Multiple sequence alignment - TraesCS4D01G255000

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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 TraesCS4D01G255000 chr4D 100.000 3005 0 0 1 3005 423905343 423908347 0.000000e+00 5550
1 TraesCS4D01G255000 chr4D 86.583 1036 88 21 1870 2880 423880695 423881704 0.000000e+00 1096
2 TraesCS4D01G255000 chr4D 82.559 1141 133 27 742 1839 423879580 423880697 0.000000e+00 944
3 TraesCS4D01G255000 chr4D 81.922 437 44 10 280 706 423879171 423879582 1.330000e-88 337
4 TraesCS4D01G255000 chr4A 92.864 2200 99 15 835 3005 40437590 40435420 0.000000e+00 3140
5 TraesCS4D01G255000 chr4A 92.823 1059 47 8 835 1881 40414058 40413017 0.000000e+00 1507
6 TraesCS4D01G255000 chr4A 91.725 568 44 3 1989 2555 40413027 40412462 0.000000e+00 785
7 TraesCS4D01G255000 chr4A 91.405 477 18 5 299 761 40438053 40437586 1.520000e-177 632
8 TraesCS4D01G255000 chr4A 90.342 497 25 5 279 761 40414541 40414054 5.470000e-177 630
9 TraesCS4D01G255000 chr4A 90.141 497 26 5 279 761 40493347 40492860 2.540000e-175 625
10 TraesCS4D01G255000 chr4A 92.035 452 20 7 835 1281 40495235 40495675 3.290000e-174 621
11 TraesCS4D01G255000 chr4A 91.593 452 19 8 835 1281 40492864 40492427 9.210000e-170 606
12 TraesCS4D01G255000 chr4A 91.500 200 8 3 569 761 40495042 40495239 1.780000e-67 267
13 TraesCS4D01G255000 chr4B 91.289 1435 104 8 1135 2557 520237441 520238866 0.000000e+00 1938
14 TraesCS4D01G255000 chr4B 82.846 2221 237 62 742 2880 520228587 520230745 0.000000e+00 1858
15 TraesCS4D01G255000 chr4B 87.487 927 50 25 53 921 520236267 520237185 0.000000e+00 1009
16 TraesCS4D01G255000 chr4B 95.493 355 4 3 2663 3005 520238916 520239270 9.410000e-155 556
17 TraesCS4D01G255000 chr4B 82.877 438 37 13 280 706 520228179 520228589 2.850000e-95 359
18 TraesCS4D01G255000 chr4B 95.361 194 7 2 906 1098 520237251 520237443 1.050000e-79 307
19 TraesCS4D01G255000 chr1A 77.159 359 76 6 1381 1737 564345822 564345468 1.410000e-48 204
20 TraesCS4D01G255000 chr1A 74.704 423 93 8 1382 1802 564576036 564576446 3.080000e-40 176
21 TraesCS4D01G255000 chr1B 76.584 363 69 12 1381 1736 653938851 653938498 5.120000e-43 185
22 TraesCS4D01G255000 chr6B 76.042 288 61 3 1439 1719 6007747 6008033 3.120000e-30 143


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 TraesCS4D01G255000 chr4D 423905343 423908347 3004 False 5550.000000 5550 100.0000 1 3005 1 chr4D.!!$F1 3004
1 TraesCS4D01G255000 chr4D 423879171 423881704 2533 False 792.333333 1096 83.6880 280 2880 3 chr4D.!!$F2 2600
2 TraesCS4D01G255000 chr4A 40435420 40438053 2633 True 1886.000000 3140 92.1345 299 3005 2 chr4A.!!$R2 2706
3 TraesCS4D01G255000 chr4A 40412462 40414541 2079 True 974.000000 1507 91.6300 279 2555 3 chr4A.!!$R1 2276
4 TraesCS4D01G255000 chr4A 40492427 40493347 920 True 615.500000 625 90.8670 279 1281 2 chr4A.!!$R3 1002
5 TraesCS4D01G255000 chr4A 40495042 40495675 633 False 444.000000 621 91.7675 569 1281 2 chr4A.!!$F1 712
6 TraesCS4D01G255000 chr4B 520228179 520230745 2566 False 1108.500000 1858 82.8615 280 2880 2 chr4B.!!$F1 2600
7 TraesCS4D01G255000 chr4B 520236267 520239270 3003 False 952.500000 1938 92.4075 53 3005 4 chr4B.!!$F2 2952

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
788 859 0.168128 GTGTGTGCAATTAGCCCGTC 59.832 55.0 0.00 0.0 44.83 4.79 F
1536 1720 0.179006 CCTGGCTTGCCTTATCCTCC 60.179 60.0 13.18 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1858 2066 1.133699 CCATGATGGGCTGAAGGCTAA 60.134 52.381 2.79 0.0 41.46 3.09 R
2775 3042 1.699634 GGGCAGAATACATAGCTCCCA 59.300 52.381 0.00 0.0 32.89 4.37 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
22 23 3.309675 GGATGACGAACGCGGATG 58.690 61.111 12.47 0.82 43.17 3.51
23 24 2.621000 GATGACGAACGCGGATGC 59.379 61.111 12.47 0.00 43.17 3.91
33 34 4.771127 GCGGATGCGAATTAGGGA 57.229 55.556 12.10 0.00 0.00 4.20
34 35 3.233355 GCGGATGCGAATTAGGGAT 57.767 52.632 12.10 0.00 0.00 3.85
35 36 1.079503 GCGGATGCGAATTAGGGATC 58.920 55.000 12.10 2.89 0.00 3.36
36 37 1.726853 CGGATGCGAATTAGGGATCC 58.273 55.000 15.54 15.54 45.74 3.36
41 42 5.712152 GATGCGAATTAGGGATCCAAAAT 57.288 39.130 15.23 9.46 0.00 1.82
42 43 6.817765 GATGCGAATTAGGGATCCAAAATA 57.182 37.500 15.23 0.00 0.00 1.40
43 44 6.824305 ATGCGAATTAGGGATCCAAAATAG 57.176 37.500 15.23 10.66 0.00 1.73
44 45 4.518970 TGCGAATTAGGGATCCAAAATAGC 59.481 41.667 15.23 18.56 0.00 2.97
45 46 4.762251 GCGAATTAGGGATCCAAAATAGCT 59.238 41.667 15.23 1.63 0.00 3.32
46 47 5.335191 GCGAATTAGGGATCCAAAATAGCTG 60.335 44.000 15.23 4.81 0.00 4.24
47 48 5.335191 CGAATTAGGGATCCAAAATAGCTGC 60.335 44.000 15.23 0.00 0.00 5.25
48 49 1.972872 AGGGATCCAAAATAGCTGCG 58.027 50.000 15.23 0.00 0.00 5.18
49 50 0.954452 GGGATCCAAAATAGCTGCGG 59.046 55.000 15.23 0.00 0.00 5.69
50 51 0.312102 GGATCCAAAATAGCTGCGGC 59.688 55.000 10.33 10.33 39.06 6.53
51 52 1.024271 GATCCAAAATAGCTGCGGCA 58.976 50.000 21.93 1.29 41.70 5.69
84 85 3.863543 CGCGCCGACATGAATGCA 61.864 61.111 0.00 0.00 0.00 3.96
91 92 1.331756 CCGACATGAATGCAGTTAGGC 59.668 52.381 0.00 0.00 0.00 3.93
92 93 1.004610 CGACATGAATGCAGTTAGGCG 60.005 52.381 0.00 0.00 36.28 5.52
102 113 1.453155 CAGTTAGGCGGCTGAAATGT 58.547 50.000 23.55 0.00 34.87 2.71
104 115 0.451783 GTTAGGCGGCTGAAATGTGG 59.548 55.000 23.55 0.00 0.00 4.17
122 133 1.649633 TGGGGAGGGTTCTAGAGCTAA 59.350 52.381 6.54 0.00 0.00 3.09
124 135 2.435069 GGGGAGGGTTCTAGAGCTAAAC 59.565 54.545 6.54 0.00 0.00 2.01
125 136 3.105283 GGGAGGGTTCTAGAGCTAAACA 58.895 50.000 6.54 0.00 0.00 2.83
136 153 6.570692 TCTAGAGCTAAACAACCGGAAATAG 58.429 40.000 9.46 4.32 0.00 1.73
153 170 6.776094 GGAAATAGATGTCCGAACTTTCAAG 58.224 40.000 0.00 0.00 0.00 3.02
160 177 1.002087 TCCGAACTTTCAAGAGCTCCC 59.998 52.381 10.93 0.00 0.00 4.30
161 178 1.443802 CGAACTTTCAAGAGCTCCCC 58.556 55.000 10.93 0.00 0.00 4.81
162 179 1.827681 GAACTTTCAAGAGCTCCCCC 58.172 55.000 10.93 0.00 0.00 5.40
199 216 4.263905 ACTTGTGGGATTTGAGAGGCATTA 60.264 41.667 0.00 0.00 0.00 1.90
201 218 4.209538 TGTGGGATTTGAGAGGCATTATG 58.790 43.478 0.00 0.00 0.00 1.90
227 244 3.804786 TTGATTACGGTAGCATCGGAA 57.195 42.857 0.00 0.00 34.76 4.30
243 260 2.169769 TCGGAACTCTCTCTCTCTCTCC 59.830 54.545 0.00 0.00 0.00 3.71
244 261 2.170607 CGGAACTCTCTCTCTCTCTCCT 59.829 54.545 0.00 0.00 0.00 3.69
246 263 3.199946 GGAACTCTCTCTCTCTCTCCTCA 59.800 52.174 0.00 0.00 0.00 3.86
247 264 4.324254 GGAACTCTCTCTCTCTCTCCTCAA 60.324 50.000 0.00 0.00 0.00 3.02
248 265 4.222124 ACTCTCTCTCTCTCTCCTCAAC 57.778 50.000 0.00 0.00 0.00 3.18
249 266 3.198068 CTCTCTCTCTCTCTCCTCAACG 58.802 54.545 0.00 0.00 0.00 4.10
264 281 1.609794 AACGGTCCTCACTCCTCCC 60.610 63.158 0.00 0.00 0.00 4.30
266 283 2.037527 GGTCCTCACTCCTCCCGT 59.962 66.667 0.00 0.00 0.00 5.28
287 334 3.481559 TTCATCTCCTCTCCCTCACTT 57.518 47.619 0.00 0.00 0.00 3.16
315 362 2.125269 CCTTACACCGGCGGGAAG 60.125 66.667 31.78 26.44 36.97 3.46
334 381 4.683432 GAGCGTGCTTCTCCAGTT 57.317 55.556 0.00 0.00 0.00 3.16
348 395 1.002430 TCCAGTTGCTGAAATCTCGCT 59.998 47.619 0.00 0.00 32.44 4.93
354 401 2.047370 TGAAATCTCGCTGCGGCA 60.047 55.556 23.03 9.30 38.60 5.69
425 472 6.042781 TGAGAACACAATCCCTTGTTAGTACT 59.957 38.462 0.00 0.00 43.05 2.73
426 473 7.233962 TGAGAACACAATCCCTTGTTAGTACTA 59.766 37.037 0.00 0.00 43.05 1.82
427 474 7.384477 AGAACACAATCCCTTGTTAGTACTAC 58.616 38.462 0.91 0.00 43.05 2.73
428 475 6.930068 ACACAATCCCTTGTTAGTACTACT 57.070 37.500 0.91 0.00 43.05 2.57
429 476 6.932947 ACACAATCCCTTGTTAGTACTACTC 58.067 40.000 0.91 0.00 43.05 2.59
430 477 6.070938 ACACAATCCCTTGTTAGTACTACTCC 60.071 42.308 0.91 0.00 43.05 3.85
431 478 5.126707 ACAATCCCTTGTTAGTACTACTCCG 59.873 44.000 0.91 0.00 43.05 4.63
728 793 4.201980 TGACCCGTGATGTTTCTCTATACG 60.202 45.833 0.00 0.00 0.00 3.06
788 859 0.168128 GTGTGTGCAATTAGCCCGTC 59.832 55.000 0.00 0.00 44.83 4.79
804 880 1.636988 CGTCGTTCATGGAAGGTACC 58.363 55.000 2.73 2.73 0.00 3.34
892 979 4.553323 CTGATTTCCTTGCTTCTTTGTGG 58.447 43.478 0.00 0.00 0.00 4.17
894 981 4.037923 TGATTTCCTTGCTTCTTTGTGGTC 59.962 41.667 0.00 0.00 0.00 4.02
939 1107 2.230994 TACGCCTGCAGAGCTCTTGG 62.231 60.000 15.27 17.07 0.00 3.61
1067 1237 6.128145 GGATCCTTTACAGAGAGCTTTTGTTC 60.128 42.308 3.84 0.00 0.00 3.18
1119 1289 9.973246 CATATGTATACACTGTTTGTTCAGTTC 57.027 33.333 7.96 0.00 44.92 3.01
1134 1304 5.163447 TGTTCAGTTCTGCTTGTAGTACTGT 60.163 40.000 18.72 0.00 42.89 3.55
1180 1350 8.298854 TGGCGATATCCATCATTTAATTCTTTG 58.701 33.333 0.00 0.00 0.00 2.77
1223 1398 5.606348 TTTTGATTACCTTGTTGGCTTGT 57.394 34.783 0.00 0.00 40.22 3.16
1224 1399 5.606348 TTTGATTACCTTGTTGGCTTGTT 57.394 34.783 0.00 0.00 40.22 2.83
1233 1408 5.104735 ACCTTGTTGGCTTGTTCCAATAAAA 60.105 36.000 6.26 0.00 46.64 1.52
1393 1576 8.856153 TTATCAGTATTGCCTTTCAGTAAACA 57.144 30.769 0.00 0.00 0.00 2.83
1429 1612 3.239449 GACCCTGGGAATGGTTTTCTTT 58.761 45.455 22.23 0.00 34.20 2.52
1505 1689 3.642705 AGTCTTTTTGCCGCTTCAAATC 58.357 40.909 0.00 0.00 36.04 2.17
1536 1720 0.179006 CCTGGCTTGCCTTATCCTCC 60.179 60.000 13.18 0.00 0.00 4.30
1575 1759 6.510536 CAAGAAGCTTCTGAAAATTCCAACT 58.489 36.000 29.09 6.19 37.65 3.16
1737 1945 6.289064 AGTCCTTTGTAAGTACAAGAACAGG 58.711 40.000 11.19 11.19 45.77 4.00
1738 1946 6.099269 AGTCCTTTGTAAGTACAAGAACAGGA 59.901 38.462 14.33 14.33 45.77 3.86
1742 1950 7.066525 CCTTTGTAAGTACAAGAACAGGAACAA 59.933 37.037 11.73 0.00 45.77 2.83
1743 1951 6.913873 TGTAAGTACAAGAACAGGAACAAC 57.086 37.500 0.00 0.00 32.40 3.32
1744 1952 6.646267 TGTAAGTACAAGAACAGGAACAACT 58.354 36.000 0.00 0.00 32.40 3.16
1745 1953 7.784037 TGTAAGTACAAGAACAGGAACAACTA 58.216 34.615 0.00 0.00 32.40 2.24
1747 1955 9.918630 GTAAGTACAAGAACAGGAACAACTATA 57.081 33.333 0.00 0.00 0.00 1.31
1750 1958 8.305317 AGTACAAGAACAGGAACAACTATACTC 58.695 37.037 0.00 0.00 0.00 2.59
1754 1962 6.257586 AGAACAGGAACAACTATACTCCTCT 58.742 40.000 0.00 0.00 36.10 3.69
1811 2019 0.248825 CGAGAGTGGAAGATGCTCCG 60.249 60.000 0.00 0.00 38.44 4.63
1909 2117 8.616076 CAAACTTCTATGTCTTCAACTTTCAGT 58.384 33.333 0.00 0.00 0.00 3.41
1911 2119 7.275920 ACTTCTATGTCTTCAACTTTCAGTGT 58.724 34.615 0.00 0.00 0.00 3.55
1914 2122 7.500992 TCTATGTCTTCAACTTTCAGTGTCTT 58.499 34.615 0.00 0.00 0.00 3.01
2281 2499 6.317140 GTCTTGATGTTGATGAGCCTTATGAA 59.683 38.462 0.00 0.00 0.00 2.57
2400 2618 0.390472 GCTCTTGACCTGGAGAACGG 60.390 60.000 0.00 0.00 0.00 4.44
2454 2672 8.995220 AGACAAGCTTCGTTTGTACAATATAAA 58.005 29.630 9.56 1.61 37.12 1.40
2515 2733 1.282570 CCGCGTGTTGCAAGACAAT 59.717 52.632 24.54 0.00 46.97 2.71
2563 2805 3.272925 GCTCCCTGCTTTAAGCCTT 57.727 52.632 14.80 0.00 41.51 4.35
2564 2806 1.550327 GCTCCCTGCTTTAAGCCTTT 58.450 50.000 14.80 0.00 41.51 3.11
2565 2807 2.723273 GCTCCCTGCTTTAAGCCTTTA 58.277 47.619 14.80 0.00 41.51 1.85
2566 2808 3.089284 GCTCCCTGCTTTAAGCCTTTAA 58.911 45.455 14.80 0.00 41.51 1.52
2567 2809 3.119459 GCTCCCTGCTTTAAGCCTTTAAC 60.119 47.826 14.80 0.00 41.51 2.01
2568 2810 3.427573 TCCCTGCTTTAAGCCTTTAACC 58.572 45.455 14.80 0.00 41.51 2.85
2569 2811 3.161866 CCCTGCTTTAAGCCTTTAACCA 58.838 45.455 14.80 0.00 41.51 3.67
2570 2812 3.769300 CCCTGCTTTAAGCCTTTAACCAT 59.231 43.478 14.80 0.00 41.51 3.55
2571 2813 4.381932 CCCTGCTTTAAGCCTTTAACCATG 60.382 45.833 14.80 0.00 41.51 3.66
2572 2814 4.220602 CCTGCTTTAAGCCTTTAACCATGT 59.779 41.667 14.80 0.00 41.51 3.21
2573 2815 5.417580 CCTGCTTTAAGCCTTTAACCATGTA 59.582 40.000 14.80 0.00 41.51 2.29
2574 2816 6.404734 CCTGCTTTAAGCCTTTAACCATGTAG 60.405 42.308 14.80 0.14 41.51 2.74
2575 2817 6.007703 TGCTTTAAGCCTTTAACCATGTAGT 58.992 36.000 14.80 0.00 41.51 2.73
2576 2818 6.150474 TGCTTTAAGCCTTTAACCATGTAGTC 59.850 38.462 14.80 0.00 41.51 2.59
2577 2819 6.674760 GCTTTAAGCCTTTAACCATGTAGTCG 60.675 42.308 5.52 0.00 34.48 4.18
2578 2820 3.261981 AGCCTTTAACCATGTAGTCGG 57.738 47.619 0.00 0.00 0.00 4.79
2579 2821 2.570302 AGCCTTTAACCATGTAGTCGGT 59.430 45.455 0.00 0.00 36.98 4.69
2580 2822 3.770933 AGCCTTTAACCATGTAGTCGGTA 59.229 43.478 0.00 0.00 33.17 4.02
2581 2823 3.867493 GCCTTTAACCATGTAGTCGGTAC 59.133 47.826 0.00 0.00 33.17 3.34
2582 2824 4.436332 CCTTTAACCATGTAGTCGGTACC 58.564 47.826 0.16 0.16 33.17 3.34
2583 2825 4.081531 CCTTTAACCATGTAGTCGGTACCA 60.082 45.833 13.54 0.00 33.17 3.25
2584 2826 5.395990 CCTTTAACCATGTAGTCGGTACCAT 60.396 44.000 13.54 0.00 33.17 3.55
2585 2827 3.814005 AACCATGTAGTCGGTACCATC 57.186 47.619 13.54 3.88 33.17 3.51
2586 2828 3.028094 ACCATGTAGTCGGTACCATCT 57.972 47.619 13.54 11.53 32.31 2.90
2587 2829 3.371965 ACCATGTAGTCGGTACCATCTT 58.628 45.455 13.54 0.00 32.31 2.40
2637 2883 5.648178 TTATGCTGTCAAACAATGCAGAT 57.352 34.783 0.00 0.00 33.68 2.90
2638 2884 6.756299 TTATGCTGTCAAACAATGCAGATA 57.244 33.333 0.00 0.00 33.68 1.98
2640 2886 3.120234 TGCTGTCAAACAATGCAGATACG 60.120 43.478 0.00 0.00 36.11 3.06
2715 2966 8.710835 TTTTTGTTTTCTTGAACCTATTCCAC 57.289 30.769 0.00 0.00 33.49 4.02
2763 3030 6.379703 AGCTCTATTCTGTCACTGATTGTAGT 59.620 38.462 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.767445 ATCCGCGTTCGTCATCCGA 61.767 57.895 4.92 0.00 45.66 4.55
4 5 2.278596 ATCCGCGTTCGTCATCCG 60.279 61.111 4.92 0.00 38.13 4.18
5 6 2.871427 GCATCCGCGTTCGTCATCC 61.871 63.158 4.92 0.00 0.00 3.51
6 7 2.621000 GCATCCGCGTTCGTCATC 59.379 61.111 4.92 0.00 0.00 2.92
16 17 1.079503 GATCCCTAATTCGCATCCGC 58.920 55.000 0.00 0.00 0.00 5.54
17 18 1.001974 TGGATCCCTAATTCGCATCCG 59.998 52.381 9.90 0.00 36.55 4.18
18 19 2.859165 TGGATCCCTAATTCGCATCC 57.141 50.000 9.90 0.00 34.64 3.51
19 20 5.712152 ATTTTGGATCCCTAATTCGCATC 57.288 39.130 9.90 0.00 0.00 3.91
20 21 5.183904 GCTATTTTGGATCCCTAATTCGCAT 59.816 40.000 9.90 0.00 0.00 4.73
21 22 4.518970 GCTATTTTGGATCCCTAATTCGCA 59.481 41.667 9.90 0.00 0.00 5.10
22 23 4.762251 AGCTATTTTGGATCCCTAATTCGC 59.238 41.667 9.90 13.40 0.00 4.70
23 24 5.335191 GCAGCTATTTTGGATCCCTAATTCG 60.335 44.000 9.90 5.23 0.00 3.34
24 25 5.335191 CGCAGCTATTTTGGATCCCTAATTC 60.335 44.000 9.90 4.91 0.00 2.17
25 26 4.520492 CGCAGCTATTTTGGATCCCTAATT 59.480 41.667 9.90 3.14 0.00 1.40
26 27 4.074970 CGCAGCTATTTTGGATCCCTAAT 58.925 43.478 9.90 11.08 0.00 1.73
27 28 3.476552 CGCAGCTATTTTGGATCCCTAA 58.523 45.455 9.90 3.53 0.00 2.69
28 29 2.224523 CCGCAGCTATTTTGGATCCCTA 60.225 50.000 9.90 0.00 0.00 3.53
29 30 1.477558 CCGCAGCTATTTTGGATCCCT 60.478 52.381 9.90 0.00 0.00 4.20
30 31 0.954452 CCGCAGCTATTTTGGATCCC 59.046 55.000 9.90 0.00 0.00 3.85
31 32 0.312102 GCCGCAGCTATTTTGGATCC 59.688 55.000 4.20 4.20 35.50 3.36
32 33 1.024271 TGCCGCAGCTATTTTGGATC 58.976 50.000 0.00 0.00 40.80 3.36
33 34 1.406539 CTTGCCGCAGCTATTTTGGAT 59.593 47.619 0.00 0.00 40.80 3.41
34 35 0.810648 CTTGCCGCAGCTATTTTGGA 59.189 50.000 0.00 0.00 40.80 3.53
35 36 0.179129 CCTTGCCGCAGCTATTTTGG 60.179 55.000 0.00 0.00 40.80 3.28
36 37 0.803380 GCCTTGCCGCAGCTATTTTG 60.803 55.000 0.00 0.00 40.80 2.44
37 38 0.967380 AGCCTTGCCGCAGCTATTTT 60.967 50.000 5.36 0.00 40.80 1.82
38 39 0.967380 AAGCCTTGCCGCAGCTATTT 60.967 50.000 7.49 0.00 40.80 1.40
39 40 1.379044 AAGCCTTGCCGCAGCTATT 60.379 52.632 7.49 0.00 40.80 1.73
40 41 1.821332 GAAGCCTTGCCGCAGCTAT 60.821 57.895 7.49 0.00 40.80 2.97
41 42 2.436646 GAAGCCTTGCCGCAGCTA 60.437 61.111 7.49 0.00 40.80 3.32
42 43 4.341783 AGAAGCCTTGCCGCAGCT 62.342 61.111 1.38 1.38 40.80 4.24
43 44 3.808656 GAGAAGCCTTGCCGCAGC 61.809 66.667 0.00 0.00 40.48 5.25
44 45 3.494336 CGAGAAGCCTTGCCGCAG 61.494 66.667 0.00 0.00 0.00 5.18
46 47 3.659089 TACCGAGAAGCCTTGCCGC 62.659 63.158 0.00 0.00 0.00 6.53
47 48 1.519455 CTACCGAGAAGCCTTGCCG 60.519 63.158 0.00 0.00 0.00 5.69
48 49 1.815840 GCTACCGAGAAGCCTTGCC 60.816 63.158 0.00 0.00 33.73 4.52
49 50 3.801129 GCTACCGAGAAGCCTTGC 58.199 61.111 0.00 0.00 33.73 4.01
84 85 1.453155 CACATTTCAGCCGCCTAACT 58.547 50.000 0.00 0.00 0.00 2.24
91 92 1.750399 CCTCCCCACATTTCAGCCG 60.750 63.158 0.00 0.00 0.00 5.52
92 93 1.380380 CCCTCCCCACATTTCAGCC 60.380 63.158 0.00 0.00 0.00 4.85
102 113 1.315903 TAGCTCTAGAACCCTCCCCA 58.684 55.000 0.00 0.00 0.00 4.96
104 115 3.105283 TGTTTAGCTCTAGAACCCTCCC 58.895 50.000 0.00 0.00 0.00 4.30
136 153 3.330267 AGCTCTTGAAAGTTCGGACATC 58.670 45.455 0.00 0.00 0.00 3.06
199 216 4.450976 TGCTACCGTAATCAAAGCATCAT 58.549 39.130 0.00 0.00 38.22 2.45
227 244 3.369471 CGTTGAGGAGAGAGAGAGAGAGT 60.369 52.174 0.00 0.00 0.00 3.24
243 260 0.528470 GAGGAGTGAGGACCGTTGAG 59.472 60.000 0.00 0.00 0.00 3.02
244 261 0.898789 GGAGGAGTGAGGACCGTTGA 60.899 60.000 0.00 0.00 0.00 3.18
246 263 1.609794 GGGAGGAGTGAGGACCGTT 60.610 63.158 0.00 0.00 0.00 4.44
247 264 2.037527 GGGAGGAGTGAGGACCGT 59.962 66.667 0.00 0.00 0.00 4.83
248 265 3.141488 CGGGAGGAGTGAGGACCG 61.141 72.222 0.00 0.00 35.01 4.79
249 266 1.192803 AAACGGGAGGAGTGAGGACC 61.193 60.000 0.00 0.00 0.00 4.46
264 281 2.103373 TGAGGGAGAGGAGATGAAACG 58.897 52.381 0.00 0.00 0.00 3.60
266 283 3.481559 AGTGAGGGAGAGGAGATGAAA 57.518 47.619 0.00 0.00 0.00 2.69
287 334 1.061546 GGTGTAAGGTGAGGGTGGAA 58.938 55.000 0.00 0.00 0.00 3.53
331 378 0.801251 GCAGCGAGATTTCAGCAACT 59.199 50.000 0.00 0.00 0.00 3.16
332 379 0.519999 CGCAGCGAGATTTCAGCAAC 60.520 55.000 9.98 0.00 0.00 4.17
334 381 2.102438 CCGCAGCGAGATTTCAGCA 61.102 57.895 18.75 0.00 0.00 4.41
354 401 0.394080 GAGCAGAAGGCCAATCAGCT 60.394 55.000 22.73 22.73 46.50 4.24
359 406 1.639635 ATCCCGAGCAGAAGGCCAAT 61.640 55.000 5.01 0.00 46.50 3.16
399 446 5.690865 ACTAACAAGGGATTGTGTTCTCAA 58.309 37.500 0.00 0.00 38.80 3.02
427 474 0.664761 CATGGCTGGCAAATACGGAG 59.335 55.000 8.35 0.00 0.00 4.63
428 475 0.254462 TCATGGCTGGCAAATACGGA 59.746 50.000 8.35 0.00 0.00 4.69
429 476 1.102154 TTCATGGCTGGCAAATACGG 58.898 50.000 8.35 0.00 0.00 4.02
430 477 3.117794 CAATTCATGGCTGGCAAATACG 58.882 45.455 8.35 0.00 0.00 3.06
431 478 3.460103 CCAATTCATGGCTGGCAAATAC 58.540 45.455 8.35 0.00 43.80 1.89
655 712 7.644986 AAGCTAATCGAATATCTTACTGCAC 57.355 36.000 0.00 0.00 0.00 4.57
728 793 5.447279 CGATTAACAATGTGCAGGGTTAGAC 60.447 44.000 0.00 0.00 0.00 2.59
788 859 1.337447 ACACGGTACCTTCCATGAACG 60.337 52.381 10.90 0.00 0.00 3.95
870 957 4.038402 ACCACAAAGAAGCAAGGAAATCAG 59.962 41.667 0.00 0.00 0.00 2.90
892 979 2.540101 CACTCACTCCAAACACGAAGAC 59.460 50.000 0.00 0.00 0.00 3.01
894 981 2.550978 ACACTCACTCCAAACACGAAG 58.449 47.619 0.00 0.00 0.00 3.79
939 1107 5.008019 TCAATCTGTTCTGACTTGCTTGTTC 59.992 40.000 0.00 0.00 0.00 3.18
1119 1289 7.891183 AAGTTTGATACAGTACTACAAGCAG 57.109 36.000 0.00 0.00 0.00 4.24
1134 1304 8.873215 TCGCCAATTTGTTTTTAAGTTTGATA 57.127 26.923 0.00 0.00 0.00 2.15
1203 1378 4.038642 GGAACAAGCCAACAAGGTAATCAA 59.961 41.667 0.00 0.00 40.61 2.57
1376 1559 5.806654 ATGGTTGTTTACTGAAAGGCAAT 57.193 34.783 0.00 0.00 39.30 3.56
1393 1576 3.203040 CCAGGGTCCATCTCTTTATGGTT 59.797 47.826 2.98 0.00 45.67 3.67
1429 1612 5.221402 CCAGATCATCAGTTAGCTTAGCAGA 60.221 44.000 7.07 0.00 0.00 4.26
1505 1689 1.751349 AAGCCAGGCCTTGCAAACAG 61.751 55.000 28.99 3.40 0.00 3.16
1575 1759 1.538512 CGTCGTTGGTAGAGAAGACCA 59.461 52.381 0.00 0.00 45.38 4.02
1737 1945 9.968870 CAAATACCTAGAGGAGTATAGTTGTTC 57.031 37.037 1.60 0.00 38.94 3.18
1738 1946 8.422566 GCAAATACCTAGAGGAGTATAGTTGTT 58.577 37.037 1.60 0.00 38.94 2.83
1742 1950 5.711036 CGGCAAATACCTAGAGGAGTATAGT 59.289 44.000 1.60 0.00 38.94 2.12
1743 1951 5.393243 GCGGCAAATACCTAGAGGAGTATAG 60.393 48.000 1.60 0.00 38.94 1.31
1744 1952 4.461781 GCGGCAAATACCTAGAGGAGTATA 59.538 45.833 1.60 0.00 38.94 1.47
1745 1953 3.258622 GCGGCAAATACCTAGAGGAGTAT 59.741 47.826 1.60 0.00 38.94 2.12
1747 1955 1.413077 GCGGCAAATACCTAGAGGAGT 59.587 52.381 1.60 0.00 38.94 3.85
1750 1958 2.622064 AAGCGGCAAATACCTAGAGG 57.378 50.000 1.45 0.00 42.17 3.69
1754 1962 3.805422 CACGATAAAGCGGCAAATACCTA 59.195 43.478 1.45 0.00 35.12 3.08
1858 2066 1.133699 CCATGATGGGCTGAAGGCTAA 60.134 52.381 2.79 0.00 41.46 3.09
1860 2068 1.229359 CCATGATGGGCTGAAGGCT 59.771 57.895 2.79 0.00 41.46 4.58
1909 2117 3.581332 CCCAAACAGAGGGTACTAAGACA 59.419 47.826 0.00 0.00 41.61 3.41
1911 2119 4.136341 TCCCAAACAGAGGGTACTAAGA 57.864 45.455 0.00 0.00 46.82 2.10
1914 2122 4.018779 CCAAATCCCAAACAGAGGGTACTA 60.019 45.833 0.00 0.00 46.82 1.82
2026 2244 8.432013 ACATACAATGCTCCATCTATAAACAGA 58.568 33.333 0.00 0.00 0.00 3.41
2225 2443 1.680522 ATCGCACGAGCATCCTCCTT 61.681 55.000 5.50 0.00 42.27 3.36
2281 2499 1.522569 GCGGTACTTGAGGCTCCAT 59.477 57.895 12.86 0.00 0.00 3.41
2400 2618 5.231568 CGTTTATCGAATAGGACAAGACCAC 59.768 44.000 0.00 0.00 42.86 4.16
2454 2672 7.581213 TGAATCACATTAAGTTCACCAGTTT 57.419 32.000 0.00 0.00 0.00 2.66
2458 2676 5.830457 TGGTTGAATCACATTAAGTTCACCA 59.170 36.000 0.00 0.00 33.52 4.17
2501 2719 5.682943 TGGTAGTAATTGTCTTGCAACAC 57.317 39.130 0.00 0.00 40.28 3.32
2556 2798 4.223477 ACCGACTACATGGTTAAAGGCTTA 59.777 41.667 0.00 0.00 33.81 3.09
2557 2799 3.008704 ACCGACTACATGGTTAAAGGCTT 59.991 43.478 0.00 0.00 33.81 4.35
2558 2800 2.570302 ACCGACTACATGGTTAAAGGCT 59.430 45.455 0.00 0.00 33.81 4.58
2559 2801 2.981898 ACCGACTACATGGTTAAAGGC 58.018 47.619 0.00 0.00 33.81 4.35
2560 2802 4.081531 TGGTACCGACTACATGGTTAAAGG 60.082 45.833 7.57 0.00 39.70 3.11
2561 2803 5.075858 TGGTACCGACTACATGGTTAAAG 57.924 43.478 7.57 0.00 39.70 1.85
2562 2804 5.422970 AGATGGTACCGACTACATGGTTAAA 59.577 40.000 7.57 0.00 39.70 1.52
2563 2805 4.957954 AGATGGTACCGACTACATGGTTAA 59.042 41.667 7.57 0.00 39.70 2.01
2564 2806 4.539726 AGATGGTACCGACTACATGGTTA 58.460 43.478 7.57 0.00 39.70 2.85
2565 2807 3.371965 AGATGGTACCGACTACATGGTT 58.628 45.455 7.57 0.00 39.70 3.67
2566 2808 3.028094 AGATGGTACCGACTACATGGT 57.972 47.619 7.57 0.00 42.34 3.55
2567 2809 4.119862 CAAAGATGGTACCGACTACATGG 58.880 47.826 7.57 0.00 0.00 3.66
2568 2810 4.755411 ACAAAGATGGTACCGACTACATG 58.245 43.478 7.57 10.87 0.00 3.21
2569 2811 5.416271 AACAAAGATGGTACCGACTACAT 57.584 39.130 7.57 0.00 0.00 2.29
2570 2812 4.877378 AACAAAGATGGTACCGACTACA 57.123 40.909 7.57 0.00 0.00 2.74
2571 2813 4.390909 CCAAACAAAGATGGTACCGACTAC 59.609 45.833 7.57 0.00 31.84 2.73
2572 2814 4.571919 CCAAACAAAGATGGTACCGACTA 58.428 43.478 7.57 0.00 31.84 2.59
2573 2815 3.408634 CCAAACAAAGATGGTACCGACT 58.591 45.455 7.57 6.12 31.84 4.18
2574 2816 2.095415 GCCAAACAAAGATGGTACCGAC 60.095 50.000 7.57 3.64 39.00 4.79
2575 2817 2.156098 GCCAAACAAAGATGGTACCGA 58.844 47.619 7.57 0.00 39.00 4.69
2576 2818 2.159382 AGCCAAACAAAGATGGTACCG 58.841 47.619 7.57 0.00 39.00 4.02
2577 2819 4.600692 AAAGCCAAACAAAGATGGTACC 57.399 40.909 4.43 4.43 39.00 3.34
2578 2820 5.596845 TCAAAAGCCAAACAAAGATGGTAC 58.403 37.500 0.00 0.00 39.00 3.34
2579 2821 5.362430 ACTCAAAAGCCAAACAAAGATGGTA 59.638 36.000 0.00 0.00 39.00 3.25
2580 2822 4.162131 ACTCAAAAGCCAAACAAAGATGGT 59.838 37.500 0.00 0.00 39.00 3.55
2581 2823 4.508861 CACTCAAAAGCCAAACAAAGATGG 59.491 41.667 0.00 0.00 39.80 3.51
2582 2824 5.111293 ACACTCAAAAGCCAAACAAAGATG 58.889 37.500 0.00 0.00 0.00 2.90
2583 2825 5.343307 ACACTCAAAAGCCAAACAAAGAT 57.657 34.783 0.00 0.00 0.00 2.40
2584 2826 4.674101 CGACACTCAAAAGCCAAACAAAGA 60.674 41.667 0.00 0.00 0.00 2.52
2585 2827 3.547468 CGACACTCAAAAGCCAAACAAAG 59.453 43.478 0.00 0.00 0.00 2.77
2586 2828 3.506810 CGACACTCAAAAGCCAAACAAA 58.493 40.909 0.00 0.00 0.00 2.83
2587 2829 2.733858 GCGACACTCAAAAGCCAAACAA 60.734 45.455 0.00 0.00 0.00 2.83
2637 2883 5.564259 GCACTTAACAGAGAGAAGAACCGTA 60.564 44.000 0.00 0.00 0.00 4.02
2638 2884 4.796618 GCACTTAACAGAGAGAAGAACCGT 60.797 45.833 0.00 0.00 0.00 4.83
2640 2886 4.888917 AGCACTTAACAGAGAGAAGAACC 58.111 43.478 0.00 0.00 0.00 3.62
2773 3040 2.421619 GCAGAATACATAGCTCCCAGC 58.578 52.381 0.00 0.00 42.84 4.85
2774 3041 2.289945 GGGCAGAATACATAGCTCCCAG 60.290 54.545 0.00 0.00 32.89 4.45
2775 3042 1.699634 GGGCAGAATACATAGCTCCCA 59.300 52.381 0.00 0.00 32.89 4.37
2776 3043 1.981495 AGGGCAGAATACATAGCTCCC 59.019 52.381 0.00 0.00 0.00 4.30
2777 3044 3.368948 GCTAGGGCAGAATACATAGCTCC 60.369 52.174 0.00 0.00 38.54 4.70
2778 3045 3.368948 GGCTAGGGCAGAATACATAGCTC 60.369 52.174 8.02 0.00 40.87 4.09
2779 3046 2.569404 GGCTAGGGCAGAATACATAGCT 59.431 50.000 8.02 0.00 40.87 3.32
2780 3047 2.303022 TGGCTAGGGCAGAATACATAGC 59.697 50.000 0.00 0.00 40.87 2.97


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

AutoCloner maintained by Alex Coulton.