Multiple sequence alignment - TraesCS3D01G425400

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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 TraesCS3D01G425400 chr3D 100.000 4445 0 0 1 4445 537913318 537908874 0.000000e+00 8209
1 TraesCS3D01G425400 chr3D 100.000 367 0 0 4803 5169 537908516 537908150 0.000000e+00 678
2 TraesCS3D01G425400 chr3A 91.407 2793 179 33 1650 4420 673442016 673439263 0.000000e+00 3771
3 TraesCS3D01G425400 chr3A 91.118 1700 85 29 1 1655 673443724 673442046 0.000000e+00 2242
4 TraesCS3D01G425400 chr3A 88.108 370 29 9 4803 5169 673439224 673438867 4.780000e-115 425
5 TraesCS3D01G425400 chr3B 92.887 1687 71 15 1 1655 712568491 712566822 0.000000e+00 2405
6 TraesCS3D01G425400 chr3B 88.858 1813 147 30 2628 4420 712565699 712563922 0.000000e+00 2178
7 TraesCS3D01G425400 chr3B 92.829 1018 48 9 1650 2643 712566792 712565776 0.000000e+00 1452
8 TraesCS3D01G425400 chr3B 90.347 259 14 4 4803 5058 712563890 712563640 3.860000e-86 329


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 TraesCS3D01G425400 chr3D 537908150 537913318 5168 True 4443.5 8209 100.00000 1 5169 2 chr3D.!!$R1 5168
1 TraesCS3D01G425400 chr3A 673438867 673443724 4857 True 2146.0 3771 90.21100 1 5169 3 chr3A.!!$R1 5168
2 TraesCS3D01G425400 chr3B 712563640 712568491 4851 True 1591.0 2405 91.23025 1 5058 4 chr3B.!!$R1 5057

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
151 152 2.032302 AGACGTTTTTGTAATGTGCGCA 59.968 40.909 5.66 5.66 0.00 6.09 F
301 306 2.442236 AGGGGTATCTTGTTGCCATG 57.558 50.000 0.00 0.00 0.00 3.66 F
920 964 3.628002 CCACAGAATGATCATTTGGGGGA 60.628 47.826 27.40 0.00 39.69 4.81 F
2716 2917 0.321034 GGCATCAGCACACAGACAGA 60.321 55.000 0.00 0.00 44.61 3.41 F
3800 4007 0.234884 CAGGTTTGAGAAACGCCGAC 59.765 55.000 0.00 0.00 42.29 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1354 1402 0.735978 TCACTTATCCTGTGCGCACG 60.736 55.000 33.22 26.22 35.58 5.34 R
1356 1404 0.894835 TCTCACTTATCCTGTGCGCA 59.105 50.000 5.66 5.66 35.58 6.09 R
2826 3027 1.588239 AGGGTCATCAAGATGCTCCA 58.412 50.000 18.33 0.00 38.65 3.86 R
4065 4275 0.687920 TGCCAAATGTCCACGGTAGA 59.312 50.000 0.00 0.00 0.00 2.59 R
4873 5091 3.951306 TGAATCAGCAAAGTTGTGTTCG 58.049 40.909 0.00 0.00 0.00 3.95 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
30 31 8.333908 TGTTTGAATTTGAAATAATGTGTGTGC 58.666 29.630 0.00 0.00 0.00 4.57
65 66 4.250464 GCTGGCATACTACAAGTTGTACA 58.750 43.478 11.75 6.61 0.00 2.90
127 128 4.762251 GGAGTTGCCATTCTTTACTTGACT 59.238 41.667 0.00 0.00 36.34 3.41
148 149 5.270853 ACTTGAGACGTTTTTGTAATGTGC 58.729 37.500 0.00 0.00 0.00 4.57
150 151 2.646250 AGACGTTTTTGTAATGTGCGC 58.354 42.857 0.00 0.00 0.00 6.09
151 152 2.032302 AGACGTTTTTGTAATGTGCGCA 59.968 40.909 5.66 5.66 0.00 6.09
152 153 2.977169 GACGTTTTTGTAATGTGCGCAT 59.023 40.909 15.91 7.01 36.80 4.73
183 187 6.536224 GCCAAAATATTTGTCCATTTCAGGAG 59.464 38.462 0.39 0.00 38.64 3.69
184 188 7.614494 CCAAAATATTTGTCCATTTCAGGAGT 58.386 34.615 0.39 0.00 38.64 3.85
185 189 7.761249 CCAAAATATTTGTCCATTTCAGGAGTC 59.239 37.037 0.39 0.00 38.64 3.36
186 190 8.306038 CAAAATATTTGTCCATTTCAGGAGTCA 58.694 33.333 0.39 0.00 38.64 3.41
187 191 7.636150 AATATTTGTCCATTTCAGGAGTCAG 57.364 36.000 0.00 0.00 38.64 3.51
188 192 3.423539 TTGTCCATTTCAGGAGTCAGG 57.576 47.619 0.00 0.00 38.64 3.86
189 193 2.619931 TGTCCATTTCAGGAGTCAGGA 58.380 47.619 0.00 0.00 38.64 3.86
190 194 3.184628 TGTCCATTTCAGGAGTCAGGAT 58.815 45.455 0.00 0.00 38.64 3.24
205 209 5.678583 AGTCAGGATCATAAGGTGTGATTG 58.321 41.667 0.00 0.00 36.49 2.67
211 215 6.070021 AGGATCATAAGGTGTGATTGAACTCA 60.070 38.462 0.00 0.00 36.49 3.41
220 225 3.826157 TGTGATTGAACTCAATTGGGGAC 59.174 43.478 10.75 3.72 45.72 4.46
225 230 4.387026 TGAACTCAATTGGGGACTGAAT 57.613 40.909 10.75 0.00 0.00 2.57
230 235 3.631250 TCAATTGGGGACTGAATTAGGC 58.369 45.455 5.42 0.00 0.00 3.93
238 243 3.531538 GGACTGAATTAGGCGAATCACA 58.468 45.455 0.00 0.00 34.11 3.58
249 254 2.755103 GGCGAATCACAGGGAAAGAATT 59.245 45.455 0.00 0.00 0.00 2.17
292 297 5.397559 CGTGGGAAAGAATTAGGGGTATCTT 60.398 44.000 0.00 0.00 33.73 2.40
301 306 2.442236 AGGGGTATCTTGTTGCCATG 57.558 50.000 0.00 0.00 0.00 3.66
311 316 7.275560 GGTATCTTGTTGCCATGTAAATCAAAC 59.724 37.037 0.00 0.00 0.00 2.93
321 326 8.511321 TGCCATGTAAATCAAACTTGTACTTAG 58.489 33.333 0.00 0.00 0.00 2.18
358 363 6.610075 ATTCCAAACTAGATGCCATTTTGT 57.390 33.333 0.00 0.00 0.00 2.83
359 364 6.418057 TTCCAAACTAGATGCCATTTTGTT 57.582 33.333 0.00 0.00 0.00 2.83
434 462 5.977129 GGAAAATTATGAAACCTATGCACGG 59.023 40.000 0.00 0.00 0.00 4.94
547 589 7.721286 CATTTTGGAATGGAGCTAGTAGTAG 57.279 40.000 0.00 0.00 39.17 2.57
548 590 6.869206 TTTTGGAATGGAGCTAGTAGTAGT 57.131 37.500 6.47 0.00 0.00 2.73
549 591 7.966339 TTTTGGAATGGAGCTAGTAGTAGTA 57.034 36.000 6.47 0.00 0.00 1.82
550 592 7.584122 TTTGGAATGGAGCTAGTAGTAGTAG 57.416 40.000 7.56 7.56 0.00 2.57
551 593 6.263412 TGGAATGGAGCTAGTAGTAGTAGT 57.737 41.667 12.61 1.51 0.00 2.73
552 594 7.384524 TGGAATGGAGCTAGTAGTAGTAGTA 57.615 40.000 12.61 0.00 0.00 1.82
553 595 7.809238 TGGAATGGAGCTAGTAGTAGTAGTAA 58.191 38.462 12.61 0.00 0.00 2.24
554 596 7.718753 TGGAATGGAGCTAGTAGTAGTAGTAAC 59.281 40.741 12.61 5.00 0.00 2.50
555 597 7.938490 GGAATGGAGCTAGTAGTAGTAGTAACT 59.062 40.741 12.61 2.91 39.91 2.24
556 598 9.995003 GAATGGAGCTAGTAGTAGTAGTAACTA 57.005 37.037 12.61 4.57 37.15 2.24
758 800 9.352191 CTCCTTCATAGAATCATTCCTTCAAAT 57.648 33.333 0.00 0.00 0.00 2.32
759 801 9.128404 TCCTTCATAGAATCATTCCTTCAAATG 57.872 33.333 0.00 0.00 37.87 2.32
829 873 7.554959 TGTTTCCTAGTGACCTAAGAGAAAT 57.445 36.000 0.00 0.00 0.00 2.17
836 880 9.372369 CCTAGTGACCTAAGAGAAATTTAACTG 57.628 37.037 0.00 0.00 0.00 3.16
906 950 4.340666 TGTGCACACAATAAACCACAGAAT 59.659 37.500 17.42 0.00 38.56 2.40
907 951 4.681025 GTGCACACAATAAACCACAGAATG 59.319 41.667 13.17 0.00 46.00 2.67
908 952 4.582240 TGCACACAATAAACCACAGAATGA 59.418 37.500 0.00 0.00 39.69 2.57
909 953 5.243507 TGCACACAATAAACCACAGAATGAT 59.756 36.000 0.00 0.00 39.69 2.45
910 954 5.801947 GCACACAATAAACCACAGAATGATC 59.198 40.000 0.00 0.00 39.69 2.92
912 956 7.541162 CACACAATAAACCACAGAATGATCAT 58.459 34.615 1.18 1.18 39.69 2.45
913 957 8.030692 CACACAATAAACCACAGAATGATCATT 58.969 33.333 20.85 20.85 39.69 2.57
914 958 8.587608 ACACAATAAACCACAGAATGATCATTT 58.412 29.630 21.57 9.39 39.69 2.32
915 959 8.865978 CACAATAAACCACAGAATGATCATTTG 58.134 33.333 21.57 20.61 39.69 2.32
916 960 8.036575 ACAATAAACCACAGAATGATCATTTGG 58.963 33.333 25.99 25.99 39.69 3.28
917 961 5.410355 AAACCACAGAATGATCATTTGGG 57.590 39.130 28.87 23.60 39.69 4.12
920 964 3.628002 CCACAGAATGATCATTTGGGGGA 60.628 47.826 27.40 0.00 39.69 4.81
1195 1243 5.751243 TTTTGTCTGCTTCTAGTTTGTCC 57.249 39.130 0.00 0.00 0.00 4.02
1209 1257 7.833786 TCTAGTTTGTCCGATGTTATGTAACT 58.166 34.615 4.71 0.00 37.12 2.24
1354 1402 5.180868 AGCAAGTTGACAGAAGATCATGTTC 59.819 40.000 7.16 0.00 0.00 3.18
1356 1404 4.887748 AGTTGACAGAAGATCATGTTCGT 58.112 39.130 0.00 0.00 0.00 3.85
1471 1519 2.286772 CCGTGGCTGTGTTCTTTTGTAC 60.287 50.000 0.00 0.00 0.00 2.90
1538 1587 5.105595 GCATTTCTTTTAGGTCCAAGCAGAT 60.106 40.000 0.00 0.00 0.00 2.90
1670 1753 9.042008 ACTTACAGTATTAAATATCGCACCAAG 57.958 33.333 0.00 0.00 0.00 3.61
1707 1790 4.945543 TCATGTGATCTCTGGGTTTTGATG 59.054 41.667 0.00 0.00 0.00 3.07
1913 1996 9.157104 TGTCAATGCATTAAGATAGTAAACGAA 57.843 29.630 12.53 0.00 0.00 3.85
2258 2361 3.031736 ACCGTGGTAGATGATACTGCTT 58.968 45.455 0.00 0.00 0.00 3.91
2319 2422 9.912634 ATCTATGACAATCGACAAAACAAATTT 57.087 25.926 0.00 0.00 0.00 1.82
2437 2542 8.279970 TCCAGTAATCAATCACAAAATGGTAG 57.720 34.615 0.00 0.00 0.00 3.18
2438 2543 8.106462 TCCAGTAATCAATCACAAAATGGTAGA 58.894 33.333 0.00 0.00 0.00 2.59
2447 2552 9.533253 CAATCACAAAATGGTAGAGTTCTTTTT 57.467 29.630 0.00 0.00 0.00 1.94
2674 2875 5.946298 TGTGATCTGTTCATCAGCATTTTC 58.054 37.500 0.00 0.00 43.32 2.29
2685 2886 6.240894 TCATCAGCATTTTCCTTACACTCTT 58.759 36.000 0.00 0.00 0.00 2.85
2716 2917 0.321034 GGCATCAGCACACAGACAGA 60.321 55.000 0.00 0.00 44.61 3.41
2826 3027 1.671054 CCGCCGACACCTTTGACAT 60.671 57.895 0.00 0.00 0.00 3.06
2918 3119 7.011482 ACGCTATAATTGGTCTCAAGTCATTTC 59.989 37.037 0.00 0.00 36.19 2.17
2926 3127 5.296780 TGGTCTCAAGTCATTTCACACTTTC 59.703 40.000 0.00 0.00 30.06 2.62
2928 3129 6.425504 GTCTCAAGTCATTTCACACTTTCAG 58.574 40.000 0.00 0.00 30.06 3.02
2941 3142 4.691216 CACACTTTCAGGGAGCTAGTAAAC 59.309 45.833 0.00 0.00 0.00 2.01
3004 3205 5.801947 GGCATTCAACATCAAATACTGTGAC 59.198 40.000 0.00 0.00 0.00 3.67
3012 3213 7.606858 ACATCAAATACTGTGACATCTTCAG 57.393 36.000 0.00 0.00 33.71 3.02
3078 3279 3.829577 CCCAAGATTTAGGGGAGGC 57.170 57.895 0.00 0.00 45.08 4.70
3090 3291 1.929494 AGGGGAGGCACATTGGAAATA 59.071 47.619 0.00 0.00 0.00 1.40
3109 3310 2.124819 ATCAAGAGCTGGCCTGCG 60.125 61.111 26.64 14.02 38.13 5.18
3143 3344 7.815068 AGTATATTGTCAGTGTTCTCAAGACAC 59.185 37.037 0.00 0.00 39.13 3.67
3166 3367 2.030540 GCAGATGCAACTTCTCAAGCAA 60.031 45.455 0.00 0.00 40.76 3.91
3175 3376 4.088823 ACTTCTCAAGCAAAATCATCGC 57.911 40.909 0.00 0.00 0.00 4.58
3197 3398 3.732219 CGCATGCAATGGATTTACACATC 59.268 43.478 19.57 0.00 46.86 3.06
3202 3403 6.527057 TGCAATGGATTTACACATCATGAA 57.473 33.333 0.00 0.00 0.00 2.57
3216 3417 4.082895 ACATCATGAACTTTCAGAAGCAGC 60.083 41.667 0.00 0.00 41.08 5.25
3217 3418 3.479489 TCATGAACTTTCAGAAGCAGCA 58.521 40.909 0.00 0.00 41.08 4.41
3221 3422 4.675510 TGAACTTTCAGAAGCAGCAAAAG 58.324 39.130 0.00 0.00 36.29 2.27
3241 3442 4.124851 AGAACCTATTAGGCGTCTGTTG 57.875 45.455 9.77 0.00 39.63 3.33
3270 3471 4.641541 TGCTTCAATTGTATCTGACCATGG 59.358 41.667 11.19 11.19 0.00 3.66
3283 3484 1.221840 CCATGGGGTCAGGAAGTCG 59.778 63.158 2.85 0.00 0.00 4.18
3286 3487 3.003763 GGGGTCAGGAAGTCGCCT 61.004 66.667 0.00 0.00 39.37 5.52
3319 3520 9.371136 CTATTCTGTGTATTGAACATGTACACT 57.629 33.333 22.77 10.38 45.16 3.55
3328 3529 3.747529 TGAACATGTACACTGCACTCATG 59.252 43.478 0.00 0.00 40.80 3.07
3335 3536 1.556451 ACACTGCACTCATGGATGCTA 59.444 47.619 18.88 8.17 42.55 3.49
3360 3561 2.233431 CCACTCTCAGGGAAGTCTTCTG 59.767 54.545 12.31 4.24 0.00 3.02
3365 3566 4.082845 TCTCAGGGAAGTCTTCTGTACAG 58.917 47.826 17.17 17.17 0.00 2.74
3370 3571 5.186797 CAGGGAAGTCTTCTGTACAGAATCT 59.813 44.000 32.76 28.22 45.40 2.40
3374 3575 7.136119 GGAAGTCTTCTGTACAGAATCTATCG 58.864 42.308 32.76 21.80 45.40 2.92
3375 3576 6.067263 AGTCTTCTGTACAGAATCTATCGC 57.933 41.667 32.76 18.80 45.40 4.58
3376 3577 5.825679 AGTCTTCTGTACAGAATCTATCGCT 59.174 40.000 32.76 20.26 45.40 4.93
3378 3579 4.837896 TCTGTACAGAATCTATCGCTGG 57.162 45.455 23.24 0.00 33.91 4.85
3379 3580 3.570125 TCTGTACAGAATCTATCGCTGGG 59.430 47.826 23.24 0.00 33.91 4.45
3380 3581 2.628178 TGTACAGAATCTATCGCTGGGG 59.372 50.000 0.00 0.00 34.05 4.96
3381 3582 2.088104 ACAGAATCTATCGCTGGGGA 57.912 50.000 0.00 0.00 34.05 4.81
3382 3583 2.614259 ACAGAATCTATCGCTGGGGAT 58.386 47.619 5.53 5.53 34.05 3.85
3383 3584 2.301296 ACAGAATCTATCGCTGGGGATG 59.699 50.000 9.85 1.97 34.05 3.51
3384 3585 2.301296 CAGAATCTATCGCTGGGGATGT 59.699 50.000 9.85 0.00 0.00 3.06
3385 3586 2.975489 AGAATCTATCGCTGGGGATGTT 59.025 45.455 9.85 3.44 0.00 2.71
3386 3587 2.847327 ATCTATCGCTGGGGATGTTG 57.153 50.000 9.85 2.06 0.00 3.33
3387 3588 1.788229 TCTATCGCTGGGGATGTTGA 58.212 50.000 9.85 3.97 0.00 3.18
3388 3589 1.688735 TCTATCGCTGGGGATGTTGAG 59.311 52.381 9.85 0.90 0.00 3.02
3389 3590 0.758734 TATCGCTGGGGATGTTGAGG 59.241 55.000 9.85 0.00 0.00 3.86
3390 3591 1.274703 ATCGCTGGGGATGTTGAGGT 61.275 55.000 0.00 0.00 0.00 3.85
3391 3592 1.746615 CGCTGGGGATGTTGAGGTG 60.747 63.158 0.00 0.00 0.00 4.00
3396 3597 0.404040 GGGGATGTTGAGGTGGTTCA 59.596 55.000 0.00 0.00 0.00 3.18
3398 3599 2.094675 GGGATGTTGAGGTGGTTCATG 58.905 52.381 0.00 0.00 0.00 3.07
3399 3600 2.094675 GGATGTTGAGGTGGTTCATGG 58.905 52.381 0.00 0.00 0.00 3.66
3417 3618 1.620819 TGGAGAACTGAAGGACTCTGC 59.379 52.381 0.00 0.00 0.00 4.26
3428 3629 2.122768 AGGACTCTGCAAGGGGAATAG 58.877 52.381 0.00 0.00 40.48 1.73
3432 3633 4.443621 GACTCTGCAAGGGGAATAGTTAC 58.556 47.826 0.00 0.00 40.48 2.50
3448 3649 8.451748 GGAATAGTTACAGAACTTAAAGGCTTG 58.548 37.037 0.00 0.00 43.70 4.01
3457 3658 6.429385 CAGAACTTAAAGGCTTGATTCAGACT 59.571 38.462 0.00 0.00 31.06 3.24
3469 3670 4.556233 TGATTCAGACTTACAACTCACCG 58.444 43.478 0.00 0.00 0.00 4.94
3481 3682 3.067106 CAACTCACCGAAAGTAGTGCAT 58.933 45.455 0.00 0.00 33.90 3.96
3489 3690 2.868583 CGAAAGTAGTGCATGATGGAGG 59.131 50.000 0.00 0.00 0.00 4.30
3504 3705 2.457598 TGGAGGTATCCTGCCGATATC 58.542 52.381 4.96 0.00 46.80 1.63
3507 3708 3.093057 GAGGTATCCTGCCGATATCTGT 58.907 50.000 8.10 0.00 43.72 3.41
3528 3729 6.264067 TCTGTGTACCTCATGAGATACATCAG 59.736 42.308 30.51 30.51 37.07 2.90
3561 3762 6.305693 GAAGCATAAAGGTTCGCTTGATAT 57.694 37.500 0.00 0.00 44.40 1.63
3566 3767 6.580041 GCATAAAGGTTCGCTTGATATGATTG 59.420 38.462 0.00 0.00 0.00 2.67
3569 3770 6.851222 AAGGTTCGCTTGATATGATTGTAG 57.149 37.500 0.00 0.00 0.00 2.74
3570 3771 5.300752 AGGTTCGCTTGATATGATTGTAGG 58.699 41.667 0.00 0.00 0.00 3.18
3578 3779 7.201504 CGCTTGATATGATTGTAGGTCATGATC 60.202 40.741 0.00 0.00 36.96 2.92
3586 3787 5.682234 TTGTAGGTCATGATCACACTGAT 57.318 39.130 9.06 0.00 40.34 2.90
3587 3788 5.014808 TGTAGGTCATGATCACACTGATG 57.985 43.478 9.06 0.00 37.20 3.07
3592 3793 4.100035 GGTCATGATCACACTGATGGTCTA 59.900 45.833 0.00 0.00 37.20 2.59
3593 3794 5.046529 GTCATGATCACACTGATGGTCTAC 58.953 45.833 0.00 0.00 37.20 2.59
3623 3824 3.006247 GAGGGAATGAGCTTGACAAGTC 58.994 50.000 16.39 12.43 0.00 3.01
3628 3829 2.890808 TGAGCTTGACAAGTCGTCTT 57.109 45.000 16.39 0.00 45.60 3.01
3643 3844 2.362397 TCGTCTTGTATCTGGGCTCATC 59.638 50.000 0.00 0.00 0.00 2.92
3652 3853 1.761198 TCTGGGCTCATCACTGATCTG 59.239 52.381 0.00 0.00 0.00 2.90
3658 3859 3.071312 GGCTCATCACTGATCTGGAATCT 59.929 47.826 4.49 0.00 0.00 2.40
3669 3870 9.205719 CACTGATCTGGAATCTGTAATTGATAG 57.794 37.037 4.49 0.00 0.00 2.08
3673 3874 9.770097 GATCTGGAATCTGTAATTGATAGACAA 57.230 33.333 0.00 0.00 42.95 3.18
3676 3877 8.908786 TGGAATCTGTAATTGATAGACAATCC 57.091 34.615 0.00 0.00 46.90 3.01
3678 3879 8.997323 GGAATCTGTAATTGATAGACAATCCAG 58.003 37.037 0.00 0.00 46.90 3.86
3684 3885 7.560991 TGTAATTGATAGACAATCCAGGCAATT 59.439 33.333 0.00 0.00 46.90 2.32
3686 3887 6.855763 TTGATAGACAATCCAGGCAATTTT 57.144 33.333 0.00 0.00 33.22 1.82
3690 3894 5.143376 AGACAATCCAGGCAATTTTCTTG 57.857 39.130 0.00 0.00 0.00 3.02
3705 3909 7.040686 GCAATTTTCTTGTAAAGGACTCCAGTA 60.041 37.037 0.00 0.00 46.24 2.74
3763 3967 4.199432 AGAAGTCGAGCAATCAGATGTT 57.801 40.909 0.00 0.00 0.00 2.71
3766 3970 4.134379 AGTCGAGCAATCAGATGTTCAT 57.866 40.909 0.00 0.00 31.60 2.57
3800 4007 0.234884 CAGGTTTGAGAAACGCCGAC 59.765 55.000 0.00 0.00 42.29 4.79
3804 4011 0.601841 TTTGAGAAACGCCGACCCTC 60.602 55.000 0.00 0.00 0.00 4.30
3805 4012 2.125633 GAGAAACGCCGACCCTCC 60.126 66.667 0.00 0.00 0.00 4.30
3812 4019 2.990479 GCCGACCCTCCATCAAGT 59.010 61.111 0.00 0.00 0.00 3.16
3866 4073 2.170166 GACCATTTGCATCCACCTTGA 58.830 47.619 0.00 0.00 0.00 3.02
3867 4074 2.165030 GACCATTTGCATCCACCTTGAG 59.835 50.000 0.00 0.00 0.00 3.02
3892 4099 3.039134 AAAAACGCGCTTCCCAGG 58.961 55.556 5.73 0.00 0.00 4.45
3916 4126 7.016563 AGGAAAAAGGCAAGGATAAACTTCAAT 59.983 33.333 0.00 0.00 0.00 2.57
3927 4137 8.934023 AGGATAAACTTCAATTTCTGGTACAA 57.066 30.769 0.00 0.00 38.70 2.41
3928 4138 9.362151 AGGATAAACTTCAATTTCTGGTACAAA 57.638 29.630 0.00 0.00 38.70 2.83
3938 4148 0.321653 CTGGTACAAAGCTCCGCCTT 60.322 55.000 0.00 0.00 38.70 4.35
3960 4170 2.092429 TGACTCCCTTGCAGAGTTTTGT 60.092 45.455 8.35 0.00 44.55 2.83
3961 4171 2.550180 GACTCCCTTGCAGAGTTTTGTC 59.450 50.000 8.35 0.00 44.55 3.18
3963 4173 3.217626 CTCCCTTGCAGAGTTTTGTCTT 58.782 45.455 0.00 0.00 0.00 3.01
3968 4178 4.260948 CCTTGCAGAGTTTTGTCTTGTCTC 60.261 45.833 0.00 0.00 0.00 3.36
3984 4194 3.479489 TGTCTCTCAATGAAGCTTGCAA 58.521 40.909 2.10 0.00 0.00 4.08
3986 4196 4.082949 TGTCTCTCAATGAAGCTTGCAATG 60.083 41.667 2.10 5.69 0.00 2.82
3987 4197 4.155462 GTCTCTCAATGAAGCTTGCAATGA 59.845 41.667 2.10 9.73 0.00 2.57
3988 4198 4.395231 TCTCTCAATGAAGCTTGCAATGAG 59.605 41.667 23.78 23.78 42.08 2.90
4036 4246 1.476074 CTCTTCGAGATGAGCTTCGC 58.524 55.000 0.58 0.00 0.00 4.70
4037 4247 0.811281 TCTTCGAGATGAGCTTCGCA 59.189 50.000 0.58 0.00 0.00 5.10
4038 4248 1.202348 TCTTCGAGATGAGCTTCGCAA 59.798 47.619 0.58 0.00 0.00 4.85
4041 4251 1.995484 TCGAGATGAGCTTCGCAAAAG 59.005 47.619 0.58 0.00 0.00 2.27
4048 4258 1.399791 GAGCTTCGCAAAAGGATCCTG 59.600 52.381 17.02 4.89 0.00 3.86
4049 4259 1.003580 AGCTTCGCAAAAGGATCCTGA 59.996 47.619 17.02 4.64 0.00 3.86
4059 4269 5.920840 GCAAAAGGATCCTGAAGTTTGTTAC 59.079 40.000 26.43 13.84 0.00 2.50
4065 4275 4.931661 TCCTGAAGTTTGTTACTCGAGT 57.068 40.909 23.66 23.66 35.54 4.18
4066 4276 4.868067 TCCTGAAGTTTGTTACTCGAGTC 58.132 43.478 23.89 9.53 35.54 3.36
4071 4281 4.416505 AGTTTGTTACTCGAGTCTACCG 57.583 45.455 23.89 0.00 28.23 4.02
4078 4288 1.339824 ACTCGAGTCTACCGTGGACAT 60.340 52.381 13.58 2.82 36.29 3.06
4113 4323 4.202441 AGACAGTCTGCAGAACAAAATGT 58.798 39.130 20.19 11.74 0.00 2.71
4124 4334 5.406477 GCAGAACAAAATGTGAGGGAATTTC 59.594 40.000 0.00 0.00 0.00 2.17
4126 4336 6.421801 CAGAACAAAATGTGAGGGAATTTCAC 59.578 38.462 2.39 2.39 44.03 3.18
4128 4338 6.484364 ACAAAATGTGAGGGAATTTCACTT 57.516 33.333 2.00 1.90 44.08 3.16
4148 4358 5.294060 CACTTGGAGTGGAAAACCAAAATTG 59.706 40.000 0.00 0.00 42.35 2.32
4149 4359 5.188751 ACTTGGAGTGGAAAACCAAAATTGA 59.811 36.000 0.00 0.00 42.02 2.57
4170 4380 9.781633 AATTGATGAATTGTTTGAAGGATGAAA 57.218 25.926 0.00 0.00 30.17 2.69
4195 4406 6.942532 AGCAGTTTAATTTCTGTCTGTGAA 57.057 33.333 0.00 0.00 34.57 3.18
4256 4467 9.109393 CTTTGTATATTGTACCTATGTTGCTGT 57.891 33.333 0.00 0.00 0.00 4.40
4277 4488 1.698506 CCTTGTGTTTGCCCCTGTAA 58.301 50.000 0.00 0.00 0.00 2.41
4279 4490 2.632512 CCTTGTGTTTGCCCCTGTAAAT 59.367 45.455 0.00 0.00 0.00 1.40
4280 4491 3.554752 CCTTGTGTTTGCCCCTGTAAATG 60.555 47.826 0.00 0.00 0.00 2.32
4281 4492 2.950781 TGTGTTTGCCCCTGTAAATGA 58.049 42.857 0.00 0.00 0.00 2.57
4282 4493 3.505386 TGTGTTTGCCCCTGTAAATGAT 58.495 40.909 0.00 0.00 0.00 2.45
4283 4494 4.667573 TGTGTTTGCCCCTGTAAATGATA 58.332 39.130 0.00 0.00 0.00 2.15
4284 4495 5.080337 TGTGTTTGCCCCTGTAAATGATAA 58.920 37.500 0.00 0.00 0.00 1.75
4285 4496 5.184864 TGTGTTTGCCCCTGTAAATGATAAG 59.815 40.000 0.00 0.00 0.00 1.73
4286 4497 4.159506 TGTTTGCCCCTGTAAATGATAAGC 59.840 41.667 0.00 0.00 0.00 3.09
4287 4498 3.951563 TGCCCCTGTAAATGATAAGCT 57.048 42.857 0.00 0.00 0.00 3.74
4288 4499 3.554934 TGCCCCTGTAAATGATAAGCTG 58.445 45.455 0.00 0.00 0.00 4.24
4289 4500 3.201930 TGCCCCTGTAAATGATAAGCTGA 59.798 43.478 0.00 0.00 0.00 4.26
4290 4501 4.207165 GCCCCTGTAAATGATAAGCTGAA 58.793 43.478 0.00 0.00 0.00 3.02
4291 4502 4.829492 GCCCCTGTAAATGATAAGCTGAAT 59.171 41.667 0.00 0.00 0.00 2.57
4292 4503 5.048434 GCCCCTGTAAATGATAAGCTGAATC 60.048 44.000 0.00 0.00 0.00 2.52
4293 4504 6.064060 CCCCTGTAAATGATAAGCTGAATCA 58.936 40.000 12.91 12.91 37.73 2.57
4294 4505 6.206243 CCCCTGTAAATGATAAGCTGAATCAG 59.794 42.308 15.11 5.78 36.82 2.90
4328 4539 6.715280 AGATATATTTGTGCTATGGAGGTGG 58.285 40.000 0.00 0.00 0.00 4.61
4341 4552 9.555411 TGCTATGGAGGTGGTATTTATATCTTA 57.445 33.333 0.00 0.00 0.00 2.10
4370 4588 6.305272 ACTGAGGATAAATCTGTGTGACAT 57.695 37.500 0.00 0.00 0.00 3.06
4389 4607 7.173218 TGTGACATGAATAAGGTTTCAGTCTTC 59.827 37.037 0.00 0.00 38.90 2.87
4420 4638 7.004086 TCGGGATATCAAAATAGAAAATGCCT 58.996 34.615 4.83 0.00 0.00 4.75
4422 4640 8.143835 CGGGATATCAAAATAGAAAATGCCTTT 58.856 33.333 4.83 0.00 0.00 3.11
4423 4641 9.264719 GGGATATCAAAATAGAAAATGCCTTTG 57.735 33.333 4.83 0.00 0.00 2.77
4424 4642 9.264719 GGATATCAAAATAGAAAATGCCTTTGG 57.735 33.333 4.83 0.00 0.00 3.28
4425 4643 9.822185 GATATCAAAATAGAAAATGCCTTTGGT 57.178 29.630 0.00 0.00 0.00 3.67
4427 4645 8.922931 ATCAAAATAGAAAATGCCTTTGGTTT 57.077 26.923 0.00 0.00 0.00 3.27
4428 4646 8.376889 TCAAAATAGAAAATGCCTTTGGTTTC 57.623 30.769 0.00 0.00 0.00 2.78
4431 4649 8.922931 AAATAGAAAATGCCTTTGGTTTCATT 57.077 26.923 0.00 0.00 33.37 2.57
4433 4651 6.866010 AGAAAATGCCTTTGGTTTCATTTC 57.134 33.333 0.00 0.00 37.94 2.17
4435 4653 7.734942 AGAAAATGCCTTTGGTTTCATTTCTA 58.265 30.769 0.00 0.00 37.94 2.10
4438 4656 6.855763 ATGCCTTTGGTTTCATTTCTATGA 57.144 33.333 0.00 0.00 39.00 2.15
4439 4657 6.662865 TGCCTTTGGTTTCATTTCTATGAA 57.337 33.333 0.00 0.00 46.38 2.57
4829 5047 6.873605 CCATTAGTAAATGCATCGAGGTATGA 59.126 38.462 0.34 0.00 41.06 2.15
4840 5058 7.389232 TGCATCGAGGTATGATATCTTCATTT 58.611 34.615 3.98 0.00 42.62 2.32
4890 5109 2.080693 ACACGAACACAACTTTGCTGA 58.919 42.857 0.00 0.00 0.00 4.26
4891 5110 2.682856 ACACGAACACAACTTTGCTGAT 59.317 40.909 0.00 0.00 0.00 2.90
4899 5118 4.098349 ACACAACTTTGCTGATTCATGTGT 59.902 37.500 12.05 12.05 43.64 3.72
4914 5133 5.159273 TCATGTGTTATGTTGGCTCTACA 57.841 39.130 0.00 0.00 0.00 2.74
4919 5138 6.649155 TGTGTTATGTTGGCTCTACATGTAT 58.351 36.000 5.91 0.00 36.89 2.29
4920 5139 7.109501 TGTGTTATGTTGGCTCTACATGTATT 58.890 34.615 5.91 0.00 36.89 1.89
4921 5140 7.609918 TGTGTTATGTTGGCTCTACATGTATTT 59.390 33.333 5.91 0.00 36.89 1.40
4922 5141 8.458843 GTGTTATGTTGGCTCTACATGTATTTT 58.541 33.333 5.91 0.00 36.89 1.82
4923 5142 8.673711 TGTTATGTTGGCTCTACATGTATTTTC 58.326 33.333 5.91 0.00 36.89 2.29
4924 5143 8.893727 GTTATGTTGGCTCTACATGTATTTTCT 58.106 33.333 5.91 0.00 36.89 2.52
4927 5146 9.632638 ATGTTGGCTCTACATGTATTTTCTATT 57.367 29.630 5.91 0.00 35.03 1.73
4959 5178 6.687647 GCTTGGAGCTATTTCCTAGAGACATT 60.688 42.308 7.53 0.00 40.98 2.71
5022 5243 3.627577 ACAAGAATGTGACAGCGAAAACT 59.372 39.130 0.00 0.00 38.69 2.66
5062 5283 2.308866 ACAAGGCCAGCTACCAATAACT 59.691 45.455 5.01 0.00 0.00 2.24
5064 5285 2.196595 AGGCCAGCTACCAATAACTGA 58.803 47.619 5.01 0.00 31.67 3.41
5065 5286 2.780010 AGGCCAGCTACCAATAACTGAT 59.220 45.455 5.01 0.00 31.67 2.90
5066 5287 3.973973 AGGCCAGCTACCAATAACTGATA 59.026 43.478 5.01 0.00 31.67 2.15
5072 5293 7.148641 CCAGCTACCAATAACTGATACTACAG 58.851 42.308 0.00 0.00 42.78 2.74
5098 5319 5.437289 TTTGTTTGCAGACCATACTTCTG 57.563 39.130 4.73 0.00 43.01 3.02
5103 5324 3.165071 TGCAGACCATACTTCTGTCAGA 58.835 45.455 0.00 0.00 42.26 3.27
5113 5334 6.094464 CCATACTTCTGTCAGATGAATTTGCA 59.906 38.462 19.66 0.00 0.00 4.08
5116 5337 3.682696 TCTGTCAGATGAATTTGCAGCT 58.317 40.909 0.00 0.00 34.31 4.24
5134 5355 5.130975 TGCAGCTATATTCTTCTGGAAGGAA 59.869 40.000 10.01 4.68 38.88 3.36
5139 5360 1.430992 TTCTTCTGGAAGGAACGGGT 58.569 50.000 10.01 0.00 38.88 5.28
5150 5371 1.070105 GAACGGGTAGTGTGTGCCA 59.930 57.895 0.00 0.00 30.82 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.503521 TGTAGAGCACACACATTATTTCAAA 57.496 32.000 0.00 0.00 30.04 2.69
27 28 3.378112 TGCCAGCAATTTATGTAGAGCAC 59.622 43.478 0.00 0.00 0.00 4.40
30 31 7.657354 TGTAGTATGCCAGCAATTTATGTAGAG 59.343 37.037 0.00 0.00 0.00 2.43
65 66 7.066284 CACGATAATGAGGAAACAAGGATTTCT 59.934 37.037 0.00 0.00 38.43 2.52
127 128 4.275662 CGCACATTACAAAAACGTCTCAA 58.724 39.130 0.00 0.00 0.00 3.02
148 149 3.354089 AATATTTTGGCGAAGGATGCG 57.646 42.857 0.00 0.00 43.07 4.73
150 151 5.043248 GGACAAATATTTTGGCGAAGGATG 58.957 41.667 0.00 0.00 0.00 3.51
151 152 4.709397 TGGACAAATATTTTGGCGAAGGAT 59.291 37.500 0.00 0.00 0.00 3.24
152 153 4.082845 TGGACAAATATTTTGGCGAAGGA 58.917 39.130 0.00 0.00 0.00 3.36
183 187 5.674525 TCAATCACACCTTATGATCCTGAC 58.325 41.667 0.00 0.00 35.72 3.51
184 188 5.955961 TCAATCACACCTTATGATCCTGA 57.044 39.130 0.00 0.00 35.72 3.86
185 189 6.118170 AGTTCAATCACACCTTATGATCCTG 58.882 40.000 0.00 0.00 35.72 3.86
186 190 6.070021 TGAGTTCAATCACACCTTATGATCCT 60.070 38.462 0.00 0.00 35.72 3.24
187 191 6.115446 TGAGTTCAATCACACCTTATGATCC 58.885 40.000 0.00 0.00 35.72 3.36
188 192 7.615582 TTGAGTTCAATCACACCTTATGATC 57.384 36.000 0.00 0.00 35.72 2.92
189 193 8.464404 CAATTGAGTTCAATCACACCTTATGAT 58.536 33.333 7.74 0.00 45.06 2.45
190 194 7.094248 CCAATTGAGTTCAATCACACCTTATGA 60.094 37.037 7.12 0.00 45.06 2.15
205 209 5.358160 CCTAATTCAGTCCCCAATTGAGTTC 59.642 44.000 7.12 0.00 28.66 3.01
211 215 2.241176 TCGCCTAATTCAGTCCCCAATT 59.759 45.455 0.00 0.00 0.00 2.32
220 225 2.874701 CCCTGTGATTCGCCTAATTCAG 59.125 50.000 0.00 0.00 33.48 3.02
225 230 2.569853 TCTTTCCCTGTGATTCGCCTAA 59.430 45.455 0.00 0.00 0.00 2.69
230 235 5.066505 CCCTTAATTCTTTCCCTGTGATTCG 59.933 44.000 0.00 0.00 0.00 3.34
238 243 9.035890 CAAAAAGATACCCTTAATTCTTTCCCT 57.964 33.333 0.00 0.00 37.42 4.20
249 254 5.474189 CCCACGAAACAAAAAGATACCCTTA 59.526 40.000 0.00 0.00 34.00 2.69
268 273 2.801077 ACCCCTAATTCTTTCCCACG 57.199 50.000 0.00 0.00 0.00 4.94
321 326 9.886132 TCTAGTTTGGAATAGAAAGGATACAAC 57.114 33.333 0.00 0.00 41.41 3.32
327 332 6.069673 TGGCATCTAGTTTGGAATAGAAAGGA 60.070 38.462 0.00 0.00 32.05 3.36
329 334 7.814264 ATGGCATCTAGTTTGGAATAGAAAG 57.186 36.000 0.00 0.00 32.05 2.62
335 340 6.610075 ACAAAATGGCATCTAGTTTGGAAT 57.390 33.333 20.49 3.75 34.28 3.01
364 369 8.815565 TTCATATAAAGTAAAAGTGGCCATGA 57.184 30.769 9.72 0.00 0.00 3.07
369 374 8.833493 ACCGTATTCATATAAAGTAAAAGTGGC 58.167 33.333 0.00 0.00 0.00 5.01
379 384 9.537192 TCCTTTACACACCGTATTCATATAAAG 57.463 33.333 0.00 0.00 0.00 1.85
434 462 8.874744 TTTTAGTTGGTTATGTTTAGGTTTGC 57.125 30.769 0.00 0.00 0.00 3.68
557 599 4.039032 CGGCGTATTCACAAACACTTTTT 58.961 39.130 0.00 0.00 0.00 1.94
758 800 4.505566 GCTTATCTGGACAGCATATTCCCA 60.506 45.833 0.00 0.00 33.45 4.37
759 801 4.006319 GCTTATCTGGACAGCATATTCCC 58.994 47.826 0.00 0.00 33.45 3.97
889 933 8.865978 CAAATGATCATTCTGTGGTTTATTGTG 58.134 33.333 20.95 6.95 0.00 3.33
906 950 1.905839 TAGCCTCCCCCAAATGATCA 58.094 50.000 0.00 0.00 0.00 2.92
907 951 2.175715 ACTTAGCCTCCCCCAAATGATC 59.824 50.000 0.00 0.00 0.00 2.92
908 952 2.217776 ACTTAGCCTCCCCCAAATGAT 58.782 47.619 0.00 0.00 0.00 2.45
909 953 1.681229 ACTTAGCCTCCCCCAAATGA 58.319 50.000 0.00 0.00 0.00 2.57
910 954 2.241176 TGTACTTAGCCTCCCCCAAATG 59.759 50.000 0.00 0.00 0.00 2.32
912 956 1.913419 CTGTACTTAGCCTCCCCCAAA 59.087 52.381 0.00 0.00 0.00 3.28
913 957 1.580059 CTGTACTTAGCCTCCCCCAA 58.420 55.000 0.00 0.00 0.00 4.12
914 958 0.326238 CCTGTACTTAGCCTCCCCCA 60.326 60.000 0.00 0.00 0.00 4.96
915 959 0.326332 ACCTGTACTTAGCCTCCCCC 60.326 60.000 0.00 0.00 0.00 5.40
916 960 0.831307 CACCTGTACTTAGCCTCCCC 59.169 60.000 0.00 0.00 0.00 4.81
917 961 0.831307 CCACCTGTACTTAGCCTCCC 59.169 60.000 0.00 0.00 0.00 4.30
920 964 1.196012 GCTCCACCTGTACTTAGCCT 58.804 55.000 0.00 0.00 0.00 4.58
1195 1243 9.529325 TTAGAATCAAGGAGTTACATAACATCG 57.471 33.333 4.67 0.00 38.62 3.84
1276 1324 9.424319 TGAAACAAACAGCTACAAAATGTTAAA 57.576 25.926 0.00 0.00 36.18 1.52
1354 1402 0.735978 TCACTTATCCTGTGCGCACG 60.736 55.000 33.22 26.22 35.58 5.34
1356 1404 0.894835 TCTCACTTATCCTGTGCGCA 59.105 50.000 5.66 5.66 35.58 6.09
1653 1702 9.950680 CATTAGAAACTTGGTGCGATATTTAAT 57.049 29.630 0.00 0.00 0.00 1.40
1654 1703 8.952278 ACATTAGAAACTTGGTGCGATATTTAA 58.048 29.630 0.00 0.00 0.00 1.52
1656 1705 7.391148 ACATTAGAAACTTGGTGCGATATTT 57.609 32.000 0.00 0.00 0.00 1.40
1657 1706 8.677148 ATACATTAGAAACTTGGTGCGATATT 57.323 30.769 0.00 0.00 0.00 1.28
1665 1748 9.295825 TCACATGAAATACATTAGAAACTTGGT 57.704 29.630 0.00 0.00 37.07 3.67
1692 1775 6.361433 TGTTTTCTACATCAAAACCCAGAGA 58.639 36.000 5.76 0.00 41.25 3.10
1707 1790 3.127721 GCTCTTCCAGCCATGTTTTCTAC 59.872 47.826 0.00 0.00 43.17 2.59
1913 1996 1.818674 GCCATTCTTGGTTGTTCCGAT 59.181 47.619 0.00 0.00 45.57 4.18
2258 2361 1.697432 CTGTGTTCTAACCTCCCACCA 59.303 52.381 0.00 0.00 0.00 4.17
2319 2422 2.914941 GGTACCAAAAGGGAAGGAGGTA 59.085 50.000 7.15 0.00 41.15 3.08
2401 2504 6.939730 TGATTGATTACTGGAACTGCACTTAA 59.060 34.615 0.00 0.00 0.00 1.85
2447 2552 6.403049 TGCTCGTGTCTCCTTTTATATCAAA 58.597 36.000 0.00 0.00 0.00 2.69
2674 2875 7.174253 TGCCTGTAAATAAACAAGAGTGTAAGG 59.826 37.037 0.00 0.00 36.80 2.69
2685 2886 4.764308 TGTGCTGATGCCTGTAAATAAACA 59.236 37.500 0.00 0.00 38.71 2.83
2716 2917 3.822167 CCAAAGAAGGCATGCCAATTTTT 59.178 39.130 37.18 26.76 38.92 1.94
2826 3027 1.588239 AGGGTCATCAAGATGCTCCA 58.412 50.000 18.33 0.00 38.65 3.86
2918 3119 4.537135 TTACTAGCTCCCTGAAAGTGTG 57.463 45.455 0.00 0.00 0.00 3.82
2926 3127 2.317530 GCTGGTTTACTAGCTCCCTG 57.682 55.000 10.55 0.00 45.52 4.45
3004 3205 0.037303 ACTGGCACCCACTGAAGATG 59.963 55.000 0.00 0.00 0.00 2.90
3012 3213 1.272212 CACCAATTAACTGGCACCCAC 59.728 52.381 2.07 0.00 40.45 4.61
3065 3266 2.091885 TCCAATGTGCCTCCCCTAAATC 60.092 50.000 0.00 0.00 0.00 2.17
3078 3279 6.263344 CAGCTCTTGATGTATTTCCAATGTG 58.737 40.000 0.00 0.00 0.00 3.21
3090 3291 1.378250 GCAGGCCAGCTCTTGATGT 60.378 57.895 13.78 0.00 0.00 3.06
3109 3310 5.488341 ACACTGACAATATACTCCAACACC 58.512 41.667 0.00 0.00 0.00 4.16
3154 3355 3.425359 CGCGATGATTTTGCTTGAGAAGT 60.425 43.478 0.00 0.00 31.94 3.01
3157 3358 1.202065 GCGCGATGATTTTGCTTGAGA 60.202 47.619 12.10 0.00 31.94 3.27
3162 3363 0.868602 GCATGCGCGATGATTTTGCT 60.869 50.000 12.10 0.00 33.31 3.91
3166 3367 3.951115 ATTGCATGCGCGATGATTT 57.049 42.105 12.10 4.36 40.97 2.17
3175 3376 3.148026 TGTGTAAATCCATTGCATGCG 57.852 42.857 14.09 0.00 36.00 4.73
3197 3398 3.909776 TGCTGCTTCTGAAAGTTCATG 57.090 42.857 0.00 0.00 36.46 3.07
3202 3403 4.440663 GGTTCTTTTGCTGCTTCTGAAAGT 60.441 41.667 0.00 0.00 34.79 2.66
3216 3417 4.935808 ACAGACGCCTAATAGGTTCTTTTG 59.064 41.667 8.28 3.05 37.80 2.44
3217 3418 5.161943 ACAGACGCCTAATAGGTTCTTTT 57.838 39.130 8.28 0.00 37.80 2.27
3221 3422 3.864003 GTCAACAGACGCCTAATAGGTTC 59.136 47.826 8.28 5.20 37.80 3.62
3241 3442 6.310197 GTCAGATACAATTGAAGCAACAGTC 58.690 40.000 13.59 0.00 0.00 3.51
3275 3476 0.902516 AGCTTCTCAGGCGACTTCCT 60.903 55.000 0.00 0.00 40.21 3.36
3283 3484 3.258971 ACACAGAATAGCTTCTCAGGC 57.741 47.619 0.00 0.00 39.78 4.85
3286 3487 7.386059 TGTTCAATACACAGAATAGCTTCTCA 58.614 34.615 0.00 0.00 39.78 3.27
3319 3520 0.181114 GGGTAGCATCCATGAGTGCA 59.819 55.000 19.78 7.37 43.63 4.57
3328 3529 0.691078 TGAGAGTGGGGGTAGCATCC 60.691 60.000 0.00 0.00 0.00 3.51
3335 3536 1.229658 CTTCCCTGAGAGTGGGGGT 60.230 63.158 0.00 0.00 44.67 4.95
3360 3561 2.891580 TCCCCAGCGATAGATTCTGTAC 59.108 50.000 0.00 0.00 39.76 2.90
3365 3566 3.070018 CAACATCCCCAGCGATAGATTC 58.930 50.000 0.00 0.00 39.76 2.52
3370 3571 0.758734 CCTCAACATCCCCAGCGATA 59.241 55.000 0.00 0.00 0.00 2.92
3374 3575 1.379044 CCACCTCAACATCCCCAGC 60.379 63.158 0.00 0.00 0.00 4.85
3375 3576 0.405585 AACCACCTCAACATCCCCAG 59.594 55.000 0.00 0.00 0.00 4.45
3376 3577 0.404040 GAACCACCTCAACATCCCCA 59.596 55.000 0.00 0.00 0.00 4.96
3378 3579 2.094675 CATGAACCACCTCAACATCCC 58.905 52.381 0.00 0.00 0.00 3.85
3379 3580 2.094675 CCATGAACCACCTCAACATCC 58.905 52.381 0.00 0.00 0.00 3.51
3380 3581 3.012518 CTCCATGAACCACCTCAACATC 58.987 50.000 0.00 0.00 0.00 3.06
3381 3582 2.644299 TCTCCATGAACCACCTCAACAT 59.356 45.455 0.00 0.00 0.00 2.71
3382 3583 2.054021 TCTCCATGAACCACCTCAACA 58.946 47.619 0.00 0.00 0.00 3.33
3383 3584 2.814336 GTTCTCCATGAACCACCTCAAC 59.186 50.000 0.00 0.00 46.89 3.18
3384 3585 3.140325 GTTCTCCATGAACCACCTCAA 57.860 47.619 0.00 0.00 46.89 3.02
3385 3586 2.859165 GTTCTCCATGAACCACCTCA 57.141 50.000 0.00 0.00 46.89 3.86
3396 3597 2.235898 GCAGAGTCCTTCAGTTCTCCAT 59.764 50.000 0.00 0.00 0.00 3.41
3398 3599 1.620819 TGCAGAGTCCTTCAGTTCTCC 59.379 52.381 0.00 0.00 0.00 3.71
3399 3600 3.324993 CTTGCAGAGTCCTTCAGTTCTC 58.675 50.000 0.00 0.00 0.00 2.87
3407 3608 1.376649 ATTCCCCTTGCAGAGTCCTT 58.623 50.000 0.00 0.00 0.00 3.36
3417 3618 8.857694 TTTAAGTTCTGTAACTATTCCCCTTG 57.142 34.615 0.00 0.00 45.37 3.61
3428 3629 7.871853 TGAATCAAGCCTTTAAGTTCTGTAAC 58.128 34.615 0.00 0.00 35.72 2.50
3432 3633 6.429385 AGTCTGAATCAAGCCTTTAAGTTCTG 59.571 38.462 0.00 0.00 0.00 3.02
3448 3649 4.806330 TCGGTGAGTTGTAAGTCTGAATC 58.194 43.478 1.59 0.00 0.00 2.52
3457 3658 4.053295 GCACTACTTTCGGTGAGTTGTAA 58.947 43.478 0.00 0.00 32.67 2.41
3469 3670 3.878778 ACCTCCATCATGCACTACTTTC 58.121 45.455 0.00 0.00 0.00 2.62
3481 3682 0.105709 TCGGCAGGATACCTCCATCA 60.106 55.000 0.00 0.00 44.79 3.07
3489 3690 3.944055 ACACAGATATCGGCAGGATAC 57.056 47.619 2.46 0.00 40.34 2.24
3528 3729 3.118223 ACCTTTATGCTTCACTAGGAGCC 60.118 47.826 11.09 0.00 0.00 4.70
3553 3754 7.605309 TGATCATGACCTACAATCATATCAAGC 59.395 37.037 0.00 0.00 34.99 4.01
3561 3762 5.187576 TCAGTGTGATCATGACCTACAATCA 59.812 40.000 0.00 0.00 0.00 2.57
3566 3767 4.141846 ACCATCAGTGTGATCATGACCTAC 60.142 45.833 0.00 0.00 34.28 3.18
3569 3770 3.118482 AGACCATCAGTGTGATCATGACC 60.118 47.826 0.00 0.00 34.28 4.02
3570 3771 4.134379 AGACCATCAGTGTGATCATGAC 57.866 45.455 0.00 0.00 34.28 3.06
3578 3779 4.887748 ACTTTCAGTAGACCATCAGTGTG 58.112 43.478 0.00 0.00 0.00 3.82
3586 3787 3.583228 TCCCTCAACTTTCAGTAGACCA 58.417 45.455 0.00 0.00 0.00 4.02
3587 3788 4.618920 TTCCCTCAACTTTCAGTAGACC 57.381 45.455 0.00 0.00 0.00 3.85
3592 3793 3.073650 AGCTCATTCCCTCAACTTTCAGT 59.926 43.478 0.00 0.00 0.00 3.41
3593 3794 3.683802 AGCTCATTCCCTCAACTTTCAG 58.316 45.455 0.00 0.00 0.00 3.02
3623 3824 2.101415 TGATGAGCCCAGATACAAGACG 59.899 50.000 0.00 0.00 0.00 4.18
3628 3829 2.750814 TCAGTGATGAGCCCAGATACA 58.249 47.619 0.00 0.00 0.00 2.29
3643 3844 9.205719 CTATCAATTACAGATTCCAGATCAGTG 57.794 37.037 0.00 0.00 0.00 3.66
3652 3853 8.908786 TGGATTGTCTATCAATTACAGATTCC 57.091 34.615 0.00 0.00 45.49 3.01
3658 3859 6.000246 TGCCTGGATTGTCTATCAATTACA 58.000 37.500 0.00 0.00 45.49 2.41
3669 3870 4.886579 ACAAGAAAATTGCCTGGATTGTC 58.113 39.130 0.00 0.00 0.00 3.18
3673 3874 5.779771 TCCTTTACAAGAAAATTGCCTGGAT 59.220 36.000 0.00 0.00 0.00 3.41
3676 3877 6.089249 AGTCCTTTACAAGAAAATTGCCTG 57.911 37.500 0.00 0.00 0.00 4.85
3678 3879 5.010617 TGGAGTCCTTTACAAGAAAATTGCC 59.989 40.000 11.33 0.00 0.00 4.52
3684 3885 6.488769 TGTACTGGAGTCCTTTACAAGAAA 57.511 37.500 16.73 0.00 0.00 2.52
3686 3887 7.973048 ATATGTACTGGAGTCCTTTACAAGA 57.027 36.000 20.70 14.66 29.86 3.02
3690 3894 8.475639 TCAAGAATATGTACTGGAGTCCTTTAC 58.524 37.037 11.33 11.61 0.00 2.01
3834 4041 1.832366 CAAATGGTCCCCATGATGCAA 59.168 47.619 0.00 0.00 44.40 4.08
3850 4057 1.856629 CCCTCAAGGTGGATGCAAAT 58.143 50.000 0.00 0.00 0.00 2.32
3851 4058 3.362040 CCCTCAAGGTGGATGCAAA 57.638 52.632 0.00 0.00 0.00 3.68
3879 4086 1.515521 CTTTTTCCTGGGAAGCGCGT 61.516 55.000 8.43 0.00 35.38 6.01
3881 4088 1.586541 CCTTTTTCCTGGGAAGCGC 59.413 57.895 0.00 0.00 35.38 5.92
3882 4089 1.178534 TGCCTTTTTCCTGGGAAGCG 61.179 55.000 2.19 0.00 35.38 4.68
3885 4092 1.219213 TCCTTGCCTTTTTCCTGGGAA 59.781 47.619 0.00 0.00 32.82 3.97
3892 4099 8.607441 AATTGAAGTTTATCCTTGCCTTTTTC 57.393 30.769 0.00 0.00 0.00 2.29
3938 4148 2.951642 CAAAACTCTGCAAGGGAGTCAA 59.048 45.455 7.48 0.00 35.24 3.18
3960 4170 3.750130 GCAAGCTTCATTGAGAGACAAGA 59.250 43.478 0.00 0.00 42.02 3.02
3961 4171 3.501062 TGCAAGCTTCATTGAGAGACAAG 59.499 43.478 0.00 0.00 42.02 3.16
3963 4173 3.130280 TGCAAGCTTCATTGAGAGACA 57.870 42.857 0.00 0.00 31.55 3.41
3968 4178 3.179830 GCTCATTGCAAGCTTCATTGAG 58.820 45.455 26.09 26.09 41.33 3.02
3988 4198 1.373570 GTACCTTCCAGCACATCTGC 58.626 55.000 0.00 0.00 44.63 4.26
4036 4246 7.277174 AGTAACAAACTTCAGGATCCTTTTG 57.723 36.000 25.29 25.29 33.35 2.44
4037 4247 6.204882 CGAGTAACAAACTTCAGGATCCTTTT 59.795 38.462 13.00 7.48 39.07 2.27
4038 4248 5.701290 CGAGTAACAAACTTCAGGATCCTTT 59.299 40.000 13.00 0.08 39.07 3.11
4041 4251 4.817517 TCGAGTAACAAACTTCAGGATCC 58.182 43.478 2.48 2.48 39.07 3.36
4048 4258 4.850470 CGGTAGACTCGAGTAACAAACTTC 59.150 45.833 20.09 7.84 39.07 3.01
4049 4259 4.276926 ACGGTAGACTCGAGTAACAAACTT 59.723 41.667 20.09 0.00 39.07 2.66
4059 4269 1.380524 ATGTCCACGGTAGACTCGAG 58.619 55.000 11.84 11.84 35.21 4.04
4065 4275 0.687920 TGCCAAATGTCCACGGTAGA 59.312 50.000 0.00 0.00 0.00 2.59
4066 4276 1.468520 CTTGCCAAATGTCCACGGTAG 59.531 52.381 0.00 0.00 0.00 3.18
4071 4281 2.227388 CTCTGACTTGCCAAATGTCCAC 59.773 50.000 0.00 0.00 0.00 4.02
4078 4288 2.435805 AGACTGTCTCTGACTTGCCAAA 59.564 45.455 4.06 0.00 33.15 3.28
4148 4358 9.028185 GCTATTTCATCCTTCAAACAATTCATC 57.972 33.333 0.00 0.00 0.00 2.92
4149 4359 8.533657 TGCTATTTCATCCTTCAAACAATTCAT 58.466 29.630 0.00 0.00 0.00 2.57
4170 4380 8.507249 GTTCACAGACAGAAATTAAACTGCTAT 58.493 33.333 0.00 0.00 37.61 2.97
4195 4406 1.348064 TGGTCTTCATCCACTTCCGT 58.652 50.000 0.00 0.00 0.00 4.69
4256 4467 1.152567 CAGGGGCAAACACAAGGGA 60.153 57.895 0.00 0.00 0.00 4.20
4301 4512 9.071276 CACCTCCATAGCACAAATATATCTTTT 57.929 33.333 0.00 0.00 0.00 2.27
4307 4518 5.904984 ACCACCTCCATAGCACAAATATA 57.095 39.130 0.00 0.00 0.00 0.86
4314 4525 7.852263 AGATATAAATACCACCTCCATAGCAC 58.148 38.462 0.00 0.00 0.00 4.40
4341 4552 9.147732 TCACACAGATTTATCCTCAGTATGTAT 57.852 33.333 0.00 0.00 37.40 2.29
4342 4553 8.414003 GTCACACAGATTTATCCTCAGTATGTA 58.586 37.037 0.00 0.00 37.40 2.29
4345 4556 7.423844 TGTCACACAGATTTATCCTCAGTAT 57.576 36.000 0.00 0.00 0.00 2.12
4349 4560 6.298441 TCATGTCACACAGATTTATCCTCA 57.702 37.500 0.00 0.00 0.00 3.86
4350 4561 7.798596 ATTCATGTCACACAGATTTATCCTC 57.201 36.000 0.00 0.00 0.00 3.71
4352 4563 8.562892 CCTTATTCATGTCACACAGATTTATCC 58.437 37.037 0.00 0.00 0.00 2.59
4353 4564 9.113838 ACCTTATTCATGTCACACAGATTTATC 57.886 33.333 0.00 0.00 0.00 1.75
4354 4565 9.466497 AACCTTATTCATGTCACACAGATTTAT 57.534 29.630 0.00 0.00 0.00 1.40
4357 4575 7.448161 TGAAACCTTATTCATGTCACACAGATT 59.552 33.333 0.00 0.00 34.50 2.40
4370 4588 5.235516 GTCCGAAGACTGAAACCTTATTCA 58.764 41.667 0.00 0.00 40.10 2.57
4389 4607 5.779922 TCTATTTTGATATCCCGAAGTCCG 58.220 41.667 0.00 0.00 38.18 4.79
4402 4620 8.922931 AAACCAAAGGCATTTTCTATTTTGAT 57.077 26.923 0.00 0.00 0.00 2.57
4873 5091 3.951306 TGAATCAGCAAAGTTGTGTTCG 58.049 40.909 0.00 0.00 0.00 3.95
4890 5109 6.179756 TGTAGAGCCAACATAACACATGAAT 58.820 36.000 0.00 0.00 0.00 2.57
4891 5110 5.555966 TGTAGAGCCAACATAACACATGAA 58.444 37.500 0.00 0.00 0.00 2.57
4919 5138 7.054491 AGCTCCAAGCAAGAAAAATAGAAAA 57.946 32.000 1.29 0.00 45.56 2.29
4920 5139 6.655078 AGCTCCAAGCAAGAAAAATAGAAA 57.345 33.333 1.29 0.00 45.56 2.52
4921 5140 7.944729 ATAGCTCCAAGCAAGAAAAATAGAA 57.055 32.000 0.00 0.00 45.56 2.10
4922 5141 7.944729 AATAGCTCCAAGCAAGAAAAATAGA 57.055 32.000 0.00 0.00 45.56 1.98
4923 5142 7.704047 GGAAATAGCTCCAAGCAAGAAAAATAG 59.296 37.037 0.00 0.00 45.56 1.73
4924 5143 7.397192 AGGAAATAGCTCCAAGCAAGAAAAATA 59.603 33.333 0.00 0.00 45.56 1.40
4925 5144 6.212187 AGGAAATAGCTCCAAGCAAGAAAAAT 59.788 34.615 0.00 0.00 45.56 1.82
4926 5145 5.539955 AGGAAATAGCTCCAAGCAAGAAAAA 59.460 36.000 0.00 0.00 45.56 1.94
4927 5146 5.079643 AGGAAATAGCTCCAAGCAAGAAAA 58.920 37.500 0.00 0.00 45.56 2.29
5022 5243 4.824479 TGTCTGCTTGTTCATCTCCATA 57.176 40.909 0.00 0.00 0.00 2.74
5085 5306 6.805016 ATTCATCTGACAGAAGTATGGTCT 57.195 37.500 9.70 0.00 32.84 3.85
5093 5314 4.156190 AGCTGCAAATTCATCTGACAGAAG 59.844 41.667 9.70 5.16 0.00 2.85
5098 5319 8.097078 AGAATATAGCTGCAAATTCATCTGAC 57.903 34.615 17.84 0.00 32.04 3.51
5103 5324 7.722728 TCCAGAAGAATATAGCTGCAAATTCAT 59.277 33.333 17.84 10.11 32.04 2.57
5113 5334 5.221541 CCGTTCCTTCCAGAAGAATATAGCT 60.222 44.000 9.00 0.00 40.79 3.32
5116 5337 4.966805 ACCCGTTCCTTCCAGAAGAATATA 59.033 41.667 9.00 0.00 40.79 0.86


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

AutoCloner maintained by Alex Coulton.