Multiple sequence alignment - TraesCS2B01G476900

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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 TraesCS2B01G476900 chr2B 100.000 3491 0 0 1 3491 673923774 673927264 0.000000e+00 6447.0
1 TraesCS2B01G476900 chr2D 87.985 3171 203 89 418 3491 563291077 563294166 0.000000e+00 3581.0
2 TraesCS2B01G476900 chr2D 89.438 445 38 7 1 438 563290623 563291065 1.420000e-153 553.0
3 TraesCS2B01G476900 chr2A 86.858 2199 120 76 1197 3299 703698915 703701040 0.000000e+00 2303.0
4 TraesCS2B01G476900 chr2A 88.789 446 33 9 32 472 703697677 703698110 6.630000e-147 531.0
5 TraesCS2B01G476900 chr2A 86.525 423 20 14 511 899 703698119 703698538 6.920000e-117 431.0
6 TraesCS2B01G476900 chr4A 94.000 50 3 0 2570 2619 46577497 46577448 3.740000e-10 76.8


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 TraesCS2B01G476900 chr2B 673923774 673927264 3490 False 6447.000000 6447 100.000000 1 3491 1 chr2B.!!$F1 3490
1 TraesCS2B01G476900 chr2D 563290623 563294166 3543 False 2067.000000 3581 88.711500 1 3491 2 chr2D.!!$F1 3490
2 TraesCS2B01G476900 chr2A 703697677 703701040 3363 False 1088.333333 2303 87.390667 32 3299 3 chr2A.!!$F1 3267

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
204 212 0.899717 CCCATGTGGTGTCCTTTGGG 60.900 60.0 0.0 0.0 38.01 4.12 F
1018 1124 0.560688 GATGGACTCCTCCTCCTCCT 59.439 60.0 0.0 0.0 37.48 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1352 1534 0.178947 GGGAGGATGGACGGAGAGAT 60.179 60.0 0.00 0.00 0.00 2.75 R
2496 2716 0.037447 GGGAAAAGGAGCAGCTCAGT 59.963 55.0 24.09 7.73 31.08 3.41 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
37 38 2.414481 CTCGACGAGTCCGAGTCTTTTA 59.586 50.000 16.83 0.00 45.89 1.52
60 61 5.565592 TCGTCTTTATTTACACTCCGCTA 57.434 39.130 0.00 0.00 0.00 4.26
80 86 4.641989 GCTATGGACAATGACCACATTTCT 59.358 41.667 6.59 0.00 43.17 2.52
85 91 1.541147 CAATGACCACATTTCTGGCGT 59.459 47.619 0.00 0.00 43.17 5.68
144 151 3.586470 TGGGTGTTTACTTCATGTGGT 57.414 42.857 0.00 0.00 0.00 4.16
172 179 1.352156 GCTCGAGATTTCGGCGTTGT 61.352 55.000 18.75 0.00 46.67 3.32
183 190 1.527380 GGCGTTGTCTTGGTTGGGA 60.527 57.895 0.00 0.00 0.00 4.37
186 194 1.165270 CGTTGTCTTGGTTGGGATCC 58.835 55.000 1.92 1.92 0.00 3.36
204 212 0.899717 CCCATGTGGTGTCCTTTGGG 60.900 60.000 0.00 0.00 38.01 4.12
212 220 1.145119 GGTGTCCTTTGGGGTTTCTCT 59.855 52.381 0.00 0.00 36.25 3.10
218 226 4.649674 GTCCTTTGGGGTTTCTCTCTTTTT 59.350 41.667 0.00 0.00 36.25 1.94
243 251 2.104111 TGCTAGCGGTGCCTTGTATTAT 59.896 45.455 10.77 0.00 0.00 1.28
267 275 5.941647 TGGTTTAACATAACCTAGGTTGCTC 59.058 40.000 33.19 15.44 46.28 4.26
331 339 4.513442 GTGCCATAATCTTGTACTCCACA 58.487 43.478 0.00 0.00 34.51 4.17
336 344 6.425114 GCCATAATCTTGTACTCCACATAGTG 59.575 42.308 0.00 0.00 36.90 2.74
340 348 9.959721 ATAATCTTGTACTCCACATAGTGTTTT 57.040 29.630 0.00 0.00 36.90 2.43
351 359 6.017440 TCCACATAGTGTTTTGTGTTTCTAGC 60.017 38.462 2.77 0.00 41.27 3.42
354 362 4.531659 AGTGTTTTGTGTTTCTAGCGTC 57.468 40.909 0.00 0.00 0.00 5.19
433 472 3.330267 GGCTCTGTCCTCTTGTAAACTG 58.670 50.000 0.00 0.00 0.00 3.16
435 474 4.381411 GCTCTGTCCTCTTGTAAACTGTT 58.619 43.478 0.00 0.00 0.00 3.16
466 507 4.893424 AAAAGTGCGTGACATGTAAAGT 57.107 36.364 0.00 0.00 0.00 2.66
469 510 4.468095 AGTGCGTGACATGTAAAGTTTC 57.532 40.909 0.00 0.00 0.00 2.78
470 511 4.127171 AGTGCGTGACATGTAAAGTTTCT 58.873 39.130 0.00 0.00 0.00 2.52
471 512 4.211374 AGTGCGTGACATGTAAAGTTTCTC 59.789 41.667 0.00 0.00 0.00 2.87
532 573 1.215423 AGTTTCTCAACAAGCACCCCT 59.785 47.619 0.00 0.00 35.05 4.79
533 574 1.609072 GTTTCTCAACAAGCACCCCTC 59.391 52.381 0.00 0.00 32.54 4.30
534 575 1.140312 TTCTCAACAAGCACCCCTCT 58.860 50.000 0.00 0.00 0.00 3.69
535 576 1.140312 TCTCAACAAGCACCCCTCTT 58.860 50.000 0.00 0.00 0.00 2.85
661 726 1.122680 GAAGCGTCGAGAAACGTTGAG 59.877 52.381 0.00 0.00 44.38 3.02
1018 1124 0.560688 GATGGACTCCTCCTCCTCCT 59.439 60.000 0.00 0.00 37.48 3.69
1275 1457 0.942962 CGTACGGCTACTTCCTCGAT 59.057 55.000 7.57 0.00 0.00 3.59
1369 1551 0.965439 CCATCTCTCCGTCCATCCTC 59.035 60.000 0.00 0.00 0.00 3.71
1372 1554 1.834822 CTCTCCGTCCATCCTCCCC 60.835 68.421 0.00 0.00 0.00 4.81
1417 1600 0.818040 GTGTTTGCCTGGGTCTTCGT 60.818 55.000 0.00 0.00 0.00 3.85
1419 1602 1.029681 GTTTGCCTGGGTCTTCGTTT 58.970 50.000 0.00 0.00 0.00 3.60
1421 1609 0.472471 TTGCCTGGGTCTTCGTTTCT 59.528 50.000 0.00 0.00 0.00 2.52
1427 1615 0.108019 GGGTCTTCGTTTCTGTGGGT 59.892 55.000 0.00 0.00 0.00 4.51
1428 1616 1.509703 GGTCTTCGTTTCTGTGGGTC 58.490 55.000 0.00 0.00 0.00 4.46
1429 1617 1.509703 GTCTTCGTTTCTGTGGGTCC 58.490 55.000 0.00 0.00 0.00 4.46
1430 1618 0.395312 TCTTCGTTTCTGTGGGTCCC 59.605 55.000 0.00 0.00 0.00 4.46
1431 1619 0.605589 CTTCGTTTCTGTGGGTCCCC 60.606 60.000 5.13 0.00 0.00 4.81
1432 1620 2.358247 CGTTTCTGTGGGTCCCCG 60.358 66.667 5.13 0.00 39.42 5.73
1433 1621 2.671963 GTTTCTGTGGGTCCCCGC 60.672 66.667 5.13 9.04 46.15 6.13
1490 1678 2.237893 TGGTATTTCTCGGGGGAAGAAC 59.762 50.000 0.00 0.00 32.64 3.01
1524 1713 3.460868 GGCCGGGGAAAAGCCATG 61.461 66.667 2.18 0.00 46.34 3.66
1526 1715 2.037208 CCGGGGAAAAGCCATGGT 59.963 61.111 14.67 0.00 38.95 3.55
1748 1937 2.685388 TGATTCCATTAAATTCCGCGCA 59.315 40.909 8.75 0.00 0.00 6.09
1787 1976 5.253335 GCTTAATTACGGTCACGATTTCAC 58.747 41.667 0.00 0.00 44.60 3.18
1826 2020 5.935945 TGGAGTTACCACTGATTTTTCTCA 58.064 37.500 0.00 0.00 44.64 3.27
1839 2033 8.190784 ACTGATTTTTCTCAACAAAGTTACTGG 58.809 33.333 0.00 0.00 0.00 4.00
1964 2167 2.805657 GCTGTTTGTTCCGTCTGGTAGT 60.806 50.000 0.00 0.00 36.30 2.73
1965 2168 3.553508 GCTGTTTGTTCCGTCTGGTAGTA 60.554 47.826 0.00 0.00 36.30 1.82
1967 2170 3.890756 TGTTTGTTCCGTCTGGTAGTAGA 59.109 43.478 0.00 0.00 36.30 2.59
1968 2171 4.525487 TGTTTGTTCCGTCTGGTAGTAGAT 59.475 41.667 0.00 0.00 36.30 1.98
1969 2172 4.713824 TTGTTCCGTCTGGTAGTAGATG 57.286 45.455 0.00 0.00 36.30 2.90
1972 2175 2.068834 CCGTCTGGTAGTAGATGGGT 57.931 55.000 6.19 0.00 45.91 4.51
1973 2176 2.385803 CCGTCTGGTAGTAGATGGGTT 58.614 52.381 6.19 0.00 45.91 4.11
1974 2177 3.559069 CCGTCTGGTAGTAGATGGGTTA 58.441 50.000 6.19 0.00 45.91 2.85
1975 2178 3.956199 CCGTCTGGTAGTAGATGGGTTAA 59.044 47.826 6.19 0.00 45.91 2.01
2031 2239 2.159627 CCTTCCGTTTCCGTTTGAGATG 59.840 50.000 0.00 0.00 0.00 2.90
2052 2260 2.991190 GGTGATTTTGCTGCATGAAGTG 59.009 45.455 1.84 0.00 0.00 3.16
2073 2281 7.158099 AGTGGAAAACTATATGGTTCTTTGC 57.842 36.000 4.79 3.32 37.36 3.68
2084 2292 3.712187 TGGTTCTTTGCGAATTGGTTTC 58.288 40.909 0.00 0.00 33.45 2.78
2175 2390 6.081049 TGTTTATCGCTAACAAACATTTCCG 58.919 36.000 0.00 0.00 37.27 4.30
2186 2401 0.250727 ACATTTCCGTGTGTGAGGGG 60.251 55.000 0.00 0.00 0.00 4.79
2218 2433 8.966868 TGATAAGACAGACATGTTACATGACTA 58.033 33.333 29.17 14.31 40.68 2.59
2219 2434 9.239002 GATAAGACAGACATGTTACATGACTAC 57.761 37.037 29.17 22.27 40.68 2.73
2220 2435 5.641709 AGACAGACATGTTACATGACTACG 58.358 41.667 29.17 19.05 40.68 3.51
2245 2460 2.146342 CGTTGAGTGATTGTCAAGCCT 58.854 47.619 0.00 0.00 34.59 4.58
2274 2494 1.153978 GGTTCATGCCATGCACACG 60.154 57.895 9.62 0.00 43.04 4.49
2279 2499 1.751544 ATGCCATGCACACGCTGAT 60.752 52.632 0.00 0.00 43.04 2.90
2439 2659 4.649705 TCCCTGGGCGAGGTGGAA 62.650 66.667 14.85 0.00 40.87 3.53
2496 2716 4.069232 CTCGCCGGCTGACAGGAA 62.069 66.667 26.68 0.00 0.00 3.36
2497 2717 4.373116 TCGCCGGCTGACAGGAAC 62.373 66.667 26.68 0.00 0.00 3.62
2498 2718 4.379243 CGCCGGCTGACAGGAACT 62.379 66.667 26.68 0.00 43.88 3.01
2527 2747 0.041684 CTTTTCCCCCAGGCCAAGAT 59.958 55.000 5.01 0.00 0.00 2.40
2530 2750 3.023116 CCCCCAGGCCAAGATCCA 61.023 66.667 5.01 0.00 0.00 3.41
2553 2787 4.044065 ACCATTACCCACCATCAGAAGAAA 59.956 41.667 0.00 0.00 0.00 2.52
2558 2792 4.145052 ACCCACCATCAGAAGAAAGAAAC 58.855 43.478 0.00 0.00 0.00 2.78
2559 2793 4.141158 ACCCACCATCAGAAGAAAGAAACT 60.141 41.667 0.00 0.00 0.00 2.66
2586 2833 4.398044 GCTTAATTACTTACAGCCAGGCAA 59.602 41.667 15.80 0.00 0.00 4.52
2662 2918 1.478510 TGTTGCGACCATGGTTTTTGT 59.521 42.857 20.85 0.00 0.00 2.83
2718 2977 7.502895 ACGAACATGATGTATAGGTTAGAGACT 59.497 37.037 0.00 0.00 0.00 3.24
2721 2980 8.768501 ACATGATGTATAGGTTAGAGACTGAA 57.231 34.615 0.00 0.00 0.00 3.02
2722 2981 8.855110 ACATGATGTATAGGTTAGAGACTGAAG 58.145 37.037 0.00 0.00 0.00 3.02
2745 3004 1.607467 GGAAATGGTGGCCAGTGCT 60.607 57.895 5.11 0.00 36.75 4.40
2746 3005 1.588082 GAAATGGTGGCCAGTGCTG 59.412 57.895 5.11 0.00 36.75 4.41
2747 3006 2.496828 GAAATGGTGGCCAGTGCTGC 62.497 60.000 5.11 0.00 36.75 5.25
2748 3007 3.518552 AATGGTGGCCAGTGCTGCT 62.519 57.895 5.11 0.00 36.75 4.24
2749 3008 3.518552 ATGGTGGCCAGTGCTGCTT 62.519 57.895 5.11 0.00 36.75 3.91
2750 3009 3.368571 GGTGGCCAGTGCTGCTTC 61.369 66.667 5.11 0.00 37.74 3.86
2751 3010 3.368571 GTGGCCAGTGCTGCTTCC 61.369 66.667 5.11 0.00 37.74 3.46
2752 3011 3.573229 TGGCCAGTGCTGCTTCCT 61.573 61.111 0.00 0.00 37.74 3.36
2753 3012 2.223443 TGGCCAGTGCTGCTTCCTA 61.223 57.895 0.00 0.00 37.74 2.94
2754 3013 1.225704 GGCCAGTGCTGCTTCCTAT 59.774 57.895 0.00 0.00 37.74 2.57
2755 3014 1.099879 GGCCAGTGCTGCTTCCTATG 61.100 60.000 0.00 0.00 37.74 2.23
2756 3015 1.722636 GCCAGTGCTGCTTCCTATGC 61.723 60.000 0.00 0.00 33.53 3.14
2757 3016 0.107312 CCAGTGCTGCTTCCTATGCT 60.107 55.000 0.00 0.00 0.00 3.79
2760 3019 1.099879 GTGCTGCTTCCTATGCTGGG 61.100 60.000 0.00 0.00 0.00 4.45
2761 3020 1.273986 TGCTGCTTCCTATGCTGGGA 61.274 55.000 0.00 0.00 0.00 4.37
2762 3021 0.817229 GCTGCTTCCTATGCTGGGAC 60.817 60.000 0.00 0.00 31.94 4.46
2764 3023 0.543277 TGCTTCCTATGCTGGGACTG 59.457 55.000 0.00 0.00 31.94 3.51
2765 3024 0.543749 GCTTCCTATGCTGGGACTGT 59.456 55.000 0.00 0.00 31.94 3.55
2766 3025 1.745141 GCTTCCTATGCTGGGACTGTG 60.745 57.143 0.00 0.00 31.94 3.66
2767 3026 0.253044 TTCCTATGCTGGGACTGTGC 59.747 55.000 0.00 0.00 31.94 4.57
2768 3027 0.618680 TCCTATGCTGGGACTGTGCT 60.619 55.000 0.00 0.00 0.00 4.40
2769 3028 0.463295 CCTATGCTGGGACTGTGCTG 60.463 60.000 0.00 0.00 0.00 4.41
2770 3029 1.078214 TATGCTGGGACTGTGCTGC 60.078 57.895 0.00 5.21 0.00 5.25
2772 3031 4.648626 GCTGGGACTGTGCTGCCA 62.649 66.667 0.00 0.00 0.00 4.92
2773 3032 2.359602 CTGGGACTGTGCTGCCAG 60.360 66.667 14.07 14.07 42.68 4.85
2774 3033 3.914579 CTGGGACTGTGCTGCCAGG 62.915 68.421 18.12 3.01 44.16 4.45
2775 3034 4.729918 GGGACTGTGCTGCCAGGG 62.730 72.222 18.12 1.47 36.75 4.45
2776 3035 4.729918 GGACTGTGCTGCCAGGGG 62.730 72.222 18.12 0.00 36.75 4.79
2777 3036 3.958860 GACTGTGCTGCCAGGGGT 61.959 66.667 18.12 3.20 36.75 4.95
2827 3121 8.973835 TTTTCTTTGTGTTTTGTAGTAGTTGG 57.026 30.769 0.00 0.00 0.00 3.77
2878 3175 4.783764 AAGGTTTTTCTAATGAAGCGGG 57.216 40.909 0.00 0.00 33.28 6.13
2892 3189 2.193536 GCGGGTGGAACATATGGGC 61.194 63.158 7.80 0.00 44.52 5.36
2910 3207 4.724399 TGGGCAAAGAAGAAACTGACATA 58.276 39.130 0.00 0.00 0.00 2.29
2985 3283 2.035617 CTTGCGAGTTGTGCGTGTGT 62.036 55.000 0.00 0.00 34.24 3.72
2990 3288 0.247655 GAGTTGTGCGTGTGTGTGTG 60.248 55.000 0.00 0.00 0.00 3.82
2991 3289 0.953471 AGTTGTGCGTGTGTGTGTGT 60.953 50.000 0.00 0.00 0.00 3.72
2992 3290 0.792729 GTTGTGCGTGTGTGTGTGTG 60.793 55.000 0.00 0.00 0.00 3.82
2993 3291 1.231296 TTGTGCGTGTGTGTGTGTGT 61.231 50.000 0.00 0.00 0.00 3.72
2994 3292 1.231296 TGTGCGTGTGTGTGTGTGTT 61.231 50.000 0.00 0.00 0.00 3.32
2997 3295 0.520412 GCGTGTGTGTGTGTGTTGAC 60.520 55.000 0.00 0.00 0.00 3.18
3034 3332 1.140252 TGGCCGGCTCTCCTTATTAAC 59.860 52.381 28.56 4.81 0.00 2.01
3058 3362 9.495572 AACTTGCTGCTAGTATAATAATTCTCC 57.504 33.333 16.64 0.00 0.00 3.71
3061 3365 7.539436 TGCTGCTAGTATAATAATTCTCCGAG 58.461 38.462 0.00 0.00 0.00 4.63
3089 3403 6.295039 TGTCGATGTTGAAAAACCTAACTC 57.705 37.500 0.00 0.00 0.00 3.01
3122 3437 5.118642 TCATGCACGTTTCATTTTCATGA 57.881 34.783 0.00 0.00 37.67 3.07
3124 3439 5.801444 TCATGCACGTTTCATTTTCATGATC 59.199 36.000 0.00 0.00 39.28 2.92
3179 3494 2.352503 ACGCCTTCATTCATGTTTGC 57.647 45.000 0.00 0.00 0.00 3.68
3199 3514 0.812014 TTGCTCGCAACGGTGAAAGA 60.812 50.000 3.55 0.00 32.14 2.52
3207 3522 2.808543 GCAACGGTGAAAGATCTCACTT 59.191 45.455 3.55 0.00 44.33 3.16
3209 3524 4.058124 CAACGGTGAAAGATCTCACTTCA 58.942 43.478 13.14 9.10 44.33 3.02
3210 3525 3.654414 ACGGTGAAAGATCTCACTTCAC 58.346 45.455 22.45 22.45 44.33 3.18
3211 3526 3.069586 ACGGTGAAAGATCTCACTTCACA 59.930 43.478 27.76 8.08 44.33 3.58
3213 3528 3.999663 GGTGAAAGATCTCACTTCACAGG 59.000 47.826 27.76 0.00 44.33 4.00
3214 3529 3.434984 GTGAAAGATCTCACTTCACAGGC 59.565 47.826 24.35 6.21 42.11 4.85
3215 3530 3.326006 TGAAAGATCTCACTTCACAGGCT 59.674 43.478 4.53 0.00 0.00 4.58
3216 3531 3.608316 AAGATCTCACTTCACAGGCTC 57.392 47.619 0.00 0.00 0.00 4.70
3217 3532 2.533916 AGATCTCACTTCACAGGCTCA 58.466 47.619 0.00 0.00 0.00 4.26
3218 3533 2.496871 AGATCTCACTTCACAGGCTCAG 59.503 50.000 0.00 0.00 0.00 3.35
3219 3534 0.319728 TCTCACTTCACAGGCTCAGC 59.680 55.000 0.00 0.00 0.00 4.26
3260 3575 4.141482 GGAACTAGCCCATCATACTTTCCA 60.141 45.833 0.00 0.00 31.98 3.53
3333 3651 3.405592 GATGTCACGCGGCGTAGGA 62.406 63.158 28.93 19.20 38.32 2.94
3375 3693 2.890945 CCGGAAACAGAAACCATTTCCT 59.109 45.455 0.00 0.00 46.17 3.36
3383 3701 4.020218 ACAGAAACCATTTCCTCGATCTCA 60.020 41.667 0.00 0.00 40.54 3.27
3390 3708 3.594603 TTTCCTCGATCTCAGTTGACC 57.405 47.619 0.00 0.00 0.00 4.02
3394 3712 3.056536 TCCTCGATCTCAGTTGACCTTTG 60.057 47.826 0.00 0.00 0.00 2.77
3429 3747 3.254024 AAATCGTGGCCGGACAGCT 62.254 57.895 12.52 0.00 33.95 4.24
3474 3792 9.716507 ATTTTAAAAATCAAGATCGATACGGTG 57.283 29.630 4.44 0.00 0.00 4.94
3475 3793 4.795970 AAAATCAAGATCGATACGGTGC 57.204 40.909 0.00 0.00 0.00 5.01
3476 3794 2.440539 ATCAAGATCGATACGGTGCC 57.559 50.000 0.00 0.00 0.00 5.01
3477 3795 0.030235 TCAAGATCGATACGGTGCCG 59.970 55.000 9.29 9.29 46.03 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.007385 AGCGGAGTGTAAATAAAGACGAT 57.993 39.130 0.00 0.00 0.00 3.73
60 61 3.765511 CCAGAAATGTGGTCATTGTCCAT 59.234 43.478 5.92 0.00 42.60 3.41
80 86 0.680601 ATGCCATTCATCACACGCCA 60.681 50.000 0.00 0.00 0.00 5.69
85 91 0.335705 ACCCCATGCCATTCATCACA 59.664 50.000 0.00 0.00 31.79 3.58
144 151 2.607187 GAAATCTCGAGCACGGAAAGA 58.393 47.619 7.81 0.00 40.21 2.52
183 190 1.272648 CCAAAGGACACCACATGGGAT 60.273 52.381 0.00 0.00 41.15 3.85
186 194 0.899717 CCCCAAAGGACACCACATGG 60.900 60.000 0.00 0.00 38.24 3.66
204 212 6.146216 GCTAGCAAAGAAAAAGAGAGAAACC 58.854 40.000 10.63 0.00 0.00 3.27
212 220 2.031157 GCACCGCTAGCAAAGAAAAAGA 60.031 45.455 16.45 0.00 0.00 2.52
218 226 0.955428 CAAGGCACCGCTAGCAAAGA 60.955 55.000 16.45 0.00 0.00 2.52
243 251 7.025537 GGAGCAACCTAGGTTATGTTAAACCA 61.026 42.308 26.66 0.00 42.37 3.67
267 275 4.510167 AAACATCTAGAGGGTTGGATGG 57.490 45.455 6.93 0.00 39.61 3.51
331 339 5.989777 AGACGCTAGAAACACAAAACACTAT 59.010 36.000 0.00 0.00 0.00 2.12
336 344 4.204370 GCAAAGACGCTAGAAACACAAAAC 59.796 41.667 0.00 0.00 0.00 2.43
340 348 2.833794 AGCAAAGACGCTAGAAACACA 58.166 42.857 0.00 0.00 41.55 3.72
369 377 2.860009 CTAGCCAGATGGACAATGCAT 58.140 47.619 2.18 0.00 37.39 3.96
445 484 4.893424 ACTTTACATGTCACGCACTTTT 57.107 36.364 0.00 0.00 0.00 2.27
466 507 8.311836 ACAACTTCGGATGTTTATAGAGAGAAA 58.688 33.333 6.54 0.00 0.00 2.52
469 510 7.484975 AGACAACTTCGGATGTTTATAGAGAG 58.515 38.462 6.54 0.00 31.07 3.20
470 511 7.406031 AGACAACTTCGGATGTTTATAGAGA 57.594 36.000 6.54 0.00 31.07 3.10
471 512 6.697892 GGAGACAACTTCGGATGTTTATAGAG 59.302 42.308 6.54 0.00 31.07 2.43
532 573 1.529152 TAGGTTGCGTGCTCCGAAGA 61.529 55.000 0.43 0.00 39.56 2.87
533 574 1.080093 TAGGTTGCGTGCTCCGAAG 60.080 57.895 0.43 0.00 39.56 3.79
534 575 1.373748 GTAGGTTGCGTGCTCCGAA 60.374 57.895 0.43 0.00 39.56 4.30
535 576 2.260434 GTAGGTTGCGTGCTCCGA 59.740 61.111 0.43 0.00 39.56 4.55
722 816 4.796495 CTTACTGGTGGGGCCGCC 62.796 72.222 18.45 10.45 46.15 6.13
770 869 4.354387 TGGTTTTATTAAGTGAGTGGGGGA 59.646 41.667 0.00 0.00 0.00 4.81
1275 1457 4.399395 CGGCAGAGGAAGCAGGCA 62.399 66.667 0.00 0.00 0.00 4.75
1346 1528 2.833582 GGACGGAGAGATGGCGGA 60.834 66.667 0.00 0.00 0.00 5.54
1349 1531 1.118356 AGGATGGACGGAGAGATGGC 61.118 60.000 0.00 0.00 0.00 4.40
1352 1534 0.178947 GGGAGGATGGACGGAGAGAT 60.179 60.000 0.00 0.00 0.00 2.75
1355 1537 2.282446 GGGGAGGATGGACGGAGA 59.718 66.667 0.00 0.00 0.00 3.71
1372 1554 1.075600 GGAGTGAGGAGGAGGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
1375 1557 3.509290 ACGGAGTGAGGAGGAGGA 58.491 61.111 0.00 0.00 42.51 3.71
1490 1678 0.732538 GCCGGCGGTCAAAATTTCTG 60.733 55.000 28.82 0.00 0.00 3.02
1570 1759 5.449862 GCACCAAGAAACGAATGGCATTATA 60.450 40.000 13.65 0.00 37.77 0.98
1760 1949 0.654160 GTGACCGTAATTAAGCCCGC 59.346 55.000 0.00 0.00 0.00 6.13
1826 2020 3.525800 ATCCTGGCCAGTAACTTTGTT 57.474 42.857 30.63 6.35 0.00 2.83
1839 2033 1.494960 AGTCTCTCCTGAATCCTGGC 58.505 55.000 0.00 0.00 0.00 4.85
1881 2079 7.396055 CAGAAGGTCAGGTAATAATCCCAAAAA 59.604 37.037 0.00 0.00 0.00 1.94
1882 2080 6.889722 CAGAAGGTCAGGTAATAATCCCAAAA 59.110 38.462 0.00 0.00 0.00 2.44
1896 2099 2.702478 TGGCATCTATCAGAAGGTCAGG 59.298 50.000 0.00 0.00 0.00 3.86
1898 2101 4.384537 CCTTTGGCATCTATCAGAAGGTCA 60.385 45.833 2.81 0.00 0.00 4.02
1901 2104 3.881688 CACCTTTGGCATCTATCAGAAGG 59.118 47.826 8.42 8.42 38.45 3.46
1964 2167 7.996644 AGTTTCTGTTCAACTTTAACCCATCTA 59.003 33.333 0.00 0.00 29.75 1.98
1965 2168 6.833933 AGTTTCTGTTCAACTTTAACCCATCT 59.166 34.615 0.00 0.00 29.75 2.90
1967 2170 6.379988 ACAGTTTCTGTTCAACTTTAACCCAT 59.620 34.615 0.00 0.00 42.59 4.00
1968 2171 5.712917 ACAGTTTCTGTTCAACTTTAACCCA 59.287 36.000 0.00 0.00 42.59 4.51
1969 2172 6.203808 ACAGTTTCTGTTCAACTTTAACCC 57.796 37.500 0.00 0.00 42.59 4.11
1970 2173 6.910972 GCTACAGTTTCTGTTCAACTTTAACC 59.089 38.462 7.70 0.00 42.59 2.85
1971 2174 7.694886 AGCTACAGTTTCTGTTCAACTTTAAC 58.305 34.615 7.70 0.00 42.59 2.01
1972 2175 7.859325 AGCTACAGTTTCTGTTCAACTTTAA 57.141 32.000 7.70 0.00 42.59 1.52
1973 2176 7.859325 AAGCTACAGTTTCTGTTCAACTTTA 57.141 32.000 7.70 0.00 42.59 1.85
1974 2177 6.759497 AAGCTACAGTTTCTGTTCAACTTT 57.241 33.333 7.70 0.00 42.59 2.66
1975 2178 6.759497 AAAGCTACAGTTTCTGTTCAACTT 57.241 33.333 7.70 4.72 42.59 2.66
2031 2239 2.991190 CACTTCATGCAGCAAAATCACC 59.009 45.455 0.00 0.00 0.00 4.02
2052 2260 6.431198 TCGCAAAGAACCATATAGTTTTCC 57.569 37.500 0.00 0.00 0.00 3.13
2084 2292 2.417933 CTGCTTGATCCTCCACTTTTCG 59.582 50.000 0.00 0.00 0.00 3.46
2086 2294 3.416156 GTCTGCTTGATCCTCCACTTTT 58.584 45.455 0.00 0.00 0.00 2.27
2087 2295 2.613977 CGTCTGCTTGATCCTCCACTTT 60.614 50.000 0.00 0.00 0.00 2.66
2088 2296 1.066573 CGTCTGCTTGATCCTCCACTT 60.067 52.381 0.00 0.00 0.00 3.16
2123 2331 8.227791 GCAATTAGTGAAAGATTCTACGTTTCA 58.772 33.333 0.00 0.00 37.75 2.69
2124 2332 8.227791 TGCAATTAGTGAAAGATTCTACGTTTC 58.772 33.333 0.00 0.00 0.00 2.78
2125 2333 8.094798 TGCAATTAGTGAAAGATTCTACGTTT 57.905 30.769 0.00 0.00 0.00 3.60
2126 2334 7.667043 TGCAATTAGTGAAAGATTCTACGTT 57.333 32.000 0.00 0.00 0.00 3.99
2128 2336 7.688372 ACATGCAATTAGTGAAAGATTCTACG 58.312 34.615 0.00 0.00 0.00 3.51
2129 2337 9.846248 AAACATGCAATTAGTGAAAGATTCTAC 57.154 29.630 0.00 0.00 0.00 2.59
2133 2341 9.507280 CGATAAACATGCAATTAGTGAAAGATT 57.493 29.630 0.00 0.00 0.00 2.40
2175 2390 1.071471 CACACCTCCCCTCACACAC 59.929 63.158 0.00 0.00 0.00 3.82
2186 2401 5.078411 ACATGTCTGTCTTATCACACCTC 57.922 43.478 0.00 0.00 0.00 3.85
2219 2434 3.049912 TGACAATCACTCAACGAACTCG 58.950 45.455 0.00 0.00 46.33 4.18
2220 2435 4.609336 GCTTGACAATCACTCAACGAACTC 60.609 45.833 0.00 0.00 0.00 3.01
2245 2460 3.291584 TGGCATGAACCAGTAAACACAA 58.708 40.909 0.00 0.00 33.75 3.33
2274 2494 9.860898 AAACAAAAGATTCAGGTTAATATCAGC 57.139 29.630 0.00 0.00 0.00 4.26
2279 2499 8.353684 TGCGAAAACAAAAGATTCAGGTTAATA 58.646 29.630 0.00 0.00 0.00 0.98
2301 2521 3.838271 GCGATGTCCCCTCTGCGA 61.838 66.667 0.00 0.00 0.00 5.10
2472 2692 2.892425 CAGCCGGCGAGGATTGAC 60.892 66.667 23.20 0.00 45.00 3.18
2494 2714 1.809547 GGAAAAGGAGCAGCTCAGTTC 59.190 52.381 24.09 20.23 31.08 3.01
2495 2715 1.546548 GGGAAAAGGAGCAGCTCAGTT 60.547 52.381 24.09 13.48 31.08 3.16
2496 2716 0.037447 GGGAAAAGGAGCAGCTCAGT 59.963 55.000 24.09 7.73 31.08 3.41
2497 2717 0.679321 GGGGAAAAGGAGCAGCTCAG 60.679 60.000 24.09 0.00 31.08 3.35
2498 2718 1.380302 GGGGAAAAGGAGCAGCTCA 59.620 57.895 24.09 0.00 31.08 4.26
2499 2719 1.379176 GGGGGAAAAGGAGCAGCTC 60.379 63.158 14.69 14.69 0.00 4.09
2500 2720 2.147433 CTGGGGGAAAAGGAGCAGCT 62.147 60.000 0.00 0.00 0.00 4.24
2501 2721 1.680314 CTGGGGGAAAAGGAGCAGC 60.680 63.158 0.00 0.00 0.00 5.25
2527 2747 1.563879 CTGATGGTGGGTAATGGTGGA 59.436 52.381 0.00 0.00 0.00 4.02
2530 2750 3.189606 TCTTCTGATGGTGGGTAATGGT 58.810 45.455 0.00 0.00 0.00 3.55
2553 2787 7.277319 GCTGTAAGTAATTAAGCGGTAGTTTCT 59.723 37.037 0.00 0.00 35.30 2.52
2558 2792 5.353938 TGGCTGTAAGTAATTAAGCGGTAG 58.646 41.667 0.00 0.00 35.30 3.18
2559 2793 5.341872 TGGCTGTAAGTAATTAAGCGGTA 57.658 39.130 0.00 0.00 35.30 4.02
2586 2833 5.192927 CACAAACCCATATATGTCACTGGT 58.807 41.667 11.73 8.15 0.00 4.00
2701 2960 7.507616 CCTTCCTTCAGTCTCTAACCTATACAT 59.492 40.741 0.00 0.00 0.00 2.29
2702 2961 6.834451 CCTTCCTTCAGTCTCTAACCTATACA 59.166 42.308 0.00 0.00 0.00 2.29
2703 2962 6.265876 CCCTTCCTTCAGTCTCTAACCTATAC 59.734 46.154 0.00 0.00 0.00 1.47
2718 2977 1.549950 GCCACCATTTCCCTTCCTTCA 60.550 52.381 0.00 0.00 0.00 3.02
2721 2980 1.388133 GGCCACCATTTCCCTTCCT 59.612 57.895 0.00 0.00 0.00 3.36
2722 2981 0.972471 CTGGCCACCATTTCCCTTCC 60.972 60.000 0.00 0.00 30.82 3.46
2745 3004 0.543277 CAGTCCCAGCATAGGAAGCA 59.457 55.000 0.00 0.00 34.43 3.91
2746 3005 0.543749 ACAGTCCCAGCATAGGAAGC 59.456 55.000 0.00 0.00 34.43 3.86
2747 3006 1.745141 GCACAGTCCCAGCATAGGAAG 60.745 57.143 0.00 0.00 34.43 3.46
2748 3007 0.253044 GCACAGTCCCAGCATAGGAA 59.747 55.000 0.00 0.00 34.43 3.36
2749 3008 0.618680 AGCACAGTCCCAGCATAGGA 60.619 55.000 0.00 0.00 0.00 2.94
2750 3009 0.463295 CAGCACAGTCCCAGCATAGG 60.463 60.000 0.00 0.00 0.00 2.57
2751 3010 1.094073 GCAGCACAGTCCCAGCATAG 61.094 60.000 0.00 0.00 0.00 2.23
2752 3011 1.078214 GCAGCACAGTCCCAGCATA 60.078 57.895 0.00 0.00 0.00 3.14
2753 3012 2.360852 GCAGCACAGTCCCAGCAT 60.361 61.111 0.00 0.00 0.00 3.79
2754 3013 4.648626 GGCAGCACAGTCCCAGCA 62.649 66.667 0.00 0.00 0.00 4.41
2755 3014 4.648626 TGGCAGCACAGTCCCAGC 62.649 66.667 0.00 0.00 0.00 4.85
2756 3015 2.359602 CTGGCAGCACAGTCCCAG 60.360 66.667 0.00 0.00 38.93 4.45
2757 3016 3.957586 CCTGGCAGCACAGTCCCA 61.958 66.667 9.56 0.00 36.75 4.37
2760 3019 2.983725 AAACCCCTGGCAGCACAGTC 62.984 60.000 9.56 0.00 36.75 3.51
2761 3020 2.983725 GAAACCCCTGGCAGCACAGT 62.984 60.000 9.56 0.00 36.75 3.55
2762 3021 2.203538 AAACCCCTGGCAGCACAG 60.204 61.111 9.56 0.00 38.21 3.66
2764 3023 2.991540 GGAAACCCCTGGCAGCAC 60.992 66.667 9.56 0.00 0.00 4.40
2776 3035 0.250770 AAGAACAGAGCCCGGGAAAC 60.251 55.000 29.31 14.55 0.00 2.78
2777 3036 1.354101 TAAGAACAGAGCCCGGGAAA 58.646 50.000 29.31 0.00 0.00 3.13
2827 3121 1.176527 CCACCATCACCATTCACCAC 58.823 55.000 0.00 0.00 0.00 4.16
2878 3175 4.016444 TCTTCTTTGCCCATATGTTCCAC 58.984 43.478 1.24 0.00 0.00 4.02
2892 3189 6.430925 TCACCCATATGTCAGTTTCTTCTTTG 59.569 38.462 1.24 0.00 0.00 2.77
2910 3207 3.331293 GGGGATTCGGTCACCCAT 58.669 61.111 0.00 0.00 45.38 4.00
2985 3283 1.522806 GCCTCCGTCAACACACACA 60.523 57.895 0.00 0.00 0.00 3.72
3034 3332 8.029522 TCGGAGAATTATTATACTAGCAGCAAG 58.970 37.037 0.00 0.00 0.00 4.01
3058 3362 2.347697 TCAACATCGACAAGACCTCG 57.652 50.000 0.00 0.00 0.00 4.63
3061 3365 4.036380 AGGTTTTTCAACATCGACAAGACC 59.964 41.667 0.00 0.00 34.15 3.85
3089 3403 3.818961 ACGTGCATGATCAGTCTTTTG 57.181 42.857 14.17 0.00 0.00 2.44
3179 3494 0.384725 CTTTCACCGTTGCGAGCAAG 60.385 55.000 11.09 3.24 36.52 4.01
3199 3514 1.066286 GCTGAGCCTGTGAAGTGAGAT 60.066 52.381 0.00 0.00 0.00 2.75
3207 3522 2.031616 GTGCTGCTGAGCCTGTGA 59.968 61.111 0.23 0.00 45.57 3.58
3209 3524 2.281345 GTGTGCTGCTGAGCCTGT 60.281 61.111 0.23 0.00 45.57 4.00
3210 3525 2.281276 TGTGTGCTGCTGAGCCTG 60.281 61.111 0.23 0.00 45.57 4.85
3211 3526 2.281345 GTGTGTGCTGCTGAGCCT 60.281 61.111 0.23 0.00 45.57 4.58
3213 3528 2.635899 GTGTGTGTGCTGCTGAGC 59.364 61.111 0.00 0.00 46.44 4.26
3214 3529 0.947660 ATCGTGTGTGTGCTGCTGAG 60.948 55.000 0.00 0.00 0.00 3.35
3215 3530 0.532640 AATCGTGTGTGTGCTGCTGA 60.533 50.000 0.00 0.00 0.00 4.26
3216 3531 0.385098 CAATCGTGTGTGTGCTGCTG 60.385 55.000 0.00 0.00 0.00 4.41
3217 3532 0.815213 ACAATCGTGTGTGTGCTGCT 60.815 50.000 0.00 0.00 36.31 4.24
3218 3533 1.648720 ACAATCGTGTGTGTGCTGC 59.351 52.632 0.00 0.00 36.31 5.25
3260 3575 0.535102 CTTCCACTTGTCCAGCCGTT 60.535 55.000 0.00 0.00 0.00 4.44
3375 3693 2.037121 TGCAAAGGTCAACTGAGATCGA 59.963 45.455 0.00 0.00 0.00 3.59
3383 3701 1.824230 TGTTGCTTGCAAAGGTCAACT 59.176 42.857 22.48 0.00 46.35 3.16
3394 3712 4.386652 ACGATTTGATTTGATGTTGCTTGC 59.613 37.500 0.00 0.00 0.00 4.01
3452 3770 5.235616 GGCACCGTATCGATCTTGATTTTTA 59.764 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.