Multiple sequence alignment - TraesCS4D01G306900

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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 TraesCS4D01G306900 chr4D 100.000 3679 0 0 1 3679 474940959 474944637 0.000000e+00 6794.0
1 TraesCS4D01G306900 chr4D 75.173 721 140 31 1407 2094 474920910 474921624 1.660000e-78 303.0
2 TraesCS4D01G306900 chr4B 94.414 3061 105 27 1 3042 599332805 599329792 0.000000e+00 4645.0
3 TraesCS4D01G306900 chr4B 75.294 1275 230 58 1410 2610 599351264 599350001 7.000000e-147 531.0
4 TraesCS4D01G306900 chr4B 73.632 1206 257 44 1411 2593 599236149 599234982 3.420000e-110 409.0
5 TraesCS4D01G306900 chr4B 90.545 275 25 1 3405 3679 599328885 599328612 2.700000e-96 363.0
6 TraesCS4D01G306900 chr4B 91.600 250 11 3 3043 3283 599329321 599329073 1.640000e-88 337.0
7 TraesCS4D01G306900 chr4A 94.045 2351 109 19 570 2903 681120278 681117942 0.000000e+00 3537.0
8 TraesCS4D01G306900 chr4A 84.284 649 60 22 2 639 681149470 681148853 2.450000e-166 595.0
9 TraesCS4D01G306900 chr4A 75.669 1270 222 58 1410 2610 681177566 681176315 1.490000e-153 553.0
10 TraesCS4D01G306900 chr4A 82.601 546 36 23 33 572 681121041 681120549 9.440000e-116 427.0
11 TraesCS4D01G306900 chr4A 82.105 95 17 0 3287 3381 664190298 664190204 8.470000e-12 82.4
12 TraesCS4D01G306900 chr3D 77.054 998 204 21 1596 2579 47755388 47756374 5.370000e-153 551.0
13 TraesCS4D01G306900 chr3D 72.868 516 110 28 1989 2489 8893188 8893688 2.290000e-32 150.0
14 TraesCS4D01G306900 chr3D 83.333 102 17 0 3279 3380 434166136 434166237 1.090000e-15 95.3
15 TraesCS4D01G306900 chr3D 80.392 102 20 0 3279 3380 550510750 550510649 1.100000e-10 78.7
16 TraesCS4D01G306900 chr3D 80.851 94 18 0 3287 3380 464321018 464321111 1.420000e-09 75.0
17 TraesCS4D01G306900 chr3A 75.000 1180 267 25 1411 2576 60193472 60194637 1.510000e-143 520.0
18 TraesCS4D01G306900 chr2D 89.831 295 27 3 3377 3670 131282801 131283093 3.470000e-100 375.0
19 TraesCS4D01G306900 chr2D 72.870 1209 261 51 1411 2593 199762672 199761505 1.630000e-93 353.0
20 TraesCS4D01G306900 chr2A 73.201 1209 257 51 1411 2593 220015550 220014383 3.470000e-100 375.0
21 TraesCS4D01G306900 chr2A 82.524 103 16 2 3279 3380 161800296 161800397 5.060000e-14 89.8
22 TraesCS4D01G306900 chrUn 88.215 297 34 1 3377 3673 25995979 25996274 1.630000e-93 353.0
23 TraesCS4D01G306900 chrUn 88.215 297 34 1 3377 3673 183930946 183930651 1.630000e-93 353.0
24 TraesCS4D01G306900 chrUn 88.215 297 34 1 3377 3673 253003728 253004023 1.630000e-93 353.0
25 TraesCS4D01G306900 chrUn 88.215 297 34 1 3377 3673 255746570 255746275 1.630000e-93 353.0
26 TraesCS4D01G306900 chrUn 88.215 297 34 1 3377 3673 318906176 318905881 1.630000e-93 353.0
27 TraesCS4D01G306900 chrUn 87.879 297 35 1 3377 3673 26075373 26075668 7.560000e-92 348.0
28 TraesCS4D01G306900 chrUn 87.879 297 35 1 3377 3673 26107926 26108221 7.560000e-92 348.0
29 TraesCS4D01G306900 chr5B 78.497 386 73 10 2213 2591 109679682 109679300 1.020000e-60 244.0
30 TraesCS4D01G306900 chr5B 80.769 104 16 3 3278 3380 534468832 534468932 1.100000e-10 78.7
31 TraesCS4D01G306900 chr5D 77.720 386 76 10 2213 2591 101422497 101422115 1.030000e-55 228.0
32 TraesCS4D01G306900 chr5A 78.167 371 71 10 2213 2576 99103860 99104227 1.030000e-55 228.0
33 TraesCS4D01G306900 chr1A 70.855 1146 272 48 1423 2537 250443971 250442857 3.720000e-50 209.0
34 TraesCS4D01G306900 chr3B 76.206 311 67 7 2223 2531 11066015 11065710 1.370000e-34 158.0
35 TraesCS4D01G306900 chr2B 82.609 92 15 1 3290 3381 23727993 23727903 3.050000e-11 80.5
36 TraesCS4D01G306900 chr2B 83.146 89 13 2 3293 3380 745782989 745783076 3.050000e-11 80.5
37 TraesCS4D01G306900 chr7B 80.392 102 20 0 3279 3380 706755211 706755110 1.100000e-10 78.7


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 TraesCS4D01G306900 chr4D 474940959 474944637 3678 False 6794.000000 6794 100.000000 1 3679 1 chr4D.!!$F2 3678
1 TraesCS4D01G306900 chr4D 474920910 474921624 714 False 303.000000 303 75.173000 1407 2094 1 chr4D.!!$F1 687
2 TraesCS4D01G306900 chr4B 599328612 599332805 4193 True 1781.666667 4645 92.186333 1 3679 3 chr4B.!!$R3 3678
3 TraesCS4D01G306900 chr4B 599350001 599351264 1263 True 531.000000 531 75.294000 1410 2610 1 chr4B.!!$R2 1200
4 TraesCS4D01G306900 chr4B 599234982 599236149 1167 True 409.000000 409 73.632000 1411 2593 1 chr4B.!!$R1 1182
5 TraesCS4D01G306900 chr4A 681117942 681121041 3099 True 1982.000000 3537 88.323000 33 2903 2 chr4A.!!$R4 2870
6 TraesCS4D01G306900 chr4A 681148853 681149470 617 True 595.000000 595 84.284000 2 639 1 chr4A.!!$R2 637
7 TraesCS4D01G306900 chr4A 681176315 681177566 1251 True 553.000000 553 75.669000 1410 2610 1 chr4A.!!$R3 1200
8 TraesCS4D01G306900 chr3D 47755388 47756374 986 False 551.000000 551 77.054000 1596 2579 1 chr3D.!!$F2 983
9 TraesCS4D01G306900 chr3A 60193472 60194637 1165 False 520.000000 520 75.000000 1411 2576 1 chr3A.!!$F1 1165
10 TraesCS4D01G306900 chr2D 199761505 199762672 1167 True 353.000000 353 72.870000 1411 2593 1 chr2D.!!$R1 1182
11 TraesCS4D01G306900 chr2A 220014383 220015550 1167 True 375.000000 375 73.201000 1411 2593 1 chr2A.!!$R1 1182
12 TraesCS4D01G306900 chr1A 250442857 250443971 1114 True 209.000000 209 70.855000 1423 2537 1 chr1A.!!$R1 1114

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
173 177 0.179161 AACCGACGCTCGATCTGAAG 60.179 55.0 8.63 0.0 43.74 3.02 F
674 978 0.295470 GCGCGCATTAATTTGCACTG 59.705 50.0 29.10 0.0 42.91 3.66 F
732 1038 0.737715 GCCAGAGACAGTGGTTAGCG 60.738 60.0 0.00 0.0 37.40 4.26 F
1177 1498 1.224069 CGGCTGATTCGCGGATGATT 61.224 55.0 3.53 0.0 32.63 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1077 1398 0.592148 GGCATCTACGTACGAGGAGG 59.408 60.0 24.41 19.81 0.00 4.30 R
2374 2779 0.935831 CGAGTACGTTTCGTGGTGCA 60.936 55.0 12.37 0.00 41.39 4.57 R
2627 3035 1.053294 CGTGACTGAACGACGACTCG 61.053 60.0 0.00 0.00 46.49 4.18 R
3035 3462 0.253327 ACTCCTGGCTCGGGAAAATC 59.747 55.0 4.55 0.00 38.58 2.17 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
59 61 2.715749 ATTCCTGATCGATGCAACCA 57.284 45.000 0.54 0.00 0.00 3.67
72 74 2.382882 TGCAACCAACAAGGAATCACA 58.617 42.857 0.00 0.00 41.22 3.58
83 85 7.283807 CCAACAAGGAATCACATATGAATCTGA 59.716 37.037 10.38 2.78 41.22 3.27
173 177 0.179161 AACCGACGCTCGATCTGAAG 60.179 55.000 8.63 0.00 43.74 3.02
187 191 5.701290 TCGATCTGAAGGAAGAAGAAAAACC 59.299 40.000 0.00 0.00 0.00 3.27
276 298 0.462047 GCCATGGACGTAACCAGGAG 60.462 60.000 18.40 1.78 43.28 3.69
332 354 5.102953 TCTGCCAGAGCACTGTTAATTAT 57.897 39.130 10.37 0.00 46.52 1.28
333 355 5.118990 TCTGCCAGAGCACTGTTAATTATC 58.881 41.667 10.37 0.00 46.52 1.75
334 356 4.842574 TGCCAGAGCACTGTTAATTATCA 58.157 39.130 10.37 0.00 46.52 2.15
335 357 5.252547 TGCCAGAGCACTGTTAATTATCAA 58.747 37.500 10.37 0.00 46.52 2.57
336 358 5.887598 TGCCAGAGCACTGTTAATTATCAAT 59.112 36.000 10.37 0.00 46.52 2.57
337 359 6.377996 TGCCAGAGCACTGTTAATTATCAATT 59.622 34.615 10.37 0.00 46.52 2.32
338 360 6.914757 GCCAGAGCACTGTTAATTATCAATTC 59.085 38.462 10.37 0.00 42.05 2.17
457 486 8.876275 CTGAAGTAGGAGTAGTACAGTACTAG 57.124 42.308 19.16 3.04 41.59 2.57
458 487 8.372877 TGAAGTAGGAGTAGTACAGTACTAGT 57.627 38.462 23.11 23.11 45.18 2.57
459 488 9.480861 TGAAGTAGGAGTAGTACAGTACTAGTA 57.519 37.037 22.99 9.46 43.18 1.82
460 489 9.744468 GAAGTAGGAGTAGTACAGTACTAGTAC 57.256 40.741 23.26 23.26 43.18 2.73
461 490 7.936584 AGTAGGAGTAGTACAGTACTAGTACG 58.063 42.308 23.94 20.37 45.96 3.67
467 496 7.607250 AGTAGTACAGTACTAGTACGAGTGTT 58.393 38.462 28.98 22.14 44.92 3.32
492 521 1.658596 CGACGCTCGATCCAAATTTCA 59.341 47.619 0.00 0.00 43.74 2.69
497 526 4.336433 ACGCTCGATCCAAATTTCATCATT 59.664 37.500 0.00 0.00 0.00 2.57
504 533 7.772292 TCGATCCAAATTTCATCATTTCTCTCT 59.228 33.333 7.22 0.00 0.00 3.10
505 534 8.404000 CGATCCAAATTTCATCATTTCTCTCTT 58.596 33.333 7.22 0.00 0.00 2.85
507 536 8.874744 TCCAAATTTCATCATTTCTCTCTTCT 57.125 30.769 0.00 0.00 0.00 2.85
543 572 3.071312 TGCATGTGGAGGAAGCAAATTTT 59.929 39.130 0.00 0.00 31.42 1.82
673 977 1.133363 CGCGCGCATTAATTTGCACT 61.133 50.000 32.61 0.00 42.91 4.40
674 978 0.295470 GCGCGCATTAATTTGCACTG 59.705 50.000 29.10 0.00 42.91 3.66
708 1013 8.834004 AAACACCATCAACTAGGAGTAGTATA 57.166 34.615 0.00 0.00 38.66 1.47
709 1014 8.466617 AACACCATCAACTAGGAGTAGTATAG 57.533 38.462 0.00 0.00 38.66 1.31
732 1038 0.737715 GCCAGAGACAGTGGTTAGCG 60.738 60.000 0.00 0.00 37.40 4.26
786 1096 5.048713 CCACTCAAAGTCCCAGTCAATTAAC 60.049 44.000 0.00 0.00 0.00 2.01
823 1133 1.466024 CGTGCGTGAAGTCTACTCCTC 60.466 57.143 0.00 0.00 0.00 3.71
1177 1498 1.224069 CGGCTGATTCGCGGATGATT 61.224 55.000 3.53 0.00 32.63 2.57
2670 3078 1.313091 GGAGATGTTTGGGTTCCGGC 61.313 60.000 0.00 0.00 0.00 6.13
2710 3118 6.260050 CGTAGTACCAACCAAAATAGATGCAT 59.740 38.462 0.00 0.00 0.00 3.96
2808 3216 9.376075 ACATCTTCTAATTTGTCATCTACAGTG 57.624 33.333 0.00 0.00 39.87 3.66
2826 3234 6.683974 ACAGTGATTGATTATAACAGTGCC 57.316 37.500 0.00 0.00 35.96 5.01
2864 3291 6.820656 GTGGTGTGATCTTCATACTTGAGATT 59.179 38.462 4.71 0.00 38.37 2.40
2865 3292 6.820152 TGGTGTGATCTTCATACTTGAGATTG 59.180 38.462 4.71 0.00 38.37 2.67
2866 3293 7.044181 GGTGTGATCTTCATACTTGAGATTGA 58.956 38.462 4.71 0.00 38.37 2.57
2868 3295 8.763356 GTGTGATCTTCATACTTGAGATTGATC 58.237 37.037 0.00 0.00 35.88 2.92
2869 3296 8.702819 TGTGATCTTCATACTTGAGATTGATCT 58.297 33.333 0.00 0.00 40.50 2.75
2870 3297 9.545105 GTGATCTTCATACTTGAGATTGATCTT 57.455 33.333 0.00 0.00 37.25 2.40
2871 3298 9.761504 TGATCTTCATACTTGAGATTGATCTTC 57.238 33.333 0.00 0.00 37.25 2.87
2872 3299 9.761504 GATCTTCATACTTGAGATTGATCTTCA 57.238 33.333 0.00 0.00 37.25 3.02
2918 3345 6.899114 ACTAAACTGATGGATTCGTTGTTTC 58.101 36.000 0.00 0.00 31.78 2.78
2947 3374 1.556911 CAGGTACAGCCCTGTGAATCT 59.443 52.381 11.02 0.00 45.81 2.40
3035 3462 4.390603 TGAATTTACAACTCCGGACAATCG 59.609 41.667 0.00 0.00 0.00 3.34
3070 3967 0.324091 GAGTTACCTGGGGTCGAGGA 60.324 60.000 0.00 0.00 37.09 3.71
3095 3992 0.682292 TGGATGCGGTGTTGTCTGTA 59.318 50.000 0.00 0.00 0.00 2.74
3125 4022 3.104014 GAGGTTCACTCGTTCGGAC 57.896 57.895 0.00 0.00 36.29 4.79
3181 4085 1.874019 CGAGGGCGACAGTTCATCG 60.874 63.158 0.00 0.00 42.55 3.84
3205 4109 0.252103 AGGTGACGGCTTAAGGAGGA 60.252 55.000 4.29 0.00 0.00 3.71
3212 4116 2.499685 CTTAAGGAGGACGGGGCG 59.500 66.667 0.00 0.00 0.00 6.13
3283 4188 1.217882 AGTTTTTGTCGTCCAGAGCG 58.782 50.000 0.00 0.00 0.00 5.03
3284 4189 0.935196 GTTTTTGTCGTCCAGAGCGT 59.065 50.000 0.00 0.00 0.00 5.07
3305 4237 0.606604 TACAGCCGGACCTCTCAAAC 59.393 55.000 5.05 0.00 0.00 2.93
3308 4240 2.890766 GCCGGACCTCTCAAACCCA 61.891 63.158 5.05 0.00 0.00 4.51
3310 4242 0.328258 CCGGACCTCTCAAACCCATT 59.672 55.000 0.00 0.00 0.00 3.16
3312 4244 2.084546 CGGACCTCTCAAACCCATTTC 58.915 52.381 0.00 0.00 0.00 2.17
3321 4253 2.099405 CAAACCCATTTCATACGCCCT 58.901 47.619 0.00 0.00 0.00 5.19
3329 4261 1.262417 TTCATACGCCCTGACTGACA 58.738 50.000 0.00 0.00 0.00 3.58
3330 4262 1.262417 TCATACGCCCTGACTGACAA 58.738 50.000 0.00 0.00 0.00 3.18
3331 4263 1.067142 TCATACGCCCTGACTGACAAC 60.067 52.381 0.00 0.00 0.00 3.32
3337 4269 0.474184 CCCTGACTGACAACCTGGTT 59.526 55.000 6.18 6.18 0.00 3.67
3343 4275 3.181469 TGACTGACAACCTGGTTACTGTC 60.181 47.826 27.82 27.82 38.91 3.51
3395 4376 2.684881 CTCAAATATGGGGCGGATATGC 59.315 50.000 0.00 0.00 0.00 3.14
3397 4378 0.107214 AATATGGGGCGGATATGCGG 60.107 55.000 18.67 0.32 35.06 5.69
3398 4379 0.980754 ATATGGGGCGGATATGCGGA 60.981 55.000 18.67 0.00 35.06 5.54
3399 4380 1.895020 TATGGGGCGGATATGCGGAC 61.895 60.000 18.67 2.18 35.06 4.79
3401 4382 4.295119 GGGCGGATATGCGGACGT 62.295 66.667 18.67 0.00 35.06 4.34
3402 4383 2.733593 GGCGGATATGCGGACGTC 60.734 66.667 18.67 7.13 35.06 4.34
3403 4384 2.733593 GCGGATATGCGGACGTCC 60.734 66.667 25.28 25.28 0.00 4.79
3479 4460 3.636231 CACCCCGAAGACCAGCCA 61.636 66.667 0.00 0.00 0.00 4.75
3484 4465 1.227089 CCGAAGACCAGCCAGATCG 60.227 63.158 0.00 0.00 0.00 3.69
3502 4483 5.945784 CAGATCGATTTCCTATCTCCTCTCT 59.054 44.000 0.00 0.00 0.00 3.10
3514 4495 3.197983 TCTCCTCTCTTCTTCCTCCTCT 58.802 50.000 0.00 0.00 0.00 3.69
3518 4499 0.179113 CTCTTCTTCCTCCTCTGCGC 60.179 60.000 0.00 0.00 0.00 6.09
3654 4635 3.364441 CCACCGTGGTACGTCCGA 61.364 66.667 9.64 0.00 40.58 4.55
3655 4636 2.703798 CCACCGTGGTACGTCCGAT 61.704 63.158 9.64 0.00 40.58 4.18
3668 4649 0.311477 GTCCGATAACTCTCCGGCTC 59.689 60.000 0.00 0.00 42.70 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 8.812513 TTCAGATTCATATGTGATTCCTTGTT 57.187 30.769 9.83 0.00 34.40 2.83
72 74 8.188799 CACAATGCAGAGTTTTCAGATTCATAT 58.811 33.333 0.00 0.00 0.00 1.78
83 85 5.179045 CTCTGTTCACAATGCAGAGTTTT 57.821 39.130 11.37 0.00 46.52 2.43
173 177 3.188667 CGGCTACTGGTTTTTCTTCTTCC 59.811 47.826 0.00 0.00 0.00 3.46
187 191 4.891727 AATCGGCGCCGGCTACTG 62.892 66.667 44.95 21.06 40.25 2.74
276 298 3.152261 GATCCCATCGTCGATCCATAC 57.848 52.381 4.34 0.00 30.64 2.39
333 355 9.825972 CCAAGTTTGTATACAACTACTGAATTG 57.174 33.333 17.85 15.78 35.28 2.32
334 356 9.787435 TCCAAGTTTGTATACAACTACTGAATT 57.213 29.630 17.85 5.32 35.28 2.17
335 357 9.436957 CTCCAAGTTTGTATACAACTACTGAAT 57.563 33.333 17.85 3.08 35.28 2.57
336 358 8.644216 TCTCCAAGTTTGTATACAACTACTGAA 58.356 33.333 17.85 8.14 35.28 3.02
337 359 8.185506 TCTCCAAGTTTGTATACAACTACTGA 57.814 34.615 17.85 12.22 35.28 3.41
338 360 9.436957 AATCTCCAAGTTTGTATACAACTACTG 57.563 33.333 17.85 12.06 35.28 2.74
389 418 4.680440 GCATTTGGTCAACAGAAACTTGGT 60.680 41.667 0.00 0.00 0.00 3.67
452 481 4.152402 GTCGGTTGAACACTCGTACTAGTA 59.848 45.833 0.00 0.00 0.00 1.82
453 482 3.058639 GTCGGTTGAACACTCGTACTAGT 60.059 47.826 0.00 0.00 0.00 2.57
455 484 2.096268 CGTCGGTTGAACACTCGTACTA 60.096 50.000 0.00 0.00 0.00 1.82
456 485 1.334419 CGTCGGTTGAACACTCGTACT 60.334 52.381 0.00 0.00 0.00 2.73
457 486 1.047739 CGTCGGTTGAACACTCGTAC 58.952 55.000 0.00 0.00 0.00 3.67
458 487 0.661187 GCGTCGGTTGAACACTCGTA 60.661 55.000 0.00 0.00 0.00 3.43
459 488 1.947642 GCGTCGGTTGAACACTCGT 60.948 57.895 0.00 0.00 0.00 4.18
460 489 1.606350 GAGCGTCGGTTGAACACTCG 61.606 60.000 0.00 0.00 0.00 4.18
461 490 1.606350 CGAGCGTCGGTTGAACACTC 61.606 60.000 5.74 0.00 36.00 3.51
467 496 1.868987 TTGGATCGAGCGTCGGTTGA 61.869 55.000 16.28 16.28 40.88 3.18
492 521 8.599624 AAAGAGAGAGAGAAGAGAGAAATGAT 57.400 34.615 0.00 0.00 0.00 2.45
497 526 7.523709 GCAAAGAAAGAGAGAGAGAAGAGAGAA 60.524 40.741 0.00 0.00 0.00 2.87
504 533 5.699915 CACATGCAAAGAAAGAGAGAGAGAA 59.300 40.000 0.00 0.00 0.00 2.87
505 534 5.236282 CACATGCAAAGAAAGAGAGAGAGA 58.764 41.667 0.00 0.00 0.00 3.10
507 536 4.040829 TCCACATGCAAAGAAAGAGAGAGA 59.959 41.667 0.00 0.00 0.00 3.10
543 572 0.251165 GCTGTACTGGCCCAAGGAAA 60.251 55.000 0.00 0.00 0.00 3.13
673 977 6.182507 AGTTGATGGTGTTTTCTACTACCA 57.817 37.500 0.00 0.00 40.09 3.25
674 978 6.817140 CCTAGTTGATGGTGTTTTCTACTACC 59.183 42.308 0.00 0.00 31.83 3.18
708 1013 0.613292 ACCACTGTCTCTGGCGATCT 60.613 55.000 0.00 0.00 31.13 2.75
709 1014 0.247736 AACCACTGTCTCTGGCGATC 59.752 55.000 0.00 0.00 31.13 3.69
732 1038 3.004002 GTGGTGCTAGTGGTTGTTTTACC 59.996 47.826 0.00 0.00 38.73 2.85
915 1225 9.709495 GAGGAAGACGAAGATTAGTAGTATAGA 57.291 37.037 0.00 0.00 0.00 1.98
921 1231 6.059484 AGAGGAGGAAGACGAAGATTAGTAG 58.941 44.000 0.00 0.00 0.00 2.57
1006 1323 2.740055 AGAGCTTGCGACGCCAAG 60.740 61.111 18.69 19.83 43.88 3.61
1077 1398 0.592148 GGCATCTACGTACGAGGAGG 59.408 60.000 24.41 19.81 0.00 4.30
1085 1406 1.651987 GCAAGCAAGGCATCTACGTA 58.348 50.000 0.00 0.00 0.00 3.57
1086 1407 1.361668 CGCAAGCAAGGCATCTACGT 61.362 55.000 0.00 0.00 0.00 3.57
1177 1498 1.744798 CGGATCTGATCAGCTGGCAAA 60.745 52.381 18.36 0.00 0.00 3.68
1526 1856 2.976840 GCCGGCGTTGCTGATGAAA 61.977 57.895 12.58 0.00 37.02 2.69
1908 2262 2.401766 CCGGCATGTTGAGCAGGTC 61.402 63.158 0.00 0.00 41.57 3.85
2374 2779 0.935831 CGAGTACGTTTCGTGGTGCA 60.936 55.000 12.37 0.00 41.39 4.57
2492 2900 3.072184 GCCTGGGTATCATCTTGATCACT 59.928 47.826 0.00 0.00 38.26 3.41
2627 3035 1.053294 CGTGACTGAACGACGACTCG 61.053 60.000 0.00 0.00 46.49 4.18
2630 3038 2.362800 GGCGTGACTGAACGACGAC 61.363 63.158 0.00 0.00 46.49 4.34
2670 3078 8.578769 GTTGGTACTACGAGTAACTTATTTTCG 58.421 37.037 10.18 0.00 39.13 3.46
2710 3118 9.551734 CTTGATCTACATTCTGTCAATGGATTA 57.448 33.333 0.00 0.00 32.14 1.75
2808 3216 7.792374 TCTTCTGGCACTGTTATAATCAATC 57.208 36.000 0.00 0.00 0.00 2.67
2826 3234 1.462283 CACACCACGATGCTTCTTCTG 59.538 52.381 0.00 0.00 0.00 3.02
2864 3291 9.140874 AGACACATCTCAAGTATATGAAGATCA 57.859 33.333 0.00 0.00 0.00 2.92
2865 3292 9.409312 CAGACACATCTCAAGTATATGAAGATC 57.591 37.037 0.00 0.00 30.42 2.75
2866 3293 9.140874 TCAGACACATCTCAAGTATATGAAGAT 57.859 33.333 0.00 0.00 30.42 2.40
2868 3295 8.628280 TCTCAGACACATCTCAAGTATATGAAG 58.372 37.037 0.00 0.00 30.42 3.02
2869 3296 8.409371 GTCTCAGACACATCTCAAGTATATGAA 58.591 37.037 0.00 0.00 30.42 2.57
2870 3297 7.777440 AGTCTCAGACACATCTCAAGTATATGA 59.223 37.037 7.77 0.00 34.60 2.15
2871 3298 7.939782 AGTCTCAGACACATCTCAAGTATATG 58.060 38.462 7.77 0.00 34.60 1.78
2872 3299 9.634021 TTAGTCTCAGACACATCTCAAGTATAT 57.366 33.333 7.77 0.00 34.60 0.86
2873 3300 9.462606 TTTAGTCTCAGACACATCTCAAGTATA 57.537 33.333 7.77 0.00 34.60 1.47
2874 3301 7.946381 TTAGTCTCAGACACATCTCAAGTAT 57.054 36.000 7.77 0.00 34.60 2.12
2875 3302 7.448777 AGTTTAGTCTCAGACACATCTCAAGTA 59.551 37.037 7.77 0.00 34.60 2.24
2876 3303 6.266558 AGTTTAGTCTCAGACACATCTCAAGT 59.733 38.462 7.77 0.00 34.60 3.16
2877 3304 6.585702 CAGTTTAGTCTCAGACACATCTCAAG 59.414 42.308 7.77 0.00 34.60 3.02
2878 3305 6.265422 TCAGTTTAGTCTCAGACACATCTCAA 59.735 38.462 7.77 0.00 34.60 3.02
2879 3306 5.770162 TCAGTTTAGTCTCAGACACATCTCA 59.230 40.000 7.77 0.00 34.60 3.27
2880 3307 6.260870 TCAGTTTAGTCTCAGACACATCTC 57.739 41.667 7.77 0.00 34.60 2.75
2881 3308 6.350864 CCATCAGTTTAGTCTCAGACACATCT 60.351 42.308 7.77 0.00 34.60 2.90
2918 3345 1.677217 GGGCTGTACCTGAAGCTTCTG 60.677 57.143 26.09 24.25 39.46 3.02
2989 3416 6.858993 TCAGTCAATTTACCAATAACAAACGC 59.141 34.615 0.00 0.00 0.00 4.84
3027 3454 1.330829 GCTCGGGAAAATCGATTGTCC 59.669 52.381 31.68 31.68 42.39 4.02
3035 3462 0.253327 ACTCCTGGCTCGGGAAAATC 59.747 55.000 4.55 0.00 38.58 2.17
3095 3992 1.000612 GAACCTCGGACTCCCCTCT 59.999 63.158 0.00 0.00 0.00 3.69
3163 4067 1.874019 CGATGAACTGTCGCCCTCG 60.874 63.158 0.00 0.00 31.85 4.63
3173 4077 0.526662 GTCACCTCCGACGATGAACT 59.473 55.000 0.00 0.00 0.00 3.01
3181 4085 0.458025 CTTAAGCCGTCACCTCCGAC 60.458 60.000 0.00 0.00 0.00 4.79
3252 4156 9.804758 TGGACGACAAAAACTTAAAATATTTGT 57.195 25.926 0.39 2.18 44.36 2.83
3255 4159 9.893305 CTCTGGACGACAAAAACTTAAAATATT 57.107 29.630 0.00 0.00 0.00 1.28
3257 4161 7.357303 GCTCTGGACGACAAAAACTTAAAATA 58.643 34.615 0.00 0.00 0.00 1.40
3279 4184 1.007618 GGTCCGGCTGTATACGCTC 60.008 63.158 15.76 8.12 0.00 5.03
3283 4188 1.688772 TGAGAGGTCCGGCTGTATAC 58.311 55.000 0.00 0.00 0.00 1.47
3284 4189 2.429610 GTTTGAGAGGTCCGGCTGTATA 59.570 50.000 0.00 0.00 0.00 1.47
3305 4237 1.134098 AGTCAGGGCGTATGAAATGGG 60.134 52.381 0.00 0.00 0.00 4.00
3308 4240 2.236146 TGTCAGTCAGGGCGTATGAAAT 59.764 45.455 0.00 0.00 0.00 2.17
3310 4242 1.262417 TGTCAGTCAGGGCGTATGAA 58.738 50.000 0.00 0.00 0.00 2.57
3312 4244 1.359848 GTTGTCAGTCAGGGCGTATG 58.640 55.000 0.00 0.00 0.00 2.39
3321 4253 2.769663 ACAGTAACCAGGTTGTCAGTCA 59.230 45.455 15.82 0.00 0.00 3.41
3329 4261 2.028385 GTGATCGGACAGTAACCAGGTT 60.028 50.000 10.50 10.50 0.00 3.50
3330 4262 1.549170 GTGATCGGACAGTAACCAGGT 59.451 52.381 0.00 0.00 0.00 4.00
3331 4263 1.548719 TGTGATCGGACAGTAACCAGG 59.451 52.381 0.00 0.00 0.00 4.45
3365 4297 1.543429 CCCATATTTGAGAGGCCCGTC 60.543 57.143 0.00 0.00 0.00 4.79
3369 4301 0.890996 CGCCCCATATTTGAGAGGCC 60.891 60.000 0.00 0.00 37.07 5.19
3436 4417 1.047801 GTGCAATTTGGGGTGAGGTT 58.952 50.000 0.00 0.00 0.00 3.50
3479 4460 6.139679 AGAGAGGAGATAGGAAATCGATCT 57.860 41.667 0.00 0.00 39.93 2.75
3484 4465 6.782494 AGGAAGAAGAGAGGAGATAGGAAATC 59.218 42.308 0.00 0.00 0.00 2.17
3502 4483 2.982130 GGCGCAGAGGAGGAAGAA 59.018 61.111 10.83 0.00 0.00 2.52
3632 4613 2.504681 CGTACCACGGTGGCGTAC 60.505 66.667 26.62 19.78 42.67 3.67
3649 4630 0.311477 GAGCCGGAGAGTTATCGGAC 59.689 60.000 5.05 0.00 45.96 4.79


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

AutoCloner maintained by Alex Coulton.