Multiple sequence alignment - TraesCS2D01G262700

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 TraesCS2D01G262700 chr2D 100.000 8358 0 0 1 8358 318909647 318918004 0.000000e+00 15435.0
1 TraesCS2D01G262700 chr2D 86.932 176 23 0 1000 1175 126149541 126149366 1.840000e-46 198.0
2 TraesCS2D01G262700 chr2A 93.804 5116 194 58 1 5036 411951128 411946056 0.000000e+00 7577.0
3 TraesCS2D01G262700 chr2A 94.116 3025 106 28 5145 8141 411946058 411943078 0.000000e+00 4534.0
4 TraesCS2D01G262700 chr2A 93.333 165 9 2 8190 8354 411926577 411926415 8.380000e-60 243.0
5 TraesCS2D01G262700 chr2A 88.068 176 21 0 1000 1175 132876425 132876250 8.500000e-50 209.0
6 TraesCS2D01G262700 chr2A 92.035 113 9 0 5032 5144 39694590 39694478 8.680000e-35 159.0
7 TraesCS2D01G262700 chr2A 92.793 111 7 1 5034 5144 78848821 78848930 8.680000e-35 159.0
8 TraesCS2D01G262700 chr2A 96.721 61 2 0 8126 8186 411926728 411926668 1.480000e-17 102.0
9 TraesCS2D01G262700 chr2B 94.918 2558 85 12 5286 7828 387703382 387705909 0.000000e+00 3962.0
10 TraesCS2D01G262700 chr2B 92.505 2735 108 43 1801 4476 387699302 387701998 0.000000e+00 3825.0
11 TraesCS2D01G262700 chr2B 93.782 1769 43 24 1 1740 387697566 387699296 0.000000e+00 2595.0
12 TraesCS2D01G262700 chr2B 95.567 564 22 3 4474 5036 387702330 387702891 0.000000e+00 900.0
13 TraesCS2D01G262700 chr2B 87.462 327 12 4 8058 8358 387707537 387707860 4.800000e-92 350.0
14 TraesCS2D01G262700 chr2B 91.818 220 8 6 7814 8030 387707263 387707475 1.760000e-76 298.0
15 TraesCS2D01G262700 chr2B 88.068 176 21 0 1000 1175 180059837 180059662 8.500000e-50 209.0
16 TraesCS2D01G262700 chr2B 94.340 106 2 4 5145 5247 387702889 387702993 8.680000e-35 159.0
17 TraesCS2D01G262700 chr5D 96.262 107 4 0 5038 5144 322949654 322949548 8.620000e-40 176.0
18 TraesCS2D01G262700 chr5D 90.741 54 5 0 6839 6892 467177492 467177439 1.160000e-08 73.1
19 TraesCS2D01G262700 chr5A 93.103 116 6 2 5030 5144 115018632 115018746 1.440000e-37 169.0
20 TraesCS2D01G262700 chr5A 90.741 54 5 0 6839 6892 587412352 587412299 1.160000e-08 73.1
21 TraesCS2D01G262700 chr4D 92.793 111 8 0 5034 5144 3754416 3754306 2.410000e-35 161.0
22 TraesCS2D01G262700 chr1A 90.909 121 9 2 5024 5144 550442986 550443104 2.410000e-35 161.0
23 TraesCS2D01G262700 chr5B 92.793 111 7 1 5034 5144 657593222 657593331 8.680000e-35 159.0
24 TraesCS2D01G262700 chr5B 90.741 54 5 0 6839 6892 573803766 573803713 1.160000e-08 73.1
25 TraesCS2D01G262700 chr4A 92.793 111 7 1 5034 5144 187572346 187572237 8.680000e-35 159.0
26 TraesCS2D01G262700 chr3B 92.105 114 8 1 5031 5144 104392890 104393002 8.680000e-35 159.0
27 TraesCS2D01G262700 chr7D 80.000 120 20 4 8068 8186 326725259 326725375 1.490000e-12 86.1
28 TraesCS2D01G262700 chrUn 82.759 87 15 0 8100 8186 85544043 85544129 2.500000e-10 78.7
29 TraesCS2D01G262700 chrUn 82.759 87 15 0 8100 8186 361522342 361522256 2.500000e-10 78.7


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 TraesCS2D01G262700 chr2D 318909647 318918004 8357 False 15435.0 15435 100.000000 1 8358 1 chr2D.!!$F1 8357
1 TraesCS2D01G262700 chr2A 411943078 411951128 8050 True 6055.5 7577 93.960000 1 8141 2 chr2A.!!$R4 8140
2 TraesCS2D01G262700 chr2B 387697566 387707860 10294 False 1727.0 3962 92.913143 1 8358 7 chr2B.!!$F1 8357

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
140 141 0.475475 TGCCTATGGGATGGAAGCTG 59.525 55.0 0.00 0.0 33.58 4.24 F
712 743 0.595310 GCCGCTGCTGCTACTACTAC 60.595 60.0 14.03 0.0 36.97 2.73 F
1476 1520 0.108138 GTACCGCATGTGCTTCCTCT 60.108 55.0 0.00 0.0 39.32 3.69 F
1477 1521 0.175760 TACCGCATGTGCTTCCTCTC 59.824 55.0 0.00 0.0 39.32 3.20 F
2758 2855 0.332972 GGCTTCTGGAACCCCTTCAT 59.667 55.0 0.00 0.0 0.00 2.57 F
3564 3678 0.881118 ACAATGCCAAGCCTTGTACG 59.119 50.0 8.23 0.0 43.33 3.67 F
5049 5503 0.702902 AACTACTCCCTCTGTCCGGA 59.297 55.0 0.00 0.0 0.00 5.14 F
6542 7357 0.035739 GCCCACCCGAACTGTCTTAA 59.964 55.0 0.00 0.0 0.00 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1331 0.638292 ACGGTATTACCTCCCTCCCA 59.362 55.000 11.05 0.0 35.66 4.37 R
2503 2599 0.738063 ACGAGTCGTTGCACAACACA 60.738 50.000 13.56 0.0 41.20 3.72 R
2970 3070 2.360801 TCTTGTAAAACAGCCAAGGTGC 59.639 45.455 0.00 0.0 36.94 5.01 R
3433 3547 3.068165 GCAATAGCTTATCACAAACCCCC 59.932 47.826 0.00 0.0 37.91 5.40 R
4686 5139 2.990740 TGAAAGGGCCAAATACAGGT 57.009 45.000 6.18 0.0 0.00 4.00 R
5134 5588 0.248289 ACCAAATGTACTCCGTCCGG 59.752 55.000 0.00 0.0 0.00 5.14 R
7025 7844 0.895100 TTTGGTGCTCCCACTGCATC 60.895 55.000 1.59 0.0 45.19 3.91 R
8244 10509 0.598419 TGTCGTGCTGCTGACTCTTG 60.598 55.000 20.49 0.0 36.10 3.02 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
22 23 4.307032 ACTATCAAATTCCAGTGCACCT 57.693 40.909 14.63 0.00 0.00 4.00
45 46 1.974265 TGAAGATGCAAACGACCCAA 58.026 45.000 0.00 0.00 0.00 4.12
87 88 1.255667 ACGAGGCACACCGAACCTAT 61.256 55.000 0.00 0.00 42.76 2.57
91 92 2.817844 GAGGCACACCGAACCTATTTTT 59.182 45.455 0.00 0.00 42.76 1.94
140 141 0.475475 TGCCTATGGGATGGAAGCTG 59.525 55.000 0.00 0.00 33.58 4.24
151 152 1.223211 GGAAGCTGAAGAGAGGGCC 59.777 63.158 0.00 0.00 0.00 5.80
349 368 8.975663 ATGTACTTGCTACTAGTCATACTACA 57.024 34.615 0.00 0.41 0.00 2.74
667 698 0.955919 AGGAGTTAAACCTGCGCTGC 60.956 55.000 9.73 0.00 36.30 5.25
668 699 1.132640 GAGTTAAACCTGCGCTGCG 59.867 57.895 19.17 19.17 0.00 5.18
712 743 0.595310 GCCGCTGCTGCTACTACTAC 60.595 60.000 14.03 0.00 36.97 2.73
734 767 9.742144 ACTACTAAACACAATAGAGAGAGAGAA 57.258 33.333 0.00 0.00 0.00 2.87
807 840 2.279517 CTCGACAGCATACGGGGC 60.280 66.667 0.00 0.00 0.00 5.80
1278 1320 2.360225 TGCCGCTGCATCACACAT 60.360 55.556 0.00 0.00 44.23 3.21
1289 1331 6.128472 CGCTGCATCACACATACATACATATT 60.128 38.462 0.00 0.00 0.00 1.28
1404 1448 1.876664 GGAAAAGCTCCTTGTCGGC 59.123 57.895 0.00 0.00 41.61 5.54
1476 1520 0.108138 GTACCGCATGTGCTTCCTCT 60.108 55.000 0.00 0.00 39.32 3.69
1477 1521 0.175760 TACCGCATGTGCTTCCTCTC 59.824 55.000 0.00 0.00 39.32 3.20
1502 1546 1.555533 GTTTCTACTGCTAGCCCCAGT 59.444 52.381 13.29 11.76 44.99 4.00
1594 1639 4.703093 TGGGTAACGATTTGATTTTCTCCC 59.297 41.667 0.00 0.00 37.60 4.30
1620 1665 1.140589 CACTCACTAGCTGGCTCGG 59.859 63.158 0.00 0.00 0.00 4.63
1743 1788 8.494433 TCTTTAATTCACATTCACCTATAGCCT 58.506 33.333 0.00 0.00 0.00 4.58
1787 1832 3.182967 GTGACACGAGAAGGCAGATTAG 58.817 50.000 0.00 0.00 0.00 1.73
1798 1843 7.753132 CGAGAAGGCAGATTAGATTATACTGAC 59.247 40.741 0.00 0.00 36.93 3.51
1799 1844 7.902087 AGAAGGCAGATTAGATTATACTGACC 58.098 38.462 0.00 0.00 37.32 4.02
1800 1845 6.613153 AGGCAGATTAGATTATACTGACCC 57.387 41.667 0.00 0.00 37.32 4.46
1801 1846 6.084738 AGGCAGATTAGATTATACTGACCCA 58.915 40.000 0.00 0.00 37.32 4.51
1844 1889 9.803315 GTAATTAGATGATTTTTGTCCCTTTCC 57.197 33.333 0.00 0.00 0.00 3.13
1880 1925 6.682020 CGTTCTAGACTCGATTGTACTACAAC 59.318 42.308 3.67 0.00 41.40 3.32
1927 1972 2.351738 CCGTCCAGTGATTTGGCTTTTC 60.352 50.000 0.00 0.00 38.16 2.29
1928 1973 2.554032 CGTCCAGTGATTTGGCTTTTCT 59.446 45.455 0.00 0.00 38.16 2.52
1952 1997 2.725723 GTGACCAAAAATCACATGCGTG 59.274 45.455 3.82 3.82 44.87 5.34
1957 2002 4.269844 ACCAAAAATCACATGCGTGTTTTC 59.730 37.500 9.37 0.00 41.83 2.29
1958 2003 4.269603 CCAAAAATCACATGCGTGTTTTCA 59.730 37.500 9.37 0.00 41.83 2.69
1960 2005 6.420588 CAAAAATCACATGCGTGTTTTCATT 58.579 32.000 9.37 2.89 41.83 2.57
1996 2045 7.156876 TCAATAATAAACACAGCTTCCAAGG 57.843 36.000 0.00 0.00 0.00 3.61
2036 2085 2.934553 CCAGTGACAGACATGCATGTAG 59.065 50.000 31.45 26.61 41.95 2.74
2039 2088 2.674852 GTGACAGACATGCATGTAGTGG 59.325 50.000 30.83 22.62 41.95 4.00
2050 2099 2.005960 ATGTAGTGGACGGAGCTCGC 62.006 60.000 7.83 0.00 43.89 5.03
2101 2150 4.318332 CCTCTCTAAACATGCAGTGAACA 58.682 43.478 0.00 0.00 0.00 3.18
2178 2229 5.845391 ATCCCTCTTCTTACTCTTCTTCG 57.155 43.478 0.00 0.00 0.00 3.79
2228 2279 5.486526 TGGCTCTTCTTTGATCTTCTTCTC 58.513 41.667 0.00 0.00 0.00 2.87
2229 2280 5.248020 TGGCTCTTCTTTGATCTTCTTCTCT 59.752 40.000 0.00 0.00 0.00 3.10
2232 2298 7.148423 GGCTCTTCTTTGATCTTCTTCTCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
2236 2302 7.552050 TCTTTGATCTTCTTCTCTTTCCTCT 57.448 36.000 0.00 0.00 0.00 3.69
2297 2369 4.407296 CCCTCTAGGTCAATCTTTGCTAGT 59.593 45.833 0.00 0.00 30.28 2.57
2298 2370 5.598830 CCCTCTAGGTCAATCTTTGCTAGTA 59.401 44.000 0.00 0.00 30.28 1.82
2299 2371 6.268847 CCCTCTAGGTCAATCTTTGCTAGTAT 59.731 42.308 0.00 0.00 30.28 2.12
2317 2389 8.426489 TGCTAGTATCTCGGTTTTATTTGGTAT 58.574 33.333 0.00 0.00 0.00 2.73
2421 2517 8.707938 AAATAAAGGTGTACGATGTACTTACC 57.292 34.615 8.41 8.18 0.00 2.85
2422 2518 5.990120 AAAGGTGTACGATGTACTTACCT 57.010 39.130 11.34 11.34 38.62 3.08
2423 2519 5.990120 AAGGTGTACGATGTACTTACCTT 57.010 39.130 18.69 18.69 40.99 3.50
2424 2520 5.320549 AGGTGTACGATGTACTTACCTTG 57.679 43.478 11.34 0.00 33.53 3.61
2425 2521 3.861689 GGTGTACGATGTACTTACCTTGC 59.138 47.826 8.41 0.00 0.00 4.01
2503 2599 6.094325 TCTCAATTCCGTGTACAACAGTTTTT 59.906 34.615 0.00 0.00 0.00 1.94
2545 2641 2.217847 CGTACGGTAACAGTATGCATGC 59.782 50.000 11.82 11.82 42.53 4.06
2560 2656 1.015868 CATGCATGTATGTCGGCACA 58.984 50.000 18.91 0.00 39.34 4.57
2613 2709 7.616313 TCCAATATACATATATGTCCGTTGCA 58.384 34.615 21.49 8.66 41.97 4.08
2675 2771 7.563924 TGTCTATATAAGGCATGGGTACCTATC 59.436 40.741 12.72 5.59 42.60 2.08
2716 2812 1.761667 CCTGGCCTCTCTCTGGGAG 60.762 68.421 3.32 0.00 43.12 4.30
2737 2834 8.333235 TGGGAGAAGTAAAGGAATTAATGCTTA 58.667 33.333 0.00 0.00 38.99 3.09
2758 2855 0.332972 GGCTTCTGGAACCCCTTCAT 59.667 55.000 0.00 0.00 0.00 2.57
2773 2873 7.610580 ACCCCTTCATTAATTCTCTCTCTAG 57.389 40.000 0.00 0.00 0.00 2.43
2877 2977 2.730069 TGTGTTGACCGTACGTACAAG 58.270 47.619 24.50 17.12 0.00 3.16
3020 3120 2.764269 AGCCAGCTCTATAAGGTTCCA 58.236 47.619 0.00 0.00 31.91 3.53
3023 3123 3.742640 GCCAGCTCTATAAGGTTCCACTG 60.743 52.174 0.00 0.00 31.91 3.66
3270 3383 7.793888 GTGAGATATATGTTTTATGTGTGCACG 59.206 37.037 13.13 0.00 0.00 5.34
3296 3409 2.119655 GCTGGCATCCTGCTTCCAG 61.120 63.158 7.37 2.94 46.63 3.86
3308 3421 1.101331 GCTTCCAGGGCAATCAAGAG 58.899 55.000 0.00 0.00 0.00 2.85
3318 3431 6.294473 CAGGGCAATCAAGAGTGATATTACT 58.706 40.000 0.00 0.00 44.02 2.24
3322 3435 7.880195 GGGCAATCAAGAGTGATATTACTACAT 59.120 37.037 0.00 0.00 44.02 2.29
3511 3625 3.492102 TGCTTCTTAGTGCTGGTTTCT 57.508 42.857 0.00 0.00 0.00 2.52
3542 3656 3.264574 TGCCAAGCATTGTACTCCC 57.735 52.632 0.00 0.00 46.99 4.30
3564 3678 0.881118 ACAATGCCAAGCCTTGTACG 59.119 50.000 8.23 0.00 43.33 3.67
3658 3772 1.343142 GTTGCAAAGGACCGGGATTTT 59.657 47.619 6.32 0.00 0.00 1.82
3662 3776 4.601084 TGCAAAGGACCGGGATTTTATTA 58.399 39.130 6.32 0.00 0.00 0.98
3684 3798 1.620524 CCCCAAAAGGCATGGACTGAT 60.621 52.381 5.66 0.00 40.56 2.90
3922 4036 9.551734 TCCTTCACATAAACATCATATCTGAAG 57.448 33.333 0.00 0.00 36.42 3.02
4106 4220 2.875933 GTTTTGTCGACCCACAGATGAA 59.124 45.455 14.12 0.00 0.00 2.57
4131 4245 7.464358 ACTTTCGAAATGTGTAGCATTCATAC 58.536 34.615 11.70 0.00 46.29 2.39
4144 4258 4.876107 AGCATTCATACGTCCTTAAACTGG 59.124 41.667 0.00 0.00 0.00 4.00
4152 4266 5.494390 ACGTCCTTAAACTGGTTAATCCT 57.506 39.130 0.00 0.00 37.07 3.24
4236 4350 6.405397 GCAACCTATGTTAAATACAAGTGGGG 60.405 42.308 0.00 0.00 40.89 4.96
4280 4394 6.979238 ACTTACAGGCAGATAAGATCGTTTAC 59.021 38.462 8.78 0.00 33.44 2.01
4508 4960 8.143193 TGTGGGATGCATGAAATTATATGAAAC 58.857 33.333 2.46 0.00 0.00 2.78
4513 4965 9.270576 GATGCATGAAATTATATGAAACTAGCG 57.729 33.333 2.46 0.00 0.00 4.26
4643 5096 9.330063 TCAAAATTATATGTTTTGCCACAAACA 57.670 25.926 16.94 8.03 43.04 2.83
4672 5125 4.017126 ACCTAAGCTTCACAAAATAGCCC 58.983 43.478 0.00 0.00 35.53 5.19
4675 5128 5.885912 CCTAAGCTTCACAAAATAGCCCTTA 59.114 40.000 0.00 0.00 35.53 2.69
4686 5139 8.511321 CACAAAATAGCCCTTATATTCGCATTA 58.489 33.333 0.00 0.00 0.00 1.90
4688 5141 7.625828 AAATAGCCCTTATATTCGCATTACC 57.374 36.000 0.00 0.00 0.00 2.85
4881 5334 6.531021 CAAGATACCCCTCCGTGTATTATTT 58.469 40.000 0.00 0.00 0.00 1.40
5044 5498 8.762481 AAAAATAAAACAACTACTCCCTCTGT 57.238 30.769 0.00 0.00 0.00 3.41
5045 5499 7.981102 AAATAAAACAACTACTCCCTCTGTC 57.019 36.000 0.00 0.00 0.00 3.51
5046 5500 4.353383 AAAACAACTACTCCCTCTGTCC 57.647 45.455 0.00 0.00 0.00 4.02
5047 5501 1.546961 ACAACTACTCCCTCTGTCCG 58.453 55.000 0.00 0.00 0.00 4.79
5048 5502 0.818296 CAACTACTCCCTCTGTCCGG 59.182 60.000 0.00 0.00 0.00 5.14
5049 5503 0.702902 AACTACTCCCTCTGTCCGGA 59.297 55.000 0.00 0.00 0.00 5.14
5050 5504 0.702902 ACTACTCCCTCTGTCCGGAA 59.297 55.000 5.23 0.00 0.00 4.30
5051 5505 1.076677 ACTACTCCCTCTGTCCGGAAA 59.923 52.381 5.23 0.00 0.00 3.13
5052 5506 2.292323 ACTACTCCCTCTGTCCGGAAAT 60.292 50.000 5.23 0.00 0.00 2.17
5053 5507 2.544844 ACTCCCTCTGTCCGGAAATA 57.455 50.000 5.23 0.00 0.00 1.40
5054 5508 2.108970 ACTCCCTCTGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
5055 5509 2.292323 ACTCCCTCTGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
5056 5510 2.766828 CTCCCTCTGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
5057 5511 2.500098 TCCCTCTGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
5058 5512 2.236395 CCCTCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
5059 5513 3.522553 CCTCTGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
5060 5514 3.522553 CTCTGTCCGGAAATACTTGTCC 58.477 50.000 5.23 0.00 0.00 4.02
5061 5515 3.170717 TCTGTCCGGAAATACTTGTCCT 58.829 45.455 5.23 0.00 0.00 3.85
5062 5516 4.346730 TCTGTCCGGAAATACTTGTCCTA 58.653 43.478 5.23 0.00 0.00 2.94
5063 5517 4.401519 TCTGTCCGGAAATACTTGTCCTAG 59.598 45.833 5.23 0.00 0.00 3.02
5064 5518 4.346730 TGTCCGGAAATACTTGTCCTAGA 58.653 43.478 5.23 0.00 0.00 2.43
5065 5519 4.773674 TGTCCGGAAATACTTGTCCTAGAA 59.226 41.667 5.23 0.00 0.00 2.10
5066 5520 5.246656 TGTCCGGAAATACTTGTCCTAGAAA 59.753 40.000 5.23 0.00 0.00 2.52
5067 5521 6.070424 TGTCCGGAAATACTTGTCCTAGAAAT 60.070 38.462 5.23 0.00 0.00 2.17
5068 5522 6.258068 GTCCGGAAATACTTGTCCTAGAAATG 59.742 42.308 5.23 0.00 0.00 2.32
5069 5523 5.527582 CCGGAAATACTTGTCCTAGAAATGG 59.472 44.000 0.00 0.00 0.00 3.16
5070 5524 6.346096 CGGAAATACTTGTCCTAGAAATGGA 58.654 40.000 0.00 0.00 0.00 3.41
5071 5525 6.992715 CGGAAATACTTGTCCTAGAAATGGAT 59.007 38.462 0.00 0.00 35.87 3.41
5072 5526 8.148351 CGGAAATACTTGTCCTAGAAATGGATA 58.852 37.037 0.00 0.00 35.87 2.59
5073 5527 9.847224 GGAAATACTTGTCCTAGAAATGGATAA 57.153 33.333 0.00 0.00 35.87 1.75
5123 5577 7.455641 AGGTCTAGATACATCCATTTCTACG 57.544 40.000 0.00 0.00 0.00 3.51
5124 5578 7.232188 AGGTCTAGATACATCCATTTCTACGA 58.768 38.462 0.00 0.00 0.00 3.43
5125 5579 7.175293 AGGTCTAGATACATCCATTTCTACGAC 59.825 40.741 0.00 0.00 0.00 4.34
5126 5580 7.040617 GGTCTAGATACATCCATTTCTACGACA 60.041 40.741 0.00 0.00 0.00 4.35
5127 5581 8.350722 GTCTAGATACATCCATTTCTACGACAA 58.649 37.037 0.00 0.00 0.00 3.18
5128 5582 8.568794 TCTAGATACATCCATTTCTACGACAAG 58.431 37.037 0.00 0.00 0.00 3.16
5129 5583 7.113658 AGATACATCCATTTCTACGACAAGT 57.886 36.000 0.00 0.00 0.00 3.16
5130 5584 8.234136 AGATACATCCATTTCTACGACAAGTA 57.766 34.615 0.00 0.00 0.00 2.24
5131 5585 8.861086 AGATACATCCATTTCTACGACAAGTAT 58.139 33.333 0.00 0.00 34.34 2.12
5132 5586 9.477484 GATACATCCATTTCTACGACAAGTATT 57.523 33.333 0.00 0.00 34.34 1.89
5133 5587 9.832445 ATACATCCATTTCTACGACAAGTATTT 57.168 29.630 0.00 0.00 34.34 1.40
5134 5588 8.197988 ACATCCATTTCTACGACAAGTATTTC 57.802 34.615 0.00 0.00 34.34 2.17
5135 5589 7.280205 ACATCCATTTCTACGACAAGTATTTCC 59.720 37.037 0.00 0.00 34.34 3.13
5136 5590 5.808540 TCCATTTCTACGACAAGTATTTCCG 59.191 40.000 0.00 0.00 34.34 4.30
5137 5591 5.006358 CCATTTCTACGACAAGTATTTCCGG 59.994 44.000 0.00 0.00 34.34 5.14
5138 5592 5.389859 TTTCTACGACAAGTATTTCCGGA 57.610 39.130 0.00 0.00 34.34 5.14
5139 5593 4.361451 TCTACGACAAGTATTTCCGGAC 57.639 45.455 1.83 0.00 34.34 4.79
5140 5594 1.986698 ACGACAAGTATTTCCGGACG 58.013 50.000 1.83 3.25 0.00 4.79
5141 5595 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
5142 5596 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
5143 5597 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
5257 5714 5.684853 ATTTTCTGATTGGGATATGGGGA 57.315 39.130 0.00 0.00 0.00 4.81
5265 5722 1.761780 GGGATATGGGGAGAGGGGGA 61.762 65.000 0.00 0.00 0.00 4.81
5295 6102 9.816787 ATTAAATCCGGTTTACACCCAATATAT 57.183 29.630 0.00 0.00 40.52 0.86
5332 6139 2.634815 AGACATGGCTTGATGGCTAG 57.365 50.000 0.00 0.00 40.14 3.42
5345 6152 2.897271 TGGCTAGGAATTTGGCTGAA 57.103 45.000 0.00 0.00 0.00 3.02
5551 6358 4.940654 TCCACATGCGAATACTGATTTTCA 59.059 37.500 0.00 0.00 0.00 2.69
5558 6365 8.740369 CATGCGAATACTGATTTTCATTTCTTC 58.260 33.333 0.00 0.00 0.00 2.87
5597 6405 6.908825 TGCACATTGAACCTAAACATAGTTC 58.091 36.000 0.00 0.00 40.23 3.01
5731 6539 6.509418 TCAATGGCTGAAACCTGTTATAAC 57.491 37.500 8.75 8.75 0.00 1.89
5802 6610 7.607607 TGCTGTTCTAGTATCATTGTTTGTGAT 59.392 33.333 0.00 0.00 39.50 3.06
5820 6628 6.631971 TGTGATAAAATGCAAGAAGTGACA 57.368 33.333 0.00 0.00 0.00 3.58
5829 6637 4.923893 TGCAAGAAGTGACATGACAAAAG 58.076 39.130 0.00 0.00 0.00 2.27
5847 6655 2.203337 TGCAAGTGTGAGTGCCCC 60.203 61.111 0.00 0.00 40.14 5.80
5859 6667 2.158385 TGAGTGCCCCAAGGTAAATGTT 60.158 45.455 0.00 0.00 34.57 2.71
5869 6677 6.007703 CCCAAGGTAAATGTTAACTTCTCCA 58.992 40.000 7.22 0.00 0.00 3.86
5873 6681 9.244799 CAAGGTAAATGTTAACTTCTCCAAAAC 57.755 33.333 7.22 0.00 0.00 2.43
5893 6701 7.973944 CCAAAACTGGAAGCCTTATTTATGTAC 59.026 37.037 0.00 0.00 37.60 2.90
5903 6711 5.399842 GCCTTATTTATGTACCCCCTCCTTT 60.400 44.000 0.00 0.00 0.00 3.11
5923 6731 1.681793 TCAGGTCTATAAGGAGCGCAC 59.318 52.381 11.47 1.97 38.56 5.34
5938 6746 3.006940 AGCGCACGGATTTTGAGATTTA 58.993 40.909 11.47 0.00 0.00 1.40
5940 6748 3.181510 GCGCACGGATTTTGAGATTTACT 60.182 43.478 0.30 0.00 0.00 2.24
5987 6795 3.728845 TGAGTTATGCGGCCTAGAAATC 58.271 45.455 0.00 2.94 0.00 2.17
6019 6827 9.630098 ACTGTAAAATTAGACTCAAAATGCATG 57.370 29.630 0.00 0.00 0.00 4.06
6123 6931 9.060347 CATTGTATAAGCATATTGAGAGTGGTT 57.940 33.333 0.00 0.00 37.36 3.67
6151 6964 6.723131 AGCGGTAAAAGATGTTCTTAGTTC 57.277 37.500 0.00 0.00 35.27 3.01
6182 6995 4.213482 GGAACGTTCATTCTTGTACTTGCT 59.787 41.667 28.24 0.00 0.00 3.91
6475 7290 1.297456 GCAGCAGCTGGAGAGTTCAC 61.297 60.000 24.13 0.00 37.91 3.18
6530 7345 3.039011 TCTAAGATTCAGTAGCCCACCC 58.961 50.000 0.00 0.00 0.00 4.61
6534 7349 0.252197 ATTCAGTAGCCCACCCGAAC 59.748 55.000 0.00 0.00 0.00 3.95
6536 7351 1.079127 CAGTAGCCCACCCGAACTG 60.079 63.158 0.00 0.00 32.39 3.16
6537 7352 1.535687 AGTAGCCCACCCGAACTGT 60.536 57.895 0.00 0.00 0.00 3.55
6538 7353 1.079336 GTAGCCCACCCGAACTGTC 60.079 63.158 0.00 0.00 0.00 3.51
6539 7354 1.229082 TAGCCCACCCGAACTGTCT 60.229 57.895 0.00 0.00 0.00 3.41
6540 7355 0.834687 TAGCCCACCCGAACTGTCTT 60.835 55.000 0.00 0.00 0.00 3.01
6541 7356 0.834687 AGCCCACCCGAACTGTCTTA 60.835 55.000 0.00 0.00 0.00 2.10
6542 7357 0.035739 GCCCACCCGAACTGTCTTAA 59.964 55.000 0.00 0.00 0.00 1.85
6586 7401 2.032290 CGTCAGATGCCAGCATTACATG 60.032 50.000 6.57 4.50 36.70 3.21
6707 7522 5.569059 CCGATCATTTGTAACTGCAAACTTC 59.431 40.000 0.00 0.00 40.58 3.01
6932 7748 7.858498 AGCACCTATAATTACTTAACCACTGT 58.142 34.615 0.00 0.00 0.00 3.55
7016 7835 2.725641 CAGCAGCAGCAGCAACAA 59.274 55.556 12.92 0.00 45.49 2.83
7025 7844 1.921887 CAGCAGCAACAACAACAACAG 59.078 47.619 0.00 0.00 0.00 3.16
7233 8064 5.764686 ACAGTTCATCTTCTTGTGTATGCAA 59.235 36.000 0.00 0.00 0.00 4.08
7339 8170 1.229359 CCTGCCTCCATGGATGCTT 59.771 57.895 33.29 0.00 36.84 3.91
7548 8379 1.577468 TGTTCAGCAACACGTACCAG 58.423 50.000 0.00 0.00 37.61 4.00
7849 10048 9.206690 AGAATCTAGATAGAAAGGAATGTCACA 57.793 33.333 5.46 0.00 35.69 3.58
7858 10057 5.960811 AGAAAGGAATGTCACATCTAGAGGA 59.039 40.000 12.12 0.00 0.00 3.71
7931 10130 8.356657 TGTGTATAGCTATGCTTTTGTTTGTTT 58.643 29.630 20.58 0.00 40.44 2.83
7932 10131 9.191995 GTGTATAGCTATGCTTTTGTTTGTTTT 57.808 29.630 20.58 0.00 40.44 2.43
7933 10132 9.190858 TGTATAGCTATGCTTTTGTTTGTTTTG 57.809 29.630 20.58 0.00 40.44 2.44
7934 10133 9.191995 GTATAGCTATGCTTTTGTTTGTTTTGT 57.808 29.630 16.77 0.00 40.44 2.83
8205 10470 2.047750 GCCCGCTGCCTATAGAGC 60.048 66.667 0.00 2.20 0.00 4.09
8206 10471 2.872388 GCCCGCTGCCTATAGAGCA 61.872 63.158 12.49 12.86 38.82 4.26
8256 10521 5.679734 ATTTAACACACAAGAGTCAGCAG 57.320 39.130 0.00 0.00 0.00 4.24
8263 10528 0.598419 CAAGAGTCAGCAGCACGACA 60.598 55.000 15.29 0.00 34.48 4.35
8333 10598 0.249398 ACATCGCCCTGAACACCTAC 59.751 55.000 0.00 0.00 0.00 3.18
8349 10614 2.292521 ACCTACCAGAAGAGATGCCTCA 60.293 50.000 0.00 0.00 41.87 3.86
8350 10615 2.102252 CCTACCAGAAGAGATGCCTCAC 59.898 54.545 0.00 0.00 41.87 3.51
8351 10616 1.949799 ACCAGAAGAGATGCCTCACT 58.050 50.000 0.00 0.00 41.87 3.41
8353 10618 1.138661 CCAGAAGAGATGCCTCACTCC 59.861 57.143 0.00 0.00 41.87 3.85
8354 10619 2.109774 CAGAAGAGATGCCTCACTCCT 58.890 52.381 0.00 0.00 41.87 3.69
8355 10620 3.295093 CAGAAGAGATGCCTCACTCCTA 58.705 50.000 0.00 0.00 41.87 2.94
8357 10622 2.080654 AGAGATGCCTCACTCCTACC 57.919 55.000 0.00 0.00 41.87 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.487762 GGGTCGTTTGCATCTTCATGAA 59.512 45.455 8.12 8.12 30.57 2.57
45 46 4.843728 TGGTGAGAAGACAAGTGAAGTTT 58.156 39.130 0.00 0.00 0.00 2.66
91 92 4.908534 GGTATCTCCAACCAGGGAAACCA 61.909 52.174 0.00 0.00 45.02 3.67
140 141 1.135053 GTAGAACGTGGCCCTCTCTTC 60.135 57.143 0.00 0.00 0.00 2.87
397 419 5.300792 TGACCCTTTTAAGTTTGACATCACC 59.699 40.000 0.00 0.00 0.00 4.02
476 502 2.147150 GACTGGAACCTCTTTGACTGC 58.853 52.381 0.00 0.00 0.00 4.40
712 743 9.787532 CTCTTTCTCTCTCTCTATTGTGTTTAG 57.212 37.037 0.00 0.00 0.00 1.85
729 762 5.241403 TCAGTCTCAGTCTCTCTTTCTCT 57.759 43.478 0.00 0.00 0.00 3.10
734 767 2.083774 CGCTCAGTCTCAGTCTCTCTT 58.916 52.381 0.00 0.00 0.00 2.85
807 840 1.153628 GATCGAGTGTGGTTCCGGG 60.154 63.158 0.00 0.00 0.00 5.73
990 1023 1.160329 CGCGACCCATCCTGATTTCC 61.160 60.000 0.00 0.00 0.00 3.13
1275 1317 5.488919 CCTCCCTCCCAATATGTATGTATGT 59.511 44.000 0.00 0.00 0.00 2.29
1276 1318 5.488919 ACCTCCCTCCCAATATGTATGTATG 59.511 44.000 0.00 0.00 0.00 2.39
1277 1319 5.676125 ACCTCCCTCCCAATATGTATGTAT 58.324 41.667 0.00 0.00 0.00 2.29
1278 1320 5.101254 ACCTCCCTCCCAATATGTATGTA 57.899 43.478 0.00 0.00 0.00 2.29
1289 1331 0.638292 ACGGTATTACCTCCCTCCCA 59.362 55.000 11.05 0.00 35.66 4.37
1476 1520 3.306780 GGGCTAGCAGTAGAAACAAGTGA 60.307 47.826 18.24 0.00 0.00 3.41
1477 1521 3.003480 GGGCTAGCAGTAGAAACAAGTG 58.997 50.000 18.24 0.00 0.00 3.16
1502 1546 3.327757 ACACAAACTCAGAATAGGCAGGA 59.672 43.478 0.00 0.00 0.00 3.86
1560 1604 5.576447 AATCGTTACCCAAATAAGCAAGG 57.424 39.130 0.00 0.00 0.00 3.61
1594 1639 1.476085 CAGCTAGTGAGTGAGGACTGG 59.524 57.143 0.00 0.00 30.16 4.00
1620 1665 2.605366 CGAGAAAGGAAATCGGAGAAGC 59.395 50.000 0.00 0.00 43.58 3.86
1740 1785 5.316987 ACATATTAATTGTCCTAGGCAGGC 58.683 41.667 2.96 0.00 42.30 4.85
1743 1788 8.655901 TCACATACATATTAATTGTCCTAGGCA 58.344 33.333 2.96 2.51 0.00 4.75
1754 1799 7.385205 GCCTTCTCGTGTCACATACATATTAAT 59.615 37.037 3.42 0.00 41.10 1.40
1755 1800 6.700081 GCCTTCTCGTGTCACATACATATTAA 59.300 38.462 3.42 0.00 41.10 1.40
1756 1801 6.183360 TGCCTTCTCGTGTCACATACATATTA 60.183 38.462 3.42 0.00 41.10 0.98
1757 1802 5.050490 GCCTTCTCGTGTCACATACATATT 58.950 41.667 3.42 0.00 41.10 1.28
1787 1832 2.039084 CTGGGGCTGGGTCAGTATAATC 59.961 54.545 0.00 0.00 33.43 1.75
1844 1889 4.553742 CGAGTCTAGAACGATGTGGATGAG 60.554 50.000 13.14 0.00 0.00 2.90
1894 1939 2.561419 CACTGGACGGGAACTAGAAAGA 59.439 50.000 0.00 0.00 0.00 2.52
1967 2012 9.461312 TGGAAGCTGTGTTTATTATTGATAGTT 57.539 29.630 0.00 0.00 0.00 2.24
1969 2014 9.941664 CTTGGAAGCTGTGTTTATTATTGATAG 57.058 33.333 0.00 0.00 0.00 2.08
1970 2015 8.902806 CCTTGGAAGCTGTGTTTATTATTGATA 58.097 33.333 0.00 0.00 0.00 2.15
1971 2016 7.615365 TCCTTGGAAGCTGTGTTTATTATTGAT 59.385 33.333 0.00 0.00 0.00 2.57
1972 2017 6.945435 TCCTTGGAAGCTGTGTTTATTATTGA 59.055 34.615 0.00 0.00 0.00 2.57
1973 2018 7.094205 ACTCCTTGGAAGCTGTGTTTATTATTG 60.094 37.037 0.00 0.00 0.00 1.90
1982 2031 1.071385 CTCACTCCTTGGAAGCTGTGT 59.929 52.381 0.00 0.00 33.01 3.72
1996 2045 1.079266 CTCACTGCCCAGCTCACTC 60.079 63.158 0.00 0.00 0.00 3.51
2036 2085 2.564553 ATTCAGCGAGCTCCGTCCAC 62.565 60.000 8.47 0.00 41.15 4.02
2039 2088 1.922570 TTAATTCAGCGAGCTCCGTC 58.077 50.000 8.47 0.00 41.15 4.79
2050 2099 3.062763 AGATGCGAGGCGATTAATTCAG 58.937 45.455 0.00 0.00 0.00 3.02
2101 2150 3.381045 CGATGTACCATGCATAAGTCGT 58.619 45.455 0.00 0.00 0.00 4.34
2178 2229 1.662044 CCACTGCTTGGCAAGAACC 59.338 57.895 30.45 13.44 39.07 3.62
2196 2247 3.118112 TCAAAGAAGAGCCAGATCCATCC 60.118 47.826 0.00 0.00 0.00 3.51
2228 2279 9.913310 AGGGAGAAGAAATAAATAAGAGGAAAG 57.087 33.333 0.00 0.00 0.00 2.62
2229 2280 9.907229 GAGGGAGAAGAAATAAATAAGAGGAAA 57.093 33.333 0.00 0.00 0.00 3.13
2232 2298 9.913310 AAAGAGGGAGAAGAAATAAATAAGAGG 57.087 33.333 0.00 0.00 0.00 3.69
2247 2313 5.564550 CATCAAAGAGGAAAAGAGGGAGAA 58.435 41.667 0.00 0.00 0.00 2.87
2317 2389 8.203681 TGTACTGTATCTAGCTGGTCTATCTA 57.796 38.462 0.00 0.00 0.00 1.98
2319 2391 6.938030 ACTGTACTGTATCTAGCTGGTCTATC 59.062 42.308 3.21 0.00 0.00 2.08
2323 2395 6.056884 ACTACTGTACTGTATCTAGCTGGTC 58.943 44.000 12.40 0.00 0.00 4.02
2324 2396 6.003859 ACTACTGTACTGTATCTAGCTGGT 57.996 41.667 12.40 2.98 0.00 4.00
2325 2397 7.424227 GTACTACTGTACTGTATCTAGCTGG 57.576 44.000 12.40 0.00 44.08 4.85
2341 2426 8.764524 AACAAAGCAAAGATCTAGTACTACTG 57.235 34.615 0.00 0.00 0.00 2.74
2351 2436 7.147949 CCCTATCAATGAACAAAGCAAAGATCT 60.148 37.037 0.00 0.00 0.00 2.75
2422 2518 8.057855 AATGGTTTCATCATTAGCGATTTGCAA 61.058 33.333 0.00 0.00 38.32 4.08
2423 2519 6.627731 AATGGTTTCATCATTAGCGATTTGCA 60.628 34.615 0.00 0.00 38.32 4.08
2424 2520 4.671377 TGGTTTCATCATTAGCGATTTGC 58.329 39.130 0.00 0.00 46.98 3.68
2425 2521 7.614908 CAAATGGTTTCATCATTAGCGATTTG 58.385 34.615 0.00 0.00 34.15 2.32
2503 2599 0.738063 ACGAGTCGTTGCACAACACA 60.738 50.000 13.56 0.00 41.20 3.72
2545 2641 4.221342 GCATAAATGTGCCGACATACATG 58.779 43.478 0.00 0.00 42.30 3.21
2560 2656 5.473066 AGCACTTGAAAACAGGCATAAAT 57.527 34.783 0.00 0.00 0.00 1.40
2613 2709 6.443206 TCAAAGAGGGAAGAAAGAGATGAGAT 59.557 38.462 0.00 0.00 0.00 2.75
2646 2742 8.074363 AGGTACCCATGCCTTATATAGACATAT 58.926 37.037 8.74 0.00 37.77 1.78
2647 2743 7.427501 AGGTACCCATGCCTTATATAGACATA 58.572 38.462 8.74 0.00 37.77 2.29
2648 2744 6.272320 AGGTACCCATGCCTTATATAGACAT 58.728 40.000 8.74 0.00 37.77 3.06
2649 2745 5.661565 AGGTACCCATGCCTTATATAGACA 58.338 41.667 8.74 0.00 37.77 3.41
2675 2771 4.381863 GTCGTCTTGTATATATGTGGCACG 59.618 45.833 13.77 0.00 0.00 5.34
2716 2812 8.858003 GCCTTAAGCATTAATTCCTTTACTTC 57.142 34.615 0.00 0.00 40.24 3.01
2773 2873 8.327941 TGTGCAGCCTATTTATCTGAATTATC 57.672 34.615 0.00 0.00 0.00 1.75
2830 2930 3.200825 CCCACCATCTTGAACCTCACTAT 59.799 47.826 0.00 0.00 0.00 2.12
2831 2931 2.571653 CCCACCATCTTGAACCTCACTA 59.428 50.000 0.00 0.00 0.00 2.74
2877 2977 5.293560 AGAAGAAGCTCTTAATCCGTATGC 58.706 41.667 0.00 0.00 36.73 3.14
2970 3070 2.360801 TCTTGTAAAACAGCCAAGGTGC 59.639 45.455 0.00 0.00 36.94 5.01
3020 3120 5.106555 CGATCCTAAACTGAACAATTGCAGT 60.107 40.000 11.59 11.59 46.59 4.40
3023 3123 4.098416 GCGATCCTAAACTGAACAATTGC 58.902 43.478 5.05 0.00 0.00 3.56
3131 3234 7.774625 TGTGGATAATGATTGAAGCATTACAGA 59.225 33.333 16.92 8.37 40.02 3.41
3200 3310 3.643763 GCTGTATAGAACCATGAGTCCG 58.356 50.000 0.00 0.00 0.00 4.79
3296 3409 7.217200 TGTAGTAATATCACTCTTGATTGCCC 58.783 38.462 0.00 0.00 39.66 5.36
3318 3431 6.770785 AGTGCTCCTTTACTGTTCAAAATGTA 59.229 34.615 0.00 0.00 0.00 2.29
3322 3435 5.499139 CAGTGCTCCTTTACTGTTCAAAA 57.501 39.130 0.00 0.00 39.48 2.44
3433 3547 3.068165 GCAATAGCTTATCACAAACCCCC 59.932 47.826 0.00 0.00 37.91 5.40
3511 3625 3.966979 TGCTTGGCATCCTTCTAATTCA 58.033 40.909 0.00 0.00 31.71 2.57
3564 3678 8.465273 AGTACTAATTATGCCTTGGAAAATCC 57.535 34.615 0.00 0.00 36.96 3.01
3658 3772 4.169856 AGTCCATGCCTTTTGGGGATAATA 59.830 41.667 0.00 0.00 44.63 0.98
3684 3798 3.820467 CTGCAAGGAAAACTCACACCATA 59.180 43.478 0.00 0.00 0.00 2.74
3808 3922 8.373981 AGCAGCAAGAGTAATCATCATAATAGT 58.626 33.333 0.00 0.00 0.00 2.12
3922 4036 6.700081 GGAAAATCCAACAACAAGAAGGTTAC 59.300 38.462 0.00 0.00 36.28 2.50
4131 4245 5.731591 AGAGGATTAACCAGTTTAAGGACG 58.268 41.667 0.00 0.00 42.04 4.79
4152 4266 6.106673 GGTGAGACAAAATCCGAGATAAAGA 58.893 40.000 0.00 0.00 0.00 2.52
4236 4350 9.334693 CTGTAAGTTTGCAACTAGAAATTCATC 57.665 33.333 0.00 0.00 41.91 2.92
4280 4394 9.720769 TGTTTACTAGGTTCTTTTCATCCTTAG 57.279 33.333 0.00 0.00 0.00 2.18
4345 4459 7.659799 GGCCAAATTTACTAAAAATGTGAAGGT 59.340 33.333 0.00 0.00 28.55 3.50
4483 4935 8.362639 AGTTTCATATAATTTCATGCATCCCAC 58.637 33.333 0.00 0.00 0.00 4.61
4643 5096 9.614792 CTATTTTGTGAAGCTTAGGTAGGTTAT 57.385 33.333 0.00 0.00 44.30 1.89
4672 5125 7.962918 GCCAAATACAGGTAATGCGAATATAAG 59.037 37.037 0.00 0.00 0.00 1.73
4675 5128 5.183140 GGCCAAATACAGGTAATGCGAATAT 59.817 40.000 0.00 0.00 0.00 1.28
4686 5139 2.990740 TGAAAGGGCCAAATACAGGT 57.009 45.000 6.18 0.00 0.00 4.00
4688 5141 4.709397 TGGTTATGAAAGGGCCAAATACAG 59.291 41.667 6.18 0.00 0.00 2.74
4776 5229 9.581289 TTCAATAACCTTCTCTTACAATCCAAA 57.419 29.630 0.00 0.00 0.00 3.28
4781 5234 9.384764 GCTACTTCAATAACCTTCTCTTACAAT 57.615 33.333 0.00 0.00 0.00 2.71
5023 5477 5.337330 CGGACAGAGGGAGTAGTTGTTTTAT 60.337 44.000 0.00 0.00 0.00 1.40
5024 5478 4.021719 CGGACAGAGGGAGTAGTTGTTTTA 60.022 45.833 0.00 0.00 0.00 1.52
5028 5482 1.546961 CGGACAGAGGGAGTAGTTGT 58.453 55.000 0.00 0.00 0.00 3.32
5029 5483 0.818296 CCGGACAGAGGGAGTAGTTG 59.182 60.000 0.00 0.00 0.00 3.16
5031 5485 0.702902 TTCCGGACAGAGGGAGTAGT 59.297 55.000 1.83 0.00 33.01 2.73
5032 5486 1.848652 TTTCCGGACAGAGGGAGTAG 58.151 55.000 1.83 0.00 33.01 2.57
5033 5487 2.544844 ATTTCCGGACAGAGGGAGTA 57.455 50.000 1.83 0.00 33.01 2.59
5034 5488 2.108970 GTATTTCCGGACAGAGGGAGT 58.891 52.381 1.83 0.00 33.01 3.85
5035 5489 2.389715 AGTATTTCCGGACAGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
5036 5490 2.500098 CAAGTATTTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
5037 5491 2.236395 ACAAGTATTTCCGGACAGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
5038 5492 3.522553 GACAAGTATTTCCGGACAGAGG 58.477 50.000 1.83 0.00 0.00 3.69
5039 5493 3.195825 AGGACAAGTATTTCCGGACAGAG 59.804 47.826 1.83 0.00 36.95 3.35
5040 5494 3.170717 AGGACAAGTATTTCCGGACAGA 58.829 45.455 1.83 0.00 36.95 3.41
5041 5495 3.611766 AGGACAAGTATTTCCGGACAG 57.388 47.619 1.83 0.00 36.95 3.51
5042 5496 4.346730 TCTAGGACAAGTATTTCCGGACA 58.653 43.478 1.83 0.00 36.95 4.02
5043 5497 4.996788 TCTAGGACAAGTATTTCCGGAC 57.003 45.455 1.83 0.00 36.95 4.79
5044 5498 6.346096 CATTTCTAGGACAAGTATTTCCGGA 58.654 40.000 0.00 0.00 36.95 5.14
5045 5499 5.527582 CCATTTCTAGGACAAGTATTTCCGG 59.472 44.000 0.00 0.00 36.95 5.14
5046 5500 6.346096 TCCATTTCTAGGACAAGTATTTCCG 58.654 40.000 0.00 0.00 36.95 4.30
5047 5501 9.847224 TTATCCATTTCTAGGACAAGTATTTCC 57.153 33.333 0.00 0.00 38.13 3.13
5097 5551 9.179909 CGTAGAAATGGATGTATCTAGACCTAT 57.820 37.037 0.00 0.00 0.00 2.57
5098 5552 8.380867 TCGTAGAAATGGATGTATCTAGACCTA 58.619 37.037 0.00 0.00 0.00 3.08
5099 5553 7.175293 GTCGTAGAAATGGATGTATCTAGACCT 59.825 40.741 0.00 0.00 39.69 3.85
5100 5554 7.040617 TGTCGTAGAAATGGATGTATCTAGACC 60.041 40.741 0.00 0.00 39.69 3.85
5101 5555 7.872881 TGTCGTAGAAATGGATGTATCTAGAC 58.127 38.462 0.00 0.00 39.69 2.59
5102 5556 8.459911 TTGTCGTAGAAATGGATGTATCTAGA 57.540 34.615 0.00 0.00 39.69 2.43
5103 5557 8.353684 ACTTGTCGTAGAAATGGATGTATCTAG 58.646 37.037 0.00 0.00 39.69 2.43
5104 5558 8.234136 ACTTGTCGTAGAAATGGATGTATCTA 57.766 34.615 0.00 0.00 39.69 1.98
5105 5559 7.113658 ACTTGTCGTAGAAATGGATGTATCT 57.886 36.000 0.00 0.00 39.69 1.98
5106 5560 9.477484 AATACTTGTCGTAGAAATGGATGTATC 57.523 33.333 0.00 0.00 39.69 2.24
5107 5561 9.832445 AAATACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
5108 5562 9.309516 GAAATACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
5109 5563 7.280205 GGAAATACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
5110 5564 7.516785 CGGAAATACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
5111 5565 6.479001 CGGAAATACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
5112 5566 5.808540 CGGAAATACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
5113 5567 5.006358 CCGGAAATACTTGTCGTAGAAATGG 59.994 44.000 0.00 0.00 39.69 3.16
5114 5568 5.808540 TCCGGAAATACTTGTCGTAGAAATG 59.191 40.000 0.00 0.00 39.69 2.32
5115 5569 5.809051 GTCCGGAAATACTTGTCGTAGAAAT 59.191 40.000 5.23 0.00 39.69 2.17
5116 5570 5.163513 GTCCGGAAATACTTGTCGTAGAAA 58.836 41.667 5.23 0.00 39.69 2.52
5117 5571 4.672542 CGTCCGGAAATACTTGTCGTAGAA 60.673 45.833 5.23 0.00 39.69 2.10
5118 5572 3.181507 CGTCCGGAAATACTTGTCGTAGA 60.182 47.826 5.23 0.00 0.00 2.59
5119 5573 3.103738 CGTCCGGAAATACTTGTCGTAG 58.896 50.000 5.23 0.00 0.00 3.51
5120 5574 2.159393 CCGTCCGGAAATACTTGTCGTA 60.159 50.000 5.23 0.00 37.50 3.43
5121 5575 1.403249 CCGTCCGGAAATACTTGTCGT 60.403 52.381 5.23 0.00 37.50 4.34
5122 5576 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
5123 5577 2.094338 ACTCCGTCCGGAAATACTTGTC 60.094 50.000 5.23 0.00 44.66 3.18
5124 5578 1.897802 ACTCCGTCCGGAAATACTTGT 59.102 47.619 5.23 0.00 44.66 3.16
5125 5579 2.667473 ACTCCGTCCGGAAATACTTG 57.333 50.000 5.23 0.00 44.66 3.16
5126 5580 3.091545 TGTACTCCGTCCGGAAATACTT 58.908 45.455 21.24 0.00 44.66 2.24
5127 5581 2.726821 TGTACTCCGTCCGGAAATACT 58.273 47.619 21.24 0.00 44.66 2.12
5128 5582 3.722728 ATGTACTCCGTCCGGAAATAC 57.277 47.619 5.23 14.34 44.66 1.89
5129 5583 4.435425 CAAATGTACTCCGTCCGGAAATA 58.565 43.478 5.23 2.87 44.66 1.40
5130 5584 3.267483 CAAATGTACTCCGTCCGGAAAT 58.733 45.455 5.23 3.83 44.66 2.17
5131 5585 2.613474 CCAAATGTACTCCGTCCGGAAA 60.613 50.000 5.23 0.00 44.66 3.13
5132 5586 1.066716 CCAAATGTACTCCGTCCGGAA 60.067 52.381 5.23 0.00 44.66 4.30
5133 5587 0.533491 CCAAATGTACTCCGTCCGGA 59.467 55.000 0.00 0.00 42.90 5.14
5134 5588 0.248289 ACCAAATGTACTCCGTCCGG 59.752 55.000 0.00 0.00 0.00 5.14
5135 5589 2.088950 AACCAAATGTACTCCGTCCG 57.911 50.000 0.00 0.00 0.00 4.79
5136 5590 5.163374 ACCTATAACCAAATGTACTCCGTCC 60.163 44.000 0.00 0.00 0.00 4.79
5137 5591 5.910614 ACCTATAACCAAATGTACTCCGTC 58.089 41.667 0.00 0.00 0.00 4.79
5138 5592 5.945144 ACCTATAACCAAATGTACTCCGT 57.055 39.130 0.00 0.00 0.00 4.69
5139 5593 7.619964 AAAACCTATAACCAAATGTACTCCG 57.380 36.000 0.00 0.00 0.00 4.63
5140 5594 9.016438 TGAAAAACCTATAACCAAATGTACTCC 57.984 33.333 0.00 0.00 0.00 3.85
5257 5714 4.668335 ACCGGATTTAATAATTCCCCCTCT 59.332 41.667 9.46 0.00 0.00 3.69
5265 5722 7.957992 TGGGTGTAAACCGGATTTAATAATT 57.042 32.000 9.46 0.00 34.50 1.40
5295 6102 8.301002 GCCATGTCTACTTGTTTACCATAAAAA 58.699 33.333 0.00 0.00 0.00 1.94
5332 6139 6.701340 AGAATTTTAGGTTCAGCCAAATTCC 58.299 36.000 10.66 0.00 43.51 3.01
5442 6249 6.372381 GGACATTGCAAGCAAGGAAATTAATT 59.628 34.615 23.91 0.00 39.72 1.40
5454 6261 2.502142 AGAGATGGACATTGCAAGCA 57.498 45.000 4.94 0.00 0.00 3.91
5455 6262 2.223203 CGAAGAGATGGACATTGCAAGC 60.223 50.000 4.94 0.00 0.00 4.01
5463 6270 1.410517 GATGGAGCGAAGAGATGGACA 59.589 52.381 0.00 0.00 0.00 4.02
5571 6379 6.003950 ACTATGTTTAGGTTCAATGTGCAGT 58.996 36.000 0.00 0.00 0.00 4.40
5572 6380 6.500684 ACTATGTTTAGGTTCAATGTGCAG 57.499 37.500 0.00 0.00 0.00 4.41
5573 6381 6.714810 AGAACTATGTTTAGGTTCAATGTGCA 59.285 34.615 0.00 0.00 0.00 4.57
5694 6502 1.955778 CCATTGAAGTGCAGGAACACA 59.044 47.619 0.00 0.00 43.23 3.72
5802 6610 6.631971 TGTCATGTCACTTCTTGCATTTTA 57.368 33.333 0.00 0.00 0.00 1.52
5820 6628 3.696051 ACTCACACTTGCACTTTTGTCAT 59.304 39.130 0.00 0.00 0.00 3.06
5829 6637 2.555547 GGGGCACTCACACTTGCAC 61.556 63.158 0.00 0.00 41.75 4.57
5847 6655 9.244799 GTTTTGGAGAAGTTAACATTTACCTTG 57.755 33.333 8.61 0.00 0.00 3.61
5869 6677 7.123697 GGGTACATAAATAAGGCTTCCAGTTTT 59.876 37.037 1.30 0.55 0.00 2.43
5873 6681 5.070685 GGGGTACATAAATAAGGCTTCCAG 58.929 45.833 1.30 0.00 0.00 3.86
5903 6711 1.681793 GTGCGCTCCTTATAGACCTGA 59.318 52.381 9.73 0.00 0.00 3.86
5923 6731 6.908825 TGGTCAAAGTAAATCTCAAAATCCG 58.091 36.000 0.00 0.00 0.00 4.18
5938 6746 7.397221 TGATTGATCTAGTTGATGGTCAAAGT 58.603 34.615 0.00 0.00 38.22 2.66
5987 6795 7.962964 TTGAGTCTAATTTTACAGTGGTCTG 57.037 36.000 0.00 0.00 46.18 3.51
6019 6827 4.157840 CCCTCCTTTGTTTATAAGGTGTGC 59.842 45.833 0.00 0.00 42.29 4.57
6073 6881 7.573710 TGTGAGTAGATGGCAAGGTAATATTT 58.426 34.615 0.00 0.00 0.00 1.40
6074 6882 7.136822 TGTGAGTAGATGGCAAGGTAATATT 57.863 36.000 0.00 0.00 0.00 1.28
6076 6884 6.747414 ATGTGAGTAGATGGCAAGGTAATA 57.253 37.500 0.00 0.00 0.00 0.98
6085 6893 5.991606 TGCTTATACAATGTGAGTAGATGGC 59.008 40.000 0.00 0.00 0.00 4.40
6116 6924 5.899299 TCTTTTACCGCTATAGAACCACTC 58.101 41.667 3.21 0.00 0.00 3.51
6123 6931 8.910944 ACTAAGAACATCTTTTACCGCTATAGA 58.089 33.333 3.21 0.00 37.89 1.98
6151 6964 6.668323 ACAAGAATGAACGTTCCTTTGTATG 58.332 36.000 24.78 18.02 29.83 2.39
6159 6972 4.213482 AGCAAGTACAAGAATGAACGTTCC 59.787 41.667 24.78 10.18 0.00 3.62
6182 6995 9.807921 AGGAAAATTATTTTCTGTCAGAGGTAA 57.192 29.630 24.01 4.73 46.31 2.85
6301 7114 9.571810 TTCCACAATTATTCAGAATTCAAATCG 57.428 29.630 8.44 0.98 0.00 3.34
6475 7290 3.433513 TCTCGATCTGATGTGCTTCAG 57.566 47.619 0.00 8.30 43.70 3.02
6530 7345 6.362820 GTCCAGTTAAGACTTAAGACAGTTCG 59.637 42.308 10.09 0.00 32.54 3.95
6534 7349 6.982852 TCAGTCCAGTTAAGACTTAAGACAG 58.017 40.000 19.81 14.93 41.87 3.51
6536 7351 6.015265 ACCTCAGTCCAGTTAAGACTTAAGAC 60.015 42.308 10.09 11.56 41.87 3.01
6537 7352 6.015350 CACCTCAGTCCAGTTAAGACTTAAGA 60.015 42.308 10.09 0.14 41.87 2.10
6538 7353 6.159988 CACCTCAGTCCAGTTAAGACTTAAG 58.840 44.000 7.93 0.00 41.87 1.85
6539 7354 5.011738 CCACCTCAGTCCAGTTAAGACTTAA 59.988 44.000 3.44 3.44 41.87 1.85
6540 7355 4.527038 CCACCTCAGTCCAGTTAAGACTTA 59.473 45.833 0.00 0.00 41.87 2.24
6541 7356 3.325135 CCACCTCAGTCCAGTTAAGACTT 59.675 47.826 0.00 0.00 41.87 3.01
6542 7357 2.900546 CCACCTCAGTCCAGTTAAGACT 59.099 50.000 0.00 0.00 45.45 3.24
6586 7401 1.317613 TGCAAGGACCACATTCACAC 58.682 50.000 0.00 0.00 0.00 3.82
6670 7485 7.447374 ACAAATGATCGGAAACTTTATCACA 57.553 32.000 0.00 0.00 31.56 3.58
6671 7486 9.274065 GTTACAAATGATCGGAAACTTTATCAC 57.726 33.333 0.00 0.00 31.56 3.06
6707 7522 2.106166 AGATGGCTCTGCAAATAGAGGG 59.894 50.000 5.09 0.00 43.49 4.30
6932 7748 3.055891 TGAAGGATCAGATCAGCAACGAA 60.056 43.478 12.66 0.00 0.00 3.85
7014 7833 2.544277 CCCACTGCATCTGTTGTTGTTG 60.544 50.000 0.00 0.00 0.00 3.33
7015 7834 1.682854 CCCACTGCATCTGTTGTTGTT 59.317 47.619 0.00 0.00 0.00 2.83
7016 7835 1.133823 TCCCACTGCATCTGTTGTTGT 60.134 47.619 0.00 0.00 0.00 3.32
7025 7844 0.895100 TTTGGTGCTCCCACTGCATC 60.895 55.000 1.59 0.00 45.19 3.91
7044 7863 1.076513 GTTTTGGGTATGGGTCTGGGT 59.923 52.381 0.00 0.00 0.00 4.51
7190 8021 9.606631 TGAACTGTGCATATTATTACATGTACA 57.393 29.630 4.68 0.00 42.85 2.90
7204 8035 5.308014 ACACAAGAAGATGAACTGTGCATA 58.692 37.500 0.07 0.00 0.00 3.14
7208 8039 5.179929 TGCATACACAAGAAGATGAACTGTG 59.820 40.000 0.00 0.00 0.00 3.66
7339 8170 2.054458 TCAAGCGTTGAGGTGGCTA 58.946 52.632 0.00 0.00 35.64 3.93
7858 10057 8.624776 GTCTCTGCAGTATTATTGCCTATTTTT 58.375 33.333 14.67 0.00 40.81 1.94
7931 10130 8.319057 ACATTCTGGTATCACTTATAGGACAA 57.681 34.615 0.00 0.00 0.00 3.18
7932 10131 7.914427 ACATTCTGGTATCACTTATAGGACA 57.086 36.000 0.00 0.00 0.00 4.02
7933 10132 8.857098 TGTACATTCTGGTATCACTTATAGGAC 58.143 37.037 0.00 0.00 0.00 3.85
7934 10133 9.429109 TTGTACATTCTGGTATCACTTATAGGA 57.571 33.333 0.00 0.00 0.00 2.94
8205 10470 4.898829 TTTTATCCGATGATTGCACCTG 57.101 40.909 0.00 0.00 32.18 4.00
8206 10471 5.380043 AGATTTTATCCGATGATTGCACCT 58.620 37.500 0.00 0.00 32.18 4.00
8207 10472 5.695851 AGATTTTATCCGATGATTGCACC 57.304 39.130 0.00 0.00 32.18 5.01
8244 10509 0.598419 TGTCGTGCTGCTGACTCTTG 60.598 55.000 20.49 0.00 36.10 3.02
8245 10510 0.598680 GTGTCGTGCTGCTGACTCTT 60.599 55.000 20.49 0.00 36.10 2.85
8256 10521 0.667792 GAGGTCTTCCTGTGTCGTGC 60.668 60.000 0.00 0.00 45.24 5.34
8263 10528 4.283722 AGATTGTTAACGAGGTCTTCCTGT 59.716 41.667 1.30 0.00 45.24 4.00
8333 10598 1.138661 GGAGTGAGGCATCTCTTCTGG 59.861 57.143 4.26 0.00 40.58 3.86


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

AutoCloner maintained by Alex Coulton.