Multiple sequence alignment - TraesCS1A01G202300

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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 TraesCS1A01G202300 chr1A 100.000 4647 0 0 1 4647 363451366 363456012 0.000000e+00 8582.0
1 TraesCS1A01G202300 chr1D 92.890 2827 83 34 15 2787 291491168 291493930 0.000000e+00 3999.0
2 TraesCS1A01G202300 chr1D 97.260 1241 32 2 2844 4084 291493929 291495167 0.000000e+00 2102.0
3 TraesCS1A01G202300 chr1D 91.546 414 19 8 4126 4529 291503589 291503996 1.460000e-154 556.0
4 TraesCS1A01G202300 chr1B 92.004 2839 99 52 15 2787 392433644 392436420 0.000000e+00 3868.0
5 TraesCS1A01G202300 chr1B 97.300 1074 29 0 2985 4058 392436787 392437860 0.000000e+00 1823.0
6 TraesCS1A01G202300 chr1B 96.429 140 5 0 2844 2983 392436419 392436558 1.010000e-56 231.0
7 TraesCS1A01G202300 chr1B 90.533 169 8 4 4126 4287 392438235 392438402 2.820000e-52 217.0
8 TraesCS1A01G202300 chr1B 81.818 176 9 12 4430 4605 392438521 392438673 4.880000e-25 126.0
9 TraesCS1A01G202300 chr1B 93.056 72 0 3 2782 2851 656234056 656234124 2.960000e-17 100.0
10 TraesCS1A01G202300 chr1B 100.000 29 0 0 4099 4127 392438194 392438222 2.000000e-03 54.7
11 TraesCS1A01G202300 chr5B 92.593 81 2 3 2786 2862 370194767 370194687 3.800000e-21 113.0
12 TraesCS1A01G202300 chr5B 91.358 81 3 2 2786 2862 370239627 370239547 1.770000e-19 108.0
13 TraesCS1A01G202300 chr7B 96.774 62 1 1 2785 2845 699186066 699186005 8.230000e-18 102.0
14 TraesCS1A01G202300 chr2B 95.312 64 3 0 2782 2845 516729480 516729543 8.230000e-18 102.0
15 TraesCS1A01G202300 chr2B 95.238 63 1 1 2785 2845 321689903 321689841 1.060000e-16 99.0
16 TraesCS1A01G202300 chr6B 95.238 63 1 1 2786 2846 418818410 418818348 1.060000e-16 99.0
17 TraesCS1A01G202300 chr3B 86.667 90 7 4 2786 2870 69360937 69361026 1.380000e-15 95.3
18 TraesCS1A01G202300 chr2D 91.429 70 3 1 2782 2851 134642339 134642405 4.950000e-15 93.5
19 TraesCS1A01G202300 chr2A 87.671 73 8 1 2528 2599 763527375 763527447 2.980000e-12 84.2


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 TraesCS1A01G202300 chr1A 363451366 363456012 4646 False 8582.000000 8582 100.000 1 4647 1 chr1A.!!$F1 4646
1 TraesCS1A01G202300 chr1D 291491168 291495167 3999 False 3050.500000 3999 95.075 15 4084 2 chr1D.!!$F2 4069
2 TraesCS1A01G202300 chr1B 392433644 392438673 5029 False 1053.283333 3868 93.014 15 4605 6 chr1B.!!$F2 4590

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
601 626 0.034896 ATCGTTCTTGGTCGGCTGTT 59.965 50.0 0.0 0.0 0.0 3.16 F
867 902 0.181114 TCAATCTCCCAGCAATCCGG 59.819 55.0 0.0 0.0 0.0 5.14 F
2797 2886 0.258194 TCCTTCCTACTCCCTCCGTC 59.742 60.0 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
1954 2005 1.937108 GCACTCAAGAACCAGGAGACG 60.937 57.143 0.0 0.0 33.0 4.18 R
2823 2912 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.0 0.0 0.0 2.71 R
4396 5062 0.104120 CAACGAGTCACCAGTCACCA 59.896 55.000 0.0 0.0 0.0 4.17 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 6.442112 ACAAAGAAAAATCTAAGACAGCAGC 58.558 36.000 0.00 0.00 0.00 5.25
65 66 6.039717 ACAAAGAAAAATCTAAGACAGCAGCA 59.960 34.615 0.00 0.00 0.00 4.41
145 147 1.003233 GAAAGAAAGCGAGGGAAGGGA 59.997 52.381 0.00 0.00 0.00 4.20
296 303 4.101077 CAGCCCCCTCTCCCTCCT 62.101 72.222 0.00 0.00 0.00 3.69
297 304 3.773154 AGCCCCCTCTCCCTCCTC 61.773 72.222 0.00 0.00 0.00 3.71
298 305 4.095400 GCCCCCTCTCCCTCCTCA 62.095 72.222 0.00 0.00 0.00 3.86
299 306 2.041405 CCCCCTCTCCCTCCTCAC 60.041 72.222 0.00 0.00 0.00 3.51
300 307 2.041405 CCCCTCTCCCTCCTCACC 60.041 72.222 0.00 0.00 0.00 4.02
344 351 2.765807 CCACGAGCTCCTCCCCAT 60.766 66.667 8.47 0.00 0.00 4.00
498 515 1.524482 GGCACCTCCCTGATCTGAC 59.476 63.158 0.38 0.00 0.00 3.51
502 519 1.836166 CACCTCCCTGATCTGACATGT 59.164 52.381 0.00 0.00 0.00 3.21
540 557 1.127225 CTTCGGTTCGTTCGTTCGC 59.873 57.895 0.00 0.00 0.00 4.70
568 593 1.866496 CGGATTCGTCGTGGTCGTC 60.866 63.158 0.00 0.00 38.33 4.20
570 595 1.154338 GATTCGTCGTGGTCGTCGT 60.154 57.895 7.05 0.00 45.27 4.34
572 597 2.791396 ATTCGTCGTGGTCGTCGTGG 62.791 60.000 7.05 0.00 45.27 4.94
573 598 4.016629 CGTCGTGGTCGTCGTGGA 62.017 66.667 0.00 0.00 41.73 4.02
574 599 2.126965 GTCGTGGTCGTCGTGGAG 60.127 66.667 0.00 0.00 38.33 3.86
601 626 0.034896 ATCGTTCTTGGTCGGCTGTT 59.965 50.000 0.00 0.00 0.00 3.16
604 629 1.228124 TTCTTGGTCGGCTGTTGGG 60.228 57.895 0.00 0.00 0.00 4.12
605 630 2.672996 CTTGGTCGGCTGTTGGGG 60.673 66.667 0.00 0.00 0.00 4.96
606 631 4.966787 TTGGTCGGCTGTTGGGGC 62.967 66.667 0.00 0.00 0.00 5.80
609 634 4.643387 GTCGGCTGTTGGGGCAGT 62.643 66.667 0.00 0.00 38.65 4.40
610 635 4.641645 TCGGCTGTTGGGGCAGTG 62.642 66.667 0.00 0.00 38.65 3.66
626 651 1.153147 GTGCGGGAGGAGGGATTTC 60.153 63.158 0.00 0.00 0.00 2.17
628 653 0.914417 TGCGGGAGGAGGGATTTCTT 60.914 55.000 0.00 0.00 0.00 2.52
636 661 1.133216 GGAGGGATTTCTTTTGCTCGC 59.867 52.381 0.00 0.00 0.00 5.03
640 665 1.622232 GATTTCTTTTGCTCGCCTGC 58.378 50.000 0.00 0.00 0.00 4.85
757 791 8.677300 TCAATTCTTTCCTGTTATTGATGCTAC 58.323 33.333 0.00 0.00 32.10 3.58
759 793 5.116180 TCTTTCCTGTTATTGATGCTACGG 58.884 41.667 0.00 0.00 0.00 4.02
806 841 4.811024 AGATATTATTATCATGGCGGCGTG 59.189 41.667 24.24 24.24 37.31 5.34
820 855 1.153628 GCGTGATTGGTACGGCTCT 60.154 57.895 0.00 0.00 41.56 4.09
837 872 0.608130 TCTAATCATGGCCGATCGGG 59.392 55.000 33.98 18.22 39.58 5.14
849 884 0.528684 CGATCGGGAGGACTGCTTTC 60.529 60.000 7.38 0.00 0.00 2.62
856 891 2.637947 GGAGGACTGCTTTCAATCTCC 58.362 52.381 0.00 0.00 0.00 3.71
867 902 0.181114 TCAATCTCCCAGCAATCCGG 59.819 55.000 0.00 0.00 0.00 5.14
895 930 5.645067 TGTTCTTCGTCTCTAATCGTTCCTA 59.355 40.000 0.00 0.00 0.00 2.94
953 1004 8.912988 TCCTCAAATGATTTTGTTTCTTGTACT 58.087 29.630 0.00 0.00 42.37 2.73
954 1005 8.971321 CCTCAAATGATTTTGTTTCTTGTACTG 58.029 33.333 0.00 0.00 42.37 2.74
955 1006 9.520204 CTCAAATGATTTTGTTTCTTGTACTGT 57.480 29.630 0.00 0.00 42.37 3.55
956 1007 9.515020 TCAAATGATTTTGTTTCTTGTACTGTC 57.485 29.630 0.00 0.00 42.37 3.51
957 1008 9.520204 CAAATGATTTTGTTTCTTGTACTGTCT 57.480 29.630 0.00 0.00 37.92 3.41
958 1009 9.736023 AAATGATTTTGTTTCTTGTACTGTCTC 57.264 29.630 0.00 0.00 0.00 3.36
959 1010 8.682936 ATGATTTTGTTTCTTGTACTGTCTCT 57.317 30.769 0.00 0.00 0.00 3.10
960 1011 7.919690 TGATTTTGTTTCTTGTACTGTCTCTG 58.080 34.615 0.00 0.00 0.00 3.35
961 1012 7.768582 TGATTTTGTTTCTTGTACTGTCTCTGA 59.231 33.333 0.00 0.00 0.00 3.27
962 1013 8.682936 ATTTTGTTTCTTGTACTGTCTCTGAT 57.317 30.769 0.00 0.00 0.00 2.90
963 1014 7.715265 TTTGTTTCTTGTACTGTCTCTGATC 57.285 36.000 0.00 0.00 0.00 2.92
964 1015 6.405278 TGTTTCTTGTACTGTCTCTGATCA 57.595 37.500 0.00 0.00 0.00 2.92
965 1016 6.216569 TGTTTCTTGTACTGTCTCTGATCAC 58.783 40.000 0.00 0.00 0.00 3.06
966 1017 5.392767 TTCTTGTACTGTCTCTGATCACC 57.607 43.478 0.00 0.00 0.00 4.02
967 1018 4.407365 TCTTGTACTGTCTCTGATCACCA 58.593 43.478 0.00 0.00 0.00 4.17
968 1019 4.832823 TCTTGTACTGTCTCTGATCACCAA 59.167 41.667 0.00 0.00 0.00 3.67
969 1020 4.521130 TGTACTGTCTCTGATCACCAAC 57.479 45.455 0.00 0.00 0.00 3.77
970 1021 3.895041 TGTACTGTCTCTGATCACCAACA 59.105 43.478 0.00 0.00 0.00 3.33
971 1022 3.674528 ACTGTCTCTGATCACCAACAG 57.325 47.619 18.37 18.37 39.90 3.16
1014 1065 1.522355 CATCATGAGCGGAGGCGTT 60.522 57.895 0.09 0.00 46.35 4.84
1017 1068 2.125512 ATGAGCGGAGGCGTTGAC 60.126 61.111 0.00 0.00 46.35 3.18
1247 1298 2.998097 CAGGGCTTGGATTCGGGA 59.002 61.111 0.00 0.00 0.00 5.14
1285 1336 1.448540 CAGCAGACATCCGTCCCAC 60.449 63.158 0.00 0.00 43.73 4.61
1397 1448 2.171725 GCACCTCGGAATGCGTACC 61.172 63.158 0.00 0.00 30.97 3.34
1418 1469 3.480133 GCTATCCCTGCACCGGGT 61.480 66.667 6.32 0.00 44.95 5.28
1468 1519 2.413310 ACCATAAATTTCGCTCCGGT 57.587 45.000 0.00 0.00 0.00 5.28
1477 1528 3.691342 CGCTCCGGTGGTTCCTCA 61.691 66.667 0.00 0.00 0.00 3.86
1588 1639 2.684881 CCACCCATTCTGACTTATGTGC 59.315 50.000 0.00 0.00 0.00 4.57
1691 1742 6.826231 ACGTATGATGGTGGAAATGATTGTAA 59.174 34.615 0.00 0.00 0.00 2.41
1954 2005 0.670162 ACGCCTTGCATATGAATGGC 59.330 50.000 24.78 24.78 39.77 4.40
1991 2042 8.015087 TCTTGAGTGCAGTAATTATTCGTTTTG 58.985 33.333 0.00 0.00 0.00 2.44
1998 2049 5.416326 CAGTAATTATTCGTTTTGTGGGGGA 59.584 40.000 0.00 0.00 0.00 4.81
2024 2075 5.957910 TTTTTGTGGCATTTGACTTTACG 57.042 34.783 0.00 0.00 0.00 3.18
2045 2096 9.814507 TTTACGTAGCACAACTAATGTTTAATG 57.185 29.630 0.00 0.00 41.46 1.90
2215 2266 2.463620 GGCTGATCACGCGATTGCA 61.464 57.895 15.93 4.60 42.97 4.08
2369 2420 2.747446 ACCTGTCGAATGTTATTGCACC 59.253 45.455 0.00 0.00 0.00 5.01
2470 2539 7.565323 AACATGTGTTAAATGCCACAAAAAT 57.435 28.000 0.00 0.00 44.10 1.82
2640 2729 9.850628 CCATTCATTGTATAATATTGCAAGGAG 57.149 33.333 4.94 6.50 34.06 3.69
2787 2876 9.628500 AAATAATTGGACACTATTCCTTCCTAC 57.372 33.333 0.00 0.00 36.51 3.18
2788 2877 6.893020 AATTGGACACTATTCCTTCCTACT 57.107 37.500 0.00 0.00 36.51 2.57
2789 2878 5.934402 TTGGACACTATTCCTTCCTACTC 57.066 43.478 0.00 0.00 36.51 2.59
2790 2879 4.287552 TGGACACTATTCCTTCCTACTCC 58.712 47.826 0.00 0.00 36.51 3.85
2791 2880 3.642377 GGACACTATTCCTTCCTACTCCC 59.358 52.174 0.00 0.00 32.24 4.30
2792 2881 4.548669 GACACTATTCCTTCCTACTCCCT 58.451 47.826 0.00 0.00 0.00 4.20
2793 2882 4.548669 ACACTATTCCTTCCTACTCCCTC 58.451 47.826 0.00 0.00 0.00 4.30
2794 2883 3.898741 CACTATTCCTTCCTACTCCCTCC 59.101 52.174 0.00 0.00 0.00 4.30
2795 2884 2.089600 ATTCCTTCCTACTCCCTCCG 57.910 55.000 0.00 0.00 0.00 4.63
2796 2885 0.708802 TTCCTTCCTACTCCCTCCGT 59.291 55.000 0.00 0.00 0.00 4.69
2797 2886 0.258194 TCCTTCCTACTCCCTCCGTC 59.742 60.000 0.00 0.00 0.00 4.79
2798 2887 0.756070 CCTTCCTACTCCCTCCGTCC 60.756 65.000 0.00 0.00 0.00 4.79
2799 2888 0.756070 CTTCCTACTCCCTCCGTCCC 60.756 65.000 0.00 0.00 0.00 4.46
2800 2889 1.512201 TTCCTACTCCCTCCGTCCCA 61.512 60.000 0.00 0.00 0.00 4.37
2801 2890 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
2802 2891 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
2803 2892 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
2804 2893 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
2805 2894 3.245514 CCTACTCCCTCCGTCCCATAATA 60.246 52.174 0.00 0.00 0.00 0.98
2806 2895 2.890814 ACTCCCTCCGTCCCATAATAG 58.109 52.381 0.00 0.00 0.00 1.73
2807 2896 2.179424 ACTCCCTCCGTCCCATAATAGT 59.821 50.000 0.00 0.00 0.00 2.12
2808 2897 2.563179 CTCCCTCCGTCCCATAATAGTG 59.437 54.545 0.00 0.00 0.00 2.74
2809 2898 2.090943 TCCCTCCGTCCCATAATAGTGT 60.091 50.000 0.00 0.00 0.00 3.55
2810 2899 2.299297 CCCTCCGTCCCATAATAGTGTC 59.701 54.545 0.00 0.00 0.00 3.67
2811 2900 2.963101 CCTCCGTCCCATAATAGTGTCA 59.037 50.000 0.00 0.00 0.00 3.58
2812 2901 3.386726 CCTCCGTCCCATAATAGTGTCAA 59.613 47.826 0.00 0.00 0.00 3.18
2813 2902 4.141801 CCTCCGTCCCATAATAGTGTCAAA 60.142 45.833 0.00 0.00 0.00 2.69
2814 2903 5.423704 TCCGTCCCATAATAGTGTCAAAA 57.576 39.130 0.00 0.00 0.00 2.44
2815 2904 5.806818 TCCGTCCCATAATAGTGTCAAAAA 58.193 37.500 0.00 0.00 0.00 1.94
2837 2926 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2838 2927 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2839 2928 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2840 2929 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2841 2930 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2842 2931 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2917 3006 4.415596 TCACATTTATTGCTTCAACCCCT 58.584 39.130 0.00 0.00 0.00 4.79
3177 3493 4.441356 GCTGTCAAAAGATCACAAACCCAA 60.441 41.667 0.00 0.00 0.00 4.12
3241 3557 4.314740 AGTCTTCGATGGCTATCTCAAC 57.685 45.455 8.55 1.75 0.00 3.18
3292 3608 1.880027 GATTGGCACGTCAAAGGTTCT 59.120 47.619 0.00 0.00 0.00 3.01
3445 3761 0.178068 TACGGAAAGAGCTGATGGCC 59.822 55.000 0.00 0.00 43.05 5.36
3526 3842 0.388907 GCGACAACCTAACTGCGGTA 60.389 55.000 0.00 0.00 33.53 4.02
3580 3896 4.778213 AATTGAGATCCCAAGATTCCGA 57.222 40.909 0.00 0.00 30.90 4.55
3657 3973 0.043940 AATGCCTGACCTCCCTCTCT 59.956 55.000 0.00 0.00 0.00 3.10
3745 4061 2.306847 GAAAGTTTTGCCCAGGTCTCA 58.693 47.619 0.00 0.00 0.00 3.27
3760 4076 2.091222 GGTCTCACCACTATAGGTCCCT 60.091 54.545 4.43 0.00 40.77 4.20
3843 4159 3.146104 AGGCAATGCTCTGTTTGTACT 57.854 42.857 4.82 0.00 0.00 2.73
3943 4259 3.119602 GCTGATCAATTTTGCTCTGCTCA 60.120 43.478 14.74 0.00 41.75 4.26
3955 4271 4.793201 TGCTCTGCTCAGGAGTTATACTA 58.207 43.478 0.00 0.00 33.73 1.82
3999 4315 7.092083 CCCCTTATCCCTCAGATGATAAATGAT 60.092 40.741 0.00 0.00 36.33 2.45
4054 4370 8.864087 AGAAATGAACTTTTAATCCTTGCTCTT 58.136 29.630 0.00 0.00 0.00 2.85
4084 4647 7.992608 TGTATTGTCTGATGGTAGCATTGTAAT 59.007 33.333 9.14 11.71 0.00 1.89
4087 4650 7.087409 TGTCTGATGGTAGCATTGTAATTTG 57.913 36.000 9.14 0.00 0.00 2.32
4088 4651 6.095300 TGTCTGATGGTAGCATTGTAATTTGG 59.905 38.462 9.14 0.00 0.00 3.28
4090 4653 6.889177 TCTGATGGTAGCATTGTAATTTGGAA 59.111 34.615 9.14 0.00 0.00 3.53
4091 4654 6.862209 TGATGGTAGCATTGTAATTTGGAAC 58.138 36.000 9.14 0.00 0.00 3.62
4092 4655 5.303747 TGGTAGCATTGTAATTTGGAACG 57.696 39.130 0.00 0.00 0.00 3.95
4093 4656 4.156922 TGGTAGCATTGTAATTTGGAACGG 59.843 41.667 0.00 0.00 0.00 4.44
4095 4658 4.701956 AGCATTGTAATTTGGAACGGAG 57.298 40.909 0.00 0.00 0.00 4.63
4096 4659 3.443681 AGCATTGTAATTTGGAACGGAGG 59.556 43.478 0.00 0.00 0.00 4.30
4219 4842 4.332637 CCGCTTGTGTGGCTGCAC 62.333 66.667 0.50 5.96 37.01 4.57
4220 4843 3.585020 CGCTTGTGTGGCTGCACA 61.585 61.111 10.49 10.49 46.30 4.57
4231 4861 1.351012 GCTGCACAGCGATGATCAC 59.649 57.895 8.12 0.00 45.29 3.06
4260 4890 6.202762 CGACGAATTTGATCATTTCTGGGATA 59.797 38.462 13.84 0.00 0.00 2.59
4262 4892 7.707104 ACGAATTTGATCATTTCTGGGATAAC 58.293 34.615 13.84 0.00 0.00 1.89
4269 4899 8.066612 TGATCATTTCTGGGATAACTTTTTCC 57.933 34.615 0.00 0.00 0.00 3.13
4312 4978 9.416284 TGGAACTTTAAAACCATATAATCCCTC 57.584 33.333 4.88 0.00 0.00 4.30
4334 5000 3.594134 GTTCCATCTTGAGGTCTCACTG 58.406 50.000 0.00 0.00 39.66 3.66
4359 5025 2.292267 CAGTGTTGCAGAAGTCCACTT 58.708 47.619 0.00 0.00 39.23 3.16
4361 5027 3.129287 CAGTGTTGCAGAAGTCCACTTTT 59.871 43.478 0.00 0.00 36.11 2.27
4389 5055 2.356665 TGCTTAGTGGCAAAGGTCAA 57.643 45.000 0.00 0.00 39.43 3.18
4390 5056 1.953686 TGCTTAGTGGCAAAGGTCAAC 59.046 47.619 0.00 0.00 39.43 3.18
4391 5057 1.953686 GCTTAGTGGCAAAGGTCAACA 59.046 47.619 0.00 0.00 0.00 3.33
4392 5058 2.360801 GCTTAGTGGCAAAGGTCAACAA 59.639 45.455 0.00 0.00 0.00 2.83
4393 5059 3.795488 GCTTAGTGGCAAAGGTCAACAAC 60.795 47.826 0.00 0.00 0.00 3.32
4394 5060 2.143876 AGTGGCAAAGGTCAACAACT 57.856 45.000 0.00 0.00 0.00 3.16
4395 5061 2.024414 AGTGGCAAAGGTCAACAACTC 58.976 47.619 0.00 0.00 0.00 3.01
4396 5062 2.024414 GTGGCAAAGGTCAACAACTCT 58.976 47.619 0.00 0.00 0.00 3.24
4397 5063 2.023673 TGGCAAAGGTCAACAACTCTG 58.976 47.619 0.00 0.00 0.00 3.35
4398 5064 1.338020 GGCAAAGGTCAACAACTCTGG 59.662 52.381 0.00 0.00 0.00 3.86
4399 5065 2.024414 GCAAAGGTCAACAACTCTGGT 58.976 47.619 0.00 0.00 0.00 4.00
4400 5066 2.223572 GCAAAGGTCAACAACTCTGGTG 60.224 50.000 0.00 0.00 42.08 4.17
4405 5071 2.620251 TCAACAACTCTGGTGACTGG 57.380 50.000 0.00 0.00 44.56 4.00
4406 5072 1.837439 TCAACAACTCTGGTGACTGGT 59.163 47.619 0.00 0.00 44.56 4.00
4407 5073 1.942657 CAACAACTCTGGTGACTGGTG 59.057 52.381 0.00 0.00 43.55 4.17
4408 5074 1.496060 ACAACTCTGGTGACTGGTGA 58.504 50.000 0.00 0.00 0.00 4.02
4409 5075 1.139058 ACAACTCTGGTGACTGGTGAC 59.861 52.381 0.00 0.00 0.00 3.67
4410 5076 1.414181 CAACTCTGGTGACTGGTGACT 59.586 52.381 0.00 0.00 0.00 3.41
4411 5077 1.333177 ACTCTGGTGACTGGTGACTC 58.667 55.000 0.00 0.00 0.00 3.36
4412 5078 0.242286 CTCTGGTGACTGGTGACTCG 59.758 60.000 0.00 0.00 0.00 4.18
4413 5079 0.467474 TCTGGTGACTGGTGACTCGT 60.467 55.000 0.00 0.00 0.00 4.18
4414 5080 0.389391 CTGGTGACTGGTGACTCGTT 59.611 55.000 0.00 0.00 0.00 3.85
4415 5081 0.104120 TGGTGACTGGTGACTCGTTG 59.896 55.000 0.00 0.00 0.00 4.10
4416 5082 0.600255 GGTGACTGGTGACTCGTTGG 60.600 60.000 0.00 0.00 0.00 3.77
4417 5083 0.600255 GTGACTGGTGACTCGTTGGG 60.600 60.000 0.00 0.00 0.00 4.12
4418 5084 1.004918 GACTGGTGACTCGTTGGGG 60.005 63.158 0.00 0.00 0.00 4.96
4419 5085 1.755393 GACTGGTGACTCGTTGGGGT 61.755 60.000 0.00 0.00 0.00 4.95
4420 5086 1.342672 ACTGGTGACTCGTTGGGGTT 61.343 55.000 0.00 0.00 0.00 4.11
4421 5087 0.884704 CTGGTGACTCGTTGGGGTTG 60.885 60.000 0.00 0.00 0.00 3.77
4422 5088 1.338890 TGGTGACTCGTTGGGGTTGA 61.339 55.000 0.00 0.00 0.00 3.18
4423 5089 0.179040 GGTGACTCGTTGGGGTTGAA 60.179 55.000 0.00 0.00 0.00 2.69
4424 5090 1.226746 GTGACTCGTTGGGGTTGAAG 58.773 55.000 0.00 0.00 0.00 3.02
4425 5091 0.107831 TGACTCGTTGGGGTTGAAGG 59.892 55.000 0.00 0.00 0.00 3.46
4426 5092 0.605589 GACTCGTTGGGGTTGAAGGG 60.606 60.000 0.00 0.00 0.00 3.95
4427 5093 1.350310 ACTCGTTGGGGTTGAAGGGT 61.350 55.000 0.00 0.00 0.00 4.34
4428 5094 0.605589 CTCGTTGGGGTTGAAGGGTC 60.606 60.000 0.00 0.00 0.00 4.46
4453 5119 3.907894 TTGGGTGCTCGTTTACATTTC 57.092 42.857 0.00 0.00 0.00 2.17
4458 5124 4.156008 GGGTGCTCGTTTACATTTCAGAAT 59.844 41.667 0.00 0.00 0.00 2.40
4514 5180 7.676947 AGAATCGGAATAAGGGATCGAATTTA 58.323 34.615 0.00 0.00 33.53 1.40
4515 5181 8.322091 AGAATCGGAATAAGGGATCGAATTTAT 58.678 33.333 0.00 0.00 33.53 1.40
4516 5182 8.494016 AATCGGAATAAGGGATCGAATTTATC 57.506 34.615 0.00 0.00 33.53 1.75
4517 5183 6.403878 TCGGAATAAGGGATCGAATTTATCC 58.596 40.000 10.81 10.81 41.96 2.59
4518 5184 6.212791 TCGGAATAAGGGATCGAATTTATCCT 59.787 38.462 16.25 4.95 42.27 3.24
4520 5186 7.148407 CGGAATAAGGGATCGAATTTATCCTTG 60.148 40.741 16.25 0.00 42.27 3.61
4521 5187 7.665974 GGAATAAGGGATCGAATTTATCCTTGT 59.334 37.037 16.25 5.89 42.27 3.16
4522 5188 9.720769 GAATAAGGGATCGAATTTATCCTTGTA 57.279 33.333 16.25 9.27 42.27 2.41
4523 5189 9.503399 AATAAGGGATCGAATTTATCCTTGTAC 57.497 33.333 16.25 0.00 42.27 2.90
4524 5190 6.749036 AGGGATCGAATTTATCCTTGTACT 57.251 37.500 16.25 5.99 42.27 2.73
4525 5191 6.760291 AGGGATCGAATTTATCCTTGTACTC 58.240 40.000 16.25 3.28 42.27 2.59
4526 5192 5.932883 GGGATCGAATTTATCCTTGTACTCC 59.067 44.000 16.25 0.00 42.27 3.85
4527 5193 6.239629 GGGATCGAATTTATCCTTGTACTCCT 60.240 42.308 16.25 0.00 42.27 3.69
4528 5194 7.217906 GGATCGAATTTATCCTTGTACTCCTT 58.782 38.462 11.65 0.00 39.93 3.36
4529 5195 7.715686 GGATCGAATTTATCCTTGTACTCCTTT 59.284 37.037 11.65 0.00 39.93 3.11
4530 5196 7.843490 TCGAATTTATCCTTGTACTCCTTTG 57.157 36.000 0.00 0.00 0.00 2.77
4531 5197 7.391620 TCGAATTTATCCTTGTACTCCTTTGT 58.608 34.615 0.00 0.00 0.00 2.83
4532 5198 8.533657 TCGAATTTATCCTTGTACTCCTTTGTA 58.466 33.333 0.00 0.00 0.00 2.41
4533 5199 8.601476 CGAATTTATCCTTGTACTCCTTTGTAC 58.399 37.037 0.00 0.00 42.10 2.90
4534 5200 8.803397 AATTTATCCTTGTACTCCTTTGTACC 57.197 34.615 0.00 0.00 41.34 3.34
4535 5201 4.838904 ATCCTTGTACTCCTTTGTACCC 57.161 45.455 0.00 0.00 41.34 3.69
4536 5202 3.589641 TCCTTGTACTCCTTTGTACCCA 58.410 45.455 0.00 0.00 41.34 4.51
4537 5203 3.975312 TCCTTGTACTCCTTTGTACCCAA 59.025 43.478 0.00 0.00 41.34 4.12
4538 5204 4.041198 TCCTTGTACTCCTTTGTACCCAAG 59.959 45.833 0.00 0.00 41.34 3.61
4566 5232 2.094675 CTCGATTGGAACATGGGCTTT 58.905 47.619 0.00 0.00 39.30 3.51
4590 5256 3.594134 CTGACCAGATTCTTCACACCTC 58.406 50.000 0.00 0.00 0.00 3.85
4605 5271 0.972883 ACCTCAAGTGCAGACTCTCC 59.027 55.000 0.00 0.00 0.00 3.71
4606 5272 0.248843 CCTCAAGTGCAGACTCTCCC 59.751 60.000 0.00 0.00 0.00 4.30
4607 5273 0.248843 CTCAAGTGCAGACTCTCCCC 59.751 60.000 0.00 0.00 0.00 4.81
4608 5274 0.178921 TCAAGTGCAGACTCTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
4609 5275 0.248843 CAAGTGCAGACTCTCCCCTC 59.751 60.000 0.00 0.00 0.00 4.30
4610 5276 0.907230 AAGTGCAGACTCTCCCCTCC 60.907 60.000 0.00 0.00 0.00 4.30
4611 5277 1.305718 GTGCAGACTCTCCCCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
4612 5278 0.033011 GTGCAGACTCTCCCCTCCTA 60.033 60.000 0.00 0.00 0.00 2.94
4613 5279 0.937441 TGCAGACTCTCCCCTCCTAT 59.063 55.000 0.00 0.00 0.00 2.57
4614 5280 1.292242 TGCAGACTCTCCCCTCCTATT 59.708 52.381 0.00 0.00 0.00 1.73
4615 5281 2.518407 TGCAGACTCTCCCCTCCTATTA 59.482 50.000 0.00 0.00 0.00 0.98
4616 5282 3.161866 GCAGACTCTCCCCTCCTATTAG 58.838 54.545 0.00 0.00 0.00 1.73
4617 5283 3.773560 CAGACTCTCCCCTCCTATTAGG 58.226 54.545 3.07 3.07 36.46 2.69
4629 5295 5.742063 CCTCCTATTAGGGTTTCGTTTTCT 58.258 41.667 9.88 0.00 35.59 2.52
4630 5296 5.816258 CCTCCTATTAGGGTTTCGTTTTCTC 59.184 44.000 9.88 0.00 35.59 2.87
4631 5297 6.351966 CCTCCTATTAGGGTTTCGTTTTCTCT 60.352 42.308 9.88 0.00 35.59 3.10
4632 5298 7.012661 TCCTATTAGGGTTTCGTTTTCTCTT 57.987 36.000 9.88 0.00 35.59 2.85
4633 5299 6.877322 TCCTATTAGGGTTTCGTTTTCTCTTG 59.123 38.462 9.88 0.00 35.59 3.02
4634 5300 5.959618 ATTAGGGTTTCGTTTTCTCTTGG 57.040 39.130 0.00 0.00 0.00 3.61
4635 5301 1.954382 AGGGTTTCGTTTTCTCTTGGC 59.046 47.619 0.00 0.00 0.00 4.52
4636 5302 1.334689 GGGTTTCGTTTTCTCTTGGCG 60.335 52.381 0.00 0.00 0.00 5.69
4637 5303 1.600485 GGTTTCGTTTTCTCTTGGCGA 59.400 47.619 0.00 0.00 0.00 5.54
4638 5304 2.601504 GGTTTCGTTTTCTCTTGGCGAC 60.602 50.000 0.00 0.00 0.00 5.19
4639 5305 2.234300 TTCGTTTTCTCTTGGCGACT 57.766 45.000 0.00 0.00 0.00 4.18
4640 5306 1.779569 TCGTTTTCTCTTGGCGACTC 58.220 50.000 0.00 0.00 0.00 3.36
4641 5307 1.340248 TCGTTTTCTCTTGGCGACTCT 59.660 47.619 0.00 0.00 0.00 3.24
4642 5308 1.721926 CGTTTTCTCTTGGCGACTCTC 59.278 52.381 0.00 0.00 0.00 3.20
4643 5309 2.070028 GTTTTCTCTTGGCGACTCTCC 58.930 52.381 0.00 0.00 0.00 3.71
4644 5310 0.243907 TTTCTCTTGGCGACTCTCCG 59.756 55.000 0.00 0.00 0.00 4.63
4645 5311 0.608308 TTCTCTTGGCGACTCTCCGA 60.608 55.000 0.00 0.00 0.00 4.55
4646 5312 1.027255 TCTCTTGGCGACTCTCCGAG 61.027 60.000 0.00 0.00 36.61 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.092846 ACTGCTTCTTATCTATACCAACCAGTT 60.093 37.037 0.00 0.00 0.00 3.16
1 2 6.384305 ACTGCTTCTTATCTATACCAACCAGT 59.616 38.462 0.00 0.00 0.00 4.00
2 3 6.703607 CACTGCTTCTTATCTATACCAACCAG 59.296 42.308 0.00 0.00 0.00 4.00
3 4 6.408092 CCACTGCTTCTTATCTATACCAACCA 60.408 42.308 0.00 0.00 0.00 3.67
4 5 5.992217 CCACTGCTTCTTATCTATACCAACC 59.008 44.000 0.00 0.00 0.00 3.77
5 6 6.480320 CACCACTGCTTCTTATCTATACCAAC 59.520 42.308 0.00 0.00 0.00 3.77
6 7 6.408092 CCACCACTGCTTCTTATCTATACCAA 60.408 42.308 0.00 0.00 0.00 3.67
7 8 5.070446 CCACCACTGCTTCTTATCTATACCA 59.930 44.000 0.00 0.00 0.00 3.25
8 9 5.542779 CCACCACTGCTTCTTATCTATACC 58.457 45.833 0.00 0.00 0.00 2.73
9 10 4.991687 GCCACCACTGCTTCTTATCTATAC 59.008 45.833 0.00 0.00 0.00 1.47
10 11 4.653801 TGCCACCACTGCTTCTTATCTATA 59.346 41.667 0.00 0.00 0.00 1.31
11 12 3.455910 TGCCACCACTGCTTCTTATCTAT 59.544 43.478 0.00 0.00 0.00 1.98
12 13 2.837591 TGCCACCACTGCTTCTTATCTA 59.162 45.455 0.00 0.00 0.00 1.98
13 14 1.630369 TGCCACCACTGCTTCTTATCT 59.370 47.619 0.00 0.00 0.00 1.98
64 65 0.539669 ACCTTTTCGCCCCTTTCCTG 60.540 55.000 0.00 0.00 0.00 3.86
65 66 0.251209 GACCTTTTCGCCCCTTTCCT 60.251 55.000 0.00 0.00 0.00 3.36
341 348 2.187946 GCAGGAGGTCGTGGATGG 59.812 66.667 2.11 0.00 32.80 3.51
343 350 2.982130 GTGCAGGAGGTCGTGGAT 59.018 61.111 0.00 0.00 34.79 3.41
344 351 3.680786 CGTGCAGGAGGTCGTGGA 61.681 66.667 0.00 0.00 32.80 4.02
427 440 1.962321 GAGAAGGGAGAAGGGCCGTC 61.962 65.000 11.87 11.87 0.00 4.79
430 443 2.736826 CGGAGAAGGGAGAAGGGCC 61.737 68.421 0.00 0.00 0.00 5.80
432 445 1.306226 ACCGGAGAAGGGAGAAGGG 60.306 63.158 9.46 0.00 35.02 3.95
433 446 1.617947 CCACCGGAGAAGGGAGAAGG 61.618 65.000 9.46 0.00 35.02 3.46
434 447 0.905337 ACCACCGGAGAAGGGAGAAG 60.905 60.000 9.46 0.00 35.02 2.85
435 448 1.157751 ACCACCGGAGAAGGGAGAA 59.842 57.895 9.46 0.00 35.02 2.87
436 449 1.609501 CACCACCGGAGAAGGGAGA 60.610 63.158 9.46 0.00 35.02 3.71
437 450 1.608717 CTCACCACCGGAGAAGGGAG 61.609 65.000 9.46 5.49 34.24 4.30
438 451 1.609501 CTCACCACCGGAGAAGGGA 60.610 63.158 9.46 0.00 34.24 4.20
498 515 0.036952 AGAGTTGCGGACAGGACATG 60.037 55.000 0.00 0.00 0.00 3.21
502 519 2.343758 GCAGAGTTGCGGACAGGA 59.656 61.111 0.00 0.00 41.13 3.86
561 586 0.109458 CGATTTCTCCACGACGACCA 60.109 55.000 0.00 0.00 0.00 4.02
568 593 1.852895 GAACGATCCGATTTCTCCACG 59.147 52.381 0.00 0.00 0.00 4.94
570 595 3.521560 CAAGAACGATCCGATTTCTCCA 58.478 45.455 0.00 0.00 0.00 3.86
572 597 3.522553 ACCAAGAACGATCCGATTTCTC 58.477 45.455 0.00 0.00 0.00 2.87
573 598 3.522553 GACCAAGAACGATCCGATTTCT 58.477 45.455 0.00 0.00 0.00 2.52
574 599 2.281762 CGACCAAGAACGATCCGATTTC 59.718 50.000 0.00 0.00 0.00 2.17
606 631 1.915078 AAATCCCTCCTCCCGCACTG 61.915 60.000 0.00 0.00 0.00 3.66
607 632 1.616628 AAATCCCTCCTCCCGCACT 60.617 57.895 0.00 0.00 0.00 4.40
608 633 1.153147 GAAATCCCTCCTCCCGCAC 60.153 63.158 0.00 0.00 0.00 5.34
609 634 0.914417 AAGAAATCCCTCCTCCCGCA 60.914 55.000 0.00 0.00 0.00 5.69
610 635 0.256177 AAAGAAATCCCTCCTCCCGC 59.744 55.000 0.00 0.00 0.00 6.13
611 636 2.369394 CAAAAGAAATCCCTCCTCCCG 58.631 52.381 0.00 0.00 0.00 5.14
806 841 3.997021 CCATGATTAGAGCCGTACCAATC 59.003 47.826 0.00 0.00 0.00 2.67
820 855 0.608130 CTCCCGATCGGCCATGATTA 59.392 55.000 29.12 4.79 0.00 1.75
837 872 2.026822 TGGGAGATTGAAAGCAGTCCTC 60.027 50.000 0.00 0.00 31.65 3.71
849 884 0.181114 TCCGGATTGCTGGGAGATTG 59.819 55.000 0.00 0.00 41.20 2.67
856 891 2.094675 AGAACATTTCCGGATTGCTGG 58.905 47.619 4.15 0.00 42.30 4.85
867 902 6.872670 ACGATTAGAGACGAAGAACATTTC 57.127 37.500 0.00 0.00 0.00 2.17
895 930 3.239861 CTTTCCGCTCCTGAAAGCT 57.760 52.632 0.00 0.00 41.41 3.74
953 1004 3.387699 TGTTCTGTTGGTGATCAGAGACA 59.612 43.478 0.00 0.05 40.91 3.41
954 1005 3.993081 CTGTTCTGTTGGTGATCAGAGAC 59.007 47.826 0.00 0.00 40.91 3.36
955 1006 3.897505 TCTGTTCTGTTGGTGATCAGAGA 59.102 43.478 0.00 0.00 40.91 3.10
956 1007 4.244066 CTCTGTTCTGTTGGTGATCAGAG 58.756 47.826 13.74 13.74 44.62 3.35
957 1008 3.643320 ACTCTGTTCTGTTGGTGATCAGA 59.357 43.478 0.00 0.00 37.71 3.27
958 1009 4.000331 ACTCTGTTCTGTTGGTGATCAG 58.000 45.455 0.00 0.00 34.39 2.90
959 1010 4.561530 GCTACTCTGTTCTGTTGGTGATCA 60.562 45.833 0.00 0.00 0.00 2.92
960 1011 3.929610 GCTACTCTGTTCTGTTGGTGATC 59.070 47.826 0.00 0.00 0.00 2.92
961 1012 3.307059 GGCTACTCTGTTCTGTTGGTGAT 60.307 47.826 0.00 0.00 0.00 3.06
962 1013 2.037251 GGCTACTCTGTTCTGTTGGTGA 59.963 50.000 0.00 0.00 0.00 4.02
963 1014 2.224281 TGGCTACTCTGTTCTGTTGGTG 60.224 50.000 0.00 0.00 0.00 4.17
964 1015 2.047061 TGGCTACTCTGTTCTGTTGGT 58.953 47.619 0.00 0.00 0.00 3.67
965 1016 2.839486 TGGCTACTCTGTTCTGTTGG 57.161 50.000 0.00 0.00 0.00 3.77
966 1017 3.993081 CTCTTGGCTACTCTGTTCTGTTG 59.007 47.826 0.00 0.00 0.00 3.33
967 1018 3.556004 GCTCTTGGCTACTCTGTTCTGTT 60.556 47.826 0.00 0.00 38.06 3.16
968 1019 2.028567 GCTCTTGGCTACTCTGTTCTGT 60.029 50.000 0.00 0.00 38.06 3.41
969 1020 2.615869 GCTCTTGGCTACTCTGTTCTG 58.384 52.381 0.00 0.00 38.06 3.02
970 1021 1.552792 GGCTCTTGGCTACTCTGTTCT 59.447 52.381 0.00 0.00 41.46 3.01
971 1022 1.406205 GGGCTCTTGGCTACTCTGTTC 60.406 57.143 0.00 0.00 41.46 3.18
1247 1298 2.369860 TGGTGAGATCAAGCTCAGTGTT 59.630 45.455 0.00 0.00 44.92 3.32
1285 1336 2.269241 GGAAGACCGGCAGGAAGG 59.731 66.667 10.86 0.00 41.02 3.46
1393 1444 1.054406 TGCAGGGATAGCAGGGGTAC 61.054 60.000 0.00 0.00 37.02 3.34
1397 1448 2.512896 GGTGCAGGGATAGCAGGG 59.487 66.667 0.00 0.00 43.63 4.45
1418 1469 2.290896 CCAACTCACCCCATAGAAAGCA 60.291 50.000 0.00 0.00 0.00 3.91
1468 1519 2.158813 GGACAAGAACAGTGAGGAACCA 60.159 50.000 0.00 0.00 0.00 3.67
1691 1742 4.009675 ACGCAATCATTCAACCACAGTAT 58.990 39.130 0.00 0.00 0.00 2.12
1694 1745 2.981805 CAACGCAATCATTCAACCACAG 59.018 45.455 0.00 0.00 0.00 3.66
1954 2005 1.937108 GCACTCAAGAACCAGGAGACG 60.937 57.143 0.00 0.00 33.00 4.18
2215 2266 2.420687 GCGGTCAAGAGAATGGGAATCT 60.421 50.000 0.00 0.00 0.00 2.40
2355 2406 2.031870 GGAGGGGGTGCAATAACATTC 58.968 52.381 0.00 0.00 0.00 2.67
2470 2539 8.968242 CATTCGACGACAAATCTGAAGATATAA 58.032 33.333 0.00 0.00 33.73 0.98
2479 2548 4.910746 ACTTCATTCGACGACAAATCTG 57.089 40.909 0.00 0.00 0.00 2.90
2640 2729 8.245701 TGTCAACAAACTGGTTTTGATTTAAC 57.754 30.769 3.81 0.00 46.76 2.01
2648 2737 8.527810 TCTTTTCTATGTCAACAAACTGGTTTT 58.472 29.630 0.00 0.00 0.00 2.43
2652 2741 8.190784 AGTTTCTTTTCTATGTCAACAAACTGG 58.809 33.333 0.00 0.00 31.89 4.00
2786 2875 2.179424 ACTATTATGGGACGGAGGGAGT 59.821 50.000 0.00 0.00 0.00 3.85
2787 2876 2.563179 CACTATTATGGGACGGAGGGAG 59.437 54.545 0.00 0.00 0.00 4.30
2788 2877 2.090943 ACACTATTATGGGACGGAGGGA 60.091 50.000 0.00 0.00 0.00 4.20
2789 2878 2.299297 GACACTATTATGGGACGGAGGG 59.701 54.545 0.00 0.00 0.00 4.30
2790 2879 2.963101 TGACACTATTATGGGACGGAGG 59.037 50.000 0.00 0.00 0.00 4.30
2791 2880 4.665833 TTGACACTATTATGGGACGGAG 57.334 45.455 0.00 0.00 0.00 4.63
2792 2881 5.423704 TTTTGACACTATTATGGGACGGA 57.576 39.130 0.00 0.00 0.00 4.69
2812 2901 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
2813 2902 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
2814 2903 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
2815 2904 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
2816 2905 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2818 2907 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2819 2908 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2820 2909 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2821 2910 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2822 2911 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2823 2912 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2824 2913 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2825 2914 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
2826 2915 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
2827 2916 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
2828 2917 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
2829 2918 1.961133 AAAATACTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
2830 2919 2.237893 TCAAAAATACTCCCTCCGTCCC 59.762 50.000 0.00 0.00 0.00 4.46
2831 2920 3.622166 TCAAAAATACTCCCTCCGTCC 57.378 47.619 0.00 0.00 0.00 4.79
2832 2921 6.510879 AATTTCAAAAATACTCCCTCCGTC 57.489 37.500 0.00 0.00 0.00 4.79
2833 2922 9.338622 CTATAATTTCAAAAATACTCCCTCCGT 57.661 33.333 0.00 0.00 0.00 4.69
2834 2923 9.555727 TCTATAATTTCAAAAATACTCCCTCCG 57.444 33.333 0.00 0.00 0.00 4.63
2837 2926 9.355916 GCCTCTATAATTTCAAAAATACTCCCT 57.644 33.333 0.00 0.00 0.00 4.20
2838 2927 9.355916 AGCCTCTATAATTTCAAAAATACTCCC 57.644 33.333 0.00 0.00 0.00 4.30
2917 3006 4.062293 CCTTGTGTTCGGTTGAGACATTA 58.938 43.478 0.00 0.00 0.00 1.90
2983 3072 7.956328 TCTACTCTGGTAATGTGTCAACTAT 57.044 36.000 0.00 0.00 0.00 2.12
3177 3493 2.877168 CTGAGCTTTTCACTCTTGCAGT 59.123 45.455 0.00 0.00 35.12 4.40
3445 3761 0.321298 ACCTTTCCGGATCGTTGTGG 60.321 55.000 4.15 2.69 36.31 4.17
3526 3842 3.594134 GTCTGCTGAGAAGCATACAACT 58.406 45.455 10.33 0.00 44.47 3.16
3580 3896 4.885907 TCCATCGAAATACTTCTCCGTACT 59.114 41.667 0.00 0.00 0.00 2.73
3657 3973 2.093658 GCGAGGGAGGAAGACATGTTTA 60.094 50.000 0.00 0.00 0.00 2.01
3745 4061 3.726837 ATTCCAGGGACCTATAGTGGT 57.273 47.619 6.30 0.00 44.10 4.16
3760 4076 8.862325 AACATGATTCTACACAACTTATTCCA 57.138 30.769 0.00 0.00 0.00 3.53
3843 4159 1.271108 TGGACAATCAAACGCTAGCCA 60.271 47.619 9.66 0.00 0.00 4.75
3888 4204 8.918202 ACTGTCATTTGTACCAGAATAAGAAA 57.082 30.769 2.13 0.00 0.00 2.52
3955 4271 6.910259 AAGGGGGAGTTCATAATTTAGACT 57.090 37.500 0.00 0.00 0.00 3.24
3973 4289 6.216251 TCATTTATCATCTGAGGGATAAGGGG 59.784 42.308 11.81 7.96 37.31 4.79
3999 4315 8.355169 GTCAGGTTTACCAACGTAGATATGATA 58.645 37.037 1.13 0.00 38.89 2.15
4007 4323 4.022589 TCTCTGTCAGGTTTACCAACGTAG 60.023 45.833 0.00 1.86 38.89 3.51
4015 4331 7.497925 AAGTTCATTTCTCTGTCAGGTTTAC 57.502 36.000 0.00 0.00 0.00 2.01
4054 4370 8.839343 CAATGCTACCATCAGACAATACAATAA 58.161 33.333 0.00 0.00 0.00 1.40
4058 4621 5.744171 ACAATGCTACCATCAGACAATACA 58.256 37.500 0.00 0.00 0.00 2.29
4064 4627 6.318648 TCCAAATTACAATGCTACCATCAGAC 59.681 38.462 0.00 0.00 0.00 3.51
4084 4647 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4087 4650 1.020437 CGTACTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
4088 4651 2.029838 TCGTACTACTCCCTCCGTTC 57.970 55.000 0.00 0.00 0.00 3.95
4090 4653 2.016096 GCTTCGTACTACTCCCTCCGT 61.016 57.143 0.00 0.00 0.00 4.69
4091 4654 0.662085 GCTTCGTACTACTCCCTCCG 59.338 60.000 0.00 0.00 0.00 4.63
4092 4655 1.948834 GAGCTTCGTACTACTCCCTCC 59.051 57.143 0.00 0.00 0.00 4.30
4093 4656 2.355444 GTGAGCTTCGTACTACTCCCTC 59.645 54.545 0.00 0.00 0.00 4.30
4095 4658 2.097791 CAGTGAGCTTCGTACTACTCCC 59.902 54.545 0.00 0.00 0.00 4.30
4096 4659 3.008330 TCAGTGAGCTTCGTACTACTCC 58.992 50.000 0.00 0.00 0.00 3.85
4129 4738 8.947055 ACAAGAAAATATTTGCAAGTTTGAGT 57.053 26.923 8.91 0.00 0.00 3.41
4134 4743 9.270640 TGCAATACAAGAAAATATTTGCAAGTT 57.729 25.926 8.91 0.00 29.72 2.66
4136 4745 9.532697 GTTGCAATACAAGAAAATATTTGCAAG 57.467 29.630 17.41 7.28 39.50 4.01
4215 4838 1.079888 ACGTGATCATCGCTGTGCA 60.080 52.632 14.78 0.00 0.00 4.57
4216 4839 1.346197 CACGTGATCATCGCTGTGC 59.654 57.895 10.90 0.00 30.01 4.57
4218 4841 2.160853 CGCACGTGATCATCGCTGT 61.161 57.895 22.23 0.00 0.00 4.40
4219 4842 1.873572 TCGCACGTGATCATCGCTG 60.874 57.895 22.23 13.02 0.00 5.18
4220 4843 1.874019 GTCGCACGTGATCATCGCT 60.874 57.895 22.23 3.51 0.00 4.93
4221 4844 2.615618 GTCGCACGTGATCATCGC 59.384 61.111 22.23 0.00 0.00 4.58
4222 4845 1.131618 TTCGTCGCACGTGATCATCG 61.132 55.000 22.23 13.11 43.14 3.84
4223 4846 1.200483 ATTCGTCGCACGTGATCATC 58.800 50.000 22.23 0.00 43.14 2.92
4224 4847 1.640428 AATTCGTCGCACGTGATCAT 58.360 45.000 22.23 0.00 43.14 2.45
4231 4861 2.719325 ATGATCAAATTCGTCGCACG 57.281 45.000 0.00 2.79 44.19 5.34
4260 4890 3.383185 TCAATGCAGTTCGGGAAAAAGTT 59.617 39.130 0.00 0.00 0.00 2.66
4262 4892 3.641437 TCAATGCAGTTCGGGAAAAAG 57.359 42.857 0.00 0.00 0.00 2.27
4267 4897 2.230992 CCAAAATCAATGCAGTTCGGGA 59.769 45.455 0.00 0.00 0.00 5.14
4269 4899 3.574284 TCCAAAATCAATGCAGTTCGG 57.426 42.857 0.00 0.00 0.00 4.30
4270 4900 4.549458 AGTTCCAAAATCAATGCAGTTCG 58.451 39.130 0.00 0.00 0.00 3.95
4271 4901 6.849588 AAAGTTCCAAAATCAATGCAGTTC 57.150 33.333 0.00 0.00 0.00 3.01
4273 4903 8.611757 GTTTTAAAGTTCCAAAATCAATGCAGT 58.388 29.630 0.00 0.00 0.00 4.40
4303 4969 4.040952 CCTCAAGATGGAACGAGGGATTAT 59.959 45.833 0.00 0.00 41.20 1.28
4312 4978 2.232452 AGTGAGACCTCAAGATGGAACG 59.768 50.000 0.70 0.00 41.85 3.95
4370 5036 1.953686 GTTGACCTTTGCCACTAAGCA 59.046 47.619 0.00 0.00 42.17 3.91
4371 5037 1.953686 TGTTGACCTTTGCCACTAAGC 59.046 47.619 0.00 0.00 0.00 3.09
4372 5038 3.632145 AGTTGTTGACCTTTGCCACTAAG 59.368 43.478 0.00 0.00 0.00 2.18
4373 5039 3.626930 AGTTGTTGACCTTTGCCACTAA 58.373 40.909 0.00 0.00 0.00 2.24
4374 5040 3.118038 AGAGTTGTTGACCTTTGCCACTA 60.118 43.478 0.00 0.00 0.00 2.74
4375 5041 2.024414 GAGTTGTTGACCTTTGCCACT 58.976 47.619 0.00 0.00 0.00 4.00
4376 5042 2.024414 AGAGTTGTTGACCTTTGCCAC 58.976 47.619 0.00 0.00 0.00 5.01
4377 5043 2.023673 CAGAGTTGTTGACCTTTGCCA 58.976 47.619 0.00 0.00 0.00 4.92
4378 5044 1.338020 CCAGAGTTGTTGACCTTTGCC 59.662 52.381 0.00 0.00 0.00 4.52
4379 5045 2.024414 ACCAGAGTTGTTGACCTTTGC 58.976 47.619 0.00 0.00 0.00 3.68
4380 5046 3.065371 GTCACCAGAGTTGTTGACCTTTG 59.935 47.826 0.00 0.00 0.00 2.77
4381 5047 3.054361 AGTCACCAGAGTTGTTGACCTTT 60.054 43.478 2.22 0.00 0.00 3.11
4382 5048 2.505819 AGTCACCAGAGTTGTTGACCTT 59.494 45.455 2.22 0.00 0.00 3.50
4383 5049 2.119495 AGTCACCAGAGTTGTTGACCT 58.881 47.619 2.22 0.00 0.00 3.85
4384 5050 2.213499 CAGTCACCAGAGTTGTTGACC 58.787 52.381 2.22 0.00 0.00 4.02
4385 5051 2.213499 CCAGTCACCAGAGTTGTTGAC 58.787 52.381 0.00 0.00 0.00 3.18
4386 5052 1.837439 ACCAGTCACCAGAGTTGTTGA 59.163 47.619 0.00 0.00 0.00 3.18
4387 5053 1.942657 CACCAGTCACCAGAGTTGTTG 59.057 52.381 0.00 0.00 0.00 3.33
4388 5054 1.837439 TCACCAGTCACCAGAGTTGTT 59.163 47.619 0.00 0.00 0.00 2.83
4389 5055 1.139058 GTCACCAGTCACCAGAGTTGT 59.861 52.381 0.00 0.00 0.00 3.32
4390 5056 1.414181 AGTCACCAGTCACCAGAGTTG 59.586 52.381 0.00 0.00 0.00 3.16
4391 5057 1.689273 GAGTCACCAGTCACCAGAGTT 59.311 52.381 0.00 0.00 0.00 3.01
4392 5058 1.333177 GAGTCACCAGTCACCAGAGT 58.667 55.000 0.00 0.00 0.00 3.24
4393 5059 0.242286 CGAGTCACCAGTCACCAGAG 59.758 60.000 0.00 0.00 0.00 3.35
4394 5060 0.467474 ACGAGTCACCAGTCACCAGA 60.467 55.000 0.00 0.00 0.00 3.86
4395 5061 0.389391 AACGAGTCACCAGTCACCAG 59.611 55.000 0.00 0.00 0.00 4.00
4396 5062 0.104120 CAACGAGTCACCAGTCACCA 59.896 55.000 0.00 0.00 0.00 4.17
4397 5063 0.600255 CCAACGAGTCACCAGTCACC 60.600 60.000 0.00 0.00 0.00 4.02
4398 5064 0.600255 CCCAACGAGTCACCAGTCAC 60.600 60.000 0.00 0.00 0.00 3.67
4399 5065 1.745890 CCCAACGAGTCACCAGTCA 59.254 57.895 0.00 0.00 0.00 3.41
4400 5066 1.004918 CCCCAACGAGTCACCAGTC 60.005 63.158 0.00 0.00 0.00 3.51
4401 5067 1.342672 AACCCCAACGAGTCACCAGT 61.343 55.000 0.00 0.00 0.00 4.00
4402 5068 0.884704 CAACCCCAACGAGTCACCAG 60.885 60.000 0.00 0.00 0.00 4.00
4403 5069 1.147376 CAACCCCAACGAGTCACCA 59.853 57.895 0.00 0.00 0.00 4.17
4404 5070 0.179040 TTCAACCCCAACGAGTCACC 60.179 55.000 0.00 0.00 0.00 4.02
4405 5071 1.226746 CTTCAACCCCAACGAGTCAC 58.773 55.000 0.00 0.00 0.00 3.67
4406 5072 0.107831 CCTTCAACCCCAACGAGTCA 59.892 55.000 0.00 0.00 0.00 3.41
4407 5073 0.605589 CCCTTCAACCCCAACGAGTC 60.606 60.000 0.00 0.00 0.00 3.36
4408 5074 1.350310 ACCCTTCAACCCCAACGAGT 61.350 55.000 0.00 0.00 0.00 4.18
4409 5075 0.605589 GACCCTTCAACCCCAACGAG 60.606 60.000 0.00 0.00 0.00 4.18
4410 5076 1.057851 AGACCCTTCAACCCCAACGA 61.058 55.000 0.00 0.00 0.00 3.85
4411 5077 0.179001 AAGACCCTTCAACCCCAACG 60.179 55.000 0.00 0.00 0.00 4.10
4412 5078 1.328279 CAAGACCCTTCAACCCCAAC 58.672 55.000 0.00 0.00 0.00 3.77
4413 5079 0.930726 ACAAGACCCTTCAACCCCAA 59.069 50.000 0.00 0.00 0.00 4.12
4414 5080 0.930726 AACAAGACCCTTCAACCCCA 59.069 50.000 0.00 0.00 0.00 4.96
4415 5081 1.686587 CAAACAAGACCCTTCAACCCC 59.313 52.381 0.00 0.00 0.00 4.95
4416 5082 1.686587 CCAAACAAGACCCTTCAACCC 59.313 52.381 0.00 0.00 0.00 4.11
4417 5083 1.686587 CCCAAACAAGACCCTTCAACC 59.313 52.381 0.00 0.00 0.00 3.77
4418 5084 2.100749 CACCCAAACAAGACCCTTCAAC 59.899 50.000 0.00 0.00 0.00 3.18
4419 5085 2.383855 CACCCAAACAAGACCCTTCAA 58.616 47.619 0.00 0.00 0.00 2.69
4420 5086 2.026905 GCACCCAAACAAGACCCTTCA 61.027 52.381 0.00 0.00 0.00 3.02
4421 5087 0.673985 GCACCCAAACAAGACCCTTC 59.326 55.000 0.00 0.00 0.00 3.46
4422 5088 0.261696 AGCACCCAAACAAGACCCTT 59.738 50.000 0.00 0.00 0.00 3.95
4423 5089 0.178990 GAGCACCCAAACAAGACCCT 60.179 55.000 0.00 0.00 0.00 4.34
4424 5090 1.515521 CGAGCACCCAAACAAGACCC 61.516 60.000 0.00 0.00 0.00 4.46
4425 5091 0.818040 ACGAGCACCCAAACAAGACC 60.818 55.000 0.00 0.00 0.00 3.85
4426 5092 1.021968 AACGAGCACCCAAACAAGAC 58.978 50.000 0.00 0.00 0.00 3.01
4427 5093 1.757682 AAACGAGCACCCAAACAAGA 58.242 45.000 0.00 0.00 0.00 3.02
4428 5094 2.356382 TGTAAACGAGCACCCAAACAAG 59.644 45.455 0.00 0.00 0.00 3.16
4458 5124 8.267894 CCCCTATAAAAAGAGAAGTCTGATTCA 58.732 37.037 0.00 0.00 31.37 2.57
4464 5130 8.450780 TTTCTCCCCTATAAAAAGAGAAGTCT 57.549 34.615 0.00 0.00 42.68 3.24
4467 5133 9.913310 ATTCTTTCTCCCCTATAAAAAGAGAAG 57.087 33.333 0.00 0.00 42.68 2.85
4470 5136 7.442666 CCGATTCTTTCTCCCCTATAAAAAGAG 59.557 40.741 0.00 0.00 37.29 2.85
4472 5138 7.280356 TCCGATTCTTTCTCCCCTATAAAAAG 58.720 38.462 0.00 0.00 0.00 2.27
4473 5139 7.202972 TCCGATTCTTTCTCCCCTATAAAAA 57.797 36.000 0.00 0.00 0.00 1.94
4474 5140 6.818281 TCCGATTCTTTCTCCCCTATAAAA 57.182 37.500 0.00 0.00 0.00 1.52
4475 5141 6.818281 TTCCGATTCTTTCTCCCCTATAAA 57.182 37.500 0.00 0.00 0.00 1.40
4514 5180 4.172807 TGGGTACAAAGGAGTACAAGGAT 58.827 43.478 6.59 0.00 44.76 3.24
4515 5181 3.589641 TGGGTACAAAGGAGTACAAGGA 58.410 45.455 6.59 0.00 44.76 3.36
4516 5182 4.041198 TCTTGGGTACAAAGGAGTACAAGG 59.959 45.833 6.59 0.00 44.76 3.61
4517 5183 5.223449 TCTTGGGTACAAAGGAGTACAAG 57.777 43.478 6.59 0.00 44.76 3.16
4518 5184 4.041198 CCTCTTGGGTACAAAGGAGTACAA 59.959 45.833 6.59 0.00 44.76 2.41
4520 5186 4.203654 CCTCTTGGGTACAAAGGAGTAC 57.796 50.000 7.47 0.00 42.78 2.73
4534 5200 0.745845 CAATCGAGCCCACCTCTTGG 60.746 60.000 0.00 0.00 46.47 3.61
4535 5201 0.745845 CCAATCGAGCCCACCTCTTG 60.746 60.000 0.00 0.00 38.49 3.02
4536 5202 0.909610 TCCAATCGAGCCCACCTCTT 60.910 55.000 0.00 0.00 38.49 2.85
4537 5203 0.909610 TTCCAATCGAGCCCACCTCT 60.910 55.000 0.00 0.00 38.49 3.69
4538 5204 0.744771 GTTCCAATCGAGCCCACCTC 60.745 60.000 0.00 0.00 37.22 3.85
4542 5208 0.394216 CCATGTTCCAATCGAGCCCA 60.394 55.000 0.00 0.00 0.00 5.36
4566 5232 2.303022 GTGTGAAGAATCTGGTCAGGGA 59.697 50.000 0.00 0.00 0.00 4.20
4590 5256 0.248843 GAGGGGAGAGTCTGCACTTG 59.751 60.000 18.43 0.00 35.20 3.16
4606 5272 5.742063 AGAAAACGAAACCCTAATAGGAGG 58.258 41.667 8.12 0.00 37.67 4.30
4607 5273 6.641474 AGAGAAAACGAAACCCTAATAGGAG 58.359 40.000 8.12 0.53 37.67 3.69
4608 5274 6.616237 AGAGAAAACGAAACCCTAATAGGA 57.384 37.500 8.12 0.00 37.67 2.94
4609 5275 6.093633 CCAAGAGAAAACGAAACCCTAATAGG 59.906 42.308 0.00 0.00 34.30 2.57
4610 5276 6.403309 GCCAAGAGAAAACGAAACCCTAATAG 60.403 42.308 0.00 0.00 0.00 1.73
4611 5277 5.413523 GCCAAGAGAAAACGAAACCCTAATA 59.586 40.000 0.00 0.00 0.00 0.98
4612 5278 4.217767 GCCAAGAGAAAACGAAACCCTAAT 59.782 41.667 0.00 0.00 0.00 1.73
4613 5279 3.566742 GCCAAGAGAAAACGAAACCCTAA 59.433 43.478 0.00 0.00 0.00 2.69
4614 5280 3.143728 GCCAAGAGAAAACGAAACCCTA 58.856 45.455 0.00 0.00 0.00 3.53
4615 5281 1.954382 GCCAAGAGAAAACGAAACCCT 59.046 47.619 0.00 0.00 0.00 4.34
4616 5282 1.334689 CGCCAAGAGAAAACGAAACCC 60.335 52.381 0.00 0.00 0.00 4.11
4617 5283 1.600485 TCGCCAAGAGAAAACGAAACC 59.400 47.619 0.00 0.00 0.00 3.27
4618 5284 2.287103 AGTCGCCAAGAGAAAACGAAAC 59.713 45.455 0.00 0.00 34.12 2.78
4619 5285 2.542595 GAGTCGCCAAGAGAAAACGAAA 59.457 45.455 0.00 0.00 34.12 3.46
4620 5286 2.132762 GAGTCGCCAAGAGAAAACGAA 58.867 47.619 0.00 0.00 34.12 3.85
4621 5287 1.340248 AGAGTCGCCAAGAGAAAACGA 59.660 47.619 0.00 0.00 0.00 3.85
4622 5288 1.721926 GAGAGTCGCCAAGAGAAAACG 59.278 52.381 0.00 0.00 0.00 3.60
4623 5289 2.070028 GGAGAGTCGCCAAGAGAAAAC 58.930 52.381 8.20 0.00 0.00 2.43
4624 5290 1.336887 CGGAGAGTCGCCAAGAGAAAA 60.337 52.381 13.75 0.00 0.00 2.29
4625 5291 0.243907 CGGAGAGTCGCCAAGAGAAA 59.756 55.000 13.75 0.00 0.00 2.52
4626 5292 0.608308 TCGGAGAGTCGCCAAGAGAA 60.608 55.000 13.75 0.00 0.00 2.87
4627 5293 1.002502 TCGGAGAGTCGCCAAGAGA 60.003 57.895 13.75 0.00 0.00 3.10
4628 5294 3.592070 TCGGAGAGTCGCCAAGAG 58.408 61.111 13.75 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.