Multiple sequence alignment - TraesCS3A01G512500

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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 TraesCS3A01G512500 chr3A 100.000 5727 0 0 1 5727 732062925 732057199 0.000000e+00 10576.0
1 TraesCS3A01G512500 chr3A 99.379 161 1 0 373 533 732062312 732062152 5.610000e-75 292.0
2 TraesCS3A01G512500 chr3A 99.379 161 1 0 614 774 732062553 732062393 5.610000e-75 292.0
3 TraesCS3A01G512500 chr3A 95.506 89 3 1 199 287 732062296 732062383 2.150000e-29 141.0
4 TraesCS3A01G512500 chr3A 95.506 89 3 1 543 630 732062639 732062727 2.150000e-29 141.0
5 TraesCS3A01G512500 chr3A 89.655 58 6 0 4153 4210 170784397 170784340 2.210000e-09 75.0
6 TraesCS3A01G512500 chr3D 95.405 3482 79 21 659 4135 602329943 602326538 0.000000e+00 5469.0
7 TraesCS3A01G512500 chr3D 92.671 846 48 8 4259 5092 602326451 602325608 0.000000e+00 1206.0
8 TraesCS3A01G512500 chr3D 93.721 637 35 3 5091 5725 602325556 602324923 0.000000e+00 950.0
9 TraesCS3A01G512500 chr3D 90.435 345 7 8 215 533 602330172 602329828 1.140000e-116 431.0
10 TraesCS3A01G512500 chr3D 91.860 172 13 1 42 212 602330652 602330481 7.420000e-59 239.0
11 TraesCS3A01G512500 chr3D 97.260 73 2 0 543 615 602330100 602330172 2.170000e-24 124.0
12 TraesCS3A01G512500 chr3D 97.368 38 1 0 614 651 602330014 602329977 1.330000e-06 65.8
13 TraesCS3A01G512500 chr3B 96.605 1679 49 6 2063 3738 809605310 809603637 0.000000e+00 2778.0
14 TraesCS3A01G512500 chr3B 94.703 1397 43 9 659 2044 809606752 809605376 0.000000e+00 2141.0
15 TraesCS3A01G512500 chr3B 90.337 1304 94 24 3803 5088 809603636 809602347 0.000000e+00 1681.0
16 TraesCS3A01G512500 chr3B 93.878 637 29 6 5091 5725 809602291 809601663 0.000000e+00 952.0
17 TraesCS3A01G512500 chr3B 88.235 561 29 14 1 533 809607188 809606637 2.250000e-178 636.0
18 TraesCS3A01G512500 chr3B 96.053 76 3 0 543 618 809606903 809606978 2.170000e-24 124.0
19 TraesCS3A01G512500 chr3B 90.385 52 5 0 4160 4211 70957524 70957473 1.030000e-07 69.4
20 TraesCS3A01G512500 chr4A 89.729 1879 151 14 2118 3992 617233178 617231338 0.000000e+00 2362.0
21 TraesCS3A01G512500 chr4A 88.330 1311 126 14 664 1962 617234562 617233267 0.000000e+00 1548.0
22 TraesCS3A01G512500 chr4A 87.266 534 37 11 4565 5092 617230947 617230439 1.070000e-161 580.0
23 TraesCS3A01G512500 chr4A 89.030 237 19 4 4258 4489 617231184 617230950 2.610000e-73 287.0
24 TraesCS3A01G512500 chr4A 87.931 58 7 0 4153 4210 475594878 475594935 1.030000e-07 69.4
25 TraesCS3A01G512500 chr5B 90.831 1625 137 8 2118 3740 702889951 702891565 0.000000e+00 2165.0
26 TraesCS3A01G512500 chr5B 87.585 1321 129 17 664 1963 702888532 702889838 0.000000e+00 1498.0
27 TraesCS3A01G512500 chr5B 86.007 536 32 15 4565 5092 702892288 702892788 8.450000e-148 534.0
28 TraesCS3A01G512500 chr5B 96.373 193 7 0 3797 3989 702891658 702891850 9.260000e-83 318.0
29 TraesCS3A01G512500 chr5B 86.555 238 24 7 4258 4489 702892050 702892285 7.360000e-64 255.0
30 TraesCS3A01G512500 chr5B 94.595 37 1 1 1926 1962 383227186 383227221 8.020000e-04 56.5
31 TraesCS3A01G512500 chr5D 91.034 1606 124 14 2118 3718 550439514 550441104 0.000000e+00 2150.0
32 TraesCS3A01G512500 chr5D 89.096 1183 103 13 664 1838 550438324 550439488 0.000000e+00 1447.0
33 TraesCS3A01G512500 chr5D 87.640 534 35 12 4565 5092 550441711 550442219 4.940000e-165 592.0
34 TraesCS3A01G512500 chr5D 90.991 222 17 3 3762 3981 550441097 550441317 4.340000e-76 296.0
35 TraesCS3A01G512500 chr5D 86.170 282 29 7 5091 5369 550442270 550442544 4.340000e-76 296.0
36 TraesCS3A01G512500 chr5D 86.885 61 6 2 4151 4210 268562098 268562157 3.700000e-07 67.6
37 TraesCS3A01G512500 chr4D 84.483 232 22 6 2300 2526 123391965 123391743 3.470000e-52 217.0
38 TraesCS3A01G512500 chr4D 84.483 232 22 6 2300 2526 134953453 134953231 3.470000e-52 217.0
39 TraesCS3A01G512500 chr1D 84.483 232 22 6 2300 2526 212455132 212455354 3.470000e-52 217.0
40 TraesCS3A01G512500 chr1A 84.483 232 22 6 2300 2526 271752595 271752817 3.470000e-52 217.0
41 TraesCS3A01G512500 chr1A 92.308 52 4 0 4158 4209 9587985 9588036 2.210000e-09 75.0
42 TraesCS3A01G512500 chr6D 78.534 191 35 5 1772 1962 429211460 429211644 2.800000e-23 121.0
43 TraesCS3A01G512500 chr6A 78.289 152 27 5 1770 1921 574410851 574410996 6.110000e-15 93.5
44 TraesCS3A01G512500 chr6A 89.130 46 3 2 5574 5617 581291053 581291098 8.020000e-04 56.5
45 TraesCS3A01G512500 chr6A 89.130 46 3 2 5574 5617 581333668 581333713 8.020000e-04 56.5
46 TraesCS3A01G512500 chr2A 84.810 79 9 3 4134 4210 78845852 78845775 6.150000e-10 76.8
47 TraesCS3A01G512500 chr2D 83.333 78 12 1 4134 4210 78563906 78563829 2.860000e-08 71.3
48 TraesCS3A01G512500 chr5A 87.931 58 7 0 4153 4210 63665822 63665879 1.030000e-07 69.4
49 TraesCS3A01G512500 chr5A 95.238 42 2 0 1898 1939 548664048 548664089 3.700000e-07 67.6
50 TraesCS3A01G512500 chr4B 86.667 60 4 3 4156 4215 650324867 650324812 4.790000e-06 63.9
51 TraesCS3A01G512500 chr1B 94.595 37 1 1 1926 1962 230816263 230816228 8.020000e-04 56.5


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 TraesCS3A01G512500 chr3A 732057199 732062925 5726 True 3720.000000 10576 99.586000 1 5727 3 chr3A.!!$R2 5726
1 TraesCS3A01G512500 chr3D 602324923 602330652 5729 True 1393.466667 5469 93.576667 42 5725 6 chr3D.!!$R1 5683
2 TraesCS3A01G512500 chr3B 809601663 809607188 5525 True 1637.600000 2778 92.751600 1 5725 5 chr3B.!!$R2 5724
3 TraesCS3A01G512500 chr4A 617230439 617234562 4123 True 1194.250000 2362 88.588750 664 5092 4 chr4A.!!$R1 4428
4 TraesCS3A01G512500 chr5B 702888532 702892788 4256 False 954.000000 2165 89.470200 664 5092 5 chr5B.!!$F2 4428
5 TraesCS3A01G512500 chr5D 550438324 550442544 4220 False 956.200000 2150 88.986200 664 5369 5 chr5D.!!$F2 4705

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
644 979 0.182537 TGGTTGTGCTTGGTGTAGCT 59.817 50.000 0.00 0.00 41.76 3.32 F
648 983 0.467804 TGTGCTTGGTGTAGCTGTCA 59.532 50.000 0.00 0.00 41.76 3.58 F
1068 1422 0.472471 AAGACAGGGACCAAAAGCGA 59.528 50.000 0.00 0.00 0.00 4.93 F
2588 3007 1.145598 ACTGATGCTCATGGCGGAG 59.854 57.895 0.00 1.95 45.43 4.63 F
2857 3276 0.093705 CTAGCTGCGCTTTGTCGTTC 59.906 55.000 9.73 0.00 40.44 3.95 F
3730 4152 0.373716 GCCGTGCTCCATCTTTTACG 59.626 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 2033 5.806654 AAACATGCACTGGGAATTAAAGT 57.193 34.783 0.00 0.0 0.00 2.66 R
2588 3007 6.294731 GGAACCATAGAATGATAAATGGGCAC 60.295 42.308 5.29 0.0 42.66 5.01 R
2677 3096 1.501741 CAACCCAATCTTGTCGGCG 59.498 57.895 0.00 0.0 0.00 6.46 R
3756 4178 1.061131 CACAAGAAGCACGGCTATTCG 59.939 52.381 0.00 0.0 38.25 3.34 R
4680 5340 0.095935 CAAATTCTCTGCCGACTGCG 59.904 55.000 0.00 0.0 45.60 5.18 R
4763 5423 0.972883 AGAGCTGACTGAAGTGTCCC 59.027 55.000 0.00 0.0 36.21 4.46 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
137 138 8.630278 ATGATAAGTACGTATATGCGATTTCC 57.370 34.615 20.38 2.78 35.59 3.13
251 558 5.837437 AGAATTGCCAAACGTGATTTTACA 58.163 33.333 0.00 0.00 0.00 2.41
274 581 7.514721 ACACTTTTCCTGGTTTGTAGAGAATA 58.485 34.615 0.00 0.00 0.00 1.75
410 719 1.347378 TGCTTGGTGTAGCTGTCATGA 59.653 47.619 0.00 0.00 41.76 3.07
411 720 2.224499 TGCTTGGTGTAGCTGTCATGAA 60.224 45.455 0.00 0.00 41.76 2.57
412 721 3.012518 GCTTGGTGTAGCTGTCATGAAT 58.987 45.455 0.00 0.00 38.15 2.57
413 722 4.191544 GCTTGGTGTAGCTGTCATGAATA 58.808 43.478 0.00 0.00 38.15 1.75
415 724 5.297776 GCTTGGTGTAGCTGTCATGAATAAT 59.702 40.000 0.00 0.00 38.15 1.28
416 725 6.483307 GCTTGGTGTAGCTGTCATGAATAATA 59.517 38.462 0.00 0.00 38.15 0.98
420 755 8.839343 TGGTGTAGCTGTCATGAATAATATTTG 58.161 33.333 0.00 0.00 0.00 2.32
453 788 9.577110 AGTGCTGATTAATATTTGTTGTGATTG 57.423 29.630 0.00 0.00 0.00 2.67
501 836 7.885399 ACTTGTTGAGTTCTTATGGATAAGCTT 59.115 33.333 3.48 3.48 39.60 3.74
502 837 7.615582 TGTTGAGTTCTTATGGATAAGCTTG 57.384 36.000 9.86 0.00 39.60 4.01
503 838 6.094048 TGTTGAGTTCTTATGGATAAGCTTGC 59.906 38.462 9.86 0.41 39.60 4.01
504 839 5.994250 TGAGTTCTTATGGATAAGCTTGCT 58.006 37.500 9.86 0.00 39.60 3.91
505 840 5.819379 TGAGTTCTTATGGATAAGCTTGCTG 59.181 40.000 9.86 0.00 39.60 4.41
506 841 4.578105 AGTTCTTATGGATAAGCTTGCTGC 59.422 41.667 9.86 2.17 39.60 5.25
536 871 7.810766 TTTTCTTTGTGAATGCCGATTATTC 57.189 32.000 0.00 0.00 34.24 1.75
537 872 6.507958 TTCTTTGTGAATGCCGATTATTCA 57.492 33.333 0.00 0.00 41.00 2.57
538 873 6.698008 TCTTTGTGAATGCCGATTATTCAT 57.302 33.333 10.59 0.00 43.90 2.57
539 874 6.497437 TCTTTGTGAATGCCGATTATTCATG 58.503 36.000 10.59 0.00 43.90 3.07
540 875 6.318396 TCTTTGTGAATGCCGATTATTCATGA 59.682 34.615 10.59 0.00 43.90 3.07
541 876 6.638096 TTGTGAATGCCGATTATTCATGAT 57.362 33.333 0.00 0.00 43.90 2.45
542 877 7.742556 TTGTGAATGCCGATTATTCATGATA 57.257 32.000 0.00 0.00 43.90 2.15
543 878 7.926674 TGTGAATGCCGATTATTCATGATAT 57.073 32.000 0.00 0.00 43.90 1.63
544 879 9.447157 TTGTGAATGCCGATTATTCATGATATA 57.553 29.630 0.00 0.00 43.90 0.86
545 880 9.617523 TGTGAATGCCGATTATTCATGATATAT 57.382 29.630 0.00 0.00 43.90 0.86
574 909 9.807921 AGAATTTATTCTCTACAAACCAGGAAA 57.192 29.630 0.00 0.00 43.27 3.13
577 912 8.990163 TTTATTCTCTACAAACCAGGAAAAGT 57.010 30.769 0.00 0.00 0.00 2.66
578 913 6.884280 ATTCTCTACAAACCAGGAAAAGTG 57.116 37.500 0.00 0.00 0.00 3.16
579 914 5.367945 TCTCTACAAACCAGGAAAAGTGT 57.632 39.130 0.00 0.00 0.00 3.55
580 915 6.488769 TCTCTACAAACCAGGAAAAGTGTA 57.511 37.500 0.00 0.00 0.00 2.90
581 916 6.891388 TCTCTACAAACCAGGAAAAGTGTAA 58.109 36.000 0.00 0.00 0.00 2.41
582 917 7.340256 TCTCTACAAACCAGGAAAAGTGTAAA 58.660 34.615 0.00 0.00 0.00 2.01
583 918 7.830201 TCTCTACAAACCAGGAAAAGTGTAAAA 59.170 33.333 0.00 0.00 0.00 1.52
584 919 8.528044 TCTACAAACCAGGAAAAGTGTAAAAT 57.472 30.769 0.00 0.00 0.00 1.82
585 920 8.626526 TCTACAAACCAGGAAAAGTGTAAAATC 58.373 33.333 0.00 0.00 0.00 2.17
586 921 7.176589 ACAAACCAGGAAAAGTGTAAAATCA 57.823 32.000 0.00 0.00 0.00 2.57
587 922 7.039270 ACAAACCAGGAAAAGTGTAAAATCAC 58.961 34.615 0.00 0.00 38.46 3.06
588 923 5.432885 ACCAGGAAAAGTGTAAAATCACG 57.567 39.130 0.00 0.00 42.40 4.35
589 924 4.885325 ACCAGGAAAAGTGTAAAATCACGT 59.115 37.500 0.00 0.00 42.40 4.49
590 925 5.358725 ACCAGGAAAAGTGTAAAATCACGTT 59.641 36.000 0.00 0.00 42.40 3.99
591 926 6.127563 ACCAGGAAAAGTGTAAAATCACGTTT 60.128 34.615 9.55 9.55 46.37 3.60
592 927 6.198216 CCAGGAAAAGTGTAAAATCACGTTTG 59.802 38.462 13.25 3.33 44.82 2.93
593 928 6.198216 CAGGAAAAGTGTAAAATCACGTTTGG 59.802 38.462 13.25 2.83 44.82 3.28
594 929 5.051307 GGAAAAGTGTAAAATCACGTTTGGC 60.051 40.000 13.25 3.27 44.82 4.52
595 930 4.640789 AAGTGTAAAATCACGTTTGGCA 57.359 36.364 0.00 0.00 42.40 4.92
596 931 4.640789 AGTGTAAAATCACGTTTGGCAA 57.359 36.364 0.00 0.00 42.40 4.52
597 932 5.195001 AGTGTAAAATCACGTTTGGCAAT 57.805 34.783 0.00 0.00 42.40 3.56
598 933 5.596845 AGTGTAAAATCACGTTTGGCAATT 58.403 33.333 0.00 0.00 42.40 2.32
599 934 5.689961 AGTGTAAAATCACGTTTGGCAATTC 59.310 36.000 0.00 0.00 42.40 2.17
600 935 5.689961 GTGTAAAATCACGTTTGGCAATTCT 59.310 36.000 0.00 0.00 0.00 2.40
601 936 6.858993 GTGTAAAATCACGTTTGGCAATTCTA 59.141 34.615 0.00 0.00 0.00 2.10
602 937 7.380065 GTGTAAAATCACGTTTGGCAATTCTAA 59.620 33.333 0.00 0.00 0.00 2.10
603 938 6.763303 AAAATCACGTTTGGCAATTCTAAC 57.237 33.333 0.00 0.00 0.00 2.34
604 939 5.446143 AATCACGTTTGGCAATTCTAACA 57.554 34.783 0.00 0.00 0.00 2.41
605 940 4.902443 TCACGTTTGGCAATTCTAACAA 57.098 36.364 0.00 0.00 0.00 2.83
606 941 5.250235 TCACGTTTGGCAATTCTAACAAA 57.750 34.783 0.00 0.00 0.00 2.83
607 942 5.038033 TCACGTTTGGCAATTCTAACAAAC 58.962 37.500 0.00 8.59 45.46 2.93
608 943 5.040635 CACGTTTGGCAATTCTAACAAACT 58.959 37.500 14.63 2.82 46.25 2.66
609 944 5.173131 CACGTTTGGCAATTCTAACAAACTC 59.827 40.000 14.63 0.00 46.25 3.01
610 945 4.679654 CGTTTGGCAATTCTAACAAACTCC 59.320 41.667 14.63 0.00 46.25 3.85
611 946 5.507315 CGTTTGGCAATTCTAACAAACTCCT 60.507 40.000 14.63 0.00 46.25 3.69
612 947 5.452078 TTGGCAATTCTAACAAACTCCTG 57.548 39.130 0.00 0.00 0.00 3.86
613 948 3.826157 TGGCAATTCTAACAAACTCCTGG 59.174 43.478 0.00 0.00 0.00 4.45
614 949 4.079253 GGCAATTCTAACAAACTCCTGGA 58.921 43.478 0.00 0.00 0.00 3.86
615 950 4.706962 GGCAATTCTAACAAACTCCTGGAT 59.293 41.667 0.00 0.00 0.00 3.41
616 951 5.885912 GGCAATTCTAACAAACTCCTGGATA 59.114 40.000 0.00 0.00 0.00 2.59
617 952 6.547510 GGCAATTCTAACAAACTCCTGGATAT 59.452 38.462 0.00 0.00 0.00 1.63
618 953 7.420800 GCAATTCTAACAAACTCCTGGATATG 58.579 38.462 0.00 0.00 0.00 1.78
619 954 7.067494 GCAATTCTAACAAACTCCTGGATATGT 59.933 37.037 0.00 0.00 0.00 2.29
620 955 8.960591 CAATTCTAACAAACTCCTGGATATGTT 58.039 33.333 19.26 19.26 35.41 2.71
626 961 8.964476 AACAAACTCCTGGATATGTTATACTG 57.036 34.615 15.86 7.32 29.89 2.74
627 962 7.509546 ACAAACTCCTGGATATGTTATACTGG 58.490 38.462 0.00 0.00 0.00 4.00
628 963 7.127339 ACAAACTCCTGGATATGTTATACTGGT 59.873 37.037 0.00 0.00 0.00 4.00
629 964 7.691993 AACTCCTGGATATGTTATACTGGTT 57.308 36.000 0.00 0.00 0.00 3.67
630 965 7.067496 ACTCCTGGATATGTTATACTGGTTG 57.933 40.000 0.00 1.91 0.00 3.77
631 966 6.615726 ACTCCTGGATATGTTATACTGGTTGT 59.384 38.462 0.00 2.36 0.00 3.32
632 967 6.826668 TCCTGGATATGTTATACTGGTTGTG 58.173 40.000 0.00 0.00 0.00 3.33
633 968 5.470098 CCTGGATATGTTATACTGGTTGTGC 59.530 44.000 0.00 0.00 0.00 4.57
634 969 6.247229 TGGATATGTTATACTGGTTGTGCT 57.753 37.500 0.00 0.00 0.00 4.40
635 970 6.658849 TGGATATGTTATACTGGTTGTGCTT 58.341 36.000 0.00 0.00 0.00 3.91
636 971 6.542005 TGGATATGTTATACTGGTTGTGCTTG 59.458 38.462 0.00 0.00 0.00 4.01
637 972 6.017109 GGATATGTTATACTGGTTGTGCTTGG 60.017 42.308 0.00 0.00 0.00 3.61
638 973 4.093472 TGTTATACTGGTTGTGCTTGGT 57.907 40.909 0.00 0.00 0.00 3.67
639 974 3.818210 TGTTATACTGGTTGTGCTTGGTG 59.182 43.478 0.00 0.00 0.00 4.17
640 975 2.656947 ATACTGGTTGTGCTTGGTGT 57.343 45.000 0.00 0.00 0.00 4.16
641 976 3.780804 ATACTGGTTGTGCTTGGTGTA 57.219 42.857 0.00 0.00 0.00 2.90
642 977 1.967319 ACTGGTTGTGCTTGGTGTAG 58.033 50.000 0.00 0.00 0.00 2.74
643 978 0.593128 CTGGTTGTGCTTGGTGTAGC 59.407 55.000 0.00 0.00 41.59 3.58
644 979 0.182537 TGGTTGTGCTTGGTGTAGCT 59.817 50.000 0.00 0.00 41.76 3.32
645 980 0.593128 GGTTGTGCTTGGTGTAGCTG 59.407 55.000 0.00 0.00 41.76 4.24
646 981 1.308998 GTTGTGCTTGGTGTAGCTGT 58.691 50.000 0.00 0.00 41.76 4.40
647 982 1.264288 GTTGTGCTTGGTGTAGCTGTC 59.736 52.381 0.00 0.00 41.76 3.51
648 983 0.467804 TGTGCTTGGTGTAGCTGTCA 59.532 50.000 0.00 0.00 41.76 3.58
649 984 1.072173 TGTGCTTGGTGTAGCTGTCAT 59.928 47.619 0.00 0.00 41.76 3.06
650 985 1.466167 GTGCTTGGTGTAGCTGTCATG 59.534 52.381 0.00 0.00 41.76 3.07
651 986 1.347378 TGCTTGGTGTAGCTGTCATGA 59.653 47.619 0.00 0.00 41.76 3.07
652 987 2.224499 TGCTTGGTGTAGCTGTCATGAA 60.224 45.455 0.00 0.00 41.76 2.57
653 988 3.012518 GCTTGGTGTAGCTGTCATGAAT 58.987 45.455 0.00 0.00 38.15 2.57
654 989 4.191544 GCTTGGTGTAGCTGTCATGAATA 58.808 43.478 0.00 0.00 38.15 1.75
655 990 4.635765 GCTTGGTGTAGCTGTCATGAATAA 59.364 41.667 0.00 0.00 38.15 1.40
656 991 5.297776 GCTTGGTGTAGCTGTCATGAATAAT 59.702 40.000 0.00 0.00 38.15 1.28
657 992 6.483307 GCTTGGTGTAGCTGTCATGAATAATA 59.517 38.462 0.00 0.00 38.15 0.98
658 993 7.173907 GCTTGGTGTAGCTGTCATGAATAATAT 59.826 37.037 0.00 0.00 38.15 1.28
659 994 8.978874 TTGGTGTAGCTGTCATGAATAATATT 57.021 30.769 0.00 0.00 0.00 1.28
660 995 8.978874 TGGTGTAGCTGTCATGAATAATATTT 57.021 30.769 0.00 0.00 0.00 1.40
661 996 8.839343 TGGTGTAGCTGTCATGAATAATATTTG 58.161 33.333 0.00 0.00 0.00 2.32
662 997 8.840321 GGTGTAGCTGTCATGAATAATATTTGT 58.160 33.333 0.00 0.00 0.00 2.83
668 1003 8.871862 GCTGTCATGAATAATATTTGTTTGCAA 58.128 29.630 0.00 0.00 0.00 4.08
694 1029 9.577110 AGTGCTGATTAATATTTGTTGTGATTG 57.423 29.630 0.00 0.00 0.00 2.67
711 1048 7.030075 TGTGATTGCATGAATAATCGACAAT 57.970 32.000 0.00 0.00 36.36 2.71
714 1051 5.833406 TTGCATGAATAATCGACAATGGT 57.167 34.783 0.00 0.00 0.00 3.55
788 1131 2.477825 CCGATTGAGCGACTGATTCAT 58.522 47.619 0.00 0.00 0.00 2.57
824 1167 4.334481 CACATCTTTCTAGCACATGCATCA 59.666 41.667 6.64 0.00 45.16 3.07
1008 1362 3.059352 AGTGAGTAAACCATGAGCCAC 57.941 47.619 0.00 0.00 0.00 5.01
1029 1383 3.127533 GGCAAGCGTACCAGCCAG 61.128 66.667 0.00 0.00 46.26 4.85
1068 1422 0.472471 AAGACAGGGACCAAAAGCGA 59.528 50.000 0.00 0.00 0.00 4.93
1100 1454 1.702957 CACCCAGGAAACCTCCAGTAA 59.297 52.381 0.00 0.00 45.24 2.24
1197 1551 4.019858 TGATAAATTCCATCCGGCAACAA 58.980 39.130 0.00 0.00 0.00 2.83
1585 1942 9.226606 TGAGTTTTGATAATTTCGTTCAGGTAT 57.773 29.630 0.00 0.00 0.00 2.73
1691 2048 5.126061 AGCAGCAATACTTTAATTCCCAGTG 59.874 40.000 0.00 0.00 0.00 3.66
2282 2701 9.485206 TCTTCGGTATTCTGCTAATTATTAACC 57.515 33.333 0.00 0.00 0.00 2.85
2494 2913 9.574516 TTATACTCAGTGTCAGATGCTTCTATA 57.425 33.333 1.16 0.00 0.00 1.31
2588 3007 1.145598 ACTGATGCTCATGGCGGAG 59.854 57.895 0.00 1.95 45.43 4.63
2755 3174 0.846693 AAGAGAGTGGTGCAAGGGTT 59.153 50.000 0.00 0.00 0.00 4.11
2827 3246 2.684943 TCCACTGAGGTTAGACCACAA 58.315 47.619 0.00 0.00 41.95 3.33
2857 3276 0.093705 CTAGCTGCGCTTTGTCGTTC 59.906 55.000 9.73 0.00 40.44 3.95
2891 3311 7.471721 TGATATGCTTTTTATTTGAGGTGACG 58.528 34.615 0.00 0.00 0.00 4.35
2926 3346 3.270877 GCCACCGATGATGTAAAGTCTT 58.729 45.455 0.00 0.00 0.00 3.01
3178 3599 9.003658 CCTTGTGTTATTGTTTGAGATAGTCTT 57.996 33.333 0.00 0.00 0.00 3.01
3227 3649 5.545658 AGTTTTATTGCATGTAGGTGTCG 57.454 39.130 0.00 0.00 0.00 4.35
3315 3737 1.675641 GACAGCGTGGGAAGGCAAT 60.676 57.895 0.00 0.00 0.00 3.56
3341 3763 1.393603 GCAAGGATGGGAAGCTAACC 58.606 55.000 0.00 0.00 0.00 2.85
3412 3834 6.739550 GCATTATTACCGTACAGTCAACAAAC 59.260 38.462 0.00 0.00 0.00 2.93
3607 4029 7.037438 TGTGAGATAAACTTAACCGGTGATAC 58.963 38.462 8.52 0.00 0.00 2.24
3723 4145 1.936547 CTTTCTAAGCCGTGCTCCATC 59.063 52.381 0.00 0.00 38.25 3.51
3728 4150 2.489938 AAGCCGTGCTCCATCTTTTA 57.510 45.000 0.00 0.00 38.25 1.52
3729 4151 1.739067 AGCCGTGCTCCATCTTTTAC 58.261 50.000 0.00 0.00 30.62 2.01
3730 4152 0.373716 GCCGTGCTCCATCTTTTACG 59.626 55.000 0.00 0.00 0.00 3.18
3731 4153 2.004583 CCGTGCTCCATCTTTTACGA 57.995 50.000 0.00 0.00 33.78 3.43
3732 4154 2.343101 CCGTGCTCCATCTTTTACGAA 58.657 47.619 0.00 0.00 33.78 3.85
3733 4155 2.936498 CCGTGCTCCATCTTTTACGAAT 59.064 45.455 0.00 0.00 33.78 3.34
3734 4156 4.116961 CCGTGCTCCATCTTTTACGAATA 58.883 43.478 0.00 0.00 33.78 1.75
3735 4157 4.209288 CCGTGCTCCATCTTTTACGAATAG 59.791 45.833 0.00 0.00 33.78 1.73
3736 4158 4.318121 CGTGCTCCATCTTTTACGAATAGC 60.318 45.833 0.00 0.00 33.78 2.97
3737 4159 4.024809 GTGCTCCATCTTTTACGAATAGCC 60.025 45.833 0.00 0.00 0.00 3.93
3738 4160 3.184581 GCTCCATCTTTTACGAATAGCCG 59.815 47.826 0.00 0.00 0.00 5.52
3739 4161 4.369182 CTCCATCTTTTACGAATAGCCGT 58.631 43.478 0.00 0.00 45.54 5.68
3740 4162 4.365723 TCCATCTTTTACGAATAGCCGTC 58.634 43.478 0.00 0.00 43.20 4.79
3741 4163 4.098960 TCCATCTTTTACGAATAGCCGTCT 59.901 41.667 0.00 0.00 43.20 4.18
3742 4164 4.444720 CCATCTTTTACGAATAGCCGTCTC 59.555 45.833 0.00 0.00 43.20 3.36
3743 4165 4.037858 TCTTTTACGAATAGCCGTCTCC 57.962 45.455 0.00 0.00 43.20 3.71
3744 4166 3.444742 TCTTTTACGAATAGCCGTCTCCA 59.555 43.478 0.00 0.00 43.20 3.86
3745 4167 4.098960 TCTTTTACGAATAGCCGTCTCCAT 59.901 41.667 0.00 0.00 43.20 3.41
3781 4203 1.726865 CCGTGCTTCTTGTGTGCAA 59.273 52.632 0.00 0.00 38.50 4.08
3799 4317 6.147821 GTGTGCAAGCTCTCTTAGATTTGTAA 59.852 38.462 0.00 0.00 29.18 2.41
3897 4415 6.071952 CCCGGATATGGAAATGTTTATTCCTG 60.072 42.308 0.73 0.00 45.40 3.86
3989 4507 7.759489 ACTATTTCATTTTACTGGTGCTTGA 57.241 32.000 0.00 0.00 0.00 3.02
4027 4546 2.854963 AGCTTGATGTGAGTTCAGCAA 58.145 42.857 0.00 0.00 40.58 3.91
4031 4550 4.394300 GCTTGATGTGAGTTCAGCAACTAT 59.606 41.667 0.00 0.00 43.37 2.12
4147 4684 5.392057 GCTACTTGCTGTCCCAAAATAAGTC 60.392 44.000 0.00 0.00 38.95 3.01
4148 4685 3.826729 ACTTGCTGTCCCAAAATAAGTCC 59.173 43.478 0.00 0.00 0.00 3.85
4149 4686 2.802719 TGCTGTCCCAAAATAAGTCCC 58.197 47.619 0.00 0.00 0.00 4.46
4150 4687 2.109128 TGCTGTCCCAAAATAAGTCCCA 59.891 45.455 0.00 0.00 0.00 4.37
4152 4689 3.761897 CTGTCCCAAAATAAGTCCCACA 58.238 45.455 0.00 0.00 0.00 4.17
4153 4690 4.148838 CTGTCCCAAAATAAGTCCCACAA 58.851 43.478 0.00 0.00 0.00 3.33
4154 4691 3.892588 TGTCCCAAAATAAGTCCCACAAC 59.107 43.478 0.00 0.00 0.00 3.32
4155 4692 4.149598 GTCCCAAAATAAGTCCCACAACT 58.850 43.478 0.00 0.00 0.00 3.16
4156 4693 4.022329 GTCCCAAAATAAGTCCCACAACTG 60.022 45.833 0.00 0.00 0.00 3.16
4157 4694 3.895041 CCCAAAATAAGTCCCACAACTGT 59.105 43.478 0.00 0.00 0.00 3.55
4158 4695 5.074115 CCCAAAATAAGTCCCACAACTGTA 58.926 41.667 0.00 0.00 0.00 2.74
4159 4696 5.183140 CCCAAAATAAGTCCCACAACTGTAG 59.817 44.000 0.00 0.00 0.00 2.74
4160 4697 5.768164 CCAAAATAAGTCCCACAACTGTAGT 59.232 40.000 0.00 0.00 0.00 2.73
4161 4698 6.938030 CCAAAATAAGTCCCACAACTGTAGTA 59.062 38.462 0.00 0.00 0.00 1.82
4162 4699 7.094933 CCAAAATAAGTCCCACAACTGTAGTAC 60.095 40.741 0.00 0.00 0.00 2.73
4163 4700 6.675413 AATAAGTCCCACAACTGTAGTACA 57.325 37.500 2.36 2.36 0.00 2.90
4164 4701 6.675413 ATAAGTCCCACAACTGTAGTACAA 57.325 37.500 4.21 0.00 0.00 2.41
4165 4702 4.332428 AGTCCCACAACTGTAGTACAAC 57.668 45.455 4.21 0.00 0.00 3.32
4166 4703 3.965347 AGTCCCACAACTGTAGTACAACT 59.035 43.478 4.21 0.00 0.00 3.16
4167 4704 4.407945 AGTCCCACAACTGTAGTACAACTT 59.592 41.667 4.21 0.00 0.00 2.66
4168 4705 5.104652 AGTCCCACAACTGTAGTACAACTTT 60.105 40.000 4.21 0.00 0.00 2.66
4169 4706 5.007332 GTCCCACAACTGTAGTACAACTTTG 59.993 44.000 4.21 10.14 0.00 2.77
4170 4707 4.879545 CCCACAACTGTAGTACAACTTTGT 59.120 41.667 14.52 14.52 44.86 2.83
4171 4708 6.050432 CCCACAACTGTAGTACAACTTTGTA 58.950 40.000 17.74 0.00 42.35 2.41
4205 4742 2.237893 GACTTATTTTGGGACGGAGGGA 59.762 50.000 0.00 0.00 0.00 4.20
4206 4743 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
4207 4744 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
4208 4745 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4209 4746 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
4210 4747 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
4211 4748 2.376695 TTGGGACGGAGGGAGTATAG 57.623 55.000 0.00 0.00 0.00 1.31
4212 4749 1.229131 TGGGACGGAGGGAGTATAGT 58.771 55.000 0.00 0.00 0.00 2.12
4213 4750 2.421725 TGGGACGGAGGGAGTATAGTA 58.578 52.381 0.00 0.00 0.00 1.82
4214 4751 2.991713 TGGGACGGAGGGAGTATAGTAT 59.008 50.000 0.00 0.00 0.00 2.12
4215 4752 3.400322 TGGGACGGAGGGAGTATAGTATT 59.600 47.826 0.00 0.00 0.00 1.89
4216 4753 4.603171 TGGGACGGAGGGAGTATAGTATTA 59.397 45.833 0.00 0.00 0.00 0.98
4311 4966 7.072263 AGAGGGTAATTTGATCCATGACTAG 57.928 40.000 0.00 0.00 0.00 2.57
4325 4980 9.368674 GATCCATGACTAGAGATGAAATGTATG 57.631 37.037 0.00 0.00 0.00 2.39
4450 5106 8.853077 AACTTGTAATCTGACATCTTGAATGA 57.147 30.769 0.00 0.00 0.00 2.57
4507 5167 0.379316 AAAGCACGGTTTCACGTTCC 59.621 50.000 0.00 0.00 46.25 3.62
4549 5209 5.660864 TGGTTCTTTTCACCTTTTTCCTCAT 59.339 36.000 0.00 0.00 35.07 2.90
4551 5211 5.200368 TCTTTTCACCTTTTTCCTCATGC 57.800 39.130 0.00 0.00 0.00 4.06
4680 5340 2.697147 TTTGGCACCCCTGAGCAGAC 62.697 60.000 0.00 0.00 0.00 3.51
4739 5399 4.393062 TGTCTACTTAAGGACGTACTTCCG 59.607 45.833 18.35 11.72 41.04 4.30
4763 5423 6.147821 CGGCTGTAGTTTGAAAGGATATATGG 59.852 42.308 0.00 0.00 0.00 2.74
4802 5462 2.032860 ATCGGACTCTTGCCATCCCG 62.033 60.000 0.00 0.00 38.41 5.14
4807 5467 2.367567 GGACTCTTGCCATCCCGTAATA 59.632 50.000 0.00 0.00 0.00 0.98
4944 5610 8.988934 GTTTAATCGCATGTTCAGATATTCCTA 58.011 33.333 0.00 0.00 0.00 2.94
5036 5702 2.677836 TGATTCATTCGCTTGCCAGTAC 59.322 45.455 0.00 0.00 0.00 2.73
5108 5828 6.666451 GCACACGTTCTAACACTTTGTTTTTG 60.666 38.462 0.00 0.00 41.45 2.44
5213 5933 4.439305 TTTGCTGCTTACCATGATTGAC 57.561 40.909 0.00 0.00 0.00 3.18
5289 6009 5.547181 TGCTACATCGTCCTTAGATATCG 57.453 43.478 0.00 0.00 0.00 2.92
5292 6012 6.374613 TGCTACATCGTCCTTAGATATCGAAT 59.625 38.462 0.00 0.00 34.38 3.34
5346 6068 9.436957 AATCTGTTTCATCGTGACTAAGTAAAT 57.563 29.630 0.00 0.00 0.00 1.40
5466 6188 4.905456 TCGGTCATTCCTTAGGTGGATATT 59.095 41.667 0.00 0.00 35.83 1.28
5513 6236 2.544267 GCATCAACTAGGTCGGTAATGC 59.456 50.000 0.00 0.00 0.00 3.56
5562 6285 7.004691 ACTAAGTAAAATTCTTGCCCTTGTCT 58.995 34.615 0.00 0.00 0.00 3.41
5563 6286 5.712152 AGTAAAATTCTTGCCCTTGTCTG 57.288 39.130 0.00 0.00 0.00 3.51
5564 6287 5.140454 AGTAAAATTCTTGCCCTTGTCTGT 58.860 37.500 0.00 0.00 0.00 3.41
5565 6288 6.303839 AGTAAAATTCTTGCCCTTGTCTGTA 58.696 36.000 0.00 0.00 0.00 2.74
5647 6371 3.454082 GACTCCTCTTCCCATTCATCACT 59.546 47.826 0.00 0.00 0.00 3.41
5725 6449 5.041015 TGTGAATATTAGGTAGGGTGGGTT 58.959 41.667 0.00 0.00 0.00 4.11
5726 6450 5.104277 TGTGAATATTAGGTAGGGTGGGTTG 60.104 44.000 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 3.499737 CCGTTGTGCCGCCATCTC 61.500 66.667 0.00 0.00 0.00 2.75
45 46 1.901650 GAAGAGAAGCCGTTGTGCCG 61.902 60.000 0.00 0.00 0.00 5.69
51 52 1.374758 CAGCCGAAGAGAAGCCGTT 60.375 57.895 0.00 0.00 0.00 4.44
251 558 8.990163 TTTATTCTCTACAAACCAGGAAAAGT 57.010 30.769 0.00 0.00 0.00 2.66
341 648 7.043854 CGAACGGAGAATGTACATTAATTACGT 60.044 37.037 20.83 21.62 0.00 3.57
410 719 9.439500 AATCAGCACTTGCAAACAAATATTATT 57.561 25.926 0.00 0.00 45.16 1.40
412 721 9.920133 TTAATCAGCACTTGCAAACAAATATTA 57.080 25.926 0.00 0.00 45.16 0.98
413 722 8.830201 TTAATCAGCACTTGCAAACAAATATT 57.170 26.923 0.00 0.18 45.16 1.28
416 725 9.439500 AATATTAATCAGCACTTGCAAACAAAT 57.561 25.926 0.00 1.01 45.16 2.32
420 755 8.243289 ACAAATATTAATCAGCACTTGCAAAC 57.757 30.769 0.00 0.00 45.16 2.93
453 788 3.944422 ACCGTTGTCGATTATTCATGC 57.056 42.857 0.00 0.00 39.71 4.06
511 846 7.869937 TGAATAATCGGCATTCACAAAGAAAAA 59.130 29.630 3.96 0.00 40.22 1.94
512 847 7.374272 TGAATAATCGGCATTCACAAAGAAAA 58.626 30.769 3.96 0.00 40.22 2.29
513 848 6.918626 TGAATAATCGGCATTCACAAAGAAA 58.081 32.000 3.96 0.00 40.22 2.52
514 849 6.507958 TGAATAATCGGCATTCACAAAGAA 57.492 33.333 3.96 0.00 37.46 2.52
515 850 6.318396 TCATGAATAATCGGCATTCACAAAGA 59.682 34.615 0.00 4.32 43.27 2.52
516 851 6.497437 TCATGAATAATCGGCATTCACAAAG 58.503 36.000 0.00 2.68 43.27 2.77
517 852 6.448207 TCATGAATAATCGGCATTCACAAA 57.552 33.333 0.00 0.00 43.27 2.83
518 853 6.638096 ATCATGAATAATCGGCATTCACAA 57.362 33.333 0.00 2.94 43.27 3.33
519 854 7.926674 ATATCATGAATAATCGGCATTCACA 57.073 32.000 0.00 1.94 43.27 3.58
551 886 9.588096 ACTTTTCCTGGTTTGTAGAGAATAAAT 57.412 29.630 0.00 0.00 0.00 1.40
552 887 8.846211 CACTTTTCCTGGTTTGTAGAGAATAAA 58.154 33.333 0.00 0.00 0.00 1.40
553 888 7.996644 ACACTTTTCCTGGTTTGTAGAGAATAA 59.003 33.333 0.00 0.00 0.00 1.40
554 889 7.514721 ACACTTTTCCTGGTTTGTAGAGAATA 58.485 34.615 0.00 0.00 0.00 1.75
555 890 6.365520 ACACTTTTCCTGGTTTGTAGAGAAT 58.634 36.000 0.00 0.00 0.00 2.40
556 891 5.751586 ACACTTTTCCTGGTTTGTAGAGAA 58.248 37.500 0.00 0.00 0.00 2.87
557 892 5.367945 ACACTTTTCCTGGTTTGTAGAGA 57.632 39.130 0.00 0.00 0.00 3.10
558 893 7.562454 TTTACACTTTTCCTGGTTTGTAGAG 57.438 36.000 0.00 0.00 0.00 2.43
559 894 7.941431 TTTTACACTTTTCCTGGTTTGTAGA 57.059 32.000 0.00 0.00 0.00 2.59
560 895 8.410141 TGATTTTACACTTTTCCTGGTTTGTAG 58.590 33.333 0.00 0.00 0.00 2.74
561 896 8.192110 GTGATTTTACACTTTTCCTGGTTTGTA 58.808 33.333 0.00 0.00 37.73 2.41
562 897 7.039270 GTGATTTTACACTTTTCCTGGTTTGT 58.961 34.615 0.00 0.00 37.73 2.83
563 898 6.198216 CGTGATTTTACACTTTTCCTGGTTTG 59.802 38.462 0.00 0.00 38.47 2.93
564 899 6.127563 ACGTGATTTTACACTTTTCCTGGTTT 60.128 34.615 0.00 0.00 38.47 3.27
565 900 5.358725 ACGTGATTTTACACTTTTCCTGGTT 59.641 36.000 0.00 0.00 38.47 3.67
566 901 4.885325 ACGTGATTTTACACTTTTCCTGGT 59.115 37.500 0.00 0.00 38.47 4.00
567 902 5.432885 ACGTGATTTTACACTTTTCCTGG 57.567 39.130 0.00 0.00 38.47 4.45
568 903 6.198216 CCAAACGTGATTTTACACTTTTCCTG 59.802 38.462 0.00 0.00 39.15 3.86
569 904 6.270064 CCAAACGTGATTTTACACTTTTCCT 58.730 36.000 0.00 0.00 39.15 3.36
570 905 5.051307 GCCAAACGTGATTTTACACTTTTCC 60.051 40.000 0.00 0.00 39.15 3.13
571 906 5.517054 TGCCAAACGTGATTTTACACTTTTC 59.483 36.000 0.00 0.00 39.15 2.29
572 907 5.411781 TGCCAAACGTGATTTTACACTTTT 58.588 33.333 0.00 0.00 40.84 2.27
573 908 5.000012 TGCCAAACGTGATTTTACACTTT 58.000 34.783 0.00 0.00 38.47 2.66
574 909 4.640789 TGCCAAACGTGATTTTACACTT 57.359 36.364 0.00 0.00 38.47 3.16
575 910 4.640789 TTGCCAAACGTGATTTTACACT 57.359 36.364 0.00 0.00 38.47 3.55
576 911 5.689961 AGAATTGCCAAACGTGATTTTACAC 59.310 36.000 0.00 0.00 37.42 2.90
577 912 5.837437 AGAATTGCCAAACGTGATTTTACA 58.163 33.333 0.00 0.00 0.00 2.41
578 913 7.380065 TGTTAGAATTGCCAAACGTGATTTTAC 59.620 33.333 0.00 0.00 0.00 2.01
579 914 7.426410 TGTTAGAATTGCCAAACGTGATTTTA 58.574 30.769 0.00 0.00 0.00 1.52
580 915 6.276847 TGTTAGAATTGCCAAACGTGATTTT 58.723 32.000 0.00 0.00 0.00 1.82
581 916 5.837437 TGTTAGAATTGCCAAACGTGATTT 58.163 33.333 0.00 0.00 0.00 2.17
582 917 5.446143 TGTTAGAATTGCCAAACGTGATT 57.554 34.783 0.00 0.00 0.00 2.57
583 918 5.446143 TTGTTAGAATTGCCAAACGTGAT 57.554 34.783 0.00 0.00 0.00 3.06
584 919 4.902443 TTGTTAGAATTGCCAAACGTGA 57.098 36.364 0.00 0.00 0.00 4.35
585 920 5.040635 AGTTTGTTAGAATTGCCAAACGTG 58.959 37.500 0.00 0.00 46.90 4.49
586 921 5.257082 AGTTTGTTAGAATTGCCAAACGT 57.743 34.783 0.00 0.00 46.90 3.99
587 922 4.679654 GGAGTTTGTTAGAATTGCCAAACG 59.320 41.667 0.00 0.00 46.90 3.60
588 923 5.691754 CAGGAGTTTGTTAGAATTGCCAAAC 59.308 40.000 0.00 0.00 44.27 2.93
589 924 5.221422 CCAGGAGTTTGTTAGAATTGCCAAA 60.221 40.000 0.00 0.00 0.00 3.28
590 925 4.280677 CCAGGAGTTTGTTAGAATTGCCAA 59.719 41.667 0.00 0.00 0.00 4.52
591 926 3.826157 CCAGGAGTTTGTTAGAATTGCCA 59.174 43.478 0.00 0.00 0.00 4.92
592 927 4.079253 TCCAGGAGTTTGTTAGAATTGCC 58.921 43.478 0.00 0.00 0.00 4.52
593 928 5.904362 ATCCAGGAGTTTGTTAGAATTGC 57.096 39.130 0.00 0.00 0.00 3.56
594 929 8.511604 ACATATCCAGGAGTTTGTTAGAATTG 57.488 34.615 0.00 0.00 0.00 2.32
601 936 7.993183 CCAGTATAACATATCCAGGAGTTTGTT 59.007 37.037 15.27 15.27 0.00 2.83
602 937 7.127339 ACCAGTATAACATATCCAGGAGTTTGT 59.873 37.037 0.00 0.00 0.00 2.83
603 938 7.509546 ACCAGTATAACATATCCAGGAGTTTG 58.490 38.462 0.00 0.00 0.00 2.93
604 939 7.691993 ACCAGTATAACATATCCAGGAGTTT 57.308 36.000 0.00 0.00 0.00 2.66
605 940 7.127339 ACAACCAGTATAACATATCCAGGAGTT 59.873 37.037 0.00 0.00 0.00 3.01
606 941 6.615726 ACAACCAGTATAACATATCCAGGAGT 59.384 38.462 0.00 0.00 0.00 3.85
607 942 6.931281 CACAACCAGTATAACATATCCAGGAG 59.069 42.308 0.00 0.00 0.00 3.69
608 943 6.687901 GCACAACCAGTATAACATATCCAGGA 60.688 42.308 0.00 0.00 0.00 3.86
609 944 5.470098 GCACAACCAGTATAACATATCCAGG 59.530 44.000 0.00 0.00 0.00 4.45
610 945 6.291377 AGCACAACCAGTATAACATATCCAG 58.709 40.000 0.00 0.00 0.00 3.86
611 946 6.247229 AGCACAACCAGTATAACATATCCA 57.753 37.500 0.00 0.00 0.00 3.41
612 947 6.017109 CCAAGCACAACCAGTATAACATATCC 60.017 42.308 0.00 0.00 0.00 2.59
613 948 6.542370 ACCAAGCACAACCAGTATAACATATC 59.458 38.462 0.00 0.00 0.00 1.63
614 949 6.318648 CACCAAGCACAACCAGTATAACATAT 59.681 38.462 0.00 0.00 0.00 1.78
615 950 5.645929 CACCAAGCACAACCAGTATAACATA 59.354 40.000 0.00 0.00 0.00 2.29
616 951 4.458989 CACCAAGCACAACCAGTATAACAT 59.541 41.667 0.00 0.00 0.00 2.71
617 952 3.818210 CACCAAGCACAACCAGTATAACA 59.182 43.478 0.00 0.00 0.00 2.41
618 953 3.818773 ACACCAAGCACAACCAGTATAAC 59.181 43.478 0.00 0.00 0.00 1.89
619 954 4.093472 ACACCAAGCACAACCAGTATAA 57.907 40.909 0.00 0.00 0.00 0.98
620 955 3.780804 ACACCAAGCACAACCAGTATA 57.219 42.857 0.00 0.00 0.00 1.47
621 956 2.656947 ACACCAAGCACAACCAGTAT 57.343 45.000 0.00 0.00 0.00 2.12
622 957 2.808933 GCTACACCAAGCACAACCAGTA 60.809 50.000 0.00 0.00 42.30 2.74
623 958 1.967319 CTACACCAAGCACAACCAGT 58.033 50.000 0.00 0.00 0.00 4.00
624 959 0.593128 GCTACACCAAGCACAACCAG 59.407 55.000 0.00 0.00 42.30 4.00
625 960 0.182537 AGCTACACCAAGCACAACCA 59.817 50.000 0.00 0.00 45.30 3.67
626 961 0.593128 CAGCTACACCAAGCACAACC 59.407 55.000 0.00 0.00 45.30 3.77
627 962 1.264288 GACAGCTACACCAAGCACAAC 59.736 52.381 0.00 0.00 45.30 3.32
628 963 1.134250 TGACAGCTACACCAAGCACAA 60.134 47.619 0.00 0.00 45.30 3.33
629 964 0.467804 TGACAGCTACACCAAGCACA 59.532 50.000 0.00 0.00 45.30 4.57
630 965 1.466167 CATGACAGCTACACCAAGCAC 59.534 52.381 0.00 0.00 45.30 4.40
631 966 1.347378 TCATGACAGCTACACCAAGCA 59.653 47.619 0.00 0.00 45.30 3.91
632 967 2.099141 TCATGACAGCTACACCAAGC 57.901 50.000 0.00 0.00 43.11 4.01
633 968 6.932356 ATTATTCATGACAGCTACACCAAG 57.068 37.500 0.00 0.00 0.00 3.61
634 969 8.978874 AATATTATTCATGACAGCTACACCAA 57.021 30.769 0.00 0.00 0.00 3.67
635 970 8.839343 CAAATATTATTCATGACAGCTACACCA 58.161 33.333 0.00 0.00 0.00 4.17
636 971 8.840321 ACAAATATTATTCATGACAGCTACACC 58.160 33.333 0.00 0.00 0.00 4.16
640 975 9.734620 GCAAACAAATATTATTCATGACAGCTA 57.265 29.630 0.00 0.00 0.00 3.32
641 976 8.252417 TGCAAACAAATATTATTCATGACAGCT 58.748 29.630 0.00 0.00 0.00 4.24
642 977 8.410030 TGCAAACAAATATTATTCATGACAGC 57.590 30.769 0.00 0.00 0.00 4.40
644 979 9.926158 ACTTGCAAACAAATATTATTCATGACA 57.074 25.926 0.00 0.00 34.74 3.58
646 981 8.871862 GCACTTGCAAACAAATATTATTCATGA 58.128 29.630 0.00 0.00 41.59 3.07
647 982 8.875803 AGCACTTGCAAACAAATATTATTCATG 58.124 29.630 0.00 0.00 45.16 3.07
648 983 8.875803 CAGCACTTGCAAACAAATATTATTCAT 58.124 29.630 0.00 0.00 45.16 2.57
649 984 8.087136 TCAGCACTTGCAAACAAATATTATTCA 58.913 29.630 0.00 0.00 45.16 2.57
650 985 8.464770 TCAGCACTTGCAAACAAATATTATTC 57.535 30.769 0.00 0.00 45.16 1.75
651 986 9.439500 AATCAGCACTTGCAAACAAATATTATT 57.561 25.926 0.00 0.00 45.16 1.40
653 988 9.920133 TTAATCAGCACTTGCAAACAAATATTA 57.080 25.926 0.00 0.00 45.16 0.98
654 989 8.830201 TTAATCAGCACTTGCAAACAAATATT 57.170 26.923 0.00 0.18 45.16 1.28
657 992 9.439500 AATATTAATCAGCACTTGCAAACAAAT 57.561 25.926 0.00 1.01 45.16 2.32
658 993 8.830201 AATATTAATCAGCACTTGCAAACAAA 57.170 26.923 0.00 0.00 45.16 2.83
659 994 8.710551 CAAATATTAATCAGCACTTGCAAACAA 58.289 29.630 0.00 0.00 45.16 2.83
660 995 7.871973 ACAAATATTAATCAGCACTTGCAAACA 59.128 29.630 0.00 0.00 45.16 2.83
661 996 8.243289 ACAAATATTAATCAGCACTTGCAAAC 57.757 30.769 0.00 0.00 45.16 2.93
662 997 8.710551 CAACAAATATTAATCAGCACTTGCAAA 58.289 29.630 0.00 0.00 45.16 3.68
668 1003 9.577110 CAATCACAACAAATATTAATCAGCACT 57.423 29.630 0.00 0.00 0.00 4.40
694 1029 6.959361 AGTAACCATTGTCGATTATTCATGC 58.041 36.000 0.00 0.00 0.00 4.06
711 1048 6.833041 TCCATAAGAACTCAACAAGTAACCA 58.167 36.000 0.00 0.00 37.17 3.67
714 1051 9.162764 GCTTATCCATAAGAACTCAACAAGTAA 57.837 33.333 10.05 0.00 41.72 2.24
788 1131 0.839277 AGATGTGGCCATGATTCCGA 59.161 50.000 9.72 0.00 0.00 4.55
824 1167 4.922206 ACAAATGGGTCATGTATCACTGT 58.078 39.130 0.00 0.00 0.00 3.55
931 1285 7.115520 CAGGCACTACAAAGATGAATAGATACG 59.884 40.741 0.00 0.00 36.02 3.06
1014 1368 2.358615 TGCTGGCTGGTACGCTTG 60.359 61.111 0.00 0.00 0.00 4.01
1029 1383 1.483827 TCTCTGTCATGATCCCTGTGC 59.516 52.381 0.00 0.00 0.00 4.57
1142 1496 4.201910 CCTTGCCAATTACACTACCAATCG 60.202 45.833 0.00 0.00 0.00 3.34
1197 1551 2.306847 ACCTTGACTTTGGCATTCGTT 58.693 42.857 0.00 0.00 0.00 3.85
1452 1809 6.072728 TGACAGAACCAGATTTTCCAATAACG 60.073 38.462 0.00 0.00 0.00 3.18
1676 2033 5.806654 AAACATGCACTGGGAATTAAAGT 57.193 34.783 0.00 0.00 0.00 2.66
1691 2048 8.066595 TGCATACATTTTAACACAAAAACATGC 58.933 29.630 13.59 13.59 39.22 4.06
1815 2172 7.211573 TCAGTCGAAGTTAACAAAGGTTGATA 58.788 34.615 8.61 0.00 37.88 2.15
2588 3007 6.294731 GGAACCATAGAATGATAAATGGGCAC 60.295 42.308 5.29 0.00 42.66 5.01
2677 3096 1.501741 CAACCCAATCTTGTCGGCG 59.498 57.895 0.00 0.00 0.00 6.46
2680 3099 4.380444 CCAATAACCAACCCAATCTTGTCG 60.380 45.833 0.00 0.00 0.00 4.35
2755 3174 6.071840 TGTCATTCTTTGCATCATCAACATCA 60.072 34.615 0.00 0.00 0.00 3.07
3178 3599 7.117956 CGTAAAGACATCTAGATAGATCCACGA 59.882 40.741 4.54 0.00 40.91 4.35
3227 3649 1.074951 CAGGTTGTCCACTTCCCCC 59.925 63.158 0.00 0.00 35.89 5.40
3315 3737 2.423373 GCTTCCCATCCTTGCCAGAATA 60.423 50.000 0.00 0.00 0.00 1.75
3341 3763 1.785041 CTGGTTCAGTGGTGGCAACG 61.785 60.000 0.00 0.00 42.51 4.10
3412 3834 1.802960 GATCATAGCGCAATGGAGTGG 59.197 52.381 11.47 0.00 0.00 4.00
3558 3980 7.064253 ACAAACTTAATAGGCACGTCTCATTAC 59.936 37.037 0.00 0.00 0.00 1.89
3607 4029 1.347050 CATCTACAGCCTGATGGAGGG 59.653 57.143 0.00 0.00 43.07 4.30
3723 4145 3.777478 TGGAGACGGCTATTCGTAAAAG 58.223 45.455 0.00 0.00 43.96 2.27
3728 4150 2.981859 AAATGGAGACGGCTATTCGT 57.018 45.000 0.00 0.00 46.83 3.85
3756 4178 1.061131 CACAAGAAGCACGGCTATTCG 59.939 52.381 0.00 0.00 38.25 3.34
3848 4366 3.521560 GCGTCTGATCAGTGGTAATCAA 58.478 45.455 21.92 0.00 31.81 2.57
3897 4415 5.402398 CATTACTTTTGAAAGGCCACTAGC 58.598 41.667 5.01 0.00 40.31 3.42
4027 4546 5.710567 GCCTCTTTTCCACACCTTTAATAGT 59.289 40.000 0.00 0.00 0.00 2.12
4031 4550 3.227614 GGCCTCTTTTCCACACCTTTAA 58.772 45.455 0.00 0.00 0.00 1.52
4082 4601 1.673665 GGCACTCCTTCAGGCAGTG 60.674 63.158 15.68 15.68 41.75 3.66
4147 4684 4.879545 ACAAAGTTGTACTACAGTTGTGGG 59.120 41.667 20.42 4.26 40.16 4.61
4170 4707 9.720769 CCCAAAATAAGTCTCTCAACTTTAGTA 57.279 33.333 0.00 0.00 40.01 1.82
4171 4708 8.437575 TCCCAAAATAAGTCTCTCAACTTTAGT 58.562 33.333 0.00 0.00 40.01 2.24
4172 4709 8.722394 GTCCCAAAATAAGTCTCTCAACTTTAG 58.278 37.037 0.00 0.00 40.01 1.85
4173 4710 7.386848 CGTCCCAAAATAAGTCTCTCAACTTTA 59.613 37.037 0.00 0.00 40.01 1.85
4174 4711 6.204882 CGTCCCAAAATAAGTCTCTCAACTTT 59.795 38.462 0.00 0.00 40.01 2.66
4177 4714 4.392138 CCGTCCCAAAATAAGTCTCTCAAC 59.608 45.833 0.00 0.00 0.00 3.18
4184 4721 2.237893 TCCCTCCGTCCCAAAATAAGTC 59.762 50.000 0.00 0.00 0.00 3.01
4213 4750 9.893975 AGGTACTGGTATACTAATGGACTTAAT 57.106 33.333 2.25 0.00 37.18 1.40
4216 4753 9.719433 TTTAGGTACTGGTATACTAATGGACTT 57.281 33.333 2.25 0.00 41.52 3.01
4299 4954 9.368674 CATACATTTCATCTCTAGTCATGGATC 57.631 37.037 0.00 0.00 0.00 3.36
4311 4966 7.224753 ACACCATTACGTCATACATTTCATCTC 59.775 37.037 0.00 0.00 0.00 2.75
4325 4980 3.803231 TGTTGTACACACACCATTACGTC 59.197 43.478 0.00 0.00 33.30 4.34
4368 5024 1.876799 CAATCCTGTACAACGGTTGCA 59.123 47.619 20.20 10.38 0.00 4.08
4375 5031 4.395854 TCATGCATGTCAATCCTGTACAAC 59.604 41.667 25.43 0.00 0.00 3.32
4494 5154 2.289547 AGTGAAATGGAACGTGAAACCG 59.710 45.455 0.00 0.00 0.00 4.44
4525 5185 5.020132 TGAGGAAAAAGGTGAAAAGAACCA 58.980 37.500 0.00 0.00 40.40 3.67
4542 5202 2.758423 TGCGAAGTAGTAGCATGAGGAA 59.242 45.455 0.00 0.00 35.81 3.36
4549 5209 2.921121 CGTCAATTGCGAAGTAGTAGCA 59.079 45.455 14.47 0.00 39.33 3.49
4551 5211 3.241678 GCACGTCAATTGCGAAGTAGTAG 60.242 47.826 22.87 7.99 0.00 2.57
4680 5340 0.095935 CAAATTCTCTGCCGACTGCG 59.904 55.000 0.00 0.00 45.60 5.18
4733 5393 2.922740 TTCAAACTACAGCCGGAAGT 57.077 45.000 5.05 4.75 0.00 3.01
4739 5399 6.431234 CCCATATATCCTTTCAAACTACAGCC 59.569 42.308 0.00 0.00 0.00 4.85
4763 5423 0.972883 AGAGCTGACTGAAGTGTCCC 59.027 55.000 0.00 0.00 36.21 4.46
4802 5462 9.331282 AGCACTGTTTTGATCTAAGGATATTAC 57.669 33.333 0.00 0.00 31.46 1.89
4807 5467 6.059787 AGAGCACTGTTTTGATCTAAGGAT 57.940 37.500 0.00 0.00 40.47 3.24
5108 5828 7.681939 TGGTAATGGTGTAACAGATTTCTTC 57.318 36.000 0.00 0.00 39.98 2.87
5213 5933 2.411069 CGCATGTTCTGACTGAAGACTG 59.589 50.000 0.00 0.00 35.01 3.51
5346 6068 9.408648 AGAGTATTTGAAAAGAACAGGAAGAAA 57.591 29.630 0.00 0.00 0.00 2.52
5491 6214 3.792401 CATTACCGACCTAGTTGATGCA 58.208 45.455 0.00 0.00 0.00 3.96
5562 6285 4.517453 GCCATTACTCAACCAACACTTACA 59.483 41.667 0.00 0.00 0.00 2.41
5563 6286 4.082949 GGCCATTACTCAACCAACACTTAC 60.083 45.833 0.00 0.00 0.00 2.34
5564 6287 4.076394 GGCCATTACTCAACCAACACTTA 58.924 43.478 0.00 0.00 0.00 2.24
5565 6288 2.890945 GGCCATTACTCAACCAACACTT 59.109 45.455 0.00 0.00 0.00 3.16
5618 6342 3.474798 TGGGAAGAGGAGTCATGTACT 57.525 47.619 0.00 0.00 42.80 2.73
5647 6371 3.289836 CATACATGGCCAAGGAATGACA 58.710 45.455 10.96 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.