Multiple sequence alignment - TraesCS7D01G483200

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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 TraesCS7D01G483200 chr7D 100.000 4639 0 0 1 4639 593240244 593235606 0.000000e+00 8567.0
1 TraesCS7D01G483200 chr7D 80.579 484 43 19 3884 4321 597515266 597515744 4.480000e-85 326.0
2 TraesCS7D01G483200 chr7D 80.165 484 45 15 3884 4321 27354046 27354524 9.690000e-82 315.0
3 TraesCS7D01G483200 chr7D 79.794 485 46 16 3884 4321 228136915 228137394 5.830000e-79 305.0
4 TraesCS7D01G483200 chr7D 79.588 485 47 19 3884 4321 39862787 39862308 2.710000e-77 300.0
5 TraesCS7D01G483200 chr7D 87.662 154 2 9 4498 4639 27354601 27354749 3.710000e-36 163.0
6 TraesCS7D01G483200 chr7D 86.928 153 3 9 4499 4639 228137470 228137617 6.210000e-34 156.0
7 TraesCS7D01G483200 chr7A 91.315 4698 259 63 19 4639 686023134 686018509 0.000000e+00 6277.0
8 TraesCS7D01G483200 chr7B 90.151 4183 242 92 17 4104 667745909 667750016 0.000000e+00 5286.0
9 TraesCS7D01G483200 chr7B 85.139 323 32 9 4109 4415 667750338 667750660 2.690000e-82 316.0
10 TraesCS7D01G483200 chr7B 93.289 149 4 3 4497 4639 667752670 667752818 1.010000e-51 215.0
11 TraesCS7D01G483200 chr7B 92.857 140 6 4 4341 4476 667752547 667752686 2.830000e-47 200.0
12 TraesCS7D01G483200 chr6A 84.354 294 31 9 3884 4168 325084231 325084518 1.640000e-69 274.0
13 TraesCS7D01G483200 chr6A 83.226 155 8 10 4498 4639 325084756 325084905 4.870000e-25 126.0
14 TraesCS7D01G483200 chr4B 87.662 154 2 9 4498 4639 20347930 20348078 3.710000e-36 163.0
15 TraesCS7D01G483200 chr4B 88.073 109 13 0 3018 3126 578227123 578227231 3.770000e-26 130.0
16 TraesCS7D01G483200 chr4B 87.931 58 7 0 2295 2352 578225906 578225963 8.330000e-08 69.4
17 TraesCS7D01G483200 chr1A 85.366 164 16 6 3884 4039 55285190 55285027 3.710000e-36 163.0
18 TraesCS7D01G483200 chr6D 89.147 129 11 3 3018 3143 291235624 291235752 1.730000e-34 158.0
19 TraesCS7D01G483200 chr1D 86.364 154 4 9 4498 4639 422493605 422493457 8.040000e-33 152.0
20 TraesCS7D01G483200 chr4A 86.364 154 1 10 4498 4639 592505381 592505236 2.890000e-32 150.0
21 TraesCS7D01G483200 chr4A 86.364 154 1 10 4498 4639 593071761 593071616 2.890000e-32 150.0
22 TraesCS7D01G483200 chr4A 85.714 154 2 10 4498 4639 592784202 592784057 1.350000e-30 145.0
23 TraesCS7D01G483200 chr4A 88.073 109 13 0 3018 3126 6635059 6634951 3.770000e-26 130.0
24 TraesCS7D01G483200 chr4D 88.073 109 13 0 3018 3126 462744650 462744542 3.770000e-26 130.0
25 TraesCS7D01G483200 chr3B 100.000 30 0 0 1765 1794 580782988 580783017 6.480000e-04 56.5
26 TraesCS7D01G483200 chr3D 100.000 28 0 0 1767 1794 442971817 442971844 8.000000e-03 52.8


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 TraesCS7D01G483200 chr7D 593235606 593240244 4638 True 8567.00 8567 100.0000 1 4639 1 chr7D.!!$R2 4638
1 TraesCS7D01G483200 chr7D 27354046 27354749 703 False 239.00 315 83.9135 3884 4639 2 chr7D.!!$F2 755
2 TraesCS7D01G483200 chr7D 228136915 228137617 702 False 230.50 305 83.3610 3884 4639 2 chr7D.!!$F3 755
3 TraesCS7D01G483200 chr7A 686018509 686023134 4625 True 6277.00 6277 91.3150 19 4639 1 chr7A.!!$R1 4620
4 TraesCS7D01G483200 chr7B 667745909 667752818 6909 False 1504.25 5286 90.3590 17 4639 4 chr7B.!!$F1 4622

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
404 414 0.176680 CCATGGAGAAGGACCGAGTG 59.823 60.0 5.56 0.00 0.00 3.51 F
1197 1238 0.103208 AGGCTAGCTACACATGCGTC 59.897 55.0 15.72 0.00 35.28 5.19 F
2260 2357 0.035881 ATACATCAGGCCGGATGCTG 59.964 55.0 36.50 21.51 46.81 4.41 F
2419 2516 0.535780 TCACAGGGCTTGCTGACTTG 60.536 55.0 0.00 0.00 36.75 3.16 F
2434 2531 1.291877 ACTTGCGCGTCCTGTTCATC 61.292 55.0 8.43 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2357 0.461693 AGCAAAGAGGCTCAGCGATC 60.462 55.000 18.26 0.50 41.05 3.69 R
2891 3010 0.031994 GTGGTGGTGGCACATGAAAC 59.968 55.000 20.82 8.79 44.52 2.78 R
3270 3416 1.968017 GCTGCTGCTGGTAGTGCAA 60.968 57.895 8.53 0.00 40.13 4.08 R
3290 3436 2.124193 TGCTGCAGGTGCTGTTGT 60.124 55.556 17.12 0.00 42.66 3.32 R
3974 4134 2.491693 CCCATAACGCAACTGACCAAAT 59.508 45.455 0.00 0.00 0.00 2.32 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
44 45 4.906618 TCTTGGTAGTTGAGGCCTTTTAG 58.093 43.478 6.77 0.00 0.00 1.85
47 48 3.181438 TGGTAGTTGAGGCCTTTTAGCAA 60.181 43.478 6.77 2.57 0.00 3.91
54 55 2.229062 GAGGCCTTTTAGCAAACTGGAC 59.771 50.000 6.77 0.00 0.00 4.02
69 70 2.175811 GACAATTGCCCGTGCGTC 59.824 61.111 5.05 0.00 41.78 5.19
89 94 4.259930 CGTCGAAACGGGTGTAAATATTCC 60.260 45.833 0.00 0.00 45.21 3.01
112 117 8.392631 TCCATAGTATGTTAGCCCATGATTAT 57.607 34.615 9.28 0.00 0.00 1.28
254 260 3.376234 TGTTATACGAAGGACGAGGTGAG 59.624 47.826 0.00 0.00 45.77 3.51
270 276 1.068748 GTGAGCGACAGAACCTTACGA 60.069 52.381 0.00 0.00 0.00 3.43
324 330 3.128764 TCCATCAGTCTTGTACACTAGCG 59.871 47.826 0.00 0.00 0.00 4.26
345 355 2.608090 GGTAACTAAGCAATGAGACCGC 59.392 50.000 0.00 0.00 0.00 5.68
382 392 5.640357 AGTAAATTAATCCACGCGTGAGAAA 59.360 36.000 39.10 25.33 0.00 2.52
398 408 1.087501 GAAACGCCATGGAGAAGGAC 58.912 55.000 23.45 5.01 0.00 3.85
399 409 0.322546 AAACGCCATGGAGAAGGACC 60.323 55.000 23.45 0.00 0.00 4.46
402 412 1.144936 GCCATGGAGAAGGACCGAG 59.855 63.158 18.40 0.00 0.00 4.63
403 413 1.617947 GCCATGGAGAAGGACCGAGT 61.618 60.000 18.40 0.00 0.00 4.18
404 414 0.176680 CCATGGAGAAGGACCGAGTG 59.823 60.000 5.56 0.00 0.00 3.51
406 416 1.550524 CATGGAGAAGGACCGAGTGAA 59.449 52.381 0.00 0.00 0.00 3.18
407 417 1.712056 TGGAGAAGGACCGAGTGAAA 58.288 50.000 0.00 0.00 0.00 2.69
408 418 1.343465 TGGAGAAGGACCGAGTGAAAC 59.657 52.381 0.00 0.00 0.00 2.78
724 745 6.426646 AAACTACTCCACAAATCACTCTCT 57.573 37.500 0.00 0.00 0.00 3.10
725 746 5.652994 ACTACTCCACAAATCACTCTCTC 57.347 43.478 0.00 0.00 0.00 3.20
740 761 9.881773 AATCACTCTCTCTAATTAATCTCTCCT 57.118 33.333 0.00 0.00 0.00 3.69
758 779 3.723097 TTCCTTGGCCCGTGTGCAA 62.723 57.895 0.00 0.00 0.00 4.08
775 801 1.202582 GCAAGCTCTCTACTTGGACGA 59.797 52.381 5.72 0.00 43.81 4.20
880 906 3.741476 GGCCGGAGCTTTGCACTG 61.741 66.667 5.05 0.00 39.73 3.66
881 907 2.980233 GCCGGAGCTTTGCACTGT 60.980 61.111 5.05 0.00 35.50 3.55
882 908 2.555547 GCCGGAGCTTTGCACTGTT 61.556 57.895 5.05 0.00 35.50 3.16
883 909 2.032981 CCGGAGCTTTGCACTGTTT 58.967 52.632 0.00 0.00 0.00 2.83
884 910 1.234821 CCGGAGCTTTGCACTGTTTA 58.765 50.000 0.00 0.00 0.00 2.01
885 911 1.197721 CCGGAGCTTTGCACTGTTTAG 59.802 52.381 0.00 0.00 0.00 1.85
886 912 2.143122 CGGAGCTTTGCACTGTTTAGA 58.857 47.619 0.00 0.00 0.00 2.10
887 913 2.096218 CGGAGCTTTGCACTGTTTAGAC 60.096 50.000 0.00 0.00 0.00 2.59
888 914 2.226674 GGAGCTTTGCACTGTTTAGACC 59.773 50.000 0.00 0.00 0.00 3.85
889 915 3.142174 GAGCTTTGCACTGTTTAGACCT 58.858 45.455 0.00 0.00 0.00 3.85
953 983 4.974438 TCCCCTCCTTGCACCGGT 62.974 66.667 0.00 0.00 0.00 5.28
954 984 4.722700 CCCCTCCTTGCACCGGTG 62.723 72.222 30.66 30.66 0.00 4.94
1112 1149 3.535962 CTCCAGCTCCTCCTCCGC 61.536 72.222 0.00 0.00 0.00 5.54
1150 1191 1.279025 GGAGGCCAACACCCCTATCA 61.279 60.000 5.01 0.00 0.00 2.15
1164 1205 6.322456 ACACCCCTATCACTATATCGATCATG 59.678 42.308 0.00 0.00 0.00 3.07
1165 1206 5.303078 ACCCCTATCACTATATCGATCATGC 59.697 44.000 0.00 0.00 0.00 4.06
1178 1219 2.287009 CGATCATGCGTACTAGTGAGCA 60.287 50.000 23.12 23.12 44.13 4.26
1179 1220 2.851805 TCATGCGTACTAGTGAGCAG 57.148 50.000 24.35 18.09 43.20 4.24
1193 1234 1.137675 TGAGCAGGCTAGCTACACATG 59.862 52.381 15.72 5.58 46.75 3.21
1196 1237 0.179100 CAGGCTAGCTACACATGCGT 60.179 55.000 15.72 0.00 35.28 5.24
1197 1238 0.103208 AGGCTAGCTACACATGCGTC 59.897 55.000 15.72 0.00 35.28 5.19
1200 1241 1.337071 GCTAGCTACACATGCGTCCTA 59.663 52.381 7.70 0.00 35.28 2.94
1201 1242 2.859032 GCTAGCTACACATGCGTCCTAC 60.859 54.545 7.70 0.00 35.28 3.18
1202 1243 0.460311 AGCTACACATGCGTCCTACC 59.540 55.000 0.00 0.00 35.28 3.18
1203 1244 0.460311 GCTACACATGCGTCCTACCT 59.540 55.000 0.00 0.00 0.00 3.08
1204 1245 1.134788 GCTACACATGCGTCCTACCTT 60.135 52.381 0.00 0.00 0.00 3.50
1205 1246 2.540515 CTACACATGCGTCCTACCTTG 58.459 52.381 0.00 0.00 0.00 3.61
1206 1247 0.685097 ACACATGCGTCCTACCTTGT 59.315 50.000 0.00 0.00 0.00 3.16
1207 1248 1.078709 CACATGCGTCCTACCTTGTG 58.921 55.000 0.00 0.00 33.00 3.33
1208 1249 0.973632 ACATGCGTCCTACCTTGTGA 59.026 50.000 0.00 0.00 0.00 3.58
1209 1250 1.066858 ACATGCGTCCTACCTTGTGAG 60.067 52.381 0.00 0.00 0.00 3.51
1215 1256 2.035449 CGTCCTACCTTGTGAGTTGTGA 59.965 50.000 0.00 0.00 0.00 3.58
1225 1270 2.166870 TGTGAGTTGTGACTAACGGTGT 59.833 45.455 0.00 0.00 39.76 4.16
1240 1297 5.416271 AACGGTGTATGTTTGTAGGAGAT 57.584 39.130 0.00 0.00 0.00 2.75
1255 1312 4.241555 GATGAGGCGCCGGTGGAT 62.242 66.667 23.20 9.63 0.00 3.41
1363 1429 1.812093 CATCGCCGCGGGTTTCTTA 60.812 57.895 29.38 0.91 0.00 2.10
1480 1546 3.682292 GAGGCCCGCCGAGACATTT 62.682 63.158 0.00 0.00 41.95 2.32
1504 1570 2.125961 GCGGACCTCCATCTACCGT 61.126 63.158 0.00 0.00 44.48 4.83
1562 1629 3.292492 TGCATGCATCATCTTCTTCCT 57.708 42.857 18.46 0.00 0.00 3.36
1595 1665 6.146347 GGAAAGAAGAACACACTAGCTAGTTG 59.854 42.308 23.94 23.50 33.46 3.16
1605 1675 3.961408 CACTAGCTAGTTGGGTAGGATGT 59.039 47.826 23.94 0.00 40.39 3.06
1619 1689 8.209802 TGGGTAGGATGTTTCTTACTTCTTAA 57.790 34.615 0.00 0.00 35.39 1.85
1620 1690 8.832735 TGGGTAGGATGTTTCTTACTTCTTAAT 58.167 33.333 0.00 0.00 35.39 1.40
1621 1691 9.682465 GGGTAGGATGTTTCTTACTTCTTAATT 57.318 33.333 0.00 0.00 35.39 1.40
1670 1745 2.743928 CCGGAGTGAACTGCTGGC 60.744 66.667 0.00 0.00 31.63 4.85
1713 1788 7.803279 AGTTTCTTTTTGTTAACCGATCTCT 57.197 32.000 2.48 0.00 0.00 3.10
1727 1802 3.138304 CGATCTCTTGGTGTTTGTGGAA 58.862 45.455 0.00 0.00 0.00 3.53
1737 1812 5.073428 TGGTGTTTGTGGAAGTAATGCATA 58.927 37.500 0.00 0.00 0.00 3.14
1842 1924 3.894547 AAGGCCGCCAAGGTACACG 62.895 63.158 13.15 0.00 43.70 4.49
1880 1963 5.537188 TGTCCAATAATCCTGCAAAAACAC 58.463 37.500 0.00 0.00 0.00 3.32
1881 1964 5.069648 TGTCCAATAATCCTGCAAAAACACA 59.930 36.000 0.00 0.00 0.00 3.72
1882 1965 5.405269 GTCCAATAATCCTGCAAAAACACAC 59.595 40.000 0.00 0.00 0.00 3.82
1924 2013 8.470002 ACTAACATGTTTTCTCTTTGCTTTTCT 58.530 29.630 17.78 0.00 0.00 2.52
1943 2032 6.391227 TTTCTCCCACAAATTTCTCAACTC 57.609 37.500 0.00 0.00 0.00 3.01
2021 2111 5.722263 CAAGCCACATCCAATCATTTTACA 58.278 37.500 0.00 0.00 0.00 2.41
2032 2122 7.696755 TCCAATCATTTTACACATCTTCATCG 58.303 34.615 0.00 0.00 0.00 3.84
2041 2131 3.181457 ACACATCTTCATCGATGCCATCT 60.181 43.478 20.81 1.29 43.54 2.90
2059 2154 5.413499 CCATCTGGTTCATGATTTGGAAAC 58.587 41.667 0.00 0.00 0.00 2.78
2221 2317 1.066587 GACTCCGGCAAGAGATCGG 59.933 63.158 9.05 0.00 44.59 4.18
2250 2347 4.356405 TGGCAACTCCATATACATCAGG 57.644 45.455 0.00 0.00 40.72 3.86
2251 2348 3.077359 GGCAACTCCATATACATCAGGC 58.923 50.000 0.00 0.00 34.01 4.85
2254 2351 1.902508 ACTCCATATACATCAGGCCGG 59.097 52.381 0.00 0.00 0.00 6.13
2255 2352 2.179427 CTCCATATACATCAGGCCGGA 58.821 52.381 8.42 8.42 0.00 5.14
2258 2355 2.283298 CATATACATCAGGCCGGATGC 58.717 52.381 36.50 0.00 46.81 3.91
2260 2357 0.035881 ATACATCAGGCCGGATGCTG 59.964 55.000 36.50 21.51 46.81 4.41
2270 2367 2.308769 CGGATGCTGATCGCTGAGC 61.309 63.158 0.00 0.00 40.11 4.26
2271 2368 1.960250 GGATGCTGATCGCTGAGCC 60.960 63.158 0.00 1.16 40.11 4.70
2283 2380 1.592064 GCTGAGCCTCTTTGCTATCC 58.408 55.000 0.00 0.00 42.95 2.59
2284 2381 1.134280 GCTGAGCCTCTTTGCTATCCA 60.134 52.381 0.00 0.00 42.95 3.41
2292 2389 4.082125 CCTCTTTGCTATCCAAAAGGTGT 58.918 43.478 0.00 0.00 42.51 4.16
2351 2448 3.257561 CGGCAGGAGTTCATCGCG 61.258 66.667 0.00 0.00 0.00 5.87
2354 2451 2.508891 GCAGGAGTTCATCGCGTCG 61.509 63.158 5.77 0.00 0.00 5.12
2419 2516 0.535780 TCACAGGGCTTGCTGACTTG 60.536 55.000 0.00 0.00 36.75 3.16
2424 2521 4.017877 GCTTGCTGACTTGCGCGT 62.018 61.111 8.43 0.00 35.36 6.01
2434 2531 1.291877 ACTTGCGCGTCCTGTTCATC 61.292 55.000 8.43 0.00 0.00 2.92
2516 2617 6.976925 GCTTTTGCATATGATCTGCTTTACTT 59.023 34.615 6.97 0.00 46.58 2.24
2525 2626 1.648467 CTGCTTTACTTGGGCCGAGC 61.648 60.000 21.17 7.87 0.00 5.03
2629 2730 7.095270 ACAGAGGAGTAACAAGGTAATTAACG 58.905 38.462 0.00 0.00 0.00 3.18
2650 2751 3.189080 CGATTGTTTCACCTGAATGAGCA 59.811 43.478 0.00 0.00 33.54 4.26
2680 2781 6.877611 AAACAAAATGTGGTACTAGTCTGG 57.122 37.500 0.00 0.00 0.00 3.86
2746 2850 8.218441 TCATCTTTTAGTCAAATGTTCGTAACG 58.782 33.333 0.00 0.00 0.00 3.18
2931 3051 3.009033 ACAGGGCTCAGTGCATTACTAAA 59.991 43.478 0.00 0.00 45.15 1.85
3006 3152 4.804139 GTGGTACAATTATCTGACCGTCTG 59.196 45.833 0.00 0.00 44.16 3.51
3014 3160 3.207547 CTGACCGTCTGTCCGCACA 62.208 63.158 0.00 0.00 43.78 4.57
3236 3382 3.065787 ATCCCCAGACATGCTGCCC 62.066 63.158 10.54 0.00 43.50 5.36
3270 3416 2.575455 CTACTGGTCCCTCCTCGCCT 62.575 65.000 0.00 0.00 37.07 5.52
3290 3436 1.968017 GCACTACCAGCAGCAGCAA 60.968 57.895 3.17 0.00 45.49 3.91
3718 3867 2.043801 GTGATAGGCCTAGGAGGAGGAT 59.956 54.545 19.33 0.00 37.67 3.24
3988 4148 5.408604 ACTTCTAGTTATTTGGTCAGTTGCG 59.591 40.000 0.00 0.00 0.00 4.85
3989 4149 4.890088 TCTAGTTATTTGGTCAGTTGCGT 58.110 39.130 0.00 0.00 0.00 5.24
4068 4234 1.133976 GGGGACATCAGGTGAATGAGG 60.134 57.143 0.00 0.00 37.04 3.86
4203 4714 5.010708 ACATTGGGGGTCAGTCTAAAATT 57.989 39.130 0.00 0.00 0.00 1.82
4258 4785 5.105513 ACGGAAGACCAAGAAACATGTTTTT 60.106 36.000 24.02 16.40 35.59 1.94
4260 4787 7.145323 CGGAAGACCAAGAAACATGTTTTTAT 58.855 34.615 24.02 11.31 35.59 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.804758 GCCTCAACTACCAAGATATATATACAC 57.195 37.037 0.00 0.00 0.00 2.90
12 13 8.978472 GGCCTCAACTACCAAGATATATATACA 58.022 37.037 0.00 0.00 0.00 2.29
13 14 9.203163 AGGCCTCAACTACCAAGATATATATAC 57.797 37.037 0.00 0.00 0.00 1.47
14 15 9.784376 AAGGCCTCAACTACCAAGATATATATA 57.216 33.333 5.23 0.00 0.00 0.86
15 16 8.686739 AAGGCCTCAACTACCAAGATATATAT 57.313 34.615 5.23 0.00 0.00 0.86
28 29 4.518970 CAGTTTGCTAAAAGGCCTCAACTA 59.481 41.667 5.23 0.00 30.29 2.24
34 35 2.239400 GTCCAGTTTGCTAAAAGGCCT 58.761 47.619 0.00 0.00 0.00 5.19
44 45 0.667184 CGGGCAATTGTCCAGTTTGC 60.667 55.000 27.87 1.30 40.62 3.68
47 48 1.805428 GCACGGGCAATTGTCCAGTT 61.805 55.000 27.87 9.35 40.62 3.16
54 55 2.450960 TTTCGACGCACGGGCAATTG 62.451 55.000 11.77 0.00 42.82 2.32
69 70 5.744666 ATGGAATATTTACACCCGTTTCG 57.255 39.130 0.00 0.00 0.00 3.46
89 94 9.896645 AAGATAATCATGGGCTAACATACTATG 57.103 33.333 0.00 0.00 0.00 2.23
140 145 8.419076 AATCACGGGCATAATTTTAAACAATC 57.581 30.769 0.00 0.00 0.00 2.67
324 330 2.608090 GCGGTCTCATTGCTTAGTTACC 59.392 50.000 0.00 0.00 0.00 2.85
382 392 2.990479 GGTCCTTCTCCATGGCGT 59.010 61.111 6.96 0.00 0.00 5.68
724 745 6.183361 GGCCAAGGAAGGAGAGATTAATTAGA 60.183 42.308 0.00 0.00 0.00 2.10
725 746 6.000840 GGCCAAGGAAGGAGAGATTAATTAG 58.999 44.000 0.00 0.00 0.00 1.73
737 758 2.852075 ACACGGGCCAAGGAAGGA 60.852 61.111 4.39 0.00 0.00 3.36
740 761 3.723097 TTGCACACGGGCCAAGGAA 62.723 57.895 4.39 0.00 0.00 3.36
758 779 2.088423 CACTCGTCCAAGTAGAGAGCT 58.912 52.381 0.00 0.00 36.03 4.09
775 801 0.110486 ATGCGTCCAAGGAAACCACT 59.890 50.000 0.00 0.00 0.00 4.00
820 846 1.064060 GAACTGTGCACTGTTCACACC 59.936 52.381 41.35 26.61 46.98 4.16
874 900 6.360370 AATAGAGAAGGTCTAAACAGTGCA 57.640 37.500 0.00 0.00 41.31 4.57
875 901 8.950208 ATAAATAGAGAAGGTCTAAACAGTGC 57.050 34.615 0.00 0.00 41.31 4.40
878 904 9.680315 CGGTATAAATAGAGAAGGTCTAAACAG 57.320 37.037 0.00 0.00 41.31 3.16
879 905 8.636213 CCGGTATAAATAGAGAAGGTCTAAACA 58.364 37.037 0.00 0.00 41.31 2.83
880 906 8.854117 TCCGGTATAAATAGAGAAGGTCTAAAC 58.146 37.037 0.00 0.00 41.31 2.01
881 907 8.854117 GTCCGGTATAAATAGAGAAGGTCTAAA 58.146 37.037 0.00 0.00 41.31 1.85
882 908 8.223330 AGTCCGGTATAAATAGAGAAGGTCTAA 58.777 37.037 0.00 0.00 41.31 2.10
883 909 7.753630 AGTCCGGTATAAATAGAGAAGGTCTA 58.246 38.462 0.00 0.00 42.22 2.59
884 910 6.612741 AGTCCGGTATAAATAGAGAAGGTCT 58.387 40.000 0.00 0.00 39.59 3.85
885 911 6.897706 AGTCCGGTATAAATAGAGAAGGTC 57.102 41.667 0.00 0.00 0.00 3.85
886 912 7.343833 TCAAAGTCCGGTATAAATAGAGAAGGT 59.656 37.037 0.00 0.00 0.00 3.50
887 913 7.652507 GTCAAAGTCCGGTATAAATAGAGAAGG 59.347 40.741 0.00 0.00 0.00 3.46
888 914 8.414778 AGTCAAAGTCCGGTATAAATAGAGAAG 58.585 37.037 0.00 0.00 0.00 2.85
889 915 8.302515 AGTCAAAGTCCGGTATAAATAGAGAA 57.697 34.615 0.00 0.00 0.00 2.87
953 983 4.645588 GTCTAAGCTAGAAGAAGGGTAGCA 59.354 45.833 0.00 0.00 41.44 3.49
954 984 4.891168 AGTCTAAGCTAGAAGAAGGGTAGC 59.109 45.833 0.00 0.00 39.64 3.58
1032 1069 2.125753 GAGAGCCAGTGGTGAGCG 60.126 66.667 11.74 0.00 0.00 5.03
1150 1191 6.817140 TCACTAGTACGCATGATCGATATAGT 59.183 38.462 0.00 0.00 0.00 2.12
1164 1205 1.002251 CTAGCCTGCTCACTAGTACGC 60.002 57.143 0.00 1.49 32.82 4.42
1165 1206 1.002251 GCTAGCCTGCTCACTAGTACG 60.002 57.143 2.29 0.00 38.50 3.67
1178 1219 0.103208 GACGCATGTGTAGCTAGCCT 59.897 55.000 12.82 1.20 0.00 4.58
1179 1220 0.876342 GGACGCATGTGTAGCTAGCC 60.876 60.000 12.82 4.27 0.00 3.93
1193 1234 1.270147 ACAACTCACAAGGTAGGACGC 60.270 52.381 0.00 0.00 0.00 5.19
1196 1237 3.305720 AGTCACAACTCACAAGGTAGGA 58.694 45.455 0.00 0.00 0.00 2.94
1197 1238 3.753294 AGTCACAACTCACAAGGTAGG 57.247 47.619 0.00 0.00 0.00 3.18
1200 1241 3.454375 CGTTAGTCACAACTCACAAGGT 58.546 45.455 0.00 0.00 36.92 3.50
1201 1242 2.800544 CCGTTAGTCACAACTCACAAGG 59.199 50.000 0.00 0.00 36.92 3.61
1202 1243 3.245284 CACCGTTAGTCACAACTCACAAG 59.755 47.826 0.00 0.00 36.92 3.16
1203 1244 3.191669 CACCGTTAGTCACAACTCACAA 58.808 45.455 0.00 0.00 36.92 3.33
1204 1245 2.166870 ACACCGTTAGTCACAACTCACA 59.833 45.455 0.00 0.00 36.92 3.58
1205 1246 2.817901 ACACCGTTAGTCACAACTCAC 58.182 47.619 0.00 0.00 36.92 3.51
1206 1247 4.038282 ACATACACCGTTAGTCACAACTCA 59.962 41.667 0.00 0.00 36.92 3.41
1207 1248 4.553323 ACATACACCGTTAGTCACAACTC 58.447 43.478 0.00 0.00 36.92 3.01
1208 1249 4.595762 ACATACACCGTTAGTCACAACT 57.404 40.909 0.00 0.00 39.66 3.16
1209 1250 5.006941 ACAAACATACACCGTTAGTCACAAC 59.993 40.000 0.00 0.00 0.00 3.32
1215 1256 5.477984 TCTCCTACAAACATACACCGTTAGT 59.522 40.000 0.00 0.00 0.00 2.24
1225 1270 3.492656 GCGCCTCATCTCCTACAAACATA 60.493 47.826 0.00 0.00 0.00 2.29
1255 1312 1.402896 CCTCCATCTTAGGCGCCTCA 61.403 60.000 36.73 23.16 0.00 3.86
1297 1363 4.570663 GTCGATCCCGTCCCAGCG 62.571 72.222 0.00 0.00 37.05 5.18
1302 1368 4.570663 CAGCCGTCGATCCCGTCC 62.571 72.222 0.00 0.00 37.05 4.79
1303 1369 3.823330 ACAGCCGTCGATCCCGTC 61.823 66.667 0.00 0.00 37.05 4.79
1304 1370 4.129737 CACAGCCGTCGATCCCGT 62.130 66.667 0.00 0.00 37.05 5.28
1305 1371 4.873129 CCACAGCCGTCGATCCCG 62.873 72.222 0.00 0.00 37.07 5.14
1306 1372 3.771160 ACCACAGCCGTCGATCCC 61.771 66.667 0.00 0.00 0.00 3.85
1307 1373 2.509336 CACCACAGCCGTCGATCC 60.509 66.667 0.00 0.00 0.00 3.36
1308 1374 2.509336 CCACCACAGCCGTCGATC 60.509 66.667 0.00 0.00 0.00 3.69
1381 1447 1.008424 CTGATCCGTCATCCCGTCG 60.008 63.158 0.00 0.00 32.98 5.12
1389 1455 0.532573 GCCAGAGTTCTGATCCGTCA 59.467 55.000 10.64 0.00 46.59 4.35
1391 1457 1.513158 CGCCAGAGTTCTGATCCGT 59.487 57.895 10.64 0.00 46.59 4.69
1392 1458 1.880340 GCGCCAGAGTTCTGATCCG 60.880 63.158 10.64 10.46 46.59 4.18
1477 1543 2.044946 GAGGTCCGCTGGCCAAAT 60.045 61.111 7.01 0.00 0.00 2.32
1504 1570 2.815684 ATCCCTACCTGGTGACGCCA 62.816 60.000 10.23 7.67 46.95 5.69
1562 1629 5.477291 AGTGTGTTCTTCTTTCCTCTCGATA 59.523 40.000 0.00 0.00 0.00 2.92
1595 1665 9.682465 AATTAAGAAGTAAGAAACATCCTACCC 57.318 33.333 0.00 0.00 0.00 3.69
1622 1692 9.132923 TGCAATAGATGTTTAGCTAGTAGTACT 57.867 33.333 8.14 8.14 0.00 2.73
1705 1780 1.806542 CCACAAACACCAAGAGATCGG 59.193 52.381 0.00 0.00 0.00 4.18
1706 1781 2.766313 TCCACAAACACCAAGAGATCG 58.234 47.619 0.00 0.00 0.00 3.69
1707 1782 4.137543 ACTTCCACAAACACCAAGAGATC 58.862 43.478 0.00 0.00 0.00 2.75
1713 1788 3.701542 TGCATTACTTCCACAAACACCAA 59.298 39.130 0.00 0.00 0.00 3.67
1743 1818 2.108514 CACCGGTGCCTGCATAGTG 61.109 63.158 24.02 0.00 0.00 2.74
1892 1981 8.025445 GCAAAGAGAAAACATGTTAGTGATGAT 58.975 33.333 12.39 0.00 0.00 2.45
1894 1983 7.365741 AGCAAAGAGAAAACATGTTAGTGATG 58.634 34.615 12.39 6.89 0.00 3.07
1911 2000 4.654091 TTTGTGGGAGAAAAGCAAAGAG 57.346 40.909 0.00 0.00 0.00 2.85
1924 2013 3.815809 ACGAGTTGAGAAATTTGTGGGA 58.184 40.909 0.00 0.00 0.00 4.37
1943 2032 3.567576 TTTATCACCAATGCACCAACG 57.432 42.857 0.00 0.00 0.00 4.10
2032 2122 4.500887 CCAAATCATGAACCAGATGGCATC 60.501 45.833 19.78 19.78 39.32 3.91
2041 2131 5.599732 CTTGTGTTTCCAAATCATGAACCA 58.400 37.500 0.00 0.00 0.00 3.67
2059 2154 8.032952 TCTAATGTAAGACTCAAATGCTTGTG 57.967 34.615 0.00 0.00 33.94 3.33
2141 2237 3.626996 CTTCAGGGCGGCCATGTCA 62.627 63.158 30.20 18.36 36.61 3.58
2258 2355 1.288350 CAAAGAGGCTCAGCGATCAG 58.712 55.000 18.26 0.00 0.00 2.90
2260 2357 0.461693 AGCAAAGAGGCTCAGCGATC 60.462 55.000 18.26 0.50 41.05 3.69
2270 2367 4.082125 ACACCTTTTGGATAGCAAAGAGG 58.918 43.478 3.16 3.16 44.07 3.69
2271 2368 4.156739 GGACACCTTTTGGATAGCAAAGAG 59.843 45.833 0.00 0.00 44.07 2.85
2283 2380 3.724374 TCTCGTAGTTGGACACCTTTTG 58.276 45.455 0.00 0.00 0.00 2.44
2284 2381 4.377897 CTTCTCGTAGTTGGACACCTTTT 58.622 43.478 0.00 0.00 0.00 2.27
2292 2389 1.819288 CAGCTCCTTCTCGTAGTTGGA 59.181 52.381 0.00 0.00 0.00 3.53
2419 2516 0.737715 AGAAGATGAACAGGACGCGC 60.738 55.000 5.73 0.00 0.00 6.86
2424 2521 2.248248 ACGTGGAGAAGATGAACAGGA 58.752 47.619 0.00 0.00 0.00 3.86
2434 2531 2.404215 CAAGGTGTGTACGTGGAGAAG 58.596 52.381 0.00 0.00 0.00 2.85
2501 2602 2.659428 GGCCCAAGTAAAGCAGATCAT 58.341 47.619 0.00 0.00 0.00 2.45
2516 2617 3.695606 GTGTGAGAGCTCGGCCCA 61.696 66.667 8.37 2.61 0.00 5.36
2525 2626 2.161012 GGTCAACATGCATGTGTGAGAG 59.839 50.000 31.98 17.08 41.61 3.20
2587 2688 1.004440 GTAGATGGATGCCCCTCGC 60.004 63.158 0.00 0.00 33.00 5.03
2596 2697 5.600484 CCTTGTTACTCCTCTGTAGATGGAT 59.400 44.000 0.00 0.00 0.00 3.41
2629 2730 4.771590 TGCTCATTCAGGTGAAACAATC 57.228 40.909 0.00 0.00 39.98 2.67
2650 2751 5.679601 AGTACCACATTTTGTTTTGGCAAT 58.320 33.333 0.00 0.00 31.76 3.56
2697 2798 4.742438 GACATTTGCGTGTCCTTTCTAA 57.258 40.909 5.64 0.00 42.04 2.10
2891 3010 0.031994 GTGGTGGTGGCACATGAAAC 59.968 55.000 20.82 8.79 44.52 2.78
3006 3152 4.012895 CGTGCCTGTTGTGCGGAC 62.013 66.667 0.00 0.00 0.00 4.79
3014 3160 3.241530 TCCTCCTGCGTGCCTGTT 61.242 61.111 0.00 0.00 0.00 3.16
3083 3229 2.069273 CTCATGTCGAAGTTGGTCACC 58.931 52.381 0.00 0.00 0.00 4.02
3236 3382 2.441532 TAGTCCTTCTCCGCCGGG 60.442 66.667 1.90 0.00 0.00 5.73
3270 3416 1.968017 GCTGCTGCTGGTAGTGCAA 60.968 57.895 8.53 0.00 40.13 4.08
3290 3436 2.124193 TGCTGCAGGTGCTGTTGT 60.124 55.556 17.12 0.00 42.66 3.32
3718 3867 2.838202 GTTCCATGTTAGTCCCTCTCCA 59.162 50.000 0.00 0.00 0.00 3.86
3771 3920 3.274095 TCATACATCGTTCCCATGCAA 57.726 42.857 0.00 0.00 0.00 4.08
3772 3921 2.998316 TCATACATCGTTCCCATGCA 57.002 45.000 0.00 0.00 0.00 3.96
3974 4134 2.491693 CCCATAACGCAACTGACCAAAT 59.508 45.455 0.00 0.00 0.00 2.32
3988 4148 7.506328 ACAGTACTTCTCAAAAACCCATAAC 57.494 36.000 0.00 0.00 0.00 1.89
3989 4149 9.226606 CATACAGTACTTCTCAAAAACCCATAA 57.773 33.333 0.00 0.00 0.00 1.90
4068 4234 4.558860 CCGCATTTTCCGAAAATTCTTCTC 59.441 41.667 15.11 2.52 38.97 2.87
4203 4714 9.967451 TCTGTTTATAAATCCAACTTCCATGTA 57.033 29.630 0.31 0.00 0.00 2.29
4260 4787 9.092876 GTTTCTCATCATTGTTGTTTTTGGTTA 57.907 29.630 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.