Multiple sequence alignment - TraesCS7A01G482100

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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 TraesCS7A01G482100 chr7A 100.000 3920 0 0 1 3920 674276187 674272268 0.000000e+00 7239.0
1 TraesCS7A01G482100 chr7A 85.127 1022 114 25 1015 2016 217202654 217203657 0.000000e+00 1011.0
2 TraesCS7A01G482100 chr7A 84.937 956 127 15 1024 1965 85030873 85031825 0.000000e+00 952.0
3 TraesCS7A01G482100 chr7A 85.042 361 42 6 2414 2771 217204277 217204628 1.340000e-94 357.0
4 TraesCS7A01G482100 chr7A 92.166 217 17 0 1024 1240 84854670 84854886 1.370000e-79 307.0
5 TraesCS7A01G482100 chr7A 93.939 99 6 0 2656 2754 85032777 85032875 2.440000e-32 150.0
6 TraesCS7A01G482100 chr7D 91.202 2296 125 33 771 3022 582304217 582301955 0.000000e+00 3049.0
7 TraesCS7A01G482100 chr7D 84.772 985 123 24 1015 1975 205131734 205132715 0.000000e+00 963.0
8 TraesCS7A01G482100 chr7D 88.462 650 72 3 1329 1976 82899312 82899960 0.000000e+00 782.0
9 TraesCS7A01G482100 chr7D 88.889 468 44 6 3013 3479 582301842 582301382 1.580000e-158 569.0
10 TraesCS7A01G482100 chr7D 91.727 411 22 3 3522 3920 582301383 582300973 9.510000e-156 560.0
11 TraesCS7A01G482100 chr7D 78.406 690 115 24 2101 2771 82902025 82902699 6.060000e-113 418.0
12 TraesCS7A01G482100 chr7D 86.479 355 36 9 2414 2764 205133340 205133686 2.860000e-101 379.0
13 TraesCS7A01G482100 chr7D 91.244 217 19 0 1024 1240 82899030 82899246 2.960000e-76 296.0
14 TraesCS7A01G482100 chr7D 89.231 130 14 0 2415 2544 83064833 83064962 3.130000e-36 163.0
15 TraesCS7A01G482100 chr7D 90.517 116 10 1 2656 2771 83065087 83065201 6.780000e-33 152.0
16 TraesCS7A01G482100 chr7D 88.785 107 11 1 2656 2761 83084591 83084697 3.180000e-26 130.0
17 TraesCS7A01G482100 chr7D 85.859 99 14 0 2831 2929 82902883 82902981 5.360000e-19 106.0
18 TraesCS7A01G482100 chr7B 89.960 2271 137 46 785 3011 650130270 650128047 0.000000e+00 2846.0
19 TraesCS7A01G482100 chr7B 88.353 953 46 13 3013 3920 650127930 650126998 0.000000e+00 1085.0
20 TraesCS7A01G482100 chr7B 85.174 951 121 12 1024 1973 32330516 32331447 0.000000e+00 957.0
21 TraesCS7A01G482100 chr7B 84.701 987 118 24 1015 1975 169433042 169434021 0.000000e+00 955.0
22 TraesCS7A01G482100 chr7B 88.509 644 73 1 1329 1971 32344793 32345436 0.000000e+00 778.0
23 TraesCS7A01G482100 chr7B 82.680 612 77 17 173 759 460586689 460587296 2.090000e-142 516.0
24 TraesCS7A01G482100 chr7B 85.596 361 40 8 2414 2771 169434642 169434993 6.190000e-98 368.0
25 TraesCS7A01G482100 chr7B 88.393 224 26 0 1024 1247 32408355 32408578 1.800000e-68 270.0
26 TraesCS7A01G482100 chr7B 90.000 130 13 0 2415 2544 32332119 32332248 6.740000e-38 169.0
27 TraesCS7A01G482100 chr7B 82.727 110 17 1 2823 2932 32332727 32332834 3.220000e-16 97.1
28 TraesCS7A01G482100 chr2B 84.314 969 139 13 1012 1972 792124686 792123723 0.000000e+00 935.0
29 TraesCS7A01G482100 chr2B 81.714 350 50 12 2415 2760 792123080 792122741 2.980000e-71 279.0
30 TraesCS7A01G482100 chr2B 84.959 246 37 0 183 428 405117189 405117434 2.340000e-62 250.0
31 TraesCS7A01G482100 chr2B 85.870 92 11 1 20 111 405117078 405117167 3.220000e-16 97.1
32 TraesCS7A01G482100 chr2B 93.023 43 3 0 20 62 464669675 464669633 3.270000e-06 63.9
33 TraesCS7A01G482100 chr2A 83.086 538 75 7 114 648 447928566 447929090 3.540000e-130 475.0
34 TraesCS7A01G482100 chr3A 81.059 623 68 21 158 759 327291669 327292262 5.970000e-123 451.0
35 TraesCS7A01G482100 chr3D 83.708 356 46 5 329 682 256986944 256987289 3.780000e-85 326.0
36 TraesCS7A01G482100 chr4A 77.487 573 97 17 191 759 642643561 642643017 8.180000e-82 315.0
37 TraesCS7A01G482100 chr6D 77.863 524 94 18 169 682 131931508 131930997 4.920000e-79 305.0
38 TraesCS7A01G482100 chr5D 78.971 447 88 6 240 682 90311790 90312234 2.290000e-77 300.0
39 TraesCS7A01G482100 chr5B 76.557 546 111 13 145 682 55544274 55544810 2.310000e-72 283.0
40 TraesCS7A01G482100 chr5B 85.950 121 7 3 1 111 584869380 584869260 1.910000e-23 121.0
41 TraesCS7A01G482100 chr2D 77.014 509 101 13 217 717 505645046 505645546 1.070000e-70 278.0
42 TraesCS7A01G482100 chrUn 86.207 116 11 1 1 111 318430977 318431092 1.910000e-23 121.0
43 TraesCS7A01G482100 chr3B 86.207 116 11 1 1 111 159564074 159564189 1.910000e-23 121.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G482100 chr7A 674272268 674276187 3919 True 7239.000000 7239 100.00000 1 3920 1 chr7A.!!$R1 3919
1 TraesCS7A01G482100 chr7A 217202654 217204628 1974 False 684.000000 1011 85.08450 1015 2771 2 chr7A.!!$F3 1756
2 TraesCS7A01G482100 chr7A 85030873 85032875 2002 False 551.000000 952 89.43800 1024 2754 2 chr7A.!!$F2 1730
3 TraesCS7A01G482100 chr7D 582300973 582304217 3244 True 1392.666667 3049 90.60600 771 3920 3 chr7D.!!$R1 3149
4 TraesCS7A01G482100 chr7D 205131734 205133686 1952 False 671.000000 963 85.62550 1015 2764 2 chr7D.!!$F4 1749
5 TraesCS7A01G482100 chr7D 82899030 82902981 3951 False 400.500000 782 85.99275 1024 2929 4 chr7D.!!$F2 1905
6 TraesCS7A01G482100 chr7B 650126998 650130270 3272 True 1965.500000 2846 89.15650 785 3920 2 chr7B.!!$R1 3135
7 TraesCS7A01G482100 chr7B 32344793 32345436 643 False 778.000000 778 88.50900 1329 1971 1 chr7B.!!$F1 642
8 TraesCS7A01G482100 chr7B 169433042 169434993 1951 False 661.500000 955 85.14850 1015 2771 2 chr7B.!!$F5 1756
9 TraesCS7A01G482100 chr7B 460586689 460587296 607 False 516.000000 516 82.68000 173 759 1 chr7B.!!$F3 586
10 TraesCS7A01G482100 chr7B 32330516 32332834 2318 False 407.700000 957 85.96700 1024 2932 3 chr7B.!!$F4 1908
11 TraesCS7A01G482100 chr2B 792122741 792124686 1945 True 607.000000 935 83.01400 1012 2760 2 chr2B.!!$R2 1748
12 TraesCS7A01G482100 chr2A 447928566 447929090 524 False 475.000000 475 83.08600 114 648 1 chr2A.!!$F1 534
13 TraesCS7A01G482100 chr3A 327291669 327292262 593 False 451.000000 451 81.05900 158 759 1 chr3A.!!$F1 601
14 TraesCS7A01G482100 chr4A 642643017 642643561 544 True 315.000000 315 77.48700 191 759 1 chr4A.!!$R1 568
15 TraesCS7A01G482100 chr6D 131930997 131931508 511 True 305.000000 305 77.86300 169 682 1 chr6D.!!$R1 513
16 TraesCS7A01G482100 chr5B 55544274 55544810 536 False 283.000000 283 76.55700 145 682 1 chr5B.!!$F1 537
17 TraesCS7A01G482100 chr2D 505645046 505645546 500 False 278.000000 278 77.01400 217 717 1 chr2D.!!$F1 500

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
644 688 0.025898 CTGCGACATCTTGTGCATCG 59.974 55.0 0.00 0.00 35.23 3.84 F
665 710 0.111253 CCAGACCACCTTCAAAGCCT 59.889 55.0 0.00 0.00 0.00 4.58 F
2352 4699 0.108945 GTGCTTTCAGGCATGCTTCC 60.109 55.0 18.92 0.18 44.34 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2352 4699 0.326048 ATGGTGTGAGAGGGAGGGAG 60.326 60.000 0.00 0.00 0.00 4.30 R
2358 4705 1.556911 ACTAGCAATGGTGTGAGAGGG 59.443 52.381 0.00 0.00 0.00 4.30 R
3717 6567 0.388649 AGTGATTCAGTCGTGCGACC 60.389 55.000 19.35 6.13 45.59 4.79 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
21 22 4.640789 AAGTCTCATGGAGTGTCGTATC 57.359 45.455 0.00 0.00 0.00 2.24
22 23 2.952978 AGTCTCATGGAGTGTCGTATCC 59.047 50.000 0.00 0.00 36.05 2.59
33 34 4.513519 CGTATCCACGCACACCAT 57.486 55.556 0.00 0.00 42.05 3.55
34 35 2.297625 CGTATCCACGCACACCATC 58.702 57.895 0.00 0.00 42.05 3.51
35 36 0.179111 CGTATCCACGCACACCATCT 60.179 55.000 0.00 0.00 42.05 2.90
36 37 1.066454 CGTATCCACGCACACCATCTA 59.934 52.381 0.00 0.00 42.05 1.98
37 38 2.480587 CGTATCCACGCACACCATCTAA 60.481 50.000 0.00 0.00 42.05 2.10
38 39 3.728845 GTATCCACGCACACCATCTAAT 58.271 45.455 0.00 0.00 0.00 1.73
39 40 2.309528 TCCACGCACACCATCTAATC 57.690 50.000 0.00 0.00 0.00 1.75
40 41 1.134521 TCCACGCACACCATCTAATCC 60.135 52.381 0.00 0.00 0.00 3.01
41 42 0.930310 CACGCACACCATCTAATCCG 59.070 55.000 0.00 0.00 0.00 4.18
42 43 0.179084 ACGCACACCATCTAATCCGG 60.179 55.000 0.00 0.00 0.00 5.14
43 44 0.179084 CGCACACCATCTAATCCGGT 60.179 55.000 0.00 0.00 0.00 5.28
46 47 3.006672 CACCATCTAATCCGGTGGC 57.993 57.895 0.00 0.00 45.32 5.01
47 48 0.535102 CACCATCTAATCCGGTGGCC 60.535 60.000 0.00 0.00 45.32 5.36
48 49 0.986019 ACCATCTAATCCGGTGGCCA 60.986 55.000 0.00 0.00 35.11 5.36
49 50 0.401738 CCATCTAATCCGGTGGCCAT 59.598 55.000 9.72 0.00 0.00 4.40
50 51 1.611673 CCATCTAATCCGGTGGCCATC 60.612 57.143 9.72 7.61 0.00 3.51
51 52 0.693049 ATCTAATCCGGTGGCCATCC 59.307 55.000 9.72 11.73 0.00 3.51
52 53 0.399949 TCTAATCCGGTGGCCATCCT 60.400 55.000 9.72 0.00 0.00 3.24
53 54 1.132977 TCTAATCCGGTGGCCATCCTA 60.133 52.381 9.72 0.00 0.00 2.94
54 55 1.276421 CTAATCCGGTGGCCATCCTAG 59.724 57.143 9.72 6.37 0.00 3.02
55 56 1.418908 AATCCGGTGGCCATCCTAGG 61.419 60.000 9.72 5.16 0.00 3.02
63 64 2.834688 CCATCCTAGGCTGCCAGG 59.165 66.667 22.65 23.00 0.00 4.45
64 65 1.767672 CCATCCTAGGCTGCCAGGA 60.768 63.158 29.42 29.42 44.90 3.86
65 66 1.753470 CATCCTAGGCTGCCAGGAG 59.247 63.158 30.11 22.20 44.06 3.69
66 67 2.146061 ATCCTAGGCTGCCAGGAGC 61.146 63.158 30.11 2.05 44.06 4.70
72 73 4.527583 GCTGCCAGGAGCCGAGAG 62.528 72.222 0.00 0.00 42.71 3.20
73 74 4.527583 CTGCCAGGAGCCGAGAGC 62.528 72.222 0.00 0.00 42.71 4.09
82 83 2.892425 GCCGAGAGCATCAACCGG 60.892 66.667 0.00 0.00 43.97 5.28
83 84 2.579201 CCGAGAGCATCAACCGGT 59.421 61.111 0.00 0.00 39.06 5.28
84 85 1.811266 CCGAGAGCATCAACCGGTG 60.811 63.158 8.52 2.16 39.06 4.94
85 86 1.079819 CGAGAGCATCAACCGGTGT 60.080 57.895 8.52 0.00 37.82 4.16
86 87 0.172578 CGAGAGCATCAACCGGTGTA 59.827 55.000 8.52 0.00 37.82 2.90
87 88 1.799181 CGAGAGCATCAACCGGTGTAG 60.799 57.143 8.52 0.79 37.82 2.74
88 89 0.108138 AGAGCATCAACCGGTGTAGC 60.108 55.000 8.52 10.88 37.82 3.58
89 90 0.391130 GAGCATCAACCGGTGTAGCA 60.391 55.000 8.52 0.00 32.76 3.49
90 91 0.391661 AGCATCAACCGGTGTAGCAG 60.392 55.000 8.52 0.00 32.76 4.24
91 92 0.391130 GCATCAACCGGTGTAGCAGA 60.391 55.000 8.52 0.00 0.00 4.26
92 93 1.359848 CATCAACCGGTGTAGCAGAC 58.640 55.000 8.52 0.00 0.00 3.51
93 94 1.066858 CATCAACCGGTGTAGCAGACT 60.067 52.381 8.52 0.00 0.00 3.24
94 95 0.601558 TCAACCGGTGTAGCAGACTC 59.398 55.000 8.52 0.00 0.00 3.36
95 96 0.603569 CAACCGGTGTAGCAGACTCT 59.396 55.000 8.52 0.00 0.00 3.24
96 97 0.889306 AACCGGTGTAGCAGACTCTC 59.111 55.000 8.52 0.00 0.00 3.20
97 98 0.251209 ACCGGTGTAGCAGACTCTCA 60.251 55.000 6.12 0.00 0.00 3.27
98 99 0.453793 CCGGTGTAGCAGACTCTCAG 59.546 60.000 0.00 0.00 0.00 3.35
99 100 0.179150 CGGTGTAGCAGACTCTCAGC 60.179 60.000 0.00 0.00 0.00 4.26
100 101 0.891373 GGTGTAGCAGACTCTCAGCA 59.109 55.000 0.00 0.00 30.69 4.41
101 102 1.403514 GGTGTAGCAGACTCTCAGCAC 60.404 57.143 0.00 0.00 30.69 4.40
102 103 1.270826 GTGTAGCAGACTCTCAGCACA 59.729 52.381 0.00 0.00 30.69 4.57
103 104 1.270826 TGTAGCAGACTCTCAGCACAC 59.729 52.381 0.00 0.00 30.69 3.82
104 105 1.270826 GTAGCAGACTCTCAGCACACA 59.729 52.381 0.00 0.00 30.69 3.72
105 106 0.975135 AGCAGACTCTCAGCACACAT 59.025 50.000 0.00 0.00 30.69 3.21
106 107 1.067000 AGCAGACTCTCAGCACACATC 60.067 52.381 0.00 0.00 30.69 3.06
107 108 1.626747 CAGACTCTCAGCACACATCG 58.373 55.000 0.00 0.00 0.00 3.84
108 109 0.108898 AGACTCTCAGCACACATCGC 60.109 55.000 0.00 0.00 0.00 4.58
109 110 0.389037 GACTCTCAGCACACATCGCA 60.389 55.000 0.00 0.00 0.00 5.10
110 111 0.248565 ACTCTCAGCACACATCGCAT 59.751 50.000 0.00 0.00 0.00 4.73
111 112 1.478105 ACTCTCAGCACACATCGCATA 59.522 47.619 0.00 0.00 0.00 3.14
112 113 1.857217 CTCTCAGCACACATCGCATAC 59.143 52.381 0.00 0.00 0.00 2.39
118 119 1.447945 CACACATCGCATACCAACCA 58.552 50.000 0.00 0.00 0.00 3.67
119 120 1.398041 CACACATCGCATACCAACCAG 59.602 52.381 0.00 0.00 0.00 4.00
127 128 2.432444 GCATACCAACCAGTGTAGCAA 58.568 47.619 0.00 0.00 0.00 3.91
142 143 0.178981 AGCAAACCCTCAGCACACAT 60.179 50.000 0.00 0.00 0.00 3.21
143 144 0.675633 GCAAACCCTCAGCACACATT 59.324 50.000 0.00 0.00 0.00 2.71
180 181 2.324014 AATCCGCCGCTGCCATCTTA 62.324 55.000 0.00 0.00 0.00 2.10
181 182 2.116983 ATCCGCCGCTGCCATCTTAT 62.117 55.000 0.00 0.00 0.00 1.73
189 190 1.820483 GCTGCCATCTTATGCCATCCA 60.820 52.381 0.00 0.00 0.00 3.41
212 215 6.458478 CCAATCTTCAAGAGAGATCAATGCAC 60.458 42.308 0.00 0.00 37.93 4.57
262 276 1.080501 CATCACGACGCCAGACAGT 60.081 57.895 0.00 0.00 0.00 3.55
271 285 1.604593 GCCAGACAGTGCCACCATT 60.605 57.895 0.00 0.00 0.00 3.16
272 286 1.181098 GCCAGACAGTGCCACCATTT 61.181 55.000 0.00 0.00 0.00 2.32
277 291 1.363443 CAGTGCCACCATTTTGCGT 59.637 52.632 0.00 0.00 0.00 5.24
286 300 0.388391 CCATTTTGCGTGCGTCCATT 60.388 50.000 0.00 0.00 0.00 3.16
291 305 1.160989 TTGCGTGCGTCCATTAACAT 58.839 45.000 0.00 0.00 0.00 2.71
300 314 2.032894 CGTCCATTAACATGCGACCATC 60.033 50.000 0.00 0.00 31.66 3.51
301 315 2.942376 GTCCATTAACATGCGACCATCA 59.058 45.455 0.00 0.00 30.26 3.07
304 318 1.745232 TTAACATGCGACCATCACCC 58.255 50.000 0.00 0.00 0.00 4.61
308 322 1.091771 CATGCGACCATCACCCAGAC 61.092 60.000 0.00 0.00 0.00 3.51
310 324 2.584608 CGACCATCACCCAGACCC 59.415 66.667 0.00 0.00 0.00 4.46
313 327 4.489771 CCATCACCCAGACCCCGC 62.490 72.222 0.00 0.00 0.00 6.13
315 329 2.063979 CATCACCCAGACCCCGCTA 61.064 63.158 0.00 0.00 0.00 4.26
330 344 2.106332 CTACCCCATGCCGTCGAC 59.894 66.667 5.18 5.18 0.00 4.20
380 418 1.601419 GCCACTCCACCGCTGTAGTA 61.601 60.000 0.00 0.00 0.00 1.82
409 447 0.261991 TCCCTCTAGCCGATGAACCT 59.738 55.000 0.00 0.00 0.00 3.50
412 450 2.035632 CCTCTAGCCGATGAACCTCTT 58.964 52.381 0.00 0.00 0.00 2.85
482 523 3.054948 TCCGACCGATTGATAAGGGTTTT 60.055 43.478 0.00 0.00 31.66 2.43
484 525 4.189231 CGACCGATTGATAAGGGTTTTCT 58.811 43.478 0.00 0.00 31.66 2.52
548 592 3.691049 CTTCAAGAAGGAAACAACGCA 57.309 42.857 1.86 0.00 34.87 5.24
574 618 4.082523 CACCATCACCGGCTCCGT 62.083 66.667 0.00 0.00 37.81 4.69
576 620 3.461773 CCATCACCGGCTCCGTCT 61.462 66.667 0.00 0.00 37.81 4.18
577 621 2.202797 CATCACCGGCTCCGTCTG 60.203 66.667 0.00 2.61 37.81 3.51
578 622 2.680352 ATCACCGGCTCCGTCTGT 60.680 61.111 0.00 0.00 37.81 3.41
622 666 1.736032 CGGATCTTGTCCCACGAGAAC 60.736 57.143 0.00 0.00 41.62 3.01
625 669 1.003718 CTTGTCCCACGAGAACCCC 60.004 63.158 0.00 0.00 31.05 4.95
627 671 1.764571 TTGTCCCACGAGAACCCCTG 61.765 60.000 0.00 0.00 0.00 4.45
629 673 4.760047 CCCACGAGAACCCCTGCG 62.760 72.222 0.00 0.00 0.00 5.18
631 675 2.432628 CACGAGAACCCCTGCGAC 60.433 66.667 0.00 0.00 0.00 5.19
632 676 2.915659 ACGAGAACCCCTGCGACA 60.916 61.111 0.00 0.00 0.00 4.35
633 677 2.283529 ACGAGAACCCCTGCGACAT 61.284 57.895 0.00 0.00 0.00 3.06
634 678 1.519455 CGAGAACCCCTGCGACATC 60.519 63.158 0.00 0.00 0.00 3.06
635 679 1.901085 GAGAACCCCTGCGACATCT 59.099 57.895 0.00 0.00 0.00 2.90
636 680 0.250513 GAGAACCCCTGCGACATCTT 59.749 55.000 0.00 0.00 0.00 2.40
637 681 0.036010 AGAACCCCTGCGACATCTTG 60.036 55.000 0.00 0.00 0.00 3.02
638 682 0.321653 GAACCCCTGCGACATCTTGT 60.322 55.000 0.00 0.00 0.00 3.16
639 683 0.606401 AACCCCTGCGACATCTTGTG 60.606 55.000 0.00 0.00 0.00 3.33
640 684 2.401766 CCCCTGCGACATCTTGTGC 61.402 63.158 0.00 0.00 0.00 4.57
641 685 1.672030 CCCTGCGACATCTTGTGCA 60.672 57.895 0.00 0.00 34.80 4.57
642 686 1.028330 CCCTGCGACATCTTGTGCAT 61.028 55.000 0.00 0.00 35.23 3.96
644 688 0.025898 CTGCGACATCTTGTGCATCG 59.974 55.000 0.00 0.00 35.23 3.84
647 692 1.723870 GACATCTTGTGCATCGGCC 59.276 57.895 0.00 0.00 40.13 6.13
665 710 0.111253 CCAGACCACCTTCAAAGCCT 59.889 55.000 0.00 0.00 0.00 4.58
674 719 2.909006 ACCTTCAAAGCCTCAGATCTGA 59.091 45.455 23.75 23.75 38.06 3.27
682 727 0.539051 CCTCAGATCTGACCACCCAC 59.461 60.000 21.67 0.00 35.46 4.61
683 728 1.269958 CTCAGATCTGACCACCCACA 58.730 55.000 21.67 0.00 35.46 4.17
684 729 1.206610 CTCAGATCTGACCACCCACAG 59.793 57.143 21.67 4.94 35.46 3.66
685 730 0.979665 CAGATCTGACCACCCACAGT 59.020 55.000 18.34 0.00 35.84 3.55
686 731 2.179427 CAGATCTGACCACCCACAGTA 58.821 52.381 18.34 0.00 35.84 2.74
687 732 2.167281 CAGATCTGACCACCCACAGTAG 59.833 54.545 18.34 0.00 35.84 2.57
688 733 0.905357 ATCTGACCACCCACAGTAGC 59.095 55.000 0.00 0.00 35.84 3.58
689 734 1.192146 TCTGACCACCCACAGTAGCC 61.192 60.000 0.00 0.00 35.84 3.93
690 735 1.152118 TGACCACCCACAGTAGCCT 60.152 57.895 0.00 0.00 0.00 4.58
691 736 1.296715 GACCACCCACAGTAGCCTG 59.703 63.158 0.00 0.00 44.68 4.85
692 737 2.045926 CCACCCACAGTAGCCTGC 60.046 66.667 0.00 0.00 42.81 4.85
693 738 2.045926 CACCCACAGTAGCCTGCC 60.046 66.667 0.00 0.00 42.81 4.85
694 739 2.529136 ACCCACAGTAGCCTGCCA 60.529 61.111 0.00 0.00 42.81 4.92
695 740 2.045926 CCCACAGTAGCCTGCCAC 60.046 66.667 0.00 0.00 42.81 5.01
696 741 2.045926 CCACAGTAGCCTGCCACC 60.046 66.667 0.00 0.00 42.81 4.61
697 742 2.434884 CACAGTAGCCTGCCACCG 60.435 66.667 0.00 0.00 42.81 4.94
698 743 4.394712 ACAGTAGCCTGCCACCGC 62.395 66.667 0.00 0.00 42.81 5.68
738 783 4.261888 CACTACCGAGTGCACCAC 57.738 61.111 14.63 7.42 46.41 4.16
739 784 1.733041 CACTACCGAGTGCACCACG 60.733 63.158 21.62 21.62 46.41 4.94
740 785 1.900016 ACTACCGAGTGCACCACGA 60.900 57.895 27.39 13.08 39.64 4.35
741 786 1.443872 CTACCGAGTGCACCACGAC 60.444 63.158 27.39 9.68 39.64 4.34
742 787 1.863662 CTACCGAGTGCACCACGACT 61.864 60.000 27.39 17.27 39.64 4.18
743 788 2.137425 TACCGAGTGCACCACGACTG 62.137 60.000 27.39 16.87 39.64 3.51
744 789 2.734723 CGAGTGCACCACGACTGG 60.735 66.667 23.36 0.00 44.26 4.00
745 790 2.734591 GAGTGCACCACGACTGGA 59.265 61.111 14.63 0.00 40.55 3.86
746 791 1.373497 GAGTGCACCACGACTGGAG 60.373 63.158 14.63 0.00 40.55 3.86
749 794 4.008933 GCACCACGACTGGAGCCT 62.009 66.667 3.50 0.00 45.78 4.58
750 795 2.047844 CACCACGACTGGAGCCTG 60.048 66.667 0.00 0.00 40.55 4.85
751 796 3.314331 ACCACGACTGGAGCCTGG 61.314 66.667 0.00 0.00 40.55 4.45
752 797 4.087892 CCACGACTGGAGCCTGGG 62.088 72.222 0.00 0.00 40.55 4.45
753 798 2.997315 CACGACTGGAGCCTGGGA 60.997 66.667 0.00 0.00 0.00 4.37
754 799 2.681778 ACGACTGGAGCCTGGGAG 60.682 66.667 0.00 0.00 0.00 4.30
755 800 3.465403 CGACTGGAGCCTGGGAGG 61.465 72.222 0.00 0.00 38.80 4.30
756 801 2.039624 GACTGGAGCCTGGGAGGA 59.960 66.667 0.00 0.00 37.67 3.71
757 802 2.040278 ACTGGAGCCTGGGAGGAG 59.960 66.667 0.00 0.00 37.67 3.69
758 803 2.767496 CTGGAGCCTGGGAGGAGG 60.767 72.222 0.00 0.00 37.67 4.30
759 804 3.284251 TGGAGCCTGGGAGGAGGA 61.284 66.667 0.00 0.00 37.67 3.71
760 805 2.041265 GGAGCCTGGGAGGAGGAA 59.959 66.667 0.00 0.00 37.67 3.36
761 806 2.371259 GGAGCCTGGGAGGAGGAAC 61.371 68.421 0.00 0.00 37.67 3.62
762 807 2.285743 AGCCTGGGAGGAGGAACC 60.286 66.667 0.00 0.00 37.67 3.62
763 808 3.787001 GCCTGGGAGGAGGAACCG 61.787 72.222 0.00 0.00 44.74 4.44
764 809 3.083997 CCTGGGAGGAGGAACCGG 61.084 72.222 0.00 0.00 44.74 5.28
765 810 2.284699 CTGGGAGGAGGAACCGGT 60.285 66.667 0.00 0.00 44.74 5.28
766 811 2.284405 TGGGAGGAGGAACCGGTC 60.284 66.667 8.04 0.72 44.74 4.79
767 812 2.039137 GGGAGGAGGAACCGGTCT 59.961 66.667 8.04 0.00 44.74 3.85
768 813 2.359967 GGGAGGAGGAACCGGTCTG 61.360 68.421 8.04 0.00 44.74 3.51
769 814 2.359967 GGAGGAGGAACCGGTCTGG 61.360 68.421 8.04 0.00 44.74 3.86
790 835 3.629398 GGTGATGAATCGGCAGAAGAATT 59.371 43.478 0.00 0.00 0.00 2.17
798 843 2.478894 TCGGCAGAAGAATTTGTTCGAC 59.521 45.455 1.09 0.00 0.00 4.20
812 857 1.082561 TCGACGTCTCGACAAACGG 60.083 57.895 14.70 0.00 44.14 4.44
813 858 2.078914 CGACGTCTCGACAAACGGG 61.079 63.158 14.70 0.00 43.06 5.28
820 865 4.368808 CGACAAACGGGCGTGCAG 62.369 66.667 0.00 0.00 38.46 4.41
850 902 1.472188 GCAACGGGTAGGTACTCTCT 58.528 55.000 0.00 0.00 41.75 3.10
852 904 1.669779 CAACGGGTAGGTACTCTCTCG 59.330 57.143 0.00 0.00 40.89 4.04
853 905 1.198713 ACGGGTAGGTACTCTCTCGA 58.801 55.000 9.91 0.00 38.31 4.04
937 989 4.463186 GCGTGGAGTATAGATACCTGGATT 59.537 45.833 0.00 0.00 33.79 3.01
978 1030 1.968017 CCGGTGACAACTGCTGCAT 60.968 57.895 1.31 0.00 0.00 3.96
1146 1198 2.568612 CTCTTCGCCGTCAGCTCA 59.431 61.111 0.00 0.00 40.39 4.26
1236 1288 0.614979 TCTCCACCTTCTCCTTCGGG 60.615 60.000 0.00 0.00 0.00 5.14
1268 1335 0.933791 ACCCATCTCCTCTCCTCCCT 60.934 60.000 0.00 0.00 0.00 4.20
1269 1336 0.178935 CCCATCTCCTCTCCTCCCTC 60.179 65.000 0.00 0.00 0.00 4.30
1270 1337 0.178935 CCATCTCCTCTCCTCCCTCC 60.179 65.000 0.00 0.00 0.00 4.30
1272 1339 1.376249 ATCTCCTCTCCTCCCTCCCC 61.376 65.000 0.00 0.00 0.00 4.81
1284 1351 2.997315 CTCCCCGGCACTCACTCA 60.997 66.667 0.00 0.00 0.00 3.41
1286 1353 3.314331 CCCCGGCACTCACTCACT 61.314 66.667 0.00 0.00 0.00 3.41
1296 1368 2.030363 CACTCACTCACTCTCTCACACC 60.030 54.545 0.00 0.00 0.00 4.16
1304 1387 0.824109 CTCTCTCACACCCGCCATTA 59.176 55.000 0.00 0.00 0.00 1.90
1310 1401 1.003851 CACACCCGCCATTACTAACG 58.996 55.000 0.00 0.00 0.00 3.18
1311 1402 0.896923 ACACCCGCCATTACTAACGA 59.103 50.000 0.00 0.00 0.00 3.85
1312 1403 1.275856 ACACCCGCCATTACTAACGAA 59.724 47.619 0.00 0.00 0.00 3.85
1316 1407 1.322338 CCGCCATTACTAACGAACACG 59.678 52.381 0.00 0.00 0.00 4.49
1317 1408 1.987770 CGCCATTACTAACGAACACGT 59.012 47.619 0.00 0.00 42.17 4.49
1413 1518 2.029666 GCGATGCTGGGCGTCTAT 59.970 61.111 9.56 0.00 41.85 1.98
1578 1683 4.189188 GCGCTCTCCTTCGCCGTA 62.189 66.667 0.00 0.00 45.01 4.02
1905 2010 1.762370 TGGTACATCGGCATGATCACT 59.238 47.619 0.00 0.00 34.13 3.41
1969 2156 1.971357 CCCTCGGCATCTGGTACTATT 59.029 52.381 0.00 0.00 0.00 1.73
1970 2157 3.162666 CCCTCGGCATCTGGTACTATTA 58.837 50.000 0.00 0.00 0.00 0.98
1971 2158 3.056749 CCCTCGGCATCTGGTACTATTAC 60.057 52.174 0.00 0.00 0.00 1.89
1972 2159 3.827302 CCTCGGCATCTGGTACTATTACT 59.173 47.826 0.00 0.00 0.00 2.24
1976 2174 6.066690 TCGGCATCTGGTACTATTACTACTT 58.933 40.000 0.00 0.00 0.00 2.24
2016 2214 5.680619 ACAACCTGACAACATTCTGAACTA 58.319 37.500 0.00 0.00 0.00 2.24
2017 2215 6.119536 ACAACCTGACAACATTCTGAACTAA 58.880 36.000 0.00 0.00 0.00 2.24
2027 4125 7.011482 ACAACATTCTGAACTAACTGACAGAAC 59.989 37.037 10.08 0.00 46.87 3.01
2095 4198 2.802667 CTTCATCGGCCTCAACGCG 61.803 63.158 3.53 3.53 0.00 6.01
2248 4582 5.726980 GAGACAGCTTCTCCATCATCTAT 57.273 43.478 12.34 0.00 44.74 1.98
2352 4699 0.108945 GTGCTTTCAGGCATGCTTCC 60.109 55.000 18.92 0.18 44.34 3.46
2358 4705 1.153005 CAGGCATGCTTCCTCCCTC 60.153 63.158 18.92 0.00 0.00 4.30
2403 4768 4.218200 TCATTTTGTTCATGTCGCCTCAAT 59.782 37.500 0.00 0.00 0.00 2.57
2404 4769 5.414144 TCATTTTGTTCATGTCGCCTCAATA 59.586 36.000 0.00 0.00 0.00 1.90
2468 4887 2.609459 CCTTGTCGCATACATCAACCTC 59.391 50.000 0.00 0.00 38.10 3.85
2794 5460 9.619316 CTTTGTTTGATTTCGGATATGTTGTAA 57.381 29.630 0.00 0.00 0.00 2.41
2842 5527 2.401568 TGCTCATCTCTCATGCCCTAA 58.598 47.619 0.00 0.00 0.00 2.69
2937 5623 6.841229 TGGAGTAGAACTAGATCACCATGATT 59.159 38.462 0.00 0.00 37.20 2.57
2973 5659 3.584406 TCCTGAAGAAAGAGAGAAGCG 57.416 47.619 0.00 0.00 0.00 4.68
3033 5841 7.784470 AGAAGTTGTGTAGAACTAGAAGGAT 57.216 36.000 0.00 0.00 35.01 3.24
3038 5846 7.124298 AGTTGTGTAGAACTAGAAGGATATGCA 59.876 37.037 0.00 0.00 34.29 3.96
3062 5870 3.044305 GCTGCGCCGTTGTCTCTT 61.044 61.111 4.18 0.00 0.00 2.85
3143 5958 1.276622 TTCTCTCTACCCAGCAACCC 58.723 55.000 0.00 0.00 0.00 4.11
3170 5985 5.473039 ACAATTAGCAGCACTGGAAATTTC 58.527 37.500 9.83 9.83 0.00 2.17
3198 6013 3.313526 GGAATGCACACTACACATCCATC 59.686 47.826 0.00 0.00 0.00 3.51
3202 6017 2.283298 CACACTACACATCCATCCAGC 58.717 52.381 0.00 0.00 0.00 4.85
3293 6109 6.560003 ATCCACATACCAAATACTCAGACA 57.440 37.500 0.00 0.00 0.00 3.41
3294 6110 6.560003 TCCACATACCAAATACTCAGACAT 57.440 37.500 0.00 0.00 0.00 3.06
3298 6114 7.970061 CCACATACCAAATACTCAGACATTTTG 59.030 37.037 0.00 0.00 0.00 2.44
3301 6117 4.220602 ACCAAATACTCAGACATTTTGCCC 59.779 41.667 0.00 0.00 0.00 5.36
3302 6118 4.381932 CCAAATACTCAGACATTTTGCCCC 60.382 45.833 0.00 0.00 0.00 5.80
3334 6150 4.100498 GGAATACTCGACAGAATTACCCCA 59.900 45.833 0.00 0.00 0.00 4.96
3395 6211 3.118482 TCCCAGATGATCTCTTCACTTGC 60.118 47.826 0.00 0.00 37.11 4.01
3485 6308 6.456988 GCCAATCTTTACTCACCAAACTATCG 60.457 42.308 0.00 0.00 0.00 2.92
3556 6379 0.037447 AGAGCAACCAGAGGGCTTTC 59.963 55.000 0.00 0.00 38.15 2.62
3622 6462 7.117236 CACATTCATCTTGGGAGTTTCAAAATG 59.883 37.037 0.00 0.00 30.85 2.32
3633 6473 3.138098 AGTTTCAAAATGCCCCCAACATT 59.862 39.130 0.00 0.00 39.38 2.71
3666 6506 0.855349 CCTCATACGCGATGCAGAAC 59.145 55.000 15.93 0.00 35.29 3.01
3677 6517 4.260579 CGCGATGCAGAACCATGTTAAATA 60.261 41.667 0.00 0.00 0.00 1.40
3690 6530 8.938801 ACCATGTTAAATATCTCCATTATGCA 57.061 30.769 0.00 0.00 0.00 3.96
3717 6567 9.702726 AAACATGATTAGAATTATTCGTCGTTG 57.297 29.630 0.00 4.93 34.02 4.10
3726 6576 2.736343 ATTCGTCGTTGGTCGCACGA 62.736 55.000 0.00 9.36 44.25 4.35
3755 6606 1.199327 CTTGCCACATTCAGCAGTCAG 59.801 52.381 0.00 0.00 40.73 3.51
3766 6617 2.544726 GCAGTCAGCAACAGTACCC 58.455 57.895 0.00 0.00 44.79 3.69
3859 6711 0.906756 TCTCCTTGGCTCCCTCACTG 60.907 60.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.381908 GGATACGACACTCCATGAGACTT 59.618 47.826 0.00 0.00 33.32 3.01
1 2 2.952978 GGATACGACACTCCATGAGACT 59.047 50.000 0.00 0.00 33.32 3.24
2 3 2.688446 TGGATACGACACTCCATGAGAC 59.312 50.000 0.00 0.00 36.63 3.36
3 4 2.688446 GTGGATACGACACTCCATGAGA 59.312 50.000 0.00 0.00 43.20 3.27
4 5 3.085443 GTGGATACGACACTCCATGAG 57.915 52.381 0.00 0.00 43.20 2.90
17 18 2.882927 TAGATGGTGTGCGTGGATAC 57.117 50.000 0.00 0.00 0.00 2.24
18 19 3.244078 GGATTAGATGGTGTGCGTGGATA 60.244 47.826 0.00 0.00 0.00 2.59
19 20 2.485479 GGATTAGATGGTGTGCGTGGAT 60.485 50.000 0.00 0.00 0.00 3.41
20 21 1.134521 GGATTAGATGGTGTGCGTGGA 60.135 52.381 0.00 0.00 0.00 4.02
21 22 1.299541 GGATTAGATGGTGTGCGTGG 58.700 55.000 0.00 0.00 0.00 4.94
22 23 0.930310 CGGATTAGATGGTGTGCGTG 59.070 55.000 0.00 0.00 0.00 5.34
23 24 0.179084 CCGGATTAGATGGTGTGCGT 60.179 55.000 0.00 0.00 0.00 5.24
24 25 0.179084 ACCGGATTAGATGGTGTGCG 60.179 55.000 9.46 0.00 33.91 5.34
25 26 1.299541 CACCGGATTAGATGGTGTGC 58.700 55.000 9.46 0.00 46.36 4.57
29 30 0.986019 TGGCCACCGGATTAGATGGT 60.986 55.000 9.46 0.00 36.10 3.55
30 31 0.401738 ATGGCCACCGGATTAGATGG 59.598 55.000 8.16 5.03 35.17 3.51
31 32 1.611673 GGATGGCCACCGGATTAGATG 60.612 57.143 8.16 0.00 0.00 2.90
32 33 0.693049 GGATGGCCACCGGATTAGAT 59.307 55.000 8.16 0.00 0.00 1.98
33 34 0.399949 AGGATGGCCACCGGATTAGA 60.400 55.000 8.16 0.00 36.29 2.10
34 35 1.276421 CTAGGATGGCCACCGGATTAG 59.724 57.143 8.16 5.84 36.29 1.73
35 36 1.348064 CTAGGATGGCCACCGGATTA 58.652 55.000 8.16 0.00 36.29 1.75
36 37 1.418908 CCTAGGATGGCCACCGGATT 61.419 60.000 8.16 0.00 36.29 3.01
37 38 1.843376 CCTAGGATGGCCACCGGAT 60.843 63.158 8.16 0.00 36.29 4.18
38 39 2.445845 CCTAGGATGGCCACCGGA 60.446 66.667 8.16 4.79 36.29 5.14
39 40 4.256180 GCCTAGGATGGCCACCGG 62.256 72.222 14.75 10.48 46.82 5.28
46 47 1.766625 CTCCTGGCAGCCTAGGATGG 61.767 65.000 27.62 11.88 41.96 3.51
47 48 1.753470 CTCCTGGCAGCCTAGGATG 59.247 63.158 23.01 23.01 41.96 3.51
48 49 2.146061 GCTCCTGGCAGCCTAGGAT 61.146 63.158 24.79 1.88 41.96 3.24
49 50 2.765807 GCTCCTGGCAGCCTAGGA 60.766 66.667 23.69 23.69 40.68 2.94
55 56 4.527583 CTCTCGGCTCCTGGCAGC 62.528 72.222 9.56 0.00 44.01 5.25
56 57 4.527583 GCTCTCGGCTCCTGGCAG 62.528 72.222 7.75 7.75 44.01 4.85
58 59 3.805891 GATGCTCTCGGCTCCTGGC 62.806 68.421 0.00 0.00 42.39 4.85
59 60 1.964608 TTGATGCTCTCGGCTCCTGG 61.965 60.000 0.00 0.00 42.39 4.45
60 61 0.809241 GTTGATGCTCTCGGCTCCTG 60.809 60.000 0.00 0.00 42.39 3.86
61 62 1.519719 GTTGATGCTCTCGGCTCCT 59.480 57.895 0.00 0.00 42.39 3.69
62 63 1.522580 GGTTGATGCTCTCGGCTCC 60.523 63.158 0.00 0.00 42.39 4.70
63 64 1.880340 CGGTTGATGCTCTCGGCTC 60.880 63.158 0.00 0.00 42.39 4.70
64 65 2.185350 CGGTTGATGCTCTCGGCT 59.815 61.111 0.00 0.00 42.39 5.52
65 66 2.892425 CCGGTTGATGCTCTCGGC 60.892 66.667 0.00 0.00 42.22 5.54
66 67 1.811266 CACCGGTTGATGCTCTCGG 60.811 63.158 2.97 0.00 45.42 4.63
67 68 0.172578 TACACCGGTTGATGCTCTCG 59.827 55.000 2.97 0.00 0.00 4.04
68 69 1.927895 CTACACCGGTTGATGCTCTC 58.072 55.000 2.97 0.00 0.00 3.20
69 70 0.108138 GCTACACCGGTTGATGCTCT 60.108 55.000 2.97 0.00 0.00 4.09
70 71 0.391130 TGCTACACCGGTTGATGCTC 60.391 55.000 2.97 0.00 0.00 4.26
71 72 0.391661 CTGCTACACCGGTTGATGCT 60.392 55.000 2.97 0.00 0.00 3.79
72 73 0.391130 TCTGCTACACCGGTTGATGC 60.391 55.000 2.97 8.09 0.00 3.91
73 74 1.066858 AGTCTGCTACACCGGTTGATG 60.067 52.381 2.97 0.00 0.00 3.07
74 75 1.204941 GAGTCTGCTACACCGGTTGAT 59.795 52.381 2.97 0.00 0.00 2.57
75 76 0.601558 GAGTCTGCTACACCGGTTGA 59.398 55.000 2.97 0.00 0.00 3.18
76 77 0.603569 AGAGTCTGCTACACCGGTTG 59.396 55.000 2.97 2.94 0.00 3.77
77 78 0.889306 GAGAGTCTGCTACACCGGTT 59.111 55.000 2.97 0.00 0.00 4.44
78 79 0.251209 TGAGAGTCTGCTACACCGGT 60.251 55.000 0.00 0.00 0.00 5.28
79 80 0.453793 CTGAGAGTCTGCTACACCGG 59.546 60.000 0.00 0.00 0.00 5.28
80 81 0.179150 GCTGAGAGTCTGCTACACCG 60.179 60.000 0.00 0.00 38.17 4.94
81 82 0.891373 TGCTGAGAGTCTGCTACACC 59.109 55.000 0.00 0.00 41.21 4.16
82 83 1.270826 TGTGCTGAGAGTCTGCTACAC 59.729 52.381 0.00 1.29 41.21 2.90
83 84 1.270826 GTGTGCTGAGAGTCTGCTACA 59.729 52.381 0.00 0.92 41.21 2.74
84 85 1.270826 TGTGTGCTGAGAGTCTGCTAC 59.729 52.381 0.00 0.85 41.21 3.58
85 86 1.620822 TGTGTGCTGAGAGTCTGCTA 58.379 50.000 0.00 0.00 41.21 3.49
86 87 0.975135 ATGTGTGCTGAGAGTCTGCT 59.025 50.000 0.00 0.00 41.21 4.24
87 88 1.357907 GATGTGTGCTGAGAGTCTGC 58.642 55.000 0.00 0.00 41.04 4.26
88 89 1.626747 CGATGTGTGCTGAGAGTCTG 58.373 55.000 0.00 0.00 0.00 3.51
89 90 0.108898 GCGATGTGTGCTGAGAGTCT 60.109 55.000 0.00 0.00 0.00 3.24
90 91 0.389037 TGCGATGTGTGCTGAGAGTC 60.389 55.000 0.00 0.00 0.00 3.36
91 92 0.248565 ATGCGATGTGTGCTGAGAGT 59.751 50.000 0.00 0.00 0.00 3.24
92 93 1.857217 GTATGCGATGTGTGCTGAGAG 59.143 52.381 0.00 0.00 0.00 3.20
93 94 1.471501 GGTATGCGATGTGTGCTGAGA 60.472 52.381 0.00 0.00 0.00 3.27
94 95 0.933097 GGTATGCGATGTGTGCTGAG 59.067 55.000 0.00 0.00 0.00 3.35
95 96 0.248843 TGGTATGCGATGTGTGCTGA 59.751 50.000 0.00 0.00 0.00 4.26
96 97 1.085893 TTGGTATGCGATGTGTGCTG 58.914 50.000 0.00 0.00 0.00 4.41
97 98 1.086696 GTTGGTATGCGATGTGTGCT 58.913 50.000 0.00 0.00 0.00 4.40
98 99 0.098728 GGTTGGTATGCGATGTGTGC 59.901 55.000 0.00 0.00 0.00 4.57
99 100 1.398041 CTGGTTGGTATGCGATGTGTG 59.602 52.381 0.00 0.00 0.00 3.82
100 101 1.003118 ACTGGTTGGTATGCGATGTGT 59.997 47.619 0.00 0.00 0.00 3.72
101 102 1.398041 CACTGGTTGGTATGCGATGTG 59.602 52.381 0.00 0.00 0.00 3.21
102 103 1.003118 ACACTGGTTGGTATGCGATGT 59.997 47.619 0.00 0.00 0.00 3.06
103 104 1.737838 ACACTGGTTGGTATGCGATG 58.262 50.000 0.00 0.00 0.00 3.84
104 105 2.741878 GCTACACTGGTTGGTATGCGAT 60.742 50.000 0.00 0.00 0.00 4.58
105 106 1.404986 GCTACACTGGTTGGTATGCGA 60.405 52.381 0.00 0.00 0.00 5.10
106 107 1.006832 GCTACACTGGTTGGTATGCG 58.993 55.000 0.00 0.00 0.00 4.73
107 108 2.107950 TGCTACACTGGTTGGTATGC 57.892 50.000 0.00 0.00 0.00 3.14
108 109 3.190535 GGTTTGCTACACTGGTTGGTATG 59.809 47.826 0.00 0.00 0.00 2.39
109 110 3.418047 GGTTTGCTACACTGGTTGGTAT 58.582 45.455 0.00 0.00 0.00 2.73
110 111 2.487625 GGGTTTGCTACACTGGTTGGTA 60.488 50.000 0.00 0.00 0.00 3.25
111 112 1.687563 GGTTTGCTACACTGGTTGGT 58.312 50.000 0.00 0.00 0.00 3.67
112 113 0.958822 GGGTTTGCTACACTGGTTGG 59.041 55.000 0.00 0.00 0.00 3.77
118 119 0.764890 TGCTGAGGGTTTGCTACACT 59.235 50.000 0.00 0.00 45.42 3.55
119 120 0.875059 GTGCTGAGGGTTTGCTACAC 59.125 55.000 0.00 0.00 0.00 2.90
180 181 4.165565 TCTCTCTTGAAGATTGGATGGCAT 59.834 41.667 0.00 0.00 32.19 4.40
181 182 3.520721 TCTCTCTTGAAGATTGGATGGCA 59.479 43.478 0.00 0.00 32.19 4.92
189 190 6.178324 TGTGCATTGATCTCTCTTGAAGATT 58.822 36.000 0.00 0.00 32.19 2.40
246 260 2.335011 CACTGTCTGGCGTCGTGA 59.665 61.111 0.00 0.00 0.00 4.35
262 276 2.028778 GCACGCAAAATGGTGGCA 59.971 55.556 0.00 0.00 34.76 4.92
271 285 0.945099 TGTTAATGGACGCACGCAAA 59.055 45.000 0.00 0.00 0.00 3.68
272 286 1.135831 CATGTTAATGGACGCACGCAA 60.136 47.619 0.00 0.00 0.00 4.85
277 291 0.724549 GTCGCATGTTAATGGACGCA 59.275 50.000 0.00 0.00 34.09 5.24
286 300 0.615850 TGGGTGATGGTCGCATGTTA 59.384 50.000 0.00 0.00 0.00 2.41
291 305 2.662596 GTCTGGGTGATGGTCGCA 59.337 61.111 0.00 0.00 0.00 5.10
300 314 3.782443 GGTAGCGGGGTCTGGGTG 61.782 72.222 0.00 0.00 0.00 4.61
304 318 2.768344 ATGGGGTAGCGGGGTCTG 60.768 66.667 0.00 0.00 0.00 3.51
310 324 4.910585 GACGGCATGGGGTAGCGG 62.911 72.222 0.00 0.00 37.15 5.52
313 327 2.106332 GTCGACGGCATGGGGTAG 59.894 66.667 0.00 0.00 0.00 3.18
315 329 4.388499 GTGTCGACGGCATGGGGT 62.388 66.667 5.01 0.00 0.00 4.95
330 344 3.487202 CATCGACAACGGCGGGTG 61.487 66.667 13.24 7.91 40.21 4.61
380 418 1.562783 GCTAGAGGGACCAGTGAACT 58.437 55.000 0.00 0.00 0.00 3.01
409 447 1.640149 TGGGGGCATCATTCTTGAAGA 59.360 47.619 0.00 0.00 34.96 2.87
412 450 2.390696 CATTGGGGGCATCATTCTTGA 58.609 47.619 0.00 0.00 36.00 3.02
465 505 3.560068 CGGAGAAAACCCTTATCAATCGG 59.440 47.826 0.00 0.00 0.00 4.18
548 592 2.272146 GTGATGGTGACGCCCCAT 59.728 61.111 1.74 1.08 45.37 4.00
576 620 3.281727 AAACCTTGTCTTCTGCTGACA 57.718 42.857 0.00 0.00 41.94 3.58
577 621 3.627577 TGAAAACCTTGTCTTCTGCTGAC 59.372 43.478 0.00 0.00 35.21 3.51
578 622 3.627577 GTGAAAACCTTGTCTTCTGCTGA 59.372 43.478 0.00 0.00 0.00 4.26
622 666 2.401766 GCACAAGATGTCGCAGGGG 61.402 63.158 0.00 0.00 0.00 4.79
625 669 0.025898 CGATGCACAAGATGTCGCAG 59.974 55.000 0.00 0.00 37.63 5.18
627 671 1.349627 CCGATGCACAAGATGTCGC 59.650 57.895 0.00 0.00 0.00 5.19
629 673 1.026182 TGGCCGATGCACAAGATGTC 61.026 55.000 0.00 0.00 40.13 3.06
631 675 0.745486 TCTGGCCGATGCACAAGATG 60.745 55.000 0.00 0.00 40.13 2.90
632 676 0.745845 GTCTGGCCGATGCACAAGAT 60.746 55.000 0.00 0.00 40.13 2.40
633 677 1.375908 GTCTGGCCGATGCACAAGA 60.376 57.895 0.00 0.00 40.13 3.02
634 678 2.401766 GGTCTGGCCGATGCACAAG 61.402 63.158 0.00 0.00 40.13 3.16
635 679 2.359850 GGTCTGGCCGATGCACAA 60.360 61.111 0.00 0.00 40.13 3.33
636 680 3.635191 TGGTCTGGCCGATGCACA 61.635 61.111 0.00 0.00 41.21 4.57
637 681 3.127533 GTGGTCTGGCCGATGCAC 61.128 66.667 0.00 0.00 41.21 4.57
638 682 4.408821 GGTGGTCTGGCCGATGCA 62.409 66.667 0.00 0.00 41.21 3.96
639 683 3.628646 AAGGTGGTCTGGCCGATGC 62.629 63.158 0.00 0.00 41.21 3.91
640 684 1.450312 GAAGGTGGTCTGGCCGATG 60.450 63.158 0.00 0.00 41.21 3.84
641 685 1.488705 TTGAAGGTGGTCTGGCCGAT 61.489 55.000 0.00 0.00 41.21 4.18
642 686 1.701031 TTTGAAGGTGGTCTGGCCGA 61.701 55.000 0.00 0.00 41.21 5.54
644 688 1.527433 GCTTTGAAGGTGGTCTGGCC 61.527 60.000 0.00 0.00 37.90 5.36
647 692 1.202806 TGAGGCTTTGAAGGTGGTCTG 60.203 52.381 0.00 0.00 0.00 3.51
665 710 1.269958 CTGTGGGTGGTCAGATCTGA 58.730 55.000 21.67 21.67 37.24 3.27
674 719 2.895424 GCAGGCTACTGTGGGTGGT 61.895 63.158 0.00 0.00 46.62 4.16
714 759 3.678717 CACTCGGTAGTGTCCGCGG 62.679 68.421 22.12 22.12 46.76 6.46
715 760 2.202440 CACTCGGTAGTGTCCGCG 60.202 66.667 0.00 0.00 46.76 6.46
722 767 1.900016 TCGTGGTGCACTCGGTAGT 60.900 57.895 25.14 0.00 36.76 2.73
723 768 1.443872 GTCGTGGTGCACTCGGTAG 60.444 63.158 25.14 10.54 36.76 3.18
724 769 1.900016 AGTCGTGGTGCACTCGGTA 60.900 57.895 25.14 11.57 36.76 4.02
725 770 3.224324 AGTCGTGGTGCACTCGGT 61.224 61.111 25.14 15.31 36.76 4.69
726 771 2.734723 CAGTCGTGGTGCACTCGG 60.735 66.667 25.14 13.02 36.76 4.63
727 772 2.734723 CCAGTCGTGGTGCACTCG 60.735 66.667 17.98 20.37 39.30 4.18
728 773 1.373497 CTCCAGTCGTGGTGCACTC 60.373 63.158 17.98 7.60 45.28 3.51
729 774 2.737180 CTCCAGTCGTGGTGCACT 59.263 61.111 17.98 0.00 45.28 4.40
733 778 2.047844 CAGGCTCCAGTCGTGGTG 60.048 66.667 0.00 0.00 45.28 4.17
734 779 3.314331 CCAGGCTCCAGTCGTGGT 61.314 66.667 0.00 0.00 45.28 4.16
735 780 4.087892 CCCAGGCTCCAGTCGTGG 62.088 72.222 0.00 0.00 46.63 4.94
736 781 2.997315 TCCCAGGCTCCAGTCGTG 60.997 66.667 0.00 0.00 0.00 4.35
737 782 2.681778 CTCCCAGGCTCCAGTCGT 60.682 66.667 0.00 0.00 0.00 4.34
738 783 3.465403 CCTCCCAGGCTCCAGTCG 61.465 72.222 0.00 0.00 0.00 4.18
739 784 2.039624 TCCTCCCAGGCTCCAGTC 59.960 66.667 0.00 0.00 34.61 3.51
740 785 2.040278 CTCCTCCCAGGCTCCAGT 59.960 66.667 0.00 0.00 34.61 4.00
741 786 2.767496 CCTCCTCCCAGGCTCCAG 60.767 72.222 0.00 0.00 34.61 3.86
742 787 2.880612 TTCCTCCTCCCAGGCTCCA 61.881 63.158 0.00 0.00 34.61 3.86
743 788 2.041265 TTCCTCCTCCCAGGCTCC 59.959 66.667 0.00 0.00 34.61 4.70
744 789 2.371259 GGTTCCTCCTCCCAGGCTC 61.371 68.421 0.00 0.00 34.61 4.70
745 790 2.285743 GGTTCCTCCTCCCAGGCT 60.286 66.667 0.00 0.00 34.61 4.58
746 791 3.787001 CGGTTCCTCCTCCCAGGC 61.787 72.222 0.00 0.00 34.61 4.85
747 792 3.083997 CCGGTTCCTCCTCCCAGG 61.084 72.222 0.00 0.00 36.46 4.45
748 793 2.284699 ACCGGTTCCTCCTCCCAG 60.285 66.667 0.00 0.00 0.00 4.45
749 794 2.284405 GACCGGTTCCTCCTCCCA 60.284 66.667 9.42 0.00 0.00 4.37
750 795 2.039137 AGACCGGTTCCTCCTCCC 59.961 66.667 9.42 0.00 0.00 4.30
751 796 2.359967 CCAGACCGGTTCCTCCTCC 61.360 68.421 9.42 0.00 0.00 4.30
752 797 3.300013 CCAGACCGGTTCCTCCTC 58.700 66.667 9.42 0.00 0.00 3.71
761 806 0.530650 CCGATTCATCACCAGACCGG 60.531 60.000 0.00 0.00 42.50 5.28
762 807 1.154205 GCCGATTCATCACCAGACCG 61.154 60.000 0.00 0.00 0.00 4.79
763 808 0.107703 TGCCGATTCATCACCAGACC 60.108 55.000 0.00 0.00 0.00 3.85
764 809 1.134699 TCTGCCGATTCATCACCAGAC 60.135 52.381 3.47 0.00 32.29 3.51
765 810 1.194218 TCTGCCGATTCATCACCAGA 58.806 50.000 3.47 3.47 33.77 3.86
766 811 1.938577 CTTCTGCCGATTCATCACCAG 59.061 52.381 0.00 0.00 0.00 4.00
767 812 1.554617 TCTTCTGCCGATTCATCACCA 59.445 47.619 0.00 0.00 0.00 4.17
768 813 2.315925 TCTTCTGCCGATTCATCACC 57.684 50.000 0.00 0.00 0.00 4.02
769 814 4.889832 AATTCTTCTGCCGATTCATCAC 57.110 40.909 0.00 0.00 0.00 3.06
798 843 3.467119 CGCCCGTTTGTCGAGACG 61.467 66.667 8.47 8.47 42.86 4.18
874 926 4.217159 GCCGCCGGTAGGTAGGTG 62.217 72.222 17.36 0.00 38.87 4.00
909 961 1.535833 ATCTATACTCCACGCTCCGG 58.464 55.000 0.00 0.00 0.00 5.14
1146 1198 1.658673 GACGAAGACGGTGGTGACT 59.341 57.895 0.00 0.00 44.46 3.41
1236 1288 0.804933 GATGGGTGCGTACGAGGAAC 60.805 60.000 21.65 10.61 0.00 3.62
1268 1335 3.311110 GTGAGTGAGTGCCGGGGA 61.311 66.667 2.18 0.00 0.00 4.81
1269 1336 3.302347 GAGTGAGTGAGTGCCGGGG 62.302 68.421 2.18 0.00 0.00 5.73
1270 1337 2.219325 GAGAGTGAGTGAGTGCCGGG 62.219 65.000 2.18 0.00 0.00 5.73
1272 1339 0.170116 GAGAGAGTGAGTGAGTGCCG 59.830 60.000 0.00 0.00 0.00 5.69
1276 1343 2.235016 GGTGTGAGAGAGTGAGTGAGT 58.765 52.381 0.00 0.00 0.00 3.41
1284 1351 1.194781 AATGGCGGGTGTGAGAGAGT 61.195 55.000 0.00 0.00 0.00 3.24
1286 1353 0.535335 GTAATGGCGGGTGTGAGAGA 59.465 55.000 0.00 0.00 0.00 3.10
1296 1368 1.322338 CGTGTTCGTTAGTAATGGCGG 59.678 52.381 2.28 0.00 0.00 6.13
1325 1416 4.770362 TGCCCAGCTGCATGCCAT 62.770 61.111 16.68 0.00 44.23 4.40
1413 1518 3.079478 ATCCAGGAGCGCTGCAGA 61.079 61.111 31.08 25.40 0.00 4.26
1485 1590 2.519541 CCGATGGCGAGGAGGAGA 60.520 66.667 0.00 0.00 40.82 3.71
1578 1683 1.530655 CTTGGCGGTGGGGAAGTTT 60.531 57.895 0.00 0.00 0.00 2.66
1988 2186 6.295249 TCAGAATGTTGTCAGGTTGTAATGA 58.705 36.000 0.00 0.00 37.40 2.57
2016 2214 4.677779 GCCACAAATGTTGTTCTGTCAGTT 60.678 41.667 0.00 0.00 43.23 3.16
2017 2215 3.181487 GCCACAAATGTTGTTCTGTCAGT 60.181 43.478 0.00 0.00 43.23 3.41
2027 4125 1.262151 GCTGCAAAGCCACAAATGTTG 59.738 47.619 0.00 0.00 0.00 3.33
2095 4198 2.125512 ACTCGAACGCTGATGGCC 60.126 61.111 0.00 0.00 37.74 5.36
2188 4522 1.822613 CATGCAGAGCAGCCCGATT 60.823 57.895 0.00 0.00 43.65 3.34
2248 4582 2.353958 AGCTCCGAGTCGGTGGTA 59.646 61.111 30.68 12.92 46.64 3.25
2314 4648 3.730761 GGCTGCACGCTGTTGAGG 61.731 66.667 0.50 0.00 39.13 3.86
2352 4699 0.326048 ATGGTGTGAGAGGGAGGGAG 60.326 60.000 0.00 0.00 0.00 4.30
2358 4705 1.556911 ACTAGCAATGGTGTGAGAGGG 59.443 52.381 0.00 0.00 0.00 4.30
2403 4768 2.965831 CGACCCCTGAATGAGAGGAATA 59.034 50.000 0.00 0.00 31.48 1.75
2404 4769 1.765314 CGACCCCTGAATGAGAGGAAT 59.235 52.381 0.00 0.00 31.48 3.01
2468 4887 1.600663 CCGAAGATGTAGTAGCAGCCG 60.601 57.143 0.00 0.00 0.00 5.52
2581 5123 7.678171 ACCACAAATACCCTCCTTCATTTTAAT 59.322 33.333 0.00 0.00 0.00 1.40
2801 5467 9.941325 TGAGCATTTTCCATATAAACAACATTT 57.059 25.926 0.00 0.00 0.00 2.32
2803 5469 9.754382 GATGAGCATTTTCCATATAAACAACAT 57.246 29.630 0.00 0.00 0.00 2.71
2808 5477 9.060347 TGAGAGATGAGCATTTTCCATATAAAC 57.940 33.333 0.00 0.00 0.00 2.01
2812 5481 6.151312 GCATGAGAGATGAGCATTTTCCATAT 59.849 38.462 0.00 0.00 0.00 1.78
2821 5490 1.436326 AGGGCATGAGAGATGAGCAT 58.564 50.000 0.00 0.00 0.00 3.79
2944 5630 6.325028 TCTCTCTTTCTTCAGGAAAACAGAGA 59.675 38.462 13.07 13.07 45.65 3.10
2953 5639 2.894126 ACGCTTCTCTCTTTCTTCAGGA 59.106 45.455 0.00 0.00 0.00 3.86
2956 5642 3.056749 GGGTACGCTTCTCTCTTTCTTCA 60.057 47.826 2.05 0.00 0.00 3.02
2973 5659 2.484241 CGCCACAAGGTAATAGGGGTAC 60.484 54.545 0.00 0.00 37.19 3.34
3062 5870 0.114168 AACTTGCTGCCCCAATGGTA 59.886 50.000 0.00 0.00 36.04 3.25
3086 5895 5.796350 ACCACTACGACAAATATCAAAGC 57.204 39.130 0.00 0.00 0.00 3.51
3143 5958 0.729116 CAGTGCTGCTAATTGTCCCG 59.271 55.000 0.00 0.00 0.00 5.14
3170 5985 4.930963 TGTGTAGTGTGCATTCCTTTTTG 58.069 39.130 0.00 0.00 0.00 2.44
3202 6017 6.755141 CAGAAAATCTATTGTGGCAAGATTGG 59.245 38.462 11.74 1.55 39.34 3.16
3290 6106 3.402110 CCTCAAAAAGGGGCAAAATGTC 58.598 45.455 0.00 0.00 42.03 3.06
3291 6107 3.490439 CCTCAAAAAGGGGCAAAATGT 57.510 42.857 0.00 0.00 42.03 2.71
3301 6117 4.575885 TGTCGAGTATTCCCTCAAAAAGG 58.424 43.478 0.00 0.00 45.77 3.11
3302 6118 5.479306 TCTGTCGAGTATTCCCTCAAAAAG 58.521 41.667 0.00 0.00 0.00 2.27
3342 6158 1.816863 TTCTCGCCAGGTGAGACCAC 61.817 60.000 29.35 0.00 46.79 4.16
3395 6211 1.903404 AACTGGAAAGGCGCCTTGG 60.903 57.895 40.75 29.45 36.26 3.61
3503 6326 2.351924 TTTGGGTCCCACTGTCAGCC 62.352 60.000 11.24 0.00 30.78 4.85
3556 6379 1.302511 GTGTGGGCACAGTGGGTAG 60.303 63.158 1.84 0.00 44.64 3.18
3622 6462 1.221566 GGATTGCAATGTTGGGGGC 59.778 57.895 18.59 0.00 0.00 5.80
3633 6473 4.631131 CGTATGAGGTTGATAGGATTGCA 58.369 43.478 0.00 0.00 0.00 4.08
3677 6517 9.358406 TCTAATCATGTTTTGCATAATGGAGAT 57.642 29.630 0.00 0.00 35.74 2.75
3717 6567 0.388649 AGTGATTCAGTCGTGCGACC 60.389 55.000 19.35 6.13 45.59 4.79
3726 6576 3.489355 TGAATGTGGCAAGTGATTCAGT 58.511 40.909 7.87 0.00 32.40 3.41
3755 6606 1.356938 GTAGCTTCGGGTACTGTTGC 58.643 55.000 0.00 0.00 43.29 4.17
3762 6613 2.240667 ACTCTGGTAGTAGCTTCGGGTA 59.759 50.000 0.00 0.00 36.36 3.69
3765 6616 2.753452 TGAACTCTGGTAGTAGCTTCGG 59.247 50.000 0.00 0.00 37.50 4.30
3766 6617 4.082679 ACTTGAACTCTGGTAGTAGCTTCG 60.083 45.833 0.00 0.00 37.50 3.79
3859 6711 2.138656 CTGTTGTGCTCTTGCTGGGC 62.139 60.000 0.00 0.00 40.48 5.36


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

AutoCloner maintained by Alex Coulton.