Multiple sequence alignment - TraesCS6D01G152100

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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 TraesCS6D01G152100 chr6D 100.000 3949 0 0 1 3949 125248439 125244491 0.000000e+00 7293.0
1 TraesCS6D01G152100 chr6D 96.000 100 4 0 3397 3496 125244992 125244893 3.160000e-36 163.0
2 TraesCS6D01G152100 chr6D 96.000 100 4 0 3448 3547 125245043 125244944 3.160000e-36 163.0
3 TraesCS6D01G152100 chr6D 95.918 49 2 0 3397 3445 125244941 125244893 3.270000e-11 80.5
4 TraesCS6D01G152100 chr6D 95.918 49 2 0 3499 3547 125245043 125244995 3.270000e-11 80.5
5 TraesCS6D01G152100 chr6B 94.010 1853 79 18 1 1827 223572972 223571126 0.000000e+00 2778.0
6 TraesCS6D01G152100 chr6B 91.492 1528 72 23 1987 3494 223570810 223569321 0.000000e+00 2049.0
7 TraesCS6D01G152100 chr6B 91.193 352 18 10 3448 3792 223569418 223569073 2.150000e-127 466.0
8 TraesCS6D01G152100 chr6B 95.522 134 6 0 1832 1965 223571002 223570869 8.590000e-52 215.0
9 TraesCS6D01G152100 chr6B 92.361 144 10 1 3649 3792 223568923 223568781 1.860000e-48 204.0
10 TraesCS6D01G152100 chr6B 90.411 146 9 5 3652 3792 223569069 223568924 1.870000e-43 187.0
11 TraesCS6D01G152100 chr6B 86.420 81 8 3 3869 3947 564311623 564311544 7.030000e-13 86.1
12 TraesCS6D01G152100 chr6B 93.617 47 3 0 3499 3545 223569418 223569372 1.970000e-08 71.3
13 TraesCS6D01G152100 chr6B 75.694 144 28 5 3766 3904 630451842 630451701 9.160000e-07 65.8
14 TraesCS6D01G152100 chr6A 93.333 1845 83 14 1 1827 155223305 155225127 0.000000e+00 2689.0
15 TraesCS6D01G152100 chr6A 93.701 1413 69 12 1978 3383 155225536 155226935 0.000000e+00 2098.0
16 TraesCS6D01G152100 chr6A 89.453 512 31 10 3448 3949 155227260 155227758 3.350000e-175 625.0
17 TraesCS6D01G152100 chr6A 94.030 134 8 0 1832 1965 155225356 155225489 1.860000e-48 204.0
18 TraesCS6D01G152100 chr6A 90.244 123 12 0 3374 3496 155227237 155227359 1.140000e-35 161.0
19 TraesCS6D01G152100 chr7B 87.383 214 27 0 1480 1693 518388301 518388088 3.050000e-61 246.0
20 TraesCS6D01G152100 chr7B 88.679 53 5 1 3896 3947 114415105 114415053 3.290000e-06 63.9
21 TraesCS6D01G152100 chr7D 86.547 223 29 1 1480 1702 489721570 489721349 1.100000e-60 244.0
22 TraesCS6D01G152100 chr7D 79.070 215 29 10 3748 3947 420766359 420766572 2.480000e-27 134.0
23 TraesCS6D01G152100 chr7A 86.099 223 27 2 1480 1702 556505921 556505703 1.830000e-58 237.0
24 TraesCS6D01G152100 chr1A 80.423 189 24 3 3772 3947 449845988 449845800 8.900000e-27 132.0
25 TraesCS6D01G152100 chr4D 79.602 201 26 12 3758 3944 13604741 13604542 3.200000e-26 130.0
26 TraesCS6D01G152100 chr4A 83.824 136 19 3 3804 3937 31431263 31431129 4.140000e-25 126.0
27 TraesCS6D01G152100 chr4A 79.104 134 20 6 3804 3933 26766649 26766520 7.030000e-13 86.1
28 TraesCS6D01G152100 chr3B 78.173 197 24 7 3770 3947 807075465 807075269 1.500000e-19 108.0
29 TraesCS6D01G152100 chr1B 76.768 198 30 9 3765 3947 138570459 138570263 3.250000e-16 97.1
30 TraesCS6D01G152100 chr2A 82.407 108 16 3 3756 3861 718389463 718389357 1.510000e-14 91.6
31 TraesCS6D01G152100 chr2B 90.909 55 3 2 3805 3858 6316588 6316641 5.470000e-09 73.1
32 TraesCS6D01G152100 chr5D 76.159 151 27 9 3804 3949 217408242 217408096 1.970000e-08 71.3
33 TraesCS6D01G152100 chr3A 74.346 191 30 16 3765 3939 155015353 155015166 3.290000e-06 63.9


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 TraesCS6D01G152100 chr6D 125244491 125248439 3948 True 1556.0 7293 96.7672 1 3949 5 chr6D.!!$R1 3948
1 TraesCS6D01G152100 chr6B 223568781 223572972 4191 True 852.9 2778 92.6580 1 3792 7 chr6B.!!$R3 3791
2 TraesCS6D01G152100 chr6A 155223305 155227758 4453 False 1155.4 2689 92.1522 1 3949 5 chr6A.!!$F1 3948


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
258 272 0.602562 ATTGTGGCCATGTTTGACGG 59.397 50.000 9.72 0.0 0.00 4.79 F
594 612 1.876156 CAGAGGCACCTGAAACTGAAC 59.124 52.381 0.00 0.0 36.29 3.18 F
2022 2317 0.178903 ACTTCTGCACTGGGGTCCTA 60.179 55.000 0.00 0.0 0.00 2.94 F
2663 2968 0.178953 AACATTGGTGCCAAGCCTCT 60.179 50.000 9.65 0.0 39.47 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1736 1770 2.151202 GCAGCAGTAAAGCACCAAGTA 58.849 47.619 0.00 0.0 36.85 2.24 R
2274 2577 0.106569 TCAATATGGTGCTGCAGGGG 60.107 55.000 17.12 0.0 0.00 4.79 R
2861 3169 0.107831 CCTTGAAGGTCACCGTTCCA 59.892 55.000 2.25 0.0 35.16 3.53 R
3718 4351 0.183014 TATCCTCGGCGTTCTCTCCT 59.817 55.000 6.85 0.0 0.00 3.69 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
103 104 4.944962 TGATACGCTGTTTCCTTCAATG 57.055 40.909 0.00 0.00 0.00 2.82
104 105 4.574892 TGATACGCTGTTTCCTTCAATGA 58.425 39.130 0.00 0.00 0.00 2.57
164 165 4.088634 ACATGTGATGTTGTTATGGCCTT 58.911 39.130 3.32 0.00 41.63 4.35
166 167 5.011943 ACATGTGATGTTGTTATGGCCTTTT 59.988 36.000 3.32 0.00 41.63 2.27
258 272 0.602562 ATTGTGGCCATGTTTGACGG 59.397 50.000 9.72 0.00 0.00 4.79
289 303 2.963432 CCACAAGGCAATCATCCAAAC 58.037 47.619 0.00 0.00 0.00 2.93
290 304 2.564062 CCACAAGGCAATCATCCAAACT 59.436 45.455 0.00 0.00 0.00 2.66
291 305 3.581755 CACAAGGCAATCATCCAAACTG 58.418 45.455 0.00 0.00 0.00 3.16
292 306 3.006110 CACAAGGCAATCATCCAAACTGT 59.994 43.478 0.00 0.00 0.00 3.55
294 308 4.832266 ACAAGGCAATCATCCAAACTGTTA 59.168 37.500 0.00 0.00 0.00 2.41
295 309 5.163513 CAAGGCAATCATCCAAACTGTTAC 58.836 41.667 0.00 0.00 0.00 2.50
296 310 4.406456 AGGCAATCATCCAAACTGTTACA 58.594 39.130 0.00 0.00 0.00 2.41
297 311 5.018809 AGGCAATCATCCAAACTGTTACAT 58.981 37.500 0.00 0.00 0.00 2.29
299 313 6.663093 AGGCAATCATCCAAACTGTTACATAA 59.337 34.615 0.00 0.00 0.00 1.90
300 314 7.342799 AGGCAATCATCCAAACTGTTACATAAT 59.657 33.333 0.00 0.00 0.00 1.28
340 356 4.883759 TGAGAATTAGACAGGGAGATCCA 58.116 43.478 0.47 0.00 38.24 3.41
345 362 7.646884 AGAATTAGACAGGGAGATCCAATTTT 58.353 34.615 0.47 0.00 38.24 1.82
489 506 4.041075 TCAAGTAACACCTCAAGCACCATA 59.959 41.667 0.00 0.00 0.00 2.74
490 507 4.634012 AGTAACACCTCAAGCACCATAA 57.366 40.909 0.00 0.00 0.00 1.90
491 508 4.324267 AGTAACACCTCAAGCACCATAAC 58.676 43.478 0.00 0.00 0.00 1.89
567 585 4.232091 ACGTTATCCCCTATGTCCATTCT 58.768 43.478 0.00 0.00 0.00 2.40
594 612 1.876156 CAGAGGCACCTGAAACTGAAC 59.124 52.381 0.00 0.00 36.29 3.18
714 732 6.998802 AGTGTCACTTTTAGAAGAGCTATGT 58.001 36.000 0.00 0.00 36.69 2.29
755 787 8.077991 GGCAGTCAACTAACGTATATACACATA 58.922 37.037 13.22 2.22 0.00 2.29
756 788 9.622004 GCAGTCAACTAACGTATATACACATAT 57.378 33.333 13.22 0.00 0.00 1.78
782 814 9.337396 TGTAAGATCTTGCTCTTCTTTGTTTTA 57.663 29.630 21.95 0.00 36.82 1.52
783 815 9.818796 GTAAGATCTTGCTCTTCTTTGTTTTAG 57.181 33.333 18.47 0.00 36.82 1.85
796 828 9.273016 CTTCTTTGTTTTAGTCAAGAGTGGATA 57.727 33.333 0.00 0.00 0.00 2.59
802 834 9.166173 TGTTTTAGTCAAGAGTGGATATCAATG 57.834 33.333 4.83 0.00 0.00 2.82
808 840 5.876460 TCAAGAGTGGATATCAATGTGTGTG 59.124 40.000 4.83 0.00 0.00 3.82
811 843 6.240894 AGAGTGGATATCAATGTGTGTGTTT 58.759 36.000 4.83 0.00 0.00 2.83
851 883 6.959639 ATTGTTATAGTATTGGTGGCTTGG 57.040 37.500 0.00 0.00 0.00 3.61
887 919 3.820467 TCAGTTGCCCTTAAATGTGTGAG 59.180 43.478 0.00 0.00 0.00 3.51
1152 1185 7.337942 AGTGTCATCATGAAGTTCCCTAAAATC 59.662 37.037 0.00 0.00 0.00 2.17
1160 1193 4.373348 AGTTCCCTAAAATCGACGAGAG 57.627 45.455 3.01 0.00 0.00 3.20
1233 1266 6.406624 CCCCTGTATGTAAAGTTGTCGACTAT 60.407 42.308 17.92 0.00 37.72 2.12
1234 1267 6.696148 CCCTGTATGTAAAGTTGTCGACTATC 59.304 42.308 17.92 7.07 37.72 2.08
1253 1286 6.762333 ACTATCGTTGGTAGTGTTAACCTTT 58.238 36.000 2.48 0.00 37.91 3.11
1279 1312 5.247507 TCTACCATGCCATCAAAATTTCG 57.752 39.130 0.00 0.00 0.00 3.46
1309 1342 7.598278 TCAAGTCTGAGAACTAGTTTGAGATC 58.402 38.462 10.02 4.50 0.00 2.75
1361 1394 9.547279 AACCTACTTGGGATAATTTTGATTTCT 57.453 29.630 0.00 0.00 41.11 2.52
1362 1395 9.190317 ACCTACTTGGGATAATTTTGATTTCTC 57.810 33.333 0.00 0.00 41.11 2.87
1567 1601 6.750660 ATCTCATTCACAGATGAGGAGATT 57.249 37.500 13.22 4.12 45.81 2.40
1588 1622 8.723942 AGATTAAAGATCTATTTGAAGCGTGT 57.276 30.769 0.00 0.00 0.00 4.49
1600 1634 6.588348 TTTGAAGCGTGTGACATATATGAG 57.412 37.500 19.63 4.65 0.00 2.90
1609 1643 4.102996 TGTGACATATATGAGCACATGGGT 59.897 41.667 26.90 4.19 39.58 4.51
1698 1732 6.609212 TCAGAAGCAGTATCCTTCATACTTCT 59.391 38.462 0.00 0.00 44.80 2.85
1700 1734 8.584157 CAGAAGCAGTATCCTTCATACTTCTAT 58.416 37.037 0.00 0.00 44.80 1.98
1730 1764 6.749923 AATACACCTGCTTTCAGAATTCTC 57.250 37.500 4.57 0.00 42.95 2.87
1736 1770 4.574013 CCTGCTTTCAGAATTCTCGCTATT 59.426 41.667 4.57 0.00 42.95 1.73
1768 1802 0.904649 ACTGCTGCTGCTACACCATA 59.095 50.000 17.00 0.00 40.48 2.74
1770 1804 2.092753 ACTGCTGCTGCTACACCATATT 60.093 45.455 17.00 0.00 40.48 1.28
1818 1852 4.211125 TGACCCAGTTCATAAAAGCAACA 58.789 39.130 0.00 0.00 0.00 3.33
1866 2124 5.446860 TCGACATAAGGAGTAGGAATCACT 58.553 41.667 0.00 0.00 0.00 3.41
1977 2235 9.699410 ATTGTCCAAGGTATAAATCATGAAAGA 57.301 29.630 0.00 0.00 0.00 2.52
1978 2236 9.699410 TTGTCCAAGGTATAAATCATGAAAGAT 57.301 29.630 0.00 0.00 0.00 2.40
2017 2312 0.321122 GTCAGACTTCTGCACTGGGG 60.321 60.000 0.99 0.00 43.46 4.96
2022 2317 0.178903 ACTTCTGCACTGGGGTCCTA 60.179 55.000 0.00 0.00 0.00 2.94
2047 2350 8.911247 AGTTTACATGTTTCTTTGTTCTGTTC 57.089 30.769 2.30 0.00 0.00 3.18
2052 2355 7.198390 ACATGTTTCTTTGTTCTGTTCTGATG 58.802 34.615 0.00 0.00 0.00 3.07
2063 2366 3.513119 TCTGTTCTGATGAGGAGACTTGG 59.487 47.826 0.00 0.00 44.43 3.61
2120 2423 2.508300 GGGATTAGGTAACCTTGAGCCA 59.492 50.000 0.00 0.00 34.61 4.75
2269 2572 3.555518 GCGTGAAAAGATTTGGTGAGTC 58.444 45.455 0.00 0.00 0.00 3.36
2274 2577 6.606768 GTGAAAAGATTTGGTGAGTCATCTC 58.393 40.000 4.73 0.00 40.79 2.75
2275 2578 5.707298 TGAAAAGATTTGGTGAGTCATCTCC 59.293 40.000 4.73 0.00 39.75 3.71
2284 2587 1.614525 AGTCATCTCCCCTGCAGCA 60.615 57.895 8.66 0.00 0.00 4.41
2285 2588 1.451028 GTCATCTCCCCTGCAGCAC 60.451 63.158 8.66 0.00 0.00 4.40
2332 2635 6.982724 TCTGAAGCATTACACATACTCTCATG 59.017 38.462 0.00 0.00 0.00 3.07
2338 2641 6.690098 GCATTACACATACTCTCATGCTTTTG 59.310 38.462 0.00 0.00 34.10 2.44
2437 2740 6.211515 GCACCATTGCTTTTATAGGAATCTG 58.788 40.000 0.00 0.00 42.33 2.90
2438 2741 6.183360 GCACCATTGCTTTTATAGGAATCTGT 60.183 38.462 0.00 0.00 42.33 3.41
2445 2750 9.733556 TTGCTTTTATAGGAATCTGTAGTTCAA 57.266 29.630 0.00 0.00 0.00 2.69
2476 2781 7.778382 ACACTTTTAGAAAGTAAATCTGGTGGT 59.222 33.333 5.81 0.00 0.00 4.16
2477 2782 8.076178 CACTTTTAGAAAGTAAATCTGGTGGTG 58.924 37.037 5.81 0.00 0.00 4.17
2485 2790 6.976934 AGTAAATCTGGTGGTGAAAACAAT 57.023 33.333 0.00 0.00 0.00 2.71
2548 2853 5.044030 TCTGGAATTACCACCTCTCTCTACT 60.044 44.000 0.00 0.00 44.64 2.57
2630 2935 1.135460 GTCTCAAGCTGCTGGCAATTC 60.135 52.381 1.35 0.00 44.79 2.17
2634 2939 3.156293 TCAAGCTGCTGGCAATTCTAAA 58.844 40.909 1.35 0.00 44.79 1.85
2663 2968 0.178953 AACATTGGTGCCAAGCCTCT 60.179 50.000 9.65 0.00 39.47 3.69
2677 2982 2.136878 CCTCTGCGGTAGGGATGCT 61.137 63.158 0.00 0.00 0.00 3.79
2721 3026 3.068024 TCGTGCTTTGGCTTTTGAAGAAT 59.932 39.130 0.00 0.00 39.59 2.40
2724 3029 5.461737 CGTGCTTTGGCTTTTGAAGAATTTA 59.538 36.000 0.00 0.00 39.59 1.40
2781 3086 3.825328 CTTAGTGCTTATTCCAGCCCAT 58.175 45.455 0.00 0.00 39.25 4.00
2822 3127 8.279970 TCATTTATGTTCACCCTGATGTTTAG 57.720 34.615 0.00 0.00 0.00 1.85
2831 3139 4.455877 CACCCTGATGTTTAGTCTTTGGTC 59.544 45.833 0.00 0.00 0.00 4.02
2947 3255 4.741676 TGAAGATGACGACGATGATGAATG 59.258 41.667 0.00 0.00 0.00 2.67
2951 3259 1.449789 GACGACGATGATGAATGAGCG 59.550 52.381 0.00 0.00 0.00 5.03
3084 3393 8.755696 TTGCCAATTATGTCTGTTTATGTTTC 57.244 30.769 0.00 0.00 0.00 2.78
3085 3394 8.121305 TGCCAATTATGTCTGTTTATGTTTCT 57.879 30.769 0.00 0.00 0.00 2.52
3086 3395 8.028354 TGCCAATTATGTCTGTTTATGTTTCTG 58.972 33.333 0.00 0.00 0.00 3.02
3088 3397 9.912634 CCAATTATGTCTGTTTATGTTTCTGTT 57.087 29.630 0.00 0.00 0.00 3.16
3116 3425 5.237344 AGAAATGAACCGAAGTTGTTGAGAG 59.763 40.000 0.00 0.00 35.94 3.20
3117 3426 2.833794 TGAACCGAAGTTGTTGAGAGG 58.166 47.619 0.00 0.00 35.94 3.69
3124 3433 3.815401 CGAAGTTGTTGAGAGGATTTGGT 59.185 43.478 0.00 0.00 0.00 3.67
3192 3501 1.821336 TTGAAAACTTTGTGCGCTCG 58.179 45.000 9.73 0.00 0.00 5.03
3455 4082 4.739195 GGCATTTAGGCGTAACAAAATCA 58.261 39.130 0.00 0.00 33.57 2.57
3456 4083 4.561213 GGCATTTAGGCGTAACAAAATCAC 59.439 41.667 0.00 0.00 33.57 3.06
3457 4084 5.157781 GCATTTAGGCGTAACAAAATCACA 58.842 37.500 0.00 0.00 0.00 3.58
3458 4085 5.631512 GCATTTAGGCGTAACAAAATCACAA 59.368 36.000 0.00 0.00 0.00 3.33
3459 4086 6.310224 GCATTTAGGCGTAACAAAATCACAAT 59.690 34.615 0.00 0.00 0.00 2.71
3460 4087 7.665471 CATTTAGGCGTAACAAAATCACAATG 58.335 34.615 0.00 0.00 0.00 2.82
3461 4088 4.846779 AGGCGTAACAAAATCACAATGT 57.153 36.364 0.00 0.00 0.00 2.71
3462 4089 4.794169 AGGCGTAACAAAATCACAATGTC 58.206 39.130 0.00 0.00 0.00 3.06
3463 4090 3.602062 GGCGTAACAAAATCACAATGTCG 59.398 43.478 0.00 0.00 0.00 4.35
3464 4091 4.459606 GCGTAACAAAATCACAATGTCGA 58.540 39.130 0.00 0.00 0.00 4.20
3465 4092 4.549599 GCGTAACAAAATCACAATGTCGAG 59.450 41.667 0.00 0.00 0.00 4.04
3466 4093 5.675970 CGTAACAAAATCACAATGTCGAGT 58.324 37.500 0.00 0.00 0.00 4.18
3467 4094 6.133392 CGTAACAAAATCACAATGTCGAGTT 58.867 36.000 0.00 0.00 0.00 3.01
3468 4095 6.084939 CGTAACAAAATCACAATGTCGAGTTG 59.915 38.462 8.50 8.50 0.00 3.16
3469 4096 4.290155 ACAAAATCACAATGTCGAGTTGC 58.710 39.130 9.69 0.00 0.00 4.17
3470 4097 4.202000 ACAAAATCACAATGTCGAGTTGCA 60.202 37.500 9.69 0.00 0.00 4.08
3471 4098 4.566545 AAATCACAATGTCGAGTTGCAA 57.433 36.364 9.69 0.00 0.00 4.08
3472 4099 3.818961 ATCACAATGTCGAGTTGCAAG 57.181 42.857 0.00 0.00 0.00 4.01
3473 4100 2.560504 TCACAATGTCGAGTTGCAAGT 58.439 42.857 6.46 6.46 0.00 3.16
3474 4101 3.723260 TCACAATGTCGAGTTGCAAGTA 58.277 40.909 6.80 0.00 0.00 2.24
3475 4102 4.314961 TCACAATGTCGAGTTGCAAGTAT 58.685 39.130 6.80 0.00 0.00 2.12
3476 4103 5.474825 TCACAATGTCGAGTTGCAAGTATA 58.525 37.500 6.80 0.00 0.00 1.47
3477 4104 6.106003 TCACAATGTCGAGTTGCAAGTATAT 58.894 36.000 6.80 0.00 0.00 0.86
3478 4105 6.593770 TCACAATGTCGAGTTGCAAGTATATT 59.406 34.615 6.80 0.11 0.00 1.28
3479 4106 7.119116 TCACAATGTCGAGTTGCAAGTATATTT 59.881 33.333 6.80 0.00 0.00 1.40
3480 4107 7.426456 CACAATGTCGAGTTGCAAGTATATTTC 59.574 37.037 6.80 0.00 0.00 2.17
3481 4108 7.119116 ACAATGTCGAGTTGCAAGTATATTTCA 59.881 33.333 6.80 2.20 0.00 2.69
3482 4109 6.403333 TGTCGAGTTGCAAGTATATTTCAC 57.597 37.500 6.80 0.00 0.00 3.18
3483 4110 6.163476 TGTCGAGTTGCAAGTATATTTCACT 58.837 36.000 6.80 0.00 0.00 3.41
3484 4111 6.090763 TGTCGAGTTGCAAGTATATTTCACTG 59.909 38.462 6.80 0.00 0.00 3.66
3485 4112 5.580691 TCGAGTTGCAAGTATATTTCACTGG 59.419 40.000 6.80 0.00 0.00 4.00
3486 4113 5.567138 AGTTGCAAGTATATTTCACTGGC 57.433 39.130 4.57 0.00 42.36 4.85
3490 4117 6.528537 TGCAAGTATATTTCACTGGCATTT 57.471 33.333 2.55 0.00 45.80 2.32
3491 4118 7.637631 TGCAAGTATATTTCACTGGCATTTA 57.362 32.000 2.55 0.00 45.80 1.40
3492 4119 7.706159 TGCAAGTATATTTCACTGGCATTTAG 58.294 34.615 2.55 0.00 45.80 1.85
3493 4120 7.141363 GCAAGTATATTTCACTGGCATTTAGG 58.859 38.462 0.00 0.00 41.75 2.69
3494 4121 6.884280 AGTATATTTCACTGGCATTTAGGC 57.116 37.500 0.00 0.00 44.50 3.93
3511 4138 9.291664 GCATTTAGGCGTAACAAAATTACAATA 57.708 29.630 0.00 0.00 0.00 1.90
3559 4186 2.107950 TTAGGCGCTTATGCTGTTGT 57.892 45.000 7.64 0.00 36.97 3.32
3694 4327 1.004927 GCGCTCAAAGTATTAGCACCG 60.005 52.381 0.00 0.00 35.98 4.94
3718 4351 1.110442 CAGGCTTTGTTGGTGACCAA 58.890 50.000 14.05 14.05 41.69 3.67
3721 4354 1.398692 GCTTTGTTGGTGACCAAGGA 58.601 50.000 18.89 6.39 44.82 3.36
3809 4739 6.971527 TCGAAGAACAAAGTACTTCAAACA 57.028 33.333 8.95 0.00 39.64 2.83
3810 4740 7.548196 TCGAAGAACAAAGTACTTCAAACAT 57.452 32.000 8.95 0.00 39.64 2.71
3849 4779 1.574134 TTCTGAAACCACCGAACGAC 58.426 50.000 0.00 0.00 0.00 4.34
3850 4780 0.460722 TCTGAAACCACCGAACGACA 59.539 50.000 0.00 0.00 0.00 4.35
3854 4784 2.159128 TGAAACCACCGAACGACAACTA 60.159 45.455 0.00 0.00 0.00 2.24
3855 4785 1.856802 AACCACCGAACGACAACTAC 58.143 50.000 0.00 0.00 0.00 2.73
3856 4786 1.035139 ACCACCGAACGACAACTACT 58.965 50.000 0.00 0.00 0.00 2.57
3857 4787 2.229792 ACCACCGAACGACAACTACTA 58.770 47.619 0.00 0.00 0.00 1.82
3858 4788 2.030805 ACCACCGAACGACAACTACTAC 60.031 50.000 0.00 0.00 0.00 2.73
3859 4789 2.589014 CACCGAACGACAACTACTACC 58.411 52.381 0.00 0.00 0.00 3.18
3860 4790 1.197721 ACCGAACGACAACTACTACCG 59.802 52.381 0.00 0.00 0.00 4.02
3861 4791 1.197721 CCGAACGACAACTACTACCGT 59.802 52.381 0.00 0.00 34.74 4.83
3862 4792 2.350772 CCGAACGACAACTACTACCGTT 60.351 50.000 0.00 0.00 44.63 4.44
3863 4793 3.120338 CCGAACGACAACTACTACCGTTA 60.120 47.826 0.00 0.00 42.47 3.18
3864 4794 4.084507 CGAACGACAACTACTACCGTTAG 58.915 47.826 0.00 0.00 42.47 2.34
3879 4809 1.006688 TTAGAACGCGCTGCTGTCA 60.007 52.632 5.73 0.00 0.00 3.58
3892 4822 2.203788 TGTCACCGCTCCCCTTCT 60.204 61.111 0.00 0.00 0.00 2.85
3893 4823 0.970937 CTGTCACCGCTCCCCTTCTA 60.971 60.000 0.00 0.00 0.00 2.10
3900 4830 3.863606 CTCCCCTTCTAGAGCCGG 58.136 66.667 0.00 0.00 0.00 6.13
3901 4831 2.444140 TCCCCTTCTAGAGCCGGC 60.444 66.667 21.89 21.89 0.00 6.13
3903 4833 2.066999 CCCCTTCTAGAGCCGGCTT 61.067 63.158 33.34 22.07 0.00 4.35
3915 4845 0.103572 GCCGGCTTACCTTGTCGATA 59.896 55.000 22.15 0.00 34.08 2.92
3935 4865 1.884235 AAAGCCAGGAAGTCTTCGTG 58.116 50.000 22.76 22.76 43.26 4.35
3944 4874 1.237285 AAGTCTTCGTGCATGTGCCC 61.237 55.000 5.68 0.00 41.18 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 7.736017 GCGTATCAACAACGAATAATCATAGTG 59.264 37.037 0.00 0.00 42.90 2.74
143 144 4.724074 AAGGCCATAACAACATCACATG 57.276 40.909 5.01 0.00 0.00 3.21
172 173 9.920946 AAGGACTCAACCAACACATTATATTAT 57.079 29.630 0.00 0.00 0.00 1.28
173 174 9.747898 AAAGGACTCAACCAACACATTATATTA 57.252 29.630 0.00 0.00 0.00 0.98
174 175 8.650143 AAAGGACTCAACCAACACATTATATT 57.350 30.769 0.00 0.00 0.00 1.28
175 176 9.747898 TTAAAGGACTCAACCAACACATTATAT 57.252 29.630 0.00 0.00 0.00 0.86
227 241 1.269517 GGCCACAATTTTCGCTTGTCA 60.270 47.619 0.00 0.00 34.69 3.58
258 272 1.080569 CCTTGTGGCCATGCGTTTC 60.081 57.895 9.72 0.00 0.00 2.78
294 308 9.851686 TCAGCATTCCAGTATTTAGAATTATGT 57.148 29.630 0.00 0.00 0.00 2.29
299 313 9.638176 AATTCTCAGCATTCCAGTATTTAGAAT 57.362 29.630 0.00 0.00 32.80 2.40
340 356 3.420893 TCACATCGGCCTCTCAAAAATT 58.579 40.909 0.00 0.00 0.00 1.82
345 362 1.194218 TCATCACATCGGCCTCTCAA 58.806 50.000 0.00 0.00 0.00 3.02
489 506 5.104374 CAGCAACAATGAAAACAGACAGTT 58.896 37.500 0.00 0.00 43.89 3.16
490 507 4.675510 CAGCAACAATGAAAACAGACAGT 58.324 39.130 0.00 0.00 0.00 3.55
491 508 3.488310 GCAGCAACAATGAAAACAGACAG 59.512 43.478 0.00 0.00 0.00 3.51
567 585 1.434188 TCAGGTGCCTCTGGAAGAAA 58.566 50.000 3.98 0.00 46.34 2.52
594 612 0.861837 GTCAAAGGTGTGCGACTGAG 59.138 55.000 0.00 0.00 0.00 3.35
600 618 0.950836 TTCATGGTCAAAGGTGTGCG 59.049 50.000 0.00 0.00 0.00 5.34
652 670 2.036089 CTCCTAGTTACTGCCGGGAATC 59.964 54.545 2.18 0.00 0.00 2.52
701 719 7.624549 ACTCCAAATTGAACATAGCTCTTCTA 58.375 34.615 0.00 0.00 0.00 2.10
714 732 4.724399 TGACTGCCTAACTCCAAATTGAA 58.276 39.130 0.00 0.00 0.00 2.69
747 765 9.703892 GAAGAGCAAGATCTTACATATGTGTAT 57.296 33.333 18.81 8.64 40.35 2.29
755 787 7.992754 AACAAAGAAGAGCAAGATCTTACAT 57.007 32.000 7.86 0.00 39.63 2.29
756 788 7.807977 AAACAAAGAAGAGCAAGATCTTACA 57.192 32.000 7.86 0.00 39.63 2.41
757 789 9.818796 CTAAAACAAAGAAGAGCAAGATCTTAC 57.181 33.333 7.86 1.97 39.63 2.34
758 790 9.561069 ACTAAAACAAAGAAGAGCAAGATCTTA 57.439 29.630 7.86 0.00 39.63 2.10
759 791 8.457238 ACTAAAACAAAGAAGAGCAAGATCTT 57.543 30.769 0.88 0.88 42.23 2.40
760 792 7.716998 TGACTAAAACAAAGAAGAGCAAGATCT 59.283 33.333 0.00 0.00 0.00 2.75
761 793 7.865707 TGACTAAAACAAAGAAGAGCAAGATC 58.134 34.615 0.00 0.00 0.00 2.75
767 799 7.128976 CACTCTTGACTAAAACAAAGAAGAGC 58.871 38.462 0.00 0.00 0.00 4.09
782 814 6.111382 CACACATTGATATCCACTCTTGACT 58.889 40.000 0.00 0.00 0.00 3.41
783 815 5.877012 ACACACATTGATATCCACTCTTGAC 59.123 40.000 0.00 0.00 0.00 3.18
796 828 6.942532 ACACTAGAAAACACACACATTGAT 57.057 33.333 0.00 0.00 0.00 2.57
802 834 3.691498 GCCAACACTAGAAAACACACAC 58.309 45.455 0.00 0.00 0.00 3.82
808 840 5.178809 ACAATAGACGCCAACACTAGAAAAC 59.821 40.000 0.00 0.00 0.00 2.43
811 843 4.530710 ACAATAGACGCCAACACTAGAA 57.469 40.909 0.00 0.00 0.00 2.10
866 898 3.820467 TCTCACACATTTAAGGGCAACTG 59.180 43.478 0.00 0.00 0.00 3.16
867 899 4.098914 TCTCACACATTTAAGGGCAACT 57.901 40.909 0.00 0.00 0.00 3.16
868 900 4.846779 TTCTCACACATTTAAGGGCAAC 57.153 40.909 0.00 0.00 0.00 4.17
869 901 7.147915 GGATATTTCTCACACATTTAAGGGCAA 60.148 37.037 0.00 0.00 0.00 4.52
870 902 6.321181 GGATATTTCTCACACATTTAAGGGCA 59.679 38.462 0.00 0.00 0.00 5.36
871 903 6.547510 AGGATATTTCTCACACATTTAAGGGC 59.452 38.462 0.00 0.00 0.00 5.19
1115 1148 4.696877 TCATGATGACACTGTTGAATGACC 59.303 41.667 0.00 0.00 0.00 4.02
1160 1193 6.749923 AGATAATCCTGCAGTTTCTCAAAC 57.250 37.500 13.81 0.00 41.69 2.93
1233 1266 7.933033 AGAATAAAAGGTTAACACTACCAACGA 59.067 33.333 8.10 0.00 38.16 3.85
1234 1267 8.091385 AGAATAAAAGGTTAACACTACCAACG 57.909 34.615 8.10 0.00 38.16 4.10
1253 1286 7.920151 CGAAATTTTGATGGCATGGTAGAATAA 59.080 33.333 3.81 0.00 0.00 1.40
1309 1342 7.190920 AGTTCAGAAACTTCAGAATTAACGG 57.809 36.000 1.29 0.00 43.28 4.44
1567 1601 6.871492 TGTCACACGCTTCAAATAGATCTTTA 59.129 34.615 0.00 0.00 0.00 1.85
1588 1622 4.980339 ACCCATGTGCTCATATATGTCA 57.020 40.909 12.42 9.00 32.47 3.58
1600 1634 4.398988 TCATTGAACTTCATACCCATGTGC 59.601 41.667 0.00 0.00 33.57 4.57
1716 1750 6.836577 AGTAATAGCGAGAATTCTGAAAGC 57.163 37.500 14.00 12.46 0.00 3.51
1720 1754 6.042777 CACCAAGTAATAGCGAGAATTCTGA 58.957 40.000 14.00 0.00 0.00 3.27
1725 1759 4.408182 AGCACCAAGTAATAGCGAGAAT 57.592 40.909 0.00 0.00 0.00 2.40
1730 1764 4.494199 GCAGTAAAGCACCAAGTAATAGCG 60.494 45.833 0.00 0.00 0.00 4.26
1736 1770 2.151202 GCAGCAGTAAAGCACCAAGTA 58.849 47.619 0.00 0.00 36.85 2.24
1784 1818 5.009631 TGAACTGGGTCATGTATTTCTTGG 58.990 41.667 0.00 0.00 0.00 3.61
1785 1819 6.764308 ATGAACTGGGTCATGTATTTCTTG 57.236 37.500 0.00 0.00 36.86 3.02
1839 2097 8.524487 GTGATTCCTACTCCTTATGTCGATTAT 58.476 37.037 0.00 0.00 0.00 1.28
1845 2103 5.755861 GCAAGTGATTCCTACTCCTTATGTC 59.244 44.000 0.00 0.00 0.00 3.06
1851 2109 4.042187 ACTTTGCAAGTGATTCCTACTCCT 59.958 41.667 0.00 0.00 41.01 3.69
1965 2223 8.673251 ACCTAGCCCTTATATCTTTCATGATTT 58.327 33.333 0.00 0.00 0.00 2.17
1966 2224 8.224620 ACCTAGCCCTTATATCTTTCATGATT 57.775 34.615 0.00 0.00 0.00 2.57
1968 2226 8.177456 TCTACCTAGCCCTTATATCTTTCATGA 58.823 37.037 0.00 0.00 0.00 3.07
1969 2227 8.367660 TCTACCTAGCCCTTATATCTTTCATG 57.632 38.462 0.00 0.00 0.00 3.07
1974 2232 9.649316 GACATATCTACCTAGCCCTTATATCTT 57.351 37.037 0.00 0.00 0.00 2.40
1975 2233 8.792734 TGACATATCTACCTAGCCCTTATATCT 58.207 37.037 0.00 0.00 0.00 1.98
1976 2234 8.998277 TGACATATCTACCTAGCCCTTATATC 57.002 38.462 0.00 0.00 0.00 1.63
1977 2235 8.792734 TCTGACATATCTACCTAGCCCTTATAT 58.207 37.037 0.00 0.00 0.00 0.86
1978 2236 8.053963 GTCTGACATATCTACCTAGCCCTTATA 58.946 40.741 2.24 0.00 0.00 0.98
1979 2237 6.893005 GTCTGACATATCTACCTAGCCCTTAT 59.107 42.308 2.24 0.00 0.00 1.73
1980 2238 6.045695 AGTCTGACATATCTACCTAGCCCTTA 59.954 42.308 10.88 0.00 0.00 2.69
1983 2241 4.668636 AGTCTGACATATCTACCTAGCCC 58.331 47.826 10.88 0.00 0.00 5.19
1985 2243 6.569610 GCAGAAGTCTGACATATCTACCTAGC 60.570 46.154 12.54 6.27 46.59 3.42
2017 2312 8.837389 AGAACAAAGAAACATGTAAACTAGGAC 58.163 33.333 0.00 0.00 0.00 3.85
2022 2317 8.739972 AGAACAGAACAAAGAAACATGTAAACT 58.260 29.630 0.00 0.00 0.00 2.66
2047 2350 4.202202 GGACATACCAAGTCTCCTCATCAG 60.202 50.000 0.00 0.00 38.79 2.90
2052 2355 3.769844 TCAAGGACATACCAAGTCTCCTC 59.230 47.826 0.00 0.00 42.04 3.71
2063 2366 5.376854 AAAGCAACACATCAAGGACATAC 57.623 39.130 0.00 0.00 0.00 2.39
2120 2423 4.733523 GCATCAACCAACGTCTCAAAAGTT 60.734 41.667 0.00 0.00 0.00 2.66
2269 2572 2.124403 GGTGCTGCAGGGGAGATG 60.124 66.667 17.12 0.00 0.00 2.90
2274 2577 0.106569 TCAATATGGTGCTGCAGGGG 60.107 55.000 17.12 0.00 0.00 4.79
2275 2578 1.766494 TTCAATATGGTGCTGCAGGG 58.234 50.000 17.12 0.00 0.00 4.45
2314 2617 7.695201 CACAAAAGCATGAGAGTATGTGTAATG 59.305 37.037 0.00 0.00 33.93 1.90
2323 2626 4.460263 ACCAACACAAAAGCATGAGAGTA 58.540 39.130 0.00 0.00 0.00 2.59
2332 2635 5.815222 ACCAAAGATTAACCAACACAAAAGC 59.185 36.000 0.00 0.00 0.00 3.51
2338 2641 6.801575 TGAGAAACCAAAGATTAACCAACAC 58.198 36.000 0.00 0.00 0.00 3.32
2427 2730 7.824779 GTGTCCTTTTGAACTACAGATTCCTAT 59.175 37.037 0.00 0.00 0.00 2.57
2432 2735 7.881775 AAAGTGTCCTTTTGAACTACAGATT 57.118 32.000 0.00 0.00 37.65 2.40
2465 2770 7.872483 GTCATAATTGTTTTCACCACCAGATTT 59.128 33.333 0.00 0.00 0.00 2.17
2485 2790 9.793259 AGAAAGGAAGTGAAAACATAGTCATAA 57.207 29.630 0.00 0.00 0.00 1.90
2607 2912 0.604780 TGCCAGCAGCTTGAGACTTC 60.605 55.000 0.00 0.00 44.23 3.01
2630 2935 5.639082 GCACCAATGTTCCAAAGGAATTTAG 59.361 40.000 1.30 0.00 44.04 1.85
2634 2939 2.302733 GGCACCAATGTTCCAAAGGAAT 59.697 45.455 1.30 0.00 44.04 3.01
2663 2968 1.558167 TTGGAAGCATCCCTACCGCA 61.558 55.000 5.34 0.00 45.95 5.69
2666 2971 2.808906 AACTTGGAAGCATCCCTACC 57.191 50.000 5.34 0.00 45.95 3.18
2724 3029 7.230510 TCCTATGCAGTTGTTGAACTTAAACAT 59.769 33.333 0.00 0.00 40.68 2.71
2808 3113 4.398319 ACCAAAGACTAAACATCAGGGTG 58.602 43.478 0.00 0.00 0.00 4.61
2831 3139 2.684881 CCAATCCATTTCCTCTGGAACG 59.315 50.000 0.00 0.00 45.57 3.95
2861 3169 0.107831 CCTTGAAGGTCACCGTTCCA 59.892 55.000 2.25 0.00 35.16 3.53
2947 3255 0.581053 GCTAATCTTCAGCTGCGCTC 59.419 55.000 9.47 0.00 36.40 5.03
2951 3259 3.003482 CAGAATGGCTAATCTTCAGCTGC 59.997 47.826 9.47 0.00 39.09 5.25
2991 3300 3.019003 GCTGCTGGAGGCTACCGAA 62.019 63.158 0.00 0.00 42.39 4.30
3084 3393 8.504005 ACAACTTCGGTTCATTTCTATTAACAG 58.496 33.333 0.00 0.00 35.78 3.16
3085 3394 8.385898 ACAACTTCGGTTCATTTCTATTAACA 57.614 30.769 0.00 0.00 35.78 2.41
3086 3395 9.113876 CAACAACTTCGGTTCATTTCTATTAAC 57.886 33.333 0.00 0.00 35.78 2.01
3088 3397 8.610248 TCAACAACTTCGGTTCATTTCTATTA 57.390 30.769 0.00 0.00 35.78 0.98
3090 3399 6.934645 TCTCAACAACTTCGGTTCATTTCTAT 59.065 34.615 0.00 0.00 35.78 1.98
3091 3400 6.285224 TCTCAACAACTTCGGTTCATTTCTA 58.715 36.000 0.00 0.00 35.78 2.10
3092 3401 5.123227 TCTCAACAACTTCGGTTCATTTCT 58.877 37.500 0.00 0.00 35.78 2.52
3093 3402 5.418310 TCTCAACAACTTCGGTTCATTTC 57.582 39.130 0.00 0.00 35.78 2.17
3094 3403 4.275936 CCTCTCAACAACTTCGGTTCATTT 59.724 41.667 0.00 0.00 35.78 2.32
3103 3412 4.821805 TCACCAAATCCTCTCAACAACTTC 59.178 41.667 0.00 0.00 0.00 3.01
3116 3425 6.223120 AGCACAAAGTTTTATCACCAAATCC 58.777 36.000 0.00 0.00 0.00 3.01
3117 3426 7.713764 AAGCACAAAGTTTTATCACCAAATC 57.286 32.000 0.00 0.00 0.00 2.17
3124 3433 5.971763 ACACCAAAGCACAAAGTTTTATCA 58.028 33.333 0.00 0.00 0.00 2.15
3192 3501 6.697395 ACTTACAATTTTGCTTCCAATACCC 58.303 36.000 0.00 0.00 0.00 3.69
3285 3597 8.311109 AGTTTGTTTCTTTCTTTAAGGAGCAAA 58.689 29.630 4.38 4.38 45.09 3.68
3286 3598 7.836842 AGTTTGTTTCTTTCTTTAAGGAGCAA 58.163 30.769 0.00 0.00 39.83 3.91
3287 3599 7.404671 AGTTTGTTTCTTTCTTTAAGGAGCA 57.595 32.000 0.00 0.00 31.39 4.26
3288 3600 9.797556 TTTAGTTTGTTTCTTTCTTTAAGGAGC 57.202 29.630 0.00 0.00 34.46 4.70
3348 3660 3.844090 GAGGGAGGCCACGAGAGC 61.844 72.222 5.01 0.00 0.00 4.09
3383 3695 2.764251 ATTTTGTCGCGCGTGCAGTC 62.764 55.000 30.98 14.04 42.97 3.51
3384 3696 2.387125 AATTTTGTCGCGCGTGCAGT 62.387 50.000 30.98 15.49 42.97 4.40
3445 4072 5.912396 GCAACTCGACATTGTGATTTTGTTA 59.088 36.000 0.00 0.00 0.00 2.41
3446 4073 4.739716 GCAACTCGACATTGTGATTTTGTT 59.260 37.500 0.00 0.00 0.00 2.83
3447 4074 4.202000 TGCAACTCGACATTGTGATTTTGT 60.202 37.500 0.00 0.00 0.00 2.83
3448 4075 4.289342 TGCAACTCGACATTGTGATTTTG 58.711 39.130 0.00 1.47 0.00 2.44
3449 4076 4.566545 TGCAACTCGACATTGTGATTTT 57.433 36.364 0.00 0.00 0.00 1.82
3450 4077 4.036734 ACTTGCAACTCGACATTGTGATTT 59.963 37.500 0.00 0.00 0.00 2.17
3451 4078 3.565482 ACTTGCAACTCGACATTGTGATT 59.435 39.130 0.00 0.00 0.00 2.57
3452 4079 3.141398 ACTTGCAACTCGACATTGTGAT 58.859 40.909 0.00 0.00 0.00 3.06
3453 4080 2.560504 ACTTGCAACTCGACATTGTGA 58.439 42.857 0.00 0.00 0.00 3.58
3454 4081 4.668576 ATACTTGCAACTCGACATTGTG 57.331 40.909 0.00 0.00 0.00 3.33
3455 4082 6.985188 AATATACTTGCAACTCGACATTGT 57.015 33.333 0.00 0.00 0.00 2.71
3456 4083 7.426456 GTGAAATATACTTGCAACTCGACATTG 59.574 37.037 0.00 1.06 0.00 2.82
3457 4084 7.334421 AGTGAAATATACTTGCAACTCGACATT 59.666 33.333 0.00 0.00 0.00 2.71
3458 4085 6.818644 AGTGAAATATACTTGCAACTCGACAT 59.181 34.615 0.00 0.00 0.00 3.06
3459 4086 6.090763 CAGTGAAATATACTTGCAACTCGACA 59.909 38.462 0.00 0.00 0.00 4.35
3460 4087 6.455646 CCAGTGAAATATACTTGCAACTCGAC 60.456 42.308 0.00 0.00 0.00 4.20
3461 4088 5.580691 CCAGTGAAATATACTTGCAACTCGA 59.419 40.000 0.00 0.00 0.00 4.04
3462 4089 5.727791 GCCAGTGAAATATACTTGCAACTCG 60.728 44.000 0.00 0.00 36.95 4.18
3463 4090 5.123820 TGCCAGTGAAATATACTTGCAACTC 59.876 40.000 0.00 0.00 41.86 3.01
3464 4091 5.009631 TGCCAGTGAAATATACTTGCAACT 58.990 37.500 0.00 0.00 41.86 3.16
3465 4092 5.309323 TGCCAGTGAAATATACTTGCAAC 57.691 39.130 0.00 0.00 41.86 4.17
3466 4093 6.528537 AATGCCAGTGAAATATACTTGCAA 57.471 33.333 6.89 0.00 45.86 4.08
3467 4094 6.528537 AAATGCCAGTGAAATATACTTGCA 57.471 33.333 5.60 5.60 46.48 4.08
3468 4095 7.141363 CCTAAATGCCAGTGAAATATACTTGC 58.859 38.462 0.00 0.00 37.34 4.01
3469 4096 7.141363 GCCTAAATGCCAGTGAAATATACTTG 58.859 38.462 0.00 0.00 0.00 3.16
3470 4097 6.017109 CGCCTAAATGCCAGTGAAATATACTT 60.017 38.462 0.00 0.00 0.00 2.24
3471 4098 5.470098 CGCCTAAATGCCAGTGAAATATACT 59.530 40.000 0.00 0.00 0.00 2.12
3472 4099 5.238650 ACGCCTAAATGCCAGTGAAATATAC 59.761 40.000 0.00 0.00 0.00 1.47
3473 4100 5.373222 ACGCCTAAATGCCAGTGAAATATA 58.627 37.500 0.00 0.00 0.00 0.86
3474 4101 4.207165 ACGCCTAAATGCCAGTGAAATAT 58.793 39.130 0.00 0.00 0.00 1.28
3475 4102 3.616219 ACGCCTAAATGCCAGTGAAATA 58.384 40.909 0.00 0.00 0.00 1.40
3476 4103 2.446435 ACGCCTAAATGCCAGTGAAAT 58.554 42.857 0.00 0.00 0.00 2.17
3477 4104 1.904287 ACGCCTAAATGCCAGTGAAA 58.096 45.000 0.00 0.00 0.00 2.69
3478 4105 2.745281 GTTACGCCTAAATGCCAGTGAA 59.255 45.455 0.00 0.00 0.00 3.18
3479 4106 2.289756 TGTTACGCCTAAATGCCAGTGA 60.290 45.455 0.00 0.00 0.00 3.41
3480 4107 2.080693 TGTTACGCCTAAATGCCAGTG 58.919 47.619 0.00 0.00 0.00 3.66
3481 4108 2.483014 TGTTACGCCTAAATGCCAGT 57.517 45.000 0.00 0.00 0.00 4.00
3482 4109 3.840890 TTTGTTACGCCTAAATGCCAG 57.159 42.857 0.00 0.00 0.00 4.85
3483 4110 4.792521 ATTTTGTTACGCCTAAATGCCA 57.207 36.364 0.00 0.00 0.00 4.92
3484 4111 6.094061 TGTAATTTTGTTACGCCTAAATGCC 58.906 36.000 0.00 0.00 0.00 4.40
3485 4112 7.569677 TTGTAATTTTGTTACGCCTAAATGC 57.430 32.000 0.00 0.00 0.00 3.56
3488 4115 9.705471 CGATATTGTAATTTTGTTACGCCTAAA 57.295 29.630 0.00 0.00 0.00 1.85
3489 4116 9.096160 TCGATATTGTAATTTTGTTACGCCTAA 57.904 29.630 0.00 0.00 0.00 2.69
3490 4117 8.645730 TCGATATTGTAATTTTGTTACGCCTA 57.354 30.769 0.00 0.00 0.00 3.93
3491 4118 7.279313 ACTCGATATTGTAATTTTGTTACGCCT 59.721 33.333 0.00 0.00 0.00 5.52
3492 4119 7.404203 ACTCGATATTGTAATTTTGTTACGCC 58.596 34.615 0.00 0.00 0.00 5.68
3493 4120 8.721476 CAACTCGATATTGTAATTTTGTTACGC 58.279 33.333 0.00 0.00 0.00 4.42
3494 4121 8.721476 GCAACTCGATATTGTAATTTTGTTACG 58.279 33.333 10.32 0.00 0.00 3.18
3511 4138 6.258727 CCAGTGAAATATACTTGCAACTCGAT 59.741 38.462 0.00 0.00 0.00 3.59
3550 4177 3.319137 TCGCTCTTTCTACAACAGCAT 57.681 42.857 0.00 0.00 0.00 3.79
3559 4186 7.924412 ACGGTATGAAAAATATCGCTCTTTCTA 59.076 33.333 0.00 0.00 31.80 2.10
3694 4327 0.954452 CACCAACAAAGCCTGAGACC 59.046 55.000 0.00 0.00 0.00 3.85
3718 4351 0.183014 TATCCTCGGCGTTCTCTCCT 59.817 55.000 6.85 0.00 0.00 3.69
3721 4354 2.634815 TAGTATCCTCGGCGTTCTCT 57.365 50.000 6.85 2.29 0.00 3.10
3818 4748 4.863131 GTGGTTTCAGAATCTCGACGTAAT 59.137 41.667 0.00 0.00 0.00 1.89
3823 4753 1.993370 CGGTGGTTTCAGAATCTCGAC 59.007 52.381 0.00 0.00 0.00 4.20
3860 4790 1.282248 TGACAGCAGCGCGTTCTAAC 61.282 55.000 8.43 1.28 0.00 2.34
3861 4791 1.006688 TGACAGCAGCGCGTTCTAA 60.007 52.632 8.43 0.00 0.00 2.10
3862 4792 1.733041 GTGACAGCAGCGCGTTCTA 60.733 57.895 8.43 0.00 0.00 2.10
3863 4793 3.038417 GTGACAGCAGCGCGTTCT 61.038 61.111 8.43 0.00 0.00 3.01
3864 4794 4.077188 GGTGACAGCAGCGCGTTC 62.077 66.667 8.43 0.00 32.24 3.95
3879 4809 1.758906 GCTCTAGAAGGGGAGCGGT 60.759 63.158 0.00 0.00 44.01 5.68
3892 4822 0.822164 GACAAGGTAAGCCGGCTCTA 59.178 55.000 32.93 20.69 40.50 2.43
3893 4823 1.597461 GACAAGGTAAGCCGGCTCT 59.403 57.895 32.93 20.65 40.50 4.09
3900 4830 3.687698 TGGCTTTTATCGACAAGGTAAGC 59.312 43.478 3.29 3.29 36.64 3.09
3901 4831 4.332819 CCTGGCTTTTATCGACAAGGTAAG 59.667 45.833 0.00 0.00 0.00 2.34
3903 4833 3.516300 TCCTGGCTTTTATCGACAAGGTA 59.484 43.478 0.00 0.00 0.00 3.08
3915 4845 2.222027 CACGAAGACTTCCTGGCTTTT 58.778 47.619 9.63 0.00 45.69 2.27



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

AutoCloner maintained by Alex Coulton.