Multiple sequence alignment - TraesCS5A01G331400

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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 TraesCS5A01G331400 chr5A 100.000 2621 0 0 1 2621 540369200 540366580 0.000000e+00 4841.0
1 TraesCS5A01G331400 chr5A 83.099 142 24 0 2374 2515 129749618 129749759 2.120000e-26 130.0
2 TraesCS5A01G331400 chr5D 90.207 1205 53 28 690 1840 426167018 426165825 0.000000e+00 1511.0
3 TraesCS5A01G331400 chr5D 93.632 424 11 6 2209 2621 426165265 426164847 1.030000e-173 619.0
4 TraesCS5A01G331400 chr5D 87.849 502 28 12 98 575 426167581 426167089 2.280000e-155 558.0
5 TraesCS5A01G331400 chr5D 91.776 304 17 5 1901 2203 426165721 426165425 1.450000e-112 416.0
6 TraesCS5A01G331400 chr5B 91.847 1018 49 21 701 1695 516039405 516038399 0.000000e+00 1389.0
7 TraesCS5A01G331400 chr5B 89.892 742 32 16 1898 2621 516033885 516033169 0.000000e+00 915.0
8 TraesCS5A01G331400 chr5B 89.226 594 31 13 98 672 516040591 516040012 0.000000e+00 712.0
9 TraesCS5A01G331400 chr5B 82.353 170 30 0 2351 2520 132588283 132588452 5.840000e-32 148.0
10 TraesCS5A01G331400 chr5B 87.059 85 11 0 1730 1814 516038399 516038315 2.150000e-16 97.1


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 TraesCS5A01G331400 chr5A 540366580 540369200 2620 True 4841.0 4841 100.000000 1 2621 1 chr5A.!!$R1 2620
1 TraesCS5A01G331400 chr5D 426164847 426167581 2734 True 776.0 1511 90.866000 98 2621 4 chr5D.!!$R1 2523
2 TraesCS5A01G331400 chr5B 516033169 516033885 716 True 915.0 915 89.892000 1898 2621 1 chr5B.!!$R1 723
3 TraesCS5A01G331400 chr5B 516038315 516040591 2276 True 732.7 1389 89.377333 98 1814 3 chr5B.!!$R2 1716

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
87 88 0.03392 GGCACTTGCTTTGGGAAAGG 59.966 55.0 0.38 0.0 41.7 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2483 1.071239 CGCATGCGTATTTCTTCGGAG 60.071 52.381 31.33 0.0 34.35 4.63 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
23 24 6.957984 ATGTATTTATATCTGCTGCTCGTG 57.042 37.500 0.00 0.00 0.00 4.35
24 25 4.686091 TGTATTTATATCTGCTGCTCGTGC 59.314 41.667 1.71 1.71 40.20 5.34
36 37 1.123655 GCTCGTGCAAACTTTTCTGC 58.876 50.000 4.26 0.00 39.41 4.26
37 38 1.268743 GCTCGTGCAAACTTTTCTGCT 60.269 47.619 4.26 0.00 39.38 4.24
38 39 2.378806 CTCGTGCAAACTTTTCTGCTG 58.621 47.619 0.00 0.00 39.38 4.41
39 40 1.742831 TCGTGCAAACTTTTCTGCTGT 59.257 42.857 0.00 0.00 39.38 4.40
40 41 2.163412 TCGTGCAAACTTTTCTGCTGTT 59.837 40.909 0.00 0.00 39.38 3.16
41 42 2.923020 CGTGCAAACTTTTCTGCTGTTT 59.077 40.909 0.00 0.00 39.38 2.83
42 43 3.367630 CGTGCAAACTTTTCTGCTGTTTT 59.632 39.130 0.00 0.00 39.38 2.43
43 44 4.640956 GTGCAAACTTTTCTGCTGTTTTG 58.359 39.130 0.00 0.00 39.38 2.44
44 45 4.152223 GTGCAAACTTTTCTGCTGTTTTGT 59.848 37.500 0.00 0.00 39.38 2.83
45 46 5.347364 GTGCAAACTTTTCTGCTGTTTTGTA 59.653 36.000 0.00 0.00 39.38 2.41
46 47 6.035975 GTGCAAACTTTTCTGCTGTTTTGTAT 59.964 34.615 0.00 0.00 39.38 2.29
47 48 6.593382 TGCAAACTTTTCTGCTGTTTTGTATT 59.407 30.769 0.00 0.00 39.38 1.89
48 49 7.761704 TGCAAACTTTTCTGCTGTTTTGTATTA 59.238 29.630 0.00 0.00 39.38 0.98
49 50 8.764287 GCAAACTTTTCTGCTGTTTTGTATTAT 58.236 29.630 0.00 0.00 35.62 1.28
58 59 9.767684 TCTGCTGTTTTGTATTATAATGAAACG 57.232 29.630 8.28 11.85 0.00 3.60
59 60 8.388319 TGCTGTTTTGTATTATAATGAAACGC 57.612 30.769 22.27 22.27 0.00 4.84
60 61 8.023706 TGCTGTTTTGTATTATAATGAAACGCA 58.976 29.630 24.43 24.43 0.00 5.24
61 62 8.311120 GCTGTTTTGTATTATAATGAAACGCAC 58.689 33.333 22.98 14.10 0.00 5.34
62 63 9.554724 CTGTTTTGTATTATAATGAAACGCACT 57.445 29.630 8.28 0.00 0.00 4.40
63 64 9.549509 TGTTTTGTATTATAATGAAACGCACTC 57.450 29.630 8.28 0.00 0.00 3.51
64 65 9.006215 GTTTTGTATTATAATGAAACGCACTCC 57.994 33.333 8.28 0.00 0.00 3.85
65 66 6.854496 TGTATTATAATGAAACGCACTCCC 57.146 37.500 8.28 0.00 0.00 4.30
66 67 5.761234 TGTATTATAATGAAACGCACTCCCC 59.239 40.000 8.28 0.00 0.00 4.81
67 68 4.497291 TTATAATGAAACGCACTCCCCT 57.503 40.909 0.00 0.00 0.00 4.79
68 69 2.107950 TAATGAAACGCACTCCCCTG 57.892 50.000 0.00 0.00 0.00 4.45
69 70 0.609131 AATGAAACGCACTCCCCTGG 60.609 55.000 0.00 0.00 0.00 4.45
70 71 3.056328 GAAACGCACTCCCCTGGC 61.056 66.667 0.00 0.00 0.00 4.85
71 72 3.842925 GAAACGCACTCCCCTGGCA 62.843 63.158 0.00 0.00 0.00 4.92
72 73 4.643387 AACGCACTCCCCTGGCAC 62.643 66.667 0.00 0.00 0.00 5.01
74 75 4.335647 CGCACTCCCCTGGCACTT 62.336 66.667 0.00 0.00 0.00 3.16
75 76 2.674380 GCACTCCCCTGGCACTTG 60.674 66.667 0.00 0.00 0.00 3.16
76 77 2.674380 CACTCCCCTGGCACTTGC 60.674 66.667 0.00 0.00 41.14 4.01
77 78 2.856000 ACTCCCCTGGCACTTGCT 60.856 61.111 0.38 0.00 41.70 3.91
78 79 2.437897 CTCCCCTGGCACTTGCTT 59.562 61.111 0.38 0.00 41.70 3.91
79 80 1.228675 CTCCCCTGGCACTTGCTTT 60.229 57.895 0.38 0.00 41.70 3.51
80 81 1.530013 CTCCCCTGGCACTTGCTTTG 61.530 60.000 0.38 0.00 41.70 2.77
81 82 2.576832 CCCCTGGCACTTGCTTTGG 61.577 63.158 0.38 1.53 41.70 3.28
82 83 2.576832 CCCTGGCACTTGCTTTGGG 61.577 63.158 0.38 6.73 41.70 4.12
83 84 1.531365 CCTGGCACTTGCTTTGGGA 60.531 57.895 0.38 0.00 41.70 4.37
84 85 1.114722 CCTGGCACTTGCTTTGGGAA 61.115 55.000 0.38 0.00 41.70 3.97
85 86 0.752054 CTGGCACTTGCTTTGGGAAA 59.248 50.000 0.38 0.00 41.70 3.13
86 87 0.752054 TGGCACTTGCTTTGGGAAAG 59.248 50.000 0.38 0.00 41.70 2.62
87 88 0.033920 GGCACTTGCTTTGGGAAAGG 59.966 55.000 0.38 0.00 41.70 3.11
88 89 0.752658 GCACTTGCTTTGGGAAAGGT 59.247 50.000 0.00 0.00 38.93 3.50
89 90 1.138859 GCACTTGCTTTGGGAAAGGTT 59.861 47.619 0.00 0.00 38.93 3.50
90 91 2.803133 GCACTTGCTTTGGGAAAGGTTC 60.803 50.000 0.00 0.00 38.93 3.62
91 92 2.695147 CACTTGCTTTGGGAAAGGTTCT 59.305 45.455 0.00 0.00 38.93 3.01
92 93 2.695147 ACTTGCTTTGGGAAAGGTTCTG 59.305 45.455 0.00 0.00 38.93 3.02
93 94 2.452600 TGCTTTGGGAAAGGTTCTGT 57.547 45.000 0.00 0.00 38.93 3.41
94 95 2.745968 TGCTTTGGGAAAGGTTCTGTT 58.254 42.857 0.00 0.00 38.93 3.16
95 96 2.693074 TGCTTTGGGAAAGGTTCTGTTC 59.307 45.455 0.00 0.00 38.93 3.18
96 97 2.035961 GCTTTGGGAAAGGTTCTGTTCC 59.964 50.000 0.00 0.00 42.28 3.62
147 148 2.460918 ACTCGCATTCGAACCTAATCG 58.539 47.619 0.00 0.00 44.98 3.34
164 165 1.705256 TCGCGTGGTTAAACTAGCAG 58.295 50.000 5.77 4.69 0.00 4.24
207 208 6.389869 TCATTATGGGGAATCTTTGGTCTACT 59.610 38.462 0.00 0.00 0.00 2.57
225 226 3.454371 ACTCAGCCGTATTATCCACAC 57.546 47.619 0.00 0.00 0.00 3.82
295 299 7.336161 AGTAGTACAATCATCTGAGTGGTAC 57.664 40.000 11.78 10.70 43.65 3.34
328 340 2.481471 GCTAGTTTGGGCGGCATCC 61.481 63.158 12.47 0.00 0.00 3.51
341 353 2.826725 GCGGCATCCTTCTAGGTAGTAT 59.173 50.000 0.00 0.00 36.53 2.12
457 496 2.503382 GCCTCTCCCCTCGATGACC 61.503 68.421 0.00 0.00 0.00 4.02
506 546 4.717988 CTCGATTAGCTGCGAGCA 57.282 55.556 18.11 0.00 45.97 4.26
507 547 3.191903 CTCGATTAGCTGCGAGCAT 57.808 52.632 18.11 0.00 45.97 3.79
508 548 0.782981 CTCGATTAGCTGCGAGCATG 59.217 55.000 18.11 0.00 45.97 4.06
510 550 0.782981 CGATTAGCTGCGAGCATGAG 59.217 55.000 0.00 0.00 45.56 2.90
575 615 1.553248 TGGATAAACACGCCTGCTAGT 59.447 47.619 0.00 0.00 0.00 2.57
576 616 1.933853 GGATAAACACGCCTGCTAGTG 59.066 52.381 0.00 0.00 43.46 2.74
577 617 1.327764 GATAAACACGCCTGCTAGTGC 59.672 52.381 0.00 0.00 41.72 4.40
578 618 0.672401 TAAACACGCCTGCTAGTGCC 60.672 55.000 0.00 0.00 41.72 5.01
579 619 2.674563 AAACACGCCTGCTAGTGCCA 62.675 55.000 0.00 0.00 41.72 4.92
580 620 2.816958 CACGCCTGCTAGTGCCAG 60.817 66.667 0.00 0.00 38.71 4.85
581 621 4.767255 ACGCCTGCTAGTGCCAGC 62.767 66.667 0.00 0.00 42.15 4.85
583 623 4.415150 GCCTGCTAGTGCCAGCCA 62.415 66.667 0.00 0.00 41.04 4.75
584 624 2.593978 CCTGCTAGTGCCAGCCAT 59.406 61.111 0.00 0.00 41.04 4.40
585 625 1.077212 CCTGCTAGTGCCAGCCATT 60.077 57.895 0.00 0.00 41.04 3.16
619 659 1.235281 CCGGACTGTCACTGACGAGA 61.235 60.000 10.38 0.00 34.95 4.04
631 671 8.068893 TGTCACTGACGAGAAAAGTTTATTAC 57.931 34.615 4.71 0.00 34.95 1.89
632 672 7.924412 TGTCACTGACGAGAAAAGTTTATTACT 59.076 33.333 4.71 0.00 35.22 2.24
633 673 8.426251 GTCACTGACGAGAAAAGTTTATTACTC 58.574 37.037 0.00 0.00 35.54 2.59
647 687 8.773404 AGTTTATTACTCCTTACACATGACAC 57.227 34.615 0.00 0.00 28.23 3.67
699 1329 1.372087 CCTGCAGCCGGAGAAATGTC 61.372 60.000 5.05 0.00 30.74 3.06
941 1589 1.417979 GAGCAGAAGAAAGCGTCGC 59.582 57.895 9.80 9.80 35.48 5.19
984 1632 1.984570 CACCGGGGAGCAGAGAGAA 60.985 63.158 6.32 0.00 0.00 2.87
985 1633 1.002274 ACCGGGGAGCAGAGAGAAT 59.998 57.895 6.32 0.00 0.00 2.40
996 1649 0.105964 AGAGAGAATAGGCGGCAGGA 60.106 55.000 13.08 0.00 0.00 3.86
1228 1881 2.813908 GCATCGTCGTGGTGTCCC 60.814 66.667 0.00 0.00 0.00 4.46
1629 2295 1.896660 GTGCTTTTGACCCGAGCCA 60.897 57.895 0.00 0.00 35.59 4.75
1632 2298 1.302832 CTTTTGACCCGAGCCAGCT 60.303 57.895 0.00 0.00 0.00 4.24
1633 2299 1.580845 CTTTTGACCCGAGCCAGCTG 61.581 60.000 6.78 6.78 0.00 4.24
1634 2300 4.704833 TTGACCCGAGCCAGCTGC 62.705 66.667 8.66 3.91 41.71 5.25
1666 2344 3.862845 GCGGACACTGTTTTGTTCAAATT 59.137 39.130 0.00 0.00 0.00 1.82
1675 2353 4.329528 TGTTTTGTTCAAATTGCAGTCAGC 59.670 37.500 0.00 0.00 45.96 4.26
1676 2354 4.389890 TTTGTTCAAATTGCAGTCAGCT 57.610 36.364 0.00 0.00 45.94 4.24
1677 2355 4.389890 TTGTTCAAATTGCAGTCAGCTT 57.610 36.364 0.00 0.00 45.94 3.74
1678 2356 3.968649 TGTTCAAATTGCAGTCAGCTTC 58.031 40.909 0.00 0.00 45.94 3.86
1695 2373 4.908730 CAGCTTCTTTCTTTCGCTTTCTTC 59.091 41.667 0.00 0.00 0.00 2.87
1696 2374 4.819088 AGCTTCTTTCTTTCGCTTTCTTCT 59.181 37.500 0.00 0.00 0.00 2.85
1697 2375 5.049749 AGCTTCTTTCTTTCGCTTTCTTCTC 60.050 40.000 0.00 0.00 0.00 2.87
1698 2376 4.974103 TCTTTCTTTCGCTTTCTTCTCG 57.026 40.909 0.00 0.00 0.00 4.04
1699 2377 4.369182 TCTTTCTTTCGCTTTCTTCTCGT 58.631 39.130 0.00 0.00 0.00 4.18
1701 2379 4.710528 TTCTTTCGCTTTCTTCTCGTTC 57.289 40.909 0.00 0.00 0.00 3.95
1702 2380 3.978687 TCTTTCGCTTTCTTCTCGTTCT 58.021 40.909 0.00 0.00 0.00 3.01
1704 2382 4.444720 TCTTTCGCTTTCTTCTCGTTCTTC 59.555 41.667 0.00 0.00 0.00 2.87
1705 2383 3.644884 TCGCTTTCTTCTCGTTCTTCT 57.355 42.857 0.00 0.00 0.00 2.85
1707 2385 3.736252 TCGCTTTCTTCTCGTTCTTCTTG 59.264 43.478 0.00 0.00 0.00 3.02
1715 2394 4.060038 TCTCGTTCTTCTTGTTGCTCTT 57.940 40.909 0.00 0.00 0.00 2.85
1721 2400 5.049818 CGTTCTTCTTGTTGCTCTTTGATCT 60.050 40.000 0.00 0.00 0.00 2.75
1747 2426 4.098044 GCAAGTGATCTGTAGCTACCACTA 59.902 45.833 24.67 7.50 34.22 2.74
1781 2460 4.002982 TCAACTGGTTGGATGAATCTTCG 58.997 43.478 12.65 0.00 40.78 3.79
1792 2476 2.011947 TGAATCTTCGAGCATGCTTGG 58.988 47.619 30.40 21.20 0.00 3.61
1793 2477 0.737219 AATCTTCGAGCATGCTTGGC 59.263 50.000 30.40 14.23 0.00 4.52
1799 2483 3.352338 GAGCATGCTTGGCTGGTGC 62.352 63.158 23.61 1.03 42.78 5.01
1802 2486 2.362120 ATGCTTGGCTGGTGCTCC 60.362 61.111 0.00 0.00 39.59 4.70
1818 2502 1.333258 GCTCCGAAGAAATACGCATGC 60.333 52.381 7.91 7.91 0.00 4.06
1826 2510 2.032549 AGAAATACGCATGCGAATCTGC 60.033 45.455 43.72 26.16 42.83 4.26
1840 2524 4.142730 GCGAATCTGCAGACATTTCTTCTT 60.143 41.667 20.97 5.77 34.15 2.52
1842 2526 5.638783 GAATCTGCAGACATTTCTTCTTGG 58.361 41.667 20.97 0.00 0.00 3.61
1843 2527 4.356405 TCTGCAGACATTTCTTCTTGGA 57.644 40.909 13.74 0.00 0.00 3.53
1844 2528 4.914983 TCTGCAGACATTTCTTCTTGGAT 58.085 39.130 13.74 0.00 0.00 3.41
1845 2529 6.053632 TCTGCAGACATTTCTTCTTGGATA 57.946 37.500 13.74 0.00 0.00 2.59
1847 2531 7.114754 TCTGCAGACATTTCTTCTTGGATAAT 58.885 34.615 13.74 0.00 0.00 1.28
1848 2532 8.267183 TCTGCAGACATTTCTTCTTGGATAATA 58.733 33.333 13.74 0.00 0.00 0.98
1849 2533 8.213518 TGCAGACATTTCTTCTTGGATAATAC 57.786 34.615 0.00 0.00 0.00 1.89
1850 2534 8.049117 TGCAGACATTTCTTCTTGGATAATACT 58.951 33.333 0.00 0.00 0.00 2.12
1853 2537 9.620259 AGACATTTCTTCTTGGATAATACTTCC 57.380 33.333 0.00 0.00 0.00 3.46
1896 2610 2.518949 GCGTGTGCACATTCCAATAAG 58.481 47.619 24.69 7.25 42.15 1.73
1978 2709 7.158021 TCAAAAGTCACACAAAAAGTTGGAAT 58.842 30.769 0.00 0.00 39.22 3.01
2003 2734 4.727507 TCTCTGCAGTATCCTCTGAAAC 57.272 45.455 14.67 0.00 37.61 2.78
2006 2737 1.559682 TGCAGTATCCTCTGAAACCCC 59.440 52.381 0.00 0.00 37.61 4.95
2013 2745 1.003118 TCCTCTGAAACCCCGTGATTG 59.997 52.381 0.00 0.00 0.00 2.67
2015 2747 0.608035 TCTGAAACCCCGTGATTGCC 60.608 55.000 0.00 0.00 0.00 4.52
2017 2749 0.178975 TGAAACCCCGTGATTGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
2050 2782 3.570926 TTCGAGAAACATACTCAGCGT 57.429 42.857 0.00 0.00 34.47 5.07
2051 2783 3.570926 TCGAGAAACATACTCAGCGTT 57.429 42.857 0.00 0.00 34.47 4.84
2052 2784 3.909430 TCGAGAAACATACTCAGCGTTT 58.091 40.909 0.00 0.00 35.63 3.60
2053 2785 4.304110 TCGAGAAACATACTCAGCGTTTT 58.696 39.130 0.00 0.00 33.18 2.43
2127 2859 1.077212 CACATCTCCAAGGCCCAGG 60.077 63.158 0.00 0.67 0.00 4.45
2139 2871 4.293671 CCCAGGTTTTCGGGCCCA 62.294 66.667 24.92 6.15 35.09 5.36
2174 2906 1.196012 CCGGTTCTAGAGCCTTCCTT 58.804 55.000 21.75 0.00 0.00 3.36
2221 3107 2.127297 CCTTCCCCTTCCCCTCCA 59.873 66.667 0.00 0.00 0.00 3.86
2227 3113 1.615262 CCCTTCCCCTCCATTCCAC 59.385 63.158 0.00 0.00 0.00 4.02
2228 3114 1.615262 CCTTCCCCTCCATTCCACC 59.385 63.158 0.00 0.00 0.00 4.61
2229 3115 1.615262 CTTCCCCTCCATTCCACCC 59.385 63.158 0.00 0.00 0.00 4.61
2230 3116 1.933812 TTCCCCTCCATTCCACCCC 60.934 63.158 0.00 0.00 0.00 4.95
2231 3117 2.616893 CCCCTCCATTCCACCCCA 60.617 66.667 0.00 0.00 0.00 4.96
2232 3118 2.683475 CCCTCCATTCCACCCCAC 59.317 66.667 0.00 0.00 0.00 4.61
2233 3119 2.683475 CCTCCATTCCACCCCACC 59.317 66.667 0.00 0.00 0.00 4.61
2256 3142 3.507713 CCACCACCACCCCCACTT 61.508 66.667 0.00 0.00 0.00 3.16
2306 3192 4.295199 ACCCCCAAAACCCTCGCC 62.295 66.667 0.00 0.00 0.00 5.54
2484 3381 4.323477 CCCGCTCCCCAACGTCAA 62.323 66.667 0.00 0.00 0.00 3.18
2492 3389 2.637025 CCAACGTCAACGCCAAGG 59.363 61.111 1.81 0.00 44.43 3.61
2592 3498 2.182030 CAAGCCCGACGAGGAGAC 59.818 66.667 0.00 0.00 45.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.349817 GCACGAGCAGCAGATATAAATACAT 59.650 40.000 0.00 0.00 41.58 2.29
1 2 4.686091 GCACGAGCAGCAGATATAAATACA 59.314 41.667 0.00 0.00 41.58 2.29
2 3 5.196809 GCACGAGCAGCAGATATAAATAC 57.803 43.478 0.00 0.00 41.58 1.89
17 18 1.123655 GCAGAAAAGTTTGCACGAGC 58.876 50.000 0.00 0.00 40.02 5.03
18 19 2.223340 ACAGCAGAAAAGTTTGCACGAG 60.223 45.455 0.00 0.00 42.67 4.18
19 20 1.742831 ACAGCAGAAAAGTTTGCACGA 59.257 42.857 0.00 0.00 42.67 4.35
20 21 2.193306 ACAGCAGAAAAGTTTGCACG 57.807 45.000 0.00 0.00 42.67 5.34
21 22 4.152223 ACAAAACAGCAGAAAAGTTTGCAC 59.848 37.500 0.00 0.00 42.67 4.57
22 23 4.314121 ACAAAACAGCAGAAAAGTTTGCA 58.686 34.783 0.00 0.00 42.67 4.08
23 24 4.926860 ACAAAACAGCAGAAAAGTTTGC 57.073 36.364 0.00 0.00 40.57 3.68
32 33 9.767684 CGTTTCATTATAATACAAAACAGCAGA 57.232 29.630 19.64 2.30 0.00 4.26
33 34 8.523464 GCGTTTCATTATAATACAAAACAGCAG 58.477 33.333 21.86 13.19 32.18 4.24
34 35 8.023706 TGCGTTTCATTATAATACAAAACAGCA 58.976 29.630 23.35 23.35 35.72 4.41
35 36 8.311120 GTGCGTTTCATTATAATACAAAACAGC 58.689 33.333 19.64 20.46 32.34 4.40
36 37 9.554724 AGTGCGTTTCATTATAATACAAAACAG 57.445 29.630 19.64 15.56 0.00 3.16
37 38 9.549509 GAGTGCGTTTCATTATAATACAAAACA 57.450 29.630 19.64 12.12 0.00 2.83
38 39 9.006215 GGAGTGCGTTTCATTATAATACAAAAC 57.994 33.333 14.43 14.43 0.00 2.43
39 40 8.185505 GGGAGTGCGTTTCATTATAATACAAAA 58.814 33.333 0.00 0.00 0.00 2.44
40 41 7.201750 GGGGAGTGCGTTTCATTATAATACAAA 60.202 37.037 0.00 0.00 0.00 2.83
41 42 6.261381 GGGGAGTGCGTTTCATTATAATACAA 59.739 38.462 0.00 0.00 0.00 2.41
42 43 5.761234 GGGGAGTGCGTTTCATTATAATACA 59.239 40.000 0.00 0.00 0.00 2.29
43 44 5.995897 AGGGGAGTGCGTTTCATTATAATAC 59.004 40.000 0.00 0.00 0.00 1.89
44 45 5.995282 CAGGGGAGTGCGTTTCATTATAATA 59.005 40.000 0.00 0.00 0.00 0.98
45 46 4.821805 CAGGGGAGTGCGTTTCATTATAAT 59.178 41.667 0.00 0.00 0.00 1.28
46 47 4.196193 CAGGGGAGTGCGTTTCATTATAA 58.804 43.478 0.00 0.00 0.00 0.98
47 48 3.433031 CCAGGGGAGTGCGTTTCATTATA 60.433 47.826 0.00 0.00 0.00 0.98
48 49 2.643551 CAGGGGAGTGCGTTTCATTAT 58.356 47.619 0.00 0.00 0.00 1.28
49 50 1.339631 CCAGGGGAGTGCGTTTCATTA 60.340 52.381 0.00 0.00 0.00 1.90
50 51 0.609131 CCAGGGGAGTGCGTTTCATT 60.609 55.000 0.00 0.00 0.00 2.57
51 52 1.002134 CCAGGGGAGTGCGTTTCAT 60.002 57.895 0.00 0.00 0.00 2.57
52 53 2.429930 CCAGGGGAGTGCGTTTCA 59.570 61.111 0.00 0.00 0.00 2.69
53 54 3.056328 GCCAGGGGAGTGCGTTTC 61.056 66.667 0.00 0.00 0.00 2.78
54 55 3.884774 TGCCAGGGGAGTGCGTTT 61.885 61.111 0.00 0.00 0.00 3.60
55 56 4.643387 GTGCCAGGGGAGTGCGTT 62.643 66.667 0.00 0.00 0.00 4.84
57 58 4.335647 AAGTGCCAGGGGAGTGCG 62.336 66.667 0.00 0.00 0.00 5.34
58 59 2.674380 CAAGTGCCAGGGGAGTGC 60.674 66.667 0.00 0.00 0.00 4.40
59 60 2.674380 GCAAGTGCCAGGGGAGTG 60.674 66.667 0.00 0.00 34.31 3.51
60 61 2.011617 AAAGCAAGTGCCAGGGGAGT 62.012 55.000 0.00 0.00 43.38 3.85
61 62 1.228675 AAAGCAAGTGCCAGGGGAG 60.229 57.895 0.00 0.00 43.38 4.30
62 63 1.531365 CAAAGCAAGTGCCAGGGGA 60.531 57.895 0.00 0.00 43.38 4.81
63 64 2.576832 CCAAAGCAAGTGCCAGGGG 61.577 63.158 0.00 0.00 43.38 4.79
64 65 2.576832 CCCAAAGCAAGTGCCAGGG 61.577 63.158 9.94 9.94 43.38 4.45
65 66 1.114722 TTCCCAAAGCAAGTGCCAGG 61.115 55.000 0.00 0.00 43.38 4.45
66 67 0.752054 TTTCCCAAAGCAAGTGCCAG 59.248 50.000 0.00 0.00 43.38 4.85
67 68 0.752054 CTTTCCCAAAGCAAGTGCCA 59.248 50.000 0.00 0.00 43.38 4.92
68 69 0.033920 CCTTTCCCAAAGCAAGTGCC 59.966 55.000 0.00 0.00 43.38 5.01
69 70 0.752658 ACCTTTCCCAAAGCAAGTGC 59.247 50.000 0.00 0.00 42.49 4.40
70 71 2.695147 AGAACCTTTCCCAAAGCAAGTG 59.305 45.455 0.00 0.00 37.18 3.16
71 72 2.695147 CAGAACCTTTCCCAAAGCAAGT 59.305 45.455 0.00 0.00 37.18 3.16
72 73 2.695147 ACAGAACCTTTCCCAAAGCAAG 59.305 45.455 0.00 0.00 37.18 4.01
73 74 2.745968 ACAGAACCTTTCCCAAAGCAA 58.254 42.857 0.00 0.00 37.18 3.91
74 75 2.452600 ACAGAACCTTTCCCAAAGCA 57.547 45.000 0.00 0.00 37.18 3.91
75 76 2.035961 GGAACAGAACCTTTCCCAAAGC 59.964 50.000 0.00 0.00 36.07 3.51
76 77 2.293399 CGGAACAGAACCTTTCCCAAAG 59.707 50.000 0.00 0.00 38.50 2.77
77 78 2.303175 CGGAACAGAACCTTTCCCAAA 58.697 47.619 0.00 0.00 38.50 3.28
78 79 1.975660 CGGAACAGAACCTTTCCCAA 58.024 50.000 0.00 0.00 38.50 4.12
79 80 0.536460 GCGGAACAGAACCTTTCCCA 60.536 55.000 0.00 0.00 38.50 4.37
80 81 0.536460 TGCGGAACAGAACCTTTCCC 60.536 55.000 0.00 0.00 38.50 3.97
81 82 1.534729 ATGCGGAACAGAACCTTTCC 58.465 50.000 0.00 0.00 38.37 3.13
82 83 3.308530 CAAATGCGGAACAGAACCTTTC 58.691 45.455 0.00 0.00 0.00 2.62
83 84 2.035832 CCAAATGCGGAACAGAACCTTT 59.964 45.455 0.00 0.00 0.00 3.11
84 85 1.613437 CCAAATGCGGAACAGAACCTT 59.387 47.619 0.00 0.00 0.00 3.50
85 86 1.247567 CCAAATGCGGAACAGAACCT 58.752 50.000 0.00 0.00 0.00 3.50
86 87 0.958822 ACCAAATGCGGAACAGAACC 59.041 50.000 0.00 0.00 0.00 3.62
87 88 2.793278 AACCAAATGCGGAACAGAAC 57.207 45.000 0.00 0.00 0.00 3.01
88 89 2.554893 GGTAACCAAATGCGGAACAGAA 59.445 45.455 0.00 0.00 0.00 3.02
89 90 2.156098 GGTAACCAAATGCGGAACAGA 58.844 47.619 0.00 0.00 0.00 3.41
90 91 1.135803 CGGTAACCAAATGCGGAACAG 60.136 52.381 0.00 0.00 0.00 3.16
91 92 0.875728 CGGTAACCAAATGCGGAACA 59.124 50.000 0.00 0.00 0.00 3.18
92 93 0.876399 ACGGTAACCAAATGCGGAAC 59.124 50.000 0.00 0.00 0.00 3.62
93 94 2.469274 TACGGTAACCAAATGCGGAA 57.531 45.000 0.00 0.00 0.00 4.30
94 95 2.093606 TCATACGGTAACCAAATGCGGA 60.094 45.455 0.00 0.00 0.00 5.54
95 96 2.281517 TCATACGGTAACCAAATGCGG 58.718 47.619 0.00 0.00 0.00 5.69
96 97 4.201871 ACATTCATACGGTAACCAAATGCG 60.202 41.667 11.66 0.00 0.00 4.73
129 130 1.205657 GCGATTAGGTTCGAATGCGA 58.794 50.000 0.00 0.00 46.33 5.10
147 148 2.157085 GTCACTGCTAGTTTAACCACGC 59.843 50.000 0.00 0.00 0.00 5.34
178 179 4.829492 CCAAAGATTCCCCATAATGAGTCC 59.171 45.833 0.00 0.00 0.00 3.85
207 208 2.764010 AGTGTGTGGATAATACGGCTGA 59.236 45.455 0.00 0.00 0.00 4.26
225 226 1.741706 CCAGGCTGCTTGTGATTAGTG 59.258 52.381 9.56 0.00 0.00 2.74
295 299 8.708742 GCCCAAACTAGCAAAATTTAAAACTAG 58.291 33.333 11.93 11.93 34.61 2.57
313 321 1.678970 GAAGGATGCCGCCCAAACT 60.679 57.895 0.00 0.00 0.00 2.66
328 340 4.641094 CGGGGAGCATATACTACCTAGAAG 59.359 50.000 4.09 0.00 40.93 2.85
341 353 2.200370 ATCGGGTCGGGGAGCATA 59.800 61.111 0.00 0.00 0.00 3.14
393 422 2.503375 CGTCGTCGTTTCTCCCGG 60.503 66.667 0.00 0.00 0.00 5.73
399 428 2.458629 GTGCGTCGTCGTCGTTTC 59.541 61.111 13.09 0.00 39.49 2.78
457 496 5.027099 CGGCATCTTTTTGTTTTGTTTTGG 58.973 37.500 0.00 0.00 0.00 3.28
499 539 4.368315 ACGAAATAATACTCATGCTCGCA 58.632 39.130 0.00 0.00 0.00 5.10
505 545 6.920210 TCTGCAGAGACGAAATAATACTCATG 59.080 38.462 13.74 0.00 0.00 3.07
506 546 7.043961 TCTGCAGAGACGAAATAATACTCAT 57.956 36.000 13.74 0.00 0.00 2.90
507 547 6.451064 TCTGCAGAGACGAAATAATACTCA 57.549 37.500 13.74 0.00 0.00 3.41
508 548 6.920758 ACATCTGCAGAGACGAAATAATACTC 59.079 38.462 22.96 0.00 0.00 2.59
510 550 6.697455 TCACATCTGCAGAGACGAAATAATAC 59.303 38.462 22.96 0.00 0.00 1.89
575 615 1.250328 CAACAGAGAAATGGCTGGCA 58.750 50.000 6.31 6.31 36.47 4.92
576 616 0.108945 GCAACAGAGAAATGGCTGGC 60.109 55.000 0.00 0.00 36.47 4.85
577 617 0.529378 GGCAACAGAGAAATGGCTGG 59.471 55.000 0.00 0.00 36.47 4.85
578 618 1.250328 TGGCAACAGAGAAATGGCTG 58.750 50.000 0.00 0.00 46.17 4.85
579 619 3.751767 TGGCAACAGAGAAATGGCT 57.248 47.368 0.00 0.00 46.17 4.75
631 671 6.605849 CAAATTCTGTGTCATGTGTAAGGAG 58.394 40.000 0.00 0.00 0.00 3.69
632 672 5.048782 GCAAATTCTGTGTCATGTGTAAGGA 60.049 40.000 0.00 0.00 0.00 3.36
633 673 5.048504 AGCAAATTCTGTGTCATGTGTAAGG 60.049 40.000 0.00 0.00 0.00 2.69
647 687 0.039798 ACGCAGTGCAGCAAATTCTG 60.040 50.000 16.83 0.85 42.51 3.02
806 1441 4.619140 GCAATCGATGGCTGCGGC 62.619 66.667 17.87 9.72 37.82 6.53
807 1442 2.890109 GAGCAATCGATGGCTGCGG 61.890 63.158 31.73 0.97 41.22 5.69
808 1443 1.829349 GAGAGCAATCGATGGCTGCG 61.829 60.000 31.73 1.60 41.22 5.18
811 1446 0.529337 CGTGAGAGCAATCGATGGCT 60.529 55.000 27.39 27.39 44.48 4.75
871 1506 5.127356 GGGTGGTGGAGCTATATGTATAGAC 59.873 48.000 10.48 4.46 38.30 2.59
916 1551 2.788191 CTTTCTTCTGCTCGGGCGGT 62.788 60.000 17.41 0.00 44.62 5.68
920 1555 1.355066 GACGCTTTCTTCTGCTCGGG 61.355 60.000 0.00 0.00 0.00 5.14
954 1602 2.047655 CCGGTGGTTTGCGCTCTA 60.048 61.111 9.73 0.00 0.00 2.43
984 1632 0.037303 CCATCAATCCTGCCGCCTAT 59.963 55.000 0.00 0.00 0.00 2.57
985 1633 1.451504 CCATCAATCCTGCCGCCTA 59.548 57.895 0.00 0.00 0.00 3.93
996 1649 0.982852 TCTCCACCTCCGCCATCAAT 60.983 55.000 0.00 0.00 0.00 2.57
1086 1739 2.685380 AGGCTCTTGACCCCGGAG 60.685 66.667 0.73 0.00 0.00 4.63
1650 2328 5.477510 TGACTGCAATTTGAACAAAACAGT 58.522 33.333 21.78 21.78 41.44 3.55
1666 2344 2.545526 CGAAAGAAAGAAGCTGACTGCA 59.454 45.455 7.11 0.00 45.94 4.41
1675 2353 5.050702 ACGAGAAGAAAGCGAAAGAAAGAAG 60.051 40.000 0.00 0.00 0.00 2.85
1676 2354 4.809426 ACGAGAAGAAAGCGAAAGAAAGAA 59.191 37.500 0.00 0.00 0.00 2.52
1677 2355 4.369182 ACGAGAAGAAAGCGAAAGAAAGA 58.631 39.130 0.00 0.00 0.00 2.52
1678 2356 4.717188 ACGAGAAGAAAGCGAAAGAAAG 57.283 40.909 0.00 0.00 0.00 2.62
1695 2373 4.271049 TCAAAGAGCAACAAGAAGAACGAG 59.729 41.667 0.00 0.00 0.00 4.18
1696 2374 4.188462 TCAAAGAGCAACAAGAAGAACGA 58.812 39.130 0.00 0.00 0.00 3.85
1697 2375 4.536364 TCAAAGAGCAACAAGAAGAACG 57.464 40.909 0.00 0.00 0.00 3.95
1698 2376 6.017605 TCAGATCAAAGAGCAACAAGAAGAAC 60.018 38.462 0.00 0.00 0.00 3.01
1699 2377 6.057533 TCAGATCAAAGAGCAACAAGAAGAA 58.942 36.000 0.00 0.00 0.00 2.52
1701 2379 5.929278 CTCAGATCAAAGAGCAACAAGAAG 58.071 41.667 0.00 0.00 0.00 2.85
1702 2380 5.936686 CTCAGATCAAAGAGCAACAAGAA 57.063 39.130 0.00 0.00 0.00 2.52
1715 2394 4.548451 ACAGATCACTTGCTCAGATCAA 57.452 40.909 0.00 0.00 40.39 2.57
1721 2400 3.131223 GGTAGCTACAGATCACTTGCTCA 59.869 47.826 24.75 0.00 32.72 4.26
1781 2460 2.882876 CACCAGCCAAGCATGCTC 59.117 61.111 22.93 8.91 36.81 4.26
1792 2476 1.666189 GTATTTCTTCGGAGCACCAGC 59.334 52.381 0.00 0.00 42.56 4.85
1793 2477 1.927174 CGTATTTCTTCGGAGCACCAG 59.073 52.381 0.00 0.00 35.59 4.00
1799 2483 1.071239 CGCATGCGTATTTCTTCGGAG 60.071 52.381 31.33 0.00 34.35 4.63
1802 2486 2.712132 TTCGCATGCGTATTTCTTCG 57.288 45.000 36.50 7.77 40.74 3.79
1818 2502 5.322310 CAAGAAGAAATGTCTGCAGATTCG 58.678 41.667 21.47 3.18 30.64 3.34
1852 2536 8.495949 CGCATTCCTGTACTAGTATTTTATTGG 58.504 37.037 5.75 1.98 0.00 3.16
1853 2537 9.042008 ACGCATTCCTGTACTAGTATTTTATTG 57.958 33.333 5.75 2.72 0.00 1.90
1855 2539 8.202137 ACACGCATTCCTGTACTAGTATTTTAT 58.798 33.333 5.75 0.00 0.00 1.40
1858 2542 5.810587 CACACGCATTCCTGTACTAGTATTT 59.189 40.000 5.75 0.00 0.00 1.40
1859 2543 5.348986 CACACGCATTCCTGTACTAGTATT 58.651 41.667 5.75 0.00 0.00 1.89
1860 2544 4.736759 GCACACGCATTCCTGTACTAGTAT 60.737 45.833 5.75 0.00 38.36 2.12
1862 2546 2.674177 GCACACGCATTCCTGTACTAGT 60.674 50.000 0.00 0.00 38.36 2.57
1863 2547 1.927174 GCACACGCATTCCTGTACTAG 59.073 52.381 0.00 0.00 38.36 2.57
1864 2548 1.273886 TGCACACGCATTCCTGTACTA 59.726 47.619 0.00 0.00 45.36 1.82
1866 2550 2.539003 TGCACACGCATTCCTGTAC 58.461 52.632 0.00 0.00 45.36 2.90
1889 2603 7.338800 AGAATATGTTTCAGTGCCTTATTGG 57.661 36.000 0.00 0.00 39.35 3.16
1896 2610 4.096984 CCTCCAAGAATATGTTTCAGTGCC 59.903 45.833 0.00 0.00 0.00 5.01
2024 2756 5.864474 GCTGAGTATGTTTCTCGAAAGAAGA 59.136 40.000 0.00 0.00 42.36 2.87
2028 2760 3.921021 ACGCTGAGTATGTTTCTCGAAAG 59.079 43.478 0.00 0.00 34.99 2.62
2030 2762 3.570926 ACGCTGAGTATGTTTCTCGAA 57.429 42.857 0.00 0.00 34.99 3.71
2031 2763 3.570926 AACGCTGAGTATGTTTCTCGA 57.429 42.857 0.00 0.00 34.99 4.04
2032 2764 4.647291 AAAACGCTGAGTATGTTTCTCG 57.353 40.909 1.38 0.00 34.92 4.04
2060 2792 8.795786 TTTTGATGTCTCTTTCCGTTAAAATG 57.204 30.769 0.00 0.00 0.00 2.32
2070 2802 3.057245 GTGGCCCTTTTGATGTCTCTTTC 60.057 47.826 0.00 0.00 0.00 2.62
2127 2859 2.273179 GGTTCCTGGGCCCGAAAAC 61.273 63.158 19.37 19.49 0.00 2.43
2174 2906 0.390078 TTATTTCCGGCGTCGCAGAA 60.390 50.000 20.50 17.62 39.69 3.02
2221 3107 3.272847 GGTGGGGTGGGGTGGAAT 61.273 66.667 0.00 0.00 0.00 3.01
2256 3142 3.618855 AACCCTAGGAGCGGAGGCA 62.619 63.158 11.48 0.00 43.41 4.75
2484 3381 1.831652 CTTGGAGAGGACCTTGGCGT 61.832 60.000 0.00 0.00 0.00 5.68
2592 3498 3.181967 CGTCGAAGGCCTTGAGCG 61.182 66.667 26.25 20.62 45.17 5.03


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

AutoCloner maintained by Alex Coulton.