Multiple sequence alignment - TraesCS4A01G209900

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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 TraesCS4A01G209900 chr4A 100.000 5374 0 0 1 5374 503633543 503628170 0.000000e+00 9925.0
1 TraesCS4A01G209900 chr4A 92.339 248 12 7 5113 5357 719682170 719682413 3.980000e-91 346.0
2 TraesCS4A01G209900 chr4A 89.222 167 15 3 2956 3121 1910533 1910369 7.060000e-49 206.0
3 TraesCS4A01G209900 chr4A 89.308 159 15 2 5115 5271 660521206 660521364 1.180000e-46 198.0
4 TraesCS4A01G209900 chr4B 91.365 2710 157 35 311 2957 128059765 128057070 0.000000e+00 3637.0
5 TraesCS4A01G209900 chr4B 91.566 1245 38 17 3812 5035 128056362 128055164 0.000000e+00 1655.0
6 TraesCS4A01G209900 chr4B 93.033 689 23 6 3117 3805 128057071 128056408 0.000000e+00 983.0
7 TraesCS4A01G209900 chr4B 92.742 248 13 3 5112 5357 596356800 596356556 2.380000e-93 353.0
8 TraesCS4A01G209900 chr4B 87.455 279 23 7 22 290 128060263 128059987 1.450000e-80 311.0
9 TraesCS4A01G209900 chr4B 85.020 247 10 10 5113 5357 345463870 345463649 5.420000e-55 226.0
10 TraesCS4A01G209900 chr4D 96.574 2014 60 7 985 2995 91242190 91240183 0.000000e+00 3328.0
11 TraesCS4A01G209900 chr4D 94.960 1250 29 12 3809 5035 91239318 91238080 0.000000e+00 1929.0
12 TraesCS4A01G209900 chr4D 91.205 921 48 10 22 912 91243374 91242457 0.000000e+00 1221.0
13 TraesCS4A01G209900 chr4D 93.964 729 31 7 3078 3805 91240077 91239361 0.000000e+00 1090.0
14 TraesCS4A01G209900 chr6B 92.664 259 12 5 5101 5357 216570072 216569819 3.060000e-97 366.0
15 TraesCS4A01G209900 chr3A 90.734 259 17 5 5102 5357 219860602 219860856 6.670000e-89 339.0
16 TraesCS4A01G209900 chr1B 92.073 164 11 2 2956 3118 41090990 41091152 4.190000e-56 230.0
17 TraesCS4A01G209900 chr5D 97.727 132 1 2 2993 3122 241844204 241844073 5.420000e-55 226.0
18 TraesCS4A01G209900 chr5D 76.500 200 37 10 4296 4489 210676614 210676419 3.420000e-17 100.0
19 TraesCS4A01G209900 chr2D 97.015 134 2 2 2986 3118 62293429 62293297 1.950000e-54 224.0
20 TraesCS4A01G209900 chr7B 84.615 247 11 10 5113 5357 72327841 72328062 2.520000e-53 220.0
21 TraesCS4A01G209900 chr7B 88.050 159 17 2 5112 5268 632473124 632473282 2.560000e-43 187.0
22 TraesCS4A01G209900 chr3D 94.366 142 5 3 2988 3128 210622419 210622558 1.170000e-51 215.0
23 TraesCS4A01G209900 chr3D 90.062 161 14 2 2959 3118 610017761 610017602 1.960000e-49 207.0
24 TraesCS4A01G209900 chr2B 90.244 164 14 2 2956 3118 211527829 211527991 4.220000e-51 213.0
25 TraesCS4A01G209900 chr5B 86.911 191 21 4 3530 3719 257332466 257332653 1.520000e-50 211.0
26 TraesCS4A01G209900 chr5B 86.911 191 21 4 3530 3719 257528636 257528823 1.520000e-50 211.0
27 TraesCS4A01G209900 chr5B 89.024 164 16 2 2956 3118 368502788 368502950 9.130000e-48 202.0
28 TraesCS4A01G209900 chr5B 87.786 131 14 2 3530 3660 261191179 261191307 9.320000e-33 152.0
29 TraesCS4A01G209900 chr3B 89.634 164 15 2 2956 3118 422472137 422472299 1.960000e-49 207.0
30 TraesCS4A01G209900 chr6D 88.406 138 14 2 5112 5247 386522463 386522600 1.200000e-36 165.0
31 TraesCS4A01G209900 chr2A 95.000 60 3 0 2951 3010 177665122 177665181 1.590000e-15 95.3
32 TraesCS4A01G209900 chr2A 94.545 55 2 1 2951 3004 177665328 177665274 3.450000e-12 84.2
33 TraesCS4A01G209900 chr2A 85.000 80 7 2 100 174 754178884 754178963 5.770000e-10 76.8


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 TraesCS4A01G209900 chr4A 503628170 503633543 5373 True 9925.0 9925 100.00000 1 5374 1 chr4A.!!$R2 5373
1 TraesCS4A01G209900 chr4B 128055164 128060263 5099 True 1646.5 3637 90.85475 22 5035 4 chr4B.!!$R3 5013
2 TraesCS4A01G209900 chr4D 91238080 91243374 5294 True 1892.0 3328 94.17575 22 5035 4 chr4D.!!$R1 5013

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
698 931 0.249741 AGACCGGGTTCAGTCAAACG 60.250 55.0 6.32 0.0 35.38 3.60 F
801 1034 0.389296 CCGTATCAACCGTGCACTCA 60.389 55.0 16.19 0.0 0.00 3.41 F
1617 2047 0.530744 CTAGTGCCCTGCGTTACTGA 59.469 55.0 0.00 0.0 0.00 3.41 F
3009 3484 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.0 0.00 0.0 0.00 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2328 0.248743 CATGCTGCCATACTTTGCGG 60.249 55.000 0.00 0.0 36.92 5.69 R
2583 3053 2.235898 GTGAGTCCTCAGGAAGCAGAAT 59.764 50.000 0.00 0.0 40.75 2.40 R
3096 3571 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.0 0.00 2.17 R
4670 5237 0.476771 ACTCACCAACCGGAAACCAT 59.523 50.000 9.46 0.0 35.59 3.55 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
79 86 7.990314 TGTAATATGTATTGCTTGAGCCTTGTA 59.010 33.333 0.00 0.00 41.18 2.41
233 245 7.837202 TGAACAATACTAATCCGAAATTCGT 57.163 32.000 14.58 0.00 38.40 3.85
245 257 5.362263 TCCGAAATTCGTAAAAGGGGATAG 58.638 41.667 14.58 0.00 38.40 2.08
262 274 7.354312 AGGGGATAGTAAACTGCAAACAATAT 58.646 34.615 0.00 0.00 0.00 1.28
281 293 8.574251 ACAATATAACACTGCAGGTTGAAATA 57.426 30.769 19.93 13.16 0.00 1.40
372 587 2.432628 CCGTGGAGACCGACAAGC 60.433 66.667 0.00 0.00 0.00 4.01
589 817 4.323477 CGTTTCGCCCCTCACCCA 62.323 66.667 0.00 0.00 0.00 4.51
606 834 1.285280 CCACCTCTTCCCATACACCA 58.715 55.000 0.00 0.00 0.00 4.17
698 931 0.249741 AGACCGGGTTCAGTCAAACG 60.250 55.000 6.32 0.00 35.38 3.60
774 1007 3.663176 CTGCACCCACCGCACAAG 61.663 66.667 0.00 0.00 35.08 3.16
778 1011 4.284550 ACCCACCGCACAAGCCAT 62.285 61.111 0.00 0.00 37.52 4.40
796 1029 0.872881 ATACGCCGTATCAACCGTGC 60.873 55.000 3.44 0.00 35.36 5.34
801 1034 0.389296 CCGTATCAACCGTGCACTCA 60.389 55.000 16.19 0.00 0.00 3.41
802 1035 1.424403 CGTATCAACCGTGCACTCAA 58.576 50.000 16.19 0.00 0.00 3.02
823 1056 4.537533 CGTGATGCGCGCGTGTAC 62.538 66.667 33.42 25.90 45.03 2.90
881 1115 4.722535 AGCCTCCGCCTTCCTCCA 62.723 66.667 0.00 0.00 34.57 3.86
1092 1521 1.038130 ACTCCGAGACCTTCATCCGG 61.038 60.000 1.33 0.00 41.36 5.14
1617 2047 0.530744 CTAGTGCCCTGCGTTACTGA 59.469 55.000 0.00 0.00 0.00 3.41
1663 2093 4.321974 GCCTAATTTTGAGTTTCCAGGGTG 60.322 45.833 0.00 0.00 0.00 4.61
1898 2328 7.254227 TCTGTGTTGTTTGTAGTCCATAAAC 57.746 36.000 0.00 0.00 38.39 2.01
2022 2452 4.654091 AATTGTTGGACAAGTGTGGAAG 57.346 40.909 0.00 0.00 41.94 3.46
2420 2884 6.768483 TCTTCCATTCAGTGAAGATTGTGTA 58.232 36.000 11.91 0.00 0.00 2.90
2454 2918 6.337356 CACCACTTAGTTGTTTCCAATTGTT 58.663 36.000 4.43 0.00 32.11 2.83
2457 2921 7.038659 CCACTTAGTTGTTTCCAATTGTTGAA 58.961 34.615 4.43 0.00 32.11 2.69
2499 2969 6.560253 ATTGATTGTTCAAGTGTAGTGGAC 57.440 37.500 0.00 0.00 44.75 4.02
2501 2971 2.519377 TGTTCAAGTGTAGTGGACGG 57.481 50.000 0.00 0.00 0.00 4.79
2583 3053 9.863845 TCTGTCACTACGAAATACAAATATCAA 57.136 29.630 0.00 0.00 0.00 2.57
2741 3214 1.260544 ATGTTGAAAGCTTCCTGGCC 58.739 50.000 0.00 0.00 0.00 5.36
2744 3217 1.172180 TTGAAAGCTTCCTGGCCACG 61.172 55.000 0.00 0.00 0.00 4.94
2760 3233 2.678336 GCCACGCTGAAGCTATAAACTT 59.322 45.455 0.10 0.00 39.32 2.66
2811 3284 2.354261 AGGTTAGCTCCCCAAGGTTA 57.646 50.000 0.00 0.00 36.91 2.85
2965 3440 5.216665 ACCTTACAATACTACTCCCTCCA 57.783 43.478 0.00 0.00 0.00 3.86
2995 3470 9.209175 CAAAATAAGTGTCTCAAGCTTAGTACT 57.791 33.333 0.00 0.00 0.00 2.73
2996 3471 8.989653 AAATAAGTGTCTCAAGCTTAGTACTC 57.010 34.615 0.00 0.00 0.00 2.59
2998 3473 3.764972 AGTGTCTCAAGCTTAGTACTCCC 59.235 47.826 0.00 0.00 0.00 4.30
3000 3475 4.017808 TGTCTCAAGCTTAGTACTCCCTC 58.982 47.826 0.00 0.00 0.00 4.30
3001 3476 3.382227 GTCTCAAGCTTAGTACTCCCTCC 59.618 52.174 0.00 0.00 0.00 4.30
3002 3477 2.359531 CTCAAGCTTAGTACTCCCTCCG 59.640 54.545 0.00 0.00 0.00 4.63
3003 3478 2.100989 CAAGCTTAGTACTCCCTCCGT 58.899 52.381 0.00 0.00 0.00 4.69
3005 3480 1.031235 GCTTAGTACTCCCTCCGTCC 58.969 60.000 0.00 0.00 0.00 4.79
3006 3481 1.689984 CTTAGTACTCCCTCCGTCCC 58.310 60.000 0.00 0.00 0.00 4.46
3007 3482 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3009 3484 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3010 3485 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3011 3486 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3012 3487 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3013 3488 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3014 3489 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3016 3491 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3017 3492 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3018 3493 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3020 3495 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3021 3496 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3022 3497 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3024 3499 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3025 3500 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3027 3502 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3028 3503 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3029 3504 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3030 3505 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3038 3513 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
3039 3514 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
3041 3516 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
3042 3517 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
3043 3518 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
3058 3533 6.199937 ACGGATGTATCTAACACTAAACGT 57.800 37.500 0.00 0.00 42.09 3.99
3059 3534 7.320443 ACGGATGTATCTAACACTAAACGTA 57.680 36.000 0.00 0.00 42.09 3.57
3060 3535 7.761409 ACGGATGTATCTAACACTAAACGTAA 58.239 34.615 0.00 0.00 42.09 3.18
3061 3536 7.698130 ACGGATGTATCTAACACTAAACGTAAC 59.302 37.037 0.00 0.00 42.09 2.50
3062 3537 7.912250 CGGATGTATCTAACACTAAACGTAACT 59.088 37.037 0.00 0.00 42.09 2.24
3066 3541 9.231297 TGTATCTAACACTAAACGTAACTAGGT 57.769 33.333 0.00 0.00 31.43 3.08
3069 3544 8.615878 TCTAACACTAAACGTAACTAGGTACA 57.384 34.615 17.91 0.00 0.00 2.90
3070 3545 9.231297 TCTAACACTAAACGTAACTAGGTACAT 57.769 33.333 17.91 0.00 0.00 2.29
3071 3546 9.495754 CTAACACTAAACGTAACTAGGTACATC 57.504 37.037 17.91 0.00 0.00 3.06
3072 3547 6.856895 ACACTAAACGTAACTAGGTACATCC 58.143 40.000 17.91 0.00 0.00 3.51
3073 3548 5.967674 CACTAAACGTAACTAGGTACATCCG 59.032 44.000 17.91 6.39 41.99 4.18
3074 3549 5.648092 ACTAAACGTAACTAGGTACATCCGT 59.352 40.000 17.91 7.03 41.99 4.69
3076 3551 6.699575 AAACGTAACTAGGTACATCCGTAT 57.300 37.500 17.91 0.00 41.99 3.06
3078 3553 6.699575 ACGTAACTAGGTACATCCGTATTT 57.300 37.500 17.91 0.00 41.99 1.40
3079 3554 7.801716 ACGTAACTAGGTACATCCGTATTTA 57.198 36.000 17.91 0.00 41.99 1.40
3080 3555 7.865707 ACGTAACTAGGTACATCCGTATTTAG 58.134 38.462 17.91 0.00 41.99 1.85
3083 3558 7.886629 AACTAGGTACATCCGTATTTAGACA 57.113 36.000 0.00 0.00 41.99 3.41
3084 3559 7.886629 ACTAGGTACATCCGTATTTAGACAA 57.113 36.000 0.00 0.00 41.99 3.18
3085 3560 8.297470 ACTAGGTACATCCGTATTTAGACAAA 57.703 34.615 0.00 0.00 41.99 2.83
3086 3561 8.921205 ACTAGGTACATCCGTATTTAGACAAAT 58.079 33.333 0.00 0.00 41.99 2.32
3087 3562 9.408069 CTAGGTACATCCGTATTTAGACAAATC 57.592 37.037 0.00 0.00 41.99 2.17
3088 3563 8.019656 AGGTACATCCGTATTTAGACAAATCT 57.980 34.615 0.00 0.00 41.99 2.40
3089 3564 9.139734 AGGTACATCCGTATTTAGACAAATCTA 57.860 33.333 0.00 0.00 41.99 1.98
3090 3565 9.754382 GGTACATCCGTATTTAGACAAATCTAA 57.246 33.333 0.00 0.00 44.17 2.10
3093 3568 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
3094 3569 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
3096 3571 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
3108 3607 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3265 3764 4.217550 AGCATAAAAAGCTAGGAACGCAAA 59.782 37.500 0.00 0.00 41.32 3.68
3267 3766 5.457140 CATAAAAAGCTAGGAACGCAAACA 58.543 37.500 0.00 0.00 0.00 2.83
3271 3770 1.070134 AGCTAGGAACGCAAACAGACA 59.930 47.619 0.00 0.00 0.00 3.41
3278 3777 2.248431 GCAAACAGACACGTCCGC 59.752 61.111 0.00 0.00 0.00 5.54
3296 3795 1.876714 CGTTGTCCGCCTATGTCCG 60.877 63.158 0.00 0.00 0.00 4.79
3339 3838 9.062524 ACTAATGTGTTGTTGCTTTAATAGTGA 57.937 29.630 0.00 0.00 0.00 3.41
3347 3846 5.183713 TGTTGCTTTAATAGTGATGCTGCTT 59.816 36.000 0.00 0.00 0.00 3.91
3364 3863 4.618489 GCTGCTTTAATTATATGCTTGCGG 59.382 41.667 0.00 0.00 0.00 5.69
3368 3867 5.287035 GCTTTAATTATATGCTTGCGGATGC 59.713 40.000 7.89 7.89 43.20 3.91
3404 3903 3.157087 CCGCCTGCATCCCTATAAAAAT 58.843 45.455 0.00 0.00 0.00 1.82
3432 3931 6.183360 GGTCCTGTAGTTGATGTGACTACTAG 60.183 46.154 13.59 9.79 46.07 2.57
3518 4017 2.627699 TCAAAAACAGGGGAAGTGATGC 59.372 45.455 0.00 0.00 0.00 3.91
3805 4304 9.249457 TCTGAGTATGACGACATCAAATTTATC 57.751 33.333 3.03 0.00 41.93 1.75
3806 4305 8.940768 TGAGTATGACGACATCAAATTTATCA 57.059 30.769 3.03 0.00 41.93 2.15
3807 4306 9.034544 TGAGTATGACGACATCAAATTTATCAG 57.965 33.333 3.03 0.00 41.93 2.90
3858 4396 6.405278 TCATCTTACAGTCTCTGTGTTGAA 57.595 37.500 11.92 0.00 45.01 2.69
3957 4498 3.066203 GGAAGAACAAGCCAAACTTCGAA 59.934 43.478 0.00 0.00 36.04 3.71
3966 4507 3.119495 AGCCAAACTTCGAAATGGTATGC 60.119 43.478 19.60 9.00 35.34 3.14
3996 4537 5.815740 TCTTGTTTTCGAAGTTTGCTAGTCT 59.184 36.000 0.00 0.00 0.00 3.24
4029 4570 2.554032 AGGCTCAGAACAAAAACCATCG 59.446 45.455 0.00 0.00 0.00 3.84
4031 4572 3.555518 GCTCAGAACAAAAACCATCGTC 58.444 45.455 0.00 0.00 0.00 4.20
4036 4577 3.568430 AGAACAAAAACCATCGTCTTCCC 59.432 43.478 0.00 0.00 0.00 3.97
4062 4603 2.691409 TTTAAGGCATCTGAGGGTCG 57.309 50.000 0.00 0.00 0.00 4.79
4063 4604 1.860641 TTAAGGCATCTGAGGGTCGA 58.139 50.000 0.00 0.00 0.00 4.20
4064 4605 1.112113 TAAGGCATCTGAGGGTCGAC 58.888 55.000 7.13 7.13 0.00 4.20
4065 4606 1.617947 AAGGCATCTGAGGGTCGACC 61.618 60.000 27.04 27.04 40.67 4.79
4066 4607 2.359169 GGCATCTGAGGGTCGACCA 61.359 63.158 34.40 15.51 43.89 4.02
4067 4608 1.142748 GCATCTGAGGGTCGACCAG 59.857 63.158 34.40 23.35 43.89 4.00
4068 4609 1.608717 GCATCTGAGGGTCGACCAGT 61.609 60.000 34.40 21.86 43.89 4.00
4069 4610 0.174389 CATCTGAGGGTCGACCAGTG 59.826 60.000 34.40 20.53 43.89 3.66
4070 4611 0.039764 ATCTGAGGGTCGACCAGTGA 59.960 55.000 34.40 24.51 43.89 3.41
4071 4612 0.039764 TCTGAGGGTCGACCAGTGAT 59.960 55.000 34.40 15.23 43.89 3.06
4072 4613 0.457851 CTGAGGGTCGACCAGTGATC 59.542 60.000 34.40 22.20 43.89 2.92
4073 4614 0.251608 TGAGGGTCGACCAGTGATCA 60.252 55.000 34.40 24.21 43.89 2.92
4074 4615 0.895530 GAGGGTCGACCAGTGATCAA 59.104 55.000 34.40 0.00 43.89 2.57
4075 4616 1.482593 GAGGGTCGACCAGTGATCAAT 59.517 52.381 34.40 9.25 43.89 2.57
4076 4617 1.482593 AGGGTCGACCAGTGATCAATC 59.517 52.381 34.40 13.91 43.89 2.67
4077 4618 1.207089 GGGTCGACCAGTGATCAATCA 59.793 52.381 34.40 0.00 39.85 2.57
4078 4619 2.544685 GGTCGACCAGTGATCAATCAG 58.455 52.381 29.75 0.00 35.02 2.90
4079 4620 2.093973 GGTCGACCAGTGATCAATCAGT 60.094 50.000 29.75 0.00 40.95 3.41
4080 4621 3.182967 GTCGACCAGTGATCAATCAGTC 58.817 50.000 3.51 11.16 38.35 3.51
4081 4622 2.825532 TCGACCAGTGATCAATCAGTCA 59.174 45.455 18.01 7.06 38.35 3.41
4082 4623 2.926200 CGACCAGTGATCAATCAGTCAC 59.074 50.000 18.01 0.00 43.85 3.67
4083 4624 3.265791 GACCAGTGATCAATCAGTCACC 58.734 50.000 14.76 0.00 44.43 4.02
4084 4625 2.909006 ACCAGTGATCAATCAGTCACCT 59.091 45.455 0.00 0.00 44.43 4.00
4085 4626 3.328931 ACCAGTGATCAATCAGTCACCTT 59.671 43.478 0.00 0.00 44.43 3.50
4086 4627 3.688185 CCAGTGATCAATCAGTCACCTTG 59.312 47.826 0.00 0.00 44.43 3.61
4087 4628 4.321718 CAGTGATCAATCAGTCACCTTGT 58.678 43.478 0.00 0.00 44.43 3.16
4421 4988 1.962144 CCGACCACAGTTCGGTAGT 59.038 57.895 5.61 0.00 41.62 2.73
4670 5237 7.889873 TCTGGTTGGAAGTCTTGAATTTTTA 57.110 32.000 0.00 0.00 0.00 1.52
4693 5280 0.531090 TTTCCGGTTGGTGAGTCGTG 60.531 55.000 0.00 0.00 36.30 4.35
4738 5325 1.201424 AGCTACCGGTTTAGGGGAAG 58.799 55.000 15.04 1.50 35.02 3.46
4801 5388 5.163550 GGCAGTTTTACTGTCCAAGAAAAGT 60.164 40.000 8.46 0.00 44.65 2.66
4906 5494 2.142357 CTCACTCGCCTGACGGAACA 62.142 60.000 0.00 0.00 43.89 3.18
4945 5533 5.356190 GGAACTGATGTGATGAATGATGTGT 59.644 40.000 0.00 0.00 0.00 3.72
4959 5547 3.081061 TGATGTGTATCCACCTGCAAAC 58.919 45.455 0.00 0.00 41.09 2.93
5042 5630 2.244946 GACACCTTGTCCCTTTCGC 58.755 57.895 0.00 0.00 41.37 4.70
5043 5631 1.566018 GACACCTTGTCCCTTTCGCG 61.566 60.000 0.00 0.00 41.37 5.87
5044 5632 1.597027 CACCTTGTCCCTTTCGCGT 60.597 57.895 5.77 0.00 0.00 6.01
5045 5633 1.147600 ACCTTGTCCCTTTCGCGTT 59.852 52.632 5.77 0.00 0.00 4.84
5046 5634 0.464916 ACCTTGTCCCTTTCGCGTTT 60.465 50.000 5.77 0.00 0.00 3.60
5047 5635 0.666374 CCTTGTCCCTTTCGCGTTTT 59.334 50.000 5.77 0.00 0.00 2.43
5048 5636 1.066454 CCTTGTCCCTTTCGCGTTTTT 59.934 47.619 5.77 0.00 0.00 1.94
5069 5657 5.669164 TTTTAGGTGCCTTGTTGTTTTCT 57.331 34.783 0.00 0.00 0.00 2.52
5070 5658 5.669164 TTTAGGTGCCTTGTTGTTTTCTT 57.331 34.783 0.00 0.00 0.00 2.52
5071 5659 3.801114 AGGTGCCTTGTTGTTTTCTTC 57.199 42.857 0.00 0.00 0.00 2.87
5072 5660 3.365472 AGGTGCCTTGTTGTTTTCTTCT 58.635 40.909 0.00 0.00 0.00 2.85
5073 5661 3.381590 AGGTGCCTTGTTGTTTTCTTCTC 59.618 43.478 0.00 0.00 0.00 2.87
5074 5662 3.381590 GGTGCCTTGTTGTTTTCTTCTCT 59.618 43.478 0.00 0.00 0.00 3.10
5075 5663 4.498177 GGTGCCTTGTTGTTTTCTTCTCTC 60.498 45.833 0.00 0.00 0.00 3.20
5076 5664 4.336713 GTGCCTTGTTGTTTTCTTCTCTCT 59.663 41.667 0.00 0.00 0.00 3.10
5077 5665 4.949856 TGCCTTGTTGTTTTCTTCTCTCTT 59.050 37.500 0.00 0.00 0.00 2.85
5078 5666 5.418840 TGCCTTGTTGTTTTCTTCTCTCTTT 59.581 36.000 0.00 0.00 0.00 2.52
5079 5667 6.071391 TGCCTTGTTGTTTTCTTCTCTCTTTT 60.071 34.615 0.00 0.00 0.00 2.27
5080 5668 6.813649 GCCTTGTTGTTTTCTTCTCTCTTTTT 59.186 34.615 0.00 0.00 0.00 1.94
5105 5693 7.739498 TTTCCCTGAGAAAACTGTGTTATAC 57.261 36.000 0.00 0.00 41.56 1.47
5106 5694 6.681729 TCCCTGAGAAAACTGTGTTATACT 57.318 37.500 0.00 0.00 0.00 2.12
5107 5695 6.464222 TCCCTGAGAAAACTGTGTTATACTG 58.536 40.000 0.00 0.00 0.00 2.74
5108 5696 6.042781 TCCCTGAGAAAACTGTGTTATACTGT 59.957 38.462 0.00 0.00 42.45 3.55
5109 5697 7.233962 TCCCTGAGAAAACTGTGTTATACTGTA 59.766 37.037 0.00 0.00 40.12 2.74
5110 5698 7.331193 CCCTGAGAAAACTGTGTTATACTGTAC 59.669 40.741 0.00 0.00 40.12 2.90
5111 5699 8.088981 CCTGAGAAAACTGTGTTATACTGTACT 58.911 37.037 0.00 0.00 40.12 2.73
5113 5701 9.903682 TGAGAAAACTGTGTTATACTGTACTAC 57.096 33.333 0.00 0.00 40.12 2.73
5127 5715 8.725405 ATACTGTACTACTAGATCATCGATGG 57.275 38.462 24.61 10.96 0.00 3.51
5128 5716 5.413213 ACTGTACTACTAGATCATCGATGGC 59.587 44.000 24.61 16.65 0.00 4.40
5129 5717 4.392138 TGTACTACTAGATCATCGATGGCG 59.608 45.833 24.61 11.16 39.35 5.69
5130 5718 2.162608 ACTACTAGATCATCGATGGCGC 59.837 50.000 24.61 13.96 37.46 6.53
5131 5719 0.109551 ACTAGATCATCGATGGCGCG 60.110 55.000 24.61 0.00 37.46 6.86
5132 5720 1.409227 CTAGATCATCGATGGCGCGC 61.409 60.000 25.94 25.94 37.46 6.86
5133 5721 4.126390 GATCATCGATGGCGCGCG 62.126 66.667 28.44 28.44 37.46 6.86
5134 5722 4.950062 ATCATCGATGGCGCGCGT 62.950 61.111 32.35 16.88 37.46 6.01
5136 5724 4.925307 CATCGATGGCGCGCGTTG 62.925 66.667 32.35 19.55 37.46 4.10
5150 5738 2.511600 GTTGCTGCGCCCGTCTAT 60.512 61.111 4.18 0.00 0.00 1.98
5151 5739 2.106683 GTTGCTGCGCCCGTCTATT 61.107 57.895 4.18 0.00 0.00 1.73
5152 5740 1.376683 TTGCTGCGCCCGTCTATTT 60.377 52.632 4.18 0.00 0.00 1.40
5153 5741 0.958382 TTGCTGCGCCCGTCTATTTT 60.958 50.000 4.18 0.00 0.00 1.82
5154 5742 0.958382 TGCTGCGCCCGTCTATTTTT 60.958 50.000 4.18 0.00 0.00 1.94
5155 5743 0.248094 GCTGCGCCCGTCTATTTTTC 60.248 55.000 4.18 0.00 0.00 2.29
5156 5744 0.026285 CTGCGCCCGTCTATTTTTCG 59.974 55.000 4.18 0.00 0.00 3.46
5157 5745 0.671163 TGCGCCCGTCTATTTTTCGT 60.671 50.000 4.18 0.00 0.00 3.85
5158 5746 0.445043 GCGCCCGTCTATTTTTCGTT 59.555 50.000 0.00 0.00 0.00 3.85
5159 5747 1.789054 GCGCCCGTCTATTTTTCGTTG 60.789 52.381 0.00 0.00 0.00 4.10
5160 5748 1.727880 CGCCCGTCTATTTTTCGTTGA 59.272 47.619 0.00 0.00 0.00 3.18
5161 5749 2.158058 CGCCCGTCTATTTTTCGTTGAA 59.842 45.455 0.00 0.00 0.00 2.69
5162 5750 3.364167 CGCCCGTCTATTTTTCGTTGAAA 60.364 43.478 0.00 0.00 0.00 2.69
5163 5751 4.670735 CGCCCGTCTATTTTTCGTTGAAAT 60.671 41.667 0.00 0.00 31.34 2.17
5164 5752 4.557301 GCCCGTCTATTTTTCGTTGAAATG 59.443 41.667 0.00 0.00 31.34 2.32
5165 5753 5.618195 GCCCGTCTATTTTTCGTTGAAATGA 60.618 40.000 0.00 0.00 31.34 2.57
5166 5754 6.551736 CCCGTCTATTTTTCGTTGAAATGAT 58.448 36.000 0.00 0.00 31.34 2.45
5167 5755 7.677747 GCCCGTCTATTTTTCGTTGAAATGATA 60.678 37.037 0.00 0.00 31.34 2.15
5168 5756 7.850982 CCCGTCTATTTTTCGTTGAAATGATAG 59.149 37.037 12.37 12.37 33.87 2.08
5169 5757 7.850982 CCGTCTATTTTTCGTTGAAATGATAGG 59.149 37.037 15.55 7.30 33.66 2.57
5170 5758 8.600625 CGTCTATTTTTCGTTGAAATGATAGGA 58.399 33.333 15.55 6.97 33.66 2.94
5176 5764 8.560355 TTTTCGTTGAAATGATAGGAATCTCA 57.440 30.769 0.00 0.00 31.34 3.27
5177 5765 8.737168 TTTCGTTGAAATGATAGGAATCTCAT 57.263 30.769 0.00 0.00 33.59 2.90
5178 5766 9.830975 TTTCGTTGAAATGATAGGAATCTCATA 57.169 29.630 0.00 0.00 31.95 2.15
5179 5767 9.830975 TTCGTTGAAATGATAGGAATCTCATAA 57.169 29.630 0.00 0.00 31.95 1.90
5180 5768 9.830975 TCGTTGAAATGATAGGAATCTCATAAA 57.169 29.630 0.00 0.00 31.95 1.40
5273 5861 9.799106 ATTCTTATGCTAATGTATTAGGCAGTT 57.201 29.630 12.23 2.50 40.01 3.16
5274 5862 8.607441 TCTTATGCTAATGTATTAGGCAGTTG 57.393 34.615 12.23 6.36 40.01 3.16
5275 5863 8.210946 TCTTATGCTAATGTATTAGGCAGTTGT 58.789 33.333 12.23 1.74 40.01 3.32
5276 5864 6.624352 ATGCTAATGTATTAGGCAGTTGTG 57.376 37.500 12.23 0.00 40.01 3.33
5277 5865 5.739959 TGCTAATGTATTAGGCAGTTGTGA 58.260 37.500 12.23 0.00 40.01 3.58
5278 5866 5.584649 TGCTAATGTATTAGGCAGTTGTGAC 59.415 40.000 12.23 0.00 40.01 3.67
5279 5867 5.584649 GCTAATGTATTAGGCAGTTGTGACA 59.415 40.000 12.23 0.00 40.01 3.58
5280 5868 6.093495 GCTAATGTATTAGGCAGTTGTGACAA 59.907 38.462 12.23 0.00 40.01 3.18
5281 5869 5.880054 ATGTATTAGGCAGTTGTGACAAC 57.120 39.130 20.12 20.12 31.79 3.32
5282 5870 4.968259 TGTATTAGGCAGTTGTGACAACT 58.032 39.130 24.14 24.14 31.79 3.16
5295 5883 7.896811 AGTTGTGACAACTGATAGTATTCTCA 58.103 34.615 28.27 0.00 0.00 3.27
5296 5884 8.535335 AGTTGTGACAACTGATAGTATTCTCAT 58.465 33.333 28.27 0.16 0.00 2.90
5297 5885 9.803315 GTTGTGACAACTGATAGTATTCTCATA 57.197 33.333 20.39 0.00 0.00 2.15
5299 5887 9.408648 TGTGACAACTGATAGTATTCTCATAGA 57.591 33.333 0.00 0.00 0.00 1.98
5300 5888 9.672086 GTGACAACTGATAGTATTCTCATAGAC 57.328 37.037 0.00 0.00 0.00 2.59
5301 5889 9.408648 TGACAACTGATAGTATTCTCATAGACA 57.591 33.333 0.00 0.00 0.00 3.41
5302 5890 9.891828 GACAACTGATAGTATTCTCATAGACAG 57.108 37.037 0.00 0.00 0.00 3.51
5303 5891 9.415008 ACAACTGATAGTATTCTCATAGACAGT 57.585 33.333 0.00 0.00 36.63 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.683917 ACATGGTATCAGAGCCGTCTC 59.316 52.381 0.00 0.00 39.65 3.36
10 11 1.781786 ACATGGTATCAGAGCCGTCT 58.218 50.000 0.00 0.00 0.00 4.18
11 12 3.728076 TTACATGGTATCAGAGCCGTC 57.272 47.619 0.00 0.00 0.00 4.79
12 13 4.442706 CTTTTACATGGTATCAGAGCCGT 58.557 43.478 0.00 0.00 0.00 5.68
13 14 3.809832 CCTTTTACATGGTATCAGAGCCG 59.190 47.826 0.00 0.00 0.00 5.52
14 15 5.036117 TCCTTTTACATGGTATCAGAGCC 57.964 43.478 0.00 0.00 0.00 4.70
15 16 8.150945 TCTATTCCTTTTACATGGTATCAGAGC 58.849 37.037 0.00 0.00 0.00 4.09
16 17 9.703892 CTCTATTCCTTTTACATGGTATCAGAG 57.296 37.037 0.00 0.00 0.00 3.35
17 18 9.434275 TCTCTATTCCTTTTACATGGTATCAGA 57.566 33.333 0.00 0.00 0.00 3.27
18 19 9.703892 CTCTCTATTCCTTTTACATGGTATCAG 57.296 37.037 0.00 0.00 0.00 2.90
19 20 9.434275 TCTCTCTATTCCTTTTACATGGTATCA 57.566 33.333 0.00 0.00 0.00 2.15
59 60 4.202441 CCTACAAGGCTCAAGCAATACAT 58.798 43.478 4.13 0.00 44.36 2.29
60 61 3.609853 CCTACAAGGCTCAAGCAATACA 58.390 45.455 4.13 0.00 44.36 2.29
233 245 7.005296 TGTTTGCAGTTTACTATCCCCTTTTA 58.995 34.615 0.00 0.00 0.00 1.52
245 257 7.593273 TGCAGTGTTATATTGTTTGCAGTTTAC 59.407 33.333 0.00 0.00 35.41 2.01
284 296 9.027202 AGAGGGCTTTCGGTTTAATAATTTTTA 57.973 29.630 0.00 0.00 0.00 1.52
291 303 4.266714 CCAAGAGGGCTTTCGGTTTAATA 58.733 43.478 0.00 0.00 30.14 0.98
292 304 3.089284 CCAAGAGGGCTTTCGGTTTAAT 58.911 45.455 0.00 0.00 30.14 1.40
358 573 3.059982 CTGGCTTGTCGGTCTCCA 58.940 61.111 0.00 0.00 0.00 3.86
372 587 2.726912 CGTGCGTTTTGCTGCTGG 60.727 61.111 0.00 0.00 46.63 4.85
444 672 0.707024 TTAATGACATGTGGGCCCCA 59.293 50.000 22.27 17.75 0.00 4.96
545 773 2.742372 CGTTGGCCGTGGAAGGAG 60.742 66.667 0.00 0.00 0.00 3.69
589 817 0.912486 GCTGGTGTATGGGAAGAGGT 59.088 55.000 0.00 0.00 0.00 3.85
593 821 0.911769 TGAGGCTGGTGTATGGGAAG 59.088 55.000 0.00 0.00 0.00 3.46
606 834 1.196766 TGTCTCTGGTGCATGAGGCT 61.197 55.000 16.07 0.00 45.15 4.58
774 1007 1.554042 CGGTTGATACGGCGTATGGC 61.554 60.000 34.60 21.87 42.51 4.40
778 1011 1.516821 GCACGGTTGATACGGCGTA 60.517 57.895 23.25 23.25 35.23 4.42
819 1052 0.682292 TGCATGAACTGGACGGTACA 59.318 50.000 0.00 0.00 0.00 2.90
821 1054 0.036765 GGTGCATGAACTGGACGGTA 60.037 55.000 3.21 0.00 46.43 4.02
822 1055 1.302511 GGTGCATGAACTGGACGGT 60.303 57.895 3.21 0.00 46.43 4.83
823 1056 2.390599 CGGTGCATGAACTGGACGG 61.391 63.158 4.50 0.00 46.43 4.79
825 1058 0.884704 ACACGGTGCATGAACTGGAC 60.885 55.000 17.35 0.00 44.87 4.02
828 1061 0.884259 TGGACACGGTGCATGAACTG 60.884 55.000 11.45 11.45 0.00 3.16
881 1115 3.467803 GCTGGTACAAGAGTCAAAGTGT 58.532 45.455 0.00 0.00 38.70 3.55
1284 1713 1.117749 AGAGGCTCCTCATATGCGCA 61.118 55.000 14.96 14.96 44.99 6.09
1359 1788 1.835693 GCTCCTCTTATGCCCAGCT 59.164 57.895 0.00 0.00 0.00 4.24
1578 2008 4.625607 AGAACTAGCAGCAAACTACCTT 57.374 40.909 0.00 0.00 0.00 3.50
1579 2009 4.773149 ACTAGAACTAGCAGCAAACTACCT 59.227 41.667 8.54 0.00 36.66 3.08
1898 2328 0.248743 CATGCTGCCATACTTTGCGG 60.249 55.000 0.00 0.00 36.92 5.69
2022 2452 5.530915 TCCATATTAGTGTTACCAATGCAGC 59.469 40.000 0.00 0.00 0.00 5.25
2039 2469 7.349598 AGCTTTGAATTAGTCAGGTCCATATT 58.650 34.615 0.00 0.00 37.61 1.28
2040 2470 6.904626 AGCTTTGAATTAGTCAGGTCCATAT 58.095 36.000 0.00 0.00 37.61 1.78
2045 2475 4.670221 CGCAAGCTTTGAATTAGTCAGGTC 60.670 45.833 0.00 0.00 37.61 3.85
2169 2632 9.507329 AATGTCAACAACTGTAGTAATGAGAAT 57.493 29.630 0.00 0.00 0.00 2.40
2420 2884 3.895041 CAACTAAGTGGTGGGGTCAAAAT 59.105 43.478 0.00 0.00 0.00 1.82
2454 2918 9.241919 TCAATTATCAAAAGCTCTACCAATTCA 57.758 29.630 0.00 0.00 0.00 2.57
2499 2969 5.760253 AGTTAAACTCATTAGGATCATGCCG 59.240 40.000 0.00 0.00 0.00 5.69
2583 3053 2.235898 GTGAGTCCTCAGGAAGCAGAAT 59.764 50.000 0.00 0.00 40.75 2.40
2744 3217 9.921637 ATAGACTGATAAGTTTATAGCTTCAGC 57.078 33.333 6.25 0.00 42.49 4.26
2760 3233 9.778741 AACAAGTTTTCTTCACATAGACTGATA 57.221 29.630 0.00 0.00 38.17 2.15
2774 3247 5.914898 AACCTAGTGCAACAAGTTTTCTT 57.085 34.783 0.00 0.00 41.43 2.52
2811 3284 7.721286 TCGATTGCCATAAAAACAACAAATT 57.279 28.000 0.00 0.00 0.00 1.82
2847 3321 6.926313 ACAGGTAGAGAAGTACTTGATTCAC 58.074 40.000 14.14 4.34 34.46 3.18
2965 3440 5.574188 AGCTTGAGACACTTATTTTGGGAT 58.426 37.500 0.00 0.00 0.00 3.85
2995 3470 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2996 3471 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2998 3473 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3000 3475 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3001 3476 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3002 3477 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3003 3478 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3012 3487 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
3013 3488 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
3014 3489 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
3016 3491 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
3017 3492 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
3034 3509 7.320443 ACGTTTAGTGTTAGATACATCCGTA 57.680 36.000 0.00 0.00 39.39 4.02
3035 3510 6.199937 ACGTTTAGTGTTAGATACATCCGT 57.800 37.500 0.00 0.00 39.39 4.69
3036 3511 7.912250 AGTTACGTTTAGTGTTAGATACATCCG 59.088 37.037 0.00 0.00 39.39 4.18
3043 3518 9.231297 TGTACCTAGTTACGTTTAGTGTTAGAT 57.769 33.333 0.00 0.00 0.00 1.98
3044 3519 8.615878 TGTACCTAGTTACGTTTAGTGTTAGA 57.384 34.615 0.00 0.00 0.00 2.10
3045 3520 9.495754 GATGTACCTAGTTACGTTTAGTGTTAG 57.504 37.037 0.00 0.00 0.00 2.34
3046 3521 8.458843 GGATGTACCTAGTTACGTTTAGTGTTA 58.541 37.037 0.00 0.00 35.41 2.41
3047 3522 7.315890 GGATGTACCTAGTTACGTTTAGTGTT 58.684 38.462 0.00 0.00 35.41 3.32
3048 3523 6.403636 CGGATGTACCTAGTTACGTTTAGTGT 60.404 42.308 0.00 0.00 36.31 3.55
3049 3524 5.967674 CGGATGTACCTAGTTACGTTTAGTG 59.032 44.000 0.00 0.00 36.31 2.74
3050 3525 5.648092 ACGGATGTACCTAGTTACGTTTAGT 59.352 40.000 0.00 0.00 36.31 2.24
3051 3526 6.124088 ACGGATGTACCTAGTTACGTTTAG 57.876 41.667 0.00 0.00 36.31 1.85
3052 3527 7.801716 ATACGGATGTACCTAGTTACGTTTA 57.198 36.000 0.00 0.00 36.31 2.01
3054 3529 6.699575 AATACGGATGTACCTAGTTACGTT 57.300 37.500 0.00 0.00 36.31 3.99
3055 3530 6.699575 AAATACGGATGTACCTAGTTACGT 57.300 37.500 0.00 0.00 36.31 3.57
3056 3531 8.012241 GTCTAAATACGGATGTACCTAGTTACG 58.988 40.741 0.00 0.00 36.31 3.18
3057 3532 8.840321 TGTCTAAATACGGATGTACCTAGTTAC 58.160 37.037 0.00 0.00 36.31 2.50
3058 3533 8.978874 TGTCTAAATACGGATGTACCTAGTTA 57.021 34.615 0.00 0.00 36.31 2.24
3059 3534 7.886629 TGTCTAAATACGGATGTACCTAGTT 57.113 36.000 0.00 0.00 36.31 2.24
3060 3535 7.886629 TTGTCTAAATACGGATGTACCTAGT 57.113 36.000 0.00 0.00 36.31 2.57
3061 3536 9.408069 GATTTGTCTAAATACGGATGTACCTAG 57.592 37.037 0.00 0.00 36.66 3.02
3062 3537 9.139734 AGATTTGTCTAAATACGGATGTACCTA 57.860 33.333 0.00 0.00 36.66 3.08
3064 3539 9.754382 TTAGATTTGTCTAAATACGGATGTACC 57.246 33.333 0.00 0.00 36.66 3.34
3067 3542 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
3068 3543 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
3070 3545 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
3071 3546 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
3079 3554 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3080 3555 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3083 3558 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3084 3559 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3085 3560 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3086 3561 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3087 3562 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3088 3563 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3089 3564 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3090 3565 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3092 3567 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3093 3568 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3094 3569 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3095 3570 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3096 3571 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3108 3607 5.036117 TGCTCATGTAATTTACTCCCTCC 57.964 43.478 7.99 0.00 0.00 4.30
3218 3717 8.837788 CTCCAGAGCATTCATTTATATGTACA 57.162 34.615 0.00 0.00 33.34 2.90
3291 3790 4.147449 CTCCTGCCATCGCGGACA 62.147 66.667 6.13 0.00 44.91 4.02
3296 3795 1.522580 GTTCCTCTCCTGCCATCGC 60.523 63.158 0.00 0.00 0.00 4.58
3300 3799 2.237143 CACATTAGTTCCTCTCCTGCCA 59.763 50.000 0.00 0.00 0.00 4.92
3339 3838 5.860182 CGCAAGCATATAATTAAAGCAGCAT 59.140 36.000 16.64 0.00 0.00 3.79
3347 3846 7.679400 GCATAGCATCCGCAAGCATATAATTAA 60.679 37.037 0.00 0.00 42.27 1.40
3356 3855 2.536673 CGCATAGCATCCGCAAGCA 61.537 57.895 0.00 0.00 42.27 3.91
3364 3863 1.212616 GACAGTGTCCGCATAGCATC 58.787 55.000 12.54 0.00 0.00 3.91
3404 3903 3.258372 GTCACATCAACTACAGGACCAGA 59.742 47.826 0.00 0.00 0.00 3.86
3432 3931 4.379652 ACTTTTGGGTGCAACAAATCATC 58.620 39.130 15.88 0.00 39.98 2.92
3637 4136 0.961019 GATGTTCAGCACTGGCCAAA 59.039 50.000 7.01 0.00 42.56 3.28
3640 4139 2.113860 TAAGATGTTCAGCACTGGCC 57.886 50.000 0.00 0.00 42.56 5.36
3681 4180 8.241367 GGTCTTAATAAATCTTTTTCGCTTCCA 58.759 33.333 0.00 0.00 0.00 3.53
3733 4232 7.652507 ACAAAGTTCACTAGCTCTACTACAAAC 59.347 37.037 0.00 0.00 0.00 2.93
3805 4304 8.055279 ACAAAATATTGGTTATCACAGTCCTG 57.945 34.615 0.00 0.00 41.01 3.86
3806 4305 8.522830 CAACAAAATATTGGTTATCACAGTCCT 58.477 33.333 5.68 0.00 41.01 3.85
3807 4306 7.275560 GCAACAAAATATTGGTTATCACAGTCC 59.724 37.037 5.68 0.00 41.01 3.85
3957 4498 4.862641 AACAAGACTAGGGCATACCATT 57.137 40.909 0.00 0.00 43.89 3.16
3966 4507 5.748592 CAAACTTCGAAAACAAGACTAGGG 58.251 41.667 0.00 0.00 0.00 3.53
4024 4565 2.698855 ATGTTCAGGGAAGACGATGG 57.301 50.000 0.00 0.00 0.00 3.51
4029 4570 4.079253 TGCCTTAAATGTTCAGGGAAGAC 58.921 43.478 0.00 0.00 0.00 3.01
4031 4572 4.952335 AGATGCCTTAAATGTTCAGGGAAG 59.048 41.667 0.00 0.00 30.91 3.46
4036 4577 4.337555 CCCTCAGATGCCTTAAATGTTCAG 59.662 45.833 0.00 0.00 0.00 3.02
4062 4603 3.055530 AGGTGACTGATTGATCACTGGTC 60.056 47.826 0.00 2.80 43.91 4.02
4063 4604 2.909006 AGGTGACTGATTGATCACTGGT 59.091 45.455 0.00 0.00 43.91 4.00
4064 4605 3.623906 AGGTGACTGATTGATCACTGG 57.376 47.619 0.00 0.00 43.91 4.00
4065 4606 4.153655 CACAAGGTGACTGATTGATCACTG 59.846 45.833 0.00 0.00 43.91 3.66
4066 4607 4.040829 TCACAAGGTGACTGATTGATCACT 59.959 41.667 0.00 0.00 43.91 3.41
4067 4608 4.318332 TCACAAGGTGACTGATTGATCAC 58.682 43.478 0.00 0.00 42.68 3.06
4068 4609 4.622260 TCACAAGGTGACTGATTGATCA 57.378 40.909 0.00 0.00 42.68 2.92
4079 4620 3.582647 ACAGATACATGGTCACAAGGTGA 59.417 43.478 0.00 0.00 40.50 4.02
4080 4621 3.942829 ACAGATACATGGTCACAAGGTG 58.057 45.455 0.00 0.00 34.45 4.00
4081 4622 4.565652 GGAACAGATACATGGTCACAAGGT 60.566 45.833 0.00 0.00 38.73 3.50
4082 4623 3.941483 GGAACAGATACATGGTCACAAGG 59.059 47.826 0.00 0.00 38.73 3.61
4083 4624 3.618594 CGGAACAGATACATGGTCACAAG 59.381 47.826 0.00 0.00 38.73 3.16
4084 4625 3.007506 ACGGAACAGATACATGGTCACAA 59.992 43.478 0.00 0.00 38.73 3.33
4085 4626 2.565391 ACGGAACAGATACATGGTCACA 59.435 45.455 0.00 0.00 38.73 3.58
4086 4627 2.930040 CACGGAACAGATACATGGTCAC 59.070 50.000 0.00 0.00 38.73 3.67
4087 4628 2.676750 GCACGGAACAGATACATGGTCA 60.677 50.000 0.00 0.00 38.73 4.02
4670 5237 0.476771 ACTCACCAACCGGAAACCAT 59.523 50.000 9.46 0.00 35.59 3.55
4693 5280 0.878416 TTTGTATGCACCGCCAGTTC 59.122 50.000 0.00 0.00 0.00 3.01
4738 5325 2.547826 GGCAGTCAAATCTACCGGTAC 58.452 52.381 11.16 0.99 0.00 3.34
4801 5388 7.385267 ACAAAGCCAGTTGAATTTTGCATATA 58.615 30.769 0.00 0.00 33.28 0.86
4906 5494 3.517901 TCAGTTCCCGACATATGGTCTTT 59.482 43.478 7.80 0.00 44.68 2.52
4945 5533 3.719268 ACAGATGTTTGCAGGTGGATA 57.281 42.857 0.00 0.00 0.00 2.59
4959 5547 1.000843 TGGACACTGGACGAACAGATG 59.999 52.381 15.85 12.37 40.97 2.90
5009 5597 1.338200 GGTGTCTCCAGGCAGTGTTAG 60.338 57.143 0.00 0.00 35.97 2.34
5046 5634 6.043854 AGAAAACAACAAGGCACCTAAAAA 57.956 33.333 0.00 0.00 0.00 1.94
5047 5635 5.669164 AGAAAACAACAAGGCACCTAAAA 57.331 34.783 0.00 0.00 0.00 1.52
5048 5636 5.420739 AGAAGAAAACAACAAGGCACCTAAA 59.579 36.000 0.00 0.00 0.00 1.85
5049 5637 4.953579 AGAAGAAAACAACAAGGCACCTAA 59.046 37.500 0.00 0.00 0.00 2.69
5050 5638 4.532834 AGAAGAAAACAACAAGGCACCTA 58.467 39.130 0.00 0.00 0.00 3.08
5051 5639 3.365472 AGAAGAAAACAACAAGGCACCT 58.635 40.909 0.00 0.00 0.00 4.00
5052 5640 3.381590 AGAGAAGAAAACAACAAGGCACC 59.618 43.478 0.00 0.00 0.00 5.01
5053 5641 4.336713 AGAGAGAAGAAAACAACAAGGCAC 59.663 41.667 0.00 0.00 0.00 5.01
5054 5642 4.526970 AGAGAGAAGAAAACAACAAGGCA 58.473 39.130 0.00 0.00 0.00 4.75
5055 5643 5.506686 AAGAGAGAAGAAAACAACAAGGC 57.493 39.130 0.00 0.00 0.00 4.35
5081 5669 7.444183 CAGTATAACACAGTTTTCTCAGGGAAA 59.556 37.037 0.00 0.00 41.58 3.13
5082 5670 6.934645 CAGTATAACACAGTTTTCTCAGGGAA 59.065 38.462 0.00 0.00 0.00 3.97
5083 5671 6.042781 ACAGTATAACACAGTTTTCTCAGGGA 59.957 38.462 0.00 0.00 0.00 4.20
5084 5672 6.231211 ACAGTATAACACAGTTTTCTCAGGG 58.769 40.000 0.00 0.00 0.00 4.45
5085 5673 8.088981 AGTACAGTATAACACAGTTTTCTCAGG 58.911 37.037 0.00 0.00 0.00 3.86
5087 5675 9.903682 GTAGTACAGTATAACACAGTTTTCTCA 57.096 33.333 0.00 0.00 0.00 3.27
5101 5689 9.819267 CCATCGATGATCTAGTAGTACAGTATA 57.181 37.037 26.86 0.00 0.00 1.47
5102 5690 7.281324 GCCATCGATGATCTAGTAGTACAGTAT 59.719 40.741 26.86 0.00 0.00 2.12
5103 5691 6.594547 GCCATCGATGATCTAGTAGTACAGTA 59.405 42.308 26.86 0.00 0.00 2.74
5104 5692 5.413213 GCCATCGATGATCTAGTAGTACAGT 59.587 44.000 26.86 0.00 0.00 3.55
5105 5693 5.446607 CGCCATCGATGATCTAGTAGTACAG 60.447 48.000 26.86 5.63 38.10 2.74
5106 5694 4.392138 CGCCATCGATGATCTAGTAGTACA 59.608 45.833 26.86 0.00 38.10 2.90
5107 5695 4.728307 GCGCCATCGATGATCTAGTAGTAC 60.728 50.000 26.86 0.00 38.10 2.73
5108 5696 3.374367 GCGCCATCGATGATCTAGTAGTA 59.626 47.826 26.86 0.00 38.10 1.82
5109 5697 2.162608 GCGCCATCGATGATCTAGTAGT 59.837 50.000 26.86 0.00 38.10 2.73
5110 5698 2.789436 CGCGCCATCGATGATCTAGTAG 60.789 54.545 26.86 8.24 38.10 2.57
5111 5699 1.130561 CGCGCCATCGATGATCTAGTA 59.869 52.381 26.86 0.00 38.10 1.82
5112 5700 0.109551 CGCGCCATCGATGATCTAGT 60.110 55.000 26.86 0.00 38.10 2.57
5113 5701 1.409227 GCGCGCCATCGATGATCTAG 61.409 60.000 26.86 13.84 38.10 2.43
5114 5702 1.444383 GCGCGCCATCGATGATCTA 60.444 57.895 26.86 0.00 38.10 1.98
5115 5703 2.736236 GCGCGCCATCGATGATCT 60.736 61.111 26.86 0.00 38.10 2.75
5116 5704 4.126390 CGCGCGCCATCGATGATC 62.126 66.667 27.72 15.86 38.10 2.92
5117 5705 4.950062 ACGCGCGCCATCGATGAT 62.950 61.111 32.58 2.28 38.10 2.45
5119 5707 4.925307 CAACGCGCGCCATCGATG 62.925 66.667 32.58 18.76 38.10 3.84
5137 5725 0.026285 CGAAAAATAGACGGGCGCAG 59.974 55.000 10.83 4.90 0.00 5.18
5138 5726 0.671163 ACGAAAAATAGACGGGCGCA 60.671 50.000 10.83 0.00 0.00 6.09
5139 5727 0.445043 AACGAAAAATAGACGGGCGC 59.555 50.000 0.00 0.00 0.00 6.53
5140 5728 1.727880 TCAACGAAAAATAGACGGGCG 59.272 47.619 0.00 0.00 0.00 6.13
5141 5729 3.817148 TTCAACGAAAAATAGACGGGC 57.183 42.857 0.00 0.00 0.00 6.13
5142 5730 5.933790 TCATTTCAACGAAAAATAGACGGG 58.066 37.500 0.00 0.00 35.11 5.28
5143 5731 7.850982 CCTATCATTTCAACGAAAAATAGACGG 59.149 37.037 16.24 5.22 35.61 4.79
5144 5732 8.600625 TCCTATCATTTCAACGAAAAATAGACG 58.399 33.333 16.24 0.00 35.61 4.18
5150 5738 9.008965 TGAGATTCCTATCATTTCAACGAAAAA 57.991 29.630 0.00 0.00 35.11 1.94
5151 5739 8.560355 TGAGATTCCTATCATTTCAACGAAAA 57.440 30.769 0.00 0.00 35.11 2.29
5152 5740 8.737168 ATGAGATTCCTATCATTTCAACGAAA 57.263 30.769 0.00 0.00 32.20 3.46
5153 5741 9.830975 TTATGAGATTCCTATCATTTCAACGAA 57.169 29.630 0.00 0.00 37.36 3.85
5154 5742 9.830975 TTTATGAGATTCCTATCATTTCAACGA 57.169 29.630 0.00 0.00 37.36 3.85
5247 5835 9.799106 AACTGCCTAATACATTAGCATAAGAAT 57.201 29.630 3.82 0.00 38.69 2.40
5248 5836 9.056005 CAACTGCCTAATACATTAGCATAAGAA 57.944 33.333 3.82 0.00 38.69 2.52
5249 5837 8.210946 ACAACTGCCTAATACATTAGCATAAGA 58.789 33.333 3.82 0.00 38.69 2.10
5250 5838 8.285394 CACAACTGCCTAATACATTAGCATAAG 58.715 37.037 3.82 1.95 38.69 1.73
5251 5839 7.990314 TCACAACTGCCTAATACATTAGCATAA 59.010 33.333 3.82 0.00 38.69 1.90
5252 5840 7.441157 GTCACAACTGCCTAATACATTAGCATA 59.559 37.037 3.82 0.00 38.69 3.14
5253 5841 6.260936 GTCACAACTGCCTAATACATTAGCAT 59.739 38.462 3.82 0.00 38.69 3.79
5254 5842 5.584649 GTCACAACTGCCTAATACATTAGCA 59.415 40.000 3.82 5.20 38.69 3.49
5255 5843 5.584649 TGTCACAACTGCCTAATACATTAGC 59.415 40.000 3.82 1.47 38.69 3.09
5256 5844 7.334421 AGTTGTCACAACTGCCTAATACATTAG 59.666 37.037 22.72 2.53 39.50 1.73
5257 5845 7.119116 CAGTTGTCACAACTGCCTAATACATTA 59.881 37.037 32.42 0.00 40.80 1.90
5258 5846 6.003950 AGTTGTCACAACTGCCTAATACATT 58.996 36.000 22.72 0.00 0.00 2.71
5259 5847 5.412594 CAGTTGTCACAACTGCCTAATACAT 59.587 40.000 32.42 1.39 40.80 2.29
5260 5848 4.754618 CAGTTGTCACAACTGCCTAATACA 59.245 41.667 32.42 0.00 40.80 2.29
5261 5849 4.994852 TCAGTTGTCACAACTGCCTAATAC 59.005 41.667 36.30 3.38 45.34 1.89
5262 5850 5.222079 TCAGTTGTCACAACTGCCTAATA 57.778 39.130 36.30 20.95 45.34 0.98
5263 5851 4.085357 TCAGTTGTCACAACTGCCTAAT 57.915 40.909 36.30 8.06 45.34 1.73
5264 5852 3.552132 TCAGTTGTCACAACTGCCTAA 57.448 42.857 36.30 21.91 45.34 2.69
5265 5853 3.769739 ATCAGTTGTCACAACTGCCTA 57.230 42.857 36.30 24.40 45.34 3.93
5266 5854 2.645838 ATCAGTTGTCACAACTGCCT 57.354 45.000 36.30 25.74 45.34 4.75
5267 5855 3.403038 ACTATCAGTTGTCACAACTGCC 58.597 45.455 36.30 6.77 45.34 4.85
5268 5856 6.591834 AGAATACTATCAGTTGTCACAACTGC 59.408 38.462 36.30 23.19 45.34 4.40
5269 5857 7.814587 TGAGAATACTATCAGTTGTCACAACTG 59.185 37.037 35.68 35.68 46.67 3.16
5270 5858 7.896811 TGAGAATACTATCAGTTGTCACAACT 58.103 34.615 17.94 17.94 0.00 3.16
5271 5859 8.709386 ATGAGAATACTATCAGTTGTCACAAC 57.291 34.615 13.16 13.16 0.00 3.32
5273 5861 9.408648 TCTATGAGAATACTATCAGTTGTCACA 57.591 33.333 0.00 0.00 0.00 3.58
5274 5862 9.672086 GTCTATGAGAATACTATCAGTTGTCAC 57.328 37.037 0.00 0.00 0.00 3.67
5275 5863 9.408648 TGTCTATGAGAATACTATCAGTTGTCA 57.591 33.333 0.00 0.00 0.00 3.58
5276 5864 9.891828 CTGTCTATGAGAATACTATCAGTTGTC 57.108 37.037 0.00 0.00 0.00 3.18
5277 5865 9.415008 ACTGTCTATGAGAATACTATCAGTTGT 57.585 33.333 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.