Multiple sequence alignment - TraesCS3A01G331000

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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 TraesCS3A01G331000 chr3A 100.000 5015 0 0 1 5015 575493512 575498526 0.000000e+00 9262
1 TraesCS3A01G331000 chr3A 100.000 1627 0 0 5225 6851 575498736 575500362 0.000000e+00 3005
2 TraesCS3A01G331000 chr3B 89.163 3165 186 80 1 3101 572744683 572747754 0.000000e+00 3799
3 TraesCS3A01G331000 chr3B 91.518 1627 97 21 5234 6851 572749431 572751025 0.000000e+00 2202
4 TraesCS3A01G331000 chr3B 85.778 893 100 20 4092 4968 572748527 572749408 0.000000e+00 920
5 TraesCS3A01G331000 chr3B 94.615 130 7 0 3967 4096 46285118 46285247 1.170000e-47 202
6 TraesCS3A01G331000 chr3B 95.604 91 4 0 3754 3844 738120246 738120336 5.540000e-31 147
7 TraesCS3A01G331000 chr3D 96.619 2100 55 6 1658 3756 437490391 437492475 0.000000e+00 3470
8 TraesCS3A01G331000 chr3D 95.254 927 30 5 4092 5015 437492603 437493518 0.000000e+00 1456
9 TraesCS3A01G331000 chr3D 92.716 810 36 10 6052 6851 437494268 437495064 0.000000e+00 1147
10 TraesCS3A01G331000 chr3D 94.648 710 34 3 5225 5934 437493533 437494238 0.000000e+00 1098
11 TraesCS3A01G331000 chr3D 89.729 886 36 27 812 1659 437489025 437489893 0.000000e+00 1081
12 TraesCS3A01G331000 chr3D 95.290 637 29 1 1 637 437487974 437488609 0.000000e+00 1009
13 TraesCS3A01G331000 chr3D 92.806 139 9 1 3967 4104 84562736 84562598 4.190000e-47 200
14 TraesCS3A01G331000 chr3D 93.333 135 9 0 3960 4094 134495869 134496003 4.190000e-47 200
15 TraesCS3A01G331000 chr3D 98.667 75 1 0 596 670 437488608 437488682 4.310000e-27 134
16 TraesCS3A01G331000 chr6B 91.892 259 20 1 1 259 711514146 711513889 1.820000e-95 361
17 TraesCS3A01G331000 chr6B 91.129 248 22 0 4 251 711512065 711511818 3.060000e-88 337
18 TraesCS3A01G331000 chr6B 90.234 256 24 1 4 259 711516834 711516580 3.960000e-87 333
19 TraesCS3A01G331000 chr6B 90.234 256 24 1 4 259 711518801 711518547 3.960000e-87 333
20 TraesCS3A01G331000 chr6B 90.947 243 22 0 3 245 711625073 711624831 1.840000e-85 327
21 TraesCS3A01G331000 chr6B 90.079 252 24 1 2 253 711521751 711521501 6.630000e-85 326
22 TraesCS3A01G331000 chr6B 89.189 259 26 2 1 259 711519786 711519530 8.570000e-84 322
23 TraesCS3A01G331000 chr6B 88.417 259 27 3 1 259 711520768 711520513 6.670000e-80 309
24 TraesCS3A01G331000 chr2B 96.063 127 5 0 3967 4093 134488796 134488670 2.500000e-49 207
25 TraesCS3A01G331000 chr7B 94.074 135 8 0 3967 4101 133487096 133486962 9.010000e-49 206
26 TraesCS3A01G331000 chr7B 97.674 86 2 0 3753 3838 542884334 542884419 1.540000e-31 148
27 TraesCS3A01G331000 chr7B 97.674 86 2 0 3753 3838 542981485 542981570 1.540000e-31 148
28 TraesCS3A01G331000 chr6A 91.667 144 11 1 3957 4099 107503257 107503114 1.510000e-46 198
29 TraesCS3A01G331000 chr5B 91.667 144 11 1 3958 4100 46633247 46633390 1.510000e-46 198
30 TraesCS3A01G331000 chr1B 94.488 127 7 0 3967 4093 41782558 41782684 5.420000e-46 196
31 TraesCS3A01G331000 chr1B 85.185 108 13 3 3754 3861 606365151 606365255 2.610000e-19 108
32 TraesCS3A01G331000 chr1A 91.034 145 10 2 3949 4093 486045758 486045899 7.010000e-45 193
33 TraesCS3A01G331000 chr1A 97.701 87 2 0 3754 3840 31314905 31314991 4.280000e-32 150
34 TraesCS3A01G331000 chr1A 87.273 110 13 1 3753 3861 584675595 584675704 2.590000e-24 124
35 TraesCS3A01G331000 chr6D 83.838 198 16 5 5972 6169 454000870 454001051 2.540000e-39 174
36 TraesCS3A01G331000 chr6D 96.552 87 3 0 3752 3838 215213522 215213608 1.990000e-30 145
37 TraesCS3A01G331000 chr5A 95.699 93 4 0 3746 3838 463600520 463600612 4.280000e-32 150
38 TraesCS3A01G331000 chr5A 96.591 88 3 0 3753 3840 395887788 395887701 5.540000e-31 147
39 TraesCS3A01G331000 chr4A 93.684 95 6 0 3751 3845 649803982 649803888 7.160000e-30 143
40 TraesCS3A01G331000 chr7D 84.397 141 19 3 3735 3873 329500236 329500097 1.200000e-27 135
41 TraesCS3A01G331000 chr7A 89.320 103 8 3 3754 3855 173487648 173487548 7.210000e-25 126
42 TraesCS3A01G331000 chr7A 86.139 101 14 0 3754 3854 63791698 63791598 7.260000e-20 110


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 TraesCS3A01G331000 chr3A 575493512 575500362 6850 False 6133.500000 9262 100.000000 1 6851 2 chr3A.!!$F1 6850
1 TraesCS3A01G331000 chr3B 572744683 572751025 6342 False 2307.000000 3799 88.819667 1 6851 3 chr3B.!!$F3 6850
2 TraesCS3A01G331000 chr3D 437487974 437495064 7090 False 1342.142857 3470 94.703286 1 6851 7 chr3D.!!$F2 6850
3 TraesCS3A01G331000 chr6B 711511818 711521751 9933 True 331.571429 361 90.167714 1 259 7 chr6B.!!$R2 258

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
542 8148 0.033781 TTTACAACGACGACCCTGGG 59.966 55.000 12.28 12.28 0.00 4.45 F
587 8193 0.325671 ATGATCCGTGACACTCCCCT 60.326 55.000 3.68 0.00 0.00 4.79 F
1813 10211 0.530870 GCTAGCCGACCAGATTGACC 60.531 60.000 2.29 0.00 0.00 4.02 F
1998 10397 1.553706 TAACCGGGAAGAGACCAGAC 58.446 55.000 6.32 0.00 0.00 3.51 F
3370 11818 0.252696 ACAGGGCATGGAGTGGTAGA 60.253 55.000 3.46 0.00 0.00 2.59 F
3421 11869 1.354368 CAAAGCTTAGTTCCCCCAGGA 59.646 52.381 0.00 0.00 41.88 3.86 F
3544 11992 2.515854 GGTCTCCCCAAAAGAACTTCC 58.484 52.381 0.00 0.00 0.00 3.46 F
4977 13445 2.715046 TCAAGGTGTGAGATTCCATGC 58.285 47.619 0.00 0.00 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 10219 1.087771 GGTTGAGCCGTGTAATCCCG 61.088 60.000 0.0 0.0 0.00 5.14 R
1911 10309 5.760484 AGGTCAATGGGCAAAACAATAAT 57.240 34.783 0.0 0.0 0.00 1.28 R
2719 11120 1.022735 CAAGTGCCCTGATGATCTGC 58.977 55.000 0.0 0.0 0.00 4.26 R
3834 12286 0.034574 TGGCCCAATTGCGATGTACT 60.035 50.000 0.0 0.0 0.00 2.73 R
4760 13224 4.372656 AGGCAAGACGCAGAGAATAATAC 58.627 43.478 0.0 0.0 45.17 1.89 R
4826 13290 5.144100 AGACTCATCTAATCGACCCAAGAT 58.856 41.667 0.0 0.0 31.46 2.40 R
5449 13917 1.535088 GCAATTCGGCTAAGCGTTTC 58.465 50.000 0.0 0.0 0.00 2.78 R
6346 14816 0.325671 TTGCGAAGGAGGAGGAGGAT 60.326 55.000 0.0 0.0 0.00 3.24 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
98 4030 4.742201 CCGGCTCCACAGTCCGTG 62.742 72.222 0.00 0.00 45.92 4.94
173 7779 3.535629 CTGCCCAGTCTGCACGGAA 62.536 63.158 0.00 0.00 34.46 4.30
183 7789 3.882888 AGTCTGCACGGAAAGATTTGAAA 59.117 39.130 0.00 0.00 0.00 2.69
344 7950 2.203422 CCACAACCTTCGGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
373 7979 4.308458 CGTGAGCCGTGGGGTTGA 62.308 66.667 0.00 0.00 31.55 3.18
415 8021 2.434185 TGTCATGAGGAACGGCGC 60.434 61.111 6.90 0.00 0.00 6.53
468 8074 4.099170 CGTTCGGGTCGTCGAGCT 62.099 66.667 22.48 0.00 40.42 4.09
542 8148 0.033781 TTTACAACGACGACCCTGGG 59.966 55.000 12.28 12.28 0.00 4.45
586 8192 1.341531 CTATGATCCGTGACACTCCCC 59.658 57.143 3.68 0.00 0.00 4.81
587 8193 0.325671 ATGATCCGTGACACTCCCCT 60.326 55.000 3.68 0.00 0.00 4.79
591 8200 2.262915 CGTGACACTCCCCTGAGC 59.737 66.667 3.68 0.00 42.74 4.26
670 8321 1.232621 GGTGCCTGTAACGTTCACCC 61.233 60.000 20.09 7.12 40.84 4.61
673 8353 1.310904 GCCTGTAACGTTCACCCAAA 58.689 50.000 2.82 0.00 0.00 3.28
689 8373 2.300152 CCCAAACTGTCTACTGAGCAGA 59.700 50.000 4.21 0.00 34.60 4.26
712 8396 6.074544 AGTGAACTACTCCGTATATTCTGC 57.925 41.667 0.00 0.00 33.17 4.26
722 8406 8.004087 ACTCCGTATATTCTGCAGTAAAGTAA 57.996 34.615 14.67 0.00 0.00 2.24
743 8578 8.614469 AGTAAACTAGTATATCGGACTGTACC 57.386 38.462 0.00 0.00 0.00 3.34
744 8579 8.213679 AGTAAACTAGTATATCGGACTGTACCA 58.786 37.037 0.00 0.00 0.00 3.25
773 8613 5.689383 TTCCAGCTGAACTTTGTATTGTC 57.311 39.130 17.39 0.00 0.00 3.18
774 8614 4.713553 TCCAGCTGAACTTTGTATTGTCA 58.286 39.130 17.39 0.00 0.00 3.58
775 8615 4.515191 TCCAGCTGAACTTTGTATTGTCAC 59.485 41.667 17.39 0.00 0.00 3.67
776 8616 4.275689 CCAGCTGAACTTTGTATTGTCACA 59.724 41.667 17.39 0.00 0.00 3.58
777 8617 5.207768 CAGCTGAACTTTGTATTGTCACAC 58.792 41.667 8.42 0.00 0.00 3.82
780 8620 6.710295 AGCTGAACTTTGTATTGTCACACATA 59.290 34.615 0.00 0.00 0.00 2.29
804 8647 3.868077 GGATCTGTGAAGAGTTTGATCGG 59.132 47.826 0.00 0.00 33.30 4.18
805 8648 4.499183 GATCTGTGAAGAGTTTGATCGGT 58.501 43.478 0.00 0.00 0.00 4.69
806 8649 3.914312 TCTGTGAAGAGTTTGATCGGTC 58.086 45.455 0.00 0.00 0.00 4.79
808 8651 2.035449 TGTGAAGAGTTTGATCGGTCGT 59.965 45.455 0.00 0.00 0.00 4.34
809 8652 2.408704 GTGAAGAGTTTGATCGGTCGTG 59.591 50.000 0.00 0.00 0.00 4.35
810 8653 2.035449 TGAAGAGTTTGATCGGTCGTGT 59.965 45.455 0.00 0.00 0.00 4.49
848 8702 0.531974 AAAGAAACGTGCCAGCGAGA 60.532 50.000 0.00 0.00 35.59 4.04
849 8703 0.531974 AAGAAACGTGCCAGCGAGAA 60.532 50.000 0.00 0.00 35.59 2.87
850 8704 0.946221 AGAAACGTGCCAGCGAGAAG 60.946 55.000 0.00 0.00 35.59 2.85
851 8705 0.944311 GAAACGTGCCAGCGAGAAGA 60.944 55.000 0.00 0.00 35.59 2.87
852 8706 0.946221 AAACGTGCCAGCGAGAAGAG 60.946 55.000 0.00 0.00 35.59 2.85
885 8739 2.584835 TGCCATTTTGTCCTGCTACT 57.415 45.000 0.00 0.00 0.00 2.57
889 8743 3.375299 GCCATTTTGTCCTGCTACTACTG 59.625 47.826 0.00 0.00 0.00 2.74
890 8744 4.579869 CCATTTTGTCCTGCTACTACTGT 58.420 43.478 0.00 0.00 0.00 3.55
891 8745 5.730550 CCATTTTGTCCTGCTACTACTGTA 58.269 41.667 0.00 0.00 0.00 2.74
892 8746 5.812642 CCATTTTGTCCTGCTACTACTGTAG 59.187 44.000 13.13 13.13 46.59 2.74
940 8794 6.015856 CCCAGACTTATCTATCTCACGTTCAT 60.016 42.308 0.00 0.00 32.25 2.57
967 8821 1.156736 CCAAACACATGTCGAGGACC 58.843 55.000 0.00 0.00 0.00 4.46
968 8822 1.270839 CCAAACACATGTCGAGGACCT 60.271 52.381 0.00 0.00 0.00 3.85
969 8823 2.069273 CAAACACATGTCGAGGACCTC 58.931 52.381 11.87 11.87 0.00 3.85
1043 8920 3.132467 AGCTACCGTGTTATCTTCTTCCC 59.868 47.826 0.00 0.00 0.00 3.97
1352 9230 4.500116 GCACTCTCTCCGGGCGTC 62.500 72.222 0.00 0.00 0.00 5.19
1478 9373 2.069273 GACAACAGTCATGGACTTCCG 58.931 52.381 0.00 0.00 41.37 4.30
1523 9420 7.124573 AGCACCAAGTGTATCATCATAGTTA 57.875 36.000 0.00 0.00 35.75 2.24
1570 9467 5.213891 TCACTCTGAGAACAGCATTTGTA 57.786 39.130 12.44 0.00 43.17 2.41
1578 9475 5.123820 TGAGAACAGCATTTGTATTGGCTAC 59.876 40.000 0.00 0.00 39.73 3.58
1606 9503 2.847901 CGAATTGCTTCAAGCTCTGTG 58.152 47.619 11.57 0.00 42.97 3.66
1607 9504 2.225019 CGAATTGCTTCAAGCTCTGTGT 59.775 45.455 11.57 0.00 42.97 3.72
1611 9508 2.420642 TGCTTCAAGCTCTGTGTGATC 58.579 47.619 11.57 0.00 42.97 2.92
1612 9509 2.224354 TGCTTCAAGCTCTGTGTGATCA 60.224 45.455 11.57 0.00 42.97 2.92
1613 9510 3.008330 GCTTCAAGCTCTGTGTGATCAT 58.992 45.455 0.71 0.00 38.45 2.45
1614 9511 3.439476 GCTTCAAGCTCTGTGTGATCATT 59.561 43.478 0.71 0.00 38.45 2.57
1652 9551 3.826729 ACATACTGCTACGATATCTGCCA 59.173 43.478 0.34 0.00 0.00 4.92
1659 9558 3.736433 GCTACGATATCTGCCAGCCATAG 60.736 52.174 0.34 0.00 0.00 2.23
1718 10116 1.311859 CTGCAGCTGTTGTTTCTCCA 58.688 50.000 16.64 0.00 0.00 3.86
1719 10117 1.002033 CTGCAGCTGTTGTTTCTCCAC 60.002 52.381 16.64 0.00 0.00 4.02
1730 10128 7.523052 GCTGTTGTTTCTCCACCATATTTTGTA 60.523 37.037 0.00 0.00 0.00 2.41
1813 10211 0.530870 GCTAGCCGACCAGATTGACC 60.531 60.000 2.29 0.00 0.00 4.02
1821 10219 2.739932 CGACCAGATTGACCAGGATGTC 60.740 54.545 0.00 0.00 35.77 3.06
1865 10263 6.237901 TGTTCTCACCTTGCAAAGTATGTAT 58.762 36.000 0.00 0.00 44.25 2.29
1911 10309 6.327887 AGCAAGGGAAAGGTTAAATTTGGTTA 59.672 34.615 0.00 0.00 0.00 2.85
1949 10347 6.393990 CATTGACCTAGACCTGTATAGCATC 58.606 44.000 0.00 0.00 0.00 3.91
1998 10397 1.553706 TAACCGGGAAGAGACCAGAC 58.446 55.000 6.32 0.00 0.00 3.51
2052 10451 5.396362 CGTGAGTTATTTCTTGTGCTTGTTG 59.604 40.000 0.00 0.00 0.00 3.33
2764 11165 1.007387 CCGCAAGAAAACTGGCACC 60.007 57.895 0.00 0.00 43.02 5.01
3235 11681 3.201290 AGATGATGCAAAGTAGAAGGCG 58.799 45.455 0.00 0.00 0.00 5.52
3252 11698 2.114056 GGCGAACGAAAAACTGAAACC 58.886 47.619 0.00 0.00 0.00 3.27
3273 11719 3.306364 CCGATACAAAGCAGCCTAGCTAT 60.306 47.826 0.00 0.00 45.89 2.97
3370 11818 0.252696 ACAGGGCATGGAGTGGTAGA 60.253 55.000 3.46 0.00 0.00 2.59
3379 11827 2.035312 AGTGGTAGACGCCGGAGT 59.965 61.111 11.88 11.88 0.00 3.85
3421 11869 1.354368 CAAAGCTTAGTTCCCCCAGGA 59.646 52.381 0.00 0.00 41.88 3.86
3445 11893 4.343814 TGGAATCCAACAAAACCTTTCCTC 59.656 41.667 0.00 0.00 33.83 3.71
3455 11903 3.297134 AACCTTTCCTCAAGTTGCTGA 57.703 42.857 0.00 0.00 0.00 4.26
3459 11907 3.251972 CCTTTCCTCAAGTTGCTGAGAAC 59.748 47.826 0.00 0.00 44.82 3.01
3462 11910 2.700371 TCCTCAAGTTGCTGAGAACTGA 59.300 45.455 0.00 0.00 44.82 3.41
3478 11926 7.670364 TGAGAACTGAGTGATGATTTTCTGTA 58.330 34.615 0.00 0.00 0.00 2.74
3529 11977 3.494048 CCTGATAGCACATTCTGGGTCTC 60.494 52.174 0.00 0.00 0.00 3.36
3544 11992 2.515854 GGTCTCCCCAAAAGAACTTCC 58.484 52.381 0.00 0.00 0.00 3.46
3562 12010 6.555812 ACTTCCGTATCTTTTTCAGTTTCC 57.444 37.500 0.00 0.00 0.00 3.13
3573 12021 8.561738 TCTTTTTCAGTTTCCTATATGTGGAC 57.438 34.615 0.00 0.00 32.65 4.02
3576 12024 7.496346 TTTCAGTTTCCTATATGTGGACTCT 57.504 36.000 0.00 0.06 32.65 3.24
3710 12162 5.785940 AGTGAAGTATCTTACCTGAACCCTT 59.214 40.000 0.00 0.00 0.00 3.95
3731 12183 6.040391 CCCTTTTTCAACCTATTGACAGTTGA 59.960 38.462 4.38 4.38 44.66 3.18
3758 12210 9.998106 TTAGATAATTGGTTTAGCTGATACTCC 57.002 33.333 0.00 0.00 37.15 3.85
3759 12211 7.454225 AGATAATTGGTTTAGCTGATACTCCC 58.546 38.462 0.00 0.00 35.26 4.30
3760 12212 5.717119 AATTGGTTTAGCTGATACTCCCT 57.283 39.130 0.00 0.00 0.00 4.20
3761 12213 4.755266 TTGGTTTAGCTGATACTCCCTC 57.245 45.455 0.00 0.00 0.00 4.30
3762 12214 3.995636 TGGTTTAGCTGATACTCCCTCT 58.004 45.455 0.00 0.00 0.00 3.69
3763 12215 3.706594 TGGTTTAGCTGATACTCCCTCTG 59.293 47.826 0.00 0.00 0.00 3.35
3764 12216 3.707102 GGTTTAGCTGATACTCCCTCTGT 59.293 47.826 0.00 0.00 0.00 3.41
3765 12217 4.894114 GGTTTAGCTGATACTCCCTCTGTA 59.106 45.833 0.00 0.00 0.00 2.74
3766 12218 5.363005 GGTTTAGCTGATACTCCCTCTGTAA 59.637 44.000 0.00 0.00 0.00 2.41
3767 12219 6.127140 GGTTTAGCTGATACTCCCTCTGTAAA 60.127 42.308 0.00 0.00 0.00 2.01
3768 12220 6.466885 TTAGCTGATACTCCCTCTGTAAAC 57.533 41.667 0.00 0.00 0.00 2.01
3769 12221 4.615513 AGCTGATACTCCCTCTGTAAACT 58.384 43.478 0.00 0.00 0.00 2.66
3770 12222 5.767670 AGCTGATACTCCCTCTGTAAACTA 58.232 41.667 0.00 0.00 0.00 2.24
3771 12223 6.195700 AGCTGATACTCCCTCTGTAAACTAA 58.804 40.000 0.00 0.00 0.00 2.24
3772 12224 6.841755 AGCTGATACTCCCTCTGTAAACTAAT 59.158 38.462 0.00 0.00 0.00 1.73
3773 12225 8.005388 AGCTGATACTCCCTCTGTAAACTAATA 58.995 37.037 0.00 0.00 0.00 0.98
3774 12226 8.808092 GCTGATACTCCCTCTGTAAACTAATAT 58.192 37.037 0.00 0.00 0.00 1.28
3780 12232 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3781 12233 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
3782 12234 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
3833 12285 9.490379 AACGCTCTTATATTAATTTACAGAGGG 57.510 33.333 21.96 21.96 42.53 4.30
3834 12286 8.867097 ACGCTCTTATATTAATTTACAGAGGGA 58.133 33.333 25.54 1.67 40.49 4.20
3835 12287 9.360093 CGCTCTTATATTAATTTACAGAGGGAG 57.640 37.037 20.74 5.24 40.49 4.30
3864 12316 4.458989 CGCAATTGGGCCATACTACATTAT 59.541 41.667 7.26 0.00 0.00 1.28
3914 12367 4.725556 TCAACTGTGTTCGAGCAAATAC 57.274 40.909 2.60 0.00 0.00 1.89
3979 12433 3.947612 TCATTACTACTCCCTCCGTCT 57.052 47.619 0.00 0.00 0.00 4.18
4001 12455 7.482743 CGTCTGGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
4002 12456 8.514594 GTCTGGAAATACTTGTCATCAAAATGA 58.485 33.333 0.00 0.00 39.63 2.57
4004 12458 9.132521 CTGGAAATACTTGTCATCAAAATGAAC 57.867 33.333 0.00 0.00 43.42 3.18
4011 12465 6.762661 ACTTGTCATCAAAATGAACAAAAGGG 59.237 34.615 0.87 0.00 43.42 3.95
4013 12467 5.365025 TGTCATCAAAATGAACAAAAGGGGA 59.635 36.000 0.00 0.00 43.42 4.81
4080 12534 9.722056 ATCTATTTTGATGACAAGTATTTTCGC 57.278 29.630 0.00 0.00 37.32 4.70
4081 12535 6.853279 ATTTTGATGACAAGTATTTTCGCG 57.147 33.333 0.00 0.00 37.32 5.87
4720 13179 6.939163 ACATTCTCTTGCTGAACTAAATCTGT 59.061 34.615 0.00 0.00 0.00 3.41
4760 13224 7.360438 GCCTTATTCTAGCTTTAATCACCATCG 60.360 40.741 0.00 0.00 0.00 3.84
4774 13238 4.546570 TCACCATCGTATTATTCTCTGCG 58.453 43.478 0.00 0.00 0.00 5.18
4783 13247 3.334583 TTATTCTCTGCGTCTTGCCTT 57.665 42.857 0.00 0.00 45.60 4.35
4826 13290 6.603201 CCTCAGAAAATTATACTTTGCCCTGA 59.397 38.462 11.46 11.46 0.00 3.86
4869 13333 7.667219 TGAGTCTTTTTGAGAGCTCCAAATATT 59.333 33.333 22.72 12.92 34.31 1.28
4915 13383 4.551702 TGCAATCTACCTAAGTGCTTCA 57.448 40.909 0.00 0.00 0.00 3.02
4919 13387 7.109501 TGCAATCTACCTAAGTGCTTCAATTA 58.890 34.615 0.00 0.00 0.00 1.40
4977 13445 2.715046 TCAAGGTGTGAGATTCCATGC 58.285 47.619 0.00 0.00 0.00 4.06
5267 13735 7.555087 TGGAATTTGGAAATGCATTTAGTAGG 58.445 34.615 24.15 0.00 0.00 3.18
5280 13748 8.116651 TGCATTTAGTAGGCAAACTATTTGAA 57.883 30.769 5.49 0.00 43.26 2.69
5281 13749 8.580720 TGCATTTAGTAGGCAAACTATTTGAAA 58.419 29.630 5.49 0.00 43.26 2.69
5425 13893 4.775664 GCCTGTTGCATTTCACAAAATTC 58.224 39.130 0.00 0.00 40.77 2.17
5431 13899 7.408123 TGTTGCATTTCACAAAATTCATGTTC 58.592 30.769 0.00 0.00 32.69 3.18
5449 13917 3.314357 TGTTCCTCATCTATACACGGTCG 59.686 47.826 0.00 0.00 0.00 4.79
5506 13974 3.733337 ACTGGATTGCTGATATCCGAAC 58.267 45.455 0.00 0.00 43.72 3.95
5561 14029 5.235305 ACCTGTATTGCGCTAATTTTGAG 57.765 39.130 9.73 1.99 0.00 3.02
5646 14114 0.374758 CCAATGTCGTCGAATGCCAG 59.625 55.000 0.00 0.00 0.00 4.85
5729 14197 5.689383 TCTGTATTTGGTCTCAGTTTTGC 57.311 39.130 0.00 0.00 0.00 3.68
5762 14232 5.703978 CACAGGTGTGGATTTGTTCAATA 57.296 39.130 1.90 0.00 42.10 1.90
5846 14316 9.911138 TTTGTAAAGGGAAACGGTAATTAAATC 57.089 29.630 0.00 0.00 0.00 2.17
5847 14317 7.750769 TGTAAAGGGAAACGGTAATTAAATCG 58.249 34.615 0.00 0.00 0.00 3.34
5878 14348 2.030371 GGAACTAACTACTCCCTCCGG 58.970 57.143 0.00 0.00 0.00 5.14
5884 14354 1.766461 CTACTCCCTCCGGCCCATT 60.766 63.158 0.00 0.00 0.00 3.16
5899 14369 1.366319 CCATTATGGGAGGGAGGGAG 58.634 60.000 2.72 0.00 32.67 4.30
5900 14370 1.366319 CATTATGGGAGGGAGGGAGG 58.634 60.000 0.00 0.00 0.00 4.30
5901 14371 0.197145 ATTATGGGAGGGAGGGAGGG 59.803 60.000 0.00 0.00 0.00 4.30
5902 14372 0.939443 TTATGGGAGGGAGGGAGGGA 60.939 60.000 0.00 0.00 0.00 4.20
5938 14408 9.523168 GGAGTATTTCAGTAGGTATCTATCACT 57.477 37.037 0.00 0.00 0.00 3.41
5988 14458 3.507162 TCCAGATCACTTGGCAAGAAA 57.493 42.857 32.50 19.48 0.00 2.52
5991 14461 3.822735 CCAGATCACTTGGCAAGAAAAGA 59.177 43.478 32.50 22.10 0.00 2.52
5992 14462 4.082895 CCAGATCACTTGGCAAGAAAAGAG 60.083 45.833 32.50 16.84 0.00 2.85
5993 14463 4.518211 CAGATCACTTGGCAAGAAAAGAGT 59.482 41.667 32.50 7.11 0.00 3.24
5994 14464 4.518211 AGATCACTTGGCAAGAAAAGAGTG 59.482 41.667 32.50 19.08 36.68 3.51
6010 14480 2.840038 AGAGTGGGTGCATTCTGTATGA 59.160 45.455 0.00 0.00 36.26 2.15
6014 14484 2.171237 TGGGTGCATTCTGTATGAGAGG 59.829 50.000 0.00 0.00 36.26 3.69
6015 14485 2.486191 GGGTGCATTCTGTATGAGAGGG 60.486 54.545 0.00 0.00 36.26 4.30
6049 14519 9.226606 CAGGTTTGGTTCTACAGTATATTTGAA 57.773 33.333 0.00 0.00 0.00 2.69
6073 14543 4.022329 GGGAATCAACGTTGACTTCCAATT 60.022 41.667 38.22 28.06 41.45 2.32
6074 14544 5.154222 GGAATCAACGTTGACTTCCAATTC 58.846 41.667 36.15 29.98 40.54 2.17
6075 14545 4.766404 ATCAACGTTGACTTCCAATTCC 57.234 40.909 31.87 0.00 40.49 3.01
6076 14546 3.546724 TCAACGTTGACTTCCAATTCCA 58.453 40.909 26.53 0.00 37.08 3.53
6077 14547 3.948473 TCAACGTTGACTTCCAATTCCAA 59.052 39.130 26.53 0.00 37.08 3.53
6078 14548 4.582656 TCAACGTTGACTTCCAATTCCAAT 59.417 37.500 26.53 0.00 37.08 3.16
6146 14616 8.932945 TCAACTGAAACTATCACATGATCTAC 57.067 34.615 0.00 0.00 36.05 2.59
6163 14633 5.823570 TGATCTACTAGGAAGGAAGAGAACG 59.176 44.000 0.00 0.00 0.00 3.95
6187 14657 4.396166 ACATTGACGCCCTTGAAATCTAAG 59.604 41.667 0.00 0.00 0.00 2.18
6200 14670 2.017559 ATCTAAGCTGGGTCGCGGAC 62.018 60.000 6.13 2.87 34.40 4.79
6209 14679 2.664436 GGTCGCGGACAAGAAACGG 61.664 63.158 6.13 0.00 33.68 4.44
6247 14717 2.415168 TCATCGTTCCGATTCAGTTTGC 59.585 45.455 0.00 0.00 44.59 3.68
6320 14790 1.738099 CCGTCTTTGCCGTCCTCAG 60.738 63.158 0.00 0.00 0.00 3.35
6329 14799 3.374402 CGTCCTCAGCTCCGGTGT 61.374 66.667 0.00 0.00 32.43 4.16
6362 14832 1.240256 CGTATCCTCCTCCTCCTTCG 58.760 60.000 0.00 0.00 0.00 3.79
6370 14840 3.665675 CTCCTCCTTCGCAACCGGG 62.666 68.421 6.32 0.00 34.56 5.73
6730 15200 3.127533 GCAGACAGCGGCGGAATT 61.128 61.111 9.78 0.00 0.00 2.17
6731 15201 2.787249 CAGACAGCGGCGGAATTG 59.213 61.111 9.78 0.00 0.00 2.32
6732 15202 2.436646 AGACAGCGGCGGAATTGG 60.437 61.111 9.78 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 7779 3.445096 CCTCCGAGCCAATTTCAAATCTT 59.555 43.478 0.00 0.00 0.00 2.40
308 7914 2.200170 GACGGGCTGCATTGTTGTCC 62.200 60.000 0.50 0.00 0.00 4.02
386 7992 3.017581 ATGACAGGCCCAGGGTCC 61.018 66.667 6.42 8.79 0.00 4.46
415 8021 3.839432 GGCTCCCTCCTTCGTCGG 61.839 72.222 0.00 0.00 0.00 4.79
468 8074 0.178926 TGGTAAGAACTGGGACCGGA 60.179 55.000 9.46 0.00 34.49 5.14
542 8148 3.491792 GCCACTCAGAGTAGGTTATCTGC 60.492 52.174 1.67 0.00 42.20 4.26
670 8321 3.986572 CACTCTGCTCAGTAGACAGTTTG 59.013 47.826 0.00 0.00 32.22 2.93
673 8353 3.147553 TCACTCTGCTCAGTAGACAGT 57.852 47.619 0.00 0.00 32.22 3.55
700 8384 8.644318 AGTTTACTTTACTGCAGAATATACGG 57.356 34.615 23.35 4.43 0.00 4.02
765 8605 6.946340 ACAGATCCTTATGTGTGACAATACA 58.054 36.000 0.00 0.00 38.14 2.29
774 8614 6.365970 AACTCTTCACAGATCCTTATGTGT 57.634 37.500 11.34 0.00 45.57 3.72
775 8615 6.875726 TCAAACTCTTCACAGATCCTTATGTG 59.124 38.462 6.50 6.50 46.52 3.21
776 8616 7.009179 TCAAACTCTTCACAGATCCTTATGT 57.991 36.000 0.00 0.00 0.00 2.29
777 8617 7.042858 CGATCAAACTCTTCACAGATCCTTATG 60.043 40.741 0.00 0.00 30.75 1.90
780 8620 5.174395 CGATCAAACTCTTCACAGATCCTT 58.826 41.667 0.00 0.00 30.75 3.36
804 8647 0.042448 GACAACGCAGGAAACACGAC 60.042 55.000 0.00 0.00 36.22 4.34
805 8648 1.484227 CGACAACGCAGGAAACACGA 61.484 55.000 0.00 0.00 36.22 4.35
806 8649 1.083657 CGACAACGCAGGAAACACG 60.084 57.895 0.00 0.00 38.05 4.49
848 8702 0.106335 CATCTCCATGCCTCGCTCTT 59.894 55.000 0.00 0.00 0.00 2.85
849 8703 1.747145 CATCTCCATGCCTCGCTCT 59.253 57.895 0.00 0.00 0.00 4.09
850 8704 4.357699 CATCTCCATGCCTCGCTC 57.642 61.111 0.00 0.00 0.00 5.03
885 8739 8.033038 CCTGACTAAACAAAGTATGCTACAGTA 58.967 37.037 0.00 0.00 0.00 2.74
889 8743 5.064834 GGCCTGACTAAACAAAGTATGCTAC 59.935 44.000 0.00 0.00 0.00 3.58
890 8744 5.183228 GGCCTGACTAAACAAAGTATGCTA 58.817 41.667 0.00 0.00 0.00 3.49
891 8745 4.010349 GGCCTGACTAAACAAAGTATGCT 58.990 43.478 0.00 0.00 0.00 3.79
892 8746 3.181510 CGGCCTGACTAAACAAAGTATGC 60.182 47.826 0.00 0.00 0.00 3.14
893 8747 3.181510 GCGGCCTGACTAAACAAAGTATG 60.182 47.826 0.00 0.00 0.00 2.39
894 8748 3.007635 GCGGCCTGACTAAACAAAGTAT 58.992 45.455 0.00 0.00 0.00 2.12
895 8749 2.419667 GCGGCCTGACTAAACAAAGTA 58.580 47.619 0.00 0.00 0.00 2.24
896 8750 1.235724 GCGGCCTGACTAAACAAAGT 58.764 50.000 0.00 0.00 0.00 2.66
897 8751 0.521735 GGCGGCCTGACTAAACAAAG 59.478 55.000 12.87 0.00 0.00 2.77
898 8752 0.891904 GGGCGGCCTGACTAAACAAA 60.892 55.000 22.87 0.00 0.00 2.83
940 8794 5.506686 TCGACATGTGTTTGGAATTTTGA 57.493 34.783 1.15 0.00 0.00 2.69
982 8846 4.404654 GACGGCTTTTGGGCAGCG 62.405 66.667 0.00 0.00 38.24 5.18
984 8848 4.404654 GCGACGGCTTTTGGGCAG 62.405 66.667 0.00 0.00 40.90 4.85
1043 8920 1.199615 GGGGGAGGAAGAAGAGACTG 58.800 60.000 0.00 0.00 0.00 3.51
1107 8985 4.487412 GCAAGCCATGACTGCCGC 62.487 66.667 0.00 0.00 0.00 6.53
1352 9230 2.240667 AGGGGGTCAGAAATCACAGATG 59.759 50.000 0.00 0.00 0.00 2.90
1478 9373 5.461078 TGCTTACTCTACAACACGAAGAAAC 59.539 40.000 0.00 0.00 0.00 2.78
1570 9467 4.498009 GCAATTCGCTATGTTGTAGCCAAT 60.498 41.667 1.83 0.00 37.26 3.16
1614 9511 6.719370 AGCAGTATGTTACATCAAGGGAAAAA 59.281 34.615 0.00 0.00 39.31 1.94
1652 9551 2.255406 CAGGGCAGATAGTCTATGGCT 58.745 52.381 0.00 0.00 39.31 4.75
1813 10211 1.538204 CCGTGTAATCCCGACATCCTG 60.538 57.143 0.00 0.00 0.00 3.86
1821 10219 1.087771 GGTTGAGCCGTGTAATCCCG 61.088 60.000 0.00 0.00 0.00 5.14
1865 10263 7.977789 TGCTTATCAGAAACATAACAACTGA 57.022 32.000 0.00 0.00 40.88 3.41
1911 10309 5.760484 AGGTCAATGGGCAAAACAATAAT 57.240 34.783 0.00 0.00 0.00 1.28
2459 10860 6.036517 ACAGCTCTATAAAGCAGAACAAATCG 59.963 38.462 0.00 0.00 45.00 3.34
2464 10865 6.042638 AGAACAGCTCTATAAAGCAGAACA 57.957 37.500 0.00 0.00 45.00 3.18
2719 11120 1.022735 CAAGTGCCCTGATGATCTGC 58.977 55.000 0.00 0.00 0.00 4.26
2764 11165 6.671614 TTACATACCCAAAAGTGCTTATCG 57.328 37.500 0.00 0.00 0.00 2.92
3235 11681 5.740406 TGTATCGGTTTCAGTTTTTCGTTC 58.260 37.500 0.00 0.00 0.00 3.95
3252 11698 2.231215 AGCTAGGCTGCTTTGTATCG 57.769 50.000 0.00 0.00 40.93 2.92
3273 11719 5.184096 TGCTGTCTAGTTGTTTTTGTTTCCA 59.816 36.000 0.00 0.00 0.00 3.53
3379 11827 1.827789 GTTGGCAGGTGTCAAGGCA 60.828 57.895 0.00 0.00 40.68 4.75
3421 11869 4.907269 AGGAAAGGTTTTGTTGGATTCCAT 59.093 37.500 6.15 0.00 37.82 3.41
3431 11879 3.769300 AGCAACTTGAGGAAAGGTTTTGT 59.231 39.130 0.00 0.00 40.51 2.83
3445 11893 3.461061 TCACTCAGTTCTCAGCAACTTG 58.539 45.455 0.00 0.00 34.17 3.16
3459 11907 8.824781 CCAGTATTACAGAAAATCATCACTCAG 58.175 37.037 0.00 0.00 0.00 3.35
3462 11910 7.112122 TGCCAGTATTACAGAAAATCATCACT 58.888 34.615 0.00 0.00 0.00 3.41
3478 11926 6.655078 AACAAAGAGTTTCATGCCAGTATT 57.345 33.333 0.00 0.00 37.03 1.89
3529 11977 3.951663 AGATACGGAAGTTCTTTTGGGG 58.048 45.455 2.25 0.00 46.40 4.96
3659 12111 6.798427 TCTGGTCCAGGATATTATAGATGC 57.202 41.667 19.11 0.00 31.51 3.91
3756 12208 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
3790 12242 8.828688 AAGAGCGTTTAGAACACTAAAATAGT 57.171 30.769 0.00 0.00 37.69 2.12
3807 12259 9.490379 CCCTCTGTAAATTAATATAAGAGCGTT 57.510 33.333 9.98 0.00 0.00 4.84
3808 12260 8.867097 TCCCTCTGTAAATTAATATAAGAGCGT 58.133 33.333 9.98 0.00 0.00 5.07
3809 12261 9.360093 CTCCCTCTGTAAATTAATATAAGAGCG 57.640 37.037 9.98 4.77 0.00 5.03
3817 12269 8.086522 GCGATGTACTCCCTCTGTAAATTAATA 58.913 37.037 0.00 0.00 0.00 0.98
3818 12270 6.929606 GCGATGTACTCCCTCTGTAAATTAAT 59.070 38.462 0.00 0.00 0.00 1.40
3819 12271 6.127281 TGCGATGTACTCCCTCTGTAAATTAA 60.127 38.462 0.00 0.00 0.00 1.40
3820 12272 5.361571 TGCGATGTACTCCCTCTGTAAATTA 59.638 40.000 0.00 0.00 0.00 1.40
3821 12273 4.161565 TGCGATGTACTCCCTCTGTAAATT 59.838 41.667 0.00 0.00 0.00 1.82
3822 12274 3.704566 TGCGATGTACTCCCTCTGTAAAT 59.295 43.478 0.00 0.00 0.00 1.40
3823 12275 3.093814 TGCGATGTACTCCCTCTGTAAA 58.906 45.455 0.00 0.00 0.00 2.01
3824 12276 2.730382 TGCGATGTACTCCCTCTGTAA 58.270 47.619 0.00 0.00 0.00 2.41
3825 12277 2.430248 TGCGATGTACTCCCTCTGTA 57.570 50.000 0.00 0.00 0.00 2.74
3826 12278 1.557099 TTGCGATGTACTCCCTCTGT 58.443 50.000 0.00 0.00 0.00 3.41
3827 12279 2.868583 CAATTGCGATGTACTCCCTCTG 59.131 50.000 0.00 0.00 0.00 3.35
3828 12280 2.158900 CCAATTGCGATGTACTCCCTCT 60.159 50.000 0.00 0.00 0.00 3.69
3829 12281 2.213499 CCAATTGCGATGTACTCCCTC 58.787 52.381 0.00 0.00 0.00 4.30
3830 12282 1.134098 CCCAATTGCGATGTACTCCCT 60.134 52.381 0.00 0.00 0.00 4.20
3831 12283 1.308998 CCCAATTGCGATGTACTCCC 58.691 55.000 0.00 0.00 0.00 4.30
3832 12284 0.663153 GCCCAATTGCGATGTACTCC 59.337 55.000 0.00 0.00 0.00 3.85
3833 12285 0.663153 GGCCCAATTGCGATGTACTC 59.337 55.000 0.00 0.00 0.00 2.59
3834 12286 0.034574 TGGCCCAATTGCGATGTACT 60.035 50.000 0.00 0.00 0.00 2.73
3835 12287 1.032014 ATGGCCCAATTGCGATGTAC 58.968 50.000 0.00 0.00 0.00 2.90
3836 12288 2.158682 AGTATGGCCCAATTGCGATGTA 60.159 45.455 0.00 0.00 31.76 2.29
3837 12289 1.032014 GTATGGCCCAATTGCGATGT 58.968 50.000 0.00 0.00 31.76 3.06
3838 12290 1.321474 AGTATGGCCCAATTGCGATG 58.679 50.000 0.00 0.00 31.76 3.84
3891 12344 4.836125 ATTTGCTCGAACACAGTTGAAT 57.164 36.364 0.00 0.00 0.00 2.57
3979 12433 8.637099 TGTTCATTTTGATGACAAGTATTTCCA 58.363 29.630 0.00 0.00 37.32 3.53
4001 12455 5.753921 CGTCTAGATACATCCCCTTTTGTTC 59.246 44.000 0.00 0.00 0.00 3.18
4002 12456 5.189145 ACGTCTAGATACATCCCCTTTTGTT 59.811 40.000 0.00 0.00 0.00 2.83
4004 12458 5.277857 ACGTCTAGATACATCCCCTTTTG 57.722 43.478 0.00 0.00 0.00 2.44
4057 12511 6.467682 GCGCGAAAATACTTGTCATCAAAATA 59.532 34.615 12.10 0.00 32.87 1.40
4076 12530 1.102809 TTATACTCCCTCCGCGCGAA 61.103 55.000 34.63 11.42 0.00 4.70
4080 12534 3.144506 TCTAGTTTATACTCCCTCCGCG 58.855 50.000 0.00 0.00 35.78 6.46
4081 12535 5.068855 AGTTTCTAGTTTATACTCCCTCCGC 59.931 44.000 0.00 0.00 35.78 5.54
4235 12689 5.885912 TCAGGTGGCTTTATTAGAACCATTC 59.114 40.000 0.00 0.00 35.58 2.67
4523 12980 5.633830 AAATGTTCTCCAGCAACATACTG 57.366 39.130 0.29 0.00 42.47 2.74
4760 13224 4.372656 AGGCAAGACGCAGAGAATAATAC 58.627 43.478 0.00 0.00 45.17 1.89
4826 13290 5.144100 AGACTCATCTAATCGACCCAAGAT 58.856 41.667 0.00 0.00 31.46 2.40
4896 13360 8.723942 ACTAATTGAAGCACTTAGGTAGATTG 57.276 34.615 8.68 0.00 33.04 2.67
4919 13387 6.712095 TGCTACTGAAATTTGACAGAATGACT 59.288 34.615 12.48 0.00 39.69 3.41
5244 13712 7.041107 TGCCTACTAAATGCATTTCCAAATTC 58.959 34.615 27.28 12.91 0.00 2.17
5267 13735 5.596845 TGTTGTCCCTTTCAAATAGTTTGC 58.403 37.500 0.00 0.00 40.43 3.68
5425 13893 5.201713 ACCGTGTATAGATGAGGAACATG 57.798 43.478 0.00 0.00 39.56 3.21
5431 13899 4.288531 GTTTCGACCGTGTATAGATGAGG 58.711 47.826 0.00 0.00 0.00 3.86
5449 13917 1.535088 GCAATTCGGCTAAGCGTTTC 58.465 50.000 0.00 0.00 0.00 2.78
5506 13974 8.066668 TGTTTGTTTAACACAACTTTTGTCTG 57.933 30.769 17.15 0.00 45.54 3.51
5561 14029 1.168714 GCACCAAAGACATGGAGGAC 58.831 55.000 0.00 0.00 43.54 3.85
5605 14073 2.100197 TCCCTGTACCACTCATTCTCG 58.900 52.381 0.00 0.00 0.00 4.04
5635 14103 1.448985 TGCTAAACCTGGCATTCGAC 58.551 50.000 0.00 0.00 33.50 4.20
5646 14114 6.017109 TGACAGTGAATCTTCTTTGCTAAACC 60.017 38.462 0.00 0.00 0.00 3.27
5846 14316 3.600388 AGTTAGTTCCAGGATTTGCTCG 58.400 45.455 0.00 0.00 0.00 5.03
5847 14317 5.735766 AGTAGTTAGTTCCAGGATTTGCTC 58.264 41.667 0.00 0.00 0.00 4.26
5884 14354 1.311464 TCCCTCCCTCCCTCCCATA 60.311 63.158 0.00 0.00 0.00 2.74
5889 14359 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
5890 14360 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
5891 14361 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
5892 14362 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
5893 14363 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
5894 14364 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
5895 14365 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
5896 14366 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
5897 14367 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
5899 14369 1.381089 ATACTCCCTCCCTCCCTCCC 61.381 65.000 0.00 0.00 0.00 4.30
5900 14370 0.568697 AATACTCCCTCCCTCCCTCC 59.431 60.000 0.00 0.00 0.00 4.30
5901 14371 2.331166 GAAATACTCCCTCCCTCCCTC 58.669 57.143 0.00 0.00 0.00 4.30
5902 14372 1.657162 TGAAATACTCCCTCCCTCCCT 59.343 52.381 0.00 0.00 0.00 4.20
5938 14408 2.158971 TGATTCCTTACTGCGCATGCTA 60.159 45.455 12.24 3.60 43.34 3.49
5988 14458 3.264193 TCATACAGAATGCACCCACTCTT 59.736 43.478 0.00 0.00 42.53 2.85
5991 14461 2.840038 TCTCATACAGAATGCACCCACT 59.160 45.455 0.00 0.00 42.53 4.00
5992 14462 3.201290 CTCTCATACAGAATGCACCCAC 58.799 50.000 0.00 0.00 42.53 4.61
5993 14463 2.171237 CCTCTCATACAGAATGCACCCA 59.829 50.000 0.00 0.00 42.53 4.51
5994 14464 2.486191 CCCTCTCATACAGAATGCACCC 60.486 54.545 0.00 0.00 42.53 4.61
6010 14480 2.666317 CAAACCTGGTGTTTTCCCTCT 58.334 47.619 0.00 0.00 44.80 3.69
6041 14511 6.659242 AGTCAACGTTGATTCCCTTCAAATAT 59.341 34.615 31.81 0.58 39.73 1.28
6045 14515 3.815809 AGTCAACGTTGATTCCCTTCAA 58.184 40.909 31.81 4.56 39.73 2.69
6049 14519 2.105821 TGGAAGTCAACGTTGATTCCCT 59.894 45.455 36.74 27.60 40.35 4.20
6073 14543 7.673504 TGTTTTCTTATGGAATGGAAGATTGGA 59.326 33.333 0.00 0.00 33.53 3.53
6074 14544 7.839907 TGTTTTCTTATGGAATGGAAGATTGG 58.160 34.615 0.00 0.00 33.53 3.16
6075 14545 9.709495 TTTGTTTTCTTATGGAATGGAAGATTG 57.291 29.630 0.00 0.00 33.53 2.67
6076 14546 9.933723 CTTTGTTTTCTTATGGAATGGAAGATT 57.066 29.630 0.00 0.00 33.53 2.40
6077 14547 8.037166 GCTTTGTTTTCTTATGGAATGGAAGAT 58.963 33.333 0.00 0.00 33.53 2.40
6078 14548 7.233348 AGCTTTGTTTTCTTATGGAATGGAAGA 59.767 33.333 0.00 0.00 33.53 2.87
6146 14616 4.993029 ATGTCGTTCTCTTCCTTCCTAG 57.007 45.455 0.00 0.00 0.00 3.02
6163 14633 2.749621 AGATTTCAAGGGCGTCAATGTC 59.250 45.455 0.00 0.00 0.00 3.06
6187 14657 3.876589 TTCTTGTCCGCGACCCAGC 62.877 63.158 8.23 0.00 0.00 4.85
6200 14670 4.380867 CCCTGGATTTGATTCCGTTTCTTG 60.381 45.833 0.00 0.00 38.74 3.02
6209 14679 3.812053 CGATGACTCCCTGGATTTGATTC 59.188 47.826 0.00 0.00 0.00 2.52
6247 14717 4.891727 CGTCGCCATCCGGGAAGG 62.892 72.222 13.96 13.96 40.01 3.46
6340 14810 1.909287 GGAGGAGGAGGATACGGCC 60.909 68.421 0.00 0.00 46.39 6.13
6341 14811 0.470268 AAGGAGGAGGAGGATACGGC 60.470 60.000 0.00 0.00 46.39 5.68
6343 14813 1.240256 CGAAGGAGGAGGAGGATACG 58.760 60.000 0.00 0.00 46.39 3.06
6344 14814 0.963225 GCGAAGGAGGAGGAGGATAC 59.037 60.000 0.00 0.00 0.00 2.24
6345 14815 0.556258 TGCGAAGGAGGAGGAGGATA 59.444 55.000 0.00 0.00 0.00 2.59
6346 14816 0.325671 TTGCGAAGGAGGAGGAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
6362 14832 2.112815 CGGAAGATTCCCCGGTTGC 61.113 63.158 0.00 0.00 44.67 4.17
6370 14840 1.442148 CCTCGACCCGGAAGATTCC 59.558 63.158 0.73 1.23 44.05 3.01
6724 15194 1.754234 CCTCCCTTGCCCAATTCCG 60.754 63.158 0.00 0.00 0.00 4.30
6725 15195 2.060383 GCCTCCCTTGCCCAATTCC 61.060 63.158 0.00 0.00 0.00 3.01
6726 15196 2.418083 CGCCTCCCTTGCCCAATTC 61.418 63.158 0.00 0.00 0.00 2.17
6727 15197 2.362889 CGCCTCCCTTGCCCAATT 60.363 61.111 0.00 0.00 0.00 2.32
6728 15198 4.447342 CCGCCTCCCTTGCCCAAT 62.447 66.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.