Multiple sequence alignment - TraesCS5A01G007000

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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 TraesCS5A01G007000 chr5A 100.000 2495 0 0 1 2495 4074873 4072379 0.000000e+00 4608
1 TraesCS5A01G007000 chr5A 79.307 1846 245 66 199 1940 4785337 4783525 0.000000e+00 1166
2 TraesCS5A01G007000 chr5A 99.638 553 1 1 1943 2495 4059045 4058494 0.000000e+00 1009
3 TraesCS5A01G007000 chr5A 96.739 552 17 1 1944 2495 581275250 581274700 0.000000e+00 918
4 TraesCS5A01G007000 chr5A 81.147 1151 171 29 804 1923 4791062 4789927 0.000000e+00 881
5 TraesCS5A01G007000 chr5A 79.070 645 100 25 199 818 4864911 4865545 6.420000e-111 411
6 TraesCS5A01G007000 chr5A 77.964 658 104 26 193 818 4874922 4875570 8.430000e-100 374
7 TraesCS5A01G007000 chr5A 77.667 600 102 25 233 807 4882291 4882883 1.110000e-88 337
8 TraesCS5A01G007000 chr5A 82.051 234 33 6 588 818 4796943 4796716 9.110000e-45 191
9 TraesCS5A01G007000 chr4A 79.596 1833 248 71 199 1940 18731881 18730084 0.000000e+00 1197
10 TraesCS5A01G007000 chr4A 81.079 1168 175 31 804 1940 18743205 18742053 0.000000e+00 891
11 TraesCS5A01G007000 chr4A 81.541 1116 156 32 804 1884 18737562 18736462 0.000000e+00 874
12 TraesCS5A01G007000 chr4A 96.636 327 8 1 1 327 17881132 17880809 7.850000e-150 540
13 TraesCS5A01G007000 chr4A 81.624 234 35 5 588 818 18743449 18743221 1.180000e-43 187
14 TraesCS5A01G007000 chr5D 79.155 1823 258 71 193 1921 3889483 3891277 0.000000e+00 1149
15 TraesCS5A01G007000 chr5D 81.383 1171 171 26 804 1940 3869629 3870786 0.000000e+00 911
16 TraesCS5A01G007000 chr5D 81.330 1173 169 31 804 1940 7120196 7119038 0.000000e+00 907
17 TraesCS5A01G007000 chr5D 80.746 1179 170 35 804 1940 3875208 3876371 0.000000e+00 867
18 TraesCS5A01G007000 chr5D 78.395 648 102 25 199 818 7126151 7125514 1.080000e-103 387
19 TraesCS5A01G007000 chr5D 82.128 235 31 7 588 818 7136263 7136036 9.110000e-45 191
20 TraesCS5A01G007000 chrUn 94.648 654 32 2 997 1650 65691742 65692392 0.000000e+00 1011
21 TraesCS5A01G007000 chr1A 98.556 554 7 1 1943 2495 45259570 45259017 0.000000e+00 977
22 TraesCS5A01G007000 chr1A 96.931 554 13 4 1943 2495 481831381 481831931 0.000000e+00 926
23 TraesCS5A01G007000 chr6B 97.473 554 10 4 1944 2495 206418056 206418607 0.000000e+00 942
24 TraesCS5A01G007000 chr6B 96.757 555 13 5 1943 2495 206424884 206425435 0.000000e+00 920
25 TraesCS5A01G007000 chr6B 96.583 556 17 2 1941 2495 660468260 660468814 0.000000e+00 920
26 TraesCS5A01G007000 chr6B 96.751 554 13 5 1944 2495 52018056 52017506 0.000000e+00 918
27 TraesCS5A01G007000 chr7A 97.101 552 15 1 1944 2495 705789303 705789853 0.000000e+00 929
28 TraesCS5A01G007000 chr5B 79.915 1180 173 39 804 1940 7383467 7382309 0.000000e+00 808
29 TraesCS5A01G007000 chr5B 79.503 1166 166 50 805 1940 7149424 7148302 0.000000e+00 761
30 TraesCS5A01G007000 chr5B 79.467 1164 164 52 805 1940 7185154 7184038 0.000000e+00 756
31 TraesCS5A01G007000 chr5B 82.242 794 105 22 999 1770 7355437 7354658 0.000000e+00 652
32 TraesCS5A01G007000 chr5B 77.984 645 95 30 199 818 7185793 7185171 6.560000e-96 361
33 TraesCS5A01G007000 chr5B 77.379 641 104 25 199 818 7305534 7304914 2.380000e-90 342
34 TraesCS5A01G007000 chr5B 79.794 485 68 20 354 818 7356471 7355997 2.390000e-85 326
35 TraesCS5A01G007000 chr5B 78.458 506 74 26 199 676 7448738 7448240 5.220000e-77 298


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 TraesCS5A01G007000 chr5A 4072379 4074873 2494 True 4608.0 4608 100.0000 1 2495 1 chr5A.!!$R2 2494
1 TraesCS5A01G007000 chr5A 4783525 4785337 1812 True 1166.0 1166 79.3070 199 1940 1 chr5A.!!$R3 1741
2 TraesCS5A01G007000 chr5A 4058494 4059045 551 True 1009.0 1009 99.6380 1943 2495 1 chr5A.!!$R1 552
3 TraesCS5A01G007000 chr5A 581274700 581275250 550 True 918.0 918 96.7390 1944 2495 1 chr5A.!!$R6 551
4 TraesCS5A01G007000 chr5A 4789927 4791062 1135 True 881.0 881 81.1470 804 1923 1 chr5A.!!$R4 1119
5 TraesCS5A01G007000 chr5A 4864911 4865545 634 False 411.0 411 79.0700 199 818 1 chr5A.!!$F1 619
6 TraesCS5A01G007000 chr5A 4874922 4875570 648 False 374.0 374 77.9640 193 818 1 chr5A.!!$F2 625
7 TraesCS5A01G007000 chr5A 4882291 4882883 592 False 337.0 337 77.6670 233 807 1 chr5A.!!$F3 574
8 TraesCS5A01G007000 chr4A 18730084 18731881 1797 True 1197.0 1197 79.5960 199 1940 1 chr4A.!!$R2 1741
9 TraesCS5A01G007000 chr4A 18736462 18737562 1100 True 874.0 874 81.5410 804 1884 1 chr4A.!!$R3 1080
10 TraesCS5A01G007000 chr4A 18742053 18743449 1396 True 539.0 891 81.3515 588 1940 2 chr4A.!!$R4 1352
11 TraesCS5A01G007000 chr5D 3889483 3891277 1794 False 1149.0 1149 79.1550 193 1921 1 chr5D.!!$F3 1728
12 TraesCS5A01G007000 chr5D 3869629 3870786 1157 False 911.0 911 81.3830 804 1940 1 chr5D.!!$F1 1136
13 TraesCS5A01G007000 chr5D 7119038 7120196 1158 True 907.0 907 81.3300 804 1940 1 chr5D.!!$R1 1136
14 TraesCS5A01G007000 chr5D 3875208 3876371 1163 False 867.0 867 80.7460 804 1940 1 chr5D.!!$F2 1136
15 TraesCS5A01G007000 chr5D 7125514 7126151 637 True 387.0 387 78.3950 199 818 1 chr5D.!!$R2 619
16 TraesCS5A01G007000 chrUn 65691742 65692392 650 False 1011.0 1011 94.6480 997 1650 1 chrUn.!!$F1 653
17 TraesCS5A01G007000 chr1A 45259017 45259570 553 True 977.0 977 98.5560 1943 2495 1 chr1A.!!$R1 552
18 TraesCS5A01G007000 chr1A 481831381 481831931 550 False 926.0 926 96.9310 1943 2495 1 chr1A.!!$F1 552
19 TraesCS5A01G007000 chr6B 206418056 206418607 551 False 942.0 942 97.4730 1944 2495 1 chr6B.!!$F1 551
20 TraesCS5A01G007000 chr6B 206424884 206425435 551 False 920.0 920 96.7570 1943 2495 1 chr6B.!!$F2 552
21 TraesCS5A01G007000 chr6B 660468260 660468814 554 False 920.0 920 96.5830 1941 2495 1 chr6B.!!$F3 554
22 TraesCS5A01G007000 chr6B 52017506 52018056 550 True 918.0 918 96.7510 1944 2495 1 chr6B.!!$R1 551
23 TraesCS5A01G007000 chr7A 705789303 705789853 550 False 929.0 929 97.1010 1944 2495 1 chr7A.!!$F1 551
24 TraesCS5A01G007000 chr5B 7382309 7383467 1158 True 808.0 808 79.9150 804 1940 1 chr5B.!!$R3 1136
25 TraesCS5A01G007000 chr5B 7148302 7149424 1122 True 761.0 761 79.5030 805 1940 1 chr5B.!!$R1 1135
26 TraesCS5A01G007000 chr5B 7184038 7185793 1755 True 558.5 756 78.7255 199 1940 2 chr5B.!!$R5 1741
27 TraesCS5A01G007000 chr5B 7354658 7356471 1813 True 489.0 652 81.0180 354 1770 2 chr5B.!!$R6 1416
28 TraesCS5A01G007000 chr5B 7304914 7305534 620 True 342.0 342 77.3790 199 818 1 chr5B.!!$R2 619

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
181 182 0.033504 GGACAGACAAGTCGCTCCAA 59.966 55.0 11.91 0.0 39.42 3.53 F
183 184 0.034059 ACAGACAAGTCGCTCCAAGG 59.966 55.0 0.00 0.0 34.09 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1463 1943 0.317603 CTGTGTTGTTGCTGCTGCTC 60.318 55.000 17.00 10.19 40.48 4.26 R
1935 2473 1.004277 ACGTTCCCCAACAGCATATGT 59.996 47.619 4.29 0.00 46.97 2.29 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
17 18 4.272100 TGAGTTTTAGTCGCGCCC 57.728 55.556 0.00 0.00 0.00 6.13
18 19 1.669440 TGAGTTTTAGTCGCGCCCT 59.331 52.632 0.00 1.62 0.00 5.19
19 20 0.669318 TGAGTTTTAGTCGCGCCCTG 60.669 55.000 0.00 0.00 0.00 4.45
20 21 0.389426 GAGTTTTAGTCGCGCCCTGA 60.389 55.000 0.00 0.00 0.00 3.86
21 22 0.389948 AGTTTTAGTCGCGCCCTGAG 60.390 55.000 0.00 0.00 0.00 3.35
22 23 0.389426 GTTTTAGTCGCGCCCTGAGA 60.389 55.000 0.00 0.00 0.00 3.27
23 24 0.535335 TTTTAGTCGCGCCCTGAGAT 59.465 50.000 0.00 0.00 0.00 2.75
24 25 0.535335 TTTAGTCGCGCCCTGAGATT 59.465 50.000 0.00 0.00 0.00 2.40
25 26 0.179111 TTAGTCGCGCCCTGAGATTG 60.179 55.000 0.00 0.00 0.00 2.67
26 27 1.320344 TAGTCGCGCCCTGAGATTGT 61.320 55.000 0.00 0.00 0.00 2.71
27 28 2.125552 TCGCGCCCTGAGATTGTG 60.126 61.111 0.00 0.00 0.00 3.33
28 29 2.434884 CGCGCCCTGAGATTGTGT 60.435 61.111 0.00 0.00 0.00 3.72
29 30 2.034879 CGCGCCCTGAGATTGTGTT 61.035 57.895 0.00 0.00 0.00 3.32
30 31 1.503542 GCGCCCTGAGATTGTGTTG 59.496 57.895 0.00 0.00 0.00 3.33
31 32 1.926511 GCGCCCTGAGATTGTGTTGG 61.927 60.000 0.00 0.00 0.00 3.77
32 33 0.606401 CGCCCTGAGATTGTGTTGGT 60.606 55.000 0.00 0.00 0.00 3.67
33 34 1.168714 GCCCTGAGATTGTGTTGGTC 58.831 55.000 0.00 0.00 0.00 4.02
34 35 1.442769 CCCTGAGATTGTGTTGGTCG 58.557 55.000 0.00 0.00 0.00 4.79
35 36 1.270839 CCCTGAGATTGTGTTGGTCGT 60.271 52.381 0.00 0.00 0.00 4.34
36 37 2.069273 CCTGAGATTGTGTTGGTCGTC 58.931 52.381 0.00 0.00 0.00 4.20
37 38 1.721389 CTGAGATTGTGTTGGTCGTCG 59.279 52.381 0.00 0.00 0.00 5.12
38 39 1.067974 TGAGATTGTGTTGGTCGTCGT 59.932 47.619 0.00 0.00 0.00 4.34
39 40 2.132762 GAGATTGTGTTGGTCGTCGTT 58.867 47.619 0.00 0.00 0.00 3.85
40 41 2.542595 GAGATTGTGTTGGTCGTCGTTT 59.457 45.455 0.00 0.00 0.00 3.60
41 42 2.286833 AGATTGTGTTGGTCGTCGTTTG 59.713 45.455 0.00 0.00 0.00 2.93
42 43 1.723220 TTGTGTTGGTCGTCGTTTGA 58.277 45.000 0.00 0.00 0.00 2.69
43 44 1.723220 TGTGTTGGTCGTCGTTTGAA 58.277 45.000 0.00 0.00 0.00 2.69
44 45 2.281517 TGTGTTGGTCGTCGTTTGAAT 58.718 42.857 0.00 0.00 0.00 2.57
45 46 2.031068 TGTGTTGGTCGTCGTTTGAATG 59.969 45.455 0.00 0.00 0.00 2.67
46 47 1.600013 TGTTGGTCGTCGTTTGAATGG 59.400 47.619 0.00 0.00 0.00 3.16
47 48 1.868498 GTTGGTCGTCGTTTGAATGGA 59.132 47.619 0.00 0.00 0.00 3.41
48 49 2.242047 TGGTCGTCGTTTGAATGGAA 57.758 45.000 0.00 0.00 0.00 3.53
49 50 1.868498 TGGTCGTCGTTTGAATGGAAC 59.132 47.619 0.00 0.00 0.00 3.62
50 51 2.140717 GGTCGTCGTTTGAATGGAACT 58.859 47.619 0.00 0.00 0.00 3.01
51 52 2.157085 GGTCGTCGTTTGAATGGAACTC 59.843 50.000 0.00 0.00 0.00 3.01
52 53 2.798283 GTCGTCGTTTGAATGGAACTCA 59.202 45.455 0.00 0.00 0.00 3.41
53 54 3.246699 GTCGTCGTTTGAATGGAACTCAA 59.753 43.478 0.00 0.00 0.00 3.02
54 55 4.062293 TCGTCGTTTGAATGGAACTCAAT 58.938 39.130 0.00 0.00 0.00 2.57
55 56 4.084066 TCGTCGTTTGAATGGAACTCAATG 60.084 41.667 0.00 0.00 0.00 2.82
56 57 4.475944 GTCGTTTGAATGGAACTCAATGG 58.524 43.478 0.00 0.00 0.00 3.16
57 58 4.215399 GTCGTTTGAATGGAACTCAATGGA 59.785 41.667 0.00 0.00 0.00 3.41
58 59 5.009631 TCGTTTGAATGGAACTCAATGGAT 58.990 37.500 0.00 0.00 0.00 3.41
59 60 6.093495 GTCGTTTGAATGGAACTCAATGGATA 59.907 38.462 0.00 0.00 0.00 2.59
60 61 6.316140 TCGTTTGAATGGAACTCAATGGATAG 59.684 38.462 0.00 0.00 0.00 2.08
61 62 6.458751 CGTTTGAATGGAACTCAATGGATAGG 60.459 42.308 0.00 0.00 0.00 2.57
62 63 4.464008 TGAATGGAACTCAATGGATAGGC 58.536 43.478 0.00 0.00 0.00 3.93
63 64 4.166725 TGAATGGAACTCAATGGATAGGCT 59.833 41.667 0.00 0.00 0.00 4.58
64 65 3.565764 TGGAACTCAATGGATAGGCTG 57.434 47.619 0.00 0.00 0.00 4.85
65 66 2.846206 TGGAACTCAATGGATAGGCTGT 59.154 45.455 0.00 0.00 0.00 4.40
66 67 3.118261 TGGAACTCAATGGATAGGCTGTC 60.118 47.826 2.15 2.15 0.00 3.51
67 68 2.898729 ACTCAATGGATAGGCTGTCG 57.101 50.000 5.11 0.00 0.00 4.35
68 69 2.388735 ACTCAATGGATAGGCTGTCGA 58.611 47.619 5.11 1.42 0.00 4.20
69 70 2.766263 ACTCAATGGATAGGCTGTCGAA 59.234 45.455 5.11 0.00 0.00 3.71
70 71 3.197766 ACTCAATGGATAGGCTGTCGAAA 59.802 43.478 5.11 0.00 0.00 3.46
71 72 3.797039 TCAATGGATAGGCTGTCGAAAG 58.203 45.455 5.11 0.00 0.00 2.62
72 73 2.874701 CAATGGATAGGCTGTCGAAAGG 59.125 50.000 4.40 0.00 0.00 3.11
73 74 1.568504 TGGATAGGCTGTCGAAAGGT 58.431 50.000 4.40 0.00 0.00 3.50
74 75 2.742348 TGGATAGGCTGTCGAAAGGTA 58.258 47.619 4.40 0.00 0.00 3.08
75 76 2.429610 TGGATAGGCTGTCGAAAGGTAC 59.570 50.000 4.40 0.00 0.00 3.34
77 78 3.243468 GGATAGGCTGTCGAAAGGTACTC 60.243 52.174 4.40 0.00 38.49 2.59
78 79 0.896226 AGGCTGTCGAAAGGTACTCC 59.104 55.000 4.40 0.00 38.49 3.85
79 80 0.458025 GGCTGTCGAAAGGTACTCCG 60.458 60.000 4.40 0.00 38.49 4.63
80 81 0.458025 GCTGTCGAAAGGTACTCCGG 60.458 60.000 4.40 0.00 38.49 5.14
81 82 0.886563 CTGTCGAAAGGTACTCCGGT 59.113 55.000 0.00 0.00 38.49 5.28
82 83 1.271656 CTGTCGAAAGGTACTCCGGTT 59.728 52.381 0.00 0.00 38.49 4.44
83 84 1.270550 TGTCGAAAGGTACTCCGGTTC 59.729 52.381 0.00 0.00 38.49 3.62
84 85 0.890683 TCGAAAGGTACTCCGGTTCC 59.109 55.000 0.00 0.00 38.49 3.62
85 86 0.893447 CGAAAGGTACTCCGGTTCCT 59.107 55.000 0.00 2.39 43.59 3.36
88 89 1.725803 AAGGTACTCCGGTTCCTTGT 58.274 50.000 16.52 5.31 46.61 3.16
89 90 0.974383 AGGTACTCCGGTTCCTTGTG 59.026 55.000 0.00 0.00 39.69 3.33
90 91 0.971386 GGTACTCCGGTTCCTTGTGA 59.029 55.000 0.00 0.00 31.36 3.58
91 92 1.345415 GGTACTCCGGTTCCTTGTGAA 59.655 52.381 0.00 0.00 31.36 3.18
92 93 2.224354 GGTACTCCGGTTCCTTGTGAAA 60.224 50.000 0.00 0.00 33.94 2.69
93 94 2.721425 ACTCCGGTTCCTTGTGAAAA 57.279 45.000 0.00 0.00 33.94 2.29
94 95 2.572290 ACTCCGGTTCCTTGTGAAAAG 58.428 47.619 0.00 0.00 33.94 2.27
95 96 2.171870 ACTCCGGTTCCTTGTGAAAAGA 59.828 45.455 0.00 0.00 33.94 2.52
96 97 3.181443 ACTCCGGTTCCTTGTGAAAAGAT 60.181 43.478 0.00 0.00 33.94 2.40
97 98 3.821033 CTCCGGTTCCTTGTGAAAAGATT 59.179 43.478 0.00 0.00 33.94 2.40
98 99 3.568007 TCCGGTTCCTTGTGAAAAGATTG 59.432 43.478 0.00 0.00 33.94 2.67
99 100 3.568007 CCGGTTCCTTGTGAAAAGATTGA 59.432 43.478 0.00 0.00 33.94 2.57
100 101 4.537015 CGGTTCCTTGTGAAAAGATTGAC 58.463 43.478 0.00 0.00 33.94 3.18
101 102 4.036262 CGGTTCCTTGTGAAAAGATTGACA 59.964 41.667 0.00 0.00 33.94 3.58
102 103 5.449862 CGGTTCCTTGTGAAAAGATTGACAA 60.450 40.000 0.00 0.00 39.79 3.18
109 110 6.609237 TGTGAAAAGATTGACAAGAGTCTG 57.391 37.500 0.00 0.00 45.20 3.51
110 111 6.115446 TGTGAAAAGATTGACAAGAGTCTGT 58.885 36.000 0.00 0.00 45.20 3.41
111 112 6.599244 TGTGAAAAGATTGACAAGAGTCTGTT 59.401 34.615 0.00 0.00 45.20 3.16
112 113 7.121168 TGTGAAAAGATTGACAAGAGTCTGTTT 59.879 33.333 0.00 0.00 45.20 2.83
113 114 7.430502 GTGAAAAGATTGACAAGAGTCTGTTTG 59.569 37.037 0.00 0.00 45.20 2.93
114 115 5.429957 AAGATTGACAAGAGTCTGTTTGC 57.570 39.130 0.00 0.00 45.20 3.68
115 116 4.454678 AGATTGACAAGAGTCTGTTTGCA 58.545 39.130 0.00 0.00 45.20 4.08
116 117 4.514441 AGATTGACAAGAGTCTGTTTGCAG 59.486 41.667 0.00 0.00 45.20 4.41
117 118 3.266510 TGACAAGAGTCTGTTTGCAGT 57.733 42.857 0.00 0.00 45.20 4.40
118 119 2.938451 TGACAAGAGTCTGTTTGCAGTG 59.062 45.455 0.00 0.00 45.20 3.66
119 120 2.939103 GACAAGAGTCTGTTTGCAGTGT 59.061 45.455 0.00 0.00 43.05 3.55
120 121 2.679837 ACAAGAGTCTGTTTGCAGTGTG 59.320 45.455 0.00 0.00 43.05 3.82
121 122 1.303309 AGAGTCTGTTTGCAGTGTGC 58.697 50.000 0.00 0.00 45.29 4.57
131 132 3.708195 GCAGTGTGCACCATGATTC 57.292 52.632 15.69 0.00 44.26 2.52
132 133 0.171903 GCAGTGTGCACCATGATTCC 59.828 55.000 15.69 0.00 44.26 3.01
133 134 1.830279 CAGTGTGCACCATGATTCCT 58.170 50.000 15.69 0.00 0.00 3.36
134 135 1.741706 CAGTGTGCACCATGATTCCTC 59.258 52.381 15.69 0.00 0.00 3.71
135 136 1.632409 AGTGTGCACCATGATTCCTCT 59.368 47.619 15.69 0.00 0.00 3.69
136 137 2.040813 AGTGTGCACCATGATTCCTCTT 59.959 45.455 15.69 0.00 0.00 2.85
137 138 2.163010 GTGTGCACCATGATTCCTCTTG 59.837 50.000 15.69 0.00 0.00 3.02
138 139 1.747355 GTGCACCATGATTCCTCTTGG 59.253 52.381 5.22 6.10 46.97 3.61
139 140 1.634973 TGCACCATGATTCCTCTTGGA 59.365 47.619 12.83 0.00 45.35 3.53
152 153 5.762179 TCCTCTTGGAAACAGTATGATGT 57.238 39.130 0.00 0.00 44.54 3.06
153 154 5.734720 TCCTCTTGGAAACAGTATGATGTC 58.265 41.667 0.00 0.00 44.54 3.06
154 155 4.568359 CCTCTTGGAAACAGTATGATGTCG 59.432 45.833 0.00 0.00 44.54 4.35
155 156 5.400066 TCTTGGAAACAGTATGATGTCGA 57.600 39.130 0.00 0.00 44.54 4.20
156 157 5.410924 TCTTGGAAACAGTATGATGTCGAG 58.589 41.667 0.00 0.00 44.54 4.04
157 158 4.123497 TGGAAACAGTATGATGTCGAGG 57.877 45.455 0.00 0.00 39.69 4.63
158 159 3.513912 TGGAAACAGTATGATGTCGAGGT 59.486 43.478 0.00 0.00 39.69 3.85
159 160 4.020573 TGGAAACAGTATGATGTCGAGGTT 60.021 41.667 0.00 0.00 39.69 3.50
160 161 4.567159 GGAAACAGTATGATGTCGAGGTTC 59.433 45.833 0.00 0.00 39.69 3.62
161 162 5.407407 AAACAGTATGATGTCGAGGTTCT 57.593 39.130 0.00 0.00 39.69 3.01
162 163 4.377839 ACAGTATGATGTCGAGGTTCTG 57.622 45.455 0.00 0.00 39.69 3.02
163 164 3.131223 ACAGTATGATGTCGAGGTTCTGG 59.869 47.826 0.00 0.00 39.69 3.86
164 165 3.381590 CAGTATGATGTCGAGGTTCTGGA 59.618 47.826 0.00 0.00 39.69 3.86
165 166 2.969628 ATGATGTCGAGGTTCTGGAC 57.030 50.000 3.63 3.63 39.18 4.02
168 169 3.432262 TGTCGAGGTTCTGGACAGA 57.568 52.632 8.34 0.00 42.52 3.41
169 170 0.959553 TGTCGAGGTTCTGGACAGAC 59.040 55.000 8.34 0.00 42.52 3.51
170 171 0.959553 GTCGAGGTTCTGGACAGACA 59.040 55.000 0.67 0.00 38.70 3.41
171 172 1.340248 GTCGAGGTTCTGGACAGACAA 59.660 52.381 0.67 0.00 38.70 3.18
172 173 1.613925 TCGAGGTTCTGGACAGACAAG 59.386 52.381 0.67 0.00 37.14 3.16
173 174 1.341531 CGAGGTTCTGGACAGACAAGT 59.658 52.381 0.67 0.00 37.14 3.16
174 175 2.608261 CGAGGTTCTGGACAGACAAGTC 60.608 54.545 0.67 0.00 37.14 3.01
175 176 1.341531 AGGTTCTGGACAGACAAGTCG 59.658 52.381 0.67 0.00 39.42 4.18
176 177 1.140816 GTTCTGGACAGACAAGTCGC 58.859 55.000 0.67 0.00 39.42 5.19
177 178 1.040646 TTCTGGACAGACAAGTCGCT 58.959 50.000 0.67 0.00 39.42 4.93
178 179 0.598562 TCTGGACAGACAAGTCGCTC 59.401 55.000 0.00 0.00 39.42 5.03
179 180 0.389166 CTGGACAGACAAGTCGCTCC 60.389 60.000 10.55 10.55 39.42 4.70
180 181 1.112916 TGGACAGACAAGTCGCTCCA 61.113 55.000 14.30 14.30 39.42 3.86
181 182 0.033504 GGACAGACAAGTCGCTCCAA 59.966 55.000 11.91 0.00 39.42 3.53
182 183 1.423395 GACAGACAAGTCGCTCCAAG 58.577 55.000 0.00 0.00 34.09 3.61
183 184 0.034059 ACAGACAAGTCGCTCCAAGG 59.966 55.000 0.00 0.00 34.09 3.61
184 185 0.671781 CAGACAAGTCGCTCCAAGGG 60.672 60.000 0.00 0.00 34.09 3.95
185 186 0.832135 AGACAAGTCGCTCCAAGGGA 60.832 55.000 0.00 0.00 34.60 4.20
217 219 1.228583 TCTCCCACTCGCTGTGTCT 60.229 57.895 7.42 0.00 44.81 3.41
218 220 1.080230 CTCCCACTCGCTGTGTCTG 60.080 63.158 7.42 0.00 44.81 3.51
223 225 3.177920 CTCGCTGTGTCTGCTCGC 61.178 66.667 0.00 0.00 0.00 5.03
227 229 2.050077 CTGTGTCTGCTCGCGTCA 60.050 61.111 5.77 4.72 0.00 4.35
231 233 1.153958 TGTCTGCTCGCGTCATCAG 60.154 57.895 5.77 9.45 0.00 2.90
261 263 1.968017 AGACAGGCGCACATTGTGG 60.968 57.895 18.05 9.43 33.64 4.17
270 272 0.324645 GCACATTGTGGGAAGGGGAT 60.325 55.000 18.05 0.00 33.64 3.85
272 274 1.005805 CACATTGTGGGAAGGGGATGA 59.994 52.381 9.00 0.00 0.00 2.92
277 286 1.715931 TGTGGGAAGGGGATGATGTTT 59.284 47.619 0.00 0.00 0.00 2.83
279 288 1.715931 TGGGAAGGGGATGATGTTTGT 59.284 47.619 0.00 0.00 0.00 2.83
282 291 2.618045 GGAAGGGGATGATGTTTGTCGT 60.618 50.000 0.00 0.00 0.00 4.34
335 344 1.883926 GGAAGCTCCGCCTAACAAAAA 59.116 47.619 0.00 0.00 0.00 1.94
340 349 4.076394 AGCTCCGCCTAACAAAAATTACA 58.924 39.130 0.00 0.00 0.00 2.41
342 351 5.034797 GCTCCGCCTAACAAAAATTACATC 58.965 41.667 0.00 0.00 0.00 3.06
343 352 5.570234 TCCGCCTAACAAAAATTACATCC 57.430 39.130 0.00 0.00 0.00 3.51
344 353 5.010933 TCCGCCTAACAAAAATTACATCCA 58.989 37.500 0.00 0.00 0.00 3.41
345 354 5.477291 TCCGCCTAACAAAAATTACATCCAA 59.523 36.000 0.00 0.00 0.00 3.53
352 365 6.112927 ACAAAAATTACATCCAACCAGCAT 57.887 33.333 0.00 0.00 0.00 3.79
362 375 3.992643 TCCAACCAGCATGACATTTTTG 58.007 40.909 0.00 0.00 39.69 2.44
364 377 3.132160 CAACCAGCATGACATTTTTGCA 58.868 40.909 0.00 0.00 39.69 4.08
485 523 8.657074 TCAAGTACCTGGATATAAAATGTTCG 57.343 34.615 0.00 0.00 0.00 3.95
554 592 9.001542 CATCCCATTTTTAAAACATGTTCATGT 57.998 29.630 12.39 11.97 36.10 3.21
556 594 7.989741 TCCCATTTTTAAAACATGTTCATGTGT 59.010 29.630 12.39 10.50 34.56 3.72
567 607 9.950680 AAACATGTTCATGTGTAGAAAACTAAG 57.049 29.630 12.39 0.00 34.56 2.18
570 610 9.817365 CATGTTCATGTGTAGAAAACTAAGAAG 57.183 33.333 4.80 0.00 0.00 2.85
658 716 8.131731 GCCATCAGTCTTAGTGGATTTTAAATC 58.868 37.037 9.03 9.03 33.53 2.17
780 858 5.345741 GCCTTAAACATAATATTGCCATGCG 59.654 40.000 0.00 0.00 0.00 4.73
781 859 6.676950 CCTTAAACATAATATTGCCATGCGA 58.323 36.000 0.00 0.00 0.00 5.10
784 862 5.710513 AACATAATATTGCCATGCGACAT 57.289 34.783 0.00 0.00 0.00 3.06
839 947 3.009143 AGAGGGGGCACTAAAGTAACTTG 59.991 47.826 0.00 0.00 0.00 3.16
846 954 4.083484 GGCACTAAAGTAACTTGCACGATT 60.083 41.667 0.00 0.00 34.76 3.34
853 961 5.095691 AGTAACTTGCACGATTTGACAAG 57.904 39.130 0.00 0.00 41.42 3.16
858 967 1.612950 TGCACGATTTGACAAGGCATT 59.387 42.857 0.00 0.00 0.00 3.56
905 1019 5.316167 TGAACCATGCATCTTTAGAAGTGT 58.684 37.500 0.00 0.00 0.00 3.55
943 1057 6.065374 TGTTTAGACAAGCCATAACTCCAAA 58.935 36.000 0.00 0.00 31.49 3.28
949 1063 6.375455 AGACAAGCCATAACTCCAAACATTAG 59.625 38.462 0.00 0.00 0.00 1.73
952 1066 7.120726 ACAAGCCATAACTCCAAACATTAGTAC 59.879 37.037 0.00 0.00 0.00 2.73
955 1069 8.545472 AGCCATAACTCCAAACATTAGTACTTA 58.455 33.333 0.00 0.00 0.00 2.24
956 1070 9.169592 GCCATAACTCCAAACATTAGTACTTAA 57.830 33.333 0.00 0.00 0.00 1.85
959 1073 9.901172 ATAACTCCAAACATTAGTACTTAAGGG 57.099 33.333 7.53 0.00 0.00 3.95
961 1075 7.621796 ACTCCAAACATTAGTACTTAAGGGAG 58.378 38.462 7.53 11.10 42.02 4.30
962 1076 6.954232 TCCAAACATTAGTACTTAAGGGAGG 58.046 40.000 7.53 0.00 0.00 4.30
963 1077 6.731919 TCCAAACATTAGTACTTAAGGGAGGA 59.268 38.462 7.53 0.00 0.00 3.71
964 1078 7.238096 TCCAAACATTAGTACTTAAGGGAGGAA 59.762 37.037 7.53 0.00 0.00 3.36
965 1079 7.336176 CCAAACATTAGTACTTAAGGGAGGAAC 59.664 40.741 7.53 0.00 0.00 3.62
979 1093 2.887152 GGAGGAACCATACATCAATGCC 59.113 50.000 0.00 0.00 38.79 4.40
986 1100 4.603131 ACCATACATCAATGCCAAGAAGT 58.397 39.130 0.00 0.00 0.00 3.01
1058 1522 3.502211 CACTCATCAACCCCACTTACAAC 59.498 47.826 0.00 0.00 0.00 3.32
1070 1534 3.135994 CACTTACAACAGTACCACCCAC 58.864 50.000 0.00 0.00 0.00 4.61
1116 1580 2.885135 TGACCAAGCACATGAGGAAT 57.115 45.000 0.00 0.00 0.00 3.01
1332 1803 3.056607 GCAACATGATGGCCAAAGTAAGT 60.057 43.478 10.96 0.64 0.00 2.24
1366 1837 4.098894 ACCCCCTTGTTATAAAGACGAGA 58.901 43.478 0.00 0.00 31.41 4.04
1407 1884 8.067751 TCTGCTGTAAGATAGATAAGTTGTGT 57.932 34.615 0.00 0.00 34.07 3.72
1482 1962 0.317603 GAGCAGCAGCAACAACACAG 60.318 55.000 3.17 0.00 45.49 3.66
1483 1963 1.947642 GCAGCAGCAACAACACAGC 60.948 57.895 0.00 0.00 41.58 4.40
1490 1986 2.613595 CAGCAACAACACAGCAGTTCTA 59.386 45.455 0.00 0.00 0.00 2.10
1494 1990 5.530915 AGCAACAACACAGCAGTTCTATTAA 59.469 36.000 0.00 0.00 0.00 1.40
1498 1994 6.525629 ACAACACAGCAGTTCTATTAACTCT 58.474 36.000 0.00 0.00 0.00 3.24
1507 2003 9.825109 AGCAGTTCTATTAACTCTCCTATTTTC 57.175 33.333 0.00 0.00 0.00 2.29
1528 2024 6.925610 TTCGATGGATAAATCTCAACCTTG 57.074 37.500 0.00 0.00 0.00 3.61
1556 2052 9.643693 GGTTCTCAAAATAATGATGTGTTGATT 57.356 29.630 0.00 0.00 0.00 2.57
1665 2167 6.998673 GGCTAGATTTGTCACCTACCATTTAT 59.001 38.462 0.00 0.00 0.00 1.40
1667 2169 9.555727 GCTAGATTTGTCACCTACCATTTATAA 57.444 33.333 0.00 0.00 0.00 0.98
1707 2212 8.519526 GTTTATGTCCATGTTTTGATTGTCCTA 58.480 33.333 0.00 0.00 0.00 2.94
1714 2219 6.316390 CCATGTTTTGATTGTCCTACTAGGTC 59.684 42.308 1.83 0.00 36.53 3.85
1726 2231 4.652881 TCCTACTAGGTCTACTGATCGTGA 59.347 45.833 1.83 0.00 36.53 4.35
1739 2244 4.590647 ACTGATCGTGAACCTATGATGGAT 59.409 41.667 0.00 0.00 0.00 3.41
1741 2246 6.025749 TGATCGTGAACCTATGATGGATAC 57.974 41.667 0.00 0.00 0.00 2.24
1742 2247 5.775195 TGATCGTGAACCTATGATGGATACT 59.225 40.000 0.00 0.00 37.61 2.12
1776 2314 6.424883 TCGACTTTAATCTCCCTCTCTACTT 58.575 40.000 0.00 0.00 0.00 2.24
1821 2359 8.744568 TCACATACTTATTGTTGCATTGGATA 57.255 30.769 0.00 0.00 0.00 2.59
1829 2367 2.746904 TGTTGCATTGGATAGGTGAACG 59.253 45.455 0.00 0.00 0.00 3.95
1839 2377 4.457603 TGGATAGGTGAACGACAATTTTGG 59.542 41.667 0.00 0.00 0.00 3.28
1842 2380 6.127730 GGATAGGTGAACGACAATTTTGGAAT 60.128 38.462 0.00 0.00 0.00 3.01
1846 2384 6.659242 AGGTGAACGACAATTTTGGAATAGAT 59.341 34.615 0.00 0.00 0.00 1.98
1856 2394 8.316214 ACAATTTTGGAATAGATTGTGAAGCAT 58.684 29.630 0.00 0.00 40.21 3.79
1858 2396 6.455360 TTTGGAATAGATTGTGAAGCATCC 57.545 37.500 0.00 0.00 0.00 3.51
1864 2402 7.229306 GGAATAGATTGTGAAGCATCCAACATA 59.771 37.037 0.00 0.00 0.00 2.29
1872 2410 7.761409 TGTGAAGCATCCAACATAGTAATTTC 58.239 34.615 0.00 0.00 0.00 2.17
1923 2461 8.744652 ACTCTATAGATCAAGCATGGTGTATAC 58.255 37.037 2.11 0.00 29.62 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.669318 CAGGGCGCGACTAAAACTCA 60.669 55.000 13.91 0.00 0.00 3.41
1 2 0.389426 TCAGGGCGCGACTAAAACTC 60.389 55.000 13.91 0.00 0.00 3.01
2 3 0.389948 CTCAGGGCGCGACTAAAACT 60.390 55.000 13.91 0.00 0.00 2.66
3 4 0.389426 TCTCAGGGCGCGACTAAAAC 60.389 55.000 13.91 0.00 0.00 2.43
4 5 0.535335 ATCTCAGGGCGCGACTAAAA 59.465 50.000 13.91 0.00 0.00 1.52
5 6 0.535335 AATCTCAGGGCGCGACTAAA 59.465 50.000 13.91 0.00 0.00 1.85
6 7 0.179111 CAATCTCAGGGCGCGACTAA 60.179 55.000 13.91 0.00 0.00 2.24
7 8 1.320344 ACAATCTCAGGGCGCGACTA 61.320 55.000 13.91 0.00 0.00 2.59
8 9 2.185350 CAATCTCAGGGCGCGACT 59.815 61.111 13.91 4.58 0.00 4.18
9 10 2.125512 ACAATCTCAGGGCGCGAC 60.126 61.111 12.10 6.99 0.00 5.19
10 11 2.125552 CACAATCTCAGGGCGCGA 60.126 61.111 12.10 0.00 0.00 5.87
11 12 2.034879 AACACAATCTCAGGGCGCG 61.035 57.895 0.00 0.00 0.00 6.86
12 13 1.503542 CAACACAATCTCAGGGCGC 59.496 57.895 0.00 0.00 0.00 6.53
13 14 0.606401 ACCAACACAATCTCAGGGCG 60.606 55.000 0.00 0.00 0.00 6.13
14 15 1.168714 GACCAACACAATCTCAGGGC 58.831 55.000 0.00 0.00 0.00 5.19
15 16 1.270839 ACGACCAACACAATCTCAGGG 60.271 52.381 0.00 0.00 0.00 4.45
16 17 2.069273 GACGACCAACACAATCTCAGG 58.931 52.381 0.00 0.00 0.00 3.86
17 18 1.721389 CGACGACCAACACAATCTCAG 59.279 52.381 0.00 0.00 0.00 3.35
18 19 1.067974 ACGACGACCAACACAATCTCA 59.932 47.619 0.00 0.00 0.00 3.27
19 20 1.779569 ACGACGACCAACACAATCTC 58.220 50.000 0.00 0.00 0.00 2.75
20 21 2.234300 AACGACGACCAACACAATCT 57.766 45.000 0.00 0.00 0.00 2.40
21 22 2.285756 TCAAACGACGACCAACACAATC 59.714 45.455 0.00 0.00 0.00 2.67
22 23 2.281517 TCAAACGACGACCAACACAAT 58.718 42.857 0.00 0.00 0.00 2.71
23 24 1.723220 TCAAACGACGACCAACACAA 58.277 45.000 0.00 0.00 0.00 3.33
24 25 1.723220 TTCAAACGACGACCAACACA 58.277 45.000 0.00 0.00 0.00 3.72
25 26 2.601266 CCATTCAAACGACGACCAACAC 60.601 50.000 0.00 0.00 0.00 3.32
26 27 1.600013 CCATTCAAACGACGACCAACA 59.400 47.619 0.00 0.00 0.00 3.33
27 28 1.868498 TCCATTCAAACGACGACCAAC 59.132 47.619 0.00 0.00 0.00 3.77
28 29 2.242047 TCCATTCAAACGACGACCAA 57.758 45.000 0.00 0.00 0.00 3.67
29 30 1.868498 GTTCCATTCAAACGACGACCA 59.132 47.619 0.00 0.00 0.00 4.02
30 31 2.140717 AGTTCCATTCAAACGACGACC 58.859 47.619 0.00 0.00 0.00 4.79
31 32 2.798283 TGAGTTCCATTCAAACGACGAC 59.202 45.455 0.00 0.00 0.00 4.34
32 33 3.100658 TGAGTTCCATTCAAACGACGA 57.899 42.857 0.00 0.00 0.00 4.20
33 34 3.870723 TTGAGTTCCATTCAAACGACG 57.129 42.857 0.00 0.00 31.98 5.12
34 35 4.215399 TCCATTGAGTTCCATTCAAACGAC 59.785 41.667 0.00 0.00 38.01 4.34
35 36 4.393834 TCCATTGAGTTCCATTCAAACGA 58.606 39.130 0.00 0.00 38.01 3.85
36 37 4.764679 TCCATTGAGTTCCATTCAAACG 57.235 40.909 0.00 0.00 38.01 3.60
37 38 6.681368 GCCTATCCATTGAGTTCCATTCAAAC 60.681 42.308 0.00 0.00 38.01 2.93
38 39 5.360714 GCCTATCCATTGAGTTCCATTCAAA 59.639 40.000 0.00 0.00 38.01 2.69
39 40 4.889409 GCCTATCCATTGAGTTCCATTCAA 59.111 41.667 0.00 0.00 38.76 2.69
40 41 4.166725 AGCCTATCCATTGAGTTCCATTCA 59.833 41.667 0.00 0.00 0.00 2.57
41 42 4.518211 CAGCCTATCCATTGAGTTCCATTC 59.482 45.833 0.00 0.00 0.00 2.67
42 43 4.079558 ACAGCCTATCCATTGAGTTCCATT 60.080 41.667 0.00 0.00 0.00 3.16
43 44 3.461085 ACAGCCTATCCATTGAGTTCCAT 59.539 43.478 0.00 0.00 0.00 3.41
44 45 2.846206 ACAGCCTATCCATTGAGTTCCA 59.154 45.455 0.00 0.00 0.00 3.53
45 46 3.471680 GACAGCCTATCCATTGAGTTCC 58.528 50.000 0.00 0.00 0.00 3.62
46 47 3.126831 CGACAGCCTATCCATTGAGTTC 58.873 50.000 0.00 0.00 0.00 3.01
47 48 2.766263 TCGACAGCCTATCCATTGAGTT 59.234 45.455 0.00 0.00 0.00 3.01
48 49 2.388735 TCGACAGCCTATCCATTGAGT 58.611 47.619 0.00 0.00 0.00 3.41
49 50 3.459232 TTCGACAGCCTATCCATTGAG 57.541 47.619 0.00 0.00 0.00 3.02
50 51 3.432186 CCTTTCGACAGCCTATCCATTGA 60.432 47.826 0.00 0.00 0.00 2.57
51 52 2.874701 CCTTTCGACAGCCTATCCATTG 59.125 50.000 0.00 0.00 0.00 2.82
52 53 2.505819 ACCTTTCGACAGCCTATCCATT 59.494 45.455 0.00 0.00 0.00 3.16
53 54 2.119495 ACCTTTCGACAGCCTATCCAT 58.881 47.619 0.00 0.00 0.00 3.41
54 55 1.568504 ACCTTTCGACAGCCTATCCA 58.431 50.000 0.00 0.00 0.00 3.41
55 56 2.694109 AGTACCTTTCGACAGCCTATCC 59.306 50.000 0.00 0.00 0.00 2.59
56 57 3.243468 GGAGTACCTTTCGACAGCCTATC 60.243 52.174 0.00 0.00 0.00 2.08
57 58 2.694109 GGAGTACCTTTCGACAGCCTAT 59.306 50.000 0.00 0.00 0.00 2.57
58 59 2.097825 GGAGTACCTTTCGACAGCCTA 58.902 52.381 0.00 0.00 0.00 3.93
59 60 0.896226 GGAGTACCTTTCGACAGCCT 59.104 55.000 0.00 0.00 0.00 4.58
60 61 0.458025 CGGAGTACCTTTCGACAGCC 60.458 60.000 0.00 0.00 0.00 4.85
61 62 0.458025 CCGGAGTACCTTTCGACAGC 60.458 60.000 0.00 0.00 0.00 4.40
62 63 0.886563 ACCGGAGTACCTTTCGACAG 59.113 55.000 9.46 0.00 0.00 3.51
63 64 1.270550 GAACCGGAGTACCTTTCGACA 59.729 52.381 9.46 0.00 0.00 4.35
64 65 1.403382 GGAACCGGAGTACCTTTCGAC 60.403 57.143 9.46 0.00 30.99 4.20
65 66 0.890683 GGAACCGGAGTACCTTTCGA 59.109 55.000 9.46 0.00 30.99 3.71
66 67 0.893447 AGGAACCGGAGTACCTTTCG 59.107 55.000 9.46 0.00 30.99 3.46
67 68 2.038164 ACAAGGAACCGGAGTACCTTTC 59.962 50.000 9.46 0.00 40.21 2.62
68 69 2.052468 ACAAGGAACCGGAGTACCTTT 58.948 47.619 9.46 5.72 40.21 3.11
69 70 1.346722 CACAAGGAACCGGAGTACCTT 59.653 52.381 9.46 13.94 42.49 3.50
70 71 0.974383 CACAAGGAACCGGAGTACCT 59.026 55.000 9.46 8.11 0.00 3.08
71 72 0.971386 TCACAAGGAACCGGAGTACC 59.029 55.000 9.46 5.61 0.00 3.34
72 73 2.825861 TTCACAAGGAACCGGAGTAC 57.174 50.000 9.46 0.00 0.00 2.73
73 74 3.388676 TCTTTTCACAAGGAACCGGAGTA 59.611 43.478 9.46 0.00 34.56 2.59
74 75 2.171870 TCTTTTCACAAGGAACCGGAGT 59.828 45.455 9.46 0.00 34.56 3.85
75 76 2.846193 TCTTTTCACAAGGAACCGGAG 58.154 47.619 9.46 0.00 34.56 4.63
76 77 3.502123 ATCTTTTCACAAGGAACCGGA 57.498 42.857 9.46 0.00 34.56 5.14
77 78 3.568007 TCAATCTTTTCACAAGGAACCGG 59.432 43.478 0.00 0.00 34.56 5.28
78 79 4.036262 TGTCAATCTTTTCACAAGGAACCG 59.964 41.667 0.00 0.00 34.56 4.44
79 80 5.514274 TGTCAATCTTTTCACAAGGAACC 57.486 39.130 0.00 0.00 34.56 3.62
80 81 6.795399 TCTTGTCAATCTTTTCACAAGGAAC 58.205 36.000 10.03 0.00 43.94 3.62
81 82 6.603201 ACTCTTGTCAATCTTTTCACAAGGAA 59.397 34.615 10.03 0.00 43.94 3.36
82 83 6.122277 ACTCTTGTCAATCTTTTCACAAGGA 58.878 36.000 10.03 0.00 43.94 3.36
83 84 6.261826 AGACTCTTGTCAATCTTTTCACAAGG 59.738 38.462 10.03 4.83 43.94 3.61
84 85 7.130917 CAGACTCTTGTCAATCTTTTCACAAG 58.869 38.462 4.59 4.59 45.20 3.16
85 86 6.599244 ACAGACTCTTGTCAATCTTTTCACAA 59.401 34.615 0.00 0.00 45.20 3.33
86 87 6.115446 ACAGACTCTTGTCAATCTTTTCACA 58.885 36.000 0.00 0.00 45.20 3.58
87 88 6.610741 ACAGACTCTTGTCAATCTTTTCAC 57.389 37.500 0.00 0.00 45.20 3.18
88 89 7.475015 CAAACAGACTCTTGTCAATCTTTTCA 58.525 34.615 0.00 0.00 45.20 2.69
89 90 6.416161 GCAAACAGACTCTTGTCAATCTTTTC 59.584 38.462 0.00 0.00 45.20 2.29
90 91 6.127647 TGCAAACAGACTCTTGTCAATCTTTT 60.128 34.615 0.00 0.00 45.20 2.27
91 92 5.357878 TGCAAACAGACTCTTGTCAATCTTT 59.642 36.000 0.00 0.00 45.20 2.52
92 93 4.883585 TGCAAACAGACTCTTGTCAATCTT 59.116 37.500 0.00 0.00 45.20 2.40
93 94 4.454678 TGCAAACAGACTCTTGTCAATCT 58.545 39.130 0.00 0.00 45.20 2.40
94 95 4.818534 TGCAAACAGACTCTTGTCAATC 57.181 40.909 0.00 0.00 45.20 2.67
113 114 0.171903 GGAATCATGGTGCACACTGC 59.828 55.000 20.43 0.95 45.29 4.40
114 115 1.741706 GAGGAATCATGGTGCACACTG 59.258 52.381 20.43 14.89 0.00 3.66
115 116 1.632409 AGAGGAATCATGGTGCACACT 59.368 47.619 20.43 1.25 0.00 3.55
116 117 2.119801 AGAGGAATCATGGTGCACAC 57.880 50.000 20.43 8.79 0.00 3.82
117 118 2.439409 CAAGAGGAATCATGGTGCACA 58.561 47.619 20.43 5.24 0.00 4.57
118 119 1.747355 CCAAGAGGAATCATGGTGCAC 59.253 52.381 8.80 8.80 36.89 4.57
119 120 1.634973 TCCAAGAGGAATCATGGTGCA 59.365 47.619 0.00 0.00 42.23 4.57
120 121 2.425143 TCCAAGAGGAATCATGGTGC 57.575 50.000 0.00 0.00 42.23 5.01
130 131 5.624509 CGACATCATACTGTTTCCAAGAGGA 60.625 44.000 0.00 0.00 43.93 3.71
131 132 4.568359 CGACATCATACTGTTTCCAAGAGG 59.432 45.833 0.00 0.00 0.00 3.69
132 133 5.410924 TCGACATCATACTGTTTCCAAGAG 58.589 41.667 0.00 0.00 0.00 2.85
133 134 5.400066 TCGACATCATACTGTTTCCAAGA 57.600 39.130 0.00 0.00 0.00 3.02
134 135 4.568359 CCTCGACATCATACTGTTTCCAAG 59.432 45.833 0.00 0.00 0.00 3.61
135 136 4.020573 ACCTCGACATCATACTGTTTCCAA 60.021 41.667 0.00 0.00 0.00 3.53
136 137 3.513912 ACCTCGACATCATACTGTTTCCA 59.486 43.478 0.00 0.00 0.00 3.53
137 138 4.124851 ACCTCGACATCATACTGTTTCC 57.875 45.455 0.00 0.00 0.00 3.13
138 139 5.289675 CAGAACCTCGACATCATACTGTTTC 59.710 44.000 0.00 0.00 0.00 2.78
139 140 5.171476 CAGAACCTCGACATCATACTGTTT 58.829 41.667 0.00 0.00 0.00 2.83
140 141 4.382040 CCAGAACCTCGACATCATACTGTT 60.382 45.833 0.00 0.00 0.00 3.16
141 142 3.131223 CCAGAACCTCGACATCATACTGT 59.869 47.826 0.00 0.00 0.00 3.55
142 143 3.381590 TCCAGAACCTCGACATCATACTG 59.618 47.826 0.00 0.00 0.00 2.74
143 144 3.381908 GTCCAGAACCTCGACATCATACT 59.618 47.826 0.00 0.00 0.00 2.12
144 145 3.130516 TGTCCAGAACCTCGACATCATAC 59.869 47.826 0.00 0.00 31.74 2.39
145 146 3.361786 TGTCCAGAACCTCGACATCATA 58.638 45.455 0.00 0.00 31.74 2.15
146 147 2.167281 CTGTCCAGAACCTCGACATCAT 59.833 50.000 0.00 0.00 36.03 2.45
147 148 1.546029 CTGTCCAGAACCTCGACATCA 59.454 52.381 0.00 0.00 36.03 3.07
148 149 1.819288 TCTGTCCAGAACCTCGACATC 59.181 52.381 0.00 0.00 36.03 3.06
149 150 1.546476 GTCTGTCCAGAACCTCGACAT 59.454 52.381 0.00 0.00 39.48 3.06
150 151 0.959553 GTCTGTCCAGAACCTCGACA 59.040 55.000 0.00 0.00 39.48 4.35
151 152 0.959553 TGTCTGTCCAGAACCTCGAC 59.040 55.000 0.00 0.00 39.48 4.20
152 153 1.613925 CTTGTCTGTCCAGAACCTCGA 59.386 52.381 0.00 0.00 39.48 4.04
153 154 1.341531 ACTTGTCTGTCCAGAACCTCG 59.658 52.381 0.00 0.00 39.48 4.63
154 155 2.608261 CGACTTGTCTGTCCAGAACCTC 60.608 54.545 0.00 0.00 39.48 3.85
155 156 1.341531 CGACTTGTCTGTCCAGAACCT 59.658 52.381 0.00 0.00 39.48 3.50
156 157 1.784525 CGACTTGTCTGTCCAGAACC 58.215 55.000 0.00 0.00 39.48 3.62
157 158 1.140816 GCGACTTGTCTGTCCAGAAC 58.859 55.000 0.00 0.00 39.48 3.01
158 159 1.000163 GAGCGACTTGTCTGTCCAGAA 60.000 52.381 0.00 0.00 39.48 3.02
159 160 0.598562 GAGCGACTTGTCTGTCCAGA 59.401 55.000 0.00 0.00 33.70 3.86
160 161 0.389166 GGAGCGACTTGTCTGTCCAG 60.389 60.000 11.19 0.00 33.70 3.86
161 162 1.112916 TGGAGCGACTTGTCTGTCCA 61.113 55.000 13.53 13.53 33.70 4.02
162 163 0.033504 TTGGAGCGACTTGTCTGTCC 59.966 55.000 9.84 9.84 33.70 4.02
163 164 1.423395 CTTGGAGCGACTTGTCTGTC 58.577 55.000 0.00 0.00 0.00 3.51
164 165 0.034059 CCTTGGAGCGACTTGTCTGT 59.966 55.000 0.00 0.00 0.00 3.41
165 166 0.671781 CCCTTGGAGCGACTTGTCTG 60.672 60.000 0.00 0.00 0.00 3.51
166 167 0.832135 TCCCTTGGAGCGACTTGTCT 60.832 55.000 0.00 0.00 0.00 3.41
167 168 0.390472 CTCCCTTGGAGCGACTTGTC 60.390 60.000 0.00 0.00 43.29 3.18
168 169 1.674057 CTCCCTTGGAGCGACTTGT 59.326 57.895 0.00 0.00 43.29 3.16
169 170 4.606071 CTCCCTTGGAGCGACTTG 57.394 61.111 0.00 0.00 43.29 3.16
190 191 4.479993 AGTGGGAGAGCATGCGGC 62.480 66.667 13.01 8.84 45.30 6.53
191 192 2.202987 GAGTGGGAGAGCATGCGG 60.203 66.667 13.01 0.00 0.00 5.69
195 196 1.986757 ACAGCGAGTGGGAGAGCAT 60.987 57.895 0.00 0.00 0.00 3.79
197 198 2.125753 CACAGCGAGTGGGAGAGC 60.126 66.667 4.63 0.00 44.69 4.09
217 219 2.125952 CCACTGATGACGCGAGCA 60.126 61.111 15.93 11.47 0.00 4.26
218 220 2.887568 CCCACTGATGACGCGAGC 60.888 66.667 15.93 4.68 0.00 5.03
245 247 2.974692 TTCCCACAATGTGCGCCTGT 62.975 55.000 8.05 0.00 31.34 4.00
261 263 2.017049 CGACAAACATCATCCCCTTCC 58.983 52.381 0.00 0.00 0.00 3.46
270 272 3.325870 CTGCTCCTTACGACAAACATCA 58.674 45.455 0.00 0.00 0.00 3.07
272 274 2.076863 GCTGCTCCTTACGACAAACAT 58.923 47.619 0.00 0.00 0.00 2.71
277 286 1.100510 ATACGCTGCTCCTTACGACA 58.899 50.000 0.00 0.00 0.00 4.35
279 288 1.878088 CCTATACGCTGCTCCTTACGA 59.122 52.381 0.00 0.00 0.00 3.43
282 291 2.158505 ACTCCCTATACGCTGCTCCTTA 60.159 50.000 0.00 0.00 0.00 2.69
335 344 3.966979 TGTCATGCTGGTTGGATGTAAT 58.033 40.909 0.00 0.00 43.72 1.89
340 349 4.571919 CAAAAATGTCATGCTGGTTGGAT 58.428 39.130 0.00 0.00 0.00 3.41
342 351 2.481185 GCAAAAATGTCATGCTGGTTGG 59.519 45.455 0.00 0.00 37.12 3.77
343 352 3.132160 TGCAAAAATGTCATGCTGGTTG 58.868 40.909 0.00 0.00 40.66 3.77
344 353 3.472283 TGCAAAAATGTCATGCTGGTT 57.528 38.095 0.00 0.00 40.66 3.67
345 354 3.472283 TTGCAAAAATGTCATGCTGGT 57.528 38.095 0.00 0.00 40.66 4.00
620 676 4.521146 AGACTGATGGCTTAACATTGGAG 58.479 43.478 0.00 0.00 0.00 3.86
634 691 9.401058 AGGATTTAAAATCCACTAAGACTGATG 57.599 33.333 1.58 0.00 40.61 3.07
795 873 6.283694 TCTAGAATTGCTCGCTTGTAATGAT 58.716 36.000 0.00 0.00 0.00 2.45
796 874 5.660460 TCTAGAATTGCTCGCTTGTAATGA 58.340 37.500 0.00 0.00 0.00 2.57
809 917 0.548510 AGTGCCCCCTCTAGAATTGC 59.451 55.000 0.00 0.00 0.00 3.56
839 947 2.352503 AATGCCTTGTCAAATCGTGC 57.647 45.000 0.00 0.00 0.00 5.34
869 980 3.181506 GCATGGTTCATTCCTCGAGTTTC 60.182 47.826 12.31 0.00 0.00 2.78
873 984 2.028420 TGCATGGTTCATTCCTCGAG 57.972 50.000 5.13 5.13 0.00 4.04
874 985 2.171237 AGATGCATGGTTCATTCCTCGA 59.829 45.455 2.46 0.00 0.00 4.04
876 987 4.996788 AAAGATGCATGGTTCATTCCTC 57.003 40.909 2.46 0.00 0.00 3.71
882 996 5.316167 ACACTTCTAAAGATGCATGGTTCA 58.684 37.500 2.46 0.00 0.00 3.18
919 1033 5.235850 TGGAGTTATGGCTTGTCTAAACA 57.764 39.130 0.00 0.00 0.00 2.83
920 1034 6.016610 TGTTTGGAGTTATGGCTTGTCTAAAC 60.017 38.462 0.00 0.00 38.42 2.01
923 1037 5.235850 TGTTTGGAGTTATGGCTTGTCTA 57.764 39.130 0.00 0.00 0.00 2.59
943 1057 6.027482 TGGTTCCTCCCTTAAGTACTAATGT 58.973 40.000 0.00 0.00 34.77 2.71
949 1063 5.945144 TGTATGGTTCCTCCCTTAAGTAC 57.055 43.478 0.97 0.00 34.77 2.73
952 1066 5.630415 TGATGTATGGTTCCTCCCTTAAG 57.370 43.478 0.00 0.00 34.77 1.85
955 1069 4.796606 CATTGATGTATGGTTCCTCCCTT 58.203 43.478 0.00 0.00 34.77 3.95
956 1070 3.435601 GCATTGATGTATGGTTCCTCCCT 60.436 47.826 0.00 0.00 34.77 4.20
957 1071 2.887152 GCATTGATGTATGGTTCCTCCC 59.113 50.000 0.00 0.00 34.77 4.30
959 1073 3.554934 TGGCATTGATGTATGGTTCCTC 58.445 45.455 0.00 0.00 0.00 3.71
961 1075 3.953612 TCTTGGCATTGATGTATGGTTCC 59.046 43.478 0.00 0.00 0.00 3.62
962 1076 5.126061 ACTTCTTGGCATTGATGTATGGTTC 59.874 40.000 7.44 0.00 0.00 3.62
963 1077 5.018809 ACTTCTTGGCATTGATGTATGGTT 58.981 37.500 7.44 0.00 0.00 3.67
964 1078 4.603131 ACTTCTTGGCATTGATGTATGGT 58.397 39.130 7.44 0.00 0.00 3.55
965 1079 5.587388 AACTTCTTGGCATTGATGTATGG 57.413 39.130 8.97 0.00 0.00 2.74
1011 1474 1.822990 ACCATGAAATGCTTGCTCCAG 59.177 47.619 0.00 0.00 44.97 3.86
1058 1522 4.715297 AGAGGTTATTAGTGGGTGGTACTG 59.285 45.833 0.00 0.00 0.00 2.74
1070 1534 4.469945 TCACCAAGGACCAGAGGTTATTAG 59.530 45.833 0.00 0.00 35.25 1.73
1116 1580 3.423539 AGCAGAAGTCCTTGCACATTA 57.576 42.857 0.00 0.00 0.00 1.90
1285 1750 9.609346 GCTAGTCTTTATGGTTTCACCTAATTA 57.391 33.333 0.00 0.00 39.58 1.40
1286 1751 8.107095 TGCTAGTCTTTATGGTTTCACCTAATT 58.893 33.333 0.00 0.00 39.58 1.40
1332 1803 1.633432 CAAGGGGGTCTGGTTACATGA 59.367 52.381 0.00 0.00 0.00 3.07
1366 1837 3.571401 CAGCAGAATTGTCCAAGGACTTT 59.429 43.478 19.20 12.83 44.80 2.66
1407 1884 2.368439 CATTCTCCGAGATTTGGCCAA 58.632 47.619 16.05 16.05 0.00 4.52
1463 1943 0.317603 CTGTGTTGTTGCTGCTGCTC 60.318 55.000 17.00 10.19 40.48 4.26
1482 1962 8.756864 CGAAAATAGGAGAGTTAATAGAACTGC 58.243 37.037 0.00 0.00 0.00 4.40
1494 1990 8.875168 AGATTTATCCATCGAAAATAGGAGAGT 58.125 33.333 0.00 0.00 32.91 3.24
1498 1994 9.273016 GTTGAGATTTATCCATCGAAAATAGGA 57.727 33.333 0.00 0.00 34.12 2.94
1507 2003 5.008019 CCACAAGGTTGAGATTTATCCATCG 59.992 44.000 0.00 0.00 0.00 3.84
1528 2024 8.081633 TCAACACATCATTATTTTGAGAACCAC 58.918 33.333 0.00 0.00 0.00 4.16
1609 2106 2.285756 CGCAGACAACCGACAAGTTTTA 59.714 45.455 0.00 0.00 0.00 1.52
1670 2172 8.593945 AACATGGACATAAACCAATACTGAAT 57.406 30.769 0.00 0.00 40.93 2.57
1671 2173 8.415950 AAACATGGACATAAACCAATACTGAA 57.584 30.769 0.00 0.00 40.93 3.02
1673 2175 8.303156 TCAAAACATGGACATAAACCAATACTG 58.697 33.333 0.00 0.00 40.93 2.74
1675 2177 9.651913 AATCAAAACATGGACATAAACCAATAC 57.348 29.630 0.00 0.00 40.93 1.89
1680 2182 6.589907 GGACAATCAAAACATGGACATAAACC 59.410 38.462 0.00 0.00 0.00 3.27
1681 2183 7.378181 AGGACAATCAAAACATGGACATAAAC 58.622 34.615 0.00 0.00 0.00 2.01
1693 2196 7.760340 CAGTAGACCTAGTAGGACAATCAAAAC 59.240 40.741 23.50 9.18 37.67 2.43
1707 2212 3.946558 GGTTCACGATCAGTAGACCTAGT 59.053 47.826 0.00 0.00 35.39 2.57
1714 2219 5.241728 TCCATCATAGGTTCACGATCAGTAG 59.758 44.000 0.00 0.00 0.00 2.57
1750 2256 7.747690 AGTAGAGAGGGAGATTAAAGTCGATA 58.252 38.462 0.00 0.00 0.00 2.92
1753 2262 6.095720 ACAAGTAGAGAGGGAGATTAAAGTCG 59.904 42.308 0.00 0.00 0.00 4.18
1766 2275 9.798994 ATGTTAACGTAATAACAAGTAGAGAGG 57.201 33.333 14.88 0.00 45.85 3.69
1806 2344 4.142403 CGTTCACCTATCCAATGCAACAAT 60.142 41.667 0.00 0.00 0.00 2.71
1821 2359 6.001460 TCTATTCCAAAATTGTCGTTCACCT 58.999 36.000 0.00 0.00 0.00 4.00
1829 2367 7.814107 TGCTTCACAATCTATTCCAAAATTGTC 59.186 33.333 0.00 0.00 39.62 3.18
1839 2377 6.441093 TGTTGGATGCTTCACAATCTATTC 57.559 37.500 1.64 0.00 0.00 1.75
1842 2380 6.653020 ACTATGTTGGATGCTTCACAATCTA 58.347 36.000 1.64 0.84 0.00 1.98
1846 2384 7.701539 AATTACTATGTTGGATGCTTCACAA 57.298 32.000 1.64 1.37 0.00 3.33
1894 2432 5.699915 CACCATGCTTGATCTATAGAGTTGG 59.300 44.000 8.70 9.00 0.00 3.77
1923 2461 9.859427 CCCAACAGCATATGTATTTAAATATGG 57.141 33.333 11.00 9.80 43.00 2.74
1924 2462 9.859427 CCCCAACAGCATATGTATTTAAATATG 57.141 33.333 11.00 7.58 43.00 1.78
1925 2463 9.821240 TCCCCAACAGCATATGTATTTAAATAT 57.179 29.630 11.00 0.37 43.00 1.28
1926 2464 9.647918 TTCCCCAACAGCATATGTATTTAAATA 57.352 29.630 3.71 3.71 43.00 1.40
1927 2465 8.421002 GTTCCCCAACAGCATATGTATTTAAAT 58.579 33.333 5.89 5.89 43.00 1.40
1930 2468 5.529430 CGTTCCCCAACAGCATATGTATTTA 59.471 40.000 4.29 0.00 43.00 1.40
1932 2470 3.882888 CGTTCCCCAACAGCATATGTATT 59.117 43.478 4.29 0.00 43.00 1.89
1935 2473 1.004277 ACGTTCCCCAACAGCATATGT 59.996 47.619 4.29 0.00 46.97 2.29


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

AutoCloner maintained by Alex Coulton.