Multiple sequence alignment - TraesCS1A01G219500

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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 TraesCS1A01G219500 chr1A 100.000 4462 0 0 1 4462 388164182 388159721 0.000000e+00 8240
1 TraesCS1A01G219500 chr1D 93.833 3162 149 24 1331 4462 308588388 308585243 0.000000e+00 4717
2 TraesCS1A01G219500 chr1D 98.020 606 8 2 1 606 308589573 308588972 0.000000e+00 1050
3 TraesCS1A01G219500 chr1D 93.168 483 27 4 783 1264 308588872 308588395 0.000000e+00 704
4 TraesCS1A01G219500 chr1D 87.302 126 5 3 633 757 308588987 308588872 2.800000e-27 134
5 TraesCS1A01G219500 chr1B 94.519 2098 91 12 2374 4462 418674267 418672185 0.000000e+00 3216
6 TraesCS1A01G219500 chr1B 90.161 1118 68 17 1285 2381 418677099 418676003 0.000000e+00 1417
7 TraesCS1A01G219500 chr1B 94.910 609 11 6 1 606 418678248 418677657 0.000000e+00 935
8 TraesCS1A01G219500 chr1B 92.901 493 18 6 782 1264 418677572 418677087 0.000000e+00 701
9 TraesCS1A01G219500 chr1B 85.833 120 6 3 633 751 418677672 418677563 2.820000e-22 117
10 TraesCS1A01G219500 chr4D 83.784 148 20 3 1001 1147 509663214 509663358 2.160000e-28 137
11 TraesCS1A01G219500 chr4B 89.091 110 10 2 1037 1145 657176374 657176266 7.790000e-28 135
12 TraesCS1A01G219500 chr5A 83.333 144 18 3 1001 1141 698507356 698507496 1.300000e-25 128


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 TraesCS1A01G219500 chr1A 388159721 388164182 4461 True 8240.00 8240 100.00000 1 4462 1 chr1A.!!$R1 4461
1 TraesCS1A01G219500 chr1D 308585243 308589573 4330 True 1651.25 4717 93.08075 1 4462 4 chr1D.!!$R1 4461
2 TraesCS1A01G219500 chr1B 418672185 418678248 6063 True 1277.20 3216 91.66480 1 4462 5 chr1B.!!$R1 4461

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
670 674 0.396695 TAACCGAGCTACCTCCTGGG 60.397 60.0 0.00 0.00 41.89 4.45 F
761 766 0.409484 AAACCCCAGAATCCACAGGG 59.591 55.0 0.00 0.00 43.88 4.45 F
1881 1928 0.032515 TGCTCCTCAACCGGATCCTA 60.033 55.0 9.46 0.00 31.43 2.94 F
2798 4589 1.086067 CACAGCTCGCCATGGTACTG 61.086 60.0 14.67 16.85 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1928 0.648301 ACCCTAGGCCTATTCCCAGT 59.352 55.000 14.30 1.94 0.00 4.00 R
1957 2004 1.276138 CTCCTGAGCCACATGTACACA 59.724 52.381 0.00 0.00 0.00 3.72 R
2900 4691 0.179171 GACGTGTGACGACCGATGAT 60.179 55.000 2.62 0.00 46.05 2.45 R
4149 5955 0.533951 CTGGAAATTTGGAGCTGGCC 59.466 55.000 0.00 0.00 0.00 5.36 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
67 68 4.517453 TCTTCCAAACAATCAGTAAACCGG 59.483 41.667 0.00 0.00 0.00 5.28
95 96 1.045407 AACGCAGAGAAGGTGTGGTA 58.955 50.000 0.00 0.00 0.00 3.25
459 463 4.804420 AGCAGGAGGGATGCCGGA 62.804 66.667 5.05 0.00 44.97 5.14
592 596 1.535226 CGATCGGATCTTACGGTTGCA 60.535 52.381 15.50 0.00 0.00 4.08
593 597 2.755650 GATCGGATCTTACGGTTGCAT 58.244 47.619 10.73 0.00 0.00 3.96
594 598 2.218953 TCGGATCTTACGGTTGCATC 57.781 50.000 0.00 0.00 0.00 3.91
595 599 1.202486 TCGGATCTTACGGTTGCATCC 60.202 52.381 3.51 3.51 0.00 3.51
605 609 2.038387 GGTTGCATCCGATACCAAGT 57.962 50.000 0.00 0.00 0.00 3.16
606 610 2.365582 GGTTGCATCCGATACCAAGTT 58.634 47.619 0.00 0.00 0.00 2.66
607 611 2.752903 GGTTGCATCCGATACCAAGTTT 59.247 45.455 0.00 0.00 0.00 2.66
608 612 3.192633 GGTTGCATCCGATACCAAGTTTT 59.807 43.478 0.00 0.00 0.00 2.43
609 613 4.321675 GGTTGCATCCGATACCAAGTTTTT 60.322 41.667 0.00 0.00 0.00 1.94
670 674 0.396695 TAACCGAGCTACCTCCTGGG 60.397 60.000 0.00 0.00 41.89 4.45
729 733 3.824133 CCTGCTCATATCATTTCCACCA 58.176 45.455 0.00 0.00 0.00 4.17
741 746 2.791383 TTCCACCAGCAACAAAATCG 57.209 45.000 0.00 0.00 0.00 3.34
745 750 2.794350 CCACCAGCAACAAAATCGAAAC 59.206 45.455 0.00 0.00 0.00 2.78
757 762 2.420058 ATCGAAACCCCAGAATCCAC 57.580 50.000 0.00 0.00 0.00 4.02
758 763 1.060729 TCGAAACCCCAGAATCCACA 58.939 50.000 0.00 0.00 0.00 4.17
759 764 1.003118 TCGAAACCCCAGAATCCACAG 59.997 52.381 0.00 0.00 0.00 3.66
760 765 1.839424 GAAACCCCAGAATCCACAGG 58.161 55.000 0.00 0.00 0.00 4.00
761 766 0.409484 AAACCCCAGAATCCACAGGG 59.591 55.000 0.00 0.00 43.88 4.45
762 767 2.155197 AACCCCAGAATCCACAGGGC 62.155 60.000 0.00 0.00 41.86 5.19
763 768 2.615465 CCCCAGAATCCACAGGGCA 61.615 63.158 0.00 0.00 40.07 5.36
764 769 1.379044 CCCAGAATCCACAGGGCAC 60.379 63.158 0.00 0.00 33.91 5.01
776 781 3.758172 GGGCACCGCTGAAGAAAA 58.242 55.556 0.00 0.00 40.86 2.29
777 782 2.037871 GGGCACCGCTGAAGAAAAA 58.962 52.632 0.00 0.00 40.86 1.94
829 834 1.985895 CCCCAGAGGTAGTCAAAGGTT 59.014 52.381 0.00 0.00 0.00 3.50
830 835 3.178865 CCCCAGAGGTAGTCAAAGGTTA 58.821 50.000 0.00 0.00 0.00 2.85
831 836 3.197983 CCCCAGAGGTAGTCAAAGGTTAG 59.802 52.174 0.00 0.00 0.00 2.34
832 837 3.838903 CCCAGAGGTAGTCAAAGGTTAGT 59.161 47.826 0.00 0.00 0.00 2.24
833 838 5.021458 CCCAGAGGTAGTCAAAGGTTAGTA 58.979 45.833 0.00 0.00 0.00 1.82
945 951 1.150536 CTCTCCCTCCCTCTCTCCG 59.849 68.421 0.00 0.00 0.00 4.63
950 956 2.440430 CTCCCTCTCTCCGGCGAA 60.440 66.667 9.30 0.00 0.00 4.70
963 969 1.664965 GGCGAAACGACACTCTGCT 60.665 57.895 0.00 0.00 33.63 4.24
976 982 2.828520 CACTCTGCTCTTGGACTAGGAA 59.171 50.000 0.00 0.00 0.00 3.36
1008 1014 1.890979 GCAGGGAGTGATGGCGATG 60.891 63.158 0.00 0.00 0.00 3.84
1011 1017 2.592861 GGAGTGATGGCGATGGGC 60.593 66.667 0.00 0.00 42.51 5.36
1147 1153 4.899239 GCATCTCCGGTCCGCCTG 62.899 72.222 5.50 1.09 0.00 4.85
1157 1163 1.079057 GTCCGCCTGTCTTCTTCCC 60.079 63.158 0.00 0.00 0.00 3.97
1199 1215 2.045926 CCTCTTGGGCTCAACGGG 60.046 66.667 0.00 0.00 0.00 5.28
1269 1285 4.917474 GGCATTCATGGCGCTTTT 57.083 50.000 7.64 0.00 43.58 2.27
1270 1286 3.142124 GGCATTCATGGCGCTTTTT 57.858 47.368 7.64 0.00 43.58 1.94
1312 1328 1.533625 TGGCTTACTTGTGGTGCATC 58.466 50.000 0.00 0.00 0.00 3.91
1313 1329 0.811281 GGCTTACTTGTGGTGCATCC 59.189 55.000 0.00 0.00 0.00 3.51
1334 1350 2.031163 GCTTCAGTGCCTCGTGGT 59.969 61.111 5.26 0.00 35.27 4.16
1339 1355 4.626081 AGTGCCTCGTGGTGGTGC 62.626 66.667 5.26 0.00 35.27 5.01
1356 1372 4.012374 TGGTGCAGATTTTCTCTTCCATC 58.988 43.478 0.00 0.00 29.16 3.51
1410 1428 4.229876 GCTTTCCTCTGTTCCATTTTTCG 58.770 43.478 0.00 0.00 0.00 3.46
1460 1478 8.221251 AGGCCTTTTAGAGGGATTATAGAAAAG 58.779 37.037 0.00 0.00 46.40 2.27
1480 1510 7.809806 AGAAAAGGAAAAGAATCATGCGTTTAG 59.190 33.333 0.00 0.00 0.00 1.85
1524 1554 2.671396 GGTCAACATTACGCGATGAACT 59.329 45.455 15.93 0.00 0.00 3.01
1589 1636 2.667969 GCATGCGGTTCTGAATTTTTCC 59.332 45.455 0.00 0.00 0.00 3.13
1803 1850 1.153568 CGTGTCCATGCTGATCGGT 60.154 57.895 2.89 0.00 0.00 4.69
1854 1901 2.260434 GGAGCAGCCGTGAACGTA 59.740 61.111 1.75 0.00 37.74 3.57
1881 1928 0.032515 TGCTCCTCAACCGGATCCTA 60.033 55.000 9.46 0.00 31.43 2.94
1945 1992 4.247258 TGCAACAATTCAAGCCAATGATC 58.753 39.130 0.00 0.00 0.00 2.92
1957 2004 5.184892 AGCCAATGATCCTTTAAGTCAGT 57.815 39.130 0.00 0.00 0.00 3.41
1970 2017 2.169832 AGTCAGTGTGTACATGTGGC 57.830 50.000 9.11 1.72 0.00 5.01
2005 2052 4.829064 AAAAATCAGTAGCACAGCGAAA 57.171 36.364 0.00 0.00 0.00 3.46
2007 2054 6.494893 AAAAATCAGTAGCACAGCGAAATA 57.505 33.333 0.00 0.00 0.00 1.40
2081 2130 3.233507 ACCCTGCATCAGTTCACAAATT 58.766 40.909 0.00 0.00 0.00 1.82
2166 2215 6.785076 TCCTGTAGATGTAATTTGTCCCAAA 58.215 36.000 0.00 0.00 0.00 3.28
2244 2293 3.378427 GTCTCCCAAATCCCAAAGAATCG 59.622 47.826 0.00 0.00 0.00 3.34
2250 2299 4.497300 CAAATCCCAAAGAATCGTTGCAT 58.503 39.130 3.38 0.00 0.00 3.96
2259 2308 5.940192 AAGAATCGTTGCATTTGACTACA 57.060 34.783 0.00 0.00 0.00 2.74
2267 2316 4.857871 TGCATTTGACTACACGATAAGC 57.142 40.909 0.00 0.00 0.00 3.09
2301 2350 4.759183 TGTAGCAAGTGCATGTGATGTTTA 59.241 37.500 6.00 0.00 45.16 2.01
2408 4199 1.407618 TCGATCCCATTGTACCTGTCG 59.592 52.381 0.00 0.00 0.00 4.35
2648 4439 4.681978 GGCGACACCGACAAGGCT 62.682 66.667 0.00 0.00 44.91 4.58
2740 4531 2.665000 CCTCTCGAGGGCAGCAAA 59.335 61.111 13.56 0.00 44.87 3.68
2795 4586 2.584064 CCACAGCTCGCCATGGTA 59.416 61.111 14.67 0.74 0.00 3.25
2798 4589 1.086067 CACAGCTCGCCATGGTACTG 61.086 60.000 14.67 16.85 0.00 2.74
2825 4616 2.487986 CCCTTTCTTCAACCAGCTCACT 60.488 50.000 0.00 0.00 0.00 3.41
2846 4637 5.184479 CACTGGGATCAATGTGATGAACTTT 59.816 40.000 0.00 0.00 37.20 2.66
2855 4646 3.772387 TGTGATGAACTTTTATGCCCCA 58.228 40.909 0.00 0.00 0.00 4.96
2900 4691 2.196229 GAGAGCGCCTCCCTCCTA 59.804 66.667 2.29 0.00 35.87 2.94
2903 4694 1.531840 GAGCGCCTCCCTCCTATCA 60.532 63.158 2.29 0.00 0.00 2.15
2909 4700 1.551452 CCTCCCTCCTATCATCGGTC 58.449 60.000 0.00 0.00 0.00 4.79
2915 4706 1.947456 CTCCTATCATCGGTCGTCACA 59.053 52.381 0.00 0.00 0.00 3.58
2999 4790 0.039911 AGCTCTTCCTCGTAGGTGGT 59.960 55.000 3.64 0.00 36.53 4.16
3017 4808 4.101585 GGTGGTATCCAGATGATCTTGTCA 59.898 45.833 0.00 0.00 36.10 3.58
3044 4835 4.971125 GTCGGCGCCATCCTAGCC 62.971 72.222 28.98 0.00 46.88 3.93
3060 4851 1.082104 GCCGCAAAGTTCAAGGACG 60.082 57.895 0.00 0.00 0.00 4.79
3167 4958 1.153628 CACATTCCTCGTCCCGACC 60.154 63.158 0.00 0.00 0.00 4.79
3188 4979 1.767681 GAGATCTGCCCACTGGAGATT 59.232 52.381 0.00 0.00 32.23 2.40
3284 5075 1.078918 CCTCTGCCGCATCAAGTCA 60.079 57.895 0.00 0.00 0.00 3.41
3345 5136 3.622630 ACGCTAGTGGTCTATCTGTTCT 58.377 45.455 8.42 0.00 0.00 3.01
3434 5225 3.265479 AGAAGATTGTTGGGGAGGAAGAG 59.735 47.826 0.00 0.00 0.00 2.85
3458 5249 5.371176 GGATAAGGAAGAGGAGGAAAAGGAT 59.629 44.000 0.00 0.00 0.00 3.24
3459 5250 6.126332 GGATAAGGAAGAGGAGGAAAAGGATT 60.126 42.308 0.00 0.00 0.00 3.01
3460 5251 7.072581 GGATAAGGAAGAGGAGGAAAAGGATTA 59.927 40.741 0.00 0.00 0.00 1.75
3461 5252 6.720217 AAGGAAGAGGAGGAAAAGGATTAA 57.280 37.500 0.00 0.00 0.00 1.40
3462 5253 6.720217 AGGAAGAGGAGGAAAAGGATTAAA 57.280 37.500 0.00 0.00 0.00 1.52
3463 5254 6.726379 AGGAAGAGGAGGAAAAGGATTAAAG 58.274 40.000 0.00 0.00 0.00 1.85
3464 5255 5.888724 GGAAGAGGAGGAAAAGGATTAAAGG 59.111 44.000 0.00 0.00 0.00 3.11
3465 5256 6.297068 GGAAGAGGAGGAAAAGGATTAAAGGA 60.297 42.308 0.00 0.00 0.00 3.36
3471 5262 3.628032 GGAAAAGGATTAAAGGAGAGGCG 59.372 47.826 0.00 0.00 0.00 5.52
3485 5276 3.600388 GAGAGGCGAGAAAGGAAAATCA 58.400 45.455 0.00 0.00 0.00 2.57
3564 5356 7.703058 AGGGAAAACATAGTACAGGATTTTG 57.297 36.000 0.00 0.00 0.00 2.44
3607 5400 7.466746 AAGTATGGTTGCATCTAATTGTGTT 57.533 32.000 0.00 0.00 0.00 3.32
3608 5401 6.855836 AGTATGGTTGCATCTAATTGTGTTG 58.144 36.000 0.00 0.00 0.00 3.33
3617 5410 3.411446 TCTAATTGTGTTGCCTGACAGG 58.589 45.455 17.83 17.83 38.80 4.00
3626 5419 4.340246 CCTGACAGGCCTGCAGCA 62.340 66.667 33.91 27.12 46.50 4.41
3642 5435 3.060615 CAGCTGCTGCCAGTTCCC 61.061 66.667 17.73 0.00 41.26 3.97
3666 5459 0.607620 ATGGCCATTTCAAACGGTGG 59.392 50.000 14.09 0.00 34.84 4.61
3667 5460 0.468214 TGGCCATTTCAAACGGTGGA 60.468 50.000 0.00 0.00 33.53 4.02
3669 5462 1.336795 GGCCATTTCAAACGGTGGAAG 60.337 52.381 0.00 0.00 33.53 3.46
3672 5465 3.192633 GCCATTTCAAACGGTGGAAGTAT 59.807 43.478 0.00 0.00 33.53 2.12
3688 5481 9.614792 GGTGGAAGTATTGATATGAAGTAACTT 57.385 33.333 1.52 1.52 0.00 2.66
3744 5546 0.758123 CTCTCAGAGGGGCTGGATTC 59.242 60.000 0.00 0.00 44.98 2.52
3758 5560 4.765856 GGCTGGATTCTCTGATTATGCATT 59.234 41.667 3.54 0.00 0.00 3.56
3814 5616 1.277579 TGGATGGCCAAACAATGCAT 58.722 45.000 10.96 0.00 42.49 3.96
3834 5636 2.908940 GTGCACAGCCCAACAGCT 60.909 61.111 13.17 0.00 46.45 4.24
4090 5892 8.545420 CCAAATAAGAATAAAATCATGCAGCAC 58.455 33.333 0.00 0.00 0.00 4.40
4132 5934 4.678840 GCATGGCTTCTTTCAACCATAAGG 60.679 45.833 0.00 0.00 40.95 2.69
4149 5955 3.692257 AAGGTCTTGAGTGACTGGATG 57.308 47.619 0.00 0.00 37.16 3.51
4192 5998 4.286297 TCCGGACAAAATCTGAAGACAT 57.714 40.909 0.00 0.00 35.44 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.406370 ACTGATTGTTTGGAAGATCACGATA 58.594 36.000 0.00 0.00 0.00 2.92
67 68 3.782244 CTCTGCGTTGCGTCTGCC 61.782 66.667 0.00 0.00 41.78 4.85
95 96 0.548510 GGAGCAGAGGTAAAGCCCAT 59.451 55.000 0.00 0.00 38.26 4.00
459 463 2.291865 GGCCATCTTTTTCCTCCTCCTT 60.292 50.000 0.00 0.00 0.00 3.36
572 576 1.129326 GCAACCGTAAGATCCGATCG 58.871 55.000 8.51 8.51 43.02 3.69
573 577 2.218953 TGCAACCGTAAGATCCGATC 57.781 50.000 0.00 0.00 43.02 3.69
574 578 2.548067 GGATGCAACCGTAAGATCCGAT 60.548 50.000 0.00 0.00 43.02 4.18
575 579 1.202486 GGATGCAACCGTAAGATCCGA 60.202 52.381 0.00 0.00 43.02 4.55
576 580 1.217882 GGATGCAACCGTAAGATCCG 58.782 55.000 0.00 0.00 43.02 4.18
620 624 2.577606 TCGGATGCCTTCCTCAAAAA 57.422 45.000 1.73 0.00 42.99 1.94
621 625 2.806945 ATCGGATGCCTTCCTCAAAA 57.193 45.000 0.00 0.00 42.99 2.44
622 626 2.158813 GGTATCGGATGCCTTCCTCAAA 60.159 50.000 16.77 0.00 42.99 2.69
623 627 1.416401 GGTATCGGATGCCTTCCTCAA 59.584 52.381 16.77 0.00 42.99 3.02
624 628 1.048601 GGTATCGGATGCCTTCCTCA 58.951 55.000 16.77 0.00 42.99 3.86
625 629 1.048601 TGGTATCGGATGCCTTCCTC 58.951 55.000 22.99 0.00 42.99 3.71
626 630 1.417890 CTTGGTATCGGATGCCTTCCT 59.582 52.381 22.99 0.00 42.99 3.36
627 631 1.141053 ACTTGGTATCGGATGCCTTCC 59.859 52.381 22.99 8.32 41.59 3.46
628 632 2.158957 TCACTTGGTATCGGATGCCTTC 60.159 50.000 22.99 0.94 35.87 3.46
629 633 1.837439 TCACTTGGTATCGGATGCCTT 59.163 47.619 22.99 7.47 35.87 4.35
630 634 1.414181 CTCACTTGGTATCGGATGCCT 59.586 52.381 22.99 3.39 35.87 4.75
631 635 1.139058 ACTCACTTGGTATCGGATGCC 59.861 52.381 17.14 17.14 35.37 4.40
632 636 2.604046 ACTCACTTGGTATCGGATGC 57.396 50.000 0.00 0.00 0.00 3.91
633 637 4.369182 GGTTACTCACTTGGTATCGGATG 58.631 47.826 0.00 0.00 0.00 3.51
670 674 4.593634 ACTAATTACTAGATGGGCCAGGAC 59.406 45.833 13.78 6.20 0.00 3.85
671 675 4.827789 ACTAATTACTAGATGGGCCAGGA 58.172 43.478 13.78 0.00 0.00 3.86
673 677 5.308825 CCAACTAATTACTAGATGGGCCAG 58.691 45.833 13.78 0.00 43.63 4.85
678 682 6.174720 TGAGCCCAACTAATTACTAGATGG 57.825 41.667 0.00 2.03 45.80 3.51
679 683 7.225538 CACTTGAGCCCAACTAATTACTAGATG 59.774 40.741 0.00 0.00 31.73 2.90
680 684 7.275920 CACTTGAGCCCAACTAATTACTAGAT 58.724 38.462 0.00 0.00 0.00 1.98
681 685 6.351881 CCACTTGAGCCCAACTAATTACTAGA 60.352 42.308 0.00 0.00 0.00 2.43
682 686 5.817816 CCACTTGAGCCCAACTAATTACTAG 59.182 44.000 0.00 0.00 0.00 2.57
683 687 5.338871 CCCACTTGAGCCCAACTAATTACTA 60.339 44.000 0.00 0.00 0.00 1.82
684 688 4.567747 CCCACTTGAGCCCAACTAATTACT 60.568 45.833 0.00 0.00 0.00 2.24
685 689 3.694566 CCCACTTGAGCCCAACTAATTAC 59.305 47.826 0.00 0.00 0.00 1.89
729 733 2.035632 TGGGGTTTCGATTTTGTTGCT 58.964 42.857 0.00 0.00 0.00 3.91
741 746 1.616994 CCCTGTGGATTCTGGGGTTTC 60.617 57.143 0.00 0.00 41.12 2.78
745 750 2.276740 GCCCTGTGGATTCTGGGG 59.723 66.667 9.91 0.00 43.76 4.96
757 762 1.172180 TTTTCTTCAGCGGTGCCCTG 61.172 55.000 10.38 0.00 0.00 4.45
758 763 0.467290 TTTTTCTTCAGCGGTGCCCT 60.467 50.000 10.38 0.00 0.00 5.19
759 764 2.037871 TTTTTCTTCAGCGGTGCCC 58.962 52.632 10.38 0.00 0.00 5.36
775 780 1.203001 TGGTCCTGCGGATTCCTTTTT 60.203 47.619 0.30 0.00 32.73 1.94
776 781 0.404040 TGGTCCTGCGGATTCCTTTT 59.596 50.000 0.30 0.00 32.73 2.27
777 782 0.322546 GTGGTCCTGCGGATTCCTTT 60.323 55.000 0.30 0.00 32.73 3.11
778 783 1.299976 GTGGTCCTGCGGATTCCTT 59.700 57.895 0.30 0.00 32.73 3.36
779 784 2.670148 GGTGGTCCTGCGGATTCCT 61.670 63.158 0.30 0.00 32.73 3.36
780 785 2.124695 GGTGGTCCTGCGGATTCC 60.125 66.667 0.00 0.00 32.73 3.01
781 786 2.511600 CGGTGGTCCTGCGGATTC 60.512 66.667 0.00 0.00 32.73 2.52
782 787 3.000819 TCGGTGGTCCTGCGGATT 61.001 61.111 0.00 0.00 32.73 3.01
783 788 3.771160 GTCGGTGGTCCTGCGGAT 61.771 66.667 0.00 0.00 32.73 4.18
786 791 4.778415 CTCGTCGGTGGTCCTGCG 62.778 72.222 0.00 0.00 0.00 5.18
787 792 3.681835 ACTCGTCGGTGGTCCTGC 61.682 66.667 0.00 0.00 0.00 4.85
829 834 1.674441 CGGCGAGGTTGACTGATACTA 59.326 52.381 0.00 0.00 0.00 1.82
830 835 0.456221 CGGCGAGGTTGACTGATACT 59.544 55.000 0.00 0.00 0.00 2.12
831 836 0.527817 CCGGCGAGGTTGACTGATAC 60.528 60.000 9.30 0.00 34.51 2.24
832 837 1.813859 CCGGCGAGGTTGACTGATA 59.186 57.895 9.30 0.00 34.51 2.15
833 838 2.579201 CCGGCGAGGTTGACTGAT 59.421 61.111 9.30 0.00 34.51 2.90
893 899 7.730364 ATATAAATTTATCGGCGGATGGATC 57.270 36.000 13.95 0.00 34.00 3.36
945 951 1.618640 GAGCAGAGTGTCGTTTCGCC 61.619 60.000 0.00 0.00 0.00 5.54
950 956 1.040646 TCCAAGAGCAGAGTGTCGTT 58.959 50.000 0.00 0.00 0.00 3.85
963 969 4.079154 TGCTCTCCTATTCCTAGTCCAAGA 60.079 45.833 0.00 0.00 0.00 3.02
976 982 1.059006 CCCTGCCCTTGCTCTCCTAT 61.059 60.000 0.00 0.00 38.71 2.57
1141 1147 0.391793 GAAGGGAAGAAGACAGGCGG 60.392 60.000 0.00 0.00 0.00 6.13
1147 1153 6.599356 ACTCTAGAAAGAAGGGAAGAAGAC 57.401 41.667 0.00 0.00 0.00 3.01
1157 1163 9.589111 GGGTTAACAATCTACTCTAGAAAGAAG 57.411 37.037 8.10 7.09 38.50 2.85
1234 1250 4.817318 TGCCATTTTAATCCCTTCCAAC 57.183 40.909 0.00 0.00 0.00 3.77
1279 1295 4.211502 GCCATGAATGCCACCCGC 62.212 66.667 0.00 0.00 38.31 6.13
1280 1296 0.751277 TAAGCCATGAATGCCACCCG 60.751 55.000 0.00 0.00 0.00 5.28
1281 1297 0.746659 GTAAGCCATGAATGCCACCC 59.253 55.000 0.00 0.00 0.00 4.61
1282 1298 1.767759 AGTAAGCCATGAATGCCACC 58.232 50.000 0.00 0.00 0.00 4.61
1283 1299 2.493278 ACAAGTAAGCCATGAATGCCAC 59.507 45.455 0.00 0.00 0.00 5.01
1284 1300 2.492881 CACAAGTAAGCCATGAATGCCA 59.507 45.455 0.00 0.00 0.00 4.92
1285 1301 2.159198 CCACAAGTAAGCCATGAATGCC 60.159 50.000 0.00 0.00 0.00 4.40
1286 1302 2.493278 ACCACAAGTAAGCCATGAATGC 59.507 45.455 0.00 0.00 0.00 3.56
1287 1303 3.674138 GCACCACAAGTAAGCCATGAATG 60.674 47.826 0.00 0.00 0.00 2.67
1288 1304 2.493278 GCACCACAAGTAAGCCATGAAT 59.507 45.455 0.00 0.00 0.00 2.57
1289 1305 1.885887 GCACCACAAGTAAGCCATGAA 59.114 47.619 0.00 0.00 0.00 2.57
1290 1306 1.202867 TGCACCACAAGTAAGCCATGA 60.203 47.619 0.00 0.00 0.00 3.07
1291 1307 1.246649 TGCACCACAAGTAAGCCATG 58.753 50.000 0.00 0.00 0.00 3.66
1292 1308 2.094675 GATGCACCACAAGTAAGCCAT 58.905 47.619 0.00 0.00 0.00 4.40
1293 1309 1.533625 GATGCACCACAAGTAAGCCA 58.466 50.000 0.00 0.00 0.00 4.75
1294 1310 0.811281 GGATGCACCACAAGTAAGCC 59.189 55.000 0.00 0.00 38.79 4.35
1295 1311 1.533625 TGGATGCACCACAAGTAAGC 58.466 50.000 4.16 0.00 44.64 3.09
1334 1350 3.507162 TGGAAGAGAAAATCTGCACCA 57.493 42.857 0.00 0.00 38.67 4.17
1356 1372 3.256383 TCATCAGCTTTTGTGTCCCAATG 59.744 43.478 0.00 0.00 31.81 2.82
1410 1428 5.983540 AGTCCTAGATCATTTTGACCTGAC 58.016 41.667 0.00 0.00 0.00 3.51
1460 1478 5.106317 TGGACTAAACGCATGATTCTTTTCC 60.106 40.000 0.00 0.00 0.00 3.13
1469 1499 4.880886 CAATGATGGACTAAACGCATGA 57.119 40.909 0.00 0.00 0.00 3.07
1758 1805 1.276421 CCAAACCTCCTCGTGACAGAT 59.724 52.381 0.00 0.00 0.00 2.90
1760 1807 0.951040 GCCAAACCTCCTCGTGACAG 60.951 60.000 0.00 0.00 0.00 3.51
1787 1834 1.221566 CCACCGATCAGCATGGACA 59.778 57.895 0.00 0.00 36.16 4.02
1803 1850 0.953471 CGGCAATGAAGACGGTTCCA 60.953 55.000 0.00 0.00 36.07 3.53
1854 1901 1.001641 GTTGAGGAGCAGCATGGGT 60.002 57.895 0.00 0.00 35.86 4.51
1881 1928 0.648301 ACCCTAGGCCTATTCCCAGT 59.352 55.000 14.30 1.94 0.00 4.00
1927 1974 5.750352 AAAGGATCATTGGCTTGAATTGT 57.250 34.783 0.00 0.00 0.00 2.71
1928 1975 7.325694 ACTTAAAGGATCATTGGCTTGAATTG 58.674 34.615 0.00 0.00 0.00 2.32
1945 1992 5.179368 CCACATGTACACACTGACTTAAAGG 59.821 44.000 0.00 0.00 0.00 3.11
1957 2004 1.276138 CTCCTGAGCCACATGTACACA 59.724 52.381 0.00 0.00 0.00 3.72
1987 2034 4.445718 CGATATTTCGCTGTGCTACTGATT 59.554 41.667 0.00 0.00 38.75 2.57
2055 2104 2.876368 GAACTGATGCAGGGTCCGGG 62.876 65.000 0.00 0.00 35.51 5.73
2081 2130 1.305219 GCTCCATACAGCCGCACAAA 61.305 55.000 0.00 0.00 32.76 2.83
2166 2215 4.371624 TCCATTGTCATCAACTTGGAGT 57.628 40.909 0.00 0.00 37.63 3.85
2244 2293 5.022021 GCTTATCGTGTAGTCAAATGCAAC 58.978 41.667 0.00 0.00 0.00 4.17
2250 2299 4.878439 ACACAGCTTATCGTGTAGTCAAA 58.122 39.130 5.80 0.00 44.32 2.69
2259 2308 5.749109 GCTACAAGATAACACAGCTTATCGT 59.251 40.000 0.00 0.00 37.94 3.73
2267 2316 4.452114 TGCACTTGCTACAAGATAACACAG 59.548 41.667 13.94 0.00 42.66 3.66
2343 2392 8.309656 ACAGTAACCACAGTAAGGTATTTAGTC 58.690 37.037 0.00 0.00 38.76 2.59
2795 4586 3.416156 GTTGAAGAAAGGGATCAGCAGT 58.584 45.455 0.00 0.00 0.00 4.40
2798 4589 2.751806 CTGGTTGAAGAAAGGGATCAGC 59.248 50.000 0.00 0.00 0.00 4.26
2825 4616 7.631161 GCATAAAAGTTCATCACATTGATCCCA 60.631 37.037 0.00 0.00 34.28 4.37
2846 4637 1.408127 CGGAACATCACTGGGGCATAA 60.408 52.381 0.00 0.00 0.00 1.90
2855 4646 2.010145 CGATTGTCCGGAACATCACT 57.990 50.000 19.45 4.07 37.82 3.41
2900 4691 0.179171 GACGTGTGACGACCGATGAT 60.179 55.000 2.62 0.00 46.05 2.45
2903 4694 0.954449 AGAGACGTGTGACGACCGAT 60.954 55.000 2.62 0.00 46.05 4.18
2915 4706 0.235665 CAAATGTTGCGCAGAGACGT 59.764 50.000 11.31 4.66 34.88 4.34
2996 4787 4.716287 TGTGACAAGATCATCTGGATACCA 59.284 41.667 0.00 0.00 40.28 3.25
2999 4790 4.652881 AGCTGTGACAAGATCATCTGGATA 59.347 41.667 0.00 0.00 40.28 2.59
3044 4835 1.135972 CCATCGTCCTTGAACTTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
3060 4851 4.713792 AGTCCTTATCCATCAACCCATC 57.286 45.455 0.00 0.00 0.00 3.51
3167 4958 1.039785 TCTCCAGTGGGCAGATCTCG 61.040 60.000 9.92 0.00 0.00 4.04
3188 4979 0.688749 TGCTCTGCCCTGCTGATCTA 60.689 55.000 0.00 0.00 36.06 1.98
3299 5090 1.663074 GCAAATCCACGCGGCAAAA 60.663 52.632 12.47 0.00 0.00 2.44
3345 5136 2.645838 AGCTTCTTTGTCTCTGGCAA 57.354 45.000 0.00 0.00 0.00 4.52
3434 5225 4.722279 TCCTTTTCCTCCTCTTCCTTATCC 59.278 45.833 0.00 0.00 0.00 2.59
3458 5249 3.170717 TCCTTTCTCGCCTCTCCTTTAA 58.829 45.455 0.00 0.00 0.00 1.52
3459 5250 2.816411 TCCTTTCTCGCCTCTCCTTTA 58.184 47.619 0.00 0.00 0.00 1.85
3460 5251 1.645710 TCCTTTCTCGCCTCTCCTTT 58.354 50.000 0.00 0.00 0.00 3.11
3461 5252 1.645710 TTCCTTTCTCGCCTCTCCTT 58.354 50.000 0.00 0.00 0.00 3.36
3462 5253 1.645710 TTTCCTTTCTCGCCTCTCCT 58.354 50.000 0.00 0.00 0.00 3.69
3463 5254 2.474410 TTTTCCTTTCTCGCCTCTCC 57.526 50.000 0.00 0.00 0.00 3.71
3464 5255 3.600388 TGATTTTCCTTTCTCGCCTCTC 58.400 45.455 0.00 0.00 0.00 3.20
3465 5256 3.703001 TGATTTTCCTTTCTCGCCTCT 57.297 42.857 0.00 0.00 0.00 3.69
3471 5262 4.324267 TCGGGAGTTGATTTTCCTTTCTC 58.676 43.478 0.00 0.00 33.85 2.87
3485 5276 2.122167 CGCTAGGAGCTCGGGAGTT 61.122 63.158 7.83 0.00 39.60 3.01
3590 5383 3.922240 CAGGCAACACAATTAGATGCAAC 59.078 43.478 12.28 0.00 38.73 4.17
3625 5418 3.060615 GGGAACTGGCAGCAGCTG 61.061 66.667 18.93 18.93 41.70 4.24
3626 5419 3.573229 TGGGAACTGGCAGCAGCT 61.573 61.111 15.89 0.00 41.70 4.24
3631 5424 1.683943 CCATATGTGGGAACTGGCAG 58.316 55.000 14.16 14.16 42.11 4.85
3642 5435 3.119173 ACCGTTTGAAATGGCCATATGTG 60.119 43.478 21.15 5.48 41.46 3.21
3708 5501 9.295825 CCTCTGAGAGACTGTTCACTTATATAT 57.704 37.037 11.82 0.00 0.00 0.86
3722 5518 1.001503 CCAGCCCCTCTGAGAGACT 59.998 63.158 11.82 2.39 45.72 3.24
3744 5546 8.350722 AGCAAAAGTCATAATGCATAATCAGAG 58.649 33.333 0.00 0.00 41.18 3.35
3814 5616 2.124529 TGTTGGGCTGTGCACGAA 60.125 55.556 13.13 0.00 32.76 3.85
3824 5626 3.055891 ACATATTTCCAAAGCTGTTGGGC 60.056 43.478 20.54 0.00 39.96 5.36
3905 5707 3.129287 CCTCCATTATGCACCAAGTGTTC 59.871 47.826 0.00 0.00 35.75 3.18
4090 5892 8.362639 AGCCATGCTAAATATTTTACCAATGAG 58.637 33.333 5.91 0.00 36.99 2.90
4132 5934 1.677217 GGCCATCCAGTCACTCAAGAC 60.677 57.143 0.00 0.00 38.81 3.01
4149 5955 0.533951 CTGGAAATTTGGAGCTGGCC 59.466 55.000 0.00 0.00 0.00 5.36
4362 6171 4.158394 GGATGCATCTGTTGTTTGTATGGT 59.842 41.667 25.28 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.