Multiple sequence alignment - TraesCS1A01G295700

Loading Multiple Alignment...

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 TraesCS1A01G295700 chr1A 100.000 2312 0 0 1 2312 490759070 490761381 0.000000e+00 4270.0
1 TraesCS1A01G295700 chr1A 99.085 656 6 0 1657 2312 490777760 490777105 0.000000e+00 1179.0
2 TraesCS1A01G295700 chr1A 87.538 979 83 19 673 1642 62794796 62793848 0.000000e+00 1096.0
3 TraesCS1A01G295700 chr1A 87.399 992 75 20 672 1640 490418011 490418975 0.000000e+00 1094.0
4 TraesCS1A01G295700 chr1A 90.747 562 45 6 764 1322 487568494 487569051 0.000000e+00 743.0
5 TraesCS1A01G295700 chr1A 89.624 559 53 4 67 624 490417028 490417582 0.000000e+00 706.0
6 TraesCS1A01G295700 chr6B 90.560 964 64 15 690 1642 679983727 679982780 0.000000e+00 1251.0
7 TraesCS1A01G295700 chr6B 84.629 566 70 9 68 624 679984361 679983804 4.340000e-152 547.0
8 TraesCS1A01G295700 chr1D 89.825 973 84 9 674 1642 63682395 63681434 0.000000e+00 1234.0
9 TraesCS1A01G295700 chr1D 90.728 604 40 9 689 1284 394492016 394491421 0.000000e+00 791.0
10 TraesCS1A01G295700 chr1D 89.703 573 53 5 764 1334 388024379 388024947 0.000000e+00 726.0
11 TraesCS1A01G295700 chr1B 89.259 931 78 11 715 1642 104481766 104480855 0.000000e+00 1146.0
12 TraesCS1A01G295700 chr1B 84.315 1154 110 28 525 1641 527287850 527288969 0.000000e+00 1062.0
13 TraesCS1A01G295700 chr1B 85.499 731 87 14 723 1447 608335898 608335181 0.000000e+00 745.0
14 TraesCS1A01G295700 chr7A 94.817 656 16 9 1657 2312 671842844 671843481 0.000000e+00 1007.0
15 TraesCS1A01G295700 chr7A 88.535 628 39 18 1691 2312 543771652 543772252 0.000000e+00 730.0
16 TraesCS1A01G295700 chr7A 97.378 267 7 0 2046 2312 466699985 466700251 2.710000e-124 455.0
17 TraesCS1A01G295700 chr5A 92.593 675 29 9 1657 2312 676326603 676325931 0.000000e+00 950.0
18 TraesCS1A01G295700 chr3D 96.507 458 10 2 1861 2312 114237201 114237658 0.000000e+00 752.0
19 TraesCS1A01G295700 chr3D 92.553 282 17 2 1657 1935 114236945 114237225 3.580000e-108 401.0
20 TraesCS1A01G295700 chr2A 88.339 626 45 15 1690 2312 632408655 632409255 0.000000e+00 726.0
21 TraesCS1A01G295700 chr2A 98.148 54 0 1 1677 1729 710876260 710876313 2.450000e-15 93.5
22 TraesCS1A01G295700 chr4B 90.289 484 29 5 1694 2159 648848070 648847587 3.260000e-173 617.0
23 TraesCS1A01G295700 chr4B 94.035 285 17 0 2028 2312 648847576 648847292 1.270000e-117 433.0
24 TraesCS1A01G295700 chr5B 88.177 406 29 2 1691 2077 38760592 38760997 1.250000e-127 466.0
25 TraesCS1A01G295700 chr5B 91.016 256 17 3 2058 2312 38760911 38761161 7.910000e-90 340.0
26 TraesCS1A01G295700 chr5B 89.130 46 5 0 265 310 439858060 439858105 8.920000e-05 58.4
27 TraesCS1A01G295700 chr7B 87.671 73 2 2 2011 2078 536774277 536774207 6.850000e-11 78.7


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 TraesCS1A01G295700 chr1A 490759070 490761381 2311 False 4270.0 4270 100.0000 1 2312 1 chr1A.!!$F2 2311
1 TraesCS1A01G295700 chr1A 490777105 490777760 655 True 1179.0 1179 99.0850 1657 2312 1 chr1A.!!$R2 655
2 TraesCS1A01G295700 chr1A 62793848 62794796 948 True 1096.0 1096 87.5380 673 1642 1 chr1A.!!$R1 969
3 TraesCS1A01G295700 chr1A 490417028 490418975 1947 False 900.0 1094 88.5115 67 1640 2 chr1A.!!$F3 1573
4 TraesCS1A01G295700 chr1A 487568494 487569051 557 False 743.0 743 90.7470 764 1322 1 chr1A.!!$F1 558
5 TraesCS1A01G295700 chr6B 679982780 679984361 1581 True 899.0 1251 87.5945 68 1642 2 chr6B.!!$R1 1574
6 TraesCS1A01G295700 chr1D 63681434 63682395 961 True 1234.0 1234 89.8250 674 1642 1 chr1D.!!$R1 968
7 TraesCS1A01G295700 chr1D 394491421 394492016 595 True 791.0 791 90.7280 689 1284 1 chr1D.!!$R2 595
8 TraesCS1A01G295700 chr1D 388024379 388024947 568 False 726.0 726 89.7030 764 1334 1 chr1D.!!$F1 570
9 TraesCS1A01G295700 chr1B 104480855 104481766 911 True 1146.0 1146 89.2590 715 1642 1 chr1B.!!$R1 927
10 TraesCS1A01G295700 chr1B 527287850 527288969 1119 False 1062.0 1062 84.3150 525 1641 1 chr1B.!!$F1 1116
11 TraesCS1A01G295700 chr1B 608335181 608335898 717 True 745.0 745 85.4990 723 1447 1 chr1B.!!$R2 724
12 TraesCS1A01G295700 chr7A 671842844 671843481 637 False 1007.0 1007 94.8170 1657 2312 1 chr7A.!!$F3 655
13 TraesCS1A01G295700 chr7A 543771652 543772252 600 False 730.0 730 88.5350 1691 2312 1 chr7A.!!$F2 621
14 TraesCS1A01G295700 chr5A 676325931 676326603 672 True 950.0 950 92.5930 1657 2312 1 chr5A.!!$R1 655
15 TraesCS1A01G295700 chr3D 114236945 114237658 713 False 576.5 752 94.5300 1657 2312 2 chr3D.!!$F1 655
16 TraesCS1A01G295700 chr2A 632408655 632409255 600 False 726.0 726 88.3390 1690 2312 1 chr2A.!!$F1 622
17 TraesCS1A01G295700 chr4B 648847292 648848070 778 True 525.0 617 92.1620 1694 2312 2 chr4B.!!$R1 618
18 TraesCS1A01G295700 chr5B 38760592 38761161 569 False 403.0 466 89.5965 1691 2312 2 chr5B.!!$F2 621

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
53 54 0.107456 ACGACATGATCATGAGGCCC 59.893 55.0 36.37 19.47 41.2 5.80 F
463 473 0.321564 CATCCGCTCCACCTCACAAA 60.322 55.0 0.00 0.00 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1632 0.391661 GGAAGATCTTGAGCACGCCA 60.392 55.0 14.0 0.0 0.00 5.69 R
1652 2148 0.603569 ACTGCTGTCCGTTAGACTGG 59.396 55.0 0.0 0.0 46.46 4.00 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
37 38 4.973055 CGGTTCACGCCCCAACGA 62.973 66.667 0.00 0.00 36.70 3.85
38 39 3.351416 GGTTCACGCCCCAACGAC 61.351 66.667 0.00 0.00 36.70 4.34
39 40 2.589442 GTTCACGCCCCAACGACA 60.589 61.111 0.00 0.00 36.70 4.35
40 41 1.964373 GTTCACGCCCCAACGACAT 60.964 57.895 0.00 0.00 36.70 3.06
41 42 1.963855 TTCACGCCCCAACGACATG 60.964 57.895 0.00 0.00 36.70 3.21
42 43 2.358125 CACGCCCCAACGACATGA 60.358 61.111 0.00 0.00 36.70 3.07
43 44 1.745115 CACGCCCCAACGACATGAT 60.745 57.895 0.00 0.00 36.70 2.45
44 45 1.449601 ACGCCCCAACGACATGATC 60.450 57.895 0.00 0.00 36.70 2.92
45 46 1.449423 CGCCCCAACGACATGATCA 60.449 57.895 0.00 0.00 34.06 2.92
46 47 0.815213 CGCCCCAACGACATGATCAT 60.815 55.000 1.18 1.18 34.06 2.45
47 48 0.664761 GCCCCAACGACATGATCATG 59.335 55.000 29.95 29.95 44.15 3.07
48 49 1.746861 GCCCCAACGACATGATCATGA 60.747 52.381 36.37 0.00 41.20 3.07
49 50 2.216046 CCCCAACGACATGATCATGAG 58.784 52.381 36.37 29.29 41.20 2.90
50 51 2.216046 CCCAACGACATGATCATGAGG 58.784 52.381 36.37 27.81 41.20 3.86
51 52 1.600957 CCAACGACATGATCATGAGGC 59.399 52.381 36.37 23.82 41.20 4.70
52 53 1.600957 CAACGACATGATCATGAGGCC 59.399 52.381 36.37 21.48 41.20 5.19
53 54 0.107456 ACGACATGATCATGAGGCCC 59.893 55.000 36.37 19.47 41.20 5.80
54 55 0.395686 CGACATGATCATGAGGCCCT 59.604 55.000 36.37 17.04 41.20 5.19
55 56 1.607509 CGACATGATCATGAGGCCCTC 60.608 57.143 36.37 22.53 41.20 4.30
56 57 1.419012 GACATGATCATGAGGCCCTCA 59.581 52.381 36.37 17.41 44.99 3.86
57 58 1.142465 ACATGATCATGAGGCCCTCAC 59.858 52.381 36.37 3.62 43.63 3.51
58 59 1.142262 CATGATCATGAGGCCCTCACA 59.858 52.381 28.37 10.05 43.63 3.58
59 60 1.514983 TGATCATGAGGCCCTCACAT 58.485 50.000 17.46 11.25 43.63 3.21
60 61 1.419012 TGATCATGAGGCCCTCACATC 59.581 52.381 17.46 19.54 43.63 3.06
61 62 0.769873 ATCATGAGGCCCTCACATCC 59.230 55.000 17.46 0.00 43.63 3.51
62 63 0.621280 TCATGAGGCCCTCACATCCA 60.621 55.000 17.46 0.00 43.63 3.41
63 64 0.465097 CATGAGGCCCTCACATCCAC 60.465 60.000 17.46 0.00 43.63 4.02
64 65 1.976132 ATGAGGCCCTCACATCCACG 61.976 60.000 17.46 0.00 43.63 4.94
65 66 2.607750 AGGCCCTCACATCCACGT 60.608 61.111 0.00 0.00 0.00 4.49
84 85 1.481363 GTCCAGGAAGGCCACTACTAC 59.519 57.143 5.01 0.00 37.29 2.73
85 86 0.831307 CCAGGAAGGCCACTACTACC 59.169 60.000 5.01 0.00 36.29 3.18
87 88 0.326332 AGGAAGGCCACTACTACCCC 60.326 60.000 5.01 0.00 36.29 4.95
88 89 1.343431 GGAAGGCCACTACTACCCCC 61.343 65.000 5.01 0.00 0.00 5.40
121 122 2.076863 AGCTTCATTTTTCGGGACTCG 58.923 47.619 0.00 0.00 40.90 4.18
125 126 2.396157 ATTTTTCGGGACTCGCGGC 61.396 57.895 14.81 0.00 40.17 6.53
141 142 4.057428 GCCGTCTGGTGAGCTCGT 62.057 66.667 9.64 0.00 37.67 4.18
143 144 1.734477 CCGTCTGGTGAGCTCGTTG 60.734 63.158 9.64 0.00 0.00 4.10
165 166 2.338577 CATGGGGAAGACATGTCCTC 57.661 55.000 22.21 18.40 40.54 3.71
312 320 4.029704 TGAAATTCGTTCGGTTTGTTTCG 58.970 39.130 0.00 0.00 39.30 3.46
358 366 1.176619 ATCACTGTCCGACGTGTCCA 61.177 55.000 17.29 5.28 33.07 4.02
394 402 5.174943 CGTTTCTGTTTTAGGGTTTTGCATC 59.825 40.000 0.00 0.00 0.00 3.91
463 473 0.321564 CATCCGCTCCACCTCACAAA 60.322 55.000 0.00 0.00 0.00 2.83
591 601 6.290605 AGGTTGCCTAGTTACGAAAACTTTA 58.709 36.000 11.97 0.00 28.47 1.85
624 635 6.654582 ACCTTGCTCAGAAAAACAATGTTTTT 59.345 30.769 29.82 29.82 34.64 1.94
625 636 7.821846 ACCTTGCTCAGAAAAACAATGTTTTTA 59.178 29.630 29.57 17.34 32.37 1.52
626 637 8.663911 CCTTGCTCAGAAAAACAATGTTTTTAA 58.336 29.630 29.57 19.94 32.37 1.52
657 668 7.609760 AAAAAGAAACAATGTTTTCTCCACC 57.390 32.000 13.00 0.00 43.62 4.61
743 1172 3.532155 AAAACTTTGGCGCCGGCA 61.532 55.556 28.98 10.12 42.47 5.69
762 1192 1.915769 GCCACTCCTCTGACCCAGT 60.916 63.158 0.00 0.00 32.61 4.00
941 1400 4.118410 GGCAAATCACAACACAATTCACA 58.882 39.130 0.00 0.00 0.00 3.58
956 1415 2.600769 ACAACCGCTCCTCGACCT 60.601 61.111 0.00 0.00 41.67 3.85
957 1416 2.182030 CAACCGCTCCTCGACCTC 59.818 66.667 0.00 0.00 41.67 3.85
958 1417 3.069318 AACCGCTCCTCGACCTCC 61.069 66.667 0.00 0.00 41.67 4.30
968 1432 3.917760 CGACCTCCTCCATCCGCC 61.918 72.222 0.00 0.00 0.00 6.13
1167 1632 0.545171 TCATCTACGAGGAGACCCGT 59.455 55.000 0.00 0.00 42.15 5.28
1347 1821 1.547372 CCCTGCAGATCCCAAAAGTTG 59.453 52.381 17.39 0.00 0.00 3.16
1376 1869 1.979469 CGCGACTTGTGTAGTTCTCTG 59.021 52.381 0.00 0.00 37.17 3.35
1398 1892 3.728076 TTGCTCTGTAGTTCGAACTGT 57.272 42.857 35.24 17.03 40.07 3.55
1493 1988 1.072806 TGTCCTGCTGCATCTCTGTTT 59.927 47.619 1.31 0.00 0.00 2.83
1502 1998 5.091431 GCTGCATCTCTGTTTATGTGAAAC 58.909 41.667 0.00 0.00 37.35 2.78
1507 2003 7.443879 TGCATCTCTGTTTATGTGAAACTGTTA 59.556 33.333 0.00 0.00 38.04 2.41
1540 2036 0.503961 GCGAAATTGTGTGTGCTTGC 59.496 50.000 0.00 0.00 0.00 4.01
1581 2077 1.073923 TCTTTTTCCTGGAGACCCTGC 59.926 52.381 0.00 0.00 0.00 4.85
1583 2079 1.065410 TTTTCCTGGAGACCCTGCCA 61.065 55.000 0.00 0.00 0.00 4.92
1590 2086 1.617947 GGAGACCCTGCCAGATCGTT 61.618 60.000 0.00 0.00 0.00 3.85
1600 2096 1.446907 CCAGATCGTTCTTGCTTGCT 58.553 50.000 0.00 0.00 0.00 3.91
1604 2100 3.058708 CAGATCGTTCTTGCTTGCTGAAA 60.059 43.478 0.00 0.00 0.00 2.69
1619 2115 5.212532 TGCTGAAAAATTTGTGTATGGCT 57.787 34.783 0.00 0.00 0.00 4.75
1629 2125 4.508551 TTGTGTATGGCTGAATCAGGAT 57.491 40.909 12.66 0.00 31.21 3.24
1642 2138 4.514066 TGAATCAGGATCATCATTTGCTCG 59.486 41.667 0.00 0.00 0.00 5.03
1643 2139 2.842457 TCAGGATCATCATTTGCTCGG 58.158 47.619 0.00 0.00 0.00 4.63
1644 2140 2.435437 TCAGGATCATCATTTGCTCGGA 59.565 45.455 0.00 0.00 0.00 4.55
1645 2141 2.547211 CAGGATCATCATTTGCTCGGAC 59.453 50.000 0.00 0.00 0.00 4.79
1646 2142 2.437281 AGGATCATCATTTGCTCGGACT 59.563 45.455 0.00 0.00 0.00 3.85
1647 2143 2.547211 GGATCATCATTTGCTCGGACTG 59.453 50.000 0.00 0.00 0.00 3.51
1648 2144 3.461061 GATCATCATTTGCTCGGACTGA 58.539 45.455 0.00 0.00 0.00 3.41
1741 2237 2.967887 AGAAAATGCTTCAGCCTTGGTT 59.032 40.909 0.00 0.00 41.18 3.67
1747 2243 1.408702 GCTTCAGCCTTGGTTGTTCAA 59.591 47.619 3.55 0.00 34.31 2.69
1755 2251 3.821033 GCCTTGGTTGTTCAATCACTAGT 59.179 43.478 0.00 0.00 0.00 2.57
2180 2909 6.214191 ACAATATGTGACTACTGTCCAGAG 57.786 41.667 0.40 0.00 42.28 3.35
2260 2990 1.670811 GCCATCCTTCCATACAACACG 59.329 52.381 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.973055 TCGTTGGGGCGTGAACCG 62.973 66.667 0.00 0.00 40.40 4.44
21 22 3.351416 GTCGTTGGGGCGTGAACC 61.351 66.667 0.00 0.00 0.00 3.62
22 23 1.964373 ATGTCGTTGGGGCGTGAAC 60.964 57.895 0.00 0.00 0.00 3.18
23 24 1.963855 CATGTCGTTGGGGCGTGAA 60.964 57.895 0.00 0.00 0.00 3.18
24 25 2.178876 ATCATGTCGTTGGGGCGTGA 62.179 55.000 0.00 0.00 33.42 4.35
25 26 1.705337 GATCATGTCGTTGGGGCGTG 61.705 60.000 0.00 0.00 0.00 5.34
26 27 1.449601 GATCATGTCGTTGGGGCGT 60.450 57.895 0.00 0.00 0.00 5.68
27 28 0.815213 ATGATCATGTCGTTGGGGCG 60.815 55.000 7.59 0.00 0.00 6.13
28 29 0.664761 CATGATCATGTCGTTGGGGC 59.335 55.000 24.87 0.00 34.23 5.80
29 30 2.216046 CTCATGATCATGTCGTTGGGG 58.784 52.381 30.01 4.14 39.72 4.96
30 31 2.216046 CCTCATGATCATGTCGTTGGG 58.784 52.381 30.01 19.64 39.72 4.12
31 32 1.600957 GCCTCATGATCATGTCGTTGG 59.399 52.381 30.01 23.82 39.72 3.77
32 33 1.600957 GGCCTCATGATCATGTCGTTG 59.399 52.381 30.01 17.59 39.72 4.10
33 34 1.475751 GGGCCTCATGATCATGTCGTT 60.476 52.381 30.01 0.00 39.72 3.85
34 35 0.107456 GGGCCTCATGATCATGTCGT 59.893 55.000 30.01 0.00 39.72 4.34
35 36 0.395686 AGGGCCTCATGATCATGTCG 59.604 55.000 30.01 22.34 39.72 4.35
36 37 1.419012 TGAGGGCCTCATGATCATGTC 59.581 52.381 32.01 20.75 39.72 3.06
37 38 1.142465 GTGAGGGCCTCATGATCATGT 59.858 52.381 36.94 13.79 42.73 3.21
38 39 1.142262 TGTGAGGGCCTCATGATCATG 59.858 52.381 36.94 26.79 42.73 3.07
39 40 1.514983 TGTGAGGGCCTCATGATCAT 58.485 50.000 36.94 1.18 42.73 2.45
40 41 1.419012 GATGTGAGGGCCTCATGATCA 59.581 52.381 36.94 28.95 42.73 2.92
41 42 1.271271 GGATGTGAGGGCCTCATGATC 60.271 57.143 36.94 33.68 42.73 2.92
42 43 0.769873 GGATGTGAGGGCCTCATGAT 59.230 55.000 36.94 29.55 42.73 2.45
43 44 0.621280 TGGATGTGAGGGCCTCATGA 60.621 55.000 36.94 26.53 42.73 3.07
44 45 0.465097 GTGGATGTGAGGGCCTCATG 60.465 60.000 36.94 0.00 42.73 3.07
45 46 1.918253 GTGGATGTGAGGGCCTCAT 59.082 57.895 36.94 23.82 42.73 2.90
46 47 2.659063 CGTGGATGTGAGGGCCTCA 61.659 63.158 32.01 32.01 38.25 3.86
47 48 2.187946 CGTGGATGTGAGGGCCTC 59.812 66.667 26.95 26.95 0.00 4.70
48 49 2.607750 ACGTGGATGTGAGGGCCT 60.608 61.111 5.25 5.25 0.00 5.19
49 50 2.125106 GACGTGGATGTGAGGGCC 60.125 66.667 0.00 0.00 0.00 5.80
50 51 2.125106 GGACGTGGATGTGAGGGC 60.125 66.667 0.00 0.00 0.00 5.19
51 52 1.219124 CTGGACGTGGATGTGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
52 53 1.219124 CCTGGACGTGGATGTGAGG 59.781 63.158 0.00 0.00 0.00 3.86
53 54 0.608130 TTCCTGGACGTGGATGTGAG 59.392 55.000 0.00 0.00 33.09 3.51
54 55 0.608130 CTTCCTGGACGTGGATGTGA 59.392 55.000 0.00 0.00 33.09 3.58
55 56 0.391661 CCTTCCTGGACGTGGATGTG 60.392 60.000 0.00 0.00 38.35 3.21
56 57 1.983224 CCTTCCTGGACGTGGATGT 59.017 57.895 0.00 0.00 38.35 3.06
57 58 1.450312 GCCTTCCTGGACGTGGATG 60.450 63.158 12.17 0.00 38.35 3.51
58 59 2.670148 GGCCTTCCTGGACGTGGAT 61.670 63.158 12.17 0.00 38.35 3.41
59 60 3.319198 GGCCTTCCTGGACGTGGA 61.319 66.667 12.17 0.00 38.35 4.02
64 65 1.481363 GTAGTAGTGGCCTTCCTGGAC 59.519 57.143 3.32 0.00 46.75 4.02
65 66 1.621622 GGTAGTAGTGGCCTTCCTGGA 60.622 57.143 3.32 0.00 38.35 3.86
90 91 1.915078 AATGAAGCTGTCGGAGGGGG 61.915 60.000 0.00 0.00 0.00 5.40
98 99 2.814336 AGTCCCGAAAAATGAAGCTGTC 59.186 45.455 0.00 0.00 0.00 3.51
99 100 2.814336 GAGTCCCGAAAAATGAAGCTGT 59.186 45.455 0.00 0.00 0.00 4.40
102 103 1.465856 GCGAGTCCCGAAAAATGAAGC 60.466 52.381 0.00 0.00 41.76 3.86
125 126 1.734477 CAACGAGCTCACCAGACGG 60.734 63.158 15.40 0.00 38.77 4.79
128 129 1.112916 TGTCCAACGAGCTCACCAGA 61.113 55.000 15.40 1.82 0.00 3.86
130 131 0.320683 CATGTCCAACGAGCTCACCA 60.321 55.000 15.40 0.63 0.00 4.17
141 142 2.512692 CATGTCTTCCCCATGTCCAA 57.487 50.000 0.00 0.00 35.94 3.53
165 166 2.715624 GGCAGCGCCTATTTTCCG 59.284 61.111 2.29 0.00 46.69 4.30
185 186 3.253677 CCTAGTCTAAATGATCGTCGGCT 59.746 47.826 0.00 0.00 0.00 5.52
282 283 5.934935 ACCGAACGAATTTCATGTAAACT 57.065 34.783 0.00 0.00 33.24 2.66
287 288 4.561735 ACAAACCGAACGAATTTCATGT 57.438 36.364 0.00 0.00 33.24 3.21
338 346 0.456312 GGACACGTCGGACAGTGATC 60.456 60.000 27.35 21.44 40.56 2.92
358 366 5.488645 AAACAGAAACGGTATTTGTTCGT 57.511 34.783 5.06 0.00 38.89 3.85
394 402 2.418334 GGTAAGTCTAAGGGCAACTCCG 60.418 54.545 0.00 0.00 34.94 4.63
554 564 1.136500 GGCAACCTAGTTCTAGGGACG 59.864 57.143 24.22 15.13 41.51 4.79
581 591 7.312899 AGCAAGGTAATTCCATAAAGTTTTCG 58.687 34.615 0.00 0.00 39.02 3.46
591 601 6.267471 TGTTTTTCTGAGCAAGGTAATTCCAT 59.733 34.615 0.00 0.00 39.02 3.41
634 645 6.706295 TGGTGGAGAAAACATTGTTTCTTTT 58.294 32.000 14.80 0.00 45.67 2.27
638 649 6.816140 TCTTTTGGTGGAGAAAACATTGTTTC 59.184 34.615 14.80 8.87 37.70 2.78
640 651 6.154363 TCTCTTTTGGTGGAGAAAACATTGTT 59.846 34.615 0.00 0.00 35.91 2.83
642 653 6.147864 TCTCTTTTGGTGGAGAAAACATTG 57.852 37.500 0.00 0.00 35.91 2.82
643 654 6.790232 TTCTCTTTTGGTGGAGAAAACATT 57.210 33.333 0.00 0.00 43.03 2.71
649 660 7.060421 ACTATTGTTTCTCTTTTGGTGGAGAA 58.940 34.615 0.00 0.00 43.89 2.87
650 661 6.601332 ACTATTGTTTCTCTTTTGGTGGAGA 58.399 36.000 0.00 0.00 36.89 3.71
651 662 6.884280 ACTATTGTTTCTCTTTTGGTGGAG 57.116 37.500 0.00 0.00 0.00 3.86
652 663 6.017440 CGAACTATTGTTTCTCTTTTGGTGGA 60.017 38.462 0.00 0.00 36.39 4.02
653 664 6.142817 CGAACTATTGTTTCTCTTTTGGTGG 58.857 40.000 0.00 0.00 36.39 4.61
654 665 5.625311 GCGAACTATTGTTTCTCTTTTGGTG 59.375 40.000 0.00 0.00 36.39 4.17
655 666 5.560183 CGCGAACTATTGTTTCTCTTTTGGT 60.560 40.000 0.00 0.00 36.39 3.67
656 667 4.846137 CGCGAACTATTGTTTCTCTTTTGG 59.154 41.667 0.00 0.00 36.39 3.28
657 668 4.318332 GCGCGAACTATTGTTTCTCTTTTG 59.682 41.667 12.10 0.00 36.39 2.44
667 678 0.098728 GCAATGGCGCGAACTATTGT 59.901 50.000 12.10 0.00 34.04 2.71
668 679 2.858729 GCAATGGCGCGAACTATTG 58.141 52.632 12.10 14.17 34.51 1.90
743 1172 1.611851 CTGGGTCAGAGGAGTGGCT 60.612 63.158 0.00 0.00 32.44 4.75
762 1192 4.329545 GGTTGCTGGAGTGGCGGA 62.330 66.667 0.00 0.00 0.00 5.54
896 1352 2.518407 GAGGTGGGGAGGGGATTTTTAT 59.482 50.000 0.00 0.00 0.00 1.40
941 1400 3.069318 GGAGGTCGAGGAGCGGTT 61.069 66.667 0.00 0.00 41.33 4.44
968 1432 3.939837 TTCTTGGCTCGAGCTGCGG 62.940 63.158 34.46 21.59 41.70 5.69
979 1443 1.285578 GCTGACGATCTCTTCTTGGC 58.714 55.000 0.00 0.00 0.00 4.52
1047 1512 1.003839 CACCTTCCTGTGGCGCTTA 60.004 57.895 7.64 0.00 32.50 3.09
1167 1632 0.391661 GGAAGATCTTGAGCACGCCA 60.392 55.000 14.00 0.00 0.00 5.69
1347 1821 1.374252 ACAAGTCGCGGTGTCATCC 60.374 57.895 6.13 0.00 0.00 3.51
1353 1827 0.782384 GAACTACACAAGTCGCGGTG 59.218 55.000 6.13 9.16 37.50 4.94
1376 1869 3.802685 ACAGTTCGAACTACAGAGCAAAC 59.197 43.478 29.28 0.00 37.08 2.93
1398 1892 3.061322 CGAACCACTTTGTTCCACGATA 58.939 45.455 0.00 0.00 41.24 2.92
1493 1988 9.554395 TCACAGAAGAAATAACAGTTTCACATA 57.446 29.630 0.00 0.00 39.88 2.29
1502 1998 5.784750 TCGCATCACAGAAGAAATAACAG 57.215 39.130 0.00 0.00 0.00 3.16
1507 2003 5.860182 CACAATTTCGCATCACAGAAGAAAT 59.140 36.000 0.00 0.00 41.53 2.17
1540 2036 2.791383 TGGCAAAACAATCCAACTCG 57.209 45.000 0.00 0.00 0.00 4.18
1581 2077 1.129998 CAGCAAGCAAGAACGATCTGG 59.870 52.381 0.00 0.00 35.59 3.86
1583 2079 2.462456 TCAGCAAGCAAGAACGATCT 57.538 45.000 0.00 0.00 37.57 2.75
1590 2086 5.177326 ACACAAATTTTTCAGCAAGCAAGA 58.823 33.333 0.00 0.00 0.00 3.02
1600 2096 7.440198 TGATTCAGCCATACACAAATTTTTCA 58.560 30.769 0.00 0.00 0.00 2.69
1604 2100 5.716228 TCCTGATTCAGCCATACACAAATTT 59.284 36.000 8.23 0.00 0.00 1.82
1619 2115 4.514066 CGAGCAAATGATGATCCTGATTCA 59.486 41.667 0.00 0.00 41.48 2.57
1629 2125 2.497273 TCTCAGTCCGAGCAAATGATGA 59.503 45.455 0.00 0.00 41.98 2.92
1645 2141 3.017442 TGTCCGTTAGACTGGATCTCAG 58.983 50.000 9.01 9.01 46.46 3.35
1646 2142 3.017442 CTGTCCGTTAGACTGGATCTCA 58.983 50.000 0.00 0.00 46.46 3.27
1647 2143 2.223618 GCTGTCCGTTAGACTGGATCTC 60.224 54.545 0.00 0.00 46.46 2.75
1648 2144 1.751924 GCTGTCCGTTAGACTGGATCT 59.248 52.381 0.00 0.00 46.46 2.75
1649 2145 1.476891 TGCTGTCCGTTAGACTGGATC 59.523 52.381 2.55 0.00 46.46 3.36
1650 2146 1.478510 CTGCTGTCCGTTAGACTGGAT 59.521 52.381 2.55 0.00 46.46 3.41
1651 2147 0.888619 CTGCTGTCCGTTAGACTGGA 59.111 55.000 2.55 0.00 46.46 3.86
1652 2148 0.603569 ACTGCTGTCCGTTAGACTGG 59.396 55.000 0.00 0.00 46.46 4.00
1653 2149 1.269723 TCACTGCTGTCCGTTAGACTG 59.730 52.381 0.00 0.00 46.46 3.51
1654 2150 1.269998 GTCACTGCTGTCCGTTAGACT 59.730 52.381 0.00 0.00 46.46 3.24
1655 2151 1.669211 GGTCACTGCTGTCCGTTAGAC 60.669 57.143 0.00 0.00 46.51 2.59
1755 2251 9.658475 CTGAACGAAAACTGTTGATTGTATTAA 57.342 29.630 0.00 0.00 0.00 1.40
1776 2272 7.735500 TGTTACATTCGTATTGTTAGCTGAAC 58.264 34.615 0.00 0.00 38.65 3.18
2260 2990 6.970484 TCTGTTAAGACATTTGAAGAAAGGC 58.030 36.000 0.00 0.00 34.72 4.35


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

AutoCloner maintained by Alex Coulton.