Multiple sequence alignment - TraesCS2A01G121700

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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 TraesCS2A01G121700 chr2A 100.000 4640 0 0 367 5006 71351083 71346444 0.000000e+00 8569.0
1 TraesCS2A01G121700 chr2A 82.267 1579 139 53 3024 4551 71165601 71164113 0.000000e+00 1234.0
2 TraesCS2A01G121700 chr2A 82.256 1578 141 49 3024 4551 71218384 71216896 0.000000e+00 1234.0
3 TraesCS2A01G121700 chr2A 82.256 1578 141 49 3024 4551 71268057 71266569 0.000000e+00 1234.0
4 TraesCS2A01G121700 chr2A 80.816 1397 142 46 3352 4700 71318810 71317492 0.000000e+00 979.0
5 TraesCS2A01G121700 chr2A 85.744 484 55 9 1989 2462 71124382 71123903 2.690000e-137 499.0
6 TraesCS2A01G121700 chr2A 85.239 481 62 6 1989 2462 71166317 71165839 2.090000e-133 486.0
7 TraesCS2A01G121700 chr2A 87.149 249 30 2 4454 4700 71312344 71312096 1.060000e-71 281.0
8 TraesCS2A01G121700 chr2A 100.000 148 0 0 1 148 71351449 71351302 1.780000e-69 274.0
9 TraesCS2A01G121700 chr2A 84.825 257 29 6 4454 4700 71210787 71210531 2.990000e-62 250.0
10 TraesCS2A01G121700 chr2A 84.825 257 29 6 4454 4700 71263416 71263160 2.990000e-62 250.0
11 TraesCS2A01G121700 chr2A 84.436 257 30 6 4454 4700 71158027 71157771 1.390000e-60 244.0
12 TraesCS2A01G121700 chr2A 84.906 106 15 1 2554 2659 71165813 71165709 6.850000e-19 106.0
13 TraesCS2A01G121700 chr2A 84.906 106 15 1 2554 2659 71218596 71218492 6.850000e-19 106.0
14 TraesCS2A01G121700 chr2D 91.004 4313 263 56 406 4699 72442973 72438767 0.000000e+00 5699.0
15 TraesCS2A01G121700 chr2D 92.367 3734 187 30 685 4386 72702589 72698922 0.000000e+00 5227.0
16 TraesCS2A01G121700 chr2D 83.118 1629 153 51 3125 4700 72660204 72658645 0.000000e+00 1373.0
17 TraesCS2A01G121700 chr2D 80.654 1101 107 45 3637 4700 72379042 72378011 0.000000e+00 756.0
18 TraesCS2A01G121700 chr2D 81.149 870 145 18 1090 1947 72426609 72425747 0.000000e+00 680.0
19 TraesCS2A01G121700 chr2D 80.233 688 123 11 980 1662 72686794 72686115 5.780000e-139 505.0
20 TraesCS2A01G121700 chr2D 84.452 283 39 5 2743 3022 181311822 181312102 1.780000e-69 274.0
21 TraesCS2A01G121700 chr2B 91.204 3979 223 48 765 4700 109936797 109932903 0.000000e+00 5291.0
22 TraesCS2A01G121700 chr2B 89.968 2462 159 42 666 3102 109983488 109981090 0.000000e+00 3097.0
23 TraesCS2A01G121700 chr2B 90.518 1466 73 19 3092 4555 109976428 109975027 0.000000e+00 1877.0
24 TraesCS2A01G121700 chr2B 83.363 1713 167 48 3024 4700 109875988 109874358 0.000000e+00 1476.0
25 TraesCS2A01G121700 chr2B 84.188 1404 120 41 3027 4409 109760098 109758776 0.000000e+00 1269.0
26 TraesCS2A01G121700 chr2B 82.428 1178 159 34 666 1833 110067324 110068463 0.000000e+00 985.0
27 TraesCS2A01G121700 chr2B 85.609 813 73 15 3024 3819 109195035 109194250 0.000000e+00 813.0
28 TraesCS2A01G121700 chr2B 81.033 1007 164 24 956 1947 109931487 109930493 0.000000e+00 776.0
29 TraesCS2A01G121700 chr2B 85.230 501 58 8 1978 2462 109876724 109876224 7.480000e-138 501.0
30 TraesCS2A01G121700 chr2B 83.069 189 23 9 2554 2735 109195275 109195089 4.010000e-36 163.0
31 TraesCS2A01G121700 chr2B 87.059 85 9 2 2652 2735 109760242 109760159 1.480000e-15 95.3
32 TraesCS2A01G121700 chr2B 84.706 85 12 1 2652 2735 109096706 109096622 3.210000e-12 84.2
33 TraesCS2A01G121700 chr2B 91.228 57 5 0 2679 2735 109876098 109876042 1.490000e-10 78.7
34 TraesCS2A01G121700 chrUn 90.859 1805 106 30 2841 4620 289940692 289942462 0.000000e+00 2364.0
35 TraesCS2A01G121700 chrUn 91.964 1655 95 21 1237 2887 289939069 289940689 0.000000e+00 2285.0
36 TraesCS2A01G121700 chrUn 83.654 1713 162 44 3024 4700 235538425 235540055 0.000000e+00 1504.0
37 TraesCS2A01G121700 chrUn 96.615 384 13 0 3376 3759 480865901 480866284 5.470000e-179 638.0
38 TraesCS2A01G121700 chrUn 85.629 501 53 10 1978 2462 235537692 235538189 4.470000e-140 508.0
39 TraesCS2A01G121700 chrUn 91.071 336 21 7 3842 4176 478508832 478509159 3.560000e-121 446.0
40 TraesCS2A01G121700 chrUn 84.825 257 29 6 4454 4700 289659153 289658897 2.990000e-62 250.0
41 TraesCS2A01G121700 chrUn 86.792 106 13 1 2554 2659 235538215 235538319 3.170000e-22 117.0
42 TraesCS2A01G121700 chr4B 87.319 276 30 5 2749 3022 464159012 464159284 1.350000e-80 311.0
43 TraesCS2A01G121700 chr7D 84.588 279 41 2 2743 3020 102552492 102552215 4.940000e-70 276.0
44 TraesCS2A01G121700 chr7A 84.698 281 38 5 2743 3020 175240550 175240828 4.940000e-70 276.0
45 TraesCS2A01G121700 chr3B 86.154 65 9 0 16 80 828340747 828340683 2.500000e-08 71.3
46 TraesCS2A01G121700 chr3D 93.617 47 2 1 12 57 66345803 66345849 8.990000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G121700 chr2A 71346444 71351449 5005 True 4421.500000 8569 100.000000 1 5006 2 chr2A.!!$R9 5005
1 TraesCS2A01G121700 chr2A 71317492 71318810 1318 True 979.000000 979 80.816000 3352 4700 1 chr2A.!!$R5 1348
2 TraesCS2A01G121700 chr2A 71263160 71268057 4897 True 742.000000 1234 83.540500 3024 4700 2 chr2A.!!$R8 1676
3 TraesCS2A01G121700 chr2A 71216896 71218596 1700 True 670.000000 1234 83.581000 2554 4551 2 chr2A.!!$R7 1997
4 TraesCS2A01G121700 chr2A 71164113 71166317 2204 True 608.666667 1234 84.137333 1989 4551 3 chr2A.!!$R6 2562
5 TraesCS2A01G121700 chr2D 72438767 72442973 4206 True 5699.000000 5699 91.004000 406 4699 1 chr2D.!!$R3 4293
6 TraesCS2A01G121700 chr2D 72698922 72702589 3667 True 5227.000000 5227 92.367000 685 4386 1 chr2D.!!$R6 3701
7 TraesCS2A01G121700 chr2D 72658645 72660204 1559 True 1373.000000 1373 83.118000 3125 4700 1 chr2D.!!$R4 1575
8 TraesCS2A01G121700 chr2D 72378011 72379042 1031 True 756.000000 756 80.654000 3637 4700 1 chr2D.!!$R1 1063
9 TraesCS2A01G121700 chr2D 72425747 72426609 862 True 680.000000 680 81.149000 1090 1947 1 chr2D.!!$R2 857
10 TraesCS2A01G121700 chr2D 72686115 72686794 679 True 505.000000 505 80.233000 980 1662 1 chr2D.!!$R5 682
11 TraesCS2A01G121700 chr2B 109981090 109983488 2398 True 3097.000000 3097 89.968000 666 3102 1 chr2B.!!$R3 2436
12 TraesCS2A01G121700 chr2B 109930493 109936797 6304 True 3033.500000 5291 86.118500 765 4700 2 chr2B.!!$R7 3935
13 TraesCS2A01G121700 chr2B 109975027 109976428 1401 True 1877.000000 1877 90.518000 3092 4555 1 chr2B.!!$R2 1463
14 TraesCS2A01G121700 chr2B 110067324 110068463 1139 False 985.000000 985 82.428000 666 1833 1 chr2B.!!$F1 1167
15 TraesCS2A01G121700 chr2B 109874358 109876724 2366 True 685.233333 1476 86.607000 1978 4700 3 chr2B.!!$R6 2722
16 TraesCS2A01G121700 chr2B 109758776 109760242 1466 True 682.150000 1269 85.623500 2652 4409 2 chr2B.!!$R5 1757
17 TraesCS2A01G121700 chr2B 109194250 109195275 1025 True 488.000000 813 84.339000 2554 3819 2 chr2B.!!$R4 1265
18 TraesCS2A01G121700 chrUn 289939069 289942462 3393 False 2324.500000 2364 91.411500 1237 4620 2 chrUn.!!$F4 3383
19 TraesCS2A01G121700 chrUn 235537692 235540055 2363 False 709.666667 1504 85.358333 1978 4700 3 chrUn.!!$F3 2722

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
552 554 0.179156 GCACATTGGGTCATCGCTTG 60.179 55.000 0.00 0.0 0.00 4.01 F
889 955 0.252513 TGGATCCCTTCGTCCCTCAA 60.253 55.000 9.90 0.0 33.45 3.02 F
1459 1525 0.877071 TCGTAAGGGAGTCACGTCAC 59.123 55.000 1.28 0.0 37.02 3.67 F
1759 1825 1.283613 ACTTTGGGTCACTGGTCACAA 59.716 47.619 0.00 0.0 0.00 3.33 F
3190 3419 0.386838 GGCTGCAATATGAAGGTGGC 59.613 55.000 0.50 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1736 0.976641 AAGGTTCGGAGCAGTGATCA 59.023 50.000 11.09 0.00 0.00 2.92 R
2558 2650 2.359900 GTGAACAATGCTCCCTCGAAT 58.640 47.619 0.00 0.00 0.00 3.34 R
2798 2923 2.888414 CCATTCCTACAAACCAAACGGT 59.112 45.455 0.00 0.00 38.95 4.83 R
3573 3818 2.878406 CTGAAGGGGTATACCATTTGCG 59.122 50.000 23.33 3.91 44.71 4.85 R
4043 4295 0.317160 TCGATCGCGGCAGGATTTAT 59.683 50.000 11.09 0.00 38.28 1.40 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
32 33 4.822026 GGAACGGATATCATTGAGGTAGG 58.178 47.826 4.83 0.00 0.00 3.18
33 34 4.322801 GGAACGGATATCATTGAGGTAGGG 60.323 50.000 4.83 0.00 0.00 3.53
34 35 4.127918 ACGGATATCATTGAGGTAGGGA 57.872 45.455 4.83 0.00 0.00 4.20
35 36 4.090090 ACGGATATCATTGAGGTAGGGAG 58.910 47.826 4.83 0.00 0.00 4.30
36 37 4.202684 ACGGATATCATTGAGGTAGGGAGA 60.203 45.833 4.83 0.00 0.00 3.71
37 38 4.400884 CGGATATCATTGAGGTAGGGAGAG 59.599 50.000 4.83 0.00 0.00 3.20
38 39 5.584913 GGATATCATTGAGGTAGGGAGAGA 58.415 45.833 4.83 0.00 0.00 3.10
39 40 5.420739 GGATATCATTGAGGTAGGGAGAGAC 59.579 48.000 4.83 0.00 0.00 3.36
40 41 3.033659 TCATTGAGGTAGGGAGAGACC 57.966 52.381 0.00 0.00 35.83 3.85
41 42 2.314852 TCATTGAGGTAGGGAGAGACCA 59.685 50.000 0.00 0.00 41.20 4.02
42 43 3.107601 CATTGAGGTAGGGAGAGACCAA 58.892 50.000 0.00 0.00 41.20 3.67
43 44 3.269592 TTGAGGTAGGGAGAGACCAAA 57.730 47.619 0.00 0.00 41.20 3.28
44 45 2.821437 TGAGGTAGGGAGAGACCAAAG 58.179 52.381 0.00 0.00 41.20 2.77
45 46 2.382305 TGAGGTAGGGAGAGACCAAAGA 59.618 50.000 0.00 0.00 41.20 2.52
46 47 3.028130 GAGGTAGGGAGAGACCAAAGAG 58.972 54.545 0.00 0.00 41.20 2.85
47 48 2.655407 AGGTAGGGAGAGACCAAAGAGA 59.345 50.000 0.00 0.00 41.20 3.10
48 49 3.273618 AGGTAGGGAGAGACCAAAGAGAT 59.726 47.826 0.00 0.00 41.20 2.75
49 50 3.639561 GGTAGGGAGAGACCAAAGAGATC 59.360 52.174 0.00 0.00 41.20 2.75
50 51 3.774842 AGGGAGAGACCAAAGAGATCT 57.225 47.619 0.00 0.00 41.20 2.75
51 52 4.073425 AGGGAGAGACCAAAGAGATCTT 57.927 45.455 0.00 0.00 41.20 2.40
52 53 5.213868 AGGGAGAGACCAAAGAGATCTTA 57.786 43.478 0.00 0.00 41.20 2.10
53 54 5.787327 AGGGAGAGACCAAAGAGATCTTAT 58.213 41.667 0.00 0.00 41.20 1.73
54 55 6.209026 AGGGAGAGACCAAAGAGATCTTATT 58.791 40.000 0.00 0.00 41.20 1.40
55 56 6.326323 AGGGAGAGACCAAAGAGATCTTATTC 59.674 42.308 0.00 0.00 41.20 1.75
56 57 6.463755 GGGAGAGACCAAAGAGATCTTATTCC 60.464 46.154 0.00 0.00 41.20 3.01
57 58 6.326323 GGAGAGACCAAAGAGATCTTATTCCT 59.674 42.308 0.00 0.00 38.79 3.36
58 59 7.507616 GGAGAGACCAAAGAGATCTTATTCCTA 59.492 40.741 0.00 0.00 38.79 2.94
59 60 8.245195 AGAGACCAAAGAGATCTTATTCCTAC 57.755 38.462 0.00 0.00 34.61 3.18
60 61 7.841729 AGAGACCAAAGAGATCTTATTCCTACA 59.158 37.037 0.00 0.00 34.61 2.74
61 62 7.787028 AGACCAAAGAGATCTTATTCCTACAC 58.213 38.462 0.00 0.00 34.61 2.90
62 63 6.574350 ACCAAAGAGATCTTATTCCTACACG 58.426 40.000 0.00 0.00 34.61 4.49
63 64 6.154706 ACCAAAGAGATCTTATTCCTACACGT 59.845 38.462 0.00 0.00 34.61 4.49
64 65 6.697892 CCAAAGAGATCTTATTCCTACACGTC 59.302 42.308 0.00 0.00 34.61 4.34
65 66 7.258441 CAAAGAGATCTTATTCCTACACGTCA 58.742 38.462 0.00 0.00 34.61 4.35
66 67 7.589958 AAGAGATCTTATTCCTACACGTCAT 57.410 36.000 0.00 0.00 33.79 3.06
67 68 7.589958 AGAGATCTTATTCCTACACGTCATT 57.410 36.000 0.00 0.00 0.00 2.57
68 69 8.693120 AGAGATCTTATTCCTACACGTCATTA 57.307 34.615 0.00 0.00 0.00 1.90
69 70 8.569641 AGAGATCTTATTCCTACACGTCATTAC 58.430 37.037 0.00 0.00 0.00 1.89
70 71 7.659186 AGATCTTATTCCTACACGTCATTACC 58.341 38.462 0.00 0.00 0.00 2.85
71 72 5.824429 TCTTATTCCTACACGTCATTACCG 58.176 41.667 0.00 0.00 0.00 4.02
72 73 2.282701 TTCCTACACGTCATTACCGC 57.717 50.000 0.00 0.00 0.00 5.68
73 74 0.457035 TCCTACACGTCATTACCGCC 59.543 55.000 0.00 0.00 0.00 6.13
74 75 0.868602 CCTACACGTCATTACCGCCG 60.869 60.000 0.00 0.00 0.00 6.46
75 76 1.477030 CTACACGTCATTACCGCCGC 61.477 60.000 0.00 0.00 0.00 6.53
76 77 2.887463 TACACGTCATTACCGCCGCC 62.887 60.000 0.00 0.00 0.00 6.13
77 78 3.766691 ACGTCATTACCGCCGCCT 61.767 61.111 0.00 0.00 0.00 5.52
78 79 2.960129 CGTCATTACCGCCGCCTC 60.960 66.667 0.00 0.00 0.00 4.70
79 80 2.588034 GTCATTACCGCCGCCTCC 60.588 66.667 0.00 0.00 0.00 4.30
80 81 2.762459 TCATTACCGCCGCCTCCT 60.762 61.111 0.00 0.00 0.00 3.69
81 82 2.189521 CATTACCGCCGCCTCCTT 59.810 61.111 0.00 0.00 0.00 3.36
82 83 2.180204 CATTACCGCCGCCTCCTTG 61.180 63.158 0.00 0.00 0.00 3.61
83 84 2.363975 ATTACCGCCGCCTCCTTGA 61.364 57.895 0.00 0.00 0.00 3.02
84 85 1.696097 ATTACCGCCGCCTCCTTGAT 61.696 55.000 0.00 0.00 0.00 2.57
85 86 2.587322 TTACCGCCGCCTCCTTGATG 62.587 60.000 0.00 0.00 0.00 3.07
92 93 4.161295 CCTCCTTGATGCCGCCGA 62.161 66.667 0.00 0.00 0.00 5.54
93 94 2.125147 CTCCTTGATGCCGCCGAA 60.125 61.111 0.00 0.00 0.00 4.30
94 95 1.745115 CTCCTTGATGCCGCCGAAA 60.745 57.895 0.00 0.00 0.00 3.46
95 96 1.302913 TCCTTGATGCCGCCGAAAA 60.303 52.632 0.00 0.00 0.00 2.29
96 97 1.137404 CCTTGATGCCGCCGAAAAG 59.863 57.895 0.00 0.00 0.00 2.27
97 98 1.586154 CCTTGATGCCGCCGAAAAGT 61.586 55.000 0.00 0.00 0.00 2.66
98 99 1.083489 CTTGATGCCGCCGAAAAGTA 58.917 50.000 0.00 0.00 0.00 2.24
99 100 1.670811 CTTGATGCCGCCGAAAAGTAT 59.329 47.619 0.00 0.00 0.00 2.12
100 101 1.013596 TGATGCCGCCGAAAAGTATG 58.986 50.000 0.00 0.00 0.00 2.39
101 102 1.295792 GATGCCGCCGAAAAGTATGA 58.704 50.000 0.00 0.00 0.00 2.15
102 103 1.261619 GATGCCGCCGAAAAGTATGAG 59.738 52.381 0.00 0.00 0.00 2.90
103 104 0.742990 TGCCGCCGAAAAGTATGAGG 60.743 55.000 0.00 0.00 0.00 3.86
104 105 2.014594 CCGCCGAAAAGTATGAGGC 58.985 57.895 0.00 0.00 44.00 4.70
107 108 2.763249 GCCGAAAAGTATGAGGCATG 57.237 50.000 0.00 0.00 46.48 4.06
108 109 1.268743 GCCGAAAAGTATGAGGCATGC 60.269 52.381 9.90 9.90 46.48 4.06
109 110 2.016318 CCGAAAAGTATGAGGCATGCA 58.984 47.619 21.36 0.00 0.00 3.96
110 111 2.423185 CCGAAAAGTATGAGGCATGCAA 59.577 45.455 21.36 4.56 0.00 4.08
111 112 3.067180 CCGAAAAGTATGAGGCATGCAAT 59.933 43.478 21.36 12.16 0.00 3.56
113 114 4.365723 GAAAAGTATGAGGCATGCAATGG 58.634 43.478 21.36 0.00 46.86 3.16
121 122 2.824952 GCATGCAATGGCGTTTTGA 58.175 47.368 14.21 0.00 46.86 2.69
122 123 0.439600 GCATGCAATGGCGTTTTGAC 59.560 50.000 14.21 0.00 46.86 3.18
123 124 1.070038 CATGCAATGGCGTTTTGACC 58.930 50.000 0.00 0.00 45.35 4.02
124 125 0.968405 ATGCAATGGCGTTTTGACCT 59.032 45.000 0.00 0.00 45.35 3.85
125 126 0.749649 TGCAATGGCGTTTTGACCTT 59.250 45.000 0.00 0.00 45.35 3.50
126 127 1.139163 GCAATGGCGTTTTGACCTTG 58.861 50.000 0.00 0.00 0.00 3.61
127 128 1.782044 CAATGGCGTTTTGACCTTGG 58.218 50.000 0.00 0.00 0.00 3.61
128 129 1.339610 CAATGGCGTTTTGACCTTGGA 59.660 47.619 0.00 0.00 0.00 3.53
129 130 1.698506 ATGGCGTTTTGACCTTGGAA 58.301 45.000 0.00 0.00 0.00 3.53
130 131 1.698506 TGGCGTTTTGACCTTGGAAT 58.301 45.000 0.00 0.00 0.00 3.01
131 132 2.865079 TGGCGTTTTGACCTTGGAATA 58.135 42.857 0.00 0.00 0.00 1.75
132 133 3.426615 TGGCGTTTTGACCTTGGAATAT 58.573 40.909 0.00 0.00 0.00 1.28
133 134 4.590918 TGGCGTTTTGACCTTGGAATATA 58.409 39.130 0.00 0.00 0.00 0.86
134 135 5.197451 TGGCGTTTTGACCTTGGAATATAT 58.803 37.500 0.00 0.00 0.00 0.86
135 136 5.654650 TGGCGTTTTGACCTTGGAATATATT 59.345 36.000 0.00 0.00 0.00 1.28
136 137 6.153680 TGGCGTTTTGACCTTGGAATATATTT 59.846 34.615 0.00 0.00 0.00 1.40
137 138 7.039270 GGCGTTTTGACCTTGGAATATATTTT 58.961 34.615 0.00 0.00 0.00 1.82
138 139 7.547722 GGCGTTTTGACCTTGGAATATATTTTT 59.452 33.333 0.00 0.00 0.00 1.94
398 399 9.865321 AGTCCTCTTTAAACCTTTTGTTAAAAC 57.135 29.630 0.00 0.00 35.67 2.43
399 400 9.090692 GTCCTCTTTAAACCTTTTGTTAAAACC 57.909 33.333 0.00 0.00 35.67 3.27
400 401 8.813951 TCCTCTTTAAACCTTTTGTTAAAACCA 58.186 29.630 0.00 0.00 35.67 3.67
401 402 9.438228 CCTCTTTAAACCTTTTGTTAAAACCAA 57.562 29.630 0.00 0.00 35.67 3.67
414 415 8.864069 TTGTTAAAACCAATGTGTATCACTTG 57.136 30.769 1.72 4.10 35.11 3.16
418 419 5.356882 AACCAATGTGTATCACTTGAACG 57.643 39.130 1.72 0.00 35.11 3.95
427 428 4.938832 TGTATCACTTGAACGGGTTTATGG 59.061 41.667 0.00 0.00 0.00 2.74
430 431 2.161609 CACTTGAACGGGTTTATGGCTC 59.838 50.000 0.00 0.00 0.00 4.70
448 449 2.671914 GCTCCTGATGCGCAATTTTTGA 60.672 45.455 17.11 5.84 0.00 2.69
449 450 3.176708 CTCCTGATGCGCAATTTTTGAG 58.823 45.455 17.11 12.15 0.00 3.02
450 451 2.557924 TCCTGATGCGCAATTTTTGAGT 59.442 40.909 17.11 0.00 32.69 3.41
451 452 3.005684 TCCTGATGCGCAATTTTTGAGTT 59.994 39.130 17.11 0.00 32.69 3.01
491 493 3.758554 GTGCATCTGTCCAAGTTTATGGT 59.241 43.478 0.00 0.00 41.46 3.55
495 497 4.715534 TCTGTCCAAGTTTATGGTCCAA 57.284 40.909 0.00 0.00 41.46 3.53
497 499 5.640147 TCTGTCCAAGTTTATGGTCCAATT 58.360 37.500 0.00 0.00 41.46 2.32
536 538 5.938125 TCCAGAATGTTCTAGGTAAAAGCAC 59.062 40.000 0.00 0.00 35.34 4.40
538 540 6.375455 CCAGAATGTTCTAGGTAAAAGCACAT 59.625 38.462 0.00 0.00 33.14 3.21
539 541 7.094205 CCAGAATGTTCTAGGTAAAAGCACATT 60.094 37.037 1.63 1.63 41.46 2.71
541 543 5.957842 TGTTCTAGGTAAAAGCACATTGG 57.042 39.130 0.00 0.00 0.00 3.16
545 547 3.237268 AGGTAAAAGCACATTGGGTCA 57.763 42.857 0.00 0.00 0.00 4.02
552 554 0.179156 GCACATTGGGTCATCGCTTG 60.179 55.000 0.00 0.00 0.00 4.01
587 589 8.752187 AGAATGCATTAGCTTTATTTTTGGAGA 58.248 29.630 12.97 0.00 42.74 3.71
588 590 9.369904 GAATGCATTAGCTTTATTTTTGGAGAA 57.630 29.630 12.97 0.00 42.74 2.87
589 591 9.723601 AATGCATTAGCTTTATTTTTGGAGAAA 57.276 25.926 11.02 0.00 42.74 2.52
590 592 9.895138 ATGCATTAGCTTTATTTTTGGAGAAAT 57.105 25.926 0.00 0.00 42.74 2.17
591 593 9.723601 TGCATTAGCTTTATTTTTGGAGAAATT 57.276 25.926 0.00 0.00 42.74 1.82
698 705 0.549169 TTAGCTAACTGGGCCACCCT 60.549 55.000 0.00 0.00 45.70 4.34
699 706 0.549169 TAGCTAACTGGGCCACCCTT 60.549 55.000 0.00 0.00 45.70 3.95
749 760 2.046023 CCATCGACCCAAGCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
751 762 2.437359 ATCGACCCAAGCAGCAGC 60.437 61.111 0.00 0.00 42.56 5.25
752 763 3.258228 ATCGACCCAAGCAGCAGCA 62.258 57.895 3.17 0.00 45.49 4.41
754 765 2.033141 GACCCAAGCAGCAGCAGA 59.967 61.111 3.17 0.00 45.49 4.26
757 768 4.099170 CCAAGCAGCAGCAGACGC 62.099 66.667 3.17 0.00 45.49 5.19
758 769 4.099170 CAAGCAGCAGCAGACGCC 62.099 66.667 3.17 0.00 45.49 5.68
821 873 5.486526 TCCATCCCCAAAATTTCGAATTTG 58.513 37.500 14.53 14.53 36.52 2.32
831 883 1.680668 TTCGAATTTGAAAAGCGGCG 58.319 45.000 0.51 0.51 0.00 6.46
859 914 0.999406 CACGCCATTTCGACGAATCT 59.001 50.000 11.71 0.00 0.00 2.40
881 936 1.479323 TCCGTAAGTTGGATCCCTTCG 59.521 52.381 9.90 11.18 0.00 3.79
889 955 0.252513 TGGATCCCTTCGTCCCTCAA 60.253 55.000 9.90 0.00 33.45 3.02
908 974 1.158904 ACCCCTCTAGATCCGATCCA 58.841 55.000 4.67 0.00 0.00 3.41
1003 1069 0.933097 CCATCTGCTCGACGAAATGG 59.067 55.000 0.00 6.44 0.00 3.16
1135 1201 2.001361 GCTCCTGCACCACATCATGC 62.001 60.000 0.00 0.00 42.40 4.06
1304 1370 1.152030 ACAGCCTCTTCCTCCACCA 60.152 57.895 0.00 0.00 0.00 4.17
1405 1471 2.029918 TCGTGGATCAGGATTGCTATCG 60.030 50.000 2.01 0.00 0.00 2.92
1453 1519 2.225382 TGGACATCGTAAGGGAGTCA 57.775 50.000 0.00 0.00 35.52 3.41
1458 1524 1.471287 CATCGTAAGGGAGTCACGTCA 59.529 52.381 1.28 0.00 37.02 4.35
1459 1525 0.877071 TCGTAAGGGAGTCACGTCAC 59.123 55.000 1.28 0.00 37.02 3.67
1665 1731 1.686355 AATGCACGTTCAACTGGGAA 58.314 45.000 0.00 0.00 0.00 3.97
1670 1736 2.293399 GCACGTTCAACTGGGAATTCTT 59.707 45.455 5.23 0.00 0.00 2.52
1759 1825 1.283613 ACTTTGGGTCACTGGTCACAA 59.716 47.619 0.00 0.00 0.00 3.33
1970 2045 5.528690 ACATCGGTGATGATAACTTTGGATG 59.471 40.000 13.36 0.00 42.09 3.51
2043 2118 5.059833 CCTAAAGGAAGATATGGACACAGC 58.940 45.833 0.00 0.00 37.39 4.40
2061 2136 5.583457 ACACAGCCGTTACAAGGATAATTAC 59.417 40.000 0.00 0.00 0.00 1.89
2250 2335 3.431415 TGAGAGCCTTTCTACTGCTACA 58.569 45.455 0.00 0.00 35.87 2.74
2253 2338 2.933260 GAGCCTTTCTACTGCTACAAGC 59.067 50.000 0.00 0.00 42.82 4.01
2286 2371 6.554982 TGTTAACTGATGCTGGAGAGGTATAT 59.445 38.462 7.22 0.00 0.00 0.86
2298 2383 7.044496 TGGAGAGGTATATCTATCACCATCA 57.956 40.000 9.75 0.00 34.62 3.07
2388 2480 2.289547 ACATGTTTTCCGGACGTTTCAG 59.710 45.455 1.83 0.00 0.00 3.02
2431 2523 5.839262 TGAACAGAATACATGTGTCGAAC 57.161 39.130 9.11 2.27 0.00 3.95
2432 2524 5.293560 TGAACAGAATACATGTGTCGAACA 58.706 37.500 9.11 0.00 44.79 3.18
2484 2576 8.287503 GTGTCAATACCTGGTTACAAAGTTTAG 58.712 37.037 3.84 0.00 0.00 1.85
2487 2579 9.802039 TCAATACCTGGTTACAAAGTTTAGATT 57.198 29.630 3.84 0.00 0.00 2.40
2558 2650 8.470805 GGAATCAGTTAGATGAAAGACTGTAGA 58.529 37.037 0.00 0.00 40.21 2.59
2609 2701 5.444613 CGTTCTCATAGGATTGTTTGTCGTG 60.445 44.000 0.00 0.00 0.00 4.35
2819 2944 3.569250 CCGTTTGGTTTGTAGGAATGG 57.431 47.619 0.00 0.00 0.00 3.16
2824 2949 5.183140 CGTTTGGTTTGTAGGAATGGATTCT 59.817 40.000 0.00 0.00 37.00 2.40
2830 2955 8.336235 TGGTTTGTAGGAATGGATTCTTATTCT 58.664 33.333 11.32 0.00 37.00 2.40
2916 3093 9.942526 ATGGAAAATTTTCTATCCTATGAACCT 57.057 29.630 25.86 2.53 33.80 3.50
2932 3109 8.043710 CCTATGAACCTAGTGACATCTCTTTTT 58.956 37.037 0.00 0.00 0.00 1.94
2968 3145 3.806380 GATGCATGTCATCTCACTTCCT 58.194 45.455 2.46 0.00 46.29 3.36
3017 3194 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
3018 3195 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
3019 3196 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
3020 3197 2.777692 CCTATGAACCAAAGGAGGCCTA 59.222 50.000 4.42 0.00 31.13 3.93
3021 3198 3.202151 CCTATGAACCAAAGGAGGCCTAA 59.798 47.826 4.42 0.00 31.13 2.69
3153 3382 6.084925 AGTTGATTCGACTTACTACTGTTCG 58.915 40.000 0.33 0.00 0.00 3.95
3190 3419 0.386838 GGCTGCAATATGAAGGTGGC 59.613 55.000 0.50 0.00 0.00 5.01
3573 3818 2.094675 ACCTTGGCACATATGTTCAGC 58.905 47.619 5.37 6.87 39.30 4.26
3754 4000 2.585330 TGACACACATTGCCATGTTCT 58.415 42.857 0.00 0.00 41.16 3.01
3801 4047 4.818546 GTGGCATATGATCTGCTTAGTGTT 59.181 41.667 6.97 0.00 39.60 3.32
3807 4054 7.041576 GCATATGATCTGCTTAGTGTTTCATCA 60.042 37.037 6.97 0.00 36.68 3.07
4043 4295 8.855804 AAGTTTATGAGGGGTCTTCTAGATAA 57.144 34.615 0.00 0.00 0.00 1.75
4066 4318 4.514577 CCTGCCGCGATCGAACCT 62.515 66.667 21.57 0.00 38.10 3.50
4067 4319 3.257561 CTGCCGCGATCGAACCTG 61.258 66.667 21.57 5.62 38.10 4.00
4115 4368 4.500499 AAGAACCCTTGATCTCCATGAG 57.500 45.455 0.00 0.00 0.00 2.90
4149 4402 4.431661 CTTTCAAAGCTTCACTGGATCC 57.568 45.455 4.20 4.20 0.00 3.36
4266 4521 9.772973 TCATATGTGTGTTCTGTAGTAACTTTT 57.227 29.630 1.90 0.00 0.00 2.27
4308 4565 6.610075 AACAAAATTATGGATGCTCCTTGT 57.390 33.333 4.21 2.90 37.46 3.16
4326 4583 2.412870 TGTCTGAATTGTGGTACAGCG 58.587 47.619 0.00 0.00 41.80 5.18
4478 4781 8.837788 TCATATGCAACAGGTAGAATATTGAG 57.162 34.615 0.00 0.00 0.00 3.02
4513 4816 1.402968 CTGCAATCATGTGTGCCTACC 59.597 52.381 17.01 0.00 40.14 3.18
4537 4840 1.640428 TGAGCAGCGAGGTATTTTCG 58.360 50.000 0.00 0.00 40.85 3.46
4555 5487 9.434559 GTATTTTCGCTCTGAATAACAAATACC 57.565 33.333 0.00 0.00 36.22 2.73
4622 5557 9.424319 TGACACAGTTAATAAGAGAGTGAATTC 57.576 33.333 0.00 0.00 0.00 2.17
4625 5560 9.219603 CACAGTTAATAAGAGAGTGAATTCCAA 57.780 33.333 2.27 0.00 0.00 3.53
4642 5578 5.941555 TTCCAATGTTTACCCACTGTTTT 57.058 34.783 0.00 0.00 0.00 2.43
4703 5959 5.065859 CGCCACATTGTACCTCAAAATATGA 59.934 40.000 0.00 0.00 39.62 2.15
4713 5969 6.446781 ACCTCAAAATATGATGCAGTCAAG 57.553 37.500 0.00 0.00 40.97 3.02
4723 5979 1.673665 GCAGTCAAGTGAGCTGGGG 60.674 63.158 0.00 0.00 0.00 4.96
4724 5980 1.757306 CAGTCAAGTGAGCTGGGGT 59.243 57.895 0.00 0.00 0.00 4.95
4738 6400 1.286553 CTGGGGTGGTTTTATGGCCTA 59.713 52.381 3.32 0.00 0.00 3.93
4756 6418 2.106166 CCTATGCTGGCAGAAGGAGATT 59.894 50.000 20.86 0.00 35.98 2.40
4768 6430 5.182001 GCAGAAGGAGATTTAAGAGCAAACA 59.818 40.000 0.00 0.00 0.00 2.83
4783 6445 2.603560 GCAAACATAGTAGAGTCGCCAC 59.396 50.000 0.00 0.00 0.00 5.01
4787 6449 3.882444 ACATAGTAGAGTCGCCACACTA 58.118 45.455 0.00 0.00 0.00 2.74
4846 6509 1.270826 TGCTAGGCTGCTATCGACATC 59.729 52.381 0.00 0.00 0.00 3.06
4893 6565 1.350193 CCGTCCAACGACTGATTCAG 58.650 55.000 12.17 12.17 46.05 3.02
4895 6567 1.670087 CGTCCAACGACTGATTCAGCT 60.670 52.381 13.64 1.29 46.05 4.24
4904 6576 3.326747 GACTGATTCAGCTTTACGGTGT 58.673 45.455 13.64 0.00 41.76 4.16
4915 6587 2.074230 TTACGGTGTGCGTCGTCCTT 62.074 55.000 0.00 0.00 40.31 3.36
4925 6597 0.526211 CGTCGTCCTTGATCCACTCA 59.474 55.000 0.00 0.00 0.00 3.41
4937 6609 4.104086 TGATCCACTCAAAGTAGTCCCAT 58.896 43.478 0.00 0.00 0.00 4.00
4959 6631 1.388547 CCTCTCCCAGAACTCTCTCG 58.611 60.000 0.00 0.00 0.00 4.04
4960 6632 1.388547 CTCTCCCAGAACTCTCTCGG 58.611 60.000 0.00 0.00 31.44 4.63
4961 6633 0.699399 TCTCCCAGAACTCTCTCGGT 59.301 55.000 0.00 0.00 32.09 4.69
4967 6639 0.315568 AGAACTCTCTCGGTGTGTGC 59.684 55.000 0.00 0.00 0.00 4.57
4968 6640 0.667792 GAACTCTCTCGGTGTGTGCC 60.668 60.000 0.00 0.00 0.00 5.01
4977 6664 4.699522 GTGTGTGCCGGGGAGGAC 62.700 72.222 2.18 0.00 45.00 3.85
4999 6686 4.794439 CCGCACCGACATGCTCGA 62.794 66.667 16.06 0.00 46.14 4.04
5000 6687 2.583319 CGCACCGACATGCTCGAT 60.583 61.111 16.06 0.00 46.14 3.59
5002 6689 1.519234 GCACCGACATGCTCGATGA 60.519 57.895 13.95 0.00 46.14 2.92
5003 6690 1.485838 GCACCGACATGCTCGATGAG 61.486 60.000 13.95 4.11 46.14 2.90
5005 6692 1.323271 ACCGACATGCTCGATGAGGT 61.323 55.000 16.06 0.00 46.14 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.386768 ACCTCAATGATATCCGTTCCG 57.613 47.619 0.00 0.00 0.00 4.30
10 11 4.322801 CCCTACCTCAATGATATCCGTTCC 60.323 50.000 0.00 0.00 0.00 3.62
11 12 4.527038 TCCCTACCTCAATGATATCCGTTC 59.473 45.833 0.00 0.00 0.00 3.95
12 13 4.489737 TCCCTACCTCAATGATATCCGTT 58.510 43.478 0.00 0.00 0.00 4.44
13 14 4.090090 CTCCCTACCTCAATGATATCCGT 58.910 47.826 0.00 0.00 0.00 4.69
14 15 4.344978 TCTCCCTACCTCAATGATATCCG 58.655 47.826 0.00 0.00 0.00 4.18
15 16 5.420739 GTCTCTCCCTACCTCAATGATATCC 59.579 48.000 0.00 0.00 0.00 2.59
16 17 5.420739 GGTCTCTCCCTACCTCAATGATATC 59.579 48.000 0.00 0.00 32.72 1.63
17 18 5.162826 TGGTCTCTCCCTACCTCAATGATAT 60.163 44.000 0.00 0.00 36.67 1.63
18 19 4.170053 TGGTCTCTCCCTACCTCAATGATA 59.830 45.833 0.00 0.00 36.67 2.15
19 20 3.051803 TGGTCTCTCCCTACCTCAATGAT 60.052 47.826 0.00 0.00 36.67 2.45
20 21 2.314852 TGGTCTCTCCCTACCTCAATGA 59.685 50.000 0.00 0.00 36.67 2.57
21 22 2.752030 TGGTCTCTCCCTACCTCAATG 58.248 52.381 0.00 0.00 36.67 2.82
22 23 3.491766 TTGGTCTCTCCCTACCTCAAT 57.508 47.619 0.00 0.00 36.67 2.57
23 24 3.173965 CTTTGGTCTCTCCCTACCTCAA 58.826 50.000 0.00 0.00 36.67 3.02
24 25 2.382305 TCTTTGGTCTCTCCCTACCTCA 59.618 50.000 0.00 0.00 36.67 3.86
25 26 3.028130 CTCTTTGGTCTCTCCCTACCTC 58.972 54.545 0.00 0.00 36.67 3.85
26 27 2.655407 TCTCTTTGGTCTCTCCCTACCT 59.345 50.000 0.00 0.00 36.67 3.08
27 28 3.103080 TCTCTTTGGTCTCTCCCTACC 57.897 52.381 0.00 0.00 36.24 3.18
28 29 4.542697 AGATCTCTTTGGTCTCTCCCTAC 58.457 47.826 0.00 0.00 34.77 3.18
29 30 4.890499 AGATCTCTTTGGTCTCTCCCTA 57.110 45.455 0.00 0.00 34.77 3.53
30 31 3.774842 AGATCTCTTTGGTCTCTCCCT 57.225 47.619 0.00 0.00 34.77 4.20
31 32 6.463755 GGAATAAGATCTCTTTGGTCTCTCCC 60.464 46.154 0.00 0.00 37.40 4.30
32 33 6.326323 AGGAATAAGATCTCTTTGGTCTCTCC 59.674 42.308 0.00 0.00 37.40 3.71
33 34 7.360113 AGGAATAAGATCTCTTTGGTCTCTC 57.640 40.000 0.00 0.00 37.40 3.20
34 35 7.841729 TGTAGGAATAAGATCTCTTTGGTCTCT 59.158 37.037 0.00 0.00 37.40 3.10
35 36 7.923878 GTGTAGGAATAAGATCTCTTTGGTCTC 59.076 40.741 0.00 0.00 37.40 3.36
36 37 7.416890 CGTGTAGGAATAAGATCTCTTTGGTCT 60.417 40.741 0.00 0.00 37.40 3.85
37 38 6.697892 CGTGTAGGAATAAGATCTCTTTGGTC 59.302 42.308 0.00 0.00 37.40 4.02
38 39 6.154706 ACGTGTAGGAATAAGATCTCTTTGGT 59.845 38.462 0.00 0.00 37.40 3.67
39 40 6.574350 ACGTGTAGGAATAAGATCTCTTTGG 58.426 40.000 0.00 0.00 37.40 3.28
40 41 7.258441 TGACGTGTAGGAATAAGATCTCTTTG 58.742 38.462 0.00 0.00 37.40 2.77
41 42 7.406031 TGACGTGTAGGAATAAGATCTCTTT 57.594 36.000 0.00 0.00 37.40 2.52
42 43 7.589958 ATGACGTGTAGGAATAAGATCTCTT 57.410 36.000 0.00 0.00 39.85 2.85
43 44 7.589958 AATGACGTGTAGGAATAAGATCTCT 57.410 36.000 0.00 0.00 0.00 3.10
44 45 7.808856 GGTAATGACGTGTAGGAATAAGATCTC 59.191 40.741 0.00 0.00 0.00 2.75
45 46 7.521748 CGGTAATGACGTGTAGGAATAAGATCT 60.522 40.741 0.00 0.00 0.00 2.75
46 47 6.581542 CGGTAATGACGTGTAGGAATAAGATC 59.418 42.308 0.00 0.00 0.00 2.75
47 48 6.444633 CGGTAATGACGTGTAGGAATAAGAT 58.555 40.000 0.00 0.00 0.00 2.40
48 49 5.734220 GCGGTAATGACGTGTAGGAATAAGA 60.734 44.000 0.00 0.00 0.00 2.10
49 50 4.443394 GCGGTAATGACGTGTAGGAATAAG 59.557 45.833 0.00 0.00 0.00 1.73
50 51 4.362279 GCGGTAATGACGTGTAGGAATAA 58.638 43.478 0.00 0.00 0.00 1.40
51 52 3.243501 GGCGGTAATGACGTGTAGGAATA 60.244 47.826 0.00 0.00 0.00 1.75
52 53 2.482490 GGCGGTAATGACGTGTAGGAAT 60.482 50.000 0.00 0.00 0.00 3.01
53 54 1.135024 GGCGGTAATGACGTGTAGGAA 60.135 52.381 0.00 0.00 0.00 3.36
54 55 0.457035 GGCGGTAATGACGTGTAGGA 59.543 55.000 0.00 0.00 0.00 2.94
55 56 0.868602 CGGCGGTAATGACGTGTAGG 60.869 60.000 0.00 0.00 35.06 3.18
56 57 1.477030 GCGGCGGTAATGACGTGTAG 61.477 60.000 9.78 0.00 44.01 2.74
57 58 1.516821 GCGGCGGTAATGACGTGTA 60.517 57.895 9.78 0.00 44.01 2.90
58 59 2.812178 GCGGCGGTAATGACGTGT 60.812 61.111 9.78 0.00 44.01 4.49
59 60 3.560278 GGCGGCGGTAATGACGTG 61.560 66.667 9.78 0.00 44.01 4.49
60 61 3.711541 GAGGCGGCGGTAATGACGT 62.712 63.158 9.78 0.00 44.01 4.34
61 62 2.960129 GAGGCGGCGGTAATGACG 60.960 66.667 9.78 0.00 45.26 4.35
62 63 2.588034 GGAGGCGGCGGTAATGAC 60.588 66.667 9.78 0.00 0.00 3.06
63 64 2.363975 AAGGAGGCGGCGGTAATGA 61.364 57.895 9.78 0.00 0.00 2.57
64 65 2.180204 CAAGGAGGCGGCGGTAATG 61.180 63.158 9.78 0.00 0.00 1.90
65 66 1.696097 ATCAAGGAGGCGGCGGTAAT 61.696 55.000 9.78 0.00 0.00 1.89
66 67 2.363975 ATCAAGGAGGCGGCGGTAA 61.364 57.895 9.78 0.00 0.00 2.85
67 68 2.762459 ATCAAGGAGGCGGCGGTA 60.762 61.111 9.78 0.00 0.00 4.02
68 69 4.473520 CATCAAGGAGGCGGCGGT 62.474 66.667 9.78 0.00 0.00 5.68
75 76 3.680620 TTCGGCGGCATCAAGGAGG 62.681 63.158 10.53 0.00 0.00 4.30
76 77 1.305219 TTTTCGGCGGCATCAAGGAG 61.305 55.000 10.53 0.00 0.00 3.69
77 78 1.302913 TTTTCGGCGGCATCAAGGA 60.303 52.632 10.53 0.00 0.00 3.36
78 79 1.137404 CTTTTCGGCGGCATCAAGG 59.863 57.895 10.53 0.00 0.00 3.61
79 80 1.083489 TACTTTTCGGCGGCATCAAG 58.917 50.000 10.53 9.51 0.00 3.02
80 81 1.400142 CATACTTTTCGGCGGCATCAA 59.600 47.619 10.53 0.00 0.00 2.57
81 82 1.013596 CATACTTTTCGGCGGCATCA 58.986 50.000 10.53 0.00 0.00 3.07
82 83 1.261619 CTCATACTTTTCGGCGGCATC 59.738 52.381 10.53 0.00 0.00 3.91
83 84 1.299541 CTCATACTTTTCGGCGGCAT 58.700 50.000 10.53 0.00 0.00 4.40
84 85 0.742990 CCTCATACTTTTCGGCGGCA 60.743 55.000 10.53 0.00 0.00 5.69
85 86 2.014594 CCTCATACTTTTCGGCGGC 58.985 57.895 7.21 0.00 0.00 6.53
86 87 0.742990 TGCCTCATACTTTTCGGCGG 60.743 55.000 7.21 0.00 43.54 6.13
87 88 1.003545 CATGCCTCATACTTTTCGGCG 60.004 52.381 0.00 0.00 43.54 6.46
88 89 1.268743 GCATGCCTCATACTTTTCGGC 60.269 52.381 6.36 0.00 41.06 5.54
89 90 2.016318 TGCATGCCTCATACTTTTCGG 58.984 47.619 16.68 0.00 0.00 4.30
90 91 3.763097 TTGCATGCCTCATACTTTTCG 57.237 42.857 16.68 0.00 0.00 3.46
91 92 4.365723 CCATTGCATGCCTCATACTTTTC 58.634 43.478 16.68 0.00 0.00 2.29
92 93 3.431207 GCCATTGCATGCCTCATACTTTT 60.431 43.478 16.68 0.00 37.47 2.27
93 94 2.101917 GCCATTGCATGCCTCATACTTT 59.898 45.455 16.68 0.00 37.47 2.66
94 95 1.684983 GCCATTGCATGCCTCATACTT 59.315 47.619 16.68 0.00 37.47 2.24
95 96 1.325355 GCCATTGCATGCCTCATACT 58.675 50.000 16.68 0.00 37.47 2.12
96 97 0.039798 CGCCATTGCATGCCTCATAC 60.040 55.000 16.68 0.00 37.32 2.39
97 98 0.466007 ACGCCATTGCATGCCTCATA 60.466 50.000 16.68 0.00 37.32 2.15
98 99 1.324740 AACGCCATTGCATGCCTCAT 61.325 50.000 16.68 1.38 37.32 2.90
99 100 1.534336 AAACGCCATTGCATGCCTCA 61.534 50.000 16.68 0.00 37.32 3.86
100 101 0.390209 AAAACGCCATTGCATGCCTC 60.390 50.000 16.68 0.00 37.32 4.70
101 102 0.671163 CAAAACGCCATTGCATGCCT 60.671 50.000 16.68 0.00 37.32 4.75
102 103 0.669932 TCAAAACGCCATTGCATGCC 60.670 50.000 16.68 0.00 37.32 4.40
103 104 0.439600 GTCAAAACGCCATTGCATGC 59.560 50.000 11.82 11.82 37.32 4.06
104 105 1.070038 GGTCAAAACGCCATTGCATG 58.930 50.000 0.00 0.00 37.32 4.06
105 106 0.968405 AGGTCAAAACGCCATTGCAT 59.032 45.000 0.00 0.00 37.32 3.96
106 107 0.749649 AAGGTCAAAACGCCATTGCA 59.250 45.000 0.00 0.00 37.32 4.08
107 108 1.139163 CAAGGTCAAAACGCCATTGC 58.861 50.000 0.00 0.00 0.00 3.56
108 109 1.339610 TCCAAGGTCAAAACGCCATTG 59.660 47.619 0.00 0.00 0.00 2.82
109 110 1.698506 TCCAAGGTCAAAACGCCATT 58.301 45.000 0.00 0.00 0.00 3.16
110 111 1.698506 TTCCAAGGTCAAAACGCCAT 58.301 45.000 0.00 0.00 0.00 4.40
111 112 1.698506 ATTCCAAGGTCAAAACGCCA 58.301 45.000 0.00 0.00 0.00 5.69
112 113 5.767816 ATATATTCCAAGGTCAAAACGCC 57.232 39.130 0.00 0.00 0.00 5.68
113 114 8.474006 AAAAATATATTCCAAGGTCAAAACGC 57.526 30.769 0.00 0.00 0.00 4.84
372 373 9.865321 GTTTTAACAAAAGGTTTAAAGAGGACT 57.135 29.630 0.00 0.00 38.31 3.85
373 374 9.090692 GGTTTTAACAAAAGGTTTAAAGAGGAC 57.909 33.333 0.00 0.00 38.31 3.85
374 375 8.813951 TGGTTTTAACAAAAGGTTTAAAGAGGA 58.186 29.630 0.00 0.00 38.31 3.71
375 376 9.438228 TTGGTTTTAACAAAAGGTTTAAAGAGG 57.562 29.630 0.00 0.00 38.31 3.69
380 381 9.503399 ACACATTGGTTTTAACAAAAGGTTTAA 57.497 25.926 0.00 0.00 40.96 1.52
382 383 7.987750 ACACATTGGTTTTAACAAAAGGTTT 57.012 28.000 0.00 0.00 40.96 3.27
383 384 9.320352 GATACACATTGGTTTTAACAAAAGGTT 57.680 29.630 0.00 0.00 43.62 3.50
384 385 8.478877 TGATACACATTGGTTTTAACAAAAGGT 58.521 29.630 0.00 0.00 0.00 3.50
385 386 8.760569 GTGATACACATTGGTTTTAACAAAAGG 58.239 33.333 0.00 0.00 34.08 3.11
386 387 9.528018 AGTGATACACATTGGTTTTAACAAAAG 57.472 29.630 4.75 0.00 36.74 2.27
387 388 9.877178 AAGTGATACACATTGGTTTTAACAAAA 57.123 25.926 4.75 0.00 36.74 2.44
388 389 9.307121 CAAGTGATACACATTGGTTTTAACAAA 57.693 29.630 4.75 0.00 36.74 2.83
389 390 8.687242 TCAAGTGATACACATTGGTTTTAACAA 58.313 29.630 4.75 0.00 36.74 2.83
390 391 8.226819 TCAAGTGATACACATTGGTTTTAACA 57.773 30.769 4.75 0.00 36.74 2.41
391 392 8.964150 GTTCAAGTGATACACATTGGTTTTAAC 58.036 33.333 4.75 0.00 36.74 2.01
392 393 7.858382 CGTTCAAGTGATACACATTGGTTTTAA 59.142 33.333 4.75 0.00 36.74 1.52
393 394 7.356540 CGTTCAAGTGATACACATTGGTTTTA 58.643 34.615 4.75 0.00 36.74 1.52
394 395 6.205784 CGTTCAAGTGATACACATTGGTTTT 58.794 36.000 4.75 0.00 36.74 2.43
395 396 5.278266 CCGTTCAAGTGATACACATTGGTTT 60.278 40.000 4.75 0.00 36.74 3.27
396 397 4.215399 CCGTTCAAGTGATACACATTGGTT 59.785 41.667 4.75 0.00 36.74 3.67
397 398 3.751175 CCGTTCAAGTGATACACATTGGT 59.249 43.478 4.75 0.00 36.74 3.67
398 399 3.126858 CCCGTTCAAGTGATACACATTGG 59.873 47.826 4.75 0.00 36.74 3.16
399 400 3.751175 ACCCGTTCAAGTGATACACATTG 59.249 43.478 4.75 6.30 36.74 2.82
400 401 4.015872 ACCCGTTCAAGTGATACACATT 57.984 40.909 4.75 0.00 36.74 2.71
401 402 3.695830 ACCCGTTCAAGTGATACACAT 57.304 42.857 4.75 0.00 36.74 3.21
402 403 3.478857 AACCCGTTCAAGTGATACACA 57.521 42.857 4.75 0.00 36.74 3.72
403 404 5.163794 CCATAAACCCGTTCAAGTGATACAC 60.164 44.000 0.00 0.00 34.10 2.90
404 405 4.938832 CCATAAACCCGTTCAAGTGATACA 59.061 41.667 0.00 0.00 0.00 2.29
414 415 1.065709 TCAGGAGCCATAAACCCGTTC 60.066 52.381 0.00 0.00 0.00 3.95
418 419 1.322442 GCATCAGGAGCCATAAACCC 58.678 55.000 0.00 0.00 0.00 4.11
427 428 1.657094 CAAAAATTGCGCATCAGGAGC 59.343 47.619 12.75 0.00 43.33 4.70
430 431 2.950433 ACTCAAAAATTGCGCATCAGG 58.050 42.857 12.75 0.00 0.00 3.86
448 449 7.721402 TGCACACTTTTGTCCATTAATTAACT 58.279 30.769 0.00 0.00 31.66 2.24
449 450 7.938563 TGCACACTTTTGTCCATTAATTAAC 57.061 32.000 0.00 0.00 31.66 2.01
450 451 8.584157 AGATGCACACTTTTGTCCATTAATTAA 58.416 29.630 0.00 0.00 31.66 1.40
451 452 8.028354 CAGATGCACACTTTTGTCCATTAATTA 58.972 33.333 0.00 0.00 31.66 1.40
464 465 2.936202 ACTTGGACAGATGCACACTTT 58.064 42.857 0.00 0.00 0.00 2.66
508 510 7.822822 GCTTTTACCTAGAACATTCTGGACTAA 59.177 37.037 6.57 0.41 37.94 2.24
510 512 6.174049 GCTTTTACCTAGAACATTCTGGACT 58.826 40.000 6.57 0.00 37.94 3.85
511 513 5.938125 TGCTTTTACCTAGAACATTCTGGAC 59.062 40.000 6.57 0.00 37.94 4.02
512 514 5.938125 GTGCTTTTACCTAGAACATTCTGGA 59.062 40.000 6.57 0.00 37.94 3.86
513 515 5.705441 TGTGCTTTTACCTAGAACATTCTGG 59.295 40.000 4.34 1.21 38.19 3.86
514 516 6.801539 TGTGCTTTTACCTAGAACATTCTG 57.198 37.500 4.34 0.00 38.19 3.02
515 517 7.094205 CCAATGTGCTTTTACCTAGAACATTCT 60.094 37.037 6.29 0.00 44.80 2.40
516 518 7.029563 CCAATGTGCTTTTACCTAGAACATTC 58.970 38.462 6.29 0.00 44.80 2.67
523 525 4.331968 TGACCCAATGTGCTTTTACCTAG 58.668 43.478 0.00 0.00 0.00 3.02
528 530 2.163412 GCGATGACCCAATGTGCTTTTA 59.837 45.455 0.00 0.00 0.00 1.52
536 538 1.402968 CTTCCAAGCGATGACCCAATG 59.597 52.381 0.00 0.00 0.00 2.82
538 540 0.960364 GCTTCCAAGCGATGACCCAA 60.960 55.000 0.00 0.00 42.88 4.12
539 541 1.377202 GCTTCCAAGCGATGACCCA 60.377 57.895 0.00 0.00 42.88 4.51
552 554 4.133078 AGCTAATGCATTCTACTGCTTCC 58.867 43.478 16.86 0.00 42.75 3.46
651 653 9.182214 CCATCTATTTCTCTGAATTTCCTCAAA 57.818 33.333 0.00 0.00 0.00 2.69
653 655 8.094284 TCCATCTATTTCTCTGAATTTCCTCA 57.906 34.615 0.00 0.00 0.00 3.86
662 664 9.373450 AGTTAGCTAATCCATCTATTTCTCTGA 57.627 33.333 9.88 0.00 0.00 3.27
663 665 9.421806 CAGTTAGCTAATCCATCTATTTCTCTG 57.578 37.037 9.88 3.30 0.00 3.35
664 666 8.592809 CCAGTTAGCTAATCCATCTATTTCTCT 58.407 37.037 9.88 0.00 0.00 3.10
698 705 1.328069 CTGTCGCGTGTGTTACCAAAA 59.672 47.619 5.77 0.00 0.00 2.44
699 706 0.931702 CTGTCGCGTGTGTTACCAAA 59.068 50.000 5.77 0.00 0.00 3.28
749 760 2.361610 CAAATGGGGGCGTCTGCT 60.362 61.111 0.00 0.00 42.25 4.24
751 762 2.361610 AGCAAATGGGGGCGTCTG 60.362 61.111 0.00 0.00 34.54 3.51
752 763 2.361610 CAGCAAATGGGGGCGTCT 60.362 61.111 0.00 0.00 34.54 4.18
821 873 0.166161 GGAGTTCTTCGCCGCTTTTC 59.834 55.000 0.00 0.00 0.00 2.29
831 883 1.128692 CGAAATGGCGTGGAGTTCTTC 59.871 52.381 0.00 0.00 0.00 2.87
859 914 2.544844 AGGGATCCAACTTACGGAGA 57.455 50.000 15.23 0.00 35.56 3.71
881 936 2.321719 GATCTAGAGGGGTTGAGGGAC 58.678 57.143 0.00 0.00 0.00 4.46
889 955 1.158904 TGGATCGGATCTAGAGGGGT 58.841 55.000 16.96 0.00 0.00 4.95
908 974 4.532126 TGGAGGAATATGCGTATGGAGATT 59.468 41.667 0.00 0.00 29.40 2.40
1075 1141 4.702081 GTCGACAGTGACGGCGCT 62.702 66.667 11.55 0.00 34.57 5.92
1084 1150 4.057428 GCTGAGGCGGTCGACAGT 62.057 66.667 18.91 0.00 33.57 3.55
1135 1201 2.742372 CCACGCCTTCAGGAACGG 60.742 66.667 0.00 0.00 37.39 4.44
1453 1519 4.640855 CACGCGGTCCAGTGACGT 62.641 66.667 12.47 0.00 42.73 4.34
1665 1731 3.265791 GTTCGGAGCAGTGATCAAGAAT 58.734 45.455 17.40 0.00 0.00 2.40
1670 1736 0.976641 AAGGTTCGGAGCAGTGATCA 59.023 50.000 11.09 0.00 0.00 2.92
1938 2013 6.931281 AGTTATCATCACCGATGTATCCAAAG 59.069 38.462 4.03 0.00 40.55 2.77
1951 2026 5.300034 TGATGCATCCAAAGTTATCATCACC 59.700 40.000 23.67 0.00 35.39 4.02
2043 2118 8.653338 CCATAATCGTAATTATCCTTGTAACGG 58.347 37.037 0.00 0.00 36.18 4.44
2250 2335 4.022849 GCATCAGTTAACAACTCCAAGCTT 60.023 41.667 8.61 0.00 40.46 3.74
2253 2338 4.083110 CCAGCATCAGTTAACAACTCCAAG 60.083 45.833 8.61 0.00 40.46 3.61
2298 2383 7.619302 AGAGAGGAAAGAGACAGATCAGTAAAT 59.381 37.037 0.00 0.00 0.00 1.40
2348 2433 3.638860 TGTCCCATGATAACTACGGTCT 58.361 45.455 0.00 0.00 0.00 3.85
2350 2435 3.709653 ACATGTCCCATGATAACTACGGT 59.290 43.478 10.96 0.00 0.00 4.83
2353 2442 6.238374 CGGAAAACATGTCCCATGATAACTAC 60.238 42.308 10.96 0.00 0.00 2.73
2371 2463 3.310501 TCTTTCTGAAACGTCCGGAAAAC 59.689 43.478 5.23 0.00 29.89 2.43
2388 2480 4.274950 TCAAGGGAACACGATGTTTCTTTC 59.725 41.667 8.44 0.00 41.28 2.62
2431 2523 4.037208 AGCAGAAGGTCAGAAATGTGTTTG 59.963 41.667 0.00 0.00 0.00 2.93
2432 2524 4.210331 AGCAGAAGGTCAGAAATGTGTTT 58.790 39.130 0.00 0.00 0.00 2.83
2529 2621 7.400339 ACAGTCTTTCATCTAACTGATTCCCTA 59.600 37.037 8.24 0.00 41.26 3.53
2530 2622 6.214412 ACAGTCTTTCATCTAACTGATTCCCT 59.786 38.462 8.24 0.00 41.26 4.20
2531 2623 6.410540 ACAGTCTTTCATCTAACTGATTCCC 58.589 40.000 8.24 0.00 41.26 3.97
2558 2650 2.359900 GTGAACAATGCTCCCTCGAAT 58.640 47.619 0.00 0.00 0.00 3.34
2609 2701 4.485163 ACACTGTTGCAACAAAGAGAAAC 58.515 39.130 30.62 2.15 38.66 2.78
2695 2819 3.579534 ACATCGGCCTTAGACTCTCTA 57.420 47.619 0.00 0.00 0.00 2.43
2781 2905 8.248253 ACCAAACGGTTCTATATGAAATTTTCC 58.752 33.333 6.68 0.00 36.30 3.13
2791 2916 6.949715 TCCTACAAACCAAACGGTTCTATAT 58.050 36.000 0.00 0.00 46.41 0.86
2798 2923 2.888414 CCATTCCTACAAACCAAACGGT 59.112 45.455 0.00 0.00 38.95 4.83
2801 2926 6.590234 AGAATCCATTCCTACAAACCAAAC 57.410 37.500 0.00 0.00 37.51 2.93
2839 2965 6.373005 TGAAATGTGAAGGATAGGAACAGA 57.627 37.500 0.00 0.00 0.00 3.41
2898 3075 8.603898 TGTCACTAGGTTCATAGGATAGAAAA 57.396 34.615 0.00 0.00 0.00 2.29
2901 3078 7.760607 AGATGTCACTAGGTTCATAGGATAGA 58.239 38.462 0.00 0.00 0.00 1.98
2932 3109 5.150715 ACATGCATCTCAGTTCCTATAGGA 58.849 41.667 18.00 18.00 43.73 2.94
3087 3315 6.651643 ACAAACTGCATACGAGTGGTTTATTA 59.348 34.615 0.00 0.00 0.00 0.98
3153 3382 4.859245 GCAGCCAAAAGAGTATTTAGCAAC 59.141 41.667 7.63 0.00 30.67 4.17
3190 3419 5.645497 CACCTTTTCAATTCCCTACTCAGAG 59.355 44.000 0.00 0.00 0.00 3.35
3397 3642 7.041107 ACCAAATTGTTATTAAGCATGCGATT 58.959 30.769 13.01 4.59 0.00 3.34
3573 3818 2.878406 CTGAAGGGGTATACCATTTGCG 59.122 50.000 23.33 3.91 44.71 4.85
3680 3926 5.529581 AAACCAACAAACCAGTAAGGATG 57.470 39.130 0.00 0.00 41.22 3.51
3681 3927 8.966868 CATATAAACCAACAAACCAGTAAGGAT 58.033 33.333 0.00 0.00 41.22 3.24
3775 4021 4.840680 ACTAAGCAGATCATATGCCACCTA 59.159 41.667 0.00 0.00 44.97 3.08
4015 4267 6.960542 TCTAGAAGACCCCTCATAAACTTCTT 59.039 38.462 0.00 0.00 42.23 2.52
4025 4277 8.242325 AGGATTTATTATCTAGAAGACCCCTCA 58.758 37.037 0.00 0.00 0.00 3.86
4043 4295 0.317160 TCGATCGCGGCAGGATTTAT 59.683 50.000 11.09 0.00 38.28 1.40
4066 4318 5.104527 AGGTCCTTGCTAACTACATAATGCA 60.105 40.000 0.00 0.00 0.00 3.96
4067 4319 5.368989 AGGTCCTTGCTAACTACATAATGC 58.631 41.667 0.00 0.00 0.00 3.56
4266 4521 8.680039 TTTTGTTTCTATTCCGGTAAGAAAGA 57.320 30.769 20.98 18.51 39.28 2.52
4308 4565 1.621317 TCCGCTGTACCACAATTCAGA 59.379 47.619 0.00 0.00 0.00 3.27
4326 4583 4.213482 AGTGAAACAACAAAGCGTATCTCC 59.787 41.667 0.00 0.00 41.43 3.71
4342 4599 3.921021 CAGTCATACTGTCGGAGTGAAAC 59.079 47.826 9.60 0.00 41.19 2.78
4459 4756 6.017852 GCTTACCTCAATATTCTACCTGTTGC 60.018 42.308 0.00 0.00 0.00 4.17
4513 4816 3.377346 AATACCTCGCTGCTCATAGTG 57.623 47.619 0.00 0.00 0.00 2.74
4537 4840 6.801862 GTGTGTTGGTATTTGTTATTCAGAGC 59.198 38.462 0.00 0.00 0.00 4.09
4596 5531 9.424319 GAATTCACTCTCTTATTAACTGTGTCA 57.576 33.333 0.00 0.00 0.00 3.58
4622 5557 5.423886 ACAAAAACAGTGGGTAAACATTGG 58.576 37.500 0.00 0.00 32.97 3.16
4625 5560 8.261522 ACAAATACAAAAACAGTGGGTAAACAT 58.738 29.630 0.00 0.00 0.00 2.71
4627 5562 7.760340 TCACAAATACAAAAACAGTGGGTAAAC 59.240 33.333 0.00 0.00 0.00 2.01
4664 5600 4.873746 TGTGGCGGAAAATTTAAATGGA 57.126 36.364 0.39 0.00 0.00 3.41
4703 5959 0.322277 CCCAGCTCACTTGACTGCAT 60.322 55.000 0.00 0.00 0.00 3.96
4713 5969 1.818674 CATAAAACCACCCCAGCTCAC 59.181 52.381 0.00 0.00 0.00 3.51
4723 5979 2.362077 CCAGCATAGGCCATAAAACCAC 59.638 50.000 5.01 0.00 42.56 4.16
4724 5980 2.665165 CCAGCATAGGCCATAAAACCA 58.335 47.619 5.01 0.00 42.56 3.67
4738 6400 2.822707 AAATCTCCTTCTGCCAGCAT 57.177 45.000 0.00 0.00 0.00 3.79
4749 6411 8.982723 TCTACTATGTTTGCTCTTAAATCTCCT 58.017 33.333 0.00 0.00 0.00 3.69
4756 6418 6.034591 GCGACTCTACTATGTTTGCTCTTAA 58.965 40.000 0.00 0.00 0.00 1.85
4768 6430 3.253677 GCATAGTGTGGCGACTCTACTAT 59.746 47.826 12.05 8.29 35.56 2.12
4783 6445 1.224075 CGGCCTTCAGATGCATAGTG 58.776 55.000 0.00 0.00 0.00 2.74
4787 6449 2.517875 GCCGGCCTTCAGATGCAT 60.518 61.111 18.11 0.00 0.00 3.96
4814 6476 1.279271 AGCCTAGCAGAAAATGGACGT 59.721 47.619 0.00 0.00 0.00 4.34
4821 6483 2.430694 TCGATAGCAGCCTAGCAGAAAA 59.569 45.455 0.00 0.00 36.85 2.29
4880 6552 2.993899 CCGTAAAGCTGAATCAGTCGTT 59.006 45.455 12.29 10.65 33.43 3.85
4904 6576 1.080093 GTGGATCAAGGACGACGCA 60.080 57.895 0.00 0.00 0.00 5.24
4915 6587 3.516586 TGGGACTACTTTGAGTGGATCA 58.483 45.455 0.00 0.00 35.62 2.92
4925 6597 3.632906 GGGAGAGGGTATGGGACTACTTT 60.633 52.174 0.00 0.00 0.00 2.66
4937 6609 2.242708 GAGAGAGTTCTGGGAGAGGGTA 59.757 54.545 0.00 0.00 32.53 3.69
4960 6632 4.699522 GTCCTCCCCGGCACACAC 62.700 72.222 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.