Multiple sequence alignment - TraesCS5A01G162600

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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 TraesCS5A01G162600 chr5A 100.000 8514 0 0 1 8514 347006077 347014590 0.000000e+00 15723.0
1 TraesCS5A01G162600 chr5A 87.407 135 13 3 4189 4320 656492270 656492137 1.480000e-32 152.0
2 TraesCS5A01G162600 chr5A 100.000 49 0 0 1660 1708 347007683 347007731 3.270000e-14 91.6
3 TraesCS5A01G162600 chr5A 100.000 49 0 0 1607 1655 347007736 347007784 3.270000e-14 91.6
4 TraesCS5A01G162600 chr5A 96.000 50 2 0 5187 5236 344542219 344542268 1.970000e-11 82.4
5 TraesCS5A01G162600 chr5B 96.359 6207 175 30 1659 7849 294770475 294764304 0.000000e+00 10163.0
6 TraesCS5A01G162600 chr5B 96.200 500 4 5 734 1221 294771306 294770810 0.000000e+00 804.0
7 TraesCS5A01G162600 chr5B 86.057 667 41 13 7849 8498 294764063 294763432 0.000000e+00 669.0
8 TraesCS5A01G162600 chr5B 98.163 381 7 0 1275 1655 294770806 294770426 0.000000e+00 665.0
9 TraesCS5A01G162600 chr5B 95.902 122 5 0 632 753 294771817 294771696 1.870000e-46 198.0
10 TraesCS5A01G162600 chr5B 94.000 50 3 0 5187 5236 293542934 293542983 9.160000e-10 76.8
11 TraesCS5A01G162600 chr5D 97.674 3569 65 11 4365 7919 261390285 261393849 0.000000e+00 6115.0
12 TraesCS5A01G162600 chr5D 95.118 1352 40 10 2290 3618 261387276 261388624 0.000000e+00 2108.0
13 TraesCS5A01G162600 chr5D 97.138 1118 22 6 541 1655 261385110 261386220 0.000000e+00 1879.0
14 TraesCS5A01G162600 chr5D 96.457 762 23 3 3609 4367 261389402 261390162 0.000000e+00 1254.0
15 TraesCS5A01G162600 chr5D 96.160 651 24 1 1659 2308 261386171 261386821 0.000000e+00 1062.0
16 TraesCS5A01G162600 chr5D 92.075 265 19 1 8234 8498 261393892 261394154 1.040000e-98 372.0
17 TraesCS5A01G162600 chr5D 86.567 134 11 6 4431 4561 248600831 248600960 3.200000e-29 141.0
18 TraesCS5A01G162600 chr5D 81.169 154 15 7 4433 4574 15417252 15417403 2.510000e-20 111.0
19 TraesCS5A01G162600 chr5D 94.000 50 3 0 5187 5236 260796409 260796360 9.160000e-10 76.8
20 TraesCS5A01G162600 chr5D 95.745 47 2 0 5186 5232 481269101 481269147 9.160000e-10 76.8
21 TraesCS5A01G162600 chr5D 100.000 28 0 0 8208 8235 261393852 261393879 1.500000e-02 52.8
22 TraesCS5A01G162600 chr3B 86.450 524 70 1 1 524 752271617 752272139 2.670000e-159 573.0
23 TraesCS5A01G162600 chr3B 88.406 138 13 3 4190 4325 636108899 636109035 6.840000e-36 163.0
24 TraesCS5A01G162600 chr3B 88.550 131 11 3 4194 4321 784665225 784665354 1.140000e-33 156.0
25 TraesCS5A01G162600 chr7A 80.000 500 100 0 4 503 166783733 166783234 3.750000e-98 370.0
26 TraesCS5A01G162600 chr7A 84.615 130 11 8 4460 4582 418103625 418103752 4.170000e-23 121.0
27 TraesCS5A01G162600 chr2D 83.251 406 58 3 1 406 342515958 342516353 1.750000e-96 364.0
28 TraesCS5A01G162600 chr2D 90.566 53 5 0 5186 5238 382456126 382456074 4.260000e-08 71.3
29 TraesCS5A01G162600 chr3A 89.510 143 12 3 4185 4325 620571841 620571982 2.440000e-40 178.0
30 TraesCS5A01G162600 chr3A 90.909 55 3 2 5186 5238 510594353 510594299 1.190000e-08 73.1
31 TraesCS5A01G162600 chr3D 87.413 143 15 3 4185 4325 476983956 476984097 2.460000e-35 161.0
32 TraesCS5A01G162600 chr3D 88.060 134 15 1 4189 4321 482007466 482007599 3.180000e-34 158.0
33 TraesCS5A01G162600 chr3D 84.348 115 13 3 4468 4581 481597882 481597772 3.250000e-19 108.0
34 TraesCS5A01G162600 chr3D 90.909 55 3 2 5186 5238 389909243 389909189 1.190000e-08 73.1
35 TraesCS5A01G162600 chr7B 83.908 174 19 9 4416 4582 368148414 368148585 3.180000e-34 158.0
36 TraesCS5A01G162600 chr2B 87.407 135 13 3 4190 4321 379972981 379973114 1.480000e-32 152.0
37 TraesCS5A01G162600 chr4B 88.430 121 14 0 1 121 522447250 522447370 6.890000e-31 147.0
38 TraesCS5A01G162600 chr1B 87.912 91 10 1 4488 4577 143039900 143039810 1.170000e-18 106.0
39 TraesCS5A01G162600 chr1D 88.000 75 8 1 4488 4561 89566855 89566929 4.230000e-13 87.9


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 TraesCS5A01G162600 chr5A 347006077 347014590 8513 False 15723.000000 15723 100.000000 1 8514 1 chr5A.!!$F2 8513
1 TraesCS5A01G162600 chr5B 294763432 294771817 8385 True 2499.800000 10163 94.536200 632 8498 5 chr5B.!!$R1 7866
2 TraesCS5A01G162600 chr5D 261385110 261394154 9044 False 1834.685714 6115 96.374571 541 8498 7 chr5D.!!$F4 7957
3 TraesCS5A01G162600 chr3B 752271617 752272139 522 False 573.000000 573 86.450000 1 524 1 chr3B.!!$F2 523

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
368 369 0.164002 GAACAGAAGAAACCGAGCGC 59.836 55.000 0.00 0.00 0.00 5.92 F
372 373 0.173708 AGAAGAAACCGAGCGCCTAG 59.826 55.000 2.29 0.00 0.00 3.02 F
514 515 0.323908 CCTAGGAGGCGATAGGGAGG 60.324 65.000 1.05 0.00 35.81 4.30 F
1605 2030 0.458370 TGATCGTCACATGGCTCACG 60.458 55.000 0.00 0.00 0.00 4.35 F
3038 3946 1.318158 GCTGCAATCAAGACCCCAGG 61.318 60.000 0.00 0.00 0.00 4.45 F
3447 4369 1.001158 GACGGGCTAGATGCAGTCTAC 60.001 57.143 0.00 0.00 42.96 2.59 F
4943 6787 2.410785 AAAGCCGCGGTAAGTTTTTC 57.589 45.000 28.70 6.22 0.00 2.29 F
5905 7752 0.890683 GTGGAAATCACTTGGGCAGG 59.109 55.000 0.00 0.00 42.86 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 2485 0.179086 TGTTGCTCACTGTTCTGCGA 60.179 50.000 0.00 0.00 0.00 5.10 R
2130 2556 0.318955 GTGGCTGTGTGAACAATGGC 60.319 55.000 4.34 4.34 0.00 4.40 R
2231 2657 2.291411 ACTACGTACCCTCACAGGTCAT 60.291 50.000 0.00 0.00 41.58 3.06 R
3292 4201 0.395862 TAAGAGGCCTAGAGCGTGCT 60.396 55.000 4.42 0.00 45.17 4.40 R
4943 6787 0.768622 TTGTACTGTGGTGAAGGGGG 59.231 55.000 0.00 0.00 0.00 5.40 R
4950 6794 3.194005 ACTGAAGGTTGTACTGTGGTG 57.806 47.619 0.00 0.00 0.00 4.17 R
6154 8001 2.092646 TGGTTCAGTCCGATTATTGGGG 60.093 50.000 0.00 0.00 0.00 4.96 R
7824 9675 0.032130 AGTGACGCTTCGAGCAAGAA 59.968 50.000 7.47 0.00 42.58 2.52 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
22 23 5.203060 GTACAGTCCTTCAAGAAGTGTCT 57.797 43.478 8.83 2.07 36.72 3.41
46 47 1.614903 CTCCAAGCATTTGAAGCACCA 59.385 47.619 0.00 0.00 36.36 4.17
48 49 1.425412 CAAGCATTTGAAGCACCAGC 58.575 50.000 0.00 0.00 37.49 4.85
52 53 0.901580 CATTTGAAGCACCAGCCCCT 60.902 55.000 0.00 0.00 43.56 4.79
53 54 0.901580 ATTTGAAGCACCAGCCCCTG 60.902 55.000 0.00 0.00 43.56 4.45
56 57 1.000396 GAAGCACCAGCCCCTGATT 60.000 57.895 0.00 0.00 43.56 2.57
59 60 1.000396 GCACCAGCCCCTGATTTCT 60.000 57.895 0.00 0.00 32.44 2.52
107 108 3.991051 CGACGCACCACCACCTCT 61.991 66.667 0.00 0.00 0.00 3.69
114 115 2.348998 CCACCACCTCTGTCTGCC 59.651 66.667 0.00 0.00 0.00 4.85
144 145 3.967715 GGTGCTTCCGAAGTGACC 58.032 61.111 9.87 11.64 0.00 4.02
172 173 1.635817 GCAGGGGCTTCCTACCATGA 61.636 60.000 0.00 0.00 46.12 3.07
173 174 0.471617 CAGGGGCTTCCTACCATGAG 59.528 60.000 0.00 0.00 46.12 2.90
176 177 1.227674 GGCTTCCTACCATGAGGCG 60.228 63.158 0.00 0.00 39.06 5.52
194 195 4.615815 ATCCTGCGCGATGGAGCC 62.616 66.667 21.51 0.00 38.30 4.70
211 212 2.721167 CCGCCAAGATGTCCTCCGA 61.721 63.158 0.00 0.00 0.00 4.55
215 216 1.320344 CCAAGATGTCCTCCGACGGA 61.320 60.000 17.28 17.28 42.37 4.69
241 242 3.071206 GACAGCCTCCTCCGCAGA 61.071 66.667 0.00 0.00 0.00 4.26
251 252 2.038007 TCCGCAGAAGAGCCCTCT 59.962 61.111 0.00 0.00 42.75 3.69
264 265 3.125573 CCTCTGACGCCGACGAGA 61.126 66.667 0.00 0.00 43.93 4.04
273 274 2.579201 CCGACGAGATGCCAAGGT 59.421 61.111 0.00 0.00 0.00 3.50
275 276 1.519455 CGACGAGATGCCAAGGTCC 60.519 63.158 0.00 0.00 0.00 4.46
284 285 2.927580 GCCAAGGTCCGAGACGACA 61.928 63.158 0.00 0.00 34.24 4.35
286 287 1.213013 CAAGGTCCGAGACGACAGG 59.787 63.158 0.00 0.00 34.24 4.00
287 288 2.637383 AAGGTCCGAGACGACAGGC 61.637 63.158 0.00 0.00 34.24 4.85
368 369 0.164002 GAACAGAAGAAACCGAGCGC 59.836 55.000 0.00 0.00 0.00 5.92
370 371 1.374758 CAGAAGAAACCGAGCGCCT 60.375 57.895 2.29 0.00 0.00 5.52
372 373 0.173708 AGAAGAAACCGAGCGCCTAG 59.826 55.000 2.29 0.00 0.00 3.02
514 515 0.323908 CCTAGGAGGCGATAGGGAGG 60.324 65.000 1.05 0.00 35.81 4.30
515 516 0.699399 CTAGGAGGCGATAGGGAGGA 59.301 60.000 0.00 0.00 0.00 3.71
516 517 0.699399 TAGGAGGCGATAGGGAGGAG 59.301 60.000 0.00 0.00 0.00 3.69
517 518 1.608046 GGAGGCGATAGGGAGGAGG 60.608 68.421 0.00 0.00 0.00 4.30
518 519 2.203714 AGGCGATAGGGAGGAGGC 60.204 66.667 0.00 0.00 0.00 4.70
519 520 2.524394 GGCGATAGGGAGGAGGCA 60.524 66.667 0.00 0.00 0.00 4.75
521 522 2.578714 GCGATAGGGAGGAGGCAGG 61.579 68.421 0.00 0.00 0.00 4.85
522 523 2.578714 CGATAGGGAGGAGGCAGGC 61.579 68.421 0.00 0.00 0.00 4.85
523 524 2.525381 ATAGGGAGGAGGCAGGCG 60.525 66.667 0.00 0.00 0.00 5.52
524 525 4.860881 TAGGGAGGAGGCAGGCGG 62.861 72.222 0.00 0.00 0.00 6.13
556 557 5.593095 GTCGGGGGCTTTTCTATTTTAGAAT 59.407 40.000 0.00 0.00 43.72 2.40
563 564 6.322456 GGCTTTTCTATTTTAGAATGAGGGCT 59.678 38.462 0.00 0.00 43.72 5.19
998 1423 1.291184 CGTTCGTGCAAGATCTGGCA 61.291 55.000 21.30 21.30 37.77 4.92
1245 1670 4.142643 ACGTCTAAAAGCGAGGAGAGTTAG 60.143 45.833 0.00 0.00 0.00 2.34
1266 1691 3.944015 AGGATGCTCTGTGATTGCTTTAC 59.056 43.478 0.00 0.00 0.00 2.01
1273 1698 6.598850 TGCTCTGTGATTGCTTTACATATTCA 59.401 34.615 0.00 0.00 0.00 2.57
1420 1845 2.252976 TGCTCAGTGTATGTTGCACA 57.747 45.000 0.00 0.00 39.17 4.57
1594 2019 3.314080 TGCTATCGTGTATGTGATCGTCA 59.686 43.478 0.00 0.00 0.00 4.35
1605 2030 0.458370 TGATCGTCACATGGCTCACG 60.458 55.000 0.00 0.00 0.00 4.35
1628 2053 5.125100 AGCATCTTAATGTGTTGGTGTTG 57.875 39.130 0.00 0.00 35.18 3.33
1629 2054 4.022068 AGCATCTTAATGTGTTGGTGTTGG 60.022 41.667 0.00 0.00 35.18 3.77
1630 2055 4.022416 GCATCTTAATGTGTTGGTGTTGGA 60.022 41.667 0.00 0.00 35.18 3.53
1631 2056 5.336690 GCATCTTAATGTGTTGGTGTTGGAT 60.337 40.000 0.00 0.00 35.18 3.41
1632 2057 6.690530 CATCTTAATGTGTTGGTGTTGGATT 58.309 36.000 0.00 0.00 0.00 3.01
1633 2058 6.083098 TCTTAATGTGTTGGTGTTGGATTG 57.917 37.500 0.00 0.00 0.00 2.67
1634 2059 3.749665 AATGTGTTGGTGTTGGATTGG 57.250 42.857 0.00 0.00 0.00 3.16
1635 2060 2.151502 TGTGTTGGTGTTGGATTGGT 57.848 45.000 0.00 0.00 0.00 3.67
1636 2061 3.298686 TGTGTTGGTGTTGGATTGGTA 57.701 42.857 0.00 0.00 0.00 3.25
1637 2062 3.838565 TGTGTTGGTGTTGGATTGGTAT 58.161 40.909 0.00 0.00 0.00 2.73
1638 2063 3.823873 TGTGTTGGTGTTGGATTGGTATC 59.176 43.478 0.00 0.00 0.00 2.24
1655 2080 9.651913 GATTGGTATCCATTTGTATTTTGTGTT 57.348 29.630 0.00 0.00 31.53 3.32
1656 2081 8.824159 TTGGTATCCATTTGTATTTTGTGTTG 57.176 30.769 0.00 0.00 31.53 3.33
1657 2082 8.183104 TGGTATCCATTTGTATTTTGTGTTGA 57.817 30.769 0.00 0.00 0.00 3.18
1658 2083 8.811017 TGGTATCCATTTGTATTTTGTGTTGAT 58.189 29.630 0.00 0.00 0.00 2.57
1661 2086 8.931385 ATCCATTTGTATTTTGTGTTGATAGC 57.069 30.769 0.00 0.00 0.00 2.97
1662 2087 7.890515 TCCATTTGTATTTTGTGTTGATAGCA 58.109 30.769 0.00 0.00 0.00 3.49
1663 2088 8.530311 TCCATTTGTATTTTGTGTTGATAGCAT 58.470 29.630 0.00 0.00 0.00 3.79
1664 2089 8.810427 CCATTTGTATTTTGTGTTGATAGCATC 58.190 33.333 0.00 0.00 0.00 3.91
1665 2090 9.577110 CATTTGTATTTTGTGTTGATAGCATCT 57.423 29.630 0.00 0.00 0.00 2.90
1672 2097 8.969121 TTTTGTGTTGATAGCATCTTAATGTG 57.031 30.769 0.00 0.00 35.18 3.21
1673 2098 7.686438 TTGTGTTGATAGCATCTTAATGTGT 57.314 32.000 0.00 0.00 35.18 3.72
1674 2099 7.686438 TGTGTTGATAGCATCTTAATGTGTT 57.314 32.000 0.00 0.00 35.18 3.32
1675 2100 7.529158 TGTGTTGATAGCATCTTAATGTGTTG 58.471 34.615 0.00 0.00 35.18 3.33
1676 2101 6.968904 GTGTTGATAGCATCTTAATGTGTTGG 59.031 38.462 0.00 0.00 35.18 3.77
1677 2102 6.658816 TGTTGATAGCATCTTAATGTGTTGGT 59.341 34.615 0.00 0.00 35.18 3.67
1678 2103 6.682423 TGATAGCATCTTAATGTGTTGGTG 57.318 37.500 0.00 0.00 35.18 4.17
1679 2104 6.179756 TGATAGCATCTTAATGTGTTGGTGT 58.820 36.000 0.00 0.00 35.18 4.16
1680 2105 6.658816 TGATAGCATCTTAATGTGTTGGTGTT 59.341 34.615 0.00 0.00 35.18 3.32
1842 2268 9.151471 GTTGTAGCACATTTCTTGAAGTATAGA 57.849 33.333 0.00 0.00 0.00 1.98
1916 2342 7.279615 TGTATTCCTTGTAGTATGTGAATGGG 58.720 38.462 0.00 0.00 0.00 4.00
1980 2406 8.511321 GTCAACATTAATTCACTGACCAATGTA 58.489 33.333 10.39 0.00 36.01 2.29
2059 2485 7.540474 TGTTTAGACTTCAGACCTAGACATT 57.460 36.000 0.00 0.00 0.00 2.71
2060 2486 7.603651 TGTTTAGACTTCAGACCTAGACATTC 58.396 38.462 0.00 0.00 0.00 2.67
2130 2556 2.710377 TGAACCATCCAAACTCATCCG 58.290 47.619 0.00 0.00 0.00 4.18
2188 2614 7.394359 TCTCTGTTTGCTAATGCCTTTTAATCT 59.606 33.333 0.00 0.00 38.71 2.40
2495 3394 1.523758 ACTGATTTGCCGTTCAGACC 58.476 50.000 12.27 0.00 41.53 3.85
2555 3454 4.510167 AATGCTTTAGTGGCTCTGGTAT 57.490 40.909 0.00 0.00 0.00 2.73
2557 3456 3.873910 TGCTTTAGTGGCTCTGGTATTC 58.126 45.455 0.00 0.00 0.00 1.75
2566 3473 5.367937 AGTGGCTCTGGTATTCTGATACATT 59.632 40.000 0.00 0.00 39.94 2.71
2590 3497 7.405469 TTGATTCGTTTTCATTTTCCATGTG 57.595 32.000 0.00 0.00 0.00 3.21
2601 3508 6.166279 TCATTTTCCATGTGTAGACTCAGTC 58.834 40.000 0.00 0.00 0.00 3.51
2698 3606 3.926527 TGTCATGTGTGATTAGCGACTTC 59.073 43.478 0.00 0.00 36.60 3.01
2840 3748 1.999648 AGGTGTCATGTGCATTGGTT 58.000 45.000 0.00 0.00 0.00 3.67
2901 3809 7.148120 TGTGCTTCTGTCTAGTATAGGTACAAC 60.148 40.741 0.00 0.00 39.78 3.32
2924 3832 6.173339 ACTGTACACAATAAACATCCCTCTG 58.827 40.000 0.00 0.00 0.00 3.35
2984 3892 7.672240 TGTACCAAGTGAATGTGTGTATTCTA 58.328 34.615 0.00 0.00 37.81 2.10
3038 3946 1.318158 GCTGCAATCAAGACCCCAGG 61.318 60.000 0.00 0.00 0.00 4.45
3059 3967 3.385111 GGTTCCTACTCCTGGTCATAGTG 59.615 52.174 0.00 0.00 0.00 2.74
3086 3994 2.741211 GCGGGTTGAAGGTCCGTC 60.741 66.667 0.00 0.00 44.97 4.79
3186 4094 2.109834 ACCCCAGTCCATGAATGTTGAA 59.890 45.455 0.00 0.00 0.00 2.69
3187 4095 3.245730 ACCCCAGTCCATGAATGTTGAAT 60.246 43.478 0.00 0.00 0.00 2.57
3292 4201 4.308458 CCGTGGTCCAGCCGAACA 62.308 66.667 3.53 0.00 41.21 3.18
3446 4368 1.319541 GACGGGCTAGATGCAGTCTA 58.680 55.000 0.00 0.00 42.96 2.59
3447 4369 1.001158 GACGGGCTAGATGCAGTCTAC 60.001 57.143 0.00 0.00 42.96 2.59
3600 4522 3.463944 GAAGTTGGAGGACTTTCGAACA 58.536 45.455 0.00 0.00 39.84 3.18
3681 5392 8.109705 ACTATATTTGACTGTTTGCATGTCAA 57.890 30.769 15.94 15.94 45.31 3.18
3682 5393 8.742777 ACTATATTTGACTGTTTGCATGTCAAT 58.257 29.630 18.71 13.64 45.94 2.57
3699 5410 4.096231 TGTCAATACATGCGCTAAAATGCT 59.904 37.500 9.73 0.00 0.00 3.79
4010 5721 5.103855 CCAATGGGGTAGGGAACAATACTTA 60.104 44.000 0.00 0.00 0.00 2.24
4117 5828 9.554724 CAACCATAATAACATTCAACACTGTAC 57.445 33.333 0.00 0.00 0.00 2.90
4238 5949 5.045140 CCCACTACCTATTTTTCCTCTCCAA 60.045 44.000 0.00 0.00 0.00 3.53
4275 5986 2.565046 TCAAGTCATGCATGTGGTCA 57.435 45.000 25.43 3.60 0.00 4.02
4396 6234 7.224557 GTGTTGGACAGTTGAAGCAAATTTATT 59.775 33.333 0.00 0.00 0.00 1.40
4715 6559 5.588958 AAATTTGCAGGCTCTTATCCTTC 57.411 39.130 0.00 0.00 0.00 3.46
4780 6624 5.067283 GCCATTGTACCGAAATATTGAACCT 59.933 40.000 0.00 0.00 0.00 3.50
4851 6695 9.556030 GTTTTTACTTTCCCTAATCATTCTTCG 57.444 33.333 0.00 0.00 0.00 3.79
4943 6787 2.410785 AAAGCCGCGGTAAGTTTTTC 57.589 45.000 28.70 6.22 0.00 2.29
4950 6794 1.542915 GCGGTAAGTTTTTCCCCCTTC 59.457 52.381 0.00 0.00 0.00 3.46
5069 6913 6.590234 AGGATGTCCCTTAAAATGTTTCAC 57.410 37.500 0.00 0.00 44.85 3.18
5070 6914 6.314917 AGGATGTCCCTTAAAATGTTTCACT 58.685 36.000 0.00 0.00 44.85 3.41
5128 6972 5.343058 GCGTGACAGTAAACTAATGACGTTA 59.657 40.000 0.00 0.00 0.00 3.18
5225 7069 4.083003 TGCGACACTTATTTTGGATTGGAC 60.083 41.667 0.00 0.00 0.00 4.02
5265 7109 6.466812 ACGTGATATGATCAATGGCTCAATA 58.533 36.000 0.00 0.00 41.69 1.90
5287 7131 5.000570 ACTGTCTACTCTACTTTGTCCCT 57.999 43.478 0.00 0.00 0.00 4.20
5347 7191 8.646356 ACATGCATTTTTGATATACACAAAACG 58.354 29.630 14.91 11.72 43.62 3.60
5377 7221 4.759782 ACACTGCCAGTATGACAATACTC 58.240 43.478 0.00 0.00 44.76 2.59
5592 7436 5.048154 TGACAAGCAATAGCATTTGTTAGCA 60.048 36.000 0.00 0.00 45.49 3.49
5593 7437 5.969423 ACAAGCAATAGCATTTGTTAGCAT 58.031 33.333 0.00 0.00 45.49 3.79
5595 7439 6.875195 ACAAGCAATAGCATTTGTTAGCATTT 59.125 30.769 0.00 0.00 45.49 2.32
5596 7440 7.063780 ACAAGCAATAGCATTTGTTAGCATTTC 59.936 33.333 0.00 0.00 45.49 2.17
5597 7441 6.044682 AGCAATAGCATTTGTTAGCATTTCC 58.955 36.000 0.00 0.00 45.49 3.13
5598 7442 6.044682 GCAATAGCATTTGTTAGCATTTCCT 58.955 36.000 0.00 0.00 41.58 3.36
5599 7443 6.536224 GCAATAGCATTTGTTAGCATTTCCTT 59.464 34.615 0.00 0.00 41.58 3.36
5601 7445 8.598075 CAATAGCATTTGTTAGCATTTCCTTTC 58.402 33.333 0.00 0.00 0.00 2.62
5602 7446 5.482006 AGCATTTGTTAGCATTTCCTTTCC 58.518 37.500 0.00 0.00 0.00 3.13
5905 7752 0.890683 GTGGAAATCACTTGGGCAGG 59.109 55.000 0.00 0.00 42.86 4.85
6154 8001 1.601412 GCTGTGAAGCTTTTGAGCACC 60.601 52.381 15.75 0.00 37.25 5.01
6185 8032 3.512329 TCGGACTGAACCAGTAATGCTAA 59.488 43.478 0.00 0.00 45.44 3.09
6436 8283 1.883084 GCCGCTCTTGTACCATCGG 60.883 63.158 0.00 0.00 39.81 4.18
6565 8412 3.140814 GGGTCAGGGAAATGGCGC 61.141 66.667 0.00 0.00 0.00 6.53
6777 8624 2.157738 CCAGAAAAGTTCAGGCCAGAG 58.842 52.381 5.01 0.00 29.18 3.35
6993 8840 6.488715 AGAATCCCTTGAAAGCTTTGTCTAT 58.511 36.000 18.30 0.00 0.00 1.98
7450 9297 1.383523 GGAAGGCGCAAGAAGCTATT 58.616 50.000 10.83 0.00 42.61 1.73
7540 9387 6.150976 ACTTGCCTCGTTTTGATGATTTATCA 59.849 34.615 0.00 0.00 43.92 2.15
7751 9602 7.172875 GGACTGAAATGATGATACCTTCTGATG 59.827 40.741 0.00 0.00 0.00 3.07
7824 9675 8.677148 AACTTCAGTATATATTTCGGTGCATT 57.323 30.769 0.00 0.00 0.00 3.56
7891 9983 2.035832 AGCACAACATACTTTTGCACCC 59.964 45.455 0.00 0.00 35.57 4.61
7895 9987 5.115480 CACAACATACTTTTGCACCCTTTT 58.885 37.500 0.00 0.00 0.00 2.27
7959 10053 2.362077 GGCAGGACACACTGAAAACATT 59.638 45.455 0.00 0.00 40.97 2.71
7976 10070 0.108377 ATTGTCATGGTAGCGACGCA 60.108 50.000 23.70 5.17 34.78 5.24
8002 10096 6.869913 TCAGGAGTTTAAACATACCTTACACG 59.130 38.462 20.06 11.96 30.91 4.49
8011 10105 6.519679 AACATACCTTACACGTATCTGACA 57.480 37.500 0.00 0.00 0.00 3.58
8019 10113 8.932791 ACCTTACACGTATCTGACAATTTTTAG 58.067 33.333 0.00 0.00 0.00 1.85
8072 10166 9.482627 TTTGATGGTAATTTGAAACATGTAACC 57.517 29.630 0.00 0.00 0.00 2.85
8077 10171 8.432805 TGGTAATTTGAAACATGTAACCCATTT 58.567 29.630 0.00 0.00 0.00 2.32
8091 10185 9.847224 ATGTAACCCATTTATAAGGAGTACTTG 57.153 33.333 0.00 0.00 40.37 3.16
8092 10186 9.049050 TGTAACCCATTTATAAGGAGTACTTGA 57.951 33.333 0.00 0.00 40.37 3.02
8093 10187 9.322773 GTAACCCATTTATAAGGAGTACTTGAC 57.677 37.037 0.00 0.00 40.37 3.18
8094 10188 7.504926 ACCCATTTATAAGGAGTACTTGACA 57.495 36.000 0.00 0.00 40.37 3.58
8095 10189 7.924541 ACCCATTTATAAGGAGTACTTGACAA 58.075 34.615 0.00 0.00 40.37 3.18
8096 10190 7.827729 ACCCATTTATAAGGAGTACTTGACAAC 59.172 37.037 0.00 0.00 40.37 3.32
8097 10191 7.827236 CCCATTTATAAGGAGTACTTGACAACA 59.173 37.037 0.00 0.00 40.37 3.33
8098 10192 9.226606 CCATTTATAAGGAGTACTTGACAACAA 57.773 33.333 0.00 0.00 40.37 2.83
8147 10241 8.770828 TGTTACATGTTTAGTTTACTTCAGAGC 58.229 33.333 2.30 0.00 0.00 4.09
8148 10242 8.770828 GTTACATGTTTAGTTTACTTCAGAGCA 58.229 33.333 2.30 0.00 0.00 4.26
8149 10243 7.986085 ACATGTTTAGTTTACTTCAGAGCAT 57.014 32.000 0.00 0.00 0.00 3.79
8150 10244 7.810658 ACATGTTTAGTTTACTTCAGAGCATG 58.189 34.615 0.00 0.00 36.08 4.06
8151 10245 6.241207 TGTTTAGTTTACTTCAGAGCATGC 57.759 37.500 10.51 10.51 0.00 4.06
8152 10246 5.107104 TGTTTAGTTTACTTCAGAGCATGCG 60.107 40.000 13.01 0.00 0.00 4.73
8153 10247 3.319137 AGTTTACTTCAGAGCATGCGA 57.681 42.857 13.01 0.05 0.00 5.10
8154 10248 2.996621 AGTTTACTTCAGAGCATGCGAC 59.003 45.455 13.01 10.86 0.00 5.19
8155 10249 2.736721 GTTTACTTCAGAGCATGCGACA 59.263 45.455 13.01 0.00 0.00 4.35
8156 10250 2.967599 TACTTCAGAGCATGCGACAT 57.032 45.000 13.01 0.00 0.00 3.06
8157 10251 1.366679 ACTTCAGAGCATGCGACATG 58.633 50.000 13.01 9.87 0.00 3.21
8163 10257 1.134610 AGAGCATGCGACATGTCATCA 60.135 47.619 24.93 20.54 0.00 3.07
8178 10272 7.218614 ACATGTCATCATTTGGTTTCAACAAT 58.781 30.769 0.00 0.00 31.78 2.71
8206 10300 3.645884 ACACAACGTGCGTAAGTAGATT 58.354 40.909 0.00 0.00 36.98 2.40
8269 10377 6.826231 TGAAAATTTCCATATACGAGCTCCAA 59.174 34.615 8.47 0.00 0.00 3.53
8286 10394 7.540400 CGAGCTCCAATTGAGTATAGAGTTATG 59.460 40.741 8.47 0.00 43.48 1.90
8288 10396 6.931281 GCTCCAATTGAGTATAGAGTTATGCA 59.069 38.462 7.12 0.00 43.48 3.96
8326 10435 0.039618 ACACCAATTGCCCCGAATCT 59.960 50.000 0.00 0.00 0.00 2.40
8353 10462 1.280457 CCAAGTCTAGAACTGGGGCT 58.720 55.000 11.92 0.00 44.57 5.19
8395 10504 1.125093 TTGAGGGCAGGGTTCTTCGA 61.125 55.000 0.00 0.00 0.00 3.71
8407 10516 2.225727 GGTTCTTCGAAAACGGAGCAAT 59.774 45.455 0.00 0.00 0.00 3.56
8474 10583 8.349245 ACATTTCAACGATGTTTCATAAAGACA 58.651 29.630 0.00 0.00 34.18 3.41
8498 10607 4.778904 ACGACAATGTTTTGTGTTATCCG 58.221 39.130 0.00 0.00 46.01 4.18
8499 10608 4.512198 ACGACAATGTTTTGTGTTATCCGA 59.488 37.500 0.00 0.00 46.01 4.55
8500 10609 5.180492 ACGACAATGTTTTGTGTTATCCGAT 59.820 36.000 0.00 0.00 46.01 4.18
8501 10610 5.507876 CGACAATGTTTTGTGTTATCCGATG 59.492 40.000 0.00 0.00 46.01 3.84
8502 10611 5.708948 ACAATGTTTTGTGTTATCCGATGG 58.291 37.500 0.00 0.00 44.36 3.51
8503 10612 4.981806 ATGTTTTGTGTTATCCGATGGG 57.018 40.909 0.00 0.00 0.00 4.00
8504 10613 3.757270 TGTTTTGTGTTATCCGATGGGT 58.243 40.909 0.00 0.00 33.83 4.51
8505 10614 3.504134 TGTTTTGTGTTATCCGATGGGTG 59.496 43.478 0.00 0.00 33.83 4.61
8506 10615 2.411628 TTGTGTTATCCGATGGGTGG 57.588 50.000 0.00 0.00 33.83 4.61
8507 10616 1.574263 TGTGTTATCCGATGGGTGGA 58.426 50.000 0.00 0.00 40.46 4.02
8509 10618 2.158827 TGTGTTATCCGATGGGTGGATG 60.159 50.000 4.80 0.00 45.70 3.51
8510 10619 2.104111 GTGTTATCCGATGGGTGGATGA 59.896 50.000 4.80 0.00 45.70 2.92
8511 10620 2.978978 TGTTATCCGATGGGTGGATGAT 59.021 45.455 4.80 0.00 45.70 2.45
8512 10621 3.007940 TGTTATCCGATGGGTGGATGATC 59.992 47.826 4.80 0.00 45.70 2.92
8513 10622 2.035910 ATCCGATGGGTGGATGATCT 57.964 50.000 0.00 0.00 44.51 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.762289 AAGACACTTCTTGAAGGACTGT 57.238 40.909 13.97 9.37 40.82 3.55
22 23 4.370917 GTGCTTCAAATGCTTGGAGAAAA 58.629 39.130 0.00 0.00 40.25 2.29
46 47 2.273449 CGCCAGAAATCAGGGGCT 59.727 61.111 0.00 0.00 44.23 5.19
48 49 1.026718 GTGACGCCAGAAATCAGGGG 61.027 60.000 7.27 7.27 40.50 4.79
52 53 3.532896 GAGGTGACGCCAGAAATCA 57.467 52.632 7.99 0.00 40.61 2.57
91 92 2.357517 CAGAGGTGGTGGTGCGTC 60.358 66.667 0.00 0.00 0.00 5.19
92 93 3.161450 ACAGAGGTGGTGGTGCGT 61.161 61.111 0.00 0.00 0.00 5.24
129 130 2.357034 GCGGTCACTTCGGAAGCA 60.357 61.111 17.37 1.83 0.00 3.91
136 137 3.755697 GCTTCAAAGCGGTCACTTC 57.244 52.632 0.00 0.00 42.88 3.01
166 167 2.507944 GCAGGATCGCCTCATGGT 59.492 61.111 0.00 0.00 44.80 3.55
176 177 3.040763 GCTCCATCGCGCAGGATC 61.041 66.667 17.69 11.34 32.53 3.36
188 189 2.268920 GACATCTTGGCGGCTCCA 59.731 61.111 11.43 0.00 44.85 3.86
191 192 2.586792 GAGGACATCTTGGCGGCT 59.413 61.111 11.43 0.00 0.00 5.52
194 195 1.519455 GTCGGAGGACATCTTGGCG 60.519 63.158 0.00 0.00 42.91 5.69
241 242 3.764466 CGGCGTCAGAGGGCTCTT 61.764 66.667 14.15 0.00 37.98 2.85
251 252 4.492160 GGCATCTCGTCGGCGTCA 62.492 66.667 10.18 0.00 39.49 4.35
264 265 1.982395 TCGTCTCGGACCTTGGCAT 60.982 57.895 0.00 0.00 0.00 4.40
275 276 4.838486 GAGCGGCCTGTCGTCTCG 62.838 72.222 0.00 0.00 0.00 4.04
343 344 3.926616 TCGGTTTCTTCTGTTCCAGATC 58.073 45.455 0.00 0.00 40.39 2.75
354 355 1.422179 GCTAGGCGCTCGGTTTCTTC 61.422 60.000 7.64 0.00 35.14 2.87
399 400 4.711949 CCCTGCTGCGTGCCTCTT 62.712 66.667 0.00 0.00 42.00 2.85
473 474 4.039357 CCCGTCGTGCGTCACTCT 62.039 66.667 8.07 0.00 39.32 3.24
484 485 4.517934 TCCTAGGCCCTCCCGTCG 62.518 72.222 2.96 0.00 39.21 5.12
486 487 4.159108 CCTCCTAGGCCCTCCCGT 62.159 72.222 2.96 0.00 39.21 5.28
507 508 4.860881 CCGCCTGCCTCCTCCCTA 62.861 72.222 0.00 0.00 0.00 3.53
526 527 4.677151 AAAGCCCCCGACTCCCCT 62.677 66.667 0.00 0.00 0.00 4.79
527 528 3.640257 GAAAAGCCCCCGACTCCCC 62.640 68.421 0.00 0.00 0.00 4.81
528 529 1.269703 TAGAAAAGCCCCCGACTCCC 61.270 60.000 0.00 0.00 0.00 4.30
529 530 0.837940 ATAGAAAAGCCCCCGACTCC 59.162 55.000 0.00 0.00 0.00 3.85
530 531 2.711978 AATAGAAAAGCCCCCGACTC 57.288 50.000 0.00 0.00 0.00 3.36
531 532 3.451402 AAAATAGAAAAGCCCCCGACT 57.549 42.857 0.00 0.00 0.00 4.18
532 533 4.520179 TCTAAAATAGAAAAGCCCCCGAC 58.480 43.478 0.00 0.00 0.00 4.79
533 534 4.847990 TCTAAAATAGAAAAGCCCCCGA 57.152 40.909 0.00 0.00 0.00 5.14
534 535 5.592688 TCATTCTAAAATAGAAAAGCCCCCG 59.407 40.000 4.11 0.00 46.81 5.73
535 536 6.040955 CCTCATTCTAAAATAGAAAAGCCCCC 59.959 42.308 4.11 0.00 46.81 5.40
536 537 6.040955 CCCTCATTCTAAAATAGAAAAGCCCC 59.959 42.308 4.11 0.00 46.81 5.80
537 538 6.461648 GCCCTCATTCTAAAATAGAAAAGCCC 60.462 42.308 4.11 0.00 46.81 5.19
538 539 6.322456 AGCCCTCATTCTAAAATAGAAAAGCC 59.678 38.462 4.11 1.25 46.81 4.35
539 540 7.340122 AGCCCTCATTCTAAAATAGAAAAGC 57.660 36.000 4.11 3.95 46.81 3.51
556 557 1.139498 TGGATGGTTGGAAGCCCTCA 61.139 55.000 0.00 0.00 0.00 3.86
697 700 2.936202 CCTACCTGATTCATGTTGGGG 58.064 52.381 12.46 1.31 0.00 4.96
1221 1646 3.341823 ACTCTCCTCGCTTTTAGACGTA 58.658 45.455 0.00 0.00 0.00 3.57
1222 1647 2.161030 ACTCTCCTCGCTTTTAGACGT 58.839 47.619 0.00 0.00 0.00 4.34
1245 1670 3.691118 TGTAAAGCAATCACAGAGCATCC 59.309 43.478 0.00 0.00 33.66 3.51
1420 1845 0.961019 AAGCACACCGCACAATTCAT 59.039 45.000 0.00 0.00 46.13 2.57
1605 2030 5.156355 CAACACCAACACATTAAGATGCTC 58.844 41.667 0.00 0.00 36.72 4.26
1629 2054 9.651913 AACACAAAATACAAATGGATACCAATC 57.348 29.630 0.00 0.00 36.95 2.67
1630 2055 9.434420 CAACACAAAATACAAATGGATACCAAT 57.566 29.630 0.00 0.00 36.95 3.16
1631 2056 8.642432 TCAACACAAAATACAAATGGATACCAA 58.358 29.630 0.00 0.00 36.95 3.67
1632 2057 8.183104 TCAACACAAAATACAAATGGATACCA 57.817 30.769 0.00 0.00 38.19 3.25
1636 2061 8.530311 TGCTATCAACACAAAATACAAATGGAT 58.470 29.630 0.00 0.00 0.00 3.41
1637 2062 7.890515 TGCTATCAACACAAAATACAAATGGA 58.109 30.769 0.00 0.00 0.00 3.41
1638 2063 8.706492 ATGCTATCAACACAAAATACAAATGG 57.294 30.769 0.00 0.00 0.00 3.16
1639 2064 9.577110 AGATGCTATCAACACAAAATACAAATG 57.423 29.630 0.00 0.00 0.00 2.32
1646 2071 9.577110 CACATTAAGATGCTATCAACACAAAAT 57.423 29.630 0.00 0.00 36.72 1.82
1647 2072 8.575589 ACACATTAAGATGCTATCAACACAAAA 58.424 29.630 0.00 0.00 36.72 2.44
1648 2073 8.109705 ACACATTAAGATGCTATCAACACAAA 57.890 30.769 0.00 0.00 36.72 2.83
1649 2074 7.686438 ACACATTAAGATGCTATCAACACAA 57.314 32.000 0.00 0.00 36.72 3.33
1650 2075 7.361971 CCAACACATTAAGATGCTATCAACACA 60.362 37.037 0.00 0.00 36.72 3.72
1651 2076 6.968904 CCAACACATTAAGATGCTATCAACAC 59.031 38.462 0.00 0.00 36.72 3.32
1652 2077 6.658816 ACCAACACATTAAGATGCTATCAACA 59.341 34.615 0.00 0.00 36.72 3.33
1653 2078 6.968904 CACCAACACATTAAGATGCTATCAAC 59.031 38.462 0.00 0.00 36.72 3.18
1654 2079 6.658816 ACACCAACACATTAAGATGCTATCAA 59.341 34.615 0.00 0.00 36.72 2.57
1655 2080 6.179756 ACACCAACACATTAAGATGCTATCA 58.820 36.000 0.00 0.00 36.72 2.15
1656 2081 6.683974 ACACCAACACATTAAGATGCTATC 57.316 37.500 0.00 0.00 36.72 2.08
1657 2082 6.127647 CCAACACCAACACATTAAGATGCTAT 60.128 38.462 0.00 0.00 36.72 2.97
1658 2083 5.182950 CCAACACCAACACATTAAGATGCTA 59.817 40.000 0.00 0.00 36.72 3.49
1659 2084 4.022068 CCAACACCAACACATTAAGATGCT 60.022 41.667 0.00 0.00 36.72 3.79
1660 2085 4.022416 TCCAACACCAACACATTAAGATGC 60.022 41.667 0.00 0.00 36.72 3.91
1661 2086 5.703978 TCCAACACCAACACATTAAGATG 57.296 39.130 0.00 0.00 39.25 2.90
1662 2087 6.295236 CCAATCCAACACCAACACATTAAGAT 60.295 38.462 0.00 0.00 0.00 2.40
1663 2088 5.010516 CCAATCCAACACCAACACATTAAGA 59.989 40.000 0.00 0.00 0.00 2.10
1664 2089 5.221422 ACCAATCCAACACCAACACATTAAG 60.221 40.000 0.00 0.00 0.00 1.85
1665 2090 4.651503 ACCAATCCAACACCAACACATTAA 59.348 37.500 0.00 0.00 0.00 1.40
1666 2091 4.219115 ACCAATCCAACACCAACACATTA 58.781 39.130 0.00 0.00 0.00 1.90
1667 2092 3.037549 ACCAATCCAACACCAACACATT 58.962 40.909 0.00 0.00 0.00 2.71
1668 2093 2.676748 ACCAATCCAACACCAACACAT 58.323 42.857 0.00 0.00 0.00 3.21
1669 2094 2.151502 ACCAATCCAACACCAACACA 57.848 45.000 0.00 0.00 0.00 3.72
1670 2095 4.434713 GATACCAATCCAACACCAACAC 57.565 45.455 0.00 0.00 0.00 3.32
1823 2249 7.492669 ACCATCGTCTATACTTCAAGAAATGTG 59.507 37.037 0.00 0.00 0.00 3.21
1842 2268 6.127842 ACAGAACAGTTTAAACAAACCATCGT 60.128 34.615 20.06 5.09 33.28 3.73
1896 2322 3.118038 GGCCCATTCACATACTACAAGGA 60.118 47.826 0.00 0.00 0.00 3.36
1899 2325 4.584638 AAGGCCCATTCACATACTACAA 57.415 40.909 0.00 0.00 0.00 2.41
1980 2406 9.373450 AGTCATATCCTGAATACTGTTGTAGAT 57.627 33.333 0.00 0.00 35.07 1.98
2059 2485 0.179086 TGTTGCTCACTGTTCTGCGA 60.179 50.000 0.00 0.00 0.00 5.10
2060 2486 0.657312 TTGTTGCTCACTGTTCTGCG 59.343 50.000 0.00 0.00 0.00 5.18
2082 2508 6.480524 TTGGATTCAGAAAATGTGTAGTCG 57.519 37.500 0.00 0.00 0.00 4.18
2130 2556 0.318955 GTGGCTGTGTGAACAATGGC 60.319 55.000 4.34 4.34 0.00 4.40
2231 2657 2.291411 ACTACGTACCCTCACAGGTCAT 60.291 50.000 0.00 0.00 41.58 3.06
2433 3332 3.575256 ACATTGCCAAGAATCTCAAGCAA 59.425 39.130 14.11 14.11 43.59 3.91
2495 3394 7.201750 GGAGTCTAGATGTGTTTCTACTACCAG 60.202 44.444 0.00 0.00 0.00 4.00
2566 3473 6.983307 ACACATGGAAAATGAAAACGAATCAA 59.017 30.769 0.00 0.00 0.00 2.57
2590 3497 8.001881 TGATTTCTATTCCTGACTGAGTCTAC 57.998 38.462 14.42 0.00 33.15 2.59
2601 3508 7.870509 TCAAGGTTGATGATTTCTATTCCTG 57.129 36.000 0.00 0.00 31.01 3.86
2744 3652 1.543208 CCAAGGCAGTGTACAAGCAGA 60.543 52.381 19.53 0.00 0.00 4.26
2746 3654 0.537143 CCCAAGGCAGTGTACAAGCA 60.537 55.000 19.53 0.00 0.00 3.91
2840 3748 4.652421 ATGCATCACTGTTGTTTTGTGA 57.348 36.364 0.00 0.00 43.53 3.58
2873 3781 8.215736 TGTACCTATACTAGACAGAAGCACATA 58.784 37.037 0.00 0.00 32.00 2.29
2901 3809 6.173339 ACAGAGGGATGTTTATTGTGTACAG 58.827 40.000 0.00 0.00 0.00 2.74
2924 3832 7.417612 ACAAAAGCATCCGTGAATATGAATAC 58.582 34.615 0.00 0.00 0.00 1.89
3017 3925 2.486966 GGGTCTTGATTGCAGCGC 59.513 61.111 0.00 0.00 0.00 5.92
3038 3946 3.385111 CCACTATGACCAGGAGTAGGAAC 59.615 52.174 0.00 0.00 0.00 3.62
3186 4094 7.611467 TCTTACAATCTTGCATACTGTTTGGAT 59.389 33.333 0.00 0.00 0.00 3.41
3187 4095 6.939730 TCTTACAATCTTGCATACTGTTTGGA 59.060 34.615 0.00 0.00 0.00 3.53
3292 4201 0.395862 TAAGAGGCCTAGAGCGTGCT 60.396 55.000 4.42 0.00 45.17 4.40
3427 4349 1.001158 GTAGACTGCATCTAGCCCGTC 60.001 57.143 6.23 0.00 40.76 4.79
3446 4368 4.295201 TGGTATAGCCCAGTTAGATGTGT 58.705 43.478 0.00 0.00 36.04 3.72
3447 4369 4.887748 CTGGTATAGCCCAGTTAGATGTG 58.112 47.826 0.00 0.00 45.81 3.21
3681 5392 3.243168 CCACAGCATTTTAGCGCATGTAT 60.243 43.478 11.47 0.00 40.15 2.29
3682 5393 2.097304 CCACAGCATTTTAGCGCATGTA 59.903 45.455 11.47 0.00 40.15 2.29
3699 5410 4.726583 ACAGTTAGAGAGTAGTCACCACA 58.273 43.478 0.00 0.00 0.00 4.17
3799 5510 7.975616 AGCGTTTGTTAATGATTAAGCATGAAT 59.024 29.630 7.03 0.00 0.00 2.57
3800 5511 7.312154 AGCGTTTGTTAATGATTAAGCATGAA 58.688 30.769 7.03 2.83 0.00 2.57
3810 5521 8.177663 CAGAGAACATTAGCGTTTGTTAATGAT 58.822 33.333 15.63 6.61 46.35 2.45
4010 5721 2.553904 CCACTGCCTCTTGGTTCAGAAT 60.554 50.000 0.00 0.00 35.27 2.40
4200 5911 6.074698 AGGTAGTGGGTTGCAACTATTTAT 57.925 37.500 27.64 12.40 31.83 1.40
4290 6001 6.148480 GGCATGATTGATGGACAGATTAGTAC 59.852 42.308 0.00 0.00 31.99 2.73
4293 6004 5.048921 GTGGCATGATTGATGGACAGATTAG 60.049 44.000 0.00 0.00 31.99 1.73
4331 6042 7.041508 TGACCACACAAATTAATGCCAAAATTC 60.042 33.333 0.00 0.00 0.00 2.17
4396 6234 5.367302 TGGATGATGCGAATCATGAACTAA 58.633 37.500 23.93 0.00 41.02 2.24
4825 6669 9.556030 CGAAGAATGATTAGGGAAAGTAAAAAC 57.444 33.333 0.00 0.00 0.00 2.43
4943 6787 0.768622 TTGTACTGTGGTGAAGGGGG 59.231 55.000 0.00 0.00 0.00 5.40
4950 6794 3.194005 ACTGAAGGTTGTACTGTGGTG 57.806 47.619 0.00 0.00 0.00 4.17
5026 6870 5.324409 TCCTTTGACAAAATATCACAGGCT 58.676 37.500 1.62 0.00 41.80 4.58
5057 6901 8.086522 AGAAGCTACGACTAGTGAAACATTTTA 58.913 33.333 0.00 0.00 41.43 1.52
5069 6913 5.527951 TGTCATAAGGAGAAGCTACGACTAG 59.472 44.000 0.00 0.00 0.00 2.57
5070 6914 5.296283 GTGTCATAAGGAGAAGCTACGACTA 59.704 44.000 0.00 0.00 0.00 2.59
5128 6972 9.533253 GGCATGTTATTTTGCTATGTTAAATCT 57.467 29.630 0.00 0.00 38.88 2.40
5225 7069 9.454585 TCATATCACGTTAAAAATAGTACTCCG 57.545 33.333 0.00 0.00 0.00 4.63
5265 7109 5.000570 AGGGACAAAGTAGAGTAGACAGT 57.999 43.478 0.00 0.00 0.00 3.55
5347 7191 3.337619 CTGGCAGTGTCAGTGCAC 58.662 61.111 29.15 19.99 46.06 4.57
5377 7221 3.541632 ACCAGCAACAATCCCGTAATAG 58.458 45.455 0.00 0.00 0.00 1.73
5595 7439 6.613028 AGCTATGTTGCGACTTGGAAAGGA 62.613 45.833 5.50 0.00 42.84 3.36
5596 7440 4.422712 AGCTATGTTGCGACTTGGAAAGG 61.423 47.826 5.50 0.00 42.84 3.11
5597 7441 2.744202 AGCTATGTTGCGACTTGGAAAG 59.256 45.455 5.50 0.00 43.64 2.62
5598 7442 2.778299 AGCTATGTTGCGACTTGGAAA 58.222 42.857 5.50 0.00 38.13 3.13
5599 7443 2.472695 AGCTATGTTGCGACTTGGAA 57.527 45.000 5.50 0.00 38.13 3.53
5601 7445 3.236816 CAAAAGCTATGTTGCGACTTGG 58.763 45.455 5.50 2.17 38.13 3.61
5602 7446 3.888934 ACAAAAGCTATGTTGCGACTTG 58.111 40.909 5.50 2.23 38.13 3.16
5754 7601 4.416620 CGTGTTACTTTTTGCAGGTTTCA 58.583 39.130 0.00 0.00 0.00 2.69
5905 7752 5.923684 CCTCGAGAACTCATTTAAGATAGGC 59.076 44.000 15.71 0.00 0.00 3.93
6061 7908 3.889538 CTGTAGATGAATCCCTACCACGA 59.110 47.826 0.00 0.00 35.57 4.35
6154 8001 2.092646 TGGTTCAGTCCGATTATTGGGG 60.093 50.000 0.00 0.00 0.00 4.96
6185 8032 5.385198 ACCAAGATTGTTGTAGAACATGGT 58.615 37.500 18.28 18.28 42.83 3.55
6565 8412 5.018539 TCACCGGACTGATAACTAAATGG 57.981 43.478 9.46 0.00 0.00 3.16
6717 8564 4.047822 GCACTCCTCTGTATCTGAAATCG 58.952 47.826 0.00 0.00 0.00 3.34
7450 9297 0.106769 TGCACCTTCTCAACTTGCCA 60.107 50.000 0.00 0.00 31.94 4.92
7824 9675 0.032130 AGTGACGCTTCGAGCAAGAA 59.968 50.000 7.47 0.00 42.58 2.52
7875 9967 4.202315 GGGAAAAGGGTGCAAAAGTATGTT 60.202 41.667 0.00 0.00 0.00 2.71
7891 9983 4.803613 CAGAAGAAAAACGTTGGGGAAAAG 59.196 41.667 0.00 0.00 0.00 2.27
7895 9987 3.007473 ACAGAAGAAAAACGTTGGGGA 57.993 42.857 0.00 0.00 0.00 4.81
7959 10053 0.527600 GATGCGTCGCTACCATGACA 60.528 55.000 19.50 0.00 34.78 3.58
7976 10070 7.548075 CGTGTAAGGTATGTTTAAACTCCTGAT 59.452 37.037 18.72 11.52 0.00 2.90
8019 10113 9.822185 ATTGCCTATAACAATTTCCAAAGATTC 57.178 29.630 0.00 0.00 34.05 2.52
8060 10154 9.185680 ACTCCTTATAAATGGGTTACATGTTTC 57.814 33.333 2.30 0.00 40.44 2.78
8072 10166 8.786826 TGTTGTCAAGTACTCCTTATAAATGG 57.213 34.615 0.00 0.00 0.00 3.16
8103 10197 9.100554 CATGTAACATCCAAAACATGCATTATT 57.899 29.630 0.00 0.00 41.77 1.40
8104 10198 8.651391 CATGTAACATCCAAAACATGCATTAT 57.349 30.769 0.00 0.00 41.77 1.28
8117 10211 9.562408 TGAAGTAAACTAAACATGTAACATCCA 57.438 29.630 0.00 0.00 0.00 3.41
8121 10215 8.770828 GCTCTGAAGTAAACTAAACATGTAACA 58.229 33.333 0.00 0.00 0.00 2.41
8122 10216 8.770828 TGCTCTGAAGTAAACTAAACATGTAAC 58.229 33.333 0.00 0.00 0.00 2.50
8128 10222 5.107104 CGCATGCTCTGAAGTAAACTAAACA 60.107 40.000 17.13 0.00 0.00 2.83
8145 10239 1.963172 ATGATGACATGTCGCATGCT 58.037 45.000 24.66 9.30 35.21 3.79
8146 10240 2.768833 AATGATGACATGTCGCATGC 57.231 45.000 25.48 7.91 36.79 4.06
8147 10241 3.181494 ACCAAATGATGACATGTCGCATG 60.181 43.478 25.48 18.49 36.79 4.06
8148 10242 3.018856 ACCAAATGATGACATGTCGCAT 58.981 40.909 21.56 21.56 36.79 4.73
8149 10243 2.435422 ACCAAATGATGACATGTCGCA 58.565 42.857 20.54 19.93 36.79 5.10
8150 10244 3.492421 AACCAAATGATGACATGTCGC 57.508 42.857 20.54 15.18 36.79 5.19
8151 10245 5.045668 TGAAACCAAATGATGACATGTCG 57.954 39.130 20.54 6.47 36.79 4.35
8152 10246 6.215121 TGTTGAAACCAAATGATGACATGTC 58.785 36.000 19.27 19.27 36.79 3.06
8153 10247 6.159299 TGTTGAAACCAAATGATGACATGT 57.841 33.333 0.00 0.00 36.79 3.21
8154 10248 7.601130 AGATTGTTGAAACCAAATGATGACATG 59.399 33.333 0.00 0.00 36.79 3.21
8155 10249 7.673180 AGATTGTTGAAACCAAATGATGACAT 58.327 30.769 0.00 0.00 38.50 3.06
8156 10250 7.053316 AGATTGTTGAAACCAAATGATGACA 57.947 32.000 0.00 0.00 0.00 3.58
8157 10251 9.079833 CATAGATTGTTGAAACCAAATGATGAC 57.920 33.333 0.00 0.00 0.00 3.06
8163 10257 8.420222 TGTGTTCATAGATTGTTGAAACCAAAT 58.580 29.630 0.00 0.00 33.90 2.32
8178 10272 2.143008 ACGCACGTTGTGTTCATAGA 57.857 45.000 0.00 0.00 37.97 1.98
8206 10300 1.060729 TCCCAACTTCCAATCCGTGA 58.939 50.000 0.00 0.00 0.00 4.35
8269 10377 7.330454 CGAAGCATGCATAACTCTATACTCAAT 59.670 37.037 21.98 0.00 0.00 2.57
8319 10427 1.065418 ACTTGGCCAACCTAGATTCGG 60.065 52.381 16.05 3.02 40.88 4.30
8326 10435 3.260884 CAGTTCTAGACTTGGCCAACCTA 59.739 47.826 16.05 16.91 36.10 3.08
8353 10462 2.801111 CGATCCACGACTCTTATCTCGA 59.199 50.000 0.00 0.00 45.77 4.04
8395 10504 8.085296 TGTTTGTAAATCATATTGCTCCGTTTT 58.915 29.630 0.00 0.00 0.00 2.43
8474 10583 5.683743 CGGATAACACAAAACATTGTCGTTT 59.316 36.000 11.69 0.00 40.79 3.60


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

AutoCloner maintained by Alex Coulton.