Multiple sequence alignment - TraesCS5A01G100600

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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 TraesCS5A01G100600 chr5A 100.000 4240 0 0 1506 5745 145681030 145676791 0.000000e+00 7830.0
1 TraesCS5A01G100600 chr5A 100.000 1135 0 0 1 1135 145682535 145681401 0.000000e+00 2097.0
2 TraesCS5A01G100600 chr5A 95.804 143 5 1 4069 4211 414133562 414133421 4.480000e-56 230.0
3 TraesCS5A01G100600 chr5A 93.421 152 10 0 4047 4198 569702134 569701983 5.790000e-55 226.0
4 TraesCS5A01G100600 chr5A 78.327 263 45 8 493 746 288258754 288259013 5.960000e-35 159.0
5 TraesCS5A01G100600 chr5B 95.144 2574 93 12 1506 4071 141905754 141903205 0.000000e+00 4032.0
6 TraesCS5A01G100600 chr5B 95.968 744 24 3 4210 4948 141903195 141902453 0.000000e+00 1203.0
7 TraesCS5A01G100600 chr5B 85.658 767 70 23 1 753 141945481 141944741 0.000000e+00 771.0
8 TraesCS5A01G100600 chr5B 95.584 317 6 4 825 1135 141906061 141905747 8.590000e-138 501.0
9 TraesCS5A01G100600 chr5B 93.443 183 7 4 5011 5193 141902292 141902115 3.410000e-67 267.0
10 TraesCS5A01G100600 chr5B 81.553 309 47 8 453 759 598047831 598047531 4.450000e-61 246.0
11 TraesCS5A01G100600 chr5B 91.667 108 8 1 5465 5571 141901582 141901475 1.290000e-31 148.0
12 TraesCS5A01G100600 chr5B 97.297 37 1 0 4943 4979 141902330 141902294 4.810000e-06 63.9
13 TraesCS5A01G100600 chr5D 93.896 1196 59 7 2881 4071 129866083 129864897 0.000000e+00 1792.0
14 TraesCS5A01G100600 chr5D 93.792 1192 35 10 1506 2689 129867296 129866136 0.000000e+00 1755.0
15 TraesCS5A01G100600 chr5D 96.682 844 13 6 4194 5032 129864899 129864066 0.000000e+00 1389.0
16 TraesCS5A01G100600 chr5D 89.078 998 79 18 1 981 129868731 129867747 0.000000e+00 1212.0
17 TraesCS5A01G100600 chr5D 91.626 203 15 1 5219 5419 129863615 129863413 4.380000e-71 279.0
18 TraesCS5A01G100600 chr5D 87.448 239 18 4 5420 5647 129863366 129863129 1.230000e-66 265.0
19 TraesCS5A01G100600 chr5D 94.262 122 2 3 5069 5190 129864067 129863951 1.270000e-41 182.0
20 TraesCS5A01G100600 chr3A 100.000 131 0 0 4068 4198 158174957 158174827 5.750000e-60 243.0
21 TraesCS5A01G100600 chr3A 97.778 135 3 0 4069 4203 584748652 584748786 3.460000e-57 233.0
22 TraesCS5A01G100600 chr3A 97.101 138 4 0 4067 4204 681617897 681617760 3.460000e-57 233.0
23 TraesCS5A01G100600 chr3A 79.283 251 32 16 512 754 595070271 595070509 2.140000e-34 158.0
24 TraesCS5A01G100600 chr3A 85.333 150 15 7 452 598 75414766 75414621 1.290000e-31 148.0
25 TraesCS5A01G100600 chr3A 90.909 77 6 1 490 565 422623457 422623381 1.020000e-17 102.0
26 TraesCS5A01G100600 chr1A 100.000 130 0 0 4068 4197 345168817 345168946 2.070000e-59 241.0
27 TraesCS5A01G100600 chr1A 98.507 134 2 0 4066 4199 14170061 14170194 2.680000e-58 237.0
28 TraesCS5A01G100600 chr1A 80.339 295 33 14 453 743 532787170 532786897 3.510000e-47 200.0
29 TraesCS5A01G100600 chr7A 97.163 141 3 1 4066 4206 729886494 729886633 2.680000e-58 237.0
30 TraesCS5A01G100600 chr7A 97.794 136 3 0 4068 4203 501074674 501074809 9.620000e-58 235.0
31 TraesCS5A01G100600 chr1D 79.798 297 38 13 451 743 435280346 435280068 4.540000e-46 196.0
32 TraesCS5A01G100600 chr1B 77.926 299 41 10 451 744 588511965 588511687 4.610000e-36 163.0
33 TraesCS5A01G100600 chr2D 84.828 145 20 2 490 634 470214267 470214125 1.670000e-30 145.0


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 TraesCS5A01G100600 chr5A 145676791 145682535 5744 True 4963.500000 7830 100.000000 1 5745 2 chr5A.!!$R3 5744
1 TraesCS5A01G100600 chr5B 141901475 141906061 4586 True 1035.816667 4032 94.850500 825 5571 6 chr5B.!!$R3 4746
2 TraesCS5A01G100600 chr5B 141944741 141945481 740 True 771.000000 771 85.658000 1 753 1 chr5B.!!$R1 752
3 TraesCS5A01G100600 chr5D 129863129 129868731 5602 True 982.000000 1792 92.397714 1 5647 7 chr5D.!!$R1 5646

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
962 1023 1.011293 TCCCTTCCCATCTCCATTCCT 59.989 52.381 0.0 0.0 0.0 3.36 F
1129 1496 0.034616 CTCATCGAAGCCCATCTCCC 59.965 60.000 0.0 0.0 0.0 4.30 F
1132 1499 0.105246 ATCGAAGCCCATCTCCCTCT 60.105 55.000 0.0 0.0 0.0 3.69 F
2178 2545 0.671472 TGCTCACATGCTTCCAGACG 60.671 55.000 0.0 0.0 0.0 4.18 F
4018 4406 0.681733 CTGCACCCTACCGCTGATAT 59.318 55.000 0.0 0.0 0.0 1.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2812 3188 0.108424 CACGGGAGGAAGAAGCTGAG 60.108 60.000 0.00 0.0 0.0 3.35 R
2897 3273 1.456705 GGGAGCACAACAAACCCCA 60.457 57.895 0.00 0.0 35.0 4.96 R
3152 3528 0.252197 CTACCTCAAACCTTCCCCCG 59.748 60.000 0.00 0.0 0.0 5.73 R
4178 4566 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.0 0.0 4.55 R
5703 6843 0.037326 TGCTAGCTTTGACCTGACGG 60.037 55.000 17.23 0.0 0.0 4.79 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
45 46 1.315257 CCCATGCCAAGGTTTCTCCG 61.315 60.000 0.00 0.00 41.99 4.63
63 64 1.568612 CGTGTCAACGCCATTCTGCT 61.569 55.000 0.00 0.00 43.98 4.24
189 190 3.242608 CCATTTGACACTAATTACCGCCG 60.243 47.826 0.00 0.00 0.00 6.46
208 209 2.742053 CCGTTGACATAACCTGAACCAG 59.258 50.000 0.00 0.00 0.00 4.00
265 267 7.108194 TGCTTGATGATTCTCTTAGTCATGTT 58.892 34.615 0.00 0.00 33.03 2.71
271 273 6.796426 TGATTCTCTTAGTCATGTTCTACCG 58.204 40.000 0.00 0.00 0.00 4.02
284 286 4.933330 TGTTCTACCGATATGAGCTCAAC 58.067 43.478 22.50 13.91 0.00 3.18
298 300 9.710900 ATATGAGCTCAACGATAATCATTGTAA 57.289 29.630 22.50 0.00 0.00 2.41
317 319 6.036577 TGTAATTGTAGAGATGACAGCACA 57.963 37.500 0.00 0.00 0.00 4.57
324 326 6.935167 TGTAGAGATGACAGCACAATTAAGA 58.065 36.000 0.00 0.00 0.00 2.10
357 359 4.706962 AGTTTATCCAGTTGGCTTTCCATC 59.293 41.667 0.00 0.00 43.05 3.51
364 366 1.784301 TTGGCTTTCCATCCCACCGA 61.784 55.000 0.00 0.00 43.05 4.69
400 404 9.958180 TTTTATTGTGAGATACCATCTTGAGAA 57.042 29.630 0.00 0.00 40.38 2.87
456 460 5.774630 CAATTTGTAGGGAAAGCCGTTTTA 58.225 37.500 0.00 0.00 33.56 1.52
658 693 4.862371 TGTGGAGGTAATATTTGGGGTTC 58.138 43.478 0.00 0.00 0.00 3.62
659 694 4.292571 TGTGGAGGTAATATTTGGGGTTCA 59.707 41.667 0.00 0.00 0.00 3.18
664 699 6.439375 GGAGGTAATATTTGGGGTTCAACTTT 59.561 38.462 0.00 0.00 34.67 2.66
713 750 5.759763 AGGCTTTTCACCTAAAATTTTGCAG 59.240 36.000 13.76 3.84 36.49 4.41
734 771 2.030274 GGTAGCATTTGGGTGTGACAAC 60.030 50.000 0.00 0.00 0.00 3.32
816 871 3.426568 GCAGGTGCAGCGGTTCTC 61.427 66.667 17.19 0.00 41.59 2.87
827 882 1.736681 AGCGGTTCTCGACACTAGTAC 59.263 52.381 0.00 0.00 42.43 2.73
828 883 1.202121 GCGGTTCTCGACACTAGTACC 60.202 57.143 0.00 0.00 42.43 3.34
829 884 2.354259 CGGTTCTCGACACTAGTACCT 58.646 52.381 0.00 0.00 42.43 3.08
962 1023 1.011293 TCCCTTCCCATCTCCATTCCT 59.989 52.381 0.00 0.00 0.00 3.36
1116 1483 1.680522 CCACCTCCCCACTCTCATCG 61.681 65.000 0.00 0.00 0.00 3.84
1129 1496 0.034616 CTCATCGAAGCCCATCTCCC 59.965 60.000 0.00 0.00 0.00 4.30
1130 1497 0.399091 TCATCGAAGCCCATCTCCCT 60.399 55.000 0.00 0.00 0.00 4.20
1131 1498 0.034616 CATCGAAGCCCATCTCCCTC 59.965 60.000 0.00 0.00 0.00 4.30
1132 1499 0.105246 ATCGAAGCCCATCTCCCTCT 60.105 55.000 0.00 0.00 0.00 3.69
1133 1500 0.757188 TCGAAGCCCATCTCCCTCTC 60.757 60.000 0.00 0.00 0.00 3.20
1134 1501 1.753368 CGAAGCCCATCTCCCTCTCC 61.753 65.000 0.00 0.00 0.00 3.71
1974 2341 2.417239 CGCCTACCAATTCGTTAAAGCA 59.583 45.455 0.00 0.00 0.00 3.91
2178 2545 0.671472 TGCTCACATGCTTCCAGACG 60.671 55.000 0.00 0.00 0.00 4.18
2235 2602 4.503314 GCCAATCCGCTTGCTGCC 62.503 66.667 0.00 0.00 38.78 4.85
2479 2846 1.160329 GCTCACGGTATGATGCCACC 61.160 60.000 0.00 0.00 36.48 4.61
2485 2852 1.540363 CGGTATGATGCCACCTGTACC 60.540 57.143 0.00 0.00 32.29 3.34
2544 2917 4.201910 TGCCTAATTAGTTCGCAATTGCTC 60.202 41.667 26.86 16.70 39.32 4.26
2603 2976 2.945008 GCTCAGTGCTATTTGTATGCCA 59.055 45.455 0.00 0.00 38.95 4.92
2742 3118 6.043243 AGAGACTGGACTCTTGATTTAAACCA 59.957 38.462 0.00 0.00 43.62 3.67
2756 3132 0.752658 AAACCAAACTGCAAGAGCCC 59.247 50.000 0.00 0.00 41.13 5.19
2785 3161 5.008118 GCCTGGAGTATTCTTTAATGCAGTC 59.992 44.000 0.00 0.00 30.79 3.51
2792 3168 4.944962 TTCTTTAATGCAGTCGACATGG 57.055 40.909 19.50 7.93 0.00 3.66
2802 3178 1.079503 GTCGACATGGGTCTTGCTTC 58.920 55.000 11.55 0.00 42.05 3.86
2806 3182 2.508526 GACATGGGTCTTGCTTCTGTT 58.491 47.619 0.00 0.00 40.99 3.16
2807 3183 2.485814 GACATGGGTCTTGCTTCTGTTC 59.514 50.000 0.00 0.00 40.99 3.18
2808 3184 1.815003 CATGGGTCTTGCTTCTGTTCC 59.185 52.381 0.00 0.00 0.00 3.62
2809 3185 0.843309 TGGGTCTTGCTTCTGTTCCA 59.157 50.000 0.00 0.00 0.00 3.53
2810 3186 1.425066 TGGGTCTTGCTTCTGTTCCAT 59.575 47.619 0.00 0.00 0.00 3.41
2811 3187 2.087646 GGGTCTTGCTTCTGTTCCATC 58.912 52.381 0.00 0.00 0.00 3.51
2812 3188 2.087646 GGTCTTGCTTCTGTTCCATCC 58.912 52.381 0.00 0.00 0.00 3.51
2836 3212 1.139853 GCTTCTTCCTCCCGTGATGAT 59.860 52.381 0.00 0.00 0.00 2.45
2897 3273 2.167037 TTTAGGGTTGCAGGGGCCT 61.167 57.895 0.84 0.00 40.13 5.19
3093 3469 2.503356 GGGAGATTGACACAGATCTGGT 59.497 50.000 26.08 19.76 32.96 4.00
3152 3528 1.418637 TGGTGGGTTACTGGTGAAGAC 59.581 52.381 0.00 0.00 0.00 3.01
3212 3588 8.682936 AGGATGTATGTTGACTGGAATTTATC 57.317 34.615 0.00 0.00 0.00 1.75
3213 3589 8.497745 AGGATGTATGTTGACTGGAATTTATCT 58.502 33.333 0.00 0.00 0.00 1.98
3245 3624 6.597672 TGTTCAAGTGTTGTTTAGTGACTGAT 59.402 34.615 0.00 0.00 0.00 2.90
3269 3648 4.580580 GGATTGAGCCATTTAACTACAGGG 59.419 45.833 0.00 0.00 0.00 4.45
3289 3668 2.380084 GGCACCTCGAGAATTACACA 57.620 50.000 15.71 0.00 0.00 3.72
3323 3709 5.562506 TCAGTAGACAGTCTGAAATACCG 57.437 43.478 13.84 0.00 37.69 4.02
3347 3733 4.490743 AGGGTTCTGTTTTGTTGTTTTCG 58.509 39.130 0.00 0.00 0.00 3.46
3372 3758 8.901748 CGGTTGTGTTTTTGTTCATATTTAGAG 58.098 33.333 0.00 0.00 0.00 2.43
3396 3782 6.824704 AGCATTGCACAATTTATGGCTTAAAT 59.175 30.769 11.91 11.41 41.31 1.40
3434 3822 6.991938 TGAGTGCCTTATTTTGCATAAAGTT 58.008 32.000 0.00 0.00 40.07 2.66
3462 3850 3.383761 CCTTGTTGAAACATGGCTGTTC 58.616 45.455 13.34 0.00 44.83 3.18
3659 4047 2.361757 CACATGGAAAGAGTGTTTGGCA 59.638 45.455 0.00 0.00 0.00 4.92
3719 4107 0.815213 TGATTGCGATGGCTGGCTAC 60.815 55.000 0.15 0.00 40.82 3.58
3812 4200 7.059156 CCCTCAGTTTCCTCTTGAAATGATAT 58.941 38.462 0.00 0.00 44.44 1.63
3893 4281 3.255725 GTTGCTGTACTATGCCACGTTA 58.744 45.455 0.00 0.00 0.00 3.18
3987 4375 5.163499 TGGTATCCGTTGCAAAAAGTTCTTT 60.163 36.000 0.00 0.00 0.00 2.52
3993 4381 5.052633 CCGTTGCAAAAAGTTCTTTTACTCG 60.053 40.000 0.00 12.60 0.00 4.18
4018 4406 0.681733 CTGCACCCTACCGCTGATAT 59.318 55.000 0.00 0.00 0.00 1.63
4077 4465 6.954352 ATTTCCTGGTTATATACTCCCTCC 57.046 41.667 0.00 0.00 0.00 4.30
4078 4466 4.043608 TCCTGGTTATATACTCCCTCCG 57.956 50.000 0.00 0.00 0.00 4.63
4079 4467 3.400322 TCCTGGTTATATACTCCCTCCGT 59.600 47.826 0.00 0.00 0.00 4.69
4080 4468 4.140853 TCCTGGTTATATACTCCCTCCGTT 60.141 45.833 0.00 0.00 0.00 4.44
4081 4469 4.220163 CCTGGTTATATACTCCCTCCGTTC 59.780 50.000 0.00 0.00 0.00 3.95
4082 4470 4.154942 TGGTTATATACTCCCTCCGTTCC 58.845 47.826 2.00 0.00 0.00 3.62
4083 4471 3.192212 GGTTATATACTCCCTCCGTTCCG 59.808 52.174 0.00 0.00 0.00 4.30
4084 4472 2.965671 ATATACTCCCTCCGTTCCGA 57.034 50.000 0.00 0.00 0.00 4.55
4085 4473 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
4086 4474 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
4087 4475 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
4088 4476 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4089 4477 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4090 4478 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4091 4479 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4092 4480 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4093 4481 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4094 4482 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4095 4483 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4096 4484 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4097 4485 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
4098 4486 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
4099 4487 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
4100 4488 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
4101 4489 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
4102 4490 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
4103 4491 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
4104 4492 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
4105 4493 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
4106 4494 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
4107 4495 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
4108 4496 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
4109 4497 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
4110 4498 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
4112 4500 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
4113 4501 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
4114 4502 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
4115 4503 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
4116 4504 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
4117 4505 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
4118 4506 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
4119 4507 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
4120 4508 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
4136 4524 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
4137 4525 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
4138 4526 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
4139 4527 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
4142 4530 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
4146 4534 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
4147 4535 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
4148 4536 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
4149 4537 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
4150 4538 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
4151 4539 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
4152 4540 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
4153 4541 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
4165 4553 6.837471 ATACCTCCGTATCTAGACAAATCC 57.163 41.667 0.00 0.00 28.45 3.01
4166 4554 4.543689 ACCTCCGTATCTAGACAAATCCA 58.456 43.478 0.00 0.00 0.00 3.41
4167 4555 4.960469 ACCTCCGTATCTAGACAAATCCAA 59.040 41.667 0.00 0.00 0.00 3.53
4168 4556 5.069251 ACCTCCGTATCTAGACAAATCCAAG 59.931 44.000 0.00 0.00 0.00 3.61
4169 4557 5.302059 CCTCCGTATCTAGACAAATCCAAGA 59.698 44.000 0.00 0.00 0.00 3.02
4170 4558 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
4171 4559 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
4172 4560 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
4173 4561 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
4174 4562 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
4175 4563 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
4176 4564 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
4178 4566 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
4179 4567 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
4180 4568 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
4181 4569 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
4182 4570 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
4183 4571 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
4184 4572 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
4423 4813 0.036010 CCTGGCAACTCTCATTCGGT 60.036 55.000 0.00 0.00 37.61 4.69
4630 5020 0.760945 CCCCCGTCTTCTATGGAGCT 60.761 60.000 0.00 0.00 36.17 4.09
4648 5038 0.745845 CTGGCTATGTTCCGCTTGCT 60.746 55.000 0.00 0.00 0.00 3.91
4879 5272 7.498570 TCTTTTAGTTTGTACCCGTACATTTGT 59.501 33.333 8.45 0.00 44.54 2.83
4909 5302 2.879756 GCAGTTACTTCCAATGCCAGGA 60.880 50.000 0.00 0.00 0.00 3.86
4984 5505 7.535139 TGTTTATCTTATGCCTTAGTTTGTGC 58.465 34.615 0.00 0.00 0.00 4.57
4985 5506 7.393234 TGTTTATCTTATGCCTTAGTTTGTGCT 59.607 33.333 0.00 0.00 0.00 4.40
4986 5507 7.938140 TTATCTTATGCCTTAGTTTGTGCTT 57.062 32.000 0.00 0.00 0.00 3.91
4987 5508 5.627499 TCTTATGCCTTAGTTTGTGCTTG 57.373 39.130 0.00 0.00 0.00 4.01
4992 5513 1.000274 CCTTAGTTTGTGCTTGGTGCC 60.000 52.381 0.00 0.00 42.00 5.01
5009 5530 2.637872 GTGCCCCTGATAAGCCTACATA 59.362 50.000 0.00 0.00 0.00 2.29
5043 5564 6.138263 TGGATCTTTTGCCTTCATCCATAAT 58.862 36.000 0.00 0.00 38.48 1.28
5045 5566 6.266103 GGATCTTTTGCCTTCATCCATAATCA 59.734 38.462 0.00 0.00 34.27 2.57
5067 5588 4.327087 CAGGTTTTCTGTCACAAAAACAGC 59.673 41.667 20.38 10.66 43.74 4.40
5068 5589 3.616821 GGTTTTCTGTCACAAAAACAGCC 59.383 43.478 20.38 4.01 43.74 4.85
5072 5593 0.032615 TGTCACAAAAACAGCCCCCT 60.033 50.000 0.00 0.00 0.00 4.79
5188 5945 4.286032 TCTTTCCAGTTGTAGGTATGCACT 59.714 41.667 0.00 0.00 0.00 4.40
5189 5946 5.482526 TCTTTCCAGTTGTAGGTATGCACTA 59.517 40.000 0.00 0.00 0.00 2.74
5190 5947 4.730949 TCCAGTTGTAGGTATGCACTAC 57.269 45.455 6.12 6.12 40.87 2.73
5191 5948 4.350245 TCCAGTTGTAGGTATGCACTACT 58.650 43.478 12.60 3.38 41.03 2.57
5192 5949 5.512298 TCCAGTTGTAGGTATGCACTACTA 58.488 41.667 12.60 4.34 41.03 1.82
5193 5950 5.593095 TCCAGTTGTAGGTATGCACTACTAG 59.407 44.000 12.60 0.00 41.03 2.57
5194 5951 5.593095 CCAGTTGTAGGTATGCACTACTAGA 59.407 44.000 12.60 1.43 41.03 2.43
5195 5952 6.238786 CCAGTTGTAGGTATGCACTACTAGAG 60.239 46.154 12.60 0.00 41.03 2.43
5196 5953 6.542735 CAGTTGTAGGTATGCACTACTAGAGA 59.457 42.308 12.60 0.00 41.03 3.10
5197 5954 7.229707 CAGTTGTAGGTATGCACTACTAGAGAT 59.770 40.741 12.60 0.00 41.03 2.75
5198 5955 7.780745 AGTTGTAGGTATGCACTACTAGAGATT 59.219 37.037 12.60 0.00 41.03 2.40
5199 5956 8.414778 GTTGTAGGTATGCACTACTAGAGATTT 58.585 37.037 12.60 0.00 41.03 2.17
5200 5957 8.534954 TGTAGGTATGCACTACTAGAGATTTT 57.465 34.615 12.60 0.00 41.03 1.82
5201 5958 8.978472 TGTAGGTATGCACTACTAGAGATTTTT 58.022 33.333 12.60 0.00 41.03 1.94
5202 5959 9.250624 GTAGGTATGCACTACTAGAGATTTTTG 57.749 37.037 0.00 0.00 38.19 2.44
5234 5991 9.781633 TTTTGGTAACTTACATTAACTCTGCTA 57.218 29.630 1.40 0.00 37.61 3.49
5235 5992 8.997621 TTGGTAACTTACATTAACTCTGCTAG 57.002 34.615 1.40 0.00 37.61 3.42
5236 5993 8.357290 TGGTAACTTACATTAACTCTGCTAGA 57.643 34.615 0.00 0.00 37.61 2.43
5237 5994 8.467598 TGGTAACTTACATTAACTCTGCTAGAG 58.532 37.037 10.48 10.48 42.75 2.43
5238 5995 8.684520 GGTAACTTACATTAACTCTGCTAGAGA 58.315 37.037 16.81 0.00 45.07 3.10
5327 6410 3.517901 ACATGTTCGTTCTCCTTGGGATA 59.482 43.478 0.00 0.00 0.00 2.59
5354 6437 1.565305 GTCTCCTGCACGATGACATC 58.435 55.000 5.28 5.28 0.00 3.06
5394 6477 3.382832 CGTGGGAAGGCGGTCTCT 61.383 66.667 0.00 0.00 0.00 3.10
5409 6492 1.153289 CTCTGGCAGCGGCAAGTAT 60.153 57.895 13.24 0.00 42.10 2.12
5435 6564 2.552315 CGGTGCACTTTCCATTAGTTGT 59.448 45.455 17.98 0.00 0.00 3.32
5477 6615 1.106944 TGCCCATATCGACGAGCTGA 61.107 55.000 3.01 0.00 0.00 4.26
5478 6616 0.664767 GCCCATATCGACGAGCTGAC 60.665 60.000 3.01 0.00 0.00 3.51
5480 6618 0.955178 CCATATCGACGAGCTGACCT 59.045 55.000 3.01 0.00 0.00 3.85
5511 6649 2.413351 GTCGCTCGCTAGCCATCA 59.587 61.111 9.66 0.00 46.68 3.07
5542 6680 3.416382 GGAAAGTTGCGGCGCGTA 61.416 61.111 28.09 15.23 0.00 4.42
5595 6734 0.538287 ACTTGGAGCTTTGGGTGAGC 60.538 55.000 0.00 0.00 40.43 4.26
5602 6741 0.600057 GCTTTGGGTGAGCAAGAAGG 59.400 55.000 0.00 0.00 39.89 3.46
5610 6749 0.601046 TGAGCAAGAAGGTGAGTGCG 60.601 55.000 0.00 0.00 41.90 5.34
5613 6752 1.672356 CAAGAAGGTGAGTGCGGGG 60.672 63.158 0.00 0.00 0.00 5.73
5647 6787 1.323412 AGTTATCTCTCGCATCGCCT 58.677 50.000 0.00 0.00 0.00 5.52
5648 6788 1.268352 AGTTATCTCTCGCATCGCCTC 59.732 52.381 0.00 0.00 0.00 4.70
5649 6789 0.238553 TTATCTCTCGCATCGCCTCG 59.761 55.000 0.00 0.00 0.00 4.63
5650 6790 2.188849 TATCTCTCGCATCGCCTCGC 62.189 60.000 0.00 0.00 0.00 5.03
5668 6808 3.775654 CCTCGCACACCCCCTCTC 61.776 72.222 0.00 0.00 0.00 3.20
5669 6809 4.135153 CTCGCACACCCCCTCTCG 62.135 72.222 0.00 0.00 0.00 4.04
5670 6810 4.671590 TCGCACACCCCCTCTCGA 62.672 66.667 0.00 0.00 0.00 4.04
5671 6811 3.461773 CGCACACCCCCTCTCGAT 61.462 66.667 0.00 0.00 0.00 3.59
5672 6812 2.125326 CGCACACCCCCTCTCGATA 61.125 63.158 0.00 0.00 0.00 2.92
5673 6813 1.742768 GCACACCCCCTCTCGATAG 59.257 63.158 0.00 0.00 0.00 2.08
5674 6814 1.749334 GCACACCCCCTCTCGATAGG 61.749 65.000 9.85 9.85 36.30 2.57
5675 6815 0.106167 CACACCCCCTCTCGATAGGA 60.106 60.000 17.98 0.00 39.15 2.94
5676 6816 0.106116 ACACCCCCTCTCGATAGGAC 60.106 60.000 17.98 0.00 39.15 3.85
5677 6817 1.150992 ACCCCCTCTCGATAGGACG 59.849 63.158 17.98 9.50 39.15 4.79
5678 6818 1.150992 CCCCCTCTCGATAGGACGT 59.849 63.158 17.98 0.00 39.15 4.34
5679 6819 1.173444 CCCCCTCTCGATAGGACGTG 61.173 65.000 17.98 1.49 39.15 4.49
5680 6820 1.173444 CCCCTCTCGATAGGACGTGG 61.173 65.000 17.98 6.92 39.15 4.94
5681 6821 1.655329 CCTCTCGATAGGACGTGGC 59.345 63.158 11.33 0.00 39.15 5.01
5682 6822 0.820074 CCTCTCGATAGGACGTGGCT 60.820 60.000 11.33 0.00 39.15 4.75
5683 6823 1.025812 CTCTCGATAGGACGTGGCTT 58.974 55.000 0.00 0.00 34.70 4.35
5684 6824 1.405821 CTCTCGATAGGACGTGGCTTT 59.594 52.381 0.00 0.00 34.70 3.51
5685 6825 1.134367 TCTCGATAGGACGTGGCTTTG 59.866 52.381 0.00 0.00 34.70 2.77
5686 6826 0.174845 TCGATAGGACGTGGCTTTGG 59.825 55.000 0.00 0.00 34.70 3.28
5687 6827 0.174845 CGATAGGACGTGGCTTTGGA 59.825 55.000 0.00 0.00 0.00 3.53
5688 6828 1.802880 CGATAGGACGTGGCTTTGGAG 60.803 57.143 0.00 0.00 0.00 3.86
5689 6829 0.541863 ATAGGACGTGGCTTTGGAGG 59.458 55.000 0.00 0.00 0.00 4.30
5690 6830 0.834687 TAGGACGTGGCTTTGGAGGT 60.835 55.000 0.00 0.00 0.00 3.85
5691 6831 0.834687 AGGACGTGGCTTTGGAGGTA 60.835 55.000 0.00 0.00 0.00 3.08
5692 6832 0.252197 GGACGTGGCTTTGGAGGTAT 59.748 55.000 0.00 0.00 0.00 2.73
5693 6833 1.369625 GACGTGGCTTTGGAGGTATG 58.630 55.000 0.00 0.00 0.00 2.39
5694 6834 0.690762 ACGTGGCTTTGGAGGTATGT 59.309 50.000 0.00 0.00 0.00 2.29
5695 6835 1.073284 ACGTGGCTTTGGAGGTATGTT 59.927 47.619 0.00 0.00 0.00 2.71
5696 6836 2.303600 ACGTGGCTTTGGAGGTATGTTA 59.696 45.455 0.00 0.00 0.00 2.41
5697 6837 2.676342 CGTGGCTTTGGAGGTATGTTAC 59.324 50.000 0.00 0.00 0.00 2.50
5698 6838 3.681593 GTGGCTTTGGAGGTATGTTACA 58.318 45.455 0.00 0.00 0.00 2.41
5699 6839 4.270008 GTGGCTTTGGAGGTATGTTACAT 58.730 43.478 2.58 2.58 0.00 2.29
5700 6840 4.705023 GTGGCTTTGGAGGTATGTTACATT 59.295 41.667 2.23 0.00 0.00 2.71
5701 6841 4.704540 TGGCTTTGGAGGTATGTTACATTG 59.295 41.667 2.23 0.00 0.00 2.82
5702 6842 4.947388 GGCTTTGGAGGTATGTTACATTGA 59.053 41.667 2.23 0.00 0.00 2.57
5703 6843 5.163652 GGCTTTGGAGGTATGTTACATTGAC 60.164 44.000 2.23 0.00 0.00 3.18
5704 6844 5.163652 GCTTTGGAGGTATGTTACATTGACC 60.164 44.000 2.23 6.17 0.00 4.02
5705 6845 4.131649 TGGAGGTATGTTACATTGACCG 57.868 45.455 2.23 0.00 35.24 4.79
5706 6846 3.516300 TGGAGGTATGTTACATTGACCGT 59.484 43.478 2.23 0.00 35.24 4.83
5707 6847 4.117685 GGAGGTATGTTACATTGACCGTC 58.882 47.826 2.23 5.86 35.24 4.79
5708 6848 4.382254 GGAGGTATGTTACATTGACCGTCA 60.382 45.833 2.23 0.00 35.24 4.35
5709 6849 4.755411 AGGTATGTTACATTGACCGTCAG 58.245 43.478 2.23 0.00 35.24 3.51
5710 6850 3.869246 GGTATGTTACATTGACCGTCAGG 59.131 47.826 2.23 1.33 45.13 3.86
5721 6861 2.755929 CCGTCAGGTCAAAGCTAGC 58.244 57.895 6.62 6.62 0.00 3.42
5722 6862 0.037326 CCGTCAGGTCAAAGCTAGCA 60.037 55.000 18.83 0.00 0.00 3.49
5723 6863 1.071605 CGTCAGGTCAAAGCTAGCAC 58.928 55.000 18.83 5.89 0.00 4.40
5724 6864 1.071605 GTCAGGTCAAAGCTAGCACG 58.928 55.000 18.83 4.51 0.00 5.34
5725 6865 0.679505 TCAGGTCAAAGCTAGCACGT 59.320 50.000 18.83 4.85 0.00 4.49
5726 6866 0.792640 CAGGTCAAAGCTAGCACGTG 59.207 55.000 18.83 12.28 0.00 4.49
5727 6867 0.320771 AGGTCAAAGCTAGCACGTGG 60.321 55.000 18.83 1.27 0.00 4.94
5728 6868 1.497722 GTCAAAGCTAGCACGTGGC 59.502 57.895 18.83 12.49 45.30 5.01
5729 6869 1.671054 TCAAAGCTAGCACGTGGCC 60.671 57.895 18.83 0.00 46.50 5.36
5730 6870 2.742372 AAAGCTAGCACGTGGCCG 60.742 61.111 18.83 5.28 46.50 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.128692 GTAGCAGAATGGCGTTGACAC 59.871 52.381 0.00 0.00 39.27 3.67
126 127 4.405116 TCCATTTTGATGGCCTATTTGC 57.595 40.909 3.32 0.00 41.43 3.68
127 128 6.164417 TCATCCATTTTGATGGCCTATTTG 57.836 37.500 3.32 0.00 41.97 2.32
128 129 5.306160 CCTCATCCATTTTGATGGCCTATTT 59.694 40.000 3.32 0.00 41.97 1.40
129 130 4.836736 CCTCATCCATTTTGATGGCCTATT 59.163 41.667 3.32 0.00 41.97 1.73
130 131 4.106825 TCCTCATCCATTTTGATGGCCTAT 59.893 41.667 3.32 0.00 41.97 2.57
131 132 3.462954 TCCTCATCCATTTTGATGGCCTA 59.537 43.478 3.32 0.00 41.97 3.93
189 190 2.159627 CGCTGGTTCAGGTTATGTCAAC 59.840 50.000 0.00 0.00 31.21 3.18
259 261 4.827284 TGAGCTCATATCGGTAGAACATGA 59.173 41.667 13.74 0.00 0.00 3.07
265 267 3.473625 TCGTTGAGCTCATATCGGTAGA 58.526 45.455 19.04 5.66 0.00 2.59
271 273 8.249327 ACAATGATTATCGTTGAGCTCATATC 57.751 34.615 27.64 13.21 44.06 1.63
298 300 8.043113 TCTTAATTGTGCTGTCATCTCTACAAT 58.957 33.333 0.00 0.00 39.59 2.71
313 315 4.631813 ACTCGGTTGATCTCTTAATTGTGC 59.368 41.667 0.00 0.00 0.00 4.57
317 319 8.265055 TGGATAAACTCGGTTGATCTCTTAATT 58.735 33.333 11.60 0.00 34.66 1.40
324 326 5.178797 CAACTGGATAAACTCGGTTGATCT 58.821 41.667 8.78 0.00 38.97 2.75
357 359 5.897377 ATAAAAATTCTCAAGTCGGTGGG 57.103 39.130 0.00 0.00 0.00 4.61
446 450 0.322546 CCCCAGAGCTAAAACGGCTT 60.323 55.000 0.00 0.00 40.40 4.35
472 476 5.913137 AATTTAATGTTCATCCGGAAGCA 57.087 34.783 9.01 0.52 35.82 3.91
566 601 7.651304 TCATGTTTCGCATAAAAATTGTCAAGT 59.349 29.630 0.00 0.00 35.74 3.16
637 672 4.862371 TGAACCCCAAATATTACCTCCAC 58.138 43.478 0.00 0.00 0.00 4.02
670 707 2.096496 CCTAAGCATTTTGACCTGCGAG 59.904 50.000 0.00 0.00 43.17 5.03
713 750 1.904287 TGTCACACCCAAATGCTACC 58.096 50.000 0.00 0.00 0.00 3.18
757 794 9.474920 CTGTGAGCAAAAATAATGGTAGAAAAA 57.525 29.630 0.00 0.00 0.00 1.94
758 795 8.087750 CCTGTGAGCAAAAATAATGGTAGAAAA 58.912 33.333 0.00 0.00 0.00 2.29
762 799 6.757897 TCCTGTGAGCAAAAATAATGGTAG 57.242 37.500 0.00 0.00 0.00 3.18
764 801 5.649782 CTCCTGTGAGCAAAAATAATGGT 57.350 39.130 0.00 0.00 0.00 3.55
816 871 2.606725 CGTAGACCAGGTACTAGTGTCG 59.393 54.545 5.39 0.00 36.02 4.35
827 882 1.214589 CCGGTGTTCGTAGACCAGG 59.785 63.158 9.05 6.95 37.56 4.45
828 883 0.815734 ATCCGGTGTTCGTAGACCAG 59.184 55.000 9.05 0.00 37.56 4.00
829 884 0.528924 CATCCGGTGTTCGTAGACCA 59.471 55.000 9.05 0.00 37.56 4.02
1105 1472 0.467384 ATGGGCTTCGATGAGAGTGG 59.533 55.000 1.89 0.00 0.00 4.00
1116 1483 2.141312 GGAGAGGGAGATGGGCTTC 58.859 63.158 0.00 0.00 0.00 3.86
1505 1872 1.687493 GAGTGGGAGTGGGAGAGGG 60.687 68.421 0.00 0.00 0.00 4.30
1506 1873 1.687493 GGAGTGGGAGTGGGAGAGG 60.687 68.421 0.00 0.00 0.00 3.69
2037 2404 2.367202 GGAGACCGAGGGGATTGCA 61.367 63.158 0.00 0.00 36.97 4.08
2178 2545 2.704193 CGCTGACGAAACGACCGAC 61.704 63.158 0.00 0.00 43.93 4.79
2235 2602 2.320587 GGTGCTGAGCGTCAGGTTG 61.321 63.158 14.19 0.00 44.43 3.77
2510 2883 5.560966 ACTAATTAGGCATGGTTCAAACG 57.439 39.130 16.73 0.00 0.00 3.60
2721 3097 6.833933 AGTTTGGTTTAAATCAAGAGTCCAGT 59.166 34.615 13.36 0.00 29.47 4.00
2742 3118 1.035139 CAACTGGGCTCTTGCAGTTT 58.965 50.000 0.00 0.00 41.91 2.66
2785 3161 1.081892 CAGAAGCAAGACCCATGTCG 58.918 55.000 0.00 0.00 46.51 4.35
2806 3182 2.114616 GAGGAAGAAGCTGAGGATGGA 58.885 52.381 0.00 0.00 0.00 3.41
2807 3183 1.140652 GGAGGAAGAAGCTGAGGATGG 59.859 57.143 0.00 0.00 0.00 3.51
2808 3184 1.140652 GGGAGGAAGAAGCTGAGGATG 59.859 57.143 0.00 0.00 0.00 3.51
2809 3185 1.506025 GGGAGGAAGAAGCTGAGGAT 58.494 55.000 0.00 0.00 0.00 3.24
2810 3186 0.972983 CGGGAGGAAGAAGCTGAGGA 60.973 60.000 0.00 0.00 0.00 3.71
2811 3187 1.261238 ACGGGAGGAAGAAGCTGAGG 61.261 60.000 0.00 0.00 0.00 3.86
2812 3188 0.108424 CACGGGAGGAAGAAGCTGAG 60.108 60.000 0.00 0.00 0.00 3.35
2836 3212 2.680352 GGTCTCTGGCGAGGTCCA 60.680 66.667 0.00 0.00 37.86 4.02
2897 3273 1.456705 GGGAGCACAACAAACCCCA 60.457 57.895 0.00 0.00 35.00 4.96
3152 3528 0.252197 CTACCTCAAACCTTCCCCCG 59.748 60.000 0.00 0.00 0.00 5.73
3212 3588 9.567848 ACTAAACAACACTTGAACACATTTTAG 57.432 29.630 0.00 0.00 0.00 1.85
3213 3589 9.347934 CACTAAACAACACTTGAACACATTTTA 57.652 29.630 0.00 0.00 0.00 1.52
3219 3595 6.021596 CAGTCACTAAACAACACTTGAACAC 58.978 40.000 0.00 0.00 0.00 3.32
3245 3624 5.192927 CCTGTAGTTAAATGGCTCAATCCA 58.807 41.667 0.00 0.00 40.97 3.41
3269 3648 1.066430 TGTGTAATTCTCGAGGTGCCC 60.066 52.381 13.56 0.00 0.00 5.36
3289 3668 8.616076 CAGACTGTCTACTGAAAAATTTCAACT 58.384 33.333 10.47 1.65 45.61 3.16
3321 3707 2.946990 ACAACAAAACAGAACCCTACGG 59.053 45.455 0.00 0.00 0.00 4.02
3323 3709 5.513849 CGAAAACAACAAAACAGAACCCTAC 59.486 40.000 0.00 0.00 0.00 3.18
3347 3733 8.699749 GCTCTAAATATGAACAAAAACACAACC 58.300 33.333 0.00 0.00 0.00 3.77
3372 3758 6.419980 TTTAAGCCATAAATTGTGCAATGC 57.580 33.333 0.00 0.00 0.00 3.56
3396 3782 5.483685 AGGCACTCAATAAGTAACAGTGA 57.516 39.130 0.00 0.00 37.28 3.41
3434 3822 3.639094 CCATGTTTCAACAAGGTTACCCA 59.361 43.478 5.88 0.00 41.54 4.51
3462 3850 0.246360 TGCAGACAGGTGGATGTACG 59.754 55.000 0.00 0.00 32.25 3.67
3514 3902 6.402550 GCATGGACAGTACAATGTTTCAGTAG 60.403 42.308 0.00 0.00 32.25 2.57
3659 4047 3.235200 GGTATCCCATGCTACAGACTCT 58.765 50.000 0.00 0.00 0.00 3.24
3812 4200 7.346471 AGCAAGAATAACTAAATAGGAGCCAA 58.654 34.615 0.00 0.00 0.00 4.52
3850 4238 2.798499 GCACATCCATCATGCTCAAAGC 60.798 50.000 0.00 0.00 42.82 3.51
3852 4240 1.402613 CGCACATCCATCATGCTCAAA 59.597 47.619 0.00 0.00 37.20 2.69
3893 4281 4.764679 TTCGTGCTGTCAAAATGCTAAT 57.235 36.364 0.00 0.00 0.00 1.73
3957 4345 0.250510 TGCAACGGATACCAGCAACA 60.251 50.000 0.00 0.00 31.42 3.33
3987 4375 2.453521 AGGGTGCAGACATACGAGTAA 58.546 47.619 0.00 0.00 0.00 2.24
3993 4381 0.529992 GCGGTAGGGTGCAGACATAC 60.530 60.000 4.96 4.96 0.00 2.39
4018 4406 5.425217 TCAGATCTAACAATCTAACCCAGCA 59.575 40.000 0.00 0.00 34.21 4.41
4078 4466 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
4079 4467 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
4080 4468 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
4081 4469 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
4082 4470 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
4083 4471 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
4084 4472 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
4086 4474 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
4087 4475 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
4088 4476 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
4089 4477 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
4090 4478 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
4091 4479 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
4092 4480 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
4093 4481 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
4094 4482 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
4095 4483 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
4096 4484 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
4110 4498 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
4111 4499 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
4112 4500 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
4113 4501 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
4116 4504 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
4120 4508 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
4121 4509 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
4122 4510 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
4123 4511 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
4124 4512 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
4125 4513 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
4126 4514 6.153067 CGGAGGTATCTAGCACTAAAATGAG 58.847 44.000 0.00 0.00 0.00 2.90
4127 4515 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
4128 4516 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
4129 4517 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
4142 4530 6.312529 TGGATTTGTCTAGATACGGAGGTAT 58.687 40.000 0.00 0.00 42.01 2.73
4143 4531 5.698104 TGGATTTGTCTAGATACGGAGGTA 58.302 41.667 0.00 0.00 0.00 3.08
4144 4532 4.543689 TGGATTTGTCTAGATACGGAGGT 58.456 43.478 0.00 0.00 0.00 3.85
4145 4533 5.302059 TCTTGGATTTGTCTAGATACGGAGG 59.698 44.000 0.00 0.00 0.00 4.30
4146 4534 6.183360 TGTCTTGGATTTGTCTAGATACGGAG 60.183 42.308 0.00 0.00 0.00 4.63
4147 4535 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
4148 4536 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
4149 4537 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
4150 4538 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
4152 4540 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
4153 4541 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
4154 4542 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
4155 4543 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
4156 4544 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
4157 4545 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
4158 4546 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
4159 4547 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
4160 4548 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
4161 4549 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
4162 4550 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
4163 4551 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
4164 4552 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
4165 4553 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
4166 4554 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4167 4555 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4168 4556 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4169 4557 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4170 4558 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4171 4559 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4172 4560 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4173 4561 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4174 4562 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4175 4563 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
4176 4564 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
4177 4565 0.251297 TGTACTCCCTCCGTTCCGAA 60.251 55.000 0.00 0.00 0.00 4.30
4178 4566 0.033796 ATGTACTCCCTCCGTTCCGA 60.034 55.000 0.00 0.00 0.00 4.55
4179 4567 0.384669 GATGTACTCCCTCCGTTCCG 59.615 60.000 0.00 0.00 0.00 4.30
4180 4568 1.409427 CAGATGTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
4181 4569 2.376109 TCAGATGTACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
4182 4570 2.526888 TCAGATGTACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
4183 4571 2.379972 CTTCAGATGTACTCCCTCCGT 58.620 52.381 0.00 0.00 0.00 4.69
4184 4572 1.683917 CCTTCAGATGTACTCCCTCCG 59.316 57.143 0.00 0.00 0.00 4.63
4185 4573 3.033659 TCCTTCAGATGTACTCCCTCC 57.966 52.381 0.00 0.00 0.00 4.30
4186 4574 4.027437 ACTTCCTTCAGATGTACTCCCTC 58.973 47.826 0.00 0.00 31.37 4.30
4187 4575 4.067944 ACTTCCTTCAGATGTACTCCCT 57.932 45.455 0.00 0.00 31.37 4.20
4188 4576 5.657302 TCTTACTTCCTTCAGATGTACTCCC 59.343 44.000 0.00 0.00 35.47 4.30
4189 4577 6.153000 TGTCTTACTTCCTTCAGATGTACTCC 59.847 42.308 0.00 0.00 35.47 3.85
4190 4578 7.159322 TGTCTTACTTCCTTCAGATGTACTC 57.841 40.000 0.00 0.00 35.47 2.59
4191 4579 7.726033 ATGTCTTACTTCCTTCAGATGTACT 57.274 36.000 0.00 0.00 35.47 2.73
4192 4580 9.685828 GATATGTCTTACTTCCTTCAGATGTAC 57.314 37.037 0.00 0.00 35.47 2.90
4423 4813 3.324846 AGAAGTACATCAGCACCAAGACA 59.675 43.478 0.31 0.00 0.00 3.41
4630 5020 1.026182 CAGCAAGCGGAACATAGCCA 61.026 55.000 0.00 0.00 0.00 4.75
4648 5038 2.815684 ATCCGTAGCCCCACCACTCA 62.816 60.000 0.00 0.00 0.00 3.41
4909 5302 1.538047 CCACTTGCCAGTAACTGCAT 58.462 50.000 0.00 0.00 0.00 3.96
4992 5513 6.294176 GCAACAATTATGTAGGCTTATCAGGG 60.294 42.308 0.00 0.00 39.40 4.45
5009 5530 4.004982 GGCAAAAGATCCATGCAACAATT 58.995 39.130 14.58 0.00 41.80 2.32
5043 5564 5.708948 CTGTTTTTGTGACAGAAAACCTGA 58.291 37.500 21.61 10.85 45.72 3.86
5045 5566 4.494484 GCTGTTTTTGTGACAGAAAACCT 58.506 39.130 21.61 0.00 45.72 3.50
5067 5588 1.202891 ACTCAAAAGTTTCGGAGGGGG 60.203 52.381 16.95 0.00 28.74 5.40
5068 5589 2.271944 ACTCAAAAGTTTCGGAGGGG 57.728 50.000 16.95 0.25 28.74 4.79
5156 5677 3.825328 ACAACTGGAAAGATCTGTTGCT 58.175 40.909 18.05 7.19 40.32 3.91
5170 5691 4.737855 AGTAGTGCATACCTACAACTGG 57.262 45.455 13.62 0.00 34.67 4.00
5172 5693 6.660800 TCTCTAGTAGTGCATACCTACAACT 58.339 40.000 13.62 0.31 34.67 3.16
5252 6335 1.265905 GGTTTCCGGCAGTTACTGTTG 59.734 52.381 14.23 6.62 33.43 3.33
5297 6380 3.309954 GGAGAACGAACATGTATGCTTCC 59.690 47.826 0.00 0.00 0.00 3.46
5394 6477 2.124736 GGATACTTGCCGCTGCCA 60.125 61.111 0.00 0.00 36.33 4.92
5463 6601 0.312416 GCAGGTCAGCTCGTCGATAT 59.688 55.000 0.00 0.00 0.00 1.63
5511 6649 1.142262 ACTTTCCACCGTAGCCAAAGT 59.858 47.619 0.00 0.00 33.42 2.66
5542 6680 1.528129 CCGCAAGCTTTTCTCCTTCT 58.472 50.000 0.00 0.00 0.00 2.85
5595 6734 1.672356 CCCCGCACTCACCTTCTTG 60.672 63.158 0.00 0.00 0.00 3.02
5602 6741 1.002624 TCATTTCCCCCGCACTCAC 60.003 57.895 0.00 0.00 0.00 3.51
5610 6749 1.272704 ACTTTGGCTCTCATTTCCCCC 60.273 52.381 0.00 0.00 0.00 5.40
5613 6752 6.118852 AGAGATAACTTTGGCTCTCATTTCC 58.881 40.000 0.00 0.00 37.25 3.13
5651 6791 3.775654 GAGAGGGGGTGTGCGAGG 61.776 72.222 0.00 0.00 0.00 4.63
5652 6792 4.135153 CGAGAGGGGGTGTGCGAG 62.135 72.222 0.00 0.00 0.00 5.03
5653 6793 2.561467 TATCGAGAGGGGGTGTGCGA 62.561 60.000 0.00 0.00 0.00 5.10
5654 6794 2.076622 CTATCGAGAGGGGGTGTGCG 62.077 65.000 0.00 0.00 0.00 5.34
5655 6795 1.742768 CTATCGAGAGGGGGTGTGC 59.257 63.158 0.00 0.00 0.00 4.57
5656 6796 0.106167 TCCTATCGAGAGGGGGTGTG 60.106 60.000 25.26 0.00 37.20 3.82
5657 6797 0.106116 GTCCTATCGAGAGGGGGTGT 60.106 60.000 25.26 0.00 37.20 4.16
5658 6798 1.173444 CGTCCTATCGAGAGGGGGTG 61.173 65.000 25.26 9.44 37.20 4.61
5659 6799 1.150992 CGTCCTATCGAGAGGGGGT 59.849 63.158 25.26 0.00 37.20 4.95
5660 6800 1.150992 ACGTCCTATCGAGAGGGGG 59.849 63.158 25.26 18.69 37.20 5.40
5661 6801 1.173444 CCACGTCCTATCGAGAGGGG 61.173 65.000 25.26 19.02 37.20 4.79
5662 6802 1.797211 GCCACGTCCTATCGAGAGGG 61.797 65.000 25.26 13.05 37.20 4.30
5663 6803 0.820074 AGCCACGTCCTATCGAGAGG 60.820 60.000 20.33 20.33 38.03 3.69
5664 6804 1.025812 AAGCCACGTCCTATCGAGAG 58.974 55.000 0.00 0.00 34.70 3.20
5665 6805 1.134367 CAAAGCCACGTCCTATCGAGA 59.866 52.381 0.00 0.00 34.70 4.04
5666 6806 1.560923 CAAAGCCACGTCCTATCGAG 58.439 55.000 0.00 0.00 34.70 4.04
5667 6807 0.174845 CCAAAGCCACGTCCTATCGA 59.825 55.000 0.00 0.00 34.70 3.59
5668 6808 0.174845 TCCAAAGCCACGTCCTATCG 59.825 55.000 0.00 0.00 0.00 2.92
5669 6809 1.473434 CCTCCAAAGCCACGTCCTATC 60.473 57.143 0.00 0.00 0.00 2.08
5670 6810 0.541863 CCTCCAAAGCCACGTCCTAT 59.458 55.000 0.00 0.00 0.00 2.57
5671 6811 0.834687 ACCTCCAAAGCCACGTCCTA 60.835 55.000 0.00 0.00 0.00 2.94
5672 6812 0.834687 TACCTCCAAAGCCACGTCCT 60.835 55.000 0.00 0.00 0.00 3.85
5673 6813 0.252197 ATACCTCCAAAGCCACGTCC 59.748 55.000 0.00 0.00 0.00 4.79
5674 6814 1.338769 ACATACCTCCAAAGCCACGTC 60.339 52.381 0.00 0.00 0.00 4.34
5675 6815 0.690762 ACATACCTCCAAAGCCACGT 59.309 50.000 0.00 0.00 0.00 4.49
5676 6816 1.821216 AACATACCTCCAAAGCCACG 58.179 50.000 0.00 0.00 0.00 4.94
5677 6817 3.681593 TGTAACATACCTCCAAAGCCAC 58.318 45.455 0.00 0.00 0.00 5.01
5678 6818 4.584638 ATGTAACATACCTCCAAAGCCA 57.415 40.909 0.00 0.00 0.00 4.75
5679 6819 4.947388 TCAATGTAACATACCTCCAAAGCC 59.053 41.667 0.00 0.00 0.00 4.35
5680 6820 5.163652 GGTCAATGTAACATACCTCCAAAGC 60.164 44.000 0.00 0.00 0.00 3.51
5681 6821 5.064707 CGGTCAATGTAACATACCTCCAAAG 59.935 44.000 0.00 0.00 0.00 2.77
5682 6822 4.938832 CGGTCAATGTAACATACCTCCAAA 59.061 41.667 0.00 0.00 0.00 3.28
5683 6823 4.020039 ACGGTCAATGTAACATACCTCCAA 60.020 41.667 0.00 0.00 0.00 3.53
5684 6824 3.516300 ACGGTCAATGTAACATACCTCCA 59.484 43.478 0.00 0.00 0.00 3.86
5685 6825 4.117685 GACGGTCAATGTAACATACCTCC 58.882 47.826 2.62 0.00 0.00 4.30
5686 6826 4.751060 TGACGGTCAATGTAACATACCTC 58.249 43.478 8.68 0.00 0.00 3.85
5687 6827 4.382685 CCTGACGGTCAATGTAACATACCT 60.383 45.833 12.54 0.00 0.00 3.08
5688 6828 3.869246 CCTGACGGTCAATGTAACATACC 59.131 47.826 12.54 0.00 0.00 2.73
5689 6829 4.501071 ACCTGACGGTCAATGTAACATAC 58.499 43.478 12.54 0.00 40.27 2.39
5690 6830 4.811969 ACCTGACGGTCAATGTAACATA 57.188 40.909 12.54 0.00 40.27 2.29
5691 6831 3.695830 ACCTGACGGTCAATGTAACAT 57.304 42.857 12.54 0.00 40.27 2.71
5703 6843 0.037326 TGCTAGCTTTGACCTGACGG 60.037 55.000 17.23 0.00 0.00 4.79
5704 6844 1.071605 GTGCTAGCTTTGACCTGACG 58.928 55.000 17.23 0.00 0.00 4.35
5705 6845 1.071605 CGTGCTAGCTTTGACCTGAC 58.928 55.000 17.23 0.93 0.00 3.51
5706 6846 0.679505 ACGTGCTAGCTTTGACCTGA 59.320 50.000 17.23 0.00 0.00 3.86
5707 6847 0.792640 CACGTGCTAGCTTTGACCTG 59.207 55.000 17.23 2.14 0.00 4.00
5708 6848 0.320771 CCACGTGCTAGCTTTGACCT 60.321 55.000 17.23 0.00 0.00 3.85
5709 6849 1.912371 GCCACGTGCTAGCTTTGACC 61.912 60.000 17.23 0.00 36.87 4.02
5710 6850 1.497722 GCCACGTGCTAGCTTTGAC 59.502 57.895 17.23 4.47 36.87 3.18
5711 6851 1.671054 GGCCACGTGCTAGCTTTGA 60.671 57.895 17.23 0.00 40.92 2.69
5712 6852 2.870372 GGCCACGTGCTAGCTTTG 59.130 61.111 17.23 9.79 40.92 2.77
5713 6853 2.742372 CGGCCACGTGCTAGCTTT 60.742 61.111 17.23 0.00 40.92 3.51


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

AutoCloner maintained by Alex Coulton.