Multiple sequence alignment - TraesCS1B01G091400

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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 TraesCS1B01G091400 chr1B 100.000 2195 0 0 1 2195 92853976 92851782 0.000000e+00 4054
1 TraesCS1B01G091400 chr1B 89.398 1179 76 15 170 1329 678498967 678500115 0.000000e+00 1439
2 TraesCS1B01G091400 chr1B 85.885 418 43 4 173 574 107795736 107795319 4.330000e-117 431
3 TraesCS1B01G091400 chr1B 96.532 173 5 1 1 172 557342247 557342075 3.570000e-73 285
4 TraesCS1B01G091400 chr1B 86.939 245 22 6 1 241 383119331 383119569 1.290000e-67 267
5 TraesCS1B01G091400 chr6B 92.407 1159 75 7 173 1329 648885616 648886763 0.000000e+00 1640
6 TraesCS1B01G091400 chr6B 92.069 1160 77 9 173 1329 648849567 648850714 0.000000e+00 1618
7 TraesCS1B01G091400 chr5B 91.810 1160 91 4 173 1329 49392136 49393294 0.000000e+00 1613
8 TraesCS1B01G091400 chr5B 91.027 1159 74 9 172 1329 10496064 10497193 0.000000e+00 1537
9 TraesCS1B01G091400 chr3B 91.817 1161 81 8 171 1329 21575814 21574666 0.000000e+00 1605
10 TraesCS1B01G091400 chr2B 91.424 1166 79 8 171 1329 311834120 311835271 0.000000e+00 1580
11 TraesCS1B01G091400 chr2B 89.637 1158 75 13 173 1329 22380453 22381566 0.000000e+00 1432
12 TraesCS1B01G091400 chr2B 95.647 850 34 3 1347 2195 311836103 311836950 0.000000e+00 1362
13 TraesCS1B01G091400 chr2B 91.837 98 8 0 2098 2195 46985923 46986020 1.060000e-28 137
14 TraesCS1B01G091400 chr2B 91.837 98 8 0 2098 2195 340339507 340339410 1.060000e-28 137
15 TraesCS1B01G091400 chr4B 91.293 1160 86 9 173 1329 108079305 108080452 0.000000e+00 1568
16 TraesCS1B01G091400 chr4B 95.607 865 35 3 1331 2195 560022832 560021971 0.000000e+00 1384
17 TraesCS1B01G091400 chr4B 86.858 1187 105 19 166 1331 222962733 222963889 0.000000e+00 1280
18 TraesCS1B01G091400 chr4B 93.173 747 48 3 1354 2100 222964719 222965462 0.000000e+00 1094
19 TraesCS1B01G091400 chr4B 96.532 173 5 1 1 172 245141063 245141235 3.570000e-73 285
20 TraesCS1B01G091400 chr4B 96.532 173 5 1 1 172 420004956 420004784 3.570000e-73 285
21 TraesCS1B01G091400 chr7B 89.632 1167 93 14 166 1329 101714636 101715777 0.000000e+00 1459
22 TraesCS1B01G091400 chr7B 97.093 172 4 1 2 172 556546427 556546598 2.760000e-74 289
23 TraesCS1B01G091400 chr7B 96.552 174 4 2 1 172 661761342 661761169 9.920000e-74 287
24 TraesCS1B01G091400 chr7B 92.373 118 7 1 2080 2195 549271842 549271725 1.350000e-37 167
25 TraesCS1B01G091400 chr2D 95.838 865 33 3 1331 2195 573298164 573299025 0.000000e+00 1395
26 TraesCS1B01G091400 chr2D 95.065 770 37 1 1331 2100 613465744 613466512 0.000000e+00 1210
27 TraesCS1B01G091400 chr2D 96.532 173 5 1 1 172 610602837 610602665 3.570000e-73 285
28 TraesCS1B01G091400 chr6D 95.974 770 30 1 1331 2100 55758 54990 0.000000e+00 1249
29 TraesCS1B01G091400 chr1D 95.195 770 36 1 1331 2100 417759479 417760247 0.000000e+00 1216
30 TraesCS1B01G091400 chr1D 94.728 626 32 1 704 1329 417758034 417758658 0.000000e+00 972
31 TraesCS1B01G091400 chr1D 83.819 309 37 12 1 300 415875759 415875455 4.610000e-72 281
32 TraesCS1B01G091400 chr5D 93.766 770 47 1 1331 2100 52596386 52597154 0.000000e+00 1155
33 TraesCS1B01G091400 chr5D 91.837 98 8 0 2098 2195 235441994 235441897 1.060000e-28 137
34 TraesCS1B01G091400 chr7A 94.484 707 39 0 1331 2037 7051440 7052146 0.000000e+00 1090
35 TraesCS1B01G091400 chr7A 94.783 115 6 0 2081 2195 114452555 114452441 1.730000e-41 180
36 TraesCS1B01G091400 chr5A 94.407 447 22 1 883 1329 693881418 693880975 0.000000e+00 684
37 TraesCS1B01G091400 chr4D 96.532 173 5 1 1 172 418251329 418251157 3.570000e-73 285
38 TraesCS1B01G091400 chr4D 94.828 116 6 0 2080 2195 437399290 437399175 4.810000e-42 182


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 TraesCS1B01G091400 chr1B 92851782 92853976 2194 True 4054 4054 100.0000 1 2195 1 chr1B.!!$R1 2194
1 TraesCS1B01G091400 chr1B 678498967 678500115 1148 False 1439 1439 89.3980 170 1329 1 chr1B.!!$F2 1159
2 TraesCS1B01G091400 chr6B 648885616 648886763 1147 False 1640 1640 92.4070 173 1329 1 chr6B.!!$F2 1156
3 TraesCS1B01G091400 chr6B 648849567 648850714 1147 False 1618 1618 92.0690 173 1329 1 chr6B.!!$F1 1156
4 TraesCS1B01G091400 chr5B 49392136 49393294 1158 False 1613 1613 91.8100 173 1329 1 chr5B.!!$F2 1156
5 TraesCS1B01G091400 chr5B 10496064 10497193 1129 False 1537 1537 91.0270 172 1329 1 chr5B.!!$F1 1157
6 TraesCS1B01G091400 chr3B 21574666 21575814 1148 True 1605 1605 91.8170 171 1329 1 chr3B.!!$R1 1158
7 TraesCS1B01G091400 chr2B 311834120 311836950 2830 False 1471 1580 93.5355 171 2195 2 chr2B.!!$F3 2024
8 TraesCS1B01G091400 chr2B 22380453 22381566 1113 False 1432 1432 89.6370 173 1329 1 chr2B.!!$F1 1156
9 TraesCS1B01G091400 chr4B 108079305 108080452 1147 False 1568 1568 91.2930 173 1329 1 chr4B.!!$F1 1156
10 TraesCS1B01G091400 chr4B 560021971 560022832 861 True 1384 1384 95.6070 1331 2195 1 chr4B.!!$R2 864
11 TraesCS1B01G091400 chr4B 222962733 222965462 2729 False 1187 1280 90.0155 166 2100 2 chr4B.!!$F3 1934
12 TraesCS1B01G091400 chr7B 101714636 101715777 1141 False 1459 1459 89.6320 166 1329 1 chr7B.!!$F1 1163
13 TraesCS1B01G091400 chr2D 573298164 573299025 861 False 1395 1395 95.8380 1331 2195 1 chr2D.!!$F1 864
14 TraesCS1B01G091400 chr2D 613465744 613466512 768 False 1210 1210 95.0650 1331 2100 1 chr2D.!!$F2 769
15 TraesCS1B01G091400 chr6D 54990 55758 768 True 1249 1249 95.9740 1331 2100 1 chr6D.!!$R1 769
16 TraesCS1B01G091400 chr1D 417758034 417760247 2213 False 1094 1216 94.9615 704 2100 2 chr1D.!!$F1 1396
17 TraesCS1B01G091400 chr5D 52596386 52597154 768 False 1155 1155 93.7660 1331 2100 1 chr5D.!!$F1 769
18 TraesCS1B01G091400 chr7A 7051440 7052146 706 False 1090 1090 94.4840 1331 2037 1 chr7A.!!$F1 706

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
818 854 0.397957 TCCTTCCATACCTAGCCGCA 60.398 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 2984 1.319541 ATCCTACGACCATCGACAGG 58.68 55.0 5.04 10.53 43.74 4.0 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
56 57 8.857098 ACTAAAGAACACACACTTAGATAGACA 58.143 33.333 0.00 0.00 0.00 3.41
57 58 9.862371 CTAAAGAACACACACTTAGATAGACAT 57.138 33.333 0.00 0.00 0.00 3.06
58 59 8.764524 AAAGAACACACACTTAGATAGACATC 57.235 34.615 0.00 0.00 0.00 3.06
59 60 6.868622 AGAACACACACTTAGATAGACATCC 58.131 40.000 0.00 0.00 0.00 3.51
60 61 5.599999 ACACACACTTAGATAGACATCCC 57.400 43.478 0.00 0.00 0.00 3.85
61 62 5.273208 ACACACACTTAGATAGACATCCCT 58.727 41.667 0.00 0.00 0.00 4.20
62 63 5.361285 ACACACACTTAGATAGACATCCCTC 59.639 44.000 0.00 0.00 0.00 4.30
63 64 5.596361 CACACACTTAGATAGACATCCCTCT 59.404 44.000 0.00 0.00 0.00 3.69
64 65 6.773200 CACACACTTAGATAGACATCCCTCTA 59.227 42.308 0.00 0.00 0.00 2.43
65 66 7.001674 ACACACTTAGATAGACATCCCTCTAG 58.998 42.308 0.00 0.00 0.00 2.43
66 67 7.001674 CACACTTAGATAGACATCCCTCTAGT 58.998 42.308 0.00 0.00 0.00 2.57
67 68 7.174253 CACACTTAGATAGACATCCCTCTAGTC 59.826 44.444 0.00 0.00 0.00 2.59
68 69 7.147284 ACACTTAGATAGACATCCCTCTAGTCA 60.147 40.741 0.00 0.00 34.80 3.41
69 70 7.888021 CACTTAGATAGACATCCCTCTAGTCAT 59.112 40.741 0.00 0.00 34.80 3.06
70 71 8.107095 ACTTAGATAGACATCCCTCTAGTCATC 58.893 40.741 0.00 0.00 34.80 2.92
71 72 6.718593 AGATAGACATCCCTCTAGTCATCT 57.281 41.667 0.00 0.00 34.80 2.90
72 73 7.822749 AGATAGACATCCCTCTAGTCATCTA 57.177 40.000 0.00 0.00 33.05 1.98
73 74 8.225863 AGATAGACATCCCTCTAGTCATCTAA 57.774 38.462 0.00 0.00 33.05 2.10
74 75 8.674173 AGATAGACATCCCTCTAGTCATCTAAA 58.326 37.037 0.00 0.00 33.05 1.85
75 76 9.474313 GATAGACATCCCTCTAGTCATCTAAAT 57.526 37.037 0.00 0.00 34.80 1.40
76 77 7.537596 AGACATCCCTCTAGTCATCTAAATG 57.462 40.000 0.00 0.00 34.80 2.32
77 78 7.301420 AGACATCCCTCTAGTCATCTAAATGA 58.699 38.462 0.00 0.00 39.63 2.57
78 79 7.955185 AGACATCCCTCTAGTCATCTAAATGAT 59.045 37.037 0.00 0.00 43.62 2.45
79 80 9.249053 GACATCCCTCTAGTCATCTAAATGATA 57.751 37.037 0.00 0.00 43.62 2.15
80 81 9.781425 ACATCCCTCTAGTCATCTAAATGATAT 57.219 33.333 0.00 0.00 43.62 1.63
82 83 9.781425 ATCCCTCTAGTCATCTAAATGATATGT 57.219 33.333 0.00 0.00 43.62 2.29
83 84 9.029368 TCCCTCTAGTCATCTAAATGATATGTG 57.971 37.037 0.00 0.00 43.62 3.21
84 85 9.029368 CCCTCTAGTCATCTAAATGATATGTGA 57.971 37.037 0.00 0.00 43.62 3.58
101 102 8.902806 TGATATGTGATCCAAATCAACTAAACC 58.097 33.333 0.00 0.00 43.42 3.27
102 103 8.821686 ATATGTGATCCAAATCAACTAAACCA 57.178 30.769 0.00 0.00 43.42 3.67
103 104 7.722949 ATGTGATCCAAATCAACTAAACCAT 57.277 32.000 0.00 0.00 43.42 3.55
104 105 6.923012 TGTGATCCAAATCAACTAAACCATG 58.077 36.000 0.00 0.00 43.42 3.66
105 106 6.493115 TGTGATCCAAATCAACTAAACCATGT 59.507 34.615 0.00 0.00 43.42 3.21
106 107 7.029563 GTGATCCAAATCAACTAAACCATGTC 58.970 38.462 0.00 0.00 43.42 3.06
107 108 5.975693 TCCAAATCAACTAAACCATGTCC 57.024 39.130 0.00 0.00 0.00 4.02
108 109 4.457603 TCCAAATCAACTAAACCATGTCCG 59.542 41.667 0.00 0.00 0.00 4.79
109 110 4.457603 CCAAATCAACTAAACCATGTCCGA 59.542 41.667 0.00 0.00 0.00 4.55
110 111 5.125417 CCAAATCAACTAAACCATGTCCGAT 59.875 40.000 0.00 0.00 0.00 4.18
111 112 6.258160 CAAATCAACTAAACCATGTCCGATC 58.742 40.000 0.00 0.00 0.00 3.69
112 113 4.545208 TCAACTAAACCATGTCCGATCA 57.455 40.909 0.00 0.00 0.00 2.92
113 114 5.097742 TCAACTAAACCATGTCCGATCAT 57.902 39.130 0.00 0.00 0.00 2.45
114 115 5.116180 TCAACTAAACCATGTCCGATCATC 58.884 41.667 0.00 0.00 0.00 2.92
115 116 4.753516 ACTAAACCATGTCCGATCATCA 57.246 40.909 0.00 0.00 0.00 3.07
116 117 4.442706 ACTAAACCATGTCCGATCATCAC 58.557 43.478 0.00 0.00 0.00 3.06
117 118 1.939974 AACCATGTCCGATCATCACG 58.060 50.000 0.00 0.00 0.00 4.35
118 119 0.824109 ACCATGTCCGATCATCACGT 59.176 50.000 0.00 0.00 0.00 4.49
119 120 1.211743 CCATGTCCGATCATCACGTG 58.788 55.000 9.94 9.94 0.00 4.49
120 121 1.202405 CCATGTCCGATCATCACGTGA 60.202 52.381 22.48 22.48 42.06 4.35
121 122 2.122564 CATGTCCGATCATCACGTGAG 58.877 52.381 24.41 15.36 40.92 3.51
122 123 1.459450 TGTCCGATCATCACGTGAGA 58.541 50.000 24.41 19.81 40.92 3.27
123 124 2.024414 TGTCCGATCATCACGTGAGAT 58.976 47.619 24.41 23.15 40.92 2.75
124 125 2.223572 TGTCCGATCATCACGTGAGATG 60.224 50.000 24.41 17.82 45.28 2.90
125 126 1.338020 TCCGATCATCACGTGAGATGG 59.662 52.381 24.41 22.63 44.30 3.51
126 127 1.338020 CCGATCATCACGTGAGATGGA 59.662 52.381 26.12 20.22 44.30 3.41
127 128 2.606551 CCGATCATCACGTGAGATGGAG 60.607 54.545 26.12 19.00 44.30 3.86
128 129 2.033927 CGATCATCACGTGAGATGGAGT 59.966 50.000 24.41 8.11 44.30 3.85
129 130 3.251004 CGATCATCACGTGAGATGGAGTA 59.749 47.826 24.41 2.74 44.30 2.59
130 131 4.083057 CGATCATCACGTGAGATGGAGTAT 60.083 45.833 24.41 7.49 44.30 2.12
131 132 4.837896 TCATCACGTGAGATGGAGTATC 57.162 45.455 24.41 0.00 44.30 2.24
133 134 4.889995 TCATCACGTGAGATGGAGTATCTT 59.110 41.667 24.41 0.00 46.12 2.40
134 135 4.902443 TCACGTGAGATGGAGTATCTTC 57.098 45.455 15.76 0.00 46.12 2.87
135 136 4.270008 TCACGTGAGATGGAGTATCTTCA 58.730 43.478 15.76 0.00 46.12 3.02
136 137 4.705023 TCACGTGAGATGGAGTATCTTCAA 59.295 41.667 15.76 0.00 46.12 2.69
137 138 5.360999 TCACGTGAGATGGAGTATCTTCAAT 59.639 40.000 15.76 0.00 46.12 2.57
138 139 5.461407 CACGTGAGATGGAGTATCTTCAATG 59.539 44.000 10.90 0.00 46.12 2.82
139 140 4.987285 CGTGAGATGGAGTATCTTCAATGG 59.013 45.833 0.00 0.00 46.12 3.16
140 141 5.452496 CGTGAGATGGAGTATCTTCAATGGT 60.452 44.000 0.00 0.00 46.12 3.55
141 142 5.757320 GTGAGATGGAGTATCTTCAATGGTG 59.243 44.000 0.00 0.00 46.12 4.17
142 143 5.662657 TGAGATGGAGTATCTTCAATGGTGA 59.337 40.000 0.00 0.00 46.12 4.02
143 144 6.156775 TGAGATGGAGTATCTTCAATGGTGAA 59.843 38.462 0.00 0.00 46.12 3.18
144 145 6.352516 AGATGGAGTATCTTCAATGGTGAAC 58.647 40.000 0.00 0.00 43.68 3.18
145 146 5.497464 TGGAGTATCTTCAATGGTGAACA 57.503 39.130 0.00 0.00 38.88 3.18
146 147 6.065976 TGGAGTATCTTCAATGGTGAACAT 57.934 37.500 0.00 0.00 38.88 2.71
147 148 6.115446 TGGAGTATCTTCAATGGTGAACATC 58.885 40.000 0.00 0.00 38.88 3.06
148 149 6.115446 GGAGTATCTTCAATGGTGAACATCA 58.885 40.000 0.00 0.00 38.88 3.07
149 150 6.037610 GGAGTATCTTCAATGGTGAACATCAC 59.962 42.308 1.88 1.88 38.88 3.06
150 151 6.715280 AGTATCTTCAATGGTGAACATCACT 58.285 36.000 10.06 0.00 46.19 3.41
151 152 7.851228 AGTATCTTCAATGGTGAACATCACTA 58.149 34.615 10.06 4.82 46.19 2.74
153 154 6.990341 TCTTCAATGGTGAACATCACTATG 57.010 37.500 9.66 7.08 45.90 2.23
154 155 6.475504 TCTTCAATGGTGAACATCACTATGT 58.524 36.000 9.66 0.00 45.90 2.29
212 213 2.775911 AGACAGAGCAATAGCAGCAA 57.224 45.000 0.00 0.00 45.49 3.91
218 219 0.606401 AGCAATAGCAGCAACGTGGT 60.606 50.000 0.00 0.00 45.49 4.16
455 460 2.303022 CGGATCAGCTAATGTACCCCAT 59.697 50.000 0.00 0.00 34.36 4.00
550 583 4.843331 GCCCCTCCCCCTCCATCA 62.843 72.222 0.00 0.00 0.00 3.07
571 604 1.304891 CCCTCCCCCAACCAATCTTA 58.695 55.000 0.00 0.00 0.00 2.10
591 624 2.267006 CACACCGCAGATGCCTCT 59.733 61.111 0.00 0.00 37.91 3.69
670 704 1.984570 CCCCCAGCTCGTCTTCTCA 60.985 63.158 0.00 0.00 0.00 3.27
737 772 3.066190 CGGCGACCACCAGAGGTA 61.066 66.667 0.00 0.00 43.38 3.08
772 808 1.619977 GCTCCCTCCTTCTCCACTACA 60.620 57.143 0.00 0.00 0.00 2.74
808 844 1.411216 GGGACGACTCCTCCTTCCATA 60.411 57.143 0.00 0.00 36.68 2.74
818 854 0.397957 TCCTTCCATACCTAGCCGCA 60.398 55.000 0.00 0.00 0.00 5.69
859 903 2.723273 CTTGAAACCCTAGCCCGAATT 58.277 47.619 0.00 0.00 0.00 2.17
930 975 6.782988 TCTTCTTCCTCTGGTTCTTCTTCTTA 59.217 38.462 0.00 0.00 0.00 2.10
1233 1297 1.806542 ACGAGCTGCTTGTGTTTATGG 59.193 47.619 21.34 0.00 0.00 2.74
1452 2357 3.776969 TCTTGCAGGTATGACTCATCCTT 59.223 43.478 0.00 0.00 0.00 3.36
2029 2936 3.670625 TGTGTACTTACAATGCCTGTCC 58.329 45.455 0.00 0.00 39.64 4.02
2043 2950 0.695803 CTGTCCCATAGGGCCCTTCT 60.696 60.000 34.04 15.99 43.94 2.85
2061 2969 4.561105 CTTCTCAGCGAGACCTAAGTTTT 58.439 43.478 7.61 0.00 38.51 2.43
2063 2971 5.312120 TCTCAGCGAGACCTAAGTTTTAG 57.688 43.478 4.47 0.00 33.35 1.85
2068 2976 5.869888 CAGCGAGACCTAAGTTTTAGTTGAT 59.130 40.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.857098 TGTCTATCTAAGTGTGTGTTCTTTAGT 58.143 33.333 0.00 0.00 0.00 2.24
31 32 9.862371 ATGTCTATCTAAGTGTGTGTTCTTTAG 57.138 33.333 0.00 0.00 0.00 1.85
32 33 9.856488 GATGTCTATCTAAGTGTGTGTTCTTTA 57.144 33.333 0.00 0.00 0.00 1.85
33 34 7.819900 GGATGTCTATCTAAGTGTGTGTTCTTT 59.180 37.037 0.00 0.00 33.68 2.52
34 35 7.324178 GGATGTCTATCTAAGTGTGTGTTCTT 58.676 38.462 0.00 0.00 33.68 2.52
35 36 6.127310 GGGATGTCTATCTAAGTGTGTGTTCT 60.127 42.308 0.00 0.00 33.68 3.01
36 37 6.043411 GGGATGTCTATCTAAGTGTGTGTTC 58.957 44.000 0.00 0.00 33.68 3.18
37 38 5.721960 AGGGATGTCTATCTAAGTGTGTGTT 59.278 40.000 0.00 0.00 33.68 3.32
38 39 5.273208 AGGGATGTCTATCTAAGTGTGTGT 58.727 41.667 0.00 0.00 33.68 3.72
39 40 5.596361 AGAGGGATGTCTATCTAAGTGTGTG 59.404 44.000 0.00 0.00 33.68 3.82
40 41 5.772004 AGAGGGATGTCTATCTAAGTGTGT 58.228 41.667 0.00 0.00 33.68 3.72
41 42 7.001674 ACTAGAGGGATGTCTATCTAAGTGTG 58.998 42.308 0.00 0.00 33.68 3.82
42 43 7.147284 TGACTAGAGGGATGTCTATCTAAGTGT 60.147 40.741 0.00 0.00 33.68 3.55
43 44 7.227873 TGACTAGAGGGATGTCTATCTAAGTG 58.772 42.308 0.00 0.00 33.68 3.16
44 45 7.395525 TGACTAGAGGGATGTCTATCTAAGT 57.604 40.000 0.00 0.00 33.68 2.24
45 46 8.328758 AGATGACTAGAGGGATGTCTATCTAAG 58.671 40.741 0.00 0.00 32.48 2.18
46 47 8.225863 AGATGACTAGAGGGATGTCTATCTAA 57.774 38.462 0.00 0.00 32.48 2.10
47 48 7.822749 AGATGACTAGAGGGATGTCTATCTA 57.177 40.000 0.00 0.00 32.48 1.98
48 49 6.718593 AGATGACTAGAGGGATGTCTATCT 57.281 41.667 0.00 0.00 33.68 1.98
49 50 8.871629 TTTAGATGACTAGAGGGATGTCTATC 57.128 38.462 0.00 0.00 0.00 2.08
50 51 9.253832 CATTTAGATGACTAGAGGGATGTCTAT 57.746 37.037 0.00 0.00 35.16 1.98
51 52 8.448816 TCATTTAGATGACTAGAGGGATGTCTA 58.551 37.037 0.00 0.00 37.37 2.59
52 53 7.301420 TCATTTAGATGACTAGAGGGATGTCT 58.699 38.462 0.00 0.00 37.37 3.41
53 54 7.531857 TCATTTAGATGACTAGAGGGATGTC 57.468 40.000 0.00 0.00 37.37 3.06
54 55 9.781425 ATATCATTTAGATGACTAGAGGGATGT 57.219 33.333 0.00 0.00 44.64 3.06
56 57 9.781425 ACATATCATTTAGATGACTAGAGGGAT 57.219 33.333 0.00 0.00 44.64 3.85
57 58 9.029368 CACATATCATTTAGATGACTAGAGGGA 57.971 37.037 0.00 0.00 44.64 4.20
58 59 9.029368 TCACATATCATTTAGATGACTAGAGGG 57.971 37.037 0.00 0.00 44.64 4.30
75 76 8.902806 GGTTTAGTTGATTTGGATCACATATCA 58.097 33.333 10.84 10.84 43.03 2.15
76 77 8.902806 TGGTTTAGTTGATTTGGATCACATATC 58.097 33.333 0.00 1.91 41.84 1.63
77 78 8.821686 TGGTTTAGTTGATTTGGATCACATAT 57.178 30.769 0.00 0.00 41.84 1.78
78 79 8.685427 CATGGTTTAGTTGATTTGGATCACATA 58.315 33.333 0.00 0.00 41.84 2.29
79 80 7.178983 ACATGGTTTAGTTGATTTGGATCACAT 59.821 33.333 0.00 0.00 41.84 3.21
80 81 6.493115 ACATGGTTTAGTTGATTTGGATCACA 59.507 34.615 0.00 0.00 41.84 3.58
81 82 6.924111 ACATGGTTTAGTTGATTTGGATCAC 58.076 36.000 0.00 0.00 41.84 3.06
82 83 6.152661 GGACATGGTTTAGTTGATTTGGATCA 59.847 38.462 0.00 0.00 40.46 2.92
83 84 6.564328 GGACATGGTTTAGTTGATTTGGATC 58.436 40.000 0.00 0.00 0.00 3.36
84 85 5.125417 CGGACATGGTTTAGTTGATTTGGAT 59.875 40.000 0.00 0.00 0.00 3.41
85 86 4.457603 CGGACATGGTTTAGTTGATTTGGA 59.542 41.667 0.00 0.00 0.00 3.53
86 87 4.457603 TCGGACATGGTTTAGTTGATTTGG 59.542 41.667 0.00 0.00 0.00 3.28
87 88 5.621197 TCGGACATGGTTTAGTTGATTTG 57.379 39.130 0.00 0.00 0.00 2.32
88 89 5.943416 TGATCGGACATGGTTTAGTTGATTT 59.057 36.000 0.00 0.00 0.00 2.17
89 90 5.496556 TGATCGGACATGGTTTAGTTGATT 58.503 37.500 0.00 0.00 0.00 2.57
90 91 5.097742 TGATCGGACATGGTTTAGTTGAT 57.902 39.130 0.00 0.00 0.00 2.57
91 92 4.545208 TGATCGGACATGGTTTAGTTGA 57.455 40.909 0.00 0.00 0.00 3.18
92 93 4.875536 TGATGATCGGACATGGTTTAGTTG 59.124 41.667 0.00 0.00 0.00 3.16
93 94 4.876107 GTGATGATCGGACATGGTTTAGTT 59.124 41.667 0.00 0.00 0.00 2.24
94 95 4.442706 GTGATGATCGGACATGGTTTAGT 58.557 43.478 0.00 0.00 0.00 2.24
95 96 3.490896 CGTGATGATCGGACATGGTTTAG 59.509 47.826 0.00 0.00 0.00 1.85
96 97 3.118920 ACGTGATGATCGGACATGGTTTA 60.119 43.478 0.00 0.00 0.00 2.01
97 98 2.279741 CGTGATGATCGGACATGGTTT 58.720 47.619 0.00 0.00 0.00 3.27
98 99 1.207089 ACGTGATGATCGGACATGGTT 59.793 47.619 0.00 0.00 0.00 3.67
99 100 0.824109 ACGTGATGATCGGACATGGT 59.176 50.000 0.00 0.00 0.00 3.55
100 101 1.202405 TCACGTGATGATCGGACATGG 60.202 52.381 15.76 0.00 29.99 3.66
101 102 2.122564 CTCACGTGATGATCGGACATG 58.877 52.381 20.40 0.00 36.48 3.21
102 103 2.024414 TCTCACGTGATGATCGGACAT 58.976 47.619 20.40 0.00 36.48 3.06
103 104 1.459450 TCTCACGTGATGATCGGACA 58.541 50.000 20.40 0.00 36.48 4.02
104 105 2.389059 CATCTCACGTGATGATCGGAC 58.611 52.381 20.40 0.00 44.71 4.79
105 106 1.338020 CCATCTCACGTGATGATCGGA 59.662 52.381 20.40 12.04 44.71 4.55
106 107 1.338020 TCCATCTCACGTGATGATCGG 59.662 52.381 20.40 21.82 44.71 4.18
107 108 2.033927 ACTCCATCTCACGTGATGATCG 59.966 50.000 20.40 15.51 44.71 3.69
108 109 3.724508 ACTCCATCTCACGTGATGATC 57.275 47.619 20.40 0.00 44.71 2.92
109 110 5.076182 AGATACTCCATCTCACGTGATGAT 58.924 41.667 20.40 19.36 44.71 2.45
110 111 4.464947 AGATACTCCATCTCACGTGATGA 58.535 43.478 20.40 18.00 44.71 2.92
111 112 4.844998 AGATACTCCATCTCACGTGATG 57.155 45.455 20.40 15.30 40.09 3.07
112 113 4.889995 TGAAGATACTCCATCTCACGTGAT 59.110 41.667 20.40 1.42 43.56 3.06
113 114 4.270008 TGAAGATACTCCATCTCACGTGA 58.730 43.478 18.88 18.88 43.56 4.35
114 115 4.639135 TGAAGATACTCCATCTCACGTG 57.361 45.455 9.94 9.94 43.56 4.49
115 116 5.452496 CCATTGAAGATACTCCATCTCACGT 60.452 44.000 0.00 0.00 43.56 4.49
116 117 4.987285 CCATTGAAGATACTCCATCTCACG 59.013 45.833 0.00 0.00 43.56 4.35
117 118 5.757320 CACCATTGAAGATACTCCATCTCAC 59.243 44.000 0.00 0.00 43.56 3.51
118 119 5.662657 TCACCATTGAAGATACTCCATCTCA 59.337 40.000 0.00 0.00 43.56 3.27
119 120 6.166984 TCACCATTGAAGATACTCCATCTC 57.833 41.667 0.00 0.00 43.56 2.75
120 121 6.070021 TGTTCACCATTGAAGATACTCCATCT 60.070 38.462 0.00 0.00 46.48 2.90
121 122 6.115446 TGTTCACCATTGAAGATACTCCATC 58.885 40.000 0.00 0.00 42.60 3.51
122 123 6.065976 TGTTCACCATTGAAGATACTCCAT 57.934 37.500 0.00 0.00 42.60 3.41
123 124 5.497464 TGTTCACCATTGAAGATACTCCA 57.503 39.130 0.00 0.00 42.60 3.86
124 125 6.037610 GTGATGTTCACCATTGAAGATACTCC 59.962 42.308 0.00 0.00 43.87 3.85
125 126 7.009568 GTGATGTTCACCATTGAAGATACTC 57.990 40.000 0.00 0.00 43.87 2.59
126 127 6.992063 GTGATGTTCACCATTGAAGATACT 57.008 37.500 0.00 0.00 43.87 2.12
163 164 9.917887 AGCTTTTTCCTAGTAGTGTATAGTAGA 57.082 33.333 0.00 0.00 0.00 2.59
212 213 1.743995 GCGGCTTCCATTACCACGT 60.744 57.895 0.00 0.00 0.00 4.49
218 219 1.034356 TAGTAGCGCGGCTTCCATTA 58.966 50.000 8.83 0.00 40.44 1.90
339 344 2.240279 CCCCTCGCTGCTACTATAAGT 58.760 52.381 0.00 0.00 0.00 2.24
409 414 6.371825 GGTCAATTTATAGTAGTAGCATGGGC 59.628 42.308 0.00 0.00 41.61 5.36
455 460 0.238289 GTGCTTCGCTGCTGCTAAAA 59.762 50.000 14.03 4.65 36.97 1.52
550 583 2.120571 ATTGGTTGGGGGAGGGGT 60.121 61.111 0.00 0.00 0.00 4.95
571 604 4.722700 GGCATCTGCGGTGTGGGT 62.723 66.667 0.00 0.00 43.26 4.51
634 668 2.282958 AGGTGGAAGGAGACGCGA 60.283 61.111 15.93 0.00 0.00 5.87
772 808 3.655211 CCCCTCTGCTGGTGCCTT 61.655 66.667 0.00 0.00 38.71 4.35
818 854 0.683412 GGTGTTAGAGGTTGGACGGT 59.317 55.000 0.00 0.00 0.00 4.83
859 903 4.383861 CTGCTGCACCTCTGCCGA 62.384 66.667 0.00 0.00 43.51 5.54
930 975 1.070604 ATGCATCAGATCCGGGGAAT 58.929 50.000 0.00 0.00 0.00 3.01
1044 1094 3.491964 CGTCCGCTATCCTCATACCAAAA 60.492 47.826 0.00 0.00 0.00 2.44
1207 1271 2.979676 CAAGCAGCTCGTGGGCAA 60.980 61.111 0.00 0.00 34.17 4.52
1213 1277 1.806542 CCATAAACACAAGCAGCTCGT 59.193 47.619 0.00 0.00 0.00 4.18
1233 1297 4.412207 GGTGAACAGAAAAACGATATGGC 58.588 43.478 0.00 0.00 0.00 4.40
1276 1341 0.252513 TTGTAGGTGGGCAGAGGCTA 60.253 55.000 0.00 0.00 40.87 3.93
1452 2357 3.146066 ACAAAGGCGAAGTAAGAATGCA 58.854 40.909 0.00 0.00 0.00 3.96
1569 2476 8.540388 ACACTATACATAGGTCAGACAAAACAT 58.460 33.333 2.17 0.00 34.69 2.71
1755 2662 7.622081 TGTTATTCTATTTGACCCCAGTCTCTA 59.378 37.037 0.00 0.00 43.91 2.43
1759 2666 6.884836 ACTTGTTATTCTATTTGACCCCAGTC 59.115 38.462 0.00 0.00 43.83 3.51
2029 2936 1.453669 GCTGAGAAGGGCCCTATGG 59.546 63.158 28.96 14.81 0.00 2.74
2043 2950 5.010314 TCAACTAAAACTTAGGTCTCGCTGA 59.990 40.000 0.00 0.00 0.00 4.26
2061 2969 7.147724 ACCATCGACAGGAAAGATAATCAACTA 60.148 37.037 12.36 0.00 0.00 2.24
2063 2971 5.817816 ACCATCGACAGGAAAGATAATCAAC 59.182 40.000 12.36 0.00 0.00 3.18
2068 2976 3.446161 ACGACCATCGACAGGAAAGATAA 59.554 43.478 12.36 0.00 43.74 1.75
2076 2984 1.319541 ATCCTACGACCATCGACAGG 58.680 55.000 5.04 10.53 43.74 4.00
2135 3043 4.990426 GGCTAAACCAACGACAGTAGTTTA 59.010 41.667 0.00 0.00 37.78 2.01


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

AutoCloner maintained by Alex Coulton.