Multiple sequence alignment - TraesCS7D01G105900

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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 TraesCS7D01G105900 chr7D 100.000 5863 0 0 1 5863 64012402 64006540 0.000000e+00 10828.0
1 TraesCS7D01G105900 chr7D 97.561 82 1 1 444 525 64011890 64011810 7.920000e-29 139.0
2 TraesCS7D01G105900 chr7D 97.561 82 1 1 513 593 64011959 64011878 7.920000e-29 139.0
3 TraesCS7D01G105900 chr7B 89.218 2328 164 43 1546 3833 5057959 5055679 0.000000e+00 2828.0
4 TraesCS7D01G105900 chr7B 92.688 1518 70 15 3924 5420 5055682 5054185 0.000000e+00 2150.0
5 TraesCS7D01G105900 chr7B 86.927 872 47 36 513 1344 5059152 5058308 0.000000e+00 917.0
6 TraesCS7D01G105900 chr7B 97.714 525 12 0 1 525 5059595 5059071 0.000000e+00 904.0
7 TraesCS7D01G105900 chr7B 92.176 524 34 5 4574 5096 5143404 5143921 0.000000e+00 734.0
8 TraesCS7D01G105900 chr7B 93.077 130 9 0 5421 5550 5053656 5053527 2.160000e-44 191.0
9 TraesCS7D01G105900 chr7B 90.588 85 8 0 5700 5784 5053448 5053364 4.800000e-21 113.0
10 TraesCS7D01G105900 chr7B 97.872 47 1 0 5816 5862 5053354 5053308 1.350000e-11 82.4
11 TraesCS7D01G105900 chr7A 87.796 1606 118 31 1344 2925 67674223 67675774 0.000000e+00 1808.0
12 TraesCS7D01G105900 chr7A 92.756 1201 72 9 3863 5050 67676867 67678065 0.000000e+00 1722.0
13 TraesCS7D01G105900 chr7A 93.750 896 43 10 2965 3852 67675773 67676663 0.000000e+00 1332.0
14 TraesCS7D01G105900 chr7A 87.674 860 48 23 513 1344 67673345 67674174 0.000000e+00 948.0
15 TraesCS7D01G105900 chr7A 95.057 526 24 2 1 525 67672902 67673426 0.000000e+00 826.0
16 TraesCS7D01G105900 chr7A 80.759 369 54 7 118 479 629879236 629879594 7.490000e-69 272.0
17 TraesCS7D01G105900 chr7A 87.500 128 7 5 5298 5419 67678307 67678431 7.920000e-29 139.0
18 TraesCS7D01G105900 chr7A 95.588 68 3 0 5677 5744 67678723 67678790 6.210000e-20 110.0
19 TraesCS7D01G105900 chr7A 92.593 54 4 0 5426 5479 67678508 67678561 1.750000e-10 78.7
20 TraesCS7D01G105900 chr2A 83.416 603 68 19 3270 3865 774908276 774907699 1.120000e-146 531.0
21 TraesCS7D01G105900 chr2A 81.063 301 54 3 109 408 764660970 764661268 2.730000e-58 237.0
22 TraesCS7D01G105900 chr5D 89.024 164 12 3 5099 5260 462454800 462454641 1.290000e-46 198.0
23 TraesCS7D01G105900 chr1B 86.585 164 15 4 5098 5259 642605725 642605883 2.170000e-39 174.0
24 TraesCS7D01G105900 chr1B 85.366 164 19 2 5097 5259 577610471 577610312 1.310000e-36 165.0
25 TraesCS7D01G105900 chr5B 85.976 164 18 2 5097 5260 581220857 581221015 2.810000e-38 171.0
26 TraesCS7D01G105900 chr4A 85.294 170 18 4 5093 5260 319821321 319821485 1.010000e-37 169.0
27 TraesCS7D01G105900 chr3A 86.709 158 14 3 5098 5254 730086959 730086808 1.010000e-37 169.0
28 TraesCS7D01G105900 chr4B 85.714 161 16 4 5097 5257 27243645 27243798 4.700000e-36 163.0
29 TraesCS7D01G105900 chr2D 84.848 165 20 4 5097 5260 8983619 8983459 1.690000e-35 161.0
30 TraesCS7D01G105900 chr6B 89.899 99 10 0 94 192 172277045 172276947 1.710000e-25 128.0


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 TraesCS7D01G105900 chr7D 64006540 64012402 5862 True 3702.000000 10828 98.374000 1 5863 3 chr7D.!!$R1 5862
1 TraesCS7D01G105900 chr7B 5053308 5059595 6287 True 1026.485714 2828 92.583429 1 5862 7 chr7B.!!$R1 5861
2 TraesCS7D01G105900 chr7B 5143404 5143921 517 False 734.000000 734 92.176000 4574 5096 1 chr7B.!!$F1 522
3 TraesCS7D01G105900 chr7A 67672902 67678790 5888 False 870.462500 1808 91.589250 1 5744 8 chr7A.!!$F2 5743
4 TraesCS7D01G105900 chr2A 774907699 774908276 577 True 531.000000 531 83.416000 3270 3865 1 chr2A.!!$R1 595

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
797 840 0.179026 TATACTCGACAGCTCCGCCT 60.179 55.0 0.45 0.0 0.00 5.52 F
1257 1338 0.967380 GAATGAAGGGGGTGTGCTGG 60.967 60.0 0.00 0.0 0.00 4.85 F
2250 2529 0.618458 TCATCACTGCCCCTAACCAC 59.382 55.0 0.00 0.0 0.00 4.16 F
2379 2668 0.823769 TGGGTGCGTAATGTGGCAAA 60.824 50.0 0.00 0.0 41.46 3.68 F
3904 4429 1.079503 GTGTGAATCAGCGGGACTTC 58.920 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1990 0.109781 CACAATGCCGGACCGAAAAG 60.110 55.0 17.49 0.0 0.00 2.27 R
2353 2638 0.537188 CATTACGCACCCAGGACTCT 59.463 55.0 0.00 0.0 0.00 3.24 R
3086 3399 0.807496 GCTGAGTTCAGTTGGCATCC 59.193 55.0 10.57 0.0 45.45 3.51 R
4094 4619 1.674359 AACACATTGGAACGACAGCA 58.326 45.0 0.00 0.0 0.00 4.41 R
5557 6897 0.178068 GCACCTACATCCCGTGTCAT 59.822 55.0 0.00 0.0 42.29 3.06 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
505 506 3.827898 GTCGTGGAGGGAGCCGAG 61.828 72.222 0.00 0.00 0.00 4.63
508 509 2.444895 GTGGAGGGAGCCGAGGAT 60.445 66.667 0.00 0.00 0.00 3.24
509 510 2.444706 TGGAGGGAGCCGAGGATG 60.445 66.667 0.00 0.00 0.00 3.51
510 511 2.123251 GGAGGGAGCCGAGGATGA 60.123 66.667 0.00 0.00 0.00 2.92
511 512 2.206536 GGAGGGAGCCGAGGATGAG 61.207 68.421 0.00 0.00 0.00 2.90
512 513 2.841988 AGGGAGCCGAGGATGAGC 60.842 66.667 0.00 0.00 0.00 4.26
513 514 3.157252 GGGAGCCGAGGATGAGCA 61.157 66.667 0.00 0.00 0.00 4.26
514 515 2.420890 GGAGCCGAGGATGAGCAG 59.579 66.667 0.00 0.00 0.00 4.24
515 516 2.280052 GAGCCGAGGATGAGCAGC 60.280 66.667 0.00 0.00 0.00 5.25
516 517 3.079478 AGCCGAGGATGAGCAGCA 61.079 61.111 0.00 0.00 0.00 4.41
517 518 2.588314 GCCGAGGATGAGCAGCAG 60.588 66.667 0.00 0.00 0.00 4.24
518 519 2.588314 CCGAGGATGAGCAGCAGC 60.588 66.667 0.00 0.00 42.56 5.25
519 520 2.186125 CGAGGATGAGCAGCAGCA 59.814 61.111 3.17 0.00 45.49 4.41
520 521 1.883544 CGAGGATGAGCAGCAGCAG 60.884 63.158 3.17 0.00 45.49 4.24
521 522 2.124653 AGGATGAGCAGCAGCAGC 60.125 61.111 3.17 0.46 45.49 5.25
672 694 4.424566 CGCCATGCCGCAAAGCTT 62.425 61.111 14.08 0.00 0.00 3.74
734 765 4.437587 GGAGGACGAGGGGACGGA 62.438 72.222 0.00 0.00 37.61 4.69
735 766 2.123812 GAGGACGAGGGGACGGAT 60.124 66.667 0.00 0.00 37.61 4.18
736 767 1.757340 GAGGACGAGGGGACGGATT 60.757 63.158 0.00 0.00 37.61 3.01
737 768 1.305887 AGGACGAGGGGACGGATTT 60.306 57.895 0.00 0.00 37.61 2.17
743 785 1.984288 GAGGGGACGGATTTGGGGAG 61.984 65.000 0.00 0.00 0.00 4.30
756 798 4.862823 GGGAGGGGACGGAGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
758 800 3.752167 GAGGGGACGGAGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
759 801 3.742248 GAGGGGACGGAGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
760 802 4.862823 GGGGACGGAGGAGGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
797 840 0.179026 TATACTCGACAGCTCCGCCT 60.179 55.000 0.45 0.00 0.00 5.52
897 945 5.047943 CCCTTCGTATATTGTACTCCTCCTG 60.048 48.000 0.00 0.00 0.00 3.86
1171 1248 2.126307 CAGGTGAGTGAGGTCGCG 60.126 66.667 0.00 0.00 0.00 5.87
1186 1267 1.299392 CGCGCGATCTCTGGATTGA 60.299 57.895 28.94 0.00 35.83 2.57
1195 1276 3.370840 TCTCTGGATTGATTGGTTGGG 57.629 47.619 0.00 0.00 0.00 4.12
1245 1326 5.163478 GGGGGAGTTGAATGAATGAATGAAG 60.163 44.000 0.00 0.00 0.00 3.02
1257 1338 0.967380 GAATGAAGGGGGTGTGCTGG 60.967 60.000 0.00 0.00 0.00 4.85
1363 1498 1.745489 GGCTAGTTGGTTGGAGGCG 60.745 63.158 0.00 0.00 0.00 5.52
1364 1499 1.745489 GCTAGTTGGTTGGAGGCGG 60.745 63.158 0.00 0.00 0.00 6.13
1390 1525 2.057137 ATGCATGTTTGGTAGCCGAT 57.943 45.000 0.00 0.00 0.00 4.18
1457 1592 3.083997 AGATGGGGGTCGCAGGTC 61.084 66.667 0.00 0.00 0.00 3.85
1485 1620 5.653769 GGAGAATCTTCACCCATTTCATTGA 59.346 40.000 0.00 0.00 32.58 2.57
1512 1648 9.736023 GAAGCAATTCAGAAATACGGAAATAAT 57.264 29.630 0.00 0.00 36.43 1.28
1521 1657 8.909671 CAGAAATACGGAAATAATACGGTAGAC 58.090 37.037 0.00 0.00 0.00 2.59
1560 1821 3.641437 GCTACATGCTTCACCAAACAA 57.359 42.857 0.00 0.00 38.95 2.83
1600 1861 3.793827 ACCCATAACAGAATGAGGGGATT 59.206 43.478 0.00 0.00 40.08 3.01
1601 1862 4.232820 ACCCATAACAGAATGAGGGGATTT 59.767 41.667 0.00 0.00 40.08 2.17
1602 1863 5.211201 CCCATAACAGAATGAGGGGATTTT 58.789 41.667 0.00 0.00 39.69 1.82
1603 1864 5.302823 CCCATAACAGAATGAGGGGATTTTC 59.697 44.000 0.00 0.00 39.69 2.29
1604 1865 5.893255 CCATAACAGAATGAGGGGATTTTCA 59.107 40.000 0.00 0.00 39.69 2.69
1605 1866 6.183360 CCATAACAGAATGAGGGGATTTTCAC 60.183 42.308 0.00 0.00 39.69 3.18
1641 1905 4.785346 AAGGGTGTATGATTGAGATGCT 57.215 40.909 0.00 0.00 0.00 3.79
1642 1906 4.082665 AGGGTGTATGATTGAGATGCTG 57.917 45.455 0.00 0.00 0.00 4.41
1648 1912 5.863935 GTGTATGATTGAGATGCTGCGTATA 59.136 40.000 0.00 0.00 0.00 1.47
1657 1924 3.513119 AGATGCTGCGTATAGTGGATCAT 59.487 43.478 0.00 0.00 0.00 2.45
1704 1971 3.278574 GCTTAATGTGTCATGGTGCCTA 58.721 45.455 0.00 0.00 0.00 3.93
1721 1988 2.167075 GCCTAGTGCCATTGCTTGATTT 59.833 45.455 0.00 0.00 38.71 2.17
1723 1990 2.088950 AGTGCCATTGCTTGATTTGC 57.911 45.000 0.00 0.00 38.71 3.68
1778 2052 3.686016 TGTGGAGTAATTTCCCTTGCTC 58.314 45.455 0.00 0.00 37.20 4.26
1779 2053 2.678336 GTGGAGTAATTTCCCTTGCTCG 59.322 50.000 0.00 0.00 38.36 5.03
1790 2064 1.136110 CCCTTGCTCGTTTTTGGTTGT 59.864 47.619 0.00 0.00 0.00 3.32
1924 2198 3.198853 CAGGAACTCTCCCTAAAGGAAGG 59.801 52.174 0.00 0.00 40.81 3.46
1942 2216 4.404098 GCGTTGGTCCCGGGATGT 62.404 66.667 29.73 0.00 0.00 3.06
1963 2237 4.699735 TGTGGCATGGTATGTTAAACAGAG 59.300 41.667 0.00 0.00 0.00 3.35
1987 2261 4.712476 ACATTTATCATCTGCCTCTGTCC 58.288 43.478 0.00 0.00 0.00 4.02
2017 2291 4.591321 ATGCCTTTCCCTTCAATCTGTA 57.409 40.909 0.00 0.00 0.00 2.74
2028 2302 7.004086 TCCCTTCAATCTGTACAATTTTCTGT 58.996 34.615 0.00 0.00 0.00 3.41
2039 2313 7.728148 TGTACAATTTTCTGTCTACACCTACA 58.272 34.615 0.00 0.00 0.00 2.74
2040 2314 7.654520 TGTACAATTTTCTGTCTACACCTACAC 59.345 37.037 0.00 0.00 0.00 2.90
2041 2315 5.995897 ACAATTTTCTGTCTACACCTACACC 59.004 40.000 0.00 0.00 0.00 4.16
2042 2316 6.183361 ACAATTTTCTGTCTACACCTACACCT 60.183 38.462 0.00 0.00 0.00 4.00
2043 2317 7.015877 ACAATTTTCTGTCTACACCTACACCTA 59.984 37.037 0.00 0.00 0.00 3.08
2044 2318 5.972107 TTTCTGTCTACACCTACACCTAC 57.028 43.478 0.00 0.00 0.00 3.18
2144 2422 7.124573 ACCAAGTTTCTTGCTAAGGAAAAAT 57.875 32.000 4.22 0.00 33.97 1.82
2173 2451 9.903682 CAATAATAATGTGGTGATCAATTCCTC 57.096 33.333 0.00 0.00 0.00 3.71
2204 2483 3.823873 TGGTCGCCAATTAAACATTCAGT 59.176 39.130 0.00 0.00 0.00 3.41
2206 2485 6.684111 TTGGTCGCCAATTAAACATTCAGTTT 60.684 34.615 7.15 0.00 44.49 2.66
2248 2527 0.912486 AGTCATCACTGCCCCTAACC 59.088 55.000 0.00 0.00 0.00 2.85
2250 2529 0.618458 TCATCACTGCCCCTAACCAC 59.382 55.000 0.00 0.00 0.00 4.16
2254 2533 2.144738 ACTGCCCCTAACCACGTGT 61.145 57.895 15.65 0.00 0.00 4.49
2266 2545 6.449698 CCTAACCACGTGTTCTACTTCTTTA 58.550 40.000 15.65 0.00 38.42 1.85
2311 2595 4.201773 TGTTTACACAAAGAGCAGTTGTCG 60.202 41.667 0.00 0.00 37.09 4.35
2328 2612 3.780902 TGTCGTATGCATGAACTAGTGG 58.219 45.455 10.16 0.00 0.00 4.00
2330 2614 2.102420 TCGTATGCATGAACTAGTGGGG 59.898 50.000 10.16 0.00 0.00 4.96
2340 2624 7.017551 TGCATGAACTAGTGGGGAGAATATATT 59.982 37.037 0.00 0.00 0.00 1.28
2363 2648 4.844349 TTTTTCTATGGAGAGTCCTGGG 57.156 45.455 0.00 0.00 37.46 4.45
2379 2668 0.823769 TGGGTGCGTAATGTGGCAAA 60.824 50.000 0.00 0.00 41.46 3.68
2385 2674 3.610677 GTGCGTAATGTGGCAAATAAACC 59.389 43.478 0.00 0.00 41.46 3.27
2387 2676 4.238514 GCGTAATGTGGCAAATAAACCAA 58.761 39.130 0.00 0.00 37.79 3.67
2484 2774 9.253832 CCTGGTTCATGTCTATCTATAAGATCT 57.746 37.037 0.00 0.00 36.20 2.75
2506 2801 7.490657 TCTTTTTGCAATACTAGTAGGAGGA 57.509 36.000 8.85 0.00 0.00 3.71
2532 2827 2.867647 GCTCCAATTTCCCTTGCAACAC 60.868 50.000 0.00 0.00 0.00 3.32
2536 2831 3.392882 CAATTTCCCTTGCAACACCTTC 58.607 45.455 0.00 0.00 0.00 3.46
2537 2832 1.408969 TTTCCCTTGCAACACCTTCC 58.591 50.000 0.00 0.00 0.00 3.46
2591 2886 3.091545 CAGGGTTATGATGTGGTTGCTT 58.908 45.455 0.00 0.00 0.00 3.91
2763 3061 5.850557 TTTGGTCAATTTTTCTCTGCAGA 57.149 34.783 17.19 17.19 0.00 4.26
2771 3069 7.811236 GTCAATTTTTCTCTGCAGAATGATGAA 59.189 33.333 18.85 14.02 38.50 2.57
2928 3231 2.490115 TGATTTATGTCACGGGGCAAAC 59.510 45.455 0.00 0.00 0.00 2.93
2930 3233 3.420300 TTTATGTCACGGGGCAAACTA 57.580 42.857 0.00 0.00 0.00 2.24
2939 3242 3.254657 CACGGGGCAAACTATCTTCAAAA 59.745 43.478 0.00 0.00 0.00 2.44
2960 3263 2.430248 AGGAAAAGGAAACCACGTGT 57.570 45.000 15.65 0.00 0.00 4.49
3101 3414 4.574674 TGATTAGGATGCCAACTGAACT 57.425 40.909 0.00 0.00 0.00 3.01
3135 3448 7.659390 TGGTATTTGGATTGAATTGGTGTTTTC 59.341 33.333 0.00 0.00 0.00 2.29
3585 3912 7.711846 TCTATGCTTCTTGTTTACTTTTGCAA 58.288 30.769 0.00 0.00 0.00 4.08
3587 3914 9.624697 CTATGCTTCTTGTTTACTTTTGCAATA 57.375 29.630 0.00 0.00 0.00 1.90
3669 3998 6.005198 TGTGAACCGGTTGATTTACCTTTAT 58.995 36.000 27.87 0.00 35.97 1.40
3762 4091 8.176105 TCCTTCTATCAAGGATCATGAGTAGAT 58.824 37.037 0.09 3.21 41.27 1.98
3873 4398 5.832539 AGAATCTAGGTATCAATGTGGGG 57.167 43.478 0.00 0.00 0.00 4.96
3892 4417 2.357154 GGGTCCATAGCTTGGTGTGAAT 60.357 50.000 12.71 0.00 46.52 2.57
3897 4422 1.725641 TAGCTTGGTGTGAATCAGCG 58.274 50.000 0.00 0.00 46.24 5.18
3904 4429 1.079503 GTGTGAATCAGCGGGACTTC 58.920 55.000 0.00 0.00 0.00 3.01
3980 4505 8.101309 TGTTTCCTCATTTCCTATCCTTATGA 57.899 34.615 0.00 0.00 0.00 2.15
4011 4536 4.586421 TGTTTTCATGACCTTTGGTGCATA 59.414 37.500 0.00 0.00 35.25 3.14
4012 4537 4.782019 TTTCATGACCTTTGGTGCATAC 57.218 40.909 0.00 0.00 35.25 2.39
4032 4557 6.475207 CATACGACACCCTTTAAAAGAATCG 58.525 40.000 0.00 6.87 0.00 3.34
4039 4564 4.643334 ACCCTTTAAAAGAATCGGTATGCC 59.357 41.667 0.00 0.00 0.00 4.40
4094 4619 4.322057 AAGACATGCTAAAACCTCCCAT 57.678 40.909 0.00 0.00 0.00 4.00
4155 4680 2.035704 CAGACAGACAGACAGTGCTCTT 59.964 50.000 0.00 0.00 0.00 2.85
4170 4696 6.202954 ACAGTGCTCTTATAGAAAACACACAC 59.797 38.462 0.00 0.00 29.87 3.82
4236 4762 3.052642 AGGGGGAGTTGATGCACATATTT 60.053 43.478 0.00 0.00 0.00 1.40
4426 4952 3.480470 AGTAAGTATGCATGCATGTCCC 58.520 45.455 37.43 23.20 37.82 4.46
4540 5068 4.803329 ATCCTGCCTTCATTATTGACCT 57.197 40.909 0.00 0.00 0.00 3.85
4628 5157 3.232213 TGTATGGAAGACAACGAGCTC 57.768 47.619 2.73 2.73 0.00 4.09
4649 5178 1.531058 GCTATTAAACCGCGCAAGGTG 60.531 52.381 8.75 0.00 45.21 4.00
4670 5199 2.674177 GCATCCTACACGCTACTGTTGT 60.674 50.000 0.00 0.00 0.00 3.32
4731 5264 3.708220 CTCCTGAACGCTCGCTCCC 62.708 68.421 0.00 0.00 0.00 4.30
4747 5288 2.588877 CCCTTGTCGGCGGCTATG 60.589 66.667 14.51 1.49 0.00 2.23
4917 5471 6.968131 ATACACTGTGTATTGTGTTAGCTG 57.032 37.500 23.99 0.00 43.88 4.24
4924 5478 0.518636 ATTGTGTTAGCTGCTGTGCG 59.481 50.000 13.43 0.00 38.13 5.34
4969 5523 1.653232 GATGCATGCGTGATGTGCG 60.653 57.895 19.18 0.00 41.61 5.34
4979 5533 1.267532 CGTGATGTGCGATTTACTGCC 60.268 52.381 0.00 0.00 0.00 4.85
5075 5831 5.431420 TGTGTGTGTTTTAAGTATGCTGG 57.569 39.130 0.00 0.00 0.00 4.85
5089 5845 0.322816 TGCTGGCAACTTGGAGATCC 60.323 55.000 0.00 0.00 37.61 3.36
5113 5877 3.083122 TGTAGGGTGTGACTAGGTCTC 57.917 52.381 0.00 0.00 33.15 3.36
5115 5879 2.223803 AGGGTGTGACTAGGTCTCAG 57.776 55.000 0.00 0.00 36.86 3.35
5152 5916 4.950050 ACCAAGTAAGTCTCAGTCAAGTG 58.050 43.478 0.00 0.00 0.00 3.16
5172 5936 6.782082 AGTGACATAACATGCTAGAGAGAA 57.218 37.500 0.00 0.00 0.00 2.87
5176 5940 8.386606 GTGACATAACATGCTAGAGAGAAAAAG 58.613 37.037 0.00 0.00 0.00 2.27
5221 5985 5.301805 TGCACGGATCTCAATGTAAGATCTA 59.698 40.000 11.66 0.00 45.56 1.98
5225 5989 5.859114 CGGATCTCAATGTAAGATCTAACGG 59.141 44.000 11.66 0.00 45.56 4.44
5236 6000 7.694886 TGTAAGATCTAACGGATATAGCATCG 58.305 38.462 0.00 0.00 34.33 3.84
5239 6003 7.197071 AGATCTAACGGATATAGCATCGATC 57.803 40.000 0.00 0.00 34.33 3.69
5264 6028 4.623932 ACTTAATGAAGTCTCAGCCACA 57.376 40.909 0.00 0.00 42.50 4.17
5280 6044 4.272018 CAGCCACATAGCAAGACACTTATC 59.728 45.833 0.00 0.00 34.23 1.75
5295 6059 6.595716 AGACACTTATCTGGAAAGGAAAATCG 59.404 38.462 0.00 0.00 0.00 3.34
5296 6060 5.123979 ACACTTATCTGGAAAGGAAAATCGC 59.876 40.000 0.00 0.00 0.00 4.58
5355 6125 6.551385 TTTTCATCAGAGCTTCTTGAGAAC 57.449 37.500 0.00 0.00 0.00 3.01
5411 6181 4.465660 TCATGTTCTCTCTCCTCCTTTCAG 59.534 45.833 0.00 0.00 0.00 3.02
5420 6190 2.504996 CTCCTCCTTTCAGCCTTGAGAT 59.495 50.000 0.00 0.00 34.15 2.75
5421 6191 2.238144 TCCTCCTTTCAGCCTTGAGATG 59.762 50.000 0.00 0.00 34.15 2.90
5422 6192 2.641305 CTCCTTTCAGCCTTGAGATGG 58.359 52.381 0.00 0.00 34.15 3.51
5423 6193 1.988107 TCCTTTCAGCCTTGAGATGGT 59.012 47.619 0.00 0.00 34.15 3.55
5424 6194 2.376518 TCCTTTCAGCCTTGAGATGGTT 59.623 45.455 0.00 0.00 34.15 3.67
5430 6715 3.523157 TCAGCCTTGAGATGGTTATTGGA 59.477 43.478 0.00 0.00 0.00 3.53
5431 6716 3.881688 CAGCCTTGAGATGGTTATTGGAG 59.118 47.826 0.00 0.00 0.00 3.86
5498 6838 2.027625 CGCTCTCACCGGTTTGTCC 61.028 63.158 2.97 0.00 0.00 4.02
5511 6851 1.527736 GTTTGTCCGTTATGTGCGTCA 59.472 47.619 0.00 0.00 0.00 4.35
5512 6852 1.141645 TTGTCCGTTATGTGCGTCAC 58.858 50.000 3.44 3.44 34.56 3.67
5534 6874 1.854280 TCCCTTCTCCCTACCTCTCTC 59.146 57.143 0.00 0.00 0.00 3.20
5550 6890 4.617486 TCGTGCACGTTCGTCGCT 62.617 61.111 35.74 0.00 44.19 4.93
5551 6891 4.394941 CGTGCACGTTCGTCGCTG 62.395 66.667 30.50 0.00 44.19 5.18
5552 6892 4.702826 GTGCACGTTCGTCGCTGC 62.703 66.667 0.00 15.80 44.19 5.25
5553 6893 4.942481 TGCACGTTCGTCGCTGCT 62.942 61.111 19.56 0.00 42.39 4.24
5554 6894 4.415501 GCACGTTCGTCGCTGCTG 62.416 66.667 0.00 0.00 44.19 4.41
5555 6895 3.030308 CACGTTCGTCGCTGCTGT 61.030 61.111 0.00 0.00 44.19 4.40
5556 6896 2.729862 ACGTTCGTCGCTGCTGTC 60.730 61.111 0.00 0.00 44.19 3.51
5557 6897 2.729491 CGTTCGTCGCTGCTGTCA 60.729 61.111 0.00 0.00 0.00 3.58
5558 6898 2.088763 CGTTCGTCGCTGCTGTCAT 61.089 57.895 0.00 0.00 0.00 3.06
5559 6899 1.417592 GTTCGTCGCTGCTGTCATG 59.582 57.895 0.00 0.00 0.00 3.07
5560 6900 1.008875 GTTCGTCGCTGCTGTCATGA 61.009 55.000 0.00 0.00 0.00 3.07
5561 6901 1.008875 TTCGTCGCTGCTGTCATGAC 61.009 55.000 19.27 19.27 0.00 3.06
5562 6902 1.734117 CGTCGCTGCTGTCATGACA 60.734 57.895 26.33 26.33 39.32 3.58
5563 6903 1.784062 GTCGCTGCTGTCATGACAC 59.216 57.895 24.56 19.87 36.21 3.67
5564 6904 1.734117 TCGCTGCTGTCATGACACG 60.734 57.895 24.56 23.83 36.21 4.49
5565 6905 2.733671 CGCTGCTGTCATGACACGG 61.734 63.158 24.56 23.31 36.21 4.94
5566 6906 2.393768 GCTGCTGTCATGACACGGG 61.394 63.158 24.56 15.92 36.21 5.28
5567 6907 1.293179 CTGCTGTCATGACACGGGA 59.707 57.895 24.56 15.73 36.21 5.14
5568 6908 0.107993 CTGCTGTCATGACACGGGAT 60.108 55.000 24.56 0.00 36.21 3.85
5569 6909 0.391528 TGCTGTCATGACACGGGATG 60.392 55.000 24.56 14.49 36.21 3.51
5571 6911 1.134818 GCTGTCATGACACGGGATGTA 60.135 52.381 24.56 0.37 43.56 2.29
5572 6912 2.814269 CTGTCATGACACGGGATGTAG 58.186 52.381 24.56 7.93 43.56 2.74
5573 6913 1.480545 TGTCATGACACGGGATGTAGG 59.519 52.381 24.56 0.00 43.56 3.18
5574 6914 1.480954 GTCATGACACGGGATGTAGGT 59.519 52.381 21.07 0.00 43.56 3.08
5575 6915 1.480545 TCATGACACGGGATGTAGGTG 59.519 52.381 0.00 0.00 43.56 4.00
5576 6916 0.178068 ATGACACGGGATGTAGGTGC 59.822 55.000 0.00 0.00 43.56 5.01
5586 6926 0.179045 ATGTAGGTGCCAGCGGATTC 60.179 55.000 0.00 0.00 0.00 2.52
5631 6971 3.031812 CGCTAATCGCTTGCATTCTTTC 58.968 45.455 0.00 0.00 36.13 2.62
5643 6983 1.250840 ATTCTTTCGCCCCCACAAGC 61.251 55.000 0.00 0.00 0.00 4.01
5657 6997 2.042831 CAAGCGGCCCTCTTCTTGG 61.043 63.158 0.00 0.00 34.04 3.61
5665 7005 0.908198 CCCTCTTCTTGGTCCTGAGG 59.092 60.000 0.00 0.00 42.72 3.86
5666 7006 0.908198 CCTCTTCTTGGTCCTGAGGG 59.092 60.000 0.00 0.00 40.25 4.30
5667 7007 0.251634 CTCTTCTTGGTCCTGAGGGC 59.748 60.000 0.00 0.00 0.00 5.19
5668 7008 1.078848 CTTCTTGGTCCTGAGGGCG 60.079 63.158 0.00 0.00 0.00 6.13
5669 7009 2.527951 CTTCTTGGTCCTGAGGGCGG 62.528 65.000 0.00 0.00 0.00 6.13
5670 7010 4.101448 CTTGGTCCTGAGGGCGGG 62.101 72.222 0.00 0.00 42.30 6.13
5674 7014 3.787001 GTCCTGAGGGCGGGGAAG 61.787 72.222 0.00 0.00 41.20 3.46
5675 7015 4.005978 TCCTGAGGGCGGGGAAGA 62.006 66.667 0.00 0.00 41.20 2.87
5679 7019 3.930012 GAGGGCGGGGAAGATCGG 61.930 72.222 0.00 0.00 0.00 4.18
5744 7084 2.225369 TGGAGATGTGACCCTCTTCTGA 60.225 50.000 2.90 0.00 0.00 3.27
5757 7097 3.181450 CCTCTTCTGACTTGACCTTTGGT 60.181 47.826 0.00 0.00 39.44 3.67
5763 7103 1.748493 GACTTGACCTTTGGTTGTGCA 59.252 47.619 0.00 0.00 35.25 4.57
5766 7106 2.363306 TGACCTTTGGTTGTGCAGAT 57.637 45.000 0.00 0.00 35.25 2.90
5769 7109 0.890683 CCTTTGGTTGTGCAGATCCC 59.109 55.000 8.39 1.11 0.00 3.85
5775 7115 1.620822 GTTGTGCAGATCCCCACTTT 58.379 50.000 12.79 0.00 33.26 2.66
5779 7119 1.675641 GCAGATCCCCACTTTGCGT 60.676 57.895 0.00 0.00 0.00 5.24
5784 7124 1.827399 ATCCCCACTTTGCGTCGAGT 61.827 55.000 0.00 0.00 0.00 4.18
5785 7125 2.317609 CCCCACTTTGCGTCGAGTG 61.318 63.158 0.00 0.52 42.21 3.51
5786 7126 1.300620 CCCACTTTGCGTCGAGTGA 60.301 57.895 12.70 0.00 44.65 3.41
5787 7127 1.557443 CCCACTTTGCGTCGAGTGAC 61.557 60.000 12.70 0.00 44.65 3.67
5789 7129 1.660575 ACTTTGCGTCGAGTGACCG 60.661 57.895 0.00 0.00 42.37 4.79
5790 7130 2.355363 TTTGCGTCGAGTGACCGG 60.355 61.111 0.00 0.00 42.37 5.28
5791 7131 2.742710 CTTTGCGTCGAGTGACCGGA 62.743 60.000 9.46 0.00 42.37 5.14
5793 7133 4.773117 GCGTCGAGTGACCGGACC 62.773 72.222 9.46 0.00 42.37 4.46
5794 7134 3.054503 CGTCGAGTGACCGGACCT 61.055 66.667 9.46 0.69 42.37 3.85
5795 7135 2.623915 CGTCGAGTGACCGGACCTT 61.624 63.158 9.46 0.00 42.37 3.50
5796 7136 1.212229 GTCGAGTGACCGGACCTTC 59.788 63.158 9.46 1.11 39.30 3.46
5797 7137 1.074423 TCGAGTGACCGGACCTTCT 59.926 57.895 9.46 0.10 0.00 2.85
5798 7138 0.538977 TCGAGTGACCGGACCTTCTT 60.539 55.000 9.46 0.00 0.00 2.52
5799 7139 0.388649 CGAGTGACCGGACCTTCTTG 60.389 60.000 9.46 1.06 0.00 3.02
5800 7140 0.966920 GAGTGACCGGACCTTCTTGA 59.033 55.000 9.46 0.00 0.00 3.02
5801 7141 1.550976 GAGTGACCGGACCTTCTTGAT 59.449 52.381 9.46 0.00 0.00 2.57
5802 7142 1.276421 AGTGACCGGACCTTCTTGATG 59.724 52.381 9.46 0.00 0.00 3.07
5803 7143 1.002087 GTGACCGGACCTTCTTGATGT 59.998 52.381 9.46 0.00 0.00 3.06
5804 7144 1.275291 TGACCGGACCTTCTTGATGTC 59.725 52.381 9.46 0.00 0.00 3.06
5805 7145 1.550976 GACCGGACCTTCTTGATGTCT 59.449 52.381 9.46 0.00 0.00 3.41
5806 7146 1.276421 ACCGGACCTTCTTGATGTCTG 59.724 52.381 9.46 0.00 35.59 3.51
5807 7147 1.363744 CGGACCTTCTTGATGTCTGC 58.636 55.000 0.00 0.00 0.00 4.26
5808 7148 1.066573 CGGACCTTCTTGATGTCTGCT 60.067 52.381 0.00 0.00 0.00 4.24
5809 7149 2.626840 GGACCTTCTTGATGTCTGCTC 58.373 52.381 0.00 0.00 0.00 4.26
5810 7150 2.266554 GACCTTCTTGATGTCTGCTCG 58.733 52.381 0.00 0.00 0.00 5.03
5811 7151 1.066573 ACCTTCTTGATGTCTGCTCGG 60.067 52.381 0.00 0.00 0.00 4.63
5812 7152 1.205655 CCTTCTTGATGTCTGCTCGGA 59.794 52.381 0.00 0.00 0.00 4.55
5813 7153 2.158986 CCTTCTTGATGTCTGCTCGGAT 60.159 50.000 0.00 0.00 0.00 4.18
5814 7154 3.068732 CCTTCTTGATGTCTGCTCGGATA 59.931 47.826 0.00 0.00 0.00 2.59
5849 7189 1.447838 CTCGGTCGTCCACAATGGG 60.448 63.158 0.00 0.00 38.32 4.00
5862 7202 3.055891 CCACAATGGGAATTGGAAGGTTC 60.056 47.826 3.70 0.00 35.93 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
344 345 4.760047 TTCTGCTTCCCGGCGCTC 62.760 66.667 7.64 0.00 34.52 5.03
501 502 2.588314 GCTGCTGCTCATCCTCGG 60.588 66.667 8.53 0.00 36.03 4.63
502 503 1.883544 CTGCTGCTGCTCATCCTCG 60.884 63.158 17.00 0.00 40.48 4.63
503 504 2.181521 GCTGCTGCTGCTCATCCTC 61.182 63.158 22.10 0.00 40.48 3.71
504 505 2.124653 GCTGCTGCTGCTCATCCT 60.125 61.111 22.10 0.00 40.48 3.24
505 506 3.574445 CGCTGCTGCTGCTCATCC 61.574 66.667 25.43 0.47 40.48 3.51
506 507 3.574445 CCGCTGCTGCTGCTCATC 61.574 66.667 25.43 1.13 40.48 2.92
556 557 3.827898 CTCGGCTCCCTCCACGAC 61.828 72.222 0.00 0.00 0.00 4.34
559 560 2.444895 ATCCTCGGCTCCCTCCAC 60.445 66.667 0.00 0.00 0.00 4.02
560 561 2.444706 CATCCTCGGCTCCCTCCA 60.445 66.667 0.00 0.00 0.00 3.86
561 562 2.123251 TCATCCTCGGCTCCCTCC 60.123 66.667 0.00 0.00 0.00 4.30
562 563 2.866726 GCTCATCCTCGGCTCCCTC 61.867 68.421 0.00 0.00 0.00 4.30
563 564 2.841988 GCTCATCCTCGGCTCCCT 60.842 66.667 0.00 0.00 0.00 4.20
564 565 3.157252 TGCTCATCCTCGGCTCCC 61.157 66.667 0.00 0.00 0.00 4.30
565 566 2.420890 CTGCTCATCCTCGGCTCC 59.579 66.667 0.00 0.00 0.00 4.70
566 567 2.280052 GCTGCTCATCCTCGGCTC 60.280 66.667 0.00 0.00 0.00 4.70
567 568 3.079478 TGCTGCTCATCCTCGGCT 61.079 61.111 0.00 0.00 35.69 5.52
568 569 2.588314 CTGCTGCTCATCCTCGGC 60.588 66.667 0.00 0.00 35.26 5.54
652 674 4.183686 CTTTGCGGCATGGCGGAG 62.184 66.667 37.92 23.42 35.06 4.63
655 677 4.424566 AAGCTTTGCGGCATGGCG 62.425 61.111 34.70 34.70 35.06 5.69
656 678 2.507769 GAAGCTTTGCGGCATGGC 60.508 61.111 9.69 9.69 34.17 4.40
657 679 2.182537 GGAAGCTTTGCGGCATGG 59.817 61.111 2.28 0.54 34.17 3.66
658 680 2.202518 CGGAAGCTTTGCGGCATG 60.203 61.111 2.28 0.91 41.03 4.06
671 693 0.613777 GGAGGAGAAGAAAGCCGGAA 59.386 55.000 5.05 0.00 0.00 4.30
672 694 1.265454 GGGAGGAGAAGAAAGCCGGA 61.265 60.000 5.05 0.00 0.00 5.14
719 750 1.305887 AAATCCGTCCCCTCGTCCT 60.306 57.895 0.00 0.00 0.00 3.85
722 753 2.666098 CCCAAATCCGTCCCCTCGT 61.666 63.158 0.00 0.00 0.00 4.18
723 754 2.189521 CCCAAATCCGTCCCCTCG 59.810 66.667 0.00 0.00 0.00 4.63
726 757 2.595655 CTCCCCAAATCCGTCCCC 59.404 66.667 0.00 0.00 0.00 4.81
727 758 2.595655 CCTCCCCAAATCCGTCCC 59.404 66.667 0.00 0.00 0.00 4.46
728 759 2.595655 CCCTCCCCAAATCCGTCC 59.404 66.667 0.00 0.00 0.00 4.79
730 761 2.126372 TCCCCTCCCCAAATCCGT 59.874 61.111 0.00 0.00 0.00 4.69
731 762 2.595655 GTCCCCTCCCCAAATCCG 59.404 66.667 0.00 0.00 0.00 4.18
732 763 2.595655 CGTCCCCTCCCCAAATCC 59.404 66.667 0.00 0.00 0.00 3.01
734 765 2.001269 CTCCGTCCCCTCCCCAAAT 61.001 63.158 0.00 0.00 0.00 2.32
735 766 2.609610 CTCCGTCCCCTCCCCAAA 60.610 66.667 0.00 0.00 0.00 3.28
736 767 4.733725 CCTCCGTCCCCTCCCCAA 62.734 72.222 0.00 0.00 0.00 4.12
743 785 4.862823 CCTCCCTCCTCCGTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
756 798 4.329545 TTCCCTGTGCACGCCTCC 62.330 66.667 13.13 0.00 0.00 4.30
758 800 3.560251 ACTTCCCTGTGCACGCCT 61.560 61.111 13.13 0.00 0.00 5.52
759 801 3.357079 CACTTCCCTGTGCACGCC 61.357 66.667 13.13 0.00 0.00 5.68
760 802 0.391130 TATCACTTCCCTGTGCACGC 60.391 55.000 13.13 0.00 37.81 5.34
761 803 2.315925 ATATCACTTCCCTGTGCACG 57.684 50.000 13.13 7.03 37.81 5.34
762 804 4.372656 GAGTATATCACTTCCCTGTGCAC 58.627 47.826 10.75 10.75 37.72 4.57
763 805 3.068165 CGAGTATATCACTTCCCTGTGCA 59.932 47.826 0.00 0.00 37.72 4.57
797 840 1.546998 GGGGAAGAAAAGGAAAGCGGA 60.547 52.381 0.00 0.00 0.00 5.54
897 945 4.631377 GGAAAAGGATAAAACAATGGCAGC 59.369 41.667 0.00 0.00 0.00 5.25
1160 1237 3.114647 GAGATCGCGCGACCTCACT 62.115 63.158 41.71 29.45 34.92 3.41
1161 1238 2.652496 GAGATCGCGCGACCTCAC 60.652 66.667 41.71 27.58 34.92 3.51
1162 1239 2.824489 AGAGATCGCGCGACCTCA 60.824 61.111 45.30 23.05 37.24 3.86
1163 1240 2.352915 CAGAGATCGCGCGACCTC 60.353 66.667 40.59 40.59 35.02 3.85
1166 1243 1.299468 AATCCAGAGATCGCGCGAC 60.299 57.895 37.37 27.03 0.00 5.19
1171 1248 2.843701 ACCAATCAATCCAGAGATCGC 58.156 47.619 0.00 0.00 0.00 4.58
1186 1267 2.990967 CCGCAGCACCCAACCAAT 60.991 61.111 0.00 0.00 0.00 3.16
1245 1326 4.974721 CACCACCAGCACACCCCC 62.975 72.222 0.00 0.00 0.00 5.40
1257 1338 0.666577 CGAGGACGAGAAACCACCAC 60.667 60.000 0.00 0.00 42.66 4.16
1286 1367 1.484227 CGAGACGAGACGAGATCGCT 61.484 60.000 1.39 0.59 43.91 4.93
1363 1498 2.446435 ACCAAACATGCATAGGTCACC 58.554 47.619 0.00 0.00 0.00 4.02
1364 1499 3.065371 GCTACCAAACATGCATAGGTCAC 59.935 47.826 13.53 6.10 33.91 3.67
1390 1525 2.105649 TCACACATTGACACCTGCCTAA 59.894 45.455 0.00 0.00 0.00 2.69
1396 1531 4.648762 TCCAATTTTCACACATTGACACCT 59.351 37.500 0.00 0.00 32.91 4.00
1398 1533 8.649841 CATAATCCAATTTTCACACATTGACAC 58.350 33.333 0.00 0.00 32.91 3.67
1399 1534 7.818446 CCATAATCCAATTTTCACACATTGACA 59.182 33.333 0.00 0.00 32.91 3.58
1481 1616 6.599244 TCCGTATTTCTGAATTGCTTCTCAAT 59.401 34.615 0.00 0.00 46.82 2.57
1483 1618 5.487433 TCCGTATTTCTGAATTGCTTCTCA 58.513 37.500 0.00 0.00 32.29 3.27
1485 1620 6.817765 TTTCCGTATTTCTGAATTGCTTCT 57.182 33.333 0.00 0.00 32.29 2.85
1521 1657 1.671261 GCTGATTCCTCCATCGATCGG 60.671 57.143 16.41 0.85 0.00 4.18
1524 1660 3.234353 TGTAGCTGATTCCTCCATCGAT 58.766 45.455 0.00 0.00 0.00 3.59
1559 1820 3.349927 GGTTAGCCCGGTTTCATACTTT 58.650 45.455 0.00 0.00 0.00 2.66
1560 1821 2.356432 GGGTTAGCCCGGTTTCATACTT 60.356 50.000 0.00 0.00 46.51 2.24
1600 1861 5.012768 CCCTTTACCCTCTAGTGAAGTGAAA 59.987 44.000 0.00 0.00 32.87 2.69
1601 1862 4.530946 CCCTTTACCCTCTAGTGAAGTGAA 59.469 45.833 0.00 0.00 32.87 3.18
1602 1863 4.094476 CCCTTTACCCTCTAGTGAAGTGA 58.906 47.826 0.00 0.00 32.87 3.41
1603 1864 3.838903 ACCCTTTACCCTCTAGTGAAGTG 59.161 47.826 0.00 0.00 32.87 3.16
1604 1865 3.838903 CACCCTTTACCCTCTAGTGAAGT 59.161 47.826 0.00 0.00 32.87 3.01
1605 1866 3.838903 ACACCCTTTACCCTCTAGTGAAG 59.161 47.826 0.00 0.00 34.15 3.02
1641 1905 3.467374 TGCAATGATCCACTATACGCA 57.533 42.857 0.00 0.00 0.00 5.24
1642 1906 4.776743 CTTTGCAATGATCCACTATACGC 58.223 43.478 6.48 0.00 0.00 4.42
1648 1912 2.753452 CTCTGCTTTGCAATGATCCACT 59.247 45.455 15.97 0.00 38.41 4.00
1657 1924 2.363038 AGTGCATTTCTCTGCTTTGCAA 59.637 40.909 0.00 0.00 44.13 4.08
1704 1971 1.621814 AGCAAATCAAGCAATGGCACT 59.378 42.857 0.00 0.00 44.61 4.40
1721 1988 1.602323 AATGCCGGACCGAAAAGCA 60.602 52.632 17.49 16.75 37.94 3.91
1723 1990 0.109781 CACAATGCCGGACCGAAAAG 60.110 55.000 17.49 0.00 0.00 2.27
1778 2052 4.260172 GCCAAGAATGAACAACCAAAAACG 60.260 41.667 0.00 0.00 0.00 3.60
1779 2053 4.875536 AGCCAAGAATGAACAACCAAAAAC 59.124 37.500 0.00 0.00 0.00 2.43
1790 2064 0.885879 CAGCAGCAGCCAAGAATGAA 59.114 50.000 0.00 0.00 43.56 2.57
1942 2216 4.018870 TCCTCTGTTTAACATACCATGCCA 60.019 41.667 0.00 0.00 0.00 4.92
1963 2237 4.712476 ACAGAGGCAGATGATAAATGTCC 58.288 43.478 0.00 0.00 0.00 4.02
1987 2261 2.711542 AGGGAAAGGCATAAGTGTTCG 58.288 47.619 0.00 0.00 0.00 3.95
2017 2291 5.995897 GGTGTAGGTGTAGACAGAAAATTGT 59.004 40.000 0.00 0.00 0.00 2.71
2028 2302 3.834231 GGGTTTGTAGGTGTAGGTGTAGA 59.166 47.826 0.00 0.00 0.00 2.59
2039 2313 4.383770 CGGATATCACTTGGGTTTGTAGGT 60.384 45.833 4.83 0.00 0.00 3.08
2040 2314 4.127171 CGGATATCACTTGGGTTTGTAGG 58.873 47.826 4.83 0.00 0.00 3.18
2041 2315 4.766375 ACGGATATCACTTGGGTTTGTAG 58.234 43.478 4.83 0.00 0.00 2.74
2042 2316 4.829872 ACGGATATCACTTGGGTTTGTA 57.170 40.909 4.83 0.00 0.00 2.41
2043 2317 3.713826 ACGGATATCACTTGGGTTTGT 57.286 42.857 4.83 0.00 0.00 2.83
2044 2318 7.094805 CCATATAACGGATATCACTTGGGTTTG 60.095 40.741 4.83 0.00 0.00 2.93
2120 2398 6.538945 TTTTTCCTTAGCAAGAAACTTGGT 57.461 33.333 17.69 17.69 0.00 3.67
2239 2518 0.609662 TAGAACACGTGGTTAGGGGC 59.390 55.000 21.57 0.00 40.63 5.80
2243 2522 6.089150 GCTAAAGAAGTAGAACACGTGGTTAG 59.911 42.308 21.57 9.50 40.63 2.34
2248 2527 4.557205 AGGCTAAAGAAGTAGAACACGTG 58.443 43.478 15.48 15.48 0.00 4.49
2250 2529 5.952033 AGTAGGCTAAAGAAGTAGAACACG 58.048 41.667 0.00 0.00 0.00 4.49
2298 2582 2.455674 TGCATACGACAACTGCTCTT 57.544 45.000 0.00 0.00 36.84 2.85
2305 2589 4.032900 CCACTAGTTCATGCATACGACAAC 59.967 45.833 0.00 0.00 0.00 3.32
2311 2595 3.388024 TCTCCCCACTAGTTCATGCATAC 59.612 47.826 0.00 0.00 0.00 2.39
2353 2638 0.537188 CATTACGCACCCAGGACTCT 59.463 55.000 0.00 0.00 0.00 3.24
2363 2648 3.610677 GGTTTATTTGCCACATTACGCAC 59.389 43.478 0.00 0.00 33.97 5.34
2484 2774 8.548877 AGAATCCTCCTACTAGTATTGCAAAAA 58.451 33.333 1.71 0.00 0.00 1.94
2506 2801 2.498885 GCAAGGGAAATTGGAGCAGAAT 59.501 45.455 0.00 0.00 0.00 2.40
2521 2816 0.542702 ATGGGAAGGTGTTGCAAGGG 60.543 55.000 0.00 0.00 0.00 3.95
2532 2827 6.786967 AATCAGAAAAGATTGATGGGAAGG 57.213 37.500 0.00 0.00 36.88 3.46
2561 2856 6.157994 ACCACATCATAACCCTGTTATACAGT 59.842 38.462 6.13 0.00 44.50 3.55
2591 2886 0.700564 AATCTCTCAGGGCTTGCCAA 59.299 50.000 14.04 0.00 0.00 4.52
2747 3045 8.703604 ATTCATCATTCTGCAGAGAAAAATTG 57.296 30.769 17.43 9.58 41.64 2.32
2752 3050 6.431852 TGACAATTCATCATTCTGCAGAGAAA 59.568 34.615 17.43 2.24 41.64 2.52
2757 3055 5.891451 ACATGACAATTCATCATTCTGCAG 58.109 37.500 7.63 7.63 40.79 4.41
2811 3114 6.993079 ACCTGAACCACTTTGGAAATAATTC 58.007 36.000 0.00 0.00 40.96 2.17
2813 3116 5.480422 GGACCTGAACCACTTTGGAAATAAT 59.520 40.000 0.00 0.00 40.96 1.28
2930 3233 8.367911 GTGGTTTCCTTTTCCTATTTTGAAGAT 58.632 33.333 0.00 0.00 0.00 2.40
2939 3242 3.818773 CACACGTGGTTTCCTTTTCCTAT 59.181 43.478 21.57 0.00 0.00 2.57
2960 3263 3.348647 TGCCTGCTGTAATTAGCTTCA 57.651 42.857 0.00 0.00 44.01 3.02
3007 3310 5.491323 AATTAGAGGTAGCATCCTTAGCC 57.509 43.478 1.37 0.00 38.02 3.93
3008 3311 7.809546 AAAAATTAGAGGTAGCATCCTTAGC 57.190 36.000 1.37 0.00 38.02 3.09
3009 3312 9.832445 TGTAAAAATTAGAGGTAGCATCCTTAG 57.168 33.333 1.37 0.00 38.02 2.18
3076 3389 7.293073 AGTTCAGTTGGCATCCTAATCAATAT 58.707 34.615 0.00 0.00 0.00 1.28
3086 3399 0.807496 GCTGAGTTCAGTTGGCATCC 59.193 55.000 10.57 0.00 45.45 3.51
3087 3400 1.736681 GAGCTGAGTTCAGTTGGCATC 59.263 52.381 10.57 0.00 45.45 3.91
3091 3404 2.149578 CCAAGAGCTGAGTTCAGTTGG 58.850 52.381 12.71 12.71 45.45 3.77
3101 3414 5.178096 TCAATCCAAATACCAAGAGCTGA 57.822 39.130 0.00 0.00 0.00 4.26
3249 3570 3.142951 TGGTACATCAACAGGGAAAACG 58.857 45.455 0.00 0.00 0.00 3.60
3615 3942 9.534565 TTAGAGTTCAGTTCAGCATATCATAAC 57.465 33.333 0.00 0.00 0.00 1.89
3624 3952 6.542005 TCACATTTTTAGAGTTCAGTTCAGCA 59.458 34.615 0.00 0.00 0.00 4.41
3625 3953 6.959361 TCACATTTTTAGAGTTCAGTTCAGC 58.041 36.000 0.00 0.00 0.00 4.26
3628 3956 6.851330 CGGTTCACATTTTTAGAGTTCAGTTC 59.149 38.462 0.00 0.00 0.00 3.01
3713 4042 2.578021 AGCAATACCACCACAATCCTCT 59.422 45.455 0.00 0.00 0.00 3.69
3762 4091 7.177184 TCCAGTTGTTACCTATGACTACACTA 58.823 38.462 0.00 0.00 0.00 2.74
3765 4097 6.495872 AGTTCCAGTTGTTACCTATGACTACA 59.504 38.462 0.00 0.00 0.00 2.74
3897 4422 2.032681 ACTTGGCTGCGAAGTCCC 59.967 61.111 21.99 0.00 26.38 4.46
3904 4429 2.357881 TGCTCAGACTTGGCTGCG 60.358 61.111 0.00 0.00 35.86 5.18
4011 4536 3.749609 CCGATTCTTTTAAAGGGTGTCGT 59.250 43.478 4.77 0.00 0.00 4.34
4012 4537 3.749609 ACCGATTCTTTTAAAGGGTGTCG 59.250 43.478 4.77 9.15 0.00 4.35
4032 4557 5.919755 AGCTTTAAGAAGAGTAGGCATACC 58.080 41.667 4.63 0.00 34.71 2.73
4094 4619 1.674359 AACACATTGGAACGACAGCA 58.326 45.000 0.00 0.00 0.00 4.41
4145 4670 6.202954 GTGTGTGTTTTCTATAAGAGCACTGT 59.797 38.462 0.00 0.00 30.34 3.55
4155 4680 7.442969 ACCTCGAATTTGTGTGTGTTTTCTATA 59.557 33.333 0.00 0.00 0.00 1.31
4170 4696 2.280628 GGAGTAGGCACCTCGAATTTG 58.719 52.381 0.00 0.00 0.00 2.32
4426 4952 8.035290 GAAATTAATTCTTTCGCGATAGGGACG 61.035 40.741 23.46 0.91 45.34 4.79
4540 5068 6.728200 CAGTTTCACAAAAGAACAGCTATCA 58.272 36.000 0.00 0.00 0.00 2.15
4649 5178 1.927174 CAACAGTAGCGTGTAGGATGC 59.073 52.381 0.00 0.00 36.77 3.91
4670 5199 6.239120 CCGGAGATAACTCGGTATAGGAAAAA 60.239 42.308 0.00 0.00 43.44 1.94
4703 5236 4.675671 CGAGCGTTCAGGAGATAACTCTTT 60.676 45.833 0.00 0.00 42.28 2.52
4704 5237 3.181495 CGAGCGTTCAGGAGATAACTCTT 60.181 47.826 0.00 0.00 42.28 2.85
4716 5249 3.302347 AAGGGGAGCGAGCGTTCAG 62.302 63.158 8.87 0.00 0.00 3.02
4731 5264 1.449601 AACATAGCCGCCGACAAGG 60.450 57.895 0.00 0.00 44.97 3.61
4741 5282 2.551071 GGACCATAGCTCCAACATAGCC 60.551 54.545 0.00 0.00 41.02 3.93
4747 5288 1.840635 AGAAGGGACCATAGCTCCAAC 59.159 52.381 0.00 0.00 0.00 3.77
4924 5478 4.826600 GTGCACATCACGAACTGC 57.173 55.556 13.17 0.00 35.76 4.40
4969 5523 0.458669 TCCGACGGAGGCAGTAAATC 59.541 55.000 13.88 0.00 0.00 2.17
5075 5831 5.302357 CTACAAAAGGATCTCCAAGTTGC 57.698 43.478 0.00 0.00 38.89 4.17
5089 5845 4.283722 AGACCTAGTCACACCCTACAAAAG 59.716 45.833 0.00 0.00 34.60 2.27
5113 5877 5.230942 ACTTGGTTAAATCTCAGTCGACTG 58.769 41.667 34.76 34.76 45.08 3.51
5115 5879 6.867293 ACTTACTTGGTTAAATCTCAGTCGAC 59.133 38.462 7.70 7.70 0.00 4.20
5152 5916 8.709386 TCTTTTTCTCTCTAGCATGTTATGTC 57.291 34.615 0.00 0.00 0.00 3.06
5188 5952 4.844998 TGAGATCCGTGCAAAATTTTCA 57.155 36.364 0.00 0.01 0.00 2.69
5190 5954 5.540911 ACATTGAGATCCGTGCAAAATTTT 58.459 33.333 0.00 0.00 0.00 1.82
5196 5960 4.200838 TCTTACATTGAGATCCGTGCAA 57.799 40.909 0.00 0.00 0.00 4.08
5201 5965 5.859114 CCGTTAGATCTTACATTGAGATCCG 59.141 44.000 12.07 7.17 46.88 4.18
5221 5985 3.939592 TCTCGATCGATGCTATATCCGTT 59.060 43.478 19.78 0.00 0.00 4.44
5225 5989 8.338986 TCATTAAGTCTCGATCGATGCTATATC 58.661 37.037 19.78 3.51 0.00 1.63
5260 6024 4.813161 CCAGATAAGTGTCTTGCTATGTGG 59.187 45.833 0.00 0.00 0.00 4.17
5263 6027 6.259608 CCTTTCCAGATAAGTGTCTTGCTATG 59.740 42.308 0.00 0.00 0.00 2.23
5264 6028 6.156949 TCCTTTCCAGATAAGTGTCTTGCTAT 59.843 38.462 0.00 0.00 0.00 2.97
5280 6044 3.641437 TGTTGCGATTTTCCTTTCCAG 57.359 42.857 0.00 0.00 0.00 3.86
5295 6059 4.512571 ACCATTTGCTCTTTGATTTGTTGC 59.487 37.500 0.00 0.00 0.00 4.17
5296 6060 5.754406 TCACCATTTGCTCTTTGATTTGTTG 59.246 36.000 0.00 0.00 0.00 3.33
5337 6107 6.489361 ACAAAATGTTCTCAAGAAGCTCTGAT 59.511 34.615 0.00 0.00 34.27 2.90
5355 6125 2.289010 GGCTCCCCTCAACAACAAAATG 60.289 50.000 0.00 0.00 0.00 2.32
5411 6181 2.620585 GCTCCAATAACCATCTCAAGGC 59.379 50.000 0.00 0.00 0.00 4.35
5420 6190 3.547746 GATTAACCGGCTCCAATAACCA 58.452 45.455 0.00 0.00 0.00 3.67
5421 6191 2.882761 GGATTAACCGGCTCCAATAACC 59.117 50.000 0.00 0.00 0.00 2.85
5422 6192 2.882761 GGGATTAACCGGCTCCAATAAC 59.117 50.000 0.00 0.00 40.11 1.89
5423 6193 2.510382 TGGGATTAACCGGCTCCAATAA 59.490 45.455 0.00 0.00 40.11 1.40
5424 6194 2.128535 TGGGATTAACCGGCTCCAATA 58.871 47.619 0.00 0.00 40.11 1.90
5430 6715 3.004090 GGGTGGGATTAACCGGCT 58.996 61.111 0.00 0.00 38.70 5.52
5431 6716 2.515290 CGGGTGGGATTAACCGGC 60.515 66.667 0.00 0.00 42.48 6.13
5498 6838 0.719465 GGGAAGTGACGCACATAACG 59.281 55.000 11.58 0.00 36.74 3.18
5511 6851 2.012236 AGAGGTAGGGAGAAGGGAAGT 58.988 52.381 0.00 0.00 0.00 3.01
5512 6852 2.246327 AGAGAGGTAGGGAGAAGGGAAG 59.754 54.545 0.00 0.00 0.00 3.46
5534 6874 4.394941 CAGCGACGAACGTGCACG 62.395 66.667 35.99 35.99 44.60 5.34
5550 6890 0.391528 CATCCCGTGTCATGACAGCA 60.392 55.000 28.54 12.85 42.74 4.41
5551 6891 0.391661 ACATCCCGTGTCATGACAGC 60.392 55.000 28.54 20.35 42.74 4.40
5552 6892 2.481969 CCTACATCCCGTGTCATGACAG 60.482 54.545 28.54 20.37 42.74 3.51
5553 6893 1.480545 CCTACATCCCGTGTCATGACA 59.519 52.381 24.56 24.56 42.29 3.58
5554 6894 1.480954 ACCTACATCCCGTGTCATGAC 59.519 52.381 19.27 19.27 42.29 3.06
5555 6895 1.480545 CACCTACATCCCGTGTCATGA 59.519 52.381 0.00 0.00 42.29 3.07
5556 6896 1.939974 CACCTACATCCCGTGTCATG 58.060 55.000 0.00 0.00 42.29 3.07
5557 6897 0.178068 GCACCTACATCCCGTGTCAT 59.822 55.000 0.00 0.00 42.29 3.06
5558 6898 1.594833 GCACCTACATCCCGTGTCA 59.405 57.895 0.00 0.00 42.29 3.58
5559 6899 1.153429 GGCACCTACATCCCGTGTC 60.153 63.158 0.00 0.00 42.29 3.67
5560 6900 1.899437 CTGGCACCTACATCCCGTGT 61.899 60.000 0.00 0.00 44.95 4.49
5561 6901 1.153369 CTGGCACCTACATCCCGTG 60.153 63.158 0.00 0.00 0.00 4.94
5562 6902 3.031417 GCTGGCACCTACATCCCGT 62.031 63.158 0.00 0.00 0.00 5.28
5563 6903 2.203070 GCTGGCACCTACATCCCG 60.203 66.667 0.00 0.00 0.00 5.14
5564 6904 2.203070 CGCTGGCACCTACATCCC 60.203 66.667 0.00 0.00 0.00 3.85
5565 6905 2.044806 ATCCGCTGGCACCTACATCC 62.045 60.000 0.00 0.00 0.00 3.51
5566 6906 0.179045 AATCCGCTGGCACCTACATC 60.179 55.000 0.00 0.00 0.00 3.06
5567 6907 0.179045 GAATCCGCTGGCACCTACAT 60.179 55.000 0.00 0.00 0.00 2.29
5568 6908 1.220749 GAATCCGCTGGCACCTACA 59.779 57.895 0.00 0.00 0.00 2.74
5569 6909 0.811616 CAGAATCCGCTGGCACCTAC 60.812 60.000 0.00 0.00 32.26 3.18
5570 6910 1.522092 CAGAATCCGCTGGCACCTA 59.478 57.895 0.00 0.00 32.26 3.08
5571 6911 2.270205 CAGAATCCGCTGGCACCT 59.730 61.111 0.00 0.00 32.26 4.00
5613 6953 2.223249 GGCGAAAGAATGCAAGCGATTA 60.223 45.455 0.00 0.00 0.00 1.75
5622 6962 1.531739 TTGTGGGGGCGAAAGAATGC 61.532 55.000 0.00 0.00 0.00 3.56
5623 6963 0.527565 CTTGTGGGGGCGAAAGAATG 59.472 55.000 0.00 0.00 0.00 2.67
5624 6964 1.250840 GCTTGTGGGGGCGAAAGAAT 61.251 55.000 0.00 0.00 0.00 2.40
5625 6965 1.901464 GCTTGTGGGGGCGAAAGAA 60.901 57.895 0.00 0.00 0.00 2.52
5643 6983 2.269241 GGACCAAGAAGAGGGCCG 59.731 66.667 0.00 0.00 46.41 6.13
5648 6988 0.251634 GCCCTCAGGACCAAGAAGAG 59.748 60.000 0.00 0.00 33.47 2.85
5649 6989 1.544825 CGCCCTCAGGACCAAGAAGA 61.545 60.000 0.00 0.00 33.47 2.87
5651 6991 2.592993 CCGCCCTCAGGACCAAGAA 61.593 63.158 0.00 0.00 33.47 2.52
5657 6997 3.787001 CTTCCCCGCCCTCAGGAC 61.787 72.222 0.00 0.00 33.47 3.85
5665 7005 2.925162 CTTGACCGATCTTCCCCGCC 62.925 65.000 0.00 0.00 0.00 6.13
5666 7006 1.521681 CTTGACCGATCTTCCCCGC 60.522 63.158 0.00 0.00 0.00 6.13
5667 7007 1.521681 GCTTGACCGATCTTCCCCG 60.522 63.158 0.00 0.00 0.00 5.73
5668 7008 0.181350 ATGCTTGACCGATCTTCCCC 59.819 55.000 0.00 0.00 0.00 4.81
5669 7009 1.134401 TCATGCTTGACCGATCTTCCC 60.134 52.381 0.00 0.00 0.00 3.97
5670 7010 2.159043 TCTCATGCTTGACCGATCTTCC 60.159 50.000 0.00 0.00 0.00 3.46
5671 7011 3.170791 TCTCATGCTTGACCGATCTTC 57.829 47.619 0.00 0.00 0.00 2.87
5672 7012 3.834489 ATCTCATGCTTGACCGATCTT 57.166 42.857 0.00 0.00 0.00 2.40
5673 7013 3.726607 GAATCTCATGCTTGACCGATCT 58.273 45.455 0.00 0.00 0.00 2.75
5674 7014 2.474359 CGAATCTCATGCTTGACCGATC 59.526 50.000 0.00 0.00 0.00 3.69
5675 7015 2.101415 TCGAATCTCATGCTTGACCGAT 59.899 45.455 0.00 0.00 0.00 4.18
5679 7019 3.063180 CCAAGTCGAATCTCATGCTTGAC 59.937 47.826 9.08 2.86 36.41 3.18
5744 7084 1.750778 CTGCACAACCAAAGGTCAAGT 59.249 47.619 0.00 0.00 33.12 3.16
5757 7097 1.619654 CAAAGTGGGGATCTGCACAA 58.380 50.000 0.00 0.00 0.00 3.33
5763 7103 1.079127 CGACGCAAAGTGGGGATCT 60.079 57.895 0.00 0.00 34.28 2.75
5766 7106 2.342279 CTCGACGCAAAGTGGGGA 59.658 61.111 0.00 0.00 34.28 4.81
5769 7109 1.557443 GGTCACTCGACGCAAAGTGG 61.557 60.000 13.35 0.00 43.61 4.00
5775 7115 4.034258 GTCCGGTCACTCGACGCA 62.034 66.667 0.00 0.00 43.61 5.24
5779 7119 0.538977 AAGAAGGTCCGGTCACTCGA 60.539 55.000 0.00 0.00 0.00 4.04
5784 7124 1.275291 GACATCAAGAAGGTCCGGTCA 59.725 52.381 0.00 0.00 0.00 4.02
5785 7125 1.550976 AGACATCAAGAAGGTCCGGTC 59.449 52.381 0.00 0.00 31.99 4.79
5786 7126 1.276421 CAGACATCAAGAAGGTCCGGT 59.724 52.381 0.00 0.00 31.99 5.28
5787 7127 2.009042 GCAGACATCAAGAAGGTCCGG 61.009 57.143 0.00 0.00 31.99 5.14
5789 7129 2.626840 GAGCAGACATCAAGAAGGTCC 58.373 52.381 0.00 0.00 31.99 4.46
5790 7130 2.266554 CGAGCAGACATCAAGAAGGTC 58.733 52.381 0.00 0.00 0.00 3.85
5791 7131 1.066573 CCGAGCAGACATCAAGAAGGT 60.067 52.381 0.00 0.00 0.00 3.50
5793 7133 2.662006 TCCGAGCAGACATCAAGAAG 57.338 50.000 0.00 0.00 0.00 2.85
5794 7134 4.342092 TCATATCCGAGCAGACATCAAGAA 59.658 41.667 0.00 0.00 0.00 2.52
5795 7135 3.891366 TCATATCCGAGCAGACATCAAGA 59.109 43.478 0.00 0.00 0.00 3.02
5796 7136 4.248691 TCATATCCGAGCAGACATCAAG 57.751 45.455 0.00 0.00 0.00 3.02
5797 7137 4.039609 ACATCATATCCGAGCAGACATCAA 59.960 41.667 0.00 0.00 0.00 2.57
5798 7138 3.575687 ACATCATATCCGAGCAGACATCA 59.424 43.478 0.00 0.00 0.00 3.07
5799 7139 4.185467 ACATCATATCCGAGCAGACATC 57.815 45.455 0.00 0.00 0.00 3.06
5800 7140 4.202295 ACAACATCATATCCGAGCAGACAT 60.202 41.667 0.00 0.00 0.00 3.06
5801 7141 3.132824 ACAACATCATATCCGAGCAGACA 59.867 43.478 0.00 0.00 0.00 3.41
5802 7142 3.722147 ACAACATCATATCCGAGCAGAC 58.278 45.455 0.00 0.00 0.00 3.51
5803 7143 4.122046 CAACAACATCATATCCGAGCAGA 58.878 43.478 0.00 0.00 0.00 4.26
5804 7144 3.249320 CCAACAACATCATATCCGAGCAG 59.751 47.826 0.00 0.00 0.00 4.24
5805 7145 3.205338 CCAACAACATCATATCCGAGCA 58.795 45.455 0.00 0.00 0.00 4.26
5806 7146 3.206150 ACCAACAACATCATATCCGAGC 58.794 45.455 0.00 0.00 0.00 5.03
5807 7147 4.496341 GCAACCAACAACATCATATCCGAG 60.496 45.833 0.00 0.00 0.00 4.63
5808 7148 3.376859 GCAACCAACAACATCATATCCGA 59.623 43.478 0.00 0.00 0.00 4.55
5809 7149 3.489059 GGCAACCAACAACATCATATCCG 60.489 47.826 0.00 0.00 0.00 4.18
5810 7150 3.701040 AGGCAACCAACAACATCATATCC 59.299 43.478 0.00 0.00 37.17 2.59
5811 7151 4.496341 CGAGGCAACCAACAACATCATATC 60.496 45.833 0.00 0.00 37.17 1.63
5812 7152 3.378112 CGAGGCAACCAACAACATCATAT 59.622 43.478 0.00 0.00 37.17 1.78
5813 7153 2.746904 CGAGGCAACCAACAACATCATA 59.253 45.455 0.00 0.00 37.17 2.15
5814 7154 1.541147 CGAGGCAACCAACAACATCAT 59.459 47.619 0.00 0.00 37.17 2.45


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

AutoCloner maintained by Alex Coulton.