Multiple sequence alignment - TraesCS4B01G305500

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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 TraesCS4B01G305500 chr4B 100.000 3323 0 0 1 3323 594359723 594356401 0.000000e+00 6137.0
1 TraesCS4B01G305500 chr4D 88.902 3343 279 59 1 3304 472166669 472163380 0.000000e+00 4034.0
2 TraesCS4B01G305500 chr4A 88.760 3025 230 57 19 2982 679076428 679073453 0.000000e+00 3602.0
3 TraesCS4B01G305500 chr7D 93.074 823 42 2 1254 2076 538599675 538598868 0.000000e+00 1190.0
4 TraesCS4B01G305500 chr7D 93.408 713 44 1 1364 2076 159703171 159703880 0.000000e+00 1053.0
5 TraesCS4B01G305500 chr7D 94.574 129 7 0 1305 1433 137915408 137915536 2.020000e-47 200.0
6 TraesCS4B01G305500 chr2D 93.804 694 41 2 1347 2039 442056976 442056284 0.000000e+00 1042.0
7 TraesCS4B01G305500 chr3D 92.131 610 44 2 1467 2076 320413817 320413212 0.000000e+00 857.0
8 TraesCS4B01G305500 chr2A 90.068 584 55 1 1493 2076 85584677 85585257 0.000000e+00 754.0
9 TraesCS4B01G305500 chr2A 93.243 148 9 1 1350 1497 85537652 85537798 2.010000e-52 217.0
10 TraesCS4B01G305500 chr1B 93.023 129 9 0 1305 1433 167949602 167949474 4.380000e-44 189.0
11 TraesCS4B01G305500 chr6D 92.308 130 10 0 1305 1434 157661293 157661164 5.660000e-43 185.0
12 TraesCS4B01G305500 chr7A 84.118 170 24 3 293 460 733065892 733065724 9.540000e-36 161.0
13 TraesCS4B01G305500 chr7A 83.333 108 14 3 492 599 732900467 732900364 2.730000e-16 97.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G305500 chr4B 594356401 594359723 3322 True 6137 6137 100.000 1 3323 1 chr4B.!!$R1 3322
1 TraesCS4B01G305500 chr4D 472163380 472166669 3289 True 4034 4034 88.902 1 3304 1 chr4D.!!$R1 3303
2 TraesCS4B01G305500 chr4A 679073453 679076428 2975 True 3602 3602 88.760 19 2982 1 chr4A.!!$R1 2963
3 TraesCS4B01G305500 chr7D 538598868 538599675 807 True 1190 1190 93.074 1254 2076 1 chr7D.!!$R1 822
4 TraesCS4B01G305500 chr7D 159703171 159703880 709 False 1053 1053 93.408 1364 2076 1 chr7D.!!$F2 712
5 TraesCS4B01G305500 chr2D 442056284 442056976 692 True 1042 1042 93.804 1347 2039 1 chr2D.!!$R1 692
6 TraesCS4B01G305500 chr3D 320413212 320413817 605 True 857 857 92.131 1467 2076 1 chr3D.!!$R1 609
7 TraesCS4B01G305500 chr2A 85584677 85585257 580 False 754 754 90.068 1493 2076 1 chr2A.!!$F2 583

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
743 774 0.179189 CGGCCGTGATCTTTTCTTGC 60.179 55.0 19.5 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 2558 0.10852 AGCATTTCCAAGCCGCAATG 60.109 50.0 0.0 0.0 0.0 2.82 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
64 65 5.766670 TCATGCAAAGATGACTTTCACTTCT 59.233 36.000 0.00 0.00 43.41 2.85
221 222 1.304381 GCCCAAGCAGGACATTCCA 60.304 57.895 0.00 0.00 39.61 3.53
276 277 2.099405 TCATCAGACTGACCATGCGTA 58.901 47.619 7.47 0.00 0.00 4.42
292 293 2.264109 CGTAGCACTGTCGATGTTCT 57.736 50.000 0.00 0.00 0.00 3.01
293 294 2.596452 CGTAGCACTGTCGATGTTCTT 58.404 47.619 0.00 0.00 0.00 2.52
319 320 7.333921 TGAGAGCTTCTGATTCAGAGAATTTTC 59.666 37.037 15.59 11.14 41.75 2.29
339 340 5.869753 TTCCCATGTGTTTTGTTTTGTTG 57.130 34.783 0.00 0.00 0.00 3.33
341 342 4.020218 TCCCATGTGTTTTGTTTTGTTGGA 60.020 37.500 0.00 0.00 0.00 3.53
342 343 4.094146 CCCATGTGTTTTGTTTTGTTGGAC 59.906 41.667 0.00 0.00 0.00 4.02
343 344 4.692625 CCATGTGTTTTGTTTTGTTGGACA 59.307 37.500 0.00 0.00 0.00 4.02
345 346 5.659048 TGTGTTTTGTTTTGTTGGACAAC 57.341 34.783 8.19 8.19 37.90 3.32
473 475 1.474077 GGATGGACAAGTGACAATGCC 59.526 52.381 0.00 0.00 0.00 4.40
610 639 4.000325 TGTAACTTCATCCATCCGTGTTG 59.000 43.478 0.00 0.00 0.00 3.33
634 663 7.066374 GAACTTCATTGTTCATCAGTACTCC 57.934 40.000 0.00 0.00 44.00 3.85
650 681 3.297134 ACTCCAACCAGTTGTGTGAAT 57.703 42.857 9.53 0.00 38.85 2.57
743 774 0.179189 CGGCCGTGATCTTTTCTTGC 60.179 55.000 19.50 0.00 0.00 4.01
758 789 5.659440 TTTCTTGCTGAAAAACCAGAACT 57.341 34.783 0.00 0.00 41.23 3.01
960 992 1.066143 ACCGTTATGGCCTGAGAGTTG 60.066 52.381 3.32 0.00 43.94 3.16
969 1001 1.672356 CTGAGAGTTGTTGCCCCGG 60.672 63.158 0.00 0.00 0.00 5.73
972 1004 2.112297 GAGTTGTTGCCCCGGTCA 59.888 61.111 0.00 0.00 0.00 4.02
973 1005 1.303317 GAGTTGTTGCCCCGGTCAT 60.303 57.895 0.00 0.00 0.00 3.06
985 1023 2.166829 CCCGGTCATCCATTTCAACAA 58.833 47.619 0.00 0.00 0.00 2.83
986 1024 2.560542 CCCGGTCATCCATTTCAACAAA 59.439 45.455 0.00 0.00 0.00 2.83
987 1025 3.574614 CCGGTCATCCATTTCAACAAAC 58.425 45.455 0.00 0.00 0.00 2.93
988 1026 3.233578 CGGTCATCCATTTCAACAAACG 58.766 45.455 0.00 0.00 0.00 3.60
989 1027 3.574614 GGTCATCCATTTCAACAAACGG 58.425 45.455 0.00 0.00 0.00 4.44
990 1028 2.986479 GTCATCCATTTCAACAAACGGC 59.014 45.455 0.00 0.00 0.00 5.68
991 1029 2.890311 TCATCCATTTCAACAAACGGCT 59.110 40.909 0.00 0.00 0.00 5.52
992 1030 3.057596 TCATCCATTTCAACAAACGGCTC 60.058 43.478 0.00 0.00 0.00 4.70
993 1031 1.265635 TCCATTTCAACAAACGGCTCG 59.734 47.619 0.00 0.00 0.00 5.03
994 1032 1.665735 CCATTTCAACAAACGGCTCGG 60.666 52.381 0.00 0.00 0.00 4.63
995 1033 1.001815 CATTTCAACAAACGGCTCGGT 60.002 47.619 0.00 0.00 0.00 4.69
1251 1289 1.489649 CTGGAGATCACCAAGATGGCT 59.510 52.381 13.21 0.00 42.67 4.75
1437 1475 4.247380 CGGGCCATGGAGGAGCTC 62.247 72.222 18.40 4.71 41.22 4.09
1911 1949 2.583520 GAGGAGCTGGAGTGCCTG 59.416 66.667 0.00 0.00 36.29 4.85
2165 2206 2.184322 GCGGCAGATGTCGGAGAA 59.816 61.111 9.09 0.00 44.35 2.87
2168 2209 0.738975 CGGCAGATGTCGGAGAACTA 59.261 55.000 0.00 0.00 39.69 2.24
2178 2219 1.382692 CGGAGAACTACGAGGGGTCC 61.383 65.000 0.00 0.00 39.85 4.46
2216 2257 3.787001 GGTCGAGGAGCCCAAGGG 61.787 72.222 0.00 0.00 38.57 3.95
2242 2283 1.003839 GGCGTGTTCACCAGGATGA 60.004 57.895 0.00 0.00 39.69 2.92
2307 2348 1.578206 GCTTGTTCCGGTGGAAGAGC 61.578 60.000 14.41 14.41 42.88 4.09
2324 2365 2.802816 AGAGCTTCAACAACAAGTAGCG 59.197 45.455 0.00 0.00 35.08 4.26
2363 2404 2.125673 GAGCCGTGTGCCGTGTAT 60.126 61.111 0.00 0.00 42.71 2.29
2364 2405 2.434185 AGCCGTGTGCCGTGTATG 60.434 61.111 0.00 0.00 42.71 2.39
2386 2427 5.870706 TGTATGTTGTACAATGTCCTTGGA 58.129 37.500 12.26 0.00 39.30 3.53
2398 2451 5.649782 ATGTCCTTGGAATTGCTAGTTTG 57.350 39.130 7.55 0.00 0.00 2.93
2419 2473 1.883275 TGTTGGGTAATTGGCGTCTTG 59.117 47.619 0.00 0.00 0.00 3.02
2420 2474 2.156098 GTTGGGTAATTGGCGTCTTGA 58.844 47.619 0.00 0.00 0.00 3.02
2423 2478 1.597663 GGGTAATTGGCGTCTTGATCG 59.402 52.381 0.00 0.00 0.00 3.69
2426 2481 0.251916 AATTGGCGTCTTGATCGGGA 59.748 50.000 0.00 0.00 0.00 5.14
2430 2485 2.815308 CGTCTTGATCGGGAGGGG 59.185 66.667 0.00 0.00 0.00 4.79
2432 2487 1.382695 GTCTTGATCGGGAGGGGGA 60.383 63.158 0.00 0.00 0.00 4.81
2442 2497 0.325272 GGGAGGGGGAGATATTTCGC 59.675 60.000 1.98 1.98 0.00 4.70
2447 2503 2.934083 GGGAGATATTTCGCTGCCC 58.066 57.895 3.33 0.00 36.72 5.36
2448 2504 0.398318 GGGAGATATTTCGCTGCCCT 59.602 55.000 3.33 0.00 36.72 5.19
2456 2512 1.737838 TTTCGCTGCCCTGTGATAAG 58.262 50.000 0.00 0.00 0.00 1.73
2463 2519 2.360165 CTGCCCTGTGATAAGAATTGCC 59.640 50.000 0.00 0.00 0.00 4.52
2471 2527 6.152661 CCTGTGATAAGAATTGCCCTTGTAAA 59.847 38.462 0.00 0.00 0.00 2.01
2476 2532 7.615365 TGATAAGAATTGCCCTTGTAAATGACT 59.385 33.333 0.00 0.00 0.00 3.41
2477 2533 9.120538 GATAAGAATTGCCCTTGTAAATGACTA 57.879 33.333 0.00 0.00 0.00 2.59
2478 2534 7.775053 AAGAATTGCCCTTGTAAATGACTAA 57.225 32.000 0.00 0.00 0.00 2.24
2504 2560 6.737720 AGTGTGTATATGTGATCACCTCAT 57.262 37.500 22.85 14.61 35.97 2.90
2508 2564 4.990426 TGTATATGTGATCACCTCATTGCG 59.010 41.667 22.85 0.00 35.97 4.85
2527 2583 2.604462 GCGGCTTGGAAATGCTATTTTG 59.396 45.455 0.00 0.00 0.00 2.44
2535 2591 0.179103 AATGCTATTTTGCAGCGCCC 60.179 50.000 2.29 0.00 46.71 6.13
2536 2592 2.278142 GCTATTTTGCAGCGCCCG 60.278 61.111 2.29 0.00 0.00 6.13
2537 2593 2.278142 CTATTTTGCAGCGCCCGC 60.278 61.111 12.24 12.24 42.33 6.13
2538 2594 3.756413 CTATTTTGCAGCGCCCGCC 62.756 63.158 16.00 0.00 43.17 6.13
2575 2638 4.701663 CGTGACATGTCAAGCCCT 57.298 55.556 29.42 0.00 41.85 5.19
2582 2658 3.072330 TGACATGTCAAGCCCTAGTTTGA 59.928 43.478 26.02 0.00 40.46 2.69
2587 2663 3.135994 GTCAAGCCCTAGTTTGAAACGA 58.864 45.455 1.97 0.00 43.71 3.85
2593 2669 2.484264 CCCTAGTTTGAAACGAAGGCAG 59.516 50.000 20.34 9.37 37.81 4.85
2606 2682 2.232941 CGAAGGCAGAAGTTGTACCCTA 59.767 50.000 0.00 0.00 0.00 3.53
2614 2690 6.183360 GGCAGAAGTTGTACCCTATCTCATTA 60.183 42.308 0.00 0.00 0.00 1.90
2618 2694 8.822805 AGAAGTTGTACCCTATCTCATTAACAA 58.177 33.333 0.00 0.00 0.00 2.83
2680 2758 3.305471 GGCATACTCGACCAACCTATCTC 60.305 52.174 0.00 0.00 0.00 2.75
2694 2772 7.669722 ACCAACCTATCTCACAACAAATACATT 59.330 33.333 0.00 0.00 0.00 2.71
2702 2780 7.860613 TCTCACAACAAATACATTACACACAG 58.139 34.615 0.00 0.00 0.00 3.66
2705 2784 5.534654 ACAACAAATACATTACACACAGCCT 59.465 36.000 0.00 0.00 0.00 4.58
2707 2786 6.985188 ACAAATACATTACACACAGCCTAG 57.015 37.500 0.00 0.00 0.00 3.02
2718 2797 9.765795 ATTACACACAGCCTAGAAGATAAATAC 57.234 33.333 0.00 0.00 0.00 1.89
2721 2800 6.480320 CACACAGCCTAGAAGATAAATACACC 59.520 42.308 0.00 0.00 0.00 4.16
2744 2823 3.930336 CAGAGGTTGCACATAAGTCTCA 58.070 45.455 0.00 0.00 0.00 3.27
2745 2824 4.511527 CAGAGGTTGCACATAAGTCTCAT 58.488 43.478 0.00 0.00 0.00 2.90
2746 2825 4.940046 CAGAGGTTGCACATAAGTCTCATT 59.060 41.667 0.00 0.00 0.00 2.57
2747 2826 4.940046 AGAGGTTGCACATAAGTCTCATTG 59.060 41.667 0.00 0.00 0.00 2.82
2748 2827 4.655963 AGGTTGCACATAAGTCTCATTGT 58.344 39.130 0.00 0.00 0.00 2.71
2749 2828 4.697352 AGGTTGCACATAAGTCTCATTGTC 59.303 41.667 0.00 0.00 0.00 3.18
2750 2829 4.455533 GGTTGCACATAAGTCTCATTGTCA 59.544 41.667 0.00 0.00 0.00 3.58
2751 2830 5.048782 GGTTGCACATAAGTCTCATTGTCAA 60.049 40.000 0.00 0.00 0.00 3.18
2752 2831 6.349611 GGTTGCACATAAGTCTCATTGTCAAT 60.350 38.462 0.00 0.00 0.00 2.57
2763 2842 4.631377 TCTCATTGTCAATTCGTCATCACC 59.369 41.667 0.00 0.00 0.00 4.02
2764 2843 3.370672 TCATTGTCAATTCGTCATCACCG 59.629 43.478 0.00 0.00 0.00 4.94
2790 2869 2.289195 ACAAGCAACCGACTCCGATTTA 60.289 45.455 0.00 0.00 38.22 1.40
2791 2870 2.005971 AGCAACCGACTCCGATTTAC 57.994 50.000 0.00 0.00 38.22 2.01
2792 2871 1.004595 GCAACCGACTCCGATTTACC 58.995 55.000 0.00 0.00 38.22 2.85
2793 2872 1.274596 CAACCGACTCCGATTTACCG 58.725 55.000 0.00 0.00 38.22 4.02
2794 2873 0.890683 AACCGACTCCGATTTACCGT 59.109 50.000 0.00 0.00 38.22 4.83
2798 2888 1.820092 GACTCCGATTTACCGTCGAC 58.180 55.000 5.18 5.18 41.40 4.20
2819 2919 2.810400 CGAAGTCCTCCCAACAACATGT 60.810 50.000 0.00 0.00 0.00 3.21
2842 2942 0.107831 AAGCCACGCTAAGGTCAACA 59.892 50.000 0.00 0.00 38.25 3.33
2850 2950 5.390567 CCACGCTAAGGTCAACAAAATAGTC 60.391 44.000 0.00 0.00 0.00 2.59
2859 2959 5.390567 GGTCAACAAAATAGTCGTCCACATC 60.391 44.000 0.00 0.00 0.00 3.06
2863 2963 0.248907 AATAGTCGTCCACATCGGCG 60.249 55.000 0.00 0.00 37.99 6.46
2870 2970 0.098728 GTCCACATCGGCGGAAAATG 59.901 55.000 7.21 5.85 31.67 2.32
2880 2980 0.101219 GCGGAAAATGAGATGGGTGC 59.899 55.000 0.00 0.00 0.00 5.01
2885 2985 0.608856 AAATGAGATGGGTGCGTGCA 60.609 50.000 0.00 0.00 0.00 4.57
2892 2995 0.181114 ATGGGTGCGTGCATGAGTAT 59.819 50.000 10.93 0.00 0.00 2.12
2894 2997 0.744414 GGGTGCGTGCATGAGTATGT 60.744 55.000 10.93 0.00 36.65 2.29
2896 2999 1.202065 GGTGCGTGCATGAGTATGTTG 60.202 52.381 10.93 0.00 36.65 3.33
2898 3001 0.587242 GCGTGCATGAGTATGTTGCG 60.587 55.000 10.93 0.00 39.23 4.85
2901 3004 0.728542 TGCATGAGTATGTTGCGCAG 59.271 50.000 11.31 0.00 39.23 5.18
2905 3008 1.155889 TGAGTATGTTGCGCAGGTTG 58.844 50.000 11.31 0.00 0.00 3.77
2926 3029 1.831736 CGGAATGTTGGACCTACTCCT 59.168 52.381 7.60 0.00 40.26 3.69
2931 3034 3.764237 TGTTGGACCTACTCCTCAAAC 57.236 47.619 7.60 0.00 40.26 2.93
2933 3036 4.485875 TGTTGGACCTACTCCTCAAACTA 58.514 43.478 7.60 0.00 40.26 2.24
2936 3039 6.126710 TGTTGGACCTACTCCTCAAACTAAAA 60.127 38.462 7.60 0.00 40.26 1.52
2976 3079 8.899427 TTCAAGGATCATTCTCATCTATCAAC 57.101 34.615 0.00 0.00 0.00 3.18
2983 3086 4.655762 TTCTCATCTATCAACGACCAGG 57.344 45.455 0.00 0.00 0.00 4.45
2984 3087 3.632333 TCTCATCTATCAACGACCAGGT 58.368 45.455 0.00 0.00 0.00 4.00
2988 3091 6.016192 TCTCATCTATCAACGACCAGGTTATC 60.016 42.308 0.00 0.00 0.00 1.75
2989 3092 5.833667 TCATCTATCAACGACCAGGTTATCT 59.166 40.000 0.00 0.00 0.00 1.98
2991 3094 5.198207 TCTATCAACGACCAGGTTATCTCA 58.802 41.667 0.00 0.00 0.00 3.27
2993 3096 4.610605 TCAACGACCAGGTTATCTCAAA 57.389 40.909 0.00 0.00 0.00 2.69
2994 3097 4.963373 TCAACGACCAGGTTATCTCAAAA 58.037 39.130 0.00 0.00 0.00 2.44
2997 3100 2.348666 CGACCAGGTTATCTCAAAAGCG 59.651 50.000 0.00 0.00 0.00 4.68
3002 3105 2.039879 AGGTTATCTCAAAAGCGTGGGT 59.960 45.455 0.00 0.00 0.00 4.51
3014 3117 4.929819 AAGCGTGGGTGAAAAGTTTATT 57.070 36.364 0.00 0.00 0.00 1.40
3015 3118 6.394025 AAAGCGTGGGTGAAAAGTTTATTA 57.606 33.333 0.00 0.00 0.00 0.98
3018 3121 4.729595 CGTGGGTGAAAAGTTTATTAGGC 58.270 43.478 0.00 0.00 0.00 3.93
3022 3125 7.214381 GTGGGTGAAAAGTTTATTAGGCTTTT 58.786 34.615 0.00 0.00 42.79 2.27
3031 3134 5.716703 AGTTTATTAGGCTTTTCATGTGGCT 59.283 36.000 0.00 2.66 39.84 4.75
3042 3145 1.903860 TCATGTGGCTTTAGGTACGGT 59.096 47.619 0.00 0.00 0.00 4.83
3045 3148 0.320946 GTGGCTTTAGGTACGGTGCA 60.321 55.000 0.00 0.00 0.00 4.57
3046 3149 0.397187 TGGCTTTAGGTACGGTGCAA 59.603 50.000 0.00 0.00 0.00 4.08
3048 3151 1.515081 GCTTTAGGTACGGTGCAACA 58.485 50.000 0.98 0.00 39.98 3.33
3049 3152 2.081462 GCTTTAGGTACGGTGCAACAT 58.919 47.619 0.98 0.00 39.98 2.71
3050 3153 2.486592 GCTTTAGGTACGGTGCAACATT 59.513 45.455 0.98 0.00 39.98 2.71
3054 3157 1.346395 AGGTACGGTGCAACATTCTCA 59.654 47.619 0.98 0.00 39.98 3.27
3058 3161 0.948623 CGGTGCAACATTCTCACGGA 60.949 55.000 0.98 0.00 39.98 4.69
3063 3166 1.061131 GCAACATTCTCACGGACGATG 59.939 52.381 0.00 0.00 0.00 3.84
3064 3167 1.061131 CAACATTCTCACGGACGATGC 59.939 52.381 0.00 0.00 0.00 3.91
3072 3175 0.526739 CACGGACGATGCGTTATCCA 60.527 55.000 9.41 0.00 43.30 3.41
3081 3184 1.208706 TGCGTTATCCATGAAGGGGA 58.791 50.000 0.00 0.00 39.14 4.81
3082 3185 1.774254 TGCGTTATCCATGAAGGGGAT 59.226 47.619 0.00 0.00 46.62 3.85
3083 3186 2.976185 TGCGTTATCCATGAAGGGGATA 59.024 45.455 0.00 0.00 43.27 2.59
3084 3187 3.007940 TGCGTTATCCATGAAGGGGATAG 59.992 47.826 0.00 0.00 45.51 2.08
3085 3188 3.600388 CGTTATCCATGAAGGGGATAGC 58.400 50.000 0.00 0.00 45.51 2.97
3101 3204 2.042686 TAGCCTTGTAGCATGCTTGG 57.957 50.000 28.02 21.92 35.34 3.61
3102 3205 0.682209 AGCCTTGTAGCATGCTTGGG 60.682 55.000 28.02 21.48 34.23 4.12
3106 3209 2.834968 GTAGCATGCTTGGGCCCC 60.835 66.667 28.02 3.99 37.74 5.80
3107 3210 3.023116 TAGCATGCTTGGGCCCCT 61.023 61.111 28.02 9.75 37.74 4.79
3110 3213 2.281091 CATGCTTGGGCCCCTCAT 59.719 61.111 22.27 16.67 37.74 2.90
3111 3214 1.382146 CATGCTTGGGCCCCTCATT 60.382 57.895 22.27 0.00 37.74 2.57
3113 3216 2.761213 GCTTGGGCCCCTCATTGG 60.761 66.667 22.27 2.26 0.00 3.16
3114 3217 2.772924 CTTGGGCCCCTCATTGGT 59.227 61.111 22.27 0.00 0.00 3.67
3116 3219 0.395724 CTTGGGCCCCTCATTGGTAC 60.396 60.000 22.27 0.00 0.00 3.34
3125 3228 1.134098 CCTCATTGGTACGCCCTTGAT 60.134 52.381 0.00 0.00 0.00 2.57
3128 3231 2.158871 TCATTGGTACGCCCTTGATACC 60.159 50.000 0.00 0.00 39.12 2.73
3130 3233 0.538118 TGGTACGCCCTTGATACCAC 59.462 55.000 0.00 0.00 42.70 4.16
3136 3239 0.535335 GCCCTTGATACCACGAGTCA 59.465 55.000 0.00 0.00 0.00 3.41
3163 3266 1.278985 TCAGGGATGCAACATCTCGTT 59.721 47.619 7.45 0.00 38.83 3.85
3172 3275 1.237285 AACATCTCGTTGCTGGTGCC 61.237 55.000 0.00 0.00 36.12 5.01
3187 3290 1.011968 GTGCCGCACACGATTCACTA 61.012 55.000 18.79 0.00 43.93 2.74
3192 3295 2.480587 CCGCACACGATTCACTATGGTA 60.481 50.000 0.00 0.00 43.93 3.25
3193 3296 2.789339 CGCACACGATTCACTATGGTAG 59.211 50.000 0.00 0.00 43.93 3.18
3194 3297 3.123804 GCACACGATTCACTATGGTAGG 58.876 50.000 0.00 0.00 0.00 3.18
3198 3301 6.513180 CACACGATTCACTATGGTAGGTAAT 58.487 40.000 0.00 0.00 0.00 1.89
3204 3307 5.134202 TCACTATGGTAGGTAATCATGCG 57.866 43.478 0.00 0.00 0.00 4.73
3205 3308 3.679980 CACTATGGTAGGTAATCATGCGC 59.320 47.826 0.00 0.00 0.00 6.09
3208 3311 1.269569 TGGTAGGTAATCATGCGCTCG 60.270 52.381 9.73 0.00 0.00 5.03
3210 3313 0.673985 TAGGTAATCATGCGCTCGCT 59.326 50.000 9.73 0.00 42.51 4.93
3227 3330 1.804372 CGCTGAGTTCCAGGCTATGTC 60.804 57.143 0.00 0.00 43.13 3.06
3228 3331 1.208052 GCTGAGTTCCAGGCTATGTCA 59.792 52.381 0.00 0.00 43.13 3.58
3231 3334 2.271800 GAGTTCCAGGCTATGTCAACG 58.728 52.381 0.00 0.00 0.00 4.10
3232 3335 0.727398 GTTCCAGGCTATGTCAACGC 59.273 55.000 0.00 0.00 0.00 4.84
3233 3336 0.392461 TTCCAGGCTATGTCAACGCC 60.392 55.000 7.49 7.49 44.09 5.68
3237 3340 1.745087 CAGGCTATGTCAACGCCAAAT 59.255 47.619 15.63 0.00 46.14 2.32
3239 3342 2.423538 AGGCTATGTCAACGCCAAATTC 59.576 45.455 15.63 0.00 46.14 2.17
3254 3362 5.123186 CGCCAAATTCTTCTACATTGGTGTA 59.877 40.000 7.95 0.00 43.33 2.90
3262 3370 5.350365 TCTTCTACATTGGTGTAATTGCGTC 59.650 40.000 0.00 0.00 40.16 5.19
3265 3373 1.466950 CATTGGTGTAATTGCGTCGGT 59.533 47.619 0.00 0.00 0.00 4.69
3271 3379 1.807981 TAATTGCGTCGGTGCCTCG 60.808 57.895 0.00 0.00 0.00 4.63
3275 3383 2.813908 GCGTCGGTGCCTCGATTT 60.814 61.111 1.96 0.00 41.40 2.17
3279 3387 1.801395 CGTCGGTGCCTCGATTTATGT 60.801 52.381 1.96 0.00 41.40 2.29
3291 3399 6.589135 CCTCGATTTATGTTAGGGTTAGGTT 58.411 40.000 0.00 0.00 0.00 3.50
3292 3400 6.704937 CCTCGATTTATGTTAGGGTTAGGTTC 59.295 42.308 0.00 0.00 0.00 3.62
3293 3401 7.185318 TCGATTTATGTTAGGGTTAGGTTCA 57.815 36.000 0.00 0.00 0.00 3.18
3295 3403 8.269317 TCGATTTATGTTAGGGTTAGGTTCATT 58.731 33.333 0.00 0.00 0.00 2.57
3298 3406 5.789574 ATGTTAGGGTTAGGTTCATTGGA 57.210 39.130 0.00 0.00 0.00 3.53
3299 3407 5.789574 TGTTAGGGTTAGGTTCATTGGAT 57.210 39.130 0.00 0.00 0.00 3.41
3302 3410 2.244769 AGGGTTAGGTTCATTGGATGGG 59.755 50.000 0.00 0.00 0.00 4.00
3303 3411 2.024369 GGGTTAGGTTCATTGGATGGGT 60.024 50.000 0.00 0.00 0.00 4.51
3304 3412 3.203487 GGGTTAGGTTCATTGGATGGGTA 59.797 47.826 0.00 0.00 0.00 3.69
3305 3413 4.204799 GGTTAGGTTCATTGGATGGGTAC 58.795 47.826 0.00 0.00 0.00 3.34
3306 3414 4.324719 GGTTAGGTTCATTGGATGGGTACA 60.325 45.833 0.00 0.00 0.00 2.90
3307 3415 5.258051 GTTAGGTTCATTGGATGGGTACAA 58.742 41.667 0.00 0.00 31.35 2.41
3308 3416 4.608170 AGGTTCATTGGATGGGTACAAT 57.392 40.909 0.00 0.00 39.53 2.71
3309 3417 5.725551 AGGTTCATTGGATGGGTACAATA 57.274 39.130 0.00 0.00 36.74 1.90
3310 3418 5.694995 AGGTTCATTGGATGGGTACAATAG 58.305 41.667 0.00 0.00 36.74 1.73
3311 3419 4.827284 GGTTCATTGGATGGGTACAATAGG 59.173 45.833 0.00 0.00 36.74 2.57
3312 3420 5.445964 GTTCATTGGATGGGTACAATAGGT 58.554 41.667 0.00 0.00 36.74 3.08
3313 3421 5.725551 TCATTGGATGGGTACAATAGGTT 57.274 39.130 0.00 0.00 36.74 3.50
3314 3422 5.445069 TCATTGGATGGGTACAATAGGTTG 58.555 41.667 0.00 0.00 36.74 3.77
3315 3423 3.943671 TGGATGGGTACAATAGGTTGG 57.056 47.619 0.00 0.00 39.70 3.77
3316 3424 3.194620 TGGATGGGTACAATAGGTTGGT 58.805 45.455 0.00 0.00 39.70 3.67
3317 3425 4.372588 TGGATGGGTACAATAGGTTGGTA 58.627 43.478 0.00 0.00 39.70 3.25
3318 3426 4.164604 TGGATGGGTACAATAGGTTGGTAC 59.835 45.833 0.00 0.00 39.70 3.34
3319 3427 4.411212 GGATGGGTACAATAGGTTGGTACT 59.589 45.833 0.00 0.00 39.70 2.73
3320 3428 5.104235 GGATGGGTACAATAGGTTGGTACTT 60.104 44.000 0.00 0.00 39.70 2.24
3321 3429 5.846528 TGGGTACAATAGGTTGGTACTTT 57.153 39.130 0.00 0.00 39.70 2.66
3322 3430 6.949117 TGGGTACAATAGGTTGGTACTTTA 57.051 37.500 0.00 0.00 39.70 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.196971 TCATCTTTGCATGACAGATGGAG 58.803 43.478 20.55 4.89 42.87 3.86
197 198 1.973812 GTCCTGCTTGGGCTTCACC 60.974 63.158 0.00 0.00 37.49 4.02
221 222 0.175073 GGTACTTGTCGGCGAGGATT 59.825 55.000 11.20 0.00 0.00 3.01
276 277 2.297315 TCTCAAGAACATCGACAGTGCT 59.703 45.455 0.00 0.00 0.00 4.40
292 293 5.735285 TTCTCTGAATCAGAAGCTCTCAA 57.265 39.130 14.44 0.00 40.18 3.02
293 294 5.936187 ATTCTCTGAATCAGAAGCTCTCA 57.064 39.130 14.44 0.00 40.18 3.27
319 320 4.094146 GTCCAACAAAACAAAACACATGGG 59.906 41.667 0.00 0.00 0.00 4.00
339 340 0.321122 CTCCAGCTCCTGTGTTGTCC 60.321 60.000 0.00 0.00 0.00 4.02
341 342 1.072159 GCTCCAGCTCCTGTGTTGT 59.928 57.895 0.00 0.00 38.21 3.32
342 343 3.978272 GCTCCAGCTCCTGTGTTG 58.022 61.111 0.00 0.00 38.21 3.33
473 475 0.729116 CTCCACTTAACAGCCATGCG 59.271 55.000 0.00 0.00 0.00 4.73
481 491 2.878406 GAGCAGCAAACTCCACTTAACA 59.122 45.455 0.00 0.00 0.00 2.41
485 495 2.283145 ATGAGCAGCAAACTCCACTT 57.717 45.000 0.00 0.00 32.98 3.16
486 496 2.157738 GAATGAGCAGCAAACTCCACT 58.842 47.619 0.00 0.00 32.98 4.00
610 639 6.650807 TGGAGTACTGATGAACAATGAAGTTC 59.349 38.462 0.00 0.00 46.22 3.01
632 661 2.100584 GCAATTCACACAACTGGTTGGA 59.899 45.455 16.33 3.30 44.45 3.53
634 663 3.162202 TGCAATTCACACAACTGGTTG 57.838 42.857 11.35 11.35 45.58 3.77
758 789 6.045955 GCTTTGGTTTAGGAACATGTGAAAA 58.954 36.000 0.00 0.00 37.51 2.29
869 901 4.726825 AGGATAAAAGAGGGAGGTGCATTA 59.273 41.667 0.00 0.00 0.00 1.90
937 969 1.221840 CTCAGGCCATAACGGTGCT 59.778 57.895 5.01 0.00 36.97 4.40
960 992 0.970427 AAATGGATGACCGGGGCAAC 60.970 55.000 6.69 3.35 39.42 4.17
969 1001 5.140591 GAGCCGTTTGTTGAAATGGATGAC 61.141 45.833 9.51 0.00 45.10 3.06
988 1026 4.899239 CTGCATCCGGACCGAGCC 62.899 72.222 17.49 1.02 0.00 4.70
989 1027 4.899239 CCTGCATCCGGACCGAGC 62.899 72.222 17.49 16.51 0.00 5.03
990 1028 4.899239 GCCTGCATCCGGACCGAG 62.899 72.222 17.49 5.68 0.00 4.63
1403 1441 0.391793 CCGCTTGTTCTTCTCCTCCC 60.392 60.000 0.00 0.00 0.00 4.30
1551 1589 2.738521 TCGTCCTTGCGCTTCAGC 60.739 61.111 9.73 0.00 37.78 4.26
2105 2146 2.184322 GCTTCATCCTCGCGTCCA 59.816 61.111 5.77 0.00 0.00 4.02
2165 2206 0.678048 GTACACGGACCCCTCGTAGT 60.678 60.000 0.00 0.00 38.94 2.73
2168 2209 3.058160 CGTACACGGACCCCTCGT 61.058 66.667 0.00 0.00 41.93 4.18
2216 2257 2.434185 TGAACACGCCCATCTCGC 60.434 61.111 0.00 0.00 0.00 5.03
2307 2348 4.795970 AAGTCGCTACTTGTTGTTGAAG 57.204 40.909 2.31 0.00 44.40 3.02
2363 2404 5.870706 TCCAAGGACATTGTACAACATACA 58.129 37.500 11.22 0.00 37.17 2.29
2364 2405 6.811253 TTCCAAGGACATTGTACAACATAC 57.189 37.500 11.22 2.57 37.17 2.39
2386 2427 6.664428 ATTACCCAACACAAACTAGCAATT 57.336 33.333 0.00 0.00 0.00 2.32
2398 2451 1.530323 AGACGCCAATTACCCAACAC 58.470 50.000 0.00 0.00 0.00 3.32
2419 2473 2.255770 AATATCTCCCCCTCCCGATC 57.744 55.000 0.00 0.00 0.00 3.69
2420 2474 2.552367 GAAATATCTCCCCCTCCCGAT 58.448 52.381 0.00 0.00 0.00 4.18
2423 2478 0.325272 GCGAAATATCTCCCCCTCCC 59.675 60.000 0.00 0.00 0.00 4.30
2426 2481 0.398318 GCAGCGAAATATCTCCCCCT 59.602 55.000 0.00 0.00 0.00 4.79
2430 2485 1.202698 ACAGGGCAGCGAAATATCTCC 60.203 52.381 0.00 0.00 0.00 3.71
2432 2487 1.486310 TCACAGGGCAGCGAAATATCT 59.514 47.619 0.00 0.00 0.00 1.98
2442 2497 2.360165 GGCAATTCTTATCACAGGGCAG 59.640 50.000 0.00 0.00 0.00 4.85
2447 2503 6.757897 TTACAAGGGCAATTCTTATCACAG 57.242 37.500 0.00 0.00 0.00 3.66
2448 2504 7.395772 TCATTTACAAGGGCAATTCTTATCACA 59.604 33.333 0.00 0.00 0.00 3.58
2456 2512 9.736023 CTTATTAGTCATTTACAAGGGCAATTC 57.264 33.333 0.00 0.00 0.00 2.17
2477 2533 8.704668 TGAGGTGATCACATATACACACTTATT 58.295 33.333 26.47 0.00 35.33 1.40
2478 2534 8.250143 TGAGGTGATCACATATACACACTTAT 57.750 34.615 26.47 0.00 35.33 1.73
2502 2558 0.108520 AGCATTTCCAAGCCGCAATG 60.109 50.000 0.00 0.00 0.00 2.82
2504 2560 1.473258 ATAGCATTTCCAAGCCGCAA 58.527 45.000 0.00 0.00 0.00 4.85
2508 2564 3.598299 TGCAAAATAGCATTTCCAAGCC 58.402 40.909 0.00 0.00 40.11 4.35
2538 2594 2.437359 CCAAGCGGCCTTCTCCAG 60.437 66.667 0.00 0.00 0.00 3.86
2550 2606 3.651480 GACATGTCACGCGCCAAGC 62.651 63.158 21.07 0.00 43.95 4.01
2551 2607 1.840630 TTGACATGTCACGCGCCAAG 61.841 55.000 27.88 0.00 39.66 3.61
2552 2608 1.840630 CTTGACATGTCACGCGCCAA 61.841 55.000 27.88 10.79 39.66 4.52
2553 2609 2.280457 TTGACATGTCACGCGCCA 60.280 55.556 27.88 9.82 39.66 5.69
2575 2638 4.448210 ACTTCTGCCTTCGTTTCAAACTA 58.552 39.130 0.00 0.00 0.00 2.24
2582 2658 2.876550 GGTACAACTTCTGCCTTCGTTT 59.123 45.455 0.00 0.00 0.00 3.60
2587 2663 4.104831 AGATAGGGTACAACTTCTGCCTT 58.895 43.478 0.00 0.00 0.00 4.35
2593 2669 9.444600 TTTGTTAATGAGATAGGGTACAACTTC 57.555 33.333 0.00 0.00 0.00 3.01
2606 2682 3.181487 GCGTGGGCATTTGTTAATGAGAT 60.181 43.478 2.25 0.00 43.12 2.75
2614 2690 1.165270 GTCTAGCGTGGGCATTTGTT 58.835 50.000 0.00 0.00 43.41 2.83
2618 2694 1.450312 GCTGTCTAGCGTGGGCATT 60.450 57.895 0.00 0.00 43.41 3.56
2637 2713 5.414454 TGCCTTTGTAGTATTCATGTTCCAC 59.586 40.000 0.00 0.00 0.00 4.02
2649 2725 4.018490 TGGTCGAGTATGCCTTTGTAGTA 58.982 43.478 0.00 0.00 0.00 1.82
2650 2726 2.829720 TGGTCGAGTATGCCTTTGTAGT 59.170 45.455 0.00 0.00 0.00 2.73
2651 2727 3.520290 TGGTCGAGTATGCCTTTGTAG 57.480 47.619 0.00 0.00 0.00 2.74
2652 2728 3.592059 GTTGGTCGAGTATGCCTTTGTA 58.408 45.455 0.00 0.00 0.00 2.41
2653 2729 2.423577 GTTGGTCGAGTATGCCTTTGT 58.576 47.619 0.00 0.00 0.00 2.83
2655 2731 1.628846 AGGTTGGTCGAGTATGCCTTT 59.371 47.619 0.00 0.00 0.00 3.11
2680 2758 5.629020 GGCTGTGTGTAATGTATTTGTTGTG 59.371 40.000 0.00 0.00 0.00 3.33
2694 2772 8.195436 GTGTATTTATCTTCTAGGCTGTGTGTA 58.805 37.037 0.00 0.00 0.00 2.90
2702 2780 4.628074 TGCGGTGTATTTATCTTCTAGGC 58.372 43.478 0.00 0.00 0.00 3.93
2705 2784 5.597182 ACCTCTGCGGTGTATTTATCTTCTA 59.403 40.000 0.00 0.00 46.80 2.10
2707 2786 4.694339 ACCTCTGCGGTGTATTTATCTTC 58.306 43.478 0.00 0.00 46.80 2.87
2731 2810 5.961843 CGAATTGACAATGAGACTTATGTGC 59.038 40.000 0.34 0.00 0.00 4.57
2732 2811 7.065216 ACGAATTGACAATGAGACTTATGTG 57.935 36.000 0.34 0.00 0.00 3.21
2733 2812 6.873605 TGACGAATTGACAATGAGACTTATGT 59.126 34.615 0.34 0.00 0.00 2.29
2734 2813 7.294676 TGACGAATTGACAATGAGACTTATG 57.705 36.000 0.34 0.00 0.00 1.90
2735 2814 7.765819 TGATGACGAATTGACAATGAGACTTAT 59.234 33.333 0.34 0.00 0.00 1.73
2736 2815 7.063426 GTGATGACGAATTGACAATGAGACTTA 59.937 37.037 0.34 0.00 0.00 2.24
2737 2816 5.934043 TGATGACGAATTGACAATGAGACTT 59.066 36.000 0.34 0.00 0.00 3.01
2738 2817 5.349817 GTGATGACGAATTGACAATGAGACT 59.650 40.000 0.34 0.00 0.00 3.24
2739 2818 5.446473 GGTGATGACGAATTGACAATGAGAC 60.446 44.000 0.34 0.73 0.00 3.36
2740 2819 4.631377 GGTGATGACGAATTGACAATGAGA 59.369 41.667 0.34 0.00 0.00 3.27
2741 2820 4.493057 CGGTGATGACGAATTGACAATGAG 60.493 45.833 0.34 1.73 0.00 2.90
2742 2821 3.370672 CGGTGATGACGAATTGACAATGA 59.629 43.478 0.34 0.00 0.00 2.57
2743 2822 3.673366 CGGTGATGACGAATTGACAATG 58.327 45.455 0.34 0.00 0.00 2.82
2744 2823 2.095853 GCGGTGATGACGAATTGACAAT 59.904 45.455 0.00 0.00 0.00 2.71
2745 2824 1.463056 GCGGTGATGACGAATTGACAA 59.537 47.619 0.00 0.00 0.00 3.18
2746 2825 1.075542 GCGGTGATGACGAATTGACA 58.924 50.000 0.00 0.00 0.00 3.58
2747 2826 1.324736 GAGCGGTGATGACGAATTGAC 59.675 52.381 0.00 0.00 0.00 3.18
2748 2827 1.204704 AGAGCGGTGATGACGAATTGA 59.795 47.619 0.00 0.00 0.00 2.57
2749 2828 1.645034 AGAGCGGTGATGACGAATTG 58.355 50.000 0.00 0.00 0.00 2.32
2750 2829 2.165641 TGTAGAGCGGTGATGACGAATT 59.834 45.455 0.00 0.00 0.00 2.17
2751 2830 1.749063 TGTAGAGCGGTGATGACGAAT 59.251 47.619 0.00 0.00 0.00 3.34
2752 2831 1.170442 TGTAGAGCGGTGATGACGAA 58.830 50.000 0.00 0.00 0.00 3.85
2790 2869 2.331132 GGAGGACTTCGTCGACGGT 61.331 63.158 35.05 26.25 40.29 4.83
2791 2870 2.484203 GGAGGACTTCGTCGACGG 59.516 66.667 35.05 23.24 40.29 4.79
2792 2871 1.859427 TTGGGAGGACTTCGTCGACG 61.859 60.000 31.30 31.30 41.45 5.12
2793 2872 0.388263 GTTGGGAGGACTTCGTCGAC 60.388 60.000 5.18 5.18 32.65 4.20
2794 2873 0.824595 TGTTGGGAGGACTTCGTCGA 60.825 55.000 0.00 0.00 32.65 4.20
2798 2888 1.806542 CATGTTGTTGGGAGGACTTCG 59.193 52.381 0.00 0.00 0.00 3.79
2803 2893 1.492599 TCACACATGTTGTTGGGAGGA 59.507 47.619 0.00 0.00 35.67 3.71
2812 2902 0.661187 GCGTGGCTTCACACATGTTG 60.661 55.000 0.00 0.00 41.38 3.33
2813 2903 0.819259 AGCGTGGCTTCACACATGTT 60.819 50.000 0.00 0.00 41.38 2.71
2814 2904 0.034756 TAGCGTGGCTTCACACATGT 59.965 50.000 0.00 0.00 41.38 3.21
2819 2919 0.320421 GACCTTAGCGTGGCTTCACA 60.320 55.000 0.00 0.00 41.27 3.58
2842 2942 2.277084 GCCGATGTGGACGACTATTTT 58.723 47.619 0.00 0.00 42.00 1.82
2859 2959 0.748005 ACCCATCTCATTTTCCGCCG 60.748 55.000 0.00 0.00 0.00 6.46
2863 2963 1.133025 CACGCACCCATCTCATTTTCC 59.867 52.381 0.00 0.00 0.00 3.13
2870 2970 1.434622 CTCATGCACGCACCCATCTC 61.435 60.000 0.00 0.00 0.00 2.75
2880 2980 0.587242 GCGCAACATACTCATGCACG 60.587 55.000 0.30 0.00 40.04 5.34
2885 2985 1.739466 CAACCTGCGCAACATACTCAT 59.261 47.619 13.05 0.00 0.00 2.90
2898 3001 1.080569 CCAACATTCCGCAACCTGC 60.081 57.895 0.00 0.00 40.69 4.85
2901 3004 0.893727 AGGTCCAACATTCCGCAACC 60.894 55.000 0.00 0.00 0.00 3.77
2905 3008 1.653151 GAGTAGGTCCAACATTCCGC 58.347 55.000 0.00 0.00 0.00 5.54
2948 3051 9.910267 TGATAGATGAGAATGATCCTTGAAAAA 57.090 29.630 0.00 0.00 24.06 1.94
2949 3052 9.910267 TTGATAGATGAGAATGATCCTTGAAAA 57.090 29.630 0.00 0.00 24.06 2.29
2969 3072 5.515797 TGAGATAACCTGGTCGTTGATAG 57.484 43.478 0.00 0.00 0.00 2.08
2972 3075 4.610605 TTTGAGATAACCTGGTCGTTGA 57.389 40.909 0.00 0.00 0.00 3.18
2976 3079 2.348666 CGCTTTTGAGATAACCTGGTCG 59.651 50.000 0.00 0.00 0.00 4.79
2983 3086 3.071479 TCACCCACGCTTTTGAGATAAC 58.929 45.455 0.00 0.00 0.00 1.89
2984 3087 3.410631 TCACCCACGCTTTTGAGATAA 57.589 42.857 0.00 0.00 0.00 1.75
2988 3091 2.099098 ACTTTTCACCCACGCTTTTGAG 59.901 45.455 0.00 0.00 0.00 3.02
2989 3092 2.096248 ACTTTTCACCCACGCTTTTGA 58.904 42.857 0.00 0.00 0.00 2.69
2991 3094 3.603158 AAACTTTTCACCCACGCTTTT 57.397 38.095 0.00 0.00 0.00 2.27
2993 3096 4.929819 AATAAACTTTTCACCCACGCTT 57.070 36.364 0.00 0.00 0.00 4.68
2994 3097 4.457949 CCTAATAAACTTTTCACCCACGCT 59.542 41.667 0.00 0.00 0.00 5.07
2997 3100 5.977489 AGCCTAATAAACTTTTCACCCAC 57.023 39.130 0.00 0.00 0.00 4.61
3014 3117 4.016444 CCTAAAGCCACATGAAAAGCCTA 58.984 43.478 0.00 0.00 0.00 3.93
3015 3118 2.827921 CCTAAAGCCACATGAAAAGCCT 59.172 45.455 0.00 0.00 0.00 4.58
3018 3121 4.142687 CCGTACCTAAAGCCACATGAAAAG 60.143 45.833 0.00 0.00 0.00 2.27
3022 3125 1.903860 ACCGTACCTAAAGCCACATGA 59.096 47.619 0.00 0.00 0.00 3.07
3023 3126 2.006888 CACCGTACCTAAAGCCACATG 58.993 52.381 0.00 0.00 0.00 3.21
3025 3128 0.320946 GCACCGTACCTAAAGCCACA 60.321 55.000 0.00 0.00 0.00 4.17
3028 3131 0.800631 GTTGCACCGTACCTAAAGCC 59.199 55.000 0.00 0.00 0.00 4.35
3031 3134 3.998341 GAGAATGTTGCACCGTACCTAAA 59.002 43.478 0.00 0.00 0.00 1.85
3042 3145 0.032815 TCGTCCGTGAGAATGTTGCA 59.967 50.000 0.00 0.00 0.00 4.08
3045 3148 1.359848 GCATCGTCCGTGAGAATGTT 58.640 50.000 0.00 0.00 0.00 2.71
3046 3149 0.802222 CGCATCGTCCGTGAGAATGT 60.802 55.000 0.00 0.00 0.00 2.71
3048 3151 0.108804 AACGCATCGTCCGTGAGAAT 60.109 50.000 0.00 0.00 39.99 2.40
3049 3152 0.522626 TAACGCATCGTCCGTGAGAA 59.477 50.000 0.00 0.00 39.99 2.87
3050 3153 0.736636 ATAACGCATCGTCCGTGAGA 59.263 50.000 0.00 0.00 39.99 3.27
3054 3157 0.387929 ATGGATAACGCATCGTCCGT 59.612 50.000 0.00 0.00 39.99 4.69
3058 3161 2.483876 CCTTCATGGATAACGCATCGT 58.516 47.619 0.00 0.00 39.18 3.73
3063 3166 2.568623 ATCCCCTTCATGGATAACGC 57.431 50.000 0.00 0.00 40.85 4.84
3064 3167 3.600388 GCTATCCCCTTCATGGATAACG 58.400 50.000 0.00 0.00 42.73 3.18
3066 3169 3.886938 AGGCTATCCCCTTCATGGATAA 58.113 45.455 0.00 0.00 42.73 1.75
3072 3175 2.373502 GCTACAAGGCTATCCCCTTCAT 59.626 50.000 0.00 0.00 43.23 2.57
3081 3184 2.579873 CCAAGCATGCTACAAGGCTAT 58.420 47.619 23.00 0.00 35.11 2.97
3082 3185 1.408683 CCCAAGCATGCTACAAGGCTA 60.409 52.381 23.00 0.00 35.11 3.93
3083 3186 0.682209 CCCAAGCATGCTACAAGGCT 60.682 55.000 23.00 0.00 38.45 4.58
3084 3187 1.811860 CCCAAGCATGCTACAAGGC 59.188 57.895 23.00 0.00 0.00 4.35
3085 3188 1.669999 GGCCCAAGCATGCTACAAGG 61.670 60.000 23.00 19.15 42.56 3.61
3101 3204 2.516225 GCGTACCAATGAGGGGCC 60.516 66.667 0.00 0.00 43.89 5.80
3102 3205 2.516225 GGCGTACCAATGAGGGGC 60.516 66.667 0.00 0.00 43.89 5.80
3106 3209 2.332063 ATCAAGGGCGTACCAATGAG 57.668 50.000 10.64 0.00 43.89 2.90
3107 3210 2.158871 GGTATCAAGGGCGTACCAATGA 60.159 50.000 8.42 8.42 43.89 2.57
3110 3213 1.065998 GTGGTATCAAGGGCGTACCAA 60.066 52.381 5.16 0.00 46.70 3.67
3111 3214 0.538118 GTGGTATCAAGGGCGTACCA 59.462 55.000 0.00 0.00 44.05 3.25
3113 3216 0.457035 TCGTGGTATCAAGGGCGTAC 59.543 55.000 0.00 0.00 0.00 3.67
3114 3217 0.742505 CTCGTGGTATCAAGGGCGTA 59.257 55.000 0.00 0.00 0.00 4.42
3116 3219 0.527817 GACTCGTGGTATCAAGGGCG 60.528 60.000 0.00 0.00 0.00 6.13
3136 3239 2.293318 TTGCATCCCTGAGCGAGGT 61.293 57.895 4.34 0.00 40.87 3.85
3141 3244 1.307097 GAGATGTTGCATCCCTGAGC 58.693 55.000 5.59 0.00 0.00 4.26
3144 3247 1.742761 AACGAGATGTTGCATCCCTG 58.257 50.000 5.59 0.00 40.00 4.45
3166 3269 3.047280 GAATCGTGTGCGGCACCA 61.047 61.111 28.57 14.84 44.97 4.17
3172 3275 1.640428 ACCATAGTGAATCGTGTGCG 58.360 50.000 0.00 0.00 39.92 5.34
3180 3283 6.166279 CGCATGATTACCTACCATAGTGAAT 58.834 40.000 0.00 0.00 0.00 2.57
3184 3287 3.578716 AGCGCATGATTACCTACCATAGT 59.421 43.478 11.47 0.00 0.00 2.12
3187 3290 2.610479 CGAGCGCATGATTACCTACCAT 60.610 50.000 11.47 0.00 0.00 3.55
3192 3295 0.877649 CAGCGAGCGCATGATTACCT 60.878 55.000 17.68 0.00 44.88 3.08
3193 3296 0.875908 TCAGCGAGCGCATGATTACC 60.876 55.000 17.68 0.00 44.88 2.85
3194 3297 0.506080 CTCAGCGAGCGCATGATTAC 59.494 55.000 17.68 0.00 44.88 1.89
3198 3301 1.807165 GAACTCAGCGAGCGCATGA 60.807 57.895 17.68 15.10 44.88 3.07
3204 3307 1.949847 TAGCCTGGAACTCAGCGAGC 61.950 60.000 0.00 0.00 42.05 5.03
3205 3308 0.749649 ATAGCCTGGAACTCAGCGAG 59.250 55.000 0.00 4.36 42.05 5.03
3208 3311 1.208052 TGACATAGCCTGGAACTCAGC 59.792 52.381 0.00 0.00 42.05 4.26
3210 3313 2.353704 CGTTGACATAGCCTGGAACTCA 60.354 50.000 0.00 0.00 0.00 3.41
3227 3330 4.858692 CCAATGTAGAAGAATTTGGCGTTG 59.141 41.667 0.00 0.00 31.29 4.10
3228 3331 4.522789 ACCAATGTAGAAGAATTTGGCGTT 59.477 37.500 0.00 0.00 40.37 4.84
3231 3334 5.391312 ACACCAATGTAGAAGAATTTGGC 57.609 39.130 0.00 0.00 40.37 4.52
3232 3335 9.357652 CAATTACACCAATGTAGAAGAATTTGG 57.642 33.333 0.00 0.00 42.29 3.28
3233 3336 8.863049 GCAATTACACCAATGTAGAAGAATTTG 58.137 33.333 0.00 0.00 42.29 2.32
3237 3340 5.703592 ACGCAATTACACCAATGTAGAAGAA 59.296 36.000 0.00 0.00 42.29 2.52
3239 3342 5.545658 ACGCAATTACACCAATGTAGAAG 57.454 39.130 0.00 0.00 42.29 2.85
3254 3362 2.852495 ATCGAGGCACCGACGCAATT 62.852 55.000 4.22 0.00 41.70 2.32
3262 3370 2.800544 CCTAACATAAATCGAGGCACCG 59.199 50.000 0.00 0.00 0.00 4.94
3265 3373 4.497291 AACCCTAACATAAATCGAGGCA 57.503 40.909 0.00 0.00 0.00 4.75
3271 3379 8.630037 CCAATGAACCTAACCCTAACATAAATC 58.370 37.037 0.00 0.00 0.00 2.17
3275 3383 6.894735 TCCAATGAACCTAACCCTAACATA 57.105 37.500 0.00 0.00 0.00 2.29
3279 3387 4.079443 CCCATCCAATGAACCTAACCCTAA 60.079 45.833 0.00 0.00 0.00 2.69
3291 3399 5.445069 CAACCTATTGTACCCATCCAATGA 58.555 41.667 0.00 0.00 33.54 2.57
3292 3400 4.584325 CCAACCTATTGTACCCATCCAATG 59.416 45.833 0.00 0.00 33.54 2.82
3293 3401 4.231890 ACCAACCTATTGTACCCATCCAAT 59.768 41.667 0.00 0.00 35.55 3.16
3295 3403 3.194620 ACCAACCTATTGTACCCATCCA 58.805 45.455 0.00 0.00 33.60 3.41
3298 3406 6.397217 AAAGTACCAACCTATTGTACCCAT 57.603 37.500 0.00 0.00 33.60 4.00
3299 3407 5.846528 AAAGTACCAACCTATTGTACCCA 57.153 39.130 0.00 0.00 33.60 4.51


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

AutoCloner maintained by Alex Coulton.