Multiple sequence alignment - TraesCS2D01G507500

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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 TraesCS2D01G507500 chr2D 100.000 8155 0 0 1 8155 601177568 601185722 0.000000e+00 15060.0
1 TraesCS2D01G507500 chr2D 98.004 952 18 1 1 951 520046622 520045671 0.000000e+00 1652.0
2 TraesCS2D01G507500 chr2D 93.750 64 2 2 4007 4070 350755879 350755940 2.420000e-15 95.3
3 TraesCS2D01G507500 chr2A 94.482 3661 153 16 3914 7545 734620247 734623887 0.000000e+00 5596.0
4 TraesCS2D01G507500 chr2A 91.762 1663 127 4 5885 7545 734525582 734523928 0.000000e+00 2303.0
5 TraesCS2D01G507500 chr2A 94.981 1056 25 5 3914 4967 734527769 734526740 0.000000e+00 1631.0
6 TraesCS2D01G507500 chr2A 95.982 871 25 7 952 1816 734618192 734619058 0.000000e+00 1406.0
7 TraesCS2D01G507500 chr2A 95.076 792 19 5 2852 3636 734619415 734620193 0.000000e+00 1229.0
8 TraesCS2D01G507500 chr2A 91.909 791 29 8 2852 3636 734528584 734527823 0.000000e+00 1074.0
9 TraesCS2D01G507500 chr2A 91.024 791 43 6 5117 5882 734526451 734525664 0.000000e+00 1042.0
10 TraesCS2D01G507500 chr2A 91.577 653 39 10 955 1599 734529549 734528905 0.000000e+00 887.0
11 TraesCS2D01G507500 chr2A 92.453 371 20 6 2323 2689 734619049 734619415 2.610000e-144 523.0
12 TraesCS2D01G507500 chr2A 94.753 324 14 2 2369 2689 734528907 734528584 1.220000e-137 501.0
13 TraesCS2D01G507500 chr2A 79.894 378 70 6 7781 8155 776101710 776102084 1.040000e-68 272.0
14 TraesCS2D01G507500 chr2B 93.106 1465 83 9 5570 7023 731311244 731312701 0.000000e+00 2130.0
15 TraesCS2D01G507500 chr2B 93.773 1076 45 16 952 2013 731304038 731305105 0.000000e+00 1596.0
16 TraesCS2D01G507500 chr2B 91.079 1177 67 17 2851 4022 731305856 731306999 0.000000e+00 1557.0
17 TraesCS2D01G507500 chr2B 93.416 729 47 1 6823 7550 731312694 731313422 0.000000e+00 1079.0
18 TraesCS2D01G507500 chr2B 93.247 696 39 8 1996 2687 731305164 731305855 0.000000e+00 1018.0
19 TraesCS2D01G507500 chr2B 94.118 527 23 6 4518 5042 731309928 731310448 0.000000e+00 795.0
20 TraesCS2D01G507500 chr2B 94.154 479 25 3 5068 5545 731310771 731311247 0.000000e+00 726.0
21 TraesCS2D01G507500 chr2B 91.036 357 28 2 4100 4455 731309577 731309930 5.730000e-131 479.0
22 TraesCS2D01G507500 chr2B 88.679 371 26 4 7551 7921 608189695 608190049 9.720000e-119 438.0
23 TraesCS2D01G507500 chr2B 88.442 199 22 1 2685 2883 138113435 138113632 1.060000e-58 239.0
24 TraesCS2D01G507500 chr2B 92.308 65 3 2 4024 4088 259022463 259022401 3.130000e-14 91.6
25 TraesCS2D01G507500 chr2B 90.000 70 5 2 4024 4092 255130669 255130601 1.130000e-13 89.8
26 TraesCS2D01G507500 chr1D 98.006 953 17 2 1 952 334243727 334244678 0.000000e+00 1653.0
27 TraesCS2D01G507500 chr1D 94.578 166 9 0 2691 2856 84712059 84712224 2.920000e-64 257.0
28 TraesCS2D01G507500 chr7D 98.004 952 17 2 1 951 56882036 56881086 0.000000e+00 1652.0
29 TraesCS2D01G507500 chr7D 97.803 956 18 3 1 954 93993989 93994943 0.000000e+00 1646.0
30 TraesCS2D01G507500 chr7D 97.597 957 21 2 1 955 47000208 46999252 0.000000e+00 1639.0
31 TraesCS2D01G507500 chr7D 97.597 957 20 3 1 954 138278145 138277189 0.000000e+00 1637.0
32 TraesCS2D01G507500 chr7D 97.471 949 22 2 1 948 612267834 612266887 0.000000e+00 1618.0
33 TraesCS2D01G507500 chr7D 97.269 952 25 1 2 952 88322615 88321664 0.000000e+00 1613.0
34 TraesCS2D01G507500 chr7D 92.079 606 46 2 7551 8155 519853919 519854523 0.000000e+00 852.0
35 TraesCS2D01G507500 chr7D 94.328 335 16 1 7551 7885 511119919 511119588 2.030000e-140 510.0
36 TraesCS2D01G507500 chr7D 94.048 168 10 0 2687 2854 312574126 312574293 1.050000e-63 255.0
37 TraesCS2D01G507500 chr7D 83.212 137 19 4 7549 7682 420767387 420767522 1.110000e-23 122.0
38 TraesCS2D01G507500 chr7D 96.552 58 0 2 4024 4081 471545323 471545378 2.420000e-15 95.3
39 TraesCS2D01G507500 chr7D 85.507 69 7 3 3773 3839 112015143 112015210 1.470000e-07 69.4
40 TraesCS2D01G507500 chr3D 97.379 954 24 1 1 953 452379924 452380877 0.000000e+00 1622.0
41 TraesCS2D01G507500 chr3D 93.567 171 11 0 2684 2854 545912164 545912334 1.050000e-63 255.0
42 TraesCS2D01G507500 chr3D 93.023 172 11 1 2682 2853 580330939 580331109 4.890000e-62 250.0
43 TraesCS2D01G507500 chr3D 88.406 69 6 2 3773 3839 6158242 6158174 1.890000e-11 82.4
44 TraesCS2D01G507500 chr5D 94.030 603 35 1 7553 8155 514469418 514470019 0.000000e+00 913.0
45 TraesCS2D01G507500 chr5D 91.291 333 16 2 7551 7883 152739406 152739087 7.510000e-120 442.0
46 TraesCS2D01G507500 chr5D 92.135 178 13 1 2684 2860 445106658 445106481 4.890000e-62 250.0
47 TraesCS2D01G507500 chr5D 91.892 74 2 4 3769 3839 41140038 41139966 5.210000e-17 100.0
48 TraesCS2D01G507500 chr5D 93.443 61 4 0 4024 4084 10897937 10897877 3.130000e-14 91.6
49 TraesCS2D01G507500 chr5D 84.146 82 7 5 1792 1869 303763780 303763701 3.160000e-09 75.0
50 TraesCS2D01G507500 chr7A 92.079 606 46 2 7551 8155 595986530 595987134 0.000000e+00 852.0
51 TraesCS2D01G507500 chr7A 93.548 62 2 2 4024 4083 193631751 193631690 3.130000e-14 91.6
52 TraesCS2D01G507500 chr7B 91.297 609 49 3 7550 8155 553135980 553136587 0.000000e+00 828.0
53 TraesCS2D01G507500 chr7B 89.515 515 52 2 7551 8065 616824788 616824276 0.000000e+00 651.0
54 TraesCS2D01G507500 chr7B 81.395 129 19 5 7557 7682 436827900 436828026 5.210000e-17 100.0
55 TraesCS2D01G507500 chr4A 89.638 608 59 3 7551 8155 565751713 565752319 0.000000e+00 771.0
56 TraesCS2D01G507500 chr4A 84.416 77 8 3 3773 3846 562283936 562283861 1.140000e-08 73.1
57 TraesCS2D01G507500 chr3A 94.345 336 18 1 7551 7885 455085012 455085347 1.570000e-141 514.0
58 TraesCS2D01G507500 chr3A 91.176 68 1 4 4024 4089 336604451 336604515 4.050000e-13 87.9
59 TraesCS2D01G507500 chr4B 75.114 880 152 42 4604 5464 1991128 1990297 4.680000e-92 350.0
60 TraesCS2D01G507500 chr1A 94.152 171 10 0 2685 2855 586112581 586112411 2.260000e-65 261.0
61 TraesCS2D01G507500 chr4D 94.578 166 9 0 2691 2856 243613274 243613439 2.920000e-64 257.0
62 TraesCS2D01G507500 chr4D 95.000 60 2 1 4012 4070 346123360 346123419 8.710000e-15 93.5
63 TraesCS2D01G507500 chr5B 80.838 334 49 12 7551 7876 545154010 545154336 1.760000e-61 248.0
64 TraesCS2D01G507500 chr5B 85.526 76 3 6 3769 3839 35254702 35254630 1.140000e-08 73.1
65 TraesCS2D01G507500 chr6A 89.062 192 20 1 2666 2857 204007732 204007922 3.800000e-58 237.0
66 TraesCS2D01G507500 chr6A 93.443 61 4 0 4021 4081 511530735 511530795 3.130000e-14 91.6
67 TraesCS2D01G507500 chr6A 85.714 70 4 6 3772 3839 104308491 104308556 1.470000e-07 69.4
68 TraesCS2D01G507500 chr3B 88.462 78 4 5 4024 4099 42471601 42471527 1.130000e-13 89.8
69 TraesCS2D01G507500 chr3B 93.333 60 3 1 4024 4083 822825925 822825983 4.050000e-13 87.9
70 TraesCS2D01G507500 chr6B 89.189 74 3 3 3771 3840 14541142 14541070 4.050000e-13 87.9
71 TraesCS2D01G507500 chr6D 88.571 70 4 4 3772 3839 406205749 406205682 1.890000e-11 82.4
72 TraesCS2D01G507500 chr1B 85.185 81 5 3 3769 3843 491239651 491239730 8.780000e-10 76.8


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 TraesCS2D01G507500 chr2D 601177568 601185722 8154 False 15060.000000 15060 100.000000 1 8155 1 chr2D.!!$F2 8154
1 TraesCS2D01G507500 chr2D 520045671 520046622 951 True 1652.000000 1652 98.004000 1 951 1 chr2D.!!$R1 950
2 TraesCS2D01G507500 chr2A 734618192 734623887 5695 False 2188.500000 5596 94.498250 952 7545 4 chr2A.!!$F2 6593
3 TraesCS2D01G507500 chr2A 734523928 734529549 5621 True 1239.666667 2303 92.667667 955 7545 6 chr2A.!!$R1 6590
4 TraesCS2D01G507500 chr2B 731304038 731313422 9384 False 1172.500000 2130 92.991125 952 7550 8 chr2B.!!$F3 6598
5 TraesCS2D01G507500 chr1D 334243727 334244678 951 False 1653.000000 1653 98.006000 1 952 1 chr1D.!!$F2 951
6 TraesCS2D01G507500 chr7D 56881086 56882036 950 True 1652.000000 1652 98.004000 1 951 1 chr7D.!!$R2 950
7 TraesCS2D01G507500 chr7D 93993989 93994943 954 False 1646.000000 1646 97.803000 1 954 1 chr7D.!!$F1 953
8 TraesCS2D01G507500 chr7D 46999252 47000208 956 True 1639.000000 1639 97.597000 1 955 1 chr7D.!!$R1 954
9 TraesCS2D01G507500 chr7D 138277189 138278145 956 True 1637.000000 1637 97.597000 1 954 1 chr7D.!!$R4 953
10 TraesCS2D01G507500 chr7D 612266887 612267834 947 True 1618.000000 1618 97.471000 1 948 1 chr7D.!!$R6 947
11 TraesCS2D01G507500 chr7D 88321664 88322615 951 True 1613.000000 1613 97.269000 2 952 1 chr7D.!!$R3 950
12 TraesCS2D01G507500 chr7D 519853919 519854523 604 False 852.000000 852 92.079000 7551 8155 1 chr7D.!!$F6 604
13 TraesCS2D01G507500 chr3D 452379924 452380877 953 False 1622.000000 1622 97.379000 1 953 1 chr3D.!!$F1 952
14 TraesCS2D01G507500 chr5D 514469418 514470019 601 False 913.000000 913 94.030000 7553 8155 1 chr5D.!!$F1 602
15 TraesCS2D01G507500 chr7A 595986530 595987134 604 False 852.000000 852 92.079000 7551 8155 1 chr7A.!!$F1 604
16 TraesCS2D01G507500 chr7B 553135980 553136587 607 False 828.000000 828 91.297000 7550 8155 1 chr7B.!!$F2 605
17 TraesCS2D01G507500 chr7B 616824276 616824788 512 True 651.000000 651 89.515000 7551 8065 1 chr7B.!!$R1 514
18 TraesCS2D01G507500 chr4A 565751713 565752319 606 False 771.000000 771 89.638000 7551 8155 1 chr4A.!!$F1 604
19 TraesCS2D01G507500 chr4B 1990297 1991128 831 True 350.000000 350 75.114000 4604 5464 1 chr4B.!!$R1 860

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
968 971 0.252742 AAAAACCCACCACCCAACCA 60.253 50.000 0.00 0.0 0.00 3.67 F
1090 1095 0.674534 CGGAGCTACCCATACCTGAC 59.325 60.000 0.00 0.0 34.64 3.51 F
2702 2818 0.463474 GCATCTGCTCCCTCTGTTCC 60.463 60.000 0.00 0.0 38.21 3.62 F
2905 3021 0.028374 AAACACGCGCACAGGTTAAC 59.972 50.000 5.73 0.0 0.00 2.01 F
3579 3716 1.002069 TCATGGAGCCCAAATGGACT 58.998 50.000 0.00 0.0 36.95 3.85 F
3738 3875 1.477553 TTGGAAGCATCCCAATCTGC 58.522 50.000 5.34 0.0 45.95 4.26 F
4515 7217 3.952967 GGGTCTTGTCTCTACCGATAACT 59.047 47.826 0.00 0.0 33.89 2.24 F
5853 8925 0.531200 GTCATTTCTCCTCGGGTCGT 59.469 55.000 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1977 0.035820 GTATTCCACTGCCCCGACAA 60.036 55.000 0.00 0.00 0.00 3.18 R
2835 2951 0.115745 ACTACTCCCTCCGTTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12 R
3636 3773 0.387239 GATGTGTTTGTTGGGAGCGC 60.387 55.000 0.00 0.00 0.00 5.92 R
4348 7049 2.125753 GACTGAGTCTGGCAGCGG 60.126 66.667 10.34 3.63 36.86 5.52 R
4515 7217 6.647334 TGTGACTTGAGCCAAATAATTTCA 57.353 33.333 0.00 0.00 0.00 2.69 R
5682 8730 3.473621 ACCCTCCACTATCCAATACCCTA 59.526 47.826 0.00 0.00 0.00 3.53 R
6177 9332 0.030101 CCTTCTTAGCTCGCTCCTCG 59.970 60.000 0.00 0.00 40.15 4.63 R
7260 10611 0.677288 CCGCCACATTATCGACCCTA 59.323 55.000 0.00 0.00 0.00 3.53 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
440 441 1.628340 TCCACCGAATTCTGTCACCAT 59.372 47.619 3.52 0.00 0.00 3.55
467 468 2.273449 GACATGGCTCACTGGGGG 59.727 66.667 0.00 0.00 0.00 5.40
515 516 0.928451 GTTGGAGTTTGCGCGTTGTC 60.928 55.000 8.43 0.00 0.00 3.18
713 714 5.455612 GGGATATCTTCAACCGGTTTGGATA 60.456 44.000 19.55 22.45 42.00 2.59
769 770 4.406003 CCTATCTATATTTAGCCAGCCGGT 59.594 45.833 1.90 0.00 33.28 5.28
897 899 7.241376 ACTTTTCTTTCGTTAATAAGATGGCG 58.759 34.615 0.00 0.00 31.00 5.69
968 971 0.252742 AAAAACCCACCACCCAACCA 60.253 50.000 0.00 0.00 0.00 3.67
969 972 0.978667 AAAACCCACCACCCAACCAC 60.979 55.000 0.00 0.00 0.00 4.16
970 973 1.881057 AAACCCACCACCCAACCACT 61.881 55.000 0.00 0.00 0.00 4.00
1090 1095 0.674534 CGGAGCTACCCATACCTGAC 59.325 60.000 0.00 0.00 34.64 3.51
1355 1381 4.332819 AGTTTATCGCTGTTGCACCTATTC 59.667 41.667 0.00 0.00 39.64 1.75
1455 1481 6.827641 TGTTGATTTGTAACGCTGAGATTAC 58.172 36.000 1.42 1.42 32.85 1.89
1542 1568 7.151976 GCTTCTGAAAAATTTTAGGTGGCTAA 58.848 34.615 3.34 0.00 0.00 3.09
1572 1598 4.426736 TTCGAAGGACTTTGGGTTTAGT 57.573 40.909 0.00 0.00 0.00 2.24
1623 1650 3.366052 TTGCCTGTTCCCCTCTTAATC 57.634 47.619 0.00 0.00 0.00 1.75
1836 1867 6.471233 TGGTTGTGTCATAAATCACCAAAA 57.529 33.333 0.00 0.00 34.14 2.44
1850 1881 3.028130 CACCAAAACCCAACTAGGTGTT 58.972 45.455 7.09 0.00 40.05 3.32
1853 1884 5.127356 CACCAAAACCCAACTAGGTGTTTTA 59.873 40.000 7.09 0.00 43.13 1.52
1855 1886 6.127281 ACCAAAACCCAACTAGGTGTTTTAAG 60.127 38.462 7.09 5.83 43.13 1.85
1856 1887 6.097129 CCAAAACCCAACTAGGTGTTTTAAGA 59.903 38.462 7.09 0.00 43.13 2.10
1857 1888 6.954487 AAACCCAACTAGGTGTTTTAAGAG 57.046 37.500 7.09 0.00 40.05 2.85
1858 1889 5.899631 ACCCAACTAGGTGTTTTAAGAGA 57.100 39.130 7.09 0.00 39.24 3.10
1859 1890 6.449830 ACCCAACTAGGTGTTTTAAGAGAT 57.550 37.500 7.09 0.00 39.24 2.75
1860 1891 7.563724 ACCCAACTAGGTGTTTTAAGAGATA 57.436 36.000 7.09 0.00 39.24 1.98
1868 1900 9.706691 CTAGGTGTTTTAAGAGATACACTTTCA 57.293 33.333 0.00 0.00 40.45 2.69
1881 1913 9.178758 GAGATACACTTTCATAACCATTTTCCT 57.821 33.333 0.00 0.00 0.00 3.36
1902 1934 5.964477 TCCTAAATCTAGCTTCTCTCCCAAA 59.036 40.000 0.00 0.00 0.00 3.28
1960 1992 0.616395 TATCTTGTCGGGGCAGTGGA 60.616 55.000 0.00 0.00 0.00 4.02
1994 2026 2.880890 AGCACATCCTGACAGTTGAAAC 59.119 45.455 0.93 0.00 0.00 2.78
2013 2046 8.863049 GTTGAAACAAAATATATGCCTCAGTTG 58.137 33.333 0.00 0.00 0.00 3.16
2016 2049 5.894807 ACAAAATATATGCCTCAGTTGTGC 58.105 37.500 0.00 0.00 0.00 4.57
2040 2149 4.335594 GCACAAGAAGCGGGTAATTCTAAT 59.664 41.667 0.00 0.00 34.71 1.73
2059 2168 6.759272 TCTAATAAGAAACATCTCGGATGGG 58.241 40.000 15.41 0.00 0.00 4.00
2125 2234 4.374689 TTCTAAAGTGTATGTTGGGGCA 57.625 40.909 0.00 0.00 0.00 5.36
2144 2253 4.532521 GGGCACAACCACTAGGATATATCT 59.467 45.833 12.42 1.94 42.05 1.98
2154 2263 9.261035 ACCACTAGGATATATCTTACATCTTGG 57.739 37.037 12.42 10.03 38.69 3.61
2155 2264 8.700051 CCACTAGGATATATCTTACATCTTGGG 58.300 40.741 12.42 2.71 36.89 4.12
2193 2302 5.391312 AGACAACATAATTTCCAACAGCC 57.609 39.130 0.00 0.00 0.00 4.85
2225 2334 1.476891 GGATGCAGTGTCTCGTAAGGA 59.523 52.381 0.00 0.00 38.47 3.36
2237 2346 1.893137 TCGTAAGGAGTGACATGTGCT 59.107 47.619 1.15 0.21 38.47 4.40
2250 2359 6.927936 AGTGACATGTGCTAGTGATATGAATC 59.072 38.462 1.15 0.00 0.00 2.52
2259 2368 8.790718 GTGCTAGTGATATGAATCAATTTGGAT 58.209 33.333 0.00 0.00 43.69 3.41
2328 2438 7.834881 AATCCATTATAACTCGGTCTCACTA 57.165 36.000 0.00 0.00 0.00 2.74
2334 2444 3.367646 AACTCGGTCTCACTAGATGGA 57.632 47.619 0.00 0.00 33.30 3.41
2339 2449 2.324541 GGTCTCACTAGATGGATGGCT 58.675 52.381 0.00 0.00 33.30 4.75
2380 2490 7.185565 TGACCAACATGGAAATTATTAGGGAA 58.814 34.615 2.85 0.00 40.96 3.97
2381 2491 7.123547 TGACCAACATGGAAATTATTAGGGAAC 59.876 37.037 2.85 0.00 40.96 3.62
2538 2654 0.586802 GTCCTGCAACCGAACAGAAC 59.413 55.000 0.00 0.00 35.90 3.01
2554 2670 4.172807 ACAGAACATCCCTAAACCCAGTA 58.827 43.478 0.00 0.00 0.00 2.74
2687 2803 1.165270 AGTTTGTTACCGCCAGCATC 58.835 50.000 0.00 0.00 0.00 3.91
2688 2804 1.165270 GTTTGTTACCGCCAGCATCT 58.835 50.000 0.00 0.00 0.00 2.90
2689 2805 1.135689 GTTTGTTACCGCCAGCATCTG 60.136 52.381 0.00 0.00 0.00 2.90
2690 2806 1.305219 TTGTTACCGCCAGCATCTGC 61.305 55.000 0.00 0.00 42.49 4.26
2701 2817 3.077617 GCATCTGCTCCCTCTGTTC 57.922 57.895 0.00 0.00 38.21 3.18
2702 2818 0.463474 GCATCTGCTCCCTCTGTTCC 60.463 60.000 0.00 0.00 38.21 3.62
2703 2819 1.202330 CATCTGCTCCCTCTGTTCCT 58.798 55.000 0.00 0.00 0.00 3.36
2704 2820 2.392662 CATCTGCTCCCTCTGTTCCTA 58.607 52.381 0.00 0.00 0.00 2.94
2705 2821 2.623418 TCTGCTCCCTCTGTTCCTAA 57.377 50.000 0.00 0.00 0.00 2.69
2706 2822 2.902608 TCTGCTCCCTCTGTTCCTAAA 58.097 47.619 0.00 0.00 0.00 1.85
2707 2823 3.454858 TCTGCTCCCTCTGTTCCTAAAT 58.545 45.455 0.00 0.00 0.00 1.40
2708 2824 4.620723 TCTGCTCCCTCTGTTCCTAAATA 58.379 43.478 0.00 0.00 0.00 1.40
2709 2825 5.219739 TCTGCTCCCTCTGTTCCTAAATAT 58.780 41.667 0.00 0.00 0.00 1.28
2710 2826 6.382087 TCTGCTCCCTCTGTTCCTAAATATA 58.618 40.000 0.00 0.00 0.00 0.86
2711 2827 6.844388 TCTGCTCCCTCTGTTCCTAAATATAA 59.156 38.462 0.00 0.00 0.00 0.98
2712 2828 7.015682 TCTGCTCCCTCTGTTCCTAAATATAAG 59.984 40.741 0.00 0.00 0.00 1.73
2713 2829 6.615726 TGCTCCCTCTGTTCCTAAATATAAGT 59.384 38.462 0.00 0.00 0.00 2.24
2714 2830 7.156000 GCTCCCTCTGTTCCTAAATATAAGTC 58.844 42.308 0.00 0.00 0.00 3.01
2715 2831 7.015779 GCTCCCTCTGTTCCTAAATATAAGTCT 59.984 40.741 0.00 0.00 0.00 3.24
2716 2832 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
2717 2833 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
2718 2834 9.907229 CCCTCTGTTCCTAAATATAAGTCTTTT 57.093 33.333 0.00 0.00 0.00 2.27
2748 2864 9.834628 ACATTTCAAATAAAGTACAACATACGG 57.165 29.630 0.00 0.00 0.00 4.02
2753 2869 9.872721 TCAAATAAAGTACAACATACGGATGTA 57.127 29.630 15.10 0.00 45.93 2.29
2791 2907 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2792 2908 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
2793 2909 8.621532 AAAGTGTAGATTCACTCATTTTGCTA 57.378 30.769 0.00 0.00 46.25 3.49
2794 2910 7.602517 AGTGTAGATTCACTCATTTTGCTAC 57.397 36.000 0.00 0.00 44.07 3.58
2795 2911 6.311445 AGTGTAGATTCACTCATTTTGCTACG 59.689 38.462 0.00 0.00 44.07 3.51
2796 2912 6.090898 GTGTAGATTCACTCATTTTGCTACGT 59.909 38.462 0.00 0.00 35.68 3.57
2797 2913 7.274904 GTGTAGATTCACTCATTTTGCTACGTA 59.725 37.037 0.00 0.00 35.68 3.57
2798 2914 7.979537 TGTAGATTCACTCATTTTGCTACGTAT 59.020 33.333 0.00 0.00 31.97 3.06
2799 2915 7.239166 AGATTCACTCATTTTGCTACGTATG 57.761 36.000 0.00 0.00 0.00 2.39
2800 2916 6.818644 AGATTCACTCATTTTGCTACGTATGT 59.181 34.615 0.00 0.00 0.00 2.29
2801 2917 7.979537 AGATTCACTCATTTTGCTACGTATGTA 59.020 33.333 0.00 0.00 0.00 2.29
2815 2931 7.862741 CTACGTATGTAGTCACTTGTTGAAA 57.137 36.000 13.15 0.00 42.61 2.69
2816 2932 8.462143 CTACGTATGTAGTCACTTGTTGAAAT 57.538 34.615 13.15 0.00 42.61 2.17
2817 2933 7.347508 ACGTATGTAGTCACTTGTTGAAATC 57.652 36.000 0.00 0.00 35.39 2.17
2818 2934 7.152645 ACGTATGTAGTCACTTGTTGAAATCT 58.847 34.615 0.00 0.00 35.39 2.40
2819 2935 7.328737 ACGTATGTAGTCACTTGTTGAAATCTC 59.671 37.037 0.00 0.00 35.39 2.75
2820 2936 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2821 2937 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2823 2939 9.778741 ATGTAGTCACTTGTTGAAATCTCTAAA 57.221 29.630 0.00 0.00 35.39 1.85
2824 2940 9.607988 TGTAGTCACTTGTTGAAATCTCTAAAA 57.392 29.630 0.00 0.00 35.39 1.52
2827 2943 9.396022 AGTCACTTGTTGAAATCTCTAAAAAGA 57.604 29.630 0.00 0.00 35.39 2.52
2828 2944 9.439537 GTCACTTGTTGAAATCTCTAAAAAGAC 57.560 33.333 0.00 0.00 35.39 3.01
2829 2945 9.396022 TCACTTGTTGAAATCTCTAAAAAGACT 57.604 29.630 0.00 0.00 0.00 3.24
2844 2960 9.169592 TCTAAAAAGACTTATATTTGGGAACGG 57.830 33.333 0.00 0.00 0.00 4.44
2845 2961 9.169592 CTAAAAAGACTTATATTTGGGAACGGA 57.830 33.333 0.00 0.00 0.00 4.69
2846 2962 7.625828 AAAAGACTTATATTTGGGAACGGAG 57.374 36.000 0.00 0.00 0.00 4.63
2847 2963 5.291905 AGACTTATATTTGGGAACGGAGG 57.708 43.478 0.00 0.00 0.00 4.30
2848 2964 4.102681 AGACTTATATTTGGGAACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
2849 2965 4.042174 ACTTATATTTGGGAACGGAGGGA 58.958 43.478 0.00 0.00 0.00 4.20
2905 3021 0.028374 AAACACGCGCACAGGTTAAC 59.972 50.000 5.73 0.00 0.00 2.01
2923 3039 2.496899 ACCGAAAGTGCATTGGAGAT 57.503 45.000 0.00 0.00 0.00 2.75
2976 3092 8.225603 AGGTATATGCAAATTAACTCAACCTG 57.774 34.615 0.00 0.00 31.48 4.00
3306 3442 6.653320 GGGCTGTAATGATATATTTTCCGTCA 59.347 38.462 0.00 0.00 0.00 4.35
3324 3460 5.046878 TCCGTCATCTTGTAACCTGTAATGT 60.047 40.000 0.00 0.00 0.00 2.71
3367 3503 4.334759 CAGTATTTCTGTGAGCAGGATTGG 59.665 45.833 0.00 0.00 42.78 3.16
3579 3716 1.002069 TCATGGAGCCCAAATGGACT 58.998 50.000 0.00 0.00 36.95 3.85
3627 3764 1.956477 CAGCACTGTAGGTTGGCTTTT 59.044 47.619 0.00 0.00 31.30 2.27
3665 3802 3.439857 ACAAACACATCATAGGCAGGT 57.560 42.857 0.00 0.00 0.00 4.00
3666 3803 3.084039 ACAAACACATCATAGGCAGGTG 58.916 45.455 0.00 0.00 35.66 4.00
3738 3875 1.477553 TTGGAAGCATCCCAATCTGC 58.522 50.000 5.34 0.00 45.95 4.26
3774 3911 5.812286 TCCTTGAGGGGATTTGTTAAGTAC 58.188 41.667 0.00 0.00 35.41 2.73
3775 3912 5.550403 TCCTTGAGGGGATTTGTTAAGTACT 59.450 40.000 0.00 0.00 35.41 2.73
3776 3913 5.880887 CCTTGAGGGGATTTGTTAAGTACTC 59.119 44.000 0.00 0.00 0.00 2.59
3777 3914 5.431179 TGAGGGGATTTGTTAAGTACTCC 57.569 43.478 0.00 0.00 0.00 3.85
3778 3915 4.226620 TGAGGGGATTTGTTAAGTACTCCC 59.773 45.833 0.00 0.00 37.81 4.30
3779 3916 4.445564 AGGGGATTTGTTAAGTACTCCCT 58.554 43.478 11.22 9.24 38.34 4.20
3780 3917 4.227527 AGGGGATTTGTTAAGTACTCCCTG 59.772 45.833 11.23 0.00 40.41 4.45
3781 3918 4.018688 GGGGATTTGTTAAGTACTCCCTGT 60.019 45.833 11.22 0.00 38.34 4.00
3783 3920 6.296605 GGGGATTTGTTAAGTACTCCCTGTAA 60.297 42.308 11.22 0.00 38.34 2.41
3784 3921 7.170277 GGGATTTGTTAAGTACTCCCTGTAAA 58.830 38.462 0.00 0.00 36.36 2.01
3785 3922 7.336176 GGGATTTGTTAAGTACTCCCTGTAAAG 59.664 40.741 0.00 0.00 36.36 1.85
3789 3926 9.856162 TTTGTTAAGTACTCCCTGTAAAGAAAT 57.144 29.630 0.00 0.00 32.25 2.17
3799 3936 8.925338 ACTCCCTGTAAAGAAATATAAGATCGT 58.075 33.333 0.00 0.00 0.00 3.73
3800 3937 9.413048 CTCCCTGTAAAGAAATATAAGATCGTC 57.587 37.037 0.00 0.00 0.00 4.20
3801 3938 9.144298 TCCCTGTAAAGAAATATAAGATCGTCT 57.856 33.333 0.00 0.00 0.00 4.18
3846 3983 5.818678 ACAGAGGGAGTACATGTTTGTAA 57.181 39.130 2.30 0.00 39.96 2.41
3853 3990 8.090788 AGGGAGTACATGTTTGTAATAGTGAT 57.909 34.615 2.30 0.00 39.96 3.06
3873 4010 8.797350 AGTGATGATTGTGTCTATTGAATTGA 57.203 30.769 0.00 0.00 0.00 2.57
3874 4011 8.671921 AGTGATGATTGTGTCTATTGAATTGAC 58.328 33.333 11.86 11.86 35.92 3.18
3877 4014 8.797350 ATGATTGTGTCTATTGAATTGACAGA 57.203 30.769 19.79 16.68 43.62 3.41
3895 4032 5.469760 TGACAGATGTGTTTGGTAGATTGTG 59.530 40.000 0.00 0.00 36.88 3.33
3904 4041 8.253810 TGTGTTTGGTAGATTGTGAAATTTCAA 58.746 29.630 22.07 8.69 39.21 2.69
4515 7217 3.952967 GGGTCTTGTCTCTACCGATAACT 59.047 47.826 0.00 0.00 33.89 2.24
4516 7218 4.202030 GGGTCTTGTCTCTACCGATAACTG 60.202 50.000 0.00 0.00 33.89 3.16
4756 7460 4.891756 AGGATGAATTGGTGAGGCTTATTG 59.108 41.667 0.00 0.00 0.00 1.90
4903 7608 8.517062 AAAGAAAATATGATCTAGCTTGCACT 57.483 30.769 0.00 0.00 0.00 4.40
5682 8730 4.274214 GCGGGTTTTCAGTTAGTTACAAGT 59.726 41.667 0.00 0.00 0.00 3.16
5730 8778 3.686241 TCAGCATGCTCTGTCATTACAAC 59.314 43.478 19.68 0.00 32.61 3.32
5751 8816 3.920841 ACCAGGTAGGGAACATTTAGGTT 59.079 43.478 0.00 0.00 43.89 3.50
5785 8850 1.067283 TGCTACTTCTGCTCTGCTGTC 60.067 52.381 0.00 0.00 0.00 3.51
5835 8900 7.630082 AGTTAGATCAGTAGTCTTCAGAGAGT 58.370 38.462 0.00 0.00 38.99 3.24
5837 8902 6.061022 AGATCAGTAGTCTTCAGAGAGTCA 57.939 41.667 0.00 0.00 36.88 3.41
5853 8925 0.531200 GTCATTTCTCCTCGGGTCGT 59.469 55.000 0.00 0.00 0.00 4.34
5876 8948 9.268268 TCGTTTGTAATCTGACTTTATGTTTCT 57.732 29.630 0.00 0.00 0.00 2.52
5877 8949 9.530129 CGTTTGTAATCTGACTTTATGTTTCTC 57.470 33.333 0.00 0.00 0.00 2.87
6044 9199 2.898705 GGTCAATGAGAGCAGTGTAGG 58.101 52.381 0.00 0.00 44.14 3.18
6103 9258 3.371702 GGGTAGGAAATGGAAAGGGAGTC 60.372 52.174 0.00 0.00 0.00 3.36
6126 9281 7.286316 AGTCTGGAAAATTTTGTGTCTGAGAAT 59.714 33.333 8.47 0.00 0.00 2.40
6138 9293 9.725019 TTTGTGTCTGAGAATATGAAACTACAT 57.275 29.630 0.00 0.00 0.00 2.29
6168 9323 6.960542 AGGTCCAGGAGTTAAAGAGAGATAAA 59.039 38.462 0.00 0.00 0.00 1.40
6177 9332 7.113437 AGTTAAAGAGAGATAAAAAGGAGGCC 58.887 38.462 0.00 0.00 0.00 5.19
6183 9338 2.436173 AGATAAAAAGGAGGCCGAGGAG 59.564 50.000 0.00 0.00 0.00 3.69
6186 9341 4.761058 AAGGAGGCCGAGGAGCGA 62.761 66.667 0.00 0.00 44.57 4.93
6198 9353 0.686112 AGGAGCGAGCTAAGAAGGCT 60.686 55.000 0.00 0.00 43.26 4.58
6212 9367 4.879197 AGAAGGCTGAAAAAGAAATGGG 57.121 40.909 0.00 0.00 0.00 4.00
6215 9370 5.366477 AGAAGGCTGAAAAAGAAATGGGAAA 59.634 36.000 0.00 0.00 0.00 3.13
6220 9375 6.165577 GCTGAAAAAGAAATGGGAAATGCTA 58.834 36.000 0.00 0.00 0.00 3.49
6245 9400 3.672511 GCTGACAACATGAAGCTGAATGG 60.673 47.826 0.00 0.45 31.35 3.16
6261 9416 0.467384 ATGGTCAGCTCCAGGAATCG 59.533 55.000 0.18 0.00 41.05 3.34
6266 9421 1.208052 TCAGCTCCAGGAATCGGAAAG 59.792 52.381 0.00 0.00 30.33 2.62
6267 9422 1.208052 CAGCTCCAGGAATCGGAAAGA 59.792 52.381 0.00 0.00 30.33 2.52
6288 9443 3.953542 AATAAAAAGGAGGCCGAGGAT 57.046 42.857 0.00 0.00 0.00 3.24
6324 9479 4.645535 TGGATTTCTTCTCAGGAAGTGTG 58.354 43.478 5.79 0.00 46.47 3.82
6364 9519 7.283127 TGGATTTGCACAATAAGATAGAGGTTC 59.717 37.037 0.00 0.00 0.00 3.62
6369 9524 8.306313 TGCACAATAAGATAGAGGTTCTAGAA 57.694 34.615 0.00 0.00 31.67 2.10
6424 9579 2.751806 GAGGCAGAAAGTGAAATGGAGG 59.248 50.000 0.00 0.00 0.00 4.30
6446 9601 1.230324 GTTGTGGCTGAGAACAGGAC 58.770 55.000 0.00 0.00 43.62 3.85
6447 9602 0.249868 TTGTGGCTGAGAACAGGACG 60.250 55.000 0.00 0.00 43.62 4.79
6453 9608 1.707632 CTGAGAACAGGACGCTGAAG 58.292 55.000 0.00 0.00 40.14 3.02
6476 9631 1.923850 TCAGCTCCAGGTAGTAGAGGT 59.076 52.381 0.00 0.00 38.84 3.85
6483 9638 2.624557 CCAGGTAGTAGAGGTCCAAGCT 60.625 54.545 0.00 0.00 0.00 3.74
6484 9639 3.372784 CCAGGTAGTAGAGGTCCAAGCTA 60.373 52.174 0.00 0.00 0.00 3.32
6535 9690 6.270064 GTTGCAGGTGTAAACATAGTTTTGT 58.730 36.000 0.03 0.00 0.00 2.83
6576 9731 6.118852 GTCAGAGGAGAAGAATAAAATGGCT 58.881 40.000 0.00 0.00 0.00 4.75
6645 9800 4.829064 TGACAATGTGAAACTAAGTGGC 57.171 40.909 0.00 0.00 38.04 5.01
6662 9817 8.306761 ACTAAGTGGCCAGATTCAAAAATTAAG 58.693 33.333 5.11 0.00 0.00 1.85
6739 9894 4.530710 AGTGTTCTAGCCGTAAACATGA 57.469 40.909 0.00 0.00 35.54 3.07
6747 9902 4.434713 AGCCGTAAACATGAATTTGGAC 57.565 40.909 0.00 0.00 0.00 4.02
6757 9912 4.657969 ACATGAATTTGGACAAAAAGGGGA 59.342 37.500 0.00 0.00 33.56 4.81
6772 9927 1.663173 GGGATGGAGCGAGCTACTC 59.337 63.158 8.93 7.56 0.00 2.59
6774 9929 1.545875 GGGATGGAGCGAGCTACTCTA 60.546 57.143 14.18 9.82 34.46 2.43
6777 9932 0.814410 TGGAGCGAGCTACTCTACCG 60.814 60.000 14.18 0.68 34.46 4.02
6810 9965 7.445096 GGATTGGAAATTGTTGGAGTTGAAAAT 59.555 33.333 0.00 0.00 0.00 1.82
6833 9988 3.161866 TGAAGGGGAAATTACAAGGCAC 58.838 45.455 0.00 0.00 0.00 5.01
6893 10242 2.031870 GGCAACTCCAACCAAAGACTT 58.968 47.619 0.00 0.00 34.01 3.01
7112 10462 3.428746 TTTGTGTTTCACCCGAACATG 57.571 42.857 0.00 0.00 39.03 3.21
7127 10477 5.220567 CCCGAACATGTTTCCTTTTGTTTTG 60.221 40.000 13.36 0.00 32.73 2.44
7199 10550 4.429854 GAGAGGGTCTCCATGCTATTTT 57.570 45.455 0.00 0.00 37.55 1.82
7209 10560 4.539726 TCCATGCTATTTTGCCTTGATCT 58.460 39.130 0.00 0.00 0.00 2.75
7218 10569 7.442364 GCTATTTTGCCTTGATCTGTCAGTATA 59.558 37.037 0.00 0.00 35.39 1.47
7253 10604 9.988815 CTCCTATCTATTATATTATGCGGCTTT 57.011 33.333 0.00 0.00 0.00 3.51
7317 10668 0.938713 TGTCGATTTGGTTCGCGTTT 59.061 45.000 5.77 0.00 38.97 3.60
7403 10754 5.335113 GCTAAATGTGATCTGCTTGTTGTGA 60.335 40.000 0.00 0.00 0.00 3.58
7404 10755 5.717078 AAATGTGATCTGCTTGTTGTGAT 57.283 34.783 0.00 0.00 0.00 3.06
7449 10800 3.517602 CACACGTCCATTCGGATTCTTA 58.482 45.455 0.00 0.00 45.33 2.10
7494 10845 2.038269 GCGGCGTCCTTTTGATCCA 61.038 57.895 9.37 0.00 0.00 3.41
7545 10896 0.995024 ATTCAGGAGTGGACTTGGGG 59.005 55.000 0.00 0.00 0.00 4.96
7564 10915 2.018515 GGTGTCTTTTTGACCGGAACA 58.981 47.619 9.46 5.02 44.75 3.18
7601 10952 9.707957 TGCCTTTTCATTATATTAGAGGGAAAA 57.292 29.630 0.00 0.00 33.36 2.29
7618 10969 6.252995 AGGGAAAAATTATACAAGACTGCCA 58.747 36.000 0.00 0.00 0.00 4.92
7623 10974 7.396540 AAAATTATACAAGACTGCCAGAAGG 57.603 36.000 0.00 0.00 38.23 3.46
7665 11018 5.130975 ACAGCAAGGAAGAAAAAGGGAAAAT 59.869 36.000 0.00 0.00 0.00 1.82
7778 11132 3.441922 CAGCACAGTAGAAGTAGAGCTCA 59.558 47.826 17.77 0.00 0.00 4.26
7927 11281 3.134127 GATGTCGCACCCAAGGCC 61.134 66.667 0.00 0.00 0.00 5.19
7966 11320 7.331791 CAGGATAAGAGCCACTAACTTTAAGT 58.668 38.462 0.00 0.00 0.00 2.24
8071 11425 0.602905 GATCCCAATTACGAGCCCGG 60.603 60.000 0.00 0.00 40.78 5.73
8076 11430 0.529992 CAATTACGAGCCCGGAGTCC 60.530 60.000 0.73 0.00 40.78 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
440 441 3.088532 GTGAGCCATGTCCCAAATAACA 58.911 45.455 0.00 0.00 0.00 2.41
467 468 2.197577 GTCTCGCTAATTGAGGCTCAC 58.802 52.381 18.55 4.19 35.23 3.51
475 476 5.890110 ACACGAATATGTCTCGCTAATTG 57.110 39.130 0.00 0.00 39.97 2.32
515 516 1.204704 TGCAAGTCCAGATAGTCCACG 59.795 52.381 0.00 0.00 0.00 4.94
672 673 0.833834 CCCGAGCTACCATCTCCCAT 60.834 60.000 0.00 0.00 0.00 4.00
713 714 3.195825 GCCTATCCTATTACATGACCGCT 59.804 47.826 0.00 0.00 0.00 5.52
769 770 0.383949 GCCAAGAAAAGACGCCACAA 59.616 50.000 0.00 0.00 0.00 3.33
968 971 5.772672 AGAGATCATATCGGAAGCAAGTAGT 59.227 40.000 0.00 0.00 0.00 2.73
969 972 6.266168 AGAGATCATATCGGAAGCAAGTAG 57.734 41.667 0.00 0.00 0.00 2.57
970 973 6.656632 AAGAGATCATATCGGAAGCAAGTA 57.343 37.500 0.00 0.00 0.00 2.24
1085 1088 7.739995 TCCCCATGATCTAATATTAGTCAGG 57.260 40.000 19.58 20.23 30.33 3.86
1269 1279 0.464452 ATACGCACTAGGCAAGGACC 59.536 55.000 0.00 0.00 45.17 4.46
1326 1352 3.501828 TGCAACAGCGATAAACTTCACAT 59.498 39.130 0.00 0.00 0.00 3.21
1455 1481 4.532276 TGAATTTCATCACAAAACCGACG 58.468 39.130 0.00 0.00 0.00 5.12
1528 1554 7.462571 AAAATCGACTTTAGCCACCTAAAAT 57.537 32.000 0.00 0.00 41.59 1.82
1572 1598 8.546597 TTCTTGTGTGAAATCGATGAAAGATA 57.453 30.769 0.00 0.00 0.00 1.98
1623 1650 6.961359 TGTTGAGTGTAGGAAAATCATACG 57.039 37.500 0.00 0.00 36.52 3.06
1836 1867 5.899631 TCTCTTAAAACACCTAGTTGGGT 57.100 39.130 0.00 0.00 41.19 4.51
1855 1886 9.178758 AGGAAAATGGTTATGAAAGTGTATCTC 57.821 33.333 0.00 0.00 0.00 2.75
1906 1938 4.739793 TCAAGGTGATTTGAGGGTGAATT 58.260 39.130 0.00 0.00 32.39 2.17
1907 1939 4.387026 TCAAGGTGATTTGAGGGTGAAT 57.613 40.909 0.00 0.00 32.39 2.57
1909 1941 3.874383 TTCAAGGTGATTTGAGGGTGA 57.126 42.857 0.00 0.00 38.25 4.02
1910 1942 4.935352 TTTTCAAGGTGATTTGAGGGTG 57.065 40.909 0.00 0.00 38.25 4.61
1911 1943 5.602145 TCAATTTTCAAGGTGATTTGAGGGT 59.398 36.000 0.00 0.00 38.25 4.34
1912 1944 6.100404 TCAATTTTCAAGGTGATTTGAGGG 57.900 37.500 0.00 0.00 38.25 4.30
1945 1977 0.035820 GTATTCCACTGCCCCGACAA 60.036 55.000 0.00 0.00 0.00 3.18
1960 1992 3.447586 AGGATGTGCTCACAGTACGTATT 59.552 43.478 8.74 0.00 45.48 1.89
1994 2026 4.971830 CGCACAACTGAGGCATATATTTTG 59.028 41.667 0.00 0.00 0.00 2.44
2003 2036 3.279116 GTGCGCACAACTGAGGCA 61.279 61.111 34.52 0.00 0.00 4.75
2040 2149 3.112263 ACCCCATCCGAGATGTTTCTTA 58.888 45.455 11.38 0.00 30.30 2.10
2059 2168 3.825328 ACAATCATATGGGAGAAGCACC 58.175 45.455 2.13 0.00 0.00 5.01
2125 2234 9.830186 AGATGTAAGATATATCCTAGTGGTTGT 57.170 33.333 9.18 0.00 34.23 3.32
2144 2253 4.370776 TGAGAGATTCCCCCAAGATGTAA 58.629 43.478 0.00 0.00 0.00 2.41
2154 2263 2.774234 TGTCTTGGATGAGAGATTCCCC 59.226 50.000 0.00 0.00 0.00 4.81
2155 2264 4.195416 GTTGTCTTGGATGAGAGATTCCC 58.805 47.826 0.00 0.00 0.00 3.97
2193 2302 1.081892 CTGCATCCGAGACACTTTGG 58.918 55.000 0.00 0.00 0.00 3.28
2225 2334 5.859205 TCATATCACTAGCACATGTCACT 57.141 39.130 0.00 0.00 0.00 3.41
2304 2414 6.732896 AGTGAGACCGAGTTATAATGGATT 57.267 37.500 7.99 0.00 0.00 3.01
2309 2419 7.232188 TCCATCTAGTGAGACCGAGTTATAAT 58.768 38.462 0.00 0.00 33.41 1.28
2310 2420 6.598503 TCCATCTAGTGAGACCGAGTTATAA 58.401 40.000 0.00 0.00 33.41 0.98
2358 2468 7.416964 TGTTCCCTAATAATTTCCATGTTGG 57.583 36.000 0.00 0.00 39.43 3.77
2520 2636 0.179234 TGTTCTGTTCGGTTGCAGGA 59.821 50.000 0.00 0.00 33.81 3.86
2538 2654 4.660771 AGAGGATTACTGGGTTTAGGGATG 59.339 45.833 0.00 0.00 0.00 3.51
2554 2670 1.202855 CGGGCATGGATGAAGAGGATT 60.203 52.381 0.00 0.00 0.00 3.01
2687 2803 3.922171 ATTTAGGAACAGAGGGAGCAG 57.078 47.619 0.00 0.00 0.00 4.24
2688 2804 6.615726 ACTTATATTTAGGAACAGAGGGAGCA 59.384 38.462 0.00 0.00 0.00 4.26
2689 2805 7.015779 AGACTTATATTTAGGAACAGAGGGAGC 59.984 40.741 0.00 0.00 0.00 4.70
2690 2806 8.485578 AGACTTATATTTAGGAACAGAGGGAG 57.514 38.462 0.00 0.00 0.00 4.30
2691 2807 8.855804 AAGACTTATATTTAGGAACAGAGGGA 57.144 34.615 0.00 0.00 0.00 4.20
2692 2808 9.907229 AAAAGACTTATATTTAGGAACAGAGGG 57.093 33.333 0.00 0.00 0.00 4.30
2722 2838 9.834628 CCGTATGTTGTACTTTATTTGAAATGT 57.165 29.630 0.00 0.00 0.00 2.71
2726 2842 9.221933 ACATCCGTATGTTGTACTTTATTTGAA 57.778 29.630 0.00 0.00 44.07 2.69
2727 2843 8.780846 ACATCCGTATGTTGTACTTTATTTGA 57.219 30.769 0.00 0.00 44.07 2.69
2771 2887 6.090898 ACGTAGCAAAATGAGTGAATCTACAC 59.909 38.462 0.00 0.00 40.60 2.90
2772 2888 6.163476 ACGTAGCAAAATGAGTGAATCTACA 58.837 36.000 0.00 0.00 0.00 2.74
2773 2889 6.648725 ACGTAGCAAAATGAGTGAATCTAC 57.351 37.500 0.00 0.00 0.00 2.59
2774 2890 7.979537 ACATACGTAGCAAAATGAGTGAATCTA 59.020 33.333 0.08 0.00 0.00 1.98
2775 2891 6.818644 ACATACGTAGCAAAATGAGTGAATCT 59.181 34.615 0.08 0.00 0.00 2.40
2776 2892 7.005062 ACATACGTAGCAAAATGAGTGAATC 57.995 36.000 0.08 0.00 0.00 2.52
2777 2893 6.985188 ACATACGTAGCAAAATGAGTGAAT 57.015 33.333 0.08 0.00 0.00 2.57
2778 2894 7.520119 CTACATACGTAGCAAAATGAGTGAA 57.480 36.000 0.08 0.00 38.84 3.18
2792 2908 8.301720 AGATTTCAACAAGTGACTACATACGTA 58.698 33.333 0.00 0.00 35.39 3.57
2793 2909 7.152645 AGATTTCAACAAGTGACTACATACGT 58.847 34.615 0.00 0.00 35.39 3.57
2794 2910 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2795 2911 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2797 2913 9.778741 TTTAGAGATTTCAACAAGTGACTACAT 57.221 29.630 0.00 0.00 35.39 2.29
2798 2914 9.607988 TTTTAGAGATTTCAACAAGTGACTACA 57.392 29.630 0.00 0.00 35.39 2.74
2801 2917 9.396022 TCTTTTTAGAGATTTCAACAAGTGACT 57.604 29.630 0.00 0.00 35.39 3.41
2802 2918 9.439537 GTCTTTTTAGAGATTTCAACAAGTGAC 57.560 33.333 0.00 0.00 35.39 3.67
2803 2919 9.396022 AGTCTTTTTAGAGATTTCAACAAGTGA 57.604 29.630 0.00 0.00 0.00 3.41
2818 2934 9.169592 CCGTTCCCAAATATAAGTCTTTTTAGA 57.830 33.333 0.00 0.00 0.00 2.10
2819 2935 9.169592 TCCGTTCCCAAATATAAGTCTTTTTAG 57.830 33.333 0.00 0.00 0.00 1.85
2820 2936 9.169592 CTCCGTTCCCAAATATAAGTCTTTTTA 57.830 33.333 0.00 0.00 0.00 1.52
2821 2937 7.122204 CCTCCGTTCCCAAATATAAGTCTTTTT 59.878 37.037 0.00 0.00 0.00 1.94
2822 2938 6.602009 CCTCCGTTCCCAAATATAAGTCTTTT 59.398 38.462 0.00 0.00 0.00 2.27
2823 2939 6.120220 CCTCCGTTCCCAAATATAAGTCTTT 58.880 40.000 0.00 0.00 0.00 2.52
2824 2940 5.397559 CCCTCCGTTCCCAAATATAAGTCTT 60.398 44.000 0.00 0.00 0.00 3.01
2825 2941 4.102681 CCCTCCGTTCCCAAATATAAGTCT 59.897 45.833 0.00 0.00 0.00 3.24
2826 2942 4.102054 TCCCTCCGTTCCCAAATATAAGTC 59.898 45.833 0.00 0.00 0.00 3.01
2827 2943 4.042174 TCCCTCCGTTCCCAAATATAAGT 58.958 43.478 0.00 0.00 0.00 2.24
2828 2944 4.102681 ACTCCCTCCGTTCCCAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
2829 2945 4.042174 ACTCCCTCCGTTCCCAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
2830 2946 3.660959 ACTCCCTCCGTTCCCAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
2831 2947 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
2832 2948 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2833 2949 1.838077 CTACTCCCTCCGTTCCCAAAT 59.162 52.381 0.00 0.00 0.00 2.32
2834 2950 1.272807 CTACTCCCTCCGTTCCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
2835 2951 0.115745 ACTACTCCCTCCGTTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
2836 2952 1.002069 TACTACTCCCTCCGTTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
2837 2953 2.149973 TTACTACTCCCTCCGTTCCC 57.850 55.000 0.00 0.00 0.00 3.97
2838 2954 3.095332 ACTTTACTACTCCCTCCGTTCC 58.905 50.000 0.00 0.00 0.00 3.62
2839 2955 3.760684 TCACTTTACTACTCCCTCCGTTC 59.239 47.826 0.00 0.00 0.00 3.95
2840 2956 3.771216 TCACTTTACTACTCCCTCCGTT 58.229 45.455 0.00 0.00 0.00 4.44
2841 2957 3.446442 TCACTTTACTACTCCCTCCGT 57.554 47.619 0.00 0.00 0.00 4.69
2842 2958 4.208746 AGATCACTTTACTACTCCCTCCG 58.791 47.826 0.00 0.00 0.00 4.63
2843 2959 7.657023 TTAAGATCACTTTACTACTCCCTCC 57.343 40.000 0.00 0.00 37.53 4.30
2845 2961 9.892130 CAAATTAAGATCACTTTACTACTCCCT 57.108 33.333 0.00 0.00 37.53 4.20
2846 2962 9.668497 ACAAATTAAGATCACTTTACTACTCCC 57.332 33.333 0.00 0.00 37.53 4.30
2905 3021 1.402968 CCATCTCCAATGCACTTTCGG 59.597 52.381 0.00 0.00 0.00 4.30
2976 3092 4.164413 AGGGACAGGAAACTAAATCTAGCC 59.836 45.833 0.00 0.00 40.21 3.93
3184 3310 9.478019 GATGTTTTCACAAATTCACTAGATACG 57.522 33.333 0.00 0.00 36.16 3.06
3254 3383 6.916387 TGTTTCGGTTAACGCAATTGAATTTA 59.084 30.769 10.34 0.00 43.86 1.40
3306 3442 5.590259 GCCATGACATTACAGGTTACAAGAT 59.410 40.000 0.00 0.00 0.00 2.40
3367 3503 5.529060 GGATCTTGGATGTTTGTATCACCTC 59.471 44.000 0.00 0.00 0.00 3.85
3385 3521 8.801882 TCTAATTTTGTATTTCGGTGGATCTT 57.198 30.769 0.00 0.00 0.00 2.40
3579 3716 4.132336 TGGCTACAAATTTTGCATGCAAA 58.868 34.783 35.80 35.80 43.23 3.68
3627 3764 1.152652 TTGGGAGCGCCAGGAAAAA 60.153 52.632 9.31 0.00 35.15 1.94
3631 3768 3.126703 TTTGTTGGGAGCGCCAGGA 62.127 57.895 9.31 0.00 35.15 3.86
3632 3769 2.597217 TTTGTTGGGAGCGCCAGG 60.597 61.111 9.31 0.00 35.15 4.45
3636 3773 0.387239 GATGTGTTTGTTGGGAGCGC 60.387 55.000 0.00 0.00 0.00 5.92
3666 3803 5.007626 TCAATAGTGACAAGTTGCAAGTGTC 59.992 40.000 25.91 25.91 41.66 3.67
3737 3874 3.717400 TCAAGGATGAGACACTATCGC 57.283 47.619 0.00 0.00 0.00 4.58
3774 3911 9.413048 GACGATCTTATATTTCTTTACAGGGAG 57.587 37.037 0.00 0.00 0.00 4.30
3775 3912 9.144298 AGACGATCTTATATTTCTTTACAGGGA 57.856 33.333 0.00 0.00 0.00 4.20
3853 3990 8.671028 CATCTGTCAATTCAATAGACACAATCA 58.329 33.333 0.00 0.00 37.36 2.57
3873 4010 5.620206 TCACAATCTACCAAACACATCTGT 58.380 37.500 0.00 0.00 0.00 3.41
3874 4011 6.558771 TTCACAATCTACCAAACACATCTG 57.441 37.500 0.00 0.00 0.00 2.90
3877 4014 8.420222 TGAAATTTCACAATCTACCAAACACAT 58.580 29.630 16.91 0.00 31.01 3.21
3904 4041 6.374417 AACTCCCAAGTACATGTCTACATT 57.626 37.500 0.00 0.00 33.48 2.71
4268 6969 6.791371 TGGGTAGATATAGTCCTAAGGTCAG 58.209 44.000 0.00 0.00 0.00 3.51
4348 7049 2.125753 GACTGAGTCTGGCAGCGG 60.126 66.667 10.34 3.63 36.86 5.52
4515 7217 6.647334 TGTGACTTGAGCCAAATAATTTCA 57.353 33.333 0.00 0.00 0.00 2.69
4516 7218 7.147976 AGTTGTGACTTGAGCCAAATAATTTC 58.852 34.615 0.00 0.00 29.87 2.17
4663 7365 7.312899 CCCCTATTGATTCACACAAAGTAAAC 58.687 38.462 0.00 0.00 0.00 2.01
5110 8124 8.668510 CATCATATGCTAAGTTATGGGGTATC 57.331 38.462 0.00 0.00 0.00 2.24
5143 8158 8.877864 TGGAGTTTTGACCACTGATTAATAAT 57.122 30.769 0.00 0.00 0.00 1.28
5682 8730 3.473621 ACCCTCCACTATCCAATACCCTA 59.526 47.826 0.00 0.00 0.00 3.53
5730 8778 4.227527 AGAACCTAAATGTTCCCTACCTGG 59.772 45.833 0.00 0.00 44.55 4.45
5751 8816 4.406972 AGAAGTAGCATGTCATTGGCTAGA 59.593 41.667 5.36 0.00 40.50 2.43
5785 8850 3.744660 ACCAAAGTAGAAGAGCAGTTGG 58.255 45.455 0.00 0.00 39.92 3.77
5835 8900 1.263356 AACGACCCGAGGAGAAATGA 58.737 50.000 0.00 0.00 0.00 2.57
5837 8902 1.346722 ACAAACGACCCGAGGAGAAAT 59.653 47.619 0.00 0.00 0.00 2.17
5876 8948 7.604545 CGAGGACTGTATGTGAATAGATAGAGA 59.395 40.741 0.00 0.00 30.68 3.10
5877 8949 7.389330 ACGAGGACTGTATGTGAATAGATAGAG 59.611 40.741 0.00 0.00 31.91 2.43
5878 8950 7.173390 CACGAGGACTGTATGTGAATAGATAGA 59.827 40.741 0.00 0.00 32.39 1.98
5879 8951 7.301789 CACGAGGACTGTATGTGAATAGATAG 58.698 42.308 0.00 0.00 32.39 2.08
6103 9258 9.350357 CATATTCTCAGACACAAAATTTTCCAG 57.650 33.333 0.00 0.00 0.00 3.86
6126 9281 6.183361 CCTGGACCTGATCATGTAGTTTCATA 60.183 42.308 3.40 0.00 0.00 2.15
6138 9293 4.425772 TCTTTAACTCCTGGACCTGATCA 58.574 43.478 0.00 0.00 0.00 2.92
6168 9323 3.775654 CGCTCCTCGGCCTCCTTT 61.776 66.667 0.00 0.00 33.78 3.11
6177 9332 0.030101 CCTTCTTAGCTCGCTCCTCG 59.970 60.000 0.00 0.00 40.15 4.63
6183 9338 1.726853 TTTCAGCCTTCTTAGCTCGC 58.273 50.000 0.00 0.00 38.95 5.03
6186 9341 6.294955 CCATTTCTTTTTCAGCCTTCTTAGCT 60.295 38.462 0.00 0.00 42.70 3.32
6198 9353 7.104939 CCATAGCATTTCCCATTTCTTTTTCA 58.895 34.615 0.00 0.00 0.00 2.69
6212 9367 4.096833 TCATGTTGTCAGCCATAGCATTTC 59.903 41.667 0.00 0.00 43.56 2.17
6215 9370 3.286329 TCATGTTGTCAGCCATAGCAT 57.714 42.857 0.00 0.00 43.56 3.79
6220 9375 1.816835 CAGCTTCATGTTGTCAGCCAT 59.183 47.619 0.00 0.00 0.00 4.40
6245 9400 0.537188 TTCCGATTCCTGGAGCTGAC 59.463 55.000 0.00 0.00 36.72 3.51
6261 9416 4.461431 TCGGCCTCCTTTTTATTTCTTTCC 59.539 41.667 0.00 0.00 0.00 3.13
6266 9421 3.617284 TCCTCGGCCTCCTTTTTATTTC 58.383 45.455 0.00 0.00 0.00 2.17
6267 9422 3.732048 TCCTCGGCCTCCTTTTTATTT 57.268 42.857 0.00 0.00 0.00 1.40
6288 9443 8.391075 AGAAGAAATCCAACTGTAAAATTCGA 57.609 30.769 0.00 0.00 0.00 3.71
6292 9447 7.944554 TCCTGAGAAGAAATCCAACTGTAAAAT 59.055 33.333 0.00 0.00 0.00 1.82
6324 9479 3.514645 CAAATCCATGTTTACAGCTGCC 58.485 45.455 15.27 0.00 0.00 4.85
6357 9512 9.520515 TTTTTATGCTCATTTTCTAGAACCTCT 57.479 29.630 4.18 0.00 0.00 3.69
6364 9519 5.973565 CGGCCTTTTTATGCTCATTTTCTAG 59.026 40.000 0.00 0.00 0.00 2.43
6369 9524 3.131046 CCTCGGCCTTTTTATGCTCATTT 59.869 43.478 0.00 0.00 0.00 2.32
6376 9531 1.014352 CGGTCCTCGGCCTTTTTATG 58.986 55.000 0.00 0.00 34.75 1.90
6424 9579 0.947244 CTGTTCTCAGCCACAACACC 59.053 55.000 0.00 0.00 34.79 4.16
6503 9658 4.142271 TGTTTACACCTGCAACCTTTTCAG 60.142 41.667 0.00 0.00 0.00 3.02
6535 9690 0.685458 GACCCCTCCAGCTTACGGTA 60.685 60.000 0.00 0.00 0.00 4.02
6576 9731 0.837691 TCTCCTTGGCTTGCTCCTCA 60.838 55.000 0.00 0.00 0.00 3.86
6739 9894 4.238669 TCCATCCCCTTTTTGTCCAAATT 58.761 39.130 0.00 0.00 0.00 1.82
6747 9902 1.098050 CTCGCTCCATCCCCTTTTTG 58.902 55.000 0.00 0.00 0.00 2.44
6757 9912 1.611519 GGTAGAGTAGCTCGCTCCAT 58.388 55.000 12.84 1.36 35.36 3.41
6772 9927 4.699925 TTTCCAATCCCTTATCCGGTAG 57.300 45.455 0.00 0.00 0.00 3.18
6774 9929 4.215109 CAATTTCCAATCCCTTATCCGGT 58.785 43.478 0.00 0.00 0.00 5.28
6777 9932 5.660864 TCCAACAATTTCCAATCCCTTATCC 59.339 40.000 0.00 0.00 0.00 2.59
6810 9965 4.953579 GTGCCTTGTAATTTCCCCTTCATA 59.046 41.667 0.00 0.00 0.00 2.15
6833 9988 5.801350 TTGTTCACTCTTCTTGTGACTTG 57.199 39.130 0.00 0.00 43.13 3.16
7159 10509 3.262151 TCTCCAACGGTGTGGATCAATAA 59.738 43.478 0.00 0.00 46.66 1.40
7171 10521 4.115270 GAGACCCTCTCCAACGGT 57.885 61.111 0.00 0.00 37.55 4.83
7199 10550 7.544804 ACATATATACTGACAGATCAAGGCA 57.455 36.000 10.08 0.00 33.30 4.75
7253 10604 5.424757 CCACATTATCGACCCTAAAGAACA 58.575 41.667 0.00 0.00 0.00 3.18
7260 10611 0.677288 CCGCCACATTATCGACCCTA 59.323 55.000 0.00 0.00 0.00 3.53
7333 10684 2.522436 ACGACCACGAAGGGGACA 60.522 61.111 0.00 0.00 43.89 4.02
7403 10754 2.081161 GGGAGCACCATGGGAGGAT 61.081 63.158 18.09 3.43 39.85 3.24
7404 10755 2.692368 GGGAGCACCATGGGAGGA 60.692 66.667 18.09 0.00 39.85 3.71
7449 10800 2.529389 AGGCGAAGTGGTTCCCCT 60.529 61.111 0.00 0.00 36.31 4.79
7473 10824 0.741221 GATCAAAAGGACGCCGCTCT 60.741 55.000 0.00 0.00 0.00 4.09
7475 10826 1.745489 GGATCAAAAGGACGCCGCT 60.745 57.895 0.00 0.00 0.00 5.52
7481 10832 2.762535 TCCGTCTGGATCAAAAGGAC 57.237 50.000 0.00 0.00 40.17 3.85
7494 10845 1.768275 TGGGCACATTGATATCCGTCT 59.232 47.619 0.00 0.00 0.00 4.18
7502 10853 2.898612 TGAACAACATGGGCACATTGAT 59.101 40.909 9.25 0.00 34.35 2.57
7601 10952 6.313519 TCCTTCTGGCAGTCTTGTATAATT 57.686 37.500 15.27 0.00 0.00 1.40
7605 10956 2.093235 GCTCCTTCTGGCAGTCTTGTAT 60.093 50.000 15.27 0.00 0.00 2.29
7618 10969 1.632409 TCATTTCCTGCTGCTCCTTCT 59.368 47.619 0.00 0.00 0.00 2.85
7623 10974 3.243002 GCTGTAATCATTTCCTGCTGCTC 60.243 47.826 0.00 0.00 0.00 4.26
7630 10981 5.819991 TCTTCCTTGCTGTAATCATTTCCT 58.180 37.500 0.00 0.00 0.00 3.36
7778 11132 2.222027 CAGAGTTTTCAAGGCCTCGTT 58.778 47.619 5.23 0.00 0.00 3.85
7937 11291 0.978146 AGTGGCTCTTATCCTGCGGT 60.978 55.000 0.00 0.00 0.00 5.68
7945 11299 9.000486 GTTTGACTTAAAGTTAGTGGCTCTTAT 58.000 33.333 0.00 0.00 0.00 1.73
7966 11320 2.360801 CCCTTTTGCGAAAGAGGTTTGA 59.639 45.455 25.31 0.00 44.03 2.69


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

AutoCloner maintained by Alex Coulton.