Multiple sequence alignment - TraesCS7D01G023600

Loading Multiple Alignment...

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 TraesCS7D01G023600 chr7D 100.000 6392 0 0 406 6797 11018742 11025133 0.000000e+00 11804.0
1 TraesCS7D01G023600 chr7D 100.000 175 0 0 1 175 11018337 11018511 2.360000e-84 324.0
2 TraesCS7D01G023600 chr7D 80.277 289 36 11 6155 6423 227657960 227658247 1.500000e-46 198.0
3 TraesCS7D01G023600 chr7D 81.463 205 34 4 5920 6122 340264695 340264493 1.520000e-36 165.0
4 TraesCS7D01G023600 chr7A 92.500 6000 272 67 559 6450 10191284 10197213 0.000000e+00 8423.0
5 TraesCS7D01G023600 chr7A 85.833 240 30 4 540 776 278230126 278230364 1.130000e-62 252.0
6 TraesCS7D01G023600 chr7A 93.548 93 6 0 6705 6797 10198096 10198188 9.190000e-29 139.0
7 TraesCS7D01G023600 chr7A 96.610 59 1 1 3 61 83936156 83936099 5.610000e-16 97.1
8 TraesCS7D01G023600 chr4A 93.270 3581 140 44 2186 5738 727117875 727114368 0.000000e+00 5184.0
9 TraesCS7D01G023600 chr4A 91.121 1588 84 21 523 2072 727119497 727117929 0.000000e+00 2098.0
10 TraesCS7D01G023600 chr4A 84.127 252 39 1 523 773 27273330 27273079 6.810000e-60 243.0
11 TraesCS7D01G023600 chr4A 83.529 255 41 1 520 773 444386187 444386441 3.170000e-58 237.0
12 TraesCS7D01G023600 chr4A 82.699 289 29 7 6157 6424 660198291 660198579 3.170000e-58 237.0
13 TraesCS7D01G023600 chr4A 92.063 126 4 3 406 525 727121344 727121219 9.060000e-39 172.0
14 TraesCS7D01G023600 chr4A 79.747 237 29 10 6159 6385 439274083 439274310 3.280000e-33 154.0
15 TraesCS7D01G023600 chr5D 82.380 647 91 17 2772 3403 82323813 82323175 6.000000e-150 542.0
16 TraesCS7D01G023600 chr5D 74.652 935 154 58 4150 5058 82319792 82318915 3.040000e-88 337.0
17 TraesCS7D01G023600 chr5D 83.934 305 25 14 6150 6432 44681544 44681846 3.120000e-68 270.0
18 TraesCS7D01G023600 chr5D 79.359 281 35 13 6160 6417 414326755 414326475 7.010000e-40 176.0
19 TraesCS7D01G023600 chr5D 85.057 174 18 5 3951 4120 82322492 82322323 3.260000e-38 171.0
20 TraesCS7D01G023600 chr5D 79.070 258 34 16 6158 6397 299727527 299727782 7.060000e-35 159.0
21 TraesCS7D01G023600 chr5D 85.135 74 7 3 1093 1164 82324561 82324490 9.460000e-09 73.1
22 TraesCS7D01G023600 chr3D 82.485 491 74 6 2781 3259 552956519 552957009 2.930000e-113 420.0
23 TraesCS7D01G023600 chr3D 89.116 147 13 3 3963 4106 552957811 552957957 5.420000e-41 180.0
24 TraesCS7D01G023600 chr3A 81.762 488 80 5 2781 3259 689360058 689360545 3.820000e-107 399.0
25 TraesCS7D01G023600 chr3A 76.080 602 100 28 4479 5058 689362799 689363378 2.420000e-69 274.0
26 TraesCS7D01G023600 chr3A 86.585 164 16 4 3963 4120 689361344 689361507 7.010000e-40 176.0
27 TraesCS7D01G023600 chr3B 78.336 637 116 15 2781 3403 733880343 733880971 6.390000e-105 392.0
28 TraesCS7D01G023600 chr3B 75.753 598 96 29 4479 5058 733883039 733883605 8.750000e-64 255.0
29 TraesCS7D01G023600 chr3B 87.195 164 15 4 3963 4120 733881631 733881794 1.510000e-41 182.0
30 TraesCS7D01G023600 chr3B 98.182 55 1 0 3 57 306581485 306581431 5.610000e-16 97.1
31 TraesCS7D01G023600 chr2B 82.866 321 45 4 6421 6738 678712910 678713223 5.190000e-71 279.0
32 TraesCS7D01G023600 chr2B 81.271 299 27 13 6155 6425 18971873 18972170 1.480000e-51 215.0
33 TraesCS7D01G023600 chr2A 81.818 352 45 13 3951 4291 48255108 48255451 1.870000e-70 278.0
34 TraesCS7D01G023600 chr2A 83.846 260 40 2 520 777 35892659 35892918 5.260000e-61 246.0
35 TraesCS7D01G023600 chr2A 83.525 261 40 3 520 777 11238950 11239210 2.450000e-59 241.0
36 TraesCS7D01G023600 chr2A 83.462 260 41 2 520 777 776394103 776394362 2.450000e-59 241.0
37 TraesCS7D01G023600 chr2A 94.231 104 6 0 6321 6424 300683119 300683016 7.060000e-35 159.0
38 TraesCS7D01G023600 chr2A 79.188 197 35 4 5925 6116 42960822 42960627 1.540000e-26 132.0
39 TraesCS7D01G023600 chr2A 76.442 208 43 4 5920 6122 101851735 101851941 2.590000e-19 108.0
40 TraesCS7D01G023600 chr2A 98.214 56 1 0 2 57 711956646 711956701 1.560000e-16 99.0
41 TraesCS7D01G023600 chr1A 84.524 252 38 1 523 773 571740326 571740075 1.460000e-61 248.0
42 TraesCS7D01G023600 chr1A 77.404 208 41 4 5920 6122 428981259 428981465 1.200000e-22 119.0
43 TraesCS7D01G023600 chr6A 84.047 257 38 3 520 774 416644549 416644804 1.890000e-60 244.0
44 TraesCS7D01G023600 chr6A 85.385 130 17 2 6155 6282 153684141 153684012 4.280000e-27 134.0
45 TraesCS7D01G023600 chr6A 96.610 59 2 0 3 61 183307413 183307471 1.560000e-16 99.0
46 TraesCS7D01G023600 chr6A 90.541 74 5 2 3 74 611563229 611563156 5.610000e-16 97.1
47 TraesCS7D01G023600 chr7B 82.639 288 29 10 6155 6423 232876292 232876577 1.140000e-57 235.0
48 TraesCS7D01G023600 chr4D 82.578 287 29 11 6157 6422 474687133 474686847 4.100000e-57 233.0
49 TraesCS7D01G023600 chr4D 89.928 139 12 2 6281 6419 127116310 127116446 1.950000e-40 178.0
50 TraesCS7D01G023600 chr4D 93.443 61 4 0 3 63 179707481 179707541 2.610000e-14 91.6
51 TraesCS7D01G023600 chr1B 74.679 624 98 28 6155 6738 535013655 535013052 8.870000e-54 222.0
52 TraesCS7D01G023600 chr1B 83.539 243 33 6 4130 4371 619259832 619259596 3.190000e-53 220.0
53 TraesCS7D01G023600 chr1B 80.515 272 24 4 6153 6395 302751642 302751913 1.510000e-41 182.0
54 TraesCS7D01G023600 chr5B 83.128 243 34 7 4130 4371 100031033 100030797 1.480000e-51 215.0
55 TraesCS7D01G023600 chr5A 79.861 288 39 3 6155 6423 276637147 276637434 6.960000e-45 193.0
56 TraesCS7D01G023600 chr5A 79.457 258 33 13 4130 4371 606331277 606331530 1.520000e-36 165.0
57 TraesCS7D01G023600 chr5A 78.155 206 38 5 5919 6118 689893850 689893646 2.570000e-24 124.0
58 TraesCS7D01G023600 chrUn 77.941 204 34 7 5920 6118 9363332 9363529 4.310000e-22 117.0
59 TraesCS7D01G023600 chr4B 79.503 161 29 4 5959 6118 549146888 549147045 2.000000e-20 111.0
60 TraesCS7D01G023600 chr4B 86.250 80 8 3 3 81 490663900 490663823 4.370000e-12 84.2
61 TraesCS7D01G023600 chr6D 96.491 57 2 0 3 59 356602677 356602621 2.020000e-15 95.3
62 TraesCS7D01G023600 chr6B 93.651 63 2 2 4 64 567715398 567715336 7.260000e-15 93.5
63 TraesCS7D01G023600 chr2D 74.519 208 47 4 5918 6120 347452939 347453145 1.210000e-12 86.1


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 TraesCS7D01G023600 chr7D 11018337 11025133 6796 False 6064.000000 11804 100.000000 1 6797 2 chr7D.!!$F2 6796
1 TraesCS7D01G023600 chr7A 10191284 10198188 6904 False 4281.000000 8423 93.024000 559 6797 2 chr7A.!!$F2 6238
2 TraesCS7D01G023600 chr4A 727114368 727121344 6976 True 2484.666667 5184 92.151333 406 5738 3 chr4A.!!$R2 5332
3 TraesCS7D01G023600 chr5D 82318915 82324561 5646 True 280.775000 542 81.806000 1093 5058 4 chr5D.!!$R2 3965
4 TraesCS7D01G023600 chr3D 552956519 552957957 1438 False 300.000000 420 85.800500 2781 4106 2 chr3D.!!$F1 1325
5 TraesCS7D01G023600 chr3A 689360058 689363378 3320 False 283.000000 399 81.475667 2781 5058 3 chr3A.!!$F1 2277
6 TraesCS7D01G023600 chr3B 733880343 733883605 3262 False 276.333333 392 80.428000 2781 5058 3 chr3B.!!$F1 2277
7 TraesCS7D01G023600 chr1B 535013052 535013655 603 True 222.000000 222 74.679000 6155 6738 1 chr1B.!!$R1 583

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
440 442 0.317938 ACTCACTCGACGTCTTGTGC 60.318 55.000 23.82 0.0 0.00 4.57 F
955 2714 1.077068 CAGCTCCGTCTCCTCCTCT 60.077 63.158 0.00 0.0 0.00 3.69 F
1852 3614 1.814527 GCCGGAAGTCGTATCTGGT 59.185 57.895 5.05 0.0 43.93 4.00 F
2981 4777 0.541392 TTGGATCGGATGGTGGTGAG 59.459 55.000 0.00 0.0 0.00 3.51 F
3245 5053 0.588252 CAGACTTGAAGGCGTTGGTG 59.412 55.000 0.00 0.0 0.00 4.17 F
3501 5490 0.678048 GTCTGCCATGTTCCTGTCCC 60.678 60.000 0.00 0.0 0.00 4.46 F
4405 9023 1.603802 TGCAGCAAGTAGTCAAGCAAC 59.396 47.619 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 3845 0.093705 GAGTTCATCAGTTCGCACGC 59.906 55.000 0.00 0.0 0.00 5.34 R
2074 3846 1.702886 AGAGTTCATCAGTTCGCACG 58.297 50.000 0.00 0.0 0.00 5.34 R
3245 5053 2.234143 GCCAGATTCCCTGCTTTATCC 58.766 52.381 0.00 0.0 41.57 2.59 R
4395 9013 1.066605 CTTGCTGCAAGTTGCTTGACT 59.933 47.619 29.38 0.0 45.31 3.41 R
4396 9014 1.484356 CTTGCTGCAAGTTGCTTGAC 58.516 50.000 29.38 14.5 45.31 3.18 R
5090 9778 1.691196 TAAGCAGGCAAGCAAACAGT 58.309 45.000 4.78 0.0 36.85 3.55 R
6068 10800 1.346365 GCGATGCACGTTCAGTTAGA 58.654 50.000 9.76 0.0 44.60 2.10 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
29 30 7.723324 ACTAAAGCTAGTACAAAGTTGAGTCA 58.277 34.615 0.00 0.00 36.56 3.41
30 31 6.846325 AAAGCTAGTACAAAGTTGAGTCAC 57.154 37.500 0.00 0.00 0.00 3.67
31 32 5.793030 AGCTAGTACAAAGTTGAGTCACT 57.207 39.130 0.00 0.00 0.00 3.41
32 33 6.163135 AGCTAGTACAAAGTTGAGTCACTT 57.837 37.500 0.00 0.00 38.74 3.16
33 34 7.286215 AGCTAGTACAAAGTTGAGTCACTTA 57.714 36.000 0.00 0.00 35.87 2.24
34 35 7.897864 AGCTAGTACAAAGTTGAGTCACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
35 36 8.368668 AGCTAGTACAAAGTTGAGTCACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
36 37 8.989980 GCTAGTACAAAGTTGAGTCACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
39 40 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
40 41 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
41 42 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
42 43 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
43 44 5.690865 AGTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
44 45 5.765182 AGTTGAGTCACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
45 46 5.560722 TGAGTCACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
46 47 5.551233 TGAGTCACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
47 48 4.911390 AGTCACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
48 49 4.010349 GTCACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
49 50 3.913799 TCACTTATTTTGGGACAGAGGGA 59.086 43.478 0.00 0.00 42.39 4.20
50 51 4.019321 TCACTTATTTTGGGACAGAGGGAG 60.019 45.833 0.00 0.00 42.39 4.30
51 52 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
52 53 5.045869 CACTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
53 54 5.731678 ACTTATTTTGGGACAGAGGGAGTAT 59.268 40.000 0.00 0.00 42.39 2.12
54 55 6.217693 ACTTATTTTGGGACAGAGGGAGTATT 59.782 38.462 0.00 0.00 42.39 1.89
55 56 5.536497 ATTTTGGGACAGAGGGAGTATTT 57.464 39.130 0.00 0.00 42.39 1.40
56 57 5.333566 TTTTGGGACAGAGGGAGTATTTT 57.666 39.130 0.00 0.00 42.39 1.82
57 58 6.457159 TTTTGGGACAGAGGGAGTATTTTA 57.543 37.500 0.00 0.00 42.39 1.52
58 59 6.652205 TTTGGGACAGAGGGAGTATTTTAT 57.348 37.500 0.00 0.00 42.39 1.40
59 60 7.758820 TTTGGGACAGAGGGAGTATTTTATA 57.241 36.000 0.00 0.00 42.39 0.98
60 61 7.758820 TTGGGACAGAGGGAGTATTTTATAA 57.241 36.000 0.00 0.00 42.39 0.98
61 62 7.758820 TGGGACAGAGGGAGTATTTTATAAA 57.241 36.000 0.00 0.00 0.00 1.40
62 63 8.165267 TGGGACAGAGGGAGTATTTTATAAAA 57.835 34.615 12.85 12.85 0.00 1.52
63 64 8.787818 TGGGACAGAGGGAGTATTTTATAAAAT 58.212 33.333 23.28 23.28 41.24 1.82
109 110 8.719560 TTTGGTGTTATATAAATCGTAGCACA 57.280 30.769 0.00 0.00 33.09 4.57
110 111 8.896320 TTGGTGTTATATAAATCGTAGCACAT 57.104 30.769 0.00 0.00 33.09 3.21
111 112 8.896320 TGGTGTTATATAAATCGTAGCACATT 57.104 30.769 0.00 0.00 33.09 2.71
112 113 9.332502 TGGTGTTATATAAATCGTAGCACATTT 57.667 29.630 0.00 0.00 33.09 2.32
124 125 9.935682 AATCGTAGCACATTTTTCATATACTTG 57.064 29.630 0.00 0.00 0.00 3.16
125 126 7.915508 TCGTAGCACATTTTTCATATACTTGG 58.084 34.615 0.00 0.00 0.00 3.61
126 127 7.551262 TCGTAGCACATTTTTCATATACTTGGT 59.449 33.333 0.00 0.00 0.00 3.67
127 128 7.850982 CGTAGCACATTTTTCATATACTTGGTC 59.149 37.037 0.00 0.00 0.00 4.02
128 129 7.701539 AGCACATTTTTCATATACTTGGTCA 57.298 32.000 0.00 0.00 0.00 4.02
129 130 8.121305 AGCACATTTTTCATATACTTGGTCAA 57.879 30.769 0.00 0.00 0.00 3.18
130 131 8.584157 AGCACATTTTTCATATACTTGGTCAAA 58.416 29.630 0.00 0.00 0.00 2.69
131 132 8.647226 GCACATTTTTCATATACTTGGTCAAAC 58.353 33.333 0.00 0.00 0.00 2.93
132 133 9.912634 CACATTTTTCATATACTTGGTCAAACT 57.087 29.630 0.00 0.00 0.00 2.66
146 147 9.744468 ACTTGGTCAAACTTAAACATAATTGAC 57.256 29.630 7.68 7.68 43.51 3.18
147 148 9.965824 CTTGGTCAAACTTAAACATAATTGACT 57.034 29.630 13.97 0.00 43.66 3.41
440 442 0.317938 ACTCACTCGACGTCTTGTGC 60.318 55.000 23.82 0.00 0.00 4.57
458 464 3.832490 TGTGCTGTAGTAATCACTGGAGT 59.168 43.478 0.00 0.00 36.14 3.85
598 2329 5.055812 GCCACATGAAAAACAAAGGAATGA 58.944 37.500 0.00 0.00 0.00 2.57
604 2335 9.048446 ACATGAAAAACAAAGGAATGATGAAAG 57.952 29.630 0.00 0.00 0.00 2.62
609 2340 3.766051 ACAAAGGAATGATGAAAGGAGGC 59.234 43.478 0.00 0.00 0.00 4.70
633 2364 6.235231 TGGAGTGGATGTTAGATTTCCTAC 57.765 41.667 0.00 0.00 0.00 3.18
643 2374 6.620678 TGTTAGATTTCCTACAAATTGCAGC 58.379 36.000 0.00 0.00 0.00 5.25
653 2384 5.346822 CCTACAAATTGCAGCACAAAAGATC 59.653 40.000 0.00 0.00 42.86 2.75
731 2462 7.761249 AGGCAAAATTCCTAAAGATTTCAATCG 59.239 33.333 0.00 0.00 34.86 3.34
745 2504 3.848272 TCAATCGTCCAAAAATCCTGC 57.152 42.857 0.00 0.00 0.00 4.85
775 2534 3.623453 GCTTGAATCAAAGGAGCCCTAGT 60.623 47.826 0.00 0.00 31.13 2.57
879 2638 6.361433 TCTCAATCAAGTACAAAAAGGTCCA 58.639 36.000 0.00 0.00 0.00 4.02
894 2653 1.199097 GGTCCACAGTGGTATTTTGCG 59.801 52.381 19.65 0.00 39.03 4.85
899 2658 3.980775 CCACAGTGGTATTTTGCGAAAAG 59.019 43.478 11.99 0.00 30.79 2.27
903 2662 4.082245 CAGTGGTATTTTGCGAAAAGGGAT 60.082 41.667 2.54 0.00 33.22 3.85
929 2688 5.010415 GGGCTTTTGATGATATTCTCCCTTG 59.990 44.000 0.00 0.00 0.00 3.61
955 2714 1.077068 CAGCTCCGTCTCCTCCTCT 60.077 63.158 0.00 0.00 0.00 3.69
1852 3614 1.814527 GCCGGAAGTCGTATCTGGT 59.185 57.895 5.05 0.00 43.93 4.00
1989 3752 6.804677 TGAAACAAGTGAAATGCAACAGTAT 58.195 32.000 0.00 0.00 0.00 2.12
1990 3753 7.264221 TGAAACAAGTGAAATGCAACAGTATT 58.736 30.769 0.00 0.00 0.00 1.89
1999 3762 8.915654 GTGAAATGCAACAGTATTTTTAAGGAG 58.084 33.333 0.00 0.00 29.47 3.69
2023 3795 7.954835 AGTGATGATTTTGGAAATGTTTCTCA 58.045 30.769 5.56 2.12 37.35 3.27
2045 3817 3.153919 TGGGGTTCAACTTGCAGAATAC 58.846 45.455 0.00 0.00 0.00 1.89
2049 3821 3.057526 GGTTCAACTTGCAGAATACCACC 60.058 47.826 0.00 0.00 0.00 4.61
2050 3822 3.500448 TCAACTTGCAGAATACCACCA 57.500 42.857 0.00 0.00 0.00 4.17
2051 3823 3.826524 TCAACTTGCAGAATACCACCAA 58.173 40.909 0.00 0.00 0.00 3.67
2052 3824 4.211125 TCAACTTGCAGAATACCACCAAA 58.789 39.130 0.00 0.00 0.00 3.28
2053 3825 4.278170 TCAACTTGCAGAATACCACCAAAG 59.722 41.667 0.00 0.00 0.00 2.77
2054 3826 2.558359 ACTTGCAGAATACCACCAAAGC 59.442 45.455 0.00 0.00 0.00 3.51
2074 3846 1.518774 CCATCCTTGGGCAATGTGC 59.481 57.895 0.00 0.00 44.08 4.57
2079 3865 4.340019 TTGGGCAATGTGCGTGCG 62.340 61.111 0.00 0.00 46.21 5.34
2102 3888 6.580791 GCGAACTGATGAACTCTATAGATGTC 59.419 42.308 2.11 4.55 0.00 3.06
2131 3917 2.038952 TGTAATGCAAGCTCCTCAGTGT 59.961 45.455 0.00 0.00 0.00 3.55
2138 3924 3.265791 CAAGCTCCTCAGTGTATTCCAC 58.734 50.000 0.00 0.00 44.89 4.02
2160 3946 5.471456 CACCTAGAAATTGAAACTGCTGACT 59.529 40.000 0.00 0.00 0.00 3.41
2161 3947 5.703130 ACCTAGAAATTGAAACTGCTGACTC 59.297 40.000 0.00 0.00 0.00 3.36
2164 3950 6.010294 AGAAATTGAAACTGCTGACTCATG 57.990 37.500 0.00 0.00 0.00 3.07
2171 3957 4.484537 AACTGCTGACTCATGAATAGCT 57.515 40.909 19.85 0.00 35.50 3.32
2177 3963 4.225984 CTGACTCATGAATAGCTAGCGAC 58.774 47.826 9.55 2.97 0.00 5.19
2178 3964 3.004839 TGACTCATGAATAGCTAGCGACC 59.995 47.826 9.55 0.55 0.00 4.79
2179 3965 2.030717 ACTCATGAATAGCTAGCGACCG 60.031 50.000 9.55 0.00 0.00 4.79
2198 3985 3.119245 ACCGAGTTAGTATTGTGTGCGAT 60.119 43.478 0.00 0.00 0.00 4.58
2213 4000 5.065090 TGTGTGCGATTGATCCTTAATTCAG 59.935 40.000 0.00 0.00 0.00 3.02
2278 4069 7.648908 TGCTTTGAATGATTGAACTTAGTTGTG 59.351 33.333 0.93 0.00 0.00 3.33
2280 4071 7.581213 TTGAATGATTGAACTTAGTTGTGGT 57.419 32.000 0.93 0.00 0.00 4.16
2285 4076 6.822442 TGATTGAACTTAGTTGTGGTAGTGA 58.178 36.000 0.93 0.00 0.00 3.41
2294 4085 1.267121 TGTGGTAGTGAAGCTCCCTC 58.733 55.000 0.00 0.00 0.00 4.30
2295 4086 1.267121 GTGGTAGTGAAGCTCCCTCA 58.733 55.000 0.00 0.00 0.00 3.86
2296 4087 1.205893 GTGGTAGTGAAGCTCCCTCAG 59.794 57.143 0.00 0.00 0.00 3.35
2297 4088 1.077169 TGGTAGTGAAGCTCCCTCAGA 59.923 52.381 0.00 0.00 0.00 3.27
2298 4089 2.180276 GGTAGTGAAGCTCCCTCAGAA 58.820 52.381 0.00 0.00 0.00 3.02
2299 4090 2.167487 GGTAGTGAAGCTCCCTCAGAAG 59.833 54.545 0.00 0.00 0.00 2.85
2300 4091 1.274712 AGTGAAGCTCCCTCAGAAGG 58.725 55.000 0.00 0.00 42.95 3.46
2361 4153 3.345508 TTATGCATTGCCATTTGCCAA 57.654 38.095 3.54 0.00 40.16 4.52
2429 4221 5.875359 AGCATTGTACTTAAAGAGGTAGTGC 59.125 40.000 0.00 0.00 0.00 4.40
2430 4222 5.642063 GCATTGTACTTAAAGAGGTAGTGCA 59.358 40.000 0.00 0.00 33.62 4.57
2431 4223 6.148811 GCATTGTACTTAAAGAGGTAGTGCAA 59.851 38.462 0.00 0.00 44.53 4.08
2432 4224 7.624344 GCATTGTACTTAAAGAGGTAGTGCAAG 60.624 40.741 9.97 5.04 43.97 4.01
2433 4225 6.659745 TGTACTTAAAGAGGTAGTGCAAGA 57.340 37.500 0.00 0.00 32.74 3.02
2434 4226 6.453092 TGTACTTAAAGAGGTAGTGCAAGAC 58.547 40.000 0.00 0.00 32.74 3.01
2435 4227 5.810080 ACTTAAAGAGGTAGTGCAAGACT 57.190 39.130 0.00 0.00 38.88 3.24
2436 4228 5.542779 ACTTAAAGAGGTAGTGCAAGACTG 58.457 41.667 0.00 0.00 35.96 3.51
2499 4293 8.989980 CCCGTCAGGATTAAGTAAAGATAATTC 58.010 37.037 0.00 0.00 41.02 2.17
2526 4320 1.339438 GGTGCTTTGATGCTCTCCTGA 60.339 52.381 0.00 0.00 0.00 3.86
2778 4574 3.362706 TCGCCTCATAGTCCTTGTACTT 58.637 45.455 0.00 0.00 0.00 2.24
2981 4777 0.541392 TTGGATCGGATGGTGGTGAG 59.459 55.000 0.00 0.00 0.00 3.51
3245 5053 0.588252 CAGACTTGAAGGCGTTGGTG 59.412 55.000 0.00 0.00 0.00 4.17
3406 5214 2.026262 TGGATGACTTTGAGGTAAGCCC 60.026 50.000 0.00 0.00 34.57 5.19
3459 5351 3.193263 CACCTGCTGTCTGATCATACAC 58.807 50.000 9.69 7.96 0.00 2.90
3501 5490 0.678048 GTCTGCCATGTTCCTGTCCC 60.678 60.000 0.00 0.00 0.00 4.46
3821 5821 8.956426 TCATAGTAATTGGCAGAAAGTTTAAGG 58.044 33.333 0.00 0.00 0.00 2.69
4164 8760 6.806751 TGTGTATAGACTGCTAAGATGTTCC 58.193 40.000 1.30 0.00 0.00 3.62
4387 9005 5.567138 ATGAATACTTGGTAGCAACTTGC 57.433 39.130 2.54 5.55 45.46 4.01
4405 9023 1.603802 TGCAGCAAGTAGTCAAGCAAC 59.396 47.619 0.00 0.00 0.00 4.17
4493 9155 5.679638 GCTCAAGTGAAGTGTTTGTTCCATT 60.680 40.000 0.00 0.00 0.00 3.16
4580 9242 4.275196 GTCTCCTAAACCAGGTTTGAACAC 59.725 45.833 25.65 12.48 45.71 3.32
4592 9255 3.065371 GGTTTGAACACTGTCTTGGTCAG 59.935 47.826 0.00 0.00 44.04 3.51
4774 9448 4.692625 TGTCAGCTACTGATTGCTTCTTTC 59.307 41.667 0.00 0.00 42.73 2.62
5090 9778 5.512753 TTGAGTTTGTGAAAGCTGCATTA 57.487 34.783 1.02 0.00 0.00 1.90
5200 9908 1.896220 TAGGAAGGTGCAGTGCAAAG 58.104 50.000 21.67 0.00 41.47 2.77
5549 10263 3.840102 TATTCGGCCAACTGATCCGCC 62.840 57.143 2.24 0.00 42.65 6.13
5558 10272 0.465705 ACTGATCCGCCATCGTCATT 59.534 50.000 0.00 0.00 33.61 2.57
5634 10349 2.860735 GCTTAGTGTAGAGATTGCGTGG 59.139 50.000 0.00 0.00 0.00 4.94
5650 10367 1.200716 CGTGGGCGACTCTACACTAAA 59.799 52.381 0.00 0.00 41.33 1.85
5690 10407 2.940410 TGAGGAACTTGTTTTCGGTGTC 59.060 45.455 0.00 0.00 41.55 3.67
5795 10512 6.644347 TCGAAGAATAATTGAGGAGCTTTCT 58.356 36.000 0.00 0.00 0.00 2.52
5797 10514 6.314896 CGAAGAATAATTGAGGAGCTTTCTGT 59.685 38.462 0.00 0.00 0.00 3.41
5826 10543 2.330231 ACATTTTCGACCAATGCACG 57.670 45.000 13.98 0.00 35.36 5.34
5847 10564 3.493350 CGATTCTTCCGTCCATTGGAGAT 60.493 47.826 5.39 0.00 36.72 2.75
5860 10578 0.106868 TGGAGATGGATGCAAGGCTG 60.107 55.000 0.00 0.00 0.00 4.85
5926 10653 5.828299 TTTTTAATATAGGCGCAAGTGCT 57.172 34.783 10.83 0.00 39.32 4.40
5937 10664 2.987149 GCGCAAGTGCTCATATATACGT 59.013 45.455 0.30 0.00 39.32 3.57
5939 10666 3.981416 CGCAAGTGCTCATATATACGTGT 59.019 43.478 0.00 0.00 39.32 4.49
5947 10674 8.622157 AGTGCTCATATATACGTGTATACATCC 58.378 37.037 13.46 5.04 31.52 3.51
5962 10691 6.759356 TGTATACATCCAACCTTATGAACACG 59.241 38.462 0.08 0.00 0.00 4.49
5974 10703 2.248280 TGAACACGCACACACCTTAT 57.752 45.000 0.00 0.00 0.00 1.73
5975 10704 2.139917 TGAACACGCACACACCTTATC 58.860 47.619 0.00 0.00 0.00 1.75
5980 10709 3.744426 ACACGCACACACCTTATCTTTAC 59.256 43.478 0.00 0.00 0.00 2.01
5983 10712 3.303495 CGCACACACCTTATCTTTACGAG 59.697 47.826 0.00 0.00 0.00 4.18
5989 10718 5.812642 CACACCTTATCTTTACGAGCATCTT 59.187 40.000 0.00 0.00 0.00 2.40
5993 10722 6.758886 ACCTTATCTTTACGAGCATCTTTGAG 59.241 38.462 0.00 0.00 0.00 3.02
5997 10726 5.403246 TCTTTACGAGCATCTTTGAGAGAC 58.597 41.667 0.00 0.00 37.17 3.36
5998 10727 5.184096 TCTTTACGAGCATCTTTGAGAGACT 59.816 40.000 0.00 0.00 37.17 3.24
6005 10734 3.867600 GCATCTTTGAGAGACTGAGCCAA 60.868 47.826 0.00 0.00 37.17 4.52
6019 10748 7.215789 AGACTGAGCCAACATATAATCTTGAG 58.784 38.462 0.00 0.00 0.00 3.02
6053 10782 3.762288 TCATTGTAGGCGTCTTGTAGTCT 59.238 43.478 0.00 0.00 0.00 3.24
6055 10784 5.593095 TCATTGTAGGCGTCTTGTAGTCTAT 59.407 40.000 0.00 0.00 0.00 1.98
6068 10800 7.808856 GTCTTGTAGTCTATGAAAACGTCTTCT 59.191 37.037 2.87 0.00 0.00 2.85
6077 10809 8.573885 TCTATGAAAACGTCTTCTCTAACTGAA 58.426 33.333 2.87 0.00 0.00 3.02
6078 10810 6.823678 TGAAAACGTCTTCTCTAACTGAAC 57.176 37.500 2.87 0.00 0.00 3.18
6085 10817 4.324936 GTCTTCTCTAACTGAACGTGCATC 59.675 45.833 0.00 0.00 0.00 3.91
6087 10819 1.321743 CTCTAACTGAACGTGCATCGC 59.678 52.381 0.00 0.00 44.19 4.58
6098 10830 0.248215 GTGCATCGCCGGAAATCTTG 60.248 55.000 5.05 0.00 0.00 3.02
6143 10875 1.760613 CCTTCGTGGGCTAAGGATACA 59.239 52.381 0.00 0.00 44.27 2.29
6144 10876 2.224066 CCTTCGTGGGCTAAGGATACAG 60.224 54.545 0.00 0.00 44.27 2.74
6145 10877 2.447408 TCGTGGGCTAAGGATACAGA 57.553 50.000 0.00 0.00 41.41 3.41
6226 10961 7.290110 TGTCTATGTGAAGAAGAGAGACAAA 57.710 36.000 0.00 0.00 44.69 2.83
6228 10963 8.370940 TGTCTATGTGAAGAAGAGAGACAAAAT 58.629 33.333 0.00 0.00 44.69 1.82
6381 11147 3.693807 ACTCTTGATGACATGGCATGTT 58.306 40.909 31.83 18.84 45.03 2.71
6443 11209 1.188863 GCCCTTCACAATGCTCCATT 58.811 50.000 0.00 0.00 34.04 3.16
6465 11446 1.003003 TGTACATGTGCTAAGGCTGCA 59.997 47.619 15.25 0.00 39.59 4.41
6472 11453 2.027285 TGTGCTAAGGCTGCAATGTAGA 60.027 45.455 1.65 0.00 42.41 2.59
6504 11487 5.708230 TCTGACGTGGCAAGGTAATAAAAAT 59.292 36.000 5.22 0.00 0.00 1.82
6528 11512 7.675161 TGAGAGATATGAGTTTATGACCCAA 57.325 36.000 0.00 0.00 0.00 4.12
6573 11558 8.426881 TTGAACCTAGGCAAAAACAATTAAAC 57.573 30.769 9.30 0.00 0.00 2.01
6639 11624 7.772166 AGCATTAAATAAGGGAAGCTTAACAC 58.228 34.615 0.00 0.00 0.00 3.32
6679 11664 7.086376 CCTATGCATTATGAACATTAGTTGCC 58.914 38.462 3.54 0.00 38.30 4.52
6702 11687 8.364142 TGCCAAACTTTTTAATACACTTAGCAT 58.636 29.630 0.00 0.00 0.00 3.79
6745 12140 5.304686 TGGGAAGTGGCCTAATTATACAG 57.695 43.478 3.32 0.00 0.00 2.74
6746 12141 4.724798 TGGGAAGTGGCCTAATTATACAGT 59.275 41.667 3.32 0.00 0.00 3.55
6782 12177 4.935205 GGCAATGGACGTATCATATTGCTA 59.065 41.667 22.38 0.00 46.10 3.49
6788 12183 5.538813 TGGACGTATCATATTGCTAGGTCTT 59.461 40.000 9.61 0.00 35.47 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.853126 TGACTCAACTTTGTACTAGCTTTAGTA 58.147 33.333 0.00 0.00 0.00 1.82
4 5 7.652507 GTGACTCAACTTTGTACTAGCTTTAGT 59.347 37.037 0.00 0.00 0.00 2.24
5 6 7.868415 AGTGACTCAACTTTGTACTAGCTTTAG 59.132 37.037 0.00 0.00 0.00 1.85
6 7 7.723324 AGTGACTCAACTTTGTACTAGCTTTA 58.277 34.615 0.00 0.00 0.00 1.85
7 8 6.583562 AGTGACTCAACTTTGTACTAGCTTT 58.416 36.000 0.00 0.00 0.00 3.51
8 9 6.163135 AGTGACTCAACTTTGTACTAGCTT 57.837 37.500 0.00 0.00 0.00 3.74
9 10 5.793030 AGTGACTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
10 11 8.535690 AATAAGTGACTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
13 14 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
14 15 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
15 16 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
16 17 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
17 18 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
18 19 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
19 20 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
20 21 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
21 22 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
22 23 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
23 24 5.513094 CCTCTGTCCCAAAATAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
24 25 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
25 26 4.263506 CCCTCTGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
26 27 4.010349 CCCTCTGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
27 28 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
28 29 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
29 30 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
30 31 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
31 32 6.652205 AATACTCCCTCTGTCCCAAAATAA 57.348 37.500 0.00 0.00 0.00 1.40
32 33 6.652205 AAATACTCCCTCTGTCCCAAAATA 57.348 37.500 0.00 0.00 0.00 1.40
33 34 5.536497 AAATACTCCCTCTGTCCCAAAAT 57.464 39.130 0.00 0.00 0.00 1.82
34 35 5.333566 AAAATACTCCCTCTGTCCCAAAA 57.666 39.130 0.00 0.00 0.00 2.44
35 36 6.652205 ATAAAATACTCCCTCTGTCCCAAA 57.348 37.500 0.00 0.00 0.00 3.28
36 37 7.758820 TTATAAAATACTCCCTCTGTCCCAA 57.241 36.000 0.00 0.00 0.00 4.12
37 38 7.758820 TTTATAAAATACTCCCTCTGTCCCA 57.241 36.000 0.00 0.00 0.00 4.37
83 84 9.332502 TGTGCTACGATTTATATAACACCAAAT 57.667 29.630 0.00 0.00 0.00 2.32
84 85 8.719560 TGTGCTACGATTTATATAACACCAAA 57.280 30.769 0.00 0.00 0.00 3.28
85 86 8.896320 ATGTGCTACGATTTATATAACACCAA 57.104 30.769 0.00 0.00 0.00 3.67
86 87 8.896320 AATGTGCTACGATTTATATAACACCA 57.104 30.769 0.00 0.00 0.00 4.17
98 99 9.935682 CAAGTATATGAAAAATGTGCTACGATT 57.064 29.630 0.00 0.00 0.00 3.34
99 100 8.559536 CCAAGTATATGAAAAATGTGCTACGAT 58.440 33.333 0.00 0.00 0.00 3.73
100 101 7.551262 ACCAAGTATATGAAAAATGTGCTACGA 59.449 33.333 0.00 0.00 0.00 3.43
101 102 7.693952 ACCAAGTATATGAAAAATGTGCTACG 58.306 34.615 0.00 0.00 0.00 3.51
102 103 8.673711 TGACCAAGTATATGAAAAATGTGCTAC 58.326 33.333 0.00 0.00 0.00 3.58
103 104 8.800370 TGACCAAGTATATGAAAAATGTGCTA 57.200 30.769 0.00 0.00 0.00 3.49
104 105 7.701539 TGACCAAGTATATGAAAAATGTGCT 57.298 32.000 0.00 0.00 0.00 4.40
105 106 8.647226 GTTTGACCAAGTATATGAAAAATGTGC 58.353 33.333 0.00 0.00 0.00 4.57
106 107 9.912634 AGTTTGACCAAGTATATGAAAAATGTG 57.087 29.630 0.00 0.00 0.00 3.21
120 121 9.744468 GTCAATTATGTTTAAGTTTGACCAAGT 57.256 29.630 0.00 0.00 34.32 3.16
121 122 9.965824 AGTCAATTATGTTTAAGTTTGACCAAG 57.034 29.630 9.31 0.00 37.70 3.61
424 426 0.595053 ACAGCACAAGACGTCGAGTG 60.595 55.000 27.92 27.92 35.19 3.51
547 2278 9.434275 TCAAACACTCCTTGATAATCCTATAGA 57.566 33.333 0.00 0.00 0.00 1.98
598 2329 0.622665 CCACTCCAGCCTCCTTTCAT 59.377 55.000 0.00 0.00 0.00 2.57
604 2335 1.139853 CTAACATCCACTCCAGCCTCC 59.860 57.143 0.00 0.00 0.00 4.30
609 2340 5.365021 AGGAAATCTAACATCCACTCCAG 57.635 43.478 0.00 0.00 35.62 3.86
633 2364 3.434299 GGGATCTTTTGTGCTGCAATTTG 59.566 43.478 2.77 0.00 36.89 2.32
643 2374 7.765819 GGAATTTTTCCTATGGGATCTTTTGTG 59.234 37.037 0.00 0.00 46.57 3.33
731 2462 5.347012 CAAATTGTGCAGGATTTTTGGAC 57.653 39.130 4.84 0.00 37.40 4.02
745 2504 5.107220 GCTCCTTTGATTCAAGCAAATTGTG 60.107 40.000 0.32 0.00 40.05 3.33
797 2556 9.605955 GAATGGCGCAACTTTTTATTTTAATTT 57.394 25.926 10.83 0.00 0.00 1.82
799 2558 8.546597 AGAATGGCGCAACTTTTTATTTTAAT 57.453 26.923 10.83 0.00 0.00 1.40
801 2560 7.570324 GCAAGAATGGCGCAACTTTTTATTTTA 60.570 33.333 10.83 0.00 0.00 1.52
879 2638 3.005367 CCCTTTTCGCAAAATACCACTGT 59.995 43.478 0.00 0.00 0.00 3.55
894 2653 2.256306 TCAAAAGCCCCATCCCTTTTC 58.744 47.619 0.00 0.00 38.74 2.29
899 2658 2.092598 ATCATCAAAAGCCCCATCCC 57.907 50.000 0.00 0.00 0.00 3.85
903 2662 4.473444 GGAGAATATCATCAAAAGCCCCA 58.527 43.478 0.00 0.00 0.00 4.96
929 2688 0.179124 GAGACGGAGCTGTGATGTCC 60.179 60.000 0.00 0.00 0.00 4.02
1738 3500 2.270205 CCGTGCAGCAGAATCCCT 59.730 61.111 0.00 0.00 0.00 4.20
1852 3614 6.324770 TCAAATCAGATAGCATACCAGAGACA 59.675 38.462 0.00 0.00 0.00 3.41
1990 3753 9.709495 CATTTCCAAAATCATCACTCCTTAAAA 57.291 29.630 0.00 0.00 0.00 1.52
1999 3762 8.653338 CATGAGAAACATTTCCAAAATCATCAC 58.347 33.333 0.68 0.00 37.92 3.06
2023 3795 2.380064 TTCTGCAAGTTGAACCCCAT 57.620 45.000 7.16 0.00 33.76 4.00
2045 3817 1.079073 AAGGATGGGGCTTTGGTGG 59.921 57.895 0.00 0.00 0.00 4.61
2072 3844 0.599991 AGTTCATCAGTTCGCACGCA 60.600 50.000 0.00 0.00 0.00 5.24
2073 3845 0.093705 GAGTTCATCAGTTCGCACGC 59.906 55.000 0.00 0.00 0.00 5.34
2074 3846 1.702886 AGAGTTCATCAGTTCGCACG 58.297 50.000 0.00 0.00 0.00 5.34
2079 3865 8.629158 ACTGACATCTATAGAGTTCATCAGTTC 58.371 37.037 20.49 4.72 40.97 3.01
2102 3888 4.637534 AGGAGCTTGCATTACACAATACTG 59.362 41.667 0.00 0.00 0.00 2.74
2131 3917 7.121168 CAGCAGTTTCAATTTCTAGGTGGAATA 59.879 37.037 0.00 0.00 0.00 1.75
2138 3924 5.702670 TGAGTCAGCAGTTTCAATTTCTAGG 59.297 40.000 0.00 0.00 0.00 3.02
2160 3946 2.226674 CTCGGTCGCTAGCTATTCATGA 59.773 50.000 13.93 0.00 0.00 3.07
2161 3947 2.030717 ACTCGGTCGCTAGCTATTCATG 60.031 50.000 13.93 0.00 0.00 3.07
2164 3950 2.778187 AACTCGGTCGCTAGCTATTC 57.222 50.000 13.93 0.17 0.00 1.75
2171 3957 3.691118 ACACAATACTAACTCGGTCGCTA 59.309 43.478 0.00 0.00 0.00 4.26
2177 3963 2.871133 TCGCACACAATACTAACTCGG 58.129 47.619 0.00 0.00 0.00 4.63
2178 3964 4.561213 TCAATCGCACACAATACTAACTCG 59.439 41.667 0.00 0.00 0.00 4.18
2179 3965 6.292381 GGATCAATCGCACACAATACTAACTC 60.292 42.308 0.00 0.00 0.00 3.01
2280 4071 2.043115 TCCTTCTGAGGGAGCTTCACTA 59.957 50.000 4.13 0.00 43.72 2.74
2285 4076 3.884037 TTTTTCCTTCTGAGGGAGCTT 57.116 42.857 8.62 0.00 43.72 3.74
2397 4189 8.514594 CCTCTTTAAGTACAATGCTTTGATGAA 58.485 33.333 18.35 1.97 36.64 2.57
2402 4194 8.230486 CACTACCTCTTTAAGTACAATGCTTTG 58.770 37.037 10.58 10.58 38.86 2.77
2429 4221 6.183360 CCATGTATCTAAACCTTGCAGTCTTG 60.183 42.308 0.00 0.00 0.00 3.02
2430 4222 5.882557 CCATGTATCTAAACCTTGCAGTCTT 59.117 40.000 0.00 0.00 0.00 3.01
2431 4223 5.045578 ACCATGTATCTAAACCTTGCAGTCT 60.046 40.000 0.00 0.00 0.00 3.24
2432 4224 5.065218 CACCATGTATCTAAACCTTGCAGTC 59.935 44.000 0.00 0.00 0.00 3.51
2433 4225 4.943705 CACCATGTATCTAAACCTTGCAGT 59.056 41.667 0.00 0.00 0.00 4.40
2434 4226 5.185454 TCACCATGTATCTAAACCTTGCAG 58.815 41.667 0.00 0.00 0.00 4.41
2435 4227 5.172687 TCACCATGTATCTAAACCTTGCA 57.827 39.130 0.00 0.00 0.00 4.08
2436 4228 5.822519 TCATCACCATGTATCTAAACCTTGC 59.177 40.000 0.00 0.00 0.00 4.01
2437 4229 7.173907 GGATCATCACCATGTATCTAAACCTTG 59.826 40.741 0.00 0.00 0.00 3.61
2499 4293 2.419324 GAGCATCAAAGCACCTCTGAAG 59.581 50.000 0.00 0.00 36.85 3.02
2526 4320 5.297776 CACACACAAGAAAATCCTCACTTCT 59.702 40.000 0.00 0.00 0.00 2.85
2789 4585 8.088463 ACAAGACTCTGATATTTTCCTCAGAT 57.912 34.615 2.98 0.00 45.01 2.90
2981 4777 5.947228 TTTCAGATGATTGTGAGTCCAAC 57.053 39.130 0.00 0.00 0.00 3.77
3245 5053 2.234143 GCCAGATTCCCTGCTTTATCC 58.766 52.381 0.00 0.00 41.57 2.59
3406 5214 8.986929 AGAAGAAAGATAAAATGACCCCATAG 57.013 34.615 0.00 0.00 31.59 2.23
3421 5311 6.825721 CAGCAGGTGGTTAATAGAAGAAAGAT 59.174 38.462 0.00 0.00 0.00 2.40
3459 5351 8.873830 AGACAACAGACAATGAAAACGATATAG 58.126 33.333 0.00 0.00 0.00 1.31
3501 5490 4.100808 AGCTAATAGCAGAGGAGGACAAAG 59.899 45.833 15.28 0.00 45.56 2.77
3579 5571 2.435418 TGGTTGAACCATTGTGGCC 58.565 52.632 14.05 0.00 44.79 5.36
4164 8760 3.258372 GCCCCTAAAGTTCCAGAAAAAGG 59.742 47.826 0.00 0.00 0.00 3.11
4340 8939 5.811796 TTGTTCTAAGCAACTACCCAGTA 57.188 39.130 0.00 0.00 33.48 2.74
4393 9011 1.603802 TGCTGCAAGTTGCTTGACTAC 59.396 47.619 27.17 10.06 45.31 2.73
4394 9012 1.965935 TGCTGCAAGTTGCTTGACTA 58.034 45.000 27.17 6.28 45.31 2.59
4395 9013 1.066605 CTTGCTGCAAGTTGCTTGACT 59.933 47.619 29.38 0.00 45.31 3.41
4396 9014 1.484356 CTTGCTGCAAGTTGCTTGAC 58.516 50.000 29.38 14.50 45.31 3.18
4405 9023 1.875514 TGCTTGACTACTTGCTGCAAG 59.124 47.619 34.07 34.07 45.85 4.01
4580 9242 1.959042 AACACAGCTGACCAAGACAG 58.041 50.000 23.35 0.00 38.27 3.51
4592 9255 6.789262 AGAATATCTGTATTGCAAACACAGC 58.211 36.000 27.49 18.20 39.60 4.40
4626 9296 7.039270 ACGCAGAACAAAAATAAAAGGAAAGT 58.961 30.769 0.00 0.00 0.00 2.66
4627 9297 7.463469 ACGCAGAACAAAAATAAAAGGAAAG 57.537 32.000 0.00 0.00 0.00 2.62
4630 9300 9.187455 GATTAACGCAGAACAAAAATAAAAGGA 57.813 29.630 0.00 0.00 0.00 3.36
4631 9301 8.973378 TGATTAACGCAGAACAAAAATAAAAGG 58.027 29.630 0.00 0.00 0.00 3.11
4637 9307 8.878769 AGTTTTTGATTAACGCAGAACAAAAAT 58.121 25.926 18.40 10.19 43.62 1.82
4639 9309 7.820044 AGTTTTTGATTAACGCAGAACAAAA 57.180 28.000 0.00 0.00 36.12 2.44
4662 9332 3.844577 ACTGCAAGCAGAGCATTTTAG 57.155 42.857 27.17 0.00 46.30 1.85
4774 9448 4.588951 TCCCACTCAGGTATAAGCATGTAG 59.411 45.833 0.00 0.00 34.66 2.74
5090 9778 1.691196 TAAGCAGGCAAGCAAACAGT 58.309 45.000 4.78 0.00 36.85 3.55
5200 9908 3.544356 GCTCAAGCAGGTTAGTTCAAC 57.456 47.619 0.00 0.00 41.59 3.18
5451 10159 3.792401 TGTAAAGCCGGTGATATGACAG 58.208 45.455 1.90 0.00 0.00 3.51
5549 10263 2.282555 CCTCGTAAGCACAATGACGATG 59.717 50.000 0.00 0.00 42.83 3.84
5558 10272 2.165641 CAGTATGGTCCTCGTAAGCACA 59.834 50.000 0.00 0.00 37.18 4.57
5634 10349 2.943449 AGCTTTAGTGTAGAGTCGCC 57.057 50.000 0.00 0.00 0.00 5.54
5650 10367 7.195374 TCCTCACTACCAAAATTGTATAGCT 57.805 36.000 0.00 0.00 0.00 3.32
5690 10407 7.251704 AGCATAACGAGTTCATATTTTCCAG 57.748 36.000 0.00 0.00 0.00 3.86
5780 10497 4.518211 CAGTTCACAGAAAGCTCCTCAATT 59.482 41.667 0.00 0.00 0.00 2.32
5826 10543 3.543680 TCTCCAATGGACGGAAGAATC 57.456 47.619 0.00 0.00 30.33 2.52
5847 10564 4.064768 CCCCCAGCCTTGCATCCA 62.065 66.667 0.00 0.00 0.00 3.41
5923 10650 8.514330 TGGATGTATACACGTATATATGAGCA 57.486 34.615 7.96 0.00 32.38 4.26
5925 10652 9.731819 GGTTGGATGTATACACGTATATATGAG 57.268 37.037 7.96 3.50 32.38 2.90
5926 10653 9.470399 AGGTTGGATGTATACACGTATATATGA 57.530 33.333 7.96 0.00 32.38 2.15
5937 10664 6.759356 CGTGTTCATAAGGTTGGATGTATACA 59.241 38.462 8.27 8.27 0.00 2.29
5939 10666 5.756347 GCGTGTTCATAAGGTTGGATGTATA 59.244 40.000 0.00 0.00 0.00 1.47
5946 10673 1.876799 TGTGCGTGTTCATAAGGTTGG 59.123 47.619 0.00 0.00 0.00 3.77
5947 10674 2.289274 TGTGTGCGTGTTCATAAGGTTG 59.711 45.455 0.00 0.00 0.00 3.77
5956 10683 2.413837 AGATAAGGTGTGTGCGTGTTC 58.586 47.619 0.00 0.00 0.00 3.18
5962 10691 3.062234 GCTCGTAAAGATAAGGTGTGTGC 59.938 47.826 0.00 0.00 0.00 4.57
5974 10703 5.184096 AGTCTCTCAAAGATGCTCGTAAAGA 59.816 40.000 0.00 0.00 36.11 2.52
5975 10704 5.288232 CAGTCTCTCAAAGATGCTCGTAAAG 59.712 44.000 0.00 0.00 36.11 1.85
5980 10709 3.437428 CTCAGTCTCTCAAAGATGCTCG 58.563 50.000 0.00 0.00 36.11 5.03
5983 10712 2.278854 GGCTCAGTCTCTCAAAGATGC 58.721 52.381 0.00 0.00 36.11 3.91
5989 10718 6.544928 TTATATGTTGGCTCAGTCTCTCAA 57.455 37.500 0.00 0.00 0.00 3.02
5993 10722 7.212976 TCAAGATTATATGTTGGCTCAGTCTC 58.787 38.462 0.00 0.00 34.59 3.36
5997 10726 8.618702 AATCTCAAGATTATATGTTGGCTCAG 57.381 34.615 3.42 0.00 42.48 3.35
5998 10727 8.985315 AAATCTCAAGATTATATGTTGGCTCA 57.015 30.769 5.71 0.00 43.41 4.26
6026 10755 7.101054 ACTACAAGACGCCTACAATGATTTTA 58.899 34.615 0.00 0.00 0.00 1.52
6030 10759 4.402793 AGACTACAAGACGCCTACAATGAT 59.597 41.667 0.00 0.00 0.00 2.45
6043 10772 7.883217 AGAAGACGTTTTCATAGACTACAAGA 58.117 34.615 19.69 0.00 0.00 3.02
6046 10775 7.450124 AGAGAAGACGTTTTCATAGACTACA 57.550 36.000 19.69 0.00 0.00 2.74
6053 10782 7.325338 CGTTCAGTTAGAGAAGACGTTTTCATA 59.675 37.037 19.69 9.92 0.00 2.15
6055 10784 5.457799 CGTTCAGTTAGAGAAGACGTTTTCA 59.542 40.000 19.69 0.00 0.00 2.69
6068 10800 1.346365 GCGATGCACGTTCAGTTAGA 58.654 50.000 9.76 0.00 44.60 2.10
6077 10809 2.435938 ATTTCCGGCGATGCACGT 60.436 55.556 9.30 0.00 44.60 4.49
6078 10810 1.705337 AAGATTTCCGGCGATGCACG 61.705 55.000 9.30 0.00 45.66 5.34
6085 10817 6.885735 AAATTTATTTCAAGATTTCCGGCG 57.114 33.333 0.00 0.00 0.00 6.46
6226 10961 7.182060 TGAGAGCCCACTCCTTTATTTTTATT 58.818 34.615 0.00 0.00 44.65 1.40
6228 10963 6.134535 TGAGAGCCCACTCCTTTATTTTTA 57.865 37.500 0.00 0.00 44.65 1.52
6233 10968 2.158696 GCATGAGAGCCCACTCCTTTAT 60.159 50.000 0.00 0.00 44.65 1.40
6269 11004 9.283768 TCTATCTCTTTCTTCTAGAGCATGTAG 57.716 37.037 0.00 0.00 39.18 2.74
6271 11006 8.710749 ATCTATCTCTTTCTTCTAGAGCATGT 57.289 34.615 0.00 0.00 39.18 3.21
6443 11209 2.487762 GCAGCCTTAGCACATGTACAAA 59.512 45.455 0.00 0.00 43.56 2.83
6480 11461 3.965379 TTATTACCTTGCCACGTCAGA 57.035 42.857 0.00 0.00 0.00 3.27
6481 11462 5.365403 TTTTTATTACCTTGCCACGTCAG 57.635 39.130 0.00 0.00 0.00 3.51
6484 11465 5.708230 TCTCATTTTTATTACCTTGCCACGT 59.292 36.000 0.00 0.00 0.00 4.49
6485 11466 6.093495 TCTCTCATTTTTATTACCTTGCCACG 59.907 38.462 0.00 0.00 0.00 4.94
6486 11467 7.391148 TCTCTCATTTTTATTACCTTGCCAC 57.609 36.000 0.00 0.00 0.00 5.01
6504 11487 7.675161 TTGGGTCATAAACTCATATCTCTCA 57.325 36.000 0.00 0.00 38.46 3.27
6528 11512 4.020662 TCAAGTGTTTGGCAGGTTCTTTTT 60.021 37.500 0.00 0.00 34.97 1.94
6532 11516 2.427095 GTTCAAGTGTTTGGCAGGTTCT 59.573 45.455 0.00 0.00 34.97 3.01
6533 11517 2.481276 GGTTCAAGTGTTTGGCAGGTTC 60.481 50.000 0.00 0.00 34.97 3.62
6535 11519 1.111277 GGTTCAAGTGTTTGGCAGGT 58.889 50.000 0.00 0.00 34.97 4.00
6537 11521 2.554032 CCTAGGTTCAAGTGTTTGGCAG 59.446 50.000 0.00 0.00 34.97 4.85
6548 11533 7.222999 CGTTTAATTGTTTTTGCCTAGGTTCAA 59.777 33.333 11.31 4.06 0.00 2.69
6573 11558 8.692110 TTTCATTCATTGATGGATTTCTTTCG 57.308 30.769 0.00 0.00 33.34 3.46
6629 11614 6.478673 GTGCTTTATTTGTTGGTGTTAAGCTT 59.521 34.615 3.48 3.48 38.02 3.74
6636 11621 6.024552 CATAGGTGCTTTATTTGTTGGTGT 57.975 37.500 0.00 0.00 0.00 4.16
6664 11649 9.606631 TTAAAAAGTTTGGCAACTAATGTTCAT 57.393 25.926 0.00 0.00 42.89 2.57
6719 12114 0.630673 ATTAGGCCACTTCCCATGCA 59.369 50.000 5.01 0.00 0.00 3.96
6723 12118 4.724798 ACTGTATAATTAGGCCACTTCCCA 59.275 41.667 5.01 0.00 0.00 4.37
6745 12140 2.406130 CATTGCCAACCAACATGTGAC 58.594 47.619 0.00 0.00 35.99 3.67
6746 12141 1.343789 CCATTGCCAACCAACATGTGA 59.656 47.619 0.00 0.00 35.99 3.58


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

AutoCloner maintained by Alex Coulton.