Multiple sequence alignment - TraesCS6D01G186200

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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 TraesCS6D01G186200 chr6D 100.000 5165 0 0 1 5165 243453186 243448022 0.000000e+00 9539.0
1 TraesCS6D01G186200 chr6D 96.040 2500 74 8 2685 5165 243425059 243422566 0.000000e+00 4045.0
2 TraesCS6D01G186200 chr6D 92.245 245 18 1 2166 2410 48088539 48088296 3.830000e-91 346.0
3 TraesCS6D01G186200 chr6D 98.507 134 2 0 1 134 354628897 354628764 2.400000e-58 237.0
4 TraesCS6D01G186200 chr6D 96.528 144 4 1 1 143 368311302 368311159 2.400000e-58 237.0
5 TraesCS6D01G186200 chr6D 96.377 138 5 0 1 138 374089462 374089325 1.450000e-55 228.0
6 TraesCS6D01G186200 chr6D 89.423 104 10 1 2632 2735 219787337 219787235 4.200000e-26 130.0
7 TraesCS6D01G186200 chr6D 87.850 107 12 1 2629 2735 323697152 323697047 1.950000e-24 124.0
8 TraesCS6D01G186200 chr6D 87.736 106 12 1 2629 2734 168219535 168219639 7.020000e-24 122.0
9 TraesCS6D01G186200 chr6D 86.916 107 13 1 2629 2735 95293690 95293795 9.090000e-23 119.0
10 TraesCS6D01G186200 chr6A 94.884 2795 109 18 773 3552 333957065 333959840 0.000000e+00 4338.0
11 TraesCS6D01G186200 chr6A 95.984 772 28 3 3842 4612 333960323 333961092 0.000000e+00 1251.0
12 TraesCS6D01G186200 chr6A 98.635 293 4 0 3554 3846 333959874 333960166 2.130000e-143 520.0
13 TraesCS6D01G186200 chr6A 88.889 108 10 2 2629 2735 457379366 457379472 1.170000e-26 132.0
14 TraesCS6D01G186200 chr6B 95.061 1478 47 6 2076 3552 334453945 334452493 0.000000e+00 2302.0
15 TraesCS6D01G186200 chr6B 93.942 1172 47 11 790 1957 334455156 334454005 0.000000e+00 1749.0
16 TraesCS6D01G186200 chr6B 94.477 688 16 5 3554 4239 334452334 334451667 0.000000e+00 1040.0
17 TraesCS6D01G186200 chr6B 91.710 386 19 2 4294 4678 334451549 334451176 1.650000e-144 523.0
18 TraesCS6D01G186200 chr6B 79.306 749 111 26 1666 2411 279090485 279089778 7.780000e-133 484.0
19 TraesCS6D01G186200 chr6B 88.670 203 20 2 4694 4895 334444536 334444336 1.440000e-60 244.0
20 TraesCS6D01G186200 chr6B 90.476 105 9 1 2631 2735 331039843 331039740 2.510000e-28 137.0
21 TraesCS6D01G186200 chr5A 88.727 275 28 3 2135 2408 671549205 671549477 2.980000e-87 333.0
22 TraesCS6D01G186200 chr7B 89.883 257 25 1 2152 2408 647000774 647001029 3.860000e-86 329.0
23 TraesCS6D01G186200 chr7B 88.934 244 21 2 1666 1909 242353111 242353348 3.910000e-76 296.0
24 TraesCS6D01G186200 chr7B 75.979 562 103 24 131 673 75586819 75587367 1.430000e-65 261.0
25 TraesCS6D01G186200 chr5D 87.805 287 25 7 1665 1949 434362548 434362270 1.390000e-85 327.0
26 TraesCS6D01G186200 chr5D 97.761 134 3 0 1 134 80418086 80417953 1.120000e-56 231.0
27 TraesCS6D01G186200 chr5D 97.080 137 3 1 1 136 563384729 563384865 4.020000e-56 230.0
28 TraesCS6D01G186200 chr5D 96.403 139 4 1 1 139 452696089 452695952 1.450000e-55 228.0
29 TraesCS6D01G186200 chr5D 88.991 109 11 1 2627 2735 162425305 162425198 3.240000e-27 134.0
30 TraesCS6D01G186200 chr5D 89.423 104 10 1 2632 2735 387237865 387237763 4.200000e-26 130.0
31 TraesCS6D01G186200 chr3D 84.412 340 46 7 1 337 104342593 104342928 1.390000e-85 327.0
32 TraesCS6D01G186200 chr3D 84.868 304 34 5 1658 1954 575968112 575967814 3.910000e-76 296.0
33 TraesCS6D01G186200 chr3D 79.947 379 63 11 131 501 471393060 471393433 3.070000e-67 267.0
34 TraesCS6D01G186200 chr3D 89.720 107 10 1 2629 2735 497902664 497902769 9.020000e-28 135.0
35 TraesCS6D01G186200 chr3D 100.000 29 0 0 2740 2768 254114671 254114643 3.000000e-03 54.7
36 TraesCS6D01G186200 chr3B 88.087 277 31 2 2135 2411 771762601 771762327 1.390000e-85 327.0
37 TraesCS6D01G186200 chr3B 88.000 275 31 2 2135 2408 750326916 750327189 1.790000e-84 324.0
38 TraesCS6D01G186200 chr3B 86.328 256 35 0 2153 2408 380516995 380517250 3.940000e-71 279.0
39 TraesCS6D01G186200 chr3B 75.185 270 42 16 525 780 227825814 227826072 2.540000e-18 104.0
40 TraesCS6D01G186200 chr7D 89.494 257 26 1 2152 2408 580318520 580318775 1.790000e-84 324.0
41 TraesCS6D01G186200 chr7D 77.739 575 81 27 130 667 139868830 139869394 5.020000e-80 309.0
42 TraesCS6D01G186200 chr7D 84.507 142 19 3 2630 2769 481177367 481177507 2.510000e-28 137.0
43 TraesCS6D01G186200 chr7D 80.315 127 11 10 665 780 53346083 53345960 3.310000e-12 84.2
44 TraesCS6D01G186200 chr1B 90.336 238 22 1 1668 1904 341934886 341934649 1.400000e-80 311.0
45 TraesCS6D01G186200 chr1B 85.496 262 31 6 1668 1928 238682768 238682513 3.070000e-67 267.0
46 TraesCS6D01G186200 chr5B 77.758 553 88 21 129 663 270630815 270630280 1.810000e-79 307.0
47 TraesCS6D01G186200 chr5B 80.247 405 65 12 131 526 523409544 523409146 1.820000e-74 291.0
48 TraesCS6D01G186200 chr5B 76.441 590 97 27 139 710 429428318 429427753 1.090000e-71 281.0
49 TraesCS6D01G186200 chr5B 95.745 141 6 0 1 141 300199605 300199465 1.450000e-55 228.0
50 TraesCS6D01G186200 chr5B 85.217 115 16 1 1841 1955 118561506 118561393 3.270000e-22 117.0
51 TraesCS6D01G186200 chr7A 77.844 501 88 19 130 620 705485508 705485021 6.540000e-74 289.0
52 TraesCS6D01G186200 chr2B 85.612 278 29 6 1668 1944 404167683 404167416 1.090000e-71 281.0
53 TraesCS6D01G186200 chrUn 84.122 296 37 7 1665 1958 74618884 74618597 1.420000e-70 278.0
54 TraesCS6D01G186200 chrUn 86.667 105 13 1 2631 2735 310883104 310883001 1.180000e-21 115.0
55 TraesCS6D01G186200 chrUn 85.047 107 15 1 2629 2735 348740513 348740618 1.970000e-19 108.0
56 TraesCS6D01G186200 chrUn 85.047 107 15 1 2629 2735 364369465 364369570 1.970000e-19 108.0
57 TraesCS6D01G186200 chrUn 85.047 107 15 1 2629 2735 374196422 374196317 1.970000e-19 108.0
58 TraesCS6D01G186200 chrUn 85.047 107 15 1 2629 2735 374198280 374198175 1.970000e-19 108.0
59 TraesCS6D01G186200 chrUn 85.047 107 15 1 2629 2735 374285583 374285478 1.970000e-19 108.0
60 TraesCS6D01G186200 chrUn 85.000 100 15 0 2636 2735 41441801 41441702 9.150000e-18 102.0
61 TraesCS6D01G186200 chr4B 79.551 401 70 12 130 524 232206665 232206271 5.090000e-70 276.0
62 TraesCS6D01G186200 chr4B 87.963 108 11 2 2629 2735 212497120 212497226 5.430000e-25 126.0
63 TraesCS6D01G186200 chr2D 92.763 152 9 2 1 152 429812840 429812691 8.710000e-53 219.0
64 TraesCS6D01G186200 chr2D 83.803 142 20 3 2629 2768 206238969 206239109 1.170000e-26 132.0
65 TraesCS6D01G186200 chr1D 86.331 139 16 2 2629 2767 438324119 438324254 1.160000e-31 148.0
66 TraesCS6D01G186200 chr1D 89.720 107 10 1 2629 2735 166827478 166827373 9.020000e-28 135.0
67 TraesCS6D01G186200 chr1D 89.720 107 10 1 2629 2735 277359726 277359831 9.020000e-28 135.0
68 TraesCS6D01G186200 chr4D 89.815 108 10 1 2628 2735 23322718 23322824 2.510000e-28 137.0
69 TraesCS6D01G186200 chr4D 87.850 107 12 1 2629 2735 423598955 423599060 1.950000e-24 124.0
70 TraesCS6D01G186200 chr4D 88.462 104 11 1 2632 2735 469604708 469604606 1.950000e-24 124.0
71 TraesCS6D01G186200 chr3A 82.979 141 19 3 2629 2767 367786447 367786310 7.020000e-24 122.0
72 TraesCS6D01G186200 chr2A 88.235 85 7 3 697 780 737234360 737234442 1.180000e-16 99.0
73 TraesCS6D01G186200 chr4A 96.970 33 1 0 2740 2772 681713068 681713100 7.220000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G186200 chr6D 243448022 243453186 5164 True 9539.000000 9539 100.0000 1 5165 1 chr6D.!!$R4 5164
1 TraesCS6D01G186200 chr6D 243422566 243425059 2493 True 4045.000000 4045 96.0400 2685 5165 1 chr6D.!!$R3 2480
2 TraesCS6D01G186200 chr6A 333957065 333961092 4027 False 2036.333333 4338 96.5010 773 4612 3 chr6A.!!$F2 3839
3 TraesCS6D01G186200 chr6B 334451176 334455156 3980 True 1403.500000 2302 93.7975 790 4678 4 chr6B.!!$R4 3888
4 TraesCS6D01G186200 chr6B 279089778 279090485 707 True 484.000000 484 79.3060 1666 2411 1 chr6B.!!$R1 745
5 TraesCS6D01G186200 chr7B 75586819 75587367 548 False 261.000000 261 75.9790 131 673 1 chr7B.!!$F1 542
6 TraesCS6D01G186200 chr7D 139868830 139869394 564 False 309.000000 309 77.7390 130 667 1 chr7D.!!$F1 537
7 TraesCS6D01G186200 chr5B 270630280 270630815 535 True 307.000000 307 77.7580 129 663 1 chr5B.!!$R2 534
8 TraesCS6D01G186200 chr5B 429427753 429428318 565 True 281.000000 281 76.4410 139 710 1 chr5B.!!$R4 571

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
772 819 0.106708 AAGAAGCGCTCCTCAACACA 59.893 50.0 12.06 0.0 0.00 3.72 F
775 822 0.179045 AAGCGCTCCTCAACACAGTT 60.179 50.0 12.06 0.0 0.00 3.16 F
1911 1966 0.329261 TGCCAGGGAAACATCTCCAG 59.671 55.0 0.00 0.0 37.20 3.86 F
2643 2745 0.466555 ACGTAAAAAGTGGCAGCCCA 60.467 50.0 9.64 0.0 39.32 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 1952 0.256177 GGGTCCTGGAGATGTTTCCC 59.744 60.000 0.00 0.00 36.35 3.97 R
2316 2417 0.400213 AAGGGTCGGTTTGAGATGCA 59.600 50.000 0.00 0.00 0.00 3.96 R
2835 2937 3.142951 TGGAATACCACAAGTTGTTCCG 58.857 45.455 15.59 6.19 41.49 4.30 R
4476 4966 0.820482 TCGTCACAACTCCCTCGTCA 60.820 55.000 0.00 0.00 0.00 4.35 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
32 33 8.952278 TGTATTCACACATGTATTTAGGTTTCC 58.048 33.333 0.00 0.00 0.00 3.13
33 34 6.489127 TTCACACATGTATTTAGGTTTCCG 57.511 37.500 0.00 0.00 0.00 4.30
34 35 5.795972 TCACACATGTATTTAGGTTTCCGA 58.204 37.500 0.00 0.00 0.00 4.55
35 36 6.411376 TCACACATGTATTTAGGTTTCCGAT 58.589 36.000 0.00 0.00 0.00 4.18
36 37 6.537301 TCACACATGTATTTAGGTTTCCGATC 59.463 38.462 0.00 0.00 0.00 3.69
37 38 6.315144 CACACATGTATTTAGGTTTCCGATCA 59.685 38.462 0.00 0.00 0.00 2.92
38 39 6.882140 ACACATGTATTTAGGTTTCCGATCAA 59.118 34.615 0.00 0.00 0.00 2.57
39 40 7.556275 ACACATGTATTTAGGTTTCCGATCAAT 59.444 33.333 0.00 0.00 0.00 2.57
40 41 9.051679 CACATGTATTTAGGTTTCCGATCAATA 57.948 33.333 0.00 0.00 0.00 1.90
41 42 9.052759 ACATGTATTTAGGTTTCCGATCAATAC 57.947 33.333 0.00 0.00 0.00 1.89
42 43 9.051679 CATGTATTTAGGTTTCCGATCAATACA 57.948 33.333 10.21 10.21 39.01 2.29
43 44 9.621629 ATGTATTTAGGTTTCCGATCAATACAA 57.378 29.630 11.29 0.66 38.47 2.41
44 45 9.621629 TGTATTTAGGTTTCCGATCAATACAAT 57.378 29.630 6.89 0.00 34.35 2.71
47 48 8.801882 TTTAGGTTTCCGATCAATACAATTCT 57.198 30.769 0.00 0.00 0.00 2.40
48 49 9.893634 TTTAGGTTTCCGATCAATACAATTCTA 57.106 29.630 0.00 0.00 0.00 2.10
49 50 9.542462 TTAGGTTTCCGATCAATACAATTCTAG 57.458 33.333 0.00 0.00 0.00 2.43
50 51 6.483640 AGGTTTCCGATCAATACAATTCTAGC 59.516 38.462 0.00 0.00 0.00 3.42
51 52 6.260050 GGTTTCCGATCAATACAATTCTAGCA 59.740 38.462 0.00 0.00 0.00 3.49
52 53 7.041098 GGTTTCCGATCAATACAATTCTAGCAT 60.041 37.037 0.00 0.00 0.00 3.79
53 54 7.425577 TTCCGATCAATACAATTCTAGCATG 57.574 36.000 0.00 0.00 0.00 4.06
54 55 6.758254 TCCGATCAATACAATTCTAGCATGA 58.242 36.000 0.00 0.00 0.00 3.07
55 56 7.216494 TCCGATCAATACAATTCTAGCATGAA 58.784 34.615 0.00 0.00 0.00 2.57
56 57 7.879677 TCCGATCAATACAATTCTAGCATGAAT 59.120 33.333 0.00 0.00 38.19 2.57
57 58 9.154847 CCGATCAATACAATTCTAGCATGAATA 57.845 33.333 0.00 0.00 35.82 1.75
214 215 0.108585 AAGCAAAGCCGTTCCTCTCA 59.891 50.000 0.00 0.00 0.00 3.27
256 260 9.759259 GAAAACATGTTCTTTTTCTTTTTCTGG 57.241 29.630 12.39 0.00 38.27 3.86
257 261 8.846943 AAACATGTTCTTTTTCTTTTTCTGGT 57.153 26.923 12.39 0.00 0.00 4.00
258 262 8.846943 AACATGTTCTTTTTCTTTTTCTGGTT 57.153 26.923 4.92 0.00 0.00 3.67
314 320 1.221466 CTCTCGCGACAGCAAAACCA 61.221 55.000 3.71 0.00 45.49 3.67
372 386 3.034721 TCGTTTATGAGAAGCACGGTT 57.965 42.857 0.00 0.00 0.00 4.44
373 387 3.395639 TCGTTTATGAGAAGCACGGTTT 58.604 40.909 0.00 0.00 0.00 3.27
408 422 1.954146 GCAAACGTGCCTCTCGTGA 60.954 57.895 0.00 0.00 45.68 4.35
411 425 1.329292 CAAACGTGCCTCTCGTGAAAA 59.671 47.619 0.00 0.00 41.38 2.29
429 443 1.981256 AACAAAACCATGCCTCTCGT 58.019 45.000 0.00 0.00 0.00 4.18
430 444 1.981256 ACAAAACCATGCCTCTCGTT 58.019 45.000 0.00 0.00 0.00 3.85
496 521 4.261888 GTGCCTCTCGCGAAAGAA 57.738 55.556 11.91 0.00 42.08 2.52
653 700 1.121789 CTTAAAAAGCCGAAAACGCGC 59.878 47.619 5.73 0.00 0.00 6.86
692 739 3.813529 AAACAAAATTCGGAGAGAGCG 57.186 42.857 0.00 0.00 38.43 5.03
700 747 3.456365 GGAGAGAGCGCCAGAGCA 61.456 66.667 2.29 0.00 39.83 4.26
722 769 2.049985 ACGTGACGTGCTCTCAGC 60.050 61.111 10.91 0.00 39.18 4.26
723 770 2.807045 CGTGACGTGCTCTCAGCC 60.807 66.667 0.00 0.00 41.51 4.85
724 771 2.433318 GTGACGTGCTCTCAGCCC 60.433 66.667 0.00 0.00 41.51 5.19
725 772 2.917227 TGACGTGCTCTCAGCCCA 60.917 61.111 0.00 0.00 41.51 5.36
726 773 2.433318 GACGTGCTCTCAGCCCAC 60.433 66.667 0.00 0.00 41.51 4.61
727 774 3.941657 GACGTGCTCTCAGCCCACC 62.942 68.421 0.00 0.00 41.51 4.61
731 778 4.704833 GCTCTCAGCCCACCGCAA 62.705 66.667 0.00 0.00 41.38 4.85
732 779 2.435586 CTCTCAGCCCACCGCAAG 60.436 66.667 0.00 0.00 41.38 4.01
733 780 3.241530 TCTCAGCCCACCGCAAGT 61.242 61.111 0.00 0.00 41.38 3.16
734 781 3.052082 CTCAGCCCACCGCAAGTG 61.052 66.667 0.00 0.00 46.83 3.16
744 791 2.183478 ACCGCAAGTGATCATTGTGA 57.817 45.000 22.26 0.00 39.89 3.58
745 792 2.079158 ACCGCAAGTGATCATTGTGAG 58.921 47.619 22.26 17.03 39.89 3.51
746 793 1.399440 CCGCAAGTGATCATTGTGAGG 59.601 52.381 22.26 16.79 39.89 3.86
747 794 1.202110 CGCAAGTGATCATTGTGAGGC 60.202 52.381 18.62 8.26 39.89 4.70
748 795 2.089980 GCAAGTGATCATTGTGAGGCT 58.910 47.619 0.00 0.00 0.00 4.58
749 796 2.490903 GCAAGTGATCATTGTGAGGCTT 59.509 45.455 0.00 0.00 0.00 4.35
750 797 3.427233 GCAAGTGATCATTGTGAGGCTTC 60.427 47.826 0.00 0.00 0.00 3.86
751 798 2.996631 AGTGATCATTGTGAGGCTTCC 58.003 47.619 0.00 0.00 0.00 3.46
752 799 1.667724 GTGATCATTGTGAGGCTTCCG 59.332 52.381 0.00 0.00 0.00 4.30
753 800 1.554617 TGATCATTGTGAGGCTTCCGA 59.445 47.619 0.00 0.00 0.00 4.55
754 801 2.027285 TGATCATTGTGAGGCTTCCGAA 60.027 45.455 0.00 0.00 0.00 4.30
755 802 2.099141 TCATTGTGAGGCTTCCGAAG 57.901 50.000 3.56 3.56 0.00 3.79
756 803 1.623311 TCATTGTGAGGCTTCCGAAGA 59.377 47.619 12.54 0.00 0.00 2.87
757 804 2.038426 TCATTGTGAGGCTTCCGAAGAA 59.962 45.455 12.54 0.00 0.00 2.52
764 811 3.787458 CTTCCGAAGAAGCGCTCC 58.213 61.111 12.06 0.00 42.97 4.70
765 812 1.216710 CTTCCGAAGAAGCGCTCCT 59.783 57.895 12.06 0.00 42.97 3.69
766 813 0.804156 CTTCCGAAGAAGCGCTCCTC 60.804 60.000 12.06 5.48 42.97 3.71
767 814 1.532604 TTCCGAAGAAGCGCTCCTCA 61.533 55.000 12.06 0.00 0.00 3.86
768 815 1.079819 CCGAAGAAGCGCTCCTCAA 60.080 57.895 12.06 0.00 0.00 3.02
769 816 1.355066 CCGAAGAAGCGCTCCTCAAC 61.355 60.000 12.06 2.99 0.00 3.18
770 817 0.667487 CGAAGAAGCGCTCCTCAACA 60.667 55.000 12.06 0.00 0.00 3.33
771 818 0.793250 GAAGAAGCGCTCCTCAACAC 59.207 55.000 12.06 0.00 0.00 3.32
772 819 0.106708 AAGAAGCGCTCCTCAACACA 59.893 50.000 12.06 0.00 0.00 3.72
773 820 0.320247 AGAAGCGCTCCTCAACACAG 60.320 55.000 12.06 0.00 0.00 3.66
774 821 0.601311 GAAGCGCTCCTCAACACAGT 60.601 55.000 12.06 0.00 0.00 3.55
775 822 0.179045 AAGCGCTCCTCAACACAGTT 60.179 50.000 12.06 0.00 0.00 3.16
776 823 0.882042 AGCGCTCCTCAACACAGTTG 60.882 55.000 2.64 3.58 0.00 3.16
777 824 1.571460 CGCTCCTCAACACAGTTGC 59.429 57.895 5.06 0.00 0.00 4.17
778 825 0.882042 CGCTCCTCAACACAGTTGCT 60.882 55.000 5.06 0.00 0.00 3.91
779 826 0.871057 GCTCCTCAACACAGTTGCTC 59.129 55.000 5.06 0.00 0.00 4.26
780 827 1.517242 CTCCTCAACACAGTTGCTCC 58.483 55.000 5.06 0.00 0.00 4.70
781 828 1.071385 CTCCTCAACACAGTTGCTCCT 59.929 52.381 5.06 0.00 0.00 3.69
782 829 1.202687 TCCTCAACACAGTTGCTCCTG 60.203 52.381 5.06 2.20 38.45 3.86
783 830 1.233019 CTCAACACAGTTGCTCCTGG 58.767 55.000 5.06 0.00 36.75 4.45
784 831 0.546122 TCAACACAGTTGCTCCTGGT 59.454 50.000 5.06 1.42 36.75 4.00
785 832 1.765904 TCAACACAGTTGCTCCTGGTA 59.234 47.619 5.06 0.00 36.75 3.25
786 833 2.171659 TCAACACAGTTGCTCCTGGTAA 59.828 45.455 5.06 0.00 36.75 2.85
787 834 3.149196 CAACACAGTTGCTCCTGGTAAT 58.851 45.455 7.87 0.00 36.75 1.89
788 835 3.059352 ACACAGTTGCTCCTGGTAATC 57.941 47.619 7.87 0.00 36.75 1.75
811 858 6.434302 TCAATCCAGGTCATTGATTTGGTAT 58.566 36.000 15.08 8.04 35.71 2.73
815 862 5.065914 CCAGGTCATTGATTTGGTATCGAT 58.934 41.667 2.16 2.16 0.00 3.59
832 879 3.213506 TCGATGGCCCATGAAATACTTG 58.786 45.455 0.00 0.00 0.00 3.16
847 894 2.629017 ACTTGGGCCCAAATTGATCT 57.371 45.000 36.16 11.14 35.33 2.75
848 895 2.906568 ACTTGGGCCCAAATTGATCTT 58.093 42.857 36.16 11.48 35.33 2.40
918 968 1.638133 CCTGAGTCGATTGCAGAGTG 58.362 55.000 12.04 0.00 0.00 3.51
919 969 0.997932 CTGAGTCGATTGCAGAGTGC 59.002 55.000 6.35 0.00 45.29 4.40
920 970 0.605083 TGAGTCGATTGCAGAGTGCT 59.395 50.000 0.00 0.00 45.31 4.40
921 971 1.001293 TGAGTCGATTGCAGAGTGCTT 59.999 47.619 0.00 0.00 45.31 3.91
922 972 1.658095 GAGTCGATTGCAGAGTGCTTC 59.342 52.381 0.00 0.00 45.31 3.86
923 973 1.274728 AGTCGATTGCAGAGTGCTTCT 59.725 47.619 0.00 0.00 45.31 2.85
924 974 2.072298 GTCGATTGCAGAGTGCTTCTT 58.928 47.619 0.00 0.00 45.31 2.52
963 1013 0.541998 TCGACTCCAGGAAGCCTTCA 60.542 55.000 6.80 0.00 0.00 3.02
964 1014 0.390472 CGACTCCAGGAAGCCTTCAC 60.390 60.000 6.80 0.00 0.00 3.18
965 1015 0.980423 GACTCCAGGAAGCCTTCACT 59.020 55.000 6.80 0.00 0.00 3.41
966 1016 0.980423 ACTCCAGGAAGCCTTCACTC 59.020 55.000 6.80 0.00 0.00 3.51
971 1021 0.912006 AGGAAGCCTTCACTCCTCCC 60.912 60.000 6.80 0.00 0.00 4.30
972 1022 1.201429 GGAAGCCTTCACTCCTCCCA 61.201 60.000 6.80 0.00 0.00 4.37
975 1026 2.224159 GCCTTCACTCCTCCCACCA 61.224 63.158 0.00 0.00 0.00 4.17
1044 1095 3.878519 CTCGTCCGAGACTCCGCC 61.879 72.222 11.12 0.00 44.53 6.13
1232 1283 3.220110 TCTCGATAAGTACGGCCTCAAT 58.780 45.455 0.00 0.00 0.00 2.57
1563 1616 5.329035 AGTTGTTGAACTGTTGAGCAATT 57.671 34.783 11.72 5.79 41.12 2.32
1571 1624 4.916983 ACTGTTGAGCAATTTGTAGCAA 57.083 36.364 0.00 0.00 0.00 3.91
1733 1786 1.208259 CCGCCAGTTTTCAGTTTTGC 58.792 50.000 0.00 0.00 0.00 3.68
1839 1894 1.067565 TGCAAAAACACAGTTTCCGCA 60.068 42.857 12.16 12.16 30.59 5.69
1879 1934 2.565391 TGTATCGGGAGAAAGCAGTTGA 59.435 45.455 0.00 0.00 45.37 3.18
1911 1966 0.329261 TGCCAGGGAAACATCTCCAG 59.671 55.000 0.00 0.00 37.20 3.86
2014 2075 0.814410 CGACGGAGGAGCTAGCTACA 60.814 60.000 28.69 0.00 0.00 2.74
2022 2083 1.305201 GAGCTAGCTACAGCGACTCT 58.695 55.000 19.38 0.00 46.52 3.24
2044 2142 1.552348 CCGCTCGAATCGATTCAGCC 61.552 60.000 32.83 22.35 37.50 4.85
2073 2171 4.504689 GCTAGCTAGCTCCTGGATTGATTT 60.505 45.833 33.71 0.00 45.62 2.17
2127 2225 1.064060 GCCGTTTGGATTGATTCGAGG 59.936 52.381 0.00 0.00 37.49 4.63
2158 2256 3.838271 GCGAGCCATCCTGGACGA 61.838 66.667 0.00 0.00 40.96 4.20
2159 2257 3.133014 CGAGCCATCCTGGACGAT 58.867 61.111 0.00 0.00 40.96 3.73
2195 2293 1.312371 GCCCTTTTATGCGCTGTCCA 61.312 55.000 9.73 0.00 0.00 4.02
2316 2417 1.415672 TTTGAGGGGTCTGTTCGGCT 61.416 55.000 0.00 0.00 0.00 5.52
2320 2421 2.045926 GGGTCTGTTCGGCTGCAT 60.046 61.111 0.50 0.00 0.00 3.96
2606 2708 7.987268 TTAGTTCAGAGTATGATTTAGCACG 57.013 36.000 0.00 0.00 37.89 5.34
2620 2722 1.217882 AGCACGGAGTTCTGTTTTCG 58.782 50.000 0.00 0.00 41.61 3.46
2633 2735 5.146482 TCTGTTTTCGTGGACGTAAAAAG 57.854 39.130 12.70 12.70 41.94 2.27
2643 2745 0.466555 ACGTAAAAAGTGGCAGCCCA 60.467 50.000 9.64 0.00 39.32 5.36
2661 2763 1.086067 CAGTGCATGTAGGTCCTGCG 61.086 60.000 0.00 0.00 39.86 5.18
3322 3424 1.533756 CCCCATCTTTGCAAATACGCG 60.534 52.381 13.23 3.53 33.35 6.01
3372 3474 2.132762 GTGCGGGTATTGAAGATACCG 58.867 52.381 8.63 0.00 43.76 4.02
3377 3479 3.067742 CGGGTATTGAAGATACCGACAGT 59.932 47.826 8.63 0.00 43.76 3.55
3378 3480 4.441079 CGGGTATTGAAGATACCGACAGTT 60.441 45.833 8.63 0.00 43.76 3.16
3379 3481 5.048507 GGGTATTGAAGATACCGACAGTTC 58.951 45.833 8.63 0.00 43.76 3.01
3453 3558 4.903045 CCTTGAGGTACAACTTCCCTTA 57.097 45.455 0.00 0.00 34.56 2.69
4177 4601 6.527023 ACTGTATCTGTGACGATTCTAAAACG 59.473 38.462 0.00 0.00 0.00 3.60
4227 4653 9.099454 AGACATCTTAACATTTTAGATTCGGAC 57.901 33.333 0.00 0.00 0.00 4.79
4470 4960 8.792830 TGGTAACTTTTATGAAGGAGAATGAG 57.207 34.615 0.00 0.00 37.61 2.90
4543 5045 5.728637 ATTTCCAATCCCTTGTTTGAGAC 57.271 39.130 0.00 0.00 0.00 3.36
4616 5118 2.572290 TCGGATGAGCTGAGATACGAA 58.428 47.619 0.00 0.00 31.93 3.85
4636 5138 5.413833 ACGAAGAGAGGTTAAGTTATGACGA 59.586 40.000 0.00 0.00 0.00 4.20
4742 5244 1.540797 GGCAGAGAGGCATGATCACTC 60.541 57.143 0.00 0.00 43.51 3.51
4771 5273 7.364408 CCAGGAAGATTGATTTTGGTGAATCAT 60.364 37.037 1.60 0.00 43.43 2.45
4787 5289 2.627515 TCATGTTATGAGAGCCAGGC 57.372 50.000 1.84 1.84 33.59 4.85
4809 5311 2.778679 GCACCACTTGATCGTCGC 59.221 61.111 0.00 0.00 0.00 5.19
4810 5312 1.738099 GCACCACTTGATCGTCGCT 60.738 57.895 0.00 0.00 0.00 4.93
4814 5316 0.994995 CCACTTGATCGTCGCTGAAG 59.005 55.000 0.00 0.00 0.00 3.02
4874 5377 1.316651 GCATTCTTCTGGGCAGGATC 58.683 55.000 0.00 0.00 0.00 3.36
4875 5378 1.409241 GCATTCTTCTGGGCAGGATCA 60.409 52.381 0.00 0.00 0.00 2.92
4901 5404 3.081409 TAGTGGAGGGAAGGGCGC 61.081 66.667 0.00 0.00 0.00 6.53
4912 5415 2.548127 GAAGGGCGCAGTTTCATGGC 62.548 60.000 10.83 0.00 0.00 4.40
4915 5418 1.734117 GGCGCAGTTTCATGGCAAC 60.734 57.895 10.83 0.00 0.00 4.17
4923 5426 1.523154 TTTCATGGCAACGGGTCTGC 61.523 55.000 0.00 0.00 42.51 4.26
4945 5465 1.064685 GGTTTAGGGGTGATGGACCTG 60.065 57.143 0.00 0.00 45.33 4.00
4946 5466 1.913419 GTTTAGGGGTGATGGACCTGA 59.087 52.381 0.00 0.00 45.33 3.86
4974 5494 0.246635 TGGTCTTGCTCTTCGGCTAC 59.753 55.000 0.00 0.00 0.00 3.58
5020 5540 1.450531 GATTCGAGGCCATGGCAAGG 61.451 60.000 36.56 23.74 44.11 3.61
5055 5575 1.800586 CGGACAAACATGTGAGGACAG 59.199 52.381 0.00 0.00 34.87 3.51
5097 5617 2.238521 GGCATGTTGGAAAAGGAGACA 58.761 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.120465 CGGAAACCTAAATACATGTGTGAATAC 58.880 37.037 9.11 0.00 0.00 1.89
8 9 8.041919 TCGGAAACCTAAATACATGTGTGAATA 58.958 33.333 9.11 0.00 0.00 1.75
9 10 6.882140 TCGGAAACCTAAATACATGTGTGAAT 59.118 34.615 9.11 0.00 0.00 2.57
10 11 6.231951 TCGGAAACCTAAATACATGTGTGAA 58.768 36.000 9.11 0.00 0.00 3.18
12 13 6.315144 TGATCGGAAACCTAAATACATGTGTG 59.685 38.462 9.11 0.00 0.00 3.82
14 15 6.918892 TGATCGGAAACCTAAATACATGTG 57.081 37.500 9.11 0.00 0.00 3.21
15 16 9.052759 GTATTGATCGGAAACCTAAATACATGT 57.947 33.333 2.69 2.69 32.10 3.21
18 19 9.621629 ATTGTATTGATCGGAAACCTAAATACA 57.378 29.630 0.00 0.00 37.29 2.29
21 22 9.408648 AGAATTGTATTGATCGGAAACCTAAAT 57.591 29.630 0.00 0.00 0.00 1.40
22 23 8.801882 AGAATTGTATTGATCGGAAACCTAAA 57.198 30.769 0.00 0.00 0.00 1.85
23 24 9.542462 CTAGAATTGTATTGATCGGAAACCTAA 57.458 33.333 0.00 0.00 0.00 2.69
24 25 7.656137 GCTAGAATTGTATTGATCGGAAACCTA 59.344 37.037 0.00 0.00 0.00 3.08
25 26 6.483640 GCTAGAATTGTATTGATCGGAAACCT 59.516 38.462 0.00 0.00 0.00 3.50
26 27 6.260050 TGCTAGAATTGTATTGATCGGAAACC 59.740 38.462 0.00 0.00 0.00 3.27
27 28 7.246674 TGCTAGAATTGTATTGATCGGAAAC 57.753 36.000 0.00 0.00 0.00 2.78
28 29 7.714813 TCATGCTAGAATTGTATTGATCGGAAA 59.285 33.333 0.00 0.00 0.00 3.13
29 30 7.216494 TCATGCTAGAATTGTATTGATCGGAA 58.784 34.615 0.00 0.00 0.00 4.30
30 31 6.758254 TCATGCTAGAATTGTATTGATCGGA 58.242 36.000 0.00 0.00 0.00 4.55
31 32 7.425577 TTCATGCTAGAATTGTATTGATCGG 57.574 36.000 0.00 0.00 0.00 4.18
108 109 7.830099 AAAAGAAGGAAATATGCCATAGAGG 57.170 36.000 0.00 0.00 41.84 3.69
137 138 2.224042 GGTTGTGCCTCTTTTGGAAAGG 60.224 50.000 1.04 0.00 0.00 3.11
241 245 4.032786 CGTGCCAACCAGAAAAAGAAAAAG 59.967 41.667 0.00 0.00 0.00 2.27
272 277 1.790387 GCTTGTGCTTTCGCGAGAT 59.210 52.632 9.59 0.00 39.65 2.75
303 309 1.251251 GAGAGGCATGGTTTTGCTGT 58.749 50.000 0.00 0.00 42.38 4.40
304 310 0.169672 CGAGAGGCATGGTTTTGCTG 59.830 55.000 0.00 0.00 42.38 4.41
359 373 0.465460 AGGCAAAACCGTGCTTCTCA 60.465 50.000 0.00 0.00 46.52 3.27
364 378 1.961277 CGAGAGGCAAAACCGTGCT 60.961 57.895 0.00 0.00 46.52 4.40
372 386 3.253955 GCTTTCGCGAGAGGCAAA 58.746 55.556 25.84 8.54 43.84 3.68
394 408 0.179094 TGTTTTCACGAGAGGCACGT 60.179 50.000 0.00 0.00 44.83 4.49
406 420 3.243367 CGAGAGGCATGGTTTTGTTTTCA 60.243 43.478 0.00 0.00 0.00 2.69
408 422 2.693074 ACGAGAGGCATGGTTTTGTTTT 59.307 40.909 0.00 0.00 0.00 2.43
411 425 1.608590 CAACGAGAGGCATGGTTTTGT 59.391 47.619 0.00 0.00 0.00 2.83
474 499 1.155424 TTTCGCGAGAGGCACGTTTT 61.155 50.000 9.59 0.00 43.84 2.43
475 500 1.557443 CTTTCGCGAGAGGCACGTTT 61.557 55.000 18.35 0.00 43.84 3.60
477 502 2.416244 TTCTTTCGCGAGAGGCACGT 62.416 55.000 24.53 0.00 43.84 4.49
496 521 0.937231 CCGCGAAATGCACGGTTTTT 60.937 50.000 8.23 0.00 46.97 1.94
577 623 1.464997 CACCGGTCTTGCTTAGCTTTC 59.535 52.381 2.59 0.00 0.00 2.62
633 680 1.121789 GCGCGTTTTCGGCTTTTTAAG 59.878 47.619 8.43 0.00 44.29 1.85
675 722 0.375106 GGCGCTCTCTCCGAATTTTG 59.625 55.000 7.64 0.00 0.00 2.44
676 723 0.036388 TGGCGCTCTCTCCGAATTTT 60.036 50.000 7.64 0.00 0.00 1.82
677 724 0.460987 CTGGCGCTCTCTCCGAATTT 60.461 55.000 7.64 0.00 0.00 1.82
678 725 1.142748 CTGGCGCTCTCTCCGAATT 59.857 57.895 7.64 0.00 0.00 2.17
679 726 1.733402 CTCTGGCGCTCTCTCCGAAT 61.733 60.000 7.64 0.00 0.00 3.34
680 727 2.361230 TCTGGCGCTCTCTCCGAA 60.361 61.111 7.64 0.00 0.00 4.30
681 728 2.826287 CTCTGGCGCTCTCTCCGA 60.826 66.667 7.64 0.00 0.00 4.55
682 729 4.567385 GCTCTGGCGCTCTCTCCG 62.567 72.222 7.64 0.00 0.00 4.63
683 730 3.456365 TGCTCTGGCGCTCTCTCC 61.456 66.667 7.64 0.00 42.25 3.71
684 731 2.202730 GTGCTCTGGCGCTCTCTC 60.203 66.667 7.64 0.00 44.66 3.20
685 732 4.127040 CGTGCTCTGGCGCTCTCT 62.127 66.667 7.64 0.00 45.75 3.10
686 733 4.121669 TCGTGCTCTGGCGCTCTC 62.122 66.667 7.64 0.00 45.75 3.20
687 734 4.427661 GTCGTGCTCTGGCGCTCT 62.428 66.667 7.64 0.00 45.75 4.09
688 735 4.724602 TGTCGTGCTCTGGCGCTC 62.725 66.667 7.64 0.00 45.75 5.03
714 761 4.704833 TTGCGGTGGGCTGAGAGC 62.705 66.667 0.00 0.00 44.05 4.09
715 762 2.435586 CTTGCGGTGGGCTGAGAG 60.436 66.667 0.00 0.00 44.05 3.20
716 763 3.241530 ACTTGCGGTGGGCTGAGA 61.242 61.111 0.00 0.00 44.05 3.27
717 764 2.809861 ATCACTTGCGGTGGGCTGAG 62.810 60.000 9.26 0.00 45.38 3.35
718 765 2.803155 GATCACTTGCGGTGGGCTGA 62.803 60.000 9.26 0.00 45.38 4.26
719 766 2.360350 ATCACTTGCGGTGGGCTG 60.360 61.111 9.26 0.00 45.38 4.85
720 767 2.045926 GATCACTTGCGGTGGGCT 60.046 61.111 9.26 0.00 45.38 5.19
721 768 1.315257 AATGATCACTTGCGGTGGGC 61.315 55.000 0.00 3.71 45.38 5.36
722 769 0.452987 CAATGATCACTTGCGGTGGG 59.547 55.000 0.00 0.00 45.38 4.61
723 770 1.135603 CACAATGATCACTTGCGGTGG 60.136 52.381 0.00 0.00 45.38 4.61
724 771 1.805943 TCACAATGATCACTTGCGGTG 59.194 47.619 0.00 0.89 46.60 4.94
725 772 2.079158 CTCACAATGATCACTTGCGGT 58.921 47.619 0.00 0.00 0.00 5.68
726 773 1.399440 CCTCACAATGATCACTTGCGG 59.601 52.381 0.00 0.00 0.00 5.69
727 774 1.202110 GCCTCACAATGATCACTTGCG 60.202 52.381 0.00 0.00 0.00 4.85
728 775 2.089980 AGCCTCACAATGATCACTTGC 58.910 47.619 0.00 0.00 0.00 4.01
729 776 3.128242 GGAAGCCTCACAATGATCACTTG 59.872 47.826 0.00 6.92 0.00 3.16
730 777 3.350833 GGAAGCCTCACAATGATCACTT 58.649 45.455 0.00 0.00 0.00 3.16
731 778 2.679059 CGGAAGCCTCACAATGATCACT 60.679 50.000 0.00 0.00 0.00 3.41
732 779 1.667724 CGGAAGCCTCACAATGATCAC 59.332 52.381 0.00 0.00 0.00 3.06
733 780 1.554617 TCGGAAGCCTCACAATGATCA 59.445 47.619 0.00 0.00 0.00 2.92
734 781 2.315925 TCGGAAGCCTCACAATGATC 57.684 50.000 0.00 0.00 0.00 2.92
735 782 2.237143 TCTTCGGAAGCCTCACAATGAT 59.763 45.455 12.90 0.00 0.00 2.45
736 783 1.623311 TCTTCGGAAGCCTCACAATGA 59.377 47.619 12.90 0.00 0.00 2.57
737 784 2.099141 TCTTCGGAAGCCTCACAATG 57.901 50.000 12.90 0.00 0.00 2.82
738 785 2.704572 CTTCTTCGGAAGCCTCACAAT 58.295 47.619 12.90 0.00 43.85 2.71
739 786 2.169832 CTTCTTCGGAAGCCTCACAA 57.830 50.000 12.90 0.50 43.85 3.33
740 787 3.914984 CTTCTTCGGAAGCCTCACA 57.085 52.632 12.90 0.00 43.85 3.58
748 795 1.215647 GAGGAGCGCTTCTTCGGAA 59.784 57.895 21.76 0.00 0.00 4.30
749 796 1.532604 TTGAGGAGCGCTTCTTCGGA 61.533 55.000 21.76 3.33 34.78 4.55
750 797 1.079819 TTGAGGAGCGCTTCTTCGG 60.080 57.895 21.76 0.00 34.78 4.30
751 798 0.667487 TGTTGAGGAGCGCTTCTTCG 60.667 55.000 21.76 0.00 34.78 3.79
752 799 0.793250 GTGTTGAGGAGCGCTTCTTC 59.207 55.000 21.76 14.89 32.77 2.87
753 800 0.106708 TGTGTTGAGGAGCGCTTCTT 59.893 50.000 21.76 5.35 0.00 2.52
754 801 0.320247 CTGTGTTGAGGAGCGCTTCT 60.320 55.000 20.88 20.88 0.00 2.85
755 802 0.601311 ACTGTGTTGAGGAGCGCTTC 60.601 55.000 13.26 10.56 0.00 3.86
756 803 0.179045 AACTGTGTTGAGGAGCGCTT 60.179 50.000 13.26 0.00 0.00 4.68
757 804 0.882042 CAACTGTGTTGAGGAGCGCT 60.882 55.000 11.27 11.27 0.00 5.92
758 805 1.571460 CAACTGTGTTGAGGAGCGC 59.429 57.895 0.00 0.00 0.00 5.92
759 806 0.882042 AGCAACTGTGTTGAGGAGCG 60.882 55.000 13.75 0.00 0.00 5.03
760 807 0.871057 GAGCAACTGTGTTGAGGAGC 59.129 55.000 13.75 0.00 0.00 4.70
761 808 1.071385 AGGAGCAACTGTGTTGAGGAG 59.929 52.381 13.75 0.00 0.00 3.69
762 809 1.131638 AGGAGCAACTGTGTTGAGGA 58.868 50.000 13.75 0.00 0.00 3.71
763 810 1.233019 CAGGAGCAACTGTGTTGAGG 58.767 55.000 13.75 0.00 33.81 3.86
764 811 1.233019 CCAGGAGCAACTGTGTTGAG 58.767 55.000 13.75 0.00 36.75 3.02
765 812 0.546122 ACCAGGAGCAACTGTGTTGA 59.454 50.000 13.75 0.00 36.75 3.18
766 813 2.254546 TACCAGGAGCAACTGTGTTG 57.745 50.000 6.12 6.12 36.75 3.33
767 814 3.181445 TGATTACCAGGAGCAACTGTGTT 60.181 43.478 0.00 0.00 36.75 3.32
768 815 2.371841 TGATTACCAGGAGCAACTGTGT 59.628 45.455 0.00 6.87 36.75 3.72
769 816 3.057969 TGATTACCAGGAGCAACTGTG 57.942 47.619 0.00 2.04 36.75 3.66
770 817 3.788227 TTGATTACCAGGAGCAACTGT 57.212 42.857 0.00 0.00 36.75 3.55
771 818 3.629398 GGATTGATTACCAGGAGCAACTG 59.371 47.826 0.00 1.04 38.21 3.16
772 819 3.266772 TGGATTGATTACCAGGAGCAACT 59.733 43.478 0.00 0.00 0.00 3.16
773 820 3.620488 TGGATTGATTACCAGGAGCAAC 58.380 45.455 0.00 0.00 0.00 4.17
774 821 3.889815 CTGGATTGATTACCAGGAGCAA 58.110 45.455 0.00 0.00 46.76 3.91
775 822 3.565764 CTGGATTGATTACCAGGAGCA 57.434 47.619 0.00 0.00 46.76 4.26
780 827 6.066690 ATCAATGACCTGGATTGATTACCAG 58.933 40.000 14.60 0.00 44.55 4.00
781 828 5.449297 TCAATGACCTGGATTGATTACCA 57.551 39.130 0.00 0.00 35.38 3.25
787 834 4.676109 ACCAAATCAATGACCTGGATTGA 58.324 39.130 16.65 11.80 42.53 2.57
788 835 6.513884 CGATACCAAATCAATGACCTGGATTG 60.514 42.308 16.65 0.78 31.98 2.67
811 858 3.213506 CAAGTATTTCATGGGCCATCGA 58.786 45.455 18.16 14.79 0.00 3.59
815 862 2.157640 CCCAAGTATTTCATGGGCCA 57.842 50.000 9.61 9.61 46.12 5.36
963 1013 0.695803 GATGGGATGGTGGGAGGAGT 60.696 60.000 0.00 0.00 0.00 3.85
964 1014 1.762522 CGATGGGATGGTGGGAGGAG 61.763 65.000 0.00 0.00 0.00 3.69
965 1015 1.766059 CGATGGGATGGTGGGAGGA 60.766 63.158 0.00 0.00 0.00 3.71
966 1016 1.130054 ATCGATGGGATGGTGGGAGG 61.130 60.000 0.00 0.00 32.92 4.30
971 1021 3.999001 CACAGATAATCGATGGGATGGTG 59.001 47.826 0.00 0.33 34.93 4.17
972 1022 3.008375 CCACAGATAATCGATGGGATGGT 59.992 47.826 0.00 0.00 34.93 3.55
975 1026 2.354103 CGCCACAGATAATCGATGGGAT 60.354 50.000 0.00 0.00 36.78 3.85
1010 1061 4.083862 GGACGACCACCCTGGAGC 62.084 72.222 0.00 0.00 40.96 4.70
1208 1259 0.039346 GGCCGTACTTATCGAGAGGC 60.039 60.000 0.00 0.00 40.49 4.70
1563 1616 4.892934 AGTTTCTGAACCCAATTGCTACAA 59.107 37.500 0.00 0.00 36.39 2.41
1571 1624 3.611025 TCCCAAGTTTCTGAACCCAAT 57.389 42.857 0.00 0.00 36.39 3.16
1607 1660 0.883833 GATCAGCCCACCAAACACTG 59.116 55.000 0.00 0.00 0.00 3.66
1733 1786 0.459759 GTTCGGGCTACTTCTTCCGG 60.460 60.000 0.00 0.00 42.44 5.14
1839 1894 1.905512 GGGCACCGTAGAAGTGGAT 59.094 57.895 0.00 0.00 40.86 3.41
1897 1952 0.256177 GGGTCCTGGAGATGTTTCCC 59.744 60.000 0.00 0.00 36.35 3.97
2022 2083 0.454196 TGAATCGATTCGAGCGGACA 59.546 50.000 28.07 10.17 39.91 4.02
2073 2171 2.820619 CGTCGCCGTAGCTAGCTCA 61.821 63.158 23.26 5.10 36.60 4.26
2127 2225 2.861375 CTCGCACGAAGCTAGCTAC 58.139 57.895 19.70 4.68 42.61 3.58
2148 2246 4.241555 GCCGCCATCGTCCAGGAT 62.242 66.667 0.00 0.00 0.00 3.24
2158 2256 1.525995 CCAAATACGGAGCCGCCAT 60.526 57.895 9.14 0.00 44.19 4.40
2159 2257 2.124901 CCAAATACGGAGCCGCCA 60.125 61.111 9.14 0.00 44.19 5.69
2316 2417 0.400213 AAGGGTCGGTTTGAGATGCA 59.600 50.000 0.00 0.00 0.00 3.96
2320 2421 3.132925 CGTTTTAAGGGTCGGTTTGAGA 58.867 45.455 0.00 0.00 0.00 3.27
2606 2708 1.525619 CGTCCACGAAAACAGAACTCC 59.474 52.381 0.00 0.00 43.02 3.85
2620 2722 1.334689 GCTGCCACTTTTTACGTCCAC 60.335 52.381 0.00 0.00 0.00 4.02
2633 2735 3.755628 CATGCACTGGGCTGCCAC 61.756 66.667 22.05 10.55 45.15 5.01
2828 2930 5.678132 ACCACAAGTTGTTCCGTTATTAC 57.322 39.130 5.57 0.00 0.00 1.89
2835 2937 3.142951 TGGAATACCACAAGTTGTTCCG 58.857 45.455 15.59 6.19 41.49 4.30
3322 3424 4.685628 CAGCAAACATTGTATTGGTTCACC 59.314 41.667 11.22 0.00 35.25 4.02
3372 3474 4.450419 CCTGATGTGACAAGAAGAACTGTC 59.550 45.833 0.00 0.00 0.00 3.51
3487 3592 7.462571 AAGTACCATTACTTTCCATGAAACC 57.537 36.000 0.00 0.00 44.77 3.27
4177 4601 9.048446 TCTATTTATAAGGGCACAAAACGATAC 57.952 33.333 0.00 0.00 0.00 2.24
4470 4960 3.813166 TCACAACTCCCTCGTCAAAATTC 59.187 43.478 0.00 0.00 0.00 2.17
4476 4966 0.820482 TCGTCACAACTCCCTCGTCA 60.820 55.000 0.00 0.00 0.00 4.35
4543 5045 2.096496 GCACATCTCTCAAATTCCCACG 59.904 50.000 0.00 0.00 0.00 4.94
4616 5118 7.337167 TCTACTCGTCATAACTTAACCTCTCT 58.663 38.462 0.00 0.00 0.00 3.10
4636 5138 8.954834 ATTGATCTATGGAGAACATCTCTACT 57.045 34.615 7.27 0.00 42.95 2.57
4742 5244 3.758554 ACCAAAATCAATCTTCCTGGTCG 59.241 43.478 0.00 0.00 29.76 4.79
4771 5273 0.913934 TGGGCCTGGCTCTCATAACA 60.914 55.000 21.13 0.00 0.00 2.41
4787 5289 2.390599 CGATCAAGTGGTGCGTGGG 61.391 63.158 0.00 0.00 0.00 4.61
4883 5386 2.901042 CGCCCTTCCCTCCACTAC 59.099 66.667 0.00 0.00 0.00 2.73
4884 5387 3.081409 GCGCCCTTCCCTCCACTA 61.081 66.667 0.00 0.00 0.00 2.74
4901 5404 0.240945 GACCCGTTGCCATGAAACTG 59.759 55.000 0.00 0.00 0.00 3.16
4923 5426 0.107361 GTCCATCACCCCTAAACCGG 60.107 60.000 0.00 0.00 0.00 5.28
4945 5465 3.996480 AGAGCAAGACCAGTGTTTACTC 58.004 45.455 0.00 1.28 34.07 2.59
4946 5466 4.381411 GAAGAGCAAGACCAGTGTTTACT 58.619 43.478 0.00 0.00 37.75 2.24
4974 5494 1.078214 TTCTCAGCCATTCCCAGCG 60.078 57.895 0.00 0.00 0.00 5.18
5020 5540 0.672711 GTCCGGTGCCAGGTTTAGTC 60.673 60.000 0.00 0.00 0.00 2.59
5055 5575 4.427312 CATTGGACCAAGCTATTGAAAGC 58.573 43.478 13.43 0.00 43.11 3.51
5123 5643 3.938963 CTGCAATTGTTGACCCGTATACT 59.061 43.478 7.40 0.00 0.00 2.12
5127 5647 2.552599 TCTGCAATTGTTGACCCGTA 57.447 45.000 7.40 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.