Multiple sequence alignment - TraesCS1B01G188300

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 TraesCS1B01G188300 chr1B 100.000 4766 0 0 1 4766 336645420 336650185 0.000000e+00 8802.0
1 TraesCS1B01G188300 chr1B 93.600 625 18 10 936 1538 434763927 434764551 0.000000e+00 913.0
2 TraesCS1B01G188300 chr1B 85.149 101 9 2 2338 2438 26507017 26506923 1.090000e-16 99.0
3 TraesCS1B01G188300 chr1D 90.451 2817 132 45 348 3086 237807217 237804460 0.000000e+00 3585.0
4 TraesCS1B01G188300 chr1D 92.705 987 41 13 3164 4126 237804325 237803346 0.000000e+00 1395.0
5 TraesCS1B01G188300 chr1D 92.941 255 11 3 4286 4534 237803268 237803015 9.750000e-97 364.0
6 TraesCS1B01G188300 chr1D 89.956 229 10 7 1 219 237807444 237807219 2.810000e-72 283.0
7 TraesCS1B01G188300 chr1D 90.805 87 6 2 4154 4240 237803347 237803263 1.080000e-21 115.0
8 TraesCS1B01G188300 chr1A 91.845 1447 48 28 727 2151 301200164 301198766 0.000000e+00 1954.0
9 TraesCS1B01G188300 chr1A 91.838 1409 73 14 3091 4479 301197700 301196314 0.000000e+00 1927.0
10 TraesCS1B01G188300 chr1A 86.105 950 84 22 2150 3086 301198733 301197819 0.000000e+00 979.0
11 TraesCS1B01G188300 chr1A 90.749 227 15 3 196 422 301200930 301200710 1.000000e-76 298.0
12 TraesCS1B01G188300 chr1A 91.558 154 10 2 492 643 301200486 301200334 4.830000e-50 209.0
13 TraesCS1B01G188300 chr1A 100.000 110 0 0 4657 4766 492653924 492654033 2.250000e-48 204.0
14 TraesCS1B01G188300 chr1A 93.396 106 3 2 4478 4580 301196280 301196176 2.300000e-33 154.0
15 TraesCS1B01G188300 chr1A 92.391 92 5 1 1 92 301201687 301201598 3.870000e-26 130.0
16 TraesCS1B01G188300 chr1A 91.071 56 2 2 136 188 301201292 301201237 6.620000e-09 73.1
17 TraesCS1B01G188300 chr3D 93.058 605 38 3 2143 2743 20623353 20622749 0.000000e+00 881.0
18 TraesCS1B01G188300 chr5B 95.190 499 18 6 1041 1538 13200662 13200169 0.000000e+00 784.0
19 TraesCS1B01G188300 chr5B 99.099 111 0 1 4654 4764 642598712 642598603 1.050000e-46 198.0
20 TraesCS1B01G188300 chr5B 90.741 108 10 0 2679 2786 503730615 503730508 1.380000e-30 145.0
21 TraesCS1B01G188300 chr6B 95.787 451 12 2 1103 1546 720461104 720460654 0.000000e+00 721.0
22 TraesCS1B01G188300 chr6B 99.107 112 1 0 4655 4766 704956171 704956060 8.090000e-48 202.0
23 TraesCS1B01G188300 chrUn 92.459 305 20 1 2442 2743 70269693 70269389 2.630000e-117 433.0
24 TraesCS1B01G188300 chr2A 92.131 305 21 1 2442 2743 610249835 610250139 1.230000e-115 427.0
25 TraesCS1B01G188300 chr5A 91.246 297 23 1 2450 2743 291396568 291396864 7.430000e-108 401.0
26 TraesCS1B01G188300 chr5A 100.000 112 0 0 4655 4766 585238446 585238335 1.740000e-49 207.0
27 TraesCS1B01G188300 chr7A 99.091 110 1 0 4657 4766 198950577 198950686 1.050000e-46 198.0
28 TraesCS1B01G188300 chr7A 97.297 37 1 0 330 366 403987521 403987485 3.980000e-06 63.9
29 TraesCS1B01G188300 chr4A 97.436 117 2 1 4650 4766 161356742 161356857 1.050000e-46 198.0
30 TraesCS1B01G188300 chr3A 99.091 110 1 0 4657 4766 16637405 16637296 1.050000e-46 198.0
31 TraesCS1B01G188300 chr3A 99.091 110 1 0 4657 4766 16640404 16640295 1.050000e-46 198.0
32 TraesCS1B01G188300 chr3A 99.091 110 1 0 4657 4766 16643601 16643492 1.050000e-46 198.0
33 TraesCS1B01G188300 chr2B 90.164 61 3 1 2382 2442 80342557 80342614 5.110000e-10 76.8


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 TraesCS1B01G188300 chr1B 336645420 336650185 4765 False 8802.0000 8802 100.000000 1 4766 1 chr1B.!!$F1 4765
1 TraesCS1B01G188300 chr1B 434763927 434764551 624 False 913.0000 913 93.600000 936 1538 1 chr1B.!!$F2 602
2 TraesCS1B01G188300 chr1D 237803015 237807444 4429 True 1148.4000 3585 91.371600 1 4534 5 chr1D.!!$R1 4533
3 TraesCS1B01G188300 chr1A 301196176 301201687 5511 True 715.5125 1954 91.119125 1 4580 8 chr1A.!!$R1 4579
4 TraesCS1B01G188300 chr3D 20622749 20623353 604 True 881.0000 881 93.058000 2143 2743 1 chr3D.!!$R1 600

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
732 1490 0.042188 CTGTGAAAACTCCACACGCG 60.042 55.0 3.53 3.53 39.36 6.01 F
734 1492 0.042448 GTGAAAACTCCACACGCGAC 60.042 55.0 15.93 0.00 34.81 5.19 F
2113 3031 0.244450 TTGGTTGGCGTCTAGTACCG 59.756 55.0 0.00 0.00 0.00 4.02 F
2407 3359 0.318120 GGTGGTGCTGGGTTGATTTG 59.682 55.0 0.00 0.00 0.00 2.32 F
2913 3885 0.324614 ATCACATGCCGTCTGGTTCA 59.675 50.0 0.00 0.00 37.67 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2525 3496 0.468226 GATGGGCTATTCCGGTGTCA 59.532 55.000 0.00 0.00 34.94 3.58 R
2555 3526 2.348660 ACGAACGGAACAAGTGACAAA 58.651 42.857 0.00 0.00 0.00 2.83 R
3540 4629 0.033504 CGTAGCCCGCCATGAAGTAT 59.966 55.000 0.00 0.00 0.00 2.12 R
3654 4743 0.250793 TGTACCGGCGGACATCAAAT 59.749 50.000 35.78 10.16 0.00 2.32 R
4714 5867 0.036388 AGAAAATTCAGAGCGGCCGA 60.036 50.000 33.48 6.95 0.00 5.54 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
39 42 0.521291 CAGCACCCCATACACGTTTG 59.479 55.000 0.00 0.00 0.00 2.93
40 43 1.211709 GCACCCCATACACGTTTGC 59.788 57.895 0.00 0.00 0.00 3.68
85 98 2.002586 CGCCACATTCTGTTACAGGAG 58.997 52.381 12.79 5.43 31.51 3.69
86 99 2.359900 GCCACATTCTGTTACAGGAGG 58.640 52.381 12.79 8.24 31.51 4.30
87 100 2.027192 GCCACATTCTGTTACAGGAGGA 60.027 50.000 12.58 0.00 31.51 3.71
102 391 6.446909 ACAGGAGGAGAAGAAGAAGAAAAT 57.553 37.500 0.00 0.00 0.00 1.82
118 407 4.260985 AGAAAATATGCACCACACGATGA 58.739 39.130 0.00 0.00 0.00 2.92
132 421 1.080093 GATGAACGTGCGGGAGACA 60.080 57.895 0.00 0.00 0.00 3.41
172 461 7.291567 GCTATTTCGAGCAAAATGATACTACC 58.708 38.462 0.00 0.00 42.36 3.18
195 518 5.338365 CCGTAGTAACTACTTTGTGCTAGG 58.662 45.833 0.90 0.00 37.73 3.02
220 811 7.491696 GGTAGTAAACTGCTCGATTTAATGACT 59.508 37.037 0.00 0.00 0.00 3.41
275 866 4.519730 ACAGTAGGACTATTGATCTACGGC 59.480 45.833 8.58 0.00 37.67 5.68
283 874 0.108520 TTGATCTACGGCCACGGTTC 60.109 55.000 2.24 0.00 46.48 3.62
433 1050 3.919197 GGACTGCTCTTCAAACGTACTAC 59.081 47.826 0.00 0.00 0.00 2.73
442 1059 6.365839 TCTTCAAACGTACTACTACTCGTTG 58.634 40.000 0.00 0.00 43.86 4.10
545 1291 2.419297 GGAGATGATGTGTCGAAGGCTT 60.419 50.000 0.00 0.00 0.00 4.35
578 1324 2.125147 CAAATGCCGCCGGAGAGA 60.125 61.111 7.68 0.00 0.00 3.10
622 1370 7.672240 AGAAAGAAAAACTAAGAGAGGACGAT 58.328 34.615 0.00 0.00 0.00 3.73
647 1395 3.303461 CCAACGCGTGAAGTTAAATGACA 60.303 43.478 14.98 0.00 0.00 3.58
656 1404 7.273381 GCGTGAAGTTAAATGACAGCAAAATAT 59.727 33.333 0.00 0.00 0.00 1.28
657 1405 9.767684 CGTGAAGTTAAATGACAGCAAAATATA 57.232 29.630 0.00 0.00 0.00 0.86
727 1485 1.807142 GCTAGCCTGTGAAAACTCCAC 59.193 52.381 2.29 0.00 35.23 4.02
728 1486 2.810400 GCTAGCCTGTGAAAACTCCACA 60.810 50.000 2.29 0.00 41.68 4.17
729 1487 1.680338 AGCCTGTGAAAACTCCACAC 58.320 50.000 0.00 0.00 39.36 3.82
730 1488 0.307760 GCCTGTGAAAACTCCACACG 59.692 55.000 0.00 0.00 39.36 4.49
732 1490 0.042188 CTGTGAAAACTCCACACGCG 60.042 55.000 3.53 3.53 39.36 6.01
734 1492 0.042448 GTGAAAACTCCACACGCGAC 60.042 55.000 15.93 0.00 34.81 5.19
799 1679 2.259818 CGCAGCCTGTCTCGAACT 59.740 61.111 0.00 0.00 0.00 3.01
800 1680 1.803519 CGCAGCCTGTCTCGAACTC 60.804 63.158 0.00 0.00 0.00 3.01
801 1681 1.803519 GCAGCCTGTCTCGAACTCG 60.804 63.158 0.00 0.00 41.45 4.18
1731 2640 5.946942 TTTCACAAGGCTAGAGATCTGAT 57.053 39.130 0.00 0.00 0.00 2.90
1962 2876 6.899892 ATCTGAGGAGGGAAGAAACTAAAT 57.100 37.500 0.00 0.00 0.00 1.40
1963 2877 6.054860 TCTGAGGAGGGAAGAAACTAAATG 57.945 41.667 0.00 0.00 0.00 2.32
1964 2878 5.785423 TCTGAGGAGGGAAGAAACTAAATGA 59.215 40.000 0.00 0.00 0.00 2.57
1965 2879 6.054860 TGAGGAGGGAAGAAACTAAATGAG 57.945 41.667 0.00 0.00 0.00 2.90
1966 2880 5.548056 TGAGGAGGGAAGAAACTAAATGAGT 59.452 40.000 0.00 0.00 41.56 3.41
1967 2881 6.729100 TGAGGAGGGAAGAAACTAAATGAGTA 59.271 38.462 0.00 0.00 37.44 2.59
1968 2882 7.236847 TGAGGAGGGAAGAAACTAAATGAGTAA 59.763 37.037 0.00 0.00 37.44 2.24
1969 2883 7.985589 AGGAGGGAAGAAACTAAATGAGTAAA 58.014 34.615 0.00 0.00 37.44 2.01
1970 2884 8.615705 AGGAGGGAAGAAACTAAATGAGTAAAT 58.384 33.333 0.00 0.00 37.44 1.40
1971 2885 8.678199 GGAGGGAAGAAACTAAATGAGTAAATG 58.322 37.037 0.00 0.00 37.44 2.32
1972 2886 9.449719 GAGGGAAGAAACTAAATGAGTAAATGA 57.550 33.333 0.00 0.00 37.44 2.57
1973 2887 9.454859 AGGGAAGAAACTAAATGAGTAAATGAG 57.545 33.333 0.00 0.00 37.44 2.90
1974 2888 9.232473 GGGAAGAAACTAAATGAGTAAATGAGT 57.768 33.333 0.00 0.00 37.44 3.41
2113 3031 0.244450 TTGGTTGGCGTCTAGTACCG 59.756 55.000 0.00 0.00 0.00 4.02
2125 3043 2.742589 TCTAGTACCGCGCTGATGATAG 59.257 50.000 5.61 1.07 0.00 2.08
2176 3128 7.496591 AGCACATGTTTTCAACTTCATCATTTT 59.503 29.630 0.00 0.00 0.00 1.82
2296 3248 4.868171 TGCTGTTGTCCGATCTACAATTAC 59.132 41.667 12.07 3.64 38.95 1.89
2299 3251 6.700081 GCTGTTGTCCGATCTACAATTACATA 59.300 38.462 12.07 0.00 38.95 2.29
2347 3299 7.725818 TGAATTTGCTGTTTGAATTGCATAA 57.274 28.000 0.00 0.00 35.27 1.90
2407 3359 0.318120 GGTGGTGCTGGGTTGATTTG 59.682 55.000 0.00 0.00 0.00 2.32
2448 3400 5.451798 GCATCCCAACGATTTAATTGGTCAT 60.452 40.000 5.14 0.00 43.36 3.06
2497 3468 8.268850 ACTACAATTTGCATAAGAAGTAGTGG 57.731 34.615 13.07 0.00 39.34 4.00
2525 3496 4.533311 AGATCATCCCTTTTTGGCAATTGT 59.467 37.500 7.40 0.00 0.00 2.71
2532 3503 2.215907 TTTTGGCAATTGTGACACCG 57.784 45.000 7.40 0.00 44.76 4.94
2537 3508 2.088423 GGCAATTGTGACACCGGAATA 58.912 47.619 9.46 0.00 30.49 1.75
2550 3521 1.072173 CCGGAATAGCCCATCATGTGA 59.928 52.381 0.00 0.00 0.00 3.58
2564 3535 6.250344 CATCATGTGATGTCTTTGTCACTT 57.750 37.500 13.53 0.00 45.10 3.16
2583 3554 3.934579 ACTTGTTCCGTTCGTTTGTTAGT 59.065 39.130 0.00 0.00 0.00 2.24
2757 3729 5.135383 TGCTGAATAAATAAGCTGCATCCT 58.865 37.500 1.02 0.00 37.82 3.24
2762 3734 6.606796 TGAATAAATAAGCTGCATCCTTTCCA 59.393 34.615 1.02 0.00 0.00 3.53
2773 3745 6.616774 TGCATCCTTTCCAATTTGAAAAAC 57.383 33.333 6.21 0.00 34.06 2.43
2778 3750 6.951971 TCCTTTCCAATTTGAAAAACAGGAA 58.048 32.000 7.60 0.00 34.06 3.36
2784 3756 9.898152 TTCCAATTTGAAAAACAGGAAACTAAT 57.102 25.926 0.00 0.00 40.21 1.73
2785 3757 9.323985 TCCAATTTGAAAAACAGGAAACTAATG 57.676 29.630 0.00 0.00 40.21 1.90
2838 3810 5.923733 TCTCTTATCTTCTTGGTGACCTC 57.076 43.478 2.11 0.00 0.00 3.85
2885 3857 3.702045 TGGGTGGACCTAAACAAAGTTTG 59.298 43.478 14.13 14.13 41.11 2.93
2904 3876 0.664761 GGGAACATCATCACATGCCG 59.335 55.000 0.00 0.00 0.00 5.69
2913 3885 0.324614 ATCACATGCCGTCTGGTTCA 59.675 50.000 0.00 0.00 37.67 3.18
2931 3903 5.053145 GGTTCAGATTAGGTCATAGCACTG 58.947 45.833 0.00 0.00 0.00 3.66
2932 3904 4.944619 TCAGATTAGGTCATAGCACTGG 57.055 45.455 0.00 0.00 0.00 4.00
2938 3910 0.830648 GGTCATAGCACTGGTAGGCA 59.169 55.000 0.00 0.00 0.00 4.75
3033 4005 0.969917 TGCAAGTTGTGGCTGTTGGT 60.970 50.000 4.48 0.00 0.00 3.67
3044 4016 1.205893 GGCTGTTGGTGGTGACAAAAA 59.794 47.619 0.00 0.00 46.06 1.94
3047 4019 4.298332 GCTGTTGGTGGTGACAAAAATAG 58.702 43.478 0.00 0.00 46.06 1.73
3068 4040 7.713764 ATAGTTGTGGAAAATCTTTTTGCAC 57.286 32.000 22.52 22.52 46.46 4.57
3086 4058 4.566004 TGCACGATTTAGTCTTGTAGCTT 58.434 39.130 0.00 0.00 0.00 3.74
3087 4059 4.625742 TGCACGATTTAGTCTTGTAGCTTC 59.374 41.667 0.00 0.00 0.00 3.86
3090 4179 5.289675 CACGATTTAGTCTTGTAGCTTCTGG 59.710 44.000 0.00 0.00 0.00 3.86
3092 4181 6.100004 CGATTTAGTCTTGTAGCTTCTGGAA 58.900 40.000 0.00 0.00 0.00 3.53
3154 4243 6.998968 TTGCACTTGTTTTGAAAATCCAAT 57.001 29.167 0.00 0.00 0.00 3.16
3156 4245 5.233902 TGCACTTGTTTTGAAAATCCAATCG 59.766 36.000 0.00 0.00 0.00 3.34
3214 4303 4.804139 GCATTGCTCTTTCTTTGATGGATG 59.196 41.667 0.16 0.00 0.00 3.51
3216 4305 6.395629 CATTGCTCTTTCTTTGATGGATGTT 58.604 36.000 0.00 0.00 0.00 2.71
3217 4306 6.409524 TTGCTCTTTCTTTGATGGATGTTT 57.590 33.333 0.00 0.00 0.00 2.83
3376 4465 1.606531 GAGCTGAAGGCCATGGAGT 59.393 57.895 18.40 0.00 43.05 3.85
3540 4629 0.659417 GCTTCTTCGTGACGTCGACA 60.659 55.000 17.16 0.00 39.58 4.35
3588 4677 3.787001 CGGACCAAGAGGGAGCCC 61.787 72.222 0.00 0.00 41.15 5.19
3654 4743 2.595095 CTTATGCAGGCCCGGGAA 59.405 61.111 29.31 6.50 0.00 3.97
3675 4764 1.537814 TTGATGTCCGCCGGTACAGT 61.538 55.000 1.63 0.00 0.00 3.55
3686 4775 2.646175 GGTACAGTGAGCTCCGGCA 61.646 63.158 12.15 0.00 41.70 5.69
3726 4815 0.339859 TACATCCTCAGAGCCCCTGT 59.660 55.000 3.97 0.00 43.38 4.00
3750 4839 1.599047 CTCGCAGGAGAACCACCAT 59.401 57.895 0.00 0.00 43.27 3.55
3986 5100 3.482436 ACCGGCTGTAAACAATCTTTGA 58.518 40.909 0.00 0.00 0.00 2.69
4068 5182 1.081892 CATCTGGCTCAACTTGTCCG 58.918 55.000 0.00 0.00 0.00 4.79
4072 5186 1.264288 CTGGCTCAACTTGTCCGAAAC 59.736 52.381 0.00 0.00 0.00 2.78
4108 5222 6.013379 AGGGATCTTCAGCGATTATTCTCTA 58.987 40.000 0.00 0.00 0.00 2.43
4133 5247 4.018960 ACATAGGCAGGGTCATAATCCATC 60.019 45.833 0.00 0.00 0.00 3.51
4166 5280 9.581289 TCTTTTATTTCTGATGGTTTGGTCTAA 57.419 29.630 0.00 0.00 0.00 2.10
4169 5283 5.705609 TTTCTGATGGTTTGGTCTAAAGC 57.294 39.130 4.08 4.08 44.86 3.51
4170 5284 3.686016 TCTGATGGTTTGGTCTAAAGCC 58.314 45.455 8.21 1.93 44.19 4.35
4206 5320 9.480053 GGAAAAATCAATGTGATCTTGAAGAAA 57.520 29.630 0.00 0.00 35.76 2.52
4208 5322 9.820725 AAAAATCAATGTGATCTTGAAGAAACA 57.179 25.926 14.04 14.04 35.76 2.83
4276 5391 1.032114 AGGGCCGTCAGCATTTAAGC 61.032 55.000 0.00 0.00 46.50 3.09
4302 5417 3.161866 TGTTATGGCCTGTCCTTTTTCC 58.838 45.455 3.32 0.00 35.26 3.13
4324 5439 3.125316 CCGCTGTCTGTTTTTGGACTATC 59.875 47.826 0.00 0.00 34.01 2.08
4392 5507 5.866092 GGTTTCTTTCATTTGATGCCTTCTC 59.134 40.000 0.00 0.00 0.00 2.87
4426 5541 0.548926 TTGCTATCTCCACCCACCCA 60.549 55.000 0.00 0.00 0.00 4.51
4580 5733 2.969443 ATTTTACACGCACAGCTGTC 57.031 45.000 18.64 11.13 0.00 3.51
4581 5734 1.657822 TTTTACACGCACAGCTGTCA 58.342 45.000 18.64 0.00 0.00 3.58
4582 5735 1.657822 TTTACACGCACAGCTGTCAA 58.342 45.000 18.64 1.52 0.00 3.18
4583 5736 0.934496 TTACACGCACAGCTGTCAAC 59.066 50.000 18.64 8.72 0.00 3.18
4584 5737 0.179097 TACACGCACAGCTGTCAACA 60.179 50.000 18.64 0.00 0.00 3.33
4585 5738 1.024046 ACACGCACAGCTGTCAACAA 61.024 50.000 18.64 0.00 0.00 2.83
4586 5739 0.098552 CACGCACAGCTGTCAACAAA 59.901 50.000 18.64 0.00 0.00 2.83
4587 5740 0.808125 ACGCACAGCTGTCAACAAAA 59.192 45.000 18.64 0.00 0.00 2.44
4588 5741 1.202177 ACGCACAGCTGTCAACAAAAG 60.202 47.619 18.64 4.10 0.00 2.27
4589 5742 1.063912 CGCACAGCTGTCAACAAAAGA 59.936 47.619 18.64 0.00 0.00 2.52
4590 5743 2.477694 CGCACAGCTGTCAACAAAAGAA 60.478 45.455 18.64 0.00 0.00 2.52
4591 5744 3.111098 GCACAGCTGTCAACAAAAGAAG 58.889 45.455 18.64 1.89 0.00 2.85
4592 5745 3.181497 GCACAGCTGTCAACAAAAGAAGA 60.181 43.478 18.64 0.00 0.00 2.87
4593 5746 4.675146 GCACAGCTGTCAACAAAAGAAGAA 60.675 41.667 18.64 0.00 0.00 2.52
4594 5747 5.032863 CACAGCTGTCAACAAAAGAAGAAG 58.967 41.667 18.64 0.00 0.00 2.85
4595 5748 4.943705 ACAGCTGTCAACAAAAGAAGAAGA 59.056 37.500 15.25 0.00 0.00 2.87
4596 5749 5.415701 ACAGCTGTCAACAAAAGAAGAAGAA 59.584 36.000 15.25 0.00 0.00 2.52
4597 5750 6.071952 ACAGCTGTCAACAAAAGAAGAAGAAA 60.072 34.615 15.25 0.00 0.00 2.52
4598 5751 6.808212 CAGCTGTCAACAAAAGAAGAAGAAAA 59.192 34.615 5.25 0.00 0.00 2.29
4599 5752 7.329226 CAGCTGTCAACAAAAGAAGAAGAAAAA 59.671 33.333 5.25 0.00 0.00 1.94
4619 5772 3.975168 AAACTGTACCGGTAGCAATCT 57.025 42.857 16.41 0.00 0.00 2.40
4620 5773 5.410355 AAAACTGTACCGGTAGCAATCTA 57.590 39.130 16.41 0.00 0.00 1.98
4621 5774 4.650754 AACTGTACCGGTAGCAATCTAG 57.349 45.455 16.41 7.45 0.00 2.43
4622 5775 2.361438 ACTGTACCGGTAGCAATCTAGC 59.639 50.000 16.41 0.00 39.32 3.42
4623 5776 2.361119 CTGTACCGGTAGCAATCTAGCA 59.639 50.000 16.41 5.05 41.98 3.49
4624 5777 2.100252 TGTACCGGTAGCAATCTAGCAC 59.900 50.000 16.41 1.11 41.98 4.40
4625 5778 0.464452 ACCGGTAGCAATCTAGCACC 59.536 55.000 4.49 0.00 41.98 5.01
4626 5779 2.886859 CGGTAGCAATCTAGCACCG 58.113 57.895 12.71 12.71 45.32 4.94
4627 5780 1.215655 CGGTAGCAATCTAGCACCGC 61.216 60.000 13.70 0.00 45.04 5.68
4628 5781 0.880718 GGTAGCAATCTAGCACCGCC 60.881 60.000 0.00 0.00 41.61 6.13
4629 5782 1.067416 TAGCAATCTAGCACCGCCG 59.933 57.895 0.00 0.00 36.85 6.46
4630 5783 2.971428 TAGCAATCTAGCACCGCCGC 62.971 60.000 0.00 0.00 36.85 6.53
4631 5784 3.630148 CAATCTAGCACCGCCGCG 61.630 66.667 5.59 5.59 36.85 6.46
4632 5785 4.143333 AATCTAGCACCGCCGCGT 62.143 61.111 12.58 0.00 36.85 6.01
4633 5786 3.659089 AATCTAGCACCGCCGCGTT 62.659 57.895 12.58 0.00 36.85 4.84
4634 5787 4.789075 TCTAGCACCGCCGCGTTC 62.789 66.667 12.58 0.00 36.85 3.95
4653 5806 3.033368 TCGTGGACGAACAATCAATCA 57.967 42.857 0.00 0.00 46.30 2.57
4654 5807 3.595173 TCGTGGACGAACAATCAATCAT 58.405 40.909 0.00 0.00 46.30 2.45
4655 5808 4.749976 TCGTGGACGAACAATCAATCATA 58.250 39.130 0.00 0.00 46.30 2.15
4656 5809 5.172205 TCGTGGACGAACAATCAATCATAA 58.828 37.500 0.00 0.00 46.30 1.90
4657 5810 5.290885 TCGTGGACGAACAATCAATCATAAG 59.709 40.000 0.00 0.00 46.30 1.73
4658 5811 5.502382 CGTGGACGAACAATCAATCATAAGG 60.502 44.000 0.00 0.00 43.02 2.69
4659 5812 4.881273 TGGACGAACAATCAATCATAAGGG 59.119 41.667 0.00 0.00 0.00 3.95
4660 5813 4.261197 GGACGAACAATCAATCATAAGGGC 60.261 45.833 0.00 0.00 0.00 5.19
4661 5814 3.632145 ACGAACAATCAATCATAAGGGCC 59.368 43.478 0.00 0.00 0.00 5.80
4662 5815 3.004734 CGAACAATCAATCATAAGGGCCC 59.995 47.826 16.46 16.46 0.00 5.80
4663 5816 2.586425 ACAATCAATCATAAGGGCCCG 58.414 47.619 18.44 1.05 0.00 6.13
4664 5817 2.091885 ACAATCAATCATAAGGGCCCGT 60.092 45.455 18.44 17.51 0.00 5.28
4665 5818 2.958355 CAATCAATCATAAGGGCCCGTT 59.042 45.455 17.88 13.55 0.00 4.44
4666 5819 2.341846 TCAATCATAAGGGCCCGTTC 57.658 50.000 17.88 0.00 0.00 3.95
4667 5820 0.944386 CAATCATAAGGGCCCGTTCG 59.056 55.000 17.88 7.69 0.00 3.95
4668 5821 0.179029 AATCATAAGGGCCCGTTCGG 60.179 55.000 17.88 6.33 0.00 4.30
4678 5831 3.395702 CCGTTCGGGGATCCACCA 61.396 66.667 15.23 0.00 41.20 4.17
4679 5832 2.186903 CGTTCGGGGATCCACCAG 59.813 66.667 15.23 8.96 41.20 4.00
4680 5833 2.124695 GTTCGGGGATCCACCAGC 60.125 66.667 15.23 0.00 41.20 4.85
4681 5834 2.285368 TTCGGGGATCCACCAGCT 60.285 61.111 15.23 0.00 41.20 4.24
4682 5835 2.367202 TTCGGGGATCCACCAGCTC 61.367 63.158 15.23 0.00 41.20 4.09
4683 5836 3.866582 CGGGGATCCACCAGCTCC 61.867 72.222 15.23 2.23 41.20 4.70
4684 5837 2.367512 GGGGATCCACCAGCTCCT 60.368 66.667 15.23 0.00 41.20 3.69
4685 5838 2.447714 GGGGATCCACCAGCTCCTC 61.448 68.421 15.23 0.00 41.20 3.71
4686 5839 1.690633 GGGATCCACCAGCTCCTCA 60.691 63.158 15.23 0.00 41.20 3.86
4687 5840 1.274703 GGGATCCACCAGCTCCTCAA 61.275 60.000 15.23 0.00 41.20 3.02
4688 5841 0.620556 GGATCCACCAGCTCCTCAAA 59.379 55.000 6.95 0.00 38.79 2.69
4689 5842 1.004745 GGATCCACCAGCTCCTCAAAA 59.995 52.381 6.95 0.00 38.79 2.44
4690 5843 2.357569 GGATCCACCAGCTCCTCAAAAT 60.358 50.000 6.95 0.00 38.79 1.82
4691 5844 3.117888 GGATCCACCAGCTCCTCAAAATA 60.118 47.826 6.95 0.00 38.79 1.40
4692 5845 3.350219 TCCACCAGCTCCTCAAAATAC 57.650 47.619 0.00 0.00 0.00 1.89
4693 5846 2.642311 TCCACCAGCTCCTCAAAATACA 59.358 45.455 0.00 0.00 0.00 2.29
4694 5847 2.749621 CCACCAGCTCCTCAAAATACAC 59.250 50.000 0.00 0.00 0.00 2.90
4695 5848 2.416547 CACCAGCTCCTCAAAATACACG 59.583 50.000 0.00 0.00 0.00 4.49
4696 5849 2.009774 CCAGCTCCTCAAAATACACGG 58.990 52.381 0.00 0.00 0.00 4.94
4697 5850 2.354704 CCAGCTCCTCAAAATACACGGA 60.355 50.000 0.00 0.00 0.00 4.69
4698 5851 2.932614 CAGCTCCTCAAAATACACGGAG 59.067 50.000 0.00 0.00 43.18 4.63
4700 5853 3.252974 CTCCTCAAAATACACGGAGCT 57.747 47.619 0.00 0.00 35.35 4.09
4701 5854 2.932614 CTCCTCAAAATACACGGAGCTG 59.067 50.000 0.00 0.00 35.35 4.24
4702 5855 2.009774 CCTCAAAATACACGGAGCTGG 58.990 52.381 0.00 0.00 0.00 4.85
4703 5856 2.009774 CTCAAAATACACGGAGCTGGG 58.990 52.381 0.00 0.00 0.00 4.45
4704 5857 1.094785 CAAAATACACGGAGCTGGGG 58.905 55.000 0.00 0.00 0.00 4.96
4705 5858 0.988832 AAAATACACGGAGCTGGGGA 59.011 50.000 0.00 0.00 0.00 4.81
4706 5859 0.541863 AAATACACGGAGCTGGGGAG 59.458 55.000 0.00 0.00 0.00 4.30
4707 5860 0.617820 AATACACGGAGCTGGGGAGT 60.618 55.000 0.00 0.00 0.00 3.85
4708 5861 0.260816 ATACACGGAGCTGGGGAGTA 59.739 55.000 0.00 0.00 0.00 2.59
4709 5862 0.682209 TACACGGAGCTGGGGAGTAC 60.682 60.000 0.00 0.00 0.00 2.73
4710 5863 2.363925 ACGGAGCTGGGGAGTACC 60.364 66.667 0.00 0.00 39.11 3.34
4711 5864 3.528370 CGGAGCTGGGGAGTACCG 61.528 72.222 0.00 0.00 41.60 4.02
4712 5865 2.363925 GGAGCTGGGGAGTACCGT 60.364 66.667 0.00 0.00 41.60 4.83
4713 5866 1.988406 GGAGCTGGGGAGTACCGTT 60.988 63.158 0.00 0.00 41.60 4.44
4714 5867 1.551019 GGAGCTGGGGAGTACCGTTT 61.551 60.000 0.00 0.00 41.60 3.60
4715 5868 0.108281 GAGCTGGGGAGTACCGTTTC 60.108 60.000 0.00 0.00 41.60 2.78
4716 5869 1.447314 GCTGGGGAGTACCGTTTCG 60.447 63.158 0.00 0.00 41.60 3.46
4726 5879 4.735132 CCGTTTCGGCCGCTCTGA 62.735 66.667 23.51 0.00 41.17 3.27
4727 5880 2.736995 CGTTTCGGCCGCTCTGAA 60.737 61.111 23.51 6.11 38.26 3.02
4728 5881 2.100631 CGTTTCGGCCGCTCTGAAT 61.101 57.895 23.51 0.00 39.64 2.57
4729 5882 1.635663 CGTTTCGGCCGCTCTGAATT 61.636 55.000 23.51 0.00 39.64 2.17
4730 5883 0.521735 GTTTCGGCCGCTCTGAATTT 59.478 50.000 23.51 0.00 39.64 1.82
4731 5884 1.068541 GTTTCGGCCGCTCTGAATTTT 60.069 47.619 23.51 0.00 39.64 1.82
4732 5885 0.802494 TTCGGCCGCTCTGAATTTTC 59.198 50.000 23.51 0.00 35.24 2.29
4733 5886 0.036388 TCGGCCGCTCTGAATTTTCT 60.036 50.000 23.51 0.00 0.00 2.52
4734 5887 1.206132 TCGGCCGCTCTGAATTTTCTA 59.794 47.619 23.51 0.00 0.00 2.10
4735 5888 1.594862 CGGCCGCTCTGAATTTTCTAG 59.405 52.381 14.67 0.00 0.00 2.43
4736 5889 1.332065 GGCCGCTCTGAATTTTCTAGC 59.668 52.381 0.00 7.66 35.19 3.42
4739 5892 1.004504 CGCTCTGAATTTTCTAGCGGC 60.005 52.381 22.00 0.00 46.57 6.53
4740 5893 2.009774 GCTCTGAATTTTCTAGCGGCA 58.990 47.619 1.45 0.00 31.05 5.69
4741 5894 2.031437 GCTCTGAATTTTCTAGCGGCAG 59.969 50.000 1.45 0.00 31.05 4.85
4742 5895 2.009774 TCTGAATTTTCTAGCGGCAGC 58.990 47.619 0.00 0.00 45.58 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 4.047059 CAACGGCCTGCCAGCAAG 62.047 66.667 9.17 0.00 35.37 4.01
59 72 3.499737 CAGAATGTGGCGCGTCCC 61.500 66.667 8.89 0.95 0.00 4.46
85 98 6.375455 TGGTGCATATTTTCTTCTTCTTCTCC 59.625 38.462 0.00 0.00 0.00 3.71
86 99 7.094634 TGTGGTGCATATTTTCTTCTTCTTCTC 60.095 37.037 0.00 0.00 0.00 2.87
87 100 6.716628 TGTGGTGCATATTTTCTTCTTCTTCT 59.283 34.615 0.00 0.00 0.00 2.85
102 391 1.355005 CGTTCATCGTGTGGTGCATA 58.645 50.000 0.00 0.00 34.52 3.14
123 412 1.355916 CTAGCTACGTGTCTCCCGC 59.644 63.158 0.00 0.00 0.00 6.13
124 413 0.463295 TCCTAGCTACGTGTCTCCCG 60.463 60.000 0.00 0.00 0.00 5.14
132 421 4.357996 GAAATAGCGTTTCCTAGCTACGT 58.642 43.478 7.72 0.00 46.99 3.57
134 423 4.604976 TCGAAATAGCGTTTCCTAGCTAC 58.395 43.478 10.66 0.00 46.99 3.58
172 461 5.105997 ACCTAGCACAAAGTAGTTACTACGG 60.106 44.000 15.73 12.09 41.37 4.02
195 518 8.408743 AGTCATTAAATCGAGCAGTTTACTAC 57.591 34.615 0.00 0.00 0.00 2.73
254 845 4.080687 GGCCGTAGATCAATAGTCCTACT 58.919 47.826 0.00 0.00 31.78 2.57
259 850 2.607282 CCGTGGCCGTAGATCAATAGTC 60.607 54.545 0.00 0.00 0.00 2.59
271 862 3.921521 TTTTTGAACCGTGGCCGT 58.078 50.000 0.00 0.00 0.00 5.68
290 881 7.349412 ACTCTATCGAGCAGTTTATACCTTT 57.651 36.000 0.00 0.00 41.09 3.11
291 882 6.963083 ACTCTATCGAGCAGTTTATACCTT 57.037 37.500 0.00 0.00 41.09 3.50
292 883 6.963083 AACTCTATCGAGCAGTTTATACCT 57.037 37.500 0.00 0.00 41.09 3.08
293 884 8.351461 ACTAAACTCTATCGAGCAGTTTATACC 58.649 37.037 19.09 0.00 40.26 2.73
294 885 9.733219 AACTAAACTCTATCGAGCAGTTTATAC 57.267 33.333 19.09 0.00 40.26 1.47
296 887 9.088512 CAAACTAAACTCTATCGAGCAGTTTAT 57.911 33.333 19.09 9.01 40.87 1.40
412 1003 4.796369 AGTAGTACGTTTGAAGAGCAGTC 58.204 43.478 0.00 0.00 0.00 3.51
433 1050 0.247974 CGTAGCGGACCAACGAGTAG 60.248 60.000 5.34 0.00 38.89 2.57
442 1059 0.590195 ATCGATACACGTAGCGGACC 59.410 55.000 14.13 0.00 44.12 4.46
489 1107 7.602517 TTTTGGTTGTACACAAAGGAAAATG 57.397 32.000 10.46 0.00 37.80 2.32
545 1291 4.502950 GGCATTTGGAAAATGACACCTTCA 60.503 41.667 15.14 0.00 35.75 3.02
578 1324 4.336889 TCTTTCGGTTCATCACTTCTGT 57.663 40.909 0.00 0.00 0.00 3.41
622 1370 1.937278 TTAACTTCACGCGTTGGTCA 58.063 45.000 10.22 0.00 0.00 4.02
660 1408 8.931385 AATGTATCCATTTTAACTACGTACGT 57.069 30.769 25.98 25.98 38.10 3.57
801 1681 1.446272 CCGGGCTGTTCGAGACTTC 60.446 63.158 0.00 0.00 0.00 3.01
802 1682 1.906824 TCCGGGCTGTTCGAGACTT 60.907 57.895 0.00 0.00 0.00 3.01
803 1683 2.282958 TCCGGGCTGTTCGAGACT 60.283 61.111 0.00 0.00 0.00 3.24
804 1684 2.126031 GTCCGGGCTGTTCGAGAC 60.126 66.667 0.00 0.00 0.00 3.36
805 1685 3.744719 CGTCCGGGCTGTTCGAGA 61.745 66.667 3.66 0.00 0.00 4.04
1116 2015 1.520192 CATGAATCCCACGTCCGGA 59.480 57.895 0.00 0.00 0.00 5.14
1731 2640 2.786578 GCAAAACACGCGAAAAATCTCA 59.213 40.909 15.93 0.00 0.00 3.27
1962 2876 9.778741 AAGACTGTCATTTTACTCATTTACTCA 57.221 29.630 10.88 0.00 0.00 3.41
1964 2878 8.507249 GCAAGACTGTCATTTTACTCATTTACT 58.493 33.333 10.88 0.00 0.00 2.24
1965 2879 8.507249 AGCAAGACTGTCATTTTACTCATTTAC 58.493 33.333 10.88 0.00 0.00 2.01
1966 2880 8.621532 AGCAAGACTGTCATTTTACTCATTTA 57.378 30.769 10.88 0.00 0.00 1.40
1967 2881 7.516198 AGCAAGACTGTCATTTTACTCATTT 57.484 32.000 10.88 0.00 0.00 2.32
1968 2882 8.621532 TTAGCAAGACTGTCATTTTACTCATT 57.378 30.769 10.88 0.00 0.00 2.57
1969 2883 8.621532 TTTAGCAAGACTGTCATTTTACTCAT 57.378 30.769 10.88 0.00 0.00 2.90
1970 2884 8.445275 TTTTAGCAAGACTGTCATTTTACTCA 57.555 30.769 10.88 0.00 0.00 3.41
1971 2885 9.899226 AATTTTAGCAAGACTGTCATTTTACTC 57.101 29.630 10.88 0.00 0.00 2.59
2081 2998 5.680619 ACGCCAACCAATCTGAATATAGAA 58.319 37.500 0.00 0.00 0.00 2.10
2113 3031 0.948141 GGAGCCACTATCATCAGCGC 60.948 60.000 0.00 0.00 0.00 5.92
2125 3043 2.507407 TCCCAAAATAGTGGAGCCAC 57.493 50.000 11.67 11.67 46.50 5.01
2176 3128 7.181569 TGAACATCTACATGACTACCAATGA 57.818 36.000 0.00 0.00 33.72 2.57
2268 3220 1.344438 AGATCGGACAACAGCAAGTGA 59.656 47.619 0.00 0.00 0.00 3.41
2296 3248 8.320396 ACTATCAATTGCTTATCACTGCTATG 57.680 34.615 0.00 0.00 0.00 2.23
2299 3251 8.152898 TCATACTATCAATTGCTTATCACTGCT 58.847 33.333 0.00 0.00 0.00 4.24
2328 3280 7.656542 TCTTCAATTATGCAATTCAAACAGCAA 59.343 29.630 0.00 0.00 40.76 3.91
2382 3334 0.777446 AACCCAGCACCACCACTAAT 59.223 50.000 0.00 0.00 0.00 1.73
2384 3336 1.057275 TCAACCCAGCACCACCACTA 61.057 55.000 0.00 0.00 0.00 2.74
2477 3429 6.377996 TCATGCCACTACTTCTTATGCAAATT 59.622 34.615 0.00 0.00 0.00 1.82
2497 3468 3.492137 GCCAAAAAGGGATGATCTCATGC 60.492 47.826 3.32 3.32 42.93 4.06
2525 3496 0.468226 GATGGGCTATTCCGGTGTCA 59.532 55.000 0.00 0.00 34.94 3.58
2550 3521 3.541632 ACGGAACAAGTGACAAAGACAT 58.458 40.909 0.00 0.00 0.00 3.06
2555 3526 2.348660 ACGAACGGAACAAGTGACAAA 58.651 42.857 0.00 0.00 0.00 2.83
2564 3535 3.062369 CACACTAACAAACGAACGGAACA 59.938 43.478 0.00 0.00 0.00 3.18
2727 3699 6.420008 GCAGCTTATTTATTCAGCAGGAAATG 59.580 38.462 0.00 0.00 39.39 2.32
2757 3729 9.726438 TTAGTTTCCTGTTTTTCAAATTGGAAA 57.274 25.926 3.75 3.75 39.03 3.13
2762 3734 8.729805 TGCATTAGTTTCCTGTTTTTCAAATT 57.270 26.923 0.00 0.00 0.00 1.82
2773 3745 2.134789 AGCCCTGCATTAGTTTCCTG 57.865 50.000 0.00 0.00 0.00 3.86
2778 3750 4.010349 GACTTGTTAGCCCTGCATTAGTT 58.990 43.478 0.00 0.00 0.00 2.24
2784 3756 2.161855 CATTGACTTGTTAGCCCTGCA 58.838 47.619 0.00 0.00 0.00 4.41
2785 3757 2.162408 GTCATTGACTTGTTAGCCCTGC 59.838 50.000 9.59 0.00 0.00 4.85
2861 3833 2.158519 ACTTTGTTTAGGTCCACCCAGG 60.159 50.000 0.00 0.00 36.42 4.45
2885 3857 0.664761 CGGCATGTGATGATGTTCCC 59.335 55.000 0.00 0.00 0.00 3.97
2904 3876 5.163405 TGCTATGACCTAATCTGAACCAGAC 60.163 44.000 0.00 0.00 43.63 3.51
2913 3885 4.835615 CCTACCAGTGCTATGACCTAATCT 59.164 45.833 0.00 0.00 0.00 2.40
2931 3903 4.117685 CGTACCACTTATCTTTGCCTACC 58.882 47.826 0.00 0.00 0.00 3.18
2932 3904 5.002464 TCGTACCACTTATCTTTGCCTAC 57.998 43.478 0.00 0.00 0.00 3.18
3033 4005 6.531503 TTTCCACAACTATTTTTGTCACCA 57.468 33.333 0.00 0.00 37.62 4.17
3044 4016 6.420604 CGTGCAAAAAGATTTTCCACAACTAT 59.579 34.615 9.53 0.00 34.62 2.12
3047 4019 4.564769 TCGTGCAAAAAGATTTTCCACAAC 59.435 37.500 9.53 3.01 34.62 3.32
3068 4040 5.651530 TCCAGAAGCTACAAGACTAAATCG 58.348 41.667 0.00 0.00 0.00 3.34
3086 4058 2.619931 TGGATTCAGACACCTTCCAGA 58.380 47.619 0.00 0.00 32.80 3.86
3087 4059 3.276857 CATGGATTCAGACACCTTCCAG 58.723 50.000 0.00 0.00 39.68 3.86
3090 4179 3.012518 CCACATGGATTCAGACACCTTC 58.987 50.000 0.00 0.00 37.39 3.46
3092 4181 2.269023 TCCACATGGATTCAGACACCT 58.731 47.619 0.00 0.00 39.78 4.00
3154 4243 5.294356 ACATTTAGCTCAAACTGTACACGA 58.706 37.500 0.00 0.00 0.00 4.35
3156 4245 8.531530 CAAAAACATTTAGCTCAAACTGTACAC 58.468 33.333 0.00 0.00 0.00 2.90
3214 4303 4.202050 TGGCTGCTCTTCTTTTCAAGAAAC 60.202 41.667 0.00 0.00 46.13 2.78
3216 4305 3.554934 TGGCTGCTCTTCTTTTCAAGAA 58.445 40.909 0.00 0.00 44.82 2.52
3217 4306 3.213206 TGGCTGCTCTTCTTTTCAAGA 57.787 42.857 0.00 0.00 35.26 3.02
3267 4356 6.537453 TTCACAACCTGGAATTTTGAAGAA 57.463 33.333 0.00 2.59 0.00 2.52
3279 4368 3.318839 TCTCAATTGCTTTCACAACCTGG 59.681 43.478 0.00 0.00 31.03 4.45
3324 4413 4.445448 GGGTGATTCTCAGCAATAGATGGT 60.445 45.833 8.41 0.00 45.96 3.55
3326 4415 4.755629 CAGGGTGATTCTCAGCAATAGATG 59.244 45.833 8.41 0.00 45.96 2.90
3331 4420 1.005097 TGCAGGGTGATTCTCAGCAAT 59.995 47.619 8.41 0.00 45.96 3.56
3376 4465 2.376109 GTCGATGTCTACCTTCTGGGA 58.624 52.381 0.00 0.00 38.76 4.37
3540 4629 0.033504 CGTAGCCCGCCATGAAGTAT 59.966 55.000 0.00 0.00 0.00 2.12
3588 4677 0.458716 GGAAGAAGCCCTCGAACGAG 60.459 60.000 15.94 15.94 41.63 4.18
3639 4728 0.754957 CAAATTCCCGGGCCTGCATA 60.755 55.000 18.49 0.00 0.00 3.14
3643 4732 0.684153 ACATCAAATTCCCGGGCCTG 60.684 55.000 18.49 3.88 0.00 4.85
3645 4734 1.391933 GGACATCAAATTCCCGGGCC 61.392 60.000 18.49 2.55 0.00 5.80
3654 4743 0.250793 TGTACCGGCGGACATCAAAT 59.749 50.000 35.78 10.16 0.00 2.32
3675 4764 4.399395 CAGGCTTGCCGGAGCTCA 62.399 66.667 17.19 0.00 42.32 4.26
3743 4832 1.941377 ATGACAATGGCAATGGTGGT 58.059 45.000 7.57 0.00 0.00 4.16
3750 4839 4.308265 CAACACATCAATGACAATGGCAA 58.692 39.130 0.00 0.00 0.00 4.52
3862 4966 9.435688 TTCGAGTTTAAAATCTGAATCTGATCA 57.564 29.630 13.26 0.00 0.00 2.92
4012 5126 9.643693 CAATTGCTCAGTTTGTAATCCTTAATT 57.356 29.630 0.00 0.00 0.00 1.40
4013 5127 8.806146 ACAATTGCTCAGTTTGTAATCCTTAAT 58.194 29.630 5.05 0.00 32.09 1.40
4014 5128 8.177119 ACAATTGCTCAGTTTGTAATCCTTAA 57.823 30.769 5.05 0.00 32.09 1.85
4015 5129 7.446931 TGACAATTGCTCAGTTTGTAATCCTTA 59.553 33.333 5.05 0.00 33.92 2.69
4016 5130 6.265196 TGACAATTGCTCAGTTTGTAATCCTT 59.735 34.615 5.05 0.00 33.92 3.36
4017 5131 5.769662 TGACAATTGCTCAGTTTGTAATCCT 59.230 36.000 5.05 0.00 33.92 3.24
4018 5132 6.012658 TGACAATTGCTCAGTTTGTAATCC 57.987 37.500 5.05 0.00 33.92 3.01
4022 5136 5.069318 TGGATGACAATTGCTCAGTTTGTA 58.931 37.500 5.05 0.00 33.92 2.41
4029 5143 2.362736 GAGCTGGATGACAATTGCTCA 58.637 47.619 5.05 9.07 44.19 4.26
4030 5144 2.362736 TGAGCTGGATGACAATTGCTC 58.637 47.619 5.05 4.31 44.77 4.26
4033 5147 4.553756 CAGATGAGCTGGATGACAATTG 57.446 45.455 3.24 3.24 41.07 2.32
4068 5182 1.444895 CCTTGCCAGCATGCGTTTC 60.445 57.895 13.01 3.73 31.97 2.78
4072 5186 2.831742 ATCCCTTGCCAGCATGCG 60.832 61.111 13.01 7.31 31.97 4.73
4108 5222 3.073062 GGATTATGACCCTGCCTATGTGT 59.927 47.826 0.00 0.00 0.00 3.72
4152 5266 6.122964 AGAATAGGCTTTAGACCAAACCATC 58.877 40.000 0.00 0.00 0.00 3.51
4167 5281 9.259832 ACATTGATTTTTCCTAAAGAATAGGCT 57.740 29.630 0.00 0.00 33.44 4.58
4168 5282 9.305925 CACATTGATTTTTCCTAAAGAATAGGC 57.694 33.333 0.00 0.00 33.44 3.93
4206 5320 3.225104 TGCCTTTTCTGATGCTCTTTGT 58.775 40.909 0.00 0.00 0.00 2.83
4208 5322 4.342359 AGATGCCTTTTCTGATGCTCTTT 58.658 39.130 0.00 0.00 0.00 2.52
4256 5371 1.745827 GCTTAAATGCTGACGGCCCTA 60.746 52.381 3.22 0.00 40.92 3.53
4276 5391 4.871933 AAGGACAGGCCATAACAAAAAG 57.128 40.909 5.01 0.00 40.02 2.27
4302 5417 1.308998 AGTCCAAAAACAGACAGCGG 58.691 50.000 0.00 0.00 35.38 5.52
4324 5439 3.544356 GCATCTGCATCATGACATGAG 57.456 47.619 22.00 14.94 43.53 2.90
4392 5507 2.100631 GCAATGGACGGTCACGAGG 61.101 63.158 10.76 0.00 44.60 4.63
4426 5541 4.282703 TGGGACGAGTTAAAAACTAGAGCT 59.717 41.667 0.00 0.00 43.03 4.09
4479 5595 2.108278 AACCACGGCAGGACCAGTAC 62.108 60.000 0.00 0.00 39.03 2.73
4480 5596 0.542467 TAACCACGGCAGGACCAGTA 60.542 55.000 0.00 0.00 39.03 2.74
4516 5669 2.014068 GCCATCCACTAGTTCCTGCAC 61.014 57.143 0.00 0.00 0.00 4.57
4597 5750 4.648651 AGATTGCTACCGGTACAGTTTTT 58.351 39.130 11.16 0.00 0.00 1.94
4598 5751 4.281898 AGATTGCTACCGGTACAGTTTT 57.718 40.909 11.16 1.98 0.00 2.43
4599 5752 3.975168 AGATTGCTACCGGTACAGTTT 57.025 42.857 11.16 3.84 0.00 2.66
4600 5753 3.181478 GCTAGATTGCTACCGGTACAGTT 60.181 47.826 11.16 5.93 0.00 3.16
4601 5754 2.361438 GCTAGATTGCTACCGGTACAGT 59.639 50.000 11.16 10.71 0.00 3.55
4602 5755 2.361119 TGCTAGATTGCTACCGGTACAG 59.639 50.000 11.16 4.88 0.00 2.74
4603 5756 2.100252 GTGCTAGATTGCTACCGGTACA 59.900 50.000 11.16 11.30 0.00 2.90
4604 5757 2.545322 GGTGCTAGATTGCTACCGGTAC 60.545 54.545 11.16 8.66 0.00 3.34
4605 5758 1.684983 GGTGCTAGATTGCTACCGGTA 59.315 52.381 14.95 14.95 0.00 4.02
4606 5759 0.464452 GGTGCTAGATTGCTACCGGT 59.536 55.000 13.98 13.98 0.00 5.28
4607 5760 0.597637 CGGTGCTAGATTGCTACCGG 60.598 60.000 0.00 0.00 45.02 5.28
4608 5761 2.886859 CGGTGCTAGATTGCTACCG 58.113 57.895 12.57 12.57 44.25 4.02
4609 5762 0.880718 GGCGGTGCTAGATTGCTACC 60.881 60.000 0.00 0.00 33.75 3.18
4610 5763 1.215655 CGGCGGTGCTAGATTGCTAC 61.216 60.000 0.00 0.00 0.00 3.58
4611 5764 1.067416 CGGCGGTGCTAGATTGCTA 59.933 57.895 0.00 0.00 0.00 3.49
4612 5765 2.202932 CGGCGGTGCTAGATTGCT 60.203 61.111 0.00 0.00 0.00 3.91
4613 5766 3.941836 GCGGCGGTGCTAGATTGC 61.942 66.667 9.78 0.00 0.00 3.56
4614 5767 3.630148 CGCGGCGGTGCTAGATTG 61.630 66.667 15.84 0.00 0.00 2.67
4615 5768 3.659089 AACGCGGCGGTGCTAGATT 62.659 57.895 27.37 6.04 0.00 2.40
4616 5769 4.143333 AACGCGGCGGTGCTAGAT 62.143 61.111 27.37 0.00 0.00 1.98
4617 5770 4.789075 GAACGCGGCGGTGCTAGA 62.789 66.667 27.37 0.00 0.00 2.43
4634 5787 5.463499 TTATGATTGATTGTTCGTCCACG 57.537 39.130 0.00 0.00 41.45 4.94
4635 5788 5.220854 CCCTTATGATTGATTGTTCGTCCAC 60.221 44.000 0.00 0.00 0.00 4.02
4636 5789 4.881273 CCCTTATGATTGATTGTTCGTCCA 59.119 41.667 0.00 0.00 0.00 4.02
4637 5790 4.261197 GCCCTTATGATTGATTGTTCGTCC 60.261 45.833 0.00 0.00 0.00 4.79
4638 5791 4.261197 GGCCCTTATGATTGATTGTTCGTC 60.261 45.833 0.00 0.00 0.00 4.20
4639 5792 3.632145 GGCCCTTATGATTGATTGTTCGT 59.368 43.478 0.00 0.00 0.00 3.85
4640 5793 3.004734 GGGCCCTTATGATTGATTGTTCG 59.995 47.826 17.04 0.00 0.00 3.95
4641 5794 3.004734 CGGGCCCTTATGATTGATTGTTC 59.995 47.826 22.43 0.00 0.00 3.18
4642 5795 2.958355 CGGGCCCTTATGATTGATTGTT 59.042 45.455 22.43 0.00 0.00 2.83
4643 5796 2.091885 ACGGGCCCTTATGATTGATTGT 60.092 45.455 22.43 1.65 0.00 2.71
4644 5797 2.586425 ACGGGCCCTTATGATTGATTG 58.414 47.619 22.43 0.90 0.00 2.67
4645 5798 3.222603 GAACGGGCCCTTATGATTGATT 58.777 45.455 22.43 0.00 0.00 2.57
4646 5799 2.810400 CGAACGGGCCCTTATGATTGAT 60.810 50.000 22.43 0.00 0.00 2.57
4647 5800 1.474320 CGAACGGGCCCTTATGATTGA 60.474 52.381 22.43 0.00 0.00 2.57
4648 5801 0.944386 CGAACGGGCCCTTATGATTG 59.056 55.000 22.43 3.46 0.00 2.67
4649 5802 0.179029 CCGAACGGGCCCTTATGATT 60.179 55.000 22.43 4.01 0.00 2.57
4650 5803 1.450211 CCGAACGGGCCCTTATGAT 59.550 57.895 22.43 0.00 0.00 2.45
4651 5804 2.904905 CCGAACGGGCCCTTATGA 59.095 61.111 22.43 0.00 0.00 2.15
4661 5814 3.385749 CTGGTGGATCCCCGAACGG 62.386 68.421 9.90 6.25 34.77 4.44
4662 5815 2.186903 CTGGTGGATCCCCGAACG 59.813 66.667 9.90 0.00 34.77 3.95
4663 5816 2.124695 GCTGGTGGATCCCCGAAC 60.125 66.667 9.90 0.00 34.77 3.95
4664 5817 2.285368 AGCTGGTGGATCCCCGAA 60.285 61.111 9.90 0.00 34.77 4.30
4665 5818 2.764128 GAGCTGGTGGATCCCCGA 60.764 66.667 9.90 0.00 34.77 5.14
4666 5819 3.866582 GGAGCTGGTGGATCCCCG 61.867 72.222 9.90 7.80 44.19 5.73
4670 5823 2.496899 TTTTGAGGAGCTGGTGGATC 57.503 50.000 0.00 0.00 0.00 3.36
4671 5824 3.266772 TGTATTTTGAGGAGCTGGTGGAT 59.733 43.478 0.00 0.00 0.00 3.41
4672 5825 2.642311 TGTATTTTGAGGAGCTGGTGGA 59.358 45.455 0.00 0.00 0.00 4.02
4673 5826 2.749621 GTGTATTTTGAGGAGCTGGTGG 59.250 50.000 0.00 0.00 0.00 4.61
4674 5827 2.416547 CGTGTATTTTGAGGAGCTGGTG 59.583 50.000 0.00 0.00 0.00 4.17
4675 5828 2.615493 CCGTGTATTTTGAGGAGCTGGT 60.615 50.000 0.00 0.00 0.00 4.00
4676 5829 2.009774 CCGTGTATTTTGAGGAGCTGG 58.990 52.381 0.00 0.00 0.00 4.85
4677 5830 2.932614 CTCCGTGTATTTTGAGGAGCTG 59.067 50.000 0.00 0.00 41.48 4.24
4678 5831 3.252974 CTCCGTGTATTTTGAGGAGCT 57.747 47.619 0.00 0.00 41.48 4.09
4681 5834 2.354704 CCAGCTCCGTGTATTTTGAGGA 60.355 50.000 0.00 0.00 0.00 3.71
4682 5835 2.009774 CCAGCTCCGTGTATTTTGAGG 58.990 52.381 0.00 0.00 0.00 3.86
4683 5836 2.009774 CCCAGCTCCGTGTATTTTGAG 58.990 52.381 0.00 0.00 0.00 3.02
4684 5837 1.339631 CCCCAGCTCCGTGTATTTTGA 60.340 52.381 0.00 0.00 0.00 2.69
4685 5838 1.094785 CCCCAGCTCCGTGTATTTTG 58.905 55.000 0.00 0.00 0.00 2.44
4686 5839 0.988832 TCCCCAGCTCCGTGTATTTT 59.011 50.000 0.00 0.00 0.00 1.82
4687 5840 0.541863 CTCCCCAGCTCCGTGTATTT 59.458 55.000 0.00 0.00 0.00 1.40
4688 5841 0.617820 ACTCCCCAGCTCCGTGTATT 60.618 55.000 0.00 0.00 0.00 1.89
4689 5842 0.260816 TACTCCCCAGCTCCGTGTAT 59.739 55.000 0.00 0.00 0.00 2.29
4690 5843 0.682209 GTACTCCCCAGCTCCGTGTA 60.682 60.000 0.00 0.00 0.00 2.90
4691 5844 1.982938 GTACTCCCCAGCTCCGTGT 60.983 63.158 0.00 0.00 0.00 4.49
4692 5845 2.722201 GGTACTCCCCAGCTCCGTG 61.722 68.421 0.00 0.00 0.00 4.94
4693 5846 2.363925 GGTACTCCCCAGCTCCGT 60.364 66.667 0.00 0.00 0.00 4.69
4694 5847 3.528370 CGGTACTCCCCAGCTCCG 61.528 72.222 0.00 0.00 34.41 4.63
4695 5848 1.551019 AAACGGTACTCCCCAGCTCC 61.551 60.000 0.00 0.00 0.00 4.70
4696 5849 0.108281 GAAACGGTACTCCCCAGCTC 60.108 60.000 0.00 0.00 0.00 4.09
4697 5850 1.885163 CGAAACGGTACTCCCCAGCT 61.885 60.000 0.00 0.00 0.00 4.24
4698 5851 1.447314 CGAAACGGTACTCCCCAGC 60.447 63.158 0.00 0.00 0.00 4.85
4699 5852 1.217244 CCGAAACGGTACTCCCCAG 59.783 63.158 1.80 0.00 42.73 4.45
4700 5853 3.379880 CCGAAACGGTACTCCCCA 58.620 61.111 1.80 0.00 42.73 4.96
4710 5863 1.635663 AATTCAGAGCGGCCGAAACG 61.636 55.000 33.48 14.37 0.00 3.60
4711 5864 0.521735 AAATTCAGAGCGGCCGAAAC 59.478 50.000 33.48 18.74 0.00 2.78
4712 5865 1.199097 GAAAATTCAGAGCGGCCGAAA 59.801 47.619 33.48 14.37 0.00 3.46
4713 5866 0.802494 GAAAATTCAGAGCGGCCGAA 59.198 50.000 33.48 14.93 0.00 4.30
4714 5867 0.036388 AGAAAATTCAGAGCGGCCGA 60.036 50.000 33.48 6.95 0.00 5.54
4715 5868 1.594862 CTAGAAAATTCAGAGCGGCCG 59.405 52.381 24.05 24.05 0.00 6.13
4716 5869 1.332065 GCTAGAAAATTCAGAGCGGCC 59.668 52.381 0.00 0.00 31.65 6.13
4717 5870 2.746623 GCTAGAAAATTCAGAGCGGC 57.253 50.000 0.00 0.00 31.65 6.53
4720 5873 2.009774 TGCCGCTAGAAAATTCAGAGC 58.990 47.619 0.00 9.01 35.98 4.09
4721 5874 2.031437 GCTGCCGCTAGAAAATTCAGAG 59.969 50.000 0.00 0.00 0.00 3.35
4722 5875 2.009774 GCTGCCGCTAGAAAATTCAGA 58.990 47.619 0.00 0.00 0.00 3.27
4723 5876 2.012673 AGCTGCCGCTAGAAAATTCAG 58.987 47.619 0.00 0.00 46.79 3.02
4724 5877 2.113860 AGCTGCCGCTAGAAAATTCA 57.886 45.000 0.00 0.00 46.79 2.57


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

AutoCloner maintained by Alex Coulton.