Multiple sequence alignment - TraesCS7A01G058800

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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 TraesCS7A01G058800 chr7A 100.000 3983 0 0 1 3983 28452785 28456767 0.000000e+00 7356
1 TraesCS7A01G058800 chr7A 77.820 266 54 3 1093 1357 19487467 19487728 4.120000e-35 159
2 TraesCS7A01G058800 chr7D 94.491 3794 128 27 223 3983 28034199 28037944 0.000000e+00 5773
3 TraesCS7A01G058800 chr4A 94.862 3270 135 16 741 3983 701756796 701760059 0.000000e+00 5077
4 TraesCS7A01G058800 chr4A 94.785 652 26 5 13 656 701756143 701756794 0.000000e+00 1009
5 TraesCS7A01G058800 chr1A 77.230 953 195 16 2986 3929 402229745 402230684 4.530000e-149 538
6 TraesCS7A01G058800 chrUn 83.158 570 90 6 3366 3931 284401434 284400867 2.120000e-142 516
7 TraesCS7A01G058800 chrUn 83.158 570 90 6 3366 3931 284407968 284407401 2.120000e-142 516
8 TraesCS7A01G058800 chrUn 83.158 570 90 6 3366 3931 302991593 302991026 2.120000e-142 516
9 TraesCS7A01G058800 chrUn 82.982 570 91 6 3366 3931 257885879 257885312 9.870000e-141 510
10 TraesCS7A01G058800 chrUn 82.105 570 96 6 3366 3931 35296487 35297054 2.150000e-132 483
11 TraesCS7A01G058800 chr3D 82.982 570 91 6 3366 3931 4958018 4957451 9.870000e-141 510
12 TraesCS7A01G058800 chr3D 82.982 570 91 6 3366 3931 9634699 9635266 9.870000e-141 510
13 TraesCS7A01G058800 chr5B 80.843 261 48 2 1085 1344 695493771 695493512 1.880000e-48 204
14 TraesCS7A01G058800 chr4B 85.906 149 16 3 484 631 617332793 617332937 1.920000e-33 154
15 TraesCS7A01G058800 chr4B 85.811 148 16 3 484 630 617328004 617328147 6.890000e-33 152
16 TraesCS7A01G058800 chr1B 84.906 159 17 5 484 639 14053458 14053612 1.920000e-33 154
17 TraesCS7A01G058800 chr1B 85.906 149 16 3 484 631 634413780 634413636 1.920000e-33 154
18 TraesCS7A01G058800 chr1B 85.811 148 16 3 484 630 14048659 14048802 6.890000e-33 152
19 TraesCS7A01G058800 chr1B 86.923 130 17 0 1093 1222 433644666 433644537 3.210000e-31 147
20 TraesCS7A01G058800 chr6A 85.811 148 16 3 484 630 83346910 83346767 6.890000e-33 152
21 TraesCS7A01G058800 chr6A 84.459 148 16 4 484 630 83351961 83351820 5.370000e-29 139
22 TraesCS7A01G058800 chr5D 74.818 274 62 7 1068 1337 555501452 555501722 2.510000e-22 117


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 TraesCS7A01G058800 chr7A 28452785 28456767 3982 False 7356 7356 100.0000 1 3983 1 chr7A.!!$F2 3982
1 TraesCS7A01G058800 chr7D 28034199 28037944 3745 False 5773 5773 94.4910 223 3983 1 chr7D.!!$F1 3760
2 TraesCS7A01G058800 chr4A 701756143 701760059 3916 False 3043 5077 94.8235 13 3983 2 chr4A.!!$F1 3970
3 TraesCS7A01G058800 chr1A 402229745 402230684 939 False 538 538 77.2300 2986 3929 1 chr1A.!!$F1 943
4 TraesCS7A01G058800 chrUn 284400867 284401434 567 True 516 516 83.1580 3366 3931 1 chrUn.!!$R2 565
5 TraesCS7A01G058800 chrUn 284407401 284407968 567 True 516 516 83.1580 3366 3931 1 chrUn.!!$R3 565
6 TraesCS7A01G058800 chrUn 302991026 302991593 567 True 516 516 83.1580 3366 3931 1 chrUn.!!$R4 565
7 TraesCS7A01G058800 chrUn 257885312 257885879 567 True 510 510 82.9820 3366 3931 1 chrUn.!!$R1 565
8 TraesCS7A01G058800 chrUn 35296487 35297054 567 False 483 483 82.1050 3366 3931 1 chrUn.!!$F1 565
9 TraesCS7A01G058800 chr3D 4957451 4958018 567 True 510 510 82.9820 3366 3931 1 chr3D.!!$R1 565
10 TraesCS7A01G058800 chr3D 9634699 9635266 567 False 510 510 82.9820 3366 3931 1 chr3D.!!$F1 565

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
786 803 0.841289 ACTTTCAAACACGGGGGAGA 59.159 50.0 0.0 0.0 0.00 3.71 F
1209 1250 0.036010 CTTTCTGCCACTGGATCGGT 60.036 55.0 0.0 0.0 0.00 4.69 F
1345 1386 0.751277 CACCAGCACAAACCTCACCA 60.751 55.0 0.0 0.0 0.00 4.17 F
2685 2726 0.958382 TACCAACCAGCATCGGCAAC 60.958 55.0 0.0 0.0 44.61 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2465 1.223187 CGGTTAACTTGTTGCGACCT 58.777 50.000 5.42 0.0 0.00 3.85 R
2958 2999 1.228552 TTTGAAGCTGGTCTGGGCC 60.229 57.895 0.00 0.0 0.00 5.80 R
2959 3000 1.246737 CCTTTGAAGCTGGTCTGGGC 61.247 60.000 0.00 0.0 0.00 5.36 R
3690 3737 0.112412 GCCTCTCAAGGAACCCCAAA 59.888 55.000 0.00 0.0 46.67 3.28 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
52 53 6.813649 CACTACAATGCACATCTAGTAACTGT 59.186 38.462 0.00 0.00 0.00 3.55
128 129 5.126108 CATTGATGAAAGAAAGCAATGCG 57.874 39.130 0.00 0.00 39.26 4.73
129 130 4.502171 TTGATGAAAGAAAGCAATGCGA 57.498 36.364 0.00 0.00 0.00 5.10
178 179 6.469782 TGTCTACATATCAGTGAGCAATCA 57.530 37.500 0.00 0.00 0.00 2.57
319 320 1.541588 GCAAGTTCCATCTGTCCAACC 59.458 52.381 0.00 0.00 0.00 3.77
328 329 3.057315 CCATCTGTCCAACCAAACACATC 60.057 47.826 0.00 0.00 0.00 3.06
333 334 3.703556 TGTCCAACCAAACACATCAACAT 59.296 39.130 0.00 0.00 0.00 2.71
336 340 6.127338 TGTCCAACCAAACACATCAACATAAA 60.127 34.615 0.00 0.00 0.00 1.40
339 343 6.705381 CCAACCAAACACATCAACATAAACAT 59.295 34.615 0.00 0.00 0.00 2.71
340 344 7.869937 CCAACCAAACACATCAACATAAACATA 59.130 33.333 0.00 0.00 0.00 2.29
345 353 9.254133 CAAACACATCAACATAAACATAACCAA 57.746 29.630 0.00 0.00 0.00 3.67
365 373 6.700352 ACCAATCCATTCCATTTTGTAGTTG 58.300 36.000 0.00 0.00 0.00 3.16
506 514 3.236816 CATTCGCTGCCTGTAAAACAAG 58.763 45.455 0.00 0.00 0.00 3.16
585 593 1.074319 GCTTTCATGCGCATGTGTGG 61.074 55.000 40.57 29.58 39.72 4.17
656 665 5.649782 ACCTCTTCCGAAGACGTATTAAA 57.350 39.130 6.75 0.00 37.88 1.52
657 666 5.405797 ACCTCTTCCGAAGACGTATTAAAC 58.594 41.667 6.75 0.00 37.88 2.01
658 667 5.184671 ACCTCTTCCGAAGACGTATTAAACT 59.815 40.000 6.75 0.00 37.88 2.66
659 668 6.098017 CCTCTTCCGAAGACGTATTAAACTT 58.902 40.000 6.75 0.00 37.88 2.66
660 669 7.094205 ACCTCTTCCGAAGACGTATTAAACTTA 60.094 37.037 6.75 0.00 37.88 2.24
661 670 7.219726 CCTCTTCCGAAGACGTATTAAACTTAC 59.780 40.741 6.75 0.00 37.88 2.34
662 671 7.029563 TCTTCCGAAGACGTATTAAACTTACC 58.970 38.462 6.75 0.00 37.88 2.85
663 672 5.650543 TCCGAAGACGTATTAAACTTACCC 58.349 41.667 0.00 0.00 37.88 3.69
664 673 5.418840 TCCGAAGACGTATTAAACTTACCCT 59.581 40.000 0.00 0.00 37.88 4.34
665 674 5.517770 CCGAAGACGTATTAAACTTACCCTG 59.482 44.000 0.00 0.00 37.88 4.45
666 675 5.005107 CGAAGACGTATTAAACTTACCCTGC 59.995 44.000 0.00 0.00 34.56 4.85
667 676 5.410355 AGACGTATTAAACTTACCCTGCA 57.590 39.130 0.00 0.00 0.00 4.41
668 677 5.797051 AGACGTATTAAACTTACCCTGCAA 58.203 37.500 0.00 0.00 0.00 4.08
669 678 6.232692 AGACGTATTAAACTTACCCTGCAAA 58.767 36.000 0.00 0.00 0.00 3.68
670 679 6.711645 AGACGTATTAAACTTACCCTGCAAAA 59.288 34.615 0.00 0.00 0.00 2.44
671 680 7.229106 AGACGTATTAAACTTACCCTGCAAAAA 59.771 33.333 0.00 0.00 0.00 1.94
720 729 2.354821 ACAAAGAAAGTGTGTTCCTCGC 59.645 45.455 0.00 0.00 0.00 5.03
731 747 4.156008 GTGTGTTCCTCGCCTATTGATTTT 59.844 41.667 0.00 0.00 0.00 1.82
735 751 6.260050 GTGTTCCTCGCCTATTGATTTTCATA 59.740 38.462 0.00 0.00 0.00 2.15
739 755 6.427853 TCCTCGCCTATTGATTTTCATACATG 59.572 38.462 0.00 0.00 0.00 3.21
775 792 9.190858 GCATGTTGTTAATATGTCACTTTCAAA 57.809 29.630 0.00 0.00 33.13 2.69
782 799 1.384525 TGTCACTTTCAAACACGGGG 58.615 50.000 0.00 0.00 0.00 5.73
786 803 0.841289 ACTTTCAAACACGGGGGAGA 59.159 50.000 0.00 0.00 0.00 3.71
792 809 1.812571 CAAACACGGGGGAGATTTCTG 59.187 52.381 0.00 0.00 0.00 3.02
821 838 5.560953 GCCGTGCTTAGTGGAATTAATCATC 60.561 44.000 0.00 0.00 0.00 2.92
822 839 5.333339 CCGTGCTTAGTGGAATTAATCATCG 60.333 44.000 0.00 0.00 0.00 3.84
823 840 5.444122 GTGCTTAGTGGAATTAATCATCGC 58.556 41.667 0.00 0.00 0.00 4.58
824 841 5.237344 GTGCTTAGTGGAATTAATCATCGCT 59.763 40.000 0.00 0.00 0.00 4.93
905 934 4.519540 TCCAAAAAGAATGGTTAGCAGC 57.480 40.909 0.00 0.00 39.09 5.25
926 955 1.403249 CCAATACGTCCGAAAGTCCGT 60.403 52.381 0.00 0.00 38.68 4.69
951 983 1.404391 ACCTCATACGAACCGCACTAG 59.596 52.381 0.00 0.00 0.00 2.57
1023 1055 0.394216 CCACCGCATCCATTTCCAGA 60.394 55.000 0.00 0.00 0.00 3.86
1083 1118 1.827399 GCACTTCTTCCCCGACTCCA 61.827 60.000 0.00 0.00 0.00 3.86
1084 1119 0.685097 CACTTCTTCCCCGACTCCAA 59.315 55.000 0.00 0.00 0.00 3.53
1166 1207 0.755686 GATCCTCTCGGCATCCTTGT 59.244 55.000 0.00 0.00 0.00 3.16
1204 1245 0.249868 CACGTCTTTCTGCCACTGGA 60.250 55.000 0.00 0.00 0.00 3.86
1209 1250 0.036010 CTTTCTGCCACTGGATCGGT 60.036 55.000 0.00 0.00 0.00 4.69
1225 1266 2.024319 GGTGTCTCGTGCAGCTCAC 61.024 63.158 0.00 6.31 42.23 3.51
1282 1323 2.142761 CCCCTCCATGGATCGCTCA 61.143 63.158 16.63 0.00 38.35 4.26
1345 1386 0.751277 CACCAGCACAAACCTCACCA 60.751 55.000 0.00 0.00 0.00 4.17
1422 1463 1.048724 TCAATGGCCTCTCGGGTAGG 61.049 60.000 3.32 0.00 37.43 3.18
1545 1586 5.337410 CCATCTCAACTCCCTATATCTGCAG 60.337 48.000 7.63 7.63 0.00 4.41
1658 1699 1.714899 GCAATACCGCCTTGCATCGT 61.715 55.000 9.16 0.00 46.44 3.73
1704 1745 4.922206 TGGACCTGCAAGTAAATCATCTT 58.078 39.130 0.00 0.00 0.00 2.40
1939 1980 4.262164 GCAATTCATTTGAGGGTCTTGTGT 60.262 41.667 0.00 0.00 37.53 3.72
2132 2173 1.213537 CCGAATTGCACCTTGCCAG 59.786 57.895 0.00 0.00 44.23 4.85
2193 2234 8.957466 GGCAATTTATCTCAACTAACTTACCTT 58.043 33.333 0.00 0.00 0.00 3.50
2370 2411 2.576191 AGAGGGAAATTCATTCACCGGA 59.424 45.455 9.46 0.00 42.85 5.14
2420 2461 6.816136 TCTCTACACAGTTGATCACTTTTCA 58.184 36.000 0.00 0.00 30.92 2.69
2424 2465 4.338964 ACACAGTTGATCACTTTTCATGCA 59.661 37.500 0.00 0.00 30.92 3.96
2685 2726 0.958382 TACCAACCAGCATCGGCAAC 60.958 55.000 0.00 0.00 44.61 4.17
2725 2766 6.723298 ACATTGACTTGTCCAATAACCAAA 57.277 33.333 0.00 0.00 33.35 3.28
2846 2887 6.183360 GCTGATGGTCTAATACAAATCGATCG 60.183 42.308 9.36 9.36 0.00 3.69
2944 2985 6.367695 CCTAAATATGTCACACAACTCGTTCA 59.632 38.462 0.00 0.00 0.00 3.18
2955 2996 3.189287 ACAACTCGTTCAATGGCTCAATC 59.811 43.478 0.00 0.00 0.00 2.67
2956 2997 2.359900 ACTCGTTCAATGGCTCAATCC 58.640 47.619 0.00 0.00 0.00 3.01
2957 2998 1.672881 CTCGTTCAATGGCTCAATCCC 59.327 52.381 0.00 0.00 0.00 3.85
2958 2999 0.378257 CGTTCAATGGCTCAATCCCG 59.622 55.000 0.00 0.00 0.00 5.14
2959 3000 0.740737 GTTCAATGGCTCAATCCCGG 59.259 55.000 0.00 0.00 0.00 5.73
3014 3055 4.384647 GCAACATTAGACCTCTCCTCCAAT 60.385 45.833 0.00 0.00 0.00 3.16
3028 3069 2.880890 CCTCCAATAATCTTTCCGGCAG 59.119 50.000 0.00 0.00 0.00 4.85
3109 3150 3.456277 AGGCTAGAAGGACAAATACCAGG 59.544 47.826 0.00 0.00 0.00 4.45
3238 3280 2.951642 GCAGTAGGCATTTGCTGGAATA 59.048 45.455 2.12 0.00 43.97 1.75
3338 3380 4.081406 AGCAAGATGTTGTTAATGCCTCA 58.919 39.130 4.33 0.00 35.92 3.86
3349 3391 1.762522 AATGCCTCAGCCGATCCGAT 61.763 55.000 0.00 0.00 38.69 4.18
3363 3405 5.062308 GCCGATCCGATTGATTCTGTAATAC 59.938 44.000 0.00 0.00 32.41 1.89
3403 3445 6.604396 TCCTACCATGAGTTAGTTCGTATCAA 59.396 38.462 0.00 0.00 0.00 2.57
3690 3737 4.040755 ACTACCCTCAAGGCTCAACATAT 58.959 43.478 0.00 0.00 40.58 1.78
3826 3873 1.067915 TGTTCGATGAGCACATGACGA 60.068 47.619 0.00 2.50 36.82 4.20
3880 3927 1.566211 ACTCTGGGATGACACCTCTG 58.434 55.000 0.00 0.00 0.00 3.35
3933 3980 0.771127 ACATGGCACCAGGTACTTGT 59.229 50.000 4.94 0.40 39.28 3.16
3953 4000 7.104290 ACTTGTCTAGACCTTGTAATTAAGCC 58.896 38.462 20.11 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.448540 GCTCCACTGCGCTATGTGT 60.449 57.895 20.64 6.44 32.76 3.72
1 2 2.176273 GGCTCCACTGCGCTATGTG 61.176 63.158 9.73 14.70 0.00 3.21
3 4 2.705934 ATCGGCTCCACTGCGCTATG 62.706 60.000 9.73 6.73 0.00 2.23
4 5 2.427540 GATCGGCTCCACTGCGCTAT 62.428 60.000 9.73 0.00 0.00 2.97
5 6 3.138930 GATCGGCTCCACTGCGCTA 62.139 63.158 9.73 0.00 0.00 4.26
6 7 4.521062 GATCGGCTCCACTGCGCT 62.521 66.667 9.73 0.00 0.00 5.92
7 8 3.138930 TAGATCGGCTCCACTGCGC 62.139 63.158 0.00 0.00 0.00 6.09
8 9 1.299468 GTAGATCGGCTCCACTGCG 60.299 63.158 0.00 0.00 0.00 5.18
9 10 1.068250 GGTAGATCGGCTCCACTGC 59.932 63.158 0.00 0.00 0.00 4.40
10 11 0.103208 GTGGTAGATCGGCTCCACTG 59.897 60.000 17.67 0.00 44.57 3.66
11 12 2.506065 GTGGTAGATCGGCTCCACT 58.494 57.895 17.67 0.00 44.57 4.00
52 53 3.057806 CACTGTGCATTGATCAAAGCAGA 60.058 43.478 32.23 29.56 44.24 4.26
77 78 8.582433 TGATCATAAAAATGCACATTGCTATG 57.418 30.769 6.59 6.59 45.31 2.23
103 104 6.662414 CATTGCTTTCTTTCATCAATGCAT 57.338 33.333 0.00 0.00 38.01 3.96
113 114 4.498323 GTGATCATCGCATTGCTTTCTTTC 59.502 41.667 7.12 0.00 0.00 2.62
128 129 4.450080 TGCTTCGATTGCTATGTGATCATC 59.550 41.667 0.00 0.00 35.70 2.92
129 130 4.383173 TGCTTCGATTGCTATGTGATCAT 58.617 39.130 0.00 0.00 38.00 2.45
146 147 9.138062 CTCACTGATATGTAGACATATTGCTTC 57.862 37.037 14.74 5.30 46.36 3.86
178 179 7.093333 TGTGTTCATGACTAGACTGATTGGTAT 60.093 37.037 0.00 0.00 0.00 2.73
259 260 2.546652 TGGAATGGAATGGAATGGCA 57.453 45.000 0.00 0.00 0.00 4.92
319 320 8.809159 TGGTTATGTTTATGTTGATGTGTTTG 57.191 30.769 0.00 0.00 0.00 2.93
328 329 8.256605 TGGAATGGATTGGTTATGTTTATGTTG 58.743 33.333 0.00 0.00 0.00 3.33
333 334 9.664332 CAAAATGGAATGGATTGGTTATGTTTA 57.336 29.630 0.00 0.00 0.00 2.01
336 340 7.256494 ACAAAATGGAATGGATTGGTTATGT 57.744 32.000 0.00 0.00 0.00 2.29
339 343 8.310382 CAACTACAAAATGGAATGGATTGGTTA 58.690 33.333 0.00 0.00 0.00 2.85
340 344 6.933514 ACTACAAAATGGAATGGATTGGTT 57.066 33.333 0.00 0.00 0.00 3.67
345 353 7.961351 TGTTTCAACTACAAAATGGAATGGAT 58.039 30.769 0.00 0.00 0.00 3.41
365 373 4.348656 GGTTCCGTTCTTCAGTTTGTTTC 58.651 43.478 0.00 0.00 0.00 2.78
415 423 6.460781 TCGAGAACCAAGTGTAATGTAATGT 58.539 36.000 0.00 0.00 0.00 2.71
506 514 1.081641 GAGCAGCACACACACATGC 60.082 57.895 0.00 0.00 42.39 4.06
570 578 3.442167 GCCCACACATGCGCATGA 61.442 61.111 46.90 13.55 41.20 3.07
585 593 2.034999 TTGTTCCCGGTGGATGCC 59.965 61.111 0.00 0.00 41.40 4.40
711 720 4.584874 TGAAAATCAATAGGCGAGGAACA 58.415 39.130 0.00 0.00 0.00 3.18
720 729 7.392673 AGGCTAGCATGTATGAAAATCAATAGG 59.607 37.037 18.24 0.00 0.00 2.57
731 747 2.608623 TGCCTAGGCTAGCATGTATGA 58.391 47.619 33.07 6.61 42.51 2.15
739 755 2.044123 AACAACATGCCTAGGCTAGC 57.956 50.000 33.07 6.04 42.51 3.42
775 792 0.613777 GACAGAAATCTCCCCCGTGT 59.386 55.000 0.00 0.00 0.00 4.49
821 838 3.181516 GCAATCACAAAGGACTCTAAGCG 60.182 47.826 0.00 0.00 0.00 4.68
822 839 3.127721 GGCAATCACAAAGGACTCTAAGC 59.872 47.826 0.00 0.00 0.00 3.09
823 840 3.372206 CGGCAATCACAAAGGACTCTAAG 59.628 47.826 0.00 0.00 0.00 2.18
824 841 3.334691 CGGCAATCACAAAGGACTCTAA 58.665 45.455 0.00 0.00 0.00 2.10
905 934 1.648504 GGACTTTCGGACGTATTGGG 58.351 55.000 0.00 0.00 0.00 4.12
926 955 1.673626 GCGGTTCGTATGAGGTTTCCA 60.674 52.381 0.00 0.00 0.00 3.53
951 983 5.545588 TCATCTAGCTTTGCTGGTGATATC 58.454 41.667 0.00 0.00 40.10 1.63
1023 1055 5.137412 AGGCTGATAGAAGAAGTAGGACT 57.863 43.478 0.00 0.00 0.00 3.85
1074 1109 2.358247 CCGTTGGTTGGAGTCGGG 60.358 66.667 0.00 0.00 37.92 5.14
1083 1118 3.591835 CTGCCGTTGCCGTTGGTT 61.592 61.111 0.00 0.00 36.33 3.67
1107 1148 4.626081 AACAGCGCGGCAAGGTCT 62.626 61.111 8.83 0.00 0.00 3.85
1166 1207 2.425592 CGGTGGTCCAGTTGCTGA 59.574 61.111 0.00 0.00 32.44 4.26
1204 1245 2.125912 GCTGCACGAGACACCGAT 60.126 61.111 0.00 0.00 0.00 4.18
1250 1291 1.062352 GGAGGGGTATGTAGGTGAGGT 60.062 57.143 0.00 0.00 0.00 3.85
1282 1323 1.903183 GAGGTTACCAAGCTGAGGAGT 59.097 52.381 12.13 0.00 39.77 3.85
1422 1463 3.072622 GGTTTCCTATAGTGGGTGGGATC 59.927 52.174 0.00 0.00 0.00 3.36
1545 1586 2.617274 GCCGGCGAGGGAATTATGC 61.617 63.158 12.58 0.00 41.48 3.14
1658 1699 7.363880 CCAGTAACTCTAGCATTTCTAAGGACA 60.364 40.741 0.00 0.00 0.00 4.02
1939 1980 1.411977 CAACTTGCCCAACCATGTTGA 59.588 47.619 8.47 0.00 45.89 3.18
2132 2173 5.698545 GGAATTGCACCTGATAGATGACTAC 59.301 44.000 0.00 0.00 0.00 2.73
2193 2234 7.092079 CAGACAGTGGATTTATTTGCAAATCA 58.908 34.615 27.28 14.88 43.66 2.57
2370 2411 1.559065 CCACGTGGTTAGGGATGGGT 61.559 60.000 26.95 0.00 0.00 4.51
2424 2465 1.223187 CGGTTAACTTGTTGCGACCT 58.777 50.000 5.42 0.00 0.00 3.85
2551 2592 3.306088 CGAGAGAGGTTAAGAAGCACCAA 60.306 47.826 0.00 0.00 35.25 3.67
2685 2726 6.319658 AGTCAATGTATTCCAACATGCTAAGG 59.680 38.462 0.00 0.00 39.98 2.69
2725 2766 6.407202 AGCTTGTCGGTATCTTTGAACTTAT 58.593 36.000 0.00 0.00 0.00 1.73
2769 2810 8.782339 AATTTTGGAAAAGAAATAGCTGGATG 57.218 30.769 0.00 0.00 0.00 3.51
2846 2887 6.581171 AGAAGTTGGAAGAAATGTCCATTC 57.419 37.500 0.00 0.00 44.62 2.67
2944 2985 2.123726 GGCCGGGATTGAGCCATT 60.124 61.111 2.18 0.00 46.34 3.16
2956 2997 4.785453 GAAGCTGGTCTGGGCCGG 62.785 72.222 5.83 5.83 37.94 6.13
2957 2998 3.551496 TTGAAGCTGGTCTGGGCCG 62.551 63.158 0.00 0.00 0.00 6.13
2958 2999 1.228552 TTTGAAGCTGGTCTGGGCC 60.229 57.895 0.00 0.00 0.00 5.80
2959 3000 1.246737 CCTTTGAAGCTGGTCTGGGC 61.247 60.000 0.00 0.00 0.00 5.36
3014 3055 3.053991 TGGGAATTCTGCCGGAAAGATTA 60.054 43.478 5.05 0.00 37.49 1.75
3109 3150 1.617322 GGTTGAGAAAACACCTCCCC 58.383 55.000 0.00 0.00 0.00 4.81
3318 3360 4.418392 GCTGAGGCATTAACAACATCTTG 58.582 43.478 0.00 0.00 38.54 3.02
3319 3361 3.445096 GGCTGAGGCATTAACAACATCTT 59.555 43.478 0.00 0.00 40.87 2.40
3338 3380 1.414181 ACAGAATCAATCGGATCGGCT 59.586 47.619 0.00 0.00 34.28 5.52
3349 3391 5.670485 ACTGATGGCGTATTACAGAATCAA 58.330 37.500 0.00 0.00 33.53 2.57
3363 3405 3.357166 GTAGGAGACTAACTGATGGCG 57.643 52.381 0.00 0.00 46.54 5.69
3690 3737 0.112412 GCCTCTCAAGGAACCCCAAA 59.888 55.000 0.00 0.00 46.67 3.28
3826 3873 1.321474 CCAAAGTCTGCCACATGTGT 58.679 50.000 23.79 1.62 0.00 3.72
3865 3912 1.833630 GATCACAGAGGTGTCATCCCA 59.166 52.381 0.00 0.00 45.45 4.37
3880 3927 1.445716 GGCATGCTGGCAGAGATCAC 61.446 60.000 20.86 0.00 43.14 3.06
3933 3980 5.425539 AGCAGGCTTAATTACAAGGTCTAGA 59.574 40.000 0.00 0.00 0.00 2.43
3953 4000 4.201724 GCTTAACAACAATAGACCGAGCAG 60.202 45.833 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.