Multiple sequence alignment - TraesCS2D01G463900

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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 TraesCS2D01G463900 chr2D 100.000 2643 0 0 1 2643 569308541 569311183 0.000000e+00 4881
1 TraesCS2D01G463900 chr2B 87.936 2611 120 68 12 2506 682137781 682140312 0.000000e+00 2896
2 TraesCS2D01G463900 chr2A 86.116 2096 111 60 9 2011 709048045 709050053 0.000000e+00 2093
3 TraesCS2D01G463900 chr2A 92.632 190 13 1 2013 2202 709051407 709051595 3.350000e-69 272
4 TraesCS2D01G463900 chr2A 94.737 76 4 0 2295 2370 709051602 709051677 4.620000e-23 119


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 TraesCS2D01G463900 chr2D 569308541 569311183 2642 False 4881 4881 100.000000 1 2643 1 chr2D.!!$F1 2642
1 TraesCS2D01G463900 chr2B 682137781 682140312 2531 False 2896 2896 87.936000 12 2506 1 chr2B.!!$F1 2494
2 TraesCS2D01G463900 chr2A 709048045 709051677 3632 False 828 2093 91.161667 9 2370 3 chr2A.!!$F1 2361

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
167 169 0.16923 CGTGACTTGACCTCGAGGAG 59.831 60.0 37.69 25.59 38.94 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2133 0.727398 GCATCCGTCAGTTGGCTTAC 59.273 55.0 0.0 0.0 0.0 2.34 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
18 19 2.876581 TTACCACTCGCCTGATCGA 58.123 52.632 0.00 0.00 36.94 3.59
19 20 1.399714 TTACCACTCGCCTGATCGAT 58.600 50.000 0.00 0.00 37.87 3.59
20 21 0.952280 TACCACTCGCCTGATCGATC 59.048 55.000 18.72 18.72 37.87 3.69
21 22 1.371022 CCACTCGCCTGATCGATCG 60.371 63.158 20.03 9.36 37.87 3.69
22 23 1.649267 CACTCGCCTGATCGATCGA 59.351 57.895 21.86 21.86 37.87 3.59
23 24 4.836892 CTCGCCTGATCGATCGAG 57.163 61.111 23.84 18.18 41.66 4.04
24 25 4.456806 TCGCCTGATCGATCGAGA 57.543 55.556 23.84 11.01 33.02 4.04
51 52 1.721487 CCAATGGCGATCAACCGTC 59.279 57.895 0.00 0.00 34.30 4.79
109 110 4.753662 AGGACGGCCCTGCTCGTA 62.754 66.667 1.76 0.00 45.61 3.43
110 111 4.509737 GGACGGCCCTGCTCGTAC 62.510 72.222 0.00 0.80 36.12 3.67
114 115 4.874977 GGCCCTGCTCGTACTCGC 62.875 72.222 0.00 0.00 36.96 5.03
136 137 3.726517 CAACCAGCAGGCGAACGG 61.727 66.667 0.00 0.00 39.06 4.44
166 168 1.863662 GCGTGACTTGACCTCGAGGA 61.864 60.000 37.69 14.23 38.94 3.71
167 169 0.169230 CGTGACTTGACCTCGAGGAG 59.831 60.000 37.69 25.59 38.94 3.69
168 170 1.249407 GTGACTTGACCTCGAGGAGT 58.751 55.000 37.69 28.62 38.94 3.85
169 171 2.434428 GTGACTTGACCTCGAGGAGTA 58.566 52.381 37.69 19.34 38.94 2.59
176 209 4.708576 TGACCTCGAGGAGTAGTATGAT 57.291 45.455 37.69 11.29 38.94 2.45
213 246 2.104111 TGAGCTAATTATGGTCACCGGG 59.896 50.000 6.32 0.00 37.07 5.73
268 307 4.656117 TGAAGCGCGGCTCGTGAA 62.656 61.111 8.83 0.00 38.25 3.18
269 308 4.135493 GAAGCGCGGCTCGTGAAC 62.135 66.667 8.83 0.00 38.25 3.18
338 377 2.162208 CGGAGTACAGTAACCGTAGCAA 59.838 50.000 15.37 0.00 40.42 3.91
365 408 1.151450 GGCACGGGATGGATGGATT 59.849 57.895 0.00 0.00 0.00 3.01
388 431 1.129998 CGGTGGTACTGTACGAGACTG 59.870 57.143 11.52 9.15 0.00 3.51
440 483 1.178276 AGCCGACAGAGAGGTTAGTG 58.822 55.000 0.00 0.00 0.00 2.74
666 760 2.390225 AGGGTTCTCACTCACTCACT 57.610 50.000 0.00 0.00 0.00 3.41
667 761 2.243810 AGGGTTCTCACTCACTCACTC 58.756 52.381 0.00 0.00 0.00 3.51
668 762 1.964223 GGGTTCTCACTCACTCACTCA 59.036 52.381 0.00 0.00 0.00 3.41
669 763 2.288518 GGGTTCTCACTCACTCACTCAC 60.289 54.545 0.00 0.00 0.00 3.51
711 805 1.381872 AGGCTCCCATACTCGTGCT 60.382 57.895 0.00 0.00 0.00 4.40
715 809 1.538419 GCTCCCATACTCGTGCTAACC 60.538 57.143 0.00 0.00 0.00 2.85
716 810 1.754803 CTCCCATACTCGTGCTAACCA 59.245 52.381 0.00 0.00 0.00 3.67
717 811 2.167693 CTCCCATACTCGTGCTAACCAA 59.832 50.000 0.00 0.00 0.00 3.67
718 812 2.568062 TCCCATACTCGTGCTAACCAAA 59.432 45.455 0.00 0.00 0.00 3.28
719 813 2.676342 CCCATACTCGTGCTAACCAAAC 59.324 50.000 0.00 0.00 0.00 2.93
720 814 2.676342 CCATACTCGTGCTAACCAAACC 59.324 50.000 0.00 0.00 0.00 3.27
721 815 3.331150 CATACTCGTGCTAACCAAACCA 58.669 45.455 0.00 0.00 0.00 3.67
725 819 1.141254 TCGTGCTAACCAAACCAAGGA 59.859 47.619 0.00 0.00 0.00 3.36
766 866 3.037431 TCTTCAAGAGCTCTCACAAGC 57.963 47.619 18.55 0.00 42.82 4.01
782 882 4.099266 TCACAAGCCACAAGTGCTATTTTT 59.901 37.500 0.00 0.00 38.34 1.94
828 950 2.159226 ACTATCCTTTCGTGAAGCTCCG 60.159 50.000 0.00 0.00 33.84 4.63
844 966 2.564975 CGGAGGTACGTTCGTGCT 59.435 61.111 8.10 0.47 0.00 4.40
845 967 1.800315 CGGAGGTACGTTCGTGCTG 60.800 63.158 8.10 0.00 0.00 4.41
917 1047 6.292328 GGAATTCTGCACTTTGTTTGTTTAGC 60.292 38.462 5.23 0.00 0.00 3.09
923 1053 4.209080 GCACTTTGTTTGTTTAGCATGGTC 59.791 41.667 0.00 0.00 0.00 4.02
924 1054 5.591099 CACTTTGTTTGTTTAGCATGGTCT 58.409 37.500 0.00 0.00 0.00 3.85
925 1055 5.459762 CACTTTGTTTGTTTAGCATGGTCTG 59.540 40.000 0.00 0.00 0.00 3.51
1003 1133 0.460811 TGAGATCTGTCGGTGCATGC 60.461 55.000 11.82 11.82 0.00 4.06
1074 1213 3.890674 GGTGAATCACCGAGCCAC 58.109 61.111 17.46 0.00 44.95 5.01
1075 1214 1.003839 GGTGAATCACCGAGCCACA 60.004 57.895 17.46 0.00 44.95 4.17
1076 1215 0.392998 GGTGAATCACCGAGCCACAT 60.393 55.000 17.46 0.00 44.95 3.21
1077 1216 1.009829 GTGAATCACCGAGCCACATC 58.990 55.000 1.10 0.00 0.00 3.06
1230 1376 3.490759 CGCAACGGCAGCTCGATT 61.491 61.111 9.87 0.00 41.24 3.34
1655 1801 3.143515 GCTAAGCCAGCCCCAAGC 61.144 66.667 0.00 0.00 45.23 4.01
1657 1803 4.424711 TAAGCCAGCCCCAAGCCG 62.425 66.667 0.00 0.00 45.47 5.52
1674 1820 1.406887 GCCGGCTTGATTTGAGTAGGA 60.407 52.381 22.15 0.00 0.00 2.94
1764 1913 0.790814 CTTCCGTTCTTCCGCTGTTC 59.209 55.000 0.00 0.00 0.00 3.18
1765 1914 0.942410 TTCCGTTCTTCCGCTGTTCG 60.942 55.000 0.00 0.00 38.08 3.95
1768 1917 1.860078 GTTCTTCCGCTGTTCGTGG 59.140 57.895 0.00 0.00 44.95 4.94
1782 1931 1.965930 CGTGGGTGTGTGTGATGGG 60.966 63.158 0.00 0.00 0.00 4.00
1790 1939 1.426983 TGTGTGTGATGGGGATTTGGA 59.573 47.619 0.00 0.00 0.00 3.53
1795 1944 1.213926 GTGATGGGGATTTGGAGAGCT 59.786 52.381 0.00 0.00 0.00 4.09
1796 1945 2.439507 GTGATGGGGATTTGGAGAGCTA 59.560 50.000 0.00 0.00 0.00 3.32
1797 1946 2.439507 TGATGGGGATTTGGAGAGCTAC 59.560 50.000 0.00 0.00 0.00 3.58
1798 1947 0.830648 TGGGGATTTGGAGAGCTACG 59.169 55.000 0.00 0.00 0.00 3.51
1979 2133 4.701956 ATGGCTAATTGTTGGAGAAACG 57.298 40.909 0.00 0.00 42.10 3.60
1992 2146 2.479275 GGAGAAACGTAAGCCAACTGAC 59.521 50.000 0.00 0.00 45.62 3.51
2002 2156 1.421410 GCCAACTGACGGATGCTACG 61.421 60.000 0.00 0.00 37.36 3.51
2283 3806 4.717629 CGCAGTGGGAACGAGCGA 62.718 66.667 0.00 0.00 46.02 4.93
2290 3813 4.742201 GGAACGAGCGAGCAGGCA 62.742 66.667 0.00 0.00 34.64 4.75
2291 3814 3.482783 GAACGAGCGAGCAGGCAC 61.483 66.667 0.00 0.00 34.64 5.01
2292 3815 3.923563 GAACGAGCGAGCAGGCACT 62.924 63.158 0.00 0.00 43.88 4.40
2293 3816 3.923563 AACGAGCGAGCAGGCACTC 62.924 63.158 0.00 0.00 34.60 3.51
2294 3817 4.426112 CGAGCGAGCAGGCACTCA 62.426 66.667 8.09 0.00 34.60 3.41
2424 3958 2.432628 GGCGTGTAGAGCAGCGTT 60.433 61.111 0.00 0.00 36.08 4.84
2425 3959 2.730672 GGCGTGTAGAGCAGCGTTG 61.731 63.158 0.00 0.00 36.08 4.10
2448 3982 3.491792 CCAAACGAGATCTAGGAGGAAGC 60.492 52.174 7.79 0.00 0.00 3.86
2449 3983 2.738587 ACGAGATCTAGGAGGAAGCA 57.261 50.000 7.79 0.00 0.00 3.91
2459 4003 3.338250 AGGAAGCATGCGGGGGAA 61.338 61.111 13.01 0.00 0.00 3.97
2493 4037 1.139734 CTCCATGGTCCAGTCGACG 59.860 63.158 12.58 5.16 42.99 5.12
2496 4040 4.129737 ATGGTCCAGTCGACGCCG 62.130 66.667 10.46 2.71 42.99 6.46
2541 4085 4.838152 GCCTCGGCTGGAATCGCA 62.838 66.667 0.00 0.00 38.26 5.10
2542 4086 2.125147 CCTCGGCTGGAATCGCAA 60.125 61.111 0.00 0.00 0.00 4.85
2543 4087 2.464459 CCTCGGCTGGAATCGCAAC 61.464 63.158 0.00 0.00 0.00 4.17
2544 4088 2.435938 TCGGCTGGAATCGCAACC 60.436 61.111 0.00 0.00 0.00 3.77
2545 4089 3.864686 CGGCTGGAATCGCAACCG 61.865 66.667 0.00 0.00 0.00 4.44
2546 4090 2.746277 GGCTGGAATCGCAACCGT 60.746 61.111 0.00 0.00 35.54 4.83
2547 4091 2.750888 GGCTGGAATCGCAACCGTC 61.751 63.158 0.00 0.00 35.54 4.79
2548 4092 3.081133 CTGGAATCGCAACCGTCG 58.919 61.111 0.00 0.00 35.54 5.12
2549 4093 2.433491 TGGAATCGCAACCGTCGG 60.433 61.111 10.48 10.48 35.54 4.79
2550 4094 2.125832 GGAATCGCAACCGTCGGA 60.126 61.111 20.51 0.00 35.54 4.55
2551 4095 2.165301 GGAATCGCAACCGTCGGAG 61.165 63.158 20.51 11.19 35.54 4.63
2552 4096 2.799540 GAATCGCAACCGTCGGAGC 61.800 63.158 20.51 19.56 35.54 4.70
2553 4097 3.583276 AATCGCAACCGTCGGAGCA 62.583 57.895 20.51 12.06 35.54 4.26
2554 4098 2.852495 AATCGCAACCGTCGGAGCAT 62.852 55.000 20.51 13.60 35.54 3.79
2555 4099 3.853330 CGCAACCGTCGGAGCATG 61.853 66.667 20.51 11.95 0.00 4.06
2556 4100 4.166011 GCAACCGTCGGAGCATGC 62.166 66.667 20.51 17.62 0.00 4.06
2557 4101 2.434884 CAACCGTCGGAGCATGCT 60.435 61.111 22.92 22.92 0.00 3.79
2558 4102 2.434884 AACCGTCGGAGCATGCTG 60.435 61.111 28.27 12.32 0.00 4.41
2559 4103 3.958147 AACCGTCGGAGCATGCTGG 62.958 63.158 28.27 21.72 0.00 4.85
2563 4107 4.393155 TCGGAGCATGCTGGCGTT 62.393 61.111 28.27 0.00 39.27 4.84
2564 4108 4.170062 CGGAGCATGCTGGCGTTG 62.170 66.667 28.27 3.95 39.27 4.10
2565 4109 4.487412 GGAGCATGCTGGCGTTGC 62.487 66.667 28.27 8.49 39.27 4.17
2575 4119 2.954611 GGCGTTGCCTTCCAGAAC 59.045 61.111 0.00 0.00 46.69 3.01
2576 4120 2.626780 GGCGTTGCCTTCCAGAACC 61.627 63.158 0.00 0.00 46.69 3.62
2577 4121 1.896660 GCGTTGCCTTCCAGAACCA 60.897 57.895 0.00 0.00 0.00 3.67
2578 4122 1.856265 GCGTTGCCTTCCAGAACCAG 61.856 60.000 0.00 0.00 0.00 4.00
2579 4123 0.250295 CGTTGCCTTCCAGAACCAGA 60.250 55.000 0.00 0.00 0.00 3.86
2580 4124 1.239347 GTTGCCTTCCAGAACCAGAC 58.761 55.000 0.00 0.00 0.00 3.51
2581 4125 0.110486 TTGCCTTCCAGAACCAGACC 59.890 55.000 0.00 0.00 0.00 3.85
2582 4126 1.002011 GCCTTCCAGAACCAGACCC 60.002 63.158 0.00 0.00 0.00 4.46
2583 4127 1.779061 GCCTTCCAGAACCAGACCCA 61.779 60.000 0.00 0.00 0.00 4.51
2584 4128 0.771127 CCTTCCAGAACCAGACCCAA 59.229 55.000 0.00 0.00 0.00 4.12
2585 4129 1.271597 CCTTCCAGAACCAGACCCAAG 60.272 57.143 0.00 0.00 0.00 3.61
2586 4130 1.421646 CTTCCAGAACCAGACCCAAGT 59.578 52.381 0.00 0.00 0.00 3.16
2587 4131 0.764890 TCCAGAACCAGACCCAAGTG 59.235 55.000 0.00 0.00 0.00 3.16
2588 4132 0.250901 CCAGAACCAGACCCAAGTGG 60.251 60.000 0.00 0.00 39.98 4.00
2589 4133 0.764890 CAGAACCAGACCCAAGTGGA 59.235 55.000 0.00 0.00 37.27 4.02
2590 4134 1.142870 CAGAACCAGACCCAAGTGGAA 59.857 52.381 0.00 0.00 37.27 3.53
2591 4135 1.421646 AGAACCAGACCCAAGTGGAAG 59.578 52.381 0.00 0.00 37.27 3.46
2592 4136 0.478507 AACCAGACCCAAGTGGAAGG 59.521 55.000 0.00 0.00 37.27 3.46
2593 4137 0.697854 ACCAGACCCAAGTGGAAGGT 60.698 55.000 0.00 0.00 37.27 3.50
2594 4138 0.478507 CCAGACCCAAGTGGAAGGTT 59.521 55.000 0.00 0.00 35.67 3.50
2595 4139 1.133482 CCAGACCCAAGTGGAAGGTTT 60.133 52.381 0.00 0.00 35.67 3.27
2596 4140 2.230660 CAGACCCAAGTGGAAGGTTTC 58.769 52.381 0.00 0.00 37.39 2.78
2606 4150 1.165270 GGAAGGTTTCCGTGATGTGG 58.835 55.000 0.00 0.00 40.59 4.17
2607 4151 1.544759 GGAAGGTTTCCGTGATGTGGT 60.545 52.381 0.00 0.00 40.59 4.16
2608 4152 1.535462 GAAGGTTTCCGTGATGTGGTG 59.465 52.381 0.00 0.00 0.00 4.17
2609 4153 0.762418 AGGTTTCCGTGATGTGGTGA 59.238 50.000 0.00 0.00 0.00 4.02
2610 4154 1.142060 AGGTTTCCGTGATGTGGTGAA 59.858 47.619 0.00 0.00 0.00 3.18
2611 4155 2.159382 GGTTTCCGTGATGTGGTGAAT 58.841 47.619 0.00 0.00 0.00 2.57
2612 4156 3.008594 AGGTTTCCGTGATGTGGTGAATA 59.991 43.478 0.00 0.00 0.00 1.75
2613 4157 3.945285 GGTTTCCGTGATGTGGTGAATAT 59.055 43.478 0.00 0.00 0.00 1.28
2614 4158 4.398044 GGTTTCCGTGATGTGGTGAATATT 59.602 41.667 0.00 0.00 0.00 1.28
2615 4159 5.105917 GGTTTCCGTGATGTGGTGAATATTT 60.106 40.000 0.00 0.00 0.00 1.40
2616 4160 5.559427 TTCCGTGATGTGGTGAATATTTG 57.441 39.130 0.00 0.00 0.00 2.32
2617 4161 4.584874 TCCGTGATGTGGTGAATATTTGT 58.415 39.130 0.00 0.00 0.00 2.83
2618 4162 4.394610 TCCGTGATGTGGTGAATATTTGTG 59.605 41.667 0.00 0.00 0.00 3.33
2619 4163 4.438608 CCGTGATGTGGTGAATATTTGTGG 60.439 45.833 0.00 0.00 0.00 4.17
2620 4164 4.438608 CGTGATGTGGTGAATATTTGTGGG 60.439 45.833 0.00 0.00 0.00 4.61
2621 4165 4.022603 TGATGTGGTGAATATTTGTGGGG 58.977 43.478 0.00 0.00 0.00 4.96
2622 4166 3.534357 TGTGGTGAATATTTGTGGGGT 57.466 42.857 0.00 0.00 0.00 4.95
2623 4167 3.161067 TGTGGTGAATATTTGTGGGGTG 58.839 45.455 0.00 0.00 0.00 4.61
2624 4168 3.181428 TGTGGTGAATATTTGTGGGGTGA 60.181 43.478 0.00 0.00 0.00 4.02
2625 4169 3.443681 GTGGTGAATATTTGTGGGGTGAG 59.556 47.826 0.00 0.00 0.00 3.51
2626 4170 3.332187 TGGTGAATATTTGTGGGGTGAGA 59.668 43.478 0.00 0.00 0.00 3.27
2627 4171 3.947834 GGTGAATATTTGTGGGGTGAGAG 59.052 47.826 0.00 0.00 0.00 3.20
2628 4172 4.324254 GGTGAATATTTGTGGGGTGAGAGA 60.324 45.833 0.00 0.00 0.00 3.10
2629 4173 5.440610 GTGAATATTTGTGGGGTGAGAGAT 58.559 41.667 0.00 0.00 0.00 2.75
2630 4174 5.888161 GTGAATATTTGTGGGGTGAGAGATT 59.112 40.000 0.00 0.00 0.00 2.40
2631 4175 6.378280 GTGAATATTTGTGGGGTGAGAGATTT 59.622 38.462 0.00 0.00 0.00 2.17
2632 4176 6.953520 TGAATATTTGTGGGGTGAGAGATTTT 59.046 34.615 0.00 0.00 0.00 1.82
2633 4177 7.454380 TGAATATTTGTGGGGTGAGAGATTTTT 59.546 33.333 0.00 0.00 0.00 1.94
2634 4178 8.893563 AATATTTGTGGGGTGAGAGATTTTTA 57.106 30.769 0.00 0.00 0.00 1.52
2635 4179 6.840780 ATTTGTGGGGTGAGAGATTTTTAG 57.159 37.500 0.00 0.00 0.00 1.85
2636 4180 4.301072 TGTGGGGTGAGAGATTTTTAGG 57.699 45.455 0.00 0.00 0.00 2.69
2637 4181 3.017442 GTGGGGTGAGAGATTTTTAGGC 58.983 50.000 0.00 0.00 0.00 3.93
2638 4182 2.919602 TGGGGTGAGAGATTTTTAGGCT 59.080 45.455 0.00 0.00 0.00 4.58
2639 4183 4.080526 GTGGGGTGAGAGATTTTTAGGCTA 60.081 45.833 0.00 0.00 0.00 3.93
2640 4184 4.726825 TGGGGTGAGAGATTTTTAGGCTAT 59.273 41.667 0.00 0.00 0.00 2.97
2641 4185 5.066593 GGGGTGAGAGATTTTTAGGCTATG 58.933 45.833 0.00 0.00 0.00 2.23
2642 4186 5.398012 GGGGTGAGAGATTTTTAGGCTATGT 60.398 44.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.337071 GATCGATCAGGCGAGTGGTAA 59.663 52.381 20.52 0.00 44.26 2.85
2 3 1.736586 GATCGATCAGGCGAGTGGT 59.263 57.895 20.52 0.00 44.26 4.16
3 4 1.371022 CGATCGATCAGGCGAGTGG 60.371 63.158 24.40 1.69 44.26 4.00
5 6 1.945522 CTCGATCGATCAGGCGAGT 59.054 57.895 24.40 0.00 44.26 4.18
6 7 4.836892 CTCGATCGATCAGGCGAG 57.163 61.111 24.40 20.20 44.26 5.03
7 8 0.533085 ACTCTCGATCGATCAGGCGA 60.533 55.000 24.40 15.25 45.22 5.54
8 9 0.110419 GACTCTCGATCGATCAGGCG 60.110 60.000 24.40 11.72 0.00 5.52
9 10 0.947960 TGACTCTCGATCGATCAGGC 59.052 55.000 24.40 19.25 0.00 4.85
11 12 1.070242 CGGTGACTCTCGATCGATCAG 60.070 57.143 24.40 18.83 0.00 2.90
13 14 0.236187 CCGGTGACTCTCGATCGATC 59.764 60.000 19.78 15.68 0.00 3.69
14 15 1.787057 GCCGGTGACTCTCGATCGAT 61.787 60.000 19.78 3.36 0.00 3.59
15 16 2.470362 GCCGGTGACTCTCGATCGA 61.470 63.158 18.32 18.32 0.00 3.59
16 17 2.024871 GCCGGTGACTCTCGATCG 59.975 66.667 9.36 9.36 0.00 3.69
17 18 1.945354 TTGGCCGGTGACTCTCGATC 61.945 60.000 1.90 0.00 0.00 3.69
18 19 1.330655 ATTGGCCGGTGACTCTCGAT 61.331 55.000 1.90 0.00 0.00 3.59
19 20 1.982395 ATTGGCCGGTGACTCTCGA 60.982 57.895 1.90 0.00 0.00 4.04
20 21 1.811266 CATTGGCCGGTGACTCTCG 60.811 63.158 1.90 0.00 0.00 4.04
21 22 1.450312 CCATTGGCCGGTGACTCTC 60.450 63.158 1.90 0.00 0.00 3.20
22 23 2.671070 CCATTGGCCGGTGACTCT 59.329 61.111 1.90 0.00 0.00 3.24
23 24 3.134127 GCCATTGGCCGGTGACTC 61.134 66.667 17.28 0.00 44.06 3.36
72 73 3.433031 CCTCGAGTCCTGAGAGATGTACT 60.433 52.174 12.31 0.00 35.43 2.73
102 103 2.089887 TTGTTGGGCGAGTACGAGCA 62.090 55.000 15.48 0.00 42.66 4.26
105 106 1.005867 GGTTGTTGGGCGAGTACGA 60.006 57.895 0.00 0.00 42.66 3.43
109 110 2.594592 GCTGGTTGTTGGGCGAGT 60.595 61.111 0.00 0.00 0.00 4.18
110 111 2.594303 TGCTGGTTGTTGGGCGAG 60.594 61.111 0.00 0.00 0.00 5.03
114 115 3.673484 CGCCTGCTGGTTGTTGGG 61.673 66.667 11.69 0.00 35.27 4.12
136 137 1.136141 CAAGTCACGCAACTCATCAGC 60.136 52.381 0.00 0.00 0.00 4.26
166 168 3.003482 GTCGTCCGCTTCATCATACTACT 59.997 47.826 0.00 0.00 0.00 2.57
167 169 3.298317 GTCGTCCGCTTCATCATACTAC 58.702 50.000 0.00 0.00 0.00 2.73
168 170 2.032290 CGTCGTCCGCTTCATCATACTA 60.032 50.000 0.00 0.00 0.00 1.82
169 171 1.268589 CGTCGTCCGCTTCATCATACT 60.269 52.381 0.00 0.00 0.00 2.12
236 269 4.812476 TCACGGGCAAGCGATCGG 62.812 66.667 18.30 0.83 0.00 4.18
268 307 2.890814 CTGTCTATTCTATCCCCCGGT 58.109 52.381 0.00 0.00 0.00 5.28
269 308 1.550976 GCTGTCTATTCTATCCCCCGG 59.449 57.143 0.00 0.00 0.00 5.73
271 310 1.909986 GGGCTGTCTATTCTATCCCCC 59.090 57.143 0.00 0.00 0.00 5.40
272 311 1.909986 GGGGCTGTCTATTCTATCCCC 59.090 57.143 0.00 0.00 44.32 4.81
338 377 0.107017 CATCCCGTGCCCAGATTCTT 60.107 55.000 0.00 0.00 0.00 2.52
365 408 1.066215 TCTCGTACAGTACCACCGCTA 60.066 52.381 5.07 0.00 0.00 4.26
388 431 0.962489 TATTAGGAGAGCAGAGCGCC 59.038 55.000 2.29 0.00 44.04 6.53
440 483 3.502595 GTGAGGAAGCCTTTACTTGGTTC 59.497 47.826 0.00 0.00 31.76 3.62
666 760 3.264947 GAGAGGCTCGTGACGTGA 58.735 61.111 11.51 0.00 0.00 4.35
711 805 3.876309 AAGAGCTCCTTGGTTTGGTTA 57.124 42.857 10.93 0.00 32.92 2.85
715 809 7.545965 CGGTATATATAAGAGCTCCTTGGTTTG 59.454 40.741 10.93 0.00 36.34 2.93
716 810 7.310485 CCGGTATATATAAGAGCTCCTTGGTTT 60.310 40.741 10.93 0.00 36.34 3.27
717 811 6.154706 CCGGTATATATAAGAGCTCCTTGGTT 59.845 42.308 10.93 0.00 36.34 3.67
718 812 5.657302 CCGGTATATATAAGAGCTCCTTGGT 59.343 44.000 10.93 0.00 36.34 3.67
719 813 5.069251 CCCGGTATATATAAGAGCTCCTTGG 59.931 48.000 10.93 0.00 36.34 3.61
720 814 5.892119 TCCCGGTATATATAAGAGCTCCTTG 59.108 44.000 10.93 0.00 36.34 3.61
721 815 6.088541 TCCCGGTATATATAAGAGCTCCTT 57.911 41.667 10.93 6.87 38.87 3.36
725 819 7.839705 TGAAGATTCCCGGTATATATAAGAGCT 59.160 37.037 0.00 0.00 0.00 4.09
766 866 4.217118 AGCAGAGAAAAATAGCACTTGTGG 59.783 41.667 2.81 0.00 0.00 4.17
782 882 1.213013 GCGACGGAGAAAGCAGAGA 59.787 57.895 0.00 0.00 0.00 3.10
828 950 1.007336 CACAGCACGAACGTACCTCC 61.007 60.000 0.00 0.00 0.00 4.30
840 962 1.154338 CGCTAGCTTTGCACAGCAC 60.154 57.895 25.71 13.80 42.84 4.40
842 964 1.423056 CTCGCTAGCTTTGCACAGC 59.577 57.895 17.16 17.16 40.44 4.40
844 966 0.034756 TTCCTCGCTAGCTTTGCACA 59.965 50.000 13.93 0.00 0.00 4.57
845 967 1.156736 TTTCCTCGCTAGCTTTGCAC 58.843 50.000 13.93 0.00 0.00 4.57
917 1047 3.052620 GCAGCAGCAGCAGACCATG 62.053 63.158 4.63 0.00 45.49 3.66
1003 1133 6.786207 ACCAAAGAAGAAGAAGAAAAAGTCG 58.214 36.000 0.00 0.00 0.00 4.18
1073 1212 2.283298 GCAGAACGATCATGTGGATGT 58.717 47.619 0.00 0.00 36.00 3.06
1074 1213 2.282407 TGCAGAACGATCATGTGGATG 58.718 47.619 0.00 0.00 36.00 3.51
1075 1214 2.696989 TGCAGAACGATCATGTGGAT 57.303 45.000 0.00 0.00 39.53 3.41
1076 1215 2.696989 ATGCAGAACGATCATGTGGA 57.303 45.000 0.00 0.00 0.00 4.02
1077 1216 3.376234 AGAAATGCAGAACGATCATGTGG 59.624 43.478 0.00 0.00 0.00 4.17
1133 1272 5.260424 TCTTGAACTGCTCTCTAGACTGAT 58.740 41.667 0.00 0.00 0.00 2.90
1230 1376 2.745884 CCATTGCTTCGGTCGCCA 60.746 61.111 0.00 0.00 0.00 5.69
1464 1610 4.202574 TGCTGGTGGTGGTGGTGG 62.203 66.667 0.00 0.00 0.00 4.61
1465 1611 2.906897 GTGCTGGTGGTGGTGGTG 60.907 66.667 0.00 0.00 0.00 4.17
1466 1612 4.204028 GGTGCTGGTGGTGGTGGT 62.204 66.667 0.00 0.00 0.00 4.16
1652 1798 2.359900 CTACTCAAATCAAGCCGGCTT 58.640 47.619 35.84 35.84 36.60 4.35
1655 1801 2.280628 GTCCTACTCAAATCAAGCCGG 58.719 52.381 0.00 0.00 0.00 6.13
1657 1803 2.673368 CACGTCCTACTCAAATCAAGCC 59.327 50.000 0.00 0.00 0.00 4.35
1662 1808 3.572584 ACGAACACGTCCTACTCAAATC 58.427 45.455 0.00 0.00 35.22 2.17
1665 1811 2.693797 GACGAACACGTCCTACTCAA 57.306 50.000 10.96 0.00 46.91 3.02
1674 1820 3.181534 CGCTAATGAATTGACGAACACGT 60.182 43.478 0.00 0.00 43.06 4.49
1764 1913 1.965930 CCCATCACACACACCCACG 60.966 63.158 0.00 0.00 0.00 4.94
1765 1914 1.603455 CCCCATCACACACACCCAC 60.603 63.158 0.00 0.00 0.00 4.61
1768 1917 1.545582 CAAATCCCCATCACACACACC 59.454 52.381 0.00 0.00 0.00 4.16
1782 1931 2.543238 CCGTACGTAGCTCTCCAAATCC 60.543 54.545 15.21 0.00 0.00 3.01
1790 1939 2.178890 CCGCTCCGTACGTAGCTCT 61.179 63.158 26.97 0.00 36.56 4.09
1795 1944 4.164664 CGTGCCGCTCCGTACGTA 62.165 66.667 15.21 0.00 33.40 3.57
1955 2109 6.207810 ACGTTTCTCCAACAATTAGCCATTAA 59.792 34.615 0.00 0.00 34.68 1.40
1979 2133 0.727398 GCATCCGTCAGTTGGCTTAC 59.273 55.000 0.00 0.00 0.00 2.34
1992 2146 1.752501 CGCTTGGAACGTAGCATCCG 61.753 60.000 8.64 0.00 39.37 4.18
2002 2156 3.119849 ACTGCAACATAATCGCTTGGAAC 60.120 43.478 0.00 0.00 0.00 3.62
2120 3632 2.029244 CGAAACAGTACTGCTAATGGCG 59.971 50.000 22.90 12.45 45.43 5.69
2123 3635 2.029244 CGGCGAAACAGTACTGCTAATG 59.971 50.000 22.90 10.14 0.00 1.90
2153 3665 1.850441 CGTTTTCGTCGTCTTCACACT 59.150 47.619 0.00 0.00 38.65 3.55
2154 3666 1.071698 CCGTTTTCGTCGTCTTCACAC 60.072 52.381 0.00 0.00 42.35 3.82
2155 3667 1.202203 CCGTTTTCGTCGTCTTCACA 58.798 50.000 0.00 0.00 42.35 3.58
2156 3668 1.450905 CTCCGTTTTCGTCGTCTTCAC 59.549 52.381 0.00 0.00 42.35 3.18
2157 3669 1.334556 TCTCCGTTTTCGTCGTCTTCA 59.665 47.619 0.00 0.00 42.35 3.02
2159 3671 2.325761 CATCTCCGTTTTCGTCGTCTT 58.674 47.619 0.00 0.00 42.35 3.01
2197 3709 2.219875 AGCCCAGGTGACAGACAGG 61.220 63.158 0.00 0.00 0.00 4.00
2283 3806 0.888285 GCTTTCAGTGAGTGCCTGCT 60.888 55.000 7.86 0.00 0.00 4.24
2290 3813 1.490490 TGGTTCAGGCTTTCAGTGAGT 59.510 47.619 0.00 0.00 0.00 3.41
2291 3814 2.149578 CTGGTTCAGGCTTTCAGTGAG 58.850 52.381 0.00 0.00 0.00 3.51
2292 3815 1.768275 TCTGGTTCAGGCTTTCAGTGA 59.232 47.619 0.00 0.00 31.51 3.41
2293 3816 1.876156 GTCTGGTTCAGGCTTTCAGTG 59.124 52.381 0.00 0.00 32.76 3.66
2294 3817 1.202818 GGTCTGGTTCAGGCTTTCAGT 60.203 52.381 0.00 0.00 36.22 3.41
2404 3936 4.436998 GCTGCTCTACACGCCCGT 62.437 66.667 0.00 0.00 0.00 5.28
2406 3938 3.934391 AACGCTGCTCTACACGCCC 62.934 63.158 0.00 0.00 0.00 6.13
2408 3940 2.772189 CAACGCTGCTCTACACGC 59.228 61.111 0.00 0.00 0.00 5.34
2409 3941 2.772189 GCAACGCTGCTCTACACG 59.228 61.111 2.93 0.00 45.74 4.49
2424 3958 1.757118 CCTCCTAGATCTCGTTTGGCA 59.243 52.381 0.00 0.00 0.00 4.92
2425 3959 2.032620 TCCTCCTAGATCTCGTTTGGC 58.967 52.381 0.00 0.00 0.00 4.52
2427 3961 3.131223 TGCTTCCTCCTAGATCTCGTTTG 59.869 47.826 0.00 0.00 0.00 2.93
2473 4017 2.187946 CGACTGGACCATGGAGCC 59.812 66.667 21.47 19.26 0.00 4.70
2477 4021 2.509336 GCGTCGACTGGACCATGG 60.509 66.667 11.19 11.19 42.99 3.66
2520 4064 4.473520 ATTCCAGCCGAGGCCGTG 62.474 66.667 10.95 3.40 43.17 4.94
2521 4065 4.162690 GATTCCAGCCGAGGCCGT 62.163 66.667 10.95 0.00 43.17 5.68
2524 4068 4.838152 TGCGATTCCAGCCGAGGC 62.838 66.667 5.89 5.89 42.33 4.70
2525 4069 2.125147 TTGCGATTCCAGCCGAGG 60.125 61.111 0.00 0.00 0.00 4.63
2526 4070 2.464459 GGTTGCGATTCCAGCCGAG 61.464 63.158 0.00 0.00 0.00 4.63
2527 4071 2.435938 GGTTGCGATTCCAGCCGA 60.436 61.111 0.00 0.00 0.00 5.54
2529 4073 2.746277 ACGGTTGCGATTCCAGCC 60.746 61.111 0.00 0.00 33.28 4.85
2530 4074 2.785258 GACGGTTGCGATTCCAGC 59.215 61.111 0.00 0.00 0.00 4.85
2531 4075 2.452813 CCGACGGTTGCGATTCCAG 61.453 63.158 5.48 0.00 0.00 3.86
2532 4076 2.433491 CCGACGGTTGCGATTCCA 60.433 61.111 5.48 0.00 0.00 3.53
2533 4077 2.125832 TCCGACGGTTGCGATTCC 60.126 61.111 14.79 0.00 0.00 3.01
2534 4078 2.799540 GCTCCGACGGTTGCGATTC 61.800 63.158 14.79 0.00 0.00 2.52
2535 4079 2.813908 GCTCCGACGGTTGCGATT 60.814 61.111 14.79 0.00 0.00 3.34
2536 4080 3.371097 ATGCTCCGACGGTTGCGAT 62.371 57.895 22.15 16.04 0.00 4.58
2537 4081 4.063967 ATGCTCCGACGGTTGCGA 62.064 61.111 22.15 14.95 0.00 5.10
2538 4082 3.853330 CATGCTCCGACGGTTGCG 61.853 66.667 22.15 10.76 0.00 4.85
2539 4083 4.166011 GCATGCTCCGACGGTTGC 62.166 66.667 21.38 21.38 0.00 4.17
2540 4084 2.434884 AGCATGCTCCGACGGTTG 60.435 61.111 16.30 9.40 0.00 3.77
2541 4085 2.434884 CAGCATGCTCCGACGGTT 60.435 61.111 19.68 0.00 0.00 4.44
2542 4086 4.457496 CCAGCATGCTCCGACGGT 62.457 66.667 19.68 0.00 31.97 4.83
2546 4090 4.393155 AACGCCAGCATGCTCCGA 62.393 61.111 32.12 0.00 31.97 4.55
2547 4091 4.170062 CAACGCCAGCATGCTCCG 62.170 66.667 26.79 26.79 31.97 4.63
2548 4092 4.487412 GCAACGCCAGCATGCTCC 62.487 66.667 19.68 11.08 37.12 4.70
2559 4103 1.856265 CTGGTTCTGGAAGGCAACGC 61.856 60.000 0.00 0.00 46.39 4.84
2560 4104 0.250295 TCTGGTTCTGGAAGGCAACG 60.250 55.000 0.00 0.00 46.39 4.10
2561 4105 1.239347 GTCTGGTTCTGGAAGGCAAC 58.761 55.000 0.00 0.00 0.00 4.17
2562 4106 0.110486 GGTCTGGTTCTGGAAGGCAA 59.890 55.000 0.00 0.00 0.00 4.52
2563 4107 1.761174 GGTCTGGTTCTGGAAGGCA 59.239 57.895 0.00 0.00 0.00 4.75
2564 4108 1.002011 GGGTCTGGTTCTGGAAGGC 60.002 63.158 0.00 0.00 0.00 4.35
2565 4109 0.771127 TTGGGTCTGGTTCTGGAAGG 59.229 55.000 0.00 0.00 0.00 3.46
2566 4110 1.421646 ACTTGGGTCTGGTTCTGGAAG 59.578 52.381 0.00 0.00 0.00 3.46
2567 4111 1.142870 CACTTGGGTCTGGTTCTGGAA 59.857 52.381 0.00 0.00 0.00 3.53
2568 4112 0.764890 CACTTGGGTCTGGTTCTGGA 59.235 55.000 0.00 0.00 0.00 3.86
2569 4113 0.250901 CCACTTGGGTCTGGTTCTGG 60.251 60.000 0.00 0.00 0.00 3.86
2570 4114 0.764890 TCCACTTGGGTCTGGTTCTG 59.235 55.000 0.00 0.00 38.11 3.02
2571 4115 1.421646 CTTCCACTTGGGTCTGGTTCT 59.578 52.381 0.00 0.00 38.11 3.01
2572 4116 1.545651 CCTTCCACTTGGGTCTGGTTC 60.546 57.143 0.00 0.00 38.11 3.62
2573 4117 0.478507 CCTTCCACTTGGGTCTGGTT 59.521 55.000 0.00 0.00 38.11 3.67
2574 4118 0.697854 ACCTTCCACTTGGGTCTGGT 60.698 55.000 0.00 0.00 38.11 4.00
2575 4119 0.478507 AACCTTCCACTTGGGTCTGG 59.521 55.000 0.00 0.00 38.11 3.86
2576 4120 2.230660 GAAACCTTCCACTTGGGTCTG 58.769 52.381 0.00 0.00 38.11 3.51
2577 4121 2.658807 GAAACCTTCCACTTGGGTCT 57.341 50.000 0.00 0.00 38.11 3.85
2587 4131 1.165270 CCACATCACGGAAACCTTCC 58.835 55.000 0.00 0.00 46.62 3.46
2588 4132 1.535462 CACCACATCACGGAAACCTTC 59.465 52.381 0.00 0.00 0.00 3.46
2589 4133 1.142060 TCACCACATCACGGAAACCTT 59.858 47.619 0.00 0.00 0.00 3.50
2590 4134 0.762418 TCACCACATCACGGAAACCT 59.238 50.000 0.00 0.00 0.00 3.50
2591 4135 1.600023 TTCACCACATCACGGAAACC 58.400 50.000 0.00 0.00 0.00 3.27
2592 4136 5.560966 AATATTCACCACATCACGGAAAC 57.439 39.130 0.00 0.00 0.00 2.78
2593 4137 5.475220 ACAAATATTCACCACATCACGGAAA 59.525 36.000 0.00 0.00 0.00 3.13
2594 4138 5.007034 ACAAATATTCACCACATCACGGAA 58.993 37.500 0.00 0.00 0.00 4.30
2595 4139 4.394610 CACAAATATTCACCACATCACGGA 59.605 41.667 0.00 0.00 0.00 4.69
2596 4140 4.438608 CCACAAATATTCACCACATCACGG 60.439 45.833 0.00 0.00 0.00 4.94
2597 4141 4.438608 CCCACAAATATTCACCACATCACG 60.439 45.833 0.00 0.00 0.00 4.35
2598 4142 4.142182 CCCCACAAATATTCACCACATCAC 60.142 45.833 0.00 0.00 0.00 3.06
2599 4143 4.022603 CCCCACAAATATTCACCACATCA 58.977 43.478 0.00 0.00 0.00 3.07
2600 4144 4.023291 ACCCCACAAATATTCACCACATC 58.977 43.478 0.00 0.00 0.00 3.06
2601 4145 3.768757 CACCCCACAAATATTCACCACAT 59.231 43.478 0.00 0.00 0.00 3.21
2602 4146 3.161067 CACCCCACAAATATTCACCACA 58.839 45.455 0.00 0.00 0.00 4.17
2603 4147 3.426615 TCACCCCACAAATATTCACCAC 58.573 45.455 0.00 0.00 0.00 4.16
2604 4148 3.332187 TCTCACCCCACAAATATTCACCA 59.668 43.478 0.00 0.00 0.00 4.17
2605 4149 3.947834 CTCTCACCCCACAAATATTCACC 59.052 47.826 0.00 0.00 0.00 4.02
2606 4150 4.843728 TCTCTCACCCCACAAATATTCAC 58.156 43.478 0.00 0.00 0.00 3.18
2607 4151 5.715439 ATCTCTCACCCCACAAATATTCA 57.285 39.130 0.00 0.00 0.00 2.57
2608 4152 7.410120 AAAATCTCTCACCCCACAAATATTC 57.590 36.000 0.00 0.00 0.00 1.75
2609 4153 7.797121 AAAAATCTCTCACCCCACAAATATT 57.203 32.000 0.00 0.00 0.00 1.28
2610 4154 7.561356 CCTAAAAATCTCTCACCCCACAAATAT 59.439 37.037 0.00 0.00 0.00 1.28
2611 4155 6.889722 CCTAAAAATCTCTCACCCCACAAATA 59.110 38.462 0.00 0.00 0.00 1.40
2612 4156 5.716703 CCTAAAAATCTCTCACCCCACAAAT 59.283 40.000 0.00 0.00 0.00 2.32
2613 4157 5.076873 CCTAAAAATCTCTCACCCCACAAA 58.923 41.667 0.00 0.00 0.00 2.83
2614 4158 4.662278 CCTAAAAATCTCTCACCCCACAA 58.338 43.478 0.00 0.00 0.00 3.33
2615 4159 3.561313 GCCTAAAAATCTCTCACCCCACA 60.561 47.826 0.00 0.00 0.00 4.17
2616 4160 3.017442 GCCTAAAAATCTCTCACCCCAC 58.983 50.000 0.00 0.00 0.00 4.61
2617 4161 2.919602 AGCCTAAAAATCTCTCACCCCA 59.080 45.455 0.00 0.00 0.00 4.96
2618 4162 3.653835 AGCCTAAAAATCTCTCACCCC 57.346 47.619 0.00 0.00 0.00 4.95
2619 4163 5.685728 ACATAGCCTAAAAATCTCTCACCC 58.314 41.667 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.