Multiple sequence alignment - TraesCS3D01G417300

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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 TraesCS3D01G417300 chr3D 100.000 4221 0 0 1 4221 528955889 528960109 0.000000e+00 7795.0
1 TraesCS3D01G417300 chr3B 86.816 1881 99 75 187 1984 699106005 699104191 0.000000e+00 1962.0
2 TraesCS3D01G417300 chr3B 88.359 1469 47 45 2249 3657 699103939 699102535 0.000000e+00 1652.0
3 TraesCS3D01G417300 chr3B 90.300 567 26 15 3662 4221 699102287 699101743 0.000000e+00 715.0
4 TraesCS3D01G417300 chr3B 82.822 815 86 26 568 1361 699508077 699507296 0.000000e+00 680.0
5 TraesCS3D01G417300 chr3B 90.000 200 15 4 2011 2207 699104137 699103940 1.950000e-63 254.0
6 TraesCS3D01G417300 chr3B 78.613 346 44 15 3039 3370 699308848 699308519 7.160000e-48 202.0
7 TraesCS3D01G417300 chr3B 79.211 279 24 21 254 531 699509787 699509542 3.380000e-36 163.0
8 TraesCS3D01G417300 chr3B 91.111 45 2 2 199 243 699509826 699509784 4.560000e-05 60.2
9 TraesCS3D01G417300 chr3A 83.702 1810 115 77 435 2149 662930817 662932541 0.000000e+00 1543.0
10 TraesCS3D01G417300 chr3A 81.857 1163 112 41 2252 3372 662932575 662933680 0.000000e+00 887.0
11 TraesCS3D01G417300 chr3A 82.807 285 29 15 3405 3670 662933685 662933968 1.960000e-58 237.0
12 TraesCS3D01G417300 chr3A 95.238 42 0 2 2067 2106 436485913 436485872 9.800000e-07 65.8
13 TraesCS3D01G417300 chr5D 95.055 182 8 1 4 185 484121461 484121281 6.910000e-73 285.0
14 TraesCS3D01G417300 chr5D 93.085 188 7 4 4 185 8770017 8769830 1.930000e-68 270.0
15 TraesCS3D01G417300 chr4D 94.054 185 7 1 1 185 4142300 4142480 1.160000e-70 278.0
16 TraesCS3D01G417300 chr4D 93.407 182 10 2 4 185 370689267 370689088 6.960000e-68 268.0
17 TraesCS3D01G417300 chr6A 87.866 239 24 3 1415 1651 585102970 585102735 4.160000e-70 276.0
18 TraesCS3D01G417300 chr6A 80.882 136 19 5 1037 1166 585103158 585103024 2.690000e-17 100.0
19 TraesCS3D01G417300 chr2A 93.548 186 10 2 1 185 639072446 639072630 4.160000e-70 276.0
20 TraesCS3D01G417300 chr1D 92.386 197 7 1 4 192 398875008 398874812 1.500000e-69 274.0
21 TraesCS3D01G417300 chr6B 91.753 194 12 2 1 190 21093514 21093707 2.500000e-67 267.0
22 TraesCS3D01G417300 chr6B 91.753 194 12 2 1 190 21096510 21096703 2.500000e-67 267.0
23 TraesCS3D01G417300 chr6B 91.753 194 12 2 1 190 21099870 21100063 2.500000e-67 267.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G417300 chr3D 528955889 528960109 4220 False 7795.000000 7795 100.000000 1 4221 1 chr3D.!!$F1 4220
1 TraesCS3D01G417300 chr3B 699101743 699106005 4262 True 1145.750000 1962 88.868750 187 4221 4 chr3B.!!$R2 4034
2 TraesCS3D01G417300 chr3B 699507296 699509826 2530 True 301.066667 680 84.381333 199 1361 3 chr3B.!!$R3 1162
3 TraesCS3D01G417300 chr3A 662930817 662933968 3151 False 889.000000 1543 82.788667 435 3670 3 chr3A.!!$F1 3235
4 TraesCS3D01G417300 chr6B 21093514 21100063 6549 False 267.000000 267 91.753000 1 190 3 chr6B.!!$F1 189

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
379 806 0.44231 CACCGAATGCAACGAATCGT 59.558 50.0 16.17 0.96 43.97 3.73 F
2000 4652 0.17668 TCTTCTCTCGCCTGCATTCC 59.823 55.0 0.00 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 6273 0.108186 CACACCCAGCGAGCTATGAA 60.108 55.0 0.0 0.0 0.00 2.57 R
3392 8079 0.107456 CGGAAGGGACTCATGGATGG 59.893 60.0 0.0 0.0 38.49 3.51 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
49 50 7.917597 AGTACTAGTATGAGTAACATCACACG 58.082 38.462 5.75 0.00 40.07 4.49
57 212 6.262193 TGAGTAACATCACACGTATCAAGA 57.738 37.500 0.00 0.00 0.00 3.02
75 230 7.594351 ATCAAGACAAGATGAGTCTATAGCA 57.406 36.000 0.00 0.00 45.11 3.49
101 256 9.801873 ATAATAAATGAAGTGTTGCATGTTACC 57.198 29.630 0.00 0.00 0.00 2.85
109 264 5.009631 AGTGTTGCATGTTACCACACATAT 58.990 37.500 15.74 0.00 35.51 1.78
110 265 5.094812 GTGTTGCATGTTACCACACATATG 58.905 41.667 10.02 0.00 35.51 1.78
111 266 4.764308 TGTTGCATGTTACCACACATATGT 59.236 37.500 1.41 1.41 40.80 2.29
112 267 5.242615 TGTTGCATGTTACCACACATATGTT 59.757 36.000 5.37 0.00 36.72 2.71
129 284 6.954684 ACATATGTTACTCCCCACTATAGAGG 59.045 42.308 6.78 8.10 31.70 3.69
132 287 5.950023 TGTTACTCCCCACTATAGAGGTAG 58.050 45.833 14.29 12.87 31.70 3.18
136 291 5.951204 ACTCCCCACTATAGAGGTAGTAAC 58.049 45.833 14.29 0.00 33.29 2.50
142 297 7.830201 CCCCACTATAGAGGTAGTAACATAGAG 59.170 44.444 14.29 0.00 33.29 2.43
180 335 7.005709 ACTCTATATTACTACCCATTGTGGC 57.994 40.000 0.00 0.00 35.79 5.01
182 337 7.954056 ACTCTATATTACTACCCATTGTGGCTA 59.046 37.037 0.00 0.00 35.79 3.93
183 338 8.362464 TCTATATTACTACCCATTGTGGCTAG 57.638 38.462 0.00 0.00 35.79 3.42
185 340 9.251440 CTATATTACTACCCATTGTGGCTAGTA 57.749 37.037 6.96 6.96 35.79 1.82
186 341 8.680820 ATATTACTACCCATTGTGGCTAGTAT 57.319 34.615 10.45 5.82 35.79 2.12
187 342 4.957684 ACTACCCATTGTGGCTAGTATC 57.042 45.455 2.84 0.00 35.79 2.24
189 344 3.845781 ACCCATTGTGGCTAGTATCAG 57.154 47.619 0.00 0.00 35.79 2.90
315 479 3.674753 CAGAAATTTCGCCATGTTTGTCC 59.325 43.478 12.42 0.00 0.00 4.02
317 481 1.243902 ATTTCGCCATGTTTGTCCGT 58.756 45.000 0.00 0.00 0.00 4.69
319 483 2.123988 TTCGCCATGTTTGTCCGTGC 62.124 55.000 0.00 0.00 0.00 5.34
359 786 7.094634 GCATATCTTTATGTTCCCGTCATCATT 60.095 37.037 0.00 0.00 37.99 2.57
365 792 0.899019 TTCCCGTCATCATTCACCGA 59.101 50.000 0.00 0.00 0.00 4.69
366 793 0.899019 TCCCGTCATCATTCACCGAA 59.101 50.000 0.00 0.00 0.00 4.30
367 794 1.484653 TCCCGTCATCATTCACCGAAT 59.515 47.619 0.00 0.00 31.86 3.34
369 796 1.003545 CCGTCATCATTCACCGAATGC 60.004 52.381 11.08 0.00 46.14 3.56
370 797 1.665169 CGTCATCATTCACCGAATGCA 59.335 47.619 11.08 0.00 46.14 3.96
371 798 2.095692 CGTCATCATTCACCGAATGCAA 59.904 45.455 11.08 0.00 46.14 4.08
372 799 3.429085 GTCATCATTCACCGAATGCAAC 58.571 45.455 11.08 6.17 46.14 4.17
374 801 1.802069 TCATTCACCGAATGCAACGA 58.198 45.000 16.17 0.00 46.14 3.85
375 802 2.147150 TCATTCACCGAATGCAACGAA 58.853 42.857 16.17 5.32 46.14 3.85
378 805 0.718904 TCACCGAATGCAACGAATCG 59.281 50.000 16.17 0.00 35.19 3.34
379 806 0.442310 CACCGAATGCAACGAATCGT 59.558 50.000 16.17 0.96 43.97 3.73
423 850 2.203224 CCCTCGGCGAGCTCTCTA 60.203 66.667 30.55 0.00 0.00 2.43
430 857 2.023461 CGAGCTCTCTACGGTGCG 59.977 66.667 12.85 0.00 0.00 5.34
431 858 2.409651 GAGCTCTCTACGGTGCGG 59.590 66.667 6.43 0.00 0.00 5.69
433 860 2.202623 GCTCTCTACGGTGCGGTG 60.203 66.667 0.00 0.00 0.00 4.94
435 862 2.675423 TCTCTACGGTGCGGTGCT 60.675 61.111 0.00 0.00 0.00 4.40
436 863 2.214181 CTCTCTACGGTGCGGTGCTT 62.214 60.000 0.00 0.00 0.00 3.91
531 958 3.597182 TGCCATCCTGGACCTATATCAA 58.403 45.455 0.00 0.00 40.96 2.57
532 959 4.178339 TGCCATCCTGGACCTATATCAAT 58.822 43.478 0.00 0.00 40.96 2.57
533 960 5.349690 TGCCATCCTGGACCTATATCAATA 58.650 41.667 0.00 0.00 40.96 1.90
535 962 6.100279 TGCCATCCTGGACCTATATCAATATC 59.900 42.308 0.00 0.00 40.96 1.63
537 964 7.202167 GCCATCCTGGACCTATATCAATATCAT 60.202 40.741 0.00 0.00 40.96 2.45
564 1002 1.693627 CACATACTCTACCGCTCCCT 58.306 55.000 0.00 0.00 0.00 4.20
582 2769 4.388499 CCCACAACCTCGTCCCGG 62.388 72.222 0.00 0.00 0.00 5.73
594 2781 1.876664 GTCCCGGCTTCTGCTTTTC 59.123 57.895 0.00 0.00 39.59 2.29
676 2884 1.383803 CCCCCTCTCCCTCCTTCAG 60.384 68.421 0.00 0.00 0.00 3.02
811 3039 3.854459 CCCTCGCGCGCTTCTTTC 61.854 66.667 30.48 0.00 0.00 2.62
812 3040 2.811317 CCTCGCGCGCTTCTTTCT 60.811 61.111 30.48 0.00 0.00 2.52
813 3041 2.383527 CCTCGCGCGCTTCTTTCTT 61.384 57.895 30.48 0.00 0.00 2.52
814 3042 1.057976 CTCGCGCGCTTCTTTCTTC 59.942 57.895 30.48 0.00 0.00 2.87
820 3048 1.291877 GCGCTTCTTTCTTCGCTCCA 61.292 55.000 0.00 0.00 43.70 3.86
823 3051 2.222908 CGCTTCTTTCTTCGCTCCATTC 60.223 50.000 0.00 0.00 0.00 2.67
833 3061 1.210155 GCTCCATTCGTGTTGGTGC 59.790 57.895 10.56 10.56 43.88 5.01
834 3062 1.875963 CTCCATTCGTGTTGGTGCC 59.124 57.895 0.00 0.00 35.64 5.01
902 3172 3.453679 ACGGCGCTCCTCTCTTCC 61.454 66.667 6.90 0.00 0.00 3.46
904 3174 2.762043 GGCGCTCCTCTCTTCCCT 60.762 66.667 7.64 0.00 0.00 4.20
907 3177 1.819905 CGCTCCTCTCTTCCCTTCC 59.180 63.158 0.00 0.00 0.00 3.46
909 3179 1.681486 GCTCCTCTCTTCCCTTCCCG 61.681 65.000 0.00 0.00 0.00 5.14
910 3180 1.001760 TCCTCTCTTCCCTTCCCGG 59.998 63.158 0.00 0.00 0.00 5.73
911 3181 1.306226 CCTCTCTTCCCTTCCCGGT 60.306 63.158 0.00 0.00 0.00 5.28
912 3182 1.617947 CCTCTCTTCCCTTCCCGGTG 61.618 65.000 0.00 0.00 0.00 4.94
913 3183 1.612442 TCTCTTCCCTTCCCGGTGG 60.612 63.158 0.00 0.00 0.00 4.61
914 3184 2.609610 TCTTCCCTTCCCGGTGGG 60.610 66.667 15.86 15.86 46.11 4.61
915 3185 2.933834 CTTCCCTTCCCGGTGGGT 60.934 66.667 19.71 0.00 44.74 4.51
916 3186 3.253838 TTCCCTTCCCGGTGGGTG 61.254 66.667 19.71 5.81 44.74 4.61
931 3201 1.682344 GGTGGGTGGGCTCCAAATC 60.682 63.158 0.00 0.00 34.18 2.17
941 3245 1.677633 CTCCAAATCCGGGCGGTTT 60.678 57.895 0.00 0.00 36.47 3.27
1675 4317 1.009829 GCGAACAGAATTCCGCTCAT 58.990 50.000 16.40 0.00 43.75 2.90
1678 4320 3.063452 GCGAACAGAATTCCGCTCATTTA 59.937 43.478 16.40 0.00 43.75 1.40
1679 4321 4.578601 CGAACAGAATTCCGCTCATTTAC 58.421 43.478 0.65 0.00 0.00 2.01
1681 4323 2.351726 ACAGAATTCCGCTCATTTACGC 59.648 45.455 0.65 0.00 0.00 4.42
1683 4325 3.063997 CAGAATTCCGCTCATTTACGCTT 59.936 43.478 0.65 0.00 0.00 4.68
1684 4326 3.063997 AGAATTCCGCTCATTTACGCTTG 59.936 43.478 0.65 0.00 0.00 4.01
1685 4327 2.087501 TTCCGCTCATTTACGCTTGA 57.912 45.000 0.00 0.00 0.00 3.02
1687 4329 1.067142 TCCGCTCATTTACGCTTGAGT 60.067 47.619 2.30 0.00 41.16 3.41
1688 4330 1.061131 CCGCTCATTTACGCTTGAGTG 59.939 52.381 6.52 6.52 45.61 3.51
1690 4332 3.375911 GCTCATTTACGCTTGAGTGAC 57.624 47.619 0.00 0.00 41.16 3.67
1692 4334 3.423645 GCTCATTTACGCTTGAGTGACAC 60.424 47.826 0.00 0.00 41.16 3.67
1693 4335 2.729360 TCATTTACGCTTGAGTGACACG 59.271 45.455 0.00 0.00 0.00 4.49
1694 4336 0.856641 TTTACGCTTGAGTGACACGC 59.143 50.000 1.90 1.90 39.82 5.34
1695 4337 0.942410 TTACGCTTGAGTGACACGCC 60.942 55.000 6.88 0.72 40.03 5.68
1696 4338 3.767230 CGCTTGAGTGACACGCCG 61.767 66.667 6.88 0.00 40.03 6.46
1697 4339 3.414700 GCTTGAGTGACACGCCGG 61.415 66.667 6.88 0.00 37.72 6.13
1698 4340 2.338620 CTTGAGTGACACGCCGGA 59.661 61.111 5.05 0.00 0.00 5.14
1699 4341 1.734477 CTTGAGTGACACGCCGGAG 60.734 63.158 5.05 3.72 0.00 4.63
1700 4342 3.858868 TTGAGTGACACGCCGGAGC 62.859 63.158 5.05 0.00 0.00 4.70
1923 4571 4.090588 TTCATCCACGTCCGGGCC 62.091 66.667 0.00 0.00 0.00 5.80
1984 4636 0.255033 GGTACAATTCCCGGCCTCTT 59.745 55.000 0.00 0.00 0.00 2.85
1986 4638 1.209747 GTACAATTCCCGGCCTCTTCT 59.790 52.381 0.00 0.00 0.00 2.85
1987 4639 0.253327 ACAATTCCCGGCCTCTTCTC 59.747 55.000 0.00 0.00 0.00 2.87
1988 4640 0.543749 CAATTCCCGGCCTCTTCTCT 59.456 55.000 0.00 0.00 0.00 3.10
1990 4642 1.395826 ATTCCCGGCCTCTTCTCTCG 61.396 60.000 0.00 0.00 0.00 4.04
1991 4643 4.214327 CCCGGCCTCTTCTCTCGC 62.214 72.222 0.00 0.00 0.00 5.03
1992 4644 4.214327 CCGGCCTCTTCTCTCGCC 62.214 72.222 0.00 0.00 38.07 5.54
1993 4645 3.144193 CGGCCTCTTCTCTCGCCT 61.144 66.667 0.00 0.00 39.34 5.52
1994 4646 2.498726 GGCCTCTTCTCTCGCCTG 59.501 66.667 0.00 0.00 38.41 4.85
1995 4647 2.202864 GCCTCTTCTCTCGCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
1996 4648 3.011635 GCCTCTTCTCTCGCCTGCA 62.012 63.158 0.00 0.00 0.00 4.41
1998 4650 0.177604 CCTCTTCTCTCGCCTGCATT 59.822 55.000 0.00 0.00 0.00 3.56
1999 4651 1.569708 CTCTTCTCTCGCCTGCATTC 58.430 55.000 0.00 0.00 0.00 2.67
2000 4652 0.176680 TCTTCTCTCGCCTGCATTCC 59.823 55.000 0.00 0.00 0.00 3.01
2003 4655 1.523258 CTCTCGCCTGCATTCCTGG 60.523 63.158 0.00 0.00 35.75 4.45
2009 4661 2.586245 CTGCATTCCTGGCCGAGA 59.414 61.111 0.00 0.00 0.00 4.04
2036 4719 7.041508 GGACTGATGATCATTTTCATGGTAGAC 60.042 40.741 10.14 0.00 36.48 2.59
2063 4746 5.916661 ATTCATTTCTCATGCTCTGCTTT 57.083 34.783 0.00 0.00 0.00 3.51
2065 4748 3.693085 TCATTTCTCATGCTCTGCTTTCC 59.307 43.478 0.00 0.00 0.00 3.13
2071 4754 2.015587 CATGCTCTGCTTTCCCTTCTC 58.984 52.381 0.00 0.00 0.00 2.87
2076 4761 1.003355 TGCTTTCCCTTCTCCTGCG 60.003 57.895 0.00 0.00 0.00 5.18
2149 6182 2.040544 CCCGGCTGCAACAAGGTAG 61.041 63.158 0.50 0.00 0.00 3.18
2154 6187 2.611971 CGGCTGCAACAAGGTAGAGTAA 60.612 50.000 0.50 0.00 0.00 2.24
2157 6190 4.322499 GGCTGCAACAAGGTAGAGTAACTA 60.322 45.833 0.50 0.00 0.00 2.24
2192 6225 4.604843 TTCTGCACTTATCATTTCGCAG 57.395 40.909 0.00 0.00 46.34 5.18
2203 6236 2.032799 TCATTTCGCAGTTGTTGTCACC 59.967 45.455 0.00 0.00 0.00 4.02
2209 6242 1.331756 GCAGTTGTTGTCACCTCACTG 59.668 52.381 0.00 0.00 0.00 3.66
2211 6244 1.837439 AGTTGTTGTCACCTCACTGGA 59.163 47.619 0.00 0.00 39.71 3.86
2212 6245 2.158900 AGTTGTTGTCACCTCACTGGAG 60.159 50.000 0.00 0.00 41.02 3.86
2213 6246 1.496060 TGTTGTCACCTCACTGGAGT 58.504 50.000 0.00 0.00 39.64 3.85
2214 6247 1.138859 TGTTGTCACCTCACTGGAGTG 59.861 52.381 0.00 0.00 46.91 3.51
2224 6257 3.693810 ACTGGAGTGAGGGAGTACC 57.306 57.895 0.00 0.00 40.67 3.34
2247 6280 5.988561 CCTCATTAGGTTCAGACTTCATAGC 59.011 44.000 0.00 0.00 38.19 2.97
2253 6286 2.857152 GTTCAGACTTCATAGCTCGCTG 59.143 50.000 0.85 0.00 0.00 5.18
2285 6318 5.296748 CAGATTTGAAACCCGGAAAAATGT 58.703 37.500 0.73 0.00 0.00 2.71
2322 6355 3.512516 GGCAAGGCCGTCATGCTC 61.513 66.667 20.10 10.45 39.62 4.26
2378 6411 3.592059 GGCAAGTCGAGGTACACAAATA 58.408 45.455 0.00 0.00 0.00 1.40
2379 6412 4.189231 GGCAAGTCGAGGTACACAAATAT 58.811 43.478 0.00 0.00 0.00 1.28
2381 6414 5.233689 GGCAAGTCGAGGTACACAAATATAC 59.766 44.000 0.00 0.00 0.00 1.47
2384 6417 5.899299 AGTCGAGGTACACAAATATACACC 58.101 41.667 0.00 0.00 0.00 4.16
2385 6418 4.736793 GTCGAGGTACACAAATATACACCG 59.263 45.833 0.00 0.00 0.00 4.94
2387 6420 5.300034 TCGAGGTACACAAATATACACCGAT 59.700 40.000 0.00 0.00 0.00 4.18
2390 6423 7.350744 AGGTACACAAATATACACCGATACA 57.649 36.000 0.00 0.00 0.00 2.29
2447 6494 3.689161 CCACGAATTGCCATCTTGAACTA 59.311 43.478 0.00 0.00 0.00 2.24
2448 6495 4.155826 CCACGAATTGCCATCTTGAACTAA 59.844 41.667 0.00 0.00 0.00 2.24
2449 6496 5.088739 CACGAATTGCCATCTTGAACTAAC 58.911 41.667 0.00 0.00 0.00 2.34
2450 6497 5.003804 ACGAATTGCCATCTTGAACTAACT 58.996 37.500 0.00 0.00 0.00 2.24
2463 6510 6.367969 TCTTGAACTAACTTATGCCGTTCTTC 59.632 38.462 0.00 0.00 36.03 2.87
2613 6856 2.829914 GCTCCCATTGCCGCATCA 60.830 61.111 0.00 0.00 0.00 3.07
2641 6888 4.141959 CCTCCTTCCTCTCTGACTGATTTC 60.142 50.000 0.00 0.00 0.00 2.17
2715 6965 1.819632 GTCGCATTTCCCGCTGGAT 60.820 57.895 0.00 0.00 41.40 3.41
3062 7322 1.965754 GCCAGGAGATCGCCACTTCT 61.966 60.000 18.44 0.00 0.00 2.85
3114 7389 6.009589 TCCAGTTTCAGCCTGAATTATGAAA 58.990 36.000 8.18 0.00 38.85 2.69
3135 7545 9.767228 ATGAAAATTCACATCACTTTCATTCAA 57.233 25.926 0.00 0.00 41.58 2.69
3138 7548 6.653526 ATTCACATCACTTTCATTCAACCA 57.346 33.333 0.00 0.00 0.00 3.67
3139 7549 5.694231 TCACATCACTTTCATTCAACCAG 57.306 39.130 0.00 0.00 0.00 4.00
3167 7577 6.254157 CACCAAAGATTCGGATGCTAAATTTG 59.746 38.462 0.00 5.92 0.00 2.32
3172 7582 4.712122 TTCGGATGCTAAATTTGTTCCC 57.288 40.909 0.00 0.00 0.00 3.97
3178 7588 5.885912 GGATGCTAAATTTGTTCCCTGTCTA 59.114 40.000 0.00 0.00 0.00 2.59
3179 7589 6.038714 GGATGCTAAATTTGTTCCCTGTCTAG 59.961 42.308 0.00 0.00 0.00 2.43
3267 7947 1.063811 GACCGGAATCCTCGACGAC 59.936 63.158 9.46 0.00 0.00 4.34
3269 7949 2.466982 CCGGAATCCTCGACGACGA 61.467 63.158 9.98 9.98 46.56 4.20
3304 7984 3.873910 TGTACATAGGGAGAAGCAAAGC 58.126 45.455 0.00 0.00 0.00 3.51
3314 8001 2.192608 GAAGCAAAGCCAGTCAGCCG 62.193 60.000 0.00 0.00 0.00 5.52
3316 8003 3.058160 CAAAGCCAGTCAGCCGGG 61.058 66.667 2.18 0.00 0.00 5.73
3336 8023 0.379669 CAAGCTTGCCATCGATCCAC 59.620 55.000 14.65 0.00 0.00 4.02
3365 8052 4.734398 AGCACTCTGAGATTCAACCTAG 57.266 45.455 12.44 0.00 0.00 3.02
3372 8059 4.081972 TCTGAGATTCAACCTAGCAGTGTC 60.082 45.833 0.00 0.00 0.00 3.67
3373 8060 3.834813 TGAGATTCAACCTAGCAGTGTCT 59.165 43.478 0.00 0.00 0.00 3.41
3374 8061 4.284490 TGAGATTCAACCTAGCAGTGTCTT 59.716 41.667 0.00 0.00 0.00 3.01
3375 8062 5.480422 TGAGATTCAACCTAGCAGTGTCTTA 59.520 40.000 0.00 0.00 0.00 2.10
3376 8063 5.725362 AGATTCAACCTAGCAGTGTCTTAC 58.275 41.667 0.00 0.00 0.00 2.34
3377 8064 5.482175 AGATTCAACCTAGCAGTGTCTTACT 59.518 40.000 0.00 0.00 41.36 2.24
3392 8079 8.989653 AGTGTCTTACTGTAGCTTCTAATTTC 57.010 34.615 0.00 0.00 38.49 2.17
3393 8080 8.035984 AGTGTCTTACTGTAGCTTCTAATTTCC 58.964 37.037 0.00 0.00 38.49 3.13
3394 8081 7.817962 GTGTCTTACTGTAGCTTCTAATTTCCA 59.182 37.037 0.00 0.00 0.00 3.53
3395 8082 8.540388 TGTCTTACTGTAGCTTCTAATTTCCAT 58.460 33.333 0.00 0.00 0.00 3.41
3396 8083 9.036671 GTCTTACTGTAGCTTCTAATTTCCATC 57.963 37.037 0.00 0.00 0.00 3.51
3397 8084 8.204836 TCTTACTGTAGCTTCTAATTTCCATCC 58.795 37.037 0.00 0.00 0.00 3.51
3398 8085 6.313519 ACTGTAGCTTCTAATTTCCATCCA 57.686 37.500 0.00 0.00 0.00 3.41
3399 8086 6.904626 ACTGTAGCTTCTAATTTCCATCCAT 58.095 36.000 0.00 0.00 0.00 3.41
3400 8087 6.769822 ACTGTAGCTTCTAATTTCCATCCATG 59.230 38.462 0.00 0.00 0.00 3.66
3401 8088 6.899089 TGTAGCTTCTAATTTCCATCCATGA 58.101 36.000 0.00 0.00 0.00 3.07
3402 8089 6.994496 TGTAGCTTCTAATTTCCATCCATGAG 59.006 38.462 0.00 0.00 0.00 2.90
3403 8090 6.011122 AGCTTCTAATTTCCATCCATGAGT 57.989 37.500 0.00 0.00 0.00 3.41
3462 8198 3.788766 CGGCCGTGCAACAGTAGC 61.789 66.667 19.50 0.00 35.74 3.58
3463 8199 3.788766 GGCCGTGCAACAGTAGCG 61.789 66.667 0.00 0.00 35.74 4.26
3464 8200 4.445545 GCCGTGCAACAGTAGCGC 62.446 66.667 0.00 0.00 35.74 5.92
3480 8219 1.783031 GCGCAGGCTAGCTCTACGTA 61.783 60.000 15.72 0.00 35.83 3.57
3481 8220 0.875728 CGCAGGCTAGCTCTACGTAT 59.124 55.000 15.72 0.00 0.00 3.06
3482 8221 1.135916 CGCAGGCTAGCTCTACGTATC 60.136 57.143 15.72 0.00 0.00 2.24
3520 8265 5.246203 TCTCCTTTCTTCTTGTGCTAAGCTA 59.754 40.000 0.00 0.00 0.00 3.32
3521 8266 5.482908 TCCTTTCTTCTTGTGCTAAGCTAG 58.517 41.667 0.00 0.00 0.00 3.42
3522 8267 4.633565 CCTTTCTTCTTGTGCTAAGCTAGG 59.366 45.833 0.00 0.00 0.00 3.02
3548 8293 1.202582 GATCGATGGGTACATAGCGCT 59.797 52.381 17.26 17.26 37.47 5.92
3551 8296 1.284982 GATGGGTACATAGCGCTGCG 61.285 60.000 22.90 19.17 37.47 5.18
3563 8308 3.409856 GCTGCGCGGTACATGAAT 58.590 55.556 19.23 0.00 0.00 2.57
3565 8310 1.934463 CTGCGCGGTACATGAATCC 59.066 57.895 8.83 0.00 0.00 3.01
3567 8312 0.107897 TGCGCGGTACATGAATCCTT 60.108 50.000 8.83 0.00 0.00 3.36
3568 8313 0.304705 GCGCGGTACATGAATCCTTG 59.695 55.000 8.83 0.00 0.00 3.61
3721 9762 3.496309 TTGCCCTGCCCACTGTGAG 62.496 63.158 9.86 0.00 0.00 3.51
3747 9788 2.240414 TGATTGGCATCTCACATCTGGT 59.760 45.455 0.00 0.00 0.00 4.00
3796 9837 0.319813 CGCTGGCGATGATGGTGATA 60.320 55.000 9.51 0.00 42.83 2.15
3801 9842 3.667360 TGGCGATGATGGTGATAATGAG 58.333 45.455 0.00 0.00 0.00 2.90
3802 9843 3.071457 TGGCGATGATGGTGATAATGAGT 59.929 43.478 0.00 0.00 0.00 3.41
3803 9844 3.434641 GGCGATGATGGTGATAATGAGTG 59.565 47.826 0.00 0.00 0.00 3.51
3804 9845 4.309933 GCGATGATGGTGATAATGAGTGA 58.690 43.478 0.00 0.00 0.00 3.41
3806 9847 4.388165 CGATGATGGTGATAATGAGTGAGC 59.612 45.833 0.00 0.00 0.00 4.26
3807 9848 5.549347 GATGATGGTGATAATGAGTGAGCT 58.451 41.667 0.00 0.00 0.00 4.09
3808 9849 4.953667 TGATGGTGATAATGAGTGAGCTC 58.046 43.478 6.82 6.82 41.97 4.09
3816 9860 6.017770 GTGATAATGAGTGAGCTCGTAGTAGT 60.018 42.308 9.64 0.00 44.48 2.73
3871 9915 0.322906 GAGAAGGTGAGGGGCAAAGG 60.323 60.000 0.00 0.00 0.00 3.11
3910 9954 1.882623 GGACAGAAGGAACAAGCAAGG 59.117 52.381 0.00 0.00 0.00 3.61
4008 10052 1.822613 CACTGGCTATGGCTGGCTG 60.823 63.158 0.00 0.00 38.73 4.85
4010 10054 3.786884 CTGGCTATGGCTGGCTGGG 62.787 68.421 0.00 0.00 38.73 4.45
4012 10056 2.276740 GCTATGGCTGGCTGGGTT 59.723 61.111 2.00 0.00 35.22 4.11
4014 10058 2.044053 TATGGCTGGCTGGGTTGC 60.044 61.111 2.00 0.00 0.00 4.17
4029 10073 0.179111 GTTGCCGATGACGATGAGGA 60.179 55.000 0.00 0.00 42.66 3.71
4039 10086 2.158798 TGACGATGAGGACTCCGTATCT 60.159 50.000 10.87 2.04 35.22 1.98
4051 10098 0.875728 CCGTATCTGTAGGAGCCTCG 59.124 60.000 0.00 0.00 0.00 4.63
4052 10099 0.238817 CGTATCTGTAGGAGCCTCGC 59.761 60.000 0.00 0.00 0.00 5.03
4053 10100 0.599060 GTATCTGTAGGAGCCTCGCC 59.401 60.000 0.00 0.00 0.00 5.54
4054 10101 0.539901 TATCTGTAGGAGCCTCGCCC 60.540 60.000 0.00 0.00 0.00 6.13
4055 10102 2.305314 ATCTGTAGGAGCCTCGCCCT 62.305 60.000 0.00 0.00 34.56 5.19
4056 10103 2.442272 TGTAGGAGCCTCGCCCTC 60.442 66.667 0.00 0.00 32.93 4.30
4097 10144 2.521105 ACGAGCAAAGTAAAGACGGT 57.479 45.000 0.00 0.00 0.00 4.83
4099 10146 1.459592 CGAGCAAAGTAAAGACGGTGG 59.540 52.381 0.00 0.00 0.00 4.61
4100 10147 2.762745 GAGCAAAGTAAAGACGGTGGA 58.237 47.619 0.00 0.00 0.00 4.02
4158 10205 2.780643 CGCCATTCACTGCGTCTG 59.219 61.111 0.00 0.00 45.43 3.51
4175 10222 3.093449 GCGTCTGCGTTTGCTTGC 61.093 61.111 0.00 0.00 43.34 4.01
4186 10233 2.669364 GTTTGCTTGCTCCTGTTCATG 58.331 47.619 0.00 0.00 0.00 3.07
4193 10240 2.359850 TCCTGTTCATGTGCGGCC 60.360 61.111 0.00 0.00 0.00 6.13
4217 10264 4.697352 GCTGCCTCAGTTAAAAAGAGATCA 59.303 41.667 0.00 0.00 33.43 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.692088 ACGTGTGATGTTACTCATACTAGTAC 58.308 38.462 4.31 0.00 35.73 2.73
34 35 6.090783 GTCTTGATACGTGTGATGTTACTCA 58.909 40.000 0.00 0.00 0.00 3.41
48 49 7.748683 GCTATAGACTCATCTTGTCTTGATACG 59.251 40.741 3.21 0.00 41.45 3.06
49 50 8.572185 TGCTATAGACTCATCTTGTCTTGATAC 58.428 37.037 3.21 0.00 41.45 2.24
75 230 9.801873 GGTAACATGCAACACTTCATTTATTAT 57.198 29.630 0.00 0.00 0.00 1.28
101 256 4.487714 AGTGGGGAGTAACATATGTGTG 57.512 45.455 9.63 0.00 38.92 3.82
109 264 4.894252 ACCTCTATAGTGGGGAGTAACA 57.106 45.455 21.82 0.00 33.22 2.41
110 265 5.951204 ACTACCTCTATAGTGGGGAGTAAC 58.049 45.833 22.09 0.00 34.02 2.50
111 266 7.129349 TGTTACTACCTCTATAGTGGGGAGTAA 59.871 40.741 28.26 28.26 38.03 2.24
112 267 6.621098 TGTTACTACCTCTATAGTGGGGAGTA 59.379 42.308 23.32 23.32 36.09 2.59
153 308 9.310449 CCACAATGGGTAGTAATATAGAGTAGT 57.690 37.037 0.00 0.00 32.67 2.73
154 309 8.251721 GCCACAATGGGTAGTAATATAGAGTAG 58.748 40.741 0.00 0.00 38.19 2.57
155 310 8.130671 GCCACAATGGGTAGTAATATAGAGTA 57.869 38.462 0.00 0.00 38.19 2.59
156 311 7.005709 GCCACAATGGGTAGTAATATAGAGT 57.994 40.000 0.00 0.00 38.19 3.24
170 325 2.224621 CCCTGATACTAGCCACAATGGG 60.225 54.545 0.00 0.00 38.19 4.00
171 326 2.705658 TCCCTGATACTAGCCACAATGG 59.294 50.000 0.00 0.00 41.55 3.16
172 327 3.495100 GGTCCCTGATACTAGCCACAATG 60.495 52.174 0.00 0.00 0.00 2.82
173 328 2.706190 GGTCCCTGATACTAGCCACAAT 59.294 50.000 0.00 0.00 0.00 2.71
176 331 1.789523 TGGTCCCTGATACTAGCCAC 58.210 55.000 0.00 0.00 0.00 5.01
177 332 2.609747 GATGGTCCCTGATACTAGCCA 58.390 52.381 0.00 0.00 0.00 4.75
180 335 1.546476 GGCGATGGTCCCTGATACTAG 59.454 57.143 0.00 0.00 0.00 2.57
182 337 0.105453 AGGCGATGGTCCCTGATACT 60.105 55.000 0.00 0.00 0.00 2.12
183 338 0.759346 AAGGCGATGGTCCCTGATAC 59.241 55.000 0.00 0.00 0.00 2.24
185 340 0.982852 TGAAGGCGATGGTCCCTGAT 60.983 55.000 0.00 0.00 0.00 2.90
186 341 1.612146 TGAAGGCGATGGTCCCTGA 60.612 57.895 0.00 0.00 0.00 3.86
187 342 1.450312 GTGAAGGCGATGGTCCCTG 60.450 63.158 0.00 0.00 0.00 4.45
189 344 2.124695 GGTGAAGGCGATGGTCCC 60.125 66.667 0.00 0.00 0.00 4.46
243 407 0.667993 TTGCGCCCTGTTTTTCTGAG 59.332 50.000 4.18 0.00 0.00 3.35
273 437 8.870160 TTTCTGAACCTGATAAACAAATTGTG 57.130 30.769 0.00 0.00 0.00 3.33
291 455 4.942852 ACAAACATGGCGAAATTTCTGAA 58.057 34.783 15.92 1.79 0.00 3.02
292 456 4.545610 GACAAACATGGCGAAATTTCTGA 58.454 39.130 15.92 0.38 0.00 3.27
295 459 2.661195 CGGACAAACATGGCGAAATTTC 59.339 45.455 8.20 8.20 0.00 2.17
359 786 0.718904 CGATTCGTTGCATTCGGTGA 59.281 50.000 10.93 0.79 0.00 4.02
374 801 1.443872 GCGGTGACTGACGACGATT 60.444 57.895 0.00 0.00 0.00 3.34
375 802 2.178521 GCGGTGACTGACGACGAT 59.821 61.111 0.00 0.00 0.00 3.73
378 805 2.710724 AAAGGGCGGTGACTGACGAC 62.711 60.000 0.00 0.00 37.40 4.34
379 806 2.035237 AAAAGGGCGGTGACTGACGA 62.035 55.000 0.00 0.00 0.00 4.20
381 808 1.534163 GTTAAAAGGGCGGTGACTGAC 59.466 52.381 0.00 0.00 0.00 3.51
383 810 0.879090 GGTTAAAAGGGCGGTGACTG 59.121 55.000 0.00 0.00 0.00 3.51
384 811 0.251033 GGGTTAAAAGGGCGGTGACT 60.251 55.000 0.00 0.00 0.00 3.41
385 812 1.246056 GGGGTTAAAAGGGCGGTGAC 61.246 60.000 0.00 0.00 0.00 3.67
386 813 1.075305 GGGGTTAAAAGGGCGGTGA 59.925 57.895 0.00 0.00 0.00 4.02
387 814 2.337246 CGGGGTTAAAAGGGCGGTG 61.337 63.158 0.00 0.00 0.00 4.94
388 815 2.034532 CGGGGTTAAAAGGGCGGT 59.965 61.111 0.00 0.00 0.00 5.68
423 850 2.665185 GAAGAAGCACCGCACCGT 60.665 61.111 0.00 0.00 0.00 4.83
430 857 1.301293 CCAGGGAGGAAGAAGCACC 59.699 63.158 0.00 0.00 41.22 5.01
431 858 0.402121 AACCAGGGAGGAAGAAGCAC 59.598 55.000 0.00 0.00 41.22 4.40
433 860 1.073923 TGAAACCAGGGAGGAAGAAGC 59.926 52.381 0.00 0.00 41.22 3.86
435 862 2.041620 CCATGAAACCAGGGAGGAAGAA 59.958 50.000 0.00 0.00 41.22 2.52
436 863 1.635487 CCATGAAACCAGGGAGGAAGA 59.365 52.381 0.00 0.00 41.22 2.87
531 958 4.082733 AGAGTATGTGCGCGTGTATGATAT 60.083 41.667 8.43 0.00 0.00 1.63
532 959 3.252458 AGAGTATGTGCGCGTGTATGATA 59.748 43.478 8.43 0.00 0.00 2.15
533 960 2.034685 AGAGTATGTGCGCGTGTATGAT 59.965 45.455 8.43 0.00 0.00 2.45
535 962 1.840181 AGAGTATGTGCGCGTGTATG 58.160 50.000 8.43 0.00 0.00 2.39
537 964 1.064505 GGTAGAGTATGTGCGCGTGTA 59.935 52.381 8.43 0.00 0.00 2.90
646 2847 2.204306 AGGGGGAGAAAGTGGGGG 60.204 66.667 0.00 0.00 0.00 5.40
776 2995 0.324943 GGAGGCAAGTAGGTTGAGCA 59.675 55.000 0.00 0.00 38.60 4.26
811 3039 0.443869 CCAACACGAATGGAGCGAAG 59.556 55.000 0.00 0.00 40.56 3.79
812 3040 0.250124 ACCAACACGAATGGAGCGAA 60.250 50.000 11.74 0.00 40.56 4.70
813 3041 0.948623 CACCAACACGAATGGAGCGA 60.949 55.000 11.74 0.00 40.56 4.93
814 3042 1.497278 CACCAACACGAATGGAGCG 59.503 57.895 11.74 0.00 40.56 5.03
820 3048 2.671619 CCCGGCACCAACACGAAT 60.672 61.111 0.00 0.00 0.00 3.34
885 3155 3.453679 GGAAGAGAGGAGCGCCGT 61.454 66.667 2.29 0.00 39.96 5.68
894 3164 1.617947 CCACCGGGAAGGGAAGAGAG 61.618 65.000 6.32 0.00 46.96 3.20
912 3182 3.238197 ATTTGGAGCCCACCCACCC 62.238 63.158 0.00 0.00 30.78 4.61
913 3183 1.682344 GATTTGGAGCCCACCCACC 60.682 63.158 0.00 0.00 30.78 4.61
914 3184 1.682344 GGATTTGGAGCCCACCCAC 60.682 63.158 0.00 0.00 30.78 4.61
915 3185 2.770130 GGATTTGGAGCCCACCCA 59.230 61.111 0.00 0.00 30.78 4.51
916 3186 2.440247 CGGATTTGGAGCCCACCC 60.440 66.667 0.00 0.00 30.78 4.61
926 3196 0.109319 CAAGAAACCGCCCGGATTTG 60.109 55.000 14.44 7.99 38.96 2.32
927 3197 1.248101 CCAAGAAACCGCCCGGATTT 61.248 55.000 14.44 9.89 38.96 2.17
1035 3340 1.814169 GTTGAGGAATCCCGCCGTC 60.814 63.158 0.00 0.00 37.58 4.79
1044 3349 2.040412 GTCCCAGTTGAGGTTGAGGAAT 59.960 50.000 0.00 0.00 0.00 3.01
1675 4317 0.856641 GCGTGTCACTCAAGCGTAAA 59.143 50.000 0.65 0.00 41.04 2.01
1681 4323 1.734477 CTCCGGCGTGTCACTCAAG 60.734 63.158 6.01 0.00 0.00 3.02
1683 4325 4.357947 GCTCCGGCGTGTCACTCA 62.358 66.667 6.01 0.00 0.00 3.41
1693 4335 3.661131 TCTATCGCTCGCTCCGGC 61.661 66.667 0.00 0.00 0.00 6.13
1694 4336 2.252855 GTCTATCGCTCGCTCCGG 59.747 66.667 0.00 0.00 0.00 5.14
1695 4337 2.127571 CGTCTATCGCTCGCTCCG 60.128 66.667 0.00 0.00 0.00 4.63
1696 4338 1.082627 GACGTCTATCGCTCGCTCC 60.083 63.158 8.70 0.00 44.19 4.70
1697 4339 1.437411 CGACGTCTATCGCTCGCTC 60.437 63.158 14.70 0.00 44.19 5.03
1698 4340 1.222766 ATCGACGTCTATCGCTCGCT 61.223 55.000 14.70 0.00 44.19 4.93
1699 4341 0.786439 GATCGACGTCTATCGCTCGC 60.786 60.000 14.70 0.00 44.19 5.03
1700 4342 0.785378 AGATCGACGTCTATCGCTCG 59.215 55.000 20.52 3.77 41.06 5.03
1701 4343 1.793532 TGAGATCGACGTCTATCGCTC 59.206 52.381 26.06 18.42 44.19 5.03
1702 4344 1.527736 GTGAGATCGACGTCTATCGCT 59.472 52.381 26.06 11.94 44.19 4.93
1703 4345 1.398705 GGTGAGATCGACGTCTATCGC 60.399 57.143 21.60 21.60 44.19 4.58
1704 4346 1.194997 GGGTGAGATCGACGTCTATCG 59.805 57.143 20.52 6.26 43.63 2.92
1705 4347 1.194997 CGGGTGAGATCGACGTCTATC 59.805 57.143 19.48 19.48 0.00 2.08
1706 4348 1.202615 TCGGGTGAGATCGACGTCTAT 60.203 52.381 14.70 8.32 0.00 1.98
1707 4349 0.176449 TCGGGTGAGATCGACGTCTA 59.824 55.000 14.70 2.39 0.00 2.59
1890 4538 3.978571 GAAGTCCTTGGGCGGCTCC 62.979 68.421 9.56 0.00 0.00 4.70
1975 4627 4.214327 GGCGAGAGAAGAGGCCGG 62.214 72.222 0.00 0.00 35.59 6.13
1984 4636 1.519246 CAGGAATGCAGGCGAGAGA 59.481 57.895 0.00 0.00 0.00 3.10
1986 4638 2.586245 CCAGGAATGCAGGCGAGA 59.414 61.111 0.00 0.00 0.00 4.04
1987 4639 3.207669 GCCAGGAATGCAGGCGAG 61.208 66.667 0.00 0.00 38.86 5.03
1991 4643 2.515523 CTCGGCCAGGAATGCAGG 60.516 66.667 2.24 0.00 0.00 4.85
1992 4644 1.523258 CTCTCGGCCAGGAATGCAG 60.523 63.158 2.24 0.00 0.00 4.41
1993 4645 2.586245 CTCTCGGCCAGGAATGCA 59.414 61.111 2.24 0.00 0.00 3.96
1994 4646 2.203126 CCTCTCGGCCAGGAATGC 60.203 66.667 2.24 0.00 31.91 3.56
1995 4647 1.144936 GTCCTCTCGGCCAGGAATG 59.855 63.158 11.78 0.00 41.94 2.67
1996 4648 1.002274 AGTCCTCTCGGCCAGGAAT 59.998 57.895 11.78 8.27 41.94 3.01
1998 4650 2.230189 ATCAGTCCTCTCGGCCAGGA 62.230 60.000 6.20 6.20 37.75 3.86
1999 4651 1.760086 ATCAGTCCTCTCGGCCAGG 60.760 63.158 2.24 1.49 0.00 4.45
2000 4652 1.039785 TCATCAGTCCTCTCGGCCAG 61.040 60.000 2.24 0.00 0.00 4.85
2003 4655 1.035923 TGATCATCAGTCCTCTCGGC 58.964 55.000 0.00 0.00 0.00 5.54
2004 4656 4.333913 AAATGATCATCAGTCCTCTCGG 57.666 45.455 9.06 0.00 0.00 4.63
2005 4657 5.354767 TGAAAATGATCATCAGTCCTCTCG 58.645 41.667 9.06 0.00 0.00 4.04
2007 4659 6.062749 CCATGAAAATGATCATCAGTCCTCT 58.937 40.000 9.06 0.00 37.96 3.69
2009 4661 5.763355 ACCATGAAAATGATCATCAGTCCT 58.237 37.500 9.06 0.00 37.96 3.85
2076 4761 3.446873 TGATCTTCTCTCTTCTCACCTGC 59.553 47.826 0.00 0.00 0.00 4.85
2192 6225 2.213499 CTCCAGTGAGGTGACAACAAC 58.787 52.381 0.00 0.00 39.02 3.32
2224 6257 6.815089 AGCTATGAAGTCTGAACCTAATGAG 58.185 40.000 0.00 0.00 0.00 2.90
2225 6258 6.460261 CGAGCTATGAAGTCTGAACCTAATGA 60.460 42.308 0.00 0.00 0.00 2.57
2226 6259 5.689514 CGAGCTATGAAGTCTGAACCTAATG 59.310 44.000 0.00 0.00 0.00 1.90
2227 6260 5.737635 GCGAGCTATGAAGTCTGAACCTAAT 60.738 44.000 0.00 0.00 0.00 1.73
2228 6261 4.440250 GCGAGCTATGAAGTCTGAACCTAA 60.440 45.833 0.00 0.00 0.00 2.69
2229 6262 3.066900 GCGAGCTATGAAGTCTGAACCTA 59.933 47.826 0.00 0.00 0.00 3.08
2230 6263 2.159170 GCGAGCTATGAAGTCTGAACCT 60.159 50.000 0.00 0.00 0.00 3.50
2231 6264 2.159170 AGCGAGCTATGAAGTCTGAACC 60.159 50.000 0.00 0.00 0.00 3.62
2232 6265 2.857152 CAGCGAGCTATGAAGTCTGAAC 59.143 50.000 0.00 0.00 0.00 3.18
2233 6266 2.159184 CCAGCGAGCTATGAAGTCTGAA 60.159 50.000 0.00 0.00 0.00 3.02
2234 6267 1.406898 CCAGCGAGCTATGAAGTCTGA 59.593 52.381 0.00 0.00 0.00 3.27
2235 6268 1.537776 CCCAGCGAGCTATGAAGTCTG 60.538 57.143 0.00 0.00 0.00 3.51
2236 6269 0.749649 CCCAGCGAGCTATGAAGTCT 59.250 55.000 0.00 0.00 0.00 3.24
2237 6270 0.461961 ACCCAGCGAGCTATGAAGTC 59.538 55.000 0.00 0.00 0.00 3.01
2238 6271 0.176680 CACCCAGCGAGCTATGAAGT 59.823 55.000 0.00 0.00 0.00 3.01
2239 6272 0.176680 ACACCCAGCGAGCTATGAAG 59.823 55.000 0.00 0.00 0.00 3.02
2240 6273 0.108186 CACACCCAGCGAGCTATGAA 60.108 55.000 0.00 0.00 0.00 2.57
2241 6274 1.517361 CACACCCAGCGAGCTATGA 59.483 57.895 0.00 0.00 0.00 2.15
2242 6275 2.176273 GCACACCCAGCGAGCTATG 61.176 63.158 0.00 0.00 0.00 2.23
2243 6276 2.187946 GCACACCCAGCGAGCTAT 59.812 61.111 0.00 0.00 0.00 2.97
2244 6277 4.082523 GGCACACCCAGCGAGCTA 62.083 66.667 0.00 0.00 0.00 3.32
2271 6304 1.765904 AGGCAAACATTTTTCCGGGTT 59.234 42.857 0.00 0.00 0.00 4.11
2322 6355 3.417969 GCACGTAGTTTATGATCTCGTCG 59.582 47.826 0.00 0.00 41.61 5.12
2378 6411 1.045407 ATGGGCGTGTATCGGTGTAT 58.955 50.000 0.00 0.00 40.26 2.29
2379 6412 0.825410 AATGGGCGTGTATCGGTGTA 59.175 50.000 0.00 0.00 40.26 2.90
2381 6414 0.742990 ACAATGGGCGTGTATCGGTG 60.743 55.000 0.00 0.00 40.26 4.94
2384 6417 1.062002 GTTGACAATGGGCGTGTATCG 59.938 52.381 0.00 0.00 43.12 2.92
2385 6418 1.400494 GGTTGACAATGGGCGTGTATC 59.600 52.381 0.00 0.00 0.00 2.24
2387 6420 0.108774 TGGTTGACAATGGGCGTGTA 59.891 50.000 0.00 0.00 0.00 2.90
2390 6423 1.115467 TTTTGGTTGACAATGGGCGT 58.885 45.000 0.00 0.00 39.21 5.68
2447 6494 4.642429 AGTTGAGAAGAACGGCATAAGTT 58.358 39.130 0.00 0.00 34.07 2.66
2448 6495 4.273148 AGTTGAGAAGAACGGCATAAGT 57.727 40.909 0.00 0.00 0.00 2.24
2449 6496 5.613358 AAAGTTGAGAAGAACGGCATAAG 57.387 39.130 0.00 0.00 0.00 1.73
2450 6497 5.757886 CAAAAGTTGAGAAGAACGGCATAA 58.242 37.500 0.00 0.00 0.00 1.90
2463 6510 4.266976 CAGAAACTGCAAGCAAAAGTTGAG 59.733 41.667 0.00 0.00 37.60 3.02
2617 6860 0.823460 CAGTCAGAGAGGAAGGAGGC 59.177 60.000 0.00 0.00 0.00 4.70
2620 6863 3.445450 CGAAATCAGTCAGAGAGGAAGGA 59.555 47.826 0.00 0.00 0.00 3.36
2622 6865 3.119173 AGCGAAATCAGTCAGAGAGGAAG 60.119 47.826 0.00 0.00 0.00 3.46
2623 6866 2.828520 AGCGAAATCAGTCAGAGAGGAA 59.171 45.455 0.00 0.00 0.00 3.36
2641 6888 1.456165 CATCTGCGATCATCAGAAGCG 59.544 52.381 15.84 6.81 43.01 4.68
2824 7080 2.360475 GCAGAAGGCCTGGTCCAC 60.360 66.667 5.69 0.00 43.13 4.02
2960 7219 1.393603 TTGCAACCATCACAAACCGA 58.606 45.000 0.00 0.00 0.00 4.69
3062 7322 0.319211 CACCGTCGTAGCTGTTGGAA 60.319 55.000 0.00 0.00 0.00 3.53
3114 7389 7.053316 TGGTTGAATGAAAGTGATGTGAATT 57.947 32.000 0.00 0.00 0.00 2.17
3135 7545 1.611673 CCGAATCTTTGGTGAGCTGGT 60.612 52.381 0.00 0.00 0.00 4.00
3138 7548 2.636830 CATCCGAATCTTTGGTGAGCT 58.363 47.619 0.00 0.00 33.22 4.09
3139 7549 1.064654 GCATCCGAATCTTTGGTGAGC 59.935 52.381 0.00 0.00 33.22 4.26
3172 7582 1.071605 GCAACGAACCTGCTAGACAG 58.928 55.000 0.00 0.14 46.77 3.51
3178 7588 4.049393 GTCTGCAACGAACCTGCT 57.951 55.556 0.00 0.00 40.59 4.24
3336 8023 0.907486 TCTCAGAGTGCTTCCATGGG 59.093 55.000 13.02 0.00 0.00 4.00
3372 8059 7.987458 TGGATGGAAATTAGAAGCTACAGTAAG 59.013 37.037 0.00 0.00 0.00 2.34
3373 8060 7.857456 TGGATGGAAATTAGAAGCTACAGTAA 58.143 34.615 0.00 0.00 0.00 2.24
3374 8061 7.432148 TGGATGGAAATTAGAAGCTACAGTA 57.568 36.000 0.00 0.00 0.00 2.74
3375 8062 6.313519 TGGATGGAAATTAGAAGCTACAGT 57.686 37.500 0.00 0.00 0.00 3.55
3376 8063 6.994496 TCATGGATGGAAATTAGAAGCTACAG 59.006 38.462 0.00 0.00 0.00 2.74
3377 8064 6.899089 TCATGGATGGAAATTAGAAGCTACA 58.101 36.000 0.00 0.00 0.00 2.74
3378 8065 6.995091 ACTCATGGATGGAAATTAGAAGCTAC 59.005 38.462 0.00 0.00 0.00 3.58
3379 8066 7.141758 ACTCATGGATGGAAATTAGAAGCTA 57.858 36.000 0.00 0.00 0.00 3.32
3380 8067 6.011122 ACTCATGGATGGAAATTAGAAGCT 57.989 37.500 0.00 0.00 0.00 3.74
3381 8068 5.240403 GGACTCATGGATGGAAATTAGAAGC 59.760 44.000 0.00 0.00 0.00 3.86
3382 8069 5.767168 GGGACTCATGGATGGAAATTAGAAG 59.233 44.000 0.00 0.00 0.00 2.85
3383 8070 5.433051 AGGGACTCATGGATGGAAATTAGAA 59.567 40.000 0.00 0.00 0.00 2.10
3384 8071 4.977739 AGGGACTCATGGATGGAAATTAGA 59.022 41.667 0.00 0.00 0.00 2.10
3385 8072 5.316158 AGGGACTCATGGATGGAAATTAG 57.684 43.478 0.00 0.00 0.00 1.73
3386 8073 5.399038 GGAAGGGACTCATGGATGGAAATTA 60.399 44.000 0.00 0.00 38.49 1.40
3387 8074 4.540715 GAAGGGACTCATGGATGGAAATT 58.459 43.478 0.00 0.00 38.49 1.82
3388 8075 3.117360 GGAAGGGACTCATGGATGGAAAT 60.117 47.826 0.00 0.00 38.49 2.17
3389 8076 2.242196 GGAAGGGACTCATGGATGGAAA 59.758 50.000 0.00 0.00 38.49 3.13
3390 8077 1.846439 GGAAGGGACTCATGGATGGAA 59.154 52.381 0.00 0.00 38.49 3.53
3391 8078 1.511613 GGAAGGGACTCATGGATGGA 58.488 55.000 0.00 0.00 38.49 3.41
3392 8079 0.107456 CGGAAGGGACTCATGGATGG 59.893 60.000 0.00 0.00 38.49 3.51
3393 8080 3.694364 CGGAAGGGACTCATGGATG 57.306 57.895 0.00 0.00 38.49 3.51
3462 8198 0.875728 ATACGTAGAGCTAGCCTGCG 59.124 55.000 28.30 28.30 43.60 5.18
3463 8199 1.880675 TGATACGTAGAGCTAGCCTGC 59.119 52.381 12.13 10.81 0.00 4.85
3464 8200 3.753797 TGATGATACGTAGAGCTAGCCTG 59.246 47.826 12.13 0.00 0.00 4.85
3476 8215 6.380560 AGGAGATGATGATGATGATGATACGT 59.619 38.462 0.00 0.00 0.00 3.57
3480 8219 7.923461 AGAAAGGAGATGATGATGATGATGAT 58.077 34.615 0.00 0.00 0.00 2.45
3481 8220 7.317722 AGAAAGGAGATGATGATGATGATGA 57.682 36.000 0.00 0.00 0.00 2.92
3482 8221 7.880713 AGAAGAAAGGAGATGATGATGATGATG 59.119 37.037 0.00 0.00 0.00 3.07
3520 8265 1.689273 GTACCCATCGATCTTGCTCCT 59.311 52.381 0.00 0.00 0.00 3.69
3521 8266 1.412710 TGTACCCATCGATCTTGCTCC 59.587 52.381 0.00 0.00 0.00 4.70
3522 8267 2.890808 TGTACCCATCGATCTTGCTC 57.109 50.000 0.00 0.00 0.00 4.26
3548 8293 0.107897 AAGGATTCATGTACCGCGCA 60.108 50.000 8.75 0.00 0.00 6.09
3551 8296 1.668419 AGCAAGGATTCATGTACCGC 58.332 50.000 0.00 0.00 0.00 5.68
3554 8299 6.939163 AGAATGGATAGCAAGGATTCATGTAC 59.061 38.462 0.00 0.00 0.00 2.90
3556 8301 5.950023 AGAATGGATAGCAAGGATTCATGT 58.050 37.500 0.00 0.00 0.00 3.21
3558 8303 5.516238 GGGAGAATGGATAGCAAGGATTCAT 60.516 44.000 0.00 0.00 0.00 2.57
3559 8304 4.202503 GGGAGAATGGATAGCAAGGATTCA 60.203 45.833 0.00 0.00 0.00 2.57
3560 8305 4.042684 AGGGAGAATGGATAGCAAGGATTC 59.957 45.833 0.00 0.00 0.00 2.52
3562 8307 3.586618 GAGGGAGAATGGATAGCAAGGAT 59.413 47.826 0.00 0.00 0.00 3.24
3563 8308 2.975489 GAGGGAGAATGGATAGCAAGGA 59.025 50.000 0.00 0.00 0.00 3.36
3565 8310 4.428294 TTGAGGGAGAATGGATAGCAAG 57.572 45.455 0.00 0.00 0.00 4.01
3567 8312 4.413189 TCATTTGAGGGAGAATGGATAGCA 59.587 41.667 0.00 0.00 34.74 3.49
3568 8313 4.978099 TCATTTGAGGGAGAATGGATAGC 58.022 43.478 0.00 0.00 34.74 2.97
3655 9457 9.667107 TGGTATTTATAATTATAGGCTGCAGAC 57.333 33.333 20.43 17.00 0.00 3.51
3689 9730 2.492881 CAGGGCAACACAATCAAGCATA 59.507 45.455 0.00 0.00 39.74 3.14
3703 9744 3.496309 CTCACAGTGGGCAGGGCAA 62.496 63.158 0.00 0.00 0.00 4.52
3721 9762 4.579340 AGATGTGAGATGCCAATCATTCAC 59.421 41.667 10.42 10.42 40.09 3.18
3732 9773 2.681848 CAGGAAACCAGATGTGAGATGC 59.318 50.000 0.00 0.00 0.00 3.91
3796 9837 5.183969 TGTACTACTACGAGCTCACTCATT 58.816 41.667 15.40 0.00 43.66 2.57
3801 9842 5.568296 CAGTTTTGTACTACTACGAGCTCAC 59.432 44.000 15.40 1.90 34.56 3.51
3802 9843 5.240183 ACAGTTTTGTACTACTACGAGCTCA 59.760 40.000 15.40 0.00 35.25 4.26
3803 9844 5.697826 ACAGTTTTGTACTACTACGAGCTC 58.302 41.667 2.73 2.73 35.25 4.09
3804 9845 5.702349 ACAGTTTTGTACTACTACGAGCT 57.298 39.130 0.00 0.00 35.25 4.09
3806 9847 8.074972 AGAAGAACAGTTTTGTACTACTACGAG 58.925 37.037 0.00 0.00 36.23 4.18
3807 9848 7.934457 AGAAGAACAGTTTTGTACTACTACGA 58.066 34.615 0.00 0.00 36.23 3.43
3808 9849 8.074972 AGAGAAGAACAGTTTTGTACTACTACG 58.925 37.037 0.00 0.00 36.23 3.51
3816 9860 6.093495 CACAACCAGAGAAGAACAGTTTTGTA 59.907 38.462 0.00 0.00 36.23 2.41
3871 9915 2.834549 TCCATGTCCTTTCTCTCACTCC 59.165 50.000 0.00 0.00 0.00 3.85
3910 9954 3.070878 ACCCACAAATCCCAAATCAACAC 59.929 43.478 0.00 0.00 0.00 3.32
3977 10021 1.294780 CCAGTGCTGTCCCTGTCTC 59.705 63.158 0.00 0.00 0.00 3.36
4008 10052 1.153449 TCATCGTCATCGGCAACCC 60.153 57.895 0.00 0.00 37.69 4.11
4010 10054 0.179111 TCCTCATCGTCATCGGCAAC 60.179 55.000 0.00 0.00 37.69 4.17
4012 10056 1.037579 AGTCCTCATCGTCATCGGCA 61.038 55.000 0.00 0.00 37.69 5.69
4014 10058 0.312416 GGAGTCCTCATCGTCATCGG 59.688 60.000 0.41 0.00 37.69 4.18
4015 10059 0.040870 CGGAGTCCTCATCGTCATCG 60.041 60.000 7.77 0.00 38.55 3.84
4020 10064 2.222886 CAGATACGGAGTCCTCATCGT 58.777 52.381 7.77 1.99 43.93 3.73
4029 10073 1.495574 AGGCTCCTACAGATACGGAGT 59.504 52.381 6.44 0.00 44.83 3.85
4039 10086 2.442272 GAGGGCGAGGCTCCTACA 60.442 66.667 9.32 0.00 31.35 2.74
4097 10144 2.501723 GCCTTGGTAGAATCAGTCTCCA 59.498 50.000 0.00 0.00 37.84 3.86
4099 10146 2.166664 ACGCCTTGGTAGAATCAGTCTC 59.833 50.000 0.00 0.00 37.84 3.36
4100 10147 2.180276 ACGCCTTGGTAGAATCAGTCT 58.820 47.619 0.00 0.00 40.71 3.24
4155 10202 1.887242 AAGCAAACGCAGACGCAGA 60.887 52.632 0.00 0.00 45.53 4.26
4158 10205 3.093449 GCAAGCAAACGCAGACGC 61.093 61.111 0.00 0.00 45.53 5.19
4166 10213 2.035066 ACATGAACAGGAGCAAGCAAAC 59.965 45.455 0.00 0.00 0.00 2.93
4167 10214 2.034939 CACATGAACAGGAGCAAGCAAA 59.965 45.455 0.00 0.00 0.00 3.68
4168 10215 1.610038 CACATGAACAGGAGCAAGCAA 59.390 47.619 0.00 0.00 0.00 3.91
4169 10216 1.241165 CACATGAACAGGAGCAAGCA 58.759 50.000 0.00 0.00 0.00 3.91
4170 10217 0.109412 GCACATGAACAGGAGCAAGC 60.109 55.000 0.00 0.00 0.00 4.01
4171 10218 0.167470 CGCACATGAACAGGAGCAAG 59.833 55.000 0.00 0.00 0.00 4.01
4172 10219 1.236616 CCGCACATGAACAGGAGCAA 61.237 55.000 0.00 0.00 0.00 3.91
4173 10220 1.672030 CCGCACATGAACAGGAGCA 60.672 57.895 0.00 0.00 0.00 4.26
4174 10221 3.044059 GCCGCACATGAACAGGAGC 62.044 63.158 0.00 0.00 0.00 4.70
4175 10222 2.401766 GGCCGCACATGAACAGGAG 61.402 63.158 0.00 0.00 0.00 3.69
4193 10240 3.067106 TCTCTTTTTAACTGAGGCAGCG 58.933 45.455 0.00 0.00 34.37 5.18
4196 10243 5.003804 GGTGATCTCTTTTTAACTGAGGCA 58.996 41.667 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.