Multiple sequence alignment - TraesCS6D01G130400

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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 TraesCS6D01G130400 chr6D 100.000 6033 0 0 1 6033 96828450 96822418 0.000000e+00 11141.0
1 TraesCS6D01G130400 chr6B 93.194 2204 121 17 3039 5234 179989590 179987408 0.000000e+00 3212.0
2 TraesCS6D01G130400 chr6B 95.175 1658 62 9 1009 2659 179991798 179990152 0.000000e+00 2603.0
3 TraesCS6D01G130400 chr6B 92.763 912 60 5 1 908 179997114 179996205 0.000000e+00 1314.0
4 TraesCS6D01G130400 chr6B 86.119 353 39 7 2695 3044 179990155 179989810 7.380000e-99 372.0
5 TraesCS6D01G130400 chr6B 96.429 84 3 0 3039 3122 179989775 179989692 8.150000e-29 139.0
6 TraesCS6D01G130400 chr6A 92.659 2166 130 17 3039 5196 115829446 115827302 0.000000e+00 3092.0
7 TraesCS6D01G130400 chr6A 94.737 1957 77 12 714 2659 115831764 115829823 0.000000e+00 3020.0
8 TraesCS6D01G130400 chr6A 92.676 669 48 1 55 722 115841096 115840428 0.000000e+00 963.0
9 TraesCS6D01G130400 chr6A 86.402 353 38 7 2695 3044 115829826 115829481 1.590000e-100 377.0
10 TraesCS6D01G130400 chr6A 100.000 29 0 0 1 29 115841125 115841097 3.000000e-03 54.7
11 TraesCS6D01G130400 chr7B 87.080 1339 136 18 3039 4357 620662031 620663352 0.000000e+00 1480.0
12 TraesCS6D01G130400 chr7B 87.841 954 70 21 1040 1951 620659940 620660889 0.000000e+00 1077.0
13 TraesCS6D01G130400 chr7B 87.732 701 55 17 1999 2689 620660884 620661563 0.000000e+00 789.0
14 TraesCS6D01G130400 chr7B 89.407 472 50 0 1 472 140024914 140025385 4.030000e-166 595.0
15 TraesCS6D01G130400 chr7B 82.991 682 84 12 5356 6031 713434972 713435627 6.740000e-164 588.0
16 TraesCS6D01G130400 chr7B 85.779 443 52 7 4606 5039 620663367 620663807 5.510000e-125 459.0
17 TraesCS6D01G130400 chr7A 86.757 1329 139 20 3042 4357 652719928 652718624 0.000000e+00 1445.0
18 TraesCS6D01G130400 chr7A 85.700 979 66 27 1040 1951 652722028 652721057 0.000000e+00 965.0
19 TraesCS6D01G130400 chr7A 87.966 698 57 17 2003 2689 652721058 652720377 0.000000e+00 798.0
20 TraesCS6D01G130400 chr7A 90.576 382 31 4 571 949 218917308 218917687 9.030000e-138 501.0
21 TraesCS6D01G130400 chr4D 92.999 957 64 3 1 956 213418704 213417750 0.000000e+00 1393.0
22 TraesCS6D01G130400 chr3B 91.245 948 78 5 1 947 252352765 252353708 0.000000e+00 1286.0
23 TraesCS6D01G130400 chr3B 76.848 514 80 26 5353 5856 522400244 522400728 2.790000e-63 254.0
24 TraesCS6D01G130400 chr3B 83.417 199 13 11 4164 4355 797640607 797640792 3.740000e-37 167.0
25 TraesCS6D01G130400 chr3B 74.863 366 64 25 5619 5971 567390698 567390348 2.270000e-29 141.0
26 TraesCS6D01G130400 chrUn 91.071 952 67 4 1 951 29528935 29528001 0.000000e+00 1271.0
27 TraesCS6D01G130400 chr2D 90.513 917 72 4 39 954 633841673 633840771 0.000000e+00 1197.0
28 TraesCS6D01G130400 chr7D 89.807 932 66 18 1040 1945 566552047 566551119 0.000000e+00 1168.0
29 TraesCS6D01G130400 chr7D 89.814 805 64 6 3563 4357 566549404 566548608 0.000000e+00 1016.0
30 TraesCS6D01G130400 chr7D 92.059 680 43 7 5355 6031 309756571 309757242 0.000000e+00 946.0
31 TraesCS6D01G130400 chr7D 89.067 686 52 14 2013 2689 566551098 566550427 0.000000e+00 830.0
32 TraesCS6D01G130400 chr7D 87.575 499 54 8 3043 3539 566549895 566549403 6.780000e-159 571.0
33 TraesCS6D01G130400 chr4B 91.620 716 30 12 5343 6033 599348312 599349022 0.000000e+00 963.0
34 TraesCS6D01G130400 chr4B 86.756 521 66 3 429 947 550668393 550668912 1.460000e-160 577.0
35 TraesCS6D01G130400 chr4B 89.510 429 45 0 1 429 550616704 550617132 1.480000e-150 544.0
36 TraesCS6D01G130400 chr4B 90.722 97 8 1 5343 5439 599347776 599347871 1.760000e-25 128.0
37 TraesCS6D01G130400 chr2B 91.342 693 33 5 5343 6031 772221762 772222431 0.000000e+00 922.0
38 TraesCS6D01G130400 chr2B 83.769 727 74 25 5343 6031 66203490 66204210 0.000000e+00 649.0
39 TraesCS6D01G130400 chr1D 85.991 671 40 19 5359 6025 269986615 269987235 0.000000e+00 669.0
40 TraesCS6D01G130400 chr5A 87.200 500 36 22 5369 5862 32158831 32159308 1.480000e-150 544.0
41 TraesCS6D01G130400 chr5A 89.136 405 43 1 543 947 479225825 479226228 2.510000e-138 503.0
42 TraesCS6D01G130400 chr3A 84.848 198 12 7 4164 4355 724897312 724897497 3.710000e-42 183.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G130400 chr6D 96822418 96828450 6032 True 11141.000000 11141 100.000000 1 6033 1 chr6D.!!$R1 6032
1 TraesCS6D01G130400 chr6B 179987408 179991798 4390 True 1581.500000 3212 92.729250 1009 5234 4 chr6B.!!$R2 4225
2 TraesCS6D01G130400 chr6B 179996205 179997114 909 True 1314.000000 1314 92.763000 1 908 1 chr6B.!!$R1 907
3 TraesCS6D01G130400 chr6A 115827302 115831764 4462 True 2163.000000 3092 91.266000 714 5196 3 chr6A.!!$R1 4482
4 TraesCS6D01G130400 chr6A 115840428 115841125 697 True 508.850000 963 96.338000 1 722 2 chr6A.!!$R2 721
5 TraesCS6D01G130400 chr7B 620659940 620663807 3867 False 951.250000 1480 87.108000 1040 5039 4 chr7B.!!$F3 3999
6 TraesCS6D01G130400 chr7B 713434972 713435627 655 False 588.000000 588 82.991000 5356 6031 1 chr7B.!!$F2 675
7 TraesCS6D01G130400 chr7A 652718624 652722028 3404 True 1069.333333 1445 86.807667 1040 4357 3 chr7A.!!$R1 3317
8 TraesCS6D01G130400 chr4D 213417750 213418704 954 True 1393.000000 1393 92.999000 1 956 1 chr4D.!!$R1 955
9 TraesCS6D01G130400 chr3B 252352765 252353708 943 False 1286.000000 1286 91.245000 1 947 1 chr3B.!!$F1 946
10 TraesCS6D01G130400 chrUn 29528001 29528935 934 True 1271.000000 1271 91.071000 1 951 1 chrUn.!!$R1 950
11 TraesCS6D01G130400 chr2D 633840771 633841673 902 True 1197.000000 1197 90.513000 39 954 1 chr2D.!!$R1 915
12 TraesCS6D01G130400 chr7D 309756571 309757242 671 False 946.000000 946 92.059000 5355 6031 1 chr7D.!!$F1 676
13 TraesCS6D01G130400 chr7D 566548608 566552047 3439 True 896.250000 1168 89.065750 1040 4357 4 chr7D.!!$R1 3317
14 TraesCS6D01G130400 chr4B 550668393 550668912 519 False 577.000000 577 86.756000 429 947 1 chr4B.!!$F2 518
15 TraesCS6D01G130400 chr4B 599347776 599349022 1246 False 545.500000 963 91.171000 5343 6033 2 chr4B.!!$F3 690
16 TraesCS6D01G130400 chr2B 772221762 772222431 669 False 922.000000 922 91.342000 5343 6031 1 chr2B.!!$F2 688
17 TraesCS6D01G130400 chr2B 66203490 66204210 720 False 649.000000 649 83.769000 5343 6031 1 chr2B.!!$F1 688
18 TraesCS6D01G130400 chr1D 269986615 269987235 620 False 669.000000 669 85.991000 5359 6025 1 chr1D.!!$F1 666

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
802 806 0.040514 CAAGCATGTTCGTCGGCAAA 60.041 50.0 0.00 0.0 0.00 3.68 F
999 1007 1.040339 GGCACCAACACTCCCAAACA 61.040 55.0 0.00 0.0 0.00 2.83 F
2556 2643 0.242017 GTGAGCCAAGTTGCATCACC 59.758 55.0 20.07 8.7 35.36 4.02 F
2840 2932 0.764890 TGTGGCCACTAGAAAGCACT 59.235 50.0 34.75 0.0 0.00 4.40 F
4322 4892 0.310543 GTGCTGAAACATGCGTTCCA 59.689 50.0 7.15 0.0 32.91 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2057 0.178301 TGTGGTGCTTTGTACGTCCA 59.822 50.0 0.00 0.0 0.00 4.02 R
2713 2805 0.460987 TTTGTGGGTTGCTTTTGGCG 60.461 50.0 0.00 0.0 45.43 5.69 R
3463 4009 0.107831 TGGCCACGCTAAGAAACACT 59.892 50.0 0.00 0.0 0.00 3.55 R
4430 5004 0.531090 TGGTTGACCGGAACAAGACG 60.531 55.0 9.46 0.0 39.43 4.18 R
5314 5898 0.242555 TCGCAGCGTGTGTATCTTCA 59.757 50.0 15.93 0.0 0.00 3.02 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
35 36 4.654915 TGCTCAAGATTGTCTTCCATCAA 58.345 39.130 0.00 0.00 33.78 2.57
68 69 1.325355 ACGACGACATATCCCCGATT 58.675 50.000 0.00 0.00 0.00 3.34
154 155 2.382770 AAGGGCCGTATGGGATGCA 61.383 57.895 0.00 0.00 38.47 3.96
157 158 0.827507 GGGCCGTATGGGATGCAATT 60.828 55.000 2.41 0.00 38.47 2.32
184 185 3.077359 GTGGGCAGATATCCAACTATGC 58.923 50.000 0.00 1.41 34.47 3.14
283 285 5.190925 ACTGGCTGTGTCCTTTTGGTATATA 59.809 40.000 0.00 0.00 41.38 0.86
513 516 4.907269 TCAGAGATTAATATGTCAGGGGCA 59.093 41.667 0.00 0.00 0.00 5.36
518 521 0.552848 AATATGTCAGGGGCAGGTGG 59.447 55.000 0.00 0.00 0.00 4.61
545 548 3.605634 CCGTGAACCATGAAGGAACATA 58.394 45.455 0.00 0.00 41.22 2.29
549 552 7.158697 CCGTGAACCATGAAGGAACATATATA 58.841 38.462 0.00 0.00 41.22 0.86
583 587 1.533187 ACCTATCCATGGGGCATTGA 58.467 50.000 13.02 0.00 31.86 2.57
617 621 1.623811 AGAGGCTCTGGCTTTACGAAA 59.376 47.619 17.96 0.00 38.98 3.46
631 635 6.706055 CTTTACGAAAAGCTGTGTATCTGA 57.294 37.500 0.00 0.00 35.98 3.27
802 806 0.040514 CAAGCATGTTCGTCGGCAAA 60.041 50.000 0.00 0.00 0.00 3.68
814 818 5.128992 TCGTCGGCAAATGAATATAGCTA 57.871 39.130 0.00 0.00 0.00 3.32
874 878 6.795399 AGTGTTGTTGTTTTCCATTCTACTG 58.205 36.000 0.00 0.00 0.00 2.74
909 913 4.887655 CAGGAGACCCTTTGTAACTTTGTT 59.112 41.667 0.00 0.00 42.02 2.83
979 987 2.172851 ATTTGGGCAGCACACATTTG 57.827 45.000 0.00 0.00 0.00 2.32
997 1005 4.268720 GGCACCAACACTCCCAAA 57.731 55.556 0.00 0.00 0.00 3.28
998 1006 1.739667 GGCACCAACACTCCCAAAC 59.260 57.895 0.00 0.00 0.00 2.93
999 1007 1.040339 GGCACCAACACTCCCAAACA 61.040 55.000 0.00 0.00 0.00 2.83
1103 1112 1.764723 AGCAACGAGATGATGGATCCA 59.235 47.619 18.88 18.88 0.00 3.41
1380 1430 1.665679 GTGATGGGTTATGTGACTGCG 59.334 52.381 0.00 0.00 0.00 5.18
1555 1608 3.585289 TCCAGATGGCTGTTTGGTAGTTA 59.415 43.478 0.00 0.00 40.63 2.24
1739 1815 7.172703 GGGTTGTATATTGCCTACTGATGTAAC 59.827 40.741 0.00 0.00 0.00 2.50
1965 2043 5.643421 ATATTCTCTTGCTCACCCATTCT 57.357 39.130 0.00 0.00 0.00 2.40
1968 2046 2.639347 TCTCTTGCTCACCCATTCTTCA 59.361 45.455 0.00 0.00 0.00 3.02
1979 2057 5.006386 CACCCATTCTTCAAAGTTCTAGCT 58.994 41.667 0.00 0.00 0.00 3.32
1984 2062 3.914312 TCTTCAAAGTTCTAGCTGGACG 58.086 45.455 0.00 0.00 0.00 4.79
2001 2079 2.292292 GGACGTACAAAGCACCACATTT 59.708 45.455 0.00 0.00 0.00 2.32
2010 2088 4.486125 AAGCACCACATTTTCCAGTTTT 57.514 36.364 0.00 0.00 0.00 2.43
2115 2198 1.276859 ATCAGATGCTGGCCCTGTCA 61.277 55.000 0.00 0.00 31.51 3.58
2127 2210 1.614317 GCCCTGTCATTTACACTGCCT 60.614 52.381 0.00 0.00 33.45 4.75
2206 2290 4.105377 CCCCTAACAATTCATCATCTCCCT 59.895 45.833 0.00 0.00 0.00 4.20
2255 2339 8.826293 TGGTGACGGTAATATCATGGTATATA 57.174 34.615 0.00 0.00 0.00 0.86
2256 2340 9.429109 TGGTGACGGTAATATCATGGTATATAT 57.571 33.333 0.00 0.00 0.00 0.86
2295 2379 3.413558 CGAAAGGCGTGTTATTAGCAAC 58.586 45.455 0.00 0.00 34.64 4.17
2302 2386 4.513692 GGCGTGTTATTAGCAACCATCATA 59.486 41.667 0.00 0.00 0.00 2.15
2304 2388 6.307155 GCGTGTTATTAGCAACCATCATATC 58.693 40.000 0.00 0.00 0.00 1.63
2309 2393 2.175878 AGCAACCATCATATCGCTCC 57.824 50.000 0.00 0.00 0.00 4.70
2341 2428 5.126869 TGACAGTCTTTGGCTGAATTTTTGA 59.873 36.000 6.16 0.00 35.09 2.69
2464 2551 1.270907 GTGGAGAGGGTGTCATGTCT 58.729 55.000 0.00 0.00 0.00 3.41
2497 2584 3.888323 TGCAGTGTTTAAGGATTGCTTCA 59.112 39.130 0.00 0.00 33.00 3.02
2542 2629 4.940654 AGCAAAATAAAGAGAGAGGTGAGC 59.059 41.667 0.00 0.00 0.00 4.26
2556 2643 0.242017 GTGAGCCAAGTTGCATCACC 59.758 55.000 20.07 8.70 35.36 4.02
2562 2649 3.770933 AGCCAAGTTGCATCACCAATATT 59.229 39.130 0.00 0.00 0.00 1.28
2563 2650 4.223477 AGCCAAGTTGCATCACCAATATTT 59.777 37.500 0.00 0.00 0.00 1.40
2594 2681 9.590451 ACAATTTGGATATCTGCTTTAATGTTG 57.410 29.630 2.05 0.00 0.00 3.33
2631 2718 2.107378 TGTAGCAGGGGTTGTGAATTGA 59.893 45.455 0.00 0.00 0.00 2.57
2682 2774 5.302360 TGGTTAACCACTCTGACATGTAAC 58.698 41.667 23.69 0.00 42.01 2.50
2689 2781 4.084537 CCACTCTGACATGTAACGTGTTTC 60.085 45.833 0.00 0.00 0.00 2.78
2690 2782 4.056050 ACTCTGACATGTAACGTGTTTCC 58.944 43.478 0.00 0.00 0.00 3.13
2691 2783 4.202223 ACTCTGACATGTAACGTGTTTCCT 60.202 41.667 0.00 0.00 0.00 3.36
2692 2784 4.304110 TCTGACATGTAACGTGTTTCCTC 58.696 43.478 0.00 0.00 0.00 3.71
2693 2785 4.038763 TCTGACATGTAACGTGTTTCCTCT 59.961 41.667 0.00 0.00 0.00 3.69
2694 2786 5.242171 TCTGACATGTAACGTGTTTCCTCTA 59.758 40.000 0.00 0.00 0.00 2.43
2695 2787 6.032956 TGACATGTAACGTGTTTCCTCTAT 57.967 37.500 0.00 0.00 0.00 1.98
2696 2788 6.460781 TGACATGTAACGTGTTTCCTCTATT 58.539 36.000 0.00 0.00 0.00 1.73
2697 2789 6.367695 TGACATGTAACGTGTTTCCTCTATTG 59.632 38.462 0.00 0.00 0.00 1.90
2708 2800 8.454106 CGTGTTTCCTCTATTGAAGATCAAAAT 58.546 33.333 0.00 0.00 40.12 1.82
2723 2815 5.414454 AGATCAAAATACTACGCCAAAAGCA 59.586 36.000 0.00 0.00 44.04 3.91
2739 2831 1.111277 AGCAACCCACAAAGTTCCAC 58.889 50.000 0.00 0.00 0.00 4.02
2746 2838 2.099098 CCCACAAAGTTCCACACTGAAC 59.901 50.000 0.00 0.00 43.95 3.18
2755 2847 2.615391 TCCACACTGAACATCCCTGTA 58.385 47.619 0.00 0.00 33.36 2.74
2758 2850 4.161565 TCCACACTGAACATCCCTGTATAC 59.838 45.833 0.00 0.00 33.36 1.47
2763 2855 6.042093 ACACTGAACATCCCTGTATACCATAG 59.958 42.308 0.00 0.00 33.36 2.23
2767 2859 8.096621 TGAACATCCCTGTATACCATAGAAAA 57.903 34.615 0.00 0.00 33.36 2.29
2783 2875 8.650490 ACCATAGAAAAGGAAACAAAATGATGT 58.350 29.630 0.00 0.00 34.24 3.06
2840 2932 0.764890 TGTGGCCACTAGAAAGCACT 59.235 50.000 34.75 0.00 0.00 4.40
2871 2963 2.158813 ACATTGGTCGTCTCCTGTTGTT 60.159 45.455 0.00 0.00 0.00 2.83
2882 2974 2.671396 CTCCTGTTGTTGTACATACGGC 59.329 50.000 0.00 0.00 0.00 5.68
2883 2975 1.392168 CCTGTTGTTGTACATACGGCG 59.608 52.381 4.80 4.80 0.00 6.46
2884 2976 1.392168 CTGTTGTTGTACATACGGCGG 59.608 52.381 13.24 0.00 0.00 6.13
2885 2977 1.270199 TGTTGTTGTACATACGGCGGT 60.270 47.619 13.24 1.39 0.00 5.68
2886 2978 1.127213 GTTGTTGTACATACGGCGGTG 59.873 52.381 13.24 12.54 0.00 4.94
2888 2980 1.205179 TGTTGTACATACGGCGGTGAT 59.795 47.619 19.03 3.66 0.00 3.06
2908 3003 4.721274 TGATTCACTGGGATATGTGGAGAA 59.279 41.667 0.00 0.00 35.15 2.87
2909 3004 4.487714 TTCACTGGGATATGTGGAGAAC 57.512 45.455 0.00 0.00 35.15 3.01
2910 3005 3.724478 TCACTGGGATATGTGGAGAACT 58.276 45.455 0.00 0.00 35.15 3.01
2911 3006 3.452264 TCACTGGGATATGTGGAGAACTG 59.548 47.826 0.00 0.00 35.15 3.16
2912 3007 2.774234 ACTGGGATATGTGGAGAACTGG 59.226 50.000 0.00 0.00 0.00 4.00
2913 3008 2.105477 CTGGGATATGTGGAGAACTGGG 59.895 54.545 0.00 0.00 0.00 4.45
2914 3009 1.421646 GGGATATGTGGAGAACTGGGG 59.578 57.143 0.00 0.00 0.00 4.96
2915 3010 2.408565 GGATATGTGGAGAACTGGGGA 58.591 52.381 0.00 0.00 0.00 4.81
2924 3023 2.100418 GGAGAACTGGGGATACGTGTAC 59.900 54.545 0.00 0.00 37.60 2.90
2990 3268 1.147153 GATAGGCTGGGACACTGGC 59.853 63.158 0.00 0.00 42.79 4.85
3062 3590 3.511362 TGCCAACAAGGAAGAAGCA 57.489 47.368 0.00 0.00 41.22 3.91
3257 3785 1.193323 ACAGATGGAGGAGCTGACTG 58.807 55.000 0.00 0.00 40.87 3.51
3258 3786 1.193323 CAGATGGAGGAGCTGACTGT 58.807 55.000 0.00 0.00 40.87 3.55
3297 3825 6.723977 TGAAATTGGGCCTTATTATGTATCCC 59.276 38.462 4.53 0.00 0.00 3.85
3327 3855 8.730680 GCTCAAAGTCCTTCATTAATGAAACTA 58.269 33.333 25.30 15.23 45.26 2.24
3458 4004 2.526888 TCCCCGTGTCTGTATCTCTT 57.473 50.000 0.00 0.00 0.00 2.85
3463 4009 4.341235 CCCCGTGTCTGTATCTCTTTATCA 59.659 45.833 0.00 0.00 0.00 2.15
3467 4013 6.404844 CCGTGTCTGTATCTCTTTATCAGTGT 60.405 42.308 0.00 0.00 0.00 3.55
3585 4143 5.833131 TCTCAAAGTAGCAAATCAAACCCTT 59.167 36.000 0.00 0.00 0.00 3.95
3666 4224 7.939039 AGAAATTATGTGACTTTCTGAACCTCA 59.061 33.333 0.00 0.00 37.72 3.86
3842 4403 4.464069 AACTATGAAGGAGAGCACTCAC 57.536 45.455 13.37 2.83 44.22 3.51
4033 4594 2.568956 TGGAGTGCTGCACTTCTCTAAT 59.431 45.455 34.11 13.77 45.44 1.73
4189 4757 7.171447 TGTTCGCCTGTTATTTTCATTTTTG 57.829 32.000 0.00 0.00 0.00 2.44
4243 4812 9.768662 ATCTATAATGAATTTCCCAAACATTGC 57.231 29.630 0.00 0.00 33.99 3.56
4296 4866 6.594547 CCTCACTAGCCATGAAATATGATCTG 59.405 42.308 0.00 0.00 0.00 2.90
4297 4867 7.307131 TCACTAGCCATGAAATATGATCTGA 57.693 36.000 0.00 0.00 0.00 3.27
4298 4868 7.157347 TCACTAGCCATGAAATATGATCTGAC 58.843 38.462 0.00 0.00 0.00 3.51
4316 4886 3.446799 TGACAAAAGTGCTGAAACATGC 58.553 40.909 0.00 0.00 0.00 4.06
4320 4890 2.405892 AAGTGCTGAAACATGCGTTC 57.594 45.000 0.00 0.00 32.91 3.95
4321 4891 0.593128 AGTGCTGAAACATGCGTTCC 59.407 50.000 7.15 0.00 32.91 3.62
4322 4892 0.310543 GTGCTGAAACATGCGTTCCA 59.689 50.000 7.15 0.00 32.91 3.53
4323 4893 1.068333 GTGCTGAAACATGCGTTCCAT 60.068 47.619 7.15 0.00 32.91 3.41
4324 4894 1.199789 TGCTGAAACATGCGTTCCATC 59.800 47.619 7.15 0.00 32.91 3.51
4325 4895 1.470098 GCTGAAACATGCGTTCCATCT 59.530 47.619 7.15 0.00 32.91 2.90
4326 4896 2.476854 GCTGAAACATGCGTTCCATCTC 60.477 50.000 7.15 0.00 32.91 2.75
4375 4945 6.127451 TGAGTTATTCTCTATGGCGAAGTGAA 60.127 38.462 6.05 6.05 43.13 3.18
4445 5019 1.364901 GTCCGTCTTGTTCCGGTCA 59.635 57.895 0.00 0.00 44.51 4.02
4454 5028 4.457949 GTCTTGTTCCGGTCAACCAATATT 59.542 41.667 0.00 0.00 35.14 1.28
4494 5068 2.382882 TGTTGAACATGCCTGTTTCCA 58.617 42.857 8.84 0.85 45.57 3.53
4504 5078 2.886523 TGCCTGTTTCCAAGAGAATGTG 59.113 45.455 0.00 0.00 33.44 3.21
4505 5079 2.887152 GCCTGTTTCCAAGAGAATGTGT 59.113 45.455 0.00 0.00 33.44 3.72
4511 5085 4.811555 TTCCAAGAGAATGTGTCAAACG 57.188 40.909 0.00 0.00 0.00 3.60
4515 5089 4.214437 CAAGAGAATGTGTCAAACGAAGC 58.786 43.478 0.00 0.00 0.00 3.86
4530 5104 3.270877 ACGAAGCCATGTTACATTCTCC 58.729 45.455 0.00 0.00 0.00 3.71
4535 5109 3.879295 AGCCATGTTACATTCTCCATTCG 59.121 43.478 0.00 0.00 0.00 3.34
4536 5110 3.876914 GCCATGTTACATTCTCCATTCGA 59.123 43.478 0.00 0.00 0.00 3.71
4550 5124 5.366482 TCCATTCGAACCATGGAGAATTA 57.634 39.130 21.47 12.68 44.50 1.40
4554 5128 8.163408 TCCATTCGAACCATGGAGAATTATTAT 58.837 33.333 21.47 2.36 44.50 1.28
4555 5129 8.796475 CCATTCGAACCATGGAGAATTATTATT 58.204 33.333 21.47 0.00 43.70 1.40
4589 5163 3.484721 CGTCAGCAGAACTATTGCATGTG 60.485 47.826 0.00 0.00 43.92 3.21
4630 5204 8.519799 TTTTGTTCTCTTAACTGGACAAGAAT 57.480 30.769 0.00 0.00 30.68 2.40
4714 5289 4.130118 CAGATCCACCAGCTATACCAAAC 58.870 47.826 0.00 0.00 0.00 2.93
4756 5331 4.039124 ACCAAACCAATGTTGACTGAATCC 59.961 41.667 0.00 0.00 34.13 3.01
4811 5386 1.484038 GGCTGGAGAGTCAGATGAGT 58.516 55.000 0.00 0.00 36.93 3.41
4850 5425 9.456147 GATCACCTAAGAGTCTAATAGATGCTA 57.544 37.037 0.00 0.00 0.00 3.49
4909 5486 7.843490 TGGCAATAGTTAGATTGACTGTAAC 57.157 36.000 3.79 0.00 44.05 2.50
4937 5514 7.396540 ACAGTTCTTAATTCCATGATGGTTC 57.603 36.000 11.87 0.00 39.03 3.62
5054 5638 0.906066 TTGCTACGCCACCATTCCTA 59.094 50.000 0.00 0.00 0.00 2.94
5057 5641 2.701423 TGCTACGCCACCATTCCTATAA 59.299 45.455 0.00 0.00 0.00 0.98
5099 5683 0.459899 TGTGCTATGTAGGCAGTCCG 59.540 55.000 0.00 0.00 40.54 4.79
5112 5696 1.476891 GCAGTCCGTGGAACATCTCTA 59.523 52.381 0.00 0.00 44.52 2.43
5114 5698 3.430929 GCAGTCCGTGGAACATCTCTATT 60.431 47.826 0.00 0.00 44.52 1.73
5122 5706 5.644644 GTGGAACATCTCTATTGGCAAAAG 58.355 41.667 3.01 2.55 44.52 2.27
5123 5707 4.158394 TGGAACATCTCTATTGGCAAAAGC 59.842 41.667 3.01 0.00 0.00 3.51
5124 5708 4.400567 GGAACATCTCTATTGGCAAAAGCT 59.599 41.667 3.01 0.00 0.00 3.74
5167 5751 2.587060 AAGGGTGGAGGGTCATCATA 57.413 50.000 0.00 0.00 0.00 2.15
5199 5783 6.640518 TCTTGTGGACTGTCCTATGTATTTC 58.359 40.000 26.03 7.28 37.46 2.17
5201 5785 6.620877 TGTGGACTGTCCTATGTATTTCTT 57.379 37.500 26.03 0.00 37.46 2.52
5205 5789 8.237267 GTGGACTGTCCTATGTATTTCTTTTTG 58.763 37.037 26.03 0.00 37.46 2.44
5206 5790 8.160765 TGGACTGTCCTATGTATTTCTTTTTGA 58.839 33.333 26.03 0.00 37.46 2.69
5207 5791 9.010029 GGACTGTCCTATGTATTTCTTTTTGAA 57.990 33.333 19.53 0.00 32.53 2.69
5219 5803 7.920160 ATTTCTTTTTGAAACAGAGGCAAAA 57.080 28.000 0.00 0.00 46.08 2.44
5240 5824 7.820648 CAAAATTTGCCTCAACTCTGTATAGT 58.179 34.615 0.00 0.00 0.00 2.12
5241 5825 8.299570 CAAAATTTGCCTCAACTCTGTATAGTT 58.700 33.333 0.00 0.00 40.33 2.24
5248 5832 3.955650 AACTCTGTATAGTTGCGTGGT 57.044 42.857 0.00 0.00 38.28 4.16
5249 5833 3.955650 ACTCTGTATAGTTGCGTGGTT 57.044 42.857 0.00 0.00 0.00 3.67
5250 5834 5.395682 AACTCTGTATAGTTGCGTGGTTA 57.604 39.130 0.00 0.00 38.28 2.85
5251 5835 5.395682 ACTCTGTATAGTTGCGTGGTTAA 57.604 39.130 0.00 0.00 0.00 2.01
5252 5836 5.166398 ACTCTGTATAGTTGCGTGGTTAAC 58.834 41.667 0.00 0.00 0.00 2.01
5253 5837 5.047519 ACTCTGTATAGTTGCGTGGTTAACT 60.048 40.000 5.42 0.00 40.09 2.24
5254 5838 5.165676 TCTGTATAGTTGCGTGGTTAACTG 58.834 41.667 5.42 0.00 37.66 3.16
5255 5839 4.247258 TGTATAGTTGCGTGGTTAACTGG 58.753 43.478 5.42 0.00 37.66 4.00
5256 5840 2.914695 TAGTTGCGTGGTTAACTGGT 57.085 45.000 5.42 0.00 37.66 4.00
5257 5841 1.305201 AGTTGCGTGGTTAACTGGTG 58.695 50.000 5.42 0.00 35.91 4.17
5258 5842 0.309612 GTTGCGTGGTTAACTGGTGG 59.690 55.000 5.42 0.00 0.00 4.61
5259 5843 0.820074 TTGCGTGGTTAACTGGTGGG 60.820 55.000 5.42 0.00 0.00 4.61
5260 5844 1.071814 GCGTGGTTAACTGGTGGGA 59.928 57.895 5.42 0.00 0.00 4.37
5261 5845 0.535553 GCGTGGTTAACTGGTGGGAA 60.536 55.000 5.42 0.00 0.00 3.97
5262 5846 1.970092 CGTGGTTAACTGGTGGGAAA 58.030 50.000 5.42 0.00 0.00 3.13
5263 5847 2.510613 CGTGGTTAACTGGTGGGAAAT 58.489 47.619 5.42 0.00 0.00 2.17
5264 5848 2.486592 CGTGGTTAACTGGTGGGAAATC 59.513 50.000 5.42 0.00 0.00 2.17
5265 5849 3.492337 GTGGTTAACTGGTGGGAAATCA 58.508 45.455 5.42 0.00 0.00 2.57
5266 5850 3.506067 GTGGTTAACTGGTGGGAAATCAG 59.494 47.826 5.42 0.00 34.91 2.90
5267 5851 3.089284 GGTTAACTGGTGGGAAATCAGG 58.911 50.000 5.42 0.00 33.19 3.86
5268 5852 3.499745 GGTTAACTGGTGGGAAATCAGGT 60.500 47.826 5.42 0.00 33.19 4.00
5269 5853 2.292828 AACTGGTGGGAAATCAGGTG 57.707 50.000 0.00 0.00 33.19 4.00
5270 5854 1.444933 ACTGGTGGGAAATCAGGTGA 58.555 50.000 0.00 0.00 33.19 4.02
5271 5855 1.780309 ACTGGTGGGAAATCAGGTGAA 59.220 47.619 0.00 0.00 33.19 3.18
5272 5856 2.224867 ACTGGTGGGAAATCAGGTGAAG 60.225 50.000 0.00 0.00 33.19 3.02
5273 5857 2.040278 CTGGTGGGAAATCAGGTGAAGA 59.960 50.000 0.00 0.00 0.00 2.87
5274 5858 2.445145 TGGTGGGAAATCAGGTGAAGAA 59.555 45.455 0.00 0.00 0.00 2.52
5275 5859 3.075882 TGGTGGGAAATCAGGTGAAGAAT 59.924 43.478 0.00 0.00 0.00 2.40
5276 5860 3.445096 GGTGGGAAATCAGGTGAAGAATG 59.555 47.826 0.00 0.00 0.00 2.67
5277 5861 4.082125 GTGGGAAATCAGGTGAAGAATGT 58.918 43.478 0.00 0.00 0.00 2.71
5278 5862 4.156739 GTGGGAAATCAGGTGAAGAATGTC 59.843 45.833 0.00 0.00 0.00 3.06
5279 5863 4.202556 TGGGAAATCAGGTGAAGAATGTCA 60.203 41.667 0.00 0.00 0.00 3.58
5280 5864 4.952335 GGGAAATCAGGTGAAGAATGTCAT 59.048 41.667 0.00 0.00 0.00 3.06
5281 5865 6.122277 GGGAAATCAGGTGAAGAATGTCATA 58.878 40.000 0.00 0.00 0.00 2.15
5282 5866 6.603201 GGGAAATCAGGTGAAGAATGTCATAA 59.397 38.462 0.00 0.00 0.00 1.90
5283 5867 7.286316 GGGAAATCAGGTGAAGAATGTCATAAT 59.714 37.037 0.00 0.00 0.00 1.28
5284 5868 9.342308 GGAAATCAGGTGAAGAATGTCATAATA 57.658 33.333 0.00 0.00 0.00 0.98
5286 5870 7.976135 ATCAGGTGAAGAATGTCATAATAGC 57.024 36.000 0.00 0.00 0.00 2.97
5287 5871 6.291377 TCAGGTGAAGAATGTCATAATAGCC 58.709 40.000 0.00 0.00 0.00 3.93
5288 5872 6.057533 CAGGTGAAGAATGTCATAATAGCCA 58.942 40.000 0.00 0.00 0.00 4.75
5289 5873 6.543465 CAGGTGAAGAATGTCATAATAGCCAA 59.457 38.462 0.00 0.00 0.00 4.52
5290 5874 6.543831 AGGTGAAGAATGTCATAATAGCCAAC 59.456 38.462 0.00 0.00 0.00 3.77
5291 5875 6.318648 GGTGAAGAATGTCATAATAGCCAACA 59.681 38.462 0.00 0.00 0.00 3.33
5292 5876 7.189512 GTGAAGAATGTCATAATAGCCAACAC 58.810 38.462 0.00 0.00 0.00 3.32
5293 5877 6.318648 TGAAGAATGTCATAATAGCCAACACC 59.681 38.462 0.00 0.00 0.00 4.16
5294 5878 4.816385 AGAATGTCATAATAGCCAACACCG 59.184 41.667 0.00 0.00 0.00 4.94
5295 5879 2.912771 TGTCATAATAGCCAACACCGG 58.087 47.619 0.00 0.00 0.00 5.28
5312 5896 4.468689 GCCCACCTCGCTACCCAC 62.469 72.222 0.00 0.00 0.00 4.61
5313 5897 3.000819 CCCACCTCGCTACCCACA 61.001 66.667 0.00 0.00 0.00 4.17
5314 5898 2.367202 CCCACCTCGCTACCCACAT 61.367 63.158 0.00 0.00 0.00 3.21
5315 5899 1.153369 CCACCTCGCTACCCACATG 60.153 63.158 0.00 0.00 0.00 3.21
5316 5900 1.613317 CCACCTCGCTACCCACATGA 61.613 60.000 0.00 0.00 0.00 3.07
5317 5901 0.249120 CACCTCGCTACCCACATGAA 59.751 55.000 0.00 0.00 0.00 2.57
5318 5902 0.537188 ACCTCGCTACCCACATGAAG 59.463 55.000 0.00 0.00 0.00 3.02
5319 5903 0.824109 CCTCGCTACCCACATGAAGA 59.176 55.000 0.00 0.00 0.00 2.87
5320 5904 1.414181 CCTCGCTACCCACATGAAGAT 59.586 52.381 0.00 0.00 0.00 2.40
5321 5905 2.628178 CCTCGCTACCCACATGAAGATA 59.372 50.000 0.00 0.00 0.00 1.98
5322 5906 3.553096 CCTCGCTACCCACATGAAGATAC 60.553 52.174 0.00 0.00 0.00 2.24
5323 5907 3.028130 TCGCTACCCACATGAAGATACA 58.972 45.455 0.00 0.00 0.00 2.29
5324 5908 3.123804 CGCTACCCACATGAAGATACAC 58.876 50.000 0.00 0.00 0.00 2.90
5325 5909 3.430236 CGCTACCCACATGAAGATACACA 60.430 47.826 0.00 0.00 0.00 3.72
5326 5910 3.871594 GCTACCCACATGAAGATACACAC 59.128 47.826 0.00 0.00 0.00 3.82
5327 5911 2.972625 ACCCACATGAAGATACACACG 58.027 47.619 0.00 0.00 0.00 4.49
5328 5912 1.665679 CCCACATGAAGATACACACGC 59.334 52.381 0.00 0.00 0.00 5.34
5329 5913 2.621338 CCACATGAAGATACACACGCT 58.379 47.619 0.00 0.00 0.00 5.07
5330 5914 2.349580 CCACATGAAGATACACACGCTG 59.650 50.000 0.00 0.00 0.00 5.18
5331 5915 2.002586 ACATGAAGATACACACGCTGC 58.997 47.619 0.00 0.00 0.00 5.25
5332 5916 1.005662 CATGAAGATACACACGCTGCG 60.006 52.381 21.91 21.91 0.00 5.18
5333 5917 0.242555 TGAAGATACACACGCTGCGA 59.757 50.000 30.47 5.85 0.00 5.10
5334 5918 0.917259 GAAGATACACACGCTGCGAG 59.083 55.000 30.47 23.73 0.00 5.03
5335 5919 0.526211 AAGATACACACGCTGCGAGA 59.474 50.000 30.47 5.34 0.00 4.04
5336 5920 0.526211 AGATACACACGCTGCGAGAA 59.474 50.000 30.47 12.17 0.00 2.87
5337 5921 0.917259 GATACACACGCTGCGAGAAG 59.083 55.000 30.47 19.76 0.00 2.85
5338 5922 0.458543 ATACACACGCTGCGAGAAGG 60.459 55.000 30.47 17.11 0.00 3.46
5339 5923 1.520600 TACACACGCTGCGAGAAGGA 61.521 55.000 30.47 12.89 0.00 3.36
5340 5924 1.664649 CACACGCTGCGAGAAGGAA 60.665 57.895 30.47 0.00 0.00 3.36
5341 5925 1.069090 ACACGCTGCGAGAAGGAAA 59.931 52.632 30.47 0.00 0.00 3.13
5418 6013 1.025041 GGTTCGAATCTGGCCCATTC 58.975 55.000 12.62 12.62 0.00 2.67
5426 6021 4.764771 TGGCCCATTCCCTGCTGC 62.765 66.667 0.00 0.00 0.00 5.25
5520 6654 1.539496 GCGACAACCACTAGACCAACA 60.539 52.381 0.00 0.00 0.00 3.33
5943 7172 5.174037 AGGGAAAGTTCATGGATTTCGTA 57.826 39.130 0.00 0.00 34.47 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.729882 GTCGTCGTTGTAATTGTGCTCT 59.270 45.455 0.00 0.00 0.00 4.09
68 69 1.201181 ACAAAAACAGCAACACGCAGA 59.799 42.857 0.00 0.00 46.13 4.26
154 155 4.665009 TGGATATCTGCCCACTCCTTAATT 59.335 41.667 2.05 0.00 0.00 1.40
157 158 3.344535 TGGATATCTGCCCACTCCTTA 57.655 47.619 2.05 0.00 0.00 2.69
184 185 7.544566 TGCTTAGTATTTCTGAAAGTAGAACGG 59.455 37.037 8.95 0.00 36.48 4.44
283 285 0.734942 CGTCGTTACGTGCTTCCCAT 60.735 55.000 4.24 0.00 44.21 4.00
518 521 3.061848 CATGGTTCACGGCCACCC 61.062 66.667 2.24 0.00 39.03 4.61
545 548 9.191479 GGATAGGTTCAGTACATGCTACTATAT 57.809 37.037 0.00 0.00 0.00 0.86
549 552 5.208890 TGGATAGGTTCAGTACATGCTACT 58.791 41.667 0.00 0.00 0.00 2.57
583 587 1.539157 GCCTCTGCAAGTTTAGGCTT 58.461 50.000 13.51 0.00 45.32 4.35
617 621 3.291584 TCTCGGATCAGATACACAGCTT 58.708 45.455 0.00 0.00 0.00 3.74
697 701 6.059484 AGGAACGGTCAGAAATACTTGAAAA 58.941 36.000 1.31 0.00 0.00 2.29
708 712 1.003118 CCAATGGAGGAACGGTCAGAA 59.997 52.381 1.31 0.00 0.00 3.02
802 806 9.253832 AGCTAACAGATGAGTAGCTATATTCAT 57.746 33.333 16.09 14.49 41.71 2.57
909 913 6.854496 ACGTCAGCTTTATGAAACACTTAA 57.146 33.333 0.00 0.00 0.00 1.85
969 977 0.879839 GTTGGTGCCCAAATGTGTGC 60.880 55.000 8.06 0.00 45.73 4.57
979 987 1.456705 TTTGGGAGTGTTGGTGCCC 60.457 57.895 0.00 0.00 41.08 5.36
989 997 5.011635 GTGAATTTGGGTAATGTTTGGGAGT 59.988 40.000 0.00 0.00 0.00 3.85
990 998 5.245977 AGTGAATTTGGGTAATGTTTGGGAG 59.754 40.000 0.00 0.00 0.00 4.30
991 999 5.151454 AGTGAATTTGGGTAATGTTTGGGA 58.849 37.500 0.00 0.00 0.00 4.37
992 1000 5.011533 TGAGTGAATTTGGGTAATGTTTGGG 59.988 40.000 0.00 0.00 0.00 4.12
994 1002 8.430801 TTTTGAGTGAATTTGGGTAATGTTTG 57.569 30.769 0.00 0.00 0.00 2.93
995 1003 9.108284 CTTTTTGAGTGAATTTGGGTAATGTTT 57.892 29.630 0.00 0.00 0.00 2.83
996 1004 7.714813 CCTTTTTGAGTGAATTTGGGTAATGTT 59.285 33.333 0.00 0.00 0.00 2.71
997 1005 7.216494 CCTTTTTGAGTGAATTTGGGTAATGT 58.784 34.615 0.00 0.00 0.00 2.71
998 1006 6.650390 CCCTTTTTGAGTGAATTTGGGTAATG 59.350 38.462 0.00 0.00 0.00 1.90
999 1007 6.744056 GCCCTTTTTGAGTGAATTTGGGTAAT 60.744 38.462 0.00 0.00 34.88 1.89
1380 1430 0.958382 TGTACGGCTGGACCAATTGC 60.958 55.000 5.15 0.00 39.03 3.56
1565 1622 6.436843 AACTCCACACTTAAACTCTTTGTG 57.563 37.500 0.00 0.00 37.83 3.33
1566 1623 8.570068 TTAAACTCCACACTTAAACTCTTTGT 57.430 30.769 0.00 0.00 0.00 2.83
1692 1763 3.447229 CCATACCCCTCATTGTCCAAAAC 59.553 47.826 0.00 0.00 0.00 2.43
1739 1815 7.500992 TCTACCCAGAAGCATTAACTCATTAG 58.499 38.462 0.00 0.00 0.00 1.73
1956 2034 5.006386 AGCTAGAACTTTGAAGAATGGGTG 58.994 41.667 0.00 0.00 0.00 4.61
1959 2037 5.123027 GTCCAGCTAGAACTTTGAAGAATGG 59.877 44.000 0.00 0.00 0.00 3.16
1965 2043 3.746045 ACGTCCAGCTAGAACTTTGAA 57.254 42.857 0.00 0.00 0.00 2.69
1968 2046 4.595762 TTGTACGTCCAGCTAGAACTTT 57.404 40.909 0.00 0.00 0.00 2.66
1979 2057 0.178301 TGTGGTGCTTTGTACGTCCA 59.822 50.000 0.00 0.00 0.00 4.02
1984 2062 4.202111 ACTGGAAAATGTGGTGCTTTGTAC 60.202 41.667 0.00 0.00 0.00 2.90
2001 2079 2.325583 AGCGACACAGAAAACTGGAA 57.674 45.000 0.00 0.00 0.00 3.53
2010 2088 5.836821 ACTTCTCATTATAGCGACACAGA 57.163 39.130 0.00 0.00 0.00 3.41
2115 2198 7.961326 AGATAAATTCCAAGGCAGTGTAAAT 57.039 32.000 0.00 0.00 0.00 1.40
2206 2290 8.629158 CCAAAATATGCAAAGGTTACAGCTATA 58.371 33.333 0.00 0.00 0.00 1.31
2255 2339 7.116233 GCCTTTCGTGTTCACAAATATTGAAAT 59.884 33.333 3.87 0.00 34.78 2.17
2256 2340 6.419413 GCCTTTCGTGTTCACAAATATTGAAA 59.581 34.615 3.87 2.85 34.78 2.69
2274 2358 3.413558 GTTGCTAATAACACGCCTTTCG 58.586 45.455 0.00 0.00 45.38 3.46
2295 2379 3.260380 AGAAGAAGGGAGCGATATGATGG 59.740 47.826 0.00 0.00 0.00 3.51
2302 2386 1.480137 CTGTCAGAAGAAGGGAGCGAT 59.520 52.381 0.00 0.00 0.00 4.58
2304 2388 0.605589 ACTGTCAGAAGAAGGGAGCG 59.394 55.000 6.91 0.00 0.00 5.03
2309 2393 2.810852 GCCAAAGACTGTCAGAAGAAGG 59.189 50.000 10.88 4.13 0.00 3.46
2341 2428 7.732025 TGTATGTTGGATCGATAACCTACATT 58.268 34.615 26.37 16.29 45.03 2.71
2464 2551 7.390823 TCCTTAAACACTGCATGATAACACTA 58.609 34.615 0.00 0.00 0.00 2.74
2497 2584 6.599244 TGCTTGTTATATCAGCAGCTTTAACT 59.401 34.615 0.00 0.00 0.00 2.24
2542 2629 5.722263 TGAAATATTGGTGATGCAACTTGG 58.278 37.500 0.00 0.00 0.00 3.61
2594 2681 8.784043 CCCCTGCTACAGTTTAATATTTCATAC 58.216 37.037 0.00 0.00 0.00 2.39
2605 2692 2.706723 TCACAACCCCTGCTACAGTTTA 59.293 45.455 0.00 0.00 0.00 2.01
2611 2698 2.749621 CTCAATTCACAACCCCTGCTAC 59.250 50.000 0.00 0.00 0.00 3.58
2682 2774 6.968131 TTGATCTTCAATAGAGGAAACACG 57.032 37.500 0.00 0.00 36.02 4.49
2689 2781 8.704234 GCGTAGTATTTTGATCTTCAATAGAGG 58.296 37.037 0.00 0.00 36.11 3.69
2690 2782 8.704234 GGCGTAGTATTTTGATCTTCAATAGAG 58.296 37.037 0.00 0.00 36.11 2.43
2691 2783 8.201464 TGGCGTAGTATTTTGATCTTCAATAGA 58.799 33.333 0.00 0.00 36.11 1.98
2692 2784 8.365399 TGGCGTAGTATTTTGATCTTCAATAG 57.635 34.615 0.00 0.00 36.11 1.73
2693 2785 8.725405 TTGGCGTAGTATTTTGATCTTCAATA 57.275 30.769 0.00 0.00 36.11 1.90
2694 2786 7.624360 TTGGCGTAGTATTTTGATCTTCAAT 57.376 32.000 0.00 0.00 36.11 2.57
2695 2787 7.441890 TTTGGCGTAGTATTTTGATCTTCAA 57.558 32.000 0.00 0.00 34.03 2.69
2696 2788 7.441890 TTTTGGCGTAGTATTTTGATCTTCA 57.558 32.000 0.00 0.00 0.00 3.02
2697 2789 6.469275 GCTTTTGGCGTAGTATTTTGATCTTC 59.531 38.462 0.00 0.00 0.00 2.87
2708 2800 1.202782 TGGGTTGCTTTTGGCGTAGTA 60.203 47.619 0.00 0.00 45.43 1.82
2713 2805 0.460987 TTTGTGGGTTGCTTTTGGCG 60.461 50.000 0.00 0.00 45.43 5.69
2723 2815 2.099405 CAGTGTGGAACTTTGTGGGTT 58.901 47.619 0.00 0.00 36.83 4.11
2739 2831 4.753516 TGGTATACAGGGATGTTCAGTG 57.246 45.455 5.01 0.00 0.00 3.66
2746 2838 7.316393 TCCTTTTCTATGGTATACAGGGATG 57.684 40.000 5.01 0.00 0.00 3.51
2758 2850 9.492973 AACATCATTTTGTTTCCTTTTCTATGG 57.507 29.630 0.00 0.00 36.43 2.74
2778 2870 9.047371 TGTCAACGTTCTATTTTTCTAACATCA 57.953 29.630 0.00 0.00 0.00 3.07
2783 2875 9.658475 CACAATGTCAACGTTCTATTTTTCTAA 57.342 29.630 0.00 0.00 0.00 2.10
2787 2879 6.417635 CAGCACAATGTCAACGTTCTATTTTT 59.582 34.615 0.00 0.00 0.00 1.94
2797 2889 0.943673 TGACCAGCACAATGTCAACG 59.056 50.000 0.00 0.00 36.16 4.10
2840 2932 2.942376 GACGACCAATGTTGCCATATCA 59.058 45.455 0.00 0.00 0.00 2.15
2861 2953 2.671396 GCCGTATGTACAACAACAGGAG 59.329 50.000 0.00 0.00 31.70 3.69
2871 2963 1.477295 TGAATCACCGCCGTATGTACA 59.523 47.619 0.00 0.00 0.00 2.90
2882 2974 3.133691 CACATATCCCAGTGAATCACCG 58.866 50.000 10.12 0.00 37.97 4.94
2883 2975 3.136443 TCCACATATCCCAGTGAATCACC 59.864 47.826 10.12 0.00 37.97 4.02
2884 2976 4.101585 TCTCCACATATCCCAGTGAATCAC 59.898 45.833 5.02 5.02 37.97 3.06
2885 2977 4.297768 TCTCCACATATCCCAGTGAATCA 58.702 43.478 0.00 0.00 37.97 2.57
2886 2978 4.963318 TCTCCACATATCCCAGTGAATC 57.037 45.455 0.00 0.00 37.97 2.52
2888 2980 4.080919 CAGTTCTCCACATATCCCAGTGAA 60.081 45.833 0.00 0.00 37.97 3.18
2908 3003 2.906268 GGGTACACGTATCCCCAGT 58.094 57.895 9.97 0.00 37.09 4.00
2913 3008 1.772836 ACTCAGGGGTACACGTATCC 58.227 55.000 0.00 0.00 35.57 2.59
2914 3009 3.505293 GGATACTCAGGGGTACACGTATC 59.495 52.174 10.69 10.69 34.99 2.24
2915 3010 3.494332 GGATACTCAGGGGTACACGTAT 58.506 50.000 0.00 0.00 0.00 3.06
2958 3235 7.829706 GTCCCAGCCTATCCCTATTTATTTTAG 59.170 40.741 0.00 0.00 0.00 1.85
2990 3268 2.354103 CCCATATCACAGCCGTATCTGG 60.354 54.545 0.00 0.00 38.36 3.86
3062 3590 0.622665 CATCTTTCTCCCTGCCCAGT 59.377 55.000 0.00 0.00 0.00 4.00
3257 3785 5.048013 CCCAATTTCAGAAAACCCTAGACAC 60.048 44.000 0.00 0.00 0.00 3.67
3258 3786 5.076873 CCCAATTTCAGAAAACCCTAGACA 58.923 41.667 0.00 0.00 0.00 3.41
3297 3825 2.503895 ATGAAGGACTTTGAGCAGGG 57.496 50.000 0.00 0.00 0.00 4.45
3327 3855 7.896811 TGAGAGTACTGAATACATGTTGTCTT 58.103 34.615 2.30 0.00 36.09 3.01
3458 4004 3.682858 GCCACGCTAAGAAACACTGATAA 59.317 43.478 0.00 0.00 0.00 1.75
3463 4009 0.107831 TGGCCACGCTAAGAAACACT 59.892 50.000 0.00 0.00 0.00 3.55
3467 4013 2.179764 GCATGGCCACGCTAAGAAA 58.820 52.632 18.36 0.00 0.00 2.52
4033 4594 5.182190 TCAAGCAACTATTTAATGCACGGAA 59.818 36.000 0.00 0.00 42.45 4.30
4067 4628 0.678950 AAAAATCAGGGTGGTTGGCG 59.321 50.000 0.00 0.00 0.00 5.69
4087 4648 2.373169 GGAGTATGGATCCCTGCATTGA 59.627 50.000 9.90 0.00 34.89 2.57
4093 4654 3.048600 TCCTTTGGAGTATGGATCCCTG 58.951 50.000 9.90 0.00 35.86 4.45
4189 4757 3.555139 GCACTCAGATCATGCAACTAGAC 59.445 47.826 0.00 0.00 39.23 2.59
4235 4804 3.311106 CTGAAGCATGAACGCAATGTTT 58.689 40.909 0.00 0.00 42.09 2.83
4243 4812 2.975410 TGAAAGCTGAAGCATGAACG 57.025 45.000 4.90 0.00 45.16 3.95
4296 4866 2.468777 CGCATGTTTCAGCACTTTTGTC 59.531 45.455 0.00 0.00 0.00 3.18
4297 4867 2.159254 ACGCATGTTTCAGCACTTTTGT 60.159 40.909 0.00 0.00 0.00 2.83
4298 4868 2.462889 ACGCATGTTTCAGCACTTTTG 58.537 42.857 0.00 0.00 0.00 2.44
4316 4886 2.847327 AGCATATGGGAGATGGAACG 57.153 50.000 4.56 0.00 0.00 3.95
4320 4890 3.708403 TGCTTAGCATATGGGAGATGG 57.292 47.619 1.39 0.00 31.71 3.51
4411 4983 9.778741 ACAAGACGGACATATACATATCAAAAT 57.221 29.630 0.00 0.00 0.00 1.82
4430 5004 0.531090 TGGTTGACCGGAACAAGACG 60.531 55.000 9.46 0.00 39.43 4.18
4494 5068 3.251004 GGCTTCGTTTGACACATTCTCTT 59.749 43.478 0.00 0.00 0.00 2.85
4504 5078 3.889196 TGTAACATGGCTTCGTTTGAC 57.111 42.857 0.00 0.00 0.00 3.18
4505 5079 4.759693 AGAATGTAACATGGCTTCGTTTGA 59.240 37.500 0.00 0.00 0.00 2.69
4511 5085 5.504665 CGAATGGAGAATGTAACATGGCTTC 60.505 44.000 0.00 0.00 0.00 3.86
4515 5089 5.220854 GGTTCGAATGGAGAATGTAACATGG 60.221 44.000 0.00 0.00 0.00 3.66
4550 5124 9.005777 TCTGCTGACGGTTTAACTTAAAATAAT 57.994 29.630 0.00 0.00 0.00 1.28
4554 5128 6.316890 AGTTCTGCTGACGGTTTAACTTAAAA 59.683 34.615 0.00 0.00 0.00 1.52
4555 5129 5.818857 AGTTCTGCTGACGGTTTAACTTAAA 59.181 36.000 0.00 0.00 0.00 1.52
4556 5130 5.362263 AGTTCTGCTGACGGTTTAACTTAA 58.638 37.500 0.00 0.00 0.00 1.85
4557 5131 4.952460 AGTTCTGCTGACGGTTTAACTTA 58.048 39.130 0.00 0.00 0.00 2.24
4630 5204 9.725019 GGGTATGTATGTCATATCAAAGAATCA 57.275 33.333 0.00 0.00 40.75 2.57
4714 5289 2.120232 GTATCCTCATGCTTGTCGTCG 58.880 52.381 0.00 0.00 0.00 5.12
4756 5331 2.095567 CACGCTTTTCACCTCTGGATTG 60.096 50.000 0.00 0.00 0.00 2.67
4811 5386 3.795688 AGGTGATCTGCTTTCCTTGAA 57.204 42.857 0.00 0.00 0.00 2.69
4850 5425 3.565307 TCCTTCTGTGTTTTGGCTTGAT 58.435 40.909 0.00 0.00 0.00 2.57
4855 5430 3.632145 TCTTCTTCCTTCTGTGTTTTGGC 59.368 43.478 0.00 0.00 0.00 4.52
4909 5486 6.488006 CCATCATGGAATTAAGAACTGTAGGG 59.512 42.308 0.00 0.00 40.96 3.53
4917 5494 8.548025 TGTCTAGAACCATCATGGAATTAAGAA 58.452 33.333 11.90 0.00 40.96 2.52
4966 5543 3.192541 AGCATGTGCACCGTCAATATA 57.807 42.857 15.69 0.00 45.16 0.86
4967 5544 2.042686 AGCATGTGCACCGTCAATAT 57.957 45.000 15.69 0.00 45.16 1.28
5086 5670 0.249398 GTTCCACGGACTGCCTACAT 59.751 55.000 0.00 0.00 0.00 2.29
5099 5683 5.643379 TTTTGCCAATAGAGATGTTCCAC 57.357 39.130 0.00 0.00 0.00 4.02
5114 5698 8.852696 CCTTCAATCAGGAAAAGCTTTTGCCA 62.853 42.308 32.06 22.48 40.67 4.92
5122 5706 3.425659 AGGTCCTTCAATCAGGAAAAGC 58.574 45.455 0.00 0.00 45.03 3.51
5123 5707 5.072741 TGAAGGTCCTTCAATCAGGAAAAG 58.927 41.667 28.64 0.00 45.84 2.27
5124 5708 5.060427 TGAAGGTCCTTCAATCAGGAAAA 57.940 39.130 28.64 4.51 45.84 2.29
5156 5740 3.464828 AGAACCCAAGTATGATGACCCT 58.535 45.455 0.00 0.00 0.00 4.34
5167 5751 1.564348 ACAGTCCACAAGAACCCAAGT 59.436 47.619 0.00 0.00 0.00 3.16
5199 5783 7.958112 CAAATTTTGCCTCTGTTTCAAAAAG 57.042 32.000 0.00 0.00 41.26 2.27
5234 5818 4.092383 CACCAGTTAACCACGCAACTATAC 59.908 45.833 0.88 0.00 33.29 1.47
5235 5819 4.247258 CACCAGTTAACCACGCAACTATA 58.753 43.478 0.88 0.00 33.29 1.31
5236 5820 3.071479 CACCAGTTAACCACGCAACTAT 58.929 45.455 0.88 0.00 33.29 2.12
5237 5821 2.485903 CACCAGTTAACCACGCAACTA 58.514 47.619 0.88 0.00 33.29 2.24
5238 5822 1.305201 CACCAGTTAACCACGCAACT 58.695 50.000 0.88 0.00 35.38 3.16
5239 5823 0.309612 CCACCAGTTAACCACGCAAC 59.690 55.000 0.88 0.00 0.00 4.17
5240 5824 0.820074 CCCACCAGTTAACCACGCAA 60.820 55.000 0.88 0.00 0.00 4.85
5241 5825 1.228003 CCCACCAGTTAACCACGCA 60.228 57.895 0.88 0.00 0.00 5.24
5242 5826 0.535553 TTCCCACCAGTTAACCACGC 60.536 55.000 0.88 0.00 0.00 5.34
5243 5827 1.970092 TTTCCCACCAGTTAACCACG 58.030 50.000 0.88 0.00 0.00 4.94
5244 5828 3.492337 TGATTTCCCACCAGTTAACCAC 58.508 45.455 0.88 0.00 0.00 4.16
5245 5829 3.499563 CCTGATTTCCCACCAGTTAACCA 60.500 47.826 0.88 0.00 0.00 3.67
5246 5830 3.089284 CCTGATTTCCCACCAGTTAACC 58.911 50.000 0.88 0.00 0.00 2.85
5247 5831 3.506067 CACCTGATTTCCCACCAGTTAAC 59.494 47.826 0.00 0.00 0.00 2.01
5248 5832 3.396276 TCACCTGATTTCCCACCAGTTAA 59.604 43.478 0.00 0.00 0.00 2.01
5249 5833 2.983192 TCACCTGATTTCCCACCAGTTA 59.017 45.455 0.00 0.00 0.00 2.24
5250 5834 1.780309 TCACCTGATTTCCCACCAGTT 59.220 47.619 0.00 0.00 0.00 3.16
5251 5835 1.444933 TCACCTGATTTCCCACCAGT 58.555 50.000 0.00 0.00 0.00 4.00
5252 5836 2.040278 TCTTCACCTGATTTCCCACCAG 59.960 50.000 0.00 0.00 0.00 4.00
5253 5837 2.061848 TCTTCACCTGATTTCCCACCA 58.938 47.619 0.00 0.00 0.00 4.17
5254 5838 2.879103 TCTTCACCTGATTTCCCACC 57.121 50.000 0.00 0.00 0.00 4.61
5255 5839 4.082125 ACATTCTTCACCTGATTTCCCAC 58.918 43.478 0.00 0.00 0.00 4.61
5256 5840 4.202556 TGACATTCTTCACCTGATTTCCCA 60.203 41.667 0.00 0.00 0.00 4.37
5257 5841 4.335416 TGACATTCTTCACCTGATTTCCC 58.665 43.478 0.00 0.00 0.00 3.97
5258 5842 7.630242 TTATGACATTCTTCACCTGATTTCC 57.370 36.000 0.00 0.00 0.00 3.13
5260 5844 8.844244 GCTATTATGACATTCTTCACCTGATTT 58.156 33.333 0.00 0.00 0.00 2.17
5261 5845 7.446625 GGCTATTATGACATTCTTCACCTGATT 59.553 37.037 0.00 0.00 0.00 2.57
5262 5846 6.939163 GGCTATTATGACATTCTTCACCTGAT 59.061 38.462 0.00 0.00 0.00 2.90
5263 5847 6.126796 TGGCTATTATGACATTCTTCACCTGA 60.127 38.462 0.00 0.00 0.00 3.86
5264 5848 6.057533 TGGCTATTATGACATTCTTCACCTG 58.942 40.000 0.00 0.00 0.00 4.00
5265 5849 6.252599 TGGCTATTATGACATTCTTCACCT 57.747 37.500 0.00 0.00 0.00 4.00
5266 5850 6.318648 TGTTGGCTATTATGACATTCTTCACC 59.681 38.462 0.00 0.00 0.00 4.02
5267 5851 7.189512 GTGTTGGCTATTATGACATTCTTCAC 58.810 38.462 0.00 0.00 0.00 3.18
5268 5852 6.318648 GGTGTTGGCTATTATGACATTCTTCA 59.681 38.462 0.00 0.00 0.00 3.02
5269 5853 6.511767 CGGTGTTGGCTATTATGACATTCTTC 60.512 42.308 0.00 0.00 0.00 2.87
5270 5854 5.296780 CGGTGTTGGCTATTATGACATTCTT 59.703 40.000 0.00 0.00 0.00 2.52
5271 5855 4.816385 CGGTGTTGGCTATTATGACATTCT 59.184 41.667 0.00 0.00 0.00 2.40
5272 5856 4.024048 CCGGTGTTGGCTATTATGACATTC 60.024 45.833 0.00 0.00 0.00 2.67
5273 5857 3.882888 CCGGTGTTGGCTATTATGACATT 59.117 43.478 0.00 0.00 0.00 2.71
5274 5858 3.476552 CCGGTGTTGGCTATTATGACAT 58.523 45.455 0.00 0.00 0.00 3.06
5275 5859 2.912771 CCGGTGTTGGCTATTATGACA 58.087 47.619 0.00 0.00 0.00 3.58
5295 5879 4.468689 GTGGGTAGCGAGGTGGGC 62.469 72.222 0.00 0.00 0.00 5.36
5296 5880 2.367202 ATGTGGGTAGCGAGGTGGG 61.367 63.158 0.00 0.00 0.00 4.61
5297 5881 1.153369 CATGTGGGTAGCGAGGTGG 60.153 63.158 0.00 0.00 0.00 4.61
5298 5882 0.249120 TTCATGTGGGTAGCGAGGTG 59.751 55.000 0.00 0.00 0.00 4.00
5299 5883 0.537188 CTTCATGTGGGTAGCGAGGT 59.463 55.000 0.00 0.00 0.00 3.85
5300 5884 0.824109 TCTTCATGTGGGTAGCGAGG 59.176 55.000 0.00 0.00 0.00 4.63
5301 5885 2.898729 ATCTTCATGTGGGTAGCGAG 57.101 50.000 0.00 0.00 0.00 5.03
5302 5886 3.028130 TGTATCTTCATGTGGGTAGCGA 58.972 45.455 0.00 0.00 0.00 4.93
5303 5887 3.123804 GTGTATCTTCATGTGGGTAGCG 58.876 50.000 0.00 0.00 0.00 4.26
5304 5888 3.871594 GTGTGTATCTTCATGTGGGTAGC 59.128 47.826 0.00 0.00 0.00 3.58
5305 5889 4.112634 CGTGTGTATCTTCATGTGGGTAG 58.887 47.826 0.00 0.00 0.00 3.18
5306 5890 3.677700 GCGTGTGTATCTTCATGTGGGTA 60.678 47.826 0.00 0.00 0.00 3.69
5307 5891 2.935238 GCGTGTGTATCTTCATGTGGGT 60.935 50.000 0.00 0.00 0.00 4.51
5308 5892 1.665679 GCGTGTGTATCTTCATGTGGG 59.334 52.381 0.00 0.00 0.00 4.61
5309 5893 2.349580 CAGCGTGTGTATCTTCATGTGG 59.650 50.000 0.00 0.00 0.00 4.17
5310 5894 2.222886 GCAGCGTGTGTATCTTCATGTG 60.223 50.000 0.00 0.00 0.00 3.21
5311 5895 2.002586 GCAGCGTGTGTATCTTCATGT 58.997 47.619 0.00 0.00 0.00 3.21
5312 5896 1.005662 CGCAGCGTGTGTATCTTCATG 60.006 52.381 6.65 0.00 0.00 3.07
5313 5897 1.135112 TCGCAGCGTGTGTATCTTCAT 60.135 47.619 15.93 0.00 0.00 2.57
5314 5898 0.242555 TCGCAGCGTGTGTATCTTCA 59.757 50.000 15.93 0.00 0.00 3.02
5315 5899 0.917259 CTCGCAGCGTGTGTATCTTC 59.083 55.000 15.93 0.00 0.00 2.87
5316 5900 0.526211 TCTCGCAGCGTGTGTATCTT 59.474 50.000 15.93 0.00 0.00 2.40
5317 5901 0.526211 TTCTCGCAGCGTGTGTATCT 59.474 50.000 15.93 0.00 0.00 1.98
5318 5902 0.917259 CTTCTCGCAGCGTGTGTATC 59.083 55.000 15.93 0.00 0.00 2.24
5319 5903 0.458543 CCTTCTCGCAGCGTGTGTAT 60.459 55.000 15.93 0.00 0.00 2.29
5320 5904 1.080772 CCTTCTCGCAGCGTGTGTA 60.081 57.895 15.93 2.18 0.00 2.90
5321 5905 2.356313 CCTTCTCGCAGCGTGTGT 60.356 61.111 15.93 0.00 0.00 3.72
5322 5906 1.221466 TTTCCTTCTCGCAGCGTGTG 61.221 55.000 15.93 9.74 0.00 3.82
5323 5907 0.946221 CTTTCCTTCTCGCAGCGTGT 60.946 55.000 15.93 0.00 0.00 4.49
5324 5908 1.630244 CCTTTCCTTCTCGCAGCGTG 61.630 60.000 15.93 13.15 0.00 5.34
5325 5909 1.374758 CCTTTCCTTCTCGCAGCGT 60.375 57.895 15.93 0.00 0.00 5.07
5326 5910 2.103042 CCCTTTCCTTCTCGCAGCG 61.103 63.158 9.06 9.06 0.00 5.18
5327 5911 0.742635 CTCCCTTTCCTTCTCGCAGC 60.743 60.000 0.00 0.00 0.00 5.25
5328 5912 0.742635 GCTCCCTTTCCTTCTCGCAG 60.743 60.000 0.00 0.00 0.00 5.18
5329 5913 1.296715 GCTCCCTTTCCTTCTCGCA 59.703 57.895 0.00 0.00 0.00 5.10
5330 5914 1.450491 GGCTCCCTTTCCTTCTCGC 60.450 63.158 0.00 0.00 0.00 5.03
5331 5915 1.222113 GGGCTCCCTTTCCTTCTCG 59.778 63.158 0.00 0.00 0.00 4.04
5332 5916 1.610327 GGGGCTCCCTTTCCTTCTC 59.390 63.158 4.74 0.00 41.34 2.87
5333 5917 3.842570 GGGGCTCCCTTTCCTTCT 58.157 61.111 4.74 0.00 41.34 2.85
5418 6013 0.758123 TTTTTCCTTTGGCAGCAGGG 59.242 50.000 13.34 0.00 0.00 4.45
5426 6021 8.499403 TGGTTATTTTTCACTTTTTCCTTTGG 57.501 30.769 0.00 0.00 0.00 3.28
5835 7060 9.504708 AAATGGATGAACTATTTTGCAAATTCA 57.495 25.926 21.78 21.78 36.52 2.57


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

AutoCloner maintained by Alex Coulton.