Multiple sequence alignment - TraesCS5B01G007200

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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 TraesCS5B01G007200 chr5B 100.000 3898 0 0 1 3898 8350878 8354775 0.000000e+00 7199.0
1 TraesCS5B01G007200 chr5B 95.362 690 28 2 2323 3009 652936582 652935894 0.000000e+00 1094.0
2 TraesCS5B01G007200 chr5B 94.670 713 25 6 1616 2325 652947069 652946367 0.000000e+00 1094.0
3 TraesCS5B01G007200 chr5B 87.413 286 28 7 2994 3276 139340414 139340694 4.860000e-84 322.0
4 TraesCS5B01G007200 chr5B 75.218 803 129 46 777 1528 8188381 8187598 2.260000e-82 316.0
5 TraesCS5B01G007200 chr5B 86.111 288 33 4 2994 3276 360621578 360621293 1.760000e-78 303.0
6 TraesCS5B01G007200 chr5B 74.783 805 126 45 777 1528 32416941 32417721 1.370000e-74 291.0
7 TraesCS5B01G007200 chr5B 75.444 338 67 12 1157 1486 656468456 656468785 2.430000e-32 150.0
8 TraesCS5B01G007200 chr5B 98.077 52 1 0 1073 1124 652947122 652947071 1.490000e-14 91.6
9 TraesCS5B01G007200 chr5A 91.044 3037 150 47 1 2991 6421182 6424142 0.000000e+00 3989.0
10 TraesCS5B01G007200 chr5A 85.147 579 54 12 3324 3898 6424253 6424803 7.310000e-157 564.0
11 TraesCS5B01G007200 chr5A 76.696 339 61 14 1157 1486 649365206 649365535 5.180000e-39 172.0
12 TraesCS5B01G007200 chr5D 92.209 2503 133 28 512 2991 8032870 8035333 0.000000e+00 3485.0
13 TraesCS5B01G007200 chr5D 85.276 489 41 15 3411 3898 8035528 8035986 3.520000e-130 475.0
14 TraesCS5B01G007200 chr5D 79.747 553 97 13 969 1511 8020005 8020552 1.700000e-103 387.0
15 TraesCS5B01G007200 chr5D 77.948 653 105 23 897 1528 7966822 7966188 4.760000e-99 372.0
16 TraesCS5B01G007200 chr5D 76.696 339 61 16 1157 1486 520839477 520839806 5.180000e-39 172.0
17 TraesCS5B01G007200 chr5D 76.331 338 64 12 1157 1486 520805317 520805646 2.410000e-37 167.0
18 TraesCS5B01G007200 chr5D 94.118 68 3 1 3343 3409 8035425 8035492 6.890000e-18 102.0
19 TraesCS5B01G007200 chr6A 88.850 287 30 2 2994 3280 552741835 552742119 6.200000e-93 351.0
20 TraesCS5B01G007200 chr6A 89.377 273 26 2 3007 3277 555243249 555243520 1.340000e-89 340.0
21 TraesCS5B01G007200 chr1B 88.112 286 28 5 2994 3276 335975138 335974856 6.240000e-88 335.0
22 TraesCS5B01G007200 chr2B 86.972 284 33 3 2994 3276 232780046 232780326 2.260000e-82 316.0
23 TraesCS5B01G007200 chr2B 86.572 283 37 1 2994 3276 769267733 769267452 1.050000e-80 311.0
24 TraesCS5B01G007200 chr7B 86.760 287 33 4 2994 3276 448005395 448005110 8.130000e-82 315.0
25 TraesCS5B01G007200 chr4B 86.014 286 35 3 2994 3276 399269764 399269481 6.330000e-78 302.0
26 TraesCS5B01G007200 chr4A 79.612 206 38 4 1284 1487 108374182 108374385 1.130000e-30 145.0
27 TraesCS5B01G007200 chr4D 79.126 206 39 4 1284 1487 357527156 357526953 5.250000e-29 139.0


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 TraesCS5B01G007200 chr5B 8350878 8354775 3897 False 7199.0 7199 100.000000 1 3898 1 chr5B.!!$F1 3897
1 TraesCS5B01G007200 chr5B 652935894 652936582 688 True 1094.0 1094 95.362000 2323 3009 1 chr5B.!!$R3 686
2 TraesCS5B01G007200 chr5B 652946367 652947122 755 True 592.8 1094 96.373500 1073 2325 2 chr5B.!!$R4 1252
3 TraesCS5B01G007200 chr5B 8187598 8188381 783 True 316.0 316 75.218000 777 1528 1 chr5B.!!$R1 751
4 TraesCS5B01G007200 chr5B 32416941 32417721 780 False 291.0 291 74.783000 777 1528 1 chr5B.!!$F2 751
5 TraesCS5B01G007200 chr5A 6421182 6424803 3621 False 2276.5 3989 88.095500 1 3898 2 chr5A.!!$F2 3897
6 TraesCS5B01G007200 chr5D 8032870 8035986 3116 False 1354.0 3485 90.534333 512 3898 3 chr5D.!!$F4 3386
7 TraesCS5B01G007200 chr5D 8020005 8020552 547 False 387.0 387 79.747000 969 1511 1 chr5D.!!$F1 542
8 TraesCS5B01G007200 chr5D 7966188 7966822 634 True 372.0 372 77.948000 897 1528 1 chr5D.!!$R1 631

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
890 921 0.179234 TGGTGGAAAACTGCACGAGA 59.821 50.0 0.00 0.0 0.00 4.04 F
2612 2739 1.333636 CGTCTTGGGAGAGGCCAGAT 61.334 60.0 5.01 0.0 38.95 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2816 2943 0.106569 CAGCCATATCAACCCCTGCA 60.107 55.0 0.00 0.0 0.0 4.41 R
3847 4076 0.098200 GACCGCGCAAAATCCTTACC 59.902 55.0 8.75 0.0 0.0 2.85 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
69 70 6.681729 ATACTCCAGAGTTAACTTGGTGAA 57.318 37.500 27.21 17.93 42.54 3.18
70 71 5.367945 ACTCCAGAGTTAACTTGGTGAAA 57.632 39.130 27.21 14.71 38.83 2.69
205 207 1.944024 CAGGTCAACCGTGTAAGCAAA 59.056 47.619 0.00 0.00 42.08 3.68
206 208 2.356382 CAGGTCAACCGTGTAAGCAAAA 59.644 45.455 0.00 0.00 42.08 2.44
229 231 5.613358 AAGTCAAGAGGAAAAGCATTACG 57.387 39.130 0.00 0.00 0.00 3.18
232 234 5.179555 AGTCAAGAGGAAAAGCATTACGTTC 59.820 40.000 0.00 0.00 0.00 3.95
233 235 5.049680 GTCAAGAGGAAAAGCATTACGTTCA 60.050 40.000 0.00 0.00 0.00 3.18
260 262 3.257933 GCTTCACGCAACCCTCAG 58.742 61.111 0.00 0.00 38.92 3.35
348 350 6.839124 TGATACCCAATCAATATTCATGCC 57.161 37.500 0.00 0.00 41.75 4.40
359 361 8.846943 ATCAATATTCATGCCGTGTTTATAGA 57.153 30.769 0.00 0.00 0.00 1.98
369 371 5.009110 TGCCGTGTTTATAGAGAGAGATGAG 59.991 44.000 0.00 0.00 0.00 2.90
377 379 9.569122 GTTTATAGAGAGAGATGAGTAGGAACT 57.431 37.037 0.00 0.00 46.37 3.01
442 446 9.959749 TTAAACAGCAAAGAAGTAACCAATTAG 57.040 29.630 0.00 0.00 0.00 1.73
604 608 5.008911 TGTTGGAATGTCATTCACAACTCAG 59.991 40.000 32.36 0.00 43.27 3.35
623 628 2.034179 CAGTGTGAAGTAGTCGTGGTCA 59.966 50.000 0.00 0.00 0.00 4.02
689 694 9.678941 CGTAGAAACATGCAGAGAGTATTATAA 57.321 33.333 0.00 0.00 0.00 0.98
755 760 7.350382 TGGCTTATTGGATGGTCAATAACTTA 58.650 34.615 6.08 0.00 41.73 2.24
769 774 7.360017 GGTCAATAACTTATTTGGCTTTGCAAC 60.360 37.037 0.00 0.00 0.00 4.17
790 802 1.223187 CACGTACGGAAAAGCAAGGT 58.777 50.000 21.06 0.00 0.00 3.50
797 809 1.606668 CGGAAAAGCAAGGTAAGTGCA 59.393 47.619 0.00 0.00 44.74 4.57
890 921 0.179234 TGGTGGAAAACTGCACGAGA 59.821 50.000 0.00 0.00 0.00 4.04
964 1026 2.827921 GAGTAGGACGTAGGAACCCAAA 59.172 50.000 0.00 0.00 0.00 3.28
1407 1512 2.029073 ATCATTCGCTACGGCCCG 59.971 61.111 0.00 0.00 34.44 6.13
1518 1623 1.811266 CTTCCGCCATGGTCGTCAG 60.811 63.158 21.61 14.83 39.52 3.51
1529 1634 2.600790 TGGTCGTCAGGAAGAGGTAAA 58.399 47.619 0.00 0.00 33.88 2.01
1535 1640 6.218746 GTCGTCAGGAAGAGGTAAAAACTTA 58.781 40.000 0.00 0.00 33.88 2.24
1541 1646 7.236847 TCAGGAAGAGGTAAAAACTTATCCTCA 59.763 37.037 11.27 0.00 44.79 3.86
1548 1653 6.891908 AGGTAAAAACTTATCCTCATGTGCAT 59.108 34.615 0.00 0.00 0.00 3.96
1549 1654 6.974622 GGTAAAAACTTATCCTCATGTGCATG 59.025 38.462 5.86 5.86 40.09 4.06
1550 1655 6.594788 AAAAACTTATCCTCATGTGCATGT 57.405 33.333 11.38 0.00 39.72 3.21
1551 1656 5.571784 AAACTTATCCTCATGTGCATGTG 57.428 39.130 11.38 9.15 39.72 3.21
1552 1657 4.226427 ACTTATCCTCATGTGCATGTGT 57.774 40.909 11.38 0.00 39.72 3.72
1570 1675 2.413796 GTGTGCGACGAAATATCAACCA 59.586 45.455 0.00 0.00 0.00 3.67
1585 1694 2.094906 TCAACCATTAGTCCGTCACTCG 60.095 50.000 0.00 0.00 36.43 4.18
1590 1699 3.428999 CCATTAGTCCGTCACTCGTCATT 60.429 47.826 0.00 0.00 36.43 2.57
1591 1700 2.913777 TAGTCCGTCACTCGTCATTG 57.086 50.000 0.00 0.00 36.43 2.82
1597 1706 1.618861 GTCACTCGTCATTGGACTCG 58.381 55.000 0.00 0.00 42.05 4.18
1676 1789 1.741770 GGTGGTGGACATGAGCGAC 60.742 63.158 0.00 0.00 0.00 5.19
2085 2200 8.370940 TCACTTGTATTTTCCCATTGCAAATAA 58.629 29.630 1.71 0.00 0.00 1.40
2086 2201 8.997323 CACTTGTATTTTCCCATTGCAAATAAA 58.003 29.630 1.71 0.00 0.00 1.40
2099 2214 7.414319 CCATTGCAAATAAAATTGTCCATGTCC 60.414 37.037 1.71 0.00 32.80 4.02
2164 2288 9.341078 GCTGGAGGGAGTATATAAGTAGTATAC 57.659 40.741 0.00 0.00 43.47 1.47
2303 2427 2.225467 GAGGCTGGCATAGAAACATCC 58.775 52.381 3.38 0.00 0.00 3.51
2523 2650 3.052082 CCACCGCTGACTGCAAGG 61.052 66.667 5.11 1.30 43.06 3.61
2612 2739 1.333636 CGTCTTGGGAGAGGCCAGAT 61.334 60.000 5.01 0.00 38.95 2.90
2899 3026 5.574188 ACTTGTTGCTCAGATTCCCTAAAT 58.426 37.500 0.00 0.00 0.00 1.40
2967 3097 7.553044 AGGCAAGGAATAAAATGACTACTGTAC 59.447 37.037 0.00 0.00 0.00 2.90
2997 3127 7.924412 TGTTTATCAGTCATTATTACGTCCTCC 59.076 37.037 0.00 0.00 0.00 4.30
2998 3128 7.591421 TTATCAGTCATTATTACGTCCTCCA 57.409 36.000 0.00 0.00 0.00 3.86
3001 3131 6.513180 TCAGTCATTATTACGTCCTCCATTC 58.487 40.000 0.00 0.00 0.00 2.67
3009 3139 9.939802 ATTATTACGTCCTCCATTCCTAAATAC 57.060 33.333 0.00 0.00 0.00 1.89
3010 3140 7.613551 ATTACGTCCTCCATTCCTAAATACT 57.386 36.000 0.00 0.00 0.00 2.12
3011 3141 5.532664 ACGTCCTCCATTCCTAAATACTC 57.467 43.478 0.00 0.00 0.00 2.59
3012 3142 4.344390 ACGTCCTCCATTCCTAAATACTCC 59.656 45.833 0.00 0.00 0.00 3.85
3013 3143 4.262506 CGTCCTCCATTCCTAAATACTCCC 60.263 50.000 0.00 0.00 0.00 4.30
3014 3144 4.908481 GTCCTCCATTCCTAAATACTCCCT 59.092 45.833 0.00 0.00 0.00 4.20
3015 3145 5.012251 GTCCTCCATTCCTAAATACTCCCTC 59.988 48.000 0.00 0.00 0.00 4.30
3016 3146 4.287326 CCTCCATTCCTAAATACTCCCTCC 59.713 50.000 0.00 0.00 0.00 4.30
3017 3147 3.901844 TCCATTCCTAAATACTCCCTCCG 59.098 47.826 0.00 0.00 0.00 4.63
3018 3148 3.646637 CCATTCCTAAATACTCCCTCCGT 59.353 47.826 0.00 0.00 0.00 4.69
3019 3149 4.262506 CCATTCCTAAATACTCCCTCCGTC 60.263 50.000 0.00 0.00 0.00 4.79
3020 3150 2.954792 TCCTAAATACTCCCTCCGTCC 58.045 52.381 0.00 0.00 0.00 4.79
3021 3151 1.612463 CCTAAATACTCCCTCCGTCCG 59.388 57.143 0.00 0.00 0.00 4.79
3022 3152 1.612463 CTAAATACTCCCTCCGTCCGG 59.388 57.143 0.00 0.00 0.00 5.14
3023 3153 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
3024 3154 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
3025 3155 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3026 3156 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3027 3157 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3028 3158 1.339097 CTCCCTCCGTCCGGAAATAT 58.661 55.000 5.23 0.00 44.66 1.28
3029 3159 1.692519 CTCCCTCCGTCCGGAAATATT 59.307 52.381 5.23 0.00 44.66 1.28
3030 3160 2.104281 CTCCCTCCGTCCGGAAATATTT 59.896 50.000 5.23 0.00 44.66 1.40
3031 3161 2.158871 TCCCTCCGTCCGGAAATATTTG 60.159 50.000 5.23 0.00 44.66 2.32
3032 3162 2.420967 CCCTCCGTCCGGAAATATTTGT 60.421 50.000 5.23 0.00 44.66 2.83
3033 3163 2.870411 CCTCCGTCCGGAAATATTTGTC 59.130 50.000 5.23 0.00 44.66 3.18
3034 3164 3.527533 CTCCGTCCGGAAATATTTGTCA 58.472 45.455 5.23 0.00 44.66 3.58
3035 3165 4.127171 CTCCGTCCGGAAATATTTGTCAT 58.873 43.478 5.23 0.00 44.66 3.06
3036 3166 4.124238 TCCGTCCGGAAATATTTGTCATC 58.876 43.478 5.23 0.00 42.05 2.92
3037 3167 3.874543 CCGTCCGGAAATATTTGTCATCA 59.125 43.478 5.23 0.00 37.50 3.07
3038 3168 4.024893 CCGTCCGGAAATATTTGTCATCAG 60.025 45.833 5.23 0.00 37.50 2.90
3039 3169 4.808895 CGTCCGGAAATATTTGTCATCAGA 59.191 41.667 5.23 0.00 0.00 3.27
3040 3170 5.293324 CGTCCGGAAATATTTGTCATCAGAA 59.707 40.000 5.23 0.00 0.00 3.02
3041 3171 6.017934 CGTCCGGAAATATTTGTCATCAGAAT 60.018 38.462 5.23 0.00 0.00 2.40
3042 3172 7.134815 GTCCGGAAATATTTGTCATCAGAATG 58.865 38.462 5.23 0.00 37.54 2.67
3043 3173 6.262944 TCCGGAAATATTTGTCATCAGAATGG 59.737 38.462 0.00 0.00 36.16 3.16
3044 3174 6.262944 CCGGAAATATTTGTCATCAGAATGGA 59.737 38.462 5.17 0.00 36.16 3.41
3045 3175 7.040201 CCGGAAATATTTGTCATCAGAATGGAT 60.040 37.037 5.17 0.00 36.16 3.41
3046 3176 9.002600 CGGAAATATTTGTCATCAGAATGGATA 57.997 33.333 5.17 0.00 36.16 2.59
3053 3183 9.865321 ATTTGTCATCAGAATGGATAAAAAGTG 57.135 29.630 0.00 0.00 36.16 3.16
3054 3184 7.395190 TGTCATCAGAATGGATAAAAAGTGG 57.605 36.000 0.00 0.00 36.16 4.00
3055 3185 6.947733 TGTCATCAGAATGGATAAAAAGTGGT 59.052 34.615 0.00 0.00 36.16 4.16
3056 3186 7.094248 TGTCATCAGAATGGATAAAAAGTGGTG 60.094 37.037 0.00 0.00 36.16 4.17
3057 3187 6.947733 TCATCAGAATGGATAAAAAGTGGTGT 59.052 34.615 0.00 0.00 36.16 4.16
3058 3188 8.106462 TCATCAGAATGGATAAAAAGTGGTGTA 58.894 33.333 0.00 0.00 36.16 2.90
3059 3189 8.906867 CATCAGAATGGATAAAAAGTGGTGTAT 58.093 33.333 0.00 0.00 36.16 2.29
3060 3190 8.506168 TCAGAATGGATAAAAAGTGGTGTATC 57.494 34.615 0.00 0.00 36.16 2.24
3061 3191 8.328758 TCAGAATGGATAAAAAGTGGTGTATCT 58.671 33.333 0.00 0.00 36.16 1.98
3062 3192 9.613428 CAGAATGGATAAAAAGTGGTGTATCTA 57.387 33.333 0.00 0.00 0.00 1.98
3063 3193 9.838339 AGAATGGATAAAAAGTGGTGTATCTAG 57.162 33.333 0.00 0.00 0.00 2.43
3064 3194 9.832445 GAATGGATAAAAAGTGGTGTATCTAGA 57.168 33.333 0.00 0.00 0.00 2.43
3066 3196 9.614792 ATGGATAAAAAGTGGTGTATCTAGAAC 57.385 33.333 0.00 0.00 0.00 3.01
3067 3197 8.822805 TGGATAAAAAGTGGTGTATCTAGAACT 58.177 33.333 0.00 0.00 0.00 3.01
3091 3221 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
3099 3229 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
3102 3232 9.621239 TCTAGATACATCCCCTTTTATTCATCT 57.379 33.333 0.00 0.00 0.00 2.90
3104 3234 8.930846 AGATACATCCCCTTTTATTCATCTTG 57.069 34.615 0.00 0.00 0.00 3.02
3105 3235 8.727149 AGATACATCCCCTTTTATTCATCTTGA 58.273 33.333 0.00 0.00 0.00 3.02
3106 3236 9.525826 GATACATCCCCTTTTATTCATCTTGAT 57.474 33.333 0.00 0.00 0.00 2.57
3107 3237 7.592885 ACATCCCCTTTTATTCATCTTGATG 57.407 36.000 4.35 4.35 33.80 3.07
3108 3238 7.356680 ACATCCCCTTTTATTCATCTTGATGA 58.643 34.615 9.02 9.02 32.39 2.92
3109 3239 7.286316 ACATCCCCTTTTATTCATCTTGATGAC 59.714 37.037 12.28 0.00 32.39 3.06
3110 3240 6.730447 TCCCCTTTTATTCATCTTGATGACA 58.270 36.000 12.28 5.64 0.00 3.58
3111 3241 7.181361 TCCCCTTTTATTCATCTTGATGACAA 58.819 34.615 12.28 7.53 34.65 3.18
3123 3253 5.470845 CTTGATGACAAGTATTTCCGGAC 57.529 43.478 1.83 0.00 45.73 4.79
3124 3254 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3125 3255 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3126 3256 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3127 3257 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3128 3258 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3129 3259 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3130 3260 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3131 3261 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3132 3262 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
3133 3263 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
3134 3264 0.032813 TTTCCGGACGGAGGGAGTAT 60.033 55.000 13.64 0.00 46.06 2.12
3135 3265 0.846015 TTCCGGACGGAGGGAGTATA 59.154 55.000 13.64 0.00 46.06 1.47
3136 3266 0.846015 TCCGGACGGAGGGAGTATAA 59.154 55.000 9.76 0.00 39.76 0.98
3137 3267 1.202855 TCCGGACGGAGGGAGTATAAG 60.203 57.143 9.76 0.00 39.76 1.73
3138 3268 1.478288 CCGGACGGAGGGAGTATAAGT 60.478 57.143 4.40 0.00 37.50 2.24
3139 3269 1.878734 CGGACGGAGGGAGTATAAGTC 59.121 57.143 0.00 0.00 0.00 3.01
3140 3270 2.486907 CGGACGGAGGGAGTATAAGTCT 60.487 54.545 0.00 0.00 0.00 3.24
3141 3271 3.564264 GGACGGAGGGAGTATAAGTCTT 58.436 50.000 0.00 0.00 0.00 3.01
3142 3272 3.959449 GGACGGAGGGAGTATAAGTCTTT 59.041 47.826 0.00 0.00 0.00 2.52
3143 3273 4.405036 GGACGGAGGGAGTATAAGTCTTTT 59.595 45.833 0.00 0.00 0.00 2.27
3144 3274 5.105023 GGACGGAGGGAGTATAAGTCTTTTT 60.105 44.000 0.00 0.00 0.00 1.94
3145 3275 6.097412 GGACGGAGGGAGTATAAGTCTTTTTA 59.903 42.308 0.00 0.00 0.00 1.52
3146 3276 7.110043 ACGGAGGGAGTATAAGTCTTTTTAG 57.890 40.000 0.00 0.00 0.00 1.85
3147 3277 6.894103 ACGGAGGGAGTATAAGTCTTTTTAGA 59.106 38.462 0.00 0.00 0.00 2.10
3148 3278 7.068470 ACGGAGGGAGTATAAGTCTTTTTAGAG 59.932 40.741 0.00 0.00 0.00 2.43
3149 3279 7.284944 CGGAGGGAGTATAAGTCTTTTTAGAGA 59.715 40.741 0.00 0.00 0.00 3.10
3150 3280 9.150028 GGAGGGAGTATAAGTCTTTTTAGAGAT 57.850 37.037 0.00 0.00 0.00 2.75
3153 3283 9.767228 GGGAGTATAAGTCTTTTTAGAGATTCC 57.233 37.037 0.00 0.00 0.00 3.01
3168 3298 8.749026 TTAGAGATTCCAATAAGAGACTACGT 57.251 34.615 0.00 0.00 0.00 3.57
3169 3299 9.842775 TTAGAGATTCCAATAAGAGACTACGTA 57.157 33.333 0.00 0.00 0.00 3.57
3170 3300 8.156994 AGAGATTCCAATAAGAGACTACGTAC 57.843 38.462 0.00 0.00 0.00 3.67
3171 3301 7.774157 AGAGATTCCAATAAGAGACTACGTACA 59.226 37.037 0.00 0.00 0.00 2.90
3172 3302 7.932335 AGATTCCAATAAGAGACTACGTACAG 58.068 38.462 0.00 0.00 0.00 2.74
3173 3303 7.774157 AGATTCCAATAAGAGACTACGTACAGA 59.226 37.037 0.00 0.00 0.00 3.41
3174 3304 6.922247 TCCAATAAGAGACTACGTACAGAG 57.078 41.667 0.00 0.00 0.00 3.35
3175 3305 5.296283 TCCAATAAGAGACTACGTACAGAGC 59.704 44.000 0.00 0.00 0.00 4.09
3176 3306 5.066117 CCAATAAGAGACTACGTACAGAGCA 59.934 44.000 0.00 0.00 0.00 4.26
3177 3307 6.404403 CCAATAAGAGACTACGTACAGAGCAA 60.404 42.308 0.00 0.00 0.00 3.91
3178 3308 6.754702 ATAAGAGACTACGTACAGAGCAAA 57.245 37.500 0.00 0.00 0.00 3.68
3179 3309 5.449107 AAGAGACTACGTACAGAGCAAAA 57.551 39.130 0.00 0.00 0.00 2.44
3180 3310 5.646577 AGAGACTACGTACAGAGCAAAAT 57.353 39.130 0.00 0.00 0.00 1.82
3181 3311 5.403246 AGAGACTACGTACAGAGCAAAATG 58.597 41.667 0.00 0.00 0.00 2.32
3182 3312 5.183331 AGAGACTACGTACAGAGCAAAATGA 59.817 40.000 0.00 0.00 0.00 2.57
3183 3313 5.403246 AGACTACGTACAGAGCAAAATGAG 58.597 41.667 0.00 0.00 0.00 2.90
3184 3314 5.047943 AGACTACGTACAGAGCAAAATGAGT 60.048 40.000 0.00 0.00 0.00 3.41
3185 3315 4.923871 ACTACGTACAGAGCAAAATGAGTG 59.076 41.667 0.00 0.00 0.00 3.51
3186 3316 3.990092 ACGTACAGAGCAAAATGAGTGA 58.010 40.909 0.00 0.00 0.00 3.41
3187 3317 4.377021 ACGTACAGAGCAAAATGAGTGAA 58.623 39.130 0.00 0.00 0.00 3.18
3188 3318 4.997395 ACGTACAGAGCAAAATGAGTGAAT 59.003 37.500 0.00 0.00 0.00 2.57
3189 3319 5.120830 ACGTACAGAGCAAAATGAGTGAATC 59.879 40.000 0.00 0.00 0.00 2.52
3190 3320 5.349817 CGTACAGAGCAAAATGAGTGAATCT 59.650 40.000 0.00 0.00 0.00 2.40
3191 3321 6.531594 CGTACAGAGCAAAATGAGTGAATCTA 59.468 38.462 0.00 0.00 0.00 1.98
3192 3322 6.734104 ACAGAGCAAAATGAGTGAATCTAC 57.266 37.500 0.00 0.00 0.00 2.59
3193 3323 6.233434 ACAGAGCAAAATGAGTGAATCTACA 58.767 36.000 0.00 0.00 0.00 2.74
3194 3324 6.148480 ACAGAGCAAAATGAGTGAATCTACAC 59.852 38.462 0.00 0.00 40.60 2.90
3237 3367 7.898014 ACATCTGTATGTAGTCCATAGTGAA 57.102 36.000 0.00 0.00 44.66 3.18
3238 3368 8.306313 ACATCTGTATGTAGTCCATAGTGAAA 57.694 34.615 0.00 0.00 44.66 2.69
3239 3369 8.928448 ACATCTGTATGTAGTCCATAGTGAAAT 58.072 33.333 0.00 0.00 44.66 2.17
3240 3370 9.770097 CATCTGTATGTAGTCCATAGTGAAATT 57.230 33.333 0.00 0.00 36.71 1.82
3242 3372 9.817809 TCTGTATGTAGTCCATAGTGAAATTTC 57.182 33.333 11.41 11.41 36.71 2.17
3243 3373 9.823647 CTGTATGTAGTCCATAGTGAAATTTCT 57.176 33.333 18.64 2.61 36.71 2.52
3267 3397 9.211485 TCTAAAAAGACTTACATTTAGGAACGG 57.789 33.333 13.94 0.00 36.48 4.44
3268 3398 9.211485 CTAAAAAGACTTACATTTAGGAACGGA 57.789 33.333 8.91 0.00 33.69 4.69
3269 3399 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
3270 3400 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3271 3401 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3272 3402 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3273 3403 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3274 3404 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
3275 3405 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
3276 3406 3.450096 ACATTTAGGAACGGAGGGAGTAC 59.550 47.826 0.00 0.00 0.00 2.73
3283 3413 6.064735 AGGAACGGAGGGAGTACTATATAG 57.935 45.833 8.27 8.27 0.00 1.31
3292 3460 8.110908 GGAGGGAGTACTATATAGTTCAGATGT 58.889 40.741 20.21 0.00 37.73 3.06
3339 3531 6.039047 ACATCAGGCTAAACAATAGAGCAATG 59.961 38.462 0.00 0.00 37.98 2.82
3340 3532 5.744171 TCAGGCTAAACAATAGAGCAATGA 58.256 37.500 0.00 0.00 37.98 2.57
3341 3533 6.179756 TCAGGCTAAACAATAGAGCAATGAA 58.820 36.000 0.00 0.00 37.98 2.57
3353 3546 8.965172 CAATAGAGCAATGAACATAATTTGAGC 58.035 33.333 0.00 0.00 0.00 4.26
3392 3585 2.595463 AACACGCTGCAGCCACAT 60.595 55.556 32.07 14.11 37.91 3.21
3433 3660 2.290008 TGAGCAAAGCGGAGTGGATAAA 60.290 45.455 0.00 0.00 0.00 1.40
3462 3689 9.696917 AATTGAAAGCAAATAAGGTCTAAACAG 57.303 29.630 0.00 0.00 37.59 3.16
3599 3826 1.330829 GCAACTCGCAAGTTATAGGGC 59.669 52.381 0.00 0.00 43.99 5.19
3625 3852 2.301296 AGCTGCTGTGTGTCTAAGACAT 59.699 45.455 0.00 0.00 44.63 3.06
3626 3853 3.511540 AGCTGCTGTGTGTCTAAGACATA 59.488 43.478 0.00 0.00 44.63 2.29
3654 3882 8.112822 TGTAAATCATGTTCTCCAAAGGGAATA 58.887 33.333 0.00 0.00 44.38 1.75
3655 3883 7.651027 AAATCATGTTCTCCAAAGGGAATAG 57.349 36.000 0.00 0.00 44.38 1.73
3659 3887 3.010138 TGTTCTCCAAAGGGAATAGGTGG 59.990 47.826 0.00 0.00 44.38 4.61
3662 3890 0.751643 CCAAAGGGAATAGGTGGCGG 60.752 60.000 0.00 0.00 35.59 6.13
3704 3932 5.129485 CCTCTAGATAAACCATGTGTCCTGT 59.871 44.000 0.00 0.00 0.00 4.00
3736 3964 1.429930 TGCCACTGGTTGAGGAACTA 58.570 50.000 0.00 0.00 41.55 2.24
3774 4003 1.398390 GCGTCATCAGTCATTTGGTCC 59.602 52.381 0.00 0.00 0.00 4.46
3823 4052 0.322906 CTGGTCCTTCTCTTTGGCCC 60.323 60.000 0.00 0.00 0.00 5.80
3839 4068 3.146218 CCCTGATCAGAGAGGGGAG 57.854 63.158 24.62 4.38 44.88 4.30
3845 4074 0.937441 ATCAGAGAGGGGAGCTGGTA 59.063 55.000 0.00 0.00 0.00 3.25
3847 4076 1.047002 CAGAGAGGGGAGCTGGTATG 58.953 60.000 0.00 0.00 0.00 2.39
3861 4090 3.243068 GCTGGTATGGTAAGGATTTTGCG 60.243 47.826 0.00 0.00 0.00 4.85
3877 4106 2.494445 CGCGGTCATAGAGCACCA 59.506 61.111 0.00 0.00 32.33 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.875675 GATAATGTTATGCTCATGAGTCTTTTC 57.124 33.333 23.38 6.70 0.00 2.29
106 107 9.258629 TGGAAGAGGATTTTCATCACAAATAAT 57.741 29.630 0.00 0.00 28.01 1.28
128 129 7.882791 TCAGTCTTTTGATATTACTTGCTGGAA 59.117 33.333 0.00 0.00 0.00 3.53
164 165 9.638239 GACCTGATGAAAGATCAGTTATCTATC 57.362 37.037 10.08 0.00 44.56 2.08
185 186 1.588674 TTGCTTACACGGTTGACCTG 58.411 50.000 0.00 0.00 0.00 4.00
205 207 6.039382 ACGTAATGCTTTTCCTCTTGACTTTT 59.961 34.615 0.00 0.00 0.00 2.27
206 208 5.531287 ACGTAATGCTTTTCCTCTTGACTTT 59.469 36.000 0.00 0.00 0.00 2.66
260 262 4.009675 TGCATTTGTATGTGGAACTCCTC 58.990 43.478 0.00 0.00 38.04 3.71
297 299 8.518702 GCATTCTTTTTCTGAGAAGTATTTCCT 58.481 33.333 0.00 0.00 36.64 3.36
347 349 6.627395 ACTCATCTCTCTCTATAAACACGG 57.373 41.667 0.00 0.00 0.00 4.94
348 350 7.658167 TCCTACTCATCTCTCTCTATAAACACG 59.342 40.741 0.00 0.00 0.00 4.49
412 414 6.699642 TGGTTACTTCTTTGCTGTTTAATTGC 59.300 34.615 0.00 0.00 0.00 3.56
522 526 9.529325 ACTTCTTTGCTTTTTAATTGGTTACTC 57.471 29.630 0.00 0.00 0.00 2.59
526 530 9.104965 GGTTACTTCTTTGCTTTTTAATTGGTT 57.895 29.630 0.00 0.00 0.00 3.67
528 532 8.655651 TGGTTACTTCTTTGCTTTTTAATTGG 57.344 30.769 0.00 0.00 0.00 3.16
604 608 2.391879 GTGACCACGACTACTTCACAC 58.608 52.381 0.00 0.00 37.20 3.82
689 694 9.300681 TCTTATTGAAAAGATGACACTTCCAAT 57.699 29.630 0.00 0.00 30.54 3.16
719 724 9.995594 ACCATCCAATAAGCCATATAATACAAT 57.004 29.630 0.00 0.00 0.00 2.71
720 725 9.461312 GACCATCCAATAAGCCATATAATACAA 57.539 33.333 0.00 0.00 0.00 2.41
721 726 8.610369 TGACCATCCAATAAGCCATATAATACA 58.390 33.333 0.00 0.00 0.00 2.29
722 727 9.461312 TTGACCATCCAATAAGCCATATAATAC 57.539 33.333 0.00 0.00 0.00 1.89
730 735 5.765510 AGTTATTGACCATCCAATAAGCCA 58.234 37.500 8.73 0.00 44.72 4.75
755 760 1.134848 ACGTGTGTTGCAAAGCCAAAT 60.135 42.857 0.00 0.00 0.00 2.32
769 774 1.070175 CCTTGCTTTTCCGTACGTGTG 60.070 52.381 15.21 0.00 0.00 3.82
890 921 5.587844 GCTCTCCATCAATTATGTCAAGTGT 59.412 40.000 0.00 0.00 33.34 3.55
951 1013 0.958876 GCTGGGTTTGGGTTCCTACG 60.959 60.000 0.00 0.00 0.00 3.51
964 1026 3.655211 CAGGAAGCTGGGCTGGGT 61.655 66.667 0.00 0.00 39.62 4.51
1066 1150 1.135257 CAGGAGAACGGTGAGCAGTAG 60.135 57.143 0.00 0.00 0.00 2.57
1407 1512 0.451135 GTGCAAACGCGATGTCTGTC 60.451 55.000 15.93 0.00 0.00 3.51
1518 1623 7.829706 ACATGAGGATAAGTTTTTACCTCTTCC 59.170 37.037 0.00 0.00 44.91 3.46
1529 1634 5.012239 ACACATGCACATGAGGATAAGTTT 58.988 37.500 17.19 0.00 41.20 2.66
1548 1653 2.413796 GGTTGATATTTCGTCGCACACA 59.586 45.455 0.00 0.00 0.00 3.72
1549 1654 2.413796 TGGTTGATATTTCGTCGCACAC 59.586 45.455 0.00 0.00 0.00 3.82
1550 1655 2.689646 TGGTTGATATTTCGTCGCACA 58.310 42.857 0.00 0.00 0.00 4.57
1551 1656 3.944422 ATGGTTGATATTTCGTCGCAC 57.056 42.857 0.00 0.00 0.00 5.34
1552 1657 5.113383 ACTAATGGTTGATATTTCGTCGCA 58.887 37.500 0.00 0.00 0.00 5.10
1554 1659 5.107989 CGGACTAATGGTTGATATTTCGTCG 60.108 44.000 0.00 0.00 0.00 5.12
1555 1660 5.751990 ACGGACTAATGGTTGATATTTCGTC 59.248 40.000 0.00 0.00 0.00 4.20
1556 1661 5.667466 ACGGACTAATGGTTGATATTTCGT 58.333 37.500 0.00 0.00 0.00 3.85
1557 1662 5.751509 TGACGGACTAATGGTTGATATTTCG 59.248 40.000 0.00 0.00 0.00 3.46
1558 1663 6.761714 AGTGACGGACTAATGGTTGATATTTC 59.238 38.462 0.00 0.00 30.86 2.17
1559 1664 6.650120 AGTGACGGACTAATGGTTGATATTT 58.350 36.000 0.00 0.00 30.86 1.40
1597 1706 2.433664 GCACCTGCAGCAATTGGC 60.434 61.111 8.66 3.57 45.30 4.52
1600 1709 4.060038 GGCGCACCTGCAGCAATT 62.060 61.111 10.83 0.00 42.21 2.32
1619 1732 4.503910 CCTCACGGATCTTGTTGATAACA 58.496 43.478 0.00 0.00 40.21 2.41
1660 1773 1.888436 GAGGTCGCTCATGTCCACCA 61.888 60.000 0.00 0.00 0.00 4.17
1676 1789 2.722201 GGTGTAGCCGGACAGGAGG 61.722 68.421 5.05 0.00 45.00 4.30
2085 2200 6.158695 ACAGTATAGGAGGACATGGACAATTT 59.841 38.462 0.00 0.00 0.00 1.82
2086 2201 5.667626 ACAGTATAGGAGGACATGGACAATT 59.332 40.000 0.00 0.00 0.00 2.32
2099 2214 9.781633 AGTAGTAGTATGACAACAGTATAGGAG 57.218 37.037 0.00 0.00 0.00 3.69
2131 2255 2.038863 TACTCCCTCCAGCTCCAAAA 57.961 50.000 0.00 0.00 0.00 2.44
2164 2288 7.173907 ACATGGAAACTGTGAATGAACTCTTAG 59.826 37.037 0.00 0.00 0.00 2.18
2224 2348 4.493057 GCGTGTGTGTCTGTTGATCATATG 60.493 45.833 0.00 0.00 0.00 1.78
2288 2412 5.509670 CGTCAGATAGGATGTTTCTATGCCA 60.510 44.000 0.00 0.00 0.00 4.92
2303 2427 2.541178 GCCGTACTCCAACGTCAGATAG 60.541 54.545 0.00 0.00 41.27 2.08
2360 2484 6.464607 GGGATCTTACCTCCTCCTGTAATTTC 60.465 46.154 0.00 0.00 33.05 2.17
2396 2520 6.268847 GGTCCTCCTCTGTTATCATGTCTAAT 59.731 42.308 0.00 0.00 0.00 1.73
2523 2650 3.279853 GGGTATCAAGTATCCGTCGAC 57.720 52.381 5.18 5.18 0.00 4.20
2591 2718 2.232298 CTGGCCTCTCCCAAGACGAC 62.232 65.000 3.32 0.00 33.73 4.34
2612 2739 1.661463 ACCTCTCAGGCCAGAAATCA 58.339 50.000 5.01 0.00 39.63 2.57
2816 2943 0.106569 CAGCCATATCAACCCCTGCA 60.107 55.000 0.00 0.00 0.00 4.41
2910 3037 5.688823 TGTGCTCATGTCGAAATAAACTTG 58.311 37.500 0.00 0.00 0.00 3.16
2991 3121 4.908481 AGGGAGTATTTAGGAATGGAGGAC 59.092 45.833 0.00 0.00 0.00 3.85
2997 3127 4.262506 GGACGGAGGGAGTATTTAGGAATG 60.263 50.000 0.00 0.00 0.00 2.67
2998 3128 3.902467 GGACGGAGGGAGTATTTAGGAAT 59.098 47.826 0.00 0.00 0.00 3.01
3001 3131 1.612463 CGGACGGAGGGAGTATTTAGG 59.388 57.143 0.00 0.00 0.00 2.69
3009 3139 1.339097 ATATTTCCGGACGGAGGGAG 58.661 55.000 13.64 0.00 46.06 4.30
3010 3140 1.797320 AATATTTCCGGACGGAGGGA 58.203 50.000 13.64 4.95 46.06 4.20
3011 3141 2.218603 CAAATATTTCCGGACGGAGGG 58.781 52.381 13.64 0.00 46.06 4.30
3012 3142 2.870411 GACAAATATTTCCGGACGGAGG 59.130 50.000 13.64 0.00 46.06 4.30
3013 3143 3.527533 TGACAAATATTTCCGGACGGAG 58.472 45.455 13.64 3.15 46.06 4.63
3014 3144 3.613494 TGACAAATATTTCCGGACGGA 57.387 42.857 1.83 9.76 43.52 4.69
3015 3145 3.874543 TGATGACAAATATTTCCGGACGG 59.125 43.478 1.83 3.96 0.00 4.79
3016 3146 4.808895 TCTGATGACAAATATTTCCGGACG 59.191 41.667 1.83 0.00 0.00 4.79
3017 3147 6.677781 TTCTGATGACAAATATTTCCGGAC 57.322 37.500 1.83 0.00 0.00 4.79
3018 3148 6.262944 CCATTCTGATGACAAATATTTCCGGA 59.737 38.462 0.00 0.00 35.16 5.14
3019 3149 6.262944 TCCATTCTGATGACAAATATTTCCGG 59.737 38.462 0.00 0.00 35.16 5.14
3020 3150 7.263100 TCCATTCTGATGACAAATATTTCCG 57.737 36.000 0.00 0.00 35.16 4.30
3027 3157 9.865321 CACTTTTTATCCATTCTGATGACAAAT 57.135 29.630 0.00 0.00 35.16 2.32
3028 3158 8.306038 CCACTTTTTATCCATTCTGATGACAAA 58.694 33.333 0.00 0.00 35.16 2.83
3029 3159 7.451255 ACCACTTTTTATCCATTCTGATGACAA 59.549 33.333 0.00 0.00 35.16 3.18
3030 3160 6.947733 ACCACTTTTTATCCATTCTGATGACA 59.052 34.615 0.00 0.00 35.16 3.58
3031 3161 7.094205 ACACCACTTTTTATCCATTCTGATGAC 60.094 37.037 0.00 0.00 35.16 3.06
3032 3162 6.947733 ACACCACTTTTTATCCATTCTGATGA 59.052 34.615 0.00 0.00 35.16 2.92
3033 3163 7.161773 ACACCACTTTTTATCCATTCTGATG 57.838 36.000 0.00 0.00 0.00 3.07
3034 3164 9.125026 GATACACCACTTTTTATCCATTCTGAT 57.875 33.333 0.00 0.00 0.00 2.90
3035 3165 8.328758 AGATACACCACTTTTTATCCATTCTGA 58.671 33.333 0.00 0.00 0.00 3.27
3036 3166 8.511604 AGATACACCACTTTTTATCCATTCTG 57.488 34.615 0.00 0.00 0.00 3.02
3037 3167 9.838339 CTAGATACACCACTTTTTATCCATTCT 57.162 33.333 0.00 0.00 0.00 2.40
3038 3168 9.832445 TCTAGATACACCACTTTTTATCCATTC 57.168 33.333 0.00 0.00 0.00 2.67
3040 3170 9.614792 GTTCTAGATACACCACTTTTTATCCAT 57.385 33.333 0.00 0.00 0.00 3.41
3041 3171 8.822805 AGTTCTAGATACACCACTTTTTATCCA 58.177 33.333 0.00 0.00 0.00 3.41
3065 3195 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
3073 3203 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
3076 3206 9.621239 AGATGAATAAAAGGGGATGTATCTAGA 57.379 33.333 0.00 0.00 0.00 2.43
3079 3209 8.727149 TCAAGATGAATAAAAGGGGATGTATCT 58.273 33.333 0.00 0.00 0.00 1.98
3080 3210 8.924511 TCAAGATGAATAAAAGGGGATGTATC 57.075 34.615 0.00 0.00 0.00 2.24
3081 3211 9.305555 CATCAAGATGAATAAAAGGGGATGTAT 57.694 33.333 4.01 0.00 41.20 2.29
3082 3212 8.501904 TCATCAAGATGAATAAAAGGGGATGTA 58.498 33.333 10.16 0.00 44.14 2.29
3083 3213 7.356680 TCATCAAGATGAATAAAAGGGGATGT 58.643 34.615 10.16 0.00 44.14 3.06
3084 3214 7.828508 TCATCAAGATGAATAAAAGGGGATG 57.171 36.000 10.16 0.00 44.14 3.51
3100 3230 8.994207 CCGTCCGGAAATACTTGTCATCAAGA 62.994 46.154 5.23 0.31 44.37 3.02
3101 3231 6.918800 CCGTCCGGAAATACTTGTCATCAAG 61.919 48.000 5.23 6.44 45.65 3.02
3102 3232 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3103 3233 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3104 3234 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3105 3235 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3106 3236 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3107 3237 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3108 3238 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3109 3239 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3110 3240 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3111 3241 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3112 3242 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3113 3243 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3114 3244 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3115 3245 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
3116 3246 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
3117 3247 0.846015 TTATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
3118 3248 1.245732 CTTATACTCCCTCCGTCCGG 58.754 60.000 0.00 0.00 0.00 5.14
3119 3249 1.878734 GACTTATACTCCCTCCGTCCG 59.121 57.143 0.00 0.00 0.00 4.79
3120 3250 3.226682 AGACTTATACTCCCTCCGTCC 57.773 52.381 0.00 0.00 0.00 4.79
3121 3251 5.595257 AAAAGACTTATACTCCCTCCGTC 57.405 43.478 0.00 0.00 0.00 4.79
3122 3252 6.894103 TCTAAAAAGACTTATACTCCCTCCGT 59.106 38.462 0.00 0.00 0.00 4.69
3123 3253 7.284944 TCTCTAAAAAGACTTATACTCCCTCCG 59.715 40.741 0.00 0.00 0.00 4.63
3124 3254 8.536340 TCTCTAAAAAGACTTATACTCCCTCC 57.464 38.462 0.00 0.00 0.00 4.30
3127 3257 9.767228 GGAATCTCTAAAAAGACTTATACTCCC 57.233 37.037 0.00 0.00 0.00 4.30
3142 3272 9.186837 ACGTAGTCTCTTATTGGAATCTCTAAA 57.813 33.333 0.00 0.00 29.74 1.85
3143 3273 8.749026 ACGTAGTCTCTTATTGGAATCTCTAA 57.251 34.615 0.00 0.00 29.74 2.10
3144 3274 9.270640 GTACGTAGTCTCTTATTGGAATCTCTA 57.729 37.037 0.00 0.00 43.93 2.43
3145 3275 7.774157 TGTACGTAGTCTCTTATTGGAATCTCT 59.226 37.037 0.00 0.00 43.93 3.10
3146 3276 7.928103 TGTACGTAGTCTCTTATTGGAATCTC 58.072 38.462 0.00 0.00 43.93 2.75
3147 3277 7.774157 TCTGTACGTAGTCTCTTATTGGAATCT 59.226 37.037 0.00 0.00 43.93 2.40
3148 3278 7.928103 TCTGTACGTAGTCTCTTATTGGAATC 58.072 38.462 0.00 0.00 43.93 2.52
3149 3279 7.468906 GCTCTGTACGTAGTCTCTTATTGGAAT 60.469 40.741 0.00 0.00 43.93 3.01
3150 3280 6.183360 GCTCTGTACGTAGTCTCTTATTGGAA 60.183 42.308 0.00 0.00 43.93 3.53
3151 3281 5.296283 GCTCTGTACGTAGTCTCTTATTGGA 59.704 44.000 0.00 0.00 43.93 3.53
3152 3282 5.066117 TGCTCTGTACGTAGTCTCTTATTGG 59.934 44.000 0.00 0.00 43.93 3.16
3153 3283 6.120378 TGCTCTGTACGTAGTCTCTTATTG 57.880 41.667 0.00 0.00 43.93 1.90
3154 3284 6.754702 TTGCTCTGTACGTAGTCTCTTATT 57.245 37.500 0.00 0.00 43.93 1.40
3155 3285 6.754702 TTTGCTCTGTACGTAGTCTCTTAT 57.245 37.500 0.00 0.00 43.93 1.73
3156 3286 6.564709 TTTTGCTCTGTACGTAGTCTCTTA 57.435 37.500 0.00 0.00 43.93 2.10
3157 3287 5.449107 TTTTGCTCTGTACGTAGTCTCTT 57.551 39.130 0.00 0.00 43.93 2.85
3158 3288 5.183331 TCATTTTGCTCTGTACGTAGTCTCT 59.817 40.000 0.00 0.00 43.93 3.10
3159 3289 5.399858 TCATTTTGCTCTGTACGTAGTCTC 58.600 41.667 0.00 0.00 43.93 3.36
3160 3290 5.047943 ACTCATTTTGCTCTGTACGTAGTCT 60.048 40.000 0.00 0.00 43.93 3.24
3161 3291 5.061064 CACTCATTTTGCTCTGTACGTAGTC 59.939 44.000 0.00 0.00 43.93 2.59
3163 3293 5.161358 TCACTCATTTTGCTCTGTACGTAG 58.839 41.667 0.00 0.00 0.00 3.51
3164 3294 5.128992 TCACTCATTTTGCTCTGTACGTA 57.871 39.130 0.00 0.00 0.00 3.57
3165 3295 3.990092 TCACTCATTTTGCTCTGTACGT 58.010 40.909 0.00 0.00 0.00 3.57
3166 3296 4.990543 TTCACTCATTTTGCTCTGTACG 57.009 40.909 0.00 0.00 0.00 3.67
3167 3297 6.734104 AGATTCACTCATTTTGCTCTGTAC 57.266 37.500 0.00 0.00 0.00 2.90
3168 3298 7.331934 GTGTAGATTCACTCATTTTGCTCTGTA 59.668 37.037 0.00 0.00 35.68 2.74
3169 3299 6.148480 GTGTAGATTCACTCATTTTGCTCTGT 59.852 38.462 0.00 0.00 35.68 3.41
3170 3300 6.370994 AGTGTAGATTCACTCATTTTGCTCTG 59.629 38.462 0.00 0.00 44.07 3.35
3171 3301 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
3172 3302 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3211 3341 9.588096 TTCACTATGGACTACATACAGATGTAT 57.412 33.333 0.00 0.00 45.42 2.29
3212 3342 8.990163 TTCACTATGGACTACATACAGATGTA 57.010 34.615 0.00 0.00 44.77 2.29
3214 3344 9.770097 AATTTCACTATGGACTACATACAGATG 57.230 33.333 0.00 0.00 41.03 2.90
3216 3346 9.817809 GAAATTTCACTATGGACTACATACAGA 57.182 33.333 13.40 0.00 41.03 3.41
3217 3347 9.823647 AGAAATTTCACTATGGACTACATACAG 57.176 33.333 19.99 0.00 41.03 2.74
3241 3371 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
3242 3372 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
3243 3373 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
3244 3374 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
3245 3375 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
3246 3376 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3247 3377 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3248 3378 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
3249 3379 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
3250 3380 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
3251 3381 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
3252 3382 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
3253 3383 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
3254 3384 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3255 3385 3.705072 AGTACTCCCTCCGTTCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
3256 3386 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3257 3387 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3258 3388 4.803329 ATAGTACTCCCTCCGTTCCTAA 57.197 45.455 0.00 0.00 0.00 2.69
3259 3389 6.732862 ACTATATAGTACTCCCTCCGTTCCTA 59.267 42.308 13.88 0.00 34.13 2.94
3260 3390 5.551189 ACTATATAGTACTCCCTCCGTTCCT 59.449 44.000 13.88 0.00 34.13 3.36
3261 3391 5.814481 ACTATATAGTACTCCCTCCGTTCC 58.186 45.833 13.88 0.00 34.13 3.62
3262 3392 6.939163 TGAACTATATAGTACTCCCTCCGTTC 59.061 42.308 15.74 7.64 34.99 3.95
3263 3393 6.845908 TGAACTATATAGTACTCCCTCCGTT 58.154 40.000 15.74 0.00 34.99 4.44
3264 3394 6.271857 TCTGAACTATATAGTACTCCCTCCGT 59.728 42.308 15.74 0.00 34.99 4.69
3265 3395 6.709281 TCTGAACTATATAGTACTCCCTCCG 58.291 44.000 15.74 5.64 34.99 4.63
3266 3396 8.110908 ACATCTGAACTATATAGTACTCCCTCC 58.889 40.741 15.74 0.27 34.99 4.30
3309 3494 7.227512 GCTCTATTGTTTAGCCTGATGTACATT 59.772 37.037 10.30 0.00 0.00 2.71
3316 3501 6.359804 TCATTGCTCTATTGTTTAGCCTGAT 58.640 36.000 0.00 0.00 35.33 2.90
3327 3519 8.965172 GCTCAAATTATGTTCATTGCTCTATTG 58.035 33.333 0.00 0.00 0.00 1.90
3332 3524 4.736793 CCGCTCAAATTATGTTCATTGCTC 59.263 41.667 0.00 0.00 0.00 4.26
3339 3531 3.609103 ATCGCCGCTCAAATTATGTTC 57.391 42.857 0.00 0.00 0.00 3.18
3340 3532 4.211374 GTCTATCGCCGCTCAAATTATGTT 59.789 41.667 0.00 0.00 0.00 2.71
3341 3533 3.741344 GTCTATCGCCGCTCAAATTATGT 59.259 43.478 0.00 0.00 0.00 2.29
3353 3546 0.171455 GGCAGATAGGTCTATCGCCG 59.829 60.000 23.74 14.23 44.11 6.46
3409 3602 2.357517 ACTCCGCTTTGCTCACCG 60.358 61.111 0.00 0.00 0.00 4.94
3438 3665 8.232913 ACTGTTTAGACCTTATTTGCTTTCAA 57.767 30.769 0.00 0.00 0.00 2.69
3462 3689 9.923143 TGCATGATTAGTTACCTACACATATAC 57.077 33.333 0.00 0.00 0.00 1.47
3470 3697 8.094548 TCCATACATGCATGATTAGTTACCTAC 58.905 37.037 32.75 0.00 0.00 3.18
3540 3767 7.161404 TGAGCTTAATCACTTGTGACTACAAT 58.839 34.615 5.53 0.00 45.16 2.71
3543 3770 7.171678 AGTTTGAGCTTAATCACTTGTGACTAC 59.828 37.037 5.53 0.00 0.00 2.73
3544 3771 7.217200 AGTTTGAGCTTAATCACTTGTGACTA 58.783 34.615 5.53 0.00 0.00 2.59
3545 3772 6.058183 AGTTTGAGCTTAATCACTTGTGACT 58.942 36.000 5.53 0.00 0.00 3.41
3546 3773 6.305693 AGTTTGAGCTTAATCACTTGTGAC 57.694 37.500 5.53 0.00 0.00 3.67
3547 3774 6.542005 TCAAGTTTGAGCTTAATCACTTGTGA 59.458 34.615 24.05 11.81 35.94 3.58
3548 3775 6.728200 TCAAGTTTGAGCTTAATCACTTGTG 58.272 36.000 24.05 10.24 35.94 3.33
3549 3776 6.942532 TCAAGTTTGAGCTTAATCACTTGT 57.057 33.333 24.05 0.54 35.94 3.16
3599 3826 0.877649 AGACACACAGCAGCTTGTCG 60.878 55.000 16.62 10.63 42.66 4.35
3602 3829 2.478134 GTCTTAGACACACAGCAGCTTG 59.522 50.000 7.59 0.00 32.09 4.01
3625 3852 8.112822 TCCCTTTGGAGAACATGATTTACAATA 58.887 33.333 0.00 0.00 35.03 1.90
3626 3853 6.953520 TCCCTTTGGAGAACATGATTTACAAT 59.046 34.615 0.00 0.00 35.03 2.71
3654 3882 0.606401 CAAACATGAGACCGCCACCT 60.606 55.000 0.00 0.00 0.00 4.00
3655 3883 1.586154 CCAAACATGAGACCGCCACC 61.586 60.000 0.00 0.00 0.00 4.61
3659 3887 1.244019 AAGCCCAAACATGAGACCGC 61.244 55.000 0.00 0.00 0.00 5.68
3662 3890 3.010420 GAGGTAAGCCCAAACATGAGAC 58.990 50.000 0.00 0.00 34.66 3.36
3704 3932 2.497138 CAGTGGCAACTCATCTGACAA 58.503 47.619 0.00 0.00 32.31 3.18
3736 3964 1.204941 CGCAAGCCCTACTCAACTAGT 59.795 52.381 0.00 0.00 42.62 2.57
3774 4003 5.179368 TGATGAAAACAACTTTCTAGCCTCG 59.821 40.000 0.00 0.00 43.42 4.63
3823 4052 1.042229 CAGCTCCCCTCTCTGATCAG 58.958 60.000 17.07 17.07 0.00 2.90
3839 4068 3.243068 CGCAAAATCCTTACCATACCAGC 60.243 47.826 0.00 0.00 0.00 4.85
3845 4074 0.738389 CCGCGCAAAATCCTTACCAT 59.262 50.000 8.75 0.00 0.00 3.55
3847 4076 0.098200 GACCGCGCAAAATCCTTACC 59.902 55.000 8.75 0.00 0.00 2.85
3861 4090 0.811616 CCTTGGTGCTCTATGACCGC 60.812 60.000 0.00 0.00 34.69 5.68


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

AutoCloner maintained by Alex Coulton.