Multiple sequence alignment - TraesCS3B01G585300

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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 TraesCS3B01G585300 chr3B 100.000 9706 0 0 1 9706 812346009 812336304 0.000000e+00 17924.0
1 TraesCS3B01G585300 chr3B 88.398 181 18 3 2241 2421 610299841 610300018 2.120000e-51 215.0
2 TraesCS3B01G585300 chr3B 98.165 109 2 0 5546 5654 505264679 505264571 3.580000e-44 191.0
3 TraesCS3B01G585300 chr3D 95.251 5707 203 29 207 5888 604674837 604669174 0.000000e+00 8975.0
4 TraesCS3B01G585300 chr3D 92.849 1832 74 22 7316 9098 604667591 604665768 0.000000e+00 2604.0
5 TraesCS3B01G585300 chr3D 94.387 1443 51 5 5889 7302 604669108 604667667 0.000000e+00 2189.0
6 TraesCS3B01G585300 chr3D 89.637 193 20 0 9 201 604675069 604674877 7.530000e-61 246.0
7 TraesCS3B01G585300 chr3D 97.196 107 3 0 5547 5653 463716971 463716865 2.150000e-41 182.0
8 TraesCS3B01G585300 chr3A 94.894 5719 206 35 207 5888 734791691 734786022 0.000000e+00 8865.0
9 TraesCS3B01G585300 chr3A 94.343 3270 95 36 5889 9099 734785956 734782718 0.000000e+00 4931.0
10 TraesCS3B01G585300 chr3A 93.273 1977 106 11 3578 5548 182639374 182637419 0.000000e+00 2889.0
11 TraesCS3B01G585300 chr3A 90.196 561 36 12 5889 6444 182636932 182636386 0.000000e+00 713.0
12 TraesCS3B01G585300 chr3A 84.254 362 53 3 9099 9460 672184376 672184733 5.580000e-92 350.0
13 TraesCS3B01G585300 chr3A 92.683 164 11 1 5652 5814 182637420 182637257 1.630000e-57 235.0
14 TraesCS3B01G585300 chr3A 96.899 129 4 0 3407 3535 182639503 182639375 5.900000e-52 217.0
15 TraesCS3B01G585300 chr7A 81.350 563 75 17 9099 9639 165445521 165444967 1.940000e-116 431.0
16 TraesCS3B01G585300 chr7A 83.967 368 50 7 9093 9460 116008378 116008736 2.600000e-90 344.0
17 TraesCS3B01G585300 chrUn 81.287 513 74 17 9142 9640 320341619 320341115 7.060000e-106 396.0
18 TraesCS3B01G585300 chr1D 88.580 324 29 6 9145 9466 442153832 442153515 4.250000e-103 387.0
19 TraesCS3B01G585300 chr5B 83.721 387 51 8 9098 9479 325960719 325960340 1.200000e-93 355.0
20 TraesCS3B01G585300 chr5B 98.131 107 2 0 5547 5653 364132666 364132772 4.630000e-43 187.0
21 TraesCS3B01G585300 chr5B 90.351 114 11 0 5701 5814 9504756 9504643 6.070000e-32 150.0
22 TraesCS3B01G585300 chr2B 83.421 380 50 9 9142 9516 763804734 763804363 3.360000e-89 340.0
23 TraesCS3B01G585300 chr4A 79.231 520 77 16 9144 9639 540918905 540918393 5.620000e-87 333.0
24 TraesCS3B01G585300 chr4A 89.744 117 10 1 5699 5813 580297819 580297703 2.180000e-31 148.0
25 TraesCS3B01G585300 chr7D 83.425 362 51 8 9099 9460 41696438 41696790 2.610000e-85 327.0
26 TraesCS3B01G585300 chr7D 95.536 112 5 0 5545 5656 514658914 514658803 7.740000e-41 180.0
27 TraesCS3B01G585300 chr7B 83.196 363 46 9 9099 9460 147267702 147268050 1.570000e-82 318.0
28 TraesCS3B01G585300 chr7B 76.136 528 67 32 9165 9642 741476858 741477376 1.270000e-53 222.0
29 TraesCS3B01G585300 chr6A 99.083 109 1 0 5546 5654 502244335 502244227 7.690000e-46 196.0
30 TraesCS3B01G585300 chr6A 96.581 117 2 2 5540 5654 222554890 222555006 9.950000e-45 193.0
31 TraesCS3B01G585300 chr6A 92.241 116 9 0 5699 5814 536253932 536253817 2.170000e-36 165.0
32 TraesCS3B01G585300 chr6A 84.286 70 10 1 9029 9097 63207360 63207429 6.290000e-07 67.6
33 TraesCS3B01G585300 chr5A 75.589 467 68 27 9277 9706 534068412 534068869 1.290000e-43 189.0
34 TraesCS3B01G585300 chr2D 92.063 126 10 0 5547 5672 473292305 473292180 2.790000e-40 178.0
35 TraesCS3B01G585300 chr6D 93.103 116 8 0 5699 5814 389973699 389973584 4.660000e-38 171.0
36 TraesCS3B01G585300 chr1A 90.598 117 11 0 5698 5814 458567870 458567986 1.310000e-33 156.0
37 TraesCS3B01G585300 chr5D 90.351 114 9 2 5701 5814 9495434 9495323 2.180000e-31 148.0
38 TraesCS3B01G585300 chr6B 87.500 72 8 1 9029 9099 119242673 119242744 2.250000e-11 82.4


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 TraesCS3B01G585300 chr3B 812336304 812346009 9705 True 17924.0 17924 100.00000 1 9706 1 chr3B.!!$R2 9705
1 TraesCS3B01G585300 chr3D 604665768 604675069 9301 True 3503.5 8975 93.03100 9 9098 4 chr3D.!!$R2 9089
2 TraesCS3B01G585300 chr3A 734782718 734791691 8973 True 6898.0 8865 94.61850 207 9099 2 chr3A.!!$R2 8892
3 TraesCS3B01G585300 chr3A 182636386 182639503 3117 True 1013.5 2889 93.26275 3407 6444 4 chr3A.!!$R1 3037
4 TraesCS3B01G585300 chr7A 165444967 165445521 554 True 431.0 431 81.35000 9099 9639 1 chr7A.!!$R1 540
5 TraesCS3B01G585300 chrUn 320341115 320341619 504 True 396.0 396 81.28700 9142 9640 1 chrUn.!!$R1 498
6 TraesCS3B01G585300 chr4A 540918393 540918905 512 True 333.0 333 79.23100 9144 9639 1 chr4A.!!$R1 495
7 TraesCS3B01G585300 chr7B 741476858 741477376 518 False 222.0 222 76.13600 9165 9642 1 chr7B.!!$F2 477

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
104 105 0.102481 CACGTTATCCTCCTGGACGG 59.898 60.000 8.02 6.99 46.51 4.79 F
977 1024 0.169009 GTTCTTGACCTTGATGCGGC 59.831 55.000 0.00 0.00 0.00 6.53 F
1372 1432 2.027385 GGTGAGGCCTGAAATGGAATC 58.973 52.381 12.00 0.00 0.00 2.52 F
2722 2798 0.179062 AGTCATCTCCGCATTCAGGC 60.179 55.000 0.00 0.00 0.00 4.85 F
3239 3315 1.490490 AGAGCACCAAGAACCAGTTCA 59.510 47.619 12.76 0.00 41.84 3.18 F
4251 4332 0.605319 CCGTGGTGCTATTGGTGTGT 60.605 55.000 0.00 0.00 0.00 3.72 F
4635 4719 2.039084 ACTTTACCTTCTGCCACTCCTG 59.961 50.000 0.00 0.00 0.00 3.86 F
5735 5822 1.728971 CGCGAGGATGGCAATATCTTC 59.271 52.381 0.00 0.00 41.24 2.87 F
5950 6294 1.416401 AGTGGGTGTTGATCTGTCGTT 59.584 47.619 0.00 0.00 0.00 3.85 F
7283 7661 3.365265 GTTGGCCTGGCACCTTCG 61.365 66.667 22.05 0.00 0.00 3.79 F
8085 8529 1.831580 GCAAGACCAAGATGAAGCCT 58.168 50.000 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1416 0.106519 CCCGATTCCATTTCAGGCCT 60.107 55.000 0.00 0.00 0.00 5.19 R
2701 2777 1.485397 CTGAATGCGGAGATGACTCG 58.515 55.000 0.00 0.00 43.44 4.18 R
3137 3213 0.107456 CCCTGGAATCACGATGGAGG 59.893 60.000 0.00 0.00 0.00 4.30 R
3677 3753 1.004745 GCCCCCTCATTCTCAAAGTCA 59.995 52.381 0.00 0.00 0.00 3.41 R
5059 5144 1.614317 CCTTGGACACCATTGGACTCC 60.614 57.143 10.37 12.36 32.01 3.85 R
5685 5772 0.684535 TTGCCATCCTGACGTCAGAA 59.315 50.000 40.21 27.12 46.59 3.02 R
5918 6262 2.004120 ACCCACTGAACCACACCCA 61.004 57.895 0.00 0.00 0.00 4.51 R
6763 7137 3.055891 GTGCAGGGAGGTATTTTTGCATT 60.056 43.478 0.03 0.00 42.64 3.56 R
7758 8201 0.179000 ACCTGGAGCATAAGAAGGCG 59.821 55.000 0.00 0.00 37.52 5.52 R
8118 8562 0.033504 TGACTCTGCCAAGGACGTTC 59.966 55.000 0.00 0.00 0.00 3.95 R
9115 9615 0.099791 AAAACTCCCGTTGCAACACG 59.900 50.000 28.01 16.67 40.02 4.49 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
42 43 4.397417 GCAGAGTTCAGATTTGTAAGGCAT 59.603 41.667 0.00 0.00 0.00 4.40
50 51 7.333528 TCAGATTTGTAAGGCATTGGTTATC 57.666 36.000 0.00 0.00 0.00 1.75
55 56 4.276642 TGTAAGGCATTGGTTATCATGCA 58.723 39.130 6.48 0.00 41.44 3.96
58 59 3.098377 AGGCATTGGTTATCATGCACAA 58.902 40.909 6.48 0.00 41.44 3.33
87 88 1.526917 CCATCCTCCCATTCCGCAC 60.527 63.158 0.00 0.00 0.00 5.34
99 100 0.174845 TTCCGCACGTTATCCTCCTG 59.825 55.000 0.00 0.00 0.00 3.86
104 105 0.102481 CACGTTATCCTCCTGGACGG 59.898 60.000 8.02 6.99 46.51 4.79
109 110 3.029570 GTTATCCTCCTGGACGGTTACT 58.970 50.000 10.66 1.06 46.51 2.24
142 143 0.730265 TTTCCATTTTCGATCCCGCG 59.270 50.000 0.00 0.00 35.37 6.46
144 145 2.327940 CATTTTCGATCCCGCGCC 59.672 61.111 0.00 0.00 35.37 6.53
162 163 1.704082 CCCTCTGGTCCCCTCTACA 59.296 63.158 0.00 0.00 0.00 2.74
189 190 3.066203 ACTCCAACAAAGTTAAGTTGCGG 59.934 43.478 13.05 10.50 42.77 5.69
194 195 3.638484 ACAAAGTTAAGTTGCGGAATGC 58.362 40.909 0.00 0.00 46.70 3.56
203 204 2.892425 GCGGAATGCGGGTGAGAG 60.892 66.667 0.00 0.00 0.00 3.20
204 205 2.892640 CGGAATGCGGGTGAGAGA 59.107 61.111 0.00 0.00 0.00 3.10
205 206 1.227089 CGGAATGCGGGTGAGAGAG 60.227 63.158 0.00 0.00 0.00 3.20
246 281 7.601705 AAATAGTATATGCTTGCACCCATTT 57.398 32.000 0.00 0.00 0.00 2.32
247 282 7.601705 AATAGTATATGCTTGCACCCATTTT 57.398 32.000 0.00 0.00 0.00 1.82
251 287 2.459060 TGCTTGCACCCATTTTGATG 57.541 45.000 0.00 0.00 0.00 3.07
262 299 4.165779 CCCATTTTGATGTAAACTCGTGC 58.834 43.478 0.00 0.00 0.00 5.34
273 310 6.102006 TGTAAACTCGTGCTTATTATGTGC 57.898 37.500 0.00 0.00 0.00 4.57
275 312 5.621197 AAACTCGTGCTTATTATGTGCAA 57.379 34.783 0.00 0.00 38.50 4.08
294 331 1.132500 ATGATTTCCCTCGACCCCTC 58.868 55.000 0.00 0.00 0.00 4.30
339 377 4.558898 CGATCCTCTTGAATAGTTACCCCG 60.559 50.000 0.00 0.00 0.00 5.73
344 382 0.176219 TGAATAGTTACCCCGCACGG 59.824 55.000 1.02 1.02 0.00 4.94
374 412 1.468914 GTTCCATTTCGCCTCCAACTC 59.531 52.381 0.00 0.00 0.00 3.01
376 414 1.351017 TCCATTTCGCCTCCAACTCTT 59.649 47.619 0.00 0.00 0.00 2.85
387 425 3.118223 CCTCCAACTCTTCACCTTATCCC 60.118 52.174 0.00 0.00 0.00 3.85
394 432 4.037927 CTCTTCACCTTATCCCCCACTAA 58.962 47.826 0.00 0.00 0.00 2.24
396 434 2.112998 TCACCTTATCCCCCACTAACG 58.887 52.381 0.00 0.00 0.00 3.18
401 439 3.455543 CCTTATCCCCCACTAACGGTAAA 59.544 47.826 0.00 0.00 0.00 2.01
427 465 5.062934 CCAACGAATTTAAGTAGCGACATGA 59.937 40.000 0.00 0.00 0.00 3.07
440 479 1.061131 CGACATGATGGTCAGTTTCGC 59.939 52.381 0.00 0.00 37.66 4.70
460 503 3.188786 GAGCGTGCGACCCATGAC 61.189 66.667 0.00 0.00 31.89 3.06
461 504 4.760047 AGCGTGCGACCCATGACC 62.760 66.667 0.00 0.00 31.89 4.02
462 505 4.760047 GCGTGCGACCCATGACCT 62.760 66.667 0.00 0.00 31.89 3.85
463 506 2.047274 CGTGCGACCCATGACCTT 60.047 61.111 0.00 0.00 31.89 3.50
465 508 1.003839 GTGCGACCCATGACCTTCA 60.004 57.895 0.00 0.00 0.00 3.02
485 528 3.417690 ACGAGAGAGCGTGGTTATTAC 57.582 47.619 0.00 0.00 43.79 1.89
491 534 2.424601 AGAGCGTGGTTATTACGTAGCA 59.575 45.455 0.00 0.00 43.09 3.49
492 535 2.787680 GAGCGTGGTTATTACGTAGCAG 59.212 50.000 0.00 0.00 43.09 4.24
510 553 4.403137 CATGGTTGGGCACGTGCG 62.403 66.667 32.35 13.60 43.26 5.34
518 561 4.307908 GGCACGTGCGCTCGTTTT 62.308 61.111 32.17 11.14 42.27 2.43
527 570 2.712466 GTGCGCTCGTTTTCAACTAAAC 59.288 45.455 9.73 0.00 35.23 2.01
530 573 4.270566 TGCGCTCGTTTTCAACTAAACTAA 59.729 37.500 9.73 0.00 36.18 2.24
536 579 7.005945 GCTCGTTTTCAACTAAACTAATTACGC 59.994 37.037 0.00 0.00 36.18 4.42
562 605 7.597743 CCTTGATATCATATTTTGGCTTTGAGC 59.402 37.037 6.17 0.00 41.46 4.26
577 620 5.511571 GCTTTGAGCCCTAATAAATCGAAC 58.488 41.667 0.00 0.00 34.48 3.95
582 625 6.411376 TGAGCCCTAATAAATCGAACAAAGA 58.589 36.000 0.00 0.00 0.00 2.52
586 629 6.511929 GCCCTAATAAATCGAACAAAGAGAGC 60.512 42.308 0.00 0.00 0.00 4.09
587 630 6.538742 CCCTAATAAATCGAACAAAGAGAGCA 59.461 38.462 0.00 0.00 0.00 4.26
588 631 7.402640 CCTAATAAATCGAACAAAGAGAGCAC 58.597 38.462 0.00 0.00 0.00 4.40
589 632 6.801539 AATAAATCGAACAAAGAGAGCACA 57.198 33.333 0.00 0.00 0.00 4.57
590 633 6.801539 ATAAATCGAACAAAGAGAGCACAA 57.198 33.333 0.00 0.00 0.00 3.33
591 634 5.695851 AAATCGAACAAAGAGAGCACAAT 57.304 34.783 0.00 0.00 0.00 2.71
592 635 6.801539 AAATCGAACAAAGAGAGCACAATA 57.198 33.333 0.00 0.00 0.00 1.90
593 636 5.786401 ATCGAACAAAGAGAGCACAATAC 57.214 39.130 0.00 0.00 0.00 1.89
594 637 4.883083 TCGAACAAAGAGAGCACAATACT 58.117 39.130 0.00 0.00 0.00 2.12
595 638 6.020971 TCGAACAAAGAGAGCACAATACTA 57.979 37.500 0.00 0.00 0.00 1.82
596 639 5.862323 TCGAACAAAGAGAGCACAATACTAC 59.138 40.000 0.00 0.00 0.00 2.73
597 640 5.633601 CGAACAAAGAGAGCACAATACTACA 59.366 40.000 0.00 0.00 0.00 2.74
607 650 7.865707 AGAGCACAATACTACACTTGAAAAAG 58.134 34.615 0.00 0.00 0.00 2.27
609 652 8.220755 AGCACAATACTACACTTGAAAAAGAA 57.779 30.769 0.00 0.00 0.00 2.52
619 662 6.887368 ACACTTGAAAAAGAAGTTTTGTTGC 58.113 32.000 0.00 0.00 39.60 4.17
627 670 9.906111 GAAAAAGAAGTTTTGTTGCATAGAAAG 57.094 29.630 0.00 0.00 39.60 2.62
631 674 4.874970 AGTTTTGTTGCATAGAAAGCCTG 58.125 39.130 0.00 0.00 0.00 4.85
650 696 3.353557 CTGAGGCTGTACTACACTACCA 58.646 50.000 0.00 0.00 0.00 3.25
869 916 4.875713 CGCCCCGAATTCCCCCAG 62.876 72.222 0.00 0.00 0.00 4.45
975 1022 1.428448 TCGTTCTTGACCTTGATGCG 58.572 50.000 0.00 0.00 0.00 4.73
977 1024 0.169009 GTTCTTGACCTTGATGCGGC 59.831 55.000 0.00 0.00 0.00 6.53
1319 1379 2.603560 CGTTGCTCCTCGTATCTTTTCC 59.396 50.000 0.00 0.00 0.00 3.13
1329 1389 3.055963 TCGTATCTTTTCCCCGTGCTTTA 60.056 43.478 0.00 0.00 0.00 1.85
1356 1416 2.747460 GCATTGCTGCTCCGGTGA 60.747 61.111 7.92 0.00 45.32 4.02
1372 1432 2.027385 GGTGAGGCCTGAAATGGAATC 58.973 52.381 12.00 0.00 0.00 2.52
1672 1732 4.610945 CTTTCAATCAGCAACTCCGTTTT 58.389 39.130 0.00 0.00 0.00 2.43
1682 1742 2.734606 CAACTCCGTTTTGCTCGTATGA 59.265 45.455 0.00 0.00 0.00 2.15
1699 1759 3.928727 ATGACATTGCTTCCACTGTTG 57.071 42.857 0.00 0.00 35.31 3.33
1700 1760 2.653726 TGACATTGCTTCCACTGTTGT 58.346 42.857 0.00 0.00 35.31 3.32
1701 1761 3.814625 TGACATTGCTTCCACTGTTGTA 58.185 40.909 0.00 0.00 35.31 2.41
1702 1762 3.563808 TGACATTGCTTCCACTGTTGTAC 59.436 43.478 0.00 0.00 35.31 2.90
1761 1821 9.784531 AGTTATGACATATTAGAGGTTCCATTG 57.215 33.333 0.00 0.00 0.00 2.82
1778 1838 7.148069 GGTTCCATTGTTCCTATTCTAAACAGG 60.148 40.741 0.00 0.00 34.64 4.00
1798 1858 6.123651 ACAGGTAAATTTGTGTGAACTGGTA 58.876 36.000 7.64 0.00 0.00 3.25
1876 1936 6.758416 TGGAAGTGATCTCATCTTAAATGACG 59.242 38.462 0.00 0.00 0.00 4.35
2024 2096 3.713003 TGTCTAGGTGGAGATGTGTCAT 58.287 45.455 0.00 0.00 0.00 3.06
2101 2173 4.675063 ATGGTTGAGTTAAAGTCCCCAT 57.325 40.909 0.00 0.00 0.00 4.00
2503 2579 7.621428 AACCATCAGTTCAACATAGATCAAG 57.379 36.000 0.00 0.00 30.99 3.02
2722 2798 0.179062 AGTCATCTCCGCATTCAGGC 60.179 55.000 0.00 0.00 0.00 4.85
2758 2834 9.762381 TTATCCCTCCTTTTAATTGTTGTATGT 57.238 29.630 0.00 0.00 0.00 2.29
2968 3044 7.041303 AGCATTGATAGCTTGATGTCAGTATTG 60.041 37.037 0.00 0.00 39.87 1.90
2969 3045 7.255035 GCATTGATAGCTTGATGTCAGTATTGT 60.255 37.037 0.00 0.00 0.00 2.71
2970 3046 9.264719 CATTGATAGCTTGATGTCAGTATTGTA 57.735 33.333 0.00 0.00 0.00 2.41
2971 3047 8.877808 TTGATAGCTTGATGTCAGTATTGTAG 57.122 34.615 0.00 0.00 0.00 2.74
2972 3048 6.925718 TGATAGCTTGATGTCAGTATTGTAGC 59.074 38.462 0.00 0.00 0.00 3.58
2973 3049 5.089970 AGCTTGATGTCAGTATTGTAGCA 57.910 39.130 0.00 0.00 0.00 3.49
2974 3050 5.491070 AGCTTGATGTCAGTATTGTAGCAA 58.509 37.500 0.00 0.00 0.00 3.91
3022 3098 6.317789 TCAGACTGATTTGAATGGTTGAAC 57.682 37.500 0.00 0.00 0.00 3.18
3043 3119 1.802960 CCTCTTTGTGCTGCTGTAGTG 59.197 52.381 0.00 0.00 0.00 2.74
3059 3135 3.991773 TGTAGTGCATGTAGTTTCGAACC 59.008 43.478 0.00 0.00 0.00 3.62
3060 3136 3.120321 AGTGCATGTAGTTTCGAACCA 57.880 42.857 0.00 0.00 0.00 3.67
3065 3141 5.523916 GTGCATGTAGTTTCGAACCATCTAT 59.476 40.000 0.00 0.00 0.00 1.98
3066 3142 5.523552 TGCATGTAGTTTCGAACCATCTATG 59.476 40.000 0.00 0.45 0.00 2.23
3137 3213 5.633830 TCTCCATTCTTCTGATGTTTTGC 57.366 39.130 0.00 0.00 0.00 3.68
3138 3214 4.460382 TCTCCATTCTTCTGATGTTTTGCC 59.540 41.667 0.00 0.00 0.00 4.52
3182 3258 3.864789 ATTTCCGAGGATATGCAACCT 57.135 42.857 9.65 9.65 39.41 3.50
3200 3276 3.053826 ACCTGGAACCTTAAGTCCTGTT 58.946 45.455 12.11 4.50 0.00 3.16
3239 3315 1.490490 AGAGCACCAAGAACCAGTTCA 59.510 47.619 12.76 0.00 41.84 3.18
3373 3449 3.818787 GCGTCCCATGGCTGCAAG 61.819 66.667 6.09 0.00 0.00 4.01
3719 3795 1.688772 ATTCAGCTCATGTGGCATCC 58.311 50.000 13.76 0.00 0.00 3.51
3834 3913 4.638421 GCACTATGCATGTTAAAGGGTGTA 59.362 41.667 10.16 0.00 44.26 2.90
3943 4022 5.586243 GGTGCTTAATGACTGAATTCTAGCA 59.414 40.000 7.05 2.34 36.12 3.49
4136 4215 9.567848 TTTTAATTTACCATCGAAGATCTTTGC 57.432 29.630 16.79 1.14 45.12 3.68
4241 4322 4.666253 AATGCTGCCCGTGGTGCT 62.666 61.111 0.00 0.00 0.00 4.40
4244 4325 2.438434 GCTGCCCGTGGTGCTATT 60.438 61.111 0.00 0.00 0.00 1.73
4251 4332 0.605319 CCGTGGTGCTATTGGTGTGT 60.605 55.000 0.00 0.00 0.00 3.72
4257 4338 4.217550 GTGGTGCTATTGGTGTGTAATTGT 59.782 41.667 0.00 0.00 0.00 2.71
4280 4361 9.524106 TTGTACATATCGTAGTTATCTGTTTGG 57.476 33.333 0.00 0.00 0.00 3.28
4282 4363 5.989777 ACATATCGTAGTTATCTGTTTGGCC 59.010 40.000 0.00 0.00 0.00 5.36
4289 4370 3.834231 AGTTATCTGTTTGGCCTGCAAAT 59.166 39.130 3.32 0.00 0.00 2.32
4290 4371 2.754946 ATCTGTTTGGCCTGCAAATG 57.245 45.000 3.32 0.00 0.00 2.32
4300 4381 2.543641 GCCTGCAAATGGCTGTAATTC 58.456 47.619 8.16 0.00 46.38 2.17
4381 4462 6.463755 GCCCTTTTTGGAAGAAAATAGAACCA 60.464 38.462 0.00 0.00 38.35 3.67
4434 4515 4.605183 TCCTTCTTGAAAAACCAGGTTCA 58.395 39.130 4.93 0.00 31.99 3.18
4475 4559 5.253330 AGTTGGTATAATGGACCTGTTGTG 58.747 41.667 0.00 0.00 37.88 3.33
4476 4560 4.919774 TGGTATAATGGACCTGTTGTGT 57.080 40.909 0.00 0.00 37.88 3.72
4477 4561 4.839121 TGGTATAATGGACCTGTTGTGTC 58.161 43.478 0.00 0.00 37.88 3.67
4569 4653 6.563010 GCATGTCTAATAAGCACGATGAAGAC 60.563 42.308 0.00 0.00 34.18 3.01
4575 4659 3.885484 AAGCACGATGAAGACAAGTTG 57.115 42.857 0.00 0.00 0.00 3.16
4635 4719 2.039084 ACTTTACCTTCTGCCACTCCTG 59.961 50.000 0.00 0.00 0.00 3.86
5059 5144 5.869344 TGTAGAAGATGTTGATGACTTTCCG 59.131 40.000 0.00 0.00 0.00 4.30
5089 5174 6.226787 CAATGGTGTCCAAGGAGATATACTC 58.773 44.000 0.00 0.00 39.95 2.59
5090 5175 4.878968 TGGTGTCCAAGGAGATATACTCA 58.121 43.478 0.00 0.00 46.54 3.41
5146 5231 4.216257 GCCTCAGTTGAATTTGAAGCTACA 59.784 41.667 0.00 0.00 30.10 2.74
5182 5267 6.752168 CAGTTTTGGAATGTCTCCTGATTTT 58.248 36.000 0.00 0.00 45.64 1.82
5735 5822 1.728971 CGCGAGGATGGCAATATCTTC 59.271 52.381 0.00 0.00 41.24 2.87
5918 6262 3.251004 GCTGTGAATTCGAAACCTTGAGT 59.749 43.478 0.00 0.00 0.00 3.41
5950 6294 1.416401 AGTGGGTGTTGATCTGTCGTT 59.584 47.619 0.00 0.00 0.00 3.85
6042 6386 6.417258 TGATCCTTGAGAAAACAGATGCATA 58.583 36.000 0.00 0.00 0.00 3.14
6073 6417 6.147164 TCGTCACCTCATTGTTTTCAGTAATC 59.853 38.462 0.00 0.00 0.00 1.75
6117 6461 9.958180 TCTCCTTATTAACTCAAATCATTGTCA 57.042 29.630 0.00 0.00 37.79 3.58
6302 6648 5.936372 TCAAGTCACCATTTCATCTTCTCTG 59.064 40.000 0.00 0.00 0.00 3.35
6347 6693 8.988934 TGTGAAAACTTAGAGCATACTAAACTG 58.011 33.333 0.00 0.00 32.95 3.16
6400 6746 6.570378 GCATTTGAGGCTTCAAGCTTAAGTAA 60.570 38.462 9.83 0.00 43.76 2.24
6406 6755 6.476378 AGGCTTCAAGCTTAAGTAATGAGAA 58.524 36.000 9.83 0.00 41.99 2.87
6468 6842 6.183360 GGGTCTCATGTGACAAATTGATAGTG 60.183 42.308 24.84 0.00 38.61 2.74
6471 6845 4.094739 TCATGTGACAAATTGATAGTGCCG 59.905 41.667 0.00 0.00 0.00 5.69
6718 7092 6.040209 TGATGATTTCCTTTTGTCATTGGG 57.960 37.500 0.00 0.00 31.86 4.12
7134 7511 4.471904 TTGCTGGTACCTGAATACTCTG 57.528 45.455 21.97 0.00 0.00 3.35
7283 7661 3.365265 GTTGGCCTGGCACCTTCG 61.365 66.667 22.05 0.00 0.00 3.79
7399 7840 8.796475 AGTGTTGCATGTTTCTTTCTATGTATT 58.204 29.630 0.00 0.00 0.00 1.89
7723 8166 4.081917 ACACAAACCCGCCTATTTATTTGG 60.082 41.667 0.00 0.00 32.58 3.28
7866 8309 6.015772 GGTATTTCTAGCACCCTTGAACAAAA 60.016 38.462 0.00 0.00 33.58 2.44
7904 8348 7.267128 TGGCATGATGATTTTGTAAGAAATCC 58.733 34.615 0.00 0.00 42.59 3.01
7918 8362 7.885297 TGTAAGAAATCCTTTTTCATGAGGTG 58.115 34.615 0.00 0.00 36.34 4.00
8085 8529 1.831580 GCAAGACCAAGATGAAGCCT 58.168 50.000 0.00 0.00 0.00 4.58
8118 8562 1.224075 CGCAGCTATCAACATCTGGG 58.776 55.000 0.00 0.00 34.14 4.45
8239 8683 0.825010 CCAGCAACCAAGGAACAGCT 60.825 55.000 0.00 0.00 0.00 4.24
8340 8784 2.109126 GGAGGGCAACGACATCAGC 61.109 63.158 0.00 0.00 37.60 4.26
8355 8799 3.706373 AGCGCCTGGTTCACGGAT 61.706 61.111 2.29 0.00 0.00 4.18
8368 8812 3.770040 CGGATGGCCTGGACGACA 61.770 66.667 3.32 0.00 0.00 4.35
8737 9183 1.229927 GTTGCCCATGCTCCCCATA 59.770 57.895 0.00 0.00 38.71 2.74
8872 9353 8.630054 AAGGACAGTGCATGTTATTTAACTTA 57.370 30.769 0.00 0.00 44.17 2.24
8873 9354 8.807948 AGGACAGTGCATGTTATTTAACTTAT 57.192 30.769 0.00 0.00 44.17 1.73
8874 9355 8.677300 AGGACAGTGCATGTTATTTAACTTATG 58.323 33.333 0.00 0.66 44.17 1.90
8899 9380 9.012161 TGATTGTTCATCTGAATATTTGTCACA 57.988 29.630 0.00 0.00 36.33 3.58
8900 9381 9.844790 GATTGTTCATCTGAATATTTGTCACAA 57.155 29.630 0.00 0.00 36.33 3.33
8903 9384 9.628746 TGTTCATCTGAATATTTGTCACAAATG 57.371 29.630 23.60 8.37 36.33 2.32
8940 9436 7.094549 TGGATAAATAGTTACAAGTGCACAACC 60.095 37.037 21.04 2.00 0.00 3.77
8941 9437 7.094549 GGATAAATAGTTACAAGTGCACAACCA 60.095 37.037 21.04 3.92 0.00 3.67
8948 9444 0.756442 AAGTGCACAACCACATGGCT 60.756 50.000 21.04 0.00 38.18 4.75
8949 9445 1.007038 GTGCACAACCACATGGCTG 60.007 57.895 13.17 0.00 39.32 4.85
8969 9465 6.040504 TGGCTGTACTAACATCTACAGTATGG 59.959 42.308 6.67 0.00 41.31 2.74
8970 9466 6.040616 GGCTGTACTAACATCTACAGTATGGT 59.959 42.308 6.67 0.00 41.31 3.55
8971 9467 7.140048 GCTGTACTAACATCTACAGTATGGTC 58.860 42.308 6.67 0.00 41.31 4.02
8972 9468 7.201794 GCTGTACTAACATCTACAGTATGGTCA 60.202 40.741 6.67 0.00 41.31 4.02
8973 9469 7.993101 TGTACTAACATCTACAGTATGGTCAC 58.007 38.462 0.00 0.00 43.62 3.67
8974 9470 7.612633 TGTACTAACATCTACAGTATGGTCACA 59.387 37.037 0.00 0.00 43.62 3.58
8977 9473 8.540388 ACTAACATCTACAGTATGGTCACATTT 58.460 33.333 0.00 0.00 43.62 2.32
8978 9474 7.615582 AACATCTACAGTATGGTCACATTTG 57.384 36.000 0.00 0.00 43.62 2.32
8979 9475 6.711277 ACATCTACAGTATGGTCACATTTGT 58.289 36.000 0.00 0.00 43.62 2.83
8980 9476 7.168219 ACATCTACAGTATGGTCACATTTGTT 58.832 34.615 0.00 0.00 43.62 2.83
9016 9516 9.736414 AGGAAAAGGGTAAAAAGACTAGAATAC 57.264 33.333 0.00 0.00 0.00 1.89
9031 9531 1.476488 GAATACGGGTTTGCAATGGCT 59.524 47.619 0.00 0.00 41.91 4.75
9056 9556 6.952773 ATAGTTTGCACAACTTTTCTACCA 57.047 33.333 16.02 1.29 0.00 3.25
9058 9558 5.591099 AGTTTGCACAACTTTTCTACCATG 58.409 37.500 8.03 0.00 0.00 3.66
9062 9562 4.642437 TGCACAACTTTTCTACCATGACAA 59.358 37.500 0.00 0.00 0.00 3.18
9160 9660 7.905265 TCTTTTTCATAATCTTCAATGGCCAA 58.095 30.769 10.96 0.00 0.00 4.52
9182 9685 3.762288 AGATCACATTTTGCTGCATCACT 59.238 39.130 1.84 0.00 0.00 3.41
9194 9697 4.343239 TGCTGCATCACTGAGATACACTAT 59.657 41.667 0.00 0.00 34.43 2.12
9195 9698 4.922692 GCTGCATCACTGAGATACACTATC 59.077 45.833 0.00 0.00 34.43 2.08
9253 9794 9.552114 TTTTTAAACTCGTGAACGTATTTGAAA 57.448 25.926 14.25 14.25 40.80 2.69
9254 9795 9.719279 TTTTAAACTCGTGAACGTATTTGAAAT 57.281 25.926 14.25 0.00 40.80 2.17
9255 9796 9.719279 TTTAAACTCGTGAACGTATTTGAAATT 57.281 25.926 13.51 0.00 40.80 1.82
9256 9797 7.603297 AAACTCGTGAACGTATTTGAAATTG 57.397 32.000 0.00 0.00 40.80 2.32
9257 9798 5.144359 ACTCGTGAACGTATTTGAAATTGC 58.856 37.500 0.00 0.00 40.80 3.56
9258 9799 4.145276 TCGTGAACGTATTTGAAATTGCG 58.855 39.130 11.16 11.16 40.80 4.85
9259 9800 4.084485 TCGTGAACGTATTTGAAATTGCGA 60.084 37.500 16.98 6.39 40.80 5.10
9260 9801 4.257447 CGTGAACGTATTTGAAATTGCGAG 59.743 41.667 16.98 0.82 34.11 5.03
9267 9808 6.804295 ACGTATTTGAAATTGCGAGCATTTTA 59.196 30.769 16.98 5.91 32.06 1.52
9420 9989 7.370383 TCTTGAATTGGCAAACATTTCTAGAC 58.630 34.615 16.18 0.00 41.64 2.59
9425 9994 4.326826 TGGCAAACATTTCTAGACTGGAG 58.673 43.478 0.00 0.00 0.00 3.86
9454 10023 4.764172 TGTTTTGGAAATTGGTGGAACAG 58.236 39.130 0.00 0.00 41.80 3.16
9529 10138 8.523464 CAACGAACATTTTAGAAAGTCACAAAG 58.477 33.333 0.00 0.00 0.00 2.77
9534 10144 9.788960 AACATTTTAGAAAGTCACAAAGAGTTC 57.211 29.630 0.00 0.00 38.96 3.01
9655 10266 7.601705 AAAATCATATTCCCGATCATTTGGT 57.398 32.000 0.00 0.00 0.00 3.67
9656 10267 7.601705 AAATCATATTCCCGATCATTTGGTT 57.398 32.000 0.00 0.00 0.00 3.67
9657 10268 7.601705 AATCATATTCCCGATCATTTGGTTT 57.398 32.000 0.00 0.00 0.00 3.27
9658 10269 7.601705 ATCATATTCCCGATCATTTGGTTTT 57.398 32.000 0.00 0.00 0.00 2.43
9659 10270 7.038154 TCATATTCCCGATCATTTGGTTTTC 57.962 36.000 0.00 0.00 0.00 2.29
9660 10271 3.840890 TTCCCGATCATTTGGTTTTCG 57.159 42.857 0.00 0.00 0.00 3.46
9661 10272 3.060736 TCCCGATCATTTGGTTTTCGA 57.939 42.857 0.00 0.00 31.74 3.71
9662 10273 3.413327 TCCCGATCATTTGGTTTTCGAA 58.587 40.909 0.00 0.00 31.74 3.71
9663 10274 3.821600 TCCCGATCATTTGGTTTTCGAAA 59.178 39.130 6.47 6.47 31.74 3.46
9664 10275 4.461081 TCCCGATCATTTGGTTTTCGAAAT 59.539 37.500 12.12 0.00 38.43 2.17
9665 10276 5.047660 TCCCGATCATTTGGTTTTCGAAATT 60.048 36.000 12.12 0.00 36.38 1.82
9666 10277 5.637387 CCCGATCATTTGGTTTTCGAAATTT 59.363 36.000 12.12 0.00 36.38 1.82
9667 10278 6.183360 CCCGATCATTTGGTTTTCGAAATTTC 60.183 38.462 12.12 8.20 36.38 2.17
9668 10279 6.364706 CCGATCATTTGGTTTTCGAAATTTCA 59.635 34.615 17.99 7.72 36.38 2.69
9669 10280 7.095857 CCGATCATTTGGTTTTCGAAATTTCAA 60.096 33.333 17.99 12.94 36.38 2.69
9670 10281 8.272176 CGATCATTTGGTTTTCGAAATTTCAAA 58.728 29.630 23.26 23.26 36.38 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.016706 CGGCAACCCTCGGTCCTT 62.017 66.667 0.00 0.00 33.12 3.36
7 8 4.785453 CTCTGCCCGGCAACCCTC 62.785 72.222 14.45 0.00 38.41 4.30
15 16 1.089920 CAAATCTGAACTCTGCCCGG 58.910 55.000 0.00 0.00 0.00 5.73
19 20 3.753272 TGCCTTACAAATCTGAACTCTGC 59.247 43.478 0.00 0.00 0.00 4.26
50 51 4.976224 TGGAGAGAAATCATTGTGCATG 57.024 40.909 0.00 0.00 0.00 4.06
55 56 4.141298 GGGAGGATGGAGAGAAATCATTGT 60.141 45.833 0.00 0.00 0.00 2.71
58 59 3.673343 TGGGAGGATGGAGAGAAATCAT 58.327 45.455 0.00 0.00 0.00 2.45
69 70 1.526917 GTGCGGAATGGGAGGATGG 60.527 63.158 0.00 0.00 0.00 3.51
99 100 0.389426 ACACGCATCAGTAACCGTCC 60.389 55.000 0.00 0.00 0.00 4.79
104 105 4.403453 GAAAATGGACACGCATCAGTAAC 58.597 43.478 0.00 0.00 0.00 2.50
109 110 1.902938 TGGAAAATGGACACGCATCA 58.097 45.000 0.00 0.00 0.00 3.07
162 163 6.183360 GCAACTTAACTTTGTTGGAGTTACCT 60.183 38.462 7.75 0.00 42.48 3.08
171 172 4.085107 GCATTCCGCAACTTAACTTTGTTG 60.085 41.667 0.00 0.00 44.33 3.33
173 174 3.638484 GCATTCCGCAACTTAACTTTGT 58.362 40.909 0.00 0.00 41.79 2.83
189 190 0.537188 TTCCTCTCTCACCCGCATTC 59.463 55.000 0.00 0.00 0.00 2.67
194 195 5.467063 GCTTATTAATTTCCTCTCTCACCCG 59.533 44.000 0.00 0.00 0.00 5.28
196 197 6.281405 TCGCTTATTAATTTCCTCTCTCACC 58.719 40.000 0.00 0.00 0.00 4.02
225 260 6.125719 TCAAAATGGGTGCAAGCATATACTA 58.874 36.000 0.00 0.00 34.77 1.82
227 262 5.261209 TCAAAATGGGTGCAAGCATATAC 57.739 39.130 0.00 0.00 34.77 1.47
228 263 5.363292 ACATCAAAATGGGTGCAAGCATATA 59.637 36.000 0.00 0.00 37.19 0.86
229 264 4.162698 ACATCAAAATGGGTGCAAGCATAT 59.837 37.500 0.00 0.00 37.19 1.78
230 265 3.514706 ACATCAAAATGGGTGCAAGCATA 59.485 39.130 0.00 0.00 37.19 3.14
231 266 2.303600 ACATCAAAATGGGTGCAAGCAT 59.696 40.909 0.00 0.00 37.19 3.79
232 267 1.693062 ACATCAAAATGGGTGCAAGCA 59.307 42.857 0.00 0.00 37.19 3.91
238 273 5.153513 CACGAGTTTACATCAAAATGGGTG 58.846 41.667 0.00 0.00 37.19 4.61
246 281 8.387354 CACATAATAAGCACGAGTTTACATCAA 58.613 33.333 0.00 0.00 0.00 2.57
247 282 7.465379 GCACATAATAAGCACGAGTTTACATCA 60.465 37.037 0.00 0.00 0.00 3.07
251 287 6.102006 TGCACATAATAAGCACGAGTTTAC 57.898 37.500 0.00 0.00 32.55 2.01
262 299 7.041167 TCGAGGGAAATCATTGCACATAATAAG 60.041 37.037 0.00 0.00 0.00 1.73
273 310 1.212935 AGGGGTCGAGGGAAATCATTG 59.787 52.381 0.00 0.00 0.00 2.82
275 312 1.132500 GAGGGGTCGAGGGAAATCAT 58.868 55.000 0.00 0.00 0.00 2.45
294 331 4.260375 CGAGGATTCAAGGCGAATAACAAG 60.260 45.833 0.00 0.00 44.65 3.16
339 377 2.953020 TGGAACATAAAAATGCCGTGC 58.047 42.857 0.00 0.00 0.00 5.34
374 412 3.431766 CGTTAGTGGGGGATAAGGTGAAG 60.432 52.174 0.00 0.00 0.00 3.02
376 414 2.112998 CGTTAGTGGGGGATAAGGTGA 58.887 52.381 0.00 0.00 0.00 4.02
387 425 2.674357 CGTTGGATTTACCGTTAGTGGG 59.326 50.000 0.00 0.00 42.61 4.61
394 432 6.806388 ACTTAAATTCGTTGGATTTACCGT 57.194 33.333 0.00 0.00 42.61 4.83
396 434 6.903479 CGCTACTTAAATTCGTTGGATTTACC 59.097 38.462 0.00 0.00 39.54 2.85
401 439 5.172934 TGTCGCTACTTAAATTCGTTGGAT 58.827 37.500 0.00 0.00 0.00 3.41
427 465 0.737715 GCTCTCGCGAAACTGACCAT 60.738 55.000 11.33 0.00 0.00 3.55
440 479 4.498520 ATGGGTCGCACGCTCTCG 62.499 66.667 0.00 0.00 42.43 4.04
454 497 1.470632 GCTCTCTCGTGAAGGTCATGG 60.471 57.143 0.00 0.00 34.27 3.66
465 508 2.223203 CGTAATAACCACGCTCTCTCGT 60.223 50.000 0.00 0.00 44.35 4.18
485 528 2.764314 GCCCAACCATGCTGCTACG 61.764 63.158 0.00 0.00 0.00 3.51
491 534 2.985282 CACGTGCCCAACCATGCT 60.985 61.111 0.82 0.00 0.00 3.79
492 535 4.722855 GCACGTGCCCAACCATGC 62.723 66.667 30.12 0.00 32.08 4.06
518 561 9.826574 ATATCAAGGCGTAATTAGTTTAGTTGA 57.173 29.630 0.00 0.00 0.00 3.18
530 573 7.394359 AGCCAAAATATGATATCAAGGCGTAAT 59.606 33.333 9.99 0.00 44.00 1.89
536 579 7.597743 GCTCAAAGCCAAAATATGATATCAAGG 59.402 37.037 9.99 6.44 34.48 3.61
562 605 6.538742 TGCTCTCTTTGTTCGATTTATTAGGG 59.461 38.462 0.00 0.00 0.00 3.53
565 608 7.899178 TGTGCTCTCTTTGTTCGATTTATTA 57.101 32.000 0.00 0.00 0.00 0.98
577 620 6.646653 TCAAGTGTAGTATTGTGCTCTCTTTG 59.353 38.462 0.00 0.00 0.00 2.77
582 625 7.715249 TCTTTTTCAAGTGTAGTATTGTGCTCT 59.285 33.333 0.00 0.00 0.00 4.09
592 635 9.191995 CAACAAAACTTCTTTTTCAAGTGTAGT 57.808 29.630 0.00 0.00 35.03 2.73
593 636 8.162245 GCAACAAAACTTCTTTTTCAAGTGTAG 58.838 33.333 0.00 0.00 35.03 2.74
594 637 7.653713 TGCAACAAAACTTCTTTTTCAAGTGTA 59.346 29.630 0.00 0.00 35.03 2.90
595 638 6.481644 TGCAACAAAACTTCTTTTTCAAGTGT 59.518 30.769 0.00 0.00 35.03 3.55
596 639 6.886307 TGCAACAAAACTTCTTTTTCAAGTG 58.114 32.000 0.00 0.00 35.03 3.16
597 640 7.671495 ATGCAACAAAACTTCTTTTTCAAGT 57.329 28.000 0.00 0.00 35.03 3.16
607 650 5.403466 CAGGCTTTCTATGCAACAAAACTTC 59.597 40.000 0.00 0.00 0.00 3.01
609 652 4.584325 TCAGGCTTTCTATGCAACAAAACT 59.416 37.500 0.00 0.00 0.00 2.66
631 674 4.401519 TCAATGGTAGTGTAGTACAGCCTC 59.598 45.833 2.39 0.00 0.00 4.70
671 718 8.102676 TGGTCAATCATCATTTCTCTCTTGTAA 58.897 33.333 0.00 0.00 0.00 2.41
672 719 7.623630 TGGTCAATCATCATTTCTCTCTTGTA 58.376 34.615 0.00 0.00 0.00 2.41
674 721 6.997239 TGGTCAATCATCATTTCTCTCTTG 57.003 37.500 0.00 0.00 0.00 3.02
676 723 8.467598 CAATTTGGTCAATCATCATTTCTCTCT 58.532 33.333 0.00 0.00 0.00 3.10
677 724 8.464404 TCAATTTGGTCAATCATCATTTCTCTC 58.536 33.333 0.00 0.00 0.00 3.20
679 726 7.490402 GGTCAATTTGGTCAATCATCATTTCTC 59.510 37.037 0.00 0.00 0.00 2.87
680 727 7.325694 GGTCAATTTGGTCAATCATCATTTCT 58.674 34.615 0.00 0.00 0.00 2.52
886 933 4.643387 GATCGGCCGGATTGGGGG 62.643 72.222 27.83 0.00 38.63 5.40
1319 1379 2.736682 CGCGGAAGTAAAGCACGGG 61.737 63.158 0.00 0.00 0.00 5.28
1329 1389 2.669569 AGCAATGCACGCGGAAGT 60.670 55.556 12.47 0.00 0.00 3.01
1356 1416 0.106519 CCCGATTCCATTTCAGGCCT 60.107 55.000 0.00 0.00 0.00 5.19
1372 1432 4.722700 CCCTGTCCCTGCAACCCG 62.723 72.222 0.00 0.00 0.00 5.28
1390 1450 1.803519 GACTCCTGCAGCGACTTCG 60.804 63.158 8.66 0.00 43.27 3.79
1470 1530 3.667282 CGACCTGTCCACCGACGT 61.667 66.667 0.00 0.00 42.37 4.34
1672 1732 2.279741 GGAAGCAATGTCATACGAGCA 58.720 47.619 0.00 0.00 0.00 4.26
1676 1736 3.002791 ACAGTGGAAGCAATGTCATACG 58.997 45.455 0.00 0.00 0.00 3.06
1682 1742 2.548057 CGTACAACAGTGGAAGCAATGT 59.452 45.455 0.00 0.00 34.67 2.71
1699 1759 6.582672 GGTACCAACTCAAACTAACTACGTAC 59.417 42.308 7.15 0.00 0.00 3.67
1700 1760 6.490040 AGGTACCAACTCAAACTAACTACGTA 59.510 38.462 15.94 0.00 0.00 3.57
1701 1761 5.302823 AGGTACCAACTCAAACTAACTACGT 59.697 40.000 15.94 0.00 0.00 3.57
1702 1762 5.776744 AGGTACCAACTCAAACTAACTACG 58.223 41.667 15.94 0.00 0.00 3.51
1778 1838 6.915843 CCAACTACCAGTTCACACAAATTTAC 59.084 38.462 0.00 0.00 36.03 2.01
1798 1858 2.304092 CACTGATATGCCATGCCAACT 58.696 47.619 0.00 0.00 0.00 3.16
2024 2096 6.832520 TGGTATAAAAGCTTTGCTCAATCA 57.167 33.333 13.54 1.03 38.25 2.57
2171 2246 7.339466 GCCTTTGAAGACATAATAAGGAGGAAA 59.661 37.037 0.00 0.00 34.18 3.13
2175 2250 7.442666 GGTAGCCTTTGAAGACATAATAAGGAG 59.557 40.741 0.00 0.00 34.18 3.69
2503 2579 2.431539 CGTCCACGTACTTCACTGC 58.568 57.895 0.00 0.00 34.11 4.40
2598 2674 8.169977 TCCATAATGATCCATTTGAAGCTTAC 57.830 34.615 0.00 0.00 35.54 2.34
2701 2777 1.485397 CTGAATGCGGAGATGACTCG 58.515 55.000 0.00 0.00 43.44 4.18
2722 2798 4.608948 AAGGAGGGATAAGATAAGTGCG 57.391 45.455 0.00 0.00 0.00 5.34
2758 2834 3.849002 GCAGAAGCTCCATGTCTGA 57.151 52.632 15.08 0.00 41.08 3.27
2968 3044 6.910536 ATAGAATGTGTTGCTACTTGCTAC 57.089 37.500 0.00 0.00 45.29 3.58
2969 3045 8.038351 TGTTATAGAATGTGTTGCTACTTGCTA 58.962 33.333 0.00 0.00 43.37 3.49
2970 3046 6.878923 TGTTATAGAATGTGTTGCTACTTGCT 59.121 34.615 0.00 0.00 43.37 3.91
2971 3047 7.072177 TGTTATAGAATGTGTTGCTACTTGC 57.928 36.000 0.00 0.00 43.25 4.01
2972 3048 8.882736 TCATGTTATAGAATGTGTTGCTACTTG 58.117 33.333 0.00 0.00 0.00 3.16
2973 3049 9.618890 ATCATGTTATAGAATGTGTTGCTACTT 57.381 29.630 0.00 0.00 0.00 2.24
2974 3050 9.265901 GATCATGTTATAGAATGTGTTGCTACT 57.734 33.333 0.00 0.00 0.00 2.57
3022 3098 1.271054 ACTACAGCAGCACAAAGAGGG 60.271 52.381 0.00 0.00 0.00 4.30
3043 3119 5.050091 CCATAGATGGTTCGAAACTACATGC 60.050 44.000 15.41 5.20 43.05 4.06
3098 3174 8.844244 AGAATGGAGAAGCACATAATTATTCAC 58.156 33.333 0.00 0.00 0.00 3.18
3105 3181 6.656902 TCAGAAGAATGGAGAAGCACATAAT 58.343 36.000 0.00 0.00 0.00 1.28
3118 3194 4.381292 GGAGGCAAAACATCAGAAGAATGG 60.381 45.833 0.00 0.00 0.00 3.16
3137 3213 0.107456 CCCTGGAATCACGATGGAGG 59.893 60.000 0.00 0.00 0.00 4.30
3138 3214 0.533755 GCCCTGGAATCACGATGGAG 60.534 60.000 0.00 0.00 0.00 3.86
3182 3258 3.975312 TGGTAACAGGACTTAAGGTTCCA 59.025 43.478 13.15 10.29 46.17 3.53
3200 3276 2.712087 TCTGGTTGCTTTACCCTTGGTA 59.288 45.455 0.00 0.00 37.09 3.25
3239 3315 3.096852 TGATGAGTGGATACCGACAAGT 58.903 45.455 0.00 0.00 0.00 3.16
3373 3449 0.398318 AACAGGAGGTGAAGAGGCAC 59.602 55.000 0.00 0.00 38.05 5.01
3677 3753 1.004745 GCCCCCTCATTCTCAAAGTCA 59.995 52.381 0.00 0.00 0.00 3.41
3719 3795 8.722342 TTTTCTTGGACGAGAAAATTAAATCG 57.278 30.769 18.80 4.99 45.66 3.34
3834 3913 5.711976 CCAACTTCTCTTTTGGTATGGATGT 59.288 40.000 0.00 0.00 37.98 3.06
3943 4022 9.820229 CAGATACAAAATACAATACACGTGTTT 57.180 29.630 28.55 16.98 30.09 2.83
4244 4325 7.774134 ACTACGATATGTACAATTACACACCA 58.226 34.615 0.00 0.00 41.12 4.17
4257 4338 7.014905 AGGCCAAACAGATAACTACGATATGTA 59.985 37.037 5.01 0.00 28.90 2.29
4275 4356 3.970721 GCCATTTGCAGGCCAAAC 58.029 55.556 5.01 0.00 45.52 2.93
4282 4363 6.140303 ACATAGAATTACAGCCATTTGCAG 57.860 37.500 0.00 0.00 44.83 4.41
4289 4370 8.892723 CAACTATGAAACATAGAATTACAGCCA 58.107 33.333 20.75 0.00 0.00 4.75
4290 4371 9.109393 TCAACTATGAAACATAGAATTACAGCC 57.891 33.333 20.75 0.00 30.99 4.85
4300 4381 8.954950 AGGAACTCATCAACTATGAAACATAG 57.045 34.615 14.64 14.64 44.05 2.23
4311 4392 7.609532 CAGAAAAGGATAAGGAACTCATCAACT 59.390 37.037 0.00 0.00 38.49 3.16
4320 4401 5.335976 CCAACTGCAGAAAAGGATAAGGAAC 60.336 44.000 23.35 0.00 0.00 3.62
4381 4462 5.494724 TCAGAGCTGATGAAAGTAAGCATT 58.505 37.500 0.00 0.00 38.14 3.56
4475 4559 3.535561 AGTGATGATTCATCCCAACGAC 58.464 45.455 21.08 12.60 39.87 4.34
4476 4560 3.912496 AGTGATGATTCATCCCAACGA 57.088 42.857 21.08 1.68 39.87 3.85
4477 4561 4.273480 GGTAAGTGATGATTCATCCCAACG 59.727 45.833 21.08 0.00 39.87 4.10
4539 4623 3.565482 CGTGCTTATTAGACATGCCCATT 59.435 43.478 0.00 0.00 0.00 3.16
4575 4659 4.436050 CCATTGTAGTTCGTTGATGCAGTC 60.436 45.833 0.00 0.00 0.00 3.51
4587 4671 3.662290 TGGTGGCCCATTGTAGTTC 57.338 52.632 0.00 0.00 35.17 3.01
4635 4719 7.544566 TGAAAACATCTTCCACGATAAGAGTAC 59.455 37.037 0.00 0.00 36.46 2.73
5059 5144 1.614317 CCTTGGACACCATTGGACTCC 60.614 57.143 10.37 12.36 32.01 3.85
5089 5174 7.201767 GGAAGGTAGTCATTTGAGAATTCCATG 60.202 40.741 0.65 0.40 34.10 3.66
5090 5175 6.830838 GGAAGGTAGTCATTTGAGAATTCCAT 59.169 38.462 0.65 0.00 34.10 3.41
5146 5231 2.919602 TCCAAAACTGGATTCTAGCCCT 59.080 45.455 0.00 0.00 32.09 5.19
5182 5267 4.217550 GCTGGGTTACTGTTTGAATGCTTA 59.782 41.667 0.00 0.00 0.00 3.09
5685 5772 0.684535 TTGCCATCCTGACGTCAGAA 59.315 50.000 40.21 27.12 46.59 3.02
5735 5822 2.029623 AGGAATTGCCATGCTTGCTAG 58.970 47.619 0.00 0.00 40.02 3.42
5918 6262 2.004120 ACCCACTGAACCACACCCA 61.004 57.895 0.00 0.00 0.00 4.51
6042 6386 6.878923 TGAAAACAATGAGGTGACGATCTATT 59.121 34.615 0.00 0.00 0.00 1.73
6073 6417 5.601662 AGGAGACATATGGAATAACACACG 58.398 41.667 7.80 0.00 29.06 4.49
6113 6457 5.065090 CAGTCAGAAAAATATCGCCATGACA 59.935 40.000 0.00 0.00 38.57 3.58
6117 6461 3.947196 TGCAGTCAGAAAAATATCGCCAT 59.053 39.130 0.00 0.00 0.00 4.40
6286 6632 5.353678 GTGAACTCCAGAGAAGATGAAATGG 59.646 44.000 0.70 0.00 0.00 3.16
6302 6648 5.597813 CACAGTAACTTCATGTGAACTCC 57.402 43.478 0.00 0.00 45.67 3.85
6347 6693 8.590719 GTTCTAGAACTACTAATACCAATGCC 57.409 38.462 25.30 0.00 38.25 4.40
6400 6746 9.682465 CCACCATAATATTCTCATCATTCTCAT 57.318 33.333 0.00 0.00 0.00 2.90
6406 6755 8.746530 GCAATTCCACCATAATATTCTCATCAT 58.253 33.333 0.00 0.00 0.00 2.45
6468 6842 3.267483 TGCTATTTCACTAGTTTCCGGC 58.733 45.455 0.00 0.00 0.00 6.13
6471 6845 5.735766 AGACCTGCTATTTCACTAGTTTCC 58.264 41.667 0.00 0.00 0.00 3.13
6718 7092 8.964420 TTTTAATGCATAGAACTGCTGTAAAC 57.036 30.769 0.00 0.00 42.75 2.01
6763 7137 3.055891 GTGCAGGGAGGTATTTTTGCATT 60.056 43.478 0.03 0.00 42.64 3.56
7024 7401 3.804036 TGGAATTAGACACCGCAATAGG 58.196 45.455 0.00 0.00 37.30 2.57
7134 7511 7.601073 AAAAGTAGGCGGTAATGTAACTAAC 57.399 36.000 0.00 0.00 0.00 2.34
7283 7661 7.545965 ACATTGCTATCAACAAGACTACACTAC 59.454 37.037 0.00 0.00 34.60 2.73
7723 8166 9.765795 ATATGGAAGTTCTTACAACTATAGTGC 57.234 33.333 6.06 0.00 0.00 4.40
7758 8201 0.179000 ACCTGGAGCATAAGAAGGCG 59.821 55.000 0.00 0.00 37.52 5.52
7904 8348 3.891366 AGTTGGGACACCTCATGAAAAAG 59.109 43.478 0.00 0.00 39.29 2.27
7918 8362 1.280421 AGGATCAGCAGAAGTTGGGAC 59.720 52.381 0.00 0.00 0.00 4.46
7962 8406 0.176910 CCCTTTCTCTCTCGCCCTTC 59.823 60.000 0.00 0.00 0.00 3.46
8118 8562 0.033504 TGACTCTGCCAAGGACGTTC 59.966 55.000 0.00 0.00 0.00 3.95
8340 8784 2.819595 CCATCCGTGAACCAGGCG 60.820 66.667 0.00 0.00 0.00 5.52
8368 8812 2.880890 AGAAATCAAAGTCTTGCAGCGT 59.119 40.909 0.00 0.00 32.14 5.07
8476 8920 9.304335 TCAAGAATCATCCAATTATATGCACAT 57.696 29.630 0.00 0.00 0.00 3.21
8477 8921 8.694581 TCAAGAATCATCCAATTATATGCACA 57.305 30.769 0.00 0.00 0.00 4.57
8718 9164 1.579140 TATGGGGAGCATGGGCAACA 61.579 55.000 0.00 0.00 44.61 3.33
8849 9324 8.673711 TCATAAGTTAAATAACATGCACTGTCC 58.326 33.333 6.13 0.00 36.98 4.02
8873 9354 9.012161 TGTGACAAATATTCAGATGAACAATCA 57.988 29.630 0.00 0.00 40.57 2.57
8874 9355 9.844790 TTGTGACAAATATTCAGATGAACAATC 57.155 29.630 0.00 0.00 36.80 2.67
8919 9415 5.358442 TGTGGTTGTGCACTTGTAACTATTT 59.642 36.000 19.41 0.00 0.00 1.40
8923 9419 2.717390 TGTGGTTGTGCACTTGTAACT 58.283 42.857 19.41 0.00 0.00 2.24
8940 9436 5.660460 TGTAGATGTTAGTACAGCCATGTG 58.340 41.667 0.00 0.00 41.57 3.21
8941 9437 5.422331 ACTGTAGATGTTAGTACAGCCATGT 59.578 40.000 8.98 0.00 46.86 3.21
8948 9444 7.612633 TGTGACCATACTGTAGATGTTAGTACA 59.387 37.037 0.00 0.00 38.95 2.90
8949 9445 7.993101 TGTGACCATACTGTAGATGTTAGTAC 58.007 38.462 0.00 0.00 30.47 2.73
8999 9499 7.095102 TGCAAACCCGTATTCTAGTCTTTTTAC 60.095 37.037 0.00 0.00 0.00 2.01
9005 9505 4.546829 TTGCAAACCCGTATTCTAGTCT 57.453 40.909 0.00 0.00 0.00 3.24
9016 9516 2.687935 ACTATTAGCCATTGCAAACCCG 59.312 45.455 1.71 0.00 41.13 5.28
9031 9531 8.453238 TGGTAGAAAAGTTGTGCAAACTATTA 57.547 30.769 12.60 3.98 0.00 0.98
9062 9562 1.848388 TGATCAGCACAATCCCCTGAT 59.152 47.619 2.32 2.32 46.01 2.90
9068 9568 5.762825 ATGTACATTGATCAGCACAATCC 57.237 39.130 1.41 0.00 36.07 3.01
9115 9615 0.099791 AAAACTCCCGTTGCAACACG 59.900 50.000 28.01 16.67 40.02 4.49
9117 9617 2.096248 AGAAAAACTCCCGTTGCAACA 58.904 42.857 28.01 9.07 32.65 3.33
9132 9632 9.218440 GGCCATTGAAGATTATGAAAAAGAAAA 57.782 29.630 0.00 0.00 0.00 2.29
9133 9633 8.373981 TGGCCATTGAAGATTATGAAAAAGAAA 58.626 29.630 0.00 0.00 0.00 2.52
9134 9634 7.905265 TGGCCATTGAAGATTATGAAAAAGAA 58.095 30.769 0.00 0.00 0.00 2.52
9135 9635 7.479352 TGGCCATTGAAGATTATGAAAAAGA 57.521 32.000 0.00 0.00 0.00 2.52
9137 9637 7.905265 TCTTGGCCATTGAAGATTATGAAAAA 58.095 30.769 6.09 0.00 0.00 1.94
9138 9638 7.479352 TCTTGGCCATTGAAGATTATGAAAA 57.521 32.000 6.09 0.00 0.00 2.29
9139 9639 7.342541 TGATCTTGGCCATTGAAGATTATGAAA 59.657 33.333 16.92 0.33 38.72 2.69
9140 9640 6.834969 TGATCTTGGCCATTGAAGATTATGAA 59.165 34.615 16.92 1.76 38.72 2.57
9160 9660 3.762288 AGTGATGCAGCAAAATGTGATCT 59.238 39.130 6.05 0.00 0.00 2.75
9194 9697 6.306199 TGATTTCACAAAATTGAGAGGGAGA 58.694 36.000 0.00 0.00 35.21 3.71
9195 9698 6.579666 TGATTTCACAAAATTGAGAGGGAG 57.420 37.500 0.00 0.00 35.21 4.30
9198 9701 7.868922 TGTTCATGATTTCACAAAATTGAGAGG 59.131 33.333 0.00 0.00 35.21 3.69
9243 9784 5.685195 AAATGCTCGCAATTTCAAATACG 57.315 34.783 0.00 0.11 0.00 3.06
9244 9785 7.948137 TGTAAAATGCTCGCAATTTCAAATAC 58.052 30.769 8.09 2.68 32.19 1.89
9245 9786 8.526218 TTGTAAAATGCTCGCAATTTCAAATA 57.474 26.923 8.09 0.00 32.19 1.40
9246 9787 7.418840 TTGTAAAATGCTCGCAATTTCAAAT 57.581 28.000 8.09 0.00 32.19 2.32
9247 9788 6.834959 TTGTAAAATGCTCGCAATTTCAAA 57.165 29.167 8.09 2.87 32.19 2.69
9248 9789 6.834959 TTTGTAAAATGCTCGCAATTTCAA 57.165 29.167 8.09 9.53 32.19 2.69
9249 9790 7.418840 AATTTGTAAAATGCTCGCAATTTCA 57.581 28.000 8.09 4.87 32.19 2.69
9250 9791 9.971744 ATAAATTTGTAAAATGCTCGCAATTTC 57.028 25.926 8.09 2.72 32.19 2.17
9251 9792 9.757859 CATAAATTTGTAAAATGCTCGCAATTT 57.242 25.926 9.57 9.57 34.04 1.82
9252 9793 9.149225 TCATAAATTTGTAAAATGCTCGCAATT 57.851 25.926 0.00 0.00 0.00 2.32
9253 9794 8.700722 TCATAAATTTGTAAAATGCTCGCAAT 57.299 26.923 0.00 0.00 0.00 3.56
9254 9795 8.431593 GTTCATAAATTTGTAAAATGCTCGCAA 58.568 29.630 0.00 0.00 0.00 4.85
9255 9796 7.596621 TGTTCATAAATTTGTAAAATGCTCGCA 59.403 29.630 0.00 0.00 0.00 5.10
9256 9797 7.892731 GTGTTCATAAATTTGTAAAATGCTCGC 59.107 33.333 0.00 0.00 0.00 5.03
9257 9798 9.128107 AGTGTTCATAAATTTGTAAAATGCTCG 57.872 29.630 0.00 0.00 0.00 5.03
9386 9955 8.498054 TGTTTGCCAATTCAAGAAAATTGTTA 57.502 26.923 8.15 0.00 42.50 2.41
9407 9976 6.187727 TGTTCCTCCAGTCTAGAAATGTTT 57.812 37.500 0.00 0.00 0.00 2.83
9420 9989 4.935352 TTCCAAAACAATGTTCCTCCAG 57.065 40.909 0.00 0.00 0.00 3.86
9425 9994 5.008514 CCACCAATTTCCAAAACAATGTTCC 59.991 40.000 0.00 0.00 0.00 3.62
9517 10107 9.841880 AAAACTTAAGAACTCTTTGTGACTTTC 57.158 29.630 10.09 0.00 37.40 2.62
9558 10168 8.409371 TCGCCAACTCAAATAATATTTATGCAA 58.591 29.630 0.00 0.00 0.00 4.08
9560 10170 8.795786 TTCGCCAACTCAAATAATATTTATGC 57.204 30.769 0.00 0.00 0.00 3.14
9567 10177 9.482627 AACAAAATTTCGCCAACTCAAATAATA 57.517 25.926 0.00 0.00 0.00 0.98
9571 10181 5.814705 TGAACAAAATTTCGCCAACTCAAAT 59.185 32.000 0.00 0.00 0.00 2.32
9639 10250 4.013728 TCGAAAACCAAATGATCGGGAAT 58.986 39.130 0.00 0.00 34.47 3.01
9640 10251 3.413327 TCGAAAACCAAATGATCGGGAA 58.587 40.909 0.00 0.00 34.47 3.97
9641 10252 3.060736 TCGAAAACCAAATGATCGGGA 57.939 42.857 0.00 0.00 34.47 5.14
9642 10253 3.840890 TTCGAAAACCAAATGATCGGG 57.159 42.857 0.00 0.00 34.47 5.14
9643 10254 6.364706 TGAAATTTCGAAAACCAAATGATCGG 59.635 34.615 15.66 0.00 34.47 4.18
9644 10255 7.332003 TGAAATTTCGAAAACCAAATGATCG 57.668 32.000 15.66 0.00 34.98 3.69


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

AutoCloner maintained by Alex Coulton.