845 4292 0.172578 TATGACGACCAGCTTGTCCG 59.827 55.000 12.05 9.63 32.64 4.79
3846 4293 1.067142 TGTATGACGACCAGCTTGTCC 60.067 52.381 12.05 0.29 32.64 4.02
3847 4294 2.094700 TCTGTATGACGACCAGCTTGTC 60.095 50.000 7.88 7.88 34.12 3.18
3849 4296 2.654749 TCTGTATGACGACCAGCTTG 57.345 50.000 0.00 0.00 0.00 4.01
3850 4297 3.895232 AATCTGTATGACGACCAGCTT 57.105 42.857 0.00 0.00 0.00 3.74
3851 4298 3.195610 TCAAATCTGTATGACGACCAGCT 59.804 43.478 0.00 0.00 0.00 4.24
3858 4305 3.684305 TGCCTGTTCAAATCTGTATGACG 59.316 43.478 0.00 0.00 0.00 4.35
3861 4308 5.413833 AGTTCTGCCTGTTCAAATCTGTATG 59.586 40.000 0.00 0.00 0.00 2.39
3873 4320 1.545651 GGCCAAGTAGTTCTGCCTGTT 60.546 52.381 11.52 0.00 39.05 3.16
3874 4321 0.036875 GGCCAAGTAGTTCTGCCTGT 59.963 55.000 11.52 0.00 39.05 4.00
3875 4322 2.859992 GGCCAAGTAGTTCTGCCTG 58.140 57.895 11.52 0.00 39.05 4.85
3877 4324 1.911057 AAAGGCCAAGTAGTTCTGCC 58.089 50.000 5.01 11.02 42.48 4.85
3879 4326 4.389374 TCAGAAAAGGCCAAGTAGTTCTG 58.611 43.478 5.01 13.59 42.03 3.02
3880 4327 4.706842 TCAGAAAAGGCCAAGTAGTTCT 57.293 40.909 5.01 1.01 0.00 3.01
3881 4328 5.966742 AATCAGAAAAGGCCAAGTAGTTC 57.033 39.130 5.01 0.00 0.00 3.01
3882 4329 6.731292 AAAATCAGAAAAGGCCAAGTAGTT 57.269 33.333 5.01 0.00 0.00 2.24
3906 4364 5.757808 TCAGTTCGAGACAAATTGATGACAA 59.242 36.000 0.00 0.00 40.42 3.18
3909 4367 5.541845 ACTCAGTTCGAGACAAATTGATGA 58.458 37.500 0.00 0.00 45.45 2.92
3917 4375 6.984474 AGTCAAAATTACTCAGTTCGAGACAA 59.016 34.615 0.00 0.00 45.45 3.18
3947 4408 3.192844 TCGCGCCCAAAAATGGTATTTAA 59.807 39.130 0.00 0.00 0.00 1.52
3953 4414 1.215117 CATCGCGCCCAAAAATGGT 59.785 52.632 0.00 0.00 0.00 3.55
3956 4417 1.459450 ACTACATCGCGCCCAAAAAT 58.541 45.000 0.00 0.00 0.00 1.82
3968 4429 8.076178 ACTTGAATGTGCAAACTAAACTACATC 58.924 33.333 0.00 0.00 0.00 3.06
3969 4430 7.940850 ACTTGAATGTGCAAACTAAACTACAT 58.059 30.769 0.00 0.00 0.00 2.29
3974 4437 7.275560 ACAGAAACTTGAATGTGCAAACTAAAC 59.724 33.333 0.00 0.00 0.00 2.01
3977 4440 6.449635 ACAGAAACTTGAATGTGCAAACTA 57.550 33.333 0.00 0.00 0.00 2.24
3979 4442 7.698836 AATACAGAAACTTGAATGTGCAAAC 57.301 32.000 0.00 0.00 0.00 2.93
3983 4446 8.579682 AAGAAAATACAGAAACTTGAATGTGC 57.420 30.769 0.00 0.00 0.00 4.57
3989 4452 9.184523 TGGAGAAAAGAAAATACAGAAACTTGA 57.815 29.630 0.00 0.00 0.00 3.02
3991 4454 8.138074 GCTGGAGAAAAGAAAATACAGAAACTT 58.862 33.333 0.00 0.00 0.00 2.66
3996 4459 6.299141 AGTGCTGGAGAAAAGAAAATACAGA 58.701 36.000 0.00 0.00 0.00 3.41
4000 4463 8.349983 GTGTTTAGTGCTGGAGAAAAGAAAATA 58.650 33.333 0.00 0.00 0.00 1.40
4004 4467 5.189928 TGTGTTTAGTGCTGGAGAAAAGAA 58.810 37.500 0.00 0.00 0.00 2.52
4011 4474 1.532868 GTGCTGTGTTTAGTGCTGGAG 59.467 52.381 0.00 0.00 0.00 3.86
4015 4478 2.364632 TGTTGTGCTGTGTTTAGTGCT 58.635 42.857 0.00 0.00 0.00 4.40
4016 4479 2.842208 TGTTGTGCTGTGTTTAGTGC 57.158 45.000 0.00 0.00 0.00 4.40
4017 4480 4.614555 TCTTGTTGTGCTGTGTTTAGTG 57.385 40.909 0.00 0.00 0.00 2.74
4018 4481 6.935741 TTATCTTGTTGTGCTGTGTTTAGT 57.064 33.333 0.00 0.00 0.00 2.24
4019 4482 7.096477 GCTTTTATCTTGTTGTGCTGTGTTTAG 60.096 37.037 0.00 0.00 0.00 1.85
4020 4483 6.695278 GCTTTTATCTTGTTGTGCTGTGTTTA 59.305 34.615 0.00 0.00 0.00 2.01
4021 4484 5.519927 GCTTTTATCTTGTTGTGCTGTGTTT 59.480 36.000 0.00 0.00 0.00 2.83
4075 4541 3.791973 AGGCGTGTCTCTTCTATCTTG 57.208 47.619 0.00 0.00 0.00 3.02
4090 4556 1.759445 AGCATCACTCATCTAAGGCGT 59.241 47.619 0.00 0.00 0.00 5.68
4344 4810 4.497340 CCGCAGTGTATTGACTTTGTTGTT 60.497 41.667 0.00 0.00 0.00 2.83
4345 4811 3.003275 CCGCAGTGTATTGACTTTGTTGT 59.997 43.478 0.00 0.00 0.00 3.32
4360 4826 0.950836 TTCATGAACCAACCGCAGTG 59.049 50.000 3.38 0.00 0.00 3.66
4366 4832 2.689983 CCCTATGCTTCATGAACCAACC 59.310 50.000 3.38 0.00 0.00 3.77
4392 4858 4.142049 ACGAACCTCTCTCATTCAAGATCC 60.142 45.833 0.00 0.00 0.00 3.36
4411 4877 1.252215 TGGCCGACATCTGGTACGAA 61.252 55.000 0.00 0.00 0.00 3.85
4414 4880 1.961394 TCTATGGCCGACATCTGGTAC 59.039 52.381 0.00 0.00 41.03 3.34


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

AutoCloner maintained by Alex Coulton.