Multiple sequence alignment - TraesCS5B01G231900

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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 TraesCS5B01G231900 chr5B 100.000 4162 0 0 1 4162 408971574 408975735 0.000000e+00 7686.0
1 TraesCS5B01G231900 chr5D 92.180 3376 126 51 522 3839 348492076 348495371 0.000000e+00 4645.0
2 TraesCS5B01G231900 chr5D 91.440 514 33 7 1 506 348491519 348492029 0.000000e+00 695.0
3 TraesCS5B01G231900 chr5D 96.875 64 0 2 4101 4162 348495374 348495437 5.690000e-19 106.0
4 TraesCS5B01G231900 chr5A 87.727 3634 185 94 310 3770 448627542 448631087 0.000000e+00 3999.0
5 TraesCS5B01G231900 chr5A 90.435 115 3 1 213 319 448627278 448627392 1.210000e-30 145.0
6 TraesCS5B01G231900 chr5A 90.541 74 7 0 3766 3839 448631271 448631344 9.520000e-17 99.0
7 TraesCS5B01G231900 chr6B 90.809 272 23 2 3833 4103 583189240 583188970 3.060000e-96 363.0
8 TraesCS5B01G231900 chr7B 91.288 264 21 2 3839 4101 700725134 700725396 3.960000e-95 359.0
9 TraesCS5B01G231900 chr7B 90.566 265 22 3 3840 4103 492756722 492756460 8.560000e-92 348.0
10 TraesCS5B01G231900 chr7B 90.840 262 21 3 3840 4100 713286188 713286447 8.560000e-92 348.0
11 TraesCS5B01G231900 chr4B 91.538 260 20 2 3840 4098 418510722 418510980 1.420000e-94 357.0
12 TraesCS5B01G231900 chr6A 91.221 262 21 2 3840 4100 610645711 610645971 5.120000e-94 355.0
13 TraesCS5B01G231900 chr3B 91.221 262 21 2 3840 4100 464610213 464610473 5.120000e-94 355.0
14 TraesCS5B01G231900 chr1D 90.530 264 23 2 3838 4100 304625115 304625377 8.560000e-92 348.0
15 TraesCS5B01G231900 chr1B 90.000 270 25 2 3832 4100 502627838 502627570 8.560000e-92 348.0
16 TraesCS5B01G231900 chr2A 100.000 28 0 0 3535 3562 517673976 517673949 8.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G231900 chr5B 408971574 408975735 4161 False 7686.000000 7686 100.000000 1 4162 1 chr5B.!!$F1 4161
1 TraesCS5B01G231900 chr5D 348491519 348495437 3918 False 1815.333333 4645 93.498333 1 4162 3 chr5D.!!$F1 4161
2 TraesCS5B01G231900 chr5A 448627278 448631344 4066 False 1414.333333 3999 89.567667 213 3839 3 chr5A.!!$F1 3626

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
890 1141 0.039074 CGACTGTCACTGGACTGACC 60.039 60.0 8.73 0.00 44.61 4.02 F
1524 1811 0.235926 GTTTCTTCGACTGCAGGCAC 59.764 55.0 22.03 4.85 0.00 5.01 F
2148 2459 0.029834 GCAGCGCCTAATTGTCATGG 59.970 55.0 2.29 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 2365 0.108992 CGCATGGCATTGACAAGCTT 60.109 50.0 16.9 0.0 32.65 3.74 R
2770 3107 0.191064 TCTTGAGAGTGGGTGGAGGT 59.809 55.0 0.0 0.0 0.00 3.85 R
3568 3949 0.467290 TGCTTTCAGCTTTTCGGGGT 60.467 50.0 0.0 0.0 42.97 4.95 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
46 47 4.334552 TGTGTATGAATTGCCATGTCAGT 58.665 39.130 0.00 0.00 0.00 3.41
107 108 6.041523 ACAAAAGCTGCCTAATTTCCTAACAA 59.958 34.615 0.00 0.00 0.00 2.83
156 157 6.892658 TGATTTTGGAGCTTTTAACTAGCA 57.107 33.333 10.47 0.00 41.11 3.49
157 158 7.466746 TGATTTTGGAGCTTTTAACTAGCAT 57.533 32.000 10.47 0.00 41.11 3.79
211 212 0.725784 GCCAAAACATCGCACTCGTG 60.726 55.000 0.00 0.00 36.96 4.35
217 218 1.227999 ACATCGCACTCGTGTTTGGG 61.228 55.000 0.00 0.00 36.96 4.12
331 499 1.913762 ACCGAACTAGCAGCCACCT 60.914 57.895 0.00 0.00 0.00 4.00
398 571 9.590451 CAATCTGCTTTAACCATTCACAATAAT 57.410 29.630 0.00 0.00 0.00 1.28
430 605 3.325293 TTTTGCACACTTTGAGGCAAA 57.675 38.095 14.30 14.30 43.43 3.68
433 608 3.540314 TGCACACTTTGAGGCAAAAAT 57.460 38.095 0.00 0.00 32.75 1.82
435 610 4.367450 TGCACACTTTGAGGCAAAAATAC 58.633 39.130 0.00 0.00 32.75 1.89
436 611 4.099266 TGCACACTTTGAGGCAAAAATACT 59.901 37.500 0.00 0.00 32.75 2.12
437 612 5.049828 GCACACTTTGAGGCAAAAATACTT 58.950 37.500 0.00 0.00 32.75 2.24
439 614 6.143919 GCACACTTTGAGGCAAAAATACTTAC 59.856 38.462 0.00 0.00 32.75 2.34
440 615 7.425606 CACACTTTGAGGCAAAAATACTTACT 58.574 34.615 0.00 0.00 32.75 2.24
466 651 5.779806 AATAACAGTGACACGTGATAAGC 57.220 39.130 25.01 7.36 0.00 3.09
527 743 3.185594 CACAAAGCCGTCGTAATTCAGAA 59.814 43.478 0.00 0.00 0.00 3.02
562 783 3.434319 CGAATTGCCGCAGCCTGT 61.434 61.111 0.00 0.00 38.69 4.00
585 806 1.245376 GGCGATTCCCGGGAACAAAA 61.245 55.000 37.91 17.08 36.91 2.44
686 908 0.179097 AAGCGGATCGAGGAAGAAGC 60.179 55.000 0.00 0.00 0.00 3.86
689 922 1.067212 GCGGATCGAGGAAGAAGCTAA 59.933 52.381 0.00 0.00 0.00 3.09
699 932 2.534757 GGAAGAAGCTAACGTACATCGC 59.465 50.000 0.00 0.00 44.19 4.58
763 1000 1.196808 GCGAATCACGAGGAAAGCAAA 59.803 47.619 0.00 0.00 45.77 3.68
778 1015 2.035632 AGCAAACCGGGAGATAGAGAG 58.964 52.381 6.32 0.00 0.00 3.20
779 1016 2.032620 GCAAACCGGGAGATAGAGAGA 58.967 52.381 6.32 0.00 0.00 3.10
784 1021 1.073125 CCGGGAGATAGAGAGAGAGCA 59.927 57.143 0.00 0.00 0.00 4.26
785 1022 2.426522 CGGGAGATAGAGAGAGAGCAG 58.573 57.143 0.00 0.00 0.00 4.24
786 1023 2.224523 CGGGAGATAGAGAGAGAGCAGT 60.225 54.545 0.00 0.00 0.00 4.40
845 1087 4.382754 CGTTTGGACTTTGGTACTACGTAC 59.617 45.833 0.00 0.00 38.19 3.67
846 1088 3.829886 TGGACTTTGGTACTACGTACG 57.170 47.619 15.01 15.01 39.64 3.67
847 1089 3.146066 TGGACTTTGGTACTACGTACGT 58.854 45.455 25.98 25.98 39.64 3.57
848 1090 4.320023 TGGACTTTGGTACTACGTACGTA 58.680 43.478 25.41 25.41 39.64 3.57
890 1141 0.039074 CGACTGTCACTGGACTGACC 60.039 60.000 8.73 0.00 44.61 4.02
891 1142 0.318762 GACTGTCACTGGACTGACCC 59.681 60.000 2.24 0.00 44.61 4.46
892 1143 1.122019 ACTGTCACTGGACTGACCCC 61.122 60.000 8.43 0.00 44.61 4.95
893 1144 2.159819 CTGTCACTGGACTGACCCCG 62.160 65.000 0.00 0.00 44.61 5.73
894 1145 2.603473 TCACTGGACTGACCCCGG 60.603 66.667 0.00 0.00 38.00 5.73
939 1190 5.705609 AGGAAATAAAACAAGTGACGCAT 57.294 34.783 0.00 0.00 0.00 4.73
940 1191 6.084326 AGGAAATAAAACAAGTGACGCATT 57.916 33.333 0.00 0.00 0.00 3.56
1107 1364 2.024319 GCTCACACACACTCGCTCC 61.024 63.158 0.00 0.00 0.00 4.70
1115 1372 0.679640 CACACTCGCTCCCTCTCTCT 60.680 60.000 0.00 0.00 0.00 3.10
1125 1382 0.880278 CCCTCTCTCTCTCTCGCTCG 60.880 65.000 0.00 0.00 0.00 5.03
1126 1383 1.498865 CCTCTCTCTCTCTCGCTCGC 61.499 65.000 0.00 0.00 0.00 5.03
1127 1384 0.530650 CTCTCTCTCTCTCGCTCGCT 60.531 60.000 0.00 0.00 0.00 4.93
1128 1385 0.747852 TCTCTCTCTCTCGCTCGCTA 59.252 55.000 0.00 0.00 0.00 4.26
1142 1399 2.105930 GCTAGCTCTCGGTGCCAG 59.894 66.667 7.70 0.00 0.00 4.85
1330 1612 4.219846 GCAGCATGAGCAGCGACG 62.220 66.667 0.00 0.00 43.44 5.12
1331 1613 2.812609 CAGCATGAGCAGCGACGT 60.813 61.111 0.00 0.00 45.49 4.34
1332 1614 2.507992 AGCATGAGCAGCGACGTC 60.508 61.111 5.18 5.18 45.49 4.34
1333 1615 3.906649 GCATGAGCAGCGACGTCG 61.907 66.667 32.57 32.57 41.58 5.12
1334 1616 3.250323 CATGAGCAGCGACGTCGG 61.250 66.667 36.13 22.87 40.23 4.79
1524 1811 0.235926 GTTTCTTCGACTGCAGGCAC 59.764 55.000 22.03 4.85 0.00 5.01
1648 1935 1.215647 CGACCTCCTGCTGGTACAC 59.784 63.158 9.73 0.40 38.03 2.90
1653 1940 0.667487 CTCCTGCTGGTACACACACG 60.667 60.000 9.73 0.00 34.23 4.49
1654 1941 2.317609 CCTGCTGGTACACACACGC 61.318 63.158 0.51 0.00 0.00 5.34
1660 1947 3.411351 GTACACACACGCTGCCCG 61.411 66.667 0.00 0.00 44.21 6.13
1661 1948 4.673298 TACACACACGCTGCCCGG 62.673 66.667 0.00 0.00 42.52 5.73
1743 2033 5.243207 AGATTTCCTCGGTCGTGTTAAAAT 58.757 37.500 0.00 0.00 0.00 1.82
1764 2054 3.390135 TCGTCGCTTTCTCTCATTGTTT 58.610 40.909 0.00 0.00 0.00 2.83
1826 2116 1.297598 GCCGGTCGCAATCAATTCG 60.298 57.895 1.90 0.00 37.47 3.34
1836 2126 2.270297 AATCAATTCGGGCTGCGTGC 62.270 55.000 0.00 0.00 41.94 5.34
1907 2200 5.297569 ACTCTTTCCTCTGTAAGCAAAGT 57.702 39.130 0.00 0.00 31.08 2.66
1910 2203 2.743636 TCCTCTGTAAGCAAAGTCCG 57.256 50.000 0.00 0.00 0.00 4.79
1921 2214 0.905337 CAAAGTCCGTCCCTCCCTCT 60.905 60.000 0.00 0.00 0.00 3.69
1953 2258 1.299773 GATCGGCTTCAGCTCTCGG 60.300 63.158 0.00 0.00 41.70 4.63
1964 2269 2.352032 GCTCTCGGTAGGCCTGTGT 61.352 63.158 17.99 0.00 0.00 3.72
1965 2270 1.889530 GCTCTCGGTAGGCCTGTGTT 61.890 60.000 17.99 0.00 0.00 3.32
2030 2339 1.830477 AGGCAAGGACAAAGCACAAAA 59.170 42.857 0.00 0.00 0.00 2.44
2051 2360 6.963049 AAATCGTAGAGTTCGCATTTAACT 57.037 33.333 0.00 0.00 43.08 2.24
2056 2365 5.975344 CGTAGAGTTCGCATTTAACTATGGA 59.025 40.000 0.00 0.00 37.31 3.41
2148 2459 0.029834 GCAGCGCCTAATTGTCATGG 59.970 55.000 2.29 0.00 0.00 3.66
2327 2658 4.899502 AGTAAAGACAGATCTGGGTGTTG 58.100 43.478 26.08 0.80 34.48 3.33
2332 2663 1.074405 ACAGATCTGGGTGTTGCATGT 59.926 47.619 26.08 0.00 34.19 3.21
2385 2716 0.250467 GACTGCTCCTGCCAAAGTCA 60.250 55.000 0.00 0.00 38.69 3.41
2421 2752 7.967854 CGTGATCACTTCATTATTTTTAAGGCA 59.032 33.333 22.95 0.00 36.54 4.75
2424 2755 8.986477 ATCACTTCATTATTTTTAAGGCACAC 57.014 30.769 0.00 0.00 0.00 3.82
2522 2853 1.789576 TTTCTCCAAGAGGCCCACCC 61.790 60.000 0.00 0.00 36.11 4.61
2546 2877 1.122019 AGAAGAACCACCCGTGCTCT 61.122 55.000 0.00 0.00 25.92 4.09
2660 2997 2.818169 GCTCAGGACACCACCACCA 61.818 63.158 0.00 0.00 0.00 4.17
2728 3065 2.181521 GTTGAAACGGGCGACACCA 61.182 57.895 0.00 0.00 42.05 4.17
2770 3107 4.319249 CGACACGCTTCACAGTCA 57.681 55.556 0.00 0.00 0.00 3.41
2784 3121 0.833834 CAGTCACCTCCACCCACTCT 60.834 60.000 0.00 0.00 0.00 3.24
3315 3672 4.808649 GCACGTAGCAGTACTCCC 57.191 61.111 0.00 0.00 44.79 4.30
3316 3673 1.226603 GCACGTAGCAGTACTCCCG 60.227 63.158 0.00 0.00 44.79 5.14
3356 3713 7.039270 TGCCGTGTAATTATATGCTCGATTAT 58.961 34.615 7.75 0.00 0.00 1.28
3357 3714 7.547722 TGCCGTGTAATTATATGCTCGATTATT 59.452 33.333 7.75 0.00 0.00 1.40
3358 3715 9.027129 GCCGTGTAATTATATGCTCGATTATTA 57.973 33.333 0.00 0.00 0.00 0.98
3422 3784 3.846360 TCTTCTCCGGATCTCGTTTTTC 58.154 45.455 3.57 0.00 37.11 2.29
3484 3858 4.487412 GGATCGTCCGTCGCCGTT 62.487 66.667 3.08 0.00 39.67 4.44
3568 3949 2.598686 TTACGGCCGCATACATACAA 57.401 45.000 28.58 2.31 0.00 2.41
3719 4113 7.088589 ACTTGAGCATACATTGTTAATCACC 57.911 36.000 0.00 0.00 0.00 4.02
3720 4114 6.658816 ACTTGAGCATACATTGTTAATCACCA 59.341 34.615 0.00 0.00 0.00 4.17
3721 4115 6.435430 TGAGCATACATTGTTAATCACCAC 57.565 37.500 0.00 0.00 0.00 4.16
3726 4120 6.094048 GCATACATTGTTAATCACCACTCACT 59.906 38.462 0.00 0.00 0.00 3.41
3770 4164 7.589574 TGGCTTCTTTCTGTTTGTTTAAAAC 57.410 32.000 0.00 0.00 0.00 2.43
3824 4407 3.445857 GATAAAGACGGTGGTAGAGCAC 58.554 50.000 3.23 3.23 0.00 4.40
3829 4412 2.125512 GGTGGTAGAGCACGGCAG 60.126 66.667 5.82 0.00 0.00 4.85
3831 4414 2.283604 TGGTAGAGCACGGCAGGA 60.284 61.111 0.00 0.00 0.00 3.86
3839 4422 2.084546 GAGCACGGCAGGATAAAAACT 58.915 47.619 0.00 0.00 0.00 2.66
3840 4423 3.055385 AGAGCACGGCAGGATAAAAACTA 60.055 43.478 0.00 0.00 0.00 2.24
3842 4425 3.007635 GCACGGCAGGATAAAAACTACT 58.992 45.455 0.00 0.00 0.00 2.57
3843 4426 3.439129 GCACGGCAGGATAAAAACTACTT 59.561 43.478 0.00 0.00 0.00 2.24
3844 4427 4.436986 GCACGGCAGGATAAAAACTACTTC 60.437 45.833 0.00 0.00 0.00 3.01
3845 4428 4.094442 CACGGCAGGATAAAAACTACTTCC 59.906 45.833 0.00 0.00 0.00 3.46
3846 4429 4.019591 ACGGCAGGATAAAAACTACTTCCT 60.020 41.667 0.00 0.00 37.29 3.36
3848 4431 5.064834 CGGCAGGATAAAAACTACTTCCTTC 59.935 44.000 0.00 0.00 34.59 3.46
3849 4432 5.944007 GGCAGGATAAAAACTACTTCCTTCA 59.056 40.000 0.00 0.00 34.59 3.02
3850 4433 6.603599 GGCAGGATAAAAACTACTTCCTTCAT 59.396 38.462 0.00 0.00 34.59 2.57
3851 4434 7.122799 GGCAGGATAAAAACTACTTCCTTCATT 59.877 37.037 0.00 0.00 34.59 2.57
3852 4435 8.184848 GCAGGATAAAAACTACTTCCTTCATTC 58.815 37.037 0.00 0.00 34.59 2.67
3853 4436 8.678199 CAGGATAAAAACTACTTCCTTCATTCC 58.322 37.037 0.00 0.00 34.59 3.01
3854 4437 8.390921 AGGATAAAAACTACTTCCTTCATTCCA 58.609 33.333 0.00 0.00 32.94 3.53
3855 4438 8.459635 GGATAAAAACTACTTCCTTCATTCCAC 58.540 37.037 0.00 0.00 0.00 4.02
3856 4439 8.934023 ATAAAAACTACTTCCTTCATTCCACA 57.066 30.769 0.00 0.00 0.00 4.17
3857 4440 7.654022 AAAAACTACTTCCTTCATTCCACAA 57.346 32.000 0.00 0.00 0.00 3.33
3858 4441 7.839680 AAAACTACTTCCTTCATTCCACAAT 57.160 32.000 0.00 0.00 0.00 2.71
3859 4442 6.824305 AACTACTTCCTTCATTCCACAATG 57.176 37.500 0.00 0.00 40.91 2.82
3860 4443 5.880901 ACTACTTCCTTCATTCCACAATGT 58.119 37.500 0.00 0.00 40.47 2.71
3861 4444 7.016153 ACTACTTCCTTCATTCCACAATGTA 57.984 36.000 0.00 0.00 40.47 2.29
3862 4445 7.106239 ACTACTTCCTTCATTCCACAATGTAG 58.894 38.462 0.00 0.00 40.47 2.74
3863 4446 5.880901 ACTTCCTTCATTCCACAATGTAGT 58.119 37.500 0.00 0.00 40.47 2.73
3864 4447 5.707298 ACTTCCTTCATTCCACAATGTAGTG 59.293 40.000 0.00 0.00 40.47 2.74
3865 4448 4.009675 TCCTTCATTCCACAATGTAGTGC 58.990 43.478 0.00 0.00 40.47 4.40
3866 4449 3.129287 CCTTCATTCCACAATGTAGTGCC 59.871 47.826 0.00 0.00 40.47 5.01
3867 4450 3.719268 TCATTCCACAATGTAGTGCCT 57.281 42.857 0.00 0.00 40.47 4.75
3868 4451 4.835284 TCATTCCACAATGTAGTGCCTA 57.165 40.909 0.00 0.00 40.47 3.93
3869 4452 5.372343 TCATTCCACAATGTAGTGCCTAT 57.628 39.130 0.00 0.00 40.47 2.57
3870 4453 6.493189 TCATTCCACAATGTAGTGCCTATA 57.507 37.500 0.00 0.00 40.47 1.31
3871 4454 6.288294 TCATTCCACAATGTAGTGCCTATAC 58.712 40.000 0.00 0.00 40.47 1.47
3872 4455 5.685520 TTCCACAATGTAGTGCCTATACA 57.314 39.130 0.00 0.00 38.18 2.29
3873 4456 5.887214 TCCACAATGTAGTGCCTATACAT 57.113 39.130 0.00 0.99 43.90 2.29
3875 4458 6.658849 TCCACAATGTAGTGCCTATACATTT 58.341 36.000 12.88 5.65 46.59 2.32
3876 4459 7.116075 TCCACAATGTAGTGCCTATACATTTT 58.884 34.615 12.88 6.95 46.59 1.82
3877 4460 7.613801 TCCACAATGTAGTGCCTATACATTTTT 59.386 33.333 12.88 4.32 46.59 1.94
3878 4461 8.898761 CCACAATGTAGTGCCTATACATTTTTA 58.101 33.333 12.88 0.00 46.59 1.52
3887 4470 9.461312 AGTGCCTATACATTTTTATGAAAGTCA 57.539 29.630 0.00 0.00 0.00 3.41
3906 4489 8.926715 AAAGTCAAACTTTATCAACTTTGACC 57.073 30.769 15.18 2.61 45.75 4.02
3907 4490 8.527810 AAAGTCAAACTTTATCAACTTTGACCA 58.472 29.630 15.18 0.00 45.75 4.02
3909 4492 8.340230 GTCAAACTTTATCAACTTTGACCAAG 57.660 34.615 9.86 9.16 43.35 3.61
3911 4494 7.973388 TCAAACTTTATCAACTTTGACCAAGTG 59.027 33.333 14.26 7.05 45.77 3.16
3912 4495 7.404671 AACTTTATCAACTTTGACCAAGTGT 57.595 32.000 14.26 6.35 45.77 3.55
3913 4496 8.514330 AACTTTATCAACTTTGACCAAGTGTA 57.486 30.769 14.26 0.00 45.77 2.90
3914 4497 8.691661 ACTTTATCAACTTTGACCAAGTGTAT 57.308 30.769 13.32 0.00 45.77 2.29
3915 4498 9.787435 ACTTTATCAACTTTGACCAAGTGTATA 57.213 29.630 13.32 0.00 45.77 1.47
3917 4500 8.786826 TTATCAACTTTGACCAAGTGTATAGG 57.213 34.615 0.00 0.00 45.77 2.57
3918 4501 5.556915 TCAACTTTGACCAAGTGTATAGGG 58.443 41.667 0.00 0.00 45.77 3.53
3919 4502 5.308497 TCAACTTTGACCAAGTGTATAGGGA 59.692 40.000 0.00 0.00 45.77 4.20
3920 4503 5.836024 ACTTTGACCAAGTGTATAGGGAA 57.164 39.130 0.00 0.00 44.70 3.97
3921 4504 6.195600 ACTTTGACCAAGTGTATAGGGAAA 57.804 37.500 0.00 0.00 44.70 3.13
3922 4505 6.790319 ACTTTGACCAAGTGTATAGGGAAAT 58.210 36.000 0.00 0.00 44.70 2.17
3923 4506 7.238710 ACTTTGACCAAGTGTATAGGGAAATT 58.761 34.615 0.00 0.00 44.70 1.82
3924 4507 7.176690 ACTTTGACCAAGTGTATAGGGAAATTG 59.823 37.037 0.00 0.00 44.70 2.32
3925 4508 6.134535 TGACCAAGTGTATAGGGAAATTGT 57.865 37.500 0.00 0.00 0.00 2.71
3926 4509 6.177610 TGACCAAGTGTATAGGGAAATTGTC 58.822 40.000 0.00 0.00 0.00 3.18
3927 4510 6.012858 TGACCAAGTGTATAGGGAAATTGTCT 60.013 38.462 0.00 0.00 0.00 3.41
3928 4511 7.181305 TGACCAAGTGTATAGGGAAATTGTCTA 59.819 37.037 0.00 0.00 0.00 2.59
3929 4512 7.336396 ACCAAGTGTATAGGGAAATTGTCTAC 58.664 38.462 0.00 0.00 0.00 2.59
3930 4513 7.037873 ACCAAGTGTATAGGGAAATTGTCTACA 60.038 37.037 0.00 0.00 0.00 2.74
3931 4514 7.993183 CCAAGTGTATAGGGAAATTGTCTACAT 59.007 37.037 0.00 0.00 0.00 2.29
3932 4515 9.046296 CAAGTGTATAGGGAAATTGTCTACATC 57.954 37.037 0.00 0.00 0.00 3.06
3933 4516 8.554490 AGTGTATAGGGAAATTGTCTACATCT 57.446 34.615 0.00 0.00 0.00 2.90
3934 4517 9.656323 AGTGTATAGGGAAATTGTCTACATCTA 57.344 33.333 0.00 0.00 0.00 1.98
3935 4518 9.694137 GTGTATAGGGAAATTGTCTACATCTAC 57.306 37.037 0.00 0.00 0.00 2.59
3936 4519 9.429109 TGTATAGGGAAATTGTCTACATCTACA 57.571 33.333 0.00 0.00 0.00 2.74
3941 4524 8.211629 AGGGAAATTGTCTACATCTACAATACC 58.788 37.037 0.00 0.00 43.66 2.73
3942 4525 7.990886 GGGAAATTGTCTACATCTACAATACCA 59.009 37.037 17.59 0.00 43.66 3.25
3943 4526 9.391006 GGAAATTGTCTACATCTACAATACCAA 57.609 33.333 14.02 0.00 43.66 3.67
3946 4529 9.733556 AATTGTCTACATCTACAATACCAAACA 57.266 29.630 0.00 0.00 43.66 2.83
3947 4530 9.905713 ATTGTCTACATCTACAATACCAAACAT 57.094 29.630 0.00 0.00 42.87 2.71
3988 4571 8.908786 ATAACTCACGATTTATCCAATGATGT 57.091 30.769 0.00 0.00 32.18 3.06
3989 4572 6.609237 ACTCACGATTTATCCAATGATGTG 57.391 37.500 0.00 0.00 32.18 3.21
3990 4573 5.008019 ACTCACGATTTATCCAATGATGTGC 59.992 40.000 0.00 0.00 32.18 4.57
3991 4574 4.880696 TCACGATTTATCCAATGATGTGCA 59.119 37.500 0.00 0.00 32.18 4.57
3992 4575 5.532032 TCACGATTTATCCAATGATGTGCAT 59.468 36.000 0.00 0.00 39.43 3.96
3994 4577 6.698329 CACGATTTATCCAATGATGTGCATTT 59.302 34.615 0.00 0.00 44.68 2.32
3995 4578 6.698329 ACGATTTATCCAATGATGTGCATTTG 59.302 34.615 0.00 0.00 44.68 2.32
3996 4579 6.144886 CGATTTATCCAATGATGTGCATTTGG 59.855 38.462 8.57 8.57 44.68 3.28
3997 4580 5.936187 TTATCCAATGATGTGCATTTGGT 57.064 34.783 12.63 6.06 44.68 3.67
3998 4581 7.415592 TTTATCCAATGATGTGCATTTGGTA 57.584 32.000 12.63 5.40 44.68 3.25
3999 4582 7.600231 TTATCCAATGATGTGCATTTGGTAT 57.400 32.000 12.63 9.03 44.68 2.73
4000 4583 5.936187 TCCAATGATGTGCATTTGGTATT 57.064 34.783 12.63 0.00 44.68 1.89
4001 4584 5.904941 TCCAATGATGTGCATTTGGTATTC 58.095 37.500 12.63 0.00 44.68 1.75
4002 4585 5.051816 CCAATGATGTGCATTTGGTATTCC 58.948 41.667 0.00 0.00 44.68 3.01
4003 4586 5.395435 CCAATGATGTGCATTTGGTATTCCA 60.395 40.000 0.00 0.00 44.68 3.53
4004 4587 4.987408 TGATGTGCATTTGGTATTCCAG 57.013 40.909 0.00 0.00 45.22 3.86
4005 4588 4.598022 TGATGTGCATTTGGTATTCCAGA 58.402 39.130 0.00 0.00 45.22 3.86
4006 4589 4.398988 TGATGTGCATTTGGTATTCCAGAC 59.601 41.667 0.00 0.00 45.22 3.51
4007 4590 2.746904 TGTGCATTTGGTATTCCAGACG 59.253 45.455 0.00 0.00 45.22 4.18
4008 4591 2.747446 GTGCATTTGGTATTCCAGACGT 59.253 45.455 0.00 0.00 45.22 4.34
4009 4592 3.936453 GTGCATTTGGTATTCCAGACGTA 59.064 43.478 0.00 0.00 45.22 3.57
4010 4593 3.936453 TGCATTTGGTATTCCAGACGTAC 59.064 43.478 0.00 0.00 45.22 3.67
4011 4594 3.311596 GCATTTGGTATTCCAGACGTACC 59.688 47.826 0.00 0.00 45.22 3.34
4012 4595 4.766375 CATTTGGTATTCCAGACGTACCT 58.234 43.478 3.28 0.00 45.22 3.08
4013 4596 5.682990 GCATTTGGTATTCCAGACGTACCTA 60.683 44.000 3.28 0.00 45.22 3.08
4014 4597 4.989279 TTGGTATTCCAGACGTACCTAC 57.011 45.455 3.28 0.00 45.22 3.18
4015 4598 4.240881 TGGTATTCCAGACGTACCTACT 57.759 45.455 3.28 0.00 39.03 2.57
4016 4599 4.603131 TGGTATTCCAGACGTACCTACTT 58.397 43.478 3.28 0.00 39.03 2.24
4017 4600 5.018809 TGGTATTCCAGACGTACCTACTTT 58.981 41.667 3.28 0.00 39.03 2.66
4018 4601 5.481473 TGGTATTCCAGACGTACCTACTTTT 59.519 40.000 3.28 0.00 39.03 2.27
4019 4602 6.014327 TGGTATTCCAGACGTACCTACTTTTT 60.014 38.462 3.28 0.00 39.03 1.94
4050 4633 8.916628 AAACATGGCCAAAGTTTATAATGTTT 57.083 26.923 28.25 22.73 40.37 2.83
4051 4634 7.903995 ACATGGCCAAAGTTTATAATGTTTG 57.096 32.000 10.96 0.00 0.00 2.93
4052 4635 7.675062 ACATGGCCAAAGTTTATAATGTTTGA 58.325 30.769 10.96 3.53 32.65 2.69
4053 4636 7.602265 ACATGGCCAAAGTTTATAATGTTTGAC 59.398 33.333 10.96 8.70 32.65 3.18
4054 4637 7.296628 TGGCCAAAGTTTATAATGTTTGACT 57.703 32.000 0.61 1.74 32.65 3.41
4055 4638 7.731054 TGGCCAAAGTTTATAATGTTTGACTT 58.269 30.769 0.61 6.82 32.65 3.01
4056 4639 7.870445 TGGCCAAAGTTTATAATGTTTGACTTC 59.130 33.333 0.61 7.58 32.65 3.01
4057 4640 8.088365 GGCCAAAGTTTATAATGTTTGACTTCT 58.912 33.333 16.30 0.85 32.65 2.85
4058 4641 8.915654 GCCAAAGTTTATAATGTTTGACTTCTG 58.084 33.333 16.30 9.31 32.65 3.02
4059 4642 9.965824 CCAAAGTTTATAATGTTTGACTTCTGT 57.034 29.630 16.30 0.00 32.65 3.41
4073 4656 9.989869 GTTTGACTTCTGTAAAAATCTATAGGC 57.010 33.333 0.00 0.00 29.00 3.93
4074 4657 9.733556 TTTGACTTCTGTAAAAATCTATAGGCA 57.266 29.630 0.00 0.00 0.00 4.75
4075 4658 8.718102 TGACTTCTGTAAAAATCTATAGGCAC 57.282 34.615 0.00 0.00 0.00 5.01
4076 4659 8.540388 TGACTTCTGTAAAAATCTATAGGCACT 58.460 33.333 0.00 0.00 46.37 4.40
4092 4675 5.031066 AGGCACTACATTATAAAAGCGGA 57.969 39.130 0.00 0.00 36.02 5.54
4093 4676 5.057149 AGGCACTACATTATAAAAGCGGAG 58.943 41.667 0.00 0.00 36.02 4.63
4094 4677 4.213482 GGCACTACATTATAAAAGCGGAGG 59.787 45.833 0.00 0.00 0.00 4.30
4095 4678 4.213482 GCACTACATTATAAAAGCGGAGGG 59.787 45.833 0.00 0.00 0.00 4.30
4096 4679 5.607477 CACTACATTATAAAAGCGGAGGGA 58.393 41.667 0.00 0.00 0.00 4.20
4097 4680 5.696724 CACTACATTATAAAAGCGGAGGGAG 59.303 44.000 0.00 0.00 0.00 4.30
4098 4681 4.772886 ACATTATAAAAGCGGAGGGAGT 57.227 40.909 0.00 0.00 0.00 3.85
4099 4682 5.881923 ACATTATAAAAGCGGAGGGAGTA 57.118 39.130 0.00 0.00 0.00 2.59
4100 4683 5.608449 ACATTATAAAAGCGGAGGGAGTAC 58.392 41.667 0.00 0.00 0.00 2.73
4101 4684 4.677673 TTATAAAAGCGGAGGGAGTACC 57.322 45.455 0.00 0.00 40.67 3.34
4102 4685 1.941377 TAAAAGCGGAGGGAGTACCA 58.059 50.000 0.00 0.00 43.89 3.25
4103 4686 1.061546 AAAAGCGGAGGGAGTACCAA 58.938 50.000 0.00 0.00 43.89 3.67
4104 4687 1.061546 AAAGCGGAGGGAGTACCAAA 58.938 50.000 0.00 0.00 43.89 3.28
4105 4688 0.613777 AAGCGGAGGGAGTACCAAAG 59.386 55.000 0.00 0.00 43.89 2.77
4106 4689 0.544595 AGCGGAGGGAGTACCAAAGT 60.545 55.000 0.00 0.00 43.89 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.446931 TGGCAATTCATACACAAGAGACTTAAA 59.553 33.333 0.00 0.00 0.00 1.52
18 19 5.124457 ACATGGCAATTCATACACAAGAGAC 59.876 40.000 0.00 0.00 0.00 3.36
33 34 5.255687 TCACAAGATTACTGACATGGCAAT 58.744 37.500 1.11 0.00 0.00 3.56
46 47 8.547481 TCCAGGTTAGTATCATCACAAGATTA 57.453 34.615 0.00 0.00 30.20 1.75
79 80 6.664428 AGGAAATTAGGCAGCTTTTGTTTA 57.336 33.333 0.00 0.00 0.00 2.01
135 136 9.559732 AAAAATGCTAGTTAAAAGCTCCAAAAT 57.440 25.926 11.25 0.00 40.73 1.82
200 201 1.070786 ACCCAAACACGAGTGCGAT 59.929 52.632 2.76 0.00 41.64 4.58
201 202 1.885388 CACCCAAACACGAGTGCGA 60.885 57.895 2.76 0.00 41.64 5.10
202 203 2.631428 CACCCAAACACGAGTGCG 59.369 61.111 2.76 0.00 44.79 5.34
211 212 2.352715 GCCAGAATACTTGCACCCAAAC 60.353 50.000 0.00 0.00 35.29 2.93
217 218 1.394917 CACGAGCCAGAATACTTGCAC 59.605 52.381 0.00 0.00 37.27 4.57
331 499 2.281484 GGAGGTCAAAGCCACGCA 60.281 61.111 0.00 0.00 0.00 5.24
335 503 1.771854 TGTTACAGGAGGTCAAAGCCA 59.228 47.619 0.00 0.00 0.00 4.75
398 571 7.600375 TCAAAGTGTGCAAAATGTTTGAGTTTA 59.400 29.630 4.93 0.00 31.88 2.01
433 608 9.748708 ACGTGTCACTGTTATTTTAAGTAAGTA 57.251 29.630 0.65 0.00 0.00 2.24
435 610 8.757789 TCACGTGTCACTGTTATTTTAAGTAAG 58.242 33.333 16.51 0.00 0.00 2.34
436 611 8.645730 TCACGTGTCACTGTTATTTTAAGTAA 57.354 30.769 16.51 0.00 0.00 2.24
437 612 8.821147 ATCACGTGTCACTGTTATTTTAAGTA 57.179 30.769 16.51 0.00 0.00 2.24
439 614 9.741168 CTTATCACGTGTCACTGTTATTTTAAG 57.259 33.333 16.51 0.00 0.00 1.85
440 615 8.225107 GCTTATCACGTGTCACTGTTATTTTAA 58.775 33.333 16.51 0.00 0.00 1.52
448 633 1.268625 TCGCTTATCACGTGTCACTGT 59.731 47.619 16.51 0.00 0.00 3.55
452 637 1.990799 CCTTCGCTTATCACGTGTCA 58.009 50.000 16.51 1.21 0.00 3.58
466 651 3.664537 GCTTTAAGTCTTTGACGCCTTCG 60.665 47.826 0.00 0.00 37.67 3.79
496 681 2.539953 CGACGGCTTTGTGCTTTGTTTA 60.540 45.455 0.00 0.00 42.39 2.01
517 713 1.134907 TCGGCGAGGGTTCTGAATTAC 60.135 52.381 4.99 0.00 0.00 1.89
527 743 0.249322 CGAAATATGTCGGCGAGGGT 60.249 55.000 11.20 1.25 37.37 4.34
562 783 4.789173 TCCCGGGAATCGCCTCCA 62.789 66.667 24.50 0.00 37.20 3.86
686 908 0.874607 GGCTGGGCGATGTACGTTAG 60.875 60.000 0.00 0.00 44.60 2.34
689 922 2.457743 TTTGGCTGGGCGATGTACGT 62.458 55.000 0.00 0.00 44.60 3.57
763 1000 1.073284 GCTCTCTCTCTATCTCCCGGT 59.927 57.143 0.00 0.00 0.00 5.28
778 1015 0.952984 GTGGTTGGCTGACTGCTCTC 60.953 60.000 4.20 0.00 42.39 3.20
779 1016 1.072159 GTGGTTGGCTGACTGCTCT 59.928 57.895 4.20 0.00 42.39 4.09
784 1021 0.550147 ATAGGGGTGGTTGGCTGACT 60.550 55.000 0.00 0.00 0.00 3.41
785 1022 0.107165 GATAGGGGTGGTTGGCTGAC 60.107 60.000 0.00 0.00 0.00 3.51
786 1023 0.253160 AGATAGGGGTGGTTGGCTGA 60.253 55.000 0.00 0.00 0.00 4.26
845 1087 3.921021 CCAAAGTCAGTTAGCAGAGTACG 59.079 47.826 0.00 0.00 0.00 3.67
846 1088 3.680458 GCCAAAGTCAGTTAGCAGAGTAC 59.320 47.826 0.00 0.00 0.00 2.73
847 1089 3.306780 GGCCAAAGTCAGTTAGCAGAGTA 60.307 47.826 0.00 0.00 0.00 2.59
848 1090 2.551071 GGCCAAAGTCAGTTAGCAGAGT 60.551 50.000 0.00 0.00 0.00 3.24
918 1169 5.118510 CCAATGCGTCACTTGTTTTATTTCC 59.881 40.000 0.00 0.00 0.00 3.13
939 1190 2.106684 TGTACATACACCAGTTGGCCAA 59.893 45.455 16.05 16.05 39.32 4.52
940 1191 1.700186 TGTACATACACCAGTTGGCCA 59.300 47.619 0.00 0.00 39.32 5.36
1020 1271 4.785453 CCTCCAACGCCAGAGCCC 62.785 72.222 0.00 0.00 34.57 5.19
1107 1364 1.498865 GCGAGCGAGAGAGAGAGAGG 61.499 65.000 0.00 0.00 0.00 3.69
1125 1382 2.105930 CTGGCACCGAGAGCTAGC 59.894 66.667 6.62 6.62 33.84 3.42
1126 1383 1.315981 TGTCTGGCACCGAGAGCTAG 61.316 60.000 0.00 0.00 41.36 3.42
1127 1384 0.898326 TTGTCTGGCACCGAGAGCTA 60.898 55.000 0.00 0.00 0.00 3.32
1128 1385 2.164865 CTTGTCTGGCACCGAGAGCT 62.165 60.000 0.00 0.00 0.00 4.09
1189 1453 1.002990 CTGTCTCCATGGTGCAGCA 60.003 57.895 22.56 22.56 0.00 4.41
1336 1618 4.821589 CAGGAAGGAGTCGCCGCC 62.822 72.222 0.31 0.31 43.43 6.13
1338 1620 3.708220 GAGCAGGAAGGAGTCGCCG 62.708 68.421 0.00 0.00 43.43 6.46
1339 1621 2.185608 GAGCAGGAAGGAGTCGCC 59.814 66.667 0.00 0.00 0.00 5.54
1340 1622 2.202676 CGAGCAGGAAGGAGTCGC 60.203 66.667 0.00 0.00 0.00 5.19
1341 1623 2.492090 CCGAGCAGGAAGGAGTCG 59.508 66.667 0.00 0.00 45.00 4.18
1342 1624 1.985116 ACCCGAGCAGGAAGGAGTC 60.985 63.158 0.00 0.00 45.00 3.36
1343 1625 2.120718 ACCCGAGCAGGAAGGAGT 59.879 61.111 0.00 0.00 45.00 3.85
1344 1626 2.581354 CACCCGAGCAGGAAGGAG 59.419 66.667 0.00 0.00 45.00 3.69
1404 1686 1.609794 GGGGAAGAGGTCGTGGAGT 60.610 63.158 0.00 0.00 0.00 3.85
1458 1745 1.878102 GCCGAAGAGGAAAACAGAGCA 60.878 52.381 0.00 0.00 45.00 4.26
1488 1775 2.457366 AACGGCGAGTTCAATTCTCT 57.543 45.000 16.62 0.00 39.16 3.10
1660 1947 1.413077 AGGATAGTAGGTTGCTTCGCC 59.587 52.381 0.00 0.00 0.00 5.54
1661 1948 2.892784 AGGATAGTAGGTTGCTTCGC 57.107 50.000 0.00 0.00 0.00 4.70
1662 1949 6.334102 AGATAAGGATAGTAGGTTGCTTCG 57.666 41.667 0.00 0.00 0.00 3.79
1663 1950 7.382759 CGAAAGATAAGGATAGTAGGTTGCTTC 59.617 40.741 0.00 0.00 0.00 3.86
1664 1951 7.210873 CGAAAGATAAGGATAGTAGGTTGCTT 58.789 38.462 0.00 0.00 0.00 3.91
1665 1952 6.739008 GCGAAAGATAAGGATAGTAGGTTGCT 60.739 42.308 0.00 0.00 0.00 3.91
1666 1953 5.405873 GCGAAAGATAAGGATAGTAGGTTGC 59.594 44.000 0.00 0.00 0.00 4.17
1667 1954 5.629849 CGCGAAAGATAAGGATAGTAGGTTG 59.370 44.000 0.00 0.00 0.00 3.77
1668 1955 5.301298 ACGCGAAAGATAAGGATAGTAGGTT 59.699 40.000 15.93 0.00 0.00 3.50
1669 1956 4.826183 ACGCGAAAGATAAGGATAGTAGGT 59.174 41.667 15.93 0.00 0.00 3.08
1670 1957 5.373981 ACGCGAAAGATAAGGATAGTAGG 57.626 43.478 15.93 0.00 0.00 3.18
1671 1958 5.392286 GGACGCGAAAGATAAGGATAGTAG 58.608 45.833 15.93 0.00 0.00 2.57
1672 1959 4.083643 CGGACGCGAAAGATAAGGATAGTA 60.084 45.833 15.93 0.00 0.00 1.82
1673 1960 3.304525 CGGACGCGAAAGATAAGGATAGT 60.305 47.826 15.93 0.00 0.00 2.12
1674 1961 3.058432 TCGGACGCGAAAGATAAGGATAG 60.058 47.826 15.93 0.00 0.00 2.08
1675 1962 2.880268 TCGGACGCGAAAGATAAGGATA 59.120 45.455 15.93 0.00 0.00 2.59
1732 2022 3.737266 AGAAAGCGACGATTTTAACACGA 59.263 39.130 12.88 0.00 0.00 4.35
1743 2033 2.724977 ACAATGAGAGAAAGCGACGA 57.275 45.000 0.00 0.00 0.00 4.20
1836 2126 3.114616 CTTCTCGTGCTGCGGTGG 61.115 66.667 0.00 0.00 41.72 4.61
1907 2200 1.927569 CTGAGAGAGGGAGGGACGGA 61.928 65.000 0.00 0.00 0.00 4.69
1910 2203 0.629058 AGTCTGAGAGAGGGAGGGAC 59.371 60.000 0.00 0.00 0.00 4.46
1921 2214 1.410517 GCCGATCAATGGAGTCTGAGA 59.589 52.381 0.00 0.00 0.00 3.27
1965 2270 2.572104 GGGCAGAGACCTAGAGGAAAAA 59.428 50.000 1.60 0.00 38.94 1.94
1971 2276 1.830408 CCGGGGCAGAGACCTAGAG 60.830 68.421 0.00 0.00 0.00 2.43
1972 2277 2.279073 CCGGGGCAGAGACCTAGA 59.721 66.667 0.00 0.00 0.00 2.43
1973 2278 2.042843 ACCGGGGCAGAGACCTAG 60.043 66.667 6.32 0.00 0.00 3.02
2030 2339 6.641314 CCATAGTTAAATGCGAACTCTACGAT 59.359 38.462 0.00 0.00 38.16 3.73
2051 2360 3.084536 TGGCATTGACAAGCTTCCATA 57.915 42.857 0.00 0.00 0.00 2.74
2056 2365 0.108992 CGCATGGCATTGACAAGCTT 60.109 50.000 16.90 0.00 32.65 3.74
2148 2459 2.555757 GCAAATCATAGGGTCATCAGGC 59.444 50.000 0.00 0.00 0.00 4.85
2204 2520 1.536766 CAATCCTACCGTACCGCGATA 59.463 52.381 8.23 0.00 44.77 2.92
2327 2658 5.818136 TCTTTGCTACCATCTAAACATGC 57.182 39.130 0.00 0.00 0.00 4.06
2385 2716 4.699637 TGAAGTGATCACGTAAAAGGTGT 58.300 39.130 19.85 0.00 35.64 4.16
2415 2746 2.261729 TCACATACCCAGTGTGCCTTA 58.738 47.619 1.58 0.00 45.01 2.69
2421 2752 5.569355 TCATTCAATTCACATACCCAGTGT 58.431 37.500 0.00 0.00 38.16 3.55
2440 2771 8.177663 GCGATCATCAACCGATTAATAATCATT 58.822 33.333 12.82 4.21 37.78 2.57
2452 2783 1.521457 GGCAGCGATCATCAACCGA 60.521 57.895 0.00 0.00 0.00 4.69
2522 2853 1.672356 CGGGTGGTTCTTCTGCCAG 60.672 63.158 0.00 0.00 35.14 4.85
2577 2908 2.040278 AGGAGGAGGAGGTGCTGG 59.960 66.667 0.00 0.00 0.00 4.85
2644 2975 1.836391 CTTGGTGGTGGTGTCCTGA 59.164 57.895 0.00 0.00 0.00 3.86
2686 3023 2.441164 GAGGAGCAGCGAGGGAGA 60.441 66.667 0.00 0.00 0.00 3.71
2770 3107 0.191064 TCTTGAGAGTGGGTGGAGGT 59.809 55.000 0.00 0.00 0.00 3.85
3137 3484 0.668535 CTCGCGTCCTCATGATGGTA 59.331 55.000 5.77 0.00 0.00 3.25
3298 3655 1.226603 CGGGAGTACTGCTACGTGC 60.227 63.158 14.52 0.00 43.25 5.34
3299 3656 1.002684 GATCGGGAGTACTGCTACGTG 60.003 57.143 14.52 0.27 0.00 4.49
3310 3667 1.757340 GGAACTCGGGATCGGGAGT 60.757 63.158 10.53 10.53 45.01 3.85
3312 3669 2.635787 ATCGGAACTCGGGATCGGGA 62.636 60.000 0.00 0.00 39.73 5.14
3313 3670 2.201022 ATCGGAACTCGGGATCGGG 61.201 63.158 0.00 0.00 43.72 5.14
3314 3671 1.007271 CATCGGAACTCGGGATCGG 60.007 63.158 0.00 0.00 39.77 4.18
3315 3672 1.661821 GCATCGGAACTCGGGATCG 60.662 63.158 0.00 0.00 39.77 3.69
3316 3673 1.301009 GGCATCGGAACTCGGGATC 60.301 63.158 0.00 0.00 39.77 3.36
3356 3713 4.422057 TCACTCACCCACTCCTTATGTAA 58.578 43.478 0.00 0.00 0.00 2.41
3357 3714 4.055710 TCACTCACCCACTCCTTATGTA 57.944 45.455 0.00 0.00 0.00 2.29
3358 3715 2.902608 TCACTCACCCACTCCTTATGT 58.097 47.619 0.00 0.00 0.00 2.29
3422 3784 3.067883 TCAGAGCATCCGAGAAGAAGATG 59.932 47.826 0.00 0.00 40.30 2.90
3484 3858 2.199652 CCGGGCTTTGTTCCTTGCA 61.200 57.895 0.00 0.00 0.00 4.08
3568 3949 0.467290 TGCTTTCAGCTTTTCGGGGT 60.467 50.000 0.00 0.00 42.97 4.95
3679 4070 5.218139 GCTCAAGTCAAGTCCATTCTTTTG 58.782 41.667 0.00 0.00 0.00 2.44
3719 4113 0.595095 GGAAGGCTTTGCAGTGAGTG 59.405 55.000 0.00 0.00 0.00 3.51
3720 4114 0.475906 AGGAAGGCTTTGCAGTGAGT 59.524 50.000 0.00 0.00 0.00 3.41
3721 4115 1.163554 GAGGAAGGCTTTGCAGTGAG 58.836 55.000 0.00 0.00 0.00 3.51
3726 4120 0.478072 TTCCAGAGGAAGGCTTTGCA 59.522 50.000 0.00 0.00 36.71 4.08
3770 4164 0.934436 CTTTGCCGGACAGCGTTTTG 60.934 55.000 5.05 0.00 34.65 2.44
3824 4407 4.514401 AGGAAGTAGTTTTTATCCTGCCG 58.486 43.478 0.00 0.00 39.03 5.69
3829 4412 8.459635 GTGGAATGAAGGAAGTAGTTTTTATCC 58.540 37.037 0.00 0.00 0.00 2.59
3831 4414 8.934023 TGTGGAATGAAGGAAGTAGTTTTTAT 57.066 30.769 0.00 0.00 0.00 1.40
3839 4422 6.878923 CACTACATTGTGGAATGAAGGAAGTA 59.121 38.462 7.20 0.00 41.49 2.24
3840 4423 5.707298 CACTACATTGTGGAATGAAGGAAGT 59.293 40.000 7.20 0.00 41.49 3.01
3842 4425 4.458989 GCACTACATTGTGGAATGAAGGAA 59.541 41.667 7.20 0.00 41.49 3.36
3843 4426 4.009675 GCACTACATTGTGGAATGAAGGA 58.990 43.478 7.20 0.00 41.49 3.36
3844 4427 3.129287 GGCACTACATTGTGGAATGAAGG 59.871 47.826 7.20 0.00 41.49 3.46
3845 4428 4.012374 AGGCACTACATTGTGGAATGAAG 58.988 43.478 7.20 0.00 41.96 3.02
3846 4429 4.032960 AGGCACTACATTGTGGAATGAA 57.967 40.909 7.20 0.00 41.96 2.57
3861 4444 9.461312 TGACTTTCATAAAAATGTATAGGCACT 57.539 29.630 0.00 0.00 46.37 4.40
3899 4482 7.176690 ACAATTTCCCTATACACTTGGTCAAAG 59.823 37.037 0.00 0.00 42.07 2.77
3900 4483 7.007723 ACAATTTCCCTATACACTTGGTCAAA 58.992 34.615 0.00 0.00 0.00 2.69
3901 4484 6.548321 ACAATTTCCCTATACACTTGGTCAA 58.452 36.000 0.00 0.00 0.00 3.18
3902 4485 6.012858 AGACAATTTCCCTATACACTTGGTCA 60.013 38.462 0.00 0.00 0.00 4.02
3903 4486 6.415573 AGACAATTTCCCTATACACTTGGTC 58.584 40.000 0.00 0.00 0.00 4.02
3904 4487 6.388619 AGACAATTTCCCTATACACTTGGT 57.611 37.500 0.00 0.00 0.00 3.67
3905 4488 7.335627 TGTAGACAATTTCCCTATACACTTGG 58.664 38.462 0.00 0.00 0.00 3.61
3906 4489 8.964476 ATGTAGACAATTTCCCTATACACTTG 57.036 34.615 0.00 0.00 0.00 3.16
3907 4490 8.993424 AGATGTAGACAATTTCCCTATACACTT 58.007 33.333 0.00 0.00 0.00 3.16
3908 4491 8.554490 AGATGTAGACAATTTCCCTATACACT 57.446 34.615 0.00 0.00 0.00 3.55
3909 4492 9.694137 GTAGATGTAGACAATTTCCCTATACAC 57.306 37.037 0.00 0.00 0.00 2.90
3910 4493 9.429109 TGTAGATGTAGACAATTTCCCTATACA 57.571 33.333 0.00 0.00 0.00 2.29
3915 4498 8.211629 GGTATTGTAGATGTAGACAATTTCCCT 58.788 37.037 5.64 0.00 42.27 4.20
3916 4499 7.990886 TGGTATTGTAGATGTAGACAATTTCCC 59.009 37.037 5.64 5.20 42.27 3.97
3917 4500 8.958119 TGGTATTGTAGATGTAGACAATTTCC 57.042 34.615 5.64 9.13 42.27 3.13
3920 4503 9.733556 TGTTTGGTATTGTAGATGTAGACAATT 57.266 29.630 5.64 0.00 42.27 2.32
3921 4504 9.905713 ATGTTTGGTATTGTAGATGTAGACAAT 57.094 29.630 5.65 5.65 45.74 2.71
3962 4545 9.996554 ACATCATTGGATAAATCGTGAGTTATA 57.003 29.630 2.86 0.00 32.50 0.98
3963 4546 8.777413 CACATCATTGGATAAATCGTGAGTTAT 58.223 33.333 2.51 2.51 34.70 1.89
3964 4547 7.254761 GCACATCATTGGATAAATCGTGAGTTA 60.255 37.037 0.00 0.00 30.87 2.24
3965 4548 6.458751 GCACATCATTGGATAAATCGTGAGTT 60.459 38.462 0.00 0.00 30.87 3.01
3966 4549 5.008019 GCACATCATTGGATAAATCGTGAGT 59.992 40.000 0.00 0.00 30.87 3.41
3967 4550 5.007921 TGCACATCATTGGATAAATCGTGAG 59.992 40.000 0.00 0.00 30.87 3.51
3968 4551 4.880696 TGCACATCATTGGATAAATCGTGA 59.119 37.500 0.00 0.00 30.87 4.35
3969 4552 5.172460 TGCACATCATTGGATAAATCGTG 57.828 39.130 0.00 0.00 30.87 4.35
3970 4553 6.395426 AATGCACATCATTGGATAAATCGT 57.605 33.333 0.00 0.00 43.40 3.73
3971 4554 6.144886 CCAAATGCACATCATTGGATAAATCG 59.855 38.462 7.93 0.00 44.23 3.34
3972 4555 6.987992 ACCAAATGCACATCATTGGATAAATC 59.012 34.615 17.12 0.00 44.23 2.17
3973 4556 6.891388 ACCAAATGCACATCATTGGATAAAT 58.109 32.000 17.12 0.00 44.23 1.40
3974 4557 6.297080 ACCAAATGCACATCATTGGATAAA 57.703 33.333 17.12 0.00 44.23 1.40
3975 4558 5.936187 ACCAAATGCACATCATTGGATAA 57.064 34.783 17.12 0.00 44.23 1.75
3976 4559 7.255906 GGAATACCAAATGCACATCATTGGATA 60.256 37.037 17.12 8.79 44.23 2.59
3977 4560 6.463331 GGAATACCAAATGCACATCATTGGAT 60.463 38.462 17.12 6.97 44.23 3.41
3978 4561 5.163426 GGAATACCAAATGCACATCATTGGA 60.163 40.000 17.12 5.42 44.23 3.53
3979 4562 5.051816 GGAATACCAAATGCACATCATTGG 58.948 41.667 11.02 11.02 44.23 3.16
3980 4563 5.662456 TGGAATACCAAATGCACATCATTG 58.338 37.500 0.00 0.00 44.23 2.82
3981 4564 5.657745 TCTGGAATACCAAATGCACATCATT 59.342 36.000 0.00 0.00 46.82 2.57
3982 4565 5.068198 GTCTGGAATACCAAATGCACATCAT 59.932 40.000 0.00 0.00 46.32 2.45
3983 4566 4.398988 GTCTGGAATACCAAATGCACATCA 59.601 41.667 0.00 0.00 46.32 3.07
3984 4567 4.496341 CGTCTGGAATACCAAATGCACATC 60.496 45.833 0.00 0.00 46.32 3.06
3985 4568 3.378112 CGTCTGGAATACCAAATGCACAT 59.622 43.478 0.00 0.00 46.32 3.21
3986 4569 2.746904 CGTCTGGAATACCAAATGCACA 59.253 45.455 0.00 0.00 46.32 4.57
3987 4570 2.747446 ACGTCTGGAATACCAAATGCAC 59.253 45.455 0.00 0.00 46.32 4.57
3988 4571 3.066291 ACGTCTGGAATACCAAATGCA 57.934 42.857 0.00 0.00 46.32 3.96
3989 4572 3.311596 GGTACGTCTGGAATACCAAATGC 59.688 47.826 0.00 0.00 46.32 3.56
3990 4573 4.766375 AGGTACGTCTGGAATACCAAATG 58.234 43.478 0.00 0.00 46.32 2.32
3991 4574 5.659971 AGTAGGTACGTCTGGAATACCAAAT 59.340 40.000 0.00 0.00 46.32 2.32
3992 4575 5.018809 AGTAGGTACGTCTGGAATACCAAA 58.981 41.667 0.00 0.00 46.32 3.28
3993 4576 4.603131 AGTAGGTACGTCTGGAATACCAA 58.397 43.478 0.00 0.00 46.32 3.67
3994 4577 4.240881 AGTAGGTACGTCTGGAATACCA 57.759 45.455 0.00 0.00 44.76 3.25
3995 4578 5.588958 AAAGTAGGTACGTCTGGAATACC 57.411 43.478 0.00 0.00 38.98 2.73
4025 4608 8.782144 CAAACATTATAAACTTTGGCCATGTTT 58.218 29.630 28.44 28.44 41.84 2.83
4026 4609 8.153550 TCAAACATTATAAACTTTGGCCATGTT 58.846 29.630 6.09 12.73 35.60 2.71
4027 4610 7.602265 GTCAAACATTATAAACTTTGGCCATGT 59.398 33.333 6.09 6.11 0.00 3.21
4028 4611 7.818930 AGTCAAACATTATAAACTTTGGCCATG 59.181 33.333 6.09 5.34 30.10 3.66
4029 4612 7.906327 AGTCAAACATTATAAACTTTGGCCAT 58.094 30.769 6.09 0.00 30.10 4.40
4030 4613 7.296628 AGTCAAACATTATAAACTTTGGCCA 57.703 32.000 0.00 0.00 30.10 5.36
4031 4614 8.088365 AGAAGTCAAACATTATAAACTTTGGCC 58.912 33.333 14.60 0.00 30.10 5.36
4032 4615 8.915654 CAGAAGTCAAACATTATAAACTTTGGC 58.084 33.333 11.97 11.97 0.00 4.52
4033 4616 9.965824 ACAGAAGTCAAACATTATAAACTTTGG 57.034 29.630 14.00 6.90 0.00 3.28
4047 4630 9.989869 GCCTATAGATTTTTACAGAAGTCAAAC 57.010 33.333 0.00 0.00 0.00 2.93
4048 4631 9.733556 TGCCTATAGATTTTTACAGAAGTCAAA 57.266 29.630 0.00 0.00 0.00 2.69
4049 4632 9.162764 GTGCCTATAGATTTTTACAGAAGTCAA 57.837 33.333 0.00 0.00 0.00 3.18
4050 4633 8.540388 AGTGCCTATAGATTTTTACAGAAGTCA 58.460 33.333 0.00 0.00 0.00 3.41
4051 4634 8.950208 AGTGCCTATAGATTTTTACAGAAGTC 57.050 34.615 0.00 0.00 0.00 3.01
4052 4635 9.819267 GTAGTGCCTATAGATTTTTACAGAAGT 57.181 33.333 0.00 0.00 0.00 3.01
4053 4636 9.817809 TGTAGTGCCTATAGATTTTTACAGAAG 57.182 33.333 0.00 0.00 0.00 2.85
4064 4647 9.587772 CGCTTTTATAATGTAGTGCCTATAGAT 57.412 33.333 0.00 0.00 0.00 1.98
4065 4648 8.033038 CCGCTTTTATAATGTAGTGCCTATAGA 58.967 37.037 0.00 0.00 0.00 1.98
4066 4649 8.033038 TCCGCTTTTATAATGTAGTGCCTATAG 58.967 37.037 0.00 0.00 0.00 1.31
4067 4650 7.898918 TCCGCTTTTATAATGTAGTGCCTATA 58.101 34.615 0.00 0.00 0.00 1.31
4068 4651 6.765403 TCCGCTTTTATAATGTAGTGCCTAT 58.235 36.000 0.00 0.00 0.00 2.57
4069 4652 6.164417 TCCGCTTTTATAATGTAGTGCCTA 57.836 37.500 0.00 0.00 0.00 3.93
4070 4653 5.031066 TCCGCTTTTATAATGTAGTGCCT 57.969 39.130 0.00 0.00 0.00 4.75
4071 4654 4.213482 CCTCCGCTTTTATAATGTAGTGCC 59.787 45.833 0.00 0.00 0.00 5.01
4072 4655 4.213482 CCCTCCGCTTTTATAATGTAGTGC 59.787 45.833 0.00 0.00 0.00 4.40
4073 4656 5.607477 TCCCTCCGCTTTTATAATGTAGTG 58.393 41.667 0.00 0.00 0.00 2.74
4074 4657 5.365895 ACTCCCTCCGCTTTTATAATGTAGT 59.634 40.000 0.00 0.00 0.00 2.73
4075 4658 5.855045 ACTCCCTCCGCTTTTATAATGTAG 58.145 41.667 0.00 0.00 0.00 2.74
4076 4659 5.881923 ACTCCCTCCGCTTTTATAATGTA 57.118 39.130 0.00 0.00 0.00 2.29
4077 4660 4.772886 ACTCCCTCCGCTTTTATAATGT 57.227 40.909 0.00 0.00 0.00 2.71
4078 4661 4.995487 GGTACTCCCTCCGCTTTTATAATG 59.005 45.833 0.00 0.00 0.00 1.90
4079 4662 4.657039 TGGTACTCCCTCCGCTTTTATAAT 59.343 41.667 0.00 0.00 0.00 1.28
4080 4663 4.032310 TGGTACTCCCTCCGCTTTTATAA 58.968 43.478 0.00 0.00 0.00 0.98
4081 4664 3.645434 TGGTACTCCCTCCGCTTTTATA 58.355 45.455 0.00 0.00 0.00 0.98
4082 4665 2.474112 TGGTACTCCCTCCGCTTTTAT 58.526 47.619 0.00 0.00 0.00 1.40
4083 4666 1.941377 TGGTACTCCCTCCGCTTTTA 58.059 50.000 0.00 0.00 0.00 1.52
4084 4667 1.061546 TTGGTACTCCCTCCGCTTTT 58.938 50.000 0.00 0.00 0.00 2.27
4085 4668 1.003233 CTTTGGTACTCCCTCCGCTTT 59.997 52.381 0.00 0.00 0.00 3.51
4086 4669 0.613777 CTTTGGTACTCCCTCCGCTT 59.386 55.000 0.00 0.00 0.00 4.68
4087 4670 0.544595 ACTTTGGTACTCCCTCCGCT 60.545 55.000 0.00 0.00 0.00 5.52
4088 4671 1.188863 TACTTTGGTACTCCCTCCGC 58.811 55.000 0.00 0.00 0.00 5.54
4089 4672 3.967332 TTTACTTTGGTACTCCCTCCG 57.033 47.619 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.