Multiple sequence alignment - TraesCS2D01G200500

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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 TraesCS2D01G200500 chr2D 100.000 3292 0 0 1 3292 152096422 152099713 0.000000e+00 6080.0
1 TraesCS2D01G200500 chr2D 81.250 112 21 0 1572 1683 337134716 337134827 1.260000e-14 91.6
2 TraesCS2D01G200500 chr2B 94.255 1201 42 12 1565 2753 210457516 210458701 0.000000e+00 1810.0
3 TraesCS2D01G200500 chr2B 94.293 841 35 4 652 1481 210456680 210457518 0.000000e+00 1275.0
4 TraesCS2D01G200500 chr2B 94.188 499 19 3 2752 3249 210460160 210460649 0.000000e+00 752.0
5 TraesCS2D01G200500 chr2B 96.359 412 7 3 246 653 210456140 210456547 0.000000e+00 671.0
6 TraesCS2D01G200500 chr2B 90.588 255 7 3 1 238 210455609 210455863 4.100000e-84 322.0
7 TraesCS2D01G200500 chr2A 93.081 1243 43 10 248 1481 149210432 149209224 0.000000e+00 1779.0
8 TraesCS2D01G200500 chr2A 92.909 973 40 17 1565 2527 149209226 149208273 0.000000e+00 1387.0
9 TraesCS2D01G200500 chr2A 91.463 246 6 4 1 231 149211127 149210882 1.140000e-84 324.0
10 TraesCS2D01G200500 chr2A 81.250 112 21 0 1572 1683 447285367 447285478 1.260000e-14 91.6
11 TraesCS2D01G200500 chr7D 86.245 269 22 4 2538 2793 360344801 360344535 9.000000e-71 278.0
12 TraesCS2D01G200500 chr7D 97.917 48 0 1 3245 3292 104684830 104684876 7.570000e-12 82.4
13 TraesCS2D01G200500 chr7A 84.249 273 27 5 2534 2793 350421395 350421664 5.450000e-63 252.0
14 TraesCS2D01G200500 chr3D 80.144 277 32 14 2534 2791 442864201 442863929 5.610000e-43 185.0
15 TraesCS2D01G200500 chr3D 88.764 89 10 0 2707 2795 4835326 4835414 3.470000e-20 110.0
16 TraesCS2D01G200500 chr3D 92.727 55 3 1 3238 3292 427021335 427021282 9.790000e-11 78.7
17 TraesCS2D01G200500 chr7B 96.078 51 2 0 3242 3292 79369734 79369784 2.110000e-12 84.2
18 TraesCS2D01G200500 chr1D 94.444 54 3 0 3239 3292 460648948 460649001 2.110000e-12 84.2
19 TraesCS2D01G200500 chr1D 94.118 51 3 0 3242 3292 86096963 86096913 9.790000e-11 78.7
20 TraesCS2D01G200500 chr1A 96.078 51 2 0 3242 3292 490503949 490503899 2.110000e-12 84.2
21 TraesCS2D01G200500 chr1B 95.918 49 2 0 3242 3290 486968832 486968784 2.720000e-11 80.5
22 TraesCS2D01G200500 chr1B 89.831 59 3 3 3235 3291 522622847 522622904 4.560000e-09 73.1
23 TraesCS2D01G200500 chr6A 92.308 52 4 0 3241 3292 553000795 553000744 1.270000e-09 75.0


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 TraesCS2D01G200500 chr2D 152096422 152099713 3291 False 6080.000000 6080 100.000000 1 3292 1 chr2D.!!$F1 3291
1 TraesCS2D01G200500 chr2B 210455609 210460649 5040 False 966.000000 1810 93.936600 1 3249 5 chr2B.!!$F1 3248
2 TraesCS2D01G200500 chr2A 149208273 149211127 2854 True 1163.333333 1779 92.484333 1 2527 3 chr2A.!!$R1 2526

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
876 1491 2.190841 ACCGCCGTTTGGACTTTGG 61.191 57.895 0.0 0.00 37.49 3.28 F
1551 2167 0.100682 GGAGAGCTTGCATGCATGTG 59.899 55.000 28.2 19.34 34.99 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1763 2384 0.030504 CGCACTTGCACATTTCCACA 59.969 50.0 1.48 0.0 42.21 4.17 R
2660 3290 0.179045 AGACTCTTTGGCAGCAACGT 60.179 50.0 0.00 0.0 0.00 3.99 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
416 874 4.913924 GCTCTGTTATGCTTCTTTGTTGTG 59.086 41.667 0.00 0.00 0.00 3.33
478 936 4.138290 TGTTAGGTGAAGCCAAATCGAAA 58.862 39.130 0.00 0.00 40.61 3.46
764 1372 4.800993 GGAGATTGACTAATGACGTCACAG 59.199 45.833 22.71 22.00 40.78 3.66
876 1491 2.190841 ACCGCCGTTTGGACTTTGG 61.191 57.895 0.00 0.00 37.49 3.28
935 1550 3.753434 ACCTCGCAGTGCTCCTCG 61.753 66.667 14.33 0.00 0.00 4.63
1094 1710 1.215382 CCGCTGAAGACGTCATCCA 59.785 57.895 19.50 10.97 35.07 3.41
1210 1826 4.125695 GCCCCGAAGAGTACGCGT 62.126 66.667 19.17 19.17 0.00 6.01
1313 1929 1.609501 CCTTCTCCGACCTCACCCA 60.610 63.158 0.00 0.00 0.00 4.51
1480 2096 1.012086 CACCGATGTCAAGATGCAGG 58.988 55.000 0.00 0.00 0.00 4.85
1481 2097 0.615331 ACCGATGTCAAGATGCAGGT 59.385 50.000 0.00 0.00 0.00 4.00
1482 2098 1.831106 ACCGATGTCAAGATGCAGGTA 59.169 47.619 0.00 0.00 0.00 3.08
1483 2099 2.205074 CCGATGTCAAGATGCAGGTAC 58.795 52.381 0.00 0.00 0.00 3.34
1484 2100 1.854743 CGATGTCAAGATGCAGGTACG 59.145 52.381 0.00 0.00 0.00 3.67
1485 2101 1.594862 GATGTCAAGATGCAGGTACGC 59.405 52.381 0.00 0.00 0.00 4.42
1486 2102 0.735978 TGTCAAGATGCAGGTACGCG 60.736 55.000 3.53 3.53 33.35 6.01
1487 2103 1.809619 TCAAGATGCAGGTACGCGC 60.810 57.895 5.73 0.00 33.35 6.86
1488 2104 2.885644 AAGATGCAGGTACGCGCG 60.886 61.111 30.96 30.96 34.39 6.86
1502 2118 3.481903 CGCGCGATGCAGTTCACT 61.482 61.111 28.94 0.00 46.97 3.41
1503 2119 2.397252 GCGCGATGCAGTTCACTC 59.603 61.111 12.10 0.00 45.45 3.51
1504 2120 3.084579 CGCGATGCAGTTCACTCC 58.915 61.111 0.00 0.00 0.00 3.85
1505 2121 2.792290 CGCGATGCAGTTCACTCCG 61.792 63.158 0.00 0.00 0.00 4.63
1506 2122 3.084579 CGATGCAGTTCACTCCGC 58.915 61.111 0.00 0.00 0.00 5.54
1507 2123 1.446792 CGATGCAGTTCACTCCGCT 60.447 57.895 0.00 0.00 0.00 5.52
1508 2124 0.179137 CGATGCAGTTCACTCCGCTA 60.179 55.000 0.00 0.00 0.00 4.26
1509 2125 1.565305 GATGCAGTTCACTCCGCTAG 58.435 55.000 0.00 0.00 0.00 3.42
1510 2126 0.176680 ATGCAGTTCACTCCGCTAGG 59.823 55.000 0.00 0.00 39.46 3.02
1511 2127 0.898326 TGCAGTTCACTCCGCTAGGA 60.898 55.000 0.00 0.00 46.11 2.94
1525 2141 3.258971 GCTAGGAAGCTTGTGATGTCT 57.741 47.619 2.10 0.00 45.85 3.41
1526 2142 3.604582 GCTAGGAAGCTTGTGATGTCTT 58.395 45.455 2.10 0.00 45.85 3.01
1527 2143 4.006319 GCTAGGAAGCTTGTGATGTCTTT 58.994 43.478 2.10 0.00 45.85 2.52
1528 2144 5.178797 GCTAGGAAGCTTGTGATGTCTTTA 58.821 41.667 2.10 0.00 45.85 1.85
1529 2145 5.064071 GCTAGGAAGCTTGTGATGTCTTTAC 59.936 44.000 2.10 0.00 45.85 2.01
1530 2146 4.973168 AGGAAGCTTGTGATGTCTTTACA 58.027 39.130 2.10 0.00 40.69 2.41
1531 2147 8.540076 GCTAGGAAGCTTGTGATGTCTTTACAT 61.540 40.741 2.10 0.00 46.17 2.29
1532 2148 5.413833 AGGAAGCTTGTGATGTCTTTACATG 59.586 40.000 2.10 0.00 46.49 3.21
1533 2149 5.392380 GGAAGCTTGTGATGTCTTTACATGG 60.392 44.000 2.10 0.00 46.49 3.66
1534 2150 4.910195 AGCTTGTGATGTCTTTACATGGA 58.090 39.130 0.00 0.00 46.49 3.41
1535 2151 4.940046 AGCTTGTGATGTCTTTACATGGAG 59.060 41.667 0.00 0.00 46.49 3.86
1536 2152 4.937620 GCTTGTGATGTCTTTACATGGAGA 59.062 41.667 0.00 0.00 46.49 3.71
1537 2153 5.064452 GCTTGTGATGTCTTTACATGGAGAG 59.936 44.000 0.00 0.00 46.49 3.20
1538 2154 4.507710 TGTGATGTCTTTACATGGAGAGC 58.492 43.478 0.00 0.00 46.49 4.09
1539 2155 4.223700 TGTGATGTCTTTACATGGAGAGCT 59.776 41.667 0.00 0.00 46.49 4.09
1540 2156 5.181748 GTGATGTCTTTACATGGAGAGCTT 58.818 41.667 0.00 0.00 46.49 3.74
1541 2157 5.064452 GTGATGTCTTTACATGGAGAGCTTG 59.936 44.000 0.00 0.00 46.49 4.01
1542 2158 3.338249 TGTCTTTACATGGAGAGCTTGC 58.662 45.455 0.00 0.00 0.00 4.01
1543 2159 3.244526 TGTCTTTACATGGAGAGCTTGCA 60.245 43.478 0.00 0.00 0.00 4.08
1544 2160 3.944015 GTCTTTACATGGAGAGCTTGCAT 59.056 43.478 0.00 0.00 38.54 3.96
1547 2163 2.489040 CATGGAGAGCTTGCATGCA 58.511 52.632 24.65 18.46 46.52 3.96
1548 2164 1.032794 CATGGAGAGCTTGCATGCAT 58.967 50.000 23.37 6.60 46.52 3.96
1549 2165 1.032794 ATGGAGAGCTTGCATGCATG 58.967 50.000 23.37 24.36 36.38 4.06
1550 2166 0.323087 TGGAGAGCTTGCATGCATGT 60.323 50.000 28.20 17.93 34.99 3.21
1551 2167 0.100682 GGAGAGCTTGCATGCATGTG 59.899 55.000 28.20 19.34 34.99 3.21
1552 2168 0.809385 GAGAGCTTGCATGCATGTGT 59.191 50.000 28.20 18.87 34.99 3.72
1553 2169 1.201647 GAGAGCTTGCATGCATGTGTT 59.798 47.619 28.20 17.10 34.99 3.32
1554 2170 1.616865 AGAGCTTGCATGCATGTGTTT 59.383 42.857 28.20 15.33 34.99 2.83
1555 2171 2.036733 AGAGCTTGCATGCATGTGTTTT 59.963 40.909 28.20 11.14 34.99 2.43
1556 2172 2.803956 GAGCTTGCATGCATGTGTTTTT 59.196 40.909 28.20 9.61 34.99 1.94
1700 2316 0.737367 ACACGGTGCGACATCATCAG 60.737 55.000 8.30 0.00 0.00 2.90
1720 2341 1.312815 CTCAATTCAATCGCCCTCCC 58.687 55.000 0.00 0.00 0.00 4.30
1735 2356 3.760684 GCCCTCCCAATTCATATGCTTAG 59.239 47.826 0.00 0.00 0.00 2.18
1736 2357 4.507335 GCCCTCCCAATTCATATGCTTAGA 60.507 45.833 0.00 0.00 0.00 2.10
1739 2360 7.405292 CCCTCCCAATTCATATGCTTAGATAA 58.595 38.462 0.00 0.00 0.00 1.75
1740 2361 7.555554 CCCTCCCAATTCATATGCTTAGATAAG 59.444 40.741 0.00 0.00 36.40 1.73
1763 2384 8.749026 AAGATAATCTGATTGTTGATCTGCTT 57.251 30.769 13.01 1.99 35.69 3.91
1857 2478 1.135199 ACGCGTACAAGTACCTGATGG 60.135 52.381 11.67 0.00 39.83 3.51
2334 2958 3.181534 GCGTAGTACGTGTTCACGTAGTA 60.182 47.826 31.31 31.31 46.46 1.82
2403 3029 4.622740 GCACTCAATAATGCCACTTCAAAC 59.377 41.667 0.00 0.00 35.73 2.93
2404 3030 5.771469 CACTCAATAATGCCACTTCAAACA 58.229 37.500 0.00 0.00 0.00 2.83
2406 3032 7.537715 CACTCAATAATGCCACTTCAAACATA 58.462 34.615 0.00 0.00 0.00 2.29
2407 3033 7.485913 CACTCAATAATGCCACTTCAAACATAC 59.514 37.037 0.00 0.00 0.00 2.39
2408 3034 7.394359 ACTCAATAATGCCACTTCAAACATACT 59.606 33.333 0.00 0.00 0.00 2.12
2409 3035 8.121305 TCAATAATGCCACTTCAAACATACTT 57.879 30.769 0.00 0.00 0.00 2.24
2413 3043 6.743575 ATGCCACTTCAAACATACTTCTAC 57.256 37.500 0.00 0.00 0.00 2.59
2435 3065 4.581493 CAAGCGCTTGTATACACATTCTG 58.419 43.478 36.23 11.53 35.92 3.02
2436 3066 2.609459 AGCGCTTGTATACACATTCTGC 59.391 45.455 2.64 4.54 33.76 4.26
2437 3067 2.286418 GCGCTTGTATACACATTCTGCC 60.286 50.000 4.68 0.00 33.76 4.85
2438 3068 2.287915 CGCTTGTATACACATTCTGCCC 59.712 50.000 4.68 0.00 33.76 5.36
2439 3069 3.545703 GCTTGTATACACATTCTGCCCT 58.454 45.455 4.68 0.00 33.76 5.19
2440 3070 3.561725 GCTTGTATACACATTCTGCCCTC 59.438 47.826 4.68 0.00 33.76 4.30
2520 3150 1.069935 GGCCGCTGAGATCTTACCC 59.930 63.158 0.00 0.00 0.00 3.69
2523 3153 0.312416 CCGCTGAGATCTTACCCTCG 59.688 60.000 0.00 0.00 32.30 4.63
2591 3221 2.706190 CTCGGTGGGGGAAATATCTTCT 59.294 50.000 0.00 0.00 0.00 2.85
2592 3222 2.704065 TCGGTGGGGGAAATATCTTCTC 59.296 50.000 0.00 0.00 0.00 2.87
2615 3245 1.606737 GGAGATGCGCACCTATCTTCC 60.607 57.143 14.90 11.34 33.97 3.46
2623 3253 1.666189 GCACCTATCTTCCGAACTTGC 59.334 52.381 0.00 0.00 0.00 4.01
2631 3261 1.740025 CTTCCGAACTTGCAGGGATTC 59.260 52.381 0.00 0.00 0.00 2.52
2654 3284 1.134367 GATTCGATGGACTGGTCGTGA 59.866 52.381 0.00 0.00 38.85 4.35
2655 3285 1.182667 TTCGATGGACTGGTCGTGAT 58.817 50.000 0.00 0.00 38.85 3.06
2656 3286 0.455815 TCGATGGACTGGTCGTGATG 59.544 55.000 0.00 0.00 38.85 3.07
2657 3287 1.148157 CGATGGACTGGTCGTGATGC 61.148 60.000 0.00 0.00 33.42 3.91
2658 3288 0.176680 GATGGACTGGTCGTGATGCT 59.823 55.000 0.00 0.00 0.00 3.79
2659 3289 1.409064 GATGGACTGGTCGTGATGCTA 59.591 52.381 0.00 0.00 0.00 3.49
2660 3290 1.262417 TGGACTGGTCGTGATGCTAA 58.738 50.000 0.00 0.00 0.00 3.09
2662 3292 1.269166 GACTGGTCGTGATGCTAACG 58.731 55.000 0.77 0.77 42.36 3.18
2664 3294 1.000506 ACTGGTCGTGATGCTAACGTT 59.999 47.619 5.88 5.88 41.70 3.99
2665 3295 1.390123 CTGGTCGTGATGCTAACGTTG 59.610 52.381 11.99 2.07 41.70 4.10
2666 3296 0.094730 GGTCGTGATGCTAACGTTGC 59.905 55.000 11.99 12.95 41.70 4.17
2676 3308 1.400242 GCTAACGTTGCTGCCAAAGAG 60.400 52.381 11.99 0.00 34.97 2.85
2690 3322 3.754965 CCAAAGAGTCTTTGGTGATCCA 58.245 45.455 39.67 0.00 42.92 3.41
2760 4852 4.106029 TGTACAATCAGACTTAGTCCGC 57.894 45.455 8.96 0.00 32.18 5.54
2761 4853 2.674796 ACAATCAGACTTAGTCCGCC 57.325 50.000 8.96 0.00 32.18 6.13
2881 4973 4.872691 AGATACAGGTCGCTTCAAAAGATG 59.127 41.667 0.00 0.00 0.00 2.90
2890 4982 5.000591 TCGCTTCAAAAGATGTATCCACAA 58.999 37.500 0.00 0.00 38.42 3.33
2921 5014 2.499289 AGAGCAACGATCTCTTGGATGT 59.501 45.455 0.00 0.00 37.63 3.06
2922 5015 3.701542 AGAGCAACGATCTCTTGGATGTA 59.298 43.478 0.00 0.00 37.63 2.29
2923 5016 4.047822 GAGCAACGATCTCTTGGATGTAG 58.952 47.826 0.00 0.00 34.33 2.74
2932 5025 3.012518 CTCTTGGATGTAGCCAAACCTG 58.987 50.000 2.98 0.00 46.58 4.00
3059 5152 4.584394 GTGTAATGTATGCGTAAGTTGGC 58.416 43.478 0.00 0.00 41.68 4.52
3083 5176 7.224167 GGCGTTTCAATTAGCTAGTGTAGTATT 59.776 37.037 0.00 0.00 0.00 1.89
3122 5215 2.246091 AAAGACTGCCCTCTCTAGCT 57.754 50.000 0.00 0.00 0.00 3.32
3177 5270 9.485591 CTTATACGTGGCTTAACTGTAAAATTG 57.514 33.333 0.00 0.00 0.00 2.32
3270 5363 5.678132 ATGAAACAAGGCAAAAGATTTGC 57.322 34.783 17.18 17.18 44.22 3.68
3271 5364 4.768583 TGAAACAAGGCAAAAGATTTGCT 58.231 34.783 22.59 9.80 44.36 3.91
3272 5365 5.911752 TGAAACAAGGCAAAAGATTTGCTA 58.088 33.333 22.59 2.70 44.36 3.49
3273 5366 6.523840 TGAAACAAGGCAAAAGATTTGCTAT 58.476 32.000 22.59 12.13 44.36 2.97
3274 5367 6.991531 TGAAACAAGGCAAAAGATTTGCTATT 59.008 30.769 22.59 16.19 44.36 1.73
3275 5368 7.498570 TGAAACAAGGCAAAAGATTTGCTATTT 59.501 29.630 22.59 17.37 44.36 1.40
3276 5369 7.806409 AACAAGGCAAAAGATTTGCTATTTT 57.194 28.000 22.59 11.38 44.36 1.82
3277 5370 7.425577 ACAAGGCAAAAGATTTGCTATTTTC 57.574 32.000 22.59 8.88 44.36 2.29
3278 5371 6.991531 ACAAGGCAAAAGATTTGCTATTTTCA 59.008 30.769 22.59 0.00 44.36 2.69
3279 5372 7.662669 ACAAGGCAAAAGATTTGCTATTTTCAT 59.337 29.630 22.59 0.99 44.36 2.57
3280 5373 8.508875 CAAGGCAAAAGATTTGCTATTTTCATT 58.491 29.630 22.59 6.88 44.36 2.57
3281 5374 8.036273 AGGCAAAAGATTTGCTATTTTCATTG 57.964 30.769 22.59 0.00 44.36 2.82
3282 5375 7.879160 AGGCAAAAGATTTGCTATTTTCATTGA 59.121 29.630 22.59 0.00 44.36 2.57
3283 5376 8.671028 GGCAAAAGATTTGCTATTTTCATTGAT 58.329 29.630 22.59 0.00 44.36 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 175 9.920133 ATATATACACAGTAATTGACTCAGCAG 57.080 33.333 0.00 0.00 35.64 4.24
764 1372 0.179124 CCCAGCGTCTTACTCTGAGC 60.179 60.000 4.19 0.00 32.99 4.26
827 1436 2.030401 GGCGGCACACGTATGTCAA 61.030 57.895 3.07 0.00 46.52 3.18
935 1550 1.450905 GCGTCGTCAAATATAGGCGAC 59.549 52.381 19.47 19.47 45.52 5.19
970 1586 1.001633 GGAAACCTTGCTCGGTAGTCA 59.998 52.381 0.00 0.00 35.89 3.41
1010 1626 1.228215 AAGGAGGAGGAGGAGGAGCT 61.228 60.000 0.00 0.00 0.00 4.09
1015 1631 1.817740 CGCTAGAAGGAGGAGGAGGAG 60.818 61.905 0.00 0.00 0.00 3.69
1018 1634 0.467290 AGCGCTAGAAGGAGGAGGAG 60.467 60.000 8.99 0.00 0.00 3.69
1080 1696 0.247460 CCTGCTGGATGACGTCTTCA 59.753 55.000 26.86 16.49 39.11 3.02
1313 1929 3.453679 GCGCCTCGAACTCCTCCT 61.454 66.667 0.00 0.00 0.00 3.69
1485 2101 3.411703 GAGTGAACTGCATCGCGCG 62.412 63.158 26.76 26.76 46.97 6.86
1486 2102 2.397252 GAGTGAACTGCATCGCGC 59.603 61.111 0.00 0.00 42.89 6.86
1487 2103 2.792290 CGGAGTGAACTGCATCGCG 61.792 63.158 0.00 0.00 35.02 5.87
1488 2104 3.084579 CGGAGTGAACTGCATCGC 58.915 61.111 2.80 0.00 33.58 4.58
1489 2105 0.179137 TAGCGGAGTGAACTGCATCG 60.179 55.000 2.80 0.00 43.72 3.84
1490 2106 1.565305 CTAGCGGAGTGAACTGCATC 58.435 55.000 2.80 0.00 43.72 3.91
1491 2107 0.176680 CCTAGCGGAGTGAACTGCAT 59.823 55.000 2.80 0.00 43.72 3.96
1492 2108 0.898326 TCCTAGCGGAGTGAACTGCA 60.898 55.000 2.80 0.00 43.72 4.41
1493 2109 0.246635 TTCCTAGCGGAGTGAACTGC 59.753 55.000 0.00 0.00 41.25 4.40
1494 2110 1.737363 GCTTCCTAGCGGAGTGAACTG 60.737 57.143 0.00 0.00 41.25 3.16
1495 2111 0.533032 GCTTCCTAGCGGAGTGAACT 59.467 55.000 0.00 0.00 41.25 3.01
1496 2112 3.052181 GCTTCCTAGCGGAGTGAAC 57.948 57.895 0.00 0.00 41.25 3.18
1505 2121 8.540076 ATGTAAAGACATCACAAGCTTCCTAGC 61.540 40.741 0.00 0.00 43.01 3.42
1506 2122 6.166279 TGTAAAGACATCACAAGCTTCCTAG 58.834 40.000 0.00 0.00 0.00 3.02
1507 2123 6.109156 TGTAAAGACATCACAAGCTTCCTA 57.891 37.500 0.00 0.00 0.00 2.94
1508 2124 4.973168 TGTAAAGACATCACAAGCTTCCT 58.027 39.130 0.00 0.00 0.00 3.36
1509 2125 5.392380 CCATGTAAAGACATCACAAGCTTCC 60.392 44.000 0.00 0.00 44.82 3.46
1510 2126 5.412594 TCCATGTAAAGACATCACAAGCTTC 59.587 40.000 0.00 0.00 44.82 3.86
1511 2127 5.316167 TCCATGTAAAGACATCACAAGCTT 58.684 37.500 0.00 0.00 44.82 3.74
1512 2128 4.910195 TCCATGTAAAGACATCACAAGCT 58.090 39.130 0.00 0.00 44.82 3.74
1513 2129 4.937620 TCTCCATGTAAAGACATCACAAGC 59.062 41.667 0.00 0.00 44.82 4.01
1514 2130 5.064452 GCTCTCCATGTAAAGACATCACAAG 59.936 44.000 0.00 0.00 44.82 3.16
1515 2131 4.937620 GCTCTCCATGTAAAGACATCACAA 59.062 41.667 0.00 0.00 44.82 3.33
1516 2132 4.223700 AGCTCTCCATGTAAAGACATCACA 59.776 41.667 0.00 0.00 44.82 3.58
1517 2133 4.764172 AGCTCTCCATGTAAAGACATCAC 58.236 43.478 0.00 0.00 44.82 3.06
1518 2134 5.181009 CAAGCTCTCCATGTAAAGACATCA 58.819 41.667 0.00 0.00 44.82 3.07
1519 2135 4.034975 GCAAGCTCTCCATGTAAAGACATC 59.965 45.833 0.00 0.00 44.82 3.06
1521 2137 3.244526 TGCAAGCTCTCCATGTAAAGACA 60.245 43.478 0.00 0.00 40.72 3.41
1522 2138 3.338249 TGCAAGCTCTCCATGTAAAGAC 58.662 45.455 0.00 0.00 0.00 3.01
1523 2139 3.701205 TGCAAGCTCTCCATGTAAAGA 57.299 42.857 0.00 0.00 0.00 2.52
1524 2140 3.488721 GCATGCAAGCTCTCCATGTAAAG 60.489 47.826 14.21 0.00 38.79 1.85
1525 2141 2.424601 GCATGCAAGCTCTCCATGTAAA 59.575 45.455 14.21 0.00 38.79 2.01
1526 2142 2.019249 GCATGCAAGCTCTCCATGTAA 58.981 47.619 14.21 0.00 38.79 2.41
1527 2143 1.065272 TGCATGCAAGCTCTCCATGTA 60.065 47.619 20.30 12.68 38.79 2.29
1528 2144 0.323087 TGCATGCAAGCTCTCCATGT 60.323 50.000 20.30 0.00 38.79 3.21
1529 2145 1.032794 ATGCATGCAAGCTCTCCATG 58.967 50.000 26.68 13.75 39.38 3.66
1530 2146 1.032794 CATGCATGCAAGCTCTCCAT 58.967 50.000 26.68 0.80 34.99 3.41
1531 2147 0.323087 ACATGCATGCAAGCTCTCCA 60.323 50.000 26.68 0.00 34.99 3.86
1532 2148 0.100682 CACATGCATGCAAGCTCTCC 59.899 55.000 26.68 0.00 34.99 3.71
1533 2149 0.809385 ACACATGCATGCAAGCTCTC 59.191 50.000 26.68 0.00 34.99 3.20
1534 2150 1.254026 AACACATGCATGCAAGCTCT 58.746 45.000 26.68 4.34 34.99 4.09
1535 2151 2.074547 AAACACATGCATGCAAGCTC 57.925 45.000 26.68 0.00 34.99 4.09
1536 2152 2.536761 AAAACACATGCATGCAAGCT 57.463 40.000 26.68 5.25 34.99 3.74
1553 2169 2.738964 GCACACGCCCTAAAACCAAAAA 60.739 45.455 0.00 0.00 0.00 1.94
1554 2170 1.202428 GCACACGCCCTAAAACCAAAA 60.202 47.619 0.00 0.00 0.00 2.44
1555 2171 0.386113 GCACACGCCCTAAAACCAAA 59.614 50.000 0.00 0.00 0.00 3.28
1556 2172 1.787057 CGCACACGCCCTAAAACCAA 61.787 55.000 0.00 0.00 33.11 3.67
1557 2173 2.255172 CGCACACGCCCTAAAACCA 61.255 57.895 0.00 0.00 33.11 3.67
1558 2174 2.559330 CGCACACGCCCTAAAACC 59.441 61.111 0.00 0.00 33.11 3.27
1559 2175 2.559330 CCGCACACGCCCTAAAAC 59.441 61.111 0.00 0.00 38.22 2.43
1560 2176 3.358707 GCCGCACACGCCCTAAAA 61.359 61.111 0.00 0.00 38.22 1.52
1561 2177 4.323477 AGCCGCACACGCCCTAAA 62.323 61.111 0.00 0.00 38.22 1.85
1562 2178 4.752879 GAGCCGCACACGCCCTAA 62.753 66.667 0.00 0.00 38.22 2.69
1700 2316 0.665298 GGAGGGCGATTGAATTGAGC 59.335 55.000 0.00 0.00 0.00 4.26
1739 2360 7.774157 ACAAGCAGATCAACAATCAGATTATCT 59.226 33.333 0.00 0.00 36.79 1.98
1740 2361 7.856398 CACAAGCAGATCAACAATCAGATTATC 59.144 37.037 0.00 0.00 36.79 1.75
1750 2371 4.341806 ACATTTCCACAAGCAGATCAACAA 59.658 37.500 0.00 0.00 0.00 2.83
1753 2374 3.305539 GCACATTTCCACAAGCAGATCAA 60.306 43.478 0.00 0.00 0.00 2.57
1756 2377 2.241160 TGCACATTTCCACAAGCAGAT 58.759 42.857 0.00 0.00 0.00 2.90
1763 2384 0.030504 CGCACTTGCACATTTCCACA 59.969 50.000 1.48 0.00 42.21 4.17
2355 2979 3.039011 GTCCACTGATTAAGCCCTCCTA 58.961 50.000 0.00 0.00 0.00 2.94
2356 2980 1.840635 GTCCACTGATTAAGCCCTCCT 59.159 52.381 0.00 0.00 0.00 3.69
2357 2981 1.559682 TGTCCACTGATTAAGCCCTCC 59.440 52.381 0.00 0.00 0.00 4.30
2358 2982 2.237392 AGTGTCCACTGATTAAGCCCTC 59.763 50.000 0.00 0.00 40.75 4.30
2413 3043 4.581493 CAGAATGTGTATACAAGCGCTTG 58.419 43.478 40.80 40.80 45.58 4.01
2428 3058 1.153086 GGCATCGAGGGCAGAATGT 60.153 57.895 19.44 0.00 39.31 2.71
2429 3059 1.895707 GGGCATCGAGGGCAGAATG 60.896 63.158 25.23 0.00 40.87 2.67
2430 3060 2.512896 GGGCATCGAGGGCAGAAT 59.487 61.111 25.23 0.00 34.52 2.40
2431 3061 4.161295 CGGGCATCGAGGGCAGAA 62.161 66.667 25.23 0.00 42.43 3.02
2438 3068 1.592669 GACATCCACGGGCATCGAG 60.593 63.158 5.71 0.00 42.43 4.04
2439 3069 2.016393 GAGACATCCACGGGCATCGA 62.016 60.000 5.71 0.00 42.43 3.59
2440 3070 1.592669 GAGACATCCACGGGCATCG 60.593 63.158 0.00 0.00 45.88 3.84
2453 3083 2.677914 TCAGGGTTGAGACTTGAGACA 58.322 47.619 0.00 0.00 0.00 3.41
2520 3150 1.815421 CCCGGCCACAAATCTCGAG 60.815 63.158 5.93 5.93 0.00 4.04
2523 3153 2.361104 TGCCCGGCCACAAATCTC 60.361 61.111 7.03 0.00 0.00 2.75
2591 3221 1.069204 GATAGGTGCGCATCTCCTTGA 59.931 52.381 29.62 9.95 39.30 3.02
2592 3222 1.069823 AGATAGGTGCGCATCTCCTTG 59.930 52.381 29.62 0.00 39.30 3.61
2615 3245 1.002366 CTCGAATCCCTGCAAGTTCG 58.998 55.000 13.14 13.14 43.34 3.95
2631 3261 1.598183 CGACCAGTCCATCGAATCTCG 60.598 57.143 0.00 0.00 40.86 4.04
2654 3284 0.958091 TTTGGCAGCAACGTTAGCAT 59.042 45.000 19.82 7.00 0.00 3.79
2655 3285 0.310543 CTTTGGCAGCAACGTTAGCA 59.689 50.000 19.82 6.56 0.00 3.49
2656 3286 0.591170 TCTTTGGCAGCAACGTTAGC 59.409 50.000 0.00 7.56 0.00 3.09
2657 3287 1.873591 ACTCTTTGGCAGCAACGTTAG 59.126 47.619 0.00 0.00 0.00 2.34
2658 3288 1.871039 GACTCTTTGGCAGCAACGTTA 59.129 47.619 0.00 0.00 0.00 3.18
2659 3289 0.663153 GACTCTTTGGCAGCAACGTT 59.337 50.000 0.00 0.00 0.00 3.99
2660 3290 0.179045 AGACTCTTTGGCAGCAACGT 60.179 50.000 0.00 0.00 0.00 3.99
2662 3292 2.544486 CCAAAGACTCTTTGGCAGCAAC 60.544 50.000 29.49 0.00 41.95 4.17
2664 3294 1.321474 CCAAAGACTCTTTGGCAGCA 58.679 50.000 29.49 0.00 41.95 4.41
2690 3322 9.787435 TTACTGGAAAATCAATTGTACTAGTGT 57.213 29.630 5.39 0.81 0.00 3.55
2698 3330 8.421249 TCAGGAATTACTGGAAAATCAATTGT 57.579 30.769 17.82 0.00 38.98 2.71
2718 3350 4.074259 CAATGTCAACCAGAACATCAGGA 58.926 43.478 0.00 0.00 0.00 3.86
2760 4852 6.316890 CCCTCAAGGCATTTTATTCATTTTGG 59.683 38.462 0.00 0.00 0.00 3.28
2761 4853 7.311364 CCCTCAAGGCATTTTATTCATTTTG 57.689 36.000 0.00 0.00 0.00 2.44
2815 4907 9.093970 GCAGTTAAAATTTGTTACTCCTGTTTT 57.906 29.630 0.00 0.00 0.00 2.43
2816 4908 8.254508 TGCAGTTAAAATTTGTTACTCCTGTTT 58.745 29.630 0.00 0.00 0.00 2.83
2817 4909 7.704899 GTGCAGTTAAAATTTGTTACTCCTGTT 59.295 33.333 0.00 0.00 0.00 3.16
2818 4910 7.068226 AGTGCAGTTAAAATTTGTTACTCCTGT 59.932 33.333 0.00 0.00 0.00 4.00
2819 4911 7.379529 CAGTGCAGTTAAAATTTGTTACTCCTG 59.620 37.037 0.00 0.00 0.00 3.86
2820 4912 7.284489 TCAGTGCAGTTAAAATTTGTTACTCCT 59.716 33.333 0.00 0.00 0.00 3.69
2881 4973 5.880332 TGCTCTGGTTTTAGATTGTGGATAC 59.120 40.000 0.00 0.00 0.00 2.24
2890 4982 5.091261 AGATCGTTGCTCTGGTTTTAGAT 57.909 39.130 0.00 0.00 0.00 1.98
2921 5014 0.613260 ATGAGACGCAGGTTTGGCTA 59.387 50.000 0.00 0.00 0.00 3.93
2922 5015 0.674895 GATGAGACGCAGGTTTGGCT 60.675 55.000 0.00 0.00 0.00 4.75
2923 5016 1.796796 GATGAGACGCAGGTTTGGC 59.203 57.895 0.00 0.00 0.00 4.52
2963 5056 3.306364 GCTGGGCATCAGACTAATATCGT 60.306 47.826 10.03 0.00 46.18 3.73
3036 5129 4.780946 GCCAACTTACGCATACATTACACG 60.781 45.833 0.00 0.00 0.00 4.49
3059 5152 9.297586 TCAATACTACACTAGCTAATTGAAACG 57.702 33.333 10.79 0.00 33.54 3.60
3083 5176 4.600692 TTTTCTGTCCTTCGTCTCATCA 57.399 40.909 0.00 0.00 0.00 3.07
3249 5342 4.768583 AGCAAATCTTTTGCCTTGTTTCA 58.231 34.783 18.48 0.00 45.98 2.69
3250 5343 7.425577 AATAGCAAATCTTTTGCCTTGTTTC 57.574 32.000 18.48 0.00 45.98 2.78
3251 5344 7.806409 AAATAGCAAATCTTTTGCCTTGTTT 57.194 28.000 18.48 10.65 45.98 2.83
3252 5345 7.498570 TGAAAATAGCAAATCTTTTGCCTTGTT 59.501 29.630 18.48 9.62 45.98 2.83
3253 5346 6.991531 TGAAAATAGCAAATCTTTTGCCTTGT 59.008 30.769 18.48 9.77 45.98 3.16
3254 5347 7.424227 TGAAAATAGCAAATCTTTTGCCTTG 57.576 32.000 18.48 0.00 45.98 3.61
3255 5348 8.508875 CAATGAAAATAGCAAATCTTTTGCCTT 58.491 29.630 18.48 11.35 45.98 4.35
3256 5349 7.879160 TCAATGAAAATAGCAAATCTTTTGCCT 59.121 29.630 18.48 10.36 45.98 4.75
3257 5350 8.031848 TCAATGAAAATAGCAAATCTTTTGCC 57.968 30.769 18.48 5.75 45.98 4.52


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

AutoCloner maintained by Alex Coulton.