Multiple sequence alignment - TraesCS5B01G287700

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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 TraesCS5B01G287700 chr5B 100.000 3475 0 0 1 3475 473643524 473640050 0.000000e+00 6418.0
1 TraesCS5B01G287700 chr5A 95.187 2036 69 14 896 2926 495869227 495867216 0.000000e+00 3190.0
2 TraesCS5B01G287700 chr5A 93.143 525 28 7 15 534 495869831 495869310 0.000000e+00 763.0
3 TraesCS5B01G287700 chr5A 92.357 471 29 3 2999 3465 495867216 495866749 0.000000e+00 664.0
4 TraesCS5B01G287700 chr5D 93.155 2060 82 27 15 2064 393806657 393804647 0.000000e+00 2968.0
5 TraesCS5B01G287700 chr5D 93.786 869 38 5 2062 2926 393804545 393803689 0.000000e+00 1291.0
6 TraesCS5B01G287700 chr5D 92.990 485 20 8 2999 3475 393803689 393803211 0.000000e+00 695.0
7 TraesCS5B01G287700 chr2A 94.545 165 7 1 2702 2864 578387555 578387719 1.600000e-63 254.0
8 TraesCS5B01G287700 chr2A 93.452 168 8 2 2697 2862 70985750 70985584 2.680000e-61 246.0
9 TraesCS5B01G287700 chr4B 92.353 170 11 1 2695 2862 178081095 178081264 1.250000e-59 241.0
10 TraesCS5B01G287700 chr4B 91.765 170 12 1 2700 2867 159566856 159566687 5.800000e-58 235.0
11 TraesCS5B01G287700 chr4B 100.000 39 0 0 2928 2966 209128815 209128777 4.810000e-09 73.1
12 TraesCS5B01G287700 chr4B 100.000 39 0 0 2928 2966 209277878 209277840 4.810000e-09 73.1
13 TraesCS5B01G287700 chr1B 92.771 166 10 1 2702 2865 533863225 533863060 4.480000e-59 239.0
14 TraesCS5B01G287700 chr1A 91.813 171 10 3 2695 2862 71070764 71070595 5.800000e-58 235.0
15 TraesCS5B01G287700 chr4A 91.765 170 11 2 2699 2866 150653310 150653478 2.090000e-57 233.0
16 TraesCS5B01G287700 chrUn 100.000 39 0 0 2928 2966 86472322 86472360 4.810000e-09 73.1
17 TraesCS5B01G287700 chrUn 100.000 39 0 0 2928 2966 221542865 221542903 4.810000e-09 73.1
18 TraesCS5B01G287700 chrUn 100.000 39 0 0 2928 2966 446966945 446966983 4.810000e-09 73.1
19 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 86517652 86517687 2.240000e-07 67.6
20 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 206785169 206785204 2.240000e-07 67.6
21 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 301688389 301688424 2.240000e-07 67.6
22 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 312173176 312173211 2.240000e-07 67.6
23 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 345388131 345388096 2.240000e-07 67.6
24 TraesCS5B01G287700 chrUn 100.000 36 0 0 2964 2999 444295923 444295888 2.240000e-07 67.6
25 TraesCS5B01G287700 chr7D 100.000 39 0 0 2928 2966 203539215 203539177 4.810000e-09 73.1
26 TraesCS5B01G287700 chr4D 100.000 39 0 0 2928 2966 123494336 123494374 4.810000e-09 73.1
27 TraesCS5B01G287700 chr4D 100.000 39 0 0 2928 2966 450986314 450986276 4.810000e-09 73.1
28 TraesCS5B01G287700 chr4D 100.000 36 0 0 2964 2999 123290225 123290260 2.240000e-07 67.6
29 TraesCS5B01G287700 chr4D 100.000 36 0 0 2964 2999 123321994 123322029 2.240000e-07 67.6
30 TraesCS5B01G287700 chr3D 100.000 39 0 0 2928 2966 308531714 308531752 4.810000e-09 73.1
31 TraesCS5B01G287700 chr6D 100.000 36 0 0 2964 2999 124504043 124504078 2.240000e-07 67.6


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 TraesCS5B01G287700 chr5B 473640050 473643524 3474 True 6418.000000 6418 100.000000 1 3475 1 chr5B.!!$R1 3474
1 TraesCS5B01G287700 chr5A 495866749 495869831 3082 True 1539.000000 3190 93.562333 15 3465 3 chr5A.!!$R1 3450
2 TraesCS5B01G287700 chr5D 393803211 393806657 3446 True 1651.333333 2968 93.310333 15 3475 3 chr5D.!!$R1 3460

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
583 589 0.040514 TGCGCCAGTTTTGTTCATCG 60.041 50.0 4.18 0.0 0.00 3.84 F
1919 1929 0.108804 TAGCACCGCTGAGCTGTAAC 60.109 55.0 10.18 0.0 41.97 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2202 0.313987 GCCCCCGAAGTTCAAAACTG 59.686 55.0 3.32 0.00 41.91 3.16 R
2954 3077 0.034616 AGACCAGCACTGAACAGAGC 59.965 55.0 14.39 14.39 43.84 4.09 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
113 115 4.798682 AGATCCCCCGGAACCGCT 62.799 66.667 0.73 0.00 34.34 5.52
147 149 2.299582 CAGCTCGATCCATCCAATCTCT 59.700 50.000 0.00 0.00 0.00 3.10
150 152 3.244009 GCTCGATCCATCCAATCTCTCAA 60.244 47.826 0.00 0.00 0.00 3.02
172 174 2.640457 CGCGTTTCGATTTCGCCG 60.640 61.111 18.40 12.23 45.85 6.46
218 222 2.560542 CCCTTCCTCTGAATCGATCGAT 59.439 50.000 24.60 24.60 36.23 3.59
224 228 1.270826 TCTGAATCGATCGATCAGCCC 59.729 52.381 31.28 20.46 33.73 5.19
287 291 1.448069 GAAATCGCCCTCTCTCCCC 59.552 63.158 0.00 0.00 0.00 4.81
288 292 2.370647 GAAATCGCCCTCTCTCCCCG 62.371 65.000 0.00 0.00 0.00 5.73
340 346 1.300080 TTCCGTCCCGTCGTTGTTC 60.300 57.895 0.00 0.00 0.00 3.18
413 419 1.279271 CCTGAAATTCACGGAGAGGGT 59.721 52.381 5.83 0.00 0.00 4.34
537 543 2.019984 ACTCTTACCCTAGGTTACGCG 58.980 52.381 3.53 3.53 37.09 6.01
553 559 5.178252 GGTTACGCGTATCTGTCTGTATCTA 59.822 44.000 21.30 0.00 0.00 1.98
554 560 6.128336 GGTTACGCGTATCTGTCTGTATCTAT 60.128 42.308 21.30 0.00 0.00 1.98
555 561 5.533533 ACGCGTATCTGTCTGTATCTATC 57.466 43.478 11.67 0.00 0.00 2.08
556 562 4.091655 ACGCGTATCTGTCTGTATCTATCG 59.908 45.833 11.67 0.00 0.00 2.92
557 563 4.492732 CGCGTATCTGTCTGTATCTATCGG 60.493 50.000 0.00 0.00 0.00 4.18
558 564 4.392445 GCGTATCTGTCTGTATCTATCGGT 59.608 45.833 0.00 0.00 0.00 4.69
560 566 6.258287 GCGTATCTGTCTGTATCTATCGGTAT 59.742 42.308 0.00 0.00 0.00 2.73
562 568 8.666573 CGTATCTGTCTGTATCTATCGGTATTT 58.333 37.037 0.00 0.00 0.00 1.40
565 571 9.698309 ATCTGTCTGTATCTATCGGTATTTTTG 57.302 33.333 0.00 0.00 0.00 2.44
566 572 7.652105 TCTGTCTGTATCTATCGGTATTTTTGC 59.348 37.037 0.00 0.00 0.00 3.68
567 573 6.419710 TGTCTGTATCTATCGGTATTTTTGCG 59.580 38.462 0.00 0.00 0.00 4.85
568 574 5.404366 TCTGTATCTATCGGTATTTTTGCGC 59.596 40.000 0.00 0.00 0.00 6.09
569 575 4.449743 TGTATCTATCGGTATTTTTGCGCC 59.550 41.667 4.18 0.00 0.00 6.53
570 576 2.907634 TCTATCGGTATTTTTGCGCCA 58.092 42.857 4.18 0.00 0.00 5.69
571 577 2.869801 TCTATCGGTATTTTTGCGCCAG 59.130 45.455 4.18 0.00 0.00 4.85
572 578 1.459450 ATCGGTATTTTTGCGCCAGT 58.541 45.000 4.18 0.00 0.00 4.00
573 579 1.240256 TCGGTATTTTTGCGCCAGTT 58.760 45.000 4.18 0.00 0.00 3.16
574 580 1.609555 TCGGTATTTTTGCGCCAGTTT 59.390 42.857 4.18 0.00 0.00 2.66
575 581 2.034812 TCGGTATTTTTGCGCCAGTTTT 59.965 40.909 4.18 0.00 0.00 2.43
576 582 2.154772 CGGTATTTTTGCGCCAGTTTTG 59.845 45.455 4.18 0.00 0.00 2.44
577 583 3.127589 GGTATTTTTGCGCCAGTTTTGT 58.872 40.909 4.18 0.00 0.00 2.83
578 584 3.558006 GGTATTTTTGCGCCAGTTTTGTT 59.442 39.130 4.18 0.00 0.00 2.83
579 585 3.942539 ATTTTTGCGCCAGTTTTGTTC 57.057 38.095 4.18 0.00 0.00 3.18
580 586 2.370281 TTTTGCGCCAGTTTTGTTCA 57.630 40.000 4.18 0.00 0.00 3.18
581 587 2.593346 TTTGCGCCAGTTTTGTTCAT 57.407 40.000 4.18 0.00 0.00 2.57
582 588 2.132740 TTGCGCCAGTTTTGTTCATC 57.867 45.000 4.18 0.00 0.00 2.92
583 589 0.040514 TGCGCCAGTTTTGTTCATCG 60.041 50.000 4.18 0.00 0.00 3.84
584 590 0.729140 GCGCCAGTTTTGTTCATCGG 60.729 55.000 0.00 0.00 0.00 4.18
585 591 0.591170 CGCCAGTTTTGTTCATCGGT 59.409 50.000 0.00 0.00 0.00 4.69
598 604 5.309638 TGTTCATCGGTATTTTTCCAGTGA 58.690 37.500 0.00 0.00 0.00 3.41
599 605 5.943416 TGTTCATCGGTATTTTTCCAGTGAT 59.057 36.000 0.00 0.00 0.00 3.06
600 606 6.128035 TGTTCATCGGTATTTTTCCAGTGATG 60.128 38.462 0.00 0.00 34.70 3.07
601 607 5.496556 TCATCGGTATTTTTCCAGTGATGT 58.503 37.500 0.00 0.00 34.92 3.06
614 620 5.630121 TCCAGTGATGTGGAAATTTGTACT 58.370 37.500 0.00 0.00 44.01 2.73
676 682 7.428282 TCTGATGCGTTAATTCACTTGTTAA 57.572 32.000 0.00 0.00 0.00 2.01
677 683 8.039603 TCTGATGCGTTAATTCACTTGTTAAT 57.960 30.769 0.00 0.00 0.00 1.40
678 684 8.511321 TCTGATGCGTTAATTCACTTGTTAATT 58.489 29.630 0.00 0.00 0.00 1.40
692 698 4.481930 TGTTAATTTTCAGAGTGTGCGG 57.518 40.909 0.00 0.00 0.00 5.69
718 724 6.697641 TTTTCAGGGTAAACTCTCATACCT 57.302 37.500 2.34 0.00 41.13 3.08
721 727 6.337185 TCAGGGTAAACTCTCATACCTAGA 57.663 41.667 0.00 0.00 41.13 2.43
722 728 6.366340 TCAGGGTAAACTCTCATACCTAGAG 58.634 44.000 0.00 0.00 44.99 2.43
723 729 5.536916 CAGGGTAAACTCTCATACCTAGAGG 59.463 48.000 5.21 0.00 43.98 3.69
727 733 4.883021 AACTCTCATACCTAGAGGACCA 57.117 45.455 1.60 0.00 43.98 4.02
746 752 5.179452 ACCACCTTAATGTCACAATAGCT 57.821 39.130 0.00 0.00 0.00 3.32
747 753 6.308015 ACCACCTTAATGTCACAATAGCTA 57.692 37.500 0.00 0.00 0.00 3.32
748 754 6.349300 ACCACCTTAATGTCACAATAGCTAG 58.651 40.000 0.00 0.00 0.00 3.42
749 755 6.070194 ACCACCTTAATGTCACAATAGCTAGT 60.070 38.462 0.00 0.00 0.00 2.57
751 757 5.817816 ACCTTAATGTCACAATAGCTAGTGC 59.182 40.000 20.52 5.78 35.76 4.40
752 758 5.817296 CCTTAATGTCACAATAGCTAGTGCA 59.183 40.000 20.52 11.24 42.74 4.57
753 759 6.316140 CCTTAATGTCACAATAGCTAGTGCAA 59.684 38.462 20.52 6.55 42.74 4.08
754 760 7.012704 CCTTAATGTCACAATAGCTAGTGCAAT 59.987 37.037 20.52 7.03 42.74 3.56
755 761 5.746307 ATGTCACAATAGCTAGTGCAATG 57.254 39.130 20.52 11.84 42.74 2.82
756 762 4.578871 TGTCACAATAGCTAGTGCAATGT 58.421 39.130 20.52 5.37 42.74 2.71
761 767 6.652900 TCACAATAGCTAGTGCAATGTTGTAA 59.347 34.615 20.52 0.00 42.74 2.41
767 773 7.031226 AGCTAGTGCAATGTTGTAATATTGG 57.969 36.000 13.54 1.53 42.74 3.16
794 800 4.537135 AGTCATGTACTCGTGTGGATTT 57.463 40.909 0.00 0.00 30.33 2.17
845 851 3.640967 AGGAGATGCTCTATGTTGGTCTC 59.359 47.826 0.00 0.00 0.00 3.36
864 870 1.677552 CAGTTCGGTGCCCTAGGTT 59.322 57.895 8.29 0.00 0.00 3.50
912 918 1.838112 TCCAACTGTCATGAATGGCC 58.162 50.000 0.00 0.00 0.00 5.36
945 952 3.684788 GGACTGCAGTCGTTTGATAATGT 59.315 43.478 34.28 2.86 45.65 2.71
978 985 3.764237 TGGACAGGGTCTAACTTGTTC 57.236 47.619 0.00 0.00 32.47 3.18
1044 1051 5.510430 AGATTGGGTTATTTCTTGGTCCTC 58.490 41.667 0.00 0.00 0.00 3.71
1192 1199 2.103094 GACACTCCATGGCACTATAGCA 59.897 50.000 6.96 0.00 35.73 3.49
1216 1223 1.536940 TGGTGTCGATCTCGTGGTAA 58.463 50.000 0.00 0.00 40.80 2.85
1230 1237 2.094130 CGTGGTAAGGTCTTCTTCTCCC 60.094 54.545 0.00 0.00 36.93 4.30
1297 1304 1.816074 TGTTGGCAGGGAACGATAAC 58.184 50.000 0.00 0.00 0.00 1.89
1840 1850 8.589335 TCACATTCTCTCTTGTAACTTGTAAC 57.411 34.615 0.00 0.00 0.00 2.50
1907 1917 4.617959 TCTCTTTTATCCGAATAGCACCG 58.382 43.478 0.00 0.00 0.00 4.94
1913 1923 2.240500 CCGAATAGCACCGCTGAGC 61.241 63.158 0.00 0.00 40.10 4.26
1914 1924 1.227089 CGAATAGCACCGCTGAGCT 60.227 57.895 1.78 5.31 44.55 4.09
1915 1925 1.485838 CGAATAGCACCGCTGAGCTG 61.486 60.000 10.18 0.00 41.97 4.24
1916 1926 0.460987 GAATAGCACCGCTGAGCTGT 60.461 55.000 10.18 0.00 41.97 4.40
1917 1927 0.824109 AATAGCACCGCTGAGCTGTA 59.176 50.000 10.18 0.00 41.97 2.74
1918 1928 0.824109 ATAGCACCGCTGAGCTGTAA 59.176 50.000 10.18 0.00 41.97 2.41
1919 1929 0.108804 TAGCACCGCTGAGCTGTAAC 60.109 55.000 10.18 0.00 41.97 2.50
2052 2062 1.610038 CCAGCACAATCAACTTCAGCA 59.390 47.619 0.00 0.00 0.00 4.41
2059 2069 5.733091 GCACAATCAACTTCAGCAACAGTTA 60.733 40.000 0.00 0.00 31.78 2.24
2097 2211 5.350504 TTGAAAAGATGGCCAGTTTTGAA 57.649 34.783 25.81 21.90 0.00 2.69
2098 2212 4.692228 TGAAAAGATGGCCAGTTTTGAAC 58.308 39.130 25.81 15.58 0.00 3.18
2187 2301 5.239306 TCGACATCATTTTTCTTGCAGAGTT 59.761 36.000 0.00 0.00 0.00 3.01
2249 2365 1.317613 AATTTCTGCTGTCACGCCAA 58.682 45.000 0.00 0.00 0.00 4.52
2497 2613 3.849563 TCTACCTCTAGCTCTCCTCAC 57.150 52.381 0.00 0.00 0.00 3.51
2550 2666 2.951642 AGTGTGTGGTTTCAGGATGTTG 59.048 45.455 0.00 0.00 37.40 3.33
2685 2801 6.219473 AGTTTCAGTTCAGCTATGATATCCG 58.781 40.000 0.00 0.00 34.73 4.18
2710 2826 3.714144 ACACTTGCATACTACTCCCTCT 58.286 45.455 0.00 0.00 0.00 3.69
2726 2842 7.068686 ACTCCCTCTGTTCCTAAATATAAGC 57.931 40.000 0.00 0.00 0.00 3.09
2728 2844 6.151049 TCCCTCTGTTCCTAAATATAAGCCT 58.849 40.000 0.00 0.00 0.00 4.58
2729 2845 6.619852 TCCCTCTGTTCCTAAATATAAGCCTT 59.380 38.462 0.00 0.00 0.00 4.35
2777 2895 3.837213 ACGGAGCAAAATGAGTGAATG 57.163 42.857 0.00 0.00 0.00 2.67
2826 2946 9.864034 CATCCGTATGTAGTTTGTATTGAAATC 57.136 33.333 0.00 0.00 0.00 2.17
2867 2990 2.694109 AGAAACGGAGGGAGTAGTATGC 59.306 50.000 0.00 0.00 0.00 3.14
2925 3048 8.768957 TTTGAAACATGAAGATCAAACAACAA 57.231 26.923 0.00 0.00 36.99 2.83
2926 3049 8.768957 TTGAAACATGAAGATCAAACAACAAA 57.231 26.923 0.00 0.00 0.00 2.83
2927 3050 8.410030 TGAAACATGAAGATCAAACAACAAAG 57.590 30.769 0.00 0.00 0.00 2.77
2928 3051 6.833342 AACATGAAGATCAAACAACAAAGC 57.167 33.333 0.00 0.00 0.00 3.51
2929 3052 6.152932 ACATGAAGATCAAACAACAAAGCT 57.847 33.333 0.00 0.00 0.00 3.74
2930 3053 6.211515 ACATGAAGATCAAACAACAAAGCTC 58.788 36.000 0.00 0.00 0.00 4.09
2931 3054 6.040166 ACATGAAGATCAAACAACAAAGCTCT 59.960 34.615 0.00 0.00 0.00 4.09
2932 3055 6.455360 TGAAGATCAAACAACAAAGCTCTT 57.545 33.333 0.00 0.00 0.00 2.85
2933 3056 6.866480 TGAAGATCAAACAACAAAGCTCTTT 58.134 32.000 0.00 0.00 0.00 2.52
2940 3063 3.041701 CAAAGCTCTTTGGCCGCA 58.958 55.556 13.11 0.00 44.47 5.69
2941 3064 1.588082 CAAAGCTCTTTGGCCGCAT 59.412 52.632 13.11 0.00 44.47 4.73
2942 3065 0.457337 CAAAGCTCTTTGGCCGCATC 60.457 55.000 13.11 0.00 44.47 3.91
2943 3066 1.926511 AAAGCTCTTTGGCCGCATCG 61.927 55.000 0.00 0.00 0.00 3.84
2953 3076 3.981308 CCGCATCGGTTGAGGTTT 58.019 55.556 1.15 0.00 42.73 3.27
2954 3077 1.501741 CCGCATCGGTTGAGGTTTG 59.498 57.895 1.15 0.00 42.73 2.93
2955 3078 1.154225 CGCATCGGTTGAGGTTTGC 60.154 57.895 0.00 0.00 0.00 3.68
2956 3079 1.577328 CGCATCGGTTGAGGTTTGCT 61.577 55.000 0.00 0.00 0.00 3.91
2957 3080 0.169009 GCATCGGTTGAGGTTTGCTC 59.831 55.000 0.00 0.00 0.00 4.26
2958 3081 1.813513 CATCGGTTGAGGTTTGCTCT 58.186 50.000 0.00 0.00 0.00 4.09
2959 3082 1.466167 CATCGGTTGAGGTTTGCTCTG 59.534 52.381 0.00 0.00 0.00 3.35
2960 3083 0.468226 TCGGTTGAGGTTTGCTCTGT 59.532 50.000 0.00 0.00 0.00 3.41
2961 3084 1.134220 TCGGTTGAGGTTTGCTCTGTT 60.134 47.619 0.00 0.00 0.00 3.16
2962 3085 1.264288 CGGTTGAGGTTTGCTCTGTTC 59.736 52.381 0.00 0.00 0.00 3.18
2963 3086 2.297701 GGTTGAGGTTTGCTCTGTTCA 58.702 47.619 0.00 0.00 0.00 3.18
2964 3087 2.291741 GGTTGAGGTTTGCTCTGTTCAG 59.708 50.000 0.00 0.00 0.00 3.02
2965 3088 2.945668 GTTGAGGTTTGCTCTGTTCAGT 59.054 45.455 0.00 0.00 0.00 3.41
2966 3089 2.564771 TGAGGTTTGCTCTGTTCAGTG 58.435 47.619 0.00 0.00 0.00 3.66
2967 3090 1.265365 GAGGTTTGCTCTGTTCAGTGC 59.735 52.381 16.61 16.61 0.00 4.40
2968 3091 1.133976 AGGTTTGCTCTGTTCAGTGCT 60.134 47.619 21.57 4.70 0.00 4.40
2969 3092 1.002033 GGTTTGCTCTGTTCAGTGCTG 60.002 52.381 21.57 0.00 0.00 4.41
2970 3093 1.002033 GTTTGCTCTGTTCAGTGCTGG 60.002 52.381 21.57 3.23 0.00 4.85
2971 3094 0.181114 TTGCTCTGTTCAGTGCTGGT 59.819 50.000 21.57 0.00 0.00 4.00
2972 3095 0.250038 TGCTCTGTTCAGTGCTGGTC 60.250 55.000 21.57 0.88 0.00 4.02
2973 3096 0.034616 GCTCTGTTCAGTGCTGGTCT 59.965 55.000 16.31 0.00 0.00 3.85
2974 3097 1.793258 CTCTGTTCAGTGCTGGTCTG 58.207 55.000 0.00 0.00 0.00 3.51
2975 3098 1.069823 CTCTGTTCAGTGCTGGTCTGT 59.930 52.381 0.00 0.00 34.86 3.41
2976 3099 1.069204 TCTGTTCAGTGCTGGTCTGTC 59.931 52.381 0.00 0.00 34.86 3.51
2977 3100 0.829990 TGTTCAGTGCTGGTCTGTCA 59.170 50.000 0.00 0.00 34.86 3.58
2978 3101 1.221414 GTTCAGTGCTGGTCTGTCAC 58.779 55.000 0.00 0.00 34.86 3.67
2979 3102 0.249447 TTCAGTGCTGGTCTGTCACG 60.249 55.000 0.00 0.00 35.97 4.35
2980 3103 2.029666 AGTGCTGGTCTGTCACGC 59.970 61.111 0.00 0.00 35.97 5.34
2981 3104 3.044305 GTGCTGGTCTGTCACGCC 61.044 66.667 0.00 0.00 0.00 5.68
2982 3105 3.545574 TGCTGGTCTGTCACGCCA 61.546 61.111 0.00 0.00 0.00 5.69
2985 3108 3.544772 TGGTCTGTCACGCCAGAA 58.455 55.556 2.05 0.00 42.81 3.02
2986 3109 1.367471 TGGTCTGTCACGCCAGAAG 59.633 57.895 2.05 0.00 42.81 2.85
2987 3110 1.367840 GGTCTGTCACGCCAGAAGT 59.632 57.895 2.05 0.00 42.81 3.01
2988 3111 0.667792 GGTCTGTCACGCCAGAAGTC 60.668 60.000 2.05 0.00 42.81 3.01
2989 3112 1.004277 GTCTGTCACGCCAGAAGTCG 61.004 60.000 2.05 0.00 42.81 4.18
2990 3113 2.355837 TGTCACGCCAGAAGTCGC 60.356 61.111 0.00 0.00 0.00 5.19
2996 3119 3.119096 GCCAGAAGTCGCGGGTTC 61.119 66.667 6.13 9.83 0.00 3.62
2997 3120 2.809601 CCAGAAGTCGCGGGTTCG 60.810 66.667 6.13 6.30 39.81 3.95
3036 3159 5.730296 TGTTTTGGGAAAGTTGAAGTGAA 57.270 34.783 0.00 0.00 0.00 3.18
3179 3305 5.592688 GCTTCAGTACCCTTTATATGGCAAA 59.407 40.000 0.00 0.00 0.00 3.68
3205 3331 5.105228 ACAGGCCATGTTTCCAATGATAAAG 60.105 40.000 5.01 0.00 39.96 1.85
3244 3373 8.229253 TGAATTATCCAATCTTGTGATTCTGG 57.771 34.615 0.00 0.00 40.61 3.86
3287 3416 3.449018 GCCTGGACTTACAAGAGATCTCA 59.551 47.826 24.39 0.57 0.00 3.27
3358 3487 0.326264 CAGCCCAGCCTCACTTAACT 59.674 55.000 0.00 0.00 0.00 2.24
3390 3519 5.990996 CCTCTTCTCTCTAGATTTGATTGGC 59.009 44.000 0.00 0.00 0.00 4.52
3399 3528 2.097825 GATTTGATTGGCTCCACAGCT 58.902 47.619 0.00 0.00 46.03 4.24
3405 3534 0.035881 TTGGCTCCACAGCTTCTCAG 59.964 55.000 0.00 0.00 46.03 3.35
3414 3543 3.118702 CCACAGCTTCTCAGACTGATGAT 60.119 47.826 5.42 0.00 35.38 2.45
3415 3544 3.866327 CACAGCTTCTCAGACTGATGATG 59.134 47.826 5.42 10.57 35.38 3.07
3469 3599 0.962855 TGGCCGTCTCTCTCTCACTG 60.963 60.000 0.00 0.00 0.00 3.66
3470 3600 1.138671 GCCGTCTCTCTCTCACTGC 59.861 63.158 0.00 0.00 0.00 4.40
3471 3601 1.590610 GCCGTCTCTCTCTCACTGCA 61.591 60.000 0.00 0.00 0.00 4.41
3472 3602 1.102154 CCGTCTCTCTCTCACTGCAT 58.898 55.000 0.00 0.00 0.00 3.96
3473 3603 1.065401 CCGTCTCTCTCTCACTGCATC 59.935 57.143 0.00 0.00 0.00 3.91
3474 3604 1.267982 CGTCTCTCTCTCACTGCATCG 60.268 57.143 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.408909 CCTTTTGTTGGGTTTACGTGTTTTT 59.591 36.000 0.00 0.00 0.00 1.94
6 7 4.930405 CCTTTTGTTGGGTTTACGTGTTTT 59.070 37.500 0.00 0.00 0.00 2.43
7 8 4.496360 CCTTTTGTTGGGTTTACGTGTTT 58.504 39.130 0.00 0.00 0.00 2.83
8 9 3.676598 GCCTTTTGTTGGGTTTACGTGTT 60.677 43.478 0.00 0.00 0.00 3.32
9 10 2.159212 GCCTTTTGTTGGGTTTACGTGT 60.159 45.455 0.00 0.00 0.00 4.49
10 11 2.159226 TGCCTTTTGTTGGGTTTACGTG 60.159 45.455 0.00 0.00 0.00 4.49
11 12 2.100087 CTGCCTTTTGTTGGGTTTACGT 59.900 45.455 0.00 0.00 0.00 3.57
12 13 2.359531 TCTGCCTTTTGTTGGGTTTACG 59.640 45.455 0.00 0.00 0.00 3.18
13 14 3.634910 TCTCTGCCTTTTGTTGGGTTTAC 59.365 43.478 0.00 0.00 0.00 2.01
113 115 1.302511 GAGCTGACCTTGGGCGAAA 60.303 57.895 0.00 0.00 0.00 3.46
147 149 1.823260 AATCGAAACGCGCGTGTTGA 61.823 50.000 37.70 37.70 40.61 3.18
150 152 1.154727 GAAATCGAAACGCGCGTGT 60.155 52.632 38.44 33.65 40.61 4.49
262 266 1.607612 GAGGGCGATTTCCTCCCAA 59.392 57.895 0.00 0.00 43.71 4.12
287 291 1.772063 GAAATCCCACGAATCGGGCG 61.772 60.000 7.80 0.00 44.11 6.13
288 292 0.463833 AGAAATCCCACGAATCGGGC 60.464 55.000 7.80 0.00 44.11 6.13
289 293 1.583054 GAGAAATCCCACGAATCGGG 58.417 55.000 7.80 1.60 46.03 5.14
290 294 1.209128 CGAGAAATCCCACGAATCGG 58.791 55.000 7.80 0.00 0.00 4.18
364 370 6.089551 CGAAATGAGAAACCAGTAGTGTACAG 59.910 42.308 0.00 0.00 0.00 2.74
368 374 3.746492 GCGAAATGAGAAACCAGTAGTGT 59.254 43.478 0.00 0.00 0.00 3.55
370 376 3.997021 CAGCGAAATGAGAAACCAGTAGT 59.003 43.478 0.00 0.00 0.00 2.73
413 419 0.400213 ACAAAATCAGAGGGCGTCCA 59.600 50.000 9.71 0.00 34.83 4.02
506 512 5.250082 CCTAGGGTAAGAGTTAAACCACCTT 59.750 44.000 0.00 0.00 34.83 3.50
553 559 1.459450 ACTGGCGCAAAAATACCGAT 58.541 45.000 10.83 0.00 0.00 4.18
554 560 1.240256 AACTGGCGCAAAAATACCGA 58.760 45.000 10.83 0.00 0.00 4.69
555 561 2.058913 AAACTGGCGCAAAAATACCG 57.941 45.000 10.83 0.00 0.00 4.02
556 562 3.127589 ACAAAACTGGCGCAAAAATACC 58.872 40.909 10.83 0.00 0.00 2.73
557 563 4.268884 TGAACAAAACTGGCGCAAAAATAC 59.731 37.500 10.83 0.00 0.00 1.89
558 564 4.433615 TGAACAAAACTGGCGCAAAAATA 58.566 34.783 10.83 0.00 0.00 1.40
560 566 2.688507 TGAACAAAACTGGCGCAAAAA 58.311 38.095 10.83 0.00 0.00 1.94
562 568 2.468831 GATGAACAAAACTGGCGCAAA 58.531 42.857 10.83 0.00 0.00 3.68
563 569 1.599171 CGATGAACAAAACTGGCGCAA 60.599 47.619 10.83 0.00 0.00 4.85
564 570 0.040514 CGATGAACAAAACTGGCGCA 60.041 50.000 10.83 0.00 0.00 6.09
565 571 0.729140 CCGATGAACAAAACTGGCGC 60.729 55.000 0.00 0.00 0.00 6.53
566 572 0.591170 ACCGATGAACAAAACTGGCG 59.409 50.000 0.00 0.00 0.00 5.69
567 573 4.434713 AATACCGATGAACAAAACTGGC 57.565 40.909 0.00 0.00 0.00 4.85
568 574 6.364976 GGAAAAATACCGATGAACAAAACTGG 59.635 38.462 0.00 0.00 0.00 4.00
569 575 6.920758 TGGAAAAATACCGATGAACAAAACTG 59.079 34.615 0.00 0.00 0.00 3.16
570 576 7.045126 TGGAAAAATACCGATGAACAAAACT 57.955 32.000 0.00 0.00 0.00 2.66
571 577 6.921307 ACTGGAAAAATACCGATGAACAAAAC 59.079 34.615 0.00 0.00 0.00 2.43
572 578 6.920758 CACTGGAAAAATACCGATGAACAAAA 59.079 34.615 0.00 0.00 0.00 2.44
573 579 6.263392 TCACTGGAAAAATACCGATGAACAAA 59.737 34.615 0.00 0.00 0.00 2.83
574 580 5.765677 TCACTGGAAAAATACCGATGAACAA 59.234 36.000 0.00 0.00 0.00 2.83
575 581 5.309638 TCACTGGAAAAATACCGATGAACA 58.690 37.500 0.00 0.00 0.00 3.18
576 582 5.873179 TCACTGGAAAAATACCGATGAAC 57.127 39.130 0.00 0.00 0.00 3.18
577 583 5.943416 ACATCACTGGAAAAATACCGATGAA 59.057 36.000 0.00 0.00 31.19 2.57
578 584 5.353956 CACATCACTGGAAAAATACCGATGA 59.646 40.000 0.00 0.00 0.00 2.92
579 585 5.449041 CCACATCACTGGAAAAATACCGATG 60.449 44.000 0.00 0.00 32.30 3.84
580 586 4.640201 CCACATCACTGGAAAAATACCGAT 59.360 41.667 0.00 0.00 32.30 4.18
581 587 4.006989 CCACATCACTGGAAAAATACCGA 58.993 43.478 0.00 0.00 32.30 4.69
582 588 4.006989 TCCACATCACTGGAAAAATACCG 58.993 43.478 0.00 0.00 37.39 4.02
583 589 5.975693 TTCCACATCACTGGAAAAATACC 57.024 39.130 0.00 0.00 45.61 2.73
598 604 5.528043 TGCACAAGTACAAATTTCCACAT 57.472 34.783 0.00 0.00 0.00 3.21
599 605 4.991153 TGCACAAGTACAAATTTCCACA 57.009 36.364 0.00 0.00 0.00 4.17
600 606 5.772521 AGATGCACAAGTACAAATTTCCAC 58.227 37.500 0.00 0.00 0.00 4.02
601 607 7.148086 GGATAGATGCACAAGTACAAATTTCCA 60.148 37.037 0.00 0.00 0.00 3.53
614 620 5.101648 TCATTCACAGGATAGATGCACAA 57.898 39.130 0.00 0.00 0.00 3.33
676 682 4.385358 AAAAACCGCACACTCTGAAAAT 57.615 36.364 0.00 0.00 0.00 1.82
677 683 3.859411 AAAAACCGCACACTCTGAAAA 57.141 38.095 0.00 0.00 0.00 2.29
701 707 5.535783 GTCCTCTAGGTATGAGAGTTTACCC 59.464 48.000 0.00 0.00 39.09 3.69
702 708 5.535783 GGTCCTCTAGGTATGAGAGTTTACC 59.464 48.000 0.00 0.00 39.09 2.85
718 724 4.422057 TGTGACATTAAGGTGGTCCTCTA 58.578 43.478 0.00 0.00 44.35 2.43
722 728 4.335594 GCTATTGTGACATTAAGGTGGTCC 59.664 45.833 0.00 0.00 0.00 4.46
723 729 5.186198 AGCTATTGTGACATTAAGGTGGTC 58.814 41.667 0.00 0.00 0.00 4.02
727 733 5.817816 GCACTAGCTATTGTGACATTAAGGT 59.182 40.000 15.35 0.00 36.38 3.50
732 738 5.649395 ACATTGCACTAGCTATTGTGACATT 59.351 36.000 15.35 7.70 42.74 2.71
736 742 5.003160 ACAACATTGCACTAGCTATTGTGA 58.997 37.500 15.35 4.61 42.74 3.58
741 747 8.786898 CCAATATTACAACATTGCACTAGCTAT 58.213 33.333 0.00 0.00 42.74 2.97
746 752 6.765915 TGCCAATATTACAACATTGCACTA 57.234 33.333 0.00 0.00 32.00 2.74
747 753 5.657826 TGCCAATATTACAACATTGCACT 57.342 34.783 0.00 0.00 32.00 4.40
748 754 5.811613 ACATGCCAATATTACAACATTGCAC 59.188 36.000 0.00 0.00 32.00 4.57
749 755 5.975282 ACATGCCAATATTACAACATTGCA 58.025 33.333 0.00 0.00 32.00 4.08
751 757 8.404765 TGACTACATGCCAATATTACAACATTG 58.595 33.333 0.00 0.00 32.94 2.82
752 758 8.518430 TGACTACATGCCAATATTACAACATT 57.482 30.769 0.00 0.00 0.00 2.71
753 759 8.570488 CATGACTACATGCCAATATTACAACAT 58.430 33.333 0.00 0.00 45.51 2.71
754 760 7.929159 CATGACTACATGCCAATATTACAACA 58.071 34.615 0.00 0.00 45.51 3.33
782 788 3.125829 CCATGACTTCAAATCCACACGAG 59.874 47.826 0.00 0.00 0.00 4.18
794 800 1.066215 CCACACGGATCCATGACTTCA 60.066 52.381 16.14 0.00 0.00 3.02
864 870 4.572389 GCTTCTCAACTCAAAACTCTGACA 59.428 41.667 0.00 0.00 0.00 3.58
912 918 3.257393 GACTGCAGTCCAACTACATGAG 58.743 50.000 32.55 0.00 39.07 2.90
1192 1199 1.135139 CACGAGATCGACACCATCCTT 59.865 52.381 9.58 0.00 43.02 3.36
1216 1223 2.769095 GCACATAGGGAGAAGAAGACCT 59.231 50.000 0.00 0.00 37.13 3.85
1297 1304 8.730680 ACTACAAAAATAATGACAGTTAGCCAG 58.269 33.333 0.00 0.00 0.00 4.85
1334 1341 9.003658 TGCAGAAAATCTCTTAGTAAAAGAAGG 57.996 33.333 0.00 0.00 29.07 3.46
1342 1349 7.441836 TGTGACTTGCAGAAAATCTCTTAGTA 58.558 34.615 0.00 0.00 29.07 1.82
1596 1604 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1597 1605 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1598 1606 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1599 1607 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
1600 1608 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
1601 1609 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
1602 1610 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
1907 1917 2.028020 AGGTTACAGGTTACAGCTCAGC 60.028 50.000 0.00 0.00 0.00 4.26
1913 1923 5.217978 TGGTTACAGGTTACAGGTTACAG 57.782 43.478 0.00 0.00 0.00 2.74
1914 1924 5.829062 ATGGTTACAGGTTACAGGTTACA 57.171 39.130 0.00 0.00 0.00 2.41
1915 1925 5.413523 CCAATGGTTACAGGTTACAGGTTAC 59.586 44.000 0.00 0.00 0.00 2.50
1916 1926 5.562635 CCAATGGTTACAGGTTACAGGTTA 58.437 41.667 0.00 0.00 0.00 2.85
1917 1927 4.403734 CCAATGGTTACAGGTTACAGGTT 58.596 43.478 0.00 0.00 0.00 3.50
1918 1928 3.812882 GCCAATGGTTACAGGTTACAGGT 60.813 47.826 0.00 0.00 0.00 4.00
1919 1929 2.752903 GCCAATGGTTACAGGTTACAGG 59.247 50.000 0.00 0.00 0.00 4.00
2052 2062 9.357161 TCAAGTTGGTAAATGGTATTAACTGTT 57.643 29.630 2.34 0.00 0.00 3.16
2059 2069 9.927668 CATCTTTTCAAGTTGGTAAATGGTATT 57.072 29.630 2.34 0.00 0.00 1.89
2088 2202 0.313987 GCCCCCGAAGTTCAAAACTG 59.686 55.000 3.32 0.00 41.91 3.16
2179 2293 1.881973 GTGCAATGGAAGAACTCTGCA 59.118 47.619 0.00 0.00 37.46 4.41
2497 2613 1.301716 CCAGTCGGGTTGGTGAGTG 60.302 63.158 0.00 0.00 35.71 3.51
2550 2666 6.582636 TCATGAATATCTGAACAGGGTGTAC 58.417 40.000 0.00 0.00 0.00 2.90
2586 2702 6.747280 GTGTCATCCAAATTACAAAATCCTCG 59.253 38.462 0.00 0.00 0.00 4.63
2685 2801 3.933332 GGGAGTAGTATGCAAGTGTTGAC 59.067 47.826 0.00 0.00 0.00 3.18
2726 2842 8.055790 AGTCCCTTATTGGAATCTCTAAAAAGG 58.944 37.037 0.00 0.00 35.80 3.11
2728 2844 9.901172 GTAGTCCCTTATTGGAATCTCTAAAAA 57.099 33.333 0.00 0.00 35.80 1.94
2729 2845 9.053472 TGTAGTCCCTTATTGGAATCTCTAAAA 57.947 33.333 0.00 0.00 35.80 1.52
2840 2963 8.804204 CATACTACTCCCTCCGTTTCTAAATAT 58.196 37.037 0.00 0.00 0.00 1.28
2841 2964 7.255730 GCATACTACTCCCTCCGTTTCTAAATA 60.256 40.741 0.00 0.00 0.00 1.40
2852 2975 1.906990 TAGCGCATACTACTCCCTCC 58.093 55.000 11.47 0.00 0.00 4.30
2914 3037 4.122046 GCCAAAGAGCTTTGTTGTTTGAT 58.878 39.130 18.52 0.00 46.19 2.57
2925 3048 2.401766 CGATGCGGCCAAAGAGCTT 61.402 57.895 2.24 0.00 0.00 3.74
2926 3049 2.821366 CGATGCGGCCAAAGAGCT 60.821 61.111 2.24 0.00 0.00 4.09
2927 3050 3.880846 CCGATGCGGCCAAAGAGC 61.881 66.667 2.24 0.00 41.17 4.09
2937 3060 1.154225 GCAAACCTCAACCGATGCG 60.154 57.895 0.00 0.00 0.00 4.73
2938 3061 0.169009 GAGCAAACCTCAACCGATGC 59.831 55.000 0.00 0.00 40.45 3.91
2939 3062 1.466167 CAGAGCAAACCTCAACCGATG 59.534 52.381 0.00 0.00 43.31 3.84
2940 3063 1.072331 ACAGAGCAAACCTCAACCGAT 59.928 47.619 0.00 0.00 43.31 4.18
2941 3064 0.468226 ACAGAGCAAACCTCAACCGA 59.532 50.000 0.00 0.00 43.31 4.69
2942 3065 1.264288 GAACAGAGCAAACCTCAACCG 59.736 52.381 0.00 0.00 43.31 4.44
2943 3066 2.291741 CTGAACAGAGCAAACCTCAACC 59.708 50.000 0.00 0.00 43.31 3.77
2944 3067 2.945668 ACTGAACAGAGCAAACCTCAAC 59.054 45.455 8.87 0.00 43.31 3.18
2945 3068 2.945008 CACTGAACAGAGCAAACCTCAA 59.055 45.455 8.87 0.00 43.31 3.02
2946 3069 2.564771 CACTGAACAGAGCAAACCTCA 58.435 47.619 8.87 0.00 43.31 3.86
2947 3070 1.265365 GCACTGAACAGAGCAAACCTC 59.735 52.381 16.59 0.00 43.16 3.85
2948 3071 1.133976 AGCACTGAACAGAGCAAACCT 60.134 47.619 21.58 2.94 45.52 3.50
2949 3072 1.002033 CAGCACTGAACAGAGCAAACC 60.002 52.381 21.58 0.00 45.52 3.27
2950 3073 1.002033 CCAGCACTGAACAGAGCAAAC 60.002 52.381 21.58 0.00 45.52 2.93
2951 3074 1.311859 CCAGCACTGAACAGAGCAAA 58.688 50.000 21.58 0.00 45.52 3.68
2952 3075 0.181114 ACCAGCACTGAACAGAGCAA 59.819 50.000 21.58 0.00 45.52 3.91
2953 3076 0.250038 GACCAGCACTGAACAGAGCA 60.250 55.000 21.58 0.00 45.52 4.26
2954 3077 0.034616 AGACCAGCACTGAACAGAGC 59.965 55.000 14.39 14.39 43.84 4.09
2955 3078 1.069823 ACAGACCAGCACTGAACAGAG 59.930 52.381 8.87 1.91 38.55 3.35
2956 3079 1.069204 GACAGACCAGCACTGAACAGA 59.931 52.381 8.87 0.00 38.55 3.41
2957 3080 1.202568 TGACAGACCAGCACTGAACAG 60.203 52.381 0.00 0.00 38.55 3.16
2958 3081 0.829990 TGACAGACCAGCACTGAACA 59.170 50.000 0.00 0.00 38.55 3.18
2959 3082 1.221414 GTGACAGACCAGCACTGAAC 58.779 55.000 0.00 0.00 38.55 3.18
2960 3083 0.249447 CGTGACAGACCAGCACTGAA 60.249 55.000 0.00 0.00 38.55 3.02
2961 3084 1.363807 CGTGACAGACCAGCACTGA 59.636 57.895 0.00 0.00 38.55 3.41
2962 3085 2.313172 GCGTGACAGACCAGCACTG 61.313 63.158 0.00 0.00 40.68 3.66
2963 3086 2.029666 GCGTGACAGACCAGCACT 59.970 61.111 0.00 0.00 0.00 4.40
2964 3087 3.044305 GGCGTGACAGACCAGCAC 61.044 66.667 0.00 0.00 0.00 4.40
2965 3088 3.519973 CTGGCGTGACAGACCAGCA 62.520 63.158 10.06 0.00 44.16 4.41
2966 3089 2.740055 CTGGCGTGACAGACCAGC 60.740 66.667 10.06 0.00 44.16 4.85
2968 3091 1.367471 CTTCTGGCGTGACAGACCA 59.633 57.895 4.55 0.00 46.44 4.02
2969 3092 0.667792 GACTTCTGGCGTGACAGACC 60.668 60.000 4.55 0.00 46.44 3.85
2970 3093 1.004277 CGACTTCTGGCGTGACAGAC 61.004 60.000 4.55 0.00 46.44 3.51
2971 3094 1.285950 CGACTTCTGGCGTGACAGA 59.714 57.895 0.07 0.07 45.22 3.41
2972 3095 2.375766 GCGACTTCTGGCGTGACAG 61.376 63.158 0.00 0.00 39.84 3.51
2973 3096 2.355837 GCGACTTCTGGCGTGACA 60.356 61.111 0.00 0.00 0.00 3.58
2974 3097 3.470567 CGCGACTTCTGGCGTGAC 61.471 66.667 0.00 0.00 46.79 3.67
2979 3102 3.119096 GAACCCGCGACTTCTGGC 61.119 66.667 8.23 0.00 0.00 4.85
2980 3103 2.809601 CGAACCCGCGACTTCTGG 60.810 66.667 8.23 0.20 0.00 3.86
2981 3104 1.801913 CTCGAACCCGCGACTTCTG 60.802 63.158 8.23 4.68 36.17 3.02
2982 3105 2.567049 CTCGAACCCGCGACTTCT 59.433 61.111 8.23 0.00 36.17 2.85
2983 3106 2.506438 CCTCGAACCCGCGACTTC 60.506 66.667 8.23 6.67 36.17 3.01
2984 3107 4.065281 CCCTCGAACCCGCGACTT 62.065 66.667 8.23 0.00 36.17 3.01
2990 3113 1.400530 ATTAGGAGCCCTCGAACCCG 61.401 60.000 0.00 0.00 34.61 5.28
2991 3114 0.837940 AATTAGGAGCCCTCGAACCC 59.162 55.000 0.00 0.00 34.61 4.11
2992 3115 2.711978 AAATTAGGAGCCCTCGAACC 57.288 50.000 0.00 0.00 34.61 3.62
2993 3116 5.123936 ACATAAAATTAGGAGCCCTCGAAC 58.876 41.667 0.00 0.00 34.61 3.95
2994 3117 5.367945 ACATAAAATTAGGAGCCCTCGAA 57.632 39.130 0.00 0.00 34.61 3.71
2995 3118 5.367945 AACATAAAATTAGGAGCCCTCGA 57.632 39.130 0.00 0.00 34.61 4.04
2996 3119 6.265577 CAAAACATAAAATTAGGAGCCCTCG 58.734 40.000 0.00 0.00 34.61 4.63
2997 3120 6.406961 CCCAAAACATAAAATTAGGAGCCCTC 60.407 42.308 0.00 0.00 34.61 4.30
3179 3305 1.619827 CATTGGAAACATGGCCTGTGT 59.380 47.619 3.32 6.40 42.32 3.72
3244 3373 6.002704 AGGCAATCAGATCAAGGAATCATAC 58.997 40.000 0.00 0.00 0.00 2.39
3287 3416 0.250124 TTTGGCACCGTCTGACGATT 60.250 50.000 29.93 14.37 46.05 3.34
3358 3487 7.969690 AATCTAGAGAGAAGAGGAATTGTGA 57.030 36.000 0.00 0.00 34.61 3.58
3390 3519 1.891811 TCAGTCTGAGAAGCTGTGGAG 59.108 52.381 0.00 0.00 0.00 3.86
3399 3528 8.625786 TTTTCAAATCATCATCAGTCTGAGAA 57.374 30.769 8.82 0.47 0.00 2.87
3405 3534 7.149569 TGGACTTTTCAAATCATCATCAGTC 57.850 36.000 0.00 0.00 0.00 3.51
3414 3543 6.930164 CCAATCATGTTGGACTTTTCAAATCA 59.070 34.615 17.28 0.00 42.06 2.57
3415 3544 6.128472 GCCAATCATGTTGGACTTTTCAAATC 60.128 38.462 23.18 4.97 42.06 2.17


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

AutoCloner maintained by Alex Coulton.