Multiple sequence alignment - TraesCS5D01G505800

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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 TraesCS5D01G505800 chr5D 100.000 7364 0 0 1 7364 531537347 531544710 0.000000e+00 13599.0
1 TraesCS5D01G505800 chr5D 100.000 1947 0 0 7590 9536 531544936 531546882 0.000000e+00 3596.0
2 TraesCS5D01G505800 chr5D 88.855 978 93 15 1750 2716 531806002 531806974 0.000000e+00 1188.0
3 TraesCS5D01G505800 chr5D 88.855 978 90 13 1750 2716 531827490 531828459 0.000000e+00 1184.0
4 TraesCS5D01G505800 chr5D 88.528 985 90 14 1750 2716 531839064 531840043 0.000000e+00 1171.0
5 TraesCS5D01G505800 chr5D 88.332 977 100 11 1750 2716 531803994 531804966 0.000000e+00 1160.0
6 TraesCS5D01G505800 chr5D 88.265 980 95 16 1750 2714 531831074 531832048 0.000000e+00 1155.0
7 TraesCS5D01G505800 chr5D 88.098 983 89 17 1752 2716 531837108 531838080 0.000000e+00 1142.0
8 TraesCS5D01G505800 chr5D 88.049 979 95 15 1749 2716 531833084 531834051 0.000000e+00 1140.0
9 TraesCS5D01G505800 chr5D 87.820 977 96 15 1750 2716 531821909 531822872 0.000000e+00 1123.0
10 TraesCS5D01G505800 chr5D 89.513 534 47 6 327 855 531826955 531827484 0.000000e+00 667.0
11 TraesCS5D01G505800 chr5D 88.454 537 52 8 327 856 531803456 531803989 2.900000e-179 640.0
12 TraesCS5D01G505800 chr5D 88.290 538 56 5 327 859 531836569 531837104 1.040000e-178 638.0
13 TraesCS5D01G505800 chr5D 88.104 538 56 7 327 859 531825354 531825888 4.860000e-177 632.0
14 TraesCS5D01G505800 chr5D 88.082 537 56 7 330 859 531830537 531831072 1.750000e-176 630.0
15 TraesCS5D01G505800 chr5D 75.944 503 77 23 7621 8085 491536128 491535632 1.610000e-52 219.0
16 TraesCS5D01G505800 chr4A 92.685 5701 260 59 1 5648 640813254 640807658 0.000000e+00 8072.0
17 TraesCS5D01G505800 chr4A 93.376 1555 80 16 5645 7192 640807575 640806037 0.000000e+00 2279.0
18 TraesCS5D01G505800 chr4A 93.919 1332 67 3 7592 8915 640805658 640804333 0.000000e+00 1999.0
19 TraesCS5D01G505800 chr4A 89.796 588 47 8 8955 9535 640804329 640803748 0.000000e+00 741.0
20 TraesCS5D01G505800 chr4A 96.875 32 1 0 7212 7243 640806039 640806008 5.000000e-03 54.7
21 TraesCS5D01G505800 chr5B 90.041 2661 207 30 1783 4402 670925412 670928055 0.000000e+00 3393.0
22 TraesCS5D01G505800 chr5B 92.330 1408 58 15 7846 9241 670931906 670933275 0.000000e+00 1956.0
23 TraesCS5D01G505800 chr5B 89.205 1408 127 13 327 1727 670923895 670925284 0.000000e+00 1735.0
24 TraesCS5D01G505800 chr5B 91.442 1262 73 11 4434 5670 670928056 670929307 0.000000e+00 1700.0
25 TraesCS5D01G505800 chr5B 89.425 1286 105 7 5669 6951 670929523 670930780 0.000000e+00 1592.0
26 TraesCS5D01G505800 chr5B 89.118 533 51 5 327 854 670989362 670989892 0.000000e+00 656.0
27 TraesCS5D01G505800 chr5B 88.312 539 56 5 327 859 670994907 670995444 2.900000e-179 640.0
28 TraesCS5D01G505800 chr5B 85.644 606 49 19 6759 7364 670930588 670931155 3.810000e-168 603.0
29 TraesCS5D01G505800 chr5B 85.263 285 14 12 7592 7849 670931553 670931836 1.580000e-67 268.0
30 TraesCS5D01G505800 chr3D 93.598 328 20 1 1 328 505171644 505171318 1.110000e-133 488.0
31 TraesCS5D01G505800 chr3D 92.683 328 24 0 1 328 104673843 104674170 3.120000e-129 473.0
32 TraesCS5D01G505800 chr7D 93.293 328 22 0 1 328 242604981 242605308 1.440000e-132 484.0
33 TraesCS5D01G505800 chr7A 92.988 328 23 0 1 328 165898070 165897743 6.700000e-131 479.0
34 TraesCS5D01G505800 chr2B 92.988 328 23 0 1 328 264568420 264568747 6.700000e-131 479.0
35 TraesCS5D01G505800 chr2B 92.988 328 22 1 1 328 784908975 784908649 2.410000e-130 477.0
36 TraesCS5D01G505800 chr6D 92.683 328 24 0 1 328 132063833 132063506 3.120000e-129 473.0
37 TraesCS5D01G505800 chr6D 92.683 328 23 1 1 328 72345713 72346039 1.120000e-128 472.0
38 TraesCS5D01G505800 chr4D 92.378 328 25 0 1 328 309779690 309779363 1.450000e-127 468.0
39 TraesCS5D01G505800 chr5A 77.445 501 72 24 7620 8085 613747227 613746733 2.640000e-65 261.0
40 TraesCS5D01G505800 chr4B 100.000 28 0 0 4265 4292 165843242 165843269 1.700000e-02 52.8


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 TraesCS5D01G505800 chr5D 531537347 531546882 9535 False 8597.500000 13599 100.0000 1 9536 2 chr5D.!!$F1 9535
1 TraesCS5D01G505800 chr5D 531803456 531806974 3518 False 996.000000 1188 88.5470 327 2716 3 chr5D.!!$F2 2389
2 TraesCS5D01G505800 chr5D 531821909 531840043 18134 False 948.200000 1184 88.3604 327 2716 10 chr5D.!!$F3 2389
3 TraesCS5D01G505800 chr4A 640803748 640813254 9506 True 2629.140000 8072 93.3302 1 9535 5 chr4A.!!$R1 9534
4 TraesCS5D01G505800 chr5B 670923895 670933275 9380 False 1606.714286 3393 89.0500 327 9241 7 chr5B.!!$F3 8914
5 TraesCS5D01G505800 chr5B 670989362 670989892 530 False 656.000000 656 89.1180 327 854 1 chr5B.!!$F1 527
6 TraesCS5D01G505800 chr5B 670994907 670995444 537 False 640.000000 640 88.3120 327 859 1 chr5B.!!$F2 532

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
315 316 0.041238 TCCTCCGATGTCAGGGAGTT 59.959 55.000 17.21 0.00 46.83 3.01 F
1360 6498 1.831580 AGCAAGAAGGCTGATTCCAC 58.168 50.000 0.00 0.00 43.89 4.02 F
1967 8798 0.036010 GCTTGCTGCCTCCACTCTAA 60.036 55.000 0.00 0.00 35.15 2.10 F
2419 12850 0.687920 TGGTTGGCGTGGTTCATAGA 59.312 50.000 0.00 0.00 0.00 1.98 F
3136 21590 0.804989 GAGTGGGAAATGCGGTTCAG 59.195 55.000 2.06 0.00 0.00 3.02 F
3138 21592 0.958822 GTGGGAAATGCGGTTCAGTT 59.041 50.000 2.06 0.00 35.44 3.16 F
4285 22746 1.197721 GGCAAGGTTGTCAGAATCACG 59.802 52.381 0.00 0.00 31.86 4.35 F
4876 23338 1.555477 CCCGTTCACAAAAGTTGCAC 58.445 50.000 0.00 0.00 0.00 4.57 F
6409 25203 0.463654 TCAATCACCATGCCCTACGC 60.464 55.000 0.00 0.00 38.31 4.42 F
6799 25597 0.387202 CCGCGACATGAGAGGAAGAT 59.613 55.000 8.23 0.00 0.00 2.40 F
8436 27503 0.512952 AGCAGCTACGCGAAAACTTG 59.487 50.000 15.93 4.37 36.85 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 6830 1.174712 AGCATGTGACAACTGGTGGC 61.175 55.000 0.00 0.00 34.82 5.01 R
3074 21527 1.960417 TCATGCGTTGTGTGGAAAGA 58.040 45.000 0.00 0.00 0.00 2.52 R
3703 22164 4.242475 CGTATTGACAAGCTTGTGAGGTA 58.758 43.478 35.67 20.14 42.43 3.08 R
4092 22553 1.331214 CAGCTGTGTTCAACCCCAAT 58.669 50.000 5.25 0.00 0.00 3.16 R
4264 22725 2.508526 GTGATTCTGACAACCTTGCCT 58.491 47.619 0.00 0.00 0.00 4.75 R
4876 23338 2.989166 GGAAGCTTGAAAATTGGAAGCG 59.011 45.455 2.10 0.00 45.53 4.68 R
6273 25067 2.563297 GGGCAAAGTCCTAAACCCG 58.437 57.895 0.00 0.00 0.00 5.28 R
6674 25472 0.916086 TGGGCCGTGATGGTTCTAAT 59.084 50.000 0.00 0.00 41.21 1.73 R
8401 27468 1.199327 CTGCTCAAGTGCCATTGTCTG 59.801 52.381 0.00 0.00 0.00 3.51 R
8448 27515 0.673644 CCACCACATTCACGACCTCC 60.674 60.000 0.00 0.00 0.00 4.30 R
9413 28505 0.251564 CTGGGGCATAACACCAACCA 60.252 55.000 0.00 0.00 33.13 3.67 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
32 33 3.482274 CGAGATTCGATCGTCGGTATCTC 60.482 52.174 15.94 23.38 44.78 2.75
56 57 6.832384 TCCATACCTAGTTCAATCTCGTTACT 59.168 38.462 0.00 0.00 0.00 2.24
59 60 5.014858 ACCTAGTTCAATCTCGTTACTGGA 58.985 41.667 0.00 0.00 0.00 3.86
71 72 6.675987 TCTCGTTACTGGAAAGTCTCTTTAC 58.324 40.000 0.00 0.00 0.00 2.01
72 73 6.489361 TCTCGTTACTGGAAAGTCTCTTTACT 59.511 38.462 6.12 0.00 0.00 2.24
76 77 7.599245 CGTTACTGGAAAGTCTCTTTACTCATT 59.401 37.037 6.12 0.00 0.00 2.57
77 78 8.927721 GTTACTGGAAAGTCTCTTTACTCATTC 58.072 37.037 6.12 0.00 0.00 2.67
79 80 8.423906 ACTGGAAAGTCTCTTTACTCATTCTA 57.576 34.615 6.12 0.00 0.00 2.10
95 96 8.423906 ACTCATTCTATAATACAAGATCCCGT 57.576 34.615 0.00 0.00 0.00 5.28
97 98 7.097192 TCATTCTATAATACAAGATCCCGTGC 58.903 38.462 0.00 0.00 0.00 5.34
98 99 5.401531 TCTATAATACAAGATCCCGTGCC 57.598 43.478 0.00 0.00 0.00 5.01
99 100 5.084519 TCTATAATACAAGATCCCGTGCCT 58.915 41.667 0.00 0.00 0.00 4.75
100 101 6.250711 TCTATAATACAAGATCCCGTGCCTA 58.749 40.000 0.00 0.00 0.00 3.93
102 103 2.973694 TACAAGATCCCGTGCCTAAC 57.026 50.000 0.00 0.00 0.00 2.34
103 104 1.276622 ACAAGATCCCGTGCCTAACT 58.723 50.000 0.00 0.00 0.00 2.24
104 105 1.207329 ACAAGATCCCGTGCCTAACTC 59.793 52.381 0.00 0.00 0.00 3.01
105 106 1.207089 CAAGATCCCGTGCCTAACTCA 59.793 52.381 0.00 0.00 0.00 3.41
106 107 1.794714 AGATCCCGTGCCTAACTCAT 58.205 50.000 0.00 0.00 0.00 2.90
121 122 6.676456 GCCTAACTCATTAGTCACATTGCTTG 60.676 42.308 0.00 0.00 36.77 4.01
187 188 1.283905 TCTCCCTCATACGGAGTGACA 59.716 52.381 3.90 0.00 46.09 3.58
192 193 3.133003 CCCTCATACGGAGTGACAAATCT 59.867 47.826 0.00 0.00 45.73 2.40
227 228 2.092323 GCCAACCCAATAGACACCTTC 58.908 52.381 0.00 0.00 0.00 3.46
272 273 3.313012 TGATCACCCAGTTACGAAGTG 57.687 47.619 0.00 0.00 45.73 3.16
315 316 0.041238 TCCTCCGATGTCAGGGAGTT 59.959 55.000 17.21 0.00 46.83 3.01
352 3473 4.349342 AGGTAGAAATGCTCATAAGGAGGG 59.651 45.833 0.00 0.00 44.22 4.30
355 3476 5.198602 AGAAATGCTCATAAGGAGGGTTT 57.801 39.130 0.00 0.00 44.22 3.27
360 3481 2.685388 GCTCATAAGGAGGGTTTGAAGC 59.315 50.000 0.00 0.00 44.22 3.86
361 3482 3.873801 GCTCATAAGGAGGGTTTGAAGCA 60.874 47.826 0.00 0.00 44.22 3.91
519 3641 9.657419 ATTCATTGGACTTGTTTTCATATTTCC 57.343 29.630 0.00 0.00 0.00 3.13
689 3811 5.503927 CCCCATGGATATCAGATAAGGTTG 58.496 45.833 15.22 0.00 0.00 3.77
690 3812 5.251468 CCCCATGGATATCAGATAAGGTTGA 59.749 44.000 15.22 0.00 0.00 3.18
692 3814 6.656693 CCCATGGATATCAGATAAGGTTGAAC 59.343 42.308 15.22 0.00 0.00 3.18
715 3841 6.991938 ACCTTTTAATGCATTAGTTCAGCAA 58.008 32.000 18.13 6.35 42.15 3.91
804 5939 6.235664 ACAACTATATGGAAGGAAAACGTGT 58.764 36.000 0.00 0.00 0.00 4.49
863 5999 4.022676 TGGCAACTATTTCCTCGTTTTTCC 60.023 41.667 0.00 0.00 37.61 3.13
864 6000 4.217767 GGCAACTATTTCCTCGTTTTTCCT 59.782 41.667 0.00 0.00 0.00 3.36
865 6001 5.391449 GCAACTATTTCCTCGTTTTTCCTC 58.609 41.667 0.00 0.00 0.00 3.71
934 6071 3.053693 TCCACCATATCCCCTTGTGAAAG 60.054 47.826 0.00 0.00 0.00 2.62
998 6135 9.244799 GTAAGTGGGTTTTATTTTCAAGAACAG 57.755 33.333 0.00 0.00 0.00 3.16
1030 6167 2.630889 AGATTGGACTGTGAGAGGGA 57.369 50.000 0.00 0.00 0.00 4.20
1114 6251 5.725362 AGAAGTTGAGCCAAGTGAGTATAC 58.275 41.667 0.00 0.00 0.00 1.47
1124 6261 5.472148 CCAAGTGAGTATACGTTGGTGTTA 58.528 41.667 15.64 0.00 34.19 2.41
1144 6281 7.132863 GTGTTAATTTGTGTCCTCAAAGAGTC 58.867 38.462 1.69 0.00 40.00 3.36
1167 6304 9.503399 AGTCAATTCTTCTTCTTTATTTACCGT 57.497 29.630 0.00 0.00 0.00 4.83
1189 6326 8.197439 ACCGTTTTCAATTTCTGATTCTTTCTT 58.803 29.630 0.00 0.00 32.78 2.52
1198 6335 4.717877 TCTGATTCTTTCTTGCCACTTCA 58.282 39.130 0.00 0.00 0.00 3.02
1254 6392 4.157840 GGACACCTTGTTTTGTGTTCTTCT 59.842 41.667 0.00 0.00 45.24 2.85
1285 6423 6.000246 TGGGATATGCAATCTAGTTTGTGA 58.000 37.500 13.68 3.46 0.00 3.58
1286 6424 6.604171 TGGGATATGCAATCTAGTTTGTGAT 58.396 36.000 13.68 9.32 0.00 3.06
1287 6425 7.744733 TGGGATATGCAATCTAGTTTGTGATA 58.255 34.615 13.68 10.78 0.00 2.15
1288 6426 8.385491 TGGGATATGCAATCTAGTTTGTGATAT 58.615 33.333 13.68 13.93 0.00 1.63
1289 6427 9.890629 GGGATATGCAATCTAGTTTGTGATATA 57.109 33.333 13.68 8.81 0.00 0.86
1351 6489 7.106439 TGATAGATATAGCTAGCAAGAAGGC 57.894 40.000 18.83 0.00 34.19 4.35
1360 6498 1.831580 AGCAAGAAGGCTGATTCCAC 58.168 50.000 0.00 0.00 43.89 4.02
1408 6546 6.151144 CGAGGGTTTTTAGGTGAGATTTTCAT 59.849 38.462 0.00 0.00 38.29 2.57
1467 6605 8.409358 AGGAAGCATGAGTTTAAATTAAGTGT 57.591 30.769 0.00 0.00 0.00 3.55
1529 6667 8.619146 ATCTCAATATTTACACAAACATTGCG 57.381 30.769 0.00 0.00 38.08 4.85
1548 6686 3.070015 TGCGTGTCATGACATAGATCCAT 59.930 43.478 30.10 0.00 43.97 3.41
1599 6737 9.135189 ACCATGTATATTGCATCTAAACAACAT 57.865 29.630 0.00 0.00 0.00 2.71
1643 6781 8.980610 TGAAGAATCTTTGCAATAACACAATTG 58.019 29.630 0.00 3.24 39.41 2.32
1692 6830 4.220163 AGAAGGGGTCGTTTGTTAGACTAG 59.780 45.833 0.00 0.00 37.52 2.57
1777 6987 7.526608 TCTCAATGGCTAACACTTAAATTTCG 58.473 34.615 0.00 0.00 0.00 3.46
1844 7072 6.266131 ACATCCCTTATTCTTCCAAGCATA 57.734 37.500 0.00 0.00 0.00 3.14
1953 8784 1.794701 GCTTGCAAAAACTAGGCTTGC 59.205 47.619 15.11 15.11 44.54 4.01
1955 8786 2.798976 TGCAAAAACTAGGCTTGCTG 57.201 45.000 19.88 6.22 44.57 4.41
1967 8798 0.036010 GCTTGCTGCCTCCACTCTAA 60.036 55.000 0.00 0.00 35.15 2.10
2236 12665 6.018433 AGGTACCATATTTCAAGCCTTCAT 57.982 37.500 15.94 0.00 0.00 2.57
2237 12666 5.829924 AGGTACCATATTTCAAGCCTTCATG 59.170 40.000 15.94 0.00 0.00 3.07
2304 12735 7.147742 TGCACATAGTTCTAGGATTGATGTACA 60.148 37.037 0.00 0.00 0.00 2.90
2367 12798 4.014406 TCATCAAGGTCTACTCTACGCAA 58.986 43.478 0.00 0.00 0.00 4.85
2419 12850 0.687920 TGGTTGGCGTGGTTCATAGA 59.312 50.000 0.00 0.00 0.00 1.98
2454 12885 9.035607 ACGACTTTAGTATCTTGAGCATAAATG 57.964 33.333 0.00 0.00 0.00 2.32
2483 12914 4.023707 CCTCCTTGCACACTAAACAAAGAG 60.024 45.833 0.00 0.00 33.56 2.85
2738 21190 5.538053 TGATTCAAAGTGAGTGAGAGAGAGT 59.462 40.000 0.00 0.00 0.00 3.24
2750 21202 4.631813 GTGAGAGAGAGTGAGAGAGAGAAC 59.368 50.000 0.00 0.00 0.00 3.01
2979 21431 7.441760 AGGTACAAACATACATAAAACACGACA 59.558 33.333 0.00 0.00 0.00 4.35
3059 21511 2.197324 GCCTGGTGGTTTGGGTCA 59.803 61.111 0.00 0.00 35.27 4.02
3063 21516 2.006805 CTGGTGGTTTGGGTCAGGGT 62.007 60.000 0.00 0.00 0.00 4.34
3072 21525 1.004361 GGGTCAGGGTGAGGGGTAT 59.996 63.158 0.00 0.00 0.00 2.73
3074 21527 1.296002 GGTCAGGGTGAGGGGTATTT 58.704 55.000 0.00 0.00 0.00 1.40
3103 21556 4.148696 CACACAACGCATGAAAATTCCTTC 59.851 41.667 0.00 0.00 0.00 3.46
3106 21559 5.406175 CACAACGCATGAAAATTCCTTCATT 59.594 36.000 0.00 0.00 42.16 2.57
3136 21590 0.804989 GAGTGGGAAATGCGGTTCAG 59.195 55.000 2.06 0.00 0.00 3.02
3138 21592 0.958822 GTGGGAAATGCGGTTCAGTT 59.041 50.000 2.06 0.00 35.44 3.16
3315 21771 9.239551 ACTTAATTAGTTATCCTTTGTTCCACC 57.760 33.333 0.00 0.00 31.29 4.61
3348 21804 6.640499 TCCTGTACTTTTTCAAAAATCATGCG 59.360 34.615 0.00 0.00 0.00 4.73
3357 21813 4.930963 TCAAAAATCATGCGTTGTCAACT 58.069 34.783 13.67 0.00 0.00 3.16
3640 22101 8.890410 ACTAACAACACCTACCGGATATATAT 57.110 34.615 9.46 0.00 0.00 0.86
3641 22102 9.979897 ACTAACAACACCTACCGGATATATATA 57.020 33.333 9.46 0.00 0.00 0.86
3735 22196 3.185594 GCTTGTCAATACGTGCTTGTACA 59.814 43.478 0.00 6.18 0.00 2.90
3891 22352 7.966246 AATTGCAATGTCAGAAATAAAAGCA 57.034 28.000 13.82 0.00 0.00 3.91
3895 22356 8.464770 TGCAATGTCAGAAATAAAAGCATAAC 57.535 30.769 0.00 0.00 0.00 1.89
3953 22414 3.751479 TGCTCAACTTCTAGTGCAAGA 57.249 42.857 0.00 0.00 32.10 3.02
4092 22553 5.543714 TGATTCTTACACTTGACGCCTTAA 58.456 37.500 0.00 0.00 0.00 1.85
4146 22607 5.424895 CCATTTGGAATTAATGGGGTCTTCA 59.575 40.000 9.72 0.00 45.36 3.02
4285 22746 1.197721 GGCAAGGTTGTCAGAATCACG 59.802 52.381 0.00 0.00 31.86 4.35
4350 22811 6.289834 TCTTAGGATAACGACAACCAAAACA 58.710 36.000 0.00 0.00 0.00 2.83
4353 22814 6.009115 AGGATAACGACAACCAAAACATTC 57.991 37.500 0.00 0.00 0.00 2.67
4355 22816 5.856455 GGATAACGACAACCAAAACATTCAG 59.144 40.000 0.00 0.00 0.00 3.02
4415 22876 9.822185 ATTCCAATTAATTTAGATTGTGAAGGC 57.178 29.630 0.00 0.00 31.92 4.35
4555 23017 2.287909 TGCGCAAGTGGGAAATAACAAC 60.288 45.455 8.16 0.00 41.68 3.32
4667 23129 4.578516 CACCACAACAGTCAAATGAAGGTA 59.421 41.667 0.00 0.00 0.00 3.08
4876 23338 1.555477 CCCGTTCACAAAAGTTGCAC 58.445 50.000 0.00 0.00 0.00 4.57
4913 23375 4.366267 AGCTTCCTCTCTTAGAATTGGGA 58.634 43.478 0.00 0.00 0.00 4.37
4979 23441 9.517609 CTAATGTACACTAGATGAAACACCTAC 57.482 37.037 5.40 0.00 32.89 3.18
4980 23442 6.904463 TGTACACTAGATGAAACACCTACA 57.096 37.500 0.00 0.00 0.00 2.74
5185 23655 5.916883 GGCAATATCGTCTTTGAATTGGATG 59.083 40.000 0.00 0.00 0.00 3.51
5274 23744 5.933617 TGAATATTGGCTGAGTGCTAAGAT 58.066 37.500 0.00 0.00 44.06 2.40
5474 23944 6.127168 CGGGATGCTGGATATTATGGTAAGTA 60.127 42.308 0.00 0.00 0.00 2.24
5489 23959 4.080469 TGGTAAGTAAAAGGGTGTGTGTCA 60.080 41.667 0.00 0.00 0.00 3.58
5502 23972 7.175104 AGGGTGTGTGTCACATATTCTTAAAT 58.825 34.615 9.31 0.00 46.32 1.40
5532 24002 7.541783 TCATGTTAATATGTGCAAACTGCTTTC 59.458 33.333 11.44 0.00 45.31 2.62
5545 24015 4.546829 ACTGCTTTCGTCCCATAAAGTA 57.453 40.909 0.00 0.00 35.56 2.24
5546 24016 4.901868 ACTGCTTTCGTCCCATAAAGTAA 58.098 39.130 0.00 0.00 35.56 2.24
5905 24696 6.319911 TGAATGATTTTACACACCACACTTGA 59.680 34.615 0.00 0.00 0.00 3.02
6023 24814 1.999735 AGATACAAATGACACACGCCG 59.000 47.619 0.00 0.00 0.00 6.46
6251 25045 2.806244 CACCAACGAACGGAAAGAGAAT 59.194 45.455 0.00 0.00 0.00 2.40
6336 25130 1.275010 TCTGCATTGCGTAGAACCTCA 59.725 47.619 3.84 0.00 32.84 3.86
6345 25139 3.128764 TGCGTAGAACCTCATACACTCTG 59.871 47.826 0.00 0.00 0.00 3.35
6407 25201 2.717639 ACTCAATCACCATGCCCTAC 57.282 50.000 0.00 0.00 0.00 3.18
6409 25203 0.463654 TCAATCACCATGCCCTACGC 60.464 55.000 0.00 0.00 38.31 4.42
6455 25249 2.134354 TGGATGCCTTGATATCCACCA 58.866 47.619 0.00 0.00 45.87 4.17
6510 25304 6.631016 CCATTGCCTCGTAATCTAAGCTATA 58.369 40.000 0.00 0.00 0.00 1.31
6537 25331 2.941064 CCGACTACTTACATCCACGAGA 59.059 50.000 0.00 0.00 0.00 4.04
6575 25372 1.133513 GCCATCACCCCAACATCCATA 60.134 52.381 0.00 0.00 0.00 2.74
6608 25405 3.641434 AAAGCATCATGTCAGCCTAGT 57.359 42.857 0.00 0.00 0.00 2.57
6655 25452 2.095768 CGTGCAACACTCCAACAATAGG 60.096 50.000 0.00 0.00 35.74 2.57
6671 25469 6.067217 ACAATAGGAAAACAGTAGCTCCAT 57.933 37.500 0.00 0.00 0.00 3.41
6674 25472 7.125811 ACAATAGGAAAACAGTAGCTCCATCTA 59.874 37.037 0.00 0.00 0.00 1.98
6693 25491 0.916086 ATTAGAACCATCACGGCCCA 59.084 50.000 0.00 0.00 39.03 5.36
6695 25493 0.907704 TAGAACCATCACGGCCCACT 60.908 55.000 0.00 0.00 39.03 4.00
6760 25558 3.308688 CCTCCATTGGGTGAGAATTGTCT 60.309 47.826 2.09 0.00 33.94 3.41
6799 25597 0.387202 CCGCGACATGAGAGGAAGAT 59.613 55.000 8.23 0.00 0.00 2.40
6876 25674 2.110420 GGGAGGGGCGTATTTCCG 59.890 66.667 0.00 0.00 0.00 4.30
6889 25687 5.048507 GCGTATTTCCGACCTCTTATTCTT 58.951 41.667 0.00 0.00 0.00 2.52
6897 25695 6.185511 TCCGACCTCTTATTCTTGTTCTCTA 58.814 40.000 0.00 0.00 0.00 2.43
7119 25917 6.823182 ACTTATGCACTCACATAACTAATGCA 59.177 34.615 0.00 0.00 44.87 3.96
7130 25928 9.278978 TCACATAACTAATGCACTAAGAAAACA 57.721 29.630 0.00 0.00 39.39 2.83
7195 25993 9.487790 AAATGTTATTGTCCCACAAGTTAATTG 57.512 29.630 0.00 0.00 41.94 2.32
7298 26096 7.420184 CATTTACAAAAATGTTGGAAGGGTC 57.580 36.000 3.26 0.00 44.62 4.46
7318 26116 4.329392 GTCGAAGGGGTTCCATTTAAAGA 58.671 43.478 0.00 0.00 34.83 2.52
7323 26121 6.605471 AAGGGGTTCCATTTAAAGATCAAC 57.395 37.500 0.00 0.00 34.83 3.18
7324 26122 5.650283 AGGGGTTCCATTTAAAGATCAACA 58.350 37.500 0.00 0.00 34.83 3.33
7325 26123 5.716703 AGGGGTTCCATTTAAAGATCAACAG 59.283 40.000 0.00 0.00 34.83 3.16
7326 26124 5.714806 GGGGTTCCATTTAAAGATCAACAGA 59.285 40.000 0.00 0.00 0.00 3.41
7327 26125 6.350194 GGGGTTCCATTTAAAGATCAACAGAC 60.350 42.308 0.00 0.00 0.00 3.51
7328 26126 6.350194 GGGTTCCATTTAAAGATCAACAGACC 60.350 42.308 0.00 0.00 0.00 3.85
7329 26127 6.208599 GGTTCCATTTAAAGATCAACAGACCA 59.791 38.462 0.00 0.00 0.00 4.02
7330 26128 7.093771 GGTTCCATTTAAAGATCAACAGACCAT 60.094 37.037 0.00 0.00 0.00 3.55
7339 26137 4.703575 AGATCAACAGACCATGGTCAAATG 59.296 41.667 39.38 31.81 46.76 2.32
7350 26148 3.815856 TGGTCAAATGTTGCACATGTT 57.184 38.095 0.00 0.00 37.97 2.71
7353 26151 5.046529 TGGTCAAATGTTGCACATGTTAAC 58.953 37.500 13.33 13.33 37.97 2.01
7356 26154 5.976534 GTCAAATGTTGCACATGTTAACTGA 59.023 36.000 18.45 13.09 37.97 3.41
7651 26619 7.561021 ACATAACATGGCGTTTGATGTTATA 57.439 32.000 15.58 0.00 46.70 0.98
7823 26818 6.372659 GCACATTGAGAATCTCCTCTACAAAA 59.627 38.462 7.91 0.00 34.92 2.44
7856 26923 9.425577 GTCTATATTTATTAAGTCAGAGCACCC 57.574 37.037 0.00 0.00 0.00 4.61
7978 27045 3.073062 GGCTAAATGATTCTGGAGCCCTA 59.927 47.826 8.40 0.00 43.02 3.53
8018 27085 3.669536 AGCTCAGGTAAACTTCAGAAGC 58.330 45.455 10.33 0.00 0.00 3.86
8021 27088 4.275936 GCTCAGGTAAACTTCAGAAGCAAA 59.724 41.667 10.33 0.00 0.00 3.68
8188 27255 5.701224 AGGAGGACATGTTTAACTGGAAAA 58.299 37.500 0.00 0.00 0.00 2.29
8195 27262 8.387354 GGACATGTTTAACTGGAAAAACTTTTG 58.613 33.333 0.00 0.00 36.70 2.44
8199 27266 3.924114 AACTGGAAAAACTTTTGGGGG 57.076 42.857 0.00 0.00 0.00 5.40
8208 27275 1.377333 CTTTTGGGGGACGCCTCTC 60.377 63.158 8.66 0.00 42.25 3.20
8209 27276 2.124507 CTTTTGGGGGACGCCTCTCA 62.125 60.000 8.66 0.00 42.25 3.27
8210 27277 2.124507 TTTTGGGGGACGCCTCTCAG 62.125 60.000 8.66 0.00 42.25 3.35
8317 27384 7.875041 AGATCAATTCATGGAACTTATCTACCG 59.125 37.037 0.00 0.00 0.00 4.02
8400 27467 5.049828 CCGAGTAACAGCAACATATCATCA 58.950 41.667 0.00 0.00 0.00 3.07
8401 27468 5.050769 CCGAGTAACAGCAACATATCATCAC 60.051 44.000 0.00 0.00 0.00 3.06
8436 27503 0.512952 AGCAGCTACGCGAAAACTTG 59.487 50.000 15.93 4.37 36.85 3.16
8601 27672 0.321653 AAGTCATCAACGTGCCTCCC 60.322 55.000 0.00 0.00 0.00 4.30
8624 27695 1.535685 GAAGCAGCCCTCCATGGAT 59.464 57.895 16.63 0.00 38.35 3.41
8742 27821 5.372343 TGCTGGACTGATGGTTATTGTAT 57.628 39.130 0.00 0.00 0.00 2.29
8744 27823 6.186957 TGCTGGACTGATGGTTATTGTATTT 58.813 36.000 0.00 0.00 0.00 1.40
8915 27999 8.522830 CCAAATCATAGTGTTGACATAAACCTT 58.477 33.333 0.00 0.00 0.00 3.50
8991 28075 9.162764 GTACCATATCTTGTTTCACATGTACTT 57.837 33.333 0.00 0.00 0.00 2.24
8992 28076 8.268850 ACCATATCTTGTTTCACATGTACTTC 57.731 34.615 0.00 0.00 0.00 3.01
9180 28266 2.664085 GCTAGACTCGAACTTGAGCAAC 59.336 50.000 0.00 0.00 39.68 4.17
9210 28296 0.842635 GAGGGAAGGACATGAGGCAT 59.157 55.000 0.00 0.00 0.00 4.40
9264 28350 2.009774 CAAGGGAGAAACATGTAGGCG 58.990 52.381 0.00 0.00 0.00 5.52
9305 28391 4.938080 AGACGGTTCAGTAATAGCATCAG 58.062 43.478 0.00 0.00 0.00 2.90
9344 28430 8.538409 AAGTTTTATTGGCTAAAATGAAGCAG 57.462 30.769 0.00 0.00 40.48 4.24
9345 28431 7.895759 AGTTTTATTGGCTAAAATGAAGCAGA 58.104 30.769 0.00 0.00 40.48 4.26
9361 28453 6.671190 TGAAGCAGAATACAAACACAATGAG 58.329 36.000 0.00 0.00 0.00 2.90
9369 28461 2.289547 ACAAACACAATGAGTACACGCC 59.710 45.455 0.00 0.00 0.00 5.68
9371 28463 0.394938 ACACAATGAGTACACGCCCA 59.605 50.000 0.00 0.00 0.00 5.36
9372 28464 1.202710 ACACAATGAGTACACGCCCAA 60.203 47.619 0.00 0.00 0.00 4.12
9375 28467 0.690762 AATGAGTACACGCCCAACCT 59.309 50.000 0.00 0.00 0.00 3.50
9377 28469 0.470766 TGAGTACACGCCCAACCTTT 59.529 50.000 0.00 0.00 0.00 3.11
9385 28477 1.315257 CGCCCAACCTTTGCATAGCT 61.315 55.000 0.00 0.00 0.00 3.32
9399 28491 7.395190 TTTGCATAGCTAGAATGAACACAAT 57.605 32.000 0.00 0.00 0.00 2.71
9400 28492 6.609237 TGCATAGCTAGAATGAACACAATC 57.391 37.500 0.00 0.00 0.00 2.67
9401 28493 5.234972 TGCATAGCTAGAATGAACACAATCG 59.765 40.000 0.00 0.00 0.00 3.34
9402 28494 5.463392 GCATAGCTAGAATGAACACAATCGA 59.537 40.000 0.00 0.00 0.00 3.59
9405 28497 8.858186 CATAGCTAGAATGAACACAATCGATAG 58.142 37.037 0.00 0.00 0.00 2.08
9413 28505 2.356313 CAATCGATAGCGGCGCCT 60.356 61.111 30.40 17.14 38.28 5.52
9432 28524 0.251564 TGGTTGGTGTTATGCCCCAG 60.252 55.000 0.00 0.00 0.00 4.45
9447 28539 0.322816 CCCAGGCAAGCAGTGTATGT 60.323 55.000 0.00 0.00 0.00 2.29
9449 28541 2.009774 CCAGGCAAGCAGTGTATGTAC 58.990 52.381 0.00 0.00 0.00 2.90
9452 28544 2.303022 AGGCAAGCAGTGTATGTACAGT 59.697 45.455 0.33 0.00 40.31 3.55
9466 28558 4.875561 TGTACAGTGCCAATACACAGTA 57.124 40.909 0.00 0.00 43.23 2.74
9468 28560 2.699954 ACAGTGCCAATACACAGTAGC 58.300 47.619 0.00 0.00 43.23 3.58
9489 28581 6.808321 AGCTGTACCTATAACCAATGAAGA 57.192 37.500 0.00 0.00 0.00 2.87
9492 28584 7.048512 GCTGTACCTATAACCAATGAAGAGTT 58.951 38.462 0.00 0.00 0.00 3.01
9503 28595 1.153349 GAAGAGTTAGCCGGCCAGG 60.153 63.158 26.15 6.38 44.97 4.45
9529 28621 4.691359 CTGCTTGGGGCCTGGCTT 62.691 66.667 19.68 0.00 40.92 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.761311 GGTATGGAGATACCGACGATC 57.239 52.381 0.00 0.00 43.81 3.69
32 33 6.918569 CAGTAACGAGATTGAACTAGGTATGG 59.081 42.308 0.00 0.00 0.00 2.74
71 72 7.276658 GCACGGGATCTTGTATTATAGAATGAG 59.723 40.741 0.00 0.00 0.00 2.90
72 73 7.097192 GCACGGGATCTTGTATTATAGAATGA 58.903 38.462 0.00 0.00 0.00 2.57
76 77 5.084519 AGGCACGGGATCTTGTATTATAGA 58.915 41.667 0.00 0.00 0.00 1.98
77 78 5.407407 AGGCACGGGATCTTGTATTATAG 57.593 43.478 0.00 0.00 0.00 1.31
79 80 5.307196 AGTTAGGCACGGGATCTTGTATTAT 59.693 40.000 0.00 0.00 0.00 1.28
82 83 3.039011 AGTTAGGCACGGGATCTTGTAT 58.961 45.455 0.00 0.00 0.00 2.29
85 86 1.207089 TGAGTTAGGCACGGGATCTTG 59.793 52.381 0.00 0.00 0.00 3.02
86 87 1.568504 TGAGTTAGGCACGGGATCTT 58.431 50.000 0.00 0.00 0.00 2.40
87 88 1.794714 ATGAGTTAGGCACGGGATCT 58.205 50.000 0.00 0.00 0.00 2.75
88 89 2.622064 AATGAGTTAGGCACGGGATC 57.378 50.000 0.00 0.00 0.00 3.36
90 91 2.429610 GACTAATGAGTTAGGCACGGGA 59.570 50.000 0.00 0.00 44.05 5.14
91 92 2.167693 TGACTAATGAGTTAGGCACGGG 59.832 50.000 0.00 0.00 46.50 5.28
97 98 6.676456 GCAAGCAATGTGACTAATGAGTTAGG 60.676 42.308 0.88 0.00 41.33 2.69
98 99 6.128200 TGCAAGCAATGTGACTAATGAGTTAG 60.128 38.462 0.00 0.00 42.45 2.34
99 100 5.704978 TGCAAGCAATGTGACTAATGAGTTA 59.295 36.000 0.00 0.00 35.45 2.24
100 101 4.520111 TGCAAGCAATGTGACTAATGAGTT 59.480 37.500 0.00 0.00 35.45 3.01
102 103 4.690184 TGCAAGCAATGTGACTAATGAG 57.310 40.909 0.00 0.00 0.00 2.90
103 104 5.050644 CTTGCAAGCAATGTGACTAATGA 57.949 39.130 14.65 0.00 35.20 2.57
121 122 7.910683 GGTAATACAACATCTTAAAGAGCTTGC 59.089 37.037 0.00 0.00 0.00 4.01
182 183 4.109050 GGATCGAGACTGAGATTTGTCAC 58.891 47.826 0.00 0.00 35.81 3.67
187 188 3.494048 GGCATGGATCGAGACTGAGATTT 60.494 47.826 0.00 0.00 0.00 2.17
192 193 1.134699 GTTGGCATGGATCGAGACTGA 60.135 52.381 0.00 0.00 0.00 3.41
227 228 3.958018 AGGTGCTCTATAGGTATCTCCG 58.042 50.000 0.00 0.00 41.99 4.63
272 273 7.044445 GGAATACTTAGTGTGTATCGAAACGTC 60.044 40.741 0.00 0.00 31.08 4.34
279 280 5.237996 TCGGAGGAATACTTAGTGTGTATCG 59.762 44.000 0.00 0.00 31.08 2.92
315 316 7.014326 AGCATTTCTACCTTATGAGATCGTGTA 59.986 37.037 0.00 0.00 0.00 2.90
360 3481 4.337274 TCATCCATATTGCTGCAACTTCTG 59.663 41.667 18.51 11.87 0.00 3.02
361 3482 4.529897 TCATCCATATTGCTGCAACTTCT 58.470 39.130 18.51 4.21 0.00 2.85
594 3716 6.349777 CCGGAAATATTGTGTTCTTTTAGCCA 60.350 38.462 0.00 0.00 0.00 4.75
689 3811 7.090173 TGCTGAACTAATGCATTAAAAGGTTC 58.910 34.615 26.76 26.76 34.35 3.62
690 3812 6.991938 TGCTGAACTAATGCATTAAAAGGTT 58.008 32.000 19.32 18.08 0.00 3.50
692 3814 7.887996 TTTGCTGAACTAATGCATTAAAAGG 57.112 32.000 19.32 10.60 36.55 3.11
694 3816 8.026026 TCGATTTGCTGAACTAATGCATTAAAA 58.974 29.630 19.32 14.56 36.55 1.52
804 5939 0.878523 CGTCGCAAGGGTTTGAGTGA 60.879 55.000 0.00 0.00 36.36 3.41
842 5977 5.181433 AGAGGAAAAACGAGGAAATAGTTGC 59.819 40.000 0.00 0.00 0.00 4.17
863 5999 4.065789 GAGGCAACCCGGATTTTATAGAG 58.934 47.826 0.73 0.00 35.76 2.43
864 6000 3.181448 GGAGGCAACCCGGATTTTATAGA 60.181 47.826 0.73 0.00 35.76 1.98
865 6001 3.146847 GGAGGCAACCCGGATTTTATAG 58.853 50.000 0.73 0.00 35.76 1.31
934 6071 6.603599 AGAGTTTTTGGTTATTATGGGAGAGC 59.396 38.462 0.00 0.00 0.00 4.09
998 6135 2.802816 GTCCAATCTACGACATGCATCC 59.197 50.000 0.00 0.00 0.00 3.51
1030 6167 2.162681 GGCATACCAACACTGCTCTTT 58.837 47.619 0.00 0.00 36.18 2.52
1114 6251 4.035792 TGAGGACACAAATTAACACCAACG 59.964 41.667 0.00 0.00 0.00 4.10
1124 6261 6.966534 ATTGACTCTTTGAGGACACAAATT 57.033 33.333 0.00 0.00 38.73 1.82
1167 6304 7.986320 TGGCAAGAAAGAATCAGAAATTGAAAA 59.014 29.630 0.00 0.00 39.77 2.29
1189 6326 2.093711 ACGTGCATAGTATGAAGTGGCA 60.094 45.455 14.52 0.39 0.00 4.92
1198 6335 6.403333 CACAAACAACTACGTGCATAGTAT 57.597 37.500 0.00 0.00 34.18 2.12
1236 6373 7.707104 AGTGAATAGAAGAACACAAAACAAGG 58.293 34.615 0.00 0.00 35.97 3.61
1254 6392 7.977818 ACTAGATTGCATATCCCAAGTGAATA 58.022 34.615 0.00 0.00 0.00 1.75
1384 6522 6.894339 TGAAAATCTCACCTAAAAACCCTC 57.106 37.500 0.00 0.00 0.00 4.30
1529 6667 4.818005 TGCAATGGATCTATGTCATGACAC 59.182 41.667 30.09 16.72 45.05 3.67
1548 6686 4.573900 ACACCACACAAATTCTTTTGCAA 58.426 34.783 0.00 0.00 45.01 4.08
1667 6805 3.497262 GTCTAACAAACGACCCCTTCTTG 59.503 47.826 0.00 0.00 0.00 3.02
1671 6809 3.306571 GCTAGTCTAACAAACGACCCCTT 60.307 47.826 0.00 0.00 0.00 3.95
1673 6811 2.614779 GCTAGTCTAACAAACGACCCC 58.385 52.381 0.00 0.00 0.00 4.95
1692 6830 1.174712 AGCATGTGACAACTGGTGGC 61.175 55.000 0.00 0.00 34.82 5.01
1777 6987 7.284820 TCCCTAAACTTTGTATACTAATGGCC 58.715 38.462 4.17 0.00 0.00 5.36
1844 7072 1.840635 GGAATGGCAGACCTTCTACCT 59.159 52.381 0.00 0.00 31.04 3.08
1903 8734 7.816640 TGTGTTTAGTTTCTAGCCAATCATTC 58.183 34.615 0.00 0.00 0.00 2.67
1953 8784 4.220382 CCTAGATCATTAGAGTGGAGGCAG 59.780 50.000 0.00 0.00 0.00 4.85
1955 8786 3.056179 GCCTAGATCATTAGAGTGGAGGC 60.056 52.174 0.00 0.00 40.13 4.70
1967 8798 3.323403 GTGCTAGTCCTTGCCTAGATCAT 59.677 47.826 0.00 0.00 35.01 2.45
2071 12487 8.856153 TTGCTATATTAGACAAACTTTGACCA 57.144 30.769 8.55 0.00 0.00 4.02
2211 12640 5.045213 TGAAGGCTTGAAATATGGTACCTCA 60.045 40.000 14.36 4.99 0.00 3.86
2261 12692 8.194104 ACTATGTGCAACTAAACATTCAAAACA 58.806 29.630 0.00 0.00 38.05 2.83
2367 12798 6.525629 GCACATAGGACTACCACATCTTATT 58.474 40.000 0.00 0.00 38.94 1.40
2419 12850 5.447757 AGATACTAAAGTCGTAGAAGGCCT 58.552 41.667 0.00 0.00 39.69 5.19
2454 12885 2.191128 AGTGTGCAAGGAGGTTCATC 57.809 50.000 0.00 0.00 0.00 2.92
2483 12914 2.933906 CCAAAATGGATGCATGCACTTC 59.066 45.455 25.37 17.76 40.96 3.01
2555 12987 8.529424 AGGTCACATGAACAATAATTGATGAT 57.471 30.769 0.00 0.00 33.22 2.45
2689 13127 5.124036 TGGATGGAATGGTTAAACCCTAG 57.876 43.478 0.00 0.00 37.50 3.02
2738 21190 6.567687 CTGAAAGTGTAGTTCTCTCTCTCA 57.432 41.667 0.00 0.00 0.00 3.27
2899 21351 2.178912 TTCTTAGACAAGGCCAACCG 57.821 50.000 5.01 0.00 42.76 4.44
2979 21431 6.870971 AGCATTTGCATTCTTGTCAAATTT 57.129 29.167 5.20 0.00 45.16 1.82
3059 21511 2.581246 GGAAAGAAATACCCCTCACCCT 59.419 50.000 0.00 0.00 0.00 4.34
3063 21516 3.396276 TGTGTGGAAAGAAATACCCCTCA 59.604 43.478 0.00 0.00 0.00 3.86
3072 21525 2.685388 TCATGCGTTGTGTGGAAAGAAA 59.315 40.909 0.00 0.00 0.00 2.52
3074 21527 1.960417 TCATGCGTTGTGTGGAAAGA 58.040 45.000 0.00 0.00 0.00 2.52
3641 22102 9.144747 GACATGATTATCAAGAGCGTGTTATAT 57.855 33.333 4.37 0.00 0.00 0.86
3642 22103 8.141268 TGACATGATTATCAAGAGCGTGTTATA 58.859 33.333 4.37 0.00 0.00 0.98
3643 22104 6.986231 TGACATGATTATCAAGAGCGTGTTAT 59.014 34.615 4.37 0.00 0.00 1.89
3644 22105 6.255670 GTGACATGATTATCAAGAGCGTGTTA 59.744 38.462 4.37 0.00 0.00 2.41
3645 22106 5.063944 GTGACATGATTATCAAGAGCGTGTT 59.936 40.000 4.37 0.00 0.00 3.32
3703 22164 4.242475 CGTATTGACAAGCTTGTGAGGTA 58.758 43.478 35.67 20.14 42.43 3.08
3973 22434 6.381801 GCCTTCATATGTGGCATTTACATAC 58.618 40.000 26.02 4.28 45.46 2.39
4092 22553 1.331214 CAGCTGTGTTCAACCCCAAT 58.669 50.000 5.25 0.00 0.00 3.16
4101 22562 3.058224 GGTTATTCACCACAGCTGTGTTC 60.058 47.826 37.55 16.29 46.42 3.18
4127 22588 5.016173 CACTTGAAGACCCCATTAATTCCA 58.984 41.667 0.00 0.00 0.00 3.53
4146 22607 7.595819 TCAAAACAATTAGATGGAACCACTT 57.404 32.000 0.00 0.00 0.00 3.16
4187 22648 2.766263 TGCTAGGATGGGTGAGTTACTG 59.234 50.000 0.00 0.00 0.00 2.74
4264 22725 2.508526 GTGATTCTGACAACCTTGCCT 58.491 47.619 0.00 0.00 0.00 4.75
4297 22758 8.762645 TGTGATCTTACTGTAGGATTTCTGATT 58.237 33.333 12.89 0.00 0.00 2.57
4423 22884 3.722147 AGAATCCCAATTCGATCGTGAG 58.278 45.455 15.94 3.97 45.01 3.51
4667 23129 6.421485 AGAAGAGCTCATTTACCACATCATT 58.579 36.000 17.77 0.00 0.00 2.57
4876 23338 2.989166 GGAAGCTTGAAAATTGGAAGCG 59.011 45.455 2.10 0.00 45.53 4.68
4913 23375 3.434940 AAGCGAAATTACCTCCCAGTT 57.565 42.857 0.00 0.00 0.00 3.16
5378 23848 9.896645 ACATTTTATCTCTATCTTGCTCTTCAA 57.103 29.630 0.00 0.00 0.00 2.69
5502 23972 9.299963 GCAGTTTGCACATATTAACATGATAAA 57.700 29.630 0.00 0.00 44.26 1.40
5525 23995 5.873179 TTTACTTTATGGGACGAAAGCAG 57.127 39.130 0.00 0.00 37.39 4.24
5532 24002 6.189677 TGCTTCAATTTACTTTATGGGACG 57.810 37.500 0.00 0.00 0.00 4.79
5905 24696 7.308649 GAGTTAGCTCGGAAAAAGGAGATTTTT 60.309 37.037 0.00 0.00 41.26 1.94
5991 24782 8.947115 GTGTCATTTGTATCTAGTTTTAGCCTT 58.053 33.333 0.00 0.00 0.00 4.35
6273 25067 2.563297 GGGCAAAGTCCTAAACCCG 58.437 57.895 0.00 0.00 0.00 5.28
6336 25130 3.779444 TGAGTTGGTCCTCAGAGTGTAT 58.221 45.455 0.00 0.00 36.57 2.29
6345 25139 1.522569 CCGGGATGAGTTGGTCCTC 59.477 63.158 0.00 0.00 34.84 3.71
6407 25201 1.207089 TGGAGTTGAAGGATAGGTGCG 59.793 52.381 0.00 0.00 0.00 5.34
6409 25203 4.444022 CCAGATGGAGTTGAAGGATAGGTG 60.444 50.000 0.00 0.00 37.39 4.00
6455 25249 2.715532 AATGTGGTGCGCTCGTGAGT 62.716 55.000 9.73 0.00 0.00 3.41
6510 25304 4.021229 TGGATGTAAGTAGTCGGTGACAT 58.979 43.478 0.00 0.00 34.60 3.06
6537 25331 1.852067 GCTTGGATCGCGGTGTGTTT 61.852 55.000 6.13 0.00 0.00 2.83
6575 25372 9.013229 TGACATGATGCTTTTAGTTAGATTTGT 57.987 29.630 0.00 0.00 0.00 2.83
6608 25405 0.963962 AACAGAAGTAAGGTCGCCGA 59.036 50.000 0.00 0.00 0.00 5.54
6655 25452 9.036671 GTTCTAATAGATGGAGCTACTGTTTTC 57.963 37.037 0.00 0.00 0.00 2.29
6671 25469 2.367567 GGGCCGTGATGGTTCTAATAGA 59.632 50.000 0.00 0.00 41.21 1.98
6674 25472 0.916086 TGGGCCGTGATGGTTCTAAT 59.084 50.000 0.00 0.00 41.21 1.73
6783 25581 2.604373 GCGAGATCTTCCTCTCATGTCG 60.604 54.545 0.00 0.00 41.49 4.35
6876 25674 7.766278 TGCAATAGAGAACAAGAATAAGAGGTC 59.234 37.037 0.00 0.00 0.00 3.85
7297 26095 4.644163 TCTTTAAATGGAACCCCTTCGA 57.356 40.909 0.00 0.00 0.00 3.71
7298 26096 4.947388 TGATCTTTAAATGGAACCCCTTCG 59.053 41.667 0.00 0.00 0.00 3.79
7318 26116 4.410099 ACATTTGACCATGGTCTGTTGAT 58.590 39.130 37.92 23.18 44.80 2.57
7323 26121 2.296752 TGCAACATTTGACCATGGTCTG 59.703 45.455 37.92 30.64 44.80 3.51
7324 26122 2.297033 GTGCAACATTTGACCATGGTCT 59.703 45.455 37.92 20.91 40.57 3.85
7325 26123 2.035704 TGTGCAACATTTGACCATGGTC 59.964 45.455 33.97 33.97 45.67 4.02
7326 26124 2.037901 TGTGCAACATTTGACCATGGT 58.962 42.857 19.89 19.89 45.67 3.55
7327 26125 2.816204 TGTGCAACATTTGACCATGG 57.184 45.000 11.19 11.19 45.67 3.66
7339 26137 5.574830 TGTTGTTTCAGTTAACATGTGCAAC 59.425 36.000 19.21 19.21 37.81 4.17
7589 26387 4.616373 CGTTCCAACTCTGAAGTAGACCTC 60.616 50.000 0.00 0.00 33.48 3.85
7590 26388 3.256136 CGTTCCAACTCTGAAGTAGACCT 59.744 47.826 0.00 0.00 33.48 3.85
7707 26702 9.100197 TCTTCACCCACTAATATAATGCAGATA 57.900 33.333 0.00 0.00 0.00 1.98
7710 26705 8.627208 AATCTTCACCCACTAATATAATGCAG 57.373 34.615 0.00 0.00 0.00 4.41
7749 26744 3.503363 CAGAACATGCCTACTGAAAGCAA 59.497 43.478 0.00 0.00 40.46 3.91
7922 26989 1.358759 CAGTTGGCACCGGTTGAAC 59.641 57.895 2.97 8.27 0.00 3.18
7944 27011 8.636213 CAGAATCATTTAGCCCTAATGTCATTT 58.364 33.333 2.79 0.00 0.00 2.32
7978 27045 4.270008 AGCTTTGAAAGTGTACACCTTGT 58.730 39.130 22.28 5.25 0.00 3.16
8049 27116 4.590850 ATCTTGTGCATAGTCAGCGATA 57.409 40.909 0.00 0.00 33.85 2.92
8188 27255 1.228459 GAGGCGTCCCCCAAAAGTT 60.228 57.895 0.00 0.00 0.00 2.66
8314 27381 1.831106 TGATGAGTAATCAGCACCGGT 59.169 47.619 7.08 0.00 40.50 5.28
8400 27467 1.242076 GCTCAAGTGCCATTGTCTGT 58.758 50.000 0.00 0.00 0.00 3.41
8401 27468 1.199327 CTGCTCAAGTGCCATTGTCTG 59.801 52.381 0.00 0.00 0.00 3.51
8436 27503 2.828933 GACCTCCTTGTCGCTCAAC 58.171 57.895 0.00 0.00 32.18 3.18
8448 27515 0.673644 CCACCACATTCACGACCTCC 60.674 60.000 0.00 0.00 0.00 4.30
8533 27601 2.159099 CGACCAGAGTATTGCTTGCCTA 60.159 50.000 0.00 0.00 0.00 3.93
8601 27672 4.120755 GGAGGGCTGCTTCCAGGG 62.121 72.222 15.57 0.00 39.54 4.45
8624 27695 2.356278 GTGAGCCTGGCCATTCCA 59.644 61.111 16.57 0.00 44.18 3.53
8628 27699 2.277737 CATGGTGAGCCTGGCCAT 59.722 61.111 16.57 8.74 43.14 4.40
8742 27821 6.528423 CACAAAGTAAAACAACATGTCGGAAA 59.472 34.615 0.00 0.00 0.00 3.13
8744 27823 5.124138 ACACAAAGTAAAACAACATGTCGGA 59.876 36.000 0.00 0.00 0.00 4.55
8915 27999 6.310941 TCTGGAAATTGTTGGATCCTGTTTA 58.689 36.000 14.23 0.00 33.89 2.01
8983 28067 9.722056 GCTTATTAATGGTTTCAGAAGTACATG 57.278 33.333 0.00 0.00 0.00 3.21
8991 28075 5.199982 TGGGGCTTATTAATGGTTTCAGA 57.800 39.130 0.00 0.00 0.00 3.27
8992 28076 5.930837 TTGGGGCTTATTAATGGTTTCAG 57.069 39.130 0.00 0.00 0.00 3.02
9180 28266 1.571457 TCCTTCCCTCCTAGGTCTCTG 59.429 57.143 9.08 0.00 31.93 3.35
9210 28296 6.016693 TCCATCTTTCAATTGCGTGAAACTTA 60.017 34.615 0.00 0.00 41.45 2.24
9264 28350 4.084537 CGTCTCCGTATGGCAATATGTTTC 60.085 45.833 0.00 0.00 34.14 2.78
9330 28416 7.594758 TGTGTTTGTATTCTGCTTCATTTTAGC 59.405 33.333 0.00 0.00 39.10 3.09
9344 28430 5.788531 GCGTGTACTCATTGTGTTTGTATTC 59.211 40.000 0.00 0.00 0.00 1.75
9345 28431 5.334569 GGCGTGTACTCATTGTGTTTGTATT 60.335 40.000 0.00 0.00 0.00 1.89
9361 28453 1.284715 GCAAAGGTTGGGCGTGTAC 59.715 57.895 0.00 0.00 0.00 2.90
9369 28461 4.883585 TCATTCTAGCTATGCAAAGGTTGG 59.116 41.667 0.00 0.00 0.00 3.77
9371 28463 5.945784 TGTTCATTCTAGCTATGCAAAGGTT 59.054 36.000 0.00 0.00 0.00 3.50
9372 28464 5.355350 GTGTTCATTCTAGCTATGCAAAGGT 59.645 40.000 0.00 0.00 0.00 3.50
9375 28467 6.816134 TTGTGTTCATTCTAGCTATGCAAA 57.184 33.333 0.00 0.00 0.00 3.68
9377 28469 5.234972 CGATTGTGTTCATTCTAGCTATGCA 59.765 40.000 0.00 0.00 0.00 3.96
9385 28477 4.982295 CCGCTATCGATTGTGTTCATTCTA 59.018 41.667 17.08 0.00 38.10 2.10
9400 28492 4.891727 AACCAGGCGCCGCTATCG 62.892 66.667 23.20 8.33 0.00 2.92
9401 28493 3.272334 CAACCAGGCGCCGCTATC 61.272 66.667 23.20 0.00 0.00 2.08
9402 28494 4.856801 CCAACCAGGCGCCGCTAT 62.857 66.667 23.20 6.39 0.00 2.97
9413 28505 0.251564 CTGGGGCATAACACCAACCA 60.252 55.000 0.00 0.00 33.13 3.67
9432 28524 2.416547 CACTGTACATACACTGCTTGCC 59.583 50.000 0.00 0.00 31.93 4.52
9437 28529 2.093306 TGGCACTGTACATACACTGC 57.907 50.000 12.58 12.58 41.90 4.40
9438 28530 5.063438 GTGTATTGGCACTGTACATACACTG 59.937 44.000 21.85 2.12 39.53 3.66
9447 28539 3.513912 AGCTACTGTGTATTGGCACTGTA 59.486 43.478 12.77 12.77 45.34 2.74
9449 28541 2.674852 CAGCTACTGTGTATTGGCACTG 59.325 50.000 0.00 0.00 41.86 3.66
9452 28544 3.369052 GGTACAGCTACTGTGTATTGGCA 60.369 47.826 10.42 0.00 45.01 4.92
9456 28548 7.562454 TGGTTATAGGTACAGCTACTGTGTATT 59.438 37.037 10.42 0.00 45.01 1.89
9466 28558 6.384305 ACTCTTCATTGGTTATAGGTACAGCT 59.616 38.462 0.00 0.00 0.00 4.24
9468 28560 9.751542 CTAACTCTTCATTGGTTATAGGTACAG 57.248 37.037 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.