Multiple sequence alignment - TraesCS7D01G372700

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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 TraesCS7D01G372700 chr7D 100.000 3218 0 0 1 3218 482135424 482132207 0.000000e+00 5943.0
1 TraesCS7D01G372700 chr7D 91.935 62 5 0 1111 1172 93949361 93949300 1.590000e-13 87.9
2 TraesCS7D01G372700 chr7B 91.713 3258 142 59 1 3218 508196701 508193532 0.000000e+00 4403.0
3 TraesCS7D01G372700 chr7B 91.935 62 5 0 1111 1172 47737291 47737352 1.590000e-13 87.9
4 TraesCS7D01G372700 chr7A 91.990 3071 110 58 1 3019 549359182 549356196 0.000000e+00 4183.0
5 TraesCS7D01G372700 chr7A 92.553 188 13 1 3031 3218 549356104 549355918 5.290000e-68 268.0
6 TraesCS7D01G372700 chr6D 91.111 90 8 0 1087 1176 153865652 153865563 4.360000e-24 122.0
7 TraesCS7D01G372700 chr6D 87.356 87 10 1 1857 1942 153865014 153864928 7.350000e-17 99.0
8 TraesCS7D01G372700 chr6A 91.111 90 8 0 1087 1176 206352502 206352413 4.360000e-24 122.0
9 TraesCS7D01G372700 chr6A 87.356 87 10 1 1857 1942 206351865 206351779 7.350000e-17 99.0
10 TraesCS7D01G372700 chr6A 93.443 61 4 0 1111 1171 591381175 591381115 1.230000e-14 91.6
11 TraesCS7D01G372700 chr6B 83.721 129 16 4 1075 1199 277624600 277624473 2.030000e-22 117.0
12 TraesCS7D01G372700 chr6B 93.443 61 4 0 1111 1171 668029995 668029935 1.230000e-14 91.6


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 TraesCS7D01G372700 chr7D 482132207 482135424 3217 True 5943.0 5943 100.0000 1 3218 1 chr7D.!!$R2 3217
1 TraesCS7D01G372700 chr7B 508193532 508196701 3169 True 4403.0 4403 91.7130 1 3218 1 chr7B.!!$R1 3217
2 TraesCS7D01G372700 chr7A 549355918 549359182 3264 True 2225.5 4183 92.2715 1 3218 2 chr7A.!!$R1 3217

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
978 1033 0.031314 CACTCACTCACTCGCACTGT 59.969 55.0 0.0 0.0 0.00 3.55 F
1256 1326 0.465824 ACTCGTGTAGCTATCCCGCT 60.466 55.0 0.0 0.0 43.83 5.52 F
1828 1902 0.961358 CGACTCCTTCCTCGTCCACT 60.961 60.0 0.0 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2077 2155 0.030369 GGTACCTACGATGTGGAGCG 59.970 60.000 4.06 0.0 36.91 5.03 R
2168 2246 0.249699 CTGGGCTTCACACACGTACA 60.250 55.000 0.00 0.0 0.00 2.90 R
2691 2779 1.228154 AGGAAAACTCGGGGTGCAC 60.228 57.895 8.80 8.8 0.00 4.57 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
136 141 2.614013 GGCCCCCTCTTCCCTTCA 60.614 66.667 0.00 0.00 0.00 3.02
140 145 1.541368 CCCCTCTTCCCTTCACCCA 60.541 63.158 0.00 0.00 0.00 4.51
141 146 1.566298 CCCCTCTTCCCTTCACCCAG 61.566 65.000 0.00 0.00 0.00 4.45
142 147 1.301293 CCTCTTCCCTTCACCCAGC 59.699 63.158 0.00 0.00 0.00 4.85
143 148 1.492133 CCTCTTCCCTTCACCCAGCA 61.492 60.000 0.00 0.00 0.00 4.41
144 149 0.401738 CTCTTCCCTTCACCCAGCAA 59.598 55.000 0.00 0.00 0.00 3.91
153 158 4.749310 ACCCAGCAAGCTCTCGCG 62.749 66.667 0.00 0.00 42.32 5.87
282 292 0.046242 TCCAACCTCCCTCCATGGAT 59.954 55.000 16.63 0.00 35.33 3.41
285 295 2.158608 CCAACCTCCCTCCATGGATTAC 60.159 54.545 16.63 0.00 38.35 1.89
287 297 2.412591 ACCTCCCTCCATGGATTACAG 58.587 52.381 16.63 8.86 38.35 2.74
299 309 5.454755 CCATGGATTACAGTTACAGGGTAGG 60.455 48.000 5.56 0.00 0.00 3.18
305 320 8.927411 GGATTACAGTTACAGGGTAGGTAATTA 58.073 37.037 0.00 0.00 33.68 1.40
351 366 5.611374 AGGCACCACTACATATGTTGTATC 58.389 41.667 20.16 10.67 40.02 2.24
359 374 9.778741 CCACTACATATGTTGTATCCTTGTATT 57.221 33.333 20.16 0.00 40.02 1.89
379 401 9.529325 TTGTATTCATGTAGTAGTCACTAATGC 57.471 33.333 0.00 0.00 38.98 3.56
386 408 3.939066 AGTAGTCACTAATGCCACAACC 58.061 45.455 0.00 0.00 31.45 3.77
390 412 1.985159 TCACTAATGCCACAACCTCCT 59.015 47.619 0.00 0.00 0.00 3.69
391 413 2.375174 TCACTAATGCCACAACCTCCTT 59.625 45.455 0.00 0.00 0.00 3.36
414 436 4.993705 AGGGAGTAGTGAATTTCAACCA 57.006 40.909 0.00 0.00 0.00 3.67
415 437 4.911390 AGGGAGTAGTGAATTTCAACCAG 58.089 43.478 0.00 0.00 0.00 4.00
416 438 3.440522 GGGAGTAGTGAATTTCAACCAGC 59.559 47.826 0.00 0.00 0.00 4.85
433 455 5.031066 ACCAGCTGAAACTACAGTTGTAA 57.969 39.130 17.39 0.00 43.87 2.41
434 456 4.814771 ACCAGCTGAAACTACAGTTGTAAC 59.185 41.667 17.39 0.00 43.87 2.50
435 457 5.057149 CCAGCTGAAACTACAGTTGTAACT 58.943 41.667 17.39 0.00 43.87 2.24
436 458 5.527582 CCAGCTGAAACTACAGTTGTAACTT 59.472 40.000 17.39 0.00 43.87 2.66
437 459 6.422223 CAGCTGAAACTACAGTTGTAACTTG 58.578 40.000 8.42 0.00 41.69 3.16
439 461 7.223971 CAGCTGAAACTACAGTTGTAACTTGTA 59.776 37.037 8.42 1.84 41.69 2.41
440 462 7.224167 AGCTGAAACTACAGTTGTAACTTGTAC 59.776 37.037 0.00 0.00 38.44 2.90
515 541 1.896220 ACTGCATGGTCACACGAAAT 58.104 45.000 0.00 0.00 0.00 2.17
560 590 1.156736 GGTGCACACATGACAGTACC 58.843 55.000 20.43 3.64 0.00 3.34
561 591 1.542328 GGTGCACACATGACAGTACCA 60.542 52.381 20.43 0.00 0.00 3.25
564 594 1.800586 GCACACATGACAGTACCACAG 59.199 52.381 0.00 0.00 0.00 3.66
658 688 3.276846 GGAACGCAAGGCACACGT 61.277 61.111 0.00 0.00 46.39 4.49
710 740 2.762327 CCCCCAAATCCATTCTTCACTG 59.238 50.000 0.00 0.00 0.00 3.66
718 748 1.081892 CATTCTTCACTGCTCCCACG 58.918 55.000 0.00 0.00 0.00 4.94
719 749 0.036010 ATTCTTCACTGCTCCCACGG 60.036 55.000 0.00 0.00 0.00 4.94
736 766 1.597461 GGTCTCCCCCTCTTTCACG 59.403 63.158 0.00 0.00 0.00 4.35
738 768 2.125512 CTCCCCCTCTTTCACGCG 60.126 66.667 3.53 3.53 0.00 6.01
763 808 3.664107 ACGCAATGTAGGCCTATGTATG 58.336 45.455 17.38 13.63 0.00 2.39
857 907 4.084147 TACAGGGGGTCCGAGGGG 62.084 72.222 0.00 0.00 38.33 4.79
924 979 1.296715 CCCACACTACACTGCTCCC 59.703 63.158 0.00 0.00 0.00 4.30
925 980 1.296715 CCACACTACACTGCTCCCC 59.703 63.158 0.00 0.00 0.00 4.81
978 1033 0.031314 CACTCACTCACTCGCACTGT 59.969 55.000 0.00 0.00 0.00 3.55
993 1052 1.227764 CTGTCACACTGCCTGCTGT 60.228 57.895 0.00 0.00 0.00 4.40
994 1053 1.504647 CTGTCACACTGCCTGCTGTG 61.505 60.000 22.50 22.50 46.63 3.66
995 1054 2.592574 TCACACTGCCTGCTGTGC 60.593 61.111 23.59 0.00 45.64 4.57
996 1055 2.593725 CACACTGCCTGCTGTGCT 60.594 61.111 23.59 11.81 45.64 4.40
997 1056 2.593725 ACACTGCCTGCTGTGCTG 60.594 61.111 23.59 6.37 45.64 4.41
1011 1070 0.842635 GTGCTGATCATTCCCTCCCT 59.157 55.000 0.00 0.00 0.00 4.20
1012 1071 1.135094 TGCTGATCATTCCCTCCCTC 58.865 55.000 0.00 0.00 0.00 4.30
1013 1072 1.344803 TGCTGATCATTCCCTCCCTCT 60.345 52.381 0.00 0.00 0.00 3.69
1014 1073 1.072015 GCTGATCATTCCCTCCCTCTG 59.928 57.143 0.00 0.00 0.00 3.35
1015 1074 1.072015 CTGATCATTCCCTCCCTCTGC 59.928 57.143 0.00 0.00 0.00 4.26
1018 1077 2.770048 ATTCCCTCCCTCTGCCCG 60.770 66.667 0.00 0.00 0.00 6.13
1019 1078 3.642741 ATTCCCTCCCTCTGCCCGT 62.643 63.158 0.00 0.00 0.00 5.28
1020 1079 4.779733 TCCCTCCCTCTGCCCGTC 62.780 72.222 0.00 0.00 0.00 4.79
1022 1081 4.787280 CCTCCCTCTGCCCGTCCT 62.787 72.222 0.00 0.00 0.00 3.85
1023 1082 3.151022 CTCCCTCTGCCCGTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1024 1083 3.670629 CTCCCTCTGCCCGTCCTCT 62.671 68.421 0.00 0.00 0.00 3.69
1025 1084 2.685380 CCCTCTGCCCGTCCTCTT 60.685 66.667 0.00 0.00 0.00 2.85
1026 1085 2.726351 CCCTCTGCCCGTCCTCTTC 61.726 68.421 0.00 0.00 0.00 2.87
1027 1086 2.726351 CCTCTGCCCGTCCTCTTCC 61.726 68.421 0.00 0.00 0.00 3.46
1028 1087 3.068691 TCTGCCCGTCCTCTTCCG 61.069 66.667 0.00 0.00 0.00 4.30
1029 1088 4.148825 CTGCCCGTCCTCTTCCGG 62.149 72.222 0.00 0.00 43.82 5.14
1181 1243 2.358300 CCCTCTCCTGTAAGCCTCACTA 60.358 54.545 0.00 0.00 0.00 2.74
1183 1245 3.626222 CCTCTCCTGTAAGCCTCACTACT 60.626 52.174 0.00 0.00 0.00 2.57
1201 1263 2.487775 ACTCCCTAGCTCTCTCTCTCA 58.512 52.381 0.00 0.00 0.00 3.27
1229 1299 1.961793 AGCTGCTCTACTCCTACTCG 58.038 55.000 0.00 0.00 0.00 4.18
1254 1324 1.805345 CCTACTCGTGTAGCTATCCCG 59.195 57.143 17.23 0.00 43.51 5.14
1256 1326 0.465824 ACTCGTGTAGCTATCCCGCT 60.466 55.000 0.00 0.00 43.83 5.52
1285 1355 8.250332 GTCCTGAGAGATAGATACATTGATTCC 58.750 40.741 0.00 0.00 0.00 3.01
1286 1356 8.176105 TCCTGAGAGATAGATACATTGATTCCT 58.824 37.037 0.00 0.00 0.00 3.36
1367 1441 1.952296 TGCATGCATGTGTGTTGTGTA 59.048 42.857 26.79 0.00 0.00 2.90
1525 1599 2.498941 GGAGATCATCGTCGCCCCA 61.499 63.158 0.00 0.00 32.58 4.96
1570 1644 3.126225 GTCGGCTCGTCGTCCTCT 61.126 66.667 0.00 0.00 0.00 3.69
1828 1902 0.961358 CGACTCCTTCCTCGTCCACT 60.961 60.000 0.00 0.00 0.00 4.00
1867 1941 2.267642 CCGCCGGAGACAATGGAA 59.732 61.111 5.05 0.00 0.00 3.53
2073 2151 2.679837 CGCACAGGCAGTTAAGATCATT 59.320 45.455 0.00 0.00 41.24 2.57
2074 2152 3.486375 CGCACAGGCAGTTAAGATCATTG 60.486 47.826 0.00 0.00 41.24 2.82
2075 2153 3.733077 GCACAGGCAGTTAAGATCATTGC 60.733 47.826 0.00 0.00 40.72 3.56
2077 2155 3.944015 ACAGGCAGTTAAGATCATTGCTC 59.056 43.478 0.00 0.00 35.23 4.26
2110 2188 1.118838 GGTACCAGCTGAGCATCTCT 58.881 55.000 17.39 0.00 34.92 3.10
2115 2193 1.270412 CCAGCTGAGCATCTCTCCATC 60.270 57.143 17.39 0.00 41.18 3.51
2143 2221 6.455246 GCACTACGTAAAATCAAGCTTAGGAC 60.455 42.308 0.00 0.00 0.00 3.85
2160 2238 6.979238 GCTTAGGACAACGATTAATCACTACT 59.021 38.462 15.57 7.67 0.00 2.57
2167 2245 6.145534 ACAACGATTAATCACTACTGTGTGTG 59.854 38.462 15.57 8.73 44.14 3.82
2168 2246 5.779922 ACGATTAATCACTACTGTGTGTGT 58.220 37.500 15.57 0.00 44.14 3.72
2186 2264 0.531090 GTGTACGTGTGTGAAGCCCA 60.531 55.000 0.00 0.00 0.00 5.36
2254 2332 0.179121 TGCCGTCACCGTCATGATAC 60.179 55.000 0.00 0.00 0.00 2.24
2378 2463 3.902261 TGCAGTACTCTTGTGCATTTG 57.098 42.857 2.83 0.00 42.20 2.32
2452 2537 6.712241 TTTAAGCGTCTCTCTTCATCAAAG 57.288 37.500 0.00 0.00 36.22 2.77
2460 2545 6.463360 GTCTCTCTTCATCAAAGGGATATCC 58.537 44.000 13.87 13.87 43.65 2.59
2493 2578 6.318648 GGTGAGGTGATATTTGCACATTCTTA 59.681 38.462 0.00 0.00 37.99 2.10
2538 2623 2.906389 AGCACTGTTCATTCTAGTCCCA 59.094 45.455 0.00 0.00 0.00 4.37
2574 2662 8.593679 CCCTAATTAAGAACAAGGTTCCAAAAT 58.406 33.333 5.54 1.65 0.00 1.82
2600 2688 7.218228 TGTAAATGGACCATCATATGAATGC 57.782 36.000 9.99 4.66 32.76 3.56
2601 2689 6.776603 TGTAAATGGACCATCATATGAATGCA 59.223 34.615 9.99 10.17 32.76 3.96
2602 2690 6.734502 AAATGGACCATCATATGAATGCAA 57.265 33.333 9.99 0.00 32.76 4.08
2603 2691 5.717078 ATGGACCATCATATGAATGCAAC 57.283 39.130 9.99 0.03 32.76 4.17
2604 2692 4.795469 TGGACCATCATATGAATGCAACT 58.205 39.130 9.99 0.00 32.76 3.16
2605 2693 5.939447 TGGACCATCATATGAATGCAACTA 58.061 37.500 9.99 0.00 32.76 2.24
2606 2694 6.545567 TGGACCATCATATGAATGCAACTAT 58.454 36.000 9.99 0.00 32.76 2.12
2637 2725 5.107143 ACAAAATTTTGAACATGTATGCGGC 60.107 36.000 32.20 0.00 40.55 6.53
2832 2920 1.128692 GCCCAAACGAGACGAAGAATG 59.871 52.381 0.00 0.00 0.00 2.67
2929 3017 5.346822 CGTGTGTAACCCTCTTGTAATACAC 59.653 44.000 6.87 6.87 41.98 2.90
2930 3018 6.225318 GTGTGTAACCCTCTTGTAATACACA 58.775 40.000 11.32 11.32 46.25 3.72
3027 3122 2.222289 CGAACTCAAATACGTCAGTGCG 60.222 50.000 0.00 5.58 31.73 5.34
3045 3220 6.424207 TCAGTGCGTTAACATTAACATGTGTA 59.576 34.615 13.47 0.00 43.34 2.90
3164 3339 5.752892 ATGACTAGTACACAGACCATACG 57.247 43.478 0.00 0.00 0.00 3.06
3192 3367 0.107508 CACCAGGCTATGTGGACCAG 60.108 60.000 0.00 0.00 38.57 4.00
3193 3368 0.547712 ACCAGGCTATGTGGACCAGT 60.548 55.000 0.00 0.00 38.57 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.134007 CGGTAATTAACTCCCCCACCC 60.134 57.143 0.00 0.00 0.00 4.61
211 221 5.283060 CGTGTAGCAAGTGATAAAGCTTT 57.717 39.130 17.30 17.30 38.47 3.51
282 292 8.899887 AGTAATTACCTACCCTGTAACTGTAA 57.100 34.615 12.05 0.00 31.47 2.41
285 295 7.287235 AGCTAGTAATTACCTACCCTGTAACTG 59.713 40.741 12.05 0.00 31.47 3.16
287 297 7.286316 TCAGCTAGTAATTACCTACCCTGTAAC 59.714 40.741 12.05 0.00 31.47 2.50
299 309 5.278022 GGCAGGCAATTCAGCTAGTAATTAC 60.278 44.000 7.57 7.57 34.17 1.89
305 320 0.394899 GGGCAGGCAATTCAGCTAGT 60.395 55.000 0.00 0.00 34.17 2.57
359 374 5.420739 TGTGGCATTAGTGACTACTACATGA 59.579 40.000 0.00 0.00 39.06 3.07
362 377 5.475719 GTTGTGGCATTAGTGACTACTACA 58.524 41.667 0.00 0.00 39.06 2.74
363 378 4.868734 GGTTGTGGCATTAGTGACTACTAC 59.131 45.833 0.00 0.00 39.06 2.73
390 412 6.843752 TGGTTGAAATTCACTACTCCCTAAA 58.156 36.000 0.00 0.00 0.00 1.85
391 413 6.442541 TGGTTGAAATTCACTACTCCCTAA 57.557 37.500 0.00 0.00 0.00 2.69
400 422 4.646492 AGTTTCAGCTGGTTGAAATTCACT 59.354 37.500 15.13 6.27 45.67 3.41
414 436 6.113411 ACAAGTTACAACTGTAGTTTCAGCT 58.887 36.000 0.00 0.00 39.66 4.24
415 437 6.359480 ACAAGTTACAACTGTAGTTTCAGC 57.641 37.500 0.00 0.00 39.66 4.26
416 438 8.644318 AGTACAAGTTACAACTGTAGTTTCAG 57.356 34.615 0.00 0.00 39.66 3.02
433 455 3.780626 ACTTCCAGGAGCTAGTACAAGT 58.219 45.455 0.00 0.00 0.00 3.16
434 456 5.419471 AGTTACTTCCAGGAGCTAGTACAAG 59.581 44.000 0.00 0.00 0.00 3.16
435 457 5.331069 AGTTACTTCCAGGAGCTAGTACAA 58.669 41.667 0.00 0.00 0.00 2.41
436 458 4.931914 AGTTACTTCCAGGAGCTAGTACA 58.068 43.478 0.00 0.00 0.00 2.90
437 459 5.918426 AAGTTACTTCCAGGAGCTAGTAC 57.082 43.478 0.00 0.00 0.00 2.73
439 461 4.593634 ACAAAGTTACTTCCAGGAGCTAGT 59.406 41.667 0.00 0.00 0.00 2.57
440 462 5.153950 ACAAAGTTACTTCCAGGAGCTAG 57.846 43.478 0.00 0.00 0.00 3.42
515 541 4.152647 TGTAAGGAGAGCTTCTGAACAGA 58.847 43.478 0.00 0.00 35.27 3.41
560 590 1.402259 CTACTCCGCTAGGACACTGTG 59.598 57.143 6.19 6.19 42.75 3.66
561 591 1.752683 CTACTCCGCTAGGACACTGT 58.247 55.000 0.00 0.00 42.75 3.55
564 594 0.382515 CTGCTACTCCGCTAGGACAC 59.617 60.000 0.00 0.00 42.75 3.67
658 688 4.100344 TGGCAGTAACTTCAAGTGTGAGTA 59.900 41.667 0.00 0.00 34.49 2.59
719 749 1.079057 GCGTGAAAGAGGGGGAGAC 60.079 63.158 0.00 0.00 0.00 3.36
738 768 2.163818 TAGGCCTACATTGCGTATGC 57.836 50.000 8.91 0.00 40.05 3.14
763 808 0.300789 GTACGCTTCCGCTTGCATAC 59.699 55.000 0.00 0.00 38.22 2.39
784 834 1.475280 GGATAGGCCGATGCGTATACA 59.525 52.381 1.80 0.00 45.79 2.29
857 907 5.050499 CAGTGAATATAAGCTACTGCACTGC 60.050 44.000 16.19 0.00 43.38 4.40
858 908 5.464722 CCAGTGAATATAAGCTACTGCACTG 59.535 44.000 19.18 19.18 46.85 3.66
859 909 5.453903 CCCAGTGAATATAAGCTACTGCACT 60.454 44.000 5.22 3.67 42.74 4.40
860 910 4.752101 CCCAGTGAATATAAGCTACTGCAC 59.248 45.833 5.22 1.61 42.74 4.57
861 911 4.653801 TCCCAGTGAATATAAGCTACTGCA 59.346 41.667 5.22 0.00 42.74 4.41
978 1033 2.592574 GCACAGCAGGCAGTGTGA 60.593 61.111 16.47 0.00 45.84 3.58
993 1052 1.135094 GAGGGAGGGAATGATCAGCA 58.865 55.000 0.09 0.00 0.00 4.41
994 1053 1.072015 CAGAGGGAGGGAATGATCAGC 59.928 57.143 0.09 0.00 0.00 4.26
995 1054 1.072015 GCAGAGGGAGGGAATGATCAG 59.928 57.143 0.09 0.00 0.00 2.90
996 1055 1.135094 GCAGAGGGAGGGAATGATCA 58.865 55.000 0.00 0.00 0.00 2.92
997 1056 0.399833 GGCAGAGGGAGGGAATGATC 59.600 60.000 0.00 0.00 0.00 2.92
1011 1070 3.068691 CGGAAGAGGACGGGCAGA 61.069 66.667 0.00 0.00 0.00 4.26
1012 1071 4.148825 CCGGAAGAGGACGGGCAG 62.149 72.222 0.00 0.00 46.08 4.85
1018 1077 3.471806 GGAGGCCCGGAAGAGGAC 61.472 72.222 0.73 0.00 0.00 3.85
1019 1078 3.680920 GAGGAGGCCCGGAAGAGGA 62.681 68.421 0.73 0.00 37.58 3.71
1020 1079 3.157949 GAGGAGGCCCGGAAGAGG 61.158 72.222 0.73 0.00 37.58 3.69
1021 1080 1.681486 GAAGAGGAGGCCCGGAAGAG 61.681 65.000 0.73 0.00 37.58 2.85
1022 1081 1.686110 GAAGAGGAGGCCCGGAAGA 60.686 63.158 0.73 0.00 37.58 2.87
1023 1082 2.736826 GGAAGAGGAGGCCCGGAAG 61.737 68.421 0.73 0.00 37.58 3.46
1024 1083 2.687566 GGAAGAGGAGGCCCGGAA 60.688 66.667 0.73 0.00 37.58 4.30
1025 1084 4.798682 GGGAAGAGGAGGCCCGGA 62.799 72.222 0.73 0.00 37.58 5.14
1026 1085 4.806339 AGGGAAGAGGAGGCCCGG 62.806 72.222 0.00 0.00 46.68 5.73
1027 1086 3.474570 CAGGGAAGAGGAGGCCCG 61.475 72.222 0.00 0.00 46.68 6.13
1028 1087 3.803162 GCAGGGAAGAGGAGGCCC 61.803 72.222 0.00 0.00 42.37 5.80
1029 1088 3.803162 GGCAGGGAAGAGGAGGCC 61.803 72.222 0.00 0.00 0.00 5.19
1030 1089 3.011517 TGGCAGGGAAGAGGAGGC 61.012 66.667 0.00 0.00 0.00 4.70
1032 1091 0.325110 TCTCTGGCAGGGAAGAGGAG 60.325 60.000 16.30 1.87 40.34 3.69
1057 1116 3.934684 GCGGAATGCAGAGCGAGC 61.935 66.667 0.00 0.00 45.45 5.03
1181 1243 2.172717 GTGAGAGAGAGAGCTAGGGAGT 59.827 54.545 0.00 0.00 0.00 3.85
1183 1245 2.438021 GAGTGAGAGAGAGAGCTAGGGA 59.562 54.545 0.00 0.00 0.00 4.20
1201 1263 3.541632 GAGTAGAGCAGCTAGTGAGAGT 58.458 50.000 0.00 0.00 32.86 3.24
1229 1299 2.412112 CTACACGAGTAGGCCGGC 59.588 66.667 21.18 21.18 43.24 6.13
1254 1324 4.824537 TGTATCTATCTCTCAGGACACAGC 59.175 45.833 0.00 0.00 0.00 4.40
1256 1326 7.062957 TCAATGTATCTATCTCTCAGGACACA 58.937 38.462 0.00 0.00 0.00 3.72
1285 1355 7.744715 CCTTAAAGTACGTAGCAATTCAAACAG 59.255 37.037 0.00 0.00 0.00 3.16
1286 1356 7.227116 ACCTTAAAGTACGTAGCAATTCAAACA 59.773 33.333 0.00 0.00 0.00 2.83
1367 1441 1.005215 CCTCCTCTTCCTGCAAACCAT 59.995 52.381 0.00 0.00 0.00 3.55
1681 1755 3.332493 CTGCCAGACGCCAATGTGC 62.332 63.158 0.00 0.00 36.24 4.57
1867 1941 1.890041 CGCGATCCTCTCCTCGTCT 60.890 63.158 0.00 0.00 37.23 4.18
2073 2151 1.433471 CTACGATGTGGAGCGAGCA 59.567 57.895 0.00 0.00 34.27 4.26
2074 2152 1.299468 CCTACGATGTGGAGCGAGC 60.299 63.158 0.00 0.00 34.27 5.03
2075 2153 1.002684 GTACCTACGATGTGGAGCGAG 60.003 57.143 0.00 0.00 34.27 5.03
2077 2155 0.030369 GGTACCTACGATGTGGAGCG 59.970 60.000 4.06 0.00 36.91 5.03
2160 2238 1.067776 TCACACACGTACACACACACA 60.068 47.619 0.00 0.00 0.00 3.72
2167 2245 0.531090 TGGGCTTCACACACGTACAC 60.531 55.000 0.00 0.00 0.00 2.90
2168 2246 0.249699 CTGGGCTTCACACACGTACA 60.250 55.000 0.00 0.00 0.00 2.90
2254 2332 9.918630 TGATATGATGTTGATACATAGTGTGAG 57.081 33.333 0.00 0.00 44.90 3.51
2357 2442 3.250762 TCAAATGCACAAGAGTACTGCAC 59.749 43.478 8.70 0.00 38.37 4.57
2400 2485 4.273480 CCGACTGAAAACAACACTTCATCT 59.727 41.667 0.00 0.00 31.40 2.90
2452 2537 3.134804 CCTCACCATATTCCGGATATCCC 59.865 52.174 16.36 0.00 0.00 3.85
2460 2545 5.106555 GCAAATATCACCTCACCATATTCCG 60.107 44.000 0.00 0.00 0.00 4.30
2538 2623 9.813446 CTTGTTCTTAATTAGGGTTACGACTAT 57.187 33.333 0.00 0.00 0.00 2.12
2574 2662 8.143193 GCATTCATATGATGGTCCATTTACAAA 58.857 33.333 6.17 0.00 33.37 2.83
2599 2687 5.622041 CAAAATTTTGTGCTTGCATAGTTGC 59.378 36.000 20.57 0.00 40.03 4.17
2600 2688 6.946165 TCAAAATTTTGTGCTTGCATAGTTG 58.054 32.000 25.98 0.56 39.18 3.16
2601 2689 7.065563 TGTTCAAAATTTTGTGCTTGCATAGTT 59.934 29.630 25.98 0.00 39.18 2.24
2602 2690 6.538021 TGTTCAAAATTTTGTGCTTGCATAGT 59.462 30.769 25.98 0.00 39.18 2.12
2603 2691 6.946165 TGTTCAAAATTTTGTGCTTGCATAG 58.054 32.000 25.98 1.17 39.18 2.23
2604 2692 6.915544 TGTTCAAAATTTTGTGCTTGCATA 57.084 29.167 25.98 5.15 39.18 3.14
2605 2693 5.814764 TGTTCAAAATTTTGTGCTTGCAT 57.185 30.435 25.98 0.00 39.18 3.96
2606 2694 5.123502 ACATGTTCAAAATTTTGTGCTTGCA 59.876 32.000 25.98 17.29 39.18 4.08
2679 2767 1.538419 GGGGTGCACGCTATCTCTTAC 60.538 57.143 29.99 9.25 0.00 2.34
2687 2775 2.386064 AAAACTCGGGGTGCACGCTA 62.386 55.000 29.99 18.71 0.00 4.26
2691 2779 1.228154 AGGAAAACTCGGGGTGCAC 60.228 57.895 8.80 8.80 0.00 4.57
2832 2920 4.142988 TGACAGATGTTTTCGGTAAATCGC 60.143 41.667 0.00 0.00 32.52 4.58
2929 3017 3.251479 TGATTCGTGACTGATCCCTTG 57.749 47.619 0.00 0.00 0.00 3.61
2930 3018 3.452264 TGATGATTCGTGACTGATCCCTT 59.548 43.478 0.00 0.00 0.00 3.95
3027 3122 8.964420 ATGCACTTACACATGTTAATGTTAAC 57.036 30.769 0.00 8.36 44.94 2.01
3045 3220 8.461222 TGATATTCTTTCAAATTCGATGCACTT 58.539 29.630 0.00 0.00 0.00 3.16
3086 3261 7.404980 TCTCCCAACTGGACCTATTTTAATACT 59.595 37.037 0.00 0.00 38.61 2.12
3192 3367 3.266510 TGATGCCTTGTGGTCATCTAC 57.733 47.619 15.10 0.00 42.24 2.59
3193 3368 3.264193 AGTTGATGCCTTGTGGTCATCTA 59.736 43.478 15.10 8.87 42.24 1.98


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

AutoCloner maintained by Alex Coulton.