Multiple sequence alignment - TraesCS7D01G103400

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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 TraesCS7D01G103400 chr7D 100.000 3353 0 0 1 3353 63379385 63376033 0.000000e+00 6192.0
1 TraesCS7D01G103400 chr7D 80.328 183 26 9 477 651 628130570 628130390 2.710000e-26 130.0
2 TraesCS7D01G103400 chr7A 93.656 1655 72 9 788 2411 66167601 66165949 0.000000e+00 2444.0
3 TraesCS7D01G103400 chr7A 90.244 779 59 9 1 765 66168361 66167586 0.000000e+00 1002.0
4 TraesCS7D01G103400 chr7A 94.248 226 12 1 2403 2628 66165927 66165703 8.910000e-91 344.0
5 TraesCS7D01G103400 chr7B 93.697 952 57 3 2403 3352 3694976 3694026 0.000000e+00 1423.0
6 TraesCS7D01G103400 chr7B 93.800 871 41 4 1554 2411 3695868 3694998 0.000000e+00 1297.0
7 TraesCS7D01G103400 chr7B 95.462 573 20 3 982 1549 3696477 3695906 0.000000e+00 909.0
8 TraesCS7D01G103400 chr7B 82.048 830 131 14 2536 3352 744666494 744665670 0.000000e+00 691.0
9 TraesCS7D01G103400 chr7B 84.198 405 29 10 1 405 3698287 3697918 8.840000e-96 361.0
10 TraesCS7D01G103400 chr7B 92.308 195 11 3 805 998 3697475 3697284 1.190000e-69 274.0
11 TraesCS7D01G103400 chr7B 93.333 75 4 1 2403 2477 3689643 3689570 3.540000e-20 110.0
12 TraesCS7D01G103400 chr7B 77.305 141 28 3 477 616 729642151 729642014 2.770000e-11 80.5
13 TraesCS7D01G103400 chr3D 84.606 812 118 5 2541 3348 602654580 602655388 0.000000e+00 800.0
14 TraesCS7D01G103400 chr6D 84.578 817 103 12 2540 3352 115318464 115317667 0.000000e+00 789.0
15 TraesCS7D01G103400 chr6D 82.275 835 130 14 2529 3352 25832406 25833233 0.000000e+00 706.0
16 TraesCS7D01G103400 chr6D 80.255 157 21 8 469 624 174399617 174399764 3.540000e-20 110.0
17 TraesCS7D01G103400 chr6A 84.314 816 114 8 2540 3352 143701797 143700993 0.000000e+00 785.0
18 TraesCS7D01G103400 chr6A 78.458 817 138 23 1557 2340 24054807 24053996 1.800000e-137 499.0
19 TraesCS7D01G103400 chr1A 83.537 820 123 10 2541 3352 464085620 464084805 0.000000e+00 756.0
20 TraesCS7D01G103400 chr1A 81.379 145 21 5 483 624 49034665 49034806 2.730000e-21 113.0
21 TraesCS7D01G103400 chr4B 83.069 821 126 11 2541 3352 211499416 211500232 0.000000e+00 734.0
22 TraesCS7D01G103400 chr4B 74.981 1299 251 47 1084 2344 600606040 600604778 6.370000e-147 531.0
23 TraesCS7D01G103400 chr4B 75.366 820 160 25 1556 2343 600517191 600516382 1.140000e-94 357.0
24 TraesCS7D01G103400 chr4D 75.251 1293 259 44 1085 2343 476229574 476228309 2.920000e-155 558.0
25 TraesCS7D01G103400 chr4D 90.196 51 5 0 574 624 35173220 35173170 2.160000e-07 67.6
26 TraesCS7D01G103400 chr4A 75.936 1068 196 35 1084 2118 683443138 683442099 3.010000e-135 492.0
27 TraesCS7D01G103400 chr5D 77.561 820 164 19 2541 3352 398372859 398372052 8.420000e-131 477.0
28 TraesCS7D01G103400 chr5D 83.051 118 18 2 504 621 526108647 526108762 4.580000e-19 106.0
29 TraesCS7D01G103400 chr6B 74.540 1304 225 69 1071 2349 42400308 42399087 1.410000e-128 470.0
30 TraesCS7D01G103400 chr6B 86.154 390 52 2 1071 1459 42406554 42406166 1.440000e-113 420.0
31 TraesCS7D01G103400 chr6B 78.554 401 74 6 1556 1944 42406087 42405687 1.540000e-63 254.0
32 TraesCS7D01G103400 chrUn 75.908 826 170 25 2541 3352 385875321 385874511 2.420000e-106 396.0
33 TraesCS7D01G103400 chr2B 86.620 284 37 1 3070 3352 687884490 687884207 2.510000e-81 313.0
34 TraesCS7D01G103400 chr2B 74.413 766 166 21 1084 1843 24882791 24883532 5.440000e-78 302.0
35 TraesCS7D01G103400 chr2A 87.407 135 13 3 1068 1200 143289073 143289205 5.790000e-33 152.0
36 TraesCS7D01G103400 chr2A 88.750 80 4 3 475 553 350700778 350700703 3.560000e-15 93.5
37 TraesCS7D01G103400 chr2A 79.545 132 21 5 494 624 94419362 94419236 4.610000e-14 89.8
38 TraesCS7D01G103400 chr2A 85.075 67 9 1 2145 2210 14890636 14890570 2.160000e-07 67.6
39 TraesCS7D01G103400 chr1D 83.217 143 22 2 482 624 282188502 282188362 2.710000e-26 130.0
40 TraesCS7D01G103400 chr2D 87.952 83 10 0 1065 1147 135511081 135511163 7.660000e-17 99.0


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 TraesCS7D01G103400 chr7D 63376033 63379385 3352 True 6192.000000 6192 100.000 1 3353 1 chr7D.!!$R1 3352
1 TraesCS7D01G103400 chr7A 66165703 66168361 2658 True 1263.333333 2444 92.716 1 2628 3 chr7A.!!$R1 2627
2 TraesCS7D01G103400 chr7B 3694026 3698287 4261 True 852.800000 1423 91.893 1 3352 5 chr7B.!!$R4 3351
3 TraesCS7D01G103400 chr7B 744665670 744666494 824 True 691.000000 691 82.048 2536 3352 1 chr7B.!!$R3 816
4 TraesCS7D01G103400 chr3D 602654580 602655388 808 False 800.000000 800 84.606 2541 3348 1 chr3D.!!$F1 807
5 TraesCS7D01G103400 chr6D 115317667 115318464 797 True 789.000000 789 84.578 2540 3352 1 chr6D.!!$R1 812
6 TraesCS7D01G103400 chr6D 25832406 25833233 827 False 706.000000 706 82.275 2529 3352 1 chr6D.!!$F1 823
7 TraesCS7D01G103400 chr6A 143700993 143701797 804 True 785.000000 785 84.314 2540 3352 1 chr6A.!!$R2 812
8 TraesCS7D01G103400 chr6A 24053996 24054807 811 True 499.000000 499 78.458 1557 2340 1 chr6A.!!$R1 783
9 TraesCS7D01G103400 chr1A 464084805 464085620 815 True 756.000000 756 83.537 2541 3352 1 chr1A.!!$R1 811
10 TraesCS7D01G103400 chr4B 211499416 211500232 816 False 734.000000 734 83.069 2541 3352 1 chr4B.!!$F1 811
11 TraesCS7D01G103400 chr4B 600604778 600606040 1262 True 531.000000 531 74.981 1084 2344 1 chr4B.!!$R2 1260
12 TraesCS7D01G103400 chr4B 600516382 600517191 809 True 357.000000 357 75.366 1556 2343 1 chr4B.!!$R1 787
13 TraesCS7D01G103400 chr4D 476228309 476229574 1265 True 558.000000 558 75.251 1085 2343 1 chr4D.!!$R2 1258
14 TraesCS7D01G103400 chr4A 683442099 683443138 1039 True 492.000000 492 75.936 1084 2118 1 chr4A.!!$R1 1034
15 TraesCS7D01G103400 chr5D 398372052 398372859 807 True 477.000000 477 77.561 2541 3352 1 chr5D.!!$R1 811
16 TraesCS7D01G103400 chr6B 42399087 42400308 1221 True 470.000000 470 74.540 1071 2349 1 chr6B.!!$R1 1278
17 TraesCS7D01G103400 chr6B 42405687 42406554 867 True 337.000000 420 82.354 1071 1944 2 chr6B.!!$R2 873
18 TraesCS7D01G103400 chrUn 385874511 385875321 810 True 396.000000 396 75.908 2541 3352 1 chrUn.!!$R1 811
19 TraesCS7D01G103400 chr2B 24882791 24883532 741 False 302.000000 302 74.413 1084 1843 1 chr2B.!!$F1 759

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
776 1145 0.031616 AAGGGGGTCACCTGCAAAAA 60.032 50.0 0.0 0.0 40.87 1.94 F
813 1182 0.394899 GAAGGTGGAGGGAGGCATTG 60.395 60.0 0.0 0.0 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 3572 0.178068 AGCGACAAAGTCCACACACT 59.822 50.0 0.0 0.0 0.0 3.55 R
2605 3964 0.321564 CTGTCCGGTTGATGGCTTCA 60.322 55.0 0.0 0.0 0.0 3.02 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
82 83 2.355197 TGATGTGTTGTATTCGGCCAG 58.645 47.619 2.24 0.00 0.00 4.85
93 94 2.358615 CGGCCAGCACTGCTACAA 60.359 61.111 2.24 0.00 36.40 2.41
94 95 2.393768 CGGCCAGCACTGCTACAAG 61.394 63.158 2.24 0.00 36.40 3.16
113 114 3.900116 CAAGCACTTGTGAACGAATAACG 59.100 43.478 4.79 0.00 40.53 3.18
162 163 2.951642 CAACATCCAACAGACACAACCT 59.048 45.455 0.00 0.00 0.00 3.50
164 165 2.951642 ACATCCAACAGACACAACCTTG 59.048 45.455 0.00 0.00 0.00 3.61
240 241 9.295825 CAACATTAGAGATATCACCTAGAGAGT 57.704 37.037 5.32 1.79 0.00 3.24
242 243 7.888021 ACATTAGAGATATCACCTAGAGAGTGG 59.112 40.741 5.32 0.00 35.87 4.00
276 277 6.867519 TTGTCACCTCCATATCTTCAAGTA 57.132 37.500 0.00 0.00 0.00 2.24
280 281 7.290948 TGTCACCTCCATATCTTCAAGTATCAT 59.709 37.037 0.00 0.00 0.00 2.45
281 282 7.601886 GTCACCTCCATATCTTCAAGTATCATG 59.398 40.741 0.00 0.00 0.00 3.07
406 763 8.918961 TCATTTTTAGTTTACACACCAAACAG 57.081 30.769 0.00 0.00 38.16 3.16
446 803 2.048603 GTCCCTGCTCAACCATGCC 61.049 63.158 0.00 0.00 0.00 4.40
452 809 1.945394 CTGCTCAACCATGCCTGATAC 59.055 52.381 0.00 0.00 0.00 2.24
453 810 1.561076 TGCTCAACCATGCCTGATACT 59.439 47.619 0.00 0.00 0.00 2.12
466 823 3.999663 GCCTGATACTAGACATCAATGGC 59.000 47.826 17.85 17.85 36.90 4.40
467 824 4.503817 GCCTGATACTAGACATCAATGGCA 60.504 45.833 22.70 0.00 40.70 4.92
468 825 5.236282 CCTGATACTAGACATCAATGGCAG 58.764 45.833 0.00 0.00 38.64 4.85
476 833 1.134818 ACATCAATGGCAGCAATGCAG 60.135 47.619 8.35 0.00 36.33 4.41
498 855 6.400568 CAGTCATGCAAGGATGGTAAATTTT 58.599 36.000 0.00 0.00 0.00 1.82
509 866 6.148811 AGGATGGTAAATTTTAGTGACACACG 59.851 38.462 8.59 0.00 39.64 4.49
510 867 6.148150 GGATGGTAAATTTTAGTGACACACGA 59.852 38.462 8.59 0.00 39.64 4.35
514 871 6.849305 GGTAAATTTTAGTGACACACGACAAG 59.151 38.462 8.59 0.00 39.64 3.16
558 917 1.005294 CACGAAGTTGCCATGCTTGC 61.005 55.000 0.00 0.00 41.61 4.01
561 920 0.389426 GAAGTTGCCATGCTTGCCAG 60.389 55.000 0.00 0.00 0.00 4.85
578 937 2.232208 GCCAGCTAAAGTTGCAATCCTT 59.768 45.455 0.59 0.00 0.00 3.36
595 954 3.735591 TCCTTGCGTAACTAAACTTGCT 58.264 40.909 0.00 0.00 0.00 3.91
626 985 0.983467 TCAGAGTTGCTATGTGCCCA 59.017 50.000 0.00 0.00 42.00 5.36
627 986 1.089920 CAGAGTTGCTATGTGCCCAC 58.910 55.000 0.00 0.00 42.00 4.61
628 987 0.391661 AGAGTTGCTATGTGCCCACG 60.392 55.000 0.00 0.00 42.00 4.94
633 999 2.125713 CTATGTGCCCACGCGTGA 60.126 61.111 39.10 20.36 38.08 4.35
641 1007 1.296056 GCCCACGCGTGACACTTATT 61.296 55.000 39.10 0.00 0.00 1.40
643 1009 1.924524 CCCACGCGTGACACTTATTAG 59.075 52.381 39.10 18.19 0.00 1.73
684 1050 4.796110 TTGATTAGGAGAAAGGGATGGG 57.204 45.455 0.00 0.00 0.00 4.00
710 1076 4.580580 GGAATGTGTAGGCAAAGATAAGGG 59.419 45.833 0.00 0.00 0.00 3.95
711 1077 5.437060 GAATGTGTAGGCAAAGATAAGGGA 58.563 41.667 0.00 0.00 0.00 4.20
765 1134 0.981943 TTCGAAGAAGGAAGGGGGTC 59.018 55.000 0.00 0.00 45.90 4.46
766 1135 0.178915 TCGAAGAAGGAAGGGGGTCA 60.179 55.000 0.00 0.00 0.00 4.02
767 1136 0.036294 CGAAGAAGGAAGGGGGTCAC 60.036 60.000 0.00 0.00 0.00 3.67
768 1137 0.328592 GAAGAAGGAAGGGGGTCACC 59.671 60.000 0.00 0.00 39.11 4.02
769 1138 0.103876 AAGAAGGAAGGGGGTCACCT 60.104 55.000 0.00 0.00 44.56 4.00
773 1142 2.840753 GGAAGGGGGTCACCTGCAA 61.841 63.158 0.00 0.00 40.87 4.08
774 1143 1.152830 GAAGGGGGTCACCTGCAAA 59.847 57.895 0.00 0.00 40.87 3.68
775 1144 0.469144 GAAGGGGGTCACCTGCAAAA 60.469 55.000 0.00 0.00 40.87 2.44
776 1145 0.031616 AAGGGGGTCACCTGCAAAAA 60.032 50.000 0.00 0.00 40.87 1.94
799 1168 7.962995 AAAAAGAAAGAAGAAGAAGGAAGGT 57.037 32.000 0.00 0.00 0.00 3.50
800 1169 6.951062 AAAGAAAGAAGAAGAAGGAAGGTG 57.049 37.500 0.00 0.00 0.00 4.00
801 1170 4.979335 AGAAAGAAGAAGAAGGAAGGTGG 58.021 43.478 0.00 0.00 0.00 4.61
802 1171 4.660771 AGAAAGAAGAAGAAGGAAGGTGGA 59.339 41.667 0.00 0.00 0.00 4.02
803 1172 4.632327 AAGAAGAAGAAGGAAGGTGGAG 57.368 45.455 0.00 0.00 0.00 3.86
813 1182 0.394899 GAAGGTGGAGGGAGGCATTG 60.395 60.000 0.00 0.00 0.00 2.82
844 1213 1.005347 CGGTCGATTGGATTGCGTTAC 60.005 52.381 0.00 0.00 0.00 2.50
853 1223 3.879427 TGGATTGCGTTACAAAAAGACG 58.121 40.909 0.00 0.00 42.86 4.18
991 1369 1.523154 GACATCGCCAAAACCCTGCA 61.523 55.000 0.00 0.00 0.00 4.41
994 1372 2.158561 ATCGCCAAAACCCTGCAAGC 62.159 55.000 0.00 0.00 0.00 4.01
1038 2237 2.905880 ACCGTCCGCCTCTATCCG 60.906 66.667 0.00 0.00 0.00 4.18
1463 2668 4.870305 CGAGAAGGTCGGTGTCAG 57.130 61.111 0.00 0.00 45.58 3.51
1501 2720 1.401148 CCGTACGTCCATGATCGATCC 60.401 57.143 22.31 5.79 0.00 3.36
1547 2789 4.229876 TGCACAGATCGATCGATAACATC 58.770 43.478 29.45 17.95 34.60 3.06
1548 2790 4.229876 GCACAGATCGATCGATAACATCA 58.770 43.478 29.45 0.36 34.60 3.07
1550 2792 5.347093 GCACAGATCGATCGATAACATCAAT 59.653 40.000 29.45 6.16 34.60 2.57
1551 2793 6.128715 GCACAGATCGATCGATAACATCAATT 60.129 38.462 29.45 5.35 34.60 2.32
1794 3076 2.045926 GTGCCCTTCATGCGAGGT 60.046 61.111 12.29 0.00 32.15 3.85
1853 3135 1.080093 TGCTCCAGCTTCGTTACCG 60.080 57.895 0.00 0.00 42.66 4.02
2044 3354 0.521867 CGCGTTCGATACCGAGTTGA 60.522 55.000 0.00 0.00 46.39 3.18
2249 3572 2.758327 ATCTGACTACCCGCCGCA 60.758 61.111 0.00 0.00 0.00 5.69
2277 3600 2.621338 GACTTTGTCGCTGATCATCCA 58.379 47.619 0.00 0.00 0.00 3.41
2418 3772 6.067217 AGTCAGGATTTGTAATTAGGTGCT 57.933 37.500 0.00 0.00 0.00 4.40
2529 3883 5.499139 ACCCTTATCGCATATTTTGTGTG 57.501 39.130 0.00 0.00 37.14 3.82
2605 3964 5.112129 ACCTAGCCCGACTTTGAATTAAT 57.888 39.130 0.00 0.00 0.00 1.40
2629 3988 1.955208 GCCATCAACCGGACAGGATTT 60.955 52.381 9.46 0.00 45.00 2.17
2638 3997 0.259938 GGACAGGATTTCAGGGGCAT 59.740 55.000 0.00 0.00 0.00 4.40
2669 4036 7.346751 ACAGGAAATTGAAAGTAGAGCAAAA 57.653 32.000 0.00 0.00 0.00 2.44
2670 4037 7.428826 ACAGGAAATTGAAAGTAGAGCAAAAG 58.571 34.615 0.00 0.00 0.00 2.27
2785 4167 2.026262 CCCACACCAACTAGCCAACTAT 60.026 50.000 0.00 0.00 0.00 2.12
2873 4256 4.471904 TCAACACTTGACTTGTCTCTGT 57.528 40.909 2.35 0.00 34.08 3.41
2878 4261 2.952978 ACTTGACTTGTCTCTGTCGTCT 59.047 45.455 2.35 0.00 36.10 4.18
3112 4498 2.241176 ACCACAAAGAAGACCCAAGACA 59.759 45.455 0.00 0.00 0.00 3.41
3113 4499 3.287222 CCACAAAGAAGACCCAAGACAA 58.713 45.455 0.00 0.00 0.00 3.18
3352 4743 1.694169 GCCTCCAGGAAGGGGATCA 60.694 63.158 0.00 0.00 42.25 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.935327 GCTAGAGAACACCGACGGCT 61.935 60.000 15.39 1.99 0.00 5.52
93 94 3.386486 TCGTTATTCGTTCACAAGTGCT 58.614 40.909 0.00 0.00 40.80 4.40
94 95 3.427528 TCTCGTTATTCGTTCACAAGTGC 59.572 43.478 0.00 0.00 40.80 4.40
109 110 7.363530 GGGCCATACATATACTTGATCTCGTTA 60.364 40.741 4.39 0.00 0.00 3.18
113 114 6.552445 AGGGCCATACATATACTTGATCTC 57.448 41.667 6.18 0.00 0.00 2.75
162 163 8.845227 TCTAGTAATTTGCACTTGATTGTTCAA 58.155 29.630 0.00 0.00 39.54 2.69
164 165 9.118236 GTTCTAGTAATTTGCACTTGATTGTTC 57.882 33.333 0.00 0.00 29.90 3.18
186 187 7.173907 CCAACATTACAGAATGACTTCAGTTCT 59.826 37.037 4.73 0.00 44.59 3.01
280 281 1.234821 GCCGACAAAACATGAGTCCA 58.765 50.000 0.00 0.00 0.00 4.02
281 282 0.165944 CGCCGACAAAACATGAGTCC 59.834 55.000 0.00 0.00 0.00 3.85
290 291 1.069296 CATTTGAGAGCGCCGACAAAA 60.069 47.619 20.81 10.30 36.19 2.44
399 402 1.114722 TTGGCCCAGCTTCTGTTTGG 61.115 55.000 0.00 0.00 0.00 3.28
406 763 1.826720 TCATGATTTTGGCCCAGCTTC 59.173 47.619 0.00 0.00 0.00 3.86
446 803 4.689812 GCTGCCATTGATGTCTAGTATCAG 59.310 45.833 10.70 0.00 36.07 2.90
452 809 3.550233 GCATTGCTGCCATTGATGTCTAG 60.550 47.826 0.16 0.00 42.88 2.43
453 810 2.359848 GCATTGCTGCCATTGATGTCTA 59.640 45.455 0.16 0.00 42.88 2.59
476 833 7.489113 CACTAAAATTTACCATCCTTGCATGAC 59.511 37.037 0.00 0.00 0.00 3.06
498 855 4.380841 AGAAACTTGTCGTGTGTCACTA 57.619 40.909 4.27 0.00 31.34 2.74
539 897 1.005294 GCAAGCATGGCAACTTCGTG 61.005 55.000 3.39 0.00 32.79 4.35
558 917 3.841643 CAAGGATTGCAACTTTAGCTGG 58.158 45.455 0.00 0.00 40.39 4.85
626 985 1.547372 ACCCTAATAAGTGTCACGCGT 59.453 47.619 5.58 5.58 0.00 6.01
627 986 2.190981 GACCCTAATAAGTGTCACGCG 58.809 52.381 3.53 3.53 0.00 6.01
628 987 2.093869 TGGACCCTAATAAGTGTCACGC 60.094 50.000 0.00 0.00 0.00 5.34
667 1033 2.632360 CCCTCCCATCCCTTTCTCCTAA 60.632 54.545 0.00 0.00 0.00 2.69
669 1035 0.327964 CCCTCCCATCCCTTTCTCCT 60.328 60.000 0.00 0.00 0.00 3.69
684 1050 3.350219 TCTTTGCCTACACATTCCCTC 57.650 47.619 0.00 0.00 0.00 4.30
724 1090 9.109393 TCGAATAAGGGATCACAAATTCTAAAG 57.891 33.333 16.02 5.29 0.00 1.85
727 1093 8.482943 TCTTCGAATAAGGGATCACAAATTCTA 58.517 33.333 16.02 6.58 0.00 2.10
729 1095 7.553881 TCTTCGAATAAGGGATCACAAATTC 57.446 36.000 0.00 10.70 0.00 2.17
775 1144 7.147828 CCACCTTCCTTCTTCTTCTTTCTTTTT 60.148 37.037 0.00 0.00 0.00 1.94
776 1145 6.322456 CCACCTTCCTTCTTCTTCTTTCTTTT 59.678 38.462 0.00 0.00 0.00 2.27
778 1147 5.132816 TCCACCTTCCTTCTTCTTCTTTCTT 59.867 40.000 0.00 0.00 0.00 2.52
779 1148 4.660771 TCCACCTTCCTTCTTCTTCTTTCT 59.339 41.667 0.00 0.00 0.00 2.52
780 1149 4.974399 TCCACCTTCCTTCTTCTTCTTTC 58.026 43.478 0.00 0.00 0.00 2.62
781 1150 4.202514 CCTCCACCTTCCTTCTTCTTCTTT 60.203 45.833 0.00 0.00 0.00 2.52
782 1151 3.329225 CCTCCACCTTCCTTCTTCTTCTT 59.671 47.826 0.00 0.00 0.00 2.52
783 1152 2.909662 CCTCCACCTTCCTTCTTCTTCT 59.090 50.000 0.00 0.00 0.00 2.85
784 1153 2.026729 CCCTCCACCTTCCTTCTTCTTC 60.027 54.545 0.00 0.00 0.00 2.87
785 1154 1.988846 CCCTCCACCTTCCTTCTTCTT 59.011 52.381 0.00 0.00 0.00 2.52
786 1155 1.152271 TCCCTCCACCTTCCTTCTTCT 59.848 52.381 0.00 0.00 0.00 2.85
787 1156 1.557371 CTCCCTCCACCTTCCTTCTTC 59.443 57.143 0.00 0.00 0.00 2.87
788 1157 1.662686 CTCCCTCCACCTTCCTTCTT 58.337 55.000 0.00 0.00 0.00 2.52
789 1158 0.252927 CCTCCCTCCACCTTCCTTCT 60.253 60.000 0.00 0.00 0.00 2.85
790 1159 1.916206 GCCTCCCTCCACCTTCCTTC 61.916 65.000 0.00 0.00 0.00 3.46
791 1160 1.925972 GCCTCCCTCCACCTTCCTT 60.926 63.158 0.00 0.00 0.00 3.36
792 1161 2.285743 GCCTCCCTCCACCTTCCT 60.286 66.667 0.00 0.00 0.00 3.36
793 1162 1.575447 AATGCCTCCCTCCACCTTCC 61.575 60.000 0.00 0.00 0.00 3.46
794 1163 0.394899 CAATGCCTCCCTCCACCTTC 60.395 60.000 0.00 0.00 0.00 3.46
795 1164 1.693640 CAATGCCTCCCTCCACCTT 59.306 57.895 0.00 0.00 0.00 3.50
796 1165 2.311854 CCAATGCCTCCCTCCACCT 61.312 63.158 0.00 0.00 0.00 4.00
797 1166 1.649271 ATCCAATGCCTCCCTCCACC 61.649 60.000 0.00 0.00 0.00 4.61
798 1167 0.466922 CATCCAATGCCTCCCTCCAC 60.467 60.000 0.00 0.00 0.00 4.02
799 1168 0.624206 TCATCCAATGCCTCCCTCCA 60.624 55.000 0.00 0.00 0.00 3.86
800 1169 0.776176 ATCATCCAATGCCTCCCTCC 59.224 55.000 0.00 0.00 0.00 4.30
801 1170 1.547223 CCATCATCCAATGCCTCCCTC 60.547 57.143 0.00 0.00 0.00 4.30
802 1171 0.481567 CCATCATCCAATGCCTCCCT 59.518 55.000 0.00 0.00 0.00 4.20
803 1172 0.479815 TCCATCATCCAATGCCTCCC 59.520 55.000 0.00 0.00 0.00 4.30
813 1182 2.341257 CAATCGACCGATCCATCATCC 58.659 52.381 5.32 0.00 33.08 3.51
906 1276 1.351017 GACCACCTCATCTCCCAACAA 59.649 52.381 0.00 0.00 0.00 2.83
1038 2237 2.510768 AGATCCATCGCCGTAGTTTC 57.489 50.000 0.00 0.00 0.00 2.78
1463 2668 0.744771 GGCCAAACGAGAGATGGGAC 60.745 60.000 0.00 0.00 40.35 4.46
1501 2720 1.808343 GTGCCCTAAAAACCCTACACG 59.192 52.381 0.00 0.00 0.00 4.49
1547 2789 2.995258 GGCTGCACAACCACATTAATTG 59.005 45.455 0.50 0.00 0.00 2.32
1548 2790 2.352617 CGGCTGCACAACCACATTAATT 60.353 45.455 0.50 0.00 0.00 1.40
1550 2792 0.595588 CGGCTGCACAACCACATTAA 59.404 50.000 0.50 0.00 0.00 1.40
1551 2793 0.250510 TCGGCTGCACAACCACATTA 60.251 50.000 0.50 0.00 0.00 1.90
1794 3076 1.748879 GATACGCTGCTTGCCCCAA 60.749 57.895 0.00 0.00 38.78 4.12
1853 3135 4.500116 GCGACGACAGGCCTCTCC 62.500 72.222 0.00 0.00 0.00 3.71
2044 3354 3.692406 GTCCTGGAGAACGCCCGT 61.692 66.667 0.00 0.00 0.00 5.28
2139 3455 1.717032 TGTGTAGCACTTCCTCCAGT 58.283 50.000 0.90 0.00 35.11 4.00
2249 3572 0.178068 AGCGACAAAGTCCACACACT 59.822 50.000 0.00 0.00 0.00 3.55
2277 3600 3.512724 CCTCCATCACAAAGAAGGCAAAT 59.487 43.478 0.00 0.00 35.06 2.32
2313 3636 1.723870 GTGCCCTGCGAACATGATC 59.276 57.895 0.00 0.00 0.00 2.92
2418 3772 7.931578 ATGGAAACGAAATGGTAATTGTAGA 57.068 32.000 0.00 0.00 0.00 2.59
2605 3964 0.321564 CTGTCCGGTTGATGGCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
2629 3988 1.212688 CCTGTAATGTGATGCCCCTGA 59.787 52.381 0.00 0.00 0.00 3.86
2638 3997 9.219603 CTCTACTTTCAATTTCCTGTAATGTGA 57.780 33.333 0.00 0.00 0.00 3.58
2669 4036 5.809001 TGTGCCATGTATCTTTCTTTCTCT 58.191 37.500 0.00 0.00 0.00 3.10
2670 4037 6.404074 CCTTGTGCCATGTATCTTTCTTTCTC 60.404 42.308 0.00 0.00 0.00 2.87
2785 4167 2.909965 GCCCGCCTTTTGTGTCCA 60.910 61.111 0.00 0.00 0.00 4.02
2852 4235 4.433615 GACAGAGACAAGTCAAGTGTTGA 58.566 43.478 2.72 0.00 37.33 3.18
2863 4246 3.312828 CCTTTGAGACGACAGAGACAAG 58.687 50.000 0.00 0.00 0.00 3.16
2873 4256 0.606604 GTAGTGGCCCTTTGAGACGA 59.393 55.000 0.00 0.00 0.00 4.20
2878 4261 0.774491 AAGGGGTAGTGGCCCTTTGA 60.774 55.000 0.00 0.00 44.95 2.69
2895 4278 0.390860 CCCATCGAGCCTAGGTGAAG 59.609 60.000 11.31 3.57 0.00 3.02
3112 4498 2.124736 CCGATGCCACCCGATGTT 60.125 61.111 0.00 0.00 0.00 2.71
3113 4499 4.175337 CCCGATGCCACCCGATGT 62.175 66.667 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.