Multiple sequence alignment - TraesCS5B01G511100

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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 TraesCS5B01G511100 chr5B 100.000 4364 0 0 1 4364 676465637 676470000 0.000000e+00 8059.0
1 TraesCS5B01G511100 chr4A 91.652 1653 99 13 1 1633 633446685 633448318 0.000000e+00 2252.0
2 TraesCS5B01G511100 chr4A 89.812 1757 158 15 2619 4363 635582480 635580733 0.000000e+00 2233.0
3 TraesCS5B01G511100 chr4A 90.947 1657 107 16 1 1633 633487676 633489313 0.000000e+00 2189.0
4 TraesCS5B01G511100 chr4A 91.181 1338 111 4 2528 3861 633448837 633450171 0.000000e+00 1810.0
5 TraesCS5B01G511100 chr4A 90.963 1339 113 5 2528 3861 633514983 633516318 0.000000e+00 1796.0
6 TraesCS5B01G511100 chr4A 90.896 1340 113 5 2528 3861 633405883 633407219 0.000000e+00 1790.0
7 TraesCS5B01G511100 chr4A 90.665 1339 117 5 2528 3861 633539579 633540914 0.000000e+00 1773.0
8 TraesCS5B01G511100 chr4A 90.359 1338 122 4 2528 3861 633721288 633722622 0.000000e+00 1749.0
9 TraesCS5B01G511100 chr4A 90.299 1340 121 6 2528 3861 633490283 633491619 0.000000e+00 1746.0
10 TraesCS5B01G511100 chr4A 91.966 1058 54 10 596 1633 633719723 633720769 0.000000e+00 1454.0
11 TraesCS5B01G511100 chr4A 86.359 931 83 19 684 1596 635849700 635848796 0.000000e+00 976.0
12 TraesCS5B01G511100 chr4A 91.973 598 43 3 1040 1633 633404767 633405363 0.000000e+00 833.0
13 TraesCS5B01G511100 chr4A 92.088 594 39 6 1045 1633 633604451 633605041 0.000000e+00 830.0
14 TraesCS5B01G511100 chr4A 91.945 509 34 2 1 509 633603181 633603682 0.000000e+00 706.0
15 TraesCS5B01G511100 chr4A 91.945 509 34 2 1 509 633648400 633648901 0.000000e+00 706.0
16 TraesCS5B01G511100 chr4A 85.007 727 51 21 919 1634 635583612 635582933 0.000000e+00 686.0
17 TraesCS5B01G511100 chr4A 92.949 468 29 3 1169 1633 633513999 633514465 0.000000e+00 678.0
18 TraesCS5B01G511100 chr4A 92.469 478 22 4 506 981 633603986 633604451 0.000000e+00 671.0
19 TraesCS5B01G511100 chr4A 91.314 472 34 2 1 472 633710317 633710781 4.760000e-179 638.0
20 TraesCS5B01G511100 chr4A 87.568 555 62 6 3814 4364 635847104 635846553 1.710000e-178 636.0
21 TraesCS5B01G511100 chr4A 91.503 459 32 2 1 459 633403787 633404238 3.710000e-175 625.0
22 TraesCS5B01G511100 chr4A 89.485 466 45 3 3901 4364 633722627 633723090 1.750000e-163 586.0
23 TraesCS5B01G511100 chr4A 89.270 466 46 3 3901 4364 633516323 633516786 8.140000e-162 580.0
24 TraesCS5B01G511100 chr4A 89.270 466 46 3 3901 4364 633651709 633652172 8.140000e-162 580.0
25 TraesCS5B01G511100 chr4A 92.941 255 11 2 547 801 633404522 633404769 8.920000e-97 364.0
26 TraesCS5B01G511100 chr4A 86.111 252 21 6 919 1166 635673499 635673258 4.330000e-65 259.0
27 TraesCS5B01G511100 chr4A 89.529 191 14 6 2236 2423 635657613 635657426 2.030000e-58 237.0
28 TraesCS5B01G511100 chr4A 88.770 187 14 6 2236 2419 635582822 635582640 5.680000e-54 222.0
29 TraesCS5B01G511100 chr4A 88.710 186 14 7 2236 2418 635671054 635670873 2.040000e-53 220.0
30 TraesCS5B01G511100 chr4A 95.536 112 4 1 2236 2347 633405475 633405585 1.250000e-40 178.0
31 TraesCS5B01G511100 chr4A 95.536 112 4 1 2236 2347 633448430 633448540 1.250000e-40 178.0
32 TraesCS5B01G511100 chr4A 95.536 112 4 1 2236 2347 633489425 633489535 1.250000e-40 178.0
33 TraesCS5B01G511100 chr4A 95.536 112 4 1 2236 2347 633720881 633720991 1.250000e-40 178.0
34 TraesCS5B01G511100 chr4A 90.000 100 8 2 3814 3913 635656292 635656195 1.270000e-25 128.0
35 TraesCS5B01G511100 chr4A 88.235 102 10 2 3812 3913 635669738 635669639 2.130000e-23 121.0
36 TraesCS5B01G511100 chr4A 94.828 58 3 0 543 600 633711084 633711141 1.670000e-14 91.6
37 TraesCS5B01G511100 chr5D 91.730 1306 102 3 2558 3861 536095981 536097282 0.000000e+00 1808.0
38 TraesCS5B01G511100 chr5D 92.681 1257 85 4 2608 3861 536005225 536006477 0.000000e+00 1805.0
39 TraesCS5B01G511100 chr5D 93.946 892 31 8 759 1633 536003363 536004248 0.000000e+00 1327.0
40 TraesCS5B01G511100 chr5D 90.705 667 51 8 670 1329 536095324 536095986 0.000000e+00 878.0
41 TraesCS5B01G511100 chr5D 89.264 503 45 6 1 501 536002024 536002519 4.790000e-174 621.0
42 TraesCS5B01G511100 chr5D 90.792 467 38 4 3901 4364 536006482 536006946 1.720000e-173 619.0
43 TraesCS5B01G511100 chr5D 89.936 467 40 6 3901 4364 536097287 536097749 2.910000e-166 595.0
44 TraesCS5B01G511100 chr5D 79.083 349 47 20 923 1259 536254956 536254622 2.640000e-52 217.0
45 TraesCS5B01G511100 chr5D 96.429 112 3 1 2236 2347 536004360 536004470 2.680000e-42 183.0
46 TraesCS5B01G511100 chrUn 92.599 581 38 3 1057 1633 410990205 410989626 0.000000e+00 830.0
47 TraesCS5B01G511100 chrUn 91.841 478 25 4 506 981 410990682 410990217 0.000000e+00 654.0
48 TraesCS5B01G511100 chrUn 89.270 466 46 3 3901 4364 370624534 370624997 8.140000e-162 580.0
49 TraesCS5B01G511100 chrUn 89.270 466 46 3 3901 4364 413320348 413320811 8.140000e-162 580.0
50 TraesCS5B01G511100 chrUn 83.385 325 42 10 1639 1955 30191035 30191355 1.540000e-74 291.0
51 TraesCS5B01G511100 chrUn 94.643 112 5 1 2236 2347 410989514 410989404 5.800000e-39 172.0
52 TraesCS5B01G511100 chr3D 87.599 379 41 5 1639 2015 464065135 464065509 6.700000e-118 435.0
53 TraesCS5B01G511100 chr3D 87.335 379 42 5 1639 2015 426169444 426169818 3.120000e-116 429.0
54 TraesCS5B01G511100 chr1D 85.492 386 46 6 1644 2026 489087229 489087607 1.140000e-105 394.0
55 TraesCS5B01G511100 chr7B 85.445 371 44 8 1638 2003 672757888 672758253 1.150000e-100 377.0
56 TraesCS5B01G511100 chr7B 84.635 384 44 11 1638 2015 672758356 672758730 6.900000e-98 368.0
57 TraesCS5B01G511100 chr4D 85.955 356 35 10 1666 2015 5590373 5590719 2.480000e-97 366.0
58 TraesCS5B01G511100 chr7A 86.834 319 34 7 1701 2015 297923092 297922778 2.500000e-92 350.0
59 TraesCS5B01G511100 chr7A 80.890 382 63 7 1642 2015 719664591 719664212 4.270000e-75 292.0


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 TraesCS5B01G511100 chr5B 676465637 676470000 4363 False 8059.000000 8059 100.000000 1 4364 1 chr5B.!!$F1 4363
1 TraesCS5B01G511100 chr4A 633539579 633540914 1335 False 1773.000000 1773 90.665000 2528 3861 1 chr4A.!!$F1 1333
2 TraesCS5B01G511100 chr4A 633446685 633450171 3486 False 1413.333333 2252 92.789667 1 3861 3 chr4A.!!$F3 3860
3 TraesCS5B01G511100 chr4A 633487676 633491619 3943 False 1371.000000 2189 92.260667 1 3861 3 chr4A.!!$F4 3860
4 TraesCS5B01G511100 chr4A 635580733 635583612 2879 True 1047.000000 2233 87.863000 919 4363 3 chr4A.!!$R1 3444
5 TraesCS5B01G511100 chr4A 633513999 633516786 2787 False 1018.000000 1796 91.060667 1169 4364 3 chr4A.!!$F5 3195
6 TraesCS5B01G511100 chr4A 633719723 633723090 3367 False 991.750000 1749 91.836500 596 4364 4 chr4A.!!$F9 3768
7 TraesCS5B01G511100 chr4A 635846553 635849700 3147 True 806.000000 976 86.963500 684 4364 2 chr4A.!!$R4 3680
8 TraesCS5B01G511100 chr4A 633403787 633407219 3432 False 758.000000 1790 92.569800 1 3861 5 chr4A.!!$F2 3860
9 TraesCS5B01G511100 chr4A 633603181 633605041 1860 False 735.666667 830 92.167333 1 1633 3 chr4A.!!$F6 1632
10 TraesCS5B01G511100 chr4A 633648400 633652172 3772 False 643.000000 706 90.607500 1 4364 2 chr4A.!!$F7 4363
11 TraesCS5B01G511100 chr4A 633710317 633711141 824 False 364.800000 638 93.071000 1 600 2 chr4A.!!$F8 599
12 TraesCS5B01G511100 chr5D 536095324 536097749 2425 False 1093.666667 1808 90.790333 670 4364 3 chr5D.!!$F2 3694
13 TraesCS5B01G511100 chr5D 536002024 536006946 4922 False 911.000000 1805 92.622400 1 4364 5 chr5D.!!$F1 4363
14 TraesCS5B01G511100 chrUn 410989404 410990682 1278 True 552.000000 830 93.027667 506 2347 3 chrUn.!!$R1 1841
15 TraesCS5B01G511100 chr7B 672757888 672758730 842 False 372.500000 377 85.040000 1638 2015 2 chr7B.!!$F1 377

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
809 1399 0.179100 TCGCTTAGGCATGCTCAGTC 60.179 55.0 18.92 0.0 38.6 3.51 F
2230 3325 0.108138 ACGAGGACTAGTTGGCATGC 60.108 55.0 9.90 9.9 0.0 4.06 F
2231 3326 0.176680 CGAGGACTAGTTGGCATGCT 59.823 55.0 18.92 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 4418 0.031212 AAATGGGTTAGGGGCATGGG 60.031 55.0 0.0 0.0 0.0 4.00 R
3302 5487 0.396811 CCACCTCTTCTTGAACGGGT 59.603 55.0 0.0 0.0 0.0 5.28 R
4089 6292 0.962356 CCTGACTGACCCCACAATGC 60.962 60.0 0.0 0.0 0.0 3.56 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
27 28 2.689658 TCTTCAACAACAGAGGAGGGA 58.310 47.619 0.00 0.00 0.00 4.20
51 53 4.521075 CATCGTTGGATGGTCGCT 57.479 55.556 0.00 0.00 45.15 4.93
76 78 2.963101 TCCACACACTAGTTGCACTACT 59.037 45.455 0.00 0.00 0.00 2.57
103 105 1.331756 GATGCAGTTGGCCGTAATGAG 59.668 52.381 9.05 0.00 43.89 2.90
127 129 0.459237 CAGTTAGAGGCCTGAGTGCG 60.459 60.000 12.00 0.00 0.00 5.34
145 147 0.820074 CGAGACGAGGTATCAGCCCT 60.820 60.000 0.00 0.00 34.11 5.19
216 218 1.669440 GGCAACCAGACTACCACGA 59.331 57.895 0.00 0.00 0.00 4.35
247 249 5.163088 GGGGTCATCAACATTAGGAGGTAAT 60.163 44.000 0.00 0.00 0.00 1.89
248 250 6.365520 GGGTCATCAACATTAGGAGGTAATT 58.634 40.000 0.00 0.00 0.00 1.40
249 251 7.420913 GGGGTCATCAACATTAGGAGGTAATTA 60.421 40.741 0.00 0.00 0.00 1.40
250 252 7.996644 GGGTCATCAACATTAGGAGGTAATTAA 59.003 37.037 0.00 0.00 0.00 1.40
258 260 2.859951 AGGAGGTAATTAACAGGGGCT 58.140 47.619 2.78 0.00 0.00 5.19
292 294 4.359706 CGATATCGGACACAACATCTTGA 58.640 43.478 17.51 0.00 35.37 3.02
354 356 5.743117 CAAAGAGAGGACCAAATCTGAGAT 58.257 41.667 0.00 0.00 0.00 2.75
365 367 2.810439 ATCTGAGATAAGCTGGCGAC 57.190 50.000 0.00 0.00 0.00 5.19
367 369 0.382158 CTGAGATAAGCTGGCGACGA 59.618 55.000 0.00 0.00 0.00 4.20
384 386 1.485066 ACGAGCAACAATAGTAGGGGG 59.515 52.381 0.00 0.00 0.00 5.40
438 441 1.533033 TGGAGAAGCGTGTGAGGGA 60.533 57.895 0.00 0.00 0.00 4.20
449 452 0.490017 TGTGAGGGAAGGGTACTGGA 59.510 55.000 0.00 0.00 0.00 3.86
459 462 1.139095 GGTACTGGAAGAGACGCCG 59.861 63.158 0.00 0.00 37.43 6.46
614 924 1.001406 GGTCTTCTGGTCTCACCACAG 59.999 57.143 0.00 0.00 44.79 3.66
636 946 2.779755 TGCAAGTGGTGGTATTCGAT 57.220 45.000 0.00 0.00 0.00 3.59
678 988 3.071023 TGCACTAGAGTACCTTGCAAGTT 59.929 43.478 24.35 13.96 40.15 2.66
679 989 4.282449 TGCACTAGAGTACCTTGCAAGTTA 59.718 41.667 24.35 12.81 40.15 2.24
680 990 4.865365 GCACTAGAGTACCTTGCAAGTTAG 59.135 45.833 24.35 12.20 33.24 2.34
681 991 5.567025 GCACTAGAGTACCTTGCAAGTTAGT 60.567 44.000 24.35 17.65 33.24 2.24
682 992 5.864474 CACTAGAGTACCTTGCAAGTTAGTG 59.136 44.000 24.35 22.08 32.42 2.74
752 1070 1.867233 GGCGCCACAGTGAGTATATTG 59.133 52.381 24.80 0.00 0.00 1.90
784 1374 1.827969 AGAGAGTTAGCGAACCAGCAT 59.172 47.619 6.04 0.00 40.15 3.79
807 1397 0.866427 CATCGCTTAGGCATGCTCAG 59.134 55.000 18.92 11.86 38.60 3.35
808 1398 0.467384 ATCGCTTAGGCATGCTCAGT 59.533 50.000 18.92 2.64 38.60 3.41
809 1399 0.179100 TCGCTTAGGCATGCTCAGTC 60.179 55.000 18.92 0.00 38.60 3.51
810 1400 0.460811 CGCTTAGGCATGCTCAGTCA 60.461 55.000 18.92 0.00 38.60 3.41
825 1415 0.315568 AGTCACAAGTCTCCGTCAGC 59.684 55.000 0.00 0.00 0.00 4.26
867 1457 4.947147 GACCAGCGTGGCCCACAA 62.947 66.667 15.45 0.00 42.67 3.33
973 1565 1.066430 GTACTTCCGCAGATCCCAACA 60.066 52.381 0.00 0.00 0.00 3.33
985 1591 4.473520 CCAACATCCGCTCCGCCT 62.474 66.667 0.00 0.00 0.00 5.52
1245 1854 2.815298 CGAGCTCGACCTCTCGGAC 61.815 68.421 32.06 0.00 45.89 4.79
1310 1919 2.979676 CCGCTGCTTGCTTGGTGA 60.980 61.111 0.00 0.00 40.11 4.02
1314 1923 0.599558 GCTGCTTGCTTGGTGATTGA 59.400 50.000 0.00 0.00 38.95 2.57
1467 2092 3.642755 GTCAAGGTCTGGCGTGTG 58.357 61.111 0.00 0.00 0.00 3.82
1541 2166 2.436646 GCGTGGTAGTGGCAGCAT 60.437 61.111 0.00 0.00 0.00 3.79
1576 2201 5.163509 GGATCTTGCCCAAGGTTTTAGATTC 60.164 44.000 8.06 0.00 38.88 2.52
1577 2202 4.998051 TCTTGCCCAAGGTTTTAGATTCT 58.002 39.130 8.06 0.00 38.88 2.40
1588 2213 8.404000 CAAGGTTTTAGATTCTGAATGGAGATG 58.596 37.037 7.78 0.00 0.00 2.90
1612 2240 3.379865 TTGTGGGGCGGCGAGATAC 62.380 63.158 12.98 4.33 0.00 2.24
1614 2242 2.196502 TGGGGCGGCGAGATACTA 59.803 61.111 12.98 0.00 0.00 1.82
1633 2261 0.681175 ACTTGGTTACCGCGGTTACT 59.319 50.000 37.14 21.13 0.00 2.24
1634 2262 1.073177 CTTGGTTACCGCGGTTACTG 58.927 55.000 37.14 25.89 0.00 2.74
1635 2263 0.392336 TTGGTTACCGCGGTTACTGT 59.608 50.000 37.14 17.19 0.00 3.55
1648 2276 5.333187 CGCGGTTACTGTGTATCTCTACTAG 60.333 48.000 0.00 0.00 0.00 2.57
1679 2770 6.721704 AAGAAGCTCAAGGTTTTCATTTCT 57.278 33.333 0.00 0.00 35.69 2.52
1685 2776 5.106357 GCTCAAGGTTTTCATTTCTCCTCTC 60.106 44.000 0.00 0.00 0.00 3.20
1689 2780 8.217799 TCAAGGTTTTCATTTCTCCTCTCTTTA 58.782 33.333 0.00 0.00 0.00 1.85
1697 2788 8.887264 TCATTTCTCCTCTCTTTAGTCTAACT 57.113 34.615 0.00 0.00 0.00 2.24
1701 2792 9.984190 TTTCTCCTCTCTTTAGTCTAACTTTTC 57.016 33.333 0.00 0.00 0.00 2.29
1722 2813 9.421399 CTTTTCTTATATATGTCCCACCCTTTT 57.579 33.333 0.00 0.00 0.00 2.27
1776 2867 6.496743 TCTGAATTTTCTCCCATCCATTCTT 58.503 36.000 0.00 0.00 0.00 2.52
1783 2874 6.401537 TTCTCCCATCCATTCTTCCTAAAA 57.598 37.500 0.00 0.00 0.00 1.52
1786 2877 8.113114 TCTCCCATCCATTCTTCCTAAAATAA 57.887 34.615 0.00 0.00 0.00 1.40
1857 2952 7.531857 TGGTAAGCAATTAAATTCTGACCAA 57.468 32.000 0.00 0.00 30.55 3.67
1858 2953 7.957002 TGGTAAGCAATTAAATTCTGACCAAA 58.043 30.769 0.00 0.00 30.55 3.28
1905 3000 6.236357 CGTGTAAATCATAGCGATTGCATAG 58.764 40.000 7.90 0.00 43.83 2.23
1921 3016 7.217070 CGATTGCATAGAAAAACTTGCTAAGAC 59.783 37.037 0.00 0.00 35.40 3.01
1976 3071 7.168972 GCAGTCACAAGCTAATCTACTAGAATG 59.831 40.741 0.00 0.00 0.00 2.67
1977 3072 8.409371 CAGTCACAAGCTAATCTACTAGAATGA 58.591 37.037 0.00 0.00 0.00 2.57
1995 3090 7.516198 AGAATGATTATATTCCCACTGCAAC 57.484 36.000 0.00 0.00 37.70 4.17
1999 3094 2.057137 ATATTCCCACTGCAACGCAT 57.943 45.000 0.00 0.00 38.13 4.73
2002 3097 3.751246 CCCACTGCAACGCATGGG 61.751 66.667 16.68 16.68 44.31 4.00
2004 3099 3.672447 CACTGCAACGCATGGGCA 61.672 61.111 10.10 0.00 41.24 5.36
2008 3103 0.173029 CTGCAACGCATGGGCAATTA 59.827 50.000 10.10 0.00 41.24 1.40
2010 3105 1.210870 GCAACGCATGGGCAATTATG 58.789 50.000 10.10 1.39 41.24 1.90
2024 3119 6.948886 TGGGCAATTATGTAGTACCAAGAAAA 59.051 34.615 0.00 0.00 0.00 2.29
2025 3120 7.451877 TGGGCAATTATGTAGTACCAAGAAAAA 59.548 33.333 0.00 0.00 0.00 1.94
2026 3121 8.474831 GGGCAATTATGTAGTACCAAGAAAAAT 58.525 33.333 0.00 0.00 0.00 1.82
2027 3122 9.869757 GGCAATTATGTAGTACCAAGAAAAATT 57.130 29.630 0.00 0.00 0.00 1.82
2091 3186 9.620660 TTCAAAATTCTTTTACCTCGATTTAGC 57.379 29.630 0.00 0.00 0.00 3.09
2114 3209 8.542497 AGCTACGTATTGAACATGAGTTTAAA 57.458 30.769 0.00 0.00 36.89 1.52
2139 3234 9.941325 AACAAAATAATCTGCAATTGTAATGGA 57.059 25.926 7.40 0.00 31.33 3.41
2140 3235 9.941325 ACAAAATAATCTGCAATTGTAATGGAA 57.059 25.926 7.40 0.00 29.89 3.53
2149 3244 9.806203 TCTGCAATTGTAATGGAATATTTCTTG 57.194 29.630 7.40 0.00 0.00 3.02
2150 3245 9.806203 CTGCAATTGTAATGGAATATTTCTTGA 57.194 29.630 7.40 0.00 0.00 3.02
2151 3246 9.585099 TGCAATTGTAATGGAATATTTCTTGAC 57.415 29.630 7.40 0.00 0.00 3.18
2152 3247 9.585099 GCAATTGTAATGGAATATTTCTTGACA 57.415 29.630 7.40 0.00 0.00 3.58
2156 3251 8.062065 TGTAATGGAATATTTCTTGACAACCC 57.938 34.615 0.00 0.00 0.00 4.11
2157 3252 7.893302 TGTAATGGAATATTTCTTGACAACCCT 59.107 33.333 0.00 0.00 0.00 4.34
2158 3253 7.797121 AATGGAATATTTCTTGACAACCCTT 57.203 32.000 0.00 0.00 0.00 3.95
2159 3254 6.834168 TGGAATATTTCTTGACAACCCTTC 57.166 37.500 0.00 0.00 0.00 3.46
2160 3255 5.414454 TGGAATATTTCTTGACAACCCTTCG 59.586 40.000 0.00 0.00 0.00 3.79
2161 3256 5.646360 GGAATATTTCTTGACAACCCTTCGA 59.354 40.000 0.00 0.00 0.00 3.71
2162 3257 6.183360 GGAATATTTCTTGACAACCCTTCGAG 60.183 42.308 0.00 0.00 0.00 4.04
2163 3258 2.543777 TTCTTGACAACCCTTCGAGG 57.456 50.000 0.00 0.00 34.30 4.63
2173 3268 3.291497 CCTTCGAGGGGAGAGTTCT 57.709 57.895 5.48 0.00 0.00 3.01
2174 3269 1.107945 CCTTCGAGGGGAGAGTTCTC 58.892 60.000 5.48 0.39 42.14 2.87
2176 3271 4.322689 CGAGGGGAGAGTTCTCGT 57.677 61.111 3.24 0.00 43.51 4.18
2177 3272 1.803943 CGAGGGGAGAGTTCTCGTG 59.196 63.158 3.24 0.00 43.51 4.35
2178 3273 0.961358 CGAGGGGAGAGTTCTCGTGT 60.961 60.000 3.24 0.00 43.51 4.49
2179 3274 0.528470 GAGGGGAGAGTTCTCGTGTG 59.472 60.000 3.24 0.00 43.76 3.82
2180 3275 0.900647 AGGGGAGAGTTCTCGTGTGG 60.901 60.000 3.24 0.00 43.76 4.17
2181 3276 1.592223 GGGAGAGTTCTCGTGTGGG 59.408 63.158 3.24 0.00 43.76 4.61
2182 3277 1.186267 GGGAGAGTTCTCGTGTGGGT 61.186 60.000 3.24 0.00 43.76 4.51
2183 3278 0.680061 GGAGAGTTCTCGTGTGGGTT 59.320 55.000 3.24 0.00 43.76 4.11
2184 3279 1.070289 GGAGAGTTCTCGTGTGGGTTT 59.930 52.381 3.24 0.00 43.76 3.27
2185 3280 2.135933 GAGAGTTCTCGTGTGGGTTTG 58.864 52.381 0.00 0.00 32.78 2.93
2186 3281 1.760613 AGAGTTCTCGTGTGGGTTTGA 59.239 47.619 0.00 0.00 0.00 2.69
2187 3282 2.368875 AGAGTTCTCGTGTGGGTTTGAT 59.631 45.455 0.00 0.00 0.00 2.57
2188 3283 3.139077 GAGTTCTCGTGTGGGTTTGATT 58.861 45.455 0.00 0.00 0.00 2.57
2189 3284 3.139077 AGTTCTCGTGTGGGTTTGATTC 58.861 45.455 0.00 0.00 0.00 2.52
2190 3285 3.139077 GTTCTCGTGTGGGTTTGATTCT 58.861 45.455 0.00 0.00 0.00 2.40
2191 3286 3.040147 TCTCGTGTGGGTTTGATTCTC 57.960 47.619 0.00 0.00 0.00 2.87
2192 3287 2.632996 TCTCGTGTGGGTTTGATTCTCT 59.367 45.455 0.00 0.00 0.00 3.10
2193 3288 3.830178 TCTCGTGTGGGTTTGATTCTCTA 59.170 43.478 0.00 0.00 0.00 2.43
2194 3289 4.466370 TCTCGTGTGGGTTTGATTCTCTAT 59.534 41.667 0.00 0.00 0.00 1.98
2195 3290 5.046591 TCTCGTGTGGGTTTGATTCTCTATT 60.047 40.000 0.00 0.00 0.00 1.73
2196 3291 5.175859 TCGTGTGGGTTTGATTCTCTATTC 58.824 41.667 0.00 0.00 0.00 1.75
2197 3292 4.032900 CGTGTGGGTTTGATTCTCTATTCG 59.967 45.833 0.00 0.00 0.00 3.34
2198 3293 3.938963 TGTGGGTTTGATTCTCTATTCGC 59.061 43.478 0.00 0.00 0.00 4.70
2199 3294 3.938963 GTGGGTTTGATTCTCTATTCGCA 59.061 43.478 0.00 0.00 0.00 5.10
2200 3295 4.034510 GTGGGTTTGATTCTCTATTCGCAG 59.965 45.833 0.00 0.00 0.00 5.18
2201 3296 4.081142 TGGGTTTGATTCTCTATTCGCAGA 60.081 41.667 0.00 0.00 0.00 4.26
2202 3297 5.059833 GGGTTTGATTCTCTATTCGCAGAT 58.940 41.667 0.00 0.00 35.04 2.90
2203 3298 6.183360 TGGGTTTGATTCTCTATTCGCAGATA 60.183 38.462 0.00 0.00 35.04 1.98
2204 3299 6.146347 GGGTTTGATTCTCTATTCGCAGATAC 59.854 42.308 0.00 0.00 35.04 2.24
2205 3300 6.926272 GGTTTGATTCTCTATTCGCAGATACT 59.074 38.462 0.00 0.00 35.04 2.12
2206 3301 7.095857 GGTTTGATTCTCTATTCGCAGATACTG 60.096 40.741 0.00 0.00 35.04 2.74
2218 3313 3.341857 CAGATACTGCTACACGAGGAC 57.658 52.381 0.00 0.00 0.00 3.85
2219 3314 2.946329 CAGATACTGCTACACGAGGACT 59.054 50.000 0.00 0.00 0.00 3.85
2220 3315 4.127907 CAGATACTGCTACACGAGGACTA 58.872 47.826 0.00 0.00 0.00 2.59
2221 3316 4.212425 CAGATACTGCTACACGAGGACTAG 59.788 50.000 0.00 0.00 0.00 2.57
2222 3317 2.493414 ACTGCTACACGAGGACTAGT 57.507 50.000 0.00 0.00 0.00 2.57
2223 3318 2.792878 ACTGCTACACGAGGACTAGTT 58.207 47.619 0.00 0.00 0.00 2.24
2224 3319 2.488545 ACTGCTACACGAGGACTAGTTG 59.511 50.000 0.00 0.00 0.00 3.16
2225 3320 1.816835 TGCTACACGAGGACTAGTTGG 59.183 52.381 0.00 0.00 0.00 3.77
2226 3321 1.469423 GCTACACGAGGACTAGTTGGC 60.469 57.143 0.00 0.00 0.00 4.52
2227 3322 1.816835 CTACACGAGGACTAGTTGGCA 59.183 52.381 0.00 0.00 0.00 4.92
2228 3323 1.267121 ACACGAGGACTAGTTGGCAT 58.733 50.000 0.00 0.00 0.00 4.40
2229 3324 1.066858 ACACGAGGACTAGTTGGCATG 60.067 52.381 0.00 0.00 0.00 4.06
2230 3325 0.108138 ACGAGGACTAGTTGGCATGC 60.108 55.000 9.90 9.90 0.00 4.06
2231 3326 0.176680 CGAGGACTAGTTGGCATGCT 59.823 55.000 18.92 0.00 0.00 3.79
2232 3327 1.406069 CGAGGACTAGTTGGCATGCTT 60.406 52.381 18.92 3.79 0.00 3.91
2233 3328 2.716217 GAGGACTAGTTGGCATGCTTT 58.284 47.619 18.92 3.43 0.00 3.51
2234 3329 3.084786 GAGGACTAGTTGGCATGCTTTT 58.915 45.455 18.92 3.79 0.00 2.27
2257 3352 7.872061 TTCTACATGGGATATGTTATCTGGT 57.128 36.000 0.00 0.00 33.76 4.00
2290 3385 0.536460 GAAGGGGGTGACAAGCGAAA 60.536 55.000 0.00 0.00 0.00 3.46
2331 3426 1.560505 GTGGTGGGAGATGGCAAATT 58.439 50.000 0.00 0.00 0.00 1.82
2376 3602 4.712122 TTCCATTCTTCCCGTAAATTGC 57.288 40.909 0.00 0.00 0.00 3.56
2380 3608 4.582656 CCATTCTTCCCGTAAATTGCCATA 59.417 41.667 0.00 0.00 0.00 2.74
2385 3613 5.300792 TCTTCCCGTAAATTGCCATATTTCC 59.699 40.000 0.00 0.00 0.00 3.13
2386 3614 4.798882 TCCCGTAAATTGCCATATTTCCT 58.201 39.130 0.00 0.00 0.00 3.36
2389 3617 6.834451 TCCCGTAAATTGCCATATTTCCTAAA 59.166 34.615 0.00 0.00 0.00 1.85
2390 3618 7.013846 TCCCGTAAATTGCCATATTTCCTAAAG 59.986 37.037 0.00 0.00 0.00 1.85
2409 3637 4.516652 AAGAAATTGCATCCTCCTAGCT 57.483 40.909 0.00 0.00 0.00 3.32
2423 3651 2.026356 TCCTAGCTAATGTTTGCTGGCA 60.026 45.455 11.09 0.00 39.49 4.92
2438 3754 6.724694 TTGCTGGCAAAATACATTCATTTC 57.275 33.333 5.47 0.00 32.44 2.17
2441 3757 7.259882 TGCTGGCAAAATACATTCATTTCTAG 58.740 34.615 0.00 0.00 0.00 2.43
2442 3758 7.122501 TGCTGGCAAAATACATTCATTTCTAGA 59.877 33.333 0.00 0.00 0.00 2.43
2443 3759 8.139989 GCTGGCAAAATACATTCATTTCTAGAT 58.860 33.333 0.00 0.00 0.00 1.98
2471 3787 4.122776 CTCTGACAAGTATTTCCGGATGG 58.877 47.826 4.15 0.00 0.00 3.51
2567 4380 0.461339 CGCAGTTACTGGGCGGTAAT 60.461 55.000 16.11 0.00 46.46 1.89
2568 4381 1.746470 GCAGTTACTGGGCGGTAATT 58.254 50.000 14.63 0.00 34.73 1.40
2577 4390 7.340999 AGTTACTGGGCGGTAATTGAATTTATT 59.659 33.333 0.00 0.00 34.73 1.40
2584 4397 6.149633 GCGGTAATTGAATTTATTGCCTAGG 58.850 40.000 3.67 3.67 36.11 3.02
2586 4399 7.309194 GCGGTAATTGAATTTATTGCCTAGGAT 60.309 37.037 14.75 0.00 36.11 3.24
2605 4418 3.251972 GGATCGAAAATCCTGATCTTGCC 59.748 47.826 0.00 0.00 38.79 4.52
2617 4802 1.295915 ATCTTGCCCCATGCCCCTAA 61.296 55.000 0.00 0.00 40.16 2.69
2670 4855 3.823304 AGCTCTTTTCATCCCTTGACAAC 59.177 43.478 0.00 0.00 32.84 3.32
2746 4931 1.197036 TCAGAACTACACGACGAGCTG 59.803 52.381 0.00 0.00 0.00 4.24
2815 5000 5.931294 AGGAGAAGACGACTGTAGATATGA 58.069 41.667 0.00 0.00 0.00 2.15
2828 5013 1.556911 AGATATGATCGATGGGGCCAC 59.443 52.381 0.54 0.00 0.00 5.01
2849 5034 2.609984 CCAACATGGCTGCGAAAATGAA 60.610 45.455 0.00 0.00 0.00 2.57
2934 5119 1.003580 TGGACATGCAAGAAGAGGGAC 59.996 52.381 0.00 0.00 0.00 4.46
2979 5164 2.024868 CGTCGTTGACATGGGCGAA 61.025 57.895 0.00 0.00 35.08 4.70
3000 5185 1.593311 GCGTTCTACTACTACGACGGC 60.593 57.143 0.00 0.00 37.47 5.68
3033 5218 0.964358 GCAGCTCCAAGAGGCATTGT 60.964 55.000 0.00 0.00 33.74 2.71
3043 5228 3.920231 AGAGGCATTGTAGATCAAGCA 57.080 42.857 0.00 0.00 39.55 3.91
3051 5236 3.526931 TGTAGATCAAGCAGTGGTAGC 57.473 47.619 0.00 0.00 0.00 3.58
3150 5335 1.135286 GCAAGCCAAGCTAATGTCACC 60.135 52.381 0.00 0.00 38.25 4.02
3158 5343 1.139058 AGCTAATGTCACCGACCATCC 59.861 52.381 0.00 0.00 0.00 3.51
3180 5365 1.159285 CTGTGCCGACATCAACACAT 58.841 50.000 4.87 0.00 41.80 3.21
3220 5405 5.791666 TCAATTTGAGCAATGCCAACATTA 58.208 33.333 0.00 0.00 44.83 1.90
3227 5412 4.209538 AGCAATGCCAACATTATCAGCTA 58.790 39.130 0.00 0.00 44.83 3.32
3246 5431 3.553922 GCTACGATAAGGAGAGCAGCAAT 60.554 47.826 0.00 0.00 30.12 3.56
3300 5485 5.408204 TGTGCGACATTATGATGATGAAC 57.592 39.130 4.20 1.74 36.73 3.18
3302 5487 5.353678 TGTGCGACATTATGATGATGAACAA 59.646 36.000 4.20 0.00 36.73 2.83
3357 5542 1.355563 CCGATCGCTCAAGTCGCTA 59.644 57.895 10.32 0.00 34.25 4.26
3367 5552 4.504461 CGCTCAAGTCGCTAATGTAATTCT 59.496 41.667 0.00 0.00 37.87 2.40
3378 5563 5.355350 GCTAATGTAATTCTGTGGCTCAAGT 59.645 40.000 0.00 0.00 37.87 3.16
3454 5639 1.350351 AGCATGCTCCAGTTTGAGAGT 59.650 47.619 16.30 0.00 34.11 3.24
3509 5694 6.536582 TGTATTGTTTGGTCCATTGTGTTTTG 59.463 34.615 0.00 0.00 0.00 2.44
3607 5792 9.495754 CTAAAGCAAATTTAGCTGATAAGTGTC 57.504 33.333 13.49 0.00 42.88 3.67
3640 5825 8.450578 TGAGAGACAACAAGATAATGTGTTTT 57.549 30.769 0.00 0.00 35.81 2.43
3643 5828 8.137437 AGAGACAACAAGATAATGTGTTTTTGG 58.863 33.333 0.00 0.00 35.81 3.28
3686 5880 9.875708 AGATAGATCACCTCTTAATACTGTCTT 57.124 33.333 0.00 0.00 35.28 3.01
3817 6015 6.449635 AGAAAAGTGTGAGTAATGTTGCAA 57.550 33.333 0.00 0.00 0.00 4.08
3831 6030 1.946768 GTTGCAAGTGCTAACCTGTGA 59.053 47.619 0.00 0.00 42.66 3.58
3870 6070 4.141287 CAGAAAAACTCACACACCCCATA 58.859 43.478 0.00 0.00 0.00 2.74
3873 6073 1.344065 AACTCACACACCCCATACGA 58.656 50.000 0.00 0.00 0.00 3.43
3874 6074 0.895530 ACTCACACACCCCATACGAG 59.104 55.000 0.00 0.00 0.00 4.18
3875 6075 0.175760 CTCACACACCCCATACGAGG 59.824 60.000 0.00 0.00 0.00 4.63
3919 6119 2.084121 TTTTAGAGGGGGTGGGGAAT 57.916 50.000 0.00 0.00 0.00 3.01
3956 6156 9.912634 CAACATGTTTACTTGACTTAATCCATT 57.087 29.630 8.77 0.00 0.00 3.16
4020 6223 7.004555 AGATGGGTTTTCCTTAAAATTCACC 57.995 36.000 0.00 0.00 36.96 4.02
4048 6251 3.181490 GGTTGACACTGGTGACCTTTTTC 60.181 47.826 2.11 0.00 30.74 2.29
4063 6266 6.265649 TGACCTTTTTCGTTGGAATTGGATTA 59.734 34.615 0.00 0.00 30.88 1.75
4086 6289 2.403252 CCGCTAGAAAATCTGGTGGT 57.597 50.000 13.36 0.00 46.56 4.16
4089 6292 3.809832 CCGCTAGAAAATCTGGTGGTATG 59.190 47.826 13.36 0.00 46.56 2.39
4104 6307 1.340991 GGTATGCATTGTGGGGTCAGT 60.341 52.381 3.54 0.00 0.00 3.41
4122 6325 5.278022 GGTCAGTCAGGAAACTTTTGATGTC 60.278 44.000 0.00 0.00 40.21 3.06
4123 6326 5.296780 GTCAGTCAGGAAACTTTTGATGTCA 59.703 40.000 0.00 0.00 40.21 3.58
4259 6462 5.361285 TGAGTTTTTAAAACTGGGCTTGCTA 59.639 36.000 25.23 1.13 0.00 3.49
4260 6463 6.127310 TGAGTTTTTAAAACTGGGCTTGCTAA 60.127 34.615 25.23 0.00 0.00 3.09
4299 6502 6.746894 TGGATTTTCCTTATATTGTTGGGGA 58.253 36.000 0.00 0.00 37.46 4.81
4300 6503 6.609616 TGGATTTTCCTTATATTGTTGGGGAC 59.390 38.462 0.00 0.00 37.46 4.46
4325 6531 9.474313 ACTTTTTAATATCTTTAGGCATGTGGA 57.526 29.630 0.00 0.00 0.00 4.02
4360 6566 2.758736 AACCAAGCTAGCTCACTCTG 57.241 50.000 19.65 12.08 0.00 3.35
4361 6567 1.930251 ACCAAGCTAGCTCACTCTGA 58.070 50.000 19.65 0.00 0.00 3.27
4362 6568 1.824230 ACCAAGCTAGCTCACTCTGAG 59.176 52.381 19.65 8.68 46.90 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.467384 CCATCCAACGATGCTCTCCT 59.533 55.000 0.00 0.00 44.00 3.69
51 53 3.659786 GTGCAACTAGTGTGTGGATGTA 58.340 45.455 0.00 0.00 0.00 2.29
76 78 1.303561 GCCAACTGCATCCTGGTCA 60.304 57.895 9.79 0.00 40.77 4.02
103 105 1.205893 CTCAGGCCTCTAACTGGTGTC 59.794 57.143 0.00 0.00 35.47 3.67
127 129 2.156098 CTAGGGCTGATACCTCGTCTC 58.844 57.143 0.00 0.00 39.54 3.36
145 147 2.363795 CGGCACTGAGGTCCCCTA 60.364 66.667 0.00 0.00 31.76 3.53
206 208 0.179119 CCCGTCCATTCGTGGTAGTC 60.179 60.000 0.00 0.00 0.00 2.59
216 218 0.695924 TGTTGATGACCCCGTCCATT 59.304 50.000 0.00 0.00 0.00 3.16
247 249 3.074281 CGGTCCAGCCCCTGTTAA 58.926 61.111 0.00 0.00 0.00 2.01
248 250 3.712907 GCGGTCCAGCCCCTGTTA 61.713 66.667 0.00 0.00 0.00 2.41
258 260 2.520020 ATATCGGTCCGCGGTCCA 60.520 61.111 34.95 24.02 0.00 4.02
354 356 1.736645 GTTGCTCGTCGCCAGCTTA 60.737 57.895 7.37 0.00 37.79 3.09
365 367 1.485066 ACCCCCTACTATTGTTGCTCG 59.515 52.381 0.00 0.00 0.00 5.03
367 369 2.846950 AGACCCCCTACTATTGTTGCT 58.153 47.619 0.00 0.00 0.00 3.91
384 386 1.141858 CCCTTCCTTGGCCATCTAGAC 59.858 57.143 6.09 0.00 0.00 2.59
438 441 0.896226 GCGTCTCTTCCAGTACCCTT 59.104 55.000 0.00 0.00 0.00 3.95
449 452 1.660575 CAACGACACGGCGTCTCTT 60.661 57.895 10.85 0.00 44.86 2.85
459 462 5.244785 TCCATGATAGACTACAACGACAC 57.755 43.478 0.00 0.00 0.00 3.67
511 821 0.882927 CCTTCGCTTCACCGTCCAAA 60.883 55.000 0.00 0.00 0.00 3.28
591 901 1.431633 TGGTGAGACCAGAAGACCCTA 59.568 52.381 0.00 0.00 44.79 3.53
614 924 3.006940 TCGAATACCACCACTTGCATTC 58.993 45.455 0.00 0.00 0.00 2.67
636 946 3.742640 GCACCACTTGGGCATTTTTGTTA 60.743 43.478 0.00 0.00 42.05 2.41
709 1024 6.072783 GCCTGATTCTGAAAATATACTGGAGC 60.073 42.308 0.00 0.00 0.00 4.70
764 1354 1.257743 TGCTGGTTCGCTAACTCTCT 58.742 50.000 0.73 0.00 35.81 3.10
765 1355 2.301577 ATGCTGGTTCGCTAACTCTC 57.698 50.000 0.73 0.00 35.81 3.20
784 1374 1.625315 AGCATGCCTAAGCGATGGATA 59.375 47.619 15.66 0.00 44.31 2.59
807 1397 0.315568 AGCTGACGGAGACTTGTGAC 59.684 55.000 0.00 0.00 0.00 3.67
808 1398 0.598562 GAGCTGACGGAGACTTGTGA 59.401 55.000 0.00 0.00 0.00 3.58
809 1399 0.315251 TGAGCTGACGGAGACTTGTG 59.685 55.000 0.00 0.00 0.00 3.33
810 1400 0.600557 CTGAGCTGACGGAGACTTGT 59.399 55.000 0.00 0.00 0.00 3.16
825 1415 1.268896 ACGGTGAACACGTGTACTGAG 60.269 52.381 28.65 19.71 43.78 3.35
867 1457 1.529244 GGCTGCCAGTGTGGAGTTT 60.529 57.895 15.17 0.00 40.96 2.66
915 1507 2.552315 GGGTTTGAGATTTGTCGAAGCA 59.448 45.455 8.57 0.00 39.26 3.91
1245 1854 1.040893 GGGGCAAAATTACCTCGGGG 61.041 60.000 0.00 0.00 38.88 5.73
1310 1919 4.565022 TCGACACACACACATACATCAAT 58.435 39.130 0.00 0.00 0.00 2.57
1314 1923 4.251543 TCTTCGACACACACACATACAT 57.748 40.909 0.00 0.00 0.00 2.29
1467 2092 2.510012 GCGCGTGGTAACTACCCC 60.510 66.667 8.43 0.00 45.87 4.95
1576 2201 5.336213 CCCACAAGAAAACATCTCCATTCAG 60.336 44.000 0.00 0.00 37.42 3.02
1577 2202 4.523943 CCCACAAGAAAACATCTCCATTCA 59.476 41.667 0.00 0.00 37.42 2.57
1588 2213 2.338620 GCCGCCCCACAAGAAAAC 59.661 61.111 0.00 0.00 0.00 2.43
1612 2240 2.094545 AGTAACCGCGGTAACCAAGTAG 60.095 50.000 34.44 0.00 0.00 2.57
1614 2242 0.681175 AGTAACCGCGGTAACCAAGT 59.319 50.000 34.44 17.08 0.00 3.16
1656 2284 6.239148 GGAGAAATGAAAACCTTGAGCTTCTT 60.239 38.462 0.00 0.00 0.00 2.52
1658 2286 5.242615 AGGAGAAATGAAAACCTTGAGCTTC 59.757 40.000 0.00 0.00 0.00 3.86
1659 2287 5.143369 AGGAGAAATGAAAACCTTGAGCTT 58.857 37.500 0.00 0.00 0.00 3.74
1660 2288 4.734266 AGGAGAAATGAAAACCTTGAGCT 58.266 39.130 0.00 0.00 0.00 4.09
1661 2289 4.764308 AGAGGAGAAATGAAAACCTTGAGC 59.236 41.667 0.00 0.00 0.00 4.26
1662 2290 6.237154 AGAGAGGAGAAATGAAAACCTTGAG 58.763 40.000 0.00 0.00 0.00 3.02
1663 2291 6.192970 AGAGAGGAGAAATGAAAACCTTGA 57.807 37.500 0.00 0.00 0.00 3.02
1664 2292 6.890979 AAGAGAGGAGAAATGAAAACCTTG 57.109 37.500 0.00 0.00 0.00 3.61
1671 2762 9.315363 AGTTAGACTAAAGAGAGGAGAAATGAA 57.685 33.333 0.00 0.00 0.00 2.57
1672 2763 8.887264 AGTTAGACTAAAGAGAGGAGAAATGA 57.113 34.615 0.00 0.00 0.00 2.57
1697 2788 9.416284 GAAAAGGGTGGGACATATATAAGAAAA 57.584 33.333 0.00 0.00 44.52 2.29
1700 2791 7.947782 AGAAAAGGGTGGGACATATATAAGA 57.052 36.000 0.00 0.00 44.52 2.10
1701 2792 8.440771 AGAAGAAAAGGGTGGGACATATATAAG 58.559 37.037 0.00 0.00 44.52 1.73
1744 2835 5.987098 TGGGAGAAAATTCAGAGATGAGAG 58.013 41.667 0.00 0.00 0.00 3.20
1757 2848 5.478503 AGGAAGAATGGATGGGAGAAAAT 57.521 39.130 0.00 0.00 0.00 1.82
1830 2925 8.592809 TGGTCAGAATTTAATTGCTTACCAAAT 58.407 29.630 8.39 0.00 36.92 2.32
1840 2935 9.643693 AGCACTTATTTGGTCAGAATTTAATTG 57.356 29.630 0.00 0.00 0.00 2.32
1858 2953 9.716507 CACGCTATTTTATTGTTAAGCACTTAT 57.283 29.630 0.00 0.00 0.00 1.73
1879 2974 3.059597 GCAATCGCTATGATTTACACGCT 60.060 43.478 0.00 0.00 45.06 5.07
1881 2976 4.451379 TGCAATCGCTATGATTTACACG 57.549 40.909 0.00 0.00 45.06 4.49
1882 2977 7.351414 TCTATGCAATCGCTATGATTTACAC 57.649 36.000 0.00 0.00 45.06 2.90
1883 2978 7.961325 TTCTATGCAATCGCTATGATTTACA 57.039 32.000 0.00 0.00 45.06 2.41
1893 2988 4.082571 AGCAAGTTTTTCTATGCAATCGCT 60.083 37.500 0.00 0.00 41.18 4.93
1929 3024 8.120030 ACTGCGCGTCTATTATTATATTGATG 57.880 34.615 8.43 0.00 0.00 3.07
1976 3071 3.563808 TGCGTTGCAGTGGGAATATAATC 59.436 43.478 0.00 0.00 33.32 1.75
1977 3072 3.550820 TGCGTTGCAGTGGGAATATAAT 58.449 40.909 0.00 0.00 33.32 1.28
1987 3082 2.495366 ATTGCCCATGCGTTGCAGTG 62.495 55.000 0.00 0.00 43.65 3.66
1988 3083 1.818959 AATTGCCCATGCGTTGCAGT 61.819 50.000 0.00 0.00 43.65 4.40
1989 3084 0.173029 TAATTGCCCATGCGTTGCAG 59.827 50.000 0.00 0.00 43.65 4.41
1995 3090 3.188460 GGTACTACATAATTGCCCATGCG 59.812 47.826 0.00 0.00 41.78 4.73
1999 3094 5.702065 TCTTGGTACTACATAATTGCCCA 57.298 39.130 0.00 0.00 0.00 5.36
2069 3164 8.601476 CGTAGCTAAATCGAGGTAAAAGAATTT 58.399 33.333 0.00 0.00 42.41 1.82
2074 3169 8.477709 CAATACGTAGCTAAATCGAGGTAAAAG 58.522 37.037 9.00 0.00 31.50 2.27
2083 3178 7.167635 ACTCATGTTCAATACGTAGCTAAATCG 59.832 37.037 0.08 0.00 0.00 3.34
2087 3182 9.642327 TTAAACTCATGTTCAATACGTAGCTAA 57.358 29.630 0.08 0.00 34.96 3.09
2114 3209 9.941325 TTCCATTACAATTGCAGATTATTTTGT 57.059 25.926 5.05 0.00 0.00 2.83
2131 3226 7.893302 AGGGTTGTCAAGAAATATTCCATTACA 59.107 33.333 0.00 0.00 0.00 2.41
2132 3227 8.293699 AGGGTTGTCAAGAAATATTCCATTAC 57.706 34.615 0.00 0.00 0.00 1.89
2133 3228 8.893563 AAGGGTTGTCAAGAAATATTCCATTA 57.106 30.769 0.00 0.00 0.00 1.90
2134 3229 7.362920 CGAAGGGTTGTCAAGAAATATTCCATT 60.363 37.037 0.00 0.00 0.00 3.16
2135 3230 6.095440 CGAAGGGTTGTCAAGAAATATTCCAT 59.905 38.462 0.00 0.00 0.00 3.41
2136 3231 5.414454 CGAAGGGTTGTCAAGAAATATTCCA 59.586 40.000 0.00 0.00 0.00 3.53
2137 3232 5.646360 TCGAAGGGTTGTCAAGAAATATTCC 59.354 40.000 0.00 0.00 0.00 3.01
2138 3233 6.183360 CCTCGAAGGGTTGTCAAGAAATATTC 60.183 42.308 0.00 0.00 0.00 1.75
2139 3234 5.648092 CCTCGAAGGGTTGTCAAGAAATATT 59.352 40.000 0.00 0.00 0.00 1.28
2140 3235 5.186198 CCTCGAAGGGTTGTCAAGAAATAT 58.814 41.667 0.00 0.00 0.00 1.28
2141 3236 4.575885 CCTCGAAGGGTTGTCAAGAAATA 58.424 43.478 0.00 0.00 0.00 1.40
2142 3237 3.412386 CCTCGAAGGGTTGTCAAGAAAT 58.588 45.455 0.00 0.00 0.00 2.17
2143 3238 2.846193 CCTCGAAGGGTTGTCAAGAAA 58.154 47.619 0.00 0.00 0.00 2.52
2144 3239 2.543777 CCTCGAAGGGTTGTCAAGAA 57.456 50.000 0.00 0.00 0.00 2.52
2155 3250 1.107945 GAGAACTCTCCCCTCGAAGG 58.892 60.000 0.00 0.00 37.02 3.46
2160 3255 0.528470 CACACGAGAACTCTCCCCTC 59.472 60.000 1.13 0.00 39.79 4.30
2161 3256 0.900647 CCACACGAGAACTCTCCCCT 60.901 60.000 1.13 0.00 39.79 4.79
2162 3257 1.592223 CCACACGAGAACTCTCCCC 59.408 63.158 1.13 0.00 39.79 4.81
2163 3258 1.186267 ACCCACACGAGAACTCTCCC 61.186 60.000 1.13 0.00 39.79 4.30
2164 3259 0.680061 AACCCACACGAGAACTCTCC 59.320 55.000 1.13 0.00 39.79 3.71
2165 3260 2.135933 CAAACCCACACGAGAACTCTC 58.864 52.381 0.00 0.00 39.55 3.20
2166 3261 1.760613 TCAAACCCACACGAGAACTCT 59.239 47.619 0.00 0.00 0.00 3.24
2167 3262 2.234300 TCAAACCCACACGAGAACTC 57.766 50.000 0.00 0.00 0.00 3.01
2168 3263 2.930826 ATCAAACCCACACGAGAACT 57.069 45.000 0.00 0.00 0.00 3.01
2169 3264 3.139077 AGAATCAAACCCACACGAGAAC 58.861 45.455 0.00 0.00 0.00 3.01
2170 3265 3.071023 AGAGAATCAAACCCACACGAGAA 59.929 43.478 0.00 0.00 37.82 2.87
2171 3266 2.632996 AGAGAATCAAACCCACACGAGA 59.367 45.455 0.00 0.00 37.82 4.04
2172 3267 3.045601 AGAGAATCAAACCCACACGAG 57.954 47.619 0.00 0.00 37.82 4.18
2173 3268 4.819105 ATAGAGAATCAAACCCACACGA 57.181 40.909 0.00 0.00 37.82 4.35
2174 3269 4.032900 CGAATAGAGAATCAAACCCACACG 59.967 45.833 0.00 0.00 37.82 4.49
2175 3270 4.201822 GCGAATAGAGAATCAAACCCACAC 60.202 45.833 0.00 0.00 37.82 3.82
2176 3271 3.938963 GCGAATAGAGAATCAAACCCACA 59.061 43.478 0.00 0.00 37.82 4.17
2177 3272 3.938963 TGCGAATAGAGAATCAAACCCAC 59.061 43.478 0.00 0.00 37.82 4.61
2178 3273 4.081142 TCTGCGAATAGAGAATCAAACCCA 60.081 41.667 0.00 0.00 37.82 4.51
2179 3274 4.442706 TCTGCGAATAGAGAATCAAACCC 58.557 43.478 0.00 0.00 37.82 4.11
2180 3275 6.926272 AGTATCTGCGAATAGAGAATCAAACC 59.074 38.462 0.00 0.00 37.82 3.27
2181 3276 7.782242 CAGTATCTGCGAATAGAGAATCAAAC 58.218 38.462 0.00 0.00 37.82 2.93
2182 3277 7.936950 CAGTATCTGCGAATAGAGAATCAAA 57.063 36.000 0.00 0.00 37.82 2.69
2198 3293 2.946329 AGTCCTCGTGTAGCAGTATCTG 59.054 50.000 0.00 0.00 34.12 2.90
2199 3294 3.284793 AGTCCTCGTGTAGCAGTATCT 57.715 47.619 0.00 0.00 0.00 1.98
2200 3295 4.128643 ACTAGTCCTCGTGTAGCAGTATC 58.871 47.826 0.00 0.00 0.00 2.24
2201 3296 4.153673 ACTAGTCCTCGTGTAGCAGTAT 57.846 45.455 0.00 0.00 0.00 2.12
2202 3297 3.623906 ACTAGTCCTCGTGTAGCAGTA 57.376 47.619 0.00 0.00 0.00 2.74
2203 3298 2.488545 CAACTAGTCCTCGTGTAGCAGT 59.511 50.000 0.00 0.00 0.00 4.40
2204 3299 2.159366 CCAACTAGTCCTCGTGTAGCAG 60.159 54.545 0.00 0.00 0.00 4.24
2205 3300 1.816835 CCAACTAGTCCTCGTGTAGCA 59.183 52.381 0.00 0.00 0.00 3.49
2206 3301 1.469423 GCCAACTAGTCCTCGTGTAGC 60.469 57.143 0.00 0.00 0.00 3.58
2207 3302 1.816835 TGCCAACTAGTCCTCGTGTAG 59.183 52.381 0.00 0.00 0.00 2.74
2208 3303 1.913778 TGCCAACTAGTCCTCGTGTA 58.086 50.000 0.00 0.00 0.00 2.90
2209 3304 1.066858 CATGCCAACTAGTCCTCGTGT 60.067 52.381 0.00 0.00 0.00 4.49
2210 3305 1.645034 CATGCCAACTAGTCCTCGTG 58.355 55.000 0.00 0.00 0.00 4.35
2211 3306 0.108138 GCATGCCAACTAGTCCTCGT 60.108 55.000 6.36 0.00 0.00 4.18
2212 3307 0.176680 AGCATGCCAACTAGTCCTCG 59.823 55.000 15.66 0.00 0.00 4.63
2213 3308 2.409948 AAGCATGCCAACTAGTCCTC 57.590 50.000 15.66 0.00 0.00 3.71
2214 3309 2.887151 AAAGCATGCCAACTAGTCCT 57.113 45.000 15.66 0.00 0.00 3.85
2215 3310 3.084786 AGAAAAGCATGCCAACTAGTCC 58.915 45.455 15.66 0.00 0.00 3.85
2216 3311 4.695455 TGTAGAAAAGCATGCCAACTAGTC 59.305 41.667 15.66 2.62 0.00 2.59
2217 3312 4.651778 TGTAGAAAAGCATGCCAACTAGT 58.348 39.130 15.66 0.00 0.00 2.57
2218 3313 5.449588 CCATGTAGAAAAGCATGCCAACTAG 60.450 44.000 15.66 2.60 40.63 2.57
2219 3314 4.398988 CCATGTAGAAAAGCATGCCAACTA 59.601 41.667 15.66 10.37 40.63 2.24
2220 3315 3.194116 CCATGTAGAAAAGCATGCCAACT 59.806 43.478 15.66 11.38 40.63 3.16
2221 3316 3.514645 CCATGTAGAAAAGCATGCCAAC 58.485 45.455 15.66 3.82 40.63 3.77
2222 3317 2.496871 CCCATGTAGAAAAGCATGCCAA 59.503 45.455 15.66 0.00 40.63 4.52
2223 3318 2.101783 CCCATGTAGAAAAGCATGCCA 58.898 47.619 15.66 3.22 40.63 4.92
2224 3319 2.378038 TCCCATGTAGAAAAGCATGCC 58.622 47.619 15.66 0.00 40.63 4.40
2225 3320 5.242393 ACATATCCCATGTAGAAAAGCATGC 59.758 40.000 10.51 10.51 40.63 4.06
2226 3321 6.889301 ACATATCCCATGTAGAAAAGCATG 57.111 37.500 0.00 0.00 41.37 4.06
2227 3322 9.236006 GATAACATATCCCATGTAGAAAAGCAT 57.764 33.333 0.00 0.00 0.00 3.79
2228 3323 8.439971 AGATAACATATCCCATGTAGAAAAGCA 58.560 33.333 0.00 0.00 0.00 3.91
2229 3324 8.725148 CAGATAACATATCCCATGTAGAAAAGC 58.275 37.037 0.00 0.00 0.00 3.51
2230 3325 9.224267 CCAGATAACATATCCCATGTAGAAAAG 57.776 37.037 0.00 0.00 0.00 2.27
2231 3326 8.723365 ACCAGATAACATATCCCATGTAGAAAA 58.277 33.333 0.00 0.00 0.00 2.29
2232 3327 8.156820 CACCAGATAACATATCCCATGTAGAAA 58.843 37.037 0.00 0.00 0.00 2.52
2233 3328 7.512402 TCACCAGATAACATATCCCATGTAGAA 59.488 37.037 0.00 0.00 0.00 2.10
2234 3329 7.016296 TCACCAGATAACATATCCCATGTAGA 58.984 38.462 0.00 0.00 0.00 2.59
2257 3352 0.329261 CCCTTCCCAGCTGACATTCA 59.671 55.000 17.39 0.00 0.00 2.57
2359 3585 6.976934 AATATGGCAATTTACGGGAAGAAT 57.023 33.333 0.00 0.00 0.00 2.40
2385 3613 6.060788 AGCTAGGAGGATGCAATTTCTTTAG 58.939 40.000 0.00 0.00 0.00 1.85
2386 3614 6.006275 AGCTAGGAGGATGCAATTTCTTTA 57.994 37.500 0.00 0.00 0.00 1.85
2389 3617 5.636903 TTAGCTAGGAGGATGCAATTTCT 57.363 39.130 0.00 0.00 0.00 2.52
2390 3618 5.767168 ACATTAGCTAGGAGGATGCAATTTC 59.233 40.000 0.00 0.00 0.00 2.17
2393 3621 4.989875 ACATTAGCTAGGAGGATGCAAT 57.010 40.909 0.00 0.00 0.00 3.56
2395 3623 4.454678 CAAACATTAGCTAGGAGGATGCA 58.545 43.478 2.85 0.00 0.00 3.96
2396 3624 3.251972 GCAAACATTAGCTAGGAGGATGC 59.748 47.826 2.85 3.74 0.00 3.91
2409 3637 7.157347 TGAATGTATTTTGCCAGCAAACATTA 58.843 30.769 23.61 10.49 44.39 1.90
2441 3757 7.222999 CCGGAAATACTTGTCAGAGAAAGTATC 59.777 40.741 14.72 7.80 44.80 2.24
2442 3758 7.042335 CCGGAAATACTTGTCAGAGAAAGTAT 58.958 38.462 0.00 10.73 46.56 2.12
2443 3759 6.209986 TCCGGAAATACTTGTCAGAGAAAGTA 59.790 38.462 0.00 7.72 41.70 2.24
2445 3761 5.479306 TCCGGAAATACTTGTCAGAGAAAG 58.521 41.667 0.00 0.00 0.00 2.62
2450 3766 3.772572 TCCATCCGGAAATACTTGTCAGA 59.227 43.478 9.01 0.00 38.83 3.27
2452 3768 3.677700 CGTCCATCCGGAAATACTTGTCA 60.678 47.826 9.01 0.00 45.20 3.58
2453 3769 2.864343 CGTCCATCCGGAAATACTTGTC 59.136 50.000 9.01 0.00 45.20 3.18
2471 3787 7.361628 GCTTAGTATATAGTCAAGTACCCCGTC 60.362 44.444 0.00 0.00 0.00 4.79
2542 4354 1.515081 GCCCAGTAACTGCGTTTGTA 58.485 50.000 0.00 0.00 0.00 2.41
2549 4362 1.400494 CAATTACCGCCCAGTAACTGC 59.600 52.381 0.00 0.00 35.14 4.40
2567 4380 7.873719 TTTCGATCCTAGGCAATAAATTCAA 57.126 32.000 2.96 0.00 0.00 2.69
2568 4381 7.873719 TTTTCGATCCTAGGCAATAAATTCA 57.126 32.000 2.96 0.00 0.00 2.57
2577 4390 3.038280 TCAGGATTTTCGATCCTAGGCA 58.962 45.455 2.96 0.00 46.22 4.75
2584 4397 3.251972 GGGCAAGATCAGGATTTTCGATC 59.748 47.826 0.00 0.00 36.59 3.69
2586 4399 2.643551 GGGCAAGATCAGGATTTTCGA 58.356 47.619 0.00 0.00 0.00 3.71
2605 4418 0.031212 AAATGGGTTAGGGGCATGGG 60.031 55.000 0.00 0.00 0.00 4.00
2746 4931 0.394899 CTGGATGGGAAGAGCCAACC 60.395 60.000 0.00 0.00 38.95 3.77
2815 5000 1.936767 ATGTTGGTGGCCCCATCGAT 61.937 55.000 13.07 0.00 44.74 3.59
2828 5013 1.067706 TCATTTTCGCAGCCATGTTGG 60.068 47.619 0.00 0.00 41.55 3.77
2849 5034 3.383223 CTCTCATTCTTCTTCCCCTCCT 58.617 50.000 0.00 0.00 0.00 3.69
2979 5164 1.929836 CCGTCGTAGTAGTAGAACGCT 59.070 52.381 6.27 0.00 36.60 5.07
3000 5185 2.879907 CTGCGTGATGGGCCAAAG 59.120 61.111 11.89 3.16 0.00 2.77
3009 5194 1.220206 CCTCTTGGAGCTGCGTGAT 59.780 57.895 0.00 0.00 34.57 3.06
3033 5218 3.099905 ACTGCTACCACTGCTTGATCTA 58.900 45.455 0.00 0.00 0.00 1.98
3051 5236 1.517242 GAGGTTCTTCCAGCACACTG 58.483 55.000 0.00 0.00 44.05 3.66
3163 5348 0.874390 ACATGTGTTGATGTCGGCAC 59.126 50.000 0.00 0.00 30.34 5.01
3202 5387 4.678574 GCTGATAATGTTGGCATTGCTCAA 60.679 41.667 8.82 8.35 44.32 3.02
3203 5388 3.181484 GCTGATAATGTTGGCATTGCTCA 60.181 43.478 8.82 6.41 44.32 4.26
3220 5405 3.491342 TGCTCTCCTTATCGTAGCTGAT 58.509 45.455 0.00 0.00 34.28 2.90
3227 5412 2.432146 TCATTGCTGCTCTCCTTATCGT 59.568 45.455 0.00 0.00 0.00 3.73
3246 5431 2.530497 GCAACCAAGTGCGTCGTCA 61.530 57.895 0.00 0.00 34.21 4.35
3277 5462 5.528320 TGTTCATCATCATAATGTCGCACAT 59.472 36.000 0.00 0.00 41.31 3.21
3280 5465 5.220835 GGTTGTTCATCATCATAATGTCGCA 60.221 40.000 0.00 0.00 34.32 5.10
3300 5485 1.873591 CACCTCTTCTTGAACGGGTTG 59.126 52.381 0.00 0.00 0.00 3.77
3302 5487 0.396811 CCACCTCTTCTTGAACGGGT 59.603 55.000 0.00 0.00 0.00 5.28
3357 5542 5.316167 TCACTTGAGCCACAGAATTACATT 58.684 37.500 0.00 0.00 0.00 2.71
3367 5552 3.806941 AAGCTTCACTTGAGCCACA 57.193 47.368 0.00 0.00 37.17 4.17
3449 5634 9.817809 TGTATATTGATTGGTAACTCAACTCTC 57.182 33.333 0.00 0.00 34.43 3.20
3490 5675 4.566360 CAGTCAAAACACAATGGACCAAAC 59.434 41.667 0.00 0.00 0.00 2.93
3509 5694 1.225855 TTCAACACCGCATCACAGTC 58.774 50.000 0.00 0.00 0.00 3.51
3573 5758 8.177663 TCAGCTAAATTTGCTTTAGATTTCTCG 58.822 33.333 11.03 0.00 46.26 4.04
3640 5825 9.642343 TCTATCTCTAGCTTCATTAGTAACCAA 57.358 33.333 0.00 0.00 0.00 3.67
3817 6015 2.180276 CCTAGGTCACAGGTTAGCACT 58.820 52.381 0.00 0.00 0.00 4.40
3831 6030 1.361543 TCTGCCAGTTCTACCCTAGGT 59.638 52.381 8.29 0.00 40.16 3.08
3870 6070 2.807676 AGGCCAATCATTTTTCCTCGT 58.192 42.857 5.01 0.00 0.00 4.18
3873 6073 6.215227 TCCATAAAAGGCCAATCATTTTTCCT 59.785 34.615 5.01 0.00 39.17 3.36
3874 6074 6.413892 TCCATAAAAGGCCAATCATTTTTCC 58.586 36.000 5.01 0.00 39.17 3.13
3875 6075 7.920160 TTCCATAAAAGGCCAATCATTTTTC 57.080 32.000 5.01 0.00 39.17 2.29
3956 6156 5.755409 TCTAGGAAAACCAAGTGATGCTA 57.245 39.130 0.00 0.00 0.00 3.49
3997 6197 6.764379 TGGTGAATTTTAAGGAAAACCCATC 58.236 36.000 0.00 0.00 37.37 3.51
3999 6199 5.900123 TCTGGTGAATTTTAAGGAAAACCCA 59.100 36.000 0.00 0.00 37.37 4.51
4020 6223 2.614057 GTCACCAGTGTCAACCTTTCTG 59.386 50.000 0.00 0.00 0.00 3.02
4033 6236 2.021457 CCAACGAAAAAGGTCACCAGT 58.979 47.619 0.00 0.00 0.00 4.00
4063 6266 3.535561 CACCAGATTTTCTAGCGGACAT 58.464 45.455 0.00 0.00 0.00 3.06
4072 6275 5.018809 ACAATGCATACCACCAGATTTTCT 58.981 37.500 0.00 0.00 0.00 2.52
4077 6280 2.658285 CCACAATGCATACCACCAGAT 58.342 47.619 0.00 0.00 0.00 2.90
4086 6289 1.632920 TGACTGACCCCACAATGCATA 59.367 47.619 0.00 0.00 0.00 3.14
4089 6292 0.962356 CCTGACTGACCCCACAATGC 60.962 60.000 0.00 0.00 0.00 3.56
4104 6307 6.550854 AGGAAATGACATCAAAAGTTTCCTGA 59.449 34.615 19.48 0.00 43.99 3.86
4122 6325 8.400947 CACATACTTCCAGATTTACAGGAAATG 58.599 37.037 0.00 0.00 42.18 2.32
4123 6326 8.109634 ACACATACTTCCAGATTTACAGGAAAT 58.890 33.333 0.00 0.00 42.18 2.17
4246 6449 4.687901 ACAAAAATTAGCAAGCCCAGTT 57.312 36.364 0.00 0.00 0.00 3.16
4247 6450 5.799827 TTACAAAAATTAGCAAGCCCAGT 57.200 34.783 0.00 0.00 0.00 4.00
4248 6451 6.397272 TCATTACAAAAATTAGCAAGCCCAG 58.603 36.000 0.00 0.00 0.00 4.45
4249 6452 6.352016 TCATTACAAAAATTAGCAAGCCCA 57.648 33.333 0.00 0.00 0.00 5.36
4250 6453 8.981647 CATATCATTACAAAAATTAGCAAGCCC 58.018 33.333 0.00 0.00 0.00 5.19
4251 6454 8.981647 CCATATCATTACAAAAATTAGCAAGCC 58.018 33.333 0.00 0.00 0.00 4.35
4299 6502 9.474313 TCCACATGCCTAAAGATATTAAAAAGT 57.526 29.630 0.00 0.00 0.00 2.66
4312 6518 4.842531 TCTTCTCATCCACATGCCTAAA 57.157 40.909 0.00 0.00 0.00 1.85
4325 6531 9.171877 CTAGCTTGGTTTTCTTATTCTTCTCAT 57.828 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.