Multiple sequence alignment - TraesCS4D01G005400

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 TraesCS4D01G005400 chr4D 100.000 3431 0 0 1 3431 3251749 3248319 0.000000e+00 6336.0
1 TraesCS4D01G005400 chr4D 82.796 1459 208 27 993 2437 3241596 3243025 0.000000e+00 1264.0
2 TraesCS4D01G005400 chr4B 91.971 2491 140 15 973 3428 3831285 3828820 0.000000e+00 3437.0
3 TraesCS4D01G005400 chr4B 82.450 1453 218 21 993 2437 3820818 3822241 0.000000e+00 1236.0
4 TraesCS4D01G005400 chr4B 89.176 425 33 11 33 456 3832272 3831860 5.080000e-143 518.0
5 TraesCS4D01G005400 chr4B 92.141 369 16 6 620 987 3831672 3831316 3.050000e-140 508.0
6 TraesCS4D01G005400 chr4B 94.690 113 5 1 469 581 3831791 3831680 1.270000e-39 174.0
7 TraesCS4D01G005400 chr4A 92.052 2441 141 26 18 2428 602271655 602274072 0.000000e+00 3384.0
8 TraesCS4D01G005400 chr4A 81.899 1464 212 38 993 2437 602307937 602306508 0.000000e+00 1186.0
9 TraesCS4D01G005400 chr4A 98.039 51 1 0 2523 2573 602274125 602274175 4.720000e-14 89.8
10 TraesCS4D01G005400 chr3A 82.818 291 45 4 69 357 426652163 426651876 4.390000e-64 255.0
11 TraesCS4D01G005400 chr3D 85.776 232 33 0 97 328 307569666 307569897 2.640000e-61 246.0
12 TraesCS4D01G005400 chr1D 83.146 267 41 4 93 357 2121814 2122078 1.230000e-59 241.0
13 TraesCS4D01G005400 chr5D 82.528 269 46 1 90 357 506156384 506156116 5.720000e-58 235.0
14 TraesCS4D01G005400 chr3B 82.759 261 45 0 97 357 413991552 413991292 2.060000e-57 233.0
15 TraesCS4D01G005400 chr1B 82.090 268 40 4 97 357 1470286 1470020 4.460000e-54 222.0
16 TraesCS4D01G005400 chr1B 81.343 268 42 4 97 357 1426478 1426744 9.650000e-51 211.0


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 TraesCS4D01G005400 chr4D 3248319 3251749 3430 True 6336.00 6336 100.0000 1 3431 1 chr4D.!!$R1 3430
1 TraesCS4D01G005400 chr4D 3241596 3243025 1429 False 1264.00 1264 82.7960 993 2437 1 chr4D.!!$F1 1444
2 TraesCS4D01G005400 chr4B 3820818 3822241 1423 False 1236.00 1236 82.4500 993 2437 1 chr4B.!!$F1 1444
3 TraesCS4D01G005400 chr4B 3828820 3832272 3452 True 1159.25 3437 91.9945 33 3428 4 chr4B.!!$R1 3395
4 TraesCS4D01G005400 chr4A 602271655 602274175 2520 False 1736.90 3384 95.0455 18 2573 2 chr4A.!!$F1 2555
5 TraesCS4D01G005400 chr4A 602306508 602307937 1429 True 1186.00 1186 81.8990 993 2437 1 chr4A.!!$R1 1444

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
600 658 1.067821 GGTCAGAGGGAGTAGATTGCG 59.932 57.143 0.0 0.0 0.0 4.85 F
1518 1637 0.109272 TTCACAGAGGCGACGATCAC 60.109 55.000 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1793 0.512952 CAAACTGTTCTTCGAGGCCG 59.487 55.0 0.0 0.0 37.07 6.13 R
2695 2845 0.742505 CGACATACCTTACCGCCTCA 59.257 55.0 0.0 0.0 0.00 3.86 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
19 20 1.410004 TCTCAAACGACTCAGGGTGT 58.590 50.000 0.00 0.00 0.00 4.16
20 21 2.589720 TCTCAAACGACTCAGGGTGTA 58.410 47.619 0.00 0.00 0.00 2.90
64 65 5.084055 CCGCTAAAAAGAAACATTACGGTC 58.916 41.667 0.00 0.00 32.53 4.79
65 66 5.334260 CCGCTAAAAAGAAACATTACGGTCA 60.334 40.000 0.00 0.00 32.53 4.02
66 67 5.562623 CGCTAAAAAGAAACATTACGGTCAC 59.437 40.000 0.00 0.00 0.00 3.67
77 78 6.300354 ACATTACGGTCACTCAAGAAAAAG 57.700 37.500 0.00 0.00 0.00 2.27
83 84 4.261197 CGGTCACTCAAGAAAAAGGAAAGG 60.261 45.833 0.00 0.00 0.00 3.11
84 85 4.038042 GGTCACTCAAGAAAAAGGAAAGGG 59.962 45.833 0.00 0.00 0.00 3.95
130 131 2.566833 TGATGGTCTGGTGAAACAGG 57.433 50.000 0.00 0.00 39.98 4.00
360 361 2.434185 AGCCACCGCGTACACATG 60.434 61.111 4.92 0.00 41.18 3.21
368 369 2.778026 CGTACACATGCACCAGCG 59.222 61.111 0.00 0.00 46.23 5.18
399 400 5.422214 TCCCATGGAAAAGAGTCTTCTAC 57.578 43.478 15.22 0.00 31.96 2.59
414 415 3.411418 CTACCACGCTCGTCGCCAT 62.411 63.158 0.00 0.00 43.23 4.40
415 416 3.693382 TACCACGCTCGTCGCCATG 62.693 63.158 0.00 0.00 43.23 3.66
418 419 4.742201 ACGCTCGTCGCCATGCTT 62.742 61.111 0.00 0.00 43.23 3.91
419 420 2.582226 CGCTCGTCGCCATGCTTA 60.582 61.111 0.00 0.00 34.21 3.09
426 427 1.831343 GTCGCCATGCTTATGCTTTG 58.169 50.000 1.96 0.49 40.48 2.77
442 443 2.540931 GCTTTGACCGTCGTTAGTTTGA 59.459 45.455 0.00 0.00 0.00 2.69
464 490 5.208121 GAGGGGAATGGGAATGATGTTTTA 58.792 41.667 0.00 0.00 0.00 1.52
466 492 4.202111 GGGGAATGGGAATGATGTTTTACG 60.202 45.833 0.00 0.00 0.00 3.18
467 493 4.359706 GGAATGGGAATGATGTTTTACGC 58.640 43.478 0.00 0.00 0.00 4.42
534 592 3.719871 TGTTCTATTGCTACTCCCTCCA 58.280 45.455 0.00 0.00 0.00 3.86
600 658 1.067821 GGTCAGAGGGAGTAGATTGCG 59.932 57.143 0.00 0.00 0.00 4.85
687 745 2.819608 ACCGGACATCAAGGAAAATGTG 59.180 45.455 9.46 0.00 36.28 3.21
695 753 5.529430 ACATCAAGGAAAATGTGTGTACGAA 59.471 36.000 0.00 0.00 34.88 3.85
914 975 7.056635 TCCCTTTTCATAGATTCCTTAAGCAG 58.943 38.462 0.00 0.00 0.00 4.24
925 986 4.365514 TCCTTAAGCAGATGGACAACAA 57.634 40.909 0.00 0.00 0.00 2.83
951 1012 1.188863 GCGTTGGGGACTACTCCTAA 58.811 55.000 0.00 0.00 37.59 2.69
1449 1568 3.636231 CTCACCTTCACCGGCCCA 61.636 66.667 0.00 0.00 0.00 5.36
1464 1583 0.833287 GCCCATCCTGCTTCTACTCA 59.167 55.000 0.00 0.00 0.00 3.41
1506 1625 1.301716 GCACGGGCTTCTTCACAGA 60.302 57.895 0.00 0.00 36.96 3.41
1511 1630 4.996976 GCTTCTTCACAGAGGCGA 57.003 55.556 0.00 0.00 41.85 5.54
1512 1631 2.450619 GCTTCTTCACAGAGGCGAC 58.549 57.895 0.00 0.00 41.85 5.19
1513 1632 1.347817 GCTTCTTCACAGAGGCGACG 61.348 60.000 0.00 0.00 41.85 5.12
1514 1633 0.241213 CTTCTTCACAGAGGCGACGA 59.759 55.000 0.00 0.00 0.00 4.20
1515 1634 0.888619 TTCTTCACAGAGGCGACGAT 59.111 50.000 0.00 0.00 0.00 3.73
1516 1635 0.452184 TCTTCACAGAGGCGACGATC 59.548 55.000 0.00 0.00 0.00 3.69
1517 1636 0.171231 CTTCACAGAGGCGACGATCA 59.829 55.000 0.00 0.00 0.00 2.92
1518 1637 0.109272 TTCACAGAGGCGACGATCAC 60.109 55.000 0.00 0.00 0.00 3.06
1519 1638 1.212751 CACAGAGGCGACGATCACA 59.787 57.895 0.00 0.00 0.00 3.58
1523 1642 2.126463 AGGCGACGATCACACGTG 60.126 61.111 15.48 15.48 46.52 4.49
1554 1673 4.760047 ATGCCGGTGCGAGTGGAC 62.760 66.667 1.90 0.00 41.78 4.02
1596 1715 2.095059 CGCTGCCTTCTTAACTTGCATT 60.095 45.455 0.00 0.00 0.00 3.56
1683 1802 2.987547 ACGTTCCTCGGCCTCGAA 60.988 61.111 0.00 0.00 45.47 3.71
1692 1811 0.391597 TCGGCCTCGAAGAACAGTTT 59.608 50.000 0.00 0.00 43.03 2.66
1695 1814 1.947456 GGCCTCGAAGAACAGTTTGTT 59.053 47.619 0.00 0.00 44.37 2.83
1762 1881 1.762957 CCTTCTTCCTCAATAGCCGGA 59.237 52.381 5.05 0.00 0.00 5.14
1842 1961 1.669265 CAGAGCACGGTCGTCTATGTA 59.331 52.381 0.00 0.00 0.00 2.29
2222 2341 1.429148 CCAGTTAGGCCGTTCGATGC 61.429 60.000 0.00 0.00 0.00 3.91
2240 2359 3.053896 CGAAAAGGCCGTGGACCC 61.054 66.667 0.00 0.00 0.00 4.46
2280 2399 2.259818 CGAGCAGTGTCGGAGCTT 59.740 61.111 7.08 0.00 39.02 3.74
2419 2538 3.512516 GCTTCATGCGGAGTGGCC 61.513 66.667 0.00 0.00 0.00 5.36
2451 2570 5.353394 AGTAGATTCGGAATTGTTAGGCA 57.647 39.130 4.47 0.00 0.00 4.75
2452 2571 5.116882 AGTAGATTCGGAATTGTTAGGCAC 58.883 41.667 4.47 0.00 0.00 5.01
2453 2572 4.222124 AGATTCGGAATTGTTAGGCACT 57.778 40.909 4.47 0.00 46.37 4.40
2454 2573 4.192317 AGATTCGGAATTGTTAGGCACTC 58.808 43.478 4.47 0.00 41.75 3.51
2456 2575 3.410631 TCGGAATTGTTAGGCACTCAA 57.589 42.857 0.00 0.00 41.75 3.02
2458 2577 4.331968 TCGGAATTGTTAGGCACTCAATT 58.668 39.130 11.43 11.43 42.84 2.32
2461 2580 4.662145 GAATTGTTAGGCACTCAATTCCG 58.338 43.478 20.14 0.00 45.72 4.30
2507 2626 4.002906 TCGTGCTAAACTGTCAAAGGAT 57.997 40.909 0.00 0.00 0.00 3.24
2622 2741 0.340208 TTTCCACCACCAAAAGGGGT 59.660 50.000 0.00 0.00 43.56 4.95
2718 2868 1.269257 GGCGGTAAGGTATGTCGGTAC 60.269 57.143 0.00 0.00 0.00 3.34
2722 2872 3.489738 CGGTAAGGTATGTCGGTACAAGG 60.490 52.174 0.00 0.00 39.58 3.61
2727 2877 3.056322 AGGTATGTCGGTACAAGGTTCAC 60.056 47.826 0.00 0.00 39.58 3.18
2733 2883 5.012239 TGTCGGTACAAGGTTCACTATACT 58.988 41.667 0.00 0.00 30.91 2.12
2734 2884 5.106038 TGTCGGTACAAGGTTCACTATACTG 60.106 44.000 0.00 0.00 30.91 2.74
2760 2910 7.754851 TGGATGTATACGCAAGAGACTATAA 57.245 36.000 0.00 0.00 43.62 0.98
2828 2978 9.573166 TTTTATGCTATAACTGCTATGGTTCAT 57.427 29.630 0.00 0.00 0.00 2.57
2846 2996 6.111382 GGTTCATGAATGTGAGATTCAGAGA 58.889 40.000 12.12 8.29 40.80 3.10
2861 3011 0.598065 AGAGAAAAACCCATGCGCAC 59.402 50.000 14.90 0.00 0.00 5.34
2869 3019 1.739929 CCCATGCGCACGTGTAGAA 60.740 57.895 14.90 6.87 0.00 2.10
2937 3087 2.352421 CGTTAACACCAGATGACTCCGT 60.352 50.000 6.39 0.00 0.00 4.69
2949 3099 3.417069 TGACTCCGTTTTCATGGTCAT 57.583 42.857 0.00 0.00 0.00 3.06
2954 3104 0.887247 CGTTTTCATGGTCATGGGCA 59.113 50.000 10.61 0.00 39.24 5.36
2962 3112 3.385433 TCATGGTCATGGGCAATTGAATC 59.615 43.478 10.34 0.00 39.24 2.52
2979 3129 6.629515 AATTGAATCTCAATGAGGGCACATTG 60.630 38.462 21.92 21.92 45.57 2.82
3134 3284 6.725369 AGATGATGTATGCTAGAAGGATCACT 59.275 38.462 0.00 0.00 0.00 3.41
3167 3317 2.102588 AGTATCATCCGTAACAGGGTGC 59.897 50.000 0.00 0.00 42.06 5.01
3169 3319 1.855295 TCATCCGTAACAGGGTGCTA 58.145 50.000 0.00 0.00 42.06 3.49
3199 3349 6.879400 AGTTGTCATTGAGTTATCTAGGGAC 58.121 40.000 0.00 0.00 0.00 4.46
3202 3352 7.584122 TGTCATTGAGTTATCTAGGGACTAC 57.416 40.000 0.00 0.00 41.75 2.73
3276 3426 6.665680 AGAGAGATACTTTTAGGCTTCACTCA 59.334 38.462 0.00 0.00 0.00 3.41
3301 3451 8.905702 CAGTATGAAAGCATTTACAAACAAGTC 58.094 33.333 0.00 0.00 39.27 3.01
3362 3512 5.223449 TGAATACAGGAACGAGAAAAGGT 57.777 39.130 0.00 0.00 0.00 3.50
3368 3518 3.187227 CAGGAACGAGAAAAGGTGTCATG 59.813 47.826 0.00 0.00 0.00 3.07
3406 3556 6.875972 AAGTAGACATAGTGATTGAAGGGT 57.124 37.500 0.00 0.00 0.00 4.34
3428 3578 4.753516 TCACTCACGGGATGTCAAATAT 57.246 40.909 0.00 0.00 0.00 1.28
3429 3579 4.693283 TCACTCACGGGATGTCAAATATC 58.307 43.478 0.00 0.00 0.00 1.63
3430 3580 4.405680 TCACTCACGGGATGTCAAATATCT 59.594 41.667 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.927014 GCTACACCCTGAGTCGTTTGAG 60.927 54.545 0.00 0.00 0.00 3.02
3 4 1.429463 GCTACACCCTGAGTCGTTTG 58.571 55.000 0.00 0.00 0.00 2.93
4 5 0.038526 CGCTACACCCTGAGTCGTTT 60.039 55.000 0.00 0.00 0.00 3.60
5 6 0.892358 TCGCTACACCCTGAGTCGTT 60.892 55.000 0.00 0.00 0.00 3.85
6 7 0.892358 TTCGCTACACCCTGAGTCGT 60.892 55.000 0.00 0.00 0.00 4.34
7 8 0.179161 CTTCGCTACACCCTGAGTCG 60.179 60.000 0.00 0.00 0.00 4.18
8 9 0.458716 GCTTCGCTACACCCTGAGTC 60.459 60.000 0.00 0.00 0.00 3.36
9 10 0.900647 AGCTTCGCTACACCCTGAGT 60.901 55.000 0.00 0.00 36.99 3.41
10 11 1.103803 TAGCTTCGCTACACCCTGAG 58.896 55.000 0.00 0.00 40.44 3.35
11 12 1.476891 CTTAGCTTCGCTACACCCTGA 59.523 52.381 0.00 0.00 41.12 3.86
12 13 1.927895 CTTAGCTTCGCTACACCCTG 58.072 55.000 0.00 0.00 41.12 4.45
13 14 0.175989 GCTTAGCTTCGCTACACCCT 59.824 55.000 0.00 0.00 41.12 4.34
14 15 0.175989 AGCTTAGCTTCGCTACACCC 59.824 55.000 0.00 0.00 41.12 4.61
15 16 2.865343 TAGCTTAGCTTCGCTACACC 57.135 50.000 13.44 0.00 41.12 4.16
16 17 6.616682 GCATTATTAGCTTAGCTTCGCTACAC 60.617 42.308 13.44 0.00 41.12 2.90
17 18 5.405571 GCATTATTAGCTTAGCTTCGCTACA 59.594 40.000 13.44 8.07 41.12 2.74
18 19 5.163943 GGCATTATTAGCTTAGCTTCGCTAC 60.164 44.000 13.44 0.00 41.12 3.58
19 20 4.929808 GGCATTATTAGCTTAGCTTCGCTA 59.070 41.667 13.44 11.33 40.44 4.26
20 21 3.748568 GGCATTATTAGCTTAGCTTCGCT 59.251 43.478 13.44 13.10 40.44 4.93
27 28 7.861630 TCTTTTTAGCGGCATTATTAGCTTAG 58.138 34.615 1.45 0.00 40.73 2.18
31 32 6.750039 TGTTTCTTTTTAGCGGCATTATTAGC 59.250 34.615 1.45 0.00 0.00 3.09
42 43 5.562623 GTGACCGTAATGTTTCTTTTTAGCG 59.437 40.000 0.00 0.00 0.00 4.26
64 65 5.594317 TCTTCCCTTTCCTTTTTCTTGAGTG 59.406 40.000 0.00 0.00 0.00 3.51
65 66 5.766590 TCTTCCCTTTCCTTTTTCTTGAGT 58.233 37.500 0.00 0.00 0.00 3.41
66 67 6.715347 TTCTTCCCTTTCCTTTTTCTTGAG 57.285 37.500 0.00 0.00 0.00 3.02
77 78 3.058432 GCGTGTACTTTTCTTCCCTTTCC 60.058 47.826 0.00 0.00 0.00 3.13
83 84 1.193874 CGGTGCGTGTACTTTTCTTCC 59.806 52.381 0.00 0.00 0.00 3.46
84 85 1.862827 ACGGTGCGTGTACTTTTCTTC 59.137 47.619 0.00 0.00 39.18 2.87
110 111 2.291153 CCCTGTTTCACCAGACCATCAT 60.291 50.000 0.00 0.00 34.23 2.45
226 227 1.078708 CAGGGCGTACCATTCCGTT 60.079 57.895 1.21 0.00 43.89 4.44
368 369 3.650298 TTCCATGGGAGCAGCAGCC 62.650 63.158 13.02 0.00 43.56 4.85
414 415 1.075542 CGACGGTCAAAGCATAAGCA 58.924 50.000 9.10 0.00 45.49 3.91
415 416 1.076332 ACGACGGTCAAAGCATAAGC 58.924 50.000 9.10 0.00 42.56 3.09
416 417 3.924686 ACTAACGACGGTCAAAGCATAAG 59.075 43.478 9.10 0.00 0.00 1.73
417 418 3.916761 ACTAACGACGGTCAAAGCATAA 58.083 40.909 9.10 0.00 0.00 1.90
418 419 3.581024 ACTAACGACGGTCAAAGCATA 57.419 42.857 9.10 0.00 0.00 3.14
419 420 2.450609 ACTAACGACGGTCAAAGCAT 57.549 45.000 9.10 0.00 0.00 3.79
426 427 1.670967 CCCCTCAAACTAACGACGGTC 60.671 57.143 0.00 0.00 0.00 4.79
442 443 3.782413 AAACATCATTCCCATTCCCCT 57.218 42.857 0.00 0.00 0.00 4.79
581 639 2.025155 TCGCAATCTACTCCCTCTGAC 58.975 52.381 0.00 0.00 0.00 3.51
621 679 8.099537 CACCCGAGTAGATTATACTTACCTCTA 58.900 40.741 0.00 0.00 0.00 2.43
914 975 3.270877 ACGCCTCTATTTGTTGTCCATC 58.729 45.455 0.00 0.00 0.00 3.51
925 986 1.761198 GTAGTCCCCAACGCCTCTATT 59.239 52.381 0.00 0.00 0.00 1.73
951 1012 6.058183 GGTGTGAAAATGTGCCTCTATCTAT 58.942 40.000 0.00 0.00 0.00 1.98
1449 1568 2.430332 GCAGAGTGAGTAGAAGCAGGAT 59.570 50.000 0.00 0.00 0.00 3.24
1464 1583 3.180984 GACGTTGAAGTCGCAGAGT 57.819 52.632 0.00 0.00 45.43 3.24
1506 1625 2.126463 CACGTGTGATCGTCGCCT 60.126 61.111 7.58 0.00 42.27 5.52
1511 1630 2.799502 CGACGCACGTGTGATCGT 60.800 61.111 34.03 25.12 45.10 3.73
1554 1673 1.171308 CCCATGTGTCCTTGCTCAAG 58.829 55.000 2.74 2.74 38.14 3.02
1596 1715 1.691219 GAACTTCCCCCATGCAGGA 59.309 57.895 0.00 0.00 41.22 3.86
1602 1721 1.562672 CCTCCACGAACTTCCCCCAT 61.563 60.000 0.00 0.00 0.00 4.00
1674 1793 0.512952 CAAACTGTTCTTCGAGGCCG 59.487 55.000 0.00 0.00 37.07 6.13
1683 1802 1.094785 AGCACGCAACAAACTGTTCT 58.905 45.000 0.00 0.00 38.77 3.01
1692 1811 1.003959 TGCCTCATAGCACGCAACA 60.004 52.632 0.00 0.00 38.00 3.33
1695 1814 2.512286 GCTGCCTCATAGCACGCA 60.512 61.111 0.00 0.00 40.81 5.24
1736 1855 1.926426 ATTGAGGAAGAAGGGCCCGG 61.926 60.000 18.44 0.00 0.00 5.73
1773 1892 1.373748 GCTCTGGTTTACGGTGCGA 60.374 57.895 0.00 0.00 35.50 5.10
1807 1926 1.003580 GCTCTGGTCCATCTTGTCCAA 59.996 52.381 0.00 0.00 0.00 3.53
1842 1961 3.050275 GCGAGGCTGCCGAAACTT 61.050 61.111 13.96 0.00 0.00 2.66
2002 2121 2.903357 CACTACGAGCCCATGCCT 59.097 61.111 0.00 0.00 38.69 4.75
2014 2133 3.204827 CGCCCAGCCATGCACTAC 61.205 66.667 0.00 0.00 0.00 2.73
2222 2341 3.053896 GGTCCACGGCCTTTTCGG 61.054 66.667 0.00 0.00 0.00 4.30
2280 2399 2.772191 ACTGCCCCATCGCCCATA 60.772 61.111 0.00 0.00 0.00 2.74
2419 2538 4.238761 TCCGAATCTACTATTCCTTGCG 57.761 45.455 0.00 0.00 0.00 4.85
2428 2547 6.097839 AGTGCCTAACAATTCCGAATCTACTA 59.902 38.462 0.00 0.00 0.00 1.82
2451 2570 1.160137 GCAGAGCAACGGAATTGAGT 58.840 50.000 0.00 0.00 41.23 3.41
2452 2571 1.446907 AGCAGAGCAACGGAATTGAG 58.553 50.000 0.00 0.00 41.23 3.02
2453 2572 2.621338 CTAGCAGAGCAACGGAATTGA 58.379 47.619 0.00 0.00 41.23 2.57
2454 2573 1.667724 CCTAGCAGAGCAACGGAATTG 59.332 52.381 0.00 0.00 41.69 2.32
2456 2575 0.905357 ACCTAGCAGAGCAACGGAAT 59.095 50.000 0.00 0.00 0.00 3.01
2458 2577 0.898326 TCACCTAGCAGAGCAACGGA 60.898 55.000 0.00 0.00 0.00 4.69
2460 2579 1.337260 ACTTCACCTAGCAGAGCAACG 60.337 52.381 0.00 0.00 0.00 4.10
2461 2580 2.072298 CACTTCACCTAGCAGAGCAAC 58.928 52.381 0.00 0.00 0.00 4.17
2507 2626 9.832445 GATACTAGAGATTTGGACCATTTGTTA 57.168 33.333 0.00 0.00 0.00 2.41
2695 2845 0.742505 CGACATACCTTACCGCCTCA 59.257 55.000 0.00 0.00 0.00 3.86
2718 2868 6.173339 ACATCCAACAGTATAGTGAACCTTG 58.827 40.000 14.61 7.89 0.00 3.61
2722 2872 7.114529 GCGTATACATCCAACAGTATAGTGAAC 59.885 40.741 14.61 0.00 34.76 3.18
2727 2877 7.368059 TCTTGCGTATACATCCAACAGTATAG 58.632 38.462 3.32 0.00 34.76 1.31
2733 2883 4.159693 AGTCTCTTGCGTATACATCCAACA 59.840 41.667 3.32 0.00 0.00 3.33
2734 2884 4.683832 AGTCTCTTGCGTATACATCCAAC 58.316 43.478 3.32 0.00 0.00 3.77
2809 2959 8.501580 CACATTCATGAACCATAGCAGTTATAG 58.498 37.037 11.07 0.00 0.00 1.31
2828 2978 6.207417 GGGTTTTTCTCTGAATCTCACATTCA 59.793 38.462 0.00 0.00 36.67 2.57
2846 2996 1.299773 CACGTGCGCATGGGTTTTT 60.300 52.632 31.55 8.46 0.00 1.94
2861 3011 5.403897 AGTTGTGTTCATGTTTCTACACG 57.596 39.130 0.00 0.00 42.81 4.49
2869 3019 9.528018 CAAAAGGTATAAAGTTGTGTTCATGTT 57.472 29.630 0.00 0.00 0.00 2.71
2910 3060 3.364023 GTCATCTGGTGTTAACGAGTTCG 59.636 47.826 0.26 0.00 46.33 3.95
2917 3067 3.314541 ACGGAGTCATCTGGTGTTAAC 57.685 47.619 0.00 0.00 29.74 2.01
2937 3087 3.581770 TCAATTGCCCATGACCATGAAAA 59.418 39.130 11.28 3.68 41.20 2.29
2949 3099 3.702548 CCTCATTGAGATTCAATTGCCCA 59.297 43.478 15.36 0.00 44.03 5.36
2954 3104 4.346730 TGTGCCCTCATTGAGATTCAATT 58.653 39.130 15.36 0.00 44.03 2.32
3017 3167 8.408601 ACCAATAACAACGTCTCGTAGTATATT 58.591 33.333 0.00 0.00 39.99 1.28
3073 3223 9.810545 CTTGGTTCAAGGATAAAAACAAGTAAA 57.189 29.630 4.39 0.00 40.93 2.01
3084 3234 5.825593 ACACTCTCTTGGTTCAAGGATAA 57.174 39.130 7.67 0.00 41.33 1.75
3093 3243 4.963318 TCATCTCAACACTCTCTTGGTT 57.037 40.909 0.00 0.00 0.00 3.67
3096 3246 6.018913 GCATACATCATCTCAACACTCTCTTG 60.019 42.308 0.00 0.00 0.00 3.02
3098 3248 5.363292 AGCATACATCATCTCAACACTCTCT 59.637 40.000 0.00 0.00 0.00 3.10
3175 3325 6.670027 AGTCCCTAGATAACTCAATGACAACT 59.330 38.462 0.00 0.00 0.00 3.16
3181 3331 7.348080 TGTGTAGTCCCTAGATAACTCAATG 57.652 40.000 0.00 0.00 0.00 2.82
3186 3336 6.672657 ACCAAATGTGTAGTCCCTAGATAACT 59.327 38.462 0.00 0.00 0.00 2.24
3196 3346 8.788325 AACTATTAAGACCAAATGTGTAGTCC 57.212 34.615 0.00 0.00 0.00 3.85
3229 3379 9.593565 TCTCTATTATCTAGAGGAGCAATTTCA 57.406 33.333 8.89 0.00 40.95 2.69
3276 3426 8.850156 AGACTTGTTTGTAAATGCTTTCATACT 58.150 29.630 0.00 0.00 31.46 2.12
3286 3436 5.820131 TCTGTGCAGACTTGTTTGTAAATG 58.180 37.500 0.00 0.00 31.41 2.32
3301 3451 1.208358 CATGCCGTTGTCTGTGCAG 59.792 57.895 0.00 0.00 37.12 4.41
3362 3512 1.262417 TCCTCGTTACTGGCATGACA 58.738 50.000 0.00 0.00 0.00 3.58
3368 3518 4.337555 TGTCTACTTATCCTCGTTACTGGC 59.662 45.833 0.00 0.00 0.00 4.85
3406 3556 2.920724 TTTGACATCCCGTGAGTGAA 57.079 45.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.