Multiple sequence alignment - TraesCS5B01G245900

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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 TraesCS5B01G245900 chr5B 100.000 3029 0 0 556 3584 427238248 427241276 0.000000e+00 5594.0
1 TraesCS5B01G245900 chr5B 100.000 168 0 0 1 168 427237693 427237860 9.660000e-81 311.0
2 TraesCS5B01G245900 chr5A 89.062 3136 174 68 556 3582 462144634 462147709 0.000000e+00 3735.0
3 TraesCS5B01G245900 chr5A 91.429 140 11 1 30 168 462144464 462144603 1.310000e-44 191.0
4 TraesCS5B01G245900 chr5D 91.149 1898 81 44 556 2401 361605909 361607771 0.000000e+00 2494.0
5 TraesCS5B01G245900 chr5D 87.234 940 52 26 2687 3581 361609990 361610906 0.000000e+00 1009.0
6 TraesCS5B01G245900 chr5D 93.491 169 10 1 1 168 361605711 361605879 2.140000e-62 250.0
7 TraesCS5B01G245900 chr5D 87.500 232 9 10 2450 2667 361607780 361608005 2.140000e-62 250.0
8 TraesCS5B01G245900 chr4D 87.027 185 24 0 1299 1483 470506936 470507120 3.630000e-50 209.0
9 TraesCS5B01G245900 chr4B 87.027 185 24 0 1299 1483 592819783 592819967 3.630000e-50 209.0
10 TraesCS5B01G245900 chr2D 85.876 177 17 6 1321 1492 557795287 557795114 7.900000e-42 182.0
11 TraesCS5B01G245900 chr6D 85.802 162 23 0 1322 1483 423675471 423675632 4.760000e-39 172.0
12 TraesCS5B01G245900 chr2B 85.799 169 17 5 1321 1484 666089796 666089630 4.760000e-39 172.0
13 TraesCS5B01G245900 chr2B 85.799 169 17 5 1321 1484 666096234 666096068 4.760000e-39 172.0
14 TraesCS5B01G245900 chr6A 84.568 162 25 0 1322 1483 568015770 568015609 1.030000e-35 161.0
15 TraesCS5B01G245900 chr6A 86.441 59 8 0 1560 1618 552265722 552265780 8.310000e-07 65.8
16 TraesCS5B01G245900 chr6B 83.146 89 15 0 1560 1648 609887524 609887612 8.250000e-12 82.4


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 TraesCS5B01G245900 chr5B 427237693 427241276 3583 False 2952.50 5594 100.0000 1 3584 2 chr5B.!!$F1 3583
1 TraesCS5B01G245900 chr5A 462144464 462147709 3245 False 1963.00 3735 90.2455 30 3582 2 chr5A.!!$F1 3552
2 TraesCS5B01G245900 chr5D 361605711 361610906 5195 False 1000.75 2494 89.8435 1 3581 4 chr5D.!!$F1 3580

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
53 54 0.462759 ACCTCGCTAGAATTGGCAGC 60.463 55.0 0.00 0.0 0.00 5.25 F
1488 1530 0.519961 ACGCGCAAAGGGTAACATTC 59.480 50.0 5.73 0.0 41.67 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 1641 0.389817 CGAAGTTGATCGCACCTCCA 60.390 55.0 0.00 0.0 35.85 3.86 R
3238 5350 0.472734 ACCCTGTGTTCTGGAGCTCT 60.473 55.0 14.64 0.0 35.11 4.09 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
47 48 0.753262 ATCGGCACCTCGCTAGAATT 59.247 50.000 0.00 0.00 41.91 2.17
53 54 0.462759 ACCTCGCTAGAATTGGCAGC 60.463 55.000 0.00 0.00 0.00 5.25
95 98 1.896220 GGTCATCACCTCAGCACAAA 58.104 50.000 0.00 0.00 40.00 2.83
154 157 4.306600 CAGGCCAAAACCAAAGTTACATC 58.693 43.478 5.01 0.00 34.19 3.06
155 158 4.039124 CAGGCCAAAACCAAAGTTACATCT 59.961 41.667 5.01 0.00 34.19 2.90
157 160 4.306600 GCCAAAACCAAAGTTACATCTGG 58.693 43.478 0.00 0.00 34.19 3.86
597 600 5.507817 GCTGAGATCAACAAATTCCAACACA 60.508 40.000 0.00 0.00 0.00 3.72
748 761 2.035066 GCCCTCCCATCAATCAAAATCG 59.965 50.000 0.00 0.00 0.00 3.34
763 776 9.073368 CAATCAAAATCGTCCTATATAGTACCG 57.927 37.037 8.92 7.59 0.00 4.02
764 777 7.750229 TCAAAATCGTCCTATATAGTACCGT 57.250 36.000 8.92 0.00 0.00 4.83
765 778 7.587629 TCAAAATCGTCCTATATAGTACCGTG 58.412 38.462 8.92 3.14 0.00 4.94
766 779 5.557891 AATCGTCCTATATAGTACCGTGC 57.442 43.478 8.92 0.00 0.00 5.34
767 780 4.277515 TCGTCCTATATAGTACCGTGCT 57.722 45.455 8.92 0.00 0.00 4.40
768 781 4.248859 TCGTCCTATATAGTACCGTGCTC 58.751 47.826 8.92 0.00 0.00 4.26
769 782 3.373439 CGTCCTATATAGTACCGTGCTCC 59.627 52.174 8.92 0.00 0.00 4.70
770 783 4.330250 GTCCTATATAGTACCGTGCTCCA 58.670 47.826 8.92 0.00 0.00 3.86
771 784 4.155644 GTCCTATATAGTACCGTGCTCCAC 59.844 50.000 8.92 0.00 0.00 4.02
777 790 3.233919 TACCGTGCTCCACCCCTCT 62.234 63.158 0.00 0.00 0.00 3.69
810 828 3.953775 AACACGCCTCCCCCAGTG 61.954 66.667 0.00 0.00 40.17 3.66
825 843 2.112297 GTGCCACTCCGTTTCCCA 59.888 61.111 0.00 0.00 0.00 4.37
845 870 3.502455 CACACGCGGCAGCATCAT 61.502 61.111 12.47 0.00 45.49 2.45
859 884 3.036819 AGCATCATTCACAGGAGAGCTA 58.963 45.455 0.00 0.00 29.88 3.32
900 938 1.048724 GTGTCCATCTCCATCCCCGA 61.049 60.000 0.00 0.00 0.00 5.14
929 967 1.971167 TCGCCAACTTGCCATGGAC 60.971 57.895 18.40 7.64 39.12 4.02
947 985 0.900647 ACAAGACCTAGCCAGCTCGT 60.901 55.000 0.00 0.00 0.00 4.18
1392 1433 3.092511 AGCCAGCGGATGACCCAT 61.093 61.111 0.00 0.00 34.14 4.00
1488 1530 0.519961 ACGCGCAAAGGGTAACATTC 59.480 50.000 5.73 0.00 41.67 2.67
1502 1544 1.140161 CATTCACAGCCGCCATTGG 59.860 57.895 0.00 0.00 0.00 3.16
1519 1561 2.269241 GCCTCCTCGACCCCTTTG 59.731 66.667 0.00 0.00 0.00 2.77
1526 1585 1.318576 CTCGACCCCTTTGCTTTTGT 58.681 50.000 0.00 0.00 0.00 2.83
1527 1586 1.681264 CTCGACCCCTTTGCTTTTGTT 59.319 47.619 0.00 0.00 0.00 2.83
1531 1590 3.816523 CGACCCCTTTGCTTTTGTTACTA 59.183 43.478 0.00 0.00 0.00 1.82
1550 1609 1.238439 AAAGTGTGCGCTATTGCTGT 58.762 45.000 9.73 0.00 36.97 4.40
1572 1632 1.064240 TCTACGTAGGGTGATCAGGCA 60.064 52.381 22.01 0.00 0.00 4.75
1578 1638 4.017126 CGTAGGGTGATCAGGCATCTATA 58.983 47.826 0.00 0.00 31.92 1.31
1581 1641 4.497516 AGGGTGATCAGGCATCTATAGTT 58.502 43.478 0.00 0.00 31.92 2.24
1722 1785 1.202940 GCCAACTTCTTCACCTTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
2034 2108 0.109412 GTAGCACGCCTACACGTTCT 60.109 55.000 8.49 0.00 45.75 3.01
2053 2127 4.895668 TCTCCCCGTACAAGTAAACAAT 57.104 40.909 0.00 0.00 0.00 2.71
2109 2184 1.074248 CCAAGGGGTTTACGGCAGT 59.926 57.895 0.00 0.00 0.00 4.40
2111 2186 1.445871 CAAGGGGTTTACGGCAGTAC 58.554 55.000 0.00 0.00 31.60 2.73
2173 2253 0.842467 AGCTGGTGCCTAGGTTTCCT 60.842 55.000 11.31 0.00 40.80 3.36
2266 2346 4.923415 ACCTCAGCAAACCTAGCTAAAAT 58.077 39.130 0.00 0.00 41.14 1.82
2267 2347 5.325239 ACCTCAGCAAACCTAGCTAAAATT 58.675 37.500 0.00 0.00 41.14 1.82
2367 2455 5.883685 ATAACCCTAGGCCTAGTAACAAC 57.116 43.478 33.00 0.00 0.00 3.32
2392 2481 5.185828 AGCTTTGCGATTCCTTCCTAAAAAT 59.814 36.000 0.00 0.00 0.00 1.82
2394 2483 7.068716 AGCTTTGCGATTCCTTCCTAAAAATAT 59.931 33.333 0.00 0.00 0.00 1.28
2450 2539 4.363034 GCCCTAGGCGTAATCTGC 57.637 61.111 2.05 0.00 39.62 4.26
2451 2540 1.664965 GCCCTAGGCGTAATCTGCG 60.665 63.158 2.05 0.00 39.62 5.18
2452 2541 1.740285 CCCTAGGCGTAATCTGCGT 59.260 57.895 2.05 0.00 0.00 5.24
2453 2542 0.956633 CCCTAGGCGTAATCTGCGTA 59.043 55.000 2.05 0.00 0.00 4.42
2454 2543 1.338973 CCCTAGGCGTAATCTGCGTAA 59.661 52.381 2.05 0.00 32.92 3.18
2455 2544 2.029290 CCCTAGGCGTAATCTGCGTAAT 60.029 50.000 2.05 0.00 32.92 1.89
2456 2545 3.243336 CCTAGGCGTAATCTGCGTAATC 58.757 50.000 0.00 0.00 32.92 1.75
2457 2546 3.057456 CCTAGGCGTAATCTGCGTAATCT 60.057 47.826 0.00 0.00 32.92 2.40
2458 2547 2.743938 AGGCGTAATCTGCGTAATCTG 58.256 47.619 0.00 0.00 0.00 2.90
2459 2548 2.361119 AGGCGTAATCTGCGTAATCTGA 59.639 45.455 0.00 0.00 0.00 3.27
2460 2549 3.005897 AGGCGTAATCTGCGTAATCTGAT 59.994 43.478 0.00 0.00 0.00 2.90
2461 2550 3.121944 GGCGTAATCTGCGTAATCTGATG 59.878 47.826 0.00 0.00 0.00 3.07
2674 2773 5.163513 GTGCAAACCAATAAAGTCCATCTG 58.836 41.667 0.00 0.00 0.00 2.90
2691 4755 3.220507 TCTGTGCAATGCAATGCTTAC 57.779 42.857 26.10 17.54 46.54 2.34
2742 4811 7.604549 TGAATTTGTTCATAATGTGCATCAGT 58.395 30.769 0.00 0.00 0.00 3.41
2777 4850 2.834549 AGAGTAGCTAGGCATGTGTTGT 59.165 45.455 0.00 0.00 0.00 3.32
2788 4861 3.443976 GCATGTGTTGTTTCTTCGGTTT 58.556 40.909 0.00 0.00 0.00 3.27
2793 4866 6.931243 TGTGTTGTTTCTTCGGTTTAAAAC 57.069 33.333 0.00 0.00 33.32 2.43
2795 4868 4.558080 TGTTGTTTCTTCGGTTTAAAACGC 59.442 37.500 20.68 6.27 35.00 4.84
2828 4914 2.224018 TGCAATGCTTCCAAACCACTTC 60.224 45.455 6.82 0.00 0.00 3.01
2833 4919 3.360867 TGCTTCCAAACCACTTCAAAGA 58.639 40.909 0.00 0.00 0.00 2.52
2913 5011 1.179174 CCGTGCTCCATAGGATCGGA 61.179 60.000 14.64 0.00 40.14 4.55
3004 5102 1.895798 TGCCAAAACACCAACAGACAA 59.104 42.857 0.00 0.00 0.00 3.18
3023 5121 5.073144 AGACAACATCTCCCTTTTAGTTCCA 59.927 40.000 0.00 0.00 28.16 3.53
3034 5132 5.761726 CCCTTTTAGTTCCAAAACGAGTAGT 59.238 40.000 0.00 0.00 40.48 2.73
3039 5137 8.524870 TTTAGTTCCAAAACGAGTAGTATGAC 57.475 34.615 0.00 0.00 40.48 3.06
3072 5170 6.797707 TCCTTAATCGGGTATACTGGATACT 58.202 40.000 9.78 0.00 40.42 2.12
3077 5175 5.784398 TCGGGTATACTGGATACTGGATA 57.216 43.478 9.78 0.00 40.09 2.59
3078 5176 6.337185 TCGGGTATACTGGATACTGGATAT 57.663 41.667 9.78 0.00 42.56 1.63
3079 5177 6.738635 TCGGGTATACTGGATACTGGATATT 58.261 40.000 9.78 0.00 42.56 1.28
3080 5178 7.875311 TCGGGTATACTGGATACTGGATATTA 58.125 38.462 9.78 0.00 42.56 0.98
3082 5180 7.997223 CGGGTATACTGGATACTGGATATTAGA 59.003 40.741 9.78 0.00 42.56 2.10
3083 5181 9.357161 GGGTATACTGGATACTGGATATTAGAG 57.643 40.741 9.78 0.00 42.56 2.43
3084 5182 9.924010 GGTATACTGGATACTGGATATTAGAGT 57.076 37.037 9.78 0.00 42.56 3.24
3089 5187 8.754080 ACTGGATACTGGATATTAGAGTAATGC 58.246 37.037 0.00 0.00 40.36 3.56
3090 5188 8.664669 TGGATACTGGATATTAGAGTAATGCA 57.335 34.615 0.00 0.00 37.61 3.96
3139 5241 4.684484 AGTCCGTTTCTGTAAAGAAGGT 57.316 40.909 0.00 0.00 0.00 3.50
3174 5278 2.414994 AAGCAGCATAGCACAGACAT 57.585 45.000 0.00 0.00 36.85 3.06
3177 5281 1.598132 GCAGCATAGCACAGACATGAG 59.402 52.381 0.00 0.00 0.00 2.90
3181 5285 1.591619 CATAGCACAGACATGAGCACG 59.408 52.381 0.00 0.00 44.51 5.34
3184 5288 1.004560 CACAGACATGAGCACGGGT 60.005 57.895 0.00 0.00 0.00 5.28
3206 5318 4.776349 TCAGGCAGTACTGAAAAGTGAAA 58.224 39.130 27.08 0.00 44.03 2.69
3207 5319 5.189928 TCAGGCAGTACTGAAAAGTGAAAA 58.810 37.500 27.08 0.00 44.03 2.29
3209 5321 4.036852 AGGCAGTACTGAAAAGTGAAAAGC 59.963 41.667 27.08 5.76 0.00 3.51
3210 5322 4.290969 GCAGTACTGAAAAGTGAAAAGCC 58.709 43.478 27.08 0.00 0.00 4.35
3211 5323 4.202010 GCAGTACTGAAAAGTGAAAAGCCA 60.202 41.667 27.08 0.00 0.00 4.75
3212 5324 5.678616 GCAGTACTGAAAAGTGAAAAGCCAA 60.679 40.000 27.08 0.00 0.00 4.52
3213 5325 6.507023 CAGTACTGAAAAGTGAAAAGCCAAT 58.493 36.000 18.45 0.00 0.00 3.16
3214 5326 6.638468 CAGTACTGAAAAGTGAAAAGCCAATC 59.362 38.462 18.45 0.00 0.00 2.67
3229 5341 1.402968 CCAATCGATGCCAAGACAAGG 59.597 52.381 0.00 0.00 0.00 3.61
3238 5350 2.705658 TGCCAAGACAAGGAGAAGAGAA 59.294 45.455 0.00 0.00 0.00 2.87
3256 5368 0.689623 AAGAGCTCCAGAACACAGGG 59.310 55.000 10.93 0.00 0.00 4.45
3257 5369 0.472734 AGAGCTCCAGAACACAGGGT 60.473 55.000 10.93 0.00 0.00 4.34
3258 5370 1.203187 AGAGCTCCAGAACACAGGGTA 60.203 52.381 10.93 0.00 0.00 3.69
3260 5372 0.389948 GCTCCAGAACACAGGGTACG 60.390 60.000 0.00 0.00 0.00 3.67
3261 5373 1.254026 CTCCAGAACACAGGGTACGA 58.746 55.000 0.00 0.00 0.00 3.43
3262 5374 1.202582 CTCCAGAACACAGGGTACGAG 59.797 57.143 0.00 0.00 0.00 4.18
3263 5375 0.966920 CCAGAACACAGGGTACGAGT 59.033 55.000 0.00 0.00 0.00 4.18
3289 5403 0.250553 GTGTCGTCCCATTGACCCAA 60.251 55.000 0.00 0.00 41.18 4.12
3372 5486 4.740634 GCATGATTGACCGAATAGTGGAGA 60.741 45.833 0.00 0.00 0.00 3.71
3377 5501 0.032017 ACCGAATAGTGGAGAGGGCT 60.032 55.000 0.00 0.00 0.00 5.19
3380 5515 1.127343 GAATAGTGGAGAGGGCTGCT 58.873 55.000 0.00 0.00 33.04 4.24
3498 5633 1.144936 CCCGAGATGTTCTGCTCCC 59.855 63.158 0.00 0.00 0.00 4.30
3514 5650 2.128035 CTCCCATCGATGTAACTTCGC 58.872 52.381 23.27 0.00 36.56 4.70
3518 5654 1.593006 CATCGATGTAACTTCGCCCAC 59.407 52.381 17.50 0.00 36.56 4.61
3551 5693 0.107165 GCCTCGCCTGGGAGTAAAAT 60.107 55.000 9.94 0.00 31.98 1.82
3556 5698 4.451900 CTCGCCTGGGAGTAAAATAATGT 58.548 43.478 3.24 0.00 0.00 2.71
3557 5699 5.454187 CCTCGCCTGGGAGTAAAATAATGTA 60.454 44.000 9.94 0.00 31.98 2.29
3558 5700 5.362263 TCGCCTGGGAGTAAAATAATGTAC 58.638 41.667 0.00 0.00 0.00 2.90
3582 5724 0.183492 AAGGCAGCAACTTCAGTGGA 59.817 50.000 0.00 0.00 0.00 4.02
3583 5725 0.250640 AGGCAGCAACTTCAGTGGAG 60.251 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.531365 CAAACCCTTCCTGCTGCCA 60.531 57.895 0.00 0.00 0.00 4.92
53 54 2.299867 CAACATTCCCAAACCCTTCCTG 59.700 50.000 0.00 0.00 0.00 3.86
567 570 5.525378 GGAATTTGTTGATCTCAGCTCGTAT 59.475 40.000 0.00 0.00 0.00 3.06
568 571 4.870426 GGAATTTGTTGATCTCAGCTCGTA 59.130 41.667 0.00 0.00 0.00 3.43
619 622 2.568090 GTGGGAAAGCGGCACATG 59.432 61.111 1.45 0.00 0.00 3.21
748 761 4.155644 GTGGAGCACGGTACTATATAGGAC 59.844 50.000 15.84 15.84 36.39 3.85
761 774 3.775654 GAGAGGGGTGGAGCACGG 61.776 72.222 0.00 0.00 34.83 4.94
762 775 3.775654 GGAGAGGGGTGGAGCACG 61.776 72.222 0.00 0.00 34.83 5.34
763 776 2.607750 TGGAGAGGGGTGGAGCAC 60.608 66.667 0.00 0.00 0.00 4.40
764 777 2.607750 GTGGAGAGGGGTGGAGCA 60.608 66.667 0.00 0.00 0.00 4.26
765 778 3.403558 GGTGGAGAGGGGTGGAGC 61.404 72.222 0.00 0.00 0.00 4.70
766 779 3.077556 CGGTGGAGAGGGGTGGAG 61.078 72.222 0.00 0.00 0.00 3.86
767 780 4.715130 CCGGTGGAGAGGGGTGGA 62.715 72.222 0.00 0.00 0.00 4.02
810 828 2.626780 GCTTGGGAAACGGAGTGGC 61.627 63.158 0.00 0.00 45.00 5.01
839 857 2.328819 AGCTCTCCTGTGAATGATGC 57.671 50.000 0.00 0.00 0.00 3.91
859 884 0.176910 GAAGCGAAGGGAGCTAAGCT 59.823 55.000 0.00 0.00 45.31 3.74
900 938 4.178169 TTGGCGACGGTTGGTGGT 62.178 61.111 0.00 0.00 0.00 4.16
929 967 0.459237 CACGAGCTGGCTAGGTCTTG 60.459 60.000 24.24 21.44 46.65 3.02
947 985 0.178964 CTCCCAAGGACCAAAAGGCA 60.179 55.000 0.00 0.00 0.00 4.75
1158 1199 2.507102 AGCATGGACGAGAACGCG 60.507 61.111 3.53 3.53 43.96 6.01
1163 1204 2.125391 GCAGCAGCATGGACGAGA 60.125 61.111 0.00 0.00 41.58 4.04
1170 1211 2.046864 AGCTTGAGGCAGCAGCATG 61.047 57.895 2.65 0.00 42.84 4.06
1250 1291 2.441348 TCATCTCGCCGCCACCTA 60.441 61.111 0.00 0.00 0.00 3.08
1392 1433 2.125872 TTGCGCTCGACGGCAATA 60.126 55.556 9.73 0.00 43.93 1.90
1502 1544 2.269241 CAAAGGGGTCGAGGAGGC 59.731 66.667 0.00 0.00 0.00 4.70
1519 1561 3.420904 GCGCACACTTTAGTAACAAAAGC 59.579 43.478 0.30 0.00 37.44 3.51
1526 1585 4.593597 GCAATAGCGCACACTTTAGTAA 57.406 40.909 11.47 0.00 0.00 2.24
1550 1609 2.651455 CCTGATCACCCTACGTAGACA 58.349 52.381 24.15 11.75 0.00 3.41
1572 1632 4.152647 TGATCGCACCTCCAACTATAGAT 58.847 43.478 6.78 0.00 0.00 1.98
1578 1638 0.687354 AGTTGATCGCACCTCCAACT 59.313 50.000 0.00 0.00 42.85 3.16
1581 1641 0.389817 CGAAGTTGATCGCACCTCCA 60.390 55.000 0.00 0.00 35.85 3.86
1722 1785 2.099263 GGTAGCGCTCATTGAGTACTGA 59.901 50.000 16.34 0.00 31.39 3.41
1769 1835 2.903357 CACCCTCACCCTCATCGG 59.097 66.667 0.00 0.00 0.00 4.18
1771 1837 2.592308 GGCACCCTCACCCTCATC 59.408 66.667 0.00 0.00 0.00 2.92
1773 1839 4.631740 TCGGCACCCTCACCCTCA 62.632 66.667 0.00 0.00 0.00 3.86
2034 2108 4.325972 GGAATTGTTTACTTGTACGGGGA 58.674 43.478 0.00 0.00 0.00 4.81
2053 2127 2.441410 TGCATATCACAAAAGCCGGAA 58.559 42.857 5.05 0.00 0.00 4.30
2137 2217 2.615447 CAGCTTGTTTCAGACTGAAGCA 59.385 45.455 25.47 25.47 44.01 3.91
2173 2253 5.220491 GGACAACGCAAAATACAAAAAGCAA 60.220 36.000 0.00 0.00 0.00 3.91
2266 2346 1.890041 CTGGAAACACGCCGGACAA 60.890 57.895 5.05 0.00 35.60 3.18
2267 2347 2.280524 CTGGAAACACGCCGGACA 60.281 61.111 5.05 0.00 35.60 4.02
2367 2455 1.457346 AGGAAGGAATCGCAAAGCTG 58.543 50.000 0.00 0.00 0.00 4.24
2401 2490 7.201145 AGCTTGAATGATGCATTTAAGTGATC 58.799 34.615 19.25 3.44 44.13 2.92
2450 2539 6.808008 AATATTTCCAGCCATCAGATTACG 57.192 37.500 0.00 0.00 0.00 3.18
2451 2540 6.865205 GCAAATATTTCCAGCCATCAGATTAC 59.135 38.462 0.00 0.00 0.00 1.89
2452 2541 6.550481 TGCAAATATTTCCAGCCATCAGATTA 59.450 34.615 0.00 0.00 0.00 1.75
2453 2542 5.364446 TGCAAATATTTCCAGCCATCAGATT 59.636 36.000 0.00 0.00 0.00 2.40
2454 2543 4.897076 TGCAAATATTTCCAGCCATCAGAT 59.103 37.500 0.00 0.00 0.00 2.90
2455 2544 4.279982 TGCAAATATTTCCAGCCATCAGA 58.720 39.130 0.00 0.00 0.00 3.27
2456 2545 4.500887 CCTGCAAATATTTCCAGCCATCAG 60.501 45.833 12.87 1.64 0.00 2.90
2457 2546 3.385433 CCTGCAAATATTTCCAGCCATCA 59.615 43.478 12.87 0.00 0.00 3.07
2458 2547 3.385755 ACCTGCAAATATTTCCAGCCATC 59.614 43.478 12.87 0.00 0.00 3.51
2459 2548 3.133362 CACCTGCAAATATTTCCAGCCAT 59.867 43.478 12.87 0.00 0.00 4.40
2460 2549 2.496871 CACCTGCAAATATTTCCAGCCA 59.503 45.455 12.87 0.00 0.00 4.75
2461 2550 2.159057 CCACCTGCAAATATTTCCAGCC 60.159 50.000 12.87 0.00 0.00 4.85
2674 2773 1.657094 GCAGTAAGCATTGCATTGCAC 59.343 47.619 29.40 21.12 45.23 4.57
2691 4755 4.994907 TTTTCATCCATGGATTCAGCAG 57.005 40.909 25.20 12.51 31.62 4.24
2742 4811 6.207614 CCTAGCTACTCTACATGCAACATCTA 59.792 42.308 0.00 0.00 0.00 1.98
2777 4850 2.286891 CCCGCGTTTTAAACCGAAGAAA 60.287 45.455 9.52 0.00 0.00 2.52
2788 4861 1.599606 ATTGCATGCCCCGCGTTTTA 61.600 50.000 16.68 0.00 0.00 1.52
2828 4914 5.640189 ATTGTTCTCTGCCTTCATCTTTG 57.360 39.130 0.00 0.00 0.00 2.77
2833 4919 4.038271 TGGAATTGTTCTCTGCCTTCAT 57.962 40.909 0.00 0.00 0.00 2.57
2913 5011 3.723172 CGCAGCTGACAACAGTGT 58.277 55.556 20.43 0.00 45.04 3.55
2975 5073 1.416030 GGTGTTTTGGCAGGAAATGGT 59.584 47.619 0.00 0.00 0.00 3.55
3004 5102 5.240844 CGTTTTGGAACTAAAAGGGAGATGT 59.759 40.000 7.73 0.00 33.88 3.06
3023 5121 9.953697 GATCTAATCAGTCATACTACTCGTTTT 57.046 33.333 0.00 0.00 0.00 2.43
3034 5132 7.674348 ACCCGATTAAGGATCTAATCAGTCATA 59.326 37.037 12.63 0.00 37.91 2.15
3039 5137 9.191479 AGTATACCCGATTAAGGATCTAATCAG 57.809 37.037 12.63 7.42 37.91 2.90
3080 5178 8.646004 ACACTGAAGATATGTATGCATTACTCT 58.354 33.333 3.54 0.00 36.58 3.24
3082 5180 7.172190 GCACACTGAAGATATGTATGCATTACT 59.828 37.037 3.54 0.00 36.58 2.24
3083 5181 7.293745 GCACACTGAAGATATGTATGCATTAC 58.706 38.462 3.54 1.81 36.58 1.89
3084 5182 6.427853 GGCACACTGAAGATATGTATGCATTA 59.572 38.462 3.54 0.00 36.58 1.90
3085 5183 5.240183 GGCACACTGAAGATATGTATGCATT 59.760 40.000 3.54 0.00 36.58 3.56
3087 5185 4.129380 GGCACACTGAAGATATGTATGCA 58.871 43.478 0.00 0.00 0.00 3.96
3088 5186 4.129380 TGGCACACTGAAGATATGTATGC 58.871 43.478 0.00 0.00 0.00 3.14
3139 5241 3.679389 CTGCTTTCTCTAAAAGGCTCCA 58.321 45.455 0.00 0.00 32.84 3.86
3174 5278 4.007644 CTGCCTGACCCGTGCTCA 62.008 66.667 0.00 0.00 0.00 4.26
3177 5281 2.434359 GTACTGCCTGACCCGTGC 60.434 66.667 0.00 0.00 0.00 5.34
3181 5285 2.224548 ACTTTTCAGTACTGCCTGACCC 60.225 50.000 18.45 0.00 41.05 4.46
3184 5288 4.415881 TTCACTTTTCAGTACTGCCTGA 57.584 40.909 18.45 10.11 39.65 3.86
3209 5321 1.402968 CCTTGTCTTGGCATCGATTGG 59.597 52.381 0.00 0.00 0.00 3.16
3210 5322 2.353889 CTCCTTGTCTTGGCATCGATTG 59.646 50.000 0.00 0.00 0.00 2.67
3211 5323 2.237143 TCTCCTTGTCTTGGCATCGATT 59.763 45.455 0.00 0.00 0.00 3.34
3212 5324 1.833630 TCTCCTTGTCTTGGCATCGAT 59.166 47.619 0.00 0.00 0.00 3.59
3213 5325 1.266178 TCTCCTTGTCTTGGCATCGA 58.734 50.000 0.00 0.00 0.00 3.59
3214 5326 2.005451 CTTCTCCTTGTCTTGGCATCG 58.995 52.381 0.00 0.00 0.00 3.84
3229 5341 3.509575 TGTTCTGGAGCTCTTCTCTTCTC 59.490 47.826 14.64 0.00 41.60 2.87
3238 5350 0.472734 ACCCTGTGTTCTGGAGCTCT 60.473 55.000 14.64 0.00 35.11 4.09
3247 5359 2.132762 CACAACTCGTACCCTGTGTTC 58.867 52.381 0.00 0.00 35.52 3.18
3256 5368 1.602877 CGACACGGCACAACTCGTAC 61.603 60.000 0.00 0.00 37.88 3.67
3257 5369 1.370778 CGACACGGCACAACTCGTA 60.371 57.895 0.00 0.00 37.88 3.43
3258 5370 2.657296 CGACACGGCACAACTCGT 60.657 61.111 0.00 0.00 40.49 4.18
3260 5372 2.308039 GGACGACACGGCACAACTC 61.308 63.158 0.00 0.00 36.10 3.01
3261 5373 2.279918 GGACGACACGGCACAACT 60.280 61.111 0.00 0.00 36.10 3.16
3262 5374 3.343421 GGGACGACACGGCACAAC 61.343 66.667 0.00 0.00 38.67 3.32
3289 5403 5.257262 GCCCTGTTCTAGAATCTTTTTCCT 58.743 41.667 8.75 0.00 0.00 3.36
3372 5486 2.348998 CAGAAACGGAGCAGCCCT 59.651 61.111 0.00 0.00 0.00 5.19
3377 5501 1.227409 TGTTCGCAGAAACGGAGCA 60.227 52.632 0.00 0.00 45.90 4.26
3405 5540 3.700970 TCGAATCAGCCGGGTGCA 61.701 61.111 28.72 17.43 44.83 4.57
3478 5613 1.144936 GAGCAGAACATCTCGGGGG 59.855 63.158 0.00 0.00 0.00 5.40
3498 5633 1.593006 GTGGGCGAAGTTACATCGATG 59.407 52.381 23.68 23.68 42.76 3.84
3518 5654 0.739813 CGAGGCTCCACCCTTTTACG 60.740 60.000 9.32 0.00 40.58 3.18
3551 5693 6.049955 AGTTGCTGCCTTTCTAGTACATTA 57.950 37.500 0.00 0.00 0.00 1.90
3556 5698 4.040461 ACTGAAGTTGCTGCCTTTCTAGTA 59.960 41.667 0.00 0.00 0.00 1.82
3557 5699 3.181450 ACTGAAGTTGCTGCCTTTCTAGT 60.181 43.478 0.00 3.07 0.00 2.57
3558 5700 3.188048 CACTGAAGTTGCTGCCTTTCTAG 59.812 47.826 0.00 2.54 0.00 2.43


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

AutoCloner maintained by Alex Coulton.