Multiple sequence alignment - TraesCS7D01G187000

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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 TraesCS7D01G187000 chr7D 100.000 2420 0 0 1 2420 139827859 139830278 0.000000e+00 4470
1 TraesCS7D01G187000 chr7B 91.241 1233 56 23 1191 2401 104757830 104759032 0.000000e+00 1631
2 TraesCS7D01G187000 chr7B 88.738 515 26 14 694 1198 104757307 104757799 3.440000e-168 601
3 TraesCS7D01G187000 chr7B 90.452 398 14 6 318 697 104755358 104755749 9.990000e-139 503
4 TraesCS7D01G187000 chr7B 89.076 238 12 5 92 321 104755044 104755275 1.420000e-72 283
5 TraesCS7D01G187000 chr7A 86.291 941 46 35 628 1521 139467812 139468716 0.000000e+00 946
6 TraesCS7D01G187000 chr7A 94.819 386 15 3 1629 2011 139468732 139469115 4.450000e-167 597
7 TraesCS7D01G187000 chr7A 88.318 428 20 15 2007 2414 139469394 139469811 1.010000e-133 486
8 TraesCS7D01G187000 chr7A 88.589 333 10 16 312 624 139454420 139454744 1.760000e-101 379
9 TraesCS7D01G187000 chr7A 91.566 166 7 4 158 321 139454188 139454348 3.130000e-54 222
10 TraesCS7D01G187000 chr6A 89.172 157 17 0 1262 1418 539865938 539866094 1.900000e-46 196
11 TraesCS7D01G187000 chr6D 88.535 157 18 0 1262 1418 393299674 393299830 8.830000e-45 191
12 TraesCS7D01G187000 chr6B 87.898 157 19 0 1262 1418 587799118 587799274 4.110000e-43 185


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 TraesCS7D01G187000 chr7D 139827859 139830278 2419 False 4470.000000 4470 100.000000 1 2420 1 chr7D.!!$F1 2419
1 TraesCS7D01G187000 chr7B 104755044 104759032 3988 False 754.500000 1631 89.876750 92 2401 4 chr7B.!!$F1 2309
2 TraesCS7D01G187000 chr7A 139467812 139469811 1999 False 676.333333 946 89.809333 628 2414 3 chr7A.!!$F2 1786
3 TraesCS7D01G187000 chr7A 139454188 139454744 556 False 300.500000 379 90.077500 158 624 2 chr7A.!!$F1 466

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
691 815 0.235926 CATGCATGCAGATCGAGCTG 59.764 55.0 25.87 25.87 38.91 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 3492 0.108774 GGATCGGAGGGATGGAAACC 59.891 60.0 0.0 0.0 34.82 3.27 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
21 22 3.877559 TCCTGTCATTAAGCATCCACTG 58.122 45.455 0.00 0.00 0.00 3.66
22 23 3.264193 TCCTGTCATTAAGCATCCACTGT 59.736 43.478 0.00 0.00 0.00 3.55
23 24 4.012374 CCTGTCATTAAGCATCCACTGTT 58.988 43.478 0.00 0.00 0.00 3.16
24 25 5.045942 TCCTGTCATTAAGCATCCACTGTTA 60.046 40.000 0.00 0.00 0.00 2.41
25 26 5.647658 CCTGTCATTAAGCATCCACTGTTAA 59.352 40.000 0.00 0.00 0.00 2.01
26 27 6.403636 CCTGTCATTAAGCATCCACTGTTAAC 60.404 42.308 0.00 0.00 0.00 2.01
27 28 6.237901 TGTCATTAAGCATCCACTGTTAACT 58.762 36.000 7.22 0.00 0.00 2.24
28 29 6.149308 TGTCATTAAGCATCCACTGTTAACTG 59.851 38.462 10.63 10.63 0.00 3.16
29 30 6.149474 GTCATTAAGCATCCACTGTTAACTGT 59.851 38.462 11.94 11.94 0.00 3.55
30 31 6.714810 TCATTAAGCATCCACTGTTAACTGTT 59.285 34.615 14.75 0.00 0.00 3.16
31 32 7.880713 TCATTAAGCATCCACTGTTAACTGTTA 59.119 33.333 14.75 7.48 0.00 2.41
32 33 8.511321 CATTAAGCATCCACTGTTAACTGTTAA 58.489 33.333 14.75 8.84 0.00 2.01
33 34 6.560253 AAGCATCCACTGTTAACTGTTAAG 57.440 37.500 14.75 5.59 0.00 1.85
34 35 4.455877 AGCATCCACTGTTAACTGTTAAGC 59.544 41.667 14.75 15.05 0.00 3.09
35 36 4.215399 GCATCCACTGTTAACTGTTAAGCA 59.785 41.667 14.75 12.36 0.00 3.91
36 37 5.106157 GCATCCACTGTTAACTGTTAAGCAT 60.106 40.000 14.75 0.00 0.00 3.79
37 38 5.940192 TCCACTGTTAACTGTTAAGCATG 57.060 39.130 14.75 10.69 0.00 4.06
38 39 5.373222 TCCACTGTTAACTGTTAAGCATGT 58.627 37.500 14.75 7.23 0.00 3.21
39 40 5.238432 TCCACTGTTAACTGTTAAGCATGTG 59.762 40.000 14.75 16.15 0.00 3.21
40 41 5.451908 CACTGTTAACTGTTAAGCATGTGG 58.548 41.667 14.75 6.01 0.00 4.17
41 42 5.008613 CACTGTTAACTGTTAAGCATGTGGT 59.991 40.000 14.75 6.50 0.00 4.16
42 43 5.592688 ACTGTTAACTGTTAAGCATGTGGTT 59.407 36.000 12.97 2.80 39.33 3.67
43 44 6.768861 ACTGTTAACTGTTAAGCATGTGGTTA 59.231 34.615 12.97 0.84 37.00 2.85
44 45 7.447238 ACTGTTAACTGTTAAGCATGTGGTTAT 59.553 33.333 12.97 0.00 37.76 1.89
45 46 8.850007 TGTTAACTGTTAAGCATGTGGTTATA 57.150 30.769 12.97 0.00 37.76 0.98
46 47 8.723311 TGTTAACTGTTAAGCATGTGGTTATAC 58.277 33.333 12.97 7.53 37.76 1.47
47 48 8.943002 GTTAACTGTTAAGCATGTGGTTATACT 58.057 33.333 12.97 0.00 37.76 2.12
50 51 8.662781 ACTGTTAAGCATGTGGTTATACTATG 57.337 34.615 5.60 0.00 37.76 2.23
51 52 7.226720 ACTGTTAAGCATGTGGTTATACTATGC 59.773 37.037 5.60 0.00 43.23 3.14
52 53 6.201997 TGTTAAGCATGTGGTTATACTATGCG 59.798 38.462 5.60 0.00 46.38 4.73
53 54 4.600692 AGCATGTGGTTATACTATGCGA 57.399 40.909 0.00 0.00 46.38 5.10
54 55 4.560128 AGCATGTGGTTATACTATGCGAG 58.440 43.478 0.00 0.00 46.38 5.03
55 56 4.280929 AGCATGTGGTTATACTATGCGAGA 59.719 41.667 0.00 0.00 46.38 4.04
56 57 5.047021 AGCATGTGGTTATACTATGCGAGAT 60.047 40.000 0.00 0.00 46.38 2.75
57 58 5.289675 GCATGTGGTTATACTATGCGAGATC 59.710 44.000 0.00 0.00 35.39 2.75
58 59 5.386958 TGTGGTTATACTATGCGAGATCC 57.613 43.478 0.00 0.00 0.00 3.36
59 60 4.830600 TGTGGTTATACTATGCGAGATCCA 59.169 41.667 0.00 0.00 0.00 3.41
60 61 5.162075 GTGGTTATACTATGCGAGATCCAC 58.838 45.833 0.00 0.00 35.61 4.02
61 62 5.047943 GTGGTTATACTATGCGAGATCCACT 60.048 44.000 0.00 0.00 38.63 4.00
62 63 5.048013 TGGTTATACTATGCGAGATCCACTG 60.048 44.000 0.00 0.00 0.00 3.66
63 64 5.047943 GGTTATACTATGCGAGATCCACTGT 60.048 44.000 0.00 0.00 0.00 3.55
64 65 6.448006 GTTATACTATGCGAGATCCACTGTT 58.552 40.000 0.00 0.00 0.00 3.16
65 66 3.895232 ACTATGCGAGATCCACTGTTT 57.105 42.857 0.00 0.00 0.00 2.83
66 67 4.207891 ACTATGCGAGATCCACTGTTTT 57.792 40.909 0.00 0.00 0.00 2.43
67 68 4.579869 ACTATGCGAGATCCACTGTTTTT 58.420 39.130 0.00 0.00 0.00 1.94
95 96 4.094887 TGTCGAATCTTAAGCATCCAAAGC 59.905 41.667 0.00 0.00 0.00 3.51
113 114 0.455005 GCGTACTCCTCCTACCACAC 59.545 60.000 0.00 0.00 0.00 3.82
131 139 2.038952 ACACAGGACAAGCTAGCAATGA 59.961 45.455 22.70 0.00 0.00 2.57
137 145 2.799412 GACAAGCTAGCAATGAGATCGG 59.201 50.000 22.70 0.22 0.00 4.18
321 332 0.679002 CCACCCATTGACCAGAGCTG 60.679 60.000 0.00 0.00 0.00 4.24
323 334 1.302285 CCCATTGACCAGAGCTGCT 59.698 57.895 0.00 0.00 0.00 4.24
324 335 1.030488 CCCATTGACCAGAGCTGCTG 61.030 60.000 7.01 0.00 44.49 4.41
347 446 1.600076 GATCTGGCGGCATCTGCAT 60.600 57.895 13.85 0.00 44.36 3.96
474 581 1.673767 TCTCCTCTCCTGGCCATTTT 58.326 50.000 5.51 0.00 0.00 1.82
491 598 3.646023 TTGCTACGTTACCGGCCGG 62.646 63.158 42.17 42.17 38.78 6.13
554 661 3.256960 GTGGCAAGTGGAGGGGGA 61.257 66.667 0.00 0.00 0.00 4.81
673 797 1.139256 TCTGTGTAAGAAACGGCACCA 59.861 47.619 0.00 0.00 29.54 4.17
686 810 1.008881 GCACCATGCATGCAGATCG 60.009 57.895 26.69 15.12 44.26 3.69
687 811 1.441732 GCACCATGCATGCAGATCGA 61.442 55.000 26.69 0.16 44.26 3.59
688 812 0.586802 CACCATGCATGCAGATCGAG 59.413 55.000 26.69 12.38 0.00 4.04
689 813 1.164662 ACCATGCATGCAGATCGAGC 61.165 55.000 26.69 6.28 0.00 5.03
690 814 0.885150 CCATGCATGCAGATCGAGCT 60.885 55.000 26.69 0.00 0.00 4.09
691 815 0.235926 CATGCATGCAGATCGAGCTG 59.764 55.000 25.87 25.87 38.91 4.24
729 2409 2.075979 AACGACCGCTAACTCCTTTC 57.924 50.000 0.00 0.00 0.00 2.62
766 2447 7.501892 AGATCTCCTTTTCCTAATCTGCATTTC 59.498 37.037 0.00 0.00 0.00 2.17
780 2461 2.235155 TGCATTTCTCTTGGCCTACGTA 59.765 45.455 3.32 0.00 0.00 3.57
781 2462 2.608090 GCATTTCTCTTGGCCTACGTAC 59.392 50.000 3.32 0.00 0.00 3.67
782 2463 2.642139 TTTCTCTTGGCCTACGTACG 57.358 50.000 15.01 15.01 0.00 3.67
783 2464 1.538047 TTCTCTTGGCCTACGTACGT 58.462 50.000 25.98 25.98 0.00 3.57
804 2485 2.430694 TCATCGACCCTGTCTTGTATGG 59.569 50.000 0.00 0.00 0.00 2.74
806 2487 2.100197 TCGACCCTGTCTTGTATGGAG 58.900 52.381 0.00 0.00 0.00 3.86
921 2616 3.558411 CGCACTTCGCAGCTAGCC 61.558 66.667 12.13 0.00 42.60 3.93
922 2617 3.558411 GCACTTCGCAGCTAGCCG 61.558 66.667 12.13 9.21 41.38 5.52
923 2618 3.558411 CACTTCGCAGCTAGCCGC 61.558 66.667 13.13 13.13 41.38 6.53
943 2638 1.139095 CGCCCACTCTACTTCCGAC 59.861 63.158 0.00 0.00 0.00 4.79
958 2653 1.080230 CGACCACACAGCCTCTCAG 60.080 63.158 0.00 0.00 0.00 3.35
986 2681 3.104602 CTTCGCTCGCCCTGCATTG 62.105 63.158 0.00 0.00 0.00 2.82
1117 2812 3.130160 GCAGCAGCAGCCAGGTAC 61.130 66.667 0.00 0.00 43.56 3.34
1118 2813 2.816958 CAGCAGCAGCCAGGTACG 60.817 66.667 0.00 0.00 43.56 3.67
1119 2814 2.997315 AGCAGCAGCCAGGTACGA 60.997 61.111 0.00 0.00 43.56 3.43
1208 2942 1.237285 AAGCCACGGTGCAAGCTTAG 61.237 55.000 17.66 0.00 43.47 2.18
1426 3172 1.340211 GCCTCCTCCGCTAGCTAGATA 60.340 57.143 25.15 7.38 0.00 1.98
1427 3173 2.361789 CCTCCTCCGCTAGCTAGATAC 58.638 57.143 25.15 5.87 0.00 2.24
1446 3192 5.484290 AGATACCTGCTCATCATCATCATCA 59.516 40.000 0.00 0.00 0.00 3.07
1447 3193 4.642466 ACCTGCTCATCATCATCATCAT 57.358 40.909 0.00 0.00 0.00 2.45
1450 3196 5.189180 CCTGCTCATCATCATCATCATCAT 58.811 41.667 0.00 0.00 0.00 2.45
1451 3197 5.295540 CCTGCTCATCATCATCATCATCATC 59.704 44.000 0.00 0.00 0.00 2.92
1452 3198 5.804639 TGCTCATCATCATCATCATCATCA 58.195 37.500 0.00 0.00 0.00 3.07
1453 3199 6.418101 TGCTCATCATCATCATCATCATCAT 58.582 36.000 0.00 0.00 0.00 2.45
1454 3200 6.317140 TGCTCATCATCATCATCATCATCATG 59.683 38.462 0.00 0.00 0.00 3.07
1485 3231 3.129871 CTGCTGATTGTCCTAAGCTAGC 58.870 50.000 6.62 6.62 36.60 3.42
1506 3252 3.610585 GCTCATCATCTACGTACAGCTCC 60.611 52.174 0.00 0.00 0.00 4.70
1578 3324 0.522180 ATATGCCGTCCGTCGATCTC 59.478 55.000 0.00 0.00 42.86 2.75
1589 3335 1.783711 CGTCGATCTCTGCAAGCATAC 59.216 52.381 0.00 0.00 0.00 2.39
1609 3355 7.545897 CATACATATGCAGATCGATCGATAC 57.454 40.000 29.45 21.14 34.60 2.24
1624 3377 2.628178 TCGATACCTAAGGACTGCATGG 59.372 50.000 0.00 0.00 0.00 3.66
1730 3492 0.893270 TTGCATGTGGTTTCCTCCCG 60.893 55.000 0.00 0.00 0.00 5.14
1879 3644 5.539048 GGTGGTGGTACTGCTAATATACTG 58.461 45.833 0.00 0.00 0.00 2.74
1889 3654 5.413213 ACTGCTAATATACTGCTCCTACTCG 59.587 44.000 0.00 0.00 0.00 4.18
1950 3715 2.092968 TGGCTTCGGCTGAATGACTATT 60.093 45.455 8.78 0.00 41.44 1.73
1951 3716 3.133901 TGGCTTCGGCTGAATGACTATTA 59.866 43.478 8.78 0.00 41.44 0.98
1992 3759 9.109393 TGATTATGTTATCTGTTAAAGCTCCAC 57.891 33.333 0.00 0.00 0.00 4.02
2066 4113 3.684788 GGTTCATGTGCTCGTTGATTACT 59.315 43.478 0.00 0.00 0.00 2.24
2085 4132 0.386352 TCAAGACAGTAACGGACGCG 60.386 55.000 3.53 3.53 0.00 6.01
2086 4133 1.731969 AAGACAGTAACGGACGCGC 60.732 57.895 5.73 0.00 0.00 6.86
2281 4336 0.322546 AAAGGGATGCCAGACGGTTC 60.323 55.000 5.86 0.00 33.28 3.62
2373 4439 1.513158 CAGTCGGCCACTACTCTGG 59.487 63.158 2.24 0.00 32.21 3.86
2414 4480 2.782615 GCATGGAACGTACGTGCC 59.217 61.111 34.56 34.56 43.30 5.01
2415 4481 2.746803 GCATGGAACGTACGTGCCC 61.747 63.158 36.84 30.27 43.29 5.36
2416 4482 2.125832 ATGGAACGTACGTGCCCG 60.126 61.111 36.84 4.69 43.29 6.13
2417 4483 3.652539 ATGGAACGTACGTGCCCGG 62.653 63.158 36.84 0.00 43.29 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.264193 ACAGTGGATGCTTAATGACAGGA 59.736 43.478 0.00 0.00 0.00 3.86
1 2 3.614092 ACAGTGGATGCTTAATGACAGG 58.386 45.455 0.00 0.00 0.00 4.00
2 3 6.372659 AGTTAACAGTGGATGCTTAATGACAG 59.627 38.462 8.61 0.00 0.00 3.51
3 4 6.149308 CAGTTAACAGTGGATGCTTAATGACA 59.851 38.462 8.61 0.00 0.00 3.58
4 5 6.149474 ACAGTTAACAGTGGATGCTTAATGAC 59.851 38.462 8.61 0.00 0.00 3.06
5 6 6.237901 ACAGTTAACAGTGGATGCTTAATGA 58.762 36.000 8.61 0.00 0.00 2.57
6 7 6.500684 ACAGTTAACAGTGGATGCTTAATG 57.499 37.500 8.61 0.00 0.00 1.90
7 8 8.630054 TTAACAGTTAACAGTGGATGCTTAAT 57.370 30.769 8.61 0.00 0.00 1.40
8 9 7.308348 GCTTAACAGTTAACAGTGGATGCTTAA 60.308 37.037 8.61 0.00 0.00 1.85
9 10 6.148811 GCTTAACAGTTAACAGTGGATGCTTA 59.851 38.462 8.61 0.00 0.00 3.09
10 11 5.048713 GCTTAACAGTTAACAGTGGATGCTT 60.049 40.000 8.61 0.00 0.00 3.91
11 12 4.455877 GCTTAACAGTTAACAGTGGATGCT 59.544 41.667 8.61 0.00 0.00 3.79
12 13 4.215399 TGCTTAACAGTTAACAGTGGATGC 59.785 41.667 8.61 11.44 0.00 3.91
13 14 5.940192 TGCTTAACAGTTAACAGTGGATG 57.060 39.130 8.61 0.00 0.00 3.51
14 15 6.003950 ACATGCTTAACAGTTAACAGTGGAT 58.996 36.000 8.61 0.00 0.00 3.41
15 16 5.238432 CACATGCTTAACAGTTAACAGTGGA 59.762 40.000 8.61 0.00 0.00 4.02
16 17 5.451908 CACATGCTTAACAGTTAACAGTGG 58.548 41.667 8.61 2.11 0.00 4.00
17 18 5.008613 ACCACATGCTTAACAGTTAACAGTG 59.991 40.000 8.61 12.74 0.00 3.66
18 19 5.130350 ACCACATGCTTAACAGTTAACAGT 58.870 37.500 8.61 2.62 0.00 3.55
19 20 5.689383 ACCACATGCTTAACAGTTAACAG 57.311 39.130 8.61 1.86 0.00 3.16
20 21 7.753309 ATAACCACATGCTTAACAGTTAACA 57.247 32.000 8.61 6.29 0.00 2.41
21 22 8.943002 AGTATAACCACATGCTTAACAGTTAAC 58.057 33.333 1.26 0.00 0.00 2.01
24 25 9.109393 CATAGTATAACCACATGCTTAACAGTT 57.891 33.333 0.00 0.00 0.00 3.16
25 26 7.226720 GCATAGTATAACCACATGCTTAACAGT 59.773 37.037 0.00 0.00 39.09 3.55
26 27 7.569408 CGCATAGTATAACCACATGCTTAACAG 60.569 40.741 0.00 0.00 39.82 3.16
27 28 6.201997 CGCATAGTATAACCACATGCTTAACA 59.798 38.462 0.00 0.00 39.82 2.41
28 29 6.422701 TCGCATAGTATAACCACATGCTTAAC 59.577 38.462 0.00 0.00 39.82 2.01
29 30 6.517605 TCGCATAGTATAACCACATGCTTAA 58.482 36.000 0.00 0.00 39.82 1.85
30 31 6.015772 TCTCGCATAGTATAACCACATGCTTA 60.016 38.462 0.00 0.00 39.82 3.09
31 32 4.956085 TCGCATAGTATAACCACATGCTT 58.044 39.130 0.00 0.00 39.82 3.91
32 33 4.280929 TCTCGCATAGTATAACCACATGCT 59.719 41.667 0.00 0.00 39.82 3.79
33 34 4.556233 TCTCGCATAGTATAACCACATGC 58.444 43.478 0.00 0.00 38.86 4.06
34 35 5.807520 GGATCTCGCATAGTATAACCACATG 59.192 44.000 0.00 0.00 0.00 3.21
35 36 5.480422 TGGATCTCGCATAGTATAACCACAT 59.520 40.000 0.00 0.00 0.00 3.21
36 37 4.830600 TGGATCTCGCATAGTATAACCACA 59.169 41.667 0.00 0.00 0.00 4.17
37 38 5.047943 AGTGGATCTCGCATAGTATAACCAC 60.048 44.000 0.00 0.00 42.61 4.16
38 39 5.048013 CAGTGGATCTCGCATAGTATAACCA 60.048 44.000 0.00 0.00 0.00 3.67
39 40 5.047943 ACAGTGGATCTCGCATAGTATAACC 60.048 44.000 0.00 0.00 0.00 2.85
40 41 6.015027 ACAGTGGATCTCGCATAGTATAAC 57.985 41.667 0.00 0.00 0.00 1.89
41 42 6.650427 AACAGTGGATCTCGCATAGTATAA 57.350 37.500 0.00 0.00 0.00 0.98
42 43 6.650427 AAACAGTGGATCTCGCATAGTATA 57.350 37.500 0.00 0.00 0.00 1.47
43 44 5.537300 AAACAGTGGATCTCGCATAGTAT 57.463 39.130 0.00 0.00 0.00 2.12
44 45 5.339008 AAAACAGTGGATCTCGCATAGTA 57.661 39.130 0.00 0.00 0.00 1.82
45 46 3.895232 AAACAGTGGATCTCGCATAGT 57.105 42.857 0.00 0.00 0.00 2.12
68 69 6.567687 TGGATGCTTAAGATTCGACAAAAA 57.432 33.333 6.67 0.00 0.00 1.94
69 70 6.567687 TTGGATGCTTAAGATTCGACAAAA 57.432 33.333 6.67 0.00 0.00 2.44
70 71 6.567687 TTTGGATGCTTAAGATTCGACAAA 57.432 33.333 6.67 6.54 0.00 2.83
71 72 5.391950 GCTTTGGATGCTTAAGATTCGACAA 60.392 40.000 6.67 0.54 0.00 3.18
72 73 4.094887 GCTTTGGATGCTTAAGATTCGACA 59.905 41.667 6.67 0.00 0.00 4.35
73 74 4.592179 GCTTTGGATGCTTAAGATTCGAC 58.408 43.478 6.67 0.00 0.00 4.20
74 75 3.309682 CGCTTTGGATGCTTAAGATTCGA 59.690 43.478 6.67 0.00 0.00 3.71
75 76 3.063997 ACGCTTTGGATGCTTAAGATTCG 59.936 43.478 6.67 0.00 0.00 3.34
76 77 4.622701 ACGCTTTGGATGCTTAAGATTC 57.377 40.909 6.67 1.57 0.00 2.52
77 78 5.186198 AGTACGCTTTGGATGCTTAAGATT 58.814 37.500 6.67 0.00 0.00 2.40
78 79 4.770795 AGTACGCTTTGGATGCTTAAGAT 58.229 39.130 6.67 0.00 0.00 2.40
79 80 4.181578 GAGTACGCTTTGGATGCTTAAGA 58.818 43.478 6.67 0.00 0.00 2.10
80 81 3.309954 GGAGTACGCTTTGGATGCTTAAG 59.690 47.826 0.00 0.00 0.00 1.85
81 82 3.055385 AGGAGTACGCTTTGGATGCTTAA 60.055 43.478 0.00 0.00 0.00 1.85
82 83 2.500098 AGGAGTACGCTTTGGATGCTTA 59.500 45.455 0.00 0.00 0.00 3.09
83 84 1.279271 AGGAGTACGCTTTGGATGCTT 59.721 47.619 0.00 0.00 0.00 3.91
84 85 0.905357 AGGAGTACGCTTTGGATGCT 59.095 50.000 0.00 0.00 0.00 3.79
85 86 1.291132 GAGGAGTACGCTTTGGATGC 58.709 55.000 0.00 0.00 0.00 3.91
86 87 1.482593 AGGAGGAGTACGCTTTGGATG 59.517 52.381 0.00 0.00 0.00 3.51
87 88 1.867363 AGGAGGAGTACGCTTTGGAT 58.133 50.000 0.00 0.00 0.00 3.41
88 89 2.097825 GTAGGAGGAGTACGCTTTGGA 58.902 52.381 0.00 0.00 0.00 3.53
89 90 1.136500 GGTAGGAGGAGTACGCTTTGG 59.864 57.143 0.00 0.00 0.00 3.28
90 91 1.822990 TGGTAGGAGGAGTACGCTTTG 59.177 52.381 0.00 0.00 0.00 2.77
95 96 1.743958 CTGTGTGGTAGGAGGAGTACG 59.256 57.143 0.00 0.00 0.00 3.67
113 114 3.257469 TCTCATTGCTAGCTTGTCCTG 57.743 47.619 17.23 4.58 0.00 3.86
278 287 5.420739 GGAGAACAATATTTTACCAGGGCAA 59.579 40.000 0.00 0.00 0.00 4.52
279 288 4.953579 GGAGAACAATATTTTACCAGGGCA 59.046 41.667 0.00 0.00 0.00 5.36
280 289 4.341235 GGGAGAACAATATTTTACCAGGGC 59.659 45.833 0.00 0.00 0.00 5.19
281 290 5.359860 GTGGGAGAACAATATTTTACCAGGG 59.640 44.000 0.00 0.00 0.00 4.45
282 291 5.359860 GGTGGGAGAACAATATTTTACCAGG 59.640 44.000 0.00 0.00 0.00 4.45
321 332 2.356793 CCGCCAGATCGATCCAGC 60.357 66.667 21.66 21.58 0.00 4.85
323 334 2.440385 GATGCCGCCAGATCGATCCA 62.440 60.000 21.66 11.58 0.00 3.41
324 335 1.739562 GATGCCGCCAGATCGATCC 60.740 63.158 21.66 5.96 0.00 3.36
347 446 4.013728 GAGAAACTCTGGAGTCTAGAGCA 58.986 47.826 28.09 0.00 44.30 4.26
491 598 4.471904 TGTGTTGGTATCATCAGTCTCC 57.528 45.455 0.00 0.00 0.00 3.71
528 635 4.497984 ACTTGCCACGTGCCCACA 62.498 61.111 10.91 2.18 40.16 4.17
673 797 0.885150 CCAGCTCGATCTGCATGCAT 60.885 55.000 22.97 7.28 32.87 3.96
678 802 0.755079 ATTAGCCAGCTCGATCTGCA 59.245 50.000 10.79 0.00 32.87 4.41
679 803 1.876322 AATTAGCCAGCTCGATCTGC 58.124 50.000 10.79 6.66 32.87 4.26
680 804 3.431572 GCTTAATTAGCCAGCTCGATCTG 59.568 47.826 9.32 9.32 44.48 2.90
681 805 3.658709 GCTTAATTAGCCAGCTCGATCT 58.341 45.455 0.00 0.00 44.48 2.75
729 2409 6.611236 AGGAAAAGGAGATCTCTCTCTTAAGG 59.389 42.308 21.81 0.00 46.11 2.69
766 2447 0.806868 TGACGTACGTAGGCCAAGAG 59.193 55.000 22.87 0.00 0.00 2.85
780 2461 0.243907 CAAGACAGGGTCGATGACGT 59.756 55.000 0.00 0.00 37.67 4.34
781 2462 0.243907 ACAAGACAGGGTCGATGACG 59.756 55.000 10.65 0.00 37.67 4.35
782 2463 3.448686 CATACAAGACAGGGTCGATGAC 58.551 50.000 10.65 0.00 37.67 3.06
783 2464 2.430694 CCATACAAGACAGGGTCGATGA 59.569 50.000 10.65 0.00 37.67 2.92
804 2485 1.380650 AGAAGACGGGGAGAGCCTC 60.381 63.158 0.00 0.00 0.00 4.70
806 2487 2.726351 CCAGAAGACGGGGAGAGCC 61.726 68.421 0.00 0.00 0.00 4.70
850 2545 4.621983 GCTTTTATAGCTAGCTAGGGAGGC 60.622 50.000 27.42 22.40 46.77 4.70
921 2616 4.796231 AAGTAGAGTGGGCGCGCG 62.796 66.667 28.44 28.44 0.00 6.86
922 2617 2.886124 GAAGTAGAGTGGGCGCGC 60.886 66.667 25.94 25.94 0.00 6.86
923 2618 2.202756 GGAAGTAGAGTGGGCGCG 60.203 66.667 0.00 0.00 0.00 6.86
924 2619 2.202756 CGGAAGTAGAGTGGGCGC 60.203 66.667 0.00 0.00 0.00 6.53
943 2638 1.080230 CGACTGAGAGGCTGTGTGG 60.080 63.158 0.00 0.00 0.00 4.17
986 2681 2.989840 CCAGACATCGTCTTCACAGAAC 59.010 50.000 0.00 0.00 41.37 3.01
1117 2812 1.058438 CTAGTCGTGTCGGTCGTCG 59.942 63.158 0.00 0.00 40.90 5.12
1118 2813 0.514691 AACTAGTCGTGTCGGTCGTC 59.485 55.000 0.00 0.00 0.00 4.20
1119 2814 0.947244 AAACTAGTCGTGTCGGTCGT 59.053 50.000 0.00 0.00 0.00 4.34
1208 2942 5.258051 TCCATAAACCTCCCATAAACACAC 58.742 41.667 0.00 0.00 0.00 3.82
1426 3172 4.041691 TGATGATGATGATGATGAGCAGGT 59.958 41.667 0.00 0.00 0.00 4.00
1427 3173 4.579869 TGATGATGATGATGATGAGCAGG 58.420 43.478 0.00 0.00 0.00 4.85
1485 3231 3.818210 AGGAGCTGTACGTAGATGATGAG 59.182 47.826 0.00 0.00 0.00 2.90
1506 3252 4.416505 GCTTAATTAGCTAGGCATGCAG 57.583 45.455 21.36 10.51 46.77 4.41
1564 3310 2.024871 GCAGAGATCGACGGACGG 59.975 66.667 0.00 0.00 42.82 4.79
1589 3335 5.180367 AGGTATCGATCGATCTGCATATG 57.820 43.478 32.50 5.91 36.17 1.78
1609 3355 2.746472 GCCTTACCATGCAGTCCTTAGG 60.746 54.545 0.00 0.00 0.00 2.69
1624 3377 6.178324 ACCAAGTAAATTAGACCAGCCTTAC 58.822 40.000 0.00 0.00 0.00 2.34
1730 3492 0.108774 GGATCGGAGGGATGGAAACC 59.891 60.000 0.00 0.00 34.82 3.27
1879 3644 3.305471 GGTGATTGATACCGAGTAGGAGC 60.305 52.174 0.00 0.00 45.00 4.70
1889 3654 6.716628 ACATACATTCATGGGTGATTGATACC 59.283 38.462 7.16 0.00 38.48 2.73
1992 3759 3.494045 TCAGTACAACAGCAGATCTCG 57.506 47.619 0.00 0.00 0.00 4.04
2028 4075 5.637810 ACATGAACCAAGAGTGTACGTATTG 59.362 40.000 0.00 0.00 0.00 1.90
2066 4113 0.386352 CGCGTCCGTTACTGTCTTGA 60.386 55.000 0.00 0.00 0.00 3.02
2085 4132 3.799755 GGGTTCGCCATCGTGTGC 61.800 66.667 0.00 0.00 39.65 4.57
2086 4133 2.358125 TGGGTTCGCCATCGTGTG 60.358 61.111 0.00 0.00 39.65 3.82
2115 4162 1.061485 CGCGAGATAGAGACGATCGA 58.939 55.000 24.34 0.00 35.47 3.59
2116 4163 0.785378 ACGCGAGATAGAGACGATCG 59.215 55.000 15.93 14.88 36.51 3.69
2117 4164 2.988493 ACTACGCGAGATAGAGACGATC 59.012 50.000 15.93 0.00 0.00 3.69
2118 4165 3.029320 ACTACGCGAGATAGAGACGAT 57.971 47.619 15.93 0.00 0.00 3.73
2305 4360 2.044946 GGCGGCCTGTCAATTCCT 60.045 61.111 12.87 0.00 0.00 3.36
2307 4362 4.179579 GCGGCGGCCTGTCAATTC 62.180 66.667 18.34 0.00 0.00 2.17
2373 4439 4.200283 CGAGAGGAGACGGGCTGC 62.200 72.222 0.00 0.00 34.75 5.25
2377 4443 2.418910 ATGCACGAGAGGAGACGGG 61.419 63.158 0.00 0.00 35.93 5.28


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

AutoCloner maintained by Alex Coulton.