Multiple sequence alignment - TraesCS5D01G199400

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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 TraesCS5D01G199400 chr5D 100.000 4298 0 0 1 4298 302017967 302022264 0.000000e+00 7938
1 TraesCS5D01G199400 chr5D 95.152 330 15 1 1540 1868 328392812 328392483 1.770000e-143 520
2 TraesCS5D01G199400 chr5A 92.446 2396 117 15 62 2405 395836650 395834267 0.000000e+00 3363
3 TraesCS5D01G199400 chr5A 93.525 1081 56 10 2401 3479 395834241 395833173 0.000000e+00 1596
4 TraesCS5D01G199400 chr5A 85.246 427 38 19 3783 4196 395833002 395832588 2.390000e-112 416
5 TraesCS5D01G199400 chr5A 95.455 88 4 0 3659 3746 395833096 395833009 1.610000e-29 141
6 TraesCS5D01G199400 chr5B 90.360 2386 127 28 1 2343 345050833 345053158 0.000000e+00 3037
7 TraesCS5D01G199400 chr5B 93.574 1027 54 10 2374 3391 345053156 345054179 0.000000e+00 1520
8 TraesCS5D01G199400 chr5B 93.976 747 34 6 3560 4298 345054389 345055132 0.000000e+00 1120
9 TraesCS5D01G199400 chr5B 93.548 93 5 1 3387 3479 345054300 345054391 2.080000e-28 137
10 TraesCS5D01G199400 chr6A 91.185 329 27 2 1540 1867 536911679 536912006 3.050000e-121 446
11 TraesCS5D01G199400 chr6A 94.318 88 5 0 3478 3565 93285788 93285701 7.500000e-28 135
12 TraesCS5D01G199400 chr7D 93.939 165 10 0 1548 1712 55445958 55446122 2.570000e-62 250
13 TraesCS5D01G199400 chr3B 97.080 137 4 0 1576 1712 612294627 612294763 9.290000e-57 231
14 TraesCS5D01G199400 chr3B 92.632 95 6 1 3478 3571 485691486 485691392 7.500000e-28 135
15 TraesCS5D01G199400 chr2D 94.681 94 5 0 3474 3567 382456028 382455935 3.460000e-31 147
16 TraesCS5D01G199400 chr2D 94.444 90 4 1 3477 3566 302248098 302248010 2.080000e-28 137
17 TraesCS5D01G199400 chr3A 89.381 113 10 2 3453 3564 698275166 698275055 1.610000e-29 141
18 TraesCS5D01G199400 chr1D 94.444 90 5 0 3473 3562 241268573 241268662 5.800000e-29 139
19 TraesCS5D01G199400 chr1D 91.089 101 8 1 3471 3570 250421755 250421655 7.500000e-28 135
20 TraesCS5D01G199400 chr6B 93.548 93 5 1 3470 3562 472612054 472612145 2.080000e-28 137
21 TraesCS5D01G199400 chr1A 91.089 101 8 1 3471 3570 320485680 320485580 7.500000e-28 135


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 TraesCS5D01G199400 chr5D 302017967 302022264 4297 False 7938.0 7938 100.0000 1 4298 1 chr5D.!!$F1 4297
1 TraesCS5D01G199400 chr5A 395832588 395836650 4062 True 1379.0 3363 91.6680 62 4196 4 chr5A.!!$R1 4134
2 TraesCS5D01G199400 chr5B 345050833 345055132 4299 False 1453.5 3037 92.8645 1 4298 4 chr5B.!!$F1 4297

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
812 871 0.244994 AGAGAGATGTTCGCTGCGTT 59.755 50.0 22.48 5.63 34.39 4.84 F
2160 2242 0.179127 ATGGACATCAGCTCACGTCG 60.179 55.0 0.00 0.00 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2400 0.180406 ATGTGGGCGTCCAAGGATAC 59.820 55.000 12.16 0.0 46.04 2.24 R
3923 4175 1.338973 CAAAAGGCAAGCTGAAGCAGA 59.661 47.619 4.90 0.0 45.16 4.26 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
40 41 2.780065 TTGTCAAAGTCACATGCAGC 57.220 45.000 0.00 0.00 0.00 5.25
48 49 5.047164 TCAAAGTCACATGCAGCCATATTTT 60.047 36.000 0.00 0.00 0.00 1.82
49 50 5.410355 AAGTCACATGCAGCCATATTTTT 57.590 34.783 0.00 0.00 0.00 1.94
56 57 3.736720 TGCAGCCATATTTTTGCACAAA 58.263 36.364 0.00 0.00 41.23 2.83
94 95 5.652518 GTGTGTAGAATTCAGGTCCTCTAC 58.347 45.833 8.44 7.87 40.36 2.59
211 220 7.482654 TGATAATTCCAGCACTAGAAAATCG 57.517 36.000 0.00 0.00 0.00 3.34
236 245 7.867909 CGCTGATGATAATTTCCAGTACTAGAA 59.132 37.037 0.00 0.00 0.00 2.10
249 258 9.545105 TTCCAGTACTAGAAAAACACGATAAAA 57.455 29.630 0.88 0.00 0.00 1.52
274 283 7.639113 AATTTATACCAAGAAGGCGAAATCA 57.361 32.000 0.00 0.00 43.14 2.57
275 284 7.823745 ATTTATACCAAGAAGGCGAAATCAT 57.176 32.000 0.00 0.00 43.14 2.45
290 299 6.237942 GGCGAAATCATGGATATGAATCTACG 60.238 42.308 0.00 0.00 45.82 3.51
309 318 4.866508 ACGCCTATAGCACTTATAAGCA 57.133 40.909 12.54 0.00 44.04 3.91
420 429 1.806542 ACAAACAATGCTGAGCTACCG 59.193 47.619 5.83 0.00 0.00 4.02
479 526 3.492756 GCAAAGCTAAGATCTAAGCCGAG 59.507 47.826 0.00 0.00 39.64 4.63
812 871 0.244994 AGAGAGATGTTCGCTGCGTT 59.755 50.000 22.48 5.63 34.39 4.84
817 876 3.254014 ATGTTCGCTGCGTTGTGCC 62.254 57.895 22.48 5.34 45.60 5.01
850 909 3.394836 GGGCTTCCCTGCTCGACT 61.395 66.667 0.00 0.00 41.34 4.18
861 924 2.166459 CCTGCTCGACTTGATAAGGTCA 59.834 50.000 0.00 0.00 34.25 4.02
869 932 2.236146 ACTTGATAAGGTCATGTGCGGA 59.764 45.455 0.00 0.00 41.94 5.54
872 935 2.159099 TGATAAGGTCATGTGCGGAGTC 60.159 50.000 0.00 0.00 0.00 3.36
897 960 2.329614 CCGTTAAAGGCCCACGTGG 61.330 63.158 28.26 28.26 31.83 4.94
1047 1123 2.835431 GCTCTCCGCTGCCTCCTA 60.835 66.667 0.00 0.00 35.14 2.94
1071 1147 3.439513 AACCGCTGCACACTCGTCA 62.440 57.895 0.00 0.00 0.00 4.35
1099 1175 2.444624 CCTCCGACGCAACACATCG 61.445 63.158 0.00 0.00 32.72 3.84
1135 1211 0.253677 CCCTAAACCCTTCCCCCTCT 60.254 60.000 0.00 0.00 0.00 3.69
1383 1459 0.249405 GCATCTCGGCCTCTCTGAAG 60.249 60.000 0.00 0.00 0.00 3.02
1413 1489 0.911525 TCCAGGAGGGCCAAGAGAAG 60.912 60.000 6.18 0.00 36.29 2.85
1426 1502 3.003763 AGAAGTCACGGGAGGGCC 61.004 66.667 0.00 0.00 0.00 5.80
1427 1503 3.319198 GAAGTCACGGGAGGGCCA 61.319 66.667 6.18 0.00 35.15 5.36
1662 1744 0.613853 ACTTCGACGGATCCTTCCCA 60.614 55.000 12.39 0.00 39.01 4.37
1721 1803 4.680237 CCACGCGGACTGGAAGCA 62.680 66.667 12.47 0.00 37.60 3.91
1887 1969 2.946762 GTTCACCTTGTCAGCGCC 59.053 61.111 2.29 0.00 0.00 6.53
1986 2068 4.481112 GCGCGGAATGTGGGCAAG 62.481 66.667 8.83 0.00 43.94 4.01
2148 2230 1.033746 CGGGCTTGCTTCATGGACAT 61.034 55.000 0.00 0.00 0.00 3.06
2154 2236 2.034104 TGCTTCATGGACATCAGCTC 57.966 50.000 12.04 0.00 0.00 4.09
2160 2242 0.179127 ATGGACATCAGCTCACGTCG 60.179 55.000 0.00 0.00 0.00 5.12
2249 2331 6.326583 AGAATAAAGGTCTCATTCCGTCCATA 59.673 38.462 0.00 0.00 30.51 2.74
2280 2362 7.614908 CACATTTTGTCAGTGAATTTTGTGAG 58.385 34.615 14.54 0.00 35.33 3.51
2287 2369 4.515191 TCAGTGAATTTTGTGAGTAGGTGC 59.485 41.667 0.00 0.00 0.00 5.01
2294 2376 0.830648 TGTGAGTAGGTGCTATGGGC 59.169 55.000 0.00 0.00 42.22 5.36
2318 2400 6.183360 GCATAAATTTTCTGCTTGTTTCCTCG 60.183 38.462 14.75 0.00 33.15 4.63
2321 2403 6.575162 AATTTTCTGCTTGTTTCCTCGTAT 57.425 33.333 0.00 0.00 0.00 3.06
2328 2410 3.618997 GCTTGTTTCCTCGTATCCTTGGA 60.619 47.826 0.00 0.00 0.00 3.53
2334 2416 1.672854 CTCGTATCCTTGGACGCCCA 61.673 60.000 0.00 0.00 41.64 5.36
2335 2417 1.520787 CGTATCCTTGGACGCCCAC 60.521 63.158 0.00 0.00 43.41 4.61
2408 2524 5.496556 CAGTTGTGATTATGTGAGGGGTAA 58.503 41.667 0.00 0.00 0.00 2.85
2412 2528 7.773690 AGTTGTGATTATGTGAGGGGTAATTAC 59.226 37.037 7.09 7.09 0.00 1.89
2437 2553 6.290294 TCACCCTCTAAACAGTAACCATAC 57.710 41.667 0.00 0.00 0.00 2.39
2439 2555 7.184161 TCACCCTCTAAACAGTAACCATACTA 58.816 38.462 0.00 0.00 40.44 1.82
2576 2692 5.353956 CACATGTCTGGTTCAATCCGAAATA 59.646 40.000 0.00 0.00 34.69 1.40
2614 2730 9.612620 CTTTTGATAAGAGTTATTTGTGTGACC 57.387 33.333 0.00 0.00 0.00 4.02
2624 2741 6.594159 AGTTATTTGTGTGACCGGATTCTTAG 59.406 38.462 9.46 0.00 0.00 2.18
2687 2804 4.160626 GTCCATACATATAGGAGGACTGGC 59.839 50.000 15.77 0.00 41.67 4.85
2688 2805 4.096681 CCATACATATAGGAGGACTGGCA 58.903 47.826 0.00 0.00 0.00 4.92
2811 2928 7.628234 AGTCTATGATGAAAGATCACTTTGGT 58.372 34.615 0.00 0.00 44.97 3.67
2937 3059 2.743636 TAGGCCAGAAACGAGTGAAG 57.256 50.000 5.01 0.00 0.00 3.02
3060 3182 0.676151 GGCTGAAAGGAGAGGCAGTG 60.676 60.000 0.00 0.00 34.93 3.66
3129 3251 1.191489 TTGTCCATGAGAGGGCGTCA 61.191 55.000 10.15 0.00 35.53 4.35
3144 3266 2.724174 GGCGTCAATTTTTGAGGAAACG 59.276 45.455 12.63 4.61 45.69 3.60
3322 3444 7.170965 AGTGTTTCATTCCATTCTGTGATACT 58.829 34.615 0.00 0.00 0.00 2.12
3406 3653 6.599244 AGCATAGTACAATTTAAGCTTGCTCA 59.401 34.615 9.86 0.00 31.54 4.26
3407 3654 7.121168 AGCATAGTACAATTTAAGCTTGCTCAA 59.879 33.333 9.86 0.00 31.54 3.02
3419 3666 0.255890 TTGCTCAAGAGGGGTATGGC 59.744 55.000 0.00 0.00 0.00 4.40
3449 3696 3.256558 GAAGATTTTTGTGGGAGCATGC 58.743 45.455 10.51 10.51 0.00 4.06
3451 3698 0.390209 ATTTTTGTGGGAGCATGCGC 60.390 50.000 13.62 13.62 38.99 6.09
3479 3726 2.143925 GGACTTGCTGTTGACTGGTAC 58.856 52.381 0.00 0.00 0.00 3.34
3480 3727 2.224305 GGACTTGCTGTTGACTGGTACT 60.224 50.000 0.00 0.00 0.00 2.73
3481 3728 3.060602 GACTTGCTGTTGACTGGTACTC 58.939 50.000 0.00 0.00 0.00 2.59
3482 3729 2.224305 ACTTGCTGTTGACTGGTACTCC 60.224 50.000 0.00 0.00 0.00 3.85
3483 3730 0.685097 TGCTGTTGACTGGTACTCCC 59.315 55.000 0.00 0.00 0.00 4.30
3484 3731 0.977395 GCTGTTGACTGGTACTCCCT 59.023 55.000 0.00 0.00 0.00 4.20
3485 3732 1.066787 GCTGTTGACTGGTACTCCCTC 60.067 57.143 0.00 0.00 0.00 4.30
3486 3733 2.530701 CTGTTGACTGGTACTCCCTCT 58.469 52.381 0.00 0.00 0.00 3.69
3487 3734 2.232452 CTGTTGACTGGTACTCCCTCTG 59.768 54.545 0.00 0.00 0.00 3.35
3488 3735 2.249139 GTTGACTGGTACTCCCTCTGT 58.751 52.381 0.00 0.00 0.00 3.41
3489 3736 3.181426 TGTTGACTGGTACTCCCTCTGTA 60.181 47.826 0.00 0.00 0.00 2.74
3490 3737 3.820195 TGACTGGTACTCCCTCTGTAA 57.180 47.619 0.00 0.00 0.00 2.41
3491 3738 4.122337 TGACTGGTACTCCCTCTGTAAA 57.878 45.455 0.00 0.00 0.00 2.01
3492 3739 4.087182 TGACTGGTACTCCCTCTGTAAAG 58.913 47.826 0.00 0.00 0.00 1.85
3493 3740 4.202641 TGACTGGTACTCCCTCTGTAAAGA 60.203 45.833 0.00 0.00 0.00 2.52
3494 3741 4.748701 ACTGGTACTCCCTCTGTAAAGAA 58.251 43.478 0.00 0.00 0.00 2.52
3495 3742 5.152934 ACTGGTACTCCCTCTGTAAAGAAA 58.847 41.667 0.00 0.00 0.00 2.52
3496 3743 5.785940 ACTGGTACTCCCTCTGTAAAGAAAT 59.214 40.000 0.00 0.00 0.00 2.17
3497 3744 6.958192 ACTGGTACTCCCTCTGTAAAGAAATA 59.042 38.462 0.00 0.00 0.00 1.40
3498 3745 7.624077 ACTGGTACTCCCTCTGTAAAGAAATAT 59.376 37.037 0.00 0.00 0.00 1.28
3499 3746 9.144298 CTGGTACTCCCTCTGTAAAGAAATATA 57.856 37.037 0.00 0.00 0.00 0.86
3500 3747 9.496710 TGGTACTCCCTCTGTAAAGAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
3501 3748 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
3504 3751 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
3505 3752 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
3506 3753 9.268282 TCCCTCTGTAAAGAAATATAAGAGTGT 57.732 33.333 0.00 0.00 0.00 3.55
3507 3754 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
3523 3770 7.426929 AAGAGTGTTTAGAGCACTATTGTTG 57.573 36.000 4.41 0.00 45.99 3.33
3524 3771 6.525629 AGAGTGTTTAGAGCACTATTGTTGT 58.474 36.000 0.00 0.00 45.99 3.32
3525 3772 6.425114 AGAGTGTTTAGAGCACTATTGTTGTG 59.575 38.462 0.00 0.00 45.99 3.33
3526 3773 6.288294 AGTGTTTAGAGCACTATTGTTGTGA 58.712 36.000 0.00 0.00 44.41 3.58
3527 3774 6.936900 AGTGTTTAGAGCACTATTGTTGTGAT 59.063 34.615 0.00 0.00 44.41 3.06
3534 3781 6.408858 AGCACTATTGTTGTGATCTAAACG 57.591 37.500 0.00 0.00 37.60 3.60
3535 3782 5.022021 GCACTATTGTTGTGATCTAAACGC 58.978 41.667 0.00 0.00 37.60 4.84
3536 3783 5.163854 GCACTATTGTTGTGATCTAAACGCT 60.164 40.000 0.00 0.00 37.60 5.07
3537 3784 6.470160 CACTATTGTTGTGATCTAAACGCTC 58.530 40.000 0.00 0.00 37.60 5.03
3538 3785 6.311445 CACTATTGTTGTGATCTAAACGCTCT 59.689 38.462 0.00 0.00 37.60 4.09
3539 3786 6.874134 ACTATTGTTGTGATCTAAACGCTCTT 59.126 34.615 0.00 0.00 0.00 2.85
3540 3787 8.033038 ACTATTGTTGTGATCTAAACGCTCTTA 58.967 33.333 0.00 0.00 0.00 2.10
3541 3788 7.849804 ATTGTTGTGATCTAAACGCTCTTAT 57.150 32.000 0.00 0.00 0.00 1.73
3542 3789 8.942338 ATTGTTGTGATCTAAACGCTCTTATA 57.058 30.769 0.00 0.00 0.00 0.98
3543 3790 8.942338 TTGTTGTGATCTAAACGCTCTTATAT 57.058 30.769 0.00 0.00 0.00 0.86
3544 3791 8.942338 TGTTGTGATCTAAACGCTCTTATATT 57.058 30.769 0.00 0.00 0.00 1.28
3545 3792 9.378551 TGTTGTGATCTAAACGCTCTTATATTT 57.621 29.630 0.00 0.00 0.00 1.40
3546 3793 9.851043 GTTGTGATCTAAACGCTCTTATATTTC 57.149 33.333 0.00 0.00 0.00 2.17
3547 3794 9.817809 TTGTGATCTAAACGCTCTTATATTTCT 57.182 29.630 0.00 0.00 0.00 2.52
3548 3795 9.817809 TGTGATCTAAACGCTCTTATATTTCTT 57.182 29.630 0.00 0.00 0.00 2.52
3553 3800 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
3554 3801 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
3555 3802 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
3556 3803 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
3557 3804 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3558 3805 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3559 3806 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3560 3807 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3561 3808 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3746 3993 8.506437 GTCAGTTTTTACATCTGAATCATGTGA 58.494 33.333 0.14 0.00 39.42 3.58
3761 4008 4.054671 TCATGTGACGAATATATTGCGCA 58.945 39.130 5.66 5.66 0.00 6.09
3923 4175 7.830099 AAGAACATCTCACTGAATCCTTTTT 57.170 32.000 0.00 0.00 0.00 1.94
3970 4222 6.608002 TGGACTGGTTATGTAAGGTTTTTGTT 59.392 34.615 0.00 0.00 0.00 2.83
4084 4341 5.241506 TCTGCATAAAAACTGGAGAGGTTTG 59.758 40.000 0.00 0.00 38.21 2.93
4098 4355 5.163673 GGAGAGGTTTGAAGAAATCTGCATC 60.164 44.000 0.00 0.00 32.31 3.91
4130 4387 1.606737 GGTCTCACAGAAGCAGACACC 60.607 57.143 0.00 0.00 38.69 4.16
4169 4426 9.696917 ATTGACAAGTTTTCTGGATGATTAAAC 57.303 29.630 0.00 0.00 0.00 2.01
4196 4453 3.340928 CATGTGAACATCTCTGAAGCCA 58.659 45.455 0.00 0.00 33.61 4.75
4200 4457 4.828939 TGTGAACATCTCTGAAGCCAAAAT 59.171 37.500 0.00 0.00 0.00 1.82
4207 4464 7.447594 ACATCTCTGAAGCCAAAATTTTCAAT 58.552 30.769 0.00 0.00 31.11 2.57
4208 4465 7.935210 ACATCTCTGAAGCCAAAATTTTCAATT 59.065 29.630 0.00 0.00 31.11 2.32
4209 4466 8.780249 CATCTCTGAAGCCAAAATTTTCAATTT 58.220 29.630 0.00 0.00 31.11 1.82
4210 4467 8.735692 TCTCTGAAGCCAAAATTTTCAATTTT 57.264 26.923 0.00 2.03 31.11 1.82
4211 4468 9.176460 TCTCTGAAGCCAAAATTTTCAATTTTT 57.824 25.926 0.00 0.00 31.11 1.94
4247 4510 1.743958 CCAAAGCATCTCTGAAGCCTG 59.256 52.381 0.00 0.00 0.00 4.85
4252 4515 1.065564 GCATCTCTGAAGCCTGAAGGT 60.066 52.381 0.00 0.00 37.57 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.913778 ATGGCTGCATGTGACTTTGA 58.086 45.000 0.50 0.00 0.00 2.69
26 27 5.410355 AAAATATGGCTGCATGTGACTTT 57.590 34.783 0.50 0.00 0.00 2.66
56 57 2.403378 ACACGGTTGCGTGCAAAGT 61.403 52.632 9.13 9.68 42.99 2.66
76 77 7.554959 ACTTTTGTAGAGGACCTGAATTCTA 57.445 36.000 0.00 0.00 0.00 2.10
211 220 9.547753 TTTCTAGTACTGGAAATTATCATCAGC 57.452 33.333 25.42 0.00 35.57 4.26
249 258 8.062065 TGATTTCGCCTTCTTGGTATAAATTT 57.938 30.769 0.00 0.00 38.35 1.82
262 271 5.947228 TTCATATCCATGATTTCGCCTTC 57.053 39.130 0.00 0.00 40.85 3.46
274 283 6.551227 TGCTATAGGCGTAGATTCATATCCAT 59.449 38.462 1.04 0.00 45.43 3.41
275 284 5.891551 TGCTATAGGCGTAGATTCATATCCA 59.108 40.000 1.04 0.00 45.43 3.41
290 299 4.894784 TGGTGCTTATAAGTGCTATAGGC 58.105 43.478 13.91 0.00 42.93 3.93
309 318 2.763933 CATCGCAGCAAGAGATATGGT 58.236 47.619 0.00 0.00 34.80 3.55
812 871 1.600511 TATCTCAACGCCTCGGCACA 61.601 55.000 8.87 0.00 42.06 4.57
817 876 0.946221 GCCCATATCTCAACGCCTCG 60.946 60.000 0.00 0.00 0.00 4.63
850 909 2.236146 ACTCCGCACATGACCTTATCAA 59.764 45.455 0.00 0.00 41.93 2.57
869 932 0.175073 CCTTTAACGGGCTAGCGACT 59.825 55.000 9.00 0.00 0.00 4.18
872 935 3.406559 GCCTTTAACGGGCTAGCG 58.593 61.111 9.00 0.00 45.57 4.26
897 960 3.544356 GCTTTCAGCCTTGTGAAGTAC 57.456 47.619 0.00 0.00 37.72 2.73
929 992 2.182030 CGTCTCAGCGGGGAGTTC 59.818 66.667 0.00 0.00 36.30 3.01
1071 1147 2.037527 GTCGGAGGAGGGTGAGGT 59.962 66.667 0.00 0.00 0.00 3.85
1099 1175 0.466372 GGGATTTGGGAGGCAGCTAC 60.466 60.000 0.00 0.00 0.00 3.58
1173 1249 4.754667 GGGGAAGACACCGGCGAC 62.755 72.222 9.30 0.00 0.00 5.19
1203 1279 1.333636 CGGCTGGGAGGTCAGAAGAT 61.334 60.000 0.00 0.00 36.93 2.40
1721 1803 2.125269 GGTTAGACGGCGCACCAT 60.125 61.111 10.83 0.00 34.57 3.55
1950 2032 1.531602 GCCAACAGCCCAGACCTTT 60.532 57.895 0.00 0.00 34.35 3.11
2037 2119 2.435059 GGCGCCTCTGTCAAGGTC 60.435 66.667 22.15 0.00 38.79 3.85
2094 2176 1.302033 CGCCTGAGCACCAAGAACT 60.302 57.895 0.00 0.00 39.83 3.01
2148 2230 1.463831 GTAAGTCTCGACGTGAGCTGA 59.536 52.381 0.00 0.00 44.86 4.26
2154 2236 0.453950 CGGGTGTAAGTCTCGACGTG 60.454 60.000 0.00 0.00 36.20 4.49
2160 2242 0.456628 GCTCCTCGGGTGTAAGTCTC 59.543 60.000 0.00 0.00 0.00 3.36
2249 2331 8.836268 AAATTCACTGACAAAATGTGCATAAT 57.164 26.923 0.00 0.00 0.00 1.28
2287 2369 6.576185 ACAAGCAGAAAATTTATGCCCATAG 58.424 36.000 19.97 9.36 40.89 2.23
2294 2376 6.863126 ACGAGGAAACAAGCAGAAAATTTATG 59.137 34.615 0.00 0.00 0.00 1.90
2296 2378 6.385649 ACGAGGAAACAAGCAGAAAATTTA 57.614 33.333 0.00 0.00 0.00 1.40
2298 2380 4.918810 ACGAGGAAACAAGCAGAAAATT 57.081 36.364 0.00 0.00 0.00 1.82
2318 2400 0.180406 ATGTGGGCGTCCAAGGATAC 59.820 55.000 12.16 0.00 46.04 2.24
2321 2403 0.608035 GAAATGTGGGCGTCCAAGGA 60.608 55.000 12.16 0.00 46.04 3.36
2328 2410 0.314935 CAAGCAAGAAATGTGGGCGT 59.685 50.000 0.00 0.00 0.00 5.68
2334 2416 7.756722 GCACATAATAGAACAAGCAAGAAATGT 59.243 33.333 0.00 0.00 0.00 2.71
2335 2417 7.972277 AGCACATAATAGAACAAGCAAGAAATG 59.028 33.333 0.00 0.00 0.00 2.32
2387 2473 7.773690 AGTAATTACCCCTCACATAATCACAAC 59.226 37.037 12.05 0.00 0.00 3.32
2408 2524 7.016858 TGGTTACTGTTTAGAGGGTGAAGTAAT 59.983 37.037 0.00 0.00 32.89 1.89
2412 2528 5.223449 TGGTTACTGTTTAGAGGGTGAAG 57.777 43.478 0.00 0.00 0.00 3.02
2437 2553 9.261180 TCAACTTCAGTTTCAGACTAACATTAG 57.739 33.333 0.00 0.00 36.65 1.73
2439 2555 7.552687 TGTCAACTTCAGTTTCAGACTAACATT 59.447 33.333 9.04 0.00 36.65 2.71
2562 2678 9.651718 GACTATTCATGTTATTTCGGATTGAAC 57.348 33.333 0.00 0.00 35.97 3.18
2600 2716 5.622770 AAGAATCCGGTCACACAAATAAC 57.377 39.130 0.00 0.00 0.00 1.89
2602 2718 6.045072 ACTAAGAATCCGGTCACACAAATA 57.955 37.500 0.00 0.00 0.00 1.40
2604 2720 4.345859 ACTAAGAATCCGGTCACACAAA 57.654 40.909 0.00 0.00 0.00 2.83
2614 2730 8.440833 ACAAAACGAATTAGAACTAAGAATCCG 58.559 33.333 0.00 0.00 0.00 4.18
2624 2741 9.673454 AAGGTTATGAACAAAACGAATTAGAAC 57.327 29.630 0.00 0.00 0.00 3.01
2644 2761 0.480690 TGCCCTGCCTGAAAAGGTTA 59.519 50.000 0.00 0.00 0.00 2.85
2687 2804 1.021390 GTCTTCCACATCCAGGCGTG 61.021 60.000 0.00 0.00 0.00 5.34
2688 2805 1.194781 AGTCTTCCACATCCAGGCGT 61.195 55.000 0.00 0.00 0.00 5.68
2937 3059 0.039618 TCACCCATTTCCCAAGCTCC 59.960 55.000 0.00 0.00 0.00 4.70
3060 3182 5.221581 ACCATCGTATGTCCATAACCCTAAC 60.222 44.000 0.00 0.00 0.00 2.34
3129 3251 5.538433 TGAGAATCCCGTTTCCTCAAAAATT 59.462 36.000 0.00 0.00 0.00 1.82
3144 3266 4.515567 ACGACTTTTGAAACTGAGAATCCC 59.484 41.667 0.00 0.00 0.00 3.85
3265 3387 1.544691 GACCGTAGCAGGTTCTGAAGA 59.455 52.381 0.00 0.00 46.09 2.87
3359 3481 5.239525 GCTTCTATGTGTTTCAAACCTCAGT 59.760 40.000 0.00 0.00 0.00 3.41
3406 3653 1.668826 TGAACAGCCATACCCCTCTT 58.331 50.000 0.00 0.00 0.00 2.85
3407 3654 1.492176 CATGAACAGCCATACCCCTCT 59.508 52.381 0.00 0.00 0.00 3.69
3419 3666 5.010922 TCCCACAAAAATCTTCCATGAACAG 59.989 40.000 0.00 0.00 0.00 3.16
3479 3726 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
3480 3727 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
3481 3728 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
3497 3744 9.155975 CAACAATAGTGCTCTAAACACTCTTAT 57.844 33.333 0.00 0.00 45.06 1.73
3498 3745 8.148351 ACAACAATAGTGCTCTAAACACTCTTA 58.852 33.333 0.00 0.00 45.06 2.10
3499 3746 6.992715 ACAACAATAGTGCTCTAAACACTCTT 59.007 34.615 0.00 0.00 45.06 2.85
3500 3747 6.425114 CACAACAATAGTGCTCTAAACACTCT 59.575 38.462 0.00 0.00 45.06 3.24
3501 3748 6.423905 TCACAACAATAGTGCTCTAAACACTC 59.576 38.462 0.00 0.00 45.06 3.51
3503 3750 6.539649 TCACAACAATAGTGCTCTAAACAC 57.460 37.500 0.00 0.00 36.93 3.32
3504 3751 7.161404 AGATCACAACAATAGTGCTCTAAACA 58.839 34.615 0.00 0.00 39.78 2.83
3505 3752 7.602517 AGATCACAACAATAGTGCTCTAAAC 57.397 36.000 0.00 0.00 39.78 2.01
3507 3754 9.151471 GTTTAGATCACAACAATAGTGCTCTAA 57.849 33.333 12.77 12.77 45.43 2.10
3508 3755 7.488150 CGTTTAGATCACAACAATAGTGCTCTA 59.512 37.037 0.00 0.00 41.26 2.43
3509 3756 6.311445 CGTTTAGATCACAACAATAGTGCTCT 59.689 38.462 0.00 0.00 42.88 4.09
3510 3757 6.470160 CGTTTAGATCACAACAATAGTGCTC 58.530 40.000 0.00 0.00 36.93 4.26
3511 3758 5.163854 GCGTTTAGATCACAACAATAGTGCT 60.164 40.000 0.00 0.00 36.93 4.40
3512 3759 5.022021 GCGTTTAGATCACAACAATAGTGC 58.978 41.667 0.00 0.00 36.93 4.40
3513 3760 6.311445 AGAGCGTTTAGATCACAACAATAGTG 59.689 38.462 0.00 0.00 37.82 2.74
3514 3761 6.398918 AGAGCGTTTAGATCACAACAATAGT 58.601 36.000 0.00 0.00 37.82 2.12
3515 3762 6.893958 AGAGCGTTTAGATCACAACAATAG 57.106 37.500 0.00 0.00 37.82 1.73
3516 3763 8.942338 ATAAGAGCGTTTAGATCACAACAATA 57.058 30.769 0.00 0.00 37.82 1.90
3517 3764 7.849804 ATAAGAGCGTTTAGATCACAACAAT 57.150 32.000 0.00 0.00 37.82 2.71
3518 3765 8.942338 ATATAAGAGCGTTTAGATCACAACAA 57.058 30.769 0.00 0.00 37.82 2.83
3519 3766 8.942338 AATATAAGAGCGTTTAGATCACAACA 57.058 30.769 0.00 0.00 37.82 3.33
3520 3767 9.851043 GAAATATAAGAGCGTTTAGATCACAAC 57.149 33.333 0.00 0.00 37.82 3.32
3521 3768 9.817809 AGAAATATAAGAGCGTTTAGATCACAA 57.182 29.630 0.00 0.00 37.82 3.33
3522 3769 9.817809 AAGAAATATAAGAGCGTTTAGATCACA 57.182 29.630 0.00 0.00 37.82 3.58
3527 3774 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
3528 3775 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
3529 3776 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
3530 3777 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
3531 3778 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
3532 3779 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
3533 3780 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3534 3781 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3535 3782 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3536 3783 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3543 3790 9.822185 GTTATAATTACTCCCTCCGTAAAGAAA 57.178 33.333 0.00 0.00 31.36 2.52
3544 3791 8.424133 GGTTATAATTACTCCCTCCGTAAAGAA 58.576 37.037 0.00 0.00 31.36 2.52
3545 3792 7.564660 TGGTTATAATTACTCCCTCCGTAAAGA 59.435 37.037 0.00 0.00 31.36 2.52
3546 3793 7.729116 TGGTTATAATTACTCCCTCCGTAAAG 58.271 38.462 0.00 0.00 31.36 1.85
3547 3794 7.673641 TGGTTATAATTACTCCCTCCGTAAA 57.326 36.000 0.00 0.00 31.36 2.01
3548 3795 7.673641 TTGGTTATAATTACTCCCTCCGTAA 57.326 36.000 0.00 0.00 0.00 3.18
3549 3796 7.673641 TTTGGTTATAATTACTCCCTCCGTA 57.326 36.000 0.00 0.00 0.00 4.02
3550 3797 6.564557 TTTGGTTATAATTACTCCCTCCGT 57.435 37.500 0.00 0.00 0.00 4.69
3551 3798 9.379791 GATATTTGGTTATAATTACTCCCTCCG 57.620 37.037 0.00 0.00 0.00 4.63
3923 4175 1.338973 CAAAAGGCAAGCTGAAGCAGA 59.661 47.619 4.90 0.00 45.16 4.26
3970 4222 6.073276 CGAAGGTCACAGTCAATGAAATGTAA 60.073 38.462 2.57 0.00 0.00 2.41
4084 4341 6.486253 TTGTACACAGATGCAGATTTCTTC 57.514 37.500 0.00 0.00 0.00 2.87
4098 4355 4.997905 CTGTGAGACCATTTGTACACAG 57.002 45.455 0.00 0.00 46.11 3.66
4130 4387 3.773117 GTCAATTGACAGCAACCCG 57.227 52.632 29.43 0.00 44.18 5.28
4169 4426 3.749609 TCAGAGATGTTCACATGCTGTTG 59.250 43.478 14.46 6.67 37.01 3.33
4210 4467 3.895232 TTGGCAAGCTACCAACAAAAA 57.105 38.095 15.37 0.00 42.23 1.94
4211 4468 3.791245 CTTTGGCAAGCTACCAACAAAA 58.209 40.909 18.26 5.72 46.66 2.44
4212 4469 3.451141 CTTTGGCAAGCTACCAACAAA 57.549 42.857 18.26 10.14 46.66 2.83
4226 4489 0.455005 GGCTTCAGAGATGCTTTGGC 59.545 55.000 5.12 0.00 33.95 4.52
4273 4536 3.428870 GCATCTTCTCAACGAGAACGAAA 59.571 43.478 2.32 0.00 42.78 3.46


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

AutoCloner maintained by Alex Coulton.