Multiple sequence alignment - TraesCS1D01G178300

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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 TraesCS1D01G178300 chr1D 100.000 4667 0 0 1 4667 253200410 253195744 0.000000e+00 8619.0
1 TraesCS1D01G178300 chr1D 90.909 110 8 2 2766 2875 50875381 50875274 3.760000e-31 147.0
2 TraesCS1D01G178300 chr1D 98.077 52 1 0 15 66 253200344 253200293 1.790000e-14 91.6
3 TraesCS1D01G178300 chr1D 98.077 52 1 0 67 118 253200396 253200345 1.790000e-14 91.6
4 TraesCS1D01G178300 chr1A 93.686 2819 121 21 15 2792 325040696 325037894 0.000000e+00 4167.0
5 TraesCS1D01G178300 chr1A 88.377 912 73 16 2877 3761 325037892 325036987 0.000000e+00 1066.0
6 TraesCS1D01G178300 chr1A 93.067 375 22 3 3762 4135 325036941 325036570 3.180000e-151 545.0
7 TraesCS1D01G178300 chr1A 94.915 118 6 0 1 118 325040762 325040645 7.970000e-43 185.0
8 TraesCS1D01G178300 chr1A 98.876 89 1 0 2791 2879 373317583 373317671 4.830000e-35 159.0
9 TraesCS1D01G178300 chr1A 98.077 52 1 0 15 66 325040644 325040593 1.790000e-14 91.6
10 TraesCS1D01G178300 chr1B 94.243 2623 97 27 201 2789 359208725 359211327 0.000000e+00 3958.0
11 TraesCS1D01G178300 chr1B 91.510 907 57 9 2874 3761 359211329 359212234 0.000000e+00 1230.0
12 TraesCS1D01G178300 chr1B 88.314 522 52 4 4151 4664 593614702 593614182 6.630000e-173 617.0
13 TraesCS1D01G178300 chr1B 90.374 374 24 6 3762 4135 359212280 359212641 9.080000e-132 481.0
14 TraesCS1D01G178300 chr1B 90.367 218 7 1 1 204 359208208 359208425 1.650000e-69 274.0
15 TraesCS1D01G178300 chr1B 100.000 52 0 0 15 66 359208274 359208325 3.840000e-16 97.1
16 TraesCS1D01G178300 chr1B 98.077 52 1 0 67 118 359208222 359208273 1.790000e-14 91.6
17 TraesCS1D01G178300 chr2B 89.777 538 50 1 4135 4667 789130601 789130064 0.000000e+00 684.0
18 TraesCS1D01G178300 chr7B 89.758 537 49 2 4136 4667 3136941 3137476 0.000000e+00 682.0
19 TraesCS1D01G178300 chr7A 88.433 536 56 6 4135 4667 403362524 403361992 3.940000e-180 641.0
20 TraesCS1D01G178300 chr4D 86.328 512 60 8 4160 4667 65150192 65149687 2.450000e-152 549.0
21 TraesCS1D01G178300 chr4D 85.234 535 74 4 4136 4667 77293048 77292516 3.180000e-151 545.0
22 TraesCS1D01G178300 chr5D 84.730 537 74 7 4135 4667 450144323 450144855 8.890000e-147 531.0
23 TraesCS1D01G178300 chr3A 83.551 535 84 3 4135 4667 458937441 458937973 9.020000e-137 497.0
24 TraesCS1D01G178300 chr7D 83.488 539 77 10 4136 4667 299151090 299151623 4.200000e-135 492.0
25 TraesCS1D01G178300 chr7D 95.833 96 3 1 2782 2877 626381617 626381711 2.250000e-33 154.0
26 TraesCS1D01G178300 chr6D 100.000 89 0 0 2790 2878 461690206 461690118 1.040000e-36 165.0
27 TraesCS1D01G178300 chr6B 98.876 89 1 0 2790 2878 459601724 459601636 4.830000e-35 159.0
28 TraesCS1D01G178300 chr6A 95.833 96 2 2 2780 2875 287115458 287115365 2.250000e-33 154.0
29 TraesCS1D01G178300 chr2A 93.269 104 5 1 2791 2894 197673589 197673488 8.090000e-33 152.0
30 TraesCS1D01G178300 chr3D 93.204 103 4 3 2773 2875 224304766 224304667 1.050000e-31 148.0
31 TraesCS1D01G178300 chr5B 90.090 111 8 3 2787 2895 63462139 63462030 1.750000e-29 141.0


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 TraesCS1D01G178300 chr1D 253195744 253200410 4666 True 2934.066667 8619 98.718000 1 4667 3 chr1D.!!$R2 4666
1 TraesCS1D01G178300 chr1A 325036570 325040762 4192 True 1210.920000 4167 93.624400 1 4135 5 chr1A.!!$R1 4134
2 TraesCS1D01G178300 chr1B 359208208 359212641 4433 False 1021.950000 3958 94.095167 1 4135 6 chr1B.!!$F1 4134
3 TraesCS1D01G178300 chr1B 593614182 593614702 520 True 617.000000 617 88.314000 4151 4664 1 chr1B.!!$R1 513
4 TraesCS1D01G178300 chr2B 789130064 789130601 537 True 684.000000 684 89.777000 4135 4667 1 chr2B.!!$R1 532
5 TraesCS1D01G178300 chr7B 3136941 3137476 535 False 682.000000 682 89.758000 4136 4667 1 chr7B.!!$F1 531
6 TraesCS1D01G178300 chr7A 403361992 403362524 532 True 641.000000 641 88.433000 4135 4667 1 chr7A.!!$R1 532
7 TraesCS1D01G178300 chr4D 65149687 65150192 505 True 549.000000 549 86.328000 4160 4667 1 chr4D.!!$R1 507
8 TraesCS1D01G178300 chr4D 77292516 77293048 532 True 545.000000 545 85.234000 4136 4667 1 chr4D.!!$R2 531
9 TraesCS1D01G178300 chr5D 450144323 450144855 532 False 531.000000 531 84.730000 4135 4667 1 chr5D.!!$F1 532
10 TraesCS1D01G178300 chr3A 458937441 458937973 532 False 497.000000 497 83.551000 4135 4667 1 chr3A.!!$F1 532
11 TraesCS1D01G178300 chr7D 299151090 299151623 533 False 492.000000 492 83.488000 4136 4667 1 chr7D.!!$F1 531

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
864 1237 0.676782 GCACAACAGGCGTATTCCCT 60.677 55.000 0.0 0.0 0.00 4.20 F
957 1333 0.787084 TGGACAGACCTCTCCTTCCT 59.213 55.000 0.0 0.0 39.86 3.36 F
958 1334 1.150135 TGGACAGACCTCTCCTTCCTT 59.850 52.381 0.0 0.0 39.86 3.36 F
2114 2524 0.177141 TCCAAAGTCTATTCCCGCCG 59.823 55.000 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2254 1.331756 GTTTCATGCTATGGACGCCAG 59.668 52.381 4.90 0.0 36.75 4.85 R
2041 2449 1.371558 GAGAGACGGTTTGGGCTGT 59.628 57.895 0.00 0.0 0.00 4.40 R
2556 2968 2.158608 ACAGCCTAGACAAAGCAGGTTT 60.159 45.455 0.00 0.0 0.00 3.27 R
4060 4554 0.939106 GTGCACCTTTCGCGCATTTT 60.939 50.000 8.75 0.0 39.67 1.82 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
126 179 2.908688 AAACATGAAGGGTTTGGCAC 57.091 45.000 0.00 0.00 37.10 5.01
128 181 1.331214 ACATGAAGGGTTTGGCACAG 58.669 50.000 0.00 0.00 42.39 3.66
141 208 1.686052 TGGCACAGATTGACAAAACCC 59.314 47.619 0.00 0.00 41.91 4.11
144 211 3.244181 GGCACAGATTGACAAAACCCATT 60.244 43.478 0.00 0.00 30.77 3.16
321 691 7.755591 TCTCTTCAGATTTTGTGTATGCAATC 58.244 34.615 0.00 0.00 0.00 2.67
341 711 7.598118 TGCAATCAATAATCAACGTTGAAACAT 59.402 29.630 32.69 21.91 41.13 2.71
360 730 5.599999 ACATAATAAGCTCTTCCGTGACT 57.400 39.130 0.00 0.00 0.00 3.41
457 827 1.224592 CAACATCCGGAGAAGGGGG 59.775 63.158 11.34 0.00 0.00 5.40
724 1094 4.424711 TCTGTGGGAATGGCGGCC 62.425 66.667 13.32 13.32 0.00 6.13
793 1163 2.355837 GACTTGCGAGTGTGCCGA 60.356 61.111 12.53 0.00 35.88 5.54
843 1216 2.592194 TCTGATCGTGTGACGCTTAAC 58.408 47.619 0.00 0.00 42.21 2.01
857 1230 0.944386 CTTAACAGCACAACAGGCGT 59.056 50.000 0.00 0.00 36.08 5.68
864 1237 0.676782 GCACAACAGGCGTATTCCCT 60.677 55.000 0.00 0.00 0.00 4.20
866 1239 1.468520 CACAACAGGCGTATTCCCTTG 59.531 52.381 0.00 0.00 0.00 3.61
945 1321 3.005539 GCCTCCTGCCTGGACAGA 61.006 66.667 16.44 0.74 40.56 3.41
955 1331 1.190643 CCTGGACAGACCTCTCCTTC 58.809 60.000 0.00 0.00 39.86 3.46
956 1332 1.190643 CTGGACAGACCTCTCCTTCC 58.809 60.000 0.00 0.00 39.86 3.46
957 1333 0.787084 TGGACAGACCTCTCCTTCCT 59.213 55.000 0.00 0.00 39.86 3.36
958 1334 1.150135 TGGACAGACCTCTCCTTCCTT 59.850 52.381 0.00 0.00 39.86 3.36
1079 1459 1.672030 TCGTCGACTCCCGTAAGCA 60.672 57.895 14.70 0.00 39.75 3.91
1142 1530 2.710096 CTTCGGGAAGCCTAATCCAA 57.290 50.000 0.00 0.00 38.80 3.53
1144 1532 1.281419 TCGGGAAGCCTAATCCAACA 58.719 50.000 0.00 0.00 38.80 3.33
1505 1894 2.558359 AGATTTCCTTGTCTTTTGCCCG 59.442 45.455 0.00 0.00 0.00 6.13
1530 1919 8.119226 CGAAACATTAGATCTGAATCTGGTTTC 58.881 37.037 5.18 19.18 43.94 2.78
1531 1920 9.171877 GAAACATTAGATCTGAATCTGGTTTCT 57.828 33.333 20.39 7.66 43.96 2.52
1604 1994 6.374417 AAGAAAGGGCTTCATAGTTCAGTA 57.626 37.500 0.00 0.00 36.40 2.74
1701 2106 8.150945 TCACTGAGCTAAAAAGTCTAGACAATT 58.849 33.333 24.44 15.53 0.00 2.32
1755 2160 3.006967 GTCACAGGTCACTCCTTGTGTAT 59.993 47.826 3.82 0.00 45.67 2.29
1767 2172 5.105310 ACTCCTTGTGTATGACTAGCGAAAT 60.105 40.000 0.00 0.00 0.00 2.17
1790 2195 6.680874 TTAGGAGACTTCAGTACTTCGATC 57.319 41.667 0.00 0.00 43.67 3.69
1797 2202 6.375736 AGACTTCAGTACTTCGATCATTCTCA 59.624 38.462 0.00 0.00 0.00 3.27
1849 2254 8.718102 TTAGAGCCTTCAAGTTGTATATTGAC 57.282 34.615 2.11 0.00 35.25 3.18
1854 2259 5.220662 CCTTCAAGTTGTATATTGACTGGCG 60.221 44.000 2.11 0.00 35.25 5.69
1943 2350 5.122239 CGCTTCAAAGACAATCATGTTAGGA 59.878 40.000 0.00 0.00 40.74 2.94
2041 2449 6.064060 TGAGCTTCTGATCCTTTTTCTTGAA 58.936 36.000 0.00 0.00 0.00 2.69
2048 2456 3.025322 TCCTTTTTCTTGAACAGCCCA 57.975 42.857 0.00 0.00 0.00 5.36
2049 2457 3.370104 TCCTTTTTCTTGAACAGCCCAA 58.630 40.909 0.00 0.00 0.00 4.12
2073 2483 6.003234 ACCGTCTCTCGACATATTGAATAG 57.997 41.667 0.00 0.00 42.86 1.73
2103 2513 3.522343 AGGGGTTGTAGGTATCCAAAGTC 59.478 47.826 0.00 0.00 0.00 3.01
2106 2516 5.368816 GGGGTTGTAGGTATCCAAAGTCTAT 59.631 44.000 0.00 0.00 0.00 1.98
2114 2524 0.177141 TCCAAAGTCTATTCCCGCCG 59.823 55.000 0.00 0.00 0.00 6.46
2259 2670 5.526479 TGATTGCATTCTAGCTGATCTTGTC 59.474 40.000 9.81 0.00 32.66 3.18
2260 2671 4.476628 TGCATTCTAGCTGATCTTGTCA 57.523 40.909 0.00 0.00 34.99 3.58
2489 2901 4.899352 AGTTGTCTCATGTAAGGCTCTT 57.101 40.909 0.00 0.00 0.00 2.85
2556 2968 7.415592 TCTTCTTCAGCTTCATTGAGATAGA 57.584 36.000 0.00 0.00 0.00 1.98
2573 2985 5.983540 AGATAGAAACCTGCTTTGTCTAGG 58.016 41.667 0.00 0.00 37.61 3.02
2650 3068 5.718649 TGACAATTTATGCGCTAGACTTC 57.281 39.130 9.73 0.00 0.00 3.01
2718 3136 4.112634 ACAGTTGAGGGGAATTTAAGCA 57.887 40.909 0.00 0.00 0.00 3.91
2758 3177 6.858993 GCTACAAAGAAGATGTACTATCCTCG 59.141 42.308 0.00 0.00 32.27 4.63
2796 3215 9.372369 GAATGACTATATAAAGCATGTACTCCC 57.628 37.037 0.00 0.00 0.00 4.30
2797 3216 8.671987 ATGACTATATAAAGCATGTACTCCCT 57.328 34.615 0.00 0.00 0.00 4.20
2798 3217 8.123639 TGACTATATAAAGCATGTACTCCCTC 57.876 38.462 0.00 0.00 0.00 4.30
2799 3218 7.950684 TGACTATATAAAGCATGTACTCCCTCT 59.049 37.037 0.00 0.00 0.00 3.69
2800 3219 8.128322 ACTATATAAAGCATGTACTCCCTCTG 57.872 38.462 0.00 0.00 0.00 3.35
2801 3220 7.730784 ACTATATAAAGCATGTACTCCCTCTGT 59.269 37.037 0.00 0.00 0.00 3.41
2802 3221 9.244292 CTATATAAAGCATGTACTCCCTCTGTA 57.756 37.037 0.00 0.00 0.00 2.74
2803 3222 6.808321 ATAAAGCATGTACTCCCTCTGTAA 57.192 37.500 0.00 0.00 0.00 2.41
2804 3223 5.499004 AAAGCATGTACTCCCTCTGTAAA 57.501 39.130 0.00 0.00 0.00 2.01
2805 3224 4.473477 AGCATGTACTCCCTCTGTAAAC 57.527 45.455 0.00 0.00 0.00 2.01
2806 3225 4.097418 AGCATGTACTCCCTCTGTAAACT 58.903 43.478 0.00 0.00 0.00 2.66
2807 3226 5.269991 AGCATGTACTCCCTCTGTAAACTA 58.730 41.667 0.00 0.00 0.00 2.24
2808 3227 5.720041 AGCATGTACTCCCTCTGTAAACTAA 59.280 40.000 0.00 0.00 0.00 2.24
2809 3228 6.384305 AGCATGTACTCCCTCTGTAAACTAAT 59.616 38.462 0.00 0.00 0.00 1.73
2810 3229 7.563924 AGCATGTACTCCCTCTGTAAACTAATA 59.436 37.037 0.00 0.00 0.00 0.98
2811 3230 8.368668 GCATGTACTCCCTCTGTAAACTAATAT 58.631 37.037 0.00 0.00 0.00 1.28
2817 3236 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2819 3238 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2869 3288 9.688592 AAACGATCTTATATTAGTTTACGGAGG 57.311 33.333 0.00 0.00 31.14 4.30
2870 3289 7.824672 ACGATCTTATATTAGTTTACGGAGGG 58.175 38.462 0.00 0.00 0.00 4.30
2871 3290 7.667219 ACGATCTTATATTAGTTTACGGAGGGA 59.333 37.037 0.00 0.00 0.00 4.20
2872 3291 8.182881 CGATCTTATATTAGTTTACGGAGGGAG 58.817 40.741 0.00 0.00 0.00 4.30
2875 3294 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2920 3339 8.040132 AGAAGTTTGATAATCAGGTGAGAAGAG 58.960 37.037 0.00 0.00 0.00 2.85
2935 3354 8.007742 AGGTGAGAAGAGAATTAGGCTTATCTA 58.992 37.037 0.00 0.00 32.66 1.98
2954 3374 5.779806 TCTAGCAGAAGAAAAATACGTGC 57.220 39.130 0.00 0.00 0.00 5.34
2960 3380 6.017440 AGCAGAAGAAAAATACGTGCAAGTAA 60.017 34.615 16.44 0.87 31.75 2.24
2970 3390 7.690952 AATACGTGCAAGTAATTCCCTTTTA 57.309 32.000 16.44 0.00 0.00 1.52
2977 3397 7.542130 GTGCAAGTAATTCCCTTTTATGTTGAG 59.458 37.037 0.00 0.00 0.00 3.02
3117 3551 5.591643 ATTAACAATAATACAGGCGCTCG 57.408 39.130 7.64 0.23 29.85 5.03
3120 3554 1.070577 CAATAATACAGGCGCTCGCAC 60.071 52.381 16.36 5.70 44.11 5.34
3121 3555 0.939577 ATAATACAGGCGCTCGCACG 60.940 55.000 16.36 8.42 44.11 5.34
3157 3591 4.524316 TTCCATTCTTTGCCATCTGTTG 57.476 40.909 0.00 0.00 0.00 3.33
3279 3727 5.904362 ATTATGCTTTCACTTCACTTCCC 57.096 39.130 0.00 0.00 0.00 3.97
3353 3801 0.670162 ATTTGCTGCACGACTTTGCT 59.330 45.000 0.00 0.00 43.41 3.91
3404 3852 6.549736 TCTTCCTCCAGAATACGAATACATCA 59.450 38.462 0.00 0.00 32.82 3.07
3448 3896 3.994392 TCTAGATCACGAAGCAAAACACC 59.006 43.478 0.00 0.00 0.00 4.16
3453 3901 1.092921 ACGAAGCAAAACACCGCAGA 61.093 50.000 0.00 0.00 0.00 4.26
3457 3905 0.593128 AGCAAAACACCGCAGACATC 59.407 50.000 0.00 0.00 0.00 3.06
3469 3917 2.931969 CGCAGACATCACAAGCTATGAA 59.068 45.455 4.80 0.00 0.00 2.57
3511 3959 5.932303 TGTTGCACTTGGTAAGTTCTAGATC 59.068 40.000 0.00 0.00 40.46 2.75
3512 3960 5.738619 TGCACTTGGTAAGTTCTAGATCA 57.261 39.130 3.70 0.00 40.46 2.92
3514 3962 4.870991 GCACTTGGTAAGTTCTAGATCACC 59.129 45.833 3.70 3.96 40.46 4.02
3530 3978 6.332976 AGATCACCCCTTTTATCTGTTGAT 57.667 37.500 0.00 0.00 36.74 2.57
3584 4032 2.238521 TCACCCTTCATTGCTTTGGTC 58.761 47.619 0.00 0.00 0.00 4.02
3627 4075 2.047274 ATCGCGACAACCACCAGG 60.047 61.111 12.93 0.00 42.21 4.45
3731 4179 1.403249 CGACCGAGTTTTCATACCCGT 60.403 52.381 0.00 0.00 0.00 5.28
3735 4183 2.613474 CCGAGTTTTCATACCCGTTGGA 60.613 50.000 0.00 0.00 34.81 3.53
3765 4258 6.026947 TGCTGTAGACCTCTAAAGAGTTTC 57.973 41.667 6.27 2.71 40.48 2.78
3837 4330 7.095899 GCTGAAAGGCTAATTGAAGAACTTTTG 60.096 37.037 0.00 0.00 30.35 2.44
3977 4471 4.337274 TGGATGATTCTGAATGTGACATGC 59.663 41.667 7.78 10.28 0.00 4.06
4005 4499 1.810853 GCCCATTCATTGCGTTGCC 60.811 57.895 0.00 0.00 0.00 4.52
4060 4554 5.418840 GGAAAGTGGAATTATTGCTTGGAGA 59.581 40.000 0.00 0.00 0.00 3.71
4069 4563 0.387112 TTGCTTGGAGAAAATGCGCG 60.387 50.000 0.00 0.00 0.00 6.86
4070 4564 1.233950 TGCTTGGAGAAAATGCGCGA 61.234 50.000 12.10 0.00 0.00 5.87
4071 4565 0.109781 GCTTGGAGAAAATGCGCGAA 60.110 50.000 12.10 0.00 0.00 4.70
4075 4569 0.521735 GGAGAAAATGCGCGAAAGGT 59.478 50.000 12.10 0.00 0.00 3.50
4114 4608 1.867233 GCAAGTTCTTGCTCTCGACAA 59.133 47.619 24.49 0.00 44.15 3.18
4117 4611 3.019933 AGTTCTTGCTCTCGACAACTC 57.980 47.619 0.00 0.00 0.00 3.01
4123 4617 1.654954 GCTCTCGACAACTCGCCCTA 61.655 60.000 0.00 0.00 39.96 3.53
4288 4790 4.368969 TCTATCGCTACTCCTATCCCCTA 58.631 47.826 0.00 0.00 0.00 3.53
4353 4855 6.248433 ACATCACACCAAATCCTAACATCTT 58.752 36.000 0.00 0.00 0.00 2.40
4399 4904 1.183030 TACCTGGACTGGGTCACACG 61.183 60.000 0.00 0.00 38.19 4.49
4448 4953 2.893398 GCCGTCTTCCACCGATCT 59.107 61.111 0.00 0.00 0.00 2.75
4449 4954 1.519455 GCCGTCTTCCACCGATCTG 60.519 63.158 0.00 0.00 0.00 2.90
4568 5073 4.736896 GCCCGTCGCCGAAACTCT 62.737 66.667 0.00 0.00 35.63 3.24
4638 5145 2.364448 GCTCCTCCTCGTCCCCTT 60.364 66.667 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.158842 TGCCATGGTTTTTGTTGGGAAG 60.159 45.455 14.67 0.00 0.00 3.46
79 132 7.116075 AGCTTGATACAAATTAATGCCATGT 57.884 32.000 0.00 0.00 0.00 3.21
126 179 7.877097 TGGAAATTAATGGGTTTTGTCAATCTG 59.123 33.333 0.00 0.00 0.00 2.90
128 181 7.877612 ACTGGAAATTAATGGGTTTTGTCAATC 59.122 33.333 0.00 0.00 0.00 2.67
141 208 5.577945 AGCGAATTTGCACTGGAAATTAATG 59.422 36.000 19.82 13.07 34.00 1.90
144 211 4.782019 AGCGAATTTGCACTGGAAATTA 57.218 36.364 19.82 0.00 34.00 1.40
341 711 4.288670 CGAGTCACGGAAGAGCTTATTA 57.711 45.455 0.00 0.00 38.46 0.98
360 730 4.002906 AGATTCTGCTTGTTTGGTACGA 57.997 40.909 0.00 0.00 0.00 3.43
531 901 3.933722 CCATCCTCCGCCGCATCT 61.934 66.667 0.00 0.00 0.00 2.90
704 1074 1.528824 CCGCCATTCCCACAGAGAT 59.471 57.895 0.00 0.00 0.00 2.75
759 1129 3.345808 CGCAACCACCTGTCCACG 61.346 66.667 0.00 0.00 0.00 4.94
793 1163 3.785189 AACACGACGGCGCAGTCTT 62.785 57.895 32.37 23.95 42.48 3.01
843 1216 0.447801 GGAATACGCCTGTTGTGCTG 59.552 55.000 0.00 0.00 0.00 4.41
849 1222 2.579410 AACAAGGGAATACGCCTGTT 57.421 45.000 0.00 0.00 0.00 3.16
850 1223 2.579410 AAACAAGGGAATACGCCTGT 57.421 45.000 0.00 0.00 0.00 4.00
857 1230 3.680937 CAGACGCGTAAAACAAGGGAATA 59.319 43.478 13.97 0.00 0.00 1.75
864 1237 2.008329 ACCAACAGACGCGTAAAACAA 58.992 42.857 13.97 0.00 0.00 2.83
866 1239 3.490526 TCTTACCAACAGACGCGTAAAAC 59.509 43.478 13.97 0.00 0.00 2.43
945 1321 1.306226 CGGGGAAGGAAGGAGAGGT 60.306 63.158 0.00 0.00 0.00 3.85
1079 1459 1.229177 GGGTTTTGGGGTGCTGGAT 60.229 57.895 0.00 0.00 0.00 3.41
1086 1466 1.384783 GGGTTTGGGGTTTTGGGGT 60.385 57.895 0.00 0.00 0.00 4.95
1142 1530 1.199097 GAATCGCGGATGTTTTGGTGT 59.801 47.619 6.13 0.00 0.00 4.16
1144 1532 1.737793 GAGAATCGCGGATGTTTTGGT 59.262 47.619 6.13 0.00 0.00 3.67
1257 1645 1.524355 CGCAGCGATGACAAGGATTAG 59.476 52.381 9.98 0.00 0.00 1.73
1505 1894 9.171877 AGAAACCAGATTCAGATCTAATGTTTC 57.828 33.333 18.53 18.53 43.85 2.78
1530 1919 4.944962 TCTCATGGCGATTTTGTTACAG 57.055 40.909 0.00 0.00 0.00 2.74
1531 1920 4.335315 GGATCTCATGGCGATTTTGTTACA 59.665 41.667 0.00 0.00 0.00 2.41
1701 2106 2.816087 GACTTGGCAATGCTTTCTCTGA 59.184 45.455 4.82 0.00 0.00 3.27
1755 2160 5.417894 TGAAGTCTCCTAATTTCGCTAGTCA 59.582 40.000 0.00 0.00 0.00 3.41
1767 2172 6.178324 TGATCGAAGTACTGAAGTCTCCTAA 58.822 40.000 0.00 0.00 0.00 2.69
1790 2195 8.298854 TCATGAGTTAAAACAACCATGAGAATG 58.701 33.333 15.31 0.00 37.46 2.67
1797 2202 6.568462 CGAAGCTCATGAGTTAAAACAACCAT 60.568 38.462 23.38 0.00 0.00 3.55
1849 2254 1.331756 GTTTCATGCTATGGACGCCAG 59.668 52.381 4.90 0.00 36.75 4.85
1854 2259 2.952310 GGAAGGGTTTCATGCTATGGAC 59.048 50.000 0.00 0.00 34.90 4.02
1892 2298 2.895404 GTGGAACTGTGGGAGTAGTACA 59.105 50.000 2.52 0.00 33.09 2.90
1943 2350 8.504005 GTGCTGTAAACAGTCATACTTGTTTAT 58.496 33.333 11.54 0.00 45.45 1.40
2041 2449 1.371558 GAGAGACGGTTTGGGCTGT 59.628 57.895 0.00 0.00 0.00 4.40
2073 2483 6.043938 TGGATACCTACAACCCCTTAATCATC 59.956 42.308 0.00 0.00 0.00 2.92
2172 2583 4.329545 GCCCCACTGCGGAGAACA 62.330 66.667 12.26 0.00 36.56 3.18
2259 2670 4.157105 TGATCAGCTCAAACACCATCATTG 59.843 41.667 0.00 0.00 0.00 2.82
2260 2671 4.338012 TGATCAGCTCAAACACCATCATT 58.662 39.130 0.00 0.00 0.00 2.57
2455 2867 8.846943 ACATGAGACAACTTCACACATATTAA 57.153 30.769 0.00 0.00 0.00 1.40
2489 2901 4.700213 GGTACTTAAGCATGCCAAAGAAGA 59.300 41.667 27.45 14.27 0.00 2.87
2556 2968 2.158608 ACAGCCTAGACAAAGCAGGTTT 60.159 45.455 0.00 0.00 0.00 3.27
2573 2985 5.638234 CCTACAAACTACAAGGAGTAACAGC 59.362 44.000 0.00 0.00 30.92 4.40
2650 3068 7.250569 ACGTTTCTGCTACATATTTTGGATTG 58.749 34.615 0.00 0.00 0.00 2.67
2718 3136 7.692460 TCTTTGTAGCTGAATCATCACAAAT 57.308 32.000 13.68 0.00 31.45 2.32
2791 3210 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
2793 3212 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2843 3262 9.688592 CCTCCGTAAACTAATATAAGATCGTTT 57.311 33.333 0.00 0.00 0.00 3.60
2844 3263 8.302438 CCCTCCGTAAACTAATATAAGATCGTT 58.698 37.037 0.00 0.00 0.00 3.85
2845 3264 7.667219 TCCCTCCGTAAACTAATATAAGATCGT 59.333 37.037 0.00 0.00 0.00 3.73
2846 3265 8.048534 TCCCTCCGTAAACTAATATAAGATCG 57.951 38.462 0.00 0.00 0.00 3.69
2847 3266 9.022884 ACTCCCTCCGTAAACTAATATAAGATC 57.977 37.037 0.00 0.00 0.00 2.75
2848 3267 8.953223 ACTCCCTCCGTAAACTAATATAAGAT 57.047 34.615 0.00 0.00 0.00 2.40
2849 3268 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2850 3269 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2851 3270 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2853 3272 9.592196 TTATGTACTCCCTCCGTAAACTAATAT 57.408 33.333 0.00 0.00 0.00 1.28
2854 3273 8.850156 GTTATGTACTCCCTCCGTAAACTAATA 58.150 37.037 0.00 0.00 0.00 0.98
2855 3274 7.342799 TGTTATGTACTCCCTCCGTAAACTAAT 59.657 37.037 0.00 0.00 0.00 1.73
2856 3275 6.663093 TGTTATGTACTCCCTCCGTAAACTAA 59.337 38.462 0.00 0.00 0.00 2.24
2857 3276 6.186957 TGTTATGTACTCCCTCCGTAAACTA 58.813 40.000 0.00 0.00 0.00 2.24
2858 3277 5.018809 TGTTATGTACTCCCTCCGTAAACT 58.981 41.667 0.00 0.00 0.00 2.66
2859 3278 5.329035 TGTTATGTACTCCCTCCGTAAAC 57.671 43.478 0.00 0.00 0.00 2.01
2860 3279 5.657745 TGATGTTATGTACTCCCTCCGTAAA 59.342 40.000 0.00 0.00 0.00 2.01
2861 3280 5.202765 TGATGTTATGTACTCCCTCCGTAA 58.797 41.667 0.00 0.00 0.00 3.18
2862 3281 4.795469 TGATGTTATGTACTCCCTCCGTA 58.205 43.478 0.00 0.00 0.00 4.02
2863 3282 3.637229 CTGATGTTATGTACTCCCTCCGT 59.363 47.826 0.00 0.00 0.00 4.69
2864 3283 3.553096 GCTGATGTTATGTACTCCCTCCG 60.553 52.174 0.00 0.00 0.00 4.63
2865 3284 3.388024 TGCTGATGTTATGTACTCCCTCC 59.612 47.826 0.00 0.00 0.00 4.30
2866 3285 4.342378 TCTGCTGATGTTATGTACTCCCTC 59.658 45.833 0.00 0.00 0.00 4.30
2867 3286 4.290093 TCTGCTGATGTTATGTACTCCCT 58.710 43.478 0.00 0.00 0.00 4.20
2868 3287 4.672587 TCTGCTGATGTTATGTACTCCC 57.327 45.455 0.00 0.00 0.00 4.30
2869 3288 6.763135 TCAAATCTGCTGATGTTATGTACTCC 59.237 38.462 6.88 0.00 32.44 3.85
2870 3289 7.708322 TCTCAAATCTGCTGATGTTATGTACTC 59.292 37.037 6.88 0.00 32.44 2.59
2871 3290 7.559486 TCTCAAATCTGCTGATGTTATGTACT 58.441 34.615 6.88 0.00 32.44 2.73
2872 3291 7.776933 TCTCAAATCTGCTGATGTTATGTAC 57.223 36.000 6.88 0.00 32.44 2.90
2875 3294 7.317842 ACTTCTCAAATCTGCTGATGTTATG 57.682 36.000 6.88 5.04 32.44 1.90
2935 3354 4.275936 ACTTGCACGTATTTTTCTTCTGCT 59.724 37.500 0.00 0.00 0.00 4.24
2951 3370 7.375053 TCAACATAAAAGGGAATTACTTGCAC 58.625 34.615 0.00 0.00 0.00 4.57
2960 3380 9.093458 ACATCTTTTCTCAACATAAAAGGGAAT 57.907 29.630 7.48 0.00 41.12 3.01
2970 3390 9.911788 ATCCTACATAACATCTTTTCTCAACAT 57.088 29.630 0.00 0.00 0.00 2.71
3097 3531 2.798283 GCGAGCGCCTGTATTATTGTTA 59.202 45.455 2.29 0.00 34.56 2.41
3117 3551 2.869233 AATGCCAAATGGATACGTGC 57.131 45.000 2.98 0.00 42.51 5.34
3157 3591 9.213799 AGATCTAAATGACAAGAAAAGACAGTC 57.786 33.333 0.00 0.00 0.00 3.51
3230 3678 2.797156 CCTTGATGATTCGGAGTTAGCG 59.203 50.000 0.00 0.00 0.00 4.26
3279 3727 5.177725 TGCATTGACTATATTGCTGCAAG 57.822 39.130 20.72 9.28 35.42 4.01
3404 3852 7.881775 AGAAAGAACCGGATGCTAATTAATT 57.118 32.000 9.46 5.89 0.00 1.40
3448 3896 2.543641 TCATAGCTTGTGATGTCTGCG 58.456 47.619 0.00 0.00 0.00 5.18
3453 3901 5.643348 TCGAACATTTCATAGCTTGTGATGT 59.357 36.000 0.00 0.00 35.19 3.06
3457 3905 5.735892 CACATCGAACATTTCATAGCTTGTG 59.264 40.000 0.00 0.00 0.00 3.33
3469 3917 1.270625 ACACGGACCACATCGAACATT 60.271 47.619 0.00 0.00 0.00 2.71
3511 3959 5.009631 TGTCATCAACAGATAAAAGGGGTG 58.990 41.667 0.00 0.00 32.81 4.61
3512 3960 5.255397 TGTCATCAACAGATAAAAGGGGT 57.745 39.130 0.00 0.00 32.81 4.95
3530 3978 6.093357 TGAAGTTAGCATCGCATATTTTGTCA 59.907 34.615 0.00 0.00 0.00 3.58
3584 4032 2.223928 CCAATTGGAGCAGGACACCTG 61.224 57.143 20.50 12.78 45.65 4.00
3627 4075 1.200948 GGAGACATGTTTTGCAGGAGC 59.799 52.381 0.00 0.00 42.57 4.70
3676 4124 5.350504 ACTGATAGAGCACAGCTACAATT 57.649 39.130 0.00 0.00 39.88 2.32
3731 4179 3.266772 AGGTCTACAGCATTCCATTCCAA 59.733 43.478 0.00 0.00 0.00 3.53
3735 4183 5.957771 TTAGAGGTCTACAGCATTCCATT 57.042 39.130 0.00 0.00 0.00 3.16
3765 4258 2.430332 CAGAGAACAGAAGAGGGGCTAG 59.570 54.545 0.00 0.00 0.00 3.42
3859 4353 9.072294 GCACCATAAACATTTATAGAAACACAC 57.928 33.333 0.00 0.00 32.39 3.82
3977 4471 3.928375 GCAATGAATGGGCAAGTTAGTTG 59.072 43.478 0.00 0.00 39.41 3.16
4005 4499 4.272489 TCTAATCCACAGGGCATGAAAAG 58.728 43.478 5.99 0.00 0.00 2.27
4060 4554 0.939106 GTGCACCTTTCGCGCATTTT 60.939 50.000 8.75 0.00 39.67 1.82
4069 4563 2.890941 GCAAGCAAGTGCACCTTTC 58.109 52.632 14.63 0.49 44.29 2.62
4111 4605 3.243434 CGATGAATACTAGGGCGAGTTGT 60.243 47.826 0.00 0.00 0.00 3.32
4114 4608 2.584236 ACGATGAATACTAGGGCGAGT 58.416 47.619 0.00 0.00 0.00 4.18
4158 4653 2.042537 AGATGCAGAGGCCGAGGA 60.043 61.111 0.00 0.00 40.13 3.71
4224 4721 3.451178 TCAGGCTTAGTGATGTACTTCCC 59.549 47.826 6.32 0.00 40.89 3.97
4266 4768 3.191273 AGGGGATAGGAGTAGCGATAGA 58.809 50.000 0.00 0.00 39.76 1.98
4269 4771 3.191273 TCTAGGGGATAGGAGTAGCGAT 58.809 50.000 0.00 0.00 31.83 4.58
4288 4790 3.383825 GGACATTCGGTACCACTACATCT 59.616 47.826 13.54 0.00 0.00 2.90
4448 4953 2.423892 GTCAGTATTCGCTCTGGAGACA 59.576 50.000 1.35 0.00 39.59 3.41
4449 4954 2.539953 CGTCAGTATTCGCTCTGGAGAC 60.540 54.545 1.35 0.00 33.13 3.36
4607 5112 2.093658 GGAGGAGCGGTGTTTCATCTAA 60.094 50.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.