Multiple sequence alignment - TraesCS2A01G331500

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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 TraesCS2A01G331500 chr2A 100.000 2171 0 0 1 2171 564498953 564501123 0.000000e+00 4010
1 TraesCS2A01G331500 chr2D 89.783 969 39 20 1 956 423876888 423875967 0.000000e+00 1186
2 TraesCS2A01G331500 chr2D 87.057 649 36 10 922 1543 423875977 423875350 0.000000e+00 689
3 TraesCS2A01G331500 chr2D 89.575 518 30 11 1659 2171 423875345 423874847 8.450000e-179 636
4 TraesCS2A01G331500 chr2B 89.898 782 30 13 617 1387 497857067 497856324 0.000000e+00 961
5 TraesCS2A01G331500 chr2B 88.047 594 25 19 1 591 497859520 497858970 0.000000e+00 662
6 TraesCS2A01G331500 chr2B 88.208 212 20 5 1962 2171 497855543 497855335 4.630000e-62 248
7 TraesCS2A01G331500 chr2B 80.247 243 30 13 1695 1922 497855787 497855548 1.330000e-37 167
8 TraesCS2A01G331500 chr4A 89.744 117 12 0 1538 1654 638172311 638172427 1.340000e-32 150
9 TraesCS2A01G331500 chr7A 91.589 107 9 0 1548 1654 163025674 163025780 4.830000e-32 148
10 TraesCS2A01G331500 chr6A 89.655 116 12 0 1546 1661 459910087 459909972 4.830000e-32 148
11 TraesCS2A01G331500 chr3B 91.589 107 9 0 1548 1654 3038027 3038133 4.830000e-32 148
12 TraesCS2A01G331500 chr3B 89.474 114 12 0 1549 1662 308391046 308390933 6.250000e-31 145
13 TraesCS2A01G331500 chr1A 88.793 116 13 0 1543 1658 474447161 474447276 2.250000e-30 143
14 TraesCS2A01G331500 chr1A 88.793 116 13 0 1549 1664 491131151 491131036 2.250000e-30 143
15 TraesCS2A01G331500 chr5B 88.136 118 14 0 1537 1654 45943847 45943964 8.080000e-30 141
16 TraesCS2A01G331500 chr4D 84.828 145 16 5 1533 1673 209212260 209212118 8.080000e-30 141


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 TraesCS2A01G331500 chr2A 564498953 564501123 2170 False 4010.0 4010 100.000 1 2171 1 chr2A.!!$F1 2170
1 TraesCS2A01G331500 chr2D 423874847 423876888 2041 True 837.0 1186 88.805 1 2171 3 chr2D.!!$R1 2170
2 TraesCS2A01G331500 chr2B 497855335 497859520 4185 True 509.5 961 86.600 1 2171 4 chr2B.!!$R1 2170

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
692 2578 0.249322 CGACCGTTCCACACAGTCTT 60.249 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 3893 0.472471 TTGCTCCCTCCGTTCACTTT 59.528 50.0 0.0 0.0 0.0 2.66 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
49 50 3.853330 CAGTGCCGTGCCGAATCG 61.853 66.667 0.00 0.00 0.00 3.34
54 55 3.853330 CCGTGCCGAATCGTGCAG 61.853 66.667 16.57 11.52 34.85 4.41
124 125 1.315257 GCCCATGGTGGTGTCATGTC 61.315 60.000 11.73 0.00 40.07 3.06
215 217 0.736325 AAAACCTCGACGGCGATCAG 60.736 55.000 16.81 9.15 46.80 2.90
311 313 4.877823 TCGAATTGATTCCATCCTGTCAAG 59.122 41.667 0.00 0.00 34.45 3.02
317 319 1.450312 CCATCCTGTCAAGCCCGTC 60.450 63.158 0.00 0.00 0.00 4.79
318 320 1.811266 CATCCTGTCAAGCCCGTCG 60.811 63.158 0.00 0.00 0.00 5.12
319 321 2.283529 ATCCTGTCAAGCCCGTCGT 61.284 57.895 0.00 0.00 0.00 4.34
320 322 2.227089 ATCCTGTCAAGCCCGTCGTC 62.227 60.000 0.00 0.00 0.00 4.20
321 323 2.432628 CTGTCAAGCCCGTCGTCC 60.433 66.667 0.00 0.00 0.00 4.79
357 359 1.689892 CCCTCCCAGTCCTAGTCTTCC 60.690 61.905 0.00 0.00 0.00 3.46
361 363 1.007238 CCCAGTCCTAGTCTTCCTCCA 59.993 57.143 0.00 0.00 0.00 3.86
367 369 3.057174 GTCCTAGTCTTCCTCCATATGCG 60.057 52.174 0.00 0.00 0.00 4.73
387 389 0.404040 TTGTCAATGGAGGACACCCC 59.596 55.000 0.00 0.00 44.38 4.95
388 390 1.303282 GTCAATGGAGGACACCCCC 59.697 63.158 0.00 0.00 35.36 5.40
389 391 1.151699 TCAATGGAGGACACCCCCA 60.152 57.895 0.00 0.00 37.25 4.96
390 392 0.774096 TCAATGGAGGACACCCCCAA 60.774 55.000 0.00 0.00 36.70 4.12
391 393 0.611896 CAATGGAGGACACCCCCAAC 60.612 60.000 0.00 0.00 36.70 3.77
392 394 1.800229 AATGGAGGACACCCCCAACC 61.800 60.000 0.00 0.00 36.70 3.77
411 413 2.180017 CAATCAGCCAAGCCGCAC 59.820 61.111 0.00 0.00 0.00 5.34
480 482 1.167851 TTCCGCAGCAAAAGATGGAG 58.832 50.000 0.00 0.00 0.00 3.86
491 493 4.617762 GCAAAAGATGGAGGAAAAGCAGAG 60.618 45.833 0.00 0.00 0.00 3.35
496 498 0.742635 GGAGGAAAAGCAGAGCCGAG 60.743 60.000 0.00 0.00 0.00 4.63
625 2511 0.747255 CCACACGGGATCGAGATTCT 59.253 55.000 0.00 0.00 40.01 2.40
662 2548 1.134371 CAACCCGGAGAGAGATTTCCC 60.134 57.143 0.73 0.00 0.00 3.97
663 2549 1.043673 ACCCGGAGAGAGATTTCCCG 61.044 60.000 0.73 0.00 39.85 5.14
667 2553 1.066303 CGGAGAGAGATTTCCCGTCAG 59.934 57.143 0.00 0.00 35.83 3.51
668 2554 1.202475 GGAGAGAGATTTCCCGTCAGC 60.202 57.143 0.00 0.00 0.00 4.26
669 2555 0.457851 AGAGAGATTTCCCGTCAGCG 59.542 55.000 0.00 0.00 37.95 5.18
692 2578 0.249322 CGACCGTTCCACACAGTCTT 60.249 55.000 0.00 0.00 0.00 3.01
735 2621 2.631428 CACACCACCGTTGAAGCG 59.369 61.111 0.00 0.00 0.00 4.68
818 2712 3.728845 TCTTTTCGAGCAAAGTGTAGCT 58.271 40.909 8.94 0.00 45.25 3.32
1120 3067 3.488090 GCCACGGCTACGACAAGC 61.488 66.667 0.00 0.00 44.60 4.01
1124 3071 1.073216 CACGGCTACGACAAGCTCAG 61.073 60.000 8.59 0.00 44.60 3.35
1128 3075 1.136872 GCTACGACAAGCTCAGCGAG 61.137 60.000 8.72 1.80 39.50 5.03
1189 3136 4.514577 CACACCCTCGCCGGCTAG 62.515 72.222 26.68 23.49 0.00 3.42
1224 3175 0.882042 CCGGCCTACTCATGTGCATC 60.882 60.000 0.00 0.00 0.00 3.91
1225 3176 0.105593 CGGCCTACTCATGTGCATCT 59.894 55.000 0.00 0.00 0.00 2.90
1226 3177 1.341209 CGGCCTACTCATGTGCATCTA 59.659 52.381 0.00 0.00 0.00 1.98
1227 3178 2.028658 CGGCCTACTCATGTGCATCTAT 60.029 50.000 0.00 0.00 0.00 1.98
1228 3179 3.332919 GGCCTACTCATGTGCATCTATG 58.667 50.000 0.00 0.00 0.00 2.23
1229 3180 3.244353 GGCCTACTCATGTGCATCTATGT 60.244 47.826 0.00 0.00 0.00 2.29
1230 3181 4.021104 GGCCTACTCATGTGCATCTATGTA 60.021 45.833 0.00 0.00 0.00 2.29
1231 3182 5.337894 GGCCTACTCATGTGCATCTATGTAT 60.338 44.000 0.00 0.00 0.00 2.29
1232 3183 5.579904 GCCTACTCATGTGCATCTATGTATG 59.420 44.000 0.00 0.00 0.00 2.39
1321 3275 0.806884 TTTTGTGTTGCTGCTGCTGC 60.807 50.000 22.51 22.51 40.48 5.25
1326 3280 0.321346 TGTTGCTGCTGCTGCTACTA 59.679 50.000 32.20 21.73 40.48 1.82
1334 3288 4.321899 GCTGCTGCTGCTACTATCTTCTAT 60.322 45.833 22.10 0.00 40.48 1.98
1349 3303 6.838401 ATCTTCTATTCCTTCTGGTCCATT 57.162 37.500 0.00 0.00 34.23 3.16
1352 3306 7.470192 TCTTCTATTCCTTCTGGTCCATTTTT 58.530 34.615 0.00 0.00 34.23 1.94
1382 3336 5.228220 CGCTCAAACTGAAGTATCTAGAACG 59.772 44.000 0.00 0.00 0.00 3.95
1387 3341 8.145767 TCAAACTGAAGTATCTAGAACGGAAAA 58.854 33.333 0.00 0.00 0.00 2.29
1388 3342 8.436200 CAAACTGAAGTATCTAGAACGGAAAAG 58.564 37.037 0.00 0.00 0.00 2.27
1389 3343 7.229581 ACTGAAGTATCTAGAACGGAAAAGT 57.770 36.000 0.00 0.00 0.00 2.66
1390 3344 7.314393 ACTGAAGTATCTAGAACGGAAAAGTC 58.686 38.462 0.00 0.00 0.00 3.01
1391 3345 7.177041 ACTGAAGTATCTAGAACGGAAAAGTCT 59.823 37.037 0.00 0.00 0.00 3.24
1392 3346 7.313646 TGAAGTATCTAGAACGGAAAAGTCTG 58.686 38.462 0.00 0.00 36.09 3.51
1393 3347 7.176165 TGAAGTATCTAGAACGGAAAAGTCTGA 59.824 37.037 0.00 0.00 33.93 3.27
1394 3348 7.463961 AGTATCTAGAACGGAAAAGTCTGAA 57.536 36.000 0.00 0.00 33.93 3.02
1395 3349 7.893658 AGTATCTAGAACGGAAAAGTCTGAAA 58.106 34.615 0.00 0.00 33.93 2.69
1406 3360 6.250951 CGGAAAAGTCTGAAATACGTCTAGAC 59.749 42.308 13.18 13.18 38.37 2.59
1412 3366 7.251994 AGTCTGAAATACGTCTAGACACATTC 58.748 38.462 22.37 18.23 40.05 2.67
1413 3367 7.121463 AGTCTGAAATACGTCTAGACACATTCT 59.879 37.037 22.37 10.08 40.05 2.40
1424 3378 4.214980 AGACACATTCTTTTCAGCAACG 57.785 40.909 0.00 0.00 0.00 4.10
1504 3462 0.817654 GCTGGAATGGTTTGGCCTAC 59.182 55.000 3.32 1.58 38.35 3.18
1523 3481 5.686913 GCCTACTTCCAGACCTTATAAACCC 60.687 48.000 0.00 0.00 0.00 4.11
1536 3657 8.458951 ACCTTATAAACCCTAAGAGGAGAAAA 57.541 34.615 0.00 0.00 37.67 2.29
1537 3658 9.070210 ACCTTATAAACCCTAAGAGGAGAAAAT 57.930 33.333 0.00 0.00 37.67 1.82
1573 3694 9.853177 ATACTCCCTCTGTTCATTTTTATAAGG 57.147 33.333 0.00 0.00 0.00 2.69
1574 3695 6.603599 ACTCCCTCTGTTCATTTTTATAAGGC 59.396 38.462 0.00 0.00 0.00 4.35
1577 3698 7.673926 TCCCTCTGTTCATTTTTATAAGGCTTT 59.326 33.333 4.45 0.00 0.00 3.51
1578 3699 7.761249 CCCTCTGTTCATTTTTATAAGGCTTTG 59.239 37.037 4.45 0.00 0.00 2.77
1579 3700 8.306761 CCTCTGTTCATTTTTATAAGGCTTTGT 58.693 33.333 4.45 0.00 0.00 2.83
1585 3706 9.968870 TTCATTTTTATAAGGCTTTGTAAACGT 57.031 25.926 4.45 0.67 32.00 3.99
1586 3707 9.968870 TCATTTTTATAAGGCTTTGTAAACGTT 57.031 25.926 4.45 0.00 32.00 3.99
1589 3710 9.798994 TTTTTATAAGGCTTTGTAAACGTTTCA 57.201 25.926 18.42 12.41 32.00 2.69
1590 3711 9.453325 TTTTATAAGGCTTTGTAAACGTTTCAG 57.547 29.630 18.42 10.47 32.00 3.02
1592 3713 4.547406 AGGCTTTGTAAACGTTTCAGAC 57.453 40.909 18.42 11.08 0.00 3.51
1594 3715 4.578928 AGGCTTTGTAAACGTTTCAGACAT 59.421 37.500 18.42 0.00 0.00 3.06
1596 3717 6.261381 AGGCTTTGTAAACGTTTCAGACATTA 59.739 34.615 18.42 7.10 0.00 1.90
1597 3718 7.040686 AGGCTTTGTAAACGTTTCAGACATTAT 60.041 33.333 18.42 0.00 0.00 1.28
1598 3719 7.060633 GGCTTTGTAAACGTTTCAGACATTATG 59.939 37.037 18.42 6.29 0.00 1.90
1599 3720 7.409343 GCTTTGTAAACGTTTCAGACATTATGC 60.409 37.037 18.42 11.69 0.00 3.14
1600 3721 6.546972 TGTAAACGTTTCAGACATTATGCA 57.453 33.333 18.42 0.00 0.00 3.96
1601 3722 6.960468 TGTAAACGTTTCAGACATTATGCAA 58.040 32.000 18.42 0.00 0.00 4.08
1602 3723 7.418408 TGTAAACGTTTCAGACATTATGCAAA 58.582 30.769 18.42 0.00 0.00 3.68
1603 3724 7.915923 TGTAAACGTTTCAGACATTATGCAAAA 59.084 29.630 18.42 0.00 0.00 2.44
1604 3725 7.945033 AAACGTTTCAGACATTATGCAAAAT 57.055 28.000 7.96 0.00 0.00 1.82
1606 3727 9.469807 AAACGTTTCAGACATTATGCAAAATAA 57.530 25.926 7.96 0.00 0.00 1.40
1608 3729 8.296713 ACGTTTCAGACATTATGCAAAATAACT 58.703 29.630 0.00 0.00 0.00 2.24
1647 3903 8.717821 TCTGAAATGACTTATAAAAGTGAACGG 58.282 33.333 0.00 0.00 46.09 4.44
1654 3910 2.467566 TAAAAGTGAACGGAGGGAGC 57.532 50.000 0.00 0.00 0.00 4.70
1656 3912 0.472471 AAAGTGAACGGAGGGAGCAA 59.528 50.000 0.00 0.00 0.00 3.91
1675 3931 6.127980 GGAGCAATAAACTACTCCCTTTTGTC 60.128 42.308 0.00 0.00 42.44 3.18
1677 3933 6.655425 AGCAATAAACTACTCCCTTTTGTCTC 59.345 38.462 0.00 0.00 0.00 3.36
1682 3938 7.898014 AAACTACTCCCTTTTGTCTCAAAAT 57.102 32.000 7.87 0.00 0.00 1.82
1792 4054 9.780413 GAAACTTTTTGCTTATGATCTCTAAGG 57.220 33.333 13.87 3.49 0.00 2.69
1849 4118 9.665719 AACAGGAAAACAAGTCAATTACAAATT 57.334 25.926 0.00 0.00 0.00 1.82
2008 4281 9.487790 TTCATCCAATTAAACTCAACCATTTTC 57.512 29.630 0.00 0.00 0.00 2.29
2141 4414 9.830975 AAAATGGTGTTCAATAACTTTAAAGCT 57.169 25.926 15.24 5.71 36.51 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.703409 CCATAACGCTCGCTGCAC 59.297 61.111 0.00 0.00 43.06 4.57
54 55 1.934463 CATCACCCATAACGCTCGC 59.066 57.895 0.00 0.00 0.00 5.03
63 64 0.527565 GCTTCAAACGCATCACCCAT 59.472 50.000 0.00 0.00 0.00 4.00
104 105 2.053865 CATGACACCACCATGGGCC 61.054 63.158 18.09 0.00 43.37 5.80
105 106 1.304381 ACATGACACCACCATGGGC 60.304 57.895 18.09 0.00 43.37 5.36
106 107 0.329261 AGACATGACACCACCATGGG 59.671 55.000 18.09 4.89 43.37 4.00
107 108 1.456296 CAGACATGACACCACCATGG 58.544 55.000 11.19 11.19 44.11 3.66
124 125 1.586028 CGGCCAACATTTGTCCCAG 59.414 57.895 2.24 0.00 0.00 4.45
250 252 4.764050 TGCGAGGGGTTATTATCAGAAA 57.236 40.909 0.00 0.00 0.00 2.52
253 255 6.403636 GCATTTATGCGAGGGGTTATTATCAG 60.404 42.308 0.00 0.00 44.67 2.90
281 283 5.113502 GATGGAATCAATTCGATTGGGAC 57.886 43.478 7.55 0.00 44.65 4.46
317 319 0.601046 CATGGATGGATGGACGGACG 60.601 60.000 0.00 0.00 0.00 4.79
318 320 0.886490 GCATGGATGGATGGACGGAC 60.886 60.000 0.00 0.00 0.00 4.79
319 321 1.451504 GCATGGATGGATGGACGGA 59.548 57.895 0.00 0.00 0.00 4.69
320 322 1.601759 GGCATGGATGGATGGACGG 60.602 63.158 0.00 0.00 0.00 4.79
321 323 1.601759 GGGCATGGATGGATGGACG 60.602 63.158 0.00 0.00 0.00 4.79
357 359 3.205338 TCCATTGACAACGCATATGGAG 58.795 45.455 4.56 0.00 39.73 3.86
361 363 3.206150 GTCCTCCATTGACAACGCATAT 58.794 45.455 0.00 0.00 32.91 1.78
387 389 1.891722 GCTTGGCTGATTGGGGTTGG 61.892 60.000 0.00 0.00 0.00 3.77
388 390 1.593265 GCTTGGCTGATTGGGGTTG 59.407 57.895 0.00 0.00 0.00 3.77
389 391 1.610379 GGCTTGGCTGATTGGGGTT 60.610 57.895 0.00 0.00 0.00 4.11
390 392 2.037847 GGCTTGGCTGATTGGGGT 59.962 61.111 0.00 0.00 0.00 4.95
391 393 3.142838 CGGCTTGGCTGATTGGGG 61.143 66.667 0.00 0.00 37.02 4.96
392 394 3.830192 GCGGCTTGGCTGATTGGG 61.830 66.667 2.25 0.00 37.02 4.12
411 413 4.892433 AGAAGATGGAAGAGGATAATGCG 58.108 43.478 0.00 0.00 0.00 4.73
480 482 2.402572 GGCTCGGCTCTGCTTTTCC 61.403 63.158 0.00 0.00 0.00 3.13
602 2345 3.723235 CTCGATCCCGTGTGGCCTG 62.723 68.421 3.32 0.00 37.05 4.85
625 2511 3.372730 GCCTTTCCGCCATGCACA 61.373 61.111 0.00 0.00 0.00 4.57
670 2556 1.663702 CTGTGTGGAACGGTCGGTC 60.664 63.158 0.00 0.00 42.39 4.79
671 2557 2.420043 CTGTGTGGAACGGTCGGT 59.580 61.111 0.00 0.00 42.39 4.69
692 2578 1.626356 ATCGCTTGCCAGGGAAGCTA 61.626 55.000 35.10 28.24 44.66 3.32
715 2601 1.795170 GCTTCAACGGTGGTGTGCAT 61.795 55.000 0.00 0.00 0.00 3.96
735 2621 0.670854 AACGAGCGCCCTTCTTTCTC 60.671 55.000 2.29 0.00 0.00 2.87
818 2712 4.145807 TCAGAGAAAATTTTAACCCGGCA 58.854 39.130 2.75 0.00 0.00 5.69
882 2776 1.104577 GGCGTGAGGGTTTTGGAACA 61.105 55.000 0.00 0.00 37.51 3.18
1142 3089 2.815647 GGCAGTCGTAGCAGGTGC 60.816 66.667 0.00 0.00 42.49 5.01
1206 3153 0.105593 AGATGCACATGAGTAGGCCG 59.894 55.000 0.00 0.00 0.00 6.13
1226 3177 9.889128 TTGCTATACATACATACATGCATACAT 57.111 29.630 0.00 0.00 36.79 2.29
1227 3178 9.717942 TTTGCTATACATACATACATGCATACA 57.282 29.630 0.00 0.00 0.00 2.29
1228 3179 9.973246 GTTTGCTATACATACATACATGCATAC 57.027 33.333 0.00 0.00 31.22 2.39
1229 3180 9.942850 AGTTTGCTATACATACATACATGCATA 57.057 29.630 0.00 0.00 33.10 3.14
1230 3181 8.724229 CAGTTTGCTATACATACATACATGCAT 58.276 33.333 0.00 0.00 33.10 3.96
1231 3182 7.714813 ACAGTTTGCTATACATACATACATGCA 59.285 33.333 0.00 0.00 33.10 3.96
1232 3183 8.011673 CACAGTTTGCTATACATACATACATGC 58.988 37.037 0.00 0.00 33.10 4.06
1321 3275 7.726291 TGGACCAGAAGGAATAGAAGATAGTAG 59.274 40.741 0.00 0.00 38.69 2.57
1326 3280 6.838401 AATGGACCAGAAGGAATAGAAGAT 57.162 37.500 0.00 0.00 38.69 2.40
1334 3288 6.072175 CGACAATAAAAATGGACCAGAAGGAA 60.072 38.462 0.00 0.00 38.69 3.36
1349 3303 6.371809 ACTTCAGTTTGAGCGACAATAAAA 57.628 33.333 0.00 0.00 38.36 1.52
1352 3306 6.631016 AGATACTTCAGTTTGAGCGACAATA 58.369 36.000 0.00 0.00 38.36 1.90
1382 3336 7.062022 GTGTCTAGACGTATTTCAGACTTTTCC 59.938 40.741 17.85 0.00 37.20 3.13
1387 3341 6.761099 ATGTGTCTAGACGTATTTCAGACT 57.239 37.500 17.85 0.00 37.20 3.24
1388 3342 7.251994 AGAATGTGTCTAGACGTATTTCAGAC 58.748 38.462 17.85 7.68 33.56 3.51
1389 3343 7.392494 AGAATGTGTCTAGACGTATTTCAGA 57.608 36.000 17.85 0.00 33.56 3.27
1390 3344 8.467402 AAAGAATGTGTCTAGACGTATTTCAG 57.533 34.615 17.85 0.00 34.56 3.02
1391 3345 8.827177 AAAAGAATGTGTCTAGACGTATTTCA 57.173 30.769 17.85 9.91 34.56 2.69
1392 3346 8.922676 TGAAAAGAATGTGTCTAGACGTATTTC 58.077 33.333 17.85 17.74 34.56 2.17
1393 3347 8.827177 TGAAAAGAATGTGTCTAGACGTATTT 57.173 30.769 17.85 11.11 34.56 1.40
1394 3348 7.063544 GCTGAAAAGAATGTGTCTAGACGTATT 59.936 37.037 17.85 18.38 34.56 1.89
1395 3349 6.531948 GCTGAAAAGAATGTGTCTAGACGTAT 59.468 38.462 17.85 11.45 34.56 3.06
1406 3360 4.214980 AGTCGTTGCTGAAAAGAATGTG 57.785 40.909 0.00 0.00 0.00 3.21
1412 3366 6.662414 TCCATATTAGTCGTTGCTGAAAAG 57.338 37.500 0.00 0.00 0.00 2.27
1413 3367 7.766738 TGTATCCATATTAGTCGTTGCTGAAAA 59.233 33.333 0.00 0.00 0.00 2.29
1424 3378 5.163602 CGAGAGCCCTGTATCCATATTAGTC 60.164 48.000 0.00 0.00 0.00 2.59
1504 3462 7.419172 CCTCTTAGGGTTTATAAGGTCTGGAAG 60.419 44.444 0.00 0.00 32.24 3.46
1563 3684 9.798994 TGAAACGTTTACAAAGCCTTATAAAAA 57.201 25.926 14.65 0.00 0.00 1.94
1565 3686 8.838365 TCTGAAACGTTTACAAAGCCTTATAAA 58.162 29.630 14.65 0.00 0.00 1.40
1566 3687 8.284693 GTCTGAAACGTTTACAAAGCCTTATAA 58.715 33.333 14.65 0.00 0.00 0.98
1569 3690 5.585445 TGTCTGAAACGTTTACAAAGCCTTA 59.415 36.000 14.65 0.00 0.00 2.69
1571 3692 3.942748 TGTCTGAAACGTTTACAAAGCCT 59.057 39.130 14.65 0.00 0.00 4.58
1572 3693 4.281525 TGTCTGAAACGTTTACAAAGCC 57.718 40.909 14.65 0.00 0.00 4.35
1573 3694 7.409343 GCATAATGTCTGAAACGTTTACAAAGC 60.409 37.037 14.65 12.84 38.14 3.51
1574 3695 7.589587 TGCATAATGTCTGAAACGTTTACAAAG 59.410 33.333 14.65 9.49 38.14 2.77
1577 3698 6.546972 TGCATAATGTCTGAAACGTTTACA 57.453 33.333 14.65 15.08 38.14 2.41
1578 3699 7.845617 TTTGCATAATGTCTGAAACGTTTAC 57.154 32.000 14.65 9.46 38.14 2.01
1580 3701 7.945033 ATTTTGCATAATGTCTGAAACGTTT 57.055 28.000 14.57 14.57 38.14 3.60
1581 3702 8.911662 GTTATTTTGCATAATGTCTGAAACGTT 58.088 29.630 12.07 0.00 40.28 3.99
1583 3704 8.673626 AGTTATTTTGCATAATGTCTGAAACG 57.326 30.769 12.07 0.00 0.00 3.60
1620 3876 9.530129 CGTTCACTTTTATAAGTCATTTCAGAC 57.470 33.333 0.00 0.00 42.67 3.51
1624 3880 8.175716 CCTCCGTTCACTTTTATAAGTCATTTC 58.824 37.037 0.00 0.00 42.67 2.17
1628 3884 5.246656 TCCCTCCGTTCACTTTTATAAGTCA 59.753 40.000 0.00 0.00 42.67 3.41
1632 3888 4.020039 TGCTCCCTCCGTTCACTTTTATAA 60.020 41.667 0.00 0.00 0.00 0.98
1633 3889 3.516300 TGCTCCCTCCGTTCACTTTTATA 59.484 43.478 0.00 0.00 0.00 0.98
1637 3893 0.472471 TTGCTCCCTCCGTTCACTTT 59.528 50.000 0.00 0.00 0.00 2.66
1638 3894 0.693049 ATTGCTCCCTCCGTTCACTT 59.307 50.000 0.00 0.00 0.00 3.16
1639 3895 1.568504 TATTGCTCCCTCCGTTCACT 58.431 50.000 0.00 0.00 0.00 3.41
1640 3896 2.396590 TTATTGCTCCCTCCGTTCAC 57.603 50.000 0.00 0.00 0.00 3.18
1641 3897 2.304761 AGTTTATTGCTCCCTCCGTTCA 59.695 45.455 0.00 0.00 0.00 3.18
1654 3910 7.979444 TGAGACAAAAGGGAGTAGTTTATTG 57.021 36.000 0.00 0.00 0.00 1.90
1656 3912 8.990163 TTTTGAGACAAAAGGGAGTAGTTTAT 57.010 30.769 5.70 0.00 0.00 1.40
1669 3925 8.792633 CCATAGGTCTTACATTTTGAGACAAAA 58.207 33.333 11.14 11.14 41.15 2.44
1670 3926 7.942341 ACCATAGGTCTTACATTTTGAGACAAA 59.058 33.333 5.26 0.00 41.15 2.83
1675 3931 7.687941 ACAACCATAGGTCTTACATTTTGAG 57.312 36.000 0.00 0.00 33.12 3.02
1677 3933 9.010029 AGTTACAACCATAGGTCTTACATTTTG 57.990 33.333 0.00 0.00 33.12 2.44
1682 3938 6.921486 TGAGTTACAACCATAGGTCTTACA 57.079 37.500 0.00 0.00 33.12 2.41
1710 3966 3.115554 GCTTGTTTGTCGACTGCAATTT 58.884 40.909 17.92 0.00 0.00 1.82
1713 3969 1.090728 TGCTTGTTTGTCGACTGCAA 58.909 45.000 17.92 16.26 31.03 4.08
1802 4064 8.585018 CCTGTTTTCCCTTAATAATGTTTGTCT 58.415 33.333 0.00 0.00 0.00 3.41
1803 4065 8.581578 TCCTGTTTTCCCTTAATAATGTTTGTC 58.418 33.333 0.00 0.00 0.00 3.18
1804 4066 8.485578 TCCTGTTTTCCCTTAATAATGTTTGT 57.514 30.769 0.00 0.00 0.00 2.83
1960 4229 2.167075 GCTTGTTGCTATTTGGCTGGAT 59.833 45.455 0.00 0.00 38.95 3.41
2008 4281 3.329386 ACTCACTGAACATGAACCATCG 58.671 45.455 0.00 0.00 0.00 3.84
2119 4392 8.001881 TCAAGCTTTAAAGTTATTGAACACCA 57.998 30.769 20.60 6.49 38.10 4.17
2141 4414 3.640967 CCTCAAAACATTTGGGTCCTCAA 59.359 43.478 2.36 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.