Multiple sequence alignment - TraesCS3B01G364700

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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 TraesCS3B01G364700 chr3B 100.000 4329 0 0 1 4329 576171833 576167505 0.000000e+00 7995.0
1 TraesCS3B01G364700 chr3B 84.054 1110 98 46 2214 3281 802681638 802680566 0.000000e+00 996.0
2 TraesCS3B01G364700 chr3B 91.827 624 28 12 3609 4230 576162162 576161560 0.000000e+00 848.0
3 TraesCS3B01G364700 chr3D 90.492 3576 173 66 7 3486 439527743 439524239 0.000000e+00 4566.0
4 TraesCS3B01G364700 chr3A 88.716 3350 168 92 7 3278 578954601 578951384 0.000000e+00 3899.0
5 TraesCS3B01G364700 chr3A 90.625 224 17 3 4009 4228 578883121 578882898 1.180000e-75 294.0
6 TraesCS3B01G364700 chr3A 83.146 178 6 7 3413 3566 578951090 578950913 1.620000e-29 141.0
7 TraesCS3B01G364700 chr3A 92.405 79 5 1 1392 1470 455035548 455035471 1.270000e-20 111.0
8 TraesCS3B01G364700 chr1A 83.273 1112 109 48 2214 3281 589577050 589575972 0.000000e+00 952.0
9 TraesCS3B01G364700 chr2A 82.268 1111 116 48 2214 3281 47574929 47573857 0.000000e+00 885.0
10 TraesCS3B01G364700 chr2A 96.970 33 1 0 3605 3637 277095343 277095375 6.050000e-04 56.5
11 TraesCS3B01G364700 chr6A 82.194 1112 117 47 2214 3281 437566191 437565117 0.000000e+00 881.0
12 TraesCS3B01G364700 chr5A 84.385 301 27 10 2214 2513 81742844 81743125 1.190000e-70 278.0
13 TraesCS3B01G364700 chr4A 83.667 300 31 10 2214 2513 526046491 526046210 2.570000e-67 267.0
14 TraesCS3B01G364700 chr7A 83.056 301 30 11 2214 2513 71387387 71387667 2.000000e-63 254.0
15 TraesCS3B01G364700 chr7A 93.939 99 6 0 3183 3281 71387766 71387864 2.700000e-32 150.0
16 TraesCS3B01G364700 chr4D 94.048 84 5 0 1388 1471 29642009 29641926 1.260000e-25 128.0
17 TraesCS3B01G364700 chr5D 92.771 83 6 0 1388 1470 378050708 378050626 2.110000e-23 121.0
18 TraesCS3B01G364700 chr2D 92.771 83 6 0 1388 1470 570985748 570985830 2.110000e-23 121.0
19 TraesCS3B01G364700 chr5B 91.566 83 7 0 1388 1470 512196603 512196521 9.840000e-22 115.0
20 TraesCS3B01G364700 chr1B 90.361 83 8 0 1388 1470 217693699 217693781 4.580000e-20 110.0
21 TraesCS3B01G364700 chr6D 93.878 49 3 0 1422 1470 156454797 156454845 1.670000e-09 75.0
22 TraesCS3B01G364700 chr7B 83.117 77 8 5 3767 3842 374771079 374771151 1.000000e-06 65.8


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 TraesCS3B01G364700 chr3B 576167505 576171833 4328 True 7995 7995 100.000 1 4329 1 chr3B.!!$R2 4328
1 TraesCS3B01G364700 chr3B 802680566 802681638 1072 True 996 996 84.054 2214 3281 1 chr3B.!!$R3 1067
2 TraesCS3B01G364700 chr3B 576161560 576162162 602 True 848 848 91.827 3609 4230 1 chr3B.!!$R1 621
3 TraesCS3B01G364700 chr3D 439524239 439527743 3504 True 4566 4566 90.492 7 3486 1 chr3D.!!$R1 3479
4 TraesCS3B01G364700 chr3A 578950913 578954601 3688 True 2020 3899 85.931 7 3566 2 chr3A.!!$R3 3559
5 TraesCS3B01G364700 chr1A 589575972 589577050 1078 True 952 952 83.273 2214 3281 1 chr1A.!!$R1 1067
6 TraesCS3B01G364700 chr2A 47573857 47574929 1072 True 885 885 82.268 2214 3281 1 chr2A.!!$R1 1067
7 TraesCS3B01G364700 chr6A 437565117 437566191 1074 True 881 881 82.194 2214 3281 1 chr6A.!!$R1 1067

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
665 720 0.170339 TCGTCCTCGTCGTCGTAGTA 59.830 55.0 1.33 0.0 38.33 1.82 F
666 721 0.569810 CGTCCTCGTCGTCGTAGTAG 59.430 60.0 1.33 0.0 38.33 2.57 F
1836 1921 0.676782 GTGTTTAGCAGGACGGGCAT 60.677 55.0 0.00 0.0 0.00 4.40 F
2043 2145 0.029035 ATCGACCGAGATACGTGTGC 59.971 55.0 0.00 0.0 40.78 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2020 0.758734 TGAAGTGGAGTGGTGACTGG 59.241 55.0 0.00 0.00 30.16 4.00 R
1922 2024 0.758734 CAGGTGAAGTGGAGTGGTGA 59.241 55.0 0.00 0.00 0.00 4.02 R
3106 3278 0.098728 AATTCAGAATTTCGGCGGCG 59.901 50.0 27.15 27.15 0.00 6.46 R
3909 4270 0.096976 CAGCCGCTACCGTTGATTTG 59.903 55.0 0.00 0.00 0.00 2.32 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
32 33 1.262151 CAGCAGCCATTTTGTTGTTGC 59.738 47.619 0.00 0.00 0.00 4.17
35 36 1.262151 CAGCCATTTTGTTGTTGCTGC 59.738 47.619 0.00 0.00 39.63 5.25
38 39 1.262151 CCATTTTGTTGTTGCTGCTGC 59.738 47.619 8.89 8.89 40.20 5.25
58 61 4.947147 TGGCCCGAGTGTGGTTGC 62.947 66.667 0.00 0.00 0.00 4.17
84 87 1.153939 CTCGAGGTCTGAGCAACCG 60.154 63.158 3.91 9.35 41.89 4.44
101 105 0.323360 CCGAGGAGAATTTTGGGGCA 60.323 55.000 0.00 0.00 0.00 5.36
111 115 1.626686 TTTTGGGGCAATCGTGATGT 58.373 45.000 0.00 0.00 0.00 3.06
261 269 2.282407 ACGCACGGTTGTTTTCTAAGT 58.718 42.857 0.00 0.00 0.00 2.24
312 321 0.180406 AGGAGCACGAGTGTTTGGTT 59.820 50.000 5.07 0.00 0.00 3.67
404 421 1.487558 ACTCACCGTTTACCAACCACT 59.512 47.619 0.00 0.00 0.00 4.00
465 488 0.984230 AAAGGAGAAGATCGCCACCA 59.016 50.000 3.00 0.00 38.94 4.17
493 523 2.046292 CACCTTGACCCAACCCATTTT 58.954 47.619 0.00 0.00 0.00 1.82
580 632 0.248580 CAAGAAACACGCAGCAGCAA 60.249 50.000 0.82 0.00 42.27 3.91
665 720 0.170339 TCGTCCTCGTCGTCGTAGTA 59.830 55.000 1.33 0.00 38.33 1.82
666 721 0.569810 CGTCCTCGTCGTCGTAGTAG 59.430 60.000 1.33 0.00 38.33 2.57
667 722 1.634702 GTCCTCGTCGTCGTAGTAGT 58.365 55.000 1.33 0.00 38.33 2.73
669 724 1.067565 TCCTCGTCGTCGTAGTAGTGT 60.068 52.381 1.33 0.00 38.33 3.55
670 725 2.163613 TCCTCGTCGTCGTAGTAGTGTA 59.836 50.000 1.33 0.00 38.33 2.90
671 726 2.280183 CCTCGTCGTCGTAGTAGTGTAC 59.720 54.545 1.33 0.00 38.33 2.90
767 822 3.069586 CCAATACATCGAGTTAGAGGGCA 59.930 47.826 0.00 0.00 0.00 5.36
980 1052 3.087781 GCTGCTCCCATCTTTTCTTCTT 58.912 45.455 0.00 0.00 0.00 2.52
985 1057 4.268359 CTCCCATCTTTTCTTCTTGAGGG 58.732 47.826 0.00 0.00 35.09 4.30
986 1058 3.916349 TCCCATCTTTTCTTCTTGAGGGA 59.084 43.478 0.00 0.00 40.31 4.20
987 1059 4.013050 CCCATCTTTTCTTCTTGAGGGAC 58.987 47.826 0.00 0.00 35.81 4.46
988 1060 4.507335 CCCATCTTTTCTTCTTGAGGGACA 60.507 45.833 0.00 0.00 35.81 4.02
989 1061 4.699257 CCATCTTTTCTTCTTGAGGGACAG 59.301 45.833 0.00 0.00 32.80 3.51
990 1062 5.513788 CCATCTTTTCTTCTTGAGGGACAGA 60.514 44.000 0.00 0.00 32.80 3.41
991 1063 5.220710 TCTTTTCTTCTTGAGGGACAGAG 57.779 43.478 0.00 0.00 0.00 3.35
992 1064 4.901849 TCTTTTCTTCTTGAGGGACAGAGA 59.098 41.667 0.00 0.00 0.00 3.10
993 1065 4.881019 TTTCTTCTTGAGGGACAGAGAG 57.119 45.455 0.00 0.00 0.00 3.20
994 1066 3.816398 TCTTCTTGAGGGACAGAGAGA 57.184 47.619 0.00 0.00 0.00 3.10
995 1067 3.696045 TCTTCTTGAGGGACAGAGAGAG 58.304 50.000 0.00 0.00 0.00 3.20
996 1068 3.332187 TCTTCTTGAGGGACAGAGAGAGA 59.668 47.826 0.00 0.00 0.00 3.10
1369 1447 3.315142 GACCGCTGCTCCATGGACA 62.315 63.158 11.44 13.08 0.00 4.02
1695 1776 4.089065 CGCGAGGTAGTTAACAACAGTTAC 59.911 45.833 0.00 0.32 0.00 2.50
1700 1781 9.070149 CGAGGTAGTTAACAACAGTTACTATTC 57.930 37.037 8.61 0.96 0.00 1.75
1701 1782 9.918630 GAGGTAGTTAACAACAGTTACTATTCA 57.081 33.333 8.61 0.00 0.00 2.57
1702 1783 9.924650 AGGTAGTTAACAACAGTTACTATTCAG 57.075 33.333 8.61 0.00 0.00 3.02
1703 1784 9.702494 GGTAGTTAACAACAGTTACTATTCAGT 57.298 33.333 8.61 0.00 38.91 3.41
1738 1823 4.974645 TTGATCCGCCATTAGATTAGGT 57.025 40.909 0.00 0.00 0.00 3.08
1836 1921 0.676782 GTGTTTAGCAGGACGGGCAT 60.677 55.000 0.00 0.00 0.00 4.40
1918 2020 2.264794 CCGCCAGGTACCACTCAC 59.735 66.667 15.94 0.00 0.00 3.51
1919 2021 2.264794 CGCCAGGTACCACTCACC 59.735 66.667 15.94 0.00 36.22 4.02
1920 2022 2.579657 CGCCAGGTACCACTCACCA 61.580 63.158 15.94 0.00 38.62 4.17
1921 2023 1.296715 GCCAGGTACCACTCACCAG 59.703 63.158 15.94 0.00 38.62 4.00
1922 2024 1.481056 GCCAGGTACCACTCACCAGT 61.481 60.000 15.94 0.00 38.62 4.00
1923 2025 0.608640 CCAGGTACCACTCACCAGTC 59.391 60.000 15.94 0.00 38.62 3.51
1997 2099 5.359756 TCGATGGAATTGACTGGTTCATAG 58.640 41.667 0.00 0.00 29.84 2.23
2002 2104 4.265073 GAATTGACTGGTTCATAGGCTGT 58.735 43.478 0.00 0.00 32.84 4.40
2011 2113 4.164796 TGGTTCATAGGCTGTTCTGATCAT 59.835 41.667 0.00 0.00 0.00 2.45
2012 2114 4.514441 GGTTCATAGGCTGTTCTGATCATG 59.486 45.833 0.00 0.00 0.00 3.07
2013 2115 5.363101 GTTCATAGGCTGTTCTGATCATGA 58.637 41.667 0.00 0.00 0.00 3.07
2014 2116 5.820404 TCATAGGCTGTTCTGATCATGAT 57.180 39.130 8.25 8.25 0.00 2.45
2015 2117 5.791666 TCATAGGCTGTTCTGATCATGATC 58.208 41.667 25.91 25.91 38.29 2.92
2016 2118 5.306160 TCATAGGCTGTTCTGATCATGATCA 59.694 40.000 31.30 31.30 44.83 2.92
2037 2139 4.023963 TCAATCAGTGATCGACCGAGATAC 60.024 45.833 5.98 0.00 0.00 2.24
2043 2145 0.029035 ATCGACCGAGATACGTGTGC 59.971 55.000 0.00 0.00 40.78 4.57
2044 2146 1.135939 CGACCGAGATACGTGTGCA 59.864 57.895 0.00 0.00 40.78 4.57
2045 2147 1.132199 CGACCGAGATACGTGTGCAC 61.132 60.000 10.75 10.75 40.78 4.57
2090 2193 2.622942 TCGGAGCATGGATATTTTTGGC 59.377 45.455 0.00 0.00 0.00 4.52
2119 2222 1.474077 GAATGTGGTGCTGATGGGTTC 59.526 52.381 0.00 0.00 0.00 3.62
2124 2227 1.168714 GGTGCTGATGGGTTCTGAAC 58.831 55.000 12.05 12.05 32.35 3.18
2126 2229 2.027192 GGTGCTGATGGGTTCTGAACTA 60.027 50.000 19.05 9.89 33.40 2.24
2127 2230 3.003480 GTGCTGATGGGTTCTGAACTAC 58.997 50.000 19.05 13.09 30.86 2.73
2130 2233 3.430929 GCTGATGGGTTCTGAACTACGAT 60.431 47.826 19.05 7.16 0.00 3.73
2317 2420 2.335933 AGGATTTCCCCTACGGTATGG 58.664 52.381 2.76 2.76 34.07 2.74
2359 2466 2.751436 GCCCTTGCAGAATCGGCA 60.751 61.111 3.50 3.50 39.50 5.69
2362 2469 1.748122 CCTTGCAGAATCGGCAGCT 60.748 57.895 8.23 0.00 43.05 4.24
2366 2473 3.823402 CAGAATCGGCAGCTGCAT 58.177 55.556 37.63 22.32 44.36 3.96
2369 2476 0.737219 AGAATCGGCAGCTGCATTTC 59.263 50.000 37.63 31.33 44.36 2.17
2370 2477 0.737219 GAATCGGCAGCTGCATTTCT 59.263 50.000 37.63 18.88 44.36 2.52
2379 2486 3.612860 GCAGCTGCATTTCTGAAATTCTG 59.387 43.478 33.36 15.95 41.59 3.02
2385 2492 5.000591 TGCATTTCTGAAATTCTGTCGGTA 58.999 37.500 12.74 0.00 0.00 4.02
2387 2494 5.967674 GCATTTCTGAAATTCTGTCGGTATG 59.032 40.000 12.74 0.94 0.00 2.39
2393 2500 1.966901 ATTCTGTCGGTATGGCGCCA 61.967 55.000 34.80 34.80 0.00 5.69
2462 2571 4.736896 GGCGTCGTGGGTCACCTC 62.737 72.222 0.00 0.00 37.76 3.85
2501 2610 3.200593 CATCTCTGCCGCTGCCAC 61.201 66.667 0.00 0.00 36.33 5.01
2576 2699 2.218953 TATTCGGGAACATGTCGAGC 57.781 50.000 0.00 0.00 34.33 5.03
2588 2720 0.317854 TGTCGAGCGCATCTTATCCG 60.318 55.000 11.47 0.00 0.00 4.18
2703 2842 2.297315 TGCACAGTCCAGAGTCTGTTAG 59.703 50.000 18.74 8.22 39.88 2.34
2804 2950 2.223021 TGTGCGCGCTTATCTGAATTTC 60.223 45.455 33.29 0.00 0.00 2.17
2809 2955 4.651994 CGCGCTTATCTGAATTTCTTTGT 58.348 39.130 5.56 0.00 0.00 2.83
2962 3112 1.088340 CATCAGGAAGCTGCAGACCG 61.088 60.000 20.43 12.70 0.00 4.79
3022 3172 1.642037 CGTGCTCAGCTGAACATGGG 61.642 60.000 25.33 13.97 0.00 4.00
3030 3182 3.117776 TCAGCTGAACATGGGCATATCTT 60.118 43.478 15.67 0.00 0.00 2.40
3091 3251 1.281899 CGGCGTTCCTCTGAAGAATC 58.718 55.000 0.00 0.00 0.00 2.52
3093 3253 1.281899 GCGTTCCTCTGAAGAATCCG 58.718 55.000 0.00 0.00 0.00 4.18
3094 3254 1.404315 GCGTTCCTCTGAAGAATCCGT 60.404 52.381 0.00 0.00 0.00 4.69
3095 3255 2.931320 GCGTTCCTCTGAAGAATCCGTT 60.931 50.000 0.00 0.00 0.00 4.44
3097 3257 2.924290 GTTCCTCTGAAGAATCCGTTCG 59.076 50.000 0.00 0.00 39.38 3.95
3099 3259 1.404181 CCTCTGAAGAATCCGTTCGCA 60.404 52.381 0.00 0.00 39.38 5.10
3106 3278 2.652893 GAATCCGTTCGCATGCTGCC 62.653 60.000 17.13 1.61 41.12 4.85
3125 3297 0.098728 CGCCGCCGAAATTCTGAATT 59.901 50.000 9.76 9.76 36.29 2.17
3126 3298 1.548986 GCCGCCGAAATTCTGAATTG 58.451 50.000 15.80 5.63 0.00 2.32
3290 3464 8.380742 TCCTAGACTTGTAGATTTCTGGAATT 57.619 34.615 0.00 0.00 0.00 2.17
3355 3605 5.417894 TCATTGTAGCCAGGTAGTATATCCG 59.582 44.000 0.00 0.00 0.00 4.18
3416 3751 5.305902 TCCTCACTGTTACTCCATTGTTGTA 59.694 40.000 0.00 0.00 0.00 2.41
3497 3837 1.958205 GAGATGATCCGCGGCAAGG 60.958 63.158 23.51 0.00 0.00 3.61
3502 3861 4.473520 ATCCGCGGCAAGGGACAG 62.474 66.667 23.51 0.00 34.58 3.51
3567 3926 8.706322 AGTTTGTAACTTGGTTGATCCTATTT 57.294 30.769 0.00 0.00 39.04 1.40
3568 3927 9.143155 AGTTTGTAACTTGGTTGATCCTATTTT 57.857 29.630 0.00 0.00 39.04 1.82
3576 3935 9.981460 ACTTGGTTGATCCTATTTTATCTTTCT 57.019 29.630 0.00 0.00 37.07 2.52
3579 3938 9.838339 TGGTTGATCCTATTTTATCTTTCTCTC 57.162 33.333 0.00 0.00 37.07 3.20
3580 3939 9.278978 GGTTGATCCTATTTTATCTTTCTCTCC 57.721 37.037 0.00 0.00 0.00 3.71
3581 3940 9.838339 GTTGATCCTATTTTATCTTTCTCTCCA 57.162 33.333 0.00 0.00 0.00 3.86
3583 3942 8.654997 TGATCCTATTTTATCTTTCTCTCCAGG 58.345 37.037 0.00 0.00 0.00 4.45
3584 3943 6.831976 TCCTATTTTATCTTTCTCTCCAGGC 58.168 40.000 0.00 0.00 0.00 4.85
3585 3944 6.386927 TCCTATTTTATCTTTCTCTCCAGGCA 59.613 38.462 0.00 0.00 0.00 4.75
3586 3945 7.072961 TCCTATTTTATCTTTCTCTCCAGGCAT 59.927 37.037 0.00 0.00 0.00 4.40
3587 3946 6.956202 ATTTTATCTTTCTCTCCAGGCATG 57.044 37.500 0.00 0.00 0.00 4.06
3588 3947 5.441718 TTTATCTTTCTCTCCAGGCATGT 57.558 39.130 0.00 0.00 0.00 3.21
3589 3948 2.775911 TCTTTCTCTCCAGGCATGTG 57.224 50.000 0.00 0.00 0.00 3.21
3590 3949 1.280133 TCTTTCTCTCCAGGCATGTGG 59.720 52.381 0.00 0.00 39.19 4.17
3591 3950 0.322816 TTTCTCTCCAGGCATGTGGC 60.323 55.000 0.00 0.00 43.74 5.01
3601 3960 1.602311 GGCATGTGGCTTCTAGATGG 58.398 55.000 7.66 0.00 44.01 3.51
3602 3961 1.602311 GCATGTGGCTTCTAGATGGG 58.398 55.000 7.66 0.00 40.25 4.00
3603 3962 1.133976 GCATGTGGCTTCTAGATGGGT 60.134 52.381 7.66 0.00 40.25 4.51
3604 3963 2.104792 GCATGTGGCTTCTAGATGGGTA 59.895 50.000 7.66 0.00 40.25 3.69
3605 3964 3.805108 GCATGTGGCTTCTAGATGGGTAG 60.805 52.174 7.66 0.00 40.25 3.18
3606 3965 3.116096 TGTGGCTTCTAGATGGGTAGT 57.884 47.619 7.66 0.00 0.00 2.73
3607 3966 3.450904 TGTGGCTTCTAGATGGGTAGTT 58.549 45.455 7.66 0.00 0.00 2.24
3618 3977 7.500992 TCTAGATGGGTAGTTGTTGATTCATC 58.499 38.462 0.00 0.00 0.00 2.92
3652 4011 9.477484 CGCTTATCTATTTTTGTCCTACACTAT 57.523 33.333 0.00 0.00 0.00 2.12
3719 4079 4.325028 TGCATGGATTTACATGGATTGC 57.675 40.909 4.97 0.00 46.40 3.56
3750 4111 2.093306 TGAGGATTGTAGTTGTGCGG 57.907 50.000 0.00 0.00 0.00 5.69
3756 4117 2.436115 GTAGTTGTGCGGAGGGCC 60.436 66.667 0.00 0.00 42.61 5.80
3843 4204 2.447443 TCGTGGTTGTAGATGCTCTCT 58.553 47.619 0.00 0.00 38.06 3.10
3848 4209 4.100189 GTGGTTGTAGATGCTCTCTGGTAT 59.900 45.833 0.27 0.00 35.28 2.73
3861 4222 8.844865 TGCTCTCTGGTATCCATATTATACAT 57.155 34.615 7.11 0.00 32.49 2.29
3894 4255 2.180946 ATATGTCCTGTCAGGCCTCA 57.819 50.000 14.64 12.78 34.61 3.86
3897 4258 1.294780 GTCCTGTCAGGCCTCACAG 59.705 63.158 28.64 28.64 39.90 3.66
3909 4270 2.548480 GGCCTCACAGCCGTAAATAATC 59.452 50.000 0.00 0.00 44.57 1.75
3918 4279 6.194508 CACAGCCGTAAATAATCAAATCAACG 59.805 38.462 0.00 0.00 0.00 4.10
3929 4290 0.036765 AAATCAACGGTAGCGGCTGA 60.037 50.000 19.72 19.48 0.00 4.26
3991 4352 4.638421 TGCACTTACATTATGTAGGTTGCC 59.362 41.667 23.86 15.02 39.68 4.52
4023 4384 0.251916 TAGCTGGTGTTCCATTCCCG 59.748 55.000 0.00 0.00 43.43 5.14
4101 4462 2.490328 TTGCAAGAAAAAGAGTGCGG 57.510 45.000 0.00 0.00 39.92 5.69
4102 4463 0.030638 TGCAAGAAAAAGAGTGCGGC 59.969 50.000 0.00 0.00 39.92 6.53
4115 4476 0.743345 GTGCGGCGAGGGTAAAGAAT 60.743 55.000 12.98 0.00 0.00 2.40
4116 4477 0.742990 TGCGGCGAGGGTAAAGAATG 60.743 55.000 12.98 0.00 0.00 2.67
4117 4478 1.436983 GCGGCGAGGGTAAAGAATGG 61.437 60.000 12.98 0.00 0.00 3.16
4118 4479 0.814010 CGGCGAGGGTAAAGAATGGG 60.814 60.000 0.00 0.00 0.00 4.00
4119 4480 0.544697 GGCGAGGGTAAAGAATGGGA 59.455 55.000 0.00 0.00 0.00 4.37
4120 4481 1.475213 GGCGAGGGTAAAGAATGGGAG 60.475 57.143 0.00 0.00 0.00 4.30
4121 4482 1.475213 GCGAGGGTAAAGAATGGGAGG 60.475 57.143 0.00 0.00 0.00 4.30
4122 4483 1.141053 CGAGGGTAAAGAATGGGAGGG 59.859 57.143 0.00 0.00 0.00 4.30
4123 4484 2.206223 GAGGGTAAAGAATGGGAGGGT 58.794 52.381 0.00 0.00 0.00 4.34
4124 4485 1.923148 AGGGTAAAGAATGGGAGGGTG 59.077 52.381 0.00 0.00 0.00 4.61
4125 4486 1.920351 GGGTAAAGAATGGGAGGGTGA 59.080 52.381 0.00 0.00 0.00 4.02
4126 4487 2.514160 GGGTAAAGAATGGGAGGGTGAT 59.486 50.000 0.00 0.00 0.00 3.06
4127 4488 3.555966 GGTAAAGAATGGGAGGGTGATG 58.444 50.000 0.00 0.00 0.00 3.07
4128 4489 3.053619 GGTAAAGAATGGGAGGGTGATGT 60.054 47.826 0.00 0.00 0.00 3.06
4129 4490 2.814805 AAGAATGGGAGGGTGATGTG 57.185 50.000 0.00 0.00 0.00 3.21
4130 4491 1.971149 AGAATGGGAGGGTGATGTGA 58.029 50.000 0.00 0.00 0.00 3.58
4131 4492 2.496297 AGAATGGGAGGGTGATGTGAT 58.504 47.619 0.00 0.00 0.00 3.06
4132 4493 2.441001 AGAATGGGAGGGTGATGTGATC 59.559 50.000 0.00 0.00 0.00 2.92
4133 4494 1.897473 ATGGGAGGGTGATGTGATCA 58.103 50.000 0.00 0.00 36.84 2.92
4134 4495 1.667595 TGGGAGGGTGATGTGATCAA 58.332 50.000 0.00 0.00 41.69 2.57
4135 4496 2.207988 TGGGAGGGTGATGTGATCAAT 58.792 47.619 0.00 0.00 41.69 2.57
4136 4497 2.092267 TGGGAGGGTGATGTGATCAATG 60.092 50.000 0.00 0.00 41.69 2.82
4137 4498 2.579873 GGAGGGTGATGTGATCAATGG 58.420 52.381 0.00 0.00 41.69 3.16
4138 4499 2.092212 GGAGGGTGATGTGATCAATGGT 60.092 50.000 0.00 0.00 41.69 3.55
4139 4500 2.947652 GAGGGTGATGTGATCAATGGTG 59.052 50.000 0.00 0.00 41.69 4.17
4140 4501 2.577563 AGGGTGATGTGATCAATGGTGA 59.422 45.455 0.00 0.00 41.69 4.02
4150 4511 8.700439 ATGTGATCAATGGTGAATATGAATGA 57.300 30.769 0.00 0.00 37.30 2.57
4218 4579 1.957177 TCGACTTGAGCTTGAGTGAGT 59.043 47.619 7.56 0.00 0.00 3.41
4230 4591 4.380531 CTTGAGTGAGTTTGGTAGCTTGA 58.619 43.478 0.00 0.00 0.00 3.02
4231 4592 3.995199 TGAGTGAGTTTGGTAGCTTGAG 58.005 45.455 0.00 0.00 0.00 3.02
4232 4593 3.244215 TGAGTGAGTTTGGTAGCTTGAGG 60.244 47.826 0.00 0.00 0.00 3.86
4233 4594 2.706190 AGTGAGTTTGGTAGCTTGAGGT 59.294 45.455 0.00 0.00 0.00 3.85
4234 4595 2.808543 GTGAGTTTGGTAGCTTGAGGTG 59.191 50.000 0.00 0.00 0.00 4.00
4235 4596 2.224523 TGAGTTTGGTAGCTTGAGGTGG 60.225 50.000 0.00 0.00 0.00 4.61
4236 4597 2.038557 GAGTTTGGTAGCTTGAGGTGGA 59.961 50.000 0.00 0.00 0.00 4.02
4237 4598 2.039084 AGTTTGGTAGCTTGAGGTGGAG 59.961 50.000 0.00 0.00 0.00 3.86
4238 4599 2.024176 TTGGTAGCTTGAGGTGGAGA 57.976 50.000 0.00 0.00 0.00 3.71
4239 4600 2.254152 TGGTAGCTTGAGGTGGAGAT 57.746 50.000 0.00 0.00 0.00 2.75
4240 4601 1.833630 TGGTAGCTTGAGGTGGAGATG 59.166 52.381 0.00 0.00 0.00 2.90
4241 4602 2.111384 GGTAGCTTGAGGTGGAGATGA 58.889 52.381 0.00 0.00 0.00 2.92
4242 4603 2.501723 GGTAGCTTGAGGTGGAGATGAA 59.498 50.000 0.00 0.00 0.00 2.57
4243 4604 3.055094 GGTAGCTTGAGGTGGAGATGAAA 60.055 47.826 0.00 0.00 0.00 2.69
4244 4605 3.795688 AGCTTGAGGTGGAGATGAAAA 57.204 42.857 0.00 0.00 0.00 2.29
4245 4606 3.416156 AGCTTGAGGTGGAGATGAAAAC 58.584 45.455 0.00 0.00 0.00 2.43
4246 4607 2.489722 GCTTGAGGTGGAGATGAAAACC 59.510 50.000 0.00 0.00 0.00 3.27
4247 4608 2.879103 TGAGGTGGAGATGAAAACCC 57.121 50.000 0.00 0.00 32.85 4.11
4248 4609 2.348472 TGAGGTGGAGATGAAAACCCT 58.652 47.619 0.00 0.00 32.85 4.34
4249 4610 3.526899 TGAGGTGGAGATGAAAACCCTA 58.473 45.455 0.00 0.00 32.85 3.53
4250 4611 3.913799 TGAGGTGGAGATGAAAACCCTAA 59.086 43.478 0.00 0.00 32.85 2.69
4251 4612 4.262617 GAGGTGGAGATGAAAACCCTAAC 58.737 47.826 0.00 0.00 32.85 2.34
4252 4613 3.010250 AGGTGGAGATGAAAACCCTAACC 59.990 47.826 0.00 0.00 32.85 2.85
4253 4614 3.353557 GTGGAGATGAAAACCCTAACCC 58.646 50.000 0.00 0.00 0.00 4.11
4254 4615 2.026636 TGGAGATGAAAACCCTAACCCG 60.027 50.000 0.00 0.00 0.00 5.28
4255 4616 2.026542 GGAGATGAAAACCCTAACCCGT 60.027 50.000 0.00 0.00 0.00 5.28
4256 4617 3.560668 GGAGATGAAAACCCTAACCCGTT 60.561 47.826 0.00 0.00 0.00 4.44
4257 4618 3.418047 AGATGAAAACCCTAACCCGTTG 58.582 45.455 0.00 0.00 0.00 4.10
4258 4619 1.320507 TGAAAACCCTAACCCGTTGC 58.679 50.000 0.00 0.00 0.00 4.17
4259 4620 1.320507 GAAAACCCTAACCCGTTGCA 58.679 50.000 0.00 0.00 0.00 4.08
4260 4621 1.268625 GAAAACCCTAACCCGTTGCAG 59.731 52.381 0.00 0.00 0.00 4.41
4261 4622 0.538746 AAACCCTAACCCGTTGCAGG 60.539 55.000 0.00 0.00 0.00 4.85
4262 4623 2.750237 CCCTAACCCGTTGCAGGC 60.750 66.667 0.00 0.00 0.00 4.85
4263 4624 2.750237 CCTAACCCGTTGCAGGCC 60.750 66.667 0.00 0.00 0.00 5.19
4264 4625 2.351276 CTAACCCGTTGCAGGCCT 59.649 61.111 0.00 0.00 0.00 5.19
4265 4626 1.745489 CTAACCCGTTGCAGGCCTC 60.745 63.158 0.00 0.00 0.00 4.70
4266 4627 2.185310 CTAACCCGTTGCAGGCCTCT 62.185 60.000 0.00 0.00 0.00 3.69
4267 4628 1.774894 TAACCCGTTGCAGGCCTCTT 61.775 55.000 0.00 0.00 0.00 2.85
4268 4629 3.058160 CCCGTTGCAGGCCTCTTG 61.058 66.667 0.00 0.00 0.00 3.02
4269 4630 3.058160 CCGTTGCAGGCCTCTTGG 61.058 66.667 0.00 0.00 0.00 3.61
4270 4631 3.058160 CGTTGCAGGCCTCTTGGG 61.058 66.667 0.00 0.00 38.36 4.12
4279 4640 4.751431 CCTCTTGGGCTGAAAGGG 57.249 61.111 0.00 0.00 0.00 3.95
4280 4641 2.078452 CCTCTTGGGCTGAAAGGGA 58.922 57.895 0.00 0.00 0.00 4.20
4281 4642 0.034670 CCTCTTGGGCTGAAAGGGAG 60.035 60.000 0.00 0.00 0.00 4.30
4282 4643 0.987294 CTCTTGGGCTGAAAGGGAGA 59.013 55.000 0.00 0.00 0.00 3.71
4283 4644 0.987294 TCTTGGGCTGAAAGGGAGAG 59.013 55.000 0.00 0.00 0.00 3.20
4284 4645 0.987294 CTTGGGCTGAAAGGGAGAGA 59.013 55.000 0.00 0.00 0.00 3.10
4285 4646 0.987294 TTGGGCTGAAAGGGAGAGAG 59.013 55.000 0.00 0.00 0.00 3.20
4286 4647 1.223211 GGGCTGAAAGGGAGAGAGC 59.777 63.158 0.00 0.00 0.00 4.09
4287 4648 1.223211 GGCTGAAAGGGAGAGAGCC 59.777 63.158 0.00 0.00 42.37 4.70
4288 4649 1.153469 GCTGAAAGGGAGAGAGCCG 60.153 63.158 0.00 0.00 0.00 5.52
4289 4650 1.519719 CTGAAAGGGAGAGAGCCGG 59.480 63.158 0.00 0.00 0.00 6.13
4290 4651 2.188207 GAAAGGGAGAGAGCCGGC 59.812 66.667 21.89 21.89 0.00 6.13
4291 4652 2.284995 AAAGGGAGAGAGCCGGCT 60.285 61.111 33.48 33.48 0.00 5.52
4292 4653 2.585791 GAAAGGGAGAGAGCCGGCTG 62.586 65.000 38.41 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.482296 AAATGGCTGCTGCACGCTTC 62.482 55.000 17.89 0.00 41.91 3.86
5 6 2.091102 AAAATGGCTGCTGCACGCTT 62.091 50.000 17.89 2.48 41.91 4.68
35 36 4.320456 ACACTCGGGCCACAGCAG 62.320 66.667 4.39 0.00 42.56 4.24
38 39 3.476031 AACCACACTCGGGCCACAG 62.476 63.158 4.39 0.93 0.00 3.66
46 47 3.767230 CGAGCGCAACCACACTCG 61.767 66.667 11.47 3.12 45.02 4.18
65 68 1.216710 GGTTGCTCAGACCTCGAGG 59.783 63.158 30.11 30.11 42.17 4.63
84 87 2.099756 CGATTGCCCCAAAATTCTCCTC 59.900 50.000 0.00 0.00 0.00 3.71
101 105 1.815421 GCGAGGCCACATCACGATT 60.815 57.895 5.01 0.00 0.00 3.34
232 240 2.527867 AACCGTGCGTTGTTCGTCC 61.528 57.895 0.00 0.00 42.13 4.79
233 241 1.367195 CAACCGTGCGTTGTTCGTC 60.367 57.895 0.00 0.00 45.79 4.20
279 288 3.617531 CGTGCTCCTGGAATACTTTCTGT 60.618 47.826 0.00 0.00 32.16 3.41
286 295 1.204941 ACACTCGTGCTCCTGGAATAC 59.795 52.381 0.00 0.00 0.00 1.89
291 300 1.230635 CCAAACACTCGTGCTCCTGG 61.231 60.000 0.00 0.00 0.00 4.45
312 321 0.607762 TAGCATTTCCGTGGCAAGCA 60.608 50.000 0.00 0.00 0.00 3.91
360 377 8.368668 AGTGAAGACAACTACTTATTGCTAACT 58.631 33.333 0.00 0.00 0.00 2.24
404 421 1.688772 CGGAAGAAGGGAGGTCGATA 58.311 55.000 0.00 0.00 0.00 2.92
440 457 3.198872 GGCGATCTTCTCCTTTTGTAGG 58.801 50.000 0.00 0.00 46.27 3.18
465 488 1.228862 GGGTCAAGGTGGCCACAAT 60.229 57.895 35.78 21.79 45.98 2.71
665 720 3.079578 TCGCTGCTAGTTGTAGTACACT 58.920 45.455 1.43 6.56 0.00 3.55
666 721 3.169733 GTCGCTGCTAGTTGTAGTACAC 58.830 50.000 1.43 0.00 0.00 2.90
667 722 2.815503 TGTCGCTGCTAGTTGTAGTACA 59.184 45.455 0.00 0.00 0.00 2.90
669 724 2.159421 GCTGTCGCTGCTAGTTGTAGTA 60.159 50.000 0.00 0.00 0.00 1.82
670 725 1.402984 GCTGTCGCTGCTAGTTGTAGT 60.403 52.381 0.00 0.00 0.00 2.73
671 726 1.272781 GCTGTCGCTGCTAGTTGTAG 58.727 55.000 0.00 0.00 0.00 2.74
710 765 1.845809 GAAAGCTGTCCACAGTGGCG 61.846 60.000 15.64 6.84 45.45 5.69
767 822 1.133976 CCGAATGATTCCTGCCTCCTT 60.134 52.381 0.00 0.00 0.00 3.36
875 930 2.266055 GACCCAACCAGAGGCGAG 59.734 66.667 0.00 0.00 0.00 5.03
876 931 2.203788 AGACCCAACCAGAGGCGA 60.204 61.111 0.00 0.00 0.00 5.54
880 935 1.376466 CACCCAGACCCAACCAGAG 59.624 63.158 0.00 0.00 0.00 3.35
980 1052 2.556766 TCTCTCTCTCTCTGTCCCTCA 58.443 52.381 0.00 0.00 0.00 3.86
985 1057 3.316308 GGAAGCATCTCTCTCTCTCTGTC 59.684 52.174 0.00 0.00 0.00 3.51
986 1058 3.290710 GGAAGCATCTCTCTCTCTCTGT 58.709 50.000 0.00 0.00 0.00 3.41
987 1059 2.291465 CGGAAGCATCTCTCTCTCTCTG 59.709 54.545 0.00 0.00 0.00 3.35
988 1060 2.575532 CGGAAGCATCTCTCTCTCTCT 58.424 52.381 0.00 0.00 0.00 3.10
1195 1273 4.760047 CGTCTTGGCCCTGGACGG 62.760 72.222 24.77 12.61 45.81 4.79
1431 1509 4.704103 AGCTCCGCCTCCCACTCA 62.704 66.667 0.00 0.00 0.00 3.41
1551 1629 1.302511 GGCGTCTTCCTTGAGCCAA 60.303 57.895 0.00 0.00 46.48 4.52
1700 1781 7.009174 GGCGGATCAAACATTAATTTACAACTG 59.991 37.037 0.00 0.00 0.00 3.16
1701 1782 7.033185 GGCGGATCAAACATTAATTTACAACT 58.967 34.615 0.00 0.00 0.00 3.16
1702 1783 6.809196 TGGCGGATCAAACATTAATTTACAAC 59.191 34.615 0.00 0.00 0.00 3.32
1703 1784 6.925211 TGGCGGATCAAACATTAATTTACAA 58.075 32.000 0.00 0.00 0.00 2.41
1704 1785 6.516739 TGGCGGATCAAACATTAATTTACA 57.483 33.333 0.00 0.00 0.00 2.41
1714 1799 5.063204 CCTAATCTAATGGCGGATCAAACA 58.937 41.667 0.00 0.00 0.00 2.83
1762 1847 4.391523 GCTTTTTGCAGGAAAGAAACAACA 59.608 37.500 21.80 0.00 42.31 3.33
1836 1921 1.289066 CGAGAGCAAGAACCCGACA 59.711 57.895 0.00 0.00 0.00 4.35
1917 2019 0.759346 GAAGTGGAGTGGTGACTGGT 59.241 55.000 0.00 0.00 30.16 4.00
1918 2020 0.758734 TGAAGTGGAGTGGTGACTGG 59.241 55.000 0.00 0.00 30.16 4.00
1919 2021 1.541233 GGTGAAGTGGAGTGGTGACTG 60.541 57.143 0.00 0.00 30.16 3.51
1920 2022 0.759346 GGTGAAGTGGAGTGGTGACT 59.241 55.000 0.00 0.00 33.98 3.41
1921 2023 0.759346 AGGTGAAGTGGAGTGGTGAC 59.241 55.000 0.00 0.00 0.00 3.67
1922 2024 0.758734 CAGGTGAAGTGGAGTGGTGA 59.241 55.000 0.00 0.00 0.00 4.02
1923 2025 0.886490 GCAGGTGAAGTGGAGTGGTG 60.886 60.000 0.00 0.00 0.00 4.17
2013 2115 8.475436 CGTATCTCGGTCGATCACTGATTGAT 62.475 46.154 11.50 9.19 39.85 2.57
2014 2116 2.365582 TCTCGGTCGATCACTGATTGA 58.634 47.619 4.99 4.99 39.85 2.57
2015 2117 2.851805 TCTCGGTCGATCACTGATTG 57.148 50.000 0.00 0.12 39.85 2.67
2016 2118 3.058846 CGTATCTCGGTCGATCACTGATT 60.059 47.826 0.00 2.91 39.85 2.57
2025 2127 1.300266 TGCACACGTATCTCGGTCGA 61.300 55.000 0.00 0.00 44.69 4.20
2029 2131 2.032924 TCATAGTGCACACGTATCTCGG 59.967 50.000 21.04 0.00 44.69 4.63
2037 2139 3.961860 CGCATTAAATCATAGTGCACACG 59.038 43.478 21.04 6.73 35.63 4.49
2043 2145 5.207768 GCCTTCACGCATTAAATCATAGTG 58.792 41.667 0.00 0.00 0.00 2.74
2044 2146 4.024893 CGCCTTCACGCATTAAATCATAGT 60.025 41.667 0.00 0.00 0.00 2.12
2045 2147 4.211164 TCGCCTTCACGCATTAAATCATAG 59.789 41.667 0.00 0.00 0.00 2.23
2090 2193 1.130955 GCACCACATTCAAAGCAACG 58.869 50.000 0.00 0.00 0.00 4.10
2317 2420 3.738282 CGTGATCGGGAAGAAGAATCATC 59.262 47.826 0.00 0.00 0.00 2.92
2359 2466 4.379186 CGACAGAATTTCAGAAATGCAGCT 60.379 41.667 15.31 5.98 0.00 4.24
2362 2469 3.820467 ACCGACAGAATTTCAGAAATGCA 59.180 39.130 15.31 0.00 0.00 3.96
2365 2472 5.066505 GCCATACCGACAGAATTTCAGAAAT 59.933 40.000 2.20 2.20 0.00 2.17
2366 2473 4.394920 GCCATACCGACAGAATTTCAGAAA 59.605 41.667 0.00 0.00 0.00 2.52
2369 2476 2.285220 CGCCATACCGACAGAATTTCAG 59.715 50.000 0.00 0.00 0.00 3.02
2370 2477 2.276201 CGCCATACCGACAGAATTTCA 58.724 47.619 0.00 0.00 0.00 2.69
2379 2486 2.972505 CCATGGCGCCATACCGAC 60.973 66.667 39.94 5.19 34.91 4.79
2385 2492 2.502093 CAAATGCCATGGCGCCAT 59.498 55.556 36.10 36.10 45.51 4.40
2387 2494 3.773404 ACCAAATGCCATGGCGCC 61.773 61.111 30.87 22.73 45.51 6.53
2393 2500 1.105457 CATCCGTCACCAAATGCCAT 58.895 50.000 0.00 0.00 0.00 4.40
2588 2720 3.043635 CGCAAGTTGATCATACTGTGC 57.956 47.619 7.16 19.85 0.00 4.57
2804 2950 1.739466 ACAGAGCACACACACACAAAG 59.261 47.619 0.00 0.00 0.00 2.77
2809 2955 0.823460 TCTGACAGAGCACACACACA 59.177 50.000 0.00 0.00 0.00 3.72
2962 3112 1.202200 CCACGTGGAGATCTCGTCTTC 60.202 57.143 31.31 2.94 37.29 2.87
3000 3150 1.010935 ATGTTCAGCTGAGCACGTCG 61.011 55.000 32.03 0.00 38.07 5.12
3022 3172 0.861837 CAACGGAGCGGAAGATATGC 59.138 55.000 0.00 0.00 0.00 3.14
3030 3182 2.260434 GCTGTACAACGGAGCGGA 59.740 61.111 0.00 0.00 0.00 5.54
3106 3278 0.098728 AATTCAGAATTTCGGCGGCG 59.901 50.000 27.15 27.15 0.00 6.46
3114 3286 9.965824 CAGTAGTACCAAAACAATTCAGAATTT 57.034 29.630 5.58 0.00 0.00 1.82
3115 3287 8.576442 CCAGTAGTACCAAAACAATTCAGAATT 58.424 33.333 2.20 2.20 0.00 2.17
3116 3288 7.942341 TCCAGTAGTACCAAAACAATTCAGAAT 59.058 33.333 0.00 0.00 0.00 2.40
3125 3297 7.776030 TCTGAATTTTCCAGTAGTACCAAAACA 59.224 33.333 0.00 0.00 33.57 2.83
3126 3298 8.161699 TCTGAATTTTCCAGTAGTACCAAAAC 57.838 34.615 0.00 0.00 33.57 2.43
3290 3464 7.127012 TGGACATCGATTTATACCAGGTAAA 57.873 36.000 2.53 0.00 0.00 2.01
3416 3751 2.228822 GGCACTTGATTGTCAAATCCGT 59.771 45.455 0.00 0.00 41.40 4.69
3452 3787 1.974236 AGAGGCTTGCACTTGTACTCT 59.026 47.619 0.00 0.00 0.00 3.24
3497 3837 2.481289 ACTTAAGCAAGCCTCTGTCC 57.519 50.000 1.29 0.00 34.94 4.02
3502 3861 4.747605 GCTGACTATACTTAAGCAAGCCTC 59.252 45.833 1.29 0.00 34.94 4.70
3554 3913 9.278978 GGAGAGAAAGATAAAATAGGATCAACC 57.721 37.037 0.00 0.00 39.35 3.77
3566 3925 5.188434 CACATGCCTGGAGAGAAAGATAAA 58.812 41.667 0.00 0.00 0.00 1.40
3567 3926 4.384537 CCACATGCCTGGAGAGAAAGATAA 60.385 45.833 0.00 0.00 32.30 1.75
3568 3927 3.135348 CCACATGCCTGGAGAGAAAGATA 59.865 47.826 0.00 0.00 32.30 1.98
3569 3928 2.092538 CCACATGCCTGGAGAGAAAGAT 60.093 50.000 0.00 0.00 32.30 2.40
3570 3929 1.280133 CCACATGCCTGGAGAGAAAGA 59.720 52.381 0.00 0.00 32.30 2.52
3571 3930 1.747709 CCACATGCCTGGAGAGAAAG 58.252 55.000 0.00 0.00 32.30 2.62
3572 3931 0.322816 GCCACATGCCTGGAGAGAAA 60.323 55.000 6.54 0.00 32.30 2.52
3573 3932 1.203441 AGCCACATGCCTGGAGAGAA 61.203 55.000 6.54 0.00 42.71 2.87
3574 3933 1.203441 AAGCCACATGCCTGGAGAGA 61.203 55.000 6.54 0.00 42.71 3.10
3575 3934 0.747283 GAAGCCACATGCCTGGAGAG 60.747 60.000 6.54 0.00 42.71 3.20
3576 3935 1.203441 AGAAGCCACATGCCTGGAGA 61.203 55.000 6.54 0.00 42.71 3.71
3577 3936 0.543277 TAGAAGCCACATGCCTGGAG 59.457 55.000 6.54 0.00 42.71 3.86
3578 3937 0.543277 CTAGAAGCCACATGCCTGGA 59.457 55.000 6.54 0.00 42.71 3.86
3579 3938 0.543277 TCTAGAAGCCACATGCCTGG 59.457 55.000 0.00 0.00 42.71 4.45
3580 3939 2.219458 CATCTAGAAGCCACATGCCTG 58.781 52.381 0.00 0.00 42.71 4.85
3581 3940 1.142465 CCATCTAGAAGCCACATGCCT 59.858 52.381 0.00 0.00 42.71 4.75
3582 3941 1.602311 CCATCTAGAAGCCACATGCC 58.398 55.000 0.00 0.00 42.71 4.40
3583 3942 1.133976 ACCCATCTAGAAGCCACATGC 60.134 52.381 0.00 0.00 41.71 4.06
3584 3943 3.389329 ACTACCCATCTAGAAGCCACATG 59.611 47.826 0.00 0.00 0.00 3.21
3585 3944 3.658725 ACTACCCATCTAGAAGCCACAT 58.341 45.455 0.00 0.00 0.00 3.21
3586 3945 3.116096 ACTACCCATCTAGAAGCCACA 57.884 47.619 0.00 0.00 0.00 4.17
3587 3946 3.197983 ACAACTACCCATCTAGAAGCCAC 59.802 47.826 0.00 0.00 0.00 5.01
3588 3947 3.450904 ACAACTACCCATCTAGAAGCCA 58.549 45.455 0.00 0.00 0.00 4.75
3589 3948 4.081087 TCAACAACTACCCATCTAGAAGCC 60.081 45.833 0.00 0.00 0.00 4.35
3590 3949 5.086104 TCAACAACTACCCATCTAGAAGC 57.914 43.478 0.00 0.00 0.00 3.86
3591 3950 7.331026 TGAATCAACAACTACCCATCTAGAAG 58.669 38.462 0.00 0.00 0.00 2.85
3592 3951 7.252612 TGAATCAACAACTACCCATCTAGAA 57.747 36.000 0.00 0.00 0.00 2.10
3593 3952 6.867519 TGAATCAACAACTACCCATCTAGA 57.132 37.500 0.00 0.00 0.00 2.43
3594 3953 6.708054 GGATGAATCAACAACTACCCATCTAG 59.292 42.308 0.00 0.00 32.26 2.43
3595 3954 6.386927 AGGATGAATCAACAACTACCCATCTA 59.613 38.462 0.00 0.00 32.26 1.98
3596 3955 5.192522 AGGATGAATCAACAACTACCCATCT 59.807 40.000 0.00 0.00 32.26 2.90
3597 3956 5.440610 AGGATGAATCAACAACTACCCATC 58.559 41.667 0.00 0.00 0.00 3.51
3598 3957 5.456921 AGGATGAATCAACAACTACCCAT 57.543 39.130 0.00 0.00 0.00 4.00
3599 3958 4.927267 AGGATGAATCAACAACTACCCA 57.073 40.909 0.00 0.00 0.00 4.51
3600 3959 5.010282 ACAAGGATGAATCAACAACTACCC 58.990 41.667 0.00 0.00 0.00 3.69
3601 3960 7.254455 CGATACAAGGATGAATCAACAACTACC 60.254 40.741 0.00 0.00 0.00 3.18
3602 3961 7.621991 CGATACAAGGATGAATCAACAACTAC 58.378 38.462 0.00 0.00 0.00 2.73
3603 3962 6.257849 GCGATACAAGGATGAATCAACAACTA 59.742 38.462 0.00 0.00 0.00 2.24
3604 3963 5.065218 GCGATACAAGGATGAATCAACAACT 59.935 40.000 0.00 0.00 0.00 3.16
3605 3964 5.065218 AGCGATACAAGGATGAATCAACAAC 59.935 40.000 0.00 0.00 0.00 3.32
3606 3965 5.185454 AGCGATACAAGGATGAATCAACAA 58.815 37.500 0.00 0.00 0.00 2.83
3607 3966 4.769688 AGCGATACAAGGATGAATCAACA 58.230 39.130 0.00 0.00 0.00 3.33
3618 3977 8.283291 GGACAAAAATAGATAAGCGATACAAGG 58.717 37.037 0.00 0.00 0.00 3.61
3652 4011 3.743911 ACGTACATTCAACGATGCAAAGA 59.256 39.130 2.27 0.00 42.90 2.52
3718 4078 8.311650 ACTACAATCCTCAAATATTGATACGC 57.688 34.615 0.00 0.00 39.30 4.42
3750 4111 4.191015 GGTCCCCATTCGGCCCTC 62.191 72.222 0.00 0.00 0.00 4.30
3796 4157 0.966370 ATCCGAGCTCCTATACGCCC 60.966 60.000 8.47 0.00 0.00 6.13
3861 4222 8.100164 TGACAGGACATATTCTCAAATTGTACA 58.900 33.333 0.00 0.00 0.00 2.90
3894 4255 6.255215 CGTTGATTTGATTATTTACGGCTGT 58.745 36.000 2.42 2.42 0.00 4.40
3899 4260 6.568601 CGCTACCGTTGATTTGATTATTTACG 59.431 38.462 0.00 0.00 0.00 3.18
3909 4270 0.096976 CAGCCGCTACCGTTGATTTG 59.903 55.000 0.00 0.00 0.00 2.32
3918 4279 0.392461 TTCACCAATCAGCCGCTACC 60.392 55.000 0.00 0.00 0.00 3.18
3929 4290 1.105457 CCGCATCACCATTCACCAAT 58.895 50.000 0.00 0.00 0.00 3.16
3991 4352 7.015292 TGGAACACCAGCTAAATATAGACTAGG 59.985 40.741 0.00 0.00 0.00 3.02
4023 4384 4.681483 GTGAGAAACTGGCTATTTGTTTGC 59.319 41.667 0.00 0.00 34.55 3.68
4062 4423 7.440523 TGCAATTTACTTGGTTGTTGTTTTT 57.559 28.000 0.00 0.00 35.25 1.94
4064 4425 6.876257 TCTTGCAATTTACTTGGTTGTTGTTT 59.124 30.769 0.00 0.00 35.25 2.83
4101 4462 1.475213 CCTCCCATTCTTTACCCTCGC 60.475 57.143 0.00 0.00 0.00 5.03
4102 4463 1.141053 CCCTCCCATTCTTTACCCTCG 59.859 57.143 0.00 0.00 0.00 4.63
4115 4476 1.667595 TTGATCACATCACCCTCCCA 58.332 50.000 0.00 0.00 39.39 4.37
4116 4477 2.579873 CATTGATCACATCACCCTCCC 58.420 52.381 0.00 0.00 39.39 4.30
4117 4478 2.092212 ACCATTGATCACATCACCCTCC 60.092 50.000 0.00 0.00 39.39 4.30
4118 4479 2.947652 CACCATTGATCACATCACCCTC 59.052 50.000 0.00 0.00 39.39 4.30
4119 4480 2.577563 TCACCATTGATCACATCACCCT 59.422 45.455 0.00 0.00 39.39 4.34
4120 4481 3.003394 TCACCATTGATCACATCACCC 57.997 47.619 0.00 0.00 39.39 4.61
4121 4482 6.487668 TCATATTCACCATTGATCACATCACC 59.512 38.462 0.00 0.00 39.39 4.02
4122 4483 7.500720 TCATATTCACCATTGATCACATCAC 57.499 36.000 0.00 0.00 39.39 3.06
4123 4484 8.573035 CATTCATATTCACCATTGATCACATCA 58.427 33.333 0.00 0.00 37.55 3.07
4124 4485 8.789762 TCATTCATATTCACCATTGATCACATC 58.210 33.333 0.00 0.00 0.00 3.06
4125 4486 8.700439 TCATTCATATTCACCATTGATCACAT 57.300 30.769 0.00 0.00 0.00 3.21
4126 4487 8.522542 TTCATTCATATTCACCATTGATCACA 57.477 30.769 0.00 0.00 0.00 3.58
4127 4488 9.976511 ATTTCATTCATATTCACCATTGATCAC 57.023 29.630 0.00 0.00 0.00 3.06
4128 4489 9.974980 CATTTCATTCATATTCACCATTGATCA 57.025 29.630 0.00 0.00 0.00 2.92
4129 4490 8.922676 GCATTTCATTCATATTCACCATTGATC 58.077 33.333 0.00 0.00 0.00 2.92
4130 4491 8.425703 TGCATTTCATTCATATTCACCATTGAT 58.574 29.630 0.00 0.00 0.00 2.57
4131 4492 7.783042 TGCATTTCATTCATATTCACCATTGA 58.217 30.769 0.00 0.00 0.00 2.57
4132 4493 8.495148 CATGCATTTCATTCATATTCACCATTG 58.505 33.333 0.00 0.00 31.79 2.82
4133 4494 7.659799 CCATGCATTTCATTCATATTCACCATT 59.340 33.333 0.00 0.00 31.79 3.16
4134 4495 7.158697 CCATGCATTTCATTCATATTCACCAT 58.841 34.615 0.00 0.00 31.79 3.55
4135 4496 6.463190 CCCATGCATTTCATTCATATTCACCA 60.463 38.462 0.00 0.00 31.79 4.17
4136 4497 5.929992 CCCATGCATTTCATTCATATTCACC 59.070 40.000 0.00 0.00 31.79 4.02
4137 4498 5.929992 CCCCATGCATTTCATTCATATTCAC 59.070 40.000 0.00 0.00 31.79 3.18
4138 4499 5.839606 TCCCCATGCATTTCATTCATATTCA 59.160 36.000 0.00 0.00 31.79 2.57
4139 4500 6.349243 TCCCCATGCATTTCATTCATATTC 57.651 37.500 0.00 0.00 31.79 1.75
4140 4501 6.750660 TTCCCCATGCATTTCATTCATATT 57.249 33.333 0.00 0.00 31.79 1.28
4150 4511 1.410153 GCTCGAATTCCCCATGCATTT 59.590 47.619 0.00 0.00 0.00 2.32
4218 4579 2.334977 TCTCCACCTCAAGCTACCAAA 58.665 47.619 0.00 0.00 0.00 3.28
4230 4591 3.010250 GGTTAGGGTTTTCATCTCCACCT 59.990 47.826 0.00 0.00 0.00 4.00
4231 4592 3.353557 GGTTAGGGTTTTCATCTCCACC 58.646 50.000 0.00 0.00 0.00 4.61
4232 4593 3.353557 GGGTTAGGGTTTTCATCTCCAC 58.646 50.000 0.00 0.00 0.00 4.02
4233 4594 2.026636 CGGGTTAGGGTTTTCATCTCCA 60.027 50.000 0.00 0.00 0.00 3.86
4234 4595 2.026542 ACGGGTTAGGGTTTTCATCTCC 60.027 50.000 0.00 0.00 0.00 3.71
4235 4596 3.345508 ACGGGTTAGGGTTTTCATCTC 57.654 47.619 0.00 0.00 0.00 2.75
4236 4597 3.418047 CAACGGGTTAGGGTTTTCATCT 58.582 45.455 0.00 0.00 0.00 2.90
4237 4598 2.094906 GCAACGGGTTAGGGTTTTCATC 60.095 50.000 0.00 0.00 0.00 2.92
4238 4599 1.890489 GCAACGGGTTAGGGTTTTCAT 59.110 47.619 0.00 0.00 0.00 2.57
4239 4600 1.320507 GCAACGGGTTAGGGTTTTCA 58.679 50.000 0.00 0.00 0.00 2.69
4240 4601 1.268625 CTGCAACGGGTTAGGGTTTTC 59.731 52.381 0.00 0.00 0.00 2.29
4241 4602 1.324383 CTGCAACGGGTTAGGGTTTT 58.676 50.000 0.00 0.00 0.00 2.43
4242 4603 0.538746 CCTGCAACGGGTTAGGGTTT 60.539 55.000 0.00 0.00 0.00 3.27
4243 4604 1.074248 CCTGCAACGGGTTAGGGTT 59.926 57.895 0.00 0.00 0.00 4.11
4244 4605 2.754375 CCTGCAACGGGTTAGGGT 59.246 61.111 0.00 0.00 0.00 4.34
4245 4606 2.750237 GCCTGCAACGGGTTAGGG 60.750 66.667 3.29 0.00 31.34 3.53
4246 4607 2.750237 GGCCTGCAACGGGTTAGG 60.750 66.667 0.00 0.00 31.34 2.69
4247 4608 1.745489 GAGGCCTGCAACGGGTTAG 60.745 63.158 12.00 0.00 31.34 2.34
4248 4609 1.774894 AAGAGGCCTGCAACGGGTTA 61.775 55.000 12.00 0.00 31.34 2.85
4249 4610 3.133365 AAGAGGCCTGCAACGGGTT 62.133 57.895 12.00 0.00 31.34 4.11
4250 4611 3.570212 AAGAGGCCTGCAACGGGT 61.570 61.111 12.00 0.00 31.34 5.28
4251 4612 3.058160 CAAGAGGCCTGCAACGGG 61.058 66.667 12.00 0.00 0.00 5.28
4252 4613 3.058160 CCAAGAGGCCTGCAACGG 61.058 66.667 12.00 0.00 0.00 4.44
4253 4614 3.058160 CCCAAGAGGCCTGCAACG 61.058 66.667 12.00 0.00 0.00 4.10
4262 4623 0.034670 CTCCCTTTCAGCCCAAGAGG 60.035 60.000 0.00 0.00 39.47 3.69
4263 4624 0.987294 TCTCCCTTTCAGCCCAAGAG 59.013 55.000 0.00 0.00 0.00 2.85
4264 4625 0.987294 CTCTCCCTTTCAGCCCAAGA 59.013 55.000 0.00 0.00 0.00 3.02
4265 4626 0.987294 TCTCTCCCTTTCAGCCCAAG 59.013 55.000 0.00 0.00 0.00 3.61
4266 4627 0.987294 CTCTCTCCCTTTCAGCCCAA 59.013 55.000 0.00 0.00 0.00 4.12
4267 4628 1.557269 GCTCTCTCCCTTTCAGCCCA 61.557 60.000 0.00 0.00 0.00 5.36
4268 4629 1.223211 GCTCTCTCCCTTTCAGCCC 59.777 63.158 0.00 0.00 0.00 5.19
4269 4630 1.223211 GGCTCTCTCCCTTTCAGCC 59.777 63.158 0.00 0.00 42.87 4.85
4270 4631 1.153469 CGGCTCTCTCCCTTTCAGC 60.153 63.158 0.00 0.00 0.00 4.26
4271 4632 1.519719 CCGGCTCTCTCCCTTTCAG 59.480 63.158 0.00 0.00 0.00 3.02
4272 4633 2.660064 GCCGGCTCTCTCCCTTTCA 61.660 63.158 22.15 0.00 0.00 2.69
4273 4634 2.188207 GCCGGCTCTCTCCCTTTC 59.812 66.667 22.15 0.00 0.00 2.62
4274 4635 2.284995 AGCCGGCTCTCTCCCTTT 60.285 61.111 27.08 0.00 0.00 3.11
4275 4636 3.080121 CAGCCGGCTCTCTCCCTT 61.080 66.667 30.29 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.