Multiple sequence alignment - TraesCS1A01G064100

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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 TraesCS1A01G064100 chr1A 100.000 5224 0 0 1 5224 45793233 45798456 0.000000e+00 9648.0
1 TraesCS1A01G064100 chr1B 93.190 4640 199 49 193 4764 65551573 65546983 0.000000e+00 6709.0
2 TraesCS1A01G064100 chr1B 85.944 249 23 7 4839 5081 65546813 65546571 6.710000e-64 255.0
3 TraesCS1A01G064100 chr1B 82.673 202 23 12 1 192 65551807 65551608 9.000000e-38 169.0
4 TraesCS1A01G064100 chr1B 93.671 79 5 0 5138 5216 65546284 65546206 9.190000e-23 119.0
5 TraesCS1A01G064100 chr1D 91.969 4719 184 85 193 4818 46186238 46181622 0.000000e+00 6434.0
6 TraesCS1A01G064100 chr1D 87.407 270 15 5 4875 5141 46181609 46181356 5.120000e-75 292.0
7 TraesCS1A01G064100 chr1D 96.203 79 3 0 5138 5216 46181302 46181224 4.250000e-26 130.0
8 TraesCS1A01G064100 chr7A 100.000 29 0 0 1698 1726 292257066 292257094 3.000000e-03 54.7


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 TraesCS1A01G064100 chr1A 45793233 45798456 5223 False 9648.000000 9648 100.000000 1 5224 1 chr1A.!!$F1 5223
1 TraesCS1A01G064100 chr1B 65546206 65551807 5601 True 1813.000000 6709 88.869500 1 5216 4 chr1B.!!$R1 5215
2 TraesCS1A01G064100 chr1D 46181224 46186238 5014 True 2285.333333 6434 91.859667 193 5216 3 chr1D.!!$R1 5023

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
981 1084 0.028902 GTCGGTGAGTGTTTGTTGGC 59.971 55.0 0.00 0.00 0.0 4.52 F
2072 2207 0.318107 AAACGTGCTTGCATGCAGTC 60.318 50.0 25.93 16.35 44.2 3.51 F
2519 2658 0.324943 GCTGTTGAAGAGGGCCTACA 59.675 55.0 5.73 5.88 0.0 2.74 F
3751 3894 0.108615 CCGACGACTCCAAAGCTGAT 60.109 55.0 0.00 0.00 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2158 2293 1.128692 GTTCAGGCATGTTCGTACAGC 59.871 52.381 0.0 4.79 37.77 4.40 R
3271 3414 0.846693 GTGCTCCCCCATCTGGTATT 59.153 55.000 0.0 0.00 0.00 1.89 R
4166 4309 0.320683 CAGCGATGTCCTTCACCACA 60.321 55.000 0.0 0.00 0.00 4.17 R
5026 5326 0.834612 TCTGACACCAGTTTCGGGTT 59.165 50.000 0.0 0.00 41.16 4.11 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
21 22 4.906747 AAAGAATGCCCAATAGCCAAAA 57.093 36.364 0.00 0.00 0.00 2.44
22 23 3.893326 AGAATGCCCAATAGCCAAAAC 57.107 42.857 0.00 0.00 0.00 2.43
24 25 3.055891 AGAATGCCCAATAGCCAAAACAC 60.056 43.478 0.00 0.00 0.00 3.32
25 26 1.709578 TGCCCAATAGCCAAAACACA 58.290 45.000 0.00 0.00 0.00 3.72
28 29 2.298729 GCCCAATAGCCAAAACACAGAA 59.701 45.455 0.00 0.00 0.00 3.02
35 36 7.095523 CCAATAGCCAAAACACAGAAATGAAAG 60.096 37.037 0.00 0.00 0.00 2.62
37 38 5.976458 AGCCAAAACACAGAAATGAAAGAA 58.024 33.333 0.00 0.00 0.00 2.52
39 40 7.049754 AGCCAAAACACAGAAATGAAAGAAAT 58.950 30.769 0.00 0.00 0.00 2.17
73 74 7.175104 ACCAATAGGCACATAAAGAGAAGAAA 58.825 34.615 0.00 0.00 39.06 2.52
74 75 7.836183 ACCAATAGGCACATAAAGAGAAGAAAT 59.164 33.333 0.00 0.00 39.06 2.17
80 81 6.597280 GGCACATAAAGAGAAGAAATGAGAGT 59.403 38.462 0.00 0.00 0.00 3.24
81 82 7.766278 GGCACATAAAGAGAAGAAATGAGAGTA 59.234 37.037 0.00 0.00 0.00 2.59
115 116 8.196771 TGTTGACTGAAGCTGAAAATAAAACAT 58.803 29.630 0.00 0.00 0.00 2.71
119 120 9.248291 GACTGAAGCTGAAAATAAAACATTTCA 57.752 29.630 0.00 0.00 41.78 2.69
138 139 9.768662 ACATTTCAACTGAAAAATAGCAATTCT 57.231 25.926 8.84 0.00 45.81 2.40
143 144 9.283768 TCAACTGAAAAATAGCAATTCTGTAGA 57.716 29.630 0.00 0.00 35.18 2.59
172 179 2.744202 GCACCGACATTTCAGATCACTT 59.256 45.455 0.00 0.00 0.00 3.16
173 180 3.425359 GCACCGACATTTCAGATCACTTG 60.425 47.826 0.00 0.00 0.00 3.16
174 181 2.744202 ACCGACATTTCAGATCACTTGC 59.256 45.455 0.00 0.00 0.00 4.01
176 183 2.222886 CGACATTTCAGATCACTTGCCG 60.223 50.000 0.00 0.00 0.00 5.69
177 184 1.470098 ACATTTCAGATCACTTGCCGC 59.530 47.619 0.00 0.00 0.00 6.53
178 185 1.741706 CATTTCAGATCACTTGCCGCT 59.258 47.619 0.00 0.00 0.00 5.52
179 186 2.760634 TTTCAGATCACTTGCCGCTA 57.239 45.000 0.00 0.00 0.00 4.26
180 187 2.299993 TTCAGATCACTTGCCGCTAG 57.700 50.000 0.00 0.00 0.00 3.42
181 188 1.186200 TCAGATCACTTGCCGCTAGT 58.814 50.000 1.26 1.26 0.00 2.57
183 190 2.758423 TCAGATCACTTGCCGCTAGTTA 59.242 45.455 4.61 0.00 0.00 2.24
184 191 3.384789 TCAGATCACTTGCCGCTAGTTAT 59.615 43.478 4.61 3.13 0.00 1.89
185 192 3.492383 CAGATCACTTGCCGCTAGTTATG 59.508 47.826 4.61 0.00 0.00 1.90
186 193 2.309528 TCACTTGCCGCTAGTTATGG 57.690 50.000 4.61 0.00 0.00 2.74
187 194 1.828595 TCACTTGCCGCTAGTTATGGA 59.171 47.619 4.61 0.00 0.00 3.41
188 195 2.235155 TCACTTGCCGCTAGTTATGGAA 59.765 45.455 4.61 0.00 0.00 3.53
189 196 3.006940 CACTTGCCGCTAGTTATGGAAA 58.993 45.455 4.61 0.00 0.00 3.13
191 198 4.096382 CACTTGCCGCTAGTTATGGAAAAT 59.904 41.667 4.61 0.00 0.00 1.82
195 239 6.952773 TGCCGCTAGTTATGGAAAATAAAT 57.047 33.333 0.00 0.00 0.00 1.40
210 254 6.478673 GGAAAATAAATTAGCAATTCCGTGGG 59.521 38.462 0.00 0.00 0.00 4.61
223 267 0.322098 CCGTGGGAGTATTTGCACCA 60.322 55.000 0.00 0.00 0.00 4.17
230 274 4.704540 TGGGAGTATTTGCACCAGTATTTG 59.295 41.667 0.00 0.00 0.00 2.32
244 289 4.191544 CAGTATTTGGAATCTCTTGCGGA 58.808 43.478 0.00 0.00 0.00 5.54
304 349 6.446318 TCAACATTAAAGTGCATCCAAGAAC 58.554 36.000 0.00 0.00 0.00 3.01
342 392 4.020307 AGCACCCAATCCCAAAACATAAAG 60.020 41.667 0.00 0.00 0.00 1.85
344 394 5.723295 CACCCAATCCCAAAACATAAAGAG 58.277 41.667 0.00 0.00 0.00 2.85
359 409 5.189736 ACATAAAGAGCACCAAGTGGAGATA 59.810 40.000 3.83 0.00 38.94 1.98
376 426 3.041946 AGATACCACTCCCACTCCAATC 58.958 50.000 0.00 0.00 0.00 2.67
378 428 1.208165 ACCACTCCCACTCCAATCCC 61.208 60.000 0.00 0.00 0.00 3.85
381 431 1.065126 CACTCCCACTCCAATCCCTTC 60.065 57.143 0.00 0.00 0.00 3.46
440 500 1.138661 GAGAGAGAGCATCCCAACAGG 59.861 57.143 0.00 0.00 33.66 4.00
472 532 1.079127 CACACGGACCATCCCTCAC 60.079 63.158 0.00 0.00 31.13 3.51
473 533 1.229209 ACACGGACCATCCCTCACT 60.229 57.895 0.00 0.00 31.13 3.41
474 534 1.258445 ACACGGACCATCCCTCACTC 61.258 60.000 0.00 0.00 31.13 3.51
475 535 0.972983 CACGGACCATCCCTCACTCT 60.973 60.000 0.00 0.00 31.13 3.24
476 536 0.684805 ACGGACCATCCCTCACTCTC 60.685 60.000 0.00 0.00 31.13 3.20
477 537 1.395826 CGGACCATCCCTCACTCTCC 61.396 65.000 0.00 0.00 31.13 3.71
478 538 1.051556 GGACCATCCCTCACTCTCCC 61.052 65.000 0.00 0.00 0.00 4.30
479 539 0.031616 GACCATCCCTCACTCTCCCT 60.032 60.000 0.00 0.00 0.00 4.20
480 540 0.031616 ACCATCCCTCACTCTCCCTC 60.032 60.000 0.00 0.00 0.00 4.30
491 551 2.689034 CTCCCTCCCCTCACCACC 60.689 72.222 0.00 0.00 0.00 4.61
514 574 2.026945 GCAGCTACCTCTCAGCTCCC 62.027 65.000 0.00 0.00 46.37 4.30
549 614 0.041238 TCAGTCCTACCACCTCCAGG 59.959 60.000 0.00 0.00 42.17 4.45
583 648 1.808133 GCTACAATTCCCAGCTCCTCG 60.808 57.143 0.00 0.00 32.46 4.63
647 716 1.466167 GCAGATATACCCGCAGCAATG 59.534 52.381 0.00 0.00 0.00 2.82
679 751 2.978010 CGCCAACCTGACACACCC 60.978 66.667 0.00 0.00 0.00 4.61
818 921 2.529744 GGTGGTTCCCCTGCAGACT 61.530 63.158 17.39 0.00 0.00 3.24
938 1041 1.520342 GGCGCAGATCTGACTGACC 60.520 63.158 27.04 14.30 39.94 4.02
940 1043 1.226802 CGCAGATCTGACTGACCGG 60.227 63.158 27.04 0.00 39.94 5.28
941 1044 1.520342 GCAGATCTGACTGACCGGC 60.520 63.158 27.04 3.37 39.94 6.13
942 1045 1.142748 CAGATCTGACTGACCGGCC 59.857 63.158 18.34 0.00 39.94 6.13
961 1064 1.533469 CGGTGTTCGTCCTCCTTCCT 61.533 60.000 0.00 0.00 0.00 3.36
981 1084 0.028902 GTCGGTGAGTGTTTGTTGGC 59.971 55.000 0.00 0.00 0.00 4.52
982 1085 1.098712 TCGGTGAGTGTTTGTTGGCC 61.099 55.000 0.00 0.00 0.00 5.36
983 1086 1.380403 CGGTGAGTGTTTGTTGGCCA 61.380 55.000 0.00 0.00 0.00 5.36
1093 1196 7.505923 AGGAGGAGGTAATAATTAATTTGTGGC 59.494 37.037 5.91 0.00 0.00 5.01
1096 1200 6.040054 GGAGGTAATAATTAATTTGTGGCGGT 59.960 38.462 5.91 0.00 0.00 5.68
1108 1212 3.435186 GGCGGTGGCTCTTGCTTC 61.435 66.667 4.81 0.00 39.81 3.86
1111 1215 2.747855 GGTGGCTCTTGCTTCGGG 60.748 66.667 0.00 0.00 39.59 5.14
1116 1221 1.021920 GGCTCTTGCTTCGGGTTCTC 61.022 60.000 0.00 0.00 39.59 2.87
1123 1228 1.005569 TGCTTCGGGTTCTCCTCTCTA 59.994 52.381 0.00 0.00 0.00 2.43
1124 1229 1.406180 GCTTCGGGTTCTCCTCTCTAC 59.594 57.143 0.00 0.00 0.00 2.59
1126 1231 3.684981 GCTTCGGGTTCTCCTCTCTACTA 60.685 52.174 0.00 0.00 0.00 1.82
1128 1233 4.792513 TCGGGTTCTCCTCTCTACTAAT 57.207 45.455 0.00 0.00 0.00 1.73
1157 1265 4.365514 TGGAGTTCTTGTGCTGGATTTA 57.634 40.909 0.00 0.00 0.00 1.40
1172 1281 8.947115 GTGCTGGATTTACTTAGATTTTACTGT 58.053 33.333 0.00 0.00 0.00 3.55
1200 1309 1.071987 TGAGCTTGCTGTGGGTCTG 59.928 57.895 0.00 0.00 0.00 3.51
1311 1424 7.131498 TCTTGAAATTGGCATATTGTTTTGC 57.869 32.000 0.00 0.00 38.14 3.68
1326 1444 4.711892 TGCTCACGCCAGCAATTA 57.288 50.000 6.42 0.00 46.65 1.40
1369 1492 7.835181 ACTAGTACTAGTTTTGATAGCCTGTCT 59.165 37.037 26.61 1.34 43.35 3.41
1371 1494 8.770010 AGTACTAGTTTTGATAGCCTGTCTAT 57.230 34.615 0.00 0.00 40.59 1.98
1610 1739 3.469739 CCAAGCTTTGCCTTTCAAATGT 58.530 40.909 0.00 0.00 43.14 2.71
1629 1758 7.442364 TCAAATGTACAGAAACTGAGGAAGAAG 59.558 37.037 0.33 0.00 35.18 2.85
1671 1800 2.838202 TCCACCAGATCTAACACCTTCC 59.162 50.000 0.00 0.00 0.00 3.46
1731 1866 4.547367 CCTCCCGCCGTTCCATCC 62.547 72.222 0.00 0.00 0.00 3.51
1839 1974 2.125391 GATGCTCCTGCGCAGACA 60.125 61.111 38.06 29.73 44.10 3.41
1843 1978 2.182791 CTCCTGCGCAGACATCGT 59.817 61.111 38.06 0.00 0.00 3.73
1878 2013 2.092049 TGGTGTATCGAGGGAAGAGCTA 60.092 50.000 0.00 0.00 0.00 3.32
1881 2016 2.231529 GTATCGAGGGAAGAGCTAGCA 58.768 52.381 18.83 0.00 0.00 3.49
1993 2128 1.808945 GAGCTCATTGTGACAGTTGGG 59.191 52.381 9.40 0.00 0.00 4.12
2072 2207 0.318107 AAACGTGCTTGCATGCAGTC 60.318 50.000 25.93 16.35 44.20 3.51
2180 2315 2.139917 TGTACGAACATGCCTGAACAC 58.860 47.619 0.00 0.00 0.00 3.32
2194 2329 0.388520 GAACACGCAAGCAAATCCCC 60.389 55.000 0.00 0.00 45.62 4.81
2195 2330 1.112315 AACACGCAAGCAAATCCCCA 61.112 50.000 0.00 0.00 45.62 4.96
2519 2658 0.324943 GCTGTTGAAGAGGGCCTACA 59.675 55.000 5.73 5.88 0.00 2.74
2703 2843 7.791029 ACTTTGTAGTTCCATTCCAAAAACAT 58.209 30.769 0.00 0.00 0.00 2.71
2768 2908 6.787085 ATGCTTTTCTTCCGCTATACATAC 57.213 37.500 0.00 0.00 0.00 2.39
2781 2921 6.462487 CCGCTATACATACTCCTTTTTCTCCA 60.462 42.308 0.00 0.00 0.00 3.86
2814 2957 9.920133 GATTGCTATACATATTCTGAGAGTCAA 57.080 33.333 0.00 0.00 0.00 3.18
3063 3206 3.161866 GGGTAGGCAAACCATCTCAAAA 58.838 45.455 10.71 0.00 41.67 2.44
3217 3360 0.737715 GCTCCAAATCTCGCAGTCGT 60.738 55.000 0.00 0.00 36.96 4.34
3221 3364 1.741770 AAATCTCGCAGTCGTGGGC 60.742 57.895 0.00 0.00 36.56 5.36
3572 3715 4.486503 GGCTGGAGCTGGCTGGAG 62.487 72.222 0.00 0.00 41.70 3.86
3751 3894 0.108615 CCGACGACTCCAAAGCTGAT 60.109 55.000 0.00 0.00 0.00 2.90
3822 3965 7.027778 ACACCAATAGTTGTGAAGAAGAAAC 57.972 36.000 0.97 0.00 0.00 2.78
3926 4069 0.692476 ACAGCATAGCCACCTCAACA 59.308 50.000 0.00 0.00 0.00 3.33
4068 4211 2.225394 ACACCAGAGAAAGGAGGCTCTA 60.225 50.000 15.23 0.00 39.36 2.43
4182 4325 1.273606 AGAGTGTGGTGAAGGACATCG 59.726 52.381 0.00 0.00 31.20 3.84
4184 4327 0.320771 GTGTGGTGAAGGACATCGCT 60.321 55.000 0.00 0.00 40.39 4.93
4186 4329 0.320771 GTGGTGAAGGACATCGCTGT 60.321 55.000 0.00 0.00 37.18 4.40
4190 4333 0.678950 TGAAGGACATCGCTGTGACA 59.321 50.000 0.00 0.00 35.14 3.58
4276 4422 5.105310 ACGGGACTATGGATTATGCAGATAC 60.105 44.000 0.00 0.00 0.00 2.24
4280 4426 7.334090 GGACTATGGATTATGCAGATACACAT 58.666 38.462 0.16 0.00 0.00 3.21
4406 4555 0.242825 TGTCGTCTGTCGGTCCATTC 59.757 55.000 0.00 0.00 40.32 2.67
4499 4652 7.522725 CGAGCAATATATTTCTTCCATGCCTTT 60.523 37.037 0.00 0.00 33.19 3.11
4500 4653 8.710749 AGCAATATATTTCTTCCATGCCTTTA 57.289 30.769 0.00 0.00 33.19 1.85
4501 4654 8.579863 AGCAATATATTTCTTCCATGCCTTTAC 58.420 33.333 0.00 0.00 33.19 2.01
4502 4655 7.538678 GCAATATATTTCTTCCATGCCTTTACG 59.461 37.037 0.00 0.00 0.00 3.18
4530 4685 4.657969 TCCCAAATTCCCAATGAACTTGTT 59.342 37.500 0.00 0.00 38.26 2.83
4563 4718 2.092914 AGCACTCTGCCCCAATAAGTAC 60.093 50.000 0.00 0.00 46.52 2.73
4569 4724 4.312487 TCTGCCCCAATAAGTACCCTATT 58.688 43.478 0.00 0.00 0.00 1.73
4693 4870 2.890474 GTGTCGGCCATGGTAGCG 60.890 66.667 14.67 0.00 0.00 4.26
4749 4926 1.188863 GCCCAGCATCCAGTTGAAAT 58.811 50.000 0.00 0.00 0.00 2.17
4750 4927 1.551883 GCCCAGCATCCAGTTGAAATT 59.448 47.619 0.00 0.00 0.00 1.82
4751 4928 2.027837 GCCCAGCATCCAGTTGAAATTT 60.028 45.455 0.00 0.00 0.00 1.82
4814 5108 7.042335 TCGAAGACATTCTCCCTTATCTTTTC 58.958 38.462 0.00 0.00 32.93 2.29
4817 5111 9.237187 GAAGACATTCTCCCTTATCTTTTCTTT 57.763 33.333 0.00 0.00 32.33 2.52
4818 5112 9.593565 AAGACATTCTCCCTTATCTTTTCTTTT 57.406 29.630 0.00 0.00 0.00 2.27
4819 5113 9.593565 AGACATTCTCCCTTATCTTTTCTTTTT 57.406 29.630 0.00 0.00 0.00 1.94
4856 5150 1.472878 TGAGGGAGAATGTCTTCGACG 59.527 52.381 0.00 0.00 36.45 5.12
4861 5155 1.921230 GAGAATGTCTTCGACGCTTCC 59.079 52.381 0.00 0.00 36.45 3.46
4863 5157 2.066262 GAATGTCTTCGACGCTTCCAA 58.934 47.619 0.00 0.00 34.95 3.53
4934 5231 9.855021 AATACACTGTAATTATGCAAACTTTCC 57.145 29.630 0.00 0.00 0.00 3.13
4936 5233 7.370383 ACACTGTAATTATGCAAACTTTCCTG 58.630 34.615 0.00 0.00 0.00 3.86
4937 5234 6.308766 CACTGTAATTATGCAAACTTTCCTGC 59.691 38.462 0.00 0.00 39.09 4.85
5018 5318 7.992608 ACCATTTTTGCCTTAATTTTGTTCTCT 59.007 29.630 0.00 0.00 0.00 3.10
5022 5322 5.125100 TGCCTTAATTTTGTTCTCTGCAG 57.875 39.130 7.63 7.63 0.00 4.41
5025 5325 5.803967 GCCTTAATTTTGTTCTCTGCAGATG 59.196 40.000 18.63 11.61 0.00 2.90
5026 5326 6.349611 GCCTTAATTTTGTTCTCTGCAGATGA 60.350 38.462 18.63 13.82 0.00 2.92
5047 5347 1.420138 ACCCGAAACTGGTGTCAGAAT 59.580 47.619 0.00 0.00 43.49 2.40
5069 5369 4.682787 TGACAATACTACCATTGAGCTCG 58.317 43.478 9.64 0.00 38.01 5.03
5206 5737 4.439057 GCAATTGATCAAGCATTCATGGT 58.561 39.130 14.54 0.00 40.78 3.55
5216 5747 1.402968 GCATTCATGGTCGAAGCACAT 59.597 47.619 0.00 0.00 0.00 3.21
5217 5748 2.159338 GCATTCATGGTCGAAGCACATT 60.159 45.455 0.00 0.00 0.00 2.71
5218 5749 3.431856 CATTCATGGTCGAAGCACATTG 58.568 45.455 0.00 0.00 0.00 2.82
5219 5750 0.804364 TCATGGTCGAAGCACATTGC 59.196 50.000 0.00 0.00 45.46 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.288810 TCTTTCATTTCTGTGTTTTGGCTAT 57.711 32.000 0.00 0.00 0.00 2.97
35 36 8.177119 TGTGCCTATTGGTTTCCATATATTTC 57.823 34.615 0.00 0.00 31.53 2.17
37 38 9.821240 TTATGTGCCTATTGGTTTCCATATATT 57.179 29.630 0.00 0.00 31.53 1.28
39 40 9.295825 CTTTATGTGCCTATTGGTTTCCATATA 57.704 33.333 0.00 0.00 31.53 0.86
45 46 7.336931 TCTTCTCTTTATGTGCCTATTGGTTTC 59.663 37.037 0.00 0.00 35.27 2.78
50 51 8.896744 TCATTTCTTCTCTTTATGTGCCTATTG 58.103 33.333 0.00 0.00 0.00 1.90
87 88 9.034544 GTTTTATTTTCAGCTTCAGTCAACATT 57.965 29.630 0.00 0.00 0.00 2.71
98 99 9.598517 TCAGTTGAAATGTTTTATTTTCAGCTT 57.401 25.926 10.68 0.00 45.29 3.74
129 130 7.065803 GGTGCAAATACTTCTACAGAATTGCTA 59.934 37.037 20.32 10.31 42.34 3.49
130 131 6.127897 GGTGCAAATACTTCTACAGAATTGCT 60.128 38.462 20.32 0.00 42.34 3.91
131 132 6.030228 GGTGCAAATACTTCTACAGAATTGC 58.970 40.000 15.95 15.95 42.26 3.56
132 133 6.092122 TCGGTGCAAATACTTCTACAGAATTG 59.908 38.462 0.00 0.00 33.01 2.32
133 134 6.092259 GTCGGTGCAAATACTTCTACAGAATT 59.908 38.462 0.00 0.00 33.01 2.17
135 136 4.927425 GTCGGTGCAAATACTTCTACAGAA 59.073 41.667 0.00 0.00 0.00 3.02
137 138 4.242475 TGTCGGTGCAAATACTTCTACAG 58.758 43.478 0.00 0.00 0.00 2.74
138 139 4.260139 TGTCGGTGCAAATACTTCTACA 57.740 40.909 0.00 0.00 0.00 2.74
139 140 5.796350 AATGTCGGTGCAAATACTTCTAC 57.204 39.130 0.00 0.00 0.00 2.59
141 142 4.759693 TGAAATGTCGGTGCAAATACTTCT 59.240 37.500 0.00 0.00 0.00 2.85
143 144 4.759693 TCTGAAATGTCGGTGCAAATACTT 59.240 37.500 0.00 0.00 0.00 2.24
172 179 6.952773 ATTTATTTTCCATAACTAGCGGCA 57.047 33.333 1.45 0.00 0.00 5.69
173 180 7.537649 GCTAATTTATTTTCCATAACTAGCGGC 59.462 37.037 0.00 0.00 0.00 6.53
174 181 8.564574 TGCTAATTTATTTTCCATAACTAGCGG 58.435 33.333 0.00 0.00 32.87 5.52
183 190 7.710475 CCACGGAATTGCTAATTTATTTTCCAT 59.290 33.333 0.00 0.00 32.53 3.41
184 191 7.038659 CCACGGAATTGCTAATTTATTTTCCA 58.961 34.615 0.00 0.00 32.53 3.53
185 192 6.478673 CCCACGGAATTGCTAATTTATTTTCC 59.521 38.462 0.00 0.00 0.00 3.13
186 193 7.262048 TCCCACGGAATTGCTAATTTATTTTC 58.738 34.615 0.00 0.00 0.00 2.29
187 194 7.093509 ACTCCCACGGAATTGCTAATTTATTTT 60.094 33.333 0.00 0.00 0.00 1.82
188 195 6.379988 ACTCCCACGGAATTGCTAATTTATTT 59.620 34.615 0.00 0.00 0.00 1.40
189 196 5.891551 ACTCCCACGGAATTGCTAATTTATT 59.108 36.000 0.00 0.00 0.00 1.40
191 198 4.850680 ACTCCCACGGAATTGCTAATTTA 58.149 39.130 0.00 0.00 0.00 1.40
195 239 4.497291 AATACTCCCACGGAATTGCTAA 57.503 40.909 0.00 0.00 0.00 3.09
210 254 6.509418 TTCCAAATACTGGTGCAAATACTC 57.491 37.500 0.00 0.00 46.51 2.59
223 267 4.487714 TCCGCAAGAGATTCCAAATACT 57.512 40.909 0.00 0.00 43.02 2.12
230 274 5.639931 GGATAAACTATCCGCAAGAGATTCC 59.360 44.000 0.00 0.00 44.75 3.01
244 289 2.305927 CGGCTGGATGGGGATAAACTAT 59.694 50.000 0.00 0.00 0.00 2.12
304 349 0.179086 GTGCTTGGGTGTTTTGGGTG 60.179 55.000 0.00 0.00 0.00 4.61
342 392 1.555075 TGGTATCTCCACTTGGTGCTC 59.445 52.381 0.00 0.00 41.93 4.26
359 409 1.208165 GGGATTGGAGTGGGAGTGGT 61.208 60.000 0.00 0.00 0.00 4.16
365 415 0.921256 AGGGAAGGGATTGGAGTGGG 60.921 60.000 0.00 0.00 0.00 4.61
371 421 1.918957 ACAGAAGAGGGAAGGGATTGG 59.081 52.381 0.00 0.00 0.00 3.16
376 426 2.764269 TGGATACAGAAGAGGGAAGGG 58.236 52.381 0.00 0.00 46.17 3.95
472 532 1.687493 GTGGTGAGGGGAGGGAGAG 60.687 68.421 0.00 0.00 0.00 3.20
473 533 2.450243 GTGGTGAGGGGAGGGAGA 59.550 66.667 0.00 0.00 0.00 3.71
474 534 2.689034 GGTGGTGAGGGGAGGGAG 60.689 72.222 0.00 0.00 0.00 4.30
475 535 4.348495 GGGTGGTGAGGGGAGGGA 62.348 72.222 0.00 0.00 0.00 4.20
477 537 4.675303 TGGGGTGGTGAGGGGAGG 62.675 72.222 0.00 0.00 0.00 4.30
478 538 3.011517 CTGGGGTGGTGAGGGGAG 61.012 72.222 0.00 0.00 0.00 4.30
491 551 1.821936 CTGAGAGGTAGCTGCTGGG 59.178 63.158 13.43 0.00 0.00 4.45
514 574 4.767255 GACAGGAGGGCACAGCGG 62.767 72.222 0.00 0.00 0.00 5.52
549 614 3.790437 TAGCTGGCTGGCTGGAGC 61.790 66.667 13.94 7.04 43.01 4.70
647 716 2.813042 GCGTGAGAGGACAGCTGC 60.813 66.667 15.27 6.61 0.00 5.25
679 751 1.497161 ACTAACGGGAAGGATGGGAG 58.503 55.000 0.00 0.00 0.00 4.30
818 921 3.055719 GCTTTACCGCTGCAGGCA 61.056 61.111 17.12 0.00 41.91 4.75
890 993 6.882140 AGATCTATCACTAGTTATCCACGGAG 59.118 42.308 0.00 0.00 0.00 4.63
891 994 6.655425 CAGATCTATCACTAGTTATCCACGGA 59.345 42.308 0.00 0.00 0.00 4.69
941 1044 1.080025 GAAGGAGGACGAACACCGG 60.080 63.158 0.00 0.00 43.93 5.28
942 1045 1.080025 GGAAGGAGGACGAACACCG 60.080 63.158 0.00 0.00 45.44 4.94
950 1053 0.898789 TCACCGACAGGAAGGAGGAC 60.899 60.000 0.00 0.00 41.02 3.85
952 1055 0.900647 ACTCACCGACAGGAAGGAGG 60.901 60.000 0.00 0.00 41.02 4.30
961 1064 1.374560 CCAACAAACACTCACCGACA 58.625 50.000 0.00 0.00 0.00 4.35
981 1084 1.055040 TGGCCCCAACAAATTCTTGG 58.945 50.000 0.00 7.58 38.37 3.61
982 1085 2.616001 CCATGGCCCCAACAAATTCTTG 60.616 50.000 0.00 0.00 38.61 3.02
983 1086 1.629861 CCATGGCCCCAACAAATTCTT 59.370 47.619 0.00 0.00 0.00 2.52
1093 1196 3.121030 CCGAAGCAAGAGCCACCG 61.121 66.667 0.00 0.00 43.56 4.94
1096 1200 1.302511 GAACCCGAAGCAAGAGCCA 60.303 57.895 0.00 0.00 43.56 4.75
1108 1212 5.855740 AAATTAGTAGAGAGGAGAACCCG 57.144 43.478 0.00 0.00 40.87 5.28
1126 1231 8.253113 CCAGCACAAGAACTCCATAAATAAATT 58.747 33.333 0.00 0.00 0.00 1.82
1128 1233 6.945435 TCCAGCACAAGAACTCCATAAATAAA 59.055 34.615 0.00 0.00 0.00 1.40
1157 1265 7.118390 CACAGCAGCTAACAGTAAAATCTAAGT 59.882 37.037 0.00 0.00 0.00 2.24
1200 1309 3.359950 AGGAAACAGCCAAATCCTGATC 58.640 45.455 0.00 0.00 40.73 2.92
1281 1394 7.844009 ACAATATGCCAATTTCAAGATTCTGT 58.156 30.769 0.00 0.00 0.00 3.41
1369 1492 5.418524 CCAACTGAAACCATCACCATGAATA 59.581 40.000 0.00 0.00 33.47 1.75
1371 1494 3.573538 CCAACTGAAACCATCACCATGAA 59.426 43.478 0.00 0.00 33.47 2.57
1464 1592 5.251932 TCCAATTGTAGGTGGAAAGATGGTA 59.748 40.000 4.43 0.00 41.02 3.25
1527 1656 5.689383 AACACAATCGCAAAGACAATACT 57.311 34.783 0.00 0.00 0.00 2.12
1528 1657 7.240674 TGATAACACAATCGCAAAGACAATAC 58.759 34.615 0.00 0.00 0.00 1.89
1529 1658 7.371126 TGATAACACAATCGCAAAGACAATA 57.629 32.000 0.00 0.00 0.00 1.90
1578 1707 2.863704 GCAAAGCTTGGGTTGTCATCAC 60.864 50.000 0.00 0.00 0.00 3.06
1610 1739 5.611374 CCAACTTCTTCCTCAGTTTCTGTA 58.389 41.667 0.00 0.00 30.48 2.74
1629 1758 1.973812 GGGGTCTCTTGCAGCCAAC 60.974 63.158 0.00 0.00 32.61 3.77
1714 1843 4.547367 GGATGGAACGGCGGGAGG 62.547 72.222 13.24 0.00 0.00 4.30
1728 1863 1.002134 CTCAGTTTGGTGCGGGGAT 60.002 57.895 0.00 0.00 0.00 3.85
1731 1866 1.672356 CTCCTCAGTTTGGTGCGGG 60.672 63.158 0.00 0.00 0.00 6.13
1878 2013 2.641305 GTCTGGATCTTGATTGCTGCT 58.359 47.619 0.00 0.00 0.00 4.24
1881 2016 1.745141 GCGGTCTGGATCTTGATTGCT 60.745 52.381 0.00 0.00 0.00 3.91
1993 2128 8.000780 AGAATGAAACCAGCCATTTAAGTATC 57.999 34.615 0.00 0.00 33.57 2.24
2072 2207 4.107622 CAGCGGCCATCAGAAAATAAAAG 58.892 43.478 2.24 0.00 0.00 2.27
2158 2293 1.128692 GTTCAGGCATGTTCGTACAGC 59.871 52.381 0.00 4.79 37.77 4.40
2180 2315 1.142314 CCATGGGGATTTGCTTGCG 59.858 57.895 2.85 0.00 35.59 4.85
2194 2329 1.273327 GTTTTGAGGAAGGCCACCATG 59.727 52.381 18.84 0.00 36.29 3.66
2195 2330 1.147817 AGTTTTGAGGAAGGCCACCAT 59.852 47.619 18.84 1.53 36.29 3.55
2748 2888 6.750148 AGGAGTATGTATAGCGGAAGAAAAG 58.250 40.000 0.00 0.00 0.00 2.27
2768 2908 3.832527 TCCTGGTTTGGAGAAAAAGGAG 58.167 45.455 0.00 0.00 33.88 3.69
2781 2921 8.439971 TCAGAATATGTATAGCAATCCTGGTTT 58.560 33.333 0.00 0.00 34.40 3.27
2814 2957 4.147321 CCTCCTTGCCTGCATTATTACAT 58.853 43.478 0.00 0.00 0.00 2.29
3063 3206 8.028938 GCACACAATATTTTTACTGATGAAGGT 58.971 33.333 0.00 0.00 0.00 3.50
3217 3360 6.945435 TCTCACTTAAAAGATGTAATTGCCCA 59.055 34.615 0.00 0.00 0.00 5.36
3270 3413 1.140312 TGCTCCCCCATCTGGTATTC 58.860 55.000 0.00 0.00 0.00 1.75
3271 3414 0.846693 GTGCTCCCCCATCTGGTATT 59.153 55.000 0.00 0.00 0.00 1.89
3356 3499 3.003275 CGAGCGCTCTCTCTCTTCTTATT 59.997 47.826 32.88 0.00 37.19 1.40
3761 3904 3.787001 GAAGGGGACAGCCGGGAG 61.787 72.222 2.18 0.00 33.83 4.30
3770 3913 2.154074 AGTGGGTGTGGAAGGGGAC 61.154 63.158 0.00 0.00 0.00 4.46
3779 3922 4.258206 ACTTTGGCAGTGGGTGTG 57.742 55.556 0.00 0.00 32.83 3.82
3822 3965 2.738147 CGTTCTTCGGTGTAGCAGG 58.262 57.895 0.00 0.00 35.71 4.85
3926 4069 3.069980 GCTCTCGTCATCCCGCACT 62.070 63.158 0.00 0.00 0.00 4.40
4022 4165 1.067669 TCTGCACTATCGATCAGTGGC 59.932 52.381 24.03 19.05 42.99 5.01
4068 4211 1.682849 TGGCTGACCCAACGCTAAT 59.317 52.632 0.00 0.00 41.82 1.73
4154 4297 1.048601 TCACCACACTCTCCACCTTC 58.951 55.000 0.00 0.00 0.00 3.46
4166 4309 0.320683 CAGCGATGTCCTTCACCACA 60.321 55.000 0.00 0.00 0.00 4.17
4167 4310 0.320771 ACAGCGATGTCCTTCACCAC 60.321 55.000 0.00 0.00 0.00 4.16
4184 4327 3.519973 CTCTGGCTGCGGTGTCACA 62.520 63.158 5.12 0.00 0.00 3.58
4186 4329 4.007644 CCTCTGGCTGCGGTGTCA 62.008 66.667 0.00 0.00 0.00 3.58
4303 4449 6.515043 AATGCAACAATTCGAAGAACTTTG 57.485 33.333 3.35 5.44 45.90 2.77
4406 4555 4.872691 TGGTTTTACACAAGCAACAAATGG 59.127 37.500 0.00 0.00 31.25 3.16
4441 4594 6.692486 AGAAGACCTGTGTACATACAAAGAG 58.308 40.000 10.33 4.15 42.83 2.85
4443 4596 9.436957 AAATAGAAGACCTGTGTACATACAAAG 57.563 33.333 0.00 2.62 40.47 2.77
4499 4652 1.916874 TGGGAATTTGGGACCATCGTA 59.083 47.619 0.00 0.00 0.00 3.43
4500 4653 0.701731 TGGGAATTTGGGACCATCGT 59.298 50.000 0.00 0.00 0.00 3.73
4501 4654 1.846007 TTGGGAATTTGGGACCATCG 58.154 50.000 0.00 0.00 32.18 3.84
4502 4655 3.373830 TCATTGGGAATTTGGGACCATC 58.626 45.455 0.00 0.00 32.18 3.51
4530 4685 4.191544 GGCAGAGTGCTACATTGACATTA 58.808 43.478 0.00 0.00 44.28 1.90
4563 4718 9.353999 GCTTTTGTGTAGACATTAAAAATAGGG 57.646 33.333 0.00 1.35 30.32 3.53
4641 4807 1.305213 ATGGCCACCACCAACCATC 60.305 57.895 8.16 0.00 44.65 3.51
4693 4870 5.189180 AGAAAGGCAACATGATTAGAGGTC 58.811 41.667 0.00 0.00 41.41 3.85
4771 5065 4.209452 TCGACACTTTGAAATGCACTTC 57.791 40.909 0.00 0.00 0.00 3.01
4782 5076 3.433615 GGGAGAATGTCTTCGACACTTTG 59.566 47.826 0.00 0.00 45.65 2.77
4783 5077 3.325135 AGGGAGAATGTCTTCGACACTTT 59.675 43.478 0.00 0.00 45.65 2.66
4829 5123 5.645497 CGAAGACATTCTCCCTCATCTTTTT 59.355 40.000 0.00 0.00 32.93 1.94
4830 5124 5.046304 TCGAAGACATTCTCCCTCATCTTTT 60.046 40.000 0.00 0.00 32.93 2.27
4831 5125 4.467795 TCGAAGACATTCTCCCTCATCTTT 59.532 41.667 0.00 0.00 32.93 2.52
4832 5126 4.026744 TCGAAGACATTCTCCCTCATCTT 58.973 43.478 0.00 0.00 32.93 2.40
4833 5127 3.636679 TCGAAGACATTCTCCCTCATCT 58.363 45.455 0.00 0.00 32.93 2.90
4856 5150 5.678132 ATTTCAAAAGTGCATTTGGAAGC 57.322 34.783 11.23 0.00 40.99 3.86
4892 5189 7.564793 ACAGTGTATTTCCACATAGATAAGCA 58.435 34.615 0.00 0.00 37.82 3.91
4893 5190 9.542462 TTACAGTGTATTTCCACATAGATAAGC 57.458 33.333 3.28 0.00 37.82 3.09
4934 5231 3.998341 CCCCAATGAACAGAATTTTGCAG 59.002 43.478 0.00 0.00 0.00 4.41
4936 5233 2.743664 GCCCCAATGAACAGAATTTTGC 59.256 45.455 0.00 0.00 0.00 3.68
4937 5234 3.008266 AGGCCCCAATGAACAGAATTTTG 59.992 43.478 0.00 0.00 0.00 2.44
4944 5241 1.607178 TGCAGGCCCCAATGAACAG 60.607 57.895 0.00 0.00 0.00 3.16
5018 5318 1.522668 CAGTTTCGGGTTCATCTGCA 58.477 50.000 0.00 0.00 0.00 4.41
5022 5322 1.804748 GACACCAGTTTCGGGTTCATC 59.195 52.381 0.00 0.00 36.19 2.92
5025 5325 1.202604 TCTGACACCAGTTTCGGGTTC 60.203 52.381 0.00 0.00 41.16 3.62
5026 5326 0.834612 TCTGACACCAGTTTCGGGTT 59.165 50.000 0.00 0.00 41.16 4.11
5047 5347 4.441495 CCGAGCTCAATGGTAGTATTGTCA 60.441 45.833 15.40 0.00 38.77 3.58
5060 5360 9.826574 TGTATTTACTAATTAACCGAGCTCAAT 57.173 29.630 15.40 2.68 0.00 2.57
5085 5556 3.119173 TGTTTTGGCTTGAACCTTGACTG 60.119 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.