Multiple sequence alignment - TraesCS1A01G223200

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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 TraesCS1A01G223200 chr1A 100.000 4606 0 0 1 4606 393455435 393460040 0.000000e+00 8506.0
1 TraesCS1A01G223200 chr1A 90.000 680 54 11 3831 4502 583818641 583817968 0.000000e+00 867.0
2 TraesCS1A01G223200 chr1D 87.679 1469 120 38 127 1579 313291735 313293158 0.000000e+00 1653.0
3 TraesCS1A01G223200 chr1D 92.518 949 52 14 1686 2630 313293158 313294091 0.000000e+00 1341.0
4 TraesCS1A01G223200 chr1D 91.235 753 51 7 3084 3830 313295262 313296005 0.000000e+00 1011.0
5 TraesCS1A01G223200 chr1D 88.124 421 27 7 2603 3019 313294092 313294493 3.220000e-131 479.0
6 TraesCS1A01G223200 chr1D 96.739 276 9 0 2811 3086 313294875 313295150 1.170000e-125 460.0
7 TraesCS1A01G223200 chr1D 91.388 209 14 2 2812 3019 313294494 313294699 2.710000e-72 283.0
8 TraesCS1A01G223200 chr1D 91.270 126 8 3 1578 1702 328440268 328440145 7.930000e-38 169.0
9 TraesCS1A01G223200 chr1D 90.076 131 9 3 2812 2940 313294700 313294828 2.850000e-37 167.0
10 TraesCS1A01G223200 chr1B 91.271 1031 65 12 2813 3830 423641838 423642856 0.000000e+00 1382.0
11 TraesCS1A01G223200 chr1B 90.338 1035 71 20 752 1773 423639353 423640371 0.000000e+00 1330.0
12 TraesCS1A01G223200 chr1B 92.141 878 43 9 1755 2630 423640387 423641240 0.000000e+00 1216.0
13 TraesCS1A01G223200 chr1B 89.810 422 38 4 2603 3019 423641241 423641662 1.890000e-148 536.0
14 TraesCS1A01G223200 chr1B 90.698 129 9 2 2812 2940 423641664 423641789 7.930000e-38 169.0
15 TraesCS1A01G223200 chr1B 80.645 186 30 6 1719 1901 19944217 19944035 6.210000e-29 139.0
16 TraesCS1A01G223200 chr2B 93.810 727 37 6 3831 4551 796674924 796675648 0.000000e+00 1086.0
17 TraesCS1A01G223200 chr2B 80.645 186 30 6 1719 1901 150888148 150887966 6.210000e-29 139.0
18 TraesCS1A01G223200 chr2B 100.000 34 0 0 4573 4606 796675650 796675683 3.850000e-06 63.9
19 TraesCS1A01G223200 chr5B 91.954 783 47 6 3831 4606 369153233 369152460 0.000000e+00 1083.0
20 TraesCS1A01G223200 chr5B 89.825 285 24 4 4216 4497 33848478 33848760 1.220000e-95 361.0
21 TraesCS1A01G223200 chr5B 93.277 119 7 1 1578 1695 50531833 50531951 1.700000e-39 174.0
22 TraesCS1A01G223200 chr5B 79.394 165 28 6 3834 3995 120296602 120296441 1.350000e-20 111.0
23 TraesCS1A01G223200 chr7D 93.379 725 39 6 3831 4549 174809788 174810509 0.000000e+00 1064.0
24 TraesCS1A01G223200 chr7D 92.800 125 6 2 1577 1701 610533491 610533370 1.320000e-40 178.0
25 TraesCS1A01G223200 chr7D 100.000 30 0 0 4577 4606 174810517 174810546 6.440000e-04 56.5
26 TraesCS1A01G223200 chr3D 89.474 399 29 10 3831 4220 286723237 286722843 4.140000e-135 492.0
27 TraesCS1A01G223200 chr3D 94.619 223 9 3 4337 4558 286722862 286722642 4.410000e-90 342.0
28 TraesCS1A01G223200 chr3A 92.857 126 7 2 1569 1692 46169216 46169091 1.020000e-41 182.0
29 TraesCS1A01G223200 chr3A 92.000 125 10 0 1570 1694 550641953 550641829 4.740000e-40 176.0
30 TraesCS1A01G223200 chr6D 94.783 115 6 0 1575 1689 222595191 222595305 3.660000e-41 180.0
31 TraesCS1A01G223200 chr4A 96.330 109 4 0 1577 1685 239632815 239632707 3.660000e-41 180.0
32 TraesCS1A01G223200 chr4A 80.749 187 29 7 1719 1901 552695826 552695643 6.210000e-29 139.0
33 TraesCS1A01G223200 chr4A 80.749 187 29 7 1719 1901 571773239 571773422 6.210000e-29 139.0
34 TraesCS1A01G223200 chr3B 95.536 112 5 0 1578 1689 12156861 12156972 3.660000e-41 180.0
35 TraesCS1A01G223200 chr2A 95.495 111 5 0 1577 1687 717816546 717816436 1.320000e-40 178.0
36 TraesCS1A01G223200 chr7B 80.645 186 30 6 1719 1901 685057039 685056857 6.210000e-29 139.0
37 TraesCS1A01G223200 chr5A 80.749 187 29 7 1719 1901 534269831 534269648 6.210000e-29 139.0
38 TraesCS1A01G223200 chr5A 95.181 83 2 2 3828 3909 689183932 689184013 3.740000e-26 130.0
39 TraesCS1A01G223200 chrUn 96.250 80 1 2 3831 3909 377500877 377500799 3.740000e-26 130.0
40 TraesCS1A01G223200 chrUn 74.850 167 31 8 31 197 83352766 83352611 1.070000e-06 65.8
41 TraesCS1A01G223200 chr4D 79.762 168 22 10 3831 3991 499297851 499297689 1.350000e-20 111.0
42 TraesCS1A01G223200 chr7A 74.850 167 31 8 31 197 698587014 698586859 1.070000e-06 65.8


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 TraesCS1A01G223200 chr1A 393455435 393460040 4605 False 8506.000000 8506 100.000000 1 4606 1 chr1A.!!$F1 4605
1 TraesCS1A01G223200 chr1A 583817968 583818641 673 True 867.000000 867 90.000000 3831 4502 1 chr1A.!!$R1 671
2 TraesCS1A01G223200 chr1D 313291735 313296005 4270 False 770.571429 1653 91.108429 127 3830 7 chr1D.!!$F1 3703
3 TraesCS1A01G223200 chr1B 423639353 423642856 3503 False 926.600000 1382 90.851600 752 3830 5 chr1B.!!$F1 3078
4 TraesCS1A01G223200 chr2B 796674924 796675683 759 False 574.950000 1086 96.905000 3831 4606 2 chr2B.!!$F1 775
5 TraesCS1A01G223200 chr5B 369152460 369153233 773 True 1083.000000 1083 91.954000 3831 4606 1 chr5B.!!$R2 775
6 TraesCS1A01G223200 chr7D 174809788 174810546 758 False 560.250000 1064 96.689500 3831 4606 2 chr7D.!!$F1 775
7 TraesCS1A01G223200 chr3D 286722642 286723237 595 True 417.000000 492 92.046500 3831 4558 2 chr3D.!!$R1 727

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
742 749 0.028374 GACAAAAACCACCGGTGTCG 59.972 55.0 31.8 20.37 35.34 4.35 F
1487 1529 0.603975 GTTCCGGGCATCTGCTATCC 60.604 60.0 0.0 0.00 41.70 2.59 F
2272 2351 0.895559 CCACTGGAAGGAAACTGGCC 60.896 60.0 0.0 0.00 42.68 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1710 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.0 0.0 0.0 0.00 4.30 R
2880 3587 0.465642 GCGCCTTAAACCTATGCCCT 60.466 55.0 0.0 0.0 0.00 5.19 R
4064 4902 0.682852 TCGGACCCCACTTGTGTAAG 59.317 55.0 0.0 0.0 39.86 2.34 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
19 20 4.504916 CAGCACGCCCTCGAGGAG 62.505 72.222 33.39 26.02 42.15 3.69
88 89 4.803426 CTGTCGGCAGCGAGGGAC 62.803 72.222 3.01 0.00 35.77 4.46
90 91 4.803426 GTCGGCAGCGAGGGACTG 62.803 72.222 0.00 0.00 41.55 3.51
95 96 3.753434 CAGCGAGGGACTGCGTCT 61.753 66.667 8.26 0.00 41.55 4.18
96 97 2.045242 AGCGAGGGACTGCGTCTA 60.045 61.111 8.26 0.00 41.55 2.59
97 98 2.102553 GCGAGGGACTGCGTCTAC 59.897 66.667 8.26 3.37 41.55 2.59
98 99 2.408241 GCGAGGGACTGCGTCTACT 61.408 63.158 8.26 7.19 41.55 2.57
99 100 1.722677 CGAGGGACTGCGTCTACTC 59.277 63.158 15.93 15.93 41.55 2.59
100 101 0.745128 CGAGGGACTGCGTCTACTCT 60.745 60.000 19.63 10.33 41.55 3.24
101 102 1.018910 GAGGGACTGCGTCTACTCTC 58.981 60.000 17.30 11.90 41.55 3.20
102 103 0.394625 AGGGACTGCGTCTACTCTCC 60.395 60.000 8.26 1.54 37.18 3.71
103 104 0.680280 GGGACTGCGTCTACTCTCCA 60.680 60.000 8.26 0.00 32.47 3.86
104 105 0.452585 GGACTGCGTCTACTCTCCAC 59.547 60.000 8.26 0.00 32.47 4.02
105 106 0.452585 GACTGCGTCTACTCTCCACC 59.547 60.000 2.10 0.00 0.00 4.61
106 107 0.251209 ACTGCGTCTACTCTCCACCA 60.251 55.000 0.00 0.00 0.00 4.17
107 108 0.171455 CTGCGTCTACTCTCCACCAC 59.829 60.000 0.00 0.00 0.00 4.16
108 109 1.248785 TGCGTCTACTCTCCACCACC 61.249 60.000 0.00 0.00 0.00 4.61
109 110 1.248785 GCGTCTACTCTCCACCACCA 61.249 60.000 0.00 0.00 0.00 4.17
110 111 1.475403 CGTCTACTCTCCACCACCAT 58.525 55.000 0.00 0.00 0.00 3.55
111 112 1.405821 CGTCTACTCTCCACCACCATC 59.594 57.143 0.00 0.00 0.00 3.51
112 113 1.405821 GTCTACTCTCCACCACCATCG 59.594 57.143 0.00 0.00 0.00 3.84
113 114 0.103208 CTACTCTCCACCACCATCGC 59.897 60.000 0.00 0.00 0.00 4.58
114 115 1.327690 TACTCTCCACCACCATCGCC 61.328 60.000 0.00 0.00 0.00 5.54
115 116 2.284625 TCTCCACCACCATCGCCT 60.285 61.111 0.00 0.00 0.00 5.52
116 117 2.187946 CTCCACCACCATCGCCTC 59.812 66.667 0.00 0.00 0.00 4.70
117 118 2.284625 TCCACCACCATCGCCTCT 60.285 61.111 0.00 0.00 0.00 3.69
118 119 2.187946 CCACCACCATCGCCTCTC 59.812 66.667 0.00 0.00 0.00 3.20
119 120 2.187946 CACCACCATCGCCTCTCC 59.812 66.667 0.00 0.00 0.00 3.71
120 121 2.039624 ACCACCATCGCCTCTCCT 59.960 61.111 0.00 0.00 0.00 3.69
121 122 1.043116 CACCACCATCGCCTCTCCTA 61.043 60.000 0.00 0.00 0.00 2.94
122 123 0.105453 ACCACCATCGCCTCTCCTAT 60.105 55.000 0.00 0.00 0.00 2.57
123 124 1.147191 ACCACCATCGCCTCTCCTATA 59.853 52.381 0.00 0.00 0.00 1.31
124 125 1.821753 CCACCATCGCCTCTCCTATAG 59.178 57.143 0.00 0.00 0.00 1.31
125 126 1.203523 CACCATCGCCTCTCCTATAGC 59.796 57.143 0.00 0.00 0.00 2.97
199 200 4.265056 GTGGTGCGGGAGTGGGTT 62.265 66.667 0.00 0.00 0.00 4.11
204 205 4.078516 GCGGGAGTGGGTTAGCGT 62.079 66.667 0.00 0.00 0.00 5.07
206 207 2.939261 CGGGAGTGGGTTAGCGTGT 61.939 63.158 0.00 0.00 0.00 4.49
208 209 1.445582 GGAGTGGGTTAGCGTGTCG 60.446 63.158 0.00 0.00 0.00 4.35
210 211 3.116531 GTGGGTTAGCGTGTCGGC 61.117 66.667 0.00 0.00 0.00 5.54
221 222 3.220658 TGTCGGCCGTGTGTCTGA 61.221 61.111 27.15 0.00 0.00 3.27
223 224 2.910479 TCGGCCGTGTGTCTGAGT 60.910 61.111 27.15 0.00 0.00 3.41
226 227 2.280119 GCCGTGTGTCTGAGTGCA 60.280 61.111 0.00 0.00 0.00 4.57
232 233 1.595382 GTGTCTGAGTGCAACGCCT 60.595 57.895 0.00 0.00 45.86 5.52
234 235 1.595382 GTCTGAGTGCAACGCCTGT 60.595 57.895 0.00 0.00 45.86 4.00
236 237 2.591429 TGAGTGCAACGCCTGTGG 60.591 61.111 0.00 0.00 45.86 4.17
243 244 2.526873 AACGCCTGTGGAGGAGGT 60.527 61.111 0.00 0.00 43.30 3.85
319 320 3.357079 GGCAACTGTGGGCACGAG 61.357 66.667 3.51 0.00 0.00 4.18
320 321 2.280797 GCAACTGTGGGCACGAGA 60.281 61.111 0.00 0.00 0.00 4.04
338 339 1.938596 AGGAGGAGGAGGAGGAGCA 60.939 63.158 0.00 0.00 0.00 4.26
404 405 4.717629 CGCAACAGACGCCCGAGA 62.718 66.667 0.00 0.00 0.00 4.04
444 445 0.319405 CGGTAGGTTTTCTCGTGGGT 59.681 55.000 0.00 0.00 0.00 4.51
445 446 1.270465 CGGTAGGTTTTCTCGTGGGTT 60.270 52.381 0.00 0.00 0.00 4.11
447 448 2.486013 GGTAGGTTTTCTCGTGGGTTGT 60.486 50.000 0.00 0.00 0.00 3.32
449 450 1.064979 AGGTTTTCTCGTGGGTTGTGT 60.065 47.619 0.00 0.00 0.00 3.72
460 461 3.578272 GTTGTGTCGCCGTTGCCA 61.578 61.111 0.00 0.00 0.00 4.92
465 466 1.673993 TGTCGCCGTTGCCATTGAT 60.674 52.632 0.00 0.00 0.00 2.57
466 467 1.226379 GTCGCCGTTGCCATTGATG 60.226 57.895 0.00 0.00 0.00 3.07
500 502 1.457643 TGGGAGACTATGAGGCGGG 60.458 63.158 0.00 0.00 0.00 6.13
521 524 8.991026 GGCGGGTTTTTAGTTTTTATTAATGTT 58.009 29.630 0.00 0.00 0.00 2.71
544 547 7.042321 TGTTTAGTTATGTTTGAAGTGGACTCG 60.042 37.037 0.00 0.00 0.00 4.18
545 548 5.209818 AGTTATGTTTGAAGTGGACTCGA 57.790 39.130 0.00 0.00 0.00 4.04
547 550 2.234300 TGTTTGAAGTGGACTCGACC 57.766 50.000 0.00 0.00 0.00 4.79
552 558 1.521450 GAAGTGGACTCGACCGTGGA 61.521 60.000 0.00 0.00 0.00 4.02
562 568 5.138125 ACTCGACCGTGGACTTTAATTTA 57.862 39.130 0.00 0.00 0.00 1.40
569 575 7.269724 CGACCGTGGACTTTAATTTAAATGTTC 59.730 37.037 0.39 0.00 0.00 3.18
643 650 0.247695 GCAGACTAAAATGCGTCGGC 60.248 55.000 0.00 0.00 42.29 5.54
646 653 1.356527 GACTAAAATGCGTCGGCCGT 61.357 55.000 27.15 5.29 38.85 5.68
660 667 1.029408 GGCCGTGTTGGATGCACATA 61.029 55.000 0.00 0.00 42.00 2.29
661 668 1.024271 GCCGTGTTGGATGCACATAT 58.976 50.000 0.00 0.00 42.00 1.78
667 674 4.060900 GTGTTGGATGCACATATCGATCT 58.939 43.478 0.00 0.00 36.88 2.75
672 679 7.445096 TGTTGGATGCACATATCGATCTAAATT 59.555 33.333 0.00 0.00 0.00 1.82
673 680 7.368480 TGGATGCACATATCGATCTAAATTG 57.632 36.000 0.00 0.00 0.00 2.32
677 684 9.539139 GATGCACATATCGATCTAAATTGAAAG 57.461 33.333 0.00 0.00 0.00 2.62
678 685 8.437360 TGCACATATCGATCTAAATTGAAAGT 57.563 30.769 0.00 0.00 0.00 2.66
681 688 8.217115 CACATATCGATCTAAATTGAAAGTCGG 58.783 37.037 0.00 0.00 0.00 4.79
685 692 5.575606 TCGATCTAAATTGAAAGTCGGACAC 59.424 40.000 11.27 2.29 0.00 3.67
686 693 5.498700 CGATCTAAATTGAAAGTCGGACACG 60.499 44.000 11.27 0.00 42.74 4.49
693 700 1.485032 AAAGTCGGACACGTGCGTTC 61.485 55.000 17.22 5.71 44.84 3.95
697 704 3.335534 GGACACGTGCGTTCGCTT 61.336 61.111 17.22 0.00 0.00 4.68
698 705 2.624264 GACACGTGCGTTCGCTTT 59.376 55.556 17.22 0.00 0.00 3.51
702 709 2.792543 CGTGCGTTCGCTTTGCTG 60.793 61.111 17.63 0.00 0.00 4.41
704 711 1.207593 GTGCGTTCGCTTTGCTGAT 59.792 52.632 17.63 0.00 0.00 2.90
705 712 0.385974 GTGCGTTCGCTTTGCTGATT 60.386 50.000 17.63 0.00 0.00 2.57
710 717 2.401720 CGTTCGCTTTGCTGATTCAAAC 59.598 45.455 0.00 0.00 32.99 2.93
719 726 3.963665 TGCTGATTCAAACGGACAAAAG 58.036 40.909 0.00 0.00 0.00 2.27
721 728 3.975035 GCTGATTCAAACGGACAAAAGAC 59.025 43.478 0.00 0.00 0.00 3.01
722 729 4.203950 TGATTCAAACGGACAAAAGACG 57.796 40.909 0.00 0.00 0.00 4.18
733 740 3.119424 GGACAAAAGACGGACAAAAACCA 60.119 43.478 0.00 0.00 0.00 3.67
735 742 3.183754 CAAAAGACGGACAAAAACCACC 58.816 45.455 0.00 0.00 0.00 4.61
738 745 3.830465 CGGACAAAAACCACCGGT 58.170 55.556 0.00 0.00 41.41 5.28
741 748 0.382873 GGACAAAAACCACCGGTGTC 59.617 55.000 31.80 20.30 35.34 3.67
742 749 0.028374 GACAAAAACCACCGGTGTCG 59.972 55.000 31.80 20.37 35.34 4.35
764 794 0.955178 CGTGTTGGGTGGCAATACAA 59.045 50.000 0.00 0.00 0.00 2.41
765 795 1.543802 CGTGTTGGGTGGCAATACAAT 59.456 47.619 0.00 0.00 0.00 2.71
777 807 3.510719 GCAATACAATTGGCACGATGTT 58.489 40.909 10.83 0.00 0.00 2.71
780 810 1.327303 ACAATTGGCACGATGTTGGT 58.673 45.000 10.83 0.00 0.00 3.67
791 821 1.463674 GATGTTGGTTGTAGGCAGGG 58.536 55.000 0.00 0.00 0.00 4.45
823 853 2.163010 TGGCTAGAGGTTAAAGACGACG 59.837 50.000 0.00 0.00 0.00 5.12
826 856 1.625511 AGAGGTTAAAGACGACGGGT 58.374 50.000 0.00 0.00 0.00 5.28
850 880 2.098117 CCCTTGGATTGAAATCTGACGC 59.902 50.000 3.21 0.00 35.73 5.19
890 920 1.593006 CGATACCGAATTGTGCTCCAC 59.407 52.381 0.00 0.00 38.22 4.02
932 973 1.733402 CTAGTCCTCTGCTCCGCCAG 61.733 65.000 0.00 0.00 0.00 4.85
988 1030 1.279271 CCTCAACCCAGATCGGAAACT 59.721 52.381 5.32 0.00 36.56 2.66
1046 1088 2.363795 CCCTCGCTCCCAGGTACA 60.364 66.667 0.00 0.00 0.00 2.90
1051 1093 2.269241 GCTCCCAGGTACACCAGC 59.731 66.667 0.38 0.00 38.89 4.85
1487 1529 0.603975 GTTCCGGGCATCTGCTATCC 60.604 60.000 0.00 0.00 41.70 2.59
1512 1554 2.165030 CTGGTGTCCCAAATCTCATTGC 59.835 50.000 0.00 0.00 41.27 3.56
1555 1597 5.987953 AGAAGAAGTGGTAGACCGTTTTAAC 59.012 40.000 0.00 0.00 39.43 2.01
1582 1624 2.086094 GGATAGGCTAGCTCGTACTCC 58.914 57.143 15.72 8.79 0.00 3.85
1583 1625 2.290450 GGATAGGCTAGCTCGTACTCCT 60.290 54.545 15.72 2.81 0.00 3.69
1584 1626 3.414269 GATAGGCTAGCTCGTACTCCTT 58.586 50.000 15.72 0.00 0.00 3.36
1587 1629 1.390565 GCTAGCTCGTACTCCTTCCA 58.609 55.000 7.70 0.00 0.00 3.53
1589 1631 2.362717 GCTAGCTCGTACTCCTTCCATT 59.637 50.000 7.70 0.00 0.00 3.16
1590 1632 3.551250 GCTAGCTCGTACTCCTTCCATTC 60.551 52.174 7.70 0.00 0.00 2.67
1595 1637 4.770795 CTCGTACTCCTTCCATTCCAAAT 58.229 43.478 0.00 0.00 0.00 2.32
1598 1640 6.110707 TCGTACTCCTTCCATTCCAAATTAC 58.889 40.000 0.00 0.00 0.00 1.89
1599 1641 6.070424 TCGTACTCCTTCCATTCCAAATTACT 60.070 38.462 0.00 0.00 0.00 2.24
1600 1642 6.258068 CGTACTCCTTCCATTCCAAATTACTC 59.742 42.308 0.00 0.00 0.00 2.59
1603 1645 5.566469 TCCTTCCATTCCAAATTACTCGTT 58.434 37.500 0.00 0.00 0.00 3.85
1604 1646 5.414454 TCCTTCCATTCCAAATTACTCGTTG 59.586 40.000 0.00 0.00 0.00 4.10
1608 1650 4.155826 CCATTCCAAATTACTCGTTGCAGA 59.844 41.667 0.00 0.00 0.00 4.26
1609 1651 5.335583 CCATTCCAAATTACTCGTTGCAGAA 60.336 40.000 0.00 0.00 0.00 3.02
1610 1652 5.759506 TTCCAAATTACTCGTTGCAGAAA 57.240 34.783 0.00 0.00 0.00 2.52
1612 1654 5.698832 TCCAAATTACTCGTTGCAGAAATG 58.301 37.500 0.00 0.00 0.00 2.32
1613 1655 4.858692 CCAAATTACTCGTTGCAGAAATGG 59.141 41.667 0.00 0.00 0.00 3.16
1615 1657 6.324819 CAAATTACTCGTTGCAGAAATGGAT 58.675 36.000 0.00 0.00 0.00 3.41
1616 1658 4.944962 TTACTCGTTGCAGAAATGGATG 57.055 40.909 0.00 0.00 0.00 3.51
1617 1659 2.783135 ACTCGTTGCAGAAATGGATGT 58.217 42.857 0.00 0.00 0.00 3.06
1619 1661 4.517285 ACTCGTTGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 0.00 2.29
1620 1662 4.572389 ACTCGTTGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 0.00 2.24
1621 1663 4.769688 TCGTTGCAGAAATGGATGTATCT 58.230 39.130 0.00 0.00 0.00 1.98
1622 1664 5.912892 TCGTTGCAGAAATGGATGTATCTA 58.087 37.500 0.00 0.00 0.00 1.98
1623 1665 5.985530 TCGTTGCAGAAATGGATGTATCTAG 59.014 40.000 0.00 0.00 0.00 2.43
1624 1666 5.985530 CGTTGCAGAAATGGATGTATCTAGA 59.014 40.000 0.00 0.00 0.00 2.43
1625 1667 6.479990 CGTTGCAGAAATGGATGTATCTAGAA 59.520 38.462 0.00 0.00 0.00 2.10
1626 1668 7.517417 CGTTGCAGAAATGGATGTATCTAGAAC 60.517 40.741 0.00 0.00 0.00 3.01
1656 1698 9.587772 AATACATTTAGATACATCGATACCTGC 57.412 33.333 0.00 0.00 0.00 4.85
1661 1703 3.568430 AGATACATCGATACCTGCGACAA 59.432 43.478 0.00 0.00 40.94 3.18
1662 1704 2.209838 ACATCGATACCTGCGACAAG 57.790 50.000 0.00 0.00 40.94 3.16
1665 1707 3.129813 ACATCGATACCTGCGACAAGTAA 59.870 43.478 0.00 0.00 40.94 2.24
1668 1710 4.357142 TCGATACCTGCGACAAGTAATTC 58.643 43.478 0.00 0.00 32.09 2.17
1671 1713 1.274167 ACCTGCGACAAGTAATTCGGA 59.726 47.619 0.00 0.00 35.73 4.55
1731 1773 3.953612 TGCGCTTCCTCATTAATTGGAAT 59.046 39.130 9.73 0.00 38.91 3.01
1732 1774 4.036734 TGCGCTTCCTCATTAATTGGAATC 59.963 41.667 9.73 12.46 38.91 2.52
1751 1794 5.694006 GGAATCGAGTATGTTTCCTCATGAG 59.306 44.000 16.24 16.24 35.66 2.90
1904 1981 9.309516 GACTTGATCCATGTACGAGTTAAATAA 57.690 33.333 0.00 0.00 0.00 1.40
2115 2193 9.850628 CAAACCATTCCATTAATGCTATATCTG 57.149 33.333 10.11 0.84 43.18 2.90
2116 2194 8.585471 AACCATTCCATTAATGCTATATCTGG 57.415 34.615 10.11 10.65 43.18 3.86
2272 2351 0.895559 CCACTGGAAGGAAACTGGCC 60.896 60.000 0.00 0.00 42.68 5.36
2293 2372 1.594194 CGCCTTTACAGCCCATGCAA 61.594 55.000 0.00 0.00 41.13 4.08
2318 2397 4.770010 GGTGGGTCCAAAATGTTCAAGATA 59.230 41.667 0.00 0.00 35.97 1.98
2333 2412 5.791336 TCAAGATATGCTGTAGTGGTAGG 57.209 43.478 0.00 0.00 0.00 3.18
2335 2414 5.302059 TCAAGATATGCTGTAGTGGTAGGAC 59.698 44.000 0.00 0.00 0.00 3.85
2401 2485 9.609346 TTATTCAAGACTTATACCAGTTAAGCC 57.391 33.333 0.00 0.00 31.22 4.35
2402 2486 6.869206 TCAAGACTTATACCAGTTAAGCCT 57.131 37.500 0.00 0.00 31.22 4.58
2403 2487 6.640518 TCAAGACTTATACCAGTTAAGCCTG 58.359 40.000 0.00 0.00 31.22 4.85
2404 2488 6.439375 TCAAGACTTATACCAGTTAAGCCTGA 59.561 38.462 0.00 0.00 34.23 3.86
2405 2489 7.125811 TCAAGACTTATACCAGTTAAGCCTGAT 59.874 37.037 0.00 0.00 34.23 2.90
2406 2490 7.439108 AGACTTATACCAGTTAAGCCTGATT 57.561 36.000 0.00 0.00 34.23 2.57
2407 2491 7.501844 AGACTTATACCAGTTAAGCCTGATTC 58.498 38.462 0.00 0.00 34.23 2.52
2408 2492 6.281405 ACTTATACCAGTTAAGCCTGATTCG 58.719 40.000 0.00 0.00 34.23 3.34
2409 2493 1.739067 ACCAGTTAAGCCTGATTCGC 58.261 50.000 0.00 0.00 34.23 4.70
2410 2494 1.003118 ACCAGTTAAGCCTGATTCGCA 59.997 47.619 0.00 0.00 34.23 5.10
2411 2495 2.083774 CCAGTTAAGCCTGATTCGCAA 58.916 47.619 0.00 0.00 34.23 4.85
2412 2496 2.096496 CCAGTTAAGCCTGATTCGCAAG 59.904 50.000 0.00 0.00 34.23 4.01
2413 2497 2.744202 CAGTTAAGCCTGATTCGCAAGT 59.256 45.455 0.00 0.00 34.23 3.16
2414 2498 3.189287 CAGTTAAGCCTGATTCGCAAGTT 59.811 43.478 0.00 0.00 34.23 2.66
2415 2499 4.391830 CAGTTAAGCCTGATTCGCAAGTTA 59.608 41.667 0.00 0.00 34.23 2.24
2416 2500 5.001232 AGTTAAGCCTGATTCGCAAGTTAA 58.999 37.500 0.00 0.00 39.48 2.01
2459 2543 1.069022 CAATGTCAACTCGGCCACAAG 60.069 52.381 2.24 0.00 0.00 3.16
2467 2551 5.813672 GTCAACTCGGCCACAAGTATTATTA 59.186 40.000 2.24 0.00 0.00 0.98
2528 2612 5.760253 AGTTCGTCTCTTTGTGATTGTTGAT 59.240 36.000 0.00 0.00 0.00 2.57
2610 2694 5.579119 TGCATTTCATCATGTTTTGCTGATC 59.421 36.000 8.98 0.00 30.94 2.92
2643 2755 4.760530 ATTCTCCGATCTTCCATGTTGA 57.239 40.909 0.00 0.00 0.00 3.18
2659 2771 6.769341 TCCATGTTGATGTGGATAGAGAATTG 59.231 38.462 0.00 0.00 39.51 2.32
2699 2811 7.856894 TCATGACATTGTATAAAATGATGCACG 59.143 33.333 20.38 9.23 39.46 5.34
2700 2812 7.082700 TGACATTGTATAAAATGATGCACGT 57.917 32.000 20.38 0.00 39.46 4.49
2773 2890 3.498927 TCGTCCTTTTAGTCTTAGCCG 57.501 47.619 0.00 0.00 0.00 5.52
2774 2891 2.821969 TCGTCCTTTTAGTCTTAGCCGT 59.178 45.455 0.00 0.00 0.00 5.68
2805 2922 3.697542 CCAAATGATGCCATCTCTGTTCA 59.302 43.478 6.21 0.00 31.40 3.18
2808 2925 3.986996 TGATGCCATCTCTGTTCAAGA 57.013 42.857 6.21 0.00 0.00 3.02
2921 3628 6.697019 GCGCCATGTGAATCTAAATAAAATGT 59.303 34.615 0.00 0.00 0.00 2.71
3024 3731 2.899303 ACTGGTTGGTTATTGAGGGG 57.101 50.000 0.00 0.00 0.00 4.79
3081 3788 4.046462 GTGCATGACAATGGTGATAATGC 58.954 43.478 0.00 0.00 38.10 3.56
3090 3911 4.623932 ATGGTGATAATGCGGTATCTGT 57.376 40.909 7.69 0.00 32.58 3.41
3094 3915 4.997395 GGTGATAATGCGGTATCTGTGATT 59.003 41.667 7.69 0.00 32.58 2.57
3112 3933 6.966021 TGTGATTTTCTTTACACTAACTGGC 58.034 36.000 0.00 0.00 34.81 4.85
3115 3936 6.206634 TGATTTTCTTTACACTAACTGGCTGG 59.793 38.462 0.00 0.00 0.00 4.85
3120 3941 4.699925 TTACACTAACTGGCTGGAAGTT 57.300 40.909 0.00 0.00 40.82 2.66
3133 3954 4.760204 GGCTGGAAGTTATGTGTGTTAGTT 59.240 41.667 0.00 0.00 35.30 2.24
3172 3993 4.712829 TCTCCCACCTTTATGTCGAATGTA 59.287 41.667 0.00 0.00 0.00 2.29
3296 4120 3.683365 GGCTGGACCAAACATTTCATT 57.317 42.857 0.00 0.00 38.86 2.57
3297 4121 4.006780 GGCTGGACCAAACATTTCATTT 57.993 40.909 0.00 0.00 38.86 2.32
3298 4122 3.747529 GGCTGGACCAAACATTTCATTTG 59.252 43.478 0.00 0.00 38.86 2.32
3299 4123 3.187022 GCTGGACCAAACATTTCATTTGC 59.813 43.478 0.00 0.00 36.01 3.68
3306 4130 4.214545 CCAAACATTTCATTTGCTGCATGT 59.785 37.500 1.84 0.00 36.01 3.21
3368 4192 5.806654 AAAGAATACATTGCAACCTGGTT 57.193 34.783 6.18 6.18 0.00 3.67
3372 4196 2.086610 ACATTGCAACCTGGTTCCTT 57.913 45.000 9.62 0.00 0.00 3.36
3423 4247 2.978156 TCCATTTGCTCTTTCAGGGT 57.022 45.000 0.00 0.00 0.00 4.34
3447 4271 3.345808 GCTCGCGCAAAGACCACA 61.346 61.111 8.75 0.00 35.78 4.17
3521 4346 1.784358 TCCCCATACTCGTAACAGGG 58.216 55.000 0.00 0.00 36.04 4.45
3558 4383 2.092882 GTAACTGACGGCGGCAGTC 61.093 63.158 44.50 30.76 45.27 3.51
3629 4454 0.879765 AAGCTGTGCTTCTGTCATGC 59.120 50.000 0.00 0.00 46.77 4.06
3639 4464 1.114627 TCTGTCATGCTATCGGTGCT 58.885 50.000 0.00 0.00 0.00 4.40
3680 4506 2.356135 AGCGCGTTACCTTGATCAATT 58.644 42.857 8.96 1.72 0.00 2.32
3689 4515 2.264813 CCTTGATCAATTTGGCTTGCG 58.735 47.619 8.96 0.00 0.00 4.85
3726 4552 5.004448 TGCCTCGAGTCCTCTGTATATTAG 58.996 45.833 12.31 0.00 0.00 1.73
3735 4561 6.211785 AGTCCTCTGTATATTAGGGCTTAAGC 59.788 42.308 19.53 19.53 42.73 3.09
3736 4562 6.014499 GTCCTCTGTATATTAGGGCTTAAGCA 60.014 42.308 27.83 8.74 44.36 3.91
3755 4581 9.462174 CTTAAGCATGTTTTGTTTATCAAGTGA 57.538 29.630 0.00 0.00 37.35 3.41
3766 4592 5.538053 TGTTTATCAAGTGAATTCTTGGCCA 59.462 36.000 0.00 0.00 43.25 5.36
3967 4804 8.604035 ACTAATAGCATGATTTACAACGTTGAG 58.396 33.333 33.66 16.40 0.00 3.02
4064 4902 5.511571 GTTGCTGAACAAGTAACTCCTTTC 58.488 41.667 0.00 0.00 45.22 2.62
4164 5027 2.728817 CTGGATCCCGGCGAGTAC 59.271 66.667 9.30 0.00 0.00 2.73
4562 5430 3.532155 GGACGCCGGATCTCAGCT 61.532 66.667 5.05 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.504916 CTCCTCGAGGGCGTGCTG 62.505 72.222 30.80 9.04 38.98 4.41
4 5 4.500116 GACTCCTCGAGGGCGTGC 62.500 72.222 30.80 16.56 38.98 5.34
5 6 3.827898 GGACTCCTCGAGGGCGTG 61.828 72.222 30.80 19.52 38.98 5.34
73 74 4.803426 CAGTCCCTCGCTGCCGAC 62.803 72.222 0.00 0.00 38.82 4.79
88 89 0.171455 GTGGTGGAGAGTAGACGCAG 59.829 60.000 0.00 0.00 0.00 5.18
89 90 1.248785 GGTGGTGGAGAGTAGACGCA 61.249 60.000 0.00 0.00 0.00 5.24
90 91 1.248785 TGGTGGTGGAGAGTAGACGC 61.249 60.000 0.00 0.00 0.00 5.19
91 92 1.405821 GATGGTGGTGGAGAGTAGACG 59.594 57.143 0.00 0.00 0.00 4.18
92 93 1.405821 CGATGGTGGTGGAGAGTAGAC 59.594 57.143 0.00 0.00 0.00 2.59
93 94 1.763968 CGATGGTGGTGGAGAGTAGA 58.236 55.000 0.00 0.00 0.00 2.59
94 95 0.103208 GCGATGGTGGTGGAGAGTAG 59.897 60.000 0.00 0.00 0.00 2.57
95 96 1.327690 GGCGATGGTGGTGGAGAGTA 61.328 60.000 0.00 0.00 0.00 2.59
96 97 2.660064 GGCGATGGTGGTGGAGAGT 61.660 63.158 0.00 0.00 0.00 3.24
97 98 2.187946 GGCGATGGTGGTGGAGAG 59.812 66.667 0.00 0.00 0.00 3.20
98 99 2.284625 AGGCGATGGTGGTGGAGA 60.285 61.111 0.00 0.00 0.00 3.71
99 100 2.187946 GAGGCGATGGTGGTGGAG 59.812 66.667 0.00 0.00 0.00 3.86
100 101 2.284625 AGAGGCGATGGTGGTGGA 60.285 61.111 0.00 0.00 0.00 4.02
101 102 2.187946 GAGAGGCGATGGTGGTGG 59.812 66.667 0.00 0.00 0.00 4.61
102 103 1.043116 TAGGAGAGGCGATGGTGGTG 61.043 60.000 0.00 0.00 0.00 4.17
103 104 0.105453 ATAGGAGAGGCGATGGTGGT 60.105 55.000 0.00 0.00 0.00 4.16
104 105 1.821753 CTATAGGAGAGGCGATGGTGG 59.178 57.143 0.00 0.00 0.00 4.61
105 106 1.203523 GCTATAGGAGAGGCGATGGTG 59.796 57.143 1.04 0.00 0.00 4.17
106 107 1.203063 TGCTATAGGAGAGGCGATGGT 60.203 52.381 1.04 0.00 0.00 3.55
107 108 1.476085 CTGCTATAGGAGAGGCGATGG 59.524 57.143 15.77 0.00 35.31 3.51
108 109 1.135141 GCTGCTATAGGAGAGGCGATG 60.135 57.143 24.04 0.00 35.31 3.84
109 110 1.181786 GCTGCTATAGGAGAGGCGAT 58.818 55.000 24.04 0.00 35.31 4.58
110 111 0.896019 GGCTGCTATAGGAGAGGCGA 60.896 60.000 24.04 0.00 35.31 5.54
111 112 1.589113 GGCTGCTATAGGAGAGGCG 59.411 63.158 24.04 0.00 35.31 5.52
112 113 1.882989 CGGGCTGCTATAGGAGAGGC 61.883 65.000 24.04 11.45 35.31 4.70
113 114 0.251386 TCGGGCTGCTATAGGAGAGG 60.251 60.000 24.04 11.83 35.31 3.69
114 115 1.173043 CTCGGGCTGCTATAGGAGAG 58.827 60.000 24.04 13.85 35.31 3.20
115 116 0.896019 GCTCGGGCTGCTATAGGAGA 60.896 60.000 24.04 3.28 35.31 3.71
116 117 1.589113 GCTCGGGCTGCTATAGGAG 59.411 63.158 16.43 16.43 36.50 3.69
117 118 1.908793 GGCTCGGGCTGCTATAGGA 60.909 63.158 7.48 0.00 38.73 2.94
118 119 2.659610 GGCTCGGGCTGCTATAGG 59.340 66.667 7.48 0.00 38.73 2.57
119 120 2.210013 TGGGCTCGGGCTGCTATAG 61.210 63.158 7.48 0.00 38.73 1.31
120 121 2.123033 TGGGCTCGGGCTGCTATA 60.123 61.111 7.48 0.00 38.73 1.31
121 122 3.866582 GTGGGCTCGGGCTGCTAT 61.867 66.667 7.48 0.00 38.73 2.97
158 159 0.689745 TCCCATTGGTACCTCTCGGG 60.690 60.000 14.36 16.69 41.89 5.14
159 160 0.753262 CTCCCATTGGTACCTCTCGG 59.247 60.000 14.36 8.24 0.00 4.63
170 171 1.978617 GCACCACACCCTCCCATTG 60.979 63.158 0.00 0.00 0.00 2.82
172 173 4.033776 CGCACCACACCCTCCCAT 62.034 66.667 0.00 0.00 0.00 4.00
199 200 4.710695 CACACGGCCGACACGCTA 62.711 66.667 35.90 0.00 34.00 4.26
204 205 3.207547 CTCAGACACACGGCCGACA 62.208 63.158 35.90 4.55 0.00 4.35
206 207 2.910479 ACTCAGACACACGGCCGA 60.910 61.111 35.90 5.21 0.00 5.54
208 209 3.044305 GCACTCAGACACACGGCC 61.044 66.667 0.00 0.00 0.00 6.13
210 211 1.821241 CGTTGCACTCAGACACACGG 61.821 60.000 0.00 0.00 0.00 4.94
217 218 1.595109 CACAGGCGTTGCACTCAGA 60.595 57.895 0.00 0.00 0.00 3.27
221 222 2.281070 CTCCACAGGCGTTGCACT 60.281 61.111 0.00 0.00 0.00 4.40
223 224 3.535629 CTCCTCCACAGGCGTTGCA 62.536 63.158 0.00 0.00 40.12 4.08
226 227 2.526873 ACCTCCTCCACAGGCGTT 60.527 61.111 0.00 0.00 40.12 4.84
232 233 1.612442 GTAGGCCACCTCCTCCACA 60.612 63.158 5.01 0.00 37.66 4.17
234 235 2.040606 GGTAGGCCACCTCCTCCA 59.959 66.667 5.01 0.00 44.79 3.86
303 304 2.280797 TCTCGTGCCCACAGTTGC 60.281 61.111 0.00 0.00 0.00 4.17
308 309 2.997315 CCTCCTCTCGTGCCCACA 60.997 66.667 0.00 0.00 0.00 4.17
318 319 1.655114 GCTCCTCCTCCTCCTCCTCT 61.655 65.000 0.00 0.00 0.00 3.69
319 320 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
320 321 1.938596 TGCTCCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
391 392 4.070552 GCCTTCTCGGGCGTCTGT 62.071 66.667 0.00 0.00 42.82 3.41
417 418 3.582780 GAGAAAACCTACCGGTACACTG 58.417 50.000 11.16 0.23 44.73 3.66
420 421 2.030007 CACGAGAAAACCTACCGGTACA 60.030 50.000 11.16 0.00 44.73 2.90
426 427 2.148768 CAACCCACGAGAAAACCTACC 58.851 52.381 0.00 0.00 0.00 3.18
428 429 2.171027 ACACAACCCACGAGAAAACCTA 59.829 45.455 0.00 0.00 0.00 3.08
429 430 1.064979 ACACAACCCACGAGAAAACCT 60.065 47.619 0.00 0.00 0.00 3.50
432 433 1.292061 CGACACAACCCACGAGAAAA 58.708 50.000 0.00 0.00 0.00 2.29
444 445 2.190170 AATGGCAACGGCGACACAA 61.190 52.632 16.62 0.00 42.47 3.33
445 446 2.593148 AATGGCAACGGCGACACA 60.593 55.556 16.62 7.38 42.47 3.72
447 448 1.673993 ATCAATGGCAACGGCGACA 60.674 52.632 16.62 7.39 42.47 4.35
449 450 3.050166 GCATCAATGGCAACGGCGA 62.050 57.895 16.62 0.00 42.47 5.54
460 461 2.420568 CGCAAGCCCAGGCATCAAT 61.421 57.895 12.03 0.00 44.88 2.57
521 524 6.643770 GTCGAGTCCACTTCAAACATAACTAA 59.356 38.462 0.00 0.00 0.00 2.24
524 527 4.151867 GGTCGAGTCCACTTCAAACATAAC 59.848 45.833 0.00 0.00 0.00 1.89
544 547 8.077386 TGAACATTTAAATTAAAGTCCACGGTC 58.923 33.333 4.43 0.00 0.00 4.79
545 548 7.942990 TGAACATTTAAATTAAAGTCCACGGT 58.057 30.769 4.43 0.00 0.00 4.83
625 632 0.373716 GGCCGACGCATTTTAGTCTG 59.626 55.000 0.00 0.00 36.38 3.51
626 633 1.082117 CGGCCGACGCATTTTAGTCT 61.082 55.000 24.07 0.00 36.38 3.24
643 650 1.261354 CGATATGTGCATCCAACACGG 59.739 52.381 0.00 0.00 41.03 4.94
646 653 4.341366 AGATCGATATGTGCATCCAACA 57.659 40.909 0.00 0.00 0.00 3.33
652 659 9.060347 ACTTTCAATTTAGATCGATATGTGCAT 57.940 29.630 2.01 0.00 0.00 3.96
660 667 6.255887 GTGTCCGACTTTCAATTTAGATCGAT 59.744 38.462 0.00 0.00 0.00 3.59
661 668 5.575606 GTGTCCGACTTTCAATTTAGATCGA 59.424 40.000 0.00 0.00 0.00 3.59
667 674 3.059461 GCACGTGTCCGACTTTCAATTTA 60.059 43.478 18.38 0.00 37.88 1.40
672 679 1.947146 CGCACGTGTCCGACTTTCA 60.947 57.895 18.38 0.00 37.88 2.69
673 680 1.485032 AACGCACGTGTCCGACTTTC 61.485 55.000 20.05 0.00 37.88 2.62
677 684 3.749373 CGAACGCACGTGTCCGAC 61.749 66.667 20.05 12.65 37.88 4.79
681 688 1.717728 CAAAGCGAACGCACGTGTC 60.718 57.895 18.38 8.63 44.88 3.67
685 692 2.498761 ATCAGCAAAGCGAACGCACG 62.499 55.000 20.66 9.56 44.88 5.34
686 693 0.385974 AATCAGCAAAGCGAACGCAC 60.386 50.000 20.66 7.54 44.88 5.34
693 700 1.069296 TCCGTTTGAATCAGCAAAGCG 60.069 47.619 0.00 0.00 38.33 4.68
695 702 3.624326 TGTCCGTTTGAATCAGCAAAG 57.376 42.857 0.00 0.00 38.33 2.77
697 704 4.097135 TCTTTTGTCCGTTTGAATCAGCAA 59.903 37.500 0.00 0.00 0.00 3.91
698 705 3.629855 TCTTTTGTCCGTTTGAATCAGCA 59.370 39.130 0.00 0.00 0.00 4.41
702 709 3.249080 TCCGTCTTTTGTCCGTTTGAATC 59.751 43.478 0.00 0.00 0.00 2.52
704 711 2.352342 GTCCGTCTTTTGTCCGTTTGAA 59.648 45.455 0.00 0.00 0.00 2.69
705 712 1.935199 GTCCGTCTTTTGTCCGTTTGA 59.065 47.619 0.00 0.00 0.00 2.69
710 717 3.103007 GTTTTTGTCCGTCTTTTGTCCG 58.897 45.455 0.00 0.00 0.00 4.79
719 726 1.096967 ACCGGTGGTTTTTGTCCGTC 61.097 55.000 6.12 0.00 41.17 4.79
721 728 1.357334 CACCGGTGGTTTTTGTCCG 59.643 57.895 27.57 0.00 42.22 4.79
722 729 0.382873 GACACCGGTGGTTTTTGTCC 59.617 55.000 36.47 11.13 31.02 4.02
737 744 4.922026 ACCCAACACGGCCGACAC 62.922 66.667 35.90 0.00 0.00 3.67
738 745 4.920112 CACCCAACACGGCCGACA 62.920 66.667 35.90 0.00 0.00 4.35
745 752 0.955178 TTGTATTGCCACCCAACACG 59.045 50.000 0.00 0.00 33.54 4.49
746 753 3.324993 CAATTGTATTGCCACCCAACAC 58.675 45.455 0.00 0.00 35.99 3.32
747 754 2.301296 CCAATTGTATTGCCACCCAACA 59.699 45.455 4.43 0.00 35.99 3.33
749 756 1.277557 GCCAATTGTATTGCCACCCAA 59.722 47.619 4.43 0.00 37.94 4.12
750 757 0.901124 GCCAATTGTATTGCCACCCA 59.099 50.000 4.43 0.00 0.00 4.51
764 794 1.327303 ACAACCAACATCGTGCCAAT 58.673 45.000 0.00 0.00 0.00 3.16
765 795 1.876799 CTACAACCAACATCGTGCCAA 59.123 47.619 0.00 0.00 0.00 4.52
772 802 1.004277 TCCCTGCCTACAACCAACATC 59.996 52.381 0.00 0.00 0.00 3.06
777 807 0.472925 TGTCTCCCTGCCTACAACCA 60.473 55.000 0.00 0.00 0.00 3.67
780 810 1.983224 GCTGTCTCCCTGCCTACAA 59.017 57.895 0.00 0.00 32.24 2.41
823 853 2.525105 TTTCAATCCAAGGGCTACCC 57.475 50.000 0.00 0.00 45.90 3.69
826 856 4.526970 GTCAGATTTCAATCCAAGGGCTA 58.473 43.478 0.00 0.00 36.04 3.93
850 880 2.094894 CGTGCAGTCATTTTCTAGCCAG 59.905 50.000 0.00 0.00 0.00 4.85
1051 1093 1.544724 TTTGAGAAATTCAGCCCGGG 58.455 50.000 19.09 19.09 37.07 5.73
1512 1554 3.654273 TCTGATACTAAAGGGGGACAGG 58.346 50.000 0.00 0.00 0.00 4.00
1555 1597 0.390860 AGCTAGCCTATCCGCAACAG 59.609 55.000 12.13 0.00 0.00 3.16
1582 1624 5.095490 GCAACGAGTAATTTGGAATGGAAG 58.905 41.667 0.00 0.00 0.00 3.46
1583 1625 4.520874 TGCAACGAGTAATTTGGAATGGAA 59.479 37.500 0.00 0.00 0.00 3.53
1584 1626 4.075682 TGCAACGAGTAATTTGGAATGGA 58.924 39.130 0.00 0.00 0.00 3.41
1587 1629 5.957842 TTCTGCAACGAGTAATTTGGAAT 57.042 34.783 0.00 0.00 0.00 3.01
1589 1631 5.335583 CCATTTCTGCAACGAGTAATTTGGA 60.336 40.000 0.00 0.00 0.00 3.53
1590 1632 4.858692 CCATTTCTGCAACGAGTAATTTGG 59.141 41.667 0.00 0.00 0.00 3.28
1595 1637 4.323417 ACATCCATTTCTGCAACGAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
1598 1640 4.813161 AGATACATCCATTTCTGCAACGAG 59.187 41.667 0.00 0.00 0.00 4.18
1599 1641 4.769688 AGATACATCCATTTCTGCAACGA 58.230 39.130 0.00 0.00 0.00 3.85
1600 1642 5.985530 TCTAGATACATCCATTTCTGCAACG 59.014 40.000 0.00 0.00 0.00 4.10
1603 1645 7.129457 AGTTCTAGATACATCCATTTCTGCA 57.871 36.000 0.00 0.00 0.00 4.41
1604 1646 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
1631 1673 7.915923 CGCAGGTATCGATGTATCTAAATGTAT 59.084 37.037 8.54 0.00 0.00 2.29
1633 1675 6.072119 TCGCAGGTATCGATGTATCTAAATGT 60.072 38.462 8.54 0.00 0.00 2.71
1634 1676 6.251589 GTCGCAGGTATCGATGTATCTAAATG 59.748 42.308 8.54 0.00 38.29 2.32
1635 1677 6.072119 TGTCGCAGGTATCGATGTATCTAAAT 60.072 38.462 8.54 0.00 38.29 1.40
1636 1678 5.239963 TGTCGCAGGTATCGATGTATCTAAA 59.760 40.000 8.54 0.00 38.29 1.85
1640 1682 3.554259 TGTCGCAGGTATCGATGTATC 57.446 47.619 8.54 0.00 38.29 2.24
1641 1683 3.318275 ACTTGTCGCAGGTATCGATGTAT 59.682 43.478 8.54 0.00 38.29 2.29
1642 1684 2.686405 ACTTGTCGCAGGTATCGATGTA 59.314 45.455 8.54 0.00 38.29 2.29
1643 1685 1.476891 ACTTGTCGCAGGTATCGATGT 59.523 47.619 8.54 0.00 38.29 3.06
1644 1686 2.209838 ACTTGTCGCAGGTATCGATG 57.790 50.000 8.54 0.00 38.29 3.84
1645 1687 4.585955 ATTACTTGTCGCAGGTATCGAT 57.414 40.909 2.16 2.16 38.29 3.59
1646 1688 4.357142 GAATTACTTGTCGCAGGTATCGA 58.643 43.478 0.00 0.00 0.00 3.59
1647 1689 3.179795 CGAATTACTTGTCGCAGGTATCG 59.820 47.826 9.09 9.09 28.22 2.92
1648 1690 3.489785 CCGAATTACTTGTCGCAGGTATC 59.510 47.826 3.46 0.18 35.93 2.24
1649 1691 3.131577 TCCGAATTACTTGTCGCAGGTAT 59.868 43.478 3.46 0.00 35.93 2.73
1650 1692 2.492881 TCCGAATTACTTGTCGCAGGTA 59.507 45.455 0.00 0.00 35.93 3.08
1651 1693 1.274167 TCCGAATTACTTGTCGCAGGT 59.726 47.619 0.00 0.91 35.93 4.00
1652 1694 2.004583 TCCGAATTACTTGTCGCAGG 57.995 50.000 0.00 0.00 35.93 4.85
1653 1695 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
1656 1698 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
1661 1703 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
1662 1704 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
1665 1707 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
1668 1710 0.102481 CATGTACTCCCTCCGTTCCG 59.898 60.000 0.00 0.00 0.00 4.30
1671 1713 2.904434 AGAAACATGTACTCCCTCCGTT 59.096 45.455 0.00 0.00 0.00 4.44
1674 1716 4.407296 AGATCAGAAACATGTACTCCCTCC 59.593 45.833 0.00 0.00 0.00 4.30
1679 1721 6.393990 ACACTCAGATCAGAAACATGTACTC 58.606 40.000 0.00 0.00 0.00 2.59
1680 1722 6.352016 ACACTCAGATCAGAAACATGTACT 57.648 37.500 0.00 0.00 0.00 2.73
1681 1723 5.287274 CGACACTCAGATCAGAAACATGTAC 59.713 44.000 0.00 0.00 0.00 2.90
1683 1725 4.240888 CGACACTCAGATCAGAAACATGT 58.759 43.478 0.00 0.00 0.00 3.21
1684 1726 4.091075 CACGACACTCAGATCAGAAACATG 59.909 45.833 0.00 0.00 0.00 3.21
1731 1773 3.181475 GGCTCATGAGGAAACATACTCGA 60.181 47.826 23.89 0.00 36.53 4.04
1732 1774 3.126831 GGCTCATGAGGAAACATACTCG 58.873 50.000 23.89 0.00 36.53 4.18
1751 1794 5.048434 AGCAGAATCTAACTTTTTGTGAGGC 60.048 40.000 0.00 0.00 0.00 4.70
1884 1961 8.921205 AGTAGGTTATTTAACTCGTACATGGAT 58.079 33.333 0.00 0.00 36.47 3.41
1904 1981 8.157476 ACATGAAAAGTTCAATAGACAGTAGGT 58.843 33.333 0.00 0.00 43.95 3.08
1936 2013 9.183368 ACCTGTACATAGAAGTAACTAGTTACC 57.817 37.037 32.51 22.10 44.79 2.85
1955 2032 7.197071 TGTTGTGAAATGAACATACCTGTAC 57.803 36.000 0.00 0.00 33.36 2.90
2115 2193 3.569701 TCAAAGTTGAAGTGCCTGATTCC 59.430 43.478 0.00 0.00 33.55 3.01
2116 2194 4.836125 TCAAAGTTGAAGTGCCTGATTC 57.164 40.909 0.00 0.00 33.55 2.52
2222 2301 3.448093 TTGTCCATAGTGGCAAATCCA 57.552 42.857 0.00 0.00 44.18 3.41
2272 2351 1.802636 CATGGGCTGTAAAGGCGTG 59.197 57.895 0.00 0.00 34.95 5.34
2318 2397 2.903784 TGTTGTCCTACCACTACAGCAT 59.096 45.455 0.00 0.00 30.73 3.79
2388 2472 3.118408 TGCGAATCAGGCTTAACTGGTAT 60.118 43.478 0.00 0.00 38.98 2.73
2398 2482 1.740025 GCTTAACTTGCGAATCAGGCT 59.260 47.619 0.00 0.00 0.00 4.58
2399 2483 1.202188 GGCTTAACTTGCGAATCAGGC 60.202 52.381 0.00 0.00 0.00 4.85
2400 2484 2.096496 CAGGCTTAACTTGCGAATCAGG 59.904 50.000 0.00 0.00 0.00 3.86
2401 2485 3.002791 TCAGGCTTAACTTGCGAATCAG 58.997 45.455 0.00 0.00 0.00 2.90
2402 2486 3.052455 TCAGGCTTAACTTGCGAATCA 57.948 42.857 0.00 0.00 0.00 2.57
2403 2487 4.622701 AATCAGGCTTAACTTGCGAATC 57.377 40.909 0.00 0.00 0.00 2.52
2404 2488 4.737054 CAAATCAGGCTTAACTTGCGAAT 58.263 39.130 0.00 0.00 0.00 3.34
2405 2489 3.611530 GCAAATCAGGCTTAACTTGCGAA 60.612 43.478 5.05 0.00 30.95 4.70
2406 2490 2.095263 GCAAATCAGGCTTAACTTGCGA 60.095 45.455 5.05 0.00 30.95 5.10
2407 2491 2.253603 GCAAATCAGGCTTAACTTGCG 58.746 47.619 5.05 0.00 30.95 4.85
2408 2492 3.302365 TGCAAATCAGGCTTAACTTGC 57.698 42.857 11.46 11.46 39.62 4.01
2409 2493 6.867816 TGTATTTGCAAATCAGGCTTAACTTG 59.132 34.615 27.28 0.00 0.00 3.16
2410 2494 6.868339 GTGTATTTGCAAATCAGGCTTAACTT 59.132 34.615 27.28 3.17 0.00 2.66
2411 2495 6.015519 TGTGTATTTGCAAATCAGGCTTAACT 60.016 34.615 27.28 3.38 0.00 2.24
2412 2496 6.155827 TGTGTATTTGCAAATCAGGCTTAAC 58.844 36.000 27.28 17.17 0.00 2.01
2413 2497 6.338214 TGTGTATTTGCAAATCAGGCTTAA 57.662 33.333 27.28 5.43 0.00 1.85
2414 2498 5.973899 TGTGTATTTGCAAATCAGGCTTA 57.026 34.783 27.28 6.20 0.00 3.09
2415 2499 4.870123 TGTGTATTTGCAAATCAGGCTT 57.130 36.364 27.28 6.19 0.00 4.35
2416 2500 4.751060 CATGTGTATTTGCAAATCAGGCT 58.249 39.130 27.28 6.95 0.00 4.58
2528 2612 7.365497 TGAGCTTCCTGATGTATCAAATCTA 57.635 36.000 0.00 0.00 36.18 1.98
2626 2738 3.534554 CACATCAACATGGAAGATCGGA 58.465 45.455 0.00 0.00 33.82 4.55
2695 2807 2.095263 AGGTAATTTGTCATGCACGTGC 60.095 45.455 33.11 33.11 42.50 5.34
2699 2811 8.810427 CAAAATATGAGGTAATTTGTCATGCAC 58.190 33.333 0.00 0.00 31.46 4.57
2700 2812 8.530311 ACAAAATATGAGGTAATTTGTCATGCA 58.470 29.630 0.00 0.00 40.62 3.96
2732 2846 7.201530 GGACGATTAACCACAGATTTTAGTGAG 60.202 40.741 0.00 0.00 37.97 3.51
2747 2861 6.257411 GGCTAAGACTAAAAGGACGATTAACC 59.743 42.308 0.00 0.00 0.00 2.85
2805 2922 6.721208 TCCAGCATTCAGAATTTAAACCTCTT 59.279 34.615 0.00 0.00 0.00 2.85
2808 2925 6.012745 AGTCCAGCATTCAGAATTTAAACCT 58.987 36.000 0.00 0.00 0.00 3.50
2880 3587 0.465642 GCGCCTTAAACCTATGCCCT 60.466 55.000 0.00 0.00 0.00 5.19
2921 3628 8.856153 TCAATTAGCCTATTGTTGTAAGTTCA 57.144 30.769 7.91 0.00 36.95 3.18
3024 3731 4.906618 TGGGACAGAAACAGATAAAGGAC 58.093 43.478 0.00 0.00 0.00 3.85
3081 3788 7.596749 AGTGTAAAGAAAATCACAGATACCG 57.403 36.000 0.00 0.00 33.84 4.02
3090 3911 6.206634 CCAGCCAGTTAGTGTAAAGAAAATCA 59.793 38.462 0.00 0.00 0.00 2.57
3094 3915 5.298989 TCCAGCCAGTTAGTGTAAAGAAA 57.701 39.130 0.00 0.00 0.00 2.52
3112 3933 6.017109 AGCAAACTAACACACATAACTTCCAG 60.017 38.462 0.00 0.00 0.00 3.86
3115 3936 8.628882 AAAAGCAAACTAACACACATAACTTC 57.371 30.769 0.00 0.00 0.00 3.01
3120 3941 7.328277 ACTGAAAAGCAAACTAACACACATA 57.672 32.000 0.00 0.00 0.00 2.29
3133 3954 4.097892 GTGGGAGAAGAAACTGAAAAGCAA 59.902 41.667 0.00 0.00 0.00 3.91
3172 3993 4.460382 CCAGATATGGCAAAAACACAGAGT 59.540 41.667 0.00 0.00 0.00 3.24
3236 4057 1.037493 ACATAACGATAGCCCGCAGA 58.963 50.000 0.00 0.00 42.67 4.26
3315 4139 9.233232 CCTCTACAAACCGCAATTATAAAATTC 57.767 33.333 0.00 0.00 32.87 2.17
3316 4140 8.962679 TCCTCTACAAACCGCAATTATAAAATT 58.037 29.630 0.00 0.00 35.65 1.82
3317 4141 8.514330 TCCTCTACAAACCGCAATTATAAAAT 57.486 30.769 0.00 0.00 0.00 1.82
3324 4148 6.827586 TTATTTCCTCTACAAACCGCAATT 57.172 33.333 0.00 0.00 0.00 2.32
3368 4192 3.404899 GTGAATCACACCCGTTTAAGGA 58.595 45.455 8.74 0.00 43.05 3.36
3399 4223 4.820716 CCCTGAAAGAGCAAATGGATAGAG 59.179 45.833 0.00 0.00 34.07 2.43
3495 4319 6.401047 TGTTACGAGTATGGGGAATAAGAG 57.599 41.667 0.00 0.00 0.00 2.85
3521 4346 2.101770 CCGTTCGTCGCCCTCTAC 59.898 66.667 0.00 0.00 38.35 2.59
3558 4383 4.087892 CTCCTCCCCTGCACCACG 62.088 72.222 0.00 0.00 0.00 4.94
3624 4449 1.807755 GCTCAAGCACCGATAGCATGA 60.808 52.381 0.00 0.00 41.59 3.07
3629 4454 2.240500 GGCGCTCAAGCACCGATAG 61.241 63.158 7.64 0.00 42.21 2.08
3639 4464 4.124351 CCCTCGTACGGCGCTCAA 62.124 66.667 16.52 0.00 41.07 3.02
3663 4489 3.119495 AGCCAAATTGATCAAGGTAACGC 60.119 43.478 14.54 9.98 46.39 4.84
3680 4506 1.207089 AGATAGTAGCACGCAAGCCAA 59.793 47.619 0.00 0.00 45.62 4.52
3689 4515 2.099263 TCGAGGCAACAGATAGTAGCAC 59.901 50.000 0.00 0.00 41.41 4.40
3726 4552 6.162777 TGATAAACAAAACATGCTTAAGCCC 58.837 36.000 24.30 0.00 41.18 5.19
3755 4581 4.105377 AGCTATACAGGATGGCCAAGAATT 59.895 41.667 10.96 0.00 42.90 2.17
3766 4592 6.789959 ACTGGAAGGAATTAGCTATACAGGAT 59.210 38.462 6.89 0.00 39.30 3.24
3805 4642 4.582701 CAAATAACTTGGTGCTGGAACA 57.417 40.909 0.00 0.00 0.00 3.18
3960 4797 1.344438 TGTCAGATTCAGCCTCAACGT 59.656 47.619 0.00 0.00 0.00 3.99
3967 4804 2.911484 CCCTACTTGTCAGATTCAGCC 58.089 52.381 0.00 0.00 0.00 4.85
4060 4898 3.146847 GGACCCCACTTGTGTAAGAAAG 58.853 50.000 0.00 0.00 37.36 2.62
4064 4902 0.682852 TCGGACCCCACTTGTGTAAG 59.317 55.000 0.00 0.00 39.86 2.34
4162 5025 3.795280 GACGCCGCGACGCTATGTA 62.795 63.158 21.79 0.00 36.19 2.29
4231 5094 3.315142 GATCCGGTGACAGCAGCCA 62.315 63.158 0.00 0.00 39.30 4.75
4235 5098 2.885113 CGAGATCCGGTGACAGCA 59.115 61.111 0.00 0.00 33.91 4.41
4425 5290 2.203788 ACCTCCTTGACCGCTCCA 60.204 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.