Multiple sequence alignment - TraesCS3D01G188500

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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 TraesCS3D01G188500 chr3D 100.000 3098 0 0 1 3098 175400514 175403611 0.000000e+00 5722.0
1 TraesCS3D01G188500 chr3D 87.023 131 17 0 2 132 394614172 394614302 6.920000e-32 148.0
2 TraesCS3D01G188500 chr3D 93.617 47 3 0 1604 1650 382753612 382753566 1.540000e-08 71.3
3 TraesCS3D01G188500 chr3D 93.617 47 3 0 1604 1650 383110639 383110593 1.540000e-08 71.3
4 TraesCS3D01G188500 chr3A 93.548 2294 62 31 159 2417 215471074 215473316 0.000000e+00 3338.0
5 TraesCS3D01G188500 chr3A 89.568 278 6 4 2635 2901 215473455 215473720 6.400000e-87 331.0
6 TraesCS3D01G188500 chr3A 81.203 133 23 1 2 132 663444777 663444645 4.230000e-19 106.0
7 TraesCS3D01G188500 chr3A 96.970 33 1 0 2473 2505 75538256 75538224 4.320000e-04 56.5
8 TraesCS3D01G188500 chr3A 92.500 40 0 3 135 174 9037607 9037643 2.000000e-03 54.7
9 TraesCS3D01G188500 chr3B 96.088 1866 49 12 174 2033 254767638 254769485 0.000000e+00 3020.0
10 TraesCS3D01G188500 chr3B 90.092 434 19 4 2029 2455 254773742 254774158 2.720000e-150 542.0
11 TraesCS3D01G188500 chr3B 93.200 250 5 1 2722 2971 254774673 254774910 1.060000e-94 357.0
12 TraesCS3D01G188500 chr3B 90.230 174 5 7 2557 2725 254774181 254774347 1.870000e-52 217.0
13 TraesCS3D01G188500 chr3B 89.908 109 10 1 2969 3077 59980833 59980726 4.170000e-29 139.0
14 TraesCS3D01G188500 chr2D 87.786 131 16 0 2 132 22787390 22787260 1.490000e-33 154.0
15 TraesCS3D01G188500 chr2D 88.034 117 13 1 2967 3083 593429700 593429585 1.500000e-28 137.0
16 TraesCS3D01G188500 chr2D 93.617 47 3 0 1603 1649 599287941 599287895 1.540000e-08 71.3
17 TraesCS3D01G188500 chr7D 90.909 110 9 1 2969 3078 579148701 579148809 2.490000e-31 147.0
18 TraesCS3D01G188500 chr7D 89.286 112 11 1 2968 3079 90544355 90544245 4.170000e-29 139.0
19 TraesCS3D01G188500 chr7D 86.667 60 4 2 2471 2526 108623512 108623571 2.580000e-06 63.9
20 TraesCS3D01G188500 chr7B 90.909 110 9 1 2969 3078 677714502 677714394 2.490000e-31 147.0
21 TraesCS3D01G188500 chr4B 89.565 115 11 1 2969 3083 654206457 654206344 8.950000e-31 145.0
22 TraesCS3D01G188500 chr4B 88.312 77 8 1 2469 2544 59232246 59232322 1.180000e-14 91.6
23 TraesCS3D01G188500 chr4B 97.500 40 1 0 2484 2523 650954617 650954578 5.540000e-08 69.4
24 TraesCS3D01G188500 chr1B 89.286 112 11 1 2967 3078 686862661 686862771 4.170000e-29 139.0
25 TraesCS3D01G188500 chr1B 83.333 132 20 2 2 132 265973389 265973519 1.510000e-23 121.0
26 TraesCS3D01G188500 chr1B 80.916 131 23 2 2 132 604104406 604104534 5.470000e-18 102.0
27 TraesCS3D01G188500 chr1D 88.034 117 11 3 2961 3076 19774674 19774788 5.390000e-28 135.0
28 TraesCS3D01G188500 chr5D 85.156 128 19 0 2 129 59236661 59236534 6.970000e-27 132.0
29 TraesCS3D01G188500 chr5D 81.148 122 22 1 2 123 371855257 371855137 2.540000e-16 97.1
30 TraesCS3D01G188500 chr5B 84.962 133 16 3 2 132 485871569 485871439 6.970000e-27 132.0
31 TraesCS3D01G188500 chr5B 94.595 37 2 0 2473 2509 360426181 360426145 1.200000e-04 58.4
32 TraesCS3D01G188500 chr2B 85.600 125 17 1 2954 3078 518517786 518517909 2.510000e-26 130.0
33 TraesCS3D01G188500 chr2B 94.737 38 1 1 135 172 620856889 620856925 1.200000e-04 58.4
34 TraesCS3D01G188500 chr2B 92.500 40 1 2 135 172 420506019 420506058 4.320000e-04 56.5
35 TraesCS3D01G188500 chr1A 78.947 133 25 2 1 132 513933052 513933182 1.530000e-13 87.9
36 TraesCS3D01G188500 chr1A 96.970 33 1 0 135 167 377023011 377022979 4.320000e-04 56.5
37 TraesCS3D01G188500 chr4D 81.308 107 13 7 1538 1641 84545794 84545692 2.560000e-11 80.5
38 TraesCS3D01G188500 chr4D 92.857 42 3 0 2473 2514 9066247 9066288 9.280000e-06 62.1
39 TraesCS3D01G188500 chr4D 94.595 37 2 0 134 170 399538058 399538094 1.200000e-04 58.4
40 TraesCS3D01G188500 chr4D 92.105 38 3 0 2473 2510 8997501 8997538 2.000000e-03 54.7
41 TraesCS3D01G188500 chr4A 81.308 107 13 7 1538 1641 497440626 497440524 2.560000e-11 80.5
42 TraesCS3D01G188500 chr6D 92.000 50 4 0 1603 1652 473103183 473103232 1.540000e-08 71.3
43 TraesCS3D01G188500 chr6B 92.157 51 2 2 1603 1652 718476178 718476227 1.540000e-08 71.3
44 TraesCS3D01G188500 chr7A 100.000 31 0 0 135 165 4709431 4709401 1.200000e-04 58.4
45 TraesCS3D01G188500 chr7A 94.737 38 0 2 135 170 244403816 244403779 1.200000e-04 58.4
46 TraesCS3D01G188500 chr6A 100.000 31 0 0 135 165 600825056 600825026 1.200000e-04 58.4
47 TraesCS3D01G188500 chr5A 100.000 31 0 0 134 164 103907619 103907589 1.200000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G188500 chr3D 175400514 175403611 3097 False 5722.0 5722 100.000 1 3098 1 chr3D.!!$F1 3097
1 TraesCS3D01G188500 chr3A 215471074 215473720 2646 False 1834.5 3338 91.558 159 2901 2 chr3A.!!$F2 2742
2 TraesCS3D01G188500 chr3B 254767638 254769485 1847 False 3020.0 3020 96.088 174 2033 1 chr3B.!!$F1 1859
3 TraesCS3D01G188500 chr3B 254773742 254774910 1168 False 372.0 542 91.174 2029 2971 3 chr3B.!!$F2 942

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
94 95 0.108424 AACTCGGATGAGCTGACAGC 60.108 55.0 20.12 20.12 46.69 4.40 F
96 97 0.108472 CTCGGATGAGCTGACAGCAA 60.108 55.0 28.43 16.81 45.56 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1441 1.136305 CTTGACGTCCCGGTGTATGAT 59.864 52.381 14.12 0.0 0.0 2.45 R
2166 2212 2.550180 TGATCACGCGAAACAATCCAAA 59.450 40.909 15.93 0.0 0.0 3.28 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
53 54 1.509703 GGAGAAACTCCGTGAACACC 58.490 55.000 1.97 0.00 41.08 4.16
54 55 1.137513 GAGAAACTCCGTGAACACCG 58.862 55.000 0.00 0.00 0.00 4.94
55 56 0.878961 AGAAACTCCGTGAACACCGC 60.879 55.000 0.00 0.00 0.00 5.68
59 60 4.595538 TCCGTGAACACCGCGCTT 62.596 61.111 5.56 0.00 46.59 4.68
60 61 4.072088 CCGTGAACACCGCGCTTC 62.072 66.667 5.56 2.56 46.59 3.86
61 62 4.072088 CGTGAACACCGCGCTTCC 62.072 66.667 5.56 0.00 42.14 3.46
62 63 4.072088 GTGAACACCGCGCTTCCG 62.072 66.667 5.56 0.00 37.57 4.30
63 64 4.595538 TGAACACCGCGCTTCCGT 62.596 61.111 5.56 0.00 36.67 4.69
64 65 4.072088 GAACACCGCGCTTCCGTG 62.072 66.667 5.56 5.64 44.18 4.94
77 78 3.047877 CCGTGCCGGGACTCAAAC 61.048 66.667 24.50 0.00 44.15 2.93
78 79 2.030562 CGTGCCGGGACTCAAACT 59.969 61.111 24.50 0.00 0.00 2.66
79 80 2.027625 CGTGCCGGGACTCAAACTC 61.028 63.158 24.50 0.00 0.00 3.01
80 81 2.027625 GTGCCGGGACTCAAACTCG 61.028 63.158 20.19 0.00 0.00 4.18
84 85 3.050703 CGGGACTCAAACTCGGATG 57.949 57.895 0.00 0.00 0.00 3.51
85 86 0.530744 CGGGACTCAAACTCGGATGA 59.469 55.000 0.00 0.00 0.00 2.92
86 87 1.469940 CGGGACTCAAACTCGGATGAG 60.470 57.143 5.72 5.72 46.69 2.90
87 88 1.646189 GGACTCAAACTCGGATGAGC 58.354 55.000 6.94 1.64 46.69 4.26
88 89 1.205893 GGACTCAAACTCGGATGAGCT 59.794 52.381 6.94 0.00 46.69 4.09
89 90 2.266554 GACTCAAACTCGGATGAGCTG 58.733 52.381 6.94 0.00 46.69 4.24
90 91 1.895798 ACTCAAACTCGGATGAGCTGA 59.104 47.619 6.94 0.00 46.69 4.26
91 92 2.266554 CTCAAACTCGGATGAGCTGAC 58.733 52.381 0.00 0.00 46.69 3.51
92 93 1.618343 TCAAACTCGGATGAGCTGACA 59.382 47.619 0.00 0.00 46.69 3.58
93 94 1.998315 CAAACTCGGATGAGCTGACAG 59.002 52.381 0.00 0.00 46.69 3.51
94 95 0.108424 AACTCGGATGAGCTGACAGC 60.108 55.000 20.12 20.12 46.69 4.40
95 96 1.253593 ACTCGGATGAGCTGACAGCA 61.254 55.000 28.43 10.12 46.69 4.41
96 97 0.108472 CTCGGATGAGCTGACAGCAA 60.108 55.000 28.43 16.81 45.56 3.91
97 98 0.390340 TCGGATGAGCTGACAGCAAC 60.390 55.000 28.43 20.84 45.56 4.17
98 99 0.390866 CGGATGAGCTGACAGCAACT 60.391 55.000 28.43 12.32 45.56 3.16
99 100 1.818642 GGATGAGCTGACAGCAACTT 58.181 50.000 28.43 18.47 45.56 2.66
100 101 2.157738 GGATGAGCTGACAGCAACTTT 58.842 47.619 28.43 8.08 45.56 2.66
101 102 3.338249 GGATGAGCTGACAGCAACTTTA 58.662 45.455 28.43 5.80 45.56 1.85
102 103 3.373439 GGATGAGCTGACAGCAACTTTAG 59.627 47.826 28.43 0.00 45.56 1.85
103 104 2.146342 TGAGCTGACAGCAACTTTAGC 58.854 47.619 28.43 8.10 45.56 3.09
104 105 2.224378 TGAGCTGACAGCAACTTTAGCT 60.224 45.455 28.43 4.94 45.56 3.32
120 121 2.358737 CTGTCCAGCCAACGGGTC 60.359 66.667 0.00 0.00 36.17 4.46
121 122 4.308458 TGTCCAGCCAACGGGTCG 62.308 66.667 0.00 0.00 36.17 4.79
122 123 3.998672 GTCCAGCCAACGGGTCGA 61.999 66.667 0.00 0.00 36.17 4.20
123 124 3.998672 TCCAGCCAACGGGTCGAC 61.999 66.667 7.13 7.13 36.17 4.20
141 142 2.084610 ACGCCCCGTCTTTAAGTTAC 57.915 50.000 0.00 0.00 33.69 2.50
142 143 1.620323 ACGCCCCGTCTTTAAGTTACT 59.380 47.619 0.00 0.00 33.69 2.24
143 144 2.265683 CGCCCCGTCTTTAAGTTACTC 58.734 52.381 0.00 0.00 0.00 2.59
144 145 2.625737 GCCCCGTCTTTAAGTTACTCC 58.374 52.381 0.00 0.00 0.00 3.85
145 146 2.679059 GCCCCGTCTTTAAGTTACTCCC 60.679 54.545 0.00 0.00 0.00 4.30
146 147 2.568509 CCCCGTCTTTAAGTTACTCCCA 59.431 50.000 0.00 0.00 0.00 4.37
147 148 3.593096 CCCGTCTTTAAGTTACTCCCAC 58.407 50.000 0.00 0.00 0.00 4.61
148 149 3.260128 CCCGTCTTTAAGTTACTCCCACT 59.740 47.826 0.00 0.00 0.00 4.00
149 150 4.463891 CCCGTCTTTAAGTTACTCCCACTA 59.536 45.833 0.00 0.00 0.00 2.74
150 151 5.128335 CCCGTCTTTAAGTTACTCCCACTAT 59.872 44.000 0.00 0.00 0.00 2.12
151 152 6.040878 CCGTCTTTAAGTTACTCCCACTATG 58.959 44.000 0.00 0.00 0.00 2.23
152 153 6.127535 CCGTCTTTAAGTTACTCCCACTATGA 60.128 42.308 0.00 0.00 0.00 2.15
153 154 6.750963 CGTCTTTAAGTTACTCCCACTATGAC 59.249 42.308 0.00 0.00 0.00 3.06
154 155 7.362747 CGTCTTTAAGTTACTCCCACTATGACT 60.363 40.741 0.00 0.00 0.00 3.41
155 156 8.964772 GTCTTTAAGTTACTCCCACTATGACTA 58.035 37.037 0.00 0.00 0.00 2.59
156 157 9.186837 TCTTTAAGTTACTCCCACTATGACTAG 57.813 37.037 0.00 0.00 0.00 2.57
157 158 5.855740 AAGTTACTCCCACTATGACTAGC 57.144 43.478 0.00 0.00 0.00 3.42
180 181 5.662447 CCTAAAGGACGAGTGTTAAGCACG 61.662 50.000 0.00 0.00 44.88 5.34
312 315 6.084326 AGAATATCACAACAACCAACCAAC 57.916 37.500 0.00 0.00 0.00 3.77
313 316 4.864704 ATATCACAACAACCAACCAACC 57.135 40.909 0.00 0.00 0.00 3.77
314 317 1.924731 TCACAACAACCAACCAACCA 58.075 45.000 0.00 0.00 0.00 3.67
315 318 2.248248 TCACAACAACCAACCAACCAA 58.752 42.857 0.00 0.00 0.00 3.67
348 351 5.323371 AGCTAGTCAGTCAATCAGTTCTC 57.677 43.478 0.00 0.00 0.00 2.87
429 432 2.874751 CCATGAAAACCGGACCGC 59.125 61.111 9.46 0.00 0.00 5.68
430 433 2.696759 CCATGAAAACCGGACCGCC 61.697 63.158 9.46 0.00 0.00 6.13
431 434 2.360726 ATGAAAACCGGACCGCCC 60.361 61.111 9.46 0.00 0.00 6.13
464 467 1.290203 CATTCGGCGCTGACAATAGT 58.710 50.000 20.84 0.00 0.00 2.12
497 500 3.119209 TGCTGATTTTGTTGTGTTGCTGA 60.119 39.130 0.00 0.00 0.00 4.26
569 572 1.281656 CGTGTCACCGCCTTTTTCC 59.718 57.895 0.00 0.00 0.00 3.13
658 671 8.638685 CAAGTAATCCATATTTGCTTTCTTGG 57.361 34.615 0.00 0.00 0.00 3.61
659 672 7.961326 AGTAATCCATATTTGCTTTCTTGGT 57.039 32.000 0.00 0.00 0.00 3.67
660 673 8.000780 AGTAATCCATATTTGCTTTCTTGGTC 57.999 34.615 0.00 0.00 0.00 4.02
661 674 7.836183 AGTAATCCATATTTGCTTTCTTGGTCT 59.164 33.333 0.00 0.00 0.00 3.85
662 675 5.902613 TCCATATTTGCTTTCTTGGTCTG 57.097 39.130 0.00 0.00 0.00 3.51
663 676 5.324409 TCCATATTTGCTTTCTTGGTCTGT 58.676 37.500 0.00 0.00 0.00 3.41
664 677 5.774690 TCCATATTTGCTTTCTTGGTCTGTT 59.225 36.000 0.00 0.00 0.00 3.16
665 678 5.865552 CCATATTTGCTTTCTTGGTCTGTTG 59.134 40.000 0.00 0.00 0.00 3.33
751 764 1.134098 TCATCCCTCTCCAAAATCCGC 60.134 52.381 0.00 0.00 0.00 5.54
865 879 1.195115 TCCCTGCCTAGTTGCTACTG 58.805 55.000 11.27 1.40 35.78 2.74
1011 1032 1.742268 GCCAAGAGCATGAAGGAGTTC 59.258 52.381 0.00 0.00 42.97 3.01
1108 1129 3.562681 TACAGGGCCAGGCTCAGGT 62.563 63.158 15.81 14.06 0.00 4.00
1926 1949 3.703127 GGGAGGGACGTGGTGGAC 61.703 72.222 0.00 0.00 0.00 4.02
2166 2212 5.508200 TTTTTCTACAAACCGTGCAAGAT 57.492 34.783 0.00 0.00 0.00 2.40
2234 2280 7.204243 AGTTAGGTTAATTATTCCCGGAGTT 57.796 36.000 0.73 0.00 0.00 3.01
2247 2301 2.496070 CCCGGAGTTGTTCATCTACTGA 59.504 50.000 0.73 0.00 32.78 3.41
2248 2302 3.133003 CCCGGAGTTGTTCATCTACTGAT 59.867 47.826 0.73 0.00 32.78 2.90
2249 2303 4.363999 CCGGAGTTGTTCATCTACTGATC 58.636 47.826 0.00 0.00 32.78 2.92
2252 2306 6.202937 CGGAGTTGTTCATCTACTGATCTAC 58.797 44.000 0.00 0.00 32.78 2.59
2253 2307 6.038825 CGGAGTTGTTCATCTACTGATCTACT 59.961 42.308 0.00 0.00 40.23 2.57
2254 2308 7.199766 GGAGTTGTTCATCTACTGATCTACTG 58.800 42.308 0.00 0.00 38.74 2.74
2255 2309 7.106439 AGTTGTTCATCTACTGATCTACTGG 57.894 40.000 0.00 0.00 37.87 4.00
2256 2310 6.892456 AGTTGTTCATCTACTGATCTACTGGA 59.108 38.462 0.00 0.00 37.87 3.86
2257 2311 7.563188 AGTTGTTCATCTACTGATCTACTGGAT 59.437 37.037 0.00 0.00 37.87 3.41
2258 2312 7.904558 TGTTCATCTACTGATCTACTGGATT 57.095 36.000 0.00 0.00 34.33 3.01
2259 2313 8.996651 TGTTCATCTACTGATCTACTGGATTA 57.003 34.615 0.00 0.00 34.33 1.75
2260 2314 9.072375 TGTTCATCTACTGATCTACTGGATTAG 57.928 37.037 0.00 0.00 41.88 1.73
2361 2417 4.289672 ACCTACCCACATGTTTGAATCTCT 59.710 41.667 0.00 0.00 0.00 3.10
2370 2426 1.283321 GTTTGAATCTCTGGGCCTCCT 59.717 52.381 4.53 0.00 0.00 3.69
2372 2428 0.984961 TGAATCTCTGGGCCTCCTGG 60.985 60.000 4.53 0.00 33.38 4.45
2382 2459 0.961753 GGCCTCCTGGTTTTGACTTG 59.038 55.000 0.00 0.00 35.27 3.16
2383 2460 1.478654 GGCCTCCTGGTTTTGACTTGA 60.479 52.381 0.00 0.00 35.27 3.02
2384 2461 2.306847 GCCTCCTGGTTTTGACTTGAA 58.693 47.619 0.00 0.00 35.27 2.69
2385 2462 2.034685 GCCTCCTGGTTTTGACTTGAAC 59.965 50.000 0.00 0.00 35.27 3.18
2386 2463 3.287222 CCTCCTGGTTTTGACTTGAACA 58.713 45.455 0.00 0.00 0.00 3.18
2387 2464 3.699038 CCTCCTGGTTTTGACTTGAACAA 59.301 43.478 0.00 0.00 0.00 2.83
2388 2465 4.159506 CCTCCTGGTTTTGACTTGAACAAA 59.840 41.667 0.00 0.00 35.81 2.83
2389 2466 5.337169 CCTCCTGGTTTTGACTTGAACAAAA 60.337 40.000 0.00 0.00 42.37 2.44
2390 2467 6.102897 TCCTGGTTTTGACTTGAACAAAAA 57.897 33.333 0.00 0.00 44.77 1.94
2391 2468 6.162777 TCCTGGTTTTGACTTGAACAAAAAG 58.837 36.000 0.00 0.00 44.77 2.27
2392 2469 5.351189 CCTGGTTTTGACTTGAACAAAAAGG 59.649 40.000 0.00 0.00 44.77 3.11
2393 2470 5.859495 TGGTTTTGACTTGAACAAAAAGGT 58.141 33.333 0.00 0.00 44.77 3.50
2394 2471 5.929415 TGGTTTTGACTTGAACAAAAAGGTC 59.071 36.000 0.00 0.00 44.77 3.85
2395 2472 5.929415 GGTTTTGACTTGAACAAAAAGGTCA 59.071 36.000 0.00 0.00 44.77 4.02
2396 2473 6.593770 GGTTTTGACTTGAACAAAAAGGTCAT 59.406 34.615 0.00 0.00 45.06 3.06
2397 2474 7.201522 GGTTTTGACTTGAACAAAAAGGTCATC 60.202 37.037 0.00 0.00 45.06 2.92
2418 2495 7.714377 GTCATCCATTTCTTCATCTCTGTATGT 59.286 37.037 0.00 0.00 0.00 2.29
2431 2508 6.834168 TCTCTGTATGTGTCACATAAGTCA 57.166 37.500 24.01 17.31 42.15 3.41
2435 2512 8.846943 TCTGTATGTGTCACATAAGTCAAAAT 57.153 30.769 24.01 0.86 42.15 1.82
2450 2527 5.908341 AGTCAAAATAACCCTTTGCGAAAA 58.092 33.333 0.00 0.00 34.43 2.29
2451 2528 5.751509 AGTCAAAATAACCCTTTGCGAAAAC 59.248 36.000 0.00 0.00 34.43 2.43
2452 2529 5.751509 GTCAAAATAACCCTTTGCGAAAACT 59.248 36.000 0.00 0.00 34.43 2.66
2453 2530 5.980715 TCAAAATAACCCTTTGCGAAAACTC 59.019 36.000 0.00 0.00 34.43 3.01
2456 2533 2.052782 ACCCTTTGCGAAAACTCTGT 57.947 45.000 0.00 0.00 0.00 3.41
2457 2534 1.947456 ACCCTTTGCGAAAACTCTGTC 59.053 47.619 0.00 0.00 0.00 3.51
2461 2538 4.420168 CCTTTGCGAAAACTCTGTCAAAA 58.580 39.130 0.00 0.00 0.00 2.44
2462 2539 4.265320 CCTTTGCGAAAACTCTGTCAAAAC 59.735 41.667 0.00 0.00 0.00 2.43
2465 2542 2.853281 GCGAAAACTCTGTCAAAACGGG 60.853 50.000 0.00 0.00 32.22 5.28
2466 2543 2.727777 GAAAACTCTGTCAAAACGGGC 58.272 47.619 0.00 0.00 32.22 6.13
2467 2544 2.052782 AAACTCTGTCAAAACGGGCT 57.947 45.000 0.00 0.00 32.22 5.19
2468 2545 1.594331 AACTCTGTCAAAACGGGCTC 58.406 50.000 0.00 0.00 32.22 4.70
2479 2556 2.045340 CGGGCTCCGGTCCAAAAT 60.045 61.111 15.44 0.00 44.15 1.82
2480 2557 1.222387 CGGGCTCCGGTCCAAAATA 59.778 57.895 15.44 0.00 44.15 1.40
2481 2558 0.393267 CGGGCTCCGGTCCAAAATAA 60.393 55.000 15.44 0.00 44.15 1.40
2482 2559 1.389555 GGGCTCCGGTCCAAAATAAG 58.610 55.000 15.44 0.00 37.14 1.73
2483 2560 1.340697 GGGCTCCGGTCCAAAATAAGT 60.341 52.381 15.44 0.00 37.14 2.24
2484 2561 1.743394 GGCTCCGGTCCAAAATAAGTG 59.257 52.381 0.00 0.00 0.00 3.16
2485 2562 2.433436 GCTCCGGTCCAAAATAAGTGT 58.567 47.619 0.00 0.00 0.00 3.55
2486 2563 2.418976 GCTCCGGTCCAAAATAAGTGTC 59.581 50.000 0.00 0.00 0.00 3.67
2487 2564 2.671396 CTCCGGTCCAAAATAAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
2488 2565 2.037511 TCCGGTCCAAAATAAGTGTCGT 59.962 45.455 0.00 0.00 0.00 4.34
2489 2566 2.158841 CCGGTCCAAAATAAGTGTCGTG 59.841 50.000 0.00 0.00 0.00 4.35
2490 2567 3.061322 CGGTCCAAAATAAGTGTCGTGA 58.939 45.455 0.00 0.00 0.00 4.35
2491 2568 3.682858 CGGTCCAAAATAAGTGTCGTGAT 59.317 43.478 0.00 0.00 0.00 3.06
2492 2569 4.153475 CGGTCCAAAATAAGTGTCGTGATT 59.847 41.667 0.00 0.00 0.00 2.57
2493 2570 5.334569 CGGTCCAAAATAAGTGTCGTGATTT 60.335 40.000 0.00 0.00 0.00 2.17
2494 2571 6.443792 GGTCCAAAATAAGTGTCGTGATTTT 58.556 36.000 0.00 0.00 32.97 1.82
2495 2572 7.571613 CGGTCCAAAATAAGTGTCGTGATTTTA 60.572 37.037 0.00 0.00 31.86 1.52
2496 2573 7.749126 GGTCCAAAATAAGTGTCGTGATTTTAG 59.251 37.037 0.00 0.00 31.86 1.85
2497 2574 8.287503 GTCCAAAATAAGTGTCGTGATTTTAGT 58.712 33.333 0.00 0.00 31.86 2.24
2498 2575 8.842280 TCCAAAATAAGTGTCGTGATTTTAGTT 58.158 29.630 0.00 0.00 31.86 2.24
2499 2576 9.458374 CCAAAATAAGTGTCGTGATTTTAGTTT 57.542 29.630 0.00 0.00 31.86 2.66
2521 2598 9.292846 AGTTTGAATTTAAACTAAAACCACGAC 57.707 29.630 22.70 0.00 46.10 4.34
2522 2599 9.074443 GTTTGAATTTAAACTAAAACCACGACA 57.926 29.630 16.30 0.00 37.52 4.35
2523 2600 8.617761 TTGAATTTAAACTAAAACCACGACAC 57.382 30.769 0.00 0.00 0.00 3.67
2524 2601 7.987649 TGAATTTAAACTAAAACCACGACACT 58.012 30.769 0.00 0.00 0.00 3.55
2525 2602 8.460428 TGAATTTAAACTAAAACCACGACACTT 58.540 29.630 0.00 0.00 0.00 3.16
2526 2603 9.292846 GAATTTAAACTAAAACCACGACACTTT 57.707 29.630 0.00 0.00 0.00 2.66
2527 2604 9.642327 AATTTAAACTAAAACCACGACACTTTT 57.358 25.926 0.00 0.00 0.00 2.27
2528 2605 9.642327 ATTTAAACTAAAACCACGACACTTTTT 57.358 25.926 0.00 0.00 0.00 1.94
2574 2651 4.966965 TTGTGTGTGACAAAATAACGGT 57.033 36.364 0.00 0.00 41.80 4.83
2587 2664 8.297470 ACAAAATAACGGTAGTAGTATCTGGA 57.703 34.615 0.00 0.00 0.00 3.86
2595 2672 4.399934 GGTAGTAGTATCTGGATAGCTGGC 59.600 50.000 0.00 0.00 0.00 4.85
2598 2675 2.255406 AGTATCTGGATAGCTGGCCTG 58.745 52.381 3.32 4.26 0.00 4.85
2599 2676 0.979665 TATCTGGATAGCTGGCCTGC 59.020 55.000 25.96 25.96 0.00 4.85
2600 2677 1.776975 ATCTGGATAGCTGGCCTGCC 61.777 60.000 28.96 15.26 0.00 4.85
2601 2678 2.367377 TGGATAGCTGGCCTGCCT 60.367 61.111 28.96 17.90 36.94 4.75
2602 2679 1.074547 TGGATAGCTGGCCTGCCTA 60.075 57.895 28.96 20.11 36.94 3.93
2603 2680 1.123861 TGGATAGCTGGCCTGCCTAG 61.124 60.000 28.96 6.84 36.94 3.02
2604 2681 1.124477 GGATAGCTGGCCTGCCTAGT 61.124 60.000 28.96 14.45 36.94 2.57
2605 2682 1.633774 GATAGCTGGCCTGCCTAGTA 58.366 55.000 28.96 16.14 36.94 1.82
2607 2684 0.261991 TAGCTGGCCTGCCTAGTACT 59.738 55.000 28.96 12.67 36.94 2.73
2838 3268 1.303309 CGCTCCCAAAGATGATGGAC 58.697 55.000 0.00 0.00 40.56 4.02
2839 3269 1.303309 GCTCCCAAAGATGATGGACG 58.697 55.000 0.00 0.00 40.56 4.79
2840 3270 1.134401 GCTCCCAAAGATGATGGACGA 60.134 52.381 0.00 0.00 40.56 4.20
2841 3271 2.555199 CTCCCAAAGATGATGGACGAC 58.445 52.381 0.00 0.00 40.56 4.34
2842 3272 1.134818 TCCCAAAGATGATGGACGACG 60.135 52.381 0.00 0.00 40.56 5.12
2843 3273 0.652592 CCAAAGATGATGGACGACGC 59.347 55.000 0.00 0.00 40.56 5.19
2844 3274 0.298707 CAAAGATGATGGACGACGCG 59.701 55.000 3.53 3.53 0.00 6.01
2845 3275 1.421410 AAAGATGATGGACGACGCGC 61.421 55.000 5.73 0.00 0.00 6.86
2846 3276 3.330853 GATGATGGACGACGCGCC 61.331 66.667 5.73 0.00 0.00 6.53
2953 3383 5.246883 AGGGTCTGCTTTTCTTAATGCAATT 59.753 36.000 0.00 0.00 41.93 2.32
2962 3392 8.071967 GCTTTTCTTAATGCAATTTGCTTTCTT 58.928 29.630 21.53 12.63 45.31 2.52
2971 3401 8.667076 ATGCAATTTGCTTTCTTTTTCTTACT 57.333 26.923 21.19 0.00 45.31 2.24
2972 3402 8.130307 TGCAATTTGCTTTCTTTTTCTTACTC 57.870 30.769 21.19 0.00 45.31 2.59
2973 3403 7.224557 TGCAATTTGCTTTCTTTTTCTTACTCC 59.775 33.333 21.19 0.00 45.31 3.85
2974 3404 7.307396 GCAATTTGCTTTCTTTTTCTTACTCCC 60.307 37.037 14.11 0.00 40.96 4.30
2975 3405 7.603180 ATTTGCTTTCTTTTTCTTACTCCCT 57.397 32.000 0.00 0.00 0.00 4.20
2976 3406 6.635030 TTGCTTTCTTTTTCTTACTCCCTC 57.365 37.500 0.00 0.00 0.00 4.30
2977 3407 5.070685 TGCTTTCTTTTTCTTACTCCCTCC 58.929 41.667 0.00 0.00 0.00 4.30
2978 3408 4.154375 GCTTTCTTTTTCTTACTCCCTCCG 59.846 45.833 0.00 0.00 0.00 4.63
2979 3409 4.968971 TTCTTTTTCTTACTCCCTCCGT 57.031 40.909 0.00 0.00 0.00 4.69
2980 3410 4.968971 TCTTTTTCTTACTCCCTCCGTT 57.031 40.909 0.00 0.00 0.00 4.44
2981 3411 4.891260 TCTTTTTCTTACTCCCTCCGTTC 58.109 43.478 0.00 0.00 0.00 3.95
2982 3412 3.308438 TTTTCTTACTCCCTCCGTTCG 57.692 47.619 0.00 0.00 0.00 3.95
2983 3413 2.205022 TTCTTACTCCCTCCGTTCGA 57.795 50.000 0.00 0.00 0.00 3.71
2984 3414 2.205022 TCTTACTCCCTCCGTTCGAA 57.795 50.000 0.00 0.00 0.00 3.71
2985 3415 2.517959 TCTTACTCCCTCCGTTCGAAA 58.482 47.619 0.00 0.00 0.00 3.46
2986 3416 3.094572 TCTTACTCCCTCCGTTCGAAAT 58.905 45.455 0.00 0.00 0.00 2.17
2987 3417 3.512724 TCTTACTCCCTCCGTTCGAAATT 59.487 43.478 0.00 0.00 0.00 1.82
2988 3418 4.706476 TCTTACTCCCTCCGTTCGAAATTA 59.294 41.667 0.00 0.00 0.00 1.40
2989 3419 3.242549 ACTCCCTCCGTTCGAAATTAC 57.757 47.619 0.00 0.00 0.00 1.89
2990 3420 2.830321 ACTCCCTCCGTTCGAAATTACT 59.170 45.455 0.00 0.00 0.00 2.24
2991 3421 3.260128 ACTCCCTCCGTTCGAAATTACTT 59.740 43.478 0.00 0.00 0.00 2.24
2992 3422 3.592059 TCCCTCCGTTCGAAATTACTTG 58.408 45.455 0.00 0.00 0.00 3.16
2993 3423 3.007182 TCCCTCCGTTCGAAATTACTTGT 59.993 43.478 0.00 0.00 0.00 3.16
2994 3424 3.749609 CCCTCCGTTCGAAATTACTTGTT 59.250 43.478 0.00 0.00 0.00 2.83
2995 3425 4.214758 CCCTCCGTTCGAAATTACTTGTTT 59.785 41.667 0.00 0.00 0.00 2.83
2996 3426 5.409214 CCCTCCGTTCGAAATTACTTGTTTA 59.591 40.000 0.00 0.00 0.00 2.01
2997 3427 6.073112 CCCTCCGTTCGAAATTACTTGTTTAA 60.073 38.462 0.00 0.00 0.00 1.52
2998 3428 7.354257 CCTCCGTTCGAAATTACTTGTTTAAA 58.646 34.615 0.00 0.00 0.00 1.52
2999 3429 7.856894 CCTCCGTTCGAAATTACTTGTTTAAAA 59.143 33.333 0.00 0.00 0.00 1.52
3000 3430 9.224058 CTCCGTTCGAAATTACTTGTTTAAAAA 57.776 29.630 0.00 0.00 0.00 1.94
3066 3496 8.889849 ATTTTTATGACAAGTAATTCCGAACG 57.110 30.769 0.00 0.00 0.00 3.95
3067 3497 6.411630 TTTATGACAAGTAATTCCGAACGG 57.588 37.500 6.94 6.94 0.00 4.44
3068 3498 3.663995 TGACAAGTAATTCCGAACGGA 57.336 42.857 12.04 12.04 43.52 4.69
3069 3499 3.581755 TGACAAGTAATTCCGAACGGAG 58.418 45.455 15.34 5.60 46.06 4.63
3070 3500 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3071 3501 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3072 3502 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3073 3503 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3074 3504 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3075 3505 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3076 3506 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
3077 3507 0.251297 TTCCGAACGGAGGGAGTACA 60.251 55.000 15.34 0.00 46.06 2.90
3078 3508 0.251297 TCCGAACGGAGGGAGTACAA 60.251 55.000 12.04 0.00 39.76 2.41
3079 3509 0.822164 CCGAACGGAGGGAGTACAAT 59.178 55.000 7.53 0.00 37.50 2.71
3080 3510 1.206371 CCGAACGGAGGGAGTACAATT 59.794 52.381 7.53 0.00 37.50 2.32
3081 3511 2.354403 CCGAACGGAGGGAGTACAATTT 60.354 50.000 7.53 0.00 37.50 1.82
3082 3512 3.332034 CGAACGGAGGGAGTACAATTTT 58.668 45.455 0.00 0.00 0.00 1.82
3083 3513 3.370061 CGAACGGAGGGAGTACAATTTTC 59.630 47.826 0.00 0.00 0.00 2.29
3084 3514 4.576879 GAACGGAGGGAGTACAATTTTCT 58.423 43.478 0.00 0.00 0.00 2.52
3085 3515 3.939066 ACGGAGGGAGTACAATTTTCTG 58.061 45.455 0.00 0.00 0.00 3.02
3086 3516 2.678336 CGGAGGGAGTACAATTTTCTGC 59.322 50.000 0.00 0.00 0.00 4.26
3087 3517 3.619979 CGGAGGGAGTACAATTTTCTGCT 60.620 47.826 0.00 0.00 0.00 4.24
3088 3518 4.382685 CGGAGGGAGTACAATTTTCTGCTA 60.383 45.833 0.00 0.00 0.00 3.49
3089 3519 4.876679 GGAGGGAGTACAATTTTCTGCTAC 59.123 45.833 0.00 0.00 0.00 3.58
3090 3520 5.488341 GAGGGAGTACAATTTTCTGCTACA 58.512 41.667 0.00 0.00 0.00 2.74
3091 3521 6.067217 AGGGAGTACAATTTTCTGCTACAT 57.933 37.500 0.00 0.00 0.00 2.29
3092 3522 6.485171 AGGGAGTACAATTTTCTGCTACATT 58.515 36.000 0.00 0.00 0.00 2.71
3093 3523 6.948309 AGGGAGTACAATTTTCTGCTACATTT 59.052 34.615 0.00 0.00 0.00 2.32
3094 3524 7.121315 AGGGAGTACAATTTTCTGCTACATTTC 59.879 37.037 0.00 0.00 0.00 2.17
3095 3525 7.121315 GGGAGTACAATTTTCTGCTACATTTCT 59.879 37.037 0.00 0.00 0.00 2.52
3096 3526 8.178313 GGAGTACAATTTTCTGCTACATTTCTC 58.822 37.037 0.00 0.00 0.00 2.87
3097 3527 7.743104 AGTACAATTTTCTGCTACATTTCTCG 58.257 34.615 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.509703 GGTGTTCACGGAGTTTCTCC 58.490 55.000 5.79 5.79 46.44 3.71
35 36 1.137513 CGGTGTTCACGGAGTTTCTC 58.862 55.000 4.84 0.00 41.61 2.87
36 37 0.878961 GCGGTGTTCACGGAGTTTCT 60.879 55.000 13.24 0.00 41.61 2.52
37 38 1.568025 GCGGTGTTCACGGAGTTTC 59.432 57.895 13.24 0.00 41.61 2.78
38 39 2.241880 CGCGGTGTTCACGGAGTTT 61.242 57.895 13.24 0.00 41.61 2.66
39 40 2.660552 CGCGGTGTTCACGGAGTT 60.661 61.111 13.24 0.00 41.61 3.01
42 43 4.595538 AAGCGCGGTGTTCACGGA 62.596 61.111 13.41 0.00 0.00 4.69
43 44 4.072088 GAAGCGCGGTGTTCACGG 62.072 66.667 13.41 6.21 0.00 4.94
44 45 4.072088 GGAAGCGCGGTGTTCACG 62.072 66.667 13.41 0.00 0.00 4.35
45 46 4.072088 CGGAAGCGCGGTGTTCAC 62.072 66.667 13.41 1.26 0.00 3.18
46 47 4.595538 ACGGAAGCGCGGTGTTCA 62.596 61.111 13.41 0.00 0.00 3.18
47 48 4.072088 CACGGAAGCGCGGTGTTC 62.072 66.667 13.41 6.50 41.41 3.18
62 63 2.027625 CGAGTTTGAGTCCCGGCAC 61.028 63.158 0.00 0.00 0.00 5.01
63 64 2.342279 CGAGTTTGAGTCCCGGCA 59.658 61.111 0.00 0.00 0.00 5.69
64 65 2.240162 ATCCGAGTTTGAGTCCCGGC 62.240 60.000 0.00 0.00 39.96 6.13
65 66 0.460284 CATCCGAGTTTGAGTCCCGG 60.460 60.000 0.00 0.00 41.36 5.73
66 67 0.530744 TCATCCGAGTTTGAGTCCCG 59.469 55.000 0.00 0.00 0.00 5.14
67 68 1.740718 GCTCATCCGAGTTTGAGTCCC 60.741 57.143 2.30 0.00 41.16 4.46
68 69 1.205893 AGCTCATCCGAGTTTGAGTCC 59.794 52.381 2.30 0.00 41.16 3.85
69 70 2.094494 TCAGCTCATCCGAGTTTGAGTC 60.094 50.000 2.30 0.00 41.16 3.36
70 71 1.895798 TCAGCTCATCCGAGTTTGAGT 59.104 47.619 2.30 0.00 41.16 3.41
71 72 2.266554 GTCAGCTCATCCGAGTTTGAG 58.733 52.381 0.00 0.00 41.71 3.02
72 73 1.618343 TGTCAGCTCATCCGAGTTTGA 59.382 47.619 0.00 0.00 41.71 2.69
73 74 1.998315 CTGTCAGCTCATCCGAGTTTG 59.002 52.381 0.00 0.00 41.71 2.93
74 75 1.674221 GCTGTCAGCTCATCCGAGTTT 60.674 52.381 17.89 0.00 41.71 2.66
75 76 0.108424 GCTGTCAGCTCATCCGAGTT 60.108 55.000 17.89 0.00 41.71 3.01
76 77 1.253593 TGCTGTCAGCTCATCCGAGT 61.254 55.000 24.76 0.00 42.97 4.18
77 78 0.108472 TTGCTGTCAGCTCATCCGAG 60.108 55.000 24.76 0.00 42.97 4.63
78 79 0.390340 GTTGCTGTCAGCTCATCCGA 60.390 55.000 24.76 0.29 42.97 4.55
79 80 0.390866 AGTTGCTGTCAGCTCATCCG 60.391 55.000 24.76 0.00 42.97 4.18
80 81 1.818642 AAGTTGCTGTCAGCTCATCC 58.181 50.000 24.76 8.64 42.97 3.51
81 82 3.181512 GCTAAAGTTGCTGTCAGCTCATC 60.182 47.826 24.76 12.32 42.97 2.92
82 83 2.746362 GCTAAAGTTGCTGTCAGCTCAT 59.254 45.455 24.76 8.24 42.97 2.90
83 84 2.146342 GCTAAAGTTGCTGTCAGCTCA 58.854 47.619 24.76 9.59 42.97 4.26
84 85 2.421619 AGCTAAAGTTGCTGTCAGCTC 58.578 47.619 24.76 17.11 42.97 4.09
85 86 2.557920 AGCTAAAGTTGCTGTCAGCT 57.442 45.000 24.76 7.53 42.97 4.24
103 104 2.358737 GACCCGTTGGCTGGACAG 60.359 66.667 0.00 0.00 33.59 3.51
104 105 4.308458 CGACCCGTTGGCTGGACA 62.308 66.667 0.00 0.00 33.59 4.02
105 106 3.998672 TCGACCCGTTGGCTGGAC 61.999 66.667 0.00 0.00 33.59 4.02
106 107 3.998672 GTCGACCCGTTGGCTGGA 61.999 66.667 3.51 0.00 33.59 3.86
122 123 1.620323 AGTAACTTAAAGACGGGGCGT 59.380 47.619 0.00 0.00 45.10 5.68
123 124 2.265683 GAGTAACTTAAAGACGGGGCG 58.734 52.381 0.00 0.00 0.00 6.13
124 125 2.625737 GGAGTAACTTAAAGACGGGGC 58.374 52.381 0.00 0.00 0.00 5.80
125 126 2.568509 TGGGAGTAACTTAAAGACGGGG 59.431 50.000 0.00 0.00 0.00 5.73
126 127 3.260128 AGTGGGAGTAACTTAAAGACGGG 59.740 47.826 0.00 0.00 0.00 5.28
127 128 4.532314 AGTGGGAGTAACTTAAAGACGG 57.468 45.455 0.00 0.00 0.00 4.79
128 129 6.750963 GTCATAGTGGGAGTAACTTAAAGACG 59.249 42.308 0.00 0.00 0.00 4.18
129 130 7.838884 AGTCATAGTGGGAGTAACTTAAAGAC 58.161 38.462 0.00 0.00 0.00 3.01
130 131 9.186837 CTAGTCATAGTGGGAGTAACTTAAAGA 57.813 37.037 0.00 0.00 0.00 2.52
131 132 7.921745 GCTAGTCATAGTGGGAGTAACTTAAAG 59.078 40.741 0.00 0.00 0.00 1.85
132 133 7.147776 GGCTAGTCATAGTGGGAGTAACTTAAA 60.148 40.741 0.00 0.00 0.00 1.52
133 134 6.323225 GGCTAGTCATAGTGGGAGTAACTTAA 59.677 42.308 0.00 0.00 0.00 1.85
134 135 5.832060 GGCTAGTCATAGTGGGAGTAACTTA 59.168 44.000 0.00 0.00 0.00 2.24
135 136 4.650131 GGCTAGTCATAGTGGGAGTAACTT 59.350 45.833 0.00 0.00 0.00 2.66
136 137 4.079096 AGGCTAGTCATAGTGGGAGTAACT 60.079 45.833 0.00 0.00 0.00 2.24
137 138 4.216708 AGGCTAGTCATAGTGGGAGTAAC 58.783 47.826 0.00 0.00 0.00 2.50
138 139 4.537945 AGGCTAGTCATAGTGGGAGTAA 57.462 45.455 0.00 0.00 0.00 2.24
139 140 5.658198 TTAGGCTAGTCATAGTGGGAGTA 57.342 43.478 0.00 0.00 0.00 2.59
140 141 4.537945 TTAGGCTAGTCATAGTGGGAGT 57.462 45.455 0.00 0.00 0.00 3.85
141 142 4.282195 CCTTTAGGCTAGTCATAGTGGGAG 59.718 50.000 0.00 0.00 0.00 4.30
142 143 4.078805 TCCTTTAGGCTAGTCATAGTGGGA 60.079 45.833 0.00 0.00 34.44 4.37
143 144 4.039366 GTCCTTTAGGCTAGTCATAGTGGG 59.961 50.000 0.00 0.00 34.44 4.61
144 145 4.261656 CGTCCTTTAGGCTAGTCATAGTGG 60.262 50.000 0.00 0.00 34.44 4.00
145 146 4.579340 TCGTCCTTTAGGCTAGTCATAGTG 59.421 45.833 0.00 0.00 34.44 2.74
146 147 4.789807 TCGTCCTTTAGGCTAGTCATAGT 58.210 43.478 0.00 0.00 34.44 2.12
147 148 4.822896 ACTCGTCCTTTAGGCTAGTCATAG 59.177 45.833 0.00 0.00 34.44 2.23
148 149 4.579340 CACTCGTCCTTTAGGCTAGTCATA 59.421 45.833 0.00 0.00 34.44 2.15
149 150 3.381908 CACTCGTCCTTTAGGCTAGTCAT 59.618 47.826 0.00 0.00 34.44 3.06
150 151 2.753452 CACTCGTCCTTTAGGCTAGTCA 59.247 50.000 0.00 0.00 34.44 3.41
151 152 2.754002 ACACTCGTCCTTTAGGCTAGTC 59.246 50.000 0.00 0.00 34.44 2.59
152 153 2.805194 ACACTCGTCCTTTAGGCTAGT 58.195 47.619 0.00 0.00 34.44 2.57
153 154 3.870633 AACACTCGTCCTTTAGGCTAG 57.129 47.619 0.00 0.00 34.44 3.42
154 155 4.381292 GCTTAACACTCGTCCTTTAGGCTA 60.381 45.833 0.00 0.00 34.44 3.93
155 156 3.616802 GCTTAACACTCGTCCTTTAGGCT 60.617 47.826 0.00 0.00 34.44 4.58
156 157 2.671888 GCTTAACACTCGTCCTTTAGGC 59.328 50.000 0.00 0.00 34.44 3.93
157 158 3.678548 GTGCTTAACACTCGTCCTTTAGG 59.321 47.826 0.00 0.00 46.41 2.69
180 181 4.021544 TGTTGGCATCCCACAAAAAGATAC 60.022 41.667 0.00 0.00 41.97 2.24
312 315 5.531287 ACTGACTAGCTTTAGGTTTGTTTGG 59.469 40.000 0.00 0.00 0.00 3.28
313 316 6.260050 TGACTGACTAGCTTTAGGTTTGTTTG 59.740 38.462 0.00 0.00 0.00 2.93
314 317 6.354130 TGACTGACTAGCTTTAGGTTTGTTT 58.646 36.000 0.00 0.00 0.00 2.83
315 318 5.925509 TGACTGACTAGCTTTAGGTTTGTT 58.074 37.500 0.00 0.00 0.00 2.83
464 467 3.014623 CAAAATCAGCAGCAGAGGATGA 58.985 45.455 0.00 0.00 30.05 2.92
497 500 1.689273 GCGATGGGTACAAGATCCTCT 59.311 52.381 0.00 0.00 0.00 3.69
569 572 8.142994 ACTGCACCGTCTAAATATAAAAGATG 57.857 34.615 0.00 0.00 0.00 2.90
658 671 6.156519 ACAAGGAGAAAACAAAACAACAGAC 58.843 36.000 0.00 0.00 0.00 3.51
659 672 6.339587 ACAAGGAGAAAACAAAACAACAGA 57.660 33.333 0.00 0.00 0.00 3.41
660 673 7.201316 CGTAACAAGGAGAAAACAAAACAACAG 60.201 37.037 0.00 0.00 0.00 3.16
661 674 6.583050 CGTAACAAGGAGAAAACAAAACAACA 59.417 34.615 0.00 0.00 0.00 3.33
662 675 6.802834 TCGTAACAAGGAGAAAACAAAACAAC 59.197 34.615 0.00 0.00 0.00 3.32
663 676 6.910995 TCGTAACAAGGAGAAAACAAAACAA 58.089 32.000 0.00 0.00 0.00 2.83
664 677 6.497785 TCGTAACAAGGAGAAAACAAAACA 57.502 33.333 0.00 0.00 0.00 2.83
665 678 7.217636 GTCTTCGTAACAAGGAGAAAACAAAAC 59.782 37.037 0.00 0.00 0.00 2.43
751 764 0.045778 TTTTAGAGGGAGGGAGGGGG 59.954 60.000 0.00 0.00 0.00 5.40
865 879 1.135083 TCGCAAAGCACTAGGAGTAGC 60.135 52.381 0.00 0.00 0.00 3.58
898 915 0.941542 GCGGAGTGTACAAGCAACAA 59.058 50.000 0.00 0.00 0.00 2.83
906 923 0.031585 GTGTGTGAGCGGAGTGTACA 59.968 55.000 0.00 0.00 0.00 2.90
907 924 1.002250 CGTGTGTGAGCGGAGTGTAC 61.002 60.000 0.00 0.00 0.00 2.90
1420 1441 1.136305 CTTGACGTCCCGGTGTATGAT 59.864 52.381 14.12 0.00 0.00 2.45
2166 2212 2.550180 TGATCACGCGAAACAATCCAAA 59.450 40.909 15.93 0.00 0.00 3.28
2234 2280 7.904558 AATCCAGTAGATCAGTAGATGAACA 57.095 36.000 0.00 0.00 42.53 3.18
2253 2307 9.952030 TCAAACAGTCATACATTAACTAATCCA 57.048 29.630 0.00 0.00 0.00 3.41
2257 2311 9.214957 CCAGTCAAACAGTCATACATTAACTAA 57.785 33.333 0.00 0.00 0.00 2.24
2258 2312 7.822334 CCCAGTCAAACAGTCATACATTAACTA 59.178 37.037 0.00 0.00 0.00 2.24
2259 2313 6.655003 CCCAGTCAAACAGTCATACATTAACT 59.345 38.462 0.00 0.00 0.00 2.24
2260 2314 6.622896 GCCCAGTCAAACAGTCATACATTAAC 60.623 42.308 0.00 0.00 0.00 2.01
2341 2395 4.567537 CCCAGAGATTCAAACATGTGGGTA 60.568 45.833 0.00 0.00 38.90 3.69
2361 2417 1.152830 GTCAAAACCAGGAGGCCCA 59.847 57.895 0.00 0.00 39.06 5.36
2370 2426 5.859495 ACCTTTTTGTTCAAGTCAAAACCA 58.141 33.333 3.80 0.00 42.07 3.67
2372 2428 7.201522 GGATGACCTTTTTGTTCAAGTCAAAAC 60.202 37.037 8.58 5.27 42.07 2.43
2382 2459 7.209475 TGAAGAAATGGATGACCTTTTTGTTC 58.791 34.615 0.05 0.05 41.49 3.18
2383 2460 7.123355 TGAAGAAATGGATGACCTTTTTGTT 57.877 32.000 0.00 0.00 41.49 2.83
2384 2461 6.729690 TGAAGAAATGGATGACCTTTTTGT 57.270 33.333 0.00 0.00 41.49 2.83
2385 2462 7.609056 AGATGAAGAAATGGATGACCTTTTTG 58.391 34.615 0.00 0.00 41.49 2.44
2386 2463 7.673082 AGAGATGAAGAAATGGATGACCTTTTT 59.327 33.333 0.00 0.00 41.49 1.94
2387 2464 7.122353 CAGAGATGAAGAAATGGATGACCTTTT 59.878 37.037 0.00 0.00 43.22 2.27
2388 2465 6.602406 CAGAGATGAAGAAATGGATGACCTTT 59.398 38.462 0.00 0.00 37.04 3.11
2389 2466 6.120905 CAGAGATGAAGAAATGGATGACCTT 58.879 40.000 0.00 0.00 37.04 3.50
2390 2467 5.191323 ACAGAGATGAAGAAATGGATGACCT 59.809 40.000 0.00 0.00 37.04 3.85
2391 2468 5.435291 ACAGAGATGAAGAAATGGATGACC 58.565 41.667 0.00 0.00 0.00 4.02
2392 2469 7.714377 ACATACAGAGATGAAGAAATGGATGAC 59.286 37.037 2.37 0.00 33.96 3.06
2393 2470 7.713942 CACATACAGAGATGAAGAAATGGATGA 59.286 37.037 2.37 0.00 33.96 2.92
2394 2471 7.498239 ACACATACAGAGATGAAGAAATGGATG 59.502 37.037 0.00 0.00 35.54 3.51
2395 2472 7.571919 ACACATACAGAGATGAAGAAATGGAT 58.428 34.615 0.00 0.00 0.00 3.41
2396 2473 6.950842 ACACATACAGAGATGAAGAAATGGA 58.049 36.000 0.00 0.00 0.00 3.41
2397 2474 6.820152 TGACACATACAGAGATGAAGAAATGG 59.180 38.462 0.00 0.00 0.00 3.16
2418 2495 8.356657 CAAAGGGTTATTTTGACTTATGTGACA 58.643 33.333 0.00 0.00 37.65 3.58
2431 2508 5.983118 CAGAGTTTTCGCAAAGGGTTATTTT 59.017 36.000 0.00 0.00 0.00 1.82
2435 2512 3.547746 ACAGAGTTTTCGCAAAGGGTTA 58.452 40.909 0.00 0.00 0.00 2.85
2450 2527 0.250338 GGAGCCCGTTTTGACAGAGT 60.250 55.000 0.00 0.00 0.00 3.24
2451 2528 1.291877 CGGAGCCCGTTTTGACAGAG 61.292 60.000 5.56 0.00 42.73 3.35
2452 2529 1.301401 CGGAGCCCGTTTTGACAGA 60.301 57.895 5.56 0.00 42.73 3.41
2453 2530 2.325082 CCGGAGCCCGTTTTGACAG 61.325 63.158 0.00 0.00 46.80 3.51
2456 2533 2.031465 GACCGGAGCCCGTTTTGA 59.969 61.111 9.46 0.00 46.80 2.69
2457 2534 3.053896 GGACCGGAGCCCGTTTTG 61.054 66.667 9.46 0.69 46.80 2.44
2461 2538 1.555477 TATTTTGGACCGGAGCCCGT 61.555 55.000 9.46 0.00 46.80 5.28
2465 2542 2.418976 GACACTTATTTTGGACCGGAGC 59.581 50.000 9.46 0.00 0.00 4.70
2466 2543 2.671396 CGACACTTATTTTGGACCGGAG 59.329 50.000 9.46 0.00 0.00 4.63
2467 2544 2.037511 ACGACACTTATTTTGGACCGGA 59.962 45.455 9.46 0.00 0.00 5.14
2468 2545 2.158841 CACGACACTTATTTTGGACCGG 59.841 50.000 0.00 0.00 0.00 5.28
2471 2548 8.287503 ACTAAAATCACGACACTTATTTTGGAC 58.712 33.333 8.95 0.00 34.97 4.02
2473 2550 9.458374 AAACTAAAATCACGACACTTATTTTGG 57.542 29.630 0.00 0.00 36.46 3.28
2496 2573 9.074443 TGTCGTGGTTTTAGTTTAAATTCAAAC 57.926 29.630 10.44 10.44 38.44 2.93
2497 2574 9.074443 GTGTCGTGGTTTTAGTTTAAATTCAAA 57.926 29.630 0.00 0.00 0.00 2.69
2498 2575 8.460428 AGTGTCGTGGTTTTAGTTTAAATTCAA 58.540 29.630 0.00 0.00 0.00 2.69
2499 2576 7.987649 AGTGTCGTGGTTTTAGTTTAAATTCA 58.012 30.769 0.00 0.00 0.00 2.57
2500 2577 8.845942 AAGTGTCGTGGTTTTAGTTTAAATTC 57.154 30.769 0.00 0.00 0.00 2.17
2501 2578 9.642327 AAAAGTGTCGTGGTTTTAGTTTAAATT 57.358 25.926 0.00 0.00 0.00 1.82
2502 2579 9.642327 AAAAAGTGTCGTGGTTTTAGTTTAAAT 57.358 25.926 0.00 0.00 0.00 1.40
2526 2603 9.753674 ACATAATAAACTCTCTCCCATCAAAAA 57.246 29.630 0.00 0.00 0.00 1.94
2527 2604 9.753674 AACATAATAAACTCTCTCCCATCAAAA 57.246 29.630 0.00 0.00 0.00 2.44
2528 2605 9.753674 AAACATAATAAACTCTCTCCCATCAAA 57.246 29.630 0.00 0.00 0.00 2.69
2529 2606 9.177608 CAAACATAATAAACTCTCTCCCATCAA 57.822 33.333 0.00 0.00 0.00 2.57
2530 2607 8.328758 ACAAACATAATAAACTCTCTCCCATCA 58.671 33.333 0.00 0.00 0.00 3.07
2531 2608 8.616076 CACAAACATAATAAACTCTCTCCCATC 58.384 37.037 0.00 0.00 0.00 3.51
2532 2609 8.109634 ACACAAACATAATAAACTCTCTCCCAT 58.890 33.333 0.00 0.00 0.00 4.00
2533 2610 7.390440 CACACAAACATAATAAACTCTCTCCCA 59.610 37.037 0.00 0.00 0.00 4.37
2534 2611 7.390718 ACACACAAACATAATAAACTCTCTCCC 59.609 37.037 0.00 0.00 0.00 4.30
2535 2612 8.230486 CACACACAAACATAATAAACTCTCTCC 58.770 37.037 0.00 0.00 0.00 3.71
2536 2613 8.988934 TCACACACAAACATAATAAACTCTCTC 58.011 33.333 0.00 0.00 0.00 3.20
2537 2614 8.774586 GTCACACACAAACATAATAAACTCTCT 58.225 33.333 0.00 0.00 0.00 3.10
2538 2615 8.556194 TGTCACACACAAACATAATAAACTCTC 58.444 33.333 0.00 0.00 29.30 3.20
2539 2616 8.445275 TGTCACACACAAACATAATAAACTCT 57.555 30.769 0.00 0.00 29.30 3.24
2568 2645 6.877855 CAGCTATCCAGATACTACTACCGTTA 59.122 42.308 0.00 0.00 0.00 3.18
2571 2648 4.636648 CCAGCTATCCAGATACTACTACCG 59.363 50.000 0.00 0.00 0.00 4.02
2573 2650 4.399934 GGCCAGCTATCCAGATACTACTAC 59.600 50.000 0.00 0.00 0.00 2.73
2574 2651 4.292571 AGGCCAGCTATCCAGATACTACTA 59.707 45.833 5.01 0.00 0.00 1.82
2575 2652 3.076785 AGGCCAGCTATCCAGATACTACT 59.923 47.826 5.01 0.00 0.00 2.57
2587 2664 1.133009 AGTACTAGGCAGGCCAGCTAT 60.133 52.381 20.55 11.53 38.92 2.97
2595 2672 4.081420 AGTTTGACATGAGTACTAGGCAGG 60.081 45.833 0.00 0.00 0.00 4.85
2598 2675 5.452077 CCCTAGTTTGACATGAGTACTAGGC 60.452 48.000 25.53 0.00 45.26 3.93
2599 2676 5.452077 GCCCTAGTTTGACATGAGTACTAGG 60.452 48.000 24.77 24.77 45.72 3.02
2600 2677 5.127194 TGCCCTAGTTTGACATGAGTACTAG 59.873 44.000 0.00 10.23 35.57 2.57
2601 2678 5.020795 TGCCCTAGTTTGACATGAGTACTA 58.979 41.667 0.00 1.00 0.00 1.82
2602 2679 3.838317 TGCCCTAGTTTGACATGAGTACT 59.162 43.478 0.00 0.00 0.00 2.73
2603 2680 4.184629 CTGCCCTAGTTTGACATGAGTAC 58.815 47.826 0.00 0.00 0.00 2.73
2604 2681 3.197766 CCTGCCCTAGTTTGACATGAGTA 59.802 47.826 0.00 0.00 0.00 2.59
2605 2682 2.026822 CCTGCCCTAGTTTGACATGAGT 60.027 50.000 0.00 0.00 0.00 3.41
2607 2684 1.985159 ACCTGCCCTAGTTTGACATGA 59.015 47.619 0.00 0.00 0.00 3.07
2641 2735 0.611896 CTTCCCGTGCCCAATTTCCT 60.612 55.000 0.00 0.00 0.00 3.36
2838 3268 2.574222 GATTAACTCCGGCGCGTCG 61.574 63.158 28.69 28.69 0.00 5.12
2839 3269 0.029834 TAGATTAACTCCGGCGCGTC 59.970 55.000 8.43 3.30 0.00 5.19
2840 3270 0.030369 CTAGATTAACTCCGGCGCGT 59.970 55.000 8.43 0.00 0.00 6.01
2841 3271 0.030369 ACTAGATTAACTCCGGCGCG 59.970 55.000 0.00 0.00 0.00 6.86
2842 3272 1.337387 AGACTAGATTAACTCCGGCGC 59.663 52.381 0.00 0.00 0.00 6.53
2843 3273 2.617308 TCAGACTAGATTAACTCCGGCG 59.383 50.000 0.00 0.00 0.00 6.46
2844 3274 4.614078 CGATCAGACTAGATTAACTCCGGC 60.614 50.000 0.00 0.00 0.00 6.13
2845 3275 4.755629 TCGATCAGACTAGATTAACTCCGG 59.244 45.833 0.00 0.00 0.00 5.14
2846 3276 5.106869 CCTCGATCAGACTAGATTAACTCCG 60.107 48.000 0.00 0.00 0.00 4.63
2847 3277 5.335348 GCCTCGATCAGACTAGATTAACTCC 60.335 48.000 0.00 0.00 0.00 3.85
2848 3278 5.239744 TGCCTCGATCAGACTAGATTAACTC 59.760 44.000 0.00 0.00 0.00 3.01
2849 3279 5.009210 GTGCCTCGATCAGACTAGATTAACT 59.991 44.000 0.00 0.00 0.00 2.24
2953 3383 5.535030 GGAGGGAGTAAGAAAAAGAAAGCAA 59.465 40.000 0.00 0.00 0.00 3.91
2962 3392 2.892852 TCGAACGGAGGGAGTAAGAAAA 59.107 45.455 0.00 0.00 0.00 2.29
2971 3401 3.007182 ACAAGTAATTTCGAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
2972 3402 3.332034 ACAAGTAATTTCGAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
2973 3403 5.352643 AAACAAGTAATTTCGAACGGAGG 57.647 39.130 0.00 0.00 0.00 4.30
2974 3404 8.770850 TTTTAAACAAGTAATTTCGAACGGAG 57.229 30.769 0.00 0.00 0.00 4.63
3040 3470 9.976255 CGTTCGGAATTACTTGTCATAAAAATA 57.024 29.630 0.00 0.00 0.00 1.40
3041 3471 7.966204 CCGTTCGGAATTACTTGTCATAAAAAT 59.034 33.333 5.19 0.00 0.00 1.82
3042 3472 7.172875 TCCGTTCGGAATTACTTGTCATAAAAA 59.827 33.333 11.66 0.00 0.00 1.94
3043 3473 6.649973 TCCGTTCGGAATTACTTGTCATAAAA 59.350 34.615 11.66 0.00 0.00 1.52
3044 3474 6.164876 TCCGTTCGGAATTACTTGTCATAAA 58.835 36.000 11.66 0.00 0.00 1.40
3045 3475 5.722263 TCCGTTCGGAATTACTTGTCATAA 58.278 37.500 11.66 0.00 0.00 1.90
3046 3476 5.327616 TCCGTTCGGAATTACTTGTCATA 57.672 39.130 11.66 0.00 0.00 2.15
3047 3477 4.181578 CTCCGTTCGGAATTACTTGTCAT 58.818 43.478 14.79 0.00 33.41 3.06
3048 3478 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
3049 3479 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3050 3480 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3051 3481 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3052 3482 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3053 3483 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3054 3484 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3055 3485 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3056 3486 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
3057 3487 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
3058 3488 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
3059 3489 0.251297 TTGTACTCCCTCCGTTCGGA 60.251 55.000 13.34 13.34 0.00 4.55
3060 3490 0.822164 ATTGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
3061 3491 2.667473 AATTGTACTCCCTCCGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
3062 3492 4.392138 CAGAAAATTGTACTCCCTCCGTTC 59.608 45.833 0.00 0.00 0.00 3.95
3063 3493 4.324267 CAGAAAATTGTACTCCCTCCGTT 58.676 43.478 0.00 0.00 0.00 4.44
3064 3494 3.868754 GCAGAAAATTGTACTCCCTCCGT 60.869 47.826 0.00 0.00 0.00 4.69
3065 3495 2.678336 GCAGAAAATTGTACTCCCTCCG 59.322 50.000 0.00 0.00 0.00 4.63
3066 3496 3.956744 AGCAGAAAATTGTACTCCCTCC 58.043 45.455 0.00 0.00 0.00 4.30
3067 3497 5.488341 TGTAGCAGAAAATTGTACTCCCTC 58.512 41.667 0.00 0.00 0.00 4.30
3068 3498 5.499004 TGTAGCAGAAAATTGTACTCCCT 57.501 39.130 0.00 0.00 0.00 4.20
3069 3499 6.759497 AATGTAGCAGAAAATTGTACTCCC 57.241 37.500 0.00 0.00 0.00 4.30
3070 3500 8.045176 AGAAATGTAGCAGAAAATTGTACTCC 57.955 34.615 0.00 0.00 0.00 3.85
3071 3501 7.900352 CGAGAAATGTAGCAGAAAATTGTACTC 59.100 37.037 0.00 0.00 0.00 2.59
3072 3502 7.743104 CGAGAAATGTAGCAGAAAATTGTACT 58.257 34.615 0.00 0.00 0.00 2.73
3073 3503 7.938971 CGAGAAATGTAGCAGAAAATTGTAC 57.061 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.