Multiple sequence alignment - TraesCS6B01G378200

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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 TraesCS6B01G378200 chr6B 100.000 8445 0 0 1 8445 653099553 653107997 0.000000e+00 15596
1 TraesCS6B01G378200 chr6B 83.178 535 81 7 6852 7383 653106371 653106899 1.650000e-131 481
2 TraesCS6B01G378200 chr6B 83.240 537 77 11 6819 7347 653106404 653106935 1.650000e-131 481
3 TraesCS6B01G378200 chr6B 83.466 502 71 8 6885 7383 653106371 653106863 2.780000e-124 457
4 TraesCS6B01G378200 chr6B 83.466 502 71 8 6819 7311 653106437 653106935 2.780000e-124 457
5 TraesCS6B01G378200 chr6B 86.550 342 32 9 8115 8445 653850328 653850666 1.730000e-96 364
6 TraesCS6B01G378200 chr6B 81.132 477 45 20 7988 8445 653709877 653710327 2.920000e-89 340
7 TraesCS6B01G378200 chr6B 84.320 338 37 10 8121 8445 653182830 653183164 4.920000e-82 316
8 TraesCS6B01G378200 chr6B 93.496 123 8 0 8323 8445 653220813 653220691 5.210000e-42 183
9 TraesCS6B01G378200 chr6B 82.778 180 25 4 86 261 653015911 653016088 1.130000e-33 156
10 TraesCS6B01G378200 chr6B 90.722 97 8 1 6298 6394 653105797 653105892 2.470000e-25 128
11 TraesCS6B01G378200 chr6D 95.590 5624 185 34 812 6394 432900195 432905796 0.000000e+00 8953
12 TraesCS6B01G378200 chr6D 87.090 1340 82 26 7175 8445 432906935 432908252 0.000000e+00 1432
13 TraesCS6B01G378200 chr6D 95.096 836 34 5 6245 7073 432905682 432906517 0.000000e+00 1310
14 TraesCS6B01G378200 chr6D 80.312 320 36 14 7935 8238 433207623 433207931 5.130000e-52 217
15 TraesCS6B01G378200 chr6D 86.341 205 17 6 8251 8445 433213033 433213236 6.640000e-51 213
16 TraesCS6B01G378200 chr6D 90.722 97 8 1 6245 6340 432905736 432905832 2.470000e-25 128
17 TraesCS6B01G378200 chr6A 95.386 2319 65 7 4849 7126 579019657 579021974 0.000000e+00 3651
18 TraesCS6B01G378200 chr6A 91.893 1838 118 18 722 2532 579015513 579017346 0.000000e+00 2540
19 TraesCS6B01G378200 chr6A 97.961 981 11 3 3878 4850 579018596 579019575 0.000000e+00 1692
20 TraesCS6B01G378200 chr6A 96.598 970 21 4 2525 3484 579017633 579018600 0.000000e+00 1598
21 TraesCS6B01G378200 chr6A 84.422 1393 129 44 7091 8445 579022181 579023523 0.000000e+00 1290
22 TraesCS6B01G378200 chr6A 91.057 861 53 14 1 856 579007715 579008556 0.000000e+00 1142
23 TraesCS6B01G378200 chr6A 90.000 110 11 0 6249 6358 579021133 579021242 8.840000e-30 143
24 TraesCS6B01G378200 chr7D 86.223 3201 275 71 3202 6294 235161810 235164952 0.000000e+00 3315
25 TraesCS6B01G378200 chr7D 84.991 1126 128 29 940 2058 235154583 235155674 0.000000e+00 1105
26 TraesCS6B01G378200 chr7D 85.177 904 120 6 6339 7232 235164907 235165806 0.000000e+00 915
27 TraesCS6B01G378200 chr7D 77.161 937 146 35 6957 7866 235165402 235166297 4.580000e-132 483
28 TraesCS6B01G378200 chr7D 89.753 283 26 3 2882 3163 235161538 235161818 8.060000e-95 359
29 TraesCS6B01G378200 chr7D 83.989 356 50 7 2246 2599 235155669 235156019 1.360000e-87 335
30 TraesCS6B01G378200 chr7A 86.107 3203 275 72 3202 6300 250033230 250036366 0.000000e+00 3293
31 TraesCS6B01G378200 chr7A 84.816 1113 122 28 940 2047 250031207 250032277 0.000000e+00 1075
32 TraesCS6B01G378200 chr7A 85.934 846 107 5 6339 7172 250036315 250037160 0.000000e+00 893
33 TraesCS6B01G378200 chr7A 88.108 555 56 7 2600 3148 250032675 250033225 0.000000e+00 651
34 TraesCS6B01G378200 chr7A 85.112 356 45 8 2246 2599 250032284 250032633 2.900000e-94 357
35 TraesCS6B01G378200 chr7A 80.117 171 28 5 2981 3147 30007747 30007915 1.150000e-23 122
36 TraesCS6B01G378200 chr7B 88.328 1328 107 15 4987 6293 211116321 211117621 0.000000e+00 1550
37 TraesCS6B01G378200 chr7B 85.156 1125 126 28 940 2058 211112096 211113185 0.000000e+00 1114
38 TraesCS6B01G378200 chr7B 84.579 1070 99 29 3202 4227 211113991 211115038 0.000000e+00 1002
39 TraesCS6B01G378200 chr7B 85.635 898 118 7 6339 7232 211117577 211118467 0.000000e+00 933
40 TraesCS6B01G378200 chr7B 88.114 774 58 17 4226 4983 211115065 211115820 0.000000e+00 889
41 TraesCS6B01G378200 chr7B 87.644 348 35 6 2820 3163 211113656 211113999 1.710000e-106 398
42 TraesCS6B01G378200 chr7B 83.708 356 51 7 2246 2599 211113180 211113530 6.320000e-86 329
43 TraesCS6B01G378200 chr7B 90.698 86 8 0 2600 2685 211113573 211113658 1.930000e-21 115


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 TraesCS6B01G378200 chr6B 653099553 653107997 8444 False 2933.333333 15596 87.345333 1 8445 6 chr6B.!!$F5 8444
1 TraesCS6B01G378200 chr6D 432900195 432908252 8057 False 2955.750000 8953 92.124500 812 8445 4 chr6D.!!$F3 7633
2 TraesCS6B01G378200 chr6A 579015513 579023523 8010 False 1819.000000 3651 92.710000 722 8445 6 chr6A.!!$F2 7723
3 TraesCS6B01G378200 chr6A 579007715 579008556 841 False 1142.000000 1142 91.057000 1 856 1 chr6A.!!$F1 855
4 TraesCS6B01G378200 chr7D 235161538 235166297 4759 False 1268.000000 3315 84.578500 2882 7866 4 chr7D.!!$F2 4984
5 TraesCS6B01G378200 chr7D 235154583 235156019 1436 False 720.000000 1105 84.490000 940 2599 2 chr7D.!!$F1 1659
6 TraesCS6B01G378200 chr7A 250031207 250037160 5953 False 1253.800000 3293 86.015400 940 7172 5 chr7A.!!$F2 6232
7 TraesCS6B01G378200 chr7B 211112096 211118467 6371 False 791.250000 1550 86.732750 940 7232 8 chr7B.!!$F1 6292

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
23 24 0.105760 TGGAGGTGTGTTGGCCAAAT 60.106 50.000 22.47 1.75 0.00 2.32 F
425 427 0.179020 TCTGCCCTGCCAATTATCGG 60.179 55.000 0.00 0.00 0.00 4.18 F
2186 2226 0.323178 AAAGTGCATCTGCCCTCCTG 60.323 55.000 0.00 0.00 41.18 3.86 F
2248 2288 1.004044 AGTGCAGATTCCAGTCCCTTG 59.996 52.381 0.00 0.00 0.00 3.61 F
2447 2491 2.483538 GCTGTGTTTGGTTGCAGGAATT 60.484 45.455 0.00 0.00 0.00 2.17 F
2518 2562 3.448093 TGGCATAACCACTTGGAATGA 57.552 42.857 15.30 0.00 46.36 2.57 F
3996 4446 2.029828 AGTGACGAAAGAGTGGCAGTAG 60.030 50.000 0.00 0.00 0.00 2.57 F
5629 6707 0.999406 CATTCTCGTTGCCAGTACCG 59.001 55.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1602 0.761187 GCTCTCATCACCCTGCCATA 59.239 55.000 0.00 0.00 0.00 2.74 R
2348 2388 1.176527 GCAGCAAAACTCCTGCCATA 58.823 50.000 1.38 0.00 46.59 2.74 R
3734 4154 0.175989 GGACCTTTACCCTCTCTGCG 59.824 60.000 0.00 0.00 0.00 5.18 R
3929 4379 3.585732 CCCTTTTCTAACTGGAGGGTGTA 59.414 47.826 0.00 0.00 41.74 2.90 R
3996 4446 8.942338 TTACAAGGTTGACTGTACATATCATC 57.058 34.615 9.99 9.29 0.00 2.92 R
4996 6068 4.557496 GCACAGATCACAAGAAAAGGAACC 60.557 45.833 0.00 0.00 0.00 3.62 R
6265 7367 0.177604 CCATCTCTGGCTGACTCACC 59.822 60.000 0.00 0.00 35.23 4.02 R
7783 9806 0.107410 ACAACCACACTTTCGGAGCA 60.107 50.000 0.00 0.00 0.00 4.26 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
23 24 0.105760 TGGAGGTGTGTTGGCCAAAT 60.106 50.000 22.47 1.75 0.00 2.32
26 27 2.514803 GAGGTGTGTTGGCCAAATAGT 58.485 47.619 22.47 2.57 0.00 2.12
65 66 5.808042 ATTCTGTCACAAATGATCTTCCG 57.192 39.130 0.00 0.00 37.14 4.30
70 71 4.929211 TGTCACAAATGATCTTCCGTACTG 59.071 41.667 0.00 0.00 37.14 2.74
86 87 6.527423 TCCGTACTGAATTGAAAGTAAGGTT 58.473 36.000 16.89 0.00 44.27 3.50
88 89 7.172019 TCCGTACTGAATTGAAAGTAAGGTTTC 59.828 37.037 16.89 0.00 44.27 2.78
117 118 6.761714 GACTTTGGTCTCTGAACTGAAAGTAA 59.238 38.462 0.00 0.00 42.47 2.24
129 130 4.522297 CTGAAAGTAAGCCGTAATCTGC 57.478 45.455 0.00 0.00 0.00 4.26
133 134 1.831736 AGTAAGCCGTAATCTGCAGGT 59.168 47.619 15.13 2.68 0.00 4.00
136 137 1.220749 GCCGTAATCTGCAGGTGGA 59.779 57.895 15.13 0.00 0.00 4.02
148 149 1.341209 GCAGGTGGAAAAAGGGAACTG 59.659 52.381 0.00 0.00 42.68 3.16
227 228 8.207545 ACAGAAGTTGAGTGAAGATTAGACTTT 58.792 33.333 0.00 0.00 0.00 2.66
228 229 9.050601 CAGAAGTTGAGTGAAGATTAGACTTTT 57.949 33.333 0.00 0.00 0.00 2.27
271 272 6.414408 AGACTCTCAAGTTGATATTTTGCG 57.586 37.500 5.91 0.00 35.28 4.85
272 273 4.974591 ACTCTCAAGTTGATATTTTGCGC 58.025 39.130 5.91 0.00 28.74 6.09
273 274 4.455533 ACTCTCAAGTTGATATTTTGCGCA 59.544 37.500 5.66 5.66 28.74 6.09
322 324 5.551233 TCGATCAATCTTCAGAAGTTTGGT 58.449 37.500 24.54 20.90 38.27 3.67
352 354 6.645790 AATCTTCATTGCTTGCCTATAAGG 57.354 37.500 0.00 0.00 38.80 2.69
356 358 6.835488 TCTTCATTGCTTGCCTATAAGGAAAT 59.165 34.615 0.00 0.00 40.57 2.17
362 364 5.163663 TGCTTGCCTATAAGGAAATTGAACG 60.164 40.000 0.00 0.00 37.67 3.95
366 368 4.335594 GCCTATAAGGAAATTGAACGTGCT 59.664 41.667 0.00 0.00 37.67 4.40
375 377 6.653320 AGGAAATTGAACGTGCTTATAAGTCA 59.347 34.615 13.91 9.43 0.00 3.41
382 384 6.259167 TGAACGTGCTTATAAGTCACACTTTT 59.741 34.615 25.79 17.61 39.51 2.27
413 415 0.403271 ATTCTGCTTGTGTCTGCCCT 59.597 50.000 0.00 0.00 0.00 5.19
420 422 0.469705 TTGTGTCTGCCCTGCCAATT 60.470 50.000 0.00 0.00 0.00 2.32
425 427 0.179020 TCTGCCCTGCCAATTATCGG 60.179 55.000 0.00 0.00 0.00 4.18
449 451 5.696724 GCACGCCAAAATATAGACAGACTAT 59.303 40.000 0.00 0.00 43.34 2.12
450 452 6.202954 GCACGCCAAAATATAGACAGACTATT 59.797 38.462 0.00 0.00 41.44 1.73
451 453 7.254795 GCACGCCAAAATATAGACAGACTATTT 60.255 37.037 0.00 0.00 41.44 1.40
475 477 1.047596 AACACACCTTGCCATGCCAA 61.048 50.000 0.00 0.00 0.00 4.52
504 506 6.951198 TGAAAGAGGAAACCCAAATAAGCATA 59.049 34.615 0.00 0.00 0.00 3.14
528 530 3.939592 GGAGCCAAATTACTGGTGTCTAC 59.060 47.826 0.00 0.00 38.86 2.59
529 531 4.323562 GGAGCCAAATTACTGGTGTCTACT 60.324 45.833 0.00 0.00 38.86 2.57
536 538 7.352739 CAAATTACTGGTGTCTACTCAAACAC 58.647 38.462 0.00 0.00 43.97 3.32
540 542 3.792401 TGGTGTCTACTCAAACACACAG 58.208 45.455 7.80 0.00 45.99 3.66
550 552 1.724582 AAACACACAGCCAACGCTCC 61.725 55.000 0.00 0.00 43.95 4.70
588 590 1.410882 GGCTGGCAACTCTAGTCTAGG 59.589 57.143 7.05 1.05 37.61 3.02
627 629 5.220710 ACCATAAGTATGATGAGCAGGAC 57.779 43.478 0.00 0.00 35.75 3.85
632 634 1.409064 GTATGATGAGCAGGACGGTGA 59.591 52.381 0.00 0.00 0.00 4.02
660 662 6.850752 AAATACCAACTCCCTTTAATGGTG 57.149 37.500 6.03 2.26 43.86 4.17
678 680 2.554893 GGTGTAAAATCTTCACCCGCAA 59.445 45.455 0.00 0.00 43.84 4.85
776 785 7.351981 GTGAAAAATAGAAAAACAACATGGGC 58.648 34.615 0.00 0.00 0.00 5.36
859 873 1.066454 CTGTTTGTCGGGGTGGTTTTC 59.934 52.381 0.00 0.00 0.00 2.29
865 879 2.544698 CGGGGTGGTTTTCGCGAAA 61.545 57.895 29.22 29.22 40.92 3.46
867 881 0.388006 GGGGTGGTTTTCGCGAAATG 60.388 55.000 32.58 0.00 0.00 2.32
875 889 3.185797 GGTTTTCGCGAAATGTACAGAGT 59.814 43.478 32.58 0.00 0.00 3.24
877 891 2.273370 TCGCGAAATGTACAGAGTCC 57.727 50.000 6.20 0.00 0.00 3.85
880 894 1.207329 GCGAAATGTACAGAGTCCCCT 59.793 52.381 0.33 0.00 0.00 4.79
882 896 2.496070 CGAAATGTACAGAGTCCCCTCA 59.504 50.000 0.33 0.00 40.40 3.86
941 965 2.579201 CCCACGGTCGAGCTGATT 59.421 61.111 13.48 0.00 0.00 2.57
1088 1112 0.460987 CTCATCCTCCACAAGTCGGC 60.461 60.000 0.00 0.00 0.00 5.54
1167 1197 1.973137 TTTAACGCGCCGCTGAATCC 61.973 55.000 5.73 0.00 0.00 3.01
1203 1233 4.492160 GCGACGATCCTGACGGCA 62.492 66.667 0.00 0.00 38.84 5.69
1401 1431 7.496346 TTGTACTCTTGGATGGATTACTCTT 57.504 36.000 0.00 0.00 0.00 2.85
1408 1439 5.359194 TGGATGGATTACTCTTCCAGTTC 57.641 43.478 0.00 0.00 46.06 3.01
1420 1451 6.522054 ACTCTTCCAGTTCAATTTCGACTAA 58.478 36.000 0.00 0.00 26.56 2.24
1430 1463 5.985781 TCAATTTCGACTAACTTCAGTTGC 58.014 37.500 2.26 0.00 38.90 4.17
1450 1483 2.860735 GCGTCTTCTAGCCAGTATTGTG 59.139 50.000 0.00 0.00 0.00 3.33
1479 1515 6.228616 AGGAACTGTTAGATCTTAAGAGGC 57.771 41.667 11.53 5.73 37.18 4.70
1480 1516 5.129650 AGGAACTGTTAGATCTTAAGAGGCC 59.870 44.000 11.53 0.00 37.18 5.19
1482 1518 4.279145 ACTGTTAGATCTTAAGAGGCCGA 58.721 43.478 11.53 0.00 0.00 5.54
1490 1526 5.654650 AGATCTTAAGAGGCCGATGTATAGG 59.345 44.000 11.53 0.00 0.00 2.57
1566 1602 3.771216 ACTTCTGTTGCCCTGATTGATT 58.229 40.909 0.00 0.00 0.00 2.57
1682 1719 3.969981 GGTACCACATTTTGTTTTCGTCG 59.030 43.478 7.15 0.00 0.00 5.12
1683 1720 4.260702 GGTACCACATTTTGTTTTCGTCGA 60.261 41.667 7.15 0.00 0.00 4.20
1687 1724 4.796312 CCACATTTTGTTTTCGTCGAAAGT 59.204 37.500 18.96 9.97 32.93 2.66
1759 1796 4.103153 TCCTTCTCGATTTAGGATGCCAAT 59.897 41.667 6.29 0.00 33.23 3.16
1831 1870 6.699688 AGGAACCCATAATCCCGGATATATA 58.300 40.000 0.73 0.00 36.31 0.86
1837 1876 8.272173 ACCCATAATCCCGGATATATAAACTTG 58.728 37.037 0.73 0.00 0.00 3.16
1940 1979 2.539274 CGAGGTGTGCACAAAATTTTGG 59.461 45.455 29.37 20.39 42.34 3.28
1993 2032 7.939039 CCTATTGTACCACAAATCAGTATCCAT 59.061 37.037 0.00 0.00 41.96 3.41
2075 2115 7.011499 TCTTATACAAAGGAGTTGCAAGGTA 57.989 36.000 0.00 0.00 41.31 3.08
2078 2118 3.157087 ACAAAGGAGTTGCAAGGTATGG 58.843 45.455 0.00 0.00 41.31 2.74
2186 2226 0.323178 AAAGTGCATCTGCCCTCCTG 60.323 55.000 0.00 0.00 41.18 3.86
2248 2288 1.004044 AGTGCAGATTCCAGTCCCTTG 59.996 52.381 0.00 0.00 0.00 3.61
2389 2432 3.439857 AAGGGAGCTTAATGTGCTGAA 57.560 42.857 0.00 0.00 41.30 3.02
2390 2433 3.659183 AGGGAGCTTAATGTGCTGAAT 57.341 42.857 0.00 0.00 41.30 2.57
2447 2491 2.483538 GCTGTGTTTGGTTGCAGGAATT 60.484 45.455 0.00 0.00 0.00 2.17
2450 2494 4.583871 TGTGTTTGGTTGCAGGAATTTTT 58.416 34.783 0.00 0.00 0.00 1.94
2481 2525 4.775236 ACTAGAAATCACAGGGCAATCTC 58.225 43.478 0.00 0.00 0.00 2.75
2518 2562 3.448093 TGGCATAACCACTTGGAATGA 57.552 42.857 15.30 0.00 46.36 2.57
2951 3339 4.752621 AACCCTTGTACCCTAATTTGGT 57.247 40.909 5.19 5.03 39.97 3.67
2995 3383 7.615403 AGTAAGATACAGATTCTTTCACAGCA 58.385 34.615 0.00 0.00 35.19 4.41
3372 3776 7.601705 AAGGGTAATGTCATATTCCCAATTG 57.398 36.000 16.92 0.00 37.56 2.32
3445 3849 5.208463 GGTTTTCTTAGAACCAAATGCCA 57.792 39.130 0.00 0.00 44.71 4.92
3715 4135 7.936950 TGAAGATCGAGTTCATATGATTCAC 57.063 36.000 6.17 1.92 0.00 3.18
3734 4154 6.877611 TTCACCCAAGTTTCTTGTTCTATC 57.122 37.500 8.37 0.00 0.00 2.08
3996 4446 2.029828 AGTGACGAAAGAGTGGCAGTAG 60.030 50.000 0.00 0.00 0.00 2.57
4309 4792 6.582672 GGCAAATCTCTAGTTTTGTTAGCAAC 59.417 38.462 12.66 0.00 37.17 4.17
4996 6068 2.275318 GCCTCTTGCTGCAGTAGTTAG 58.725 52.381 16.64 5.58 36.87 2.34
5000 6072 3.926616 TCTTGCTGCAGTAGTTAGGTTC 58.073 45.455 16.64 0.00 0.00 3.62
5005 6077 4.072839 GCTGCAGTAGTTAGGTTCCTTTT 58.927 43.478 16.64 0.00 0.00 2.27
5055 6127 4.256920 CATCTCAACCTTACTTGGTCTGG 58.743 47.826 0.00 0.00 39.83 3.86
5555 6630 4.717233 TCACAACAAAGCACTCAACATT 57.283 36.364 0.00 0.00 0.00 2.71
5605 6680 5.769662 ACCTGAGTTAAAATCTGCAACATCA 59.230 36.000 0.00 0.00 0.00 3.07
5629 6707 0.999406 CATTCTCGTTGCCAGTACCG 59.001 55.000 0.00 0.00 0.00 4.02
5695 6776 2.046892 CCTCCTCGGGTGCAACAG 60.047 66.667 3.06 0.00 39.98 3.16
5800 6881 4.158394 GCAAATCCTACAAATGCTCCTTCA 59.842 41.667 0.00 0.00 34.29 3.02
6009 7111 1.490490 TGCTCAACACCCAGAACTTCT 59.510 47.619 0.00 0.00 0.00 2.85
6265 7367 2.091112 CGTGAAGCAGCCAGAGACG 61.091 63.158 0.00 0.00 0.00 4.18
6309 7429 2.267324 GCCAGAGACAGTGAGGCC 59.733 66.667 0.00 0.00 39.42 5.19
6347 7485 1.908340 GCCAGAGATGGTGAGGCAGT 61.908 60.000 0.00 0.00 44.59 4.40
6606 7777 4.565652 CCCTGTGTTTAGAGCACCAGTAAT 60.566 45.833 0.00 0.00 36.11 1.89
6772 7943 6.648725 GCAAACAAAATAGGTGCCAAGAAATA 59.351 34.615 0.00 0.00 0.00 1.40
6947 8184 2.976490 GCTCCTGCCACTGGACCAT 61.976 63.158 0.00 0.00 0.00 3.55
6949 8186 1.538629 TCCTGCCACTGGACCATCA 60.539 57.895 0.00 0.00 0.00 3.07
7027 8264 1.073923 GGAACACCACCAGTCAGGAAT 59.926 52.381 0.00 0.00 41.22 3.01
7029 8266 3.054361 GGAACACCACCAGTCAGGAATAT 60.054 47.826 0.00 0.00 41.22 1.28
7072 8309 2.047179 GTCAGGAACACGGCTCCC 60.047 66.667 0.00 0.00 32.95 4.30
7108 8345 1.534235 AGTCAGGAACACGGCTCCT 60.534 57.895 0.00 0.00 44.53 3.69
7111 8348 4.021925 AGGAACACGGCTCCTGGC 62.022 66.667 1.77 0.00 41.96 4.85
7112 8349 4.329545 GGAACACGGCTCCTGGCA 62.330 66.667 0.00 0.00 44.01 4.92
7113 8350 3.050275 GAACACGGCTCCTGGCAC 61.050 66.667 0.00 0.00 44.01 5.01
7114 8351 3.537206 GAACACGGCTCCTGGCACT 62.537 63.158 0.00 0.00 44.01 4.40
7115 8352 3.832237 AACACGGCTCCTGGCACTG 62.832 63.158 0.00 0.00 44.01 3.66
7124 8361 3.749981 CTGGCACTGGAACACCAC 58.250 61.111 0.00 0.00 28.77 4.16
7125 8362 1.898574 CTGGCACTGGAACACCACC 60.899 63.158 0.00 0.00 28.77 4.61
7126 8363 2.978010 GGCACTGGAACACCACCG 60.978 66.667 0.00 0.00 0.00 4.94
7127 8364 2.978010 GCACTGGAACACCACCGG 60.978 66.667 0.00 0.00 39.46 5.28
7128 8365 2.978010 CACTGGAACACCACCGGC 60.978 66.667 0.00 0.00 37.30 6.13
7129 8366 4.265056 ACTGGAACACCACCGGCC 62.265 66.667 0.00 0.00 37.30 6.13
7130 8367 4.263572 CTGGAACACCACCGGCCA 62.264 66.667 0.00 0.00 0.00 5.36
7131 8368 4.263572 TGGAACACCACCGGCCAG 62.264 66.667 0.00 0.00 0.00 4.85
7133 8370 3.948719 GAACACCACCGGCCAGGA 61.949 66.667 18.74 0.00 45.00 3.86
7134 8371 3.485346 GAACACCACCGGCCAGGAA 62.485 63.158 18.74 0.00 45.00 3.36
7135 8372 3.785122 AACACCACCGGCCAGGAAC 62.785 63.158 18.74 0.00 45.00 3.62
7136 8373 3.953775 CACCACCGGCCAGGAACT 61.954 66.667 18.74 0.00 45.00 3.01
7137 8374 3.175710 ACCACCGGCCAGGAACTT 61.176 61.111 18.74 0.00 45.00 2.66
7150 8775 3.842925 GAACTTGGCTCCCGGCACA 62.843 63.158 0.00 0.00 46.30 4.57
7160 8785 3.964875 CCGGCACAGCAACACCAC 61.965 66.667 0.00 0.00 0.00 4.16
7161 8786 2.901840 CGGCACAGCAACACCACT 60.902 61.111 0.00 0.00 0.00 4.00
7180 8805 1.255667 TAGTCAGGAACACGGCTCCC 61.256 60.000 0.00 0.00 32.95 4.30
7193 8818 3.357079 CTCCCGGCACTGCAACAC 61.357 66.667 2.82 0.00 0.00 3.32
7198 8823 3.964875 GGCACTGCAACACCACCG 61.965 66.667 2.82 0.00 0.00 4.94
7222 8847 1.891919 GAACTTGCTCACCGGCACA 60.892 57.895 0.00 0.00 42.27 4.57
7234 8859 2.978010 GGCACAGGAACACCACCG 60.978 66.667 0.00 0.00 0.00 4.94
7235 8860 2.978010 GCACAGGAACACCACCGG 60.978 66.667 0.00 0.00 0.00 5.28
7236 8861 2.978010 CACAGGAACACCACCGGC 60.978 66.667 0.00 0.00 0.00 6.13
7237 8862 4.265056 ACAGGAACACCACCGGCC 62.265 66.667 0.00 0.00 0.00 6.13
7238 8863 4.263572 CAGGAACACCACCGGCCA 62.264 66.667 0.00 0.00 0.00 5.36
7239 8864 3.953775 AGGAACACCACCGGCCAG 61.954 66.667 0.00 0.00 0.00 4.85
7241 8866 3.948719 GAACACCACCGGCCAGGA 61.949 66.667 18.74 0.00 45.00 3.86
7242 8867 3.485346 GAACACCACCGGCCAGGAA 62.485 63.158 18.74 0.00 45.00 3.36
7243 8868 3.785122 AACACCACCGGCCAGGAAC 62.785 63.158 18.74 0.00 45.00 3.62
7244 8869 3.953775 CACCACCGGCCAGGAACT 61.954 66.667 18.74 0.00 45.00 3.01
7245 8870 3.637273 ACCACCGGCCAGGAACTC 61.637 66.667 18.74 0.00 45.00 3.01
7246 8871 4.760047 CCACCGGCCAGGAACTCG 62.760 72.222 18.74 0.00 45.00 4.18
7249 8874 4.821589 CCGGCCAGGAACTCGCTC 62.822 72.222 2.24 0.00 43.67 5.03
7250 8875 4.069232 CGGCCAGGAACTCGCTCA 62.069 66.667 2.24 0.00 43.67 4.26
7251 8876 2.435059 GGCCAGGAACTCGCTCAC 60.435 66.667 0.00 0.00 43.67 3.51
7252 8877 2.435059 GCCAGGAACTCGCTCACC 60.435 66.667 0.00 0.00 40.14 4.02
7253 8878 2.125912 CCAGGAACTCGCTCACCG 60.126 66.667 0.00 0.00 34.60 4.94
7254 8879 2.125912 CAGGAACTCGCTCACCGG 60.126 66.667 0.00 0.00 34.60 5.28
7255 8880 4.070552 AGGAACTCGCTCACCGGC 62.071 66.667 0.00 0.00 37.59 6.13
7256 8881 4.373116 GGAACTCGCTCACCGGCA 62.373 66.667 0.00 0.00 37.59 5.69
7257 8882 3.112709 GAACTCGCTCACCGGCAC 61.113 66.667 0.00 0.00 37.59 5.01
7258 8883 3.858868 GAACTCGCTCACCGGCACA 62.859 63.158 0.00 0.00 37.59 4.57
7259 8884 3.865929 AACTCGCTCACCGGCACAG 62.866 63.158 0.00 0.00 37.59 3.66
7260 8885 4.363990 CTCGCTCACCGGCACAGT 62.364 66.667 0.00 0.00 37.59 3.55
7261 8886 3.865929 CTCGCTCACCGGCACAGTT 62.866 63.158 0.00 0.00 37.59 3.16
7262 8887 2.048597 CGCTCACCGGCACAGTTA 60.049 61.111 0.00 0.00 0.00 2.24
7263 8888 2.380410 CGCTCACCGGCACAGTTAC 61.380 63.158 0.00 0.00 0.00 2.50
7264 8889 1.301401 GCTCACCGGCACAGTTACA 60.301 57.895 0.00 0.00 0.00 2.41
7265 8890 1.566018 GCTCACCGGCACAGTTACAC 61.566 60.000 0.00 0.00 0.00 2.90
7266 8891 0.949105 CTCACCGGCACAGTTACACC 60.949 60.000 0.00 0.00 0.00 4.16
7267 8892 1.227704 CACCGGCACAGTTACACCA 60.228 57.895 0.00 0.00 0.00 4.17
7268 8893 1.227734 ACCGGCACAGTTACACCAC 60.228 57.895 0.00 0.00 0.00 4.16
7269 8894 1.964373 CCGGCACAGTTACACCACC 60.964 63.158 0.00 0.00 0.00 4.61
7281 9112 3.175710 ACCACCGGCCAGGAACTT 61.176 61.111 18.74 0.00 45.00 2.66
7362 9370 0.605589 GCCAGGAACTTGCTTACCGT 60.606 55.000 0.00 0.00 44.36 4.83
7428 9436 1.356494 GGGGCTAGCAAGGGGAATCT 61.356 60.000 18.24 0.00 0.00 2.40
7568 9576 1.052124 CCCCCGTGTATGCTCCCTTA 61.052 60.000 0.00 0.00 0.00 2.69
7698 9713 0.916581 GCGATCGCAATTGCCTTTTC 59.083 50.000 33.89 14.04 41.49 2.29
7735 9758 1.067846 GTCGTATCAGTGTGGCTGTGA 60.068 52.381 0.00 0.00 45.23 3.58
7750 9773 0.460109 TGTGAGGATTGACGATGGCG 60.460 55.000 0.00 0.00 44.79 5.69
7759 9782 4.796231 ACGATGGCGCGTCAGGTC 62.796 66.667 21.72 12.30 41.22 3.85
7781 9804 1.063006 CCGTTCCATCTGCATTGCG 59.937 57.895 3.84 0.00 0.00 4.85
7783 9806 1.647545 CGTTCCATCTGCATTGCGGT 61.648 55.000 16.77 2.38 36.18 5.68
7788 9811 2.117156 ATCTGCATTGCGGTGCTCC 61.117 57.895 16.77 0.00 45.27 4.70
7813 9847 6.391227 AAAGTGTGGTTGTTAGATTTCCTG 57.609 37.500 0.00 0.00 0.00 3.86
7814 9848 5.304686 AGTGTGGTTGTTAGATTTCCTGA 57.695 39.130 0.00 0.00 0.00 3.86
7838 9872 1.135199 GCATGAGTTGGCTGTTGGATG 60.135 52.381 0.00 0.00 0.00 3.51
7841 9875 1.271543 TGAGTTGGCTGTTGGATGAGG 60.272 52.381 0.00 0.00 0.00 3.86
7868 9903 4.996758 TGTTGGTGACAGAAGATGTGTATG 59.003 41.667 0.00 0.00 44.17 2.39
7869 9904 5.221621 TGTTGGTGACAGAAGATGTGTATGA 60.222 40.000 0.00 0.00 44.17 2.15
7870 9905 4.820897 TGGTGACAGAAGATGTGTATGAC 58.179 43.478 0.00 0.00 44.17 3.06
7874 9909 6.350194 GGTGACAGAAGATGTGTATGACTGTA 60.350 42.308 0.00 0.00 44.17 2.74
7875 9910 7.261325 GTGACAGAAGATGTGTATGACTGTAT 58.739 38.462 0.00 0.00 44.17 2.29
7876 9911 8.406297 GTGACAGAAGATGTGTATGACTGTATA 58.594 37.037 0.00 0.00 44.17 1.47
7877 9912 8.406297 TGACAGAAGATGTGTATGACTGTATAC 58.594 37.037 0.00 0.00 44.17 1.47
7896 9931 2.844195 ATGGTGGTTGCAGCCTGGA 61.844 57.895 21.11 4.37 0.00 3.86
7897 9932 2.985847 GGTGGTTGCAGCCTGGAC 60.986 66.667 21.11 10.42 0.00 4.02
7898 9933 2.985847 GTGGTTGCAGCCTGGACC 60.986 66.667 21.11 8.64 0.00 4.46
7900 9935 2.036256 GGTTGCAGCCTGGACCAT 59.964 61.111 13.08 0.00 0.00 3.55
7901 9936 2.048603 GGTTGCAGCCTGGACCATC 61.049 63.158 13.08 0.00 0.00 3.51
7902 9937 1.303561 GTTGCAGCCTGGACCATCA 60.304 57.895 0.00 0.00 0.00 3.07
7903 9938 1.001764 TTGCAGCCTGGACCATCAG 60.002 57.895 0.00 0.00 34.70 2.90
7958 10017 3.256631 AGTGTGCCATTCAATTTGGTCTC 59.743 43.478 0.00 0.00 36.57 3.36
8040 10109 1.141881 GACATGGACGGCGATCAGT 59.858 57.895 16.62 10.75 0.00 3.41
8090 10171 2.014068 GCTAACAAGCCAGGCCAGTAG 61.014 57.143 8.22 6.26 0.00 2.57
8126 10217 8.424133 AGTTTAGAACAATCAAGGCTTCAAAAT 58.576 29.630 0.00 0.00 0.00 1.82
8164 10255 7.200455 AGCAGTAAAATAACACCACAAACTTC 58.800 34.615 0.00 0.00 0.00 3.01
8214 10305 2.211806 TCCAGAACCGGTAAAACAACG 58.788 47.619 8.00 0.00 0.00 4.10
8219 10310 4.687483 CAGAACCGGTAAAACAACGATACT 59.313 41.667 8.00 0.00 0.00 2.12
8244 10335 4.337836 TCATTCCAAGTCTCATCTCTCTCG 59.662 45.833 0.00 0.00 0.00 4.04
8246 10337 2.023673 CCAAGTCTCATCTCTCTCGCT 58.976 52.381 0.00 0.00 0.00 4.93
8255 10346 1.364721 TCTCTCTCGCTCTCTTCACG 58.635 55.000 0.00 0.00 0.00 4.35
8264 10355 2.095466 CGCTCTCTTCACGTCTCTTCTT 60.095 50.000 0.00 0.00 0.00 2.52
8403 10502 3.813724 CACAGCTAAGCATGCATATCAGT 59.186 43.478 21.98 8.22 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 8.659925 AGATCATTTGTGACAGAATAAGCTAG 57.340 34.615 0.00 0.00 0.00 3.42
37 38 9.102757 GAAGATCATTTGTGACAGAATAAGCTA 57.897 33.333 0.00 0.00 0.00 3.32
47 48 4.929211 CAGTACGGAAGATCATTTGTGACA 59.071 41.667 0.00 0.00 0.00 3.58
108 109 3.932710 TGCAGATTACGGCTTACTTTCAG 59.067 43.478 0.00 0.00 38.02 3.02
117 118 1.221840 CCACCTGCAGATTACGGCT 59.778 57.895 17.39 0.00 38.02 5.52
120 121 3.119849 CCTTTTTCCACCTGCAGATTACG 60.120 47.826 17.39 0.00 0.00 3.18
129 130 2.944129 TCAGTTCCCTTTTTCCACCTG 58.056 47.619 0.00 0.00 0.00 4.00
133 134 7.125053 ACAGTTTAAATCAGTTCCCTTTTTCCA 59.875 33.333 0.00 0.00 0.00 3.53
223 224 9.736023 CTAAACAAGCAGTGAAGATTAAAAAGT 57.264 29.630 0.00 0.00 0.00 2.66
227 228 8.677148 AGTCTAAACAAGCAGTGAAGATTAAA 57.323 30.769 0.00 0.00 0.00 1.52
228 229 8.150945 AGAGTCTAAACAAGCAGTGAAGATTAA 58.849 33.333 0.00 0.00 0.00 1.40
240 241 6.793492 ATCAACTTGAGAGTCTAAACAAGC 57.207 37.500 16.22 0.00 42.00 4.01
271 272 4.946478 AGTATGATGAGTAGGAAGGTGC 57.054 45.455 0.00 0.00 0.00 5.01
272 273 5.053145 GCAAGTATGATGAGTAGGAAGGTG 58.947 45.833 0.00 0.00 0.00 4.00
273 274 4.202161 CGCAAGTATGATGAGTAGGAAGGT 60.202 45.833 0.00 0.00 0.00 3.50
322 324 5.477984 AGGCAAGCAATGAAGATTACAAAGA 59.522 36.000 0.00 0.00 0.00 2.52
352 354 7.268447 GTGTGACTTATAAGCACGTTCAATTTC 59.732 37.037 23.15 8.87 36.51 2.17
356 358 5.294356 AGTGTGACTTATAAGCACGTTCAA 58.706 37.500 23.15 11.27 36.51 2.69
362 364 5.757886 TGCAAAAGTGTGACTTATAAGCAC 58.242 37.500 22.55 22.55 37.47 4.40
375 377 8.090214 AGCAGAATATAAACAATGCAAAAGTGT 58.910 29.630 0.00 0.00 39.18 3.55
382 384 6.923012 ACACAAGCAGAATATAAACAATGCA 58.077 32.000 0.00 0.00 36.15 3.96
420 422 3.991773 GTCTATATTTTGGCGTGCCGATA 59.008 43.478 6.37 5.30 39.42 2.92
425 427 3.871594 AGTCTGTCTATATTTTGGCGTGC 59.128 43.478 0.00 0.00 0.00 5.34
427 429 7.226720 CCAAATAGTCTGTCTATATTTTGGCGT 59.773 37.037 10.43 0.00 38.41 5.68
430 432 7.502226 TGGCCAAATAGTCTGTCTATATTTTGG 59.498 37.037 0.61 15.25 42.84 3.28
441 443 2.884639 GTGTGTTGGCCAAATAGTCTGT 59.115 45.455 22.47 0.00 0.00 3.41
449 451 1.519719 GCAAGGTGTGTTGGCCAAA 59.480 52.632 22.47 8.06 0.00 3.28
450 452 2.430610 GGCAAGGTGTGTTGGCCAA 61.431 57.895 16.05 16.05 45.03 4.52
451 453 2.837291 GGCAAGGTGTGTTGGCCA 60.837 61.111 0.00 0.00 45.03 5.36
475 477 8.478066 GCTTATTTGGGTTTCCTCTTTCAATAT 58.522 33.333 0.00 0.00 0.00 1.28
504 506 1.710809 ACACCAGTAATTTGGCTCCCT 59.289 47.619 0.00 0.00 42.18 4.20
528 530 0.592247 GCGTTGGCTGTGTGTTTGAG 60.592 55.000 0.00 0.00 35.83 3.02
529 531 1.431440 GCGTTGGCTGTGTGTTTGA 59.569 52.632 0.00 0.00 35.83 2.69
540 542 2.480555 CATTGACGGAGCGTTGGC 59.519 61.111 0.00 0.00 41.37 4.52
615 617 1.607801 CCTCACCGTCCTGCTCATCA 61.608 60.000 0.00 0.00 0.00 3.07
715 717 9.694137 GTCCGCTTCTATTGTAGACTTATTTAT 57.306 33.333 0.00 0.00 33.84 1.40
716 718 8.910944 AGTCCGCTTCTATTGTAGACTTATTTA 58.089 33.333 0.00 0.00 33.84 1.40
776 785 1.226974 ATGCGTCGGAGATCCAACG 60.227 57.895 7.99 7.99 40.67 4.10
824 836 7.226720 CCCGACAAACAGCTATATATGAAAAGT 59.773 37.037 0.00 0.00 0.00 2.66
859 873 1.278238 GGGACTCTGTACATTTCGCG 58.722 55.000 0.00 0.00 0.00 5.87
893 907 2.356278 TGGATGACCCAGCTTGGC 59.644 61.111 3.14 0.00 40.82 4.52
901 915 2.352814 CGTTAGATCGGATGGATGACCC 60.353 54.545 0.00 0.00 34.82 4.46
902 916 2.947852 CGTTAGATCGGATGGATGACC 58.052 52.381 0.00 0.00 34.82 4.02
931 948 1.001293 ACTGCAACAGAATCAGCTCGA 59.999 47.619 0.78 0.00 35.18 4.04
941 965 0.250295 CGGGGAAAGACTGCAACAGA 60.250 55.000 0.78 0.00 35.18 3.41
1088 1112 3.157949 GAAGGGCGAGGAGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
1167 1197 4.849329 GGCGAGTACCTGCGGACG 62.849 72.222 0.00 0.00 0.00 4.79
1168 1198 4.849329 CGGCGAGTACCTGCGGAC 62.849 72.222 0.00 0.00 33.74 4.79
1203 1233 3.233980 TGCGTCACCTCCTGCAGT 61.234 61.111 13.81 0.00 32.73 4.40
1401 1431 6.285224 TGAAGTTAGTCGAAATTGAACTGGA 58.715 36.000 0.00 0.00 30.94 3.86
1408 1439 4.840772 CGCAACTGAAGTTAGTCGAAATTG 59.159 41.667 0.00 0.00 36.32 2.32
1420 1451 2.610727 GGCTAGAAGACGCAACTGAAGT 60.611 50.000 0.00 0.00 0.00 3.01
1430 1463 3.448686 CCACAATACTGGCTAGAAGACG 58.551 50.000 3.17 0.00 0.00 4.18
1450 1483 2.166664 AGATCTAACAGTTCCTGACGCC 59.833 50.000 0.00 0.00 35.18 5.68
1452 1485 6.853720 TCTTAAGATCTAACAGTTCCTGACG 58.146 40.000 0.00 0.00 35.18 4.35
1479 1515 7.495934 ACAAACTGAATTTCTCCTATACATCGG 59.504 37.037 0.00 0.00 0.00 4.18
1480 1516 8.425577 ACAAACTGAATTTCTCCTATACATCG 57.574 34.615 0.00 0.00 0.00 3.84
1482 1518 9.965902 AGAACAAACTGAATTTCTCCTATACAT 57.034 29.630 0.00 0.00 0.00 2.29
1490 1526 7.377131 GCAACAGTAGAACAAACTGAATTTCTC 59.623 37.037 10.02 0.00 45.89 2.87
1566 1602 0.761187 GCTCTCATCACCCTGCCATA 59.239 55.000 0.00 0.00 0.00 2.74
1682 1719 9.372369 AGCTACAATACAGACAGAAATACTTTC 57.628 33.333 0.00 0.00 39.96 2.62
1683 1720 9.155975 CAGCTACAATACAGACAGAAATACTTT 57.844 33.333 0.00 0.00 0.00 2.66
1713 1750 7.177216 AGGAGCATCTGATAAACAAATGAAACA 59.823 33.333 0.00 0.00 29.19 2.83
1724 1761 5.798125 ATCGAGAAGGAGCATCTGATAAA 57.202 39.130 0.00 0.00 33.73 1.40
1759 1796 3.161866 GGGTGAAACAGAAATTAGGCCA 58.838 45.455 5.01 0.00 39.98 5.36
1923 1962 3.730362 GCCAACCAAAATTTTGTGCACAC 60.730 43.478 21.56 9.81 36.45 3.82
1940 1979 2.436417 TGACCTTAAGCAGATGCCAAC 58.564 47.619 0.14 0.00 43.38 3.77
1993 2032 6.099341 CCATATAGCATACATAGCACGACAA 58.901 40.000 0.00 0.00 0.00 3.18
2075 2115 6.576778 AGTAAGTAAATCCAAGTAGGCCAT 57.423 37.500 5.01 0.00 37.29 4.40
2272 2312 2.900106 GCTGGGTTGCTCTGGACCT 61.900 63.158 0.00 0.00 36.18 3.85
2348 2388 1.176527 GCAGCAAAACTCCTGCCATA 58.823 50.000 1.38 0.00 46.59 2.74
2389 2432 1.606531 GGGTCCTGAGCAGCTCAAT 59.393 57.895 25.35 0.00 40.18 2.57
2390 2433 2.947532 CGGGTCCTGAGCAGCTCAA 61.948 63.158 25.35 9.66 40.18 3.02
2450 2494 6.823689 GCCCTGTGATTTCTAGTAATCTTCAA 59.176 38.462 19.20 0.94 35.89 2.69
2460 2504 3.806521 CGAGATTGCCCTGTGATTTCTAG 59.193 47.826 0.00 0.00 0.00 2.43
2481 2525 3.070429 GCCAAATGCAGGAATCTAACG 57.930 47.619 0.00 0.00 40.77 3.18
2896 3284 3.131396 CAACGAAAACTGGAGCTAGTGT 58.869 45.455 0.00 0.00 0.00 3.55
3372 3776 9.877178 CTAGGAATATTACCATGGTAATGAGAC 57.123 37.037 41.67 31.59 46.80 3.36
3560 3964 1.404391 CTGTGCATCAATCAGCCTTCC 59.596 52.381 0.00 0.00 0.00 3.46
3715 4135 3.751175 TGCGATAGAACAAGAAACTTGGG 59.249 43.478 14.51 0.00 39.76 4.12
3734 4154 0.175989 GGACCTTTACCCTCTCTGCG 59.824 60.000 0.00 0.00 0.00 5.18
3823 4251 4.989168 AGCCAGTTTTCTGTAGAAACTACG 59.011 41.667 6.56 2.01 45.68 3.51
3929 4379 3.585732 CCCTTTTCTAACTGGAGGGTGTA 59.414 47.826 0.00 0.00 41.74 2.90
3996 4446 8.942338 TTACAAGGTTGACTGTACATATCATC 57.058 34.615 9.99 9.29 0.00 2.92
4996 6068 4.557496 GCACAGATCACAAGAAAAGGAACC 60.557 45.833 0.00 0.00 0.00 3.62
5000 6072 3.152341 AGGCACAGATCACAAGAAAAGG 58.848 45.455 0.00 0.00 0.00 3.11
5005 6077 6.155221 ACTTTATCTAGGCACAGATCACAAGA 59.845 38.462 15.26 0.00 36.63 3.02
5055 6127 9.422196 GTTATATGCGAATGAGAACTAAACAAC 57.578 33.333 0.00 0.00 0.00 3.32
5407 6481 5.643379 ACAATGTTTGACTTGTTGACACT 57.357 34.783 0.00 0.00 31.74 3.55
5605 6680 3.272574 ACTGGCAACGAGAATGATGAT 57.727 42.857 0.00 0.00 42.51 2.45
5695 6776 2.124778 GCAGCTTGAGGAGGAGCC 60.125 66.667 0.00 0.00 39.71 4.70
5965 7067 4.268687 GTCTGTGTTCCAGGCTCG 57.731 61.111 0.00 0.00 42.76 5.03
6009 7111 1.060729 TGTAGGGGCACTGCAGTTTA 58.939 50.000 18.94 2.25 36.86 2.01
6265 7367 0.177604 CCATCTCTGGCTGACTCACC 59.822 60.000 0.00 0.00 35.23 4.02
6309 7429 2.179517 GACTCACCGTCTCTGGCG 59.820 66.667 0.00 0.00 39.61 5.69
6347 7485 2.640302 GCTGCCTCACCGTCTCTGA 61.640 63.158 0.00 0.00 0.00 3.27
6532 7688 1.812922 CTTCTGGCTGGCAGTAGCG 60.813 63.158 27.51 12.61 44.60 4.26
6606 7777 4.630644 AGAGCTTTGGTCTTCTTCATGA 57.369 40.909 0.00 0.00 37.04 3.07
6772 7943 1.001248 ATGCTGCTTCTGGGCCATT 59.999 52.632 6.72 0.00 0.00 3.16
6796 7967 4.438744 GCCATTGCGCTACTATTTGAGTTT 60.439 41.667 9.73 0.00 39.81 2.66
6944 8181 1.406539 AGCCGCATTTTTAGCTGATGG 59.593 47.619 0.00 0.00 33.41 3.51
6947 8184 1.094785 GGAGCCGCATTTTTAGCTGA 58.905 50.000 0.00 0.00 35.23 4.26
6949 8186 1.098050 CAGGAGCCGCATTTTTAGCT 58.902 50.000 0.00 0.00 38.56 3.32
7027 8264 0.913934 TTCCAGTGCCAGGAGCCATA 60.914 55.000 0.00 0.00 42.71 2.74
7029 8266 2.853542 TTCCAGTGCCAGGAGCCA 60.854 61.111 0.00 0.00 42.71 4.75
7072 8309 2.978010 GGTGGTGTTCCAGTGCCG 60.978 66.667 0.00 0.00 45.24 5.69
7074 8311 3.749981 CTGGTGGTGTTCCAGTGC 58.250 61.111 4.06 0.00 45.24 4.40
7108 8345 2.194597 GGTGGTGTTCCAGTGCCA 59.805 61.111 0.00 0.00 45.24 4.92
7109 8346 2.978010 CGGTGGTGTTCCAGTGCC 60.978 66.667 0.00 0.00 45.24 5.01
7110 8347 2.978010 CCGGTGGTGTTCCAGTGC 60.978 66.667 0.00 0.00 45.24 4.40
7111 8348 2.978010 GCCGGTGGTGTTCCAGTG 60.978 66.667 1.90 0.00 45.24 3.66
7112 8349 4.265056 GGCCGGTGGTGTTCCAGT 62.265 66.667 1.90 0.00 45.24 4.00
7113 8350 4.263572 TGGCCGGTGGTGTTCCAG 62.264 66.667 1.90 0.00 45.24 3.86
7114 8351 4.263572 CTGGCCGGTGGTGTTCCA 62.264 66.667 2.29 0.00 42.05 3.53
7116 8353 3.485346 TTCCTGGCCGGTGGTGTTC 62.485 63.158 11.58 0.00 0.00 3.18
7117 8354 3.494254 TTCCTGGCCGGTGGTGTT 61.494 61.111 11.58 0.00 0.00 3.32
7118 8355 4.265056 GTTCCTGGCCGGTGGTGT 62.265 66.667 11.58 0.00 0.00 4.16
7119 8356 3.491598 AAGTTCCTGGCCGGTGGTG 62.492 63.158 11.58 0.00 0.00 4.17
7120 8357 3.175710 AAGTTCCTGGCCGGTGGT 61.176 61.111 11.58 0.00 0.00 4.16
7121 8358 2.672996 CAAGTTCCTGGCCGGTGG 60.673 66.667 11.58 6.88 0.00 4.61
7122 8359 2.672996 CCAAGTTCCTGGCCGGTG 60.673 66.667 11.58 0.98 0.00 4.94
7128 8365 2.045926 CGGGAGCCAAGTTCCTGG 60.046 66.667 0.00 0.00 35.97 4.45
7129 8366 2.045926 CCGGGAGCCAAGTTCCTG 60.046 66.667 0.00 0.00 38.73 3.86
7130 8367 4.035102 GCCGGGAGCCAAGTTCCT 62.035 66.667 2.18 0.00 33.37 3.36
7131 8368 4.344865 TGCCGGGAGCCAAGTTCC 62.345 66.667 2.18 0.00 42.71 3.62
7132 8369 3.056328 GTGCCGGGAGCCAAGTTC 61.056 66.667 2.18 0.00 42.71 3.01
7133 8370 3.850098 CTGTGCCGGGAGCCAAGTT 62.850 63.158 2.18 0.00 42.71 2.66
7134 8371 4.335647 CTGTGCCGGGAGCCAAGT 62.336 66.667 2.18 0.00 42.71 3.16
7150 8775 1.717032 TCCTGACTAGTGGTGTTGCT 58.283 50.000 0.00 0.00 0.00 3.91
7152 8777 3.131396 GTGTTCCTGACTAGTGGTGTTG 58.869 50.000 0.00 0.00 0.00 3.33
7160 8785 0.173708 GGAGCCGTGTTCCTGACTAG 59.826 60.000 0.00 0.00 30.11 2.57
7161 8786 1.255667 GGGAGCCGTGTTCCTGACTA 61.256 60.000 6.71 0.00 33.37 2.59
7180 8805 3.964875 GGTGGTGTTGCAGTGCCG 61.965 66.667 13.72 0.00 0.00 5.69
7188 8813 3.783362 TTCCTGGCCGGTGGTGTTG 62.783 63.158 11.58 0.00 0.00 3.33
7191 8816 3.491598 AAGTTCCTGGCCGGTGGTG 62.492 63.158 11.58 0.00 0.00 4.17
7192 8817 3.175710 AAGTTCCTGGCCGGTGGT 61.176 61.111 11.58 0.00 0.00 4.16
7193 8818 2.672996 CAAGTTCCTGGCCGGTGG 60.673 66.667 11.58 6.88 0.00 4.61
7198 8823 1.973812 GGTGAGCAAGTTCCTGGCC 60.974 63.158 0.00 0.00 28.98 5.36
7213 8838 2.978010 GGTGTTCCTGTGCCGGTG 60.978 66.667 1.90 0.00 0.00 4.94
7222 8847 3.953775 CTGGCCGGTGGTGTTCCT 61.954 66.667 2.29 0.00 34.23 3.36
7234 8859 2.435059 GTGAGCGAGTTCCTGGCC 60.435 66.667 0.00 0.00 35.84 5.36
7235 8860 2.435059 GGTGAGCGAGTTCCTGGC 60.435 66.667 0.00 0.00 35.46 4.85
7236 8861 2.125912 CGGTGAGCGAGTTCCTGG 60.126 66.667 0.00 0.00 0.00 4.45
7237 8862 2.125912 CCGGTGAGCGAGTTCCTG 60.126 66.667 5.27 0.00 0.00 3.86
7238 8863 4.070552 GCCGGTGAGCGAGTTCCT 62.071 66.667 5.27 0.00 0.00 3.36
7239 8864 4.373116 TGCCGGTGAGCGAGTTCC 62.373 66.667 5.27 0.00 34.65 3.62
7240 8865 3.112709 GTGCCGGTGAGCGAGTTC 61.113 66.667 5.27 0.00 34.65 3.01
7241 8866 3.865929 CTGTGCCGGTGAGCGAGTT 62.866 63.158 5.27 0.00 34.65 3.01
7242 8867 4.363990 CTGTGCCGGTGAGCGAGT 62.364 66.667 5.27 0.00 34.65 4.18
7243 8868 2.486636 TAACTGTGCCGGTGAGCGAG 62.487 60.000 5.27 0.00 34.65 5.03
7244 8869 2.566570 TAACTGTGCCGGTGAGCGA 61.567 57.895 5.27 0.00 34.65 4.93
7245 8870 2.048597 TAACTGTGCCGGTGAGCG 60.049 61.111 1.90 0.00 34.65 5.03
7246 8871 1.301401 TGTAACTGTGCCGGTGAGC 60.301 57.895 1.90 0.00 0.00 4.26
7247 8872 0.949105 GGTGTAACTGTGCCGGTGAG 60.949 60.000 1.90 0.00 36.74 3.51
7248 8873 1.070105 GGTGTAACTGTGCCGGTGA 59.930 57.895 1.90 0.00 36.74 4.02
7249 8874 1.227704 TGGTGTAACTGTGCCGGTG 60.228 57.895 1.90 0.00 36.74 4.94
7250 8875 1.227734 GTGGTGTAACTGTGCCGGT 60.228 57.895 1.90 0.00 36.74 5.28
7251 8876 1.964373 GGTGGTGTAACTGTGCCGG 60.964 63.158 0.00 0.00 36.74 6.13
7252 8877 2.314647 CGGTGGTGTAACTGTGCCG 61.315 63.158 0.00 0.00 36.74 5.69
7253 8878 1.964373 CCGGTGGTGTAACTGTGCC 60.964 63.158 0.00 0.00 36.74 5.01
7254 8879 2.613506 GCCGGTGGTGTAACTGTGC 61.614 63.158 1.90 0.00 36.74 4.57
7255 8880 1.964373 GGCCGGTGGTGTAACTGTG 60.964 63.158 1.90 0.00 36.74 3.66
7256 8881 2.391724 CTGGCCGGTGGTGTAACTGT 62.392 60.000 2.29 0.00 36.74 3.55
7257 8882 1.671054 CTGGCCGGTGGTGTAACTG 60.671 63.158 2.29 0.00 36.74 3.16
7258 8883 2.747686 CTGGCCGGTGGTGTAACT 59.252 61.111 2.29 0.00 36.74 2.24
7259 8884 2.359478 CCTGGCCGGTGGTGTAAC 60.359 66.667 11.58 0.00 0.00 2.50
7260 8885 2.148052 TTCCTGGCCGGTGGTGTAA 61.148 57.895 11.58 0.00 0.00 2.41
7261 8886 2.527123 TTCCTGGCCGGTGGTGTA 60.527 61.111 11.58 0.00 0.00 2.90
7262 8887 4.265056 GTTCCTGGCCGGTGGTGT 62.265 66.667 11.58 0.00 0.00 4.16
7263 8888 3.491598 AAGTTCCTGGCCGGTGGTG 62.492 63.158 11.58 0.00 0.00 4.17
7264 8889 3.175710 AAGTTCCTGGCCGGTGGT 61.176 61.111 11.58 0.00 0.00 4.16
7265 8890 2.672996 CAAGTTCCTGGCCGGTGG 60.673 66.667 11.58 6.88 0.00 4.61
7266 8891 3.365265 GCAAGTTCCTGGCCGGTG 61.365 66.667 11.58 2.44 0.00 4.94
7267 8892 3.553095 GAGCAAGTTCCTGGCCGGT 62.553 63.158 11.58 0.00 28.98 5.28
7268 8893 2.747855 GAGCAAGTTCCTGGCCGG 60.748 66.667 3.88 3.88 28.98 6.13
7269 8894 2.032528 TGAGCAAGTTCCTGGCCG 59.967 61.111 0.00 0.00 28.98 6.13
7281 9112 3.555324 TTCCTGTGCCGGTGAGCA 61.555 61.111 1.90 0.00 41.46 4.26
7362 9370 2.825982 CTGGTGGTGTTCCGGTGA 59.174 61.111 0.00 0.00 36.30 4.02
7568 9576 4.038402 CCTCAGCAACTTGGTTCAGAAAAT 59.962 41.667 0.00 0.00 0.00 1.82
7640 9648 2.557452 CCCTAACAATTGGGTTCTGCCT 60.557 50.000 10.83 0.00 38.65 4.75
7641 9649 1.824852 CCCTAACAATTGGGTTCTGCC 59.175 52.381 10.83 0.00 38.65 4.85
7698 9713 1.828832 GACGACGCAGATCCTACAAG 58.171 55.000 0.00 0.00 0.00 3.16
7735 9758 2.586079 CGCGCCATCGTCAATCCT 60.586 61.111 0.00 0.00 38.14 3.24
7764 9787 1.063006 CCGCAATGCAGATGGAACG 59.937 57.895 5.91 0.00 0.00 3.95
7781 9804 0.818040 AACCACACTTTCGGAGCACC 60.818 55.000 0.00 0.00 0.00 5.01
7783 9806 0.107410 ACAACCACACTTTCGGAGCA 60.107 50.000 0.00 0.00 0.00 4.26
7788 9811 5.238650 AGGAAATCTAACAACCACACTTTCG 59.761 40.000 0.00 0.00 0.00 3.46
7813 9847 1.242076 ACAGCCAACTCATGCACTTC 58.758 50.000 0.00 0.00 0.00 3.01
7814 9848 1.338973 CAACAGCCAACTCATGCACTT 59.661 47.619 0.00 0.00 0.00 3.16
7838 9872 2.910688 TCTGTCACCAACAAGACCTC 57.089 50.000 0.00 0.00 37.45 3.85
7841 9875 4.024556 CACATCTTCTGTCACCAACAAGAC 60.025 45.833 0.00 0.00 37.45 3.01
7868 9903 3.605634 TGCAACCACCATGTATACAGTC 58.394 45.455 11.91 0.00 0.00 3.51
7869 9904 3.609853 CTGCAACCACCATGTATACAGT 58.390 45.455 11.91 1.76 0.00 3.55
7870 9905 2.355756 GCTGCAACCACCATGTATACAG 59.644 50.000 11.91 1.09 0.00 2.74
7874 9909 0.332632 AGGCTGCAACCACCATGTAT 59.667 50.000 9.23 0.00 0.00 2.29
7875 9910 0.608856 CAGGCTGCAACCACCATGTA 60.609 55.000 9.23 0.00 0.00 2.29
7876 9911 1.904865 CAGGCTGCAACCACCATGT 60.905 57.895 9.23 0.00 0.00 3.21
7877 9912 2.642254 CCAGGCTGCAACCACCATG 61.642 63.158 9.56 0.00 0.00 3.66
7897 9932 4.872691 GTCAACAGATTCAGTACCTGATGG 59.127 45.833 3.46 0.00 40.39 3.51
7898 9933 5.482006 TGTCAACAGATTCAGTACCTGATG 58.518 41.667 3.46 2.43 40.39 3.07
7900 9935 5.545063 TTGTCAACAGATTCAGTACCTGA 57.455 39.130 3.46 0.00 38.87 3.86
7901 9936 6.808008 AATTGTCAACAGATTCAGTACCTG 57.192 37.500 0.00 0.00 0.00 4.00
7902 9937 6.772716 ACAAATTGTCAACAGATTCAGTACCT 59.227 34.615 0.00 0.00 0.00 3.08
7903 9938 6.970484 ACAAATTGTCAACAGATTCAGTACC 58.030 36.000 0.00 0.00 0.00 3.34
7922 9981 2.362077 GGCACACTCAAAGGTGACAAAT 59.638 45.455 1.52 0.00 42.68 2.32
8006 10075 4.735132 TCTTCGAGGGGCGCAACG 62.735 66.667 10.83 9.09 40.61 4.10
8090 10171 5.407387 TGATTGTTCTAAACTGTTCCGTAGC 59.593 40.000 0.00 0.00 0.00 3.58
8126 10217 6.909550 ATTTTACTGCTTATGGGTTGTGAA 57.090 33.333 0.00 0.00 0.00 3.18
8164 10255 4.412796 TTTGGAGTGCCAGAGATATGAG 57.587 45.455 0.00 0.00 46.91 2.90
8214 10305 9.023962 AGAGATGAGACTTGGAATGATAGTATC 57.976 37.037 2.97 2.97 32.31 2.24
8219 10310 6.206438 CGAGAGAGATGAGACTTGGAATGATA 59.794 42.308 0.00 0.00 0.00 2.15
8244 10335 3.241701 CAAGAAGAGACGTGAAGAGAGC 58.758 50.000 0.00 0.00 0.00 4.09
8246 10337 2.029828 GGCAAGAAGAGACGTGAAGAGA 60.030 50.000 0.00 0.00 0.00 3.10
8255 10346 5.934625 TCATTTCTGTTAGGCAAGAAGAGAC 59.065 40.000 0.00 0.00 0.00 3.36
8403 10502 2.635714 CTCTGCCTATTCATGCACACA 58.364 47.619 0.00 0.00 33.17 3.72


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

AutoCloner maintained by Alex Coulton.