Multiple sequence alignment - TraesCS2A01G131600

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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 TraesCS2A01G131600 chr2A 100.000 4196 0 0 1 4196 79166170 79170365 0.000000e+00 7749.0
1 TraesCS2A01G131600 chr2B 92.999 2928 146 24 852 3767 122007606 122010486 0.000000e+00 4217.0
2 TraesCS2A01G131600 chr2B 86.957 368 22 11 3834 4196 122010511 122010857 1.410000e-104 390.0
3 TraesCS2A01G131600 chr2B 89.668 271 22 3 307 572 121999078 121999347 1.440000e-89 340.0
4 TraesCS2A01G131600 chr2B 92.149 242 16 1 76 314 121994930 121995171 5.200000e-89 339.0
5 TraesCS2A01G131600 chr2B 95.876 97 4 0 731 827 122007439 122007535 1.560000e-34 158.0
6 TraesCS2A01G131600 chr2B 94.828 58 2 1 1 57 121994874 121994931 5.780000e-14 89.8
7 TraesCS2A01G131600 chr2D 93.266 2866 117 28 919 3774 78709406 78712205 0.000000e+00 4154.0
8 TraesCS2A01G131600 chr2D 90.221 634 50 5 1 628 78703862 78704489 0.000000e+00 817.0
9 TraesCS2A01G131600 chr2D 85.417 288 18 2 3824 4111 78712213 78712476 1.150000e-70 278.0
10 TraesCS2A01G131600 chr2D 94.792 96 3 2 730 824 78704487 78704581 9.400000e-32 148.0
11 TraesCS2A01G131600 chr7A 94.828 116 5 1 626 740 269960427 269960312 3.330000e-41 180.0
12 TraesCS2A01G131600 chr6A 94.167 120 4 3 614 732 55731042 55730925 3.330000e-41 180.0
13 TraesCS2A01G131600 chr7D 93.388 121 6 2 614 733 288465650 288465531 1.200000e-40 178.0
14 TraesCS2A01G131600 chr7D 94.737 114 5 1 621 733 21093719 21093606 4.310000e-40 176.0
15 TraesCS2A01G131600 chr5A 95.536 112 4 1 624 734 9470798 9470909 1.200000e-40 178.0
16 TraesCS2A01G131600 chr5A 93.333 120 5 3 614 732 375844355 375844472 1.550000e-39 174.0
17 TraesCS2A01G131600 chr3D 91.406 128 9 2 629 755 530418946 530419072 1.550000e-39 174.0
18 TraesCS2A01G131600 chr4B 91.870 123 9 1 612 733 565865840 565865962 2.010000e-38 171.0
19 TraesCS2A01G131600 chr5D 90.698 129 8 4 607 733 560426065 560426191 7.210000e-38 169.0
20 TraesCS2A01G131600 chr3B 90.385 52 4 1 738 788 20024979 20024928 2.710000e-07 67.6


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 TraesCS2A01G131600 chr2A 79166170 79170365 4195 False 7749.000000 7749 100.0000 1 4196 1 chr2A.!!$F1 4195
1 TraesCS2A01G131600 chr2B 122007439 122010857 3418 False 1588.333333 4217 91.9440 731 4196 3 chr2B.!!$F2 3465
2 TraesCS2A01G131600 chr2B 121994874 121999347 4473 False 256.266667 340 92.2150 1 572 3 chr2B.!!$F1 571
3 TraesCS2A01G131600 chr2D 78709406 78712476 3070 False 2216.000000 4154 89.3415 919 4111 2 chr2D.!!$F2 3192
4 TraesCS2A01G131600 chr2D 78703862 78704581 719 False 482.500000 817 92.5065 1 824 2 chr2D.!!$F1 823

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
739 4683 0.541863 ACGGAGGGAGTAGCATTTGG 59.458 55.0 0.00 0.00 0.0 3.28 F
1548 5547 0.462581 CTAAGCGGGCATTCAGAGCA 60.463 55.0 0.00 0.00 0.0 4.26 F
1962 5961 0.104304 GATGGTCGCATCTTACCGGT 59.896 55.0 13.98 13.98 38.7 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 5620 0.448990 TCATCAAACAGCTGCATCGC 59.551 50.0 15.27 0.0 0.00 4.58 R
3032 7031 0.105039 GATTCGAAGCGGAGTCCCAT 59.895 55.0 3.35 0.0 0.00 4.00 R
3809 7820 0.031917 TGTACCCTTGGCGGATAGGA 60.032 55.0 0.00 0.0 33.13 2.94 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
32 33 9.686683 AGCCTTATCTTTTTGTGATAACTACAT 57.313 29.630 0.00 0.00 34.11 2.29
58 60 8.256611 AGACATGTATCACACAAAGATGTAAC 57.743 34.615 0.00 0.00 41.55 2.50
59 61 8.097038 AGACATGTATCACACAAAGATGTAACT 58.903 33.333 0.00 0.00 41.55 2.24
60 62 9.366216 GACATGTATCACACAAAGATGTAACTA 57.634 33.333 0.00 0.00 41.55 2.24
61 63 9.719355 ACATGTATCACACAAAGATGTAACTAA 57.281 29.630 0.00 0.00 41.55 2.24
63 65 8.771920 TGTATCACACAAAGATGTAACTAAGG 57.228 34.615 0.00 0.00 37.82 2.69
64 66 8.590204 TGTATCACACAAAGATGTAACTAAGGA 58.410 33.333 0.00 0.00 37.82 3.36
65 67 9.601217 GTATCACACAAAGATGTAACTAAGGAT 57.399 33.333 0.00 0.00 37.82 3.24
66 68 7.905604 TCACACAAAGATGTAACTAAGGATG 57.094 36.000 0.00 0.00 37.82 3.51
67 69 6.371548 TCACACAAAGATGTAACTAAGGATGC 59.628 38.462 0.00 0.00 37.82 3.91
68 70 6.149308 CACACAAAGATGTAACTAAGGATGCA 59.851 38.462 0.00 0.00 37.82 3.96
69 71 6.886459 ACACAAAGATGTAACTAAGGATGCAT 59.114 34.615 0.00 0.00 37.82 3.96
70 72 8.046708 ACACAAAGATGTAACTAAGGATGCATA 58.953 33.333 0.00 0.00 37.82 3.14
71 73 8.338259 CACAAAGATGTAACTAAGGATGCATAC 58.662 37.037 0.00 0.00 37.82 2.39
72 74 7.499232 ACAAAGATGTAACTAAGGATGCATACC 59.501 37.037 4.93 6.18 38.24 2.73
73 75 5.784177 AGATGTAACTAAGGATGCATACCG 58.216 41.667 4.93 0.00 0.00 4.02
74 76 5.538813 AGATGTAACTAAGGATGCATACCGA 59.461 40.000 4.93 0.00 0.00 4.69
75 77 5.801531 TGTAACTAAGGATGCATACCGAT 57.198 39.130 4.93 3.96 0.00 4.18
76 78 6.904463 TGTAACTAAGGATGCATACCGATA 57.096 37.500 4.93 4.83 0.00 2.92
140 162 8.629158 GTTAGTCCCATATGCATTTGTCATTAA 58.371 33.333 14.86 6.46 0.00 1.40
144 166 6.040729 TCCCATATGCATTTGTCATTAACCAG 59.959 38.462 14.86 0.00 0.00 4.00
167 189 6.262944 CAGCTATAGGTAAATCAATTGCCACA 59.737 38.462 3.68 0.00 45.52 4.17
198 220 8.827177 ATATGTAATAGTTTCCCGTACACATG 57.173 34.615 0.00 0.00 28.50 3.21
233 258 6.438741 TGCTAGCTCATATATTCAGCCTAAGT 59.561 38.462 17.23 0.00 33.28 2.24
237 262 6.496565 AGCTCATATATTCAGCCTAAGTCAGT 59.503 38.462 9.07 0.00 33.28 3.41
240 265 8.484214 TCATATATTCAGCCTAAGTCAGTCTT 57.516 34.615 0.00 0.00 39.89 3.01
384 4323 7.653311 CCAAAAGATGAAAGAAATTTCGGACTT 59.347 33.333 12.42 10.20 33.80 3.01
385 4324 8.482429 CAAAAGATGAAAGAAATTTCGGACTTG 58.518 33.333 12.42 4.93 33.80 3.16
393 4332 1.156736 ATTTCGGACTTGAGGCAACG 58.843 50.000 0.00 0.00 46.39 4.10
430 4371 9.888878 CAGAATTTATTTGCACATCGATCTAAT 57.111 29.630 0.00 0.00 0.00 1.73
482 4426 5.794687 TTCTAGGACGTAACATTTGCATG 57.205 39.130 0.00 0.00 36.34 4.06
539 4483 5.129485 ACTGGATCGAGGATCAATTTGTAGT 59.871 40.000 9.72 0.00 40.50 2.73
580 4524 6.989169 GGAACTCAGTATCATAGCTGAATGTT 59.011 38.462 0.00 0.00 40.68 2.71
591 4535 8.229253 TCATAGCTGAATGTTATGCATCTTTT 57.771 30.769 0.19 0.00 38.98 2.27
618 4562 5.129368 ACAATACTACCATGGGAAAGCAT 57.871 39.130 18.09 3.89 0.00 3.79
628 4572 5.536161 ACCATGGGAAAGCATTGATATGTAC 59.464 40.000 18.09 0.00 34.12 2.90
629 4573 5.047802 CCATGGGAAAGCATTGATATGTACC 60.048 44.000 2.85 0.00 34.12 3.34
630 4574 4.469657 TGGGAAAGCATTGATATGTACCC 58.530 43.478 0.00 0.00 35.02 3.69
631 4575 3.826729 GGGAAAGCATTGATATGTACCCC 59.173 47.826 0.00 0.00 34.12 4.95
632 4576 4.447762 GGGAAAGCATTGATATGTACCCCT 60.448 45.833 0.00 0.00 34.12 4.79
633 4577 4.762251 GGAAAGCATTGATATGTACCCCTC 59.238 45.833 0.00 0.00 34.12 4.30
634 4578 4.373156 AAGCATTGATATGTACCCCTCC 57.627 45.455 0.00 0.00 34.12 4.30
635 4579 2.303022 AGCATTGATATGTACCCCTCCG 59.697 50.000 0.00 0.00 34.12 4.63
636 4580 2.038557 GCATTGATATGTACCCCTCCGT 59.961 50.000 0.00 0.00 34.12 4.69
637 4581 3.496160 GCATTGATATGTACCCCTCCGTT 60.496 47.826 0.00 0.00 34.12 4.44
638 4582 4.714632 CATTGATATGTACCCCTCCGTTT 58.285 43.478 0.00 0.00 0.00 3.60
639 4583 4.411256 TTGATATGTACCCCTCCGTTTC 57.589 45.455 0.00 0.00 0.00 2.78
640 4584 3.376636 TGATATGTACCCCTCCGTTTCA 58.623 45.455 0.00 0.00 0.00 2.69
641 4585 3.775866 TGATATGTACCCCTCCGTTTCAA 59.224 43.478 0.00 0.00 0.00 2.69
642 4586 4.225492 TGATATGTACCCCTCCGTTTCAAA 59.775 41.667 0.00 0.00 0.00 2.69
643 4587 3.732048 ATGTACCCCTCCGTTTCAAAT 57.268 42.857 0.00 0.00 0.00 2.32
644 4588 3.512219 TGTACCCCTCCGTTTCAAATT 57.488 42.857 0.00 0.00 0.00 1.82
645 4589 4.637387 TGTACCCCTCCGTTTCAAATTA 57.363 40.909 0.00 0.00 0.00 1.40
646 4590 4.325972 TGTACCCCTCCGTTTCAAATTAC 58.674 43.478 0.00 0.00 0.00 1.89
647 4591 3.801307 ACCCCTCCGTTTCAAATTACT 57.199 42.857 0.00 0.00 0.00 2.24
648 4592 3.682696 ACCCCTCCGTTTCAAATTACTC 58.317 45.455 0.00 0.00 0.00 2.59
649 4593 2.676342 CCCCTCCGTTTCAAATTACTCG 59.324 50.000 0.00 0.00 0.00 4.18
650 4594 3.332034 CCCTCCGTTTCAAATTACTCGT 58.668 45.455 0.00 0.00 0.00 4.18
651 4595 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
652 4596 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
653 4597 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
654 4598 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
655 4599 3.395671 CGTTTCAAATTACTCGTCGCAG 58.604 45.455 0.00 0.00 0.00 5.18
656 4600 3.120616 CGTTTCAAATTACTCGTCGCAGA 59.879 43.478 0.00 0.00 0.00 4.26
657 4601 4.375606 CGTTTCAAATTACTCGTCGCAGAA 60.376 41.667 0.00 0.00 39.69 3.02
658 4602 5.437263 GTTTCAAATTACTCGTCGCAGAAA 58.563 37.500 0.00 0.00 39.69 2.52
659 4603 5.856126 TTCAAATTACTCGTCGCAGAAAT 57.144 34.783 0.00 0.00 39.69 2.17
660 4604 5.203358 TCAAATTACTCGTCGCAGAAATG 57.797 39.130 0.00 0.00 39.69 2.32
661 4605 4.092821 TCAAATTACTCGTCGCAGAAATGG 59.907 41.667 0.00 0.00 39.69 3.16
662 4606 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
663 4607 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
664 4608 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
665 4609 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
666 4610 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
667 4611 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
668 4612 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
669 4613 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
670 4614 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
671 4615 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
672 4616 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
673 4617 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
674 4618 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
675 4619 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
676 4620 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
677 4621 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
678 4622 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
705 4649 7.825331 ATATCTAGATACATCCATACCCACG 57.175 40.000 14.71 0.00 0.00 4.94
706 4650 5.251182 TCTAGATACATCCATACCCACGA 57.749 43.478 0.00 0.00 0.00 4.35
707 4651 5.008331 TCTAGATACATCCATACCCACGAC 58.992 45.833 0.00 0.00 0.00 4.34
708 4652 3.572642 AGATACATCCATACCCACGACA 58.427 45.455 0.00 0.00 0.00 4.35
709 4653 3.964688 AGATACATCCATACCCACGACAA 59.035 43.478 0.00 0.00 0.00 3.18
710 4654 2.691409 ACATCCATACCCACGACAAG 57.309 50.000 0.00 0.00 0.00 3.16
711 4655 1.906574 ACATCCATACCCACGACAAGT 59.093 47.619 0.00 0.00 0.00 3.16
712 4656 3.101437 ACATCCATACCCACGACAAGTA 58.899 45.455 0.00 0.00 0.00 2.24
713 4657 3.516300 ACATCCATACCCACGACAAGTAA 59.484 43.478 0.00 0.00 0.00 2.24
714 4658 4.163458 ACATCCATACCCACGACAAGTAAT 59.837 41.667 0.00 0.00 0.00 1.89
715 4659 4.829872 TCCATACCCACGACAAGTAATT 57.170 40.909 0.00 0.00 0.00 1.40
716 4660 4.761975 TCCATACCCACGACAAGTAATTC 58.238 43.478 0.00 0.00 0.00 2.17
717 4661 3.554324 CCATACCCACGACAAGTAATTCG 59.446 47.826 0.00 0.00 41.14 3.34
718 4662 2.088950 ACCCACGACAAGTAATTCGG 57.911 50.000 0.00 0.00 39.63 4.30
719 4663 1.619827 ACCCACGACAAGTAATTCGGA 59.380 47.619 0.00 0.00 39.63 4.55
720 4664 2.037511 ACCCACGACAAGTAATTCGGAA 59.962 45.455 0.00 0.00 39.63 4.30
721 4665 2.414138 CCCACGACAAGTAATTCGGAAC 59.586 50.000 0.00 0.00 39.63 3.62
737 4681 1.209747 GGAACGGAGGGAGTAGCATTT 59.790 52.381 0.00 0.00 0.00 2.32
739 4683 0.541863 ACGGAGGGAGTAGCATTTGG 59.458 55.000 0.00 0.00 0.00 3.28
845 4806 7.337436 TGATGATCTTTGATTTGTATGCACTGA 59.663 33.333 0.00 0.00 0.00 3.41
848 4809 9.176460 TGATCTTTGATTTGTATGCACTGAATA 57.824 29.630 0.00 0.00 0.00 1.75
867 4857 7.763071 ACTGAATATTAAGTAACACCCGTCTTC 59.237 37.037 3.38 0.00 0.00 2.87
1030 5020 3.150335 CTAGGAGAGCTGCGGCCA 61.150 66.667 15.55 0.00 39.73 5.36
1045 5035 4.873129 CCACGCTGCTATCGCCGT 62.873 66.667 0.00 0.00 35.01 5.68
1206 5205 4.704103 AGCCCCTGCGTGAGAGGA 62.704 66.667 0.00 0.00 44.33 3.71
1404 5403 4.463879 CTCAGGTGCTGCTCGGGG 62.464 72.222 0.00 0.00 0.00 5.73
1485 5484 2.672996 GACCGGGTGCTGTGCAAT 60.673 61.111 3.30 0.00 41.47 3.56
1492 5491 1.578926 GTGCTGTGCAATGCCGTTA 59.421 52.632 1.53 0.00 41.47 3.18
1512 5511 3.728076 ATCGATATGTACGCCAAGTGT 57.272 42.857 0.00 0.00 0.00 3.55
1548 5547 0.462581 CTAAGCGGGCATTCAGAGCA 60.463 55.000 0.00 0.00 0.00 4.26
1641 5640 1.792993 GCGATGCAGCTGTTTGATGAC 60.793 52.381 16.64 0.00 33.12 3.06
1810 5809 0.604578 GGCTGGCATGCTTTCTTTGA 59.395 50.000 18.92 0.00 0.00 2.69
1823 5822 0.909610 TCTTTGATGGACCTCGGCCT 60.910 55.000 0.00 0.00 0.00 5.19
1928 5927 1.513586 GCTCAATGAACGCTGCTGC 60.514 57.895 5.34 5.34 0.00 5.25
1962 5961 0.104304 GATGGTCGCATCTTACCGGT 59.896 55.000 13.98 13.98 38.70 5.28
2031 6030 1.458398 GCAGGGAGGAAGAAGCTTTC 58.542 55.000 0.00 0.00 0.00 2.62
2094 6093 1.961277 GTTCACCCTCACCAGTGCG 60.961 63.158 0.00 0.00 33.90 5.34
2257 6256 3.728864 CGCTTGCAGGATGTTTGACATAC 60.729 47.826 0.00 0.00 39.27 2.39
2370 6369 7.313646 ACAGAATGATTGCAGAAAAGATCAAG 58.686 34.615 0.88 0.00 39.69 3.02
2415 6414 2.168521 TGTTCTATCTGCCTGTAGCCAC 59.831 50.000 0.00 0.00 42.71 5.01
2616 6615 2.688507 ACATTACTGTCAGCTTGTCGG 58.311 47.619 0.00 0.00 0.00 4.79
2838 6837 3.004210 ACATTGTGCATACTTTTGTCGCA 59.996 39.130 0.00 0.00 38.24 5.10
2975 6974 1.700186 GGAGGAACAAAGGGAGACAGT 59.300 52.381 0.00 0.00 0.00 3.55
3032 7031 0.548031 GGGATCATCAGCACTCCCAA 59.452 55.000 1.58 0.00 45.66 4.12
3042 7041 1.221840 CACTCCCAATGGGACTCCG 59.778 63.158 18.77 10.46 46.17 4.63
3252 7251 1.667212 ACACGTGGGTCGAAGTTTTTC 59.333 47.619 21.57 0.00 42.86 2.29
3261 7260 3.747010 GGTCGAAGTTTTTCCTCCTTCTC 59.253 47.826 0.00 0.00 33.94 2.87
3262 7261 3.747010 GTCGAAGTTTTTCCTCCTTCTCC 59.253 47.826 0.00 0.00 33.94 3.71
3309 7311 2.331451 GCACACTCGGTTGTTGCC 59.669 61.111 0.00 0.00 0.00 4.52
3327 7329 1.732917 CGCCAGCACCTTTCAACAA 59.267 52.632 0.00 0.00 0.00 2.83
3334 7336 0.738389 CACCTTTCAACAACGCACCT 59.262 50.000 0.00 0.00 0.00 4.00
3335 7337 1.021968 ACCTTTCAACAACGCACCTC 58.978 50.000 0.00 0.00 0.00 3.85
3336 7338 0.041312 CCTTTCAACAACGCACCTCG 60.041 55.000 0.00 0.00 45.38 4.63
3345 7347 2.202797 CGCACCTCGTCATCCTGG 60.203 66.667 0.00 0.00 0.00 4.45
3346 7348 2.982130 GCACCTCGTCATCCTGGT 59.018 61.111 0.00 0.00 0.00 4.00
3347 7349 1.153549 GCACCTCGTCATCCTGGTC 60.154 63.158 0.00 0.00 0.00 4.02
3351 7353 2.678580 TCGTCATCCTGGTCGCCA 60.679 61.111 0.00 0.00 0.00 5.69
3359 7361 1.228124 CCTGGTCGCCACCTTTGAA 60.228 57.895 1.09 0.00 44.17 2.69
3361 7363 0.535102 CTGGTCGCCACCTTTGAACT 60.535 55.000 1.09 0.00 44.17 3.01
3367 7369 1.971695 CCACCTTTGAACTCCGCCC 60.972 63.158 0.00 0.00 0.00 6.13
3384 7386 1.204704 GCCCCTTCTTTGTAATGGTGC 59.795 52.381 0.00 0.00 0.00 5.01
3450 7453 2.045340 GATGGGTGACAACGGGGG 60.045 66.667 0.00 0.00 0.00 5.40
3535 7538 2.357034 GGTCGCGTGGCTTCTTCA 60.357 61.111 5.77 0.00 0.00 3.02
3540 7543 2.334946 GCGTGGCTTCTTCATGGCA 61.335 57.895 0.00 0.00 36.39 4.92
3571 7574 1.901464 GGTGGACATGCGGTTGGTT 60.901 57.895 0.00 0.00 0.00 3.67
3572 7575 1.285641 GTGGACATGCGGTTGGTTG 59.714 57.895 0.00 0.00 0.00 3.77
3606 7609 1.705997 AAGGTTGAGGAAGGTGCGGT 61.706 55.000 0.00 0.00 0.00 5.68
3665 7676 2.654877 GGGTCGAAGGAGTGCGAA 59.345 61.111 0.00 0.00 38.36 4.70
3670 7681 1.006102 CGAAGGAGTGCGAAGTGGT 60.006 57.895 0.00 0.00 0.00 4.16
3671 7682 1.284982 CGAAGGAGTGCGAAGTGGTG 61.285 60.000 0.00 0.00 0.00 4.17
3672 7683 0.951040 GAAGGAGTGCGAAGTGGTGG 60.951 60.000 0.00 0.00 0.00 4.61
3673 7684 1.696097 AAGGAGTGCGAAGTGGTGGT 61.696 55.000 0.00 0.00 0.00 4.16
3675 7686 1.069090 GAGTGCGAAGTGGTGGTGA 59.931 57.895 0.00 0.00 0.00 4.02
3676 7687 0.531974 GAGTGCGAAGTGGTGGTGAA 60.532 55.000 0.00 0.00 0.00 3.18
3677 7688 0.532862 AGTGCGAAGTGGTGGTGAAG 60.533 55.000 0.00 0.00 0.00 3.02
3678 7689 1.227823 TGCGAAGTGGTGGTGAAGG 60.228 57.895 0.00 0.00 0.00 3.46
3679 7690 2.617274 GCGAAGTGGTGGTGAAGGC 61.617 63.158 0.00 0.00 0.00 4.35
3680 7691 1.966451 CGAAGTGGTGGTGAAGGCC 60.966 63.158 0.00 0.00 0.00 5.19
3681 7692 1.150536 GAAGTGGTGGTGAAGGCCA 59.849 57.895 5.01 0.00 35.93 5.36
3682 7693 0.467290 GAAGTGGTGGTGAAGGCCAA 60.467 55.000 5.01 0.00 40.68 4.52
3683 7694 0.032615 AAGTGGTGGTGAAGGCCAAA 60.033 50.000 5.01 0.00 40.68 3.28
3684 7695 0.188342 AGTGGTGGTGAAGGCCAAAT 59.812 50.000 5.01 0.00 40.68 2.32
3685 7696 0.603065 GTGGTGGTGAAGGCCAAATC 59.397 55.000 5.01 0.00 40.68 2.17
3686 7697 0.541764 TGGTGGTGAAGGCCAAATCC 60.542 55.000 5.01 2.48 40.68 3.01
3687 7698 1.595093 GGTGGTGAAGGCCAAATCCG 61.595 60.000 5.01 0.00 40.68 4.18
3688 7699 0.608035 GTGGTGAAGGCCAAATCCGA 60.608 55.000 5.01 0.00 40.68 4.55
3689 7700 0.608035 TGGTGAAGGCCAAATCCGAC 60.608 55.000 5.01 0.00 35.25 4.79
3690 7701 1.644786 GGTGAAGGCCAAATCCGACG 61.645 60.000 5.01 0.00 0.00 5.12
3691 7702 0.953960 GTGAAGGCCAAATCCGACGT 60.954 55.000 5.01 0.00 0.00 4.34
3692 7703 0.953471 TGAAGGCCAAATCCGACGTG 60.953 55.000 5.01 0.00 0.00 4.49
3693 7704 2.253414 GAAGGCCAAATCCGACGTGC 62.253 60.000 5.01 0.00 0.00 5.34
3694 7705 3.053291 GGCCAAATCCGACGTGCA 61.053 61.111 0.00 0.00 0.00 4.57
3717 7728 1.303236 CCGGGACAGTGCAATTGGA 60.303 57.895 7.72 0.23 0.00 3.53
3774 7785 3.414700 GGCGACTGTGCACGGAAG 61.415 66.667 31.98 23.22 36.28 3.46
3775 7786 2.355837 GCGACTGTGCACGGAAGA 60.356 61.111 31.98 2.76 34.15 2.87
3776 7787 2.375766 GCGACTGTGCACGGAAGAG 61.376 63.158 31.98 15.81 34.15 2.85
3784 7795 4.735132 CACGGAAGAGCGGGCGAA 62.735 66.667 0.00 0.00 0.00 4.70
3785 7796 4.436998 ACGGAAGAGCGGGCGAAG 62.437 66.667 0.00 0.00 0.00 3.79
3786 7797 4.436998 CGGAAGAGCGGGCGAAGT 62.437 66.667 0.00 0.00 0.00 3.01
3805 7816 2.218953 TCGAATGCGATTGGTAGGAC 57.781 50.000 0.00 0.00 42.51 3.85
3806 7817 1.478916 TCGAATGCGATTGGTAGGACA 59.521 47.619 0.00 0.00 42.51 4.02
3807 7818 1.593006 CGAATGCGATTGGTAGGACAC 59.407 52.381 0.00 0.00 40.82 3.67
3808 7819 1.593006 GAATGCGATTGGTAGGACACG 59.407 52.381 0.00 0.00 0.00 4.49
3809 7820 0.535335 ATGCGATTGGTAGGACACGT 59.465 50.000 0.00 0.00 0.00 4.49
3810 7821 0.108992 TGCGATTGGTAGGACACGTC 60.109 55.000 0.00 0.00 0.00 4.34
3819 7830 2.416260 GGACACGTCCTATCCGCC 59.584 66.667 9.04 0.00 46.16 6.13
3820 7831 2.420568 GGACACGTCCTATCCGCCA 61.421 63.158 9.04 0.00 46.16 5.69
3821 7832 1.514087 GACACGTCCTATCCGCCAA 59.486 57.895 0.00 0.00 0.00 4.52
3822 7833 0.527817 GACACGTCCTATCCGCCAAG 60.528 60.000 0.00 0.00 0.00 3.61
3823 7834 1.227263 CACGTCCTATCCGCCAAGG 60.227 63.158 0.00 0.00 42.97 3.61
3824 7835 2.421739 CGTCCTATCCGCCAAGGG 59.578 66.667 0.00 0.00 41.52 3.95
3825 7836 2.432300 CGTCCTATCCGCCAAGGGT 61.432 63.158 0.00 0.00 41.52 4.34
3826 7837 1.111116 CGTCCTATCCGCCAAGGGTA 61.111 60.000 0.00 0.00 41.52 3.69
3827 7838 0.391966 GTCCTATCCGCCAAGGGTAC 59.608 60.000 0.00 0.00 41.52 3.34
3828 7839 0.031917 TCCTATCCGCCAAGGGTACA 60.032 55.000 0.00 0.00 41.52 2.90
3829 7840 0.834612 CCTATCCGCCAAGGGTACAA 59.165 55.000 0.00 0.00 41.52 2.41
3832 7843 2.296073 ATCCGCCAAGGGTACAAAAA 57.704 45.000 0.00 0.00 41.52 1.94
3844 7855 2.034179 GGTACAAAAACAGTGTCAGCCC 59.966 50.000 0.00 0.00 0.00 5.19
3845 7856 2.143876 ACAAAAACAGTGTCAGCCCT 57.856 45.000 0.00 0.00 0.00 5.19
3846 7857 2.456577 ACAAAAACAGTGTCAGCCCTT 58.543 42.857 0.00 0.00 0.00 3.95
3847 7858 2.831526 ACAAAAACAGTGTCAGCCCTTT 59.168 40.909 0.00 0.00 0.00 3.11
3908 7919 3.623466 TTATATCACTCCCGGGGAAGA 57.377 47.619 23.50 17.72 0.00 2.87
3909 7920 2.723530 ATATCACTCCCGGGGAAGAT 57.276 50.000 25.38 25.38 33.27 2.40
3911 7922 1.596496 ATCACTCCCGGGGAAGATTT 58.404 50.000 23.50 1.59 0.00 2.17
3944 7955 5.512942 TTTGAGGATCTTGGTGTCCATTA 57.487 39.130 0.00 0.00 36.96 1.90
3945 7956 5.512942 TTGAGGATCTTGGTGTCCATTAA 57.487 39.130 0.00 0.00 36.96 1.40
4100 8113 4.021719 ACCTACGTAAAAGCTGTGCTCTTA 60.022 41.667 0.00 0.00 38.25 2.10
4146 8159 6.800892 GCTCTTTACGTAATATTCCTACTCCG 59.199 42.308 9.18 0.00 0.00 4.63
4169 8184 7.787904 TCCGTCCATATATATAAGGCCTAATGT 59.212 37.037 5.16 1.10 0.00 2.71
4179 8194 2.711542 AGGCCTAATGTGTTTTCCGAG 58.288 47.619 1.29 0.00 0.00 4.63
4184 8199 4.662145 CCTAATGTGTTTTCCGAGAATGC 58.338 43.478 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.366216 GTTACATCTTTGTGTGATACATGTCTA 57.634 33.333 0.00 0.00 39.48 2.59
57 59 5.967088 GATGTATCGGTATGCATCCTTAGT 58.033 41.667 0.19 0.00 44.80 2.24
64 66 5.893824 TCCTCTATGATGTATCGGTATGCAT 59.106 40.000 3.79 3.79 40.65 3.96
65 67 5.261216 TCCTCTATGATGTATCGGTATGCA 58.739 41.667 0.00 0.00 31.89 3.96
66 68 5.734786 GCTCCTCTATGATGTATCGGTATGC 60.735 48.000 0.00 0.00 0.00 3.14
67 69 5.358160 TGCTCCTCTATGATGTATCGGTATG 59.642 44.000 0.00 0.00 0.00 2.39
68 70 5.510430 TGCTCCTCTATGATGTATCGGTAT 58.490 41.667 0.00 0.00 0.00 2.73
69 71 4.918588 TGCTCCTCTATGATGTATCGGTA 58.081 43.478 0.00 0.00 0.00 4.02
70 72 3.767711 TGCTCCTCTATGATGTATCGGT 58.232 45.455 0.00 0.00 0.00 4.69
71 73 4.219507 AGTTGCTCCTCTATGATGTATCGG 59.780 45.833 0.00 0.00 0.00 4.18
72 74 5.384063 AGTTGCTCCTCTATGATGTATCG 57.616 43.478 0.00 0.00 0.00 2.92
73 75 6.991938 AGAAGTTGCTCCTCTATGATGTATC 58.008 40.000 0.00 0.00 0.00 2.24
74 76 6.992664 AGAAGTTGCTCCTCTATGATGTAT 57.007 37.500 0.00 0.00 0.00 2.29
75 77 6.798427 AAGAAGTTGCTCCTCTATGATGTA 57.202 37.500 0.00 0.00 0.00 2.29
76 78 5.690464 AAGAAGTTGCTCCTCTATGATGT 57.310 39.130 0.00 0.00 0.00 3.06
140 162 5.770162 GGCAATTGATTTACCTATAGCTGGT 59.230 40.000 10.34 0.00 41.28 4.00
144 166 6.039270 TGTGTGGCAATTGATTTACCTATAGC 59.961 38.462 10.34 0.00 0.00 2.97
167 189 9.918630 GTACGGGAAACTATTACATATATGTGT 57.081 33.333 25.48 16.80 41.89 3.72
233 258 4.317530 TGCTAGTTCCCTCTAAGACTGA 57.682 45.455 0.00 0.00 0.00 3.41
237 262 5.710646 AGATCATGCTAGTTCCCTCTAAGA 58.289 41.667 0.00 0.00 0.00 2.10
240 265 9.775539 ATTATAAGATCATGCTAGTTCCCTCTA 57.224 33.333 0.00 0.00 0.00 2.43
287 312 8.542926 AGCATATACTATGTGGATCAAGCAATA 58.457 33.333 0.00 0.00 0.00 1.90
344 4283 7.447374 TCATCTTTTGGTCAAACGAACATAT 57.553 32.000 6.70 0.00 33.30 1.78
352 4291 9.920826 GAAATTTCTTTCATCTTTTGGTCAAAC 57.079 29.630 11.05 0.00 40.45 2.93
364 4303 6.317857 CCTCAAGTCCGAAATTTCTTTCATC 58.682 40.000 15.92 1.68 40.72 2.92
393 4332 6.647481 TGCAAATAAATTCTGGATATGCATGC 59.353 34.615 11.82 11.82 36.46 4.06
430 4371 7.821846 TGTGTGTGCTGTAATCTGACAATAATA 59.178 33.333 0.00 0.00 0.00 0.98
434 4375 4.388485 TGTGTGTGCTGTAATCTGACAAT 58.612 39.130 0.00 0.00 0.00 2.71
482 4426 7.698130 CACATAAATCAAAACTACAAGCTAGGC 59.302 37.037 0.00 0.00 0.00 3.93
591 4535 6.376018 GCTTTCCCATGGTAGTATTGTACAAA 59.624 38.462 13.23 0.00 0.00 2.83
595 4539 5.702065 TGCTTTCCCATGGTAGTATTGTA 57.298 39.130 11.73 0.00 0.00 2.41
596 4540 4.584638 TGCTTTCCCATGGTAGTATTGT 57.415 40.909 11.73 0.00 0.00 2.71
597 4541 5.593909 TCAATGCTTTCCCATGGTAGTATTG 59.406 40.000 26.18 26.18 38.43 1.90
598 4542 5.765510 TCAATGCTTTCCCATGGTAGTATT 58.234 37.500 11.73 12.51 0.00 1.89
599 4543 5.387113 TCAATGCTTTCCCATGGTAGTAT 57.613 39.130 11.73 7.20 0.00 2.12
618 4562 3.775866 TGAAACGGAGGGGTACATATCAA 59.224 43.478 0.00 0.00 0.00 2.57
628 4572 2.676342 CGAGTAATTTGAAACGGAGGGG 59.324 50.000 0.00 0.00 0.00 4.79
629 4573 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
630 4574 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
631 4575 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
632 4576 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
633 4577 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
634 4578 3.120616 TCTGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
635 4579 4.640805 TCTGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
636 4580 5.660629 TTTCTGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.00 0.00 2.69
637 4581 5.390461 CCATTTCTGCGACGAGTAATTTGAA 60.390 40.000 0.00 0.00 0.00 2.69
638 4582 4.092821 CCATTTCTGCGACGAGTAATTTGA 59.907 41.667 0.00 0.00 0.00 2.69
639 4583 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
640 4584 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
641 4585 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
642 4586 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
643 4587 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
644 4588 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
645 4589 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
646 4590 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
647 4591 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
648 4592 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
649 4593 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
650 4594 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
651 4595 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
652 4596 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
679 4623 9.521841 CGTGGGTATGGATGTATCTAGATATAT 57.478 37.037 18.82 18.82 0.00 0.86
680 4624 8.720537 TCGTGGGTATGGATGTATCTAGATATA 58.279 37.037 15.43 13.22 0.00 0.86
681 4625 7.502895 GTCGTGGGTATGGATGTATCTAGATAT 59.497 40.741 15.43 1.62 0.00 1.63
682 4626 6.827251 GTCGTGGGTATGGATGTATCTAGATA 59.173 42.308 8.44 8.44 0.00 1.98
683 4627 5.652891 GTCGTGGGTATGGATGTATCTAGAT 59.347 44.000 10.73 10.73 0.00 1.98
684 4628 5.008331 GTCGTGGGTATGGATGTATCTAGA 58.992 45.833 0.00 0.00 0.00 2.43
685 4629 4.765339 TGTCGTGGGTATGGATGTATCTAG 59.235 45.833 0.00 0.00 0.00 2.43
686 4630 4.732065 TGTCGTGGGTATGGATGTATCTA 58.268 43.478 0.00 0.00 0.00 1.98
687 4631 3.572642 TGTCGTGGGTATGGATGTATCT 58.427 45.455 0.00 0.00 0.00 1.98
688 4632 4.202223 ACTTGTCGTGGGTATGGATGTATC 60.202 45.833 0.00 0.00 0.00 2.24
689 4633 3.709653 ACTTGTCGTGGGTATGGATGTAT 59.290 43.478 0.00 0.00 0.00 2.29
690 4634 3.101437 ACTTGTCGTGGGTATGGATGTA 58.899 45.455 0.00 0.00 0.00 2.29
691 4635 1.906574 ACTTGTCGTGGGTATGGATGT 59.093 47.619 0.00 0.00 0.00 3.06
692 4636 2.691409 ACTTGTCGTGGGTATGGATG 57.309 50.000 0.00 0.00 0.00 3.51
693 4637 5.365619 GAATTACTTGTCGTGGGTATGGAT 58.634 41.667 0.00 0.00 0.00 3.41
694 4638 4.678574 CGAATTACTTGTCGTGGGTATGGA 60.679 45.833 0.00 0.00 32.61 3.41
695 4639 3.554324 CGAATTACTTGTCGTGGGTATGG 59.446 47.826 0.00 0.00 32.61 2.74
696 4640 3.554324 CCGAATTACTTGTCGTGGGTATG 59.446 47.826 0.00 0.00 35.48 2.39
697 4641 3.448301 TCCGAATTACTTGTCGTGGGTAT 59.552 43.478 0.00 0.00 35.48 2.73
698 4642 2.824936 TCCGAATTACTTGTCGTGGGTA 59.175 45.455 0.00 0.00 35.48 3.69
699 4643 1.619827 TCCGAATTACTTGTCGTGGGT 59.380 47.619 0.00 0.00 35.48 4.51
700 4644 2.373540 TCCGAATTACTTGTCGTGGG 57.626 50.000 0.00 0.00 35.48 4.61
701 4645 2.091588 CGTTCCGAATTACTTGTCGTGG 59.908 50.000 0.00 0.00 35.48 4.94
702 4646 2.091588 CCGTTCCGAATTACTTGTCGTG 59.908 50.000 0.00 0.00 35.48 4.35
703 4647 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
704 4648 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
705 4649 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
706 4650 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
707 4651 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
708 4652 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
709 4653 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
710 4654 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
711 4655 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
712 4656 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
713 4657 1.400737 CTACTCCCTCCGTTCCGAAT 58.599 55.000 0.00 0.00 0.00 3.34
714 4658 1.318158 GCTACTCCCTCCGTTCCGAA 61.318 60.000 0.00 0.00 0.00 4.30
715 4659 1.751927 GCTACTCCCTCCGTTCCGA 60.752 63.158 0.00 0.00 0.00 4.55
716 4660 1.392710 ATGCTACTCCCTCCGTTCCG 61.393 60.000 0.00 0.00 0.00 4.30
717 4661 0.831307 AATGCTACTCCCTCCGTTCC 59.169 55.000 0.00 0.00 0.00 3.62
718 4662 2.280628 CAAATGCTACTCCCTCCGTTC 58.719 52.381 0.00 0.00 0.00 3.95
719 4663 1.065418 CCAAATGCTACTCCCTCCGTT 60.065 52.381 0.00 0.00 0.00 4.44
720 4664 0.541863 CCAAATGCTACTCCCTCCGT 59.458 55.000 0.00 0.00 0.00 4.69
721 4665 0.815615 GCCAAATGCTACTCCCTCCG 60.816 60.000 0.00 0.00 36.87 4.63
722 4666 3.102090 GCCAAATGCTACTCCCTCC 57.898 57.895 0.00 0.00 36.87 4.30
737 4681 3.003275 GTCATTTCGTTCAACAAGAGCCA 59.997 43.478 0.00 0.00 0.00 4.75
739 4683 4.474226 AGTCATTTCGTTCAACAAGAGC 57.526 40.909 0.00 0.00 0.00 4.09
745 4689 6.526566 ACAACTCTAGTCATTTCGTTCAAC 57.473 37.500 0.00 0.00 0.00 3.18
835 4796 8.557029 GGGTGTTACTTAATATTCAGTGCATAC 58.443 37.037 11.74 7.14 0.00 2.39
837 4798 6.260050 CGGGTGTTACTTAATATTCAGTGCAT 59.740 38.462 11.74 0.00 0.00 3.96
845 4806 6.044682 CGGAAGACGGGTGTTACTTAATATT 58.955 40.000 0.00 0.00 39.42 1.28
848 4809 3.853475 CGGAAGACGGGTGTTACTTAAT 58.147 45.455 0.00 0.00 39.42 1.40
850 4811 1.067635 GCGGAAGACGGGTGTTACTTA 60.068 52.381 0.00 0.00 44.51 2.24
876 4866 2.123033 GAGGGAGGAGAGAGGGGC 60.123 72.222 0.00 0.00 0.00 5.80
879 4869 0.689412 GGTTGGAGGGAGGAGAGAGG 60.689 65.000 0.00 0.00 0.00 3.69
880 4870 0.689412 GGGTTGGAGGGAGGAGAGAG 60.689 65.000 0.00 0.00 0.00 3.20
881 4871 1.392534 GGGTTGGAGGGAGGAGAGA 59.607 63.158 0.00 0.00 0.00 3.10
882 4872 2.060980 CGGGTTGGAGGGAGGAGAG 61.061 68.421 0.00 0.00 0.00 3.20
883 4873 2.038975 CGGGTTGGAGGGAGGAGA 59.961 66.667 0.00 0.00 0.00 3.71
884 4874 3.083997 CCGGGTTGGAGGGAGGAG 61.084 72.222 0.00 0.00 42.00 3.69
975 4965 1.815421 GATGGCCGCTGGTGTAGTG 60.815 63.158 0.00 0.00 36.65 2.74
1045 5035 4.816984 GGGAGGCGGGAGAGTCGA 62.817 72.222 0.00 0.00 0.00 4.20
1206 5205 0.392998 GTGCATCGTGGAAGTGGGAT 60.393 55.000 0.00 0.00 0.00 3.85
1241 5240 2.278013 CGCTCCTCGTAGGCGTTC 60.278 66.667 0.00 0.00 43.28 3.95
1380 5379 4.767255 CAGCACCTGAGGACGGCC 62.767 72.222 4.99 0.00 32.44 6.13
1418 5417 3.869272 GGATGCGCTTGCCTGACG 61.869 66.667 9.73 0.00 38.03 4.35
1422 5421 2.831742 CCATGGATGCGCTTGCCT 60.832 61.111 5.56 0.00 38.03 4.75
1485 5484 2.587956 GCGTACATATCGATAACGGCA 58.412 47.619 22.68 0.00 40.21 5.69
1492 5491 3.381045 CACACTTGGCGTACATATCGAT 58.619 45.455 2.16 2.16 0.00 3.59
1548 5547 4.814294 GCGTCGACCTCGGCCATT 62.814 66.667 10.58 0.00 41.58 3.16
1621 5620 0.448990 TCATCAAACAGCTGCATCGC 59.551 50.000 15.27 0.00 0.00 4.58
1624 5623 1.736126 CGAGTCATCAAACAGCTGCAT 59.264 47.619 15.27 0.00 0.00 3.96
1810 5809 3.790437 CTGCAGGCCGAGGTCCAT 61.790 66.667 5.57 0.00 0.00 3.41
1928 5927 4.084849 GCGACCATCTATCAAAGATCAACG 60.085 45.833 0.00 0.00 43.42 4.10
1962 5961 2.351641 GCTCCATGCAAATTTCACGTCA 60.352 45.455 0.00 0.00 42.31 4.35
2031 6030 0.721718 GCATCAACCGGAAGAACTCG 59.278 55.000 9.46 0.00 0.00 4.18
2148 6147 1.226717 CCCTAGCTTCTCGACGCAC 60.227 63.158 0.00 0.00 0.00 5.34
2195 6194 4.036380 ACTTAGCATACATGTCGACGATGA 59.964 41.667 24.96 14.16 0.00 2.92
2415 6414 1.081892 CTTCACTGACCAATCTGCCG 58.918 55.000 0.00 0.00 0.00 5.69
2481 6480 5.058149 TGCAATTGTAATGTTCGATGCTT 57.942 34.783 7.40 0.00 0.00 3.91
2487 6486 5.159925 TCAACCATGCAATTGTAATGTTCG 58.840 37.500 16.94 10.77 0.00 3.95
2616 6615 1.168714 GCTCCATGTCCTTGTGAACC 58.831 55.000 0.00 0.00 0.00 3.62
2739 6738 3.804325 TCAAACTTCTGAGCTTCGAAGTG 59.196 43.478 25.24 15.98 46.55 3.16
2850 6849 2.315925 TTTCAGATGATCTCGGGTGC 57.684 50.000 0.00 0.00 0.00 5.01
2975 6974 2.677914 TCTCACTGTGGAACCTCAGAA 58.322 47.619 23.70 13.14 39.18 3.02
3032 7031 0.105039 GATTCGAAGCGGAGTCCCAT 59.895 55.000 3.35 0.00 0.00 4.00
3042 7041 3.425492 GCAGGTTCTTGAAGATTCGAAGC 60.425 47.826 4.98 4.98 34.94 3.86
3252 7251 1.681486 GCGGGAAGAGGAGAAGGAGG 61.681 65.000 0.00 0.00 0.00 4.30
3291 7293 2.477176 GGCAACAACCGAGTGTGCA 61.477 57.895 0.00 0.00 31.36 4.57
3309 7311 0.594796 GTTGTTGAAAGGTGCTGGCG 60.595 55.000 0.00 0.00 0.00 5.69
3334 7336 2.678580 TGGCGACCAGGATGACGA 60.679 61.111 0.00 0.00 39.69 4.20
3335 7337 2.509336 GTGGCGACCAGGATGACG 60.509 66.667 0.00 0.00 39.69 4.35
3336 7338 2.125106 GGTGGCGACCAGGATGAC 60.125 66.667 13.75 0.00 42.59 3.06
3337 7339 1.488705 AAAGGTGGCGACCAGGATGA 61.489 55.000 20.91 0.00 45.98 2.92
3338 7340 1.002134 AAAGGTGGCGACCAGGATG 60.002 57.895 20.91 0.00 45.98 3.51
3339 7341 1.002134 CAAAGGTGGCGACCAGGAT 60.002 57.895 20.91 0.11 45.98 3.24
3340 7342 1.701031 TTCAAAGGTGGCGACCAGGA 61.701 55.000 20.91 10.99 45.98 3.86
3341 7343 1.228124 TTCAAAGGTGGCGACCAGG 60.228 57.895 20.91 8.76 45.98 4.45
3342 7344 0.535102 AGTTCAAAGGTGGCGACCAG 60.535 55.000 20.91 9.48 45.98 4.00
3343 7345 0.534203 GAGTTCAAAGGTGGCGACCA 60.534 55.000 20.91 0.00 45.98 4.02
3344 7346 1.235281 GGAGTTCAAAGGTGGCGACC 61.235 60.000 10.38 10.38 43.52 4.79
3345 7347 1.566018 CGGAGTTCAAAGGTGGCGAC 61.566 60.000 0.00 0.00 0.00 5.19
3346 7348 1.301401 CGGAGTTCAAAGGTGGCGA 60.301 57.895 0.00 0.00 0.00 5.54
3347 7349 2.966309 GCGGAGTTCAAAGGTGGCG 61.966 63.158 0.00 0.00 0.00 5.69
3351 7353 1.716028 AAGGGGCGGAGTTCAAAGGT 61.716 55.000 0.00 0.00 0.00 3.50
3359 7361 1.061546 TTACAAAGAAGGGGCGGAGT 58.938 50.000 0.00 0.00 0.00 3.85
3361 7363 1.340600 CCATTACAAAGAAGGGGCGGA 60.341 52.381 0.00 0.00 0.00 5.54
3471 7474 2.103538 GTGCCAATGCTGCCATCG 59.896 61.111 0.00 0.00 38.71 3.84
3535 7538 2.611800 TCCCACTGCTCCTGCCAT 60.612 61.111 0.00 0.00 38.71 4.40
3540 7543 2.608988 CCACCTCCCACTGCTCCT 60.609 66.667 0.00 0.00 0.00 3.69
3571 7574 1.272536 ACCTTCGCTCTCCTACCTTCA 60.273 52.381 0.00 0.00 0.00 3.02
3572 7575 1.476477 ACCTTCGCTCTCCTACCTTC 58.524 55.000 0.00 0.00 0.00 3.46
3606 7609 2.634453 TCTCTGGTTGACATGAAGCTCA 59.366 45.455 0.00 0.00 0.00 4.26
3665 7676 0.188342 ATTTGGCCTTCACCACCACT 59.812 50.000 3.32 0.00 40.19 4.00
3670 7681 0.608035 GTCGGATTTGGCCTTCACCA 60.608 55.000 3.32 0.00 38.16 4.17
3671 7682 1.644786 CGTCGGATTTGGCCTTCACC 61.645 60.000 3.32 1.69 0.00 4.02
3672 7683 0.953960 ACGTCGGATTTGGCCTTCAC 60.954 55.000 3.32 0.00 0.00 3.18
3673 7684 0.953471 CACGTCGGATTTGGCCTTCA 60.953 55.000 3.32 0.00 0.00 3.02
3675 7686 2.332654 GCACGTCGGATTTGGCCTT 61.333 57.895 3.32 0.00 0.00 4.35
3676 7687 2.746277 GCACGTCGGATTTGGCCT 60.746 61.111 3.32 0.00 0.00 5.19
3677 7688 3.039202 CTGCACGTCGGATTTGGCC 62.039 63.158 0.00 0.00 0.00 5.36
3678 7689 1.970917 CTCTGCACGTCGGATTTGGC 61.971 60.000 0.00 0.00 0.00 4.52
3679 7690 1.361668 CCTCTGCACGTCGGATTTGG 61.362 60.000 0.00 0.00 0.00 3.28
3680 7691 1.970917 GCCTCTGCACGTCGGATTTG 61.971 60.000 0.00 0.00 37.47 2.32
3681 7692 1.741770 GCCTCTGCACGTCGGATTT 60.742 57.895 0.00 0.00 37.47 2.17
3682 7693 2.125512 GCCTCTGCACGTCGGATT 60.126 61.111 0.00 0.00 37.47 3.01
3683 7694 4.148825 GGCCTCTGCACGTCGGAT 62.149 66.667 0.00 0.00 40.13 4.18
3690 7701 4.767255 CTGTCCCGGCCTCTGCAC 62.767 72.222 0.00 0.00 40.13 4.57
3692 7703 4.767255 CACTGTCCCGGCCTCTGC 62.767 72.222 0.00 0.00 0.00 4.26
3693 7704 4.767255 GCACTGTCCCGGCCTCTG 62.767 72.222 0.00 0.00 0.00 3.35
3717 7728 0.179073 CTTCTCCGATCGCCATGGTT 60.179 55.000 14.67 0.00 0.00 3.67
3770 7781 2.509561 GACTTCGCCCGCTCTTCC 60.510 66.667 0.00 0.00 0.00 3.46
3771 7782 2.814183 TTCGACTTCGCCCGCTCTTC 62.814 60.000 0.00 0.00 39.60 2.87
3772 7783 2.227089 ATTCGACTTCGCCCGCTCTT 62.227 55.000 0.00 0.00 39.60 2.85
3773 7784 2.711922 ATTCGACTTCGCCCGCTCT 61.712 57.895 0.00 0.00 39.60 4.09
3774 7785 2.202756 ATTCGACTTCGCCCGCTC 60.203 61.111 0.00 0.00 39.60 5.03
3775 7786 2.509336 CATTCGACTTCGCCCGCT 60.509 61.111 0.00 0.00 39.60 5.52
3776 7787 4.223964 GCATTCGACTTCGCCCGC 62.224 66.667 0.00 0.00 39.60 6.13
3777 7788 3.913573 CGCATTCGACTTCGCCCG 61.914 66.667 0.00 0.00 39.60 6.13
3778 7789 2.508439 TCGCATTCGACTTCGCCC 60.508 61.111 0.00 0.00 40.21 6.13
3805 7816 1.227263 CCTTGGCGGATAGGACGTG 60.227 63.158 0.00 0.00 33.13 4.49
3806 7817 2.432300 CCCTTGGCGGATAGGACGT 61.432 63.158 0.00 0.00 33.13 4.34
3807 7818 1.111116 TACCCTTGGCGGATAGGACG 61.111 60.000 0.00 0.00 33.13 4.79
3808 7819 0.391966 GTACCCTTGGCGGATAGGAC 59.608 60.000 0.00 0.00 33.13 3.85
3809 7820 0.031917 TGTACCCTTGGCGGATAGGA 60.032 55.000 0.00 0.00 33.13 2.94
3810 7821 0.834612 TTGTACCCTTGGCGGATAGG 59.165 55.000 0.00 0.00 33.16 2.57
3811 7822 2.702592 TTTGTACCCTTGGCGGATAG 57.297 50.000 0.00 0.00 33.16 2.08
3812 7823 3.083293 GTTTTTGTACCCTTGGCGGATA 58.917 45.455 0.00 0.00 33.16 2.59
3813 7824 1.890489 GTTTTTGTACCCTTGGCGGAT 59.110 47.619 0.00 0.00 33.16 4.18
3814 7825 1.320507 GTTTTTGTACCCTTGGCGGA 58.679 50.000 0.00 0.00 33.16 5.54
3815 7826 1.000717 CTGTTTTTGTACCCTTGGCGG 60.001 52.381 0.00 0.00 0.00 6.13
3816 7827 1.679153 ACTGTTTTTGTACCCTTGGCG 59.321 47.619 0.00 0.00 0.00 5.69
3817 7828 2.429250 ACACTGTTTTTGTACCCTTGGC 59.571 45.455 0.00 0.00 0.00 4.52
3818 7829 3.697045 TGACACTGTTTTTGTACCCTTGG 59.303 43.478 0.00 0.00 0.00 3.61
3819 7830 4.733523 GCTGACACTGTTTTTGTACCCTTG 60.734 45.833 0.00 0.00 0.00 3.61
3820 7831 3.380320 GCTGACACTGTTTTTGTACCCTT 59.620 43.478 0.00 0.00 0.00 3.95
3821 7832 2.949644 GCTGACACTGTTTTTGTACCCT 59.050 45.455 0.00 0.00 0.00 4.34
3822 7833 2.034179 GGCTGACACTGTTTTTGTACCC 59.966 50.000 0.00 0.00 0.00 3.69
3823 7834 2.034179 GGGCTGACACTGTTTTTGTACC 59.966 50.000 0.00 0.00 0.00 3.34
3824 7835 2.949644 AGGGCTGACACTGTTTTTGTAC 59.050 45.455 0.00 0.00 0.00 2.90
3825 7836 3.290948 AGGGCTGACACTGTTTTTGTA 57.709 42.857 0.00 0.00 0.00 2.41
3826 7837 2.143876 AGGGCTGACACTGTTTTTGT 57.856 45.000 0.00 0.00 0.00 2.83
3827 7838 3.131046 AGAAAGGGCTGACACTGTTTTTG 59.869 43.478 0.00 0.00 0.00 2.44
3828 7839 3.365472 AGAAAGGGCTGACACTGTTTTT 58.635 40.909 0.00 0.00 0.00 1.94
3829 7840 3.018423 AGAAAGGGCTGACACTGTTTT 57.982 42.857 0.00 0.00 0.00 2.43
3832 7843 1.212935 ACAAGAAAGGGCTGACACTGT 59.787 47.619 0.00 0.00 0.00 3.55
3920 7931 4.177537 TGGACACCAAGATCCTCAAAAA 57.822 40.909 0.00 0.00 35.86 1.94
3921 7932 3.874383 TGGACACCAAGATCCTCAAAA 57.126 42.857 0.00 0.00 35.86 2.44
3922 7933 4.387026 AATGGACACCAAGATCCTCAAA 57.613 40.909 0.00 0.00 36.95 2.69
3923 7934 5.250543 TCTTAATGGACACCAAGATCCTCAA 59.749 40.000 0.00 0.00 36.95 3.02
3924 7935 4.782691 TCTTAATGGACACCAAGATCCTCA 59.217 41.667 0.00 0.00 36.95 3.86
3925 7936 5.359194 TCTTAATGGACACCAAGATCCTC 57.641 43.478 0.00 0.00 36.95 3.71
3926 7937 5.688807 CATCTTAATGGACACCAAGATCCT 58.311 41.667 7.06 0.00 36.95 3.24
3944 7955 2.749621 GGTCGCTTCATTGTTCCATCTT 59.250 45.455 0.00 0.00 0.00 2.40
3945 7956 2.026822 AGGTCGCTTCATTGTTCCATCT 60.027 45.455 0.00 0.00 0.00 2.90
3954 7965 3.871594 CCGATCTTAAAGGTCGCTTCATT 59.128 43.478 0.00 0.00 34.25 2.57
3955 7966 3.132289 TCCGATCTTAAAGGTCGCTTCAT 59.868 43.478 0.00 0.00 34.25 2.57
3959 7970 2.376109 TCTCCGATCTTAAAGGTCGCT 58.624 47.619 0.00 0.00 34.25 4.93
4112 8125 8.500753 AATATTACGTAAAGAGCACATCCAAA 57.499 30.769 12.81 0.00 0.00 3.28
4113 8126 7.225931 GGAATATTACGTAAAGAGCACATCCAA 59.774 37.037 12.81 0.00 0.00 3.53
4114 8127 6.704493 GGAATATTACGTAAAGAGCACATCCA 59.296 38.462 12.81 0.00 0.00 3.41
4116 8129 7.948278 AGGAATATTACGTAAAGAGCACATC 57.052 36.000 12.81 3.02 0.00 3.06
4119 8132 7.594386 GGAGTAGGAATATTACGTAAAGAGCAC 59.406 40.741 12.81 5.15 0.00 4.40
4159 8172 2.304761 TCTCGGAAAACACATTAGGCCT 59.695 45.455 11.78 11.78 0.00 5.19
4169 8184 3.004315 GTCAAAGGCATTCTCGGAAAACA 59.996 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.