Multiple sequence alignment - TraesCS3D01G180400

Loading Multiple Alignment...

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 TraesCS3D01G180400 chr3D 100.000 2798 0 0 2232 5029 162409866 162407069 0.000000e+00 5168
1 TraesCS3D01G180400 chr3D 100.000 2003 0 0 1 2003 162412097 162410095 0.000000e+00 3699
2 TraesCS3D01G180400 chr3D 87.712 236 26 1 1678 1913 162410345 162410113 6.420000e-69 272
3 TraesCS3D01G180400 chr3D 87.712 236 26 1 1753 1985 162410420 162410185 6.420000e-69 272
4 TraesCS3D01G180400 chr3D 92.453 159 12 0 2247 2405 162410415 162410257 1.410000e-55 228
5 TraesCS3D01G180400 chr3D 86.857 175 17 3 1821 1989 162409866 162409692 1.850000e-44 191
6 TraesCS3D01G180400 chr3D 86.857 175 17 3 2232 2406 162410277 162410109 1.850000e-44 191
7 TraesCS3D01G180400 chr3B 96.170 2794 85 9 2243 5028 239310084 239307305 0.000000e+00 4547
8 TraesCS3D01G180400 chr3B 92.482 1636 65 17 299 1919 239312063 239310471 0.000000e+00 2287
9 TraesCS3D01G180400 chr3B 91.333 300 26 0 1 300 239323471 239323172 1.300000e-110 411
10 TraesCS3D01G180400 chr3B 93.487 261 13 3 3913 4171 422225608 422225350 7.900000e-103 385
11 TraesCS3D01G180400 chr3B 86.182 275 29 4 1735 2003 239310175 239309904 6.370000e-74 289
12 TraesCS3D01G180400 chr3B 92.784 194 14 0 1810 2003 239310175 239309982 1.070000e-71 281
13 TraesCS3D01G180400 chr3B 85.253 217 19 6 1685 1888 239310078 239309862 1.420000e-50 211
14 TraesCS3D01G180400 chr3A 95.759 2806 103 6 2232 5028 194707699 194704901 0.000000e+00 4508
15 TraesCS3D01G180400 chr3A 94.056 2002 83 17 1 1985 194710185 194708203 0.000000e+00 3005
16 TraesCS3D01G180400 chr3A 90.820 305 22 3 1678 1976 194708444 194708140 2.180000e-108 403
17 TraesCS3D01G180400 chr3A 87.023 262 22 5 1646 1904 194708392 194708140 8.240000e-73 285
18 TraesCS3D01G180400 chr3A 88.038 209 19 2 1711 1913 194707734 194707526 5.030000e-60 243
19 TraesCS3D01G180400 chr3A 90.230 174 14 2 2232 2402 194708376 194708203 1.820000e-54 224
20 TraesCS3D01G180400 chr3A 85.388 219 19 8 1683 1888 194707684 194707466 1.100000e-51 215
21 TraesCS3D01G180400 chr3A 84.305 223 26 5 2233 2452 194708450 194708234 5.100000e-50 209
22 TraesCS3D01G180400 chr3A 84.951 206 28 1 2247 2452 194708514 194708312 6.600000e-49 206
23 TraesCS3D01G180400 chr3A 89.506 162 14 1 2232 2393 194708298 194708140 8.540000e-48 202
24 TraesCS3D01G180400 chr3A 90.667 150 11 1 2275 2421 194707734 194707585 3.970000e-46 196
25 TraesCS3D01G180400 chr5B 93.103 261 14 3 3913 4171 452131827 452132085 3.670000e-101 379
26 TraesCS3D01G180400 chr7D 85.303 347 47 4 998 1342 234126676 234127020 6.190000e-94 355
27 TraesCS3D01G180400 chr7A 90.286 175 10 6 4000 4171 642738396 642738566 6.550000e-54 222
28 TraesCS3D01G180400 chr2A 89.655 174 11 6 4000 4170 687064262 687064431 1.100000e-51 215
29 TraesCS3D01G180400 chr2A 90.991 111 10 0 3914 4024 687064143 687064253 3.140000e-32 150


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 TraesCS3D01G180400 chr3D 162407069 162412097 5028 True 1431.571429 5168 91.655857 1 5029 7 chr3D.!!$R1 5028
1 TraesCS3D01G180400 chr3B 239307305 239312063 4758 True 1523.000000 4547 90.574200 299 5028 5 chr3B.!!$R3 4729
2 TraesCS3D01G180400 chr3A 194704901 194710185 5284 True 881.454545 4508 89.158455 1 5028 11 chr3A.!!$R1 5027

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
690 707 0.034896 AACTGAACGGCCGATTCTGT 59.965 50.000 35.90 31.38 39.19 3.41 F
960 984 0.179089 CCTCATTCACAGGCGAGGAG 60.179 60.000 0.00 0.00 46.71 3.69 F
961 985 0.820226 CTCATTCACAGGCGAGGAGA 59.180 55.000 0.00 0.00 0.00 3.71 F
962 986 1.205655 CTCATTCACAGGCGAGGAGAA 59.794 52.381 0.00 0.00 0.00 2.87 F
1992 2429 0.043485 AGGGAAAGGAGGAGGAGGTC 59.957 60.000 0.00 0.00 0.00 3.85 F
3375 4012 0.038744 CCATGGAGCACCCTGAACTT 59.961 55.000 5.56 0.00 34.45 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 2416 0.252012 CACTGTGACCTCCTCCTCCT 60.252 60.0 0.32 0.0 0.00 3.69 R
1981 2418 0.543174 ACCACTGTGACCTCCTCCTC 60.543 60.0 9.86 0.0 0.00 3.71 R
1983 2420 0.832135 TCACCACTGTGACCTCCTCC 60.832 60.0 9.86 0.0 46.40 4.30 R
2347 2972 0.957395 ACATTCTTCTGCCTGCCACG 60.957 55.0 0.00 0.0 0.00 4.94 R
3476 4113 0.326618 TCCCCTTCCAGACCTCATCC 60.327 60.0 0.00 0.0 0.00 3.51 R
4675 5315 0.895530 TTGCTGTTCCCTCTAGGTCG 59.104 55.0 0.00 0.0 36.75 4.79 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
57 58 5.360591 ACAATAGTCGATTGACCATCTTCC 58.639 41.667 12.07 0.00 46.94 3.46
124 125 1.344763 CACTCCTCTTCCTTGACGGTT 59.655 52.381 0.00 0.00 0.00 4.44
184 185 2.352229 CAAAGCGTGGTGTGTGCG 60.352 61.111 0.00 0.00 0.00 5.34
229 236 7.442666 TGTGTGTAAATGTGATGTTGCTAACTA 59.557 33.333 0.00 0.00 0.00 2.24
273 280 0.525668 GACATGCTGCTGCTTGATGC 60.526 55.000 29.76 17.76 44.17 3.91
295 302 2.299993 TGCGCTGCTATATATGCTCC 57.700 50.000 9.73 0.00 0.00 4.70
460 469 8.082242 GCATAAAAGGATTTGTGGGTATACATC 58.918 37.037 5.01 0.00 39.02 3.06
555 564 9.909043 CATATCGTTTTCGTGTTCATATTTACA 57.091 29.630 0.00 0.00 44.46 2.41
627 636 6.949715 ACCAAGGGTATTATAGACGTTTCAA 58.050 36.000 0.00 0.00 32.11 2.69
663 680 5.814188 TGTCACAATCTCATACTGCAATCTC 59.186 40.000 0.00 0.00 0.00 2.75
674 691 9.160496 CTCATACTGCAATCTCTTAAAAGAACT 57.840 33.333 0.00 0.00 34.03 3.01
675 692 8.939929 TCATACTGCAATCTCTTAAAAGAACTG 58.060 33.333 0.00 0.00 34.03 3.16
690 707 0.034896 AACTGAACGGCCGATTCTGT 59.965 50.000 35.90 31.38 39.19 3.41
691 708 0.892755 ACTGAACGGCCGATTCTGTA 59.107 50.000 35.90 14.18 36.73 2.74
692 709 1.480954 ACTGAACGGCCGATTCTGTAT 59.519 47.619 35.90 16.04 36.73 2.29
693 710 2.093658 ACTGAACGGCCGATTCTGTATT 60.094 45.455 35.90 13.40 36.73 1.89
694 711 2.540101 CTGAACGGCCGATTCTGTATTC 59.460 50.000 35.90 22.07 0.00 1.75
695 712 2.167693 TGAACGGCCGATTCTGTATTCT 59.832 45.455 35.90 0.00 0.00 2.40
724 742 6.449698 GCAGTTTCCTGAAATCTGATTTTGA 58.550 36.000 16.14 10.76 41.50 2.69
729 747 8.972349 GTTTCCTGAAATCTGATTTTGAAGAAC 58.028 33.333 16.14 13.84 31.47 3.01
744 762 1.884235 AGAACGTGGAGCTGAAAAGG 58.116 50.000 0.00 0.00 0.00 3.11
784 802 2.025155 GAGAACATGGAGCCGAGAGTA 58.975 52.381 0.00 0.00 0.00 2.59
799 818 0.815734 GAGTAGCCCTAGTTCGCACA 59.184 55.000 0.00 0.00 0.00 4.57
898 917 2.002977 CTCCCCTCCCCTGATTGCA 61.003 63.158 0.00 0.00 0.00 4.08
960 984 0.179089 CCTCATTCACAGGCGAGGAG 60.179 60.000 0.00 0.00 46.71 3.69
961 985 0.820226 CTCATTCACAGGCGAGGAGA 59.180 55.000 0.00 0.00 0.00 3.71
962 986 1.205655 CTCATTCACAGGCGAGGAGAA 59.794 52.381 0.00 0.00 0.00 2.87
1602 1631 2.039613 GGAGCCCCTATTTGAGATGGAG 59.960 54.545 0.00 0.00 0.00 3.86
1603 1632 2.039613 GAGCCCCTATTTGAGATGGAGG 59.960 54.545 0.00 0.00 0.00 4.30
1604 1633 2.057922 GCCCCTATTTGAGATGGAGGA 58.942 52.381 0.00 0.00 0.00 3.71
1914 2351 1.566211 CAGAGAAGGAAGAGGAGGCA 58.434 55.000 0.00 0.00 0.00 4.75
1981 2418 4.479786 CCTGAACTAGAGAAGGGAAAGG 57.520 50.000 0.00 0.00 0.00 3.11
1982 2419 4.097418 CCTGAACTAGAGAAGGGAAAGGA 58.903 47.826 0.00 0.00 0.00 3.36
1983 2420 4.161377 CCTGAACTAGAGAAGGGAAAGGAG 59.839 50.000 0.00 0.00 0.00 3.69
1984 2421 4.097418 TGAACTAGAGAAGGGAAAGGAGG 58.903 47.826 0.00 0.00 0.00 4.30
1985 2422 4.202792 TGAACTAGAGAAGGGAAAGGAGGA 60.203 45.833 0.00 0.00 0.00 3.71
1986 2423 3.989056 ACTAGAGAAGGGAAAGGAGGAG 58.011 50.000 0.00 0.00 0.00 3.69
1987 2424 2.262266 AGAGAAGGGAAAGGAGGAGG 57.738 55.000 0.00 0.00 0.00 4.30
1988 2425 1.725182 AGAGAAGGGAAAGGAGGAGGA 59.275 52.381 0.00 0.00 0.00 3.71
1989 2426 2.115427 GAGAAGGGAAAGGAGGAGGAG 58.885 57.143 0.00 0.00 0.00 3.69
1990 2427 1.208706 GAAGGGAAAGGAGGAGGAGG 58.791 60.000 0.00 0.00 0.00 4.30
1991 2428 0.498685 AAGGGAAAGGAGGAGGAGGT 59.501 55.000 0.00 0.00 0.00 3.85
1992 2429 0.043485 AGGGAAAGGAGGAGGAGGTC 59.957 60.000 0.00 0.00 0.00 3.85
1993 2430 0.252742 GGGAAAGGAGGAGGAGGTCA 60.253 60.000 0.00 0.00 0.00 4.02
1994 2431 0.906066 GGAAAGGAGGAGGAGGTCAC 59.094 60.000 0.00 0.00 0.00 3.67
1995 2432 1.645710 GAAAGGAGGAGGAGGTCACA 58.354 55.000 0.00 0.00 0.00 3.58
1996 2433 1.552792 GAAAGGAGGAGGAGGTCACAG 59.447 57.143 0.00 0.00 0.00 3.66
1997 2434 0.489567 AAGGAGGAGGAGGTCACAGT 59.510 55.000 0.00 0.00 0.00 3.55
1998 2435 0.252012 AGGAGGAGGAGGTCACAGTG 60.252 60.000 0.00 0.00 0.00 3.66
1999 2436 1.261238 GGAGGAGGAGGTCACAGTGG 61.261 65.000 0.00 0.00 0.00 4.00
2000 2437 0.543174 GAGGAGGAGGTCACAGTGGT 60.543 60.000 0.00 0.00 0.00 4.16
2001 2438 0.833834 AGGAGGAGGTCACAGTGGTG 60.834 60.000 0.00 0.00 46.66 4.17
2291 2913 0.957395 CGTGGCAGGCAGAAGAATGT 60.957 55.000 0.00 0.00 0.00 2.71
2300 2922 1.268899 GCAGAAGAATGTTGTGCAGCT 59.731 47.619 7.37 0.00 38.41 4.24
2415 3040 2.042230 GAGGAGGAAGCCCCGGTA 60.042 66.667 0.00 0.00 40.87 4.02
2505 3130 2.120940 TCAGTAAGGGGCCGTGGA 59.879 61.111 0.00 0.00 0.00 4.02
2609 3234 1.347707 TGAGGACCTGCTTGTTTCGAT 59.652 47.619 0.00 0.00 0.00 3.59
2621 3246 3.829886 TGTTTCGATGACATTGAAGGC 57.170 42.857 16.01 13.69 34.33 4.35
2864 3489 0.753848 GAGAAGGACGAGGAGGAGGG 60.754 65.000 0.00 0.00 0.00 4.30
2906 3534 0.693049 AGGCGGAAGAAGAACATGGT 59.307 50.000 0.00 0.00 0.00 3.55
2910 3538 2.268298 CGGAAGAAGAACATGGTACCG 58.732 52.381 7.57 0.00 0.00 4.02
3090 3727 2.233431 CACAGTTCTTGAGGAGGAGGAG 59.767 54.545 0.00 0.00 0.00 3.69
3091 3728 1.830477 CAGTTCTTGAGGAGGAGGAGG 59.170 57.143 0.00 0.00 0.00 4.30
3092 3729 1.719378 AGTTCTTGAGGAGGAGGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
3093 3730 2.107366 GTTCTTGAGGAGGAGGAGGAG 58.893 57.143 0.00 0.00 0.00 3.69
3094 3731 0.633921 TCTTGAGGAGGAGGAGGAGG 59.366 60.000 0.00 0.00 0.00 4.30
3095 3732 0.398381 CTTGAGGAGGAGGAGGAGGG 60.398 65.000 0.00 0.00 0.00 4.30
3190 3827 1.228094 GGGGATAAGGCAGCAGCTC 60.228 63.158 0.00 0.00 41.70 4.09
3375 4012 0.038744 CCATGGAGCACCCTGAACTT 59.961 55.000 5.56 0.00 34.45 2.66
3433 4070 0.397816 GGAGAGGAAGAGGGCTGCTA 60.398 60.000 0.00 0.00 0.00 3.49
3474 4111 0.243636 GGAAAAAGGATGTGGTGGCG 59.756 55.000 0.00 0.00 0.00 5.69
3476 4113 1.184970 AAAAAGGATGTGGTGGCGGG 61.185 55.000 0.00 0.00 0.00 6.13
3495 4132 0.326618 GGATGAGGTCTGGAAGGGGA 60.327 60.000 0.00 0.00 0.00 4.81
3548 4185 5.420409 GAATAACGTTCCTCAGGAAGACAT 58.580 41.667 6.31 0.00 42.88 3.06
3561 4198 3.452627 AGGAAGACATCATGGTGGTAGAC 59.547 47.826 11.45 0.00 0.00 2.59
3629 4266 0.040425 GTTGTGACCGTGGTGAATGC 60.040 55.000 0.00 0.00 0.00 3.56
3751 4388 1.525077 GAACAGGGTGGTGCGAACA 60.525 57.895 0.00 0.00 0.00 3.18
3787 4424 0.397941 CAGTGCCCAGTCTTCTTCCA 59.602 55.000 0.00 0.00 0.00 3.53
3801 4438 1.566703 TCTTCCAACAACAAGGGTGGA 59.433 47.619 0.00 0.00 0.00 4.02
3802 4439 2.024846 TCTTCCAACAACAAGGGTGGAA 60.025 45.455 11.78 11.78 34.69 3.53
3804 4441 1.006043 TCCAACAACAAGGGTGGAACA 59.994 47.619 0.00 0.00 39.98 3.18
3909 4546 9.542462 TGCAAGTCAATGAGGTAATATAGTTAC 57.458 33.333 0.00 0.00 0.00 2.50
4058 4695 8.560374 ACTGCTTGCTAAGTTTAAGAGTTAAAG 58.440 33.333 0.00 0.00 35.91 1.85
4186 4823 1.742831 TGCATGTTTCGTTCCTATGCC 59.257 47.619 0.00 0.00 42.48 4.40
4209 4846 7.231317 TGCCTGATACAGAAGTTCAAGAAAAAT 59.769 33.333 5.50 0.00 32.44 1.82
4276 4913 8.635765 AAGATGCTTTGGTTGTTATTCTTCTA 57.364 30.769 0.00 0.00 0.00 2.10
4284 4921 8.950007 TTGGTTGTTATTCTTCTATCCCTTTT 57.050 30.769 0.00 0.00 0.00 2.27
4387 5024 3.580895 AGGTTGTTGTCACCTTGGTTTTT 59.419 39.130 0.00 0.00 0.00 1.94
4450 5090 5.785243 AGTCCTGTCTGCTACTTCTAAAAC 58.215 41.667 0.00 0.00 0.00 2.43
4534 5174 4.202245 TCATCCTTTTTCCCTACTCACG 57.798 45.455 0.00 0.00 0.00 4.35
4675 5315 4.510038 TTACTCGTTCAGTTACAGGACC 57.490 45.455 0.00 0.00 36.43 4.46
4691 5331 1.104630 GACCGACCTAGAGGGAACAG 58.895 60.000 0.00 0.00 40.27 3.16
4703 5343 1.494721 AGGGAACAGCAAAGACAGGAA 59.505 47.619 0.00 0.00 0.00 3.36
4712 5352 2.101415 GCAAAGACAGGAAACCAAAGCT 59.899 45.455 0.00 0.00 0.00 3.74
4742 5382 8.737168 AAGGATGAAATTCGATATTTGACTGA 57.263 30.769 9.35 0.00 0.00 3.41
4821 5461 9.055248 CGAATCTTTTCAGTGTATGATGAAAAC 57.945 33.333 8.57 0.71 45.59 2.43
4943 5583 5.072741 CAAGCCATGTTGCCCTAATATAGT 58.927 41.667 0.00 0.00 0.00 2.12
4957 5597 9.343539 GCCCTAATATAGTCTTTTGTCAGATTT 57.656 33.333 0.00 0.00 0.00 2.17
5028 5668 5.241949 CCTGGCTATAATACGAGACTTGAGT 59.758 44.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.804989 GAGGCTTCCAATCACAACGG 59.195 55.000 0.00 0.00 0.00 4.44
108 109 0.955919 GGCAACCGTCAAGGAAGAGG 60.956 60.000 0.00 0.00 45.00 3.69
124 125 0.112995 AAATGAGTTGGGCAGAGGCA 59.887 50.000 0.00 0.00 43.71 4.75
173 174 3.504273 TGCACACGCACACACCAC 61.504 61.111 0.00 0.00 45.36 4.16
184 185 3.004002 CACACATCCATATCCATGCACAC 59.996 47.826 0.00 0.00 0.00 3.82
193 194 7.552458 TCACATTTACACACACATCCATATC 57.448 36.000 0.00 0.00 0.00 1.63
229 236 4.519540 AAGCAAAACATCAAGCCGTTAT 57.480 36.364 0.00 0.00 0.00 1.89
233 240 2.221517 CCAAAAGCAAAACATCAAGCCG 59.778 45.455 0.00 0.00 0.00 5.52
273 280 1.995484 AGCATATATAGCAGCGCAACG 59.005 47.619 11.47 0.00 0.00 4.10
460 469 3.992643 TGAAAGTTGCAATTGACATGGG 58.007 40.909 10.34 0.00 0.00 4.00
524 533 4.091365 TGAACACGAAAACGATATGAGCAG 59.909 41.667 0.00 0.00 0.00 4.24
566 575 7.681939 ACCAATGTGAGTTATTTCGTATTGT 57.318 32.000 0.00 0.00 0.00 2.71
569 578 8.671028 GGTTAACCAATGTGAGTTATTTCGTAT 58.329 33.333 20.12 0.00 35.64 3.06
570 579 7.660617 TGGTTAACCAATGTGAGTTATTTCGTA 59.339 33.333 25.19 0.00 44.35 3.43
571 580 6.487331 TGGTTAACCAATGTGAGTTATTTCGT 59.513 34.615 25.19 0.00 44.35 3.85
572 581 6.904498 TGGTTAACCAATGTGAGTTATTTCG 58.096 36.000 25.19 0.00 44.35 3.46
627 636 6.466812 TGAGATTGTGACATGAGTTGTATGT 58.533 36.000 0.00 0.00 39.18 2.29
663 680 2.803956 TCGGCCGTTCAGTTCTTTTAAG 59.196 45.455 27.15 0.00 0.00 1.85
674 691 2.167693 AGAATACAGAATCGGCCGTTCA 59.832 45.455 29.35 14.08 0.00 3.18
675 692 2.540101 CAGAATACAGAATCGGCCGTTC 59.460 50.000 27.15 25.26 0.00 3.95
724 742 2.158813 TCCTTTTCAGCTCCACGTTCTT 60.159 45.455 0.00 0.00 0.00 2.52
729 747 0.955919 GGGTCCTTTTCAGCTCCACG 60.956 60.000 0.00 0.00 0.00 4.94
784 802 1.221840 CCATGTGCGAACTAGGGCT 59.778 57.895 0.00 0.00 0.00 5.19
799 818 1.009997 TTCTGGGATTTGGAGGCCAT 58.990 50.000 5.01 0.00 31.53 4.40
1602 1631 4.459089 GGCGCCTCCACAGTCTCC 62.459 72.222 22.15 0.00 34.01 3.71
1603 1632 3.363844 GAGGCGCCTCCACAGTCTC 62.364 68.421 40.99 17.67 37.11 3.36
1604 1633 3.386237 GAGGCGCCTCCACAGTCT 61.386 66.667 40.99 12.50 37.11 3.24
1622 1651 1.228894 TTCCTCTGCTCTCCACGGT 60.229 57.895 0.00 0.00 0.00 4.83
1967 2404 2.933825 TCCTCCTCCTTTCCCTTCTCTA 59.066 50.000 0.00 0.00 0.00 2.43
1976 2413 1.552792 CTGTGACCTCCTCCTCCTTTC 59.447 57.143 0.00 0.00 0.00 2.62
1977 2414 1.132689 ACTGTGACCTCCTCCTCCTTT 60.133 52.381 0.00 0.00 0.00 3.11
1978 2415 0.489567 ACTGTGACCTCCTCCTCCTT 59.510 55.000 0.00 0.00 0.00 3.36
1979 2416 0.252012 CACTGTGACCTCCTCCTCCT 60.252 60.000 0.32 0.00 0.00 3.69
1980 2417 1.261238 CCACTGTGACCTCCTCCTCC 61.261 65.000 9.86 0.00 0.00 4.30
1981 2418 0.543174 ACCACTGTGACCTCCTCCTC 60.543 60.000 9.86 0.00 0.00 3.71
1982 2419 0.833834 CACCACTGTGACCTCCTCCT 60.834 60.000 9.86 0.00 45.76 3.69
1983 2420 0.832135 TCACCACTGTGACCTCCTCC 60.832 60.000 9.86 0.00 46.40 4.30
1984 2421 2.746697 TCACCACTGTGACCTCCTC 58.253 57.895 9.86 0.00 46.40 3.71
2291 2913 1.228245 GGTTCAGGGAGCTGCACAA 60.228 57.895 7.79 0.00 0.00 3.33
2300 2922 2.415983 TTCCTTCTCTGGTTCAGGGA 57.584 50.000 0.00 0.00 39.45 4.20
2347 2972 0.957395 ACATTCTTCTGCCTGCCACG 60.957 55.000 0.00 0.00 0.00 4.94
2348 2973 1.068055 CAACATTCTTCTGCCTGCCAC 60.068 52.381 0.00 0.00 0.00 5.01
2352 2977 2.486982 CTCCACAACATTCTTCTGCCTG 59.513 50.000 0.00 0.00 0.00 4.85
2415 3040 1.071471 CCCTCTGCGGTTTGTCACT 59.929 57.895 0.00 0.00 0.00 3.41
2465 3090 1.097232 CATCTTCGGAGGCAATTGCA 58.903 50.000 30.32 8.07 44.36 4.08
2601 3226 3.189080 CAGCCTTCAATGTCATCGAAACA 59.811 43.478 6.48 6.48 0.00 2.83
2609 3234 2.715046 CCTTAGCAGCCTTCAATGTCA 58.285 47.619 0.00 0.00 0.00 3.58
2734 3359 3.181487 GCATTGGCACCATTATCGAAAGT 60.181 43.478 0.00 0.00 40.72 2.66
2864 3489 2.667318 CGACGTGTCACCACCATGC 61.667 63.158 0.00 0.00 38.41 4.06
2906 3534 1.207089 CCTTCTCTGGTTCATGCGGTA 59.793 52.381 0.00 0.00 0.00 4.02
2910 3538 3.055530 TCTCTTCCTTCTCTGGTTCATGC 60.056 47.826 0.00 0.00 0.00 4.06
2998 3626 2.012673 CTTTGGAGGCAGTGATACAGC 58.987 52.381 0.00 0.00 0.00 4.40
3190 3827 3.988976 TCTTTTGACCTCTCCATCCAG 57.011 47.619 0.00 0.00 0.00 3.86
3375 4012 2.158711 GGTGGCATCCTCATCATTCTCA 60.159 50.000 0.00 0.00 0.00 3.27
3413 4050 3.087666 GCAGCCCTCTTCCTCTCCG 62.088 68.421 0.00 0.00 0.00 4.63
3418 4055 0.327000 ACCATAGCAGCCCTCTTCCT 60.327 55.000 0.00 0.00 0.00 3.36
3433 4070 2.281484 AACACGGCGCTTCACCAT 60.281 55.556 6.90 0.00 0.00 3.55
3474 4111 1.348775 CCCTTCCAGACCTCATCCCC 61.349 65.000 0.00 0.00 0.00 4.81
3476 4113 0.326618 TCCCCTTCCAGACCTCATCC 60.327 60.000 0.00 0.00 0.00 3.51
3495 4132 0.473117 TCCTTCCAACCCTTCCTCGT 60.473 55.000 0.00 0.00 0.00 4.18
3538 4175 2.795231 ACCACCATGATGTCTTCCTG 57.205 50.000 0.00 0.00 0.00 3.86
3548 4185 4.715534 TTTTCCTTGTCTACCACCATGA 57.284 40.909 0.00 0.00 0.00 3.07
3561 4198 3.434299 GCACAGGCAATTCATTTTCCTTG 59.566 43.478 0.00 0.00 40.72 3.61
3597 4234 0.770499 TCACAACTGGCAGATTCCCA 59.230 50.000 23.66 0.00 0.00 4.37
3614 4251 2.358125 CCGCATTCACCACGGTCA 60.358 61.111 0.00 0.00 42.01 4.02
3629 4266 2.656002 TGACTTCTCTATCCTCACCCG 58.344 52.381 0.00 0.00 0.00 5.28
3710 4347 2.432874 TCCTCACTCTTGTTGTCGGAAA 59.567 45.455 0.00 0.00 0.00 3.13
3751 4388 3.556004 GCACTGGCAACTCTAGAAGAACT 60.556 47.826 0.00 0.00 40.72 3.01
3787 4424 3.118445 CCATTTGTTCCACCCTTGTTGTT 60.118 43.478 0.00 0.00 0.00 2.83
3801 4438 8.697507 AATCAACTCTAGAAGAACCATTTGTT 57.302 30.769 0.00 0.00 40.81 2.83
3802 4439 7.939039 TGAATCAACTCTAGAAGAACCATTTGT 59.061 33.333 0.00 0.00 0.00 2.83
3804 4441 7.609532 CCTGAATCAACTCTAGAAGAACCATTT 59.390 37.037 0.00 0.00 0.00 2.32
4058 4695 6.767902 ACCTATCCACACAATCATAACACATC 59.232 38.462 0.00 0.00 0.00 3.06
4387 5024 1.768275 TGCTTCAGTCAAACTCCCAGA 59.232 47.619 0.00 0.00 0.00 3.86
4450 5090 4.187694 GGAAGCAGACAGGACTATCTTTG 58.812 47.826 0.00 0.00 0.00 2.77
4534 5174 7.823149 AAAAGAACATAATGCATCTTGAAGC 57.177 32.000 13.96 4.78 30.44 3.86
4675 5315 0.895530 TTGCTGTTCCCTCTAGGTCG 59.104 55.000 0.00 0.00 36.75 4.79
4691 5331 2.101415 AGCTTTGGTTTCCTGTCTTTGC 59.899 45.455 0.00 0.00 0.00 3.68
4703 5343 4.657814 TCATCCTTCCTTAGCTTTGGTT 57.342 40.909 0.00 0.00 0.00 3.67
4712 5352 9.845740 TCAAATATCGAATTTCATCCTTCCTTA 57.154 29.630 0.00 0.00 0.00 2.69
4821 5461 3.058450 CAGTGAAGAGTGCAAGAGACAG 58.942 50.000 0.00 0.00 0.00 3.51
4957 5597 6.899393 ATGGCTTCACAATAAACAAGAGAA 57.101 33.333 0.00 0.00 0.00 2.87
4962 5602 9.814899 CCATAAATATGGCTTCACAATAAACAA 57.185 29.630 6.53 0.00 45.92 2.83


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

AutoCloner maintained by Alex Coulton.