Multiple sequence alignment - TraesCS3B01G328400

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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 TraesCS3B01G328400 chr3B 100.000 4369 0 0 1 4369 530235103 530239471 0.000000e+00 8069.0
1 TraesCS3B01G328400 chr3B 88.095 84 5 4 4290 4369 115549490 115549572 1.290000e-15 95.3
2 TraesCS3B01G328400 chr3A 91.006 2913 88 53 1 2843 526507575 526510383 0.000000e+00 3768.0
3 TraesCS3B01G328400 chr3A 92.614 853 26 21 2976 3809 526510410 526511244 0.000000e+00 1192.0
4 TraesCS3B01G328400 chr3A 100.000 32 0 0 4282 4313 526512892 526512923 4.720000e-05 60.2
5 TraesCS3B01G328400 chr3D 92.450 2000 62 34 1985 3936 403936023 403937981 0.000000e+00 2774.0
6 TraesCS3B01G328400 chr3D 92.480 1968 69 29 1 1932 403932666 403934590 0.000000e+00 2741.0
7 TraesCS3B01G328400 chr3D 92.258 155 10 2 3938 4091 551486668 551486515 7.360000e-53 219.0
8 TraesCS3B01G328400 chr3D 93.878 98 5 1 4093 4190 403937986 403938082 3.520000e-31 147.0
9 TraesCS3B01G328400 chr3D 100.000 34 0 0 4282 4315 403939538 403939571 3.650000e-06 63.9
10 TraesCS3B01G328400 chr5B 92.638 163 11 1 3937 4098 308556948 308557110 2.630000e-57 233.0
11 TraesCS3B01G328400 chr5B 94.915 59 3 0 4311 4369 246909452 246909394 4.650000e-15 93.5
12 TraesCS3B01G328400 chr1B 92.903 155 8 2 3937 4091 174641569 174641720 5.690000e-54 222.0
13 TraesCS3B01G328400 chr1B 90.683 161 14 1 3937 4097 628047823 628047664 3.420000e-51 213.0
14 TraesCS3B01G328400 chr1B 95.238 63 3 0 4307 4369 661980629 661980691 2.780000e-17 100.0
15 TraesCS3B01G328400 chr7B 91.824 159 12 1 3937 4095 94187031 94186874 2.050000e-53 220.0
16 TraesCS3B01G328400 chr7B 91.463 164 7 3 3937 4095 633239102 633239263 7.360000e-53 219.0
17 TraesCS3B01G328400 chr7B 87.500 80 7 3 4292 4369 115521535 115521613 6.020000e-14 89.8
18 TraesCS3B01G328400 chr2B 92.308 156 11 1 3937 4092 771215291 771215137 2.050000e-53 220.0
19 TraesCS3B01G328400 chr2B 96.721 61 2 0 4309 4369 762012677 762012737 7.730000e-18 102.0
20 TraesCS3B01G328400 chr5A 91.304 161 11 2 3937 4095 29678306 29678147 2.650000e-52 217.0
21 TraesCS3B01G328400 chr5A 90.123 162 13 3 3937 4098 101083427 101083269 1.590000e-49 207.0
22 TraesCS3B01G328400 chr4D 91.720 157 12 1 3937 4093 35722329 35722484 2.650000e-52 217.0
23 TraesCS3B01G328400 chr2D 91.720 157 11 1 3937 4093 537187758 537187912 2.650000e-52 217.0
24 TraesCS3B01G328400 chr7D 90.625 160 14 1 3937 4096 629623556 629623714 1.230000e-50 211.0
25 TraesCS3B01G328400 chr5D 90.625 160 13 2 3937 4095 410591970 410592128 1.230000e-50 211.0
26 TraesCS3B01G328400 chr1A 88.757 169 17 2 3937 4104 578019515 578019682 5.730000e-49 206.0
27 TraesCS3B01G328400 chrUn 95.312 64 3 0 4306 4369 79618366 79618429 7.730000e-18 102.0
28 TraesCS3B01G328400 chr7A 95.312 64 3 0 4306 4369 223677319 223677256 7.730000e-18 102.0
29 TraesCS3B01G328400 chr6A 93.939 66 2 1 4304 4369 465250105 465250168 1.000000e-16 99.0
30 TraesCS3B01G328400 chr4B 91.176 68 6 0 4302 4369 568553114 568553047 4.650000e-15 93.5


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 TraesCS3B01G328400 chr3B 530235103 530239471 4368 False 8069.000 8069 100.000 1 4369 1 chr3B.!!$F2 4368
1 TraesCS3B01G328400 chr3A 526507575 526512923 5348 False 1673.400 3768 94.540 1 4313 3 chr3A.!!$F1 4312
2 TraesCS3B01G328400 chr3D 403932666 403939571 6905 False 1431.475 2774 94.702 1 4315 4 chr3D.!!$F1 4314

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
918 963 0.249531 TTACGCAACTCGCTGGTTCA 60.250 50.0 0.00 0.0 43.23 3.18 F
1898 1964 0.179048 TACTTCATGCATGCCTCCGG 60.179 55.0 22.25 0.0 0.00 5.14 F
2571 4055 0.744414 GTGGTACGGCACATGCAGAT 60.744 55.0 11.07 0.0 44.36 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 3465 0.390998 TGCCGAAATCGTGCTCATGA 60.391 50.0 14.27 0.00 36.80 3.07 R
2977 4476 0.659427 TCGAAACGTCACGTGAGAGT 59.341 50.0 20.73 18.95 39.99 3.24 R
4190 5762 0.036010 TCTAAGGGCTCTTGCAGTGC 60.036 55.0 9.76 8.58 41.91 4.40 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
100 113 2.341846 ATTCCCGCGTAACATGGAAT 57.658 45.000 16.30 16.30 41.58 3.01
165 178 1.068333 CATGCCCGTTTTCTGACCAAG 60.068 52.381 0.00 0.00 0.00 3.61
233 246 1.572085 CTGACACGCTTTCCTGCCTG 61.572 60.000 0.00 0.00 0.00 4.85
277 290 3.649277 GACACGGTCGAGCCATGCT 62.649 63.158 9.39 0.00 43.88 3.79
296 313 6.344500 CATGCTAATGGAGTCTGAAACTACT 58.656 40.000 0.00 0.00 39.86 2.57
297 314 7.492524 CATGCTAATGGAGTCTGAAACTACTA 58.507 38.462 0.00 0.00 39.86 1.82
298 315 7.101652 TGCTAATGGAGTCTGAAACTACTAG 57.898 40.000 0.00 0.00 39.86 2.57
299 316 6.663953 TGCTAATGGAGTCTGAAACTACTAGT 59.336 38.462 0.00 0.00 39.86 2.57
300 317 7.832685 TGCTAATGGAGTCTGAAACTACTAGTA 59.167 37.037 1.89 1.89 39.86 1.82
301 318 8.347035 GCTAATGGAGTCTGAAACTACTAGTAG 58.653 40.741 25.30 25.30 39.86 2.57
302 319 6.702716 ATGGAGTCTGAAACTACTAGTAGC 57.297 41.667 26.54 13.16 39.86 3.58
304 321 4.948621 GGAGTCTGAAACTACTAGTAGCCA 59.051 45.833 26.54 20.04 38.74 4.75
305 322 5.595133 GGAGTCTGAAACTACTAGTAGCCAT 59.405 44.000 26.54 14.57 38.74 4.40
309 331 6.975772 GTCTGAAACTACTAGTAGCCATGAAG 59.024 42.308 26.54 16.95 36.66 3.02
332 354 3.287867 ACGAATGAGAAGAATGGCCAT 57.712 42.857 14.09 14.09 0.00 4.40
333 355 3.209410 ACGAATGAGAAGAATGGCCATC 58.791 45.455 21.08 12.71 0.00 3.51
334 356 2.222678 CGAATGAGAAGAATGGCCATCG 59.777 50.000 21.08 11.35 0.00 3.84
356 378 3.187227 GTCTCCCGCTCGTAATCGTAATA 59.813 47.826 0.00 0.00 38.33 0.98
358 380 4.456911 TCTCCCGCTCGTAATCGTAATAAT 59.543 41.667 0.00 0.00 38.33 1.28
359 381 4.726416 TCCCGCTCGTAATCGTAATAATC 58.274 43.478 0.00 0.00 38.33 1.75
360 382 4.216042 TCCCGCTCGTAATCGTAATAATCA 59.784 41.667 0.00 0.00 38.33 2.57
361 383 4.557690 CCCGCTCGTAATCGTAATAATCAG 59.442 45.833 0.00 0.00 38.33 2.90
362 384 4.557690 CCGCTCGTAATCGTAATAATCAGG 59.442 45.833 0.00 0.00 38.33 3.86
363 385 4.557690 CGCTCGTAATCGTAATAATCAGGG 59.442 45.833 0.00 0.00 38.33 4.45
364 386 4.326548 GCTCGTAATCGTAATAATCAGGGC 59.673 45.833 0.00 0.00 38.33 5.19
369 391 2.479837 TCGTAATAATCAGGGCAAGCG 58.520 47.619 0.00 0.00 0.00 4.68
428 450 1.270274 CGCAGCAGATCAGATCTAGCT 59.730 52.381 22.09 22.09 41.27 3.32
551 581 1.067582 GATCCATGGACGGACGGAC 59.932 63.158 18.99 0.00 38.07 4.79
552 582 2.679132 GATCCATGGACGGACGGACG 62.679 65.000 18.99 0.00 38.07 4.79
553 583 4.508128 CCATGGACGGACGGACGG 62.508 72.222 5.56 0.00 38.39 4.79
554 584 3.445687 CATGGACGGACGGACGGA 61.446 66.667 6.00 0.00 38.39 4.69
631 661 1.571215 CCGCCTCGCTTAAAACCGTT 61.571 55.000 0.00 0.00 0.00 4.44
663 693 1.615883 CCATCTTCGACGATCCATCCT 59.384 52.381 0.66 0.00 0.00 3.24
829 873 1.154338 GCAAGCAAGTGTAGCAGCG 60.154 57.895 0.00 0.00 0.00 5.18
831 875 0.867746 CAAGCAAGTGTAGCAGCGAA 59.132 50.000 0.00 0.00 0.00 4.70
910 955 1.058748 CACCGCATTACGCAACTCG 59.941 57.895 0.00 0.00 42.60 4.18
911 956 2.021380 CCGCATTACGCAACTCGC 59.979 61.111 0.00 0.00 42.60 5.03
912 957 2.452813 CCGCATTACGCAACTCGCT 61.453 57.895 0.00 0.00 42.60 4.93
913 958 1.296145 CGCATTACGCAACTCGCTG 60.296 57.895 0.00 0.00 42.60 5.18
914 959 1.060937 GCATTACGCAACTCGCTGG 59.939 57.895 0.00 0.00 43.23 4.85
915 960 1.635663 GCATTACGCAACTCGCTGGT 61.636 55.000 0.00 0.00 43.23 4.00
916 961 0.796312 CATTACGCAACTCGCTGGTT 59.204 50.000 0.00 0.00 43.23 3.67
917 962 1.076332 ATTACGCAACTCGCTGGTTC 58.924 50.000 0.00 0.00 43.23 3.62
918 963 0.249531 TTACGCAACTCGCTGGTTCA 60.250 50.000 0.00 0.00 43.23 3.18
919 964 0.666274 TACGCAACTCGCTGGTTCAG 60.666 55.000 0.00 0.00 43.23 3.02
1029 1086 4.891727 CCGCCCAAGATCCCGACG 62.892 72.222 0.00 0.00 0.00 5.12
1030 1087 4.891727 CGCCCAAGATCCCGACGG 62.892 72.222 6.99 6.99 0.00 4.79
1032 1089 4.891727 CCCAAGATCCCGACGGCG 62.892 72.222 1.94 1.94 37.24 6.46
1500 1557 6.993786 TGCGATTCCTTGATTAATGTGTTA 57.006 33.333 0.00 0.00 0.00 2.41
1514 1571 9.878599 GATTAATGTGTTAATTATCAACCTCGG 57.121 33.333 0.00 0.00 39.88 4.63
1541 1603 2.606272 GGACCGACCGAATTATGTGTTC 59.394 50.000 0.00 0.00 0.00 3.18
1542 1604 3.518590 GACCGACCGAATTATGTGTTCT 58.481 45.455 0.00 0.00 0.00 3.01
1648 1710 5.346011 CACAACGCTGCAGGTACATATATAG 59.654 44.000 17.12 0.00 0.00 1.31
1649 1711 4.720649 ACGCTGCAGGTACATATATAGG 57.279 45.455 17.12 0.00 0.00 2.57
1650 1712 4.341487 ACGCTGCAGGTACATATATAGGA 58.659 43.478 17.12 0.00 0.00 2.94
1651 1713 4.399618 ACGCTGCAGGTACATATATAGGAG 59.600 45.833 17.12 0.00 0.00 3.69
1652 1714 4.399618 CGCTGCAGGTACATATATAGGAGT 59.600 45.833 17.12 0.00 0.00 3.85
1653 1715 5.589050 CGCTGCAGGTACATATATAGGAGTA 59.411 44.000 17.12 0.00 0.00 2.59
1654 1716 6.458478 CGCTGCAGGTACATATATAGGAGTAC 60.458 46.154 17.12 7.67 36.88 2.73
1655 1717 6.603997 GCTGCAGGTACATATATAGGAGTACT 59.396 42.308 17.12 0.00 37.55 2.73
1656 1718 7.415765 GCTGCAGGTACATATATAGGAGTACTG 60.416 44.444 17.12 12.20 37.55 2.74
1657 1719 7.696017 TGCAGGTACATATATAGGAGTACTGA 58.304 38.462 0.00 0.00 37.55 3.41
1716 1782 4.335874 ACAGTCTAATGAGCTAGTACGTGG 59.664 45.833 0.00 0.00 0.00 4.94
1735 1801 4.378459 CGTGGAAAACTCATAACTTCTGGC 60.378 45.833 0.00 0.00 0.00 4.85
1886 1952 2.171840 ACGCCACTCACTCTACTTCAT 58.828 47.619 0.00 0.00 0.00 2.57
1898 1964 0.179048 TACTTCATGCATGCCTCCGG 60.179 55.000 22.25 0.00 0.00 5.14
1918 1984 2.606108 GCCTTTAATTTTGTCGCCCAG 58.394 47.619 0.00 0.00 0.00 4.45
1988 2208 3.009301 AGATGTACGCTACGTAATGCC 57.991 47.619 0.82 0.00 43.95 4.40
2180 3656 7.231607 CGATGTATACGTACCCATTAATTTGC 58.768 38.462 0.00 0.00 0.00 3.68
2230 3706 0.928229 ATACCGATGTTTTCGCTCGC 59.072 50.000 0.00 0.00 46.71 5.03
2285 3762 2.034812 CGTGCACTAGAGGGTTAGATCC 59.965 54.545 16.19 0.00 0.00 3.36
2287 3764 3.643792 GTGCACTAGAGGGTTAGATCCAT 59.356 47.826 10.32 0.00 0.00 3.41
2354 3831 4.380945 CCATGTGGGGTGGGGTGG 62.381 72.222 0.00 0.00 32.98 4.61
2355 3832 4.380945 CATGTGGGGTGGGGTGGG 62.381 72.222 0.00 0.00 0.00 4.61
2570 4054 1.375396 GTGGTACGGCACATGCAGA 60.375 57.895 11.07 0.00 44.36 4.26
2571 4055 0.744414 GTGGTACGGCACATGCAGAT 60.744 55.000 11.07 0.00 44.36 2.90
2672 4156 4.023193 GTGCACTGGTAGCATTTAACAACT 60.023 41.667 10.32 0.00 44.79 3.16
2691 4175 2.969950 ACTCTACTGTACCCACTTGCAA 59.030 45.455 0.00 0.00 0.00 4.08
2692 4176 3.006967 ACTCTACTGTACCCACTTGCAAG 59.993 47.826 24.84 24.84 0.00 4.01
2693 4177 2.076863 CTACTGTACCCACTTGCAAGC 58.923 52.381 26.27 9.35 0.00 4.01
2694 4178 0.884704 ACTGTACCCACTTGCAAGCG 60.885 55.000 26.27 17.05 0.00 4.68
2695 4179 2.187599 CTGTACCCACTTGCAAGCGC 62.188 60.000 26.27 0.00 39.24 5.92
2721 4205 3.858129 GCGCACGTTAAGGGTATATGCTA 60.858 47.826 0.30 0.00 0.00 3.49
2724 4208 4.092968 GCACGTTAAGGGTATATGCTATGC 59.907 45.833 0.00 0.00 0.00 3.14
2821 4311 5.091552 ACCCAGGAGTTAATCTGACAAGTA 58.908 41.667 0.00 0.00 33.11 2.24
2825 4315 6.477033 CCAGGAGTTAATCTGACAAGTAATCG 59.523 42.308 5.39 0.00 33.11 3.34
2902 4392 2.176798 TGTCCCCTTCCAATTTGACTGT 59.823 45.455 0.00 0.00 0.00 3.55
2904 4394 1.812571 CCCCTTCCAATTTGACTGTCG 59.187 52.381 2.98 0.00 0.00 4.35
2910 4400 3.659786 TCCAATTTGACTGTCGTGTAGG 58.340 45.455 2.98 3.02 0.00 3.18
2922 4415 5.818857 ACTGTCGTGTAGGTGTAAAAATGTT 59.181 36.000 0.00 0.00 0.00 2.71
2931 4424 4.277423 AGGTGTAAAAATGTTCAGTTCGGG 59.723 41.667 0.00 0.00 0.00 5.14
2977 4476 4.024302 CGTACGCTCATGGTGTCTATCTAA 60.024 45.833 0.52 0.00 39.59 2.10
2998 4497 2.287427 ACTCTCACGTGACGTTTCGATT 60.287 45.455 15.76 0.53 38.32 3.34
3001 4500 1.782569 TCACGTGACGTTTCGATTGTC 59.217 47.619 15.76 5.52 38.32 3.18
3137 4643 0.238553 GCTTTTCAAGGACGGTCAGC 59.761 55.000 10.76 4.62 0.00 4.26
3290 4796 1.123861 ACCAGCAGCAGAACCTCAGA 61.124 55.000 0.00 0.00 0.00 3.27
3391 4898 2.569059 CGATCATTGCATGTCCCTTCT 58.431 47.619 0.00 0.00 0.00 2.85
3435 4946 0.475632 ACCTGGGAGGGAACACATGA 60.476 55.000 0.00 0.00 40.58 3.07
3438 4949 1.073763 CTGGGAGGGAACACATGACAA 59.926 52.381 0.00 0.00 0.00 3.18
3441 4952 2.154462 GGAGGGAACACATGACAACAG 58.846 52.381 0.00 0.00 0.00 3.16
3467 4982 2.487762 TGAATGAAACCGTCCATGCTTC 59.512 45.455 0.00 0.00 0.00 3.86
3470 4985 2.151202 TGAAACCGTCCATGCTTCTTC 58.849 47.619 0.00 0.00 0.00 2.87
3522 5041 5.069318 TGACCTGTGTATCATTCTTTGCAA 58.931 37.500 0.00 0.00 0.00 4.08
3581 5102 0.180406 AACTGAAGTGTGCCTCCGTT 59.820 50.000 0.00 0.00 0.00 4.44
3582 5103 0.532862 ACTGAAGTGTGCCTCCGTTG 60.533 55.000 0.00 0.00 0.00 4.10
3583 5104 0.532862 CTGAAGTGTGCCTCCGTTGT 60.533 55.000 0.00 0.00 0.00 3.32
3584 5105 0.753867 TGAAGTGTGCCTCCGTTGTA 59.246 50.000 0.00 0.00 0.00 2.41
3585 5106 1.139256 TGAAGTGTGCCTCCGTTGTAA 59.861 47.619 0.00 0.00 0.00 2.41
3586 5107 2.224426 TGAAGTGTGCCTCCGTTGTAAT 60.224 45.455 0.00 0.00 0.00 1.89
3587 5108 2.561478 AGTGTGCCTCCGTTGTAATT 57.439 45.000 0.00 0.00 0.00 1.40
3794 5318 5.551233 TGTATATGTGGGCTTATGCTTCTC 58.449 41.667 0.13 0.00 39.59 2.87
3814 5338 7.766738 GCTTCTCTTTTGTACTAGCTTTATCCT 59.233 37.037 0.00 0.00 0.00 3.24
3833 5357 3.500680 TCCTTTTGTTACGATGCTTCACC 59.499 43.478 0.08 0.00 0.00 4.02
3888 5412 1.120530 GGAGGGCCGATGAAACTCTA 58.879 55.000 0.00 0.00 0.00 2.43
3903 5427 7.953158 TGAAACTCTACTCAGAAACTCATTG 57.047 36.000 0.00 0.00 0.00 2.82
3926 5450 3.693085 CAGTGGATCCAACTTTGATCCTG 59.307 47.826 18.20 12.18 43.82 3.86
3927 5451 3.019564 GTGGATCCAACTTTGATCCTGG 58.980 50.000 18.20 0.00 43.82 4.45
3936 5460 5.246883 CCAACTTTGATCCTGGGAAAATTCT 59.753 40.000 0.00 0.00 0.00 2.40
3937 5461 5.990120 ACTTTGATCCTGGGAAAATTCTG 57.010 39.130 0.00 0.00 0.00 3.02
3939 5463 5.478332 ACTTTGATCCTGGGAAAATTCTGAC 59.522 40.000 0.00 0.00 0.00 3.51
3940 5464 4.656100 TGATCCTGGGAAAATTCTGACA 57.344 40.909 0.00 0.00 0.00 3.58
3941 5465 5.197224 TGATCCTGGGAAAATTCTGACAT 57.803 39.130 0.00 0.00 0.00 3.06
3942 5466 6.325993 TGATCCTGGGAAAATTCTGACATA 57.674 37.500 0.00 0.00 0.00 2.29
3943 5467 6.359804 TGATCCTGGGAAAATTCTGACATAG 58.640 40.000 0.00 0.00 0.00 2.23
3944 5468 5.779241 TCCTGGGAAAATTCTGACATAGT 57.221 39.130 0.00 0.00 0.00 2.12
3945 5469 6.139679 TCCTGGGAAAATTCTGACATAGTT 57.860 37.500 0.00 0.00 0.00 2.24
3946 5470 7.265599 TCCTGGGAAAATTCTGACATAGTTA 57.734 36.000 0.00 0.00 0.00 2.24
3947 5471 7.872138 TCCTGGGAAAATTCTGACATAGTTAT 58.128 34.615 0.00 0.00 0.00 1.89
3948 5472 7.775093 TCCTGGGAAAATTCTGACATAGTTATG 59.225 37.037 0.00 0.00 39.55 1.90
3963 5487 8.011844 ACATAGTTATGTCACATCTAAGCTGA 57.988 34.615 0.00 0.00 42.96 4.26
3964 5488 8.646004 ACATAGTTATGTCACATCTAAGCTGAT 58.354 33.333 0.00 0.00 42.96 2.90
3965 5489 8.923683 CATAGTTATGTCACATCTAAGCTGATG 58.076 37.037 11.48 11.48 46.61 3.07
3976 5500 7.741027 CATCTAAGCTGATGTCCATTATGTT 57.259 36.000 5.99 0.00 39.05 2.71
3977 5501 8.162878 CATCTAAGCTGATGTCCATTATGTTT 57.837 34.615 5.99 0.00 39.05 2.83
3978 5502 7.558161 TCTAAGCTGATGTCCATTATGTTTG 57.442 36.000 0.00 0.00 0.00 2.93
3979 5503 7.112122 TCTAAGCTGATGTCCATTATGTTTGT 58.888 34.615 0.00 0.00 0.00 2.83
3980 5504 5.571784 AGCTGATGTCCATTATGTTTGTG 57.428 39.130 0.00 0.00 0.00 3.33
3981 5505 4.400251 AGCTGATGTCCATTATGTTTGTGG 59.600 41.667 0.00 0.00 0.00 4.17
3982 5506 4.158394 GCTGATGTCCATTATGTTTGTGGT 59.842 41.667 0.00 0.00 34.61 4.16
3983 5507 5.356751 GCTGATGTCCATTATGTTTGTGGTA 59.643 40.000 0.00 0.00 34.61 3.25
3984 5508 6.039717 GCTGATGTCCATTATGTTTGTGGTAT 59.960 38.462 0.00 0.00 34.61 2.73
3985 5509 7.416664 GCTGATGTCCATTATGTTTGTGGTATT 60.417 37.037 0.00 0.00 34.61 1.89
3986 5510 8.359875 TGATGTCCATTATGTTTGTGGTATTT 57.640 30.769 0.00 0.00 34.61 1.40
3987 5511 8.811017 TGATGTCCATTATGTTTGTGGTATTTT 58.189 29.630 0.00 0.00 34.61 1.82
3988 5512 9.651913 GATGTCCATTATGTTTGTGGTATTTTT 57.348 29.630 0.00 0.00 34.61 1.94
4037 5561 9.926751 TTTTTGTTGTTGCATTACATATTTGTG 57.073 25.926 0.00 0.00 36.53 3.33
4038 5562 7.649370 TTGTTGTTGCATTACATATTTGTGG 57.351 32.000 0.00 0.00 36.53 4.17
4039 5563 6.162079 TGTTGTTGCATTACATATTTGTGGG 58.838 36.000 0.00 0.00 36.53 4.61
4040 5564 6.015095 TGTTGTTGCATTACATATTTGTGGGA 60.015 34.615 0.00 0.00 36.53 4.37
4041 5565 6.206395 TGTTGCATTACATATTTGTGGGAG 57.794 37.500 0.00 0.00 36.53 4.30
4042 5566 4.916983 TGCATTACATATTTGTGGGAGC 57.083 40.909 0.00 0.00 36.53 4.70
4043 5567 4.535781 TGCATTACATATTTGTGGGAGCT 58.464 39.130 0.00 0.00 36.53 4.09
4044 5568 4.955450 TGCATTACATATTTGTGGGAGCTT 59.045 37.500 0.00 0.00 36.53 3.74
4045 5569 6.125719 TGCATTACATATTTGTGGGAGCTTA 58.874 36.000 0.00 0.00 36.53 3.09
4046 5570 6.262944 TGCATTACATATTTGTGGGAGCTTAG 59.737 38.462 0.00 0.00 36.53 2.18
4047 5571 6.486657 GCATTACATATTTGTGGGAGCTTAGA 59.513 38.462 0.00 0.00 36.53 2.10
4048 5572 7.175641 GCATTACATATTTGTGGGAGCTTAGAT 59.824 37.037 0.00 0.00 36.53 1.98
4049 5573 8.509690 CATTACATATTTGTGGGAGCTTAGATG 58.490 37.037 0.00 0.00 36.53 2.90
4050 5574 6.006275 ACATATTTGTGGGAGCTTAGATGT 57.994 37.500 0.00 0.00 33.85 3.06
4051 5575 5.824624 ACATATTTGTGGGAGCTTAGATGTG 59.175 40.000 0.00 0.00 33.85 3.21
4052 5576 4.574674 ATTTGTGGGAGCTTAGATGTGA 57.425 40.909 0.00 0.00 0.00 3.58
4053 5577 3.334583 TTGTGGGAGCTTAGATGTGAC 57.665 47.619 0.00 0.00 0.00 3.67
4054 5578 2.256306 TGTGGGAGCTTAGATGTGACA 58.744 47.619 0.00 0.00 0.00 3.58
4055 5579 2.840038 TGTGGGAGCTTAGATGTGACAT 59.160 45.455 0.00 0.00 0.00 3.06
4056 5580 3.118629 TGTGGGAGCTTAGATGTGACATC 60.119 47.826 17.46 17.46 0.00 3.06
4057 5581 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
4058 5582 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
4059 5583 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
4060 5584 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
4061 5585 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
4062 5586 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
4063 5587 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
4064 5588 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
4121 5693 1.002134 CCCGTCCAGCCTTCACATT 60.002 57.895 0.00 0.00 0.00 2.71
4126 5698 2.554032 CGTCCAGCCTTCACATTTTTCT 59.446 45.455 0.00 0.00 0.00 2.52
4127 5699 3.610114 CGTCCAGCCTTCACATTTTTCTG 60.610 47.826 0.00 0.00 0.00 3.02
4162 5734 2.230992 TGCACAACCCTGCATATTTGTC 59.769 45.455 4.45 2.37 42.36 3.18
4167 5739 6.629128 CACAACCCTGCATATTTGTCAATTA 58.371 36.000 4.45 0.00 29.65 1.40
4199 5854 5.466728 ACCGATTAGTATAATGCACTGCAAG 59.533 40.000 8.03 0.00 43.62 4.01
4229 5885 3.330701 AGATTTTCAGTACTGCTCCCCAA 59.669 43.478 18.45 3.14 0.00 4.12
4233 5889 1.623811 TCAGTACTGCTCCCCAAGAAC 59.376 52.381 18.45 0.00 0.00 3.01
4235 5891 1.625818 AGTACTGCTCCCCAAGAACTG 59.374 52.381 0.00 0.00 0.00 3.16
4315 7259 9.614792 AAGAAAATAACAGAACTGTCAACTACT 57.385 29.630 7.93 2.84 44.13 2.57
4316 7260 9.262358 AGAAAATAACAGAACTGTCAACTACTC 57.738 33.333 7.93 1.09 44.13 2.59
4317 7261 7.964604 AAATAACAGAACTGTCAACTACTCC 57.035 36.000 7.93 0.00 44.13 3.85
4318 7262 4.338379 AACAGAACTGTCAACTACTCCC 57.662 45.455 7.93 0.00 44.13 4.30
4319 7263 3.577919 ACAGAACTGTCAACTACTCCCT 58.422 45.455 1.32 0.00 40.24 4.20
4320 7264 3.574826 ACAGAACTGTCAACTACTCCCTC 59.425 47.826 1.32 0.00 40.24 4.30
4321 7265 3.056465 CAGAACTGTCAACTACTCCCTCC 60.056 52.174 0.00 0.00 0.00 4.30
4322 7266 1.546961 ACTGTCAACTACTCCCTCCG 58.453 55.000 0.00 0.00 0.00 4.63
4323 7267 1.203025 ACTGTCAACTACTCCCTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
4324 7268 1.473278 CTGTCAACTACTCCCTCCGTC 59.527 57.143 0.00 0.00 0.00 4.79
4325 7269 0.816373 GTCAACTACTCCCTCCGTCC 59.184 60.000 0.00 0.00 0.00 4.79
4326 7270 0.406750 TCAACTACTCCCTCCGTCCA 59.593 55.000 0.00 0.00 0.00 4.02
4327 7271 0.818296 CAACTACTCCCTCCGTCCAG 59.182 60.000 0.00 0.00 0.00 3.86
4328 7272 0.702902 AACTACTCCCTCCGTCCAGA 59.297 55.000 0.00 0.00 0.00 3.86
4329 7273 0.702902 ACTACTCCCTCCGTCCAGAA 59.297 55.000 0.00 0.00 0.00 3.02
4330 7274 1.076677 ACTACTCCCTCCGTCCAGAAA 59.923 52.381 0.00 0.00 0.00 2.52
4331 7275 2.292323 ACTACTCCCTCCGTCCAGAAAT 60.292 50.000 0.00 0.00 0.00 2.17
4332 7276 2.544844 ACTCCCTCCGTCCAGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
4333 7277 2.108970 ACTCCCTCCGTCCAGAAATAC 58.891 52.381 0.00 0.00 0.00 1.89
4334 7278 2.292323 ACTCCCTCCGTCCAGAAATACT 60.292 50.000 0.00 0.00 0.00 2.12
4335 7279 2.766828 CTCCCTCCGTCCAGAAATACTT 59.233 50.000 0.00 0.00 0.00 2.24
4336 7280 2.500098 TCCCTCCGTCCAGAAATACTTG 59.500 50.000 0.00 0.00 0.00 3.16
4337 7281 2.236395 CCCTCCGTCCAGAAATACTTGT 59.764 50.000 0.00 0.00 0.00 3.16
4338 7282 3.522553 CCTCCGTCCAGAAATACTTGTC 58.477 50.000 0.00 0.00 0.00 3.18
4339 7283 3.056107 CCTCCGTCCAGAAATACTTGTCA 60.056 47.826 0.00 0.00 0.00 3.58
4340 7284 4.383118 CCTCCGTCCAGAAATACTTGTCAT 60.383 45.833 0.00 0.00 0.00 3.06
4341 7285 4.755411 TCCGTCCAGAAATACTTGTCATC 58.245 43.478 0.00 0.00 0.00 2.92
4342 7286 4.221924 TCCGTCCAGAAATACTTGTCATCA 59.778 41.667 0.00 0.00 0.00 3.07
4343 7287 4.935205 CCGTCCAGAAATACTTGTCATCAA 59.065 41.667 0.00 0.00 0.00 2.57
4344 7288 5.411361 CCGTCCAGAAATACTTGTCATCAAA 59.589 40.000 0.00 0.00 32.87 2.69
4345 7289 6.072728 CCGTCCAGAAATACTTGTCATCAAAA 60.073 38.462 0.00 0.00 32.87 2.44
4346 7290 7.362056 CCGTCCAGAAATACTTGTCATCAAAAT 60.362 37.037 0.00 0.00 32.87 1.82
4347 7291 7.482743 CGTCCAGAAATACTTGTCATCAAAATG 59.517 37.037 0.00 0.00 32.87 2.32
4348 7292 8.514594 GTCCAGAAATACTTGTCATCAAAATGA 58.485 33.333 0.00 0.00 39.63 2.57
4349 7293 9.076781 TCCAGAAATACTTGTCATCAAAATGAA 57.923 29.630 0.00 0.00 43.42 2.57
4350 7294 9.865321 CCAGAAATACTTGTCATCAAAATGAAT 57.135 29.630 0.00 0.00 43.42 2.57
4358 7302 9.918630 ACTTGTCATCAAAATGAATAAAAGAGG 57.081 29.630 0.00 0.00 43.42 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 53 7.108194 TCTCTTTATCACGACACCTTCTACTA 58.892 38.462 0.00 0.00 0.00 1.82
100 113 4.579340 AGATCTCACCGCGTCTAATTCTAA 59.421 41.667 4.92 0.00 0.00 2.10
233 246 3.100207 TGGGAATGGATGGAAAGGAAC 57.900 47.619 0.00 0.00 0.00 3.62
277 290 7.284944 GGCTACTAGTAGTTTCAGACTCCATTA 59.715 40.741 26.76 0.00 39.86 1.90
296 313 4.404394 TCATTCGTTCCTTCATGGCTACTA 59.596 41.667 0.00 0.00 35.26 1.82
297 314 3.197766 TCATTCGTTCCTTCATGGCTACT 59.802 43.478 0.00 0.00 35.26 2.57
298 315 3.531538 TCATTCGTTCCTTCATGGCTAC 58.468 45.455 0.00 0.00 35.26 3.58
299 316 3.450817 TCTCATTCGTTCCTTCATGGCTA 59.549 43.478 0.00 0.00 35.26 3.93
300 317 2.237143 TCTCATTCGTTCCTTCATGGCT 59.763 45.455 0.00 0.00 35.26 4.75
301 318 2.632377 TCTCATTCGTTCCTTCATGGC 58.368 47.619 0.00 0.00 35.26 4.40
302 319 4.507710 TCTTCTCATTCGTTCCTTCATGG 58.492 43.478 0.00 0.00 37.10 3.66
304 321 5.587844 CCATTCTTCTCATTCGTTCCTTCAT 59.412 40.000 0.00 0.00 0.00 2.57
305 322 4.937620 CCATTCTTCTCATTCGTTCCTTCA 59.062 41.667 0.00 0.00 0.00 3.02
309 331 2.356069 GGCCATTCTTCTCATTCGTTCC 59.644 50.000 0.00 0.00 0.00 3.62
332 354 1.769098 CGATTACGAGCGGGAGACGA 61.769 60.000 0.00 0.00 43.47 4.20
333 355 1.368969 CGATTACGAGCGGGAGACG 60.369 63.158 0.00 0.00 43.57 4.18
334 356 0.940126 TACGATTACGAGCGGGAGAC 59.060 55.000 0.00 0.00 39.39 3.36
356 378 0.966875 TGATTGCGCTTGCCCTGATT 60.967 50.000 9.73 0.00 38.03 2.57
358 380 2.033911 TGATTGCGCTTGCCCTGA 59.966 55.556 9.73 0.00 38.03 3.86
359 381 2.488355 CTGATTGCGCTTGCCCTG 59.512 61.111 9.73 0.00 38.03 4.45
360 382 3.446570 GCTGATTGCGCTTGCCCT 61.447 61.111 9.73 0.00 38.03 5.19
361 383 3.695022 CTGCTGATTGCGCTTGCCC 62.695 63.158 9.73 0.00 46.63 5.36
362 384 2.202570 CTGCTGATTGCGCTTGCC 60.203 61.111 9.73 0.00 46.63 4.52
363 385 2.879462 GCTGCTGATTGCGCTTGC 60.879 61.111 9.73 6.34 46.63 4.01
364 386 1.514228 CAGCTGCTGATTGCGCTTG 60.514 57.895 24.88 0.00 44.46 4.01
369 391 1.226974 CCATGCAGCTGCTGATTGC 60.227 57.895 36.61 18.37 42.66 3.56
428 450 4.783621 GGCCGGATGTCAGCAGCA 62.784 66.667 5.05 0.00 31.62 4.41
460 482 2.432628 GCTGCAAGTAGCCGTCGT 60.433 61.111 0.00 0.00 44.83 4.34
551 581 0.887836 TCGATCTATCCACCCGTCCG 60.888 60.000 0.00 0.00 0.00 4.79
552 582 0.597072 GTCGATCTATCCACCCGTCC 59.403 60.000 0.00 0.00 0.00 4.79
553 583 1.267261 CTGTCGATCTATCCACCCGTC 59.733 57.143 0.00 0.00 0.00 4.79
554 584 1.319541 CTGTCGATCTATCCACCCGT 58.680 55.000 0.00 0.00 0.00 5.28
631 661 0.918983 GAAGATGGTGGTGGGGATCA 59.081 55.000 0.00 0.00 0.00 2.92
663 693 1.683441 GCGGGAAGGAAGGAAGGAA 59.317 57.895 0.00 0.00 0.00 3.36
829 873 4.251543 GGCATAGAGAGTAGCCTTCTTC 57.748 50.000 0.00 0.00 43.70 2.87
923 968 1.432270 GCCACGCCAAAGCTAGCTAG 61.432 60.000 19.70 16.84 36.60 3.42
1155 1212 4.057428 GCCACCGAGTCGCTCAGT 62.057 66.667 7.12 0.00 0.00 3.41
1158 1215 3.991536 GAAGGCCACCGAGTCGCTC 62.992 68.421 5.01 0.00 0.00 5.03
1209 1266 2.992114 AGCCTGTCGAAGTCGCCT 60.992 61.111 0.00 0.00 39.60 5.52
1350 1407 1.548973 CCGGATTAGCATCGTCGTGC 61.549 60.000 0.00 10.56 45.38 5.34
1351 1408 0.030235 TCCGGATTAGCATCGTCGTG 59.970 55.000 0.00 0.00 0.00 4.35
1500 1557 3.458118 TCCATGGACCGAGGTTGATAATT 59.542 43.478 11.44 0.00 0.00 1.40
1514 1571 0.107848 AATTCGGTCGGTCCATGGAC 60.108 55.000 33.14 33.14 43.87 4.02
1541 1603 3.570125 TGACGATTAGCCAGTATCCTGAG 59.430 47.826 0.00 0.00 41.50 3.35
1542 1604 3.562182 TGACGATTAGCCAGTATCCTGA 58.438 45.455 0.00 0.00 41.50 3.86
1648 1710 1.472376 GCAGCAGGTGATCAGTACTCC 60.472 57.143 3.02 0.00 0.00 3.85
1649 1711 1.480137 AGCAGCAGGTGATCAGTACTC 59.520 52.381 3.02 0.00 0.00 2.59
1650 1712 1.566211 AGCAGCAGGTGATCAGTACT 58.434 50.000 3.02 0.00 0.00 2.73
1651 1713 2.801342 GCTAGCAGCAGGTGATCAGTAC 60.801 54.545 10.63 0.00 41.89 2.73
1652 1714 1.410517 GCTAGCAGCAGGTGATCAGTA 59.589 52.381 10.63 0.00 41.89 2.74
1653 1715 0.177604 GCTAGCAGCAGGTGATCAGT 59.822 55.000 10.63 0.00 41.89 3.41
1654 1716 0.464870 AGCTAGCAGCAGGTGATCAG 59.535 55.000 18.83 0.00 45.56 2.90
1655 1717 1.685517 CTAGCTAGCAGCAGGTGATCA 59.314 52.381 18.83 0.00 45.56 2.92
1656 1718 1.686052 ACTAGCTAGCAGCAGGTGATC 59.314 52.381 20.91 0.00 45.56 2.92
1657 1719 1.786937 ACTAGCTAGCAGCAGGTGAT 58.213 50.000 20.91 0.00 45.56 3.06
1716 1782 5.966742 AAGGCCAGAAGTTATGAGTTTTC 57.033 39.130 5.01 0.00 0.00 2.29
1735 1801 5.564714 GCACTAGCTCGCCCTTTATTAAGG 61.565 50.000 3.38 3.38 43.25 2.69
1898 1964 2.606108 CTGGGCGACAAAATTAAAGGC 58.394 47.619 0.00 0.00 0.00 4.35
1918 1984 0.601046 GCTTTCTTGCAAAGGGGTGC 60.601 55.000 0.00 0.00 46.24 5.01
1988 2208 3.991605 CGTGTCTACGGAATTTCCTTG 57.008 47.619 13.45 1.64 46.23 3.61
2010 3465 0.390998 TGCCGAAATCGTGCTCATGA 60.391 50.000 14.27 0.00 36.80 3.07
2180 3656 2.417586 TCGTGGTATGTCGTGAGTACAG 59.582 50.000 0.00 0.00 0.00 2.74
2230 3706 0.590984 TTTGTGTCATTGTGTGCGCG 60.591 50.000 0.00 0.00 0.00 6.86
2285 3762 3.449227 CAGCCAGCCTGCACCATG 61.449 66.667 0.00 0.00 34.21 3.66
2356 3833 3.739613 GATCCCACCCCACCCCAC 61.740 72.222 0.00 0.00 0.00 4.61
2357 3834 3.611974 ATGATCCCACCCCACCCCA 62.612 63.158 0.00 0.00 0.00 4.96
2358 3835 2.699938 ATGATCCCACCCCACCCC 60.700 66.667 0.00 0.00 0.00 4.95
2359 3836 1.580066 TTCATGATCCCACCCCACCC 61.580 60.000 0.00 0.00 0.00 4.61
2360 3837 0.557729 ATTCATGATCCCACCCCACC 59.442 55.000 0.00 0.00 0.00 4.61
2361 3838 1.215173 TCATTCATGATCCCACCCCAC 59.785 52.381 0.00 0.00 0.00 4.61
2362 3839 1.496001 CTCATTCATGATCCCACCCCA 59.504 52.381 0.00 0.00 36.02 4.96
2363 3840 1.776667 TCTCATTCATGATCCCACCCC 59.223 52.381 0.00 0.00 36.02 4.95
2364 3841 3.683802 GATCTCATTCATGATCCCACCC 58.316 50.000 0.00 0.00 36.02 4.61
2365 3842 3.007290 TCGATCTCATTCATGATCCCACC 59.993 47.826 0.00 0.00 36.62 4.61
2366 3843 4.263018 TCGATCTCATTCATGATCCCAC 57.737 45.455 0.00 0.00 36.62 4.61
2367 3844 4.529377 TGATCGATCTCATTCATGATCCCA 59.471 41.667 25.02 0.00 36.62 4.37
2368 3845 5.082251 TGATCGATCTCATTCATGATCCC 57.918 43.478 25.02 0.00 36.62 3.85
2462 3939 0.447406 CATTTGGATCACGCGAGCAA 59.553 50.000 15.93 1.44 0.00 3.91
2463 3940 1.980951 GCATTTGGATCACGCGAGCA 61.981 55.000 15.93 0.00 0.00 4.26
2672 4156 2.289444 GCTTGCAAGTGGGTACAGTAGA 60.289 50.000 26.55 0.00 0.00 2.59
2699 4183 1.193874 GCATATACCCTTAACGTGCGC 59.806 52.381 0.00 0.00 0.00 6.09
2721 4205 5.295292 GCTTGTGATAGAATACACACAGCAT 59.705 40.000 18.85 0.00 44.81 3.79
2724 4208 5.292834 CCAGCTTGTGATAGAATACACACAG 59.707 44.000 0.00 0.00 44.81 3.66
2773 4263 1.359130 CCCCAAACATCCTCCCTTTCT 59.641 52.381 0.00 0.00 0.00 2.52
2774 4264 1.619704 CCCCCAAACATCCTCCCTTTC 60.620 57.143 0.00 0.00 0.00 2.62
2821 4311 8.880750 GCTAGAGTTAATTAGTTTTGACCGATT 58.119 33.333 0.00 0.00 0.00 3.34
2825 4315 7.119262 TGCTGCTAGAGTTAATTAGTTTTGACC 59.881 37.037 0.00 0.00 0.00 4.02
2878 4368 2.558359 GTCAAATTGGAAGGGGACACTG 59.442 50.000 0.00 0.00 0.00 3.66
2902 4392 6.050432 ACTGAACATTTTTACACCTACACGA 58.950 36.000 0.00 0.00 0.00 4.35
2904 4394 6.849305 CGAACTGAACATTTTTACACCTACAC 59.151 38.462 0.00 0.00 0.00 2.90
2910 4400 5.177725 ACCCGAACTGAACATTTTTACAC 57.822 39.130 0.00 0.00 0.00 2.90
2922 4415 9.675464 AAGTAATAATTCATTAACCCGAACTGA 57.325 29.630 0.00 0.00 30.84 3.41
2931 4424 7.927048 ACGAGGGCAAGTAATAATTCATTAAC 58.073 34.615 0.00 0.00 30.84 2.01
2977 4476 0.659427 TCGAAACGTCACGTGAGAGT 59.341 50.000 20.73 18.95 39.99 3.24
2998 4497 1.802337 CGGACACCTCGTTCTGGACA 61.802 60.000 0.00 0.00 0.00 4.02
3001 4500 1.372997 CACGGACACCTCGTTCTGG 60.373 63.158 0.00 0.00 38.94 3.86
3137 4643 0.698238 TGATTGGGTGGGAAGGAGTG 59.302 55.000 0.00 0.00 0.00 3.51
3378 4885 2.747460 GCGCAGAAGGGACATGCA 60.747 61.111 0.30 0.00 39.97 3.96
3435 4946 3.550639 CGGTTTCATTCATGCACTGTTGT 60.551 43.478 0.00 0.00 0.00 3.32
3438 4949 2.226437 GACGGTTTCATTCATGCACTGT 59.774 45.455 0.00 4.05 34.78 3.55
3441 4952 1.539388 TGGACGGTTTCATTCATGCAC 59.461 47.619 0.00 0.00 0.00 4.57
3476 4991 7.759433 GTCAATGGACAAGAAAAAGAAACAAGA 59.241 33.333 0.00 0.00 43.73 3.02
3477 4992 7.010460 GGTCAATGGACAAGAAAAAGAAACAAG 59.990 37.037 1.86 0.00 46.17 3.16
3478 4993 6.816140 GGTCAATGGACAAGAAAAAGAAACAA 59.184 34.615 1.86 0.00 46.17 2.83
3480 4995 6.476706 CAGGTCAATGGACAAGAAAAAGAAAC 59.523 38.462 1.86 0.00 46.17 2.78
3481 4996 6.154363 ACAGGTCAATGGACAAGAAAAAGAAA 59.846 34.615 1.86 0.00 46.17 2.52
3547 5066 8.020819 CACACTTCAGTTTTTCTTCACAGTAAA 58.979 33.333 0.00 0.00 0.00 2.01
3548 5067 7.526608 CACACTTCAGTTTTTCTTCACAGTAA 58.473 34.615 0.00 0.00 0.00 2.24
3550 5069 5.619981 GCACACTTCAGTTTTTCTTCACAGT 60.620 40.000 0.00 0.00 0.00 3.55
3551 5070 4.795278 GCACACTTCAGTTTTTCTTCACAG 59.205 41.667 0.00 0.00 0.00 3.66
3552 5071 4.380444 GGCACACTTCAGTTTTTCTTCACA 60.380 41.667 0.00 0.00 0.00 3.58
3553 5072 4.105486 GGCACACTTCAGTTTTTCTTCAC 58.895 43.478 0.00 0.00 0.00 3.18
3554 5073 4.016444 AGGCACACTTCAGTTTTTCTTCA 58.984 39.130 0.00 0.00 0.00 3.02
3557 5076 2.952310 GGAGGCACACTTCAGTTTTTCT 59.048 45.455 0.00 0.00 0.00 2.52
3558 5077 2.287009 CGGAGGCACACTTCAGTTTTTC 60.287 50.000 0.00 0.00 0.00 2.29
3581 5102 7.041303 TGCTACACACGGAATTTACAAATTACA 60.041 33.333 9.68 0.00 38.81 2.41
3582 5103 7.299586 TGCTACACACGGAATTTACAAATTAC 58.700 34.615 0.05 0.17 38.64 1.89
3583 5104 7.436430 TGCTACACACGGAATTTACAAATTA 57.564 32.000 0.05 0.00 38.64 1.40
3584 5105 6.320494 TGCTACACACGGAATTTACAAATT 57.680 33.333 0.00 0.00 41.06 1.82
3585 5106 5.950758 TGCTACACACGGAATTTACAAAT 57.049 34.783 0.00 0.00 0.00 2.32
3586 5107 5.950758 ATGCTACACACGGAATTTACAAA 57.049 34.783 0.00 0.00 0.00 2.83
3587 5108 5.694816 CAATGCTACACACGGAATTTACAA 58.305 37.500 0.00 0.00 0.00 2.41
3814 5338 5.761234 AGTTAGGTGAAGCATCGTAACAAAA 59.239 36.000 9.79 0.00 37.37 2.44
3869 5393 1.120530 TAGAGTTTCATCGGCCCTCC 58.879 55.000 0.00 0.00 0.00 4.30
3888 5412 3.144506 CCACTGCAATGAGTTTCTGAGT 58.855 45.455 0.00 0.00 0.00 3.41
3903 5427 3.772060 GATCAAAGTTGGATCCACTGC 57.228 47.619 15.91 8.01 36.09 4.40
3939 5463 8.923683 CATCAGCTTAGATGTGACATAACTATG 58.076 37.037 0.00 0.92 40.35 2.23
3953 5477 7.776969 ACAAACATAATGGACATCAGCTTAGAT 59.223 33.333 0.00 0.00 0.00 1.98
3954 5478 7.066163 CACAAACATAATGGACATCAGCTTAGA 59.934 37.037 0.00 0.00 0.00 2.10
3955 5479 7.191551 CACAAACATAATGGACATCAGCTTAG 58.808 38.462 0.00 0.00 0.00 2.18
3956 5480 6.095300 CCACAAACATAATGGACATCAGCTTA 59.905 38.462 0.00 0.00 35.33 3.09
3957 5481 5.105635 CCACAAACATAATGGACATCAGCTT 60.106 40.000 0.00 0.00 35.33 3.74
3958 5482 4.400251 CCACAAACATAATGGACATCAGCT 59.600 41.667 0.00 0.00 35.33 4.24
3959 5483 4.158394 ACCACAAACATAATGGACATCAGC 59.842 41.667 0.00 0.00 36.94 4.26
3960 5484 5.902613 ACCACAAACATAATGGACATCAG 57.097 39.130 0.00 0.00 36.94 2.90
3961 5485 7.953005 AATACCACAAACATAATGGACATCA 57.047 32.000 0.00 0.00 36.94 3.07
3962 5486 9.651913 AAAAATACCACAAACATAATGGACATC 57.348 29.630 0.00 0.00 36.94 3.06
4011 5535 9.926751 CACAAATATGTAATGCAACAACAAAAA 57.073 25.926 0.00 0.00 37.82 1.94
4012 5536 8.554528 CCACAAATATGTAATGCAACAACAAAA 58.445 29.630 0.00 0.00 37.82 2.44
4013 5537 7.172190 CCCACAAATATGTAATGCAACAACAAA 59.828 33.333 0.00 0.00 37.82 2.83
4014 5538 6.648310 CCCACAAATATGTAATGCAACAACAA 59.352 34.615 0.00 0.00 37.82 2.83
4015 5539 6.015095 TCCCACAAATATGTAATGCAACAACA 60.015 34.615 0.00 0.00 37.82 3.33
4016 5540 6.393990 TCCCACAAATATGTAATGCAACAAC 58.606 36.000 0.00 0.00 37.82 3.32
4017 5541 6.596309 TCCCACAAATATGTAATGCAACAA 57.404 33.333 0.00 0.00 37.82 2.83
4018 5542 5.394005 GCTCCCACAAATATGTAATGCAACA 60.394 40.000 0.00 0.00 37.82 3.33
4019 5543 5.043248 GCTCCCACAAATATGTAATGCAAC 58.957 41.667 0.00 0.00 37.82 4.17
4020 5544 4.955450 AGCTCCCACAAATATGTAATGCAA 59.045 37.500 0.00 0.00 37.82 4.08
4021 5545 4.535781 AGCTCCCACAAATATGTAATGCA 58.464 39.130 0.00 0.00 37.82 3.96
4022 5546 5.520376 AAGCTCCCACAAATATGTAATGC 57.480 39.130 0.00 0.00 37.82 3.56
4023 5547 8.509690 CATCTAAGCTCCCACAAATATGTAATG 58.490 37.037 0.00 0.00 37.82 1.90
4024 5548 8.220559 ACATCTAAGCTCCCACAAATATGTAAT 58.779 33.333 0.00 0.00 37.82 1.89
4025 5549 7.498900 CACATCTAAGCTCCCACAAATATGTAA 59.501 37.037 0.00 0.00 37.82 2.41
4026 5550 6.992123 CACATCTAAGCTCCCACAAATATGTA 59.008 38.462 0.00 0.00 37.82 2.29
4027 5551 5.824624 CACATCTAAGCTCCCACAAATATGT 59.175 40.000 0.00 0.00 41.61 2.29
4028 5552 6.017605 GTCACATCTAAGCTCCCACAAATATG 60.018 42.308 0.00 0.00 0.00 1.78
4029 5553 6.058183 GTCACATCTAAGCTCCCACAAATAT 58.942 40.000 0.00 0.00 0.00 1.28
4030 5554 5.045942 TGTCACATCTAAGCTCCCACAAATA 60.046 40.000 0.00 0.00 0.00 1.40
4031 5555 4.263462 TGTCACATCTAAGCTCCCACAAAT 60.263 41.667 0.00 0.00 0.00 2.32
4032 5556 3.072330 TGTCACATCTAAGCTCCCACAAA 59.928 43.478 0.00 0.00 0.00 2.83
4033 5557 2.637382 TGTCACATCTAAGCTCCCACAA 59.363 45.455 0.00 0.00 0.00 3.33
4034 5558 2.256306 TGTCACATCTAAGCTCCCACA 58.744 47.619 0.00 0.00 0.00 4.17
4035 5559 3.462021 GATGTCACATCTAAGCTCCCAC 58.538 50.000 10.81 0.00 0.00 4.61
4036 5560 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
4037 5561 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
4038 5562 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
4039 5563 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
4067 5591 9.950496 ATCAGTTTGTCTAATTCACAACTAGAT 57.050 29.630 0.00 4.49 33.42 1.98
4070 5594 9.990360 TGTATCAGTTTGTCTAATTCACAACTA 57.010 29.630 3.00 0.00 33.42 2.24
4071 5595 8.902540 TGTATCAGTTTGTCTAATTCACAACT 57.097 30.769 3.00 2.57 33.42 3.16
4072 5596 8.774586 ACTGTATCAGTTTGTCTAATTCACAAC 58.225 33.333 3.00 0.78 42.59 3.32
4073 5597 8.902540 ACTGTATCAGTTTGTCTAATTCACAA 57.097 30.769 0.00 0.00 42.59 3.33
4089 5613 1.411612 GGACGGGGGTAACTGTATCAG 59.588 57.143 0.00 0.00 37.52 2.90
4090 5614 1.273154 TGGACGGGGGTAACTGTATCA 60.273 52.381 0.00 0.00 0.00 2.15
4091 5615 1.411612 CTGGACGGGGGTAACTGTATC 59.588 57.143 0.00 0.00 0.00 2.24
4105 5629 2.554032 AGAAAAATGTGAAGGCTGGACG 59.446 45.455 0.00 0.00 0.00 4.79
4121 5693 4.037327 TGCACCAAATCATCGAACAGAAAA 59.963 37.500 0.00 0.00 0.00 2.29
4126 5698 2.225467 TGTGCACCAAATCATCGAACA 58.775 42.857 15.69 0.00 0.00 3.18
4127 5699 2.979813 GTTGTGCACCAAATCATCGAAC 59.020 45.455 15.69 3.98 34.07 3.95
4162 5734 9.938280 TTATACTAATCGGTGGGAGAATAATTG 57.062 33.333 0.00 0.00 0.00 2.32
4167 5739 6.013725 TGCATTATACTAATCGGTGGGAGAAT 60.014 38.462 0.00 0.00 0.00 2.40
4190 5762 0.036010 TCTAAGGGCTCTTGCAGTGC 60.036 55.000 9.76 8.58 41.91 4.40
4199 5854 4.572795 GCAGTACTGAAAATCTAAGGGCTC 59.427 45.833 27.08 0.00 0.00 4.70
4229 5885 5.585390 CAAAGATTTGTGCAGTTCAGTTCT 58.415 37.500 0.00 0.00 33.59 3.01
4253 5909 5.069119 TGACAGAGAGAAGAAACACTGCTAA 59.931 40.000 0.00 0.00 34.02 3.09
4259 5915 7.251704 TGAAATTGACAGAGAGAAGAAACAC 57.748 36.000 0.00 0.00 0.00 3.32
4315 7259 2.500098 CAAGTATTTCTGGACGGAGGGA 59.500 50.000 0.00 0.00 0.00 4.20
4316 7260 2.236395 ACAAGTATTTCTGGACGGAGGG 59.764 50.000 0.00 0.00 0.00 4.30
4317 7261 3.056107 TGACAAGTATTTCTGGACGGAGG 60.056 47.826 0.00 0.00 0.00 4.30
4318 7262 4.188247 TGACAAGTATTTCTGGACGGAG 57.812 45.455 0.00 0.00 0.00 4.63
4319 7263 4.221924 TGATGACAAGTATTTCTGGACGGA 59.778 41.667 0.00 0.00 0.00 4.69
4320 7264 4.503910 TGATGACAAGTATTTCTGGACGG 58.496 43.478 0.00 0.00 0.00 4.79
4321 7265 6.480524 TTTGATGACAAGTATTTCTGGACG 57.519 37.500 0.00 0.00 37.32 4.79
4322 7266 8.514594 TCATTTTGATGACAAGTATTTCTGGAC 58.485 33.333 0.00 0.00 37.32 4.02
4323 7267 8.634335 TCATTTTGATGACAAGTATTTCTGGA 57.366 30.769 0.00 0.00 37.32 3.86
4324 7268 9.865321 ATTCATTTTGATGACAAGTATTTCTGG 57.135 29.630 0.00 0.00 37.32 3.86
4332 7276 9.918630 CCTCTTTTATTCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16


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

AutoCloner maintained by Alex Coulton.