Multiple sequence alignment - TraesCS6B01G097400

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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 TraesCS6B01G097400 chr6B 100.000 3941 0 0 1 3941 75029400 75025460 0.000000e+00 7278.0
1 TraesCS6B01G097400 chr6B 92.132 788 43 8 1821 2599 73901905 73901128 0.000000e+00 1094.0
2 TraesCS6B01G097400 chr6B 89.213 890 76 14 924 1799 73902776 73901893 0.000000e+00 1094.0
3 TraesCS6B01G097400 chr6B 94.311 334 18 1 1 333 73947715 73947382 9.770000e-141 510.0
4 TraesCS6B01G097400 chr6B 87.004 454 23 18 2632 3051 73901018 73900567 2.750000e-131 479.0
5 TraesCS6B01G097400 chr6B 94.208 259 13 2 1 257 73903286 73903028 1.030000e-105 394.0
6 TraesCS6B01G097400 chr6B 97.980 99 2 0 235 333 73902894 73902796 5.240000e-39 172.0
7 TraesCS6B01G097400 chr6B 87.234 94 8 2 3145 3235 75000152 75000060 1.940000e-18 104.0
8 TraesCS6B01G097400 chr6B 98.246 57 1 0 867 923 73902799 73902743 2.510000e-17 100.0
9 TraesCS6B01G097400 chr6B 86.170 94 9 2 3145 3235 74907091 74906999 9.010000e-17 99.0
10 TraesCS6B01G097400 chr6B 96.491 57 2 0 867 923 73947385 73947329 1.170000e-15 95.3
11 TraesCS6B01G097400 chr6B 83.529 85 13 1 493 576 228605953 228606037 1.170000e-10 78.7
12 TraesCS6B01G097400 chr6A 91.029 1360 60 23 1821 3139 39494156 39492818 0.000000e+00 1779.0
13 TraesCS6B01G097400 chr6A 91.146 881 71 7 924 1799 39495022 39494144 0.000000e+00 1188.0
14 TraesCS6B01G097400 chr6A 93.418 471 27 4 1 469 39495862 39495394 0.000000e+00 695.0
15 TraesCS6B01G097400 chr6A 94.505 364 14 4 562 923 39495346 39494987 1.240000e-154 556.0
16 TraesCS6B01G097400 chr6A 94.595 74 4 0 753 826 35340414 35340341 8.950000e-22 115.0
17 TraesCS6B01G097400 chr6D 93.316 763 38 6 1821 2580 35623172 35622420 0.000000e+00 1114.0
18 TraesCS6B01G097400 chr6D 89.064 887 70 15 924 1799 35624030 35623160 0.000000e+00 1075.0
19 TraesCS6B01G097400 chr6D 93.173 498 25 4 2643 3139 35622269 35621780 0.000000e+00 723.0
20 TraesCS6B01G097400 chr6D 93.133 466 25 5 1 463 35624875 35624414 0.000000e+00 676.0
21 TraesCS6B01G097400 chr6D 94.595 370 15 5 554 923 35624361 35623997 5.720000e-158 568.0
22 TraesCS6B01G097400 chr5A 92.253 697 50 4 3246 3941 484426483 484427176 0.000000e+00 985.0
23 TraesCS6B01G097400 chr5A 87.822 698 79 6 3246 3941 23942973 23943666 0.000000e+00 813.0
24 TraesCS6B01G097400 chr5D 90.688 698 61 4 3245 3941 463921774 463921080 0.000000e+00 926.0
25 TraesCS6B01G097400 chr7B 89.189 703 64 11 3245 3941 35307639 35306943 0.000000e+00 867.0
26 TraesCS6B01G097400 chr2B 89.115 689 61 10 3257 3941 530128846 530128168 0.000000e+00 845.0
27 TraesCS6B01G097400 chr2B 93.243 74 5 0 753 826 220521010 220521083 4.160000e-20 110.0
28 TraesCS6B01G097400 chr1B 88.682 698 69 9 3247 3941 514187191 514186501 0.000000e+00 843.0
29 TraesCS6B01G097400 chr1B 95.946 74 3 0 753 826 393120099 393120172 1.920000e-23 121.0
30 TraesCS6B01G097400 chr1B 90.141 71 4 3 504 572 92616643 92616712 5.420000e-14 89.8
31 TraesCS6B01G097400 chr7A 88.210 687 75 6 3257 3941 128861193 128860511 0.000000e+00 815.0
32 TraesCS6B01G097400 chr7A 94.595 74 4 0 753 826 675219640 675219713 8.950000e-22 115.0
33 TraesCS6B01G097400 chr3A 89.780 636 64 1 3264 3898 736944689 736944054 0.000000e+00 813.0
34 TraesCS6B01G097400 chr3A 94.595 74 4 0 753 826 625654679 625654606 8.950000e-22 115.0
35 TraesCS6B01G097400 chr2A 87.535 706 82 5 3237 3941 663489825 663490525 0.000000e+00 811.0
36 TraesCS6B01G097400 chr2A 85.366 82 9 3 493 572 2694824 2694904 9.080000e-12 82.4
37 TraesCS6B01G097400 chr4A 94.595 74 4 0 753 826 597781494 597781567 8.950000e-22 115.0
38 TraesCS6B01G097400 chrUn 87.234 94 8 2 3145 3235 457196606 457196514 1.940000e-18 104.0
39 TraesCS6B01G097400 chr1A 87.059 85 8 3 493 575 251695783 251695700 4.190000e-15 93.5
40 TraesCS6B01G097400 chr1A 85.366 82 9 3 493 572 160152612 160152692 9.080000e-12 82.4
41 TraesCS6B01G097400 chr2D 85.882 85 8 4 493 575 157901272 157901190 1.950000e-13 87.9
42 TraesCS6B01G097400 chr3B 84.848 66 7 3 508 571 634233434 634233370 3.290000e-06 63.9
43 TraesCS6B01G097400 chr3B 93.023 43 2 1 535 576 829370684 829370642 1.180000e-05 62.1
44 TraesCS6B01G097400 chr3B 79.545 88 15 3 493 578 270151086 270151000 4.250000e-05 60.2
45 TraesCS6B01G097400 chr7D 80.247 81 13 3 493 572 389080507 389080429 1.530000e-04 58.4


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 TraesCS6B01G097400 chr6B 75025460 75029400 3940 True 7278.0 7278 100.0000 1 3941 1 chr6B.!!$R3 3940
1 TraesCS6B01G097400 chr6B 73900567 73903286 2719 True 555.5 1094 93.1305 1 3051 6 chr6B.!!$R4 3050
2 TraesCS6B01G097400 chr6A 39492818 39495862 3044 True 1054.5 1779 92.5245 1 3139 4 chr6A.!!$R2 3138
3 TraesCS6B01G097400 chr6D 35621780 35624875 3095 True 831.2 1114 92.6562 1 3139 5 chr6D.!!$R1 3138
4 TraesCS6B01G097400 chr5A 484426483 484427176 693 False 985.0 985 92.2530 3246 3941 1 chr5A.!!$F2 695
5 TraesCS6B01G097400 chr5A 23942973 23943666 693 False 813.0 813 87.8220 3246 3941 1 chr5A.!!$F1 695
6 TraesCS6B01G097400 chr5D 463921080 463921774 694 True 926.0 926 90.6880 3245 3941 1 chr5D.!!$R1 696
7 TraesCS6B01G097400 chr7B 35306943 35307639 696 True 867.0 867 89.1890 3245 3941 1 chr7B.!!$R1 696
8 TraesCS6B01G097400 chr2B 530128168 530128846 678 True 845.0 845 89.1150 3257 3941 1 chr2B.!!$R1 684
9 TraesCS6B01G097400 chr1B 514186501 514187191 690 True 843.0 843 88.6820 3247 3941 1 chr1B.!!$R1 694
10 TraesCS6B01G097400 chr7A 128860511 128861193 682 True 815.0 815 88.2100 3257 3941 1 chr7A.!!$R1 684
11 TraesCS6B01G097400 chr3A 736944054 736944689 635 True 813.0 813 89.7800 3264 3898 1 chr3A.!!$R2 634
12 TraesCS6B01G097400 chr2A 663489825 663490525 700 False 811.0 811 87.5350 3237 3941 1 chr2A.!!$F2 704

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
391 555 0.107017 CGACCCAATGCCTCCATTCT 60.107 55.0 0.00 0.00 39.6 2.40 F
931 1105 0.324943 GACTTGCTAGCCTTCCACCA 59.675 55.0 13.29 0.00 0.0 4.17 F
932 1106 0.326264 ACTTGCTAGCCTTCCACCAG 59.674 55.0 13.29 0.00 0.0 4.00 F
1215 1393 0.439985 CTCACAATGGCGTCGACTTG 59.560 55.0 14.70 13.29 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2450 0.179001 AGTAACACAGTGGGTTGGCC 60.179 55.0 21.20 8.48 0.00 5.36 R
2430 2630 0.108615 GTTGAGGCTCTTCGCTAGCA 60.109 55.0 16.45 0.00 41.93 3.49 R
2533 2733 0.179000 GGTCTTGGACGATGCTGGAT 59.821 55.0 0.00 0.00 32.65 3.41 R
3181 3520 0.248094 GCTAAACAGCGCCCGATTTC 60.248 55.0 2.29 0.00 0.00 2.17 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
96 99 1.508632 TGCCTGCTTGTCTTCGTTAC 58.491 50.000 0.00 0.00 0.00 2.50
158 161 2.558359 GGACACTGTCCCCTGAAATTTG 59.442 50.000 16.54 0.00 46.19 2.32
231 235 7.639461 CAGTTGGCAAAATTTTGTTGTATTGTC 59.361 33.333 27.13 10.72 40.24 3.18
389 553 0.331278 TTCGACCCAATGCCTCCATT 59.669 50.000 0.00 0.00 42.26 3.16
391 555 0.107017 CGACCCAATGCCTCCATTCT 60.107 55.000 0.00 0.00 39.60 2.40
399 563 2.957402 TGCCTCCATTCTTGTTCTGT 57.043 45.000 0.00 0.00 0.00 3.41
427 591 3.713764 AGAGGCAGATACCATTAGCAGTT 59.286 43.478 0.00 0.00 0.00 3.16
430 594 2.880890 GCAGATACCATTAGCAGTTGGG 59.119 50.000 4.18 0.00 37.32 4.12
497 661 1.919240 AACAATCGGTTTTCCTCCCC 58.081 50.000 0.00 0.00 35.82 4.81
512 676 3.582662 CCCCCGGCCCACAATATA 58.417 61.111 0.00 0.00 0.00 0.86
513 677 1.847686 CCCCCGGCCCACAATATAA 59.152 57.895 0.00 0.00 0.00 0.98
515 679 0.768622 CCCCGGCCCACAATATAAGA 59.231 55.000 0.00 0.00 0.00 2.10
516 680 1.354368 CCCCGGCCCACAATATAAGAT 59.646 52.381 0.00 0.00 0.00 2.40
517 681 2.618045 CCCCGGCCCACAATATAAGATC 60.618 54.545 0.00 0.00 0.00 2.75
518 682 2.346803 CCGGCCCACAATATAAGATCG 58.653 52.381 0.00 0.00 0.00 3.69
519 683 2.289444 CCGGCCCACAATATAAGATCGT 60.289 50.000 0.00 0.00 0.00 3.73
520 684 3.399330 CGGCCCACAATATAAGATCGTT 58.601 45.455 0.00 0.00 0.00 3.85
521 685 3.813166 CGGCCCACAATATAAGATCGTTT 59.187 43.478 0.00 0.00 0.00 3.60
523 687 5.220970 CGGCCCACAATATAAGATCGTTTTT 60.221 40.000 0.00 0.00 0.00 1.94
524 688 6.206498 GGCCCACAATATAAGATCGTTTTTC 58.794 40.000 0.00 0.00 0.00 2.29
526 690 7.254852 GCCCACAATATAAGATCGTTTTTCAA 58.745 34.615 0.00 0.00 0.00 2.69
527 691 7.432252 GCCCACAATATAAGATCGTTTTTCAAG 59.568 37.037 0.00 0.00 0.00 3.02
530 694 7.967854 CACAATATAAGATCGTTTTTCAAGCCA 59.032 33.333 0.00 0.00 0.00 4.75
532 696 8.798153 CAATATAAGATCGTTTTTCAAGCCAAC 58.202 33.333 0.00 0.00 0.00 3.77
533 697 3.643159 AGATCGTTTTTCAAGCCAACC 57.357 42.857 0.00 0.00 0.00 3.77
535 699 4.394729 AGATCGTTTTTCAAGCCAACCTA 58.605 39.130 0.00 0.00 0.00 3.08
536 700 4.455877 AGATCGTTTTTCAAGCCAACCTAG 59.544 41.667 0.00 0.00 0.00 3.02
537 701 3.547746 TCGTTTTTCAAGCCAACCTAGT 58.452 40.909 0.00 0.00 0.00 2.57
538 702 3.949113 TCGTTTTTCAAGCCAACCTAGTT 59.051 39.130 0.00 0.00 0.00 2.24
539 703 4.399934 TCGTTTTTCAAGCCAACCTAGTTT 59.600 37.500 0.00 0.00 0.00 2.66
540 704 4.502645 CGTTTTTCAAGCCAACCTAGTTTG 59.497 41.667 0.00 0.00 0.00 2.93
541 705 5.656480 GTTTTTCAAGCCAACCTAGTTTGA 58.344 37.500 0.87 0.00 0.00 2.69
542 706 5.923733 TTTTCAAGCCAACCTAGTTTGAA 57.076 34.783 0.87 0.00 36.35 2.69
543 707 5.923733 TTTCAAGCCAACCTAGTTTGAAA 57.076 34.783 0.87 10.25 42.27 2.69
544 708 5.923733 TTCAAGCCAACCTAGTTTGAAAA 57.076 34.783 0.87 0.00 35.51 2.29
545 709 5.923733 TCAAGCCAACCTAGTTTGAAAAA 57.076 34.783 0.87 0.00 0.00 1.94
546 710 5.656480 TCAAGCCAACCTAGTTTGAAAAAC 58.344 37.500 0.87 0.00 0.00 2.43
547 711 5.186021 TCAAGCCAACCTAGTTTGAAAAACA 59.814 36.000 0.87 0.00 0.00 2.83
548 712 5.869649 AGCCAACCTAGTTTGAAAAACAT 57.130 34.783 0.87 0.00 0.00 2.71
549 713 5.842907 AGCCAACCTAGTTTGAAAAACATC 58.157 37.500 0.87 0.00 0.00 3.06
550 714 5.598417 AGCCAACCTAGTTTGAAAAACATCT 59.402 36.000 0.87 0.00 0.00 2.90
551 715 6.098266 AGCCAACCTAGTTTGAAAAACATCTT 59.902 34.615 0.87 0.00 0.00 2.40
552 716 7.286775 AGCCAACCTAGTTTGAAAAACATCTTA 59.713 33.333 0.87 0.00 0.00 2.10
553 717 8.088365 GCCAACCTAGTTTGAAAAACATCTTAT 58.912 33.333 0.87 0.00 0.00 1.73
572 746 5.667626 TCTTATATTATGGGATGGAGGGAGC 59.332 44.000 0.00 0.00 0.00 4.70
598 772 2.490509 CTGATTTGGCTGACAGATTGCA 59.509 45.455 6.65 0.00 32.90 4.08
601 775 3.306917 TTTGGCTGACAGATTGCATTG 57.693 42.857 6.65 0.00 0.00 2.82
621 795 7.662669 TGCATTGTGATTGTGCTCTGTATATAT 59.337 33.333 0.00 0.00 39.52 0.86
627 801 8.303156 GTGATTGTGCTCTGTATATATCACTCT 58.697 37.037 0.00 0.00 38.24 3.24
659 833 8.716674 ATGAATTCCCATGCTGATACTATTTT 57.283 30.769 2.27 0.00 0.00 1.82
666 840 6.243900 CCATGCTGATACTATTTTGGAGGAT 58.756 40.000 0.00 0.00 0.00 3.24
667 841 6.718454 CCATGCTGATACTATTTTGGAGGATT 59.282 38.462 0.00 0.00 0.00 3.01
668 842 7.232127 CCATGCTGATACTATTTTGGAGGATTT 59.768 37.037 0.00 0.00 0.00 2.17
705 879 7.096106 CGAATTACTGATGTGTTGTGCAAATTT 60.096 33.333 0.00 0.00 0.00 1.82
715 889 7.467623 TGTGTTGTGCAAATTTATTTGTTTCC 58.532 30.769 14.66 1.73 46.63 3.13
800 974 6.106673 CCTTGTGGTAGTTATCTTGGTACAG 58.893 44.000 0.00 0.00 42.39 2.74
840 1014 3.073062 ACTGTAATTGGAGAAGGTGCAGT 59.927 43.478 0.00 0.00 0.00 4.40
909 1083 7.719483 TCATTCTTCCATCAGAATAAATTGGC 58.281 34.615 0.00 0.00 40.86 4.52
910 1084 7.562454 TCATTCTTCCATCAGAATAAATTGGCT 59.438 33.333 0.00 0.00 40.86 4.75
911 1085 8.853126 CATTCTTCCATCAGAATAAATTGGCTA 58.147 33.333 0.00 0.00 40.86 3.93
912 1086 8.455903 TTCTTCCATCAGAATAAATTGGCTAG 57.544 34.615 0.00 0.00 32.82 3.42
913 1087 7.805163 TCTTCCATCAGAATAAATTGGCTAGA 58.195 34.615 0.00 0.00 32.82 2.43
914 1088 7.716998 TCTTCCATCAGAATAAATTGGCTAGAC 59.283 37.037 0.00 0.00 32.82 2.59
915 1089 7.141758 TCCATCAGAATAAATTGGCTAGACT 57.858 36.000 0.00 0.00 0.00 3.24
916 1090 7.577303 TCCATCAGAATAAATTGGCTAGACTT 58.423 34.615 0.00 0.00 0.00 3.01
917 1091 7.500227 TCCATCAGAATAAATTGGCTAGACTTG 59.500 37.037 0.00 0.00 0.00 3.16
918 1092 6.683974 TCAGAATAAATTGGCTAGACTTGC 57.316 37.500 0.00 0.00 0.00 4.01
919 1093 6.418101 TCAGAATAAATTGGCTAGACTTGCT 58.582 36.000 8.78 0.00 0.00 3.91
920 1094 7.564793 TCAGAATAAATTGGCTAGACTTGCTA 58.435 34.615 8.78 0.00 0.00 3.49
929 1103 3.172229 CTAGACTTGCTAGCCTTCCAC 57.828 52.381 13.29 0.00 40.15 4.02
930 1104 0.615850 AGACTTGCTAGCCTTCCACC 59.384 55.000 13.29 0.00 0.00 4.61
931 1105 0.324943 GACTTGCTAGCCTTCCACCA 59.675 55.000 13.29 0.00 0.00 4.17
932 1106 0.326264 ACTTGCTAGCCTTCCACCAG 59.674 55.000 13.29 0.00 0.00 4.00
933 1107 0.615331 CTTGCTAGCCTTCCACCAGA 59.385 55.000 13.29 0.00 0.00 3.86
934 1108 1.003580 CTTGCTAGCCTTCCACCAGAA 59.996 52.381 13.29 0.00 0.00 3.02
986 1161 5.253330 TCAGAGTTTCTTCTTTGTGTGGTT 58.747 37.500 0.00 0.00 0.00 3.67
1003 1178 1.134220 GGTTACTGGAATCGGCCATGA 60.134 52.381 2.24 0.00 37.30 3.07
1005 1180 1.199615 TACTGGAATCGGCCATGACA 58.800 50.000 2.24 0.00 37.30 3.58
1017 1192 3.114616 ATGACAGTGCTGCGACGC 61.115 61.111 14.19 14.19 0.00 5.19
1044 1219 2.193536 GGCACTCCGGTTGCTGTTT 61.194 57.895 23.93 0.00 0.00 2.83
1045 1220 0.887387 GGCACTCCGGTTGCTGTTTA 60.887 55.000 23.93 0.00 0.00 2.01
1047 1222 1.539827 GCACTCCGGTTGCTGTTTATT 59.460 47.619 19.62 0.00 0.00 1.40
1131 1309 1.011968 CGGCGATCTTTGTGTTCGGA 61.012 55.000 0.00 0.00 38.08 4.55
1189 1367 1.990060 GGGACCAGTGCCAGAGCTA 60.990 63.158 3.11 0.00 41.16 3.32
1215 1393 0.439985 CTCACAATGGCGTCGACTTG 59.560 55.000 14.70 13.29 0.00 3.16
1313 1491 3.317711 TCACACGCTTTTGAATCAATGGT 59.682 39.130 0.00 0.00 0.00 3.55
1339 1517 1.547820 GGCTGTCTGTCTGATCAGTGA 59.452 52.381 21.92 15.18 36.85 3.41
1365 1543 2.034687 GCAGCTGTCCACATGGGT 59.965 61.111 16.64 0.00 38.11 4.51
1435 1613 2.560861 CATTGGGCAACACGACGG 59.439 61.111 0.00 0.00 39.74 4.79
1548 1727 3.428045 GCCACATCTGCTGTAACATTTCC 60.428 47.826 0.00 0.00 35.91 3.13
1554 1733 1.271108 TGCTGTAACATTTCCGCCTCA 60.271 47.619 0.00 0.00 0.00 3.86
1560 1739 3.643159 AACATTTCCGCCTCAGTTTTC 57.357 42.857 0.00 0.00 0.00 2.29
1563 1742 1.604604 TTTCCGCCTCAGTTTTCCTG 58.395 50.000 0.00 0.00 42.97 3.86
1570 1749 3.219281 GCCTCAGTTTTCCTGGTTTACA 58.781 45.455 0.00 0.00 41.83 2.41
1571 1750 3.826729 GCCTCAGTTTTCCTGGTTTACAT 59.173 43.478 0.00 0.00 41.83 2.29
1697 1891 9.562583 TTTGTTCTATATTTTAATGTTCACCGC 57.437 29.630 0.00 0.00 0.00 5.68
1753 1947 8.989980 ACTACCTAAAGTTGAGAAAATTCTTCG 58.010 33.333 0.00 0.00 37.73 3.79
1797 1991 4.953579 ACTTTCTCCTGTACTCCATCTCTC 59.046 45.833 0.00 0.00 0.00 3.20
1798 1992 4.871871 TTCTCCTGTACTCCATCTCTCT 57.128 45.455 0.00 0.00 0.00 3.10
1799 1993 4.431416 TCTCCTGTACTCCATCTCTCTC 57.569 50.000 0.00 0.00 0.00 3.20
1800 1994 4.044308 TCTCCTGTACTCCATCTCTCTCT 58.956 47.826 0.00 0.00 0.00 3.10
1801 1995 4.476846 TCTCCTGTACTCCATCTCTCTCTT 59.523 45.833 0.00 0.00 0.00 2.85
1802 1996 5.044476 TCTCCTGTACTCCATCTCTCTCTTT 60.044 44.000 0.00 0.00 0.00 2.52
1803 1997 5.584913 TCCTGTACTCCATCTCTCTCTTTT 58.415 41.667 0.00 0.00 0.00 2.27
1804 1998 6.019748 TCCTGTACTCCATCTCTCTCTTTTT 58.980 40.000 0.00 0.00 0.00 1.94
1827 2021 5.941948 TTTTTCTTCGGAAAGACTCCATC 57.058 39.130 0.00 0.00 45.74 3.51
1828 2022 4.891992 TTTCTTCGGAAAGACTCCATCT 57.108 40.909 0.00 0.00 45.74 2.90
1829 2023 4.457834 TTCTTCGGAAAGACTCCATCTC 57.542 45.455 0.00 0.00 45.74 2.75
1830 2024 3.702792 TCTTCGGAAAGACTCCATCTCT 58.297 45.455 0.00 0.00 45.74 3.10
1853 2047 6.427853 TCTCTTTAATGTCATGAACCACACAG 59.572 38.462 0.00 0.00 0.00 3.66
1874 2068 7.938490 ACACAGAATTTAAAATCTGGCCATTTT 59.062 29.630 28.41 18.53 45.80 1.82
1973 2167 7.850419 AGATGATGATCATATTACCAGGGAGAT 59.150 37.037 8.54 0.00 37.20 2.75
2021 2215 5.897050 GAGTACTTCTCGGATCTCAAACAT 58.103 41.667 0.00 0.00 33.25 2.71
2060 2254 4.373116 GGTGCCTTCGGAGCGTCA 62.373 66.667 0.00 0.00 0.00 4.35
2066 2260 1.374758 CTTCGGAGCGTCAGCCTTT 60.375 57.895 0.00 0.00 46.67 3.11
2090 2284 3.054875 TGTCCAAGTCCATCTTCCTCATG 60.055 47.826 0.00 0.00 33.63 3.07
2135 2329 1.271102 GACTTCTTCTCGCAGGACACT 59.729 52.381 0.00 0.00 0.00 3.55
2141 2335 3.573772 CTCGCAGGACACTTCGCCA 62.574 63.158 0.00 0.00 33.29 5.69
2251 2450 1.734465 GTTCCATCAGGCTTCAACTCG 59.266 52.381 0.00 0.00 33.74 4.18
2258 2458 2.626780 GGCTTCAACTCGGCCAACC 61.627 63.158 2.24 0.00 44.69 3.77
2266 2466 3.476031 CTCGGCCAACCCACTGTGT 62.476 63.158 2.24 0.00 0.00 3.72
2267 2467 2.518349 CGGCCAACCCACTGTGTT 60.518 61.111 2.24 0.00 0.00 3.32
2268 2468 1.228003 CGGCCAACCCACTGTGTTA 60.228 57.895 2.24 0.00 0.00 2.41
2269 2469 1.512156 CGGCCAACCCACTGTGTTAC 61.512 60.000 2.24 0.00 0.00 2.50
2288 2488 8.773645 TGTGTTACTTATGTTCAACTCTGAATG 58.226 33.333 0.00 0.00 43.39 2.67
2317 2517 1.798234 GCATGGTTGTGCTGCAGACA 61.798 55.000 20.43 15.84 41.82 3.41
2430 2630 4.421479 CGTCGAGCCGCTGAACCT 62.421 66.667 0.00 0.00 0.00 3.50
2452 2652 3.464628 GCGAAGAGCCTCAACGAC 58.535 61.111 13.09 3.16 40.81 4.34
2583 2790 3.439129 AGGTAAAACCGCAGCATTCTAAC 59.561 43.478 0.00 0.00 44.90 2.34
2640 2930 2.089936 GGCAACGTACGTGCATCGA 61.090 57.895 29.99 0.00 42.86 3.59
2988 3311 1.227383 GGGGCCGATCCAAGTCAAT 59.773 57.895 0.00 0.00 36.21 2.57
2989 3312 0.819666 GGGGCCGATCCAAGTCAATC 60.820 60.000 0.00 0.00 36.21 2.67
2991 3314 1.408822 GGGCCGATCCAAGTCAATCTT 60.409 52.381 0.00 0.00 36.21 2.40
3064 3389 5.587043 GTCCAATTGGGTGTCGATTAATGTA 59.413 40.000 24.29 0.00 38.11 2.29
3094 3432 0.396435 TTGGGGCAGACACACACTAG 59.604 55.000 0.00 0.00 0.00 2.57
3101 3439 3.005472 GGCAGACACACACTAGTTACTCA 59.995 47.826 0.00 0.00 0.00 3.41
3116 3455 2.979401 ACTCATCGATCGATTCTCGG 57.021 50.000 27.45 15.94 40.88 4.63
3139 3478 2.029828 CACACTGACCTGAGTACTGGAC 60.030 54.545 0.00 0.00 38.29 4.02
3140 3479 1.200252 CACTGACCTGAGTACTGGACG 59.800 57.143 0.00 0.00 38.29 4.79
3141 3480 0.171455 CTGACCTGAGTACTGGACGC 59.829 60.000 0.00 0.00 38.29 5.19
3142 3481 1.248785 TGACCTGAGTACTGGACGCC 61.249 60.000 0.00 0.00 38.29 5.68
3143 3482 1.946475 GACCTGAGTACTGGACGCCC 61.946 65.000 0.00 0.00 38.29 6.13
3144 3483 2.490217 CTGAGTACTGGACGCCCG 59.510 66.667 0.00 0.00 34.29 6.13
3145 3484 3.701604 CTGAGTACTGGACGCCCGC 62.702 68.421 0.00 0.00 34.29 6.13
3146 3485 4.849329 GAGTACTGGACGCCCGCG 62.849 72.222 7.69 7.69 46.03 6.46
3159 3498 4.742201 CCGCGTGGAGGAGGTGTG 62.742 72.222 10.20 0.00 37.49 3.82
3169 3508 4.025401 GAGGTGTGCGCCCGTTTG 62.025 66.667 4.18 0.00 0.00 2.93
3178 3517 4.526152 GCCCGTTTGCGTAAACTG 57.474 55.556 23.63 18.06 43.13 3.16
3179 3518 1.943293 GCCCGTTTGCGTAAACTGA 59.057 52.632 23.63 0.00 43.13 3.41
3180 3519 0.308376 GCCCGTTTGCGTAAACTGAA 59.692 50.000 23.63 0.00 43.13 3.02
3181 3520 1.662026 GCCCGTTTGCGTAAACTGAAG 60.662 52.381 23.63 10.35 43.13 3.02
3182 3521 1.868498 CCCGTTTGCGTAAACTGAAGA 59.132 47.619 23.63 0.00 43.13 2.87
3183 3522 2.288458 CCCGTTTGCGTAAACTGAAGAA 59.712 45.455 23.63 0.00 43.13 2.52
3184 3523 3.242804 CCCGTTTGCGTAAACTGAAGAAA 60.243 43.478 23.63 0.00 43.13 2.52
3185 3524 4.533222 CCGTTTGCGTAAACTGAAGAAAT 58.467 39.130 23.63 0.00 43.13 2.17
3186 3525 4.611366 CCGTTTGCGTAAACTGAAGAAATC 59.389 41.667 23.63 0.00 43.13 2.17
3187 3526 4.314708 CGTTTGCGTAAACTGAAGAAATCG 59.685 41.667 23.63 5.86 43.13 3.34
3188 3527 4.398549 TTGCGTAAACTGAAGAAATCGG 57.601 40.909 0.00 0.00 40.53 4.18
3189 3528 2.739913 TGCGTAAACTGAAGAAATCGGG 59.260 45.455 0.00 0.00 38.87 5.14
3190 3529 2.475685 GCGTAAACTGAAGAAATCGGGC 60.476 50.000 0.00 0.00 38.87 6.13
3191 3530 2.222729 CGTAAACTGAAGAAATCGGGCG 60.223 50.000 0.00 0.00 38.87 6.13
3192 3531 0.521735 AAACTGAAGAAATCGGGCGC 59.478 50.000 0.00 0.00 38.87 6.53
3193 3532 0.321653 AACTGAAGAAATCGGGCGCT 60.322 50.000 7.64 0.00 38.87 5.92
3194 3533 1.021390 ACTGAAGAAATCGGGCGCTG 61.021 55.000 7.64 0.00 38.87 5.18
3195 3534 1.003839 TGAAGAAATCGGGCGCTGT 60.004 52.632 7.64 0.00 0.00 4.40
3196 3535 0.605319 TGAAGAAATCGGGCGCTGTT 60.605 50.000 7.64 0.00 0.00 3.16
3197 3536 0.521735 GAAGAAATCGGGCGCTGTTT 59.478 50.000 7.64 3.39 0.00 2.83
3198 3537 1.735571 GAAGAAATCGGGCGCTGTTTA 59.264 47.619 7.64 0.00 0.00 2.01
3199 3538 1.369625 AGAAATCGGGCGCTGTTTAG 58.630 50.000 7.64 0.00 0.00 1.85
3200 3539 0.248094 GAAATCGGGCGCTGTTTAGC 60.248 55.000 7.64 0.00 46.62 3.09
3212 3551 3.665745 CTGTTTAGCATTTGCCAAGGT 57.334 42.857 0.00 0.00 43.38 3.50
3213 3552 3.319755 CTGTTTAGCATTTGCCAAGGTG 58.680 45.455 0.00 0.00 43.38 4.00
3214 3553 2.961741 TGTTTAGCATTTGCCAAGGTGA 59.038 40.909 0.00 0.00 43.38 4.02
3215 3554 3.386078 TGTTTAGCATTTGCCAAGGTGAA 59.614 39.130 0.00 0.00 43.38 3.18
3216 3555 3.940209 TTAGCATTTGCCAAGGTGAAG 57.060 42.857 0.00 0.00 43.38 3.02
3217 3556 0.971386 AGCATTTGCCAAGGTGAAGG 59.029 50.000 0.00 0.00 43.38 3.46
3225 3564 0.593128 CCAAGGTGAAGGCTGAAACG 59.407 55.000 0.00 0.00 0.00 3.60
3226 3565 1.308998 CAAGGTGAAGGCTGAAACGT 58.691 50.000 0.00 0.00 0.00 3.99
3227 3566 2.489971 CAAGGTGAAGGCTGAAACGTA 58.510 47.619 0.00 0.00 0.00 3.57
3228 3567 2.165319 AGGTGAAGGCTGAAACGTAC 57.835 50.000 0.00 0.00 0.00 3.67
3229 3568 0.788391 GGTGAAGGCTGAAACGTACG 59.212 55.000 15.01 15.01 0.00 3.67
3230 3569 1.494824 GTGAAGGCTGAAACGTACGT 58.505 50.000 16.72 16.72 0.00 3.57
3231 3570 1.862827 GTGAAGGCTGAAACGTACGTT 59.137 47.619 27.15 27.15 40.45 3.99
3232 3571 2.097056 GTGAAGGCTGAAACGTACGTTC 60.097 50.000 31.79 23.72 37.35 3.95
3233 3572 1.458445 GAAGGCTGAAACGTACGTTCC 59.542 52.381 31.79 26.55 37.35 3.62
3234 3573 0.390124 AGGCTGAAACGTACGTTCCA 59.610 50.000 31.79 25.61 37.35 3.53
3235 3574 0.788391 GGCTGAAACGTACGTTCCAG 59.212 55.000 34.50 34.50 42.25 3.86
3236 3575 0.788391 GCTGAAACGTACGTTCCAGG 59.212 55.000 37.24 23.93 40.18 4.45
3237 3576 1.425412 CTGAAACGTACGTTCCAGGG 58.575 55.000 32.26 14.61 36.93 4.45
3238 3577 1.000060 CTGAAACGTACGTTCCAGGGA 60.000 52.381 32.26 14.01 36.93 4.20
3239 3578 1.000060 TGAAACGTACGTTCCAGGGAG 60.000 52.381 31.79 0.00 37.35 4.30
3240 3579 0.320160 AAACGTACGTTCCAGGGAGC 60.320 55.000 31.79 0.00 37.35 4.70
3241 3580 1.183676 AACGTACGTTCCAGGGAGCT 61.184 55.000 27.15 1.65 32.09 4.09
3242 3581 1.139095 CGTACGTTCCAGGGAGCTC 59.861 63.158 7.22 4.71 0.00 4.09
3243 3582 1.592400 CGTACGTTCCAGGGAGCTCA 61.592 60.000 17.19 0.00 0.00 4.26
3244 3583 0.824759 GTACGTTCCAGGGAGCTCAT 59.175 55.000 17.19 0.00 0.00 2.90
3245 3584 1.207329 GTACGTTCCAGGGAGCTCATT 59.793 52.381 17.19 0.00 0.00 2.57
3246 3585 0.693049 ACGTTCCAGGGAGCTCATTT 59.307 50.000 17.19 0.00 0.00 2.32
3247 3586 1.073923 ACGTTCCAGGGAGCTCATTTT 59.926 47.619 17.19 0.00 0.00 1.82
3248 3587 2.162681 CGTTCCAGGGAGCTCATTTTT 58.837 47.619 17.19 0.00 0.00 1.94
3249 3588 2.162408 CGTTCCAGGGAGCTCATTTTTC 59.838 50.000 17.19 0.00 0.00 2.29
3250 3589 3.425659 GTTCCAGGGAGCTCATTTTTCT 58.574 45.455 17.19 0.00 0.00 2.52
3251 3590 3.814504 TCCAGGGAGCTCATTTTTCTT 57.185 42.857 17.19 0.00 0.00 2.52
3252 3591 4.118168 TCCAGGGAGCTCATTTTTCTTT 57.882 40.909 17.19 0.00 0.00 2.52
3253 3592 4.482990 TCCAGGGAGCTCATTTTTCTTTT 58.517 39.130 17.19 0.00 0.00 2.27
3254 3593 4.524328 TCCAGGGAGCTCATTTTTCTTTTC 59.476 41.667 17.19 0.00 0.00 2.29
3255 3594 4.479619 CAGGGAGCTCATTTTTCTTTTCG 58.520 43.478 17.19 0.00 0.00 3.46
3319 3658 4.314522 TGGGATACACAATTGGTCATGT 57.685 40.909 10.83 7.48 39.74 3.21
3398 3737 5.216566 GCGATGTGCTTCATAGTTAACAA 57.783 39.130 8.61 0.00 41.73 2.83
3548 3887 2.092753 ACGATGAAGTGATGAATGCCCT 60.093 45.455 0.00 0.00 0.00 5.19
3574 3913 2.283460 GCCAGGGCCAAAGCTTCT 60.283 61.111 6.18 0.00 39.73 2.85
3633 3972 0.676782 CCTTCAACTACAAGGGCCGG 60.677 60.000 0.00 0.00 37.37 6.13
3765 4105 2.151502 TTGGTTTTGCCTGAACTGGA 57.848 45.000 2.01 0.00 38.35 3.86
3768 4108 0.317854 GTTTTGCCTGAACTGGACGC 60.318 55.000 2.01 0.00 0.00 5.19
3791 4131 1.864565 GCCTCGCCATTTGTGTTTTT 58.135 45.000 0.00 0.00 0.00 1.94
3795 4135 3.620821 CCTCGCCATTTGTGTTTTTGTTT 59.379 39.130 0.00 0.00 0.00 2.83
3821 4161 5.065914 AGCTGTATTTTGTATGATCGCCAT 58.934 37.500 0.00 0.00 39.25 4.40
3828 4168 5.482163 TTTGTATGATCGCCATATCCTGA 57.518 39.130 1.67 0.00 39.69 3.86
3869 4209 0.840288 TGGGTTGCTTGAGGGCTCTA 60.840 55.000 0.00 0.00 0.00 2.43
3873 4213 2.290323 GGTTGCTTGAGGGCTCTAGAAA 60.290 50.000 0.00 0.00 35.03 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.003648 AGTCAGATTACGCCTTTTTCCTG 58.996 43.478 0.00 0.00 0.00 3.86
96 99 0.541392 TGATTCGGACATCACCCCTG 59.459 55.000 0.00 0.00 0.00 4.45
370 534 0.331278 AATGGAGGCATTGGGTCGAA 59.669 50.000 0.00 0.00 0.00 3.71
399 563 5.590259 GCTAATGGTATCTGCCTCTGAAAAA 59.410 40.000 0.00 0.00 0.00 1.94
411 575 4.862641 AACCCAACTGCTAATGGTATCT 57.137 40.909 0.00 0.00 34.79 1.98
497 661 2.711542 GATCTTATATTGTGGGCCGGG 58.288 52.381 2.18 0.00 0.00 5.73
499 663 3.040147 ACGATCTTATATTGTGGGCCG 57.960 47.619 0.00 0.00 0.00 6.13
501 665 6.791303 TGAAAAACGATCTTATATTGTGGGC 58.209 36.000 0.00 0.00 0.00 5.36
502 666 7.432252 GCTTGAAAAACGATCTTATATTGTGGG 59.568 37.037 0.00 0.00 0.00 4.61
503 667 7.432252 GGCTTGAAAAACGATCTTATATTGTGG 59.568 37.037 0.00 0.00 0.00 4.17
504 668 7.967854 TGGCTTGAAAAACGATCTTATATTGTG 59.032 33.333 0.00 0.00 0.00 3.33
505 669 8.050778 TGGCTTGAAAAACGATCTTATATTGT 57.949 30.769 0.00 0.00 0.00 2.71
506 670 8.798153 GTTGGCTTGAAAAACGATCTTATATTG 58.202 33.333 0.00 0.00 0.00 1.90
507 671 7.973944 GGTTGGCTTGAAAAACGATCTTATATT 59.026 33.333 0.00 0.00 0.00 1.28
508 672 7.339466 AGGTTGGCTTGAAAAACGATCTTATAT 59.661 33.333 0.00 0.00 0.00 0.86
509 673 6.657541 AGGTTGGCTTGAAAAACGATCTTATA 59.342 34.615 0.00 0.00 0.00 0.98
510 674 5.476945 AGGTTGGCTTGAAAAACGATCTTAT 59.523 36.000 0.00 0.00 0.00 1.73
512 676 3.636764 AGGTTGGCTTGAAAAACGATCTT 59.363 39.130 0.00 0.00 0.00 2.40
513 677 3.222603 AGGTTGGCTTGAAAAACGATCT 58.777 40.909 0.00 0.00 0.00 2.75
515 679 4.142038 ACTAGGTTGGCTTGAAAAACGAT 58.858 39.130 0.00 0.00 0.00 3.73
516 680 3.547746 ACTAGGTTGGCTTGAAAAACGA 58.452 40.909 0.00 0.00 0.00 3.85
517 681 3.982576 ACTAGGTTGGCTTGAAAAACG 57.017 42.857 0.00 0.00 0.00 3.60
518 682 5.656480 TCAAACTAGGTTGGCTTGAAAAAC 58.344 37.500 20.25 0.00 0.00 2.43
519 683 5.923733 TCAAACTAGGTTGGCTTGAAAAA 57.076 34.783 20.25 0.00 0.00 1.94
520 684 5.923733 TTCAAACTAGGTTGGCTTGAAAA 57.076 34.783 20.25 2.68 34.10 2.29
521 685 5.923733 TTTCAAACTAGGTTGGCTTGAAA 57.076 34.783 20.25 10.25 41.34 2.69
523 687 5.186021 TGTTTTTCAAACTAGGTTGGCTTGA 59.814 36.000 20.25 0.00 0.00 3.02
524 688 5.415221 TGTTTTTCAAACTAGGTTGGCTTG 58.585 37.500 20.25 0.00 0.00 4.01
526 690 5.598417 AGATGTTTTTCAAACTAGGTTGGCT 59.402 36.000 20.25 3.19 0.00 4.75
527 691 5.842907 AGATGTTTTTCAAACTAGGTTGGC 58.157 37.500 20.25 6.80 0.00 4.52
542 706 9.759473 CCTCCATCCCATAATATAAGATGTTTT 57.241 33.333 9.45 0.00 33.95 2.43
543 707 8.339247 CCCTCCATCCCATAATATAAGATGTTT 58.661 37.037 9.45 0.00 33.95 2.83
544 708 7.688534 TCCCTCCATCCCATAATATAAGATGTT 59.311 37.037 9.45 0.00 33.95 2.71
545 709 7.206251 TCCCTCCATCCCATAATATAAGATGT 58.794 38.462 9.45 0.00 33.95 3.06
546 710 7.691293 GCTCCCTCCATCCCATAATATAAGATG 60.691 44.444 5.26 5.26 35.24 2.90
547 711 6.331307 GCTCCCTCCATCCCATAATATAAGAT 59.669 42.308 0.00 0.00 0.00 2.40
548 712 5.667626 GCTCCCTCCATCCCATAATATAAGA 59.332 44.000 0.00 0.00 0.00 2.10
549 713 5.429762 TGCTCCCTCCATCCCATAATATAAG 59.570 44.000 0.00 0.00 0.00 1.73
550 714 5.358306 TGCTCCCTCCATCCCATAATATAA 58.642 41.667 0.00 0.00 0.00 0.98
551 715 4.971282 CTGCTCCCTCCATCCCATAATATA 59.029 45.833 0.00 0.00 0.00 0.86
552 716 3.784763 CTGCTCCCTCCATCCCATAATAT 59.215 47.826 0.00 0.00 0.00 1.28
553 717 3.184628 CTGCTCCCTCCATCCCATAATA 58.815 50.000 0.00 0.00 0.00 0.98
554 718 1.991070 CTGCTCCCTCCATCCCATAAT 59.009 52.381 0.00 0.00 0.00 1.28
555 719 1.345422 ACTGCTCCCTCCATCCCATAA 60.345 52.381 0.00 0.00 0.00 1.90
556 720 0.268869 ACTGCTCCCTCCATCCCATA 59.731 55.000 0.00 0.00 0.00 2.74
557 721 0.625683 AACTGCTCCCTCCATCCCAT 60.626 55.000 0.00 0.00 0.00 4.00
560 724 0.179936 CAGAACTGCTCCCTCCATCC 59.820 60.000 0.00 0.00 0.00 3.51
572 746 3.405831 TCTGTCAGCCAAATCAGAACTG 58.594 45.455 0.00 0.00 34.61 3.16
598 772 9.212641 GTGATATATACAGAGCACAATCACAAT 57.787 33.333 7.13 0.00 40.89 2.71
601 775 8.303156 AGAGTGATATATACAGAGCACAATCAC 58.697 37.037 0.00 0.00 41.30 3.06
621 795 3.949754 GGGAATTCATTGATGCAGAGTGA 59.050 43.478 7.93 0.00 0.00 3.41
627 801 3.035363 AGCATGGGAATTCATTGATGCA 58.965 40.909 22.00 0.00 38.92 3.96
672 846 9.051027 CACAACACATCAGTAATTCGAATTTAC 57.949 33.333 27.10 20.59 0.00 2.01
705 879 8.740123 ATTATCACATGGTACGGAAACAAATA 57.260 30.769 0.00 0.00 0.00 1.40
715 889 3.625313 TGCCACAATTATCACATGGTACG 59.375 43.478 0.00 0.00 32.71 3.67
800 974 9.908152 AATTACAGTTACTTGCTCCATTAAAAC 57.092 29.630 0.00 0.00 0.00 2.43
840 1014 0.108804 GCTAAGCTCAGTGCACCGTA 60.109 55.000 14.63 0.00 45.94 4.02
909 1083 2.159028 GGTGGAAGGCTAGCAAGTCTAG 60.159 54.545 18.24 0.00 46.01 2.43
910 1084 1.831736 GGTGGAAGGCTAGCAAGTCTA 59.168 52.381 18.24 5.29 36.37 2.59
911 1085 0.615850 GGTGGAAGGCTAGCAAGTCT 59.384 55.000 18.24 0.57 40.22 3.24
912 1086 0.324943 TGGTGGAAGGCTAGCAAGTC 59.675 55.000 18.24 9.87 29.69 3.01
913 1087 0.326264 CTGGTGGAAGGCTAGCAAGT 59.674 55.000 18.24 0.00 32.49 3.16
914 1088 0.615331 TCTGGTGGAAGGCTAGCAAG 59.385 55.000 18.24 0.80 32.49 4.01
915 1089 1.064003 TTCTGGTGGAAGGCTAGCAA 58.936 50.000 18.24 0.00 32.49 3.91
916 1090 1.289160 ATTCTGGTGGAAGGCTAGCA 58.711 50.000 18.24 0.00 37.36 3.49
917 1091 3.560636 TTATTCTGGTGGAAGGCTAGC 57.439 47.619 6.04 6.04 37.36 3.42
918 1092 5.300286 CCAATTTATTCTGGTGGAAGGCTAG 59.700 44.000 0.00 0.00 37.36 3.42
919 1093 5.200483 CCAATTTATTCTGGTGGAAGGCTA 58.800 41.667 0.00 0.00 37.36 3.93
920 1094 4.026052 CCAATTTATTCTGGTGGAAGGCT 58.974 43.478 0.00 0.00 37.36 4.58
921 1095 3.430790 GCCAATTTATTCTGGTGGAAGGC 60.431 47.826 0.00 0.00 37.36 4.35
922 1096 4.026052 AGCCAATTTATTCTGGTGGAAGG 58.974 43.478 0.00 0.00 37.36 3.46
923 1097 6.038714 GTCTAGCCAATTTATTCTGGTGGAAG 59.961 42.308 0.00 0.00 37.36 3.46
924 1098 5.885912 GTCTAGCCAATTTATTCTGGTGGAA 59.114 40.000 0.00 0.00 38.41 3.53
925 1099 5.191722 AGTCTAGCCAATTTATTCTGGTGGA 59.808 40.000 0.00 0.00 34.97 4.02
926 1100 5.440610 AGTCTAGCCAATTTATTCTGGTGG 58.559 41.667 0.00 0.00 34.97 4.61
927 1101 6.678900 GCAAGTCTAGCCAATTTATTCTGGTG 60.679 42.308 0.00 0.00 34.97 4.17
928 1102 5.358160 GCAAGTCTAGCCAATTTATTCTGGT 59.642 40.000 0.00 0.00 34.97 4.00
929 1103 5.591877 AGCAAGTCTAGCCAATTTATTCTGG 59.408 40.000 0.00 0.00 35.67 3.86
930 1104 6.690194 AGCAAGTCTAGCCAATTTATTCTG 57.310 37.500 0.00 0.00 0.00 3.02
971 1146 4.764050 TCCAGTAACCACACAAAGAAGA 57.236 40.909 0.00 0.00 0.00 2.87
972 1147 5.334105 CGATTCCAGTAACCACACAAAGAAG 60.334 44.000 0.00 0.00 0.00 2.85
986 1161 1.138859 CTGTCATGGCCGATTCCAGTA 59.861 52.381 0.00 0.00 39.89 2.74
1017 1192 3.726517 CGGAGTGCCACCAAAGCG 61.727 66.667 0.00 0.00 0.00 4.68
1022 1197 4.947147 GCAACCGGAGTGCCACCA 62.947 66.667 19.98 0.00 0.00 4.17
1093 1268 1.384191 GAACCACCCTGGAGGCAAT 59.616 57.895 0.00 0.00 40.96 3.56
1095 1270 3.256960 GGAACCACCCTGGAGGCA 61.257 66.667 0.00 0.00 40.96 4.75
1131 1309 1.893786 GACATCGGCAGTGGAGTCT 59.106 57.895 0.00 0.00 0.00 3.24
1189 1367 0.110486 ACGCCATTGTGAGGGAAGTT 59.890 50.000 0.00 0.00 0.00 2.66
1230 1408 2.193536 GTTGCTGAACCTGCCCGTT 61.194 57.895 0.00 0.00 0.00 4.44
1286 1464 4.064388 TGATTCAAAAGCGTGTGATCAGA 58.936 39.130 0.00 0.00 0.00 3.27
1313 1491 2.601666 AGACAGACAGCCGAGCCA 60.602 61.111 0.00 0.00 0.00 4.75
1339 1517 1.610522 GTGGACAGCTGCAAAGTTCAT 59.389 47.619 15.27 0.00 0.00 2.57
1554 1733 9.920946 ATATATGTCATGTAAACCAGGAAAACT 57.079 29.630 0.00 0.00 35.29 2.66
1560 1739 6.998074 ACCACATATATGTCATGTAAACCAGG 59.002 38.462 15.60 11.24 39.39 4.45
1697 1891 5.188434 TCATCTGCTCCACCTAAATTCTTG 58.812 41.667 0.00 0.00 0.00 3.02
1753 1947 6.833342 AGTTGTTGCTTTGATTGAACAATC 57.167 33.333 17.35 17.35 45.55 2.67
1814 2008 7.334858 ACATTAAAGAGAGATGGAGTCTTTCC 58.665 38.462 0.01 0.00 46.98 3.13
1815 2009 8.037758 TGACATTAAAGAGAGATGGAGTCTTTC 58.962 37.037 0.01 0.00 40.28 2.62
1816 2010 7.911651 TGACATTAAAGAGAGATGGAGTCTTT 58.088 34.615 0.00 0.00 42.03 2.52
1817 2011 7.487822 TGACATTAAAGAGAGATGGAGTCTT 57.512 36.000 0.00 0.00 37.29 3.01
1818 2012 7.344093 TCATGACATTAAAGAGAGATGGAGTCT 59.656 37.037 0.00 0.00 40.81 3.24
1819 2013 7.495901 TCATGACATTAAAGAGAGATGGAGTC 58.504 38.462 0.00 0.00 0.00 3.36
1820 2014 7.429374 TCATGACATTAAAGAGAGATGGAGT 57.571 36.000 0.00 0.00 0.00 3.85
1821 2015 7.226325 GGTTCATGACATTAAAGAGAGATGGAG 59.774 40.741 0.00 0.00 0.00 3.86
1822 2016 7.050377 GGTTCATGACATTAAAGAGAGATGGA 58.950 38.462 0.00 0.00 0.00 3.41
1823 2017 6.825213 TGGTTCATGACATTAAAGAGAGATGG 59.175 38.462 0.00 0.00 0.00 3.51
1824 2018 7.335171 TGTGGTTCATGACATTAAAGAGAGATG 59.665 37.037 0.00 0.00 0.00 2.90
1825 2019 7.335422 GTGTGGTTCATGACATTAAAGAGAGAT 59.665 37.037 0.00 0.00 0.00 2.75
1826 2020 6.650807 GTGTGGTTCATGACATTAAAGAGAGA 59.349 38.462 0.00 0.00 0.00 3.10
1827 2021 6.427853 TGTGTGGTTCATGACATTAAAGAGAG 59.572 38.462 0.00 0.00 0.00 3.20
1828 2022 6.295249 TGTGTGGTTCATGACATTAAAGAGA 58.705 36.000 0.00 0.00 0.00 3.10
1829 2023 6.427853 TCTGTGTGGTTCATGACATTAAAGAG 59.572 38.462 0.00 0.00 0.00 2.85
1830 2024 6.295249 TCTGTGTGGTTCATGACATTAAAGA 58.705 36.000 0.00 0.00 0.00 2.52
1853 2047 7.112122 AGGGAAAATGGCCAGATTTTAAATTC 58.888 34.615 13.05 1.86 36.00 2.17
1973 2167 3.119637 TCTGCTTCGTCATGTTGATCGTA 60.120 43.478 0.00 0.00 0.00 3.43
2019 2213 1.300481 CTGGCTGACAGCATCTGATG 58.700 55.000 27.87 13.26 44.75 3.07
2060 2254 1.140312 TGGACTTGGACAGAAAGGCT 58.860 50.000 0.00 0.00 32.88 4.58
2066 2260 2.834549 GAGGAAGATGGACTTGGACAGA 59.165 50.000 0.00 0.00 39.13 3.41
2135 2329 4.373116 GCGGTGGAGTCTGGCGAA 62.373 66.667 0.00 0.00 0.00 4.70
2251 2450 0.179001 AGTAACACAGTGGGTTGGCC 60.179 55.000 21.20 8.48 0.00 5.36
2258 2458 6.706270 AGAGTTGAACATAAGTAACACAGTGG 59.294 38.462 5.31 0.00 0.00 4.00
2268 2468 9.288576 TGATTTCATTCAGAGTTGAACATAAGT 57.711 29.630 0.00 0.00 45.54 2.24
2317 2517 2.890766 CGCCCCCAGGTTGTACAGT 61.891 63.158 0.00 0.00 34.57 3.55
2430 2630 0.108615 GTTGAGGCTCTTCGCTAGCA 60.109 55.000 16.45 0.00 41.93 3.49
2533 2733 0.179000 GGTCTTGGACGATGCTGGAT 59.821 55.000 0.00 0.00 32.65 3.41
2583 2790 7.922811 TGTACTGTACTTGATATCAGCTTGATG 59.077 37.037 17.98 0.00 37.70 3.07
2787 3078 1.978580 GGAAGTCCCAGAAGAGGAACA 59.021 52.381 0.00 0.00 34.43 3.18
2912 3203 3.924073 CGTGGAATGATACAAAGACGACA 59.076 43.478 0.00 0.00 0.00 4.35
2988 3311 2.357637 CACGAAAGGCAAAAGACCAAGA 59.642 45.455 0.00 0.00 0.00 3.02
2989 3312 2.543653 CCACGAAAGGCAAAAGACCAAG 60.544 50.000 0.00 0.00 0.00 3.61
2991 3314 1.028905 CCACGAAAGGCAAAAGACCA 58.971 50.000 0.00 0.00 0.00 4.02
2992 3315 3.865700 CCACGAAAGGCAAAAGACC 57.134 52.632 0.00 0.00 0.00 3.85
3022 3346 2.813100 CAATTGGCGCCAGTTGTTC 58.187 52.632 41.00 12.26 38.36 3.18
3054 3379 8.717821 CCCCAATTGTATGTAGTACATTAATCG 58.282 37.037 20.52 11.13 42.63 3.34
3064 3389 3.265737 TGTCTGCCCCAATTGTATGTAGT 59.734 43.478 4.43 0.00 0.00 2.73
3116 3455 0.969894 AGTACTCAGGTCAGTGTGCC 59.030 55.000 0.00 0.00 0.00 5.01
3142 3481 4.742201 CACACCTCCTCCACGCGG 62.742 72.222 12.47 0.00 0.00 6.46
3152 3491 4.025401 CAAACGGGCGCACACCTC 62.025 66.667 11.77 0.00 0.00 3.85
3165 3504 4.611366 CCGATTTCTTCAGTTTACGCAAAC 59.389 41.667 2.90 2.90 43.71 2.93
3166 3505 4.319911 CCCGATTTCTTCAGTTTACGCAAA 60.320 41.667 0.00 0.00 0.00 3.68
3167 3506 3.187637 CCCGATTTCTTCAGTTTACGCAA 59.812 43.478 0.00 0.00 0.00 4.85
3168 3507 2.739913 CCCGATTTCTTCAGTTTACGCA 59.260 45.455 0.00 0.00 0.00 5.24
3169 3508 2.475685 GCCCGATTTCTTCAGTTTACGC 60.476 50.000 0.00 0.00 0.00 4.42
3170 3509 2.222729 CGCCCGATTTCTTCAGTTTACG 60.223 50.000 0.00 0.00 0.00 3.18
3171 3510 2.475685 GCGCCCGATTTCTTCAGTTTAC 60.476 50.000 0.00 0.00 0.00 2.01
3172 3511 1.735571 GCGCCCGATTTCTTCAGTTTA 59.264 47.619 0.00 0.00 0.00 2.01
3173 3512 0.521735 GCGCCCGATTTCTTCAGTTT 59.478 50.000 0.00 0.00 0.00 2.66
3174 3513 0.321653 AGCGCCCGATTTCTTCAGTT 60.322 50.000 2.29 0.00 0.00 3.16
3175 3514 1.021390 CAGCGCCCGATTTCTTCAGT 61.021 55.000 2.29 0.00 0.00 3.41
3176 3515 1.021390 ACAGCGCCCGATTTCTTCAG 61.021 55.000 2.29 0.00 0.00 3.02
3177 3516 0.605319 AACAGCGCCCGATTTCTTCA 60.605 50.000 2.29 0.00 0.00 3.02
3178 3517 0.521735 AAACAGCGCCCGATTTCTTC 59.478 50.000 2.29 0.00 0.00 2.87
3179 3518 1.737793 CTAAACAGCGCCCGATTTCTT 59.262 47.619 2.29 0.00 0.00 2.52
3180 3519 1.369625 CTAAACAGCGCCCGATTTCT 58.630 50.000 2.29 0.00 0.00 2.52
3181 3520 0.248094 GCTAAACAGCGCCCGATTTC 60.248 55.000 2.29 0.00 0.00 2.17
3182 3521 0.958382 TGCTAAACAGCGCCCGATTT 60.958 50.000 2.29 2.14 37.69 2.17
3183 3522 0.748005 ATGCTAAACAGCGCCCGATT 60.748 50.000 2.29 0.00 37.69 3.34
3184 3523 0.748005 AATGCTAAACAGCGCCCGAT 60.748 50.000 2.29 0.00 37.69 4.18
3185 3524 0.958382 AAATGCTAAACAGCGCCCGA 60.958 50.000 2.29 0.00 37.69 5.14
3186 3525 0.798009 CAAATGCTAAACAGCGCCCG 60.798 55.000 2.29 0.00 37.69 6.13
3187 3526 1.078201 GCAAATGCTAAACAGCGCCC 61.078 55.000 2.29 0.00 38.21 6.13
3188 3527 1.078201 GGCAAATGCTAAACAGCGCC 61.078 55.000 2.29 0.00 41.70 6.53
3189 3528 0.388391 TGGCAAATGCTAAACAGCGC 60.388 50.000 0.00 0.00 41.70 5.92
3190 3529 1.987770 CTTGGCAAATGCTAAACAGCG 59.012 47.619 0.00 0.00 40.95 5.18
3191 3530 2.289010 ACCTTGGCAAATGCTAAACAGC 60.289 45.455 0.00 0.00 40.95 4.40
3192 3531 3.005684 TCACCTTGGCAAATGCTAAACAG 59.994 43.478 0.00 1.04 40.95 3.16
3193 3532 2.961741 TCACCTTGGCAAATGCTAAACA 59.038 40.909 0.00 0.00 40.95 2.83
3194 3533 3.658757 TCACCTTGGCAAATGCTAAAC 57.341 42.857 0.00 0.00 40.95 2.01
3195 3534 3.006752 CCTTCACCTTGGCAAATGCTAAA 59.993 43.478 0.00 0.68 40.95 1.85
3196 3535 2.562298 CCTTCACCTTGGCAAATGCTAA 59.438 45.455 0.00 4.65 41.70 3.09
3197 3536 2.170166 CCTTCACCTTGGCAAATGCTA 58.830 47.619 0.00 0.00 41.70 3.49
3198 3537 0.971386 CCTTCACCTTGGCAAATGCT 59.029 50.000 0.00 0.00 41.70 3.79
3199 3538 3.520187 CCTTCACCTTGGCAAATGC 57.480 52.632 0.00 0.00 41.14 3.56
3206 3545 0.593128 CGTTTCAGCCTTCACCTTGG 59.407 55.000 0.00 0.00 0.00 3.61
3207 3546 1.308998 ACGTTTCAGCCTTCACCTTG 58.691 50.000 0.00 0.00 0.00 3.61
3208 3547 2.490991 GTACGTTTCAGCCTTCACCTT 58.509 47.619 0.00 0.00 0.00 3.50
3209 3548 1.604693 CGTACGTTTCAGCCTTCACCT 60.605 52.381 7.22 0.00 0.00 4.00
3210 3549 0.788391 CGTACGTTTCAGCCTTCACC 59.212 55.000 7.22 0.00 0.00 4.02
3211 3550 1.494824 ACGTACGTTTCAGCCTTCAC 58.505 50.000 16.72 0.00 0.00 3.18
3212 3551 2.129607 GAACGTACGTTTCAGCCTTCA 58.870 47.619 32.14 0.00 38.60 3.02
3213 3552 1.458445 GGAACGTACGTTTCAGCCTTC 59.542 52.381 32.14 17.85 38.60 3.46
3214 3553 1.202557 TGGAACGTACGTTTCAGCCTT 60.203 47.619 32.94 11.25 38.56 4.35
3215 3554 0.390124 TGGAACGTACGTTTCAGCCT 59.610 50.000 32.94 12.02 38.56 4.58
3216 3555 2.903284 TGGAACGTACGTTTCAGCC 58.097 52.632 32.94 27.47 38.56 4.85
3219 3558 1.000060 CTCCCTGGAACGTACGTTTCA 60.000 52.381 33.73 33.73 40.93 2.69
3220 3559 1.706443 CTCCCTGGAACGTACGTTTC 58.294 55.000 32.14 30.39 38.60 2.78
3221 3560 0.320160 GCTCCCTGGAACGTACGTTT 60.320 55.000 32.14 17.47 38.60 3.60
3222 3561 1.183676 AGCTCCCTGGAACGTACGTT 61.184 55.000 32.17 32.17 41.54 3.99
3223 3562 1.593296 GAGCTCCCTGGAACGTACGT 61.593 60.000 16.72 16.72 0.00 3.57
3224 3563 1.139095 GAGCTCCCTGGAACGTACG 59.861 63.158 15.01 15.01 0.00 3.67
3225 3564 0.824759 ATGAGCTCCCTGGAACGTAC 59.175 55.000 12.15 0.00 0.00 3.67
3226 3565 1.568504 AATGAGCTCCCTGGAACGTA 58.431 50.000 12.15 0.00 0.00 3.57
3227 3566 0.693049 AAATGAGCTCCCTGGAACGT 59.307 50.000 12.15 0.00 0.00 3.99
3228 3567 1.826385 AAAATGAGCTCCCTGGAACG 58.174 50.000 12.15 0.00 0.00 3.95
3229 3568 3.425659 AGAAAAATGAGCTCCCTGGAAC 58.574 45.455 12.15 0.00 0.00 3.62
3230 3569 3.814504 AGAAAAATGAGCTCCCTGGAA 57.185 42.857 12.15 0.00 0.00 3.53
3231 3570 3.814504 AAGAAAAATGAGCTCCCTGGA 57.185 42.857 12.15 0.00 0.00 3.86
3232 3571 4.616835 CGAAAAGAAAAATGAGCTCCCTGG 60.617 45.833 12.15 0.00 0.00 4.45
3233 3572 4.216257 TCGAAAAGAAAAATGAGCTCCCTG 59.784 41.667 12.15 0.00 0.00 4.45
3234 3573 4.398319 TCGAAAAGAAAAATGAGCTCCCT 58.602 39.130 12.15 0.00 0.00 4.20
3235 3574 4.379918 CCTCGAAAAGAAAAATGAGCTCCC 60.380 45.833 12.15 0.00 0.00 4.30
3236 3575 4.379918 CCCTCGAAAAGAAAAATGAGCTCC 60.380 45.833 12.15 0.00 0.00 4.70
3237 3576 4.379918 CCCCTCGAAAAGAAAAATGAGCTC 60.380 45.833 6.82 6.82 0.00 4.09
3238 3577 3.507622 CCCCTCGAAAAGAAAAATGAGCT 59.492 43.478 0.00 0.00 0.00 4.09
3239 3578 3.255888 ACCCCTCGAAAAGAAAAATGAGC 59.744 43.478 0.00 0.00 0.00 4.26
3240 3579 6.569179 TTACCCCTCGAAAAGAAAAATGAG 57.431 37.500 0.00 0.00 0.00 2.90
3241 3580 6.963083 TTTACCCCTCGAAAAGAAAAATGA 57.037 33.333 0.00 0.00 0.00 2.57
3309 3648 2.673775 TGGTGTTCCACATGACCAAT 57.326 45.000 0.00 0.00 39.03 3.16
3319 3658 2.026356 CCATGTCTGGTATGGTGTTCCA 60.026 50.000 0.00 0.00 41.90 3.53
3347 3686 5.753721 AAATTTGCACTCTCTAGAGGTCT 57.246 39.130 19.67 0.00 46.13 3.85
3574 3913 0.829990 TGGAGGCAATAGCATGTCGA 59.170 50.000 0.00 0.00 44.61 4.20
3633 3972 0.817654 GGGCAACTACATTGGAAGCC 59.182 55.000 0.00 0.00 38.88 4.35
3742 4082 3.622612 CCAGTTCAGGCAAAACCAAAAAG 59.377 43.478 0.00 0.00 43.14 2.27
3772 4112 1.526464 CAAAAACACAAATGGCGAGGC 59.474 47.619 0.00 0.00 0.00 4.70
3775 4115 4.690748 TCAAAACAAAAACACAAATGGCGA 59.309 33.333 0.00 0.00 0.00 5.54
3791 4131 7.962373 CGATCATACAAAATACAGCTCAAAACA 59.038 33.333 0.00 0.00 0.00 2.83
3795 4135 5.007626 GGCGATCATACAAAATACAGCTCAA 59.992 40.000 0.00 0.00 0.00 3.02
3821 4161 4.104261 TCATCGAGAGGTACCTTCAGGATA 59.896 45.833 17.53 0.00 38.94 2.59
3828 4168 1.757699 GGCTTCATCGAGAGGTACCTT 59.242 52.381 17.53 6.07 0.00 3.50
3869 4209 6.786967 AAGCTATCCATGAAGCAATTTTCT 57.213 33.333 14.48 0.00 41.32 2.52
3873 4213 4.037208 CGGAAAGCTATCCATGAAGCAATT 59.963 41.667 14.48 9.90 41.32 2.32


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

AutoCloner maintained by Alex Coulton.