Multiple sequence alignment - TraesCS7A01G250000

Loading Multiple Alignment...

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 TraesCS7A01G250000 chr7A 100.000 4008 0 0 1 4008 232591820 232587813 0.000000e+00 7402
1 TraesCS7A01G250000 chr7D 93.860 3290 133 32 223 3493 220280077 220276838 0.000000e+00 4892
2 TraesCS7A01G250000 chr7D 94.808 520 20 4 3495 4008 220276597 220276079 0.000000e+00 804
3 TraesCS7A01G250000 chr7D 97.500 240 5 1 4 243 220280333 220280095 3.730000e-110 409
4 TraesCS7A01G250000 chr7B 93.827 1944 75 19 560 2482 179253234 179255153 0.000000e+00 2883
5 TraesCS7A01G250000 chr7B 94.135 1023 48 5 2502 3517 179255143 179256160 0.000000e+00 1546
6 TraesCS7A01G250000 chr7B 94.716 511 22 3 3502 4008 179256182 179256691 0.000000e+00 789
7 TraesCS7A01G250000 chr5B 76.580 269 47 14 3390 3645 457123459 457123194 2.510000e-27 134


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 TraesCS7A01G250000 chr7A 232587813 232591820 4007 True 7402.000000 7402 100.000000 1 4008 1 chr7A.!!$R1 4007
1 TraesCS7A01G250000 chr7D 220276079 220280333 4254 True 2035.000000 4892 95.389333 4 4008 3 chr7D.!!$R1 4004
2 TraesCS7A01G250000 chr7B 179253234 179256691 3457 False 1739.333333 2883 94.226000 560 4008 3 chr7B.!!$F1 3448

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
57 58 0.037590 TCGCTGCCATTAAAGGGTGT 59.962 50.0 0.00 0.0 0.00 4.16 F
609 653 0.447406 TGCCGTCGATTGATGCAAAG 59.553 50.0 7.47 0.0 33.49 2.77 F
1393 1461 0.324614 TGCTCACCATGTCCGTCAAT 59.675 50.0 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 1070 0.317479 GACGGTGCAGGTGACTAACT 59.683 55.0 0.0 0.0 40.21 2.24 R
2494 2562 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.0 0.0 0.0 0.00 3.82 R
3071 3139 0.035725 CAGCATCAGGAAGCTCCACA 60.036 55.0 0.0 0.0 39.61 4.17 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
57 58 0.037590 TCGCTGCCATTAAAGGGTGT 59.962 50.000 0.00 0.00 0.00 4.16
64 65 2.614057 GCCATTAAAGGGTGTCATCTCG 59.386 50.000 0.00 0.00 0.00 4.04
133 134 3.782656 AAACACCGGTGGAGAGTAATT 57.217 42.857 36.47 17.43 34.19 1.40
137 138 1.203994 ACCGGTGGAGAGTAATTGTCG 59.796 52.381 6.12 0.00 0.00 4.35
184 185 6.456449 GGCATCATTGTTTGCAAGAAATCATC 60.456 38.462 0.00 0.00 40.66 2.92
188 189 3.809234 TGTTTGCAAGAAATCATCGTCG 58.191 40.909 0.00 0.00 0.00 5.12
300 337 2.538449 ACACTTAACGACAAGTTGAGCG 59.462 45.455 10.54 14.61 46.66 5.03
478 518 5.070180 TCGCTATAGACTACAGTAGACAGGT 59.930 44.000 14.94 1.63 0.00 4.00
479 519 5.759273 CGCTATAGACTACAGTAGACAGGTT 59.241 44.000 14.94 0.00 0.00 3.50
505 545 8.867112 TTTTTAGACACAACTACAGTAGACAG 57.133 34.615 14.94 5.96 0.00 3.51
518 558 6.003859 ACAGTAGACAGGTAGCTACAGTAT 57.996 41.667 24.75 20.08 39.48 2.12
521 561 6.425721 CAGTAGACAGGTAGCTACAGTATCTC 59.574 46.154 24.75 14.84 39.48 2.75
609 653 0.447406 TGCCGTCGATTGATGCAAAG 59.553 50.000 7.47 0.00 33.49 2.77
767 820 2.170607 CTGGATCGACAAGGTGGGTTAT 59.829 50.000 0.00 0.00 0.00 1.89
770 823 4.410883 TGGATCGACAAGGTGGGTTATATT 59.589 41.667 0.00 0.00 0.00 1.28
779 832 6.043243 ACAAGGTGGGTTATATTCTCATCGAT 59.957 38.462 0.00 0.00 0.00 3.59
794 847 0.607217 TCGATTATCGCCCTCCGCTA 60.607 55.000 10.02 0.00 40.21 4.26
798 851 0.601558 TTATCGCCCTCCGCTATGTC 59.398 55.000 0.00 0.00 36.73 3.06
811 872 3.179830 CGCTATGTCCGATTATGGTAGC 58.820 50.000 0.00 0.00 31.27 3.58
839 900 6.400568 CAATTTCCACCATGCTGTAGATTTT 58.599 36.000 0.00 0.00 0.00 1.82
840 901 5.389859 TTTCCACCATGCTGTAGATTTTG 57.610 39.130 0.00 0.00 0.00 2.44
860 921 2.145397 GGGGGAAAGAGAAACCATCC 57.855 55.000 0.00 0.00 0.00 3.51
864 925 2.290071 GGGAAAGAGAAACCATCCGTCA 60.290 50.000 0.00 0.00 0.00 4.35
885 947 4.586421 TCAACAGCAATGTCCATGGTTTTA 59.414 37.500 12.58 0.00 0.00 1.52
910 972 1.077429 CTCCCCCTTTAGCACTGCC 60.077 63.158 0.00 0.00 0.00 4.85
933 995 2.284627 CGGATTACGCCTTTTTCGTACG 60.285 50.000 9.53 9.53 41.41 3.67
934 996 2.667969 GGATTACGCCTTTTTCGTACGT 59.332 45.455 16.05 0.00 41.41 3.57
935 997 3.857093 GGATTACGCCTTTTTCGTACGTA 59.143 43.478 16.05 1.99 41.41 3.57
936 998 4.259411 GGATTACGCCTTTTTCGTACGTAC 60.259 45.833 15.90 15.90 41.41 3.67
947 1009 4.968812 TTCGTACGTACCATCAGATCAA 57.031 40.909 19.67 0.00 0.00 2.57
963 1025 6.292923 TCAGATCAATGTGTGCATATGATGA 58.707 36.000 6.97 0.63 35.29 2.92
964 1026 6.940298 TCAGATCAATGTGTGCATATGATGAT 59.060 34.615 6.97 5.15 35.29 2.45
965 1027 8.098286 TCAGATCAATGTGTGCATATGATGATA 58.902 33.333 6.97 0.00 35.29 2.15
966 1028 8.893727 CAGATCAATGTGTGCATATGATGATAT 58.106 33.333 6.97 0.61 35.29 1.63
998 1060 5.979517 CCAACTGAACCTTCTTGTTTGATTC 59.020 40.000 0.00 0.00 0.00 2.52
1002 1064 6.000891 TGAACCTTCTTGTTTGATTCGATG 57.999 37.500 0.00 0.00 0.00 3.84
1004 1066 5.613358 ACCTTCTTGTTTGATTCGATGTC 57.387 39.130 0.00 0.00 0.00 3.06
1005 1067 4.455877 ACCTTCTTGTTTGATTCGATGTCC 59.544 41.667 0.00 0.00 0.00 4.02
1006 1068 4.697352 CCTTCTTGTTTGATTCGATGTCCT 59.303 41.667 0.00 0.00 0.00 3.85
1007 1069 5.182001 CCTTCTTGTTTGATTCGATGTCCTT 59.818 40.000 0.00 0.00 0.00 3.36
1008 1070 6.371548 CCTTCTTGTTTGATTCGATGTCCTTA 59.628 38.462 0.00 0.00 0.00 2.69
1009 1071 6.968131 TCTTGTTTGATTCGATGTCCTTAG 57.032 37.500 0.00 0.00 0.00 2.18
1024 1086 2.565834 TCCTTAGTTAGTCACCTGCACC 59.434 50.000 0.00 0.00 0.00 5.01
1097 1159 3.761897 CACCAGGGTTCCAAACTGATAA 58.238 45.455 0.00 0.00 34.21 1.75
1139 1207 3.166657 GCTTCATCGCATTTCAGTTGTC 58.833 45.455 0.00 0.00 0.00 3.18
1225 1293 1.834263 CTCAGGGAGAAAGGGTTCGAT 59.166 52.381 0.00 0.00 38.90 3.59
1282 1350 4.421479 CTGCCGAACCTCGACGCT 62.421 66.667 0.00 0.00 43.74 5.07
1393 1461 0.324614 TGCTCACCATGTCCGTCAAT 59.675 50.000 0.00 0.00 0.00 2.57
1403 1471 0.716108 GTCCGTCAATGACAAGCTCG 59.284 55.000 14.24 0.00 32.91 5.03
1655 1723 3.664025 CTCGTCGGCCTTGGCATCA 62.664 63.158 14.04 0.00 0.00 3.07
1720 1788 3.262660 ACATCATGGGATACAGCATCGAT 59.737 43.478 0.00 0.00 34.12 3.59
1723 1791 5.482163 TCATGGGATACAGCATCGATAAA 57.518 39.130 0.00 0.00 34.12 1.40
1724 1792 5.863965 TCATGGGATACAGCATCGATAAAA 58.136 37.500 0.00 0.00 34.12 1.52
1732 1800 0.658536 GCATCGATAAAAGGCTGCGC 60.659 55.000 0.00 0.00 0.00 6.09
1756 1824 0.390472 CTGCCGAGTTCCTCAAGTCC 60.390 60.000 0.00 0.00 0.00 3.85
1819 1887 5.692115 TGAATTTCCCTAGCATACTGTCA 57.308 39.130 0.00 0.00 0.00 3.58
1825 1893 2.033550 CCCTAGCATACTGTCACGAGAC 59.966 54.545 6.00 6.00 45.19 3.36
2056 2124 1.380112 GAGGAGCCTGGAGTACCGT 60.380 63.158 0.00 0.00 39.42 4.83
2080 2148 6.538021 GTCACAAGATACTCAAGCAGATGAAT 59.462 38.462 0.00 0.00 0.00 2.57
2164 2232 1.424638 TGATCCCAGTAGCTTAGGGC 58.575 55.000 11.80 1.94 42.52 5.19
2168 2236 1.700042 CCCAGTAGCTTAGGGCCTGG 61.700 65.000 18.53 10.23 44.56 4.45
2175 2243 0.621082 GCTTAGGGCCTGGTCTTCTT 59.379 55.000 18.53 0.00 34.27 2.52
2218 2286 9.407380 TGTAGCATGTTTTATATTCAGGTGAAT 57.593 29.630 10.03 10.03 45.77 2.57
2306 2374 8.435430 GCATTTTGCTTTAACTAGATGTTTTCC 58.565 33.333 0.00 0.00 40.96 3.13
2358 2426 7.524717 ACAAGTGGCTTGAGTATGTATTTTT 57.475 32.000 14.81 0.00 43.42 1.94
2394 2462 3.004734 AGGAAAGCGTGTGAATTTTCCAG 59.995 43.478 14.98 0.00 46.97 3.86
2473 2541 6.089016 CACAGTCACCTAATTACACAGTTACG 59.911 42.308 0.00 0.00 0.00 3.18
2482 2550 1.003851 ACACAGTTACGCACACACAC 58.996 50.000 0.00 0.00 0.00 3.82
2483 2551 1.003108 CACAGTTACGCACACACACA 58.997 50.000 0.00 0.00 0.00 3.72
2484 2552 1.003851 ACAGTTACGCACACACACAC 58.996 50.000 0.00 0.00 0.00 3.82
2485 2553 1.003108 CAGTTACGCACACACACACA 58.997 50.000 0.00 0.00 0.00 3.72
2486 2554 1.003851 AGTTACGCACACACACACAC 58.996 50.000 0.00 0.00 0.00 3.82
2487 2555 0.722282 GTTACGCACACACACACACA 59.278 50.000 0.00 0.00 0.00 3.72
2488 2556 0.722282 TTACGCACACACACACACAC 59.278 50.000 0.00 0.00 0.00 3.82
2489 2557 0.389948 TACGCACACACACACACACA 60.390 50.000 0.00 0.00 0.00 3.72
2490 2558 1.225991 CGCACACACACACACACAC 60.226 57.895 0.00 0.00 0.00 3.82
2491 2559 1.872468 GCACACACACACACACACA 59.128 52.632 0.00 0.00 0.00 3.72
2492 2560 0.454285 GCACACACACACACACACAC 60.454 55.000 0.00 0.00 0.00 3.82
2493 2561 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2494 2562 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2495 2563 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2513 2581 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
2588 2656 2.821969 CAGTGCCTACTCAGCCAAATTT 59.178 45.455 0.00 0.00 34.07 1.82
2721 2789 6.183361 ACTCTTGCATACCATCTCAATCAGAT 60.183 38.462 0.00 0.00 43.33 2.90
2777 2845 6.717084 AGTAGTGGAGAATTTTGGGAAGAAAG 59.283 38.462 0.00 0.00 0.00 2.62
2783 2851 8.115384 TGGAGAATTTTGGGAAGAAAGATGATA 58.885 33.333 0.00 0.00 0.00 2.15
2878 2946 3.674997 CTGTGTACAACCTTACCTGCAT 58.325 45.455 0.00 0.00 0.00 3.96
3020 3088 3.760684 GTGGATCTGAAAATGCTCCAGTT 59.239 43.478 0.00 0.00 36.71 3.16
3071 3139 4.325119 GCTGATGAAGAGCATATGGATGT 58.675 43.478 4.56 0.00 37.34 3.06
3139 3207 4.509616 CGAACCCACTGTATGACCATTAA 58.490 43.478 0.00 0.00 0.00 1.40
3140 3208 5.123227 CGAACCCACTGTATGACCATTAAT 58.877 41.667 0.00 0.00 0.00 1.40
3149 3217 8.458052 CACTGTATGACCATTAATTTGTTAGCA 58.542 33.333 0.00 0.00 0.00 3.49
3156 3225 7.870445 TGACCATTAATTTGTTAGCACTTTTCC 59.130 33.333 0.00 0.00 0.00 3.13
3202 3271 3.184541 CTGCTAATGGAAACTGCAATGC 58.815 45.455 0.00 0.00 33.07 3.56
3319 3388 6.321945 TCATATGCAGCCTGACAAACATATTT 59.678 34.615 0.00 0.00 30.39 1.40
3329 3398 8.296713 GCCTGACAAACATATTTCTCAAGTAAA 58.703 33.333 0.00 0.00 0.00 2.01
3433 3507 3.626028 ACTTTTCATGCGTTTGTCCTC 57.374 42.857 0.00 0.00 0.00 3.71
3466 3540 7.896383 AAGCCATAAAAGCCTGTCATATTTA 57.104 32.000 0.00 0.00 0.00 1.40
3468 3542 7.945134 AGCCATAAAAGCCTGTCATATTTAAG 58.055 34.615 0.00 0.00 0.00 1.85
3474 3548 5.379706 AGCCTGTCATATTTAAGAAGCCT 57.620 39.130 0.00 0.00 0.00 4.58
3475 3549 5.372373 AGCCTGTCATATTTAAGAAGCCTC 58.628 41.667 0.00 0.00 0.00 4.70
3477 3551 5.238214 GCCTGTCATATTTAAGAAGCCTCTG 59.762 44.000 0.00 0.00 30.03 3.35
3496 3812 5.047306 CCTCTGCGGGTTAGACATGAATATA 60.047 44.000 0.00 0.00 0.00 0.86
3499 3815 7.450074 TCTGCGGGTTAGACATGAATATATTT 58.550 34.615 0.00 0.00 0.00 1.40
3500 3816 7.936847 TCTGCGGGTTAGACATGAATATATTTT 59.063 33.333 0.00 0.00 0.00 1.82
3681 4038 4.978186 AGACAAAATGCGATGTTGAGATG 58.022 39.130 6.18 0.00 0.00 2.90
3689 4046 2.606725 GCGATGTTGAGATGGAAGAGTG 59.393 50.000 0.00 0.00 0.00 3.51
3699 4056 6.542821 TGAGATGGAAGAGTGGTTTATTGTT 58.457 36.000 0.00 0.00 0.00 2.83
3702 4059 7.661040 AGATGGAAGAGTGGTTTATTGTTTTG 58.339 34.615 0.00 0.00 0.00 2.44
3725 4082 6.927416 TGCATATTCATTTTCAGAGTTGCTT 58.073 32.000 0.00 0.00 0.00 3.91
3733 4090 7.394016 TCATTTTCAGAGTTGCTTACCTGATA 58.606 34.615 0.00 0.00 35.44 2.15
3757 4114 7.093322 AGTTTCAAGCATTTTAGAGGCATAG 57.907 36.000 0.00 0.00 0.00 2.23
3827 4184 5.812642 CCACTGTACTGGTCATTATTCTCAC 59.187 44.000 4.66 0.00 0.00 3.51
3862 4219 1.215014 TGTCAGAGCTTGCGTCAACG 61.215 55.000 0.00 0.00 43.27 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.860078 GGCAAAACAGAGGTCGACG 59.140 57.895 9.92 0.00 0.00 5.12
1 2 1.566018 CCGGCAAAACAGAGGTCGAC 61.566 60.000 7.13 7.13 0.00 4.20
2 3 1.301401 CCGGCAAAACAGAGGTCGA 60.301 57.895 0.00 0.00 0.00 4.20
57 58 0.676782 TGAGCGAGACACCGAGATGA 60.677 55.000 0.00 0.00 0.00 2.92
64 65 0.528684 GCCTACATGAGCGAGACACC 60.529 60.000 0.00 0.00 0.00 4.16
133 134 1.180456 TAGGGTTTGCTCCGACGACA 61.180 55.000 0.00 0.00 0.00 4.35
137 138 2.774687 TCTTTTAGGGTTTGCTCCGAC 58.225 47.619 0.00 0.00 0.00 4.79
184 185 2.358737 AAGGGCTTTGCTCCGACG 60.359 61.111 0.00 0.00 0.00 5.12
188 189 1.967535 GGAACAAGGGCTTTGCTCC 59.032 57.895 14.89 14.89 42.92 4.70
285 322 2.148916 TCATCGCTCAACTTGTCGTT 57.851 45.000 6.25 0.00 35.88 3.85
505 545 2.228059 TGGCGAGATACTGTAGCTACC 58.772 52.381 21.01 14.49 0.00 3.18
609 653 4.735338 GTCTAAAAATGGCTTATCTTGCGC 59.265 41.667 0.00 0.00 0.00 6.09
767 820 4.098044 GGAGGGCGATAATCGATGAGAATA 59.902 45.833 0.00 0.00 43.74 1.75
770 823 1.819288 GGAGGGCGATAATCGATGAGA 59.181 52.381 0.00 0.00 43.74 3.27
794 847 2.038557 GGGTGCTACCATAATCGGACAT 59.961 50.000 7.49 0.00 41.02 3.06
798 851 2.631160 TTGGGTGCTACCATAATCGG 57.369 50.000 7.49 0.00 41.02 4.18
811 872 1.066716 CAGCATGGTGGAAATTGGGTG 60.067 52.381 17.24 0.00 0.00 4.61
846 907 3.815401 CTGTTGACGGATGGTTTCTCTTT 59.185 43.478 0.00 0.00 0.00 2.52
851 912 1.234821 TGCTGTTGACGGATGGTTTC 58.765 50.000 0.00 0.00 0.00 2.78
860 921 1.135603 CCATGGACATTGCTGTTGACG 60.136 52.381 5.56 0.00 35.14 4.35
864 925 4.558496 CGTAAAACCATGGACATTGCTGTT 60.558 41.667 21.47 0.00 35.14 3.16
885 947 2.284112 TAAAGGGGGAGCGGTCGT 60.284 61.111 8.77 0.00 0.00 4.34
910 972 1.461897 ACGAAAAAGGCGTAATCCGTG 59.538 47.619 0.00 0.00 40.65 4.94
933 995 3.940852 TGCACACATTGATCTGATGGTAC 59.059 43.478 12.30 0.00 0.00 3.34
934 996 4.219264 TGCACACATTGATCTGATGGTA 57.781 40.909 12.30 0.00 0.00 3.25
935 997 3.076079 TGCACACATTGATCTGATGGT 57.924 42.857 12.30 6.38 0.00 3.55
936 998 5.472137 TCATATGCACACATTGATCTGATGG 59.528 40.000 12.30 5.93 37.74 3.51
964 1026 9.613428 CAAGAAGGTTCAGTTGGTTCATATATA 57.387 33.333 0.00 0.00 0.00 0.86
965 1027 8.109634 ACAAGAAGGTTCAGTTGGTTCATATAT 58.890 33.333 0.00 0.00 0.00 0.86
966 1028 7.458397 ACAAGAAGGTTCAGTTGGTTCATATA 58.542 34.615 0.00 0.00 0.00 0.86
998 1060 4.673441 CAGGTGACTAACTAAGGACATCG 58.327 47.826 0.00 0.00 40.21 3.84
1002 1064 3.586892 GTGCAGGTGACTAACTAAGGAC 58.413 50.000 0.00 0.00 40.21 3.85
1004 1066 2.674177 CGGTGCAGGTGACTAACTAAGG 60.674 54.545 0.00 0.00 40.21 2.69
1005 1067 2.029290 ACGGTGCAGGTGACTAACTAAG 60.029 50.000 0.00 0.00 40.21 2.18
1006 1068 1.965643 ACGGTGCAGGTGACTAACTAA 59.034 47.619 0.00 0.00 40.21 2.24
1007 1069 1.542915 GACGGTGCAGGTGACTAACTA 59.457 52.381 0.00 0.00 40.21 2.24
1008 1070 0.317479 GACGGTGCAGGTGACTAACT 59.683 55.000 0.00 0.00 40.21 2.24
1009 1071 1.007336 CGACGGTGCAGGTGACTAAC 61.007 60.000 0.00 0.00 40.21 2.34
1097 1159 6.070951 AGCATCATACATATAATGCCAGGT 57.929 37.500 3.76 0.00 44.34 4.00
1139 1207 2.983433 CAGGGCTAATCTCTGCACG 58.017 57.895 0.00 0.00 37.72 5.34
1208 1276 1.834263 CTCATCGAACCCTTTCTCCCT 59.166 52.381 0.00 0.00 0.00 4.20
1393 1461 2.741092 GTGGGGACGAGCTTGTCA 59.259 61.111 30.70 12.50 40.72 3.58
1403 1471 4.699522 GCACTGGACCGTGGGGAC 62.700 72.222 15.24 0.00 35.47 4.46
1655 1723 0.833287 CCGATCATGACCTCCCTGTT 59.167 55.000 0.00 0.00 0.00 3.16
1732 1800 4.035843 AGGAACTCGGCAGTAGGG 57.964 61.111 0.00 0.00 30.14 3.53
2056 2124 5.665916 TCATCTGCTTGAGTATCTTGTGA 57.334 39.130 0.00 0.00 34.92 3.58
2080 2148 1.762370 TCACTGAGACTGCACCTTGAA 59.238 47.619 0.00 0.00 0.00 2.69
2164 2232 3.323403 ACTGAAGAGACAAGAAGACCAGG 59.677 47.826 0.00 0.00 0.00 4.45
2168 2236 4.202264 TGGGAACTGAAGAGACAAGAAGAC 60.202 45.833 0.00 0.00 0.00 3.01
2175 2243 3.055819 GCTACATGGGAACTGAAGAGACA 60.056 47.826 0.00 0.00 0.00 3.41
2296 2364 4.320494 GCACTGAACATTCGGAAAACATCT 60.320 41.667 7.45 0.00 37.03 2.90
2358 2426 5.123820 CACGCTTTCCTTGGAAGAAATATGA 59.876 40.000 2.16 0.00 33.01 2.15
2374 2442 2.726241 GCTGGAAAATTCACACGCTTTC 59.274 45.455 0.00 0.00 0.00 2.62
2394 2462 8.804743 CATTTGAAATGAATAGAACATGACAGC 58.195 33.333 12.37 0.00 0.00 4.40
2443 2511 7.178628 ACTGTGTAATTAGGTGACTGTGATAGT 59.821 37.037 0.00 0.00 43.88 2.12
2473 2541 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
2482 2550 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2483 2551 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2484 2552 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2485 2553 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2486 2554 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2487 2555 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2488 2556 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2489 2557 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2490 2558 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2491 2559 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2492 2560 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2493 2561 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2494 2562 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2495 2563 0.250510 TGGTGTGTGTGTGTGTGTGT 60.251 50.000 0.00 0.00 0.00 3.72
2588 2656 6.894339 TCTTTCAGATACACTGTACACAGA 57.106 37.500 16.05 0.00 46.59 3.41
2721 2789 0.321671 GCTACACTGGAGTTGCCTGA 59.678 55.000 0.00 0.00 38.83 3.86
2777 2845 4.694509 GTCATGGTCAGGAAGCATATCATC 59.305 45.833 0.00 0.00 44.18 2.92
2783 2851 3.377253 AATGTCATGGTCAGGAAGCAT 57.623 42.857 0.00 0.00 46.92 3.79
2843 2911 5.682943 TGTACACAGCCAAGAAATTGTAC 57.317 39.130 0.00 0.00 39.72 2.90
2845 2913 4.202111 GGTTGTACACAGCCAAGAAATTGT 60.202 41.667 10.06 0.00 45.24 2.71
2945 3013 9.723601 ATTTTAACTGCAAAATGACCACATTAT 57.276 25.926 0.00 0.00 44.67 1.28
3020 3088 3.494626 CGCTTGCTCACTTTAGTCTTTCA 59.505 43.478 0.00 0.00 0.00 2.69
3054 3122 3.455543 TCCACACATCCATATGCTCTTCA 59.544 43.478 0.00 0.00 36.50 3.02
3071 3139 0.035725 CAGCATCAGGAAGCTCCACA 60.036 55.000 0.00 0.00 39.61 4.17
3181 3250 3.184541 GCATTGCAGTTTCCATTAGCAG 58.815 45.455 3.15 0.00 36.47 4.24
3202 3271 1.105167 CCTGGTATGGCATGCACCTG 61.105 60.000 21.36 20.29 33.28 4.00
3266 3335 2.932614 CGGGCATTCAGTAAACTCTCAG 59.067 50.000 0.00 0.00 0.00 3.35
3269 3338 1.679032 GGCGGGCATTCAGTAAACTCT 60.679 52.381 0.00 0.00 0.00 3.24
3413 3487 2.948979 TGAGGACAAACGCATGAAAAGT 59.051 40.909 0.00 0.00 0.00 2.66
3433 3507 4.646492 AGGCTTTTATGGCTTATGGACTTG 59.354 41.667 0.00 0.00 40.00 3.16
3466 3540 0.250513 CTAACCCGCAGAGGCTTCTT 59.749 55.000 0.00 0.00 39.21 2.52
3468 3542 0.460459 GTCTAACCCGCAGAGGCTTC 60.460 60.000 0.00 0.00 39.21 3.86
3474 3548 4.955811 ATATTCATGTCTAACCCGCAGA 57.044 40.909 0.00 0.00 0.00 4.26
3475 3549 7.672983 AAATATATTCATGTCTAACCCGCAG 57.327 36.000 0.00 0.00 0.00 5.18
3477 3551 8.094798 TCAAAATATATTCATGTCTAACCCGC 57.905 34.615 0.00 0.00 0.00 6.13
3499 3815 9.743057 CTTTAAATGTGTTCATGTTAACCTCAA 57.257 29.630 2.48 0.00 34.19 3.02
3500 3816 9.126151 TCTTTAAATGTGTTCATGTTAACCTCA 57.874 29.630 2.48 0.00 34.19 3.86
3539 3896 7.198390 GCTTTAGTGATGCATGTATGTTCAAT 58.802 34.615 2.46 0.00 0.00 2.57
3546 3903 4.635765 ACAACGCTTTAGTGATGCATGTAT 59.364 37.500 2.46 0.00 32.51 2.29
3681 4038 5.596845 TGCAAAACAATAAACCACTCTTCC 58.403 37.500 0.00 0.00 0.00 3.46
3699 4056 7.380536 AGCAACTCTGAAAATGAATATGCAAA 58.619 30.769 0.00 0.00 32.76 3.68
3702 4059 7.433425 GGTAAGCAACTCTGAAAATGAATATGC 59.567 37.037 0.00 0.00 0.00 3.14
3714 4071 6.014584 TGAAACTATCAGGTAAGCAACTCTGA 60.015 38.462 10.55 10.55 38.75 3.27
3725 4082 9.383519 CTCTAAAATGCTTGAAACTATCAGGTA 57.616 33.333 0.00 0.00 39.77 3.08
3733 4090 5.990120 ATGCCTCTAAAATGCTTGAAACT 57.010 34.783 0.00 0.00 0.00 2.66
3757 4114 5.725110 ATATTGATGCAGACAAGTTCGAC 57.275 39.130 13.10 0.00 0.00 4.20
3802 4159 5.104941 TGAGAATAATGACCAGTACAGTGGG 60.105 44.000 7.96 0.00 42.54 4.61
3844 4201 1.215655 ACGTTGACGCAAGCTCTGAC 61.216 55.000 3.05 0.00 44.43 3.51
3862 4219 2.743928 CCCCGACTCAGCTGCAAC 60.744 66.667 9.47 1.25 0.00 4.17


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

AutoCloner maintained by Alex Coulton.