Multiple sequence alignment - TraesCS1B01G402400

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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 TraesCS1B01G402400 chr1B 100.000 4128 0 0 1 4128 632173578 632169451 0.000000e+00 7624.0
1 TraesCS1B01G402400 chr1B 85.171 263 26 6 1777 2031 632169858 632169601 1.470000e-64 257.0
2 TraesCS1B01G402400 chr1B 85.171 263 26 6 3721 3978 632171802 632171548 1.470000e-64 257.0
3 TraesCS1B01G402400 chr1B 96.694 121 4 0 1 121 526256533 526256653 7.000000e-48 202.0
4 TraesCS1B01G402400 chr1B 83.810 210 25 4 417 621 632195238 632195033 1.510000e-44 191.0
5 TraesCS1B01G402400 chr1B 84.848 99 11 2 1098 1195 632172434 632172339 3.400000e-16 97.1
6 TraesCS1B01G402400 chr1B 84.848 99 11 2 1145 1240 632172481 632172384 3.400000e-16 97.1
7 TraesCS1B01G402400 chr1A 93.797 2821 130 21 405 3191 551657684 551654875 0.000000e+00 4198.0
8 TraesCS1B01G402400 chr1A 85.200 973 65 33 3213 4124 551654881 551653927 0.000000e+00 926.0
9 TraesCS1B01G402400 chr1A 87.356 261 20 6 3721 3976 551656291 551656039 1.880000e-73 287.0
10 TraesCS1B01G402400 chr1A 95.200 125 6 0 1 125 516701517 516701641 9.050000e-47 198.0
11 TraesCS1B01G402400 chr1A 95.614 114 5 0 246 359 551657812 551657699 2.530000e-42 183.0
12 TraesCS1B01G402400 chr1A 82.710 214 27 5 412 620 551664452 551664244 9.120000e-42 182.0
13 TraesCS1B01G402400 chr1A 84.848 99 11 2 1098 1195 551656923 551656828 3.400000e-16 97.1
14 TraesCS1B01G402400 chr1A 100.000 30 0 0 2578 2607 551655542 551655513 5.760000e-04 56.5
15 TraesCS1B01G402400 chr1D 96.266 723 26 1 1145 1867 460169068 460168347 0.000000e+00 1184.0
16 TraesCS1B01G402400 chr1D 90.715 797 51 14 405 1187 460169769 460168982 0.000000e+00 1040.0
17 TraesCS1B01G402400 chr1D 95.392 651 27 1 2539 3186 460167841 460167191 0.000000e+00 1033.0
18 TraesCS1B01G402400 chr1D 94.886 528 24 3 2083 2607 460168349 460167822 0.000000e+00 822.0
19 TraesCS1B01G402400 chr1D 91.837 196 15 1 170 365 460169964 460169770 5.260000e-69 272.0
20 TraesCS1B01G402400 chr1D 86.087 115 9 2 463 573 460172946 460172835 2.610000e-22 117.0
21 TraesCS1B01G402400 chr1D 100.000 33 0 0 2575 2607 460167904 460167872 1.240000e-05 62.1
22 TraesCS1B01G402400 chr3A 95.968 124 5 0 1 124 533634617 533634494 7.000000e-48 202.0
23 TraesCS1B01G402400 chr2A 96.694 121 4 0 1 121 54689349 54689469 7.000000e-48 202.0
24 TraesCS1B01G402400 chr6A 95.200 125 6 0 1 125 531419942 531420066 9.050000e-47 198.0
25 TraesCS1B01G402400 chr4B 95.200 125 6 0 1 125 437403328 437403452 9.050000e-47 198.0
26 TraesCS1B01G402400 chr4B 97.436 39 1 0 3567 3605 614779174 614779136 2.660000e-07 67.6
27 TraesCS1B01G402400 chr2B 95.200 125 6 0 1 125 761975822 761975698 9.050000e-47 198.0
28 TraesCS1B01G402400 chr7A 95.868 121 5 0 1 121 61814447 61814567 3.260000e-46 196.0
29 TraesCS1B01G402400 chr5A 95.161 124 6 0 1 124 589003385 589003262 3.260000e-46 196.0
30 TraesCS1B01G402400 chr5A 94.595 37 2 0 3561 3597 631619147 631619183 1.600000e-04 58.4
31 TraesCS1B01G402400 chr5A 100.000 31 0 0 3567 3597 631641446 631641476 1.600000e-04 58.4
32 TraesCS1B01G402400 chr7B 89.552 67 3 4 3562 3626 709320670 709320734 9.510000e-12 82.4


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 TraesCS1B01G402400 chr1B 632169451 632173578 4127 True 1666.440000 7624 88.007600 1 4128 5 chr1B.!!$R2 4127
1 TraesCS1B01G402400 chr1A 551653927 551657812 3885 True 957.933333 4198 91.135833 246 4124 6 chr1A.!!$R2 3878
2 TraesCS1B01G402400 chr1D 460167191 460172946 5755 True 647.157143 1184 93.597571 170 3186 7 chr1D.!!$R1 3016

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
42 43 0.110554 CAAAAGTCCGTTTACGCCCG 60.111 55.0 0.0 0.0 38.18 6.13 F
563 3396 0.178953 ATCCCCTGCTTGTGCTTGTT 60.179 50.0 0.0 0.0 40.48 2.83 F
2404 5261 0.179012 GGAACCCCACGAACAGGAAA 60.179 55.0 0.0 0.0 0.00 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 4890 0.181350 GGCATTGGCTGGCTAGTAGT 59.819 55.0 2.42 0.0 46.59 2.73 R
2435 5292 1.491505 GCGCACCTAGATTCGCTTCC 61.492 60.0 0.30 0.0 43.70 3.46 R
4063 7040 0.244994 TGTTGGTGTTGGTTGTGTGC 59.755 50.0 0.00 0.0 0.00 4.57 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
18 19 3.729004 GTCGAAAGCGGACACAAAG 57.271 52.632 0.00 0.00 38.28 2.77
20 21 1.438710 CGAAAGCGGACACAAAGCG 60.439 57.895 0.00 0.00 35.78 4.68
22 23 1.503818 GAAAGCGGACACAAAGCGGA 61.504 55.000 0.00 0.00 35.78 5.54
24 25 2.933878 AAGCGGACACAAAGCGGACA 62.934 55.000 0.00 0.00 35.78 4.02
25 26 2.539338 GCGGACACAAAGCGGACAA 61.539 57.895 0.00 0.00 0.00 3.18
26 27 2.018544 CGGACACAAAGCGGACAAA 58.981 52.632 0.00 0.00 0.00 2.83
27 28 0.378962 CGGACACAAAGCGGACAAAA 59.621 50.000 0.00 0.00 0.00 2.44
29 30 1.404035 GGACACAAAGCGGACAAAAGT 59.596 47.619 0.00 0.00 0.00 2.66
30 31 2.540973 GGACACAAAGCGGACAAAAGTC 60.541 50.000 0.00 0.00 0.00 3.01
40 41 1.069703 GGACAAAAGTCCGTTTACGCC 60.070 52.381 0.00 0.00 38.18 5.68
41 42 0.946528 ACAAAAGTCCGTTTACGCCC 59.053 50.000 0.00 0.00 38.18 6.13
42 43 0.110554 CAAAAGTCCGTTTACGCCCG 60.111 55.000 0.00 0.00 38.18 6.13
43 44 1.844771 AAAAGTCCGTTTACGCCCGC 61.845 55.000 0.00 0.00 38.18 6.13
63 64 3.423154 GCTGGGCCGTCTCGTTTG 61.423 66.667 0.00 0.00 0.00 2.93
64 65 2.030562 CTGGGCCGTCTCGTTTGT 59.969 61.111 0.00 0.00 0.00 2.83
65 66 1.597027 CTGGGCCGTCTCGTTTGTT 60.597 57.895 0.00 0.00 0.00 2.83
66 67 1.153127 TGGGCCGTCTCGTTTGTTT 60.153 52.632 0.00 0.00 0.00 2.83
67 68 0.748729 TGGGCCGTCTCGTTTGTTTT 60.749 50.000 0.00 0.00 0.00 2.43
68 69 0.382873 GGGCCGTCTCGTTTGTTTTT 59.617 50.000 0.00 0.00 0.00 1.94
86 87 1.316651 TTTTTACCCCAAACGGACGG 58.683 50.000 0.00 0.00 0.00 4.79
87 88 0.536915 TTTTACCCCAAACGGACGGG 60.537 55.000 0.00 0.00 43.05 5.28
100 101 4.468769 ACGGGGGCGGACAGGATA 62.469 66.667 0.00 0.00 0.00 2.59
101 102 3.616721 CGGGGGCGGACAGGATAG 61.617 72.222 0.00 0.00 0.00 2.08
103 104 3.242291 GGGGCGGACAGGATAGGG 61.242 72.222 0.00 0.00 0.00 3.53
105 106 2.508751 GGGCGGACAGGATAGGGTC 61.509 68.421 0.00 0.00 0.00 4.46
107 108 2.728817 CGGACAGGATAGGGTCGC 59.271 66.667 0.00 0.00 34.87 5.19
108 109 2.728817 GGACAGGATAGGGTCGCG 59.271 66.667 0.00 0.00 34.87 5.87
109 110 2.027751 GACAGGATAGGGTCGCGC 59.972 66.667 0.00 0.00 0.00 6.86
111 112 4.647615 CAGGATAGGGTCGCGCGG 62.648 72.222 31.69 11.75 0.00 6.46
113 114 4.944372 GGATAGGGTCGCGCGGTG 62.944 72.222 31.69 1.17 0.00 4.94
114 115 4.944372 GATAGGGTCGCGCGGTGG 62.944 72.222 31.69 0.71 0.00 4.61
123 124 4.681978 GCGCGGTGGAGTTGGTCT 62.682 66.667 8.83 0.00 0.00 3.85
125 126 1.597027 CGCGGTGGAGTTGGTCTTT 60.597 57.895 0.00 0.00 0.00 2.52
126 127 1.841663 CGCGGTGGAGTTGGTCTTTG 61.842 60.000 0.00 0.00 0.00 2.77
127 128 1.515521 GCGGTGGAGTTGGTCTTTGG 61.516 60.000 0.00 0.00 0.00 3.28
128 129 0.179029 CGGTGGAGTTGGTCTTTGGT 60.179 55.000 0.00 0.00 0.00 3.67
129 130 1.605753 GGTGGAGTTGGTCTTTGGTC 58.394 55.000 0.00 0.00 0.00 4.02
131 132 1.124780 TGGAGTTGGTCTTTGGTCGA 58.875 50.000 0.00 0.00 0.00 4.20
132 133 1.070134 TGGAGTTGGTCTTTGGTCGAG 59.930 52.381 0.00 0.00 0.00 4.04
133 134 1.343465 GGAGTTGGTCTTTGGTCGAGA 59.657 52.381 0.00 0.00 0.00 4.04
134 135 2.610727 GGAGTTGGTCTTTGGTCGAGAG 60.611 54.545 0.00 0.00 0.00 3.20
135 136 2.296471 GAGTTGGTCTTTGGTCGAGAGA 59.704 50.000 0.00 0.00 38.16 3.10
136 137 2.900546 AGTTGGTCTTTGGTCGAGAGAT 59.099 45.455 0.00 0.00 45.19 2.75
137 138 2.996621 GTTGGTCTTTGGTCGAGAGATG 59.003 50.000 0.00 0.00 45.19 2.90
138 139 1.550524 TGGTCTTTGGTCGAGAGATGG 59.449 52.381 0.00 0.00 45.19 3.51
139 140 1.134670 GGTCTTTGGTCGAGAGATGGG 60.135 57.143 0.00 0.00 45.19 4.00
141 142 0.905357 CTTTGGTCGAGAGATGGGGT 59.095 55.000 0.00 0.00 45.19 4.95
142 143 0.902531 TTTGGTCGAGAGATGGGGTC 59.097 55.000 0.00 0.00 45.19 4.46
143 144 0.252057 TTGGTCGAGAGATGGGGTCA 60.252 55.000 0.00 0.00 45.19 4.02
145 146 0.902531 GGTCGAGAGATGGGGTCAAA 59.097 55.000 0.00 0.00 45.19 2.69
146 147 1.134670 GGTCGAGAGATGGGGTCAAAG 60.135 57.143 0.00 0.00 45.19 2.77
147 148 1.134670 GTCGAGAGATGGGGTCAAAGG 60.135 57.143 0.00 0.00 45.19 3.11
148 149 0.179000 CGAGAGATGGGGTCAAAGGG 59.821 60.000 0.00 0.00 0.00 3.95
149 150 1.584724 GAGAGATGGGGTCAAAGGGA 58.415 55.000 0.00 0.00 0.00 4.20
150 151 1.210722 GAGAGATGGGGTCAAAGGGAC 59.789 57.143 0.00 0.00 46.20 4.46
173 174 3.782656 AAAATTAGGACGGGTCTGTGT 57.217 42.857 0.00 0.00 0.00 3.72
187 3001 3.132111 GGTCTGTGTTTGGGTCACATTTT 59.868 43.478 0.00 0.00 43.39 1.82
193 3007 3.066064 TGTTTGGGTCACATTTTCTGTCG 59.934 43.478 0.00 0.00 35.29 4.35
204 3018 2.045561 TTTCTGTCGGTTTGCTCCAA 57.954 45.000 0.00 0.00 0.00 3.53
215 3029 1.433053 TTGCTCCAAACGGACACACG 61.433 55.000 0.00 0.00 40.31 4.49
217 3031 1.885388 CTCCAAACGGACACACGCA 60.885 57.895 0.00 0.00 37.37 5.24
218 3032 1.227704 TCCAAACGGACACACGCAT 60.228 52.632 0.00 0.00 37.37 4.73
227 3041 2.607180 CGGACACACGCATATGAAATGA 59.393 45.455 6.97 0.00 0.00 2.57
241 3055 3.797039 TGAAATGAGATCTAGCGTTGGG 58.203 45.455 0.00 0.00 0.00 4.12
308 3122 4.180496 CCCAACGGCTAGACGAAC 57.820 61.111 28.11 0.00 37.61 3.95
344 3158 1.964223 TCTCCATCGAGCCTCATAACC 59.036 52.381 0.00 0.00 35.94 2.85
365 3187 2.364973 TGCCCCATACCTCGAGCA 60.365 61.111 6.99 0.00 0.00 4.26
366 3188 2.374830 CTGCCCCATACCTCGAGCAG 62.375 65.000 6.99 5.74 41.43 4.24
376 3198 2.011540 CCTCGAGCAGGTAAAAGGAC 57.988 55.000 6.99 0.00 37.53 3.85
377 3199 1.550976 CCTCGAGCAGGTAAAAGGACT 59.449 52.381 6.99 0.00 37.53 3.85
378 3200 2.611518 CTCGAGCAGGTAAAAGGACTG 58.388 52.381 0.00 0.00 35.40 3.51
379 3201 2.231478 CTCGAGCAGGTAAAAGGACTGA 59.769 50.000 0.00 0.00 34.21 3.41
380 3202 2.231478 TCGAGCAGGTAAAAGGACTGAG 59.769 50.000 0.00 0.00 34.21 3.35
381 3203 2.351455 GAGCAGGTAAAAGGACTGAGC 58.649 52.381 0.00 0.00 34.21 4.26
382 3204 1.699634 AGCAGGTAAAAGGACTGAGCA 59.300 47.619 0.00 0.00 34.21 4.26
383 3205 2.106511 AGCAGGTAAAAGGACTGAGCAA 59.893 45.455 0.00 0.00 34.21 3.91
384 3206 2.226674 GCAGGTAAAAGGACTGAGCAAC 59.773 50.000 0.00 0.00 34.21 4.17
385 3207 2.814336 CAGGTAAAAGGACTGAGCAACC 59.186 50.000 0.00 0.00 34.21 3.77
386 3208 1.804748 GGTAAAAGGACTGAGCAACCG 59.195 52.381 0.00 0.00 0.00 4.44
387 3209 2.490991 GTAAAAGGACTGAGCAACCGT 58.509 47.619 0.00 0.00 0.00 4.83
388 3210 1.308998 AAAAGGACTGAGCAACCGTG 58.691 50.000 0.00 0.00 0.00 4.94
389 3211 0.535102 AAAGGACTGAGCAACCGTGG 60.535 55.000 0.00 0.00 0.00 4.94
390 3212 3.050275 GGACTGAGCAACCGTGGC 61.050 66.667 0.00 0.00 0.00 5.01
391 3213 2.031163 GACTGAGCAACCGTGGCT 59.969 61.111 0.00 0.00 46.07 4.75
397 3219 3.712907 GCAACCGTGGCTCCCCTA 61.713 66.667 0.00 0.00 0.00 3.53
398 3220 2.584608 CAACCGTGGCTCCCCTAG 59.415 66.667 0.00 0.00 0.00 3.02
399 3221 2.687566 AACCGTGGCTCCCCTAGG 60.688 66.667 0.06 0.06 35.44 3.02
400 3222 3.557695 AACCGTGGCTCCCCTAGGT 62.558 63.158 8.29 0.00 41.22 3.08
401 3223 2.172229 AACCGTGGCTCCCCTAGGTA 62.172 60.000 8.29 0.00 39.50 3.08
402 3224 1.833049 CCGTGGCTCCCCTAGGTAG 60.833 68.421 8.29 6.02 0.00 3.18
403 3225 1.833049 CGTGGCTCCCCTAGGTAGG 60.833 68.421 8.29 2.52 43.25 3.18
418 3240 4.141205 CTAGGTAGGTAGCTAGGTTCACCT 60.141 50.000 18.11 18.11 45.74 4.00
424 3246 1.853963 AGCTAGGTTCACCTCGTGAT 58.146 50.000 0.39 0.00 44.77 3.06
539 3372 2.035626 ACCTCGCCCACCCAATTG 59.964 61.111 0.00 0.00 0.00 2.32
563 3396 0.178953 ATCCCCTGCTTGTGCTTGTT 60.179 50.000 0.00 0.00 40.48 2.83
591 3430 2.091389 AGATGGAGAAGGAGCTCTAGCA 60.091 50.000 14.64 0.00 45.16 3.49
678 3517 9.330063 CATTAGTATCTTCTTTGATGGCTTGTA 57.670 33.333 0.00 0.00 0.00 2.41
694 3533 4.105486 GCTTGTAATTTCCTTGAATCGGC 58.895 43.478 0.00 0.00 0.00 5.54
722 3561 5.186198 TCCTTCTGCAACTATTTAAGCTCC 58.814 41.667 0.00 0.00 0.00 4.70
724 3563 3.531538 TCTGCAACTATTTAAGCTCCGG 58.468 45.455 0.00 0.00 0.00 5.14
741 3580 1.523758 CGGGGAGTTTCTCTGGTTTG 58.476 55.000 0.00 0.00 0.00 2.93
755 3594 4.335416 TCTGGTTTGAATCTAGGGCAAAG 58.665 43.478 6.02 0.00 32.76 2.77
785 3626 5.068234 TGTTCGGTAAAGAGACATCGATT 57.932 39.130 0.00 0.00 0.00 3.34
820 3661 6.590068 CCATGGTCTGAATAGTGAGAGATTT 58.410 40.000 2.57 0.00 0.00 2.17
828 3669 6.475504 TGAATAGTGAGAGATTTGGCAAGAA 58.524 36.000 0.00 0.00 0.00 2.52
837 3679 8.137437 TGAGAGATTTGGCAAGAAAACTTTTAG 58.863 33.333 0.00 0.00 0.00 1.85
841 3683 5.669164 TTGGCAAGAAAACTTTTAGTGGT 57.331 34.783 0.00 0.00 0.00 4.16
848 3690 9.308318 GCAAGAAAACTTTTAGTGGTTGATTTA 57.692 29.630 0.00 0.00 0.00 1.40
859 3701 6.590234 AGTGGTTGATTTAATTGTTCTCCC 57.410 37.500 0.00 0.00 0.00 4.30
866 3708 2.396590 TAATTGTTCTCCCGGAGTGC 57.603 50.000 14.36 8.83 0.00 4.40
871 3713 0.322546 GTTCTCCCGGAGTGCCATTT 60.323 55.000 14.36 0.00 0.00 2.32
875 3717 0.539986 TCCCGGAGTGCCATTTAGAC 59.460 55.000 0.73 0.00 0.00 2.59
921 3769 9.542462 TTTACTACAATGGTTATGCATACTCTC 57.458 33.333 5.74 0.00 0.00 3.20
1059 3907 2.547642 GGATGACTGCATAGACCTCTGC 60.548 54.545 0.00 1.05 38.87 4.26
1106 3954 1.984570 TTCCTGCAGGGAGAGTCGG 60.985 63.158 32.23 4.54 46.01 4.79
1133 3987 7.548427 GTCAGAGTCAGATTCAGAATTTGATGA 59.452 37.037 17.15 14.14 34.92 2.92
1151 4005 2.440409 TGAAAATGCTGAAGGAGGAGC 58.560 47.619 0.00 0.00 35.65 4.70
1319 4173 5.121454 AGTCAGAGTTTGATTCAGAAATCGC 59.879 40.000 0.00 0.00 43.61 4.58
1381 4235 0.663153 AAGGTGCAGCGTGAAGAAAC 59.337 50.000 10.78 0.00 0.00 2.78
1390 4244 2.870411 AGCGTGAAGAAACTGTACAACC 59.130 45.455 0.00 0.00 0.00 3.77
1421 4275 7.041235 CCATGGATTAGATGAAGAGAAGAAAGC 60.041 40.741 5.56 0.00 0.00 3.51
1785 4639 8.333186 GCAGAAATATCAAAATTCAAGATTGCC 58.667 33.333 0.00 0.00 0.00 4.52
1908 4762 2.208132 TGCACAATTGGTCCGGTTAT 57.792 45.000 10.83 0.00 0.00 1.89
1953 4807 3.416156 AGCAAAGAGGGTTAAAGCTGAG 58.584 45.455 0.00 0.00 0.00 3.35
1954 4808 2.095008 GCAAAGAGGGTTAAAGCTGAGC 60.095 50.000 0.00 0.00 0.00 4.26
1992 4846 5.799827 AGAAGTCTAACCTATCTGGATGC 57.200 43.478 0.00 0.00 39.71 3.91
1998 4852 0.401105 ACCTATCTGGATGCCTGCCT 60.401 55.000 0.00 0.00 39.71 4.75
2029 4883 2.119801 AGAATATGCATCCATCGGCC 57.880 50.000 0.19 0.00 32.85 6.13
2035 4889 1.300388 GCATCCATCGGCCAAATGC 60.300 57.895 2.24 6.30 36.33 3.56
2036 4890 2.018727 GCATCCATCGGCCAAATGCA 62.019 55.000 15.78 0.00 43.89 3.96
2037 4891 0.249155 CATCCATCGGCCAAATGCAC 60.249 55.000 2.24 0.00 43.89 4.57
2041 4895 1.382522 CATCGGCCAAATGCACTACT 58.617 50.000 2.24 0.00 43.89 2.57
2048 4902 1.672881 CCAAATGCACTACTAGCCAGC 59.327 52.381 0.00 0.00 0.00 4.85
2078 4932 7.052873 GCCTCTGATAATTATACATGATGCCT 58.947 38.462 0.00 0.00 0.00 4.75
2079 4933 7.226325 GCCTCTGATAATTATACATGATGCCTC 59.774 40.741 0.00 0.00 0.00 4.70
2080 4934 7.714377 CCTCTGATAATTATACATGATGCCTCC 59.286 40.741 0.00 0.00 0.00 4.30
2100 4954 5.452078 TCCTCTTTTATTGTTTGTGCAGG 57.548 39.130 0.00 0.00 0.00 4.85
2102 4956 3.988819 TCTTTTATTGTTTGTGCAGGCC 58.011 40.909 0.00 0.00 0.00 5.19
2186 5040 3.660865 ACAGTTTTACACGATGGAGGTC 58.339 45.455 0.00 0.00 0.00 3.85
2393 5250 1.204146 GTGCTATCAGAGGAACCCCA 58.796 55.000 0.00 0.00 33.88 4.96
2404 5261 0.179012 GGAACCCCACGAACAGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
2435 5292 2.341168 GGCGCATCAAATGTGTTTAACG 59.659 45.455 10.83 0.00 42.56 3.18
2498 5355 2.825861 TGAGGTAAAGTCGGTGAACC 57.174 50.000 0.00 0.00 0.00 3.62
2501 5358 3.071892 TGAGGTAAAGTCGGTGAACCAAT 59.928 43.478 0.00 0.00 35.14 3.16
2508 5365 4.819105 AGTCGGTGAACCAATAAGATCA 57.181 40.909 0.00 0.00 35.14 2.92
2716 5624 2.091112 CGAGAACCAGTCGCAGCAG 61.091 63.158 0.00 0.00 0.00 4.24
2770 5678 6.681777 AGATCAACTGAAAATACTGTTTGCC 58.318 36.000 0.00 0.00 31.53 4.52
2802 5713 3.845781 TCAGGATGGAAGCTGGAATAC 57.154 47.619 0.00 0.00 36.16 1.89
2905 5816 8.434392 TGGGTAATATATTTGAGGACTGTAACC 58.566 37.037 2.68 0.61 0.00 2.85
2927 5838 1.070758 TCTTGGTGCTTCAGGTCACTC 59.929 52.381 0.00 0.00 33.91 3.51
3003 5915 1.022735 CCAACTGAGGATGCTGATGC 58.977 55.000 0.00 0.00 40.20 3.91
3061 5973 1.134491 TCATCACCAGCTGCAGAGATG 60.134 52.381 20.43 19.42 35.21 2.90
3064 5976 2.271173 CCAGCTGCAGAGATGCCA 59.729 61.111 20.43 0.00 34.01 4.92
3139 6051 9.319143 AGAAGGAAAGAGTGATATTTTATCGTG 57.681 33.333 0.00 0.00 0.00 4.35
3158 6070 2.778299 TGGCTTGTCCAGTTCACATAC 58.222 47.619 0.00 0.00 40.72 2.39
3162 6074 4.332819 GGCTTGTCCAGTTCACATACATAC 59.667 45.833 0.00 0.00 34.01 2.39
3181 6093 2.643551 ACTGTGGCCGGAATAATTCTG 58.356 47.619 5.05 0.00 35.78 3.02
3185 6097 3.279434 GTGGCCGGAATAATTCTGTCTT 58.721 45.455 5.05 0.00 34.15 3.01
3186 6098 3.694566 GTGGCCGGAATAATTCTGTCTTT 59.305 43.478 5.05 0.00 34.15 2.52
3187 6099 3.945285 TGGCCGGAATAATTCTGTCTTTC 59.055 43.478 5.05 0.00 34.15 2.62
3188 6100 4.200092 GGCCGGAATAATTCTGTCTTTCT 58.800 43.478 5.05 0.00 34.15 2.52
3189 6101 4.035675 GGCCGGAATAATTCTGTCTTTCTG 59.964 45.833 5.05 0.00 34.15 3.02
3190 6102 4.636206 GCCGGAATAATTCTGTCTTTCTGT 59.364 41.667 5.05 0.00 34.15 3.41
3191 6103 5.220681 GCCGGAATAATTCTGTCTTTCTGTC 60.221 44.000 5.05 0.00 34.15 3.51
3192 6104 5.294552 CCGGAATAATTCTGTCTTTCTGTCC 59.705 44.000 0.00 0.00 34.15 4.02
3193 6105 5.294552 CGGAATAATTCTGTCTTTCTGTCCC 59.705 44.000 0.00 0.00 0.00 4.46
3194 6106 6.418946 GGAATAATTCTGTCTTTCTGTCCCT 58.581 40.000 0.00 0.00 0.00 4.20
3195 6107 6.540551 GGAATAATTCTGTCTTTCTGTCCCTC 59.459 42.308 0.00 0.00 0.00 4.30
3196 6108 4.982241 AATTCTGTCTTTCTGTCCCTCA 57.018 40.909 0.00 0.00 0.00 3.86
3197 6109 4.982241 ATTCTGTCTTTCTGTCCCTCAA 57.018 40.909 0.00 0.00 0.00 3.02
3198 6110 4.771114 TTCTGTCTTTCTGTCCCTCAAA 57.229 40.909 0.00 0.00 0.00 2.69
3199 6111 4.771114 TCTGTCTTTCTGTCCCTCAAAA 57.229 40.909 0.00 0.00 0.00 2.44
3200 6112 5.110814 TCTGTCTTTCTGTCCCTCAAAAA 57.889 39.130 0.00 0.00 0.00 1.94
3244 6156 5.260424 TGTGAAACCTGGTGCATACATAAT 58.740 37.500 0.00 0.00 34.36 1.28
3254 6166 7.078249 TGGTGCATACATAATCAGATAACCT 57.922 36.000 0.00 0.00 0.00 3.50
3256 6168 6.372659 GGTGCATACATAATCAGATAACCTGG 59.627 42.308 0.00 0.00 43.12 4.45
3288 6200 1.760192 AAAGAGTGATGATGGCTGCC 58.240 50.000 12.87 12.87 0.00 4.85
3293 6205 0.179119 GTGATGATGGCTGCCTTTGC 60.179 55.000 21.03 6.95 38.26 3.68
3298 6210 0.031721 GATGGCTGCCTTTGCTATGC 59.968 55.000 21.03 0.00 38.71 3.14
3299 6211 0.396695 ATGGCTGCCTTTGCTATGCT 60.397 50.000 21.03 0.00 38.71 3.79
3346 6258 2.292984 TGGGGTAAAAGGGTGTGGTTTT 60.293 45.455 0.00 0.00 0.00 2.43
3358 6270 0.190069 GTGGTTTTCCCCCTTTCCCT 59.810 55.000 0.00 0.00 39.73 4.20
3359 6271 0.945760 TGGTTTTCCCCCTTTCCCTT 59.054 50.000 0.00 0.00 39.73 3.95
3361 6273 1.697432 GGTTTTCCCCCTTTCCCTTTG 59.303 52.381 0.00 0.00 0.00 2.77
3401 6313 4.142182 TGGCCTTTGAGAACTTTCAGTTTG 60.142 41.667 3.32 0.00 38.80 2.93
3405 6317 6.490534 CCTTTGAGAACTTTCAGTTTGTCTC 58.509 40.000 0.00 0.00 38.80 3.36
3408 6320 5.118990 TGAGAACTTTCAGTTTGTCTCTGG 58.881 41.667 0.00 0.00 38.80 3.86
3412 6324 5.871396 ACTTTCAGTTTGTCTCTGGTAGA 57.129 39.130 0.00 0.00 34.15 2.59
3435 6347 7.740805 AGAGAGTCTAAACCTTTGTTCTTCAT 58.259 34.615 0.00 0.00 32.15 2.57
3441 6353 3.160679 ACCTTTGTTCTTCATCCCCTG 57.839 47.619 0.00 0.00 0.00 4.45
3445 6357 1.067295 TGTTCTTCATCCCCTGCTGT 58.933 50.000 0.00 0.00 0.00 4.40
3497 6409 0.468029 GCTGGGTGATAACATGGGGG 60.468 60.000 0.00 0.00 0.00 5.40
3520 6432 2.631418 TTCGTTTTGTGCGGTTTTCA 57.369 40.000 0.00 0.00 0.00 2.69
3524 6436 3.927142 TCGTTTTGTGCGGTTTTCATTTT 59.073 34.783 0.00 0.00 0.00 1.82
3526 6438 5.575606 TCGTTTTGTGCGGTTTTCATTTTTA 59.424 32.000 0.00 0.00 0.00 1.52
3560 6472 3.187700 CGTTGAGGCGCTATTTTACTCT 58.812 45.455 7.64 0.00 0.00 3.24
3573 6485 7.634817 CGCTATTTTACTCTATGTTTTGTTCCG 59.365 37.037 0.00 0.00 0.00 4.30
3720 6637 3.007398 CAGAACCAGGTCCTCTATATGCC 59.993 52.174 0.00 0.00 0.00 4.40
3721 6638 2.795291 ACCAGGTCCTCTATATGCCA 57.205 50.000 0.00 0.00 0.00 4.92
3722 6639 3.060479 ACCAGGTCCTCTATATGCCAA 57.940 47.619 0.00 0.00 0.00 4.52
3723 6640 2.975489 ACCAGGTCCTCTATATGCCAAG 59.025 50.000 0.00 0.00 0.00 3.61
3724 6641 3.242867 CCAGGTCCTCTATATGCCAAGA 58.757 50.000 0.00 0.00 0.00 3.02
3725 6642 3.843027 CCAGGTCCTCTATATGCCAAGAT 59.157 47.826 0.00 0.00 0.00 2.40
3726 6643 4.081198 CCAGGTCCTCTATATGCCAAGATC 60.081 50.000 0.00 0.00 0.00 2.75
3727 6644 3.766591 AGGTCCTCTATATGCCAAGATCG 59.233 47.826 0.00 0.00 0.00 3.69
3728 6645 3.516615 GTCCTCTATATGCCAAGATCGC 58.483 50.000 0.00 0.00 0.00 4.58
3729 6646 3.194542 GTCCTCTATATGCCAAGATCGCT 59.805 47.826 0.00 0.00 0.00 4.93
3730 6647 3.834813 TCCTCTATATGCCAAGATCGCTT 59.165 43.478 0.00 0.00 33.74 4.68
3731 6648 4.284490 TCCTCTATATGCCAAGATCGCTTT 59.716 41.667 0.00 0.00 30.14 3.51
3732 6649 4.999950 CCTCTATATGCCAAGATCGCTTTT 59.000 41.667 0.00 0.00 30.14 2.27
3733 6650 5.121454 CCTCTATATGCCAAGATCGCTTTTC 59.879 44.000 0.00 0.00 30.14 2.29
3742 6703 5.277974 GCCAAGATCGCTTTTCTTATATGCA 60.278 40.000 0.00 0.00 32.27 3.96
3767 6728 2.482864 GACTTGTTTGCCCCAACAATG 58.517 47.619 6.45 4.70 0.00 2.82
3781 6743 6.741240 GCCCCAACAATGAAAATGACTACTTT 60.741 38.462 0.00 0.00 0.00 2.66
3784 6746 7.169645 CCCAACAATGAAAATGACTACTTTGTG 59.830 37.037 0.00 0.00 33.34 3.33
3797 6759 6.868864 TGACTACTTTGTGACAGATTTCTAGC 59.131 38.462 0.00 0.00 0.00 3.42
3798 6760 6.166982 ACTACTTTGTGACAGATTTCTAGCC 58.833 40.000 0.00 0.00 0.00 3.93
3799 6761 5.234466 ACTTTGTGACAGATTTCTAGCCT 57.766 39.130 0.00 0.00 0.00 4.58
3800 6762 5.625150 ACTTTGTGACAGATTTCTAGCCTT 58.375 37.500 0.00 0.00 0.00 4.35
3801 6763 6.064717 ACTTTGTGACAGATTTCTAGCCTTT 58.935 36.000 0.00 0.00 0.00 3.11
3802 6764 6.547510 ACTTTGTGACAGATTTCTAGCCTTTT 59.452 34.615 0.00 0.00 0.00 2.27
3803 6765 7.719633 ACTTTGTGACAGATTTCTAGCCTTTTA 59.280 33.333 0.00 0.00 0.00 1.52
3804 6766 7.672983 TTGTGACAGATTTCTAGCCTTTTAG 57.327 36.000 0.00 0.00 0.00 1.85
3805 6767 6.173339 TGTGACAGATTTCTAGCCTTTTAGG 58.827 40.000 0.00 0.00 38.80 2.69
3806 6768 5.586643 GTGACAGATTTCTAGCCTTTTAGGG 59.413 44.000 0.00 0.00 35.37 3.53
3815 6777 1.444917 GCCTTTTAGGGCGCGCTAAT 61.445 55.000 37.39 18.98 42.82 1.73
3823 6785 1.647084 GGCGCGCTAATAAACCCTG 59.353 57.895 32.29 0.00 0.00 4.45
3835 6797 8.567948 CGCTAATAAACCCTGACATAATTCATT 58.432 33.333 0.00 0.00 0.00 2.57
3855 6817 5.982516 TCATTTGCACAATTTGTCAGGTTAC 59.017 36.000 0.00 0.00 0.00 2.50
3885 6847 6.238759 GGTCGGAGATTTTAATAGCAGCAAAT 60.239 38.462 0.00 0.00 40.67 2.32
3887 6849 8.507249 GTCGGAGATTTTAATAGCAGCAAATAT 58.493 33.333 0.00 0.00 40.67 1.28
3916 6878 1.761784 CTGATCTGCTTGGAGGTAGCT 59.238 52.381 0.00 0.00 39.38 3.32
3917 6879 2.961741 CTGATCTGCTTGGAGGTAGCTA 59.038 50.000 0.00 0.00 39.38 3.32
3940 6902 8.726988 GCTAGAAGTCTAATCTATCTCGATGTT 58.273 37.037 0.00 0.00 0.00 2.71
3972 6934 8.114331 TCATTCAGGTAAAATATGCATCCATC 57.886 34.615 0.19 0.00 32.85 3.51
3974 6936 5.003160 TCAGGTAAAATATGCATCCATCGG 58.997 41.667 0.19 0.00 32.85 4.18
3980 6942 2.291209 TATGCATCCATCGGCCATTT 57.709 45.000 0.19 0.00 32.85 2.32
3983 6945 1.136695 TGCATCCATCGGCCATTTTTC 59.863 47.619 2.24 0.00 0.00 2.29
3984 6946 1.538849 GCATCCATCGGCCATTTTTCC 60.539 52.381 2.24 0.00 0.00 3.13
3985 6947 1.032014 ATCCATCGGCCATTTTTCCG 58.968 50.000 2.24 0.00 46.52 4.30
4041 7018 1.909700 AAACACGATGAGCCCACATT 58.090 45.000 0.00 0.00 0.00 2.71
4050 7027 4.576993 GCCCACATTCGGCTTTTG 57.423 55.556 0.00 0.00 43.48 2.44
4078 7055 2.307934 AAATGCACACAACCAACACC 57.692 45.000 0.00 0.00 0.00 4.16
4082 7059 0.244994 GCACACAACCAACACCAACA 59.755 50.000 0.00 0.00 0.00 3.33
4083 7060 1.989430 CACACAACCAACACCAACAC 58.011 50.000 0.00 0.00 0.00 3.32
4095 7072 1.925847 CACCAACACACACAAACATGC 59.074 47.619 0.00 0.00 0.00 4.06
4097 7074 1.136695 CCAACACACACAAACATGCCT 59.863 47.619 0.00 0.00 0.00 4.75
4124 7101 9.418045 GCAACTAGCAAAATAATAAGACCAAAA 57.582 29.630 0.00 0.00 44.79 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.384353 GCTTTGTGTCCGCTTTCGAC 60.384 55.000 0.00 0.00 38.10 4.20
1 2 1.827315 CGCTTTGTGTCCGCTTTCGA 61.827 55.000 0.00 0.00 38.10 3.71
2 3 1.438710 CGCTTTGTGTCCGCTTTCG 60.439 57.895 0.00 0.00 0.00 3.46
3 4 1.082104 CCGCTTTGTGTCCGCTTTC 60.082 57.895 0.00 0.00 0.00 2.62
4 5 1.525077 TCCGCTTTGTGTCCGCTTT 60.525 52.632 0.00 0.00 0.00 3.51
5 6 2.110213 TCCGCTTTGTGTCCGCTT 59.890 55.556 0.00 0.00 0.00 4.68
6 7 2.665185 GTCCGCTTTGTGTCCGCT 60.665 61.111 0.00 0.00 0.00 5.52
7 8 2.054140 TTTGTCCGCTTTGTGTCCGC 62.054 55.000 0.00 0.00 0.00 5.54
8 9 0.378962 TTTTGTCCGCTTTGTGTCCG 59.621 50.000 0.00 0.00 0.00 4.79
9 10 1.404035 ACTTTTGTCCGCTTTGTGTCC 59.596 47.619 0.00 0.00 0.00 4.02
10 11 2.716398 GACTTTTGTCCGCTTTGTGTC 58.284 47.619 0.00 0.00 43.37 3.67
22 23 0.946528 GGGCGTAAACGGACTTTTGT 59.053 50.000 4.49 0.00 40.23 2.83
24 25 1.844771 GCGGGCGTAAACGGACTTTT 61.845 55.000 4.49 0.00 40.23 2.27
25 26 2.319841 GCGGGCGTAAACGGACTTT 61.320 57.895 4.49 0.00 40.23 2.66
26 27 2.739671 GCGGGCGTAAACGGACTT 60.740 61.111 4.49 0.00 40.23 3.01
46 47 3.423154 CAAACGAGACGGCCCAGC 61.423 66.667 0.00 0.00 0.00 4.85
47 48 1.164041 AAACAAACGAGACGGCCCAG 61.164 55.000 0.00 0.00 0.00 4.45
48 49 0.748729 AAAACAAACGAGACGGCCCA 60.749 50.000 0.00 0.00 0.00 5.36
49 50 0.382873 AAAAACAAACGAGACGGCCC 59.617 50.000 0.00 0.00 0.00 5.80
50 51 3.930400 AAAAACAAACGAGACGGCC 57.070 47.368 0.00 0.00 0.00 6.13
67 68 1.316651 CCGTCCGTTTGGGGTAAAAA 58.683 50.000 0.00 0.00 36.01 1.94
68 69 0.536915 CCCGTCCGTTTGGGGTAAAA 60.537 55.000 0.00 0.00 42.05 1.52
69 70 1.072852 CCCGTCCGTTTGGGGTAAA 59.927 57.895 0.00 0.00 42.05 2.01
70 71 2.749016 CCCGTCCGTTTGGGGTAA 59.251 61.111 0.00 0.00 42.05 2.85
84 85 3.616721 CTATCCTGTCCGCCCCCG 61.617 72.222 0.00 0.00 0.00 5.73
85 86 3.242291 CCTATCCTGTCCGCCCCC 61.242 72.222 0.00 0.00 0.00 5.40
86 87 3.242291 CCCTATCCTGTCCGCCCC 61.242 72.222 0.00 0.00 0.00 5.80
87 88 2.446036 ACCCTATCCTGTCCGCCC 60.446 66.667 0.00 0.00 0.00 6.13
88 89 2.857744 CGACCCTATCCTGTCCGCC 61.858 68.421 0.00 0.00 0.00 6.13
89 90 2.728817 CGACCCTATCCTGTCCGC 59.271 66.667 0.00 0.00 0.00 5.54
90 91 2.728817 GCGACCCTATCCTGTCCG 59.271 66.667 0.00 0.00 0.00 4.79
91 92 2.728817 CGCGACCCTATCCTGTCC 59.271 66.667 0.00 0.00 0.00 4.02
92 93 2.027751 GCGCGACCCTATCCTGTC 59.972 66.667 12.10 0.00 0.00 3.51
93 94 3.900892 CGCGCGACCCTATCCTGT 61.901 66.667 28.94 0.00 0.00 4.00
94 95 4.647615 CCGCGCGACCCTATCCTG 62.648 72.222 34.63 6.11 0.00 3.86
97 98 4.944372 CCACCGCGCGACCCTATC 62.944 72.222 34.63 0.00 0.00 2.08
107 108 1.597027 AAAGACCAACTCCACCGCG 60.597 57.895 0.00 0.00 0.00 6.46
108 109 1.515521 CCAAAGACCAACTCCACCGC 61.516 60.000 0.00 0.00 0.00 5.68
109 110 0.179029 ACCAAAGACCAACTCCACCG 60.179 55.000 0.00 0.00 0.00 4.94
111 112 1.202604 TCGACCAAAGACCAACTCCAC 60.203 52.381 0.00 0.00 0.00 4.02
112 113 1.070134 CTCGACCAAAGACCAACTCCA 59.930 52.381 0.00 0.00 0.00 3.86
113 114 1.343465 TCTCGACCAAAGACCAACTCC 59.657 52.381 0.00 0.00 0.00 3.85
114 115 2.296471 TCTCTCGACCAAAGACCAACTC 59.704 50.000 0.00 0.00 0.00 3.01
115 116 2.317040 TCTCTCGACCAAAGACCAACT 58.683 47.619 0.00 0.00 0.00 3.16
116 117 2.814280 TCTCTCGACCAAAGACCAAC 57.186 50.000 0.00 0.00 0.00 3.77
117 118 2.028112 CCATCTCTCGACCAAAGACCAA 60.028 50.000 0.00 0.00 0.00 3.67
118 119 1.550524 CCATCTCTCGACCAAAGACCA 59.449 52.381 0.00 0.00 0.00 4.02
119 120 1.134670 CCCATCTCTCGACCAAAGACC 60.135 57.143 0.00 0.00 0.00 3.85
121 122 1.195115 CCCCATCTCTCGACCAAAGA 58.805 55.000 0.00 0.00 0.00 2.52
122 123 0.905357 ACCCCATCTCTCGACCAAAG 59.095 55.000 0.00 0.00 0.00 2.77
123 124 0.902531 GACCCCATCTCTCGACCAAA 59.097 55.000 0.00 0.00 0.00 3.28
125 126 0.252057 TTGACCCCATCTCTCGACCA 60.252 55.000 0.00 0.00 0.00 4.02
126 127 0.902531 TTTGACCCCATCTCTCGACC 59.097 55.000 0.00 0.00 0.00 4.79
127 128 1.134670 CCTTTGACCCCATCTCTCGAC 60.135 57.143 0.00 0.00 0.00 4.20
128 129 1.195115 CCTTTGACCCCATCTCTCGA 58.805 55.000 0.00 0.00 0.00 4.04
129 130 0.179000 CCCTTTGACCCCATCTCTCG 59.821 60.000 0.00 0.00 0.00 4.04
131 132 1.290134 GTCCCTTTGACCCCATCTCT 58.710 55.000 0.00 0.00 38.09 3.10
132 133 0.991920 TGTCCCTTTGACCCCATCTC 59.008 55.000 0.00 0.00 43.78 2.75
133 134 1.455822 TTGTCCCTTTGACCCCATCT 58.544 50.000 0.00 0.00 43.78 2.90
134 135 2.302587 TTTGTCCCTTTGACCCCATC 57.697 50.000 0.00 0.00 43.78 3.51
135 136 2.785357 TTTTGTCCCTTTGACCCCAT 57.215 45.000 0.00 0.00 43.78 4.00
136 137 2.552093 TTTTTGTCCCTTTGACCCCA 57.448 45.000 0.00 0.00 43.78 4.96
153 154 3.782656 ACACAGACCCGTCCTAATTTT 57.217 42.857 0.00 0.00 0.00 1.82
154 155 3.782656 AACACAGACCCGTCCTAATTT 57.217 42.857 0.00 0.00 0.00 1.82
155 156 3.408634 CAAACACAGACCCGTCCTAATT 58.591 45.455 0.00 0.00 0.00 1.40
157 158 1.071071 CCAAACACAGACCCGTCCTAA 59.929 52.381 0.00 0.00 0.00 2.69
158 159 0.682852 CCAAACACAGACCCGTCCTA 59.317 55.000 0.00 0.00 0.00 2.94
159 160 1.450211 CCAAACACAGACCCGTCCT 59.550 57.895 0.00 0.00 0.00 3.85
160 161 1.599797 CCCAAACACAGACCCGTCC 60.600 63.158 0.00 0.00 0.00 4.79
161 162 0.883370 GACCCAAACACAGACCCGTC 60.883 60.000 0.00 0.00 0.00 4.79
163 164 1.147376 TGACCCAAACACAGACCCG 59.853 57.895 0.00 0.00 0.00 5.28
164 165 0.106918 TGTGACCCAAACACAGACCC 60.107 55.000 0.00 0.00 42.20 4.46
165 166 3.487576 TGTGACCCAAACACAGACC 57.512 52.632 0.00 0.00 42.20 3.85
170 171 4.359706 GACAGAAAATGTGACCCAAACAC 58.640 43.478 0.00 0.00 44.17 3.32
171 172 3.066064 CGACAGAAAATGTGACCCAAACA 59.934 43.478 0.00 0.00 44.17 2.83
172 173 3.550030 CCGACAGAAAATGTGACCCAAAC 60.550 47.826 0.00 0.00 44.17 2.93
173 174 2.621055 CCGACAGAAAATGTGACCCAAA 59.379 45.455 0.00 0.00 44.17 3.28
187 3001 1.305201 GTTTGGAGCAAACCGACAGA 58.695 50.000 0.00 0.00 45.32 3.41
204 3018 2.087501 TTCATATGCGTGTGTCCGTT 57.912 45.000 2.35 0.00 0.00 4.44
215 3029 6.401903 CCAACGCTAGATCTCATTTCATATGC 60.402 42.308 0.00 0.00 0.00 3.14
217 3031 6.169094 CCCAACGCTAGATCTCATTTCATAT 58.831 40.000 0.00 0.00 0.00 1.78
218 3032 5.511373 CCCCAACGCTAGATCTCATTTCATA 60.511 44.000 0.00 0.00 0.00 2.15
227 3041 0.541863 CCAACCCCAACGCTAGATCT 59.458 55.000 0.00 0.00 0.00 2.75
304 3118 6.344232 GGAGATTCCATATTCGACTCGTTCG 61.344 48.000 0.00 3.24 42.15 3.95
308 3122 4.505313 TGGAGATTCCATATTCGACTCG 57.495 45.455 0.00 0.00 42.67 4.18
344 3158 2.109799 CGAGGTATGGGGCAGCAG 59.890 66.667 0.00 0.00 0.00 4.24
365 3187 2.550208 CGGTTGCTCAGTCCTTTTACCT 60.550 50.000 0.00 0.00 0.00 3.08
366 3188 1.804748 CGGTTGCTCAGTCCTTTTACC 59.195 52.381 0.00 0.00 0.00 2.85
367 3189 2.223377 CACGGTTGCTCAGTCCTTTTAC 59.777 50.000 0.00 0.00 0.00 2.01
368 3190 2.489971 CACGGTTGCTCAGTCCTTTTA 58.510 47.619 0.00 0.00 0.00 1.52
369 3191 1.308998 CACGGTTGCTCAGTCCTTTT 58.691 50.000 0.00 0.00 0.00 2.27
370 3192 0.535102 CCACGGTTGCTCAGTCCTTT 60.535 55.000 0.00 0.00 0.00 3.11
371 3193 1.071471 CCACGGTTGCTCAGTCCTT 59.929 57.895 0.00 0.00 0.00 3.36
372 3194 2.743718 CCACGGTTGCTCAGTCCT 59.256 61.111 0.00 0.00 0.00 3.85
373 3195 3.050275 GCCACGGTTGCTCAGTCC 61.050 66.667 0.00 0.00 0.00 3.85
374 3196 2.031163 AGCCACGGTTGCTCAGTC 59.969 61.111 0.12 0.00 32.41 3.51
380 3202 3.682292 CTAGGGGAGCCACGGTTGC 62.682 68.421 0.00 0.00 0.00 4.17
381 3203 2.584608 CTAGGGGAGCCACGGTTG 59.415 66.667 0.00 0.00 0.00 3.77
382 3204 2.172229 TACCTAGGGGAGCCACGGTT 62.172 60.000 14.81 0.00 36.25 4.44
383 3205 2.584873 CTACCTAGGGGAGCCACGGT 62.585 65.000 14.81 0.00 36.25 4.83
384 3206 1.833049 CTACCTAGGGGAGCCACGG 60.833 68.421 14.81 0.00 36.25 4.94
385 3207 1.833049 CCTACCTAGGGGAGCCACG 60.833 68.421 14.81 0.00 39.86 4.94
386 3208 4.297207 CCTACCTAGGGGAGCCAC 57.703 66.667 14.81 0.00 39.86 5.01
395 3217 4.141205 AGGTGAACCTAGCTACCTACCTAG 60.141 50.000 0.00 0.00 46.48 3.02
396 3218 3.790408 AGGTGAACCTAGCTACCTACCTA 59.210 47.826 0.00 0.00 46.48 3.08
397 3219 2.586368 AGGTGAACCTAGCTACCTACCT 59.414 50.000 0.00 3.71 46.48 3.08
398 3220 3.029483 AGGTGAACCTAGCTACCTACC 57.971 52.381 0.00 1.58 46.48 3.18
418 3240 2.504026 GTCACTGCGCGATCACGA 60.504 61.111 12.10 0.00 42.66 4.35
459 3281 0.909623 GGGTTTCATCGGGAAGGAGA 59.090 55.000 0.00 0.00 36.72 3.71
539 3372 1.034292 GCACAAGCAGGGGATCCTTC 61.034 60.000 12.58 4.59 42.67 3.46
563 3396 2.756907 CTCCTTCTCCATCTTCCCAGA 58.243 52.381 0.00 0.00 0.00 3.86
591 3430 1.001860 GCTCTTCAGCTCAGTGGAACT 59.998 52.381 0.00 0.00 46.57 3.01
678 3517 4.098501 GGAGAATGCCGATTCAAGGAAATT 59.901 41.667 0.00 0.00 40.59 1.82
694 3533 7.066766 AGCTTAAATAGTTGCAGAAGGAGAATG 59.933 37.037 0.00 0.00 0.00 2.67
722 3561 1.071699 TCAAACCAGAGAAACTCCCCG 59.928 52.381 0.00 0.00 0.00 5.73
724 3563 4.657013 AGATTCAAACCAGAGAAACTCCC 58.343 43.478 0.00 0.00 0.00 4.30
755 3594 3.056322 TCTCTTTACCGAACAAGTAGGCC 60.056 47.826 0.00 0.00 0.00 5.19
789 3630 2.832643 ATTCAGACCATGGCATCCAA 57.167 45.000 13.04 0.00 36.95 3.53
790 3631 2.779430 ACTATTCAGACCATGGCATCCA 59.221 45.455 13.04 0.00 38.19 3.41
791 3632 3.144506 CACTATTCAGACCATGGCATCC 58.855 50.000 13.04 0.00 0.00 3.51
795 3636 3.386078 TCTCTCACTATTCAGACCATGGC 59.614 47.826 13.04 4.70 0.00 4.40
805 3646 6.992063 TTCTTGCCAAATCTCTCACTATTC 57.008 37.500 0.00 0.00 0.00 1.75
820 3661 5.186021 TCAACCACTAAAAGTTTTCTTGCCA 59.814 36.000 3.60 0.00 40.37 4.92
837 3679 5.399013 CGGGAGAACAATTAAATCAACCAC 58.601 41.667 0.00 0.00 0.00 4.16
841 3683 5.414454 CACTCCGGGAGAACAATTAAATCAA 59.586 40.000 30.13 0.00 33.32 2.57
848 3690 0.322546 GGCACTCCGGGAGAACAATT 60.323 55.000 30.13 3.74 33.32 2.32
855 3697 0.830648 TCTAAATGGCACTCCGGGAG 59.169 55.000 22.40 22.40 35.52 4.30
859 3701 0.463833 GGGGTCTAAATGGCACTCCG 60.464 60.000 0.00 0.00 34.14 4.63
866 3708 9.273137 AGATACATCTAATAGGGGTCTAAATGG 57.727 37.037 0.00 0.00 34.85 3.16
977 3825 6.795098 TTGCTACACGAATAATCTGTGTTT 57.205 33.333 11.70 0.00 40.83 2.83
1106 3954 6.169094 TCAAATTCTGAATCTGACTCTGACC 58.831 40.000 2.35 0.00 0.00 4.02
1133 3987 1.844687 GGCTCCTCCTTCAGCATTTT 58.155 50.000 0.00 0.00 37.38 1.82
1151 4005 3.013219 TCTGAATCAGACTCTGACTCGG 58.987 50.000 17.00 17.00 43.63 4.63
1319 4173 2.095364 GCAAGTCCTTTGTCATGCTCTG 60.095 50.000 0.00 0.00 39.08 3.35
1381 4235 3.912496 TCCATGGATCAGGTTGTACAG 57.088 47.619 11.44 0.00 0.00 2.74
1390 4244 7.242322 TCTCTTCATCTAATCCATGGATCAG 57.758 40.000 27.45 22.60 33.08 2.90
1421 4275 5.126061 CCAAAACCAATCTCCCTCACATAAG 59.874 44.000 0.00 0.00 0.00 1.73
1644 4498 2.125461 TCGCTGCTATCACATTCTCG 57.875 50.000 0.00 0.00 0.00 4.04
1700 4554 2.828549 CAACCACCGGCCCTATGC 60.829 66.667 0.00 0.00 40.16 3.14
1707 4561 3.361977 ACAATCGCAACCACCGGC 61.362 61.111 0.00 0.00 0.00 6.13
1710 4564 1.234821 TCTTCACAATCGCAACCACC 58.765 50.000 0.00 0.00 0.00 4.61
1785 4639 0.579630 TCGCCGCGCATATAACAAAG 59.420 50.000 8.75 0.00 0.00 2.77
1863 4717 8.877864 AATGAATTATGTCAGGGTTTGTAAGA 57.122 30.769 0.00 0.00 0.00 2.10
1908 4762 3.493334 TCTTAAAGTCTCCGACCTCACA 58.507 45.455 0.00 0.00 32.18 3.58
1998 4852 7.289310 TGGATGCATATTCTACCTGAATGAAA 58.711 34.615 0.00 0.00 44.40 2.69
2029 4883 1.672881 GGCTGGCTAGTAGTGCATTTG 59.327 52.381 0.00 0.00 0.00 2.32
2035 4889 1.303309 GCATTGGCTGGCTAGTAGTG 58.697 55.000 2.00 0.00 36.96 2.74
2036 4890 0.181350 GGCATTGGCTGGCTAGTAGT 59.819 55.000 2.42 0.00 46.59 2.73
2037 4891 3.012560 GGCATTGGCTGGCTAGTAG 57.987 57.895 2.42 0.00 46.59 2.57
2048 4902 8.797350 TCATGTATAATTATCAGAGGCATTGG 57.203 34.615 0.00 0.00 0.00 3.16
2078 4932 4.261994 GCCTGCACAAACAATAAAAGAGGA 60.262 41.667 0.00 0.00 0.00 3.71
2079 4933 3.989817 GCCTGCACAAACAATAAAAGAGG 59.010 43.478 0.00 0.00 0.00 3.69
2080 4934 3.989817 GGCCTGCACAAACAATAAAAGAG 59.010 43.478 0.00 0.00 0.00 2.85
2100 4954 5.532779 CCTCCAAGTTATCCAAATAGAAGGC 59.467 44.000 0.00 0.00 0.00 4.35
2102 4956 7.281100 GTCACCTCCAAGTTATCCAAATAGAAG 59.719 40.741 0.00 0.00 0.00 2.85
2336 5193 1.606668 TGGCTTTCCGTGACAAATGAC 59.393 47.619 0.00 0.00 34.14 3.06
2393 5250 3.490761 CCAGCAACATTTTTCCTGTTCGT 60.491 43.478 0.00 0.00 34.69 3.85
2435 5292 1.491505 GCGCACCTAGATTCGCTTCC 61.492 60.000 0.30 0.00 43.70 3.46
2716 5624 2.266554 CTCGACTCATTCTTGACCTGC 58.733 52.381 0.00 0.00 0.00 4.85
2770 5678 2.038952 TCCATCCTGATGCCTAATTCCG 59.961 50.000 1.49 0.00 37.49 4.30
2905 5816 0.249868 TGACCTGAAGCACCAAGACG 60.250 55.000 0.00 0.00 0.00 4.18
2917 5828 4.890158 TCAATTAAGCAGAGTGACCTGA 57.110 40.909 5.45 0.00 36.29 3.86
3061 5973 1.105759 GTTCAGATCCATGGCCTGGC 61.106 60.000 24.48 11.05 45.52 4.85
3064 5976 0.549950 CCAGTTCAGATCCATGGCCT 59.450 55.000 6.96 3.53 0.00 5.19
3139 6051 2.778299 TGTATGTGAACTGGACAAGCC 58.222 47.619 0.00 0.00 37.10 4.35
3158 6070 4.214119 CAGAATTATTCCGGCCACAGTATG 59.786 45.833 2.24 0.00 46.00 2.39
3162 6074 2.614057 GACAGAATTATTCCGGCCACAG 59.386 50.000 2.24 0.00 0.00 3.66
3204 6116 9.520515 AGGTTTCACAATACAGAAAGACATATT 57.479 29.630 0.00 0.00 34.69 1.28
3205 6117 8.950210 CAGGTTTCACAATACAGAAAGACATAT 58.050 33.333 0.00 0.00 34.69 1.78
3206 6118 7.390440 CCAGGTTTCACAATACAGAAAGACATA 59.610 37.037 0.00 0.00 34.69 2.29
3207 6119 6.207417 CCAGGTTTCACAATACAGAAAGACAT 59.793 38.462 0.00 0.00 34.69 3.06
3208 6120 5.530915 CCAGGTTTCACAATACAGAAAGACA 59.469 40.000 0.00 0.00 34.69 3.41
3209 6121 5.531287 ACCAGGTTTCACAATACAGAAAGAC 59.469 40.000 0.00 0.00 34.69 3.01
3210 6122 5.530915 CACCAGGTTTCACAATACAGAAAGA 59.469 40.000 0.00 0.00 34.69 2.52
3211 6123 5.762045 CACCAGGTTTCACAATACAGAAAG 58.238 41.667 0.00 0.00 34.69 2.62
3244 6156 1.048724 CCTCCGCCCAGGTTATCTGA 61.049 60.000 0.00 0.00 46.18 3.27
3272 6184 1.404391 CAAAGGCAGCCATCATCACTC 59.596 52.381 15.80 0.00 0.00 3.51
3325 6237 0.935194 AACCACACCCTTTTACCCCA 59.065 50.000 0.00 0.00 0.00 4.96
3346 6258 2.435104 ACTTACAAAGGGAAAGGGGGA 58.565 47.619 0.00 0.00 0.00 4.81
3358 6270 2.890311 CACATGCCCTCCAACTTACAAA 59.110 45.455 0.00 0.00 0.00 2.83
3359 6271 2.513753 CACATGCCCTCCAACTTACAA 58.486 47.619 0.00 0.00 0.00 2.41
3361 6273 1.463674 CCACATGCCCTCCAACTTAC 58.536 55.000 0.00 0.00 0.00 2.34
3405 6317 6.347859 ACAAAGGTTTAGACTCTCTACCAG 57.652 41.667 10.59 4.69 0.00 4.00
3408 6320 8.142551 TGAAGAACAAAGGTTTAGACTCTCTAC 58.857 37.037 0.00 0.00 37.36 2.59
3412 6324 6.937465 GGATGAAGAACAAAGGTTTAGACTCT 59.063 38.462 0.00 0.00 37.36 3.24
3417 6329 5.183904 CAGGGGATGAAGAACAAAGGTTTAG 59.816 44.000 0.00 0.00 37.36 1.85
3422 6334 1.821136 GCAGGGGATGAAGAACAAAGG 59.179 52.381 0.00 0.00 0.00 3.11
3441 6353 2.100991 GCATGCACCGCTAACAGC 59.899 61.111 14.21 0.00 38.02 4.40
3497 6409 1.619983 AACCGCACAAAACGAAACAC 58.380 45.000 0.00 0.00 0.00 3.32
3539 6451 3.187700 AGAGTAAAATAGCGCCTCAACG 58.812 45.455 2.29 0.00 0.00 4.10
3540 6452 5.753921 ACATAGAGTAAAATAGCGCCTCAAC 59.246 40.000 2.29 0.00 0.00 3.18
3541 6453 5.914033 ACATAGAGTAAAATAGCGCCTCAA 58.086 37.500 2.29 0.00 0.00 3.02
3542 6454 5.531122 ACATAGAGTAAAATAGCGCCTCA 57.469 39.130 2.29 0.00 0.00 3.86
3543 6455 6.846325 AAACATAGAGTAAAATAGCGCCTC 57.154 37.500 2.29 0.85 0.00 4.70
3544 6456 6.598064 ACAAAACATAGAGTAAAATAGCGCCT 59.402 34.615 2.29 0.00 0.00 5.52
3545 6457 6.782150 ACAAAACATAGAGTAAAATAGCGCC 58.218 36.000 2.29 0.00 0.00 6.53
3546 6458 7.428472 GGAACAAAACATAGAGTAAAATAGCGC 59.572 37.037 0.00 0.00 0.00 5.92
3547 6459 7.634817 CGGAACAAAACATAGAGTAAAATAGCG 59.365 37.037 0.00 0.00 0.00 4.26
3548 6460 8.448615 ACGGAACAAAACATAGAGTAAAATAGC 58.551 33.333 0.00 0.00 0.00 2.97
3553 6465 9.715121 AGATAACGGAACAAAACATAGAGTAAA 57.285 29.630 0.00 0.00 0.00 2.01
3560 6472 8.731275 ATCATCAGATAACGGAACAAAACATA 57.269 30.769 0.00 0.00 31.14 2.29
3573 6485 5.010719 TCGGGTTCCACTATCATCAGATAAC 59.989 44.000 0.00 0.00 36.35 1.89
3636 6548 8.337118 TCCAGAGAGAATAATTCCAGGTTATT 57.663 34.615 0.00 0.00 35.16 1.40
3648 6560 3.969976 CACCCTCCATCCAGAGAGAATAA 59.030 47.826 0.00 0.00 35.82 1.40
3650 6562 2.406559 CACCCTCCATCCAGAGAGAAT 58.593 52.381 0.00 0.00 35.82 2.40
3651 6563 1.871418 CACCCTCCATCCAGAGAGAA 58.129 55.000 0.00 0.00 35.82 2.87
3655 6572 2.914289 GGCACCCTCCATCCAGAG 59.086 66.667 0.00 0.00 0.00 3.35
3693 6610 3.953542 AGAGGACCTGGTTCTGTTTTT 57.046 42.857 13.67 0.00 0.00 1.94
3720 6637 6.718388 TGTGCATATAAGAAAAGCGATCTTG 58.282 36.000 10.66 0.00 37.67 3.02
3721 6638 6.925610 TGTGCATATAAGAAAAGCGATCTT 57.074 33.333 0.00 6.85 40.18 2.40
3722 6639 6.510157 CGTTGTGCATATAAGAAAAGCGATCT 60.510 38.462 0.00 0.00 0.00 2.75
3723 6640 5.617187 CGTTGTGCATATAAGAAAAGCGATC 59.383 40.000 0.00 0.00 0.00 3.69
3724 6641 5.293324 TCGTTGTGCATATAAGAAAAGCGAT 59.707 36.000 0.00 0.00 0.00 4.58
3725 6642 4.627900 TCGTTGTGCATATAAGAAAAGCGA 59.372 37.500 0.00 0.00 0.00 4.93
3726 6643 4.723862 GTCGTTGTGCATATAAGAAAAGCG 59.276 41.667 0.00 0.00 0.00 4.68
3727 6644 5.869350 AGTCGTTGTGCATATAAGAAAAGC 58.131 37.500 0.00 0.00 0.00 3.51
3728 6645 7.298122 ACAAGTCGTTGTGCATATAAGAAAAG 58.702 34.615 0.00 0.00 45.58 2.27
3729 6646 7.197071 ACAAGTCGTTGTGCATATAAGAAAA 57.803 32.000 0.00 0.00 45.58 2.29
3730 6647 6.795098 ACAAGTCGTTGTGCATATAAGAAA 57.205 33.333 0.00 0.00 45.58 2.52
3731 6648 6.795098 AACAAGTCGTTGTGCATATAAGAA 57.205 33.333 0.00 0.00 46.68 2.52
3732 6649 6.598525 CAAACAAGTCGTTGTGCATATAAGA 58.401 36.000 0.00 0.00 46.68 2.10
3733 6650 5.283717 GCAAACAAGTCGTTGTGCATATAAG 59.716 40.000 0.00 0.00 46.68 1.73
3767 6728 9.387123 GAAATCTGTCACAAAGTAGTCATTTTC 57.613 33.333 0.00 0.00 0.00 2.29
3781 6743 6.173339 CCTAAAAGGCTAGAAATCTGTCACA 58.827 40.000 0.00 0.00 0.00 3.58
3797 6759 1.873698 TATTAGCGCGCCCTAAAAGG 58.126 50.000 30.33 0.00 31.62 3.11
3798 6760 3.547413 GGTTTATTAGCGCGCCCTAAAAG 60.547 47.826 30.33 0.00 31.62 2.27
3799 6761 2.355444 GGTTTATTAGCGCGCCCTAAAA 59.645 45.455 30.33 20.10 31.62 1.52
3800 6762 1.941975 GGTTTATTAGCGCGCCCTAAA 59.058 47.619 30.33 23.82 31.62 1.85
3801 6763 1.585297 GGTTTATTAGCGCGCCCTAA 58.415 50.000 30.33 21.19 0.00 2.69
3802 6764 0.249996 GGGTTTATTAGCGCGCCCTA 60.250 55.000 30.33 12.40 33.58 3.53
3803 6765 1.525306 GGGTTTATTAGCGCGCCCT 60.525 57.895 30.33 13.66 33.58 5.19
3804 6766 1.525306 AGGGTTTATTAGCGCGCCC 60.525 57.895 30.33 19.71 36.46 6.13
3805 6767 0.812412 TCAGGGTTTATTAGCGCGCC 60.812 55.000 30.33 10.46 0.00 6.53
3806 6768 0.303796 GTCAGGGTTTATTAGCGCGC 59.696 55.000 26.66 26.66 0.00 6.86
3807 6769 1.647346 TGTCAGGGTTTATTAGCGCG 58.353 50.000 0.00 0.00 0.00 6.86
3808 6770 5.941948 ATTATGTCAGGGTTTATTAGCGC 57.058 39.130 0.00 0.00 0.00 5.92
3809 6771 7.490962 TGAATTATGTCAGGGTTTATTAGCG 57.509 36.000 0.00 0.00 0.00 4.26
3815 6777 7.039434 TGTGCAAATGAATTATGTCAGGGTTTA 60.039 33.333 0.00 0.00 0.00 2.01
3823 6785 8.710551 TGACAAATTGTGCAAATGAATTATGTC 58.289 29.630 2.20 17.04 33.50 3.06
3835 6797 3.378742 ACGTAACCTGACAAATTGTGCAA 59.621 39.130 2.20 0.00 0.00 4.08
3855 6817 5.981315 TGCTATTAAAATCTCCGACCTTACG 59.019 40.000 0.00 0.00 0.00 3.18
3917 6879 7.865385 GCAAACATCGAGATAGATTAGACTTCT 59.135 37.037 0.00 0.00 0.00 2.85
3940 6902 6.559810 CATATTTTACCTGAATGAACGGCAA 58.440 36.000 0.00 0.00 0.00 4.52
3974 6936 9.959749 TTTAAGTCAATATATCGGAAAAATGGC 57.040 29.630 0.00 0.00 0.00 4.40
4041 7018 4.862018 GCATTTTAACTATGCAAAAGCCGA 59.138 37.500 14.02 0.00 45.93 5.54
4050 7027 5.226396 TGGTTGTGTGCATTTTAACTATGC 58.774 37.500 12.62 12.62 46.63 3.14
4060 7037 1.189752 TGGTGTTGGTTGTGTGCATT 58.810 45.000 0.00 0.00 0.00 3.56
4063 7040 0.244994 TGTTGGTGTTGGTTGTGTGC 59.755 50.000 0.00 0.00 0.00 4.57
4064 7041 1.270826 TGTGTTGGTGTTGGTTGTGTG 59.729 47.619 0.00 0.00 0.00 3.82
4078 7055 2.195096 CAGGCATGTTTGTGTGTGTTG 58.805 47.619 0.00 0.00 0.00 3.33
4082 7059 0.822811 TTGCAGGCATGTTTGTGTGT 59.177 45.000 0.00 0.00 0.00 3.72
4083 7060 1.202440 AGTTGCAGGCATGTTTGTGTG 60.202 47.619 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.