Multiple sequence alignment - TraesCS5A01G537000

Loading Multiple Alignment...

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 TraesCS5A01G537000 chr5A 100.000 8042 0 0 1 8042 693625191 693633232 0.000000e+00 14851.0
1 TraesCS5A01G537000 chr5A 79.880 666 107 21 21 680 441136925 441137569 5.690000e-126 462.0
2 TraesCS5A01G537000 chr5A 90.698 86 6 2 7480 7565 693632627 693632710 6.600000e-21 113.0
3 TraesCS5A01G537000 chr5A 90.698 86 6 2 7437 7520 693632670 693632755 6.600000e-21 113.0
4 TraesCS5A01G537000 chr4D 92.154 5391 192 71 747 6011 508256608 508261893 0.000000e+00 7398.0
5 TraesCS5A01G537000 chr4D 96.016 1481 54 5 6056 7533 508261898 508263376 0.000000e+00 2403.0
6 TraesCS5A01G537000 chr4D 95.851 482 16 1 7564 8041 508264401 508264882 0.000000e+00 776.0
7 TraesCS5A01G537000 chr4D 81.640 561 93 6 72 631 460649139 460648588 2.650000e-124 457.0
8 TraesCS5A01G537000 chr4B 92.210 2195 115 21 1747 3910 659589483 659587314 0.000000e+00 3055.0
9 TraesCS5A01G537000 chr4B 92.812 1920 115 17 5656 7564 659585585 659583678 0.000000e+00 2760.0
10 TraesCS5A01G537000 chr4B 93.643 1699 62 11 3934 5608 659587259 659585583 0.000000e+00 2497.0
11 TraesCS5A01G537000 chr4B 91.584 606 27 3 6816 7419 656829116 656828533 0.000000e+00 815.0
12 TraesCS5A01G537000 chr4B 89.786 607 40 12 7453 8038 656828532 656827927 0.000000e+00 758.0
13 TraesCS5A01G537000 chr4B 95.354 452 21 0 7590 8041 659583580 659583129 0.000000e+00 719.0
14 TraesCS5A01G537000 chr4B 84.155 669 40 25 1086 1714 659590121 659589479 8.990000e-164 588.0
15 TraesCS5A01G537000 chr4B 87.413 286 22 6 677 956 659590463 659590186 4.680000e-82 316.0
16 TraesCS5A01G537000 chr4B 100.000 62 0 0 996 1057 659590181 659590120 1.830000e-21 115.0
17 TraesCS5A01G537000 chr4B 88.372 86 9 1 7480 7565 659583805 659583721 1.430000e-17 102.0
18 TraesCS5A01G537000 chr4B 85.714 70 8 1 7496 7565 656828532 656828465 1.120000e-08 73.1
19 TraesCS5A01G537000 chrUn 80.368 652 106 17 31 679 39246724 39247356 7.300000e-130 475.0
20 TraesCS5A01G537000 chr7D 80.435 644 102 20 24 662 133886919 133887543 3.400000e-128 470.0
21 TraesCS5A01G537000 chr7B 79.755 652 102 22 21 662 100358686 100359317 5.730000e-121 446.0
22 TraesCS5A01G537000 chr7B 79.278 637 105 17 33 662 680192448 680193064 3.470000e-113 420.0
23 TraesCS5A01G537000 chr3D 78.869 672 108 24 24 686 511055372 511056018 2.680000e-114 424.0
24 TraesCS5A01G537000 chr3D 100.000 28 0 0 7852 7879 488903043 488903070 1.500000e-02 52.8
25 TraesCS5A01G537000 chr3D 100.000 28 0 0 7852 7879 488950113 488950140 1.500000e-02 52.8
26 TraesCS5A01G537000 chr2B 78.955 651 105 26 21 662 120562011 120561384 1.610000e-111 414.0
27 TraesCS5A01G537000 chr2B 100.000 28 0 0 7852 7879 798591448 798591421 1.500000e-02 52.8
28 TraesCS5A01G537000 chr2B 100.000 28 0 0 7852 7879 798730336 798730363 1.500000e-02 52.8
29 TraesCS5A01G537000 chr3B 78.659 656 111 19 17 662 644146440 644145804 7.510000e-110 409.0
30 TraesCS5A01G537000 chr1B 76.596 282 54 12 7766 8041 403578187 403578462 2.340000e-30 145.0
31 TraesCS5A01G537000 chr1B 86.735 98 12 1 7944 8041 18386023 18386119 3.070000e-19 108.0
32 TraesCS5A01G537000 chr1D 86.957 92 11 1 7950 8041 13042849 13042759 1.430000e-17 102.0
33 TraesCS5A01G537000 chr3A 100.000 28 0 0 7852 7879 632041211 632041184 1.500000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G537000 chr5A 693625191 693633232 8041 False 5025.666667 14851 93.798667 1 8042 3 chr5A.!!$F2 8041
1 TraesCS5A01G537000 chr5A 441136925 441137569 644 False 462.000000 462 79.880000 21 680 1 chr5A.!!$F1 659
2 TraesCS5A01G537000 chr4D 508256608 508264882 8274 False 3525.666667 7398 94.673667 747 8041 3 chr4D.!!$F1 7294
3 TraesCS5A01G537000 chr4D 460648588 460649139 551 True 457.000000 457 81.640000 72 631 1 chr4D.!!$R1 559
4 TraesCS5A01G537000 chr4B 659583129 659590463 7334 True 1269.000000 3055 91.744875 677 8041 8 chr4B.!!$R2 7364
5 TraesCS5A01G537000 chr4B 656827927 656829116 1189 True 548.700000 815 89.028000 6816 8038 3 chr4B.!!$R1 1222
6 TraesCS5A01G537000 chrUn 39246724 39247356 632 False 475.000000 475 80.368000 31 679 1 chrUn.!!$F1 648
7 TraesCS5A01G537000 chr7D 133886919 133887543 624 False 470.000000 470 80.435000 24 662 1 chr7D.!!$F1 638
8 TraesCS5A01G537000 chr7B 100358686 100359317 631 False 446.000000 446 79.755000 21 662 1 chr7B.!!$F1 641
9 TraesCS5A01G537000 chr7B 680192448 680193064 616 False 420.000000 420 79.278000 33 662 1 chr7B.!!$F2 629
10 TraesCS5A01G537000 chr3D 511055372 511056018 646 False 424.000000 424 78.869000 24 686 1 chr3D.!!$F3 662
11 TraesCS5A01G537000 chr2B 120561384 120562011 627 True 414.000000 414 78.955000 21 662 1 chr2B.!!$R1 641
12 TraesCS5A01G537000 chr3B 644145804 644146440 636 True 409.000000 409 78.659000 17 662 1 chr3B.!!$R1 645

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
634 644 0.035534 TCGTTGTACTGCCATGCCAT 60.036 50.0 0.00 0.00 0.00 4.40 F
2019 2104 0.040958 CACGTGAGCTTTCCTGCAAC 60.041 55.0 10.90 0.00 34.99 4.17 F
2721 2816 0.036010 TCTTTGGCTGCTGGCTAGTC 60.036 55.0 17.87 0.00 41.46 2.59 F
3822 3921 0.400213 TCGTTTGACCCTTCCAGCAT 59.600 50.0 0.00 0.00 0.00 3.79 F
3927 4038 0.452987 ATGTGATGTGCGTGATTGCC 59.547 50.0 0.00 0.00 0.00 4.52 F
3949 4091 1.218844 AATAACTACACCCCGGGCAT 58.781 50.0 17.73 1.11 0.00 4.40 F
3951 4093 1.339644 TAACTACACCCCGGGCATCC 61.340 60.0 17.73 0.00 0.00 3.51 F
5679 5856 1.235724 GCCGTTAGACCTTTTGCTGT 58.764 50.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 2530 0.036388 GCTACCTGGCAGCACTAACA 60.036 55.000 14.08 0.0 38.93 2.41 R
3911 4022 0.390472 TACGGCAATCACGCACATCA 60.390 50.000 0.00 0.0 34.00 3.07 R
3912 4023 0.724549 TTACGGCAATCACGCACATC 59.275 50.000 0.00 0.0 34.00 3.06 R
5369 5546 1.612463 GCCCTGGATTCAGATTGATGC 59.388 52.381 1.24 0.0 43.49 3.91 R
5654 5831 3.687698 GCAAAAGGTCTAACGGCAGATAA 59.312 43.478 0.00 0.0 0.00 1.75 R
5662 5839 4.510340 ACAGTAACAGCAAAAGGTCTAACG 59.490 41.667 0.00 0.0 0.00 3.18 R
5873 6050 6.014413 TGCTCCATTTGAAAATTTCTCCATCA 60.014 34.615 7.29 0.0 0.00 3.07 R
7562 8727 0.822164 GAGGTTAAGGCACCGCTAGA 59.178 55.000 0.00 0.0 42.33 2.43 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.462427 AATATACGTGCGGCCAACA 57.538 47.368 2.24 0.00 0.00 3.33
19 20 1.740297 AATATACGTGCGGCCAACAA 58.260 45.000 2.24 0.00 0.00 2.83
58 66 1.290134 CCTAGGGTTTCCTCTGCCTT 58.710 55.000 0.00 0.00 43.66 4.35
81 89 3.537874 GGCACTATCGCCGGTCCT 61.538 66.667 1.90 0.00 43.52 3.85
91 99 2.272797 CCGGTCCTCCTCGTCTCT 59.727 66.667 0.00 0.00 0.00 3.10
97 105 1.304547 CCTCCTCGTCTCTGGTGGT 60.305 63.158 0.00 0.00 33.61 4.16
130 138 3.771160 GCGTGGTGGATCCCGACT 61.771 66.667 9.90 0.00 33.75 4.18
136 144 1.596934 GTGGATCCCGACTCTTGCA 59.403 57.895 9.90 0.00 0.00 4.08
137 145 0.179000 GTGGATCCCGACTCTTGCAT 59.821 55.000 9.90 0.00 0.00 3.96
139 147 0.179000 GGATCCCGACTCTTGCATGT 59.821 55.000 0.00 0.00 0.00 3.21
191 199 4.334481 CGAGTTTTGTTAGGGTTTGTGTCT 59.666 41.667 0.00 0.00 0.00 3.41
249 258 1.564348 TGAATAAGGTTCTCCCTGCCC 59.436 52.381 0.00 0.00 45.47 5.36
253 262 3.650950 GGTTCTCCCTGCCCAGCA 61.651 66.667 0.00 0.00 36.92 4.41
291 300 3.183172 CGTATAGCATCATCAGTGTGTGC 59.817 47.826 0.00 0.00 37.89 4.57
294 303 1.066929 AGCATCATCAGTGTGTGCGTA 60.067 47.619 0.00 0.00 40.43 4.42
296 305 1.929169 CATCATCAGTGTGTGCGTAGG 59.071 52.381 0.00 0.00 0.00 3.18
298 307 0.246360 CATCAGTGTGTGCGTAGGGA 59.754 55.000 0.00 0.00 0.00 4.20
303 312 1.375396 TGTGTGCGTAGGGATGTGC 60.375 57.895 0.00 0.00 0.00 4.57
351 360 1.204704 TGCTTGGATCTGGTCGTAGTG 59.795 52.381 0.00 0.00 0.00 2.74
354 363 0.963856 TGGATCTGGTCGTAGTGCGT 60.964 55.000 0.00 0.00 42.13 5.24
355 364 0.172803 GGATCTGGTCGTAGTGCGTT 59.827 55.000 0.00 0.00 42.13 4.84
356 365 1.403780 GGATCTGGTCGTAGTGCGTTT 60.404 52.381 0.00 0.00 42.13 3.60
357 366 2.159338 GGATCTGGTCGTAGTGCGTTTA 60.159 50.000 0.00 0.00 42.13 2.01
358 367 2.336554 TCTGGTCGTAGTGCGTTTAC 57.663 50.000 0.00 0.00 42.13 2.01
359 368 0.979811 CTGGTCGTAGTGCGTTTACG 59.020 55.000 0.00 7.82 43.82 3.18
374 383 2.232239 TTACGACTCTACGTTCGTGC 57.768 50.000 20.11 0.00 44.14 5.34
382 391 3.165890 CTCTACGTTCGTGCGTATTCAA 58.834 45.455 8.14 0.00 44.76 2.69
390 399 3.331150 TCGTGCGTATTCAAGTTGGATT 58.669 40.909 0.92 0.00 0.00 3.01
399 408 6.037172 CGTATTCAAGTTGGATTCTTCCGATT 59.963 38.462 0.92 0.00 45.89 3.34
414 423 4.707030 TCCGATTTACGCTACTCTTCAA 57.293 40.909 0.00 0.00 41.07 2.69
451 460 0.615331 CTGGTGTGCTGGTCCTATGT 59.385 55.000 0.00 0.00 0.00 2.29
454 463 0.324943 GTGTGCTGGTCCTATGTGGT 59.675 55.000 0.00 0.00 37.07 4.16
483 492 2.163815 CGACGACTTCCCAACTGTCTAT 59.836 50.000 0.00 0.00 0.00 1.98
485 494 3.926616 ACGACTTCCCAACTGTCTATTG 58.073 45.455 0.00 0.00 0.00 1.90
575 585 5.472478 AGTGTTTGTAGTCGTCACTAGATGA 59.528 40.000 0.00 0.00 35.67 2.92
581 591 6.579865 TGTAGTCGTCACTAGATGATCTACA 58.420 40.000 16.80 16.80 43.05 2.74
631 641 2.031683 GGTATTCGTTGTACTGCCATGC 59.968 50.000 0.00 0.00 0.00 4.06
632 642 1.094785 ATTCGTTGTACTGCCATGCC 58.905 50.000 0.00 0.00 0.00 4.40
633 643 0.250510 TTCGTTGTACTGCCATGCCA 60.251 50.000 0.00 0.00 0.00 4.92
634 644 0.035534 TCGTTGTACTGCCATGCCAT 60.036 50.000 0.00 0.00 0.00 4.40
635 645 1.208293 TCGTTGTACTGCCATGCCATA 59.792 47.619 0.00 0.00 0.00 2.74
636 646 1.330521 CGTTGTACTGCCATGCCATAC 59.669 52.381 0.00 0.00 0.00 2.39
641 651 2.742428 ACTGCCATGCCATACTTGAT 57.258 45.000 0.00 0.00 0.00 2.57
671 681 9.983804 GAATAAATCGGAAGTTTATTCGAAAGT 57.016 29.630 15.59 0.00 43.17 2.66
723 733 3.365666 CCTCGTGTTTACTCGTAAGCTGA 60.366 47.826 0.00 3.40 34.81 4.26
724 734 3.818387 TCGTGTTTACTCGTAAGCTGAG 58.182 45.455 0.00 0.00 39.40 3.35
725 735 2.341760 CGTGTTTACTCGTAAGCTGAGC 59.658 50.000 0.00 0.00 36.94 4.26
726 736 2.666994 GTGTTTACTCGTAAGCTGAGCC 59.333 50.000 0.00 0.00 36.94 4.70
727 737 2.297880 TGTTTACTCGTAAGCTGAGCCA 59.702 45.455 0.00 0.00 36.94 4.75
744 754 1.898574 CAAGCCAGTGTCACCACCC 60.899 63.158 0.00 0.00 42.88 4.61
745 755 2.382770 AAGCCAGTGTCACCACCCA 61.383 57.895 0.00 0.00 42.88 4.51
747 757 1.228552 GCCAGTGTCACCACCCAAT 60.229 57.895 0.00 0.00 42.88 3.16
801 811 5.952033 ACTACTAGAAGTTAAGCAAGTCGG 58.048 41.667 0.00 0.00 0.00 4.79
844 860 1.459592 CGGCTTCCTATAAAATCGGCG 59.540 52.381 0.00 0.00 0.00 6.46
849 865 0.949105 CCTATAAAATCGGCGCGCCT 60.949 55.000 43.60 29.18 0.00 5.52
887 903 0.383590 CTCCATCGTCATCGTCAGCT 59.616 55.000 0.00 0.00 38.33 4.24
888 904 0.101219 TCCATCGTCATCGTCAGCTG 59.899 55.000 7.63 7.63 38.33 4.24
890 906 1.227089 ATCGTCATCGTCAGCTGCC 60.227 57.895 9.47 0.00 38.33 4.85
891 907 1.670949 ATCGTCATCGTCAGCTGCCT 61.671 55.000 9.47 0.00 38.33 4.75
892 908 1.029947 TCGTCATCGTCAGCTGCCTA 61.030 55.000 9.47 0.00 38.33 3.93
893 909 0.867753 CGTCATCGTCAGCTGCCTAC 60.868 60.000 9.47 0.74 0.00 3.18
930 946 1.139654 CTCCAGCCGAGGAATCATCAA 59.860 52.381 0.00 0.00 37.20 2.57
953 975 4.405116 AAACAAATGCCACTGTGATTGT 57.595 36.364 9.86 11.41 32.78 2.71
956 978 1.624336 AATGCCACTGTGATTGTGCT 58.376 45.000 9.86 0.00 34.38 4.40
957 979 1.624336 ATGCCACTGTGATTGTGCTT 58.376 45.000 9.86 0.00 34.38 3.91
958 980 0.669619 TGCCACTGTGATTGTGCTTG 59.330 50.000 9.86 0.00 34.38 4.01
959 981 0.670162 GCCACTGTGATTGTGCTTGT 59.330 50.000 9.86 0.00 34.38 3.16
960 982 1.601162 GCCACTGTGATTGTGCTTGTG 60.601 52.381 9.86 0.00 34.38 3.33
961 983 1.601162 CCACTGTGATTGTGCTTGTGC 60.601 52.381 9.86 0.00 40.20 4.57
962 984 0.308684 ACTGTGATTGTGCTTGTGCG 59.691 50.000 0.00 0.00 43.34 5.34
978 1000 3.479370 CGCGAGCCAAGGAGAAAG 58.521 61.111 0.00 0.00 0.00 2.62
979 1001 2.103042 CGCGAGCCAAGGAGAAAGG 61.103 63.158 0.00 0.00 0.00 3.11
980 1002 1.746991 GCGAGCCAAGGAGAAAGGG 60.747 63.158 0.00 0.00 0.00 3.95
981 1003 1.078143 CGAGCCAAGGAGAAAGGGG 60.078 63.158 0.00 0.00 0.00 4.79
982 1004 1.304617 GAGCCAAGGAGAAAGGGGG 59.695 63.158 0.00 0.00 0.00 5.40
1218 1246 0.395311 TCGCCTACTCCAAGATCCGT 60.395 55.000 0.00 0.00 0.00 4.69
1383 1414 3.586174 TCTCATCCCATCTGATTGATCCC 59.414 47.826 0.00 0.00 32.05 3.85
1384 1415 2.303890 TCATCCCATCTGATTGATCCCG 59.696 50.000 0.00 0.00 32.05 5.14
1385 1416 0.397941 TCCCATCTGATTGATCCCGC 59.602 55.000 0.00 0.00 32.05 6.13
1386 1417 0.607489 CCCATCTGATTGATCCCGCC 60.607 60.000 0.00 0.00 32.05 6.13
1387 1418 0.952497 CCATCTGATTGATCCCGCCG 60.952 60.000 0.00 0.00 32.05 6.46
1388 1419 1.302033 ATCTGATTGATCCCGCCGC 60.302 57.895 0.00 0.00 0.00 6.53
1389 1420 2.738213 ATCTGATTGATCCCGCCGCC 62.738 60.000 0.00 0.00 0.00 6.13
1390 1421 4.908687 TGATTGATCCCGCCGCCG 62.909 66.667 0.00 0.00 0.00 6.46
1410 1441 4.810661 GCGCGCTCCTCTGCTTCT 62.811 66.667 26.67 0.00 0.00 2.85
1411 1442 2.581953 CGCGCTCCTCTGCTTCTC 60.582 66.667 5.56 0.00 0.00 2.87
1451 1482 9.586435 AAGAATCGAATTTTATTTTTAGCCTGG 57.414 29.630 0.00 0.00 0.00 4.45
1504 1543 7.786030 TCTGTTATTAGAAGACAGATTCAGGG 58.214 38.462 1.60 0.00 43.38 4.45
1508 1547 3.197927 AGAAGACAGATTCAGGGAGGT 57.802 47.619 0.00 0.00 0.00 3.85
1509 1548 3.525862 AGAAGACAGATTCAGGGAGGTT 58.474 45.455 0.00 0.00 0.00 3.50
1572 1625 3.057969 TGGCGATGATCTTCAACTGTT 57.942 42.857 9.10 0.00 0.00 3.16
1635 1707 2.187685 CAGGTGGAGCTATGCGCA 59.812 61.111 14.96 14.96 42.61 6.09
1645 1717 5.352569 GTGGAGCTATGCGCATAGATAAAAT 59.647 40.000 45.73 28.37 39.82 1.82
1699 1776 4.416620 CTGTAAAGCTAGAGAGACCAACG 58.583 47.826 0.00 0.00 0.00 4.10
1799 1879 2.179427 TCAGAATCATCGACACCCACT 58.821 47.619 0.00 0.00 0.00 4.00
1816 1896 3.077359 CCACTTCCCAGATCTTCACAAC 58.923 50.000 0.00 0.00 0.00 3.32
1847 1927 3.331150 CTGCGACATTTACCAACCTACA 58.669 45.455 0.00 0.00 0.00 2.74
1848 1928 3.331150 TGCGACATTTACCAACCTACAG 58.669 45.455 0.00 0.00 0.00 2.74
1849 1929 3.244284 TGCGACATTTACCAACCTACAGT 60.244 43.478 0.00 0.00 0.00 3.55
1850 1930 4.021280 TGCGACATTTACCAACCTACAGTA 60.021 41.667 0.00 0.00 0.00 2.74
1851 1931 4.328169 GCGACATTTACCAACCTACAGTAC 59.672 45.833 0.00 0.00 0.00 2.73
1852 1932 4.560035 CGACATTTACCAACCTACAGTACG 59.440 45.833 0.00 0.00 0.00 3.67
1853 1933 5.473039 GACATTTACCAACCTACAGTACGT 58.527 41.667 0.00 0.00 0.00 3.57
1858 1938 7.753309 TTTACCAACCTACAGTACGTACTAA 57.247 36.000 26.95 16.98 34.13 2.24
1860 1940 6.013842 ACCAACCTACAGTACGTACTAAAC 57.986 41.667 26.95 2.16 34.13 2.01
1862 1942 6.088824 CCAACCTACAGTACGTACTAAACTG 58.911 44.000 26.95 19.37 44.89 3.16
1910 1995 7.834068 AATTACCTGGATTAATCGATCGATG 57.166 36.000 29.99 17.10 34.70 3.84
1990 2075 2.049372 AGCAACTGCCCCTTTTGAATT 58.951 42.857 0.00 0.00 43.38 2.17
2019 2104 0.040958 CACGTGAGCTTTCCTGCAAC 60.041 55.000 10.90 0.00 34.99 4.17
2166 2261 5.132502 CCATCTTTTCCTTTTTGCCCTTTT 58.867 37.500 0.00 0.00 0.00 2.27
2167 2262 5.593909 CCATCTTTTCCTTTTTGCCCTTTTT 59.406 36.000 0.00 0.00 0.00 1.94
2192 2287 4.017499 ACATTACATTTTACAGCCCCCTCT 60.017 41.667 0.00 0.00 0.00 3.69
2195 2290 1.005924 CATTTTACAGCCCCCTCTGGT 59.994 52.381 0.00 0.00 38.36 4.00
2208 2303 3.386402 CCCCTCTGGTGAAGAAGTATCTC 59.614 52.174 0.00 0.00 33.77 2.75
2267 2362 2.209064 CTGTGCTGGGCATGTGAAGC 62.209 60.000 8.23 8.23 41.91 3.86
2428 2523 3.251004 GTGAAACTGTGAACCATCCTGTC 59.749 47.826 0.00 0.00 0.00 3.51
2430 2525 4.346709 TGAAACTGTGAACCATCCTGTCTA 59.653 41.667 0.00 0.00 0.00 2.59
2432 2527 6.212589 TGAAACTGTGAACCATCCTGTCTATA 59.787 38.462 0.00 0.00 0.00 1.31
2433 2528 5.860941 ACTGTGAACCATCCTGTCTATAG 57.139 43.478 0.00 0.00 0.00 1.31
2434 2529 5.273208 ACTGTGAACCATCCTGTCTATAGT 58.727 41.667 0.00 0.00 0.00 2.12
2435 2530 5.721960 ACTGTGAACCATCCTGTCTATAGTT 59.278 40.000 0.00 0.00 0.00 2.24
2617 2712 4.787598 ACAACACTTTCTGATTCGCATTC 58.212 39.130 0.00 0.00 0.00 2.67
2618 2713 4.161333 CAACACTTTCTGATTCGCATTCC 58.839 43.478 0.00 0.00 0.00 3.01
2658 2753 3.397849 TGGCACATGCTTAAAATTGCA 57.602 38.095 3.48 0.00 43.67 4.08
2688 2783 3.573538 TGGCAGAAAACTACACATTGCAT 59.426 39.130 0.00 0.00 0.00 3.96
2721 2816 0.036010 TCTTTGGCTGCTGGCTAGTC 60.036 55.000 17.87 0.00 41.46 2.59
2733 2828 1.007618 GCTAGTCGGTCCGGTATGC 60.008 63.158 12.29 7.87 0.00 3.14
2796 2891 8.322906 TCACTTCTTTTACATGAATCGATTGT 57.677 30.769 16.96 10.93 0.00 2.71
2801 2896 8.948853 TCTTTTACATGAATCGATTGTGTTTC 57.051 30.769 23.13 8.68 0.00 2.78
2837 2932 6.663523 CCCCATAAAGTATGTCTGGTTTTCTT 59.336 38.462 0.00 0.00 34.36 2.52
2904 2999 7.878477 AAATGCATGACTTTGTTAGAATGTG 57.122 32.000 0.00 0.00 0.00 3.21
2914 3009 7.743104 ACTTTGTTAGAATGTGCTCTTTATCG 58.257 34.615 0.00 0.00 0.00 2.92
2976 3071 2.449464 TGGGCAAGTCTCATTGAATGG 58.551 47.619 5.20 0.00 31.55 3.16
2978 3073 1.202222 GGCAAGTCTCATTGAATGGCG 60.202 52.381 5.20 0.00 40.36 5.69
3034 3129 2.362077 CTGCAGGTTTTGGTTGCTAACT 59.638 45.455 5.57 0.00 38.60 2.24
3062 3157 8.853077 ATCATCTAAAATTTCGCCAGATATCA 57.147 30.769 5.32 0.00 0.00 2.15
3334 3432 5.950549 AGCAGATTGTCCATTCAGAATTCTT 59.049 36.000 4.86 0.00 0.00 2.52
3416 3514 2.171659 TCCACAACAGCTTGAGGTAACA 59.828 45.455 2.34 0.00 38.80 2.41
3593 3691 5.915758 CCTCAGTACACTATATTCAAGTCGC 59.084 44.000 0.00 0.00 0.00 5.19
3594 3692 6.238786 CCTCAGTACACTATATTCAAGTCGCT 60.239 42.308 0.00 0.00 0.00 4.93
3599 3697 8.656849 AGTACACTATATTCAAGTCGCTTTTTG 58.343 33.333 0.00 0.00 0.00 2.44
3660 3759 7.433719 TCGAAATAATGGGTTTTGCATTTATCG 59.566 33.333 0.00 0.00 0.00 2.92
3708 3807 9.346725 GCCATTCTAACTCTGTTTTAATTTGAG 57.653 33.333 0.00 0.00 0.00 3.02
3782 3881 6.295180 CCCCGTCTAGAAGAATTAAGGATACC 60.295 46.154 7.30 0.00 37.17 2.73
3805 3904 4.205996 CGCAGACACTTATCTCTGATTTCG 59.794 45.833 0.00 0.00 36.75 3.46
3822 3921 0.400213 TCGTTTGACCCTTCCAGCAT 59.600 50.000 0.00 0.00 0.00 3.79
3823 3922 1.202879 TCGTTTGACCCTTCCAGCATT 60.203 47.619 0.00 0.00 0.00 3.56
3918 4029 7.830940 TGATTTTATTTTGGATGTGATGTGC 57.169 32.000 0.00 0.00 0.00 4.57
3919 4030 6.530887 TGATTTTATTTTGGATGTGATGTGCG 59.469 34.615 0.00 0.00 0.00 5.34
3921 4032 2.702898 TTTTGGATGTGATGTGCGTG 57.297 45.000 0.00 0.00 0.00 5.34
3922 4033 1.889545 TTTGGATGTGATGTGCGTGA 58.110 45.000 0.00 0.00 0.00 4.35
3923 4034 2.112380 TTGGATGTGATGTGCGTGAT 57.888 45.000 0.00 0.00 0.00 3.06
3924 4035 2.112380 TGGATGTGATGTGCGTGATT 57.888 45.000 0.00 0.00 0.00 2.57
3926 4037 1.532505 GGATGTGATGTGCGTGATTGC 60.533 52.381 0.00 0.00 0.00 3.56
3927 4038 0.452987 ATGTGATGTGCGTGATTGCC 59.547 50.000 0.00 0.00 0.00 4.52
3928 4039 1.226101 GTGATGTGCGTGATTGCCG 60.226 57.895 0.00 0.00 0.00 5.69
3932 4043 1.330521 GATGTGCGTGATTGCCGTAAT 59.669 47.619 0.00 0.00 0.00 1.89
3949 4091 1.218844 AATAACTACACCCCGGGCAT 58.781 50.000 17.73 1.11 0.00 4.40
3951 4093 1.339644 TAACTACACCCCGGGCATCC 61.340 60.000 17.73 0.00 0.00 3.51
3991 4133 7.497909 GCCCAAACTATCACTAAATACTGCTTA 59.502 37.037 0.00 0.00 0.00 3.09
4049 4191 5.452078 CCTCAAAAGGCAGAATAACAACA 57.548 39.130 0.00 0.00 35.37 3.33
4156 4308 4.124970 TCTTCATGCTGATATGCTGTGTC 58.875 43.478 0.00 0.00 0.00 3.67
4244 4396 6.267471 ACATGGAAAATGTTGTGGTACTTGAT 59.733 34.615 0.00 0.00 0.00 2.57
4319 4472 3.319689 TCGCATCCATGATTCATGCAATT 59.680 39.130 19.26 2.86 42.65 2.32
4575 4749 3.632643 TGAGCTTTCATATGTGGAGCA 57.367 42.857 21.06 6.65 37.37 4.26
4577 4751 3.943381 TGAGCTTTCATATGTGGAGCAAG 59.057 43.478 21.06 9.91 37.37 4.01
4595 4770 9.028284 TGGAGCAAGATAAAAGAGAAAATGAAT 57.972 29.630 0.00 0.00 0.00 2.57
4618 4793 9.952188 GAATTTTAGCTTTCTGTTGTTCTTACT 57.048 29.630 0.00 0.00 0.00 2.24
4722 4897 9.123709 GAATCGTCAGATGAAGATGACTATAAC 57.876 37.037 11.24 0.00 41.26 1.89
4771 4946 1.463553 TTCTGCTGCGAGTCCTGACA 61.464 55.000 0.00 0.00 0.00 3.58
4816 4991 1.737236 GCAACGATGTCCAGCAATACA 59.263 47.619 0.00 0.00 0.00 2.29
4971 5146 5.362556 ACAATGTTGGAAAAGATCTGACG 57.637 39.130 0.00 0.00 0.00 4.35
5004 5179 5.365403 TGCCTGTTTACTTTAATGAACCG 57.635 39.130 0.00 0.00 0.00 4.44
5060 5235 6.252233 TGGAATATTCTCATTTGTTGGACCA 58.748 36.000 14.95 0.00 0.00 4.02
5070 5245 5.599242 TCATTTGTTGGACCATGCATATGAT 59.401 36.000 19.19 0.00 36.36 2.45
5118 5293 5.713389 TCATCCTTCATGCATCTTTCTTGTT 59.287 36.000 0.00 0.00 31.70 2.83
5126 5301 9.545105 TTCATGCATCTTTCTTGTTATTTGTTT 57.455 25.926 0.00 0.00 0.00 2.83
5127 5302 9.545105 TCATGCATCTTTCTTGTTATTTGTTTT 57.455 25.926 0.00 0.00 0.00 2.43
5152 5327 8.425577 TTTTGTTTTTGTTTCTGTCTTGTCAA 57.574 26.923 0.00 0.00 0.00 3.18
5292 5467 2.512705 TGCAACATGGCATCTGTTACA 58.487 42.857 6.18 4.70 39.25 2.41
5362 5539 9.681062 AAACTAGCTGGCTATAATTTTTCAGTA 57.319 29.630 0.00 0.00 0.00 2.74
5536 5713 5.767665 TGAAAATGGAATCCGTTTCTTCTCA 59.232 36.000 18.76 15.28 41.31 3.27
5558 5735 7.660208 TCTCAGAAAAGGTCAGTTATTGGTAAC 59.340 37.037 0.00 0.00 40.40 2.50
5574 5751 9.941325 TTATTGGTAACGATGGAACTAAGTTTA 57.059 29.630 0.00 0.00 42.18 2.01
5588 5765 8.349983 GGAACTAAGTTTAGCAAGTTTCATTCA 58.650 33.333 0.00 0.00 32.51 2.57
5599 5776 6.040166 AGCAAGTTTCATTCAGTGAGAATTGT 59.960 34.615 3.42 0.00 44.48 2.71
5648 5825 9.997482 TCTACAAACAGTTGTAATTTCACTTTC 57.003 29.630 1.38 0.00 46.91 2.62
5654 5831 8.732746 ACAGTTGTAATTTCACTTTCTACTGT 57.267 30.769 10.44 10.44 38.05 3.55
5662 5839 7.617041 ATTTCACTTTCTACTGTTATCTGCC 57.383 36.000 0.00 0.00 0.00 4.85
5679 5856 1.235724 GCCGTTAGACCTTTTGCTGT 58.764 50.000 0.00 0.00 0.00 4.40
5689 5866 4.510340 AGACCTTTTGCTGTTACTGTTACG 59.490 41.667 0.00 0.00 0.00 3.18
5852 6029 2.957402 TTCAGCTTGATCCTGTTGGT 57.043 45.000 0.00 0.00 34.23 3.67
5873 6050 9.620660 GTTGGTGTTTTAACATTAGAATTCGAT 57.379 29.630 0.00 0.00 41.59 3.59
6022 6199 3.181474 GCAGGTCTCATAGTAGTGAACCC 60.181 52.174 0.00 0.00 33.53 4.11
6024 6201 4.712337 CAGGTCTCATAGTAGTGAACCCTT 59.288 45.833 0.00 0.00 33.53 3.95
6025 6202 5.187967 CAGGTCTCATAGTAGTGAACCCTTT 59.812 44.000 0.00 0.00 33.53 3.11
6026 6203 5.785940 AGGTCTCATAGTAGTGAACCCTTTT 59.214 40.000 0.00 0.00 33.53 2.27
6027 6204 6.272558 AGGTCTCATAGTAGTGAACCCTTTTT 59.727 38.462 0.00 0.00 33.53 1.94
6072 6249 8.600449 AAAATCTGAACTTCTTACTCTCTGTG 57.400 34.615 0.00 0.00 0.00 3.66
6237 6414 6.523201 CGACAGGTAAAACAGAACATAAATGC 59.477 38.462 0.00 0.00 0.00 3.56
6328 6505 2.733956 TGCAAGGTTCAAGGAGTTGTT 58.266 42.857 0.00 0.00 34.98 2.83
6614 6791 3.320826 AGCTCCGTTTTTGCCTATTGTTT 59.679 39.130 0.00 0.00 0.00 2.83
6667 6844 1.379443 ACCGGATCAGCGACACCTA 60.379 57.895 9.46 0.00 0.00 3.08
6694 6871 2.093341 TGGGGAGTACGATAAAGCCAAC 60.093 50.000 0.00 0.00 0.00 3.77
6768 6945 5.497464 TGTTCTCCTACATGTTCATGGAA 57.503 39.130 2.30 7.31 0.00 3.53
6770 6947 6.484288 TGTTCTCCTACATGTTCATGGAAAT 58.516 36.000 2.30 0.00 0.00 2.17
6771 6948 7.629157 TGTTCTCCTACATGTTCATGGAAATA 58.371 34.615 2.30 1.83 0.00 1.40
6909 7094 1.364901 GTTCGACAGGGACACCGAA 59.635 57.895 0.00 0.00 43.47 4.30
7013 7198 4.580995 TGAATTGCCCGACAAGAAAACTTA 59.419 37.500 0.00 0.00 42.87 2.24
7029 7214 1.038280 CTTATCCGGTTCCCGCTAGT 58.962 55.000 0.00 0.00 46.86 2.57
7063 7248 8.715191 ATAGCTCAATTATGTAGCAGCTATTC 57.285 34.615 5.14 0.00 40.40 1.75
7151 7337 2.167075 GCTTTCCCAATCCTCATTGTGG 59.833 50.000 0.00 0.00 38.22 4.17
7165 7351 3.710165 TCATTGTGGAGAGATGAGCTCAT 59.290 43.478 29.09 29.09 46.45 2.90
7214 7400 8.809468 ATACTATGACATACGACTATGGACAT 57.191 34.615 0.00 1.87 36.44 3.06
7407 7593 4.558095 GCTGATCAAGAATGTTTGTGCAGT 60.558 41.667 0.00 0.00 35.17 4.40
7482 7669 6.757897 TTTATGTTGCACTTATCTCCAAGG 57.242 37.500 0.00 0.00 0.00 3.61
7529 8694 5.748402 TGTTGCACTTATCTCCAAGATCAT 58.252 37.500 0.00 0.00 36.20 2.45
7535 8700 7.157347 GCACTTATCTCCAAGATCATGACATA 58.843 38.462 0.00 0.00 36.20 2.29
7582 8764 0.527817 CTAGCGGTGCCTTAACCTCG 60.528 60.000 0.00 0.00 38.14 4.63
7594 8830 2.060326 TAACCTCGACAAGCAACTCG 57.940 50.000 0.00 0.00 0.00 4.18
7615 8851 1.300971 GCATTCTGCAGAGCCGTTGA 61.301 55.000 17.43 0.00 44.26 3.18
7627 8863 4.693566 CAGAGCCGTTGATAAACACCTAAA 59.306 41.667 0.00 0.00 0.00 1.85
7629 8865 5.180680 AGAGCCGTTGATAAACACCTAAAAC 59.819 40.000 0.00 0.00 0.00 2.43
7671 8907 7.039853 TGCTCTTACAAATTTTCATCACCATCA 60.040 33.333 0.00 0.00 0.00 3.07
7903 9139 0.110238 CCTTGTCAATGTCGTTGGCG 60.110 55.000 4.97 0.00 45.46 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.011333 GTTGTTGGCCGCACGTATAT 58.989 50.000 0.00 0.00 0.00 0.86
2 3 1.020333 GGTTGTTGGCCGCACGTATA 61.020 55.000 0.00 0.00 0.00 1.47
3 4 2.329614 GGTTGTTGGCCGCACGTAT 61.330 57.895 0.00 0.00 0.00 3.06
4 5 2.973600 GGTTGTTGGCCGCACGTA 60.974 61.111 0.00 0.00 0.00 3.57
12 13 3.056328 GGAGAGGCGGTTGTTGGC 61.056 66.667 0.00 0.00 0.00 4.52
13 14 2.359975 GGGAGAGGCGGTTGTTGG 60.360 66.667 0.00 0.00 0.00 3.77
14 15 2.359975 GGGGAGAGGCGGTTGTTG 60.360 66.667 0.00 0.00 0.00 3.33
15 16 2.002018 TTTGGGGAGAGGCGGTTGTT 62.002 55.000 0.00 0.00 0.00 2.83
16 17 2.002018 TTTTGGGGAGAGGCGGTTGT 62.002 55.000 0.00 0.00 0.00 3.32
17 18 0.825840 TTTTTGGGGAGAGGCGGTTG 60.826 55.000 0.00 0.00 0.00 3.77
18 19 1.539665 TTTTTGGGGAGAGGCGGTT 59.460 52.632 0.00 0.00 0.00 4.44
19 20 3.257133 TTTTTGGGGAGAGGCGGT 58.743 55.556 0.00 0.00 0.00 5.68
39 47 1.210722 GAAGGCAGAGGAAACCCTAGG 59.789 57.143 0.06 0.06 33.25 3.02
81 89 0.112606 AAGACCACCAGAGACGAGGA 59.887 55.000 0.00 0.00 0.00 3.71
91 99 1.570857 CCATGGCCCTAAGACCACCA 61.571 60.000 0.00 0.00 39.19 4.17
130 138 2.202236 GAGCCCTCCCACATGCAAGA 62.202 60.000 0.00 0.00 0.00 3.02
136 144 1.789576 AAAACGGAGCCCTCCCACAT 61.790 55.000 8.68 0.00 46.96 3.21
137 145 2.002018 AAAAACGGAGCCCTCCCACA 62.002 55.000 8.68 0.00 46.96 4.17
139 147 0.326927 CTAAAAACGGAGCCCTCCCA 59.673 55.000 8.68 0.00 46.96 4.37
191 199 3.549423 CGTCGTGTTGTCTTCCTGAGTAA 60.549 47.826 0.00 0.00 0.00 2.24
258 267 1.374252 GCTATACGCACCATCGGGG 60.374 63.158 0.00 0.00 44.81 5.73
272 281 2.207590 CGCACACACTGATGATGCTAT 58.792 47.619 0.00 0.00 38.52 2.97
287 296 0.036164 AAAGCACATCCCTACGCACA 59.964 50.000 0.00 0.00 0.00 4.57
291 300 1.278238 GTCGAAAGCACATCCCTACG 58.722 55.000 0.00 0.00 0.00 3.51
294 303 1.079127 CCGTCGAAAGCACATCCCT 60.079 57.895 0.00 0.00 0.00 4.20
296 305 0.931005 GATCCGTCGAAAGCACATCC 59.069 55.000 0.00 0.00 0.00 3.51
298 307 1.066858 ACAGATCCGTCGAAAGCACAT 60.067 47.619 0.00 0.00 0.00 3.21
351 360 1.570528 CGAACGTAGAGTCGTAAACGC 59.429 52.381 9.32 0.00 43.38 4.84
354 363 2.574322 GCACGAACGTAGAGTCGTAAA 58.426 47.619 12.22 0.00 46.06 2.01
355 364 1.462378 CGCACGAACGTAGAGTCGTAA 60.462 52.381 12.22 0.00 46.06 3.18
356 365 0.093535 CGCACGAACGTAGAGTCGTA 59.906 55.000 12.22 0.00 46.06 3.43
358 367 0.093535 TACGCACGAACGTAGAGTCG 59.906 55.000 5.86 5.86 46.19 4.18
359 368 3.955429 TACGCACGAACGTAGAGTC 57.045 52.632 9.91 0.00 46.19 3.36
374 383 4.868171 TCGGAAGAATCCAACTTGAATACG 59.132 41.667 0.00 0.00 46.97 3.06
382 391 3.621715 GCGTAAATCGGAAGAATCCAACT 59.378 43.478 0.00 0.00 46.97 3.16
451 460 0.956633 AAGTCGTCGTGCTAAGACCA 59.043 50.000 0.00 0.00 35.33 4.02
454 463 0.524862 GGGAAGTCGTCGTGCTAAGA 59.475 55.000 0.00 0.00 0.00 2.10
536 545 0.676184 ACACTGAAGCGAGCTGAAGA 59.324 50.000 12.42 0.00 0.00 2.87
631 641 8.552083 TCCGATTTATTCATCATCAAGTATGG 57.448 34.615 0.00 0.00 36.15 2.74
633 643 9.784531 ACTTCCGATTTATTCATCATCAAGTAT 57.215 29.630 0.00 0.00 0.00 2.12
634 644 9.613428 AACTTCCGATTTATTCATCATCAAGTA 57.387 29.630 0.00 0.00 0.00 2.24
635 645 8.511604 AACTTCCGATTTATTCATCATCAAGT 57.488 30.769 0.00 0.00 0.00 3.16
691 701 1.823169 AAACACGAGGCCCGCTTAGA 61.823 55.000 12.78 0.00 43.32 2.10
723 733 2.113986 GGTGACACTGGCTTGGCT 59.886 61.111 5.39 0.00 0.00 4.75
724 734 2.203337 TGGTGACACTGGCTTGGC 60.203 61.111 5.39 0.00 33.40 4.52
744 754 0.730840 GGTCCGGTCCGCTTAAATTG 59.269 55.000 5.50 0.00 0.00 2.32
745 755 0.393402 GGGTCCGGTCCGCTTAAATT 60.393 55.000 11.79 0.00 0.00 1.82
747 757 2.664398 GGGTCCGGTCCGCTTAAA 59.336 61.111 11.79 0.00 0.00 1.52
801 811 2.868787 GGAAGTCGTCGTCGTCGC 60.869 66.667 7.01 3.07 38.33 5.19
849 865 4.816984 GGGGCGGAGGAGACGAGA 62.817 72.222 0.00 0.00 0.00 4.04
854 870 4.779733 GGAGTGGGGCGGAGGAGA 62.780 72.222 0.00 0.00 0.00 3.71
869 885 0.101219 CAGCTGACGATGACGATGGA 59.899 55.000 8.42 0.00 42.66 3.41
887 903 0.559699 GGGAGGTAGGTAGGTAGGCA 59.440 60.000 0.00 0.00 0.00 4.75
888 904 0.859064 AGGGAGGTAGGTAGGTAGGC 59.141 60.000 0.00 0.00 0.00 3.93
890 906 1.428525 GGGAGGGAGGTAGGTAGGTAG 59.571 61.905 0.00 0.00 0.00 3.18
891 907 1.013066 AGGGAGGGAGGTAGGTAGGTA 59.987 57.143 0.00 0.00 0.00 3.08
892 908 0.254687 AGGGAGGGAGGTAGGTAGGT 60.255 60.000 0.00 0.00 0.00 3.08
893 909 0.483770 GAGGGAGGGAGGTAGGTAGG 59.516 65.000 0.00 0.00 0.00 3.18
930 946 5.064962 CACAATCACAGTGGCATTTGTTTTT 59.935 36.000 0.00 0.83 33.43 1.94
943 959 0.308684 CGCACAAGCACAATCACAGT 59.691 50.000 0.00 0.00 42.27 3.55
956 978 4.617520 TCCTTGGCTCGCGCACAA 62.618 61.111 8.75 5.46 38.10 3.33
958 980 4.742201 TCTCCTTGGCTCGCGCAC 62.742 66.667 8.75 0.00 38.10 5.34
959 981 3.529341 TTTCTCCTTGGCTCGCGCA 62.529 57.895 8.75 0.00 38.10 6.09
960 982 2.742372 TTTCTCCTTGGCTCGCGC 60.742 61.111 0.00 0.00 0.00 6.86
961 983 2.103042 CCTTTCTCCTTGGCTCGCG 61.103 63.158 0.00 0.00 0.00 5.87
962 984 1.746991 CCCTTTCTCCTTGGCTCGC 60.747 63.158 0.00 0.00 0.00 5.03
963 985 1.078143 CCCCTTTCTCCTTGGCTCG 60.078 63.158 0.00 0.00 0.00 5.03
964 986 1.304617 CCCCCTTTCTCCTTGGCTC 59.695 63.158 0.00 0.00 0.00 4.70
965 987 3.513027 CCCCCTTTCTCCTTGGCT 58.487 61.111 0.00 0.00 0.00 4.75
980 1002 4.534824 TCGTCGATCCCCTCCCCC 62.535 72.222 0.00 0.00 0.00 5.40
981 1003 3.225061 GTCGTCGATCCCCTCCCC 61.225 72.222 0.00 0.00 0.00 4.81
982 1004 3.593794 CGTCGTCGATCCCCTCCC 61.594 72.222 0.00 0.00 39.71 4.30
983 1005 2.515523 TCGTCGTCGATCCCCTCC 60.516 66.667 0.00 0.00 41.35 4.30
1131 1159 0.874390 CGATGTTGGTCCACTTGTGG 59.126 55.000 13.24 13.24 0.00 4.17
1393 1424 4.810661 AGAAGCAGAGGAGCGCGC 62.811 66.667 26.66 26.66 40.15 6.86
1394 1425 2.555565 AAGAGAAGCAGAGGAGCGCG 62.556 60.000 0.00 0.00 40.15 6.86
1395 1426 0.390998 AAAGAGAAGCAGAGGAGCGC 60.391 55.000 0.00 0.00 40.15 5.92
1396 1427 1.639280 GAAAGAGAAGCAGAGGAGCG 58.361 55.000 0.00 0.00 40.15 5.03
1397 1428 1.406751 GGGAAAGAGAAGCAGAGGAGC 60.407 57.143 0.00 0.00 0.00 4.70
1398 1429 1.209261 GGGGAAAGAGAAGCAGAGGAG 59.791 57.143 0.00 0.00 0.00 3.69
1399 1430 1.280457 GGGGAAAGAGAAGCAGAGGA 58.720 55.000 0.00 0.00 0.00 3.71
1400 1431 0.987294 TGGGGAAAGAGAAGCAGAGG 59.013 55.000 0.00 0.00 0.00 3.69
1401 1432 1.339535 GGTGGGGAAAGAGAAGCAGAG 60.340 57.143 0.00 0.00 0.00 3.35
1402 1433 0.693049 GGTGGGGAAAGAGAAGCAGA 59.307 55.000 0.00 0.00 0.00 4.26
1403 1434 0.322906 GGGTGGGGAAAGAGAAGCAG 60.323 60.000 0.00 0.00 0.00 4.24
1404 1435 1.767692 GGGTGGGGAAAGAGAAGCA 59.232 57.895 0.00 0.00 0.00 3.91
1405 1436 1.377333 CGGGTGGGGAAAGAGAAGC 60.377 63.158 0.00 0.00 0.00 3.86
1406 1437 0.690762 TTCGGGTGGGGAAAGAGAAG 59.309 55.000 0.00 0.00 0.00 2.85
1407 1438 1.142060 TTTCGGGTGGGGAAAGAGAA 58.858 50.000 0.00 0.00 0.00 2.87
1408 1439 2.857087 TTTCGGGTGGGGAAAGAGA 58.143 52.632 0.00 0.00 0.00 3.10
1445 1476 0.548510 GGGCAAGAATCTACCAGGCT 59.451 55.000 4.86 0.00 0.00 4.58
1446 1477 0.548510 AGGGCAAGAATCTACCAGGC 59.451 55.000 4.86 0.00 0.00 4.85
1447 1478 3.372440 AAAGGGCAAGAATCTACCAGG 57.628 47.619 4.86 0.00 0.00 4.45
1488 1527 3.197927 ACCTCCCTGAATCTGTCTTCT 57.802 47.619 0.00 0.00 0.00 2.85
1504 1543 1.068541 GTGGAACAATGGCGAAACCTC 60.069 52.381 0.00 0.00 44.16 3.85
1572 1625 9.597170 GATTATTATCATCAGAGCAGAGCATTA 57.403 33.333 0.00 0.00 0.00 1.90
1645 1717 8.867112 TTTGTTTGTTTGTTTGTTACTGTGTA 57.133 26.923 0.00 0.00 0.00 2.90
1699 1776 0.317938 AACTCAGAGTGACGTGACGC 60.318 55.000 4.25 0.00 0.00 5.19
1706 1783 0.109039 GAGGCCGAACTCAGAGTGAC 60.109 60.000 3.05 0.92 37.44 3.67
1799 1879 3.149196 GCTTGTTGTGAAGATCTGGGAA 58.851 45.455 0.00 0.00 0.00 3.97
1827 1907 3.244284 ACTGTAGGTTGGTAAATGTCGCA 60.244 43.478 0.00 0.00 0.00 5.10
1881 1966 9.850628 CGATCGATTAATCCAGGTAATTAACTA 57.149 33.333 10.26 0.00 32.87 2.24
1883 1968 8.752766 TCGATCGATTAATCCAGGTAATTAAC 57.247 34.615 15.15 0.00 32.87 2.01
1890 1975 3.832490 TCCATCGATCGATTAATCCAGGT 59.168 43.478 27.45 0.89 31.62 4.00
1893 1978 5.394553 CCATCTCCATCGATCGATTAATCCA 60.395 44.000 27.45 10.28 31.62 3.41
1990 2075 2.833533 GCTCACGTGTGCTTTGCCA 61.834 57.895 29.80 1.58 0.00 4.92
2166 2261 6.257586 AGGGGGCTGTAAAATGTAATGTAAA 58.742 36.000 0.00 0.00 0.00 2.01
2167 2262 5.833340 AGGGGGCTGTAAAATGTAATGTAA 58.167 37.500 0.00 0.00 0.00 2.41
2173 2268 2.241176 CCAGAGGGGGCTGTAAAATGTA 59.759 50.000 0.00 0.00 34.06 2.29
2192 2287 3.024547 CGGAGGAGATACTTCTTCACCA 58.975 50.000 0.00 0.00 37.94 4.17
2428 2523 4.122776 CCTGGCAGCACTAACAACTATAG 58.877 47.826 9.56 0.00 0.00 1.31
2430 2525 2.305927 ACCTGGCAGCACTAACAACTAT 59.694 45.455 9.56 0.00 0.00 2.12
2432 2527 0.474184 ACCTGGCAGCACTAACAACT 59.526 50.000 9.56 0.00 0.00 3.16
2433 2528 2.076863 CTACCTGGCAGCACTAACAAC 58.923 52.381 9.56 0.00 0.00 3.32
2434 2529 1.610624 GCTACCTGGCAGCACTAACAA 60.611 52.381 14.08 0.00 38.93 2.83
2435 2530 0.036388 GCTACCTGGCAGCACTAACA 60.036 55.000 14.08 0.00 38.93 2.41
2579 2674 4.457603 AGTGTTGTTTGTTCACAGCTACAA 59.542 37.500 0.00 0.00 34.94 2.41
2597 2692 3.820467 TGGAATGCGAATCAGAAAGTGTT 59.180 39.130 0.00 0.00 0.00 3.32
2617 2712 2.091541 ACTGTTTGTGTGGTTCTGTGG 58.908 47.619 0.00 0.00 0.00 4.17
2618 2713 3.500982 CAACTGTTTGTGTGGTTCTGTG 58.499 45.455 0.00 0.00 0.00 3.66
2658 2753 5.105554 TGTGTAGTTTTCTGCCAAAACATGT 60.106 36.000 18.40 0.00 41.29 3.21
2688 2783 6.991531 AGCAGCCAAAGAATTGAATTGTTTTA 59.008 30.769 9.93 0.00 38.94 1.52
2721 2816 1.223187 GTAATTGGCATACCGGACCG 58.777 55.000 9.46 6.99 39.70 4.79
2733 2828 4.963276 ACACAATCATCGGTGTAATTGG 57.037 40.909 13.01 6.20 45.77 3.16
2801 2896 9.965824 GACATACTTTATGGGGATGTTTTAATG 57.034 33.333 0.00 0.00 40.47 1.90
3016 3111 6.744112 TGATAAAGTTAGCAACCAAAACCTG 58.256 36.000 0.00 0.00 0.00 4.00
3051 3146 2.669924 CACGGAATGATGATATCTGGCG 59.330 50.000 3.98 0.00 0.00 5.69
3062 3157 6.036083 CGTCTGATTTACTTTCACGGAATGAT 59.964 38.462 6.55 0.00 37.11 2.45
3212 3310 6.051074 TGCATCATTCTGGTCATACAGTAAG 58.949 40.000 0.00 0.00 39.48 2.34
3334 3432 8.664798 GTTGTTTCATCTGTGTATAATACTGCA 58.335 33.333 0.00 0.00 0.00 4.41
3416 3514 4.699257 CCTAGCAGCAAGTCTTGAGAAAAT 59.301 41.667 16.99 0.00 0.00 1.82
3500 3598 2.642139 ATGCTTTCTTGCAATCCACG 57.358 45.000 0.00 0.00 46.61 4.94
3544 3642 2.057922 AGGGACCACACAGTTGATTCT 58.942 47.619 0.00 0.00 0.00 2.40
3545 3643 2.154462 CAGGGACCACACAGTTGATTC 58.846 52.381 0.00 0.00 0.00 2.52
3660 3759 8.621532 TGGCTACTGATTATTTCATAATCCAC 57.378 34.615 12.06 0.98 46.68 4.02
3756 3855 3.387050 TCCTTAATTCTTCTAGACGGGGC 59.613 47.826 0.00 0.00 0.00 5.80
3761 3860 6.746120 TGCGGTATCCTTAATTCTTCTAGAC 58.254 40.000 0.00 0.00 0.00 2.59
3782 3881 4.205996 CGAAATCAGAGATAAGTGTCTGCG 59.794 45.833 0.00 0.00 43.48 5.18
3805 3904 1.963515 ACAATGCTGGAAGGGTCAAAC 59.036 47.619 0.00 0.00 0.00 2.93
3842 3941 9.829507 CAATAGAAATGAGGATCTTTCTACAGT 57.170 33.333 13.96 4.23 42.18 3.55
3910 4021 1.226101 CGGCAATCACGCACATCAC 60.226 57.895 0.00 0.00 0.00 3.06
3911 4022 0.390472 TACGGCAATCACGCACATCA 60.390 50.000 0.00 0.00 34.00 3.07
3912 4023 0.724549 TTACGGCAATCACGCACATC 59.275 50.000 0.00 0.00 34.00 3.06
3913 4024 1.378531 ATTACGGCAATCACGCACAT 58.621 45.000 0.00 0.00 34.00 3.21
3914 4025 2.011540 TATTACGGCAATCACGCACA 57.988 45.000 0.00 0.00 34.00 4.57
3915 4026 2.350498 AGTTATTACGGCAATCACGCAC 59.650 45.455 0.00 0.00 34.00 5.34
3917 4028 3.552699 TGTAGTTATTACGGCAATCACGC 59.447 43.478 0.00 0.00 34.87 5.34
3918 4029 4.026310 GGTGTAGTTATTACGGCAATCACG 60.026 45.833 0.00 0.00 34.87 4.35
3919 4030 4.271776 GGGTGTAGTTATTACGGCAATCAC 59.728 45.833 0.00 0.00 34.87 3.06
3921 4032 3.811497 GGGGTGTAGTTATTACGGCAATC 59.189 47.826 0.00 0.00 34.87 2.67
3922 4033 3.742013 CGGGGTGTAGTTATTACGGCAAT 60.742 47.826 0.00 0.00 34.87 3.56
3923 4034 2.418471 CGGGGTGTAGTTATTACGGCAA 60.418 50.000 0.00 0.00 34.87 4.52
3924 4035 1.136695 CGGGGTGTAGTTATTACGGCA 59.863 52.381 0.00 0.00 34.87 5.69
3926 4037 1.069049 CCCGGGGTGTAGTTATTACGG 59.931 57.143 14.71 0.00 39.76 4.02
3927 4038 1.538849 GCCCGGGGTGTAGTTATTACG 60.539 57.143 25.28 0.00 34.87 3.18
3928 4039 1.485895 TGCCCGGGGTGTAGTTATTAC 59.514 52.381 25.28 0.00 0.00 1.89
3932 4043 1.339644 GGATGCCCGGGGTGTAGTTA 61.340 60.000 25.28 0.00 0.00 2.24
4002 4144 8.576442 GGTCAATCAAACTGATTTTCCTCTTAA 58.424 33.333 0.00 0.00 44.03 1.85
4049 4191 2.158519 ACCCAAAATTTCCGGTCTGACT 60.159 45.455 7.85 0.00 0.00 3.41
4072 4224 1.681229 ACTGGGAATAAGCAGGGGAA 58.319 50.000 0.00 0.00 0.00 3.97
4120 4272 3.733077 GCATGAAGAGCAGGTTATTGCAC 60.733 47.826 0.00 0.00 46.47 4.57
4319 4472 8.405531 CCAAATTGATATTTTTCCTCGAAGCTA 58.594 33.333 0.00 0.00 31.63 3.32
4553 4727 3.691118 TGCTCCACATATGAAAGCTCAAC 59.309 43.478 20.88 2.04 36.15 3.18
4722 4897 7.919690 TGAAACTTTGTCTTGTATCACAGAAG 58.080 34.615 0.00 0.00 0.00 2.85
4771 4946 5.591472 TCGAATTTGAATGCTTCATCCTCAT 59.409 36.000 0.00 0.00 39.84 2.90
5004 5179 9.199982 TCAAAGCATTTTTGAAGAGATGAAATC 57.800 29.630 0.19 0.00 39.41 2.17
5060 5235 6.496743 ACCTTTAGGCCATAATCATATGCAT 58.503 36.000 5.01 3.79 37.13 3.96
5070 5245 7.836685 TGACATTTTCATACCTTTAGGCCATAA 59.163 33.333 5.01 0.00 39.32 1.90
5091 5266 5.446860 AGAAAGATGCATGAAGGATGACAT 58.553 37.500 2.46 0.00 33.87 3.06
5126 5301 8.425577 TGACAAGACAGAAACAAAAACAAAAA 57.574 26.923 0.00 0.00 0.00 1.94
5127 5302 8.425577 TTGACAAGACAGAAACAAAAACAAAA 57.574 26.923 0.00 0.00 0.00 2.44
5128 5303 8.494347 CATTGACAAGACAGAAACAAAAACAAA 58.506 29.630 0.00 0.00 0.00 2.83
5129 5304 7.869937 TCATTGACAAGACAGAAACAAAAACAA 59.130 29.630 0.00 0.00 0.00 2.83
5130 5305 7.374272 TCATTGACAAGACAGAAACAAAAACA 58.626 30.769 0.00 0.00 0.00 2.83
5131 5306 7.810766 TCATTGACAAGACAGAAACAAAAAC 57.189 32.000 0.00 0.00 0.00 2.43
5319 5494 5.405873 GCTAGTTTCCAGACTAACAGTGAAC 59.594 44.000 0.00 0.00 32.10 3.18
5362 5539 5.691896 TGGATTCAGATTGATGCTCAGAAT 58.308 37.500 0.00 0.00 33.24 2.40
5369 5546 1.612463 GCCCTGGATTCAGATTGATGC 59.388 52.381 1.24 0.00 43.49 3.91
5536 5713 6.527423 TCGTTACCAATAACTGACCTTTTCT 58.473 36.000 0.00 0.00 38.89 2.52
5558 5735 6.481954 AACTTGCTAAACTTAGTTCCATCG 57.518 37.500 0.00 0.00 33.32 3.84
5574 5751 6.040166 ACAATTCTCACTGAATGAAACTTGCT 59.960 34.615 0.00 0.00 43.99 3.91
5648 5825 4.338682 AGGTCTAACGGCAGATAACAGTAG 59.661 45.833 0.00 0.00 0.00 2.57
5654 5831 3.687698 GCAAAAGGTCTAACGGCAGATAA 59.312 43.478 0.00 0.00 0.00 1.75
5662 5839 4.510340 ACAGTAACAGCAAAAGGTCTAACG 59.490 41.667 0.00 0.00 0.00 3.18
5679 5856 8.340618 ACTTCAGGTATAGTTCGTAACAGTAA 57.659 34.615 0.00 0.00 0.00 2.24
5873 6050 6.014413 TGCTCCATTTGAAAATTTCTCCATCA 60.014 34.615 7.29 0.00 0.00 3.07
6053 6230 3.641436 TGGCACAGAGAGTAAGAAGTTCA 59.359 43.478 5.50 0.00 0.00 3.18
6054 6231 4.258702 TGGCACAGAGAGTAAGAAGTTC 57.741 45.455 0.00 0.00 0.00 3.01
6072 6249 4.857509 TTAATGGTTGTTGTAACCTGGC 57.142 40.909 9.91 0.00 40.88 4.85
6237 6414 2.879103 ACATAGGTTGTGGGAACTGG 57.121 50.000 0.00 0.00 37.11 4.00
6328 6505 1.796017 TGGTACCGCCAATATCCTCA 58.204 50.000 7.57 0.00 45.94 3.86
6614 6791 4.489737 TCTGTTGGAGGAAGTTTCTCCTA 58.510 43.478 27.36 19.27 46.33 2.94
6667 6844 4.039366 GCTTTATCGTACTCCCCATTCTCT 59.961 45.833 0.00 0.00 0.00 3.10
6694 6871 1.819288 TCCAACCGTAGCTTCTCAGAG 59.181 52.381 0.00 0.00 0.00 3.35
7029 7214 8.258007 GCTACATAATTGAGCTATATACCCACA 58.742 37.037 0.00 0.00 33.28 4.17
7165 7351 6.381498 TTGTTTACATACAGGGGAGATGAA 57.619 37.500 0.00 0.00 0.00 2.57
7236 7422 3.201290 CCTACTACATCTTGCAAGCCTG 58.799 50.000 21.99 21.20 0.00 4.85
7383 7569 2.912967 GCACAAACATTCTTGATCAGCG 59.087 45.455 0.00 0.00 0.00 5.18
7407 7593 4.322650 GCAGAATTGCTGGGATTTGGTTAA 60.323 41.667 0.00 0.00 46.95 2.01
7433 7619 5.734720 TGTCAAGTATGTCCTGATCTTTCC 58.265 41.667 0.00 0.00 0.00 3.13
7505 7693 5.748402 TGATCTTGGAGATAAGTGCAACAT 58.252 37.500 0.00 0.00 35.10 2.71
7509 7697 5.104817 TGTCATGATCTTGGAGATAAGTGCA 60.105 40.000 0.00 0.00 34.53 4.57
7511 7699 8.366401 AGTATGTCATGATCTTGGAGATAAGTG 58.634 37.037 0.00 0.00 34.53 3.16
7548 8713 3.198068 CCGCTAGATAAGTGCAACACAT 58.802 45.455 0.00 0.00 41.43 3.21
7549 8714 2.028476 ACCGCTAGATAAGTGCAACACA 60.028 45.455 0.00 0.00 41.43 3.72
7550 8715 2.348666 CACCGCTAGATAAGTGCAACAC 59.651 50.000 0.00 0.00 41.43 3.32
7551 8716 2.616960 CACCGCTAGATAAGTGCAACA 58.383 47.619 0.00 0.00 41.43 3.33
7556 8721 2.604046 AAGGCACCGCTAGATAAGTG 57.396 50.000 0.00 0.00 35.34 3.16
7557 8722 3.181468 GGTTAAGGCACCGCTAGATAAGT 60.181 47.826 0.00 0.00 0.00 2.24
7558 8723 3.069729 AGGTTAAGGCACCGCTAGATAAG 59.930 47.826 0.00 0.00 42.33 1.73
7559 8724 3.036091 AGGTTAAGGCACCGCTAGATAA 58.964 45.455 0.00 0.00 42.33 1.75
7560 8725 2.626743 GAGGTTAAGGCACCGCTAGATA 59.373 50.000 0.00 0.00 42.33 1.98
7561 8726 1.413077 GAGGTTAAGGCACCGCTAGAT 59.587 52.381 0.00 0.00 42.33 1.98
7562 8727 0.822164 GAGGTTAAGGCACCGCTAGA 59.178 55.000 0.00 0.00 42.33 2.43
7627 8863 9.899226 GTAAGAGCAGAACAGAATAAAAATGTT 57.101 29.630 0.00 0.00 39.76 2.71
7629 8865 9.897744 TTGTAAGAGCAGAACAGAATAAAAATG 57.102 29.630 0.00 0.00 0.00 2.32
7671 8907 9.675464 TTTATTGTATTTTAGAACCTCGGTGAT 57.325 29.630 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.