Multiple sequence alignment - TraesCS2B01G175600

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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 TraesCS2B01G175600 chr2B 100.000 3942 0 0 1 3942 150711534 150707593 0.000000e+00 7280.0
1 TraesCS2B01G175600 chr2A 92.828 1980 89 20 1 1950 98137912 98135956 0.000000e+00 2820.0
2 TraesCS2B01G175600 chr2A 92.620 664 22 10 1948 2589 98135730 98135072 0.000000e+00 929.0
3 TraesCS2B01G175600 chr2A 94.970 497 18 1 3238 3727 98124857 98124361 0.000000e+00 773.0
4 TraesCS2B01G175600 chr2A 85.867 467 16 11 2762 3195 98127479 98127030 6.010000e-123 451.0
5 TraesCS2B01G175600 chr2A 93.074 231 6 3 3722 3942 98124323 98124093 2.940000e-86 329.0
6 TraesCS2B01G175600 chr2A 91.156 147 4 3 2637 2774 98135062 98134916 1.450000e-44 191.0
7 TraesCS2B01G175600 chr2D 93.709 1224 49 17 1 1209 99133467 99132257 0.000000e+00 1808.0
8 TraesCS2B01G175600 chr2D 90.765 1072 59 17 1540 2598 99131554 99130510 0.000000e+00 1395.0
9 TraesCS2B01G175600 chr2D 95.046 323 16 0 1261 1583 99131864 99131542 3.510000e-140 508.0
10 TraesCS2B01G175600 chr2D 93.833 227 5 1 3725 3942 99129367 99129141 2.270000e-87 333.0
11 TraesCS2B01G175600 chr2D 96.512 172 6 0 3556 3727 99129580 99129409 6.450000e-73 285.0
12 TraesCS2B01G175600 chr2D 84.691 307 16 12 3231 3529 99129862 99129579 1.080000e-70 278.0
13 TraesCS2B01G175600 chr2D 83.946 299 23 13 2637 2916 99130505 99130213 3.020000e-66 263.0
14 TraesCS2B01G175600 chr3D 92.893 788 19 15 1 788 284205170 284204420 0.000000e+00 1110.0
15 TraesCS2B01G175600 chr7B 91.117 788 33 14 1 788 29704330 29705080 0.000000e+00 1033.0
16 TraesCS2B01G175600 chr3B 93.986 582 21 8 207 788 245914580 245914013 0.000000e+00 869.0
17 TraesCS2B01G175600 chr3B 95.489 133 6 0 1 133 245921775 245921643 3.090000e-51 213.0
18 TraesCS2B01G175600 chr6A 99.194 124 1 0 2293 2416 24832741 24832864 1.430000e-54 224.0
19 TraesCS2B01G175600 chr6A 89.831 177 7 7 1018 1194 24832428 24832593 2.390000e-52 217.0
20 TraesCS2B01G175600 chr6A 91.156 147 4 3 2637 2774 24832959 24833105 1.450000e-44 191.0
21 TraesCS2B01G175600 chr6A 92.157 102 7 1 1403 1503 24832585 24832686 4.110000e-30 143.0
22 TraesCS2B01G175600 chr6A 95.506 89 3 1 2501 2589 24832862 24832949 1.480000e-29 141.0
23 TraesCS2B01G175600 chr6A 97.297 37 1 0 2042 2078 24832681 24832717 3.290000e-06 63.9
24 TraesCS2B01G175600 chr6A 100.000 28 0 0 2189 2216 24832715 24832742 7.000000e-03 52.8
25 TraesCS2B01G175600 chr5B 89.655 116 9 1 3582 3694 340322451 340322336 1.140000e-30 145.0
26 TraesCS2B01G175600 chr5D 91.228 57 4 1 2739 2794 284110145 284110089 4.220000e-10 76.8


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 TraesCS2B01G175600 chr2B 150707593 150711534 3941 True 7280.000000 7280 100.000000 1 3942 1 chr2B.!!$R1 3941
1 TraesCS2B01G175600 chr2A 98134916 98137912 2996 True 1313.333333 2820 92.201333 1 2774 3 chr2A.!!$R2 2773
2 TraesCS2B01G175600 chr2A 98124093 98127479 3386 True 517.666667 773 91.303667 2762 3942 3 chr2A.!!$R1 1180
3 TraesCS2B01G175600 chr2D 99129141 99133467 4326 True 695.714286 1808 91.214571 1 3942 7 chr2D.!!$R1 3941
4 TraesCS2B01G175600 chr3D 284204420 284205170 750 True 1110.000000 1110 92.893000 1 788 1 chr3D.!!$R1 787
5 TraesCS2B01G175600 chr7B 29704330 29705080 750 False 1033.000000 1033 91.117000 1 788 1 chr7B.!!$F1 787
6 TraesCS2B01G175600 chr3B 245914013 245914580 567 True 869.000000 869 93.986000 207 788 1 chr3B.!!$R1 581

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
399 400 0.874175 CGTTGCAGAGGAACACGTCA 60.874 55.0 2.49 0.0 0.0 4.35 F
1120 1149 0.045469 AGGAAGCAAGGGGGAGAGAT 59.955 55.0 0.00 0.0 0.0 2.75 F
1458 1832 0.106369 AGTCCCATCCCGATCGTGTA 60.106 55.0 15.09 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1270 0.108585 GATATTCGCAGGGGGAGCAA 59.891 55.0 0.0 0.0 0.0 3.91 R
2592 3265 0.261991 TGGATCGGAGGGAGTAGCTT 59.738 55.0 0.0 0.0 0.0 3.74 R
2950 3662 1.014352 ACAGTTGTGTTTCGTCAGGC 58.986 50.0 0.0 0.0 30.3 4.85 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
119 120 1.820010 ATGCAGTCTGGAGCGACACA 61.820 55.000 1.14 0.00 36.38 3.72
120 121 1.079543 GCAGTCTGGAGCGACACAT 60.080 57.895 1.14 0.00 36.38 3.21
399 400 0.874175 CGTTGCAGAGGAACACGTCA 60.874 55.000 2.49 0.00 0.00 4.35
923 944 2.746359 GGCGGATCCTGGATCTGG 59.254 66.667 35.10 26.37 43.46 3.86
1021 1049 4.237207 GCTGCGCCTACCCCCTAC 62.237 72.222 4.18 0.00 0.00 3.18
1022 1050 3.547513 CTGCGCCTACCCCCTACC 61.548 72.222 4.18 0.00 0.00 3.18
1027 1055 2.203596 CCTACCCCCTACCGCGAT 60.204 66.667 8.23 0.00 0.00 4.58
1107 1136 3.621394 GCGATCGCACGAGGAAGC 61.621 66.667 33.89 0.18 41.49 3.86
1113 1142 2.747855 GCACGAGGAAGCAAGGGG 60.748 66.667 0.00 0.00 0.00 4.79
1115 1144 2.203938 ACGAGGAAGCAAGGGGGA 60.204 61.111 0.00 0.00 0.00 4.81
1116 1145 2.294078 ACGAGGAAGCAAGGGGGAG 61.294 63.158 0.00 0.00 0.00 4.30
1117 1146 1.990060 CGAGGAAGCAAGGGGGAGA 60.990 63.158 0.00 0.00 0.00 3.71
1118 1147 1.911471 GAGGAAGCAAGGGGGAGAG 59.089 63.158 0.00 0.00 0.00 3.20
1119 1148 0.618968 GAGGAAGCAAGGGGGAGAGA 60.619 60.000 0.00 0.00 0.00 3.10
1120 1149 0.045469 AGGAAGCAAGGGGGAGAGAT 59.955 55.000 0.00 0.00 0.00 2.75
1121 1150 0.472044 GGAAGCAAGGGGGAGAGATC 59.528 60.000 0.00 0.00 0.00 2.75
1176 1205 2.441532 TTCGCTCCCTACTCCCGG 60.442 66.667 0.00 0.00 0.00 5.73
1231 1269 2.456840 CCCCCTTCCTCCCTGTCT 59.543 66.667 0.00 0.00 0.00 3.41
1232 1270 1.229984 CCCCCTTCCTCCCTGTCTT 60.230 63.158 0.00 0.00 0.00 3.01
1253 1293 1.768684 GCTCCCCCTGCGAATATCCA 61.769 60.000 0.00 0.00 0.00 3.41
1256 1296 0.537371 CCCCCTGCGAATATCCAACC 60.537 60.000 0.00 0.00 0.00 3.77
1258 1632 0.884704 CCCTGCGAATATCCAACCGG 60.885 60.000 0.00 0.00 0.00 5.28
1259 1633 1.507141 CCTGCGAATATCCAACCGGC 61.507 60.000 0.00 0.00 0.00 6.13
1380 1754 4.280677 TGCCAATCTCCGAAATTTGAGTTT 59.719 37.500 0.00 0.00 0.00 2.66
1382 1756 5.800438 GCCAATCTCCGAAATTTGAGTTTAC 59.200 40.000 0.00 0.00 0.00 2.01
1404 1778 8.654230 TTACATATGCTCTGAATCTTCTGTTC 57.346 34.615 1.58 0.00 0.00 3.18
1458 1832 0.106369 AGTCCCATCCCGATCGTGTA 60.106 55.000 15.09 0.00 0.00 2.90
1559 1934 5.276489 GGCATCATGATGTTTGTTATTTGCG 60.276 40.000 31.09 6.55 40.80 4.85
1780 2186 4.439700 CCATGCTAATTGCTCTTCCACAAG 60.440 45.833 0.00 0.00 43.37 3.16
1809 2215 7.425577 TCGTTGATATCAAAATGAGCATAGG 57.574 36.000 19.55 0.42 37.63 2.57
1811 2217 7.498900 TCGTTGATATCAAAATGAGCATAGGTT 59.501 33.333 19.55 0.00 37.63 3.50
1839 2245 8.950208 ATCTTAATGTAGTTCCTGAGCTTTAC 57.050 34.615 0.00 0.00 0.00 2.01
1844 2250 3.746045 AGTTCCTGAGCTTTACGTGAA 57.254 42.857 0.00 0.00 0.00 3.18
1879 2288 4.078537 TGGACATATATTTGGCATTCCCG 58.921 43.478 1.21 0.00 35.87 5.14
1880 2289 3.443681 GGACATATATTTGGCATTCCCGG 59.556 47.826 0.00 0.00 35.87 5.73
1885 2294 1.402107 ATTTGGCATTCCCGGGCATC 61.402 55.000 18.49 4.75 40.74 3.91
1896 2305 1.142870 CCCGGGCATCCAAGAGATTTA 59.857 52.381 8.08 0.00 30.59 1.40
1939 2355 5.894807 ACACTTTTTCCAGTTGAGTGAATG 58.105 37.500 8.60 0.00 39.97 2.67
2083 2730 6.817765 TCTTGTTTGAAGGATGGTATGTTC 57.182 37.500 0.00 0.00 0.00 3.18
2084 2731 5.710099 TCTTGTTTGAAGGATGGTATGTTCC 59.290 40.000 0.00 0.00 0.00 3.62
2085 2732 4.340617 TGTTTGAAGGATGGTATGTTCCC 58.659 43.478 0.00 0.00 32.05 3.97
2086 2733 4.044065 TGTTTGAAGGATGGTATGTTCCCT 59.956 41.667 0.00 0.00 32.05 4.20
2087 2734 3.931907 TGAAGGATGGTATGTTCCCTG 57.068 47.619 0.00 0.00 32.05 4.45
2128 2775 8.498358 CAGCCTTTGTTTTTCCTTTATCATTTC 58.502 33.333 0.00 0.00 0.00 2.17
2135 2782 4.963276 TTCCTTTATCATTTCGCACCTG 57.037 40.909 0.00 0.00 0.00 4.00
2175 2840 4.598807 ACTGATGGGATTATGGTATGCTCA 59.401 41.667 0.00 0.00 0.00 4.26
2463 3128 9.559732 TTCAAGAGAAAACATCAAGATCTACAA 57.440 29.630 0.00 0.00 0.00 2.41
2555 3222 4.655963 TCTCAGAACCCTTTTCTTCCATG 58.344 43.478 0.00 0.00 0.00 3.66
2589 3262 9.506042 TCCATTGTACTGTCCATATCCATATAT 57.494 33.333 0.00 0.00 0.00 0.86
2606 3279 7.232188 TCCATATATATAAGCTACTCCCTCCG 58.768 42.308 0.00 0.00 0.00 4.63
2607 3280 7.073343 TCCATATATATAAGCTACTCCCTCCGA 59.927 40.741 0.00 0.00 0.00 4.55
2608 3281 7.891183 CCATATATATAAGCTACTCCCTCCGAT 59.109 40.741 0.00 0.00 0.00 4.18
2609 3282 8.952278 CATATATATAAGCTACTCCCTCCGATC 58.048 40.741 0.00 0.00 0.00 3.69
2610 3283 2.289592 TAAGCTACTCCCTCCGATCC 57.710 55.000 0.00 0.00 0.00 3.36
2611 3284 0.261991 AAGCTACTCCCTCCGATCCA 59.738 55.000 0.00 0.00 0.00 3.41
2612 3285 0.485099 AGCTACTCCCTCCGATCCAT 59.515 55.000 0.00 0.00 0.00 3.41
2613 3286 1.711375 AGCTACTCCCTCCGATCCATA 59.289 52.381 0.00 0.00 0.00 2.74
2614 3287 1.819903 GCTACTCCCTCCGATCCATAC 59.180 57.143 0.00 0.00 0.00 2.39
2615 3288 2.818216 GCTACTCCCTCCGATCCATACA 60.818 54.545 0.00 0.00 0.00 2.29
2616 3289 1.705873 ACTCCCTCCGATCCATACAC 58.294 55.000 0.00 0.00 0.00 2.90
2617 3290 1.063190 ACTCCCTCCGATCCATACACA 60.063 52.381 0.00 0.00 0.00 3.72
2618 3291 2.251818 CTCCCTCCGATCCATACACAT 58.748 52.381 0.00 0.00 0.00 3.21
2619 3292 3.181422 ACTCCCTCCGATCCATACACATA 60.181 47.826 0.00 0.00 0.00 2.29
2620 3293 4.026744 CTCCCTCCGATCCATACACATAT 58.973 47.826 0.00 0.00 0.00 1.78
2621 3294 3.769300 TCCCTCCGATCCATACACATATG 59.231 47.826 0.00 0.00 38.38 1.78
2631 3304 4.128925 CATACACATATGGATCGGAGGG 57.871 50.000 7.80 0.00 35.45 4.30
2632 3305 2.398754 ACACATATGGATCGGAGGGA 57.601 50.000 7.80 0.00 0.00 4.20
2633 3306 2.251818 ACACATATGGATCGGAGGGAG 58.748 52.381 7.80 0.00 0.00 4.30
2634 3307 2.251818 CACATATGGATCGGAGGGAGT 58.748 52.381 7.80 0.00 0.00 3.85
2635 3308 3.181422 ACACATATGGATCGGAGGGAGTA 60.181 47.826 7.80 0.00 0.00 2.59
2649 3322 4.202212 GGAGGGAGTAAAGAGAAGATCTGC 60.202 50.000 0.00 0.00 38.67 4.26
2650 3323 4.357325 AGGGAGTAAAGAGAAGATCTGCA 58.643 43.478 2.79 0.00 38.67 4.41
2699 3372 1.474077 CTGCACTGAATAAAGGCACCC 59.526 52.381 0.00 0.00 0.00 4.61
2893 3586 4.119136 AGCATTGCAACCTGTACAAAAAC 58.881 39.130 11.91 0.00 0.00 2.43
2894 3587 4.119136 GCATTGCAACCTGTACAAAAACT 58.881 39.130 0.00 0.00 0.00 2.66
2895 3588 5.068460 AGCATTGCAACCTGTACAAAAACTA 59.932 36.000 11.91 0.00 0.00 2.24
2937 3649 5.102953 TGGCATTTCTAGAGCACTGTATT 57.897 39.130 4.99 0.00 0.00 1.89
3092 3822 3.171828 TTCTGGGAGCCGAAACGCA 62.172 57.895 0.00 0.00 0.00 5.24
3099 3829 4.084888 GCCGAAACGCAACTCCCG 62.085 66.667 0.00 0.00 0.00 5.14
3113 3843 0.099791 CTCCCGTTTGTTTGCGTGTT 59.900 50.000 0.00 0.00 0.00 3.32
3185 3956 2.425143 TCTTCATTCATGGACAGCCC 57.575 50.000 0.00 0.00 0.00 5.19
3197 3982 1.486726 GGACAGCCCTTACTACATGCT 59.513 52.381 0.00 0.00 0.00 3.79
3204 5488 4.884164 AGCCCTTACTACATGCTGAAAATC 59.116 41.667 0.00 0.00 0.00 2.17
3205 5489 4.640201 GCCCTTACTACATGCTGAAAATCA 59.360 41.667 0.00 0.00 0.00 2.57
3215 5499 9.371136 CTACATGCTGAAAATCAGTTTAGTAGA 57.629 33.333 16.88 0.00 45.94 2.59
3218 5502 6.173339 TGCTGAAAATCAGTTTAGTAGAGGG 58.827 40.000 8.97 0.00 45.94 4.30
3219 5503 5.065346 GCTGAAAATCAGTTTAGTAGAGGGC 59.935 44.000 8.97 0.00 45.94 5.19
3223 5507 5.606348 AATCAGTTTAGTAGAGGGCAGAG 57.394 43.478 0.00 0.00 0.00 3.35
3224 5508 2.761208 TCAGTTTAGTAGAGGGCAGAGC 59.239 50.000 0.00 0.00 0.00 4.09
3226 5510 3.055819 CAGTTTAGTAGAGGGCAGAGCAA 60.056 47.826 0.00 0.00 0.00 3.91
3227 5511 3.777522 AGTTTAGTAGAGGGCAGAGCAAT 59.222 43.478 0.00 0.00 0.00 3.56
3228 5512 4.123506 GTTTAGTAGAGGGCAGAGCAATC 58.876 47.826 0.00 0.00 0.00 2.67
3235 5526 1.842562 AGGGCAGAGCAATCTACACAT 59.157 47.619 0.00 0.00 0.00 3.21
3363 6278 1.470051 AAAAGGCGTGAACAAGGTGT 58.530 45.000 0.00 0.00 0.00 4.16
3375 6290 4.275689 TGAACAAGGTGTCAATCATCACAC 59.724 41.667 0.00 0.00 41.95 3.82
3421 6336 2.771372 TGATACCCAGCATCACTAGCAA 59.229 45.455 0.00 0.00 0.00 3.91
3433 6349 5.766222 CATCACTAGCAAAAGCAAGAACTT 58.234 37.500 0.00 0.00 0.00 2.66
3500 6423 2.579410 ACAAGACACCCCCAATGTAC 57.421 50.000 0.00 0.00 0.00 2.90
3629 6552 4.802563 CAGTATCTACACACAGCATGACAG 59.197 45.833 0.00 0.00 39.69 3.51
3798 6765 4.260990 CGTTGAACACCTTGAATAGCAACA 60.261 41.667 0.00 0.00 35.40 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1016 1044 1.227263 CAGGTTGATCGCGGTAGGG 60.227 63.158 6.13 0.00 0.00 3.53
1017 1045 0.527817 GTCAGGTTGATCGCGGTAGG 60.528 60.000 6.13 0.00 0.00 3.18
1018 1046 0.527817 GGTCAGGTTGATCGCGGTAG 60.528 60.000 6.13 0.00 0.00 3.18
1019 1047 1.514087 GGTCAGGTTGATCGCGGTA 59.486 57.895 6.13 0.00 0.00 4.02
1020 1048 2.264794 GGTCAGGTTGATCGCGGT 59.735 61.111 6.13 0.00 0.00 5.68
1021 1049 2.885644 CGGTCAGGTTGATCGCGG 60.886 66.667 6.13 0.00 44.44 6.46
1027 1055 4.329545 GCTGGCCGGTCAGGTTGA 62.330 66.667 35.68 0.00 43.70 3.18
1073 1102 2.325082 GCGCCGGACAAACACTGAT 61.325 57.895 5.05 0.00 0.00 2.90
1074 1103 2.970324 GCGCCGGACAAACACTGA 60.970 61.111 5.05 0.00 0.00 3.41
1075 1104 4.368808 CGCGCCGGACAAACACTG 62.369 66.667 5.05 0.00 0.00 3.66
1076 1105 3.876589 ATCGCGCCGGACAAACACT 62.877 57.895 5.05 0.00 0.00 3.55
1077 1106 3.362851 GATCGCGCCGGACAAACAC 62.363 63.158 5.05 0.00 0.00 3.32
1078 1107 3.115892 GATCGCGCCGGACAAACA 61.116 61.111 5.05 0.00 0.00 2.83
1079 1108 4.204891 CGATCGCGCCGGACAAAC 62.205 66.667 5.05 0.00 0.00 2.93
1107 1136 2.468301 TCTCTGATCTCTCCCCCTTG 57.532 55.000 0.00 0.00 0.00 3.61
1113 1142 2.821969 GCTCCTCATCTCTGATCTCTCC 59.178 54.545 0.00 0.00 0.00 3.71
1115 1144 3.493334 CTGCTCCTCATCTCTGATCTCT 58.507 50.000 0.00 0.00 0.00 3.10
1116 1145 2.029649 GCTGCTCCTCATCTCTGATCTC 60.030 54.545 0.00 0.00 0.00 2.75
1117 1146 1.965643 GCTGCTCCTCATCTCTGATCT 59.034 52.381 0.00 0.00 0.00 2.75
1118 1147 1.336148 CGCTGCTCCTCATCTCTGATC 60.336 57.143 0.00 0.00 0.00 2.92
1119 1148 0.675083 CGCTGCTCCTCATCTCTGAT 59.325 55.000 0.00 0.00 0.00 2.90
1120 1149 0.394899 TCGCTGCTCCTCATCTCTGA 60.395 55.000 0.00 0.00 0.00 3.27
1121 1150 0.031043 CTCGCTGCTCCTCATCTCTG 59.969 60.000 0.00 0.00 0.00 3.35
1229 1267 1.852157 ATTCGCAGGGGGAGCAAAGA 61.852 55.000 0.00 0.00 0.00 2.52
1231 1269 0.550914 ATATTCGCAGGGGGAGCAAA 59.449 50.000 0.00 0.00 0.00 3.68
1232 1270 0.108585 GATATTCGCAGGGGGAGCAA 59.891 55.000 0.00 0.00 0.00 3.91
1253 1293 2.579201 CTGAGATGACCGCCGGTT 59.421 61.111 11.54 0.00 35.25 4.44
1256 1296 3.133014 ATCCTGAGATGACCGCCG 58.867 61.111 0.00 0.00 0.00 6.46
1288 1662 1.617850 CGGAGCAAGATCTAGCCAGAT 59.382 52.381 0.00 0.00 44.51 2.90
1380 1754 7.147672 TGGAACAGAAGATTCAGAGCATATGTA 60.148 37.037 4.29 0.00 0.00 2.29
1382 1756 6.053650 TGGAACAGAAGATTCAGAGCATATG 58.946 40.000 0.00 0.00 0.00 1.78
1404 1778 0.464036 TATACGCAGCCTTCACCTGG 59.536 55.000 0.00 0.00 0.00 4.45
1458 1832 0.247736 GAGGCTTCTGATGTGTCGGT 59.752 55.000 0.00 0.00 32.33 4.69
1464 1838 1.627329 TCTGCTTGAGGCTTCTGATGT 59.373 47.619 0.00 0.00 42.39 3.06
1482 1856 4.464008 TGACCTGCTTGAATTTTGACTCT 58.536 39.130 0.00 0.00 0.00 3.24
1559 1934 5.705609 ATAACACCATGAACAAGGAACAC 57.294 39.130 3.07 0.00 0.00 3.32
1595 2000 9.464714 GATCAAGCTAAATACTCGTCTAATTGA 57.535 33.333 0.00 0.00 0.00 2.57
1780 2186 9.669353 ATGCTCATTTTGATATCAACGATTTAC 57.331 29.630 17.76 6.16 35.28 2.01
1809 2215 7.550906 AGCTCAGGAACTACATTAAGATCAAAC 59.449 37.037 0.00 0.00 36.02 2.93
1811 2217 7.187824 AGCTCAGGAACTACATTAAGATCAA 57.812 36.000 0.00 0.00 36.02 2.57
1839 2245 3.123621 GTCCATAAGCTGAACAGTTCACG 59.876 47.826 12.24 9.61 35.46 4.35
1844 2250 9.060347 CAAATATATGTCCATAAGCTGAACAGT 57.940 33.333 3.77 0.00 0.00 3.55
1879 2288 4.156455 TCACTAAATCTCTTGGATGCCC 57.844 45.455 0.00 0.00 34.45 5.36
1880 2289 6.705863 ATTTCACTAAATCTCTTGGATGCC 57.294 37.500 0.00 0.00 34.45 4.40
1885 2294 9.918630 ACATTCAAATTTCACTAAATCTCTTGG 57.081 29.630 0.00 0.00 34.12 3.61
1939 2355 7.471657 ACGGAAAACCACATTCAAATTTAAC 57.528 32.000 0.00 0.00 0.00 2.01
2027 2674 4.597079 ACTATCTGCAAAACACAAACACG 58.403 39.130 0.00 0.00 0.00 4.49
2083 2730 3.191371 GCTGGTTATCAAAGTGAACAGGG 59.809 47.826 0.00 0.00 0.00 4.45
2084 2731 3.191371 GGCTGGTTATCAAAGTGAACAGG 59.809 47.826 0.00 0.00 0.00 4.00
2085 2732 4.074970 AGGCTGGTTATCAAAGTGAACAG 58.925 43.478 0.00 0.00 0.00 3.16
2086 2733 4.098914 AGGCTGGTTATCAAAGTGAACA 57.901 40.909 0.00 0.00 0.00 3.18
2087 2734 5.221244 ACAAAGGCTGGTTATCAAAGTGAAC 60.221 40.000 0.00 0.00 0.00 3.18
2128 2775 0.387622 CCAATTGCAACTCAGGTGCG 60.388 55.000 10.90 0.00 0.00 5.34
2135 2782 4.305989 TCAGTCAAACCAATTGCAACTC 57.694 40.909 0.00 0.00 38.98 3.01
2350 3015 2.042979 TGAGCAGAAAGGGGGCTTTAAT 59.957 45.455 0.00 0.00 38.15 1.40
2437 3102 9.559732 TTGTAGATCTTGATGTTTTCTCTTGAA 57.440 29.630 0.00 0.00 0.00 2.69
2438 3103 9.730705 ATTGTAGATCTTGATGTTTTCTCTTGA 57.269 29.630 0.00 0.00 0.00 3.02
2463 3128 6.978674 ATGGATTTCTCAATCAGCAATGAT 57.021 33.333 0.00 0.00 40.77 2.45
2589 3262 3.332783 TGGATCGGAGGGAGTAGCTTATA 59.667 47.826 0.00 0.00 0.00 0.98
2590 3263 2.110188 TGGATCGGAGGGAGTAGCTTAT 59.890 50.000 0.00 0.00 0.00 1.73
2591 3264 1.497716 TGGATCGGAGGGAGTAGCTTA 59.502 52.381 0.00 0.00 0.00 3.09
2592 3265 0.261991 TGGATCGGAGGGAGTAGCTT 59.738 55.000 0.00 0.00 0.00 3.74
2594 3267 1.819903 GTATGGATCGGAGGGAGTAGC 59.180 57.143 0.00 0.00 0.00 3.58
2595 3268 2.820787 GTGTATGGATCGGAGGGAGTAG 59.179 54.545 0.00 0.00 0.00 2.57
2596 3269 2.176148 TGTGTATGGATCGGAGGGAGTA 59.824 50.000 0.00 0.00 0.00 2.59
2597 3270 1.063190 TGTGTATGGATCGGAGGGAGT 60.063 52.381 0.00 0.00 0.00 3.85
2598 3271 1.704641 TGTGTATGGATCGGAGGGAG 58.295 55.000 0.00 0.00 0.00 4.30
2599 3272 2.398754 ATGTGTATGGATCGGAGGGA 57.601 50.000 0.00 0.00 0.00 4.20
2600 3273 4.128925 CATATGTGTATGGATCGGAGGG 57.871 50.000 0.00 0.00 35.16 4.30
2610 3283 3.769300 TCCCTCCGATCCATATGTGTATG 59.231 47.826 1.24 0.00 37.93 2.39
2611 3284 4.026744 CTCCCTCCGATCCATATGTGTAT 58.973 47.826 1.24 0.00 0.00 2.29
2612 3285 3.181422 ACTCCCTCCGATCCATATGTGTA 60.181 47.826 1.24 0.00 0.00 2.90
2613 3286 2.251818 CTCCCTCCGATCCATATGTGT 58.748 52.381 1.24 0.00 0.00 3.72
2614 3287 2.251818 ACTCCCTCCGATCCATATGTG 58.748 52.381 1.24 0.00 0.00 3.21
2615 3288 2.704190 ACTCCCTCCGATCCATATGT 57.296 50.000 1.24 0.00 0.00 2.29
2616 3289 4.772624 TCTTTACTCCCTCCGATCCATATG 59.227 45.833 0.00 0.00 0.00 1.78
2617 3290 5.011982 TCTTTACTCCCTCCGATCCATAT 57.988 43.478 0.00 0.00 0.00 1.78
2618 3291 4.105858 TCTCTTTACTCCCTCCGATCCATA 59.894 45.833 0.00 0.00 0.00 2.74
2619 3292 3.117093 TCTCTTTACTCCCTCCGATCCAT 60.117 47.826 0.00 0.00 0.00 3.41
2620 3293 2.243994 TCTCTTTACTCCCTCCGATCCA 59.756 50.000 0.00 0.00 0.00 3.41
2621 3294 2.946785 TCTCTTTACTCCCTCCGATCC 58.053 52.381 0.00 0.00 0.00 3.36
2622 3295 4.208746 TCTTCTCTTTACTCCCTCCGATC 58.791 47.826 0.00 0.00 0.00 3.69
2623 3296 4.252570 TCTTCTCTTTACTCCCTCCGAT 57.747 45.455 0.00 0.00 0.00 4.18
2624 3297 3.733883 TCTTCTCTTTACTCCCTCCGA 57.266 47.619 0.00 0.00 0.00 4.55
2625 3298 4.037446 CAGATCTTCTCTTTACTCCCTCCG 59.963 50.000 0.00 0.00 29.16 4.63
2626 3299 4.202212 GCAGATCTTCTCTTTACTCCCTCC 60.202 50.000 0.00 0.00 29.16 4.30
2627 3300 4.404073 TGCAGATCTTCTCTTTACTCCCTC 59.596 45.833 0.00 0.00 29.16 4.30
2628 3301 4.357325 TGCAGATCTTCTCTTTACTCCCT 58.643 43.478 0.00 0.00 29.16 4.20
2629 3302 4.744795 TGCAGATCTTCTCTTTACTCCC 57.255 45.455 0.00 0.00 29.16 4.30
2630 3303 5.669477 ACATGCAGATCTTCTCTTTACTCC 58.331 41.667 0.00 0.00 29.16 3.85
2631 3304 6.456718 GCAACATGCAGATCTTCTCTTTACTC 60.457 42.308 0.00 0.00 44.26 2.59
2632 3305 5.353678 GCAACATGCAGATCTTCTCTTTACT 59.646 40.000 0.00 0.00 44.26 2.24
2633 3306 5.567552 GCAACATGCAGATCTTCTCTTTAC 58.432 41.667 0.00 0.00 44.26 2.01
2634 3307 5.808042 GCAACATGCAGATCTTCTCTTTA 57.192 39.130 0.00 0.00 44.26 1.85
2635 3308 4.698583 GCAACATGCAGATCTTCTCTTT 57.301 40.909 0.00 0.00 44.26 2.52
2699 3372 8.060090 GCATGTTCTTTTCTTTGAAATCACAAG 58.940 33.333 0.00 0.00 0.00 3.16
2842 3535 7.866898 GGCTTTCACCATAAAAATTTGCAAATT 59.133 29.630 27.73 27.73 40.15 1.82
2884 3577 9.685828 TTGGCACTCAATTATTAGTTTTTGTAC 57.314 29.630 0.00 0.00 0.00 2.90
2950 3662 1.014352 ACAGTTGTGTTTCGTCAGGC 58.986 50.000 0.00 0.00 30.30 4.85
3099 3829 5.622041 ACAATATACGAACACGCAAACAAAC 59.378 36.000 0.00 0.00 0.00 2.93
3113 3843 5.048921 GGATCTCCGAACTCACAATATACGA 60.049 44.000 0.00 0.00 0.00 3.43
3197 3982 6.013725 TCTGCCCTCTACTAAACTGATTTTCA 60.014 38.462 0.00 0.00 0.00 2.69
3198 5482 6.407202 TCTGCCCTCTACTAAACTGATTTTC 58.593 40.000 0.00 0.00 0.00 2.29
3204 5488 2.497675 TGCTCTGCCCTCTACTAAACTG 59.502 50.000 0.00 0.00 0.00 3.16
3205 5489 2.821437 TGCTCTGCCCTCTACTAAACT 58.179 47.619 0.00 0.00 0.00 2.66
3215 5499 1.279496 TGTGTAGATTGCTCTGCCCT 58.721 50.000 0.00 0.00 33.54 5.19
3218 5502 1.945394 CCCATGTGTAGATTGCTCTGC 59.055 52.381 0.00 0.00 34.93 4.26
3219 5503 3.272574 ACCCATGTGTAGATTGCTCTG 57.727 47.619 0.00 0.00 32.66 3.35
3223 5507 5.504010 CGATTTGTACCCATGTGTAGATTGC 60.504 44.000 0.00 0.00 0.00 3.56
3224 5508 5.584649 ACGATTTGTACCCATGTGTAGATTG 59.415 40.000 0.00 0.00 0.00 2.67
3226 5510 5.353394 ACGATTTGTACCCATGTGTAGAT 57.647 39.130 0.00 0.00 0.00 1.98
3227 5511 4.675933 CGACGATTTGTACCCATGTGTAGA 60.676 45.833 0.00 0.00 0.00 2.59
3228 5512 3.550275 CGACGATTTGTACCCATGTGTAG 59.450 47.826 0.00 0.00 0.00 2.74
3235 5526 3.731089 ACTTTTCGACGATTTGTACCCA 58.269 40.909 0.00 0.00 0.00 4.51
3340 6255 4.822896 ACACCTTGTTCACGCCTTTTATAA 59.177 37.500 0.00 0.00 0.00 0.98
3363 6278 1.811359 TGCATTGCGTGTGATGATTGA 59.189 42.857 3.84 0.00 0.00 2.57
3375 6290 2.987821 TGATGTTGTGAATTGCATTGCG 59.012 40.909 3.84 0.00 0.00 4.85
3812 6779 4.135153 CGAGCTAGCCTGCCGTGT 62.135 66.667 12.13 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.