Multiple sequence alignment - TraesCS2D01G037000

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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 TraesCS2D01G037000 chr2D 100.000 3496 0 0 1 3496 13775579 13772084 0.000000e+00 6457.0
1 TraesCS2D01G037000 chr2A 93.882 2566 123 26 947 3496 15964212 15961665 0.000000e+00 3838.0
2 TraesCS2D01G037000 chr2A 81.234 762 68 31 1 730 15966784 15966066 2.370000e-151 545.0
3 TraesCS2D01G037000 chr2A 92.453 53 2 2 657 708 560849669 560849618 1.350000e-09 75.0
4 TraesCS2D01G037000 chr2B 92.542 2628 128 28 897 3496 25073597 25071010 0.000000e+00 3705.0
5 TraesCS2D01G037000 chr2B 80.065 306 31 9 421 708 25074008 25073715 2.130000e-47 200.0
6 TraesCS2D01G037000 chr2B 92.000 50 4 0 657 706 773655613 773655662 1.740000e-08 71.3


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 TraesCS2D01G037000 chr2D 13772084 13775579 3495 True 6457.0 6457 100.0000 1 3496 1 chr2D.!!$R1 3495
1 TraesCS2D01G037000 chr2A 15961665 15966784 5119 True 2191.5 3838 87.5580 1 3496 2 chr2A.!!$R2 3495
2 TraesCS2D01G037000 chr2B 25071010 25074008 2998 True 1952.5 3705 86.3035 421 3496 2 chr2B.!!$R1 3075

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
109 111 0.388134 ACTTTGGTCGTCGTCCATCG 60.388 55.0 12.02 8.62 41.41 3.84 F
1020 2718 0.180642 TATAAAACGGCGCCCATGGA 59.819 50.0 23.46 3.82 0.00 3.41 F
1735 3469 0.676782 AATTCAGGCGTTCCTTCGGG 60.677 55.0 0.00 0.00 41.93 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 3105 0.031314 CGTCCAGCGACAGATAGCAT 59.969 55.0 0.00 0.0 44.77 3.79 R
2474 4215 0.042880 CACGTAAACAGCGCAAACGA 60.043 50.0 21.01 0.0 43.93 3.85 R
2941 4684 0.319555 CTCGACACCAAAAGCCGAGA 60.320 55.0 0.00 0.0 46.62 4.04 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
39 41 5.765182 CCATACAGTATGAAAGATTGGTCCC 59.235 44.000 20.55 0.00 39.69 4.46
40 42 4.927267 ACAGTATGAAAGATTGGTCCCA 57.073 40.909 0.00 0.00 39.69 4.37
41 43 5.456921 ACAGTATGAAAGATTGGTCCCAT 57.543 39.130 0.00 0.00 39.69 4.00
42 44 5.195940 ACAGTATGAAAGATTGGTCCCATG 58.804 41.667 0.00 0.00 39.69 3.66
82 84 1.371558 GCTCCAACCTCCACGTCTT 59.628 57.895 0.00 0.00 0.00 3.01
102 104 3.411351 CCGCCACTTTGGTCGTCG 61.411 66.667 7.81 0.00 40.46 5.12
109 111 0.388134 ACTTTGGTCGTCGTCCATCG 60.388 55.000 12.02 8.62 41.41 3.84
117 119 4.736739 TCGTCCATCGACTGGTCT 57.263 55.556 11.91 0.00 46.08 3.85
120 122 1.817209 GTCCATCGACTGGTCTCCC 59.183 63.158 11.91 0.00 46.08 4.30
124 126 1.982395 ATCGACTGGTCTCCCGCAA 60.982 57.895 0.00 0.00 0.00 4.85
134 136 2.427506 GTCTCCCGCAAGAGTGAAATT 58.572 47.619 0.31 0.00 43.02 1.82
136 138 2.813754 TCTCCCGCAAGAGTGAAATTTG 59.186 45.455 0.00 0.00 43.02 2.32
167 174 2.616960 TGATCAAAATCGTGGAGTCGG 58.383 47.619 0.00 0.00 34.39 4.79
187 194 7.106239 AGTCGGTCATAATCAAACTCTCAAAT 58.894 34.615 0.00 0.00 0.00 2.32
214 221 6.128472 CCAAATTCTAAAAATCAGCACCTTGC 60.128 38.462 0.00 0.00 45.46 4.01
235 249 3.750130 GCACTTCCTAGCATCACCATATG 59.250 47.826 0.00 0.00 0.00 1.78
246 260 5.008331 GCATCACCATATGTCAAGGATCAT 58.992 41.667 1.24 0.00 0.00 2.45
247 261 6.013119 AGCATCACCATATGTCAAGGATCATA 60.013 38.462 1.24 0.00 0.00 2.15
248 262 6.827251 GCATCACCATATGTCAAGGATCATAT 59.173 38.462 1.24 0.00 37.62 1.78
249 263 7.989170 GCATCACCATATGTCAAGGATCATATA 59.011 37.037 1.24 0.00 36.07 0.86
284 300 2.482721 ACATCCTTACAGAAAAACCGCG 59.517 45.455 0.00 0.00 0.00 6.46
286 302 3.383620 TCCTTACAGAAAAACCGCGTA 57.616 42.857 4.92 0.00 0.00 4.42
304 320 2.221906 TAGCTTCCCGACAACCTCGC 62.222 60.000 0.00 0.00 41.46 5.03
305 321 2.434359 CTTCCCGACAACCTCGCC 60.434 66.667 0.00 0.00 41.46 5.54
306 322 4.367023 TTCCCGACAACCTCGCCG 62.367 66.667 0.00 0.00 41.46 6.46
359 375 1.896220 CCTTCTTTGCAGTGCACCTA 58.104 50.000 19.58 0.00 38.71 3.08
360 376 1.808945 CCTTCTTTGCAGTGCACCTAG 59.191 52.381 19.58 15.24 38.71 3.02
378 394 2.034532 CCTCAGCCATGGTGCACA 59.965 61.111 20.43 5.24 0.00 4.57
380 396 1.601477 CTCAGCCATGGTGCACACA 60.601 57.895 20.43 14.54 0.00 3.72
391 407 2.104622 TGGTGCACACAATCTCTCTCAA 59.895 45.455 20.43 0.00 0.00 3.02
392 408 2.481952 GGTGCACACAATCTCTCTCAAC 59.518 50.000 20.43 0.00 0.00 3.18
404 420 0.798771 CTCTCAACAGCTACGTCGGC 60.799 60.000 0.00 0.00 0.00 5.54
479 495 3.686016 TGTGTTGAGGATTAAGGAAGGC 58.314 45.455 0.00 0.00 0.00 4.35
510 528 4.827692 TGCAAGTTATCGGTCTGTATGTT 58.172 39.130 0.00 0.00 0.00 2.71
517 551 2.683968 TCGGTCTGTATGTTGACTTGC 58.316 47.619 0.00 0.00 34.01 4.01
524 558 5.565259 GTCTGTATGTTGACTTGCATTTTCG 59.435 40.000 0.00 0.00 0.00 3.46
534 568 0.958091 TGCATTTTCGAGTGGTTGGG 59.042 50.000 0.00 0.00 0.00 4.12
538 572 3.673323 GCATTTTCGAGTGGTTGGGATTC 60.673 47.826 0.00 0.00 0.00 2.52
549 583 3.173151 GGTTGGGATTCCAGGTTTTGAT 58.827 45.455 4.80 0.00 45.04 2.57
550 584 4.202727 TGGTTGGGATTCCAGGTTTTGATA 60.203 41.667 4.80 0.00 45.04 2.15
551 585 4.775253 GGTTGGGATTCCAGGTTTTGATAA 59.225 41.667 4.80 0.00 45.04 1.75
564 598 6.204688 CAGGTTTTGATAATAAGCTCGCCATA 59.795 38.462 0.00 0.00 30.26 2.74
571 605 4.836125 AATAAGCTCGCCATAACAATGG 57.164 40.909 0.00 0.00 44.44 3.16
607 641 3.126831 CAGCTCCTATCCGTTGTTCATC 58.873 50.000 0.00 0.00 0.00 2.92
608 642 3.034635 AGCTCCTATCCGTTGTTCATCT 58.965 45.455 0.00 0.00 0.00 2.90
611 645 4.794655 GCTCCTATCCGTTGTTCATCTCTC 60.795 50.000 0.00 0.00 0.00 3.20
628 662 6.317140 TCATCTCTCAAACCAAACATATGAGC 59.683 38.462 10.38 0.00 37.89 4.26
632 666 1.102978 AACCAAACATATGAGCGGCC 58.897 50.000 10.38 0.00 0.00 6.13
647 681 1.956477 GCGGCCATCTTCAACCATTAT 59.044 47.619 2.24 0.00 0.00 1.28
720 754 2.619590 GGATACCCACCGTCACCAAAAT 60.620 50.000 0.00 0.00 0.00 1.82
729 804 4.806247 CACCGTCACCAAAATCTATCTCTC 59.194 45.833 0.00 0.00 0.00 3.20
730 805 4.045104 CCGTCACCAAAATCTATCTCTCG 58.955 47.826 0.00 0.00 0.00 4.04
733 808 5.230306 CGTCACCAAAATCTATCTCTCGAAC 59.770 44.000 0.00 0.00 0.00 3.95
738 813 7.066284 CACCAAAATCTATCTCTCGAACCAAAT 59.934 37.037 0.00 0.00 0.00 2.32
763 838 0.469917 CACCGGGGCAATCATAGTCT 59.530 55.000 6.32 0.00 0.00 3.24
774 849 6.593382 GGGCAATCATAGTCTATCTCAATGTC 59.407 42.308 0.00 0.00 0.00 3.06
779 854 9.775854 AATCATAGTCTATCTCAATGTCCTTTG 57.224 33.333 0.00 0.00 0.00 2.77
875 951 7.202016 TCTGAAAGCAAAAACTGTAGGTATG 57.798 36.000 0.00 0.00 0.00 2.39
879 955 9.727859 TGAAAGCAAAAACTGTAGGTATGTATA 57.272 29.630 0.00 0.00 0.00 1.47
883 959 9.509956 AGCAAAAACTGTAGGTATGTATAAACA 57.490 29.630 0.00 0.00 40.69 2.83
894 970 8.477419 AGGTATGTATAAACATCAAAATGGGG 57.523 34.615 0.00 0.00 42.92 4.96
895 971 7.015195 AGGTATGTATAAACATCAAAATGGGGC 59.985 37.037 0.00 0.00 42.92 5.80
896 972 7.015195 GGTATGTATAAACATCAAAATGGGGCT 59.985 37.037 0.00 0.00 42.92 5.19
897 973 9.073475 GTATGTATAAACATCAAAATGGGGCTA 57.927 33.333 0.00 0.00 42.92 3.93
898 974 8.725606 ATGTATAAACATCAAAATGGGGCTAT 57.274 30.769 0.00 0.00 42.92 2.97
899 975 9.821240 ATGTATAAACATCAAAATGGGGCTATA 57.179 29.630 0.00 0.00 42.92 1.31
941 1017 9.079833 CCTAAATCAAAGCTTAACACATGATTG 57.920 33.333 18.01 9.67 37.52 2.67
943 1019 8.752766 AAATCAAAGCTTAACACATGATTGAG 57.247 30.769 18.01 0.78 37.52 3.02
944 1020 5.702865 TCAAAGCTTAACACATGATTGAGC 58.297 37.500 17.42 17.42 38.58 4.26
953 2645 2.756207 CACATGATTGAGCCATCCACAA 59.244 45.455 0.00 0.00 0.00 3.33
955 2647 1.452110 TGATTGAGCCATCCACAACG 58.548 50.000 0.00 0.00 0.00 4.10
988 2681 5.468540 ACTGAAAATCCCAAAGCTTTACC 57.531 39.130 12.25 0.00 0.00 2.85
991 2684 4.217550 TGAAAATCCCAAAGCTTTACCGAG 59.782 41.667 12.25 0.00 0.00 4.63
1009 2703 2.280708 CGAGTCCCAACGCTATAAAACG 59.719 50.000 0.00 0.00 0.00 3.60
1020 2718 0.180642 TATAAAACGGCGCCCATGGA 59.819 50.000 23.46 3.82 0.00 3.41
1048 2746 2.997897 ACACACCCTCTCCGCTCC 60.998 66.667 0.00 0.00 0.00 4.70
1049 2747 4.135153 CACACCCTCTCCGCTCCG 62.135 72.222 0.00 0.00 0.00 4.63
1050 2748 4.680537 ACACCCTCTCCGCTCCGT 62.681 66.667 0.00 0.00 0.00 4.69
1051 2749 3.382832 CACCCTCTCCGCTCCGTT 61.383 66.667 0.00 0.00 0.00 4.44
1052 2750 3.069318 ACCCTCTCCGCTCCGTTC 61.069 66.667 0.00 0.00 0.00 3.95
1053 2751 3.839432 CCCTCTCCGCTCCGTTCC 61.839 72.222 0.00 0.00 0.00 3.62
1212 2931 2.425592 CCCAAGACGACCACAGCA 59.574 61.111 0.00 0.00 0.00 4.41
1213 2932 1.003355 CCCAAGACGACCACAGCAT 60.003 57.895 0.00 0.00 0.00 3.79
1219 2938 3.545481 CGACCACAGCATCGTCGC 61.545 66.667 0.00 0.00 42.37 5.19
1220 2939 2.432456 GACCACAGCATCGTCGCA 60.432 61.111 1.90 0.00 0.00 5.10
1221 2940 2.433145 ACCACAGCATCGTCGCAG 60.433 61.111 1.90 0.00 0.00 5.18
1222 2941 3.857854 CCACAGCATCGTCGCAGC 61.858 66.667 1.90 1.14 0.00 5.25
1223 2942 3.857854 CACAGCATCGTCGCAGCC 61.858 66.667 5.32 0.00 0.00 4.85
1224 2943 4.377708 ACAGCATCGTCGCAGCCA 62.378 61.111 5.32 0.00 0.00 4.75
1273 2992 4.070552 GCTCCTCCTCGCCAACGT 62.071 66.667 0.00 0.00 41.18 3.99
1275 2994 2.599281 TCCTCCTCGCCAACGTCA 60.599 61.111 0.00 0.00 41.18 4.35
1277 2996 1.811266 CCTCCTCGCCAACGTCATG 60.811 63.158 0.00 0.00 41.18 3.07
1475 3209 2.372264 GACCTGTACTGGACCGTCATA 58.628 52.381 24.19 0.00 0.00 2.15
1685 3419 3.495729 ACCTGGTGGTGGATGTCC 58.504 61.111 0.00 0.00 46.51 4.02
1706 3440 0.747283 TCTTCGCCGTCTACCTCTCC 60.747 60.000 0.00 0.00 0.00 3.71
1734 3468 1.165270 AAATTCAGGCGTTCCTTCGG 58.835 50.000 0.00 0.00 41.93 4.30
1735 3469 0.676782 AATTCAGGCGTTCCTTCGGG 60.677 55.000 0.00 0.00 41.93 5.14
1738 3472 4.394712 AGGCGTTCCTTCGGGCAG 62.395 66.667 0.00 0.00 40.66 4.85
1740 3474 3.119096 GCGTTCCTTCGGGCAGTC 61.119 66.667 0.00 0.00 34.44 3.51
1744 3478 0.951040 GTTCCTTCGGGCAGTCACTG 60.951 60.000 0.00 0.00 34.44 3.66
1782 3519 5.689383 TTCAGAACTTTTGGTACATGAGC 57.311 39.130 0.00 0.00 39.30 4.26
1857 3597 2.161609 GGTCGAAATTCATGGTGGTCAC 59.838 50.000 0.00 0.00 0.00 3.67
1872 3612 1.671845 GGTCACAAACTTGTTACGCCA 59.328 47.619 0.00 0.00 39.91 5.69
1885 3625 3.234386 GTTACGCCAGATTGACAAAAGC 58.766 45.455 0.00 0.00 0.00 3.51
1923 3663 2.028748 GCAGGTGTTTCTGATTGGCATT 60.029 45.455 0.00 0.00 36.93 3.56
1926 3666 3.642848 AGGTGTTTCTGATTGGCATTTGT 59.357 39.130 0.00 0.00 0.00 2.83
2001 3741 1.083806 TGGCGACGATTGTCTGCATC 61.084 55.000 22.68 12.39 43.21 3.91
2002 3742 1.270968 GCGACGATTGTCTGCATCG 59.729 57.895 18.87 5.16 43.21 3.84
2007 3747 2.514592 ATTGTCTGCATCGCCGGG 60.515 61.111 2.18 0.00 0.00 5.73
2079 3819 3.489229 GGAACGAAAAACTGAAGCAGCTT 60.489 43.478 7.60 7.60 34.37 3.74
2399 4139 4.484912 GAGACCTAGGATTCCAGGTGTAT 58.515 47.826 23.40 13.42 45.32 2.29
2403 4143 5.755849 ACCTAGGATTCCAGGTGTATTTTG 58.244 41.667 17.98 0.00 43.64 2.44
2412 4152 2.627699 CAGGTGTATTTTGTGTTGGCCT 59.372 45.455 3.32 0.00 0.00 5.19
2441 4181 2.165167 CTCCATGTTGCTCACCATGTT 58.835 47.619 6.64 0.00 37.37 2.71
2450 4190 1.197721 GCTCACCATGTTGTTCCTTCG 59.802 52.381 0.00 0.00 0.00 3.79
2451 4191 2.494059 CTCACCATGTTGTTCCTTCGT 58.506 47.619 0.00 0.00 0.00 3.85
2457 4198 2.129823 TGTTGTTCCTTCGTCTCGTC 57.870 50.000 0.00 0.00 0.00 4.20
2461 4202 0.793853 GTTCCTTCGTCTCGTCTCGC 60.794 60.000 0.00 0.00 0.00 5.03
2464 4205 1.578117 CTTCGTCTCGTCTCGCGTC 60.578 63.158 5.77 0.00 42.13 5.19
2474 4215 1.823828 GTCTCGCGTCGTGATTATGT 58.176 50.000 9.25 0.00 32.30 2.29
2536 4279 4.679373 ACATGTATCCTGATCACCTGTC 57.321 45.455 0.00 0.00 0.00 3.51
2539 4282 4.471904 TGTATCCTGATCACCTGTCAAC 57.528 45.455 0.00 0.00 0.00 3.18
2542 4285 5.719563 TGTATCCTGATCACCTGTCAACTTA 59.280 40.000 0.00 0.00 0.00 2.24
2753 4496 4.681483 GCAGCAAGGTCTTTTACATCAAAC 59.319 41.667 0.00 0.00 0.00 2.93
2840 4583 1.152247 AGCCACTGTGACCTCCTCA 60.152 57.895 9.86 0.00 0.00 3.86
2941 4684 0.537143 TCATTCACCTTGCAGGCGTT 60.537 50.000 2.50 0.00 39.63 4.84
3023 4766 1.513158 CTCGACAACCGGAGCATCT 59.487 57.895 9.46 0.00 39.14 2.90
3151 4894 1.507141 CGTTATGGATTGCTCCGGCC 61.507 60.000 0.00 0.00 45.37 6.13
3287 5030 3.573967 GAGGAGCAAGGAAATTTGTTGGA 59.426 43.478 0.00 0.00 0.00 3.53
3420 5163 1.655959 CGCCGTTTTGTTGGTTCCG 60.656 57.895 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 17 5.765182 GGGACCAATCTTTCATACTGTATGG 59.235 44.000 23.57 11.89 36.81 2.74
39 41 1.074319 GCCTTGTTGACGCATGCATG 61.074 55.000 22.70 22.70 0.00 4.06
40 42 1.213537 GCCTTGTTGACGCATGCAT 59.786 52.632 19.57 0.36 0.00 3.96
41 43 1.525718 ATGCCTTGTTGACGCATGCA 61.526 50.000 19.57 0.00 41.55 3.96
42 44 1.213537 ATGCCTTGTTGACGCATGC 59.786 52.632 7.91 7.91 41.55 4.06
117 119 2.582052 ACAAATTTCACTCTTGCGGGA 58.418 42.857 0.00 0.00 0.00 5.14
120 122 8.755018 AGATTTAAAACAAATTTCACTCTTGCG 58.245 29.630 0.00 0.00 32.27 4.85
136 138 9.405587 TCCACGATTTTGATCAAGATTTAAAAC 57.594 29.630 12.36 0.18 0.00 2.43
152 154 2.762535 ATGACCGACTCCACGATTTT 57.237 45.000 0.00 0.00 35.09 1.82
155 157 2.956333 TGATTATGACCGACTCCACGAT 59.044 45.455 0.00 0.00 35.09 3.73
156 158 2.371306 TGATTATGACCGACTCCACGA 58.629 47.619 0.00 0.00 35.09 4.35
167 174 9.912634 TTTGGAATTTGAGAGTTTGATTATGAC 57.087 29.630 0.00 0.00 0.00 3.06
187 194 7.301868 AGGTGCTGATTTTTAGAATTTGGAA 57.698 32.000 0.00 0.00 0.00 3.53
195 202 4.144297 AGTGCAAGGTGCTGATTTTTAGA 58.856 39.130 1.43 0.00 45.31 2.10
214 221 4.965814 ACATATGGTGATGCTAGGAAGTG 58.034 43.478 7.80 0.00 0.00 3.16
223 237 4.392047 TGATCCTTGACATATGGTGATGC 58.608 43.478 7.80 0.00 0.00 3.91
249 263 9.263446 TCTGTAAGGATGTTTGTAAGGTACTAT 57.737 33.333 0.00 0.00 38.49 2.12
250 264 8.654485 TCTGTAAGGATGTTTGTAAGGTACTA 57.346 34.615 0.00 0.00 38.49 1.82
284 300 0.458025 CGAGGTTGTCGGGAAGCTAC 60.458 60.000 0.00 0.00 45.58 3.58
286 302 2.657237 CGAGGTTGTCGGGAAGCT 59.343 61.111 0.00 0.00 45.58 3.74
340 356 1.808945 CTAGGTGCACTGCAAAGAAGG 59.191 52.381 17.98 0.00 41.47 3.46
359 375 3.654143 TGCACCATGGCTGAGGCT 61.654 61.111 13.04 0.00 38.73 4.58
360 376 3.446570 GTGCACCATGGCTGAGGC 61.447 66.667 13.04 8.77 37.82 4.70
378 394 3.508012 ACGTAGCTGTTGAGAGAGATTGT 59.492 43.478 0.00 0.00 0.00 2.71
380 396 3.181505 CGACGTAGCTGTTGAGAGAGATT 60.182 47.826 0.00 0.00 0.00 2.40
412 428 1.021390 AGAAATCAAGAGCGCGTGGG 61.021 55.000 8.43 0.00 0.00 4.61
415 431 1.071605 GACAGAAATCAAGAGCGCGT 58.928 50.000 8.43 0.00 0.00 6.01
419 435 3.485378 CGAGATCGACAGAAATCAAGAGC 59.515 47.826 0.00 0.00 43.02 4.09
424 440 3.444034 ACTTCCGAGATCGACAGAAATCA 59.556 43.478 3.31 0.00 43.02 2.57
479 495 2.222796 CCGATAACTTGCATCACACACG 60.223 50.000 0.00 0.00 0.00 4.49
510 528 2.571212 ACCACTCGAAAATGCAAGTCA 58.429 42.857 0.00 0.00 0.00 3.41
517 551 3.119495 GGAATCCCAACCACTCGAAAATG 60.119 47.826 0.00 0.00 0.00 2.32
524 558 0.698818 ACCTGGAATCCCAACCACTC 59.301 55.000 0.00 0.00 42.98 3.51
534 568 7.355778 CGAGCTTATTATCAAAACCTGGAATC 58.644 38.462 0.00 0.00 0.00 2.52
538 572 4.261197 GGCGAGCTTATTATCAAAACCTGG 60.261 45.833 0.00 0.00 0.00 4.45
549 583 5.940192 CCATTGTTATGGCGAGCTTATTA 57.060 39.130 0.00 0.00 44.64 0.98
550 584 4.836125 CCATTGTTATGGCGAGCTTATT 57.164 40.909 0.00 0.00 44.64 1.40
564 598 4.717280 TGTGGTTACCCTTTTTCCATTGTT 59.283 37.500 0.00 0.00 0.00 2.83
571 605 2.557056 GGAGCTGTGGTTACCCTTTTTC 59.443 50.000 0.00 0.00 0.00 2.29
593 627 5.175859 GGTTTGAGAGATGAACAACGGATA 58.824 41.667 0.00 0.00 0.00 2.59
607 641 4.201851 CCGCTCATATGTTTGGTTTGAGAG 60.202 45.833 1.90 0.00 36.72 3.20
608 642 3.689161 CCGCTCATATGTTTGGTTTGAGA 59.311 43.478 1.90 0.00 36.72 3.27
611 645 2.529151 GCCGCTCATATGTTTGGTTTG 58.471 47.619 1.90 0.00 0.00 2.93
628 662 3.213506 TGATAATGGTTGAAGATGGCCG 58.786 45.455 0.00 0.00 0.00 6.13
632 666 7.713942 TGAGTGAGATGATAATGGTTGAAGATG 59.286 37.037 0.00 0.00 0.00 2.90
647 681 8.690203 TTTTTCTATTTGGTTGAGTGAGATGA 57.310 30.769 0.00 0.00 0.00 2.92
673 707 2.255406 CAGCTGACTAGGGATAGCCAT 58.745 52.381 8.42 0.00 36.86 4.40
709 743 4.921547 TCGAGAGATAGATTTTGGTGACG 58.078 43.478 0.00 0.00 33.31 4.35
720 754 5.068723 GGGTGTATTTGGTTCGAGAGATAGA 59.931 44.000 0.00 0.00 41.60 1.98
729 804 0.800012 CGGTGGGTGTATTTGGTTCG 59.200 55.000 0.00 0.00 0.00 3.95
730 805 1.170442 CCGGTGGGTGTATTTGGTTC 58.830 55.000 0.00 0.00 0.00 3.62
733 808 4.329831 CCCGGTGGGTGTATTTGG 57.670 61.111 0.00 0.00 38.25 3.28
752 827 9.775854 AAAGGACATTGAGATAGACTATGATTG 57.224 33.333 0.00 0.00 0.00 2.67
754 829 8.932610 ACAAAGGACATTGAGATAGACTATGAT 58.067 33.333 0.00 0.00 34.38 2.45
755 830 8.311395 ACAAAGGACATTGAGATAGACTATGA 57.689 34.615 0.00 0.00 34.38 2.15
763 838 6.475504 ACACATGACAAAGGACATTGAGATA 58.524 36.000 0.00 0.00 34.38 1.98
774 849 3.131709 AGAGTGGACACATGACAAAGG 57.868 47.619 0.00 0.00 0.00 3.11
814 890 6.463995 AAATACGCACATGGGAATAAACAT 57.536 33.333 0.00 0.00 0.00 2.71
823 899 4.433186 TGAAGAAAAATACGCACATGGG 57.567 40.909 0.00 0.00 0.00 4.00
879 955 7.251321 TGTTTATAGCCCCATTTTGATGTTT 57.749 32.000 0.00 0.00 0.00 2.83
880 956 6.865834 TGTTTATAGCCCCATTTTGATGTT 57.134 33.333 0.00 0.00 0.00 2.71
881 957 6.610830 TGATGTTTATAGCCCCATTTTGATGT 59.389 34.615 0.00 0.00 0.00 3.06
882 958 7.053316 TGATGTTTATAGCCCCATTTTGATG 57.947 36.000 0.00 0.00 0.00 3.07
883 959 7.673641 TTGATGTTTATAGCCCCATTTTGAT 57.326 32.000 0.00 0.00 0.00 2.57
884 960 7.487822 TTTGATGTTTATAGCCCCATTTTGA 57.512 32.000 0.00 0.00 0.00 2.69
885 961 8.614346 CATTTTGATGTTTATAGCCCCATTTTG 58.386 33.333 0.00 0.00 0.00 2.44
886 962 7.774625 CCATTTTGATGTTTATAGCCCCATTTT 59.225 33.333 0.00 0.00 0.00 1.82
887 963 7.281841 CCATTTTGATGTTTATAGCCCCATTT 58.718 34.615 0.00 0.00 0.00 2.32
888 964 6.183361 CCCATTTTGATGTTTATAGCCCCATT 60.183 38.462 0.00 0.00 0.00 3.16
889 965 5.307716 CCCATTTTGATGTTTATAGCCCCAT 59.692 40.000 0.00 0.00 0.00 4.00
890 966 4.653341 CCCATTTTGATGTTTATAGCCCCA 59.347 41.667 0.00 0.00 0.00 4.96
891 967 4.040339 CCCCATTTTGATGTTTATAGCCCC 59.960 45.833 0.00 0.00 0.00 5.80
892 968 4.503123 GCCCCATTTTGATGTTTATAGCCC 60.503 45.833 0.00 0.00 0.00 5.19
893 969 4.503123 GGCCCCATTTTGATGTTTATAGCC 60.503 45.833 0.00 0.00 0.00 3.93
894 970 4.344968 AGGCCCCATTTTGATGTTTATAGC 59.655 41.667 0.00 0.00 0.00 2.97
895 971 7.595819 TTAGGCCCCATTTTGATGTTTATAG 57.404 36.000 0.00 0.00 0.00 1.31
896 972 7.979786 TTTAGGCCCCATTTTGATGTTTATA 57.020 32.000 0.00 0.00 0.00 0.98
897 973 6.882768 TTTAGGCCCCATTTTGATGTTTAT 57.117 33.333 0.00 0.00 0.00 1.40
898 974 6.441924 TGATTTAGGCCCCATTTTGATGTTTA 59.558 34.615 0.00 0.00 0.00 2.01
899 975 5.250313 TGATTTAGGCCCCATTTTGATGTTT 59.750 36.000 0.00 0.00 0.00 2.83
941 1017 1.970917 CTTCGCGTTGTGGATGGCTC 61.971 60.000 5.77 0.00 0.00 4.70
943 1019 2.480555 CTTCGCGTTGTGGATGGC 59.519 61.111 5.77 0.00 0.00 4.40
944 1020 2.398554 CCCTTCGCGTTGTGGATGG 61.399 63.158 5.77 0.00 0.00 3.51
953 2645 0.179040 TTTCAGTTTCCCCTTCGCGT 60.179 50.000 5.77 0.00 0.00 6.01
955 2647 2.094700 GGATTTTCAGTTTCCCCTTCGC 60.095 50.000 0.00 0.00 0.00 4.70
967 2659 4.217550 TCGGTAAAGCTTTGGGATTTTCAG 59.782 41.667 22.02 1.94 35.09 3.02
988 2681 2.280708 CGTTTTATAGCGTTGGGACTCG 59.719 50.000 0.00 0.00 0.00 4.18
991 2684 1.063027 GCCGTTTTATAGCGTTGGGAC 59.937 52.381 0.00 0.00 0.00 4.46
1009 2703 3.747976 GTGTGTTCCATGGGCGCC 61.748 66.667 21.18 21.18 0.00 6.53
1020 2718 0.039035 AGGGTGTGTGTTGGTGTGTT 59.961 50.000 0.00 0.00 0.00 3.32
1049 2747 2.035442 GTTGGGAGCTGAGCGGAAC 61.035 63.158 0.00 0.00 0.00 3.62
1050 2748 2.347490 GTTGGGAGCTGAGCGGAA 59.653 61.111 0.00 0.00 0.00 4.30
1051 2749 2.922503 TGTTGGGAGCTGAGCGGA 60.923 61.111 0.00 0.00 0.00 5.54
1052 2750 2.743928 GTGTTGGGAGCTGAGCGG 60.744 66.667 0.00 0.00 0.00 5.52
1053 2751 3.114616 CGTGTTGGGAGCTGAGCG 61.115 66.667 0.00 0.00 0.00 5.03
1167 2886 1.406180 GAAGGCGAGGTAGAAGAGGAC 59.594 57.143 0.00 0.00 0.00 3.85
1204 2923 2.433145 CTGCGACGATGCTGTGGT 60.433 61.111 0.00 0.00 35.36 4.16
1223 2942 4.742201 CACGAGGACACCGGGCTG 62.742 72.222 6.32 0.00 0.00 4.85
1273 2992 1.067846 CGACGTTGAGGAGGAACATGA 60.068 52.381 0.00 0.00 0.00 3.07
1275 2994 1.067776 GTCGACGTTGAGGAGGAACAT 60.068 52.381 5.51 0.00 0.00 2.71
1277 2996 0.728466 CGTCGACGTTGAGGAGGAAC 60.728 60.000 29.08 0.00 34.11 3.62
1382 3105 0.031314 CGTCCAGCGACAGATAGCAT 59.969 55.000 0.00 0.00 44.77 3.79
1439 3173 4.114997 TCGATGAGCTGCGACGCA 62.115 61.111 22.99 22.99 36.92 5.24
1685 3419 1.064357 GAGAGGTAGACGGCGAAGAAG 59.936 57.143 16.62 0.00 0.00 2.85
1706 3440 0.734889 CGCCTGAATTTACCTGCTGG 59.265 55.000 8.29 8.29 39.83 4.85
1734 3468 0.524862 CAAGCATTCCAGTGACTGCC 59.475 55.000 7.16 0.00 45.52 4.85
1735 3469 0.109412 GCAAGCATTCCAGTGACTGC 60.109 55.000 7.16 0.00 44.93 4.40
1738 3472 1.610522 ACAAGCAAGCATTCCAGTGAC 59.389 47.619 0.00 0.00 0.00 3.67
1740 3474 2.806608 AACAAGCAAGCATTCCAGTG 57.193 45.000 0.00 0.00 0.00 3.66
1744 3478 3.981211 TCTGAAAACAAGCAAGCATTCC 58.019 40.909 0.00 0.00 0.00 3.01
1782 3519 6.582295 CAGGGTATTTCTTCAAACACATTTCG 59.418 38.462 0.00 0.00 0.00 3.46
1857 3597 4.219033 GTCAATCTGGCGTAACAAGTTTG 58.781 43.478 0.00 0.00 0.00 2.93
1872 3612 0.238289 CACGCCGCTTTTGTCAATCT 59.762 50.000 0.00 0.00 0.00 2.40
1885 3625 1.729131 GCATCCAACAAACACGCCG 60.729 57.895 0.00 0.00 0.00 6.46
1923 3663 4.178861 GCGTACATCGGCAGACAA 57.821 55.556 0.00 0.00 40.26 3.18
1989 3729 2.537560 CCCGGCGATGCAGACAATC 61.538 63.158 9.30 0.00 0.00 2.67
1990 3730 2.514592 CCCGGCGATGCAGACAAT 60.515 61.111 9.30 0.00 0.00 2.71
2079 3819 3.998672 GGGACTGTCGGTTCGCCA 61.999 66.667 1.07 0.00 37.00 5.69
2399 4139 2.183679 AGGAACAAGGCCAACACAAAA 58.816 42.857 5.01 0.00 0.00 2.44
2403 4143 1.609072 GAGAAGGAACAAGGCCAACAC 59.391 52.381 5.01 0.00 0.00 3.32
2412 4152 3.149196 GAGCAACATGGAGAAGGAACAA 58.851 45.455 0.00 0.00 0.00 2.83
2441 4181 0.516001 CGAGACGAGACGAAGGAACA 59.484 55.000 0.00 0.00 0.00 3.18
2457 4198 0.764801 CGACATAATCACGACGCGAG 59.235 55.000 15.93 9.24 0.00 5.03
2461 4202 2.678705 GCAAACGACATAATCACGACG 58.321 47.619 0.00 0.00 0.00 5.12
2464 4205 1.060553 AGCGCAAACGACATAATCACG 59.939 47.619 11.47 0.00 43.93 4.35
2474 4215 0.042880 CACGTAAACAGCGCAAACGA 60.043 50.000 21.01 0.00 43.93 3.85
2536 4279 7.881142 TGAACAAGTTTGGGATACATAAGTTG 58.119 34.615 7.09 7.09 37.01 3.16
2539 4282 8.279970 TGATGAACAAGTTTGGGATACATAAG 57.720 34.615 0.00 0.00 39.74 1.73
2542 4285 7.121382 AGATGATGAACAAGTTTGGGATACAT 58.879 34.615 0.00 0.00 39.74 2.29
2753 4496 9.679596 CGGACAAACTAACTTATATTGTTTACG 57.320 33.333 0.00 0.00 34.59 3.18
2764 4507 6.594937 AGTGTTTTGTCGGACAAACTAACTTA 59.405 34.615 30.14 14.91 46.53 2.24
2840 4583 1.369689 CGAGGTCGTTGTCGTCGTT 60.370 57.895 0.00 0.00 38.05 3.85
2941 4684 0.319555 CTCGACACCAAAAGCCGAGA 60.320 55.000 0.00 0.00 46.62 4.04
3023 4766 2.345991 GCTGCACCCGTAGAACCA 59.654 61.111 0.00 0.00 0.00 3.67
3287 5030 4.777896 TGCTCCTTATCCTCTTGTTACTGT 59.222 41.667 0.00 0.00 0.00 3.55
3420 5163 1.228154 AGACCAAGGAAACACCGCC 60.228 57.895 0.00 0.00 44.74 6.13


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

AutoCloner maintained by Alex Coulton.