Multiple sequence alignment - TraesCS6D01G205700

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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 TraesCS6D01G205700 chr6D 100.000 3156 0 0 433 3588 291492592 291489437 0.000000e+00 5829
1 TraesCS6D01G205700 chr6D 89.910 446 35 8 3149 3588 223127475 223127034 1.870000e-157 566
2 TraesCS6D01G205700 chr6D 100.000 78 0 0 1 78 291493024 291492947 1.040000e-30 145
3 TraesCS6D01G205700 chr6A 93.887 2732 103 30 433 3144 431920887 431923574 0.000000e+00 4061
4 TraesCS6D01G205700 chr6A 89.404 453 38 6 3142 3588 109133030 109133478 2.420000e-156 562
5 TraesCS6D01G205700 chr6B 93.747 2255 97 17 759 3000 452618561 452616338 0.000000e+00 3343
6 TraesCS6D01G205700 chr6B 84.706 255 20 7 518 766 452618969 452618728 1.670000e-58 237
7 TraesCS6D01G205700 chr2D 92.291 454 25 7 3141 3588 52040497 52040048 1.410000e-178 636
8 TraesCS6D01G205700 chr2D 91.256 446 28 7 3146 3588 29146298 29145861 6.630000e-167 597
9 TraesCS6D01G205700 chr2A 91.685 445 28 7 3146 3588 767387288 767387725 3.060000e-170 608
10 TraesCS6D01G205700 chr5D 90.646 449 33 8 3146 3588 103995494 103995049 3.990000e-164 588
11 TraesCS6D01G205700 chr5A 89.933 447 27 15 3146 3588 184222608 184223040 8.700000e-156 560
12 TraesCS6D01G205700 chr4A 88.985 463 36 12 3136 3588 545779548 545780005 3.130000e-155 558
13 TraesCS6D01G205700 chr1A 89.111 450 36 7 3142 3588 312851502 312851941 6.770000e-152 547


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 TraesCS6D01G205700 chr6D 291489437 291493024 3587 True 2987 5829 100.0000 1 3588 2 chr6D.!!$R2 3587
1 TraesCS6D01G205700 chr6A 431920887 431923574 2687 False 4061 4061 93.8870 433 3144 1 chr6A.!!$F2 2711
2 TraesCS6D01G205700 chr6B 452616338 452618969 2631 True 1790 3343 89.2265 518 3000 2 chr6B.!!$R1 2482

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
68 69 0.034574 AATGGGCTTGCATACGTGGA 60.035 50.0 0.0 0.0 0.0 4.02 F
867 1059 0.038526 CCTCGTACACACTCCACCAC 60.039 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1714 2.51160 GCGACCACGGGATTGAGG 60.512 66.667 0.0 0.0 40.15 3.86 R
2589 2783 0.03779 GCCACCCATCGCTATCTCTC 60.038 60.000 0.0 0.0 0.00 3.20 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
21 22 3.319137 AGTCGAAAGAGCAATGCTACA 57.681 42.857 8.12 0.00 43.49 2.74
22 23 3.866651 AGTCGAAAGAGCAATGCTACAT 58.133 40.909 8.12 0.00 43.49 2.29
23 24 3.620374 AGTCGAAAGAGCAATGCTACATG 59.380 43.478 8.12 0.00 43.49 3.21
24 25 2.352651 TCGAAAGAGCAATGCTACATGC 59.647 45.455 8.12 0.00 39.88 4.06
25 26 4.174282 TCGAAAGAGCAATGCTACATGCA 61.174 43.478 8.12 0.00 46.05 3.96
26 27 6.199996 TCGAAAGAGCAATGCTACATGCAC 62.200 45.833 8.12 0.00 45.29 4.57
36 37 3.788333 GCTACATGCACATGATGGTTT 57.212 42.857 17.19 0.00 41.20 3.27
37 38 4.114058 GCTACATGCACATGATGGTTTT 57.886 40.909 17.19 0.00 41.20 2.43
38 39 4.497300 GCTACATGCACATGATGGTTTTT 58.503 39.130 17.19 0.00 41.20 1.94
59 60 4.364415 TTTACGTATTCAATGGGCTTGC 57.636 40.909 0.00 0.00 34.66 4.01
60 61 1.832883 ACGTATTCAATGGGCTTGCA 58.167 45.000 0.00 0.00 34.66 4.08
61 62 2.378038 ACGTATTCAATGGGCTTGCAT 58.622 42.857 0.00 0.00 34.66 3.96
62 63 3.550820 ACGTATTCAATGGGCTTGCATA 58.449 40.909 0.00 0.00 34.66 3.14
63 64 3.315191 ACGTATTCAATGGGCTTGCATAC 59.685 43.478 0.00 1.11 39.28 2.39
64 65 3.888934 GTATTCAATGGGCTTGCATACG 58.111 45.455 0.00 0.00 35.33 3.06
65 66 1.832883 TTCAATGGGCTTGCATACGT 58.167 45.000 0.00 0.00 34.66 3.57
66 67 1.093972 TCAATGGGCTTGCATACGTG 58.906 50.000 0.00 0.00 34.66 4.49
67 68 0.101040 CAATGGGCTTGCATACGTGG 59.899 55.000 0.00 0.00 0.00 4.94
68 69 0.034574 AATGGGCTTGCATACGTGGA 60.035 50.000 0.00 0.00 0.00 4.02
69 70 0.464373 ATGGGCTTGCATACGTGGAG 60.464 55.000 0.00 0.00 0.00 3.86
70 71 1.078426 GGGCTTGCATACGTGGAGT 60.078 57.895 0.00 0.00 0.00 3.85
71 72 1.369091 GGGCTTGCATACGTGGAGTG 61.369 60.000 0.00 0.00 0.00 3.51
72 73 0.673644 GGCTTGCATACGTGGAGTGT 60.674 55.000 0.00 0.00 0.00 3.55
73 74 1.156736 GCTTGCATACGTGGAGTGTT 58.843 50.000 0.00 0.00 0.00 3.32
74 75 2.343101 GCTTGCATACGTGGAGTGTTA 58.657 47.619 0.00 0.00 0.00 2.41
75 76 2.936498 GCTTGCATACGTGGAGTGTTAT 59.064 45.455 0.00 0.00 0.00 1.89
76 77 3.242413 GCTTGCATACGTGGAGTGTTATG 60.242 47.826 0.00 0.00 0.00 1.90
77 78 3.878160 TGCATACGTGGAGTGTTATGA 57.122 42.857 0.00 0.00 0.00 2.15
501 506 3.130516 TCGAAAGTAGGAGTACATGGCAG 59.869 47.826 0.00 0.00 0.00 4.85
503 508 4.434520 GAAAGTAGGAGTACATGGCAGTC 58.565 47.826 0.00 0.00 0.00 3.51
575 581 1.754803 CATCGACCACCTACCAGCTAA 59.245 52.381 0.00 0.00 0.00 3.09
579 587 2.344025 GACCACCTACCAGCTAAAACG 58.656 52.381 0.00 0.00 0.00 3.60
860 1052 4.065281 GCCGGCCTCGTACACACT 62.065 66.667 18.11 0.00 33.95 3.55
861 1053 2.181021 CCGGCCTCGTACACACTC 59.819 66.667 0.00 0.00 33.95 3.51
862 1054 2.181021 CGGCCTCGTACACACTCC 59.819 66.667 0.00 0.00 0.00 3.85
863 1055 2.632544 CGGCCTCGTACACACTCCA 61.633 63.158 0.00 0.00 0.00 3.86
864 1056 1.080025 GGCCTCGTACACACTCCAC 60.080 63.158 0.00 0.00 0.00 4.02
865 1057 1.080025 GCCTCGTACACACTCCACC 60.080 63.158 0.00 0.00 0.00 4.61
866 1058 1.812686 GCCTCGTACACACTCCACCA 61.813 60.000 0.00 0.00 0.00 4.17
867 1059 0.038526 CCTCGTACACACTCCACCAC 60.039 60.000 0.00 0.00 0.00 4.16
891 1084 2.047151 AAACAACTCCGCACGCACAG 62.047 55.000 0.00 0.00 0.00 3.66
935 1128 0.670546 CGAAACCCACGACAGAGCAT 60.671 55.000 0.00 0.00 0.00 3.79
938 1131 0.615331 AACCCACGACAGAGCATCAT 59.385 50.000 0.00 0.00 37.82 2.45
939 1132 0.176680 ACCCACGACAGAGCATCATC 59.823 55.000 0.00 0.00 37.82 2.92
1134 1327 4.778415 CCGGTCGGTGCTCGTGAG 62.778 72.222 0.55 0.00 40.32 3.51
1374 1567 2.970324 TGGGCGCAGTTCGTGTTC 60.970 61.111 10.83 0.00 41.07 3.18
1535 1728 4.778143 GCGCCTCAATCCCGTGGT 62.778 66.667 0.00 0.00 0.00 4.16
1539 1732 2.264480 CTCAATCCCGTGGTCGCA 59.736 61.111 0.00 0.00 35.54 5.10
1743 1936 3.067601 TCATATATCTGAACACACGGCGT 59.932 43.478 6.77 6.77 0.00 5.68
1897 2090 1.376553 GGAGACAAGCAGAGGCACC 60.377 63.158 0.00 0.00 44.61 5.01
2025 2218 4.723309 ACCTCGACGGTAATAATCCTACT 58.277 43.478 4.93 0.00 46.73 2.57
2026 2219 4.759183 ACCTCGACGGTAATAATCCTACTC 59.241 45.833 4.93 0.00 46.73 2.59
2073 2267 3.240606 CTGTTCCGTGCCGTGCAAG 62.241 63.158 0.00 2.87 41.47 4.01
2085 2279 1.612469 CGTGCAAGTCGTGAGCTGAG 61.612 60.000 0.00 0.00 0.00 3.35
2167 2361 2.513259 GGTGGACAAGGTCGTGGGA 61.513 63.158 0.00 0.00 32.65 4.37
2601 2795 4.515191 GTGAGACTGAAGAGAGATAGCGAT 59.485 45.833 0.00 0.00 0.00 4.58
2602 2796 4.514816 TGAGACTGAAGAGAGATAGCGATG 59.485 45.833 0.00 0.00 0.00 3.84
2674 2872 0.968405 ACGCGTGGGTTAGGACTTAA 59.032 50.000 12.93 0.00 0.00 1.85
2811 3019 1.001406 AGCTCACCTTCGTTCTTCTGG 59.999 52.381 0.00 0.00 0.00 3.86
2957 3169 2.520979 CTTGGTTCGCGTTTGTCAAAA 58.479 42.857 5.77 0.00 0.00 2.44
3019 3231 8.974238 TCTATAGTGAATCCCTTCGTTTTCTTA 58.026 33.333 0.00 0.00 33.86 2.10
3030 3242 4.789095 TCGTTTTCTTAGTGTGTGCTTC 57.211 40.909 0.00 0.00 0.00 3.86
3035 3247 6.526674 CGTTTTCTTAGTGTGTGCTTCTTTTT 59.473 34.615 0.00 0.00 0.00 1.94
3037 3249 5.751243 TCTTAGTGTGTGCTTCTTTTTCC 57.249 39.130 0.00 0.00 0.00 3.13
3040 3252 1.673920 GTGTGTGCTTCTTTTTCCGGA 59.326 47.619 0.00 0.00 0.00 5.14
3055 3267 8.688151 TCTTTTTCCGGAGAAACTTTCAAATAA 58.312 29.630 15.74 0.00 41.69 1.40
3088 3300 2.548057 GTCATGACAGAACAAAAGGCGA 59.452 45.455 21.07 0.00 0.00 5.54
3089 3301 3.189287 GTCATGACAGAACAAAAGGCGAT 59.811 43.478 21.07 0.00 0.00 4.58
3093 3305 1.531149 ACAGAACAAAAGGCGATCACG 59.469 47.619 0.00 0.00 42.93 4.35
3094 3306 1.531149 CAGAACAAAAGGCGATCACGT 59.469 47.619 0.00 0.00 41.98 4.49
3133 3345 1.135915 CTGAGGTGACTGATCCCTTCG 59.864 57.143 0.00 0.00 44.43 3.79
3144 3356 1.139058 GATCCCTTCGAGCCTGCTAAA 59.861 52.381 0.00 0.00 0.00 1.85
3145 3357 0.981183 TCCCTTCGAGCCTGCTAAAA 59.019 50.000 0.00 0.00 0.00 1.52
3146 3358 1.066143 TCCCTTCGAGCCTGCTAAAAG 60.066 52.381 0.00 0.00 0.00 2.27
3147 3359 0.729690 CCTTCGAGCCTGCTAAAAGC 59.270 55.000 0.00 0.00 42.82 3.51
3158 3370 0.659957 GCTAAAAGCATCTCCAGCCG 59.340 55.000 0.00 0.00 41.89 5.52
3159 3371 2.014068 GCTAAAAGCATCTCCAGCCGT 61.014 52.381 0.00 0.00 41.89 5.68
3160 3372 2.359900 CTAAAAGCATCTCCAGCCGTT 58.640 47.619 0.00 0.00 0.00 4.44
3161 3373 0.883833 AAAAGCATCTCCAGCCGTTG 59.116 50.000 0.00 0.00 0.00 4.10
3173 3385 4.101448 CCGTTGGCCTCCCAGGAG 62.101 72.222 3.32 6.73 43.37 3.69
3181 3393 3.309582 CTCCCAGGAGGCGCTAAA 58.690 61.111 7.64 0.00 38.51 1.85
3182 3394 1.832912 CTCCCAGGAGGCGCTAAAT 59.167 57.895 7.64 0.00 38.51 1.40
3183 3395 1.048601 CTCCCAGGAGGCGCTAAATA 58.951 55.000 7.64 0.00 38.51 1.40
3184 3396 1.625818 CTCCCAGGAGGCGCTAAATAT 59.374 52.381 7.64 0.00 38.51 1.28
3185 3397 1.623811 TCCCAGGAGGCGCTAAATATC 59.376 52.381 7.64 0.00 34.51 1.63
3186 3398 1.673033 CCCAGGAGGCGCTAAATATCG 60.673 57.143 7.64 0.00 0.00 2.92
3191 3403 3.574780 GCGCTAAATATCGCCCCC 58.425 61.111 0.00 0.00 45.01 5.40
3222 3434 4.383602 CGAAAACCGCGTGCTGGG 62.384 66.667 4.92 0.00 0.00 4.45
3230 3442 4.722700 GCGTGCTGGGGGTGTGAT 62.723 66.667 0.00 0.00 0.00 3.06
3231 3443 2.436646 CGTGCTGGGGGTGTGATC 60.437 66.667 0.00 0.00 0.00 2.92
3232 3444 2.044946 GTGCTGGGGGTGTGATCC 60.045 66.667 0.00 0.00 0.00 3.36
3233 3445 3.338250 TGCTGGGGGTGTGATCCC 61.338 66.667 0.00 0.00 46.31 3.85
3262 3474 4.151417 CGCCCACGCATCTTTTTG 57.849 55.556 0.00 0.00 34.03 2.44
3263 3475 1.578926 CGCCCACGCATCTTTTTGA 59.421 52.632 0.00 0.00 34.03 2.69
3264 3476 0.039617 CGCCCACGCATCTTTTTGAA 60.040 50.000 0.00 0.00 34.03 2.69
3265 3477 1.601663 CGCCCACGCATCTTTTTGAAA 60.602 47.619 0.00 0.00 34.03 2.69
3266 3478 2.478831 GCCCACGCATCTTTTTGAAAA 58.521 42.857 0.00 0.00 34.03 2.29
3267 3479 2.220824 GCCCACGCATCTTTTTGAAAAC 59.779 45.455 0.00 0.00 34.03 2.43
3268 3480 2.799978 CCCACGCATCTTTTTGAAAACC 59.200 45.455 0.00 0.00 0.00 3.27
3269 3481 3.452474 CCACGCATCTTTTTGAAAACCA 58.548 40.909 0.00 0.00 0.00 3.67
3270 3482 3.245048 CCACGCATCTTTTTGAAAACCAC 59.755 43.478 0.00 0.00 0.00 4.16
3271 3483 3.862267 CACGCATCTTTTTGAAAACCACA 59.138 39.130 0.00 0.00 0.00 4.17
3272 3484 4.328440 CACGCATCTTTTTGAAAACCACAA 59.672 37.500 0.00 0.00 0.00 3.33
3273 3485 4.932200 ACGCATCTTTTTGAAAACCACAAA 59.068 33.333 0.00 0.00 35.81 2.83
3274 3486 5.163903 ACGCATCTTTTTGAAAACCACAAAC 60.164 36.000 0.00 0.00 37.05 2.93
3275 3487 5.063312 CGCATCTTTTTGAAAACCACAAACT 59.937 36.000 0.00 0.00 37.05 2.66
3276 3488 6.254589 CGCATCTTTTTGAAAACCACAAACTA 59.745 34.615 0.00 0.00 37.05 2.24
3277 3489 7.515059 CGCATCTTTTTGAAAACCACAAACTAG 60.515 37.037 0.00 0.00 37.05 2.57
3278 3490 7.254421 GCATCTTTTTGAAAACCACAAACTAGG 60.254 37.037 0.00 0.00 37.05 3.02
3279 3491 6.103330 TCTTTTTGAAAACCACAAACTAGGC 58.897 36.000 0.00 0.00 37.05 3.93
3280 3492 3.701532 TTGAAAACCACAAACTAGGCG 57.298 42.857 0.00 0.00 0.00 5.52
3281 3493 1.335496 TGAAAACCACAAACTAGGCGC 59.665 47.619 0.00 0.00 0.00 6.53
3282 3494 1.335496 GAAAACCACAAACTAGGCGCA 59.665 47.619 10.83 0.00 0.00 6.09
3283 3495 1.394618 AAACCACAAACTAGGCGCAA 58.605 45.000 10.83 0.00 0.00 4.85
3284 3496 1.394618 AACCACAAACTAGGCGCAAA 58.605 45.000 10.83 0.00 0.00 3.68
3285 3497 1.616159 ACCACAAACTAGGCGCAAAT 58.384 45.000 10.83 0.00 0.00 2.32
3286 3498 1.960689 ACCACAAACTAGGCGCAAATT 59.039 42.857 10.83 0.00 0.00 1.82
3287 3499 2.030274 ACCACAAACTAGGCGCAAATTC 60.030 45.455 10.83 0.00 0.00 2.17
3288 3500 2.030363 CCACAAACTAGGCGCAAATTCA 60.030 45.455 10.83 0.00 0.00 2.57
3289 3501 3.551863 CCACAAACTAGGCGCAAATTCAA 60.552 43.478 10.83 0.00 0.00 2.69
3290 3502 3.425193 CACAAACTAGGCGCAAATTCAAC 59.575 43.478 10.83 0.00 0.00 3.18
3291 3503 2.986479 CAAACTAGGCGCAAATTCAACC 59.014 45.455 10.83 0.00 0.00 3.77
3292 3504 1.904287 ACTAGGCGCAAATTCAACCA 58.096 45.000 10.83 0.00 0.00 3.67
3293 3505 2.235016 ACTAGGCGCAAATTCAACCAA 58.765 42.857 10.83 0.00 0.00 3.67
3294 3506 2.625790 ACTAGGCGCAAATTCAACCAAA 59.374 40.909 10.83 0.00 0.00 3.28
3295 3507 1.864565 AGGCGCAAATTCAACCAAAC 58.135 45.000 10.83 0.00 0.00 2.93
3296 3508 1.412343 AGGCGCAAATTCAACCAAACT 59.588 42.857 10.83 0.00 0.00 2.66
3297 3509 2.158971 AGGCGCAAATTCAACCAAACTT 60.159 40.909 10.83 0.00 0.00 2.66
3298 3510 2.220824 GGCGCAAATTCAACCAAACTTC 59.779 45.455 10.83 0.00 0.00 3.01
3299 3511 2.097444 GCGCAAATTCAACCAAACTTCG 60.097 45.455 0.30 0.00 0.00 3.79
3300 3512 2.470999 CGCAAATTCAACCAAACTTCGG 59.529 45.455 0.00 0.00 0.00 4.30
3301 3513 2.220824 GCAAATTCAACCAAACTTCGGC 59.779 45.455 0.00 0.00 0.00 5.54
3302 3514 2.415697 AATTCAACCAAACTTCGGCG 57.584 45.000 0.00 0.00 0.00 6.46
3303 3515 1.600023 ATTCAACCAAACTTCGGCGA 58.400 45.000 4.99 4.99 0.00 5.54
3304 3516 0.941542 TTCAACCAAACTTCGGCGAG 59.058 50.000 10.46 7.26 0.00 5.03
3305 3517 0.179067 TCAACCAAACTTCGGCGAGT 60.179 50.000 10.46 7.95 0.00 4.18
3306 3518 0.661020 CAACCAAACTTCGGCGAGTT 59.339 50.000 10.46 13.71 41.44 3.01
3307 3519 0.942252 AACCAAACTTCGGCGAGTTC 59.058 50.000 19.64 0.00 38.86 3.01
3308 3520 0.179067 ACCAAACTTCGGCGAGTTCA 60.179 50.000 19.64 2.43 38.86 3.18
3309 3521 1.156736 CCAAACTTCGGCGAGTTCAT 58.843 50.000 19.64 7.54 38.86 2.57
3310 3522 2.289195 ACCAAACTTCGGCGAGTTCATA 60.289 45.455 19.64 1.40 38.86 2.15
3311 3523 2.093783 CCAAACTTCGGCGAGTTCATAC 59.906 50.000 19.64 0.00 38.86 2.39
3312 3524 2.734606 CAAACTTCGGCGAGTTCATACA 59.265 45.455 19.64 0.05 38.86 2.29
3313 3525 2.961526 ACTTCGGCGAGTTCATACAT 57.038 45.000 10.46 0.00 0.00 2.29
3314 3526 4.380841 AACTTCGGCGAGTTCATACATA 57.619 40.909 10.46 0.00 34.94 2.29
3315 3527 4.585955 ACTTCGGCGAGTTCATACATAT 57.414 40.909 10.46 0.00 0.00 1.78
3316 3528 4.945246 ACTTCGGCGAGTTCATACATATT 58.055 39.130 10.46 0.00 0.00 1.28
3317 3529 5.357257 ACTTCGGCGAGTTCATACATATTT 58.643 37.500 10.46 0.00 0.00 1.40
3318 3530 6.509656 ACTTCGGCGAGTTCATACATATTTA 58.490 36.000 10.46 0.00 0.00 1.40
3319 3531 6.982141 ACTTCGGCGAGTTCATACATATTTAA 59.018 34.615 10.46 0.00 0.00 1.52
3320 3532 7.493320 ACTTCGGCGAGTTCATACATATTTAAA 59.507 33.333 10.46 0.00 0.00 1.52
3321 3533 7.773864 TCGGCGAGTTCATACATATTTAAAA 57.226 32.000 4.99 0.00 0.00 1.52
3322 3534 8.373048 TCGGCGAGTTCATACATATTTAAAAT 57.627 30.769 4.99 0.00 0.00 1.82
3323 3535 9.478768 TCGGCGAGTTCATACATATTTAAAATA 57.521 29.630 4.99 0.00 0.00 1.40
3362 3574 2.398252 AAAAAGCTACTAGGCCCGTC 57.602 50.000 0.00 0.00 0.00 4.79
3363 3575 0.175073 AAAAGCTACTAGGCCCGTCG 59.825 55.000 0.00 0.00 0.00 5.12
3364 3576 0.969409 AAAGCTACTAGGCCCGTCGT 60.969 55.000 0.00 0.00 0.00 4.34
3365 3577 1.382692 AAGCTACTAGGCCCGTCGTC 61.383 60.000 0.00 0.00 0.00 4.20
3366 3578 3.020627 CTACTAGGCCCGTCGTCG 58.979 66.667 0.00 0.00 0.00 5.12
3367 3579 3.178569 CTACTAGGCCCGTCGTCGC 62.179 68.421 0.00 0.00 35.54 5.19
3405 3617 4.767255 CGCCGCCCTTGAAGCTCT 62.767 66.667 0.00 0.00 0.00 4.09
3406 3618 2.584608 GCCGCCCTTGAAGCTCTA 59.415 61.111 0.00 0.00 0.00 2.43
3407 3619 1.815840 GCCGCCCTTGAAGCTCTAC 60.816 63.158 0.00 0.00 0.00 2.59
3408 3620 1.596934 CCGCCCTTGAAGCTCTACA 59.403 57.895 0.00 0.00 0.00 2.74
3409 3621 0.179000 CCGCCCTTGAAGCTCTACAT 59.821 55.000 0.00 0.00 0.00 2.29
3410 3622 1.293924 CGCCCTTGAAGCTCTACATG 58.706 55.000 0.00 0.00 0.00 3.21
3411 3623 1.020437 GCCCTTGAAGCTCTACATGC 58.980 55.000 0.00 0.00 0.00 4.06
3412 3624 1.673168 CCCTTGAAGCTCTACATGCC 58.327 55.000 0.00 0.00 0.00 4.40
3413 3625 1.293924 CCTTGAAGCTCTACATGCCG 58.706 55.000 0.00 0.00 0.00 5.69
3414 3626 1.134699 CCTTGAAGCTCTACATGCCGA 60.135 52.381 0.00 0.00 0.00 5.54
3415 3627 2.200067 CTTGAAGCTCTACATGCCGAG 58.800 52.381 7.33 7.33 0.00 4.63
3416 3628 0.461548 TGAAGCTCTACATGCCGAGG 59.538 55.000 12.24 0.00 0.00 4.63
3417 3629 0.747255 GAAGCTCTACATGCCGAGGA 59.253 55.000 12.24 0.00 0.00 3.71
3418 3630 0.749649 AAGCTCTACATGCCGAGGAG 59.250 55.000 12.24 5.62 0.00 3.69
3419 3631 1.300542 GCTCTACATGCCGAGGAGC 60.301 63.158 12.24 10.62 41.65 4.70
3420 3632 1.365633 CTCTACATGCCGAGGAGCC 59.634 63.158 0.00 0.00 0.00 4.70
3421 3633 1.075970 TCTACATGCCGAGGAGCCT 60.076 57.895 0.00 0.00 0.00 4.58
3422 3634 1.068753 CTACATGCCGAGGAGCCTG 59.931 63.158 0.00 0.00 34.88 4.85
3423 3635 1.680522 CTACATGCCGAGGAGCCTGT 61.681 60.000 0.00 0.39 43.00 4.00
3424 3636 0.396556 TACATGCCGAGGAGCCTGTA 60.397 55.000 0.00 0.00 41.17 2.74
3425 3637 1.068753 CATGCCGAGGAGCCTGTAG 59.931 63.158 0.00 0.00 0.00 2.74
3426 3638 1.075970 ATGCCGAGGAGCCTGTAGA 60.076 57.895 0.00 0.00 0.00 2.59
3427 3639 0.687757 ATGCCGAGGAGCCTGTAGAA 60.688 55.000 0.00 0.00 0.00 2.10
3428 3640 1.142097 GCCGAGGAGCCTGTAGAAC 59.858 63.158 0.00 0.00 0.00 3.01
3429 3641 1.324005 GCCGAGGAGCCTGTAGAACT 61.324 60.000 0.00 0.00 0.00 3.01
3430 3642 1.187087 CCGAGGAGCCTGTAGAACTT 58.813 55.000 0.00 0.00 0.00 2.66
3431 3643 1.135333 CCGAGGAGCCTGTAGAACTTC 59.865 57.143 0.00 0.00 0.00 3.01
3432 3644 1.819288 CGAGGAGCCTGTAGAACTTCA 59.181 52.381 0.00 0.00 0.00 3.02
3433 3645 2.428890 CGAGGAGCCTGTAGAACTTCAT 59.571 50.000 0.00 0.00 0.00 2.57
3434 3646 3.736433 CGAGGAGCCTGTAGAACTTCATG 60.736 52.174 0.00 0.00 0.00 3.07
3435 3647 3.177228 AGGAGCCTGTAGAACTTCATGT 58.823 45.455 0.00 0.00 0.00 3.21
3436 3648 4.353777 AGGAGCCTGTAGAACTTCATGTA 58.646 43.478 0.00 0.00 0.00 2.29
3437 3649 4.404073 AGGAGCCTGTAGAACTTCATGTAG 59.596 45.833 0.00 0.00 0.00 2.74
3438 3650 4.160626 GGAGCCTGTAGAACTTCATGTAGT 59.839 45.833 0.00 0.00 0.00 2.73
3439 3651 5.331876 AGCCTGTAGAACTTCATGTAGTC 57.668 43.478 5.37 0.42 0.00 2.59
3440 3652 4.772624 AGCCTGTAGAACTTCATGTAGTCA 59.227 41.667 5.37 0.00 0.00 3.41
3441 3653 4.865365 GCCTGTAGAACTTCATGTAGTCAC 59.135 45.833 5.37 5.41 0.00 3.67
3442 3654 5.411781 CCTGTAGAACTTCATGTAGTCACC 58.588 45.833 5.37 0.00 0.00 4.02
3443 3655 5.055642 TGTAGAACTTCATGTAGTCACCG 57.944 43.478 5.37 0.00 0.00 4.94
3444 3656 2.960819 AGAACTTCATGTAGTCACCGC 58.039 47.619 5.37 0.00 0.00 5.68
3445 3657 2.000447 GAACTTCATGTAGTCACCGCC 59.000 52.381 5.37 0.00 0.00 6.13
3446 3658 0.108804 ACTTCATGTAGTCACCGCCG 60.109 55.000 0.00 0.00 0.00 6.46
3447 3659 1.421410 CTTCATGTAGTCACCGCCGC 61.421 60.000 0.00 0.00 0.00 6.53
3448 3660 2.845752 TTCATGTAGTCACCGCCGCC 62.846 60.000 0.00 0.00 0.00 6.13
3449 3661 4.508128 ATGTAGTCACCGCCGCCG 62.508 66.667 0.00 0.00 0.00 6.46
3469 3681 4.808238 GTCGTCGTCGTCGCCTCC 62.808 72.222 7.01 0.00 38.33 4.30
3471 3683 4.517703 CGTCGTCGTCGCCTCCTC 62.518 72.222 0.00 0.00 36.96 3.71
3472 3684 4.176851 GTCGTCGTCGCCTCCTCC 62.177 72.222 0.00 0.00 36.96 4.30
3500 3712 4.741239 TCCCTGCTGGACCCCTCC 62.741 72.222 11.88 0.00 38.61 4.30
3501 3713 4.748798 CCCTGCTGGACCCCTCCT 62.749 72.222 11.88 0.00 37.48 3.69
3502 3714 3.086600 CCTGCTGGACCCCTCCTC 61.087 72.222 2.92 0.00 37.48 3.71
3503 3715 2.284921 CTGCTGGACCCCTCCTCA 60.285 66.667 0.00 0.00 37.48 3.86
3504 3716 2.284921 TGCTGGACCCCTCCTCAG 60.285 66.667 0.00 0.00 37.48 3.35
3505 3717 3.086600 GCTGGACCCCTCCTCAGG 61.087 72.222 0.00 0.00 37.48 3.86
3506 3718 2.452114 CTGGACCCCTCCTCAGGT 59.548 66.667 0.00 0.00 38.30 4.00
3507 3719 1.229658 CTGGACCCCTCCTCAGGTT 60.230 63.158 0.00 0.00 38.30 3.50
3508 3720 1.538876 TGGACCCCTCCTCAGGTTG 60.539 63.158 0.00 0.00 38.30 3.77
3509 3721 2.301738 GGACCCCTCCTCAGGTTGG 61.302 68.421 0.00 0.00 38.30 3.77
3510 3722 2.936032 ACCCCTCCTCAGGTTGGC 60.936 66.667 0.00 0.00 38.30 4.52
3511 3723 4.101448 CCCCTCCTCAGGTTGGCG 62.101 72.222 0.00 0.00 38.30 5.69
3512 3724 4.785453 CCCTCCTCAGGTTGGCGC 62.785 72.222 0.00 0.00 38.30 6.53
3532 3744 4.483243 CGGGTTGGATGGTCCGGG 62.483 72.222 0.00 0.00 40.17 5.73
3533 3745 4.123545 GGGTTGGATGGTCCGGGG 62.124 72.222 0.00 0.00 40.17 5.73
3534 3746 4.123545 GGTTGGATGGTCCGGGGG 62.124 72.222 0.00 0.00 40.17 5.40
3535 3747 4.815108 GTTGGATGGTCCGGGGGC 62.815 72.222 0.00 0.00 40.17 5.80
3550 3762 4.176851 GGCGTCCTCGTCCTCGTC 62.177 72.222 0.00 0.00 39.49 4.20
3551 3763 4.517703 GCGTCCTCGTCCTCGTCG 62.518 72.222 0.00 0.00 39.49 5.12
3552 3764 4.517703 CGTCCTCGTCCTCGTCGC 62.518 72.222 0.00 0.00 38.33 5.19
3553 3765 3.126225 GTCCTCGTCCTCGTCGCT 61.126 66.667 0.00 0.00 38.33 4.93
3554 3766 3.125573 TCCTCGTCCTCGTCGCTG 61.126 66.667 0.00 0.00 38.33 5.18
3555 3767 3.432588 CCTCGTCCTCGTCGCTGT 61.433 66.667 0.00 0.00 38.33 4.40
3556 3768 2.098680 CTCGTCCTCGTCGCTGTC 59.901 66.667 0.00 0.00 38.33 3.51
3557 3769 3.703939 CTCGTCCTCGTCGCTGTCG 62.704 68.421 0.00 0.00 38.33 4.35
3558 3770 3.785499 CGTCCTCGTCGCTGTCGA 61.785 66.667 0.00 0.00 43.28 4.20
3565 3777 4.386245 GTCGCTGTCGAGGATCAC 57.614 61.111 0.00 0.00 46.46 3.06
3566 3778 1.226717 GTCGCTGTCGAGGATCACC 60.227 63.158 0.00 0.00 46.46 4.02
3567 3779 1.677633 TCGCTGTCGAGGATCACCA 60.678 57.895 0.00 0.00 40.21 4.17
3568 3780 1.517257 CGCTGTCGAGGATCACCAC 60.517 63.158 0.00 0.00 38.94 4.16
3570 3782 1.517257 CTGTCGAGGATCACCACGC 60.517 63.158 0.00 0.00 46.66 5.34
3571 3783 2.202756 GTCGAGGATCACCACGCC 60.203 66.667 0.00 0.00 46.66 5.68
3572 3784 3.822192 TCGAGGATCACCACGCCG 61.822 66.667 0.00 0.00 46.66 6.46
3573 3785 4.129737 CGAGGATCACCACGCCGT 62.130 66.667 0.00 0.00 42.39 5.68
3574 3786 2.509336 GAGGATCACCACGCCGTG 60.509 66.667 10.95 10.95 38.94 4.94
3575 3787 4.760047 AGGATCACCACGCCGTGC 62.760 66.667 12.68 0.00 38.94 5.34
3576 3788 4.760047 GGATCACCACGCCGTGCT 62.760 66.667 12.68 0.00 35.97 4.40
3577 3789 3.188786 GATCACCACGCCGTGCTC 61.189 66.667 12.68 1.78 33.57 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.664107 TGTAGCATTGCTCTTTCGACTT 58.336 40.909 15.81 0.00 40.44 3.01
1 2 3.319137 TGTAGCATTGCTCTTTCGACT 57.681 42.857 15.81 0.00 40.44 4.18
2 3 3.786818 GCATGTAGCATTGCTCTTTCGAC 60.787 47.826 15.81 7.23 44.79 4.20
3 4 2.352651 GCATGTAGCATTGCTCTTTCGA 59.647 45.455 15.81 0.00 44.79 3.71
4 5 2.713011 GCATGTAGCATTGCTCTTTCG 58.287 47.619 15.81 2.70 44.79 3.46
16 17 3.788333 AAACCATCATGTGCATGTAGC 57.212 42.857 11.38 0.00 45.96 3.58
36 37 5.164954 GCAAGCCCATTGAATACGTAAAAA 58.835 37.500 0.00 0.00 41.83 1.94
37 38 4.218635 TGCAAGCCCATTGAATACGTAAAA 59.781 37.500 0.00 0.00 41.83 1.52
38 39 3.759086 TGCAAGCCCATTGAATACGTAAA 59.241 39.130 0.00 0.00 41.83 2.01
39 40 3.348119 TGCAAGCCCATTGAATACGTAA 58.652 40.909 0.00 0.00 41.83 3.18
40 41 2.992593 TGCAAGCCCATTGAATACGTA 58.007 42.857 0.00 0.00 41.83 3.57
41 42 1.832883 TGCAAGCCCATTGAATACGT 58.167 45.000 0.00 0.00 41.83 3.57
42 43 3.888934 GTATGCAAGCCCATTGAATACG 58.111 45.455 0.00 0.00 46.01 3.06
44 45 3.314913 CACGTATGCAAGCCCATTGAATA 59.685 43.478 0.00 0.00 41.83 1.75
45 46 2.099592 CACGTATGCAAGCCCATTGAAT 59.900 45.455 0.00 0.00 41.83 2.57
46 47 1.472082 CACGTATGCAAGCCCATTGAA 59.528 47.619 0.00 0.00 41.83 2.69
47 48 1.093972 CACGTATGCAAGCCCATTGA 58.906 50.000 0.00 0.00 41.83 2.57
48 49 0.101040 CCACGTATGCAAGCCCATTG 59.899 55.000 0.00 0.00 42.20 2.82
49 50 0.034574 TCCACGTATGCAAGCCCATT 60.035 50.000 0.00 0.00 0.00 3.16
50 51 0.464373 CTCCACGTATGCAAGCCCAT 60.464 55.000 0.00 0.00 0.00 4.00
51 52 1.078497 CTCCACGTATGCAAGCCCA 60.078 57.895 0.00 0.00 0.00 5.36
52 53 1.078426 ACTCCACGTATGCAAGCCC 60.078 57.895 0.00 0.00 0.00 5.19
53 54 0.673644 ACACTCCACGTATGCAAGCC 60.674 55.000 0.00 0.00 0.00 4.35
54 55 1.156736 AACACTCCACGTATGCAAGC 58.843 50.000 0.00 0.00 0.00 4.01
55 56 4.180817 TCATAACACTCCACGTATGCAAG 58.819 43.478 0.00 0.00 0.00 4.01
56 57 4.195225 TCATAACACTCCACGTATGCAA 57.805 40.909 0.00 0.00 0.00 4.08
57 58 3.878160 TCATAACACTCCACGTATGCA 57.122 42.857 0.00 0.00 0.00 3.96
458 459 5.653330 TCGACCTCAATAATACTACACACCA 59.347 40.000 0.00 0.00 0.00 4.17
501 506 3.630312 TGCAAACCCTCTTAACTGTTGAC 59.370 43.478 2.69 0.00 0.00 3.18
503 508 4.853924 ATGCAAACCCTCTTAACTGTTG 57.146 40.909 2.69 0.00 0.00 3.33
618 632 5.908916 GCTACACGAGTTTCTTTCTTTCT 57.091 39.130 0.00 0.00 0.00 2.52
692 706 3.842923 AGCGGCTGACCAGATCGG 61.843 66.667 0.00 2.55 42.50 4.18
825 1017 2.677848 GGGGGAGGAAAGCTGACC 59.322 66.667 0.00 0.00 0.00 4.02
853 1045 0.691413 TGGTGGTGGTGGAGTGTGTA 60.691 55.000 0.00 0.00 0.00 2.90
854 1046 1.567208 TTGGTGGTGGTGGAGTGTGT 61.567 55.000 0.00 0.00 0.00 3.72
855 1047 0.395036 TTTGGTGGTGGTGGAGTGTG 60.395 55.000 0.00 0.00 0.00 3.82
856 1048 0.395173 GTTTGGTGGTGGTGGAGTGT 60.395 55.000 0.00 0.00 0.00 3.55
857 1049 0.395036 TGTTTGGTGGTGGTGGAGTG 60.395 55.000 0.00 0.00 0.00 3.51
858 1050 0.333312 TTGTTTGGTGGTGGTGGAGT 59.667 50.000 0.00 0.00 0.00 3.85
859 1051 0.744281 GTTGTTTGGTGGTGGTGGAG 59.256 55.000 0.00 0.00 0.00 3.86
860 1052 0.333312 AGTTGTTTGGTGGTGGTGGA 59.667 50.000 0.00 0.00 0.00 4.02
861 1053 0.744281 GAGTTGTTTGGTGGTGGTGG 59.256 55.000 0.00 0.00 0.00 4.61
862 1054 0.744281 GGAGTTGTTTGGTGGTGGTG 59.256 55.000 0.00 0.00 0.00 4.17
863 1055 0.750182 CGGAGTTGTTTGGTGGTGGT 60.750 55.000 0.00 0.00 0.00 4.16
864 1056 2.029743 CGGAGTTGTTTGGTGGTGG 58.970 57.895 0.00 0.00 0.00 4.61
865 1057 1.358759 GCGGAGTTGTTTGGTGGTG 59.641 57.895 0.00 0.00 0.00 4.17
866 1058 1.077357 TGCGGAGTTGTTTGGTGGT 60.077 52.632 0.00 0.00 0.00 4.16
867 1059 1.358759 GTGCGGAGTTGTTTGGTGG 59.641 57.895 0.00 0.00 0.00 4.61
891 1084 0.739813 CGGGTCGGTTGATTCTGTCC 60.740 60.000 0.00 0.00 0.00 4.02
935 1128 1.830477 TGGACATGGACATGACGATGA 59.170 47.619 22.48 2.38 41.20 2.92
938 1131 0.249120 GGTGGACATGGACATGACGA 59.751 55.000 18.38 7.27 41.20 4.20
939 1132 0.250234 AGGTGGACATGGACATGACG 59.750 55.000 18.38 0.00 41.20 4.35
940 1133 1.740380 CGAGGTGGACATGGACATGAC 60.740 57.143 18.38 12.09 41.20 3.06
1122 1315 4.778415 CCGACCTCACGAGCACCG 62.778 72.222 0.00 0.00 45.44 4.94
1521 1714 2.511600 GCGACCACGGGATTGAGG 60.512 66.667 0.00 0.00 40.15 3.86
1743 1936 3.371063 GACGCTGACCACTCCGGA 61.371 66.667 2.93 2.93 38.63 5.14
1897 2090 2.821366 GCCCAGCGACATGACCAG 60.821 66.667 0.00 0.00 0.00 4.00
2073 2267 1.005630 AACCTGCTCAGCTCACGAC 60.006 57.895 0.00 0.00 0.00 4.34
2085 2279 2.350772 CCTGAACAATCAACGAACCTGC 60.351 50.000 0.00 0.00 34.49 4.85
2584 2778 2.890311 ACCCATCGCTATCTCTCTTCAG 59.110 50.000 0.00 0.00 0.00 3.02
2585 2779 2.625314 CACCCATCGCTATCTCTCTTCA 59.375 50.000 0.00 0.00 0.00 3.02
2586 2780 2.029470 CCACCCATCGCTATCTCTCTTC 60.029 54.545 0.00 0.00 0.00 2.87
2587 2781 1.967066 CCACCCATCGCTATCTCTCTT 59.033 52.381 0.00 0.00 0.00 2.85
2588 2782 1.626686 CCACCCATCGCTATCTCTCT 58.373 55.000 0.00 0.00 0.00 3.10
2589 2783 0.037790 GCCACCCATCGCTATCTCTC 60.038 60.000 0.00 0.00 0.00 3.20
2590 2784 0.470833 AGCCACCCATCGCTATCTCT 60.471 55.000 0.00 0.00 32.26 3.10
2591 2785 0.037790 GAGCCACCCATCGCTATCTC 60.038 60.000 0.00 0.00 34.84 2.75
2592 2786 0.760567 TGAGCCACCCATCGCTATCT 60.761 55.000 0.00 0.00 34.84 1.98
2601 2795 0.251297 CTTGACCAATGAGCCACCCA 60.251 55.000 0.00 0.00 0.00 4.51
2602 2796 1.598701 GCTTGACCAATGAGCCACCC 61.599 60.000 0.00 0.00 0.00 4.61
3019 3231 1.676006 CCGGAAAAAGAAGCACACACT 59.324 47.619 0.00 0.00 0.00 3.55
3030 3242 8.865590 TTATTTGAAAGTTTCTCCGGAAAAAG 57.134 30.769 16.33 0.00 42.22 2.27
3035 3247 8.172352 TGAATTTATTTGAAAGTTTCTCCGGA 57.828 30.769 16.33 2.93 0.00 5.14
3081 3293 1.518572 CGCCTACGTGATCGCCTTT 60.519 57.895 0.00 0.00 41.18 3.11
3144 3356 4.308526 CAACGGCTGGAGATGCTT 57.691 55.556 0.00 0.00 0.00 3.91
3156 3368 4.101448 CTCCTGGGAGGCCAACGG 62.101 72.222 5.01 0.00 38.51 4.44
3164 3376 1.048601 TATTTAGCGCCTCCTGGGAG 58.951 55.000 2.29 9.53 41.63 4.30
3165 3377 1.623811 GATATTTAGCGCCTCCTGGGA 59.376 52.381 2.29 0.00 37.23 4.37
3166 3378 1.673033 CGATATTTAGCGCCTCCTGGG 60.673 57.143 2.29 0.00 38.36 4.45
3167 3379 1.714794 CGATATTTAGCGCCTCCTGG 58.285 55.000 2.29 0.00 0.00 4.45
3205 3417 4.383602 CCCAGCACGCGGTTTTCG 62.384 66.667 12.47 0.00 42.76 3.46
3206 3418 4.038080 CCCCAGCACGCGGTTTTC 62.038 66.667 12.47 0.00 0.00 2.29
3213 3425 4.722700 ATCACACCCCCAGCACGC 62.723 66.667 0.00 0.00 0.00 5.34
3214 3426 2.436646 GATCACACCCCCAGCACG 60.437 66.667 0.00 0.00 0.00 5.34
3215 3427 2.044946 GGATCACACCCCCAGCAC 60.045 66.667 0.00 0.00 0.00 4.40
3216 3428 3.338250 GGGATCACACCCCCAGCA 61.338 66.667 0.00 0.00 43.81 4.41
3245 3457 0.039617 TTCAAAAAGATGCGTGGGCG 60.040 50.000 0.00 0.00 44.10 6.13
3246 3458 2.147436 TTTCAAAAAGATGCGTGGGC 57.853 45.000 0.00 0.00 40.52 5.36
3247 3459 2.799978 GGTTTTCAAAAAGATGCGTGGG 59.200 45.455 0.00 0.00 0.00 4.61
3248 3460 3.245048 GTGGTTTTCAAAAAGATGCGTGG 59.755 43.478 0.00 0.00 0.00 4.94
3249 3461 3.862267 TGTGGTTTTCAAAAAGATGCGTG 59.138 39.130 0.00 0.00 0.00 5.34
3250 3462 4.116747 TGTGGTTTTCAAAAAGATGCGT 57.883 36.364 0.00 0.00 0.00 5.24
3251 3463 5.063312 AGTTTGTGGTTTTCAAAAAGATGCG 59.937 36.000 0.00 0.00 33.55 4.73
3252 3464 6.421377 AGTTTGTGGTTTTCAAAAAGATGC 57.579 33.333 0.00 0.00 33.55 3.91
3253 3465 7.254421 GCCTAGTTTGTGGTTTTCAAAAAGATG 60.254 37.037 0.00 0.00 33.55 2.90
3254 3466 6.761242 GCCTAGTTTGTGGTTTTCAAAAAGAT 59.239 34.615 0.00 0.00 33.55 2.40
3255 3467 6.103330 GCCTAGTTTGTGGTTTTCAAAAAGA 58.897 36.000 0.00 0.00 33.55 2.52
3256 3468 5.005299 CGCCTAGTTTGTGGTTTTCAAAAAG 59.995 40.000 0.00 0.00 33.55 2.27
3257 3469 4.865365 CGCCTAGTTTGTGGTTTTCAAAAA 59.135 37.500 0.00 0.00 36.71 1.94
3258 3470 4.425520 CGCCTAGTTTGTGGTTTTCAAAA 58.574 39.130 0.00 0.00 36.71 2.44
3259 3471 3.735514 GCGCCTAGTTTGTGGTTTTCAAA 60.736 43.478 0.00 0.00 33.28 2.69
3260 3472 2.223618 GCGCCTAGTTTGTGGTTTTCAA 60.224 45.455 0.00 0.00 0.00 2.69
3261 3473 1.335496 GCGCCTAGTTTGTGGTTTTCA 59.665 47.619 0.00 0.00 0.00 2.69
3262 3474 1.335496 TGCGCCTAGTTTGTGGTTTTC 59.665 47.619 4.18 0.00 0.00 2.29
3263 3475 1.394618 TGCGCCTAGTTTGTGGTTTT 58.605 45.000 4.18 0.00 0.00 2.43
3264 3476 1.394618 TTGCGCCTAGTTTGTGGTTT 58.605 45.000 4.18 0.00 0.00 3.27
3265 3477 1.394618 TTTGCGCCTAGTTTGTGGTT 58.605 45.000 4.18 0.00 0.00 3.67
3266 3478 1.616159 ATTTGCGCCTAGTTTGTGGT 58.384 45.000 4.18 0.00 0.00 4.16
3267 3479 2.030363 TGAATTTGCGCCTAGTTTGTGG 60.030 45.455 4.18 0.00 0.00 4.17
3268 3480 3.281341 TGAATTTGCGCCTAGTTTGTG 57.719 42.857 4.18 0.00 0.00 3.33
3269 3481 3.552068 GGTTGAATTTGCGCCTAGTTTGT 60.552 43.478 4.18 0.00 0.00 2.83
3270 3482 2.986479 GGTTGAATTTGCGCCTAGTTTG 59.014 45.455 4.18 0.00 0.00 2.93
3271 3483 2.625790 TGGTTGAATTTGCGCCTAGTTT 59.374 40.909 4.18 0.00 0.00 2.66
3272 3484 2.235016 TGGTTGAATTTGCGCCTAGTT 58.765 42.857 4.18 0.00 0.00 2.24
3273 3485 1.904287 TGGTTGAATTTGCGCCTAGT 58.096 45.000 4.18 0.00 0.00 2.57
3274 3486 2.986479 GTTTGGTTGAATTTGCGCCTAG 59.014 45.455 4.18 0.00 0.00 3.02
3275 3487 2.625790 AGTTTGGTTGAATTTGCGCCTA 59.374 40.909 4.18 0.00 0.00 3.93
3276 3488 1.412343 AGTTTGGTTGAATTTGCGCCT 59.588 42.857 4.18 0.00 0.00 5.52
3277 3489 1.864565 AGTTTGGTTGAATTTGCGCC 58.135 45.000 4.18 0.00 0.00 6.53
3278 3490 2.097444 CGAAGTTTGGTTGAATTTGCGC 60.097 45.455 0.00 0.00 0.00 6.09
3279 3491 2.470999 CCGAAGTTTGGTTGAATTTGCG 59.529 45.455 0.29 0.00 0.00 4.85
3280 3492 2.220824 GCCGAAGTTTGGTTGAATTTGC 59.779 45.455 10.98 0.00 0.00 3.68
3281 3493 2.470999 CGCCGAAGTTTGGTTGAATTTG 59.529 45.455 10.98 0.00 0.00 2.32
3282 3494 2.359531 TCGCCGAAGTTTGGTTGAATTT 59.640 40.909 10.98 0.00 0.00 1.82
3283 3495 1.950909 TCGCCGAAGTTTGGTTGAATT 59.049 42.857 10.98 0.00 0.00 2.17
3284 3496 1.535462 CTCGCCGAAGTTTGGTTGAAT 59.465 47.619 10.98 0.00 0.00 2.57
3285 3497 0.941542 CTCGCCGAAGTTTGGTTGAA 59.058 50.000 10.98 0.00 0.00 2.69
3286 3498 0.179067 ACTCGCCGAAGTTTGGTTGA 60.179 50.000 10.98 8.25 0.00 3.18
3287 3499 0.661020 AACTCGCCGAAGTTTGGTTG 59.339 50.000 10.98 4.32 36.02 3.77
3288 3500 0.942252 GAACTCGCCGAAGTTTGGTT 59.058 50.000 10.98 0.00 39.55 3.67
3289 3501 0.179067 TGAACTCGCCGAAGTTTGGT 60.179 50.000 10.98 0.00 39.55 3.67
3290 3502 1.156736 ATGAACTCGCCGAAGTTTGG 58.843 50.000 4.57 4.57 39.55 3.28
3291 3503 2.734606 TGTATGAACTCGCCGAAGTTTG 59.265 45.455 4.02 0.00 39.55 2.93
3292 3504 3.034721 TGTATGAACTCGCCGAAGTTT 57.965 42.857 4.02 0.00 39.55 2.66
3293 3505 2.736144 TGTATGAACTCGCCGAAGTT 57.264 45.000 2.37 2.37 42.10 2.66
3294 3506 2.961526 ATGTATGAACTCGCCGAAGT 57.038 45.000 0.00 0.00 0.00 3.01
3295 3507 5.907197 AAATATGTATGAACTCGCCGAAG 57.093 39.130 0.00 0.00 0.00 3.79
3296 3508 7.773864 TTTAAATATGTATGAACTCGCCGAA 57.226 32.000 0.00 0.00 0.00 4.30
3297 3509 7.773864 TTTTAAATATGTATGAACTCGCCGA 57.226 32.000 0.00 0.00 0.00 5.54
3343 3555 1.405121 CGACGGGCCTAGTAGCTTTTT 60.405 52.381 0.84 0.00 0.00 1.94
3344 3556 0.175073 CGACGGGCCTAGTAGCTTTT 59.825 55.000 0.84 0.00 0.00 2.27
3345 3557 0.969409 ACGACGGGCCTAGTAGCTTT 60.969 55.000 0.84 0.00 0.00 3.51
3346 3558 1.379576 ACGACGGGCCTAGTAGCTT 60.380 57.895 0.84 0.00 0.00 3.74
3347 3559 1.823041 GACGACGGGCCTAGTAGCT 60.823 63.158 0.84 0.00 0.00 3.32
3348 3560 2.720605 GACGACGGGCCTAGTAGC 59.279 66.667 0.84 0.00 0.00 3.58
3349 3561 3.020627 CGACGACGGGCCTAGTAG 58.979 66.667 0.84 6.59 35.72 2.57
3350 3562 3.204827 GCGACGACGGGCCTAGTA 61.205 66.667 9.67 0.00 40.15 1.82
3388 3600 3.371097 TAGAGCTTCAAGGGCGGCG 62.371 63.158 0.51 0.51 34.52 6.46
3389 3601 1.815840 GTAGAGCTTCAAGGGCGGC 60.816 63.158 0.00 0.00 34.52 6.53
3390 3602 0.179000 ATGTAGAGCTTCAAGGGCGG 59.821 55.000 0.00 0.00 34.52 6.13
3391 3603 1.293924 CATGTAGAGCTTCAAGGGCG 58.706 55.000 0.00 0.00 34.52 6.13
3392 3604 1.020437 GCATGTAGAGCTTCAAGGGC 58.980 55.000 0.00 0.00 0.00 5.19
3393 3605 1.673168 GGCATGTAGAGCTTCAAGGG 58.327 55.000 0.00 0.00 0.00 3.95
3394 3606 1.134699 TCGGCATGTAGAGCTTCAAGG 60.135 52.381 0.00 0.00 0.00 3.61
3395 3607 2.200067 CTCGGCATGTAGAGCTTCAAG 58.800 52.381 6.63 0.00 0.00 3.02
3396 3608 1.134699 CCTCGGCATGTAGAGCTTCAA 60.135 52.381 12.24 0.00 33.39 2.69
3397 3609 0.461548 CCTCGGCATGTAGAGCTTCA 59.538 55.000 12.24 0.00 33.39 3.02
3398 3610 0.747255 TCCTCGGCATGTAGAGCTTC 59.253 55.000 12.24 0.00 33.39 3.86
3399 3611 0.749649 CTCCTCGGCATGTAGAGCTT 59.250 55.000 12.24 0.00 33.39 3.74
3400 3612 1.743321 GCTCCTCGGCATGTAGAGCT 61.743 60.000 12.24 0.00 45.11 4.09
3401 3613 1.300542 GCTCCTCGGCATGTAGAGC 60.301 63.158 12.24 10.16 42.74 4.09
3402 3614 1.112315 AGGCTCCTCGGCATGTAGAG 61.112 60.000 11.14 11.14 41.46 2.43
3403 3615 1.075970 AGGCTCCTCGGCATGTAGA 60.076 57.895 0.00 0.00 41.46 2.59
3404 3616 1.068753 CAGGCTCCTCGGCATGTAG 59.931 63.158 0.00 0.00 38.88 2.74
3405 3617 3.220222 CAGGCTCCTCGGCATGTA 58.780 61.111 0.00 0.00 38.88 2.29
3408 3620 0.687757 TTCTACAGGCTCCTCGGCAT 60.688 55.000 0.00 0.00 41.46 4.40
3409 3621 1.304962 TTCTACAGGCTCCTCGGCA 60.305 57.895 0.00 0.00 41.46 5.69
3410 3622 1.142097 GTTCTACAGGCTCCTCGGC 59.858 63.158 0.00 0.00 38.75 5.54
3411 3623 1.135333 GAAGTTCTACAGGCTCCTCGG 59.865 57.143 0.00 0.00 0.00 4.63
3412 3624 1.819288 TGAAGTTCTACAGGCTCCTCG 59.181 52.381 4.17 0.00 0.00 4.63
3413 3625 3.196685 ACATGAAGTTCTACAGGCTCCTC 59.803 47.826 0.00 0.00 0.00 3.71
3414 3626 3.177228 ACATGAAGTTCTACAGGCTCCT 58.823 45.455 0.00 0.00 0.00 3.69
3415 3627 3.618690 ACATGAAGTTCTACAGGCTCC 57.381 47.619 0.00 0.00 0.00 4.70
3416 3628 5.105716 TGACTACATGAAGTTCTACAGGCTC 60.106 44.000 0.00 0.00 0.00 4.70
3417 3629 4.772624 TGACTACATGAAGTTCTACAGGCT 59.227 41.667 0.00 0.00 0.00 4.58
3418 3630 4.865365 GTGACTACATGAAGTTCTACAGGC 59.135 45.833 0.00 0.00 0.00 4.85
3419 3631 5.411781 GGTGACTACATGAAGTTCTACAGG 58.588 45.833 0.00 0.00 0.00 4.00
3420 3632 5.096169 CGGTGACTACATGAAGTTCTACAG 58.904 45.833 0.00 0.00 0.00 2.74
3421 3633 4.617530 GCGGTGACTACATGAAGTTCTACA 60.618 45.833 0.00 0.00 0.00 2.74
3422 3634 3.858238 GCGGTGACTACATGAAGTTCTAC 59.142 47.826 0.00 0.00 0.00 2.59
3423 3635 3.119245 GGCGGTGACTACATGAAGTTCTA 60.119 47.826 0.00 0.00 0.00 2.10
3424 3636 2.353803 GGCGGTGACTACATGAAGTTCT 60.354 50.000 0.00 0.00 0.00 3.01
3425 3637 2.000447 GGCGGTGACTACATGAAGTTC 59.000 52.381 0.00 0.00 0.00 3.01
3426 3638 1.671850 CGGCGGTGACTACATGAAGTT 60.672 52.381 0.00 0.00 0.00 2.66
3427 3639 0.108804 CGGCGGTGACTACATGAAGT 60.109 55.000 0.00 0.00 0.00 3.01
3428 3640 1.421410 GCGGCGGTGACTACATGAAG 61.421 60.000 9.78 0.00 0.00 3.02
3429 3641 1.447140 GCGGCGGTGACTACATGAA 60.447 57.895 9.78 0.00 0.00 2.57
3430 3642 2.183300 GCGGCGGTGACTACATGA 59.817 61.111 9.78 0.00 0.00 3.07
3431 3643 2.890474 GGCGGCGGTGACTACATG 60.890 66.667 9.78 0.00 0.00 3.21
3432 3644 4.508128 CGGCGGCGGTGACTACAT 62.508 66.667 25.36 0.00 0.00 2.29
3483 3695 4.741239 GGAGGGGTCCAGCAGGGA 62.741 72.222 0.00 0.00 45.89 4.20
3484 3696 4.748798 AGGAGGGGTCCAGCAGGG 62.749 72.222 0.00 0.00 34.83 4.45
3485 3697 3.086600 GAGGAGGGGTCCAGCAGG 61.087 72.222 0.00 0.00 0.00 4.85
3486 3698 2.284921 TGAGGAGGGGTCCAGCAG 60.285 66.667 0.00 0.00 0.00 4.24
3487 3699 2.284921 CTGAGGAGGGGTCCAGCA 60.285 66.667 0.00 0.00 0.00 4.41
3488 3700 3.086600 CCTGAGGAGGGGTCCAGC 61.087 72.222 0.00 0.00 35.40 4.85
3489 3701 1.229658 AACCTGAGGAGGGGTCCAG 60.230 63.158 4.99 0.00 44.84 3.86
3490 3702 1.538876 CAACCTGAGGAGGGGTCCA 60.539 63.158 4.99 0.00 44.84 4.02
3491 3703 2.301738 CCAACCTGAGGAGGGGTCC 61.302 68.421 4.99 0.00 44.84 4.46
3492 3704 2.972819 GCCAACCTGAGGAGGGGTC 61.973 68.421 4.99 0.00 44.84 4.46
3493 3705 2.936032 GCCAACCTGAGGAGGGGT 60.936 66.667 4.99 0.00 44.84 4.95
3494 3706 4.101448 CGCCAACCTGAGGAGGGG 62.101 72.222 4.99 11.41 44.84 4.79
3495 3707 4.785453 GCGCCAACCTGAGGAGGG 62.785 72.222 4.99 7.20 44.84 4.30
3515 3727 4.483243 CCCGGACCATCCAACCCG 62.483 72.222 0.73 0.00 41.47 5.28
3516 3728 4.123545 CCCCGGACCATCCAACCC 62.124 72.222 0.73 0.00 35.91 4.11
3517 3729 4.123545 CCCCCGGACCATCCAACC 62.124 72.222 0.73 0.00 35.91 3.77
3518 3730 4.815108 GCCCCCGGACCATCCAAC 62.815 72.222 0.73 0.00 35.91 3.77
3533 3745 4.176851 GACGAGGACGAGGACGCC 62.177 72.222 0.00 0.00 43.96 5.68
3534 3746 4.517703 CGACGAGGACGAGGACGC 62.518 72.222 0.00 0.00 43.96 5.19
3535 3747 4.517703 GCGACGAGGACGAGGACG 62.518 72.222 0.00 0.00 42.66 4.79
3536 3748 3.126225 AGCGACGAGGACGAGGAC 61.126 66.667 0.00 0.00 42.66 3.85
3537 3749 3.125573 CAGCGACGAGGACGAGGA 61.126 66.667 0.00 0.00 42.66 3.71
3538 3750 3.384014 GACAGCGACGAGGACGAGG 62.384 68.421 0.00 0.00 42.66 4.63
3539 3751 2.098680 GACAGCGACGAGGACGAG 59.901 66.667 0.00 0.00 42.66 4.18
3540 3752 3.785499 CGACAGCGACGAGGACGA 61.785 66.667 0.00 0.00 43.06 4.20
3541 3753 3.785499 TCGACAGCGACGAGGACG 61.785 66.667 0.00 1.71 42.51 4.79
3546 3758 1.743995 TGATCCTCGACAGCGACGA 60.744 57.895 0.00 0.00 42.51 4.20
3547 3759 1.583967 GTGATCCTCGACAGCGACG 60.584 63.158 0.00 0.00 42.51 5.12
3548 3760 1.226717 GGTGATCCTCGACAGCGAC 60.227 63.158 0.00 0.00 42.51 5.19
3549 3761 1.677633 TGGTGATCCTCGACAGCGA 60.678 57.895 0.00 0.00 45.71 4.93
3550 3762 1.517257 GTGGTGATCCTCGACAGCG 60.517 63.158 0.00 0.00 37.33 5.18
3551 3763 4.504132 GTGGTGATCCTCGACAGC 57.496 61.111 0.00 0.00 35.47 4.40
3557 3769 2.509336 CACGGCGTGGTGATCCTC 60.509 66.667 31.19 0.00 40.38 3.71
3558 3770 4.760047 GCACGGCGTGGTGATCCT 62.760 66.667 37.33 0.00 40.38 3.24
3559 3771 4.760047 AGCACGGCGTGGTGATCC 62.760 66.667 39.47 22.36 42.86 3.36
3560 3772 3.188786 GAGCACGGCGTGGTGATC 61.189 66.667 43.90 27.89 44.55 2.92


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

AutoCloner maintained by Alex Coulton.