Multiple sequence alignment - TraesCS4D01G070900

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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 TraesCS4D01G070900 chr4D 100.000 2399 0 0 1 2399 46174987 46177385 0.000000e+00 4431.0
1 TraesCS4D01G070900 chr4D 88.707 735 51 13 1696 2399 46187704 46186971 0.000000e+00 869.0
2 TraesCS4D01G070900 chr7D 90.239 1004 72 13 621 1604 451854846 451855843 0.000000e+00 1288.0
3 TraesCS4D01G070900 chr7D 89.888 89 9 0 2238 2326 564687413 564687325 5.420000e-22 115.0
4 TraesCS4D01G070900 chr7D 82.432 74 8 3 555 623 90254556 90254629 2.580000e-05 60.2
5 TraesCS4D01G070900 chr4A 88.163 1056 89 22 642 1684 680377236 680378268 0.000000e+00 1225.0
6 TraesCS4D01G070900 chr4A 91.769 571 43 3 1832 2399 552833268 552832699 0.000000e+00 791.0
7 TraesCS4D01G070900 chr4A 92.016 501 36 2 1903 2399 552816771 552817271 0.000000e+00 701.0
8 TraesCS4D01G070900 chr4A 84.029 551 42 8 1 506 552843974 552843425 2.770000e-134 488.0
9 TraesCS4D01G070900 chr4A 86.321 212 17 5 1700 1902 552816534 552816742 1.120000e-53 220.0
10 TraesCS4D01G070900 chr4A 80.531 113 8 3 1702 1814 552843329 552843231 9.200000e-10 75.0
11 TraesCS4D01G070900 chr2A 88.363 1014 96 14 607 1604 735684439 735685446 0.000000e+00 1199.0
12 TraesCS4D01G070900 chr2A 88.673 980 87 16 640 1603 735685939 735686910 0.000000e+00 1173.0
13 TraesCS4D01G070900 chr5D 88.469 1006 80 21 607 1604 173765299 173764322 0.000000e+00 1182.0
14 TraesCS4D01G070900 chr5D 87.200 125 16 0 1560 1684 173764332 173764208 2.490000e-30 143.0
15 TraesCS4D01G070900 chr1A 87.551 980 99 15 640 1604 549573489 549574460 0.000000e+00 1112.0
16 TraesCS4D01G070900 chr1A 83.217 143 20 3 1560 1699 5870465 5870606 6.960000e-26 128.0
17 TraesCS4D01G070900 chr7B 90.459 828 62 9 626 1443 23071134 23070314 0.000000e+00 1075.0
18 TraesCS4D01G070900 chr1D 90.382 811 65 7 640 1443 20402901 20402097 0.000000e+00 1053.0
19 TraesCS4D01G070900 chr6B 88.575 884 71 11 642 1498 701468490 701467610 0.000000e+00 1046.0
20 TraesCS4D01G070900 chr4B 88.251 732 54 13 1700 2399 67354539 67353808 0.000000e+00 846.0
21 TraesCS4D01G070900 chr4B 92.231 502 32 5 1902 2399 67543907 67543409 0.000000e+00 704.0
22 TraesCS4D01G070900 chr4B 91.018 501 41 4 1903 2399 67094947 67095447 0.000000e+00 673.0
23 TraesCS4D01G070900 chr4B 90.283 494 41 6 1907 2399 67485199 67484712 7.230000e-180 640.0
24 TraesCS4D01G070900 chr4B 84.729 406 40 12 169 557 67089316 67089716 1.040000e-103 387.0
25 TraesCS4D01G070900 chr4B 93.789 161 9 1 1696 1856 67544159 67544000 8.570000e-60 241.0
26 TraesCS4D01G070900 chr4B 90.964 166 10 2 1696 1856 67491351 67491186 4.020000e-53 219.0
27 TraesCS4D01G070900 chr4B 89.697 165 13 2 1738 1902 67089748 67089908 8.690000e-50 207.0
28 TraesCS4D01G070900 chr4B 86.301 146 12 3 412 557 67491487 67491350 4.130000e-33 152.0
29 TraesCS4D01G070900 chr4B 85.430 151 9 6 412 557 67544301 67544159 6.910000e-31 145.0
30 TraesCS4D01G070900 chr4B 94.030 67 3 1 438 504 67354645 67354580 1.520000e-17 100.0
31 TraesCS4D01G070900 chr5A 84.416 154 22 2 1560 1711 617125611 617125458 1.490000e-32 150.0
32 TraesCS4D01G070900 chr5A 84.173 139 21 1 1561 1698 617121837 617121975 1.500000e-27 134.0
33 TraesCS4D01G070900 chr3D 85.271 129 19 0 1561 1689 126399032 126399160 1.500000e-27 134.0
34 TraesCS4D01G070900 chr6D 92.308 78 6 0 2249 2326 7294608 7294531 7.010000e-21 111.0


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 TraesCS4D01G070900 chr4D 46174987 46177385 2398 False 4431.000000 4431 100.000000 1 2399 1 chr4D.!!$F1 2398
1 TraesCS4D01G070900 chr4D 46186971 46187704 733 True 869.000000 869 88.707000 1696 2399 1 chr4D.!!$R1 703
2 TraesCS4D01G070900 chr7D 451854846 451855843 997 False 1288.000000 1288 90.239000 621 1604 1 chr7D.!!$F2 983
3 TraesCS4D01G070900 chr4A 680377236 680378268 1032 False 1225.000000 1225 88.163000 642 1684 1 chr4A.!!$F1 1042
4 TraesCS4D01G070900 chr4A 552832699 552833268 569 True 791.000000 791 91.769000 1832 2399 1 chr4A.!!$R1 567
5 TraesCS4D01G070900 chr4A 552816534 552817271 737 False 460.500000 701 89.168500 1700 2399 2 chr4A.!!$F2 699
6 TraesCS4D01G070900 chr4A 552843231 552843974 743 True 281.500000 488 82.280000 1 1814 2 chr4A.!!$R2 1813
7 TraesCS4D01G070900 chr2A 735684439 735686910 2471 False 1186.000000 1199 88.518000 607 1604 2 chr2A.!!$F1 997
8 TraesCS4D01G070900 chr5D 173764208 173765299 1091 True 662.500000 1182 87.834500 607 1684 2 chr5D.!!$R1 1077
9 TraesCS4D01G070900 chr1A 549573489 549574460 971 False 1112.000000 1112 87.551000 640 1604 1 chr1A.!!$F2 964
10 TraesCS4D01G070900 chr7B 23070314 23071134 820 True 1075.000000 1075 90.459000 626 1443 1 chr7B.!!$R1 817
11 TraesCS4D01G070900 chr1D 20402097 20402901 804 True 1053.000000 1053 90.382000 640 1443 1 chr1D.!!$R1 803
12 TraesCS4D01G070900 chr6B 701467610 701468490 880 True 1046.000000 1046 88.575000 642 1498 1 chr6B.!!$R1 856
13 TraesCS4D01G070900 chr4B 67094947 67095447 500 False 673.000000 673 91.018000 1903 2399 1 chr4B.!!$F1 496
14 TraesCS4D01G070900 chr4B 67353808 67354645 837 True 473.000000 846 91.140500 438 2399 2 chr4B.!!$R2 1961
15 TraesCS4D01G070900 chr4B 67543409 67544301 892 True 363.333333 704 90.483333 412 2399 3 chr4B.!!$R4 1987
16 TraesCS4D01G070900 chr4B 67089316 67089908 592 False 297.000000 387 87.213000 169 1902 2 chr4B.!!$F2 1733

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
603 694 0.109458 ACGCGCACGAGATAAACTGA 60.109 50.0 5.73 0.0 43.93 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 2860 0.106167 AGGACGAGCAGCTATACCCA 60.106 55.0 0.0 0.0 0.0 4.51 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 1.588667 CAAACCAGCACGCCAACAC 60.589 57.895 0.00 0.00 0.00 3.32
36 37 4.327680 GCCAACACAGAAGGAAACTATCT 58.672 43.478 0.00 0.00 42.68 1.98
59 60 3.264947 CTGTTTCCATCGATCAAGCTCA 58.735 45.455 0.00 0.00 0.00 4.26
61 62 1.926561 TTCCATCGATCAAGCTCACG 58.073 50.000 0.00 0.00 0.00 4.35
65 66 3.068165 TCCATCGATCAAGCTCACGTATT 59.932 43.478 0.00 0.00 0.00 1.89
104 129 5.120830 GCATGTTTTGATCGAGTGAGTTACT 59.879 40.000 0.00 0.00 44.02 2.24
105 130 6.310467 GCATGTTTTGATCGAGTGAGTTACTA 59.690 38.462 0.00 0.00 40.53 1.82
106 131 7.010552 GCATGTTTTGATCGAGTGAGTTACTAT 59.989 37.037 0.00 0.00 40.53 2.12
115 140 5.986936 CGAGTGAGTTACTATCATTCGCTA 58.013 41.667 7.71 0.00 45.55 4.26
117 142 6.357503 CGAGTGAGTTACTATCATTCGCTAAC 59.642 42.308 7.71 0.00 45.55 2.34
119 144 6.096423 AGTGAGTTACTATCATTCGCTAACCA 59.904 38.462 0.00 0.00 38.04 3.67
120 145 6.924060 GTGAGTTACTATCATTCGCTAACCAT 59.076 38.462 0.00 0.00 0.00 3.55
121 146 7.438459 GTGAGTTACTATCATTCGCTAACCATT 59.562 37.037 0.00 0.00 0.00 3.16
123 148 6.641314 AGTTACTATCATTCGCTAACCATTCG 59.359 38.462 0.00 0.00 0.00 3.34
124 149 5.196341 ACTATCATTCGCTAACCATTCGA 57.804 39.130 0.00 0.00 0.00 3.71
125 150 5.784177 ACTATCATTCGCTAACCATTCGAT 58.216 37.500 0.00 0.00 31.96 3.59
127 152 4.053469 TCATTCGCTAACCATTCGATCA 57.947 40.909 0.00 0.00 31.96 2.92
129 154 4.507756 TCATTCGCTAACCATTCGATCAAG 59.492 41.667 0.00 0.00 31.96 3.02
143 172 5.545658 TCGATCAAGTGGTTAATCTTTGC 57.454 39.130 0.00 0.00 0.00 3.68
149 178 7.672983 TCAAGTGGTTAATCTTTGCTTCTAG 57.327 36.000 0.00 0.00 0.00 2.43
153 182 5.181245 GTGGTTAATCTTTGCTTCTAGTGCA 59.819 40.000 8.62 8.62 38.80 4.57
154 183 5.767665 TGGTTAATCTTTGCTTCTAGTGCAA 59.232 36.000 17.29 17.29 46.90 4.08
194 226 5.278315 CCATATGCATGTCATCTTTGGAGTG 60.278 44.000 10.16 0.00 36.63 3.51
204 236 6.088824 GTCATCTTTGGAGTGCAGTAATTTG 58.911 40.000 0.00 0.00 0.00 2.32
205 237 6.003326 TCATCTTTGGAGTGCAGTAATTTGA 58.997 36.000 0.00 0.00 0.00 2.69
207 239 6.072112 TCTTTGGAGTGCAGTAATTTGAAC 57.928 37.500 0.00 0.00 0.00 3.18
208 240 5.592282 TCTTTGGAGTGCAGTAATTTGAACA 59.408 36.000 0.00 0.00 0.00 3.18
210 242 5.437289 TGGAGTGCAGTAATTTGAACAAG 57.563 39.130 0.00 0.00 0.00 3.16
211 243 4.887071 TGGAGTGCAGTAATTTGAACAAGT 59.113 37.500 0.00 0.00 0.00 3.16
212 244 5.215160 GGAGTGCAGTAATTTGAACAAGTG 58.785 41.667 0.00 0.00 0.00 3.16
213 245 5.221048 GGAGTGCAGTAATTTGAACAAGTGT 60.221 40.000 0.00 0.00 0.00 3.55
312 345 1.240641 TTGGCATCGCAACGGAATGT 61.241 50.000 0.00 0.00 0.00 2.71
334 367 9.855021 AATGTTCACTCCTTTTTATTTAATCCG 57.145 29.630 0.00 0.00 0.00 4.18
365 398 4.034975 GGTGCAGCAGTGAGATATTTCTTC 59.965 45.833 11.86 0.00 30.30 2.87
507 558 9.451206 AGACCCATTCCCAATAATGAATAAAAT 57.549 29.630 0.00 0.00 38.84 1.82
557 648 4.657013 AGAAAGCAGAACCCTCCTTTAAG 58.343 43.478 0.00 0.00 0.00 1.85
560 651 2.026729 AGCAGAACCCTCCTTTAAGAGC 60.027 50.000 0.00 0.00 32.17 4.09
562 653 3.623453 GCAGAACCCTCCTTTAAGAGCAT 60.623 47.826 0.00 0.00 32.17 3.79
563 654 4.593956 CAGAACCCTCCTTTAAGAGCATT 58.406 43.478 0.00 0.00 32.17 3.56
564 655 5.012893 CAGAACCCTCCTTTAAGAGCATTT 58.987 41.667 0.00 0.00 32.17 2.32
565 656 5.124617 CAGAACCCTCCTTTAAGAGCATTTC 59.875 44.000 0.00 0.00 32.17 2.17
566 657 3.969553 ACCCTCCTTTAAGAGCATTTCC 58.030 45.455 0.00 0.00 32.17 3.13
567 658 3.333680 ACCCTCCTTTAAGAGCATTTCCA 59.666 43.478 0.00 0.00 32.17 3.53
568 659 4.202673 ACCCTCCTTTAAGAGCATTTCCAA 60.203 41.667 0.00 0.00 32.17 3.53
569 660 4.158579 CCCTCCTTTAAGAGCATTTCCAAC 59.841 45.833 0.00 0.00 32.17 3.77
570 661 4.766891 CCTCCTTTAAGAGCATTTCCAACA 59.233 41.667 0.00 0.00 32.17 3.33
571 662 5.105997 CCTCCTTTAAGAGCATTTCCAACAG 60.106 44.000 0.00 0.00 32.17 3.16
572 663 4.218417 TCCTTTAAGAGCATTTCCAACAGC 59.782 41.667 0.00 0.00 0.00 4.40
573 664 4.488879 CTTTAAGAGCATTTCCAACAGCC 58.511 43.478 0.00 0.00 0.00 4.85
574 665 0.883833 AAGAGCATTTCCAACAGCCG 59.116 50.000 0.00 0.00 0.00 5.52
575 666 1.153958 GAGCATTTCCAACAGCCGC 60.154 57.895 0.00 0.00 0.00 6.53
576 667 2.504681 GCATTTCCAACAGCCGCG 60.505 61.111 0.00 0.00 0.00 6.46
577 668 2.953821 CATTTCCAACAGCCGCGT 59.046 55.556 4.92 0.00 0.00 6.01
578 669 1.154225 CATTTCCAACAGCCGCGTC 60.154 57.895 4.92 0.00 0.00 5.19
579 670 1.599518 ATTTCCAACAGCCGCGTCA 60.600 52.632 4.92 0.00 0.00 4.35
580 671 1.169661 ATTTCCAACAGCCGCGTCAA 61.170 50.000 4.92 0.00 0.00 3.18
581 672 1.377366 TTTCCAACAGCCGCGTCAAA 61.377 50.000 4.92 0.00 0.00 2.69
582 673 1.377366 TTCCAACAGCCGCGTCAAAA 61.377 50.000 4.92 0.00 0.00 2.44
583 674 1.370414 CCAACAGCCGCGTCAAAAG 60.370 57.895 4.92 0.00 0.00 2.27
584 675 1.646540 CAACAGCCGCGTCAAAAGA 59.353 52.632 4.92 0.00 0.00 2.52
585 676 0.657368 CAACAGCCGCGTCAAAAGAC 60.657 55.000 4.92 0.00 0.00 3.01
593 684 2.923177 CGTCAAAAGACGCGCACGA 61.923 57.895 5.73 0.00 43.93 4.35
594 685 1.154836 GTCAAAAGACGCGCACGAG 60.155 57.895 5.73 0.00 43.93 4.18
595 686 1.299544 TCAAAAGACGCGCACGAGA 60.300 52.632 5.73 0.00 43.93 4.04
596 687 0.666274 TCAAAAGACGCGCACGAGAT 60.666 50.000 5.73 0.00 43.93 2.75
597 688 0.989164 CAAAAGACGCGCACGAGATA 59.011 50.000 5.73 0.00 43.93 1.98
598 689 1.388768 CAAAAGACGCGCACGAGATAA 59.611 47.619 5.73 0.00 43.93 1.75
599 690 1.705256 AAAGACGCGCACGAGATAAA 58.295 45.000 5.73 0.00 43.93 1.40
600 691 0.989890 AAGACGCGCACGAGATAAAC 59.010 50.000 5.73 0.00 43.93 2.01
601 692 0.170561 AGACGCGCACGAGATAAACT 59.829 50.000 5.73 0.00 43.93 2.66
602 693 0.294887 GACGCGCACGAGATAAACTG 59.705 55.000 5.73 0.00 43.93 3.16
603 694 0.109458 ACGCGCACGAGATAAACTGA 60.109 50.000 5.73 0.00 43.93 3.41
604 695 0.567968 CGCGCACGAGATAAACTGAG 59.432 55.000 8.75 0.00 43.93 3.35
605 696 1.630148 GCGCACGAGATAAACTGAGT 58.370 50.000 0.30 0.00 0.00 3.41
610 701 5.389098 GCGCACGAGATAAACTGAGTTTTTA 60.389 40.000 16.49 0.00 37.01 1.52
617 708 0.110823 AACTGAGTTTTTAGCGCGCG 60.111 50.000 28.44 28.44 0.00 6.86
618 709 1.225745 CTGAGTTTTTAGCGCGCGG 60.226 57.895 33.06 13.66 0.00 6.46
619 710 2.097728 GAGTTTTTAGCGCGCGGG 59.902 61.111 33.06 20.05 0.00 6.13
622 713 3.436055 TTTTTAGCGCGCGGGCAT 61.436 55.556 42.76 30.58 39.92 4.40
738 843 1.258445 CGGCTACCCCACACTCTCTT 61.258 60.000 0.00 0.00 0.00 2.85
746 851 2.289945 CCCCACACTCTCTTTTCCTCTG 60.290 54.545 0.00 0.00 0.00 3.35
891 1002 1.025812 CAGCTGGTACTACTCCGAGG 58.974 60.000 5.57 0.00 0.00 4.63
1133 1244 2.838748 ATCACCGAGGAGGACGAGCA 62.839 60.000 0.00 0.00 45.00 4.26
1191 1302 2.107141 GCCGACGAGCAAGCCTAT 59.893 61.111 0.00 0.00 0.00 2.57
1242 1353 4.351938 CCGTTGGACAGGCGTCGA 62.352 66.667 0.00 0.00 43.61 4.20
1244 1355 2.028484 GTTGGACAGGCGTCGACA 59.972 61.111 17.16 0.00 43.61 4.35
1252 1363 2.811317 GGCGTCGACAGAAGGCTG 60.811 66.667 17.16 0.00 45.22 4.85
1468 1623 7.755822 GGACCGTAGTTTTATCTATCTATGCTG 59.244 40.741 0.00 0.00 0.00 4.41
1558 1716 7.987268 TTTAAAAATGTGTACGCAATGTTCA 57.013 28.000 14.03 0.00 0.00 3.18
1626 1862 2.644992 CTGCCCACCACGCTTTTC 59.355 61.111 0.00 0.00 0.00 2.29
1629 1865 2.494530 GCCCACCACGCTTTTCCAA 61.495 57.895 0.00 0.00 0.00 3.53
1686 1922 2.047655 CGTTGGGCGGCTGTTAGA 60.048 61.111 9.56 0.00 36.85 2.10
1687 1923 2.100631 CGTTGGGCGGCTGTTAGAG 61.101 63.158 9.56 0.00 36.85 2.43
1688 1924 1.295423 GTTGGGCGGCTGTTAGAGA 59.705 57.895 9.56 0.00 0.00 3.10
1689 1925 0.741221 GTTGGGCGGCTGTTAGAGAG 60.741 60.000 9.56 0.00 0.00 3.20
1690 1926 1.899437 TTGGGCGGCTGTTAGAGAGG 61.899 60.000 9.56 0.00 0.00 3.69
1691 1927 2.501610 GGCGGCTGTTAGAGAGGG 59.498 66.667 0.00 0.00 0.00 4.30
1693 1929 1.142097 GCGGCTGTTAGAGAGGGTC 59.858 63.158 0.00 0.00 0.00 4.46
1695 1931 2.022754 GCGGCTGTTAGAGAGGGTCTA 61.023 57.143 0.00 0.00 36.64 2.59
1696 1932 2.376109 CGGCTGTTAGAGAGGGTCTAA 58.624 52.381 0.00 0.00 44.19 2.10
1785 2025 1.805539 CGGCATCGCTCTCGTTTCA 60.806 57.895 0.00 0.00 36.96 2.69
1796 2036 2.554462 CTCTCGTTTCAGTCTCTCACCA 59.446 50.000 0.00 0.00 0.00 4.17
1822 2062 1.324718 CGCGATATATATACCGCCGC 58.675 55.000 22.81 18.30 44.18 6.53
1823 2063 1.334329 CGCGATATATATACCGCCGCA 60.334 52.381 22.81 0.00 44.18 5.69
1824 2064 2.316792 GCGATATATATACCGCCGCAG 58.683 52.381 19.10 0.00 41.59 5.18
1865 2129 1.357907 CTCGCAAGCTTCTTCTCCTG 58.642 55.000 0.00 0.00 37.18 3.86
1893 2161 1.889530 CGGTCTCGGCTTTCCTTCCT 61.890 60.000 0.00 0.00 0.00 3.36
1974 2303 2.032799 TCGTTTCCTGTGTGAATTGTGC 59.967 45.455 0.00 0.00 0.00 4.57
1975 2304 2.223456 CGTTTCCTGTGTGAATTGTGCA 60.223 45.455 0.00 0.00 0.00 4.57
2085 2851 4.671590 TCCTCCGCCTCCGTGTCA 62.672 66.667 0.00 0.00 0.00 3.58
2268 3052 2.048597 ATCGCGTCGCTGGTCAAA 60.049 55.556 16.36 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.387855 GCTAAATACGTGAGCTTGATCGATG 60.388 44.000 0.54 0.00 33.28 3.84
59 60 4.142026 TGCATGGAGTAGTGCTAAATACGT 60.142 41.667 0.00 0.00 41.78 3.57
61 62 5.760253 ACATGCATGGAGTAGTGCTAAATAC 59.240 40.000 29.41 0.00 41.78 1.89
65 66 3.912496 ACATGCATGGAGTAGTGCTAA 57.088 42.857 29.41 0.00 41.78 3.09
104 129 5.778862 TGATCGAATGGTTAGCGAATGATA 58.221 37.500 0.00 0.00 37.60 2.15
105 130 4.631131 TGATCGAATGGTTAGCGAATGAT 58.369 39.130 0.00 0.00 37.60 2.45
106 131 4.053469 TGATCGAATGGTTAGCGAATGA 57.947 40.909 0.00 0.00 37.60 2.57
117 142 6.683974 AAGATTAACCACTTGATCGAATGG 57.316 37.500 8.97 8.97 38.26 3.16
119 144 6.375455 AGCAAAGATTAACCACTTGATCGAAT 59.625 34.615 0.00 0.00 29.57 3.34
120 145 5.705441 AGCAAAGATTAACCACTTGATCGAA 59.295 36.000 0.00 0.00 29.57 3.71
121 146 5.245531 AGCAAAGATTAACCACTTGATCGA 58.754 37.500 0.00 0.00 29.57 3.59
123 148 7.150783 AGAAGCAAAGATTAACCACTTGATC 57.849 36.000 0.00 0.00 0.00 2.92
124 149 7.885399 ACTAGAAGCAAAGATTAACCACTTGAT 59.115 33.333 0.00 0.00 0.00 2.57
125 150 7.173218 CACTAGAAGCAAAGATTAACCACTTGA 59.827 37.037 0.00 0.00 0.00 3.02
127 152 6.072452 GCACTAGAAGCAAAGATTAACCACTT 60.072 38.462 0.00 0.00 0.00 3.16
129 154 5.181245 TGCACTAGAAGCAAAGATTAACCAC 59.819 40.000 11.24 0.00 39.39 4.16
175 207 1.814394 GCACTCCAAAGATGACATGCA 59.186 47.619 0.00 0.00 31.52 3.96
179 211 2.936919 ACTGCACTCCAAAGATGACA 57.063 45.000 0.00 0.00 0.00 3.58
194 226 5.181690 TGGACACTTGTTCAAATTACTGC 57.818 39.130 0.00 0.00 28.85 4.40
204 236 4.510340 ACTCAAACGTATGGACACTTGTTC 59.490 41.667 0.00 0.00 0.00 3.18
205 237 4.448210 ACTCAAACGTATGGACACTTGTT 58.552 39.130 0.00 0.00 0.00 2.83
207 239 6.094739 CATACTCAAACGTATGGACACTTG 57.905 41.667 0.00 0.00 41.78 3.16
312 345 7.148373 CCGTCGGATTAAATAAAAAGGAGTGAA 60.148 37.037 4.91 0.00 0.00 3.18
334 367 1.672356 ACTGCTGCACCATTCCGTC 60.672 57.895 0.00 0.00 0.00 4.79
365 398 6.628919 TCATCATTGGTTAGATTCATGCTG 57.371 37.500 0.00 0.00 0.00 4.41
455 501 3.857854 GCGGCTGCTGTGTGATCG 61.858 66.667 11.21 0.00 38.39 3.69
507 558 9.415544 GAGTTTGTCGGTTTTACTCTAGAATAA 57.584 33.333 0.00 0.00 34.00 1.40
508 559 8.579006 TGAGTTTGTCGGTTTTACTCTAGAATA 58.421 33.333 0.00 0.00 36.91 1.75
531 622 2.039613 AGGAGGGTTCTGCTTTCTTGAG 59.960 50.000 0.00 0.00 38.61 3.02
557 648 1.153958 GCGGCTGTTGGAAATGCTC 60.154 57.895 0.00 0.00 0.00 4.26
560 651 1.154225 GACGCGGCTGTTGGAAATG 60.154 57.895 12.47 0.00 0.00 2.32
562 653 1.377366 TTTGACGCGGCTGTTGGAAA 61.377 50.000 15.80 0.00 0.00 3.13
563 654 1.377366 TTTTGACGCGGCTGTTGGAA 61.377 50.000 15.80 0.00 0.00 3.53
564 655 1.781025 CTTTTGACGCGGCTGTTGGA 61.781 55.000 15.80 0.00 0.00 3.53
565 656 1.370414 CTTTTGACGCGGCTGTTGG 60.370 57.895 15.80 0.00 0.00 3.77
566 657 0.657368 GTCTTTTGACGCGGCTGTTG 60.657 55.000 15.80 0.72 39.89 3.33
567 658 1.647084 GTCTTTTGACGCGGCTGTT 59.353 52.632 15.80 0.00 39.89 3.16
568 659 3.330275 GTCTTTTGACGCGGCTGT 58.670 55.556 15.80 0.00 39.89 4.40
576 667 1.154836 CTCGTGCGCGTCTTTTGAC 60.155 57.895 20.50 0.00 45.55 3.18
577 668 0.666274 ATCTCGTGCGCGTCTTTTGA 60.666 50.000 20.50 9.60 39.49 2.69
578 669 0.989164 TATCTCGTGCGCGTCTTTTG 59.011 50.000 20.50 4.63 39.49 2.44
579 670 1.705256 TTATCTCGTGCGCGTCTTTT 58.295 45.000 20.50 4.26 39.49 2.27
580 671 1.389106 GTTTATCTCGTGCGCGTCTTT 59.611 47.619 20.50 6.02 39.49 2.52
581 672 0.989890 GTTTATCTCGTGCGCGTCTT 59.010 50.000 20.50 7.81 39.49 3.01
582 673 0.170561 AGTTTATCTCGTGCGCGTCT 59.829 50.000 20.50 8.00 39.49 4.18
583 674 0.294887 CAGTTTATCTCGTGCGCGTC 59.705 55.000 20.50 0.00 39.49 5.19
584 675 0.109458 TCAGTTTATCTCGTGCGCGT 60.109 50.000 20.50 2.64 39.49 6.01
585 676 0.567968 CTCAGTTTATCTCGTGCGCG 59.432 55.000 14.79 14.79 39.92 6.86
586 677 1.630148 ACTCAGTTTATCTCGTGCGC 58.370 50.000 0.00 0.00 0.00 6.09
587 678 4.647291 AAAACTCAGTTTATCTCGTGCG 57.353 40.909 2.38 0.00 34.43 5.34
588 679 6.016111 GCTAAAAACTCAGTTTATCTCGTGC 58.984 40.000 2.38 0.00 34.43 5.34
589 680 6.234213 CGCTAAAAACTCAGTTTATCTCGTG 58.766 40.000 2.38 0.00 34.43 4.35
590 681 5.163982 GCGCTAAAAACTCAGTTTATCTCGT 60.164 40.000 2.38 0.00 34.43 4.18
591 682 5.248834 GCGCTAAAAACTCAGTTTATCTCG 58.751 41.667 2.38 6.85 34.43 4.04
592 683 5.248834 CGCGCTAAAAACTCAGTTTATCTC 58.751 41.667 2.38 0.00 34.43 2.75
593 684 4.435651 GCGCGCTAAAAACTCAGTTTATCT 60.436 41.667 26.67 0.00 34.43 1.98
594 685 3.779238 GCGCGCTAAAAACTCAGTTTATC 59.221 43.478 26.67 0.00 34.43 1.75
595 686 3.723835 CGCGCGCTAAAAACTCAGTTTAT 60.724 43.478 30.48 0.00 34.43 1.40
596 687 2.410517 CGCGCGCTAAAAACTCAGTTTA 60.411 45.455 30.48 0.00 34.43 2.01
597 688 1.659211 CGCGCGCTAAAAACTCAGTTT 60.659 47.619 30.48 0.00 37.34 2.66
598 689 0.110823 CGCGCGCTAAAAACTCAGTT 60.111 50.000 30.48 0.00 0.00 3.16
599 690 1.491563 CGCGCGCTAAAAACTCAGT 59.508 52.632 30.48 0.00 0.00 3.41
600 691 1.225745 CCGCGCGCTAAAAACTCAG 60.226 57.895 30.48 9.02 0.00 3.35
601 692 2.673114 CCCGCGCGCTAAAAACTCA 61.673 57.895 30.48 0.00 0.00 3.41
602 693 2.097728 CCCGCGCGCTAAAAACTC 59.902 61.111 30.48 0.00 0.00 3.01
603 694 4.097863 GCCCGCGCGCTAAAAACT 62.098 61.111 30.48 0.00 0.00 2.66
604 695 3.677099 ATGCCCGCGCGCTAAAAAC 62.677 57.895 30.48 12.62 38.08 2.43
605 696 3.389727 GATGCCCGCGCGCTAAAAA 62.390 57.895 30.48 11.21 38.08 1.94
619 710 2.862674 TAGTTTCCCGCCACCGATGC 62.863 60.000 0.00 0.00 36.29 3.91
622 713 2.975536 CTAGTTTCCCGCCACCGA 59.024 61.111 0.00 0.00 36.29 4.69
725 820 1.981495 AGAGGAAAAGAGAGTGTGGGG 59.019 52.381 0.00 0.00 0.00 4.96
726 821 2.370189 ACAGAGGAAAAGAGAGTGTGGG 59.630 50.000 0.00 0.00 0.00 4.61
738 843 2.733218 CGCGCGTGACAGAGGAAA 60.733 61.111 24.19 0.00 0.00 3.13
761 872 1.668151 GAAGCAACGAGGAAGCGGT 60.668 57.895 0.00 0.00 35.12 5.68
891 1002 4.773117 GACGTCGCCAGACCGGAC 62.773 72.222 9.46 0.10 44.28 4.79
916 1027 1.376037 GTCTTGAAGGTGCCGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
969 1080 2.507102 CTGCCTAGGCGTCACGTG 60.507 66.667 28.28 9.94 45.51 4.49
996 1107 1.971357 ACGTCCTGGAAGTTCATCTGT 59.029 47.619 9.58 0.00 0.00 3.41
1117 1228 2.752238 CTGCTCGTCCTCCTCGGT 60.752 66.667 0.00 0.00 0.00 4.69
1191 1302 4.704833 GCCGTCTGCTCTGCCCAA 62.705 66.667 0.00 0.00 36.87 4.12
1197 1308 2.740055 CGCTTTGCCGTCTGCTCT 60.740 61.111 0.00 0.00 42.00 4.09
1222 1333 1.890510 GACGCCTGTCCAACGGTTT 60.891 57.895 0.00 0.00 39.30 3.27
1226 1337 3.103911 GTCGACGCCTGTCCAACG 61.104 66.667 0.00 0.00 42.37 4.10
1244 1355 0.460284 CGATAACGCCACAGCCTTCT 60.460 55.000 0.00 0.00 34.57 2.85
1274 1385 1.922135 CTGCCCACCATTTTCGACGG 61.922 60.000 0.00 0.00 0.00 4.79
1278 1389 0.953471 TCGACTGCCCACCATTTTCG 60.953 55.000 0.00 0.00 0.00 3.46
1531 1689 9.856803 GAACATTGCGTACACATTTTTAAAAAT 57.143 25.926 18.40 18.40 39.07 1.82
1533 1691 8.407457 TGAACATTGCGTACACATTTTTAAAA 57.593 26.923 0.00 0.00 0.00 1.52
1543 1701 1.725931 GCAGCTGAACATTGCGTACAC 60.726 52.381 20.43 0.00 0.00 2.90
1607 1843 4.892965 AAAGCGTGGTGGGCAGCA 62.893 61.111 0.00 0.00 36.34 4.41
1615 1851 1.001815 CATCGTTTGGAAAAGCGTGGT 60.002 47.619 0.00 0.00 0.00 4.16
1686 1922 0.708802 TCCTTCCCGTTAGACCCTCT 59.291 55.000 0.00 0.00 0.00 3.69
1687 1923 1.565067 TTCCTTCCCGTTAGACCCTC 58.435 55.000 0.00 0.00 0.00 4.30
1688 1924 2.034436 TTTCCTTCCCGTTAGACCCT 57.966 50.000 0.00 0.00 0.00 4.34
1689 1925 4.492494 TTATTTCCTTCCCGTTAGACCC 57.508 45.455 0.00 0.00 0.00 4.46
1690 1926 5.677567 TGATTATTTCCTTCCCGTTAGACC 58.322 41.667 0.00 0.00 0.00 3.85
1691 1927 7.497909 TGATTGATTATTTCCTTCCCGTTAGAC 59.502 37.037 0.00 0.00 0.00 2.59
1693 1929 7.801716 TGATTGATTATTTCCTTCCCGTTAG 57.198 36.000 0.00 0.00 0.00 2.34
1695 1931 7.475137 TTTGATTGATTATTTCCTTCCCGTT 57.525 32.000 0.00 0.00 0.00 4.44
1696 1932 7.468631 CGATTTGATTGATTATTTCCTTCCCGT 60.469 37.037 0.00 0.00 0.00 5.28
1697 1933 6.857964 CGATTTGATTGATTATTTCCTTCCCG 59.142 38.462 0.00 0.00 0.00 5.14
1698 1934 7.014230 TCCGATTTGATTGATTATTTCCTTCCC 59.986 37.037 0.00 0.00 0.00 3.97
1699 1935 7.940850 TCCGATTTGATTGATTATTTCCTTCC 58.059 34.615 0.00 0.00 0.00 3.46
1700 1936 9.237846 GTTCCGATTTGATTGATTATTTCCTTC 57.762 33.333 0.00 0.00 0.00 3.46
1785 2025 1.468985 CGTGGAGATGGTGAGAGACT 58.531 55.000 0.00 0.00 0.00 3.24
1796 2036 5.608676 CGGTATATATATCGCGTGGAGAT 57.391 43.478 12.23 0.00 29.40 2.75
1893 2161 1.243902 CCTTTTTAAGGCCTGCGTCA 58.756 50.000 5.69 0.00 42.78 4.35
1974 2303 2.878406 GTGGTTACCCATGGATCGATTG 59.122 50.000 15.22 0.00 44.35 2.67
1975 2304 2.158667 GGTGGTTACCCATGGATCGATT 60.159 50.000 15.22 0.00 44.35 3.34
2085 2851 2.232452 GCAGCTATACCCATCGTCATCT 59.768 50.000 0.00 0.00 0.00 2.90
2094 2860 0.106167 AGGACGAGCAGCTATACCCA 60.106 55.000 0.00 0.00 0.00 4.51
2100 2866 1.822613 CGGGTAGGACGAGCAGCTA 60.823 63.158 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.