Multiple sequence alignment - TraesCS3A01G465000

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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 TraesCS3A01G465000 chr3A 100.000 3763 0 0 1 3763 699548701 699544939 0.000000e+00 6950.0
1 TraesCS3A01G465000 chr3A 82.861 741 122 5 2185 2924 699105262 699105998 0.000000e+00 660.0
2 TraesCS3A01G465000 chr3A 75.505 396 74 13 2364 2754 584112192 584111815 5.000000e-39 172.0
3 TraesCS3A01G465000 chr3D 96.670 2943 78 12 30 2961 565147332 565144399 0.000000e+00 4874.0
4 TraesCS3A01G465000 chr3D 93.878 539 22 3 3150 3680 565144406 565143871 0.000000e+00 802.0
5 TraesCS3A01G465000 chr3D 83.051 472 72 6 1938 2407 564493426 564493891 4.490000e-114 422.0
6 TraesCS3A01G465000 chr3D 89.109 202 7 9 2961 3152 615015281 615015085 1.750000e-58 237.0
7 TraesCS3A01G465000 chr3D 92.308 52 4 0 3680 3731 565143723 565143672 1.450000e-09 75.0
8 TraesCS3A01G465000 chr3B 96.729 1284 41 1 1678 2961 752914516 752915798 0.000000e+00 2137.0
9 TraesCS3A01G465000 chr3B 94.980 737 29 5 527 1256 752913347 752914082 0.000000e+00 1149.0
10 TraesCS3A01G465000 chr3B 94.246 504 23 4 28 531 752912329 752912826 0.000000e+00 765.0
11 TraesCS3A01G465000 chr3B 92.683 533 33 3 3150 3680 752915791 752916319 0.000000e+00 763.0
12 TraesCS3A01G465000 chr3B 97.034 236 7 0 1241 1476 752914281 752914516 7.570000e-107 398.0
13 TraesCS3A01G465000 chr3B 77.342 587 119 12 2176 2754 580787006 580786426 6.020000e-88 335.0
14 TraesCS3A01G465000 chr5B 79.756 657 121 10 2101 2750 248389154 248388503 2.050000e-127 466.0
15 TraesCS3A01G465000 chr5B 77.068 266 57 4 973 1236 24146490 24146227 2.340000e-32 150.0
16 TraesCS3A01G465000 chr5B 100.000 29 0 0 1 29 538407181 538407153 2.000000e-03 54.7
17 TraesCS3A01G465000 chr7D 79.145 585 104 15 2176 2750 89290031 89290607 4.560000e-104 388.0
18 TraesCS3A01G465000 chr7D 92.857 182 6 4 2973 3153 601400754 601400929 1.340000e-64 257.0
19 TraesCS3A01G465000 chr7D 80.899 89 9 7 1076 1160 546753330 546753414 3.140000e-06 63.9
20 TraesCS3A01G465000 chr7D 100.000 29 0 0 1 29 400800847 400800819 2.000000e-03 54.7
21 TraesCS3A01G465000 chr7B 78.767 584 107 15 2176 2750 40194776 40195351 3.550000e-100 375.0
22 TraesCS3A01G465000 chr5A 77.622 572 104 20 2194 2750 42282017 42281455 3.620000e-85 326.0
23 TraesCS3A01G465000 chr5A 83.085 201 30 4 2761 2960 297721372 297721175 2.990000e-41 180.0
24 TraesCS3A01G465000 chr5D 93.333 195 7 3 2956 3149 542392523 542392712 2.210000e-72 283.0
25 TraesCS3A01G465000 chr6D 91.935 186 9 3 2964 3149 464777424 464777245 4.820000e-64 255.0
26 TraesCS3A01G465000 chr6D 91.489 188 10 3 2962 3149 119112680 119112499 1.730000e-63 254.0
27 TraesCS3A01G465000 chr6D 89.394 198 6 9 2962 3149 69950 69758 6.280000e-58 235.0
28 TraesCS3A01G465000 chr6B 93.258 178 5 4 2973 3149 42737443 42737614 4.820000e-64 255.0
29 TraesCS3A01G465000 chr6B 100.000 29 0 0 1 29 432486253 432486225 2.000000e-03 54.7
30 TraesCS3A01G465000 chr6B 96.875 32 0 1 1 32 293105782 293105752 7.000000e-03 52.8
31 TraesCS3A01G465000 chr6B 96.875 32 0 1 1 32 593369881 593369851 7.000000e-03 52.8
32 TraesCS3A01G465000 chr1D 92.697 178 6 4 2973 3149 2853758 2853587 2.240000e-62 250.0
33 TraesCS3A01G465000 chrUn 89.362 188 14 3 2962 3149 161599815 161599996 8.130000e-57 231.0
34 TraesCS3A01G465000 chr7A 78.090 178 29 9 1054 1226 630034602 630034774 1.850000e-18 104.0
35 TraesCS3A01G465000 chr7A 100.000 29 0 0 1 29 687925411 687925439 2.000000e-03 54.7
36 TraesCS3A01G465000 chr4D 100.000 29 0 0 1 29 371127568 371127596 2.000000e-03 54.7
37 TraesCS3A01G465000 chr4A 100.000 29 0 0 1 29 465260514 465260542 2.000000e-03 54.7
38 TraesCS3A01G465000 chr2A 96.875 32 0 1 1 32 424568239 424568209 7.000000e-03 52.8


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 TraesCS3A01G465000 chr3A 699544939 699548701 3762 True 6950.0 6950 100.000000 1 3763 1 chr3A.!!$R2 3762
1 TraesCS3A01G465000 chr3A 699105262 699105998 736 False 660.0 660 82.861000 2185 2924 1 chr3A.!!$F1 739
2 TraesCS3A01G465000 chr3D 565143672 565147332 3660 True 1917.0 4874 94.285333 30 3731 3 chr3D.!!$R2 3701
3 TraesCS3A01G465000 chr3B 752912329 752916319 3990 False 1042.4 2137 95.134400 28 3680 5 chr3B.!!$F1 3652
4 TraesCS3A01G465000 chr3B 580786426 580787006 580 True 335.0 335 77.342000 2176 2754 1 chr3B.!!$R1 578
5 TraesCS3A01G465000 chr5B 248388503 248389154 651 True 466.0 466 79.756000 2101 2750 1 chr5B.!!$R2 649
6 TraesCS3A01G465000 chr7D 89290031 89290607 576 False 388.0 388 79.145000 2176 2750 1 chr7D.!!$F1 574
7 TraesCS3A01G465000 chr7B 40194776 40195351 575 False 375.0 375 78.767000 2176 2750 1 chr7B.!!$F1 574
8 TraesCS3A01G465000 chr5A 42281455 42282017 562 True 326.0 326 77.622000 2194 2750 1 chr5A.!!$R1 556

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
165 166 0.531532 CCCAGAGACGCCAATAGCAG 60.532 60.000 0.00 0.0 44.04 4.24 F
322 323 2.439553 TTTGCCAGGGGTGGTGATCC 62.440 60.000 0.00 0.0 0.00 3.36 F
1315 2063 2.608268 TGCATTGCACAAAATGGATCG 58.392 42.857 7.38 0.0 37.89 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2961 2.289274 CGGTTGCACATGACACTTAACA 59.711 45.455 0.0 0.0 0.00 2.41 R
2190 3139 3.265221 TCAATGAGAGAACCCTGCAAGAT 59.735 43.478 0.0 0.0 34.07 2.40 R
3148 4110 0.036952 TCTAGCACAGCAGACCAAGC 60.037 55.000 0.0 0.0 0.00 4.01 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
26 27 4.353437 GTCGAACCGCCGTCCTGT 62.353 66.667 0.00 0.00 0.00 4.00
40 41 4.873827 GCCGTCCTGTAACAATGAATCTAA 59.126 41.667 0.00 0.00 0.00 2.10
41 42 5.006746 GCCGTCCTGTAACAATGAATCTAAG 59.993 44.000 0.00 0.00 0.00 2.18
42 43 6.338146 CCGTCCTGTAACAATGAATCTAAGA 58.662 40.000 0.00 0.00 0.00 2.10
57 58 8.268850 TGAATCTAAGATTTTACCACAAGCTC 57.731 34.615 0.00 0.00 0.00 4.09
73 74 7.178628 ACCACAAGCTCTAATCTCTAAGTTACA 59.821 37.037 0.00 0.00 0.00 2.41
154 155 2.463047 ACTAGGATGACCCCAGAGAC 57.537 55.000 0.00 0.00 36.73 3.36
163 164 1.227674 CCCCAGAGACGCCAATAGC 60.228 63.158 0.00 0.00 38.52 2.97
164 165 1.522092 CCCAGAGACGCCAATAGCA 59.478 57.895 0.00 0.00 44.04 3.49
165 166 0.531532 CCCAGAGACGCCAATAGCAG 60.532 60.000 0.00 0.00 44.04 4.24
246 247 2.777094 AGCTGCTCTTTCTTTGTCTCC 58.223 47.619 0.00 0.00 0.00 3.71
322 323 2.439553 TTTGCCAGGGGTGGTGATCC 62.440 60.000 0.00 0.00 0.00 3.36
483 485 8.211629 GGTAATAGGTGGATCTAACAAGTCATT 58.788 37.037 0.00 0.00 0.00 2.57
560 1087 7.125963 GCCTATTACCAGGGTAATAAGAGCTAT 59.874 40.741 23.96 6.45 46.46 2.97
577 1104 4.922206 AGCTATGTTTTTCACCAGGATCA 58.078 39.130 0.00 0.00 0.00 2.92
594 1127 3.486383 GATCAAGTCCCTGTTTGGTGAA 58.514 45.455 0.00 0.00 0.00 3.18
641 1174 8.894768 ATGAAAGATAATTGCTACTAGTGTCC 57.105 34.615 5.39 0.00 0.00 4.02
655 1188 4.884744 ACTAGTGTCCAGTGTCTATGCTAG 59.115 45.833 0.00 0.00 0.00 3.42
706 1239 5.920903 TGCTAATACGTATAGCCAAAAGGT 58.079 37.500 22.80 5.00 36.09 3.50
1315 2063 2.608268 TGCATTGCACAAAATGGATCG 58.392 42.857 7.38 0.00 37.89 3.69
1485 2432 8.856490 ATGTTCTTAGTTTTGTTGTGATGTTC 57.144 30.769 0.00 0.00 0.00 3.18
1486 2433 8.050778 TGTTCTTAGTTTTGTTGTGATGTTCT 57.949 30.769 0.00 0.00 0.00 3.01
1487 2434 8.519526 TGTTCTTAGTTTTGTTGTGATGTTCTT 58.480 29.630 0.00 0.00 0.00 2.52
1488 2435 9.997482 GTTCTTAGTTTTGTTGTGATGTTCTTA 57.003 29.630 0.00 0.00 0.00 2.10
1490 2437 9.391006 TCTTAGTTTTGTTGTGATGTTCTTAGT 57.609 29.630 0.00 0.00 0.00 2.24
1492 2439 9.997482 TTAGTTTTGTTGTGATGTTCTTAGTTC 57.003 29.630 0.00 0.00 0.00 3.01
1493 2440 8.281212 AGTTTTGTTGTGATGTTCTTAGTTCT 57.719 30.769 0.00 0.00 0.00 3.01
1494 2441 8.739972 AGTTTTGTTGTGATGTTCTTAGTTCTT 58.260 29.630 0.00 0.00 0.00 2.52
1495 2442 9.997482 GTTTTGTTGTGATGTTCTTAGTTCTTA 57.003 29.630 0.00 0.00 0.00 2.10
1607 2554 8.755696 TTTTTGTGTTATGGTTGCATATCTTC 57.244 30.769 0.00 0.00 0.00 2.87
1608 2555 7.701539 TTTGTGTTATGGTTGCATATCTTCT 57.298 32.000 0.00 0.00 0.00 2.85
1609 2556 7.701539 TTGTGTTATGGTTGCATATCTTCTT 57.298 32.000 0.00 0.00 0.00 2.52
1610 2557 7.320443 TGTGTTATGGTTGCATATCTTCTTC 57.680 36.000 0.00 0.00 0.00 2.87
1611 2558 6.318648 TGTGTTATGGTTGCATATCTTCTTCC 59.681 38.462 0.00 0.00 0.00 3.46
1612 2559 6.318648 GTGTTATGGTTGCATATCTTCTTCCA 59.681 38.462 0.00 0.00 0.00 3.53
1613 2560 7.013655 GTGTTATGGTTGCATATCTTCTTCCAT 59.986 37.037 0.00 0.00 37.96 3.41
1614 2561 7.013559 TGTTATGGTTGCATATCTTCTTCCATG 59.986 37.037 0.00 0.00 36.17 3.66
1615 2562 4.858850 TGGTTGCATATCTTCTTCCATGT 58.141 39.130 0.00 0.00 0.00 3.21
1616 2563 4.641541 TGGTTGCATATCTTCTTCCATGTG 59.358 41.667 0.00 0.00 0.00 3.21
1617 2564 4.498682 GGTTGCATATCTTCTTCCATGTGC 60.499 45.833 0.00 0.00 37.57 4.57
1618 2565 4.160642 TGCATATCTTCTTCCATGTGCT 57.839 40.909 0.00 0.00 37.84 4.40
1619 2566 4.529897 TGCATATCTTCTTCCATGTGCTT 58.470 39.130 0.00 0.00 37.84 3.91
1620 2567 5.683681 TGCATATCTTCTTCCATGTGCTTA 58.316 37.500 0.00 0.00 37.84 3.09
1621 2568 6.121590 TGCATATCTTCTTCCATGTGCTTAA 58.878 36.000 0.00 0.00 37.84 1.85
1622 2569 6.038603 TGCATATCTTCTTCCATGTGCTTAAC 59.961 38.462 0.00 0.00 37.84 2.01
1623 2570 6.261826 GCATATCTTCTTCCATGTGCTTAACT 59.738 38.462 0.00 0.00 35.04 2.24
1624 2571 7.519649 GCATATCTTCTTCCATGTGCTTAACTC 60.520 40.741 0.00 0.00 35.04 3.01
1625 2572 5.489792 TCTTCTTCCATGTGCTTAACTCT 57.510 39.130 0.00 0.00 0.00 3.24
1626 2573 6.605471 TCTTCTTCCATGTGCTTAACTCTA 57.395 37.500 0.00 0.00 0.00 2.43
1627 2574 7.187824 TCTTCTTCCATGTGCTTAACTCTAT 57.812 36.000 0.00 0.00 0.00 1.98
1628 2575 7.624549 TCTTCTTCCATGTGCTTAACTCTATT 58.375 34.615 0.00 0.00 0.00 1.73
1629 2576 8.758829 TCTTCTTCCATGTGCTTAACTCTATTA 58.241 33.333 0.00 0.00 0.00 0.98
1630 2577 9.383519 CTTCTTCCATGTGCTTAACTCTATTAA 57.616 33.333 0.00 0.00 0.00 1.40
1631 2578 9.733556 TTCTTCCATGTGCTTAACTCTATTAAA 57.266 29.630 0.00 0.00 0.00 1.52
1632 2579 9.733556 TCTTCCATGTGCTTAACTCTATTAAAA 57.266 29.630 0.00 0.00 0.00 1.52
1635 2582 9.515226 TCCATGTGCTTAACTCTATTAAAAAGT 57.485 29.630 0.00 0.00 0.00 2.66
1636 2583 9.559958 CCATGTGCTTAACTCTATTAAAAAGTG 57.440 33.333 0.00 0.00 0.00 3.16
1639 2586 9.332502 TGTGCTTAACTCTATTAAAAAGTGTCA 57.667 29.630 0.00 0.00 0.00 3.58
1646 2593 9.715121 AACTCTATTAAAAAGTGTCATACCGAA 57.285 29.630 0.00 0.00 0.00 4.30
1647 2594 9.715121 ACTCTATTAAAAAGTGTCATACCGAAA 57.285 29.630 0.00 0.00 0.00 3.46
1652 2599 8.789881 TTAAAAAGTGTCATACCGAAATTGTG 57.210 30.769 0.00 0.00 0.00 3.33
1653 2600 6.627395 AAAAGTGTCATACCGAAATTGTGA 57.373 33.333 0.00 0.00 0.00 3.58
1654 2601 6.627395 AAAGTGTCATACCGAAATTGTGAA 57.373 33.333 0.00 0.00 0.00 3.18
1655 2602 6.627395 AAGTGTCATACCGAAATTGTGAAA 57.373 33.333 0.00 0.00 0.00 2.69
1656 2603 6.627395 AGTGTCATACCGAAATTGTGAAAA 57.373 33.333 0.00 0.00 0.00 2.29
1657 2604 7.214467 AGTGTCATACCGAAATTGTGAAAAT 57.786 32.000 0.00 0.00 0.00 1.82
1658 2605 8.330466 AGTGTCATACCGAAATTGTGAAAATA 57.670 30.769 0.00 0.00 0.00 1.40
1659 2606 8.788806 AGTGTCATACCGAAATTGTGAAAATAA 58.211 29.630 0.00 0.00 0.00 1.40
1660 2607 8.846607 GTGTCATACCGAAATTGTGAAAATAAC 58.153 33.333 0.00 0.00 0.00 1.89
1661 2608 8.788806 TGTCATACCGAAATTGTGAAAATAACT 58.211 29.630 0.00 0.00 0.00 2.24
1737 2684 9.852091 AATTAGTTAGACGAAACTTACTACTGG 57.148 33.333 7.63 0.00 40.20 4.00
1930 2877 7.122501 TGGATTCTTGTATGCAAATATGTGTGT 59.877 33.333 0.00 0.00 33.73 3.72
1985 2932 6.772233 TGTCCTTTTGCATATATGTAGCATGT 59.228 34.615 14.14 0.00 38.19 3.21
2130 3077 3.258872 TGAGTTCCATTTCCAATTGGCTG 59.741 43.478 20.33 15.43 32.80 4.85
2131 3078 3.242011 AGTTCCATTTCCAATTGGCTGT 58.758 40.909 20.33 4.60 32.80 4.40
2307 3260 5.697082 AGGAGAGCAAGAAGAAGATGATT 57.303 39.130 0.00 0.00 0.00 2.57
2539 3497 3.688673 CCTCACAGAATTGAGCTCTTTCC 59.311 47.826 16.19 2.07 41.61 3.13
2574 3532 4.501198 GCGAGTCATGTAGCTTAAGAAGAC 59.499 45.833 6.67 4.29 0.00 3.01
2725 3683 6.419484 ACAAATAAAACTTAAGCCTGCCTT 57.581 33.333 1.29 0.00 37.57 4.35
2862 3824 3.903467 AGGGCTCTAAAAATGGTGATCC 58.097 45.455 0.00 0.00 0.00 3.36
2961 3923 1.270893 GGTGAAGGGTGACTTGGTCTC 60.271 57.143 0.00 0.00 40.21 3.36
2962 3924 1.416401 GTGAAGGGTGACTTGGTCTCA 59.584 52.381 0.00 0.00 40.21 3.27
2964 3926 2.038952 TGAAGGGTGACTTGGTCTCATG 59.961 50.000 0.00 0.00 40.21 3.07
2965 3927 0.987294 AGGGTGACTTGGTCTCATGG 59.013 55.000 0.00 0.00 33.15 3.66
2966 3928 0.693049 GGGTGACTTGGTCTCATGGT 59.307 55.000 0.00 0.00 33.15 3.55
2967 3929 1.073923 GGGTGACTTGGTCTCATGGTT 59.926 52.381 0.00 0.00 33.15 3.67
2968 3930 2.489073 GGGTGACTTGGTCTCATGGTTT 60.489 50.000 0.00 0.00 33.15 3.27
2969 3931 3.222603 GGTGACTTGGTCTCATGGTTTT 58.777 45.455 0.00 0.00 33.15 2.43
2970 3932 4.394729 GGTGACTTGGTCTCATGGTTTTA 58.605 43.478 0.00 0.00 33.15 1.52
2971 3933 4.825085 GGTGACTTGGTCTCATGGTTTTAA 59.175 41.667 0.00 0.00 33.15 1.52
2972 3934 5.300792 GGTGACTTGGTCTCATGGTTTTAAA 59.699 40.000 0.00 0.00 33.15 1.52
2973 3935 6.015434 GGTGACTTGGTCTCATGGTTTTAAAT 60.015 38.462 0.00 0.00 33.15 1.40
2974 3936 7.175990 GGTGACTTGGTCTCATGGTTTTAAATA 59.824 37.037 0.00 0.00 33.15 1.40
2975 3937 8.237267 GTGACTTGGTCTCATGGTTTTAAATAG 58.763 37.037 0.00 0.00 33.15 1.73
2976 3938 7.094377 TGACTTGGTCTCATGGTTTTAAATAGC 60.094 37.037 0.00 0.00 33.15 2.97
2977 3939 6.152831 ACTTGGTCTCATGGTTTTAAATAGCC 59.847 38.462 0.00 0.00 0.00 3.93
2978 3940 4.953579 TGGTCTCATGGTTTTAAATAGCCC 59.046 41.667 0.00 0.00 0.00 5.19
2979 3941 4.036380 GGTCTCATGGTTTTAAATAGCCCG 59.964 45.833 0.00 0.00 0.00 6.13
2980 3942 3.630312 TCTCATGGTTTTAAATAGCCCGC 59.370 43.478 0.00 0.00 0.00 6.13
2981 3943 3.626930 TCATGGTTTTAAATAGCCCGCT 58.373 40.909 0.00 0.00 0.00 5.52
2982 3944 4.783055 TCATGGTTTTAAATAGCCCGCTA 58.217 39.130 0.00 0.00 0.00 4.26
2983 3945 5.381757 TCATGGTTTTAAATAGCCCGCTAT 58.618 37.500 3.31 3.31 40.63 2.97
2984 3946 6.535540 TCATGGTTTTAAATAGCCCGCTATA 58.464 36.000 9.56 0.00 38.20 1.31
2985 3947 6.653320 TCATGGTTTTAAATAGCCCGCTATAG 59.347 38.462 9.56 0.00 38.20 1.31
2986 3948 4.758165 TGGTTTTAAATAGCCCGCTATAGC 59.242 41.667 15.09 15.09 38.20 2.97
2987 3949 5.001874 GGTTTTAAATAGCCCGCTATAGCT 58.998 41.667 21.98 6.31 43.20 3.32
2988 3950 5.121925 GGTTTTAAATAGCCCGCTATAGCTC 59.878 44.000 21.98 11.04 40.56 4.09
2989 3951 4.467198 TTAAATAGCCCGCTATAGCTCC 57.533 45.455 21.98 10.06 40.56 4.70
2990 3952 0.818296 AATAGCCCGCTATAGCTCCG 59.182 55.000 21.98 10.15 40.56 4.63
2991 3953 1.668101 ATAGCCCGCTATAGCTCCGC 61.668 60.000 21.98 18.46 40.56 5.54
2992 3954 2.766306 TAGCCCGCTATAGCTCCGCT 62.766 60.000 24.41 24.41 43.41 5.52
2993 3955 2.341101 GCCCGCTATAGCTCCGCTA 61.341 63.158 21.98 0.00 45.55 4.26
3011 3973 4.469625 GCTATAGCGTTTAGAAAAGGCC 57.530 45.455 9.40 0.00 0.00 5.19
3012 3974 3.250280 GCTATAGCGTTTAGAAAAGGCCC 59.750 47.826 9.40 0.00 0.00 5.80
3013 3975 2.118313 TAGCGTTTAGAAAAGGCCCC 57.882 50.000 0.00 0.00 0.00 5.80
3014 3976 0.958876 AGCGTTTAGAAAAGGCCCCG 60.959 55.000 0.00 0.00 0.00 5.73
3015 3977 1.504900 CGTTTAGAAAAGGCCCCGC 59.495 57.895 0.00 0.00 0.00 6.13
3016 3978 1.504900 GTTTAGAAAAGGCCCCGCG 59.495 57.895 0.00 0.00 0.00 6.46
3017 3979 2.337246 TTTAGAAAAGGCCCCGCGC 61.337 57.895 0.00 0.00 0.00 6.86
3018 3980 2.757980 TTTAGAAAAGGCCCCGCGCT 62.758 55.000 5.56 0.00 37.74 5.92
3019 3981 1.901654 TTAGAAAAGGCCCCGCGCTA 61.902 55.000 5.56 0.00 37.74 4.26
3020 3982 1.901654 TAGAAAAGGCCCCGCGCTAA 61.902 55.000 5.56 0.00 37.74 3.09
3021 3983 2.750237 AAAAGGCCCCGCGCTAAG 60.750 61.111 5.56 0.00 37.74 2.18
3022 3984 3.262448 AAAAGGCCCCGCGCTAAGA 62.262 57.895 5.56 0.00 37.74 2.10
3023 3985 3.682292 AAAGGCCCCGCGCTAAGAG 62.682 63.158 5.56 0.00 37.74 2.85
3025 3987 4.893601 GGCCCCGCGCTAAGAGTC 62.894 72.222 5.56 0.00 37.74 3.36
3026 3988 3.839432 GCCCCGCGCTAAGAGTCT 61.839 66.667 5.56 0.00 0.00 3.24
3027 3989 2.893398 CCCCGCGCTAAGAGTCTT 59.107 61.111 10.87 10.87 0.00 3.01
3028 3990 1.218316 CCCCGCGCTAAGAGTCTTT 59.782 57.895 11.40 0.00 0.00 2.52
3029 3991 0.391263 CCCCGCGCTAAGAGTCTTTT 60.391 55.000 11.40 0.00 0.00 2.27
3030 3992 0.721718 CCCGCGCTAAGAGTCTTTTG 59.278 55.000 11.40 6.00 0.00 2.44
3031 3993 1.429463 CCGCGCTAAGAGTCTTTTGT 58.571 50.000 11.40 0.00 0.00 2.83
3032 3994 1.798813 CCGCGCTAAGAGTCTTTTGTT 59.201 47.619 11.40 0.00 0.00 2.83
3033 3995 2.159827 CCGCGCTAAGAGTCTTTTGTTC 60.160 50.000 11.40 0.00 0.00 3.18
3034 3996 2.475111 CGCGCTAAGAGTCTTTTGTTCA 59.525 45.455 11.40 0.00 0.00 3.18
3035 3997 3.059868 CGCGCTAAGAGTCTTTTGTTCAA 60.060 43.478 11.40 0.00 0.00 2.69
3036 3998 4.551990 CGCGCTAAGAGTCTTTTGTTCAAA 60.552 41.667 11.40 0.00 0.00 2.69
3037 3999 4.671068 GCGCTAAGAGTCTTTTGTTCAAAC 59.329 41.667 11.40 0.00 0.00 2.93
3038 4000 5.729454 GCGCTAAGAGTCTTTTGTTCAAACA 60.729 40.000 11.40 0.00 37.08 2.83
3039 4001 5.677178 CGCTAAGAGTCTTTTGTTCAAACAC 59.323 40.000 11.40 0.00 38.92 3.32
3040 4002 6.456988 CGCTAAGAGTCTTTTGTTCAAACACT 60.457 38.462 11.40 8.10 38.92 3.55
3041 4003 7.251281 GCTAAGAGTCTTTTGTTCAAACACTT 58.749 34.615 11.40 6.95 38.92 3.16
3042 4004 7.218963 GCTAAGAGTCTTTTGTTCAAACACTTG 59.781 37.037 11.40 0.00 38.92 3.16
3043 4005 6.817765 AGAGTCTTTTGTTCAAACACTTGA 57.182 33.333 0.00 0.00 39.87 3.02
3044 4006 6.846350 AGAGTCTTTTGTTCAAACACTTGAG 58.154 36.000 0.00 0.62 42.48 3.02
3045 4007 5.402398 AGTCTTTTGTTCAAACACTTGAGC 58.598 37.500 0.00 0.00 42.48 4.26
3050 4012 4.511617 TGTTCAAACACTTGAGCAAACA 57.488 36.364 2.42 0.00 46.13 2.83
3051 4013 5.070770 TGTTCAAACACTTGAGCAAACAT 57.929 34.783 2.42 0.00 46.13 2.71
3052 4014 5.477510 TGTTCAAACACTTGAGCAAACATT 58.522 33.333 2.42 0.00 46.13 2.71
3053 4015 5.931146 TGTTCAAACACTTGAGCAAACATTT 59.069 32.000 2.42 0.00 46.13 2.32
3054 4016 6.426328 TGTTCAAACACTTGAGCAAACATTTT 59.574 30.769 2.42 0.00 46.13 1.82
3055 4017 7.600375 TGTTCAAACACTTGAGCAAACATTTTA 59.400 29.630 2.42 0.00 46.13 1.52
3056 4018 8.439286 GTTCAAACACTTGAGCAAACATTTTAA 58.561 29.630 0.00 0.00 42.48 1.52
3057 4019 8.539770 TCAAACACTTGAGCAAACATTTTAAA 57.460 26.923 0.00 0.00 36.62 1.52
3058 4020 9.160496 TCAAACACTTGAGCAAACATTTTAAAT 57.840 25.926 0.00 0.00 36.62 1.40
3061 4023 8.298030 ACACTTGAGCAAACATTTTAAATAGC 57.702 30.769 0.00 0.00 0.00 2.97
3062 4024 8.143835 ACACTTGAGCAAACATTTTAAATAGCT 58.856 29.630 0.00 0.00 0.00 3.32
3063 4025 8.642020 CACTTGAGCAAACATTTTAAATAGCTC 58.358 33.333 18.09 18.09 45.40 4.09
3065 4027 6.248201 GAGCAAACATTTTAAATAGCTCGC 57.752 37.500 13.51 4.83 38.00 5.03
3066 4028 5.954335 AGCAAACATTTTAAATAGCTCGCT 58.046 33.333 0.00 0.00 0.00 4.93
3067 4029 7.083875 AGCAAACATTTTAAATAGCTCGCTA 57.916 32.000 0.53 0.53 0.00 4.26
3068 4030 7.707104 AGCAAACATTTTAAATAGCTCGCTAT 58.293 30.769 5.63 5.63 40.63 2.97
3069 4031 8.836413 AGCAAACATTTTAAATAGCTCGCTATA 58.164 29.630 11.49 0.00 38.20 1.31
3070 4032 9.107367 GCAAACATTTTAAATAGCTCGCTATAG 57.893 33.333 11.49 0.00 38.20 1.31
3071 4033 9.107367 CAAACATTTTAAATAGCTCGCTATAGC 57.893 33.333 15.09 15.09 43.11 2.97
3077 4039 2.958576 GCTCGCTATAGCTCCGCT 59.041 61.111 21.98 0.00 43.41 5.52
3078 4040 2.172534 GCTCGCTATAGCTCCGCTA 58.827 57.895 21.98 0.00 45.55 4.26
3086 4048 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
3087 4049 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
3088 4050 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
3089 4051 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
3090 4052 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
3099 4061 6.503616 CTATAGCACGCTATAGCATTTAGC 57.496 41.667 25.42 17.69 46.26 3.09
3110 4072 1.383523 GCATTTAGCTGAGGTCCACC 58.616 55.000 0.00 0.00 41.15 4.61
3111 4073 1.656652 CATTTAGCTGAGGTCCACCG 58.343 55.000 0.00 0.00 42.08 4.94
3112 4074 1.066143 CATTTAGCTGAGGTCCACCGT 60.066 52.381 0.00 0.00 42.08 4.83
3113 4075 1.927487 TTTAGCTGAGGTCCACCGTA 58.073 50.000 0.00 0.00 42.08 4.02
3114 4076 1.180029 TTAGCTGAGGTCCACCGTAC 58.820 55.000 0.00 0.00 42.08 3.67
3115 4077 0.682209 TAGCTGAGGTCCACCGTACC 60.682 60.000 0.00 0.00 42.08 3.34
3116 4078 2.882876 CTGAGGTCCACCGTACCG 59.117 66.667 0.00 0.00 42.15 4.02
3117 4079 3.352338 CTGAGGTCCACCGTACCGC 62.352 68.421 0.00 0.00 42.15 5.68
3118 4080 3.066814 GAGGTCCACCGTACCGCT 61.067 66.667 0.00 0.00 42.15 5.52
3119 4081 1.750399 GAGGTCCACCGTACCGCTA 60.750 63.158 0.00 0.00 42.15 4.26
3120 4082 1.304381 AGGTCCACCGTACCGCTAA 60.304 57.895 0.00 0.00 42.15 3.09
3121 4083 1.140375 GGTCCACCGTACCGCTAAG 59.860 63.158 0.00 0.00 0.00 2.18
3122 4084 1.315257 GGTCCACCGTACCGCTAAGA 61.315 60.000 0.00 0.00 0.00 2.10
3123 4085 0.100146 GTCCACCGTACCGCTAAGAG 59.900 60.000 0.00 0.00 0.00 2.85
3124 4086 1.033746 TCCACCGTACCGCTAAGAGG 61.034 60.000 0.00 0.00 0.00 3.69
3125 4087 1.226888 CACCGTACCGCTAAGAGGC 60.227 63.158 0.00 0.00 0.00 4.70
3126 4088 1.379576 ACCGTACCGCTAAGAGGCT 60.380 57.895 0.00 0.00 0.00 4.58
3127 4089 0.969409 ACCGTACCGCTAAGAGGCTT 60.969 55.000 0.00 0.00 0.00 4.35
3128 4090 1.027357 CCGTACCGCTAAGAGGCTTA 58.973 55.000 0.00 0.00 0.00 3.09
3129 4091 1.001597 CCGTACCGCTAAGAGGCTTAG 60.002 57.143 9.30 9.30 0.00 2.18
3130 4092 1.599916 CGTACCGCTAAGAGGCTTAGC 60.600 57.143 22.75 22.75 42.82 3.09
3133 4095 3.619054 GCTAAGAGGCTTAGCGCG 58.381 61.111 19.61 0.00 38.12 6.86
3134 4096 2.590401 GCTAAGAGGCTTAGCGCGC 61.590 63.158 26.66 26.66 38.12 6.86
3135 4097 1.066587 CTAAGAGGCTTAGCGCGCT 59.933 57.895 38.01 38.01 40.44 5.92
3136 4098 0.311165 CTAAGAGGCTTAGCGCGCTA 59.689 55.000 35.48 35.48 40.44 4.26
3137 4099 0.959553 TAAGAGGCTTAGCGCGCTAT 59.040 50.000 38.51 25.42 40.44 2.97
3138 4100 0.105039 AAGAGGCTTAGCGCGCTATT 59.895 50.000 38.51 26.01 40.44 1.73
3139 4101 0.105039 AGAGGCTTAGCGCGCTATTT 59.895 50.000 38.51 24.06 40.44 1.40
3140 4102 1.340248 AGAGGCTTAGCGCGCTATTTA 59.660 47.619 38.51 24.25 40.44 1.40
3141 4103 2.132762 GAGGCTTAGCGCGCTATTTAA 58.867 47.619 38.51 25.53 40.44 1.52
3142 4104 2.542595 GAGGCTTAGCGCGCTATTTAAA 59.457 45.455 38.51 25.16 40.44 1.52
3143 4105 2.940410 AGGCTTAGCGCGCTATTTAAAA 59.060 40.909 38.51 24.43 40.44 1.52
3144 4106 3.033873 GGCTTAGCGCGCTATTTAAAAC 58.966 45.455 38.51 21.47 40.44 2.43
3145 4107 3.242641 GGCTTAGCGCGCTATTTAAAACT 60.243 43.478 38.51 14.50 40.44 2.66
3146 4108 4.340263 GCTTAGCGCGCTATTTAAAACTT 58.660 39.130 38.51 13.94 0.00 2.66
3147 4109 4.791676 GCTTAGCGCGCTATTTAAAACTTT 59.208 37.500 38.51 13.72 0.00 2.66
3148 4110 5.275280 GCTTAGCGCGCTATTTAAAACTTTG 60.275 40.000 38.51 15.49 0.00 2.77
3149 4111 2.914838 AGCGCGCTATTTAAAACTTTGC 59.085 40.909 35.79 0.00 0.00 3.68
3150 4112 2.914838 GCGCGCTATTTAAAACTTTGCT 59.085 40.909 26.67 0.00 0.00 3.91
3151 4113 3.363724 GCGCGCTATTTAAAACTTTGCTT 59.636 39.130 26.67 0.00 0.00 3.91
3152 4114 4.718168 GCGCGCTATTTAAAACTTTGCTTG 60.718 41.667 26.67 0.00 0.00 4.01
3153 4115 4.201485 CGCGCTATTTAAAACTTTGCTTGG 60.201 41.667 5.56 0.00 0.00 3.61
3154 4116 4.684242 GCGCTATTTAAAACTTTGCTTGGT 59.316 37.500 0.00 0.00 0.00 3.67
3157 4119 6.088085 CGCTATTTAAAACTTTGCTTGGTCTG 59.912 38.462 0.00 0.00 0.00 3.51
3247 4209 0.539207 TGTATGCTTGCTTGGCACCA 60.539 50.000 0.00 0.00 42.69 4.17
3271 4233 2.629137 TGGATGTTGCAGATTTTGTGCT 59.371 40.909 0.00 0.00 41.78 4.40
3272 4234 2.991190 GGATGTTGCAGATTTTGTGCTG 59.009 45.455 0.00 0.00 41.78 4.41
3273 4235 2.512485 TGTTGCAGATTTTGTGCTGG 57.488 45.000 0.00 0.00 41.78 4.85
3551 4521 5.607119 TTGCATAAAGTTCTTCGTCCTTC 57.393 39.130 0.00 0.00 0.00 3.46
3552 4522 4.637276 TGCATAAAGTTCTTCGTCCTTCA 58.363 39.130 0.00 0.00 0.00 3.02
3572 4542 6.147656 CCTTCAATCCAAAGTGTATTTTTGCC 59.852 38.462 0.00 0.00 34.88 4.52
3598 4568 5.396057 AGTTCCTCTAGATTCAGGCTAGA 57.604 43.478 0.00 0.00 41.38 2.43
3637 4607 3.937814 TGGCATGTAACACTAACAGAGG 58.062 45.455 0.00 0.00 0.00 3.69
3710 4828 3.160679 ACAGGGGAAATGAGTTCAAGG 57.839 47.619 0.00 0.00 38.06 3.61
3712 4830 1.428912 AGGGGAAATGAGTTCAAGGCA 59.571 47.619 0.00 0.00 38.06 4.75
3720 4838 6.460953 GGAAATGAGTTCAAGGCAACAGTTTA 60.461 38.462 0.00 0.00 38.06 2.01
3727 4845 5.437289 TCAAGGCAACAGTTTACATCAAG 57.563 39.130 0.00 0.00 41.41 3.02
3731 4849 6.560253 AGGCAACAGTTTACATCAAGTTAG 57.440 37.500 0.00 0.00 41.41 2.34
3732 4850 6.062095 AGGCAACAGTTTACATCAAGTTAGT 58.938 36.000 0.00 0.00 41.41 2.24
3733 4851 6.546034 AGGCAACAGTTTACATCAAGTTAGTT 59.454 34.615 0.00 0.00 41.41 2.24
3734 4852 7.068226 AGGCAACAGTTTACATCAAGTTAGTTT 59.932 33.333 0.00 0.00 41.41 2.66
3735 4853 7.704899 GGCAACAGTTTACATCAAGTTAGTTTT 59.295 33.333 0.00 0.00 0.00 2.43
3736 4854 9.724839 GCAACAGTTTACATCAAGTTAGTTTTA 57.275 29.630 0.00 0.00 0.00 1.52
3752 4870 9.433153 AGTTAGTTTTATAAGCTACAAGTGACC 57.567 33.333 0.00 0.00 0.00 4.02
3753 4871 9.211485 GTTAGTTTTATAAGCTACAAGTGACCA 57.789 33.333 0.00 0.00 0.00 4.02
3754 4872 9.953565 TTAGTTTTATAAGCTACAAGTGACCAT 57.046 29.630 0.00 0.00 0.00 3.55
3755 4873 8.494016 AGTTTTATAAGCTACAAGTGACCATC 57.506 34.615 0.00 0.00 0.00 3.51
3756 4874 7.277981 AGTTTTATAAGCTACAAGTGACCATCG 59.722 37.037 0.00 0.00 0.00 3.84
3757 4875 2.386661 AAGCTACAAGTGACCATCGG 57.613 50.000 0.00 0.00 0.00 4.18
3758 4876 0.537188 AGCTACAAGTGACCATCGGG 59.463 55.000 0.00 0.00 41.29 5.14
3759 4877 0.535335 GCTACAAGTGACCATCGGGA 59.465 55.000 0.00 0.00 38.05 5.14
3760 4878 1.739371 GCTACAAGTGACCATCGGGAC 60.739 57.143 0.00 0.00 38.05 4.46
3761 4879 1.548719 CTACAAGTGACCATCGGGACA 59.451 52.381 0.00 0.00 36.48 4.02
3762 4880 0.762418 ACAAGTGACCATCGGGACAA 59.238 50.000 0.00 0.00 40.50 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.476534 TTACAGGACGGCGGTTCGAC 62.477 60.000 13.24 0.00 0.00 4.20
10 11 2.267351 TTACAGGACGGCGGTTCGA 61.267 57.895 13.24 0.00 0.00 3.71
11 12 2.090524 GTTACAGGACGGCGGTTCG 61.091 63.158 13.24 0.00 0.00 3.95
12 13 0.600782 TTGTTACAGGACGGCGGTTC 60.601 55.000 13.24 0.00 0.00 3.62
13 14 0.035739 ATTGTTACAGGACGGCGGTT 59.964 50.000 13.24 0.00 0.00 4.44
14 15 0.672401 CATTGTTACAGGACGGCGGT 60.672 55.000 13.24 0.00 0.00 5.68
15 16 0.390603 TCATTGTTACAGGACGGCGG 60.391 55.000 13.24 0.00 0.00 6.13
16 17 1.434555 TTCATTGTTACAGGACGGCG 58.565 50.000 4.80 4.80 0.00 6.46
17 18 3.270877 AGATTCATTGTTACAGGACGGC 58.729 45.455 0.00 0.00 0.00 5.68
18 19 6.338146 TCTTAGATTCATTGTTACAGGACGG 58.662 40.000 0.00 0.00 0.00 4.79
19 20 8.425577 AATCTTAGATTCATTGTTACAGGACG 57.574 34.615 0.99 0.00 0.00 4.79
40 41 7.856415 AGAGATTAGAGCTTGTGGTAAAATCT 58.144 34.615 0.00 0.00 37.65 2.40
41 42 9.601217 TTAGAGATTAGAGCTTGTGGTAAAATC 57.399 33.333 0.00 0.00 0.00 2.17
42 43 9.606631 CTTAGAGATTAGAGCTTGTGGTAAAAT 57.393 33.333 0.00 0.00 0.00 1.82
79 80 8.651589 TGACTGGACTTCTCTTAGATTTTCTA 57.348 34.615 0.00 0.00 0.00 2.10
129 130 1.049402 GGGGTCATCCTAGTAGGTGC 58.951 60.000 16.02 9.37 36.53 5.01
240 241 6.313519 AGTATTATTGCTTTCCAGGAGACA 57.686 37.500 0.00 0.00 0.00 3.41
246 247 8.974060 TTAACCCTAGTATTATTGCTTTCCAG 57.026 34.615 0.00 0.00 0.00 3.86
306 307 4.129148 GGGATCACCACCCCTGGC 62.129 72.222 0.00 0.00 42.08 4.85
322 323 7.503566 TGAATTGCCTTTCTGGAATATTAGAGG 59.496 37.037 0.00 0.00 38.35 3.69
483 485 0.252239 TGAAGGGCTGCCTGACTCTA 60.252 55.000 19.68 0.00 0.00 2.43
560 1087 3.888930 GGACTTGATCCTGGTGAAAAACA 59.111 43.478 0.00 0.00 45.22 2.83
577 1104 3.382083 AAGTTCACCAAACAGGGACTT 57.618 42.857 0.00 0.00 43.89 3.01
594 1127 8.267620 TCATAAGGATGATGTTCCTGATAAGT 57.732 34.615 0.00 0.00 45.63 2.24
641 1174 4.820897 TCAAACCACTAGCATAGACACTG 58.179 43.478 0.00 0.00 42.77 3.66
655 1188 4.180057 TGCTCACACAAAAATCAAACCAC 58.820 39.130 0.00 0.00 0.00 4.16
753 1286 7.008021 TGCAGATTGAGATGGCTATAATACA 57.992 36.000 0.00 0.00 0.00 2.29
829 1362 7.637631 TTGCTAGGACAAAATGCATTATACA 57.362 32.000 13.39 0.00 33.50 2.29
888 1422 9.988350 CAGTTTGGTATGAATACATGAGTTTAC 57.012 33.333 0.00 0.00 37.87 2.01
1275 2023 4.398988 TGCATGTGATGGGATTGAACTTAC 59.601 41.667 0.00 0.00 0.00 2.34
1371 2119 2.907696 TCCACCTTCGATCCCAACTTTA 59.092 45.455 0.00 0.00 0.00 1.85
1581 2528 9.369904 GAAGATATGCAACCATAACACAAAAAT 57.630 29.630 0.00 0.00 37.47 1.82
1582 2529 8.584157 AGAAGATATGCAACCATAACACAAAAA 58.416 29.630 0.00 0.00 37.47 1.94
1583 2530 8.121305 AGAAGATATGCAACCATAACACAAAA 57.879 30.769 0.00 0.00 37.47 2.44
1584 2531 7.701539 AGAAGATATGCAACCATAACACAAA 57.298 32.000 0.00 0.00 37.47 2.83
1585 2532 7.148086 GGAAGAAGATATGCAACCATAACACAA 60.148 37.037 0.00 0.00 37.47 3.33
1586 2533 6.318648 GGAAGAAGATATGCAACCATAACACA 59.681 38.462 0.00 0.00 37.47 3.72
1587 2534 6.318648 TGGAAGAAGATATGCAACCATAACAC 59.681 38.462 0.00 0.00 37.47 3.32
1588 2535 6.422333 TGGAAGAAGATATGCAACCATAACA 58.578 36.000 0.00 0.00 37.47 2.41
1589 2536 6.942532 TGGAAGAAGATATGCAACCATAAC 57.057 37.500 0.00 0.00 37.47 1.89
1590 2537 7.013559 CACATGGAAGAAGATATGCAACCATAA 59.986 37.037 0.00 0.00 37.47 1.90
1591 2538 6.487668 CACATGGAAGAAGATATGCAACCATA 59.512 38.462 0.00 0.00 38.25 2.74
1592 2539 5.301045 CACATGGAAGAAGATATGCAACCAT 59.699 40.000 0.00 0.00 37.36 3.55
1593 2540 4.641541 CACATGGAAGAAGATATGCAACCA 59.358 41.667 0.00 0.00 0.00 3.67
1594 2541 4.498682 GCACATGGAAGAAGATATGCAACC 60.499 45.833 0.00 0.00 0.00 3.77
1595 2542 4.337555 AGCACATGGAAGAAGATATGCAAC 59.662 41.667 0.00 0.00 34.27 4.17
1596 2543 4.529897 AGCACATGGAAGAAGATATGCAA 58.470 39.130 0.00 0.00 34.27 4.08
1597 2544 4.160642 AGCACATGGAAGAAGATATGCA 57.839 40.909 0.00 0.00 34.27 3.96
1598 2545 6.261826 AGTTAAGCACATGGAAGAAGATATGC 59.738 38.462 0.00 0.00 0.00 3.14
1599 2546 7.714377 AGAGTTAAGCACATGGAAGAAGATATG 59.286 37.037 0.00 0.00 0.00 1.78
1600 2547 7.800092 AGAGTTAAGCACATGGAAGAAGATAT 58.200 34.615 0.00 0.00 0.00 1.63
1601 2548 7.187824 AGAGTTAAGCACATGGAAGAAGATA 57.812 36.000 0.00 0.00 0.00 1.98
1602 2549 6.059787 AGAGTTAAGCACATGGAAGAAGAT 57.940 37.500 0.00 0.00 0.00 2.40
1603 2550 5.489792 AGAGTTAAGCACATGGAAGAAGA 57.510 39.130 0.00 0.00 0.00 2.87
1604 2551 7.856145 AATAGAGTTAAGCACATGGAAGAAG 57.144 36.000 0.00 0.00 0.00 2.85
1605 2552 9.733556 TTTAATAGAGTTAAGCACATGGAAGAA 57.266 29.630 0.00 0.00 0.00 2.52
1606 2553 9.733556 TTTTAATAGAGTTAAGCACATGGAAGA 57.266 29.630 0.00 0.00 0.00 2.87
1609 2556 9.515226 ACTTTTTAATAGAGTTAAGCACATGGA 57.485 29.630 0.00 0.00 0.00 3.41
1610 2557 9.559958 CACTTTTTAATAGAGTTAAGCACATGG 57.440 33.333 0.00 0.00 0.00 3.66
1613 2560 9.332502 TGACACTTTTTAATAGAGTTAAGCACA 57.667 29.630 0.00 0.00 0.00 4.57
1620 2567 9.715121 TTCGGTATGACACTTTTTAATAGAGTT 57.285 29.630 0.00 0.00 0.00 3.01
1621 2568 9.715121 TTTCGGTATGACACTTTTTAATAGAGT 57.285 29.630 0.00 0.00 0.00 3.24
1626 2573 9.405587 CACAATTTCGGTATGACACTTTTTAAT 57.594 29.630 0.00 0.00 0.00 1.40
1627 2574 8.622157 TCACAATTTCGGTATGACACTTTTTAA 58.378 29.630 0.00 0.00 0.00 1.52
1628 2575 8.155821 TCACAATTTCGGTATGACACTTTTTA 57.844 30.769 0.00 0.00 0.00 1.52
1629 2576 7.033530 TCACAATTTCGGTATGACACTTTTT 57.966 32.000 0.00 0.00 0.00 1.94
1630 2577 6.627395 TCACAATTTCGGTATGACACTTTT 57.373 33.333 0.00 0.00 0.00 2.27
1631 2578 6.627395 TTCACAATTTCGGTATGACACTTT 57.373 33.333 0.00 0.00 0.00 2.66
1632 2579 6.627395 TTTCACAATTTCGGTATGACACTT 57.373 33.333 0.00 0.00 0.00 3.16
1633 2580 6.627395 TTTTCACAATTTCGGTATGACACT 57.373 33.333 0.00 0.00 0.00 3.55
1634 2581 8.846607 GTTATTTTCACAATTTCGGTATGACAC 58.153 33.333 0.00 0.00 0.00 3.67
1635 2582 8.788806 AGTTATTTTCACAATTTCGGTATGACA 58.211 29.630 0.00 0.00 0.00 3.58
1722 2669 8.457261 ACACTATAGTTCCAGTAGTAAGTTTCG 58.543 37.037 1.56 0.00 0.00 3.46
1930 2877 4.785914 TCTTGGTATAACATCCTCCAACCA 59.214 41.667 0.00 0.00 34.93 3.67
2014 2961 2.289274 CGGTTGCACATGACACTTAACA 59.711 45.455 0.00 0.00 0.00 2.41
2190 3139 3.265221 TCAATGAGAGAACCCTGCAAGAT 59.735 43.478 0.00 0.00 34.07 2.40
2284 3234 6.805016 AATCATCTTCTTCTTGCTCTCCTA 57.195 37.500 0.00 0.00 0.00 2.94
2307 3260 4.020396 TGCTACCCCGTCAACTAATTGTAA 60.020 41.667 0.00 0.00 37.11 2.41
2539 3497 0.108186 TGACTCGCCAATAGTGCCAG 60.108 55.000 0.00 0.00 0.00 4.85
2574 3532 3.495377 TCCTTTGTTACGGAAATCACACG 59.505 43.478 0.00 0.00 0.00 4.49
2725 3683 4.593206 ACCAAGTCACCTTCACTGAGATAA 59.407 41.667 0.00 0.00 0.00 1.75
2765 3723 5.759059 TCATGGATCTTCTTAAGCCACATT 58.241 37.500 0.00 0.00 0.00 2.71
2837 3796 4.998051 TCACCATTTTTAGAGCCCTTTCT 58.002 39.130 0.00 0.00 0.00 2.52
2862 3824 2.224281 TGGAAGTAACAGCAGTGTCCAG 60.224 50.000 0.00 0.00 35.08 3.86
2961 3923 5.705609 ATAGCGGGCTATTTAAAACCATG 57.294 39.130 7.36 0.00 35.92 3.66
2962 3924 5.414765 GCTATAGCGGGCTATTTAAAACCAT 59.585 40.000 17.49 0.00 39.65 3.55
2964 3926 5.292671 GCTATAGCGGGCTATTTAAAACC 57.707 43.478 17.49 0.00 39.65 3.27
2990 3952 3.250280 GGGCCTTTTCTAAACGCTATAGC 59.750 47.826 15.09 15.09 37.78 2.97
2991 3953 3.813724 GGGGCCTTTTCTAAACGCTATAG 59.186 47.826 0.84 0.00 0.00 1.31
2992 3954 3.742013 CGGGGCCTTTTCTAAACGCTATA 60.742 47.826 0.84 0.00 0.00 1.31
2993 3955 2.651455 GGGGCCTTTTCTAAACGCTAT 58.349 47.619 0.84 0.00 0.00 2.97
2994 3956 1.676615 CGGGGCCTTTTCTAAACGCTA 60.677 52.381 0.84 0.00 0.00 4.26
2995 3957 0.958876 CGGGGCCTTTTCTAAACGCT 60.959 55.000 0.84 0.00 0.00 5.07
2996 3958 1.504900 CGGGGCCTTTTCTAAACGC 59.495 57.895 0.84 0.00 0.00 4.84
2997 3959 1.504900 GCGGGGCCTTTTCTAAACG 59.495 57.895 0.84 0.00 0.00 3.60
2998 3960 1.504900 CGCGGGGCCTTTTCTAAAC 59.495 57.895 0.84 0.00 0.00 2.01
2999 3961 2.337246 GCGCGGGGCCTTTTCTAAA 61.337 57.895 8.83 0.00 34.80 1.85
3000 3962 1.901654 TAGCGCGGGGCCTTTTCTAA 61.902 55.000 13.87 0.00 45.17 2.10
3001 3963 1.901654 TTAGCGCGGGGCCTTTTCTA 61.902 55.000 13.87 0.00 45.17 2.10
3002 3964 3.262448 TTAGCGCGGGGCCTTTTCT 62.262 57.895 13.87 0.00 45.17 2.52
3003 3965 2.748647 TTAGCGCGGGGCCTTTTC 60.749 61.111 13.87 0.00 45.17 2.29
3004 3966 2.750237 CTTAGCGCGGGGCCTTTT 60.750 61.111 13.87 0.00 45.17 2.27
3005 3967 3.682292 CTCTTAGCGCGGGGCCTTT 62.682 63.158 13.87 0.00 45.17 3.11
3006 3968 4.162690 CTCTTAGCGCGGGGCCTT 62.163 66.667 13.87 0.00 45.17 4.35
3008 3970 4.893601 GACTCTTAGCGCGGGGCC 62.894 72.222 13.87 0.00 45.17 5.80
3009 3971 2.854187 AAAGACTCTTAGCGCGGGGC 62.854 60.000 8.83 9.26 44.05 5.80
3010 3972 0.391263 AAAAGACTCTTAGCGCGGGG 60.391 55.000 8.83 0.00 0.00 5.73
3011 3973 0.721718 CAAAAGACTCTTAGCGCGGG 59.278 55.000 8.83 0.00 0.00 6.13
3012 3974 1.429463 ACAAAAGACTCTTAGCGCGG 58.571 50.000 8.83 0.00 0.00 6.46
3013 3975 2.475111 TGAACAAAAGACTCTTAGCGCG 59.525 45.455 0.00 0.00 0.00 6.86
3014 3976 4.468095 TTGAACAAAAGACTCTTAGCGC 57.532 40.909 0.00 0.00 0.00 5.92
3015 3977 5.677178 GTGTTTGAACAAAAGACTCTTAGCG 59.323 40.000 1.47 0.00 41.21 4.26
3016 3978 6.786207 AGTGTTTGAACAAAAGACTCTTAGC 58.214 36.000 1.47 0.00 46.48 3.09
3023 3985 5.160641 TGCTCAAGTGTTTGAACAAAAGAC 58.839 37.500 1.47 2.88 42.48 3.01
3024 3986 5.384063 TGCTCAAGTGTTTGAACAAAAGA 57.616 34.783 1.47 0.00 42.48 2.52
3028 3990 4.876125 TGTTTGCTCAAGTGTTTGAACAA 58.124 34.783 0.00 2.89 43.77 2.83
3029 3991 4.511617 TGTTTGCTCAAGTGTTTGAACA 57.488 36.364 0.00 0.00 42.48 3.18
3030 3992 6.407475 AAATGTTTGCTCAAGTGTTTGAAC 57.593 33.333 0.00 0.00 42.48 3.18
3031 3993 8.539770 TTAAAATGTTTGCTCAAGTGTTTGAA 57.460 26.923 0.00 0.00 42.48 2.69
3032 3994 8.539770 TTTAAAATGTTTGCTCAAGTGTTTGA 57.460 26.923 0.00 0.00 40.92 2.69
3035 3997 8.764287 GCTATTTAAAATGTTTGCTCAAGTGTT 58.236 29.630 0.00 0.00 0.00 3.32
3036 3998 8.143835 AGCTATTTAAAATGTTTGCTCAAGTGT 58.856 29.630 0.00 0.00 0.00 3.55
3037 3999 8.524870 AGCTATTTAAAATGTTTGCTCAAGTG 57.475 30.769 0.00 0.00 0.00 3.16
3038 4000 7.538678 CGAGCTATTTAAAATGTTTGCTCAAGT 59.461 33.333 17.23 0.00 43.84 3.16
3039 4001 7.461938 GCGAGCTATTTAAAATGTTTGCTCAAG 60.462 37.037 17.23 7.88 43.84 3.02
3040 4002 6.307800 GCGAGCTATTTAAAATGTTTGCTCAA 59.692 34.615 17.23 0.00 43.84 3.02
3041 4003 5.799936 GCGAGCTATTTAAAATGTTTGCTCA 59.200 36.000 17.23 0.00 43.84 4.26
3042 4004 6.030228 AGCGAGCTATTTAAAATGTTTGCTC 58.970 36.000 12.99 11.96 41.29 4.26
3043 4005 5.954335 AGCGAGCTATTTAAAATGTTTGCT 58.046 33.333 12.99 12.99 0.00 3.91
3044 4006 7.914537 ATAGCGAGCTATTTAAAATGTTTGC 57.085 32.000 11.48 10.00 35.92 3.68
3045 4007 9.107367 GCTATAGCGAGCTATTTAAAATGTTTG 57.893 33.333 20.87 0.00 39.65 2.93
3070 4032 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
3071 4033 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
3091 4053 1.383523 GGTGGACCTCAGCTAAATGC 58.616 55.000 0.00 0.00 40.48 3.56
3092 4054 1.066143 ACGGTGGACCTCAGCTAAATG 60.066 52.381 0.00 0.00 41.41 2.32
3093 4055 1.276622 ACGGTGGACCTCAGCTAAAT 58.723 50.000 0.00 0.00 41.41 1.40
3094 4056 1.547372 GTACGGTGGACCTCAGCTAAA 59.453 52.381 0.00 0.00 41.41 1.85
3095 4057 1.180029 GTACGGTGGACCTCAGCTAA 58.820 55.000 0.00 0.00 41.41 3.09
3096 4058 0.682209 GGTACGGTGGACCTCAGCTA 60.682 60.000 0.00 0.00 41.41 3.32
3097 4059 1.982938 GGTACGGTGGACCTCAGCT 60.983 63.158 0.00 0.00 41.41 4.24
3098 4060 2.577593 GGTACGGTGGACCTCAGC 59.422 66.667 0.00 0.00 40.26 4.26
3111 4073 2.137129 GCTAAGCCTCTTAGCGGTAC 57.863 55.000 18.95 0.00 38.12 3.34
3116 4078 2.590401 GCGCGCTAAGCCTCTTAGC 61.590 63.158 26.67 22.09 44.76 3.09
3117 4079 0.311165 TAGCGCGCTAAGCCTCTTAG 59.689 55.000 36.77 8.76 44.76 2.18
3118 4080 0.959553 ATAGCGCGCTAAGCCTCTTA 59.040 50.000 40.90 20.62 44.76 2.10
3119 4081 0.105039 AATAGCGCGCTAAGCCTCTT 59.895 50.000 40.90 27.25 44.76 2.85
3120 4082 0.105039 AAATAGCGCGCTAAGCCTCT 59.895 50.000 40.90 23.18 44.76 3.69
3121 4083 1.779569 TAAATAGCGCGCTAAGCCTC 58.220 50.000 40.90 6.44 44.76 4.70
3122 4084 2.234300 TTAAATAGCGCGCTAAGCCT 57.766 45.000 40.90 26.65 44.76 4.58
3123 4085 3.033873 GTTTTAAATAGCGCGCTAAGCC 58.966 45.455 40.90 21.36 44.76 4.35
3124 4086 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
3125 4087 5.275280 GCAAAGTTTTAAATAGCGCGCTAAG 60.275 40.000 40.90 16.80 31.73 2.18
3126 4088 4.555747 GCAAAGTTTTAAATAGCGCGCTAA 59.444 37.500 40.90 26.03 31.73 3.09
3127 4089 4.092816 GCAAAGTTTTAAATAGCGCGCTA 58.907 39.130 39.72 39.72 0.00 4.26
3128 4090 2.914838 GCAAAGTTTTAAATAGCGCGCT 59.085 40.909 38.01 38.01 0.00 5.92
3129 4091 2.914838 AGCAAAGTTTTAAATAGCGCGC 59.085 40.909 26.66 26.66 0.00 6.86
3130 4092 4.201485 CCAAGCAAAGTTTTAAATAGCGCG 60.201 41.667 0.00 0.00 0.00 6.86
3131 4093 4.684242 ACCAAGCAAAGTTTTAAATAGCGC 59.316 37.500 0.00 0.00 0.00 5.92
3132 4094 6.088085 CAGACCAAGCAAAGTTTTAAATAGCG 59.912 38.462 0.00 0.00 0.00 4.26
3133 4095 6.128822 GCAGACCAAGCAAAGTTTTAAATAGC 60.129 38.462 0.00 0.00 0.00 2.97
3134 4096 7.115378 CAGCAGACCAAGCAAAGTTTTAAATAG 59.885 37.037 0.00 0.00 0.00 1.73
3135 4097 6.922957 CAGCAGACCAAGCAAAGTTTTAAATA 59.077 34.615 0.00 0.00 0.00 1.40
3136 4098 5.754890 CAGCAGACCAAGCAAAGTTTTAAAT 59.245 36.000 0.00 0.00 0.00 1.40
3137 4099 5.108517 CAGCAGACCAAGCAAAGTTTTAAA 58.891 37.500 0.00 0.00 0.00 1.52
3138 4100 4.159506 ACAGCAGACCAAGCAAAGTTTTAA 59.840 37.500 0.00 0.00 0.00 1.52
3139 4101 3.699038 ACAGCAGACCAAGCAAAGTTTTA 59.301 39.130 0.00 0.00 0.00 1.52
3140 4102 2.497273 ACAGCAGACCAAGCAAAGTTTT 59.503 40.909 0.00 0.00 0.00 2.43
3141 4103 2.102578 ACAGCAGACCAAGCAAAGTTT 58.897 42.857 0.00 0.00 0.00 2.66
3142 4104 1.406539 CACAGCAGACCAAGCAAAGTT 59.593 47.619 0.00 0.00 0.00 2.66
3143 4105 1.027357 CACAGCAGACCAAGCAAAGT 58.973 50.000 0.00 0.00 0.00 2.66
3144 4106 0.318445 GCACAGCAGACCAAGCAAAG 60.318 55.000 0.00 0.00 0.00 2.77
3145 4107 0.752743 AGCACAGCAGACCAAGCAAA 60.753 50.000 0.00 0.00 0.00 3.68
3146 4108 0.108396 TAGCACAGCAGACCAAGCAA 59.892 50.000 0.00 0.00 0.00 3.91
3147 4109 0.321034 CTAGCACAGCAGACCAAGCA 60.321 55.000 0.00 0.00 0.00 3.91
3148 4110 0.036952 TCTAGCACAGCAGACCAAGC 60.037 55.000 0.00 0.00 0.00 4.01
3149 4111 1.274728 AGTCTAGCACAGCAGACCAAG 59.725 52.381 13.84 0.00 37.39 3.61
3150 4112 1.342074 AGTCTAGCACAGCAGACCAA 58.658 50.000 13.84 0.00 37.39 3.67
3151 4113 2.215942 TAGTCTAGCACAGCAGACCA 57.784 50.000 13.84 3.26 37.39 4.02
3152 4114 3.810310 ATTAGTCTAGCACAGCAGACC 57.190 47.619 13.84 2.74 37.39 3.85
3153 4115 5.897050 ACTTATTAGTCTAGCACAGCAGAC 58.103 41.667 11.16 11.16 37.15 3.51
3154 4116 6.137794 GACTTATTAGTCTAGCACAGCAGA 57.862 41.667 4.61 0.00 45.99 4.26
3194 4156 2.479566 ATGGCGCGGATAAGATTCAT 57.520 45.000 8.83 0.00 0.00 2.57
3247 4209 4.619863 GCACAAAATCTGCAACATCCATCT 60.620 41.667 0.00 0.00 34.56 2.90
3271 4233 5.937540 CACATAACAATACTCAGTTCCACCA 59.062 40.000 0.00 0.00 0.00 4.17
3272 4234 5.163754 GCACATAACAATACTCAGTTCCACC 60.164 44.000 0.00 0.00 0.00 4.61
3273 4235 5.163754 GGCACATAACAATACTCAGTTCCAC 60.164 44.000 0.00 0.00 0.00 4.02
3501 4469 1.956477 CTTTGAACCAAGGGGACACTG 59.044 52.381 0.00 0.00 38.05 3.66
3551 4521 8.600449 TTTAGGCAAAAATACACTTTGGATTG 57.400 30.769 0.00 0.00 29.78 2.67
3552 4522 8.428852 ACTTTAGGCAAAAATACACTTTGGATT 58.571 29.630 0.00 0.00 30.72 3.01
3572 4542 6.478512 AGCCTGAATCTAGAGGAACTTTAG 57.521 41.667 0.00 0.00 43.58 1.85
3615 4585 4.517285 CCTCTGTTAGTGTTACATGCCAT 58.483 43.478 0.00 0.00 0.00 4.40
3629 4599 6.946340 TCACTTGAAATATCAGCCTCTGTTA 58.054 36.000 0.00 0.00 36.78 2.41
3637 4607 7.369803 TCTCAGTTTCACTTGAAATATCAGC 57.630 36.000 7.63 0.00 44.69 4.26
3710 4828 8.628882 AAAACTAACTTGATGTAAACTGTTGC 57.371 30.769 0.00 0.00 0.00 4.17
3727 4845 9.211485 TGGTCACTTGTAGCTTATAAAACTAAC 57.789 33.333 0.00 0.00 0.00 2.34
3731 4849 7.399523 CGATGGTCACTTGTAGCTTATAAAAC 58.600 38.462 0.00 0.00 0.00 2.43
3732 4850 6.537301 CCGATGGTCACTTGTAGCTTATAAAA 59.463 38.462 0.00 0.00 0.00 1.52
3733 4851 6.046593 CCGATGGTCACTTGTAGCTTATAAA 58.953 40.000 0.00 0.00 0.00 1.40
3734 4852 5.452776 CCCGATGGTCACTTGTAGCTTATAA 60.453 44.000 0.00 0.00 0.00 0.98
3735 4853 4.038763 CCCGATGGTCACTTGTAGCTTATA 59.961 45.833 0.00 0.00 0.00 0.98
3736 4854 3.181465 CCCGATGGTCACTTGTAGCTTAT 60.181 47.826 0.00 0.00 0.00 1.73
3737 4855 2.167693 CCCGATGGTCACTTGTAGCTTA 59.832 50.000 0.00 0.00 0.00 3.09
3738 4856 1.066143 CCCGATGGTCACTTGTAGCTT 60.066 52.381 0.00 0.00 0.00 3.74
3739 4857 0.537188 CCCGATGGTCACTTGTAGCT 59.463 55.000 0.00 0.00 0.00 3.32
3740 4858 0.535335 TCCCGATGGTCACTTGTAGC 59.465 55.000 0.00 0.00 0.00 3.58
3741 4859 1.548719 TGTCCCGATGGTCACTTGTAG 59.451 52.381 0.00 0.00 0.00 2.74
3742 4860 1.634960 TGTCCCGATGGTCACTTGTA 58.365 50.000 0.00 0.00 0.00 2.41
3743 4861 0.762418 TTGTCCCGATGGTCACTTGT 59.238 50.000 0.00 0.00 28.93 3.16
3744 4862 3.623848 TTGTCCCGATGGTCACTTG 57.376 52.632 0.00 0.00 28.93 3.16


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

AutoCloner maintained by Alex Coulton.