Multiple sequence alignment - TraesCS5A01G469200

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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 TraesCS5A01G469200 chr5A 100.000 5419 0 0 1 5419 646213943 646208525 0.000000e+00 10008.0
1 TraesCS5A01G469200 chr5D 91.171 3885 227 42 6 3824 519654513 519650679 0.000000e+00 5168.0
2 TraesCS5A01G469200 chr5D 89.581 1478 92 33 3915 5377 519650663 519649233 0.000000e+00 1820.0
3 TraesCS5A01G469200 chr5D 93.478 46 2 1 4982 5026 437563638 437563593 3.500000e-07 67.6
4 TraesCS5A01G469200 chr5B 90.764 3898 233 60 2 3824 654498630 654494785 0.000000e+00 5086.0
5 TraesCS5A01G469200 chr5B 90.399 1104 67 19 3915 4994 654494769 654493681 0.000000e+00 1415.0
6 TraesCS5A01G469200 chr5B 87.464 351 21 11 5032 5377 654493512 654493180 3.060000e-102 383.0
7 TraesCS5A01G469200 chr7B 84.920 809 87 12 2746 3522 576427705 576428510 0.000000e+00 785.0
8 TraesCS5A01G469200 chr4A 85.777 457 61 4 2752 3205 654154639 654155094 1.060000e-131 481.0
9 TraesCS5A01G469200 chr4A 85.683 454 61 4 2746 3196 654184063 654184515 4.910000e-130 475.0
10 TraesCS5A01G469200 chr4A 97.619 42 1 0 4982 5023 511131880 511131921 7.530000e-09 73.1
11 TraesCS5A01G469200 chr4A 97.561 41 1 0 4983 5023 714743815 714743775 2.710000e-08 71.3
12 TraesCS5A01G469200 chr4A 93.333 45 2 1 4983 5026 143697445 143697401 1.260000e-06 65.8
13 TraesCS5A01G469200 chr4A 97.059 34 1 0 4996 5029 683427036 683427003 2.110000e-04 58.4
14 TraesCS5A01G469200 chrUn 81.769 554 73 12 2800 3327 34342080 34342631 6.440000e-119 438.0
15 TraesCS5A01G469200 chr3B 81.769 554 73 12 2800 3327 5471286 5471837 6.440000e-119 438.0
16 TraesCS5A01G469200 chr3B 81.227 554 76 12 2800 3327 5487286 5486735 6.490000e-114 422.0
17 TraesCS5A01G469200 chr1B 81.655 556 70 14 2800 3327 684585998 684585447 3.000000e-117 433.0
18 TraesCS5A01G469200 chr6D 93.878 49 1 2 4980 5026 291239462 291239510 7.530000e-09 73.1


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 TraesCS5A01G469200 chr5A 646208525 646213943 5418 True 10008.000000 10008 100.000000 1 5419 1 chr5A.!!$R1 5418
1 TraesCS5A01G469200 chr5D 519649233 519654513 5280 True 3494.000000 5168 90.376000 6 5377 2 chr5D.!!$R2 5371
2 TraesCS5A01G469200 chr5B 654493180 654498630 5450 True 2294.666667 5086 89.542333 2 5377 3 chr5B.!!$R1 5375
3 TraesCS5A01G469200 chr7B 576427705 576428510 805 False 785.000000 785 84.920000 2746 3522 1 chr7B.!!$F1 776
4 TraesCS5A01G469200 chrUn 34342080 34342631 551 False 438.000000 438 81.769000 2800 3327 1 chrUn.!!$F1 527
5 TraesCS5A01G469200 chr3B 5471286 5471837 551 False 438.000000 438 81.769000 2800 3327 1 chr3B.!!$F1 527
6 TraesCS5A01G469200 chr3B 5486735 5487286 551 True 422.000000 422 81.227000 2800 3327 1 chr3B.!!$R1 527
7 TraesCS5A01G469200 chr1B 684585447 684585998 551 True 433.000000 433 81.655000 2800 3327 1 chr1B.!!$R1 527

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
939 979 0.451783 GCCGATTTTTCCATGAGCGT 59.548 50.000 0.00 0.0 0.00 5.07 F
1638 1701 0.035343 AGAGCCGCTTTAGGGTTTCC 60.035 55.000 0.00 0.0 42.85 3.13 F
1658 1721 1.931172 CCATTTAACCGACGGCAGTAG 59.069 52.381 15.39 0.0 0.00 2.57 F
2968 3049 1.605710 CAAAGCTGTTCTGTCACCCTG 59.394 52.381 0.00 0.0 0.00 4.45 F
3821 3961 0.460635 GGCCATGCATTTGTGCGAAT 60.461 50.000 0.00 0.0 37.69 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2303 2370 2.113860 TGCAGGCTCCAATGAACTAC 57.886 50.000 0.0 0.0 0.00 2.73 R
2852 2933 3.179048 GGCGAAAGAAACATATTGTGGC 58.821 45.455 0.0 0.0 0.00 5.01 R
3648 3771 1.806496 TGGCCTGCCAGTATAGACAT 58.194 50.000 6.8 0.0 41.89 3.06 R
4092 4237 0.168788 CGTACTTGCTGCCATTGTGG 59.831 55.000 0.0 0.0 41.55 4.17 R
5175 5477 0.250234 GCATCACCTCACCTGTGCTA 59.750 55.000 0.0 0.0 33.71 3.49 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
41 43 3.764885 GAAATGGTGGATTTCGACTGG 57.235 47.619 0.00 0.00 40.43 4.00
60 62 4.811024 ACTGGTCTATGTGTAAATGCATCG 59.189 41.667 0.00 0.00 0.00 3.84
61 63 4.765273 TGGTCTATGTGTAAATGCATCGT 58.235 39.130 0.00 0.00 0.00 3.73
62 64 5.908341 TGGTCTATGTGTAAATGCATCGTA 58.092 37.500 0.00 0.00 0.00 3.43
71 73 5.740569 GTGTAAATGCATCGTAGTTACTCGA 59.259 40.000 15.64 8.72 40.28 4.04
108 110 3.802948 AAGCAAATACTCGACCGATCT 57.197 42.857 0.00 0.00 0.00 2.75
111 113 2.971915 GCAAATACTCGACCGATCTACG 59.028 50.000 0.00 0.00 42.18 3.51
134 136 1.396648 CAAATGCATCGCCGTTACTCA 59.603 47.619 0.00 0.00 0.00 3.41
160 162 6.120157 CGTATACATATCACACAAGCAAACG 58.880 40.000 3.32 0.00 0.00 3.60
161 163 3.201726 ACATATCACACAAGCAAACGC 57.798 42.857 0.00 0.00 0.00 4.84
163 165 3.191162 ACATATCACACAAGCAAACGCAT 59.809 39.130 0.00 0.00 0.00 4.73
167 171 3.367607 TCACACAAGCAAACGCATAAAC 58.632 40.909 0.00 0.00 0.00 2.01
169 173 1.713404 CACAAGCAAACGCATAAACCG 59.287 47.619 0.00 0.00 0.00 4.44
173 177 1.341369 GCAAACGCATAAACCGCACC 61.341 55.000 0.00 0.00 0.00 5.01
184 188 2.125310 CCGCACCGCCATTACTCA 60.125 61.111 0.00 0.00 0.00 3.41
189 193 0.999406 CACCGCCATTACTCAACGAG 59.001 55.000 0.00 0.00 35.52 4.18
199 203 5.050769 CCATTACTCAACGAGCATATCACAC 60.051 44.000 0.00 0.00 32.04 3.82
200 204 3.592898 ACTCAACGAGCATATCACACA 57.407 42.857 0.00 0.00 32.04 3.72
212 216 1.227999 ATCACACACCTCAAACGGCG 61.228 55.000 4.80 4.80 0.00 6.46
217 221 0.953960 ACACCTCAAACGGCGAATCC 60.954 55.000 16.62 0.00 0.00 3.01
257 262 1.286501 GCATCGCCATTACTCGACAA 58.713 50.000 0.00 0.00 37.55 3.18
259 264 2.536928 GCATCGCCATTACTCGACAAAC 60.537 50.000 0.00 0.00 37.55 2.93
283 288 5.004630 CACATCACACAACAATCAACACAAC 59.995 40.000 0.00 0.00 0.00 3.32
287 292 5.985530 TCACACAACAATCAACACAACAAAA 59.014 32.000 0.00 0.00 0.00 2.44
293 298 7.040823 ACAACAATCAACACAACAAAACCAATT 60.041 29.630 0.00 0.00 0.00 2.32
294 299 7.071014 ACAATCAACACAACAAAACCAATTC 57.929 32.000 0.00 0.00 0.00 2.17
295 300 6.878389 ACAATCAACACAACAAAACCAATTCT 59.122 30.769 0.00 0.00 0.00 2.40
296 301 8.037758 ACAATCAACACAACAAAACCAATTCTA 58.962 29.630 0.00 0.00 0.00 2.10
299 304 7.831753 TCAACACAACAAAACCAATTCTAAGA 58.168 30.769 0.00 0.00 0.00 2.10
320 325 5.128919 AGAAGATTTGGATCTCAATTCCCG 58.871 41.667 11.77 0.00 41.78 5.14
321 326 3.825328 AGATTTGGATCTCAATTCCCGG 58.175 45.455 0.00 0.00 38.21 5.73
322 327 2.435372 TTTGGATCTCAATTCCCGGG 57.565 50.000 16.85 16.85 34.98 5.73
358 363 2.042639 ATCAATGGTGGGGGCTGC 60.043 61.111 0.00 0.00 0.00 5.25
360 365 3.384532 CAATGGTGGGGGCTGCAC 61.385 66.667 0.50 0.00 0.00 4.57
365 370 4.767255 GTGGGGGCTGCACGAGAG 62.767 72.222 0.50 0.00 0.00 3.20
405 415 1.614824 AGGCCTTGTGAGAGAGGGG 60.615 63.158 0.00 0.00 33.52 4.79
417 431 5.966935 TGTGAGAGAGGGGAGAGATATTTTT 59.033 40.000 0.00 0.00 0.00 1.94
491 509 2.725203 TTCGCCCACCAACTTCCTCG 62.725 60.000 0.00 0.00 0.00 4.63
493 511 2.750350 CCCACCAACTTCCTCGCT 59.250 61.111 0.00 0.00 0.00 4.93
661 684 4.838486 CGACCGCGTCTCTCCAGC 62.838 72.222 4.92 0.00 0.00 4.85
662 685 4.500116 GACCGCGTCTCTCCAGCC 62.500 72.222 4.92 0.00 0.00 4.85
753 788 2.562738 CCCCCTTTTCGAGCTCAAAATT 59.437 45.455 15.40 0.00 0.00 1.82
756 791 2.658325 CCTTTTCGAGCTCAAAATTGCG 59.342 45.455 15.40 7.64 0.00 4.85
775 810 0.653114 GGCTTTTCCGCTCGATTCTC 59.347 55.000 0.00 0.00 0.00 2.87
812 847 4.460263 CATTGATTTCCTCCGGTTATCCA 58.540 43.478 0.00 0.00 0.00 3.41
819 854 2.645797 TCCTCCGGTTATCCAAGGTTTT 59.354 45.455 0.00 0.00 37.49 2.43
830 865 3.935172 TCCAAGGTTTTCCCCTGATTTT 58.065 40.909 0.00 0.00 41.86 1.82
834 869 2.299013 AGGTTTTCCCCTGATTTTTCGC 59.701 45.455 0.00 0.00 41.86 4.70
939 979 0.451783 GCCGATTTTTCCATGAGCGT 59.548 50.000 0.00 0.00 0.00 5.07
1358 1410 2.014128 ACAATAACCCGTGCATAGTGC 58.986 47.619 0.00 0.00 45.29 4.40
1474 1532 3.096092 TCCAATCCAAACTAATGGGTGC 58.904 45.455 0.00 0.00 41.05 5.01
1508 1567 4.099573 AGTCCAGGAGTTATGTATCAACGG 59.900 45.833 0.00 0.00 0.00 4.44
1549 1608 8.931775 GTTGGTATGATTTTAATTTGTTCACCC 58.068 33.333 0.00 0.00 0.00 4.61
1567 1626 1.588082 CCCAACTGTGCCTGAATGC 59.412 57.895 0.00 0.00 0.00 3.56
1579 1642 2.503331 CCTGAATGCACAAGGTGTACA 58.497 47.619 0.00 0.00 35.75 2.90
1583 1646 4.006989 TGAATGCACAAGGTGTACATACC 58.993 43.478 0.00 0.00 33.49 2.73
1596 1659 5.416083 GTGTACATACCTACACAGCAATCA 58.584 41.667 0.00 0.00 44.11 2.57
1636 1699 0.690762 TGAGAGCCGCTTTAGGGTTT 59.309 50.000 0.00 0.00 42.85 3.27
1637 1700 1.338769 TGAGAGCCGCTTTAGGGTTTC 60.339 52.381 0.00 0.00 42.85 2.78
1638 1701 0.035343 AGAGCCGCTTTAGGGTTTCC 60.035 55.000 0.00 0.00 42.85 3.13
1658 1721 1.931172 CCATTTAACCGACGGCAGTAG 59.069 52.381 15.39 0.00 0.00 2.57
1669 1732 2.954318 GACGGCAGTAGTACCTCCAATA 59.046 50.000 0.00 0.00 0.00 1.90
1677 1740 7.178628 GGCAGTAGTACCTCCAATAATCTGATA 59.821 40.741 0.00 0.00 0.00 2.15
1779 1842 6.711579 TGTTTTAGTTTGCGTCTTGTTCTAG 58.288 36.000 0.00 0.00 0.00 2.43
1844 1907 7.593875 GTGTACAACACGGGTGTATATTAAA 57.406 36.000 4.68 0.00 44.13 1.52
1870 1933 8.907222 AAATAAAACCATTTTCATTCTGCTGT 57.093 26.923 0.00 0.00 34.19 4.40
2229 2293 6.377146 ACATTACTGTGCCTAATCCGATTTTT 59.623 34.615 0.00 0.00 33.22 1.94
2240 2304 6.150976 CCTAATCCGATTTTTGCATAGCCATA 59.849 38.462 0.00 0.00 0.00 2.74
2241 2305 6.594788 AATCCGATTTTTGCATAGCCATAT 57.405 33.333 0.00 0.00 0.00 1.78
2242 2306 7.701539 AATCCGATTTTTGCATAGCCATATA 57.298 32.000 0.00 0.00 0.00 0.86
2243 2307 7.701539 ATCCGATTTTTGCATAGCCATATAA 57.298 32.000 0.00 0.00 0.00 0.98
2244 2308 6.908825 TCCGATTTTTGCATAGCCATATAAC 58.091 36.000 0.00 0.00 0.00 1.89
2245 2309 6.714810 TCCGATTTTTGCATAGCCATATAACT 59.285 34.615 0.00 0.00 0.00 2.24
2246 2310 7.880713 TCCGATTTTTGCATAGCCATATAACTA 59.119 33.333 0.00 0.00 0.00 2.24
2247 2311 8.511321 CCGATTTTTGCATAGCCATATAACTAA 58.489 33.333 0.00 0.00 0.00 2.24
2248 2312 9.329913 CGATTTTTGCATAGCCATATAACTAAC 57.670 33.333 0.00 0.00 0.00 2.34
2254 2321 8.378172 TGCATAGCCATATAACTAACTGAAAC 57.622 34.615 0.00 0.00 0.00 2.78
2258 2325 9.726438 ATAGCCATATAACTAACTGAAACCATC 57.274 33.333 0.00 0.00 0.00 3.51
2276 2343 4.956075 ACCATCAGTTTTCTTGTGACCTTT 59.044 37.500 0.00 0.00 0.00 3.11
2524 2591 3.317993 GGTATGTGTGCTTGGACTGTTTT 59.682 43.478 0.00 0.00 0.00 2.43
2578 2646 7.221450 TCCTTTATTGTACACAGTAAGTTGCT 58.779 34.615 0.00 0.00 31.28 3.91
2580 2648 7.803189 CCTTTATTGTACACAGTAAGTTGCTTG 59.197 37.037 0.00 0.00 31.28 4.01
2582 2650 8.890124 TTATTGTACACAGTAAGTTGCTTGTA 57.110 30.769 0.00 9.95 0.00 2.41
2593 2661 5.689383 AAGTTGCTTGTATGTTGGTGTAG 57.311 39.130 0.00 0.00 0.00 2.74
2666 2741 9.586732 AACATGGGTACACATATATGCTTTAAT 57.413 29.630 11.03 0.00 0.00 1.40
2736 2811 4.552355 CAAGAGCATGTGCATTGAAAGAA 58.448 39.130 14.19 0.00 45.16 2.52
2750 2825 2.964464 TGAAAGAAAAGCATCTTGGCCA 59.036 40.909 0.00 0.00 39.54 5.36
2852 2933 6.086222 CACTTTATTCCCGTTCATGTTTCTG 58.914 40.000 0.00 0.00 0.00 3.02
2965 3046 2.288666 TGTCAAAGCTGTTCTGTCACC 58.711 47.619 0.00 0.00 0.00 4.02
2968 3049 1.605710 CAAAGCTGTTCTGTCACCCTG 59.394 52.381 0.00 0.00 0.00 4.45
2971 3052 2.047061 AGCTGTTCTGTCACCCTGTTA 58.953 47.619 0.00 0.00 0.00 2.41
3000 3081 9.556030 GCTTTTACAGTGTCCTAATAAATGTTC 57.444 33.333 0.00 0.00 0.00 3.18
3007 3090 6.149474 AGTGTCCTAATAAATGTTCTGTGTGC 59.851 38.462 0.00 0.00 0.00 4.57
3017 3100 2.672874 TGTTCTGTGTGCGCAGATAATC 59.327 45.455 12.22 0.00 43.99 1.75
3235 3347 9.928236 GAGTTGATGCTTGAAATTATACTTCTC 57.072 33.333 0.00 0.00 0.00 2.87
3269 3381 5.829924 CCACTTGATAATTTCCTGGCTGTAT 59.170 40.000 0.00 0.00 0.00 2.29
3581 3704 9.345517 CATTTTGTTACAGAATGATACCACTTG 57.654 33.333 19.72 0.00 37.92 3.16
3614 3737 7.554835 TGTTGTCTAGCAATTATAAAATCCCGT 59.445 33.333 3.47 0.00 39.55 5.28
3617 3740 7.936847 TGTCTAGCAATTATAAAATCCCGTGAT 59.063 33.333 0.00 0.00 0.00 3.06
3633 3756 4.568359 CCCGTGATTCTCAATGAGTTACAG 59.432 45.833 10.36 0.00 0.00 2.74
3653 3786 2.636893 AGCTCTCCTGTTTCACATGTCT 59.363 45.455 0.00 0.00 0.00 3.41
3693 3833 9.877178 ATTAGTAATGTCTCTTTACTGGACAAG 57.123 33.333 14.15 0.00 42.14 3.16
3726 3866 5.458891 ACTGCTAAAGTAACAGTACTGTCG 58.541 41.667 28.04 11.71 44.13 4.35
3749 3889 5.853282 CGATGTTTTGAAGTCTTGGCTAAAG 59.147 40.000 0.00 0.00 37.22 1.85
3760 3900 4.154195 GTCTTGGCTAAAGAAATCGCTTGA 59.846 41.667 4.29 0.00 46.51 3.02
3772 3912 3.791973 ATCGCTTGACTACCTGAAGAG 57.208 47.619 0.00 0.00 0.00 2.85
3774 3914 2.488545 TCGCTTGACTACCTGAAGAGTC 59.511 50.000 0.00 0.00 42.08 3.36
3782 3922 7.718334 TGACTACCTGAAGAGTCAATGATAA 57.282 36.000 2.34 0.00 46.93 1.75
3790 3930 9.918630 CCTGAAGAGTCAATGATAACAAAATTT 57.081 29.630 0.00 0.00 31.88 1.82
3807 3947 6.546772 ACAAAATTTTGAGACAAAATGGCCAT 59.453 30.769 32.20 14.09 40.55 4.40
3821 3961 0.460635 GGCCATGCATTTGTGCGAAT 60.461 50.000 0.00 0.00 37.69 3.34
3824 3964 2.928757 GCCATGCATTTGTGCGAATAAA 59.071 40.909 0.00 0.00 37.69 1.40
3825 3965 3.370366 GCCATGCATTTGTGCGAATAAAA 59.630 39.130 0.00 0.00 37.69 1.52
3826 3966 4.492895 GCCATGCATTTGTGCGAATAAAAG 60.493 41.667 0.00 0.00 37.69 2.27
3827 3967 4.033129 CCATGCATTTGTGCGAATAAAAGG 59.967 41.667 0.00 0.00 37.69 3.11
3828 3968 2.992543 TGCATTTGTGCGAATAAAAGGC 59.007 40.909 4.68 4.68 40.10 4.35
3829 3969 3.253230 GCATTTGTGCGAATAAAAGGCT 58.747 40.909 4.45 0.00 37.55 4.58
3830 3970 3.679502 GCATTTGTGCGAATAAAAGGCTT 59.320 39.130 0.00 0.00 37.55 4.35
3831 3971 4.152223 GCATTTGTGCGAATAAAAGGCTTT 59.848 37.500 6.68 6.68 37.55 3.51
3832 3972 5.610975 CATTTGTGCGAATAAAAGGCTTTG 58.389 37.500 14.19 1.35 0.00 2.77
3835 3975 4.295051 TGTGCGAATAAAAGGCTTTGTTC 58.705 39.130 14.19 18.04 38.57 3.18
3836 3976 4.037446 TGTGCGAATAAAAGGCTTTGTTCT 59.963 37.500 24.06 10.57 39.33 3.01
3837 3977 4.382754 GTGCGAATAAAAGGCTTTGTTCTG 59.617 41.667 24.06 19.98 39.33 3.02
3839 3979 5.239744 TGCGAATAAAAGGCTTTGTTCTGTA 59.760 36.000 24.06 17.72 39.33 2.74
3841 3981 7.119992 TGCGAATAAAAGGCTTTGTTCTGTATA 59.880 33.333 24.06 10.11 39.33 1.47
3848 3988 8.525290 AAAGGCTTTGTTCTGTATATTATGCT 57.475 30.769 12.53 0.00 0.00 3.79
3849 3989 8.525290 AAGGCTTTGTTCTGTATATTATGCTT 57.475 30.769 0.00 0.00 0.00 3.91
3850 3990 8.525290 AGGCTTTGTTCTGTATATTATGCTTT 57.475 30.769 0.00 0.00 0.00 3.51
3851 3991 8.624776 AGGCTTTGTTCTGTATATTATGCTTTC 58.375 33.333 0.00 0.00 0.00 2.62
3852 3992 8.405531 GGCTTTGTTCTGTATATTATGCTTTCA 58.594 33.333 0.00 0.00 0.00 2.69
3853 3993 9.956720 GCTTTGTTCTGTATATTATGCTTTCAT 57.043 29.630 0.00 0.00 36.73 2.57
3856 3996 8.394971 TGTTCTGTATATTATGCTTTCATGGG 57.605 34.615 0.00 0.00 34.22 4.00
3857 3997 8.217111 TGTTCTGTATATTATGCTTTCATGGGA 58.783 33.333 0.00 0.00 34.22 4.37
3858 3998 8.725148 GTTCTGTATATTATGCTTTCATGGGAG 58.275 37.037 0.00 0.00 34.22 4.30
3859 3999 6.881065 TCTGTATATTATGCTTTCATGGGAGC 59.119 38.462 12.51 12.51 39.33 4.70
3866 4006 4.025040 TGCTTTCATGGGAGCATATAGG 57.975 45.455 16.61 0.00 43.46 2.57
3867 4007 3.395607 TGCTTTCATGGGAGCATATAGGT 59.604 43.478 16.61 0.00 43.46 3.08
3868 4008 4.597075 TGCTTTCATGGGAGCATATAGGTA 59.403 41.667 16.61 0.00 43.46 3.08
3869 4009 4.938226 GCTTTCATGGGAGCATATAGGTAC 59.062 45.833 13.98 0.00 38.73 3.34
3874 4014 2.541466 GGGAGCATATAGGTACCTGCT 58.459 52.381 25.33 23.76 45.80 4.24
3877 4017 3.260269 AGCATATAGGTACCTGCTCCA 57.740 47.619 25.33 3.93 40.85 3.86
3878 4018 3.796111 AGCATATAGGTACCTGCTCCAT 58.204 45.455 25.33 11.87 40.85 3.41
3879 4019 4.171234 AGCATATAGGTACCTGCTCCATT 58.829 43.478 25.33 0.79 40.85 3.16
3880 4020 4.019860 AGCATATAGGTACCTGCTCCATTG 60.020 45.833 25.33 12.35 40.85 2.82
3881 4021 2.938956 ATAGGTACCTGCTCCATTGC 57.061 50.000 25.33 0.00 0.00 3.56
3882 4022 1.578897 TAGGTACCTGCTCCATTGCA 58.421 50.000 25.33 0.00 41.05 4.08
3883 4023 0.921896 AGGTACCTGCTCCATTGCAT 59.078 50.000 15.42 0.00 42.48 3.96
3884 4024 2.126882 AGGTACCTGCTCCATTGCATA 58.873 47.619 15.42 0.00 42.48 3.14
3885 4025 2.713167 AGGTACCTGCTCCATTGCATAT 59.287 45.455 15.42 0.00 42.48 1.78
3886 4026 2.816087 GGTACCTGCTCCATTGCATATG 59.184 50.000 4.06 0.00 42.48 1.78
3887 4027 1.325355 ACCTGCTCCATTGCATATGC 58.675 50.000 21.09 21.09 42.48 3.14
3901 4041 4.644103 GCATATGCATGGTTTCAACTCT 57.356 40.909 22.84 0.00 41.59 3.24
3902 4042 5.756195 GCATATGCATGGTTTCAACTCTA 57.244 39.130 22.84 0.00 41.59 2.43
3903 4043 6.323203 GCATATGCATGGTTTCAACTCTAT 57.677 37.500 22.84 0.00 41.59 1.98
3904 4044 6.147581 GCATATGCATGGTTTCAACTCTATG 58.852 40.000 22.84 1.08 41.59 2.23
3905 4045 6.016860 GCATATGCATGGTTTCAACTCTATGA 60.017 38.462 22.84 0.00 41.59 2.15
3906 4046 7.469043 GCATATGCATGGTTTCAACTCTATGAA 60.469 37.037 22.84 0.00 41.59 2.57
3907 4047 5.627499 TGCATGGTTTCAACTCTATGAAC 57.373 39.130 0.00 0.00 38.95 3.18
3908 4048 5.069318 TGCATGGTTTCAACTCTATGAACA 58.931 37.500 0.00 0.00 38.95 3.18
3909 4049 5.048782 TGCATGGTTTCAACTCTATGAACAC 60.049 40.000 0.00 0.00 38.95 3.32
3910 4050 5.048782 GCATGGTTTCAACTCTATGAACACA 60.049 40.000 0.00 0.00 38.95 3.72
3911 4051 6.373779 CATGGTTTCAACTCTATGAACACAC 58.626 40.000 0.00 0.00 38.95 3.82
3912 4052 4.819630 TGGTTTCAACTCTATGAACACACC 59.180 41.667 0.00 0.00 38.95 4.16
3913 4053 4.819630 GGTTTCAACTCTATGAACACACCA 59.180 41.667 5.09 0.00 38.95 4.17
3914 4054 5.277828 GGTTTCAACTCTATGAACACACCAC 60.278 44.000 5.09 0.00 38.95 4.16
3915 4055 4.955811 TCAACTCTATGAACACACCACT 57.044 40.909 0.00 0.00 0.00 4.00
3916 4056 4.631131 TCAACTCTATGAACACACCACTG 58.369 43.478 0.00 0.00 0.00 3.66
3917 4057 4.100963 TCAACTCTATGAACACACCACTGT 59.899 41.667 0.00 0.00 0.00 3.55
3918 4058 5.303333 TCAACTCTATGAACACACCACTGTA 59.697 40.000 0.00 0.00 0.00 2.74
3919 4059 5.801531 ACTCTATGAACACACCACTGTAA 57.198 39.130 0.00 0.00 0.00 2.41
3920 4060 5.539048 ACTCTATGAACACACCACTGTAAC 58.461 41.667 0.00 0.00 0.00 2.50
3925 4065 5.303747 TGAACACACCACTGTAACTTTTG 57.696 39.130 0.00 0.00 0.00 2.44
3935 4075 6.655848 ACCACTGTAACTTTTGACACTGTTAA 59.344 34.615 0.00 0.00 0.00 2.01
3948 4092 9.710979 TTTGACACTGTTAATTTCTAAGAAACG 57.289 29.630 0.00 0.00 0.00 3.60
3949 4093 7.349711 TGACACTGTTAATTTCTAAGAAACGC 58.650 34.615 0.00 0.00 0.00 4.84
3950 4094 7.225931 TGACACTGTTAATTTCTAAGAAACGCT 59.774 33.333 0.00 0.00 0.00 5.07
3985 4129 7.308348 CCAACAAACGAACTGGTCATAGTTTAT 60.308 37.037 0.00 0.00 40.78 1.40
3986 4130 7.739498 ACAAACGAACTGGTCATAGTTTATT 57.261 32.000 0.00 0.00 40.78 1.40
3987 4131 8.161699 ACAAACGAACTGGTCATAGTTTATTT 57.838 30.769 0.00 0.00 40.78 1.40
3988 4132 8.626526 ACAAACGAACTGGTCATAGTTTATTTT 58.373 29.630 0.00 0.00 40.78 1.82
3991 4135 8.260270 ACGAACTGGTCATAGTTTATTTTACC 57.740 34.615 0.00 0.00 40.78 2.85
4020 4164 6.267471 TCAAGGGATGTTTGAGCATAAACTTT 59.733 34.615 14.34 5.09 40.36 2.66
4065 4210 8.421249 TTTGACACTATTTTCATTGGAATCCT 57.579 30.769 0.00 0.00 31.93 3.24
4093 4238 8.753497 AATCTTACCCATATTTTCTCTTGTCC 57.247 34.615 0.00 0.00 0.00 4.02
4096 4241 5.255397 ACCCATATTTTCTCTTGTCCACA 57.745 39.130 0.00 0.00 0.00 4.17
4154 4299 2.185350 CAGGAGCTCGCGTCCATT 59.815 61.111 15.70 0.00 36.43 3.16
4226 4371 4.166888 ATCCGCATGCTGGACGCT 62.167 61.111 26.26 13.18 38.60 5.07
4263 4408 4.410400 CACCACCCCCTTCGGAGC 62.410 72.222 0.00 0.00 0.00 4.70
4264 4409 4.974438 ACCACCCCCTTCGGAGCA 62.974 66.667 0.00 0.00 0.00 4.26
4397 4542 0.889186 TGTTTGCCTCGAAGAAGGGC 60.889 55.000 5.71 5.71 45.45 5.19
4425 4570 3.654020 GGAAGGCATGATCCGCGC 61.654 66.667 0.00 0.00 0.00 6.86
4586 4739 6.302313 GTGTTTTGATGATACGGACGAAAAAG 59.698 38.462 0.00 0.00 0.00 2.27
4693 4848 3.766545 TCCAATCCCCTCTTGTTTTCAG 58.233 45.455 0.00 0.00 0.00 3.02
4697 4859 5.163311 CCAATCCCCTCTTGTTTTCAGTTTT 60.163 40.000 0.00 0.00 0.00 2.43
4822 4986 8.600449 TGATTACATTGTTGGGATTTTCAAAC 57.400 30.769 0.00 0.00 0.00 2.93
4896 5064 5.215252 TCCCTGAACAGAAAGTTACTCAG 57.785 43.478 3.19 0.00 41.51 3.35
4935 5103 8.978874 TGCAGTAGTTGATATTTGTTGGATAT 57.021 30.769 0.00 0.00 0.00 1.63
4978 5146 3.981071 TGTCAATCCCAGTGGACTAAG 57.019 47.619 11.95 0.00 45.58 2.18
4994 5162 5.136105 GGACTAAGAAATACTCCCTCCGTA 58.864 45.833 0.00 0.00 0.00 4.02
4996 5164 4.892345 ACTAAGAAATACTCCCTCCGTACC 59.108 45.833 0.00 0.00 0.00 3.34
4997 5165 3.393426 AGAAATACTCCCTCCGTACCA 57.607 47.619 0.00 0.00 0.00 3.25
4998 5166 3.924922 AGAAATACTCCCTCCGTACCAT 58.075 45.455 0.00 0.00 0.00 3.55
5000 5168 5.078256 AGAAATACTCCCTCCGTACCATAG 58.922 45.833 0.00 0.00 0.00 2.23
5003 5171 5.793034 ATACTCCCTCCGTACCATAGTAT 57.207 43.478 0.00 0.00 0.00 2.12
5004 5172 6.898171 ATACTCCCTCCGTACCATAGTATA 57.102 41.667 0.00 0.00 29.35 1.47
5005 5173 5.589367 ACTCCCTCCGTACCATAGTATAA 57.411 43.478 0.00 0.00 0.00 0.98
5007 5175 5.311649 ACTCCCTCCGTACCATAGTATAAGA 59.688 44.000 0.00 0.00 0.00 2.10
5008 5176 5.813383 TCCCTCCGTACCATAGTATAAGAG 58.187 45.833 0.00 0.00 0.00 2.85
5009 5177 4.398673 CCCTCCGTACCATAGTATAAGAGC 59.601 50.000 0.00 0.00 0.00 4.09
5011 5179 4.645535 TCCGTACCATAGTATAAGAGCGT 58.354 43.478 0.00 0.00 0.00 5.07
5012 5180 5.065914 TCCGTACCATAGTATAAGAGCGTT 58.934 41.667 0.00 0.00 0.00 4.84
5013 5181 5.532406 TCCGTACCATAGTATAAGAGCGTTT 59.468 40.000 0.00 0.00 0.00 3.60
5014 5182 6.039717 TCCGTACCATAGTATAAGAGCGTTTT 59.960 38.462 0.00 0.00 0.00 2.43
5015 5183 6.698766 CCGTACCATAGTATAAGAGCGTTTTT 59.301 38.462 0.00 0.00 0.00 1.94
5016 5184 7.306399 CCGTACCATAGTATAAGAGCGTTTTTG 60.306 40.741 0.00 0.00 0.00 2.44
5017 5185 7.433131 CGTACCATAGTATAAGAGCGTTTTTGA 59.567 37.037 0.00 0.00 0.00 2.69
5018 5186 7.535489 ACCATAGTATAAGAGCGTTTTTGAC 57.465 36.000 0.00 0.00 0.00 3.18
5020 5188 7.064253 ACCATAGTATAAGAGCGTTTTTGACAC 59.936 37.037 0.00 0.00 0.00 3.67
5021 5189 7.277981 CCATAGTATAAGAGCGTTTTTGACACT 59.722 37.037 0.00 0.00 0.00 3.55
5022 5190 9.297586 CATAGTATAAGAGCGTTTTTGACACTA 57.702 33.333 0.00 0.00 0.00 2.74
5024 5192 8.015409 AGTATAAGAGCGTTTTTGACACTAAC 57.985 34.615 0.00 0.00 0.00 2.34
5025 5193 7.871463 AGTATAAGAGCGTTTTTGACACTAACT 59.129 33.333 0.00 0.00 0.00 2.24
5026 5194 5.405331 AAGAGCGTTTTTGACACTAACTC 57.595 39.130 0.00 0.00 0.00 3.01
5027 5195 4.694339 AGAGCGTTTTTGACACTAACTCT 58.306 39.130 0.00 0.00 0.00 3.24
5028 5196 4.745620 AGAGCGTTTTTGACACTAACTCTC 59.254 41.667 9.34 9.34 35.13 3.20
5030 5198 4.873827 AGCGTTTTTGACACTAACTCTCAA 59.126 37.500 0.00 0.00 0.00 3.02
5097 5399 9.391006 GAACCTTATACAATACAAAGATGTCCA 57.609 33.333 0.00 0.00 41.05 4.02
5099 5401 9.747898 ACCTTATACAATACAAAGATGTCCAAA 57.252 29.630 0.00 0.00 41.05 3.28
5117 5419 9.696917 ATGTCCAAACTCAAGTTATTTCAAATC 57.303 29.630 0.00 0.00 37.25 2.17
5174 5476 9.695884 TTATTTCAGCATTTTTGAAAACGAAAC 57.304 25.926 4.73 0.00 44.83 2.78
5175 5477 6.959671 TTCAGCATTTTTGAAAACGAAACT 57.040 29.167 0.00 0.00 31.98 2.66
5245 5547 1.971695 CCCGGTCAGCAAACCTTCC 60.972 63.158 0.00 0.00 37.15 3.46
5249 5551 1.971695 GTCAGCAAACCTTCCCCCG 60.972 63.158 0.00 0.00 0.00 5.73
5250 5552 3.373565 CAGCAAACCTTCCCCCGC 61.374 66.667 0.00 0.00 0.00 6.13
5251 5553 3.897122 AGCAAACCTTCCCCCGCA 61.897 61.111 0.00 0.00 0.00 5.69
5253 5555 3.361977 CAAACCTTCCCCCGCACG 61.362 66.667 0.00 0.00 0.00 5.34
5254 5556 4.653888 AAACCTTCCCCCGCACGG 62.654 66.667 1.02 1.02 0.00 4.94
5401 5703 4.065281 CGACGCCGTCCCTTTCCT 62.065 66.667 12.26 0.00 0.00 3.36
5402 5704 2.125633 GACGCCGTCCCTTTCCTC 60.126 66.667 5.81 0.00 0.00 3.71
5403 5705 3.660732 GACGCCGTCCCTTTCCTCC 62.661 68.421 5.81 0.00 0.00 4.30
5404 5706 4.814294 CGCCGTCCCTTTCCTCCG 62.814 72.222 0.00 0.00 0.00 4.63
5405 5707 4.468689 GCCGTCCCTTTCCTCCGG 62.469 72.222 0.00 0.00 41.50 5.14
5406 5708 4.468689 CCGTCCCTTTCCTCCGGC 62.469 72.222 0.00 0.00 0.00 6.13
5407 5709 3.702048 CGTCCCTTTCCTCCGGCA 61.702 66.667 0.00 0.00 0.00 5.69
5408 5710 2.046217 GTCCCTTTCCTCCGGCAC 60.046 66.667 0.00 0.00 0.00 5.01
5409 5711 3.327404 TCCCTTTCCTCCGGCACC 61.327 66.667 0.00 0.00 0.00 5.01
5410 5712 3.646715 CCCTTTCCTCCGGCACCA 61.647 66.667 0.00 0.00 0.00 4.17
5411 5713 2.359975 CCTTTCCTCCGGCACCAC 60.360 66.667 0.00 0.00 0.00 4.16
5412 5714 2.359975 CTTTCCTCCGGCACCACC 60.360 66.667 0.00 0.00 0.00 4.61
5413 5715 3.172106 TTTCCTCCGGCACCACCA 61.172 61.111 0.00 0.00 39.03 4.17
5414 5716 3.485346 TTTCCTCCGGCACCACCAC 62.485 63.158 0.00 0.00 39.03 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.081804 ACCAGTCGAAATCCACCATTTC 58.918 45.455 0.00 0.00 45.01 2.17
28 30 3.513912 ACACATAGACCAGTCGAAATCCA 59.486 43.478 0.00 0.00 34.09 3.41
30 32 7.621991 CATTTACACATAGACCAGTCGAAATC 58.378 38.462 0.00 0.00 34.09 2.17
39 41 4.765273 ACGATGCATTTACACATAGACCA 58.235 39.130 0.00 0.00 0.00 4.02
41 43 7.464830 AACTACGATGCATTTACACATAGAC 57.535 36.000 0.00 0.00 0.00 2.59
60 62 6.954852 GCGATATGTATCTGTCGAGTAACTAC 59.045 42.308 0.00 0.00 36.25 2.73
61 63 6.183360 CGCGATATGTATCTGTCGAGTAACTA 60.183 42.308 0.00 0.00 36.25 2.24
62 64 5.389620 CGCGATATGTATCTGTCGAGTAACT 60.390 44.000 0.00 0.00 36.25 2.24
71 73 4.499037 TGCTTACGCGATATGTATCTGT 57.501 40.909 15.93 0.00 39.65 3.41
97 99 0.098200 TTGTGCGTAGATCGGTCGAG 59.902 55.000 10.36 0.00 40.26 4.04
101 103 1.006832 GCATTTGTGCGTAGATCGGT 58.993 50.000 0.00 0.00 40.26 4.69
108 110 1.427419 GGCGATGCATTTGTGCGTA 59.573 52.632 0.00 0.00 37.69 4.42
111 113 0.179176 TAACGGCGATGCATTTGTGC 60.179 50.000 16.62 3.04 0.00 4.57
134 136 7.461107 GTTTGCTTGTGTGATATGTATACGTT 58.539 34.615 2.23 0.00 0.00 3.99
137 139 5.901884 GCGTTTGCTTGTGTGATATGTATAC 59.098 40.000 0.00 0.00 38.39 1.47
138 140 5.582665 TGCGTTTGCTTGTGTGATATGTATA 59.417 36.000 0.00 0.00 43.34 1.47
160 162 2.278182 AATGGCGGTGCGGTTTATGC 62.278 55.000 0.00 0.00 0.00 3.14
161 163 1.018148 TAATGGCGGTGCGGTTTATG 58.982 50.000 0.00 0.00 0.00 1.90
163 165 0.036199 AGTAATGGCGGTGCGGTTTA 60.036 50.000 0.00 0.00 0.00 2.01
167 171 1.743623 TTGAGTAATGGCGGTGCGG 60.744 57.895 0.00 0.00 0.00 5.69
169 173 1.017177 TCGTTGAGTAATGGCGGTGC 61.017 55.000 0.00 0.00 0.00 5.01
173 177 1.290203 ATGCTCGTTGAGTAATGGCG 58.710 50.000 0.00 0.00 31.39 5.69
184 188 2.233676 TGAGGTGTGTGATATGCTCGTT 59.766 45.455 0.00 0.00 0.00 3.85
189 193 2.095853 CCGTTTGAGGTGTGTGATATGC 59.904 50.000 0.00 0.00 0.00 3.14
199 203 1.644786 GGGATTCGCCGTTTGAGGTG 61.645 60.000 0.00 0.00 42.87 4.00
200 204 1.376812 GGGATTCGCCGTTTGAGGT 60.377 57.895 0.00 0.00 37.63 3.85
212 216 1.679680 TGTGTAGATCGGTCGGGATTC 59.320 52.381 0.00 0.00 0.00 2.52
217 221 2.357327 TTTGTGTGTAGATCGGTCGG 57.643 50.000 0.00 0.00 0.00 4.79
220 224 3.052455 TGCATTTGTGTGTAGATCGGT 57.948 42.857 0.00 0.00 0.00 4.69
223 227 3.546815 GGCGATGCATTTGTGTGTAGATC 60.547 47.826 0.00 0.00 0.00 2.75
257 262 5.101628 GTGTTGATTGTTGTGTGATGTGTT 58.898 37.500 0.00 0.00 0.00 3.32
259 264 4.670347 TGTGTTGATTGTTGTGTGATGTG 58.330 39.130 0.00 0.00 0.00 3.21
293 298 7.995488 GGGAATTGAGATCCAAATCTTCTTAGA 59.005 37.037 10.11 0.00 42.46 2.10
294 299 7.041508 CGGGAATTGAGATCCAAATCTTCTTAG 60.042 40.741 10.11 0.00 42.46 2.18
295 300 6.767902 CGGGAATTGAGATCCAAATCTTCTTA 59.232 38.462 10.11 0.00 42.46 2.10
296 301 5.591877 CGGGAATTGAGATCCAAATCTTCTT 59.408 40.000 10.11 0.00 42.46 2.52
299 304 4.210331 CCGGGAATTGAGATCCAAATCTT 58.790 43.478 0.00 0.00 42.46 2.40
358 363 2.156098 GTCCTCCTATAGGCTCTCGTG 58.844 57.143 14.50 0.00 46.10 4.35
360 365 1.074084 TGGTCCTCCTATAGGCTCTCG 59.926 57.143 14.50 0.00 46.10 4.04
362 367 2.225496 CCATGGTCCTCCTATAGGCTCT 60.225 54.545 14.50 0.00 46.10 4.09
363 368 2.183679 CCATGGTCCTCCTATAGGCTC 58.816 57.143 14.50 4.17 46.10 4.70
364 369 1.509961 ACCATGGTCCTCCTATAGGCT 59.490 52.381 13.00 0.00 46.10 4.58
365 370 1.625818 CACCATGGTCCTCCTATAGGC 59.374 57.143 16.53 0.00 46.10 3.93
366 371 2.158158 TCCACCATGGTCCTCCTATAGG 60.158 54.545 16.53 13.07 40.89 2.57
367 372 3.169099 CTCCACCATGGTCCTCCTATAG 58.831 54.545 16.53 0.00 39.03 1.31
368 373 2.158158 CCTCCACCATGGTCCTCCTATA 60.158 54.545 16.53 0.00 39.03 1.31
369 374 1.415126 CCTCCACCATGGTCCTCCTAT 60.415 57.143 16.53 0.00 39.03 2.57
370 375 0.031111 CCTCCACCATGGTCCTCCTA 60.031 60.000 16.53 0.00 39.03 2.94
491 509 2.893449 GCGCGGGGTATAAAGCAGC 61.893 63.158 8.83 0.00 0.00 5.25
493 511 1.401318 TAGGCGCGGGGTATAAAGCA 61.401 55.000 8.83 0.00 0.00 3.91
654 677 0.620700 GGAAACCCTAGGGCTGGAGA 60.621 60.000 28.88 0.00 39.32 3.71
655 678 1.915983 GGAAACCCTAGGGCTGGAG 59.084 63.158 28.88 3.00 39.32 3.86
658 681 2.124695 GCGGAAACCCTAGGGCTG 60.125 66.667 28.88 17.34 39.32 4.85
661 684 2.743179 GGAGGCGGAAACCCTAGGG 61.743 68.421 27.36 27.36 42.03 3.53
662 685 1.687297 GAGGAGGCGGAAACCCTAGG 61.687 65.000 0.06 0.06 32.01 3.02
689 712 2.737180 CCGCGTGGAGATGGCTAT 59.263 61.111 10.20 0.00 37.49 2.97
690 713 4.221422 GCCGCGTGGAGATGGCTA 62.221 66.667 21.76 0.00 44.16 3.93
737 772 2.660490 CCGCAATTTTGAGCTCGAAAA 58.340 42.857 28.54 23.42 33.36 2.29
741 776 0.109597 AAGCCGCAATTTTGAGCTCG 60.110 50.000 9.64 0.00 38.04 5.03
742 777 2.070262 AAAGCCGCAATTTTGAGCTC 57.930 45.000 6.82 6.82 38.04 4.09
756 791 0.653114 GAGAATCGAGCGGAAAAGCC 59.347 55.000 0.00 0.00 38.01 4.35
770 805 1.227263 CCGATTCGTGCCCGAGAAT 60.227 57.895 5.20 0.00 45.24 2.40
812 847 3.244078 GCGAAAAATCAGGGGAAAACCTT 60.244 43.478 0.00 0.00 39.34 3.50
819 854 2.043980 GCCGCGAAAAATCAGGGGA 61.044 57.895 8.23 0.00 39.96 4.81
852 887 4.473520 AGCACCAATCGCCTCGGG 62.474 66.667 0.00 0.00 0.00 5.14
1358 1410 4.201851 CCTTCGGCTGAAACATGTATGAAG 60.202 45.833 9.73 5.38 32.66 3.02
1474 1532 5.712152 AACTCCTGGACTTTTTGCAATAG 57.288 39.130 0.00 3.62 0.00 1.73
1508 1567 2.830293 ACCAACTCTTACCCCCTACTC 58.170 52.381 0.00 0.00 0.00 2.59
1549 1608 1.180456 TGCATTCAGGCACAGTTGGG 61.180 55.000 0.00 0.00 39.25 4.12
1579 1642 3.912496 TGCTGATTGCTGTGTAGGTAT 57.088 42.857 0.00 0.00 43.37 2.73
1583 1646 5.756950 CAATTTTGCTGATTGCTGTGTAG 57.243 39.130 0.00 0.00 43.37 2.74
1636 1699 0.391927 CTGCCGTCGGTTAAATGGGA 60.392 55.000 13.94 0.00 0.00 4.37
1637 1700 0.675522 ACTGCCGTCGGTTAAATGGG 60.676 55.000 13.94 0.00 0.00 4.00
1638 1701 1.931172 CTACTGCCGTCGGTTAAATGG 59.069 52.381 13.94 0.00 33.08 3.16
1646 1709 1.722636 GGAGGTACTACTGCCGTCGG 61.723 65.000 6.99 6.99 41.55 4.79
1677 1740 7.442062 GGCATGGCTAAATTAAGCACAAAATAT 59.558 33.333 12.86 0.00 44.64 1.28
1698 1761 7.774536 CAGATATCTGCAACATGCTGGCATG 62.775 48.000 27.38 27.38 46.02 4.06
1713 1776 6.127111 ACCATAGCAGGAATAGCAGATATCTG 60.127 42.308 25.64 25.64 46.40 2.90
1779 1842 4.997395 TGAGAATGGACTCTTTGCAAGTAC 59.003 41.667 0.00 0.00 37.73 2.73
1820 1883 7.593875 TTTAATATACACCCGTGTTGTACAC 57.406 36.000 5.69 0.00 45.26 2.90
1844 1907 9.341078 ACAGCAGAATGAAAATGGTTTTATTTT 57.659 25.926 0.00 0.00 41.55 1.82
1861 1924 7.889469 AGAACATCAACAATTAACAGCAGAAT 58.111 30.769 0.00 0.00 0.00 2.40
1870 1933 8.681806 TCAACTTGTGAGAACATCAACAATTAA 58.318 29.630 0.00 0.00 40.43 1.40
1961 2024 2.966050 TGGACAAAGCAAAACCACAAC 58.034 42.857 0.00 0.00 0.00 3.32
1962 2025 3.055530 ACATGGACAAAGCAAAACCACAA 60.056 39.130 0.00 0.00 33.38 3.33
2229 2293 7.444183 GGTTTCAGTTAGTTATATGGCTATGCA 59.556 37.037 0.00 0.00 0.00 3.96
2249 2313 5.163561 GGTCACAAGAAAACTGATGGTTTCA 60.164 40.000 8.89 0.00 46.18 2.69
2250 2314 5.067805 AGGTCACAAGAAAACTGATGGTTTC 59.932 40.000 0.00 0.00 46.18 2.78
2254 2321 5.520376 AAAGGTCACAAGAAAACTGATGG 57.480 39.130 0.00 0.00 0.00 3.51
2258 2325 6.528072 GTGAGAAAAAGGTCACAAGAAAACTG 59.472 38.462 0.00 0.00 42.31 3.16
2260 2327 6.871044 GTGAGAAAAAGGTCACAAGAAAAC 57.129 37.500 0.00 0.00 42.31 2.43
2303 2370 2.113860 TGCAGGCTCCAATGAACTAC 57.886 50.000 0.00 0.00 0.00 2.73
2304 2371 2.618816 CCTTGCAGGCTCCAATGAACTA 60.619 50.000 0.00 0.00 0.00 2.24
2524 2591 4.365514 TGGAGATGCAACAGGAAAAGTA 57.634 40.909 0.00 0.00 0.00 2.24
2552 2620 7.717875 AGCAACTTACTGTGTACAATAAAGGAA 59.282 33.333 0.00 0.00 0.00 3.36
2553 2621 7.221450 AGCAACTTACTGTGTACAATAAAGGA 58.779 34.615 0.00 0.00 0.00 3.36
2554 2622 7.435068 AGCAACTTACTGTGTACAATAAAGG 57.565 36.000 0.00 0.00 0.00 3.11
2555 2623 8.342634 ACAAGCAACTTACTGTGTACAATAAAG 58.657 33.333 0.00 2.18 0.00 1.85
2557 2625 7.795482 ACAAGCAACTTACTGTGTACAATAA 57.205 32.000 0.00 0.00 0.00 1.40
2558 2626 8.931775 CATACAAGCAACTTACTGTGTACAATA 58.068 33.333 0.00 0.00 0.00 1.90
2559 2627 7.444183 ACATACAAGCAACTTACTGTGTACAAT 59.556 33.333 0.00 0.00 0.00 2.71
2560 2628 6.764085 ACATACAAGCAACTTACTGTGTACAA 59.236 34.615 0.00 0.00 0.00 2.41
2561 2629 6.285224 ACATACAAGCAACTTACTGTGTACA 58.715 36.000 0.00 0.00 0.00 2.90
2564 2632 5.008613 CCAACATACAAGCAACTTACTGTGT 59.991 40.000 0.00 0.00 0.00 3.72
2567 2635 5.008613 ACACCAACATACAAGCAACTTACTG 59.991 40.000 0.00 0.00 0.00 2.74
2636 2710 6.265196 AGCATATATGTGTACCCATGTTTTGG 59.735 38.462 14.14 0.00 46.00 3.28
2666 2741 8.514594 CCTGATACAATTTCTTAGCTTTGAACA 58.485 33.333 0.00 0.00 0.00 3.18
2736 2811 4.088634 TGATTAACTGGCCAAGATGCTTT 58.911 39.130 7.01 0.00 0.00 3.51
2852 2933 3.179048 GGCGAAAGAAACATATTGTGGC 58.821 45.455 0.00 0.00 0.00 5.01
2965 3046 5.473504 AGGACACTGTAAAAGCATTAACAGG 59.526 40.000 12.13 5.67 42.95 4.00
3007 3090 4.551603 GCAGTAAGCAACAGATTATCTGCG 60.552 45.833 20.82 13.69 45.15 5.18
3235 3347 6.980397 GGAAATTATCAAGTGGGCATACAAAG 59.020 38.462 0.00 0.00 0.00 2.77
3269 3381 5.932303 CCCGAAATCAGTGAACTCTAGAAAA 59.068 40.000 0.00 0.00 0.00 2.29
3330 3447 4.093998 CAGGTTTTGGAATCACAGAGATCG 59.906 45.833 0.00 0.00 35.39 3.69
3563 3686 7.418337 TTCTAGCAAGTGGTATCATTCTGTA 57.582 36.000 0.00 0.00 0.00 2.74
3566 3689 6.893583 ACATTCTAGCAAGTGGTATCATTCT 58.106 36.000 0.00 0.00 0.00 2.40
3612 3735 5.005203 GAGCTGTAACTCATTGAGAATCACG 59.995 44.000 20.33 5.25 39.99 4.35
3614 3737 6.291648 AGAGCTGTAACTCATTGAGAATCA 57.708 37.500 20.33 13.00 40.83 2.57
3617 3740 4.774726 AGGAGAGCTGTAACTCATTGAGAA 59.225 41.667 20.33 5.15 39.26 2.87
3648 3771 1.806496 TGGCCTGCCAGTATAGACAT 58.194 50.000 6.80 0.00 41.89 3.06
3726 3866 6.970484 TCTTTAGCCAAGACTTCAAAACATC 58.030 36.000 0.00 0.00 36.51 3.06
3749 3889 4.495422 TCTTCAGGTAGTCAAGCGATTTC 58.505 43.478 0.00 0.00 0.00 2.17
3760 3900 7.482169 TGTTATCATTGACTCTTCAGGTAGT 57.518 36.000 0.00 0.00 31.71 2.73
3782 3922 5.884792 TGGCCATTTTGTCTCAAAATTTTGT 59.115 32.000 25.98 5.81 39.18 2.83
3790 3930 1.969208 TGCATGGCCATTTTGTCTCAA 59.031 42.857 17.92 0.00 0.00 3.02
3824 3964 8.525290 AAGCATAATATACAGAACAAAGCCTT 57.475 30.769 0.00 0.00 0.00 4.35
3825 3965 8.525290 AAAGCATAATATACAGAACAAAGCCT 57.475 30.769 0.00 0.00 0.00 4.58
3826 3966 8.405531 TGAAAGCATAATATACAGAACAAAGCC 58.594 33.333 0.00 0.00 0.00 4.35
3827 3967 9.956720 ATGAAAGCATAATATACAGAACAAAGC 57.043 29.630 0.00 0.00 31.57 3.51
3830 3970 8.849168 CCCATGAAAGCATAATATACAGAACAA 58.151 33.333 0.00 0.00 32.27 2.83
3831 3971 8.217111 TCCCATGAAAGCATAATATACAGAACA 58.783 33.333 0.00 0.00 32.27 3.18
3832 3972 8.621532 TCCCATGAAAGCATAATATACAGAAC 57.378 34.615 0.00 0.00 32.27 3.01
3835 3975 6.656270 TGCTCCCATGAAAGCATAATATACAG 59.344 38.462 15.42 0.00 43.30 2.74
3836 3976 6.541907 TGCTCCCATGAAAGCATAATATACA 58.458 36.000 15.42 0.00 43.30 2.29
3846 3986 4.026356 ACCTATATGCTCCCATGAAAGC 57.974 45.455 11.17 11.17 39.02 3.51
3847 3987 5.249393 AGGTACCTATATGCTCCCATGAAAG 59.751 44.000 14.41 0.00 32.85 2.62
3848 3988 5.013079 CAGGTACCTATATGCTCCCATGAAA 59.987 44.000 15.80 0.00 32.85 2.69
3849 3989 4.532126 CAGGTACCTATATGCTCCCATGAA 59.468 45.833 15.80 0.00 32.85 2.57
3850 3990 4.096681 CAGGTACCTATATGCTCCCATGA 58.903 47.826 15.80 0.00 32.85 3.07
3851 3991 3.369892 GCAGGTACCTATATGCTCCCATG 60.370 52.174 15.80 0.00 35.78 3.66
3852 3992 2.840651 GCAGGTACCTATATGCTCCCAT 59.159 50.000 15.80 0.00 35.78 4.00
3853 3993 2.158158 AGCAGGTACCTATATGCTCCCA 60.158 50.000 15.80 0.00 45.57 4.37
3854 3994 2.541466 AGCAGGTACCTATATGCTCCC 58.459 52.381 15.80 0.00 45.57 4.30
3858 3998 4.256920 CAATGGAGCAGGTACCTATATGC 58.743 47.826 15.80 14.99 38.97 3.14
3859 3999 4.256920 GCAATGGAGCAGGTACCTATATG 58.743 47.826 15.80 4.06 0.00 1.78
3860 4000 3.909995 TGCAATGGAGCAGGTACCTATAT 59.090 43.478 15.80 2.91 40.11 0.86
3861 4001 3.313791 TGCAATGGAGCAGGTACCTATA 58.686 45.455 15.80 0.00 40.11 1.31
3862 4002 2.126882 TGCAATGGAGCAGGTACCTAT 58.873 47.619 15.80 6.27 40.11 2.57
3863 4003 1.578897 TGCAATGGAGCAGGTACCTA 58.421 50.000 15.80 0.00 40.11 3.08
3864 4004 2.386864 TGCAATGGAGCAGGTACCT 58.613 52.632 9.21 9.21 40.11 3.08
3880 4020 4.644103 AGAGTTGAAACCATGCATATGC 57.356 40.909 21.09 21.09 42.50 3.14
3881 4021 7.500720 TCATAGAGTTGAAACCATGCATATG 57.499 36.000 0.00 0.00 0.00 1.78
3882 4022 7.557358 TGTTCATAGAGTTGAAACCATGCATAT 59.443 33.333 0.00 0.00 37.36 1.78
3883 4023 6.883756 TGTTCATAGAGTTGAAACCATGCATA 59.116 34.615 0.00 0.00 37.36 3.14
3884 4024 5.711506 TGTTCATAGAGTTGAAACCATGCAT 59.288 36.000 0.00 0.00 37.36 3.96
3885 4025 5.048782 GTGTTCATAGAGTTGAAACCATGCA 60.049 40.000 0.00 0.00 37.36 3.96
3886 4026 5.048782 TGTGTTCATAGAGTTGAAACCATGC 60.049 40.000 0.00 0.00 37.36 4.06
3887 4027 6.373779 GTGTGTTCATAGAGTTGAAACCATG 58.626 40.000 0.00 0.00 37.36 3.66
3888 4028 5.473504 GGTGTGTTCATAGAGTTGAAACCAT 59.526 40.000 0.00 0.00 37.36 3.55
3889 4029 4.819630 GGTGTGTTCATAGAGTTGAAACCA 59.180 41.667 0.00 0.00 37.36 3.67
3890 4030 4.819630 TGGTGTGTTCATAGAGTTGAAACC 59.180 41.667 0.00 0.00 37.36 3.27
3891 4031 5.527582 AGTGGTGTGTTCATAGAGTTGAAAC 59.472 40.000 0.00 0.00 37.36 2.78
3892 4032 5.527214 CAGTGGTGTGTTCATAGAGTTGAAA 59.473 40.000 0.00 0.00 37.36 2.69
3893 4033 5.056480 CAGTGGTGTGTTCATAGAGTTGAA 58.944 41.667 0.00 0.00 33.32 2.69
3894 4034 4.100963 ACAGTGGTGTGTTCATAGAGTTGA 59.899 41.667 0.00 0.00 34.75 3.18
3895 4035 4.380531 ACAGTGGTGTGTTCATAGAGTTG 58.619 43.478 0.00 0.00 34.75 3.16
3896 4036 4.689612 ACAGTGGTGTGTTCATAGAGTT 57.310 40.909 0.00 0.00 34.75 3.01
3897 4037 5.304614 AGTTACAGTGGTGTGTTCATAGAGT 59.695 40.000 0.00 0.00 37.52 3.24
3898 4038 5.784177 AGTTACAGTGGTGTGTTCATAGAG 58.216 41.667 0.00 0.00 37.52 2.43
3899 4039 5.801531 AGTTACAGTGGTGTGTTCATAGA 57.198 39.130 0.00 0.00 37.52 1.98
3900 4040 6.861065 AAAGTTACAGTGGTGTGTTCATAG 57.139 37.500 0.00 0.00 37.52 2.23
3901 4041 6.824196 TCAAAAGTTACAGTGGTGTGTTCATA 59.176 34.615 0.00 0.00 37.52 2.15
3902 4042 5.650266 TCAAAAGTTACAGTGGTGTGTTCAT 59.350 36.000 0.00 0.00 37.52 2.57
3903 4043 5.004448 TCAAAAGTTACAGTGGTGTGTTCA 58.996 37.500 0.00 0.00 37.52 3.18
3904 4044 5.106475 TGTCAAAAGTTACAGTGGTGTGTTC 60.106 40.000 0.00 0.00 37.52 3.18
3905 4045 4.762765 TGTCAAAAGTTACAGTGGTGTGTT 59.237 37.500 0.00 0.00 37.52 3.32
3906 4046 4.155280 GTGTCAAAAGTTACAGTGGTGTGT 59.845 41.667 0.00 0.00 37.52 3.72
3907 4047 4.394920 AGTGTCAAAAGTTACAGTGGTGTG 59.605 41.667 0.00 0.00 37.52 3.82
3908 4048 4.394920 CAGTGTCAAAAGTTACAGTGGTGT 59.605 41.667 4.72 0.00 41.36 4.16
3909 4049 4.394920 ACAGTGTCAAAAGTTACAGTGGTG 59.605 41.667 13.93 0.00 46.62 4.17
3910 4050 4.585879 ACAGTGTCAAAAGTTACAGTGGT 58.414 39.130 13.93 1.42 46.62 4.16
3911 4051 5.560966 AACAGTGTCAAAAGTTACAGTGG 57.439 39.130 13.93 0.96 46.62 4.00
3913 4053 9.783256 GAAATTAACAGTGTCAAAAGTTACAGT 57.217 29.630 0.00 0.00 0.00 3.55
3925 4065 7.573627 AGCGTTTCTTAGAAATTAACAGTGTC 58.426 34.615 10.77 0.00 0.00 3.67
3935 4075 7.136772 GGTGTTAACAAGCGTTTCTTAGAAAT 58.863 34.615 10.51 0.00 36.52 2.17
3950 4094 5.154932 CAGTTCGTTTGTTGGTGTTAACAA 58.845 37.500 10.51 0.00 45.78 2.83
3956 4100 1.741145 GACCAGTTCGTTTGTTGGTGT 59.259 47.619 0.00 0.00 43.65 4.16
3991 4135 4.589216 TGCTCAAACATCCCTTGAAAAG 57.411 40.909 0.00 0.00 45.69 2.27
4050 4194 9.408648 GGTAAGATTAGAGGATTCCAATGAAAA 57.591 33.333 5.29 0.00 33.32 2.29
4092 4237 0.168788 CGTACTTGCTGCCATTGTGG 59.831 55.000 0.00 0.00 41.55 4.17
4093 4238 0.454957 GCGTACTTGCTGCCATTGTG 60.455 55.000 0.00 0.00 0.00 3.33
4226 4371 0.815734 GAGGGATCGTCGTGAGGAAA 59.184 55.000 0.00 0.00 0.00 3.13
4263 4408 1.442184 CCGTCGTGTCCTCGTCTTG 60.442 63.158 0.00 0.00 0.00 3.02
4264 4409 1.575576 CTCCGTCGTGTCCTCGTCTT 61.576 60.000 0.00 0.00 0.00 3.01
4397 4542 3.830192 GCCTTCCCATTGCTGCCG 61.830 66.667 0.00 0.00 0.00 5.69
4430 4575 1.300465 CGTCTCAGGGGCATGATCG 60.300 63.158 0.00 0.00 0.00 3.69
4432 4577 0.620556 AAACGTCTCAGGGGCATGAT 59.379 50.000 0.00 0.00 0.00 2.45
4754 4918 3.381590 TCAGTGATCAGTAACCATCTCCG 59.618 47.826 1.86 0.00 0.00 4.63
4755 4919 4.404073 AGTCAGTGATCAGTAACCATCTCC 59.596 45.833 1.86 0.00 0.00 3.71
4834 4998 7.463431 ACTTGGTCAACCTACAAATTGGTATA 58.537 34.615 0.00 0.00 35.17 1.47
4835 4999 6.311735 ACTTGGTCAACCTACAAATTGGTAT 58.688 36.000 0.00 0.00 35.17 2.73
4845 5013 4.952460 TGTGAGTAACTTGGTCAACCTAC 58.048 43.478 0.10 0.00 36.82 3.18
4850 5018 7.201785 GGAAGAAATTGTGAGTAACTTGGTCAA 60.202 37.037 0.00 0.00 0.00 3.18
4896 5064 9.846248 ATCAACTACTGCAAAAATTACAGATTC 57.154 29.630 0.00 0.00 35.38 2.52
4906 5074 8.417106 TCCAACAAATATCAACTACTGCAAAAA 58.583 29.630 0.00 0.00 0.00 1.94
4935 5103 7.551585 ACAATTCATGGGCATTTATTCGTTTA 58.448 30.769 0.00 0.00 0.00 2.01
4936 5104 6.405538 ACAATTCATGGGCATTTATTCGTTT 58.594 32.000 0.00 0.00 0.00 3.60
4978 5146 4.831710 ACTATGGTACGGAGGGAGTATTTC 59.168 45.833 0.00 0.00 0.00 2.17
4994 5162 7.064253 GTGTCAAAAACGCTCTTATACTATGGT 59.936 37.037 0.00 0.00 35.42 3.55
4996 5164 8.186178 AGTGTCAAAAACGCTCTTATACTATG 57.814 34.615 0.00 0.00 45.69 2.23
4997 5165 9.865321 TTAGTGTCAAAAACGCTCTTATACTAT 57.135 29.630 0.00 0.00 45.69 2.12
4998 5166 9.132521 GTTAGTGTCAAAAACGCTCTTATACTA 57.867 33.333 0.00 0.00 45.69 1.82
5000 5168 8.015409 AGTTAGTGTCAAAAACGCTCTTATAC 57.985 34.615 0.00 0.00 45.69 1.47
5003 5171 6.278363 AGAGTTAGTGTCAAAAACGCTCTTA 58.722 36.000 0.00 0.00 45.69 2.10
5004 5172 5.116882 AGAGTTAGTGTCAAAAACGCTCTT 58.883 37.500 0.00 0.00 45.69 2.85
5005 5173 4.694339 AGAGTTAGTGTCAAAAACGCTCT 58.306 39.130 0.00 0.00 45.69 4.09
5008 5176 4.789095 TGAGAGTTAGTGTCAAAAACGC 57.211 40.909 0.00 0.00 38.74 4.84
5056 5355 9.995003 TGTATAAGGTTCAAAAATGCTTCAATT 57.005 25.926 0.00 0.00 0.00 2.32
5057 5356 9.995003 TTGTATAAGGTTCAAAAATGCTTCAAT 57.005 25.926 0.00 0.00 0.00 2.57
5070 5369 9.391006 GGACATCTTTGTATTGTATAAGGTTCA 57.609 33.333 0.00 0.00 35.79 3.18
5099 5401 9.561069 ACACTAGTGATTTGAAATAACTTGAGT 57.439 29.630 29.30 15.43 0.00 3.41
5117 5419 8.612619 ACACAGAATTTGTAAAAGACACTAGTG 58.387 33.333 21.44 21.44 38.16 2.74
5162 5464 3.942748 ACCTGTGCTAGTTTCGTTTTCAA 59.057 39.130 0.00 0.00 0.00 2.69
5163 5465 3.311322 CACCTGTGCTAGTTTCGTTTTCA 59.689 43.478 0.00 0.00 0.00 2.69
5164 5466 3.558418 TCACCTGTGCTAGTTTCGTTTTC 59.442 43.478 0.00 0.00 0.00 2.29
5167 5469 2.548067 CCTCACCTGTGCTAGTTTCGTT 60.548 50.000 0.00 0.00 0.00 3.85
5168 5470 1.000955 CCTCACCTGTGCTAGTTTCGT 59.999 52.381 0.00 0.00 0.00 3.85
5169 5471 1.000955 ACCTCACCTGTGCTAGTTTCG 59.999 52.381 0.00 0.00 0.00 3.46
5171 5473 2.047061 TCACCTCACCTGTGCTAGTTT 58.953 47.619 0.00 0.00 33.71 2.66
5173 5475 1.552337 CATCACCTCACCTGTGCTAGT 59.448 52.381 0.00 0.00 33.71 2.57
5174 5476 1.741732 GCATCACCTCACCTGTGCTAG 60.742 57.143 0.00 0.00 33.71 3.42
5175 5477 0.250234 GCATCACCTCACCTGTGCTA 59.750 55.000 0.00 0.00 33.71 3.49
5384 5686 3.984200 GAGGAAAGGGACGGCGTCG 62.984 68.421 31.02 8.42 43.02 5.12
5385 5687 2.125633 GAGGAAAGGGACGGCGTC 60.126 66.667 30.72 30.72 0.00 5.19
5386 5688 3.703127 GGAGGAAAGGGACGGCGT 61.703 66.667 14.65 14.65 0.00 5.68
5387 5689 4.814294 CGGAGGAAAGGGACGGCG 62.814 72.222 4.80 4.80 0.00 6.46


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

AutoCloner maintained by Alex Coulton.