Multiple sequence alignment - TraesCS7A01G541700

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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 TraesCS7A01G541700 chr7A 100.000 2333 0 0 1 2333 718266187 718263855 0.000000e+00 4309.0
1 TraesCS7A01G541700 chr7A 87.842 658 52 11 710 1340 718344179 718343523 0.000000e+00 747.0
2 TraesCS7A01G541700 chr7A 85.714 525 47 9 1818 2331 718343039 718342532 1.590000e-146 529.0
3 TraesCS7A01G541700 chr7A 84.232 501 71 8 863 1357 718440851 718440353 4.510000e-132 481.0
4 TraesCS7A01G541700 chr7A 76.955 486 78 22 936 1405 718522975 718522508 1.790000e-61 246.0
5 TraesCS7A01G541700 chr7A 76.749 486 79 23 936 1405 718518072 718517605 8.330000e-60 241.0
6 TraesCS7A01G541700 chr7A 87.805 205 11 8 403 602 718344455 718344260 6.490000e-56 228.0
7 TraesCS7A01G541700 chr7A 87.000 100 10 1 1420 1516 379030523 379030424 2.450000e-20 110.0
8 TraesCS7A01G541700 chr7A 86.813 91 11 1 413 503 718427689 718427600 1.480000e-17 100.0
9 TraesCS7A01G541700 chr7D 92.818 1824 114 12 1 1811 623358258 623360077 0.000000e+00 2627.0
10 TraesCS7A01G541700 chr7D 88.214 560 33 9 1805 2331 623360109 623360668 2.530000e-179 638.0
11 TraesCS7A01G541700 chr7D 88.724 337 38 0 946 1282 622995395 622995731 1.670000e-111 412.0
12 TraesCS7A01G541700 chr7D 88.000 100 9 1 1420 1516 336159859 336159760 5.270000e-22 115.0
13 TraesCS7A01G541700 chr7D 80.159 126 11 2 788 913 622995222 622995333 5.340000e-12 82.4
14 TraesCS7A01G541700 chr7B 89.255 1061 95 13 761 1814 720829232 720828184 0.000000e+00 1310.0
15 TraesCS7A01G541700 chr7B 87.044 548 48 6 1805 2331 720828155 720827610 4.290000e-167 597.0
16 TraesCS7A01G541700 chr7B 83.278 598 58 11 788 1357 720948744 720948161 1.600000e-141 512.0
17 TraesCS7A01G541700 chr7B 83.154 279 22 16 403 664 720829571 720829301 5.010000e-57 231.0
18 TraesCS7A01G541700 chr7B 82.482 274 29 10 403 664 720933157 720932891 3.020000e-54 222.0
19 TraesCS7A01G541700 chr7B 83.108 148 17 5 1019 1159 720925644 720925498 6.770000e-26 128.0
20 TraesCS7A01G541700 chr7B 89.000 100 8 1 1420 1516 310413065 310413164 1.130000e-23 121.0
21 TraesCS7A01G541700 chr7B 94.286 70 4 0 1411 1480 504190092 504190161 8.820000e-20 108.0
22 TraesCS7A01G541700 chr7B 94.737 57 3 0 413 469 720873910 720873854 3.190000e-14 89.8
23 TraesCS7A01G541700 chr7B 90.000 60 4 2 38 97 720829623 720829566 2.490000e-10 76.8
24 TraesCS7A01G541700 chr7B 90.741 54 4 1 38 91 720873973 720873921 1.160000e-08 71.3
25 TraesCS7A01G541700 chr4A 84.802 329 37 9 90 405 115029059 115029387 3.740000e-83 318.0
26 TraesCS7A01G541700 chr4A 84.194 310 38 6 106 404 130592390 130592081 8.160000e-75 291.0
27 TraesCS7A01G541700 chr4A 83.758 314 39 7 106 407 5129025 5129338 1.050000e-73 287.0
28 TraesCS7A01G541700 chr6A 85.577 312 33 5 106 405 377064156 377064467 1.350000e-82 316.0
29 TraesCS7A01G541700 chr6A 85.256 312 34 6 106 405 418145507 418145818 6.260000e-81 311.0
30 TraesCS7A01G541700 chr2A 83.792 327 38 8 90 403 671197849 671197525 1.750000e-76 296.0
31 TraesCS7A01G541700 chr2A 83.601 311 39 5 106 404 176182129 176181819 4.910000e-72 281.0
32 TraesCS7A01G541700 chr2A 84.314 102 13 1 1412 1510 53078409 53078510 1.910000e-16 97.1
33 TraesCS7A01G541700 chr5A 82.727 330 44 8 91 407 119906776 119907105 4.910000e-72 281.0
34 TraesCS7A01G541700 chrUn 85.586 111 13 2 1067 1174 171673433 171673323 1.890000e-21 113.0
35 TraesCS7A01G541700 chrUn 79.882 169 23 8 1013 1174 171732843 171733007 1.890000e-21 113.0
36 TraesCS7A01G541700 chr2D 84.146 82 13 0 1417 1498 589757250 589757331 1.920000e-11 80.5


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 TraesCS7A01G541700 chr7A 718263855 718266187 2332 True 4309.000000 4309 100.000000 1 2333 1 chr7A.!!$R2 2332
1 TraesCS7A01G541700 chr7A 718342532 718344455 1923 True 501.333333 747 87.120333 403 2331 3 chr7A.!!$R7 1928
2 TraesCS7A01G541700 chr7D 623358258 623360668 2410 False 1632.500000 2627 90.516000 1 2331 2 chr7D.!!$F2 2330
3 TraesCS7A01G541700 chr7D 622995222 622995731 509 False 247.200000 412 84.441500 788 1282 2 chr7D.!!$F1 494
4 TraesCS7A01G541700 chr7B 720827610 720829623 2013 True 553.700000 1310 87.363250 38 2331 4 chr7B.!!$R4 2293
5 TraesCS7A01G541700 chr7B 720948161 720948744 583 True 512.000000 512 83.278000 788 1357 1 chr7B.!!$R3 569

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
925 997 0.039617 TTCGCTTGGCCGTTTGAATG 60.04 50.0 0.0 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2201 1.442769 GTGCATCTTGTGGACGATGT 58.557 50.0 0.0 0.0 39.44 3.06 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 7.870445 GCTTAATGTGGGACATTTTGTTTCTTA 59.130 33.333 7.23 0.00 45.80 2.10
85 86 8.732531 CAAGAGTCCAATTTATTAACCGGTTTA 58.267 33.333 27.64 18.10 0.00 2.01
104 105 9.006839 CCGGTTTAACCTTACTATCTTCTTTTT 57.993 33.333 12.66 0.00 35.66 1.94
115 116 7.215719 ACTATCTTCTTTTTGTTTACAGGGC 57.784 36.000 0.00 0.00 0.00 5.19
116 117 7.004691 ACTATCTTCTTTTTGTTTACAGGGCT 58.995 34.615 0.00 0.00 0.00 5.19
117 118 5.767816 TCTTCTTTTTGTTTACAGGGCTC 57.232 39.130 0.00 0.00 0.00 4.70
119 120 5.654650 TCTTCTTTTTGTTTACAGGGCTCAA 59.345 36.000 0.00 0.00 0.00 3.02
121 122 6.478512 TCTTTTTGTTTACAGGGCTCAATT 57.521 33.333 0.00 0.00 0.00 2.32
122 123 6.279882 TCTTTTTGTTTACAGGGCTCAATTG 58.720 36.000 0.00 0.00 0.00 2.32
127 128 6.227298 TGTTTACAGGGCTCAATTGAAAAA 57.773 33.333 9.88 0.00 0.00 1.94
128 129 6.825610 TGTTTACAGGGCTCAATTGAAAAAT 58.174 32.000 9.88 0.00 0.00 1.82
129 130 6.928492 TGTTTACAGGGCTCAATTGAAAAATC 59.072 34.615 9.88 0.00 0.00 2.17
130 131 6.916360 TTACAGGGCTCAATTGAAAAATCT 57.084 33.333 9.88 0.74 0.00 2.40
131 132 5.397142 ACAGGGCTCAATTGAAAAATCTC 57.603 39.130 9.88 0.00 0.00 2.75
132 133 4.834496 ACAGGGCTCAATTGAAAAATCTCA 59.166 37.500 9.88 0.00 0.00 3.27
134 135 4.221482 AGGGCTCAATTGAAAAATCTCACC 59.779 41.667 9.88 2.05 0.00 4.02
136 137 5.511202 GGGCTCAATTGAAAAATCTCACCAA 60.511 40.000 9.88 0.00 0.00 3.67
138 139 5.406477 GCTCAATTGAAAAATCTCACCAACC 59.594 40.000 9.88 0.00 0.00 3.77
140 141 6.882656 TCAATTGAAAAATCTCACCAACCAA 58.117 32.000 5.45 0.00 0.00 3.67
142 143 4.935352 TGAAAAATCTCACCAACCAAGG 57.065 40.909 0.00 0.00 0.00 3.61
143 144 4.285863 TGAAAAATCTCACCAACCAAGGT 58.714 39.130 0.00 0.00 44.48 3.50
144 145 5.450453 TGAAAAATCTCACCAACCAAGGTA 58.550 37.500 0.00 0.00 40.77 3.08
145 146 5.534654 TGAAAAATCTCACCAACCAAGGTAG 59.465 40.000 0.00 0.00 40.77 3.18
146 147 4.993705 AAATCTCACCAACCAAGGTAGA 57.006 40.909 0.00 0.00 40.77 2.59
147 148 5.520748 AAATCTCACCAACCAAGGTAGAT 57.479 39.130 0.00 0.00 40.77 1.98
149 150 3.516586 TCTCACCAACCAAGGTAGATGA 58.483 45.455 0.00 0.00 40.77 2.92
150 151 4.104086 TCTCACCAACCAAGGTAGATGAT 58.896 43.478 0.00 0.00 40.77 2.45
151 152 4.080919 TCTCACCAACCAAGGTAGATGATG 60.081 45.833 0.00 0.00 40.77 3.07
152 153 3.843619 TCACCAACCAAGGTAGATGATGA 59.156 43.478 0.00 0.00 40.77 2.92
153 154 4.080919 TCACCAACCAAGGTAGATGATGAG 60.081 45.833 0.00 0.00 40.77 2.90
154 155 3.846588 ACCAACCAAGGTAGATGATGAGT 59.153 43.478 0.00 0.00 40.98 3.41
155 156 5.030147 ACCAACCAAGGTAGATGATGAGTA 58.970 41.667 0.00 0.00 40.98 2.59
156 157 5.104900 ACCAACCAAGGTAGATGATGAGTAC 60.105 44.000 0.00 0.00 40.98 2.73
157 158 5.129485 CCAACCAAGGTAGATGATGAGTACT 59.871 44.000 0.00 0.00 0.00 2.73
158 159 6.323996 CCAACCAAGGTAGATGATGAGTACTA 59.676 42.308 0.00 0.00 0.00 1.82
159 160 7.015682 CCAACCAAGGTAGATGATGAGTACTAT 59.984 40.741 0.00 0.00 0.00 2.12
161 162 9.656323 AACCAAGGTAGATGATGAGTACTATAA 57.344 33.333 0.00 0.00 0.00 0.98
194 195 6.918022 AGTTTGTAAAAGCACTGAACTAATGC 59.082 34.615 0.00 0.00 39.74 3.56
195 196 5.029650 TGTAAAAGCACTGAACTAATGCG 57.970 39.130 0.00 0.00 44.25 4.73
198 199 4.568152 AAAGCACTGAACTAATGCGTTT 57.432 36.364 0.00 0.00 44.25 3.60
199 200 3.542712 AGCACTGAACTAATGCGTTTG 57.457 42.857 0.00 0.00 44.25 2.93
200 201 2.878406 AGCACTGAACTAATGCGTTTGT 59.122 40.909 0.00 0.00 44.25 2.83
203 204 4.846137 GCACTGAACTAATGCGTTTGTAAG 59.154 41.667 6.17 9.49 0.00 2.34
224 225 9.632807 TGTAAGAAATATGTTTACCAATGCAAC 57.367 29.630 0.00 0.00 0.00 4.17
272 273 4.595762 ACATGCAGTGCTCAATTTTCTT 57.404 36.364 17.60 0.00 0.00 2.52
279 280 9.880157 ATGCAGTGCTCAATTTTCTTTTAATAT 57.120 25.926 17.60 0.00 0.00 1.28
333 334 8.816640 AATCTAAACATGTGATGGAAAACAAC 57.183 30.769 0.00 0.00 33.60 3.32
340 341 7.429633 ACATGTGATGGAAAACAACGAAATTA 58.570 30.769 0.00 0.00 33.60 1.40
397 398 7.571025 AGATAGCCCTATAAACCGAAAAAGAA 58.429 34.615 0.00 0.00 0.00 2.52
565 570 3.510388 CGTAGGACATTGCAAGAGAGA 57.490 47.619 4.94 0.00 0.00 3.10
566 571 3.443037 CGTAGGACATTGCAAGAGAGAG 58.557 50.000 4.94 0.00 0.00 3.20
567 572 3.129462 CGTAGGACATTGCAAGAGAGAGA 59.871 47.826 4.94 0.00 0.00 3.10
602 610 1.949525 CCCACAGAAAATATGGCCTCG 59.050 52.381 3.32 0.00 31.66 4.63
609 630 4.456911 CAGAAAATATGGCCTCGTATGCAT 59.543 41.667 3.32 3.79 0.00 3.96
628 653 3.525537 CATGTCTACAGTAACCCTGCAG 58.474 50.000 6.78 6.78 45.68 4.41
644 669 3.432890 CCTGCAGAGAAGATTAACCCTCC 60.433 52.174 17.39 0.00 0.00 4.30
646 671 2.483889 GCAGAGAAGATTAACCCTCCCG 60.484 54.545 0.00 0.00 0.00 5.14
659 684 0.249911 CCTCCCGTAATAGCCTGTGC 60.250 60.000 0.00 0.00 37.95 4.57
680 705 9.497030 CTGTGCGTGTTGCTTTATAATATAAAA 57.503 29.630 6.87 0.00 46.63 1.52
681 706 9.279904 TGTGCGTGTTGCTTTATAATATAAAAC 57.720 29.630 6.87 3.63 46.63 2.43
682 707 9.279904 GTGCGTGTTGCTTTATAATATAAAACA 57.720 29.630 6.87 5.96 46.63 2.83
683 708 9.497030 TGCGTGTTGCTTTATAATATAAAACAG 57.503 29.630 6.87 0.00 46.63 3.16
731 757 4.633175 TGTGTGTAAACATACGTCCACAT 58.367 39.130 0.00 0.00 40.30 3.21
736 762 6.754675 TGTGTAAACATACGTCCACATATGAG 59.245 38.462 10.38 0.54 33.73 2.90
785 833 4.578516 CAGTCTGACCACATACAAAACCAA 59.421 41.667 3.76 0.00 0.00 3.67
791 839 1.067915 CACATACAAAACCAAGGCCCG 60.068 52.381 0.00 0.00 0.00 6.13
797 845 2.994643 AAAACCAAGGCCCGGGTGAG 62.995 60.000 24.63 9.88 37.50 3.51
855 903 0.732880 CTACCGCGGAGAACAGTGTG 60.733 60.000 35.90 0.00 0.00 3.82
917 986 3.864686 CCACGATTCGCTTGGCCG 61.865 66.667 5.86 0.00 0.00 6.13
925 997 0.039617 TTCGCTTGGCCGTTTGAATG 60.040 50.000 0.00 0.00 0.00 2.67
930 1008 3.003275 CGCTTGGCCGTTTGAATGTATAT 59.997 43.478 0.00 0.00 0.00 0.86
932 1010 4.556699 GCTTGGCCGTTTGAATGTATATCC 60.557 45.833 0.00 0.00 0.00 2.59
933 1011 3.482436 TGGCCGTTTGAATGTATATCCC 58.518 45.455 0.00 0.00 0.00 3.85
934 1012 3.117851 TGGCCGTTTGAATGTATATCCCA 60.118 43.478 0.00 0.00 0.00 4.37
1005 1090 2.825836 CCAGCGAGCCCAATGGAC 60.826 66.667 0.00 0.00 34.60 4.02
1011 1096 3.918253 GAGCCCAATGGACCACGCA 62.918 63.158 0.00 0.00 0.00 5.24
1228 1313 4.459089 GGAGGTCTGTGGCCGCTC 62.459 72.222 18.96 5.86 0.00 5.03
1230 1315 2.037367 AGGTCTGTGGCCGCTCTA 59.963 61.111 18.96 0.00 0.00 2.43
1406 1491 0.892755 TTCTGGTGCTAGGTACGTGG 59.107 55.000 0.00 0.00 0.00 4.94
1440 1525 5.915175 ACTACTCCCTCCGATTCAAAATAC 58.085 41.667 0.00 0.00 0.00 1.89
1510 1598 3.714280 TGACAATTATGGATCCGAGGGAA 59.286 43.478 7.39 0.00 34.34 3.97
1610 1698 4.947883 TGGATTCCTAGAGACCTTCTTGA 58.052 43.478 3.95 0.00 37.36 3.02
1625 1714 5.476945 ACCTTCTTGATATTTGGGTTGACAC 59.523 40.000 0.00 0.00 0.00 3.67
1807 1935 7.793036 AGTTAGCCTCCGTAAGATAGATTTTT 58.207 34.615 0.00 0.00 43.02 1.94
1811 1939 7.435305 AGCCTCCGTAAGATAGATTTTTAGAC 58.565 38.462 0.00 0.00 43.02 2.59
1841 1969 3.181520 GCGTTTCTAGTGCCTGTTACATG 60.182 47.826 0.00 0.00 0.00 3.21
1846 1974 3.838317 TCTAGTGCCTGTTACATGGTCTT 59.162 43.478 0.00 0.00 0.00 3.01
1924 2062 5.013704 TCCTATTTGTCCTTACAGAGGCAAA 59.986 40.000 13.18 13.18 46.13 3.68
2012 2160 4.781934 AGCTGATTACTACAAATCCCCAC 58.218 43.478 0.00 0.00 35.40 4.61
2032 2180 8.723365 TCCCCACAAAGAGTATAATGTAATCAT 58.277 33.333 0.00 0.00 35.59 2.45
2042 2190 6.986817 AGTATAATGTAATCATCATAGCGGCC 59.013 38.462 0.00 0.00 32.56 6.13
2053 2201 5.891551 TCATCATAGCGGCCTATAGATTACA 59.108 40.000 0.00 0.00 33.01 2.41
2090 2238 2.126467 CACAACACGCCTTGAAATTGG 58.874 47.619 0.00 0.00 0.00 3.16
2095 2243 0.975887 ACGCCTTGAAATTGGCCATT 59.024 45.000 6.09 0.00 45.90 3.16
2169 2318 0.112412 ATGGGCGACAAAAGGGTTCT 59.888 50.000 0.00 0.00 0.00 3.01
2182 2331 4.961438 AAGGGTTCTCTTTACGTAACCA 57.039 40.909 15.57 2.30 42.61 3.67
2314 2477 1.376466 GCTGGAGGAAAGACTGGCA 59.624 57.895 0.00 0.00 0.00 4.92
2331 2494 8.023021 AGACTGGCAGACATTATCATAAAGTA 57.977 34.615 23.66 0.00 0.00 2.24
2332 2495 8.486210 AGACTGGCAGACATTATCATAAAGTAA 58.514 33.333 23.66 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 5.860941 TTTTCAATTGAGCCCTGTAAACA 57.139 34.783 8.41 0.00 0.00 2.83
112 113 4.021192 TGGTGAGATTTTTCAATTGAGCCC 60.021 41.667 8.41 0.00 0.00 5.19
114 115 5.406477 GGTTGGTGAGATTTTTCAATTGAGC 59.594 40.000 8.41 0.00 0.00 4.26
115 116 6.514947 TGGTTGGTGAGATTTTTCAATTGAG 58.485 36.000 8.41 0.00 0.00 3.02
116 117 6.477053 TGGTTGGTGAGATTTTTCAATTGA 57.523 33.333 3.38 3.38 0.00 2.57
117 118 6.203338 CCTTGGTTGGTGAGATTTTTCAATTG 59.797 38.462 0.00 0.00 0.00 2.32
119 120 5.366477 ACCTTGGTTGGTGAGATTTTTCAAT 59.634 36.000 0.00 0.00 39.17 2.57
121 122 4.285863 ACCTTGGTTGGTGAGATTTTTCA 58.714 39.130 0.00 0.00 39.17 2.69
122 123 4.937201 ACCTTGGTTGGTGAGATTTTTC 57.063 40.909 0.00 0.00 39.17 2.29
127 128 4.104086 TCATCTACCTTGGTTGGTGAGAT 58.896 43.478 11.95 5.00 41.05 2.75
128 129 3.516586 TCATCTACCTTGGTTGGTGAGA 58.483 45.455 11.95 2.97 41.05 3.27
129 130 3.981071 TCATCTACCTTGGTTGGTGAG 57.019 47.619 11.95 0.00 41.05 3.51
130 131 3.843619 TCATCATCTACCTTGGTTGGTGA 59.156 43.478 16.81 16.81 41.05 4.02
131 132 4.194640 CTCATCATCTACCTTGGTTGGTG 58.805 47.826 7.94 7.94 41.05 4.17
132 133 3.846588 ACTCATCATCTACCTTGGTTGGT 59.153 43.478 0.00 0.00 43.66 3.67
134 135 6.227298 AGTACTCATCATCTACCTTGGTTG 57.773 41.667 0.00 0.00 0.00 3.77
136 137 9.830186 ATTATAGTACTCATCATCTACCTTGGT 57.170 33.333 0.00 0.00 0.00 3.67
168 169 8.073768 GCATTAGTTCAGTGCTTTTACAAACTA 58.926 33.333 0.00 0.00 36.02 2.24
169 170 6.918022 GCATTAGTTCAGTGCTTTTACAAACT 59.082 34.615 0.00 0.00 36.02 2.66
170 171 6.129457 CGCATTAGTTCAGTGCTTTTACAAAC 60.129 38.462 0.00 0.00 36.74 2.93
173 174 4.513692 ACGCATTAGTTCAGTGCTTTTACA 59.486 37.500 0.00 0.00 36.74 2.41
174 175 5.030874 ACGCATTAGTTCAGTGCTTTTAC 57.969 39.130 0.00 0.00 36.74 2.01
175 176 5.682943 AACGCATTAGTTCAGTGCTTTTA 57.317 34.783 0.00 0.00 36.74 1.52
179 180 2.878406 ACAAACGCATTAGTTCAGTGCT 59.122 40.909 0.00 0.00 36.74 4.40
180 181 3.268013 ACAAACGCATTAGTTCAGTGC 57.732 42.857 0.00 0.00 32.43 4.40
181 182 6.223138 TCTTACAAACGCATTAGTTCAGTG 57.777 37.500 0.00 0.00 32.43 3.66
182 183 6.854496 TTCTTACAAACGCATTAGTTCAGT 57.146 33.333 0.00 0.00 32.43 3.41
183 184 9.988350 ATATTTCTTACAAACGCATTAGTTCAG 57.012 29.630 0.00 0.00 32.43 3.02
184 185 9.767684 CATATTTCTTACAAACGCATTAGTTCA 57.232 29.630 0.00 0.00 32.43 3.18
185 186 9.769093 ACATATTTCTTACAAACGCATTAGTTC 57.231 29.630 0.00 0.00 32.43 3.01
191 192 8.516234 TGGTAAACATATTTCTTACAAACGCAT 58.484 29.630 0.00 0.00 0.00 4.73
192 193 7.872881 TGGTAAACATATTTCTTACAAACGCA 58.127 30.769 0.00 0.00 0.00 5.24
193 194 8.730970 TTGGTAAACATATTTCTTACAAACGC 57.269 30.769 0.00 0.00 0.00 4.84
198 199 9.632807 GTTGCATTGGTAAACATATTTCTTACA 57.367 29.630 0.00 0.00 0.00 2.41
199 200 9.632807 TGTTGCATTGGTAAACATATTTCTTAC 57.367 29.630 0.00 0.00 0.00 2.34
203 204 9.757859 CAATTGTTGCATTGGTAAACATATTTC 57.242 29.630 0.00 0.00 34.04 2.17
249 250 5.051891 AGAAAATTGAGCACTGCATGTAC 57.948 39.130 3.30 0.00 0.00 2.90
310 311 6.261158 TCGTTGTTTTCCATCACATGTTTAGA 59.739 34.615 0.00 0.00 0.00 2.10
313 314 5.255710 TCGTTGTTTTCCATCACATGTTT 57.744 34.783 0.00 0.00 0.00 2.83
397 398 6.006449 GGCACCAAAATCATGATATACTCCT 58.994 40.000 9.04 0.00 0.00 3.69
409 410 3.068732 TGAAAACATCGGCACCAAAATCA 59.931 39.130 0.00 0.00 0.00 2.57
507 508 6.704493 GTGTATGTGACTGTACTTTCCTTTCA 59.296 38.462 0.00 0.00 0.00 2.69
602 610 5.050490 CAGGGTTACTGTAGACATGCATAC 58.950 45.833 0.00 0.00 42.42 2.39
628 653 5.548181 ATTACGGGAGGGTTAATCTTCTC 57.452 43.478 0.00 0.00 0.00 2.87
644 669 0.459585 ACACGCACAGGCTATTACGG 60.460 55.000 0.00 0.00 38.10 4.02
646 671 1.202031 GCAACACGCACAGGCTATTAC 60.202 52.381 0.00 0.00 41.79 1.89
696 722 1.774110 ACACACATGGGCTTTTGACA 58.226 45.000 0.00 0.00 0.00 3.58
700 726 4.953940 ATGTTTACACACATGGGCTTTT 57.046 36.364 0.00 0.00 35.97 2.27
702 728 3.438781 CGTATGTTTACACACATGGGCTT 59.561 43.478 0.00 0.00 37.93 4.35
708 734 4.633175 TGTGGACGTATGTTTACACACAT 58.367 39.130 13.73 0.00 40.61 3.21
743 774 6.988580 CAGACTGCCAAGATTCAATATGTCTA 59.011 38.462 0.00 0.00 31.09 2.59
752 783 1.699083 TGGTCAGACTGCCAAGATTCA 59.301 47.619 14.01 0.00 0.00 2.57
855 903 2.128771 TCTGGTGCTAATTGCCCTTC 57.871 50.000 0.00 0.00 42.00 3.46
917 986 6.511767 CGTGAGCTTGGGATATACATTCAAAC 60.512 42.308 0.00 0.00 0.00 2.93
925 997 2.364324 TGACCGTGAGCTTGGGATATAC 59.636 50.000 5.74 0.00 0.00 1.47
930 1008 2.741092 GTGACCGTGAGCTTGGGA 59.259 61.111 5.74 0.00 0.00 4.37
932 1010 2.358737 GGGTGACCGTGAGCTTGG 60.359 66.667 0.00 0.00 43.64 3.61
1005 1090 4.363990 AGCTCGTCCTGTGCGTGG 62.364 66.667 0.00 0.00 41.88 4.94
1011 1096 2.283532 AGGCTCAGCTCGTCCTGT 60.284 61.111 0.00 0.00 34.47 4.00
1188 1273 3.300667 CTTCCAAGCGTGCGCAGTC 62.301 63.158 12.22 5.33 44.88 3.51
1228 1313 1.742768 GCTCCTCGGACACCCATAG 59.257 63.158 0.00 0.00 0.00 2.23
1230 1315 3.083997 GGCTCCTCGGACACCCAT 61.084 66.667 0.00 0.00 0.00 4.00
1305 1390 1.251527 GGAGGGACAAGTCGAGCTCA 61.252 60.000 15.40 0.00 0.00 4.26
1406 1491 3.384146 GGAGGGAGTAGTAGCTAAACACC 59.616 52.174 12.76 12.76 0.00 4.16
1440 1525 4.741676 ACCTTAGTTCAAAACTACGACACG 59.258 41.667 5.26 0.00 43.30 4.49
1480 1565 8.512966 TCGGATCCATAATTGTCACAATTTTA 57.487 30.769 20.74 4.63 0.00 1.52
1503 1591 3.118956 AGCTTGAGACAAGTATTCCCTCG 60.119 47.826 12.07 0.00 0.00 4.63
1510 1598 4.040952 ACAACAGGAGCTTGAGACAAGTAT 59.959 41.667 12.07 3.07 0.00 2.12
1610 1698 6.989759 GGAACTTTTTGTGTCAACCCAAATAT 59.010 34.615 0.00 0.00 31.20 1.28
1625 1714 5.275067 TCTGGTGAAATGGGAACTTTTTG 57.725 39.130 0.00 0.00 37.77 2.44
1631 1720 5.975693 TTACAATCTGGTGAAATGGGAAC 57.024 39.130 0.00 0.00 0.00 3.62
1807 1935 3.825014 ACTAGAAACGCACTGAAGGTCTA 59.175 43.478 0.00 0.00 0.00 2.59
1811 1939 1.461127 GCACTAGAAACGCACTGAAGG 59.539 52.381 0.00 0.00 0.00 3.46
1841 1969 7.113825 GCAAATTGCAATTCATTTTCAAAGACC 59.886 33.333 24.28 0.00 44.26 3.85
1989 2135 4.816925 GTGGGGATTTGTAGTAATCAGCTC 59.183 45.833 0.00 0.00 36.46 4.09
2001 2147 7.182060 ACATTATACTCTTTGTGGGGATTTGT 58.818 34.615 0.00 0.00 0.00 2.83
2032 2180 5.014202 TGTGTAATCTATAGGCCGCTATGA 58.986 41.667 0.00 0.00 0.00 2.15
2037 2185 3.179830 CGATGTGTAATCTATAGGCCGC 58.820 50.000 0.00 0.00 0.00 6.53
2042 2190 7.649057 TCTTGTGGACGATGTGTAATCTATAG 58.351 38.462 0.00 0.00 0.00 1.31
2053 2201 1.442769 GTGCATCTTGTGGACGATGT 58.557 50.000 0.00 0.00 39.44 3.06
2090 2238 2.941720 CAACAGAGCTAAGGAGAATGGC 59.058 50.000 0.00 0.00 0.00 4.40
2095 2243 1.474478 CTCGCAACAGAGCTAAGGAGA 59.526 52.381 0.00 0.00 0.00 3.71
2232 2394 7.891561 TGAGTGAACAATTTTATCCGGAAATT 58.108 30.769 9.01 7.59 37.22 1.82
2233 2395 7.461182 TGAGTGAACAATTTTATCCGGAAAT 57.539 32.000 9.01 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.