Multiple sequence alignment - TraesCS6D01G234100

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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 TraesCS6D01G234100 chr6D 100.000 5553 0 0 1 5553 328328197 328333749 0.000000e+00 10255.0
1 TraesCS6D01G234100 chr6D 99.000 100 1 0 5454 5553 377190223 377190322 4.420000e-41 180.0
2 TraesCS6D01G234100 chr6B 95.509 3830 91 27 1 3808 492188692 492192462 0.000000e+00 6045.0
3 TraesCS6D01G234100 chr6B 93.219 1165 46 11 3807 4939 492192586 492193749 0.000000e+00 1683.0
4 TraesCS6D01G234100 chr6B 85.632 696 23 14 4640 5324 492193449 492194078 0.000000e+00 660.0
5 TraesCS6D01G234100 chr6B 95.775 71 3 0 5324 5394 492194047 492194117 1.260000e-21 115.0
6 TraesCS6D01G234100 chr6A 90.735 3033 172 52 1 2993 467042117 467045080 0.000000e+00 3943.0
7 TraesCS6D01G234100 chr6A 95.726 1006 36 1 3122 4120 467045269 467046274 0.000000e+00 1613.0
8 TraesCS6D01G234100 chr6A 92.193 871 30 11 4184 5050 467046268 467047104 0.000000e+00 1197.0
9 TraesCS6D01G234100 chr6A 87.108 287 15 6 5132 5406 467047141 467047417 6.990000e-79 305.0
10 TraesCS6D01G234100 chr4B 84.444 1755 187 40 1196 2931 633936590 633934903 0.000000e+00 1650.0
11 TraesCS6D01G234100 chr4B 84.016 1758 174 44 1196 2931 634079578 634077906 0.000000e+00 1591.0
12 TraesCS6D01G234100 chr4B 86.203 935 94 13 3184 4103 633934108 633933194 0.000000e+00 979.0
13 TraesCS6D01G234100 chr4B 86.813 364 39 4 4206 4560 634076675 634076312 1.120000e-106 398.0
14 TraesCS6D01G234100 chr4B 90.753 292 27 0 4267 4558 633933113 633932822 1.880000e-104 390.0
15 TraesCS6D01G234100 chr4B 87.742 310 38 0 3785 4094 634077010 634076701 4.090000e-96 363.0
16 TraesCS6D01G234100 chr4B 76.101 159 26 8 987 1136 633936772 633936617 7.720000e-09 73.1
17 TraesCS6D01G234100 chr5A 84.005 1763 184 36 1196 2933 673932652 673934341 0.000000e+00 1604.0
18 TraesCS6D01G234100 chr5A 84.073 1758 173 42 1196 2931 673836065 673837737 0.000000e+00 1596.0
19 TraesCS6D01G234100 chr5A 84.567 1121 119 27 3029 4121 673934524 673935618 0.000000e+00 1062.0
20 TraesCS6D01G234100 chr5A 88.154 363 39 4 4201 4560 673935629 673935990 3.970000e-116 429.0
21 TraesCS6D01G234100 chr5A 89.796 294 30 0 4267 4560 673839073 673839366 1.460000e-100 377.0
22 TraesCS6D01G234100 chr5A 87.987 308 37 0 3787 4094 673838670 673838977 1.140000e-96 364.0
23 TraesCS6D01G234100 chr5A 94.000 100 6 0 5454 5553 545643600 545643501 9.630000e-33 152.0
24 TraesCS6D01G234100 chr4D 83.891 1763 174 52 1196 2934 494514059 494512383 0.000000e+00 1581.0
25 TraesCS6D01G234100 chr4D 82.720 1765 187 51 1196 2936 494476255 494474585 0.000000e+00 1461.0
26 TraesCS6D01G234100 chr4D 84.473 1082 115 27 3060 4121 494474374 494473326 0.000000e+00 1018.0
27 TraesCS6D01G234100 chr4D 86.116 605 53 10 3203 3796 494512068 494511484 1.700000e-174 623.0
28 TraesCS6D01G234100 chr4D 86.877 381 45 5 4184 4560 494473333 494472954 6.650000e-114 422.0
29 TraesCS6D01G234100 chr4D 86.575 365 40 4 4205 4560 494511125 494510761 1.450000e-105 394.0
30 TraesCS6D01G234100 chr4D 80.747 509 59 15 3160 3645 494507690 494507198 1.470000e-95 361.0
31 TraesCS6D01G234100 chr4D 87.220 313 40 0 3785 4097 494511459 494511147 1.900000e-94 357.0
32 TraesCS6D01G234100 chr4D 87.665 227 25 2 2709 2932 494508121 494507895 1.530000e-65 261.0
33 TraesCS6D01G234100 chr4D 97.436 39 1 0 987 1025 494476437 494476399 3.590000e-07 67.6
34 TraesCS6D01G234100 chr1D 84.093 899 134 7 3170 4063 8921594 8920700 0.000000e+00 859.0
35 TraesCS6D01G234100 chr1D 81.596 614 105 5 3457 4069 8958602 8959208 8.300000e-138 501.0
36 TraesCS6D01G234100 chr1D 85.714 315 44 1 4251 4564 8920551 8920237 1.150000e-86 331.0
37 TraesCS6D01G234100 chr1B 82.301 904 150 9 3171 4068 12108949 12108050 0.000000e+00 774.0
38 TraesCS6D01G234100 chr1B 93.939 99 6 0 5454 5552 641020175 641020077 3.470000e-32 150.0
39 TraesCS6D01G234100 chr1A 81.869 888 133 14 3183 4063 10157072 10156206 0.000000e+00 723.0
40 TraesCS6D01G234100 chr1A 83.876 614 88 9 1900 2503 10159839 10159227 4.820000e-160 575.0
41 TraesCS6D01G234100 chr1A 95.960 99 4 0 5454 5552 265627639 265627541 1.600000e-35 161.0
42 TraesCS6D01G234100 chr1A 95.960 99 4 0 5454 5552 592554598 592554696 1.600000e-35 161.0
43 TraesCS6D01G234100 chr1A 81.651 109 19 1 1692 1800 10159995 10159888 7.660000e-14 89.8
44 TraesCS6D01G234100 chr5D 99.000 100 1 0 5454 5553 288551569 288551668 4.420000e-41 180.0
45 TraesCS6D01G234100 chr2D 96.000 100 4 0 5454 5553 31903111 31903012 4.450000e-36 163.0
46 TraesCS6D01G234100 chr2D 95.000 100 5 0 5454 5553 633444916 633444817 2.070000e-34 158.0
47 TraesCS6D01G234100 chr7D 94.000 100 6 0 5454 5553 3720267 3720366 9.630000e-33 152.0


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 TraesCS6D01G234100 chr6D 328328197 328333749 5552 False 10255.000000 10255 100.000000 1 5553 1 chr6D.!!$F1 5552
1 TraesCS6D01G234100 chr6B 492188692 492194117 5425 False 2125.750000 6045 92.533750 1 5394 4 chr6B.!!$F1 5393
2 TraesCS6D01G234100 chr6A 467042117 467047417 5300 False 1764.500000 3943 91.440500 1 5406 4 chr6A.!!$F1 5405
3 TraesCS6D01G234100 chr4B 634076312 634079578 3266 True 784.000000 1591 86.190333 1196 4560 3 chr4B.!!$R2 3364
4 TraesCS6D01G234100 chr4B 633932822 633936772 3950 True 773.025000 1650 84.375250 987 4558 4 chr4B.!!$R1 3571
5 TraesCS6D01G234100 chr5A 673932652 673935990 3338 False 1031.666667 1604 85.575333 1196 4560 3 chr5A.!!$F2 3364
6 TraesCS6D01G234100 chr5A 673836065 673839366 3301 False 779.000000 1596 87.285333 1196 4560 3 chr5A.!!$F1 3364
7 TraesCS6D01G234100 chr4D 494472954 494476437 3483 True 742.150000 1461 87.876500 987 4560 4 chr4D.!!$R1 3573
8 TraesCS6D01G234100 chr4D 494507198 494514059 6861 True 596.166667 1581 85.369000 1196 4560 6 chr4D.!!$R2 3364
9 TraesCS6D01G234100 chr1D 8920237 8921594 1357 True 595.000000 859 84.903500 3170 4564 2 chr1D.!!$R1 1394
10 TraesCS6D01G234100 chr1D 8958602 8959208 606 False 501.000000 501 81.596000 3457 4069 1 chr1D.!!$F1 612
11 TraesCS6D01G234100 chr1B 12108050 12108949 899 True 774.000000 774 82.301000 3171 4068 1 chr1B.!!$R1 897
12 TraesCS6D01G234100 chr1A 10156206 10159995 3789 True 462.600000 723 82.465333 1692 4063 3 chr1A.!!$R2 2371

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
28 29 0.108281 GTTAAGCCGACCTCCTGTCC 60.108 60.000 0.00 0.00 41.18 4.02 F
263 269 0.249996 TCTTTTTCCACGGGGTCGAC 60.250 55.000 7.13 7.13 40.11 4.20 F
370 378 0.390209 ATTGGGCGTGTACGGTGTAC 60.390 55.000 6.55 0.22 40.23 2.90 F
1392 1457 0.530744 CATCGTCCCCTTCGTTCTCA 59.469 55.000 0.00 0.00 0.00 3.27 F
1402 1470 0.944311 TTCGTTCTCACCGAAGCAGC 60.944 55.000 0.00 0.00 39.22 5.25 F
1802 1903 2.262915 CGAGGAGCGCAAGTCCTT 59.737 61.111 16.94 2.54 44.32 3.36 F
4080 6618 1.809619 TGCGTATCGGTGCTTCTGC 60.810 57.895 0.00 0.00 40.20 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1170 1223 1.223487 GGAGTTGGAGCCGGCATTA 59.777 57.895 31.54 11.2 0.00 1.90 R
1362 1427 2.202932 GACGATGCCTGCGGTGAT 60.203 61.111 0.00 0.0 0.00 3.06 R
1802 1903 2.852075 ACTTGGGAGGTCGGGCAA 60.852 61.111 0.00 0.0 0.00 4.52 R
3086 5354 0.732571 AACAGCGAACACAACAGTGG 59.267 50.000 0.00 0.0 37.58 4.00 R
3117 5393 5.794687 TGTAAAGTTCTGCAATATGTCCG 57.205 39.130 0.00 0.0 0.00 4.79 R
4148 6719 2.648059 ACATGCCTGCCTACTGAATTC 58.352 47.619 0.00 0.0 0.00 2.17 R
5150 8695 0.038526 AGTCGCTCTTACAACACGGG 60.039 55.000 0.00 0.0 0.00 5.28 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
27 28 0.458025 CGTTAAGCCGACCTCCTGTC 60.458 60.000 0.00 0.00 40.81 3.51
28 29 0.108281 GTTAAGCCGACCTCCTGTCC 60.108 60.000 0.00 0.00 41.18 4.02
29 30 0.252103 TTAAGCCGACCTCCTGTCCT 60.252 55.000 0.00 0.00 41.18 3.85
30 31 0.970937 TAAGCCGACCTCCTGTCCTG 60.971 60.000 0.00 0.00 41.18 3.86
31 32 2.997897 GCCGACCTCCTGTCCTGT 60.998 66.667 0.00 0.00 41.18 4.00
32 33 1.681327 GCCGACCTCCTGTCCTGTA 60.681 63.158 0.00 0.00 41.18 2.74
38 39 0.323542 CCTCCTGTCCTGTACCGTCT 60.324 60.000 0.00 0.00 0.00 4.18
96 98 4.459390 TCCGTCCAAATCACGAGATTAA 57.541 40.909 8.55 0.00 43.52 1.40
103 105 4.032900 CCAAATCACGAGATTAAGACGGTG 59.967 45.833 8.55 1.96 43.52 4.94
106 108 2.163010 TCACGAGATTAAGACGGTGACC 59.837 50.000 0.00 0.00 0.00 4.02
107 109 7.880695 AATCACGAGATTAAGACGGTGACCG 62.881 48.000 24.23 24.23 46.62 4.79
117 119 2.049802 GGTGACCGAGAAACGCGA 60.050 61.111 15.93 0.00 41.07 5.87
118 120 2.370393 GGTGACCGAGAAACGCGAC 61.370 63.158 15.93 3.56 41.07 5.19
119 121 2.049802 TGACCGAGAAACGCGACC 60.050 61.111 15.93 0.22 41.07 4.79
126 128 0.524862 GAGAAACGCGACCTAGTGGA 59.475 55.000 15.93 0.00 37.04 4.02
127 129 1.134560 GAGAAACGCGACCTAGTGGAT 59.865 52.381 15.93 0.00 37.04 3.41
140 142 2.437002 TGGATTTACCGGTGGCGC 60.437 61.111 19.93 0.00 42.61 6.53
232 238 6.039605 AGCATGCATGTACAATGCTTTGTATA 59.960 34.615 26.79 21.33 46.91 1.47
233 239 6.142798 GCATGCATGTACAATGCTTTGTATAC 59.857 38.462 26.79 16.52 46.91 1.47
263 269 0.249996 TCTTTTTCCACGGGGTCGAC 60.250 55.000 7.13 7.13 40.11 4.20
317 325 0.741221 GATTGGCACGAGTGAGACCC 60.741 60.000 7.50 0.00 0.00 4.46
319 327 1.691195 TTGGCACGAGTGAGACCCAA 61.691 55.000 7.50 8.00 0.00 4.12
370 378 0.390209 ATTGGGCGTGTACGGTGTAC 60.390 55.000 6.55 0.22 40.23 2.90
371 379 2.125952 GGGCGTGTACGGTGTACC 60.126 66.667 6.55 0.00 40.23 3.34
388 400 2.109425 ACCGTACATTTTCTCCTGCC 57.891 50.000 0.00 0.00 0.00 4.85
457 469 4.284234 ACACCTAAAATACCGTACTGTGGT 59.716 41.667 0.00 0.00 43.62 4.16
458 470 5.480073 ACACCTAAAATACCGTACTGTGGTA 59.520 40.000 0.00 0.44 45.55 3.25
503 523 4.939052 TTTCTTCTCGTCTCTTTCACCT 57.061 40.909 0.00 0.00 0.00 4.00
626 646 2.093128 ACCCAAATCTTCGATTAGCGGT 60.093 45.455 0.00 0.00 41.33 5.68
664 684 6.381420 TGTTTAATCTCTTTCCCAACCAACAA 59.619 34.615 0.00 0.00 0.00 2.83
667 697 2.021457 CTCTTTCCCAACCAACAACGT 58.979 47.619 0.00 0.00 0.00 3.99
838 878 3.823330 CCCGAACCCTCTCCGTCG 61.823 72.222 0.00 0.00 0.00 5.12
839 879 4.493747 CCGAACCCTCTCCGTCGC 62.494 72.222 0.00 0.00 0.00 5.19
840 880 4.493747 CGAACCCTCTCCGTCGCC 62.494 72.222 0.00 0.00 0.00 5.54
841 881 4.144703 GAACCCTCTCCGTCGCCC 62.145 72.222 0.00 0.00 0.00 6.13
842 882 4.698625 AACCCTCTCCGTCGCCCT 62.699 66.667 0.00 0.00 0.00 5.19
846 886 4.824515 CTCTCCGTCGCCCTCCCT 62.825 72.222 0.00 0.00 0.00 4.20
847 887 4.816984 TCTCCGTCGCCCTCCCTC 62.817 72.222 0.00 0.00 0.00 4.30
851 891 3.136123 CGTCGCCCTCCCTCGTTA 61.136 66.667 0.00 0.00 0.00 3.18
852 892 2.703798 CGTCGCCCTCCCTCGTTAA 61.704 63.158 0.00 0.00 0.00 2.01
853 893 1.821258 GTCGCCCTCCCTCGTTAAT 59.179 57.895 0.00 0.00 0.00 1.40
854 894 1.035139 GTCGCCCTCCCTCGTTAATA 58.965 55.000 0.00 0.00 0.00 0.98
855 895 1.617357 GTCGCCCTCCCTCGTTAATAT 59.383 52.381 0.00 0.00 0.00 1.28
856 896 1.891150 TCGCCCTCCCTCGTTAATATC 59.109 52.381 0.00 0.00 0.00 1.63
857 897 1.616865 CGCCCTCCCTCGTTAATATCA 59.383 52.381 0.00 0.00 0.00 2.15
858 898 2.609737 CGCCCTCCCTCGTTAATATCAC 60.610 54.545 0.00 0.00 0.00 3.06
859 899 2.633481 GCCCTCCCTCGTTAATATCACT 59.367 50.000 0.00 0.00 0.00 3.41
860 900 3.306156 GCCCTCCCTCGTTAATATCACTC 60.306 52.174 0.00 0.00 0.00 3.51
861 901 3.258622 CCCTCCCTCGTTAATATCACTCC 59.741 52.174 0.00 0.00 0.00 3.85
862 902 3.057456 CCTCCCTCGTTAATATCACTCCG 60.057 52.174 0.00 0.00 0.00 4.63
863 903 3.559069 TCCCTCGTTAATATCACTCCGT 58.441 45.455 0.00 0.00 0.00 4.69
892 932 4.090057 GACTTGCAACGCTCGGCC 62.090 66.667 0.00 0.00 0.00 6.13
893 933 4.626081 ACTTGCAACGCTCGGCCT 62.626 61.111 0.00 0.00 0.00 5.19
949 993 2.203938 AAAGGTGGGAGGGAGCGA 60.204 61.111 0.00 0.00 0.00 4.93
1392 1457 0.530744 CATCGTCCCCTTCGTTCTCA 59.469 55.000 0.00 0.00 0.00 3.27
1402 1470 0.944311 TTCGTTCTCACCGAAGCAGC 60.944 55.000 0.00 0.00 39.22 5.25
1802 1903 2.262915 CGAGGAGCGCAAGTCCTT 59.737 61.111 16.94 2.54 44.32 3.36
3086 5354 4.695455 TGCTAATTGTTGGACTTAGAGTGC 59.305 41.667 0.00 0.00 37.06 4.40
3117 5393 4.146443 GTGTTCGCTGTTAATCACAAAAGC 59.854 41.667 0.00 0.00 33.87 3.51
3688 6065 5.048507 GTGTTCGGGAATACTATGAAGACC 58.951 45.833 1.60 0.00 29.50 3.85
4080 6618 1.809619 TGCGTATCGGTGCTTCTGC 60.810 57.895 0.00 0.00 40.20 4.26
4148 6719 4.448060 GGAACTTTCCTCTGTTACTTGTCG 59.552 45.833 0.34 0.00 44.11 4.35
4315 6897 3.776781 TACCCGGGTGCGATGGTG 61.777 66.667 36.97 0.00 32.27 4.17
4586 7168 1.691434 AGGGCTAGAAGATACAGCAGC 59.309 52.381 0.00 0.00 37.02 5.25
4867 8383 3.450115 GGTAGGCCAGCGTCGAGT 61.450 66.667 5.01 0.00 34.09 4.18
4937 8454 3.853330 CATGGCGAACGGTGCGAG 61.853 66.667 13.82 0.00 0.00 5.03
4958 8475 2.368011 GGACGGAGGGGGAAGGAAG 61.368 68.421 0.00 0.00 0.00 3.46
4959 8476 2.285442 ACGGAGGGGGAAGGAAGG 60.285 66.667 0.00 0.00 0.00 3.46
4960 8477 3.090532 CGGAGGGGGAAGGAAGGG 61.091 72.222 0.00 0.00 0.00 3.95
4961 8478 3.421386 GGAGGGGGAAGGAAGGGC 61.421 72.222 0.00 0.00 0.00 5.19
4968 8485 1.378514 GGAAGGAAGGGCGCAATCA 60.379 57.895 10.83 0.00 0.00 2.57
5037 8570 4.152402 GTCTTCTGAAGCATCTTACGCAAA 59.848 41.667 12.54 0.00 0.00 3.68
5127 8672 2.836360 CCATGGTGGCTGCCATCC 60.836 66.667 28.06 25.98 45.47 3.51
5128 8673 3.214123 CATGGTGGCTGCCATCCG 61.214 66.667 28.06 15.97 45.47 4.18
5129 8674 4.511246 ATGGTGGCTGCCATCCGG 62.511 66.667 28.06 0.00 45.47 5.14
5135 8680 4.195334 GCTGCCATCCGGTCCCAT 62.195 66.667 0.00 0.00 33.28 4.00
5136 8681 2.203252 CTGCCATCCGGTCCCATG 60.203 66.667 0.00 0.00 33.28 3.66
5137 8682 3.779850 CTGCCATCCGGTCCCATGG 62.780 68.421 14.21 14.21 42.39 3.66
5138 8683 3.488569 GCCATCCGGTCCCATGGA 61.489 66.667 21.09 2.89 42.11 3.41
5139 8684 2.831770 CCATCCGGTCCCATGGAG 59.168 66.667 15.22 3.25 42.11 3.86
5140 8685 2.822637 CCATCCGGTCCCATGGAGG 61.823 68.421 15.22 11.09 42.11 4.30
5141 8686 3.171388 ATCCGGTCCCATGGAGGC 61.171 66.667 15.22 4.61 37.76 4.70
5142 8687 3.721172 ATCCGGTCCCATGGAGGCT 62.721 63.158 15.22 0.00 37.76 4.58
5143 8688 4.181010 CCGGTCCCATGGAGGCTG 62.181 72.222 15.22 9.99 35.39 4.85
5144 8689 4.864334 CGGTCCCATGGAGGCTGC 62.864 72.222 15.22 0.00 35.39 5.25
5145 8690 4.512914 GGTCCCATGGAGGCTGCC 62.513 72.222 15.22 11.65 35.39 4.85
5146 8691 4.864334 GTCCCATGGAGGCTGCCG 62.864 72.222 15.22 0.00 35.39 5.69
5148 8693 3.882326 CCCATGGAGGCTGCCGAT 61.882 66.667 15.22 4.01 35.39 4.18
5149 8694 2.593725 CCATGGAGGCTGCCGATG 60.594 66.667 13.96 15.71 0.00 3.84
5150 8695 3.285215 CATGGAGGCTGCCGATGC 61.285 66.667 13.96 2.40 38.26 3.91
5206 8763 0.967380 GCAGGGGATGTGGGTTTCAG 60.967 60.000 0.00 0.00 0.00 3.02
5221 8778 0.891373 TTCAGACCGGAGCTTGAGAG 59.109 55.000 9.46 0.00 0.00 3.20
5236 8793 2.037901 TGAGAGGCATTGAGAGGCTAG 58.962 52.381 0.00 0.00 42.47 3.42
5309 8897 4.260538 GCTAGCTGAACTCAATGAAATCCG 60.261 45.833 7.70 0.00 0.00 4.18
5324 8912 0.732880 ATCCGCACGAACGAAGAGTG 60.733 55.000 0.14 0.00 38.77 3.51
5325 8913 1.371267 CCGCACGAACGAAGAGTGA 60.371 57.895 0.14 0.00 38.06 3.41
5326 8914 0.937699 CCGCACGAACGAAGAGTGAA 60.938 55.000 0.14 0.00 38.06 3.18
5327 8915 0.158928 CGCACGAACGAAGAGTGAAC 59.841 55.000 0.14 0.00 38.06 3.18
5328 8916 1.488527 GCACGAACGAAGAGTGAACT 58.511 50.000 0.14 0.00 38.06 3.01
5336 9759 6.477688 ACGAACGAAGAGTGAACTCAATAAAA 59.522 34.615 12.76 0.00 45.21 1.52
5338 9761 7.684489 CGAACGAAGAGTGAACTCAATAAAATC 59.316 37.037 12.76 2.14 45.21 2.17
5339 9762 7.365840 ACGAAGAGTGAACTCAATAAAATCC 57.634 36.000 12.76 0.00 45.21 3.01
5340 9763 7.162082 ACGAAGAGTGAACTCAATAAAATCCT 58.838 34.615 12.76 0.00 45.21 3.24
5345 9768 8.324306 AGAGTGAACTCAATAAAATCCTCATGA 58.676 33.333 12.76 0.00 45.21 3.07
5346 9769 8.868522 AGTGAACTCAATAAAATCCTCATGAA 57.131 30.769 0.00 0.00 0.00 2.57
5348 9771 7.693951 GTGAACTCAATAAAATCCTCATGAACG 59.306 37.037 0.00 0.00 0.00 3.95
5351 9774 7.978982 ACTCAATAAAATCCTCATGAACGAAG 58.021 34.615 0.00 0.00 0.00 3.79
5410 9833 7.891183 TGGTTGCTTAAAGGGAATTAGAATACA 59.109 33.333 0.00 0.00 0.00 2.29
5411 9834 8.406297 GGTTGCTTAAAGGGAATTAGAATACAG 58.594 37.037 0.00 0.00 0.00 2.74
5412 9835 7.568199 TGCTTAAAGGGAATTAGAATACAGC 57.432 36.000 0.00 0.00 0.00 4.40
5413 9836 6.546034 TGCTTAAAGGGAATTAGAATACAGCC 59.454 38.462 0.00 0.00 0.00 4.85
5414 9837 6.773200 GCTTAAAGGGAATTAGAATACAGCCT 59.227 38.462 0.00 0.00 0.00 4.58
5415 9838 7.937394 GCTTAAAGGGAATTAGAATACAGCCTA 59.063 37.037 0.00 0.00 0.00 3.93
5421 9844 9.338968 AGGGAATTAGAATACAGCCTATTATCA 57.661 33.333 0.00 0.00 0.00 2.15
5431 9854 9.896645 AATACAGCCTATTATCATTCCATAGTG 57.103 33.333 0.00 0.00 0.00 2.74
5432 9855 7.559335 ACAGCCTATTATCATTCCATAGTGA 57.441 36.000 0.00 0.00 0.00 3.41
5434 9857 7.880195 ACAGCCTATTATCATTCCATAGTGAAC 59.120 37.037 0.00 0.00 0.00 3.18
5435 9858 7.063898 CAGCCTATTATCATTCCATAGTGAACG 59.936 40.741 0.00 0.00 0.00 3.95
5436 9859 6.183360 GCCTATTATCATTCCATAGTGAACGC 60.183 42.308 0.00 0.00 0.00 4.84
5437 9860 7.099764 CCTATTATCATTCCATAGTGAACGCT 58.900 38.462 0.00 0.00 0.00 5.07
5438 9861 6.791887 ATTATCATTCCATAGTGAACGCTG 57.208 37.500 0.00 0.00 0.00 5.18
5439 9862 2.905075 TCATTCCATAGTGAACGCTGG 58.095 47.619 0.00 0.00 0.00 4.85
5440 9863 2.236146 TCATTCCATAGTGAACGCTGGT 59.764 45.455 0.00 0.00 0.00 4.00
5443 9866 1.621317 TCCATAGTGAACGCTGGTTGA 59.379 47.619 0.00 0.00 36.24 3.18
5444 9867 1.732259 CCATAGTGAACGCTGGTTGAC 59.268 52.381 0.00 0.00 40.10 3.18
5445 9868 1.732259 CATAGTGAACGCTGGTTGACC 59.268 52.381 0.00 0.00 40.60 4.02
5446 9869 0.319211 TAGTGAACGCTGGTTGACCG 60.319 55.000 0.00 0.00 40.60 4.79
5447 9870 2.280524 TGAACGCTGGTTGACCGG 60.281 61.111 0.00 0.00 45.30 5.28
5448 9871 2.029964 GAACGCTGGTTGACCGGA 59.970 61.111 9.46 0.00 45.36 5.14
5451 9874 4.379243 CGCTGGTTGACCGGAGCT 62.379 66.667 9.46 0.00 45.36 4.09
5452 9875 2.435059 GCTGGTTGACCGGAGCTC 60.435 66.667 9.46 4.71 45.36 4.09
5455 9878 1.533033 TGGTTGACCGGAGCTCTGA 60.533 57.895 24.60 0.56 39.43 3.27
5456 9879 1.216710 GGTTGACCGGAGCTCTGAG 59.783 63.158 24.60 15.73 0.00 3.35
5457 9880 1.446966 GTTGACCGGAGCTCTGAGC 60.447 63.158 24.60 21.72 42.84 4.26
5471 9894 3.250521 GCTCTGAGCTGAAGATTAATGGC 59.749 47.826 21.93 0.00 38.45 4.40
5472 9895 4.449131 CTCTGAGCTGAAGATTAATGGCA 58.551 43.478 0.00 0.00 0.00 4.92
5474 9897 3.548770 TGAGCTGAAGATTAATGGCAGG 58.451 45.455 0.00 0.00 0.00 4.85
5478 9901 5.206587 AGCTGAAGATTAATGGCAGGAAAT 58.793 37.500 0.00 0.00 0.00 2.17
5479 9902 6.367983 AGCTGAAGATTAATGGCAGGAAATA 58.632 36.000 0.00 0.00 0.00 1.40
5480 9903 6.264067 AGCTGAAGATTAATGGCAGGAAATAC 59.736 38.462 0.00 0.00 0.00 1.89
5482 9905 7.255730 GCTGAAGATTAATGGCAGGAAATACAT 60.256 37.037 0.00 0.00 0.00 2.29
5485 9908 7.756395 AGATTAATGGCAGGAAATACATCTG 57.244 36.000 0.00 0.00 0.00 2.90
5486 9909 6.718454 AGATTAATGGCAGGAAATACATCTGG 59.282 38.462 0.00 0.00 0.00 3.86
5488 9911 1.215173 TGGCAGGAAATACATCTGGGG 59.785 52.381 0.00 0.00 0.00 4.96
5489 9912 1.322442 GCAGGAAATACATCTGGGGC 58.678 55.000 0.00 0.00 0.00 5.80
5490 9913 1.410083 GCAGGAAATACATCTGGGGCA 60.410 52.381 0.00 0.00 0.00 5.36
5493 9916 4.728772 CAGGAAATACATCTGGGGCAATA 58.271 43.478 0.00 0.00 0.00 1.90
5495 9918 5.010012 CAGGAAATACATCTGGGGCAATAAC 59.990 44.000 0.00 0.00 0.00 1.89
5496 9919 4.280929 GGAAATACATCTGGGGCAATAACC 59.719 45.833 0.00 0.00 0.00 2.85
5497 9920 4.534647 AATACATCTGGGGCAATAACCA 57.465 40.909 0.00 0.00 35.05 3.67
5498 9921 2.917713 ACATCTGGGGCAATAACCAA 57.082 45.000 0.00 0.00 36.09 3.67
5499 9922 2.738743 ACATCTGGGGCAATAACCAAG 58.261 47.619 0.00 0.00 36.09 3.61
5501 9924 2.507407 TCTGGGGCAATAACCAAGAC 57.493 50.000 0.00 0.00 36.09 3.01
5503 9926 2.026262 TCTGGGGCAATAACCAAGACTC 60.026 50.000 0.00 0.00 36.09 3.36
5505 9928 2.378547 TGGGGCAATAACCAAGACTCTT 59.621 45.455 0.00 0.00 32.89 2.85
5506 9929 3.181423 TGGGGCAATAACCAAGACTCTTT 60.181 43.478 0.00 0.00 32.89 2.52
5507 9930 3.193479 GGGGCAATAACCAAGACTCTTTG 59.807 47.826 0.00 0.00 0.00 2.77
5518 9941 3.073274 AGACTCTTTGGTTATGGCCAC 57.927 47.619 8.16 0.00 38.42 5.01
5519 9942 2.644798 AGACTCTTTGGTTATGGCCACT 59.355 45.455 8.16 0.00 38.42 4.00
5520 9943 3.844211 AGACTCTTTGGTTATGGCCACTA 59.156 43.478 8.16 0.00 38.42 2.74
5522 9945 5.665812 AGACTCTTTGGTTATGGCCACTATA 59.334 40.000 8.16 0.00 38.42 1.31
5523 9946 5.930135 ACTCTTTGGTTATGGCCACTATAG 58.070 41.667 8.16 0.00 38.42 1.31
5525 9948 6.330250 ACTCTTTGGTTATGGCCACTATAGAT 59.670 38.462 8.16 0.00 38.42 1.98
5527 9950 7.907389 TCTTTGGTTATGGCCACTATAGATAG 58.093 38.462 8.16 0.00 38.42 2.08
5528 9951 6.620877 TTGGTTATGGCCACTATAGATAGG 57.379 41.667 8.16 6.52 38.42 2.57
5532 9955 6.012771 GGTTATGGCCACTATAGATAGGGTTT 60.013 42.308 8.16 0.00 31.80 3.27
5533 9956 7.459234 GTTATGGCCACTATAGATAGGGTTTT 58.541 38.462 8.16 0.00 31.80 2.43
5534 9957 5.562298 TGGCCACTATAGATAGGGTTTTC 57.438 43.478 0.00 0.00 31.80 2.29
5535 9958 4.972568 TGGCCACTATAGATAGGGTTTTCA 59.027 41.667 0.00 0.00 31.80 2.69
5537 9960 5.940470 GGCCACTATAGATAGGGTTTTCATG 59.060 44.000 6.78 0.00 31.80 3.07
5538 9961 6.465894 GGCCACTATAGATAGGGTTTTCATGT 60.466 42.308 6.78 0.00 31.80 3.21
5539 9962 6.651225 GCCACTATAGATAGGGTTTTCATGTC 59.349 42.308 6.78 0.00 31.80 3.06
5540 9963 7.162082 CCACTATAGATAGGGTTTTCATGTCC 58.838 42.308 6.78 0.00 31.80 4.02
5542 9965 7.657761 CACTATAGATAGGGTTTTCATGTCCAC 59.342 40.741 6.78 0.00 34.69 4.02
5543 9966 6.831664 ATAGATAGGGTTTTCATGTCCACT 57.168 37.500 0.00 0.00 0.00 4.00
5544 9967 7.931015 ATAGATAGGGTTTTCATGTCCACTA 57.069 36.000 0.00 0.00 0.00 2.74
5545 9968 6.636454 AGATAGGGTTTTCATGTCCACTAA 57.364 37.500 0.00 0.00 0.00 2.24
5546 9969 7.213178 AGATAGGGTTTTCATGTCCACTAAT 57.787 36.000 0.00 0.00 0.00 1.73
5547 9970 7.643123 AGATAGGGTTTTCATGTCCACTAATT 58.357 34.615 0.00 0.00 0.00 1.40
5548 9971 5.982890 AGGGTTTTCATGTCCACTAATTG 57.017 39.130 0.00 0.00 0.00 2.32
5550 9973 4.081697 GGGTTTTCATGTCCACTAATTGGG 60.082 45.833 0.00 0.00 46.92 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.243907 CAGTGGACAGACGGTACAGG 59.756 60.000 0.00 0.00 42.35 4.00
28 29 0.959553 ACAGTGGACAGACGGTACAG 59.040 55.000 0.00 0.00 42.35 2.74
29 30 0.671796 CACAGTGGACAGACGGTACA 59.328 55.000 0.00 0.00 38.28 2.90
30 31 0.672342 ACACAGTGGACAGACGGTAC 59.328 55.000 5.31 0.00 0.00 3.34
31 32 1.405872 AACACAGTGGACAGACGGTA 58.594 50.000 5.31 0.00 0.00 4.02
32 33 1.405872 TAACACAGTGGACAGACGGT 58.594 50.000 5.31 0.00 0.00 4.83
38 39 3.007506 ACGATGGAATAACACAGTGGACA 59.992 43.478 5.31 0.00 0.00 4.02
103 105 0.522915 CTAGGTCGCGTTTCTCGGTC 60.523 60.000 5.77 0.00 40.26 4.79
106 108 0.797249 CCACTAGGTCGCGTTTCTCG 60.797 60.000 5.77 1.21 43.12 4.04
107 109 0.524862 TCCACTAGGTCGCGTTTCTC 59.475 55.000 5.77 0.00 35.89 2.87
108 110 1.183549 ATCCACTAGGTCGCGTTTCT 58.816 50.000 5.77 4.90 35.89 2.52
109 111 2.005971 AATCCACTAGGTCGCGTTTC 57.994 50.000 5.77 0.00 35.89 2.78
110 112 2.467566 AAATCCACTAGGTCGCGTTT 57.532 45.000 5.77 0.00 35.89 3.60
111 113 2.417787 GGTAAATCCACTAGGTCGCGTT 60.418 50.000 5.77 0.00 35.89 4.84
112 114 1.135721 GGTAAATCCACTAGGTCGCGT 59.864 52.381 5.77 0.00 35.89 6.01
113 115 1.849097 GGTAAATCCACTAGGTCGCG 58.151 55.000 0.00 0.00 35.89 5.87
114 116 1.537562 CCGGTAAATCCACTAGGTCGC 60.538 57.143 0.00 0.00 35.89 5.19
115 117 1.753073 ACCGGTAAATCCACTAGGTCG 59.247 52.381 4.49 0.00 35.89 4.79
116 118 2.159000 CCACCGGTAAATCCACTAGGTC 60.159 54.545 6.87 0.00 35.89 3.85
117 119 1.835531 CCACCGGTAAATCCACTAGGT 59.164 52.381 6.87 0.00 35.89 3.08
118 120 1.474498 GCCACCGGTAAATCCACTAGG 60.474 57.143 6.87 0.34 35.57 3.02
119 121 1.805120 CGCCACCGGTAAATCCACTAG 60.805 57.143 6.87 0.00 35.57 2.57
232 238 2.971330 TGGAAAAAGATTGGCACCATGT 59.029 40.909 0.00 0.00 0.00 3.21
233 239 3.328505 GTGGAAAAAGATTGGCACCATG 58.671 45.455 0.00 0.00 0.00 3.66
263 269 0.944386 CGGCCATGTTTAAGGATCGG 59.056 55.000 2.24 0.00 0.00 4.18
317 325 2.502510 GTTGCCATCGCTGCGTTG 60.503 61.111 22.48 22.44 35.36 4.10
319 327 3.726517 GTGTTGCCATCGCTGCGT 61.727 61.111 22.48 6.62 35.36 5.24
370 378 2.009774 CAGGCAGGAGAAAATGTACGG 58.990 52.381 0.00 0.00 0.00 4.02
371 379 2.009774 CCAGGCAGGAGAAAATGTACG 58.990 52.381 0.00 0.00 41.22 3.67
372 380 3.350219 TCCAGGCAGGAGAAAATGTAC 57.650 47.619 0.00 0.00 43.07 2.90
388 400 0.248907 CGGCAGTACACCGTATCCAG 60.249 60.000 16.76 0.00 45.70 3.86
417 429 2.607771 GGTGTAAAGTAAGGCGTGACGA 60.608 50.000 10.10 0.00 0.00 4.20
462 474 5.944599 AGAAAAGATCGTGTACTCCTGTAGA 59.055 40.000 0.00 0.00 0.00 2.59
463 475 6.197364 AGAAAAGATCGTGTACTCCTGTAG 57.803 41.667 0.00 0.00 0.00 2.74
652 672 2.122167 GGCACGTTGTTGGTTGGGA 61.122 57.895 0.00 0.00 0.00 4.37
655 675 1.585002 CGTGGCACGTTGTTGGTTG 60.585 57.895 30.56 0.00 36.74 3.77
838 878 2.633481 AGTGATATTAACGAGGGAGGGC 59.367 50.000 0.00 0.00 0.00 5.19
839 879 3.258622 GGAGTGATATTAACGAGGGAGGG 59.741 52.174 0.00 0.00 0.00 4.30
840 880 3.057456 CGGAGTGATATTAACGAGGGAGG 60.057 52.174 0.00 0.00 0.00 4.30
841 881 3.568853 ACGGAGTGATATTAACGAGGGAG 59.431 47.826 0.00 0.00 42.51 4.30
842 882 3.559069 ACGGAGTGATATTAACGAGGGA 58.441 45.455 0.00 0.00 42.51 4.20
861 901 4.835891 AGTCTAGGGCCCCGGACG 62.836 72.222 28.16 11.72 36.71 4.79
862 902 2.365237 AAGTCTAGGGCCCCGGAC 60.365 66.667 27.76 27.76 33.78 4.79
863 903 2.365105 CAAGTCTAGGGCCCCGGA 60.365 66.667 21.43 14.75 0.00 5.14
1170 1223 1.223487 GGAGTTGGAGCCGGCATTA 59.777 57.895 31.54 11.20 0.00 1.90
1362 1427 2.202932 GACGATGCCTGCGGTGAT 60.203 61.111 0.00 0.00 0.00 3.06
1392 1457 4.749310 CTCGCCTGCTGCTTCGGT 62.749 66.667 0.00 0.00 38.05 4.69
1802 1903 2.852075 ACTTGGGAGGTCGGGCAA 60.852 61.111 0.00 0.00 0.00 4.52
2994 4612 9.762933 TTTTTGAGAAAATTCCTACATGAAAGG 57.237 29.630 0.00 6.10 31.19 3.11
3052 4778 5.476599 TCCAACAATTAGCATGCTGTTTACT 59.523 36.000 30.42 7.84 29.70 2.24
3086 5354 0.732571 AACAGCGAACACAACAGTGG 59.267 50.000 0.00 0.00 37.58 4.00
3117 5393 5.794687 TGTAAAGTTCTGCAATATGTCCG 57.205 39.130 0.00 0.00 0.00 4.79
4148 6719 2.648059 ACATGCCTGCCTACTGAATTC 58.352 47.619 0.00 0.00 0.00 2.17
4315 6897 2.554893 GTCATCTACATCTCGGAGGACC 59.445 54.545 4.96 0.00 35.58 4.46
4586 7168 2.906458 CCAGGCTCCTGCAGGTAG 59.094 66.667 31.58 25.61 42.35 3.18
4758 8271 2.923020 AGCGTGCTTTCAACAAAAGTTG 59.077 40.909 2.09 2.09 45.23 3.16
4939 8456 3.937372 TTCCTTCCCCCTCCGTCCC 62.937 68.421 0.00 0.00 0.00 4.46
4940 8457 2.285144 TTCCTTCCCCCTCCGTCC 60.285 66.667 0.00 0.00 0.00 4.79
4941 8458 2.368011 CCTTCCTTCCCCCTCCGTC 61.368 68.421 0.00 0.00 0.00 4.79
4942 8459 2.285442 CCTTCCTTCCCCCTCCGT 60.285 66.667 0.00 0.00 0.00 4.69
4943 8460 3.090532 CCCTTCCTTCCCCCTCCG 61.091 72.222 0.00 0.00 0.00 4.63
4945 8462 3.798511 CGCCCTTCCTTCCCCCTC 61.799 72.222 0.00 0.00 0.00 4.30
4949 8466 2.043953 ATTGCGCCCTTCCTTCCC 60.044 61.111 4.18 0.00 0.00 3.97
4950 8467 1.378514 TGATTGCGCCCTTCCTTCC 60.379 57.895 4.18 0.00 0.00 3.46
4951 8468 1.803289 GTGATTGCGCCCTTCCTTC 59.197 57.895 4.18 0.00 0.00 3.46
4953 8470 2.436646 CGTGATTGCGCCCTTCCT 60.437 61.111 4.18 0.00 0.00 3.36
4961 8478 2.202260 CACAGCAGCGTGATTGCG 60.202 61.111 10.72 0.00 45.98 4.85
4968 8485 1.889105 CTTCACACCACAGCAGCGT 60.889 57.895 0.00 0.00 0.00 5.07
5124 8669 3.171388 GCCTCCATGGGACCGGAT 61.171 66.667 9.46 0.00 36.00 4.18
5125 8670 4.414956 AGCCTCCATGGGACCGGA 62.415 66.667 9.46 0.00 36.00 5.14
5126 8671 4.181010 CAGCCTCCATGGGACCGG 62.181 72.222 13.02 0.00 36.00 5.28
5127 8672 4.864334 GCAGCCTCCATGGGACCG 62.864 72.222 13.02 0.00 36.00 4.79
5128 8673 4.512914 GGCAGCCTCCATGGGACC 62.513 72.222 13.02 0.89 36.00 4.46
5129 8674 4.864334 CGGCAGCCTCCATGGGAC 62.864 72.222 13.02 1.33 36.00 4.46
5131 8676 3.882326 ATCGGCAGCCTCCATGGG 61.882 66.667 13.02 2.26 36.00 4.00
5132 8677 2.593725 CATCGGCAGCCTCCATGG 60.594 66.667 10.54 4.97 39.35 3.66
5133 8678 3.285215 GCATCGGCAGCCTCCATG 61.285 66.667 10.54 9.95 40.72 3.66
5141 8686 3.803082 CAACACGGGCATCGGCAG 61.803 66.667 3.86 0.00 44.45 4.85
5142 8687 2.733319 TTACAACACGGGCATCGGCA 62.733 55.000 3.86 0.00 44.45 5.69
5143 8688 1.977594 CTTACAACACGGGCATCGGC 61.978 60.000 3.86 0.00 44.45 5.54
5144 8689 0.390603 TCTTACAACACGGGCATCGG 60.391 55.000 3.86 0.00 44.45 4.18
5145 8690 0.999406 CTCTTACAACACGGGCATCG 59.001 55.000 0.00 0.00 45.88 3.84
5146 8691 0.727398 GCTCTTACAACACGGGCATC 59.273 55.000 0.00 0.00 0.00 3.91
5147 8692 1.019278 CGCTCTTACAACACGGGCAT 61.019 55.000 0.00 0.00 0.00 4.40
5148 8693 1.666553 CGCTCTTACAACACGGGCA 60.667 57.895 0.00 0.00 0.00 5.36
5149 8694 1.373748 TCGCTCTTACAACACGGGC 60.374 57.895 0.00 0.00 0.00 6.13
5150 8695 0.038526 AGTCGCTCTTACAACACGGG 60.039 55.000 0.00 0.00 0.00 5.28
5151 8696 1.060713 CAGTCGCTCTTACAACACGG 58.939 55.000 0.00 0.00 0.00 4.94
5152 8697 1.060713 CCAGTCGCTCTTACAACACG 58.939 55.000 0.00 0.00 0.00 4.49
5206 8763 1.965754 ATGCCTCTCAAGCTCCGGTC 61.966 60.000 0.00 0.00 0.00 4.79
5221 8778 2.224257 CCTCTTCTAGCCTCTCAATGCC 60.224 54.545 0.00 0.00 0.00 4.40
5236 8793 1.207791 TCAATGAGCCCCTCCTCTTC 58.792 55.000 0.00 0.00 33.02 2.87
5309 8897 1.452399 GAGTTCACTCTTCGTTCGTGC 59.548 52.381 0.00 0.00 39.81 5.34
5324 8912 7.974675 TCGTTCATGAGGATTTTATTGAGTTC 58.025 34.615 0.00 0.00 0.00 3.01
5325 8913 7.921786 TCGTTCATGAGGATTTTATTGAGTT 57.078 32.000 0.00 0.00 0.00 3.01
5326 8914 7.824289 TCTTCGTTCATGAGGATTTTATTGAGT 59.176 33.333 0.00 0.00 0.00 3.41
5327 8915 8.201554 TCTTCGTTCATGAGGATTTTATTGAG 57.798 34.615 0.00 0.00 0.00 3.02
5328 8916 7.824289 ACTCTTCGTTCATGAGGATTTTATTGA 59.176 33.333 0.00 0.00 31.67 2.57
5336 9759 4.543590 ACAACTCTTCGTTCATGAGGAT 57.456 40.909 0.00 0.00 32.27 3.24
5338 9761 5.207768 CAAAACAACTCTTCGTTCATGAGG 58.792 41.667 0.00 0.00 32.27 3.86
5339 9762 5.207768 CCAAAACAACTCTTCGTTCATGAG 58.792 41.667 0.00 0.00 32.27 2.90
5340 9763 4.497340 GCCAAAACAACTCTTCGTTCATGA 60.497 41.667 0.00 0.00 32.27 3.07
5345 9768 2.357952 GGAGCCAAAACAACTCTTCGTT 59.642 45.455 0.00 0.00 35.88 3.85
5346 9769 1.947456 GGAGCCAAAACAACTCTTCGT 59.053 47.619 0.00 0.00 0.00 3.85
5348 9771 3.130340 TGTTGGAGCCAAAACAACTCTTC 59.870 43.478 3.05 0.00 43.54 2.87
5351 9774 3.518634 TTGTTGGAGCCAAAACAACTC 57.481 42.857 3.05 0.00 43.54 3.01
5410 9833 7.099764 CGTTCACTATGGAATGATAATAGGCT 58.900 38.462 0.00 0.00 36.16 4.58
5411 9834 6.183360 GCGTTCACTATGGAATGATAATAGGC 60.183 42.308 0.00 0.00 36.16 3.93
5412 9835 7.063898 CAGCGTTCACTATGGAATGATAATAGG 59.936 40.741 0.00 0.00 36.16 2.57
5413 9836 7.063898 CCAGCGTTCACTATGGAATGATAATAG 59.936 40.741 0.00 0.00 36.16 1.73
5414 9837 6.873605 CCAGCGTTCACTATGGAATGATAATA 59.126 38.462 0.00 0.00 36.16 0.98
5415 9838 5.702670 CCAGCGTTCACTATGGAATGATAAT 59.297 40.000 0.00 0.00 36.16 1.28
5416 9839 5.056480 CCAGCGTTCACTATGGAATGATAA 58.944 41.667 0.00 0.00 36.16 1.75
5417 9840 4.100963 ACCAGCGTTCACTATGGAATGATA 59.899 41.667 0.00 0.00 36.16 2.15
5418 9841 3.118261 ACCAGCGTTCACTATGGAATGAT 60.118 43.478 0.00 0.00 36.16 2.45
5419 9842 2.236146 ACCAGCGTTCACTATGGAATGA 59.764 45.455 0.00 0.00 36.16 2.57
5420 9843 2.632377 ACCAGCGTTCACTATGGAATG 58.368 47.619 0.00 0.00 36.62 2.67
5421 9844 3.009723 CAACCAGCGTTCACTATGGAAT 58.990 45.455 0.00 0.00 36.62 3.01
5424 9847 1.732259 GTCAACCAGCGTTCACTATGG 59.268 52.381 0.00 0.00 38.83 2.74
5425 9848 1.732259 GGTCAACCAGCGTTCACTATG 59.268 52.381 0.00 0.00 35.64 2.23
5426 9849 1.671850 CGGTCAACCAGCGTTCACTAT 60.672 52.381 0.00 0.00 41.29 2.12
5427 9850 0.319211 CGGTCAACCAGCGTTCACTA 60.319 55.000 0.00 0.00 41.29 2.74
5428 9851 1.594293 CGGTCAACCAGCGTTCACT 60.594 57.895 0.00 0.00 41.29 3.41
5429 9852 2.604174 CCGGTCAACCAGCGTTCAC 61.604 63.158 0.00 0.00 44.91 3.18
5430 9853 2.280524 CCGGTCAACCAGCGTTCA 60.281 61.111 0.00 0.00 44.91 3.18
5431 9854 2.027625 CTCCGGTCAACCAGCGTTC 61.028 63.158 0.00 0.00 44.91 3.95
5432 9855 2.030562 CTCCGGTCAACCAGCGTT 59.969 61.111 0.00 0.00 44.91 4.84
5434 9857 4.379243 AGCTCCGGTCAACCAGCG 62.379 66.667 0.00 0.00 46.00 5.18
5435 9858 2.435059 GAGCTCCGGTCAACCAGC 60.435 66.667 0.87 0.96 35.83 4.85
5436 9859 1.079543 CAGAGCTCCGGTCAACCAG 60.080 63.158 10.93 0.00 35.14 4.00
5437 9860 1.533033 TCAGAGCTCCGGTCAACCA 60.533 57.895 10.93 0.00 35.14 3.67
5438 9861 1.216710 CTCAGAGCTCCGGTCAACC 59.783 63.158 10.93 0.00 31.89 3.77
5439 9862 1.446966 GCTCAGAGCTCCGGTCAAC 60.447 63.158 15.78 0.00 38.45 3.18
5440 9863 2.973899 GCTCAGAGCTCCGGTCAA 59.026 61.111 15.78 0.00 38.45 3.18
5451 9874 4.449131 CTGCCATTAATCTTCAGCTCAGA 58.551 43.478 0.00 0.00 0.00 3.27
5452 9875 3.564644 CCTGCCATTAATCTTCAGCTCAG 59.435 47.826 0.00 0.00 0.00 3.35
5455 9878 3.939740 TCCTGCCATTAATCTTCAGCT 57.060 42.857 0.00 0.00 0.00 4.24
5456 9879 4.989279 TTTCCTGCCATTAATCTTCAGC 57.011 40.909 0.00 0.00 0.00 4.26
5457 9880 7.572523 TGTATTTCCTGCCATTAATCTTCAG 57.427 36.000 0.00 0.00 0.00 3.02
5458 9881 8.000709 AGATGTATTTCCTGCCATTAATCTTCA 58.999 33.333 0.00 0.00 0.00 3.02
5459 9882 8.295288 CAGATGTATTTCCTGCCATTAATCTTC 58.705 37.037 0.00 0.00 0.00 2.87
5462 9885 6.071728 CCCAGATGTATTTCCTGCCATTAATC 60.072 42.308 0.00 0.00 0.00 1.75
5463 9886 5.776716 CCCAGATGTATTTCCTGCCATTAAT 59.223 40.000 0.00 0.00 0.00 1.40
5464 9887 5.139727 CCCAGATGTATTTCCTGCCATTAA 58.860 41.667 0.00 0.00 0.00 1.40
5465 9888 4.447616 CCCCAGATGTATTTCCTGCCATTA 60.448 45.833 0.00 0.00 0.00 1.90
5469 9892 1.986882 CCCCAGATGTATTTCCTGCC 58.013 55.000 0.00 0.00 0.00 4.85
5470 9893 1.322442 GCCCCAGATGTATTTCCTGC 58.678 55.000 0.00 0.00 0.00 4.85
5471 9894 2.734755 TGCCCCAGATGTATTTCCTG 57.265 50.000 0.00 0.00 0.00 3.86
5472 9895 3.979501 ATTGCCCCAGATGTATTTCCT 57.020 42.857 0.00 0.00 0.00 3.36
5474 9897 4.892934 TGGTTATTGCCCCAGATGTATTTC 59.107 41.667 0.00 0.00 0.00 2.17
5478 9901 3.525609 TCTTGGTTATTGCCCCAGATGTA 59.474 43.478 0.00 0.00 31.04 2.29
5479 9902 2.311542 TCTTGGTTATTGCCCCAGATGT 59.688 45.455 0.00 0.00 31.04 3.06
5480 9903 2.689983 GTCTTGGTTATTGCCCCAGATG 59.310 50.000 0.00 0.00 31.04 2.90
5482 9905 1.992557 AGTCTTGGTTATTGCCCCAGA 59.007 47.619 0.00 0.00 31.04 3.86
5485 9908 2.808906 AGAGTCTTGGTTATTGCCCC 57.191 50.000 0.00 0.00 0.00 5.80
5486 9909 3.193479 CCAAAGAGTCTTGGTTATTGCCC 59.807 47.826 6.06 0.00 40.94 5.36
5496 9919 3.191371 GTGGCCATAACCAAAGAGTCTTG 59.809 47.826 9.72 0.00 42.70 3.02
5497 9920 3.074538 AGTGGCCATAACCAAAGAGTCTT 59.925 43.478 9.72 0.00 42.70 3.01
5498 9921 2.644798 AGTGGCCATAACCAAAGAGTCT 59.355 45.455 9.72 0.00 42.70 3.24
5499 9922 3.073274 AGTGGCCATAACCAAAGAGTC 57.927 47.619 9.72 0.00 42.70 3.36
5501 9924 6.174720 TCTATAGTGGCCATAACCAAAGAG 57.825 41.667 9.72 0.00 42.70 2.85
5503 9926 7.106239 CCTATCTATAGTGGCCATAACCAAAG 58.894 42.308 9.72 0.87 42.70 2.77
5505 9928 5.487488 CCCTATCTATAGTGGCCATAACCAA 59.513 44.000 9.72 0.00 42.70 3.67
5506 9929 5.030147 CCCTATCTATAGTGGCCATAACCA 58.970 45.833 9.72 0.00 37.38 3.67
5507 9930 5.030820 ACCCTATCTATAGTGGCCATAACC 58.969 45.833 9.72 0.00 0.00 2.85
5508 9931 6.622427 AACCCTATCTATAGTGGCCATAAC 57.378 41.667 9.72 0.00 0.00 1.89
5509 9932 7.293771 TGAAAACCCTATCTATAGTGGCCATAA 59.706 37.037 9.72 0.00 0.00 1.90
5510 9933 6.790461 TGAAAACCCTATCTATAGTGGCCATA 59.210 38.462 9.72 2.66 0.00 2.74
5512 9935 4.972568 TGAAAACCCTATCTATAGTGGCCA 59.027 41.667 0.00 0.00 0.00 5.36
5514 9937 6.534634 ACATGAAAACCCTATCTATAGTGGC 58.465 40.000 0.00 0.00 0.00 5.01
5515 9938 7.162082 GGACATGAAAACCCTATCTATAGTGG 58.838 42.308 0.00 1.44 0.00 4.00
5518 9941 7.967908 AGTGGACATGAAAACCCTATCTATAG 58.032 38.462 0.00 0.00 0.00 1.31
5519 9942 7.931015 AGTGGACATGAAAACCCTATCTATA 57.069 36.000 0.00 0.00 0.00 1.31
5520 9943 6.831664 AGTGGACATGAAAACCCTATCTAT 57.168 37.500 0.00 0.00 0.00 1.98
5522 9945 6.636454 TTAGTGGACATGAAAACCCTATCT 57.364 37.500 0.00 0.00 0.00 1.98
5523 9946 7.707104 CAATTAGTGGACATGAAAACCCTATC 58.293 38.462 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.