Multiple sequence alignment - TraesCS1D01G113400

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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 TraesCS1D01G113400 chr1D 100.000 5217 0 0 1 5217 109820076 109814860 0.000000e+00 9635.0
1 TraesCS1D01G113400 chr1D 85.156 512 66 5 9 519 196099462 196098960 2.790000e-142 516.0
2 TraesCS1D01G113400 chr1D 81.437 334 40 12 1491 1819 484188773 484189089 2.410000e-63 254.0
3 TraesCS1D01G113400 chr1D 97.368 38 1 0 4960 4997 109815022 109814985 1.210000e-06 65.8
4 TraesCS1D01G113400 chr1D 97.368 38 1 0 5055 5092 109815117 109815080 1.210000e-06 65.8
5 TraesCS1D01G113400 chr1A 91.173 2889 170 35 8 2859 113542503 113539663 0.000000e+00 3843.0
6 TraesCS1D01G113400 chr1A 93.306 1449 66 7 2859 4304 113539591 113538171 0.000000e+00 2109.0
7 TraesCS1D01G113400 chr1A 93.778 450 24 3 4385 4832 113537985 113537538 0.000000e+00 673.0
8 TraesCS1D01G113400 chr1B 93.883 1455 74 6 2859 4312 165817448 165816008 0.000000e+00 2180.0
9 TraesCS1D01G113400 chr1B 88.698 1398 97 38 791 2151 165819694 165818321 0.000000e+00 1650.0
10 TraesCS1D01G113400 chr1B 90.654 856 56 15 4367 5217 165816011 165815175 0.000000e+00 1116.0
11 TraesCS1D01G113400 chr1B 94.366 710 36 4 2151 2859 165818226 165817520 0.000000e+00 1086.0
12 TraesCS1D01G113400 chr1B 85.127 511 66 4 9 519 269204831 269205331 1.000000e-141 514.0
13 TraesCS1D01G113400 chr1B 92.664 259 16 3 4961 5217 165813036 165812779 2.290000e-98 370.0
14 TraesCS1D01G113400 chr1B 97.368 38 1 0 4960 4997 165812940 165812903 1.210000e-06 65.8
15 TraesCS1D01G113400 chr1B 97.368 38 1 0 4960 4997 165815336 165815299 1.210000e-06 65.8
16 TraesCS1D01G113400 chr1B 97.368 38 1 0 5055 5092 165815432 165815395 1.210000e-06 65.8
17 TraesCS1D01G113400 chr1B 83.333 72 7 1 522 593 269205377 269205443 1.570000e-05 62.1
18 TraesCS1D01G113400 chr2A 84.152 448 63 4 3 450 666839651 666840090 1.340000e-115 427.0
19 TraesCS1D01G113400 chr2A 97.561 41 0 1 4312 4352 142699875 142699914 9.370000e-08 69.4
20 TraesCS1D01G113400 chr2A 95.349 43 1 1 4308 4350 582637477 582637518 3.370000e-07 67.6
21 TraesCS1D01G113400 chr5A 81.712 514 84 6 7 519 301241561 301241057 2.250000e-113 420.0
22 TraesCS1D01G113400 chr5A 97.561 41 0 1 4312 4352 37144802 37144763 9.370000e-08 69.4
23 TraesCS1D01G113400 chr5A 97.561 41 0 1 4312 4352 640919887 640919926 9.370000e-08 69.4
24 TraesCS1D01G113400 chr6D 82.520 492 70 11 31 519 159381847 159381369 8.080000e-113 418.0
25 TraesCS1D01G113400 chr6D 87.838 74 8 1 529 602 447095366 447095438 9.310000e-13 86.1
26 TraesCS1D01G113400 chr2B 81.818 506 82 4 9 514 410998295 410997800 2.910000e-112 416.0
27 TraesCS1D01G113400 chr2B 81.818 506 77 8 2 507 773826110 773825620 1.350000e-110 411.0
28 TraesCS1D01G113400 chr5D 81.107 524 81 12 1 519 410370285 410370795 2.260000e-108 403.0
29 TraesCS1D01G113400 chr5D 97.561 41 0 1 4312 4352 148233695 148233656 9.370000e-08 69.4
30 TraesCS1D01G113400 chr7D 81.737 334 39 11 1491 1819 564891695 564891379 5.180000e-65 259.0
31 TraesCS1D01G113400 chr3D 81.437 334 40 10 1491 1819 33324471 33324787 2.410000e-63 254.0
32 TraesCS1D01G113400 chr3D 97.561 41 0 1 4312 4352 546706671 546706710 9.370000e-08 69.4
33 TraesCS1D01G113400 chr7A 76.923 208 24 12 415 601 661972118 661971914 4.300000e-16 97.1
34 TraesCS1D01G113400 chr7A 97.561 41 0 1 4312 4352 461930570 461930531 9.370000e-08 69.4
35 TraesCS1D01G113400 chr7A 97.561 41 0 1 4312 4352 461936127 461936088 9.370000e-08 69.4
36 TraesCS1D01G113400 chr6A 97.561 41 0 1 4312 4352 603075311 603075350 9.370000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G113400 chr1D 109814860 109820076 5216 True 9635.000000 9635 100.000000 1 5217 1 chr1D.!!$R1 5216
1 TraesCS1D01G113400 chr1D 196098960 196099462 502 True 516.000000 516 85.156000 9 519 1 chr1D.!!$R2 510
2 TraesCS1D01G113400 chr1A 113537538 113542503 4965 True 2208.333333 3843 92.752333 8 4832 3 chr1A.!!$R1 4824
3 TraesCS1D01G113400 chr1B 165812779 165819694 6915 True 824.925000 2180 94.046125 791 5217 8 chr1B.!!$R1 4426
4 TraesCS1D01G113400 chr1B 269204831 269205443 612 False 288.050000 514 84.230000 9 593 2 chr1B.!!$F1 584
5 TraesCS1D01G113400 chr5A 301241057 301241561 504 True 420.000000 420 81.712000 7 519 1 chr5A.!!$R2 512
6 TraesCS1D01G113400 chr5D 410370285 410370795 510 False 403.000000 403 81.107000 1 519 1 chr5D.!!$F1 518

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
69 70 0.322975 GGCTCATCGCATGGGTCTAT 59.677 55.0 9.86 0.0 41.67 1.98 F
674 722 0.597637 CCCATCACGGTCGTAGATGC 60.598 60.0 19.98 0.0 40.67 3.91 F
1482 1541 1.403814 CTCCGTCTCTGGATTAGCCA 58.596 55.0 0.00 0.0 46.96 4.75 F
2358 2556 2.795231 ACTGCAATGGCTAGTGACAT 57.205 45.0 0.20 0.0 45.42 3.06 F
3382 3657 0.764890 TGCCTTGTCAACTACAGGCT 59.235 50.0 12.60 0.0 45.31 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1657 0.340208 AGCCCAACTCTAGCCTACCT 59.660 55.000 0.0 0.0 0.00 3.08 R
2553 2754 1.621317 TGTCGGTCAATAGTGAGGCAA 59.379 47.619 0.0 0.0 33.27 4.52 R
2878 3152 0.449388 GAAGGCATTGGAGCGACAAG 59.551 55.000 0.0 0.0 33.23 3.16 R
3478 3753 0.510359 GTTCTGCACAGTTCAGCGAG 59.490 55.000 0.0 0.0 0.00 5.03 R
4362 4649 0.107410 TGGTGCAGGTATTAAGGCCG 60.107 55.000 0.0 0.0 0.00 6.13 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
55 56 2.755876 ATGAGGACGAGCGGCTCA 60.756 61.111 27.83 10.13 0.00 4.26
69 70 0.322975 GGCTCATCGCATGGGTCTAT 59.677 55.000 9.86 0.00 41.67 1.98
72 73 1.541588 CTCATCGCATGGGTCTATCGA 59.458 52.381 9.86 0.56 0.00 3.59
85 86 0.598562 CTATCGACGGTCCCTCATGG 59.401 60.000 1.91 0.00 0.00 3.66
212 213 1.896660 GGGTCGCCAAGTTGAAGCA 60.897 57.895 3.87 0.00 0.00 3.91
270 271 3.156293 CATCATCCTCTCTGACTCCGAT 58.844 50.000 0.00 0.00 0.00 4.18
462 468 6.525578 AGTGTAAGAACTTATCCGATGACA 57.474 37.500 0.00 0.00 0.00 3.58
482 488 7.639113 TGACAAACTAAGTTGATCTTTTGGT 57.361 32.000 0.00 0.00 37.56 3.67
494 500 5.108517 TGATCTTTTGGTTGTTGCAAAGTC 58.891 37.500 0.00 0.00 0.00 3.01
510 537 7.908827 TGCAAAGTCTGTTAATATCCGTTTA 57.091 32.000 0.00 0.00 0.00 2.01
520 547 6.018588 TGTTAATATCCGTTTACAGCCGATTG 60.019 38.462 0.00 0.00 0.00 2.67
536 584 2.784380 CGATTGCGTAGACTAGCTCAAC 59.216 50.000 0.00 0.00 0.00 3.18
549 597 5.775686 ACTAGCTCAACGTTACATGTGTAA 58.224 37.500 9.11 1.62 38.10 2.41
593 641 2.223665 TGAGATACGCAGATGCAGAGTG 60.224 50.000 5.55 0.00 42.21 3.51
604 652 7.657354 ACGCAGATGCAGAGTGATAAATATTAA 59.343 33.333 5.55 0.00 42.21 1.40
606 654 9.985318 GCAGATGCAGAGTGATAAATATTAATC 57.015 33.333 0.00 0.00 41.59 1.75
623 671 8.988064 ATATTAATCTTGTCTATTCGATGCGT 57.012 30.769 0.00 0.00 0.00 5.24
644 692 2.032634 GCATCCGCGTGTTTGAGGA 61.033 57.895 4.92 0.00 42.23 3.71
647 695 3.423154 CCGCGTGTTTGAGGAGCC 61.423 66.667 4.92 0.00 0.00 4.70
661 709 1.843851 AGGAGCCGAATTAACCCATCA 59.156 47.619 0.00 0.00 0.00 3.07
674 722 0.597637 CCCATCACGGTCGTAGATGC 60.598 60.000 19.98 0.00 40.67 3.91
684 732 3.550678 CGGTCGTAGATGCTCTTAAAACC 59.449 47.826 0.00 0.00 40.67 3.27
689 737 3.983044 AGATGCTCTTAAAACCGGACT 57.017 42.857 9.46 0.00 0.00 3.85
796 846 9.424319 TCTCTCAGTGTACATCAAAAGAATTAC 57.576 33.333 0.00 0.00 0.00 1.89
797 847 8.547967 TCTCAGTGTACATCAAAAGAATTACC 57.452 34.615 0.00 0.00 0.00 2.85
911 963 3.992427 GCTTTCCAGCCAGAAAAATCAAG 59.008 43.478 0.95 0.00 40.61 3.02
1142 1194 3.523087 TTCGCCGTAAGCAGTGCCA 62.523 57.895 12.58 0.00 44.04 4.92
1414 1468 4.456535 TGTTGATTTTCGAGAACCCTGAA 58.543 39.130 0.00 0.00 0.00 3.02
1432 1486 4.464008 CTGAATTCCCCTAGCTGCAAATA 58.536 43.478 1.02 0.00 0.00 1.40
1482 1541 1.403814 CTCCGTCTCTGGATTAGCCA 58.596 55.000 0.00 0.00 46.96 4.75
1495 1589 5.437060 TGGATTAGCCAATCAAGGACTTAC 58.563 41.667 7.19 0.00 45.87 2.34
1560 1657 4.634012 TTAGCTTCCTTGCCTTACTTGA 57.366 40.909 0.00 0.00 0.00 3.02
1640 1737 4.508124 GTGTGTTAGTCAAGTGAGGTTCAG 59.492 45.833 0.00 0.00 0.00 3.02
1710 1808 6.017852 GCCAGTGAATTATTTCTACCACTAGC 60.018 42.308 0.00 0.00 33.72 3.42
1733 1831 6.153680 AGCTACATTCTGTCCATATAGCCTAC 59.846 42.308 0.00 0.00 27.77 3.18
1790 1888 9.874205 TTCTTTGATTAATTGATGGTTTCATCC 57.126 29.630 4.22 0.00 46.92 3.51
1914 2017 8.611051 AGTTATACAACTGAACCCTTCTCTAT 57.389 34.615 0.00 0.00 43.50 1.98
1955 2058 4.695455 TCACTAAATACAGTTTCTGCAGGC 59.305 41.667 15.13 4.80 34.37 4.85
2210 2408 9.323985 CTTTCTTCTACCTTTCAGGATTATCTG 57.676 37.037 0.00 0.00 37.67 2.90
2314 2512 5.957842 TGGGACAATGTTATTGTGAGTTC 57.042 39.130 11.52 0.00 31.92 3.01
2347 2545 7.538303 TGTGTTAGTGTATCATACTGCAATG 57.462 36.000 0.00 0.00 0.00 2.82
2349 2547 5.527214 TGTTAGTGTATCATACTGCAATGGC 59.473 40.000 0.00 0.00 41.68 4.40
2358 2556 2.795231 ACTGCAATGGCTAGTGACAT 57.205 45.000 0.20 0.00 45.42 3.06
2373 2571 6.128661 GCTAGTGACATCGTGTGTTTGAAATA 60.129 38.462 0.00 0.00 42.36 1.40
2376 2574 4.754618 TGACATCGTGTGTTTGAAATAGCT 59.245 37.500 0.00 0.00 42.36 3.32
2383 2581 5.051106 CGTGTGTTTGAAATAGCTTTTTGGG 60.051 40.000 6.89 0.00 0.00 4.12
2477 2675 6.074648 ACATTTCCCTGGTTCAGTTGAATTA 58.925 36.000 0.00 0.00 36.33 1.40
2478 2676 6.015434 ACATTTCCCTGGTTCAGTTGAATTAC 60.015 38.462 0.00 0.00 36.33 1.89
2526 2727 4.054780 TGTAGGTGAATCCTCGTATTGC 57.945 45.455 0.00 0.00 44.42 3.56
2553 2754 3.492102 AGGTTGCCGCTATGTCATTAT 57.508 42.857 0.00 0.00 0.00 1.28
2576 2778 2.803492 GCCTCACTATTGACCGACATCC 60.803 54.545 0.00 0.00 0.00 3.51
2828 3030 2.940410 GGTATGTATGTGTTTCGGTGGG 59.060 50.000 0.00 0.00 0.00 4.61
2865 3139 5.993748 TTTTTATACCAAGCCTCCCTTTG 57.006 39.130 0.00 0.00 0.00 2.77
2878 3152 2.278330 CCTTTGAGCACCCCCTTGC 61.278 63.158 0.00 0.00 43.34 4.01
3229 3504 1.340889 TGCATGGTTGAAGCTTTGGAC 59.659 47.619 0.00 0.00 0.00 4.02
3236 3511 2.205022 TGAAGCTTTGGACAGGATGG 57.795 50.000 0.00 0.00 43.62 3.51
3267 3542 6.980397 AGCAAATACTTCAAGGTTTTTCTGTG 59.020 34.615 0.00 0.00 0.00 3.66
3268 3543 6.978080 GCAAATACTTCAAGGTTTTTCTGTGA 59.022 34.615 0.00 0.00 0.00 3.58
3269 3544 7.653311 GCAAATACTTCAAGGTTTTTCTGTGAT 59.347 33.333 0.00 0.00 0.00 3.06
3270 3545 9.533253 CAAATACTTCAAGGTTTTTCTGTGATT 57.467 29.630 0.00 0.00 0.00 2.57
3276 3551 5.420421 TCAAGGTTTTTCTGTGATTTCACCA 59.580 36.000 8.16 0.00 45.88 4.17
3283 3558 9.914923 GTTTTTCTGTGATTTCACCATTTTTAC 57.085 29.630 8.16 0.00 45.88 2.01
3303 3578 6.956102 TTACTTCCCCAAGGTTTACTGATA 57.044 37.500 0.00 0.00 33.37 2.15
3382 3657 0.764890 TGCCTTGTCAACTACAGGCT 59.235 50.000 12.60 0.00 45.31 4.58
3456 3731 2.991190 CTGCTGTTAAGGCATGCTTTTG 59.009 45.455 20.95 9.70 39.07 2.44
3478 3753 5.974108 TGCCCTACTAGTAGTTGATTGTTC 58.026 41.667 24.84 6.14 0.00 3.18
3480 3755 6.127423 TGCCCTACTAGTAGTTGATTGTTCTC 60.127 42.308 24.84 5.02 0.00 2.87
3494 3769 2.904664 TTCTCGCTGAACTGTGCAG 58.095 52.632 11.62 11.62 36.47 4.41
3496 3771 0.389025 TCTCGCTGAACTGTGCAGAA 59.611 50.000 20.05 5.62 35.39 3.02
3497 3772 0.510359 CTCGCTGAACTGTGCAGAAC 59.490 55.000 20.05 1.71 35.39 3.01
3498 3773 0.179086 TCGCTGAACTGTGCAGAACA 60.179 50.000 20.05 0.00 35.39 3.18
3499 3774 0.870393 CGCTGAACTGTGCAGAACAT 59.130 50.000 20.05 0.00 38.39 2.71
3500 3775 2.068519 CGCTGAACTGTGCAGAACATA 58.931 47.619 20.05 0.00 38.39 2.29
3501 3776 2.159787 CGCTGAACTGTGCAGAACATAC 60.160 50.000 20.05 0.00 38.39 2.39
3502 3777 2.160417 GCTGAACTGTGCAGAACATACC 59.840 50.000 20.05 0.00 38.39 2.73
3503 3778 2.412870 TGAACTGTGCAGAACATACCG 58.587 47.619 6.17 0.00 38.39 4.02
3504 3779 1.128692 GAACTGTGCAGAACATACCGC 59.871 52.381 6.17 0.00 38.39 5.68
3505 3780 0.321671 ACTGTGCAGAACATACCGCT 59.678 50.000 6.17 0.00 38.39 5.52
3506 3781 1.002366 CTGTGCAGAACATACCGCTC 58.998 55.000 0.00 0.00 38.39 5.03
3627 3913 2.025981 TGCACTATGATGGCAGTTTCCT 60.026 45.455 0.00 0.00 32.95 3.36
3644 3930 1.918262 TCCTTGATTGGTGCTCATCCT 59.082 47.619 0.00 0.00 0.00 3.24
3650 3936 0.391130 TTGGTGCTCATCCTGCGTAC 60.391 55.000 0.00 0.00 0.00 3.67
3658 3944 0.870307 CATCCTGCGTACGTAGCACC 60.870 60.000 25.61 4.64 40.01 5.01
3686 3972 3.318839 CCTTGGAGCAATCTTGTTGTTCA 59.681 43.478 6.89 0.00 32.32 3.18
3693 3980 4.883585 AGCAATCTTGTTGTTCAACTCAGA 59.116 37.500 15.18 15.18 32.18 3.27
3728 4015 7.039882 TCGGTTCAATAGGAAAGTCAATAGAC 58.960 38.462 0.00 0.00 45.31 2.59
3767 4054 5.248477 ACTGTTTCTGGTGACATACAGGTAT 59.752 40.000 0.00 0.00 43.10 2.73
3806 4093 0.526211 TTGCTGTCGCGAGATACAGT 59.474 50.000 21.99 0.00 44.03 3.55
4275 4562 3.244318 TGAGCTGCATTCTCTTGAGAACA 60.244 43.478 14.36 8.79 0.00 3.18
4280 4567 5.506982 GCTGCATTCTCTTGAGAACACTTTT 60.507 40.000 14.36 0.00 0.00 2.27
4306 4593 4.759693 TGATGGCACGTTCTTCTTTTACAT 59.240 37.500 0.00 0.00 0.00 2.29
4307 4594 5.935206 TGATGGCACGTTCTTCTTTTACATA 59.065 36.000 0.00 0.00 0.00 2.29
4308 4595 5.600908 TGGCACGTTCTTCTTTTACATAC 57.399 39.130 0.00 0.00 0.00 2.39
4309 4596 5.302360 TGGCACGTTCTTCTTTTACATACT 58.698 37.500 0.00 0.00 0.00 2.12
4310 4597 5.761234 TGGCACGTTCTTCTTTTACATACTT 59.239 36.000 0.00 0.00 0.00 2.24
4311 4598 6.930164 TGGCACGTTCTTCTTTTACATACTTA 59.070 34.615 0.00 0.00 0.00 2.24
4312 4599 7.117236 TGGCACGTTCTTCTTTTACATACTTAG 59.883 37.037 0.00 0.00 0.00 2.18
4313 4600 7.412672 GGCACGTTCTTCTTTTACATACTTAGG 60.413 40.741 0.00 0.00 0.00 2.69
4314 4601 7.453838 CACGTTCTTCTTTTACATACTTAGGC 58.546 38.462 0.00 0.00 0.00 3.93
4315 4602 6.592994 ACGTTCTTCTTTTACATACTTAGGCC 59.407 38.462 0.00 0.00 0.00 5.19
4316 4603 6.036844 CGTTCTTCTTTTACATACTTAGGCCC 59.963 42.308 0.00 0.00 0.00 5.80
4317 4604 5.997843 TCTTCTTTTACATACTTAGGCCCC 58.002 41.667 0.00 0.00 0.00 5.80
4318 4605 4.411256 TCTTTTACATACTTAGGCCCCG 57.589 45.455 0.00 0.00 0.00 5.73
4319 4606 3.776417 TCTTTTACATACTTAGGCCCCGT 59.224 43.478 0.00 0.00 0.00 5.28
4320 4607 4.225717 TCTTTTACATACTTAGGCCCCGTT 59.774 41.667 0.00 0.00 0.00 4.44
4321 4608 3.825143 TTACATACTTAGGCCCCGTTC 57.175 47.619 0.00 0.00 0.00 3.95
4322 4609 0.462789 ACATACTTAGGCCCCGTTCG 59.537 55.000 0.00 0.00 0.00 3.95
4323 4610 0.249741 CATACTTAGGCCCCGTTCGG 60.250 60.000 0.00 4.08 0.00 4.30
4324 4611 0.688749 ATACTTAGGCCCCGTTCGGT 60.689 55.000 0.00 0.00 0.00 4.69
4325 4612 1.606885 TACTTAGGCCCCGTTCGGTG 61.607 60.000 0.00 0.00 0.00 4.94
4326 4613 2.924101 TTAGGCCCCGTTCGGTGT 60.924 61.111 0.00 0.00 0.00 4.16
4327 4614 2.847435 CTTAGGCCCCGTTCGGTGTC 62.847 65.000 0.00 0.00 0.00 3.67
4330 4617 4.404098 GCCCCGTTCGGTGTCCAT 62.404 66.667 10.36 0.00 0.00 3.41
4331 4618 2.125269 CCCCGTTCGGTGTCCATC 60.125 66.667 10.36 0.00 0.00 3.51
4332 4619 2.125269 CCCGTTCGGTGTCCATCC 60.125 66.667 10.36 0.00 0.00 3.51
4334 4621 3.186047 CGTTCGGTGTCCATCCGC 61.186 66.667 0.00 0.00 46.49 5.54
4335 4622 2.264794 GTTCGGTGTCCATCCGCT 59.735 61.111 0.00 0.00 46.49 5.52
4336 4623 1.810030 GTTCGGTGTCCATCCGCTC 60.810 63.158 0.00 0.00 46.49 5.03
4337 4624 3.014085 TTCGGTGTCCATCCGCTCC 62.014 63.158 0.00 0.00 46.49 4.70
4338 4625 3.770040 CGGTGTCCATCCGCTCCA 61.770 66.667 0.00 0.00 41.48 3.86
4339 4626 2.125106 GGTGTCCATCCGCTCCAC 60.125 66.667 0.00 0.00 0.00 4.02
4340 4627 2.660064 GGTGTCCATCCGCTCCACT 61.660 63.158 0.00 0.00 0.00 4.00
4341 4628 1.448540 GTGTCCATCCGCTCCACTG 60.449 63.158 0.00 0.00 0.00 3.66
4342 4629 2.512515 GTCCATCCGCTCCACTGC 60.513 66.667 0.00 0.00 0.00 4.40
4343 4630 2.685017 TCCATCCGCTCCACTGCT 60.685 61.111 0.00 0.00 0.00 4.24
4344 4631 2.202987 CCATCCGCTCCACTGCTC 60.203 66.667 0.00 0.00 0.00 4.26
4345 4632 2.202987 CATCCGCTCCACTGCTCC 60.203 66.667 0.00 0.00 0.00 4.70
4346 4633 2.364842 ATCCGCTCCACTGCTCCT 60.365 61.111 0.00 0.00 0.00 3.69
4347 4634 2.729479 ATCCGCTCCACTGCTCCTG 61.729 63.158 0.00 0.00 0.00 3.86
4349 4636 4.079850 CGCTCCACTGCTCCTGCT 62.080 66.667 0.00 0.00 40.48 4.24
4350 4637 2.125188 GCTCCACTGCTCCTGCTC 60.125 66.667 0.00 0.00 40.48 4.26
4351 4638 2.583520 CTCCACTGCTCCTGCTCC 59.416 66.667 0.00 0.00 40.48 4.70
4352 4639 1.988956 CTCCACTGCTCCTGCTCCT 60.989 63.158 0.00 0.00 40.48 3.69
4353 4640 2.241479 CTCCACTGCTCCTGCTCCTG 62.241 65.000 0.00 0.00 40.48 3.86
4354 4641 2.436292 CACTGCTCCTGCTCCTGC 60.436 66.667 0.00 0.00 40.48 4.85
4355 4642 2.607134 ACTGCTCCTGCTCCTGCT 60.607 61.111 0.00 0.00 40.48 4.24
4356 4643 2.187424 CTGCTCCTGCTCCTGCTC 59.813 66.667 0.00 0.00 40.48 4.26
4357 4644 3.388703 CTGCTCCTGCTCCTGCTCC 62.389 68.421 0.00 0.00 40.48 4.70
4358 4645 4.527583 GCTCCTGCTCCTGCTCCG 62.528 72.222 0.00 0.00 40.48 4.63
4359 4646 4.527583 CTCCTGCTCCTGCTCCGC 62.528 72.222 0.00 0.00 40.48 5.54
4361 4648 4.527583 CCTGCTCCTGCTCCGCTC 62.528 72.222 0.00 0.00 40.48 5.03
4362 4649 4.527583 CTGCTCCTGCTCCGCTCC 62.528 72.222 0.00 0.00 40.48 4.70
4393 4846 0.729116 CTGCACCAGCGTATTTCCTG 59.271 55.000 0.00 0.00 46.23 3.86
4446 4899 9.959749 ACGTACAGAAAATGTGAAAATAATGTT 57.040 25.926 0.00 0.00 43.80 2.71
4566 5020 1.239347 GGCTTGGACACCTGAACTTC 58.761 55.000 0.00 0.00 0.00 3.01
4585 5039 1.298157 CGACTCTGCATGCGGGAAAA 61.298 55.000 25.97 6.06 0.00 2.29
4760 5214 7.377131 GGACGAATAAATGCAAAATCTTAGCTC 59.623 37.037 0.00 0.00 0.00 4.09
4761 5215 7.761409 ACGAATAAATGCAAAATCTTAGCTCA 58.239 30.769 0.00 0.00 0.00 4.26
4774 5228 3.813166 TCTTAGCTCACTTGTTTTTCCCG 59.187 43.478 0.00 0.00 0.00 5.14
4807 5262 4.290155 CAACAGTTTGTGCCATGTACTTC 58.710 43.478 0.00 0.00 0.00 3.01
4808 5263 3.820557 ACAGTTTGTGCCATGTACTTCT 58.179 40.909 0.00 0.00 0.00 2.85
4809 5264 4.207165 ACAGTTTGTGCCATGTACTTCTT 58.793 39.130 0.00 0.00 0.00 2.52
4846 5303 2.042464 AGGAGCTCTGCCGATTTCATA 58.958 47.619 14.64 0.00 0.00 2.15
4847 5304 2.435805 AGGAGCTCTGCCGATTTCATAA 59.564 45.455 14.64 0.00 0.00 1.90
4876 5333 7.977853 AGATATGAAAAAGCAAGCAAATACAGG 59.022 33.333 0.00 0.00 0.00 4.00
4883 5340 3.009033 AGCAAGCAAATACAGGTGACCTA 59.991 43.478 2.59 0.00 29.64 3.08
4888 5345 6.368779 AGCAAATACAGGTGACCTAGTTTA 57.631 37.500 2.59 0.00 29.64 2.01
4897 5354 6.771267 ACAGGTGACCTAGTTTAAAAGGAAAG 59.229 38.462 2.59 0.00 36.66 2.62
4900 5357 6.938596 GGTGACCTAGTTTAAAAGGAAAGCTA 59.061 38.462 12.06 0.00 36.66 3.32
4914 5371 3.444034 GGAAAGCTATCCTGAAAACCACC 59.556 47.826 0.00 0.00 36.50 4.61
4916 5373 1.992557 AGCTATCCTGAAAACCACCCA 59.007 47.619 0.00 0.00 0.00 4.51
4929 5386 6.205658 TGAAAACCACCCAAAACAAGAAAAAG 59.794 34.615 0.00 0.00 0.00 2.27
4931 5388 3.841255 ACCACCCAAAACAAGAAAAAGGA 59.159 39.130 0.00 0.00 0.00 3.36
4933 5390 5.045213 ACCACCCAAAACAAGAAAAAGGAAT 60.045 36.000 0.00 0.00 0.00 3.01
4934 5391 5.885352 CCACCCAAAACAAGAAAAAGGAATT 59.115 36.000 0.00 0.00 0.00 2.17
4956 5416 3.771577 AAAAACAACACAACCCCAACA 57.228 38.095 0.00 0.00 0.00 3.33
4963 5423 0.247185 CACAACCCCAACATGGATGC 59.753 55.000 0.00 0.00 40.96 3.91
4966 5426 1.066716 CAACCCCAACATGGATGCAAG 60.067 52.381 0.00 0.00 40.96 4.01
5008 5468 7.980662 TCAAATCATGAAAAACAGACACACATT 59.019 29.630 0.00 0.00 34.30 2.71
5015 5476 7.766283 TGAAAAACAGACACACATTTGACATA 58.234 30.769 0.00 0.00 0.00 2.29
5045 5506 9.696572 ATGAAATCTACACCTACTTCAGTAGTA 57.303 33.333 12.11 0.32 44.88 1.82
5131 5592 8.009622 TCTTAATTTATCATTGGAATGCAGCA 57.990 30.769 0.00 0.00 36.36 4.41
5174 5635 5.578157 AAGTAGCTTTCCTACCTTCCAAA 57.422 39.130 0.00 0.00 46.21 3.28
5180 5641 4.082190 GCTTTCCTACCTTCCAAAACCATC 60.082 45.833 0.00 0.00 0.00 3.51
5201 8058 6.017605 CCATCTGATAGAAACTCAAAATCCCG 60.018 42.308 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 3.458163 GCCATGAGGGACCGTCGA 61.458 66.667 9.55 0.00 40.01 4.20
212 213 0.399233 GACCACCCTATCCTGCTCCT 60.399 60.000 0.00 0.00 0.00 3.69
270 271 4.509883 CGATCGCCGTCGTCGTCA 62.510 66.667 0.26 0.00 36.88 4.35
285 289 2.738521 GAGGTGCAGCTTTCGCGA 60.739 61.111 21.18 3.71 42.32 5.87
367 371 1.002544 CTTCCTTCTCGGGTCTTTGCT 59.997 52.381 0.00 0.00 0.00 3.91
442 448 7.829378 AGTTTGTCATCGGATAAGTTCTTAC 57.171 36.000 0.00 0.00 0.00 2.34
462 468 7.277760 GCAACAACCAAAAGATCAACTTAGTTT 59.722 33.333 0.00 0.00 37.93 2.66
482 488 6.205853 ACGGATATTAACAGACTTTGCAACAA 59.794 34.615 0.00 0.00 0.00 2.83
494 500 5.045215 TCGGCTGTAAACGGATATTAACAG 58.955 41.667 0.00 0.00 0.00 3.16
510 537 1.065701 CTAGTCTACGCAATCGGCTGT 59.934 52.381 0.00 0.00 41.67 4.40
527 575 6.887376 ATTACACATGTAACGTTGAGCTAG 57.113 37.500 11.99 0.00 42.55 3.42
549 597 9.730705 CTCATATCCGGCATTTTATATCCATAT 57.269 33.333 0.00 0.00 0.00 1.78
604 652 4.219802 CGTACGCATCGAATAGACAAGAT 58.780 43.478 0.52 0.00 0.00 2.40
606 654 2.151360 GCGTACGCATCGAATAGACAAG 59.849 50.000 33.90 0.00 41.49 3.16
607 655 2.114056 GCGTACGCATCGAATAGACAA 58.886 47.619 33.90 0.00 41.49 3.18
640 688 2.158813 TGATGGGTTAATTCGGCTCCTC 60.159 50.000 0.00 0.00 0.00 3.71
644 692 1.663695 CGTGATGGGTTAATTCGGCT 58.336 50.000 0.00 0.00 0.00 5.52
647 695 1.591158 CGACCGTGATGGGTTAATTCG 59.409 52.381 0.00 0.00 44.64 3.34
698 746 3.627395 ATAGTTGAGAATTCGGGTGCA 57.373 42.857 0.00 0.00 0.00 4.57
704 754 8.717821 TGTAGGTGAAAAATAGTTGAGAATTCG 58.282 33.333 0.00 0.00 0.00 3.34
796 846 6.851222 AGAATTGTCTGCGTAATTATCTGG 57.149 37.500 0.00 0.00 30.83 3.86
849 900 9.730420 CTTCGATATTTAACAAGTTATTTGGGG 57.270 33.333 0.00 0.00 41.25 4.96
883 935 2.363306 TCTGGCTGGAAAGCAGAAAA 57.637 45.000 0.00 0.00 36.33 2.29
958 1010 3.646162 GTGGAAGGGTTTTCTTTTGGGAT 59.354 43.478 0.00 0.00 0.00 3.85
1142 1194 7.511959 AAAAGAAAAGAAAATAGGAGACGCT 57.488 32.000 0.00 0.00 0.00 5.07
1179 1233 1.281867 AGAAATCAGGGAACGGATGCA 59.718 47.619 0.00 0.00 44.88 3.96
1385 1439 9.408648 AGGGTTCTCGAAAATCAACAAATATAT 57.591 29.630 0.00 0.00 0.00 0.86
1432 1486 6.375174 TCAACACTAACAGCATCTAATTGCAT 59.625 34.615 0.00 0.00 45.23 3.96
1452 1506 3.368427 CCAGAGACGGAGCTAATTCAACA 60.368 47.826 0.00 0.00 0.00 3.33
1495 1589 6.180472 ACATGGTACTATTTGTCCAAGGAAG 58.820 40.000 0.00 0.00 32.51 3.46
1533 1630 6.722328 AGTAAGGCAAGGAAGCTAAAGTAAT 58.278 36.000 0.00 0.00 34.17 1.89
1560 1657 0.340208 AGCCCAACTCTAGCCTACCT 59.660 55.000 0.00 0.00 0.00 3.08
1640 1737 8.265764 AGATCCACTTTACTTGACCTAATTACC 58.734 37.037 0.00 0.00 0.00 2.85
1733 1831 2.286872 GACTGATCCAGCATCAACCTG 58.713 52.381 0.00 0.00 41.25 4.00
1790 1888 3.041874 CTCCACTGAGCAGCTAACG 57.958 57.895 0.00 0.00 0.00 3.18
2347 2545 2.080286 AACACACGATGTCACTAGCC 57.920 50.000 0.00 0.00 42.31 3.93
2349 2547 5.651172 TTTCAAACACACGATGTCACTAG 57.349 39.130 0.00 0.00 42.31 2.57
2358 2556 5.746245 CCAAAAAGCTATTTCAAACACACGA 59.254 36.000 0.00 0.00 0.00 4.35
2373 2571 4.321230 CGAGCAAGTATTTCCCAAAAAGCT 60.321 41.667 0.00 0.00 0.00 3.74
2376 2574 4.825085 AGACGAGCAAGTATTTCCCAAAAA 59.175 37.500 0.00 0.00 0.00 1.94
2383 2581 7.988904 ATAACTGTAGACGAGCAAGTATTTC 57.011 36.000 0.00 0.00 0.00 2.17
2526 2727 2.058798 CATAGCGGCAACCTATACACG 58.941 52.381 1.45 0.00 31.44 4.49
2553 2754 1.621317 TGTCGGTCAATAGTGAGGCAA 59.379 47.619 0.00 0.00 33.27 4.52
2576 2778 4.820284 AAGAGAAAAGAAAAGAGCACCG 57.180 40.909 0.00 0.00 0.00 4.94
2578 2780 6.016693 AGCCTTAAGAGAAAAGAAAAGAGCAC 60.017 38.462 3.36 0.00 0.00 4.40
2615 2817 3.127721 GTCTCCAAGCATCCAACTTTAGC 59.872 47.826 0.00 0.00 0.00 3.09
2814 3016 2.304761 AGATACACCCACCGAAACACAT 59.695 45.455 0.00 0.00 0.00 3.21
2878 3152 0.449388 GAAGGCATTGGAGCGACAAG 59.551 55.000 0.00 0.00 33.23 3.16
3181 3456 2.184830 CAGGGATGATGCCACTGCG 61.185 63.158 5.58 0.00 41.78 5.18
3184 3459 1.983691 CTATCCAGGGATGATGCCACT 59.016 52.381 11.08 0.00 36.17 4.00
3193 3468 2.729383 TGCATCTCCTATCCAGGGAT 57.271 50.000 6.04 6.04 42.87 3.85
3229 3504 4.210331 AGTATTTGCTTAAGGCCATCCTG 58.790 43.478 5.01 0.00 43.40 3.86
3236 3511 5.644977 ACCTTGAAGTATTTGCTTAAGGC 57.355 39.130 4.29 0.00 35.31 4.35
3238 3513 9.750125 AGAAAAACCTTGAAGTATTTGCTTAAG 57.250 29.630 0.00 0.00 0.00 1.85
3267 3542 6.353404 TGGGGAAGTAAAAATGGTGAAATC 57.647 37.500 0.00 0.00 0.00 2.17
3268 3543 6.239858 CCTTGGGGAAGTAAAAATGGTGAAAT 60.240 38.462 0.00 0.00 33.58 2.17
3269 3544 5.071115 CCTTGGGGAAGTAAAAATGGTGAAA 59.929 40.000 0.00 0.00 33.58 2.69
3270 3545 4.591072 CCTTGGGGAAGTAAAAATGGTGAA 59.409 41.667 0.00 0.00 33.58 3.18
3271 3546 4.156477 CCTTGGGGAAGTAAAAATGGTGA 58.844 43.478 0.00 0.00 33.58 4.02
3276 3551 7.070629 TCAGTAAACCTTGGGGAAGTAAAAAT 58.929 34.615 0.00 0.00 36.25 1.82
3283 3558 6.001449 TCATATCAGTAAACCTTGGGGAAG 57.999 41.667 0.00 0.00 36.25 3.46
3303 3578 8.678199 GCCTAAGCTAAGAAGTATGTTTTTCAT 58.322 33.333 0.00 0.00 36.97 2.57
3317 3592 6.439636 AATCACCATATGCCTAAGCTAAGA 57.560 37.500 0.00 0.00 40.80 2.10
3319 3594 9.667107 GTAATAATCACCATATGCCTAAGCTAA 57.333 33.333 0.00 0.00 40.80 3.09
3382 3657 6.351286 CCATATCATCCTCATCGGTCACAATA 60.351 42.308 0.00 0.00 0.00 1.90
3456 3731 6.223351 AGAACAATCAACTACTAGTAGGGC 57.777 41.667 29.05 10.41 37.49 5.19
3460 3735 6.373495 TCAGCGAGAACAATCAACTACTAGTA 59.627 38.462 1.89 1.89 0.00 1.82
3478 3753 0.510359 GTTCTGCACAGTTCAGCGAG 59.490 55.000 0.00 0.00 0.00 5.03
3480 3755 0.870393 ATGTTCTGCACAGTTCAGCG 59.130 50.000 0.00 0.00 39.40 5.18
3494 3769 3.747193 CAAACATGTGAGCGGTATGTTC 58.253 45.455 13.05 0.00 42.40 3.18
3496 3771 1.468520 GCAAACATGTGAGCGGTATGT 59.531 47.619 0.00 0.00 36.66 2.29
3497 3772 1.739466 AGCAAACATGTGAGCGGTATG 59.261 47.619 14.77 0.00 0.00 2.39
3498 3773 1.739466 CAGCAAACATGTGAGCGGTAT 59.261 47.619 14.77 0.00 0.00 2.73
3499 3774 1.155889 CAGCAAACATGTGAGCGGTA 58.844 50.000 14.77 0.00 0.00 4.02
3500 3775 0.534877 TCAGCAAACATGTGAGCGGT 60.535 50.000 17.73 0.00 0.00 5.68
3501 3776 0.806868 ATCAGCAAACATGTGAGCGG 59.193 50.000 14.77 14.38 0.00 5.52
3502 3777 1.736126 AGATCAGCAAACATGTGAGCG 59.264 47.619 14.77 10.90 31.84 5.03
3503 3778 3.439476 AGAAGATCAGCAAACATGTGAGC 59.561 43.478 13.32 13.32 0.00 4.26
3504 3779 4.936411 AGAGAAGATCAGCAAACATGTGAG 59.064 41.667 0.00 0.00 0.00 3.51
3505 3780 4.903054 AGAGAAGATCAGCAAACATGTGA 58.097 39.130 0.00 0.00 0.00 3.58
3506 3781 5.411977 AGAAGAGAAGATCAGCAAACATGTG 59.588 40.000 0.00 0.00 0.00 3.21
3627 3913 1.466856 GCAGGATGAGCACCAATCAA 58.533 50.000 0.00 0.00 39.69 2.57
3650 3936 0.515564 CCAAGGAAAACGGTGCTACG 59.484 55.000 0.00 0.00 40.31 3.51
3658 3944 3.004734 ACAAGATTGCTCCAAGGAAAACG 59.995 43.478 0.00 0.00 0.00 3.60
3686 3972 4.537135 ACCGAACATATGTGTCTGAGTT 57.463 40.909 9.63 0.00 37.67 3.01
3693 3980 5.984725 TCCTATTGAACCGAACATATGTGT 58.015 37.500 9.63 0.00 41.28 3.72
3728 4015 3.944422 AACAGTTACACACAAGAAGCG 57.056 42.857 0.00 0.00 0.00 4.68
3767 4054 1.301716 GTCCGCTTGTTCCAGCTCA 60.302 57.895 0.00 0.00 37.68 4.26
3806 4093 0.532573 GGTTGATCACCGAGAGCTCA 59.467 55.000 17.77 0.00 35.12 4.26
3888 4175 1.764571 TTCCTCTTGGGTGGTGACCG 61.765 60.000 0.00 0.00 44.23 4.79
4306 4593 1.305213 ACCGAACGGGGCCTAAGTA 60.305 57.895 17.44 0.00 41.60 2.24
4307 4594 2.605601 ACCGAACGGGGCCTAAGT 60.606 61.111 17.44 0.00 41.60 2.24
4308 4595 2.125269 CACCGAACGGGGCCTAAG 60.125 66.667 17.44 0.00 41.60 2.18
4309 4596 2.924101 ACACCGAACGGGGCCTAA 60.924 61.111 15.64 0.00 44.03 2.69
4310 4597 3.384532 GACACCGAACGGGGCCTA 61.385 66.667 15.64 0.00 44.03 3.93
4313 4600 4.404098 ATGGACACCGAACGGGGC 62.404 66.667 15.64 8.22 44.03 5.80
4314 4601 2.125269 GATGGACACCGAACGGGG 60.125 66.667 14.15 14.15 46.10 5.73
4315 4602 2.125269 GGATGGACACCGAACGGG 60.125 66.667 17.44 8.83 43.62 5.28
4322 4609 2.125106 GTGGAGCGGATGGACACC 60.125 66.667 0.00 0.00 0.00 4.16
4323 4610 1.448540 CAGTGGAGCGGATGGACAC 60.449 63.158 0.00 0.00 0.00 3.67
4324 4611 2.981302 CAGTGGAGCGGATGGACA 59.019 61.111 0.00 0.00 0.00 4.02
4325 4612 2.512515 GCAGTGGAGCGGATGGAC 60.513 66.667 0.00 0.00 0.00 4.02
4326 4613 2.685017 AGCAGTGGAGCGGATGGA 60.685 61.111 0.00 0.00 40.15 3.41
4327 4614 2.202987 GAGCAGTGGAGCGGATGG 60.203 66.667 0.00 0.00 40.15 3.51
4328 4615 2.202987 GGAGCAGTGGAGCGGATG 60.203 66.667 0.00 0.00 40.15 3.51
4329 4616 2.364842 AGGAGCAGTGGAGCGGAT 60.365 61.111 0.00 0.00 40.15 4.18
4330 4617 3.385384 CAGGAGCAGTGGAGCGGA 61.385 66.667 0.00 0.00 40.15 5.54
4332 4619 4.079850 AGCAGGAGCAGTGGAGCG 62.080 66.667 0.00 0.00 45.49 5.03
4333 4620 2.125188 GAGCAGGAGCAGTGGAGC 60.125 66.667 0.00 0.00 45.49 4.70
4334 4621 1.988956 AGGAGCAGGAGCAGTGGAG 60.989 63.158 0.00 0.00 45.49 3.86
4335 4622 2.121385 AGGAGCAGGAGCAGTGGA 59.879 61.111 0.00 0.00 45.49 4.02
4336 4623 2.268280 CAGGAGCAGGAGCAGTGG 59.732 66.667 0.00 0.00 45.49 4.00
4337 4624 2.436292 GCAGGAGCAGGAGCAGTG 60.436 66.667 0.00 0.00 45.49 3.66
4338 4625 2.607134 AGCAGGAGCAGGAGCAGT 60.607 61.111 0.00 0.00 45.49 4.40
4339 4626 2.187424 GAGCAGGAGCAGGAGCAG 59.813 66.667 0.00 0.00 45.49 4.24
4340 4627 3.397439 GGAGCAGGAGCAGGAGCA 61.397 66.667 0.00 0.00 45.49 4.26
4341 4628 4.527583 CGGAGCAGGAGCAGGAGC 62.528 72.222 0.00 0.00 45.49 4.70
4357 4644 0.600255 CAGGTATTAAGGCCGGAGCG 60.600 60.000 5.05 0.00 41.24 5.03
4358 4645 0.885150 GCAGGTATTAAGGCCGGAGC 60.885 60.000 5.05 0.00 38.76 4.70
4359 4646 0.468226 TGCAGGTATTAAGGCCGGAG 59.532 55.000 5.05 0.00 0.00 4.63
4360 4647 0.179468 GTGCAGGTATTAAGGCCGGA 59.821 55.000 5.05 0.00 0.00 5.14
4361 4648 0.818040 GGTGCAGGTATTAAGGCCGG 60.818 60.000 0.00 0.00 0.00 6.13
4362 4649 0.107410 TGGTGCAGGTATTAAGGCCG 60.107 55.000 0.00 0.00 0.00 6.13
4363 4650 1.680338 CTGGTGCAGGTATTAAGGCC 58.320 55.000 0.00 0.00 0.00 5.19
4364 4651 1.025041 GCTGGTGCAGGTATTAAGGC 58.975 55.000 0.00 0.00 39.41 4.35
4365 4652 1.299541 CGCTGGTGCAGGTATTAAGG 58.700 55.000 0.00 0.00 39.64 2.69
4393 4846 3.277211 TACGCCAGTCTGACGGTGC 62.277 63.158 22.80 16.65 36.18 5.01
4446 4899 0.467384 TAACGAAACCCACAACCCGA 59.533 50.000 0.00 0.00 0.00 5.14
4566 5020 1.298157 TTTTCCCGCATGCAGAGTCG 61.298 55.000 19.57 0.00 0.00 4.18
4608 5062 2.223711 TGAAAGCCACGAAAGAAAAGCC 60.224 45.455 0.00 0.00 0.00 4.35
4760 5214 2.425668 ACAAGGACGGGAAAAACAAGTG 59.574 45.455 0.00 0.00 0.00 3.16
4761 5215 2.730382 ACAAGGACGGGAAAAACAAGT 58.270 42.857 0.00 0.00 0.00 3.16
4774 5228 4.351192 CACAAACTGTTGCTAACAAGGAC 58.649 43.478 0.00 0.00 41.61 3.85
4809 5264 1.952990 TCCTGCTTGCATCGTGAAAAA 59.047 42.857 0.00 0.00 0.00 1.94
4814 5269 2.789917 GCTCCTGCTTGCATCGTG 59.210 61.111 0.00 0.00 36.03 4.35
4866 5323 7.443259 TTTAAACTAGGTCACCTGTATTTGC 57.557 36.000 6.61 0.00 34.61 3.68
4876 5333 6.879276 AGCTTTCCTTTTAAACTAGGTCAC 57.121 37.500 5.95 0.00 33.15 3.67
4883 5340 8.706322 TTTCAGGATAGCTTTCCTTTTAAACT 57.294 30.769 21.77 0.00 43.88 2.66
4888 5345 5.838521 TGGTTTTCAGGATAGCTTTCCTTTT 59.161 36.000 21.77 0.30 43.88 2.27
4897 5354 2.507407 TGGGTGGTTTTCAGGATAGC 57.493 50.000 0.00 0.00 0.00 2.97
4900 5357 3.379452 TGTTTTGGGTGGTTTTCAGGAT 58.621 40.909 0.00 0.00 0.00 3.24
4943 5403 1.631405 CATCCATGTTGGGGTTGTGT 58.369 50.000 0.00 0.00 38.32 3.72
4953 5413 3.384146 TCACACAAACTTGCATCCATGTT 59.616 39.130 0.00 0.00 39.99 2.71
4954 5414 2.957680 TCACACAAACTTGCATCCATGT 59.042 40.909 0.00 0.00 0.00 3.21
4955 5415 3.243468 TGTCACACAAACTTGCATCCATG 60.243 43.478 0.00 0.00 0.00 3.66
4956 5416 2.957680 TGTCACACAAACTTGCATCCAT 59.042 40.909 0.00 0.00 0.00 3.41
4963 5423 6.702972 TTTGAAACATGTCACACAAACTTG 57.297 33.333 0.00 0.00 0.00 3.16
4966 5426 6.884096 TGATTTGAAACATGTCACACAAAC 57.116 33.333 16.06 12.40 31.77 2.93
4997 5457 7.361894 TCATGTTTATGTCAAATGTGTGTCTG 58.638 34.615 0.00 0.00 35.73 3.51
4999 5459 8.572828 TTTCATGTTTATGTCAAATGTGTGTC 57.427 30.769 0.00 0.00 35.73 3.67
5000 5460 9.195411 GATTTCATGTTTATGTCAAATGTGTGT 57.805 29.630 0.00 0.00 35.73 3.72
5001 5461 9.414295 AGATTTCATGTTTATGTCAAATGTGTG 57.586 29.630 0.00 0.00 35.73 3.82
5008 5468 8.862325 AGGTGTAGATTTCATGTTTATGTCAA 57.138 30.769 0.00 0.00 35.73 3.18
5015 5476 8.157476 ACTGAAGTAGGTGTAGATTTCATGTTT 58.843 33.333 0.00 0.00 0.00 2.83
5039 5500 8.671921 CAAAATTGCATCTCTTCACATACTACT 58.328 33.333 0.00 0.00 0.00 2.57
5045 5506 5.924254 CACACAAAATTGCATCTCTTCACAT 59.076 36.000 0.00 0.00 0.00 3.21
5117 5578 1.469703 TCGTCTTGCTGCATTCCAATG 59.530 47.619 1.84 0.00 39.40 2.82
5174 5635 7.340487 GGGATTTTGAGTTTCTATCAGATGGTT 59.660 37.037 0.00 0.00 0.00 3.67
5180 5641 4.635765 TGCGGGATTTTGAGTTTCTATCAG 59.364 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.