Multiple sequence alignment - TraesCS1B01G132400

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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 TraesCS1B01G132400 chr1B 100.000 4542 0 0 1 4542 166595588 166591047 0.000000e+00 8388.0
1 TraesCS1B01G132400 chr1D 93.603 4049 171 43 1 4032 109976916 109972939 0.000000e+00 5962.0
2 TraesCS1B01G132400 chr1D 90.813 283 15 5 4210 4483 109972956 109972676 7.180000e-98 368.0
3 TraesCS1B01G132400 chr1D 91.139 79 4 3 4146 4222 381977150 381977073 2.240000e-18 104.0
4 TraesCS1B01G132400 chr1A 92.904 3678 156 42 4 3663 113862123 113858533 0.000000e+00 5249.0
5 TraesCS1B01G132400 chr1A 93.824 340 16 4 3696 4032 113858533 113858196 1.460000e-139 507.0
6 TraesCS1B01G132400 chr1A 89.150 341 18 9 4210 4542 113858213 113857884 1.520000e-109 407.0
7 TraesCS1B01G132400 chr3B 79.085 306 49 12 2294 2590 79121444 79121743 3.580000e-46 196.0
8 TraesCS1B01G132400 chr3B 88.571 140 16 0 995 1134 79120327 79120466 2.170000e-38 171.0
9 TraesCS1B01G132400 chr3B 77.033 209 28 11 4034 4224 732862409 732862203 8.040000e-18 102.0
10 TraesCS1B01G132400 chr3D 78.689 305 51 12 2294 2590 49639510 49639808 1.670000e-44 191.0
11 TraesCS1B01G132400 chr3D 86.250 160 19 3 995 1151 49638360 49638519 2.170000e-38 171.0
12 TraesCS1B01G132400 chr3A 88.571 140 16 0 995 1134 63065925 63066064 2.170000e-38 171.0
13 TraesCS1B01G132400 chr3A 76.547 307 58 11 2294 2590 63067031 63067333 6.080000e-34 156.0
14 TraesCS1B01G132400 chr7A 96.296 81 3 0 4241 4321 149285001 149284921 2.850000e-27 134.0
15 TraesCS1B01G132400 chr2B 92.405 79 5 1 4147 4224 154494413 154494491 1.340000e-20 111.0
16 TraesCS1B01G132400 chr2B 92.405 79 5 1 4147 4224 154605844 154605766 1.340000e-20 111.0
17 TraesCS1B01G132400 chr6D 91.358 81 5 2 4146 4224 363386350 363386430 4.800000e-20 110.0
18 TraesCS1B01G132400 chr2A 89.412 85 5 4 4143 4224 310535799 310535882 2.240000e-18 104.0
19 TraesCS1B01G132400 chr6B 89.873 79 7 1 4147 4224 290223107 290223185 2.890000e-17 100.0
20 TraesCS1B01G132400 chr4D 89.873 79 7 1 4147 4224 51077858 51077936 2.890000e-17 100.0
21 TraesCS1B01G132400 chr5D 86.076 79 9 2 4147 4224 322989618 322989541 2.910000e-12 84.2


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 TraesCS1B01G132400 chr1B 166591047 166595588 4541 True 8388.000000 8388 100.000000 1 4542 1 chr1B.!!$R1 4541
1 TraesCS1B01G132400 chr1D 109972676 109976916 4240 True 3165.000000 5962 92.208000 1 4483 2 chr1D.!!$R2 4482
2 TraesCS1B01G132400 chr1A 113857884 113862123 4239 True 2054.333333 5249 91.959333 4 4542 3 chr1A.!!$R1 4538

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
387 401 0.031043 CGGTTGACTGTACACGTGGA 59.969 55.0 21.57 9.0 0.00 4.02 F
894 908 0.810648 TTGGCTGATCGAAATGGCAC 59.189 50.0 9.84 0.0 34.78 5.01 F
1823 1847 0.461548 TCTGCTCCCTTCATGTAGCG 59.538 55.0 0.00 0.0 37.80 4.26 F
2502 2534 0.613292 TGGGTGTTGGTGTTGCAACT 60.613 50.0 28.61 0.0 32.91 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1796 0.674895 GATGCCAGCTCGTCAAGGTT 60.675 55.000 0.00 0.00 31.91 3.50 R
2490 2522 1.093972 CAGTCACAGTTGCAACACCA 58.906 50.000 30.11 9.20 0.00 4.17 R
3502 3536 1.207329 GAGCTCCACATCGGTACCTTT 59.793 52.381 10.90 0.00 35.57 3.11 R
4026 4082 0.104671 CAAACAAACAGGGCCTGTGG 59.895 55.000 38.18 32.15 44.62 4.17 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
23 24 1.850345 GGGTGGAAGGATGGTGGATTA 59.150 52.381 0.00 0.00 0.00 1.75
27 28 4.165372 GGTGGAAGGATGGTGGATTAAGTA 59.835 45.833 0.00 0.00 0.00 2.24
84 85 1.222567 GGTGGATGGGGTTGTCCTAT 58.777 55.000 0.00 0.00 39.65 2.57
125 126 1.065851 TGTGCTACTCGTTCACGACAA 59.934 47.619 0.00 0.00 44.22 3.18
128 129 2.984471 TGCTACTCGTTCACGACAATTC 59.016 45.455 0.00 0.00 44.22 2.17
138 139 3.511699 TCACGACAATTCTCTTCATCGG 58.488 45.455 0.00 0.00 33.97 4.18
154 155 4.326826 TCATCGGTTCTCAAAGCTTTGAT 58.673 39.130 35.40 20.05 45.26 2.57
155 156 4.154737 TCATCGGTTCTCAAAGCTTTGATG 59.845 41.667 35.40 28.10 45.26 3.07
156 157 2.226437 TCGGTTCTCAAAGCTTTGATGC 59.774 45.455 35.40 26.78 45.26 3.91
157 158 2.589014 GGTTCTCAAAGCTTTGATGCG 58.411 47.619 35.40 25.64 45.26 4.73
158 159 2.226437 GGTTCTCAAAGCTTTGATGCGA 59.774 45.455 35.40 27.20 45.26 5.10
159 160 3.229552 GTTCTCAAAGCTTTGATGCGAC 58.770 45.455 35.40 26.11 45.26 5.19
225 232 3.449227 AGCGGCGATGAAGGACGA 61.449 61.111 12.98 0.00 38.46 4.20
228 235 1.226974 CGGCGATGAAGGACGACAT 60.227 57.895 0.00 0.00 38.46 3.06
231 238 0.924090 GCGATGAAGGACGACATCAC 59.076 55.000 0.00 0.00 41.75 3.06
234 241 0.541863 ATGAAGGACGACATCACCCC 59.458 55.000 0.00 0.00 0.00 4.95
296 310 1.013596 TGTGTTTCTTGTCTGTGCCG 58.986 50.000 0.00 0.00 0.00 5.69
361 375 0.111878 CGTGTCGCGTGTTGTACTTG 60.112 55.000 5.77 0.00 35.54 3.16
370 384 0.319211 TGTTGTACTTGGACGCTCGG 60.319 55.000 0.00 0.00 0.00 4.63
375 389 0.038892 TACTTGGACGCTCGGTTGAC 60.039 55.000 0.00 0.00 0.00 3.18
383 397 1.334992 CGCTCGGTTGACTGTACACG 61.335 60.000 0.00 0.00 0.00 4.49
387 401 0.031043 CGGTTGACTGTACACGTGGA 59.969 55.000 21.57 9.00 0.00 4.02
390 404 2.132762 GTTGACTGTACACGTGGAAGG 58.867 52.381 21.57 10.04 0.00 3.46
391 405 1.405872 TGACTGTACACGTGGAAGGT 58.594 50.000 21.57 13.41 33.66 3.50
421 435 8.512966 CCTTTGGAAAAGGGAAACAAAATAAA 57.487 30.769 10.39 0.00 33.79 1.40
422 436 8.961634 CCTTTGGAAAAGGGAAACAAAATAAAA 58.038 29.630 10.39 0.00 33.79 1.52
464 478 4.037923 ACAACCATCACTACAAAAAGGCAG 59.962 41.667 0.00 0.00 0.00 4.85
466 480 4.074970 ACCATCACTACAAAAAGGCAGAG 58.925 43.478 0.00 0.00 0.00 3.35
507 521 2.661718 GAAGGTGGTCCCTGTTTGAAA 58.338 47.619 0.00 0.00 45.47 2.69
508 522 2.838637 AGGTGGTCCCTGTTTGAAAA 57.161 45.000 0.00 0.00 44.08 2.29
537 551 5.047802 AGCAAATTCAACAGGTATTCAGTGG 60.048 40.000 0.00 0.00 0.00 4.00
549 563 5.069781 AGGTATTCAGTGGAGAGTCAATAGC 59.930 44.000 0.00 0.00 0.00 2.97
555 569 2.111384 TGGAGAGTCAATAGCTCCCAC 58.889 52.381 0.00 0.00 46.01 4.61
556 570 2.111384 GGAGAGTCAATAGCTCCCACA 58.889 52.381 0.00 0.00 41.84 4.17
814 828 3.770040 CCCAGATCCACCGACGCA 61.770 66.667 0.00 0.00 0.00 5.24
829 843 4.868900 GCAGCGCGCGGTATGTTG 62.869 66.667 35.47 22.45 0.00 3.33
853 867 1.003718 CCCTCCCGCTCGTTTCTTT 60.004 57.895 0.00 0.00 0.00 2.52
866 880 0.880278 TTTCTTTGCAGAGCGCTCGT 60.880 50.000 30.39 16.76 43.06 4.18
894 908 0.810648 TTGGCTGATCGAAATGGCAC 59.189 50.000 9.84 0.00 34.78 5.01
898 912 1.303309 CTGATCGAAATGGCACCTCC 58.697 55.000 0.00 0.00 0.00 4.30
1197 1213 2.610694 CGTGCTTGGTGCTCTGTGG 61.611 63.158 0.00 0.00 43.37 4.17
1244 1260 2.639286 GCTCTTGGGTTGTGCACG 59.361 61.111 13.13 0.00 0.00 5.34
1284 1300 6.500684 TTAACACCAGATGATTTTCAGCTC 57.499 37.500 0.00 0.00 39.11 4.09
1432 1455 1.404391 TGGAGCTAGCGTACTTACTGC 59.596 52.381 9.55 0.00 0.00 4.40
1477 1501 4.891992 ATGAACAGGTTGTGTAGCTACT 57.108 40.909 23.84 0.68 39.03 2.57
1479 1503 3.386726 TGAACAGGTTGTGTAGCTACTGT 59.613 43.478 23.84 15.49 39.03 3.55
1481 1505 3.991367 ACAGGTTGTGTAGCTACTGTTC 58.009 45.455 23.84 12.25 37.75 3.18
1482 1506 3.244112 ACAGGTTGTGTAGCTACTGTTCC 60.244 47.826 23.84 18.96 37.75 3.62
1483 1507 2.969950 AGGTTGTGTAGCTACTGTTCCA 59.030 45.455 23.84 10.24 31.41 3.53
1484 1508 3.389983 AGGTTGTGTAGCTACTGTTCCAA 59.610 43.478 23.84 14.79 31.41 3.53
1485 1509 4.131596 GGTTGTGTAGCTACTGTTCCAAA 58.868 43.478 23.84 6.01 0.00 3.28
1486 1510 4.577283 GGTTGTGTAGCTACTGTTCCAAAA 59.423 41.667 23.84 2.05 0.00 2.44
1487 1511 5.066764 GGTTGTGTAGCTACTGTTCCAAAAA 59.933 40.000 23.84 1.27 0.00 1.94
1627 1651 5.914898 AACTTGTTAGCTTTGACTTGGTT 57.085 34.783 0.00 0.00 0.00 3.67
1628 1652 5.914898 ACTTGTTAGCTTTGACTTGGTTT 57.085 34.783 0.00 0.00 0.00 3.27
1629 1653 6.280855 ACTTGTTAGCTTTGACTTGGTTTT 57.719 33.333 0.00 0.00 0.00 2.43
1631 1655 7.832769 ACTTGTTAGCTTTGACTTGGTTTTTA 58.167 30.769 0.00 0.00 0.00 1.52
1632 1656 7.973944 ACTTGTTAGCTTTGACTTGGTTTTTAG 59.026 33.333 0.00 0.00 0.00 1.85
1633 1657 6.801575 TGTTAGCTTTGACTTGGTTTTTAGG 58.198 36.000 0.00 0.00 0.00 2.69
1634 1658 6.603997 TGTTAGCTTTGACTTGGTTTTTAGGA 59.396 34.615 0.00 0.00 0.00 2.94
1635 1659 5.774498 AGCTTTGACTTGGTTTTTAGGAG 57.226 39.130 0.00 0.00 0.00 3.69
1639 1663 7.175119 AGCTTTGACTTGGTTTTTAGGAGTATC 59.825 37.037 0.00 0.00 0.00 2.24
1677 1701 7.156876 TGTTGCTTATTTCCTTGTGAATAGG 57.843 36.000 0.00 0.00 31.67 2.57
1686 1710 4.620723 TCCTTGTGAATAGGGAGAGCTTA 58.379 43.478 0.00 0.00 33.41 3.09
1772 1796 5.016051 TGGAATTTTGTTTTGCAGCTACA 57.984 34.783 0.00 0.00 0.00 2.74
1820 1844 3.582647 TCACTTTCTGCTCCCTTCATGTA 59.417 43.478 0.00 0.00 0.00 2.29
1823 1847 0.461548 TCTGCTCCCTTCATGTAGCG 59.538 55.000 0.00 0.00 37.80 4.26
1847 1871 5.220931 GCTATGGATGAAGTTTTTCGAGCAT 60.221 40.000 0.00 0.00 36.04 3.79
1886 1910 1.208052 ACTGTCATGGGATTCGGAGTG 59.792 52.381 0.00 0.00 0.00 3.51
2103 2134 5.835257 TGTAACACACTTACTTTCGCTAGT 58.165 37.500 0.00 0.00 0.00 2.57
2154 2186 9.388672 AGTTAGGGTGCAGGTTAATTATATCTA 57.611 33.333 0.00 0.00 0.00 1.98
2157 2189 8.276453 AGGGTGCAGGTTAATTATATCTAAGT 57.724 34.615 0.00 0.00 0.00 2.24
2419 2451 7.770433 TCTGTTCATTACTTCCATACCATCTTG 59.230 37.037 0.00 0.00 0.00 3.02
2490 2522 0.744281 CCGTGCTTCTTTTGGGTGTT 59.256 50.000 0.00 0.00 0.00 3.32
2502 2534 0.613292 TGGGTGTTGGTGTTGCAACT 60.613 50.000 28.61 0.00 32.91 3.16
2548 2580 1.286248 GGGGTCCATACTGTCCTTGT 58.714 55.000 0.00 0.00 0.00 3.16
2574 2606 0.920664 TTATCACGACTTGCATCGCG 59.079 50.000 9.55 0.00 46.22 5.87
2603 2635 5.705441 TCGTATCCTTTGATGACAGCTTTTT 59.295 36.000 0.00 0.00 32.18 1.94
2616 2648 5.027293 ACAGCTTTTTCCTTTTCTTGCAT 57.973 34.783 0.00 0.00 0.00 3.96
2617 2649 4.812626 ACAGCTTTTTCCTTTTCTTGCATG 59.187 37.500 0.00 0.00 0.00 4.06
2630 2662 8.780249 CCTTTTCTTGCATGAATCAAAATTTCT 58.220 29.630 15.04 0.00 0.00 2.52
2719 2752 6.688578 ACGTGATGACTGTTCATTACTACTT 58.311 36.000 7.65 0.00 43.44 2.24
2743 2776 7.739022 TTGTTACATTCACGTATTACTACCG 57.261 36.000 0.00 0.00 0.00 4.02
2777 2811 5.128205 GTGGTTTTGTAGTCCTTAACCAGT 58.872 41.667 5.32 0.00 46.29 4.00
2855 2889 6.382859 TGCTATATCAGTCTTGTCCTTACCAA 59.617 38.462 0.00 0.00 0.00 3.67
2965 2999 1.461127 GGTAAGTCACGAAGCAGCTTG 59.539 52.381 13.91 7.69 0.00 4.01
3312 3346 5.183140 GCAGGTACCTTGCTTTTCAAATCTA 59.817 40.000 13.15 0.00 33.65 1.98
3413 3447 7.390440 TGTTTATAAATCCCTGTGTGTTCTCTG 59.610 37.037 0.31 0.00 0.00 3.35
3487 3521 4.051237 GCAAAGTTGAAAATGGAGGTGAC 58.949 43.478 0.00 0.00 0.00 3.67
3502 3536 1.135199 GGTGACGACGATGAGCCTTTA 60.135 52.381 0.00 0.00 0.00 1.85
3557 3591 4.083696 GGGCGTGAAAATTTCGTCTCTTAA 60.084 41.667 0.97 0.00 0.00 1.85
3569 3603 0.177141 TCTCTTAAACGGCGGATGGG 59.823 55.000 13.24 0.00 0.00 4.00
3663 3719 7.444299 AGCAATGGACATTTCAGTTACAATTT 58.556 30.769 0.00 0.00 0.00 1.82
3664 3720 7.933033 AGCAATGGACATTTCAGTTACAATTTT 59.067 29.630 0.00 0.00 0.00 1.82
3665 3721 8.011106 GCAATGGACATTTCAGTTACAATTTTG 58.989 33.333 0.00 0.00 0.00 2.44
3666 3722 9.044150 CAATGGACATTTCAGTTACAATTTTGT 57.956 29.630 1.08 1.08 44.86 2.83
3667 3723 8.592105 ATGGACATTTCAGTTACAATTTTGTG 57.408 30.769 6.21 0.00 42.31 3.33
3668 3724 7.551585 TGGACATTTCAGTTACAATTTTGTGT 58.448 30.769 6.21 0.00 42.31 3.72
3669 3725 8.037758 TGGACATTTCAGTTACAATTTTGTGTT 58.962 29.630 6.21 0.00 42.31 3.32
3670 3726 8.878769 GGACATTTCAGTTACAATTTTGTGTTT 58.121 29.630 6.21 0.00 42.31 2.83
3743 3799 6.710295 GGTTTTACCTTCCAAAATTGCAGATT 59.290 34.615 0.00 0.00 34.73 2.40
3759 3815 6.985188 TGCAGATTTACCATGAAACTAGAC 57.015 37.500 0.00 0.00 0.00 2.59
3765 3821 3.340814 ACCATGAAACTAGACAGCAGG 57.659 47.619 0.00 0.00 0.00 4.85
3823 3879 5.290493 TCTCACTGTAACTTCATGTTGGT 57.710 39.130 0.00 0.00 39.55 3.67
3833 3889 2.851263 TCATGTTGGTACACTGGTCC 57.149 50.000 0.00 0.00 39.29 4.46
3869 3925 5.304357 CCATTCTTTTTGTACCAAAGGTCCT 59.696 40.000 12.44 0.00 37.09 3.85
3947 4003 7.074653 TGTACTTTCAGATTTACCTTGGACT 57.925 36.000 0.00 0.00 0.00 3.85
3948 4004 7.514721 TGTACTTTCAGATTTACCTTGGACTT 58.485 34.615 0.00 0.00 0.00 3.01
3950 4006 9.498176 GTACTTTCAGATTTACCTTGGACTTTA 57.502 33.333 0.00 0.00 0.00 1.85
3951 4007 8.990163 ACTTTCAGATTTACCTTGGACTTTAA 57.010 30.769 0.00 0.00 0.00 1.52
3963 4019 5.863935 CCTTGGACTTTAAAGTAATGCAAGC 59.136 40.000 20.58 5.92 39.88 4.01
4017 4073 8.608185 AATAACCAGGTTCATTTCCATGTAAT 57.392 30.769 8.57 0.00 0.00 1.89
4018 4074 9.707957 AATAACCAGGTTCATTTCCATGTAATA 57.292 29.630 8.57 0.00 0.00 0.98
4019 4075 7.404671 AACCAGGTTCATTTCCATGTAATAC 57.595 36.000 0.00 0.00 0.00 1.89
4020 4076 6.489603 ACCAGGTTCATTTCCATGTAATACA 58.510 36.000 0.00 0.00 0.00 2.29
4021 4077 6.951198 ACCAGGTTCATTTCCATGTAATACAA 59.049 34.615 0.00 0.00 0.00 2.41
4022 4078 7.453126 ACCAGGTTCATTTCCATGTAATACAAA 59.547 33.333 0.00 0.00 0.00 2.83
4023 4079 7.759433 CCAGGTTCATTTCCATGTAATACAAAC 59.241 37.037 0.00 0.00 0.00 2.93
4024 4080 8.303156 CAGGTTCATTTCCATGTAATACAAACA 58.697 33.333 0.00 0.00 0.00 2.83
4025 4081 8.522830 AGGTTCATTTCCATGTAATACAAACAG 58.477 33.333 0.00 0.00 0.00 3.16
4026 4082 7.275560 GGTTCATTTCCATGTAATACAAACAGC 59.724 37.037 0.00 0.00 0.00 4.40
4027 4083 6.862209 TCATTTCCATGTAATACAAACAGCC 58.138 36.000 0.00 0.00 0.00 4.85
4028 4084 6.435591 TCATTTCCATGTAATACAAACAGCCA 59.564 34.615 0.00 0.00 0.00 4.75
4029 4085 5.637006 TTCCATGTAATACAAACAGCCAC 57.363 39.130 0.00 0.00 0.00 5.01
4030 4086 4.657013 TCCATGTAATACAAACAGCCACA 58.343 39.130 0.00 0.00 0.00 4.17
4031 4087 4.699735 TCCATGTAATACAAACAGCCACAG 59.300 41.667 0.00 0.00 0.00 3.66
4032 4088 4.142403 CCATGTAATACAAACAGCCACAGG 60.142 45.833 0.00 0.00 0.00 4.00
4042 4098 2.521708 GCCACAGGCCCTGTTTGT 60.522 61.111 15.33 0.00 42.59 2.83
4043 4099 2.133641 GCCACAGGCCCTGTTTGTT 61.134 57.895 15.33 0.00 42.59 2.83
4044 4100 1.685355 GCCACAGGCCCTGTTTGTTT 61.685 55.000 15.33 0.00 42.59 2.83
4045 4101 0.104671 CCACAGGCCCTGTTTGTTTG 59.895 55.000 15.33 1.23 42.59 2.93
4046 4102 0.104671 CACAGGCCCTGTTTGTTTGG 59.895 55.000 15.33 0.00 42.59 3.28
4047 4103 1.048160 ACAGGCCCTGTTTGTTTGGG 61.048 55.000 11.57 0.00 42.59 4.12
4052 4108 2.708216 CCCTGTTTGTTTGGGCTTTT 57.292 45.000 0.00 0.00 33.88 2.27
4053 4109 2.287769 CCCTGTTTGTTTGGGCTTTTG 58.712 47.619 0.00 0.00 33.88 2.44
4054 4110 1.670295 CCTGTTTGTTTGGGCTTTTGC 59.330 47.619 0.00 0.00 46.64 3.68
4055 4111 2.631267 CTGTTTGTTTGGGCTTTTGCT 58.369 42.857 0.00 0.00 46.54 3.91
4056 4112 3.009026 CTGTTTGTTTGGGCTTTTGCTT 58.991 40.909 0.00 0.00 46.54 3.91
4057 4113 3.416156 TGTTTGTTTGGGCTTTTGCTTT 58.584 36.364 0.00 0.00 46.54 3.51
4058 4114 3.823304 TGTTTGTTTGGGCTTTTGCTTTT 59.177 34.783 0.00 0.00 46.54 2.27
4059 4115 4.165036 GTTTGTTTGGGCTTTTGCTTTTG 58.835 39.130 0.00 0.00 46.54 2.44
4060 4116 1.742268 TGTTTGGGCTTTTGCTTTTGC 59.258 42.857 0.00 0.00 46.54 3.68
4080 4136 4.604843 GCTTTTGCAGCTTTTTCACTTT 57.395 36.364 0.00 0.00 46.27 2.66
4081 4137 4.336932 GCTTTTGCAGCTTTTTCACTTTG 58.663 39.130 0.00 0.00 46.27 2.77
4082 4138 4.336932 CTTTTGCAGCTTTTTCACTTTGC 58.663 39.130 0.00 0.00 0.00 3.68
4083 4139 2.965572 TGCAGCTTTTTCACTTTGCT 57.034 40.000 0.00 0.00 33.00 3.91
4084 4140 2.813061 TGCAGCTTTTTCACTTTGCTC 58.187 42.857 0.00 0.00 33.00 4.26
4085 4141 2.166050 TGCAGCTTTTTCACTTTGCTCA 59.834 40.909 0.00 0.00 33.00 4.26
4086 4142 3.189285 GCAGCTTTTTCACTTTGCTCAA 58.811 40.909 0.00 0.00 0.00 3.02
4087 4143 3.618150 GCAGCTTTTTCACTTTGCTCAAA 59.382 39.130 0.00 0.00 0.00 2.69
4088 4144 4.093261 GCAGCTTTTTCACTTTGCTCAAAA 59.907 37.500 0.00 0.00 0.00 2.44
4089 4145 5.390779 GCAGCTTTTTCACTTTGCTCAAAAA 60.391 36.000 0.00 0.00 0.00 1.94
4090 4146 6.245724 CAGCTTTTTCACTTTGCTCAAAAAG 58.754 36.000 10.14 10.14 43.84 2.27
4115 4171 7.880160 CTATAGAAGCTCCTACATAGATGCT 57.120 40.000 0.00 0.00 34.78 3.79
4116 4172 8.292444 CTATAGAAGCTCCTACATAGATGCTT 57.708 38.462 14.05 14.05 41.01 3.91
4117 4173 5.885449 AGAAGCTCCTACATAGATGCTTT 57.115 39.130 14.81 6.99 39.66 3.51
4118 4174 6.245890 AGAAGCTCCTACATAGATGCTTTT 57.754 37.500 14.81 9.65 39.66 2.27
4119 4175 6.054295 AGAAGCTCCTACATAGATGCTTTTG 58.946 40.000 14.81 0.00 39.66 2.44
4120 4176 4.712476 AGCTCCTACATAGATGCTTTTGG 58.288 43.478 0.00 0.00 31.34 3.28
4121 4177 4.410228 AGCTCCTACATAGATGCTTTTGGA 59.590 41.667 0.00 0.00 31.34 3.53
4122 4178 4.754114 GCTCCTACATAGATGCTTTTGGAG 59.246 45.833 0.00 0.00 40.85 3.86
4137 4193 6.232139 CTTTTGGAGCTTTTATGGCTTTTG 57.768 37.500 0.00 0.00 40.40 2.44
4138 4194 3.959535 TGGAGCTTTTATGGCTTTTGG 57.040 42.857 0.00 0.00 40.40 3.28
4139 4195 3.505386 TGGAGCTTTTATGGCTTTTGGA 58.495 40.909 0.00 0.00 40.40 3.53
4140 4196 3.511146 TGGAGCTTTTATGGCTTTTGGAG 59.489 43.478 0.00 0.00 40.40 3.86
4166 4222 8.401490 CTCAATATTTAGGAGCTTTTATGGCT 57.599 34.615 0.00 0.00 43.26 4.75
4167 4223 8.766994 TCAATATTTAGGAGCTTTTATGGCTT 57.233 30.769 0.00 0.00 40.40 4.35
4168 4224 9.200817 TCAATATTTAGGAGCTTTTATGGCTTT 57.799 29.630 0.00 0.00 40.40 3.51
4169 4225 9.822185 CAATATTTAGGAGCTTTTATGGCTTTT 57.178 29.630 0.00 0.00 40.40 2.27
4171 4227 9.822185 ATATTTAGGAGCTTTTATGGCTTTTTG 57.178 29.630 0.00 0.00 40.40 2.44
4172 4228 4.541973 AGGAGCTTTTATGGCTTTTTGG 57.458 40.909 0.00 0.00 40.40 3.28
4173 4229 3.261643 AGGAGCTTTTATGGCTTTTTGGG 59.738 43.478 0.00 0.00 40.40 4.12
4174 4230 3.007940 GGAGCTTTTATGGCTTTTTGGGT 59.992 43.478 0.00 0.00 40.40 4.51
4175 4231 4.221924 GGAGCTTTTATGGCTTTTTGGGTA 59.778 41.667 0.00 0.00 40.40 3.69
4176 4232 5.279758 GGAGCTTTTATGGCTTTTTGGGTAA 60.280 40.000 0.00 0.00 40.40 2.85
4177 4233 6.181206 AGCTTTTATGGCTTTTTGGGTAAA 57.819 33.333 0.00 0.00 36.56 2.01
4178 4234 6.230472 AGCTTTTATGGCTTTTTGGGTAAAG 58.770 36.000 0.00 0.00 36.56 1.85
4179 4235 5.995282 GCTTTTATGGCTTTTTGGGTAAAGT 59.005 36.000 0.00 0.00 37.43 2.66
4180 4236 6.073276 GCTTTTATGGCTTTTTGGGTAAAGTG 60.073 38.462 0.00 0.00 37.43 3.16
4181 4237 6.732896 TTTATGGCTTTTTGGGTAAAGTGA 57.267 33.333 0.00 0.00 37.43 3.41
4182 4238 6.732896 TTATGGCTTTTTGGGTAAAGTGAA 57.267 33.333 0.00 0.00 37.43 3.18
4183 4239 5.622346 ATGGCTTTTTGGGTAAAGTGAAA 57.378 34.783 0.00 0.00 37.43 2.69
4184 4240 5.422214 TGGCTTTTTGGGTAAAGTGAAAA 57.578 34.783 0.00 0.00 37.43 2.29
4185 4241 5.995446 TGGCTTTTTGGGTAAAGTGAAAAT 58.005 33.333 0.00 0.00 37.43 1.82
4186 4242 6.052360 TGGCTTTTTGGGTAAAGTGAAAATC 58.948 36.000 0.00 0.00 37.43 2.17
4187 4243 6.126911 TGGCTTTTTGGGTAAAGTGAAAATCT 60.127 34.615 0.00 0.00 37.43 2.40
4188 4244 6.202762 GGCTTTTTGGGTAAAGTGAAAATCTG 59.797 38.462 0.00 0.00 37.43 2.90
4189 4245 6.292865 GCTTTTTGGGTAAAGTGAAAATCTGC 60.293 38.462 0.00 0.00 37.43 4.26
4190 4246 5.860941 TTTGGGTAAAGTGAAAATCTGCA 57.139 34.783 0.00 0.00 0.00 4.41
4191 4247 5.860941 TTGGGTAAAGTGAAAATCTGCAA 57.139 34.783 0.00 0.00 0.00 4.08
4192 4248 5.860941 TGGGTAAAGTGAAAATCTGCAAA 57.139 34.783 0.00 0.00 0.00 3.68
4193 4249 6.227298 TGGGTAAAGTGAAAATCTGCAAAA 57.773 33.333 0.00 0.00 0.00 2.44
4194 4250 6.279882 TGGGTAAAGTGAAAATCTGCAAAAG 58.720 36.000 0.00 0.00 0.00 2.27
4195 4251 5.177511 GGGTAAAGTGAAAATCTGCAAAAGC 59.822 40.000 0.00 0.00 0.00 3.51
4196 4252 5.752955 GGTAAAGTGAAAATCTGCAAAAGCA 59.247 36.000 0.00 0.00 0.00 3.91
4197 4253 5.978934 AAAGTGAAAATCTGCAAAAGCAG 57.021 34.783 11.04 11.04 39.01 4.24
4205 4261 3.523606 TCTGCAAAAGCAGAAGCAAAA 57.476 38.095 16.93 0.00 42.91 2.44
4206 4262 3.450578 TCTGCAAAAGCAGAAGCAAAAG 58.549 40.909 16.93 0.00 42.91 2.27
4207 4263 1.935199 TGCAAAAGCAGAAGCAAAAGC 59.065 42.857 0.00 0.00 45.49 3.51
4208 4264 2.207590 GCAAAAGCAGAAGCAAAAGCT 58.792 42.857 0.00 0.00 45.49 3.74
4209 4265 2.220363 GCAAAAGCAGAAGCAAAAGCTC 59.780 45.455 0.00 0.00 45.49 4.09
4210 4266 3.450578 CAAAAGCAGAAGCAAAAGCTCA 58.549 40.909 0.00 0.00 45.49 4.26
4215 4271 3.119029 AGCAGAAGCAAAAGCTCAAACAA 60.119 39.130 0.00 0.00 45.49 2.83
4217 4273 4.493057 GCAGAAGCAAAAGCTCAAACAAAC 60.493 41.667 0.00 0.00 41.58 2.93
4219 4275 4.866486 AGAAGCAAAAGCTCAAACAAACAG 59.134 37.500 0.00 0.00 0.00 3.16
4220 4276 3.524541 AGCAAAAGCTCAAACAAACAGG 58.475 40.909 0.00 0.00 0.00 4.00
4223 4279 0.752658 AAGCTCAAACAAACAGGGCC 59.247 50.000 0.00 0.00 0.00 5.80
4250 4306 1.732259 CAAGGAGGAATCGGTGTTTCG 59.268 52.381 0.00 0.00 0.00 3.46
4286 4342 5.426504 TGAAACATTTGCACCAATCTTGTT 58.573 33.333 0.00 0.00 0.00 2.83
4299 4355 7.632898 GCACCAATCTTGTTATCTGTAGAGGTA 60.633 40.741 0.00 0.00 0.00 3.08
4306 4362 7.989170 TCTTGTTATCTGTAGAGGTATACACGA 59.011 37.037 5.01 0.00 32.36 4.35
4328 4384 5.794945 CGATGCCTGTTTTTACTTACACATG 59.205 40.000 0.00 0.00 0.00 3.21
4389 4452 7.828717 ACATCACACAGGTCATATATCAAAACA 59.171 33.333 0.00 0.00 0.00 2.83
4416 4479 2.863137 GAGCTAGCAACTGCACATACTC 59.137 50.000 18.83 0.00 45.16 2.59
4420 4483 0.449388 GCAACTGCACATACTCCAGC 59.551 55.000 0.00 0.00 41.59 4.85
4429 4492 3.440173 GCACATACTCCAGCTTGCTAAAA 59.560 43.478 0.00 0.00 0.00 1.52
4489 4553 7.611467 TCTCTCATTTAACTGCCATGTTGTAAT 59.389 33.333 0.00 0.00 0.00 1.89
4501 4565 3.889196 TGTTGTAATTGTCAGTTCCGC 57.111 42.857 0.00 0.00 0.00 5.54
4510 4574 0.385974 GTCAGTTCCGCACAATGCAC 60.386 55.000 1.20 0.00 45.36 4.57
4517 4581 1.134281 CGCACAATGCACGCATACA 59.866 52.632 4.68 0.00 45.36 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.775890 TGTCGTCGAGGAAGACTACTT 58.224 47.619 9.78 0.00 40.61 2.24
27 28 1.887198 ACAATGTCGTCGAGGAAGACT 59.113 47.619 9.78 0.00 40.61 3.24
93 94 7.926018 TGAACGAGTAGCACATATCATTGTAAT 59.074 33.333 0.00 0.00 0.00 1.89
125 126 4.633565 GCTTTGAGAACCGATGAAGAGAAT 59.366 41.667 0.00 0.00 0.00 2.40
128 129 3.594134 AGCTTTGAGAACCGATGAAGAG 58.406 45.455 0.00 0.00 0.00 2.85
159 160 4.817087 CCAAAGAATTGTCGGTGCACCG 62.817 54.545 45.04 45.04 45.76 4.94
172 179 3.160269 CAAGCTCCTCCAACCAAAGAAT 58.840 45.455 0.00 0.00 0.00 2.40
252 266 9.619727 CATCTCACGTAATAGAAAATTACAACG 57.380 33.333 8.22 0.00 34.96 4.10
315 329 3.003068 CCGTAGAACATACTCGAACCGAT 59.997 47.826 0.00 0.00 34.61 4.18
346 360 0.935831 CGTCCAAGTACAACACGCGA 60.936 55.000 15.93 0.00 0.00 5.87
361 375 0.731855 GTACAGTCAACCGAGCGTCC 60.732 60.000 0.00 0.00 0.00 4.79
370 384 2.132762 CCTTCCACGTGTACAGTCAAC 58.867 52.381 15.65 0.00 0.00 3.18
375 389 0.391597 ACCACCTTCCACGTGTACAG 59.608 55.000 15.65 6.84 0.00 2.74
396 410 8.512966 TTTATTTTGTTTCCCTTTTCCAAAGG 57.487 30.769 8.14 8.14 37.17 3.11
450 464 2.623416 GCCAACTCTGCCTTTTTGTAGT 59.377 45.455 0.00 0.00 0.00 2.73
464 478 5.473504 TCCTCTTGTCTTAATTTGCCAACTC 59.526 40.000 0.00 0.00 0.00 3.01
466 480 5.705609 TCCTCTTGTCTTAATTTGCCAAC 57.294 39.130 0.00 0.00 0.00 3.77
507 521 9.995003 TGAATACCTGTTGAATTTGCTAAAATT 57.005 25.926 0.00 0.00 46.37 1.82
508 522 9.643693 CTGAATACCTGTTGAATTTGCTAAAAT 57.356 29.630 0.00 0.00 37.61 1.82
523 537 3.779444 TGACTCTCCACTGAATACCTGT 58.221 45.455 0.00 0.00 0.00 4.00
537 551 2.480416 CGTGTGGGAGCTATTGACTCTC 60.480 54.545 0.00 0.00 35.06 3.20
549 563 4.680237 TCGCTTGCCGTGTGGGAG 62.680 66.667 0.00 0.00 36.70 4.30
814 828 3.186047 GACAACATACCGCGCGCT 61.186 61.111 30.48 14.92 0.00 5.92
844 858 1.569493 GCGCTCTGCAAAGAAACGA 59.431 52.632 0.00 0.00 45.45 3.85
866 880 1.708193 CGATCAGCCAATCGCAGCAA 61.708 55.000 5.51 0.00 41.71 3.91
898 912 3.060615 GAGCACCTGCAGGCAAGG 61.061 66.667 33.06 19.83 45.16 3.61
1164 1179 1.119635 GCACGAACACGTACGTAACA 58.880 50.000 22.34 0.00 40.76 2.41
1197 1213 6.090088 CACGCCATAGATAGATCTAGCAAAAC 59.910 42.308 19.62 4.71 42.20 2.43
1244 1260 5.321516 GTGTTAATAATCTGAACCGTGCAC 58.678 41.667 6.82 6.82 0.00 4.57
1284 1300 1.203052 CTTGGCCAAAGCTACCACATG 59.797 52.381 20.91 0.00 39.73 3.21
1432 1455 5.620098 ACGAAAAACAATCAAAGCTTTCG 57.380 34.783 9.23 8.47 46.36 3.46
1446 1469 6.031471 ACACAACCTGTTCATTACGAAAAAC 58.969 36.000 0.00 0.00 34.69 2.43
1493 1517 2.084546 GGACATGCTACACAACCCTTC 58.915 52.381 0.00 0.00 0.00 3.46
1631 1655 9.829507 CAACATTCAGAAATAAGAGATACTCCT 57.170 33.333 0.00 0.00 0.00 3.69
1632 1656 8.555361 GCAACATTCAGAAATAAGAGATACTCC 58.445 37.037 0.00 0.00 0.00 3.85
1633 1657 9.323985 AGCAACATTCAGAAATAAGAGATACTC 57.676 33.333 0.00 0.00 0.00 2.59
1634 1658 9.678260 AAGCAACATTCAGAAATAAGAGATACT 57.322 29.630 0.00 0.00 0.00 2.12
1691 1715 8.411683 GGCATCTCATATTCTCATTCACTTTTT 58.588 33.333 0.00 0.00 0.00 1.94
1757 1781 3.445450 TCAAGGTTGTAGCTGCAAAACAA 59.555 39.130 19.29 6.87 0.00 2.83
1772 1796 0.674895 GATGCCAGCTCGTCAAGGTT 60.675 55.000 0.00 0.00 31.91 3.50
1820 1844 3.063997 CGAAAAACTTCATCCATAGCGCT 59.936 43.478 17.26 17.26 0.00 5.92
1823 1847 4.094887 TGCTCGAAAAACTTCATCCATAGC 59.905 41.667 0.00 0.00 0.00 2.97
1847 1871 6.545666 TGACAGTTCTTGAATCAAAAGCCTTA 59.454 34.615 0.00 0.00 0.00 2.69
1862 1886 2.571653 TCCGAATCCCATGACAGTTCTT 59.428 45.455 0.00 0.00 0.00 2.52
1922 1946 3.070015 AGCCAACAGAATTGAAACCAAGG 59.930 43.478 0.00 0.00 0.00 3.61
2103 2134 4.675146 GCCAAGTAACTATTGTCGTACCGA 60.675 45.833 0.00 0.00 0.00 4.69
2155 2187 4.705023 AGTTTCTTGCACAAACAAGGTACT 59.295 37.500 18.35 5.68 45.77 2.73
2156 2188 4.993905 AGTTTCTTGCACAAACAAGGTAC 58.006 39.130 18.35 3.79 45.77 3.34
2157 2189 5.652994 AAGTTTCTTGCACAAACAAGGTA 57.347 34.783 18.35 0.00 45.77 3.08
2419 2451 7.748241 GCAGTCAAGTCAGAAAATGTTTAGATC 59.252 37.037 0.00 0.00 0.00 2.75
2490 2522 1.093972 CAGTCACAGTTGCAACACCA 58.906 50.000 30.11 9.20 0.00 4.17
2502 2534 4.793678 GCATTGAGTTGCAAATCAGTCACA 60.794 41.667 26.36 14.18 42.31 3.58
2548 2580 2.816672 TGCAAGTCGTGATAATTGCCAA 59.183 40.909 6.57 0.00 45.76 4.52
2574 2606 5.484173 TGTCATCAAAGGATACGATTTGC 57.516 39.130 0.00 0.00 46.39 3.68
2603 2635 8.680039 AAATTTTGATTCATGCAAGAAAAGGA 57.320 26.923 8.64 0.00 0.00 3.36
2616 2648 8.680039 AAAAGATGCCAAGAAATTTTGATTCA 57.320 26.923 0.00 0.00 0.00 2.57
2719 2752 7.312154 ACGGTAGTAATACGTGAATGTAACAA 58.688 34.615 0.00 0.00 39.64 2.83
2743 2776 5.155643 ACTACAAAACCACACGACAAAAAC 58.844 37.500 0.00 0.00 0.00 2.43
2777 2811 7.676004 TCTGAATAGTGTTTGTCATCTGGTAA 58.324 34.615 0.00 0.00 0.00 2.85
2855 2889 5.065218 GCCGATAAGAAACAGTGTCAATGAT 59.935 40.000 7.39 0.00 0.00 2.45
2965 2999 4.441792 ACAATGTCAAAAGAAGTTTGCCC 58.558 39.130 0.00 0.00 45.38 5.36
3413 3447 3.054878 CACCTTCTTTTGACTGCAATGC 58.945 45.455 0.00 0.00 33.25 3.56
3445 3479 4.012374 TGCCCAAAGAATCAGAGATCAAC 58.988 43.478 0.00 0.00 0.00 3.18
3502 3536 1.207329 GAGCTCCACATCGGTACCTTT 59.793 52.381 10.90 0.00 35.57 3.11
3557 3591 1.695242 TGTATAATCCCATCCGCCGTT 59.305 47.619 0.00 0.00 0.00 4.44
3675 3731 9.155975 CATTTTACTGCTTTAGATAGTGACACT 57.844 33.333 13.68 13.68 0.00 3.55
3676 3732 9.151471 TCATTTTACTGCTTTAGATAGTGACAC 57.849 33.333 0.00 0.00 0.00 3.67
3677 3733 9.890629 ATCATTTTACTGCTTTAGATAGTGACA 57.109 29.630 0.00 0.00 0.00 3.58
3685 3741 9.896645 AGAATCAGATCATTTTACTGCTTTAGA 57.103 29.630 0.00 0.00 0.00 2.10
3688 3744 9.635520 CAAAGAATCAGATCATTTTACTGCTTT 57.364 29.630 0.00 0.00 0.00 3.51
3689 3745 8.248945 CCAAAGAATCAGATCATTTTACTGCTT 58.751 33.333 0.00 0.00 0.00 3.91
3690 3746 7.613022 TCCAAAGAATCAGATCATTTTACTGCT 59.387 33.333 0.00 0.00 0.00 4.24
3691 3747 7.765307 TCCAAAGAATCAGATCATTTTACTGC 58.235 34.615 0.00 0.00 0.00 4.40
3692 3748 8.404000 CCTCCAAAGAATCAGATCATTTTACTG 58.596 37.037 0.00 0.00 0.00 2.74
3693 3749 7.559170 CCCTCCAAAGAATCAGATCATTTTACT 59.441 37.037 0.00 0.00 0.00 2.24
3694 3750 7.340487 ACCCTCCAAAGAATCAGATCATTTTAC 59.660 37.037 0.00 0.00 0.00 2.01
3695 3751 7.413446 ACCCTCCAAAGAATCAGATCATTTTA 58.587 34.615 0.00 0.00 0.00 1.52
3743 3799 4.286032 ACCTGCTGTCTAGTTTCATGGTAA 59.714 41.667 0.00 0.00 0.00 2.85
3759 3815 8.131100 CCAGATACAATTTTACAATACCTGCTG 58.869 37.037 0.00 0.00 0.00 4.41
3823 3879 2.022195 GTCTATCTGCGGACCAGTGTA 58.978 52.381 0.00 0.00 42.38 2.90
3833 3889 5.352569 ACAAAAAGAATGGAGTCTATCTGCG 59.647 40.000 0.00 0.00 37.31 5.18
3869 3925 3.565482 GTCTTGCACAATTCTTGACCTCA 59.435 43.478 0.00 0.00 0.00 3.86
3921 3977 6.371825 GTCCAAGGTAAATCTGAAAGTACAGG 59.628 42.308 0.00 0.00 38.31 4.00
3947 4003 7.135089 TGTACATCGCTTGCATTACTTTAAA 57.865 32.000 0.00 0.00 0.00 1.52
3948 4004 6.729391 TGTACATCGCTTGCATTACTTTAA 57.271 33.333 0.00 0.00 0.00 1.52
3950 4006 5.818136 ATGTACATCGCTTGCATTACTTT 57.182 34.783 1.41 0.00 0.00 2.66
3951 4007 5.818136 AATGTACATCGCTTGCATTACTT 57.182 34.783 9.23 0.00 0.00 2.24
3963 4019 7.596749 ACTCCTTAAACTGAAATGTACATCG 57.403 36.000 9.23 1.16 0.00 3.84
4025 4081 1.685355 AAACAAACAGGGCCTGTGGC 61.685 55.000 38.18 0.00 44.62 5.01
4026 4082 0.104671 CAAACAAACAGGGCCTGTGG 59.895 55.000 38.18 32.15 44.62 4.17
4027 4083 0.104671 CCAAACAAACAGGGCCTGTG 59.895 55.000 38.18 28.10 44.62 3.66
4029 4085 1.747774 CCCAAACAAACAGGGCCTG 59.252 57.895 31.62 31.62 35.44 4.85
4030 4086 4.293610 CCCAAACAAACAGGGCCT 57.706 55.556 0.00 0.00 35.44 5.19
4033 4089 2.287769 CAAAAGCCCAAACAAACAGGG 58.712 47.619 0.00 0.00 45.68 4.45
4034 4090 1.670295 GCAAAAGCCCAAACAAACAGG 59.330 47.619 0.00 0.00 0.00 4.00
4035 4091 2.631267 AGCAAAAGCCCAAACAAACAG 58.369 42.857 0.00 0.00 0.00 3.16
4036 4092 2.777832 AGCAAAAGCCCAAACAAACA 57.222 40.000 0.00 0.00 0.00 2.83
4037 4093 4.165036 CAAAAGCAAAAGCCCAAACAAAC 58.835 39.130 0.00 0.00 0.00 2.93
4038 4094 3.366781 GCAAAAGCAAAAGCCCAAACAAA 60.367 39.130 0.00 0.00 0.00 2.83
4039 4095 2.163211 GCAAAAGCAAAAGCCCAAACAA 59.837 40.909 0.00 0.00 0.00 2.83
4040 4096 1.742268 GCAAAAGCAAAAGCCCAAACA 59.258 42.857 0.00 0.00 0.00 2.83
4041 4097 2.016318 AGCAAAAGCAAAAGCCCAAAC 58.984 42.857 0.00 0.00 0.00 2.93
4042 4098 2.416680 AGCAAAAGCAAAAGCCCAAA 57.583 40.000 0.00 0.00 0.00 3.28
4043 4099 2.416680 AAGCAAAAGCAAAAGCCCAA 57.583 40.000 0.00 0.00 0.00 4.12
4044 4100 2.416680 AAAGCAAAAGCAAAAGCCCA 57.583 40.000 0.00 0.00 0.00 5.36
4045 4101 2.795681 GCAAAAGCAAAAGCAAAAGCCC 60.796 45.455 0.00 0.00 0.00 5.19
4046 4102 2.159407 TGCAAAAGCAAAAGCAAAAGCC 60.159 40.909 0.00 0.00 33.48 4.35
4047 4103 3.103007 CTGCAAAAGCAAAAGCAAAAGC 58.897 40.909 0.00 0.00 36.44 3.51
4060 4116 4.093850 AGCAAAGTGAAAAAGCTGCAAAAG 59.906 37.500 1.02 0.00 33.67 2.27
4061 4117 4.002316 AGCAAAGTGAAAAAGCTGCAAAA 58.998 34.783 1.02 0.00 33.67 2.44
4062 4118 3.598299 AGCAAAGTGAAAAAGCTGCAAA 58.402 36.364 1.02 0.00 33.67 3.68
4063 4119 3.189285 GAGCAAAGTGAAAAAGCTGCAA 58.811 40.909 1.02 0.00 35.36 4.08
4064 4120 2.166050 TGAGCAAAGTGAAAAAGCTGCA 59.834 40.909 1.02 0.00 35.36 4.41
4065 4121 2.813061 TGAGCAAAGTGAAAAAGCTGC 58.187 42.857 0.00 0.00 35.36 5.25
4066 4122 5.783100 TTTTGAGCAAAGTGAAAAAGCTG 57.217 34.783 0.00 0.00 35.36 4.24
4067 4123 6.413018 CTTTTTGAGCAAAGTGAAAAAGCT 57.587 33.333 0.00 0.00 38.11 3.74
4091 4147 7.880160 AGCATCTATGTAGGAGCTTCTATAG 57.120 40.000 4.67 5.27 32.63 1.31
4092 4148 8.657387 AAAGCATCTATGTAGGAGCTTCTATA 57.343 34.615 4.67 2.38 40.36 1.31
4093 4149 7.552050 AAAGCATCTATGTAGGAGCTTCTAT 57.448 36.000 4.67 0.00 40.36 1.98
4094 4150 6.985653 AAAGCATCTATGTAGGAGCTTCTA 57.014 37.500 15.20 0.00 40.36 2.10
4095 4151 5.885449 AAAGCATCTATGTAGGAGCTTCT 57.115 39.130 0.00 0.00 40.36 2.85
4096 4152 5.238214 CCAAAAGCATCTATGTAGGAGCTTC 59.762 44.000 15.20 0.00 40.36 3.86
4097 4153 5.104360 TCCAAAAGCATCTATGTAGGAGCTT 60.104 40.000 11.45 11.45 41.79 3.74
4098 4154 4.410228 TCCAAAAGCATCTATGTAGGAGCT 59.590 41.667 0.00 0.00 36.10 4.09
4099 4155 4.708177 TCCAAAAGCATCTATGTAGGAGC 58.292 43.478 0.00 0.00 0.00 4.70
4114 4170 5.179929 CCAAAAGCCATAAAAGCTCCAAAAG 59.820 40.000 0.00 0.00 40.49 2.27
4115 4171 5.062528 CCAAAAGCCATAAAAGCTCCAAAA 58.937 37.500 0.00 0.00 40.49 2.44
4116 4172 4.346418 TCCAAAAGCCATAAAAGCTCCAAA 59.654 37.500 0.00 0.00 40.49 3.28
4117 4173 3.900601 TCCAAAAGCCATAAAAGCTCCAA 59.099 39.130 0.00 0.00 40.49 3.53
4118 4174 3.505386 TCCAAAAGCCATAAAAGCTCCA 58.495 40.909 0.00 0.00 40.49 3.86
4119 4175 3.677148 GCTCCAAAAGCCATAAAAGCTCC 60.677 47.826 0.00 0.00 45.92 4.70
4120 4176 3.515630 GCTCCAAAAGCCATAAAAGCTC 58.484 45.455 0.00 0.00 45.92 4.09
4121 4177 3.599730 GCTCCAAAAGCCATAAAAGCT 57.400 42.857 0.00 0.00 45.92 3.74
4132 4188 6.733145 GCTCCTAAATATTGAGCTCCAAAAG 58.267 40.000 12.15 0.00 46.19 2.27
4133 4189 6.699575 GCTCCTAAATATTGAGCTCCAAAA 57.300 37.500 12.15 0.00 46.19 2.44
4141 4197 8.401490 AGCCATAAAAGCTCCTAAATATTGAG 57.599 34.615 0.00 0.00 34.91 3.02
4142 4198 8.766994 AAGCCATAAAAGCTCCTAAATATTGA 57.233 30.769 0.00 0.00 40.49 2.57
4143 4199 9.822185 AAAAGCCATAAAAGCTCCTAAATATTG 57.178 29.630 0.00 0.00 40.49 1.90
4145 4201 9.822185 CAAAAAGCCATAAAAGCTCCTAAATAT 57.178 29.630 0.00 0.00 40.49 1.28
4146 4202 8.257306 CCAAAAAGCCATAAAAGCTCCTAAATA 58.743 33.333 0.00 0.00 40.49 1.40
4147 4203 7.105588 CCAAAAAGCCATAAAAGCTCCTAAAT 58.894 34.615 0.00 0.00 40.49 1.40
4148 4204 6.463360 CCAAAAAGCCATAAAAGCTCCTAAA 58.537 36.000 0.00 0.00 40.49 1.85
4149 4205 5.046663 CCCAAAAAGCCATAAAAGCTCCTAA 60.047 40.000 0.00 0.00 40.49 2.69
4150 4206 4.466015 CCCAAAAAGCCATAAAAGCTCCTA 59.534 41.667 0.00 0.00 40.49 2.94
4151 4207 3.261643 CCCAAAAAGCCATAAAAGCTCCT 59.738 43.478 0.00 0.00 40.49 3.69
4152 4208 3.007940 ACCCAAAAAGCCATAAAAGCTCC 59.992 43.478 0.00 0.00 40.49 4.70
4153 4209 4.271696 ACCCAAAAAGCCATAAAAGCTC 57.728 40.909 0.00 0.00 40.49 4.09
4154 4210 5.816955 TTACCCAAAAAGCCATAAAAGCT 57.183 34.783 0.00 0.00 44.19 3.74
4155 4211 5.995282 ACTTTACCCAAAAAGCCATAAAAGC 59.005 36.000 0.00 0.00 39.59 3.51
4156 4212 7.213678 TCACTTTACCCAAAAAGCCATAAAAG 58.786 34.615 0.00 0.00 39.59 2.27
4157 4213 7.125792 TCACTTTACCCAAAAAGCCATAAAA 57.874 32.000 0.00 0.00 39.59 1.52
4158 4214 6.732896 TCACTTTACCCAAAAAGCCATAAA 57.267 33.333 0.00 0.00 39.59 1.40
4159 4215 6.732896 TTCACTTTACCCAAAAAGCCATAA 57.267 33.333 0.00 0.00 39.59 1.90
4160 4216 6.732896 TTTCACTTTACCCAAAAAGCCATA 57.267 33.333 0.00 0.00 39.59 2.74
4161 4217 5.622346 TTTCACTTTACCCAAAAAGCCAT 57.378 34.783 0.00 0.00 39.59 4.40
4162 4218 5.422214 TTTTCACTTTACCCAAAAAGCCA 57.578 34.783 0.00 0.00 39.59 4.75
4163 4219 6.202762 CAGATTTTCACTTTACCCAAAAAGCC 59.797 38.462 0.00 0.00 39.59 4.35
4164 4220 6.292865 GCAGATTTTCACTTTACCCAAAAAGC 60.293 38.462 0.00 0.00 39.59 3.51
4165 4221 6.760770 TGCAGATTTTCACTTTACCCAAAAAG 59.239 34.615 0.00 0.00 41.35 2.27
4166 4222 6.644347 TGCAGATTTTCACTTTACCCAAAAA 58.356 32.000 0.00 0.00 0.00 1.94
4167 4223 6.227298 TGCAGATTTTCACTTTACCCAAAA 57.773 33.333 0.00 0.00 0.00 2.44
4168 4224 5.860941 TGCAGATTTTCACTTTACCCAAA 57.139 34.783 0.00 0.00 0.00 3.28
4169 4225 5.860941 TTGCAGATTTTCACTTTACCCAA 57.139 34.783 0.00 0.00 0.00 4.12
4170 4226 5.860941 TTTGCAGATTTTCACTTTACCCA 57.139 34.783 0.00 0.00 0.00 4.51
4171 4227 5.177511 GCTTTTGCAGATTTTCACTTTACCC 59.822 40.000 0.00 0.00 46.58 3.69
4172 4228 6.215477 GCTTTTGCAGATTTTCACTTTACC 57.785 37.500 0.00 0.00 46.58 2.85
4188 4244 2.657960 GCTTTTGCTTCTGCTTTTGC 57.342 45.000 0.00 0.00 43.94 3.68
4201 4257 2.609002 GCCCTGTTTGTTTGAGCTTTTG 59.391 45.455 0.00 0.00 0.00 2.44
4202 4258 2.419990 GGCCCTGTTTGTTTGAGCTTTT 60.420 45.455 0.00 0.00 0.00 2.27
4203 4259 1.138859 GGCCCTGTTTGTTTGAGCTTT 59.861 47.619 0.00 0.00 0.00 3.51
4204 4260 0.752658 GGCCCTGTTTGTTTGAGCTT 59.247 50.000 0.00 0.00 0.00 3.74
4205 4261 0.396974 TGGCCCTGTTTGTTTGAGCT 60.397 50.000 0.00 0.00 0.00 4.09
4206 4262 0.249447 GTGGCCCTGTTTGTTTGAGC 60.249 55.000 0.00 0.00 0.00 4.26
4207 4263 1.067516 CTGTGGCCCTGTTTGTTTGAG 59.932 52.381 0.00 0.00 0.00 3.02
4208 4264 1.110442 CTGTGGCCCTGTTTGTTTGA 58.890 50.000 0.00 0.00 0.00 2.69
4209 4265 0.823460 ACTGTGGCCCTGTTTGTTTG 59.177 50.000 0.00 0.00 0.00 2.93
4210 4266 1.480545 GAACTGTGGCCCTGTTTGTTT 59.519 47.619 14.54 0.00 35.60 2.83
4215 4271 0.468029 CCTTGAACTGTGGCCCTGTT 60.468 55.000 13.66 13.66 37.86 3.16
4217 4273 0.607489 CTCCTTGAACTGTGGCCCTG 60.607 60.000 0.00 0.00 0.00 4.45
4219 4275 1.303643 CCTCCTTGAACTGTGGCCC 60.304 63.158 0.00 0.00 0.00 5.80
4220 4276 0.110486 TTCCTCCTTGAACTGTGGCC 59.890 55.000 0.00 0.00 0.00 5.36
4223 4279 2.289694 ACCGATTCCTCCTTGAACTGTG 60.290 50.000 0.00 0.00 0.00 3.66
4250 4306 5.670341 GCAAATGTTTCATTGCTTCATCTGC 60.670 40.000 3.41 0.00 46.42 4.26
4286 4342 5.646793 GGCATCGTGTATACCTCTACAGATA 59.353 44.000 0.00 0.00 32.45 1.98
4299 4355 6.651643 TGTAAGTAAAAACAGGCATCGTGTAT 59.348 34.615 0.00 0.00 32.02 2.29
4306 4362 5.469479 GCATGTGTAAGTAAAAACAGGCAT 58.531 37.500 6.43 0.00 46.45 4.40
4343 4400 8.025445 GTGATGTTGCAAGAATTTGTCTTCTAT 58.975 33.333 0.00 0.00 45.25 1.98
4389 4452 3.265791 GTGCAGTTGCTAGCTCATTACT 58.734 45.455 17.23 8.48 42.66 2.24
4416 4479 1.880027 ACGGAACTTTTAGCAAGCTGG 59.120 47.619 4.53 0.00 0.00 4.85
4420 4483 6.730960 TGGTATAACGGAACTTTTAGCAAG 57.269 37.500 0.00 0.00 0.00 4.01
4429 4492 5.474532 GGTTTTTCCTTGGTATAACGGAACT 59.525 40.000 0.00 0.00 35.42 3.01
4456 4519 7.092137 TGGCAGTTAAATGAGAGATGAATTG 57.908 36.000 7.18 0.00 0.00 2.32
4489 4553 0.310543 GCATTGTGCGGAACTGACAA 59.689 50.000 0.00 0.00 31.71 3.18
4501 4565 3.061028 CCATTTTGTATGCGTGCATTGTG 59.939 43.478 13.20 3.84 37.82 3.33
4510 4574 2.514902 CGGTGAACCATTTTGTATGCG 58.485 47.619 0.00 0.00 35.14 4.73
4517 4581 3.292460 TGAAGAACCGGTGAACCATTTT 58.708 40.909 8.52 0.00 35.14 1.82


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

AutoCloner maintained by Alex Coulton.