Multiple sequence alignment - TraesCS2D01G388000

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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 TraesCS2D01G388000 chr2D 100.000 3900 0 0 1 3900 493202570 493198671 0.000000e+00 7203
1 TraesCS2D01G388000 chr2B 92.566 3955 175 48 1 3900 581598533 581594643 0.000000e+00 5565
2 TraesCS2D01G388000 chr2A 91.929 2416 114 32 1145 3536 640221829 640224187 0.000000e+00 3306
3 TraesCS2D01G388000 chr2A 91.905 803 41 6 1 794 640220585 640221372 0.000000e+00 1101
4 TraesCS2D01G388000 chr2A 93.261 371 7 6 3530 3900 640224217 640224569 7.420000e-147 531
5 TraesCS2D01G388000 chr2A 86.528 193 20 3 818 1004 640221570 640221762 1.420000e-49 207
6 TraesCS2D01G388000 chr7D 83.582 469 56 15 933 1396 635515208 635515660 1.680000e-113 420


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 TraesCS2D01G388000 chr2D 493198671 493202570 3899 True 7203.00 7203 100.00000 1 3900 1 chr2D.!!$R1 3899
1 TraesCS2D01G388000 chr2B 581594643 581598533 3890 True 5565.00 5565 92.56600 1 3900 1 chr2B.!!$R1 3899
2 TraesCS2D01G388000 chr2A 640220585 640224569 3984 False 1286.25 3306 90.90575 1 3900 4 chr2A.!!$F1 3899

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
579 617 1.067669 TCGTCCTCTATCACTGCATGC 59.932 52.381 11.82 11.82 0.0 4.06 F
1542 1775 0.107643 TTCATGAGGCACCAACGACA 59.892 50.000 0.00 0.00 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 2202 0.030504 ATGATCTGACGAGAGCTGCG 59.969 55.0 0.0 0.0 35.5 5.18 R
2899 3143 0.179045 GCTCAACGATGGCAGGGTAT 60.179 55.0 0.0 0.0 0.0 2.73 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
36 38 2.586792 GCAGTGAAGCGGGGATCT 59.413 61.111 0.00 0.00 0.00 2.75
67 69 6.900194 TGTTTAGGGAGATGAAATTCCTAGG 58.100 40.000 0.82 0.82 32.45 3.02
81 83 9.695155 TGAAATTCCTAGGGAGGTTAAAAATAG 57.305 33.333 9.46 0.00 44.19 1.73
82 84 9.696572 GAAATTCCTAGGGAGGTTAAAAATAGT 57.303 33.333 9.46 0.00 44.19 2.12
108 110 1.127343 CCTTTTTGCTTGGACCCCAA 58.873 50.000 0.00 0.00 41.69 4.12
213 215 2.288763 CCGTTTGGCTTTTGTATTGCCT 60.289 45.455 0.00 0.00 46.23 4.75
307 310 4.118410 TCGCGTGTTTTTCTACCTAACAA 58.882 39.130 5.77 0.00 33.96 2.83
425 428 3.307762 GGTCAAGGTGCAGAAGGATAACT 60.308 47.826 0.00 0.00 0.00 2.24
426 429 3.935828 GTCAAGGTGCAGAAGGATAACTC 59.064 47.826 0.00 0.00 0.00 3.01
427 430 3.582647 TCAAGGTGCAGAAGGATAACTCA 59.417 43.478 0.00 0.00 0.00 3.41
428 431 3.902881 AGGTGCAGAAGGATAACTCAG 57.097 47.619 0.00 0.00 0.00 3.35
429 432 3.177228 AGGTGCAGAAGGATAACTCAGT 58.823 45.455 0.00 0.00 0.00 3.41
430 433 3.055530 AGGTGCAGAAGGATAACTCAGTG 60.056 47.826 0.00 0.00 0.00 3.66
431 434 3.265791 GTGCAGAAGGATAACTCAGTGG 58.734 50.000 0.00 0.00 0.00 4.00
432 435 2.906389 TGCAGAAGGATAACTCAGTGGT 59.094 45.455 0.00 0.00 0.00 4.16
433 436 3.055819 TGCAGAAGGATAACTCAGTGGTC 60.056 47.826 0.00 0.00 0.00 4.02
434 437 3.055819 GCAGAAGGATAACTCAGTGGTCA 60.056 47.826 0.00 0.00 0.00 4.02
435 438 4.563580 GCAGAAGGATAACTCAGTGGTCAA 60.564 45.833 0.00 0.00 0.00 3.18
436 439 4.932200 CAGAAGGATAACTCAGTGGTCAAC 59.068 45.833 0.00 0.00 0.00 3.18
484 503 1.493772 CGTGAACGAACTGTGCCTTA 58.506 50.000 0.00 0.00 43.02 2.69
487 509 2.610374 GTGAACGAACTGTGCCTTACAA 59.390 45.455 0.00 0.00 39.20 2.41
536 574 1.085091 ATATCGCTACGCTACGGAGG 58.915 55.000 0.00 0.00 38.40 4.30
579 617 1.067669 TCGTCCTCTATCACTGCATGC 59.932 52.381 11.82 11.82 0.00 4.06
612 650 3.619929 GCCGTATAGTTTGAACGTTCCAT 59.380 43.478 24.78 12.32 34.90 3.41
637 675 1.657181 CTTGCAAAACCGCGTGACC 60.657 57.895 4.92 0.00 33.35 4.02
707 759 6.246332 CGACGTTGAAGTACATATTTTGCTTG 59.754 38.462 0.00 0.00 0.00 4.01
714 766 3.317603 ACATATTTTGCTTGGGTGTGC 57.682 42.857 0.00 0.00 0.00 4.57
827 1053 3.931578 TCTGCCAGAAACTTAGCTTCTC 58.068 45.455 0.00 0.00 30.58 2.87
870 1097 3.404899 TGTTGTTTTCGGAGATGGTACC 58.595 45.455 4.43 4.43 35.04 3.34
900 1131 5.287992 CGTAAGATTAGGAGACGACAAAACC 59.712 44.000 0.00 0.00 43.02 3.27
1044 1277 0.962356 ACAAATGGAGGCGCAAGAGG 60.962 55.000 10.83 0.00 43.02 3.69
1086 1319 1.147824 ATCCCATTCTCAGGCAGCG 59.852 57.895 0.00 0.00 0.00 5.18
1107 1340 4.281947 GCCTCCTACTACGCCGCC 62.282 72.222 0.00 0.00 0.00 6.13
1113 1346 3.350909 CTACTACGCCGCCTGCACA 62.351 63.158 0.00 0.00 41.33 4.57
1114 1347 3.350909 TACTACGCCGCCTGCACAG 62.351 63.158 0.00 0.00 41.33 3.66
1115 1348 4.435436 CTACGCCGCCTGCACAGA 62.435 66.667 0.00 0.00 41.33 3.41
1116 1349 4.435436 TACGCCGCCTGCACAGAG 62.435 66.667 0.00 0.00 41.33 3.35
1278 1511 3.528370 CCGGAGCTGTACGGGGAG 61.528 72.222 12.04 0.00 46.08 4.30
1308 1541 2.925170 AGCCTGCTGGAGTTCGGT 60.925 61.111 14.77 0.00 34.57 4.69
1473 1706 2.850130 AACGGTGGCCAGGTACCA 60.850 61.111 15.94 0.00 36.76 3.25
1481 1714 0.825840 GGCCAGGTACCAAAACTGCA 60.826 55.000 15.94 0.00 0.00 4.41
1524 1757 1.996798 TCAACTGTCTCCGGAGTCTT 58.003 50.000 30.17 13.64 0.00 3.01
1525 1758 1.887198 TCAACTGTCTCCGGAGTCTTC 59.113 52.381 30.17 18.51 0.00 2.87
1527 1760 2.223803 ACTGTCTCCGGAGTCTTCAT 57.776 50.000 30.17 10.25 0.00 2.57
1528 1761 1.821753 ACTGTCTCCGGAGTCTTCATG 59.178 52.381 30.17 16.05 0.00 3.07
1530 1763 2.095461 TGTCTCCGGAGTCTTCATGAG 58.905 52.381 30.17 2.24 0.00 2.90
1531 1764 1.407258 GTCTCCGGAGTCTTCATGAGG 59.593 57.143 30.17 0.00 0.00 3.86
1533 1766 0.614697 TCCGGAGTCTTCATGAGGCA 60.615 55.000 0.00 0.00 30.26 4.75
1534 1767 0.460987 CCGGAGTCTTCATGAGGCAC 60.461 60.000 0.00 0.11 30.26 5.01
1535 1768 0.460987 CGGAGTCTTCATGAGGCACC 60.461 60.000 0.00 3.28 37.37 5.01
1536 1769 0.615331 GGAGTCTTCATGAGGCACCA 59.385 55.000 0.00 0.00 40.12 4.17
1537 1770 1.003580 GGAGTCTTCATGAGGCACCAA 59.996 52.381 0.00 0.00 40.12 3.67
1538 1771 2.079925 GAGTCTTCATGAGGCACCAAC 58.920 52.381 0.00 0.00 30.26 3.77
1539 1772 0.798776 GTCTTCATGAGGCACCAACG 59.201 55.000 0.00 0.00 0.00 4.10
1540 1773 0.684535 TCTTCATGAGGCACCAACGA 59.315 50.000 0.00 0.00 0.00 3.85
1541 1774 0.798776 CTTCATGAGGCACCAACGAC 59.201 55.000 0.00 0.00 0.00 4.34
1542 1775 0.107643 TTCATGAGGCACCAACGACA 59.892 50.000 0.00 0.00 0.00 4.35
1543 1776 0.602638 TCATGAGGCACCAACGACAC 60.603 55.000 0.00 0.00 0.00 3.67
1544 1777 1.302511 ATGAGGCACCAACGACACC 60.303 57.895 0.00 0.00 0.00 4.16
1545 1778 2.050836 ATGAGGCACCAACGACACCA 62.051 55.000 0.00 0.00 0.00 4.17
1546 1779 1.961277 GAGGCACCAACGACACCAG 60.961 63.158 0.00 0.00 0.00 4.00
1547 1780 3.660111 GGCACCAACGACACCAGC 61.660 66.667 0.00 0.00 0.00 4.85
1548 1781 3.660111 GCACCAACGACACCAGCC 61.660 66.667 0.00 0.00 0.00 4.85
1549 1782 2.203139 CACCAACGACACCAGCCA 60.203 61.111 0.00 0.00 0.00 4.75
1550 1783 2.203153 ACCAACGACACCAGCCAC 60.203 61.111 0.00 0.00 0.00 5.01
1644 1877 2.342648 GAGCACCCGAACCTCGTT 59.657 61.111 0.00 0.00 38.40 3.85
1780 2013 3.391665 CTCCCATGGGACGTCAGGC 62.392 68.421 30.62 0.00 39.76 4.85
1821 2054 2.093288 TGCTGAAGGGTTGCTCTATCTG 60.093 50.000 0.00 0.00 0.00 2.90
1867 2102 0.255890 TAACCAATCTGCCCTCCAGC 59.744 55.000 0.00 0.00 41.50 4.85
1961 2202 1.348036 AGGCAGACAGTTTCTACACCC 59.652 52.381 0.00 0.00 31.12 4.61
1971 2212 1.934220 TTCTACACCCGCAGCTCTCG 61.934 60.000 0.00 0.00 0.00 4.04
1986 2227 2.405172 CTCTCGTCAGATCATGGCATG 58.595 52.381 21.42 21.42 30.75 4.06
2024 2268 4.116926 TGCATGGAAAAGGCAGGG 57.883 55.556 0.00 0.00 41.54 4.45
2025 2269 2.285024 TGCATGGAAAAGGCAGGGC 61.285 57.895 0.00 0.00 41.54 5.19
2051 2295 5.748402 TCAATTATCATCACAGCCTGAACT 58.252 37.500 0.00 0.00 30.60 3.01
2057 2301 9.664332 ATTATCATCACAGCCTGAACTATTATC 57.336 33.333 0.00 0.00 30.60 1.75
2058 2302 6.484364 TCATCACAGCCTGAACTATTATCA 57.516 37.500 0.00 0.00 30.60 2.15
2059 2303 7.071069 TCATCACAGCCTGAACTATTATCAT 57.929 36.000 0.00 0.00 30.60 2.45
2060 2304 7.512130 TCATCACAGCCTGAACTATTATCATT 58.488 34.615 0.00 0.00 30.60 2.57
2061 2305 8.650490 TCATCACAGCCTGAACTATTATCATTA 58.350 33.333 0.00 0.00 30.60 1.90
2062 2306 9.445878 CATCACAGCCTGAACTATTATCATTAT 57.554 33.333 0.00 0.00 30.60 1.28
2236 2480 3.904136 ATGTGCAAACTTCACTACAGC 57.096 42.857 0.00 0.00 35.58 4.40
2241 2485 2.357637 GCAAACTTCACTACAGCAACCA 59.642 45.455 0.00 0.00 0.00 3.67
2265 2509 4.141869 GCTCAATTTCCTTGGGTTGCATAT 60.142 41.667 0.00 0.00 37.67 1.78
2266 2510 5.068987 GCTCAATTTCCTTGGGTTGCATATA 59.931 40.000 0.00 0.00 37.67 0.86
2274 2518 3.380471 TGGGTTGCATATAGCCAAACT 57.620 42.857 5.33 0.00 44.83 2.66
2316 2560 3.327626 CATATGGAGCATCTCACAGAGC 58.672 50.000 0.00 0.00 33.73 4.09
2317 2561 0.469070 ATGGAGCATCTCACAGAGCC 59.531 55.000 0.00 0.00 33.73 4.70
2318 2562 1.227205 GGAGCATCTCACAGAGCCG 60.227 63.158 0.00 0.00 33.73 5.52
2319 2563 1.515020 GAGCATCTCACAGAGCCGT 59.485 57.895 0.00 0.00 0.00 5.68
2320 2564 0.527385 GAGCATCTCACAGAGCCGTC 60.527 60.000 0.00 0.00 0.00 4.79
2321 2565 1.216444 GCATCTCACAGAGCCGTCA 59.784 57.895 0.00 0.00 0.00 4.35
2548 2792 0.597637 CCGACAGCGAACAGTTCAGT 60.598 55.000 13.82 8.22 40.82 3.41
2660 2904 1.815817 AAAGAACCGCCCCACAATGC 61.816 55.000 0.00 0.00 0.00 3.56
2851 3095 2.753452 AGGTGAGAATGCAAATGCTCAG 59.247 45.455 6.97 0.00 42.66 3.35
2899 3143 3.749064 GCTGCTCCTCGGACGTGA 61.749 66.667 0.00 0.00 0.00 4.35
2932 3176 4.126437 TCGTTGAGCTCTTGATTTTGACA 58.874 39.130 16.19 0.00 0.00 3.58
2935 3179 5.447573 GTTGAGCTCTTGATTTTGACAGAC 58.552 41.667 16.19 0.00 0.00 3.51
3012 3257 6.389906 AGAAATTTAGTTTTCTCCAATGCCG 58.610 36.000 0.00 0.00 41.01 5.69
3015 3260 7.404671 AATTTAGTTTTCTCCAATGCCGTAT 57.595 32.000 0.00 0.00 0.00 3.06
3019 3264 2.620251 TTCTCCAATGCCGTATCTGG 57.380 50.000 0.00 0.00 0.00 3.86
3043 3288 7.147976 GGCAATTGATGAGTAAAGTTTGAAGT 58.852 34.615 10.34 0.00 0.00 3.01
3104 3350 4.475944 CAGTTATGCCTTTCTTTTGTCGG 58.524 43.478 0.00 0.00 0.00 4.79
3105 3351 4.215399 CAGTTATGCCTTTCTTTTGTCGGA 59.785 41.667 0.00 0.00 0.00 4.55
3154 3400 9.860650 ATACATGAAAATGGTGCCTACTATTTA 57.139 29.630 0.00 0.00 44.20 1.40
3242 3502 7.121315 AGGAAGCACACTAATTGGAACTTAATC 59.879 37.037 0.00 0.00 0.00 1.75
3243 3503 7.094377 GGAAGCACACTAATTGGAACTTAATCA 60.094 37.037 0.00 0.00 0.00 2.57
3353 3613 3.239861 AGCACCTGAGCTGTAAAGC 57.760 52.632 0.00 0.00 44.66 3.51
3363 3623 1.980052 CTGTAAAGCCCAGGACGGA 59.020 57.895 0.00 0.00 36.56 4.69
3535 3836 4.876107 CCCAAGAAACGTTCTATGCTATGT 59.124 41.667 0.00 0.00 39.61 2.29
3536 3837 5.354234 CCCAAGAAACGTTCTATGCTATGTT 59.646 40.000 0.00 0.00 39.61 2.71
3578 3879 6.939163 AGCTCATGACACAGAAAGTTAAATCT 59.061 34.615 0.00 0.00 0.00 2.40
3610 3911 1.941294 GCATCAGCATCCTCTTCAGTG 59.059 52.381 0.00 0.00 41.58 3.66
3612 3913 1.649321 TCAGCATCCTCTTCAGTGGT 58.351 50.000 0.00 0.00 0.00 4.16
3765 4066 1.209019 AGCAGGTCATGAGTCATCACC 59.791 52.381 17.92 17.92 38.57 4.02
3845 4146 2.800544 GCACTTGACGTTCACTGTGTAT 59.199 45.455 7.79 0.00 35.16 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 9.449719 GAATTTCATCTCCCTAAACAAGACTTA 57.550 33.333 0.00 0.00 0.00 2.24
80 82 5.221441 GGTCCAAGCAAAAAGGAAACATACT 60.221 40.000 0.00 0.00 32.30 2.12
81 83 4.988540 GGTCCAAGCAAAAAGGAAACATAC 59.011 41.667 0.00 0.00 32.30 2.39
82 84 4.039852 GGGTCCAAGCAAAAAGGAAACATA 59.960 41.667 0.00 0.00 32.30 2.29
142 144 1.523095 GGATAGCATTCACGAGCGTTC 59.477 52.381 0.00 0.00 35.48 3.95
147 149 3.742433 AGGAAGGATAGCATTCACGAG 57.258 47.619 7.75 0.00 36.57 4.18
213 215 3.515502 TCCATCAACAAACAACCACCAAA 59.484 39.130 0.00 0.00 0.00 3.28
267 269 2.604855 GCGAGACTCGAGTTCAACAGAA 60.605 50.000 28.43 0.00 43.74 3.02
307 310 1.306148 CATGTGATGGCTGATCGCTT 58.694 50.000 8.94 3.12 41.51 4.68
425 428 2.622942 GCCAAGAAATGTTGACCACTGA 59.377 45.455 0.00 0.00 0.00 3.41
426 429 2.361757 TGCCAAGAAATGTTGACCACTG 59.638 45.455 0.00 0.00 0.00 3.66
427 430 2.624838 CTGCCAAGAAATGTTGACCACT 59.375 45.455 0.00 0.00 0.00 4.00
428 431 2.863704 GCTGCCAAGAAATGTTGACCAC 60.864 50.000 0.00 0.00 0.00 4.16
429 432 1.340889 GCTGCCAAGAAATGTTGACCA 59.659 47.619 0.00 0.00 0.00 4.02
430 433 1.337167 GGCTGCCAAGAAATGTTGACC 60.337 52.381 15.17 0.00 0.00 4.02
431 434 1.666888 CGGCTGCCAAGAAATGTTGAC 60.667 52.381 20.29 0.00 0.00 3.18
432 435 0.597568 CGGCTGCCAAGAAATGTTGA 59.402 50.000 20.29 0.00 0.00 3.18
433 436 0.388907 CCGGCTGCCAAGAAATGTTG 60.389 55.000 20.29 0.00 0.00 3.33
434 437 1.535204 CCCGGCTGCCAAGAAATGTT 61.535 55.000 20.29 0.00 0.00 2.71
435 438 1.978617 CCCGGCTGCCAAGAAATGT 60.979 57.895 20.29 0.00 0.00 2.71
436 439 1.678635 TCCCGGCTGCCAAGAAATG 60.679 57.895 20.29 0.00 0.00 2.32
484 503 2.158957 TCGCCACTTCTTCTCACTTTGT 60.159 45.455 0.00 0.00 0.00 2.83
487 509 2.484889 GTTCGCCACTTCTTCTCACTT 58.515 47.619 0.00 0.00 0.00 3.16
579 617 0.319555 CTATACGGCCGTCATGGGTG 60.320 60.000 38.01 14.95 38.63 4.61
612 650 2.887889 CGGTTTTGCAAGTCGCGGA 61.888 57.895 6.13 0.00 46.97 5.54
707 759 0.321671 TCAAGAGCTGTAGCACACCC 59.678 55.000 6.65 0.00 45.16 4.61
714 766 4.614535 GCACCAACAAATCAAGAGCTGTAG 60.615 45.833 0.00 0.00 0.00 2.74
769 821 7.543947 AAAAAGTGATTTGGAAAAGCTTCAG 57.456 32.000 0.00 0.00 32.75 3.02
827 1053 0.036875 GGGGAAGGGCTAATCGATGG 59.963 60.000 0.00 0.00 0.00 3.51
870 1097 4.035324 TCGTCTCCTAATCTTACGCTTCTG 59.965 45.833 0.00 0.00 33.75 3.02
917 1148 5.299279 TCACAAAGAGAAACACCAAAGATCC 59.701 40.000 0.00 0.00 0.00 3.36
918 1149 6.377327 TCACAAAGAGAAACACCAAAGATC 57.623 37.500 0.00 0.00 0.00 2.75
1066 1299 0.822532 GCTGCCTGAGAATGGGATGG 60.823 60.000 0.00 0.00 0.00 3.51
1068 1301 1.147824 CGCTGCCTGAGAATGGGAT 59.852 57.895 0.00 0.00 0.00 3.85
1086 1319 4.281947 GCGTAGTAGGAGGCCGCC 62.282 72.222 19.43 19.43 38.52 6.13
1290 1523 2.435586 CCGAACTCCAGCAGGCTG 60.436 66.667 10.94 10.94 43.26 4.85
1308 1541 3.443925 CCACGGAGCTCGCTGAGA 61.444 66.667 7.83 0.00 43.89 3.27
1473 1706 4.453136 GTGATGGAATTGCATTGCAGTTTT 59.547 37.500 18.81 11.06 43.84 2.43
1481 1714 8.533657 TGAATTCTTTAGTGATGGAATTGCATT 58.466 29.630 14.12 0.88 38.15 3.56
1524 1757 0.602638 GTGTCGTTGGTGCCTCATGA 60.603 55.000 0.00 0.00 0.00 3.07
1525 1758 1.577328 GGTGTCGTTGGTGCCTCATG 61.577 60.000 0.00 0.00 0.00 3.07
1527 1760 2.110213 GGTGTCGTTGGTGCCTCA 59.890 61.111 0.00 0.00 0.00 3.86
1528 1761 1.961277 CTGGTGTCGTTGGTGCCTC 60.961 63.158 0.00 0.00 0.00 4.70
1530 1763 3.660111 GCTGGTGTCGTTGGTGCC 61.660 66.667 0.00 0.00 0.00 5.01
1531 1764 3.660111 GGCTGGTGTCGTTGGTGC 61.660 66.667 0.00 0.00 0.00 5.01
1533 1766 2.203153 GTGGCTGGTGTCGTTGGT 60.203 61.111 0.00 0.00 0.00 3.67
1534 1767 1.961277 GAGTGGCTGGTGTCGTTGG 60.961 63.158 0.00 0.00 0.00 3.77
1535 1768 1.069765 AGAGTGGCTGGTGTCGTTG 59.930 57.895 0.00 0.00 0.00 4.10
1536 1769 1.069765 CAGAGTGGCTGGTGTCGTT 59.930 57.895 0.00 0.00 41.07 3.85
1537 1770 1.188219 ATCAGAGTGGCTGGTGTCGT 61.188 55.000 0.00 0.00 44.98 4.34
1538 1771 0.459237 GATCAGAGTGGCTGGTGTCG 60.459 60.000 0.00 0.00 44.98 4.35
1539 1772 0.901124 AGATCAGAGTGGCTGGTGTC 59.099 55.000 0.00 0.00 44.98 3.67
1540 1773 0.612229 CAGATCAGAGTGGCTGGTGT 59.388 55.000 0.00 0.00 44.98 4.16
1541 1774 0.900421 TCAGATCAGAGTGGCTGGTG 59.100 55.000 0.00 0.00 44.98 4.17
1542 1775 1.761784 GATCAGATCAGAGTGGCTGGT 59.238 52.381 5.44 0.00 44.98 4.00
1543 1776 1.269673 CGATCAGATCAGAGTGGCTGG 60.270 57.143 11.12 0.00 44.98 4.85
1544 1777 1.868930 GCGATCAGATCAGAGTGGCTG 60.869 57.143 11.12 0.00 46.31 4.85
1545 1778 0.388659 GCGATCAGATCAGAGTGGCT 59.611 55.000 11.12 0.00 0.00 4.75
1546 1779 0.599728 GGCGATCAGATCAGAGTGGC 60.600 60.000 11.12 4.42 0.00 5.01
1547 1780 1.039068 AGGCGATCAGATCAGAGTGG 58.961 55.000 11.12 0.00 0.00 4.00
1548 1781 1.269673 CCAGGCGATCAGATCAGAGTG 60.270 57.143 11.12 2.32 0.00 3.51
1549 1782 1.039068 CCAGGCGATCAGATCAGAGT 58.961 55.000 11.12 0.00 0.00 3.24
1550 1783 0.319727 GCCAGGCGATCAGATCAGAG 60.320 60.000 11.12 0.00 0.00 3.35
1644 1877 1.432251 GCAGTAGCCGACGAGCTTA 59.568 57.895 14.55 1.38 41.41 3.09
1821 2054 3.909086 AAGCTCAAGGCCCTCGTGC 62.909 63.158 0.00 0.20 43.05 5.34
1867 2102 1.048724 TCCTAAGAGGGTGATGGGCG 61.049 60.000 0.00 0.00 35.59 6.13
1911 2147 5.236911 TGCTCAAAACAAGCAAATTCATTCC 59.763 36.000 0.00 0.00 46.29 3.01
1961 2202 0.030504 ATGATCTGACGAGAGCTGCG 59.969 55.000 0.00 0.00 35.50 5.18
1971 2212 3.560481 CAGTTCTCATGCCATGATCTGAC 59.440 47.826 20.15 12.26 38.85 3.51
1986 2227 7.834068 TGCAGTAGTTCATAATTCAGTTCTC 57.166 36.000 0.00 0.00 0.00 2.87
2023 2267 3.548818 GGCTGTGATGATAATTGAACGCC 60.549 47.826 0.00 0.00 0.00 5.68
2024 2268 3.313526 AGGCTGTGATGATAATTGAACGC 59.686 43.478 0.00 0.00 0.00 4.84
2025 2269 4.571984 TCAGGCTGTGATGATAATTGAACG 59.428 41.667 15.27 0.00 0.00 3.95
2085 2329 9.135843 CTTGAAATCGCGGTATATAATCTACAA 57.864 33.333 6.13 0.00 0.00 2.41
2192 2436 4.199310 CCACTGTAGATACATGGGTTTGG 58.801 47.826 0.00 0.00 35.36 3.28
2236 2480 2.028748 CCCAAGGAAATTGAGCTGGTTG 60.029 50.000 0.00 0.00 41.83 3.77
2241 2485 1.620323 GCAACCCAAGGAAATTGAGCT 59.380 47.619 0.00 0.00 41.83 4.09
2313 2557 2.531206 GTAATGAGTGTCTGACGGCTC 58.469 52.381 18.94 18.94 0.00 4.70
2316 2560 3.594603 AAGGTAATGAGTGTCTGACGG 57.405 47.619 2.98 0.00 0.00 4.79
2317 2561 3.123621 GCAAAGGTAATGAGTGTCTGACG 59.876 47.826 2.98 0.00 0.00 4.35
2318 2562 4.065088 TGCAAAGGTAATGAGTGTCTGAC 58.935 43.478 0.00 0.00 0.00 3.51
2319 2563 4.350368 TGCAAAGGTAATGAGTGTCTGA 57.650 40.909 0.00 0.00 0.00 3.27
2320 2564 5.437289 TTTGCAAAGGTAATGAGTGTCTG 57.563 39.130 8.05 0.00 0.00 3.51
2321 2565 6.265196 TGAATTTGCAAAGGTAATGAGTGTCT 59.735 34.615 18.19 0.00 0.00 3.41
2482 2726 1.141053 AGCTTCTGTTCGTTCTTGGGT 59.859 47.619 0.00 0.00 0.00 4.51
2548 2792 1.827344 AGCCTTGTGTCGATGATCTCA 59.173 47.619 0.00 0.00 0.00 3.27
2645 2889 2.990967 CAGCATTGTGGGGCGGTT 60.991 61.111 0.00 0.00 34.54 4.44
2660 2904 1.197430 AGCCTCTCAACCACCTCCAG 61.197 60.000 0.00 0.00 0.00 3.86
2851 3095 2.617774 GAGCATCAATCTTCTCCTTGCC 59.382 50.000 0.00 0.00 33.17 4.52
2899 3143 0.179045 GCTCAACGATGGCAGGGTAT 60.179 55.000 0.00 0.00 0.00 2.73
3012 3257 7.559590 ACTTTACTCATCAATTGCCAGATAC 57.440 36.000 0.00 0.00 0.00 2.24
3015 3260 6.489700 TCAAACTTTACTCATCAATTGCCAGA 59.510 34.615 0.00 0.00 0.00 3.86
3019 3264 7.358683 GCACTTCAAACTTTACTCATCAATTGC 60.359 37.037 0.00 0.00 0.00 3.56
3020 3265 7.864379 AGCACTTCAAACTTTACTCATCAATTG 59.136 33.333 0.00 0.00 0.00 2.32
3021 3266 7.864379 CAGCACTTCAAACTTTACTCATCAATT 59.136 33.333 0.00 0.00 0.00 2.32
3043 3288 3.181427 ACCTATTTTTACCACCACCAGCA 60.181 43.478 0.00 0.00 0.00 4.41
3104 3350 8.879342 ATACAAATTACTAGCTCATGTGAGTC 57.121 34.615 11.35 4.53 43.85 3.36
3105 3351 9.751542 GTATACAAATTACTAGCTCATGTGAGT 57.248 33.333 11.35 0.00 43.85 3.41
3203 3449 2.351418 GTGCTTCCTTTGCCAACAAAAC 59.649 45.455 0.00 0.00 44.90 2.43
3243 3503 8.919145 GCTATCCTTCCTATAGTGTGCTTATAT 58.081 37.037 0.00 0.00 30.91 0.86
3353 3613 1.202348 GCAAAGAAAATCCGTCCTGGG 59.798 52.381 0.00 0.00 38.76 4.45
3494 3759 7.368198 TCTTGGGGTTTTAGCAAGTTTATTT 57.632 32.000 0.00 0.00 0.00 1.40
3578 3879 1.829222 TGCTGATGCTGACTGAGATGA 59.171 47.619 0.00 0.00 40.48 2.92
3765 4066 3.119245 CCCATTGCTGAGAACTGAATTGG 60.119 47.826 0.00 0.00 0.00 3.16
3845 4146 4.337060 CGCGTCGATATCGGCCCA 62.337 66.667 23.08 1.95 41.58 5.36


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

AutoCloner maintained by Alex Coulton.