Multiple sequence alignment - TraesCS5B01G226500

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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 TraesCS5B01G226500 chr5B 100.000 6864 0 0 1 6864 403541873 403548736 0.000000e+00 12676.0
1 TraesCS5B01G226500 chr5B 96.875 128 4 0 3844 3971 70795653 70795780 1.500000e-51 215.0
2 TraesCS5B01G226500 chr5B 98.361 122 2 0 3844 3965 478495172 478495051 1.500000e-51 215.0
3 TraesCS5B01G226500 chr5B 94.928 138 4 3 3843 3977 522656861 522656724 5.390000e-51 213.0
4 TraesCS5B01G226500 chr5B 89.855 69 7 0 17 85 590185916 590185848 9.480000e-14 89.8
5 TraesCS5B01G226500 chr5D 90.784 3939 203 68 17 3844 343285097 343288986 0.000000e+00 5116.0
6 TraesCS5B01G226500 chr5D 94.526 1772 55 17 4733 6481 343289769 343291521 0.000000e+00 2697.0
7 TraesCS5B01G226500 chr5D 90.571 700 31 13 3990 4670 343289089 343289772 0.000000e+00 894.0
8 TraesCS5B01G226500 chr5D 91.477 352 15 4 6528 6864 343291610 343291961 2.900000e-128 470.0
9 TraesCS5B01G226500 chr5D 96.825 126 4 0 3843 3968 420228286 420228161 1.940000e-50 211.0
10 TraesCS5B01G226500 chr5D 100.000 29 0 0 3961 3989 343288988 343289016 3.000000e-03 54.7
11 TraesCS5B01G226500 chr5A 91.105 3811 195 64 135 3847 444262451 444266215 0.000000e+00 5027.0
12 TraesCS5B01G226500 chr5A 92.214 2055 108 23 4266 6268 444266787 444268841 0.000000e+00 2861.0
13 TraesCS5B01G226500 chr5A 94.649 299 12 2 6568 6864 444269188 444269484 1.740000e-125 460.0
14 TraesCS5B01G226500 chr5A 91.753 291 15 4 3990 4271 444266315 444266605 4.990000e-106 396.0
15 TraesCS5B01G226500 chr5A 88.827 179 9 3 6312 6479 444268845 444269023 6.980000e-50 209.0
16 TraesCS5B01G226500 chr5A 94.545 55 1 1 82 136 444262360 444262412 4.410000e-12 84.2
17 TraesCS5B01G226500 chr5A 100.000 31 0 0 3959 3989 444266212 444266242 2.670000e-04 58.4
18 TraesCS5B01G226500 chr7D 97.674 129 2 1 3840 3967 600971093 600970965 3.220000e-53 220.0
19 TraesCS5B01G226500 chr6B 99.167 120 1 0 3843 3962 130306165 130306046 4.170000e-52 217.0
20 TraesCS5B01G226500 chr3D 98.374 123 1 1 3845 3967 7308174 7308053 1.500000e-51 215.0
21 TraesCS5B01G226500 chr2D 95.455 132 5 1 3835 3965 460869579 460869448 6.980000e-50 209.0
22 TraesCS5B01G226500 chr2D 94.161 137 7 1 3838 3974 95519666 95519531 2.510000e-49 207.0
23 TraesCS5B01G226500 chr2D 91.176 68 5 1 17 84 458739644 458739578 2.640000e-14 91.6
24 TraesCS5B01G226500 chr6D 92.308 78 5 1 17 93 363326020 363326097 7.280000e-20 110.0
25 TraesCS5B01G226500 chr3A 93.939 66 4 0 17 82 608345664 608345599 4.380000e-17 100.0
26 TraesCS5B01G226500 chr2B 93.750 64 4 0 17 80 218285023 218284960 5.670000e-16 97.1
27 TraesCS5B01G226500 chr1D 92.188 64 5 0 17 80 469601179 469601116 2.640000e-14 91.6
28 TraesCS5B01G226500 chr4A 89.706 68 6 1 17 84 614570454 614570388 1.230000e-12 86.1
29 TraesCS5B01G226500 chr4D 86.957 69 8 1 17 85 447984030 447984097 7.380000e-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 TraesCS5B01G226500 chr5B 403541873 403548736 6863 False 12676.000000 12676 100.0000 1 6864 1 chr5B.!!$F2 6863
1 TraesCS5B01G226500 chr5D 343285097 343291961 6864 False 1846.340000 5116 93.4716 17 6864 5 chr5D.!!$F1 6847
2 TraesCS5B01G226500 chr5A 444262360 444269484 7124 False 1299.371429 5027 93.2990 82 6864 7 chr5A.!!$F1 6782

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
663 738 0.030504 TTCGTTCGTTCGTGCCTGTA 59.969 50.000 2.67 0.00 0.00 2.74 F
664 739 0.386352 TCGTTCGTTCGTGCCTGTAG 60.386 55.000 2.67 0.00 0.00 2.74 F
1806 1998 0.173481 CAGAGCCGAAGATCGTTCCA 59.827 55.000 0.00 0.00 38.40 3.53 F
2598 2796 0.871592 TGAAGAAGATGATCGCGGCG 60.872 55.000 17.70 17.70 0.00 6.46 F
2875 3076 0.537188 AGCCAGTACGAATGGTCAGG 59.463 55.000 1.96 0.00 40.17 3.86 F
3168 3369 0.691078 ATCGTACCACCCCAGAGCAT 60.691 55.000 0.00 0.00 0.00 3.79 F
3958 4173 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
4693 5190 1.221293 GTCCAGCTCAGCATGCTCT 59.779 57.895 19.68 9.66 38.92 4.09 F
5369 5869 0.461548 TGGAGGAGTCGATGCACATC 59.538 55.000 0.31 0.31 34.56 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1656 0.313233 CGTCGAAAGCGCGTTCATAC 60.313 55.0 30.39 25.19 37.46 2.39 R
2329 2521 0.466007 TGGAAAGACAGCTGCAGCAA 60.466 50.0 38.24 10.68 45.16 3.91 R
2635 2833 0.537188 TCCTTCTCCGAATGCTCCAC 59.463 55.0 0.00 0.00 0.00 4.02 R
3939 4154 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.00 44.66 2.12 R
3944 4159 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.0 5.23 0.00 44.66 4.30 R
4867 5365 0.827368 GGTCCTCTGGTGATCTCCAC 59.173 60.0 12.50 2.91 44.95 4.02 R
5199 5697 0.322816 AGACATCGCACCATTGGCTT 60.323 50.0 1.54 0.00 0.00 4.35 R
5830 6354 0.540365 CCAAGCAGGGGAAGAGCAAA 60.540 55.0 0.00 0.00 0.00 3.68 R
6642 7304 0.606130 TGTCACGCCACTGAATGCAT 60.606 50.0 0.00 0.00 0.00 3.96 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
33 34 9.814899 TTTGAGATGAAAATTTACAAAGCTTGA 57.185 25.926 0.00 0.00 0.00 3.02
56 57 8.492673 TGACTTTGAGTAAAGCTAATATGTGG 57.507 34.615 0.00 0.00 45.72 4.17
58 59 8.494016 ACTTTGAGTAAAGCTAATATGTGGAC 57.506 34.615 0.00 0.00 45.72 4.02
71 72 9.659830 GCTAATATGTGGACTAAATAAAAACGG 57.340 33.333 0.00 0.00 0.00 4.44
75 76 7.611213 ATGTGGACTAAATAAAAACGGAGAG 57.389 36.000 0.00 0.00 0.00 3.20
76 77 6.761312 TGTGGACTAAATAAAAACGGAGAGA 58.239 36.000 0.00 0.00 0.00 3.10
77 78 6.872020 TGTGGACTAAATAAAAACGGAGAGAG 59.128 38.462 0.00 0.00 0.00 3.20
80 81 8.031277 TGGACTAAATAAAAACGGAGAGAGTAC 58.969 37.037 0.00 0.00 0.00 2.73
225 275 4.717629 CAAGACACGCGCCTCGGA 62.718 66.667 5.73 0.00 43.86 4.55
270 320 3.471806 GTCCGCTTCCTCTCCCCC 61.472 72.222 0.00 0.00 0.00 5.40
368 431 2.030946 GCACGAATGGAAAGGATCTTCG 59.969 50.000 8.84 8.84 43.10 3.79
369 432 2.609459 CACGAATGGAAAGGATCTTCGG 59.391 50.000 13.43 2.25 42.09 4.30
392 455 3.525800 AATAAAGTGCAGGTGAAGGGT 57.474 42.857 0.00 0.00 0.00 4.34
393 456 2.561478 TAAAGTGCAGGTGAAGGGTC 57.439 50.000 0.00 0.00 0.00 4.46
394 457 0.178990 AAAGTGCAGGTGAAGGGTCC 60.179 55.000 0.00 0.00 0.00 4.46
395 458 2.358737 GTGCAGGTGAAGGGTCCG 60.359 66.667 0.00 0.00 0.00 4.79
396 459 3.636231 TGCAGGTGAAGGGTCCGG 61.636 66.667 0.00 0.00 0.00 5.14
397 460 4.410400 GCAGGTGAAGGGTCCGGG 62.410 72.222 0.00 0.00 0.00 5.73
398 461 2.928396 CAGGTGAAGGGTCCGGGT 60.928 66.667 0.00 0.00 0.00 5.28
553 616 2.283388 TCCACCGGCGGTAGAAGT 60.283 61.111 33.65 4.57 32.11 3.01
554 617 1.001020 TCCACCGGCGGTAGAAGTA 60.001 57.895 33.65 5.22 32.11 2.24
555 618 1.033746 TCCACCGGCGGTAGAAGTAG 61.034 60.000 33.65 17.37 32.11 2.57
556 619 1.033746 CCACCGGCGGTAGAAGTAGA 61.034 60.000 33.65 0.00 32.11 2.59
557 620 0.813184 CACCGGCGGTAGAAGTAGAA 59.187 55.000 33.65 0.00 32.11 2.10
558 621 0.813821 ACCGGCGGTAGAAGTAGAAC 59.186 55.000 33.31 0.00 32.11 3.01
560 623 0.101939 CGGCGGTAGAAGTAGAACCC 59.898 60.000 0.00 0.00 0.00 4.11
562 625 1.188863 GCGGTAGAAGTAGAACCCCA 58.811 55.000 0.00 0.00 0.00 4.96
564 627 1.136500 CGGTAGAAGTAGAACCCCAGC 59.864 57.143 0.00 0.00 0.00 4.85
565 628 1.136500 GGTAGAAGTAGAACCCCAGCG 59.864 57.143 0.00 0.00 0.00 5.18
567 630 1.449778 GAAGTAGAACCCCAGCGCC 60.450 63.158 2.29 0.00 0.00 6.53
568 631 3.310860 AAGTAGAACCCCAGCGCCG 62.311 63.158 2.29 0.00 0.00 6.46
569 632 4.832608 GTAGAACCCCAGCGCCGG 62.833 72.222 2.29 1.87 0.00 6.13
659 734 2.166985 CGTTCGTTCGTTCGTGCC 59.833 61.111 2.67 0.00 0.00 5.01
661 736 1.200839 GTTCGTTCGTTCGTGCCTG 59.799 57.895 2.67 0.00 0.00 4.85
662 737 1.227031 TTCGTTCGTTCGTGCCTGT 60.227 52.632 2.67 0.00 0.00 4.00
663 738 0.030504 TTCGTTCGTTCGTGCCTGTA 59.969 50.000 2.67 0.00 0.00 2.74
664 739 0.386352 TCGTTCGTTCGTGCCTGTAG 60.386 55.000 2.67 0.00 0.00 2.74
788 890 3.827898 CCGTGCCTCGTCTCCCTC 61.828 72.222 0.00 0.00 37.94 4.30
789 891 4.180946 CGTGCCTCGTCTCCCTCG 62.181 72.222 0.00 0.00 34.52 4.63
790 892 4.500116 GTGCCTCGTCTCCCTCGC 62.500 72.222 0.00 0.00 0.00 5.03
835 937 7.619698 ACATAGCATAGCTTACCATACATAGGA 59.380 37.037 0.00 0.00 40.44 2.94
941 1071 4.266070 GGCGCGGCAGATACGAGA 62.266 66.667 29.32 0.00 32.84 4.04
1195 1344 0.689412 GTCTTCCTCCTCCTCCCCAG 60.689 65.000 0.00 0.00 0.00 4.45
1226 1383 0.999712 ATTCCATCTCCCGTGGGTTT 59.000 50.000 4.53 0.00 37.34 3.27
1248 1410 2.356741 GGGGTTTCTGAATTCCCGATCA 60.357 50.000 18.41 0.00 40.72 2.92
1286 1458 1.302511 GGTGGCACGACTGATTGGT 60.303 57.895 12.17 0.00 0.00 3.67
1291 1463 1.298859 GCACGACTGATTGGTGGGTC 61.299 60.000 0.00 0.00 32.42 4.46
1319 1496 0.893270 TTTGTTGTCATCAGGGGCGG 60.893 55.000 0.00 0.00 0.00 6.13
1332 1509 1.764854 GGGCGGGGATAAGGAGACA 60.765 63.158 0.00 0.00 0.00 3.41
1561 1741 2.363018 CCTCTCCGTCCAGCCTCA 60.363 66.667 0.00 0.00 0.00 3.86
1599 1779 1.097547 AGATGCCTGAAATTCCGCGG 61.098 55.000 22.12 22.12 0.00 6.46
1625 1805 1.594293 CGGTGGTTTCGACAGCAGT 60.594 57.895 3.25 0.00 36.19 4.40
1626 1806 1.831389 CGGTGGTTTCGACAGCAGTG 61.831 60.000 3.25 0.00 36.19 3.66
1656 1836 1.682684 GGAGGAGGAGGAGCACGAA 60.683 63.158 0.00 0.00 0.00 3.85
1657 1837 1.513622 GAGGAGGAGGAGCACGAAC 59.486 63.158 0.00 0.00 0.00 3.95
1660 1840 1.216710 GAGGAGGAGCACGAACAGG 59.783 63.158 0.00 0.00 0.00 4.00
1664 1844 1.339151 GGAGGAGCACGAACAGGAAAT 60.339 52.381 0.00 0.00 0.00 2.17
1665 1845 2.427506 GAGGAGCACGAACAGGAAATT 58.572 47.619 0.00 0.00 0.00 1.82
1734 1923 1.827969 GAAGCAGAGGAAGCAGAGGTA 59.172 52.381 0.00 0.00 0.00 3.08
1744 1933 3.514309 GGAAGCAGAGGTACTAGTGGAAA 59.486 47.826 5.39 0.00 41.55 3.13
1745 1934 4.020485 GGAAGCAGAGGTACTAGTGGAAAA 60.020 45.833 5.39 0.00 41.55 2.29
1746 1935 5.512576 GGAAGCAGAGGTACTAGTGGAAAAA 60.513 44.000 5.39 0.00 41.55 1.94
1806 1998 0.173481 CAGAGCCGAAGATCGTTCCA 59.827 55.000 0.00 0.00 38.40 3.53
1824 2016 2.356553 GCCACGCACAACTACCGA 60.357 61.111 0.00 0.00 0.00 4.69
1830 2022 1.820519 ACGCACAACTACCGATTCCTA 59.179 47.619 0.00 0.00 0.00 2.94
1958 2150 1.849976 GAACGGAGAGTGGTCGACGT 61.850 60.000 9.92 0.00 40.22 4.34
1996 2188 1.662446 TTCGTCACGGCGAAAGACC 60.662 57.895 16.62 3.08 46.11 3.85
2091 2283 2.811317 GCGAGCTCCGTGTCCAAG 60.811 66.667 8.47 0.00 41.15 3.61
2329 2521 2.685380 CCCTGGAGGAAGCCGACT 60.685 66.667 0.00 0.00 38.24 4.18
2476 2668 1.008329 GTACAGAGAGGACGACGAGG 58.992 60.000 0.00 0.00 0.00 4.63
2497 2689 2.046217 GAACACCCCGAGAAGCCC 60.046 66.667 0.00 0.00 0.00 5.19
2518 2710 2.759973 AGGCCGAGGCGAAGATCA 60.760 61.111 8.14 0.00 43.06 2.92
2521 2713 1.666234 GCCGAGGCGAAGATCATCC 60.666 63.158 0.00 0.00 0.00 3.51
2598 2796 0.871592 TGAAGAAGATGATCGCGGCG 60.872 55.000 17.70 17.70 0.00 6.46
2762 2960 2.084610 TCGTCTCATCAAGCAGTTGG 57.915 50.000 0.00 0.00 34.09 3.77
2793 2991 1.451028 GAGCCCACAGCCATCAGAC 60.451 63.158 0.00 0.00 45.47 3.51
2805 3006 2.815589 GCCATCAGACAGGGAACTTGTT 60.816 50.000 0.00 0.00 40.21 2.83
2838 3039 3.253432 GTCATCCACCTGAACTTGTTTCC 59.747 47.826 0.00 0.00 32.58 3.13
2875 3076 0.537188 AGCCAGTACGAATGGTCAGG 59.463 55.000 1.96 0.00 40.17 3.86
3117 3318 1.261089 CACAAAGCAATTGCCCAAACG 59.739 47.619 26.45 11.80 43.13 3.60
3141 3342 2.627699 TGATCGGTCATATGCAGCAGTA 59.372 45.455 0.00 0.00 0.00 2.74
3168 3369 0.691078 ATCGTACCACCCCAGAGCAT 60.691 55.000 0.00 0.00 0.00 3.79
3188 3389 4.034975 GCATTCAGAGCAGGAATTCAGTAC 59.965 45.833 7.93 0.00 32.86 2.73
3220 3421 4.878968 TCAGTATGGAGTAATCCCTCACA 58.121 43.478 6.78 0.00 36.16 3.58
3221 3422 4.649674 TCAGTATGGAGTAATCCCTCACAC 59.350 45.833 6.78 0.00 36.16 3.82
3230 3431 2.770164 ATCCCTCACACCGAGAAAAG 57.230 50.000 0.00 0.00 45.45 2.27
3330 3531 1.807573 CGAGAAGGCCAAGTCGCTC 60.808 63.158 5.01 0.91 0.00 5.03
3504 3705 1.070786 GTCGGAGTCACCAAAGGCA 59.929 57.895 0.00 0.00 38.90 4.75
3676 3878 5.484715 TGCCTAACTACACATTACCAGTTC 58.515 41.667 0.00 0.00 33.47 3.01
3680 3882 7.578189 GCCTAACTACACATTACCAGTTCACTA 60.578 40.741 0.00 0.00 33.47 2.74
3682 3884 6.034161 ACTACACATTACCAGTTCACTACC 57.966 41.667 0.00 0.00 0.00 3.18
3684 3886 4.638304 ACACATTACCAGTTCACTACCAC 58.362 43.478 0.00 0.00 0.00 4.16
3689 3891 5.881923 TTACCAGTTCACTACCACTTCTT 57.118 39.130 0.00 0.00 0.00 2.52
3764 3979 7.981142 TCTAATAGGAAAAATTAGGTTGCACG 58.019 34.615 0.00 0.00 37.47 5.34
3821 4036 6.128063 GCTCCATGATCTAGTATTCAATTGGC 60.128 42.308 5.42 0.00 0.00 4.52
3844 4059 6.862608 GGCTCATCATAATCGCAGATATCTAG 59.137 42.308 4.54 3.01 45.12 2.43
3845 4060 7.424803 GCTCATCATAATCGCAGATATCTAGT 58.575 38.462 4.54 0.00 45.12 2.57
3846 4061 8.563732 GCTCATCATAATCGCAGATATCTAGTA 58.436 37.037 4.54 0.00 45.12 1.82
3847 4062 9.877137 CTCATCATAATCGCAGATATCTAGTAC 57.123 37.037 4.54 0.00 45.12 2.73
3848 4063 9.620259 TCATCATAATCGCAGATATCTAGTACT 57.380 33.333 4.54 0.00 45.12 2.73
3849 4064 9.877137 CATCATAATCGCAGATATCTAGTACTC 57.123 37.037 4.54 0.00 45.12 2.59
3850 4065 8.439993 TCATAATCGCAGATATCTAGTACTCC 57.560 38.462 4.54 0.00 45.12 3.85
3851 4066 7.499563 TCATAATCGCAGATATCTAGTACTCCC 59.500 40.741 4.54 0.00 45.12 4.30
3852 4067 4.912317 TCGCAGATATCTAGTACTCCCT 57.088 45.455 4.54 0.00 0.00 4.20
3853 4068 4.834534 TCGCAGATATCTAGTACTCCCTC 58.165 47.826 4.54 0.00 0.00 4.30
3854 4069 3.942748 CGCAGATATCTAGTACTCCCTCC 59.057 52.174 4.54 0.00 0.00 4.30
3855 4070 3.942748 GCAGATATCTAGTACTCCCTCCG 59.057 52.174 4.54 0.00 0.00 4.63
3856 4071 4.566070 GCAGATATCTAGTACTCCCTCCGT 60.566 50.000 4.54 0.00 0.00 4.69
3857 4072 5.180271 CAGATATCTAGTACTCCCTCCGTC 58.820 50.000 4.54 0.00 0.00 4.79
3858 4073 2.955342 ATCTAGTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
3859 4074 1.588239 TCTAGTACTCCCTCCGTCCA 58.412 55.000 0.00 0.00 0.00 4.02
3860 4075 1.489649 TCTAGTACTCCCTCCGTCCAG 59.510 57.143 0.00 0.00 0.00 3.86
3861 4076 1.489649 CTAGTACTCCCTCCGTCCAGA 59.510 57.143 0.00 0.00 0.00 3.86
3862 4077 0.702902 AGTACTCCCTCCGTCCAGAA 59.297 55.000 0.00 0.00 0.00 3.02
3863 4078 1.076677 AGTACTCCCTCCGTCCAGAAA 59.923 52.381 0.00 0.00 0.00 2.52
3864 4079 2.108970 GTACTCCCTCCGTCCAGAAAT 58.891 52.381 0.00 0.00 0.00 2.17
3865 4080 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
3866 4081 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
3867 4082 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
3868 4083 2.362717 CTCCCTCCGTCCAGAAATACTC 59.637 54.545 0.00 0.00 0.00 2.59
3869 4084 1.067212 CCCTCCGTCCAGAAATACTCG 59.933 57.143 0.00 0.00 0.00 4.18
3870 4085 1.749634 CCTCCGTCCAGAAATACTCGT 59.250 52.381 0.00 0.00 0.00 4.18
3871 4086 2.223525 CCTCCGTCCAGAAATACTCGTC 60.224 54.545 0.00 0.00 0.00 4.20
3872 4087 1.399440 TCCGTCCAGAAATACTCGTCG 59.601 52.381 0.00 0.00 0.00 5.12
3873 4088 1.533338 CCGTCCAGAAATACTCGTCGG 60.533 57.143 0.00 0.00 0.00 4.79
3874 4089 1.399440 CGTCCAGAAATACTCGTCGGA 59.601 52.381 0.00 0.00 0.00 4.55
3875 4090 2.539142 CGTCCAGAAATACTCGTCGGAG 60.539 54.545 0.00 0.00 46.13 4.63
3876 4091 2.022195 TCCAGAAATACTCGTCGGAGG 58.978 52.381 0.00 0.00 44.93 4.30
3877 4092 2.022195 CCAGAAATACTCGTCGGAGGA 58.978 52.381 0.00 0.00 44.93 3.71
3878 4093 2.426024 CCAGAAATACTCGTCGGAGGAA 59.574 50.000 1.73 0.00 44.93 3.36
3879 4094 3.068307 CCAGAAATACTCGTCGGAGGAAT 59.932 47.826 1.73 0.00 44.93 3.01
3880 4095 4.045104 CAGAAATACTCGTCGGAGGAATG 58.955 47.826 1.73 0.00 44.93 2.67
3881 4096 3.068307 AGAAATACTCGTCGGAGGAATGG 59.932 47.826 1.73 0.00 44.93 3.16
3882 4097 2.359981 ATACTCGTCGGAGGAATGGA 57.640 50.000 1.73 0.00 44.93 3.41
3883 4098 2.359981 TACTCGTCGGAGGAATGGAT 57.640 50.000 1.73 0.00 44.93 3.41
3884 4099 0.747255 ACTCGTCGGAGGAATGGATG 59.253 55.000 1.73 0.00 44.93 3.51
3885 4100 0.747255 CTCGTCGGAGGAATGGATGT 59.253 55.000 1.73 0.00 36.61 3.06
3886 4101 1.954382 CTCGTCGGAGGAATGGATGTA 59.046 52.381 1.73 0.00 36.61 2.29
3887 4102 2.558795 CTCGTCGGAGGAATGGATGTAT 59.441 50.000 1.73 0.00 36.61 2.29
3888 4103 2.557056 TCGTCGGAGGAATGGATGTATC 59.443 50.000 0.00 0.00 0.00 2.24
3889 4104 2.558795 CGTCGGAGGAATGGATGTATCT 59.441 50.000 0.00 0.00 0.00 1.98
3890 4105 3.756963 CGTCGGAGGAATGGATGTATCTA 59.243 47.826 0.00 0.00 0.00 1.98
3891 4106 4.142578 CGTCGGAGGAATGGATGTATCTAG 60.143 50.000 0.00 0.00 0.00 2.43
3892 4107 5.010933 GTCGGAGGAATGGATGTATCTAGA 58.989 45.833 0.00 0.00 0.00 2.43
3893 4108 5.654650 GTCGGAGGAATGGATGTATCTAGAT 59.345 44.000 10.73 10.73 0.00 1.98
3894 4109 5.654209 TCGGAGGAATGGATGTATCTAGATG 59.346 44.000 15.79 0.00 0.00 2.90
3895 4110 5.420421 CGGAGGAATGGATGTATCTAGATGT 59.580 44.000 15.79 1.25 0.00 3.06
3896 4111 6.603599 CGGAGGAATGGATGTATCTAGATGTA 59.396 42.308 15.79 4.44 0.00 2.29
3897 4112 7.286546 CGGAGGAATGGATGTATCTAGATGTAT 59.713 40.741 15.79 9.11 0.00 2.29
3898 4113 8.986991 GGAGGAATGGATGTATCTAGATGTATT 58.013 37.037 15.79 6.57 0.00 1.89
3935 4150 7.760131 ACATTCATTTTTATGCATTTCTCCG 57.240 32.000 3.54 0.00 0.00 4.63
3936 4151 7.546358 ACATTCATTTTTATGCATTTCTCCGA 58.454 30.769 3.54 0.00 0.00 4.55
3937 4152 7.489113 ACATTCATTTTTATGCATTTCTCCGAC 59.511 33.333 3.54 0.00 0.00 4.79
3938 4153 6.507958 TCATTTTTATGCATTTCTCCGACA 57.492 33.333 3.54 0.00 0.00 4.35
3939 4154 6.918626 TCATTTTTATGCATTTCTCCGACAA 58.081 32.000 3.54 0.00 0.00 3.18
3940 4155 7.028962 TCATTTTTATGCATTTCTCCGACAAG 58.971 34.615 3.54 0.00 0.00 3.16
3941 4156 5.957842 TTTTATGCATTTCTCCGACAAGT 57.042 34.783 3.54 0.00 0.00 3.16
3942 4157 7.441890 TTTTTATGCATTTCTCCGACAAGTA 57.558 32.000 3.54 0.00 0.00 2.24
3943 4158 7.624360 TTTTATGCATTTCTCCGACAAGTAT 57.376 32.000 3.54 0.00 0.00 2.12
3944 4159 7.624360 TTTATGCATTTCTCCGACAAGTATT 57.376 32.000 3.54 0.00 0.00 1.89
3945 4160 7.624360 TTATGCATTTCTCCGACAAGTATTT 57.376 32.000 3.54 0.00 0.00 1.40
3946 4161 5.545658 TGCATTTCTCCGACAAGTATTTC 57.454 39.130 0.00 0.00 0.00 2.17
3947 4162 4.394920 TGCATTTCTCCGACAAGTATTTCC 59.605 41.667 0.00 0.00 0.00 3.13
3948 4163 4.494199 GCATTTCTCCGACAAGTATTTCCG 60.494 45.833 0.00 0.00 0.00 4.30
3949 4164 2.953466 TCTCCGACAAGTATTTCCGG 57.047 50.000 0.00 0.00 41.36 5.14
3950 4165 2.449464 TCTCCGACAAGTATTTCCGGA 58.551 47.619 0.00 0.00 45.74 5.14
3951 4166 2.165030 TCTCCGACAAGTATTTCCGGAC 59.835 50.000 1.83 0.00 43.47 4.79
3952 4167 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
3953 4168 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
3954 4169 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
3955 4170 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
3956 4171 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3957 4172 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3958 4173 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4046 4334 3.868077 CCTTCTAATGAGGAAACGCTCAG 59.132 47.826 0.00 0.00 32.74 3.35
4050 4338 2.663826 ATGAGGAAACGCTCAGAGTC 57.336 50.000 0.00 0.00 32.74 3.36
4051 4339 1.621992 TGAGGAAACGCTCAGAGTCT 58.378 50.000 0.00 0.00 0.00 3.24
4113 4405 8.842358 TCTAACTAAAATTCACCGAAGTTGAT 57.158 30.769 0.00 0.00 30.27 2.57
4376 4861 3.454812 ACCGGTAAAAGCTATGGTGATCT 59.545 43.478 4.49 0.00 0.00 2.75
4426 4915 8.258708 ACTTAATGACCCAGATTCAGTACTTAC 58.741 37.037 0.00 0.00 0.00 2.34
4438 4927 6.469782 TTCAGTACTTACCCTTATTACCCG 57.530 41.667 0.00 0.00 0.00 5.28
4454 4943 1.450531 CCCGAAGAGATTGCATGGGC 61.451 60.000 0.00 0.00 41.68 5.36
4567 5063 1.265095 ACTGCAGAAATGCTGTTCACG 59.735 47.619 23.35 0.00 46.62 4.35
4571 5067 1.526887 CAGAAATGCTGTTCACGTCGT 59.473 47.619 0.00 0.00 39.85 4.34
4574 5070 2.717580 AATGCTGTTCACGTCGTCTA 57.282 45.000 0.00 0.00 0.00 2.59
4635 5132 6.959639 TTTTAAAGCAGTTCAAGGACAGAT 57.040 33.333 0.00 0.00 0.00 2.90
4643 5140 2.662006 TCAAGGACAGATGAAGCTCG 57.338 50.000 0.00 0.00 0.00 5.03
4693 5190 1.221293 GTCCAGCTCAGCATGCTCT 59.779 57.895 19.68 9.66 38.92 4.09
4712 5209 6.240894 TGCTCTGTGAAATGGATTTCTTACT 58.759 36.000 12.22 0.00 44.85 2.24
4715 5212 8.084684 GCTCTGTGAAATGGATTTCTTACTTTT 58.915 33.333 12.22 0.00 44.85 2.27
4716 5213 9.617975 CTCTGTGAAATGGATTTCTTACTTTTC 57.382 33.333 12.22 0.00 44.85 2.29
4753 5251 6.034683 CCTTTAGTTAACGTGCTGATGTACTC 59.965 42.308 0.00 0.00 0.00 2.59
5098 5596 2.027625 GTTTGTGGAGGACGAGCCG 61.028 63.158 0.00 0.00 43.43 5.52
5199 5697 7.922382 AGAGGTGAGGATTCTGAAATTTTAGA 58.078 34.615 8.50 8.50 0.00 2.10
5219 5717 0.541392 AGCCAATGGTGCGATGTCTA 59.459 50.000 0.00 0.00 0.00 2.59
5220 5718 0.940126 GCCAATGGTGCGATGTCTAG 59.060 55.000 0.00 0.00 0.00 2.43
5222 5720 1.935873 CCAATGGTGCGATGTCTAGTG 59.064 52.381 0.00 0.00 0.00 2.74
5223 5721 2.418609 CCAATGGTGCGATGTCTAGTGA 60.419 50.000 0.00 0.00 0.00 3.41
5240 5738 9.453572 TGTCTAGTGATGAATTTAGCTTGAAAT 57.546 29.630 0.00 0.00 0.00 2.17
5241 5739 9.713740 GTCTAGTGATGAATTTAGCTTGAAATG 57.286 33.333 0.00 0.00 0.00 2.32
5253 5753 9.844257 ATTTAGCTTGAAATGTAGAGCTCTAAT 57.156 29.630 24.85 16.52 43.86 1.73
5254 5754 8.879342 TTAGCTTGAAATGTAGAGCTCTAATC 57.121 34.615 24.85 18.93 43.86 1.75
5369 5869 0.461548 TGGAGGAGTCGATGCACATC 59.538 55.000 0.31 0.31 34.56 3.06
5408 5908 1.664649 CGACAAAGAGCCGCAGACA 60.665 57.895 0.00 0.00 0.00 3.41
5531 6039 7.650903 AGCTTTACTTTACACAGTACTACACAC 59.349 37.037 0.00 0.00 0.00 3.82
5569 6077 6.649141 TGATTTGCTACAGTACCTTACAAGTG 59.351 38.462 0.00 0.00 0.00 3.16
5584 6108 2.146342 CAAGTGCTTCCACCTACTGTG 58.854 52.381 0.00 0.00 43.09 3.66
5807 6331 2.256306 TCATGCTGGTAGACAACAGGA 58.744 47.619 0.00 0.00 39.38 3.86
5830 6354 1.073199 CCACAGGGAGGCTTCGTTT 59.927 57.895 0.00 0.00 35.59 3.60
5867 6391 5.151389 GCTTGGAGTACAAAACATAAACCG 58.849 41.667 0.00 0.00 38.91 4.44
5897 6421 9.793252 CTGATTTTGTTCTCTTCTTTTTCTTCA 57.207 29.630 0.00 0.00 0.00 3.02
5898 6422 9.573133 TGATTTTGTTCTCTTCTTTTTCTTCAC 57.427 29.630 0.00 0.00 0.00 3.18
5904 6438 4.412199 TCTCTTCTTTTTCTTCACCCTCCA 59.588 41.667 0.00 0.00 0.00 3.86
5932 6466 3.707611 TGTAATCCACGGCTTGTAGGTAT 59.292 43.478 0.00 0.00 0.00 2.73
5991 6526 0.892755 CAGCTTACACAGGTCGGGTA 59.107 55.000 0.00 0.00 0.00 3.69
6100 6636 4.993029 AGCTAGCTAGGAAACAGTACAG 57.007 45.455 17.69 0.00 0.00 2.74
6258 6809 1.095228 ACCAACTGTTCACGGCACAG 61.095 55.000 8.81 8.81 46.18 3.66
6379 6945 3.693572 AGCTCCCCTCTGGCCTCT 61.694 66.667 3.32 0.00 0.00 3.69
6499 7085 2.123897 AACTGGCCGGCTTTGTGT 60.124 55.556 28.56 14.73 0.00 3.72
6512 7098 2.210116 CTTTGTGTCCTACGCTTGTGT 58.790 47.619 0.00 0.00 0.00 3.72
6517 7103 1.063951 GTCCTACGCTTGTGTCGTCG 61.064 60.000 0.00 0.00 40.89 5.12
6566 7226 9.620660 GCTTTAATTCAAAAGGTAAATTCGAGA 57.379 29.630 3.50 0.00 37.03 4.04
6593 7255 1.230650 TGGAGAGGAGGAGAGGGGA 60.231 63.158 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.814899 TCAAGCTTTGTAAATTTTCATCTCAAA 57.185 25.926 0.00 0.00 0.00 2.69
8 9 9.248291 GTCAAGCTTTGTAAATTTTCATCTCAA 57.752 29.630 0.00 0.00 0.00 3.02
9 10 8.632679 AGTCAAGCTTTGTAAATTTTCATCTCA 58.367 29.630 0.00 0.00 0.00 3.27
10 11 9.468532 AAGTCAAGCTTTGTAAATTTTCATCTC 57.531 29.630 0.00 0.00 32.57 2.75
11 12 9.822185 AAAGTCAAGCTTTGTAAATTTTCATCT 57.178 25.926 0.00 0.00 45.00 2.90
29 30 9.979270 CACATATTAGCTTTACTCAAAGTCAAG 57.021 33.333 0.00 0.00 42.71 3.02
33 34 8.322091 AGTCCACATATTAGCTTTACTCAAAGT 58.678 33.333 0.00 0.00 42.71 2.66
45 46 9.659830 CCGTTTTTATTTAGTCCACATATTAGC 57.340 33.333 0.00 0.00 0.00 3.09
54 55 7.001099 ACTCTCTCCGTTTTTATTTAGTCCA 57.999 36.000 0.00 0.00 0.00 4.02
63 64 6.899393 TGGTTAGTACTCTCTCCGTTTTTA 57.101 37.500 0.00 0.00 0.00 1.52
66 67 4.586001 TGTTGGTTAGTACTCTCTCCGTTT 59.414 41.667 0.00 0.00 0.00 3.60
67 68 4.022503 GTGTTGGTTAGTACTCTCTCCGTT 60.023 45.833 0.00 0.00 0.00 4.44
68 69 3.505293 GTGTTGGTTAGTACTCTCTCCGT 59.495 47.826 0.00 0.00 0.00 4.69
69 70 3.119566 GGTGTTGGTTAGTACTCTCTCCG 60.120 52.174 0.00 0.00 0.00 4.63
70 71 3.119566 CGGTGTTGGTTAGTACTCTCTCC 60.120 52.174 0.00 0.00 0.00 3.71
71 72 3.119566 CCGGTGTTGGTTAGTACTCTCTC 60.120 52.174 0.00 0.00 0.00 3.20
72 73 2.824341 CCGGTGTTGGTTAGTACTCTCT 59.176 50.000 0.00 0.00 0.00 3.10
75 76 3.320626 GTTCCGGTGTTGGTTAGTACTC 58.679 50.000 0.00 0.00 0.00 2.59
76 77 2.288395 CGTTCCGGTGTTGGTTAGTACT 60.288 50.000 0.00 0.00 0.00 2.73
77 78 2.061028 CGTTCCGGTGTTGGTTAGTAC 58.939 52.381 0.00 0.00 0.00 2.73
80 81 2.088950 ATCGTTCCGGTGTTGGTTAG 57.911 50.000 0.00 0.00 0.00 2.34
100 101 5.046878 CCAACATATGGCAGCCATTGATTAT 60.047 40.000 32.20 16.14 42.23 1.28
101 102 4.281435 CCAACATATGGCAGCCATTGATTA 59.719 41.667 32.20 14.40 42.23 1.75
224 274 1.002087 AGATGTTTCACGGGTGAGGTC 59.998 52.381 1.37 0.47 41.13 3.85
225 275 1.056660 AGATGTTTCACGGGTGAGGT 58.943 50.000 1.37 0.00 41.13 3.85
230 280 0.889186 GCACCAGATGTTTCACGGGT 60.889 55.000 0.00 0.00 0.00 5.28
258 308 2.764547 GGGACGGGGGAGAGGAAG 60.765 72.222 0.00 0.00 0.00 3.46
299 362 4.144297 TCCTGATGTGTTTTCCTTCCTTG 58.856 43.478 0.00 0.00 0.00 3.61
335 398 2.159585 CCATTCGTGCTGTTATTTCGCA 60.160 45.455 0.00 0.00 0.00 5.10
368 431 3.193479 CCTTCACCTGCACTTTATTTCCC 59.807 47.826 0.00 0.00 0.00 3.97
369 432 3.193479 CCCTTCACCTGCACTTTATTTCC 59.807 47.826 0.00 0.00 0.00 3.13
502 565 3.758931 GATTTGTGGCGGGTGGGC 61.759 66.667 0.00 0.00 42.69 5.36
539 602 0.813821 GTTCTACTTCTACCGCCGGT 59.186 55.000 15.63 15.63 40.16 5.28
544 607 1.136500 GCTGGGGTTCTACTTCTACCG 59.864 57.143 0.00 0.00 32.61 4.02
545 608 1.136500 CGCTGGGGTTCTACTTCTACC 59.864 57.143 0.00 0.00 0.00 3.18
546 609 1.471153 GCGCTGGGGTTCTACTTCTAC 60.471 57.143 0.00 0.00 0.00 2.59
547 610 0.822164 GCGCTGGGGTTCTACTTCTA 59.178 55.000 0.00 0.00 0.00 2.10
549 612 1.449778 GGCGCTGGGGTTCTACTTC 60.450 63.158 7.64 0.00 0.00 3.01
550 613 2.669240 GGCGCTGGGGTTCTACTT 59.331 61.111 7.64 0.00 0.00 2.24
705 807 2.510238 GGCAGCTGCGATTCGACT 60.510 61.111 31.19 0.42 43.26 4.18
786 888 2.676016 GATCGAGCAGTGGAGGCGAG 62.676 65.000 0.00 0.00 34.25 5.03
787 889 2.755876 ATCGAGCAGTGGAGGCGA 60.756 61.111 0.00 0.00 36.08 5.54
788 890 2.279120 GATCGAGCAGTGGAGGCG 60.279 66.667 0.00 0.00 36.08 5.52
789 891 2.279120 CGATCGAGCAGTGGAGGC 60.279 66.667 10.26 0.00 0.00 4.70
790 892 1.448119 TAGCGATCGAGCAGTGGAGG 61.448 60.000 21.57 0.00 40.15 4.30
791 893 0.317436 GTAGCGATCGAGCAGTGGAG 60.317 60.000 21.57 0.00 40.15 3.86
792 894 1.029947 TGTAGCGATCGAGCAGTGGA 61.030 55.000 21.57 0.00 40.15 4.02
821 923 2.036733 GGCAGCGTCCTATGTATGGTAA 59.963 50.000 0.00 0.00 0.00 2.85
893 1015 1.373497 CGATCCTGCCGTCCTATGC 60.373 63.158 0.00 0.00 0.00 3.14
941 1071 0.698238 TCCAAGCCAACATAGCCACT 59.302 50.000 0.00 0.00 0.00 4.00
995 1138 2.588877 CGACGACATCCATGGCCC 60.589 66.667 6.96 0.00 29.87 5.80
1195 1344 4.445019 GGGAGATGGAATTCAGTCTTACCC 60.445 50.000 7.93 12.44 0.00 3.69
1226 1383 1.068948 TCGGGAATTCAGAAACCCCA 58.931 50.000 18.39 7.67 39.20 4.96
1258 1420 4.332637 GTGCCACCAACAGCAGCG 62.333 66.667 0.00 0.00 40.28 5.18
1259 1421 4.332637 CGTGCCACCAACAGCAGC 62.333 66.667 0.00 0.00 40.28 5.25
1260 1422 2.591429 TCGTGCCACCAACAGCAG 60.591 61.111 0.00 0.00 40.28 4.24
1262 1424 2.591715 AGTCGTGCCACCAACAGC 60.592 61.111 0.00 0.00 0.00 4.40
1263 1425 0.603707 ATCAGTCGTGCCACCAACAG 60.604 55.000 0.00 0.00 0.00 3.16
1264 1426 0.179032 AATCAGTCGTGCCACCAACA 60.179 50.000 0.00 0.00 0.00 3.33
1286 1458 3.436243 ACAACAAAAACAAGGAGACCCA 58.564 40.909 0.00 0.00 33.88 4.51
1291 1463 5.284079 CCTGATGACAACAAAAACAAGGAG 58.716 41.667 0.00 0.00 0.00 3.69
1319 1496 3.895041 CCTCTTCTCTGTCTCCTTATCCC 59.105 52.174 0.00 0.00 0.00 3.85
1476 1656 0.313233 CGTCGAAAGCGCGTTCATAC 60.313 55.000 30.39 25.19 37.46 2.39
1479 1659 2.353723 TCGTCGAAAGCGCGTTCA 60.354 55.556 30.39 17.49 37.92 3.18
1599 1779 4.735358 GAAACCACCGGGGCCTCC 62.735 72.222 6.32 0.51 42.05 4.30
1625 1805 0.906756 CTCCTCCTTCTGGACTGGCA 60.907 60.000 0.00 0.00 37.46 4.92
1626 1806 1.621672 CCTCCTCCTTCTGGACTGGC 61.622 65.000 0.00 0.00 37.46 4.85
1656 1836 2.107950 TCGGCGATTGAATTTCCTGT 57.892 45.000 4.99 0.00 0.00 4.00
1657 1837 3.548818 GGAATCGGCGATTGAATTTCCTG 60.549 47.826 36.79 0.00 31.89 3.86
1660 1840 3.691049 TGGAATCGGCGATTGAATTTC 57.309 42.857 36.79 22.52 31.89 2.17
1664 1844 1.597195 CGAATGGAATCGGCGATTGAA 59.403 47.619 36.79 24.50 39.12 2.69
1665 1845 1.217001 CGAATGGAATCGGCGATTGA 58.783 50.000 36.79 23.49 39.12 2.57
1706 1895 3.184683 CCTCTGCTTCGTGCTCGC 61.185 66.667 2.69 0.00 43.37 5.03
1734 1923 5.984323 GTCGTCTTCTTCTTTTTCCACTAGT 59.016 40.000 0.00 0.00 0.00 2.57
1744 1933 3.246619 GCTCATCGTCGTCTTCTTCTTT 58.753 45.455 0.00 0.00 0.00 2.52
1745 1934 2.229062 TGCTCATCGTCGTCTTCTTCTT 59.771 45.455 0.00 0.00 0.00 2.52
1746 1935 1.813178 TGCTCATCGTCGTCTTCTTCT 59.187 47.619 0.00 0.00 0.00 2.85
1783 1975 2.226896 CGATCTTCGGCTCTGCGTG 61.227 63.158 0.00 0.00 36.00 5.34
1806 1998 2.167398 ATCGGTAGTTGTGCGTGGCT 62.167 55.000 0.00 0.00 0.00 4.75
1979 2171 2.049802 GGTCTTTCGCCGTGACGA 60.050 61.111 6.54 0.00 41.04 4.20
2289 2481 1.318158 CCATGGCCTTGAGCACCTTC 61.318 60.000 19.85 0.00 46.50 3.46
2325 2517 1.226686 AAGACAGCTGCAGCAAGTCG 61.227 55.000 36.84 25.00 46.10 4.18
2329 2521 0.466007 TGGAAAGACAGCTGCAGCAA 60.466 50.000 38.24 10.68 45.16 3.91
2462 2654 3.878519 CCGCCTCGTCGTCCTCTC 61.879 72.222 0.00 0.00 0.00 3.20
2497 2689 2.303549 ATCTTCGCCTCGGCCTCTTG 62.304 60.000 0.00 0.00 37.98 3.02
2518 2710 2.368878 GCTCCCCTCCCCTTGGAT 60.369 66.667 0.00 0.00 40.80 3.41
2521 2713 4.120755 GCTGCTCCCCTCCCCTTG 62.121 72.222 0.00 0.00 0.00 3.61
2579 2777 0.871592 CGCCGCGATCATCTTCTTCA 60.872 55.000 8.23 0.00 0.00 3.02
2625 2823 2.842394 AATGCTCCACGCTGTCCTCG 62.842 60.000 0.00 0.00 40.11 4.63
2629 2827 2.456119 CCGAATGCTCCACGCTGTC 61.456 63.158 0.00 0.00 40.11 3.51
2635 2833 0.537188 TCCTTCTCCGAATGCTCCAC 59.463 55.000 0.00 0.00 0.00 4.02
2762 2960 0.755698 TGGGCTCCTCTCGGTATCAC 60.756 60.000 0.00 0.00 0.00 3.06
2793 2991 2.224209 ACTCGTACCAACAAGTTCCCTG 60.224 50.000 0.00 0.00 0.00 4.45
2805 3006 3.367288 TGGATGACCACTCGTACCA 57.633 52.632 0.00 0.00 41.77 3.25
2829 3030 4.164221 TCTTCTCTGTCAAGGGAAACAAGT 59.836 41.667 0.00 0.00 42.47 3.16
2838 3039 2.075338 GCTGCTTCTTCTCTGTCAAGG 58.925 52.381 0.00 0.00 0.00 3.61
2875 3076 3.309961 TCTCTTGTCATCAGTGTCTGC 57.690 47.619 0.00 0.00 0.00 4.26
3117 3318 3.069289 TGCTGCATATGACCGATCATTC 58.931 45.455 6.97 0.00 43.40 2.67
3141 3342 1.030457 GGGTGGTACGATCGTCAGAT 58.970 55.000 26.48 1.51 40.38 2.90
3168 3369 4.528206 TCTGTACTGAATTCCTGCTCTGAA 59.472 41.667 2.27 0.00 0.00 3.02
3188 3389 7.980662 GGATTACTCCATACTGATGATCATCTG 59.019 40.741 30.37 30.37 41.64 2.90
3220 3421 1.416401 TGGCTCTGAACTTTTCTCGGT 59.584 47.619 0.00 0.00 0.00 4.69
3221 3422 2.169832 TGGCTCTGAACTTTTCTCGG 57.830 50.000 0.00 0.00 0.00 4.63
3230 3431 2.777832 ATCCTCTGTTGGCTCTGAAC 57.222 50.000 0.00 0.00 0.00 3.18
3330 3531 1.202782 TCCTTATCCTCCTCCTCGTCG 60.203 57.143 0.00 0.00 0.00 5.12
3471 3672 1.038130 CCGACTCCTCCAGGATCGTT 61.038 60.000 18.24 0.00 44.46 3.85
3504 3705 0.613777 GTTTGAGGTCCTCCATCGGT 59.386 55.000 16.60 0.00 35.89 4.69
3662 3864 4.347000 AGTGGTAGTGAACTGGTAATGTGT 59.653 41.667 0.00 0.00 0.00 3.72
3737 3945 9.788960 GTGCAACCTAATTTTTCCTATTAGAAG 57.211 33.333 0.00 0.00 37.64 2.85
3764 3979 0.875059 CGTTTCAGAGAAAGGTGGGC 59.125 55.000 4.52 0.00 0.00 5.36
3821 4036 9.877137 GTACTAGATATCTGCGATTATGATGAG 57.123 37.037 15.79 2.41 0.00 2.90
3844 4059 1.553706 TTTCTGGACGGAGGGAGTAC 58.446 55.000 0.00 0.00 0.00 2.73
3845 4060 2.544844 ATTTCTGGACGGAGGGAGTA 57.455 50.000 0.00 0.00 0.00 2.59
3846 4061 2.108970 GTATTTCTGGACGGAGGGAGT 58.891 52.381 0.00 0.00 0.00 3.85
3847 4062 2.362717 GAGTATTTCTGGACGGAGGGAG 59.637 54.545 0.00 0.00 0.00 4.30
3848 4063 2.385803 GAGTATTTCTGGACGGAGGGA 58.614 52.381 0.00 0.00 0.00 4.20
3849 4064 1.067212 CGAGTATTTCTGGACGGAGGG 59.933 57.143 0.00 0.00 0.00 4.30
3850 4065 1.749634 ACGAGTATTTCTGGACGGAGG 59.250 52.381 0.00 0.00 0.00 4.30
3851 4066 2.539142 CGACGAGTATTTCTGGACGGAG 60.539 54.545 0.00 0.00 36.75 4.63
3852 4067 1.399440 CGACGAGTATTTCTGGACGGA 59.601 52.381 0.00 0.00 36.75 4.69
3853 4068 1.823828 CGACGAGTATTTCTGGACGG 58.176 55.000 0.00 0.00 36.75 4.79
3854 4069 1.399440 TCCGACGAGTATTTCTGGACG 59.601 52.381 0.00 0.00 38.91 4.79
3855 4070 2.223525 CCTCCGACGAGTATTTCTGGAC 60.224 54.545 0.00 0.00 33.93 4.02
3856 4071 2.022195 CCTCCGACGAGTATTTCTGGA 58.978 52.381 0.00 0.00 33.93 3.86
3857 4072 2.022195 TCCTCCGACGAGTATTTCTGG 58.978 52.381 0.00 0.00 33.93 3.86
3858 4073 3.777465 TTCCTCCGACGAGTATTTCTG 57.223 47.619 0.00 0.00 33.93 3.02
3859 4074 3.068307 CCATTCCTCCGACGAGTATTTCT 59.932 47.826 0.00 0.00 33.93 2.52
3860 4075 3.067742 TCCATTCCTCCGACGAGTATTTC 59.932 47.826 0.00 0.00 33.93 2.17
3861 4076 3.028850 TCCATTCCTCCGACGAGTATTT 58.971 45.455 0.00 0.00 33.93 1.40
3862 4077 2.662866 TCCATTCCTCCGACGAGTATT 58.337 47.619 0.00 0.00 33.93 1.89
3863 4078 2.359981 TCCATTCCTCCGACGAGTAT 57.640 50.000 0.00 0.00 33.93 2.12
3864 4079 1.954382 CATCCATTCCTCCGACGAGTA 59.046 52.381 0.00 0.00 33.93 2.59
3865 4080 0.747255 CATCCATTCCTCCGACGAGT 59.253 55.000 0.00 0.00 33.93 4.18
3866 4081 0.747255 ACATCCATTCCTCCGACGAG 59.253 55.000 0.00 0.00 35.72 4.18
3867 4082 2.061509 TACATCCATTCCTCCGACGA 57.938 50.000 0.00 0.00 0.00 4.20
3868 4083 2.558795 AGATACATCCATTCCTCCGACG 59.441 50.000 0.00 0.00 0.00 5.12
3869 4084 5.010933 TCTAGATACATCCATTCCTCCGAC 58.989 45.833 0.00 0.00 0.00 4.79
3870 4085 5.256806 TCTAGATACATCCATTCCTCCGA 57.743 43.478 0.00 0.00 0.00 4.55
3871 4086 5.420421 ACATCTAGATACATCCATTCCTCCG 59.580 44.000 4.54 0.00 0.00 4.63
3872 4087 6.865834 ACATCTAGATACATCCATTCCTCC 57.134 41.667 4.54 0.00 0.00 4.30
3909 4124 9.467258 CGGAGAAATGCATAAAAATGAATGTAT 57.533 29.630 0.00 0.00 30.86 2.29
3910 4125 8.681806 TCGGAGAAATGCATAAAAATGAATGTA 58.318 29.630 0.00 0.00 0.00 2.29
3911 4126 7.489113 GTCGGAGAAATGCATAAAAATGAATGT 59.511 33.333 0.00 0.00 39.69 2.71
3912 4127 7.488792 TGTCGGAGAAATGCATAAAAATGAATG 59.511 33.333 0.00 0.00 39.69 2.67
3913 4128 7.546358 TGTCGGAGAAATGCATAAAAATGAAT 58.454 30.769 0.00 0.00 39.69 2.57
3914 4129 6.918626 TGTCGGAGAAATGCATAAAAATGAA 58.081 32.000 0.00 0.00 39.69 2.57
3915 4130 6.507958 TGTCGGAGAAATGCATAAAAATGA 57.492 33.333 0.00 0.00 39.69 2.57
3916 4131 6.808212 ACTTGTCGGAGAAATGCATAAAAATG 59.192 34.615 0.00 0.00 39.69 2.32
3917 4132 6.924111 ACTTGTCGGAGAAATGCATAAAAAT 58.076 32.000 0.00 0.00 39.69 1.82
3918 4133 6.325919 ACTTGTCGGAGAAATGCATAAAAA 57.674 33.333 0.00 0.00 39.69 1.94
3919 4134 5.957842 ACTTGTCGGAGAAATGCATAAAA 57.042 34.783 0.00 0.00 39.69 1.52
3920 4135 7.624360 AATACTTGTCGGAGAAATGCATAAA 57.376 32.000 0.00 0.00 39.69 1.40
3921 4136 7.201696 GGAAATACTTGTCGGAGAAATGCATAA 60.202 37.037 0.00 0.00 39.69 1.90
3922 4137 6.260050 GGAAATACTTGTCGGAGAAATGCATA 59.740 38.462 0.00 0.00 39.69 3.14
3923 4138 5.066505 GGAAATACTTGTCGGAGAAATGCAT 59.933 40.000 0.00 0.00 39.69 3.96
3924 4139 4.394920 GGAAATACTTGTCGGAGAAATGCA 59.605 41.667 0.00 0.00 39.69 3.96
3925 4140 4.494199 CGGAAATACTTGTCGGAGAAATGC 60.494 45.833 0.00 0.00 39.69 3.56
3926 4141 4.034048 CCGGAAATACTTGTCGGAGAAATG 59.966 45.833 0.00 0.00 42.94 2.32
3927 4142 4.081309 TCCGGAAATACTTGTCGGAGAAAT 60.081 41.667 0.00 0.00 43.84 2.17
3928 4143 3.258872 TCCGGAAATACTTGTCGGAGAAA 59.741 43.478 0.00 0.00 43.84 2.52
3929 4144 2.827322 TCCGGAAATACTTGTCGGAGAA 59.173 45.455 0.00 0.00 43.84 2.87
3930 4145 2.449464 TCCGGAAATACTTGTCGGAGA 58.551 47.619 0.00 0.00 43.84 3.71
3931 4146 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
3932 4147 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
3933 4148 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
3934 4149 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
3935 4150 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3936 4151 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3937 4152 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3938 4153 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3939 4154 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3940 4155 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3941 4156 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3942 4157 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3943 4158 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3944 4159 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3945 4160 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
3946 4161 1.920610 ATAATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
3947 4162 3.057456 CAGAATAATACTCCCTCCGTCCG 60.057 52.174 0.00 0.00 0.00 4.79
3948 4163 3.896272 ACAGAATAATACTCCCTCCGTCC 59.104 47.826 0.00 0.00 0.00 4.79
3949 4164 6.002704 TCTACAGAATAATACTCCCTCCGTC 58.997 44.000 0.00 0.00 0.00 4.79
3950 4165 5.950023 TCTACAGAATAATACTCCCTCCGT 58.050 41.667 0.00 0.00 0.00 4.69
3951 4166 8.577048 TTATCTACAGAATAATACTCCCTCCG 57.423 38.462 0.00 0.00 0.00 4.63
3953 4168 9.810545 GCATTATCTACAGAATAATACTCCCTC 57.189 37.037 0.00 0.00 0.00 4.30
3954 4169 9.554053 AGCATTATCTACAGAATAATACTCCCT 57.446 33.333 0.00 0.00 0.00 4.20
4051 4339 9.418045 GCCAGTTTAAAATTCTAAGCATGTTAA 57.582 29.630 0.00 0.00 0.00 2.01
4086 4378 9.280174 TCAACTTCGGTGAATTTTAGTTAGAAT 57.720 29.630 0.00 0.00 0.00 2.40
4101 4393 0.958091 TTTGCCCATCAACTTCGGTG 59.042 50.000 0.00 0.00 33.73 4.94
4103 4395 1.067635 CCTTTTGCCCATCAACTTCGG 60.068 52.381 0.00 0.00 33.73 4.30
4113 4405 1.074889 GTTAGAGACCCCTTTTGCCCA 59.925 52.381 0.00 0.00 0.00 5.36
4251 4549 4.526970 TCAGTTATTTCCCCTGCATTCTC 58.473 43.478 0.00 0.00 0.00 2.87
4262 4747 5.652014 TGTGTGATCCCAATCAGTTATTTCC 59.348 40.000 0.00 0.00 42.53 3.13
4291 4776 9.331282 CAAGAGAAGATAGGTTTTTCGGATTAT 57.669 33.333 0.00 0.00 0.00 1.28
4401 4890 7.711339 GGTAAGTACTGAATCTGGGTCATTAAG 59.289 40.741 0.00 0.00 0.00 1.85
4426 4915 4.065789 GCAATCTCTTCGGGTAATAAGGG 58.934 47.826 0.00 0.00 0.00 3.95
4454 4943 7.211966 ACCAATTGAAGAACATCTCTCTTTG 57.788 36.000 7.12 0.00 33.24 2.77
4561 5057 4.032104 ACAAAAGTTGTAGACGACGTGAAC 59.968 41.667 4.58 3.59 43.27 3.18
4567 5063 6.639686 TCATAGACACAAAAGTTGTAGACGAC 59.360 38.462 0.00 0.00 43.23 4.34
4571 5067 6.989759 TGCTTCATAGACACAAAAGTTGTAGA 59.010 34.615 0.00 0.00 43.23 2.59
4574 5070 6.639632 ATGCTTCATAGACACAAAAGTTGT 57.360 33.333 0.00 0.00 46.75 3.32
4625 5122 2.376808 ACGAGCTTCATCTGTCCTTG 57.623 50.000 0.00 0.00 0.00 3.61
4643 5140 5.371115 TGTTGCCAGTATAAAGCAAGAAC 57.629 39.130 5.76 0.00 46.40 3.01
4675 5172 1.090625 CAGAGCATGCTGAGCTGGAC 61.091 60.000 28.27 7.90 43.58 4.02
4715 5212 9.822185 ACGTTAACTAAAGGAACTAAAGAAAGA 57.178 29.630 3.71 0.00 38.49 2.52
4716 5213 9.859692 CACGTTAACTAAAGGAACTAAAGAAAG 57.140 33.333 3.71 0.00 38.49 2.62
4727 5225 4.890088 ACATCAGCACGTTAACTAAAGGA 58.110 39.130 3.71 0.00 0.00 3.36
4734 5232 5.120208 ACATTGAGTACATCAGCACGTTAAC 59.880 40.000 0.00 0.00 39.68 2.01
4753 5251 4.216902 TGGAGAAAATCTGCAGTGACATTG 59.783 41.667 14.67 0.00 39.98 2.82
4867 5365 0.827368 GGTCCTCTGGTGATCTCCAC 59.173 60.000 12.50 2.91 44.95 4.02
4879 5377 2.442272 CGGTCCGATGGGTCCTCT 60.442 66.667 4.91 0.00 39.15 3.69
5199 5697 0.322816 AGACATCGCACCATTGGCTT 60.323 50.000 1.54 0.00 0.00 4.35
5219 5717 9.453572 TCTACATTTCAAGCTAAATTCATCACT 57.546 29.630 0.00 0.00 0.00 3.41
5220 5718 9.713740 CTCTACATTTCAAGCTAAATTCATCAC 57.286 33.333 0.00 0.00 0.00 3.06
5222 5720 8.619546 AGCTCTACATTTCAAGCTAAATTCATC 58.380 33.333 0.00 0.00 43.04 2.92
5223 5721 8.517062 AGCTCTACATTTCAAGCTAAATTCAT 57.483 30.769 0.00 0.00 43.04 2.57
5240 5738 6.437477 TCCAAACTTCAGATTAGAGCTCTACA 59.563 38.462 23.17 14.27 0.00 2.74
5241 5739 6.868622 TCCAAACTTCAGATTAGAGCTCTAC 58.131 40.000 23.17 12.71 0.00 2.59
5243 5743 6.558488 ATCCAAACTTCAGATTAGAGCTCT 57.442 37.500 22.17 22.17 0.00 4.09
5253 5753 3.072915 TCCTCTGCAATCCAAACTTCAGA 59.927 43.478 0.00 0.00 0.00 3.27
5254 5754 3.190118 GTCCTCTGCAATCCAAACTTCAG 59.810 47.826 0.00 0.00 0.00 3.02
5369 5869 1.952367 GCCTTGATGAACTCCCACAGG 60.952 57.143 0.00 0.00 0.00 4.00
5408 5908 1.377725 CAAGCCCTTCAGCACCGAT 60.378 57.895 0.00 0.00 34.23 4.18
5531 6039 1.027357 CAAATCATCTCCTTGCCGGG 58.973 55.000 2.18 0.00 0.00 5.73
5584 6108 3.269178 CCTCTTCTCTTTCTGCATCACC 58.731 50.000 0.00 0.00 0.00 4.02
5807 6331 0.985490 GAAGCCTCCCTGTGGATCCT 60.985 60.000 14.23 0.00 40.80 3.24
5830 6354 0.540365 CCAAGCAGGGGAAGAGCAAA 60.540 55.000 0.00 0.00 0.00 3.68
5867 6391 9.444534 GAAAAAGAAGAGAACAAAATCAGAGAC 57.555 33.333 0.00 0.00 0.00 3.36
5895 6419 1.735926 TTACATGGTGTGGAGGGTGA 58.264 50.000 0.00 0.00 0.00 4.02
5897 6421 1.564348 GGATTACATGGTGTGGAGGGT 59.436 52.381 0.00 0.00 0.00 4.34
5898 6422 1.563879 TGGATTACATGGTGTGGAGGG 59.436 52.381 0.00 0.00 0.00 4.30
5991 6526 7.490657 TGTTTATCAGGTTACAGTCATAGGT 57.509 36.000 0.00 0.00 0.00 3.08
6100 6636 4.202050 GGTGATGGATGGCTTCATTACAAC 60.202 45.833 2.60 0.00 33.34 3.32
6169 6705 9.938280 TTCATTACAACTTGTGCTAGTAGTATT 57.062 29.630 4.57 0.00 0.00 1.89
6363 6929 3.478274 CAGAGGCCAGAGGGGAGC 61.478 72.222 5.01 0.00 40.01 4.70
6379 6945 1.745890 CACGAGGACTGTTCACCCA 59.254 57.895 0.00 0.00 0.00 4.51
6499 7085 1.208358 CGACGACACAAGCGTAGGA 59.792 57.895 0.00 0.00 42.77 2.94
6512 7098 6.637658 GGAAATCACCAAAAATAAAACGACGA 59.362 34.615 0.00 0.00 0.00 4.20
6517 7103 6.645003 AGCGAGGAAATCACCAAAAATAAAAC 59.355 34.615 0.00 0.00 0.00 2.43
6566 7226 0.689623 CCTCCTCTCCACAGCAAACT 59.310 55.000 0.00 0.00 0.00 2.66
6593 7255 1.510480 GCTGCTTTCAACGGTGAGCT 61.510 55.000 14.86 0.00 34.49 4.09
6642 7304 0.606130 TGTCACGCCACTGAATGCAT 60.606 50.000 0.00 0.00 0.00 3.96
6782 7459 0.806868 ACATGCATCTTCCAGTTGCG 59.193 50.000 0.00 0.00 42.31 4.85
6784 7461 3.064958 CAGCTACATGCATCTTCCAGTTG 59.935 47.826 0.00 0.00 45.94 3.16


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

AutoCloner maintained by Alex Coulton.