Multiple sequence alignment - TraesCS5D01G194800

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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 TraesCS5D01G194800 chr5D 100.000 4273 0 0 1 4273 298717107 298721379 0.000000e+00 7891.0
1 TraesCS5D01G194800 chr5D 92.705 562 39 2 3700 4260 466574132 466573572 0.000000e+00 809.0
2 TraesCS5D01G194800 chr5D 87.273 55 3 3 1772 1824 291502954 291502902 4.610000e-05 60.2
3 TraesCS5D01G194800 chr5D 90.476 42 2 2 1772 1811 447816542 447816501 2.000000e-03 54.7
4 TraesCS5D01G194800 chr5A 96.619 1597 48 3 1805 3398 400418475 400420068 0.000000e+00 2645.0
5 TraesCS5D01G194800 chr5A 96.451 1606 51 3 1805 3407 400495140 400493538 0.000000e+00 2645.0
6 TraesCS5D01G194800 chr5A 85.212 825 72 16 253 1069 400416914 400417696 0.000000e+00 802.0
7 TraesCS5D01G194800 chr5A 85.212 825 72 16 253 1069 400496701 400495919 0.000000e+00 802.0
8 TraesCS5D01G194800 chr5A 94.432 431 17 3 1197 1627 400417772 400418195 0.000000e+00 656.0
9 TraesCS5D01G194800 chr5A 94.050 437 19 3 1197 1633 400495843 400495414 0.000000e+00 656.0
10 TraesCS5D01G194800 chr5A 88.446 251 22 2 2 252 400416635 400416878 3.230000e-76 296.0
11 TraesCS5D01G194800 chr5A 88.048 251 23 2 2 252 400496980 400496737 1.500000e-74 291.0
12 TraesCS5D01G194800 chr5A 94.215 121 4 3 3570 3690 400420181 400420298 9.440000e-42 182.0
13 TraesCS5D01G194800 chr5A 92.308 130 7 3 3570 3699 400493434 400493308 9.440000e-42 182.0
14 TraesCS5D01G194800 chr5A 93.388 121 5 2 1618 1735 400418349 400418469 4.390000e-40 176.0
15 TraesCS5D01G194800 chr5A 93.388 121 5 2 1618 1735 400495266 400495146 4.390000e-40 176.0
16 TraesCS5D01G194800 chr5B 96.663 959 28 1 1820 2774 339466819 339467777 0.000000e+00 1591.0
17 TraesCS5D01G194800 chr5B 88.377 955 52 30 823 1735 339465859 339466796 0.000000e+00 1094.0
18 TraesCS5D01G194800 chr5B 93.989 549 29 2 2771 3319 339472953 339473497 0.000000e+00 828.0
19 TraesCS5D01G194800 chr5B 89.496 476 48 2 253 728 339458252 339458725 6.110000e-168 601.0
20 TraesCS5D01G194800 chr5B 91.165 249 9 4 3316 3563 339474653 339474889 4.120000e-85 326.0
21 TraesCS5D01G194800 chr5B 88.976 127 12 2 3570 3696 339474927 339475051 5.720000e-34 156.0
22 TraesCS5D01G194800 chr2D 89.725 1236 118 4 2042 3277 651648786 651650012 0.000000e+00 1570.0
23 TraesCS5D01G194800 chr2D 77.233 1388 277 27 1866 3232 602451910 602450541 0.000000e+00 776.0
24 TraesCS5D01G194800 chr2D 92.697 178 13 0 1866 2043 651648311 651648488 1.520000e-64 257.0
25 TraesCS5D01G194800 chr2A 89.297 1252 122 7 2042 3293 776023008 776021769 0.000000e+00 1559.0
26 TraesCS5D01G194800 chr2A 89.091 220 22 1 1824 2043 776023500 776023283 5.440000e-69 272.0
27 TraesCS5D01G194800 chr2A 92.308 39 1 2 1772 1808 647341313 647341351 2.000000e-03 54.7
28 TraesCS5D01G194800 chr2A 88.889 45 2 3 1772 1814 543175356 543175399 8.000000e-03 52.8
29 TraesCS5D01G194800 chrUn 88.844 1237 127 5 2042 3277 23653102 23651876 0.000000e+00 1509.0
30 TraesCS5D01G194800 chrUn 89.091 220 22 1 1824 2043 23653612 23653395 5.440000e-69 272.0
31 TraesCS5D01G194800 chr7D 94.504 564 29 2 3699 4261 245380031 245379469 0.000000e+00 869.0
32 TraesCS5D01G194800 chr7D 91.637 562 45 2 3700 4260 99047472 99046912 0.000000e+00 776.0
33 TraesCS5D01G194800 chr7D 88.889 45 3 2 1772 1814 600225093 600225137 2.000000e-03 54.7
34 TraesCS5D01G194800 chr3D 92.718 563 37 4 3700 4260 601190261 601190821 0.000000e+00 809.0
35 TraesCS5D01G194800 chr4A 92.580 566 37 4 3699 4260 740958738 740959302 0.000000e+00 808.0
36 TraesCS5D01G194800 chr4A 73.346 1073 247 31 2054 3102 37785236 37784179 1.130000e-95 361.0
37 TraesCS5D01G194800 chr4A 72.738 818 184 30 2260 3056 37317707 37318506 5.520000e-59 239.0
38 TraesCS5D01G194800 chr4A 92.105 38 2 1 1772 1808 728942649 728942612 8.000000e-03 52.8
39 TraesCS5D01G194800 chr1A 92.553 564 38 3 3699 4261 504684359 504683799 0.000000e+00 806.0
40 TraesCS5D01G194800 chr7B 92.199 564 41 3 3699 4260 485414964 485415526 0.000000e+00 795.0
41 TraesCS5D01G194800 chr6D 91.489 564 45 3 3699 4261 440214524 440215085 0.000000e+00 773.0
42 TraesCS5D01G194800 chr6D 87.200 125 16 0 117 241 336475209 336475333 4.450000e-30 143.0
43 TraesCS5D01G194800 chr2B 77.056 1386 281 27 1866 3231 732568840 732567472 0.000000e+00 763.0
44 TraesCS5D01G194800 chr2B 94.444 36 1 1 1764 1799 82718599 82718633 2.000000e-03 54.7
45 TraesCS5D01G194800 chr3B 90.925 562 47 4 3700 4260 223040966 223041524 0.000000e+00 752.0
46 TraesCS5D01G194800 chr3B 89.362 47 3 2 1772 1818 744608589 744608633 1.660000e-04 58.4
47 TraesCS5D01G194800 chr4B 72.668 1072 256 29 2054 3102 526737124 526736067 5.330000e-84 322.0
48 TraesCS5D01G194800 chr4D 72.749 822 183 35 2260 3059 428941608 428940806 5.520000e-59 239.0
49 TraesCS5D01G194800 chr6A 93.671 79 5 0 163 241 476215737 476215815 7.510000e-23 119.0
50 TraesCS5D01G194800 chr1D 100.000 28 0 0 1772 1799 318090053 318090080 8.000000e-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 TraesCS5D01G194800 chr5D 298717107 298721379 4272 False 7891.000000 7891 100.000000 1 4273 1 chr5D.!!$F1 4272
1 TraesCS5D01G194800 chr5D 466573572 466574132 560 True 809.000000 809 92.705000 3700 4260 1 chr5D.!!$R3 560
2 TraesCS5D01G194800 chr5A 400416635 400420298 3663 False 792.833333 2645 92.052000 2 3690 6 chr5A.!!$F1 3688
3 TraesCS5D01G194800 chr5A 400493308 400496980 3672 True 792.000000 2645 91.576167 2 3699 6 chr5A.!!$R1 3697
4 TraesCS5D01G194800 chr5B 339465859 339467777 1918 False 1342.500000 1591 92.520000 823 2774 2 chr5B.!!$F2 1951
5 TraesCS5D01G194800 chr5B 339472953 339475051 2098 False 436.666667 828 91.376667 2771 3696 3 chr5B.!!$F3 925
6 TraesCS5D01G194800 chr2D 651648311 651650012 1701 False 913.500000 1570 91.211000 1866 3277 2 chr2D.!!$F1 1411
7 TraesCS5D01G194800 chr2D 602450541 602451910 1369 True 776.000000 776 77.233000 1866 3232 1 chr2D.!!$R1 1366
8 TraesCS5D01G194800 chr2A 776021769 776023500 1731 True 915.500000 1559 89.194000 1824 3293 2 chr2A.!!$R1 1469
9 TraesCS5D01G194800 chrUn 23651876 23653612 1736 True 890.500000 1509 88.967500 1824 3277 2 chrUn.!!$R1 1453
10 TraesCS5D01G194800 chr7D 245379469 245380031 562 True 869.000000 869 94.504000 3699 4261 1 chr7D.!!$R2 562
11 TraesCS5D01G194800 chr7D 99046912 99047472 560 True 776.000000 776 91.637000 3700 4260 1 chr7D.!!$R1 560
12 TraesCS5D01G194800 chr3D 601190261 601190821 560 False 809.000000 809 92.718000 3700 4260 1 chr3D.!!$F1 560
13 TraesCS5D01G194800 chr4A 740958738 740959302 564 False 808.000000 808 92.580000 3699 4260 1 chr4A.!!$F2 561
14 TraesCS5D01G194800 chr4A 37784179 37785236 1057 True 361.000000 361 73.346000 2054 3102 1 chr4A.!!$R1 1048
15 TraesCS5D01G194800 chr4A 37317707 37318506 799 False 239.000000 239 72.738000 2260 3056 1 chr4A.!!$F1 796
16 TraesCS5D01G194800 chr1A 504683799 504684359 560 True 806.000000 806 92.553000 3699 4261 1 chr1A.!!$R1 562
17 TraesCS5D01G194800 chr7B 485414964 485415526 562 False 795.000000 795 92.199000 3699 4260 1 chr7B.!!$F1 561
18 TraesCS5D01G194800 chr6D 440214524 440215085 561 False 773.000000 773 91.489000 3699 4261 1 chr6D.!!$F2 562
19 TraesCS5D01G194800 chr2B 732567472 732568840 1368 True 763.000000 763 77.056000 1866 3231 1 chr2B.!!$R1 1365
20 TraesCS5D01G194800 chr3B 223040966 223041524 558 False 752.000000 752 90.925000 3700 4260 1 chr3B.!!$F1 560
21 TraesCS5D01G194800 chr4B 526736067 526737124 1057 True 322.000000 322 72.668000 2054 3102 1 chr4B.!!$R1 1048
22 TraesCS5D01G194800 chr4D 428940806 428941608 802 True 239.000000 239 72.749000 2260 3059 1 chr4D.!!$R1 799

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
700 736 0.036022 TGATCGGCCACACATGACAA 59.964 50.0 2.24 0.00 0.0 3.18 F
703 739 0.179032 TCGGCCACACATGACAACTT 60.179 50.0 2.24 0.00 0.0 2.66 F
1135 1186 0.320858 TTGCTTTGCCCACGATCGTA 60.321 50.0 22.26 1.63 0.0 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 2103 0.037697 ACACGCGGAACAGCAAGATA 60.038 50.0 12.47 0.0 36.85 1.98 R
3092 3724 0.033504 ACGTCTTGTGCGTCTTCCAT 59.966 50.0 0.00 0.0 38.23 3.41 R
3459 5254 1.092921 TCGCGCCAAGACACTGTTTT 61.093 50.0 0.00 0.0 0.00 2.43 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
60 61 3.491652 GTCGCAGCCGCCTTCTTC 61.492 66.667 0.00 0.00 33.11 2.87
92 93 2.904866 TGGGACACGTTTGCAGCC 60.905 61.111 0.00 0.00 0.00 4.85
105 106 2.586245 CAGCCCATGCGGAGAAGA 59.414 61.111 4.56 0.00 44.33 2.87
114 115 2.805353 CGGAGAAGACACACGCCG 60.805 66.667 0.00 0.00 42.03 6.46
157 158 1.595109 TGCAGACTTGTGCCTCGTG 60.595 57.895 0.00 0.00 43.28 4.35
162 163 1.222115 GACTTGTGCCTCGTGACCAC 61.222 60.000 0.00 0.00 0.00 4.16
174 175 1.540363 CGTGACCACTAACTTGTGCCT 60.540 52.381 0.00 0.00 36.68 4.75
175 176 2.288579 CGTGACCACTAACTTGTGCCTA 60.289 50.000 0.00 0.00 36.68 3.93
176 177 3.326747 GTGACCACTAACTTGTGCCTAG 58.673 50.000 0.00 0.00 36.68 3.02
177 178 2.969950 TGACCACTAACTTGTGCCTAGT 59.030 45.455 0.00 0.00 36.68 2.57
178 179 3.006537 TGACCACTAACTTGTGCCTAGTC 59.993 47.826 0.00 0.00 36.68 2.59
179 180 2.969950 ACCACTAACTTGTGCCTAGTCA 59.030 45.455 0.00 0.00 36.68 3.41
180 181 3.006967 ACCACTAACTTGTGCCTAGTCAG 59.993 47.826 0.00 0.00 36.68 3.51
181 182 3.589988 CACTAACTTGTGCCTAGTCAGG 58.410 50.000 0.00 0.00 45.77 3.86
182 183 3.258372 CACTAACTTGTGCCTAGTCAGGA 59.742 47.826 0.00 0.00 45.91 3.86
183 184 2.841442 AACTTGTGCCTAGTCAGGAC 57.159 50.000 0.00 0.00 45.91 3.85
184 185 1.717032 ACTTGTGCCTAGTCAGGACA 58.283 50.000 1.84 0.00 45.91 4.02
185 186 1.344763 ACTTGTGCCTAGTCAGGACAC 59.655 52.381 1.84 9.77 45.91 3.67
187 188 1.717032 TGTGCCTAGTCAGGACACTT 58.283 50.000 14.79 0.00 45.91 3.16
188 189 2.884320 TGTGCCTAGTCAGGACACTTA 58.116 47.619 14.79 0.09 45.91 2.24
189 190 2.826128 TGTGCCTAGTCAGGACACTTAG 59.174 50.000 14.79 0.00 45.91 2.18
190 191 2.826725 GTGCCTAGTCAGGACACTTAGT 59.173 50.000 1.84 0.00 45.91 2.24
191 192 3.090037 TGCCTAGTCAGGACACTTAGTC 58.910 50.000 1.84 0.00 45.91 2.59
236 237 3.872603 AGCCACGCCACCAGTGAA 61.873 61.111 0.00 0.00 41.83 3.18
240 241 0.036388 CCACGCCACCAGTGAACTAT 60.036 55.000 0.00 0.00 41.83 2.12
241 242 1.078709 CACGCCACCAGTGAACTATG 58.921 55.000 0.00 0.00 41.83 2.23
249 285 5.506317 GCCACCAGTGAACTATGAAATATGC 60.506 44.000 0.00 0.00 0.00 3.14
251 287 5.009010 CACCAGTGAACTATGAAATATGCCC 59.991 44.000 0.00 0.00 0.00 5.36
262 298 5.857471 TGAAATATGCCCTGGATTGAAAG 57.143 39.130 0.00 0.00 0.00 2.62
269 305 0.443869 CCTGGATTGAAAGTGACGCG 59.556 55.000 3.53 3.53 0.00 6.01
270 306 0.179215 CTGGATTGAAAGTGACGCGC 60.179 55.000 5.73 0.00 0.00 6.86
275 311 0.249531 TTGAAAGTGACGCGCCACTA 60.250 50.000 28.30 10.58 45.82 2.74
282 318 0.245266 TGACGCGCCACTAATGAAGA 59.755 50.000 5.73 0.00 0.00 2.87
354 390 0.912486 ATGTGTAGGCAGGGAAGTCC 59.088 55.000 0.00 0.00 0.00 3.85
355 391 0.472925 TGTGTAGGCAGGGAAGTCCA 60.473 55.000 0.00 0.00 38.24 4.02
361 397 1.575447 GGCAGGGAAGTCCAGGGAAT 61.575 60.000 0.00 0.00 38.24 3.01
373 409 0.447801 CAGGGAATCGGCTTCAAACG 59.552 55.000 0.00 0.00 35.41 3.60
390 426 3.961480 AACGAGAGGAATGTGACATGA 57.039 42.857 0.00 0.00 0.00 3.07
391 427 3.961480 ACGAGAGGAATGTGACATGAA 57.039 42.857 0.00 0.00 0.00 2.57
394 430 4.021104 ACGAGAGGAATGTGACATGAAAGA 60.021 41.667 0.00 0.00 0.00 2.52
422 458 0.908910 AGTCCATGGTATTGTCGGCA 59.091 50.000 12.58 0.00 0.00 5.69
447 483 0.746204 TGCAAGCACCAAAGACGACA 60.746 50.000 0.00 0.00 0.00 4.35
464 500 0.397254 ACACTATGACGAGGGAGGGG 60.397 60.000 0.00 0.00 0.00 4.79
470 506 2.617538 ACGAGGGAGGGGAGGAGA 60.618 66.667 0.00 0.00 0.00 3.71
478 514 0.898789 GAGGGGAGGAGACGTCACAA 60.899 60.000 19.50 0.00 0.00 3.33
479 515 0.471211 AGGGGAGGAGACGTCACAAA 60.471 55.000 19.50 0.00 0.00 2.83
483 519 2.076863 GGAGGAGACGTCACAAAATGG 58.923 52.381 19.50 0.00 0.00 3.16
492 528 3.251004 ACGTCACAAAATGGAAGAAGAGC 59.749 43.478 0.00 0.00 0.00 4.09
493 529 3.250762 CGTCACAAAATGGAAGAAGAGCA 59.749 43.478 0.00 0.00 0.00 4.26
505 541 0.729690 GAAGAGCAGGGAAATGTCGC 59.270 55.000 0.00 0.00 36.97 5.19
509 545 3.093278 CAGGGAAATGTCGCTCGC 58.907 61.111 0.00 0.00 44.79 5.03
546 582 5.470098 TCAGGATGAAGTGTGCTCTAAAAAC 59.530 40.000 0.00 0.00 45.97 2.43
547 583 4.452455 AGGATGAAGTGTGCTCTAAAAACG 59.548 41.667 0.00 0.00 0.00 3.60
548 584 3.602390 TGAAGTGTGCTCTAAAAACGC 57.398 42.857 0.00 0.00 0.00 4.84
549 585 2.289547 TGAAGTGTGCTCTAAAAACGCC 59.710 45.455 0.00 0.00 0.00 5.68
550 586 1.235724 AGTGTGCTCTAAAAACGCCC 58.764 50.000 0.00 0.00 0.00 6.13
551 587 0.240145 GTGTGCTCTAAAAACGCCCC 59.760 55.000 0.00 0.00 0.00 5.80
552 588 0.179015 TGTGCTCTAAAAACGCCCCA 60.179 50.000 0.00 0.00 0.00 4.96
555 591 0.955905 GCTCTAAAAACGCCCCACAA 59.044 50.000 0.00 0.00 0.00 3.33
559 595 1.268625 CTAAAAACGCCCCACAACCTC 59.731 52.381 0.00 0.00 0.00 3.85
590 626 0.590195 GCATGCAGGCTCGATTTAGG 59.410 55.000 17.57 0.00 0.00 2.69
627 663 4.303853 CGATGGAGCTCGTAACGG 57.696 61.111 7.83 0.00 34.00 4.44
646 682 2.096496 CGGCTCTGCTCGATTGATTTTT 59.904 45.455 0.00 0.00 0.00 1.94
685 721 3.558418 ACATGCGGTTATTTACGGTGATC 59.442 43.478 0.00 0.00 0.00 2.92
686 722 2.195096 TGCGGTTATTTACGGTGATCG 58.805 47.619 0.00 0.00 45.88 3.69
687 723 1.523934 GCGGTTATTTACGGTGATCGG 59.476 52.381 0.00 0.00 44.45 4.18
695 731 1.609635 TACGGTGATCGGCCACACAT 61.610 55.000 20.76 13.24 44.45 3.21
700 736 0.036022 TGATCGGCCACACATGACAA 59.964 50.000 2.24 0.00 0.00 3.18
703 739 0.179032 TCGGCCACACATGACAACTT 60.179 50.000 2.24 0.00 0.00 2.66
708 744 2.293122 GCCACACATGACAACTTTGCTA 59.707 45.455 0.00 0.00 0.00 3.49
712 748 4.512944 CACACATGACAACTTTGCTAGAGT 59.487 41.667 0.00 0.00 0.00 3.24
733 769 5.017490 AGTAGCTCTAAAACTAGTGGCTGA 58.983 41.667 0.00 0.00 32.90 4.26
735 771 3.835395 AGCTCTAAAACTAGTGGCTGAGT 59.165 43.478 0.00 0.00 0.00 3.41
749 785 1.006220 TGAGTCGACGCATGCAACT 60.006 52.632 18.48 14.42 0.00 3.16
755 791 1.742900 CGACGCATGCAACTAGGACG 61.743 60.000 19.57 8.40 0.00 4.79
757 793 2.703409 GCATGCAACTAGGACGCG 59.297 61.111 14.21 3.53 0.00 6.01
762 798 0.961857 TGCAACTAGGACGCGGTCTA 60.962 55.000 12.47 10.71 32.47 2.59
776 812 3.675228 CGCGGTCTATAACACTCTTTGGT 60.675 47.826 0.00 0.00 0.00 3.67
782 818 7.601508 CGGTCTATAACACTCTTTGGTAACTTT 59.398 37.037 0.00 0.00 28.55 2.66
783 819 9.281371 GGTCTATAACACTCTTTGGTAACTTTT 57.719 33.333 0.00 0.00 28.55 2.27
811 847 3.979789 TGGCATGCCACAACTACG 58.020 55.556 35.59 0.00 41.89 3.51
820 856 1.554042 CCACAACTACGTCCGCACAC 61.554 60.000 0.00 0.00 0.00 3.82
917 953 4.062991 GACAATTTCACCGGTTACTCTGT 58.937 43.478 2.97 6.19 0.00 3.41
970 1013 2.535984 GTCCATTCACTAACGCATCTCG 59.464 50.000 0.00 0.00 45.38 4.04
1014 1061 4.142816 GGAGTGACAATGAGGAATTTCGTG 60.143 45.833 0.00 0.00 0.00 4.35
1036 1083 4.202398 TGGAGAAATCAGTGCTCTCTTTGT 60.202 41.667 13.24 0.00 36.61 2.83
1069 1116 1.271543 TGCTCCAAGGTCAGTTGATGG 60.272 52.381 0.00 0.00 0.00 3.51
1070 1117 1.271597 GCTCCAAGGTCAGTTGATGGT 60.272 52.381 1.41 0.00 32.90 3.55
1072 1119 3.559171 GCTCCAAGGTCAGTTGATGGTTA 60.559 47.826 1.41 0.00 32.90 2.85
1073 1120 4.848357 CTCCAAGGTCAGTTGATGGTTAT 58.152 43.478 1.41 0.00 32.90 1.89
1074 1121 5.255397 TCCAAGGTCAGTTGATGGTTATT 57.745 39.130 1.41 0.00 32.90 1.40
1075 1122 6.381498 TCCAAGGTCAGTTGATGGTTATTA 57.619 37.500 1.41 0.00 32.90 0.98
1076 1123 6.785076 TCCAAGGTCAGTTGATGGTTATTAA 58.215 36.000 1.41 0.00 32.90 1.40
1077 1124 7.235079 TCCAAGGTCAGTTGATGGTTATTAAA 58.765 34.615 1.41 0.00 32.90 1.52
1079 1126 9.184523 CCAAGGTCAGTTGATGGTTATTAAATA 57.815 33.333 0.00 0.00 0.00 1.40
1082 1129 9.614792 AGGTCAGTTGATGGTTATTAAATACTC 57.385 33.333 0.00 0.00 0.00 2.59
1083 1130 8.837389 GGTCAGTTGATGGTTATTAAATACTCC 58.163 37.037 0.00 0.00 0.00 3.85
1085 1132 9.613428 TCAGTTGATGGTTATTAAATACTCCAG 57.387 33.333 0.00 0.00 0.00 3.86
1086 1133 8.345565 CAGTTGATGGTTATTAAATACTCCAGC 58.654 37.037 0.00 0.00 32.90 4.85
1087 1134 7.226720 AGTTGATGGTTATTAAATACTCCAGCG 59.773 37.037 0.00 0.00 34.65 5.18
1088 1135 5.995282 TGATGGTTATTAAATACTCCAGCGG 59.005 40.000 0.00 0.00 34.65 5.52
1089 1136 5.362105 TGGTTATTAAATACTCCAGCGGT 57.638 39.130 0.00 0.00 0.00 5.68
1090 1137 5.747342 TGGTTATTAAATACTCCAGCGGTT 58.253 37.500 0.00 0.00 0.00 4.44
1091 1138 6.887013 TGGTTATTAAATACTCCAGCGGTTA 58.113 36.000 0.00 0.00 0.00 2.85
1092 1139 7.337167 TGGTTATTAAATACTCCAGCGGTTAA 58.663 34.615 0.00 0.00 0.00 2.01
1093 1140 7.994334 TGGTTATTAAATACTCCAGCGGTTAAT 59.006 33.333 0.00 0.00 0.00 1.40
1094 1141 9.492973 GGTTATTAAATACTCCAGCGGTTAATA 57.507 33.333 0.00 0.00 0.00 0.98
1099 1146 6.720112 AATACTCCAGCGGTTAATAGTGTA 57.280 37.500 0.00 0.00 0.00 2.90
1102 1149 6.328641 ACTCCAGCGGTTAATAGTGTATAG 57.671 41.667 0.00 0.00 0.00 1.31
1127 1178 0.537188 TTTTCGGTTTGCTTTGCCCA 59.463 45.000 0.00 0.00 0.00 5.36
1133 1184 0.729140 GTTTGCTTTGCCCACGATCG 60.729 55.000 14.88 14.88 0.00 3.69
1135 1186 0.320858 TTGCTTTGCCCACGATCGTA 60.321 50.000 22.26 1.63 0.00 3.43
1148 1199 6.196571 CCCACGATCGTAAATGGAATTTTAC 58.803 40.000 22.26 0.00 46.10 2.01
1149 1200 6.183360 CCCACGATCGTAAATGGAATTTTACA 60.183 38.462 22.26 0.00 46.10 2.41
1151 1202 8.552865 CCACGATCGTAAATGGAATTTTACATA 58.447 33.333 22.26 0.00 46.10 2.29
1152 1203 9.365311 CACGATCGTAAATGGAATTTTACATAC 57.635 33.333 22.26 0.00 46.10 2.39
1153 1204 8.553696 ACGATCGTAAATGGAATTTTACATACC 58.446 33.333 21.32 0.00 46.10 2.73
1154 1205 8.013378 CGATCGTAAATGGAATTTTACATACCC 58.987 37.037 7.03 0.00 46.10 3.69
1157 1208 7.830201 TCGTAAATGGAATTTTACATACCCTGT 59.170 33.333 7.59 0.00 46.10 4.00
1158 1209 9.111613 CGTAAATGGAATTTTACATACCCTGTA 57.888 33.333 7.59 0.00 46.10 2.74
1170 1221 9.675464 TTTACATACCCTGTAATTAAGGTGAAG 57.325 33.333 11.54 5.73 46.88 3.02
1171 1222 6.659824 ACATACCCTGTAATTAAGGTGAAGG 58.340 40.000 11.54 2.49 35.91 3.46
1173 1224 7.128883 ACATACCCTGTAATTAAGGTGAAGGAT 59.871 37.037 11.54 0.00 35.91 3.24
1177 1228 5.066505 CCTGTAATTAAGGTGAAGGATGTGC 59.933 44.000 0.00 0.00 0.00 4.57
1193 1260 2.454538 TGTGCATATGGGCATGAAACA 58.545 42.857 4.56 0.00 46.92 2.83
1209 1289 4.295870 TGAAACACACTGACGTATGTCTC 58.704 43.478 15.91 3.61 45.70 3.36
1212 1292 2.885266 ACACACTGACGTATGTCTCTGT 59.115 45.455 15.91 12.93 45.70 3.41
1219 1299 5.134202 TGACGTATGTCTCTGTTTGATGT 57.866 39.130 15.91 0.00 45.70 3.06
1312 1392 5.492895 TGAGTCTTTCTGGTGTTGTTTGTA 58.507 37.500 0.00 0.00 0.00 2.41
1327 1407 8.656849 GTGTTGTTTGTATCGATCTTAATCTGT 58.343 33.333 0.00 0.00 0.00 3.41
1328 1408 8.655970 TGTTGTTTGTATCGATCTTAATCTGTG 58.344 33.333 0.00 0.00 0.00 3.66
1329 1409 7.234187 TGTTTGTATCGATCTTAATCTGTGC 57.766 36.000 0.00 0.00 0.00 4.57
1330 1410 6.816140 TGTTTGTATCGATCTTAATCTGTGCA 59.184 34.615 0.00 0.00 0.00 4.57
1370 1450 7.041372 GCAGCCTCCAAAAACGAAATCTATATA 60.041 37.037 0.00 0.00 0.00 0.86
1371 1451 9.003658 CAGCCTCCAAAAACGAAATCTATATAT 57.996 33.333 0.00 0.00 0.00 0.86
1372 1452 9.003658 AGCCTCCAAAAACGAAATCTATATATG 57.996 33.333 0.00 0.00 0.00 1.78
1373 1453 8.237267 GCCTCCAAAAACGAAATCTATATATGG 58.763 37.037 0.00 0.00 0.00 2.74
1457 1539 1.557443 CGTCGTGGTTTCAGTGCCTC 61.557 60.000 0.00 0.00 0.00 4.70
1463 1545 1.228657 GGTTTCAGTGCCTCGGTGAC 61.229 60.000 0.00 0.00 0.00 3.67
1735 1983 8.743085 ATATATACATACCGACCGAATGTACT 57.257 34.615 14.88 10.48 38.53 2.73
1737 1985 4.037858 ACATACCGACCGAATGTACTTC 57.962 45.455 8.04 0.00 32.21 3.01
1738 1986 3.181483 ACATACCGACCGAATGTACTTCC 60.181 47.826 8.04 0.00 32.21 3.46
1739 1987 1.553706 ACCGACCGAATGTACTTCCT 58.446 50.000 0.00 0.00 0.00 3.36
1740 1988 1.475682 ACCGACCGAATGTACTTCCTC 59.524 52.381 0.00 0.00 0.00 3.71
1742 1990 2.479730 CCGACCGAATGTACTTCCTCTG 60.480 54.545 0.00 0.00 0.00 3.35
1743 1991 2.163815 CGACCGAATGTACTTCCTCTGT 59.836 50.000 0.00 0.00 0.00 3.41
1744 1992 3.376234 CGACCGAATGTACTTCCTCTGTA 59.624 47.826 0.00 0.00 0.00 2.74
1745 1993 4.142534 CGACCGAATGTACTTCCTCTGTAA 60.143 45.833 0.00 0.00 0.00 2.41
1746 1994 5.450137 CGACCGAATGTACTTCCTCTGTAAT 60.450 44.000 0.00 0.00 0.00 1.89
1747 1995 6.238566 CGACCGAATGTACTTCCTCTGTAATA 60.239 42.308 0.00 0.00 0.00 0.98
1748 1996 7.414222 ACCGAATGTACTTCCTCTGTAATAA 57.586 36.000 0.00 0.00 0.00 1.40
1749 1997 7.844009 ACCGAATGTACTTCCTCTGTAATAAA 58.156 34.615 0.00 0.00 0.00 1.40
1750 1998 7.763071 ACCGAATGTACTTCCTCTGTAATAAAC 59.237 37.037 0.00 0.00 0.00 2.01
1751 1999 7.980099 CCGAATGTACTTCCTCTGTAATAAACT 59.020 37.037 0.00 0.00 0.00 2.66
1846 2103 3.577341 TGCAGTGCATGTGACGAAGTTT 61.577 45.455 15.37 0.00 34.64 2.66
3092 3724 2.161831 CGACAAGCTCATTGCCGAA 58.838 52.632 0.00 0.00 46.42 4.30
3197 3829 2.047179 GACCACCCTTCGCAGACC 60.047 66.667 0.00 0.00 34.32 3.85
3257 3889 0.463295 CAGCCTCCGAGCACATCATT 60.463 55.000 0.00 0.00 34.23 2.57
3363 5157 8.689061 TCTTTTATGTAGTTCTACGCCATCTAA 58.311 33.333 5.66 0.00 0.00 2.10
3434 5228 4.051922 GGATCGTGTTCCACTATCATCAC 58.948 47.826 10.01 0.00 38.00 3.06
3497 5292 5.874895 GCGAAAGGGAAACAAATAGTAGT 57.125 39.130 0.00 0.00 0.00 2.73
3498 5293 6.973229 GCGAAAGGGAAACAAATAGTAGTA 57.027 37.500 0.00 0.00 0.00 1.82
3499 5294 7.368480 GCGAAAGGGAAACAAATAGTAGTAA 57.632 36.000 0.00 0.00 0.00 2.24
3518 5313 5.306394 AGTAAAAGAGAAGGAAAGGGAACG 58.694 41.667 0.00 0.00 0.00 3.95
3535 5330 1.197812 ACGTCCCCATGTTACTACCC 58.802 55.000 0.00 0.00 0.00 3.69
3536 5331 1.196911 CGTCCCCATGTTACTACCCA 58.803 55.000 0.00 0.00 0.00 4.51
3537 5332 1.555992 CGTCCCCATGTTACTACCCAA 59.444 52.381 0.00 0.00 0.00 4.12
3587 5413 2.817258 CCCATGTTGCGAGGTCTTAAAA 59.183 45.455 0.00 0.00 0.00 1.52
3684 5510 9.415544 ACAAAGATAAATGTCAATCTTTCTTGC 57.584 29.630 7.67 0.00 45.02 4.01
3746 5572 4.321718 CGGCCTCTGAATCATAATGATGT 58.678 43.478 0.00 0.00 37.15 3.06
3811 5639 7.333423 AGTCATAAAAGTATTACAGCTCGCAAA 59.667 33.333 0.00 0.00 0.00 3.68
3910 5739 4.411927 AGACTCCTATCCTGTTATGCGAT 58.588 43.478 0.00 0.00 0.00 4.58
3938 5767 3.800531 CCGAACCGGTTGAATATAACCT 58.199 45.455 27.87 0.00 46.29 3.50
3955 5786 2.481441 ACCTGTGCTATCATCTCCCAA 58.519 47.619 0.00 0.00 0.00 4.12
4120 5952 2.638480 TATAGCCCAAAGAAGCGCAT 57.362 45.000 11.47 0.00 0.00 4.73
4174 6006 1.278127 GCTCAACCCTAGCTAACCACA 59.722 52.381 0.00 0.00 37.01 4.17
4177 6009 3.178046 TCAACCCTAGCTAACCACATCA 58.822 45.455 0.00 0.00 0.00 3.07
4265 6097 3.602103 GGCGAATGGGCATGACAA 58.398 55.556 0.00 0.00 41.77 3.18
4266 6098 1.889454 GGCGAATGGGCATGACAAA 59.111 52.632 0.00 0.00 41.77 2.83
4267 6099 0.458370 GGCGAATGGGCATGACAAAC 60.458 55.000 0.00 0.00 41.77 2.93
4268 6100 0.527565 GCGAATGGGCATGACAAACT 59.472 50.000 0.00 0.00 0.00 2.66
4269 6101 1.468054 GCGAATGGGCATGACAAACTC 60.468 52.381 0.00 0.00 0.00 3.01
4270 6102 1.202065 CGAATGGGCATGACAAACTCG 60.202 52.381 0.00 0.00 0.00 4.18
4271 6103 1.812571 GAATGGGCATGACAAACTCGT 59.187 47.619 0.00 0.00 0.00 4.18
4272 6104 1.453155 ATGGGCATGACAAACTCGTC 58.547 50.000 0.00 0.00 36.40 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.452733 CCGCTCACCCCTTCGTCC 62.453 72.222 0.00 0.00 0.00 4.79
60 61 4.963878 CCATCGAAGAACTGGGGG 57.036 61.111 0.00 0.00 43.58 5.40
65 66 0.966920 ACGTGTCCCATCGAAGAACT 59.033 50.000 0.00 0.00 43.58 3.01
88 89 1.817099 GTCTTCTCCGCATGGGCTG 60.817 63.158 3.80 0.00 38.10 4.85
90 91 2.109126 GTGTCTTCTCCGCATGGGC 61.109 63.158 3.80 0.00 35.24 5.36
91 92 1.021390 GTGTGTCTTCTCCGCATGGG 61.021 60.000 2.06 2.06 35.24 4.00
92 93 1.354337 CGTGTGTCTTCTCCGCATGG 61.354 60.000 0.00 0.00 0.00 3.66
97 98 2.805353 CGGCGTGTGTCTTCTCCG 60.805 66.667 0.00 0.00 0.00 4.63
105 106 3.612681 ACTAGTGCCGGCGTGTGT 61.613 61.111 23.90 15.27 0.00 3.72
112 113 1.206132 TGGTATTGTCACTAGTGCCGG 59.794 52.381 18.45 0.00 0.00 6.13
114 115 3.262420 CACTGGTATTGTCACTAGTGCC 58.738 50.000 18.45 7.59 46.57 5.01
157 158 3.006537 TGACTAGGCACAAGTTAGTGGTC 59.993 47.826 0.00 0.00 39.87 4.02
162 163 3.258372 TGTCCTGACTAGGCACAAGTTAG 59.742 47.826 0.00 0.00 44.22 2.34
181 182 5.148651 ACAAGTATGTGGGACTAAGTGTC 57.851 43.478 0.00 0.00 40.67 3.67
197 198 2.287308 GCATTTTCACACGCCACAAGTA 60.287 45.455 0.00 0.00 0.00 2.24
205 206 1.007502 TGGCTGCATTTTCACACGC 60.008 52.632 0.50 0.00 0.00 5.34
234 235 6.716628 TCAATCCAGGGCATATTTCATAGTTC 59.283 38.462 0.00 0.00 0.00 3.01
236 237 6.204852 TCAATCCAGGGCATATTTCATAGT 57.795 37.500 0.00 0.00 0.00 2.12
240 241 5.127519 CACTTTCAATCCAGGGCATATTTCA 59.872 40.000 0.00 0.00 0.00 2.69
241 242 5.360714 TCACTTTCAATCCAGGGCATATTTC 59.639 40.000 0.00 0.00 0.00 2.17
249 285 0.804989 GCGTCACTTTCAATCCAGGG 59.195 55.000 0.00 0.00 0.00 4.45
251 287 0.179215 GCGCGTCACTTTCAATCCAG 60.179 55.000 8.43 0.00 0.00 3.86
262 298 0.370273 CTTCATTAGTGGCGCGTCAC 59.630 55.000 35.18 35.18 37.89 3.67
269 305 3.265791 CCAGACTGTCTTCATTAGTGGC 58.734 50.000 7.77 0.00 0.00 5.01
270 306 4.248859 CACCAGACTGTCTTCATTAGTGG 58.751 47.826 7.77 7.21 0.00 4.00
275 311 1.421268 TGCCACCAGACTGTCTTCATT 59.579 47.619 7.77 0.00 0.00 2.57
282 318 1.901591 CAGAAATGCCACCAGACTGT 58.098 50.000 0.93 0.00 0.00 3.55
307 343 4.329545 TCTCCGCTGGCCCAACAC 62.330 66.667 0.00 0.00 0.00 3.32
354 390 0.447801 CGTTTGAAGCCGATTCCCTG 59.552 55.000 0.00 0.00 37.08 4.45
355 391 0.323629 TCGTTTGAAGCCGATTCCCT 59.676 50.000 0.00 0.00 37.08 4.20
361 397 0.677288 TTCCTCTCGTTTGAAGCCGA 59.323 50.000 0.00 0.00 0.00 5.54
373 409 4.328440 CGTCTTTCATGTCACATTCCTCTC 59.672 45.833 0.00 0.00 0.00 3.20
422 458 0.825010 CTTTGGTGCTTGCAGTCCCT 60.825 55.000 0.00 0.00 0.00 4.20
431 467 2.902705 TAGTGTCGTCTTTGGTGCTT 57.097 45.000 0.00 0.00 0.00 3.91
432 468 2.299013 TCATAGTGTCGTCTTTGGTGCT 59.701 45.455 0.00 0.00 0.00 4.40
434 470 2.661675 CGTCATAGTGTCGTCTTTGGTG 59.338 50.000 0.00 0.00 0.00 4.17
435 471 2.555325 TCGTCATAGTGTCGTCTTTGGT 59.445 45.455 0.00 0.00 31.27 3.67
437 473 3.172050 CCTCGTCATAGTGTCGTCTTTG 58.828 50.000 0.00 0.00 31.27 2.77
447 483 0.186386 CTCCCCTCCCTCGTCATAGT 59.814 60.000 0.00 0.00 0.00 2.12
464 500 3.040147 TCCATTTTGTGACGTCTCCTC 57.960 47.619 17.92 5.50 0.00 3.71
470 506 3.251004 GCTCTTCTTCCATTTTGTGACGT 59.749 43.478 0.00 0.00 0.00 4.34
478 514 3.814504 TTCCCTGCTCTTCTTCCATTT 57.185 42.857 0.00 0.00 0.00 2.32
479 515 3.814504 TTTCCCTGCTCTTCTTCCATT 57.185 42.857 0.00 0.00 0.00 3.16
483 519 2.675348 CGACATTTCCCTGCTCTTCTTC 59.325 50.000 0.00 0.00 0.00 2.87
492 528 2.802667 CGCGAGCGACATTTCCCTG 61.803 63.158 12.58 0.00 42.83 4.45
493 529 2.509336 CGCGAGCGACATTTCCCT 60.509 61.111 12.58 0.00 42.83 4.20
505 541 0.030101 TGAAAAAGGTTTGGCGCGAG 59.970 50.000 12.10 0.00 0.00 5.03
540 576 1.320507 GAGGTTGTGGGGCGTTTTTA 58.679 50.000 0.00 0.00 0.00 1.52
546 582 0.322997 TATTTGGAGGTTGTGGGGCG 60.323 55.000 0.00 0.00 0.00 6.13
547 583 1.756538 CATATTTGGAGGTTGTGGGGC 59.243 52.381 0.00 0.00 0.00 5.80
548 584 2.387757 CCATATTTGGAGGTTGTGGGG 58.612 52.381 0.00 0.00 46.92 4.96
559 595 1.616865 CCTGCATGCCTCCATATTTGG 59.383 52.381 16.68 0.00 45.15 3.28
573 609 0.839946 ACCCTAAATCGAGCCTGCAT 59.160 50.000 0.00 0.00 0.00 3.96
584 620 6.953520 TCATGTTTTTGGAGATCACCCTAAAT 59.046 34.615 6.73 0.00 30.80 1.40
590 626 3.751175 TCGTCATGTTTTTGGAGATCACC 59.249 43.478 1.62 1.62 0.00 4.02
627 663 3.432782 CCAAAAATCAATCGAGCAGAGC 58.567 45.455 0.00 0.00 0.00 4.09
646 682 4.097135 CGCATGTGTAATATTTTGACCCCA 59.903 41.667 0.00 0.00 0.00 4.96
665 701 2.798283 CGATCACCGTAAATAACCGCAT 59.202 45.455 0.00 0.00 0.00 4.73
666 702 2.195096 CGATCACCGTAAATAACCGCA 58.805 47.619 0.00 0.00 0.00 5.69
685 721 0.667993 AAAGTTGTCATGTGTGGCCG 59.332 50.000 0.00 0.00 0.00 6.13
686 722 1.869342 GCAAAGTTGTCATGTGTGGCC 60.869 52.381 0.00 0.00 0.00 5.36
687 723 1.067516 AGCAAAGTTGTCATGTGTGGC 59.932 47.619 0.00 0.00 0.00 5.01
708 744 5.126384 CAGCCACTAGTTTTAGAGCTACTCT 59.874 44.000 2.23 2.23 43.83 3.24
712 748 5.017490 ACTCAGCCACTAGTTTTAGAGCTA 58.983 41.667 10.48 0.00 37.69 3.32
718 754 3.365666 CGTCGACTCAGCCACTAGTTTTA 60.366 47.826 14.70 0.00 0.00 1.52
721 757 0.522180 CGTCGACTCAGCCACTAGTT 59.478 55.000 14.70 0.00 0.00 2.24
724 760 1.313091 ATGCGTCGACTCAGCCACTA 61.313 55.000 14.30 0.00 0.00 2.74
733 769 0.458543 CCTAGTTGCATGCGTCGACT 60.459 55.000 14.09 15.58 33.12 4.18
735 771 0.457853 GTCCTAGTTGCATGCGTCGA 60.458 55.000 14.09 3.99 0.00 4.20
749 785 2.874701 GAGTGTTATAGACCGCGTCCTA 59.125 50.000 4.92 6.25 32.18 2.94
755 791 3.858247 ACCAAAGAGTGTTATAGACCGC 58.142 45.455 0.00 0.00 0.00 5.68
757 793 8.843885 AAAGTTACCAAAGAGTGTTATAGACC 57.156 34.615 0.00 0.00 0.00 3.85
787 823 7.575963 ACGTAGTTGTGGCATGCCATATTAAA 61.576 38.462 40.32 25.15 44.62 1.52
788 824 6.148064 ACGTAGTTGTGGCATGCCATATTAA 61.148 40.000 40.32 27.70 44.62 1.40
789 825 4.684757 ACGTAGTTGTGGCATGCCATATTA 60.685 41.667 40.32 27.48 44.62 0.98
791 827 2.421388 ACGTAGTTGTGGCATGCCATAT 60.421 45.455 40.32 25.96 44.62 1.78
792 828 1.065782 ACGTAGTTGTGGCATGCCATA 60.066 47.619 40.32 35.22 44.62 2.74
793 829 0.322456 ACGTAGTTGTGGCATGCCAT 60.322 50.000 40.32 27.12 44.62 4.40
794 830 1.072332 ACGTAGTTGTGGCATGCCA 59.928 52.632 35.59 35.59 37.78 4.92
795 831 3.981308 ACGTAGTTGTGGCATGCC 58.019 55.556 30.54 30.54 37.78 4.40
807 843 0.240145 TTCAGAGTGTGCGGACGTAG 59.760 55.000 1.60 0.00 0.00 3.51
808 844 0.039798 GTTCAGAGTGTGCGGACGTA 60.040 55.000 1.60 0.00 0.00 3.57
809 845 1.299926 GTTCAGAGTGTGCGGACGT 60.300 57.895 1.60 0.00 0.00 4.34
810 846 1.007271 AGTTCAGAGTGTGCGGACG 60.007 57.895 1.60 0.00 0.00 4.79
811 847 1.560860 GCAGTTCAGAGTGTGCGGAC 61.561 60.000 0.00 0.00 0.00 4.79
820 856 2.557920 AACCAAGAGGCAGTTCAGAG 57.442 50.000 0.00 0.00 39.06 3.35
900 936 2.036733 CAGGACAGAGTAACCGGTGAAA 59.963 50.000 8.52 0.00 0.00 2.69
917 953 8.074613 AGGTAAATATATATAAGCACGCAGGA 57.925 34.615 0.00 0.00 0.00 3.86
970 1013 2.351111 CCTCTCAGTTACTCGTACCGAC 59.649 54.545 0.00 0.00 0.00 4.79
971 1014 2.625737 CCTCTCAGTTACTCGTACCGA 58.374 52.381 0.00 0.00 0.00 4.69
972 1015 1.669779 CCCTCTCAGTTACTCGTACCG 59.330 57.143 0.00 0.00 0.00 4.02
973 1016 2.944349 CTCCCTCTCAGTTACTCGTACC 59.056 54.545 0.00 0.00 0.00 3.34
1014 1061 4.322567 ACAAAGAGAGCACTGATTTCTCC 58.677 43.478 0.00 0.00 38.45 3.71
1021 1068 4.890158 TCCATAACAAAGAGAGCACTGA 57.110 40.909 0.00 0.00 0.00 3.41
1022 1069 5.426504 AGATCCATAACAAAGAGAGCACTG 58.573 41.667 0.00 0.00 0.00 3.66
1023 1070 5.188555 TGAGATCCATAACAAAGAGAGCACT 59.811 40.000 0.00 0.00 0.00 4.40
1072 1119 8.208903 ACACTATTAACCGCTGGAGTATTTAAT 58.791 33.333 1.50 4.28 0.00 1.40
1073 1120 7.558604 ACACTATTAACCGCTGGAGTATTTAA 58.441 34.615 1.50 0.00 0.00 1.52
1074 1121 7.116075 ACACTATTAACCGCTGGAGTATTTA 57.884 36.000 1.50 0.00 0.00 1.40
1075 1122 5.985911 ACACTATTAACCGCTGGAGTATTT 58.014 37.500 1.50 0.00 0.00 1.40
1076 1123 5.609533 ACACTATTAACCGCTGGAGTATT 57.390 39.130 1.50 0.00 0.00 1.89
1077 1124 6.912951 ATACACTATTAACCGCTGGAGTAT 57.087 37.500 1.50 0.00 0.00 2.12
1079 1126 5.832060 ACTATACACTATTAACCGCTGGAGT 59.168 40.000 1.50 0.00 0.00 3.85
1080 1127 6.328641 ACTATACACTATTAACCGCTGGAG 57.671 41.667 1.50 0.00 0.00 3.86
1082 1129 7.174599 AGACTACTATACACTATTAACCGCTGG 59.825 40.741 0.00 0.00 0.00 4.85
1083 1130 8.097078 AGACTACTATACACTATTAACCGCTG 57.903 38.462 0.00 0.00 0.00 5.18
1085 1132 9.741647 AAAAGACTACTATACACTATTAACCGC 57.258 33.333 0.00 0.00 0.00 5.68
1092 1139 9.798994 CAAACCGAAAAGACTACTATACACTAT 57.201 33.333 0.00 0.00 0.00 2.12
1093 1140 7.756722 GCAAACCGAAAAGACTACTATACACTA 59.243 37.037 0.00 0.00 0.00 2.74
1094 1141 6.589139 GCAAACCGAAAAGACTACTATACACT 59.411 38.462 0.00 0.00 0.00 3.55
1095 1142 6.589139 AGCAAACCGAAAAGACTACTATACAC 59.411 38.462 0.00 0.00 0.00 2.90
1099 1146 6.567891 GCAAAGCAAACCGAAAAGACTACTAT 60.568 38.462 0.00 0.00 0.00 2.12
1102 1149 3.729217 GCAAAGCAAACCGAAAAGACTAC 59.271 43.478 0.00 0.00 0.00 2.73
1127 1178 8.553696 GGTATGTAAAATTCCATTTACGATCGT 58.446 33.333 25.94 25.94 44.82 3.73
1148 1199 6.895782 TCCTTCACCTTAATTACAGGGTATG 58.104 40.000 14.39 7.20 35.46 2.39
1149 1200 7.128883 ACATCCTTCACCTTAATTACAGGGTAT 59.871 37.037 14.39 0.95 35.46 2.73
1151 1202 5.253096 ACATCCTTCACCTTAATTACAGGGT 59.747 40.000 14.39 7.88 35.46 4.34
1152 1203 5.590259 CACATCCTTCACCTTAATTACAGGG 59.410 44.000 14.39 7.39 35.46 4.45
1153 1204 5.066505 GCACATCCTTCACCTTAATTACAGG 59.933 44.000 10.43 10.43 37.45 4.00
1154 1205 5.647658 TGCACATCCTTCACCTTAATTACAG 59.352 40.000 0.00 0.00 0.00 2.74
1157 1208 7.448161 CCATATGCACATCCTTCACCTTAATTA 59.552 37.037 0.00 0.00 0.00 1.40
1158 1209 6.266103 CCATATGCACATCCTTCACCTTAATT 59.734 38.462 0.00 0.00 0.00 1.40
1159 1210 5.771666 CCATATGCACATCCTTCACCTTAAT 59.228 40.000 0.00 0.00 0.00 1.40
1160 1211 5.132502 CCATATGCACATCCTTCACCTTAA 58.867 41.667 0.00 0.00 0.00 1.85
1163 1214 2.158564 CCCATATGCACATCCTTCACCT 60.159 50.000 0.00 0.00 0.00 4.00
1165 1216 1.610522 GCCCATATGCACATCCTTCAC 59.389 52.381 0.00 0.00 0.00 3.18
1167 1218 1.985473 TGCCCATATGCACATCCTTC 58.015 50.000 0.00 0.00 36.04 3.46
1169 1220 1.426215 TCATGCCCATATGCACATCCT 59.574 47.619 0.00 0.00 45.48 3.24
1170 1221 1.913778 TCATGCCCATATGCACATCC 58.086 50.000 0.00 0.00 45.48 3.51
1171 1222 3.068448 TGTTTCATGCCCATATGCACATC 59.932 43.478 0.00 0.00 45.48 3.06
1173 1224 2.166050 GTGTTTCATGCCCATATGCACA 59.834 45.455 0.00 0.00 45.48 4.57
1177 1228 3.695556 TCAGTGTGTTTCATGCCCATATG 59.304 43.478 0.00 0.00 0.00 1.78
1193 1260 4.037565 TCAAACAGAGACATACGTCAGTGT 59.962 41.667 0.00 0.00 45.23 3.55
1209 1289 3.507233 ACAATGCACCCTACATCAAACAG 59.493 43.478 0.00 0.00 0.00 3.16
1212 1292 3.088532 GGACAATGCACCCTACATCAAA 58.911 45.455 0.00 0.00 0.00 2.69
1219 1299 1.278985 CAGACTGGACAATGCACCCTA 59.721 52.381 0.00 0.00 0.00 3.53
1312 1392 4.383173 TGCATGCACAGATTAAGATCGAT 58.617 39.130 18.46 0.00 37.37 3.59
1370 1450 6.647334 TGTCACACAACAATATCAAACCAT 57.353 33.333 0.00 0.00 0.00 3.55
1371 1451 6.456795 TTGTCACACAACAATATCAAACCA 57.543 33.333 0.00 0.00 34.31 3.67
1372 1452 7.199766 TCTTTGTCACACAACAATATCAAACC 58.800 34.615 0.00 0.00 37.90 3.27
1373 1453 8.627487 TTCTTTGTCACACAACAATATCAAAC 57.373 30.769 0.00 0.00 37.90 2.93
1375 1455 8.246871 TGTTTCTTTGTCACACAACAATATCAA 58.753 29.630 0.00 0.00 37.90 2.57
1376 1456 7.766283 TGTTTCTTTGTCACACAACAATATCA 58.234 30.769 0.00 0.00 37.90 2.15
1434 1516 2.268298 GCACTGAAACCACGACGATAT 58.732 47.619 0.00 0.00 0.00 1.63
1436 1518 0.949105 GGCACTGAAACCACGACGAT 60.949 55.000 0.00 0.00 0.00 3.73
1438 1520 1.557443 GAGGCACTGAAACCACGACG 61.557 60.000 0.00 0.00 41.55 5.12
1463 1545 1.048724 TGTAGAGGGGCTTCATCGGG 61.049 60.000 0.00 0.00 0.00 5.14
1722 1970 2.163815 ACAGAGGAAGTACATTCGGTCG 59.836 50.000 0.00 0.00 38.95 4.79
1723 1971 3.870633 ACAGAGGAAGTACATTCGGTC 57.129 47.619 0.00 0.00 38.95 4.79
1799 2047 7.425606 TCATGTACTACATCTACGTACTCGTA 58.574 38.462 0.00 0.85 41.91 3.43
1800 2048 6.276091 TCATGTACTACATCTACGTACTCGT 58.724 40.000 0.00 0.00 44.19 4.18
1801 2049 6.760161 TCATGTACTACATCTACGTACTCG 57.240 41.667 0.00 0.00 36.53 4.18
1802 2050 7.016466 GCATCATGTACTACATCTACGTACTC 58.984 42.308 0.00 0.00 36.53 2.59
1803 2051 6.485648 TGCATCATGTACTACATCTACGTACT 59.514 38.462 0.00 0.00 36.53 2.73
1804 2052 6.665465 TGCATCATGTACTACATCTACGTAC 58.335 40.000 0.00 0.00 36.53 3.67
1805 2053 6.485648 ACTGCATCATGTACTACATCTACGTA 59.514 38.462 0.00 0.00 36.53 3.57
1806 2054 5.299531 ACTGCATCATGTACTACATCTACGT 59.700 40.000 0.00 0.00 36.53 3.57
1807 2055 5.626955 CACTGCATCATGTACTACATCTACG 59.373 44.000 0.00 0.00 36.53 3.51
1808 2056 5.403766 GCACTGCATCATGTACTACATCTAC 59.596 44.000 0.00 0.00 36.53 2.59
1809 2057 5.068987 TGCACTGCATCATGTACTACATCTA 59.931 40.000 0.00 0.00 32.53 1.98
1810 2058 4.141869 TGCACTGCATCATGTACTACATCT 60.142 41.667 0.00 0.00 32.53 2.90
1811 2059 4.122046 TGCACTGCATCATGTACTACATC 58.878 43.478 0.00 0.00 32.53 3.06
1812 2060 4.141233 TGCACTGCATCATGTACTACAT 57.859 40.909 0.00 0.00 34.31 2.29
1813 2061 3.608316 TGCACTGCATCATGTACTACA 57.392 42.857 0.00 0.00 31.71 2.74
1846 2103 0.037697 ACACGCGGAACAGCAAGATA 60.038 50.000 12.47 0.00 36.85 1.98
3092 3724 0.033504 ACGTCTTGTGCGTCTTCCAT 59.966 50.000 0.00 0.00 38.23 3.41
3352 5146 7.561021 TTTATTGCATTCTTTAGATGGCGTA 57.439 32.000 0.00 0.00 0.00 4.42
3434 5228 5.445939 CGGTTTTGTTCCGTTATCTGATGAG 60.446 44.000 0.00 0.00 42.62 2.90
3459 5254 1.092921 TCGCGCCAAGACACTGTTTT 61.093 50.000 0.00 0.00 0.00 2.43
3497 5292 5.300411 ACGTTCCCTTTCCTTCTCTTTTA 57.700 39.130 0.00 0.00 0.00 1.52
3498 5293 4.135306 GACGTTCCCTTTCCTTCTCTTTT 58.865 43.478 0.00 0.00 0.00 2.27
3499 5294 3.496337 GGACGTTCCCTTTCCTTCTCTTT 60.496 47.826 0.00 0.00 0.00 2.52
3518 5313 2.306512 TGTTGGGTAGTAACATGGGGAC 59.693 50.000 0.00 0.00 33.43 4.46
3535 5330 5.591877 CCCTTTCTATTCCATTCCTCTGTTG 59.408 44.000 0.00 0.00 0.00 3.33
3536 5331 5.492524 TCCCTTTCTATTCCATTCCTCTGTT 59.507 40.000 0.00 0.00 0.00 3.16
3537 5332 5.039645 TCCCTTTCTATTCCATTCCTCTGT 58.960 41.667 0.00 0.00 0.00 3.41
3563 5358 1.450312 GACCTCGCAACATGGGGAG 60.450 63.158 8.49 8.49 44.77 4.30
3565 5360 0.251916 TAAGACCTCGCAACATGGGG 59.748 55.000 0.00 0.00 0.00 4.96
3567 5362 4.497473 TTTTTAAGACCTCGCAACATGG 57.503 40.909 0.00 0.00 0.00 3.66
3628 5454 5.888161 GGGATTCTTCCTTGTATTCACACAT 59.112 40.000 0.00 0.00 42.20 3.21
3629 5455 5.253330 GGGATTCTTCCTTGTATTCACACA 58.747 41.667 0.00 0.00 42.20 3.72
3630 5456 4.332819 CGGGATTCTTCCTTGTATTCACAC 59.667 45.833 0.00 0.00 42.20 3.82
3733 5559 8.645814 AGATGGTTGCATACATCATTATGATT 57.354 30.769 24.43 0.77 44.50 2.57
3811 5639 5.452078 TCATTTCTTTTGTTTCGCTCCAT 57.548 34.783 0.00 0.00 0.00 3.41
3826 5654 9.415544 GATTTTGAGCATGTACTTTTCATTTCT 57.584 29.630 0.00 0.00 0.00 2.52
3938 5767 2.779430 ACCATTGGGAGATGATAGCACA 59.221 45.455 7.78 0.00 38.05 4.57
4090 5922 9.243105 GCTTCTTTGGGCTATATGGAATTATAA 57.757 33.333 0.00 0.00 0.00 0.98
4093 5925 5.705441 CGCTTCTTTGGGCTATATGGAATTA 59.295 40.000 0.00 0.00 0.00 1.40
4120 5952 4.036027 GGCTCGTATTCGGATCGGAATATA 59.964 45.833 28.22 20.91 40.09 0.86
4174 6006 6.070897 TGACATTGAATCGTTGTTTGTGAT 57.929 33.333 0.00 0.00 0.00 3.06
4177 6009 5.743398 CAGTTGACATTGAATCGTTGTTTGT 59.257 36.000 0.00 0.00 0.00 2.83
4253 6085 1.453155 GACGAGTTTGTCATGCCCAT 58.547 50.000 0.00 0.00 38.75 4.00


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

AutoCloner maintained by Alex Coulton.