Multiple sequence alignment - TraesCS4D01G308500

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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 TraesCS4D01G308500 chr4D 100.000 4643 0 0 1 4643 476318847 476314205 0.000000e+00 8575.0
1 TraesCS4D01G308500 chr4B 96.434 1935 51 9 774 2697 600673424 600671497 0.000000e+00 3175.0
2 TraesCS4D01G308500 chr4B 96.852 1239 31 5 2782 4017 600671499 600670266 0.000000e+00 2065.0
3 TraesCS4D01G308500 chr4B 87.227 321 37 4 364 681 600675840 600675521 3.410000e-96 363.0
4 TraesCS4D01G308500 chr4B 96.774 93 3 0 4549 4641 600669392 600669300 6.220000e-34 156.0
5 TraesCS4D01G308500 chr4B 97.143 70 2 0 4119 4188 600670139 600670070 8.160000e-23 119.0
6 TraesCS4D01G308500 chr4A 89.770 2395 141 45 1845 4187 683501171 683498829 0.000000e+00 2970.0
7 TraesCS4D01G308500 chr4A 93.924 576 30 2 1277 1848 683501838 683501264 0.000000e+00 865.0
8 TraesCS4D01G308500 chr4A 93.548 434 23 5 774 1204 683502565 683502134 3.920000e-180 641.0
9 TraesCS4D01G308500 chr4A 77.193 570 95 17 25 565 683534808 683534245 2.720000e-77 300.0
10 TraesCS4D01G308500 chr4A 79.558 362 25 16 4202 4517 683498761 683498403 3.640000e-51 213.0
11 TraesCS4D01G308500 chr4A 86.607 112 13 2 3016 3126 41899275 41899385 6.310000e-24 122.0
12 TraesCS4D01G308500 chr3A 85.163 337 25 10 1345 1681 323691 323380 5.800000e-84 322.0
13 TraesCS4D01G308500 chr3A 84.711 242 26 7 2032 2270 402084069 402083836 1.000000e-56 231.0
14 TraesCS4D01G308500 chr7D 83.014 365 29 10 1345 1686 575915282 575914928 2.720000e-77 300.0
15 TraesCS4D01G308500 chr3B 82.661 248 36 7 2025 2267 42700332 42700087 3.640000e-51 213.0
16 TraesCS4D01G308500 chr2B 84.713 157 11 6 2029 2184 210454936 210455080 1.350000e-30 145.0
17 TraesCS4D01G308500 chr2D 84.967 153 10 7 2029 2179 152095749 152095890 4.840000e-30 143.0
18 TraesCS4D01G308500 chr2D 86.607 112 13 2 3016 3126 433218769 433218879 6.310000e-24 122.0
19 TraesCS4D01G308500 chr2D 93.878 49 2 1 4212 4260 83962473 83962520 6.440000e-09 73.1
20 TraesCS4D01G308500 chr2D 90.566 53 5 0 2896 2948 433218663 433218715 2.320000e-08 71.3
21 TraesCS4D01G308500 chr2A 87.500 112 12 2 3016 3126 554014369 554014259 1.360000e-25 128.0
22 TraesCS4D01G308500 chr2A 88.571 105 8 4 2081 2184 149211770 149211669 1.750000e-24 124.0
23 TraesCS4D01G308500 chr2A 85.714 70 8 2 706 774 257883168 257883236 6.440000e-09 73.1
24 TraesCS4D01G308500 chr2A 89.286 56 6 0 2896 2951 554014473 554014418 2.320000e-08 71.3
25 TraesCS4D01G308500 chr5D 86.607 112 13 2 3016 3126 34271840 34271730 6.310000e-24 122.0
26 TraesCS4D01G308500 chr5D 87.500 64 6 2 4217 4279 322789851 322789789 6.440000e-09 73.1
27 TraesCS4D01G308500 chr6A 95.745 47 2 0 4217 4263 448702220 448702174 4.980000e-10 76.8
28 TraesCS4D01G308500 chr6A 93.878 49 2 1 4217 4264 432824797 432824749 6.440000e-09 73.1
29 TraesCS4D01G308500 chr1A 90.164 61 3 2 4216 4275 208881708 208881766 4.980000e-10 76.8
30 TraesCS4D01G308500 chrUn 93.878 49 2 1 4217 4264 75920478 75920526 6.440000e-09 73.1
31 TraesCS4D01G308500 chr7B 93.878 49 2 1 4217 4264 15482281 15482233 6.440000e-09 73.1
32 TraesCS4D01G308500 chr5A 87.500 64 6 2 4217 4279 419367729 419367667 6.440000e-09 73.1
33 TraesCS4D01G308500 chr1D 93.878 49 2 1 4217 4264 200548923 200548971 6.440000e-09 73.1


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 TraesCS4D01G308500 chr4D 476314205 476318847 4642 True 8575.00 8575 100.000 1 4643 1 chr4D.!!$R1 4642
1 TraesCS4D01G308500 chr4B 600669300 600675840 6540 True 1175.60 3175 94.886 364 4641 5 chr4B.!!$R1 4277
2 TraesCS4D01G308500 chr4A 683498403 683502565 4162 True 1172.25 2970 89.200 774 4517 4 chr4A.!!$R2 3743
3 TraesCS4D01G308500 chr4A 683534245 683534808 563 True 300.00 300 77.193 25 565 1 chr4A.!!$R1 540

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
523 551 0.035152 TTGCGATCATGGCAGAGGTT 60.035 50.0 0.00 0.0 42.12 3.50 F
729 760 0.036577 GCATCGCTAGCAGATCCCAT 60.037 55.0 16.45 0.0 0.00 4.00 F
741 772 0.112412 GATCCCATAAACCGGGCCAT 59.888 55.0 6.32 0.0 44.11 4.40 F
1519 3791 0.471780 TCAGCTCAGTGACCCAGGAA 60.472 55.0 0.00 0.0 0.00 3.36 F
2047 4423 0.675633 GGCTGTGTTTGGTTGATGCT 59.324 50.0 0.00 0.0 0.00 3.79 F
2683 5075 2.292103 TTGCTGCACTGGTTCAAAAC 57.708 45.0 0.00 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 3906 1.869132 GGTTAAGTCGCCACGTTTTCT 59.131 47.619 0.00 0.0 0.00 2.52 R
2295 4679 2.569404 GGGTGTTCTGAAGATGAGACCT 59.431 50.000 0.00 0.0 0.00 3.85 R
2736 5128 2.675658 ACACCACCATTAAAGCAGGT 57.324 45.000 0.00 0.0 35.65 4.00 R
2925 5405 0.391661 CCTGCACGCAAGGTAGATGT 60.392 55.000 0.00 0.0 46.39 3.06 R
3288 5783 1.187087 GATCGAGTGGTCAAGAGGGT 58.813 55.000 0.00 0.0 0.00 4.34 R
4447 7187 0.817634 TGTGTTTGGTGGCCTTCTCG 60.818 55.000 3.32 0.0 0.00 4.04 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
44 45 7.589958 TTGGTACTCCATAATTTTGTGTTGT 57.410 32.000 0.00 0.00 43.91 3.32
62 63 5.845953 GTGTTGTCACAACTATCGAAACATG 59.154 40.000 21.23 0.00 43.37 3.21
64 65 4.061596 TGTCACAACTATCGAAACATGCA 58.938 39.130 0.00 0.00 0.00 3.96
75 76 2.406024 CGAAACATGCATGCAACTCAAC 59.594 45.455 26.68 13.35 0.00 3.18
107 108 8.702163 AAAGGTCTTTAACTTGTGAATGTTTG 57.298 30.769 0.00 0.00 0.00 2.93
113 114 8.134895 TCTTTAACTTGTGAATGTTTGGTGATC 58.865 33.333 0.00 0.00 0.00 2.92
114 115 7.581213 TTAACTTGTGAATGTTTGGTGATCT 57.419 32.000 0.00 0.00 0.00 2.75
116 117 6.469782 ACTTGTGAATGTTTGGTGATCTTT 57.530 33.333 0.00 0.00 0.00 2.52
117 118 6.877236 ACTTGTGAATGTTTGGTGATCTTTT 58.123 32.000 0.00 0.00 0.00 2.27
118 119 6.757947 ACTTGTGAATGTTTGGTGATCTTTTG 59.242 34.615 0.00 0.00 0.00 2.44
119 120 6.462552 TGTGAATGTTTGGTGATCTTTTGA 57.537 33.333 0.00 0.00 0.00 2.69
123 124 3.230134 TGTTTGGTGATCTTTTGAGGGG 58.770 45.455 0.00 0.00 0.00 4.79
128 131 3.075882 TGGTGATCTTTTGAGGGGTTGAT 59.924 43.478 0.00 0.00 0.00 2.57
129 132 3.445096 GGTGATCTTTTGAGGGGTTGATG 59.555 47.826 0.00 0.00 0.00 3.07
151 154 5.188434 TGATCTTCCAACTAGCATCTTTGG 58.812 41.667 3.23 3.23 41.12 3.28
154 157 4.228210 TCTTCCAACTAGCATCTTTGGGAT 59.772 41.667 8.71 0.00 40.31 3.85
157 160 5.437060 TCCAACTAGCATCTTTGGGATAAC 58.563 41.667 8.71 0.00 40.31 1.89
161 164 7.041098 CCAACTAGCATCTTTGGGATAACATAC 60.041 40.741 1.89 0.00 36.84 2.39
165 168 7.902920 AGCATCTTTGGGATAACATACAATT 57.097 32.000 0.00 0.00 32.64 2.32
167 170 9.592196 AGCATCTTTGGGATAACATACAATTAT 57.408 29.630 0.00 0.00 32.64 1.28
174 178 9.913310 TTGGGATAACATACAATTATGTCTTCA 57.087 29.630 0.00 0.00 46.45 3.02
224 251 9.773328 ATTTTCATAAAGTCATCAATGTACACG 57.227 29.630 0.00 0.00 0.00 4.49
225 252 6.902224 TCATAAAGTCATCAATGTACACGG 57.098 37.500 0.00 0.00 0.00 4.94
227 254 2.024176 AGTCATCAATGTACACGGCC 57.976 50.000 0.00 0.00 0.00 6.13
236 263 0.038343 TGTACACGGCCGGTCTAAAC 60.038 55.000 31.76 18.02 0.00 2.01
240 267 0.672401 CACGGCCGGTCTAAACACAT 60.672 55.000 31.76 0.00 0.00 3.21
246 273 2.415512 GCCGGTCTAAACACATCTTCAC 59.584 50.000 1.90 0.00 0.00 3.18
248 275 3.306780 CCGGTCTAAACACATCTTCACCT 60.307 47.826 0.00 0.00 0.00 4.00
249 276 3.927142 CGGTCTAAACACATCTTCACCTC 59.073 47.826 0.00 0.00 0.00 3.85
251 278 5.491982 GGTCTAAACACATCTTCACCTCAT 58.508 41.667 0.00 0.00 0.00 2.90
254 281 7.363880 GGTCTAAACACATCTTCACCTCATCTA 60.364 40.741 0.00 0.00 0.00 1.98
258 285 6.305272 ACACATCTTCACCTCATCTACATT 57.695 37.500 0.00 0.00 0.00 2.71
265 292 8.306313 TCTTCACCTCATCTACATTAGCTTTA 57.694 34.615 0.00 0.00 0.00 1.85
266 293 8.928448 TCTTCACCTCATCTACATTAGCTTTAT 58.072 33.333 0.00 0.00 0.00 1.40
269 296 7.867909 TCACCTCATCTACATTAGCTTTATTCG 59.132 37.037 0.00 0.00 0.00 3.34
276 303 9.982651 ATCTACATTAGCTTTATTCGTACACAT 57.017 29.630 0.00 0.00 0.00 3.21
294 321 4.103153 ACACATCTTCCTCCTCTTTGTGAA 59.897 41.667 7.11 0.00 37.14 3.18
302 330 4.163078 TCCTCCTCTTTGTGAATCTCCATC 59.837 45.833 0.00 0.00 0.00 3.51
303 331 4.163839 CCTCCTCTTTGTGAATCTCCATCT 59.836 45.833 0.00 0.00 0.00 2.90
314 342 6.325804 TGTGAATCTCCATCTGTGATATGAGT 59.674 38.462 0.00 0.00 0.00 3.41
315 343 7.506938 TGTGAATCTCCATCTGTGATATGAGTA 59.493 37.037 0.00 0.00 0.00 2.59
316 344 8.028354 GTGAATCTCCATCTGTGATATGAGTAG 58.972 40.741 0.00 0.00 0.00 2.57
424 452 9.838339 AATAATTGTTTGGTGTGGTTTTCATTA 57.162 25.926 0.00 0.00 0.00 1.90
437 465 6.912591 GTGGTTTTCATTAATCATCGCCTTAG 59.087 38.462 0.00 0.00 0.00 2.18
461 489 7.186972 AGGCAATGGATTATGATAATGGTGAT 58.813 34.615 1.80 0.00 0.00 3.06
478 506 3.248602 GGTGATTGATTGACTATGGCGAC 59.751 47.826 0.00 0.00 0.00 5.19
503 531 1.518352 CCGATGATGCAACGACCGA 60.518 57.895 0.00 0.00 31.46 4.69
504 532 0.875908 CCGATGATGCAACGACCGAT 60.876 55.000 0.00 0.00 31.46 4.18
518 546 1.162181 ACCGATTGCGATCATGGCAG 61.162 55.000 14.39 0.00 42.12 4.85
519 547 0.881600 CCGATTGCGATCATGGCAGA 60.882 55.000 14.39 0.00 42.12 4.26
523 551 0.035152 TTGCGATCATGGCAGAGGTT 60.035 50.000 0.00 0.00 42.12 3.50
524 552 0.829990 TGCGATCATGGCAGAGGTTA 59.170 50.000 0.00 0.00 35.04 2.85
534 562 4.846779 TGGCAGAGGTTAAAATCACAAC 57.153 40.909 0.00 0.00 0.00 3.32
573 602 4.225267 TCCAACCATCTTCTCTAAGTTCCC 59.775 45.833 0.00 0.00 34.13 3.97
579 608 5.423610 CCATCTTCTCTAAGTTCCCAAGAGA 59.576 44.000 0.00 0.00 43.01 3.10
587 616 0.889186 GTTCCCAAGAGAGCGGCAAA 60.889 55.000 1.45 0.00 0.00 3.68
591 620 1.167851 CCAAGAGAGCGGCAAAATGA 58.832 50.000 1.45 0.00 0.00 2.57
599 628 0.248843 GCGGCAAAATGAAATGGGGA 59.751 50.000 0.00 0.00 0.00 4.81
601 630 2.620242 CGGCAAAATGAAATGGGGAAG 58.380 47.619 0.00 0.00 0.00 3.46
602 631 2.233431 CGGCAAAATGAAATGGGGAAGA 59.767 45.455 0.00 0.00 0.00 2.87
603 632 3.599343 GGCAAAATGAAATGGGGAAGAC 58.401 45.455 0.00 0.00 0.00 3.01
604 633 3.007831 GGCAAAATGAAATGGGGAAGACA 59.992 43.478 0.00 0.00 0.00 3.41
605 634 3.996363 GCAAAATGAAATGGGGAAGACAC 59.004 43.478 0.00 0.00 0.00 3.67
625 655 1.806542 CCACCGTCAAACTCATGGAAG 59.193 52.381 0.00 0.00 0.00 3.46
650 680 1.769026 TGAGACGGGAGGATGAAGAG 58.231 55.000 0.00 0.00 0.00 2.85
651 681 1.006043 TGAGACGGGAGGATGAAGAGT 59.994 52.381 0.00 0.00 0.00 3.24
656 687 1.686428 CGGGAGGATGAAGAGTGAGGA 60.686 57.143 0.00 0.00 0.00 3.71
663 694 6.015772 GGAGGATGAAGAGTGAGGAATAGTAC 60.016 46.154 0.00 0.00 0.00 2.73
681 712 0.905337 ACGAAAGAGGAGAGGGGTGG 60.905 60.000 0.00 0.00 0.00 4.61
682 713 1.617947 CGAAAGAGGAGAGGGGTGGG 61.618 65.000 0.00 0.00 0.00 4.61
683 714 1.229984 AAAGAGGAGAGGGGTGGGG 60.230 63.158 0.00 0.00 0.00 4.96
685 716 2.041405 GAGGAGAGGGGTGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
687 718 2.041405 GGAGAGGGGTGGGGAGAG 60.041 72.222 0.00 0.00 0.00 3.20
688 719 2.041405 GAGAGGGGTGGGGAGAGG 60.041 72.222 0.00 0.00 0.00 3.69
690 721 4.825679 GAGGGGTGGGGAGAGGGG 62.826 77.778 0.00 0.00 0.00 4.79
707 738 2.345991 GTGGCAGGGTGCGTCTTA 59.654 61.111 0.00 0.00 46.21 2.10
715 746 0.872021 GGGTGCGTCTTAGAGCATCG 60.872 60.000 8.95 0.00 44.82 3.84
717 748 0.526524 GTGCGTCTTAGAGCATCGCT 60.527 55.000 14.24 0.00 45.69 4.93
721 752 1.002359 CGTCTTAGAGCATCGCTAGCA 60.002 52.381 16.45 2.17 39.88 3.49
723 754 2.292016 GTCTTAGAGCATCGCTAGCAGA 59.708 50.000 16.45 13.24 39.88 4.26
724 755 3.057596 GTCTTAGAGCATCGCTAGCAGAT 60.058 47.826 16.45 14.92 39.88 2.90
728 759 1.117749 AGCATCGCTAGCAGATCCCA 61.118 55.000 16.45 0.00 36.99 4.37
729 760 0.036577 GCATCGCTAGCAGATCCCAT 60.037 55.000 16.45 0.00 0.00 4.00
732 763 3.866066 GCATCGCTAGCAGATCCCATAAA 60.866 47.826 16.45 0.00 0.00 1.40
733 764 3.386768 TCGCTAGCAGATCCCATAAAC 57.613 47.619 16.45 0.00 0.00 2.01
734 765 2.037251 TCGCTAGCAGATCCCATAAACC 59.963 50.000 16.45 0.00 0.00 3.27
736 767 2.872038 GCTAGCAGATCCCATAAACCGG 60.872 54.545 10.63 0.00 0.00 5.28
737 768 0.474184 AGCAGATCCCATAAACCGGG 59.526 55.000 6.32 0.00 46.03 5.73
740 771 0.991355 AGATCCCATAAACCGGGCCA 60.991 55.000 6.32 0.00 44.11 5.36
741 772 0.112412 GATCCCATAAACCGGGCCAT 59.888 55.000 6.32 0.00 44.11 4.40
743 774 1.530655 CCCATAAACCGGGCCATCC 60.531 63.158 6.32 0.00 36.72 3.51
802 2843 7.313731 AGGATGACCTAACTATCTATTTCCCA 58.686 38.462 0.00 0.00 45.83 4.37
844 2886 4.804139 CCGTATGATCTAGAGCGTTTGTTT 59.196 41.667 8.22 0.00 0.00 2.83
860 2902 1.513373 TTTCTGATCCGACGTCGCG 60.513 57.895 31.73 23.52 38.18 5.87
865 2907 0.877213 TGATCCGACGTCGCGAGATA 60.877 55.000 31.73 16.19 45.19 1.98
904 2946 1.300971 GGTAGGTTTTTCGTCCCCGC 61.301 60.000 0.00 0.00 0.00 6.13
1274 3539 1.293924 TAGAGCAGAGTACGCGTACC 58.706 55.000 38.10 29.63 36.75 3.34
1275 3540 0.675837 AGAGCAGAGTACGCGTACCA 60.676 55.000 38.10 11.24 36.75 3.25
1321 3586 2.485122 GCTTTTCATGGCGTCCCG 59.515 61.111 0.00 0.00 0.00 5.14
1464 3736 2.080693 TGCGATGTATGGGTTGTGTTC 58.919 47.619 0.00 0.00 0.00 3.18
1519 3791 0.471780 TCAGCTCAGTGACCCAGGAA 60.472 55.000 0.00 0.00 0.00 3.36
1634 3906 8.531982 GCTGGAATCTAGGACATATATGTTGTA 58.468 37.037 19.19 12.39 41.95 2.41
2047 4423 0.675633 GGCTGTGTTTGGTTGATGCT 59.324 50.000 0.00 0.00 0.00 3.79
2161 4537 2.837947 TCTGTGAGAGGAATGGTGGAT 58.162 47.619 0.00 0.00 0.00 3.41
2225 4601 2.954318 CCAAGATTTGATAGGCACCCAG 59.046 50.000 0.00 0.00 0.00 4.45
2269 4650 2.418609 GCAGCAAACCAAACAGACCTTT 60.419 45.455 0.00 0.00 0.00 3.11
2295 4679 9.865152 TCCCATGAATGTTATCAATCTTCATTA 57.135 29.630 0.00 0.00 35.06 1.90
2348 4739 8.705594 TGGTGATTTTTATGGTTACCTTGAAAA 58.294 29.630 17.55 17.55 33.33 2.29
2517 4908 2.439507 CTGGGTACATAGGTTGGATGCT 59.560 50.000 0.00 0.00 0.00 3.79
2524 4915 7.256547 GGGTACATAGGTTGGATGCTTATCTTA 60.257 40.741 0.00 0.00 0.00 2.10
2538 4929 8.978874 ATGCTTATCTTACATGGTTATTGTCA 57.021 30.769 0.00 0.00 0.00 3.58
2608 5000 8.883731 ACTCTTGCAGTGTTACAATCATATAAC 58.116 33.333 0.00 0.00 32.26 1.89
2683 5075 2.292103 TTGCTGCACTGGTTCAAAAC 57.708 45.000 0.00 0.00 0.00 2.43
2694 5086 4.947388 ACTGGTTCAAAACTCTTGTTGCTA 59.053 37.500 0.00 0.00 36.39 3.49
2695 5087 5.417580 ACTGGTTCAAAACTCTTGTTGCTAA 59.582 36.000 0.00 0.00 36.39 3.09
2696 5088 6.071616 ACTGGTTCAAAACTCTTGTTGCTAAA 60.072 34.615 0.00 0.00 36.39 1.85
2697 5089 6.096695 TGGTTCAAAACTCTTGTTGCTAAAC 58.903 36.000 0.00 0.00 36.39 2.01
2698 5090 6.071616 TGGTTCAAAACTCTTGTTGCTAAACT 60.072 34.615 0.00 0.00 37.19 2.66
2699 5091 7.121463 TGGTTCAAAACTCTTGTTGCTAAACTA 59.879 33.333 0.00 0.00 37.19 2.24
2700 5092 8.135529 GGTTCAAAACTCTTGTTGCTAAACTAT 58.864 33.333 0.00 0.00 37.19 2.12
2701 5093 9.516314 GTTCAAAACTCTTGTTGCTAAACTATT 57.484 29.630 0.00 0.00 37.19 1.73
2705 5097 9.869757 AAAACTCTTGTTGCTAAACTATTTTGT 57.130 25.926 0.00 0.00 37.19 2.83
2706 5098 9.516314 AAACTCTTGTTGCTAAACTATTTTGTC 57.484 29.630 0.00 0.00 37.19 3.18
2707 5099 8.451908 ACTCTTGTTGCTAAACTATTTTGTCT 57.548 30.769 0.00 0.00 37.19 3.41
2708 5100 8.903820 ACTCTTGTTGCTAAACTATTTTGTCTT 58.096 29.630 0.00 0.00 37.19 3.01
2709 5101 9.387123 CTCTTGTTGCTAAACTATTTTGTCTTC 57.613 33.333 0.00 0.00 37.19 2.87
2710 5102 8.898761 TCTTGTTGCTAAACTATTTTGTCTTCA 58.101 29.630 0.00 0.00 37.19 3.02
2711 5103 9.683069 CTTGTTGCTAAACTATTTTGTCTTCAT 57.317 29.630 0.00 0.00 37.19 2.57
2742 5134 3.857157 TTTTGGTCAGTCTAACCTGCT 57.143 42.857 0.00 0.00 37.69 4.24
2743 5135 3.857157 TTTGGTCAGTCTAACCTGCTT 57.143 42.857 0.00 0.00 37.69 3.91
2744 5136 3.857157 TTGGTCAGTCTAACCTGCTTT 57.143 42.857 0.00 0.00 37.69 3.51
2745 5137 4.967084 TTGGTCAGTCTAACCTGCTTTA 57.033 40.909 0.00 0.00 37.69 1.85
2746 5138 4.967084 TGGTCAGTCTAACCTGCTTTAA 57.033 40.909 0.00 0.00 37.69 1.52
2747 5139 5.499004 TGGTCAGTCTAACCTGCTTTAAT 57.501 39.130 0.00 0.00 37.69 1.40
2748 5140 5.245531 TGGTCAGTCTAACCTGCTTTAATG 58.754 41.667 0.00 0.00 37.69 1.90
2749 5141 4.636206 GGTCAGTCTAACCTGCTTTAATGG 59.364 45.833 0.00 0.00 33.78 3.16
2750 5142 5.246307 GTCAGTCTAACCTGCTTTAATGGT 58.754 41.667 0.00 0.00 35.29 3.55
2751 5143 5.122396 GTCAGTCTAACCTGCTTTAATGGTG 59.878 44.000 0.00 0.00 33.89 4.17
2752 5144 4.396166 CAGTCTAACCTGCTTTAATGGTGG 59.604 45.833 0.00 0.00 33.89 4.61
2753 5145 4.042934 AGTCTAACCTGCTTTAATGGTGGT 59.957 41.667 0.00 0.00 33.89 4.16
2754 5146 4.156008 GTCTAACCTGCTTTAATGGTGGTG 59.844 45.833 0.00 0.00 33.89 4.17
2755 5147 2.675658 ACCTGCTTTAATGGTGGTGT 57.324 45.000 0.00 0.00 32.16 4.16
2756 5148 2.957474 ACCTGCTTTAATGGTGGTGTT 58.043 42.857 0.00 0.00 32.16 3.32
2757 5149 3.304829 ACCTGCTTTAATGGTGGTGTTT 58.695 40.909 0.00 0.00 32.16 2.83
2758 5150 3.709141 ACCTGCTTTAATGGTGGTGTTTT 59.291 39.130 0.00 0.00 32.16 2.43
2759 5151 4.163268 ACCTGCTTTAATGGTGGTGTTTTT 59.837 37.500 0.00 0.00 32.16 1.94
2760 5152 4.511082 CCTGCTTTAATGGTGGTGTTTTTG 59.489 41.667 0.00 0.00 0.00 2.44
2761 5153 3.873952 TGCTTTAATGGTGGTGTTTTTGC 59.126 39.130 0.00 0.00 0.00 3.68
2762 5154 3.249799 GCTTTAATGGTGGTGTTTTTGCC 59.750 43.478 0.00 0.00 0.00 4.52
2763 5155 4.446371 CTTTAATGGTGGTGTTTTTGCCA 58.554 39.130 0.00 0.00 0.00 4.92
2764 5156 4.487714 TTAATGGTGGTGTTTTTGCCAA 57.512 36.364 0.00 0.00 36.41 4.52
2765 5157 3.574354 AATGGTGGTGTTTTTGCCAAT 57.426 38.095 0.00 0.00 36.41 3.16
2766 5158 3.574354 ATGGTGGTGTTTTTGCCAATT 57.426 38.095 0.00 0.00 36.41 2.32
2767 5159 4.696479 ATGGTGGTGTTTTTGCCAATTA 57.304 36.364 0.00 0.00 36.41 1.40
2768 5160 4.696479 TGGTGGTGTTTTTGCCAATTAT 57.304 36.364 0.00 0.00 36.41 1.28
2769 5161 5.041191 TGGTGGTGTTTTTGCCAATTATT 57.959 34.783 0.00 0.00 36.41 1.40
2770 5162 5.440610 TGGTGGTGTTTTTGCCAATTATTT 58.559 33.333 0.00 0.00 36.41 1.40
2771 5163 5.297776 TGGTGGTGTTTTTGCCAATTATTTG 59.702 36.000 0.00 0.00 36.41 2.32
2772 5164 5.211454 GTGGTGTTTTTGCCAATTATTTGC 58.789 37.500 0.00 0.00 36.41 3.68
2773 5165 4.883585 TGGTGTTTTTGCCAATTATTTGCA 59.116 33.333 0.00 0.00 0.00 4.08
2774 5166 5.357878 TGGTGTTTTTGCCAATTATTTGCAA 59.642 32.000 11.60 11.60 31.53 4.08
2775 5167 5.685068 GGTGTTTTTGCCAATTATTTGCAAC 59.315 36.000 14.63 6.64 32.45 4.17
2776 5168 6.261118 GTGTTTTTGCCAATTATTTGCAACA 58.739 32.000 14.63 8.87 32.45 3.33
2777 5169 6.414402 GTGTTTTTGCCAATTATTTGCAACAG 59.586 34.615 14.63 0.00 32.45 3.16
2778 5170 6.317140 TGTTTTTGCCAATTATTTGCAACAGA 59.683 30.769 14.63 2.83 32.45 3.41
2779 5171 6.932356 TTTTGCCAATTATTTGCAACAGAA 57.068 29.167 14.63 5.79 32.45 3.02
2780 5172 6.932356 TTTGCCAATTATTTGCAACAGAAA 57.068 29.167 14.63 0.00 32.45 2.52
2925 5405 2.710471 TCACCTGGCATGCTTATATGGA 59.290 45.455 18.92 4.41 0.00 3.41
2970 5465 5.887214 ACATTTTCCTTGGCCTTTTTAGT 57.113 34.783 3.32 0.00 0.00 2.24
3288 5783 3.603158 TGCTGAAGGCGATACTGTAAA 57.397 42.857 0.00 0.00 45.43 2.01
3593 6089 1.911766 GGACCTGTCGGAGGAACCA 60.912 63.158 8.26 0.00 46.33 3.67
3677 6175 4.063998 TCATCATACACAGCTTGCCTAG 57.936 45.455 0.00 0.00 0.00 3.02
3806 6305 3.068024 TCAAAGGCACAATCAGTTGAACC 59.932 43.478 0.00 0.00 38.71 3.62
3808 6307 1.145738 AGGCACAATCAGTTGAACCCT 59.854 47.619 0.00 0.00 38.71 4.34
3842 6345 7.856145 CTTTTCCAGCATGATTACTCTTACT 57.144 36.000 0.00 0.00 39.69 2.24
3847 6350 6.155221 TCCAGCATGATTACTCTTACTCTTGT 59.845 38.462 0.00 0.00 39.69 3.16
3913 6416 5.348997 AGACTGAATTGCTTAAGTTACTCGC 59.651 40.000 4.02 0.00 0.00 5.03
3932 6435 2.258726 GGCGTGTTTGGTGGAGTCC 61.259 63.158 0.73 0.73 0.00 3.85
3963 6468 3.569701 TGAAGGAGGCTTGAATGTTCAAC 59.430 43.478 4.16 2.79 41.88 3.18
4055 6568 9.459640 TCTAACACAGTTTATATTGTAGATCGC 57.540 33.333 0.00 0.00 0.00 4.58
4056 6569 7.478520 AACACAGTTTATATTGTAGATCGCC 57.521 36.000 0.00 0.00 0.00 5.54
4066 6579 3.013276 TGTAGATCGCCGCAATTCTAG 57.987 47.619 0.00 0.00 0.00 2.43
4074 6587 1.959042 CCGCAATTCTAGATGGCAGT 58.041 50.000 10.28 0.00 0.00 4.40
4099 6612 1.079503 GAGCTCATCGGTTTGTGTCC 58.920 55.000 9.40 0.00 0.00 4.02
4102 6615 2.301870 AGCTCATCGGTTTGTGTCCTTA 59.698 45.455 0.00 0.00 0.00 2.69
4110 6623 6.288941 TCGGTTTGTGTCCTTAATCTATGA 57.711 37.500 0.00 0.00 0.00 2.15
4134 6665 5.573337 AATTCTACATTGGAAAGAGCAGC 57.427 39.130 0.00 0.00 0.00 5.25
4188 6719 6.430925 TGGTTCAATGTTTTCCATGTCTAGAG 59.569 38.462 0.00 0.00 32.82 2.43
4189 6720 6.317857 GTTCAATGTTTTCCATGTCTAGAGC 58.682 40.000 0.00 0.00 32.82 4.09
4190 6721 5.559770 TCAATGTTTTCCATGTCTAGAGCA 58.440 37.500 0.00 0.00 32.82 4.26
4191 6722 5.645067 TCAATGTTTTCCATGTCTAGAGCAG 59.355 40.000 0.00 0.00 32.82 4.24
4192 6723 4.623932 TGTTTTCCATGTCTAGAGCAGT 57.376 40.909 0.00 0.00 0.00 4.40
4193 6724 5.738619 TGTTTTCCATGTCTAGAGCAGTA 57.261 39.130 0.00 0.00 0.00 2.74
4194 6725 6.109156 TGTTTTCCATGTCTAGAGCAGTAA 57.891 37.500 0.00 0.00 0.00 2.24
4196 6727 6.595326 TGTTTTCCATGTCTAGAGCAGTAATG 59.405 38.462 0.00 0.00 0.00 1.90
4197 6728 4.327982 TCCATGTCTAGAGCAGTAATGC 57.672 45.455 7.15 7.15 0.00 3.56
4199 6730 4.162131 TCCATGTCTAGAGCAGTAATGCAA 59.838 41.667 18.53 1.29 37.25 4.08
4229 6815 7.739498 TTTTTCATTGTTACTCCCTCTGTAC 57.261 36.000 0.00 0.00 0.00 2.90
4231 6817 5.401531 TCATTGTTACTCCCTCTGTACAC 57.598 43.478 0.00 0.00 0.00 2.90
4239 6825 9.925545 TGTTACTCCCTCTGTACACTAATATAA 57.074 33.333 0.00 0.00 0.00 0.98
4243 6829 7.444792 ACTCCCTCTGTACACTAATATAAGACG 59.555 40.741 0.00 0.00 0.00 4.18
4262 6848 9.924650 ATAAGACGTTTTAGATCACTAAAGTGT 57.075 29.630 9.81 0.00 45.40 3.55
4278 6991 8.308931 CACTAAAGTGTATAGTGTACAAAGGGA 58.691 37.037 0.00 0.00 43.31 4.20
4279 6992 8.529476 ACTAAAGTGTATAGTGTACAAAGGGAG 58.471 37.037 0.00 0.00 32.50 4.30
4280 6993 6.930068 AAGTGTATAGTGTACAAAGGGAGT 57.070 37.500 0.00 0.00 0.00 3.85
4289 7002 4.868734 GTGTACAAAGGGAGTAGTACATGC 59.131 45.833 0.00 0.00 45.70 4.06
4306 7019 2.284754 TGCTTGTGGTGGCATTCTTA 57.715 45.000 0.00 0.00 33.23 2.10
4319 7032 6.238759 GGTGGCATTCTTACAATATCAGGAAC 60.239 42.308 0.00 0.00 0.00 3.62
4320 7033 6.318648 GTGGCATTCTTACAATATCAGGAACA 59.681 38.462 0.00 0.00 0.00 3.18
4363 7079 9.586150 CTCGTATACATGCTATCAAACAAAATC 57.414 33.333 3.32 0.00 0.00 2.17
4371 7087 7.686438 TGCTATCAAACAAAATCTCAGCTTA 57.314 32.000 0.00 0.00 0.00 3.09
4433 7173 1.028130 CTAGAGCCAGCATGTCTCGA 58.972 55.000 0.00 0.00 32.42 4.04
4447 7187 0.537188 TCTCGATGGAGAACAAGGGC 59.463 55.000 4.77 0.00 46.11 5.19
4473 7213 1.153046 CCACCAAACACACCCTCGT 60.153 57.895 0.00 0.00 0.00 4.18
4534 7274 6.369890 CCATGGTATAAGAGGATGAAATCGTG 59.630 42.308 2.57 0.00 46.86 4.35
4537 7277 7.735917 TGGTATAAGAGGATGAAATCGTGATT 58.264 34.615 0.00 0.00 46.86 2.57
4550 7290 8.148807 TGAAATCGTGATTTTTGTCTTCTACA 57.851 30.769 9.06 0.00 40.77 2.74
4551 7291 8.282592 TGAAATCGTGATTTTTGTCTTCTACAG 58.717 33.333 9.06 0.00 40.77 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.630054 AGTACCAATATTAAGTGAGCAAAACA 57.370 30.769 0.00 0.00 0.00 2.83
7 8 6.553953 TGGAGTACCAATATTAAGTGAGCA 57.446 37.500 0.00 0.00 43.91 4.26
21 22 7.255312 GTGACAACACAAAATTATGGAGTACCA 60.255 37.037 0.00 0.00 46.63 3.25
22 23 7.081976 GTGACAACACAAAATTATGGAGTACC 58.918 38.462 0.00 0.00 45.32 3.34
39 40 5.559991 GCATGTTTCGATAGTTGTGACAACA 60.560 40.000 27.89 15.38 37.40 3.33
40 41 4.846137 GCATGTTTCGATAGTTGTGACAAC 59.154 41.667 20.12 20.12 37.40 3.32
44 45 4.437255 GCATGCATGTTTCGATAGTTGTGA 60.437 41.667 26.79 0.00 37.40 3.58
53 54 1.878734 TGAGTTGCATGCATGTTTCGA 59.121 42.857 26.79 8.47 0.00 3.71
55 56 2.406024 CGTTGAGTTGCATGCATGTTTC 59.594 45.455 26.79 16.19 0.00 2.78
56 57 2.223782 ACGTTGAGTTGCATGCATGTTT 60.224 40.909 26.79 7.35 0.00 2.83
62 63 2.118228 TTTCACGTTGAGTTGCATGC 57.882 45.000 11.82 11.82 0.00 4.06
84 85 6.379988 ACCAAACATTCACAAGTTAAAGACCT 59.620 34.615 0.00 0.00 0.00 3.85
86 87 7.254852 TCACCAAACATTCACAAGTTAAAGAC 58.745 34.615 0.00 0.00 0.00 3.01
87 88 7.397892 TCACCAAACATTCACAAGTTAAAGA 57.602 32.000 0.00 0.00 0.00 2.52
107 108 3.154827 TCAACCCCTCAAAAGATCACC 57.845 47.619 0.00 0.00 0.00 4.02
113 114 4.400567 GGAAGATCATCAACCCCTCAAAAG 59.599 45.833 0.00 0.00 0.00 2.27
114 115 4.202663 TGGAAGATCATCAACCCCTCAAAA 60.203 41.667 0.00 0.00 0.00 2.44
116 117 2.918934 TGGAAGATCATCAACCCCTCAA 59.081 45.455 0.00 0.00 0.00 3.02
117 118 2.561187 TGGAAGATCATCAACCCCTCA 58.439 47.619 0.00 0.00 0.00 3.86
118 119 3.054065 AGTTGGAAGATCATCAACCCCTC 60.054 47.826 16.72 0.03 40.96 4.30
119 120 2.922283 AGTTGGAAGATCATCAACCCCT 59.078 45.455 16.72 2.92 40.96 4.79
123 124 6.054295 AGATGCTAGTTGGAAGATCATCAAC 58.946 40.000 14.12 14.12 40.52 3.18
128 131 5.188434 CCAAAGATGCTAGTTGGAAGATCA 58.812 41.667 3.50 0.00 43.82 2.92
129 132 4.578105 CCCAAAGATGCTAGTTGGAAGATC 59.422 45.833 9.97 0.00 43.82 2.75
198 202 9.773328 CGTGTACATTGATGACTTTATGAAAAT 57.227 29.630 0.00 0.00 0.00 1.82
199 203 8.233868 CCGTGTACATTGATGACTTTATGAAAA 58.766 33.333 0.00 0.00 0.00 2.29
203 207 5.501715 GCCGTGTACATTGATGACTTTATG 58.498 41.667 0.00 0.00 0.00 1.90
204 208 4.574828 GGCCGTGTACATTGATGACTTTAT 59.425 41.667 0.00 0.00 0.00 1.40
206 210 2.747446 GGCCGTGTACATTGATGACTTT 59.253 45.455 0.00 0.00 0.00 2.66
217 242 0.038343 GTTTAGACCGGCCGTGTACA 60.038 55.000 26.12 9.70 0.00 2.90
218 243 0.038343 TGTTTAGACCGGCCGTGTAC 60.038 55.000 26.12 15.72 0.00 2.90
221 248 0.672401 ATGTGTTTAGACCGGCCGTG 60.672 55.000 26.12 18.04 0.00 4.94
224 251 2.007608 GAAGATGTGTTTAGACCGGCC 58.992 52.381 0.00 0.00 0.00 6.13
225 252 2.415512 GTGAAGATGTGTTTAGACCGGC 59.584 50.000 0.00 0.00 0.00 6.13
227 254 3.926616 AGGTGAAGATGTGTTTAGACCG 58.073 45.455 0.00 0.00 0.00 4.79
236 263 6.423302 GCTAATGTAGATGAGGTGAAGATGTG 59.577 42.308 0.00 0.00 0.00 3.21
240 267 6.798427 AAGCTAATGTAGATGAGGTGAAGA 57.202 37.500 0.00 0.00 0.00 2.87
246 273 9.130312 GTACGAATAAAGCTAATGTAGATGAGG 57.870 37.037 0.00 0.00 0.00 3.86
248 275 9.459640 GTGTACGAATAAAGCTAATGTAGATGA 57.540 33.333 0.00 0.00 0.00 2.92
249 276 9.244799 TGTGTACGAATAAAGCTAATGTAGATG 57.755 33.333 0.00 0.00 0.00 2.90
251 278 9.459640 GATGTGTACGAATAAAGCTAATGTAGA 57.540 33.333 0.00 0.00 0.00 2.59
254 281 8.718102 AAGATGTGTACGAATAAAGCTAATGT 57.282 30.769 0.00 0.00 0.00 2.71
258 285 7.108841 AGGAAGATGTGTACGAATAAAGCTA 57.891 36.000 0.00 0.00 0.00 3.32
265 292 4.282496 AGAGGAGGAAGATGTGTACGAAT 58.718 43.478 0.00 0.00 0.00 3.34
266 293 3.698289 AGAGGAGGAAGATGTGTACGAA 58.302 45.455 0.00 0.00 0.00 3.85
269 296 4.932200 CACAAAGAGGAGGAAGATGTGTAC 59.068 45.833 0.00 0.00 33.76 2.90
276 303 4.223923 GGAGATTCACAAAGAGGAGGAAGA 59.776 45.833 0.00 0.00 0.00 2.87
294 321 5.421693 GGCTACTCATATCACAGATGGAGAT 59.578 44.000 13.74 0.50 0.00 2.75
332 360 9.551734 CAAAGGAAATGACTATCACATATGAGA 57.448 33.333 10.38 7.61 38.57 3.27
333 361 9.334947 ACAAAGGAAATGACTATCACATATGAG 57.665 33.333 10.38 0.87 38.57 2.90
408 436 5.621104 GCGATGATTAATGAAAACCACACCA 60.621 40.000 0.00 0.00 0.00 4.17
437 465 6.839124 TCACCATTATCATAATCCATTGCC 57.161 37.500 0.00 0.00 0.00 4.52
452 480 5.469760 CGCCATAGTCAATCAATCACCATTA 59.530 40.000 0.00 0.00 0.00 1.90
461 489 3.261580 CACTGTCGCCATAGTCAATCAA 58.738 45.455 0.00 0.00 0.00 2.57
473 501 3.490759 CATCGGCACACTGTCGCC 61.491 66.667 7.54 7.54 46.34 5.54
478 506 0.179181 GTTGCATCATCGGCACACTG 60.179 55.000 0.00 0.00 41.75 3.66
479 507 1.638388 CGTTGCATCATCGGCACACT 61.638 55.000 0.00 0.00 41.75 3.55
487 515 2.373735 CAATCGGTCGTTGCATCATC 57.626 50.000 0.00 0.00 0.00 2.92
503 531 0.182061 ACCTCTGCCATGATCGCAAT 59.818 50.000 0.00 0.00 35.40 3.56
504 532 0.035152 AACCTCTGCCATGATCGCAA 60.035 50.000 0.00 0.00 35.40 4.85
508 536 5.357878 TGTGATTTTAACCTCTGCCATGATC 59.642 40.000 0.00 0.00 0.00 2.92
523 551 5.112686 GTTGCCAACAAGGTTGTGATTTTA 58.887 37.500 1.91 0.00 41.31 1.52
524 552 3.902881 TGCCAACAAGGTTGTGATTTT 57.097 38.095 8.16 0.00 41.31 1.82
534 562 0.754957 TGGAGGTGTTGCCAACAAGG 60.755 55.000 12.63 0.00 44.16 3.61
573 602 2.995466 TTCATTTTGCCGCTCTCTTG 57.005 45.000 0.00 0.00 0.00 3.02
579 608 0.249955 CCCCATTTCATTTTGCCGCT 59.750 50.000 0.00 0.00 0.00 5.52
587 616 3.165071 GTGGTGTCTTCCCCATTTCATT 58.835 45.455 0.00 0.00 32.32 2.57
591 620 0.251165 CGGTGGTGTCTTCCCCATTT 60.251 55.000 0.00 0.00 32.32 2.32
599 628 1.208535 TGAGTTTGACGGTGGTGTCTT 59.791 47.619 0.00 0.00 39.64 3.01
601 630 1.531149 CATGAGTTTGACGGTGGTGTC 59.469 52.381 0.00 0.00 39.37 3.67
602 631 1.593196 CATGAGTTTGACGGTGGTGT 58.407 50.000 0.00 0.00 0.00 4.16
603 632 0.874390 CCATGAGTTTGACGGTGGTG 59.126 55.000 0.00 0.00 0.00 4.17
604 633 0.762418 TCCATGAGTTTGACGGTGGT 59.238 50.000 0.00 0.00 0.00 4.16
605 634 1.806542 CTTCCATGAGTTTGACGGTGG 59.193 52.381 0.00 0.00 0.00 4.61
625 655 0.179000 ATCCTCCCGTCTCATTGTGC 59.821 55.000 0.00 0.00 0.00 4.57
650 680 5.589452 TCTCCTCTTTCGTACTATTCCTCAC 59.411 44.000 0.00 0.00 0.00 3.51
651 681 5.752650 TCTCCTCTTTCGTACTATTCCTCA 58.247 41.667 0.00 0.00 0.00 3.86
656 687 4.216708 CCCCTCTCCTCTTTCGTACTATT 58.783 47.826 0.00 0.00 0.00 1.73
663 694 1.617947 CCCACCCCTCTCCTCTTTCG 61.618 65.000 0.00 0.00 0.00 3.46
683 714 3.721706 CACCCTGCCACCCCTCTC 61.722 72.222 0.00 0.00 0.00 3.20
690 721 1.741770 CTAAGACGCACCCTGCCAC 60.742 63.158 0.00 0.00 41.12 5.01
691 722 1.888436 CTCTAAGACGCACCCTGCCA 61.888 60.000 0.00 0.00 41.12 4.92
692 723 1.153549 CTCTAAGACGCACCCTGCC 60.154 63.158 0.00 0.00 41.12 4.85
693 724 1.811679 GCTCTAAGACGCACCCTGC 60.812 63.158 0.00 0.00 40.69 4.85
694 725 0.176680 ATGCTCTAAGACGCACCCTG 59.823 55.000 0.00 0.00 39.21 4.45
695 726 0.461961 GATGCTCTAAGACGCACCCT 59.538 55.000 0.00 0.00 39.21 4.34
701 732 1.002359 TGCTAGCGATGCTCTAAGACG 60.002 52.381 10.77 0.00 40.44 4.18
703 734 2.576615 TCTGCTAGCGATGCTCTAAGA 58.423 47.619 10.77 0.63 40.44 2.10
707 738 0.602562 GGATCTGCTAGCGATGCTCT 59.397 55.000 23.40 6.58 40.44 4.09
715 746 2.417719 CGGTTTATGGGATCTGCTAGC 58.582 52.381 8.10 8.10 0.00 3.42
757 788 2.182537 CCTCCGTCCCGTAAACCG 59.817 66.667 0.00 0.00 0.00 4.44
758 789 2.125391 GCCTCCGTCCCGTAAACC 60.125 66.667 0.00 0.00 0.00 3.27
759 790 2.507769 CGCCTCCGTCCCGTAAAC 60.508 66.667 0.00 0.00 0.00 2.01
760 791 2.676121 TCGCCTCCGTCCCGTAAA 60.676 61.111 0.00 0.00 35.54 2.01
761 792 3.136123 CTCGCCTCCGTCCCGTAA 61.136 66.667 0.00 0.00 35.54 3.18
765 796 3.917760 CATCCTCGCCTCCGTCCC 61.918 72.222 0.00 0.00 35.54 4.46
766 797 2.833582 TCATCCTCGCCTCCGTCC 60.834 66.667 0.00 0.00 35.54 4.79
767 798 2.413765 GTCATCCTCGCCTCCGTC 59.586 66.667 0.00 0.00 35.54 4.79
769 800 1.107538 TTAGGTCATCCTCGCCTCCG 61.108 60.000 0.00 0.00 43.94 4.63
770 801 0.389757 GTTAGGTCATCCTCGCCTCC 59.610 60.000 0.00 0.00 43.94 4.30
771 802 1.404843 AGTTAGGTCATCCTCGCCTC 58.595 55.000 0.00 0.00 43.94 4.70
776 2817 7.455008 TGGGAAATAGATAGTTAGGTCATCCTC 59.545 40.741 0.00 0.00 43.94 3.71
810 2851 7.148950 GCTCTAGATCATACGGAATAAAACGTG 60.149 40.741 0.00 0.00 43.93 4.49
844 2886 2.810012 CTCGCGACGTCGGATCAGA 61.810 63.158 36.13 19.51 40.23 3.27
1121 3163 4.748798 AGAGCCTGGAGGTGGGGG 62.749 72.222 0.00 0.00 37.57 5.40
1274 3539 7.276658 GGTCTGGCTAGTGAATTAATCGATATG 59.723 40.741 0.00 0.00 0.00 1.78
1275 3540 7.324178 GGTCTGGCTAGTGAATTAATCGATAT 58.676 38.462 0.00 0.00 0.00 1.63
1321 3586 4.151157 GCTGAAACATCTGCAATTTTCACC 59.849 41.667 7.31 0.53 34.90 4.02
1464 3736 3.414700 GTGTGCAGAAGCGACCCG 61.415 66.667 0.00 0.00 46.23 5.28
1519 3791 5.615925 ACTGGACTAAGTGAAGACTTTGT 57.384 39.130 0.00 0.00 46.63 2.83
1634 3906 1.869132 GGTTAAGTCGCCACGTTTTCT 59.131 47.619 0.00 0.00 0.00 2.52
1678 3950 3.393800 CGGATGGCTCTAAATCGATTGT 58.606 45.455 12.25 4.85 0.00 2.71
1913 4289 8.518430 AGGCAAGGAAATTTAAATTGTGTTTT 57.482 26.923 14.04 0.00 0.00 2.43
2047 4423 4.323417 CAACATTTGGTAGGCTAGTGTGA 58.677 43.478 0.00 0.00 0.00 3.58
2161 4537 4.713792 AATTTTTGGTTGCCAATGGGTA 57.286 36.364 0.00 0.00 43.55 3.69
2269 4650 8.771521 AATGAAGATTGATAACATTCATGGGA 57.228 30.769 0.00 0.00 39.77 4.37
2295 4679 2.569404 GGGTGTTCTGAAGATGAGACCT 59.431 50.000 0.00 0.00 0.00 3.85
2524 4915 6.773638 AGAGAGAACTTGACAATAACCATGT 58.226 36.000 0.00 0.00 0.00 3.21
2538 4929 8.261522 ACTTAGACAAACTTGAAGAGAGAACTT 58.738 33.333 0.00 0.00 0.00 2.66
2608 5000 3.067742 ACCATACGGACCTCAACTAATCG 59.932 47.826 0.00 0.00 35.59 3.34
2683 5075 9.387123 GAAGACAAAATAGTTTAGCAACAAGAG 57.613 33.333 0.00 0.00 35.05 2.85
2721 5113 4.164843 AGCAGGTTAGACTGACCAAAAA 57.835 40.909 17.98 0.00 40.97 1.94
2722 5114 3.857157 AGCAGGTTAGACTGACCAAAA 57.143 42.857 17.98 0.00 40.97 2.44
2723 5115 3.857157 AAGCAGGTTAGACTGACCAAA 57.143 42.857 17.98 0.00 40.97 3.28
2724 5116 3.857157 AAAGCAGGTTAGACTGACCAA 57.143 42.857 17.98 0.00 40.97 3.67
2725 5117 4.967084 TTAAAGCAGGTTAGACTGACCA 57.033 40.909 17.98 0.00 40.97 4.02
2726 5118 4.636206 CCATTAAAGCAGGTTAGACTGACC 59.364 45.833 8.36 8.36 40.97 4.02
2727 5119 5.122396 CACCATTAAAGCAGGTTAGACTGAC 59.878 44.000 0.00 0.00 40.97 3.51
2728 5120 5.245531 CACCATTAAAGCAGGTTAGACTGA 58.754 41.667 0.00 0.00 40.97 3.41
2729 5121 4.396166 CCACCATTAAAGCAGGTTAGACTG 59.604 45.833 0.00 0.00 41.41 3.51
2730 5122 4.042934 ACCACCATTAAAGCAGGTTAGACT 59.957 41.667 0.00 0.00 32.15 3.24
2731 5123 4.156008 CACCACCATTAAAGCAGGTTAGAC 59.844 45.833 0.00 0.00 32.15 2.59
2732 5124 4.202524 ACACCACCATTAAAGCAGGTTAGA 60.203 41.667 0.00 0.00 32.15 2.10
2733 5125 4.079253 ACACCACCATTAAAGCAGGTTAG 58.921 43.478 0.00 0.00 32.15 2.34
2734 5126 4.107127 ACACCACCATTAAAGCAGGTTA 57.893 40.909 0.00 0.00 32.15 2.85
2735 5127 2.957474 ACACCACCATTAAAGCAGGTT 58.043 42.857 0.00 0.00 32.15 3.50
2736 5128 2.675658 ACACCACCATTAAAGCAGGT 57.324 45.000 0.00 0.00 35.65 4.00
2737 5129 4.335400 AAAACACCACCATTAAAGCAGG 57.665 40.909 0.00 0.00 0.00 4.85
2738 5130 4.024977 GCAAAAACACCACCATTAAAGCAG 60.025 41.667 0.00 0.00 0.00 4.24
2739 5131 3.873952 GCAAAAACACCACCATTAAAGCA 59.126 39.130 0.00 0.00 0.00 3.91
2740 5132 3.249799 GGCAAAAACACCACCATTAAAGC 59.750 43.478 0.00 0.00 0.00 3.51
2741 5133 4.446371 TGGCAAAAACACCACCATTAAAG 58.554 39.130 0.00 0.00 0.00 1.85
2742 5134 4.487714 TGGCAAAAACACCACCATTAAA 57.512 36.364 0.00 0.00 0.00 1.52
2743 5135 4.487714 TTGGCAAAAACACCACCATTAA 57.512 36.364 0.00 0.00 35.10 1.40
2744 5136 4.696479 ATTGGCAAAAACACCACCATTA 57.304 36.364 3.01 0.00 35.10 1.90
2745 5137 3.574354 ATTGGCAAAAACACCACCATT 57.426 38.095 3.01 0.00 35.10 3.16
2746 5138 3.574354 AATTGGCAAAAACACCACCAT 57.426 38.095 3.01 0.00 35.10 3.55
2747 5139 4.696479 ATAATTGGCAAAAACACCACCA 57.304 36.364 3.01 0.00 35.10 4.17
2748 5140 5.756849 CAAATAATTGGCAAAAACACCACC 58.243 37.500 3.01 0.00 35.10 4.61
2749 5141 5.211454 GCAAATAATTGGCAAAAACACCAC 58.789 37.500 3.01 0.00 37.02 4.16
2750 5142 4.883585 TGCAAATAATTGGCAAAAACACCA 59.116 33.333 3.01 0.00 37.02 4.17
2751 5143 5.429957 TGCAAATAATTGGCAAAAACACC 57.570 34.783 3.01 0.00 37.02 4.16
2752 5144 6.261118 TGTTGCAAATAATTGGCAAAAACAC 58.739 32.000 3.01 0.00 35.70 3.32
2753 5145 6.317140 TCTGTTGCAAATAATTGGCAAAAACA 59.683 30.769 3.01 3.67 35.70 2.83
2754 5146 6.723282 TCTGTTGCAAATAATTGGCAAAAAC 58.277 32.000 3.01 0.00 35.70 2.43
2755 5147 6.932356 TCTGTTGCAAATAATTGGCAAAAA 57.068 29.167 3.01 0.00 35.70 1.94
2756 5148 6.932356 TTCTGTTGCAAATAATTGGCAAAA 57.068 29.167 3.01 3.20 35.70 2.44
2757 5149 6.932356 TTTCTGTTGCAAATAATTGGCAAA 57.068 29.167 3.01 0.00 35.70 3.68
2758 5150 6.932356 TTTTCTGTTGCAAATAATTGGCAA 57.068 29.167 0.00 0.68 37.02 4.52
2759 5151 6.932356 TTTTTCTGTTGCAAATAATTGGCA 57.068 29.167 0.00 0.00 37.02 4.92
2780 5172 3.864243 CCACATATGCAGGCATGTTTTT 58.136 40.909 16.61 0.00 37.82 1.94
2848 5328 2.505407 TGCTGCCACCATAGTTATCTGT 59.495 45.455 0.00 0.00 0.00 3.41
2925 5405 0.391661 CCTGCACGCAAGGTAGATGT 60.392 55.000 0.00 0.00 46.39 3.06
2970 5465 3.420893 ACCATTGAGCGGAGAAAAATGA 58.579 40.909 0.00 0.00 31.34 2.57
3004 5499 2.675348 GCAGTAGCTGACAAGATGAACC 59.325 50.000 0.00 0.00 37.91 3.62
3288 5783 1.187087 GATCGAGTGGTCAAGAGGGT 58.813 55.000 0.00 0.00 0.00 4.34
3565 6060 1.202463 CCGACAGGTCCATCATCAGTC 60.202 57.143 0.00 0.00 0.00 3.51
3593 6089 7.444487 CACTCATCATGACTGATATCAACCAAT 59.556 37.037 6.90 0.00 40.20 3.16
3677 6175 7.272084 GTGACAACAGAAATGCAATTCTCATAC 59.728 37.037 14.19 6.25 37.56 2.39
3806 6305 1.753073 CTGGAAAAGCAGGGCATAAGG 59.247 52.381 0.00 0.00 0.00 2.69
3842 6345 5.989477 TCCTTCTTCAAAACTCTCACAAGA 58.011 37.500 0.00 0.00 0.00 3.02
3852 6355 8.079809 TGGACGAAATATTTCCTTCTTCAAAAC 58.920 33.333 20.01 5.56 33.68 2.43
3913 6416 2.590575 ACTCCACCAAACACGCCG 60.591 61.111 0.00 0.00 0.00 6.46
3932 6435 3.753272 TCAAGCCTCCTTCAAAATTCTCG 59.247 43.478 0.00 0.00 0.00 4.04
3963 6468 4.624024 CCAAACACATAAGAATGCAAGCTG 59.376 41.667 0.00 0.00 36.50 4.24
4032 6545 6.200286 CGGCGATCTACAATATAAACTGTGTT 59.800 38.462 0.00 0.00 0.00 3.32
4055 6568 1.600957 CACTGCCATCTAGAATTGCGG 59.399 52.381 15.10 15.10 0.00 5.69
4056 6569 2.543012 CTCACTGCCATCTAGAATTGCG 59.457 50.000 0.00 0.05 0.00 4.85
4066 6579 2.507339 GAGCTCTACTCACTGCCATC 57.493 55.000 6.43 0.00 45.49 3.51
4110 6623 6.015180 TGCTGCTCTTTCCAATGTAGAATTTT 60.015 34.615 0.00 0.00 0.00 1.82
4134 6665 5.350914 TCAAAGAACAAGGCAAACAACATTG 59.649 36.000 0.00 0.00 0.00 2.82
4261 6847 8.511604 TGTACTACTCCCTTTGTACACTATAC 57.488 38.462 0.00 0.00 39.85 1.47
4262 6848 9.128404 CATGTACTACTCCCTTTGTACACTATA 57.872 37.037 0.00 0.00 44.94 1.31
4263 6849 7.417570 GCATGTACTACTCCCTTTGTACACTAT 60.418 40.741 0.00 0.00 44.94 2.12
4273 6986 3.055094 CCACAAGCATGTACTACTCCCTT 60.055 47.826 0.00 0.00 37.82 3.95
4278 6991 2.615493 GCCACCACAAGCATGTACTACT 60.615 50.000 0.00 0.00 37.82 2.57
4279 6992 1.737793 GCCACCACAAGCATGTACTAC 59.262 52.381 0.00 0.00 37.82 2.73
4280 6993 1.349357 TGCCACCACAAGCATGTACTA 59.651 47.619 0.00 0.00 37.82 1.82
4289 7002 4.789012 ATTGTAAGAATGCCACCACAAG 57.211 40.909 0.00 0.00 30.23 3.16
4306 7019 7.822822 GTGTAGTTACCTTGTTCCTGATATTGT 59.177 37.037 0.00 0.00 0.00 2.71
4319 7032 3.240069 CGAGTTCGGTGTAGTTACCTTG 58.760 50.000 0.00 0.00 38.62 3.61
4320 7033 2.887152 ACGAGTTCGGTGTAGTTACCTT 59.113 45.455 6.48 0.00 44.95 3.50
4328 7041 3.628942 AGCATGTATACGAGTTCGGTGTA 59.371 43.478 6.48 0.00 44.95 2.90
4433 7173 0.984230 TTCTCGCCCTTGTTCTCCAT 59.016 50.000 0.00 0.00 0.00 3.41
4447 7187 0.817634 TGTGTTTGGTGGCCTTCTCG 60.818 55.000 3.32 0.00 0.00 4.04
4480 7220 1.598130 GCAACAGACTCCACGCCTT 60.598 57.895 0.00 0.00 0.00 4.35
4530 7270 6.745116 TCTCTGTAGAAGACAAAAATCACGA 58.255 36.000 0.00 0.00 37.70 4.35
4534 7274 9.606631 ACCATATCTCTGTAGAAGACAAAAATC 57.393 33.333 0.00 0.00 37.70 2.17
4551 7291 9.950496 ACCATATCAGAAACATAACCATATCTC 57.050 33.333 0.00 0.00 0.00 2.75
4568 7446 8.366401 AGAAAGAGATGTATCACACCATATCAG 58.634 37.037 0.00 0.00 32.96 2.90


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

AutoCloner maintained by Alex Coulton.