Multiple sequence alignment - TraesCS1D01G376200

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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 TraesCS1D01G376200 chr1D 100.000 2712 0 0 1 2712 452619793 452622504 0.000000e+00 5009
1 TraesCS1D01G376200 chr1D 87.535 722 59 17 1014 1722 435274487 435273784 0.000000e+00 806
2 TraesCS1D01G376200 chr1B 92.621 1423 71 12 1312 2711 622701239 622702650 0.000000e+00 2015
3 TraesCS1D01G376200 chr1B 87.049 749 57 24 989 1722 588498486 588497763 0.000000e+00 809
4 TraesCS1D01G376200 chr1B 93.534 464 22 3 812 1274 622700382 622700838 0.000000e+00 684
5 TraesCS1D01G376200 chr1B 85.203 615 69 14 23 627 622699579 622700181 1.780000e-171 612
6 TraesCS1D01G376200 chr1B 87.006 177 19 2 625 797 622700222 622700398 2.130000e-46 196
7 TraesCS1D01G376200 chr2D 90.446 1120 73 16 1081 2174 25919670 25918559 0.000000e+00 1445
8 TraesCS1D01G376200 chr1A 88.085 1217 67 26 861 2045 547384729 547385899 0.000000e+00 1373
9 TraesCS1D01G376200 chr1A 88.509 731 51 15 1014 1722 532776362 532775643 0.000000e+00 854
10 TraesCS1D01G376200 chr1A 82.744 707 90 19 1037 1729 532762222 532761534 3.860000e-168 601
11 TraesCS1D01G376200 chr1A 86.052 423 35 10 23 442 547383873 547384274 1.490000e-117 433
12 TraesCS1D01G376200 chr1A 92.342 222 13 4 2494 2712 547387608 547387828 2.030000e-81 313
13 TraesCS1D01G376200 chr1A 93.122 189 12 1 1995 2183 547385894 547386081 2.660000e-70 276
14 TraesCS1D01G376200 chr1A 93.827 81 1 2 2429 2506 547386076 547386155 4.740000e-23 119
15 TraesCS1D01G376200 chr7A 87.898 1132 72 23 1073 2179 10419848 10418757 0.000000e+00 1271
16 TraesCS1D01G376200 chr7A 89.024 82 9 0 2610 2691 10418675 10418594 4.780000e-18 102
17 TraesCS1D01G376200 chr6A 88.186 838 64 16 1185 1995 407124008 407124837 0.000000e+00 966
18 TraesCS1D01G376200 chr2A 88.485 165 15 4 2018 2179 767489301 767489138 2.130000e-46 196
19 TraesCS1D01G376200 chr2A 89.024 82 9 0 2610 2691 767489056 767488975 4.780000e-18 102


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 TraesCS1D01G376200 chr1D 452619793 452622504 2711 False 5009.00 5009 100.0000 1 2712 1 chr1D.!!$F1 2711
1 TraesCS1D01G376200 chr1D 435273784 435274487 703 True 806.00 806 87.5350 1014 1722 1 chr1D.!!$R1 708
2 TraesCS1D01G376200 chr1B 622699579 622702650 3071 False 876.75 2015 89.5910 23 2711 4 chr1B.!!$F1 2688
3 TraesCS1D01G376200 chr1B 588497763 588498486 723 True 809.00 809 87.0490 989 1722 1 chr1B.!!$R1 733
4 TraesCS1D01G376200 chr2D 25918559 25919670 1111 True 1445.00 1445 90.4460 1081 2174 1 chr2D.!!$R1 1093
5 TraesCS1D01G376200 chr1A 532775643 532776362 719 True 854.00 854 88.5090 1014 1722 1 chr1A.!!$R2 708
6 TraesCS1D01G376200 chr1A 532761534 532762222 688 True 601.00 601 82.7440 1037 1729 1 chr1A.!!$R1 692
7 TraesCS1D01G376200 chr1A 547383873 547387828 3955 False 502.80 1373 90.6856 23 2712 5 chr1A.!!$F1 2689
8 TraesCS1D01G376200 chr7A 10418594 10419848 1254 True 686.50 1271 88.4610 1073 2691 2 chr7A.!!$R1 1618
9 TraesCS1D01G376200 chr6A 407124008 407124837 829 False 966.00 966 88.1860 1185 1995 1 chr6A.!!$F1 810

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
367 373 0.035317 TGCTACCTCCACAGCAACAG 59.965 55.0 0.0 0.0 44.49 3.16 F
369 375 0.035317 CTACCTCCACAGCAACAGCA 59.965 55.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 2005 0.108207 CAGATCAGGGTGGCATCCTC 59.892 60.0 18.61 6.35 31.06 3.71 R
2027 2733 0.390340 CAGAGCAGCGGCAGAAGTAA 60.390 55.0 12.44 0.00 44.61 2.24 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
49 50 5.450818 TTTGAACCCCTATGCTATGTTCT 57.549 39.130 0.00 0.00 36.98 3.01
50 51 4.422073 TGAACCCCTATGCTATGTTCTG 57.578 45.455 0.00 0.00 36.98 3.02
51 52 4.037222 TGAACCCCTATGCTATGTTCTGA 58.963 43.478 0.00 0.00 36.98 3.27
68 69 8.969260 ATGTTCTGAATGCTATTGATCTGTTA 57.031 30.769 0.00 0.00 0.00 2.41
69 70 8.969260 TGTTCTGAATGCTATTGATCTGTTAT 57.031 30.769 0.00 0.00 0.00 1.89
111 112 8.644216 TCATTTTATTGCCATCTGATTTAGCAT 58.356 29.630 7.39 2.75 32.67 3.79
113 114 4.866508 ATTGCCATCTGATTTAGCATGG 57.133 40.909 7.39 0.00 37.25 3.66
118 119 4.261489 GCCATCTGATTTAGCATGGTTGAG 60.261 45.833 1.12 0.00 36.89 3.02
124 125 6.061022 TGATTTAGCATGGTTGAGGTTCTA 57.939 37.500 1.12 0.00 0.00 2.10
131 132 6.426587 AGCATGGTTGAGGTTCTAAATGTAT 58.573 36.000 0.00 0.00 0.00 2.29
172 173 2.846371 GCCCTCCATGCGATGTATC 58.154 57.895 0.00 0.00 0.00 2.24
182 183 1.001974 TGCGATGTATCTGGCCATACC 59.998 52.381 5.51 0.00 39.84 2.73
186 187 3.494223 CGATGTATCTGGCCATACCACAA 60.494 47.826 5.51 0.00 46.36 3.33
197 198 4.460263 GCCATACCACAATGTCTCCATTA 58.540 43.478 0.00 0.00 39.28 1.90
203 204 3.243301 CCACAATGTCTCCATTAGCATGC 60.243 47.826 10.51 10.51 39.28 4.06
240 242 0.179134 AGCAGTTGTATCGACGAGGC 60.179 55.000 3.01 0.00 0.00 4.70
244 246 2.930040 CAGTTGTATCGACGAGGCATTT 59.070 45.455 3.01 0.00 0.00 2.32
366 372 2.141312 TGCTACCTCCACAGCAACA 58.859 52.632 0.00 0.00 44.49 3.33
367 373 0.035317 TGCTACCTCCACAGCAACAG 59.965 55.000 0.00 0.00 44.49 3.16
368 374 1.301677 GCTACCTCCACAGCAACAGC 61.302 60.000 0.00 0.00 37.73 4.40
369 375 0.035317 CTACCTCCACAGCAACAGCA 59.965 55.000 0.00 0.00 0.00 4.41
371 377 2.623915 CCTCCACAGCAACAGCAGC 61.624 63.158 0.00 0.00 0.00 5.25
373 379 1.152902 TCCACAGCAACAGCAGCTT 60.153 52.632 0.00 0.00 41.14 3.74
374 380 1.007734 CCACAGCAACAGCAGCTTG 60.008 57.895 0.00 0.00 41.14 4.01
375 381 1.731433 CCACAGCAACAGCAGCTTGT 61.731 55.000 0.00 0.00 41.14 3.16
376 382 0.594028 CACAGCAACAGCAGCTTGTG 60.594 55.000 9.29 9.29 41.14 3.33
388 395 2.159421 GCAGCTTGTGTTCAGATGATGG 60.159 50.000 0.00 0.00 0.00 3.51
389 396 2.089980 AGCTTGTGTTCAGATGATGGC 58.910 47.619 0.00 0.00 0.00 4.40
404 411 4.901197 TGATGGCTGTTACCAAAGTCTA 57.099 40.909 0.00 0.00 44.65 2.59
407 415 5.705441 TGATGGCTGTTACCAAAGTCTAAAG 59.295 40.000 0.00 0.00 44.65 1.85
410 418 4.151867 GGCTGTTACCAAAGTCTAAAGTCG 59.848 45.833 0.00 0.00 0.00 4.18
439 447 4.202161 ACTTTGTGTGGTTGTGTTTGAACA 60.202 37.500 0.00 0.00 36.38 3.18
460 468 4.018960 ACATCCTGAACATCTTTAGCACCT 60.019 41.667 0.00 0.00 0.00 4.00
472 480 3.868619 TTAGCACCTTGTACCCTGTTT 57.131 42.857 0.00 0.00 0.00 2.83
475 483 4.173290 AGCACCTTGTACCCTGTTTTTA 57.827 40.909 0.00 0.00 0.00 1.52
477 485 3.633065 GCACCTTGTACCCTGTTTTTACA 59.367 43.478 0.00 0.00 0.00 2.41
504 518 5.378230 TTGCACTCCATGGATCTTTATCT 57.622 39.130 16.63 0.00 32.29 1.98
532 628 3.223674 TGATGTCGTATCTGCCTCCTA 57.776 47.619 4.56 0.00 0.00 2.94
548 644 4.802248 GCCTCCTACCATCTGTGAATGATC 60.802 50.000 0.00 0.00 0.00 2.92
558 654 6.400834 CCATCTGTGAATGATCGAATCGAATC 60.401 42.308 10.12 8.60 39.99 2.52
559 655 5.591099 TCTGTGAATGATCGAATCGAATCA 58.409 37.500 10.12 13.83 39.99 2.57
560 656 6.218746 TCTGTGAATGATCGAATCGAATCAT 58.781 36.000 10.12 15.37 39.99 2.45
565 661 6.646240 TGAATGATCGAATCGAATCATAGCAA 59.354 34.615 21.46 11.10 39.99 3.91
627 723 2.351738 GGTTTTTCATGTTCCTGCGAGG 60.352 50.000 0.00 0.00 36.46 4.63
628 724 2.552315 GTTTTTCATGTTCCTGCGAGGA 59.448 45.455 1.25 1.25 44.10 3.71
654 794 2.029073 CAGCACGGACCAACGTCT 59.971 61.111 0.00 0.00 46.75 4.18
682 822 1.271102 GCCGCCACATTTCCTTTTACA 59.729 47.619 0.00 0.00 0.00 2.41
698 838 4.510038 TTTACAGGAACTACAGACGGAC 57.490 45.455 0.00 0.00 36.02 4.79
711 854 4.465886 ACAGACGGACTAGCTGATATCTT 58.534 43.478 3.98 0.00 33.94 2.40
722 865 8.184304 ACTAGCTGATATCTTACCTCGATTTT 57.816 34.615 3.98 0.00 0.00 1.82
726 869 8.085296 AGCTGATATCTTACCTCGATTTTACTG 58.915 37.037 3.98 0.00 0.00 2.74
734 877 5.012328 ACCTCGATTTTACTGGAGATGTC 57.988 43.478 0.00 0.00 0.00 3.06
737 880 3.446161 TCGATTTTACTGGAGATGTCGGT 59.554 43.478 0.00 0.00 0.00 4.69
756 899 5.758296 GTCGGTAGCAAATTGGATGAATCTA 59.242 40.000 0.00 0.00 0.00 1.98
759 902 7.173218 TCGGTAGCAAATTGGATGAATCTATTC 59.827 37.037 0.00 0.00 37.31 1.75
787 963 3.577649 TGTTCGACAGAGTCTGAATCC 57.422 47.619 26.86 10.97 35.18 3.01
788 964 2.890945 TGTTCGACAGAGTCTGAATCCA 59.109 45.455 26.86 12.50 35.18 3.41
789 965 3.320826 TGTTCGACAGAGTCTGAATCCAA 59.679 43.478 26.86 6.91 35.18 3.53
790 966 4.021104 TGTTCGACAGAGTCTGAATCCAAT 60.021 41.667 26.86 1.65 35.18 3.16
791 967 4.808414 TCGACAGAGTCTGAATCCAATT 57.192 40.909 26.86 0.83 35.18 2.32
792 968 5.152623 TCGACAGAGTCTGAATCCAATTT 57.847 39.130 26.86 0.04 35.18 1.82
793 969 5.171476 TCGACAGAGTCTGAATCCAATTTC 58.829 41.667 26.86 9.09 35.18 2.17
794 970 4.331168 CGACAGAGTCTGAATCCAATTTCC 59.669 45.833 26.86 0.67 35.18 3.13
795 971 5.495640 GACAGAGTCTGAATCCAATTTCCT 58.504 41.667 26.86 0.00 35.18 3.36
796 972 5.885465 ACAGAGTCTGAATCCAATTTCCTT 58.115 37.500 26.86 0.00 35.18 3.36
797 973 6.310149 ACAGAGTCTGAATCCAATTTCCTTT 58.690 36.000 26.86 0.00 35.18 3.11
798 974 6.779539 ACAGAGTCTGAATCCAATTTCCTTTT 59.220 34.615 26.86 0.00 35.18 2.27
799 975 7.288621 ACAGAGTCTGAATCCAATTTCCTTTTT 59.711 33.333 26.86 0.00 35.18 1.94
850 1026 5.630061 TGTGCATTTTGTATTCTGATCGTG 58.370 37.500 0.00 0.00 0.00 4.35
855 1031 4.944962 TTTGTATTCTGATCGTGCCAAG 57.055 40.909 0.00 0.00 0.00 3.61
869 1119 3.365265 CAAGTGGGCTGGCGGTTC 61.365 66.667 0.00 0.00 0.00 3.62
901 1151 2.106332 GGGTCCAGTACATCGGCG 59.894 66.667 0.00 0.00 0.00 6.46
966 1229 1.001631 TCTCTCGCTCCATCCCCAA 59.998 57.895 0.00 0.00 0.00 4.12
967 1230 1.144936 CTCTCGCTCCATCCCCAAC 59.855 63.158 0.00 0.00 0.00 3.77
968 1231 1.612146 TCTCGCTCCATCCCCAACA 60.612 57.895 0.00 0.00 0.00 3.33
969 1232 0.982852 TCTCGCTCCATCCCCAACAT 60.983 55.000 0.00 0.00 0.00 2.71
970 1233 0.533755 CTCGCTCCATCCCCAACATC 60.534 60.000 0.00 0.00 0.00 3.06
1182 1452 4.690719 CGCAACCCCGTGCACCTA 62.691 66.667 12.15 0.00 45.19 3.08
1295 1585 1.139095 CCCACTTCGTACGCTCCTC 59.861 63.158 11.24 0.00 0.00 3.71
1308 1963 1.541672 CTCCTCTCCTCCCCCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
1309 1964 0.998945 CTCCTCTCCTCCCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
1325 1980 0.097674 CTCTTTGCCATTTCGCCGAG 59.902 55.000 0.00 0.00 0.00 4.63
1341 1996 3.633609 GAGCAGCTGGTGGGCATGA 62.634 63.158 25.60 0.00 34.17 3.07
1347 2005 4.343323 TGGTGGGCATGACGGGTG 62.343 66.667 0.00 0.00 0.00 4.61
1353 2015 1.524621 GGCATGACGGGTGAGGATG 60.525 63.158 0.00 0.00 0.00 3.51
1542 2223 3.891049 AGCGCCATTTTTCTATCTCCTT 58.109 40.909 2.29 0.00 0.00 3.36
1559 2240 4.702131 TCTCCTTTTCTTTCTAGCATTGCC 59.298 41.667 4.70 0.00 0.00 4.52
1617 2298 2.954753 GCGTCAAGTTCGCCACCAG 61.955 63.158 0.00 0.00 46.61 4.00
1722 2404 4.868171 GGCAATCGAGTGACAAGTATGTTA 59.132 41.667 18.43 0.00 40.74 2.41
1723 2405 5.523916 GGCAATCGAGTGACAAGTATGTTAT 59.476 40.000 18.43 0.00 40.74 1.89
1724 2406 6.414079 GCAATCGAGTGACAAGTATGTTATG 58.586 40.000 18.43 0.00 40.74 1.90
1725 2407 6.036083 GCAATCGAGTGACAAGTATGTTATGT 59.964 38.462 18.43 0.00 40.74 2.29
1726 2408 7.413000 GCAATCGAGTGACAAGTATGTTATGTT 60.413 37.037 18.43 0.00 40.74 2.71
1782 2476 5.957798 TCTCATGATGAAACATTTTGCCTC 58.042 37.500 0.00 0.00 0.00 4.70
1837 2542 4.491676 TGGTAATAGTTCGTTGCAGTCTC 58.508 43.478 0.00 0.00 0.00 3.36
1980 2685 6.747414 TGAACCACTAGGCATATTCAGTAT 57.253 37.500 0.00 0.00 39.06 2.12
1981 2686 6.524734 TGAACCACTAGGCATATTCAGTATG 58.475 40.000 0.00 0.00 42.57 2.39
2004 2710 4.099266 GGATCACTTCAGTCTGCTCAGTAT 59.901 45.833 0.00 0.00 0.00 2.12
2027 2733 2.092538 ACTTCTTGCTGCTGCTCCATAT 60.093 45.455 17.00 0.00 40.48 1.78
2030 2736 3.470709 TCTTGCTGCTGCTCCATATTAC 58.529 45.455 17.00 0.00 40.48 1.89
2075 2827 7.119992 GTGAAGAGAGGAAGAAAGGAAATAACC 59.880 40.741 0.00 0.00 0.00 2.85
2150 2902 8.093927 ACTGAAATCTTCTAGGAACTGAAGAAG 58.906 37.037 9.07 5.20 46.80 2.85
2235 2987 8.549548 TGCTTGTATCATGTTTGTTTGAATTTG 58.450 29.630 0.00 0.00 0.00 2.32
2238 2990 7.849496 TGTATCATGTTTGTTTGAATTTGCAC 58.151 30.769 0.00 0.00 0.00 4.57
2239 2991 5.731599 TCATGTTTGTTTGAATTTGCACC 57.268 34.783 0.00 0.00 0.00 5.01
2246 2998 2.736192 GTTTGAATTTGCACCGGATTGG 59.264 45.455 9.46 0.00 46.41 3.16
2261 3013 5.615289 CCGGATTGGTTCTTCATTAGAGAT 58.385 41.667 0.00 0.00 33.51 2.75
2277 3029 6.968131 TTAGAGATCGACTCCAACAATTTG 57.032 37.500 10.24 0.00 45.96 2.32
2279 3031 5.551233 AGAGATCGACTCCAACAATTTGAA 58.449 37.500 2.79 0.00 45.96 2.69
2291 3043 6.267471 TCCAACAATTTGAACTCTTAGCCAAT 59.733 34.615 2.79 0.00 34.24 3.16
2333 3085 1.596260 CACGCTCATATTGTGCTCTGG 59.404 52.381 0.82 0.00 34.97 3.86
2366 3118 3.507622 GGAAAGTGGGAGAAGGAACAATG 59.492 47.826 0.00 0.00 0.00 2.82
2369 3121 2.307098 AGTGGGAGAAGGAACAATGGAG 59.693 50.000 0.00 0.00 0.00 3.86
2395 3147 3.836562 GAGAAGTAAGGCGGGGGATAATA 59.163 47.826 0.00 0.00 0.00 0.98
2528 4747 0.690762 ACAGTAAGCATCAACCCCGT 59.309 50.000 0.00 0.00 0.00 5.28
2682 4904 3.879295 ACAATAGAATTGATGACCGCCTG 59.121 43.478 6.64 0.00 0.00 4.85
2696 4918 0.965866 CGCCTGTAGGACTGACTGGA 60.966 60.000 1.17 0.00 37.96 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.772393 AGATATGGGTACAACAGTTTGGA 57.228 39.130 0.00 0.00 37.00 3.53
2 3 8.964476 ATAGAAGATATGGGTACAACAGTTTG 57.036 34.615 0.00 0.00 38.83 2.93
3 4 9.975218 AAATAGAAGATATGGGTACAACAGTTT 57.025 29.630 0.00 0.00 0.00 2.66
4 5 9.396022 CAAATAGAAGATATGGGTACAACAGTT 57.604 33.333 0.00 0.00 0.00 3.16
5 6 8.768397 TCAAATAGAAGATATGGGTACAACAGT 58.232 33.333 0.00 0.00 0.00 3.55
6 7 9.613428 TTCAAATAGAAGATATGGGTACAACAG 57.387 33.333 0.00 0.00 0.00 3.16
7 8 9.391006 GTTCAAATAGAAGATATGGGTACAACA 57.609 33.333 0.00 0.00 36.78 3.33
8 9 8.837389 GGTTCAAATAGAAGATATGGGTACAAC 58.163 37.037 0.00 0.00 36.78 3.32
9 10 7.996644 GGGTTCAAATAGAAGATATGGGTACAA 59.003 37.037 0.00 0.00 36.78 2.41
10 11 7.420913 GGGGTTCAAATAGAAGATATGGGTACA 60.421 40.741 0.00 0.00 36.78 2.90
11 12 6.940867 GGGGTTCAAATAGAAGATATGGGTAC 59.059 42.308 0.00 0.00 36.78 3.34
12 13 6.855061 AGGGGTTCAAATAGAAGATATGGGTA 59.145 38.462 0.00 0.00 36.78 3.69
13 14 5.676811 AGGGGTTCAAATAGAAGATATGGGT 59.323 40.000 0.00 0.00 36.78 4.51
14 15 6.206180 AGGGGTTCAAATAGAAGATATGGG 57.794 41.667 0.00 0.00 36.78 4.00
15 16 7.337942 GCATAGGGGTTCAAATAGAAGATATGG 59.662 40.741 0.00 0.00 36.78 2.74
16 17 8.105829 AGCATAGGGGTTCAAATAGAAGATATG 58.894 37.037 0.00 0.00 36.78 1.78
17 18 8.224620 AGCATAGGGGTTCAAATAGAAGATAT 57.775 34.615 0.00 0.00 36.78 1.63
18 19 7.633018 AGCATAGGGGTTCAAATAGAAGATA 57.367 36.000 0.00 0.00 36.78 1.98
19 20 6.521527 AGCATAGGGGTTCAAATAGAAGAT 57.478 37.500 0.00 0.00 36.78 2.40
20 21 5.975988 AGCATAGGGGTTCAAATAGAAGA 57.024 39.130 0.00 0.00 36.78 2.87
21 22 7.227156 ACATAGCATAGGGGTTCAAATAGAAG 58.773 38.462 0.00 0.00 36.78 2.85
49 50 8.510243 ACACAATAACAGATCAATAGCATTCA 57.490 30.769 0.00 0.00 0.00 2.57
50 51 9.793252 AAACACAATAACAGATCAATAGCATTC 57.207 29.630 0.00 0.00 0.00 2.67
51 52 9.793252 GAAACACAATAACAGATCAATAGCATT 57.207 29.630 0.00 0.00 0.00 3.56
111 112 9.016438 GGTAAAATACATTTAGAACCTCAACCA 57.984 33.333 6.56 0.00 34.21 3.67
131 132 5.163581 GCGACTACCTCAGATACTGGTAAAA 60.164 44.000 0.00 0.00 36.11 1.52
172 173 5.519068 TGGAGACATTGTGGTATGGCCAG 62.519 52.174 13.05 0.00 41.94 4.85
197 198 1.696063 AAACAAGTGGACAGCATGCT 58.304 45.000 16.30 16.30 42.53 3.79
226 228 7.956420 ATATTAAAATGCCTCGTCGATACAA 57.044 32.000 0.00 0.00 0.00 2.41
254 259 7.759489 ACACCAGAAGCTCATGTTTTAATAA 57.241 32.000 0.00 0.00 0.00 1.40
255 260 7.592938 CAACACCAGAAGCTCATGTTTTAATA 58.407 34.615 0.00 0.00 31.25 0.98
264 269 1.072806 TCTGCAACACCAGAAGCTCAT 59.927 47.619 0.00 0.00 38.81 2.90
266 271 1.597742 TTCTGCAACACCAGAAGCTC 58.402 50.000 0.81 0.00 44.49 4.09
267 272 3.806941 TTCTGCAACACCAGAAGCT 57.193 47.368 0.81 0.00 44.49 3.74
364 370 1.878088 CATCTGAACACAAGCTGCTGT 59.122 47.619 1.35 0.48 0.00 4.40
366 372 2.556144 TCATCTGAACACAAGCTGCT 57.444 45.000 0.00 0.00 0.00 4.24
367 373 2.159421 CCATCATCTGAACACAAGCTGC 60.159 50.000 0.00 0.00 0.00 5.25
368 374 2.159421 GCCATCATCTGAACACAAGCTG 60.159 50.000 0.00 0.00 0.00 4.24
369 375 2.089980 GCCATCATCTGAACACAAGCT 58.910 47.619 0.00 0.00 0.00 3.74
371 377 3.079578 ACAGCCATCATCTGAACACAAG 58.920 45.455 0.00 0.00 35.61 3.16
373 379 2.865119 ACAGCCATCATCTGAACACA 57.135 45.000 0.00 0.00 35.61 3.72
374 380 3.375299 GGTAACAGCCATCATCTGAACAC 59.625 47.826 0.00 0.00 35.61 3.32
375 381 3.008923 TGGTAACAGCCATCATCTGAACA 59.991 43.478 0.00 0.00 46.17 3.18
376 382 3.609853 TGGTAACAGCCATCATCTGAAC 58.390 45.455 0.00 0.00 46.17 3.18
404 411 2.097466 CACACAAAGTGCCTTCGACTTT 59.903 45.455 0.00 0.00 43.01 2.66
407 415 3.825812 CACACAAAGTGCCTTCGAC 57.174 52.632 0.00 0.00 42.15 4.20
439 447 4.851639 AGGTGCTAAAGATGTTCAGGAT 57.148 40.909 0.00 0.00 0.00 3.24
460 468 7.014326 TGCAATACATGTAAAAACAGGGTACAA 59.986 33.333 10.14 0.00 31.85 2.41
472 480 5.504853 TCCATGGAGTGCAATACATGTAAA 58.495 37.500 31.40 17.44 39.14 2.01
475 483 3.650281 TCCATGGAGTGCAATACATGT 57.350 42.857 31.40 2.69 39.14 3.21
477 485 4.719026 AGATCCATGGAGTGCAATACAT 57.281 40.909 21.33 5.92 0.00 2.29
504 518 4.363138 GCAGATACGACATCATGAACAGA 58.637 43.478 0.00 0.00 0.00 3.41
532 628 4.053983 CGATTCGATCATTCACAGATGGT 58.946 43.478 0.00 0.00 0.00 3.55
548 644 4.777140 TGTGTTGCTATGATTCGATTCG 57.223 40.909 0.00 0.00 0.00 3.34
565 661 5.359576 ACAACATACCAACTTCAACATGTGT 59.640 36.000 0.00 0.00 0.00 3.72
581 677 5.757320 AGAGCATAGCATCTCAACAACATAC 59.243 40.000 0.00 0.00 0.00 2.39
582 678 5.756833 CAGAGCATAGCATCTCAACAACATA 59.243 40.000 0.00 0.00 0.00 2.29
636 776 3.041940 GACGTTGGTCCGTGCTGG 61.042 66.667 0.00 0.00 41.98 4.85
637 777 2.029073 AGACGTTGGTCCGTGCTG 59.971 61.111 0.00 0.00 44.54 4.41
642 782 2.738521 CCAGCAGACGTTGGTCCG 60.739 66.667 0.00 0.00 44.54 4.79
644 784 2.280797 TGCCAGCAGACGTTGGTC 60.281 61.111 5.91 0.00 44.96 4.02
682 822 2.026075 AGCTAGTCCGTCTGTAGTTCCT 60.026 50.000 0.00 0.00 0.00 3.36
694 834 4.093703 CGAGGTAAGATATCAGCTAGTCCG 59.906 50.000 5.32 0.00 0.00 4.79
696 836 6.995511 ATCGAGGTAAGATATCAGCTAGTC 57.004 41.667 5.32 0.00 0.00 2.59
698 838 9.562583 GTAAAATCGAGGTAAGATATCAGCTAG 57.437 37.037 5.32 1.15 0.00 3.42
711 854 5.220989 CGACATCTCCAGTAAAATCGAGGTA 60.221 44.000 0.00 0.00 0.00 3.08
722 865 2.430248 TGCTACCGACATCTCCAGTA 57.570 50.000 0.00 0.00 0.00 2.74
726 869 2.614057 CCAATTTGCTACCGACATCTCC 59.386 50.000 0.00 0.00 0.00 3.71
734 877 6.808008 ATAGATTCATCCAATTTGCTACCG 57.192 37.500 0.00 0.00 0.00 4.02
737 880 6.712095 AGCGAATAGATTCATCCAATTTGCTA 59.288 34.615 17.79 0.00 42.55 3.49
756 899 3.909430 TCTGTCGAACAGTTTAGCGAAT 58.091 40.909 12.62 0.00 46.03 3.34
759 902 2.657372 GACTCTGTCGAACAGTTTAGCG 59.343 50.000 12.62 0.00 46.03 4.26
800 976 7.069826 AGGAAATTGGATTCAGTGTCTCAAAAA 59.930 33.333 0.00 0.00 0.00 1.94
801 977 6.550854 AGGAAATTGGATTCAGTGTCTCAAAA 59.449 34.615 0.00 0.00 0.00 2.44
802 978 6.070656 AGGAAATTGGATTCAGTGTCTCAAA 58.929 36.000 0.00 0.00 0.00 2.69
803 979 5.634118 AGGAAATTGGATTCAGTGTCTCAA 58.366 37.500 0.00 0.00 0.00 3.02
804 980 5.246981 AGGAAATTGGATTCAGTGTCTCA 57.753 39.130 0.00 0.00 0.00 3.27
805 981 5.474876 ACAAGGAAATTGGATTCAGTGTCTC 59.525 40.000 0.00 0.00 43.68 3.36
806 982 5.242393 CACAAGGAAATTGGATTCAGTGTCT 59.758 40.000 0.00 0.00 43.68 3.41
807 983 5.464168 CACAAGGAAATTGGATTCAGTGTC 58.536 41.667 0.00 0.00 43.68 3.67
808 984 4.262164 GCACAAGGAAATTGGATTCAGTGT 60.262 41.667 0.00 0.00 43.68 3.55
809 985 4.240096 GCACAAGGAAATTGGATTCAGTG 58.760 43.478 0.00 0.00 43.68 3.66
810 986 3.896888 TGCACAAGGAAATTGGATTCAGT 59.103 39.130 0.00 0.00 43.68 3.41
869 1119 2.828549 CCCGGCCCAAGAAATCGG 60.829 66.667 0.00 0.00 40.32 4.18
928 1190 1.172812 GGCCACGGCAAAGAAGAACT 61.173 55.000 10.83 0.00 44.11 3.01
983 1246 2.024306 GCATCCCTGGTAGCTTTTCCC 61.024 57.143 0.00 0.00 0.00 3.97
996 1259 3.069980 GCTGACGAGACGCATCCCT 62.070 63.158 0.00 0.00 0.00 4.20
1176 1445 1.516603 GAAGGCGTCGTCTAGGTGC 60.517 63.158 0.00 0.00 0.00 5.01
1295 1585 1.631071 GGCAAAGAGAGGGGGAGGAG 61.631 65.000 0.00 0.00 0.00 3.69
1308 1963 1.514873 GCTCGGCGAAATGGCAAAG 60.515 57.895 12.13 0.00 45.16 2.77
1309 1964 2.198906 CTGCTCGGCGAAATGGCAAA 62.199 55.000 19.73 1.65 45.16 3.68
1325 1980 3.446570 GTCATGCCCACCAGCTGC 61.447 66.667 8.66 0.00 0.00 5.25
1341 1996 3.717294 GGTGGCATCCTCACCCGT 61.717 66.667 2.07 0.00 46.58 5.28
1347 2005 0.108207 CAGATCAGGGTGGCATCCTC 59.892 60.000 18.61 6.35 31.06 3.71
1353 2015 2.187946 CCGTCAGATCAGGGTGGC 59.812 66.667 0.00 0.00 0.00 5.01
1542 2223 3.056607 GCAAGGGCAATGCTAGAAAGAAA 60.057 43.478 4.82 0.00 40.64 2.52
1559 2240 6.540189 AGCATTACTATTAGTTGTCAGCAAGG 59.460 38.462 0.85 0.00 34.94 3.61
1617 2298 1.078759 CTCGTCGTCCATGAAGCACC 61.079 60.000 0.00 0.00 0.00 5.01
1722 2404 8.917088 CCTATTCCAAATGGTTCTAATCAACAT 58.083 33.333 0.00 0.00 36.34 2.71
1723 2405 8.112822 TCCTATTCCAAATGGTTCTAATCAACA 58.887 33.333 0.00 0.00 36.34 3.33
1724 2406 8.406297 GTCCTATTCCAAATGGTTCTAATCAAC 58.594 37.037 0.00 0.00 36.34 3.18
1725 2407 7.282224 CGTCCTATTCCAAATGGTTCTAATCAA 59.718 37.037 0.00 0.00 36.34 2.57
1726 2408 6.765989 CGTCCTATTCCAAATGGTTCTAATCA 59.234 38.462 0.00 0.00 36.34 2.57
1799 2504 4.935352 TTACCAACAAAGCTGCAATCTT 57.065 36.364 1.02 0.00 0.00 2.40
1859 2564 5.967088 TGAAGTGATCTACTACTCTTTGCC 58.033 41.667 0.00 0.00 39.18 4.52
1980 2685 2.233186 CTGAGCAGACTGAAGTGATCCA 59.767 50.000 6.65 0.00 0.00 3.41
1981 2686 2.233431 ACTGAGCAGACTGAAGTGATCC 59.767 50.000 6.65 0.00 0.00 3.36
2004 2710 1.072173 TGGAGCAGCAGCAAGAAGTAA 59.928 47.619 3.17 0.00 45.49 2.24
2027 2733 0.390340 CAGAGCAGCGGCAGAAGTAA 60.390 55.000 12.44 0.00 44.61 2.24
2030 2736 1.670406 AACAGAGCAGCGGCAGAAG 60.670 57.895 12.44 0.18 44.61 2.85
2075 2827 2.163818 TTGTGAACTAAGCAGACCGG 57.836 50.000 0.00 0.00 0.00 5.28
2153 2905 6.877322 GCCTAGTGGTTCAAGTTATTCTGTTA 59.123 38.462 0.00 0.00 35.27 2.41
2238 2990 5.023533 TCTCTAATGAAGAACCAATCCGG 57.976 43.478 0.00 0.00 42.50 5.14
2239 2991 5.403766 CGATCTCTAATGAAGAACCAATCCG 59.596 44.000 0.00 0.00 32.46 4.18
2246 2998 6.137794 TGGAGTCGATCTCTAATGAAGAAC 57.862 41.667 12.62 0.00 42.40 3.01
2261 3013 4.703897 AGAGTTCAAATTGTTGGAGTCGA 58.296 39.130 0.00 0.00 44.58 4.20
2277 3029 5.580297 CAGTTCTCAGATTGGCTAAGAGTTC 59.420 44.000 0.00 0.00 0.00 3.01
2279 3031 4.081198 CCAGTTCTCAGATTGGCTAAGAGT 60.081 45.833 0.00 0.00 0.00 3.24
2291 3043 1.340248 GAACCACGTCCAGTTCTCAGA 59.660 52.381 12.96 0.00 39.42 3.27
2316 3068 2.338577 ACCCAGAGCACAATATGAGC 57.661 50.000 0.00 0.00 34.10 4.26
2333 3085 2.374170 TCCCACTTTCCTGAAACCTACC 59.626 50.000 0.00 0.00 0.00 3.18
2366 3118 0.802607 CGCCTTACTTCTCACGCTCC 60.803 60.000 0.00 0.00 0.00 4.70
2369 3121 1.810030 CCCGCCTTACTTCTCACGC 60.810 63.158 0.00 0.00 0.00 5.34
2395 3147 0.613260 TGTCTTTGCTACTCCCGCAT 59.387 50.000 0.00 0.00 37.22 4.73
2682 4904 4.220821 TGTCTCATTTCCAGTCAGTCCTAC 59.779 45.833 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.