Multiple sequence alignment - TraesCS4D01G315700

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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 TraesCS4D01G315700 chr4D 100.000 2813 0 0 1 2813 481172131 481174943 0.000000e+00 5195.0
1 TraesCS4D01G315700 chr4B 86.708 978 74 18 1784 2734 609504743 609505691 0.000000e+00 1035.0
2 TraesCS4D01G315700 chr4B 86.397 963 76 31 1 943 609502383 609503310 0.000000e+00 1002.0
3 TraesCS4D01G315700 chr4B 84.158 202 27 3 981 1177 609503319 609503520 1.030000e-44 191.0
4 TraesCS4D01G315700 chr4B 93.333 75 5 0 2739 2813 609505775 609505849 8.240000e-21 111.0
5 TraesCS4D01G315700 chr5A 89.157 415 25 4 627 1037 662334121 662333723 1.500000e-137 499.0
6 TraesCS4D01G315700 chr5A 88.272 324 28 5 319 632 662334515 662334192 2.050000e-101 379.0
7 TraesCS4D01G315700 chr5A 90.941 287 12 7 1 280 662334796 662334517 9.510000e-100 374.0
8 TraesCS4D01G315700 chr5A 91.139 237 15 2 2455 2686 662332261 662332026 1.630000e-82 316.0
9 TraesCS4D01G315700 chr5A 85.526 152 10 5 1088 1227 662333713 662333562 6.280000e-32 148.0
10 TraesCS4D01G315700 chr5A 98.649 74 1 0 1251 1324 662333487 662333414 6.320000e-27 132.0
11 TraesCS4D01G315700 chr5A 91.304 92 8 0 2722 2813 662332032 662331941 2.940000e-25 126.0
12 TraesCS4D01G315700 chr5A 87.838 74 6 1 2255 2325 662332403 662332330 1.800000e-12 84.2
13 TraesCS4D01G315700 chr2D 85.024 414 50 3 1387 1788 37246004 37246417 7.250000e-111 411.0
14 TraesCS4D01G315700 chr2A 86.686 338 45 0 1387 1724 42026843 42026506 2.650000e-100 375.0
15 TraesCS4D01G315700 chr2A 72.770 426 78 27 1223 1633 131711568 131711970 2.960000e-20 110.0
16 TraesCS4D01G315700 chr2A 90.476 42 4 0 2225 2266 712054193 712054152 3.910000e-04 56.5
17 TraesCS4D01G315700 chr2B 80.000 410 72 6 1387 1788 64807580 64807173 7.620000e-76 294.0
18 TraesCS4D01G315700 chr2B 92.424 132 10 0 1224 1355 64863939 64863808 3.700000e-44 189.0
19 TraesCS4D01G315700 chr1A 77.426 505 75 26 1226 1713 11530587 11531069 5.970000e-67 265.0
20 TraesCS4D01G315700 chr1A 81.319 91 16 1 2171 2261 419033839 419033928 3.890000e-09 73.1
21 TraesCS4D01G315700 chr1A 93.478 46 2 1 2217 2262 331272235 331272191 1.810000e-07 67.6
22 TraesCS4D01G315700 chr4A 80.347 173 31 2 1224 1394 742751305 742751476 8.180000e-26 128.0
23 TraesCS4D01G315700 chr4A 79.769 173 32 2 1224 1394 743383886 743384057 3.810000e-24 122.0
24 TraesCS4D01G315700 chr7D 84.127 126 20 0 1224 1349 2052555 2052680 3.810000e-24 122.0
25 TraesCS4D01G315700 chrUn 78.824 170 36 0 1225 1394 265076215 265076046 6.370000e-22 115.0
26 TraesCS4D01G315700 chr1D 82.418 91 15 1 2171 2261 325484579 325484490 8.350000e-11 78.7
27 TraesCS4D01G315700 chr1D 90.385 52 5 0 2209 2260 53260562 53260511 5.030000e-08 69.4
28 TraesCS4D01G315700 chr3B 93.750 48 3 0 2190 2237 756662939 756662986 3.890000e-09 73.1
29 TraesCS4D01G315700 chr1B 81.319 91 16 1 2171 2261 437599791 437599702 3.890000e-09 73.1
30 TraesCS4D01G315700 chr1B 93.478 46 2 1 2217 2262 355408309 355408265 1.810000e-07 67.6
31 TraesCS4D01G315700 chr3D 81.481 81 12 3 2172 2251 454901709 454901787 2.340000e-06 63.9


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 TraesCS4D01G315700 chr4D 481172131 481174943 2812 False 5195.000 5195 100.00000 1 2813 1 chr4D.!!$F1 2812
1 TraesCS4D01G315700 chr4B 609502383 609505849 3466 False 584.750 1035 87.64900 1 2813 4 chr4B.!!$F1 2812
2 TraesCS4D01G315700 chr5A 662331941 662334796 2855 True 257.275 499 90.35325 1 2813 8 chr5A.!!$R1 2812

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
739 842 0.179084 TGCATACGGCTAGGCTCAAC 60.179 55.0 15.11 0.77 45.15 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 3486 0.039618 GAATGGCAGTGGGGAAGGAA 59.96 55.0 0.0 0.0 0.0 3.36 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
54 56 4.689612 AAGGTCATGTCTTACTGTGTGT 57.310 40.909 0.00 0.00 0.00 3.72
85 87 6.229936 AGGCTAGTTTTCCATTATCACGTA 57.770 37.500 0.00 0.00 0.00 3.57
95 97 6.718522 TCCATTATCACGTACTCACCATAA 57.281 37.500 0.00 0.00 0.00 1.90
106 108 2.228822 ACTCACCATAAAGGCGCAAAAG 59.771 45.455 10.83 0.00 43.14 2.27
206 208 6.906659 TCTTATATTTCCGACGACCTACATC 58.093 40.000 0.00 0.00 0.00 3.06
215 222 4.980434 CCGACGACCTACATCGATAATTTT 59.020 41.667 0.00 0.00 45.13 1.82
298 305 3.072476 AGCAAGACTAAGTTAACCTGGCA 59.928 43.478 0.88 0.00 0.00 4.92
309 316 4.428845 CCTGGCAAGGCTGATGTT 57.571 55.556 0.00 0.00 36.56 2.71
313 320 1.246056 TGGCAAGGCTGATGTTGAGC 61.246 55.000 0.00 0.00 35.57 4.26
322 329 2.670414 GCTGATGTTGAGCTCACAGTAC 59.330 50.000 24.76 17.93 33.37 2.73
328 335 0.817654 TGAGCTCACAGTACGGATGG 59.182 55.000 13.74 0.00 0.00 3.51
390 397 3.431207 CCAGGTACGGTTGGTTATCGATT 60.431 47.826 1.71 0.00 0.00 3.34
397 404 4.400251 ACGGTTGGTTATCGATTCTCTGTA 59.600 41.667 1.71 0.00 0.00 2.74
478 486 8.158169 TGTGAATATGAAATCTTGTAGGATGC 57.842 34.615 0.00 0.00 0.00 3.91
529 537 2.785258 GAATGCGGTCTCGGTTGC 59.215 61.111 0.00 0.00 36.79 4.17
543 560 4.178169 TTGCCCACGGACACGGTT 62.178 61.111 0.00 0.00 46.48 4.44
544 561 4.612412 TGCCCACGGACACGGTTC 62.612 66.667 0.00 0.00 46.48 3.62
570 587 8.230486 CGTCTGTTGCTACTGATTTTATCTTTT 58.770 33.333 10.67 0.00 35.15 2.27
684 785 6.215845 GCTGTGGTTTGTTAGTGAATGAATT 58.784 36.000 0.00 0.00 0.00 2.17
703 804 5.822519 TGAATTGCTGTGGTCCATCTTATAC 59.177 40.000 0.00 0.00 0.00 1.47
716 819 4.510340 CCATCTTATACGCTGGTACCAAAC 59.490 45.833 17.11 10.23 0.00 2.93
730 833 0.881118 CCAAACTGTTGCATACGGCT 59.119 50.000 0.00 0.00 45.15 5.52
739 842 0.179084 TGCATACGGCTAGGCTCAAC 60.179 55.000 15.11 0.77 45.15 3.18
764 867 6.374565 TTGAGCCCAACAAATTGAAAAATG 57.625 33.333 0.00 0.00 38.15 2.32
801 904 4.155063 TGCACATTGGCACATATCTAGT 57.845 40.909 0.00 0.00 39.25 2.57
863 969 1.845809 GCACGGCACTCTCCTTGTTG 61.846 60.000 0.00 0.00 0.00 3.33
889 997 6.669125 TGGTTTCATTTCATTCAAGTGGAT 57.331 33.333 0.00 0.00 0.00 3.41
940 1048 5.444122 GCCATTGTTATCTCGTTGATTAGC 58.556 41.667 0.00 0.00 36.65 3.09
946 1054 5.685954 TGTTATCTCGTTGATTAGCATCGTC 59.314 40.000 1.01 0.00 39.91 4.20
949 1057 3.857665 TCTCGTTGATTAGCATCGTCAAC 59.142 43.478 11.76 11.76 45.00 3.18
959 1067 1.668919 GCATCGTCAACTCGTTGGAGA 60.669 52.381 9.66 9.45 43.27 3.71
964 1072 2.251893 GTCAACTCGTTGGAGATCGAC 58.748 52.381 9.66 0.00 43.27 4.20
977 1085 4.753662 TCGACCGGGTGGCTAGCT 62.754 66.667 15.72 0.00 39.70 3.32
1005 1113 1.093972 TTGCTGATACAACCATGGCG 58.906 50.000 13.04 5.85 0.00 5.69
1067 1180 4.735132 CTTCAAGGGCGTCGGCGA 62.735 66.667 16.53 4.99 41.24 5.54
1080 1193 2.186903 GGCGACGGTGATGACCAT 59.813 61.111 1.19 0.00 43.33 3.55
1082 1195 2.813179 GCGACGGTGATGACCATGC 61.813 63.158 1.19 0.00 43.33 4.06
1083 1196 2.173669 CGACGGTGATGACCATGCC 61.174 63.158 1.19 0.00 43.33 4.40
1128 1241 2.507944 GTCATCTCCGCCATGCCT 59.492 61.111 0.00 0.00 0.00 4.75
1138 1251 1.893808 GCCATGCCTACCATCACCG 60.894 63.158 0.00 0.00 29.71 4.94
1257 1464 3.374402 CGACTGCGTCCCTCTGGT 61.374 66.667 3.65 0.00 0.00 4.00
1333 1832 1.130613 GCTGATCAACACGCACGTC 59.869 57.895 0.00 0.00 0.00 4.34
1382 2133 1.687494 GACTGCAAGATCGTCCACGC 61.687 60.000 0.00 0.00 36.92 5.34
1408 2159 1.143684 GGAAGCCCAAGGATATGCTGA 59.856 52.381 0.00 0.00 33.59 4.26
1413 2164 2.227388 GCCCAAGGATATGCTGATTTCG 59.773 50.000 0.00 0.00 0.00 3.46
1425 2176 0.592637 TGATTTCGCTGTGGCACTTG 59.407 50.000 19.83 12.53 38.60 3.16
1429 2180 1.218875 TTCGCTGTGGCACTTGTACG 61.219 55.000 19.83 14.26 38.60 3.67
1437 2188 1.601903 TGGCACTTGTACGAAAGCTTG 59.398 47.619 0.00 0.00 0.00 4.01
1439 2190 1.602377 GCACTTGTACGAAAGCTTGGT 59.398 47.619 0.00 3.99 0.00 3.67
1440 2191 2.602217 GCACTTGTACGAAAGCTTGGTG 60.602 50.000 0.00 0.00 0.00 4.17
1462 2213 4.514577 CAGAGGGCGGCACCTACG 62.515 72.222 12.47 1.83 42.10 3.51
1475 2226 2.404995 CCTACGCGTTCTCCGACCT 61.405 63.158 20.78 0.00 39.56 3.85
1476 2227 1.226323 CTACGCGTTCTCCGACCTG 60.226 63.158 20.78 0.00 39.56 4.00
1477 2228 1.919956 CTACGCGTTCTCCGACCTGT 61.920 60.000 20.78 0.00 39.56 4.00
1488 2254 3.449042 GACCTGTTCGAGAACGCG 58.551 61.111 3.53 3.53 43.94 6.01
1494 2260 2.733218 TTCGAGAACGCGTGCCAG 60.733 61.111 14.98 8.04 39.58 4.85
1540 2306 2.035312 ACCACGTCCTCGGCTACT 59.965 61.111 0.00 0.00 41.85 2.57
1605 2377 2.959071 GAGGAGATGCTGCGCGAC 60.959 66.667 12.10 0.88 0.00 5.19
1706 2479 1.949015 GACATCGTGACGCTGTGCAG 61.949 60.000 19.55 0.00 36.36 4.41
1717 2490 2.796425 CTGTGCAGCATCGAGACGC 61.796 63.158 0.00 0.00 0.00 5.19
1718 2491 3.558411 GTGCAGCATCGAGACGCC 61.558 66.667 0.00 0.00 0.00 5.68
1722 2495 3.893763 AGCATCGAGACGCCGAGG 61.894 66.667 0.00 3.36 42.21 4.63
1754 2539 3.202906 CCAAGAAGACCGTCTTTGTCAA 58.797 45.455 14.96 0.00 36.73 3.18
1758 2543 4.120589 AGAAGACCGTCTTTGTCAAGTTC 58.879 43.478 14.96 0.00 36.73 3.01
1767 2552 4.072088 GTCAAGTTCCCGCACGCG 62.072 66.667 3.53 3.53 39.44 6.01
1769 2554 3.645975 CAAGTTCCCGCACGCGTT 61.646 61.111 10.22 0.00 37.81 4.84
1778 2563 1.128611 CGCACGCGTTCTTCTTCAG 59.871 57.895 10.22 0.00 34.35 3.02
1792 2806 3.906720 TCTTCAGGAAAGGGGTTATCG 57.093 47.619 0.00 0.00 35.54 2.92
1809 2823 7.248437 GGGTTATCGTTATTTGGTTCAAGAAG 58.752 38.462 0.00 0.00 0.00 2.85
1857 2871 5.966742 AGATGAATGAATGCATCTCCATG 57.033 39.130 7.83 0.00 45.99 3.66
1858 2872 5.631119 AGATGAATGAATGCATCTCCATGA 58.369 37.500 7.83 0.00 45.99 3.07
1868 2882 2.432146 GCATCTCCATGACTAGTGTGGA 59.568 50.000 20.08 20.08 39.61 4.02
1897 2927 2.048503 GCAAAGCAGCCTGCCTTG 60.049 61.111 21.06 21.06 46.52 3.61
1909 2939 3.345808 GCCTTGTGCGACGCAGAA 61.346 61.111 27.78 27.78 40.08 3.02
1931 2961 1.295357 AACGGATCGCACGCATTTCA 61.295 50.000 0.00 0.00 34.00 2.69
2054 3084 2.626088 AGAAGTAACGTGTAGCCGTC 57.374 50.000 0.00 0.00 40.85 4.79
2132 3168 0.650512 ACTTGTCACTTTGCGACACG 59.349 50.000 0.00 0.00 42.88 4.49
2167 3203 3.466723 TGGAATGGGGTGATGAATGGTAT 59.533 43.478 0.00 0.00 0.00 2.73
2180 3216 5.134202 TGAATGGTATATGTACTGCCTCG 57.866 43.478 0.00 0.00 0.00 4.63
2181 3217 4.021456 TGAATGGTATATGTACTGCCTCGG 60.021 45.833 0.00 0.00 0.00 4.63
2185 3221 4.021916 GGTATATGTACTGCCTCGGGTAT 58.978 47.826 0.00 0.00 0.00 2.73
2193 3229 1.334869 CTGCCTCGGGTATCAAAATGC 59.665 52.381 0.00 0.00 0.00 3.56
2203 3239 5.504665 CGGGTATCAAAATGCAAGACATCTC 60.505 44.000 0.00 0.00 38.34 2.75
2207 3243 5.784750 TCAAAATGCAAGACATCTCTACG 57.215 39.130 0.00 0.00 38.34 3.51
2208 3244 4.631377 TCAAAATGCAAGACATCTCTACGG 59.369 41.667 0.00 0.00 38.34 4.02
2211 3247 3.678056 TGCAAGACATCTCTACGGTTT 57.322 42.857 0.00 0.00 0.00 3.27
2216 3252 6.653320 TGCAAGACATCTCTACGGTTTAAATT 59.347 34.615 0.00 0.00 0.00 1.82
2219 3255 8.383619 CAAGACATCTCTACGGTTTAAATTGAG 58.616 37.037 0.00 0.00 0.00 3.02
2223 3259 4.630069 TCTCTACGGTTTAAATTGAGCTGC 59.370 41.667 0.00 0.00 0.00 5.25
2224 3260 4.320023 TCTACGGTTTAAATTGAGCTGCA 58.680 39.130 1.02 0.00 0.00 4.41
2230 3266 5.006165 CGGTTTAAATTGAGCTGCAAAAACA 59.994 36.000 17.07 0.00 40.48 2.83
2329 3384 2.731571 CCCTCGCCCGATTTCAGGA 61.732 63.158 0.00 0.00 0.00 3.86
2340 3395 4.115516 CCGATTTCAGGAGTAGACACATG 58.884 47.826 0.00 0.00 0.00 3.21
2342 3397 5.039984 CGATTTCAGGAGTAGACACATGAG 58.960 45.833 0.00 0.00 0.00 2.90
2343 3398 5.393569 CGATTTCAGGAGTAGACACATGAGT 60.394 44.000 0.00 0.00 0.00 3.41
2421 3476 0.692756 TTGGGCCGGACAGATCCATA 60.693 55.000 11.00 0.00 46.67 2.74
2422 3477 0.473694 TGGGCCGGACAGATCCATAT 60.474 55.000 11.00 0.00 46.67 1.78
2423 3478 0.250513 GGGCCGGACAGATCCATATC 59.749 60.000 11.00 0.00 46.67 1.63
2424 3479 0.976641 GGCCGGACAGATCCATATCA 59.023 55.000 5.05 0.00 46.67 2.15
2425 3480 1.556911 GGCCGGACAGATCCATATCAT 59.443 52.381 5.05 0.00 46.67 2.45
2426 3481 2.419297 GGCCGGACAGATCCATATCATC 60.419 54.545 5.05 0.00 46.67 2.92
2427 3482 2.499289 GCCGGACAGATCCATATCATCT 59.501 50.000 5.05 0.00 46.67 2.90
2428 3483 3.055530 GCCGGACAGATCCATATCATCTT 60.056 47.826 5.05 0.00 46.67 2.40
2429 3484 4.753233 CCGGACAGATCCATATCATCTTC 58.247 47.826 0.00 0.00 46.67 2.87
2430 3485 4.419280 CGGACAGATCCATATCATCTTCG 58.581 47.826 0.00 0.00 46.67 3.79
2431 3486 4.082517 CGGACAGATCCATATCATCTTCGT 60.083 45.833 0.00 0.00 46.67 3.85
2432 3487 5.565637 CGGACAGATCCATATCATCTTCGTT 60.566 44.000 0.00 0.00 46.67 3.85
2433 3488 5.866633 GGACAGATCCATATCATCTTCGTTC 59.133 44.000 0.00 0.00 45.47 3.95
2434 3489 5.788450 ACAGATCCATATCATCTTCGTTCC 58.212 41.667 0.00 0.00 34.28 3.62
2435 3490 5.541868 ACAGATCCATATCATCTTCGTTCCT 59.458 40.000 0.00 0.00 34.28 3.36
2436 3491 6.042552 ACAGATCCATATCATCTTCGTTCCTT 59.957 38.462 0.00 0.00 34.28 3.36
2437 3492 6.589523 CAGATCCATATCATCTTCGTTCCTTC 59.410 42.308 0.00 0.00 34.28 3.46
2438 3493 5.215252 TCCATATCATCTTCGTTCCTTCC 57.785 43.478 0.00 0.00 0.00 3.46
2439 3494 4.040461 TCCATATCATCTTCGTTCCTTCCC 59.960 45.833 0.00 0.00 0.00 3.97
2440 3495 4.319177 CATATCATCTTCGTTCCTTCCCC 58.681 47.826 0.00 0.00 0.00 4.81
2446 3501 2.359975 CGTTCCTTCCCCACTGCC 60.360 66.667 0.00 0.00 0.00 4.85
2484 3539 4.525912 TGTGAGCGCTGATATGATATGT 57.474 40.909 18.48 0.00 0.00 2.29
2553 3613 6.160576 AGCAACAAGTCAACCATTAACAAT 57.839 33.333 0.00 0.00 0.00 2.71
2619 3682 2.201732 TCGAATAATCAAGCGTGCTCC 58.798 47.619 0.00 0.00 0.00 4.70
2621 3684 2.033407 CGAATAATCAAGCGTGCTCCAG 60.033 50.000 0.00 0.00 0.00 3.86
2679 3742 0.685097 CAGAAAAGGACCGTGGAGGA 59.315 55.000 0.00 0.00 45.00 3.71
2699 3762 3.304928 GGAAGGAGACATGCAAAGTTGTG 60.305 47.826 0.00 0.00 0.00 3.33
2736 3799 3.119708 GCAGCCAGAGGAAAACTTACATG 60.120 47.826 0.00 0.00 0.00 3.21
2757 3900 1.729470 ATCGATCCTCACGCGAGCTT 61.729 55.000 15.93 0.00 38.00 3.74
2790 3933 3.558931 TTGTTTCACTCTCAGGCTCAA 57.441 42.857 0.00 0.00 0.00 3.02
2797 3940 0.179140 CTCTCAGGCTCAACTCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 22 6.226787 AGACATGACCTTACATATAGCTTGC 58.773 40.000 0.00 0.00 0.00 4.01
54 56 9.561069 GATAATGGAAAACTAGCCTTCATAAGA 57.439 33.333 6.71 0.00 0.00 2.10
95 97 4.513198 TGCTTATTAACTTTTGCGCCTT 57.487 36.364 4.18 0.00 0.00 4.35
106 108 7.876896 TTTTCCCGTTCAATTGCTTATTAAC 57.123 32.000 0.00 0.00 0.00 2.01
206 208 8.928270 ACCTCTAACTGACAGTAAAATTATCG 57.072 34.615 8.91 0.00 0.00 2.92
215 222 3.510360 GCCTCAACCTCTAACTGACAGTA 59.490 47.826 8.91 0.00 0.00 2.74
267 274 1.728971 CTTAGTCTTGCTCTGTTGCCG 59.271 52.381 0.00 0.00 0.00 5.69
298 305 1.072806 TGTGAGCTCAACATCAGCCTT 59.927 47.619 20.19 0.00 37.63 4.35
309 316 0.817654 CCATCCGTACTGTGAGCTCA 59.182 55.000 13.74 13.74 0.00 4.26
313 320 1.878522 GCGCCATCCGTACTGTGAG 60.879 63.158 0.00 0.00 39.71 3.51
415 422 4.712476 AGCAGATTTCATACTCACATCCC 58.288 43.478 0.00 0.00 0.00 3.85
458 466 7.083062 TCCAGCATCCTACAAGATTTCATAT 57.917 36.000 0.00 0.00 0.00 1.78
471 479 1.141657 GCAGTCCATTCCAGCATCCTA 59.858 52.381 0.00 0.00 0.00 2.94
478 486 0.393537 GTCAGGGCAGTCCATTCCAG 60.394 60.000 0.00 0.00 38.24 3.86
529 537 4.289245 ACGAACCGTGTCCGTGGG 62.289 66.667 0.00 0.00 39.18 4.61
534 542 1.828331 GCAACAGACGAACCGTGTCC 61.828 60.000 0.00 0.00 41.37 4.02
543 560 6.631016 AGATAAAATCAGTAGCAACAGACGA 58.369 36.000 0.00 0.00 0.00 4.20
544 561 6.893958 AGATAAAATCAGTAGCAACAGACG 57.106 37.500 0.00 0.00 0.00 4.18
570 587 6.339587 ACGGCAATCAGAAAGGAAAATAAA 57.660 33.333 0.00 0.00 0.00 1.40
684 785 2.483013 GCGTATAAGATGGACCACAGCA 60.483 50.000 0.00 0.00 38.15 4.41
703 804 0.040425 GCAACAGTTTGGTACCAGCG 60.040 55.000 15.65 7.48 32.81 5.18
716 819 0.179073 AGCCTAGCCGTATGCAACAG 60.179 55.000 0.00 0.00 44.83 3.16
739 842 6.434018 TTTTTCAATTTGTTGGGCTCAAAG 57.566 33.333 0.00 0.00 38.02 2.77
801 904 2.869636 GCCATTTCAAAATGAACGGCCA 60.870 45.455 15.35 0.00 46.72 5.36
863 969 7.153985 TCCACTTGAATGAAATGAAACCATTC 58.846 34.615 0.00 0.00 43.73 2.67
889 997 5.898174 GATGCAATCCAGATTTGACATCAA 58.102 37.500 15.95 0.00 37.38 2.57
923 1031 5.685954 TGACGATGCTAATCAACGAGATAAC 59.314 40.000 0.00 0.00 42.63 1.89
940 1048 2.347697 TCTCCAACGAGTTGACGATG 57.652 50.000 16.66 0.83 42.93 3.84
946 1054 1.630148 GGTCGATCTCCAACGAGTTG 58.370 55.000 8.87 8.87 39.16 3.16
949 1057 1.064296 CCGGTCGATCTCCAACGAG 59.936 63.158 0.00 0.00 39.16 4.18
959 1067 2.635787 TAGCTAGCCACCCGGTCGAT 62.636 60.000 12.13 0.00 33.28 3.59
964 1072 0.674534 CTAGTTAGCTAGCCACCCGG 59.325 60.000 12.13 0.00 38.35 5.73
977 1085 5.739959 TGGTTGTATCAGCAATGCTAGTTA 58.260 37.500 7.70 0.00 36.40 2.24
990 1098 1.453015 GGCCGCCATGGTTGTATCA 60.453 57.895 14.67 0.00 41.21 2.15
995 1103 2.535485 TAGAGTGGCCGCCATGGTTG 62.535 60.000 16.96 6.37 41.21 3.77
1050 1160 4.735132 TCGCCGACGCCCTTGAAG 62.735 66.667 0.00 0.00 39.84 3.02
1071 1184 1.522092 GGAGACGGCATGGTCATCA 59.478 57.895 0.00 0.00 39.42 3.07
1073 1186 2.746375 GGGGAGACGGCATGGTCAT 61.746 63.158 0.00 0.00 39.42 3.06
1257 1464 2.568612 CGCTGAAGAGGCTGTCGA 59.431 61.111 0.00 0.00 0.00 4.20
1333 1832 2.650116 CGACAGGAGGGAGTGGTGG 61.650 68.421 0.00 0.00 0.00 4.61
1358 1867 1.078848 ACGATCTTGCAGTCTGGGC 60.079 57.895 1.14 0.00 0.00 5.36
1362 1871 0.109086 CGTGGACGATCTTGCAGTCT 60.109 55.000 0.00 0.00 43.02 3.24
1382 2133 2.220786 ATCCTTGGGCTTCCTGCAGG 62.221 60.000 27.87 27.87 45.15 4.85
1390 2141 3.607490 AATCAGCATATCCTTGGGCTT 57.393 42.857 0.00 0.00 33.60 4.35
1408 2159 1.535462 GTACAAGTGCCACAGCGAAAT 59.465 47.619 0.00 0.00 44.31 2.17
1413 2164 0.941542 TTTCGTACAAGTGCCACAGC 59.058 50.000 0.00 0.00 40.48 4.40
1425 2176 0.788391 CCGTCACCAAGCTTTCGTAC 59.212 55.000 0.00 0.00 0.00 3.67
1429 2180 0.884704 TCTGCCGTCACCAAGCTTTC 60.885 55.000 0.00 0.00 0.00 2.62
1475 2226 3.033764 GGCACGCGTTCTCGAACA 61.034 61.111 10.22 0.00 41.20 3.18
1476 2227 3.000080 CTGGCACGCGTTCTCGAAC 62.000 63.158 10.22 0.00 39.71 3.95
1477 2228 2.733218 CTGGCACGCGTTCTCGAA 60.733 61.111 10.22 0.00 39.71 3.71
1504 2270 4.820744 CCAGATGGGGCCGTTGGG 62.821 72.222 0.00 0.00 0.00 4.12
1525 2291 2.490217 CCAGTAGCCGAGGACGTG 59.510 66.667 0.00 0.00 37.88 4.49
1538 2304 4.079850 CTCTGCTCGCCTGCCAGT 62.080 66.667 0.00 0.00 0.00 4.00
1650 2422 1.586564 CTCCTCGATCGCCGTGAAC 60.587 63.158 11.09 0.00 39.75 3.18
1683 2456 4.796231 AGCGTCACGATGTCCGCC 62.796 66.667 0.00 0.00 46.85 6.13
1706 2479 4.933064 CCCTCGGCGTCTCGATGC 62.933 72.222 6.85 2.54 42.40 3.91
1707 2480 4.271816 CCCCTCGGCGTCTCGATG 62.272 72.222 6.85 0.00 38.55 3.84
1726 2499 2.815647 GGTCTTCTTGGCGCCGAG 60.816 66.667 34.36 34.36 0.00 4.63
1737 2510 3.247886 GGAACTTGACAAAGACGGTCTTC 59.752 47.826 22.62 11.96 35.27 2.87
1740 2513 1.871676 GGGAACTTGACAAAGACGGTC 59.128 52.381 0.00 0.00 36.84 4.79
1754 2539 3.802418 AAGAACGCGTGCGGGAACT 62.802 57.895 14.98 8.74 44.69 3.01
1758 2543 3.011760 GAAGAAGAACGCGTGCGGG 62.012 63.158 14.98 10.80 44.69 6.13
1767 2552 3.510531 ACCCCTTTCCTGAAGAAGAAC 57.489 47.619 0.00 0.00 37.57 3.01
1769 2554 4.081087 CGATAACCCCTTTCCTGAAGAAGA 60.081 45.833 0.00 0.00 37.57 2.87
1778 2563 4.951715 ACCAAATAACGATAACCCCTTTCC 59.048 41.667 0.00 0.00 0.00 3.13
1792 2806 9.459640 GGTTTCTTACTTCTTGAACCAAATAAC 57.540 33.333 0.00 0.00 0.00 1.89
1847 2861 2.432146 TCCACACTAGTCATGGAGATGC 59.568 50.000 17.89 0.00 37.60 3.91
1857 2871 2.169352 AGATGCACCATCCACACTAGTC 59.831 50.000 0.00 0.00 41.36 2.59
1858 2872 2.191400 AGATGCACCATCCACACTAGT 58.809 47.619 0.00 0.00 41.36 2.57
1909 2939 0.239879 AATGCGTGCGATCCGTTTTT 59.760 45.000 0.00 0.00 0.00 1.94
1921 2951 2.663879 GCAAGAGTGAGTGAAATGCGTG 60.664 50.000 0.00 0.00 0.00 5.34
1931 2961 0.679505 TGTTAGGCGCAAGAGTGAGT 59.320 50.000 10.83 0.00 43.02 3.41
2024 3054 5.706916 ACACGTTACTTCTACACGATTGAT 58.293 37.500 0.00 0.00 37.37 2.57
2054 3084 4.669197 GCTGTTCGTTAGTACCATTTGCTG 60.669 45.833 0.00 0.00 0.00 4.41
2059 3089 3.248266 GTCGCTGTTCGTTAGTACCATT 58.752 45.455 0.00 0.00 39.67 3.16
2061 3091 1.068333 GGTCGCTGTTCGTTAGTACCA 60.068 52.381 0.00 0.00 39.67 3.25
2132 3168 1.952296 CCATTCCATGTCTTAGGCAGC 59.048 52.381 0.00 0.00 0.00 5.25
2138 3174 3.785325 TCATCACCCCATTCCATGTCTTA 59.215 43.478 0.00 0.00 0.00 2.10
2154 3190 6.467677 AGGCAGTACATATACCATTCATCAC 58.532 40.000 0.00 0.00 30.88 3.06
2167 3203 3.232720 TGATACCCGAGGCAGTACATA 57.767 47.619 0.00 0.00 0.00 2.29
2180 3216 5.591877 AGAGATGTCTTGCATTTTGATACCC 59.408 40.000 0.00 0.00 38.06 3.69
2181 3217 6.690194 AGAGATGTCTTGCATTTTGATACC 57.310 37.500 0.00 0.00 38.06 2.73
2185 3221 4.631377 CCGTAGAGATGTCTTGCATTTTGA 59.369 41.667 0.00 0.00 38.06 2.69
2193 3229 8.251750 TCAATTTAAACCGTAGAGATGTCTTG 57.748 34.615 0.00 0.00 33.84 3.02
2203 3239 4.678509 TGCAGCTCAATTTAAACCGTAG 57.321 40.909 0.00 0.00 0.00 3.51
2207 3243 6.356757 TGTTTTTGCAGCTCAATTTAAACC 57.643 33.333 14.84 5.62 34.44 3.27
2208 3244 7.854534 AGATGTTTTTGCAGCTCAATTTAAAC 58.145 30.769 12.67 12.67 35.25 2.01
2216 3252 9.142515 CAAAATATAAGATGTTTTTGCAGCTCA 57.857 29.630 0.00 0.00 33.59 4.26
2247 3283 4.156373 GTCCCGCTGATTAGTACTATCTCC 59.844 50.000 2.79 0.00 0.00 3.71
2251 3287 6.492429 TGTTATGTCCCGCTGATTAGTACTAT 59.508 38.462 2.79 0.00 0.00 2.12
2329 3384 5.745312 TGAATGGAACTCATGTGTCTACT 57.255 39.130 0.03 0.00 35.99 2.57
2340 3395 2.416431 GCCTGCATGTTGAATGGAACTC 60.416 50.000 0.00 0.00 0.00 3.01
2342 3397 1.273048 TGCCTGCATGTTGAATGGAAC 59.727 47.619 0.00 0.00 0.00 3.62
2343 3398 1.546923 CTGCCTGCATGTTGAATGGAA 59.453 47.619 0.00 0.00 0.00 3.53
2421 3476 2.092914 GTGGGGAAGGAACGAAGATGAT 60.093 50.000 0.00 0.00 0.00 2.45
2422 3477 1.278127 GTGGGGAAGGAACGAAGATGA 59.722 52.381 0.00 0.00 0.00 2.92
2423 3478 1.279271 AGTGGGGAAGGAACGAAGATG 59.721 52.381 0.00 0.00 0.00 2.90
2424 3479 1.279271 CAGTGGGGAAGGAACGAAGAT 59.721 52.381 0.00 0.00 0.00 2.40
2425 3480 0.685097 CAGTGGGGAAGGAACGAAGA 59.315 55.000 0.00 0.00 0.00 2.87
2426 3481 0.955919 GCAGTGGGGAAGGAACGAAG 60.956 60.000 0.00 0.00 0.00 3.79
2427 3482 1.072505 GCAGTGGGGAAGGAACGAA 59.927 57.895 0.00 0.00 0.00 3.85
2428 3483 2.747686 GCAGTGGGGAAGGAACGA 59.252 61.111 0.00 0.00 0.00 3.85
2429 3484 2.359975 GGCAGTGGGGAAGGAACG 60.360 66.667 0.00 0.00 0.00 3.95
2430 3485 0.251787 AATGGCAGTGGGGAAGGAAC 60.252 55.000 0.00 0.00 0.00 3.62
2431 3486 0.039618 GAATGGCAGTGGGGAAGGAA 59.960 55.000 0.00 0.00 0.00 3.36
2432 3487 1.691219 GAATGGCAGTGGGGAAGGA 59.309 57.895 0.00 0.00 0.00 3.36
2433 3488 1.380380 GGAATGGCAGTGGGGAAGG 60.380 63.158 0.00 0.00 0.00 3.46
2434 3489 0.040204 AAGGAATGGCAGTGGGGAAG 59.960 55.000 0.00 0.00 0.00 3.46
2435 3490 0.039618 GAAGGAATGGCAGTGGGGAA 59.960 55.000 0.00 0.00 0.00 3.97
2436 3491 1.691219 GAAGGAATGGCAGTGGGGA 59.309 57.895 0.00 0.00 0.00 4.81
2437 3492 1.380380 GGAAGGAATGGCAGTGGGG 60.380 63.158 0.00 0.00 0.00 4.96
2438 3493 0.394899 GAGGAAGGAATGGCAGTGGG 60.395 60.000 0.00 0.00 0.00 4.61
2439 3494 0.745845 CGAGGAAGGAATGGCAGTGG 60.746 60.000 0.00 0.00 0.00 4.00
2440 3495 0.745845 CCGAGGAAGGAATGGCAGTG 60.746 60.000 0.00 0.00 0.00 3.66
2446 3501 2.093500 TCACATGTCCGAGGAAGGAATG 60.093 50.000 0.00 0.00 42.77 2.67
2484 3539 4.568956 TCGATCTGCATTTGAAGAAGTGA 58.431 39.130 0.00 0.00 32.47 3.41
2553 3613 8.573885 CCCATCTAACTCGTTGAACTATGTATA 58.426 37.037 0.00 0.00 0.00 1.47
2572 3632 5.011431 CACTAGTTCATCATGAGCCCATCTA 59.989 44.000 0.09 0.00 0.00 1.98
2679 3742 2.624838 CCACAACTTTGCATGTCTCCTT 59.375 45.455 0.00 0.00 0.00 3.36
2699 3762 3.621892 CTGCGCCTTGCTTGCTTCC 62.622 63.158 4.18 0.00 46.63 3.46
2718 3781 4.572389 CGATCCATGTAAGTTTTCCTCTGG 59.428 45.833 0.00 0.00 0.00 3.86
2723 3786 5.674933 GGATCGATCCATGTAAGTTTTCC 57.325 43.478 34.65 7.84 46.38 3.13
2757 3900 0.392336 GAAACAATGGGTGCCTTGCA 59.608 50.000 0.00 0.00 35.60 4.08


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

AutoCloner maintained by Alex Coulton.