Multiple sequence alignment - TraesCS6A01G385100

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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 TraesCS6A01G385100 chr6A 100.000 3599 0 0 1 3599 603101360 603104958 0.000000e+00 6647
1 TraesCS6A01G385100 chr6A 89.364 2642 245 20 550 3158 603092933 603095571 0.000000e+00 3290
2 TraesCS6A01G385100 chr6A 91.711 2232 179 5 550 2777 603082799 603085028 0.000000e+00 3092
3 TraesCS6A01G385100 chr6A 83.697 2061 287 43 550 2581 18462358 18464398 0.000000e+00 1899
4 TraesCS6A01G385100 chr6A 83.394 548 91 0 1 548 603082119 603082666 3.210000e-140 508
5 TraesCS6A01G385100 chr6A 86.266 466 46 12 2813 3261 603085017 603085481 1.160000e-134 490
6 TraesCS6A01G385100 chr6A 86.182 275 33 4 3272 3543 603085459 603085731 3.510000e-75 292
7 TraesCS6A01G385100 chr6A 88.542 96 7 2 3473 3567 603047853 603047945 2.940000e-21 113
8 TraesCS6A01G385100 chr6D 90.480 2416 210 6 550 2949 456425681 456428092 0.000000e+00 3169
9 TraesCS6A01G385100 chr6D 88.260 2155 216 15 550 2688 456409728 456411861 0.000000e+00 2543
10 TraesCS6A01G385100 chr6D 83.657 2062 286 38 550 2581 17501491 17503531 0.000000e+00 1893
11 TraesCS6A01G385100 chr6D 85.584 548 79 0 1 548 456425001 456425548 3.120000e-160 575
12 TraesCS6A01G385100 chr6D 94.163 257 15 0 3002 3258 456428104 456428360 3.370000e-105 392
13 TraesCS6A01G385100 chr6D 91.018 167 15 0 2890 3056 456412088 456412254 3.620000e-55 226
14 TraesCS6A01G385100 chr6B 90.318 2293 211 6 695 2980 693937001 693939289 0.000000e+00 2994
15 TraesCS6A01G385100 chr6B 86.110 2743 302 39 550 3234 693928285 693931006 0.000000e+00 2881
16 TraesCS6A01G385100 chr6B 83.375 1997 299 21 606 2581 31689136 31687152 0.000000e+00 1818
17 TraesCS6A01G385100 chr6B 83.250 2012 292 34 597 2581 30890981 30892974 0.000000e+00 1807
18 TraesCS6A01G385100 chr6B 81.488 551 96 5 1 548 693935807 693936354 7.090000e-122 448
19 TraesCS6A01G385100 chr6B 80.328 549 106 2 1 548 693927605 693928152 7.190000e-112 414
20 TraesCS6A01G385100 chr6B 87.625 299 21 9 3279 3571 693939622 693939910 2.070000e-87 333
21 TraesCS6A01G385100 chr6B 78.689 244 22 17 3295 3536 693931016 693931231 6.270000e-28 135
22 TraesCS6A01G385100 chr1A 74.044 497 111 15 61 548 530162698 530162211 1.710000e-43 187


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 TraesCS6A01G385100 chr6A 603101360 603104958 3598 False 6647.000000 6647 100.000000 1 3599 1 chr6A.!!$F4 3598
1 TraesCS6A01G385100 chr6A 603092933 603095571 2638 False 3290.000000 3290 89.364000 550 3158 1 chr6A.!!$F3 2608
2 TraesCS6A01G385100 chr6A 18462358 18464398 2040 False 1899.000000 1899 83.697000 550 2581 1 chr6A.!!$F1 2031
3 TraesCS6A01G385100 chr6A 603082119 603085731 3612 False 1095.500000 3092 86.888250 1 3543 4 chr6A.!!$F5 3542
4 TraesCS6A01G385100 chr6D 17501491 17503531 2040 False 1893.000000 1893 83.657000 550 2581 1 chr6D.!!$F1 2031
5 TraesCS6A01G385100 chr6D 456409728 456412254 2526 False 1384.500000 2543 89.639000 550 3056 2 chr6D.!!$F2 2506
6 TraesCS6A01G385100 chr6D 456425001 456428360 3359 False 1378.666667 3169 90.075667 1 3258 3 chr6D.!!$F3 3257
7 TraesCS6A01G385100 chr6B 31687152 31689136 1984 True 1818.000000 1818 83.375000 606 2581 1 chr6B.!!$R1 1975
8 TraesCS6A01G385100 chr6B 30890981 30892974 1993 False 1807.000000 1807 83.250000 597 2581 1 chr6B.!!$F1 1984
9 TraesCS6A01G385100 chr6B 693935807 693939910 4103 False 1258.333333 2994 86.477000 1 3571 3 chr6B.!!$F3 3570
10 TraesCS6A01G385100 chr6B 693927605 693931231 3626 False 1143.333333 2881 81.709000 1 3536 3 chr6B.!!$F2 3535

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
530 531 0.036010 ACATGCTAGGTGGTGTGCTC 60.036 55.000 0.00 0.00 0.00 4.26 F
765 897 0.478072 AGTTCACAGGTCCATTGCCA 59.522 50.000 0.00 0.00 0.00 4.92 F
1557 2061 1.066152 GGAAGGTACGGATCGGTGTAC 59.934 57.143 15.62 13.07 40.12 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2472 0.469892 CAAGGCCAAAGTCCCCAACT 60.470 55.000 5.01 0.00 41.10 3.16 R
2294 2813 1.559219 TCCCTGGAAATGCATTCTCGA 59.441 47.619 13.38 8.86 38.18 4.04 R
3182 3882 1.732259 CGTTGTTATTTCCTCGCTGCT 59.268 47.619 0.00 0.00 0.00 4.24 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
32 33 4.038361 CGTCATCACTTACCAATCTCTCG 58.962 47.826 0.00 0.00 0.00 4.04
50 51 2.346803 TCGGCAGTGCAAAGAATCTAC 58.653 47.619 18.61 0.00 0.00 2.59
57 58 3.997021 AGTGCAAAGAATCTACTTCACCG 59.003 43.478 0.00 0.00 36.24 4.94
68 69 2.335316 ACTTCACCGCAAACCAACTA 57.665 45.000 0.00 0.00 0.00 2.24
75 76 1.276989 CCGCAAACCAACTAGAGGGTA 59.723 52.381 9.88 0.00 36.05 3.69
97 98 3.983420 CCCTGAGGGCCTTGGCAA 61.983 66.667 7.89 0.00 35.35 4.52
98 99 2.118076 CCTGAGGGCCTTGGCAAA 59.882 61.111 7.89 0.00 0.00 3.68
110 111 4.203618 GGCAAACTCGGTAGCCTC 57.796 61.111 10.89 0.00 43.70 4.70
116 117 2.217510 AACTCGGTAGCCTCTTCTCA 57.782 50.000 0.00 0.00 0.00 3.27
120 121 3.633065 ACTCGGTAGCCTCTTCTCAATAC 59.367 47.826 0.00 0.00 0.00 1.89
130 131 3.886505 CTCTTCTCAATACGCCTAGGAGT 59.113 47.826 22.43 22.43 0.00 3.85
171 172 2.889512 TCCCTACAGCTCTCTTCAACA 58.110 47.619 0.00 0.00 0.00 3.33
199 200 5.607939 TCTCTAATAGAATTTGGCGTGGA 57.392 39.130 0.00 0.00 0.00 4.02
200 201 5.601662 TCTCTAATAGAATTTGGCGTGGAG 58.398 41.667 0.00 0.00 0.00 3.86
210 211 2.107950 TGGCGTGGAGGTAAATGAAG 57.892 50.000 0.00 0.00 0.00 3.02
212 213 2.568062 TGGCGTGGAGGTAAATGAAGTA 59.432 45.455 0.00 0.00 0.00 2.24
218 219 2.210961 GAGGTAAATGAAGTAGGCGGC 58.789 52.381 0.00 0.00 0.00 6.53
236 237 3.343617 CGGCAAACTTCCCTCAGATTTA 58.656 45.455 0.00 0.00 0.00 1.40
344 345 7.505248 TCAACTGAGATATCTGAGCTAGATGTT 59.495 37.037 17.97 2.52 45.66 2.71
345 346 7.218228 ACTGAGATATCTGAGCTAGATGTTG 57.782 40.000 17.97 0.00 45.66 3.33
346 347 6.777091 ACTGAGATATCTGAGCTAGATGTTGT 59.223 38.462 17.97 0.00 45.66 3.32
349 350 8.160106 TGAGATATCTGAGCTAGATGTTGTCTA 58.840 37.037 10.74 0.00 45.66 2.59
439 440 8.415553 TGGAATAAATCAGTTCATGGCAAATAG 58.584 33.333 0.00 0.00 0.00 1.73
464 465 2.237392 GCAGGACTGGGAGTTTATGACT 59.763 50.000 1.01 0.00 42.70 3.41
491 492 1.599518 AAATTGCACACGCCTCCGA 60.600 52.632 0.00 0.00 37.32 4.55
530 531 0.036010 ACATGCTAGGTGGTGTGCTC 60.036 55.000 0.00 0.00 0.00 4.26
548 549 0.615331 TCCCTAGCTCAGTTGCCAAG 59.385 55.000 0.00 0.00 0.00 3.61
571 703 5.665812 AGTGACACCATAGGAAGGCTAAATA 59.334 40.000 0.84 0.00 0.00 1.40
572 704 6.157994 AGTGACACCATAGGAAGGCTAAATAA 59.842 38.462 0.84 0.00 0.00 1.40
616 748 4.426704 ACATAACCTACTGACAGGGTTCT 58.573 43.478 16.62 7.34 41.69 3.01
652 784 3.838317 TGGGAACTTGACACAGCTACTAT 59.162 43.478 0.00 0.00 0.00 2.12
703 835 2.172483 GACTCTTCCGGCAAGCCTCA 62.172 60.000 9.73 0.00 31.26 3.86
765 897 0.478072 AGTTCACAGGTCCATTGCCA 59.522 50.000 0.00 0.00 0.00 4.92
774 906 3.512724 CAGGTCCATTGCCAAAAGAGATT 59.487 43.478 0.00 0.00 0.00 2.40
808 940 2.035632 CCCTGTCAGACACCCTAGATC 58.964 57.143 0.00 0.00 0.00 2.75
871 1003 1.200020 GCGACCTAACAAAGCTTGCAT 59.800 47.619 0.00 0.00 0.00 3.96
939 1071 2.892852 ACTCAGCAATTGCCAAAGCTTA 59.107 40.909 26.45 3.05 43.38 3.09
946 1078 4.511082 GCAATTGCCAAAGCTTAACAGAAA 59.489 37.500 20.06 0.00 40.80 2.52
969 1101 3.194968 TCAGGTTGGACGATAACTCCTTC 59.805 47.826 0.00 0.00 0.00 3.46
981 1113 6.128227 ACGATAACTCCTTCGATAGTAGCATC 60.128 42.308 0.00 0.00 38.67 3.91
993 1125 6.101296 TCGATAGTAGCATCCCCTCATCTATA 59.899 42.308 0.00 0.00 37.40 1.31
1028 1160 6.535150 CGAGGTCTCATGTTGCTAAATCTTAA 59.465 38.462 0.00 0.00 0.00 1.85
1029 1161 7.225538 CGAGGTCTCATGTTGCTAAATCTTAAT 59.774 37.037 0.00 0.00 0.00 1.40
1067 1568 5.065731 CAGGTGTGATTCCTCAAGATTTAGC 59.934 44.000 0.00 0.00 31.85 3.09
1152 1653 6.254157 CAGAAAACTTGGAAAATATGGCATCG 59.746 38.462 1.65 0.00 0.00 3.84
1206 1707 2.198827 ATGGCAAAGTTCCATCACGA 57.801 45.000 0.00 0.00 40.08 4.35
1212 1713 3.403038 CAAAGTTCCATCACGAGGAGTT 58.597 45.455 0.00 0.00 36.33 3.01
1241 1742 4.895668 ATGCATCTGGGTTTTCATTTGT 57.104 36.364 0.00 0.00 0.00 2.83
1279 1780 6.979238 GCTTTGTGGTGGTATACTAGAGTTAG 59.021 42.308 2.25 0.00 0.00 2.34
1354 1855 7.689313 GCCATTTGACTATCATCCTAGTTACCA 60.689 40.741 0.00 0.00 32.11 3.25
1359 1860 7.726216 TGACTATCATCCTAGTTACCACAATG 58.274 38.462 0.00 0.00 32.11 2.82
1362 1863 3.521531 TCATCCTAGTTACCACAATGGCA 59.478 43.478 0.00 0.00 42.67 4.92
1385 1886 4.676546 GGCATAATTCTGGCTTTGAGTTC 58.323 43.478 9.78 0.00 38.58 3.01
1557 2061 1.066152 GGAAGGTACGGATCGGTGTAC 59.934 57.143 15.62 13.07 40.12 2.90
1617 2121 8.154856 ACAGTAGCTGTAAAGGTTTTTGATCTA 58.845 33.333 0.00 0.00 43.46 1.98
1677 2181 3.380637 GTGAGGCACTTAGTAAGATCCGA 59.619 47.826 16.89 6.44 41.55 4.55
1875 2379 2.032426 TGCAGTTGATATTGCTGATGCG 59.968 45.455 0.00 0.00 43.34 4.73
1968 2472 6.475504 TCTCAATGAGGATTTAGTTGCTCAA 58.524 36.000 10.71 0.00 45.50 3.02
2190 2696 3.467803 CGAAGGTGGTCAAGTTTCTTCT 58.532 45.455 0.00 0.00 0.00 2.85
2293 2812 1.963515 GGTTGACCCTGCAGAAACATT 59.036 47.619 17.39 0.00 0.00 2.71
2294 2813 2.365293 GGTTGACCCTGCAGAAACATTT 59.635 45.455 17.39 0.00 0.00 2.32
2488 3016 2.528041 CATCAGAGATGCTGCTGCTA 57.472 50.000 17.00 3.79 44.52 3.49
2511 3039 3.071602 CGATTCACAGGATAAGGGATGGT 59.928 47.826 0.00 0.00 0.00 3.55
2614 3149 1.003545 CTTGAACTGGCTTCACACACG 60.004 52.381 0.00 0.00 38.70 4.49
2688 3230 5.435686 TGATATGTTAGTTTCTGGCTGGT 57.564 39.130 0.00 0.00 0.00 4.00
2739 3281 3.018423 TGCAGCCTATCTGTCACTCTA 57.982 47.619 0.00 0.00 44.66 2.43
2777 3330 3.571590 TGGTTTGTATATTGGGATGCCC 58.428 45.455 0.00 0.00 45.71 5.36
2883 3466 9.307121 GACTGCATGATATATTCGCTAATAACT 57.693 33.333 0.00 0.00 31.44 2.24
2915 3514 2.561478 TCTGTACTTTGTTCCCAGGC 57.439 50.000 0.00 0.00 0.00 4.85
2929 3528 1.156736 CCAGGCGTTTAAGTGGTCAG 58.843 55.000 0.00 0.00 0.00 3.51
3048 3746 4.218852 GGAGAAAGGATATCCGGTACTCAG 59.781 50.000 26.21 0.00 42.08 3.35
3061 3759 1.757118 GTACTCAGCATACTCCAGGCA 59.243 52.381 0.00 0.00 36.03 4.75
3084 3782 3.501828 GTCATTACAGTGCCATGTCACAA 59.498 43.478 9.89 0.00 39.35 3.33
3182 3882 5.510861 GGAACAGAGAGGCAGTGTTAAGTAA 60.511 44.000 0.00 0.00 34.55 2.24
3234 3934 8.159344 AGAAAAAGGAAGTGAACATTACTGAG 57.841 34.615 0.00 0.00 0.00 3.35
3312 4012 9.890629 AATAATAACTGCTACTGAGACATCAAA 57.109 29.630 0.00 0.00 34.23 2.69
3321 4022 7.601508 TGCTACTGAGACATCAAATATATGCTG 59.398 37.037 0.00 0.00 34.23 4.41
3375 4076 1.067060 GCCGCTTCAAAGTTTTGACCT 59.933 47.619 6.79 0.00 45.99 3.85
3450 4157 0.310854 GACCAGAAACCAACAAGGCG 59.689 55.000 0.00 0.00 43.14 5.52
3468 4175 5.813080 AGGCGTCCTTCATGTAAAAATAC 57.187 39.130 0.00 0.00 0.00 1.89
3469 4176 5.250200 AGGCGTCCTTCATGTAAAAATACA 58.750 37.500 0.00 0.00 0.00 2.29
3470 4177 5.708230 AGGCGTCCTTCATGTAAAAATACAA 59.292 36.000 0.00 0.00 33.21 2.41
3471 4178 6.377146 AGGCGTCCTTCATGTAAAAATACAAT 59.623 34.615 0.00 0.00 33.21 2.71
3544 4254 4.883021 ACTCCTACTAGTCTCCCATTCA 57.117 45.455 0.00 0.00 0.00 2.57
3550 4260 7.005296 TCCTACTAGTCTCCCATTCAAGATAC 58.995 42.308 0.00 0.00 0.00 2.24
3551 4261 7.007723 CCTACTAGTCTCCCATTCAAGATACT 58.992 42.308 0.00 0.00 0.00 2.12
3552 4262 6.723298 ACTAGTCTCCCATTCAAGATACTG 57.277 41.667 0.00 0.00 0.00 2.74
3567 4277 7.099764 TCAAGATACTGACAGAGTGAAAATCC 58.900 38.462 10.08 0.00 35.96 3.01
3568 4278 6.865834 AGATACTGACAGAGTGAAAATCCT 57.134 37.500 10.08 0.00 35.96 3.24
3569 4279 7.962995 AGATACTGACAGAGTGAAAATCCTA 57.037 36.000 10.08 0.00 35.96 2.94
3570 4280 8.006298 AGATACTGACAGAGTGAAAATCCTAG 57.994 38.462 10.08 0.00 35.96 3.02
3571 4281 5.413309 ACTGACAGAGTGAAAATCCTAGG 57.587 43.478 10.08 0.82 31.75 3.02
3572 4282 4.841246 ACTGACAGAGTGAAAATCCTAGGT 59.159 41.667 10.08 0.00 31.75 3.08
3573 4283 5.152623 TGACAGAGTGAAAATCCTAGGTG 57.847 43.478 9.08 0.00 0.00 4.00
3574 4284 3.935828 GACAGAGTGAAAATCCTAGGTGC 59.064 47.826 9.08 0.00 0.00 5.01
3575 4285 3.274288 CAGAGTGAAAATCCTAGGTGCC 58.726 50.000 9.08 0.00 0.00 5.01
3576 4286 2.239907 AGAGTGAAAATCCTAGGTGCCC 59.760 50.000 9.08 0.00 0.00 5.36
3577 4287 1.285078 AGTGAAAATCCTAGGTGCCCC 59.715 52.381 9.08 0.00 0.00 5.80
3578 4288 1.005450 GTGAAAATCCTAGGTGCCCCA 59.995 52.381 9.08 0.36 0.00 4.96
3579 4289 1.713647 TGAAAATCCTAGGTGCCCCAA 59.286 47.619 9.08 0.00 0.00 4.12
3580 4290 2.110899 TGAAAATCCTAGGTGCCCCAAA 59.889 45.455 9.08 0.00 0.00 3.28
3581 4291 2.231716 AAATCCTAGGTGCCCCAAAC 57.768 50.000 9.08 0.00 0.00 2.93
3582 4292 1.080638 AATCCTAGGTGCCCCAAACA 58.919 50.000 9.08 0.00 0.00 2.83
3583 4293 1.080638 ATCCTAGGTGCCCCAAACAA 58.919 50.000 9.08 0.00 0.00 2.83
3584 4294 1.080638 TCCTAGGTGCCCCAAACAAT 58.919 50.000 9.08 0.00 0.00 2.71
3585 4295 2.280103 TCCTAGGTGCCCCAAACAATA 58.720 47.619 9.08 0.00 0.00 1.90
3586 4296 2.856231 TCCTAGGTGCCCCAAACAATAT 59.144 45.455 9.08 0.00 0.00 1.28
3587 4297 4.048600 TCCTAGGTGCCCCAAACAATATA 58.951 43.478 9.08 0.00 0.00 0.86
3588 4298 4.667858 TCCTAGGTGCCCCAAACAATATAT 59.332 41.667 9.08 0.00 0.00 0.86
3589 4299 5.852807 TCCTAGGTGCCCCAAACAATATATA 59.147 40.000 9.08 0.00 0.00 0.86
3590 4300 6.507485 TCCTAGGTGCCCCAAACAATATATAT 59.493 38.462 9.08 0.00 0.00 0.86
3591 4301 7.685052 TCCTAGGTGCCCCAAACAATATATATA 59.315 37.037 9.08 0.00 0.00 0.86
3592 4302 8.333235 CCTAGGTGCCCCAAACAATATATATAA 58.667 37.037 0.00 0.00 0.00 0.98
3593 4303 9.396022 CTAGGTGCCCCAAACAATATATATAAG 57.604 37.037 0.00 0.00 0.00 1.73
3594 4304 7.182060 AGGTGCCCCAAACAATATATATAAGG 58.818 38.462 0.00 0.00 0.00 2.69
3595 4305 6.951778 GGTGCCCCAAACAATATATATAAGGT 59.048 38.462 0.00 0.00 0.00 3.50
3596 4306 7.122204 GGTGCCCCAAACAATATATATAAGGTC 59.878 40.741 0.00 0.00 0.00 3.85
3597 4307 7.888546 GTGCCCCAAACAATATATATAAGGTCT 59.111 37.037 0.00 0.00 0.00 3.85
3598 4308 8.107095 TGCCCCAAACAATATATATAAGGTCTC 58.893 37.037 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.753272 TGAAGTAGATTCTTTGCACTGCC 59.247 43.478 0.00 0.00 38.83 4.85
50 51 2.480419 CTCTAGTTGGTTTGCGGTGAAG 59.520 50.000 0.00 0.00 0.00 3.02
57 58 2.039348 TGGTACCCTCTAGTTGGTTTGC 59.961 50.000 10.07 3.69 36.04 3.68
97 98 2.217510 TGAGAAGAGGCTACCGAGTT 57.782 50.000 0.00 0.00 0.00 3.01
98 99 2.217510 TTGAGAAGAGGCTACCGAGT 57.782 50.000 0.00 0.00 0.00 4.18
110 111 5.769484 TTACTCCTAGGCGTATTGAGAAG 57.231 43.478 12.35 0.00 0.00 2.85
116 117 4.900054 AGGTGATTTACTCCTAGGCGTATT 59.100 41.667 12.35 3.81 40.22 1.89
120 121 2.959707 AGAGGTGATTTACTCCTAGGCG 59.040 50.000 2.96 0.00 41.80 5.52
130 131 2.265367 TGGTGCCTGAGAGGTGATTTA 58.735 47.619 0.00 0.00 37.80 1.40
187 188 3.426615 TCATTTACCTCCACGCCAAATT 58.573 40.909 0.00 0.00 0.00 1.82
188 189 3.080300 TCATTTACCTCCACGCCAAAT 57.920 42.857 0.00 0.00 0.00 2.32
191 192 1.349688 ACTTCATTTACCTCCACGCCA 59.650 47.619 0.00 0.00 0.00 5.69
199 200 1.557832 TGCCGCCTACTTCATTTACCT 59.442 47.619 0.00 0.00 0.00 3.08
200 201 2.032680 TGCCGCCTACTTCATTTACC 57.967 50.000 0.00 0.00 0.00 2.85
210 211 1.002502 AGGGAAGTTTGCCGCCTAC 60.003 57.895 0.00 0.00 44.30 3.18
212 213 2.034221 GAGGGAAGTTTGCCGCCT 59.966 61.111 0.00 0.00 44.30 5.52
240 241 2.901042 GAGGTTCGGGAGGCGATT 59.099 61.111 0.00 0.00 0.00 3.34
244 245 3.839432 CCTCGAGGTTCGGGAGGC 61.839 72.222 24.04 0.00 44.60 4.70
344 345 4.746535 TCCAGTGAAGTTGTTGTAGACA 57.253 40.909 0.00 0.00 36.19 3.41
345 346 5.357257 TCTTCCAGTGAAGTTGTTGTAGAC 58.643 41.667 0.00 0.00 46.66 2.59
346 347 5.607939 TCTTCCAGTGAAGTTGTTGTAGA 57.392 39.130 0.00 0.00 46.66 2.59
349 350 4.202050 GCAATCTTCCAGTGAAGTTGTTGT 60.202 41.667 0.00 0.00 46.66 3.32
362 363 3.744940 ATTTCTGGAGGCAATCTTCCA 57.255 42.857 0.00 0.00 0.00 3.53
380 381 1.006281 TCTGGGCAGAGCATTCCAATT 59.994 47.619 0.00 0.00 32.82 2.32
418 419 7.537715 CACACTATTTGCCATGAACTGATTTA 58.462 34.615 0.00 0.00 0.00 1.40
439 440 0.179018 AAACTCCCAGTCCTGCACAC 60.179 55.000 0.00 0.00 0.00 3.82
464 465 2.346847 GCGTGTGCAATTTGTCAACAAA 59.653 40.909 10.48 10.48 44.41 2.83
491 492 8.761689 AGCATGTTGAATTGGAGGTTAAATATT 58.238 29.630 0.00 0.00 0.00 1.28
530 531 0.326264 ACTTGGCAACTGAGCTAGGG 59.674 55.000 0.00 0.00 37.61 3.53
548 549 3.906720 TTAGCCTTCCTATGGTGTCAC 57.093 47.619 0.00 0.00 0.00 3.67
571 703 6.099269 TGTTCTAACTCCAGGACTTGTAGTTT 59.901 38.462 0.90 0.00 32.85 2.66
572 704 5.601313 TGTTCTAACTCCAGGACTTGTAGTT 59.399 40.000 1.28 1.28 34.86 2.24
591 723 4.426704 ACCCTGTCAGTAGGTTATGTTCT 58.573 43.478 0.00 0.00 36.02 3.01
595 727 5.178797 CAAGAACCCTGTCAGTAGGTTATG 58.821 45.833 12.07 10.74 43.88 1.90
616 748 1.145900 TTCCCAAGGGAGGATGGCAA 61.146 55.000 8.06 0.00 46.06 4.52
738 870 5.964958 ATGGACCTGTGAACTTATTGTTG 57.035 39.130 0.00 0.00 39.30 3.33
765 897 8.107729 AGGGACGATAGGTTAAAAATCTCTTTT 58.892 33.333 0.00 0.00 43.77 2.27
774 906 4.773674 TCTGACAGGGACGATAGGTTAAAA 59.226 41.667 1.81 0.00 43.77 1.52
808 940 4.037923 ACCAACAAAGTAATTGCCTGACAG 59.962 41.667 0.00 0.00 43.13 3.51
871 1003 7.902920 AGTTGTTCCGGGATAAGTATAAGTA 57.097 36.000 0.00 0.00 0.00 2.24
939 1071 3.485463 TCGTCCAACCTGATTTCTGTT 57.515 42.857 0.00 0.00 0.00 3.16
946 1078 3.375699 AGGAGTTATCGTCCAACCTGAT 58.624 45.455 0.00 0.00 36.43 2.90
969 1101 3.360867 AGATGAGGGGATGCTACTATCG 58.639 50.000 0.00 0.00 0.00 2.92
981 1113 4.083110 CGCATTTTGCTTATAGATGAGGGG 60.083 45.833 0.00 0.00 42.25 4.79
993 1125 1.896220 TGAGACCTCGCATTTTGCTT 58.104 45.000 0.00 0.00 42.25 3.91
1028 1160 3.498397 CACACCTGAAAGCGTGTTCTTAT 59.502 43.478 0.00 0.00 42.88 1.73
1029 1161 2.869801 CACACCTGAAAGCGTGTTCTTA 59.130 45.455 0.00 0.00 42.88 2.10
1133 1634 4.889409 ACATCGATGCCATATTTTCCAAGT 59.111 37.500 25.11 0.00 0.00 3.16
1152 1653 4.024670 AGGACAGGTCTAACTGGTACATC 58.975 47.826 0.00 0.00 42.75 3.06
1206 1707 5.888161 CCCAGATGCATTACTAAAAACTCCT 59.112 40.000 0.00 0.00 0.00 3.69
1212 1713 7.531857 TGAAAACCCAGATGCATTACTAAAA 57.468 32.000 0.00 0.00 0.00 1.52
1241 1742 1.419387 CACAAAGCCCCAAATTCCCAA 59.581 47.619 0.00 0.00 0.00 4.12
1354 1855 2.696707 CCAGAATTATGCCTGCCATTGT 59.303 45.455 0.00 0.00 35.34 2.71
1359 1860 1.406903 AAGCCAGAATTATGCCTGCC 58.593 50.000 0.00 0.00 0.00 4.85
1362 1863 3.973425 ACTCAAAGCCAGAATTATGCCT 58.027 40.909 0.00 0.00 0.00 4.75
1385 1886 5.214417 TCATTGTGAAGAAAACAAGCATCG 58.786 37.500 0.00 0.00 40.64 3.84
1467 1971 6.708054 CCAATTCAGCATAAGTAACTCTAGGG 59.292 42.308 0.00 0.00 0.00 3.53
1557 2061 2.565210 TGAGCAGCAAACAACACTTG 57.435 45.000 0.00 0.00 0.00 3.16
1617 2121 1.131638 TGGAAGAGCCAGACTGTTGT 58.868 50.000 0.93 0.00 43.33 3.32
1718 2222 4.638421 TGAAGTCGTTTTGGTTTGAGTCAT 59.362 37.500 0.00 0.00 0.00 3.06
1968 2472 0.469892 CAAGGCCAAAGTCCCCAACT 60.470 55.000 5.01 0.00 41.10 3.16
2190 2696 3.664107 GAAGCTGTACACATCTCCACAA 58.336 45.455 0.00 0.00 0.00 3.33
2293 2812 2.026356 TCCCTGGAAATGCATTCTCGAA 60.026 45.455 13.38 4.45 38.18 3.71
2294 2813 1.559219 TCCCTGGAAATGCATTCTCGA 59.441 47.619 13.38 8.86 38.18 4.04
2384 2903 3.248125 GGCATGTTCCATTGTGTTGTTTG 59.752 43.478 0.00 0.00 0.00 2.93
2387 2906 2.037901 TGGCATGTTCCATTGTGTTGT 58.962 42.857 0.00 0.00 0.00 3.32
2488 3016 3.071602 CCATCCCTTATCCTGTGAATCGT 59.928 47.826 0.00 0.00 0.00 3.73
2511 3039 8.087750 CCCTCATTTTGTCTTGCTTTAACATAA 58.912 33.333 0.00 0.00 0.00 1.90
2605 3140 6.348132 CCATTAATTAAGAGTGCGTGTGTGAA 60.348 38.462 3.94 0.00 0.00 3.18
2614 3149 7.762382 ACTACAAAGCCATTAATTAAGAGTGC 58.238 34.615 3.94 3.96 0.00 4.40
2688 3230 6.592994 CAGATCAACAAGCTAAGAGAACATCA 59.407 38.462 0.00 0.00 0.00 3.07
2727 3269 4.835615 ACTGTTGAAGGTAGAGTGACAGAT 59.164 41.667 7.50 0.00 37.17 2.90
2739 3281 7.833285 ACAAACCATATTAACTGTTGAAGGT 57.167 32.000 2.69 2.84 0.00 3.50
2781 3334 9.219603 CCGATACAAATGATATTACCAGTTCAT 57.780 33.333 0.00 0.00 0.00 2.57
2872 3446 2.874086 TGTCCGATCGAGTTATTAGCGA 59.126 45.455 18.66 0.00 38.51 4.93
2874 3448 5.921408 AGATTTGTCCGATCGAGTTATTAGC 59.079 40.000 18.66 0.00 0.00 3.09
2883 3466 4.713824 AAGTACAGATTTGTCCGATCGA 57.286 40.909 18.66 0.00 38.76 3.59
2915 3514 6.984474 ACCATCATATACTGACCACTTAAACG 59.016 38.462 0.00 0.00 36.48 3.60
3022 3720 4.528596 AGTACCGGATATCCTTTCTCCATG 59.471 45.833 19.61 0.61 0.00 3.66
3048 3746 2.338577 AATGACTGCCTGGAGTATGC 57.661 50.000 0.00 0.00 0.00 3.14
3061 3759 3.244526 TGTGACATGGCACTGTAATGACT 60.245 43.478 31.07 0.00 39.49 3.41
3182 3882 1.732259 CGTTGTTATTTCCTCGCTGCT 59.268 47.619 0.00 0.00 0.00 4.24
3321 4022 6.910995 ACTACATCTTATAGGATGCGTACAC 58.089 40.000 21.31 0.00 44.81 2.90
3361 4062 7.148069 GGAAGAAGAAGAAGGTCAAAACTTTGA 60.148 37.037 0.69 0.69 44.31 2.69
3375 4076 2.569404 GCTGGAGGAGGAAGAAGAAGAA 59.431 50.000 0.00 0.00 0.00 2.52
3544 4254 7.251321 AGGATTTTCACTCTGTCAGTATCTT 57.749 36.000 0.00 0.00 32.21 2.40
3550 4260 5.174395 CACCTAGGATTTTCACTCTGTCAG 58.826 45.833 17.98 0.00 0.00 3.51
3551 4261 4.563580 GCACCTAGGATTTTCACTCTGTCA 60.564 45.833 17.98 0.00 0.00 3.58
3552 4262 3.935828 GCACCTAGGATTTTCACTCTGTC 59.064 47.826 17.98 0.00 0.00 3.51
3571 4281 7.888546 AGACCTTATATATATTGTTTGGGGCAC 59.111 37.037 0.00 0.00 0.00 5.01
3572 4282 7.995663 AGACCTTATATATATTGTTTGGGGCA 58.004 34.615 0.00 0.00 0.00 5.36
3573 4283 8.507524 GAGACCTTATATATATTGTTTGGGGC 57.492 38.462 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.