Multiple sequence alignment - TraesCS2D01G401800

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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 TraesCS2D01G401800 chr2D 100.000 7094 0 0 1 7094 516703120 516710213 0.000000e+00 13101.0
1 TraesCS2D01G401800 chr2D 91.000 100 9 0 6653 6752 516811880 516811979 1.240000e-27 135.0
2 TraesCS2D01G401800 chr2A 94.056 4559 148 29 673 5194 660509227 660513699 0.000000e+00 6804.0
3 TraesCS2D01G401800 chr2A 90.056 1780 106 31 5356 7091 660513698 660515450 0.000000e+00 2241.0
4 TraesCS2D01G401800 chr2A 96.757 185 5 1 5182 5365 746756979 746757163 2.490000e-79 307.0
5 TraesCS2D01G401800 chr2B 93.123 2792 109 20 686 3427 608444292 608447050 0.000000e+00 4015.0
6 TraesCS2D01G401800 chr2B 96.472 1559 40 6 3645 5194 608447044 608448596 0.000000e+00 2560.0
7 TraesCS2D01G401800 chr2B 91.818 1320 67 21 5356 6653 608448595 608449895 0.000000e+00 1801.0
8 TraesCS2D01G401800 chr2B 84.375 672 98 5 1 670 504316596 504317262 0.000000e+00 652.0
9 TraesCS2D01G401800 chr2B 89.083 458 22 10 6652 7091 608449960 608450407 1.740000e-150 544.0
10 TraesCS2D01G401800 chr1A 89.866 671 66 2 1 670 533320665 533321334 0.000000e+00 861.0
11 TraesCS2D01G401800 chr1A 86.720 497 65 1 176 671 460292860 460292364 1.040000e-152 551.0
12 TraesCS2D01G401800 chr1A 88.492 252 28 1 426 676 58839300 58839049 3.220000e-78 303.0
13 TraesCS2D01G401800 chr4B 89.568 671 70 0 1 671 562362751 562362081 0.000000e+00 852.0
14 TraesCS2D01G401800 chr6B 89.286 672 69 3 1 670 666776548 666777218 0.000000e+00 839.0
15 TraesCS2D01G401800 chr6B 88.276 145 13 4 529 671 51384412 51384554 3.400000e-38 171.0
16 TraesCS2D01G401800 chr6B 97.561 41 1 0 678 718 195277492 195277452 3.550000e-08 71.3
17 TraesCS2D01G401800 chr6B 88.462 52 5 1 3663 3713 451927500 451927449 2.140000e-05 62.1
18 TraesCS2D01G401800 chr6A 89.185 601 59 2 1 598 101431256 101430659 0.000000e+00 745.0
19 TraesCS2D01G401800 chr6A 97.561 41 1 0 678 718 131937843 131937803 3.550000e-08 71.3
20 TraesCS2D01G401800 chr5B 81.990 583 98 7 96 675 586471748 586472326 8.270000e-134 488.0
21 TraesCS2D01G401800 chr5A 100.000 169 0 0 5190 5358 651496989 651496821 5.340000e-81 313.0
22 TraesCS2D01G401800 chr4D 98.837 172 2 0 5193 5364 75782217 75782046 2.490000e-79 307.0
23 TraesCS2D01G401800 chr4A 97.222 180 4 1 5188 5366 362067906 362068085 3.220000e-78 303.0
24 TraesCS2D01G401800 chr4A 95.187 187 8 1 5174 5360 582530159 582529974 1.940000e-75 294.0
25 TraesCS2D01G401800 chr7A 97.207 179 4 1 5180 5357 324925209 324925031 1.160000e-77 302.0
26 TraesCS2D01G401800 chr7A 92.683 41 2 1 688 728 176417739 176417778 2.760000e-04 58.4
27 TraesCS2D01G401800 chr7D 95.676 185 6 2 5175 5358 381797774 381797957 5.380000e-76 296.0
28 TraesCS2D01G401800 chr7D 78.491 265 44 8 4639 4892 619630720 619630982 2.050000e-35 161.0
29 TraesCS2D01G401800 chr1D 95.699 186 5 3 5175 5358 331539448 331539264 5.380000e-76 296.0
30 TraesCS2D01G401800 chr1B 94.764 191 8 2 5179 5367 336774398 336774588 5.380000e-76 296.0
31 TraesCS2D01G401800 chr3B 84.906 265 32 5 4497 4759 778446712 778446454 1.960000e-65 261.0
32 TraesCS2D01G401800 chrUn 88.780 205 22 1 469 672 29597483 29597279 4.250000e-62 250.0


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 TraesCS2D01G401800 chr2D 516703120 516710213 7093 False 13101.0 13101 100.000 1 7094 1 chr2D.!!$F1 7093
1 TraesCS2D01G401800 chr2A 660509227 660515450 6223 False 4522.5 6804 92.056 673 7091 2 chr2A.!!$F2 6418
2 TraesCS2D01G401800 chr2B 608444292 608450407 6115 False 2230.0 4015 92.624 686 7091 4 chr2B.!!$F2 6405
3 TraesCS2D01G401800 chr2B 504316596 504317262 666 False 652.0 652 84.375 1 670 1 chr2B.!!$F1 669
4 TraesCS2D01G401800 chr1A 533320665 533321334 669 False 861.0 861 89.866 1 670 1 chr1A.!!$F1 669
5 TraesCS2D01G401800 chr4B 562362081 562362751 670 True 852.0 852 89.568 1 671 1 chr4B.!!$R1 670
6 TraesCS2D01G401800 chr6B 666776548 666777218 670 False 839.0 839 89.286 1 670 1 chr6B.!!$F2 669
7 TraesCS2D01G401800 chr6A 101430659 101431256 597 True 745.0 745 89.185 1 598 1 chr6A.!!$R1 597
8 TraesCS2D01G401800 chr5B 586471748 586472326 578 False 488.0 488 81.990 96 675 1 chr5B.!!$F1 579

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
359 367 0.678048 GTCGAGAAGCAATGGCCCTT 60.678 55.0 0.00 0.00 42.56 3.95 F
604 615 1.029947 GTGTGGCTCATAAACCCCCG 61.030 60.0 0.00 0.00 0.00 5.73 F
1389 1435 0.958876 CCCCAGGTTTTGCGTCTACC 60.959 60.0 0.00 0.00 0.00 3.18 F
2482 2548 0.387929 GTGGAATGGATGCTGCATGG 59.612 55.0 21.53 0.00 0.00 3.66 F
2545 2611 2.620627 GGGGTGGGTTTCTCAATCGATT 60.621 50.0 4.39 4.39 0.00 3.34 F
3464 3536 0.376152 GCTGCCACATCGATTCACTG 59.624 55.0 0.00 0.00 0.00 3.66 F
3472 3544 0.460311 ATCGATTCACTGTCGGGTCC 59.540 55.0 0.00 0.00 39.45 4.46 F
5204 5289 0.041386 AGGCTTCTACTCCCTCCGTT 59.959 55.0 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1435 0.247736 AAGTGAGAGCAACTAGGCCG 59.752 55.000 0.00 0.0 0.00 6.13 R
1845 1910 1.084018 ATGGAGAGGGAAAGGGCAAA 58.916 50.000 0.00 0.0 0.00 3.68 R
3164 3232 0.324552 ATATGCACTGGGCTTGGCAA 60.325 50.000 2.50 0.0 45.15 4.52 R
3436 3508 0.250234 GATGTGGCAGCTACTGGTCA 59.750 55.000 10.64 0.0 31.21 4.02 R
3661 3733 0.460635 TGCGTGCTCCCGGTATTTAC 60.461 55.000 0.00 0.0 0.00 2.01 R
5187 5272 0.460722 GGAACGGAGGGAGTAGAAGC 59.539 60.000 0.00 0.0 0.00 3.86 R
5341 5426 3.716431 TGTTAATACTCCCTCCGTTCCT 58.284 45.455 0.00 0.0 0.00 3.36 R
6541 6651 0.036765 TTTATGCGGCAAGACGAGGT 60.037 50.000 6.82 0.0 35.47 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.676471 GGGCCATCTGGTTTGCGT 60.676 61.111 4.39 0.00 37.57 5.24
114 116 1.749634 GAGAGCTGGCTGATTGCAAAT 59.250 47.619 1.71 0.00 45.15 2.32
211 216 2.899256 CAAAAATCAGGGTGGATGGTGT 59.101 45.455 0.00 0.00 0.00 4.16
271 279 2.650116 GCAGAGACCAGAGCGGGAA 61.650 63.158 0.00 0.00 40.22 3.97
281 289 1.146263 GAGCGGGAAGTACATGGGG 59.854 63.158 0.00 0.00 0.00 4.96
287 295 1.202651 GGGAAGTACATGGGGTCATCG 60.203 57.143 0.00 0.00 0.00 3.84
359 367 0.678048 GTCGAGAAGCAATGGCCCTT 60.678 55.000 0.00 0.00 42.56 3.95
438 447 3.585289 TCAGGACATAAACCTTGGCACTA 59.415 43.478 0.00 0.00 35.35 2.74
450 459 3.307691 CCTTGGCACTAGAGGAATGAACA 60.308 47.826 0.00 0.00 32.11 3.18
458 467 2.898705 AGAGGAATGAACACGAGCATC 58.101 47.619 0.00 0.00 0.00 3.91
507 516 7.121974 ACTCAATTTCATAGTTGTGTCTTCG 57.878 36.000 0.00 0.00 29.08 3.79
533 543 3.329386 TGAAGGCAGAGTTTCGAATCAG 58.671 45.455 8.83 0.00 0.00 2.90
604 615 1.029947 GTGTGGCTCATAAACCCCCG 61.030 60.000 0.00 0.00 0.00 5.73
723 735 4.095932 GCTTAAGGCGCCAAATAGTAACTT 59.904 41.667 31.54 12.46 0.00 2.66
724 736 5.554822 TTAAGGCGCCAAATAGTAACTTG 57.445 39.130 31.54 0.00 0.00 3.16
891 920 6.302615 CGATTTGCTTTCAACACAACAAAAA 58.697 32.000 0.00 0.00 31.52 1.94
892 921 6.960431 CGATTTGCTTTCAACACAACAAAAAT 59.040 30.769 0.00 0.00 31.52 1.82
947 979 5.175859 TCTAAGACAGCCGGTTAAATCTTG 58.824 41.667 16.89 9.99 0.00 3.02
1354 1400 2.190538 GGTACTTGGGTAGGTTGGCTA 58.809 52.381 0.00 0.00 0.00 3.93
1356 1402 2.040342 ACTTGGGTAGGTTGGCTACT 57.960 50.000 0.00 0.00 0.00 2.57
1365 1411 1.630878 AGGTTGGCTACTCCCTCTTTG 59.369 52.381 0.00 0.00 0.00 2.77
1385 1431 1.815817 ATTGCCCCAGGTTTTGCGTC 61.816 55.000 0.00 0.00 0.00 5.19
1387 1433 1.302993 GCCCCAGGTTTTGCGTCTA 60.303 57.895 0.00 0.00 0.00 2.59
1389 1435 0.958876 CCCCAGGTTTTGCGTCTACC 60.959 60.000 0.00 0.00 0.00 3.18
1483 1532 2.124570 CAGATTGGGGCTGTCGGG 60.125 66.667 0.00 0.00 0.00 5.14
1521 1571 6.664515 TCGGATAATCGATAAATTGTTTGGC 58.335 36.000 0.00 0.00 33.92 4.52
1788 1853 1.823041 GAGCTCCTCATGCCCTTGC 60.823 63.158 0.87 0.00 38.26 4.01
1845 1910 2.193536 GCCGGGTTCTTTGTGCTGT 61.194 57.895 2.18 0.00 0.00 4.40
1892 1957 4.176271 TGATATTTGAGCATCTATCGGCG 58.824 43.478 0.00 0.00 34.92 6.46
1968 2033 4.315803 TCAACCTAGTTCTGTTTGCTAGC 58.684 43.478 8.10 8.10 32.96 3.42
1970 2035 2.907042 ACCTAGTTCTGTTTGCTAGCCT 59.093 45.455 13.29 1.47 32.96 4.58
2089 2154 6.455246 CGGTAAAACCTCTAAGCGATTTCTTC 60.455 42.308 0.00 0.00 35.66 2.87
2151 2216 5.763204 TGTTCTCCTTTTGGAACAGTATGTC 59.237 40.000 4.69 0.00 46.80 3.06
2244 2309 7.791029 TGTACTGCTTTGGAAGATATATCACA 58.209 34.615 15.08 7.88 0.00 3.58
2303 2369 2.345560 ACCCCTACTTTGTTACCTGCT 58.654 47.619 0.00 0.00 0.00 4.24
2479 2545 1.179152 CTTGTGGAATGGATGCTGCA 58.821 50.000 4.13 4.13 0.00 4.41
2482 2548 0.387929 GTGGAATGGATGCTGCATGG 59.612 55.000 21.53 0.00 0.00 3.66
2545 2611 2.620627 GGGGTGGGTTTCTCAATCGATT 60.621 50.000 4.39 4.39 0.00 3.34
2593 2659 6.605471 AATAAAACCAGACTGGAATTTCCC 57.395 37.500 28.56 0.00 40.96 3.97
2769 2835 3.247648 CGCTTGTACACTGCTTTACTTGT 59.752 43.478 15.31 0.00 0.00 3.16
3164 3232 6.261826 GCAATTCACTTGATCCTACAATAGCT 59.738 38.462 0.00 0.00 36.97 3.32
3196 3264 4.019950 CCAGTGCATATCCATGACTATCCA 60.020 45.833 0.00 0.00 33.67 3.41
3312 3381 8.197439 CCTCTTTTCCTGAAACAAATGTTACTT 58.803 33.333 0.00 0.00 37.25 2.24
3430 3502 7.424803 TGAGAACACTGTCAAATGTTAATTGG 58.575 34.615 2.82 0.00 39.13 3.16
3431 3503 6.215845 AGAACACTGTCAAATGTTAATTGGC 58.784 36.000 2.82 0.00 39.13 4.52
3432 3504 5.528043 ACACTGTCAAATGTTAATTGGCA 57.472 34.783 0.00 0.00 39.87 4.92
3436 3508 6.869913 CACTGTCAAATGTTAATTGGCAATCT 59.130 34.615 14.04 6.66 41.41 2.40
3464 3536 0.376152 GCTGCCACATCGATTCACTG 59.624 55.000 0.00 0.00 0.00 3.66
3472 3544 0.460311 ATCGATTCACTGTCGGGTCC 59.540 55.000 0.00 0.00 39.45 4.46
3535 3607 8.293699 AGTTCCCTGGAAATGATGTAATAAAC 57.706 34.615 0.00 0.00 35.75 2.01
3536 3608 7.893302 AGTTCCCTGGAAATGATGTAATAAACA 59.107 33.333 0.00 0.00 37.98 2.83
3537 3609 8.695456 GTTCCCTGGAAATGATGTAATAAACAT 58.305 33.333 0.00 0.00 42.64 2.71
3570 3642 7.093354 AGTCTTATCGATTACACCATATGCTG 58.907 38.462 1.71 0.00 0.00 4.41
3615 3687 8.943002 GCCTTACAAGACTTAAAAGTAGCATTA 58.057 33.333 0.00 0.00 39.88 1.90
3661 3733 3.644966 TGGATGTTAAGGCCCAGTAAG 57.355 47.619 0.00 0.00 0.00 2.34
3678 3750 2.304751 AAGTAAATACCGGGAGCACG 57.695 50.000 6.32 0.00 0.00 5.34
3807 3879 3.853307 GCTGTTGTGACTTGGCAATGTAC 60.853 47.826 0.00 0.62 0.00 2.90
4279 4351 5.491078 TGTTTAATCTCACAGGGGAATAGGT 59.509 40.000 0.00 0.00 0.00 3.08
4365 4437 9.844790 TGTAGCTTTTTCATGTCATCTTTATTG 57.155 29.630 0.00 0.00 0.00 1.90
4442 4515 4.844998 TCTATCCAGATCTCGCTCTTTG 57.155 45.455 0.00 0.00 0.00 2.77
4518 4601 8.383318 TGTTGCTTCATTTATCTTATAGCTCC 57.617 34.615 0.00 0.00 0.00 4.70
4551 4634 8.686334 TCTTTTTGATGCAGATACCCTTATTTC 58.314 33.333 0.00 0.00 0.00 2.17
4599 4682 4.497291 TTGGGCCCTATACTGTTTAGTG 57.503 45.455 25.70 0.00 37.78 2.74
4829 4912 2.693074 TCTTTCCAAGTTGGCCTGTTTC 59.307 45.455 17.68 0.00 37.47 2.78
4830 4913 2.452600 TTCCAAGTTGGCCTGTTTCT 57.547 45.000 17.68 0.00 37.47 2.52
4977 5062 2.039348 TGTGTTCCCTGCTAAACCCTAC 59.961 50.000 0.00 0.00 0.00 3.18
5038 5123 3.574396 CCTTGGAGATTACGCATCCTCTA 59.426 47.826 0.00 0.00 34.04 2.43
5187 5272 4.656112 AGTGGGGAATATGTGAGTTCTAGG 59.344 45.833 0.00 0.00 0.00 3.02
5192 5277 5.071115 GGGAATATGTGAGTTCTAGGCTTCT 59.929 44.000 0.00 0.00 0.00 2.85
5193 5278 6.267928 GGGAATATGTGAGTTCTAGGCTTCTA 59.732 42.308 0.00 0.00 0.00 2.10
5194 5279 7.149307 GGAATATGTGAGTTCTAGGCTTCTAC 58.851 42.308 0.00 0.00 0.00 2.59
5195 5280 7.014808 GGAATATGTGAGTTCTAGGCTTCTACT 59.985 40.741 0.00 0.00 0.00 2.57
5196 5281 5.845391 ATGTGAGTTCTAGGCTTCTACTC 57.155 43.478 12.78 12.78 0.00 2.59
5197 5282 4.017808 TGTGAGTTCTAGGCTTCTACTCC 58.982 47.826 15.46 9.98 0.00 3.85
5198 5283 3.382227 GTGAGTTCTAGGCTTCTACTCCC 59.618 52.174 15.46 5.26 0.00 4.30
5199 5284 3.269906 TGAGTTCTAGGCTTCTACTCCCT 59.730 47.826 15.46 0.00 0.00 4.20
5200 5285 3.887110 GAGTTCTAGGCTTCTACTCCCTC 59.113 52.174 0.00 0.00 0.00 4.30
5201 5286 2.960384 GTTCTAGGCTTCTACTCCCTCC 59.040 54.545 0.00 0.00 0.00 4.30
5202 5287 1.143277 TCTAGGCTTCTACTCCCTCCG 59.857 57.143 0.00 0.00 0.00 4.63
5203 5288 0.924823 TAGGCTTCTACTCCCTCCGT 59.075 55.000 0.00 0.00 0.00 4.69
5204 5289 0.041386 AGGCTTCTACTCCCTCCGTT 59.959 55.000 0.00 0.00 0.00 4.44
5205 5290 0.460722 GGCTTCTACTCCCTCCGTTC 59.539 60.000 0.00 0.00 0.00 3.95
5206 5291 0.460722 GCTTCTACTCCCTCCGTTCC 59.539 60.000 0.00 0.00 0.00 3.62
5207 5292 1.960953 GCTTCTACTCCCTCCGTTCCT 60.961 57.143 0.00 0.00 0.00 3.36
5208 5293 2.686118 GCTTCTACTCCCTCCGTTCCTA 60.686 54.545 0.00 0.00 0.00 2.94
5209 5294 3.629087 CTTCTACTCCCTCCGTTCCTAA 58.371 50.000 0.00 0.00 0.00 2.69
5210 5295 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
5211 5296 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
5212 5297 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
5213 5298 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
5214 5299 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
5215 5300 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5216 5301 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5217 5302 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5218 5303 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5219 5304 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5220 5305 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5221 5306 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5222 5307 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
5223 5308 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
5224 5309 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
5225 5310 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
5226 5311 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
5239 5324 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
5240 5325 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
5241 5326 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
5242 5327 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
5243 5328 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
5244 5329 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
5245 5330 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
5246 5331 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
5247 5332 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
5249 5334 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
5250 5335 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
5251 5336 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
5252 5337 7.870954 AGATTTCAACAAGTGACTACATACGAA 59.129 33.333 0.00 0.00 35.39 3.85
5253 5338 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
5254 5339 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
5255 5340 4.514781 ACAAGTGACTACATACGAAGCA 57.485 40.909 0.00 0.00 0.00 3.91
5256 5341 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
5257 5342 5.294356 ACAAGTGACTACATACGAAGCAAA 58.706 37.500 0.00 0.00 0.00 3.68
5258 5343 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
5259 5344 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
5260 5345 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
5261 5346 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
5262 5347 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
5263 5348 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
5264 5349 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
5265 5350 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
5266 5351 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
5267 5352 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
5268 5353 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
5269 5354 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
5270 5355 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
5271 5356 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
5272 5357 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
5273 5358 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
5306 5391 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
5308 5393 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
5309 5394 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
5310 5395 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
5311 5396 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
5312 5397 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
5313 5398 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
5314 5399 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
5315 5400 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
5316 5401 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
5317 5402 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
5318 5403 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
5319 5404 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
5320 5405 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
5321 5406 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
5322 5407 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
5323 5408 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
5324 5409 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
5325 5410 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
5326 5411 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
5327 5412 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
5328 5413 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
5329 5414 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
5333 5418 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
5334 5419 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
5351 5436 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
5352 5437 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5353 5438 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5354 5439 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5374 5459 9.110502 GAGGGAGTATTAACAAATCTTTACTGG 57.889 37.037 0.00 0.00 0.00 4.00
5451 5536 0.379669 GCATGTGCTCACAGTATGGC 59.620 55.000 8.74 3.91 45.48 4.40
5687 5772 1.069765 CGGGAGCACAAGTGACAGT 59.930 57.895 4.04 0.00 0.00 3.55
5759 5844 0.981277 CGGATAGTTGGGGAGGTGGT 60.981 60.000 0.00 0.00 0.00 4.16
5760 5845 0.546598 GGATAGTTGGGGAGGTGGTG 59.453 60.000 0.00 0.00 0.00 4.17
5761 5846 0.546598 GATAGTTGGGGAGGTGGTGG 59.453 60.000 0.00 0.00 0.00 4.61
5841 5926 3.378112 ACGATTTAACCATGTGCAGGATG 59.622 43.478 0.00 0.00 40.87 3.51
5878 5963 4.320202 CCATAACACGTGAAACAAGGAAGG 60.320 45.833 25.01 5.91 35.74 3.46
5883 5968 0.178961 GTGAAACAAGGAAGGGGCCT 60.179 55.000 0.84 0.00 40.93 5.19
5890 5975 0.113190 AAGGAAGGGGCCTTCTGTTG 59.887 55.000 0.84 0.00 44.89 3.33
5916 6001 2.754946 TTACTGGTAACCTTCTGCGG 57.245 50.000 0.00 0.00 0.00 5.69
5959 6046 1.009675 CAAGTTCACGGTGTGCTGC 60.010 57.895 8.17 0.00 32.98 5.25
6076 6163 7.106439 TGATTGTTACAACTTCAATTGGTGT 57.894 32.000 5.42 7.73 32.90 4.16
6156 6244 5.490159 CCCTTGTTTACCGATGTACCTAAA 58.510 41.667 0.00 0.00 0.00 1.85
6159 6247 6.259387 CCTTGTTTACCGATGTACCTAAATCC 59.741 42.308 0.00 0.00 0.00 3.01
6168 6256 6.813649 CCGATGTACCTAAATCCTGTGATATG 59.186 42.308 0.00 0.00 0.00 1.78
6190 6278 7.943079 ATGATTGTTTGGACATCATACTTCA 57.057 32.000 0.00 0.00 34.85 3.02
6284 6373 7.655236 TTTTGCATGAACTGTTTATTCCATG 57.345 32.000 12.31 12.31 0.00 3.66
6447 6546 7.010552 CCTGTTTCTCATAGTGTATGCAAGTAC 59.989 40.741 0.00 0.00 36.14 2.73
6448 6547 7.382898 TGTTTCTCATAGTGTATGCAAGTACA 58.617 34.615 0.00 0.00 36.14 2.90
6449 6548 7.545615 TGTTTCTCATAGTGTATGCAAGTACAG 59.454 37.037 0.34 0.00 35.40 2.74
6450 6549 6.775594 TCTCATAGTGTATGCAAGTACAGT 57.224 37.500 11.53 11.53 40.40 3.55
6451 6550 7.875327 TCTCATAGTGTATGCAAGTACAGTA 57.125 36.000 14.44 14.44 41.92 2.74
6452 6551 8.288689 TCTCATAGTGTATGCAAGTACAGTAA 57.711 34.615 15.56 3.90 41.37 2.24
6453 6552 8.188799 TCTCATAGTGTATGCAAGTACAGTAAC 58.811 37.037 15.56 0.16 41.37 2.50
6454 6553 7.832769 TCATAGTGTATGCAAGTACAGTAACA 58.167 34.615 15.56 6.05 41.37 2.41
6476 6575 6.463360 ACACTTTCAATTGGTTCTTTTGTGT 58.537 32.000 5.42 7.18 0.00 3.72
6487 6586 9.705290 ATTGGTTCTTTTGTGTGGTATTTTATC 57.295 29.630 0.00 0.00 0.00 1.75
6495 6594 6.073447 TGTGTGGTATTTTATCATGGACCT 57.927 37.500 0.00 0.00 0.00 3.85
6496 6595 5.885352 TGTGTGGTATTTTATCATGGACCTG 59.115 40.000 0.00 0.00 0.00 4.00
6497 6596 5.885912 GTGTGGTATTTTATCATGGACCTGT 59.114 40.000 0.00 0.00 0.00 4.00
6498 6597 6.038271 GTGTGGTATTTTATCATGGACCTGTC 59.962 42.308 0.00 0.00 0.00 3.51
6499 6598 6.069673 TGTGGTATTTTATCATGGACCTGTCT 60.070 38.462 0.00 0.00 0.00 3.41
6500 6599 6.483640 GTGGTATTTTATCATGGACCTGTCTC 59.516 42.308 0.00 0.00 0.00 3.36
6501 6600 6.386927 TGGTATTTTATCATGGACCTGTCTCT 59.613 38.462 0.00 0.00 0.00 3.10
6502 6601 7.567250 TGGTATTTTATCATGGACCTGTCTCTA 59.433 37.037 0.00 0.00 0.00 2.43
6503 6602 8.091449 GGTATTTTATCATGGACCTGTCTCTAG 58.909 40.741 0.00 0.00 0.00 2.43
6504 6603 5.537300 TTTATCATGGACCTGTCTCTAGC 57.463 43.478 0.00 0.00 0.00 3.42
6505 6604 2.836636 TCATGGACCTGTCTCTAGCT 57.163 50.000 0.00 0.00 0.00 3.32
6509 6608 4.586421 TCATGGACCTGTCTCTAGCTTATG 59.414 45.833 0.00 0.00 0.00 1.90
6707 6893 7.752239 CAGCTAATTCATTTTTACAGTGGAGTG 59.248 37.037 0.00 0.00 0.00 3.51
6834 7024 1.227943 GCACAGTTCTGTGGCTCCA 60.228 57.895 26.98 0.00 39.97 3.86
6857 7062 1.153588 CCAAATCCCAATGCGCACC 60.154 57.895 14.90 0.00 0.00 5.01
6858 7063 1.516821 CAAATCCCAATGCGCACCG 60.517 57.895 14.90 6.57 0.00 4.94
6859 7064 1.677300 AAATCCCAATGCGCACCGA 60.677 52.632 14.90 6.07 0.00 4.69
6860 7065 1.037030 AAATCCCAATGCGCACCGAT 61.037 50.000 14.90 8.46 0.00 4.18
6889 7110 1.459348 CAGGCAAAACCCCAACCCT 60.459 57.895 0.00 0.00 40.58 4.34
6890 7111 1.459348 AGGCAAAACCCCAACCCTG 60.459 57.895 0.00 0.00 40.58 4.45
6984 7207 2.670148 ATTCTCGCCCCCTGACACC 61.670 63.158 0.00 0.00 0.00 4.16
6985 7208 4.631740 TCTCGCCCCCTGACACCA 62.632 66.667 0.00 0.00 0.00 4.17
7028 7251 1.409412 CTGATTCGATTCGCGTAGGG 58.591 55.000 5.77 0.00 41.80 3.53
7080 7303 4.189188 CCCGCGGTCCGTACTCAG 62.189 72.222 26.12 0.00 34.38 3.35
7082 7305 2.202440 CGCGGTCCGTACTCAGTG 60.202 66.667 13.94 0.00 0.00 3.66
7091 7314 1.898154 GTACTCAGTGCATCCGGGT 59.102 57.895 0.00 0.00 0.00 5.28
7092 7315 0.179108 GTACTCAGTGCATCCGGGTC 60.179 60.000 0.00 0.00 0.00 4.46
7093 7316 1.327690 TACTCAGTGCATCCGGGTCC 61.328 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.329889 ATGGAGGGCTTGCCGTCA 61.330 61.111 28.07 17.85 0.00 4.35
67 68 7.013750 TGAGGTATTTTGTGACAAACATAAGCA 59.986 33.333 10.72 3.33 38.99 3.91
70 71 8.684386 TCTGAGGTATTTTGTGACAAACATAA 57.316 30.769 10.72 0.00 38.99 1.90
114 116 4.186136 ACGGGTCGTCTCCTTTGA 57.814 55.556 0.00 0.00 33.69 2.69
173 178 3.737559 TTTGCATAACCATGAGGAGGT 57.262 42.857 0.00 0.00 42.34 3.85
211 216 1.295792 GTCGTTGGCTCTGTTGACAA 58.704 50.000 0.00 0.00 0.00 3.18
271 279 0.691078 AGCCGATGACCCCATGTACT 60.691 55.000 0.00 0.00 32.09 2.73
281 289 1.683917 ACACTCCTGATAGCCGATGAC 59.316 52.381 0.00 0.00 0.00 3.06
287 295 0.181350 CCCCAACACTCCTGATAGCC 59.819 60.000 0.00 0.00 0.00 3.93
359 367 4.041567 TGAGTTAATGAGAGGTCCAAAGCA 59.958 41.667 0.00 0.00 0.00 3.91
438 447 2.736719 CGATGCTCGTGTTCATTCCTCT 60.737 50.000 0.00 0.00 34.72 3.69
458 467 4.791411 GCAGTAGCTCTAATCTCCTTCACG 60.791 50.000 0.00 0.00 37.91 4.35
507 516 3.131396 TCGAAACTCTGCCTTCAAAGAC 58.869 45.455 0.00 0.00 0.00 3.01
604 615 6.672266 TCATAGGGATACAATTCAGGTCTC 57.328 41.667 0.00 0.00 39.74 3.36
671 683 9.003658 CATTTATAGGCTATTCTGTTAACTGGG 57.996 37.037 13.08 0.90 0.00 4.45
1168 1214 2.156917 TGCTTGCACAGAGGATTTGAG 58.843 47.619 0.00 0.00 0.00 3.02
1354 1400 0.332972 GGGGCAATCAAAGAGGGAGT 59.667 55.000 0.00 0.00 0.00 3.85
1356 1402 0.332632 CTGGGGCAATCAAAGAGGGA 59.667 55.000 0.00 0.00 0.00 4.20
1365 1411 1.079888 CGCAAAACCTGGGGCAATC 60.080 57.895 0.00 0.00 34.37 2.67
1385 1431 0.386113 GAGAGCAACTAGGCCGGTAG 59.614 60.000 1.90 0.00 0.00 3.18
1387 1433 1.609501 TGAGAGCAACTAGGCCGGT 60.610 57.895 1.90 0.00 0.00 5.28
1389 1435 0.247736 AAGTGAGAGCAACTAGGCCG 59.752 55.000 0.00 0.00 0.00 6.13
1483 1532 7.857569 TCGATTATCCGAAAACAACATAATCC 58.142 34.615 0.00 0.00 34.79 3.01
1511 1561 3.006110 CCTGTCACTGATGCCAAACAATT 59.994 43.478 0.00 0.00 0.00 2.32
1521 1571 4.000331 AGTTCTGAACCTGTCACTGATG 58.000 45.455 16.48 0.00 31.13 3.07
1788 1853 1.668628 GGGTGTTTTGTATTGCGCCAG 60.669 52.381 4.18 0.00 33.52 4.85
1845 1910 1.084018 ATGGAGAGGGAAAGGGCAAA 58.916 50.000 0.00 0.00 0.00 3.68
2001 2066 2.955660 ACAAATTTCTGTTCCTGCGGAA 59.044 40.909 6.01 6.01 39.66 4.30
2178 2243 1.717937 GCGCAAGATGCCACAGTAG 59.282 57.895 0.30 0.00 41.12 2.57
2244 2309 6.115448 AGACAGAACTTACCTAAACATGCT 57.885 37.500 0.00 0.00 0.00 3.79
2303 2369 1.527034 CAGAACCAAAGCTAGCTGCA 58.473 50.000 20.16 0.00 45.94 4.41
2380 2446 3.616956 AACAGCTTAGCATCAGCACTA 57.383 42.857 7.07 0.00 45.49 2.74
2438 2504 2.789491 TGCATTGTTCAAACGCATCA 57.211 40.000 8.29 0.00 0.00 3.07
2479 2545 3.456380 ACAAGGCACTGGTAAATCCAT 57.544 42.857 0.00 0.00 43.49 3.41
2593 2659 2.744202 CCTTTGACTCCATTTCACTCCG 59.256 50.000 0.00 0.00 0.00 4.63
2701 2767 5.111989 CGTCATGTTCAGTCATAACCATCT 58.888 41.667 0.00 0.00 0.00 2.90
2769 2835 3.223435 TCGCCAACTTTCCAAATTACCA 58.777 40.909 0.00 0.00 0.00 3.25
3133 3201 3.057033 AGGATCAAGTGAATTGCTGCAAC 60.057 43.478 18.51 5.59 38.89 4.17
3164 3232 0.324552 ATATGCACTGGGCTTGGCAA 60.325 50.000 2.50 0.00 45.15 4.52
3196 3264 6.128486 TGCACACACCCATCATTAATAAGAT 58.872 36.000 0.00 0.00 0.00 2.40
3312 3381 8.674263 AAAATTTATGCATGTGAAAACAAGGA 57.326 26.923 10.16 0.00 0.00 3.36
3392 3464 7.714813 TGACAGTGTTCTCAATATTCAAACTCA 59.285 33.333 0.00 0.00 0.00 3.41
3430 3502 1.012841 GCAGCTACTGGTCAGATTGC 58.987 55.000 4.84 5.89 31.21 3.56
3431 3503 1.065926 TGGCAGCTACTGGTCAGATTG 60.066 52.381 4.84 0.00 31.21 2.67
3432 3504 1.065854 GTGGCAGCTACTGGTCAGATT 60.066 52.381 0.70 0.00 31.21 2.40
3436 3508 0.250234 GATGTGGCAGCTACTGGTCA 59.750 55.000 10.64 0.00 31.21 4.02
3511 3583 8.062065 TGTTTATTACATCATTTCCAGGGAAC 57.938 34.615 0.00 0.00 33.41 3.62
3536 3608 9.909644 GGTGTAATCGATAAGACTACATTACAT 57.090 33.333 9.46 0.00 42.53 2.29
3537 3609 8.905850 TGGTGTAATCGATAAGACTACATTACA 58.094 33.333 9.46 4.08 42.53 2.41
3538 3610 9.909644 ATGGTGTAATCGATAAGACTACATTAC 57.090 33.333 9.46 1.78 42.53 1.89
3542 3614 8.027189 GCATATGGTGTAATCGATAAGACTACA 58.973 37.037 4.56 0.01 39.00 2.74
3543 3615 8.244802 AGCATATGGTGTAATCGATAAGACTAC 58.755 37.037 6.62 0.00 32.59 2.73
3544 3616 8.244113 CAGCATATGGTGTAATCGATAAGACTA 58.756 37.037 23.73 0.00 38.61 2.59
3545 3617 7.039714 TCAGCATATGGTGTAATCGATAAGACT 60.040 37.037 28.83 0.00 43.46 3.24
3546 3618 7.090808 TCAGCATATGGTGTAATCGATAAGAC 58.909 38.462 28.83 0.00 43.46 3.01
3547 3619 7.227049 TCAGCATATGGTGTAATCGATAAGA 57.773 36.000 28.83 7.46 43.46 2.10
3548 3620 7.600375 AGTTCAGCATATGGTGTAATCGATAAG 59.400 37.037 28.83 4.74 43.46 1.73
3549 3621 7.441836 AGTTCAGCATATGGTGTAATCGATAA 58.558 34.615 28.83 14.10 43.46 1.75
3570 3642 7.756722 TGTAAGGCATTAACTCGTAAGTAGTTC 59.243 37.037 0.00 0.00 38.23 3.01
3615 3687 9.574516 AAAGTTTCAAACTATGACTCCTATGTT 57.425 29.630 2.38 0.00 41.91 2.71
3661 3733 0.460635 TGCGTGCTCCCGGTATTTAC 60.461 55.000 0.00 0.00 0.00 2.01
3678 3750 7.307337 CCTGTTTGGATTGAGTGTAAATTTTGC 60.307 37.037 0.00 0.00 38.35 3.68
3727 3799 5.835113 ACAATAATGGTATGGCACTCAAC 57.165 39.130 0.00 0.00 0.00 3.18
3737 3809 9.369904 GCAAGTGAAATCAAACAATAATGGTAT 57.630 29.630 0.00 0.00 0.00 2.73
3807 3879 1.299316 CACAAGCTGCACCAAACGG 60.299 57.895 1.02 0.00 0.00 4.44
4020 4092 9.299963 CAAATTTGATAATCTGGTAAAATCGCA 57.700 29.630 13.08 0.00 0.00 5.10
4279 4351 4.481368 ACAACTCAAAGTGTGGACAGTA 57.519 40.909 0.00 0.00 0.00 2.74
4365 4437 9.162793 CATGTTCTAATCTGTTTAATTCATCGC 57.837 33.333 0.00 0.00 0.00 4.58
4518 4601 8.725148 GGGTATCTGCATCAAAAAGATATGTAG 58.275 37.037 0.00 0.00 35.83 2.74
4551 4634 2.793933 CTGAAATTCAGGATTGCAGCG 58.206 47.619 14.85 0.00 42.94 5.18
4866 4951 5.882000 CAGGTAATCACAGAAACATGATGGA 59.118 40.000 0.00 0.00 35.71 3.41
4867 4952 5.649395 ACAGGTAATCACAGAAACATGATGG 59.351 40.000 0.00 0.00 35.71 3.51
4977 5062 2.753452 TGACTGGTTACCTAAGAGCTCG 59.247 50.000 8.37 0.00 0.00 5.03
5038 5123 6.444704 TGACTTCTTCAGGATCTATAGGGTT 58.555 40.000 0.00 0.00 0.00 4.11
5187 5272 0.460722 GGAACGGAGGGAGTAGAAGC 59.539 60.000 0.00 0.00 0.00 3.86
5192 5277 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
5193 5278 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
5194 5279 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
5195 5280 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
5196 5281 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
5197 5282 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
5198 5283 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
5199 5284 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
5200 5285 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
5213 5298 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
5214 5299 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
5215 5300 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
5216 5301 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
5217 5302 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
5218 5303 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
5219 5304 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
5220 5305 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
5221 5306 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
5222 5307 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
5223 5308 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
5224 5309 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
5225 5310 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
5226 5311 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
5227 5312 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
5228 5313 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
5229 5314 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
5230 5315 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
5231 5316 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
5232 5317 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
5233 5318 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
5234 5319 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
5235 5320 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
5236 5321 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
5237 5322 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
5238 5323 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
5239 5324 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
5240 5325 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
5241 5326 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
5242 5327 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
5243 5328 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
5244 5329 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
5245 5330 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
5246 5331 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
5247 5332 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
5248 5333 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
5249 5334 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
5250 5335 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
5280 5365 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
5282 5367 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
5283 5368 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
5284 5369 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
5285 5370 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
5286 5371 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
5287 5372 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
5288 5373 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
5289 5374 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
5290 5375 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
5291 5376 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
5307 5392 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
5308 5393 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
5325 5410 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
5326 5411 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
5327 5412 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
5328 5413 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
5329 5414 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
5330 5415 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
5331 5416 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
5332 5417 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
5333 5418 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
5334 5419 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
5335 5420 8.591940 GTTAATACTCCCTCCGTTCCTAAATAT 58.408 37.037 0.00 0.00 0.00 1.28
5336 5421 7.564660 TGTTAATACTCCCTCCGTTCCTAAATA 59.435 37.037 0.00 0.00 0.00 1.40
5337 5422 6.384886 TGTTAATACTCCCTCCGTTCCTAAAT 59.615 38.462 0.00 0.00 0.00 1.40
5338 5423 5.721000 TGTTAATACTCCCTCCGTTCCTAAA 59.279 40.000 0.00 0.00 0.00 1.85
5339 5424 5.271598 TGTTAATACTCCCTCCGTTCCTAA 58.728 41.667 0.00 0.00 0.00 2.69
5340 5425 4.870636 TGTTAATACTCCCTCCGTTCCTA 58.129 43.478 0.00 0.00 0.00 2.94
5341 5426 3.716431 TGTTAATACTCCCTCCGTTCCT 58.284 45.455 0.00 0.00 0.00 3.36
5342 5427 4.476628 TTGTTAATACTCCCTCCGTTCC 57.523 45.455 0.00 0.00 0.00 3.62
5343 5428 6.346896 AGATTTGTTAATACTCCCTCCGTTC 58.653 40.000 0.00 0.00 0.00 3.95
5344 5429 6.309389 AGATTTGTTAATACTCCCTCCGTT 57.691 37.500 0.00 0.00 0.00 4.44
5345 5430 5.952347 AGATTTGTTAATACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
5346 5431 7.985752 AGTAAAGATTTGTTAATACTCCCTCCG 59.014 37.037 0.00 0.00 0.00 4.63
5347 5432 9.110502 CAGTAAAGATTTGTTAATACTCCCTCC 57.889 37.037 0.00 0.00 0.00 4.30
5348 5433 9.110502 CCAGTAAAGATTTGTTAATACTCCCTC 57.889 37.037 0.00 0.00 0.00 4.30
5349 5434 7.556635 GCCAGTAAAGATTTGTTAATACTCCCT 59.443 37.037 0.00 0.00 0.00 4.20
5350 5435 7.338449 TGCCAGTAAAGATTTGTTAATACTCCC 59.662 37.037 0.00 0.00 0.00 4.30
5351 5436 8.276252 TGCCAGTAAAGATTTGTTAATACTCC 57.724 34.615 0.00 0.00 0.00 3.85
5374 5459 9.443283 GAGACATGATAAAATGAAGTGTATTGC 57.557 33.333 0.00 0.00 0.00 3.56
5451 5536 4.191033 ACAGAAGCATGAGAACAGAGAG 57.809 45.455 0.00 0.00 0.00 3.20
5687 5772 0.263172 TTTTGCCCTTCAAGACCCCA 59.737 50.000 0.00 0.00 35.84 4.96
5761 5846 3.550437 AGCCATCAGGTGTCTTATCAC 57.450 47.619 0.00 0.00 37.19 3.06
5841 5926 6.745450 CACGTGTTATGGTTTGAAACATATCC 59.255 38.462 7.58 0.00 35.72 2.59
5847 5932 5.800941 TGTTTCACGTGTTATGGTTTGAAAC 59.199 36.000 16.51 14.05 46.75 2.78
5878 5963 4.500265 TTCTGCAACAGAAGGCCC 57.500 55.556 0.00 0.00 44.27 5.80
5883 5968 6.016610 GGTTACCAGTAATTTCTGCAACAGAA 60.017 38.462 19.72 5.94 46.93 3.02
5884 5969 5.472137 GGTTACCAGTAATTTCTGCAACAGA 59.528 40.000 19.72 0.00 38.87 3.41
5890 5975 6.183309 CAGAAGGTTACCAGTAATTTCTGC 57.817 41.667 21.62 9.65 39.61 4.26
5916 6001 1.861440 CAACAAAATTGGCCAGCGC 59.139 52.632 5.11 0.00 0.00 5.92
5937 6022 1.714899 GCACACCGTGAACTTGCACT 61.715 55.000 5.28 0.00 35.23 4.40
5938 6023 1.298339 GCACACCGTGAACTTGCAC 60.298 57.895 5.28 0.00 35.23 4.57
5959 6046 2.373938 GCTGCAGCTACCTACAACG 58.626 57.895 31.33 0.00 38.21 4.10
5984 6071 4.138290 CACAGAGACTACCGTATCAGGAT 58.862 47.826 0.00 0.00 33.87 3.24
6040 6127 6.148811 AGTTGTAACAATCAATTCCCTGTACG 59.851 38.462 0.00 0.00 0.00 3.67
6156 6244 6.425735 TGTCCAAACAATCATATCACAGGAT 58.574 36.000 0.00 0.00 33.09 3.24
6159 6247 7.324354 TGATGTCCAAACAATCATATCACAG 57.676 36.000 0.00 0.00 39.30 3.66
6168 6256 9.722056 GTAATGAAGTATGATGTCCAAACAATC 57.278 33.333 0.00 0.00 39.30 2.67
6175 6263 9.599866 CTTTACAGTAATGAAGTATGATGTCCA 57.400 33.333 0.00 0.00 0.00 4.02
6190 6278 5.499004 TTCCACCAGCTCTTTACAGTAAT 57.501 39.130 0.00 0.00 0.00 1.89
6284 6373 6.747280 ACTAATTTATTTCACACGCAAGATGC 59.253 34.615 0.00 0.00 40.69 3.91
6447 6546 8.594687 CAAAAGAACCAATTGAAAGTGTTACTG 58.405 33.333 7.12 0.00 0.00 2.74
6448 6547 8.311109 ACAAAAGAACCAATTGAAAGTGTTACT 58.689 29.630 7.12 0.05 0.00 2.24
6449 6548 8.379902 CACAAAAGAACCAATTGAAAGTGTTAC 58.620 33.333 7.12 0.00 0.00 2.50
6450 6549 8.091449 ACACAAAAGAACCAATTGAAAGTGTTA 58.909 29.630 7.12 0.00 32.04 2.41
6451 6550 6.934083 ACACAAAAGAACCAATTGAAAGTGTT 59.066 30.769 7.12 1.62 32.04 3.32
6452 6551 6.368516 CACACAAAAGAACCAATTGAAAGTGT 59.631 34.615 7.12 7.17 35.92 3.55
6453 6552 6.183360 CCACACAAAAGAACCAATTGAAAGTG 60.183 38.462 7.12 6.60 0.00 3.16
6454 6553 5.874261 CCACACAAAAGAACCAATTGAAAGT 59.126 36.000 7.12 0.00 0.00 2.66
6476 6575 6.386927 AGAGACAGGTCCATGATAAAATACCA 59.613 38.462 0.00 0.00 0.00 3.25
6487 6586 4.343526 ACATAAGCTAGAGACAGGTCCATG 59.656 45.833 0.00 0.00 0.00 3.66
6495 6594 3.628032 CGTCCTGACATAAGCTAGAGACA 59.372 47.826 0.00 0.00 0.00 3.41
6496 6595 3.003897 CCGTCCTGACATAAGCTAGAGAC 59.996 52.174 0.00 0.00 0.00 3.36
6497 6596 3.118000 TCCGTCCTGACATAAGCTAGAGA 60.118 47.826 0.00 0.00 0.00 3.10
6498 6597 3.215151 TCCGTCCTGACATAAGCTAGAG 58.785 50.000 0.00 0.00 0.00 2.43
6499 6598 3.292492 TCCGTCCTGACATAAGCTAGA 57.708 47.619 0.00 0.00 0.00 2.43
6500 6599 4.386867 TTTCCGTCCTGACATAAGCTAG 57.613 45.455 0.00 0.00 0.00 3.42
6501 6600 4.755411 CTTTTCCGTCCTGACATAAGCTA 58.245 43.478 0.00 0.00 0.00 3.32
6502 6601 3.600388 CTTTTCCGTCCTGACATAAGCT 58.400 45.455 0.00 0.00 0.00 3.74
6503 6602 2.096013 GCTTTTCCGTCCTGACATAAGC 59.904 50.000 0.00 0.00 0.00 3.09
6504 6603 3.334691 TGCTTTTCCGTCCTGACATAAG 58.665 45.455 0.00 0.00 0.00 1.73
6505 6604 3.410631 TGCTTTTCCGTCCTGACATAA 57.589 42.857 0.00 0.00 0.00 1.90
6509 6608 1.666189 GCTATGCTTTTCCGTCCTGAC 59.334 52.381 0.00 0.00 0.00 3.51
6541 6651 0.036765 TTTATGCGGCAAGACGAGGT 60.037 50.000 6.82 0.00 35.47 3.85
6585 6698 6.350110 GCCAGCTTCAACCATTTTACATCTAA 60.350 38.462 0.00 0.00 0.00 2.10
6586 6699 5.125417 GCCAGCTTCAACCATTTTACATCTA 59.875 40.000 0.00 0.00 0.00 1.98
6685 6871 7.721842 TGTCCACTCCACTGTAAAAATGAATTA 59.278 33.333 0.00 0.00 0.00 1.40
6689 6875 5.042463 TGTCCACTCCACTGTAAAAATGA 57.958 39.130 0.00 0.00 0.00 2.57
6707 6893 4.900635 ATTTTCTTGTCGGCATATGTCC 57.099 40.909 0.75 4.02 0.00 4.02
6834 7024 1.039233 CGCATTGGGATTTGGGAGCT 61.039 55.000 0.00 0.00 0.00 4.09
6857 7062 0.683412 TGCCTGGATCTGGATCATCG 59.317 55.000 11.93 0.77 39.54 3.84
6858 7063 2.945080 TTGCCTGGATCTGGATCATC 57.055 50.000 11.93 0.00 39.54 2.92
6859 7064 3.294214 GTTTTGCCTGGATCTGGATCAT 58.706 45.455 11.93 0.00 39.54 2.45
6860 7065 2.621407 GGTTTTGCCTGGATCTGGATCA 60.621 50.000 11.93 0.00 39.54 2.92
6889 7110 3.625897 CTGTCTGGGGACGGCACA 61.626 66.667 0.00 0.00 44.83 4.57
6890 7111 3.311110 TCTGTCTGGGGACGGCAC 61.311 66.667 0.00 0.00 45.68 5.01
6949 7172 0.392998 AATGTGCCGACCACCTGATC 60.393 55.000 4.15 0.00 44.01 2.92
7007 7230 1.001706 CCTACGCGAATCGAATCAGGA 60.002 52.381 15.93 0.00 41.67 3.86
7072 7295 1.226974 CCCGGATGCACTGAGTACG 60.227 63.158 0.73 0.00 0.00 3.67
7074 7297 1.327690 GGACCCGGATGCACTGAGTA 61.328 60.000 0.73 0.00 0.00 2.59
7075 7298 2.660064 GGACCCGGATGCACTGAGT 61.660 63.158 0.73 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.