Multiple sequence alignment - TraesCS2B01G475400

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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 TraesCS2B01G475400 chr2B 100.000 2482 0 0 1 2482 672645462 672647943 0.000000e+00 4584.0
1 TraesCS2B01G475400 chr2B 83.712 1584 121 59 240 1752 672797813 672796296 0.000000e+00 1369.0
2 TraesCS2B01G475400 chr2B 92.034 703 47 9 1784 2482 442930391 442931088 0.000000e+00 979.0
3 TraesCS2B01G475400 chr2B 83.173 933 101 39 784 1694 673050616 673051514 0.000000e+00 802.0
4 TraesCS2B01G475400 chr2B 81.320 803 91 35 783 1545 673003358 673004141 4.570000e-167 597.0
5 TraesCS2B01G475400 chr2B 81.175 834 68 45 958 1784 672668543 672669294 2.750000e-164 588.0
6 TraesCS2B01G475400 chr2B 86.717 527 47 14 948 1464 673092853 673093366 4.630000e-157 564.0
7 TraesCS2B01G475400 chr2B 83.151 457 40 16 55 496 673001952 673002386 1.390000e-102 383.0
8 TraesCS2B01G475400 chr2B 92.135 89 7 0 254 342 672777474 672777386 2.590000e-25 126.0
9 TraesCS2B01G475400 chr2B 79.825 114 14 8 784 892 672666928 672667037 9.520000e-10 75.0
10 TraesCS2B01G475400 chr2B 95.000 40 2 0 853 892 672776346 672776307 2.060000e-06 63.9
11 TraesCS2B01G475400 chr2B 100.000 30 0 0 782 811 672776427 672776398 3.450000e-04 56.5
12 TraesCS2B01G475400 chr2D 81.641 1645 131 64 116 1695 562684057 562685595 0.000000e+00 1206.0
13 TraesCS2B01G475400 chr2D 85.250 800 65 31 832 1616 562753829 562754590 0.000000e+00 774.0
14 TraesCS2B01G475400 chr2D 82.747 881 89 37 958 1792 562587776 562588639 0.000000e+00 726.0
15 TraesCS2B01G475400 chr2D 85.614 709 66 19 965 1655 562807767 562808457 0.000000e+00 712.0
16 TraesCS2B01G475400 chr2D 86.501 563 52 11 941 1492 562785426 562785975 4.570000e-167 597.0
17 TraesCS2B01G475400 chr2D 89.882 425 35 3 1068 1492 562735069 562735485 7.810000e-150 540.0
18 TraesCS2B01G475400 chr2D 81.873 662 65 31 784 1420 562845035 562845666 7.920000e-140 507.0
19 TraesCS2B01G475400 chr2D 88.199 322 20 6 307 619 562734528 562734840 3.900000e-98 368.0
20 TraesCS2B01G475400 chr2D 86.441 295 24 4 319 606 562784991 562785276 2.400000e-80 309.0
21 TraesCS2B01G475400 chr2D 96.694 121 2 2 783 902 562839392 562839511 1.510000e-47 200.0
22 TraesCS2B01G475400 chr2D 93.333 45 3 0 240 284 562734487 562734531 1.590000e-07 67.6
23 TraesCS2B01G475400 chr7B 93.059 706 41 5 1781 2482 450577634 450576933 0.000000e+00 1026.0
24 TraesCS2B01G475400 chrUn 92.555 685 47 2 1801 2482 444183090 444183773 0.000000e+00 979.0
25 TraesCS2B01G475400 chr7D 92.034 703 44 8 1783 2482 192260382 192259689 0.000000e+00 977.0
26 TraesCS2B01G475400 chr6A 91.655 707 48 7 1779 2482 103275438 103276136 0.000000e+00 968.0
27 TraesCS2B01G475400 chr6B 91.489 705 53 7 1782 2482 40535896 40536597 0.000000e+00 963.0
28 TraesCS2B01G475400 chr2A 91.193 704 50 8 1782 2482 761145149 761144455 0.000000e+00 946.0
29 TraesCS2B01G475400 chr2A 83.414 826 74 28 573 1379 703207108 703207889 0.000000e+00 708.0
30 TraesCS2B01G475400 chr2A 85.501 669 50 24 1057 1718 703337532 703338160 0.000000e+00 654.0
31 TraesCS2B01G475400 chr2A 92.991 428 27 1 1068 1492 703291191 703291618 2.710000e-174 621.0
32 TraesCS2B01G475400 chr2A 90.023 441 31 5 1021 1450 703282312 703282750 2.160000e-155 558.0
33 TraesCS2B01G475400 chr2A 86.667 330 11 14 263 578 703206525 703206835 3.960000e-88 335.0
34 TraesCS2B01G475400 chr2A 80.165 242 8 19 1375 1616 703208508 703208709 7.150000e-31 145.0
35 TraesCS2B01G475400 chr2A 74.380 242 25 24 784 1018 703337334 703337545 4.430000e-08 69.4
36 TraesCS2B01G475400 chr4D 91.193 704 49 11 1782 2482 108213939 108214632 0.000000e+00 944.0
37 TraesCS2B01G475400 chr7A 90.960 708 52 7 1779 2482 468937715 468937016 0.000000e+00 942.0


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 TraesCS2B01G475400 chr2B 672645462 672647943 2481 False 4584.0 4584 100.000000 1 2482 1 chr2B.!!$F2 2481
1 TraesCS2B01G475400 chr2B 672796296 672797813 1517 True 1369.0 1369 83.712000 240 1752 1 chr2B.!!$R1 1512
2 TraesCS2B01G475400 chr2B 442930391 442931088 697 False 979.0 979 92.034000 1784 2482 1 chr2B.!!$F1 698
3 TraesCS2B01G475400 chr2B 673050616 673051514 898 False 802.0 802 83.173000 784 1694 1 chr2B.!!$F3 910
4 TraesCS2B01G475400 chr2B 673092853 673093366 513 False 564.0 564 86.717000 948 1464 1 chr2B.!!$F4 516
5 TraesCS2B01G475400 chr2B 673001952 673004141 2189 False 490.0 597 82.235500 55 1545 2 chr2B.!!$F6 1490
6 TraesCS2B01G475400 chr2B 672666928 672669294 2366 False 331.5 588 80.500000 784 1784 2 chr2B.!!$F5 1000
7 TraesCS2B01G475400 chr2D 562684057 562685595 1538 False 1206.0 1206 81.641000 116 1695 1 chr2D.!!$F2 1579
8 TraesCS2B01G475400 chr2D 562753829 562754590 761 False 774.0 774 85.250000 832 1616 1 chr2D.!!$F3 784
9 TraesCS2B01G475400 chr2D 562587776 562588639 863 False 726.0 726 82.747000 958 1792 1 chr2D.!!$F1 834
10 TraesCS2B01G475400 chr2D 562807767 562808457 690 False 712.0 712 85.614000 965 1655 1 chr2D.!!$F4 690
11 TraesCS2B01G475400 chr2D 562845035 562845666 631 False 507.0 507 81.873000 784 1420 1 chr2D.!!$F6 636
12 TraesCS2B01G475400 chr2D 562784991 562785975 984 False 453.0 597 86.471000 319 1492 2 chr2D.!!$F8 1173
13 TraesCS2B01G475400 chr2D 562734487 562735485 998 False 325.2 540 90.471333 240 1492 3 chr2D.!!$F7 1252
14 TraesCS2B01G475400 chr7B 450576933 450577634 701 True 1026.0 1026 93.059000 1781 2482 1 chr7B.!!$R1 701
15 TraesCS2B01G475400 chrUn 444183090 444183773 683 False 979.0 979 92.555000 1801 2482 1 chrUn.!!$F1 681
16 TraesCS2B01G475400 chr7D 192259689 192260382 693 True 977.0 977 92.034000 1783 2482 1 chr7D.!!$R1 699
17 TraesCS2B01G475400 chr6A 103275438 103276136 698 False 968.0 968 91.655000 1779 2482 1 chr6A.!!$F1 703
18 TraesCS2B01G475400 chr6B 40535896 40536597 701 False 963.0 963 91.489000 1782 2482 1 chr6B.!!$F1 700
19 TraesCS2B01G475400 chr2A 761144455 761145149 694 True 946.0 946 91.193000 1782 2482 1 chr2A.!!$R1 700
20 TraesCS2B01G475400 chr2A 703206525 703208709 2184 False 396.0 708 83.415333 263 1616 3 chr2A.!!$F3 1353
21 TraesCS2B01G475400 chr2A 703337334 703338160 826 False 361.7 654 79.940500 784 1718 2 chr2A.!!$F4 934
22 TraesCS2B01G475400 chr4D 108213939 108214632 693 False 944.0 944 91.193000 1782 2482 1 chr4D.!!$F1 700
23 TraesCS2B01G475400 chr7A 468937016 468937715 699 True 942.0 942 90.960000 1779 2482 1 chr7A.!!$R1 703

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
860 1956 0.172803 GGTCGACCTAGCACGATTGT 59.827 55.0 27.64 0.0 40.5 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 5079 0.802494 CCATTTCGTTCCGAACCAGG 59.198 55.0 5.67 0.0 45.64 4.45 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
20 21 2.559698 TTGATCCCTTCAACGCTCAA 57.440 45.000 0.00 0.00 39.44 3.02
21 22 2.787473 TGATCCCTTCAACGCTCAAT 57.213 45.000 0.00 0.00 0.00 2.57
22 23 2.358957 TGATCCCTTCAACGCTCAATG 58.641 47.619 0.00 0.00 0.00 2.82
23 24 1.672881 GATCCCTTCAACGCTCAATGG 59.327 52.381 0.00 0.00 0.00 3.16
24 25 0.960364 TCCCTTCAACGCTCAATGGC 60.960 55.000 0.00 0.00 0.00 4.40
25 26 1.243342 CCCTTCAACGCTCAATGGCA 61.243 55.000 0.00 0.00 0.00 4.92
26 27 0.597568 CCTTCAACGCTCAATGGCAA 59.402 50.000 0.00 0.00 0.00 4.52
27 28 1.666888 CCTTCAACGCTCAATGGCAAC 60.667 52.381 0.00 0.00 0.00 4.17
28 29 0.313672 TTCAACGCTCAATGGCAACC 59.686 50.000 0.00 0.00 0.00 3.77
29 30 1.442520 CAACGCTCAATGGCAACCG 60.443 57.895 0.00 0.00 0.00 4.44
30 31 3.267597 AACGCTCAATGGCAACCGC 62.268 57.895 0.00 0.00 37.44 5.68
31 32 3.736100 CGCTCAATGGCAACCGCA 61.736 61.111 0.00 0.00 41.24 5.69
32 33 2.180017 GCTCAATGGCAACCGCAG 59.820 61.111 0.00 0.00 41.24 5.18
33 34 2.180017 CTCAATGGCAACCGCAGC 59.820 61.111 0.00 0.00 41.24 5.25
34 35 2.282391 TCAATGGCAACCGCAGCT 60.282 55.556 0.00 0.00 41.24 4.24
35 36 2.126228 CAATGGCAACCGCAGCTG 60.126 61.111 10.11 10.11 41.24 4.24
36 37 4.060038 AATGGCAACCGCAGCTGC 62.060 61.111 29.12 29.12 41.24 5.25
40 41 3.969802 GCAACCGCAGCTGCAACT 61.970 61.111 36.03 17.73 42.21 3.16
41 42 2.050714 CAACCGCAGCTGCAACTG 60.051 61.111 36.03 24.42 42.21 3.16
42 43 3.289834 AACCGCAGCTGCAACTGG 61.290 61.111 36.03 29.49 42.21 4.00
46 47 3.060615 GCAGCTGCAACTGGGAGG 61.061 66.667 33.36 0.00 41.59 4.30
48 49 2.433446 AGCTGCAACTGGGAGGTG 59.567 61.111 1.02 0.00 44.53 4.00
49 50 2.674380 GCTGCAACTGGGAGGTGG 60.674 66.667 0.00 0.00 32.34 4.61
50 51 2.839098 CTGCAACTGGGAGGTGGT 59.161 61.111 0.00 0.00 32.34 4.16
51 52 1.151450 CTGCAACTGGGAGGTGGTT 59.849 57.895 0.00 0.00 32.34 3.67
52 53 0.890996 CTGCAACTGGGAGGTGGTTC 60.891 60.000 0.00 0.00 32.34 3.62
53 54 1.603739 GCAACTGGGAGGTGGTTCC 60.604 63.158 0.00 0.00 32.34 3.62
83 84 1.669760 GAAACGTGCACGATCCCCA 60.670 57.895 42.94 0.00 43.02 4.96
101 102 3.153919 CCCAAGCTAGCTAAACAAACCA 58.846 45.455 19.70 0.00 0.00 3.67
102 103 3.057526 CCCAAGCTAGCTAAACAAACCAC 60.058 47.826 19.70 0.00 0.00 4.16
103 104 3.821033 CCAAGCTAGCTAAACAAACCACT 59.179 43.478 19.70 0.00 0.00 4.00
105 106 3.676093 AGCTAGCTAAACAAACCACTCC 58.324 45.455 17.69 0.00 0.00 3.85
106 107 3.072476 AGCTAGCTAAACAAACCACTCCA 59.928 43.478 17.69 0.00 0.00 3.86
107 108 3.188667 GCTAGCTAAACAAACCACTCCAC 59.811 47.826 7.70 0.00 0.00 4.02
108 109 3.577805 AGCTAAACAAACCACTCCACT 57.422 42.857 0.00 0.00 0.00 4.00
109 110 3.898482 AGCTAAACAAACCACTCCACTT 58.102 40.909 0.00 0.00 0.00 3.16
111 112 5.442391 AGCTAAACAAACCACTCCACTTAA 58.558 37.500 0.00 0.00 0.00 1.85
112 113 5.889289 AGCTAAACAAACCACTCCACTTAAA 59.111 36.000 0.00 0.00 0.00 1.52
113 114 5.975344 GCTAAACAAACCACTCCACTTAAAC 59.025 40.000 0.00 0.00 0.00 2.01
114 115 5.986501 AAACAAACCACTCCACTTAAACA 57.013 34.783 0.00 0.00 0.00 2.83
127 131 7.885399 ACTCCACTTAAACAGCTCAATAATCTT 59.115 33.333 0.00 0.00 0.00 2.40
138 142 7.544566 ACAGCTCAATAATCTTGCATTTTTCTG 59.455 33.333 0.00 0.00 0.00 3.02
139 143 7.544566 CAGCTCAATAATCTTGCATTTTTCTGT 59.455 33.333 0.00 0.00 0.00 3.41
145 149 5.972107 ATCTTGCATTTTTCTGTAGCAGT 57.028 34.783 0.00 0.00 36.47 4.40
157 161 2.432146 CTGTAGCAGTATCCTTGAGCCA 59.568 50.000 0.00 0.00 0.00 4.75
180 184 4.751600 AGAAGTTTTAAAGGCTGCAAATGC 59.248 37.500 0.50 0.00 42.50 3.56
253 267 1.153765 CCGAGCGCAGACAAGATCA 60.154 57.895 11.47 0.00 0.00 2.92
410 440 9.322776 CTGTTCTGTATTTTCTTTTCTTCATCG 57.677 33.333 0.00 0.00 0.00 3.84
413 443 7.298122 TCTGTATTTTCTTTTCTTCATCGTGC 58.702 34.615 0.00 0.00 0.00 5.34
418 448 2.987149 TCTTTTCTTCATCGTGCGTCTC 59.013 45.455 0.00 0.00 0.00 3.36
651 1694 0.322277 ACGACTAGAGGAGGCACGAA 60.322 55.000 0.00 0.00 28.99 3.85
668 1711 4.328983 GCACGAACGAATTCTTCTCCAATA 59.671 41.667 3.52 0.00 32.12 1.90
724 1771 8.651391 TGTATTTTCGAGAGTTTTCAAGTACA 57.349 30.769 0.00 0.00 0.00 2.90
725 1772 9.100554 TGTATTTTCGAGAGTTTTCAAGTACAA 57.899 29.630 0.00 0.00 0.00 2.41
743 1791 6.558909 AGTACAAGTACGGCTACATTTCTAC 58.441 40.000 4.85 0.00 40.80 2.59
744 1792 5.395682 ACAAGTACGGCTACATTTCTACA 57.604 39.130 0.00 0.00 0.00 2.74
745 1793 5.408356 ACAAGTACGGCTACATTTCTACAG 58.592 41.667 0.00 0.00 0.00 2.74
746 1794 5.047519 ACAAGTACGGCTACATTTCTACAGT 60.048 40.000 0.00 0.00 0.00 3.55
747 1795 6.151648 ACAAGTACGGCTACATTTCTACAGTA 59.848 38.462 0.00 0.00 0.00 2.74
748 1796 6.374565 AGTACGGCTACATTTCTACAGTAG 57.625 41.667 0.47 0.47 38.54 2.57
765 1813 8.486210 TCTACAGTAGCCTTCACAAAATATCAT 58.514 33.333 2.26 0.00 0.00 2.45
842 1938 0.978146 ATGTCTCCTTCGGGACCTGG 60.978 60.000 0.00 0.00 39.58 4.45
843 1939 1.609794 GTCTCCTTCGGGACCTGGT 60.610 63.158 0.00 0.00 39.58 4.00
844 1940 1.305046 TCTCCTTCGGGACCTGGTC 60.305 63.158 18.65 18.65 39.58 4.02
848 1944 2.993264 TTCGGGACCTGGTCGACC 60.993 66.667 28.17 28.17 32.65 4.79
860 1956 0.172803 GGTCGACCTAGCACGATTGT 59.827 55.000 27.64 0.00 40.50 2.71
924 2025 3.124270 CCAGCGCACGGTATTGCA 61.124 61.111 11.47 0.00 43.15 4.08
989 3561 2.750141 ATACGAGCCTTCCACTCCTA 57.250 50.000 0.00 0.00 0.00 2.94
1036 3624 2.043450 CCTCCCTCTCCTCGCACT 60.043 66.667 0.00 0.00 0.00 4.40
1041 3629 1.388065 CCCTCTCCTCGCACTACCAG 61.388 65.000 0.00 0.00 0.00 4.00
1052 3663 1.016130 CACTACCAGAAGCGCACCAG 61.016 60.000 11.47 0.00 0.00 4.00
1071 3682 0.175302 GCAAGCTCAGCTCTGCTCTA 59.825 55.000 20.27 0.00 38.25 2.43
1123 3755 6.126623 ACACACACATACCAATATACCATGGA 60.127 38.462 21.47 2.01 39.12 3.41
1466 4767 7.096271 CGACAAGATCCGAATTCAGAAGAATAG 60.096 40.741 6.22 0.00 43.52 1.73
1470 4771 4.611943 TCCGAATTCAGAAGAATAGAGCG 58.388 43.478 6.22 0.00 43.52 5.03
1479 4807 7.803279 TCAGAAGAATAGAGCGTCTGTATTA 57.197 36.000 8.49 0.00 40.93 0.98
1557 4885 1.974875 CACCAGATGCAGCTTGCCA 60.975 57.895 0.00 0.00 44.23 4.92
1558 4886 1.677966 ACCAGATGCAGCTTGCCAG 60.678 57.895 0.00 0.00 44.23 4.85
1559 4887 2.490217 CAGATGCAGCTTGCCAGC 59.510 61.111 0.00 0.46 44.23 4.85
1659 5012 2.806945 TGGCAAGCTATTTAGGCTGT 57.193 45.000 0.00 0.00 40.19 4.40
1677 5031 1.762471 TCCGGGTGGGACGAAATTT 59.238 52.632 0.00 0.00 40.94 1.82
1702 5056 1.967779 TGATTCTTGGTCGGTCTGTGA 59.032 47.619 0.00 0.00 0.00 3.58
1719 5079 4.332543 TCTGTGATGTGCCGATGAATTTAC 59.667 41.667 0.00 0.00 0.00 2.01
1720 5080 3.376859 TGTGATGTGCCGATGAATTTACC 59.623 43.478 0.00 0.00 0.00 2.85
1764 5126 3.760684 ACCATGGATCTGAAGAAAGCAAC 59.239 43.478 21.47 0.00 0.00 4.17
1766 5128 2.426522 TGGATCTGAAGAAAGCAACCG 58.573 47.619 0.00 0.00 0.00 4.44
1777 5139 4.074970 AGAAAGCAACCGAACATGATTCT 58.925 39.130 0.00 0.00 0.00 2.40
1984 5355 3.530265 ATGCCTATGTCGAAACGGTTA 57.470 42.857 0.00 0.00 0.00 2.85
1989 5360 2.088950 ATGTCGAAACGGTTAGTGGG 57.911 50.000 0.00 0.00 0.00 4.61
2084 5458 3.007635 GCTTGAATAGCGGTTGGTACTT 58.992 45.455 0.00 0.00 40.71 2.24
2097 5471 3.945981 TGGTACTTCGCATGTTGTAGA 57.054 42.857 0.00 0.00 0.00 2.59
2214 5588 4.682778 AAGCGACCATAGTAAGGCATAA 57.317 40.909 0.00 0.00 0.00 1.90
2219 5593 4.021894 CGACCATAGTAAGGCATAAGCTCT 60.022 45.833 0.00 0.00 41.70 4.09
2248 5623 8.290325 CCCTTATTAGCGATTTGAACCTATTTC 58.710 37.037 0.00 0.00 34.41 2.17
2262 5637 6.715718 TGAACCTATTTCAAATACCGTCCAAA 59.284 34.615 0.00 0.00 41.51 3.28
2283 5658 6.430616 CCAAACAATGACCAAAAATATTGGCT 59.569 34.615 7.12 0.00 43.23 4.75
2430 5805 4.539083 TGGCCAGTTGCGTCGTGT 62.539 61.111 0.00 0.00 42.61 4.49
2433 5808 2.530497 GCCAGTTGCGTCGTGTGAA 61.530 57.895 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.559698 TTGAGCGTTGAAGGGATCAA 57.440 45.000 0.00 0.00 45.71 2.57
6 7 1.243342 TGCCATTGAGCGTTGAAGGG 61.243 55.000 0.00 0.00 34.65 3.95
7 8 0.597568 TTGCCATTGAGCGTTGAAGG 59.402 50.000 0.00 0.00 34.65 3.46
8 9 1.666888 GGTTGCCATTGAGCGTTGAAG 60.667 52.381 0.00 0.00 34.65 3.02
9 10 0.313672 GGTTGCCATTGAGCGTTGAA 59.686 50.000 0.00 0.00 34.65 2.69
10 11 1.851021 CGGTTGCCATTGAGCGTTGA 61.851 55.000 0.00 0.00 34.65 3.18
11 12 1.442520 CGGTTGCCATTGAGCGTTG 60.443 57.895 0.00 0.00 34.65 4.10
12 13 2.953821 CGGTTGCCATTGAGCGTT 59.046 55.556 0.00 0.00 34.65 4.84
13 14 3.737172 GCGGTTGCCATTGAGCGT 61.737 61.111 0.00 0.00 38.84 5.07
14 15 3.672255 CTGCGGTTGCCATTGAGCG 62.672 63.158 0.00 0.00 41.78 5.03
15 16 2.180017 CTGCGGTTGCCATTGAGC 59.820 61.111 0.00 0.00 41.78 4.26
16 17 2.180017 GCTGCGGTTGCCATTGAG 59.820 61.111 0.00 0.00 41.78 3.02
17 18 2.282391 AGCTGCGGTTGCCATTGA 60.282 55.556 0.00 0.00 41.78 2.57
18 19 2.126228 CAGCTGCGGTTGCCATTG 60.126 61.111 0.00 0.00 41.78 2.82
19 20 4.060038 GCAGCTGCGGTTGCCATT 62.060 61.111 25.23 0.00 42.55 3.16
24 25 2.050714 CAGTTGCAGCTGCGGTTG 60.051 61.111 32.11 24.17 45.83 3.77
25 26 3.289834 CCAGTTGCAGCTGCGGTT 61.290 61.111 32.11 17.55 45.83 4.44
28 29 3.429141 CTCCCAGTTGCAGCTGCG 61.429 66.667 32.11 16.37 45.83 5.18
29 30 3.060615 CCTCCCAGTTGCAGCTGC 61.061 66.667 31.89 31.89 42.50 5.25
30 31 1.970114 CACCTCCCAGTTGCAGCTG 60.970 63.158 22.44 22.44 36.31 4.24
31 32 2.433446 CACCTCCCAGTTGCAGCT 59.567 61.111 0.00 0.00 0.00 4.24
32 33 2.674380 CCACCTCCCAGTTGCAGC 60.674 66.667 0.00 0.00 0.00 5.25
33 34 0.890996 GAACCACCTCCCAGTTGCAG 60.891 60.000 0.00 0.00 0.00 4.41
34 35 1.150536 GAACCACCTCCCAGTTGCA 59.849 57.895 0.00 0.00 0.00 4.08
35 36 1.603739 GGAACCACCTCCCAGTTGC 60.604 63.158 0.00 0.00 35.41 4.17
36 37 4.821935 GGAACCACCTCCCAGTTG 57.178 61.111 0.00 0.00 35.41 3.16
53 54 1.022451 CACGTTTCGTACCATGGGGG 61.022 60.000 18.09 4.56 38.32 5.40
54 55 1.641123 GCACGTTTCGTACCATGGGG 61.641 60.000 18.09 4.96 38.32 4.96
55 56 0.951525 TGCACGTTTCGTACCATGGG 60.952 55.000 18.09 0.00 38.32 4.00
56 57 0.165079 GTGCACGTTTCGTACCATGG 59.835 55.000 11.19 11.19 38.32 3.66
57 58 0.179260 CGTGCACGTTTCGTACCATG 60.179 55.000 30.50 0.00 38.32 3.66
58 59 0.318869 TCGTGCACGTTTCGTACCAT 60.319 50.000 35.74 0.00 38.32 3.55
59 60 0.318869 ATCGTGCACGTTTCGTACCA 60.319 50.000 35.74 16.09 38.32 3.25
60 61 0.364515 GATCGTGCACGTTTCGTACC 59.635 55.000 35.74 13.12 38.32 3.34
61 62 0.364515 GGATCGTGCACGTTTCGTAC 59.635 55.000 35.74 16.63 38.32 3.67
83 84 4.072839 GGAGTGGTTTGTTTAGCTAGCTT 58.927 43.478 24.88 7.25 0.00 3.74
101 102 7.398024 AGATTATTGAGCTGTTTAAGTGGAGT 58.602 34.615 0.00 0.00 0.00 3.85
102 103 7.856145 AGATTATTGAGCTGTTTAAGTGGAG 57.144 36.000 0.00 0.00 0.00 3.86
103 104 7.362056 GCAAGATTATTGAGCTGTTTAAGTGGA 60.362 37.037 0.00 0.00 0.00 4.02
105 106 7.307694 TGCAAGATTATTGAGCTGTTTAAGTG 58.692 34.615 0.00 0.00 0.00 3.16
106 107 7.452880 TGCAAGATTATTGAGCTGTTTAAGT 57.547 32.000 0.00 0.00 0.00 2.24
107 108 8.922058 AATGCAAGATTATTGAGCTGTTTAAG 57.078 30.769 0.00 0.00 0.00 1.85
108 109 9.709495 AAAATGCAAGATTATTGAGCTGTTTAA 57.291 25.926 0.00 0.00 0.00 1.52
109 110 9.709495 AAAAATGCAAGATTATTGAGCTGTTTA 57.291 25.926 0.00 0.00 0.00 2.01
111 112 8.092687 AGAAAAATGCAAGATTATTGAGCTGTT 58.907 29.630 0.00 0.00 0.00 3.16
112 113 7.544566 CAGAAAAATGCAAGATTATTGAGCTGT 59.455 33.333 0.00 0.00 0.00 4.40
113 114 7.544566 ACAGAAAAATGCAAGATTATTGAGCTG 59.455 33.333 0.00 0.00 0.00 4.24
114 115 7.609056 ACAGAAAAATGCAAGATTATTGAGCT 58.391 30.769 0.00 0.00 0.00 4.09
127 131 5.818136 GGATACTGCTACAGAAAAATGCA 57.182 39.130 0.78 0.00 35.18 3.96
145 149 6.659242 CCTTTAAAACTTCTGGCTCAAGGATA 59.341 38.462 0.00 0.00 31.56 2.59
157 161 4.751600 GCATTTGCAGCCTTTAAAACTTCT 59.248 37.500 0.00 0.00 41.59 2.85
189 193 1.442688 GCGGCAGCTAACAAGCAAC 60.443 57.895 0.00 0.00 41.01 4.17
233 247 4.742201 TCTTGTCTGCGCTCGGCC 62.742 66.667 9.73 0.00 42.61 6.13
234 248 2.510238 ATCTTGTCTGCGCTCGGC 60.510 61.111 9.73 1.22 43.96 5.54
235 249 1.144565 CTGATCTTGTCTGCGCTCGG 61.145 60.000 9.73 0.00 0.00 4.63
236 250 1.750572 GCTGATCTTGTCTGCGCTCG 61.751 60.000 9.73 0.00 41.11 5.03
237 251 2.005220 GCTGATCTTGTCTGCGCTC 58.995 57.895 9.73 0.00 41.11 5.03
238 252 4.198625 GCTGATCTTGTCTGCGCT 57.801 55.556 9.73 0.00 41.11 5.92
410 440 6.032722 ACGTGATATTTTTATGAGACGCAC 57.967 37.500 0.00 0.00 0.00 5.34
413 443 8.336498 ACTGTACGTGATATTTTTATGAGACG 57.664 34.615 0.00 0.00 0.00 4.18
452 482 3.487376 CGCCAATAATCGACACAAATGCT 60.487 43.478 0.00 0.00 0.00 3.79
464 494 1.607148 GGTTAGCCCACGCCAATAATC 59.393 52.381 0.00 0.00 34.57 1.75
499 529 3.643320 TGCCAACATAGGACTGATAGGAG 59.357 47.826 0.00 0.00 0.00 3.69
720 1767 6.324819 TGTAGAAATGTAGCCGTACTTGTAC 58.675 40.000 1.13 1.13 0.00 2.90
721 1768 6.151648 ACTGTAGAAATGTAGCCGTACTTGTA 59.848 38.462 0.00 0.00 0.00 2.41
722 1769 5.047519 ACTGTAGAAATGTAGCCGTACTTGT 60.048 40.000 0.00 0.00 0.00 3.16
723 1770 5.408356 ACTGTAGAAATGTAGCCGTACTTG 58.592 41.667 0.00 0.00 0.00 3.16
724 1771 5.656213 ACTGTAGAAATGTAGCCGTACTT 57.344 39.130 0.00 0.00 0.00 2.24
725 1772 6.374565 CTACTGTAGAAATGTAGCCGTACT 57.625 41.667 9.22 0.00 0.00 2.73
743 1791 9.113838 AGTTATGATATTTTGTGAAGGCTACTG 57.886 33.333 0.00 0.00 0.00 2.74
744 1792 9.686683 AAGTTATGATATTTTGTGAAGGCTACT 57.313 29.630 0.00 0.00 0.00 2.57
842 1938 1.546834 GACAATCGTGCTAGGTCGAC 58.453 55.000 7.13 7.13 38.85 4.20
844 1940 2.566997 CGACAATCGTGCTAGGTCG 58.433 57.895 0.00 0.00 44.13 4.79
914 2010 2.125832 CGGGTCGTGCAATACCGT 60.126 61.111 11.52 0.00 39.70 4.83
989 3561 1.901085 GAGCGAGTTGGGTGAGGAT 59.099 57.895 0.00 0.00 0.00 3.24
1036 3624 2.047274 GCTGGTGCGCTTCTGGTA 60.047 61.111 9.73 0.00 0.00 3.25
1041 3629 3.319926 GAGCTTGCTGGTGCGCTTC 62.320 63.158 9.73 1.18 43.34 3.86
1052 3663 0.175302 TAGAGCAGAGCTGAGCTTGC 59.825 55.000 24.22 24.22 42.04 4.01
1466 4767 7.201308 CGATGATTCTTCATAATACAGACGCTC 60.201 40.741 1.09 0.00 42.73 5.03
1470 4771 7.591795 ACGACGATGATTCTTCATAATACAGAC 59.408 37.037 0.00 0.00 42.73 3.51
1479 4807 3.971150 GGAGACGACGATGATTCTTCAT 58.029 45.455 0.00 0.00 45.39 2.57
1513 4841 2.351244 CGGTCCAGGCTAGAGCACA 61.351 63.158 12.40 0.00 44.36 4.57
1659 5012 0.110869 AAAATTTCGTCCCACCCGGA 59.889 50.000 0.73 0.00 38.83 5.14
1670 5023 6.021596 CGACCAAGAATCAGGTAAAATTTCG 58.978 40.000 0.00 0.00 38.50 3.46
1677 5031 3.056107 CAGACCGACCAAGAATCAGGTAA 60.056 47.826 0.00 0.00 38.50 2.85
1702 5056 2.951642 CCAGGTAAATTCATCGGCACAT 59.048 45.455 0.00 0.00 0.00 3.21
1719 5079 0.802494 CCATTTCGTTCCGAACCAGG 59.198 55.000 5.67 0.00 45.64 4.45
1720 5080 1.803334 TCCATTTCGTTCCGAACCAG 58.197 50.000 5.67 0.00 45.64 4.00
1737 5097 4.494091 TTCTTCAGATCCATGGTCTTCC 57.506 45.455 12.58 0.00 0.00 3.46
1741 5101 3.614092 TGCTTTCTTCAGATCCATGGTC 58.386 45.455 12.58 8.86 0.00 4.02
1799 5161 9.665264 GCTACATTTTAAGATAATAAAAGCGCT 57.335 29.630 2.64 2.64 37.95 5.92
1887 5250 9.108284 CTTTTTATCAGATTTTTGGTGTTTGGT 57.892 29.630 0.00 0.00 0.00 3.67
2084 5458 4.081917 TGTGGTCTATTCTACAACATGCGA 60.082 41.667 0.00 0.00 0.00 5.10
2097 5471 5.292765 CACTCGCTTCATATGTGGTCTATT 58.707 41.667 1.90 0.00 0.00 1.73
2182 5556 9.740239 CTTACTATGGTCGCTTTAGTTATGTAA 57.260 33.333 0.00 0.00 0.00 2.41
2189 5563 3.449737 TGCCTTACTATGGTCGCTTTAGT 59.550 43.478 0.00 0.00 0.00 2.24
2191 5565 4.682778 ATGCCTTACTATGGTCGCTTTA 57.317 40.909 0.00 0.00 0.00 1.85
2214 5588 2.667470 TCGCTAATAAGGGTGAGAGCT 58.333 47.619 0.00 0.00 37.01 4.09
2219 5593 4.879545 GGTTCAAATCGCTAATAAGGGTGA 59.120 41.667 0.00 0.00 37.01 4.02
2248 5623 4.022762 TGGTCATTGTTTGGACGGTATTTG 60.023 41.667 0.00 0.00 34.87 2.32
2262 5637 7.602265 GTGTTAGCCAATATTTTTGGTCATTGT 59.398 33.333 7.57 0.00 41.53 2.71
2283 5658 1.624312 TGTATCCGCCCACAAGTGTTA 59.376 47.619 0.00 0.00 0.00 2.41
2430 5805 4.265893 TGTGCTAACCAAAGACAACTTCA 58.734 39.130 0.00 0.00 35.05 3.02
2433 5808 4.013728 TGTTGTGCTAACCAAAGACAACT 58.986 39.130 12.90 0.00 44.33 3.16


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

AutoCloner maintained by Alex Coulton.