Multiple sequence alignment - TraesCS6B01G293700

Loading Multiple Alignment...

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 TraesCS6B01G293700 chr6B 100.000 5748 0 0 668 6415 527928640 527934387 0.000000e+00 10615.0
1 TraesCS6B01G293700 chr6B 100.000 359 0 0 1 359 527927973 527928331 0.000000e+00 664.0
2 TraesCS6B01G293700 chr6B 92.366 131 10 0 3182 3312 542584872 542584742 3.050000e-43 187.0
3 TraesCS6B01G293700 chr6D 94.457 3121 112 22 3319 6410 351411806 351408718 0.000000e+00 4748.0
4 TraesCS6B01G293700 chr6D 97.190 2135 35 13 668 2786 351414584 351412459 0.000000e+00 3587.0
5 TraesCS6B01G293700 chr6D 96.774 403 7 3 2784 3181 351412203 351411802 0.000000e+00 667.0
6 TraesCS6B01G293700 chr6D 94.737 361 13 2 1 359 351414992 351414636 2.020000e-154 556.0
7 TraesCS6B01G293700 chr6A 93.640 3003 125 32 3311 6266 491917081 491920064 0.000000e+00 4427.0
8 TraesCS6B01G293700 chr6A 91.876 2585 94 52 668 3188 491914554 491917086 0.000000e+00 3504.0
9 TraesCS6B01G293700 chr6A 92.201 359 21 4 1 359 491914150 491914501 9.600000e-138 501.0
10 TraesCS6B01G293700 chr6A 91.139 158 12 2 6254 6410 491920363 491920519 5.040000e-51 213.0
11 TraesCS6B01G293700 chr7B 78.458 506 52 31 5385 5858 147727355 147727835 1.760000e-70 278.0
12 TraesCS6B01G293700 chr7B 87.654 243 12 8 4086 4312 147724334 147724574 3.810000e-67 267.0
13 TraesCS6B01G293700 chr7B 93.846 130 8 0 3183 3312 295083165 295083294 5.070000e-46 196.0
14 TraesCS6B01G293700 chr7B 80.903 288 20 19 6013 6269 147728730 147729013 1.820000e-45 195.0
15 TraesCS6B01G293700 chr7B 93.182 132 9 0 3188 3319 668203320 668203189 1.820000e-45 195.0
16 TraesCS6B01G293700 chr7B 84.286 70 3 3 5904 5969 147727857 147727922 1.930000e-05 62.1
17 TraesCS6B01G293700 chr5B 82.941 340 26 15 6058 6387 440022253 440021936 1.760000e-70 278.0
18 TraesCS6B01G293700 chr5B 85.514 214 13 7 5478 5679 440023429 440023222 2.340000e-49 207.0
19 TraesCS6B01G293700 chr5B 80.124 322 17 25 4897 5194 440025112 440024814 5.070000e-46 196.0
20 TraesCS6B01G293700 chr5B 78.367 245 15 15 5820 6048 440022612 440022390 2.430000e-24 124.0
21 TraesCS6B01G293700 chr5B 94.444 72 4 0 3393 3464 440026882 440026811 1.890000e-20 111.0
22 TraesCS6B01G293700 chr5B 87.368 95 4 5 4690 4776 440026421 440026327 1.140000e-17 102.0
23 TraesCS6B01G293700 chr5D 82.188 320 17 14 4897 5194 370746695 370746394 8.310000e-59 239.0
24 TraesCS6B01G293700 chr5D 84.259 216 18 8 5473 5679 370746307 370746099 5.070000e-46 196.0
25 TraesCS6B01G293700 chr5D 82.941 170 17 6 3315 3478 370747992 370747829 6.700000e-30 143.0
26 TraesCS6B01G293700 chr5D 88.421 95 3 5 4690 4776 370747411 370747317 2.450000e-19 108.0
27 TraesCS6B01G293700 chr5A 84.932 219 13 9 5473 5679 473324075 473323865 3.030000e-48 204.0
28 TraesCS6B01G293700 chr5A 84.706 170 17 5 3315 3478 473331580 473331414 1.850000e-35 161.0
29 TraesCS6B01G293700 chr2D 91.912 136 11 0 3180 3315 468789305 468789170 2.360000e-44 191.0
30 TraesCS6B01G293700 chr2B 91.971 137 9 2 3181 3315 104819597 104819461 2.360000e-44 191.0
31 TraesCS6B01G293700 chr2B 92.537 134 9 1 3179 3312 655599884 655599752 2.360000e-44 191.0
32 TraesCS6B01G293700 chr2B 91.852 135 11 0 3179 3313 185104929 185105063 8.490000e-44 189.0
33 TraesCS6B01G293700 chr2B 81.890 127 12 3 3186 3312 82752892 82753007 5.290000e-16 97.1
34 TraesCS6B01G293700 chr2A 93.077 130 9 0 3183 3312 630094751 630094622 2.360000e-44 191.0
35 TraesCS6B01G293700 chr4B 91.852 135 9 2 3186 3320 180671163 180671295 3.050000e-43 187.0


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 TraesCS6B01G293700 chr6B 527927973 527934387 6414 False 5639.500 10615 100.00000 1 6415 2 chr6B.!!$F1 6414
1 TraesCS6B01G293700 chr6D 351408718 351414992 6274 True 2389.500 4748 95.78950 1 6410 4 chr6D.!!$R1 6409
2 TraesCS6B01G293700 chr6A 491914150 491920519 6369 False 2161.250 4427 92.21400 1 6410 4 chr6A.!!$F1 6409
3 TraesCS6B01G293700 chr7B 147724334 147729013 4679 False 200.525 278 82.82525 4086 6269 4 chr7B.!!$F2 2183

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
908 913 0.690744 AGCCCAACCAGCAACCTTTT 60.691 50.000 0.00 0.0 0.00 2.27 F
1779 1794 0.250901 AAGGATGCATGGGCGTATCC 60.251 55.000 2.46 0.0 45.35 2.59 F
1955 1971 0.329261 TTGCAGGTGAGGGGATCTTG 59.671 55.000 0.00 0.0 0.00 3.02 F
2135 2162 0.788391 GCACCACTCGACCTTTAACG 59.212 55.000 0.00 0.0 0.00 3.18 F
3202 3538 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.0 0.00 3.28 F
3205 3541 1.073098 ACTCCCTCCGTCCCAAATTT 58.927 50.000 0.00 0.0 0.00 1.82 F
3206 3542 1.427753 ACTCCCTCCGTCCCAAATTTT 59.572 47.619 0.00 0.0 0.00 1.82 F
3677 4028 1.447838 GGCGAAATGACAGAGCGGA 60.448 57.895 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2230 1.107945 TGCATGACCGACCGAAGATA 58.892 50.000 0.00 0.00 0.00 1.98 R
3183 3519 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73 R
3186 3522 1.073098 AAATTTGGGACGGAGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85 R
4003 4359 0.820871 GCAGGCACTAGCTAGACTGT 59.179 55.000 27.45 2.30 41.70 3.55 R
4409 4789 0.253044 ACGGCTGGATGCTTGTATGT 59.747 50.000 0.00 0.00 42.39 2.29 R
4812 5911 1.687660 AGTCCATTTGCATGCAACACA 59.312 42.857 31.99 18.74 35.46 3.72 R
5221 7707 9.122613 CAGATTGCGATCGGTATATATCATAAG 57.877 37.037 18.30 0.00 37.37 1.73 R
5549 8051 1.156322 TCTGGTTCCCTCCTCCTCCT 61.156 60.000 0.00 0.00 0.00 3.69 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
36 37 3.768757 CCTCCCAATTTATTGTTCAGGCA 59.231 43.478 2.13 0.00 36.06 4.75
48 49 3.499338 TGTTCAGGCATCACTTGGAAAT 58.501 40.909 0.00 0.00 0.00 2.17
83 84 7.817418 AAAACACAGCCAGTAAATCTTCTAA 57.183 32.000 0.00 0.00 0.00 2.10
126 127 3.096092 CCGGGAAAATTCTGGAATTCCA 58.904 45.455 25.53 25.53 45.30 3.53
134 135 7.178451 GGAAAATTCTGGAATTCCAAACTAGGA 59.822 37.037 26.87 16.72 46.97 2.94
135 136 8.670521 AAAATTCTGGAATTCCAAACTAGGAT 57.329 30.769 26.87 12.90 46.97 3.24
136 137 7.651027 AATTCTGGAATTCCAAACTAGGATG 57.349 36.000 26.87 12.64 46.97 3.51
137 138 4.526970 TCTGGAATTCCAAACTAGGATGC 58.473 43.478 26.87 0.00 46.97 3.91
153 154 3.136763 GGATGCATGTAGTCTGTCCATG 58.863 50.000 2.46 0.00 39.13 3.66
155 156 3.979101 TGCATGTAGTCTGTCCATGAA 57.021 42.857 11.17 1.06 38.56 2.57
170 171 4.039124 GTCCATGAAAACACCAACCTGAAT 59.961 41.667 0.00 0.00 0.00 2.57
250 251 8.030106 CGATAAGGGAATAATACCTCACTTCTC 58.970 40.741 0.00 0.00 36.67 2.87
733 736 3.876914 CTCCAAGCAACAAGTTACACTCA 59.123 43.478 0.00 0.00 0.00 3.41
908 913 0.690744 AGCCCAACCAGCAACCTTTT 60.691 50.000 0.00 0.00 0.00 2.27
920 925 3.525268 CAACCTTTTGCCAACTCTGTT 57.475 42.857 0.00 0.00 0.00 3.16
1053 1059 1.284785 CCCCAGCTCCAAATTAGTCCA 59.715 52.381 0.00 0.00 0.00 4.02
1676 1691 3.555956 CGTTAGCAGCCGTTAGATGATTT 59.444 43.478 0.00 0.00 0.00 2.17
1711 1726 1.950216 GCTAGCAAAGTAGGCAATCCC 59.050 52.381 10.63 0.00 0.00 3.85
1753 1768 3.005050 TCTTGTGCTGGCATTCAAAAGAG 59.995 43.478 14.73 0.00 0.00 2.85
1778 1793 0.877071 CAAGGATGCATGGGCGTATC 59.123 55.000 2.46 0.00 45.35 2.24
1779 1794 0.250901 AAGGATGCATGGGCGTATCC 60.251 55.000 2.46 0.00 45.35 2.59
1955 1971 0.329261 TTGCAGGTGAGGGGATCTTG 59.671 55.000 0.00 0.00 0.00 3.02
1994 2010 5.594317 GTCCATGGTTAGCTCATTGGTTATT 59.406 40.000 12.58 0.00 0.00 1.40
2135 2162 0.788391 GCACCACTCGACCTTTAACG 59.212 55.000 0.00 0.00 0.00 3.18
2339 2381 2.454941 GGGGTGAGGAGAGGGGAA 59.545 66.667 0.00 0.00 0.00 3.97
2399 2441 3.376234 TGAGCAGCACAAAGATAAGCATC 59.624 43.478 0.00 0.00 0.00 3.91
2823 3130 1.826385 ACTTGCTGTGTATGCTTCCC 58.174 50.000 0.00 0.00 0.00 3.97
2826 3133 2.988010 TGCTGTGTATGCTTCCCTAG 57.012 50.000 0.00 0.00 0.00 3.02
2828 3135 2.571653 TGCTGTGTATGCTTCCCTAGTT 59.428 45.455 0.00 0.00 0.00 2.24
2829 3136 3.198872 GCTGTGTATGCTTCCCTAGTTC 58.801 50.000 0.00 0.00 0.00 3.01
2830 3137 3.369471 GCTGTGTATGCTTCCCTAGTTCA 60.369 47.826 0.00 0.00 0.00 3.18
2832 3139 5.453339 GCTGTGTATGCTTCCCTAGTTCATA 60.453 44.000 0.00 0.00 0.00 2.15
2834 3141 6.759272 TGTGTATGCTTCCCTAGTTCATATC 58.241 40.000 0.00 0.00 0.00 1.63
2835 3142 6.326323 TGTGTATGCTTCCCTAGTTCATATCA 59.674 38.462 0.00 0.00 0.00 2.15
2836 3143 6.870965 GTGTATGCTTCCCTAGTTCATATCAG 59.129 42.308 0.00 0.00 0.00 2.90
2837 3144 4.342862 TGCTTCCCTAGTTCATATCAGC 57.657 45.455 0.00 0.00 0.00 4.26
2947 3280 6.163476 TGATCAGTATTGTACAAGTGTCACC 58.837 40.000 14.65 2.43 0.00 4.02
3113 3446 2.094286 CGAGTCTTCAGTCCAGCAATCT 60.094 50.000 0.00 0.00 0.00 2.40
3182 3518 3.250040 GCAACAACTCGAGGTAACAACAT 59.750 43.478 18.41 0.00 41.41 2.71
3183 3519 4.449743 GCAACAACTCGAGGTAACAACATA 59.550 41.667 18.41 0.00 41.41 2.29
3184 3520 5.614013 GCAACAACTCGAGGTAACAACATAC 60.614 44.000 18.41 0.00 41.41 2.39
3185 3521 5.464030 ACAACTCGAGGTAACAACATACT 57.536 39.130 18.41 0.00 41.41 2.12
3186 3522 6.579666 ACAACTCGAGGTAACAACATACTA 57.420 37.500 18.41 0.00 41.41 1.82
3187 3523 6.385033 ACAACTCGAGGTAACAACATACTAC 58.615 40.000 18.41 0.00 41.41 2.73
3188 3524 6.208204 ACAACTCGAGGTAACAACATACTACT 59.792 38.462 18.41 0.00 41.41 2.57
3189 3525 6.434018 ACTCGAGGTAACAACATACTACTC 57.566 41.667 18.41 0.00 41.41 2.59
3190 3526 5.356470 ACTCGAGGTAACAACATACTACTCC 59.644 44.000 18.41 0.00 41.41 3.85
3191 3527 4.641989 TCGAGGTAACAACATACTACTCCC 59.358 45.833 0.00 0.00 41.41 4.30
3192 3528 4.643784 CGAGGTAACAACATACTACTCCCT 59.356 45.833 0.00 0.00 41.41 4.20
3193 3529 5.221009 CGAGGTAACAACATACTACTCCCTC 60.221 48.000 0.00 0.00 41.41 4.30
3194 3530 4.961099 AGGTAACAACATACTACTCCCTCC 59.039 45.833 0.00 0.00 41.41 4.30
3195 3531 4.202090 GGTAACAACATACTACTCCCTCCG 60.202 50.000 0.00 0.00 0.00 4.63
3196 3532 3.097342 ACAACATACTACTCCCTCCGT 57.903 47.619 0.00 0.00 0.00 4.69
3197 3533 3.022406 ACAACATACTACTCCCTCCGTC 58.978 50.000 0.00 0.00 0.00 4.79
3198 3534 2.361438 CAACATACTACTCCCTCCGTCC 59.639 54.545 0.00 0.00 0.00 4.79
3199 3535 1.133544 ACATACTACTCCCTCCGTCCC 60.134 57.143 0.00 0.00 0.00 4.46
3200 3536 1.133575 CATACTACTCCCTCCGTCCCA 60.134 57.143 0.00 0.00 0.00 4.37
3201 3537 1.002069 TACTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3202 3538 0.115745 ACTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3203 3539 1.273666 ACTACTCCCTCCGTCCCAAAT 60.274 52.381 0.00 0.00 0.00 2.32
3204 3540 1.838077 CTACTCCCTCCGTCCCAAATT 59.162 52.381 0.00 0.00 0.00 1.82
3205 3541 1.073098 ACTCCCTCCGTCCCAAATTT 58.927 50.000 0.00 0.00 0.00 1.82
3206 3542 1.427753 ACTCCCTCCGTCCCAAATTTT 59.572 47.619 0.00 0.00 0.00 1.82
3207 3543 2.158370 ACTCCCTCCGTCCCAAATTTTT 60.158 45.455 0.00 0.00 0.00 1.94
3230 3566 7.786305 TTTGTCTTACGTTTGTCTAGATACG 57.214 36.000 17.85 17.85 39.71 3.06
3231 3567 5.872635 TGTCTTACGTTTGTCTAGATACGG 58.127 41.667 21.25 9.85 38.26 4.02
3232 3568 5.643348 TGTCTTACGTTTGTCTAGATACGGA 59.357 40.000 21.25 14.49 38.26 4.69
3233 3569 6.317140 TGTCTTACGTTTGTCTAGATACGGAT 59.683 38.462 21.25 9.88 38.26 4.18
3234 3570 7.495606 TGTCTTACGTTTGTCTAGATACGGATA 59.504 37.037 21.25 10.24 38.26 2.59
3235 3571 8.502387 GTCTTACGTTTGTCTAGATACGGATAT 58.498 37.037 21.25 9.14 38.26 1.63
3236 3572 9.710900 TCTTACGTTTGTCTAGATACGGATATA 57.289 33.333 21.25 8.44 38.26 0.86
3237 3573 9.752274 CTTACGTTTGTCTAGATACGGATATAC 57.248 37.037 21.25 0.00 38.26 1.47
3238 3574 7.138692 ACGTTTGTCTAGATACGGATATACC 57.861 40.000 21.25 0.00 38.26 2.73
3239 3575 6.939163 ACGTTTGTCTAGATACGGATATACCT 59.061 38.462 21.25 3.69 38.26 3.08
3240 3576 8.097038 ACGTTTGTCTAGATACGGATATACCTA 58.903 37.037 21.25 0.00 38.26 3.08
3241 3577 8.939929 CGTTTGTCTAGATACGGATATACCTAA 58.060 37.037 13.86 0.00 36.31 2.69
3267 3603 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
3268 3604 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
3269 3605 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
3270 3606 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
3271 3607 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
3272 3608 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
3273 3609 5.518847 ACGTGACTTGATACATCCGTATTTG 59.481 40.000 0.00 0.00 38.48 2.32
3274 3610 5.051039 CGTGACTTGATACATCCGTATTTGG 60.051 44.000 0.00 0.00 38.48 3.28
3275 3611 6.046593 GTGACTTGATACATCCGTATTTGGA 58.953 40.000 0.00 0.00 43.58 3.53
3276 3612 6.018994 GTGACTTGATACATCCGTATTTGGAC 60.019 42.308 0.00 0.00 41.85 4.02
3277 3613 5.984725 ACTTGATACATCCGTATTTGGACA 58.015 37.500 0.00 0.00 41.85 4.02
3278 3614 6.411376 ACTTGATACATCCGTATTTGGACAA 58.589 36.000 0.00 0.00 41.85 3.18
3279 3615 6.882140 ACTTGATACATCCGTATTTGGACAAA 59.118 34.615 0.00 0.00 41.85 2.83
3280 3616 6.671614 TGATACATCCGTATTTGGACAAAC 57.328 37.500 0.00 0.00 41.85 2.93
3281 3617 5.587043 TGATACATCCGTATTTGGACAAACC 59.413 40.000 0.00 0.00 41.85 3.27
3282 3618 4.028993 ACATCCGTATTTGGACAAACCT 57.971 40.909 0.00 0.00 41.85 3.50
3283 3619 5.168647 ACATCCGTATTTGGACAAACCTA 57.831 39.130 0.00 0.00 41.85 3.08
3284 3620 5.562635 ACATCCGTATTTGGACAAACCTAA 58.437 37.500 0.00 0.00 41.85 2.69
3285 3621 5.646360 ACATCCGTATTTGGACAAACCTAAG 59.354 40.000 0.00 0.00 41.85 2.18
3286 3622 5.486735 TCCGTATTTGGACAAACCTAAGA 57.513 39.130 0.00 0.00 36.89 2.10
3287 3623 5.240121 TCCGTATTTGGACAAACCTAAGAC 58.760 41.667 0.00 0.00 40.34 3.01
3288 3624 4.998672 CCGTATTTGGACAAACCTAAGACA 59.001 41.667 0.00 0.00 42.51 3.41
3289 3625 5.470777 CCGTATTTGGACAAACCTAAGACAA 59.529 40.000 0.00 0.00 42.51 3.18
3290 3626 6.348213 CCGTATTTGGACAAACCTAAGACAAG 60.348 42.308 0.00 0.00 42.51 3.16
3291 3627 6.425721 CGTATTTGGACAAACCTAAGACAAGA 59.574 38.462 0.00 0.00 42.51 3.02
3292 3628 7.041644 CGTATTTGGACAAACCTAAGACAAGAA 60.042 37.037 0.00 0.00 42.51 2.52
3293 3629 7.839680 ATTTGGACAAACCTAAGACAAGAAT 57.160 32.000 0.00 0.00 36.89 2.40
3294 3630 7.654022 TTTGGACAAACCTAAGACAAGAATT 57.346 32.000 0.00 0.00 39.86 2.17
3295 3631 7.654022 TTGGACAAACCTAAGACAAGAATTT 57.346 32.000 0.00 0.00 39.86 1.82
3296 3632 7.654022 TGGACAAACCTAAGACAAGAATTTT 57.346 32.000 0.00 0.00 39.86 1.82
3297 3633 7.488322 TGGACAAACCTAAGACAAGAATTTTG 58.512 34.615 0.00 0.00 39.86 2.44
3298 3634 6.923508 GGACAAACCTAAGACAAGAATTTTGG 59.076 38.462 0.00 0.00 35.41 3.28
3299 3635 7.201875 GGACAAACCTAAGACAAGAATTTTGGA 60.202 37.037 0.00 0.00 35.41 3.53
3300 3636 8.073467 ACAAACCTAAGACAAGAATTTTGGAA 57.927 30.769 0.00 0.00 0.00 3.53
3301 3637 7.979537 ACAAACCTAAGACAAGAATTTTGGAAC 59.020 33.333 0.00 0.00 0.00 3.62
3302 3638 6.313744 ACCTAAGACAAGAATTTTGGAACG 57.686 37.500 0.00 0.00 0.00 3.95
3303 3639 5.240844 ACCTAAGACAAGAATTTTGGAACGG 59.759 40.000 0.00 0.00 0.00 4.44
3304 3640 5.472137 CCTAAGACAAGAATTTTGGAACGGA 59.528 40.000 0.00 0.00 0.00 4.69
3305 3641 5.438761 AAGACAAGAATTTTGGAACGGAG 57.561 39.130 0.00 0.00 0.00 4.63
3306 3642 3.821033 AGACAAGAATTTTGGAACGGAGG 59.179 43.478 0.00 0.00 0.00 4.30
3307 3643 2.890945 ACAAGAATTTTGGAACGGAGGG 59.109 45.455 0.00 0.00 0.00 4.30
3308 3644 3.153919 CAAGAATTTTGGAACGGAGGGA 58.846 45.455 0.00 0.00 0.00 4.20
3309 3645 3.073274 AGAATTTTGGAACGGAGGGAG 57.927 47.619 0.00 0.00 0.00 4.30
3317 3653 2.024655 TGGAACGGAGGGAGTACTACAT 60.025 50.000 7.57 0.00 0.00 2.29
3334 3670 2.288666 ACATACAACGCCATTGCTAGG 58.711 47.619 0.00 0.00 42.62 3.02
3357 3695 5.046807 GGTAGCTTCTTTGTTGGTACTCCTA 60.047 44.000 0.00 0.00 35.69 2.94
3373 3711 7.040494 GGTACTCCTAGTTTTGTATTCTGGTC 58.960 42.308 0.00 0.00 0.00 4.02
3405 3745 5.987953 GCTGCTATATCACATGAGAGAACAA 59.012 40.000 0.00 0.00 0.00 2.83
3407 3748 5.979517 TGCTATATCACATGAGAGAACAACG 59.020 40.000 0.00 0.00 0.00 4.10
3677 4028 1.447838 GGCGAAATGACAGAGCGGA 60.448 57.895 0.00 0.00 0.00 5.54
3701 4052 7.825270 GGAGTACAGCTAGCTATAAGTCTATCA 59.175 40.741 18.86 0.00 0.00 2.15
3788 4139 5.183140 GTCAAAAGCTGCTGGTAATTTCCTA 59.817 40.000 1.35 0.00 0.00 2.94
3881 4237 3.245016 TGTTTGGGCTCTTCATCTCATGT 60.245 43.478 0.00 0.00 0.00 3.21
4003 4359 3.161866 GGGTGCTTTTAGGATCAAACCA 58.838 45.455 0.00 0.00 0.00 3.67
4027 4383 3.769844 AGTCTAGCTAGTGCCTGCTTTAA 59.230 43.478 20.10 0.00 40.35 1.52
4248 4618 9.504710 GCATACATATATACTTTCCACGACTAG 57.495 37.037 0.00 0.00 0.00 2.57
4320 4698 5.413833 AGAAGTTACATCAGAAGCAACATGG 59.586 40.000 0.00 0.00 0.00 3.66
4358 4738 7.986889 TGCTATACACAATTAATCTCTCTTGCA 59.013 33.333 0.00 0.00 0.00 4.08
4501 4881 4.398319 GGCCAACTGTATAGCCATGTAAT 58.602 43.478 0.00 0.00 45.07 1.89
4502 4882 4.216257 GGCCAACTGTATAGCCATGTAATG 59.784 45.833 0.00 0.00 45.07 1.90
4503 4883 4.821805 GCCAACTGTATAGCCATGTAATGT 59.178 41.667 0.00 0.00 44.81 2.71
4504 4884 5.995282 GCCAACTGTATAGCCATGTAATGTA 59.005 40.000 0.00 0.00 44.81 2.29
4506 4886 7.519970 GCCAACTGTATAGCCATGTAATGTAAC 60.520 40.741 0.00 0.00 44.81 2.50
4507 4887 7.041372 CCAACTGTATAGCCATGTAATGTAACC 60.041 40.741 0.00 0.00 44.81 2.85
4508 4888 6.531021 ACTGTATAGCCATGTAATGTAACCC 58.469 40.000 0.00 0.00 44.81 4.11
4509 4889 6.329197 ACTGTATAGCCATGTAATGTAACCCT 59.671 38.462 0.00 0.00 44.81 4.34
4510 4890 7.511371 ACTGTATAGCCATGTAATGTAACCCTA 59.489 37.037 0.00 0.00 44.81 3.53
4511 4891 8.265108 TGTATAGCCATGTAATGTAACCCTAA 57.735 34.615 0.00 0.00 44.81 2.69
4512 4892 8.715842 TGTATAGCCATGTAATGTAACCCTAAA 58.284 33.333 0.00 0.00 44.81 1.85
4513 4893 9.216117 GTATAGCCATGTAATGTAACCCTAAAG 57.784 37.037 0.00 0.00 44.81 1.85
4514 4894 6.074698 AGCCATGTAATGTAACCCTAAAGT 57.925 37.500 0.00 0.00 44.81 2.66
4536 4916 7.857404 AGTAAACTGTATAGCCATGTAGGAT 57.143 36.000 0.00 0.00 41.22 3.24
4576 4957 8.391075 ACATGTTTATTTAGATAATGACCGGG 57.609 34.615 6.32 0.00 0.00 5.73
4579 4960 7.221450 TGTTTATTTAGATAATGACCGGGGAG 58.779 38.462 6.32 0.00 0.00 4.30
4602 4983 7.712205 GGAGCATATGATATGTATGTGCATGTA 59.288 37.037 13.48 0.00 42.77 2.29
4812 5911 2.972819 GCCTTTTCCCGCCTCTCCT 61.973 63.158 0.00 0.00 0.00 3.69
4944 7392 7.846101 ATTCAATTCCTTCCTTTGTCTTTCT 57.154 32.000 0.00 0.00 0.00 2.52
4947 7395 7.716612 TCAATTCCTTCCTTTGTCTTTCTTTC 58.283 34.615 0.00 0.00 0.00 2.62
4957 7405 4.918810 TGTCTTTCTTTCCCTTTTGCTC 57.081 40.909 0.00 0.00 0.00 4.26
5180 7666 3.562639 CATGCATGCATCTTTCCGG 57.437 52.632 30.07 13.50 33.90 5.14
5228 7714 5.707242 CAGCATGCATTTCCTCTTATGAT 57.293 39.130 21.98 0.00 0.00 2.45
5247 7733 9.122613 CTTATGATATATACCGATCGCAATCTG 57.877 37.037 10.32 0.00 0.00 2.90
5315 7801 4.015406 TGCCCCAATGTCGTCGCT 62.015 61.111 0.00 0.00 0.00 4.93
5318 7804 1.153369 CCCCAATGTCGTCGCTGAT 60.153 57.895 0.00 0.00 0.00 2.90
5339 7825 4.451150 GCCGCCGACCTGATGTCA 62.451 66.667 0.00 0.00 44.71 3.58
5345 7831 1.607801 CCGACCTGATGTCAGCTCCA 61.608 60.000 4.48 0.00 44.71 3.86
5825 8353 2.633860 TGCACAACACACACACACA 58.366 47.368 0.00 0.00 0.00 3.72
5826 8354 0.239613 TGCACAACACACACACACAC 59.760 50.000 0.00 0.00 0.00 3.82
5849 8377 0.510359 CGAGCTTGAAGAGTGTGTGC 59.490 55.000 0.00 0.00 0.00 4.57
5866 8394 4.520618 CATGTGTGCGTGCACTTC 57.479 55.556 23.86 17.01 46.30 3.01
5867 8395 1.648174 CATGTGTGCGTGCACTTCA 59.352 52.632 23.86 21.16 46.30 3.02
5868 8396 0.239082 CATGTGTGCGTGCACTTCAT 59.761 50.000 23.86 22.18 46.30 2.57
5869 8397 0.239082 ATGTGTGCGTGCACTTCATG 59.761 50.000 23.86 0.00 46.30 3.07
5909 8447 5.012148 AGACAGAGCTGCTAGGTTAAGAAAA 59.988 40.000 0.15 0.00 0.00 2.29
5943 8485 5.606348 TTTGTTATGCCACAAGAAAGGTT 57.394 34.783 0.00 0.00 37.93 3.50
5988 9306 5.526115 ACATATATGCGTGTGTACTGTACC 58.474 41.667 12.79 7.36 0.00 3.34
6138 9495 3.018856 CTGGCTGGATTTGCAGTTCATA 58.981 45.455 0.97 0.00 0.00 2.15
6219 9579 7.848223 TGTTTGATCATATGTCTACCAAGTG 57.152 36.000 1.90 0.00 0.00 3.16
6322 9993 5.860941 TTTTCATTGGTTAAGACAAGCCA 57.139 34.783 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.945543 GGTTCGTCATGTAGGGGTAAAAAT 59.054 41.667 0.00 0.00 0.00 1.82
126 127 5.395768 GGACAGACTACATGCATCCTAGTTT 60.396 44.000 12.77 6.64 0.00 2.66
134 135 4.492494 TTCATGGACAGACTACATGCAT 57.508 40.909 0.00 0.00 41.22 3.96
135 136 3.979101 TTCATGGACAGACTACATGCA 57.021 42.857 0.00 0.00 41.22 3.96
136 137 4.455533 TGTTTTCATGGACAGACTACATGC 59.544 41.667 0.00 0.00 41.22 4.06
137 138 5.106555 GGTGTTTTCATGGACAGACTACATG 60.107 44.000 0.00 0.00 42.44 3.21
153 154 2.034053 TGCGATTCAGGTTGGTGTTTTC 59.966 45.455 0.00 0.00 0.00 2.29
155 156 1.686355 TGCGATTCAGGTTGGTGTTT 58.314 45.000 0.00 0.00 0.00 2.83
733 736 4.097892 GGATGTGTTGTGTGAAAAAGAGGT 59.902 41.667 0.00 0.00 0.00 3.85
908 913 2.902486 AGAGAGATCAACAGAGTTGGCA 59.098 45.455 9.72 0.00 0.00 4.92
920 925 3.584733 TGTGGCTAGCTAGAGAGATCA 57.415 47.619 25.15 10.40 0.00 2.92
1034 1040 2.369394 GTGGACTAATTTGGAGCTGGG 58.631 52.381 0.00 0.00 0.00 4.45
1047 1053 2.609610 GTGGCAGGGGGTGGACTA 60.610 66.667 0.00 0.00 0.00 2.59
1680 1695 6.628398 GCCTACTTTGCTAGCTAGAAGAAGAA 60.628 42.308 25.15 4.17 0.00 2.52
1681 1696 5.163499 GCCTACTTTGCTAGCTAGAAGAAGA 60.163 44.000 25.15 11.82 0.00 2.87
1682 1697 5.047188 GCCTACTTTGCTAGCTAGAAGAAG 58.953 45.833 25.15 22.23 0.00 2.85
1711 1726 4.901814 AGAAATGCAAGATTCGATCAACG 58.098 39.130 0.00 0.00 44.09 4.10
1753 1768 1.602311 CCCATGCATCCTTGTCTAGC 58.398 55.000 0.00 0.00 0.00 3.42
1778 1793 1.341531 AGCTTAGCCTGTACTATGCGG 59.658 52.381 0.00 0.00 44.07 5.69
1779 1794 2.294791 AGAGCTTAGCCTGTACTATGCG 59.705 50.000 0.00 0.00 44.07 4.73
1994 2010 8.196771 ACACAAGTGATCAAAGCTCAATTAAAA 58.803 29.630 7.28 0.00 30.49 1.52
2016 2036 1.273606 GTTGAGGAGAGCTAGCACACA 59.726 52.381 18.83 6.16 0.00 3.72
2017 2037 1.734047 CGTTGAGGAGAGCTAGCACAC 60.734 57.143 18.83 9.41 0.00 3.82
2192 2227 2.460918 CATGACCGACCGAAGATACAC 58.539 52.381 0.00 0.00 0.00 2.90
2195 2230 1.107945 TGCATGACCGACCGAAGATA 58.892 50.000 0.00 0.00 0.00 1.98
2339 2381 5.511373 GGTTTTTATTGAAAAGCTGCCCTCT 60.511 40.000 8.18 0.00 46.84 3.69
2399 2441 1.444212 CGCATTTGCTTCCCGTTGG 60.444 57.895 0.51 0.00 39.32 3.77
2508 2550 6.439675 TTCATATCAATGGATGTGTGTGTG 57.560 37.500 6.71 0.00 41.74 3.82
2509 2551 8.789762 CATATTCATATCAATGGATGTGTGTGT 58.210 33.333 6.71 0.00 41.74 3.72
2510 2552 9.005777 TCATATTCATATCAATGGATGTGTGTG 57.994 33.333 6.71 0.00 39.83 3.82
2511 2553 9.577222 TTCATATTCATATCAATGGATGTGTGT 57.423 29.630 6.71 0.69 39.83 3.72
2823 3130 7.315890 TGATGAATACCGCTGATATGAACTAG 58.684 38.462 0.00 0.00 0.00 2.57
2826 3133 5.928839 ACTGATGAATACCGCTGATATGAAC 59.071 40.000 0.00 0.00 0.00 3.18
2828 3135 5.728637 ACTGATGAATACCGCTGATATGA 57.271 39.130 0.00 0.00 0.00 2.15
2829 3136 5.928264 TCAACTGATGAATACCGCTGATATG 59.072 40.000 0.00 0.00 34.30 1.78
2830 3137 6.101650 TCAACTGATGAATACCGCTGATAT 57.898 37.500 0.00 0.00 34.30 1.63
2832 3139 4.406648 TCAACTGATGAATACCGCTGAT 57.593 40.909 0.00 0.00 34.30 2.90
2834 3141 4.333649 ACAATCAACTGATGAATACCGCTG 59.666 41.667 0.00 0.00 42.54 5.18
2835 3142 4.517285 ACAATCAACTGATGAATACCGCT 58.483 39.130 0.00 0.00 42.54 5.52
2836 3143 4.572389 AGACAATCAACTGATGAATACCGC 59.428 41.667 0.00 0.00 42.54 5.68
2837 3144 6.481134 CAAGACAATCAACTGATGAATACCG 58.519 40.000 0.00 0.00 42.54 4.02
3092 3425 2.094286 AGATTGCTGGACTGAAGACTCG 60.094 50.000 0.00 0.00 0.00 4.18
3113 3446 1.546923 TGCTCGTTCCCGTCAAGATTA 59.453 47.619 0.00 0.00 35.01 1.75
3182 3518 1.002069 TTGGGACGGAGGGAGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
3183 3519 0.115745 TTTGGGACGGAGGGAGTAGT 59.884 55.000 0.00 0.00 0.00 2.73
3184 3520 1.497161 ATTTGGGACGGAGGGAGTAG 58.503 55.000 0.00 0.00 0.00 2.57
3185 3521 1.961133 AATTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3186 3522 1.073098 AAATTTGGGACGGAGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85
3187 3523 2.215942 AAAATTTGGGACGGAGGGAG 57.784 50.000 0.00 0.00 0.00 4.30
3188 3524 2.687003 AAAAATTTGGGACGGAGGGA 57.313 45.000 0.00 0.00 0.00 4.20
3204 3540 8.693504 CGTATCTAGACAAACGTAAGACAAAAA 58.306 33.333 13.30 0.00 43.62 1.94
3205 3541 7.326789 CCGTATCTAGACAAACGTAAGACAAAA 59.673 37.037 17.76 0.00 43.62 2.44
3206 3542 6.803320 CCGTATCTAGACAAACGTAAGACAAA 59.197 38.462 17.76 0.00 43.62 2.83
3207 3543 6.149308 TCCGTATCTAGACAAACGTAAGACAA 59.851 38.462 17.76 0.00 43.62 3.18
3208 3544 5.643348 TCCGTATCTAGACAAACGTAAGACA 59.357 40.000 17.76 0.00 43.62 3.41
3209 3545 6.111768 TCCGTATCTAGACAAACGTAAGAC 57.888 41.667 17.76 0.00 43.62 3.01
3210 3546 6.932356 ATCCGTATCTAGACAAACGTAAGA 57.068 37.500 17.76 11.21 43.62 2.10
3212 3548 8.721478 GGTATATCCGTATCTAGACAAACGTAA 58.279 37.037 17.76 9.60 33.63 3.18
3213 3549 8.097038 AGGTATATCCGTATCTAGACAAACGTA 58.903 37.037 17.76 7.35 41.99 3.57
3214 3550 6.939163 AGGTATATCCGTATCTAGACAAACGT 59.061 38.462 17.76 7.50 41.99 3.99
3215 3551 7.375106 AGGTATATCCGTATCTAGACAAACG 57.625 40.000 14.17 14.17 41.99 3.60
3241 3577 8.761497 CGGATGTATCAAGTCACGTTTTAATAT 58.239 33.333 0.00 0.00 0.00 1.28
3242 3578 7.760794 ACGGATGTATCAAGTCACGTTTTAATA 59.239 33.333 0.00 0.00 0.00 0.98
3243 3579 6.592607 ACGGATGTATCAAGTCACGTTTTAAT 59.407 34.615 0.00 0.00 0.00 1.40
3244 3580 5.927689 ACGGATGTATCAAGTCACGTTTTAA 59.072 36.000 0.00 0.00 0.00 1.52
3245 3581 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
3246 3582 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
3247 3583 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
3248 3584 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
3249 3585 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
3250 3586 5.051039 CCAAATACGGATGTATCAAGTCACG 60.051 44.000 0.00 0.00 40.42 4.35
3251 3587 6.018994 GTCCAAATACGGATGTATCAAGTCAC 60.019 42.308 0.00 0.00 40.42 3.67
3252 3588 6.046593 GTCCAAATACGGATGTATCAAGTCA 58.953 40.000 0.00 0.00 40.42 3.41
3253 3589 6.046593 TGTCCAAATACGGATGTATCAAGTC 58.953 40.000 0.00 0.00 40.42 3.01
3254 3590 5.984725 TGTCCAAATACGGATGTATCAAGT 58.015 37.500 0.00 0.00 40.42 3.16
3255 3591 6.918892 TTGTCCAAATACGGATGTATCAAG 57.081 37.500 0.00 0.00 40.42 3.02
3256 3592 6.094325 GGTTTGTCCAAATACGGATGTATCAA 59.906 38.462 0.00 0.00 36.90 2.57
3257 3593 5.587043 GGTTTGTCCAAATACGGATGTATCA 59.413 40.000 0.00 0.00 36.90 2.15
3258 3594 5.820947 AGGTTTGTCCAAATACGGATGTATC 59.179 40.000 0.00 0.00 38.31 2.24
3259 3595 5.751586 AGGTTTGTCCAAATACGGATGTAT 58.248 37.500 0.00 0.00 39.79 2.29
3260 3596 5.168647 AGGTTTGTCCAAATACGGATGTA 57.831 39.130 0.00 0.00 37.41 2.29
3261 3597 4.028993 AGGTTTGTCCAAATACGGATGT 57.971 40.909 0.00 0.00 37.41 3.06
3262 3598 5.878116 TCTTAGGTTTGTCCAAATACGGATG 59.122 40.000 0.00 0.00 37.41 3.51
3263 3599 5.878669 GTCTTAGGTTTGTCCAAATACGGAT 59.121 40.000 0.00 0.00 37.41 4.18
3264 3600 5.221682 TGTCTTAGGTTTGTCCAAATACGGA 60.222 40.000 0.00 0.00 39.02 4.69
3265 3601 4.998672 TGTCTTAGGTTTGTCCAAATACGG 59.001 41.667 0.00 0.00 39.02 4.02
3266 3602 6.425721 TCTTGTCTTAGGTTTGTCCAAATACG 59.574 38.462 0.00 0.00 39.02 3.06
3267 3603 7.739498 TCTTGTCTTAGGTTTGTCCAAATAC 57.261 36.000 0.00 0.00 39.02 1.89
3268 3604 8.934023 ATTCTTGTCTTAGGTTTGTCCAAATA 57.066 30.769 0.00 0.00 39.02 1.40
3269 3605 7.839680 ATTCTTGTCTTAGGTTTGTCCAAAT 57.160 32.000 0.00 0.00 39.02 2.32
3270 3606 7.654022 AATTCTTGTCTTAGGTTTGTCCAAA 57.346 32.000 0.00 0.00 39.02 3.28
3271 3607 7.654022 AAATTCTTGTCTTAGGTTTGTCCAA 57.346 32.000 0.00 0.00 39.02 3.53
3272 3608 7.417342 CCAAAATTCTTGTCTTAGGTTTGTCCA 60.417 37.037 0.00 0.00 39.02 4.02
3273 3609 6.923508 CCAAAATTCTTGTCTTAGGTTTGTCC 59.076 38.462 0.00 0.00 0.00 4.02
3274 3610 7.712797 TCCAAAATTCTTGTCTTAGGTTTGTC 58.287 34.615 0.00 0.00 0.00 3.18
3275 3611 7.654022 TCCAAAATTCTTGTCTTAGGTTTGT 57.346 32.000 0.00 0.00 0.00 2.83
3276 3612 7.167468 CGTTCCAAAATTCTTGTCTTAGGTTTG 59.833 37.037 0.00 0.00 0.00 2.93
3277 3613 7.200455 CGTTCCAAAATTCTTGTCTTAGGTTT 58.800 34.615 0.00 0.00 0.00 3.27
3278 3614 6.238925 CCGTTCCAAAATTCTTGTCTTAGGTT 60.239 38.462 0.00 0.00 0.00 3.50
3279 3615 5.240844 CCGTTCCAAAATTCTTGTCTTAGGT 59.759 40.000 0.00 0.00 0.00 3.08
3280 3616 5.472137 TCCGTTCCAAAATTCTTGTCTTAGG 59.528 40.000 0.00 0.00 0.00 2.69
3281 3617 6.348540 CCTCCGTTCCAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
3282 3618 5.472137 CCTCCGTTCCAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
3283 3619 4.278419 CCTCCGTTCCAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
3284 3620 3.821033 CCTCCGTTCCAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
3285 3621 3.057526 CCCTCCGTTCCAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
3286 3622 2.890945 CCCTCCGTTCCAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
3287 3623 3.153919 TCCCTCCGTTCCAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
3288 3624 3.181433 ACTCCCTCCGTTCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3289 3625 2.375509 ACTCCCTCCGTTCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
3290 3626 2.791655 ACTCCCTCCGTTCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
3291 3627 2.971901 ACTCCCTCCGTTCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
3292 3628 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
3293 3629 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
3294 3630 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
3295 3631 2.225091 TGTAGTACTCCCTCCGTTCCAA 60.225 50.000 0.00 0.00 0.00 3.53
3296 3632 1.355381 TGTAGTACTCCCTCCGTTCCA 59.645 52.381 0.00 0.00 0.00 3.53
3297 3633 2.134789 TGTAGTACTCCCTCCGTTCC 57.865 55.000 0.00 0.00 0.00 3.62
3298 3634 4.202441 TGTATGTAGTACTCCCTCCGTTC 58.798 47.826 0.00 0.00 34.27 3.95
3299 3635 4.240881 TGTATGTAGTACTCCCTCCGTT 57.759 45.455 0.00 0.00 34.27 4.44
3300 3636 3.939740 TGTATGTAGTACTCCCTCCGT 57.060 47.619 0.00 0.00 34.27 4.69
3301 3637 3.003068 CGTTGTATGTAGTACTCCCTCCG 59.997 52.174 0.00 0.00 34.27 4.63
3302 3638 3.243334 GCGTTGTATGTAGTACTCCCTCC 60.243 52.174 0.00 0.00 34.27 4.30
3303 3639 3.243334 GGCGTTGTATGTAGTACTCCCTC 60.243 52.174 0.00 0.00 34.27 4.30
3304 3640 2.692041 GGCGTTGTATGTAGTACTCCCT 59.308 50.000 0.00 0.00 34.27 4.20
3305 3641 2.428171 TGGCGTTGTATGTAGTACTCCC 59.572 50.000 0.00 0.00 34.27 4.30
3306 3642 3.788333 TGGCGTTGTATGTAGTACTCC 57.212 47.619 0.00 0.00 34.27 3.85
3307 3643 4.025979 GCAATGGCGTTGTATGTAGTACTC 60.026 45.833 19.84 0.00 40.07 2.59
3308 3644 3.869246 GCAATGGCGTTGTATGTAGTACT 59.131 43.478 19.84 0.00 40.07 2.73
3309 3645 4.191662 GCAATGGCGTTGTATGTAGTAC 57.808 45.455 19.84 0.00 40.07 2.73
3334 3670 4.895961 AGGAGTACCAACAAAGAAGCTAC 58.104 43.478 0.00 0.00 38.94 3.58
3357 3695 4.323417 TGCATCGACCAGAATACAAAACT 58.677 39.130 0.00 0.00 0.00 2.66
3405 3745 3.629087 AGTGTAGGATTAGGTACTGCGT 58.371 45.455 0.00 0.00 41.52 5.24
3677 4028 9.575868 TTTGATAGACTTATAGCTAGCTGTACT 57.424 33.333 27.68 18.73 0.00 2.73
3701 4052 8.306761 AGTTTTTCTGTCTCACAAGAATGTTTT 58.693 29.630 0.00 0.00 37.82 2.43
3788 4139 4.003648 ACTTTGTTGCTTTAGCGCTCTAT 58.996 39.130 16.34 0.00 45.83 1.98
3853 4209 6.126796 TGAGATGAAGAGCCCAAACATGTATA 60.127 38.462 0.00 0.00 0.00 1.47
3856 4212 3.245016 TGAGATGAAGAGCCCAAACATGT 60.245 43.478 0.00 0.00 0.00 3.21
3881 4237 7.447238 TGACGAATACCTGTAGACATCATCATA 59.553 37.037 0.00 0.00 0.00 2.15
3977 4333 4.657814 TGATCCTAAAAGCACCCTCTTT 57.342 40.909 0.00 0.00 37.86 2.52
4003 4359 0.820871 GCAGGCACTAGCTAGACTGT 59.179 55.000 27.45 2.30 41.70 3.55
4027 4383 7.555965 ACAAAGGAATAAGAGTTTGTTTTGCT 58.444 30.769 0.00 0.00 39.51 3.91
4185 4549 8.041323 CCTATGGCTAGACGGATATGTTTAATT 58.959 37.037 0.00 0.00 0.00 1.40
4358 4738 0.757188 AGCTAGCTACGCCTGGTCAT 60.757 55.000 17.69 0.00 0.00 3.06
4409 4789 0.253044 ACGGCTGGATGCTTGTATGT 59.747 50.000 0.00 0.00 42.39 2.29
4501 4881 8.260114 GGCTATACAGTTTACTTTAGGGTTACA 58.740 37.037 0.00 0.00 0.00 2.41
4502 4882 8.260114 TGGCTATACAGTTTACTTTAGGGTTAC 58.740 37.037 0.00 0.00 0.00 2.50
4503 4883 8.378115 TGGCTATACAGTTTACTTTAGGGTTA 57.622 34.615 0.00 0.00 0.00 2.85
4504 4884 7.261688 TGGCTATACAGTTTACTTTAGGGTT 57.738 36.000 0.00 0.00 0.00 4.11
4506 4886 7.280356 ACATGGCTATACAGTTTACTTTAGGG 58.720 38.462 0.00 0.00 0.00 3.53
4507 4887 9.477484 CTACATGGCTATACAGTTTACTTTAGG 57.523 37.037 0.00 0.00 0.00 2.69
4508 4888 9.477484 CCTACATGGCTATACAGTTTACTTTAG 57.523 37.037 0.00 0.00 0.00 1.85
4509 4889 9.204337 TCCTACATGGCTATACAGTTTACTTTA 57.796 33.333 0.00 0.00 35.26 1.85
4510 4890 8.086143 TCCTACATGGCTATACAGTTTACTTT 57.914 34.615 0.00 0.00 35.26 2.66
4511 4891 7.670605 TCCTACATGGCTATACAGTTTACTT 57.329 36.000 0.00 0.00 35.26 2.24
4512 4892 7.857404 ATCCTACATGGCTATACAGTTTACT 57.143 36.000 0.00 0.00 35.26 2.24
4513 4893 8.251721 CCTATCCTACATGGCTATACAGTTTAC 58.748 40.741 0.00 0.00 35.26 2.01
4514 4894 7.399191 CCCTATCCTACATGGCTATACAGTTTA 59.601 40.741 0.00 0.00 35.26 2.01
4536 4916 7.966339 ATAAACATGTACACTACTCACCCTA 57.034 36.000 0.00 0.00 0.00 3.53
4576 4957 6.541278 ACATGCACATACATATCATATGCTCC 59.459 38.462 4.41 0.00 33.99 4.70
4579 4960 8.118607 GTGTACATGCACATACATATCATATGC 58.881 37.037 13.45 0.00 39.07 3.14
4684 5079 7.040271 TGGGAGGTAAAAAGCTGTGTAATTAAC 60.040 37.037 0.00 0.00 0.00 2.01
4685 5080 7.005296 TGGGAGGTAAAAAGCTGTGTAATTAA 58.995 34.615 0.00 0.00 0.00 1.40
4812 5911 1.687660 AGTCCATTTGCATGCAACACA 59.312 42.857 31.99 18.74 35.46 3.72
5221 7707 9.122613 CAGATTGCGATCGGTATATATCATAAG 57.877 37.037 18.30 0.00 37.37 1.73
5227 7713 9.817809 ATTAAACAGATTGCGATCGGTATATAT 57.182 29.630 18.56 8.55 39.34 0.86
5228 7714 9.297586 GATTAAACAGATTGCGATCGGTATATA 57.702 33.333 18.56 10.45 39.34 0.86
5235 7721 5.641777 TCAGATTAAACAGATTGCGATCG 57.358 39.130 11.69 11.69 37.37 3.69
5247 7733 7.929941 AAGGAGAAGGAACATCAGATTAAAC 57.070 36.000 0.00 0.00 0.00 2.01
5315 7801 3.469970 AGGTCGGCGGCATCATCA 61.470 61.111 15.59 0.00 0.00 3.07
5318 7804 3.469970 ATCAGGTCGGCGGCATCA 61.470 61.111 15.59 0.00 0.00 3.07
5339 7825 3.369381 CGACAATCGGAATGGAGCT 57.631 52.632 0.00 0.00 36.00 4.09
5549 8051 1.156322 TCTGGTTCCCTCCTCCTCCT 61.156 60.000 0.00 0.00 0.00 3.69
5769 8288 3.044059 GCAGGCAGGCAAGCTAACG 62.044 63.158 0.00 0.00 34.17 3.18
5821 8349 1.269723 TCTTCAAGCTCGATCGTGTGT 59.730 47.619 15.94 1.69 0.00 3.72
5822 8350 1.916651 CTCTTCAAGCTCGATCGTGTG 59.083 52.381 15.94 8.13 0.00 3.82
5823 8351 1.542030 ACTCTTCAAGCTCGATCGTGT 59.458 47.619 15.94 0.88 0.00 4.49
5824 8352 1.916651 CACTCTTCAAGCTCGATCGTG 59.083 52.381 15.94 14.19 0.00 4.35
5825 8353 1.542030 ACACTCTTCAAGCTCGATCGT 59.458 47.619 15.94 0.00 0.00 3.73
5826 8354 1.916651 CACACTCTTCAAGCTCGATCG 59.083 52.381 9.36 9.36 0.00 3.69
5860 8388 4.806571 CAGCATGCCATGAAGTGC 57.193 55.556 15.66 0.84 37.84 4.40
5909 8447 5.183904 GTGGCATAACAAAAAGATGAGACCT 59.816 40.000 0.00 0.00 0.00 3.85
5988 9306 2.304092 ACATGCTTGCATGGTCCATAG 58.696 47.619 30.86 10.93 36.91 2.23
6138 9495 5.122396 CACCTTTACTGATTCGCTTTAGCTT 59.878 40.000 0.00 0.00 39.32 3.74
6219 9579 3.554731 GCGGTAAAAGTATAGTGCAGTCC 59.445 47.826 0.00 0.00 0.00 3.85
6270 9941 2.614013 ATGGTGGGTGGAGGGACC 60.614 66.667 0.00 0.00 39.54 4.46
6322 9993 7.338449 ACCGCAATAGAGTAATTGTTGGTTAAT 59.662 33.333 8.75 0.00 41.14 1.40


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

AutoCloner maintained by Alex Coulton.