Multiple sequence alignment - TraesCS6A01G342700

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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 TraesCS6A01G342700 chr6A 100.000 3117 0 0 1 3117 575239103 575242219 0.000000e+00 5757
1 TraesCS6A01G342700 chr6A 90.234 983 73 17 797 1768 575176290 575177260 0.000000e+00 1262
2 TraesCS6A01G342700 chr6A 93.304 687 27 6 1773 2453 575177310 575177983 0.000000e+00 996
3 TraesCS6A01G342700 chr6A 93.304 687 27 6 1773 2453 575183725 575184398 0.000000e+00 996
4 TraesCS6A01G342700 chr6A 93.023 387 27 0 961 1347 575253338 575253724 1.620000e-157 566
5 TraesCS6A01G342700 chr6A 88.811 429 39 6 1769 2189 575254090 575254517 4.610000e-143 518
6 TraesCS6A01G342700 chr6A 90.645 310 26 2 1461 1768 575253732 575254040 2.890000e-110 409
7 TraesCS6A01G342700 chr6A 90.955 199 16 1 2454 2652 575178039 575178235 1.840000e-67 267
8 TraesCS6A01G342700 chr6A 90.955 199 16 1 2454 2652 575184454 575184650 1.840000e-67 267
9 TraesCS6A01G342700 chr6A 90.050 201 17 3 2454 2652 575254903 575255102 1.110000e-64 257
10 TraesCS6A01G342700 chr6A 87.336 229 14 8 4 229 575145632 575145848 6.680000e-62 248
11 TraesCS6A01G342700 chr6A 90.833 120 11 0 1649 1768 575183556 575183675 8.950000e-36 161
12 TraesCS6A01G342700 chr6B 90.476 1134 78 16 234 1349 648021585 648022706 0.000000e+00 1469
13 TraesCS6A01G342700 chr6B 92.079 707 47 6 1565 2266 648022774 648023476 0.000000e+00 987
14 TraesCS6A01G342700 chr6B 97.248 327 8 1 2652 2977 166591863 166592189 1.260000e-153 553
15 TraesCS6A01G342700 chr6B 85.017 287 35 4 2172 2452 648040132 648040416 5.090000e-73 285
16 TraesCS6A01G342700 chr6B 92.386 197 14 1 2 198 648021298 648021493 2.370000e-71 279
17 TraesCS6A01G342700 chr6B 91.000 200 16 2 2454 2652 648040461 648040659 5.120000e-68 268
18 TraesCS6A01G342700 chr6B 82.243 214 16 9 2461 2652 648023599 648023812 6.920000e-37 165
19 TraesCS6A01G342700 chr6B 95.181 83 4 0 655 737 200777326 200777244 7.010000e-27 132
20 TraesCS6A01G342700 chr6B 88.636 88 3 4 2371 2456 648023474 648023556 1.980000e-17 100
21 TraesCS6A01G342700 chr2A 98.283 466 8 0 2652 3117 660515822 660516287 0.000000e+00 817
22 TraesCS6A01G342700 chr2A 98.069 466 8 1 2652 3117 729397645 729398109 0.000000e+00 809
23 TraesCS6A01G342700 chr2A 98.286 350 6 0 2652 3001 164708691 164708342 5.710000e-172 614
24 TraesCS6A01G342700 chr3A 97.083 480 13 1 2638 3117 634124059 634124537 0.000000e+00 808
25 TraesCS6A01G342700 chr3A 98.333 120 2 0 2998 3117 22815749 22815630 8.760000e-51 211
26 TraesCS6A01G342700 chr5A 95.338 429 7 1 2689 3117 83627271 83626856 0.000000e+00 669
27 TraesCS6A01G342700 chr5A 93.148 467 10 2 2651 3117 280760734 280761178 0.000000e+00 665
28 TraesCS6A01G342700 chr5A 90.426 94 8 1 643 735 702253176 702253269 4.220000e-24 122
29 TraesCS6A01G342700 chr5B 97.436 351 9 0 2651 3001 586868315 586867965 1.600000e-167 599
30 TraesCS6A01G342700 chr5B 91.489 94 7 1 643 735 62182455 62182548 9.070000e-26 128
31 TraesCS6A01G342700 chr4A 97.429 350 9 0 2652 3001 680563623 680563972 5.750000e-167 597
32 TraesCS6A01G342700 chr4A 97.590 332 8 0 2652 2983 59318649 59318318 1.250000e-158 569
33 TraesCS6A01G342700 chr4A 96.687 332 11 0 2652 2983 58529615 58529946 1.260000e-153 553
34 TraesCS6A01G342700 chr7A 89.733 487 8 9 2651 3117 708314401 708314865 4.480000e-163 584
35 TraesCS6A01G342700 chr4B 96.667 120 4 0 2998 3117 5074739 5074620 1.900000e-47 200
36 TraesCS6A01G342700 chr4B 93.103 87 6 0 649 735 31517966 31518052 9.070000e-26 128
37 TraesCS6A01G342700 chr5D 96.581 117 4 0 2998 3114 444900127 444900243 8.820000e-46 195
38 TraesCS6A01G342700 chr3B 89.899 99 9 1 638 735 40942743 40942841 3.260000e-25 126
39 TraesCS6A01G342700 chr1B 86.325 117 10 4 653 768 606612823 606612934 4.220000e-24 122
40 TraesCS6A01G342700 chr3D 88.119 101 10 2 636 735 138076220 138076319 5.460000e-23 119
41 TraesCS6A01G342700 chr7D 74.598 311 48 22 525 819 561963201 561963496 1.180000e-19 108


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 TraesCS6A01G342700 chr6A 575239103 575242219 3116 False 5757.000000 5757 100.000000 1 3117 1 chr6A.!!$F2 3116
1 TraesCS6A01G342700 chr6A 575176290 575178235 1945 False 841.666667 1262 91.497667 797 2652 3 chr6A.!!$F3 1855
2 TraesCS6A01G342700 chr6A 575183556 575184650 1094 False 474.666667 996 91.697333 1649 2652 3 chr6A.!!$F4 1003
3 TraesCS6A01G342700 chr6A 575253338 575255102 1764 False 437.500000 566 90.632250 961 2652 4 chr6A.!!$F5 1691
4 TraesCS6A01G342700 chr6B 648021298 648023812 2514 False 600.000000 1469 89.164000 2 2652 5 chr6B.!!$F2 2650
5 TraesCS6A01G342700 chr6B 648040132 648040659 527 False 276.500000 285 88.008500 2172 2652 2 chr6B.!!$F3 480

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
833 945 1.002087 ACCAGATTGAACAGACCGACC 59.998 52.381 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2201 2450 0.038343 CCAACTGCCCACGGATTTTG 60.038 55.0 0.0 0.0 0.0 2.44 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
96 97 3.119495 GGCCGCTGTTGATGTTTTTAGAT 60.119 43.478 0.00 0.00 0.00 1.98
99 100 6.265577 GCCGCTGTTGATGTTTTTAGATATT 58.734 36.000 0.00 0.00 0.00 1.28
153 154 9.528018 GTTCTGTAGAAATTGAACCAAAAATGA 57.472 29.630 0.00 0.00 35.58 2.57
160 161 9.410556 AGAAATTGAACCAAAAATGACTAATCG 57.589 29.630 0.00 0.00 0.00 3.34
164 165 7.731882 TGAACCAAAAATGACTAATCGTGTA 57.268 32.000 0.00 0.00 0.00 2.90
168 169 8.205131 ACCAAAAATGACTAATCGTGTATACC 57.795 34.615 0.00 0.00 0.00 2.73
255 331 3.584834 ACAAAAACTGCACAGGTTTGAC 58.415 40.909 24.26 0.00 46.74 3.18
268 344 6.566942 GCACAGGTTTGACAAATGTATTCGTA 60.567 38.462 3.49 0.00 0.00 3.43
321 401 9.371136 TGTACAAAATGTTTGCATAGTTCAAAA 57.629 25.926 0.00 0.00 35.49 2.44
606 707 8.062448 ACGAAGAAACGAAGAAAATCAAAGTAG 58.938 33.333 0.00 0.00 37.03 2.57
607 708 7.530861 CGAAGAAACGAAGAAAATCAAAGTAGG 59.469 37.037 0.00 0.00 35.09 3.18
679 780 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
686 787 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
689 790 6.238648 CGTCCCAAAATAAGTGTCTCAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
701 802 9.880157 AAGTGTCTCAAGTTTAGTACAACTTTA 57.120 29.630 8.25 1.80 43.17 1.85
751 852 6.832384 ACACTTATTCTATTCTAGGACGGACA 59.168 38.462 0.00 0.00 0.00 4.02
772 873 7.913297 CGGACAGAGTAGAAAATTGAAAAACAA 59.087 33.333 0.00 0.00 42.95 2.83
833 945 1.002087 ACCAGATTGAACAGACCGACC 59.998 52.381 0.00 0.00 0.00 4.79
903 1016 5.780984 CCCGTAGTTGATTCCTATTAGGAC 58.219 45.833 12.12 2.88 45.78 3.85
914 1027 8.148351 TGATTCCTATTAGGACTCGTTATTTGG 58.852 37.037 19.58 0.00 45.78 3.28
916 1029 4.684703 CCTATTAGGACTCGTTATTTGGCG 59.315 45.833 3.41 0.00 37.67 5.69
918 1031 2.005971 AGGACTCGTTATTTGGCGTC 57.994 50.000 0.00 0.00 0.00 5.19
919 1032 1.549170 AGGACTCGTTATTTGGCGTCT 59.451 47.619 0.00 0.00 0.00 4.18
957 1070 2.696707 AGGAATCGTTATTACTGGCGGA 59.303 45.455 0.00 0.00 34.77 5.54
999 1112 2.202453 GCGTCTCGGTCGGAGTTC 60.202 66.667 7.24 2.45 43.60 3.01
1080 1193 1.448922 CGGCTAGGAAGAGGACTCCG 61.449 65.000 0.00 0.00 0.00 4.63
1146 1259 2.999739 AAACGGCGGAAGAAGCGGAA 63.000 55.000 13.24 0.00 38.16 4.30
1371 1488 6.609212 ACTTCTTCTCATTAGCACTATCTCCA 59.391 38.462 0.00 0.00 0.00 3.86
1376 1493 7.609097 TCTCATTAGCACTATCTCCAATTCT 57.391 36.000 0.00 0.00 0.00 2.40
1444 1564 9.695526 TCCTTATCAACTGTCAATTGAAAAATG 57.304 29.630 10.35 6.83 39.43 2.32
1445 1565 9.695526 CCTTATCAACTGTCAATTGAAAAATGA 57.304 29.630 10.35 11.93 39.43 2.57
1452 1572 8.400184 ACTGTCAATTGAAAAATGAGATCTCA 57.600 30.769 27.03 27.03 44.59 3.27
1869 2047 2.343843 CGAATTGCTTCTCTGAGTCGTG 59.656 50.000 4.32 0.00 0.00 4.35
1919 2097 1.004440 GCCGTTCCTCAGAAGCAGT 60.004 57.895 0.00 0.00 30.91 4.40
1951 2129 2.877300 GCCTGCATCAAAGACCAAGAGA 60.877 50.000 0.00 0.00 0.00 3.10
2281 2534 5.129485 TCTTTTTGCAAAGATTTGGTGGGTA 59.871 36.000 12.41 0.00 42.99 3.69
2305 2560 9.109393 GTATTTCCATTGCACTAACATAAGAGA 57.891 33.333 0.00 0.00 0.00 3.10
2341 2596 2.221906 GAACTAGTTGGCCTCGGCGA 62.222 60.000 14.14 10.14 43.06 5.54
2428 2694 6.552350 TCCTTACATACGAAATAGTAGGCCTT 59.448 38.462 12.58 0.00 32.26 4.35
2577 2920 9.334693 GCTTAGCATTATATTTTGCATGTAGTC 57.665 33.333 0.00 0.00 41.35 2.59
2578 2921 9.533983 CTTAGCATTATATTTTGCATGTAGTCG 57.466 33.333 10.95 0.00 41.35 4.18
2642 2986 4.644234 TGAGTGTTGGTGATTGATGTTGTT 59.356 37.500 0.00 0.00 0.00 2.83
2652 2996 6.437928 GTGATTGATGTTGTTGCTTTGTAGA 58.562 36.000 0.00 0.00 0.00 2.59
2653 2997 6.580041 GTGATTGATGTTGTTGCTTTGTAGAG 59.420 38.462 0.00 0.00 0.00 2.43
2654 2998 6.262944 TGATTGATGTTGTTGCTTTGTAGAGT 59.737 34.615 0.00 0.00 0.00 3.24
2655 2999 7.443879 TGATTGATGTTGTTGCTTTGTAGAGTA 59.556 33.333 0.00 0.00 0.00 2.59
2656 3000 7.561021 TTGATGTTGTTGCTTTGTAGAGTAA 57.439 32.000 0.00 0.00 0.00 2.24
2657 3001 7.561021 TGATGTTGTTGCTTTGTAGAGTAAA 57.439 32.000 0.00 0.00 0.00 2.01
2658 3002 8.165239 TGATGTTGTTGCTTTGTAGAGTAAAT 57.835 30.769 0.00 0.00 0.00 1.40
2659 3003 8.629158 TGATGTTGTTGCTTTGTAGAGTAAATT 58.371 29.630 0.00 0.00 0.00 1.82
2660 3004 8.801715 ATGTTGTTGCTTTGTAGAGTAAATTG 57.198 30.769 0.00 0.00 0.00 2.32
2661 3005 6.695278 TGTTGTTGCTTTGTAGAGTAAATTGC 59.305 34.615 0.00 0.00 0.00 3.56
2662 3006 6.384258 TGTTGCTTTGTAGAGTAAATTGCA 57.616 33.333 0.00 0.00 0.00 4.08
2663 3007 6.205784 TGTTGCTTTGTAGAGTAAATTGCAC 58.794 36.000 0.00 0.00 0.00 4.57
2664 3008 6.183360 TGTTGCTTTGTAGAGTAAATTGCACA 60.183 34.615 0.00 0.00 0.00 4.57
2665 3009 6.000891 TGCTTTGTAGAGTAAATTGCACAG 57.999 37.500 0.00 0.00 0.00 3.66
2666 3010 5.762711 TGCTTTGTAGAGTAAATTGCACAGA 59.237 36.000 0.00 0.00 0.00 3.41
2667 3011 6.262049 TGCTTTGTAGAGTAAATTGCACAGAA 59.738 34.615 0.00 0.00 0.00 3.02
2668 3012 6.798959 GCTTTGTAGAGTAAATTGCACAGAAG 59.201 38.462 0.00 0.00 0.00 2.85
2669 3013 7.520614 GCTTTGTAGAGTAAATTGCACAGAAGT 60.521 37.037 0.00 0.00 0.00 3.01
2670 3014 8.896320 TTTGTAGAGTAAATTGCACAGAAGTA 57.104 30.769 0.00 0.00 0.00 2.24
2671 3015 9.502091 TTTGTAGAGTAAATTGCACAGAAGTAT 57.498 29.630 0.00 0.00 0.00 2.12
2672 3016 8.703604 TGTAGAGTAAATTGCACAGAAGTATC 57.296 34.615 0.00 0.00 0.00 2.24
2673 3017 8.311109 TGTAGAGTAAATTGCACAGAAGTATCA 58.689 33.333 0.00 0.00 0.00 2.15
2674 3018 9.319143 GTAGAGTAAATTGCACAGAAGTATCAT 57.681 33.333 0.00 0.00 0.00 2.45
2676 3020 9.890629 AGAGTAAATTGCACAGAAGTATCATAA 57.109 29.630 0.00 0.00 0.00 1.90
2681 3025 6.698008 TTGCACAGAAGTATCATAATTGGG 57.302 37.500 0.00 0.00 0.00 4.12
2682 3026 5.132502 TGCACAGAAGTATCATAATTGGGG 58.867 41.667 0.00 0.00 0.00 4.96
2683 3027 4.022849 GCACAGAAGTATCATAATTGGGGC 60.023 45.833 0.00 0.00 0.00 5.80
2684 3028 5.132502 CACAGAAGTATCATAATTGGGGCA 58.867 41.667 0.00 0.00 0.00 5.36
2685 3029 5.771666 CACAGAAGTATCATAATTGGGGCAT 59.228 40.000 0.00 0.00 0.00 4.40
2686 3030 6.266103 CACAGAAGTATCATAATTGGGGCATT 59.734 38.462 0.00 0.00 0.00 3.56
2687 3031 6.266103 ACAGAAGTATCATAATTGGGGCATTG 59.734 38.462 0.00 0.00 0.00 2.82
2688 3032 5.776716 AGAAGTATCATAATTGGGGCATTGG 59.223 40.000 0.00 0.00 0.00 3.16
2689 3033 5.337956 AGTATCATAATTGGGGCATTGGA 57.662 39.130 0.00 0.00 0.00 3.53
2690 3034 5.714863 AGTATCATAATTGGGGCATTGGAA 58.285 37.500 0.00 0.00 0.00 3.53
2691 3035 6.142498 AGTATCATAATTGGGGCATTGGAAA 58.858 36.000 0.00 0.00 0.00 3.13
2692 3036 4.751767 TCATAATTGGGGCATTGGAAAC 57.248 40.909 0.00 0.00 0.00 2.78
2693 3037 4.099633 TCATAATTGGGGCATTGGAAACA 58.900 39.130 0.00 0.00 39.83 2.83
2694 3038 4.161942 TCATAATTGGGGCATTGGAAACAG 59.838 41.667 0.00 0.00 44.54 3.16
2695 3039 2.323999 ATTGGGGCATTGGAAACAGA 57.676 45.000 0.00 0.00 44.54 3.41
2696 3040 2.323999 TTGGGGCATTGGAAACAGAT 57.676 45.000 0.00 0.00 44.54 2.90
2697 3041 2.323999 TGGGGCATTGGAAACAGATT 57.676 45.000 0.00 0.00 44.54 2.40
2698 3042 1.901159 TGGGGCATTGGAAACAGATTG 59.099 47.619 0.00 0.00 44.54 2.67
2699 3043 1.207811 GGGGCATTGGAAACAGATTGG 59.792 52.381 0.00 0.00 44.54 3.16
2700 3044 1.901833 GGGCATTGGAAACAGATTGGT 59.098 47.619 0.00 0.00 44.54 3.67
2701 3045 3.096092 GGGCATTGGAAACAGATTGGTA 58.904 45.455 0.00 0.00 44.54 3.25
2702 3046 3.119137 GGGCATTGGAAACAGATTGGTAC 60.119 47.826 0.00 0.00 44.54 3.34
2703 3047 3.119137 GGCATTGGAAACAGATTGGTACC 60.119 47.826 4.43 4.43 44.54 3.34
2704 3048 3.509575 GCATTGGAAACAGATTGGTACCA 59.490 43.478 11.60 11.60 44.54 3.25
2705 3049 4.021544 GCATTGGAAACAGATTGGTACCAA 60.022 41.667 28.95 28.95 44.54 3.67
2706 3050 5.713025 CATTGGAAACAGATTGGTACCAAG 58.287 41.667 30.00 19.80 44.54 3.61
2707 3051 4.447138 TGGAAACAGATTGGTACCAAGT 57.553 40.909 30.00 20.42 36.04 3.16
2708 3052 4.798882 TGGAAACAGATTGGTACCAAGTT 58.201 39.130 30.00 24.38 36.04 2.66
2709 3053 5.205056 TGGAAACAGATTGGTACCAAGTTT 58.795 37.500 29.45 29.45 35.78 2.66
2710 3054 5.068460 TGGAAACAGATTGGTACCAAGTTTG 59.932 40.000 32.10 27.90 34.35 2.93
2711 3055 7.862622 TGGAAACAGATTGGTACCAAGTTTGG 61.863 42.308 32.10 22.13 44.83 3.28
2727 3071 8.879342 CCAAGTTTGGTAATTTTTACATGTCA 57.121 30.769 0.00 0.00 43.43 3.58
2728 3072 8.977505 CCAAGTTTGGTAATTTTTACATGTCAG 58.022 33.333 0.00 0.00 43.43 3.51
2729 3073 9.528018 CAAGTTTGGTAATTTTTACATGTCAGT 57.472 29.630 0.00 0.00 0.00 3.41
2740 3084 7.905604 TTTTACATGTCAGTATCAAGTCTGG 57.094 36.000 0.00 0.00 33.13 3.86
2741 3085 4.478206 ACATGTCAGTATCAAGTCTGGG 57.522 45.455 0.00 0.00 33.13 4.45
2742 3086 3.198635 ACATGTCAGTATCAAGTCTGGGG 59.801 47.826 0.00 0.00 33.13 4.96
2743 3087 1.555075 TGTCAGTATCAAGTCTGGGGC 59.445 52.381 0.00 0.00 33.13 5.80
2744 3088 1.834263 GTCAGTATCAAGTCTGGGGCT 59.166 52.381 0.00 0.00 33.13 5.19
2745 3089 3.031736 GTCAGTATCAAGTCTGGGGCTA 58.968 50.000 0.00 0.00 33.13 3.93
2746 3090 3.643792 GTCAGTATCAAGTCTGGGGCTAT 59.356 47.826 0.00 0.00 33.13 2.97
2747 3091 4.833380 GTCAGTATCAAGTCTGGGGCTATA 59.167 45.833 0.00 0.00 33.13 1.31
2748 3092 4.833380 TCAGTATCAAGTCTGGGGCTATAC 59.167 45.833 0.00 0.00 33.13 1.47
2749 3093 3.827302 AGTATCAAGTCTGGGGCTATACG 59.173 47.826 0.00 0.00 0.00 3.06
2750 3094 2.154567 TCAAGTCTGGGGCTATACGT 57.845 50.000 0.00 0.00 0.00 3.57
2751 3095 2.463752 TCAAGTCTGGGGCTATACGTT 58.536 47.619 0.00 0.00 0.00 3.99
2752 3096 3.634504 TCAAGTCTGGGGCTATACGTTA 58.365 45.455 0.00 0.00 0.00 3.18
2753 3097 3.382546 TCAAGTCTGGGGCTATACGTTAC 59.617 47.826 0.00 0.00 0.00 2.50
2754 3098 3.022557 AGTCTGGGGCTATACGTTACA 57.977 47.619 0.00 0.00 0.00 2.41
2755 3099 3.368248 AGTCTGGGGCTATACGTTACAA 58.632 45.455 0.00 0.00 0.00 2.41
2756 3100 3.770933 AGTCTGGGGCTATACGTTACAAA 59.229 43.478 0.00 0.00 0.00 2.83
2757 3101 4.223477 AGTCTGGGGCTATACGTTACAAAA 59.777 41.667 0.00 0.00 0.00 2.44
2758 3102 4.937015 GTCTGGGGCTATACGTTACAAAAA 59.063 41.667 0.00 0.00 0.00 1.94
2759 3103 5.064325 GTCTGGGGCTATACGTTACAAAAAG 59.936 44.000 0.00 0.00 0.00 2.27
2760 3104 4.263435 TGGGGCTATACGTTACAAAAAGG 58.737 43.478 0.00 0.00 0.00 3.11
2761 3105 4.263418 TGGGGCTATACGTTACAAAAAGGT 60.263 41.667 0.00 0.00 0.00 3.50
2762 3106 4.333649 GGGGCTATACGTTACAAAAAGGTC 59.666 45.833 0.00 0.00 0.00 3.85
2763 3107 5.181009 GGGCTATACGTTACAAAAAGGTCT 58.819 41.667 0.00 0.00 0.00 3.85
2764 3108 6.340522 GGGCTATACGTTACAAAAAGGTCTA 58.659 40.000 0.00 0.00 0.00 2.59
2765 3109 6.818142 GGGCTATACGTTACAAAAAGGTCTAA 59.182 38.462 0.00 0.00 0.00 2.10
2766 3110 7.334171 GGGCTATACGTTACAAAAAGGTCTAAA 59.666 37.037 0.00 0.00 0.00 1.85
2767 3111 8.886719 GGCTATACGTTACAAAAAGGTCTAAAT 58.113 33.333 0.00 0.00 0.00 1.40
2768 3112 9.911980 GCTATACGTTACAAAAAGGTCTAAATC 57.088 33.333 0.00 0.00 0.00 2.17
2770 3114 5.682869 ACGTTACAAAAAGGTCTAAATCGC 58.317 37.500 0.00 0.00 0.00 4.58
2771 3115 4.779523 CGTTACAAAAAGGTCTAAATCGCG 59.220 41.667 0.00 0.00 0.00 5.87
2772 3116 5.613142 CGTTACAAAAAGGTCTAAATCGCGT 60.613 40.000 5.77 0.00 0.00 6.01
2773 3117 6.399880 CGTTACAAAAAGGTCTAAATCGCGTA 60.400 38.462 5.77 0.00 0.00 4.42
2774 3118 7.458677 GTTACAAAAAGGTCTAAATCGCGTAT 58.541 34.615 5.77 0.00 0.00 3.06
2775 3119 8.594687 GTTACAAAAAGGTCTAAATCGCGTATA 58.405 33.333 5.77 0.00 0.00 1.47
2776 3120 7.599630 ACAAAAAGGTCTAAATCGCGTATAA 57.400 32.000 5.77 0.00 0.00 0.98
2777 3121 8.031848 ACAAAAAGGTCTAAATCGCGTATAAA 57.968 30.769 5.77 0.00 0.00 1.40
2778 3122 7.959109 ACAAAAAGGTCTAAATCGCGTATAAAC 59.041 33.333 5.77 0.00 0.00 2.01
2792 3136 4.733460 CGTATAAACGCGTATTGACAGTG 58.267 43.478 14.46 0.00 43.12 3.66
2793 3137 4.263677 CGTATAAACGCGTATTGACAGTGT 59.736 41.667 14.46 0.00 43.12 3.55
2794 3138 5.451982 CGTATAAACGCGTATTGACAGTGTA 59.548 40.000 14.46 0.00 43.12 2.90
2795 3139 6.141211 CGTATAAACGCGTATTGACAGTGTAT 59.859 38.462 14.46 0.00 43.12 2.29
2796 3140 4.835199 AAACGCGTATTGACAGTGTATC 57.165 40.909 14.46 0.00 0.00 2.24
2797 3141 3.777465 ACGCGTATTGACAGTGTATCT 57.223 42.857 11.67 0.00 0.00 1.98
2799 3143 3.128068 ACGCGTATTGACAGTGTATCTGA 59.872 43.478 11.67 0.00 46.27 3.27
2800 3144 3.482472 CGCGTATTGACAGTGTATCTGAC 59.518 47.826 0.00 0.00 46.27 3.51
2801 3145 3.797256 GCGTATTGACAGTGTATCTGACC 59.203 47.826 0.00 0.00 46.27 4.02
2802 3146 4.035684 CGTATTGACAGTGTATCTGACCG 58.964 47.826 0.00 0.00 46.27 4.79
2803 3147 3.526931 ATTGACAGTGTATCTGACCGG 57.473 47.619 0.00 0.00 46.27 5.28
2804 3148 0.530744 TGACAGTGTATCTGACCGGC 59.469 55.000 0.00 0.00 46.27 6.13
2805 3149 0.525668 GACAGTGTATCTGACCGGCG 60.526 60.000 0.00 0.00 46.27 6.46
2806 3150 1.226974 CAGTGTATCTGACCGGCGG 60.227 63.158 27.06 27.06 46.27 6.13
2807 3151 2.106332 GTGTATCTGACCGGCGGG 59.894 66.667 31.78 13.02 40.11 6.13
2808 3152 3.151710 TGTATCTGACCGGCGGGG 61.152 66.667 31.78 19.20 43.62 5.73
2809 3153 4.603946 GTATCTGACCGGCGGGGC 62.604 72.222 31.78 21.76 44.16 5.80
2828 3172 4.385405 AGCCTGTCAGCTGCCGAC 62.385 66.667 9.47 9.03 42.95 4.79
2830 3174 4.363990 CCTGTCAGCTGCCGACGT 62.364 66.667 9.47 0.00 36.11 4.34
2831 3175 3.108289 CTGTCAGCTGCCGACGTG 61.108 66.667 9.47 3.47 36.11 4.49
2832 3176 4.662961 TGTCAGCTGCCGACGTGG 62.663 66.667 9.47 0.00 42.50 4.94
2857 3201 0.179070 TTTTTGCAGAAAACCCCCGC 60.179 50.000 0.00 0.00 30.56 6.13
2858 3202 1.330655 TTTTGCAGAAAACCCCCGCA 61.331 50.000 0.00 0.00 0.00 5.69
2859 3203 2.022240 TTTGCAGAAAACCCCCGCAC 62.022 55.000 0.00 0.00 31.10 5.34
2860 3204 4.038080 GCAGAAAACCCCCGCACG 62.038 66.667 0.00 0.00 0.00 5.34
2861 3205 3.361977 CAGAAAACCCCCGCACGG 61.362 66.667 1.02 1.02 0.00 4.94
2882 3226 4.271816 CGCCCGGTCTGGATCGAG 62.272 72.222 0.00 0.00 42.00 4.04
2883 3227 3.917760 GCCCGGTCTGGATCGAGG 61.918 72.222 4.78 5.76 42.00 4.63
2884 3228 3.227276 CCCGGTCTGGATCGAGGG 61.227 72.222 4.78 0.00 42.00 4.30
2885 3229 3.227276 CCGGTCTGGATCGAGGGG 61.227 72.222 4.78 0.99 42.00 4.79
2886 3230 2.123854 CGGTCTGGATCGAGGGGA 60.124 66.667 4.78 0.00 37.01 4.81
2887 3231 2.196925 CGGTCTGGATCGAGGGGAG 61.197 68.421 4.78 0.00 37.01 4.30
2888 3232 1.834822 GGTCTGGATCGAGGGGAGG 60.835 68.421 4.78 0.00 0.00 4.30
2889 3233 1.230497 GTCTGGATCGAGGGGAGGA 59.770 63.158 4.78 0.00 0.00 3.71
2890 3234 0.178947 GTCTGGATCGAGGGGAGGAT 60.179 60.000 4.78 0.00 0.00 3.24
2891 3235 0.113385 TCTGGATCGAGGGGAGGATC 59.887 60.000 4.78 0.00 38.63 3.36
2904 3248 4.916314 GGATCCCCTCGAGCCCGA 62.916 72.222 6.99 1.62 41.58 5.14
2920 3264 4.728058 GAGCTCCTCTCGCATCAC 57.272 61.111 0.87 0.00 31.20 3.06
2921 3265 1.067250 GAGCTCCTCTCGCATCACC 59.933 63.158 0.87 0.00 31.20 4.02
2922 3266 2.279120 GCTCCTCTCGCATCACCG 60.279 66.667 0.00 0.00 0.00 4.94
2923 3267 2.279120 CTCCTCTCGCATCACCGC 60.279 66.667 0.00 0.00 0.00 5.68
2924 3268 3.781770 CTCCTCTCGCATCACCGCC 62.782 68.421 0.00 0.00 0.00 6.13
3009 3353 4.845580 CTGCTCGCGGCCCAAGAT 62.846 66.667 6.13 0.00 40.92 2.40
3010 3354 4.838152 TGCTCGCGGCCCAAGATC 62.838 66.667 6.13 0.00 40.92 2.75
3018 3362 2.892425 GCCCAAGATCGGCGACAG 60.892 66.667 13.76 1.84 36.47 3.51
3019 3363 2.202932 CCCAAGATCGGCGACAGG 60.203 66.667 13.76 11.74 0.00 4.00
3020 3364 2.202932 CCAAGATCGGCGACAGGG 60.203 66.667 13.76 8.12 0.00 4.45
3021 3365 2.892425 CAAGATCGGCGACAGGGC 60.892 66.667 13.76 0.00 37.98 5.19
3045 3389 4.640855 CGACGTGGTGGTGCGACT 62.641 66.667 0.00 0.00 0.00 4.18
3046 3390 3.036084 GACGTGGTGGTGCGACTG 61.036 66.667 0.00 0.00 0.00 3.51
3076 3420 3.833645 TCGGGCCGAGACGAATGG 61.834 66.667 27.46 0.00 36.01 3.16
3080 3424 2.496817 GCCGAGACGAATGGCTCT 59.503 61.111 0.00 0.00 45.40 4.09
3081 3425 1.734137 GCCGAGACGAATGGCTCTA 59.266 57.895 0.00 0.00 45.40 2.43
3082 3426 0.595310 GCCGAGACGAATGGCTCTAC 60.595 60.000 0.00 0.00 45.40 2.59
3083 3427 1.025812 CCGAGACGAATGGCTCTACT 58.974 55.000 0.00 0.00 0.00 2.57
3084 3428 1.268794 CCGAGACGAATGGCTCTACTG 60.269 57.143 0.00 0.00 0.00 2.74
3085 3429 1.846541 GAGACGAATGGCTCTACTGC 58.153 55.000 0.00 0.00 0.00 4.40
3093 3437 2.496817 GCTCTACTGCCACTCCGG 59.503 66.667 0.00 0.00 38.11 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.096705 ACAAACAGATCAACAGATTGGTTTCA 59.903 34.615 0.00 0.00 36.39 2.69
32 33 3.314331 CAGTCCCGGCCACTGTCT 61.314 66.667 19.12 0.00 37.15 3.41
73 74 1.039856 AAAAACATCAACAGCGGCCT 58.960 45.000 0.00 0.00 0.00 5.19
99 100 9.790389 AAAAACGTCTAATCATGTGTACAAAAA 57.210 25.926 0.00 0.00 0.00 1.94
153 154 9.834628 CAAACATTTTTGGTATACACGATTAGT 57.165 29.630 5.01 0.00 38.82 2.24
160 161 8.635877 TTGTCACAAACATTTTTGGTATACAC 57.364 30.769 9.06 0.00 45.65 2.90
228 229 6.952773 AACCTGTGCAGTTTTTGTATAGAA 57.047 33.333 0.00 0.00 33.47 2.10
229 230 6.544197 TCAAACCTGTGCAGTTTTTGTATAGA 59.456 34.615 16.39 1.05 33.47 1.98
230 231 6.636850 GTCAAACCTGTGCAGTTTTTGTATAG 59.363 38.462 16.39 0.00 34.09 1.31
231 232 6.095580 TGTCAAACCTGTGCAGTTTTTGTATA 59.904 34.615 16.39 7.51 34.09 1.47
233 234 4.218635 TGTCAAACCTGTGCAGTTTTTGTA 59.781 37.500 16.39 9.24 34.09 2.41
235 236 3.583806 TGTCAAACCTGTGCAGTTTTTG 58.416 40.909 13.19 13.19 33.89 2.44
236 237 3.951775 TGTCAAACCTGTGCAGTTTTT 57.048 38.095 0.13 0.00 0.00 1.94
237 238 3.951775 TTGTCAAACCTGTGCAGTTTT 57.048 38.095 0.13 0.00 0.00 2.43
239 240 3.195396 ACATTTGTCAAACCTGTGCAGTT 59.805 39.130 0.00 0.00 0.00 3.16
284 360 7.254252 GCAAACATTTTGTACATTGTACAAGCA 60.254 33.333 30.61 24.33 38.47 3.91
496 597 7.639113 TCTTCTTCCAACACATGTTTACTTT 57.361 32.000 0.00 0.00 35.83 2.66
581 682 7.530861 CCTACTTTGATTTTCTTCGTTTCTTCG 59.469 37.037 0.00 0.00 0.00 3.79
589 690 8.311650 TCTTCTTCCTACTTTGATTTTCTTCG 57.688 34.615 0.00 0.00 0.00 3.79
636 737 8.275040 AGGGAGTATGTTATATGCTTTCAGTTT 58.725 33.333 0.00 0.00 0.00 2.66
646 747 4.159879 GGGACGGAGGGAGTATGTTATATG 59.840 50.000 0.00 0.00 0.00 1.78
722 823 8.414778 CCGTCCTAGAATAGAATAAGTGTCTTT 58.585 37.037 0.00 0.00 42.77 2.52
725 826 7.013083 TGTCCGTCCTAGAATAGAATAAGTGTC 59.987 40.741 0.00 0.00 42.77 3.67
731 832 6.839454 ACTCTGTCCGTCCTAGAATAGAATA 58.161 40.000 0.00 0.00 42.77 1.75
732 833 5.697067 ACTCTGTCCGTCCTAGAATAGAAT 58.303 41.667 0.00 0.00 42.77 2.40
733 834 5.113446 ACTCTGTCCGTCCTAGAATAGAA 57.887 43.478 0.00 0.00 42.77 2.10
734 835 4.774660 ACTCTGTCCGTCCTAGAATAGA 57.225 45.455 0.00 0.00 42.77 1.98
735 836 5.856156 TCTACTCTGTCCGTCCTAGAATAG 58.144 45.833 0.00 0.00 38.80 1.73
741 842 5.713389 TCAATTTTCTACTCTGTCCGTCCTA 59.287 40.000 0.00 0.00 0.00 2.94
744 845 6.780706 TTTCAATTTTCTACTCTGTCCGTC 57.219 37.500 0.00 0.00 0.00 4.79
833 945 1.376683 TTTCCAATCCGGTCGCTGG 60.377 57.895 0.00 4.40 35.57 4.85
934 1047 3.454375 CGCCAGTAATAACGATTCCTGT 58.546 45.455 0.00 0.00 29.24 4.00
935 1048 2.800544 CCGCCAGTAATAACGATTCCTG 59.199 50.000 0.00 0.00 30.69 3.86
957 1070 2.033755 CAGAGTCGACGACCTCGGT 61.034 63.158 23.76 5.33 43.16 4.69
999 1112 0.982704 CTCTAGCCTGGGGATCCATG 59.017 60.000 15.23 2.40 43.11 3.66
1065 1178 0.922738 TCCCCGGAGTCCTCTTCCTA 60.923 60.000 0.73 0.00 0.00 2.94
1080 1193 1.057275 GGATCCTTCTCCACCTCCCC 61.057 65.000 3.84 0.00 35.24 4.81
1126 1239 2.474712 CGCTTCTTCCGCCGTTTC 59.525 61.111 0.00 0.00 0.00 2.78
1132 1245 0.097150 GACAATTCCGCTTCTTCCGC 59.903 55.000 0.00 0.00 0.00 5.54
1146 1259 2.584791 GCGTTTTTCAGCATCGACAAT 58.415 42.857 0.00 0.00 0.00 2.71
1382 1499 5.622346 AGGAGTTGACCTAGATTTCCATC 57.378 43.478 0.00 0.00 38.65 3.51
1384 1501 4.401519 CGTAGGAGTTGACCTAGATTTCCA 59.598 45.833 0.00 0.00 42.29 3.53
1437 1557 8.983307 ATTTGAAAGCTGAGATCTCATTTTTC 57.017 30.769 31.31 31.31 39.54 2.29
1444 1564 8.242053 TGATCAAAATTTGAAAGCTGAGATCTC 58.758 33.333 16.21 16.21 43.95 2.75
1445 1565 8.118976 TGATCAAAATTTGAAAGCTGAGATCT 57.881 30.769 12.75 0.00 43.95 2.75
1452 1572 9.428097 GGTAATCTTGATCAAAATTTGAAAGCT 57.572 29.630 12.08 2.06 43.95 3.74
1510 1630 4.056050 AGTTCAATTCGGCGTATATGACC 58.944 43.478 6.85 2.90 0.00 4.02
1519 1639 5.212194 CCCAAAATATAGTTCAATTCGGCG 58.788 41.667 0.00 0.00 0.00 6.46
1555 1677 4.381612 GGGTCATCAGTTGATTCGACTGTA 60.382 45.833 26.20 16.75 43.99 2.74
1559 1681 2.673368 GTGGGTCATCAGTTGATTCGAC 59.327 50.000 0.00 0.00 36.54 4.20
1670 1792 5.008019 CAGAGCAAGTTCAGCAAAGTCTTTA 59.992 40.000 0.00 0.00 0.00 1.85
1808 1983 5.760253 CCAACTCAAACTCACTCTGTAACAT 59.240 40.000 0.00 0.00 0.00 2.71
1809 1984 5.116180 CCAACTCAAACTCACTCTGTAACA 58.884 41.667 0.00 0.00 0.00 2.41
1810 1985 4.024809 GCCAACTCAAACTCACTCTGTAAC 60.025 45.833 0.00 0.00 0.00 2.50
1812 1987 3.494398 GGCCAACTCAAACTCACTCTGTA 60.494 47.826 0.00 0.00 0.00 2.74
1869 2047 1.688197 CATGGCCATAAATGTCCCCAC 59.312 52.381 20.30 0.00 0.00 4.61
1919 2097 0.179037 GATGCAGGCACTATGGCAGA 60.179 55.000 5.10 0.00 46.46 4.26
1926 2104 1.350684 TGGTCTTTGATGCAGGCACTA 59.649 47.619 0.00 0.00 36.02 2.74
1929 2107 1.202915 TCTTGGTCTTTGATGCAGGCA 60.203 47.619 0.00 0.00 0.00 4.75
1951 2129 3.190118 GCATAAGCTCAGCAAAGAACAGT 59.810 43.478 0.00 0.00 37.91 3.55
2088 2266 3.364460 TTAGCAGCTTGGCCATAGAAA 57.636 42.857 6.09 0.00 0.00 2.52
2125 2305 2.868583 CCTTGCATCAGGTATCACTTCG 59.131 50.000 0.00 0.00 0.00 3.79
2201 2450 0.038343 CCAACTGCCCACGGATTTTG 60.038 55.000 0.00 0.00 0.00 2.44
2281 2534 7.831193 ACTCTCTTATGTTAGTGCAATGGAAAT 59.169 33.333 0.00 0.00 0.00 2.17
2305 2560 2.891580 AGTTCGTGTATGTCCAGTGACT 59.108 45.455 0.00 0.00 42.28 3.41
2642 2986 5.762711 TCTGTGCAATTTACTCTACAAAGCA 59.237 36.000 0.00 0.00 0.00 3.91
2655 2999 8.199449 CCCAATTATGATACTTCTGTGCAATTT 58.801 33.333 0.00 0.00 0.00 1.82
2656 3000 7.201938 CCCCAATTATGATACTTCTGTGCAATT 60.202 37.037 0.00 0.00 0.00 2.32
2657 3001 6.266103 CCCCAATTATGATACTTCTGTGCAAT 59.734 38.462 0.00 0.00 0.00 3.56
2658 3002 5.593909 CCCCAATTATGATACTTCTGTGCAA 59.406 40.000 0.00 0.00 0.00 4.08
2659 3003 5.132502 CCCCAATTATGATACTTCTGTGCA 58.867 41.667 0.00 0.00 0.00 4.57
2660 3004 4.022849 GCCCCAATTATGATACTTCTGTGC 60.023 45.833 0.00 0.00 0.00 4.57
2661 3005 5.132502 TGCCCCAATTATGATACTTCTGTG 58.867 41.667 0.00 0.00 0.00 3.66
2662 3006 5.387113 TGCCCCAATTATGATACTTCTGT 57.613 39.130 0.00 0.00 0.00 3.41
2663 3007 6.294899 CCAATGCCCCAATTATGATACTTCTG 60.295 42.308 0.00 0.00 0.00 3.02
2664 3008 5.776716 CCAATGCCCCAATTATGATACTTCT 59.223 40.000 0.00 0.00 0.00 2.85
2665 3009 5.774690 TCCAATGCCCCAATTATGATACTTC 59.225 40.000 0.00 0.00 0.00 3.01
2666 3010 5.714863 TCCAATGCCCCAATTATGATACTT 58.285 37.500 0.00 0.00 0.00 2.24
2667 3011 5.337956 TCCAATGCCCCAATTATGATACT 57.662 39.130 0.00 0.00 0.00 2.12
2668 3012 6.183360 TGTTTCCAATGCCCCAATTATGATAC 60.183 38.462 0.00 0.00 0.00 2.24
2669 3013 5.901853 TGTTTCCAATGCCCCAATTATGATA 59.098 36.000 0.00 0.00 0.00 2.15
2670 3014 4.720773 TGTTTCCAATGCCCCAATTATGAT 59.279 37.500 0.00 0.00 0.00 2.45
2671 3015 4.099633 TGTTTCCAATGCCCCAATTATGA 58.900 39.130 0.00 0.00 0.00 2.15
2672 3016 4.161942 TCTGTTTCCAATGCCCCAATTATG 59.838 41.667 0.00 0.00 0.00 1.90
2673 3017 4.360889 TCTGTTTCCAATGCCCCAATTAT 58.639 39.130 0.00 0.00 0.00 1.28
2674 3018 3.784178 TCTGTTTCCAATGCCCCAATTA 58.216 40.909 0.00 0.00 0.00 1.40
2675 3019 2.618794 TCTGTTTCCAATGCCCCAATT 58.381 42.857 0.00 0.00 0.00 2.32
2676 3020 2.323999 TCTGTTTCCAATGCCCCAAT 57.676 45.000 0.00 0.00 0.00 3.16
2677 3021 2.302445 CAATCTGTTTCCAATGCCCCAA 59.698 45.455 0.00 0.00 0.00 4.12
2678 3022 1.901159 CAATCTGTTTCCAATGCCCCA 59.099 47.619 0.00 0.00 0.00 4.96
2679 3023 1.207811 CCAATCTGTTTCCAATGCCCC 59.792 52.381 0.00 0.00 0.00 5.80
2680 3024 1.901833 ACCAATCTGTTTCCAATGCCC 59.098 47.619 0.00 0.00 0.00 5.36
2681 3025 3.119137 GGTACCAATCTGTTTCCAATGCC 60.119 47.826 7.15 0.00 0.00 4.40
2682 3026 3.509575 TGGTACCAATCTGTTTCCAATGC 59.490 43.478 13.60 0.00 0.00 3.56
2683 3027 5.243730 ACTTGGTACCAATCTGTTTCCAATG 59.756 40.000 27.24 13.08 35.20 2.82
2684 3028 5.393866 ACTTGGTACCAATCTGTTTCCAAT 58.606 37.500 27.24 0.00 35.20 3.16
2685 3029 4.798882 ACTTGGTACCAATCTGTTTCCAA 58.201 39.130 27.24 0.85 35.20 3.53
2686 3030 4.447138 ACTTGGTACCAATCTGTTTCCA 57.553 40.909 27.24 1.40 35.20 3.53
2687 3031 5.508994 CCAAACTTGGTACCAATCTGTTTCC 60.509 44.000 27.81 0.00 43.43 3.13
2688 3032 5.528870 CCAAACTTGGTACCAATCTGTTTC 58.471 41.667 27.81 0.00 43.43 2.78
2689 3033 5.529581 CCAAACTTGGTACCAATCTGTTT 57.470 39.130 27.24 26.59 43.43 2.83
2703 3047 9.528018 ACTGACATGTAAAAATTACCAAACTTG 57.472 29.630 0.00 0.00 0.00 3.16
2714 3058 8.950210 CCAGACTTGATACTGACATGTAAAAAT 58.050 33.333 0.00 0.00 36.38 1.82
2715 3059 7.390440 CCCAGACTTGATACTGACATGTAAAAA 59.610 37.037 0.00 0.00 36.38 1.94
2716 3060 6.878923 CCCAGACTTGATACTGACATGTAAAA 59.121 38.462 0.00 0.00 36.38 1.52
2717 3061 6.406370 CCCAGACTTGATACTGACATGTAAA 58.594 40.000 0.00 0.00 36.38 2.01
2718 3062 5.104941 CCCCAGACTTGATACTGACATGTAA 60.105 44.000 0.00 0.00 36.38 2.41
2719 3063 4.405680 CCCCAGACTTGATACTGACATGTA 59.594 45.833 0.00 0.00 36.38 2.29
2720 3064 3.198635 CCCCAGACTTGATACTGACATGT 59.801 47.826 0.00 0.00 36.38 3.21
2721 3065 3.801698 CCCCAGACTTGATACTGACATG 58.198 50.000 0.00 0.00 36.38 3.21
2722 3066 2.171448 GCCCCAGACTTGATACTGACAT 59.829 50.000 0.00 0.00 36.38 3.06
2723 3067 1.555075 GCCCCAGACTTGATACTGACA 59.445 52.381 0.00 0.00 36.38 3.58
2724 3068 1.834263 AGCCCCAGACTTGATACTGAC 59.166 52.381 0.00 0.00 36.38 3.51
2725 3069 2.254152 AGCCCCAGACTTGATACTGA 57.746 50.000 0.00 0.00 36.38 3.41
2726 3070 4.321304 CGTATAGCCCCAGACTTGATACTG 60.321 50.000 0.00 0.00 0.00 2.74
2727 3071 3.827302 CGTATAGCCCCAGACTTGATACT 59.173 47.826 0.00 0.00 0.00 2.12
2728 3072 3.573110 ACGTATAGCCCCAGACTTGATAC 59.427 47.826 0.00 0.00 0.00 2.24
2729 3073 3.840991 ACGTATAGCCCCAGACTTGATA 58.159 45.455 0.00 0.00 0.00 2.15
2730 3074 2.679082 ACGTATAGCCCCAGACTTGAT 58.321 47.619 0.00 0.00 0.00 2.57
2731 3075 2.154567 ACGTATAGCCCCAGACTTGA 57.845 50.000 0.00 0.00 0.00 3.02
2732 3076 2.981859 AACGTATAGCCCCAGACTTG 57.018 50.000 0.00 0.00 0.00 3.16
2733 3077 3.368248 TGTAACGTATAGCCCCAGACTT 58.632 45.455 0.00 0.00 0.00 3.01
2734 3078 3.022557 TGTAACGTATAGCCCCAGACT 57.977 47.619 0.00 0.00 0.00 3.24
2735 3079 3.806625 TTGTAACGTATAGCCCCAGAC 57.193 47.619 0.00 0.00 0.00 3.51
2736 3080 4.822685 TTTTGTAACGTATAGCCCCAGA 57.177 40.909 0.00 0.00 0.00 3.86
2737 3081 4.334481 CCTTTTTGTAACGTATAGCCCCAG 59.666 45.833 0.00 0.00 0.00 4.45
2738 3082 4.263418 ACCTTTTTGTAACGTATAGCCCCA 60.263 41.667 0.00 0.00 0.00 4.96
2739 3083 4.264253 ACCTTTTTGTAACGTATAGCCCC 58.736 43.478 0.00 0.00 0.00 5.80
2740 3084 5.181009 AGACCTTTTTGTAACGTATAGCCC 58.819 41.667 0.00 0.00 0.00 5.19
2741 3085 7.832503 TTAGACCTTTTTGTAACGTATAGCC 57.167 36.000 0.00 0.00 0.00 3.93
2742 3086 9.911980 GATTTAGACCTTTTTGTAACGTATAGC 57.088 33.333 0.00 0.00 0.00 2.97
2744 3088 8.594687 GCGATTTAGACCTTTTTGTAACGTATA 58.405 33.333 0.00 0.00 0.00 1.47
2745 3089 7.458677 GCGATTTAGACCTTTTTGTAACGTAT 58.541 34.615 0.00 0.00 0.00 3.06
2746 3090 6.399880 CGCGATTTAGACCTTTTTGTAACGTA 60.400 38.462 0.00 0.00 0.00 3.57
2747 3091 5.613142 CGCGATTTAGACCTTTTTGTAACGT 60.613 40.000 0.00 0.00 0.00 3.99
2748 3092 4.779523 CGCGATTTAGACCTTTTTGTAACG 59.220 41.667 0.00 0.00 0.00 3.18
2749 3093 5.682869 ACGCGATTTAGACCTTTTTGTAAC 58.317 37.500 15.93 0.00 0.00 2.50
2750 3094 5.927954 ACGCGATTTAGACCTTTTTGTAA 57.072 34.783 15.93 0.00 0.00 2.41
2751 3095 8.700722 TTATACGCGATTTAGACCTTTTTGTA 57.299 30.769 15.93 0.00 0.00 2.41
2752 3096 7.599630 TTATACGCGATTTAGACCTTTTTGT 57.400 32.000 15.93 0.00 0.00 2.83
2753 3097 7.161418 CGTTTATACGCGATTTAGACCTTTTTG 59.839 37.037 15.93 0.00 41.41 2.44
2754 3098 7.175410 CGTTTATACGCGATTTAGACCTTTTT 58.825 34.615 15.93 0.00 41.41 1.94
2755 3099 6.699063 CGTTTATACGCGATTTAGACCTTTT 58.301 36.000 15.93 0.00 41.41 2.27
2756 3100 6.264909 CGTTTATACGCGATTTAGACCTTT 57.735 37.500 15.93 0.00 41.41 3.11
2757 3101 5.878261 CGTTTATACGCGATTTAGACCTT 57.122 39.130 15.93 0.00 41.41 3.50
2771 3115 5.691508 ACACTGTCAATACGCGTTTATAC 57.308 39.130 20.78 12.22 0.00 1.47
2772 3116 7.377662 CAGATACACTGTCAATACGCGTTTATA 59.622 37.037 20.78 0.00 41.30 0.98
2773 3117 6.198403 CAGATACACTGTCAATACGCGTTTAT 59.802 38.462 20.78 1.77 41.30 1.40
2774 3118 5.513849 CAGATACACTGTCAATACGCGTTTA 59.486 40.000 20.78 0.00 41.30 2.01
2775 3119 4.326278 CAGATACACTGTCAATACGCGTTT 59.674 41.667 20.78 6.76 41.30 3.60
2776 3120 3.857665 CAGATACACTGTCAATACGCGTT 59.142 43.478 20.78 1.87 41.30 4.84
2777 3121 3.128068 TCAGATACACTGTCAATACGCGT 59.872 43.478 19.17 19.17 45.86 6.01
2778 3122 3.482472 GTCAGATACACTGTCAATACGCG 59.518 47.826 3.53 3.53 45.86 6.01
2779 3123 3.797256 GGTCAGATACACTGTCAATACGC 59.203 47.826 0.00 0.00 45.86 4.42
2780 3124 4.035684 CGGTCAGATACACTGTCAATACG 58.964 47.826 0.00 0.00 45.86 3.06
2781 3125 4.360563 CCGGTCAGATACACTGTCAATAC 58.639 47.826 0.00 0.00 45.86 1.89
2782 3126 3.181479 GCCGGTCAGATACACTGTCAATA 60.181 47.826 1.90 0.00 45.86 1.90
2783 3127 2.418746 GCCGGTCAGATACACTGTCAAT 60.419 50.000 1.90 0.00 45.86 2.57
2784 3128 1.067142 GCCGGTCAGATACACTGTCAA 60.067 52.381 1.90 0.00 45.86 3.18
2785 3129 0.530744 GCCGGTCAGATACACTGTCA 59.469 55.000 1.90 0.00 45.86 3.58
2786 3130 0.525668 CGCCGGTCAGATACACTGTC 60.526 60.000 1.90 0.00 45.86 3.51
2787 3131 1.511305 CGCCGGTCAGATACACTGT 59.489 57.895 1.90 0.00 45.86 3.55
2788 3132 1.226974 CCGCCGGTCAGATACACTG 60.227 63.158 1.90 0.00 46.97 3.66
2789 3133 2.423898 CCCGCCGGTCAGATACACT 61.424 63.158 1.90 0.00 0.00 3.55
2790 3134 2.106332 CCCGCCGGTCAGATACAC 59.894 66.667 1.90 0.00 0.00 2.90
2791 3135 3.151710 CCCCGCCGGTCAGATACA 61.152 66.667 1.90 0.00 0.00 2.29
2792 3136 4.603946 GCCCCGCCGGTCAGATAC 62.604 72.222 1.90 0.00 0.00 2.24
2811 3155 4.385405 GTCGGCAGCTGACAGGCT 62.385 66.667 26.87 0.00 44.10 4.58
2813 3157 4.363990 ACGTCGGCAGCTGACAGG 62.364 66.667 29.82 18.72 39.51 4.00
2814 3158 3.108289 CACGTCGGCAGCTGACAG 61.108 66.667 29.82 23.81 39.51 3.51
2815 3159 4.662961 CCACGTCGGCAGCTGACA 62.663 66.667 29.82 3.69 39.51 3.58
2838 3182 0.179070 GCGGGGGTTTTCTGCAAAAA 60.179 50.000 0.00 0.00 36.58 1.94
2839 3183 1.330655 TGCGGGGGTTTTCTGCAAAA 61.331 50.000 0.00 0.00 42.74 2.44
2840 3184 1.758514 TGCGGGGGTTTTCTGCAAA 60.759 52.632 0.00 0.00 42.74 3.68
2841 3185 2.123683 TGCGGGGGTTTTCTGCAA 60.124 55.556 0.00 0.00 42.74 4.08
2842 3186 2.909965 GTGCGGGGGTTTTCTGCA 60.910 61.111 0.00 0.00 43.38 4.41
2843 3187 4.038080 CGTGCGGGGGTTTTCTGC 62.038 66.667 0.00 0.00 37.06 4.26
2844 3188 3.361977 CCGTGCGGGGGTTTTCTG 61.362 66.667 2.15 0.00 0.00 3.02
2865 3209 4.271816 CTCGATCCAGACCGGGCG 62.272 72.222 6.32 0.00 35.22 6.13
2866 3210 3.917760 CCTCGATCCAGACCGGGC 61.918 72.222 6.32 0.52 34.36 6.13
2867 3211 3.227276 CCCTCGATCCAGACCGGG 61.227 72.222 6.32 0.00 34.36 5.73
2868 3212 3.227276 CCCCTCGATCCAGACCGG 61.227 72.222 0.00 0.00 0.00 5.28
2869 3213 2.123854 TCCCCTCGATCCAGACCG 60.124 66.667 0.00 0.00 0.00 4.79
2870 3214 1.834822 CCTCCCCTCGATCCAGACC 60.835 68.421 0.00 0.00 0.00 3.85
2871 3215 0.178947 ATCCTCCCCTCGATCCAGAC 60.179 60.000 0.00 0.00 0.00 3.51
2872 3216 0.113385 GATCCTCCCCTCGATCCAGA 59.887 60.000 0.00 0.00 30.64 3.86
2873 3217 2.664825 GATCCTCCCCTCGATCCAG 58.335 63.158 0.00 0.00 30.64 3.86
2874 3218 4.954768 GATCCTCCCCTCGATCCA 57.045 61.111 0.00 0.00 30.64 3.41
2875 3219 4.121906 GGATCCTCCCCTCGATCC 57.878 66.667 3.84 0.57 45.81 3.36
2887 3231 4.916314 TCGGGCTCGAGGGGATCC 62.916 72.222 15.58 1.92 40.88 3.36
2903 3247 1.067250 GGTGATGCGAGAGGAGCTC 59.933 63.158 4.71 4.71 39.19 4.09
2904 3248 2.780094 CGGTGATGCGAGAGGAGCT 61.780 63.158 0.00 0.00 39.19 4.09
2905 3249 2.279120 CGGTGATGCGAGAGGAGC 60.279 66.667 0.00 0.00 38.77 4.70
2906 3250 2.279120 GCGGTGATGCGAGAGGAG 60.279 66.667 0.00 0.00 32.19 3.69
2907 3251 3.838271 GGCGGTGATGCGAGAGGA 61.838 66.667 0.00 0.00 35.06 3.71
2992 3336 4.845580 ATCTTGGGCCGCGAGCAG 62.846 66.667 8.23 3.34 46.50 4.24
2993 3337 4.838152 GATCTTGGGCCGCGAGCA 62.838 66.667 8.23 0.00 46.50 4.26
3002 3346 2.202932 CCTGTCGCCGATCTTGGG 60.203 66.667 0.00 0.00 0.00 4.12
3003 3347 2.202932 CCCTGTCGCCGATCTTGG 60.203 66.667 0.00 0.00 0.00 3.61
3004 3348 2.892425 GCCCTGTCGCCGATCTTG 60.892 66.667 0.00 0.00 0.00 3.02
3005 3349 4.514577 CGCCCTGTCGCCGATCTT 62.515 66.667 0.00 0.00 0.00 2.40
3028 3372 4.640855 AGTCGCACCACCACGTCG 62.641 66.667 0.00 0.00 0.00 5.12
3029 3373 3.036084 CAGTCGCACCACCACGTC 61.036 66.667 0.00 0.00 0.00 4.34
3034 3378 4.760047 ATCCGCAGTCGCACCACC 62.760 66.667 0.00 0.00 38.40 4.61
3035 3379 3.490759 CATCCGCAGTCGCACCAC 61.491 66.667 0.00 0.00 38.40 4.16
3042 3386 4.148825 AGTCCGGCATCCGCAGTC 62.149 66.667 0.00 0.00 46.86 3.51
3043 3387 4.148825 GAGTCCGGCATCCGCAGT 62.149 66.667 0.00 0.00 46.86 4.40
3059 3403 3.833645 CCATTCGTCTCGGCCCGA 61.834 66.667 5.37 5.37 0.00 5.14
3063 3407 0.595310 GTAGAGCCATTCGTCTCGGC 60.595 60.000 0.00 0.00 46.62 5.54
3064 3408 1.025812 AGTAGAGCCATTCGTCTCGG 58.974 55.000 0.00 0.00 34.66 4.63
3065 3409 1.862008 GCAGTAGAGCCATTCGTCTCG 60.862 57.143 0.00 0.00 34.66 4.04
3066 3410 1.846541 GCAGTAGAGCCATTCGTCTC 58.153 55.000 0.00 0.00 0.00 3.36
3076 3420 2.496817 CCGGAGTGGCAGTAGAGC 59.503 66.667 0.00 0.00 0.00 4.09


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

AutoCloner maintained by Alex Coulton.