Multiple sequence alignment - TraesCS3A01G016200

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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 TraesCS3A01G016200 chr3A 100.000 4052 0 0 1 4052 10498344 10502395 0.000000e+00 7483.0
1 TraesCS3A01G016200 chr3A 89.106 3075 268 25 682 3724 10264340 10261301 0.000000e+00 3760.0
2 TraesCS3A01G016200 chr3A 91.979 374 25 5 3157 3527 10252339 10251968 1.670000e-143 520.0
3 TraesCS3A01G016200 chr3A 86.473 207 25 2 3781 3987 10261296 10261093 1.470000e-54 224.0
4 TraesCS3A01G016200 chr3A 92.157 102 8 0 282 383 10267286 10267185 1.170000e-30 145.0
5 TraesCS3A01G016200 chr3A 93.023 86 3 2 3639 3724 10248302 10248220 5.500000e-24 122.0
6 TraesCS3A01G016200 chr3A 100.000 52 0 0 3725 3776 209415881 209415830 3.330000e-16 97.1
7 TraesCS3A01G016200 chr3A 100.000 29 0 0 617 645 10264596 10264568 2.000000e-03 54.7
8 TraesCS3A01G016200 chr7B 89.106 3075 268 25 682 3724 440825564 440822525 0.000000e+00 3760.0
9 TraesCS3A01G016200 chr7B 86.473 207 25 2 3781 3987 440822520 440822317 1.470000e-54 224.0
10 TraesCS3A01G016200 chr7B 100.000 29 0 0 617 645 440825820 440825792 2.000000e-03 54.7
11 TraesCS3A01G016200 chr5B 89.106 3075 268 25 682 3724 319324880 319321841 0.000000e+00 3760.0
12 TraesCS3A01G016200 chr5B 86.473 207 25 2 3781 3987 319321836 319321633 1.470000e-54 224.0
13 TraesCS3A01G016200 chr5B 100.000 29 0 0 617 645 319325136 319325108 2.000000e-03 54.7
14 TraesCS3A01G016200 chrUn 88.715 2295 198 17 918 3176 35542232 35539963 0.000000e+00 2747.0
15 TraesCS3A01G016200 chrUn 88.715 2295 198 17 918 3176 244205908 244208177 0.000000e+00 2747.0
16 TraesCS3A01G016200 chrUn 85.043 1150 144 14 1953 3093 301607667 301606537 0.000000e+00 1146.0
17 TraesCS3A01G016200 chrUn 86.391 654 33 20 3090 3724 301606291 301605675 0.000000e+00 664.0
18 TraesCS3A01G016200 chrUn 90.933 386 24 9 3343 3724 35688129 35688507 3.610000e-140 508.0
19 TraesCS3A01G016200 chrUn 91.667 360 14 9 1 344 35542928 35542569 6.090000e-133 484.0
20 TraesCS3A01G016200 chrUn 91.667 360 14 9 1 344 244205212 244205571 6.090000e-133 484.0
21 TraesCS3A01G016200 chrUn 97.842 139 3 0 429 567 35542474 35542336 1.460000e-59 241.0
22 TraesCS3A01G016200 chrUn 97.842 139 3 0 429 567 244205666 244205804 1.460000e-59 241.0
23 TraesCS3A01G016200 chrUn 92.481 133 7 1 3777 3906 35688508 35688640 1.920000e-43 187.0
24 TraesCS3A01G016200 chrUn 91.379 116 10 0 3872 3987 35539323 35539208 4.190000e-35 159.0
25 TraesCS3A01G016200 chrUn 91.379 116 10 0 3872 3987 244208817 244208932 4.190000e-35 159.0
26 TraesCS3A01G016200 chrUn 91.071 112 10 0 3876 3987 34583065 34582954 7.010000e-33 152.0
27 TraesCS3A01G016200 chr3D 90.970 897 45 15 2847 3724 4946429 4947308 0.000000e+00 1175.0
28 TraesCS3A01G016200 chr3D 83.217 1150 166 20 1918 3052 28210640 28209503 0.000000e+00 1029.0
29 TraesCS3A01G016200 chr3D 87.824 386 32 9 3343 3724 4464941 4464567 4.810000e-119 438.0
30 TraesCS3A01G016200 chr3D 91.943 211 16 1 3777 3987 4947309 4947518 1.100000e-75 294.0
31 TraesCS3A01G016200 chr3D 92.308 104 8 0 280 383 4940597 4940700 9.070000e-32 148.0
32 TraesCS3A01G016200 chr3D 93.750 64 4 0 3924 3987 4464235 4464172 3.330000e-16 97.1
33 TraesCS3A01G016200 chr5D 81.752 1096 184 10 1967 3054 9102777 9103864 0.000000e+00 902.0
34 TraesCS3A01G016200 chr5D 77.815 604 103 19 1188 1777 9089042 9089628 1.080000e-90 344.0
35 TraesCS3A01G016200 chr5D 93.750 80 3 2 3973 4052 297491677 297491600 7.110000e-23 119.0
36 TraesCS3A01G016200 chr5A 80.215 743 129 9 2315 3052 7181808 7182537 3.560000e-150 542.0
37 TraesCS3A01G016200 chr5A 93.750 80 4 1 3973 4052 8173047 8172969 7.110000e-23 119.0
38 TraesCS3A01G016200 chr2A 97.260 73 2 0 3980 4052 57694612 57694684 1.530000e-24 124.0
39 TraesCS3A01G016200 chr4B 96.000 75 3 0 3978 4052 603233860 603233934 5.500000e-24 122.0
40 TraesCS3A01G016200 chr2B 96.000 75 3 0 3978 4052 490134300 490134374 5.500000e-24 122.0
41 TraesCS3A01G016200 chr2B 96.000 75 3 0 3978 4052 490167247 490167321 5.500000e-24 122.0
42 TraesCS3A01G016200 chr1B 96.000 75 3 0 3978 4052 63411276 63411350 5.500000e-24 122.0
43 TraesCS3A01G016200 chr1B 96.000 75 3 0 3978 4052 441156482 441156408 5.500000e-24 122.0
44 TraesCS3A01G016200 chr1B 96.000 75 3 0 3978 4052 447890019 447890093 5.500000e-24 122.0
45 TraesCS3A01G016200 chr3B 100.000 52 0 0 3725 3776 173941705 173941756 3.330000e-16 97.1
46 TraesCS3A01G016200 chr2D 100.000 52 0 0 3725 3776 291703789 291703840 3.330000e-16 97.1
47 TraesCS3A01G016200 chr6D 98.113 53 0 1 3725 3776 57943811 57943759 1.550000e-14 91.6
48 TraesCS3A01G016200 chr4D 98.113 53 0 1 3725 3776 123397978 123398030 1.550000e-14 91.6
49 TraesCS3A01G016200 chr4D 98.113 53 0 1 3725 3776 134959464 134959516 1.550000e-14 91.6
50 TraesCS3A01G016200 chr4D 98.113 53 0 1 3725 3776 241112268 241112320 1.550000e-14 91.6
51 TraesCS3A01G016200 chr1A 98.113 53 0 1 3725 3776 94576669 94576721 1.550000e-14 91.6
52 TraesCS3A01G016200 chr1A 98.113 53 0 1 3725 3776 94577351 94577403 1.550000e-14 91.6
53 TraesCS3A01G016200 chr7D 92.308 52 4 0 2309 2360 176160383 176160434 1.560000e-09 75.0


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 TraesCS3A01G016200 chr3A 10498344 10502395 4051 False 7483.000000 7483 100.000000 1 4052 1 chr3A.!!$F1 4051
1 TraesCS3A01G016200 chr3A 10261093 10267286 6193 True 1045.925000 3760 91.934000 282 3987 4 chr3A.!!$R3 3705
2 TraesCS3A01G016200 chr3A 10248220 10252339 4119 True 321.000000 520 92.501000 3157 3724 2 chr3A.!!$R2 567
3 TraesCS3A01G016200 chr7B 440822317 440825820 3503 True 1346.233333 3760 91.859667 617 3987 3 chr7B.!!$R1 3370
4 TraesCS3A01G016200 chr5B 319321633 319325136 3503 True 1346.233333 3760 91.859667 617 3987 3 chr5B.!!$R1 3370
5 TraesCS3A01G016200 chrUn 35539208 35542928 3720 True 907.750000 2747 92.400750 1 3987 4 chrUn.!!$R2 3986
6 TraesCS3A01G016200 chrUn 244205212 244208932 3720 False 907.750000 2747 92.400750 1 3987 4 chrUn.!!$F2 3986
7 TraesCS3A01G016200 chrUn 301605675 301607667 1992 True 905.000000 1146 85.717000 1953 3724 2 chrUn.!!$R3 1771
8 TraesCS3A01G016200 chrUn 35688129 35688640 511 False 347.500000 508 91.707000 3343 3906 2 chrUn.!!$F1 563
9 TraesCS3A01G016200 chr3D 28209503 28210640 1137 True 1029.000000 1029 83.217000 1918 3052 1 chr3D.!!$R1 1134
10 TraesCS3A01G016200 chr3D 4946429 4947518 1089 False 734.500000 1175 91.456500 2847 3987 2 chr3D.!!$F2 1140
11 TraesCS3A01G016200 chr3D 4464172 4464941 769 True 267.550000 438 90.787000 3343 3987 2 chr3D.!!$R2 644
12 TraesCS3A01G016200 chr5D 9102777 9103864 1087 False 902.000000 902 81.752000 1967 3054 1 chr5D.!!$F2 1087
13 TraesCS3A01G016200 chr5D 9089042 9089628 586 False 344.000000 344 77.815000 1188 1777 1 chr5D.!!$F1 589
14 TraesCS3A01G016200 chr5A 7181808 7182537 729 False 542.000000 542 80.215000 2315 3052 1 chr5A.!!$F1 737

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
334 351 0.107643 TCTGTGATTCCCGTGCAACA 59.892 50.0 0.0 0.0 35.74 3.33 F
1806 4450 0.105760 ATTGGTGTGCCTCCCAACAA 60.106 50.0 0.7 0.0 43.17 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2245 4904 0.179000 AGGCGACCAAGGATGATGAC 59.821 55.0 0.0 0.0 0.0 3.06 R
3337 6297 0.033642 GTAGCTGCCGTTCCTATCCC 59.966 60.0 0.0 0.0 0.0 3.85 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 3.167485 TCCTGCCTTTCCGAACTTACTA 58.833 45.455 0.00 0.00 0.00 1.82
77 78 8.798859 TCCGAACTTACTAGATTAGTGTTAGT 57.201 34.615 0.00 0.00 39.81 2.24
101 102 3.855689 AATTGCACTGCTGGTTGATAC 57.144 42.857 1.98 0.00 0.00 2.24
132 133 5.174037 TGGTGTTTATTAGTCCCTTGAGG 57.826 43.478 0.00 0.00 0.00 3.86
139 140 1.652947 TAGTCCCTTGAGGTCCCAAC 58.347 55.000 0.00 0.00 36.75 3.77
151 152 4.041198 TGAGGTCCCAACTTTCTTTCGTAT 59.959 41.667 0.00 0.00 0.00 3.06
203 204 8.577939 CGTGTGAAAATTTGAACATGCTATTAG 58.422 33.333 10.94 0.00 0.00 1.73
274 275 1.457346 ATACTGCAGCTGCTTGGAAC 58.543 50.000 36.61 9.26 42.66 3.62
275 276 0.397941 TACTGCAGCTGCTTGGAACT 59.602 50.000 36.61 16.64 42.66 3.01
276 277 0.888285 ACTGCAGCTGCTTGGAACTC 60.888 55.000 36.61 7.74 42.66 3.01
277 278 0.887836 CTGCAGCTGCTTGGAACTCA 60.888 55.000 36.61 14.40 42.66 3.41
280 293 2.866028 GCTGCTTGGAACTCAGCG 59.134 61.111 0.00 0.00 42.86 5.18
285 298 0.514691 GCTTGGAACTCAGCGTCTTG 59.485 55.000 0.00 0.00 0.00 3.02
334 351 0.107643 TCTGTGATTCCCGTGCAACA 59.892 50.000 0.00 0.00 35.74 3.33
345 362 1.609061 CCGTGCAACAGAGAAGGATGT 60.609 52.381 0.00 0.00 35.74 3.06
361 378 1.137872 GATGTCCAGAGCCTCGTCATT 59.862 52.381 0.00 0.00 0.00 2.57
365 382 1.347707 TCCAGAGCCTCGTCATTTTGT 59.652 47.619 0.00 0.00 0.00 2.83
388 405 5.127682 GTGTTCTCTGGCCAATATGGATTTT 59.872 40.000 7.01 0.00 40.96 1.82
395 412 4.529769 TGGCCAATATGGATTTTTGTGACA 59.470 37.500 0.61 0.00 40.96 3.58
397 414 5.351189 GGCCAATATGGATTTTTGTGACAAC 59.649 40.000 0.00 0.00 40.96 3.32
398 415 5.351189 GCCAATATGGATTTTTGTGACAACC 59.649 40.000 0.00 0.00 40.96 3.77
422 596 2.369860 CCCTTGACTAGCCTATCATGCA 59.630 50.000 0.00 0.00 0.00 3.96
424 598 4.001652 CCTTGACTAGCCTATCATGCATG 58.998 47.826 21.07 21.07 0.00 4.06
425 599 3.049708 TGACTAGCCTATCATGCATGC 57.950 47.619 22.25 11.82 0.00 4.06
426 600 2.636403 TGACTAGCCTATCATGCATGCT 59.364 45.455 22.25 16.85 36.11 3.79
427 601 3.001414 GACTAGCCTATCATGCATGCTG 58.999 50.000 22.25 14.33 33.63 4.41
562 773 1.311859 CTTCTGGAAGCAGCAACACA 58.688 50.000 0.00 0.00 0.00 3.72
567 778 4.842574 TCTGGAAGCAGCAACACATATTA 58.157 39.130 0.00 0.00 0.00 0.98
568 779 5.439721 TCTGGAAGCAGCAACACATATTAT 58.560 37.500 0.00 0.00 0.00 1.28
569 780 5.887598 TCTGGAAGCAGCAACACATATTATT 59.112 36.000 0.00 0.00 0.00 1.40
581 792 7.806487 GCAACACATATTATTGGTCATGATCTG 59.194 37.037 7.64 0.00 0.00 2.90
583 794 7.748677 ACACATATTATTGGTCATGATCTGGA 58.251 34.615 7.64 0.00 0.00 3.86
584 795 8.219868 ACACATATTATTGGTCATGATCTGGAA 58.780 33.333 7.64 0.00 0.00 3.53
586 797 8.219868 ACATATTATTGGTCATGATCTGGAACA 58.780 33.333 7.64 1.45 0.00 3.18
587 798 9.070179 CATATTATTGGTCATGATCTGGAACAA 57.930 33.333 16.41 16.41 44.10 2.83
588 799 7.959658 ATTATTGGTCATGATCTGGAACAAA 57.040 32.000 17.52 6.74 43.30 2.83
591 802 3.507233 TGGTCATGATCTGGAACAAAAGC 59.493 43.478 7.64 0.00 38.70 3.51
592 803 3.760684 GGTCATGATCTGGAACAAAAGCT 59.239 43.478 0.00 0.00 38.70 3.74
594 805 5.159209 GTCATGATCTGGAACAAAAGCTTG 58.841 41.667 0.00 0.00 38.70 4.01
596 807 4.836125 TGATCTGGAACAAAAGCTTGAC 57.164 40.909 0.00 0.00 38.70 3.18
597 808 4.464008 TGATCTGGAACAAAAGCTTGACT 58.536 39.130 0.00 0.00 38.70 3.41
598 809 4.276678 TGATCTGGAACAAAAGCTTGACTG 59.723 41.667 0.00 0.38 38.70 3.51
600 811 4.016444 TCTGGAACAAAAGCTTGACTGTT 58.984 39.130 17.22 17.22 38.70 3.16
601 812 4.462483 TCTGGAACAAAAGCTTGACTGTTT 59.538 37.500 17.91 0.00 38.70 2.83
602 813 4.493547 TGGAACAAAAGCTTGACTGTTTG 58.506 39.130 17.91 12.19 36.33 2.93
603 814 3.306973 GGAACAAAAGCTTGACTGTTTGC 59.693 43.478 17.91 9.74 36.33 3.68
604 815 2.529151 ACAAAAGCTTGACTGTTTGCG 58.471 42.857 0.00 0.00 36.33 4.85
645 3028 3.677424 GCTGGGAGCATCTCGGTAATATC 60.677 52.174 0.00 0.00 46.32 1.63
646 3029 2.492088 TGGGAGCATCTCGGTAATATCG 59.508 50.000 0.00 0.00 39.79 2.92
647 3030 2.531206 GGAGCATCTCGGTAATATCGC 58.469 52.381 0.00 0.00 33.73 4.58
648 3031 2.177977 GAGCATCTCGGTAATATCGCG 58.822 52.381 0.00 0.00 0.00 5.87
649 3032 1.810755 AGCATCTCGGTAATATCGCGA 59.189 47.619 13.09 13.09 0.00 5.87
653 3185 4.275662 CATCTCGGTAATATCGCGATCTC 58.724 47.826 27.45 13.70 30.95 2.75
658 3190 5.093457 TCGGTAATATCGCGATCTCAAATC 58.907 41.667 27.45 10.42 0.00 2.17
677 3209 7.208777 TCAAATCTGAATGCTCTCATAGAGAC 58.791 38.462 8.11 0.66 45.07 3.36
678 3210 6.982160 AATCTGAATGCTCTCATAGAGACT 57.018 37.500 8.11 0.00 45.07 3.24
684 3216 2.757314 TGCTCTCATAGAGACTGTGGTG 59.243 50.000 8.11 0.00 45.07 4.17
730 3306 8.524870 AAACTATCAATTTGTTAGCTTTGCAG 57.475 30.769 12.40 0.00 0.00 4.41
735 3311 7.840342 TCAATTTGTTAGCTTTGCAGAAAAA 57.160 28.000 0.00 0.00 0.00 1.94
736 3312 8.436046 TCAATTTGTTAGCTTTGCAGAAAAAT 57.564 26.923 0.00 0.00 0.00 1.82
737 3313 8.336806 TCAATTTGTTAGCTTTGCAGAAAAATG 58.663 29.630 0.00 0.00 0.00 2.32
739 3315 7.608308 TTTGTTAGCTTTGCAGAAAAATGTT 57.392 28.000 0.00 0.00 0.00 2.71
753 3329 9.396938 GCAGAAAAATGTTAAAATGGGAAATTG 57.603 29.630 0.00 0.00 0.00 2.32
775 3352 3.769300 GGGTGGAAGGCAATAATTCTGTT 59.231 43.478 0.00 0.00 0.00 3.16
794 3371 0.394488 TTGGCTGTTTTGACGGGTCA 60.394 50.000 0.00 0.00 37.91 4.02
799 3376 2.413837 CTGTTTTGACGGGTCACTAGG 58.586 52.381 0.04 0.00 39.66 3.02
812 3389 2.089980 TCACTAGGCCGTAGACAAGTC 58.910 52.381 14.03 0.00 32.41 3.01
816 3393 3.884091 ACTAGGCCGTAGACAAGTCTATG 59.116 47.826 18.27 18.27 43.32 2.23
856 3433 6.367695 TCGTTCAAACTGAAATCGACATGTAT 59.632 34.615 0.00 0.00 38.22 2.29
858 3435 6.421377 TCAAACTGAAATCGACATGTATGG 57.579 37.500 0.00 0.00 0.00 2.74
862 3439 5.496556 ACTGAAATCGACATGTATGGGAAA 58.503 37.500 0.00 0.00 0.00 3.13
865 3442 5.885352 TGAAATCGACATGTATGGGAAATGT 59.115 36.000 0.00 0.00 37.24 2.71
868 3445 5.607939 TCGACATGTATGGGAAATGTAGT 57.392 39.130 0.00 0.00 34.74 2.73
872 3449 2.912771 TGTATGGGAAATGTAGTGGCG 58.087 47.619 0.00 0.00 0.00 5.69
885 3462 2.823628 GTGGCGAAGACTACACCAC 58.176 57.895 5.28 5.28 43.57 4.16
908 3495 0.321122 CTCCTGTTGGCCAGTGAGTC 60.321 60.000 5.11 0.00 39.74 3.36
1036 3632 1.079503 GTTGTGCGTCCTCTTGATCC 58.920 55.000 0.00 0.00 0.00 3.36
1160 3756 1.329292 CGTCCTCTCTCTAACGAGCAG 59.671 57.143 0.00 0.00 37.31 4.24
1284 3880 1.296715 GTTCTCCATCACGCCCAGT 59.703 57.895 0.00 0.00 0.00 4.00
1294 3890 1.832608 ACGCCCAGTGACTCTGACA 60.833 57.895 6.09 0.00 46.27 3.58
1295 3891 1.373497 CGCCCAGTGACTCTGACAC 60.373 63.158 6.09 0.00 46.27 3.67
1396 4013 1.071019 CAATCAGGACGACGACGGTG 61.071 60.000 12.58 6.26 44.46 4.94
1397 4014 2.209064 AATCAGGACGACGACGGTGG 62.209 60.000 12.58 0.00 44.46 4.61
1431 4048 1.079503 GTTTCTTCGCCATCGAGCTT 58.920 50.000 0.00 0.00 46.34 3.74
1447 4064 0.602905 GCTTGACACCGTAGCCAACT 60.603 55.000 0.00 0.00 0.00 3.16
1448 4065 1.148310 CTTGACACCGTAGCCAACTG 58.852 55.000 0.00 0.00 0.00 3.16
1456 4073 0.320374 CGTAGCCAACTGGGAGTTCA 59.680 55.000 0.00 0.00 36.03 3.18
1558 4175 3.254892 GACAATGTCGAGAAGGACTTCC 58.745 50.000 8.37 0.00 40.33 3.46
1559 4176 2.632996 ACAATGTCGAGAAGGACTTCCA 59.367 45.455 8.37 0.54 40.33 3.53
1560 4177 2.996621 CAATGTCGAGAAGGACTTCCAC 59.003 50.000 8.37 4.43 40.33 4.02
1561 4178 1.996798 TGTCGAGAAGGACTTCCACT 58.003 50.000 8.37 0.00 40.33 4.00
1562 4179 2.317040 TGTCGAGAAGGACTTCCACTT 58.683 47.619 8.37 0.00 40.33 3.16
1572 4189 3.652869 AGGACTTCCACTTCTTCAATCCA 59.347 43.478 0.00 0.00 38.89 3.41
1680 4312 1.789523 ATAAGCCCTCTTCACCGCTA 58.210 50.000 0.00 0.00 33.85 4.26
1696 4328 2.696707 CCGCTATTGTCTTACTACCCCA 59.303 50.000 0.00 0.00 0.00 4.96
1701 4333 5.047235 GCTATTGTCTTACTACCCCATCGAT 60.047 44.000 0.00 0.00 0.00 3.59
1781 4416 0.390472 GTCGGTTTCTCTGCCTCCAG 60.390 60.000 0.00 0.00 40.54 3.86
1792 4427 2.671070 CCTCCAGCGGTGATTGGT 59.329 61.111 17.83 0.00 35.89 3.67
1793 4428 1.746615 CCTCCAGCGGTGATTGGTG 60.747 63.158 17.83 0.00 35.89 4.17
1794 4429 1.003355 CTCCAGCGGTGATTGGTGT 60.003 57.895 17.83 0.00 35.89 4.16
1796 4431 2.562912 CAGCGGTGATTGGTGTGC 59.437 61.111 9.50 0.00 0.00 4.57
1797 4432 2.672996 AGCGGTGATTGGTGTGCC 60.673 61.111 0.00 0.00 0.00 5.01
1799 4434 2.690778 GCGGTGATTGGTGTGCCTC 61.691 63.158 0.00 0.00 35.27 4.70
1800 4435 2.040544 CGGTGATTGGTGTGCCTCC 61.041 63.158 0.00 0.00 35.27 4.30
1801 4436 1.678970 GGTGATTGGTGTGCCTCCC 60.679 63.158 0.00 0.00 35.27 4.30
1802 4437 1.074775 GTGATTGGTGTGCCTCCCA 59.925 57.895 0.00 0.00 35.27 4.37
1803 4438 0.539438 GTGATTGGTGTGCCTCCCAA 60.539 55.000 0.00 0.00 44.40 4.12
1806 4450 0.105760 ATTGGTGTGCCTCCCAACAA 60.106 50.000 0.70 0.00 43.17 2.83
1810 4454 1.416030 GGTGTGCCTCCCAACAAATTT 59.584 47.619 0.00 0.00 0.00 1.82
1828 4472 4.617253 ATTTTTGGGTGGAGCTTTAACC 57.383 40.909 5.14 5.14 0.00 2.85
1852 4496 2.561037 GGACCGGCCAAACCACTTG 61.561 63.158 0.00 0.00 39.03 3.16
1944 4591 0.893727 AAGTCGTCAAATGGGTGCCC 60.894 55.000 0.00 0.00 0.00 5.36
1959 4606 2.484770 GGTGCCCGCAACTATATCTTCA 60.485 50.000 0.00 0.00 0.00 3.02
1984 4634 4.849518 TGCCATACTTGCAGGTATAACAA 58.150 39.130 19.85 5.21 34.05 2.83
1995 4645 4.142600 GCAGGTATAACAACTTGCCTTCTG 60.143 45.833 0.08 0.00 44.27 3.02
1996 4646 5.003804 CAGGTATAACAACTTGCCTTCTGT 58.996 41.667 0.00 0.00 0.00 3.41
2024 4680 1.067295 TGGTGGTGCAAGAAGAGGAT 58.933 50.000 0.00 0.00 0.00 3.24
2025 4681 1.271543 TGGTGGTGCAAGAAGAGGATG 60.272 52.381 0.00 0.00 0.00 3.51
2100 4759 4.373116 GACCTCCGCCGAGCAACA 62.373 66.667 0.00 0.00 34.49 3.33
2110 4769 0.454957 CCGAGCAACAAATGGCTTCG 60.455 55.000 0.00 0.00 41.22 3.79
2190 4849 1.153309 CTCTGGCATGGACATCGCA 60.153 57.895 0.00 0.00 0.00 5.10
2224 4883 3.382832 CGGAGTCGAAGCAGGGGT 61.383 66.667 0.00 0.00 39.00 4.95
2229 4888 1.122019 AGTCGAAGCAGGGGTTGACT 61.122 55.000 0.00 0.00 31.84 3.41
2245 4904 3.049708 TGACTGAATTCACAGCTGAGG 57.950 47.619 23.35 12.34 41.06 3.86
2259 4918 1.211457 GCTGAGGTCATCATCCTTGGT 59.789 52.381 0.00 0.00 37.28 3.67
2286 4945 0.531311 GACACCGAAACCTTGTCCGT 60.531 55.000 0.00 0.00 34.72 4.69
2312 4971 2.046285 GCTATTGCCGGCACAAGGT 61.046 57.895 32.95 15.32 31.96 3.50
2325 4984 0.892063 ACAAGGTCGAGCTTCTCCTC 59.108 55.000 26.13 0.00 0.00 3.71
2365 5024 1.748329 CGGCAGCCTGGATAGCTACA 61.748 60.000 10.54 0.00 38.95 2.74
2406 5068 1.276138 ACGATGCTCTCATGGTGTCAA 59.724 47.619 0.00 0.00 39.65 3.18
2423 5085 3.754850 TGTCAAAGGCTTCACATCATCAG 59.245 43.478 0.00 0.00 0.00 2.90
2435 5097 2.943680 ATCATCAGAGGCGTCGCGTG 62.944 60.000 18.31 11.56 0.00 5.34
2638 5312 1.536073 CCCTGAGCTGACGAGGTTCA 61.536 60.000 0.00 0.00 0.00 3.18
2685 5359 0.459237 TTGCGTTTGGTGCCTTTGTG 60.459 50.000 0.00 0.00 0.00 3.33
2911 5585 4.189580 GGCCCAGCATCCGCCTTA 62.190 66.667 0.00 0.00 39.70 2.69
2925 5599 1.540363 CGCCTTATCATGCGGTACCTT 60.540 52.381 10.90 0.00 46.65 3.50
3055 5729 4.764823 GTCTGTCTGGAGGTAGATGATAGG 59.235 50.000 0.00 0.00 0.00 2.57
3121 6052 5.516062 GGGGTGGTGTTAGGTTTAGAAGAAT 60.516 44.000 0.00 0.00 0.00 2.40
3255 6214 5.740290 TCGGAAATTCTCTCAGGTTACTT 57.260 39.130 0.00 0.00 0.00 2.24
3264 6224 4.410883 TCTCTCAGGTTACTTTCCCACAAA 59.589 41.667 0.00 0.00 0.00 2.83
3337 6297 3.349006 GTGGCTGCCAGTGTCACG 61.349 66.667 24.10 0.00 32.34 4.35
3357 6317 1.041437 GGATAGGAACGGCAGCTACT 58.959 55.000 0.00 0.00 0.00 2.57
3411 6386 2.350522 CAGGTCTGTTCCTTCCATTCG 58.649 52.381 0.00 0.00 35.37 3.34
3422 6398 2.095853 CCTTCCATTCGTCCATTGTTCG 59.904 50.000 0.00 0.00 0.00 3.95
3471 6447 6.885735 TTTGCAAGCTCAAAAAGTCTTAAC 57.114 33.333 0.00 0.00 33.47 2.01
3490 6467 9.118236 GTCTTAACTCTTTGGATTGAAAAATCG 57.882 33.333 0.00 0.00 0.00 3.34
3503 6484 5.041951 TGAAAAATCGACCAAAATCCTCG 57.958 39.130 0.00 0.00 0.00 4.63
3523 10104 4.370049 TCGAACGTCCAGTGAAACAAATA 58.630 39.130 0.00 0.00 41.43 1.40
3561 10142 5.871834 ACTGCCAACATTGTTAGTTACCTA 58.128 37.500 0.86 0.00 0.00 3.08
3582 10163 1.308998 AGTGGTGAAAAGGAGCAACG 58.691 50.000 0.00 0.00 0.00 4.10
3594 10179 3.248024 AGGAGCAACGGAATCCCATATA 58.752 45.455 0.00 0.00 33.30 0.86
3595 10180 3.846588 AGGAGCAACGGAATCCCATATAT 59.153 43.478 0.00 0.00 33.30 0.86
3637 10224 5.828299 TTTTCTTGTGACGGTTCAAGATT 57.172 34.783 21.25 0.00 45.77 2.40
3648 10243 2.427506 GTTCAAGATTGGTTCGAGCCT 58.572 47.619 19.73 0.00 0.00 4.58
3659 10254 2.007608 GTTCGAGCCTTATTTTCCGCT 58.992 47.619 0.00 0.00 0.00 5.52
3660 10255 2.396590 TCGAGCCTTATTTTCCGCTT 57.603 45.000 0.00 0.00 0.00 4.68
3725 10322 9.436957 TTTTTCTATCTCATTAGTGTTGGACTC 57.563 33.333 0.00 0.00 35.96 3.36
3726 10323 7.718334 TTCTATCTCATTAGTGTTGGACTCA 57.282 36.000 0.00 0.00 35.96 3.41
3727 10324 7.904558 TCTATCTCATTAGTGTTGGACTCAT 57.095 36.000 0.00 0.00 35.96 2.90
3728 10325 7.720442 TCTATCTCATTAGTGTTGGACTCATG 58.280 38.462 0.00 0.00 37.56 3.07
3729 10326 4.507710 TCTCATTAGTGTTGGACTCATGC 58.492 43.478 0.00 0.00 36.56 4.06
3730 10327 4.223700 TCTCATTAGTGTTGGACTCATGCT 59.776 41.667 0.00 0.00 36.56 3.79
3731 10328 4.256110 TCATTAGTGTTGGACTCATGCTG 58.744 43.478 0.00 0.00 36.56 4.41
3732 10329 2.768253 TAGTGTTGGACTCATGCTGG 57.232 50.000 0.00 0.00 35.96 4.85
3733 10330 0.767375 AGTGTTGGACTCATGCTGGT 59.233 50.000 0.00 0.00 0.00 4.00
3734 10331 1.160137 GTGTTGGACTCATGCTGGTC 58.840 55.000 0.00 0.00 0.00 4.02
3735 10332 0.764271 TGTTGGACTCATGCTGGTCA 59.236 50.000 12.71 0.00 34.49 4.02
3736 10333 1.142667 TGTTGGACTCATGCTGGTCAA 59.857 47.619 12.71 2.31 34.49 3.18
3737 10334 2.224843 TGTTGGACTCATGCTGGTCAAT 60.225 45.455 12.71 0.00 34.49 2.57
3738 10335 2.408271 TGGACTCATGCTGGTCAATC 57.592 50.000 12.71 0.99 34.49 2.67
3739 10336 1.629861 TGGACTCATGCTGGTCAATCA 59.370 47.619 12.71 2.91 34.49 2.57
3740 10337 2.040145 TGGACTCATGCTGGTCAATCAA 59.960 45.455 12.71 0.00 34.49 2.57
3741 10338 3.285484 GGACTCATGCTGGTCAATCAAT 58.715 45.455 12.71 0.00 34.49 2.57
3742 10339 3.066342 GGACTCATGCTGGTCAATCAATG 59.934 47.826 12.71 0.00 34.49 2.82
3743 10340 3.943381 GACTCATGCTGGTCAATCAATGA 59.057 43.478 7.92 0.00 35.05 2.57
3759 10356 9.788889 TCAATCAATGACAATGATAAGCTCTAT 57.211 29.630 6.43 0.00 36.53 1.98
3807 10404 6.183361 ACCTAACCAGTTCTTGTCTCTGAAAT 60.183 38.462 0.00 0.00 0.00 2.17
3808 10405 6.712547 CCTAACCAGTTCTTGTCTCTGAAATT 59.287 38.462 0.00 0.00 0.00 1.82
3819 10419 8.786898 TCTTGTCTCTGAAATTTTATTGTCAGG 58.213 33.333 0.00 0.00 38.42 3.86
3877 10480 8.655935 TCCAGATAATAATATGCAGTCTCTGA 57.344 34.615 0.00 0.00 32.44 3.27
3973 10763 5.912149 ATCCCTAGCTTGAACCATATGAA 57.088 39.130 3.65 0.00 0.00 2.57
4000 10790 9.862149 AATTAATAATACTCCCTCCATTTTCGT 57.138 29.630 0.00 0.00 0.00 3.85
4008 10798 7.005709 ACTCCCTCCATTTTCGTATATAAGG 57.994 40.000 0.00 0.00 0.00 2.69
4009 10799 5.801380 TCCCTCCATTTTCGTATATAAGGC 58.199 41.667 0.00 0.00 0.00 4.35
4010 10800 4.941873 CCCTCCATTTTCGTATATAAGGCC 59.058 45.833 0.00 0.00 0.00 5.19
4011 10801 5.514136 CCCTCCATTTTCGTATATAAGGCCA 60.514 44.000 5.01 0.00 0.00 5.36
4012 10802 5.411669 CCTCCATTTTCGTATATAAGGCCAC 59.588 44.000 5.01 0.00 0.00 5.01
4013 10803 6.182507 TCCATTTTCGTATATAAGGCCACT 57.817 37.500 5.01 0.00 0.00 4.00
4014 10804 7.305813 TCCATTTTCGTATATAAGGCCACTA 57.694 36.000 5.01 0.00 0.00 2.74
4015 10805 7.913789 TCCATTTTCGTATATAAGGCCACTAT 58.086 34.615 5.01 3.84 0.00 2.12
4016 10806 8.038944 TCCATTTTCGTATATAAGGCCACTATC 58.961 37.037 5.01 0.00 0.00 2.08
4017 10807 7.822334 CCATTTTCGTATATAAGGCCACTATCA 59.178 37.037 5.01 0.00 0.00 2.15
4018 10808 9.214957 CATTTTCGTATATAAGGCCACTATCAA 57.785 33.333 5.01 0.00 0.00 2.57
4019 10809 9.787435 ATTTTCGTATATAAGGCCACTATCAAA 57.213 29.630 5.01 0.00 0.00 2.69
4020 10810 9.616156 TTTTCGTATATAAGGCCACTATCAAAA 57.384 29.630 5.01 3.33 0.00 2.44
4021 10811 9.787435 TTTCGTATATAAGGCCACTATCAAAAT 57.213 29.630 5.01 0.00 0.00 1.82
4022 10812 9.787435 TTCGTATATAAGGCCACTATCAAAATT 57.213 29.630 5.01 0.00 0.00 1.82
4030 10820 8.776376 AAGGCCACTATCAAAATTACAATTTG 57.224 30.769 5.01 0.00 38.53 2.32
4031 10821 6.818142 AGGCCACTATCAAAATTACAATTTGC 59.182 34.615 5.01 0.00 38.53 3.68
4032 10822 6.593382 GGCCACTATCAAAATTACAATTTGCA 59.407 34.615 0.00 0.00 38.53 4.08
4033 10823 7.118971 GGCCACTATCAAAATTACAATTTGCAA 59.881 33.333 0.00 0.00 38.53 4.08
4034 10824 7.956943 GCCACTATCAAAATTACAATTTGCAAC 59.043 33.333 0.00 0.00 38.53 4.17
4035 10825 9.206870 CCACTATCAAAATTACAATTTGCAACT 57.793 29.630 0.00 0.00 38.53 3.16
4044 10834 8.702163 AATTACAATTTGCAACTATACAAGGC 57.298 30.769 0.00 0.00 0.00 4.35
4045 10835 5.072040 ACAATTTGCAACTATACAAGGCC 57.928 39.130 0.00 0.00 0.00 5.19
4046 10836 4.526262 ACAATTTGCAACTATACAAGGCCA 59.474 37.500 5.01 0.00 0.00 5.36
4047 10837 4.718940 ATTTGCAACTATACAAGGCCAC 57.281 40.909 5.01 0.00 0.00 5.01
4048 10838 3.433306 TTGCAACTATACAAGGCCACT 57.567 42.857 5.01 0.00 0.00 4.00
4049 10839 4.561500 TTGCAACTATACAAGGCCACTA 57.438 40.909 5.01 0.00 0.00 2.74
4050 10840 4.561500 TGCAACTATACAAGGCCACTAA 57.438 40.909 5.01 0.00 0.00 2.24
4051 10841 4.258543 TGCAACTATACAAGGCCACTAAC 58.741 43.478 5.01 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 9.155975 CAGTGCAATTTCTACTAACACTAATCT 57.844 33.333 0.00 0.00 35.27 2.40
77 78 3.485394 TCAACCAGCAGTGCAATTTCTA 58.515 40.909 19.20 0.00 0.00 2.10
89 90 4.214545 CCAAACGTTTAGTATCAACCAGCA 59.785 41.667 14.20 0.00 0.00 4.41
101 102 7.173735 AGGGACTAATAAACACCAAACGTTTAG 59.826 37.037 14.20 9.28 38.45 1.85
132 133 4.070009 ACCATACGAAAGAAAGTTGGGAC 58.930 43.478 0.00 0.00 0.00 4.46
139 140 4.396166 AGGAATGCACCATACGAAAGAAAG 59.604 41.667 0.00 0.00 0.00 2.62
274 275 0.315251 TGGTCAGTCAAGACGCTGAG 59.685 55.000 0.00 0.00 41.71 3.35
275 276 0.750249 TTGGTCAGTCAAGACGCTGA 59.250 50.000 0.00 0.00 39.42 4.26
276 277 1.581934 TTTGGTCAGTCAAGACGCTG 58.418 50.000 0.00 0.00 39.42 5.18
277 278 2.325583 TTTTGGTCAGTCAAGACGCT 57.674 45.000 0.00 0.00 39.42 5.07
280 293 5.757850 AAGACATTTTGGTCAGTCAAGAC 57.242 39.130 0.00 0.00 40.29 3.01
285 298 6.206634 TGGTGAATAAGACATTTTGGTCAGTC 59.793 38.462 0.00 0.00 40.29 3.51
334 351 1.008206 AGGCTCTGGACATCCTTCTCT 59.992 52.381 0.00 0.00 36.82 3.10
345 362 1.347707 ACAAAATGACGAGGCTCTGGA 59.652 47.619 13.50 0.00 0.00 3.86
361 378 3.763360 CCATATTGGCCAGAGAACACAAA 59.237 43.478 5.11 0.00 0.00 2.83
365 382 4.524802 AATCCATATTGGCCAGAGAACA 57.475 40.909 5.11 0.00 37.47 3.18
422 596 3.686016 CCACAAGGTTAGGTTACAGCAT 58.314 45.455 0.00 0.00 0.00 3.79
447 657 0.599558 TGAGTTTCTTGGCTGCATGC 59.400 50.000 11.82 11.82 41.94 4.06
562 773 9.645128 TTTGTTCCAGATCATGACCAATAATAT 57.355 29.630 0.00 0.00 0.00 1.28
567 778 5.337009 GCTTTTGTTCCAGATCATGACCAAT 60.337 40.000 0.00 0.00 0.00 3.16
568 779 4.022068 GCTTTTGTTCCAGATCATGACCAA 60.022 41.667 0.00 0.00 0.00 3.67
569 780 3.507233 GCTTTTGTTCCAGATCATGACCA 59.493 43.478 0.00 0.00 0.00 4.02
581 792 3.306973 GCAAACAGTCAAGCTTTTGTTCC 59.693 43.478 16.66 10.13 32.97 3.62
583 794 2.923020 CGCAAACAGTCAAGCTTTTGTT 59.077 40.909 12.58 12.58 35.43 2.83
584 795 2.529151 CGCAAACAGTCAAGCTTTTGT 58.471 42.857 0.00 0.00 32.71 2.83
586 797 1.802508 GCCGCAAACAGTCAAGCTTTT 60.803 47.619 0.00 0.00 0.00 2.27
587 798 0.249031 GCCGCAAACAGTCAAGCTTT 60.249 50.000 0.00 0.00 0.00 3.51
588 799 1.360192 GCCGCAAACAGTCAAGCTT 59.640 52.632 0.00 0.00 0.00 3.74
591 802 2.252260 CCGCCGCAAACAGTCAAG 59.748 61.111 0.00 0.00 0.00 3.02
592 803 3.959975 GCCGCCGCAAACAGTCAA 61.960 61.111 0.00 0.00 34.03 3.18
594 805 4.389576 CTGCCGCCGCAAACAGTC 62.390 66.667 0.47 0.00 46.66 3.51
615 839 3.335356 ATGCTCCCAGCCTTCCACG 62.335 63.158 0.00 0.00 41.51 4.94
645 3028 2.543012 AGCATTCAGATTTGAGATCGCG 59.457 45.455 0.00 0.00 34.15 5.87
646 3029 3.808726 AGAGCATTCAGATTTGAGATCGC 59.191 43.478 0.00 0.00 34.15 4.58
647 3030 5.048507 TGAGAGCATTCAGATTTGAGATCG 58.951 41.667 0.00 0.00 34.15 3.69
648 3031 8.089597 TCTATGAGAGCATTCAGATTTGAGATC 58.910 37.037 0.00 0.00 35.94 2.75
649 3032 7.964624 TCTATGAGAGCATTCAGATTTGAGAT 58.035 34.615 0.00 0.00 35.94 2.75
653 3185 7.170151 CAGTCTCTATGAGAGCATTCAGATTTG 59.830 40.741 0.00 0.00 42.04 2.32
658 3190 5.283294 CACAGTCTCTATGAGAGCATTCAG 58.717 45.833 0.00 0.00 42.04 3.02
714 3288 7.790823 ACATTTTTCTGCAAAGCTAACAAAT 57.209 28.000 0.00 0.00 0.00 2.32
717 3291 8.709386 TTTAACATTTTTCTGCAAAGCTAACA 57.291 26.923 0.00 0.00 0.00 2.41
725 3299 8.511604 TTTCCCATTTTAACATTTTTCTGCAA 57.488 26.923 0.00 0.00 0.00 4.08
730 3306 8.855110 ACCCAATTTCCCATTTTAACATTTTTC 58.145 29.630 0.00 0.00 0.00 2.29
735 3311 5.549619 TCCACCCAATTTCCCATTTTAACAT 59.450 36.000 0.00 0.00 0.00 2.71
736 3312 4.907875 TCCACCCAATTTCCCATTTTAACA 59.092 37.500 0.00 0.00 0.00 2.41
737 3313 5.491323 TCCACCCAATTTCCCATTTTAAC 57.509 39.130 0.00 0.00 0.00 2.01
739 3315 4.534103 CCTTCCACCCAATTTCCCATTTTA 59.466 41.667 0.00 0.00 0.00 1.52
753 3329 3.365472 ACAGAATTATTGCCTTCCACCC 58.635 45.455 0.00 0.00 0.00 4.61
775 3352 0.394488 TGACCCGTCAAAACAGCCAA 60.394 50.000 0.00 0.00 36.53 4.52
794 3371 2.510928 AGACTTGTCTACGGCCTAGT 57.489 50.000 0.00 0.00 0.00 2.57
799 3376 1.854227 GCCATAGACTTGTCTACGGC 58.146 55.000 25.26 25.26 43.00 5.68
856 3433 1.626321 TCTTCGCCACTACATTTCCCA 59.374 47.619 0.00 0.00 0.00 4.37
858 3435 2.973945 AGTCTTCGCCACTACATTTCC 58.026 47.619 0.00 0.00 0.00 3.13
865 3442 1.913778 TGGTGTAGTCTTCGCCACTA 58.086 50.000 7.61 0.00 40.01 2.74
868 3445 0.317160 CAGTGGTGTAGTCTTCGCCA 59.683 55.000 7.61 7.61 42.18 5.69
872 3449 3.057174 CAGGAGTCAGTGGTGTAGTCTTC 60.057 52.174 0.00 0.00 0.00 2.87
885 3462 4.709840 CTGGCCAACAGGAGTCAG 57.290 61.111 7.01 0.00 43.70 3.51
908 3495 6.342338 AGGAGCAGGGTAAGTATTAATACG 57.658 41.667 17.77 5.30 38.28 3.06
1036 3632 2.414994 ACACCATCATGGCAAGAGAG 57.585 50.000 2.52 0.00 42.67 3.20
1284 3880 1.666011 GCCGGAAGTGTCAGAGTCA 59.334 57.895 5.05 0.00 0.00 3.41
1314 3910 1.342374 GGGGCCAAGGAGATGACAAAT 60.342 52.381 4.39 0.00 0.00 2.32
1431 4048 1.369692 CCAGTTGGCTACGGTGTCA 59.630 57.895 0.00 0.00 0.00 3.58
1447 4064 6.194967 TGTTGTCTATATCTCTGAACTCCCA 58.805 40.000 0.00 0.00 0.00 4.37
1448 4065 6.716934 TGTTGTCTATATCTCTGAACTCCC 57.283 41.667 0.00 0.00 0.00 4.30
1456 4073 6.461648 CCGACATGGTTGTTGTCTATATCTCT 60.462 42.308 0.00 0.00 41.05 3.10
1538 4155 2.632996 TGGAAGTCCTTCTCGACATTGT 59.367 45.455 6.97 0.00 39.45 2.71
1554 4171 4.645535 TCAGTGGATTGAAGAAGTGGAAG 58.354 43.478 0.00 0.00 0.00 3.46
1555 4172 4.347876 TCTCAGTGGATTGAAGAAGTGGAA 59.652 41.667 0.00 0.00 0.00 3.53
1556 4173 3.903714 TCTCAGTGGATTGAAGAAGTGGA 59.096 43.478 0.00 0.00 0.00 4.02
1557 4174 3.999663 GTCTCAGTGGATTGAAGAAGTGG 59.000 47.826 0.00 0.00 0.00 4.00
1558 4175 4.892433 AGTCTCAGTGGATTGAAGAAGTG 58.108 43.478 0.00 0.00 0.00 3.16
1559 4176 5.559148 AAGTCTCAGTGGATTGAAGAAGT 57.441 39.130 0.00 0.00 0.00 3.01
1560 4177 6.229733 AGAAAGTCTCAGTGGATTGAAGAAG 58.770 40.000 0.00 0.00 0.00 2.85
1561 4178 6.179906 AGAAAGTCTCAGTGGATTGAAGAA 57.820 37.500 0.00 0.00 0.00 2.52
1562 4179 5.815233 AGAAAGTCTCAGTGGATTGAAGA 57.185 39.130 0.00 0.00 0.00 2.87
1593 4210 1.004679 CACCCAAACCTGCATTGGC 60.005 57.895 11.42 0.00 44.87 4.52
1633 4265 1.956170 CAGGAGCAAGCGTGACGTT 60.956 57.895 6.91 0.00 0.00 3.99
1680 4312 5.148502 AGATCGATGGGGTAGTAAGACAAT 58.851 41.667 0.54 0.00 0.00 2.71
1696 4328 2.237143 TGAGGACCTTTGCAAGATCGAT 59.763 45.455 0.00 0.00 0.00 3.59
1701 4333 3.576078 TTCTTGAGGACCTTTGCAAGA 57.424 42.857 16.45 16.45 43.38 3.02
1781 4416 2.672996 AGGCACACCAATCACCGC 60.673 61.111 0.00 0.00 39.06 5.68
1792 4427 3.539604 CAAAAATTTGTTGGGAGGCACA 58.460 40.909 0.00 0.00 33.59 4.57
1793 4428 2.877786 CCAAAAATTTGTTGGGAGGCAC 59.122 45.455 10.14 0.00 41.64 5.01
1794 4429 3.205784 CCAAAAATTTGTTGGGAGGCA 57.794 42.857 10.14 0.00 41.64 4.75
1800 4435 2.877786 GCTCCACCCAAAAATTTGTTGG 59.122 45.455 10.93 10.93 44.42 3.77
1801 4436 3.807553 AGCTCCACCCAAAAATTTGTTG 58.192 40.909 5.27 0.00 36.45 3.33
1802 4437 4.502105 AAGCTCCACCCAAAAATTTGTT 57.498 36.364 5.27 0.00 36.45 2.83
1803 4438 4.502105 AAAGCTCCACCCAAAAATTTGT 57.498 36.364 5.27 0.00 36.45 2.83
1806 4450 4.658435 AGGTTAAAGCTCCACCCAAAAATT 59.342 37.500 5.50 0.00 0.00 1.82
1810 4454 2.091555 ACAGGTTAAAGCTCCACCCAAA 60.092 45.455 5.50 0.00 0.00 3.28
1828 4472 1.029947 GGTTTGGCCGGTCCATACAG 61.030 60.000 26.73 0.00 45.22 2.74
1984 4634 2.154462 CCATCGAAACAGAAGGCAAGT 58.846 47.619 0.00 0.00 0.00 3.16
1995 4645 1.169661 TGCACCACCACCATCGAAAC 61.170 55.000 0.00 0.00 0.00 2.78
1996 4646 0.466372 TTGCACCACCACCATCGAAA 60.466 50.000 0.00 0.00 0.00 3.46
2024 4680 3.513119 CCAGTCTTCATTCCTCTCTGACA 59.487 47.826 0.00 0.00 0.00 3.58
2025 4681 3.118811 CCCAGTCTTCATTCCTCTCTGAC 60.119 52.174 0.00 0.00 0.00 3.51
2100 4759 2.422597 TGATTGTCGTCGAAGCCATTT 58.577 42.857 0.00 0.00 0.00 2.32
2110 4769 2.076863 CCCAAGGAGTTGATTGTCGTC 58.923 52.381 0.00 0.00 35.46 4.20
2190 4849 2.344203 CGAGGAGACCCGCTTCACT 61.344 63.158 0.00 0.00 37.58 3.41
2224 4883 3.181451 ACCTCAGCTGTGAATTCAGTCAA 60.181 43.478 17.19 0.00 37.70 3.18
2229 4888 3.008266 TGATGACCTCAGCTGTGAATTCA 59.992 43.478 17.19 14.99 32.67 2.57
2245 4904 0.179000 AGGCGACCAAGGATGATGAC 59.821 55.000 0.00 0.00 0.00 3.06
2259 4918 1.081242 GTTTCGGTGTCGTAGGCGA 60.081 57.895 0.00 0.00 45.79 5.54
2312 4971 1.654317 GTAGACGAGGAGAAGCTCGA 58.346 55.000 0.00 0.00 44.85 4.04
2325 4984 0.736636 TGGGCATGTACTCGTAGACG 59.263 55.000 0.00 0.00 41.45 4.18
2365 5024 1.200760 TGCCTAGTCTGGGTGTGCAT 61.201 55.000 3.91 0.00 0.00 3.96
2402 5064 4.005650 TCTGATGATGTGAAGCCTTTGAC 58.994 43.478 0.00 0.00 0.00 3.18
2406 5068 2.683152 GCCTCTGATGATGTGAAGCCTT 60.683 50.000 0.00 0.00 0.00 4.35
2435 5097 2.187163 GGAGGTACAGAAGCCCGC 59.813 66.667 0.00 0.00 0.00 6.13
2638 5312 1.827789 TTGCTTTGGTCGCCTTGCT 60.828 52.632 0.00 0.00 0.00 3.91
2685 5359 0.902531 TACCACAAGCCACCTCTAGC 59.097 55.000 0.00 0.00 0.00 3.42
2794 5468 0.944311 CTTGGGTCAACGGTGTCGAG 60.944 60.000 0.00 0.00 40.11 4.04
2911 5585 1.202806 CCCATCAAGGTACCGCATGAT 60.203 52.381 19.17 19.17 34.66 2.45
2925 5599 2.625617 GGGCAAAGGTAAATCCCCATCA 60.626 50.000 0.00 0.00 36.75 3.07
3055 5729 6.183361 ACAATAGATAAACCCTCCTGGATGTC 60.183 42.308 0.00 0.00 38.00 3.06
3121 6052 5.519183 TTTCTCATTTTCTCCCCATCAGA 57.481 39.130 0.00 0.00 0.00 3.27
3157 6088 1.925847 GCCACACACACAAACACATTG 59.074 47.619 0.00 0.00 44.95 2.82
3235 6194 5.648526 GGGAAAGTAACCTGAGAGAATTTCC 59.351 44.000 9.94 9.94 42.28 3.13
3255 6214 4.350816 TCCTGAGAAAGAGATTTGTGGGAA 59.649 41.667 0.00 0.00 0.00 3.97
3337 6297 0.033642 GTAGCTGCCGTTCCTATCCC 59.966 60.000 0.00 0.00 0.00 3.85
3357 6317 1.975680 GGAAGGTGTACAGGACAGGAA 59.024 52.381 0.00 0.00 39.29 3.36
3411 6386 2.000447 GGAGCTACACGAACAATGGAC 59.000 52.381 0.00 0.00 0.00 4.02
3471 6447 6.012658 TGGTCGATTTTTCAATCCAAAGAG 57.987 37.500 0.00 0.00 36.18 2.85
3487 6464 2.268298 CGTTCGAGGATTTTGGTCGAT 58.732 47.619 0.00 0.00 42.01 3.59
3488 6465 1.000060 ACGTTCGAGGATTTTGGTCGA 60.000 47.619 0.00 0.00 40.81 4.20
3490 6467 1.730612 GGACGTTCGAGGATTTTGGTC 59.269 52.381 0.00 0.00 0.00 4.02
3503 6484 7.924103 AATTTATTTGTTTCACTGGACGTTC 57.076 32.000 0.00 0.00 0.00 3.95
3523 10104 0.108396 GCAGTTGGTGGGGCAAATTT 59.892 50.000 0.00 0.00 0.00 1.82
3561 10142 3.074412 CGTTGCTCCTTTTCACCACTAT 58.926 45.455 0.00 0.00 0.00 2.12
3628 10215 2.427506 AGGCTCGAACCAATCTTGAAC 58.572 47.619 7.76 0.00 0.00 3.18
3637 10224 2.352388 CGGAAAATAAGGCTCGAACCA 58.648 47.619 7.76 0.00 0.00 3.67
3648 10243 3.677190 TCCTCGGAAAAGCGGAAAATAA 58.323 40.909 0.00 0.00 0.00 1.40
3733 10330 9.788889 ATAGAGCTTATCATTGTCATTGATTGA 57.211 29.630 13.86 5.02 35.50 2.57
3762 10359 9.438228 GTTAGGTTAGCTTCAATAGACTCTTTT 57.562 33.333 0.00 0.00 0.00 2.27
3763 10360 8.041919 GGTTAGGTTAGCTTCAATAGACTCTTT 58.958 37.037 0.00 0.00 0.00 2.52
3764 10361 7.180408 TGGTTAGGTTAGCTTCAATAGACTCTT 59.820 37.037 0.00 0.00 0.00 2.85
3765 10362 6.668283 TGGTTAGGTTAGCTTCAATAGACTCT 59.332 38.462 0.00 0.00 0.00 3.24
3766 10363 6.875076 TGGTTAGGTTAGCTTCAATAGACTC 58.125 40.000 0.00 0.00 0.00 3.36
3767 10364 6.440965 ACTGGTTAGGTTAGCTTCAATAGACT 59.559 38.462 0.00 0.00 0.00 3.24
3768 10365 6.641474 ACTGGTTAGGTTAGCTTCAATAGAC 58.359 40.000 0.00 0.00 0.00 2.59
3769 10366 6.869206 ACTGGTTAGGTTAGCTTCAATAGA 57.131 37.500 0.00 0.00 0.00 1.98
3770 10367 7.331791 AGAACTGGTTAGGTTAGCTTCAATAG 58.668 38.462 0.00 0.00 0.00 1.73
3771 10368 7.253905 AGAACTGGTTAGGTTAGCTTCAATA 57.746 36.000 0.00 0.00 0.00 1.90
3772 10369 6.128138 AGAACTGGTTAGGTTAGCTTCAAT 57.872 37.500 0.00 0.00 0.00 2.57
3773 10370 5.562298 AGAACTGGTTAGGTTAGCTTCAA 57.438 39.130 0.00 0.00 0.00 2.69
3774 10371 5.163237 ACAAGAACTGGTTAGGTTAGCTTCA 60.163 40.000 0.00 0.00 0.00 3.02
3775 10372 5.306394 ACAAGAACTGGTTAGGTTAGCTTC 58.694 41.667 0.00 0.00 0.00 3.86
3807 10404 4.016444 GCAGACATCCCCTGACAATAAAA 58.984 43.478 0.00 0.00 33.65 1.52
3808 10405 3.010027 TGCAGACATCCCCTGACAATAAA 59.990 43.478 0.00 0.00 33.65 1.40
3819 10419 3.490890 GCGTCTTGCAGACATCCC 58.509 61.111 14.09 0.07 45.30 3.85
3906 10509 1.285962 CCATCTGTCCCATTGTCCCTT 59.714 52.381 0.00 0.00 0.00 3.95
3987 10777 4.941873 GGCCTTATATACGAAAATGGAGGG 59.058 45.833 0.00 0.00 0.00 4.30
3988 10778 5.411669 GTGGCCTTATATACGAAAATGGAGG 59.588 44.000 3.32 0.00 0.00 4.30
3989 10779 6.231211 AGTGGCCTTATATACGAAAATGGAG 58.769 40.000 3.32 0.00 0.00 3.86
3990 10780 6.182507 AGTGGCCTTATATACGAAAATGGA 57.817 37.500 3.32 0.00 0.00 3.41
3991 10781 7.822334 TGATAGTGGCCTTATATACGAAAATGG 59.178 37.037 3.32 0.00 0.00 3.16
3992 10782 8.771920 TGATAGTGGCCTTATATACGAAAATG 57.228 34.615 3.32 0.00 0.00 2.32
3993 10783 9.787435 TTTGATAGTGGCCTTATATACGAAAAT 57.213 29.630 3.32 0.00 0.00 1.82
3994 10784 9.616156 TTTTGATAGTGGCCTTATATACGAAAA 57.384 29.630 3.32 4.04 0.00 2.29
3995 10785 9.787435 ATTTTGATAGTGGCCTTATATACGAAA 57.213 29.630 3.32 4.12 0.00 3.46
3996 10786 9.787435 AATTTTGATAGTGGCCTTATATACGAA 57.213 29.630 3.32 0.00 0.00 3.85
4004 10794 9.868277 CAAATTGTAATTTTGATAGTGGCCTTA 57.132 29.630 3.32 0.00 36.52 2.69
4005 10795 7.334171 GCAAATTGTAATTTTGATAGTGGCCTT 59.666 33.333 3.32 0.00 36.52 4.35
4006 10796 6.818142 GCAAATTGTAATTTTGATAGTGGCCT 59.182 34.615 3.32 0.00 36.52 5.19
4007 10797 6.593382 TGCAAATTGTAATTTTGATAGTGGCC 59.407 34.615 0.00 0.00 36.52 5.36
4008 10798 7.593875 TGCAAATTGTAATTTTGATAGTGGC 57.406 32.000 0.04 0.36 36.52 5.01
4009 10799 9.206870 AGTTGCAAATTGTAATTTTGATAGTGG 57.793 29.630 0.00 0.00 36.52 4.00
4018 10808 9.150348 GCCTTGTATAGTTGCAAATTGTAATTT 57.850 29.630 4.05 0.00 39.07 1.82
4019 10809 7.763985 GGCCTTGTATAGTTGCAAATTGTAATT 59.236 33.333 4.05 0.00 0.00 1.40
4020 10810 7.093552 TGGCCTTGTATAGTTGCAAATTGTAAT 60.094 33.333 4.05 0.00 0.00 1.89
4021 10811 6.209589 TGGCCTTGTATAGTTGCAAATTGTAA 59.790 34.615 4.05 0.00 0.00 2.41
4022 10812 5.712446 TGGCCTTGTATAGTTGCAAATTGTA 59.288 36.000 4.05 0.00 0.00 2.41
4023 10813 4.526262 TGGCCTTGTATAGTTGCAAATTGT 59.474 37.500 4.05 0.00 0.00 2.71
4024 10814 4.864247 GTGGCCTTGTATAGTTGCAAATTG 59.136 41.667 4.05 0.00 0.00 2.32
4025 10815 4.772100 AGTGGCCTTGTATAGTTGCAAATT 59.228 37.500 4.05 0.00 0.00 1.82
4026 10816 4.344104 AGTGGCCTTGTATAGTTGCAAAT 58.656 39.130 3.32 4.23 0.00 2.32
4027 10817 3.761897 AGTGGCCTTGTATAGTTGCAAA 58.238 40.909 3.32 0.00 0.00 3.68
4028 10818 3.433306 AGTGGCCTTGTATAGTTGCAA 57.567 42.857 3.32 0.00 0.00 4.08
4029 10819 4.258543 GTTAGTGGCCTTGTATAGTTGCA 58.741 43.478 3.32 0.00 0.00 4.08
4030 10820 4.877323 GTTAGTGGCCTTGTATAGTTGC 57.123 45.455 3.32 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.