Multiple sequence alignment - TraesCS4B01G267200

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 TraesCS4B01G267200 chr4B 100.000 5661 0 0 1 5661 539970750 539965090 0.000000e+00 10455.0
1 TraesCS4B01G267200 chr4A 92.359 3298 130 49 545 3767 30560956 30557706 0.000000e+00 4582.0
2 TraesCS4B01G267200 chr4A 89.444 1923 120 36 3770 5661 30557669 30555799 0.000000e+00 2350.0
3 TraesCS4B01G267200 chr4A 89.686 223 10 2 1 210 30561417 30561195 7.230000e-69 272.0
4 TraesCS4B01G267200 chr4A 80.068 296 19 19 227 517 30561211 30560951 3.480000e-42 183.0
5 TraesCS4B01G267200 chr4D 94.771 2639 105 14 2488 5094 437517428 437514791 0.000000e+00 4078.0
6 TraesCS4B01G267200 chr4D 91.566 2158 108 39 269 2414 437519612 437517517 0.000000e+00 2909.0
7 TraesCS4B01G267200 chr4D 92.958 213 12 2 1 210 437519838 437519626 1.980000e-79 307.0
8 TraesCS4B01G267200 chr5A 96.970 33 1 0 5116 5148 144390350 144390382 7.920000e-04 56.5


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 TraesCS4B01G267200 chr4B 539965090 539970750 5660 True 10455.000000 10455 100.000000 1 5661 1 chr4B.!!$R1 5660
1 TraesCS4B01G267200 chr4A 30555799 30561417 5618 True 1846.750000 4582 87.889250 1 5661 4 chr4A.!!$R1 5660
2 TraesCS4B01G267200 chr4D 437514791 437519838 5047 True 2431.333333 4078 93.098333 1 5094 3 chr4D.!!$R1 5093

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
706 736 0.106719 CTCCTCTTCGAGCCTCTCCT 60.107 60.0 0.0 0.0 0.00 3.69 F
2191 2275 0.036388 ATCCACGTTGCTTCCATCGT 60.036 50.0 0.0 0.0 45.36 3.73 F
4040 4225 0.244994 CTCTCACCTTCCACGGACAG 59.755 60.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 2755 0.543277 TAGGATCTGCAGCCAACTGG 59.457 55.0 9.47 0.0 44.63 4.00 R
4078 4264 0.383949 TGCAAAAGAACGGTGAAGCC 59.616 50.0 0.00 0.0 0.00 4.35 R
5442 5645 0.322456 GCATGGGCACTGGTGACTAA 60.322 55.0 6.53 0.0 39.02 2.24 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
19 20 1.227263 ACTGACAACGCACGAGCTT 60.227 52.632 2.73 0.00 39.10 3.74
138 152 2.347490 GAGGCGTTTCCAGGAGCA 59.653 61.111 1.79 0.00 37.29 4.26
196 210 4.662961 CACGAGCACCACGGAGCA 62.663 66.667 8.24 0.00 34.21 4.26
197 211 4.363990 ACGAGCACCACGGAGCAG 62.364 66.667 8.24 4.19 34.21 4.24
198 212 4.056125 CGAGCACCACGGAGCAGA 62.056 66.667 8.24 0.00 34.21 4.26
199 213 2.125753 GAGCACCACGGAGCAGAG 60.126 66.667 8.24 0.00 34.21 3.35
200 214 2.601666 AGCACCACGGAGCAGAGA 60.602 61.111 8.24 0.00 34.21 3.10
201 215 2.125753 GCACCACGGAGCAGAGAG 60.126 66.667 0.17 0.00 0.00 3.20
202 216 2.125753 CACCACGGAGCAGAGAGC 60.126 66.667 0.00 0.00 46.19 4.09
211 225 3.660621 GCAGAGAGCGCCACTTTT 58.339 55.556 2.29 0.00 0.00 2.27
212 226 1.952263 GCAGAGAGCGCCACTTTTT 59.048 52.632 2.29 0.00 0.00 1.94
252 266 2.750350 CGCCACTTGGGAAGGAGT 59.250 61.111 0.00 0.00 40.01 3.85
260 281 4.062032 GGGAAGGAGTTGGGGCCC 62.062 72.222 18.17 18.17 0.00 5.80
261 282 4.062032 GGAAGGAGTTGGGGCCCC 62.062 72.222 36.14 36.14 0.00 5.80
262 283 4.426313 GAAGGAGTTGGGGCCCCG 62.426 72.222 36.00 0.00 39.42 5.73
358 379 2.585869 CGGACCGCGGAATCATTCG 61.586 63.158 35.90 16.56 0.00 3.34
363 384 2.931386 GCGGAATCATTCGCGGAG 59.069 61.111 6.13 0.00 42.48 4.63
364 385 1.883084 GCGGAATCATTCGCGGAGT 60.883 57.895 6.13 0.00 42.48 3.85
365 386 1.822250 GCGGAATCATTCGCGGAGTC 61.822 60.000 6.13 4.33 42.48 3.36
366 387 0.249073 CGGAATCATTCGCGGAGTCT 60.249 55.000 6.13 0.00 30.61 3.24
367 388 1.492720 GGAATCATTCGCGGAGTCTC 58.507 55.000 6.13 0.00 30.61 3.36
389 410 4.735132 TTCGCCCCTCGCAGTTCG 62.735 66.667 0.00 0.00 37.30 3.95
398 419 0.366871 CTCGCAGTTCGTCGGAATTG 59.633 55.000 0.00 0.00 41.38 2.32
409 430 2.159707 CGTCGGAATTGCAGAATCGTTT 60.160 45.455 0.00 0.00 0.00 3.60
560 588 1.642037 CCTCGCAGCACACCAATCTG 61.642 60.000 0.00 0.00 0.00 2.90
569 597 2.965805 CACCAATCTGTGTGGGCAT 58.034 52.632 0.00 0.00 40.75 4.40
662 691 0.248949 GAAGTGCGGTCGATACCTCC 60.249 60.000 0.00 0.00 44.35 4.30
663 692 1.673808 AAGTGCGGTCGATACCTCCC 61.674 60.000 0.00 0.00 44.35 4.30
664 693 2.125961 GTGCGGTCGATACCTCCCT 61.126 63.158 0.00 0.00 44.35 4.20
665 694 1.826921 TGCGGTCGATACCTCCCTC 60.827 63.158 0.00 0.00 44.35 4.30
666 695 1.826921 GCGGTCGATACCTCCCTCA 60.827 63.158 0.00 0.00 44.35 3.86
667 696 1.179814 GCGGTCGATACCTCCCTCAT 61.180 60.000 0.00 0.00 44.35 2.90
669 698 0.882474 GGTCGATACCTCCCTCATCG 59.118 60.000 0.00 0.00 43.08 3.84
670 699 0.882474 GTCGATACCTCCCTCATCGG 59.118 60.000 3.67 0.00 41.38 4.18
671 700 0.894184 TCGATACCTCCCTCATCGGC 60.894 60.000 3.67 0.00 41.38 5.54
673 702 1.536662 ATACCTCCCTCATCGGCCC 60.537 63.158 0.00 0.00 0.00 5.80
674 703 2.326529 ATACCTCCCTCATCGGCCCA 62.327 60.000 0.00 0.00 0.00 5.36
706 736 0.106719 CTCCTCTTCGAGCCTCTCCT 60.107 60.000 0.00 0.00 0.00 3.69
729 759 4.129148 GCCATTCCCTTCCGCCCT 62.129 66.667 0.00 0.00 0.00 5.19
855 909 2.774687 CCGCCTAACCCGCTATAAATT 58.225 47.619 0.00 0.00 0.00 1.82
939 993 2.601804 GCACTCGAAAACCTCTCTCTC 58.398 52.381 0.00 0.00 0.00 3.20
940 994 2.230266 GCACTCGAAAACCTCTCTCTCT 59.770 50.000 0.00 0.00 0.00 3.10
944 998 4.261801 CTCGAAAACCTCTCTCTCTCTCT 58.738 47.826 0.00 0.00 0.00 3.10
948 1002 4.927267 AAACCTCTCTCTCTCTCTCTCA 57.073 45.455 0.00 0.00 0.00 3.27
949 1003 3.914426 ACCTCTCTCTCTCTCTCTCAC 57.086 52.381 0.00 0.00 0.00 3.51
950 1004 3.454858 ACCTCTCTCTCTCTCTCTCACT 58.545 50.000 0.00 0.00 0.00 3.41
951 1005 3.452627 ACCTCTCTCTCTCTCTCTCACTC 59.547 52.174 0.00 0.00 0.00 3.51
952 1006 3.181461 CCTCTCTCTCTCTCTCTCACTCC 60.181 56.522 0.00 0.00 0.00 3.85
953 1007 3.449918 TCTCTCTCTCTCTCTCACTCCA 58.550 50.000 0.00 0.00 0.00 3.86
954 1008 3.843619 TCTCTCTCTCTCTCTCACTCCAA 59.156 47.826 0.00 0.00 0.00 3.53
956 1010 3.329225 TCTCTCTCTCTCTCACTCCAACA 59.671 47.826 0.00 0.00 0.00 3.33
957 1011 3.684908 TCTCTCTCTCTCACTCCAACAG 58.315 50.000 0.00 0.00 0.00 3.16
958 1012 3.073798 TCTCTCTCTCTCACTCCAACAGT 59.926 47.826 0.00 0.00 34.67 3.55
959 1013 3.826157 CTCTCTCTCTCACTCCAACAGTT 59.174 47.826 0.00 0.00 30.26 3.16
960 1014 4.219115 TCTCTCTCTCACTCCAACAGTTT 58.781 43.478 0.00 0.00 30.26 2.66
962 1016 2.805099 CTCTCTCACTCCAACAGTTTGC 59.195 50.000 0.00 0.00 30.26 3.68
964 1018 2.547211 CTCTCACTCCAACAGTTTGCAG 59.453 50.000 0.00 0.00 30.26 4.41
1221 1280 1.550374 TCCTCTCCTCCCCTCCCTT 60.550 63.158 0.00 0.00 0.00 3.95
1247 1306 4.169102 CGCGCAGTGCTTCTCTTA 57.831 55.556 14.33 0.00 43.27 2.10
1332 1393 1.798813 CGGTGTTTCAGTAACTCAGCC 59.201 52.381 0.00 0.00 37.64 4.85
1470 1538 0.456142 CGTTCTCGGATCGCTGTCAA 60.456 55.000 0.00 0.00 0.00 3.18
1588 1656 4.573201 ACGGTCTCATTTTCGACTTTTTGA 59.427 37.500 0.00 0.00 0.00 2.69
1602 1670 3.755378 ACTTTTTGAGAGAATGCGATGCT 59.245 39.130 0.00 0.00 0.00 3.79
1943 2012 4.719273 TGTTTCCCCAGGTTTTCTGATTTT 59.281 37.500 0.00 0.00 46.18 1.82
1950 2019 6.493458 CCCCAGGTTTTCTGATTTTCTCTTTA 59.507 38.462 0.00 0.00 46.18 1.85
2022 2106 2.098607 GGCTACGTGCAGTGTAGTATGA 59.901 50.000 21.09 0.00 45.15 2.15
2086 2170 6.890814 TCCTTTTAACTCTGTTTTTGGTGGTA 59.109 34.615 0.00 0.00 0.00 3.25
2178 2262 0.719465 GTAAGTTGTCGCCATCCACG 59.281 55.000 0.00 0.00 0.00 4.94
2180 2264 0.534203 AAGTTGTCGCCATCCACGTT 60.534 50.000 0.00 0.00 0.00 3.99
2182 2266 2.612567 TTGTCGCCATCCACGTTGC 61.613 57.895 0.00 0.00 0.00 4.17
2191 2275 0.036388 ATCCACGTTGCTTCCATCGT 60.036 50.000 0.00 0.00 45.36 3.73
2192 2276 0.250124 TCCACGTTGCTTCCATCGTT 60.250 50.000 0.00 0.00 42.82 3.85
2193 2277 1.001068 TCCACGTTGCTTCCATCGTTA 59.999 47.619 0.00 0.00 42.82 3.18
2194 2278 2.006888 CCACGTTGCTTCCATCGTTAT 58.993 47.619 0.00 0.00 42.82 1.89
2196 2280 3.000925 CCACGTTGCTTCCATCGTTATAC 59.999 47.826 0.00 0.00 42.82 1.47
2259 2343 5.240891 TCATTTGAGACTGATGGTGAGTTC 58.759 41.667 0.00 0.00 0.00 3.01
2263 2347 5.233083 TGAGACTGATGGTGAGTTCAATT 57.767 39.130 0.00 0.00 0.00 2.32
2478 2592 3.239587 TCCAATTTGATGCTGCATGTG 57.760 42.857 21.53 9.42 0.00 3.21
2600 2723 4.393680 TCATTGTACCGGTCAAAATGCTAC 59.606 41.667 22.68 10.57 0.00 3.58
2632 2755 7.097192 TGTTGACTGTATATGTTCCAGACTTC 58.903 38.462 0.00 0.00 0.00 3.01
2694 2817 6.953520 TGATTTTTCAGGTAAACCCAGATGAT 59.046 34.615 0.00 0.00 36.42 2.45
2706 2829 3.181429 ACCCAGATGATCTTGTGTTTGGT 60.181 43.478 0.00 3.07 0.00 3.67
2974 3102 9.859427 ACAACTTGACATATATTCCAACATTTG 57.141 29.630 0.00 0.00 0.00 2.32
3075 3210 9.236691 CTGCGAATATGCTTAAAACAATAACAT 57.763 29.630 0.00 0.00 35.36 2.71
3349 3487 4.709250 AGTTCAAGGAGAAGAACAAGGTC 58.291 43.478 7.88 0.00 44.94 3.85
3469 3607 3.068873 ACAAGAACGAGGCAGAGATATCC 59.931 47.826 0.00 0.00 0.00 2.59
3496 3634 1.272092 ACACTGTATGCCATTGCCTGT 60.272 47.619 0.00 0.00 36.33 4.00
3508 3646 2.439156 GCCTGTGTCATGGAGGGC 60.439 66.667 0.00 0.00 0.00 5.19
3511 3649 1.448540 CTGTGTCATGGAGGGCGTC 60.449 63.158 0.00 0.00 0.00 5.19
3598 3736 7.068348 ACTGTACCTGTATATAGTGTCTGGTTG 59.932 40.741 5.37 1.72 34.78 3.77
3634 3772 1.999648 TCTTTTGTGCAGGGCTGATT 58.000 45.000 0.00 0.00 0.00 2.57
3706 3844 2.027385 GGCCAGACCAAGATGAAATCC 58.973 52.381 0.00 0.00 41.11 3.01
3718 3856 2.074547 TGAAATCCGTCTTGGTCGAC 57.925 50.000 7.13 7.13 39.52 4.20
3801 3974 4.686091 CAGACATTTCTCTGTTACGAAGCA 59.314 41.667 0.00 0.00 34.10 3.91
3865 4048 3.266772 TCAGCTACAACCATCTTGGGAAT 59.733 43.478 0.00 0.00 43.37 3.01
4032 4217 2.098443 GTCGATCTGTCTCTCACCTTCC 59.902 54.545 0.00 0.00 0.00 3.46
4040 4225 0.244994 CTCTCACCTTCCACGGACAG 59.755 60.000 0.00 0.00 0.00 3.51
4090 4276 2.674796 ATACTGAGGCTTCACCGTTC 57.325 50.000 0.00 0.00 46.52 3.95
4101 4287 3.848554 GCTTCACCGTTCTTTTGCAGTAC 60.849 47.826 0.00 0.00 0.00 2.73
4248 4434 2.202987 GATCTGGTGCTCCTGGCG 60.203 66.667 11.25 0.00 45.43 5.69
4325 4511 6.203915 CGAGATATGTTGCTAGTCTACTCTGT 59.796 42.308 0.00 0.00 0.00 3.41
4358 4544 2.091885 ACTTTGGGAGCCAAACTGAAGA 60.092 45.455 0.00 0.00 46.92 2.87
4364 4550 2.414691 GGAGCCAAACTGAAGATTTCGC 60.415 50.000 0.00 0.00 0.00 4.70
4367 4553 2.589014 CCAAACTGAAGATTTCGCTGC 58.411 47.619 0.00 0.00 0.00 5.25
4379 4565 0.890542 TTCGCTGCTCCACTTGCATT 60.891 50.000 0.00 0.00 39.86 3.56
4489 4675 7.553334 TCGACTGTTTGCTCTAAATAACCTAT 58.447 34.615 0.00 0.00 0.00 2.57
4519 4705 1.992170 AGACGATTAACTGACGTGCC 58.008 50.000 0.00 0.00 40.29 5.01
4615 4801 0.615331 AGAACATCATGAGGGCGTGT 59.385 50.000 12.66 2.52 32.75 4.49
4666 4852 0.888619 TGGAGTACAAGTGAGGAGCG 59.111 55.000 0.00 0.00 0.00 5.03
4802 4988 5.732247 GCTTGTCTTTAGTTTCCTTTGCGAA 60.732 40.000 0.00 0.00 0.00 4.70
4812 5001 2.436417 TCCTTTGCGAATCTTTCCCTG 58.564 47.619 0.00 0.00 0.00 4.45
4816 5005 3.426787 TTGCGAATCTTTCCCTGGTTA 57.573 42.857 0.00 0.00 0.00 2.85
4818 5007 3.343617 TGCGAATCTTTCCCTGGTTAAG 58.656 45.455 0.00 0.00 0.00 1.85
4819 5008 3.244770 TGCGAATCTTTCCCTGGTTAAGT 60.245 43.478 0.00 0.00 0.00 2.24
4822 5011 5.413523 GCGAATCTTTCCCTGGTTAAGTTTA 59.586 40.000 0.00 0.00 0.00 2.01
4823 5012 6.622245 GCGAATCTTTCCCTGGTTAAGTTTAC 60.622 42.308 0.00 0.00 0.00 2.01
4831 5027 3.073356 CCTGGTTAAGTTTACCCCAGTGA 59.927 47.826 8.53 0.00 40.88 3.41
4865 5061 2.603652 GCGAGACTATTTCGGCTCTCTC 60.604 54.545 0.00 0.00 38.45 3.20
4866 5062 2.031508 CGAGACTATTTCGGCTCTCTCC 60.032 54.545 0.00 0.00 34.56 3.71
4868 5064 2.032620 GACTATTTCGGCTCTCTCCCA 58.967 52.381 0.00 0.00 0.00 4.37
4869 5065 2.431057 GACTATTTCGGCTCTCTCCCAA 59.569 50.000 0.00 0.00 0.00 4.12
4879 5075 0.251386 TCTCTCCCAAGTCTCTGCGT 60.251 55.000 0.00 0.00 0.00 5.24
5061 5264 4.455533 GTGTGCTTTTATCATGTCACCTCA 59.544 41.667 0.00 0.00 0.00 3.86
5062 5265 5.048782 GTGTGCTTTTATCATGTCACCTCAA 60.049 40.000 0.00 0.00 0.00 3.02
5121 5324 4.576216 TGCAAGCGGAAAATCAAGTAAA 57.424 36.364 0.00 0.00 0.00 2.01
5148 5351 5.523552 GCATAAAATTACCACAATTCAGGCC 59.476 40.000 0.00 0.00 0.00 5.19
5152 5355 1.367346 TACCACAATTCAGGCCTGGA 58.633 50.000 32.23 26.17 0.00 3.86
5176 5379 2.038033 CCGGAAAACTACCACTTCTCCA 59.962 50.000 0.00 0.00 0.00 3.86
5214 5417 8.836268 AACTATCACAAAATTAGTCCGTTGTA 57.164 30.769 0.00 0.00 33.04 2.41
5250 5453 3.694566 GTGGTGGAATGGCTAGGTTTTAG 59.305 47.826 0.00 0.00 0.00 1.85
5269 5472 6.757897 TTTAGTGCCATTTATGACAAGGAG 57.242 37.500 0.00 0.00 0.00 3.69
5278 5481 0.625683 ATGACAAGGAGGGCCCATCT 60.626 55.000 27.56 18.14 37.41 2.90
5283 5486 1.277580 AAGGAGGGCCCATCTGTCAG 61.278 60.000 27.56 0.00 37.41 3.51
5284 5487 2.191641 GAGGGCCCATCTGTCAGC 59.808 66.667 27.56 0.00 0.00 4.26
5329 5532 1.807981 CGCCCGCTGACGAACATTA 60.808 57.895 0.00 0.00 43.93 1.90
5330 5533 1.752501 CGCCCGCTGACGAACATTAG 61.753 60.000 0.00 0.00 43.93 1.73
5331 5534 2.006772 CCCGCTGACGAACATTAGC 58.993 57.895 0.00 0.00 43.93 3.09
5332 5535 0.460284 CCCGCTGACGAACATTAGCT 60.460 55.000 0.00 0.00 43.93 3.32
5334 5537 2.120232 CCGCTGACGAACATTAGCTAG 58.880 52.381 0.00 0.00 43.93 3.42
5335 5538 1.518929 CGCTGACGAACATTAGCTAGC 59.481 52.381 6.62 6.62 43.93 3.42
5336 5539 1.861575 GCTGACGAACATTAGCTAGCC 59.138 52.381 12.13 0.00 33.53 3.93
5337 5540 2.474816 CTGACGAACATTAGCTAGCCC 58.525 52.381 12.13 0.00 0.00 5.19
5338 5541 1.202371 TGACGAACATTAGCTAGCCCG 60.202 52.381 12.13 6.50 0.00 6.13
5339 5542 0.822164 ACGAACATTAGCTAGCCCGT 59.178 50.000 12.13 7.12 0.00 5.28
5340 5543 1.206371 ACGAACATTAGCTAGCCCGTT 59.794 47.619 12.13 9.63 0.00 4.44
5341 5544 1.859080 CGAACATTAGCTAGCCCGTTC 59.141 52.381 12.13 16.57 0.00 3.95
5342 5545 2.481449 CGAACATTAGCTAGCCCGTTCT 60.481 50.000 22.88 6.02 32.52 3.01
5343 5546 3.243301 CGAACATTAGCTAGCCCGTTCTA 60.243 47.826 22.88 5.20 32.52 2.10
5344 5547 4.690122 GAACATTAGCTAGCCCGTTCTAA 58.310 43.478 20.38 10.29 32.09 2.10
5345 5548 4.056092 ACATTAGCTAGCCCGTTCTAAC 57.944 45.455 12.13 0.00 0.00 2.34
5346 5549 3.181468 ACATTAGCTAGCCCGTTCTAACC 60.181 47.826 12.13 0.00 0.00 2.85
5347 5550 1.027357 TAGCTAGCCCGTTCTAACCG 58.973 55.000 12.13 0.00 0.00 4.44
5348 5551 0.969409 AGCTAGCCCGTTCTAACCGT 60.969 55.000 12.13 0.00 0.00 4.83
5349 5552 0.804933 GCTAGCCCGTTCTAACCGTG 60.805 60.000 2.29 0.00 0.00 4.94
5350 5553 0.529378 CTAGCCCGTTCTAACCGTGT 59.471 55.000 0.00 0.00 0.00 4.49
5351 5554 0.527565 TAGCCCGTTCTAACCGTGTC 59.472 55.000 0.00 0.00 0.00 3.67
5352 5555 1.005867 GCCCGTTCTAACCGTGTCA 60.006 57.895 0.00 0.00 0.00 3.58
5353 5556 0.600782 GCCCGTTCTAACCGTGTCAA 60.601 55.000 0.00 0.00 0.00 3.18
5354 5557 1.868469 CCCGTTCTAACCGTGTCAAA 58.132 50.000 0.00 0.00 0.00 2.69
5355 5558 2.211806 CCCGTTCTAACCGTGTCAAAA 58.788 47.619 0.00 0.00 0.00 2.44
5356 5559 2.032636 CCCGTTCTAACCGTGTCAAAAC 60.033 50.000 0.00 0.00 0.00 2.43
5357 5560 2.347846 CCGTTCTAACCGTGTCAAAACG 60.348 50.000 0.00 0.00 43.20 3.60
5396 5599 6.206634 CACTCTCACTAAGTTCTTCTCACTCT 59.793 42.308 0.00 0.00 0.00 3.24
5397 5600 7.389330 CACTCTCACTAAGTTCTTCTCACTCTA 59.611 40.741 0.00 0.00 0.00 2.43
5410 5613 3.788708 TCTCACTCTATTCTCCTCTCCCA 59.211 47.826 0.00 0.00 0.00 4.37
5428 5631 2.093075 CCCATGCTCTCTCAATGACACT 60.093 50.000 0.00 0.00 0.00 3.55
5442 5645 1.692749 ACACTGACCACCCCACTGT 60.693 57.895 0.00 0.00 0.00 3.55
5450 5653 0.036306 CCACCCCACTGTTAGTCACC 59.964 60.000 0.00 0.00 0.00 4.02
5451 5654 0.762418 CACCCCACTGTTAGTCACCA 59.238 55.000 0.00 0.00 0.00 4.17
5469 5672 2.359850 GTGCCCATGCCTTCGTGA 60.360 61.111 0.00 0.00 36.33 4.35
5472 5675 0.825425 TGCCCATGCCTTCGTGAAAA 60.825 50.000 0.00 0.00 36.33 2.29
5473 5676 0.388520 GCCCATGCCTTCGTGAAAAC 60.389 55.000 0.00 0.00 0.00 2.43
5474 5677 0.243636 CCCATGCCTTCGTGAAAACC 59.756 55.000 0.00 0.00 0.00 3.27
5475 5678 0.109781 CCATGCCTTCGTGAAAACCG 60.110 55.000 0.00 0.00 0.00 4.44
5476 5679 0.109781 CATGCCTTCGTGAAAACCGG 60.110 55.000 0.00 0.00 0.00 5.28
5477 5680 0.536460 ATGCCTTCGTGAAAACCGGT 60.536 50.000 0.00 0.00 0.00 5.28
5478 5681 1.281656 GCCTTCGTGAAAACCGGTG 59.718 57.895 8.52 0.00 0.00 4.94
5479 5682 1.281656 CCTTCGTGAAAACCGGTGC 59.718 57.895 8.52 0.77 0.00 5.01
5480 5683 1.281656 CTTCGTGAAAACCGGTGCC 59.718 57.895 8.52 0.14 0.00 5.01
5481 5684 2.125202 CTTCGTGAAAACCGGTGCCC 62.125 60.000 8.52 0.00 0.00 5.36
5482 5685 2.888464 TTCGTGAAAACCGGTGCCCA 62.888 55.000 8.52 2.96 0.00 5.36
5483 5686 2.265182 CGTGAAAACCGGTGCCCAT 61.265 57.895 8.52 0.00 0.00 4.00
5484 5687 1.288752 GTGAAAACCGGTGCCCATG 59.711 57.895 8.52 0.00 0.00 3.66
5485 5688 2.261361 GAAAACCGGTGCCCATGC 59.739 61.111 8.52 0.00 38.26 4.06
5486 5689 3.295304 GAAAACCGGTGCCCATGCC 62.295 63.158 8.52 0.00 36.33 4.40
5487 5690 3.826265 AAAACCGGTGCCCATGCCT 62.826 57.895 8.52 0.00 36.33 4.75
5488 5691 3.826265 AAACCGGTGCCCATGCCTT 62.826 57.895 8.52 0.00 36.33 4.35
5489 5692 4.740822 ACCGGTGCCCATGCCTTC 62.741 66.667 6.12 0.00 36.33 3.46
5492 5695 3.443045 GGTGCCCATGCCTTCGTG 61.443 66.667 0.00 0.00 36.33 4.35
5493 5696 3.443045 GTGCCCATGCCTTCGTGG 61.443 66.667 0.00 0.00 46.66 4.94
5503 5706 3.373226 CTTCGTGGAAGGACGGGA 58.627 61.111 0.00 0.00 39.88 5.14
5512 5715 2.286127 GAAGGACGGGAAGGAGAGCG 62.286 65.000 0.00 0.00 0.00 5.03
5520 5723 1.213013 GAAGGAGAGCGCTGACGAA 59.787 57.895 18.48 0.00 43.93 3.85
5525 5728 1.068287 GAGAGCGCTGACGAAGACAC 61.068 60.000 18.48 0.00 43.93 3.67
5528 5731 2.375766 GCGCTGACGAAGACACCAG 61.376 63.158 0.00 0.00 43.93 4.00
5580 5783 9.791820 GAGTACTTTGTAAGTATTCTCTTCTCC 57.208 37.037 12.24 0.00 45.05 3.71
5581 5784 9.310449 AGTACTTTGTAAGTATTCTCTTCTCCA 57.690 33.333 2.92 0.00 45.05 3.86
5593 5796 5.615925 TCTCTTCTCCAATTAGTTAGGGC 57.384 43.478 0.00 0.00 0.00 5.19
5605 5808 3.859061 AGTTAGGGCTAGGGTTATTGC 57.141 47.619 0.00 0.00 0.00 3.56
5617 5820 5.505181 AGGGTTATTGCATTCGAGGATAT 57.495 39.130 0.00 0.00 0.00 1.63
5648 5851 7.174253 TGTTTCTTACTTTATTGCACCGATTCT 59.826 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 2.028125 ATAGACACGGTCCATGGGCG 62.028 60.000 13.02 9.30 32.18 6.13
89 91 1.770658 CTTCCCCATGGAGCATAGACA 59.229 52.381 15.22 0.00 43.07 3.41
209 223 7.148590 GCTTTCTGCTTGTCTCAAAAAGAAAAA 60.149 33.333 14.34 0.00 35.58 1.94
210 224 6.311200 GCTTTCTGCTTGTCTCAAAAAGAAAA 59.689 34.615 14.34 0.00 35.58 2.29
211 225 5.807011 GCTTTCTGCTTGTCTCAAAAAGAAA 59.193 36.000 13.48 13.48 35.58 2.52
212 226 5.343249 GCTTTCTGCTTGTCTCAAAAAGAA 58.657 37.500 7.90 5.87 35.58 2.52
213 227 4.496341 CGCTTTCTGCTTGTCTCAAAAAGA 60.496 41.667 7.90 1.32 40.11 2.52
214 228 3.727723 CGCTTTCTGCTTGTCTCAAAAAG 59.272 43.478 0.00 0.00 40.11 2.27
215 229 3.694734 CGCTTTCTGCTTGTCTCAAAAA 58.305 40.909 0.00 0.00 40.11 1.94
216 230 2.541588 GCGCTTTCTGCTTGTCTCAAAA 60.542 45.455 0.00 0.00 40.11 2.44
217 231 1.002468 GCGCTTTCTGCTTGTCTCAAA 60.002 47.619 0.00 0.00 40.11 2.69
218 232 0.588252 GCGCTTTCTGCTTGTCTCAA 59.412 50.000 0.00 0.00 40.11 3.02
219 233 1.230635 GGCGCTTTCTGCTTGTCTCA 61.231 55.000 7.64 0.00 40.11 3.27
220 234 1.230635 TGGCGCTTTCTGCTTGTCTC 61.231 55.000 7.64 0.00 40.11 3.36
221 235 1.227943 TGGCGCTTTCTGCTTGTCT 60.228 52.632 7.64 0.00 40.11 3.41
222 236 1.081840 GTGGCGCTTTCTGCTTGTC 60.082 57.895 7.64 0.00 40.11 3.18
223 237 1.103398 AAGTGGCGCTTTCTGCTTGT 61.103 50.000 7.64 0.00 40.11 3.16
224 238 0.662374 CAAGTGGCGCTTTCTGCTTG 60.662 55.000 11.25 9.20 40.11 4.01
225 239 1.656441 CAAGTGGCGCTTTCTGCTT 59.344 52.632 11.25 0.16 40.11 3.91
226 240 2.263741 CCAAGTGGCGCTTTCTGCT 61.264 57.895 11.25 0.00 40.11 4.24
227 241 2.256461 CCAAGTGGCGCTTTCTGC 59.744 61.111 11.25 0.00 34.69 4.26
232 246 2.282462 CCTTCCCAAGTGGCGCTT 60.282 61.111 7.64 7.64 38.08 4.68
350 371 0.872021 GCGAGACTCCGCGAATGATT 60.872 55.000 8.23 0.00 45.86 2.57
359 380 3.533691 GCGAAACGCGAGACTCCG 61.534 66.667 15.93 8.38 44.55 4.63
389 410 3.163594 CAAACGATTCTGCAATTCCGAC 58.836 45.455 0.00 0.00 0.00 4.79
398 419 6.926272 AGATAGTAGATTCCAAACGATTCTGC 59.074 38.462 0.00 0.00 35.19 4.26
409 430 5.351740 CACGCGAGATAGATAGTAGATTCCA 59.648 44.000 15.93 0.00 0.00 3.53
517 545 0.948623 GGCGTCACATGCACACAGTA 60.949 55.000 0.00 0.00 0.00 2.74
555 583 2.742428 ATGCTATGCCCACACAGATT 57.258 45.000 0.00 0.00 0.00 2.40
560 588 2.001872 GCAAAAATGCTATGCCCACAC 58.998 47.619 0.00 0.00 34.03 3.82
569 597 5.404968 CACTCCAAAAATCGCAAAAATGCTA 59.595 36.000 0.00 0.00 0.00 3.49
663 692 4.592192 ACGCGATGGGCCGATGAG 62.592 66.667 15.93 0.00 38.94 2.90
664 693 4.585526 GACGCGATGGGCCGATGA 62.586 66.667 15.93 0.00 38.94 2.92
671 700 3.447025 GAGGAAGGGACGCGATGGG 62.447 68.421 15.93 0.00 0.00 4.00
673 702 2.107141 GGAGGAAGGGACGCGATG 59.893 66.667 15.93 0.00 0.00 3.84
674 703 2.042843 AGGAGGAAGGGACGCGAT 60.043 61.111 15.93 0.00 0.00 4.58
706 736 2.272146 GAAGGGAATGGCAGCCGA 59.728 61.111 7.03 0.00 0.00 5.54
709 739 3.521796 GCGGAAGGGAATGGCAGC 61.522 66.667 0.00 0.00 0.00 5.25
711 741 4.440829 GGGCGGAAGGGAATGGCA 62.441 66.667 0.00 0.00 0.00 4.92
712 742 4.129148 AGGGCGGAAGGGAATGGC 62.129 66.667 0.00 0.00 0.00 4.40
763 793 4.704833 GGCGAGACAGCTTGGCCA 62.705 66.667 0.00 0.00 43.49 5.36
913 967 1.890510 GGTTTTCGAGTGCGGTGGT 60.891 57.895 0.00 0.00 38.28 4.16
939 993 4.305769 CAAACTGTTGGAGTGAGAGAGAG 58.694 47.826 0.00 0.00 34.02 3.20
940 994 3.493350 GCAAACTGTTGGAGTGAGAGAGA 60.493 47.826 0.00 0.00 34.02 3.10
944 998 2.564771 CTGCAAACTGTTGGAGTGAGA 58.435 47.619 0.00 0.00 45.45 3.27
950 1004 2.951642 CTCTTTCCTGCAAACTGTTGGA 59.048 45.455 0.00 0.00 35.10 3.53
951 1005 2.951642 TCTCTTTCCTGCAAACTGTTGG 59.048 45.455 0.00 0.00 35.10 3.77
952 1006 3.004106 CCTCTCTTTCCTGCAAACTGTTG 59.996 47.826 0.00 0.00 37.83 3.33
953 1007 3.217626 CCTCTCTTTCCTGCAAACTGTT 58.782 45.455 0.00 0.00 0.00 3.16
954 1008 2.487986 CCCTCTCTTTCCTGCAAACTGT 60.488 50.000 0.00 0.00 0.00 3.55
956 1010 2.039613 CTCCCTCTCTTTCCTGCAAACT 59.960 50.000 0.00 0.00 0.00 2.66
957 1011 2.039084 TCTCCCTCTCTTTCCTGCAAAC 59.961 50.000 0.00 0.00 0.00 2.93
958 1012 2.304180 CTCTCCCTCTCTTTCCTGCAAA 59.696 50.000 0.00 0.00 0.00 3.68
959 1013 1.905215 CTCTCCCTCTCTTTCCTGCAA 59.095 52.381 0.00 0.00 0.00 4.08
960 1014 1.077828 TCTCTCCCTCTCTTTCCTGCA 59.922 52.381 0.00 0.00 0.00 4.41
962 1016 2.622942 CGATCTCTCCCTCTCTTTCCTG 59.377 54.545 0.00 0.00 0.00 3.86
964 1018 2.938838 TCGATCTCTCCCTCTCTTTCC 58.061 52.381 0.00 0.00 0.00 3.13
1470 1538 5.568620 AAACAGAATCCAACACTAGAGGT 57.431 39.130 0.00 0.00 0.00 3.85
1602 1670 1.929230 TCTTGCAGACGACAACGAAA 58.071 45.000 0.00 0.00 42.66 3.46
1670 1738 3.575630 CATGTCGTATTACGGAGATGGG 58.424 50.000 15.69 0.00 42.81 4.00
1971 2040 9.919416 ATGCATTGCAATACCCAATATATACTA 57.081 29.630 16.46 0.00 43.62 1.82
1972 2041 8.689061 CATGCATTGCAATACCCAATATATACT 58.311 33.333 16.46 0.00 43.62 2.12
1974 2043 8.592529 ACATGCATTGCAATACCCAATATATA 57.407 30.769 16.46 0.00 43.62 0.86
1975 2044 7.484993 ACATGCATTGCAATACCCAATATAT 57.515 32.000 16.46 0.00 43.62 0.86
1984 2063 2.896168 AGCCAACATGCATTGCAATAC 58.104 42.857 16.46 7.23 43.62 1.89
2022 2106 1.040646 TCTTCTGTCGACAAGTGGCT 58.959 50.000 20.49 0.00 0.00 4.75
2086 2170 2.665000 CCACGAGCATCACCCTGT 59.335 61.111 0.00 0.00 33.17 4.00
2178 2262 9.640963 AGATTATAGTATAACGATGGAAGCAAC 57.359 33.333 4.71 0.00 0.00 4.17
2180 2264 9.639601 CAAGATTATAGTATAACGATGGAAGCA 57.360 33.333 4.71 0.00 0.00 3.91
2217 2301 4.972514 TGAGACATGCACTACTGTAGAG 57.027 45.455 21.01 14.19 0.00 2.43
2259 2343 6.438425 CCCATGAGATCCCCCTAAATTAATTG 59.562 42.308 0.39 0.00 0.00 2.32
2263 2347 3.333680 GCCCATGAGATCCCCCTAAATTA 59.666 47.826 0.00 0.00 0.00 1.40
2478 2592 5.170748 CCCTTCAACCAACATTAAATCAGC 58.829 41.667 0.00 0.00 0.00 4.26
2600 2723 3.181475 ACATATACAGTCAACAGAGCCCG 60.181 47.826 0.00 0.00 0.00 6.13
2632 2755 0.543277 TAGGATCTGCAGCCAACTGG 59.457 55.000 9.47 0.00 44.63 4.00
2694 2817 0.754957 CCCAGCCACCAAACACAAGA 60.755 55.000 0.00 0.00 0.00 3.02
2706 2829 1.077501 GCTGCTAATGTCCCAGCCA 60.078 57.895 0.62 0.00 44.60 4.75
2870 2993 0.889994 TGTGCCCTTGATGACATTGC 59.110 50.000 0.00 0.00 0.00 3.56
2988 3116 3.311322 CACGCACCAAACTCAGAGTTTTA 59.689 43.478 23.64 0.00 45.38 1.52
3215 3353 9.146984 TGGAGTAACATTTTTATGAGTAACTCG 57.853 33.333 0.00 0.00 32.35 4.18
3227 3365 5.061721 AGGACTGGTGGAGTAACATTTTT 57.938 39.130 0.00 0.00 33.83 1.94
3349 3487 1.531149 CAAAGCACCACTACCTTGTCG 59.469 52.381 0.00 0.00 0.00 4.35
3469 3607 2.127271 TGGCATACAGTGTTGATGGG 57.873 50.000 0.00 0.00 0.00 4.00
3496 3634 3.399181 GGGACGCCCTCCATGACA 61.399 66.667 7.58 0.00 41.63 3.58
3598 3736 6.363357 CACAAAAGAAACTAACATAAGCCTGC 59.637 38.462 0.00 0.00 0.00 4.85
3634 3772 6.094048 GGCAGTTGTTCTTAATAGCAAGATCA 59.906 38.462 0.00 0.00 34.59 2.92
3706 3844 1.269621 ACAAGGAAGTCGACCAAGACG 60.270 52.381 13.01 0.00 45.26 4.18
3715 3853 0.588252 CAGCACCAACAAGGAAGTCG 59.412 55.000 0.00 0.00 41.22 4.18
3718 3856 1.691196 TTCCAGCACCAACAAGGAAG 58.309 50.000 0.00 0.00 41.22 3.46
3801 3974 9.077885 ACAAGAACAGAAACCACATATGTTTAT 57.922 29.630 5.37 0.00 36.13 1.40
3859 4042 1.487300 TCATCCCGTCGTTATTCCCA 58.513 50.000 0.00 0.00 0.00 4.37
3865 4048 2.624838 GGATAGGTTCATCCCGTCGTTA 59.375 50.000 0.00 0.00 38.91 3.18
3928 4111 1.278985 GAGACCATGTCATCCACCACA 59.721 52.381 0.00 0.00 34.60 4.17
4040 4225 4.045636 AGTTTTTGCACCAACAGTCATC 57.954 40.909 9.35 0.00 0.00 2.92
4078 4264 0.383949 TGCAAAAGAACGGTGAAGCC 59.616 50.000 0.00 0.00 0.00 4.35
4215 4401 3.284617 CAGATCAAGAATGATGGGTGCA 58.715 45.455 0.00 0.00 46.30 4.57
4248 4434 0.463474 GAATCCTGGTGCTGAGCTCC 60.463 60.000 18.05 18.05 41.88 4.70
4325 4511 4.765856 GGCTCCCAAAGTATATCTCGACTA 59.234 45.833 0.00 0.00 0.00 2.59
4358 4544 0.890542 TGCAAGTGGAGCAGCGAAAT 60.891 50.000 0.00 0.00 37.02 2.17
4364 4550 2.060326 CACAAATGCAAGTGGAGCAG 57.940 50.000 8.85 0.00 46.36 4.24
4398 4584 1.001393 GGCAACCGGATGGAAGGAA 60.001 57.895 9.46 0.00 39.21 3.36
4519 4705 5.308825 ACCTGTTAACAGAGGAATTCAGTG 58.691 41.667 32.50 15.63 46.59 3.66
4683 4869 3.507009 GTACGGTCGCTCTCGGCT 61.507 66.667 0.00 0.00 40.74 5.52
4739 4925 1.471964 CGATCTCGCCTTCTTCTTCG 58.528 55.000 0.00 0.00 0.00 3.79
4802 4988 5.517833 GGGGTAAACTTAACCAGGGAAAGAT 60.518 44.000 5.92 0.00 42.46 2.40
4812 5001 4.070009 CACTCACTGGGGTAAACTTAACC 58.930 47.826 0.00 0.00 39.87 2.85
4816 5005 2.508300 ACACACTCACTGGGGTAAACTT 59.492 45.455 0.00 0.00 0.00 2.66
4818 5007 2.218603 CACACACTCACTGGGGTAAAC 58.781 52.381 0.00 0.00 0.00 2.01
4819 5008 1.841277 ACACACACTCACTGGGGTAAA 59.159 47.619 0.00 0.00 0.00 2.01
4822 5011 1.696097 GGACACACACTCACTGGGGT 61.696 60.000 0.00 0.00 0.00 4.95
4823 5012 1.071471 GGACACACACTCACTGGGG 59.929 63.158 0.00 0.00 0.00 4.96
4831 5027 0.249489 GTCTCGCAAGGACACACACT 60.249 55.000 0.00 0.00 37.45 3.55
4865 5061 2.832931 CAAGACGCAGAGACTTGGG 58.167 57.895 8.18 0.00 44.77 4.12
4868 5064 1.067495 GCTACCAAGACGCAGAGACTT 60.067 52.381 0.00 0.00 35.33 3.01
4869 5065 0.528470 GCTACCAAGACGCAGAGACT 59.472 55.000 0.00 0.00 0.00 3.24
4879 5075 3.445008 AGTCCATGAGAAGCTACCAAGA 58.555 45.455 0.00 0.00 0.00 3.02
5061 5264 3.057337 CCGTCCCTGAACGACCTT 58.943 61.111 0.00 0.00 45.37 3.50
5062 5265 3.692406 GCCGTCCCTGAACGACCT 61.692 66.667 0.00 0.00 45.37 3.85
5121 5324 8.143835 GCCTGAATTGTGGTAATTTTATGCTAT 58.856 33.333 0.00 0.00 0.00 2.97
5145 5348 0.323451 AGTTTTCCGGATTCCAGGCC 60.323 55.000 4.15 0.00 0.00 5.19
5148 5351 3.007635 GTGGTAGTTTTCCGGATTCCAG 58.992 50.000 4.15 0.00 0.00 3.86
5152 5355 4.565028 GGAGAAGTGGTAGTTTTCCGGATT 60.565 45.833 4.15 0.00 0.00 3.01
5201 5404 6.882678 AGTGCCTTTTAATACAACGGACTAAT 59.117 34.615 0.00 0.00 0.00 1.73
5208 5411 5.410439 ACCACTAGTGCCTTTTAATACAACG 59.590 40.000 17.86 0.47 0.00 4.10
5210 5413 5.708230 CCACCACTAGTGCCTTTTAATACAA 59.292 40.000 17.86 0.00 45.83 2.41
5214 5417 4.650972 TCCACCACTAGTGCCTTTTAAT 57.349 40.909 17.86 0.00 45.83 1.40
5250 5453 2.689983 CCCTCCTTGTCATAAATGGCAC 59.310 50.000 0.00 0.00 42.90 5.01
5278 5481 2.280797 GCTGACGTTGGGCTGACA 60.281 61.111 0.00 0.00 0.00 3.58
5317 5520 2.474816 GGGCTAGCTAATGTTCGTCAG 58.525 52.381 15.72 0.00 0.00 3.51
5319 5522 1.202382 ACGGGCTAGCTAATGTTCGTC 60.202 52.381 15.72 0.00 0.00 4.20
5320 5523 0.822164 ACGGGCTAGCTAATGTTCGT 59.178 50.000 15.72 10.19 0.00 3.85
5321 5524 1.859080 GAACGGGCTAGCTAATGTTCG 59.141 52.381 15.72 9.61 0.00 3.95
5322 5525 3.180891 AGAACGGGCTAGCTAATGTTC 57.819 47.619 22.51 22.51 36.77 3.18
5323 5526 4.439968 GTTAGAACGGGCTAGCTAATGTT 58.560 43.478 15.72 13.47 0.00 2.71
5324 5527 3.181468 GGTTAGAACGGGCTAGCTAATGT 60.181 47.826 15.72 5.32 0.00 2.71
5325 5528 3.391049 GGTTAGAACGGGCTAGCTAATG 58.609 50.000 15.72 4.66 0.00 1.90
5326 5529 2.035576 CGGTTAGAACGGGCTAGCTAAT 59.964 50.000 15.72 0.00 0.00 1.73
5327 5530 1.406539 CGGTTAGAACGGGCTAGCTAA 59.593 52.381 15.72 0.98 0.00 3.09
5329 5532 0.969409 ACGGTTAGAACGGGCTAGCT 60.969 55.000 15.72 0.00 33.99 3.32
5330 5533 0.804933 CACGGTTAGAACGGGCTAGC 60.805 60.000 6.04 6.04 33.99 3.42
5331 5534 0.529378 ACACGGTTAGAACGGGCTAG 59.471 55.000 5.15 0.00 38.56 3.42
5332 5535 0.527565 GACACGGTTAGAACGGGCTA 59.472 55.000 5.15 0.00 38.56 3.93
5334 5537 0.600782 TTGACACGGTTAGAACGGGC 60.601 55.000 5.15 0.00 38.56 6.13
5335 5538 1.868469 TTTGACACGGTTAGAACGGG 58.132 50.000 5.15 0.00 41.32 5.28
5336 5539 2.347846 CGTTTTGACACGGTTAGAACGG 60.348 50.000 12.92 0.00 36.47 4.44
5337 5540 2.535166 TCGTTTTGACACGGTTAGAACG 59.465 45.455 13.91 13.91 40.74 3.95
5350 5553 2.356553 CGGCTCGGGTCGTTTTGA 60.357 61.111 0.00 0.00 35.65 2.69
5351 5554 3.419759 CCGGCTCGGGTCGTTTTG 61.420 66.667 9.17 0.00 44.15 2.44
5396 5599 3.141838 AGAGAGCATGGGAGAGGAGAATA 59.858 47.826 0.00 0.00 0.00 1.75
5397 5600 2.090606 AGAGAGCATGGGAGAGGAGAAT 60.091 50.000 0.00 0.00 0.00 2.40
5410 5613 3.369261 GGTCAGTGTCATTGAGAGAGCAT 60.369 47.826 0.00 0.00 0.00 3.79
5428 5631 1.053424 GACTAACAGTGGGGTGGTCA 58.947 55.000 0.00 0.00 0.00 4.02
5442 5645 0.322456 GCATGGGCACTGGTGACTAA 60.322 55.000 6.53 0.00 39.02 2.24
5450 5653 2.360350 ACGAAGGCATGGGCACTG 60.360 61.111 0.00 0.00 43.71 3.66
5451 5654 2.360350 CACGAAGGCATGGGCACT 60.360 61.111 0.00 0.00 43.71 4.40
5476 5679 3.443045 CCACGAAGGCATGGGCAC 61.443 66.667 0.00 0.00 43.71 5.01
5477 5680 3.203086 TTCCACGAAGGCATGGGCA 62.203 57.895 0.00 0.00 43.71 5.36
5478 5681 2.361104 TTCCACGAAGGCATGGGC 60.361 61.111 0.00 0.00 36.56 5.36
5479 5682 3.909662 CTTCCACGAAGGCATGGG 58.090 61.111 0.00 0.00 36.16 4.00
5486 5689 0.389948 CTTCCCGTCCTTCCACGAAG 60.390 60.000 0.00 0.00 42.69 3.79
5487 5690 1.669440 CTTCCCGTCCTTCCACGAA 59.331 57.895 0.00 0.00 42.69 3.85
5488 5691 2.280552 CCTTCCCGTCCTTCCACGA 61.281 63.158 0.00 0.00 42.69 4.35
5489 5692 2.227089 CTCCTTCCCGTCCTTCCACG 62.227 65.000 0.00 0.00 39.61 4.94
5490 5693 0.903454 TCTCCTTCCCGTCCTTCCAC 60.903 60.000 0.00 0.00 0.00 4.02
5491 5694 0.614979 CTCTCCTTCCCGTCCTTCCA 60.615 60.000 0.00 0.00 0.00 3.53
5492 5695 1.962321 GCTCTCCTTCCCGTCCTTCC 61.962 65.000 0.00 0.00 0.00 3.46
5493 5696 1.518302 GCTCTCCTTCCCGTCCTTC 59.482 63.158 0.00 0.00 0.00 3.46
5494 5697 2.352032 CGCTCTCCTTCCCGTCCTT 61.352 63.158 0.00 0.00 0.00 3.36
5495 5698 2.756283 CGCTCTCCTTCCCGTCCT 60.756 66.667 0.00 0.00 0.00 3.85
5496 5699 4.516195 GCGCTCTCCTTCCCGTCC 62.516 72.222 0.00 0.00 0.00 4.79
5497 5700 3.453679 AGCGCTCTCCTTCCCGTC 61.454 66.667 2.64 0.00 0.00 4.79
5498 5701 3.764466 CAGCGCTCTCCTTCCCGT 61.764 66.667 7.13 0.00 0.00 5.28
5503 5706 1.214062 CTTCGTCAGCGCTCTCCTT 59.786 57.895 7.13 0.00 38.14 3.36
5512 5715 3.555428 GCTGGTGTCTTCGTCAGC 58.445 61.111 0.00 0.00 44.34 4.26
5520 5723 3.321648 TCGCCCATGCTGGTGTCT 61.322 61.111 2.07 0.00 35.17 3.41
5525 5728 3.958147 AAGTCGTCGCCCATGCTGG 62.958 63.158 0.00 0.00 37.25 4.85
5528 5731 1.815421 ATGAAGTCGTCGCCCATGC 60.815 57.895 0.00 0.00 0.00 4.06
5535 5738 1.191944 CGATGTCCATGAAGTCGTCG 58.808 55.000 0.00 0.78 34.08 5.12
5580 5783 6.206829 GCAATAACCCTAGCCCTAACTAATTG 59.793 42.308 0.00 0.00 0.00 2.32
5581 5784 6.126303 TGCAATAACCCTAGCCCTAACTAATT 60.126 38.462 0.00 0.00 0.00 1.40
5593 5796 4.336889 TCCTCGAATGCAATAACCCTAG 57.663 45.455 0.00 0.00 0.00 3.02
5622 5825 6.811253 ATCGGTGCAATAAAGTAAGAAACA 57.189 33.333 0.00 0.00 0.00 2.83
5623 5826 7.527457 AGAATCGGTGCAATAAAGTAAGAAAC 58.473 34.615 0.00 0.00 0.00 2.78
5624 5827 7.681939 AGAATCGGTGCAATAAAGTAAGAAA 57.318 32.000 0.00 0.00 0.00 2.52
5627 5830 7.526608 TCAAAGAATCGGTGCAATAAAGTAAG 58.473 34.615 0.00 0.00 0.00 2.34
5629 5832 7.552687 AGATCAAAGAATCGGTGCAATAAAGTA 59.447 33.333 0.00 0.00 0.00 2.24
5631 5834 6.789262 AGATCAAAGAATCGGTGCAATAAAG 58.211 36.000 0.00 0.00 0.00 1.85
5635 5838 4.142315 CCAAGATCAAAGAATCGGTGCAAT 60.142 41.667 0.00 0.00 0.00 3.56
5638 5841 2.749621 ACCAAGATCAAAGAATCGGTGC 59.250 45.455 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.