Multiple sequence alignment - TraesCS7D01G064900

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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 TraesCS7D01G064900 chr7D 100.000 3820 0 0 1 3820 36046147 36042328 0.000000e+00 7055.0
1 TraesCS7D01G064900 chr7D 90.272 1285 112 9 1732 3010 35552400 35553677 0.000000e+00 1668.0
2 TraesCS7D01G064900 chr7D 96.075 1019 40 0 1822 2840 35798298 35797280 0.000000e+00 1661.0
3 TraesCS7D01G064900 chr7D 92.727 715 41 5 928 1640 35799166 35798461 0.000000e+00 1022.0
4 TraesCS7D01G064900 chr7D 98.810 168 2 0 3197 3364 100234174 100234007 2.230000e-77 300.0
5 TraesCS7D01G064900 chr7D 96.610 177 6 0 3187 3363 604569378 604569202 1.040000e-75 294.0
6 TraesCS7D01G064900 chr7D 92.857 112 8 0 3003 3114 35796971 35796860 3.050000e-36 163.0
7 TraesCS7D01G064900 chr7D 73.451 565 93 35 35 571 21621120 21620585 3.950000e-35 159.0
8 TraesCS7D01G064900 chr4A 94.611 2264 101 7 935 3198 687830965 687833207 0.000000e+00 3485.0
9 TraesCS7D01G064900 chr4A 94.408 2271 109 7 931 3198 687892464 687894719 0.000000e+00 3474.0
10 TraesCS7D01G064900 chr4A 94.281 2273 97 9 928 3198 687813418 687815659 0.000000e+00 3446.0
11 TraesCS7D01G064900 chr4A 93.198 2264 110 8 935 3198 687919283 687921502 0.000000e+00 3288.0
12 TraesCS7D01G064900 chr4A 90.205 1950 173 11 994 2937 688375390 688373453 0.000000e+00 2527.0
13 TraesCS7D01G064900 chr4A 90.154 1950 174 11 994 2937 688327787 688325850 0.000000e+00 2521.0
14 TraesCS7D01G064900 chr4A 93.571 1011 52 5 2191 3198 687866393 687867393 0.000000e+00 1495.0
15 TraesCS7D01G064900 chr4A 84.666 1213 140 19 1815 3022 687870239 687871410 0.000000e+00 1168.0
16 TraesCS7D01G064900 chr4A 85.052 863 94 24 3 852 687812580 687813420 0.000000e+00 846.0
17 TraesCS7D01G064900 chr4A 91.884 345 27 1 940 1284 687928551 687928894 7.420000e-132 481.0
18 TraesCS7D01G064900 chr4A 85.106 282 33 9 3543 3819 687816020 687816297 2.910000e-71 279.0
19 TraesCS7D01G064900 chr4A 87.917 240 25 4 3363 3600 687833210 687833447 2.910000e-71 279.0
20 TraesCS7D01G064900 chr4A 85.106 282 33 9 3543 3819 687895080 687895357 2.910000e-71 279.0
21 TraesCS7D01G064900 chr4A 88.646 229 22 4 3363 3588 687894722 687894949 3.760000e-70 276.0
22 TraesCS7D01G064900 chr4A 88.210 229 23 4 3363 3588 687815662 687815889 1.750000e-68 270.0
23 TraesCS7D01G064900 chr4A 85.824 261 29 8 3563 3819 687921883 687922139 1.750000e-68 270.0
24 TraesCS7D01G064900 chr4A 87.879 231 24 4 3363 3591 687867396 687867624 6.290000e-68 268.0
25 TraesCS7D01G064900 chr4A 87.773 229 23 5 3363 3588 687921505 687921731 2.930000e-66 263.0
26 TraesCS7D01G064900 chr4A 83.974 156 19 4 2860 3010 687829137 687829291 1.110000e-30 145.0
27 TraesCS7D01G064900 chr4A 71.649 582 124 24 1 564 608240276 608239718 5.180000e-24 122.0
28 TraesCS7D01G064900 chr7A 95.242 2186 88 7 928 3109 35696528 35698701 0.000000e+00 3446.0
29 TraesCS7D01G064900 chr7A 94.213 743 42 1 978 1720 35746355 35747096 0.000000e+00 1133.0
30 TraesCS7D01G064900 chr7A 86.334 461 53 9 3363 3820 35706941 35707394 9.530000e-136 494.0
31 TraesCS7D01G064900 chr7A 84.272 426 30 16 429 852 35696140 35696530 7.740000e-102 381.0
32 TraesCS7D01G064900 chr7A 90.972 288 13 3 1 277 35694767 35695052 3.600000e-100 375.0
33 TraesCS7D01G064900 chr7A 79.054 148 21 6 417 561 694994724 694994864 4.060000e-15 93.5
34 TraesCS7D01G064900 chr7A 78.689 122 16 6 417 537 695091742 695091854 5.290000e-09 73.1
35 TraesCS7D01G064900 chr7A 97.143 35 1 0 503 537 694659906 694659940 4.120000e-05 60.2
36 TraesCS7D01G064900 chr2D 98.810 168 2 0 3194 3361 44329498 44329665 2.230000e-77 300.0
37 TraesCS7D01G064900 chr2D 98.235 170 3 0 3194 3363 591952206 591952037 8.020000e-77 298.0
38 TraesCS7D01G064900 chr2D 74.558 566 95 30 35 571 617981378 617980833 6.470000e-48 202.0
39 TraesCS7D01G064900 chr2D 90.526 95 6 3 850 942 378290893 378290800 5.180000e-24 122.0
40 TraesCS7D01G064900 chr2D 86.567 67 9 0 427 493 14225457 14225391 1.470000e-09 75.0
41 TraesCS7D01G064900 chr3D 97.175 177 4 1 3189 3365 563837756 563837581 8.020000e-77 298.0
42 TraesCS7D01G064900 chr3D 97.143 175 5 0 3193 3367 402850800 402850626 2.890000e-76 296.0
43 TraesCS7D01G064900 chr3D 74.188 585 102 29 11 567 48268358 48268921 8.370000e-47 198.0
44 TraesCS7D01G064900 chr3D 94.186 86 4 1 846 930 45429582 45429497 3.100000e-26 130.0
45 TraesCS7D01G064900 chr6D 97.674 172 4 0 3195 3366 5180429 5180258 2.890000e-76 296.0
46 TraesCS7D01G064900 chr6D 96.610 177 5 1 3190 3366 448381535 448381710 3.730000e-75 292.0
47 TraesCS7D01G064900 chr1D 96.629 178 5 1 3184 3360 115018772 115018595 1.040000e-75 294.0
48 TraesCS7D01G064900 chr1D 75.394 508 90 26 11 493 398480915 398481412 2.990000e-51 213.0
49 TraesCS7D01G064900 chr1D 74.106 587 108 27 11 571 246041654 246042222 6.470000e-48 202.0
50 TraesCS7D01G064900 chr1D 95.349 86 3 1 848 933 487321430 487321514 6.660000e-28 135.0
51 TraesCS7D01G064900 chr1D 75.403 248 37 13 33 260 332211861 332211618 8.730000e-17 99.0
52 TraesCS7D01G064900 chr4D 75.294 510 87 26 11 493 44042830 44043327 1.390000e-49 207.0
53 TraesCS7D01G064900 chrUn 72.978 507 95 28 1 485 126948435 126947949 5.150000e-29 139.0
54 TraesCS7D01G064900 chr5A 94.186 86 3 2 846 930 670543091 670543007 3.100000e-26 130.0
55 TraesCS7D01G064900 chr5B 76.384 271 45 12 1 255 691474704 691474437 1.110000e-25 128.0
56 TraesCS7D01G064900 chr5D 95.062 81 3 1 850 930 277244592 277244671 4.010000e-25 126.0
57 TraesCS7D01G064900 chr5D 90.722 97 3 2 850 941 456610433 456610338 1.440000e-24 124.0
58 TraesCS7D01G064900 chr1A 91.579 95 2 2 840 929 90811244 90811151 4.010000e-25 126.0
59 TraesCS7D01G064900 chr1A 91.579 95 1 5 850 939 584082814 584082906 1.440000e-24 124.0
60 TraesCS7D01G064900 chr1B 89.109 101 6 2 842 937 543485668 543485768 1.860000e-23 121.0
61 TraesCS7D01G064900 chr6A 100.000 28 0 0 503 530 71087447 71087420 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G064900 chr7D 36042328 36046147 3819 True 7055.000000 7055 100.000000 1 3820 1 chr7D.!!$R2 3819
1 TraesCS7D01G064900 chr7D 35552400 35553677 1277 False 1668.000000 1668 90.272000 1732 3010 1 chr7D.!!$F1 1278
2 TraesCS7D01G064900 chr7D 35796860 35799166 2306 True 948.666667 1661 93.886333 928 3114 3 chr7D.!!$R5 2186
3 TraesCS7D01G064900 chr4A 688373453 688375390 1937 True 2527.000000 2527 90.205000 994 2937 1 chr4A.!!$R3 1943
4 TraesCS7D01G064900 chr4A 688325850 688327787 1937 True 2521.000000 2521 90.154000 994 2937 1 chr4A.!!$R2 1943
5 TraesCS7D01G064900 chr4A 687892464 687895357 2893 False 1343.000000 3474 89.386667 931 3819 3 chr4A.!!$F5 2888
6 TraesCS7D01G064900 chr4A 687829137 687833447 4310 False 1303.000000 3485 88.834000 935 3600 3 chr4A.!!$F3 2665
7 TraesCS7D01G064900 chr4A 687919283 687922139 2856 False 1273.666667 3288 88.931667 935 3819 3 chr4A.!!$F6 2884
8 TraesCS7D01G064900 chr4A 687812580 687816297 3717 False 1210.250000 3446 88.162250 3 3819 4 chr4A.!!$F2 3816
9 TraesCS7D01G064900 chr4A 687866393 687871410 5017 False 977.000000 1495 88.705333 1815 3591 3 chr4A.!!$F4 1776
10 TraesCS7D01G064900 chr7A 35694767 35698701 3934 False 1400.666667 3446 90.162000 1 3109 3 chr7A.!!$F6 3108
11 TraesCS7D01G064900 chr7A 35746355 35747096 741 False 1133.000000 1133 94.213000 978 1720 1 chr7A.!!$F2 742
12 TraesCS7D01G064900 chr2D 617980833 617981378 545 True 202.000000 202 74.558000 35 571 1 chr2D.!!$R4 536
13 TraesCS7D01G064900 chr1D 246041654 246042222 568 False 202.000000 202 74.106000 11 571 1 chr1D.!!$F1 560

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
360 1153 0.107214 ATGGTTAGTGTGGATGGCCG 60.107 55.0 0.00 0.00 36.79 6.13 F
507 1470 0.321996 TGTGTGCGCACCCATTAGTA 59.678 50.0 35.72 13.53 44.65 1.82 F
1847 3880 0.810648 GATTCAAGAACATGGCCGCA 59.189 50.0 0.00 0.00 0.00 5.69 F
2525 4563 0.322456 CCTTCATCTTGCCCACCGAA 60.322 55.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 2183 0.387622 CGTAGGCGTCCGTGAAGAAA 60.388 55.0 0.0 0.0 0.00 2.52 R
2255 4293 0.600255 GCGTGCGGGCTATCTTGTAT 60.600 55.0 0.0 0.0 0.00 2.29 R
2729 4795 0.251608 CTTCCACCATTTCCCCGGTT 60.252 55.0 0.0 0.0 31.41 4.44 R
3443 5740 0.911045 AATACCCCCTCGGTCGGTTT 60.911 55.0 0.0 0.0 43.58 3.27 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
191 212 5.278266 GGTTACATTGTTGAAAGCACTGCTA 60.278 40.000 3.33 0.00 38.25 3.49
287 1077 2.094854 GCTCTTGACTGCCATTTCCTTG 60.095 50.000 0.00 0.00 0.00 3.61
292 1082 0.963962 ACTGCCATTTCCTTGCTGTG 59.036 50.000 0.00 0.00 36.10 3.66
297 1087 0.169672 CATTTCCTTGCTGTGAGGCG 59.830 55.000 0.00 0.00 34.17 5.52
337 1128 7.430992 TTTCTCAATGTCTTTGTGATCTGAG 57.569 36.000 0.00 0.00 37.59 3.35
347 1138 5.721480 TCTTTGTGATCTGAGGAGATGGTTA 59.279 40.000 0.00 0.00 39.19 2.85
358 1149 2.565841 GAGATGGTTAGTGTGGATGGC 58.434 52.381 0.00 0.00 0.00 4.40
360 1153 0.107214 ATGGTTAGTGTGGATGGCCG 60.107 55.000 0.00 0.00 36.79 6.13
364 1157 0.958382 TTAGTGTGGATGGCCGTTGC 60.958 55.000 0.00 0.00 36.79 4.17
400 1193 8.492673 TGATAACTGTTTTGATCGCTTCTTAT 57.507 30.769 0.00 0.00 0.00 1.73
430 1227 4.041691 TCTTTTCACTTTCCTCCACCTAGG 59.958 45.833 7.41 7.41 38.06 3.02
477 1440 2.322161 CTCTTTGCTGGCGTCATTTTG 58.678 47.619 0.00 0.00 0.00 2.44
478 1441 1.680735 TCTTTGCTGGCGTCATTTTGT 59.319 42.857 0.00 0.00 0.00 2.83
479 1442 1.788308 CTTTGCTGGCGTCATTTTGTG 59.212 47.619 0.00 0.00 0.00 3.33
492 1455 3.254411 TCATTTTGTGTGTGTGTGTGTGT 59.746 39.130 0.00 0.00 0.00 3.72
507 1470 0.321996 TGTGTGCGCACCCATTAGTA 59.678 50.000 35.72 13.53 44.65 1.82
526 1489 4.517285 AGTATTGGTTGTGTGCATCCTAG 58.483 43.478 0.00 0.00 35.89 3.02
540 1503 5.880332 GTGCATCCTAGTTATGAAAAGACCA 59.120 40.000 6.52 0.00 0.00 4.02
564 1527 5.938125 AGGTCCATACTCATTGTGTTTGTAC 59.062 40.000 8.00 3.64 0.00 2.90
642 1605 3.269538 TGTTTCCGTCCTTTTGTCTCA 57.730 42.857 0.00 0.00 0.00 3.27
658 1621 4.699637 TGTCTCAATACGGAACAACTGTT 58.300 39.130 0.00 0.00 41.64 3.16
685 1648 2.417719 GTCTTCATTCTGTTGCCGTCT 58.582 47.619 0.00 0.00 0.00 4.18
853 1817 5.246307 AGTACAGGGCAAAAATCACTACTC 58.754 41.667 0.00 0.00 0.00 2.59
857 1821 3.017442 GGGCAAAAATCACTACTCCCTC 58.983 50.000 0.00 0.00 0.00 4.30
859 1823 2.678336 GCAAAAATCACTACTCCCTCCG 59.322 50.000 0.00 0.00 0.00 4.63
861 1825 4.622220 GCAAAAATCACTACTCCCTCCGTA 60.622 45.833 0.00 0.00 0.00 4.02
863 1827 5.750352 AAAATCACTACTCCCTCCGTAAA 57.250 39.130 0.00 0.00 0.00 2.01
864 1828 4.732672 AATCACTACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
868 1832 5.513233 TCACTACTCCCTCCGTAAACTAAT 58.487 41.667 0.00 0.00 0.00 1.73
869 1833 5.359009 TCACTACTCCCTCCGTAAACTAATG 59.641 44.000 0.00 0.00 0.00 1.90
870 1834 5.126707 CACTACTCCCTCCGTAAACTAATGT 59.873 44.000 0.00 0.00 0.00 2.71
871 1835 6.319658 CACTACTCCCTCCGTAAACTAATGTA 59.680 42.308 0.00 0.00 0.00 2.29
872 1836 6.891908 ACTACTCCCTCCGTAAACTAATGTAA 59.108 38.462 0.00 0.00 0.00 2.41
873 1837 6.218108 ACTCCCTCCGTAAACTAATGTAAG 57.782 41.667 0.00 0.00 0.00 2.34
874 1838 5.954150 ACTCCCTCCGTAAACTAATGTAAGA 59.046 40.000 0.00 0.00 0.00 2.10
875 1839 6.096564 ACTCCCTCCGTAAACTAATGTAAGAG 59.903 42.308 0.00 0.00 0.00 2.85
876 1840 5.954150 TCCCTCCGTAAACTAATGTAAGAGT 59.046 40.000 0.00 0.00 0.00 3.24
877 1841 6.040878 CCCTCCGTAAACTAATGTAAGAGTG 58.959 44.000 0.00 0.00 0.00 3.51
880 1844 7.601508 CCTCCGTAAACTAATGTAAGAGTGTTT 59.398 37.037 0.00 0.00 0.00 2.83
882 1846 9.630098 TCCGTAAACTAATGTAAGAGTGTTTAG 57.370 33.333 0.00 0.00 32.78 1.85
892 1856 9.862371 AATGTAAGAGTGTTTAGATCACTAGTG 57.138 33.333 17.17 17.17 44.68 2.74
906 1870 5.899120 TCACTAGTGATCTAAACGCTCTT 57.101 39.130 21.74 0.00 34.14 2.85
908 1872 7.569639 TCACTAGTGATCTAAACGCTCTTAT 57.430 36.000 21.74 0.00 34.14 1.73
909 1873 8.672823 TCACTAGTGATCTAAACGCTCTTATA 57.327 34.615 21.74 0.00 34.14 0.98
910 1874 9.286170 TCACTAGTGATCTAAACGCTCTTATAT 57.714 33.333 21.74 0.00 34.14 0.86
911 1875 9.900710 CACTAGTGATCTAAACGCTCTTATATT 57.099 33.333 18.45 0.00 0.00 1.28
923 1887 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
925 1889 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
926 1890 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
927 1891 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
931 1895 9.632638 TTATATTAGTTTACAGAGGGAGTACGT 57.367 33.333 0.00 0.00 0.00 3.57
933 1897 4.780275 AGTTTACAGAGGGAGTACGTTC 57.220 45.455 0.00 0.00 0.00 3.95
956 1920 7.677454 TCTATATATGGCAAACATGAAGCAG 57.323 36.000 0.00 0.00 40.82 4.24
1167 2132 3.382832 CTGGAGGCCCTCGACGTT 61.383 66.667 4.29 0.00 0.00 3.99
1218 2183 4.856801 GTCATCGCCGGCATGGGT 62.857 66.667 28.98 2.79 38.63 4.51
1425 2390 3.108343 CGGATCTACGGCGTCACT 58.892 61.111 19.21 0.87 0.00 3.41
1483 2448 1.228124 TCCTTCCACAACAAGCCCG 60.228 57.895 0.00 0.00 0.00 6.13
1599 2564 1.006102 CAACAAGAGGACTCGCGGT 60.006 57.895 6.13 2.39 34.09 5.68
1611 2576 3.272334 CGCGGTGCCTTCATAGCC 61.272 66.667 0.00 0.00 0.00 3.93
1722 2810 6.967767 CGCTTCTCTTTTCTCTCGTCTAATTA 59.032 38.462 0.00 0.00 0.00 1.40
1840 3873 5.177326 GCTCTCTGTGAGATTCAAGAACAT 58.823 41.667 10.70 0.00 45.39 2.71
1847 3880 0.810648 GATTCAAGAACATGGCCGCA 59.189 50.000 0.00 0.00 0.00 5.69
1911 3944 3.457263 TACTCATGCTCGGCGCCA 61.457 61.111 28.98 12.94 38.05 5.69
1958 3991 3.766644 CATGAAGATGCCCGAGACA 57.233 52.632 0.00 0.00 0.00 3.41
2181 4219 3.083293 GTCGTCTTCTACTCCCTCAACT 58.917 50.000 0.00 0.00 0.00 3.16
2255 4293 2.036414 AGCCCTCTCGAGCAGACA 59.964 61.111 7.81 0.00 0.00 3.41
2285 4323 3.511595 CGCACGCAGGCCATCATT 61.512 61.111 5.01 0.00 0.00 2.57
2514 4552 1.352352 CCAACTCCACCACCTTCATCT 59.648 52.381 0.00 0.00 0.00 2.90
2525 4563 0.322456 CCTTCATCTTGCCCACCGAA 60.322 55.000 0.00 0.00 0.00 4.30
2729 4795 4.659529 AGGGATGTCACTCGAGGATATA 57.340 45.455 18.41 0.00 0.00 0.86
2743 4809 3.329814 GAGGATATAACCGGGGAAATGGT 59.670 47.826 6.32 0.00 41.20 3.55
2846 4916 1.462616 CATTCATCCCGGTTGCTGAA 58.537 50.000 0.00 4.21 32.63 3.02
2848 4918 1.462616 TTCATCCCGGTTGCTGAATG 58.537 50.000 0.00 0.00 0.00 2.67
2849 4919 0.394216 TCATCCCGGTTGCTGAATGG 60.394 55.000 0.00 0.00 0.00 3.16
2850 4920 0.394216 CATCCCGGTTGCTGAATGGA 60.394 55.000 0.00 0.00 0.00 3.41
2851 4921 0.552848 ATCCCGGTTGCTGAATGGAT 59.447 50.000 0.00 0.00 0.00 3.41
2852 4922 0.331278 TCCCGGTTGCTGAATGGATT 59.669 50.000 0.00 0.00 0.00 3.01
2853 4923 1.562008 TCCCGGTTGCTGAATGGATTA 59.438 47.619 0.00 0.00 0.00 1.75
2854 4924 2.174639 TCCCGGTTGCTGAATGGATTAT 59.825 45.455 0.00 0.00 0.00 1.28
2855 4925 3.392947 TCCCGGTTGCTGAATGGATTATA 59.607 43.478 0.00 0.00 0.00 0.98
2985 5061 6.967199 GTGGCAATAACACAAGTAAATCTAGC 59.033 38.462 0.00 0.00 38.67 3.42
3016 5312 8.854312 GCAAATAGTAGAGCAAATTTCAGTTTC 58.146 33.333 0.00 0.00 0.00 2.78
3036 5332 2.113777 TCACCCCTTCCTTTACTCCTCT 59.886 50.000 0.00 0.00 0.00 3.69
3074 5370 4.213906 GCCGCTGGTTTAGTACAACTTTAA 59.786 41.667 0.00 0.00 0.00 1.52
3141 5437 3.852578 ACAAGATATTGAACCCAGGACCT 59.147 43.478 7.16 0.00 0.00 3.85
3162 5458 0.531974 GGAGGTTGTGAGCACGTTGA 60.532 55.000 0.00 0.00 0.00 3.18
3184 5480 1.348036 AGCCACTAGAACCAACCAGAC 59.652 52.381 0.00 0.00 0.00 3.51
3187 5483 3.007614 GCCACTAGAACCAACCAGACTTA 59.992 47.826 0.00 0.00 0.00 2.24
3194 5490 6.875972 AGAACCAACCAGACTTAGTGATAT 57.124 37.500 0.00 0.00 0.00 1.63
3198 5494 9.694137 GAACCAACCAGACTTAGTGATATATAC 57.306 37.037 0.00 0.00 0.00 1.47
3199 5495 9.435570 AACCAACCAGACTTAGTGATATATACT 57.564 33.333 0.00 0.00 0.00 2.12
3200 5496 9.080097 ACCAACCAGACTTAGTGATATATACTC 57.920 37.037 0.00 0.00 0.00 2.59
3201 5497 8.524487 CCAACCAGACTTAGTGATATATACTCC 58.476 40.741 0.00 0.00 0.00 3.85
3202 5498 8.524487 CAACCAGACTTAGTGATATATACTCCC 58.476 40.741 0.00 0.00 0.00 4.30
3203 5499 8.002431 ACCAGACTTAGTGATATATACTCCCT 57.998 38.462 0.00 0.00 0.00 4.20
3204 5500 8.110908 ACCAGACTTAGTGATATATACTCCCTC 58.889 40.741 0.00 0.00 0.00 4.30
3205 5501 7.558444 CCAGACTTAGTGATATATACTCCCTCC 59.442 44.444 0.00 0.00 0.00 4.30
3206 5502 7.281324 CAGACTTAGTGATATATACTCCCTCCG 59.719 44.444 0.00 0.00 0.00 4.63
3207 5503 7.030234 ACTTAGTGATATATACTCCCTCCGT 57.970 40.000 0.00 0.00 0.00 4.69
3208 5504 7.468496 ACTTAGTGATATATACTCCCTCCGTT 58.532 38.462 0.00 0.00 0.00 4.44
3209 5505 7.611079 ACTTAGTGATATATACTCCCTCCGTTC 59.389 40.741 0.00 0.00 0.00 3.95
3210 5506 5.262804 AGTGATATATACTCCCTCCGTTCC 58.737 45.833 0.00 0.00 0.00 3.62
3211 5507 5.015391 AGTGATATATACTCCCTCCGTTCCT 59.985 44.000 0.00 0.00 0.00 3.36
3212 5508 6.217074 AGTGATATATACTCCCTCCGTTCCTA 59.783 42.308 0.00 0.00 0.00 2.94
3213 5509 6.888632 GTGATATATACTCCCTCCGTTCCTAA 59.111 42.308 0.00 0.00 0.00 2.69
3214 5510 7.395489 GTGATATATACTCCCTCCGTTCCTAAA 59.605 40.741 0.00 0.00 0.00 1.85
3215 5511 8.120538 TGATATATACTCCCTCCGTTCCTAAAT 58.879 37.037 0.00 0.00 0.00 1.40
3216 5512 9.638176 GATATATACTCCCTCCGTTCCTAAATA 57.362 37.037 0.00 0.00 0.00 1.40
3217 5513 7.715266 ATATACTCCCTCCGTTCCTAAATAC 57.285 40.000 0.00 0.00 0.00 1.89
3218 5514 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
3219 5515 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
3220 5516 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
3221 5517 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
3222 5518 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
3223 5519 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
3224 5520 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3225 5521 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3226 5522 6.653740 CCTCCGTTCCTAAATACTTGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
3227 5523 7.174426 CCTCCGTTCCTAAATACTTGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
3228 5524 9.211485 CTCCGTTCCTAAATACTTGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
3229 5525 9.211485 TCCGTTCCTAAATACTTGTCTTTTTAG 57.789 33.333 0.00 0.00 33.47 1.85
3230 5526 8.448615 CCGTTCCTAAATACTTGTCTTTTTAGG 58.551 37.037 12.11 12.11 46.30 2.69
3231 5527 7.961283 CGTTCCTAAATACTTGTCTTTTTAGGC 59.039 37.037 13.09 3.06 45.31 3.93
3232 5528 8.789762 GTTCCTAAATACTTGTCTTTTTAGGCA 58.210 33.333 13.09 2.93 45.31 4.75
3233 5529 9.528489 TTCCTAAATACTTGTCTTTTTAGGCAT 57.472 29.630 13.09 0.00 45.31 4.40
3234 5530 9.528489 TCCTAAATACTTGTCTTTTTAGGCATT 57.472 29.630 13.09 0.00 45.31 3.56
3239 5535 9.476202 AATACTTGTCTTTTTAGGCATTTCAAC 57.524 29.630 0.00 0.00 0.00 3.18
3240 5536 6.872920 ACTTGTCTTTTTAGGCATTTCAACA 58.127 32.000 0.00 0.00 0.00 3.33
3241 5537 7.327214 ACTTGTCTTTTTAGGCATTTCAACAA 58.673 30.769 0.00 0.00 0.00 2.83
3242 5538 7.492344 ACTTGTCTTTTTAGGCATTTCAACAAG 59.508 33.333 0.00 0.00 43.26 3.16
3243 5539 6.872920 TGTCTTTTTAGGCATTTCAACAAGT 58.127 32.000 0.00 0.00 0.00 3.16
3244 5540 6.756074 TGTCTTTTTAGGCATTTCAACAAGTG 59.244 34.615 0.00 0.00 0.00 3.16
3245 5541 6.978080 GTCTTTTTAGGCATTTCAACAAGTGA 59.022 34.615 0.00 0.00 0.00 3.41
3246 5542 6.978080 TCTTTTTAGGCATTTCAACAAGTGAC 59.022 34.615 0.00 0.00 35.39 3.67
3247 5543 6.463995 TTTTAGGCATTTCAACAAGTGACT 57.536 33.333 0.00 0.00 40.60 3.41
3248 5544 7.575414 TTTTAGGCATTTCAACAAGTGACTA 57.425 32.000 0.00 0.00 38.51 2.59
3249 5545 6.554334 TTAGGCATTTCAACAAGTGACTAC 57.446 37.500 0.00 0.00 39.07 2.73
3250 5546 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
3251 5547 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
3252 5548 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
3253 5549 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
3254 5550 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
3255 5551 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
3256 5552 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3257 5553 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3258 5554 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
3259 5555 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
3260 5556 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
3276 5572 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
3277 5573 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
3319 5615 9.977762 CATACATCCGTATGTGATATTCATTTG 57.022 33.333 3.56 0.00 46.70 2.32
3320 5616 9.942850 ATACATCCGTATGTGATATTCATTTGA 57.057 29.630 3.56 0.00 45.99 2.69
3321 5617 8.675705 ACATCCGTATGTGATATTCATTTGAA 57.324 30.769 0.00 0.00 44.79 2.69
3322 5618 9.119418 ACATCCGTATGTGATATTCATTTGAAA 57.881 29.630 0.00 0.00 44.79 2.69
3325 5621 8.075574 TCCGTATGTGATATTCATTTGAAATGC 58.924 33.333 12.86 0.00 37.61 3.56
3326 5622 7.326789 CCGTATGTGATATTCATTTGAAATGCC 59.673 37.037 12.86 1.28 37.61 4.40
3327 5623 8.077991 CGTATGTGATATTCATTTGAAATGCCT 58.922 33.333 12.86 5.36 37.61 4.75
3330 5626 8.750515 TGTGATATTCATTTGAAATGCCTAGA 57.249 30.769 12.86 0.00 37.61 2.43
3331 5627 9.187996 TGTGATATTCATTTGAAATGCCTAGAA 57.812 29.630 12.86 2.59 37.61 2.10
3336 5632 7.523293 TTCATTTGAAATGCCTAGAAAGACA 57.477 32.000 12.86 0.00 0.00 3.41
3337 5633 7.523293 TCATTTGAAATGCCTAGAAAGACAA 57.477 32.000 12.86 0.00 0.00 3.18
3338 5634 8.125978 TCATTTGAAATGCCTAGAAAGACAAT 57.874 30.769 12.86 0.00 0.00 2.71
3339 5635 8.587608 TCATTTGAAATGCCTAGAAAGACAATT 58.412 29.630 12.86 0.00 0.00 2.32
3340 5636 9.859427 CATTTGAAATGCCTAGAAAGACAATTA 57.141 29.630 4.82 0.00 0.00 1.40
3347 5643 9.920946 AATGCCTAGAAAGACAATTATTTAGGA 57.079 29.630 0.00 0.00 0.00 2.94
3348 5644 9.920946 ATGCCTAGAAAGACAATTATTTAGGAA 57.079 29.630 0.00 0.00 0.00 3.36
3349 5645 9.174166 TGCCTAGAAAGACAATTATTTAGGAAC 57.826 33.333 0.00 0.00 0.00 3.62
3350 5646 8.336080 GCCTAGAAAGACAATTATTTAGGAACG 58.664 37.037 0.00 0.00 0.00 3.95
3351 5647 8.827677 CCTAGAAAGACAATTATTTAGGAACGG 58.172 37.037 0.00 0.00 0.00 4.44
3352 5648 9.595823 CTAGAAAGACAATTATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3353 5649 8.494016 AGAAAGACAATTATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3354 5650 7.553044 AGAAAGACAATTATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3355 5651 5.681639 AGACAATTATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3356 5652 5.427481 AGACAATTATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3357 5653 5.681639 ACAATTATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3358 5654 5.191124 ACAATTATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3359 5655 6.384886 ACAATTATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3360 5656 5.859205 TTATTTAGGAACGGAGGGAGTAC 57.141 43.478 0.00 0.00 0.00 2.73
3361 5657 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
3413 5709 2.550830 ACTGTAGCAGACCAAACCAG 57.449 50.000 2.91 0.00 35.18 4.00
3424 5721 1.071699 ACCAAACCAGCACTGTACGAT 59.928 47.619 0.00 0.00 0.00 3.73
3430 5727 2.183300 GCACTGTACGATCGGGCA 59.817 61.111 20.98 15.87 0.00 5.36
3442 5739 1.961180 ATCGGGCAGGACACTGTAGC 61.961 60.000 0.00 0.00 46.62 3.58
3443 5740 2.942796 CGGGCAGGACACTGTAGCA 61.943 63.158 0.00 0.00 46.62 3.49
3474 5771 4.525487 CGAGGGGGTATTGTAGCTAATGTA 59.475 45.833 0.00 0.00 0.00 2.29
3724 6201 6.678245 GCAAACAATATTACAAATTTGCGAGC 59.322 34.615 18.12 3.50 41.53 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 212 4.162320 TGAAGATAAGGTCGAGCAAATCCT 59.838 41.667 18.15 8.53 0.00 3.24
287 1077 1.571460 CAACAGAACGCCTCACAGC 59.429 57.895 0.00 0.00 0.00 4.40
292 1082 3.606886 TTCTCCAACAGAACGCCTC 57.393 52.632 0.00 0.00 36.08 4.70
316 1106 5.485620 TCCTCAGATCACAAAGACATTGAG 58.514 41.667 0.00 0.00 41.85 3.02
317 1107 5.246883 TCTCCTCAGATCACAAAGACATTGA 59.753 40.000 0.00 0.00 41.85 2.57
318 1108 5.485620 TCTCCTCAGATCACAAAGACATTG 58.514 41.667 0.00 0.00 44.95 2.82
324 1115 4.484537 ACCATCTCCTCAGATCACAAAG 57.515 45.455 0.00 0.00 37.25 2.77
335 1126 3.181461 CCATCCACACTAACCATCTCCTC 60.181 52.174 0.00 0.00 0.00 3.71
337 1128 2.746472 GCCATCCACACTAACCATCTCC 60.746 54.545 0.00 0.00 0.00 3.71
347 1138 2.672996 GCAACGGCCATCCACACT 60.673 61.111 2.24 0.00 0.00 3.55
358 1149 1.493772 TCAACGAACTACAGCAACGG 58.506 50.000 0.00 0.00 0.00 4.44
360 1153 5.176958 ACAGTTATCAACGAACTACAGCAAC 59.823 40.000 0.00 0.00 35.36 4.17
364 1157 7.847487 TCAAAACAGTTATCAACGAACTACAG 58.153 34.615 0.00 0.00 35.36 2.74
407 1204 4.041691 CCTAGGTGGAGGAAAGTGAAAAGA 59.958 45.833 0.00 0.00 39.15 2.52
430 1227 5.952033 AGTCATACAAGACCGAAACTCTAC 58.048 41.667 0.00 0.00 39.34 2.59
477 1440 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
478 1441 3.033166 GCGCACACACACACACACA 62.033 57.895 0.30 0.00 0.00 3.72
479 1442 2.277247 GCGCACACACACACACAC 60.277 61.111 0.30 0.00 0.00 3.82
492 1455 1.065053 ACCAATACTAATGGGTGCGCA 60.065 47.619 5.66 5.66 38.08 6.09
507 1470 3.439857 ACTAGGATGCACACAACCAAT 57.560 42.857 0.00 0.00 41.12 3.16
526 1489 6.415573 AGTATGGACCTGGTCTTTTCATAAC 58.584 40.000 25.01 16.17 32.47 1.89
540 1503 4.985538 ACAAACACAATGAGTATGGACCT 58.014 39.130 0.00 0.00 0.00 3.85
642 1605 3.460103 ACGACAACAGTTGTTCCGTATT 58.540 40.909 24.24 7.16 45.52 1.89
658 1621 3.049912 CAACAGAATGAAGACGACGACA 58.950 45.455 0.00 0.00 39.69 4.35
734 1697 7.921786 TTCTCCGAAGAACACATAAATTGAT 57.078 32.000 0.00 0.00 36.59 2.57
791 1755 4.235360 GTCCCGTGGAATATGATTACGAG 58.765 47.826 0.00 0.00 36.94 4.18
831 1795 4.395231 GGAGTAGTGATTTTTGCCCTGTAC 59.605 45.833 0.00 0.00 0.00 2.90
853 1817 6.040878 CACTCTTACATTAGTTTACGGAGGG 58.959 44.000 0.00 0.00 0.00 4.30
857 1821 9.630098 TCTAAACACTCTTACATTAGTTTACGG 57.370 33.333 0.00 0.00 32.23 4.02
868 1832 8.631480 TCACTAGTGATCTAAACACTCTTACA 57.369 34.615 21.74 0.00 45.58 2.41
884 1848 5.899120 AAGAGCGTTTAGATCACTAGTGA 57.101 39.130 27.07 27.07 44.59 3.41
885 1849 9.900710 AATATAAGAGCGTTTAGATCACTAGTG 57.099 33.333 17.17 17.17 37.82 2.74
897 1861 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
898 1862 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
899 1863 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
900 1864 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
901 1865 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
905 1869 9.632638 ACGTACTCCCTCTGTAAACTAATATAA 57.367 33.333 0.00 0.00 0.00 0.98
906 1870 9.632638 AACGTACTCCCTCTGTAAACTAATATA 57.367 33.333 0.00 0.00 0.00 0.86
908 1872 7.831193 AGAACGTACTCCCTCTGTAAACTAATA 59.169 37.037 0.00 0.00 0.00 0.98
909 1873 6.662663 AGAACGTACTCCCTCTGTAAACTAAT 59.337 38.462 0.00 0.00 0.00 1.73
910 1874 6.006449 AGAACGTACTCCCTCTGTAAACTAA 58.994 40.000 0.00 0.00 0.00 2.24
911 1875 5.564550 AGAACGTACTCCCTCTGTAAACTA 58.435 41.667 0.00 0.00 0.00 2.24
913 1877 4.780275 AGAACGTACTCCCTCTGTAAAC 57.220 45.455 0.00 0.00 0.00 2.01
915 1879 9.445878 CATATATAGAACGTACTCCCTCTGTAA 57.554 37.037 0.00 0.00 0.00 2.41
916 1880 8.045507 CCATATATAGAACGTACTCCCTCTGTA 58.954 40.741 0.00 0.00 0.00 2.74
918 1882 6.183360 GCCATATATAGAACGTACTCCCTCTG 60.183 46.154 0.00 0.00 0.00 3.35
919 1883 5.887035 GCCATATATAGAACGTACTCCCTCT 59.113 44.000 0.00 0.00 0.00 3.69
920 1884 5.651139 TGCCATATATAGAACGTACTCCCTC 59.349 44.000 0.00 0.00 0.00 4.30
921 1885 5.577100 TGCCATATATAGAACGTACTCCCT 58.423 41.667 0.00 0.00 0.00 4.20
922 1886 5.909621 TGCCATATATAGAACGTACTCCC 57.090 43.478 0.00 0.00 0.00 4.30
923 1887 7.149973 TGTTTGCCATATATAGAACGTACTCC 58.850 38.462 0.00 0.00 0.00 3.85
925 1889 8.364894 TCATGTTTGCCATATATAGAACGTACT 58.635 33.333 0.00 0.00 30.71 2.73
926 1890 8.528917 TCATGTTTGCCATATATAGAACGTAC 57.471 34.615 0.00 0.00 30.71 3.67
927 1891 9.203421 CTTCATGTTTGCCATATATAGAACGTA 57.797 33.333 0.00 0.00 30.71 3.57
929 1893 7.017645 GCTTCATGTTTGCCATATATAGAACG 58.982 38.462 0.00 0.00 30.71 3.95
930 1894 7.874940 TGCTTCATGTTTGCCATATATAGAAC 58.125 34.615 0.00 0.00 30.71 3.01
931 1895 7.720957 ACTGCTTCATGTTTGCCATATATAGAA 59.279 33.333 0.00 0.00 30.71 2.10
933 1897 7.444629 ACTGCTTCATGTTTGCCATATATAG 57.555 36.000 0.00 0.00 30.71 1.31
974 1938 3.518303 AGCGGTAGTCTCTGGGTAAAAAT 59.482 43.478 0.00 0.00 0.00 1.82
1182 2147 1.906574 ACGATGGTGGTGAAGTGGTAT 59.093 47.619 0.00 0.00 0.00 2.73
1218 2183 0.387622 CGTAGGCGTCCGTGAAGAAA 60.388 55.000 0.00 0.00 0.00 2.52
1425 2390 1.059098 ACACCACCATGAGCTTGAGA 58.941 50.000 0.00 0.00 0.00 3.27
1611 2576 1.485838 CCTGCATAGCGAAGACTGCG 61.486 60.000 0.00 0.00 37.44 5.18
1668 2671 7.896811 TGTAGATTAAGAATGAGATACGGCAT 58.103 34.615 0.00 0.00 0.00 4.40
1768 2859 3.252554 TCCCAAAACCCTTTATGCAGT 57.747 42.857 0.00 0.00 0.00 4.40
1840 3873 2.049767 TCAGTCTCGTATGCGGCCA 61.050 57.895 2.24 0.00 38.89 5.36
1847 3880 1.018148 CGAGCTGGTCAGTCTCGTAT 58.982 55.000 23.38 0.00 43.37 3.06
1911 3944 0.621571 TAGGTGAGCAGGGCAGGAAT 60.622 55.000 0.00 0.00 0.00 3.01
2015 4048 2.748647 TCGATGTCGAGGACCGCA 60.749 61.111 0.21 0.00 44.22 5.69
2255 4293 0.600255 GCGTGCGGGCTATCTTGTAT 60.600 55.000 0.00 0.00 0.00 2.29
2514 4552 1.770294 GGGAATATTTCGGTGGGCAA 58.230 50.000 0.00 0.00 0.00 4.52
2729 4795 0.251608 CTTCCACCATTTCCCCGGTT 60.252 55.000 0.00 0.00 31.41 4.44
2743 4809 2.038426 TGAGATGGTTCGCTTTCTTCCA 59.962 45.455 0.00 0.00 0.00 3.53
2818 4884 1.202651 CCGGGATGAATGGTACTGGTC 60.203 57.143 0.00 0.00 0.00 4.02
2985 5061 8.623903 TGAAATTTGCTCTACTATTTGCTATGG 58.376 33.333 0.00 0.00 0.00 2.74
3016 5312 2.552367 AGAGGAGTAAAGGAAGGGGTG 58.448 52.381 0.00 0.00 0.00 4.61
3036 5332 4.202419 ACCAGCGGCAAGTAATATGGATAA 60.202 41.667 1.45 0.00 0.00 1.75
3074 5370 8.141909 TGTCGCTGCTTTAGTATATTTCTGTAT 58.858 33.333 0.00 0.00 0.00 2.29
3082 5378 7.599245 GGATTACTTGTCGCTGCTTTAGTATAT 59.401 37.037 0.00 0.00 0.00 0.86
3084 5380 5.753921 GGATTACTTGTCGCTGCTTTAGTAT 59.246 40.000 0.00 0.00 0.00 2.12
3141 5437 1.978455 AACGTGCTCACAACCTCCCA 61.978 55.000 0.00 0.00 0.00 4.37
3162 5458 3.197983 GTCTGGTTGGTTCTAGTGGCTAT 59.802 47.826 0.00 0.00 0.00 2.97
3184 5480 7.067251 GGAACGGAGGGAGTATATATCACTAAG 59.933 44.444 0.00 0.00 28.03 2.18
3187 5483 5.015391 AGGAACGGAGGGAGTATATATCACT 59.985 44.000 0.00 0.00 31.50 3.41
3194 5490 6.856757 AGTATTTAGGAACGGAGGGAGTATA 58.143 40.000 0.00 0.00 0.00 1.47
3198 5494 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3199 5495 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3200 5496 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3201 5497 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3202 5498 7.668525 AAAAGACAAGTATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
3203 5499 9.211485 CTAAAAAGACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 33.69 4.69
3213 5509 9.476202 GTTGAAATGCCTAAAAAGACAAGTATT 57.524 29.630 0.00 0.00 0.00 1.89
3214 5510 8.637986 TGTTGAAATGCCTAAAAAGACAAGTAT 58.362 29.630 0.00 0.00 0.00 2.12
3215 5511 8.001881 TGTTGAAATGCCTAAAAAGACAAGTA 57.998 30.769 0.00 0.00 0.00 2.24
3216 5512 6.872920 TGTTGAAATGCCTAAAAAGACAAGT 58.127 32.000 0.00 0.00 0.00 3.16
3217 5513 7.492344 ACTTGTTGAAATGCCTAAAAAGACAAG 59.508 33.333 0.00 0.00 43.36 3.16
3218 5514 7.277539 CACTTGTTGAAATGCCTAAAAAGACAA 59.722 33.333 0.00 0.00 0.00 3.18
3219 5515 6.756074 CACTTGTTGAAATGCCTAAAAAGACA 59.244 34.615 0.00 0.00 0.00 3.41
3220 5516 6.978080 TCACTTGTTGAAATGCCTAAAAAGAC 59.022 34.615 0.00 0.00 0.00 3.01
3221 5517 6.978080 GTCACTTGTTGAAATGCCTAAAAAGA 59.022 34.615 0.00 0.00 35.39 2.52
3222 5518 6.980397 AGTCACTTGTTGAAATGCCTAAAAAG 59.020 34.615 0.00 0.00 35.39 2.27
3223 5519 6.872920 AGTCACTTGTTGAAATGCCTAAAAA 58.127 32.000 0.00 0.00 35.39 1.94
3224 5520 6.463995 AGTCACTTGTTGAAATGCCTAAAA 57.536 33.333 0.00 0.00 35.39 1.52
3225 5521 6.544197 TGTAGTCACTTGTTGAAATGCCTAAA 59.456 34.615 0.00 0.00 35.39 1.85
3226 5522 6.058833 TGTAGTCACTTGTTGAAATGCCTAA 58.941 36.000 0.00 0.00 35.39 2.69
3227 5523 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
3228 5524 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
3229 5525 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
3230 5526 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
3231 5527 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
3232 5528 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3233 5529 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3234 5530 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
3235 5531 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
3236 5532 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
3237 5533 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
3238 5534 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
3239 5535 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
3240 5536 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
3241 5537 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
3242 5538 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
3243 5539 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
3244 5540 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
3245 5541 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
3246 5542 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
3247 5543 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
3248 5544 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
3249 5545 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
3250 5546 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
3251 5547 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
3252 5548 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
3253 5549 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
3294 5590 9.942850 TCAAATGAATATCACATACGGATGTAT 57.057 29.630 14.23 10.02 44.82 2.29
3295 5591 9.771534 TTCAAATGAATATCACATACGGATGTA 57.228 29.630 14.23 0.00 44.82 2.29
3296 5592 9.119418 TTTCAAATGAATATCACATACGGATGT 57.881 29.630 7.68 7.68 39.20 3.06
3299 5595 8.075574 GCATTTCAAATGAATATCACATACGGA 58.924 33.333 14.65 0.00 33.54 4.69
3300 5596 7.326789 GGCATTTCAAATGAATATCACATACGG 59.673 37.037 14.65 0.00 33.54 4.02
3301 5597 8.077991 AGGCATTTCAAATGAATATCACATACG 58.922 33.333 14.65 0.00 33.54 3.06
3304 5600 9.358406 TCTAGGCATTTCAAATGAATATCACAT 57.642 29.630 14.65 0.00 33.54 3.21
3305 5601 8.750515 TCTAGGCATTTCAAATGAATATCACA 57.249 30.769 14.65 0.00 33.54 3.58
3310 5606 9.241919 TGTCTTTCTAGGCATTTCAAATGAATA 57.758 29.630 14.65 4.67 29.10 1.75
3311 5607 8.125978 TGTCTTTCTAGGCATTTCAAATGAAT 57.874 30.769 14.65 3.70 29.10 2.57
3312 5608 7.523293 TGTCTTTCTAGGCATTTCAAATGAA 57.477 32.000 14.65 0.00 29.10 2.57
3313 5609 7.523293 TTGTCTTTCTAGGCATTTCAAATGA 57.477 32.000 14.65 0.00 35.56 2.57
3314 5610 8.767478 AATTGTCTTTCTAGGCATTTCAAATG 57.233 30.769 5.68 5.68 35.56 2.32
3321 5617 9.920946 TCCTAAATAATTGTCTTTCTAGGCATT 57.079 29.630 0.00 0.00 35.56 3.56
3322 5618 9.920946 TTCCTAAATAATTGTCTTTCTAGGCAT 57.079 29.630 0.00 0.00 35.56 4.40
3323 5619 9.174166 GTTCCTAAATAATTGTCTTTCTAGGCA 57.826 33.333 0.00 0.00 33.22 4.75
3324 5620 8.336080 CGTTCCTAAATAATTGTCTTTCTAGGC 58.664 37.037 0.00 0.00 0.00 3.93
3325 5621 8.827677 CCGTTCCTAAATAATTGTCTTTCTAGG 58.172 37.037 0.00 0.00 0.00 3.02
3326 5622 9.595823 TCCGTTCCTAAATAATTGTCTTTCTAG 57.404 33.333 0.00 0.00 0.00 2.43
3327 5623 9.595823 CTCCGTTCCTAAATAATTGTCTTTCTA 57.404 33.333 0.00 0.00 0.00 2.10
3328 5624 7.553044 CCTCCGTTCCTAAATAATTGTCTTTCT 59.447 37.037 0.00 0.00 0.00 2.52
3329 5625 7.201705 CCCTCCGTTCCTAAATAATTGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
3330 5626 6.602009 CCCTCCGTTCCTAAATAATTGTCTTT 59.398 38.462 0.00 0.00 0.00 2.52
3331 5627 6.069847 TCCCTCCGTTCCTAAATAATTGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
3332 5628 5.427481 TCCCTCCGTTCCTAAATAATTGTCT 59.573 40.000 0.00 0.00 0.00 3.41
3333 5629 5.677567 TCCCTCCGTTCCTAAATAATTGTC 58.322 41.667 0.00 0.00 0.00 3.18
3334 5630 5.191124 ACTCCCTCCGTTCCTAAATAATTGT 59.809 40.000 0.00 0.00 0.00 2.71
3335 5631 5.681639 ACTCCCTCCGTTCCTAAATAATTG 58.318 41.667 0.00 0.00 0.00 2.32
3336 5632 5.970501 ACTCCCTCCGTTCCTAAATAATT 57.029 39.130 0.00 0.00 0.00 1.40
3337 5633 5.901276 TGTACTCCCTCCGTTCCTAAATAAT 59.099 40.000 0.00 0.00 0.00 1.28
3338 5634 5.271598 TGTACTCCCTCCGTTCCTAAATAA 58.728 41.667 0.00 0.00 0.00 1.40
3339 5635 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3340 5636 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3341 5637 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3342 5638 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3343 5639 3.749954 GCTATGTACTCCCTCCGTTCCTA 60.750 52.174 0.00 0.00 0.00 2.94
3344 5640 2.946785 CTATGTACTCCCTCCGTTCCT 58.053 52.381 0.00 0.00 0.00 3.36
3345 5641 1.340568 GCTATGTACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
3346 5642 2.029623 TGCTATGTACTCCCTCCGTTC 58.970 52.381 0.00 0.00 0.00 3.95
3347 5643 1.755380 GTGCTATGTACTCCCTCCGTT 59.245 52.381 0.00 0.00 0.00 4.44
3348 5644 1.341679 TGTGCTATGTACTCCCTCCGT 60.342 52.381 0.00 0.00 0.00 4.69
3349 5645 1.338337 CTGTGCTATGTACTCCCTCCG 59.662 57.143 0.00 0.00 0.00 4.63
3350 5646 2.389715 ACTGTGCTATGTACTCCCTCC 58.610 52.381 0.00 0.00 0.00 4.30
3351 5647 4.160626 AGAAACTGTGCTATGTACTCCCTC 59.839 45.833 0.00 0.00 0.00 4.30
3352 5648 4.097418 AGAAACTGTGCTATGTACTCCCT 58.903 43.478 0.00 0.00 0.00 4.20
3353 5649 4.473477 AGAAACTGTGCTATGTACTCCC 57.527 45.455 0.00 0.00 0.00 4.30
3354 5650 7.265673 TGATAAGAAACTGTGCTATGTACTCC 58.734 38.462 0.00 0.00 0.00 3.85
3355 5651 8.596380 GTTGATAAGAAACTGTGCTATGTACTC 58.404 37.037 0.00 0.00 0.00 2.59
3356 5652 8.094548 TGTTGATAAGAAACTGTGCTATGTACT 58.905 33.333 0.00 0.00 0.00 2.73
3357 5653 8.251750 TGTTGATAAGAAACTGTGCTATGTAC 57.748 34.615 0.00 0.00 0.00 2.90
3358 5654 8.840833 TTGTTGATAAGAAACTGTGCTATGTA 57.159 30.769 0.00 0.00 0.00 2.29
3359 5655 7.661437 TCTTGTTGATAAGAAACTGTGCTATGT 59.339 33.333 0.00 0.00 33.96 2.29
3360 5656 8.032952 TCTTGTTGATAAGAAACTGTGCTATG 57.967 34.615 0.00 0.00 33.96 2.23
3361 5657 8.621532 TTCTTGTTGATAAGAAACTGTGCTAT 57.378 30.769 1.11 0.00 42.09 2.97
3413 5709 1.878522 CTGCCCGATCGTACAGTGC 60.879 63.158 20.60 11.43 0.00 4.40
3424 5721 2.646175 GCTACAGTGTCCTGCCCGA 61.646 63.158 0.00 0.00 42.81 5.14
3430 5727 1.045407 TCGGTTTGCTACAGTGTCCT 58.955 50.000 0.00 0.00 0.00 3.85
3442 5739 1.619807 ATACCCCCTCGGTCGGTTTG 61.620 60.000 0.00 0.00 43.58 2.93
3443 5740 0.911045 AATACCCCCTCGGTCGGTTT 60.911 55.000 0.00 0.00 43.58 3.27
3610 6046 4.732923 TGAAAAATTGTTCGCACTTTCGAG 59.267 37.500 3.92 0.00 39.82 4.04
3612 6048 5.368552 TTGAAAAATTGTTCGCACTTTCG 57.631 34.783 3.92 0.00 30.23 3.46
3697 6174 8.249327 TCGCAAATTTGTAATATTGTTTGCAT 57.751 26.923 19.03 1.82 46.96 3.96
3698 6175 7.621013 GCTCGCAAATTTGTAATATTGTTTGCA 60.621 33.333 19.03 14.76 46.96 4.08
3699 6176 6.678245 GCTCGCAAATTTGTAATATTGTTTGC 59.322 34.615 19.03 17.52 44.61 3.68
3700 6177 7.727955 TGCTCGCAAATTTGTAATATTGTTTG 58.272 30.769 19.03 3.65 0.00 2.93
3703 6180 9.748708 ATAATGCTCGCAAATTTGTAATATTGT 57.251 25.926 19.03 9.40 0.00 2.71
3708 6185 8.700722 TCAAATAATGCTCGCAAATTTGTAAT 57.299 26.923 25.57 4.19 40.41 1.89
3711 6188 7.418840 TTTCAAATAATGCTCGCAAATTTGT 57.581 28.000 25.57 0.53 40.41 2.83
3715 6192 6.423302 TGTGTTTTCAAATAATGCTCGCAAAT 59.577 30.769 0.00 0.00 0.00 2.32
3720 6197 7.159437 TGTTTGTGTTTTCAAATAATGCTCG 57.841 32.000 0.00 0.00 39.09 5.03


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

AutoCloner maintained by Alex Coulton.