Multiple sequence alignment - TraesCS2D01G126600

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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 TraesCS2D01G126600 chr2D 100.000 8395 0 0 1 8395 73579184 73570790 0.000000e+00 15503.0
1 TraesCS2D01G126600 chr2D 100.000 1145 0 0 8757 9901 73570428 73569284 0.000000e+00 2115.0
2 TraesCS2D01G126600 chr2D 77.066 702 89 34 5327 5977 353021905 353022585 1.230000e-88 339.0
3 TraesCS2D01G126600 chr2D 82.031 128 16 5 2810 2933 11147601 11147477 1.760000e-17 102.0
4 TraesCS2D01G126600 chr2B 95.795 7538 239 33 888 8395 111462242 111454753 0.000000e+00 12092.0
5 TraesCS2D01G126600 chr2B 87.031 879 48 32 1 856 111463157 111462322 0.000000e+00 931.0
6 TraesCS2D01G126600 chr2B 91.165 532 22 12 9388 9901 111454217 111453693 0.000000e+00 699.0
7 TraesCS2D01G126600 chr2B 91.089 202 9 4 8948 9144 111454560 111454363 2.120000e-66 265.0
8 TraesCS2D01G126600 chr2B 98.649 148 2 0 8757 8904 111454703 111454556 7.630000e-66 263.0
9 TraesCS2D01G126600 chr2B 90.909 99 3 4 9268 9366 247368538 247368630 2.900000e-25 128.0
10 TraesCS2D01G126600 chr2B 89.888 89 4 3 9271 9359 175632193 175632110 1.050000e-19 110.0
11 TraesCS2D01G126600 chr2B 81.061 132 13 8 2803 2926 135236590 135236717 2.940000e-15 95.3
12 TraesCS2D01G126600 chr2A 97.518 5278 99 15 1553 6814 73165431 73160170 0.000000e+00 8992.0
13 TraesCS2D01G126600 chr2A 97.284 1583 32 5 6813 8395 73160081 73158510 0.000000e+00 2675.0
14 TraesCS2D01G126600 chr2A 91.525 649 33 7 859 1492 73166069 73165428 0.000000e+00 874.0
15 TraesCS2D01G126600 chr2A 89.610 539 26 12 9370 9899 73157826 73157309 0.000000e+00 658.0
16 TraesCS2D01G126600 chr2A 87.614 549 28 15 3 544 73166850 73166335 1.420000e-167 601.0
17 TraesCS2D01G126600 chr2A 88.889 486 32 14 8757 9225 73158459 73157979 6.670000e-161 579.0
18 TraesCS2D01G126600 chr2A 75.385 455 54 25 5554 5965 471219615 471220054 6.150000e-37 167.0
19 TraesCS2D01G126600 chr2A 90.110 91 3 4 9267 9357 182008966 182009050 8.130000e-21 113.0
20 TraesCS2D01G126600 chr4A 89.691 97 4 4 9265 9360 697388893 697388802 1.750000e-22 119.0
21 TraesCS2D01G126600 chr1B 89.583 96 6 4 9266 9360 355408267 355408359 1.750000e-22 119.0
22 TraesCS2D01G126600 chr1A 89.583 96 6 4 9266 9360 331272193 331272285 1.750000e-22 119.0
23 TraesCS2D01G126600 chr1A 87.629 97 8 2 9267 9360 53035372 53035467 1.050000e-19 110.0
24 TraesCS2D01G126600 chr3A 91.358 81 4 3 9265 9343 416139201 416139280 3.780000e-19 108.0
25 TraesCS2D01G126600 chr5A 88.298 94 4 4 9266 9359 3397789 3397703 1.360000e-18 106.0
26 TraesCS2D01G126600 chrUn 87.912 91 8 3 2835 2924 360547633 360547721 4.890000e-18 104.0
27 TraesCS2D01G126600 chr6B 87.912 91 8 3 2835 2924 100709974 100709886 4.890000e-18 104.0
28 TraesCS2D01G126600 chr6B 87.912 91 8 3 2835 2924 100745219 100745131 4.890000e-18 104.0
29 TraesCS2D01G126600 chr6B 89.412 85 6 3 2842 2926 292765182 292765263 4.890000e-18 104.0
30 TraesCS2D01G126600 chr6D 80.986 142 7 13 2803 2929 147894387 147894251 2.940000e-15 95.3
31 TraesCS2D01G126600 chr7D 79.562 137 19 8 2802 2932 459940389 459940256 1.370000e-13 89.8


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 TraesCS2D01G126600 chr2D 73569284 73579184 9900 True 8809.0 15503 100.000000 1 9901 2 chr2D.!!$R2 9900
1 TraesCS2D01G126600 chr2D 353021905 353022585 680 False 339.0 339 77.066000 5327 5977 1 chr2D.!!$F1 650
2 TraesCS2D01G126600 chr2B 111453693 111463157 9464 True 2850.0 12092 92.745800 1 9901 5 chr2B.!!$R2 9900
3 TraesCS2D01G126600 chr2A 73157309 73166850 9541 True 2396.5 8992 92.073333 3 9899 6 chr2A.!!$R1 9896

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
580 604 0.032130 GCGAGTGAGTGGTGTTCTCA 59.968 55.000 0.0 0.0 39.25 3.27 F
712 736 0.246635 CCGAATCTGGTCCACGTCTT 59.753 55.000 0.0 0.0 0.00 3.01 F
1417 1506 0.319083 CCACATTGGCAGCACACATT 59.681 50.000 0.0 0.0 0.00 2.71 F
2681 2776 1.078759 CGTTCCAGGTGATGTCTCGC 61.079 60.000 0.0 0.0 0.00 5.03 F
2849 2944 1.205179 TCGTACTTGGTGTGTGTGTGT 59.795 47.619 0.0 0.0 0.00 3.72 F
4565 4673 0.458543 CGACTATGAGGCAGCGTTGT 60.459 55.000 0.0 0.0 0.00 3.32 F
5584 5710 1.139654 GATCATGCTGCCACAGGTCTA 59.860 52.381 0.0 0.0 31.21 2.59 F
5795 5956 2.438021 GGACATGCTGGAGGTAACCATA 59.562 50.000 0.0 0.0 39.34 2.74 F
7194 7459 2.928731 GCGTATCCAGAGAATGCCTAGC 60.929 54.545 0.0 0.0 0.00 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2322 2417 0.034574 ATTATTGTGGCGGCAGTCCA 60.035 50.000 13.91 3.82 0.00 4.02 R
2712 2807 9.753674 TCCATTGGTGAAGACTAAATAGAAAAT 57.246 29.630 1.86 0.00 0.00 1.82 R
3185 3281 1.187974 TCCAATTTCCTACCGCGAGA 58.812 50.000 8.23 0.00 0.00 4.04 R
4565 4673 2.151202 GGCAATTCTGAGTTTCGTGGA 58.849 47.619 0.00 0.00 0.00 4.02 R
4612 4720 4.575885 ACGGAGCTGAATTTAGCACTTTA 58.424 39.130 22.65 0.00 46.07 1.85 R
6294 6462 1.595382 GTGTGCACGACAGAAGGCT 60.595 57.895 13.13 0.00 34.28 4.58 R
7194 7459 1.885887 TCAAATTCCAAGCCTGGTTCG 59.114 47.619 0.15 0.00 43.97 3.95 R
7701 7966 9.656040 TTGAGACAAATCCAATCCAATATTTTG 57.344 29.630 0.00 0.00 0.00 2.44 R
8921 9241 0.179067 TCTTCGCGGTCCTTTGTTGT 60.179 50.000 6.13 0.00 0.00 3.32 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
227 228 2.361104 GCCCGGATCCACAAAGCA 60.361 61.111 13.41 0.00 0.00 3.91
228 229 1.754234 GCCCGGATCCACAAAGCAT 60.754 57.895 13.41 0.00 0.00 3.79
240 241 0.685458 CAAAGCATGGGGGAAGGGAG 60.685 60.000 0.00 0.00 0.00 4.30
341 351 1.445731 GTCGTTAACGTCACACTCACG 59.554 52.381 25.98 0.00 43.13 4.35
356 372 1.070445 CACGCCCCTCATCATCTCC 59.930 63.158 0.00 0.00 0.00 3.71
375 391 3.412408 GGCACCTTCTCCCCCTCC 61.412 72.222 0.00 0.00 0.00 4.30
377 393 2.456840 CACCTTCTCCCCCTCCCT 59.543 66.667 0.00 0.00 0.00 4.20
378 394 1.690985 CACCTTCTCCCCCTCCCTC 60.691 68.421 0.00 0.00 0.00 4.30
381 397 4.089757 TTCTCCCCCTCCCTCCCG 62.090 72.222 0.00 0.00 0.00 5.14
383 399 3.436028 CTCCCCCTCCCTCCCGTA 61.436 72.222 0.00 0.00 0.00 4.02
384 400 3.752816 CTCCCCCTCCCTCCCGTAC 62.753 73.684 0.00 0.00 0.00 3.67
385 401 4.874533 CCCCCTCCCTCCCGTACC 62.875 77.778 0.00 0.00 0.00 3.34
386 402 3.763757 CCCCTCCCTCCCGTACCT 61.764 72.222 0.00 0.00 0.00 3.08
387 403 2.123382 CCCTCCCTCCCGTACCTC 60.123 72.222 0.00 0.00 0.00 3.85
428 444 1.614824 AGCCTCCTCCCTCCTTGTG 60.615 63.158 0.00 0.00 0.00 3.33
429 445 1.920835 GCCTCCTCCCTCCTTGTGT 60.921 63.158 0.00 0.00 0.00 3.72
431 447 1.068121 CCTCCTCCCTCCTTGTGTTT 58.932 55.000 0.00 0.00 0.00 2.83
434 450 0.111253 CCTCCCTCCTTGTGTTTGCT 59.889 55.000 0.00 0.00 0.00 3.91
436 452 0.178992 TCCCTCCTTGTGTTTGCTGG 60.179 55.000 0.00 0.00 0.00 4.85
495 519 2.824489 GCTCGCCCAAGGTAAGCC 60.824 66.667 0.00 0.00 0.00 4.35
498 522 2.511600 CGCCCAAGGTAAGCCTCG 60.512 66.667 0.00 0.00 46.33 4.63
499 523 2.824489 GCCCAAGGTAAGCCTCGC 60.824 66.667 0.00 0.00 46.33 5.03
502 526 2.511600 CAAGGTAAGCCTCGCCCG 60.512 66.667 0.00 0.00 46.33 6.13
503 527 4.468689 AAGGTAAGCCTCGCCCGC 62.469 66.667 0.00 0.00 46.33 6.13
506 530 4.893601 GTAAGCCTCGCCCGCTCC 62.894 72.222 0.00 0.00 34.84 4.70
532 556 0.669625 CCCCTGTTTCTCGGTTCGTC 60.670 60.000 0.00 0.00 0.00 4.20
542 566 4.373116 GGTTCGTCGGCAGGCAGA 62.373 66.667 0.00 0.00 0.00 4.26
570 594 1.917782 GAGTGAGCGAGCGAGTGAGT 61.918 60.000 0.00 0.00 0.00 3.41
575 599 2.645567 CGAGCGAGTGAGTGGTGT 59.354 61.111 0.00 0.00 0.00 4.16
576 600 1.007271 CGAGCGAGTGAGTGGTGTT 60.007 57.895 0.00 0.00 0.00 3.32
577 601 1.004277 CGAGCGAGTGAGTGGTGTTC 61.004 60.000 0.00 0.00 0.00 3.18
578 602 0.315568 GAGCGAGTGAGTGGTGTTCT 59.684 55.000 0.00 0.00 0.00 3.01
580 604 0.032130 GCGAGTGAGTGGTGTTCTCA 59.968 55.000 0.00 0.00 39.25 3.27
581 605 1.538204 GCGAGTGAGTGGTGTTCTCAA 60.538 52.381 0.00 0.00 42.42 3.02
598 622 4.560128 TCTCAACTTCTGATTCGTTCCTG 58.440 43.478 0.00 0.00 32.14 3.86
616 640 3.184683 CGTTCGCCTCTGAGCTGC 61.185 66.667 0.00 0.00 0.00 5.25
618 642 2.099431 GTTCGCCTCTGAGCTGCTG 61.099 63.158 7.01 0.00 0.00 4.41
712 736 0.246635 CCGAATCTGGTCCACGTCTT 59.753 55.000 0.00 0.00 0.00 3.01
713 737 1.630148 CGAATCTGGTCCACGTCTTC 58.370 55.000 0.00 0.00 0.00 2.87
717 741 2.522436 TGGTCCACGTCTTCCCGT 60.522 61.111 0.00 0.00 42.87 5.28
726 750 2.429571 TCTTCCCGTCGCGAAACG 60.430 61.111 12.06 12.53 45.62 3.60
845 870 4.154015 TCACGGAAGCATTAACAATGAGTG 59.846 41.667 3.11 4.93 41.46 3.51
846 871 3.119849 ACGGAAGCATTAACAATGAGTGC 60.120 43.478 3.11 0.00 41.46 4.40
847 872 3.429085 GGAAGCATTAACAATGAGTGCG 58.571 45.455 3.11 0.00 41.46 5.34
848 873 3.119849 GGAAGCATTAACAATGAGTGCGT 60.120 43.478 3.11 0.00 41.46 5.24
849 874 3.476295 AGCATTAACAATGAGTGCGTG 57.524 42.857 3.11 0.00 41.46 5.34
851 876 2.731968 GCATTAACAATGAGTGCGTGGG 60.732 50.000 3.11 0.00 41.46 4.61
853 878 0.687920 TAACAATGAGTGCGTGGGGA 59.312 50.000 0.00 0.00 0.00 4.81
873 916 0.464036 TCCCTTGGATCCGTGATTCG 59.536 55.000 7.39 0.00 39.52 3.34
911 987 2.059541 GCGGATTCATCCTTACGCTAC 58.940 52.381 4.30 0.00 44.93 3.58
958 1045 2.381109 CTGACGCATTCAGCTCCTG 58.619 57.895 0.00 0.00 45.51 3.86
977 1064 2.050714 CCTTGCTGCGCTTGTGTG 60.051 61.111 9.73 0.00 0.00 3.82
1173 1260 2.359975 GGCCAGGTTTCAGTCCCG 60.360 66.667 0.00 0.00 0.00 5.14
1353 1442 1.539388 TCCATGTGTTCATTCAACCGC 59.461 47.619 0.00 0.00 33.51 5.68
1370 1459 1.002134 GCCCTCTTGCTTGCTGGTA 60.002 57.895 0.00 0.00 0.00 3.25
1417 1506 0.319083 CCACATTGGCAGCACACATT 59.681 50.000 0.00 0.00 0.00 2.71
1458 1551 7.475015 GCTGAATGCTATGTATCTTTTGTTGA 58.525 34.615 0.00 0.00 38.95 3.18
1495 1588 5.261209 TGCTTATATGACCATTTGGCAAC 57.739 39.130 0.00 0.00 39.32 4.17
1701 1794 9.547279 ACTTTGGATCCTGAAGGTAATATTTTT 57.453 29.630 23.57 4.98 36.34 1.94
1721 1814 6.497785 TTTTAAACTGAACGTCTCAAACCA 57.502 33.333 0.00 0.00 32.17 3.67
1817 1910 4.021822 CGTGCGTTGCTACAGAATTTATG 58.978 43.478 0.00 0.00 0.00 1.90
1864 1957 1.450312 GCTTGTGCCGCCATAGTCT 60.450 57.895 0.00 0.00 0.00 3.24
1865 1958 1.709147 GCTTGTGCCGCCATAGTCTG 61.709 60.000 0.00 0.00 0.00 3.51
2258 2353 9.597681 AGGAATCAAGATAAATGCAAGGATAAT 57.402 29.630 0.00 0.00 0.00 1.28
2317 2412 3.637229 CTGATGGTTGGTATAGTCCGAGT 59.363 47.826 0.00 0.00 0.00 4.18
2322 2417 3.446516 GGTTGGTATAGTCCGAGTTGAGT 59.553 47.826 0.00 0.00 0.00 3.41
2681 2776 1.078759 CGTTCCAGGTGATGTCTCGC 61.079 60.000 0.00 0.00 0.00 5.03
2692 2787 3.736252 GTGATGTCTCGCGCTTGTAATAT 59.264 43.478 5.56 0.00 0.00 1.28
2693 2788 4.209288 GTGATGTCTCGCGCTTGTAATATT 59.791 41.667 5.56 0.00 0.00 1.28
2694 2789 4.808895 TGATGTCTCGCGCTTGTAATATTT 59.191 37.500 5.56 0.00 0.00 1.40
2749 2844 6.655003 GTCTTCACCAATGGAGTATCTGAAAA 59.345 38.462 6.16 0.00 32.53 2.29
2849 2944 1.205179 TCGTACTTGGTGTGTGTGTGT 59.795 47.619 0.00 0.00 0.00 3.72
2850 2945 1.326245 CGTACTTGGTGTGTGTGTGTG 59.674 52.381 0.00 0.00 0.00 3.82
2865 2960 1.301423 GTGTGGCGTGGACTTGTTTA 58.699 50.000 0.00 0.00 0.00 2.01
2881 2977 6.512297 ACTTGTTTATTACCTTGTTTGGCTG 58.488 36.000 0.00 0.00 0.00 4.85
3185 3281 3.323979 AGGTTGTCGTCACAGGAAGTAAT 59.676 43.478 0.00 0.00 32.71 1.89
3681 3777 1.523938 GATAGAACCCTGCCACGCC 60.524 63.158 0.00 0.00 0.00 5.68
3865 3973 2.438021 ACTTCTTGTTGACTGGGCAGTA 59.562 45.455 0.00 0.00 42.66 2.74
4261 4369 6.888105 TGCATATTGTCACAGGAAGAGATTA 58.112 36.000 0.00 0.00 0.00 1.75
4298 4406 5.897250 AGGAGTTGGACAAAAAGGTAAATGT 59.103 36.000 0.00 0.00 0.00 2.71
4353 4461 4.797471 TGTCATCACTGCAAATGTAAAGC 58.203 39.130 0.00 0.00 0.00 3.51
4565 4673 0.458543 CGACTATGAGGCAGCGTTGT 60.459 55.000 0.00 0.00 0.00 3.32
4896 5004 7.148120 CCATATTTCCTGCATAGCTTCCTAATG 60.148 40.741 0.00 0.00 0.00 1.90
4899 5007 3.711190 TCCTGCATAGCTTCCTAATGACA 59.289 43.478 0.00 0.00 0.00 3.58
4905 5016 6.261603 TGCATAGCTTCCTAATGACAATTCTG 59.738 38.462 0.00 0.00 0.00 3.02
5584 5710 1.139654 GATCATGCTGCCACAGGTCTA 59.860 52.381 0.00 0.00 31.21 2.59
5795 5956 2.438021 GGACATGCTGGAGGTAACCATA 59.562 50.000 0.00 0.00 39.34 2.74
5894 6062 5.694995 AGAAGTTTGGATCTCTTTGGACAA 58.305 37.500 0.00 0.00 0.00 3.18
5938 6106 5.344066 CACGAGTATCAGAAACACTGCTAT 58.656 41.667 0.00 0.00 45.38 2.97
6013 6181 4.377841 GCTACTTGAGTCTGCATGTCAAAC 60.378 45.833 6.89 0.00 30.00 2.93
6089 6257 6.748333 TTTCTCAATCTAAGGCATGTGAAG 57.252 37.500 0.00 0.00 30.08 3.02
6294 6462 7.122204 TCTGTTCGATCTTCTACAGGTAATTCA 59.878 37.037 11.64 0.00 38.75 2.57
6304 6472 3.944087 ACAGGTAATTCAGCCTTCTGTC 58.056 45.455 0.00 0.00 41.10 3.51
6657 6825 6.486657 AGCATTGTGATGTTGTACTTAGTTGT 59.513 34.615 0.00 0.00 35.63 3.32
7194 7459 2.928731 GCGTATCCAGAGAATGCCTAGC 60.929 54.545 0.00 0.00 0.00 3.42
7386 7651 6.962686 TGCTACATCAGATGATAAATTGTGC 58.037 36.000 17.81 7.58 32.63 4.57
7701 7966 5.870978 ACAGCATTGACAGCCAATAAATTTC 59.129 36.000 0.00 0.00 43.27 2.17
8279 8551 4.708177 CCCCATCAACTTCAGACGAATAT 58.292 43.478 0.00 0.00 0.00 1.28
8904 9224 0.896940 AACGGACAAGGCCTAGTCGA 60.897 55.000 5.16 0.00 35.63 4.20
8905 9225 1.139095 CGGACAAGGCCTAGTCGAC 59.861 63.158 5.16 7.70 35.63 4.20
8906 9226 1.516423 GGACAAGGCCTAGTCGACC 59.484 63.158 13.01 1.05 35.63 4.79
8907 9227 1.139095 GACAAGGCCTAGTCGACCG 59.861 63.158 13.01 3.50 0.00 4.79
8908 9228 2.280823 GACAAGGCCTAGTCGACCGG 62.281 65.000 13.01 14.34 0.00 5.28
8909 9229 3.459063 AAGGCCTAGTCGACCGGC 61.459 66.667 28.89 28.89 43.03 6.13
8910 9230 4.753662 AGGCCTAGTCGACCGGCA 62.754 66.667 33.92 11.44 45.53 5.69
8911 9231 3.766691 GGCCTAGTCGACCGGCAA 61.767 66.667 33.92 9.59 45.53 4.52
8912 9232 2.263540 GCCTAGTCGACCGGCAAA 59.736 61.111 30.69 5.20 43.25 3.68
8913 9233 1.153429 GCCTAGTCGACCGGCAAAT 60.153 57.895 30.69 8.72 43.25 2.32
8914 9234 1.152383 GCCTAGTCGACCGGCAAATC 61.152 60.000 30.69 9.89 43.25 2.17
8915 9235 0.870307 CCTAGTCGACCGGCAAATCG 60.870 60.000 13.01 2.96 39.72 3.34
8916 9236 0.179145 CTAGTCGACCGGCAAATCGT 60.179 55.000 13.01 0.00 39.38 3.73
8917 9237 1.064505 CTAGTCGACCGGCAAATCGTA 59.935 52.381 13.01 0.00 39.38 3.43
8918 9238 0.179145 AGTCGACCGGCAAATCGTAG 60.179 55.000 13.01 0.00 39.38 3.51
8919 9239 1.140161 TCGACCGGCAAATCGTAGG 59.860 57.895 11.42 0.00 39.38 3.18
8920 9240 1.140161 CGACCGGCAAATCGTAGGA 59.860 57.895 0.00 0.00 33.63 2.94
8921 9241 0.458889 CGACCGGCAAATCGTAGGAA 60.459 55.000 0.00 0.00 33.63 3.36
8922 9242 1.004595 GACCGGCAAATCGTAGGAAC 58.995 55.000 0.00 0.00 0.00 3.62
8923 9243 0.322322 ACCGGCAAATCGTAGGAACA 59.678 50.000 0.00 0.00 0.00 3.18
8924 9244 1.270947 ACCGGCAAATCGTAGGAACAA 60.271 47.619 0.00 0.00 0.00 2.83
8925 9245 1.129811 CCGGCAAATCGTAGGAACAAC 59.870 52.381 0.00 0.00 0.00 3.32
8926 9246 1.801771 CGGCAAATCGTAGGAACAACA 59.198 47.619 0.00 0.00 0.00 3.33
8927 9247 2.224549 CGGCAAATCGTAGGAACAACAA 59.775 45.455 0.00 0.00 0.00 2.83
8928 9248 3.304123 CGGCAAATCGTAGGAACAACAAA 60.304 43.478 0.00 0.00 0.00 2.83
8929 9249 4.226761 GGCAAATCGTAGGAACAACAAAG 58.773 43.478 0.00 0.00 0.00 2.77
8930 9250 4.226761 GCAAATCGTAGGAACAACAAAGG 58.773 43.478 0.00 0.00 0.00 3.11
8931 9251 4.023536 GCAAATCGTAGGAACAACAAAGGA 60.024 41.667 0.00 0.00 0.00 3.36
8932 9252 5.449304 CAAATCGTAGGAACAACAAAGGAC 58.551 41.667 0.00 0.00 0.00 3.85
8933 9253 3.116079 TCGTAGGAACAACAAAGGACC 57.884 47.619 0.00 0.00 0.00 4.46
8934 9254 1.796459 CGTAGGAACAACAAAGGACCG 59.204 52.381 0.00 0.00 0.00 4.79
8935 9255 1.534163 GTAGGAACAACAAAGGACCGC 59.466 52.381 0.00 0.00 0.00 5.68
8936 9256 1.164041 AGGAACAACAAAGGACCGCG 61.164 55.000 0.00 0.00 0.00 6.46
8937 9257 1.161563 GGAACAACAAAGGACCGCGA 61.162 55.000 8.23 0.00 0.00 5.87
8938 9258 0.658897 GAACAACAAAGGACCGCGAA 59.341 50.000 8.23 0.00 0.00 4.70
8939 9259 0.661020 AACAACAAAGGACCGCGAAG 59.339 50.000 8.23 0.00 0.00 3.79
8940 9260 0.179067 ACAACAAAGGACCGCGAAGA 60.179 50.000 8.23 0.00 0.00 2.87
8941 9261 0.941542 CAACAAAGGACCGCGAAGAA 59.058 50.000 8.23 0.00 0.00 2.52
8942 9262 0.942252 AACAAAGGACCGCGAAGAAC 59.058 50.000 8.23 0.00 0.00 3.01
8943 9263 1.219522 ACAAAGGACCGCGAAGAACG 61.220 55.000 8.23 0.00 45.66 3.95
8949 9269 2.049433 CCGCGAAGAACGGTCAGT 60.049 61.111 8.23 0.00 45.70 3.41
8950 9270 2.087009 CCGCGAAGAACGGTCAGTC 61.087 63.158 8.23 0.00 45.70 3.51
8951 9271 2.426183 CGCGAAGAACGGTCAGTCG 61.426 63.158 18.94 18.94 42.83 4.18
8974 9294 0.668706 CCGAGCGGGATCATGATCAC 60.669 60.000 31.49 28.64 39.54 3.06
9020 9340 1.001517 TGGTGTATTGCCGCCATGT 60.002 52.632 0.00 0.00 40.01 3.21
9085 9414 3.244345 CCGCTCATAATTTTTCGACGCTA 59.756 43.478 0.00 0.00 0.00 4.26
9090 9419 6.511121 GCTCATAATTTTTCGACGCTATGGAA 60.511 38.462 0.00 0.00 0.00 3.53
9144 9476 3.866883 ACCGGCTTGTGAAATAAATGG 57.133 42.857 0.00 0.00 0.00 3.16
9178 9513 3.762407 TTTTGTCGTCAAGATCTCCCA 57.238 42.857 0.00 0.00 34.88 4.37
9179 9514 3.981071 TTTGTCGTCAAGATCTCCCAT 57.019 42.857 0.00 0.00 34.88 4.00
9182 9517 1.405821 GTCGTCAAGATCTCCCATCGT 59.594 52.381 0.00 0.00 0.00 3.73
9187 9523 3.632604 GTCAAGATCTCCCATCGTGTCTA 59.367 47.826 0.00 0.00 0.00 2.59
9194 9530 0.249073 CCCATCGTGTCTAGCCTTCG 60.249 60.000 0.00 0.00 0.00 3.79
9196 9532 0.179137 CATCGTGTCTAGCCTTCGCA 60.179 55.000 0.00 0.00 37.52 5.10
9203 9539 2.742053 TGTCTAGCCTTCGCATGTTTTC 59.258 45.455 0.00 0.00 37.52 2.29
9204 9540 3.003480 GTCTAGCCTTCGCATGTTTTCT 58.997 45.455 0.00 0.00 37.52 2.52
9213 9549 4.039151 TCGCATGTTTTCTTTTTCTGCA 57.961 36.364 0.00 0.00 0.00 4.41
9215 9551 5.767269 TCGCATGTTTTCTTTTTCTGCATA 58.233 33.333 0.00 0.00 0.00 3.14
9255 9679 1.004745 TCAAGGCCCTGAAATGGAGTC 59.995 52.381 0.10 0.00 0.00 3.36
9263 9687 2.422519 CCTGAAATGGAGTCCCTGATGG 60.423 54.545 6.74 0.00 0.00 3.51
9273 9697 2.103153 TCCCTGATGGATGTACTCCC 57.897 55.000 8.36 3.66 44.23 4.30
9275 9699 1.974236 CCCTGATGGATGTACTCCCTC 59.026 57.143 8.36 8.50 44.23 4.30
9276 9700 1.974236 CCTGATGGATGTACTCCCTCC 59.026 57.143 8.36 3.94 44.23 4.30
9277 9701 1.615883 CTGATGGATGTACTCCCTCCG 59.384 57.143 8.36 2.83 44.23 4.63
9279 9703 2.176148 TGATGGATGTACTCCCTCCGTA 59.824 50.000 8.36 0.00 44.23 4.02
9281 9705 1.326328 GGATGTACTCCCTCCGTACC 58.674 60.000 0.00 0.00 38.19 3.34
9282 9706 1.410648 GGATGTACTCCCTCCGTACCA 60.411 57.143 0.00 0.00 38.19 3.25
9283 9707 2.381911 GATGTACTCCCTCCGTACCAA 58.618 52.381 0.00 0.00 37.11 3.67
9284 9708 2.307496 TGTACTCCCTCCGTACCAAA 57.693 50.000 0.00 0.00 37.11 3.28
9285 9709 2.607499 TGTACTCCCTCCGTACCAAAA 58.393 47.619 0.00 0.00 37.11 2.44
9286 9710 3.175594 TGTACTCCCTCCGTACCAAAAT 58.824 45.455 0.00 0.00 37.11 1.82
9287 9711 4.352009 TGTACTCCCTCCGTACCAAAATA 58.648 43.478 0.00 0.00 37.11 1.40
9288 9712 4.964262 TGTACTCCCTCCGTACCAAAATAT 59.036 41.667 0.00 0.00 37.11 1.28
9289 9713 6.135454 TGTACTCCCTCCGTACCAAAATATA 58.865 40.000 0.00 0.00 37.11 0.86
9290 9714 6.610830 TGTACTCCCTCCGTACCAAAATATAA 59.389 38.462 0.00 0.00 37.11 0.98
9291 9715 6.170846 ACTCCCTCCGTACCAAAATATAAG 57.829 41.667 0.00 0.00 0.00 1.73
9292 9716 5.901276 ACTCCCTCCGTACCAAAATATAAGA 59.099 40.000 0.00 0.00 0.00 2.10
9293 9717 6.165700 TCCCTCCGTACCAAAATATAAGAC 57.834 41.667 0.00 0.00 0.00 3.01
9294 9718 5.662208 TCCCTCCGTACCAAAATATAAGACA 59.338 40.000 0.00 0.00 0.00 3.41
9295 9719 5.989777 CCCTCCGTACCAAAATATAAGACAG 59.010 44.000 0.00 0.00 0.00 3.51
9296 9720 6.407752 CCCTCCGTACCAAAATATAAGACAGT 60.408 42.308 0.00 0.00 0.00 3.55
9297 9721 7.046033 CCTCCGTACCAAAATATAAGACAGTT 58.954 38.462 0.00 0.00 0.00 3.16
9298 9722 7.551617 CCTCCGTACCAAAATATAAGACAGTTT 59.448 37.037 0.00 0.00 0.00 2.66
9299 9723 8.851541 TCCGTACCAAAATATAAGACAGTTTT 57.148 30.769 0.00 0.00 0.00 2.43
9300 9724 9.287373 TCCGTACCAAAATATAAGACAGTTTTT 57.713 29.630 0.00 0.00 0.00 1.94
9301 9725 9.337091 CCGTACCAAAATATAAGACAGTTTTTG 57.663 33.333 0.00 0.00 37.14 2.44
9302 9726 8.846607 CGTACCAAAATATAAGACAGTTTTTGC 58.153 33.333 0.00 0.00 36.45 3.68
9303 9727 9.685828 GTACCAAAATATAAGACAGTTTTTGCA 57.314 29.630 0.00 0.00 36.45 4.08
9304 9728 8.816640 ACCAAAATATAAGACAGTTTTTGCAG 57.183 30.769 0.00 0.00 36.45 4.41
9305 9729 8.421002 ACCAAAATATAAGACAGTTTTTGCAGT 58.579 29.630 0.00 0.00 36.45 4.40
9306 9730 9.260002 CCAAAATATAAGACAGTTTTTGCAGTT 57.740 29.630 0.00 0.00 36.45 3.16
9311 9735 9.846248 ATATAAGACAGTTTTTGCAGTTCATTC 57.154 29.630 0.00 0.00 0.00 2.67
9312 9736 5.581126 AGACAGTTTTTGCAGTTCATTCA 57.419 34.783 0.00 0.00 0.00 2.57
9313 9737 6.152932 AGACAGTTTTTGCAGTTCATTCAT 57.847 33.333 0.00 0.00 0.00 2.57
9314 9738 6.576185 AGACAGTTTTTGCAGTTCATTCATT 58.424 32.000 0.00 0.00 0.00 2.57
9315 9739 7.043565 AGACAGTTTTTGCAGTTCATTCATTT 58.956 30.769 0.00 0.00 0.00 2.32
9316 9740 7.550196 AGACAGTTTTTGCAGTTCATTCATTTT 59.450 29.630 0.00 0.00 0.00 1.82
9317 9741 7.465989 ACAGTTTTTGCAGTTCATTCATTTTG 58.534 30.769 0.00 0.00 0.00 2.44
9318 9742 7.333921 ACAGTTTTTGCAGTTCATTCATTTTGA 59.666 29.630 0.00 0.00 0.00 2.69
9319 9743 8.176365 CAGTTTTTGCAGTTCATTCATTTTGAA 58.824 29.630 0.00 0.00 41.09 2.69
9340 9764 9.522804 TTTGAACTGCAAAAACGTCTTATATTT 57.477 25.926 0.00 0.00 43.18 1.40
9341 9765 9.522804 TTGAACTGCAAAAACGTCTTATATTTT 57.477 25.926 0.00 0.00 32.46 1.82
9342 9766 8.963130 TGAACTGCAAAAACGTCTTATATTTTG 58.037 29.630 13.82 13.82 42.66 2.44
9343 9767 9.176181 GAACTGCAAAAACGTCTTATATTTTGA 57.824 29.630 19.73 8.16 42.48 2.69
9344 9768 9.691362 AACTGCAAAAACGTCTTATATTTTGAT 57.309 25.926 19.73 6.17 42.48 2.57
9352 9776 7.948278 ACGTCTTATATTTTGATACAGAGGC 57.052 36.000 0.00 0.00 0.00 4.70
9353 9777 7.497595 ACGTCTTATATTTTGATACAGAGGCA 58.502 34.615 0.00 0.00 0.00 4.75
9354 9778 7.653713 ACGTCTTATATTTTGATACAGAGGCAG 59.346 37.037 0.00 0.00 0.00 4.85
9355 9779 7.653713 CGTCTTATATTTTGATACAGAGGCAGT 59.346 37.037 0.00 0.00 0.00 4.40
9356 9780 9.982651 GTCTTATATTTTGATACAGAGGCAGTA 57.017 33.333 0.00 0.00 0.00 2.74
9357 9781 9.982651 TCTTATATTTTGATACAGAGGCAGTAC 57.017 33.333 0.00 0.00 0.00 2.73
9358 9782 9.764363 CTTATATTTTGATACAGAGGCAGTACA 57.236 33.333 0.00 0.00 0.00 2.90
9360 9784 6.932356 ATTTTGATACAGAGGCAGTACATG 57.068 37.500 0.00 0.00 0.00 3.21
9367 9791 3.011818 CAGAGGCAGTACATGATTTGCA 58.988 45.455 17.16 0.00 38.27 4.08
9368 9792 3.441222 CAGAGGCAGTACATGATTTGCAA 59.559 43.478 17.16 0.00 38.27 4.08
9392 9816 3.397482 TGCTCTCTGAGAAAGCTGTTTC 58.603 45.455 9.44 0.00 42.25 2.78
9416 9849 8.818141 TCTTCTTTGTATAGTCTTGTTGTGAG 57.182 34.615 0.00 0.00 0.00 3.51
9423 9856 0.861837 GTCTTGTTGTGAGCCGTGAG 59.138 55.000 0.00 0.00 0.00 3.51
9528 9961 0.037139 TGTTGCTTTGCATCATGGCC 60.037 50.000 0.00 0.00 38.76 5.36
9531 9964 2.360767 GCTTTGCATCATGGCCCCA 61.361 57.895 0.00 0.00 0.00 4.96
9546 9979 8.365060 TCATGGCCCCATTTATTATTCTATTG 57.635 34.615 0.00 0.00 33.90 1.90
9589 10024 6.708949 TGAAGCTTAGGTTTAGTTAGGTTGTG 59.291 38.462 0.00 0.00 0.00 3.33
9743 10183 1.228215 CGGCATGGCATATGGTGGA 60.228 57.895 20.37 0.00 0.00 4.02
9744 10184 0.609957 CGGCATGGCATATGGTGGAT 60.610 55.000 20.37 0.00 0.00 3.41
9745 10185 0.892755 GGCATGGCATATGGTGGATG 59.107 55.000 15.47 0.00 0.00 3.51
9746 10186 1.624336 GCATGGCATATGGTGGATGT 58.376 50.000 0.00 0.00 0.00 3.06
9835 10281 8.684386 TCTACATGACTTTTATTTGTGGACAA 57.316 30.769 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.415426 GCTCTCTGCTCCGCTACC 59.585 66.667 0.00 0.00 38.95 3.18
13 14 2.657944 CGATGCGCTCTCTGCTCC 60.658 66.667 9.73 0.00 40.11 4.70
97 98 2.503546 GAGGAGGTAGCTGCTGCC 59.496 66.667 26.79 26.79 40.80 4.85
98 99 2.503546 GGAGGAGGTAGCTGCTGC 59.496 66.667 21.40 19.76 40.05 5.25
99 100 2.439104 GGGGAGGAGGTAGCTGCTG 61.439 68.421 21.40 0.00 0.00 4.41
100 101 2.041405 GGGGAGGAGGTAGCTGCT 60.041 66.667 16.43 16.43 0.00 4.24
101 102 2.365635 TGGGGAGGAGGTAGCTGC 60.366 66.667 5.14 5.14 0.00 5.25
102 103 2.439104 GCTGGGGAGGAGGTAGCTG 61.439 68.421 0.00 0.00 0.00 4.24
227 228 2.204448 TTGCCTCCCTTCCCCCAT 60.204 61.111 0.00 0.00 0.00 4.00
228 229 3.264845 GTTGCCTCCCTTCCCCCA 61.265 66.667 0.00 0.00 0.00 4.96
335 345 0.689080 AGATGATGAGGGGCGTGAGT 60.689 55.000 0.00 0.00 0.00 3.41
341 351 1.759881 CCAGGAGATGATGAGGGGC 59.240 63.158 0.00 0.00 0.00 5.80
356 372 2.612115 AGGGGGAGAAGGTGCCAG 60.612 66.667 0.00 0.00 38.84 4.85
375 391 2.832201 GGACGGAGGTACGGGAGG 60.832 72.222 0.00 0.00 38.39 4.30
377 393 1.755395 CATGGACGGAGGTACGGGA 60.755 63.158 0.00 0.00 38.39 5.14
378 394 2.812499 CATGGACGGAGGTACGGG 59.188 66.667 0.00 0.00 38.39 5.28
381 397 0.386113 GAGAGCATGGACGGAGGTAC 59.614 60.000 0.00 0.00 0.00 3.34
382 398 1.101635 CGAGAGCATGGACGGAGGTA 61.102 60.000 0.00 0.00 0.00 3.08
383 399 2.418910 CGAGAGCATGGACGGAGGT 61.419 63.158 0.00 0.00 0.00 3.85
384 400 2.415010 CGAGAGCATGGACGGAGG 59.585 66.667 0.00 0.00 0.00 4.30
428 444 0.681243 GGAGGGGATCACCAGCAAAC 60.681 60.000 18.46 0.00 42.91 2.93
429 445 1.691219 GGAGGGGATCACCAGCAAA 59.309 57.895 18.46 0.00 42.91 3.68
431 447 2.692368 GGGAGGGGATCACCAGCA 60.692 66.667 18.46 0.00 42.91 4.41
436 452 3.162154 GGACGGGGAGGGGATCAC 61.162 72.222 0.00 0.00 0.00 3.06
502 526 3.952799 AACAGGGGAGGGAGGGAGC 62.953 68.421 0.00 0.00 0.00 4.70
503 527 1.229984 AAACAGGGGAGGGAGGGAG 60.230 63.158 0.00 0.00 0.00 4.30
504 528 1.229853 GAAACAGGGGAGGGAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
506 530 1.617947 CGAGAAACAGGGGAGGGAGG 61.618 65.000 0.00 0.00 0.00 4.30
508 532 1.612442 CCGAGAAACAGGGGAGGGA 60.612 63.158 0.00 0.00 0.00 4.20
509 533 1.489560 AACCGAGAAACAGGGGAGGG 61.490 60.000 0.00 0.00 0.00 4.30
515 539 1.007336 CCGACGAACCGAGAAACAGG 61.007 60.000 0.00 0.00 0.00 4.00
542 566 3.753434 CGCTCACTCACCGAGGCT 61.753 66.667 0.00 0.00 33.35 4.58
570 594 4.058124 CGAATCAGAAGTTGAGAACACCA 58.942 43.478 0.00 0.00 39.68 4.17
575 599 4.991056 CAGGAACGAATCAGAAGTTGAGAA 59.009 41.667 0.00 0.00 39.68 2.87
576 600 4.560128 CAGGAACGAATCAGAAGTTGAGA 58.440 43.478 0.00 0.00 39.68 3.27
577 601 3.124297 GCAGGAACGAATCAGAAGTTGAG 59.876 47.826 0.00 0.00 39.68 3.02
578 602 3.067106 GCAGGAACGAATCAGAAGTTGA 58.933 45.455 0.00 0.00 40.85 3.18
580 604 2.069273 CGCAGGAACGAATCAGAAGTT 58.931 47.619 0.00 0.00 34.06 2.66
581 605 1.000955 ACGCAGGAACGAATCAGAAGT 59.999 47.619 0.00 0.00 36.70 3.01
598 622 3.184683 CAGCTCAGAGGCGAACGC 61.185 66.667 10.81 10.81 41.06 4.84
654 678 1.409521 CGCATTCTACCATTTCCCCCA 60.410 52.381 0.00 0.00 0.00 4.96
742 766 7.536895 TTCGAGAATCAGTAGTACTCAGTAC 57.463 40.000 6.89 6.89 35.59 2.73
830 854 2.518949 CCACGCACTCATTGTTAATGC 58.481 47.619 0.00 0.00 38.77 3.56
853 878 1.070758 CGAATCACGGATCCAAGGGAT 59.929 52.381 13.41 5.51 46.28 3.85
977 1064 2.436292 CAGAGCAGGCAGGCAGAC 60.436 66.667 0.00 0.00 35.83 3.51
1173 1260 0.394565 ACTCACAGGTGAAGACAGCC 59.605 55.000 3.45 0.00 44.43 4.85
1328 1417 5.222631 GGTTGAATGAACACATGGAAGTTC 58.777 41.667 16.39 16.39 43.31 3.01
1353 1442 3.498774 ATATACCAGCAAGCAAGAGGG 57.501 47.619 0.00 0.00 0.00 4.30
1412 1501 8.201554 TCAGCTAAGTTGATAAGCTTAATGTG 57.798 34.615 10.85 0.00 43.97 3.21
1413 1502 8.792830 TTCAGCTAAGTTGATAAGCTTAATGT 57.207 30.769 10.85 0.00 43.97 2.71
1417 1506 7.251704 GCATTCAGCTAAGTTGATAAGCTTA 57.748 36.000 8.99 8.99 43.97 3.09
1467 1560 4.843220 AATGGTCATATAAGCAGCAAGC 57.157 40.909 0.00 0.00 46.19 4.01
1468 1561 5.526115 CCAAATGGTCATATAAGCAGCAAG 58.474 41.667 0.00 0.00 0.00 4.01
1495 1588 1.466024 GGACTAGTCTGACGAACAGCG 60.466 57.143 21.88 0.00 45.38 5.18
1657 1750 2.057922 AGTTTTGCTGAGGGAAGGAGA 58.942 47.619 0.00 0.00 0.00 3.71
1701 1794 5.008217 CCATTGGTTTGAGACGTTCAGTTTA 59.992 40.000 0.00 0.00 37.07 2.01
1710 1803 4.216257 AGTTGATTCCATTGGTTTGAGACG 59.784 41.667 1.86 0.00 0.00 4.18
1721 1814 1.176527 CGGTGCCAGTTGATTCCATT 58.823 50.000 0.00 0.00 0.00 3.16
1864 1957 3.625313 TCTTCATTTTGCACGAACTCACA 59.375 39.130 0.00 0.00 0.00 3.58
1865 1958 4.209452 TCTTCATTTTGCACGAACTCAC 57.791 40.909 0.00 0.00 0.00 3.51
2317 2412 3.555324 TGGCGGCAGTCCACTCAA 61.555 61.111 7.97 0.00 0.00 3.02
2322 2417 0.034574 ATTATTGTGGCGGCAGTCCA 60.035 50.000 13.91 3.82 0.00 4.02
2712 2807 9.753674 TCCATTGGTGAAGACTAAATAGAAAAT 57.246 29.630 1.86 0.00 0.00 1.82
2729 2824 8.739039 TGTTTATTTTCAGATACTCCATTGGTG 58.261 33.333 1.86 2.59 0.00 4.17
2821 2916 4.753107 CACACACCAAGTACGATAAGGTTT 59.247 41.667 0.00 0.00 0.00 3.27
2849 2944 3.075884 GGTAATAAACAAGTCCACGCCA 58.924 45.455 0.00 0.00 0.00 5.69
2850 2945 3.340928 AGGTAATAAACAAGTCCACGCC 58.659 45.455 0.00 0.00 0.00 5.68
2865 2960 2.627699 CACCACAGCCAAACAAGGTAAT 59.372 45.455 0.00 0.00 0.00 1.89
3045 3141 5.918576 AGCTTATAAACGGAAACAAAAGTGC 59.081 36.000 0.00 0.00 0.00 4.40
3078 3174 3.181479 TGCGATAAGGGTGCTAAGTACAG 60.181 47.826 0.00 0.00 0.00 2.74
3089 3185 4.955811 TGAACTATGATGCGATAAGGGT 57.044 40.909 0.00 0.00 0.00 4.34
3185 3281 1.187974 TCCAATTTCCTACCGCGAGA 58.812 50.000 8.23 0.00 0.00 4.04
3865 3973 6.155475 TGAACAAGATGAAAACCCGAATTT 57.845 33.333 0.00 0.00 0.00 1.82
4175 4283 3.692101 TCAGTGAAACGAGAAGCCAAAAA 59.308 39.130 0.00 0.00 45.86 1.94
4261 4369 2.222027 CAACTCCTTCTTTGCCTTCGT 58.778 47.619 0.00 0.00 0.00 3.85
4465 4573 2.238521 GGGTTCCATGAGCAAAGTCAA 58.761 47.619 0.00 0.00 0.00 3.18
4534 4642 4.537965 CCTCATAGTCGACGTCCTATTTG 58.462 47.826 10.58 3.15 0.00 2.32
4565 4673 2.151202 GGCAATTCTGAGTTTCGTGGA 58.849 47.619 0.00 0.00 0.00 4.02
4612 4720 4.575885 ACGGAGCTGAATTTAGCACTTTA 58.424 39.130 22.65 0.00 46.07 1.85
4896 5004 8.227791 TCGCAGAATTTACTAAACAGAATTGTC 58.772 33.333 0.00 0.00 36.23 3.18
4905 5016 7.527457 AGACCAAATCGCAGAATTTACTAAAC 58.473 34.615 0.00 0.00 43.58 2.01
5584 5710 8.314021 GGAATTGAAGGTCTAAATTTTCCACAT 58.686 33.333 0.00 0.00 32.32 3.21
5894 6062 3.102052 CAGAAAGTTGGCTGCAACAAT 57.898 42.857 14.29 5.48 37.52 2.71
5938 6106 7.775093 AGAATATAACTGCTTTGCATTACCTCA 59.225 33.333 0.00 0.00 38.13 3.86
6089 6257 7.095649 GGCATGTAAAAGAACATCAGGAAAAAC 60.096 37.037 0.00 0.00 38.01 2.43
6223 6391 3.072915 TCTCCAGCCAGAGTGATTTTTCA 59.927 43.478 0.89 0.00 35.28 2.69
6294 6462 1.595382 GTGTGCACGACAGAAGGCT 60.595 57.895 13.13 0.00 34.28 4.58
6534 6702 7.298122 CAGAAGCACGTATAACTGTGAAAAAT 58.702 34.615 0.00 0.00 38.36 1.82
7194 7459 1.885887 TCAAATTCCAAGCCTGGTTCG 59.114 47.619 0.15 0.00 43.97 3.95
7701 7966 9.656040 TTGAGACAAATCCAATCCAATATTTTG 57.344 29.630 0.00 0.00 0.00 2.44
7845 8110 1.623811 CCAATCATAGTACCCCCTCCG 59.376 57.143 0.00 0.00 0.00 4.63
8257 8529 2.472695 TTCGTCTGAAGTTGATGGGG 57.527 50.000 0.00 0.00 0.00 4.96
8279 8551 3.175594 ACAAGTTCTCCCGGGTGTTATA 58.824 45.455 22.86 0.00 0.00 0.98
8326 8598 2.674177 GCTTAGAAAGGCTACGCTGACA 60.674 50.000 0.00 0.00 40.24 3.58
8904 9224 0.322322 TGTTCCTACGATTTGCCGGT 59.678 50.000 1.90 0.00 0.00 5.28
8905 9225 1.129811 GTTGTTCCTACGATTTGCCGG 59.870 52.381 0.00 0.00 0.00 6.13
8906 9226 1.801771 TGTTGTTCCTACGATTTGCCG 59.198 47.619 0.00 0.00 0.00 5.69
8907 9227 3.907894 TTGTTGTTCCTACGATTTGCC 57.092 42.857 0.00 0.00 0.00 4.52
8908 9228 4.023536 TCCTTTGTTGTTCCTACGATTTGC 60.024 41.667 0.00 0.00 0.00 3.68
8909 9229 5.449304 GTCCTTTGTTGTTCCTACGATTTG 58.551 41.667 0.00 0.00 0.00 2.32
8910 9230 4.517832 GGTCCTTTGTTGTTCCTACGATTT 59.482 41.667 0.00 0.00 0.00 2.17
8911 9231 4.070009 GGTCCTTTGTTGTTCCTACGATT 58.930 43.478 0.00 0.00 0.00 3.34
8912 9232 3.671716 GGTCCTTTGTTGTTCCTACGAT 58.328 45.455 0.00 0.00 0.00 3.73
8913 9233 2.546373 CGGTCCTTTGTTGTTCCTACGA 60.546 50.000 0.00 0.00 0.00 3.43
8914 9234 1.796459 CGGTCCTTTGTTGTTCCTACG 59.204 52.381 0.00 0.00 0.00 3.51
8915 9235 1.534163 GCGGTCCTTTGTTGTTCCTAC 59.466 52.381 0.00 0.00 0.00 3.18
8916 9236 1.874739 CGCGGTCCTTTGTTGTTCCTA 60.875 52.381 0.00 0.00 0.00 2.94
8917 9237 1.164041 CGCGGTCCTTTGTTGTTCCT 61.164 55.000 0.00 0.00 0.00 3.36
8918 9238 1.161563 TCGCGGTCCTTTGTTGTTCC 61.162 55.000 6.13 0.00 0.00 3.62
8919 9239 0.658897 TTCGCGGTCCTTTGTTGTTC 59.341 50.000 6.13 0.00 0.00 3.18
8920 9240 0.661020 CTTCGCGGTCCTTTGTTGTT 59.339 50.000 6.13 0.00 0.00 2.83
8921 9241 0.179067 TCTTCGCGGTCCTTTGTTGT 60.179 50.000 6.13 0.00 0.00 3.32
8922 9242 0.941542 TTCTTCGCGGTCCTTTGTTG 59.058 50.000 6.13 0.00 0.00 3.33
8923 9243 0.942252 GTTCTTCGCGGTCCTTTGTT 59.058 50.000 6.13 0.00 0.00 2.83
8924 9244 1.219522 CGTTCTTCGCGGTCCTTTGT 61.220 55.000 6.13 0.00 0.00 2.83
8925 9245 1.491563 CGTTCTTCGCGGTCCTTTG 59.508 57.895 6.13 0.00 0.00 2.77
8926 9246 1.666872 CCGTTCTTCGCGGTCCTTT 60.667 57.895 6.13 0.00 43.84 3.11
8927 9247 2.048503 CCGTTCTTCGCGGTCCTT 60.049 61.111 6.13 0.00 43.84 3.36
8933 9253 2.426183 CGACTGACCGTTCTTCGCG 61.426 63.158 0.00 0.00 38.35 5.87
8934 9254 1.335697 GACGACTGACCGTTCTTCGC 61.336 60.000 4.84 0.00 43.49 4.70
8935 9255 1.058590 CGACGACTGACCGTTCTTCG 61.059 60.000 0.00 3.64 43.49 3.79
8936 9256 1.335697 GCGACGACTGACCGTTCTTC 61.336 60.000 0.00 0.00 43.49 2.87
8937 9257 1.371389 GCGACGACTGACCGTTCTT 60.371 57.895 0.00 0.00 43.49 2.52
8938 9258 2.254651 GCGACGACTGACCGTTCT 59.745 61.111 0.00 0.00 43.49 3.01
8939 9259 2.804090 GGCGACGACTGACCGTTC 60.804 66.667 0.00 0.00 43.49 3.95
8958 9278 0.316522 CTCGTGATCATGATCCCGCT 59.683 55.000 28.81 0.00 38.32 5.52
8987 9307 8.545472 GGCAATACACCACCTTATTATCCTATA 58.455 37.037 0.00 0.00 0.00 1.31
8988 9308 7.402862 GGCAATACACCACCTTATTATCCTAT 58.597 38.462 0.00 0.00 0.00 2.57
8989 9309 6.519382 CGGCAATACACCACCTTATTATCCTA 60.519 42.308 0.00 0.00 0.00 2.94
8990 9310 5.631119 GGCAATACACCACCTTATTATCCT 58.369 41.667 0.00 0.00 0.00 3.24
9011 9331 3.499737 CTCAACGGACATGGCGGC 61.500 66.667 5.94 0.00 0.00 6.53
9020 9340 2.254546 ACAAACATCAGCTCAACGGA 57.745 45.000 0.00 0.00 0.00 4.69
9113 9442 4.693283 TCACAAGCCGGTTTGATATAGAG 58.307 43.478 34.14 15.25 0.00 2.43
9168 9503 2.625790 GCTAGACACGATGGGAGATCTT 59.374 50.000 0.00 0.00 0.00 2.40
9175 9510 0.249073 CGAAGGCTAGACACGATGGG 60.249 60.000 9.12 0.00 0.00 4.00
9177 9512 0.179137 TGCGAAGGCTAGACACGATG 60.179 55.000 17.15 0.00 40.82 3.84
9178 9513 0.747255 ATGCGAAGGCTAGACACGAT 59.253 50.000 17.15 6.79 40.82 3.73
9179 9514 0.179137 CATGCGAAGGCTAGACACGA 60.179 55.000 17.15 5.04 40.82 4.35
9182 9517 2.472695 AAACATGCGAAGGCTAGACA 57.527 45.000 0.00 0.00 40.82 3.41
9187 9523 3.733443 AAAAGAAAACATGCGAAGGCT 57.267 38.095 0.00 0.00 40.82 4.58
9194 9530 9.321590 GAAAATATGCAGAAAAAGAAAACATGC 57.678 29.630 0.00 0.00 0.00 4.06
9227 9647 0.321564 TCAGGGCCTTGAATCACACG 60.322 55.000 16.40 0.00 0.00 4.49
9263 9687 2.062971 TGGTACGGAGGGAGTACATC 57.937 55.000 8.48 0.00 44.45 3.06
9265 9689 2.307496 TTTGGTACGGAGGGAGTACA 57.693 50.000 8.48 0.00 44.45 2.90
9266 9690 3.900966 ATTTTGGTACGGAGGGAGTAC 57.099 47.619 0.00 0.00 42.58 2.73
9268 9692 5.901276 TCTTATATTTTGGTACGGAGGGAGT 59.099 40.000 0.00 0.00 0.00 3.85
9271 9695 5.920903 TGTCTTATATTTTGGTACGGAGGG 58.079 41.667 0.00 0.00 0.00 4.30
9273 9697 8.488651 AAACTGTCTTATATTTTGGTACGGAG 57.511 34.615 0.00 0.00 0.00 4.63
9275 9699 9.337091 CAAAAACTGTCTTATATTTTGGTACGG 57.663 33.333 5.60 0.00 37.34 4.02
9276 9700 8.846607 GCAAAAACTGTCTTATATTTTGGTACG 58.153 33.333 12.42 0.00 39.90 3.67
9277 9701 9.685828 TGCAAAAACTGTCTTATATTTTGGTAC 57.314 29.630 12.42 0.00 39.90 3.34
9279 9703 8.421002 ACTGCAAAAACTGTCTTATATTTTGGT 58.579 29.630 12.42 3.67 39.90 3.67
9285 9709 9.846248 GAATGAACTGCAAAAACTGTCTTATAT 57.154 29.630 0.00 0.00 0.00 0.86
9286 9710 8.845227 TGAATGAACTGCAAAAACTGTCTTATA 58.155 29.630 0.00 0.00 0.00 0.98
9287 9711 7.715657 TGAATGAACTGCAAAAACTGTCTTAT 58.284 30.769 0.00 0.00 0.00 1.73
9288 9712 7.094508 TGAATGAACTGCAAAAACTGTCTTA 57.905 32.000 0.00 0.00 0.00 2.10
9289 9713 5.964758 TGAATGAACTGCAAAAACTGTCTT 58.035 33.333 0.00 0.00 0.00 3.01
9290 9714 5.581126 TGAATGAACTGCAAAAACTGTCT 57.419 34.783 0.00 0.00 0.00 3.41
9291 9715 6.833342 AATGAATGAACTGCAAAAACTGTC 57.167 33.333 0.00 0.00 0.00 3.51
9292 9716 7.333921 TCAAAATGAATGAACTGCAAAAACTGT 59.666 29.630 0.00 0.00 0.00 3.55
9293 9717 7.686519 TCAAAATGAATGAACTGCAAAAACTG 58.313 30.769 0.00 0.00 0.00 3.16
9294 9718 7.846644 TCAAAATGAATGAACTGCAAAAACT 57.153 28.000 0.00 0.00 0.00 2.66
9314 9738 9.522804 AAATATAAGACGTTTTTGCAGTTCAAA 57.477 25.926 0.00 0.00 42.50 2.69
9315 9739 9.522804 AAAATATAAGACGTTTTTGCAGTTCAA 57.477 25.926 0.00 0.00 0.00 2.69
9316 9740 8.963130 CAAAATATAAGACGTTTTTGCAGTTCA 58.037 29.630 7.67 0.00 33.75 3.18
9317 9741 9.176181 TCAAAATATAAGACGTTTTTGCAGTTC 57.824 29.630 13.47 0.00 38.38 3.01
9318 9742 9.691362 ATCAAAATATAAGACGTTTTTGCAGTT 57.309 25.926 13.47 0.00 38.38 3.16
9326 9750 8.827677 GCCTCTGTATCAAAATATAAGACGTTT 58.172 33.333 0.00 0.00 0.00 3.60
9327 9751 7.985184 TGCCTCTGTATCAAAATATAAGACGTT 59.015 33.333 0.00 0.00 0.00 3.99
9328 9752 7.497595 TGCCTCTGTATCAAAATATAAGACGT 58.502 34.615 0.00 0.00 0.00 4.34
9329 9753 7.653713 ACTGCCTCTGTATCAAAATATAAGACG 59.346 37.037 0.00 0.00 0.00 4.18
9330 9754 8.894768 ACTGCCTCTGTATCAAAATATAAGAC 57.105 34.615 0.00 0.00 0.00 3.01
9331 9755 9.982651 GTACTGCCTCTGTATCAAAATATAAGA 57.017 33.333 0.00 0.00 0.00 2.10
9332 9756 9.764363 TGTACTGCCTCTGTATCAAAATATAAG 57.236 33.333 0.00 0.00 0.00 1.73
9334 9758 9.710900 CATGTACTGCCTCTGTATCAAAATATA 57.289 33.333 0.00 0.00 0.00 0.86
9335 9759 8.432013 TCATGTACTGCCTCTGTATCAAAATAT 58.568 33.333 0.00 0.00 0.00 1.28
9336 9760 7.791029 TCATGTACTGCCTCTGTATCAAAATA 58.209 34.615 0.00 0.00 0.00 1.40
9337 9761 6.653020 TCATGTACTGCCTCTGTATCAAAAT 58.347 36.000 0.00 0.00 0.00 1.82
9338 9762 6.048732 TCATGTACTGCCTCTGTATCAAAA 57.951 37.500 0.00 0.00 0.00 2.44
9339 9763 5.675684 TCATGTACTGCCTCTGTATCAAA 57.324 39.130 0.00 0.00 0.00 2.69
9340 9764 5.876651 ATCATGTACTGCCTCTGTATCAA 57.123 39.130 0.00 0.00 0.00 2.57
9341 9765 5.876651 AATCATGTACTGCCTCTGTATCA 57.123 39.130 0.00 0.00 0.00 2.15
9342 9766 5.049818 GCAAATCATGTACTGCCTCTGTATC 60.050 44.000 0.00 0.00 0.00 2.24
9343 9767 4.818546 GCAAATCATGTACTGCCTCTGTAT 59.181 41.667 0.00 0.00 0.00 2.29
9344 9768 4.191544 GCAAATCATGTACTGCCTCTGTA 58.808 43.478 0.00 0.00 0.00 2.74
9345 9769 3.012518 GCAAATCATGTACTGCCTCTGT 58.987 45.455 0.00 0.00 0.00 3.41
9346 9770 3.011818 TGCAAATCATGTACTGCCTCTG 58.988 45.455 11.34 0.00 33.78 3.35
9347 9771 3.354948 TGCAAATCATGTACTGCCTCT 57.645 42.857 11.34 0.00 33.78 3.69
9348 9772 4.644103 ATTGCAAATCATGTACTGCCTC 57.356 40.909 1.71 0.00 33.78 4.70
9349 9773 5.172934 CAAATTGCAAATCATGTACTGCCT 58.827 37.500 1.71 0.11 33.78 4.75
9350 9774 4.201744 GCAAATTGCAAATCATGTACTGCC 60.202 41.667 13.73 0.00 44.26 4.85
9351 9775 4.889241 GCAAATTGCAAATCATGTACTGC 58.111 39.130 13.73 0.00 44.26 4.40
9367 9791 4.396522 ACAGCTTTCTCAGAGAGCAAATT 58.603 39.130 18.96 0.00 41.41 1.82
9368 9792 4.018484 ACAGCTTTCTCAGAGAGCAAAT 57.982 40.909 18.96 1.34 41.41 2.32
9392 9816 7.360438 GGCTCACAACAAGACTATACAAAGAAG 60.360 40.741 0.00 0.00 0.00 2.85
9395 9819 5.163953 CGGCTCACAACAAGACTATACAAAG 60.164 44.000 0.00 0.00 0.00 2.77
9399 9823 3.612860 CACGGCTCACAACAAGACTATAC 59.387 47.826 0.00 0.00 0.00 1.47
9404 9837 0.861837 CTCACGGCTCACAACAAGAC 59.138 55.000 0.00 0.00 0.00 3.01
9416 9849 0.735632 CAGACTTCAGAGCTCACGGC 60.736 60.000 17.77 2.79 42.19 5.68
9423 9856 1.338579 CCCAGGTTCAGACTTCAGAGC 60.339 57.143 0.00 0.00 0.00 4.09
9589 10024 2.029623 AGTGATGAATTGGCATCTGGC 58.970 47.619 8.21 0.00 43.89 4.85
9628 10063 1.798813 ACCTTCAAAAAGCTAGCGACG 59.201 47.619 9.55 0.00 0.00 5.12
9635 10070 3.146847 CGACCCTAACCTTCAAAAAGCT 58.853 45.455 0.00 0.00 0.00 3.74
9743 10183 0.319405 GGGCAAGCAAGCAAGAACAT 59.681 50.000 2.78 0.00 35.83 2.71
9744 10184 0.756442 AGGGCAAGCAAGCAAGAACA 60.756 50.000 2.78 0.00 35.83 3.18
9745 10185 0.390492 AAGGGCAAGCAAGCAAGAAC 59.610 50.000 2.78 0.00 35.83 3.01
9746 10186 1.122227 AAAGGGCAAGCAAGCAAGAA 58.878 45.000 2.78 0.00 35.83 2.52
9807 10253 7.750903 GTCCACAAATAAAAGTCATGTAGAAGC 59.249 37.037 0.00 0.00 0.00 3.86
9858 10309 0.597118 TTGCGCTGTTGCCATCAAAC 60.597 50.000 9.73 0.00 33.37 2.93
9873 10325 5.174761 TCAATTTCAATTTCCGAAGTTTGCG 59.825 36.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.