Multiple sequence alignment - TraesCS7D01G232300

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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 TraesCS7D01G232300 chr7D 100.000 4787 0 0 1 4787 193588220 193583434 0.000000e+00 8841.0
1 TraesCS7D01G232300 chr7D 84.270 89 12 2 231 319 96106024 96105938 8.540000e-13 86.1
2 TraesCS7D01G232300 chr7A 92.846 3299 144 52 131 3384 203043116 203039865 0.000000e+00 4700.0
3 TraesCS7D01G232300 chr7A 90.603 1394 104 11 3398 4787 203039814 203038444 0.000000e+00 1823.0
4 TraesCS7D01G232300 chr7A 86.585 82 10 1 238 319 99506242 99506162 6.600000e-14 89.8
5 TraesCS7D01G232300 chr7B 93.738 1533 37 23 1859 3390 157218767 157217293 0.000000e+00 2244.0
6 TraesCS7D01G232300 chr7B 93.344 1307 66 13 469 1755 157220104 157218799 0.000000e+00 1912.0
7 TraesCS7D01G232300 chr7B 84.248 1422 142 40 3388 4787 157217258 157215897 0.000000e+00 1310.0
8 TraesCS7D01G232300 chr7B 86.747 498 48 10 3 486 157220620 157220127 5.450000e-149 538.0
9 TraesCS7D01G232300 chr7B 89.130 46 2 2 76 121 538569467 538569425 2.000000e-03 54.7
10 TraesCS7D01G232300 chr4D 91.842 711 50 6 1947 2652 3611496 3610789 0.000000e+00 985.0
11 TraesCS7D01G232300 chr4D 89.445 739 71 7 2652 3386 3610720 3609985 0.000000e+00 926.0
12 TraesCS7D01G232300 chr4D 88.221 399 34 5 3584 3982 3609361 3608976 9.380000e-127 464.0
13 TraesCS7D01G232300 chr4D 89.062 256 25 2 1157 1410 3612748 3612494 1.000000e-81 315.0
14 TraesCS7D01G232300 chr4D 87.050 139 11 3 3463 3601 3609667 3609536 2.980000e-32 150.0
15 TraesCS7D01G232300 chr4B 90.204 735 67 5 2652 3383 59233300 59234032 0.000000e+00 953.0
16 TraesCS7D01G232300 chr4B 90.780 705 53 9 1947 2646 59232528 59233225 0.000000e+00 931.0
17 TraesCS7D01G232300 chr4B 87.713 293 14 4 3646 3938 59234141 59234411 5.980000e-84 322.0
18 TraesCS7D01G232300 chr4B 87.170 265 31 2 1148 1410 59231464 59231727 1.010000e-76 298.0
19 TraesCS7D01G232300 chr4B 93.478 46 2 1 852 896 59227866 59227911 3.090000e-07 67.6
20 TraesCS7D01G232300 chr6D 81.675 191 34 1 1171 1360 360680990 360681180 1.780000e-34 158.0
21 TraesCS7D01G232300 chr6A 81.250 192 35 1 1170 1360 501791969 501792160 2.310000e-33 154.0
22 TraesCS7D01G232300 chr6B 80.435 184 36 0 1171 1354 542223761 542223944 1.800000e-29 141.0
23 TraesCS7D01G232300 chr6B 89.062 64 4 1 73 133 404377831 404377768 5.140000e-10 76.8
24 TraesCS7D01G232300 chr2B 84.091 132 14 5 240 368 744218290 744218417 2.340000e-23 121.0
25 TraesCS7D01G232300 chr2B 79.213 178 31 5 218 391 793184251 793184426 8.420000e-23 119.0
26 TraesCS7D01G232300 chr2B 87.342 79 7 3 242 319 318210486 318210410 2.370000e-13 87.9
27 TraesCS7D01G232300 chr2D 83.333 132 15 6 239 368 610045243 610045117 1.090000e-21 115.0
28 TraesCS7D01G232300 chr1D 78.409 176 27 5 219 391 485199536 485199703 2.360000e-18 104.0
29 TraesCS7D01G232300 chr1A 78.090 178 27 8 219 391 582519780 582519950 8.480000e-18 102.0
30 TraesCS7D01G232300 chr3D 82.022 89 15 1 4035 4122 545636539 545636451 1.850000e-09 75.0


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 TraesCS7D01G232300 chr7D 193583434 193588220 4786 True 8841.00 8841 100.00000 1 4787 1 chr7D.!!$R2 4786
1 TraesCS7D01G232300 chr7A 203038444 203043116 4672 True 3261.50 4700 91.72450 131 4787 2 chr7A.!!$R2 4656
2 TraesCS7D01G232300 chr7B 157215897 157220620 4723 True 1501.00 2244 89.51925 3 4787 4 chr7B.!!$R2 4784
3 TraesCS7D01G232300 chr4D 3608976 3612748 3772 True 568.00 985 89.12400 1157 3982 5 chr4D.!!$R1 2825
4 TraesCS7D01G232300 chr4B 59227866 59234411 6545 False 514.32 953 89.86900 852 3938 5 chr4B.!!$F1 3086

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
29 30 0.173481 CGACGGAGGAGCTCAAATCA 59.827 55.0 17.19 0.0 31.08 2.57 F
634 702 0.790814 CTTCTCGCCCACTTTTCGAC 59.209 55.0 0.00 0.0 0.00 4.20 F
1663 5874 1.112113 TGAGTAATCCGACTGCCCTC 58.888 55.0 0.00 0.0 0.00 4.30 F
2140 6368 0.546598 ACCCAGCCTATGTTACTGCC 59.453 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 4814 1.012486 GGTACCGACCGCTGTTCAAG 61.012 60.000 0.0 0.0 35.52 3.02 R
1856 6083 1.201414 TGCAGCAAAGCTCACATGATG 59.799 47.619 0.0 0.0 36.40 3.07 R
3638 8388 0.396435 TCCACATCAGAAACACGGCT 59.604 50.000 0.0 0.0 0.00 5.52 R
3789 8539 0.107993 GCCGAGGGTTGGGTTACTAC 60.108 60.000 0.0 0.0 0.00 2.73 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
29 30 0.173481 CGACGGAGGAGCTCAAATCA 59.827 55.000 17.19 0.00 31.08 2.57
33 34 1.012841 GGAGGAGCTCAAATCAAGCG 58.987 55.000 17.19 0.00 44.59 4.68
36 37 1.308069 GGAGCTCAAATCAAGCGGCA 61.308 55.000 17.19 0.00 44.59 5.69
90 92 2.951458 GGAAAAGTGGCGGAACCG 59.049 61.111 9.00 9.00 43.94 4.44
133 135 3.932580 GATCTGGCGACGTGGTGCA 62.933 63.158 0.00 0.00 0.00 4.57
149 151 2.125350 CAGAGGGACGCAAGGAGC 60.125 66.667 0.00 0.00 46.39 4.70
192 197 2.931649 GGGGGAGGAACCAACGGA 60.932 66.667 0.00 0.00 41.20 4.69
212 217 1.680989 GGGCATTTACGGGTGGCTT 60.681 57.895 0.00 0.00 40.40 4.35
216 221 1.271102 GCATTTACGGGTGGCTTTCAA 59.729 47.619 0.00 0.00 0.00 2.69
330 335 9.636879 ACATATCTACATCATTCGATTGAAGAG 57.363 33.333 16.76 12.39 37.57 2.85
427 444 9.428097 GAGATGAAAACCAAAGCTAATGAATTT 57.572 29.630 1.14 2.63 0.00 1.82
501 565 3.228749 GCATGACTCACACAAACATTCG 58.771 45.455 0.00 0.00 0.00 3.34
508 572 1.864711 CACACAAACATTCGTCGAGGT 59.135 47.619 4.85 0.00 0.00 3.85
551 615 2.425592 CAGCAGTGGTCCGGTTCA 59.574 61.111 0.00 0.00 0.00 3.18
562 626 2.355716 GGTCCGGTTCATTGATCCTTCA 60.356 50.000 0.00 0.00 0.00 3.02
569 637 4.082125 GTTCATTGATCCTTCACCACCTT 58.918 43.478 0.00 0.00 0.00 3.50
573 641 2.907892 TGATCCTTCACCACCTTCTCT 58.092 47.619 0.00 0.00 0.00 3.10
634 702 0.790814 CTTCTCGCCCACTTTTCGAC 59.209 55.000 0.00 0.00 0.00 4.20
647 715 4.809426 CACTTTTCGACTGGACAACTACTT 59.191 41.667 0.00 0.00 0.00 2.24
775 856 3.896133 CATGCATGCCCTCACGCC 61.896 66.667 14.93 0.00 28.85 5.68
903 986 2.510906 GGCCCTCACTGTGTGTGT 59.489 61.111 7.79 0.00 46.27 3.72
1105 1226 3.383185 TCGGTTTGATTCCTGCAAGTTTT 59.617 39.130 0.00 0.00 0.00 2.43
1107 1228 4.441792 GGTTTGATTCCTGCAAGTTTTGT 58.558 39.130 0.00 0.00 0.00 2.83
1110 1231 6.536941 GGTTTGATTCCTGCAAGTTTTGTTTA 59.463 34.615 0.00 0.00 0.00 2.01
1134 2081 2.725221 AGAAGTACTACGGTCGGGAT 57.275 50.000 0.00 0.00 0.00 3.85
1173 4647 5.212934 GTTTTGATTTCTGTCTTCCCGTTC 58.787 41.667 0.00 0.00 0.00 3.95
1223 4697 2.663196 GGCGTGTTCTACCAGGCT 59.337 61.111 5.92 0.00 43.74 4.58
1340 4814 3.692406 ACCGACGACAAGGAGGGC 61.692 66.667 0.00 0.00 0.00 5.19
1390 4867 7.605449 TCATCCCAATTCTTCTCATGTTTTTC 58.395 34.615 0.00 0.00 0.00 2.29
1450 5577 4.746729 TGTAATGCAATTCATGTGCTTCC 58.253 39.130 8.11 0.00 42.69 3.46
1532 5743 1.414919 ACGTAGTGAAGTTGGCAGGAA 59.585 47.619 0.00 0.00 42.51 3.36
1534 5745 2.416547 CGTAGTGAAGTTGGCAGGAATG 59.583 50.000 0.00 0.00 0.00 2.67
1663 5874 1.112113 TGAGTAATCCGACTGCCCTC 58.888 55.000 0.00 0.00 0.00 4.30
1669 5880 1.826385 ATCCGACTGCCCTCTTTTTG 58.174 50.000 0.00 0.00 0.00 2.44
1814 6041 5.107109 TGACAGACAATTGATGGTTTTCG 57.893 39.130 13.59 0.00 0.00 3.46
1890 6117 2.585330 TGCTGCAGGATCAGTTCAAAA 58.415 42.857 17.12 0.00 36.49 2.44
2140 6368 0.546598 ACCCAGCCTATGTTACTGCC 59.453 55.000 0.00 0.00 0.00 4.85
2912 7213 5.364778 TGTTGGGGTCTATGAAATACATCG 58.635 41.667 0.00 0.00 40.07 3.84
3023 7325 5.567138 ACTCAATAATGCCAGTTTGTAGC 57.433 39.130 0.00 0.00 0.00 3.58
3027 7329 7.557719 ACTCAATAATGCCAGTTTGTAGCTAAT 59.442 33.333 0.00 0.00 0.00 1.73
3091 7399 6.823689 GCCTCTGTAAATTCTGTTCAATCCTA 59.176 38.462 0.00 0.00 0.00 2.94
3117 7425 1.787012 GCCATGGCACTTGTTTCTTG 58.213 50.000 32.08 0.00 41.49 3.02
3128 7437 5.215160 CACTTGTTTCTTGATGGCTGTTAC 58.785 41.667 0.00 0.00 0.00 2.50
3185 7494 7.846066 AGGAGAATGATGCAGTACCTTATATC 58.154 38.462 0.00 0.00 0.00 1.63
3386 7697 4.036852 GTGTTTTTATCTCAGCATAGGCCC 59.963 45.833 0.00 0.00 42.56 5.80
3393 7741 0.764369 TCAGCATAGGCCCTACCCAG 60.764 60.000 0.00 0.00 42.56 4.45
3427 7776 9.893305 CTTTTAACAAAACTATGGACGAATTCT 57.107 29.630 3.52 0.00 0.00 2.40
3477 8036 6.889301 ATGGATTCTGCATATGGTAACTTG 57.111 37.500 4.56 0.00 37.61 3.16
3506 8065 6.054860 TCCTTTCCTTCATAAGTGGAGAAG 57.945 41.667 0.00 0.00 38.72 2.85
3554 8113 7.331934 AGCAATGTACATACAACTAAGACAGTG 59.668 37.037 9.21 0.00 39.99 3.66
3607 8357 5.220931 GCCTAGATCAGTTTATGCCTGTTTG 60.221 44.000 0.00 0.00 0.00 2.93
3638 8388 0.320421 GCTTTGCTACCGACTGACCA 60.320 55.000 0.00 0.00 0.00 4.02
3768 8518 2.097038 CGTCAAGGAAGGCGAGCTG 61.097 63.158 0.00 0.00 0.00 4.24
3787 8537 0.902531 GGCCAGCCAGTACAAGTAGA 59.097 55.000 3.12 0.00 35.81 2.59
3788 8538 1.134670 GGCCAGCCAGTACAAGTAGAG 60.135 57.143 3.12 0.00 35.81 2.43
3789 8539 1.134670 GCCAGCCAGTACAAGTAGAGG 60.135 57.143 0.00 0.00 0.00 3.69
3790 8540 2.180276 CCAGCCAGTACAAGTAGAGGT 58.820 52.381 0.00 0.00 0.00 3.85
3791 8541 3.362706 CCAGCCAGTACAAGTAGAGGTA 58.637 50.000 0.00 0.00 0.00 3.08
3792 8542 3.381908 CCAGCCAGTACAAGTAGAGGTAG 59.618 52.174 0.00 0.00 0.00 3.18
4033 8800 4.090761 TCTATAACCGGACACCGTATCT 57.909 45.455 9.46 0.00 46.80 1.98
4042 8809 0.623723 ACACCGTATCTGCCCCAAAT 59.376 50.000 0.00 0.00 0.00 2.32
4117 8884 1.079888 GGCAAATCCAGCCCAAACG 60.080 57.895 0.00 0.00 46.50 3.60
4127 8894 3.353836 CCCAAACGCACGGACTGG 61.354 66.667 0.00 0.00 0.00 4.00
4129 8896 2.972505 CAAACGCACGGACTGGCT 60.973 61.111 0.00 0.00 0.00 4.75
4146 8913 0.538287 GCTGGCAACTCCCATATCCC 60.538 60.000 0.00 0.00 33.64 3.85
4147 8914 0.846015 CTGGCAACTCCCATATCCCA 59.154 55.000 0.00 0.00 33.64 4.37
4151 8918 1.522900 CAACTCCCATATCCCACCCT 58.477 55.000 0.00 0.00 0.00 4.34
4175 8942 0.753262 GGTGATATCTGGACGCACCT 59.247 55.000 3.98 0.00 44.23 4.00
4176 8943 1.961394 GGTGATATCTGGACGCACCTA 59.039 52.381 3.98 0.00 44.23 3.08
4198 8965 1.219664 CGTCGGATTTGGCCCACTA 59.780 57.895 0.00 0.00 0.00 2.74
4297 9064 3.846588 ACTCACTTCCCACAGTATCCAAT 59.153 43.478 0.00 0.00 0.00 3.16
4305 9072 3.713764 CCCACAGTATCCAATCTCCTCTT 59.286 47.826 0.00 0.00 0.00 2.85
4325 9092 4.592426 GCGAGTTTCGGCCTAGTT 57.408 55.556 0.00 0.00 40.84 2.24
4342 9109 1.280421 AGTTCTTCATGGAGGGCACTC 59.720 52.381 7.70 7.70 43.20 3.51
4348 9115 1.383109 ATGGAGGGCACTCGATCCA 60.383 57.895 10.51 3.02 44.93 3.41
4352 9119 1.965754 GAGGGCACTCGATCCAGCTT 61.966 60.000 0.00 0.00 33.35 3.74
4354 9121 1.880340 GGCACTCGATCCAGCTTCG 60.880 63.158 0.00 0.00 37.94 3.79
4391 9158 0.107459 GACTGGGTGCTCATCCCTTC 60.107 60.000 0.00 0.00 44.84 3.46
4392 9159 0.548682 ACTGGGTGCTCATCCCTTCT 60.549 55.000 0.00 0.00 44.84 2.85
4400 9167 1.333177 CTCATCCCTTCTAGTCCCGG 58.667 60.000 0.00 0.00 0.00 5.73
4413 9180 2.122813 CCCGGGGAGTAGATGGCT 60.123 66.667 14.71 0.00 0.00 4.75
4417 9184 1.749334 CGGGGAGTAGATGGCTGTCC 61.749 65.000 0.00 0.00 0.00 4.02
4418 9185 0.399233 GGGGAGTAGATGGCTGTCCT 60.399 60.000 0.00 0.00 32.08 3.85
4419 9186 1.044611 GGGAGTAGATGGCTGTCCTC 58.955 60.000 0.00 0.00 32.08 3.71
4420 9187 1.689575 GGGAGTAGATGGCTGTCCTCA 60.690 57.143 0.00 0.00 32.08 3.86
4440 9207 4.821589 GCTCTCCAACGCTCCCGG 62.822 72.222 0.00 0.00 39.22 5.73
4500 9269 0.550914 TCCATTGGGCGCTAGGATTT 59.449 50.000 7.64 0.00 0.00 2.17
4512 9281 2.545946 GCTAGGATTTCGTTGATGGAGC 59.454 50.000 0.00 0.00 0.00 4.70
4525 9294 2.223900 TGATGGAGCGTCATGAGCTTAG 60.224 50.000 17.18 0.74 46.13 2.18
4526 9295 1.474330 TGGAGCGTCATGAGCTTAGA 58.526 50.000 17.18 5.75 46.13 2.10
4567 9337 1.802508 GCGCTTCAAGTGCCAAAGTTT 60.803 47.619 12.22 0.00 45.45 2.66
4582 9352 5.473504 GCCAAAGTTTAGAGTTGAAGATGGA 59.526 40.000 0.00 0.00 0.00 3.41
4616 9386 2.203070 GTTGGCGATGAGGGCGAT 60.203 61.111 0.00 0.00 34.76 4.58
4634 9405 2.159226 CGATTAAGCCTCGAGAGTGGTT 60.159 50.000 15.71 11.67 46.17 3.67
4637 9408 2.640316 AAGCCTCGAGAGTGGTTTTT 57.360 45.000 15.71 0.00 44.07 1.94
4677 9448 7.489435 TCTTCTTCTCTATCTGCATAAAACGTG 59.511 37.037 0.00 0.00 0.00 4.49
4719 9490 3.574284 AAGCAAAGCATTCGCATGTTA 57.426 38.095 0.00 0.00 42.27 2.41
4737 9508 4.091549 TGTTATACCTCGAGTTTCCTGGT 58.908 43.478 12.31 3.44 35.05 4.00
4769 9540 4.725790 ATTTTGCTAGGATGTGCTTTCC 57.274 40.909 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.273179 CCTCCGTCGTTGTCCTCCA 61.273 63.158 0.00 0.00 0.00 3.86
1 2 1.935327 CTCCTCCGTCGTTGTCCTCC 61.935 65.000 0.00 0.00 0.00 4.30
9 10 0.173708 GATTTGAGCTCCTCCGTCGT 59.826 55.000 12.15 0.00 0.00 4.34
45 46 1.167851 CAAATCACTGCATCCACCGT 58.832 50.000 0.00 0.00 0.00 4.83
56 57 0.035317 TCCGCTGACTGCAAATCACT 59.965 50.000 5.11 0.00 43.06 3.41
57 58 0.874390 TTCCGCTGACTGCAAATCAC 59.126 50.000 5.11 0.00 43.06 3.06
58 59 1.603456 TTTCCGCTGACTGCAAATCA 58.397 45.000 5.11 0.70 43.06 2.57
68 70 2.668185 TTCCGCCACTTTTCCGCTGA 62.668 55.000 0.00 0.00 0.00 4.26
115 117 3.188786 GCACCACGTCGCCAGATC 61.189 66.667 0.00 0.00 0.00 2.75
118 120 4.662961 TCTGCACCACGTCGCCAG 62.663 66.667 0.00 0.00 0.00 4.85
174 178 4.404098 CCGTTGGTTCCTCCCCCG 62.404 72.222 0.00 0.00 34.77 5.73
187 191 0.750182 CCCGTAAATGCCCATCCGTT 60.750 55.000 0.00 0.00 0.00 4.44
192 197 1.756561 GCCACCCGTAAATGCCCAT 60.757 57.895 0.00 0.00 0.00 4.00
202 207 2.959707 TGTAAAATTGAAAGCCACCCGT 59.040 40.909 0.00 0.00 0.00 5.28
212 217 6.785076 TGACCACCCTAGATGTAAAATTGAA 58.215 36.000 0.00 0.00 0.00 2.69
216 221 4.788617 ACCTGACCACCCTAGATGTAAAAT 59.211 41.667 0.00 0.00 0.00 1.82
501 565 1.197721 CACATTTCTTGCCACCTCGAC 59.802 52.381 0.00 0.00 0.00 4.20
508 572 0.313672 GGAACGCACATTTCTTGCCA 59.686 50.000 0.00 0.00 36.57 4.92
551 615 3.848975 AGAGAAGGTGGTGAAGGATCAAT 59.151 43.478 0.00 0.00 37.30 2.57
562 626 1.539124 GGTGGGGAGAGAAGGTGGT 60.539 63.158 0.00 0.00 0.00 4.16
634 702 2.550830 AGTGCCAAGTAGTTGTCCAG 57.449 50.000 9.42 0.00 30.95 3.86
647 715 3.430862 GCGCCGATGAAAGTGCCA 61.431 61.111 0.00 0.00 33.38 4.92
860 942 2.037144 GGACGGGTAGATAAAGCCTCA 58.963 52.381 0.00 0.00 34.76 3.86
903 986 1.402896 GGAGGCGATGGGAGTGATGA 61.403 60.000 0.00 0.00 0.00 2.92
1105 1226 6.566564 CGACCGTAGTACTTCTTCAGTAAACA 60.567 42.308 0.00 0.00 39.86 2.83
1107 1228 5.106555 CCGACCGTAGTACTTCTTCAGTAAA 60.107 44.000 0.00 0.00 39.86 2.01
1110 1231 2.746362 CCGACCGTAGTACTTCTTCAGT 59.254 50.000 0.00 0.00 39.87 3.41
1124 2064 1.263356 TTCTTCAGAATCCCGACCGT 58.737 50.000 0.00 0.00 0.00 4.83
1134 2081 3.629855 TCAAAACACGGCATTCTTCAGAA 59.370 39.130 0.00 0.00 38.56 3.02
1340 4814 1.012486 GGTACCGACCGCTGTTCAAG 61.012 60.000 0.00 0.00 35.52 3.02
1450 5577 6.502652 TGTATTCACAAATTGTTCACACAGG 58.497 36.000 0.00 0.00 33.22 4.00
1522 5733 2.547855 GGTTTTGACCATTCCTGCCAAC 60.548 50.000 0.00 0.00 0.00 3.77
1532 5743 4.906618 AGTTCGATACAGGTTTTGACCAT 58.093 39.130 0.00 0.00 0.00 3.55
1534 5745 4.566987 AGAGTTCGATACAGGTTTTGACC 58.433 43.478 0.00 0.00 0.00 4.02
1761 5988 3.521560 TCAGAACACGGCTGCTTATTAG 58.478 45.455 0.00 0.00 33.45 1.73
1814 6041 8.793592 AGTTTGGGAAATTGTGATAAACTAGAC 58.206 33.333 0.00 0.00 35.75 2.59
1856 6083 1.201414 TGCAGCAAAGCTCACATGATG 59.799 47.619 0.00 0.00 36.40 3.07
2140 6368 2.680312 TTGCCTTCTTGATCCTCTCG 57.320 50.000 0.00 0.00 0.00 4.04
2998 7300 5.897377 ACAAACTGGCATTATTGAGTACC 57.103 39.130 12.23 0.00 0.00 3.34
3046 7354 6.151817 AGAGGCATAGATCAACCTTTGTTTTC 59.848 38.462 0.00 0.00 30.95 2.29
3117 7425 4.770795 AGGACACAATAGTAACAGCCATC 58.229 43.478 0.00 0.00 0.00 3.51
3128 7437 7.336679 TGGACACAATTCAATAGGACACAATAG 59.663 37.037 0.00 0.00 0.00 1.73
3393 7741 7.978975 TCCATAGTTTTGTTAAAAGCATATGGC 59.021 33.333 17.58 0.00 37.48 4.40
3427 7776 8.043113 TCGGAATAACTGACTAGTGACTACTTA 58.957 37.037 0.00 0.00 38.36 2.24
3428 7777 6.883217 TCGGAATAACTGACTAGTGACTACTT 59.117 38.462 0.00 0.00 38.36 2.24
3429 7778 6.413052 TCGGAATAACTGACTAGTGACTACT 58.587 40.000 0.00 0.00 40.99 2.57
3430 7779 6.674694 TCGGAATAACTGACTAGTGACTAC 57.325 41.667 0.00 0.00 37.19 2.73
3477 8036 6.264518 TCCACTTATGAAGGAAAGGAAAACAC 59.735 38.462 0.00 0.00 0.00 3.32
3506 8065 8.783833 TGCTCTTGATATAGATTATTCCTTGC 57.216 34.615 0.00 0.00 0.00 4.01
3554 8113 1.182667 GTGATGGTTAAGGTTGCCCC 58.817 55.000 0.00 0.00 0.00 5.80
3607 8357 2.504681 CAAAGCGCGGCAATGGAC 60.505 61.111 8.83 0.00 0.00 4.02
3638 8388 0.396435 TCCACATCAGAAACACGGCT 59.604 50.000 0.00 0.00 0.00 5.52
3768 8518 0.902531 TCTACTTGTACTGGCTGGCC 59.097 55.000 4.43 4.43 0.00 5.36
3787 8537 1.565067 CGAGGGTTGGGTTACTACCT 58.435 55.000 0.00 0.00 43.45 3.08
3788 8538 0.538584 CCGAGGGTTGGGTTACTACC 59.461 60.000 0.00 0.00 43.24 3.18
3789 8539 0.107993 GCCGAGGGTTGGGTTACTAC 60.108 60.000 0.00 0.00 0.00 2.73
3790 8540 1.606885 CGCCGAGGGTTGGGTTACTA 61.607 60.000 0.00 0.00 0.00 1.82
3791 8541 2.951101 CGCCGAGGGTTGGGTTACT 61.951 63.158 0.00 0.00 0.00 2.24
3792 8542 2.435410 CGCCGAGGGTTGGGTTAC 60.435 66.667 0.00 0.00 0.00 2.50
3847 8599 6.198778 CACTCATACAACAACACAATGGTTTG 59.801 38.462 0.00 0.00 38.86 2.93
3878 8630 6.428159 GCAGACATCCATTATTTCCGTTCTAT 59.572 38.462 0.00 0.00 0.00 1.98
3879 8631 5.758296 GCAGACATCCATTATTTCCGTTCTA 59.242 40.000 0.00 0.00 0.00 2.10
3995 8761 7.168302 CGGTTATAGATGCTCTAGACACAAAAG 59.832 40.741 0.00 0.00 31.67 2.27
4062 8829 3.305110 GCAATTTTGTGTCCGGTTAGTG 58.695 45.455 0.00 0.00 0.00 2.74
4066 8833 1.115467 TGGCAATTTTGTGTCCGGTT 58.885 45.000 0.00 0.00 0.00 4.44
4127 8894 0.538287 GGGATATGGGAGTTGCCAGC 60.538 60.000 0.00 0.00 38.95 4.85
4129 8896 0.550914 GTGGGATATGGGAGTTGCCA 59.449 55.000 0.00 0.00 38.95 4.92
4147 8914 4.956700 CGTCCAGATATCACCATATAGGGT 59.043 45.833 2.45 2.45 43.89 4.34
4151 8918 4.159693 GGTGCGTCCAGATATCACCATATA 59.840 45.833 5.32 0.00 44.79 0.86
4158 8925 1.961394 GGTAGGTGCGTCCAGATATCA 59.039 52.381 5.32 0.00 39.02 2.15
4162 8929 1.898154 GTGGTAGGTGCGTCCAGAT 59.102 57.895 0.75 0.00 39.02 2.90
4163 8930 2.632544 CGTGGTAGGTGCGTCCAGA 61.633 63.158 0.75 0.00 39.02 3.86
4175 8942 1.078988 GGCCAAATCCGACGTGGTA 60.079 57.895 0.00 0.00 39.52 3.25
4176 8943 2.359478 GGCCAAATCCGACGTGGT 60.359 61.111 0.00 0.00 39.52 4.16
4198 8965 2.450304 TGGGATCGGATGGGCCAT 60.450 61.111 21.39 21.39 35.94 4.40
4297 9064 0.526662 GAAACTCGCCGAAGAGGAGA 59.473 55.000 10.92 0.00 46.87 3.71
4305 9072 3.060020 CTAGGCCGAAACTCGCCGA 62.060 63.158 0.00 0.00 39.71 5.54
4325 9092 0.614697 TCGAGTGCCCTCCATGAAGA 60.615 55.000 0.00 0.00 33.93 2.87
4342 9109 1.336440 AGACATCTCGAAGCTGGATCG 59.664 52.381 0.00 0.00 41.53 3.69
4348 9115 1.686052 GGATCCAGACATCTCGAAGCT 59.314 52.381 6.95 0.00 0.00 3.74
4352 9119 1.598882 CTCGGATCCAGACATCTCGA 58.401 55.000 13.41 0.00 0.00 4.04
4354 9121 1.611491 GTCCTCGGATCCAGACATCTC 59.389 57.143 13.41 0.00 0.00 2.75
4391 9158 1.548128 CCATCTACTCCCCGGGACTAG 60.548 61.905 26.32 18.71 0.00 2.57
4392 9159 0.481567 CCATCTACTCCCCGGGACTA 59.518 60.000 26.32 5.94 0.00 2.59
4400 9167 1.044611 GAGGACAGCCATCTACTCCC 58.955 60.000 0.00 0.00 36.29 4.30
4413 9180 0.681733 GTTGGAGAGCAGTGAGGACA 59.318 55.000 0.00 0.00 0.00 4.02
4417 9184 0.735632 GAGCGTTGGAGAGCAGTGAG 60.736 60.000 0.00 0.00 35.48 3.51
4418 9185 1.290324 GAGCGTTGGAGAGCAGTGA 59.710 57.895 0.00 0.00 35.48 3.41
4419 9186 1.739562 GGAGCGTTGGAGAGCAGTG 60.740 63.158 0.00 0.00 35.48 3.66
4420 9187 2.659610 GGAGCGTTGGAGAGCAGT 59.340 61.111 0.00 0.00 35.48 4.40
4458 9227 1.323412 CCTCCGGATCGATGAAGACT 58.677 55.000 3.57 0.00 0.00 3.24
4500 9269 0.530288 TCATGACGCTCCATCAACGA 59.470 50.000 0.00 0.00 0.00 3.85
4512 9281 0.101399 AGCGGTCTAAGCTCATGACG 59.899 55.000 0.00 0.00 41.83 4.35
4525 9294 3.720949 AACAAAAGGGTTAAAGCGGTC 57.279 42.857 0.00 0.00 0.00 4.79
4526 9295 3.787785 CAAACAAAAGGGTTAAAGCGGT 58.212 40.909 0.00 0.00 0.00 5.68
4567 9337 7.504238 GGAGACTATCTTCCATCTTCAACTCTA 59.496 40.741 0.00 0.00 0.00 2.43
4582 9352 3.198853 GCCAACCTTGAGGAGACTATCTT 59.801 47.826 3.59 0.00 44.43 2.40
4616 9386 3.764237 AAAACCACTCTCGAGGCTTAA 57.236 42.857 13.56 0.00 0.00 1.85
4672 9443 1.226547 CACCTTTTGCGTGCACGTT 60.227 52.632 36.80 12.55 42.22 3.99
4677 9448 1.008538 CACCTCACCTTTTGCGTGC 60.009 57.895 0.00 0.00 0.00 5.34
4719 9490 2.233922 CACACCAGGAAACTCGAGGTAT 59.766 50.000 18.41 1.54 40.21 2.73
4737 9508 6.265196 ACATCCTAGCAAAATTGAAGAACACA 59.735 34.615 0.00 0.00 0.00 3.72
4769 9540 4.148230 CGACCCTGACGTCTTTCG 57.852 61.111 17.92 14.37 46.00 3.46


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

AutoCloner maintained by Alex Coulton.