Multiple sequence alignment - TraesCS7B01G126600

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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 TraesCS7B01G126600 chr7B 100.000 4976 0 0 1 4976 150591420 150586445 0.000000e+00 9190.0
1 TraesCS7B01G126600 chr7B 100.000 28 0 0 133 160 561155841 561155814 9.000000e-03 52.8
2 TraesCS7B01G126600 chr7D 89.984 2536 127 54 2180 4644 182338029 182335550 0.000000e+00 3158.0
3 TraesCS7B01G126600 chr7D 95.700 1465 57 4 723 2183 182339522 182338060 0.000000e+00 2351.0
4 TraesCS7B01G126600 chr7D 88.593 263 10 6 4714 4976 182335526 182335284 8.100000e-78 302.0
5 TraesCS7B01G126600 chr7D 90.323 62 6 0 1145 1206 488779341 488779402 1.150000e-11 82.4
6 TraesCS7B01G126600 chr7A 91.251 1223 85 17 723 1929 189324206 189325422 0.000000e+00 1646.0
7 TraesCS7B01G126600 chr7A 85.322 1165 77 42 3464 4590 189327693 189328801 0.000000e+00 1118.0
8 TraesCS7B01G126600 chr7A 86.773 688 60 15 1 672 189323535 189324207 0.000000e+00 737.0
9 TraesCS7B01G126600 chr7A 88.654 379 32 6 4607 4976 189330199 189330575 7.600000e-123 451.0
10 TraesCS7B01G126600 chr7A 90.323 62 6 0 1145 1206 556156184 556156245 1.150000e-11 82.4
11 TraesCS7B01G126600 chr1B 78.067 538 53 29 3464 3955 369000633 369001151 3.790000e-71 279.0
12 TraesCS7B01G126600 chr1B 77.509 538 54 31 3464 3955 339237219 339237735 1.370000e-65 261.0
13 TraesCS7B01G126600 chrUn 97.222 108 3 0 925 1032 211163733 211163840 3.060000e-42 183.0
14 TraesCS7B01G126600 chrUn 100.000 49 0 0 874 922 211163738 211163690 1.910000e-14 91.6
15 TraesCS7B01G126600 chr5D 97.222 108 3 0 925 1032 394579493 394579600 3.060000e-42 183.0
16 TraesCS7B01G126600 chr5D 100.000 49 0 0 874 922 394579498 394579450 1.910000e-14 91.6
17 TraesCS7B01G126600 chr6D 95.495 111 5 0 925 1035 86887382 86887272 1.420000e-40 178.0
18 TraesCS7B01G126600 chr6D 97.959 49 1 0 874 922 86887377 86887425 8.880000e-13 86.1


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 TraesCS7B01G126600 chr7B 150586445 150591420 4975 True 9190 9190 100.000000 1 4976 1 chr7B.!!$R1 4975
1 TraesCS7B01G126600 chr7D 182335284 182339522 4238 True 1937 3158 91.425667 723 4976 3 chr7D.!!$R1 4253
2 TraesCS7B01G126600 chr7A 189323535 189330575 7040 False 988 1646 88.000000 1 4976 4 chr7A.!!$F2 4975
3 TraesCS7B01G126600 chr1B 369000633 369001151 518 False 279 279 78.067000 3464 3955 1 chr1B.!!$F2 491
4 TraesCS7B01G126600 chr1B 339237219 339237735 516 False 261 261 77.509000 3464 3955 1 chr1B.!!$F1 491

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
278 291 0.177141 TGTCCCCGAATTCGTCCATC 59.823 55.0 25.10 12.28 37.74 3.51 F
1489 1509 0.179134 CCTTCACGCTCTTCCTACCG 60.179 60.0 0.00 0.00 0.00 4.02 F
1606 1626 0.248907 AGTTCGCCCATATGACGTCG 60.249 55.0 11.62 2.21 0.00 5.12 F
2507 2630 0.595095 GCAAGTCAGAAAGGGCACTG 59.405 55.0 0.00 0.00 35.72 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1601 0.381801 CATATGGGCGAACTGGTTGC 59.618 55.0 0.00 0.0 0.00 4.17 R
2954 3124 0.947244 GCCTGTCACAAGGTTGTCAG 59.053 55.0 5.10 5.1 39.91 3.51 R
3225 3956 1.144969 GCGTCGACAGAAACCATTGA 58.855 50.0 17.16 0.0 0.00 2.57 R
4491 5446 0.319555 GAAGTGTAGCACTGTCCGCA 60.320 55.0 2.31 0.0 44.62 5.69 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
64 67 1.475403 TTCTCTCACCCTAAGGCGAG 58.525 55.000 0.00 0.00 42.77 5.03
88 97 2.373707 CCTCCTCCCCTCCAAGCTG 61.374 68.421 0.00 0.00 0.00 4.24
113 122 1.846712 GCTAGCCCATGGATCCTCCC 61.847 65.000 15.22 0.00 35.03 4.30
114 123 1.151810 TAGCCCATGGATCCTCCCC 60.152 63.158 15.22 0.00 35.03 4.81
166 175 3.663815 ATCCCGGTGCCTCGACTCT 62.664 63.158 0.00 0.00 0.00 3.24
168 177 4.803426 CCGGTGCCTCGACTCTGC 62.803 72.222 0.00 0.00 0.00 4.26
170 179 3.695606 GGTGCCTCGACTCTGCCA 61.696 66.667 0.00 0.00 0.00 4.92
173 182 1.004560 TGCCTCGACTCTGCCAAAG 60.005 57.895 0.00 0.00 0.00 2.77
177 186 2.870435 GCCTCGACTCTGCCAAAGTTTA 60.870 50.000 0.00 0.00 0.00 2.01
203 212 4.360951 AGGATTTGTTAAGTTCCCACGA 57.639 40.909 0.00 0.00 0.00 4.35
206 215 3.842007 TTTGTTAAGTTCCCACGAGGA 57.158 42.857 0.00 0.00 45.68 3.71
214 223 1.970114 TCCCACGAGGACGACACTC 60.970 63.158 0.00 0.00 40.93 3.51
227 236 2.561733 GACACTCGGTCGAATGATGA 57.438 50.000 8.80 0.00 36.65 2.92
230 239 0.809385 ACTCGGTCGAATGATGACGT 59.191 50.000 0.00 0.00 37.22 4.34
278 291 0.177141 TGTCCCCGAATTCGTCCATC 59.823 55.000 25.10 12.28 37.74 3.51
280 293 0.177141 TCCCCGAATTCGTCCATCAC 59.823 55.000 25.10 0.00 37.74 3.06
296 309 3.001838 CCATCACGACGAAAACAACAAGA 59.998 43.478 0.00 0.00 0.00 3.02
302 315 3.122948 CGACGAAAACAACAAGATCCGAT 59.877 43.478 0.00 0.00 0.00 4.18
326 339 8.693120 ATGAGGTTAGAGTTTCTCATCGTATA 57.307 34.615 0.00 0.00 41.48 1.47
349 362 1.569708 ACGCAACATGCAAAAACTGG 58.430 45.000 2.99 0.00 45.36 4.00
351 364 2.099921 ACGCAACATGCAAAAACTGGTA 59.900 40.909 2.99 0.00 45.36 3.25
352 365 3.243704 ACGCAACATGCAAAAACTGGTAT 60.244 39.130 2.99 0.00 45.36 2.73
354 367 4.920340 CGCAACATGCAAAAACTGGTATTA 59.080 37.500 2.99 0.00 45.36 0.98
355 368 5.576384 CGCAACATGCAAAAACTGGTATTAT 59.424 36.000 2.99 0.00 45.36 1.28
357 370 7.434897 CGCAACATGCAAAAACTGGTATTATAT 59.565 33.333 2.99 0.00 45.36 0.86
358 371 9.743057 GCAACATGCAAAAACTGGTATTATATA 57.257 29.630 0.00 0.00 44.26 0.86
391 406 3.832527 AGGTTTGGCTTGAGTGTTACAT 58.167 40.909 0.00 0.00 0.00 2.29
395 410 5.918576 GGTTTGGCTTGAGTGTTACATTTAC 59.081 40.000 0.00 0.00 0.00 2.01
420 435 6.980397 CCATAAATAAACCAGAAATGTCAGCC 59.020 38.462 0.00 0.00 0.00 4.85
422 437 6.610075 AAATAAACCAGAAATGTCAGCCAT 57.390 33.333 0.00 0.00 34.36 4.40
466 481 5.818136 TTAAGCATGTTAGATGTTGCCTC 57.182 39.130 0.00 0.00 35.71 4.70
493 509 0.460284 GCTTGCTGGCGCTAAGAGTA 60.460 55.000 7.64 0.00 36.97 2.59
522 538 4.192000 GTGACAGGCACGATCTGG 57.808 61.111 0.00 0.00 37.83 3.86
553 569 6.377146 GGTGCTTCAGATTTAAGGGTTCAATA 59.623 38.462 0.00 0.00 0.00 1.90
554 570 7.093945 GGTGCTTCAGATTTAAGGGTTCAATAA 60.094 37.037 0.00 0.00 0.00 1.40
555 571 7.755373 GTGCTTCAGATTTAAGGGTTCAATAAC 59.245 37.037 0.00 0.00 34.66 1.89
556 572 6.967199 GCTTCAGATTTAAGGGTTCAATAACG 59.033 38.462 0.00 0.00 36.39 3.18
557 573 6.995511 TCAGATTTAAGGGTTCAATAACGG 57.004 37.500 0.00 0.00 36.39 4.44
558 574 5.355910 TCAGATTTAAGGGTTCAATAACGGC 59.644 40.000 0.00 0.00 36.39 5.68
579 595 2.223203 CGACGGCGACTATAACTTCAGT 60.223 50.000 16.62 0.00 40.82 3.41
580 596 3.001634 CGACGGCGACTATAACTTCAGTA 59.998 47.826 16.62 0.00 40.82 2.74
585 601 5.454877 CGGCGACTATAACTTCAGTACTTTC 59.545 44.000 0.00 0.00 0.00 2.62
602 619 3.058224 ACTTTCGTCTTAAAGGCACATGC 60.058 43.478 0.00 0.00 40.16 4.06
604 621 1.804151 TCGTCTTAAAGGCACATGCAC 59.196 47.619 6.15 0.00 44.36 4.57
618 635 4.539870 CACATGCACGAAGATTTTTCAGT 58.460 39.130 0.00 0.00 0.00 3.41
620 637 5.459762 CACATGCACGAAGATTTTTCAGTTT 59.540 36.000 0.00 0.00 0.00 2.66
621 638 5.459762 ACATGCACGAAGATTTTTCAGTTTG 59.540 36.000 0.00 0.00 0.00 2.93
622 639 4.992688 TGCACGAAGATTTTTCAGTTTGT 58.007 34.783 0.00 0.00 0.00 2.83
623 640 5.034152 TGCACGAAGATTTTTCAGTTTGTC 58.966 37.500 0.00 0.00 0.00 3.18
624 641 5.034152 GCACGAAGATTTTTCAGTTTGTCA 58.966 37.500 0.00 0.00 0.00 3.58
625 642 5.687285 GCACGAAGATTTTTCAGTTTGTCAT 59.313 36.000 0.00 0.00 0.00 3.06
626 643 6.129352 GCACGAAGATTTTTCAGTTTGTCATC 60.129 38.462 0.00 0.00 0.00 2.92
627 644 6.085458 CACGAAGATTTTTCAGTTTGTCATCG 59.915 38.462 0.00 0.00 34.30 3.84
628 645 6.018262 ACGAAGATTTTTCAGTTTGTCATCGA 60.018 34.615 5.08 0.00 32.98 3.59
629 646 7.017645 CGAAGATTTTTCAGTTTGTCATCGAT 58.982 34.615 0.00 0.00 31.04 3.59
635 652 9.612620 ATTTTTCAGTTTGTCATCGATAAGTTC 57.387 29.630 0.00 0.00 0.00 3.01
648 665 5.881447 TCGATAAGTTCAGTCTTGTAGCTC 58.119 41.667 0.00 0.00 0.00 4.09
670 687 9.780186 AGCTCTAGTAGTTGTTCAGTAAATTTT 57.220 29.630 0.00 0.00 0.00 1.82
676 693 9.281371 AGTAGTTGTTCAGTAAATTTTACTCCC 57.719 33.333 17.00 9.57 0.00 4.30
677 694 9.281371 GTAGTTGTTCAGTAAATTTTACTCCCT 57.719 33.333 17.00 9.93 0.00 4.20
678 695 8.392372 AGTTGTTCAGTAAATTTTACTCCCTC 57.608 34.615 17.00 9.76 0.00 4.30
679 696 7.447545 AGTTGTTCAGTAAATTTTACTCCCTCC 59.552 37.037 17.00 6.21 0.00 4.30
680 697 5.935789 TGTTCAGTAAATTTTACTCCCTCCG 59.064 40.000 17.00 7.14 0.00 4.63
681 698 5.750352 TCAGTAAATTTTACTCCCTCCGT 57.250 39.130 17.00 0.00 0.00 4.69
682 699 6.117975 TCAGTAAATTTTACTCCCTCCGTT 57.882 37.500 17.00 0.00 0.00 4.44
683 700 6.536447 TCAGTAAATTTTACTCCCTCCGTTT 58.464 36.000 17.00 0.00 0.00 3.60
684 701 6.999871 TCAGTAAATTTTACTCCCTCCGTTTT 59.000 34.615 17.00 0.00 0.00 2.43
685 702 8.156165 TCAGTAAATTTTACTCCCTCCGTTTTA 58.844 33.333 17.00 0.00 0.00 1.52
686 703 8.785946 CAGTAAATTTTACTCCCTCCGTTTTAA 58.214 33.333 17.00 0.00 0.00 1.52
687 704 9.353431 AGTAAATTTTACTCCCTCCGTTTTAAA 57.647 29.630 14.66 0.00 0.00 1.52
688 705 9.964303 GTAAATTTTACTCCCTCCGTTTTAAAA 57.036 29.630 11.27 0.00 0.00 1.52
693 710 8.922931 TTTACTCCCTCCGTTTTAAAATAAGT 57.077 30.769 3.52 3.73 0.00 2.24
694 711 8.922931 TTACTCCCTCCGTTTTAAAATAAGTT 57.077 30.769 3.52 0.00 0.00 2.66
695 712 7.210718 ACTCCCTCCGTTTTAAAATAAGTTG 57.789 36.000 3.52 0.00 0.00 3.16
696 713 6.999871 ACTCCCTCCGTTTTAAAATAAGTTGA 59.000 34.615 3.52 0.00 0.00 3.18
697 714 7.174426 ACTCCCTCCGTTTTAAAATAAGTTGAG 59.826 37.037 3.52 9.20 0.00 3.02
698 715 6.999871 TCCCTCCGTTTTAAAATAAGTTGAGT 59.000 34.615 3.52 0.00 0.00 3.41
699 716 7.173735 TCCCTCCGTTTTAAAATAAGTTGAGTC 59.826 37.037 3.52 0.00 0.00 3.36
700 717 7.040961 CCCTCCGTTTTAAAATAAGTTGAGTCA 60.041 37.037 3.52 0.00 0.00 3.41
701 718 7.801783 CCTCCGTTTTAAAATAAGTTGAGTCAC 59.198 37.037 3.52 0.00 0.00 3.67
702 719 8.441312 TCCGTTTTAAAATAAGTTGAGTCACT 57.559 30.769 3.52 0.00 0.00 3.41
703 720 8.895737 TCCGTTTTAAAATAAGTTGAGTCACTT 58.104 29.630 3.52 11.17 40.28 3.16
714 731 7.653767 AAGTTGAGTCACTTATTTTAGGACG 57.346 36.000 0.00 0.00 35.10 4.79
715 732 6.989659 AGTTGAGTCACTTATTTTAGGACGA 58.010 36.000 0.00 0.00 33.84 4.20
716 733 7.439381 AGTTGAGTCACTTATTTTAGGACGAA 58.561 34.615 0.00 0.00 33.84 3.85
717 734 7.929785 AGTTGAGTCACTTATTTTAGGACGAAA 59.070 33.333 0.00 0.00 33.84 3.46
718 735 7.884816 TGAGTCACTTATTTTAGGACGAAAG 57.115 36.000 0.00 0.00 33.84 2.62
719 736 6.872020 TGAGTCACTTATTTTAGGACGAAAGG 59.128 38.462 0.00 0.00 33.84 3.11
720 737 7.001099 AGTCACTTATTTTAGGACGAAAGGA 57.999 36.000 0.00 0.00 33.84 3.36
721 738 7.097834 AGTCACTTATTTTAGGACGAAAGGAG 58.902 38.462 0.00 0.00 33.84 3.69
815 832 4.823790 TGAAGTAAAGCTTTCGGGTTTC 57.176 40.909 16.57 13.00 43.47 2.78
850 869 2.540101 GCCGGAAAGTTATCATCGTCTG 59.460 50.000 5.05 0.00 0.00 3.51
864 883 1.944024 TCGTCTGGCAAAAACGTTCAT 59.056 42.857 0.00 0.00 37.64 2.57
865 884 2.032377 TCGTCTGGCAAAAACGTTCATC 60.032 45.455 0.00 0.00 37.64 2.92
866 885 2.286713 CGTCTGGCAAAAACGTTCATCA 60.287 45.455 0.00 0.00 0.00 3.07
867 886 3.701241 GTCTGGCAAAAACGTTCATCAA 58.299 40.909 0.00 0.00 0.00 2.57
1284 1304 2.519541 CGAGCCGAGGGATCTGGA 60.520 66.667 0.00 0.00 35.75 3.86
1340 1360 2.511600 CGTTCTGATCCGTGGGCC 60.512 66.667 0.00 0.00 0.00 5.80
1486 1506 0.963856 TCGCCTTCACGCTCTTCCTA 60.964 55.000 0.00 0.00 0.00 2.94
1489 1509 0.179134 CCTTCACGCTCTTCCTACCG 60.179 60.000 0.00 0.00 0.00 4.02
1558 1578 0.526310 GTGCTCTCATCATCGCGTCA 60.526 55.000 5.77 0.00 0.00 4.35
1576 1596 2.029844 ACTCTTCGCGCTCAAAGGC 61.030 57.895 5.56 0.00 0.00 4.35
1606 1626 0.248907 AGTTCGCCCATATGACGTCG 60.249 55.000 11.62 2.21 0.00 5.12
1664 1685 7.985634 TGTCTGTTCATTTGCTTTAGTTTTC 57.014 32.000 0.00 0.00 0.00 2.29
1671 1692 8.968242 GTTCATTTGCTTTAGTTTTCGAAGAAT 58.032 29.630 0.00 0.00 45.90 2.40
1828 1862 6.723298 AGTGCTCTATACAGACAGCTAAAT 57.277 37.500 0.00 0.00 0.00 1.40
1833 1867 6.584563 GCTCTATACAGACAGCTAAATACTGC 59.415 42.308 0.00 0.00 38.79 4.40
1855 1889 2.839486 TCTGCTAGTTTGGTCCTGTG 57.161 50.000 0.00 0.00 0.00 3.66
2019 2091 0.734889 GGTGGATCGACTGGCAAATG 59.265 55.000 7.84 0.00 0.00 2.32
2094 2169 9.753674 TCCATATAACCTTTCTGAGTTGATTTT 57.246 29.630 0.00 0.00 0.00 1.82
2170 2245 8.295288 AGAAAGAAAATCTATGCTGACAAGTTG 58.705 33.333 0.00 0.00 0.00 3.16
2216 2324 7.831193 AGTTTCTCATAGTGCCTGATAACAAAT 59.169 33.333 0.00 0.00 0.00 2.32
2283 2391 7.025963 CCGATTATACCATTACCTCTTACGAC 58.974 42.308 0.00 0.00 0.00 4.34
2300 2408 2.166664 ACGACAGAGAACCAATAGCTCC 59.833 50.000 0.00 0.00 0.00 4.70
2326 2434 7.192852 AGACTGTGATCTTACATCAAGGATT 57.807 36.000 0.00 0.00 34.76 3.01
2371 2483 4.094294 GTGGATCTTTGCGTGCATAACTTA 59.906 41.667 0.00 0.00 0.00 2.24
2372 2484 4.697828 TGGATCTTTGCGTGCATAACTTAA 59.302 37.500 0.00 0.00 0.00 1.85
2507 2630 0.595095 GCAAGTCAGAAAGGGCACTG 59.405 55.000 0.00 0.00 35.72 3.66
2508 2631 1.972872 CAAGTCAGAAAGGGCACTGT 58.027 50.000 0.00 0.00 35.84 3.55
2509 2632 2.301346 CAAGTCAGAAAGGGCACTGTT 58.699 47.619 0.00 0.00 35.84 3.16
2544 2667 3.584848 ACACAGATCAAGTAGGCCTTTCT 59.415 43.478 12.58 7.55 0.00 2.52
2619 2757 5.393866 AGTCAATCTGGTTGTTGGGTTTAT 58.606 37.500 0.00 0.00 38.95 1.40
2627 2765 5.070001 TGGTTGTTGGGTTTATCTCTTGAG 58.930 41.667 0.00 0.00 0.00 3.02
2695 2836 5.465724 GGACGTTTCTAACTCATGAACTGTT 59.534 40.000 0.00 0.17 0.00 3.16
2702 2867 9.436957 TTTCTAACTCATGAACTGTTCCTTATC 57.563 33.333 17.26 0.00 0.00 1.75
2734 2899 1.476488 ACACAACCTGGAAAACTGCAC 59.524 47.619 0.00 0.00 0.00 4.57
2799 2964 6.348950 CCGTTGAACCATTAGCATCAAACTTA 60.349 38.462 0.00 0.00 33.93 2.24
2806 2971 8.995027 ACCATTAGCATCAAACTTATATTCCA 57.005 30.769 0.00 0.00 0.00 3.53
2879 3045 8.024285 TGAGACTCGAAAGAAAGAGAGAAATAC 58.976 37.037 0.00 0.00 41.32 1.89
2954 3124 4.529109 AAGAAGTGAGAGTAGTGGAAGC 57.471 45.455 0.00 0.00 0.00 3.86
3034 3233 2.108250 ACCAGGTGCAACATAAGGAGTT 59.892 45.455 3.64 0.00 39.98 3.01
3044 3243 6.162777 GCAACATAAGGAGTTTTGGCATTTA 58.837 36.000 0.00 0.00 0.00 1.40
3053 3252 7.966812 AGGAGTTTTGGCATTTATTTTTCTCT 58.033 30.769 0.00 0.00 0.00 3.10
3055 3254 8.090831 GGAGTTTTGGCATTTATTTTTCTCTCT 58.909 33.333 0.00 0.00 0.00 3.10
3139 3612 2.691409 TCCTGTCGATGGGTTCAATC 57.309 50.000 7.44 0.00 0.00 2.67
3223 3954 0.599991 TGTAACTGCTGGTCTGCACG 60.600 55.000 0.00 0.00 38.12 5.34
3225 3956 0.608130 TAACTGCTGGTCTGCACGAT 59.392 50.000 0.00 0.00 38.12 3.73
3242 3973 2.993899 ACGATCAATGGTTTCTGTCGAC 59.006 45.455 9.11 9.11 0.00 4.20
3248 3979 1.132640 GGTTTCTGTCGACGCATGC 59.867 57.895 11.62 7.91 0.00 4.06
3421 4153 7.996385 ACAAAAGCTGTTGATACAAAGTAGTT 58.004 30.769 23.64 0.00 32.99 2.24
3455 4312 9.173939 CTGTACTTGCTCAGTTTTCTTTTAATG 57.826 33.333 0.00 0.00 36.88 1.90
3471 4354 7.622713 TCTTTTAATGGGATGCATTCAAATGT 58.377 30.769 7.43 0.00 38.65 2.71
3507 4391 9.766277 CTGATAAGAGAACTTGCATAACTTTTC 57.234 33.333 0.00 0.00 37.53 2.29
3633 4535 4.562757 CGATCCTCCAGGTGTGTCTTTTTA 60.563 45.833 0.00 0.00 36.34 1.52
3637 4539 4.938226 CCTCCAGGTGTGTCTTTTTATCTC 59.062 45.833 0.00 0.00 0.00 2.75
3647 4549 8.283291 GTGTGTCTTTTTATCTCGTCTTCATTT 58.717 33.333 0.00 0.00 0.00 2.32
3651 4553 8.713271 GTCTTTTTATCTCGTCTTCATTTCAGT 58.287 33.333 0.00 0.00 0.00 3.41
3652 4554 8.712363 TCTTTTTATCTCGTCTTCATTTCAGTG 58.288 33.333 0.00 0.00 0.00 3.66
3702 4618 2.658285 GGCCATGATTTGATGACCAGA 58.342 47.619 0.00 0.00 0.00 3.86
3710 4626 7.094890 CCATGATTTGATGACCAGAGCTATAAC 60.095 40.741 0.00 0.00 0.00 1.89
3719 4635 4.528920 ACCAGAGCTATAACGTCTTCTCT 58.471 43.478 0.00 0.00 0.00 3.10
3803 4720 2.757314 TGGAAACAATTCAGTGTGCACA 59.243 40.909 17.42 17.42 37.29 4.57
3983 4913 6.817140 AGAATTTTTAGCTCGTAACCCTAGTG 59.183 38.462 0.00 0.00 0.00 2.74
4078 5008 3.087031 TCGACCGAAAGTATCTTGTCCT 58.913 45.455 0.00 0.00 0.00 3.85
4086 5016 5.651530 GAAAGTATCTTGTCCTGATCGACA 58.348 41.667 0.00 0.00 40.98 4.35
4125 5055 0.840722 ACCGTGACCCCTTCCTTCAT 60.841 55.000 0.00 0.00 0.00 2.57
4204 5134 4.994852 GGTTTGTTGAGCTACTGTATGTGA 59.005 41.667 0.00 0.00 0.00 3.58
4205 5135 5.468746 GGTTTGTTGAGCTACTGTATGTGAA 59.531 40.000 0.00 0.00 0.00 3.18
4206 5136 6.347725 GGTTTGTTGAGCTACTGTATGTGAAG 60.348 42.308 0.00 0.00 0.00 3.02
4207 5137 5.468540 TGTTGAGCTACTGTATGTGAAGT 57.531 39.130 0.00 0.00 0.00 3.01
4208 5138 5.853936 TGTTGAGCTACTGTATGTGAAGTT 58.146 37.500 0.00 0.00 0.00 2.66
4209 5139 5.926542 TGTTGAGCTACTGTATGTGAAGTTC 59.073 40.000 0.00 0.00 0.00 3.01
4210 5140 5.073311 TGAGCTACTGTATGTGAAGTTCC 57.927 43.478 0.00 0.00 0.00 3.62
4211 5141 4.526650 TGAGCTACTGTATGTGAAGTTCCA 59.473 41.667 0.00 0.00 0.00 3.53
4212 5142 5.187772 TGAGCTACTGTATGTGAAGTTCCAT 59.812 40.000 0.00 6.29 0.00 3.41
4213 5143 6.054860 AGCTACTGTATGTGAAGTTCCATT 57.945 37.500 10.78 0.00 0.00 3.16
4214 5144 5.877012 AGCTACTGTATGTGAAGTTCCATTG 59.123 40.000 10.78 6.31 0.00 2.82
4215 5145 5.643777 GCTACTGTATGTGAAGTTCCATTGT 59.356 40.000 10.78 10.11 0.00 2.71
4216 5146 6.149474 GCTACTGTATGTGAAGTTCCATTGTT 59.851 38.462 10.78 0.44 0.00 2.83
4217 5147 7.333423 GCTACTGTATGTGAAGTTCCATTGTTA 59.667 37.037 10.78 0.00 0.00 2.41
4218 5148 7.672983 ACTGTATGTGAAGTTCCATTGTTAG 57.327 36.000 10.78 7.90 0.00 2.34
4219 5149 6.149474 ACTGTATGTGAAGTTCCATTGTTAGC 59.851 38.462 10.78 0.00 0.00 3.09
4220 5150 6.237901 TGTATGTGAAGTTCCATTGTTAGCT 58.762 36.000 10.78 0.00 0.00 3.32
4221 5151 6.714810 TGTATGTGAAGTTCCATTGTTAGCTT 59.285 34.615 10.78 0.00 0.00 3.74
4222 5152 7.880713 TGTATGTGAAGTTCCATTGTTAGCTTA 59.119 33.333 10.78 0.00 0.00 3.09
4265 5205 0.037590 ACTGCAGATTTACGGGCCAA 59.962 50.000 23.35 0.00 0.00 4.52
4294 5244 2.539476 CGAAAGTGGCTGTTGCTTTTT 58.461 42.857 0.00 0.00 39.59 1.94
4295 5245 2.282290 CGAAAGTGGCTGTTGCTTTTTG 59.718 45.455 0.00 0.00 39.59 2.44
4296 5246 1.655484 AAGTGGCTGTTGCTTTTTGC 58.345 45.000 0.00 0.00 43.25 3.68
4297 5247 0.826062 AGTGGCTGTTGCTTTTTGCT 59.174 45.000 0.00 0.00 43.37 3.91
4298 5248 0.932399 GTGGCTGTTGCTTTTTGCTG 59.068 50.000 0.00 0.00 43.37 4.41
4299 5249 0.810823 TGGCTGTTGCTTTTTGCTGC 60.811 50.000 0.00 0.00 43.37 5.25
4300 5250 0.531311 GGCTGTTGCTTTTTGCTGCT 60.531 50.000 0.00 0.00 43.37 4.24
4301 5251 1.292992 GCTGTTGCTTTTTGCTGCTT 58.707 45.000 0.00 0.00 43.37 3.91
4302 5252 1.667212 GCTGTTGCTTTTTGCTGCTTT 59.333 42.857 0.00 0.00 43.37 3.51
4303 5253 2.096335 GCTGTTGCTTTTTGCTGCTTTT 59.904 40.909 0.00 0.00 43.37 2.27
4304 5254 3.676540 CTGTTGCTTTTTGCTGCTTTTG 58.323 40.909 0.00 0.00 43.37 2.44
4308 5258 2.415857 TGCTTTTTGCTGCTTTTGTGTG 59.584 40.909 0.00 0.00 43.37 3.82
4328 5278 2.700371 TGTGTGTGAGAAGTGTCTGGAT 59.300 45.455 0.00 0.00 32.80 3.41
4329 5279 3.243873 TGTGTGTGAGAAGTGTCTGGATC 60.244 47.826 0.00 0.00 32.80 3.36
4339 5289 5.779771 AGAAGTGTCTGGATCTTCTCTCTTT 59.220 40.000 11.85 0.00 42.50 2.52
4340 5290 5.659440 AGTGTCTGGATCTTCTCTCTTTC 57.341 43.478 0.00 0.00 0.00 2.62
4341 5291 5.332743 AGTGTCTGGATCTTCTCTCTTTCT 58.667 41.667 0.00 0.00 0.00 2.52
4342 5292 5.779771 AGTGTCTGGATCTTCTCTCTTTCTT 59.220 40.000 0.00 0.00 0.00 2.52
4343 5293 6.951198 AGTGTCTGGATCTTCTCTCTTTCTTA 59.049 38.462 0.00 0.00 0.00 2.10
4344 5294 7.453126 AGTGTCTGGATCTTCTCTCTTTCTTAA 59.547 37.037 0.00 0.00 0.00 1.85
4345 5295 8.091449 GTGTCTGGATCTTCTCTCTTTCTTAAA 58.909 37.037 0.00 0.00 0.00 1.52
4378 5329 1.529865 GTGCAGGGTTCGAGTGTAAAC 59.470 52.381 0.00 0.00 0.00 2.01
4379 5330 1.414919 TGCAGGGTTCGAGTGTAAACT 59.585 47.619 0.00 0.00 0.00 2.66
4380 5331 2.158871 TGCAGGGTTCGAGTGTAAACTT 60.159 45.455 0.00 0.00 0.00 2.66
4381 5332 2.479275 GCAGGGTTCGAGTGTAAACTTC 59.521 50.000 0.00 0.00 0.00 3.01
4382 5333 3.724374 CAGGGTTCGAGTGTAAACTTCA 58.276 45.455 0.00 0.00 0.00 3.02
4384 5335 4.389077 CAGGGTTCGAGTGTAAACTTCATC 59.611 45.833 0.00 0.00 0.00 2.92
4385 5336 4.283722 AGGGTTCGAGTGTAAACTTCATCT 59.716 41.667 0.00 0.00 0.00 2.90
4387 5338 6.014840 AGGGTTCGAGTGTAAACTTCATCTAA 60.015 38.462 0.00 0.00 0.00 2.10
4388 5339 6.647895 GGGTTCGAGTGTAAACTTCATCTAAA 59.352 38.462 0.00 0.00 0.00 1.85
4466 5421 6.990939 GCTAGGTAGTAGTTTATTTTGGGAGG 59.009 42.308 0.00 0.00 0.00 4.30
4467 5422 7.147602 GCTAGGTAGTAGTTTATTTTGGGAGGA 60.148 40.741 0.00 0.00 0.00 3.71
4488 5443 4.452455 GGAGAAGCGAGAGATTTGTTGAAA 59.548 41.667 0.00 0.00 41.48 2.69
4489 5444 5.349824 AGAAGCGAGAGATTTGTTGAAAC 57.650 39.130 0.00 0.00 41.48 2.78
4490 5445 4.816385 AGAAGCGAGAGATTTGTTGAAACA 59.184 37.500 0.00 0.00 41.48 2.83
4491 5446 5.471456 AGAAGCGAGAGATTTGTTGAAACAT 59.529 36.000 0.00 0.00 41.48 2.71
4493 5448 3.605486 GCGAGAGATTTGTTGAAACATGC 59.395 43.478 0.00 0.00 38.95 4.06
4494 5449 3.842428 CGAGAGATTTGTTGAAACATGCG 59.158 43.478 0.00 0.00 38.95 4.73
4495 5450 4.161333 GAGAGATTTGTTGAAACATGCGG 58.839 43.478 0.00 0.00 38.95 5.69
4496 5451 3.820467 AGAGATTTGTTGAAACATGCGGA 59.180 39.130 0.00 0.00 38.95 5.54
4497 5452 3.900941 AGATTTGTTGAAACATGCGGAC 58.099 40.909 0.00 0.00 38.95 4.79
4553 5508 6.401367 CCTCAAACAAAAACTGAAGCAACAAG 60.401 38.462 0.00 0.00 0.00 3.16
4568 5523 1.080093 CAAGGCGCTAGAACACGGA 60.080 57.895 7.64 0.00 0.00 4.69
4593 6899 1.336609 ACCTTTCGTCTCGCTAACACC 60.337 52.381 0.00 0.00 0.00 4.16
4600 6906 0.608130 TCTCGCTAACACCAGCACAT 59.392 50.000 0.00 0.00 41.88 3.21
4605 6911 2.005451 GCTAACACCAGCACATCTGAG 58.995 52.381 0.00 0.00 45.72 3.35
4617 6954 1.133982 ACATCTGAGTGAGCTACTGCG 59.866 52.381 0.00 0.00 45.42 5.18
4636 6973 2.388121 CGTGCTGCCAGAAAGAAAAAG 58.612 47.619 0.00 0.00 0.00 2.27
4637 6974 2.747436 GTGCTGCCAGAAAGAAAAAGG 58.253 47.619 0.00 0.00 0.00 3.11
4676 7020 1.586028 GCCGTTCACATGGTTGCAT 59.414 52.632 0.00 0.00 0.00 3.96
4681 7025 1.046204 TTCACATGGTTGCATTGCCA 58.954 45.000 6.12 7.48 39.33 4.92
4696 7040 0.749818 TGCCACTCGAGCCAACAAAA 60.750 50.000 13.61 0.00 0.00 2.44
4711 7055 1.713078 ACAAAATGGCTCCTCTCCCTT 59.287 47.619 0.00 0.00 0.00 3.95
4712 7056 2.110721 ACAAAATGGCTCCTCTCCCTTT 59.889 45.455 0.00 0.00 0.00 3.11
4732 7076 1.967779 TCAAGGTTCTGTCCGTCATCA 59.032 47.619 0.00 0.00 0.00 3.07
4757 7101 3.757745 CACGAATTGTGTATGAACCCC 57.242 47.619 0.00 0.00 43.88 4.95
4788 7134 3.069289 GGATACGCTCATCATGCAATCA 58.931 45.455 0.00 0.00 0.00 2.57
4798 7144 4.340097 TCATCATGCAATCAGAAATCCACC 59.660 41.667 0.00 0.00 0.00 4.61
4948 7306 4.492160 CGAGGCAGCGGCGAGTAA 62.492 66.667 12.98 0.00 42.47 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.765695 ATACCCAAAGTGCATCCTATATTTG 57.234 36.000 0.00 0.00 0.00 2.32
88 97 2.349100 ATCCATGGGCTAGCTGGTGC 62.349 60.000 18.20 0.00 40.05 5.01
166 175 5.836358 ACAAATCCTAACCTAAACTTTGGCA 59.164 36.000 0.00 0.00 0.00 4.92
168 177 9.908152 CTTAACAAATCCTAACCTAAACTTTGG 57.092 33.333 0.00 0.00 0.00 3.28
173 182 8.517878 GGGAACTTAACAAATCCTAACCTAAAC 58.482 37.037 0.00 0.00 32.41 2.01
177 186 6.008331 GTGGGAACTTAACAAATCCTAACCT 58.992 40.000 0.00 0.00 32.41 3.50
209 218 1.467543 CGTCATCATTCGACCGAGTGT 60.468 52.381 13.19 1.00 34.17 3.55
210 219 1.191944 CGTCATCATTCGACCGAGTG 58.808 55.000 8.35 8.35 33.86 3.51
214 223 1.989864 TGAAACGTCATCATTCGACCG 59.010 47.619 0.00 0.00 0.00 4.79
225 234 1.271163 GGACCCAAGGATGAAACGTCA 60.271 52.381 0.00 0.00 38.41 4.35
227 236 1.003233 GAGGACCCAAGGATGAAACGT 59.997 52.381 0.00 0.00 0.00 3.99
230 239 1.635487 CCAGAGGACCCAAGGATGAAA 59.365 52.381 0.00 0.00 0.00 2.69
240 249 1.627297 AATCGAAGCCCAGAGGACCC 61.627 60.000 0.00 0.00 33.47 4.46
241 250 0.462759 CAATCGAAGCCCAGAGGACC 60.463 60.000 0.00 0.00 33.47 4.46
278 291 3.541711 GGATCTTGTTGTTTTCGTCGTG 58.458 45.455 0.00 0.00 0.00 4.35
280 293 2.473609 TCGGATCTTGTTGTTTTCGTCG 59.526 45.455 0.00 0.00 0.00 5.12
283 296 4.436050 CCTCATCGGATCTTGTTGTTTTCG 60.436 45.833 0.00 0.00 33.16 3.46
285 298 4.398319 ACCTCATCGGATCTTGTTGTTTT 58.602 39.130 0.00 0.00 36.31 2.43
287 300 3.703001 ACCTCATCGGATCTTGTTGTT 57.297 42.857 0.00 0.00 36.31 2.83
288 301 3.703001 AACCTCATCGGATCTTGTTGT 57.297 42.857 0.00 0.00 36.31 3.32
296 309 4.956700 TGAGAAACTCTAACCTCATCGGAT 59.043 41.667 0.00 0.00 36.31 4.18
302 315 8.568794 CATATACGATGAGAAACTCTAACCTCA 58.431 37.037 0.00 0.00 39.60 3.86
357 370 9.832445 CTCAAGCCAAACCTATAAACTATCTTA 57.168 33.333 0.00 0.00 0.00 2.10
358 371 8.329502 ACTCAAGCCAAACCTATAAACTATCTT 58.670 33.333 0.00 0.00 0.00 2.40
359 372 7.770897 CACTCAAGCCAAACCTATAAACTATCT 59.229 37.037 0.00 0.00 0.00 1.98
361 374 7.402862 ACACTCAAGCCAAACCTATAAACTAT 58.597 34.615 0.00 0.00 0.00 2.12
362 375 6.775708 ACACTCAAGCCAAACCTATAAACTA 58.224 36.000 0.00 0.00 0.00 2.24
363 376 5.631119 ACACTCAAGCCAAACCTATAAACT 58.369 37.500 0.00 0.00 0.00 2.66
364 377 5.959618 ACACTCAAGCCAAACCTATAAAC 57.040 39.130 0.00 0.00 0.00 2.01
365 378 6.999272 TGTAACACTCAAGCCAAACCTATAAA 59.001 34.615 0.00 0.00 0.00 1.40
366 379 6.535540 TGTAACACTCAAGCCAAACCTATAA 58.464 36.000 0.00 0.00 0.00 0.98
367 380 6.116711 TGTAACACTCAAGCCAAACCTATA 57.883 37.500 0.00 0.00 0.00 1.31
395 410 6.980397 GGCTGACATTTCTGGTTTATTTATGG 59.020 38.462 0.00 0.00 0.00 2.74
440 455 5.300286 GGCAACATCTAACATGCTTAATCCT 59.700 40.000 0.00 0.00 38.79 3.24
445 460 4.842574 TGAGGCAACATCTAACATGCTTA 58.157 39.130 0.00 0.00 38.79 3.09
453 468 4.523943 AGCATGTTTTGAGGCAACATCTAA 59.476 37.500 0.00 0.00 41.91 2.10
466 481 1.893168 GCGCCAGCAAGCATGTTTTG 61.893 55.000 0.00 0.00 44.35 2.44
522 538 7.054751 ACCCTTAAATCTGAAGCACCTAATAC 58.945 38.462 0.00 0.00 0.00 1.89
553 569 1.992233 TTATAGTCGCCGTCGCCGTT 61.992 55.000 0.00 0.00 35.26 4.44
554 570 2.472059 TTATAGTCGCCGTCGCCGT 61.472 57.895 0.00 0.00 35.26 5.68
555 571 2.007641 GTTATAGTCGCCGTCGCCG 61.008 63.158 0.00 0.00 35.26 6.46
556 572 0.248784 AAGTTATAGTCGCCGTCGCC 60.249 55.000 0.00 0.00 35.26 5.54
557 573 1.118833 GAAGTTATAGTCGCCGTCGC 58.881 55.000 0.00 0.00 35.26 5.19
558 574 2.223203 ACTGAAGTTATAGTCGCCGTCG 60.223 50.000 0.00 0.00 0.00 5.12
579 595 4.153475 GCATGTGCCTTTAAGACGAAAGTA 59.847 41.667 0.00 0.00 39.06 2.24
580 596 3.058224 GCATGTGCCTTTAAGACGAAAGT 60.058 43.478 0.00 0.00 41.05 2.66
585 601 1.464023 CGTGCATGTGCCTTTAAGACG 60.464 52.381 2.07 0.27 41.18 4.18
602 619 6.085458 CGATGACAAACTGAAAAATCTTCGTG 59.915 38.462 0.00 0.00 32.34 4.35
604 621 6.362686 TCGATGACAAACTGAAAAATCTTCG 58.637 36.000 0.00 0.00 35.97 3.79
618 635 6.929049 ACAAGACTGAACTTATCGATGACAAA 59.071 34.615 8.54 0.00 0.00 2.83
620 637 6.025749 ACAAGACTGAACTTATCGATGACA 57.974 37.500 8.54 0.41 0.00 3.58
621 638 6.197468 GCTACAAGACTGAACTTATCGATGAC 59.803 42.308 8.54 0.00 0.00 3.06
622 639 6.095580 AGCTACAAGACTGAACTTATCGATGA 59.904 38.462 8.54 0.00 0.00 2.92
623 640 6.269315 AGCTACAAGACTGAACTTATCGATG 58.731 40.000 8.54 0.00 0.00 3.84
624 641 6.320164 AGAGCTACAAGACTGAACTTATCGAT 59.680 38.462 2.16 2.16 0.00 3.59
625 642 5.648526 AGAGCTACAAGACTGAACTTATCGA 59.351 40.000 0.00 0.00 0.00 3.59
626 643 5.885881 AGAGCTACAAGACTGAACTTATCG 58.114 41.667 0.00 0.00 0.00 2.92
627 644 7.992008 ACTAGAGCTACAAGACTGAACTTATC 58.008 38.462 0.00 0.00 0.00 1.75
628 645 7.948034 ACTAGAGCTACAAGACTGAACTTAT 57.052 36.000 0.00 0.00 0.00 1.73
629 646 8.102047 ACTACTAGAGCTACAAGACTGAACTTA 58.898 37.037 0.00 0.00 0.00 2.24
635 652 6.503589 ACAACTACTAGAGCTACAAGACTG 57.496 41.667 0.00 0.00 0.00 3.51
670 687 8.156165 TCAACTTATTTTAAAACGGAGGGAGTA 58.844 33.333 1.97 0.00 0.00 2.59
671 688 6.999871 TCAACTTATTTTAAAACGGAGGGAGT 59.000 34.615 1.97 0.00 0.00 3.85
672 689 7.174426 ACTCAACTTATTTTAAAACGGAGGGAG 59.826 37.037 1.97 13.16 0.00 4.30
673 690 6.999871 ACTCAACTTATTTTAAAACGGAGGGA 59.000 34.615 1.97 3.96 0.00 4.20
674 691 7.040961 TGACTCAACTTATTTTAAAACGGAGGG 60.041 37.037 1.97 0.00 0.00 4.30
675 692 7.801783 GTGACTCAACTTATTTTAAAACGGAGG 59.198 37.037 1.97 0.00 0.00 4.30
676 693 8.557029 AGTGACTCAACTTATTTTAAAACGGAG 58.443 33.333 1.97 4.41 0.00 4.63
677 694 8.441312 AGTGACTCAACTTATTTTAAAACGGA 57.559 30.769 1.97 0.00 0.00 4.69
689 706 8.579006 TCGTCCTAAAATAAGTGACTCAACTTA 58.421 33.333 0.00 0.00 44.52 2.24
690 707 7.439381 TCGTCCTAAAATAAGTGACTCAACTT 58.561 34.615 0.00 0.00 42.89 2.66
691 708 6.989659 TCGTCCTAAAATAAGTGACTCAACT 58.010 36.000 0.00 0.00 0.00 3.16
692 709 7.647907 TTCGTCCTAAAATAAGTGACTCAAC 57.352 36.000 0.00 0.00 0.00 3.18
693 710 7.386848 CCTTTCGTCCTAAAATAAGTGACTCAA 59.613 37.037 0.00 0.00 0.00 3.02
694 711 6.872020 CCTTTCGTCCTAAAATAAGTGACTCA 59.128 38.462 0.00 0.00 0.00 3.41
695 712 7.095270 TCCTTTCGTCCTAAAATAAGTGACTC 58.905 38.462 0.00 0.00 0.00 3.36
696 713 7.001099 TCCTTTCGTCCTAAAATAAGTGACT 57.999 36.000 0.00 0.00 0.00 3.41
697 714 6.872547 ACTCCTTTCGTCCTAAAATAAGTGAC 59.127 38.462 0.00 0.00 0.00 3.67
698 715 7.001099 ACTCCTTTCGTCCTAAAATAAGTGA 57.999 36.000 0.00 0.00 0.00 3.41
699 716 8.943909 ATACTCCTTTCGTCCTAAAATAAGTG 57.056 34.615 0.00 0.00 0.00 3.16
704 721 9.901172 AACATAATACTCCTTTCGTCCTAAAAT 57.099 29.630 0.00 0.00 0.00 1.82
705 722 9.729281 AAACATAATACTCCTTTCGTCCTAAAA 57.271 29.630 0.00 0.00 0.00 1.52
706 723 9.158233 CAAACATAATACTCCTTTCGTCCTAAA 57.842 33.333 0.00 0.00 0.00 1.85
707 724 8.533657 TCAAACATAATACTCCTTTCGTCCTAA 58.466 33.333 0.00 0.00 0.00 2.69
708 725 8.070034 TCAAACATAATACTCCTTTCGTCCTA 57.930 34.615 0.00 0.00 0.00 2.94
709 726 6.942976 TCAAACATAATACTCCTTTCGTCCT 58.057 36.000 0.00 0.00 0.00 3.85
710 727 6.258068 CCTCAAACATAATACTCCTTTCGTCC 59.742 42.308 0.00 0.00 0.00 4.79
711 728 6.817140 ACCTCAAACATAATACTCCTTTCGTC 59.183 38.462 0.00 0.00 0.00 4.20
712 729 6.708285 ACCTCAAACATAATACTCCTTTCGT 58.292 36.000 0.00 0.00 0.00 3.85
713 730 8.888579 ATACCTCAAACATAATACTCCTTTCG 57.111 34.615 0.00 0.00 0.00 3.46
741 758 4.193865 CGAAATACCCGGACCAAAAGTAT 58.806 43.478 0.73 0.00 0.00 2.12
815 832 2.658593 CGGCGAAGTATCCAGCGG 60.659 66.667 0.00 0.00 0.00 5.52
850 869 6.062021 CGTAATTTTGATGAACGTTTTTGCC 58.938 36.000 0.46 0.00 0.00 4.52
1486 1506 3.403624 ATGAGCACCATGACCGGT 58.596 55.556 6.92 6.92 41.07 5.28
1558 1578 2.029844 GCCTTTGAGCGCGAAGAGT 61.030 57.895 18.13 0.00 37.67 3.24
1581 1601 0.381801 CATATGGGCGAACTGGTTGC 59.618 55.000 0.00 0.00 0.00 4.17
1589 1609 0.456628 TTCGACGTCATATGGGCGAA 59.543 50.000 15.91 15.91 35.69 4.70
1606 1626 4.759782 TGCAGCAATAGAGTACCTCTTTC 58.240 43.478 0.00 0.00 41.50 2.62
1642 1662 7.022055 TCGAAAACTAAAGCAAATGAACAGA 57.978 32.000 0.00 0.00 0.00 3.41
1671 1692 7.868922 TCACTCGCAAACAAGACTATTAGTAAA 59.131 33.333 0.00 0.00 0.00 2.01
1676 1697 5.168569 CCTCACTCGCAAACAAGACTATTA 58.831 41.667 0.00 0.00 0.00 0.98
1692 1713 4.141111 AGGGTAATCTCTACTCCCTCACTC 60.141 50.000 0.00 0.00 44.32 3.51
1761 1789 4.654091 ACTTGTTTCCACATGTTCCAAG 57.346 40.909 0.00 6.87 37.91 3.61
1815 1849 3.981071 TGGCAGTATTTAGCTGTCTGT 57.019 42.857 0.00 0.00 39.16 3.41
1833 1867 2.026822 ACAGGACCAAACTAGCAGATGG 60.027 50.000 0.00 0.00 38.91 3.51
1855 1889 4.697352 GCAGGTCCCATGATATTCACATAC 59.303 45.833 0.00 0.00 0.00 2.39
1898 1932 3.399440 GCTATGCTACAGCTGATCCTT 57.601 47.619 23.35 8.11 42.66 3.36
2051 2123 2.874014 TGGAGCACAATCAACCAATGA 58.126 42.857 0.00 0.00 43.67 2.57
2052 2124 3.880047 ATGGAGCACAATCAACCAATG 57.120 42.857 0.00 0.00 34.28 2.82
2053 2125 6.040842 GGTTATATGGAGCACAATCAACCAAT 59.959 38.462 8.99 0.00 34.42 3.16
2094 2169 7.614192 GGAGATTTGGGGAAGAAAATACTTACA 59.386 37.037 0.00 0.00 32.81 2.41
2184 2259 7.672983 TCAGGCACTATGAGAAACTAAAAAG 57.327 36.000 0.00 0.00 36.02 2.27
2185 2260 9.733556 TTATCAGGCACTATGAGAAACTAAAAA 57.266 29.630 0.00 0.00 36.02 1.94
2216 2324 8.798402 CAATTTGGGTAGTGATGGTTACTTTTA 58.202 33.333 0.00 0.00 0.00 1.52
2225 2333 3.131046 GCCTTCAATTTGGGTAGTGATGG 59.869 47.826 0.00 0.00 38.00 3.51
2283 2391 2.690497 TCTCGGAGCTATTGGTTCTCTG 59.310 50.000 0.00 0.00 35.19 3.35
2300 2408 5.039984 CCTTGATGTAAGATCACAGTCTCG 58.960 45.833 0.00 0.00 38.76 4.04
2371 2483 7.164803 CCTTAAACTCCTCTTCTCAAGTGATT 58.835 38.462 0.00 0.00 0.00 2.57
2372 2484 6.296145 CCCTTAAACTCCTCTTCTCAAGTGAT 60.296 42.308 0.00 0.00 0.00 3.06
2507 2630 4.355543 TCTGTGTGCTCAGTTTTTCAAC 57.644 40.909 0.00 0.00 36.85 3.18
2508 2631 4.639755 TGATCTGTGTGCTCAGTTTTTCAA 59.360 37.500 0.00 0.00 36.85 2.69
2509 2632 4.198530 TGATCTGTGTGCTCAGTTTTTCA 58.801 39.130 0.00 0.00 36.85 2.69
2544 2667 7.012327 CACTGAGTTTGAATAGGTTGACTGAAA 59.988 37.037 0.00 0.00 0.00 2.69
2619 2757 3.662759 ACCACCAAAAACCTCAAGAGA 57.337 42.857 0.00 0.00 0.00 3.10
2627 2765 2.384828 AGACCTGAACCACCAAAAACC 58.615 47.619 0.00 0.00 0.00 3.27
2695 2836 9.369904 GGTTGTGTAAAACTATAACGATAAGGA 57.630 33.333 0.00 0.00 0.00 3.36
2702 2867 7.424227 TTCCAGGTTGTGTAAAACTATAACG 57.576 36.000 0.00 0.00 0.00 3.18
2734 2899 7.672983 TTTTAGAAGGACTTTACAGAGCATG 57.327 36.000 0.00 0.00 0.00 4.06
2775 2940 5.046910 AGTTTGATGCTAATGGTTCAACG 57.953 39.130 0.00 0.00 0.00 4.10
2799 2964 3.456380 AGGCCAGTTGTTGTGGAATAT 57.544 42.857 5.01 0.00 37.23 1.28
2806 2971 2.106511 ACTGTGATAGGCCAGTTGTTGT 59.893 45.455 5.01 0.00 38.76 3.32
2889 3055 4.142816 GCTCTACAACACAACCTTATGCTG 60.143 45.833 0.00 0.00 0.00 4.41
2899 3065 6.935167 TCAGATCATAAGCTCTACAACACAA 58.065 36.000 0.00 0.00 0.00 3.33
2903 3069 6.020281 CGTGTTCAGATCATAAGCTCTACAAC 60.020 42.308 0.00 0.00 0.00 3.32
2954 3124 0.947244 GCCTGTCACAAGGTTGTCAG 59.053 55.000 5.10 5.10 39.91 3.51
3034 3233 7.233348 AGGTGAGAGAGAAAAATAAATGCCAAA 59.767 33.333 0.00 0.00 0.00 3.28
3055 3254 6.737720 AATATTCTGTCTGCTCATAGGTGA 57.262 37.500 0.00 0.00 0.00 4.02
3139 3612 5.719173 TCCACAAGACAAACAAAGGAAAAG 58.281 37.500 0.00 0.00 0.00 2.27
3223 3954 2.222819 GCGTCGACAGAAACCATTGATC 60.223 50.000 17.16 0.00 0.00 2.92
3225 3956 1.144969 GCGTCGACAGAAACCATTGA 58.855 50.000 17.16 0.00 0.00 2.57
3242 3973 3.766151 ACAGAATCAGAAATTGCATGCG 58.234 40.909 14.09 0.00 0.00 4.73
3248 3979 6.218019 TGGAGCAAAACAGAATCAGAAATTG 58.782 36.000 0.00 0.00 0.00 2.32
3322 4054 6.481954 AGGAAAGAGCTGTAAATTTGTACG 57.518 37.500 0.00 0.00 0.00 3.67
3403 4135 7.415206 GGGCCATTAACTACTTTGTATCAACAG 60.415 40.741 4.39 0.00 36.83 3.16
3421 4153 1.912731 TGAGCAAGTACAGGGCCATTA 59.087 47.619 6.18 0.00 0.00 1.90
3455 4312 3.374745 CGCTTACATTTGAATGCATCCC 58.625 45.455 0.00 0.00 40.04 3.85
3471 4354 6.282199 AGTTCTCTTATCAGAAACCGCTTA 57.718 37.500 0.00 0.00 34.11 3.09
3507 4391 4.753107 TGTAAACGGTAGCCTCTGAAAAAG 59.247 41.667 0.00 0.00 0.00 2.27
3509 4393 4.202284 ACTGTAAACGGTAGCCTCTGAAAA 60.202 41.667 0.00 0.00 32.82 2.29
3633 4535 3.265791 GGCACTGAAATGAAGACGAGAT 58.734 45.455 0.00 0.00 0.00 2.75
3637 4539 3.837213 AATGGCACTGAAATGAAGACG 57.163 42.857 0.00 0.00 0.00 4.18
3647 4549 5.738783 GCTTGTTAAAAGGAAATGGCACTGA 60.739 40.000 0.00 0.00 0.00 3.41
3651 4553 4.953940 AGCTTGTTAAAAGGAAATGGCA 57.046 36.364 0.00 0.00 0.00 4.92
3652 4554 5.056480 ACAAGCTTGTTAAAAGGAAATGGC 58.944 37.500 26.36 0.00 38.47 4.40
3702 4618 5.298276 CAGAAGGAGAGAAGACGTTATAGCT 59.702 44.000 0.00 0.00 0.00 3.32
3710 4626 6.090088 CACAAAATACAGAAGGAGAGAAGACG 59.910 42.308 0.00 0.00 0.00 4.18
3719 4635 6.889177 TCATTATGCCACAAAATACAGAAGGA 59.111 34.615 0.00 0.00 0.00 3.36
3803 4720 3.019564 GGCTTGAGTTATCCAAGTGCAT 58.980 45.455 0.00 0.00 42.11 3.96
3813 4730 6.374417 TCTTAAACAGGAGGCTTGAGTTAT 57.626 37.500 0.00 0.00 0.00 1.89
4013 4943 3.421844 ACTTCAGGAATTACAAGGGCAC 58.578 45.455 0.00 0.00 0.00 5.01
4046 4976 2.561733 TTCGGTCGATCAGCAACTAG 57.438 50.000 0.00 0.00 0.00 2.57
4078 5008 7.826252 TCTGATATCTCTATCATGTGTCGATCA 59.174 37.037 3.98 0.00 42.17 2.92
4086 5016 8.049721 TCACGGTATCTGATATCTCTATCATGT 58.950 37.037 3.98 0.00 42.17 3.21
4125 5055 3.826157 CTGTAAATGGCAGTGGAAAGGAA 59.174 43.478 0.00 0.00 0.00 3.36
4204 5134 7.575720 GCACAAGATAAGCTAACAATGGAACTT 60.576 37.037 0.00 0.00 0.00 2.66
4205 5135 6.127897 GCACAAGATAAGCTAACAATGGAACT 60.128 38.462 0.00 0.00 0.00 3.01
4206 5136 6.030228 GCACAAGATAAGCTAACAATGGAAC 58.970 40.000 0.00 0.00 0.00 3.62
4207 5137 5.709631 TGCACAAGATAAGCTAACAATGGAA 59.290 36.000 0.00 0.00 0.00 3.53
4208 5138 5.252547 TGCACAAGATAAGCTAACAATGGA 58.747 37.500 0.00 0.00 0.00 3.41
4209 5139 5.565592 TGCACAAGATAAGCTAACAATGG 57.434 39.130 0.00 0.00 0.00 3.16
4210 5140 9.571810 TTATTTGCACAAGATAAGCTAACAATG 57.428 29.630 0.00 0.00 0.00 2.82
4212 5142 9.624697 CTTTATTTGCACAAGATAAGCTAACAA 57.375 29.630 0.00 0.00 0.00 2.83
4213 5143 8.792633 ACTTTATTTGCACAAGATAAGCTAACA 58.207 29.630 0.00 0.00 0.00 2.41
4214 5144 9.626045 AACTTTATTTGCACAAGATAAGCTAAC 57.374 29.630 0.00 0.00 0.00 2.34
4251 5181 3.945640 ATAACCTTGGCCCGTAAATCT 57.054 42.857 0.00 0.00 0.00 2.40
4252 5182 3.501062 GCTATAACCTTGGCCCGTAAATC 59.499 47.826 0.00 0.00 0.00 2.17
4265 5205 2.236395 ACAGCCACTTTCGCTATAACCT 59.764 45.455 0.00 0.00 33.91 3.50
4294 5244 0.887247 ACACACACACAAAAGCAGCA 59.113 45.000 0.00 0.00 0.00 4.41
4295 5245 1.135431 TCACACACACACAAAAGCAGC 60.135 47.619 0.00 0.00 0.00 5.25
4296 5246 2.419673 TCTCACACACACACAAAAGCAG 59.580 45.455 0.00 0.00 0.00 4.24
4297 5247 2.431454 TCTCACACACACACAAAAGCA 58.569 42.857 0.00 0.00 0.00 3.91
4298 5248 3.119849 ACTTCTCACACACACACAAAAGC 60.120 43.478 0.00 0.00 0.00 3.51
4299 5249 4.083324 ACACTTCTCACACACACACAAAAG 60.083 41.667 0.00 0.00 0.00 2.27
4300 5250 3.818210 ACACTTCTCACACACACACAAAA 59.182 39.130 0.00 0.00 0.00 2.44
4301 5251 3.407698 ACACTTCTCACACACACACAAA 58.592 40.909 0.00 0.00 0.00 2.83
4302 5252 3.000041 GACACTTCTCACACACACACAA 59.000 45.455 0.00 0.00 0.00 3.33
4303 5253 2.233676 AGACACTTCTCACACACACACA 59.766 45.455 0.00 0.00 0.00 3.72
4304 5254 2.604914 CAGACACTTCTCACACACACAC 59.395 50.000 0.00 0.00 0.00 3.82
4308 5258 2.890808 TCCAGACACTTCTCACACAC 57.109 50.000 0.00 0.00 0.00 3.82
4344 5294 3.263170 ACCCTGCACAACCTTTTCTTTTT 59.737 39.130 0.00 0.00 0.00 1.94
4345 5295 2.837591 ACCCTGCACAACCTTTTCTTTT 59.162 40.909 0.00 0.00 0.00 2.27
4349 5299 1.269051 CGAACCCTGCACAACCTTTTC 60.269 52.381 0.00 0.00 0.00 2.29
4358 5308 1.529865 GTTTACACTCGAACCCTGCAC 59.470 52.381 0.00 0.00 0.00 4.57
4364 5314 7.647907 TTTAGATGAAGTTTACACTCGAACC 57.352 36.000 0.00 0.00 30.45 3.62
4384 5335 7.827819 TCCGTAAACTTCACATCTGATTTAG 57.172 36.000 0.00 0.00 0.00 1.85
4385 5336 7.876068 ACTTCCGTAAACTTCACATCTGATTTA 59.124 33.333 0.00 0.00 0.00 1.40
4387 5338 6.231211 ACTTCCGTAAACTTCACATCTGATT 58.769 36.000 0.00 0.00 0.00 2.57
4388 5339 5.794894 ACTTCCGTAAACTTCACATCTGAT 58.205 37.500 0.00 0.00 0.00 2.90
4466 5421 5.050091 TGTTTCAACAAATCTCTCGCTTCTC 60.050 40.000 0.00 0.00 35.67 2.87
4467 5422 4.816385 TGTTTCAACAAATCTCTCGCTTCT 59.184 37.500 0.00 0.00 35.67 2.85
4488 5443 0.670546 GTGTAGCACTGTCCGCATGT 60.671 55.000 0.00 0.00 0.00 3.21
4489 5444 0.390340 AGTGTAGCACTGTCCGCATG 60.390 55.000 0.53 0.00 43.63 4.06
4490 5445 0.321671 AAGTGTAGCACTGTCCGCAT 59.678 50.000 2.31 0.00 44.62 4.73
4491 5446 0.319555 GAAGTGTAGCACTGTCCGCA 60.320 55.000 2.31 0.00 44.62 5.69
4493 5448 2.148916 TTGAAGTGTAGCACTGTCCG 57.851 50.000 2.31 0.00 44.62 4.79
4494 5449 3.664107 TGATTGAAGTGTAGCACTGTCC 58.336 45.455 2.31 0.00 44.62 4.02
4495 5450 4.310769 ACTGATTGAAGTGTAGCACTGTC 58.689 43.478 2.31 4.16 44.62 3.51
4496 5451 4.342862 ACTGATTGAAGTGTAGCACTGT 57.657 40.909 2.31 0.00 44.62 3.55
4497 5452 5.237127 TCAAACTGATTGAAGTGTAGCACTG 59.763 40.000 2.31 0.00 44.94 3.66
4553 5508 2.442188 CGTTCCGTGTTCTAGCGCC 61.442 63.158 2.29 0.00 0.00 6.53
4568 5523 2.308039 GCGAGACGAAAGGTGCGTT 61.308 57.895 0.00 0.00 42.77 4.84
4593 6899 2.166050 AGTAGCTCACTCAGATGTGCTG 59.834 50.000 11.47 0.00 46.15 4.41
4600 6906 0.523519 CACGCAGTAGCTCACTCAGA 59.476 55.000 0.00 0.00 41.61 3.27
4605 6911 2.734673 GCAGCACGCAGTAGCTCAC 61.735 63.158 0.00 0.00 41.61 3.51
4617 6954 2.362077 TCCTTTTTCTTTCTGGCAGCAC 59.638 45.455 10.34 0.00 0.00 4.40
4662 7006 1.046204 TGGCAATGCAACCATGTGAA 58.954 45.000 7.79 0.00 0.00 3.18
4696 7040 1.563410 CTTGAAAGGGAGAGGAGCCAT 59.437 52.381 0.00 0.00 0.00 4.40
4711 7055 2.367241 TGATGACGGACAGAACCTTGAA 59.633 45.455 0.00 0.00 0.00 2.69
4712 7056 1.967779 TGATGACGGACAGAACCTTGA 59.032 47.619 0.00 0.00 0.00 3.02
4798 7144 0.890996 GTCCAACCAGCCACTTCCTG 60.891 60.000 0.00 0.00 0.00 3.86
4828 7174 3.181575 CGAAAAGATTGTGAAAAACCGGC 59.818 43.478 0.00 0.00 0.00 6.13
4907 7265 4.180946 CCTCCTCCTCGACGCACG 62.181 72.222 0.00 0.00 44.09 5.34
4948 7306 0.954452 CTGCTTCGGTTTCCTTGCTT 59.046 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.