Multiple sequence alignment - TraesCS2D01G435600

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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 TraesCS2D01G435600 chr2D 100.000 6370 0 0 1 6370 546689177 546682808 0.000000e+00 11764.0
1 TraesCS2D01G435600 chr2D 91.882 2550 131 27 987 3520 546815329 546812840 0.000000e+00 3493.0
2 TraesCS2D01G435600 chr2D 90.019 1052 64 19 3561 4608 546812827 546811813 0.000000e+00 1323.0
3 TraesCS2D01G435600 chr2D 95.808 501 21 0 4615 5115 546809035 546808535 0.000000e+00 809.0
4 TraesCS2D01G435600 chr2D 86.258 604 51 16 5776 6370 546734372 546733792 1.510000e-175 627.0
5 TraesCS2D01G435600 chr2D 80.632 759 69 46 5636 6370 546807590 546806886 3.400000e-142 516.0
6 TraesCS2D01G435600 chr2D 86.705 346 26 9 6031 6370 546638363 546638032 3.630000e-97 366.0
7 TraesCS2D01G435600 chr2D 90.558 233 14 6 5114 5345 546808478 546808253 1.040000e-77 302.0
8 TraesCS2D01G435600 chr2D 92.361 144 4 3 5847 5983 546638520 546638377 1.400000e-46 198.0
9 TraesCS2D01G435600 chr2D 85.714 140 14 5 5442 5576 546808242 546808104 6.660000e-30 143.0
10 TraesCS2D01G435600 chr2D 100.000 32 0 0 3532 3563 546685604 546685573 6.900000e-05 60.2
11 TraesCS2D01G435600 chr2D 96.970 33 1 0 5581 5613 546808079 546808047 8.920000e-04 56.5
12 TraesCS2D01G435600 chr2B 95.203 2543 81 11 987 3520 653598260 653595750 0.000000e+00 3982.0
13 TraesCS2D01G435600 chr2B 94.099 1576 66 12 3561 5115 653595737 653594168 0.000000e+00 2370.0
14 TraesCS2D01G435600 chr2B 95.878 558 22 1 399 956 561230603 561230047 0.000000e+00 902.0
15 TraesCS2D01G435600 chr2B 95.389 347 16 0 605 951 496568861 496568515 2.600000e-153 553.0
16 TraesCS2D01G435600 chr2B 94.444 198 11 0 6173 6370 653592888 653592691 8.020000e-79 305.0
17 TraesCS2D01G435600 chr2B 85.043 234 21 7 5114 5345 653594111 653593890 6.430000e-55 226.0
18 TraesCS2D01G435600 chr2B 95.192 104 4 1 192 295 561230706 561230604 5.110000e-36 163.0
19 TraesCS2D01G435600 chr2B 86.429 140 13 5 5442 5576 653593879 653593741 1.430000e-31 148.0
20 TraesCS2D01G435600 chr2B 96.970 33 1 0 5581 5613 653593716 653593684 8.920000e-04 56.5
21 TraesCS2D01G435600 chr2A 91.026 1716 81 26 987 2667 689753790 689755467 0.000000e+00 2248.0
22 TraesCS2D01G435600 chr2A 90.416 1586 93 22 3561 5115 689757747 689759304 0.000000e+00 2032.0
23 TraesCS2D01G435600 chr2A 91.389 871 46 7 2652 3520 689756891 689757734 0.000000e+00 1166.0
24 TraesCS2D01G435600 chr2A 83.957 748 64 29 5639 6370 689760379 689761086 0.000000e+00 665.0
25 TraesCS2D01G435600 chr2A 85.455 605 45 23 5776 6370 689768874 689769445 1.980000e-164 590.0
26 TraesCS2D01G435600 chr2A 83.690 607 64 27 5776 6370 689804177 689804760 2.020000e-149 540.0
27 TraesCS2D01G435600 chr2A 78.049 451 58 17 5119 5544 689759365 689759799 4.930000e-61 246.0
28 TraesCS2D01G435600 chr2A 90.385 52 1 3 5563 5613 689759863 689759911 1.480000e-06 65.8
29 TraesCS2D01G435600 chr1D 95.996 949 36 2 1 949 204268442 204269388 0.000000e+00 1541.0
30 TraesCS2D01G435600 chr1D 95.579 950 42 0 1 950 422174755 422175704 0.000000e+00 1522.0
31 TraesCS2D01G435600 chr3A 95.781 948 40 0 1 948 671356997 671357944 0.000000e+00 1530.0
32 TraesCS2D01G435600 chr3A 80.854 867 106 30 1502 2330 152725029 152724185 1.510000e-175 627.0
33 TraesCS2D01G435600 chr5D 94.277 961 44 4 1 960 42936417 42937367 0.000000e+00 1459.0
34 TraesCS2D01G435600 chr5B 94.142 956 49 2 1 955 472071520 472072469 0.000000e+00 1448.0
35 TraesCS2D01G435600 chr5B 87.681 276 23 2 1644 1909 636520727 636521001 1.720000e-80 311.0
36 TraesCS2D01G435600 chr4D 95.036 826 41 0 126 951 278216502 278215677 0.000000e+00 1299.0
37 TraesCS2D01G435600 chr4D 97.744 133 3 0 1 133 278225268 278225136 4.970000e-56 230.0
38 TraesCS2D01G435600 chr7D 84.642 853 85 23 1496 2330 72328698 72329522 0.000000e+00 808.0
39 TraesCS2D01G435600 chr3D 95.718 397 15 1 558 952 604607879 604607483 6.960000e-179 638.0
40 TraesCS2D01G435600 chr4A 81.110 847 93 32 1502 2330 8930663 8929866 3.260000e-172 616.0
41 TraesCS2D01G435600 chr5A 91.870 369 25 4 6005 6370 377362689 377362323 1.580000e-140 510.0
42 TraesCS2D01G435600 chr4B 83.806 494 45 16 1502 1981 314827615 314827143 2.730000e-118 436.0
43 TraesCS2D01G435600 chr4B 83.813 278 31 3 1642 1909 514540812 514540539 1.060000e-62 252.0
44 TraesCS2D01G435600 chr7B 83.402 482 49 13 1502 1970 349588339 349587876 9.880000e-113 418.0
45 TraesCS2D01G435600 chr7B 87.004 277 25 2 1640 1906 365341523 365341798 1.040000e-77 302.0
46 TraesCS2D01G435600 chr6B 87.097 279 23 6 1642 1909 630113757 630113481 2.890000e-78 303.0
47 TraesCS2D01G435600 chr6B 86.738 279 23 5 1642 1909 630079906 630079631 1.340000e-76 298.0
48 TraesCS2D01G435600 chr6A 88.710 124 14 0 6247 6370 560545014 560544891 1.110000e-32 152.0
49 TraesCS2D01G435600 chr6D 87.903 124 15 0 6247 6370 417888971 417888848 5.150000e-31 147.0


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 TraesCS2D01G435600 chr2D 546682808 546689177 6369 True 5912.100000 11764 100.000000 1 6370 2 chr2D.!!$R3 6369
1 TraesCS2D01G435600 chr2D 546806886 546815329 8443 True 948.928571 3493 90.226143 987 6370 7 chr2D.!!$R4 5383
2 TraesCS2D01G435600 chr2D 546733792 546734372 580 True 627.000000 627 86.258000 5776 6370 1 chr2D.!!$R1 594
3 TraesCS2D01G435600 chr2B 653592691 653598260 5569 True 1181.250000 3982 92.031333 987 6370 6 chr2B.!!$R3 5383
4 TraesCS2D01G435600 chr2B 561230047 561230706 659 True 532.500000 902 95.535000 192 956 2 chr2B.!!$R2 764
5 TraesCS2D01G435600 chr2A 689753790 689761086 7296 False 1070.466667 2248 87.537000 987 6370 6 chr2A.!!$F3 5383
6 TraesCS2D01G435600 chr2A 689768874 689769445 571 False 590.000000 590 85.455000 5776 6370 1 chr2A.!!$F1 594
7 TraesCS2D01G435600 chr2A 689804177 689804760 583 False 540.000000 540 83.690000 5776 6370 1 chr2A.!!$F2 594
8 TraesCS2D01G435600 chr1D 204268442 204269388 946 False 1541.000000 1541 95.996000 1 949 1 chr1D.!!$F1 948
9 TraesCS2D01G435600 chr1D 422174755 422175704 949 False 1522.000000 1522 95.579000 1 950 1 chr1D.!!$F2 949
10 TraesCS2D01G435600 chr3A 671356997 671357944 947 False 1530.000000 1530 95.781000 1 948 1 chr3A.!!$F1 947
11 TraesCS2D01G435600 chr3A 152724185 152725029 844 True 627.000000 627 80.854000 1502 2330 1 chr3A.!!$R1 828
12 TraesCS2D01G435600 chr5D 42936417 42937367 950 False 1459.000000 1459 94.277000 1 960 1 chr5D.!!$F1 959
13 TraesCS2D01G435600 chr5B 472071520 472072469 949 False 1448.000000 1448 94.142000 1 955 1 chr5B.!!$F1 954
14 TraesCS2D01G435600 chr4D 278215677 278216502 825 True 1299.000000 1299 95.036000 126 951 1 chr4D.!!$R1 825
15 TraesCS2D01G435600 chr7D 72328698 72329522 824 False 808.000000 808 84.642000 1496 2330 1 chr7D.!!$F1 834
16 TraesCS2D01G435600 chr4A 8929866 8930663 797 True 616.000000 616 81.110000 1502 2330 1 chr4A.!!$R1 828

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
591 592 0.102481 ATGTACGAGATGTGGACGCC 59.898 55.0 0.0 0.00 0.00 5.68 F
670 671 0.108615 AGCGGAGGTTGAATCAGACG 60.109 55.0 0.0 0.00 27.67 4.18 F
1613 1632 1.329256 GCGAAGGCTAGGATGTAGGA 58.671 55.0 0.0 0.00 35.83 2.94 F
2214 2294 2.628178 TGGACTACTTGTGTGACTCCTG 59.372 50.0 0.0 0.00 0.00 3.86 F
2989 4527 0.395312 GTCCCTCACTTTCCGTGGAA 59.605 55.0 0.0 0.00 43.94 3.53 F
4074 5618 1.089920 CATGTACAGGCTTGACTGGC 58.910 55.0 1.4 1.35 42.75 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2509 1.203112 TGCATCCCAACCAGCCTAAAA 60.203 47.619 0.0 0.0 0.00 1.52 R
2559 2642 4.599241 GCATATATATCAGGGGGTGCCTAT 59.401 45.833 0.0 0.0 0.00 2.57 R
2826 4349 1.200483 CATGACTAAGTACCAGCGCG 58.800 55.000 0.0 0.0 0.00 6.86 R
4212 5756 1.393603 GGCTTCTATCTTGTTGCCCC 58.606 55.000 0.0 0.0 34.81 5.80 R
4534 6080 0.668706 CACAACCACAGGAGAGAGCG 60.669 60.000 0.0 0.0 0.00 5.03 R
5375 9770 0.035439 AATCACCCTAACTGCCCACG 60.035 55.000 0.0 0.0 0.00 4.94 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
59 60 4.796231 GGCGACGCGACACATCCT 62.796 66.667 15.93 0.00 33.63 3.24
432 433 3.363341 GCTAGGCTAGCCGATCATATC 57.637 52.381 31.69 6.59 45.95 1.63
433 434 2.035321 GCTAGGCTAGCCGATCATATCC 59.965 54.545 31.69 6.54 45.95 2.59
591 592 0.102481 ATGTACGAGATGTGGACGCC 59.898 55.000 0.00 0.00 0.00 5.68
593 594 2.042259 TACGAGATGTGGACGCCGT 61.042 57.895 0.00 0.00 0.00 5.68
670 671 0.108615 AGCGGAGGTTGAATCAGACG 60.109 55.000 0.00 0.00 27.67 4.18
967 968 2.496899 AAACTCAGGTATGCCACTGG 57.503 50.000 1.54 0.00 37.19 4.00
1062 1078 2.900528 GTGAAGTCACCACAGACCG 58.099 57.895 0.00 0.00 40.85 4.79
1081 1098 1.565156 GCACAATGCTTCCGACGACA 61.565 55.000 0.00 0.00 40.96 4.35
1366 1383 2.280592 GGGTGCGTCCACGTTTCT 60.281 61.111 0.36 0.00 43.00 2.52
1474 1491 3.459232 TGAAGTGTCTGAGGTTGTGAG 57.541 47.619 0.00 0.00 0.00 3.51
1482 1499 2.103094 TCTGAGGTTGTGAGTTGGTGAG 59.897 50.000 0.00 0.00 0.00 3.51
1487 1504 1.599542 GTTGTGAGTTGGTGAGTGAGC 59.400 52.381 0.00 0.00 0.00 4.26
1489 1506 2.316108 TGTGAGTTGGTGAGTGAGCTA 58.684 47.619 0.00 0.00 0.00 3.32
1504 1521 2.069273 GAGCTACATTCTTGCGTGTGT 58.931 47.619 0.00 0.00 0.00 3.72
1540 1557 2.858260 GCGCAGTGTTTGTTGTTATGCT 60.858 45.455 0.30 0.00 0.00 3.79
1613 1632 1.329256 GCGAAGGCTAGGATGTAGGA 58.671 55.000 0.00 0.00 35.83 2.94
1745 1814 4.151867 CCATGAGATGTGAATGCTATGACG 59.848 45.833 0.00 0.00 0.00 4.35
2117 2192 3.929610 GGAGTTGATCTCTGCTTGTGTAC 59.070 47.826 0.00 0.00 42.40 2.90
2214 2294 2.628178 TGGACTACTTGTGTGACTCCTG 59.372 50.000 0.00 0.00 0.00 3.86
2225 2305 3.508012 GTGTGACTCCTGATACTCTGTGT 59.492 47.826 0.00 0.00 0.00 3.72
2244 2324 7.497595 TCTGTGTACTAGTTTGACTCAACAAT 58.502 34.615 0.00 0.00 0.00 2.71
2247 2327 9.772973 TGTGTACTAGTTTGACTCAACAATATT 57.227 29.630 0.00 0.00 0.00 1.28
2333 2413 8.958119 TCAACTATGAAGAAACATATACCACC 57.042 34.615 0.00 0.00 33.21 4.61
2356 2436 6.457851 CTTTTGCAAGGAAAAATCTGCTAC 57.542 37.500 0.00 0.00 0.00 3.58
2357 2437 5.528043 TTTGCAAGGAAAAATCTGCTACA 57.472 34.783 0.00 0.00 0.00 2.74
2483 2565 7.936496 TTTCATGTGCACCATAGAAAAGATA 57.064 32.000 15.69 0.00 32.55 1.98
2492 2574 6.094048 GCACCATAGAAAAGATAGCAGTTCAA 59.906 38.462 0.00 0.00 0.00 2.69
2559 2642 9.529325 CCTATCGACAATAAAAGAACACATAGA 57.471 33.333 0.00 0.00 0.00 1.98
2826 4349 2.104792 TGCATGGTAGAGTTAGGATGCC 59.895 50.000 0.00 0.00 36.25 4.40
2867 4390 8.811017 TCATGTCCTTTTGCCATTTCTTAAATA 58.189 29.630 0.00 0.00 0.00 1.40
2872 4395 8.646900 TCCTTTTGCCATTTCTTAAATAACACT 58.353 29.630 0.00 0.00 0.00 3.55
2873 4396 9.271828 CCTTTTGCCATTTCTTAAATAACACTT 57.728 29.630 0.00 0.00 0.00 3.16
2923 4446 1.922821 AACCACTGCAGGGTTCTGT 59.077 52.632 25.31 11.02 45.26 3.41
2924 4447 1.136828 AACCACTGCAGGGTTCTGTA 58.863 50.000 25.31 0.00 45.26 2.74
2925 4448 1.362224 ACCACTGCAGGGTTCTGTAT 58.638 50.000 19.93 0.00 42.78 2.29
2926 4449 2.546899 ACCACTGCAGGGTTCTGTATA 58.453 47.619 19.93 0.00 42.78 1.47
2927 4450 2.501723 ACCACTGCAGGGTTCTGTATAG 59.498 50.000 19.93 0.00 42.78 1.31
2928 4451 2.158900 CCACTGCAGGGTTCTGTATAGG 60.159 54.545 19.93 0.00 42.78 2.57
2929 4452 2.119495 ACTGCAGGGTTCTGTATAGGG 58.881 52.381 19.93 0.00 42.78 3.53
2930 4453 2.119495 CTGCAGGGTTCTGTATAGGGT 58.881 52.381 5.57 0.00 42.78 4.34
2931 4454 1.837439 TGCAGGGTTCTGTATAGGGTG 59.163 52.381 0.00 0.00 42.78 4.61
2932 4455 1.838077 GCAGGGTTCTGTATAGGGTGT 59.162 52.381 0.00 0.00 42.78 4.16
2933 4456 2.238898 GCAGGGTTCTGTATAGGGTGTT 59.761 50.000 0.00 0.00 42.78 3.32
2934 4457 3.308188 GCAGGGTTCTGTATAGGGTGTTT 60.308 47.826 0.00 0.00 42.78 2.83
2935 4458 4.080751 GCAGGGTTCTGTATAGGGTGTTTA 60.081 45.833 0.00 0.00 42.78 2.01
2936 4459 5.397559 GCAGGGTTCTGTATAGGGTGTTTAT 60.398 44.000 0.00 0.00 42.78 1.40
2937 4460 6.183361 GCAGGGTTCTGTATAGGGTGTTTATA 60.183 42.308 0.00 0.00 42.78 0.98
2989 4527 0.395312 GTCCCTCACTTTCCGTGGAA 59.605 55.000 0.00 0.00 43.94 3.53
2991 4529 2.235402 GTCCCTCACTTTCCGTGGAATA 59.765 50.000 1.47 0.00 43.94 1.75
3075 4613 2.089350 AGGGCCTTAGGGGTAGAATCAT 60.089 50.000 0.00 0.00 37.43 2.45
3124 4662 8.493607 TGTATGGAGTGATTGAATCCTTGATAA 58.506 33.333 2.26 0.00 34.04 1.75
3170 4708 7.390823 TCTTATACAGTACATTGCACTGGAAA 58.609 34.615 18.84 10.03 46.25 3.13
3172 4710 4.771590 ACAGTACATTGCACTGGAAATG 57.228 40.909 18.84 8.04 46.25 2.32
3226 4765 4.215399 GCACTTAGACCACTGCAATGTTTA 59.785 41.667 0.00 0.00 0.00 2.01
3330 4870 6.255596 GGACAAATCCTAAGTTCAGAAACC 57.744 41.667 0.00 0.00 42.45 3.27
3357 4897 7.713507 TGCGGATTACTTAAGTGTAGCATTATT 59.286 33.333 18.56 0.00 0.00 1.40
3528 5068 9.640952 ACTGGTATACATTGCTTTATGGTAATT 57.359 29.630 5.01 0.00 0.00 1.40
3529 5069 9.897744 CTGGTATACATTGCTTTATGGTAATTG 57.102 33.333 5.01 0.00 0.00 2.32
3530 5070 9.634021 TGGTATACATTGCTTTATGGTAATTGA 57.366 29.630 5.01 0.00 0.00 2.57
3534 5074 7.054491 ACATTGCTTTATGGTAATTGATCCC 57.946 36.000 0.00 0.00 0.00 3.85
3535 5075 6.041979 ACATTGCTTTATGGTAATTGATCCCC 59.958 38.462 0.00 0.00 0.00 4.81
3536 5076 5.136068 TGCTTTATGGTAATTGATCCCCA 57.864 39.130 0.00 0.00 0.00 4.96
3537 5077 5.523588 TGCTTTATGGTAATTGATCCCCAA 58.476 37.500 0.00 0.00 39.41 4.12
3538 5078 5.960811 TGCTTTATGGTAATTGATCCCCAAA 59.039 36.000 0.00 0.00 38.43 3.28
3539 5079 6.614906 TGCTTTATGGTAATTGATCCCCAAAT 59.385 34.615 0.00 0.00 38.43 2.32
3540 5080 7.786943 TGCTTTATGGTAATTGATCCCCAAATA 59.213 33.333 0.00 0.00 38.43 1.40
3541 5081 8.088365 GCTTTATGGTAATTGATCCCCAAATAC 58.912 37.037 0.00 0.00 39.34 1.89
3548 5088 6.950860 AATTGATCCCCAAATACCAAAAGT 57.049 33.333 0.00 0.00 38.43 2.66
3549 5089 6.950860 ATTGATCCCCAAATACCAAAAGTT 57.049 33.333 0.00 0.00 38.43 2.66
3550 5090 5.993748 TGATCCCCAAATACCAAAAGTTC 57.006 39.130 0.00 0.00 0.00 3.01
3551 5091 4.775253 TGATCCCCAAATACCAAAAGTTCC 59.225 41.667 0.00 0.00 0.00 3.62
3552 5092 3.158676 TCCCCAAATACCAAAAGTTCCG 58.841 45.455 0.00 0.00 0.00 4.30
3553 5093 2.894765 CCCCAAATACCAAAAGTTCCGT 59.105 45.455 0.00 0.00 0.00 4.69
3554 5094 3.057104 CCCCAAATACCAAAAGTTCCGTC 60.057 47.826 0.00 0.00 0.00 4.79
3555 5095 3.570550 CCCAAATACCAAAAGTTCCGTCA 59.429 43.478 0.00 0.00 0.00 4.35
3556 5096 4.320935 CCCAAATACCAAAAGTTCCGTCAG 60.321 45.833 0.00 0.00 0.00 3.51
3557 5097 4.517453 CCAAATACCAAAAGTTCCGTCAGA 59.483 41.667 0.00 0.00 0.00 3.27
3558 5098 5.009210 CCAAATACCAAAAGTTCCGTCAGAA 59.991 40.000 0.00 0.00 0.00 3.02
3559 5099 6.460399 CCAAATACCAAAAGTTCCGTCAGAAA 60.460 38.462 0.00 0.00 35.85 2.52
3594 5134 3.158676 TCCCCAAATACCAAAAGTTCCG 58.841 45.455 0.00 0.00 0.00 4.30
3700 5240 7.976414 AATTGATCCCAACTTCATATGGAAA 57.024 32.000 2.13 0.00 39.12 3.13
3764 5306 3.322191 TTGGGGTTTCTAGCCAAAGTT 57.678 42.857 0.00 0.00 43.97 2.66
3829 5371 1.899814 TCACGCCATCTTAACCTCTGT 59.100 47.619 0.00 0.00 0.00 3.41
3862 5405 7.761409 TCATAATGAAACCAGCATTTACAGTC 58.239 34.615 0.00 0.00 37.22 3.51
3865 5408 4.072131 TGAAACCAGCATTTACAGTCCTC 58.928 43.478 0.00 0.00 0.00 3.71
4074 5618 1.089920 CATGTACAGGCTTGACTGGC 58.910 55.000 1.40 1.35 42.75 4.85
4128 5672 5.569413 CACGAACACAAGGGAAATATAAGC 58.431 41.667 0.00 0.00 0.00 3.09
4212 5756 1.686355 TGTGCAAAGGTAACCCACAG 58.314 50.000 0.00 0.00 33.07 3.66
4263 5807 1.264749 ACCATAGAGCCCGTGAAGCA 61.265 55.000 0.00 0.00 0.00 3.91
4300 5844 3.876914 TGAACGCCCTATTGATGTTGATC 59.123 43.478 0.00 0.00 0.00 2.92
4319 5863 2.392613 CTTTGCCCTGTGTGTGCGAC 62.393 60.000 0.00 0.00 0.00 5.19
4324 5868 3.394874 CTGTGTGTGCGACCGTCG 61.395 66.667 16.72 16.72 43.89 5.12
4387 5931 5.397334 GCAACCTCTGATCCTCTAAATTCCT 60.397 44.000 0.00 0.00 0.00 3.36
4436 5982 7.615757 AGCCTTAGCAGTTTATTGGACTAATTT 59.384 33.333 0.00 0.00 43.56 1.82
4458 6004 6.469782 TTTCATTGCTTGATTCCTTATCCC 57.530 37.500 0.00 0.00 33.34 3.85
4495 6041 7.758076 TCAAGATTCATCTTTGATTTGTGATGC 59.242 33.333 0.00 0.00 44.28 3.91
4497 6043 7.481642 AGATTCATCTTTGATTTGTGATGCTC 58.518 34.615 0.00 0.00 37.00 4.26
4530 6076 2.564504 TGCTCATAGATATTGCTCGCCT 59.435 45.455 0.00 0.00 0.00 5.52
4534 6080 5.390356 GCTCATAGATATTGCTCGCCTTTTC 60.390 44.000 0.00 0.00 0.00 2.29
4575 6121 4.102524 TGGAACAACTGACTAGGTCATGTT 59.897 41.667 15.13 15.13 43.71 2.71
4576 6122 5.305902 TGGAACAACTGACTAGGTCATGTTA 59.694 40.000 15.17 3.90 42.21 2.41
4608 6154 2.907458 AGCCTTTTAAGTGATGGCCT 57.093 45.000 3.32 0.00 44.19 5.19
4610 6156 3.510459 AGCCTTTTAAGTGATGGCCTTT 58.490 40.909 3.32 0.00 44.19 3.11
4611 6157 3.903714 AGCCTTTTAAGTGATGGCCTTTT 59.096 39.130 3.32 0.00 44.19 2.27
4613 6159 5.542251 AGCCTTTTAAGTGATGGCCTTTTAA 59.458 36.000 3.32 0.00 44.19 1.52
4617 8934 3.825908 AAGTGATGGCCTTTTAAGGGA 57.174 42.857 3.32 0.00 46.56 4.20
4701 9018 4.040217 TGCAAACATTTAGGCATCCTTGTT 59.960 37.500 0.00 0.00 34.69 2.83
4834 9152 3.600388 GCTGCTACTTCTGCTTTCCTAA 58.400 45.455 0.00 0.00 0.00 2.69
4857 9175 1.769733 CGAAAAATGTGGTGGCTGTG 58.230 50.000 0.00 0.00 0.00 3.66
4880 9198 2.417239 CAGCTCGGAGGATATAGTCGAC 59.583 54.545 7.70 7.70 0.00 4.20
4923 9241 4.406456 TCTTATGTGCTTGGATTGTTGGT 58.594 39.130 0.00 0.00 0.00 3.67
4966 9284 0.676466 TGCAATCGGCCTTACTGTGG 60.676 55.000 0.00 0.00 43.89 4.17
5035 9353 3.741476 CCAGCGTTGCAAGGAGCC 61.741 66.667 22.64 5.30 44.83 4.70
5117 9493 6.554334 TCTGTAACTGCAAATACTTGAACC 57.446 37.500 9.28 0.00 34.14 3.62
5154 9530 7.518848 GCTGAACGTATCATGATGCTGAATTAA 60.519 37.037 18.72 2.02 37.44 1.40
5163 9539 8.620116 TCATGATGCTGAATTAATATTCCGAA 57.380 30.769 0.00 0.00 39.56 4.30
5174 9550 4.918810 AATATTCCGAAGCCCATCAAAC 57.081 40.909 0.00 0.00 0.00 2.93
5188 9564 1.798725 CAAACGAAGCGGCTGCATG 60.799 57.895 21.93 11.21 46.23 4.06
5222 9598 3.813166 CGTCCAAGTGGTTGTATCAGTTT 59.187 43.478 0.00 0.00 36.34 2.66
5246 9639 1.202927 AGTCCAATGGTCACAACTGGG 60.203 52.381 0.00 0.00 35.44 4.45
5263 9656 0.530288 GGGCGCCTTAATTTTGCAGA 59.470 50.000 28.56 0.00 0.00 4.26
5345 9740 7.175641 ACTGAGTATTTAGCCATTGGAATATGC 59.824 37.037 6.95 0.00 0.00 3.14
5353 9748 3.556213 GCCATTGGAATATGCATGCACAT 60.556 43.478 25.37 15.63 0.00 3.21
5373 9768 3.631145 TGTGCATCAAGTTTCAGAAGC 57.369 42.857 0.00 0.00 0.00 3.86
5375 9770 3.251729 TGTGCATCAAGTTTCAGAAGCTC 59.748 43.478 0.00 0.00 30.45 4.09
5376 9771 2.481568 TGCATCAAGTTTCAGAAGCTCG 59.518 45.455 0.00 0.00 30.45 5.03
5377 9772 2.481952 GCATCAAGTTTCAGAAGCTCGT 59.518 45.455 0.00 0.00 0.00 4.18
5378 9773 3.666374 GCATCAAGTTTCAGAAGCTCGTG 60.666 47.826 0.00 0.00 0.00 4.35
5380 9775 1.532868 CAAGTTTCAGAAGCTCGTGGG 59.467 52.381 0.00 0.00 0.00 4.61
5381 9776 0.603975 AGTTTCAGAAGCTCGTGGGC 60.604 55.000 0.00 0.00 0.00 5.36
5383 9778 0.603707 TTTCAGAAGCTCGTGGGCAG 60.604 55.000 0.00 0.00 34.17 4.85
5385 9780 1.302033 CAGAAGCTCGTGGGCAGTT 60.302 57.895 0.00 0.00 34.17 3.16
5387 9782 0.247736 AGAAGCTCGTGGGCAGTTAG 59.752 55.000 0.00 0.00 34.17 2.34
5388 9783 0.741221 GAAGCTCGTGGGCAGTTAGG 60.741 60.000 0.00 0.00 34.17 2.69
5389 9784 2.125106 GCTCGTGGGCAGTTAGGG 60.125 66.667 0.00 0.00 0.00 3.53
5390 9785 2.955881 GCTCGTGGGCAGTTAGGGT 61.956 63.158 0.00 0.00 0.00 4.34
5394 9789 0.035439 CGTGGGCAGTTAGGGTGATT 60.035 55.000 0.00 0.00 0.00 2.57
5395 9790 1.208535 CGTGGGCAGTTAGGGTGATTA 59.791 52.381 0.00 0.00 0.00 1.75
5397 9792 3.014623 GTGGGCAGTTAGGGTGATTAAC 58.985 50.000 0.00 0.00 0.00 2.01
5398 9793 2.916934 TGGGCAGTTAGGGTGATTAACT 59.083 45.455 0.00 0.00 40.91 2.24
5400 9795 3.694566 GGGCAGTTAGGGTGATTAACTTG 59.305 47.826 0.00 0.00 38.85 3.16
5401 9796 4.332828 GGCAGTTAGGGTGATTAACTTGT 58.667 43.478 0.00 0.00 38.85 3.16
5402 9797 4.395231 GGCAGTTAGGGTGATTAACTTGTC 59.605 45.833 0.00 0.00 38.85 3.18
5403 9798 5.246307 GCAGTTAGGGTGATTAACTTGTCT 58.754 41.667 0.00 0.00 38.85 3.41
5404 9799 6.403878 GCAGTTAGGGTGATTAACTTGTCTA 58.596 40.000 0.00 0.00 38.85 2.59
5405 9800 6.313164 GCAGTTAGGGTGATTAACTTGTCTAC 59.687 42.308 0.00 0.00 38.85 2.59
5406 9801 6.530534 CAGTTAGGGTGATTAACTTGTCTACG 59.469 42.308 0.00 0.00 38.85 3.51
5407 9802 6.435277 AGTTAGGGTGATTAACTTGTCTACGA 59.565 38.462 0.00 0.00 37.95 3.43
5428 9823 4.083643 CGAACGGTACTTAGACTTGTCTCA 60.084 45.833 6.55 0.00 0.00 3.27
5433 9828 5.344884 GGTACTTAGACTTGTCTCATGAGC 58.655 45.833 18.36 13.24 0.00 4.26
5434 9829 4.464069 ACTTAGACTTGTCTCATGAGCC 57.536 45.455 18.36 7.43 0.00 4.70
5435 9830 4.093011 ACTTAGACTTGTCTCATGAGCCT 58.907 43.478 18.36 9.59 0.00 4.58
5438 9833 2.636893 AGACTTGTCTCATGAGCCTGTT 59.363 45.455 18.36 1.81 0.00 3.16
5440 9835 4.469227 AGACTTGTCTCATGAGCCTGTTAT 59.531 41.667 18.36 0.00 0.00 1.89
5471 9870 4.457949 CACTACAATTGTGGTTAGGGTTCC 59.542 45.833 23.37 0.00 37.67 3.62
5484 9883 0.539669 GGGTTCCAAAGGACCACCAG 60.540 60.000 8.69 0.00 35.03 4.00
5500 9899 4.514066 ACCACCAGTCTACAAATTTTCGTC 59.486 41.667 0.00 0.00 0.00 4.20
5544 9946 1.761244 CGAACAGCTCGTGTGCACAA 61.761 55.000 23.59 6.00 42.89 3.33
5546 9948 0.588252 AACAGCTCGTGTGCACAATC 59.412 50.000 23.59 9.45 40.26 2.67
5547 9949 1.131218 CAGCTCGTGTGCACAATCG 59.869 57.895 23.59 21.68 34.99 3.34
5548 9950 2.202222 GCTCGTGTGCACAATCGC 60.202 61.111 23.59 19.20 0.00 4.58
5549 9951 2.476051 CTCGTGTGCACAATCGCC 59.524 61.111 23.59 7.80 0.00 5.54
5552 9959 3.047280 GTGTGCACAATCGCCGGA 61.047 61.111 23.59 0.00 0.00 5.14
5554 9961 4.166011 GTGCACAATCGCCGGAGC 62.166 66.667 13.17 0.00 0.00 4.70
5566 9992 1.078143 CCGGAGCCAAAGAAGGAGG 60.078 63.158 0.00 0.00 0.00 4.30
5572 9998 1.881903 GCCAAAGAAGGAGGCTTGCC 61.882 60.000 2.97 2.97 44.92 4.52
5576 10021 4.035102 GAAGGAGGCTTGCCGGGT 62.035 66.667 2.18 0.00 0.00 5.28
5635 10105 2.797837 GCATTAGCTGCCCACATGA 58.202 52.632 0.00 0.00 45.66 3.07
5637 10107 0.659427 CATTAGCTGCCCACATGACG 59.341 55.000 0.00 0.00 0.00 4.35
5638 10108 1.097547 ATTAGCTGCCCACATGACGC 61.098 55.000 0.00 0.00 0.00 5.19
5639 10109 2.462125 TTAGCTGCCCACATGACGCA 62.462 55.000 0.00 2.68 0.00 5.24
5722 10684 0.528466 TGTCGCGATTGATCAGGAGC 60.528 55.000 14.06 1.94 0.00 4.70
5723 10685 1.068083 TCGCGATTGATCAGGAGCC 59.932 57.895 3.71 0.00 0.00 4.70
5740 10702 3.124921 CCGACGTGGTGGGATTGC 61.125 66.667 0.00 0.00 33.13 3.56
5741 10703 2.358125 CGACGTGGTGGGATTGCA 60.358 61.111 0.00 0.00 0.00 4.08
5742 10704 2.390599 CGACGTGGTGGGATTGCAG 61.391 63.158 0.00 0.00 0.00 4.41
5743 10705 2.034066 ACGTGGTGGGATTGCAGG 59.966 61.111 0.00 0.00 0.00 4.85
5744 10706 3.443045 CGTGGTGGGATTGCAGGC 61.443 66.667 0.00 0.00 0.00 4.85
5745 10707 2.036256 GTGGTGGGATTGCAGGCT 59.964 61.111 0.00 0.00 0.00 4.58
5761 10723 4.531912 CTTGCAGCGCGCCTCATG 62.532 66.667 30.33 20.85 41.33 3.07
5774 10736 3.144120 CTCATGGAGGAGCCCGACG 62.144 68.421 0.00 0.00 34.97 5.12
5821 10786 9.593134 ACAAACAGCAAAGTACATATTTTGAAA 57.407 25.926 10.16 0.00 35.65 2.69
5961 10946 1.155042 CCAGAGCTGCTTCAACAGTC 58.845 55.000 2.53 0.00 39.96 3.51
5983 10978 4.443063 TCAACATCGTCTTGAAACGTACTG 59.557 41.667 0.00 0.00 43.08 2.74
5985 10980 2.787601 TCGTCTTGAAACGTACTGCT 57.212 45.000 0.00 0.00 43.08 4.24
5986 10981 3.088194 TCGTCTTGAAACGTACTGCTT 57.912 42.857 0.00 0.00 43.08 3.91
5988 10983 2.792674 CGTCTTGAAACGTACTGCTTGA 59.207 45.455 0.00 0.00 37.86 3.02
5989 10984 3.361724 CGTCTTGAAACGTACTGCTTGAC 60.362 47.826 0.00 0.00 37.86 3.18
5990 10985 2.792674 TCTTGAAACGTACTGCTTGACG 59.207 45.455 0.00 3.78 44.57 4.35
5991 10986 2.495409 TGAAACGTACTGCTTGACGA 57.505 45.000 10.97 0.00 41.60 4.20
5992 10987 3.021269 TGAAACGTACTGCTTGACGAT 57.979 42.857 10.97 0.00 41.60 3.73
6089 11089 1.024579 GCCCACACTACAATCCGGTG 61.025 60.000 0.00 0.00 37.05 4.94
6143 11163 3.784701 AGCTTATCACGTCGATGAAGT 57.215 42.857 12.58 0.00 35.39 3.01
6222 11249 2.742372 CTTGGCTTGGTACGCGCT 60.742 61.111 5.73 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 2.128507 CAGCTACCGGGAGTCCCTC 61.129 68.421 26.04 9.50 42.67 4.30
419 420 3.081710 TCTTCCGGATATGATCGGCTA 57.918 47.619 4.15 0.00 45.31 3.93
432 433 1.089920 CATGAACAGGCTTCTTCCGG 58.910 55.000 0.00 0.00 0.00 5.14
433 434 1.734465 GTCATGAACAGGCTTCTTCCG 59.266 52.381 0.00 0.00 0.00 4.30
591 592 5.756950 TTCGTATAGCAAGAAGTTCAACG 57.243 39.130 5.50 3.73 0.00 4.10
593 594 6.876789 TCCATTTCGTATAGCAAGAAGTTCAA 59.123 34.615 5.50 0.00 0.00 2.69
688 689 8.327941 TGATAATTATCCATTAGCTGAACTGC 57.672 34.615 20.29 0.00 35.16 4.40
851 852 5.489792 GATGATAGCATCCCAGGAACTAA 57.510 43.478 9.91 0.00 44.12 2.24
878 879 9.294030 CATTTACAAGATGGTGAGAAATAAAGC 57.706 33.333 0.00 0.00 0.00 3.51
982 983 6.707608 GGCAGAAGAGGAAATCAAATGTTTTT 59.292 34.615 0.00 0.00 0.00 1.94
983 984 6.226052 GGCAGAAGAGGAAATCAAATGTTTT 58.774 36.000 0.00 0.00 0.00 2.43
984 985 5.565439 CGGCAGAAGAGGAAATCAAATGTTT 60.565 40.000 0.00 0.00 0.00 2.83
985 986 4.082571 CGGCAGAAGAGGAAATCAAATGTT 60.083 41.667 0.00 0.00 0.00 2.71
1062 1078 1.132640 GTCGTCGGAAGCATTGTGC 59.867 57.895 0.00 0.00 45.46 4.57
1280 1297 0.252284 AGGAGGACTTGGTCGGTCAT 60.252 55.000 0.00 0.00 35.61 3.06
1474 1491 3.931578 AGAATGTAGCTCACTCACCAAC 58.068 45.455 0.00 0.00 0.00 3.77
1482 1499 2.069273 ACACGCAAGAATGTAGCTCAC 58.931 47.619 0.00 0.00 43.62 3.51
1489 1506 2.058798 CGACTACACACGCAAGAATGT 58.941 47.619 0.00 0.00 40.83 2.71
1540 1557 1.228276 TATGCAACCACCACGCCAA 60.228 52.632 0.00 0.00 0.00 4.52
1718 1787 2.029623 GCATTCACATCTCATGGCCTT 58.970 47.619 3.32 0.00 33.60 4.35
1745 1814 4.510340 ACATCGACCGGCAATAGTTTATTC 59.490 41.667 0.00 0.00 0.00 1.75
1927 1996 5.958380 ACCTATTGTATCACTGAGGACAAGA 59.042 40.000 12.48 8.63 35.41 3.02
2000 2075 8.208903 GTCCTTGCCCAGTTTAGATAAAGTATA 58.791 37.037 0.00 0.00 0.00 1.47
2001 2076 7.054751 GTCCTTGCCCAGTTTAGATAAAGTAT 58.945 38.462 0.00 0.00 0.00 2.12
2117 2192 4.093115 GCTTGATGAGTCTGATCACAACTG 59.907 45.833 10.08 0.00 29.39 3.16
2214 2294 8.041829 TGAGTCAAACTAGTACACAGAGTATC 57.958 38.462 0.00 0.00 34.67 2.24
2325 2405 6.732896 TTTTTCCTTGCAAAAGGTGGTATA 57.267 33.333 0.00 0.00 40.81 1.47
2333 2413 5.984926 TGTAGCAGATTTTTCCTTGCAAAAG 59.015 36.000 0.00 0.00 0.00 2.27
2346 2426 6.636705 TCGTACCAGTAAATGTAGCAGATTT 58.363 36.000 0.00 0.00 0.00 2.17
2349 2429 5.184479 AGTTCGTACCAGTAAATGTAGCAGA 59.816 40.000 0.00 0.00 0.00 4.26
2350 2430 5.408356 AGTTCGTACCAGTAAATGTAGCAG 58.592 41.667 0.00 0.00 0.00 4.24
2351 2431 5.395682 AGTTCGTACCAGTAAATGTAGCA 57.604 39.130 0.00 0.00 0.00 3.49
2352 2432 5.063060 CCAAGTTCGTACCAGTAAATGTAGC 59.937 44.000 0.00 0.00 0.00 3.58
2353 2433 6.309737 GTCCAAGTTCGTACCAGTAAATGTAG 59.690 42.308 0.00 0.00 0.00 2.74
2354 2434 6.158598 GTCCAAGTTCGTACCAGTAAATGTA 58.841 40.000 0.00 0.00 0.00 2.29
2355 2435 4.992951 GTCCAAGTTCGTACCAGTAAATGT 59.007 41.667 0.00 0.00 0.00 2.71
2356 2436 4.090930 CGTCCAAGTTCGTACCAGTAAATG 59.909 45.833 0.00 0.00 0.00 2.32
2357 2437 4.240096 CGTCCAAGTTCGTACCAGTAAAT 58.760 43.478 0.00 0.00 0.00 1.40
2427 2509 1.203112 TGCATCCCAACCAGCCTAAAA 60.203 47.619 0.00 0.00 0.00 1.52
2492 2574 8.532977 AGCGCAAGTAAAAACAATTAATCAAT 57.467 26.923 11.47 0.00 41.68 2.57
2559 2642 4.599241 GCATATATATCAGGGGGTGCCTAT 59.401 45.833 0.00 0.00 0.00 2.57
2826 4349 1.200483 CATGACTAAGTACCAGCGCG 58.800 55.000 0.00 0.00 0.00 6.86
2872 4395 5.342433 CAGCTGTTTCACAACAATGAAGAA 58.658 37.500 5.25 0.00 42.53 2.52
2873 4396 4.734402 GCAGCTGTTTCACAACAATGAAGA 60.734 41.667 16.64 0.00 42.53 2.87
2907 4430 2.158900 CCTATACAGAACCCTGCAGTGG 60.159 54.545 13.81 15.65 44.16 4.00
2926 4449 9.664777 TGTAACCTCACTATATATAAACACCCT 57.335 33.333 0.00 0.00 0.00 4.34
2927 4450 9.924650 CTGTAACCTCACTATATATAAACACCC 57.075 37.037 0.00 0.00 0.00 4.61
2935 4458 9.830186 AACCAGATCTGTAACCTCACTATATAT 57.170 33.333 21.11 0.00 0.00 0.86
2936 4459 9.078990 CAACCAGATCTGTAACCTCACTATATA 57.921 37.037 21.11 0.00 0.00 0.86
2937 4460 7.015682 CCAACCAGATCTGTAACCTCACTATAT 59.984 40.741 21.11 0.00 0.00 0.86
3177 4715 7.222000 ACCGAAATTTGTAGCCAAGAATAAA 57.778 32.000 0.00 0.00 0.00 1.40
3330 4870 4.430007 TGCTACACTTAAGTAATCCGCAG 58.570 43.478 8.04 0.00 0.00 5.18
3357 4897 4.871871 TGCTAATTTTACCCCTGGATCA 57.128 40.909 0.00 0.00 0.00 2.92
3523 5063 7.847096 ACTTTTGGTATTTGGGGATCAATTAC 58.153 34.615 0.00 0.00 39.55 1.89
3525 5065 6.950860 ACTTTTGGTATTTGGGGATCAATT 57.049 33.333 0.00 0.00 34.98 2.32
3526 5066 6.070251 GGAACTTTTGGTATTTGGGGATCAAT 60.070 38.462 0.00 0.00 34.98 2.57
3527 5067 5.247337 GGAACTTTTGGTATTTGGGGATCAA 59.753 40.000 0.00 0.00 0.00 2.57
3528 5068 4.775253 GGAACTTTTGGTATTTGGGGATCA 59.225 41.667 0.00 0.00 0.00 2.92
3529 5069 4.142249 CGGAACTTTTGGTATTTGGGGATC 60.142 45.833 0.00 0.00 0.00 3.36
3530 5070 3.767131 CGGAACTTTTGGTATTTGGGGAT 59.233 43.478 0.00 0.00 0.00 3.85
3531 5071 3.158676 CGGAACTTTTGGTATTTGGGGA 58.841 45.455 0.00 0.00 0.00 4.81
3532 5072 2.894765 ACGGAACTTTTGGTATTTGGGG 59.105 45.455 0.00 0.00 0.00 4.96
3533 5073 3.570550 TGACGGAACTTTTGGTATTTGGG 59.429 43.478 0.00 0.00 0.00 4.12
3534 5074 4.517453 TCTGACGGAACTTTTGGTATTTGG 59.483 41.667 0.00 0.00 0.00 3.28
3535 5075 5.682943 TCTGACGGAACTTTTGGTATTTG 57.317 39.130 0.00 0.00 0.00 2.32
3536 5076 6.702716 TTTCTGACGGAACTTTTGGTATTT 57.297 33.333 0.00 0.00 33.13 1.40
3537 5077 6.702716 TTTTCTGACGGAACTTTTGGTATT 57.297 33.333 0.00 0.00 33.13 1.89
3538 5078 6.702716 TTTTTCTGACGGAACTTTTGGTAT 57.297 33.333 0.00 0.00 33.13 2.73
3558 5098 3.306472 TGGGGAGTGCTTACAGTTTTT 57.694 42.857 0.00 0.00 0.00 1.94
3559 5099 3.306472 TTGGGGAGTGCTTACAGTTTT 57.694 42.857 0.00 0.00 0.00 2.43
3604 5144 2.441001 CCCAGCATGTCTAGGGAGAATT 59.559 50.000 13.97 0.00 44.30 2.17
3629 5169 7.446769 TGCTCCACATTAGTAACTCAAAACTA 58.553 34.615 0.00 0.00 0.00 2.24
3700 5240 5.487433 GGCAAATAAACAAGCCCATTAGTT 58.513 37.500 0.00 0.00 41.25 2.24
3862 5405 7.572523 TTATCAATCAAGCAAACATAGGAGG 57.427 36.000 0.00 0.00 0.00 4.30
3865 5408 9.590451 ACAAATTATCAATCAAGCAAACATAGG 57.410 29.630 0.00 0.00 0.00 2.57
4074 5618 1.892474 ACAATTTTGACCACCCCATCG 59.108 47.619 0.00 0.00 0.00 3.84
4212 5756 1.393603 GGCTTCTATCTTGTTGCCCC 58.606 55.000 0.00 0.00 34.81 5.80
4263 5807 2.226437 GCGTTCATCATTGGTGTTCAGT 59.774 45.455 0.00 0.00 0.00 3.41
4319 5863 3.353836 CAAACACAGGCCCGACGG 61.354 66.667 6.99 6.99 0.00 4.79
4324 5868 1.199097 CGTACAATCAAACACAGGCCC 59.801 52.381 0.00 0.00 0.00 5.80
4436 5982 4.895297 GGGGATAAGGAATCAAGCAATGAA 59.105 41.667 0.00 0.00 42.54 2.57
4458 6004 5.916318 AGATGAATCTTGAACTAGCAGAGG 58.084 41.667 0.00 0.00 31.97 3.69
4495 6041 2.808523 TGAGCACTGACTCTTGTGAG 57.191 50.000 0.00 0.00 45.43 3.51
4497 6043 4.446994 TCTATGAGCACTGACTCTTGTG 57.553 45.455 0.00 0.00 37.58 3.33
4530 6076 1.048601 ACCACAGGAGAGAGCGAAAA 58.951 50.000 0.00 0.00 0.00 2.29
4534 6080 0.668706 CACAACCACAGGAGAGAGCG 60.669 60.000 0.00 0.00 0.00 5.03
4608 6154 7.595819 AGTTGATTTCATGTGTCCCTTAAAA 57.404 32.000 0.00 0.00 0.00 1.52
4610 6156 7.942341 ACTAAGTTGATTTCATGTGTCCCTTAA 59.058 33.333 0.00 0.00 0.00 1.85
4611 6157 7.458397 ACTAAGTTGATTTCATGTGTCCCTTA 58.542 34.615 0.00 0.04 0.00 2.69
4613 6159 5.880901 ACTAAGTTGATTTCATGTGTCCCT 58.119 37.500 0.00 0.00 0.00 4.20
4617 8934 7.807977 ACAGAACTAAGTTGATTTCATGTGT 57.192 32.000 0.00 0.00 0.00 3.72
4647 8964 4.380531 TCTCGAGACAAGAGCAACAAAAT 58.619 39.130 12.08 0.00 35.79 1.82
4701 9018 7.660208 GGTCAAAGTCATTAGACCTGTAGAAAA 59.340 37.037 0.00 0.00 46.15 2.29
4834 9152 1.344114 AGCCACCACATTTTTCGCATT 59.656 42.857 0.00 0.00 0.00 3.56
4857 9175 2.417239 CGACTATATCCTCCGAGCTGAC 59.583 54.545 0.00 0.00 0.00 3.51
4862 9180 1.394227 GCGTCGACTATATCCTCCGAG 59.606 57.143 14.70 0.00 0.00 4.63
4863 9181 1.001746 AGCGTCGACTATATCCTCCGA 59.998 52.381 14.70 0.00 0.00 4.55
4880 9198 2.071540 TCTGAACAAGCAAGATCAGCG 58.928 47.619 9.76 0.00 38.05 5.18
4923 9241 2.290387 TGCTGCATTTAGGGACCGTAAA 60.290 45.455 18.96 18.96 0.00 2.01
4966 9284 4.186159 CACCATCAAATTTTCATGCCTCC 58.814 43.478 0.00 0.00 0.00 4.30
5117 9493 5.637809 TGATACGTTCAGCTAGTGTTGTAG 58.362 41.667 0.00 0.00 0.00 2.74
5154 9530 2.878406 CGTTTGATGGGCTTCGGAATAT 59.122 45.455 0.00 0.00 0.00 1.28
5158 9534 0.035598 TTCGTTTGATGGGCTTCGGA 59.964 50.000 0.00 0.00 0.00 4.55
5163 9539 2.040544 CCGCTTCGTTTGATGGGCT 61.041 57.895 0.00 0.00 32.76 5.19
5174 9550 1.512734 GAAACATGCAGCCGCTTCG 60.513 57.895 0.00 0.00 39.64 3.79
5222 9598 2.172505 AGTTGTGACCATTGGACTGTCA 59.827 45.455 10.37 0.00 36.71 3.58
5246 9639 2.346099 TGTCTGCAAAATTAAGGCGC 57.654 45.000 0.00 0.00 0.00 6.53
5312 9706 7.933577 CCAATGGCTAAATACTCAGTGAAGATA 59.066 37.037 0.00 0.00 0.00 1.98
5325 9719 6.210984 TGCATGCATATTCCAATGGCTAAATA 59.789 34.615 18.46 0.00 0.00 1.40
5353 9748 3.216800 AGCTTCTGAAACTTGATGCACA 58.783 40.909 0.00 0.00 36.30 4.57
5369 9764 0.741221 CCTAACTGCCCACGAGCTTC 60.741 60.000 0.00 0.00 0.00 3.86
5373 9768 1.079127 CACCCTAACTGCCCACGAG 60.079 63.158 0.00 0.00 0.00 4.18
5375 9770 0.035439 AATCACCCTAACTGCCCACG 60.035 55.000 0.00 0.00 0.00 4.94
5376 9771 3.014623 GTTAATCACCCTAACTGCCCAC 58.985 50.000 0.00 0.00 0.00 4.61
5377 9772 2.916934 AGTTAATCACCCTAACTGCCCA 59.083 45.455 0.00 0.00 38.02 5.36
5378 9773 3.646736 AGTTAATCACCCTAACTGCCC 57.353 47.619 0.00 0.00 38.02 5.36
5380 9775 5.246307 AGACAAGTTAATCACCCTAACTGC 58.754 41.667 0.00 0.00 39.11 4.40
5381 9776 6.530534 CGTAGACAAGTTAATCACCCTAACTG 59.469 42.308 0.00 0.00 39.11 3.16
5383 9778 6.624423 TCGTAGACAAGTTAATCACCCTAAC 58.376 40.000 0.00 0.00 0.00 2.34
5385 9780 6.623549 CGTTCGTAGACAAGTTAATCACCCTA 60.624 42.308 0.00 0.00 34.32 3.53
5387 9782 4.325472 CGTTCGTAGACAAGTTAATCACCC 59.675 45.833 0.00 0.00 34.32 4.61
5388 9783 4.325472 CCGTTCGTAGACAAGTTAATCACC 59.675 45.833 0.00 0.00 34.32 4.02
5389 9784 4.919754 ACCGTTCGTAGACAAGTTAATCAC 59.080 41.667 0.00 0.00 34.32 3.06
5390 9785 5.125100 ACCGTTCGTAGACAAGTTAATCA 57.875 39.130 0.00 0.00 34.32 2.57
5394 9789 5.689383 AAGTACCGTTCGTAGACAAGTTA 57.311 39.130 0.00 0.00 34.32 2.24
5395 9790 4.574599 AAGTACCGTTCGTAGACAAGTT 57.425 40.909 0.00 0.00 34.32 2.66
5397 9792 5.121454 AGTCTAAGTACCGTTCGTAGACAAG 59.879 44.000 23.26 0.76 43.72 3.16
5398 9793 4.997395 AGTCTAAGTACCGTTCGTAGACAA 59.003 41.667 23.26 0.00 43.72 3.18
5400 9795 5.106908 ACAAGTCTAAGTACCGTTCGTAGAC 60.107 44.000 17.59 17.59 42.60 2.59
5401 9796 4.997395 ACAAGTCTAAGTACCGTTCGTAGA 59.003 41.667 0.00 0.00 0.00 2.59
5402 9797 5.121454 AGACAAGTCTAAGTACCGTTCGTAG 59.879 44.000 0.00 0.00 38.35 3.51
5403 9798 4.997395 AGACAAGTCTAAGTACCGTTCGTA 59.003 41.667 0.00 0.00 38.35 3.43
5404 9799 3.817647 AGACAAGTCTAAGTACCGTTCGT 59.182 43.478 0.00 0.00 38.35 3.85
5405 9800 4.083643 TGAGACAAGTCTAAGTACCGTTCG 60.084 45.833 2.15 0.00 40.61 3.95
5406 9801 5.368256 TGAGACAAGTCTAAGTACCGTTC 57.632 43.478 2.15 0.00 40.61 3.95
5407 9802 5.475909 TCATGAGACAAGTCTAAGTACCGTT 59.524 40.000 2.15 0.00 40.61 4.44
5428 9823 8.491134 TGTAGTGGTTTTATATAACAGGCTCAT 58.509 33.333 8.11 0.00 0.00 2.90
5471 9870 3.485463 TTGTAGACTGGTGGTCCTTTG 57.515 47.619 0.00 0.00 45.54 2.77
5484 9883 8.385858 GGTAGTTATGGACGAAAATTTGTAGAC 58.614 37.037 0.00 0.00 0.00 2.59
5500 9899 9.140286 CGATGAAATATGTAGTGGTAGTTATGG 57.860 37.037 0.00 0.00 0.00 2.74
5544 9946 1.450312 CTTCTTTGGCTCCGGCGAT 60.450 57.895 9.30 0.00 39.81 4.58
5546 9948 3.127533 CCTTCTTTGGCTCCGGCG 61.128 66.667 0.00 0.00 39.81 6.46
5547 9949 1.746991 CTCCTTCTTTGGCTCCGGC 60.747 63.158 0.00 0.00 37.82 6.13
5548 9950 1.078143 CCTCCTTCTTTGGCTCCGG 60.078 63.158 0.00 0.00 0.00 5.14
5549 9951 1.746991 GCCTCCTTCTTTGGCTCCG 60.747 63.158 0.00 0.00 43.05 4.63
5554 9961 1.589716 CGGCAAGCCTCCTTCTTTGG 61.590 60.000 9.73 0.00 0.00 3.28
5576 10021 4.263572 CCTGCACCCCAACCGTGA 62.264 66.667 0.00 0.00 32.77 4.35
5635 10105 4.119363 ATGGAGCTGGCCATGCGT 62.119 61.111 5.51 0.00 46.62 5.24
5652 10614 3.138798 GCCCGTCCTGTCTCGCTA 61.139 66.667 0.00 0.00 0.00 4.26
5722 10684 2.435938 CAATCCCACCACGTCGGG 60.436 66.667 7.76 7.76 44.60 5.14
5723 10685 3.124921 GCAATCCCACCACGTCGG 61.125 66.667 0.00 2.92 42.50 4.79
5756 10718 2.818132 GTCGGGCTCCTCCATGAG 59.182 66.667 0.00 0.00 36.21 2.90
5757 10719 3.147595 CGTCGGGCTCCTCCATGA 61.148 66.667 0.00 0.00 36.21 3.07
5759 10721 3.461773 CACGTCGGGCTCCTCCAT 61.462 66.667 0.00 0.00 36.21 3.41
5769 10731 4.180946 CCTCTCGCTCCACGTCGG 62.181 72.222 0.00 0.00 44.19 4.79
5772 10734 2.344203 CCTTCCTCTCGCTCCACGT 61.344 63.158 0.00 0.00 44.19 4.49
5774 10736 1.216710 CACCTTCCTCTCGCTCCAC 59.783 63.158 0.00 0.00 0.00 4.02
5843 10810 9.025041 TCACTCTGATTTCTTTGAGTATCTGTA 57.975 33.333 0.00 0.00 37.64 2.74
5961 10946 4.688063 CAGTACGTTTCAAGACGATGTTG 58.312 43.478 0.00 0.00 45.47 3.33
5983 10978 6.973474 AGTCTGTATTAGTTACATCGTCAAGC 59.027 38.462 0.00 0.00 40.02 4.01
5985 10980 9.170734 ACTAGTCTGTATTAGTTACATCGTCAA 57.829 33.333 0.00 0.00 40.02 3.18
5986 10981 8.610035 CACTAGTCTGTATTAGTTACATCGTCA 58.390 37.037 0.00 0.00 40.02 4.35
5988 10983 8.503458 ACACTAGTCTGTATTAGTTACATCGT 57.497 34.615 0.00 0.00 40.02 3.73
6008 11003 3.565482 ACGTGACGAGGTCTTTTACACTA 59.435 43.478 13.70 0.00 33.15 2.74
6048 11048 7.284489 TGGGCAAATTAATCTACAAGGTATGAC 59.716 37.037 0.00 0.00 0.00 3.06
6050 11050 7.068103 TGTGGGCAAATTAATCTACAAGGTATG 59.932 37.037 0.00 0.00 0.00 2.39
6051 11051 7.068226 GTGTGGGCAAATTAATCTACAAGGTAT 59.932 37.037 0.00 0.00 0.00 2.73
6054 11054 5.418840 AGTGTGGGCAAATTAATCTACAAGG 59.581 40.000 0.00 0.00 0.00 3.61
6056 11056 6.943146 TGTAGTGTGGGCAAATTAATCTACAA 59.057 34.615 0.00 0.00 34.46 2.41
6057 11057 6.477253 TGTAGTGTGGGCAAATTAATCTACA 58.523 36.000 0.00 0.00 34.82 2.74
6058 11058 6.995511 TGTAGTGTGGGCAAATTAATCTAC 57.004 37.500 0.00 0.00 0.00 2.59
6059 11059 7.284489 GGATTGTAGTGTGGGCAAATTAATCTA 59.716 37.037 0.00 0.00 0.00 1.98
6089 11089 0.674534 CTACATAGCCGGTGGAGTCC 59.325 60.000 1.90 0.73 0.00 3.85
6143 11163 3.706373 GCCGGGAGAAGGTGCTGA 61.706 66.667 2.18 0.00 0.00 4.26
6222 11249 3.510388 CTGTGGTAGCTTCGAAGATGA 57.490 47.619 28.95 9.55 35.04 2.92
6327 11357 2.122729 CCAGGGGTGTGGAGGAGA 59.877 66.667 0.00 0.00 40.44 3.71


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

AutoCloner maintained by Alex Coulton.