Multiple sequence alignment - TraesCS7A01G148600

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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 TraesCS7A01G148600 chr7A 100.000 5451 0 0 1 5451 101857891 101863341 0.000000e+00 10067
1 TraesCS7A01G148600 chr7A 94.286 70 4 0 584 653 101858543 101858474 2.080000e-19 108
2 TraesCS7A01G148600 chr7A 90.000 80 3 1 579 653 509222371 509222450 1.250000e-16 99
3 TraesCS7A01G148600 chr7B 95.097 4467 206 8 1 4459 54724165 54728626 0.000000e+00 7023
4 TraesCS7A01G148600 chr7B 90.909 429 29 4 4459 4887 54728668 54729086 7.920000e-158 568
5 TraesCS7A01G148600 chr7B 89.286 84 2 3 575 653 8983977 8984058 1.250000e-16 99
6 TraesCS7A01G148600 chr7D 95.606 4210 175 5 256 4459 99461465 99465670 0.000000e+00 6741
7 TraesCS7A01G148600 chr7D 86.083 1006 73 26 4462 5451 99465719 99466673 0.000000e+00 1020
8 TraesCS7A01G148600 chr7D 91.860 258 19 2 1 257 99461048 99461304 5.190000e-95 359
9 TraesCS7A01G148600 chr7D 89.286 84 2 3 575 653 66954725 66954806 1.250000e-16 99
10 TraesCS7A01G148600 chr6B 94.286 70 4 0 590 659 525557609 525557540 2.080000e-19 108
11 TraesCS7A01G148600 chr4B 88.043 92 5 2 573 659 41531506 41531416 2.690000e-18 104
12 TraesCS7A01G148600 chr5D 89.286 84 4 1 575 653 281024878 281024795 3.470000e-17 100


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 TraesCS7A01G148600 chr7A 101857891 101863341 5450 False 10067.000000 10067 100.000 1 5451 1 chr7A.!!$F1 5450
1 TraesCS7A01G148600 chr7B 54724165 54729086 4921 False 3795.500000 7023 93.003 1 4887 2 chr7B.!!$F2 4886
2 TraesCS7A01G148600 chr7D 99461048 99466673 5625 False 2706.666667 6741 91.183 1 5451 3 chr7D.!!$F2 5450

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
889 1060 0.318869 TGCTGCCATTTTTGTGCTCG 60.319 50.0 0.0 0.00 0.00 5.03 F
1638 1809 0.550914 ACTGCACCAAGTTGGAGGAA 59.449 50.0 28.8 13.19 40.96 3.36 F
3147 3318 0.108585 TGAACTCCACACCAAGCTCC 59.891 55.0 0.0 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2070 0.107703 TGAGGTTGCTCAATAGGCCG 60.108 55.0 0.0 0.0 0.0 6.13 R
3255 3426 0.865769 GTGCAACCTTGAATCGACGT 59.134 50.0 0.0 0.0 0.0 4.34 R
5013 5240 0.103608 TTCCAGGGAAGGGAAAGGGA 60.104 55.0 0.0 0.0 41.3 4.20 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
87 88 2.502745 TGGATTCCCAGCTATTTCCCT 58.497 47.619 0.00 0.00 37.58 4.20
88 89 2.175499 TGGATTCCCAGCTATTTCCCTG 59.825 50.000 0.00 0.00 37.58 4.45
95 96 3.193479 CCCAGCTATTTCCCTGTTTGTTC 59.807 47.826 0.00 0.00 0.00 3.18
109 110 6.209391 CCCTGTTTGTTCCTCTGTTTATCATT 59.791 38.462 0.00 0.00 0.00 2.57
166 168 3.665190 AGTTTAAGCACTCTTCTTCCCG 58.335 45.455 0.00 0.00 33.85 5.14
178 180 4.932146 TCTTCTTCCCGCAAAAAGAAAAG 58.068 39.130 6.04 0.00 40.09 2.27
292 456 1.895131 CCTAGCAATTGCCAACTTGGT 59.105 47.619 26.45 8.25 40.46 3.67
309 473 6.590234 ACTTGGTCCTCAATTTAATTGACC 57.410 37.500 15.46 15.62 43.84 4.02
494 659 3.053544 AGGAACCCAGATTCGAGTCTAGA 60.054 47.826 10.40 0.00 0.00 2.43
536 701 1.609841 GGTTGTTCGAGGTTCGGGATT 60.610 52.381 0.00 0.00 40.88 3.01
582 747 6.884832 TGACCACAACCCTTAGATATTACTG 58.115 40.000 0.00 0.00 0.00 2.74
587 752 5.665812 ACAACCCTTAGATATTACTGCCTCA 59.334 40.000 0.00 0.00 0.00 3.86
715 885 4.600062 AGGAGTCATAAACCATGAAACCC 58.400 43.478 0.00 0.00 45.28 4.11
721 891 5.242838 GTCATAAACCATGAAACCCAACTCA 59.757 40.000 0.00 0.00 45.28 3.41
729 899 5.068460 CCATGAAACCCAACTCACAGTTTTA 59.932 40.000 0.00 0.00 36.03 1.52
765 935 4.595762 AAGCTCTTGTTAGGACGTACAA 57.404 40.909 0.00 0.35 33.54 2.41
889 1060 0.318869 TGCTGCCATTTTTGTGCTCG 60.319 50.000 0.00 0.00 0.00 5.03
908 1079 2.492088 TCGGGATGTAATATCTGCGAGG 59.508 50.000 0.00 0.00 0.00 4.63
911 1082 2.996621 GGATGTAATATCTGCGAGGCAC 59.003 50.000 0.00 0.00 33.79 5.01
1050 1221 7.469260 TGTTTCTCTTCTTAAGTTTGGTTTCG 58.531 34.615 1.63 0.00 0.00 3.46
1128 1299 9.866655 AATCTCATATTGCCTAGTTCCATAAAA 57.133 29.630 0.00 0.00 0.00 1.52
1184 1355 4.021102 ACTGGACTGGAATTAGTTGTGG 57.979 45.455 0.00 0.00 0.00 4.17
1257 1428 5.783360 TGGTTCACTAGGAGTTCAAATAGGA 59.217 40.000 0.00 0.00 0.00 2.94
1364 1535 3.762407 TGAACAGTTGGATCTTTCCGA 57.238 42.857 0.00 0.00 45.89 4.55
1535 1706 5.584551 AAACTCAGTGGTTCTATCCCTTT 57.415 39.130 0.00 0.00 0.00 3.11
1550 1721 7.110155 TCTATCCCTTTATCAGTTGGTGAAAC 58.890 38.462 0.00 0.00 39.19 2.78
1577 1748 6.438425 ACAAGCCTTAGATCATTTTGGTTGAT 59.562 34.615 15.99 0.00 36.54 2.57
1581 1752 6.038356 CCTTAGATCATTTTGGTTGATGCAC 58.962 40.000 0.00 0.00 34.03 4.57
1603 1774 4.080129 ACAATGCATTATCTGGAGGTCTGT 60.080 41.667 12.53 0.00 0.00 3.41
1638 1809 0.550914 ACTGCACCAAGTTGGAGGAA 59.449 50.000 28.80 13.19 40.96 3.36
1660 1831 3.194542 ACTCTATCTGCTGGATAATCGGC 59.805 47.826 0.00 0.00 36.59 5.54
1695 1866 4.015872 TCCGAAAACCTTGAGCTATGTT 57.984 40.909 0.00 0.00 0.00 2.71
1822 1993 2.516225 GGGGCGGTATTCCAGCAC 60.516 66.667 7.31 3.89 36.47 4.40
1899 2070 1.429423 CCAAATTCCGGCTTCGCTC 59.571 57.895 0.00 0.00 0.00 5.03
2019 2190 5.762218 GCTAGAGTTGGATCATAACATGCTT 59.238 40.000 12.74 0.00 0.00 3.91
2079 2250 5.105595 ACACTTGCAGAAGCTCTTTCTTTTT 60.106 36.000 0.00 0.00 43.68 1.94
2111 2282 1.612442 CCGGGGAGTTTCCTGAGGA 60.612 63.158 0.00 0.00 36.57 3.71
2223 2394 8.181904 AGTTATTGGAGAACATCACATTGTTT 57.818 30.769 0.00 0.00 39.85 2.83
2359 2530 2.777692 AGGAAAAGACTCAGGGTGTTGA 59.222 45.455 0.00 0.00 31.54 3.18
2367 2538 1.273327 CTCAGGGTGTTGATTTTGGGC 59.727 52.381 0.00 0.00 0.00 5.36
2379 2550 6.183360 TGTTGATTTTGGGCTTCAATCTTCTT 60.183 34.615 0.00 0.00 34.98 2.52
2485 2656 5.843673 TCCACATTTTAGAAACTGTGCAA 57.156 34.783 16.07 7.11 43.83 4.08
2486 2657 5.830912 TCCACATTTTAGAAACTGTGCAAG 58.169 37.500 16.07 6.83 43.83 4.01
2582 2753 8.964476 AATACTACAATGATAAACTGGTCAGG 57.036 34.615 2.87 0.00 0.00 3.86
2640 2811 4.262036 GGAAACTTGGTGAATTTGGGAGTC 60.262 45.833 0.00 0.00 0.00 3.36
2667 2838 5.552870 ACCTCTCACAAAACAGTCTACAT 57.447 39.130 0.00 0.00 0.00 2.29
2712 2883 6.090483 TCTAGTTGCTCCAAGCTGTATATC 57.910 41.667 0.11 0.00 42.97 1.63
2719 2890 4.622695 GCTCCAAGCTGTATATCCTGGATC 60.623 50.000 13.54 0.00 38.45 3.36
2753 2924 1.002257 TGCATGGTTCGGCACTCAT 60.002 52.632 0.00 0.00 34.58 2.90
2889 3060 1.251251 GCAACATTCTTGGAGGCAGT 58.749 50.000 0.00 0.00 0.00 4.40
2898 3069 1.839994 CTTGGAGGCAGTATCCCTTCA 59.160 52.381 0.00 0.00 36.17 3.02
2901 3072 2.334023 GGAGGCAGTATCCCTTCATCT 58.666 52.381 0.00 0.00 31.41 2.90
2946 3117 2.758423 TGCATTGAATCTCAGCAGCAAT 59.242 40.909 0.00 0.00 30.39 3.56
3050 3221 1.152383 GGTCTCGGCGCATTAGGAAC 61.152 60.000 10.83 0.00 0.00 3.62
3147 3318 0.108585 TGAACTCCACACCAAGCTCC 59.891 55.000 0.00 0.00 0.00 4.70
3150 3321 0.398318 ACTCCACACCAAGCTCCTTC 59.602 55.000 0.00 0.00 0.00 3.46
3162 3333 4.221262 CCAAGCTCCTTCAATGGAAATTCA 59.779 41.667 0.00 0.00 35.43 2.57
3171 3342 4.012374 TCAATGGAAATTCAGGTCTCTGC 58.988 43.478 0.00 0.00 40.69 4.26
3172 3343 2.099141 TGGAAATTCAGGTCTCTGCG 57.901 50.000 0.00 0.00 40.69 5.18
3182 3353 1.290324 GTCTCTGCGTCTCTTGCCA 59.710 57.895 0.00 0.00 0.00 4.92
3192 3363 2.072298 GTCTCTTGCCATGACAGTGAC 58.928 52.381 0.00 0.08 0.00 3.67
3211 3382 4.626604 GTGACTCTTCTTGCAAGAGATCTG 59.373 45.833 27.02 18.38 44.96 2.90
3217 3388 4.548451 TCTTGCAAGAGATCTGATGTGT 57.452 40.909 25.16 0.00 0.00 3.72
3225 3396 4.248859 AGAGATCTGATGTGTTGAAACCG 58.751 43.478 0.00 0.00 0.00 4.44
3273 3444 1.588674 AACGTCGATTCAAGGTTGCA 58.411 45.000 0.00 0.00 0.00 4.08
3339 3510 5.304101 ACTTATCCTCTGCTGTATCCTTCTG 59.696 44.000 0.00 0.00 0.00 3.02
3340 3511 1.759445 TCCTCTGCTGTATCCTTCTGC 59.241 52.381 0.00 0.00 0.00 4.26
3454 3625 8.562892 AGACAGAAAACTTTGATGACAAGTATG 58.437 33.333 0.00 0.00 37.32 2.39
3480 3651 1.742880 CACAGGTGCTCATGGGACG 60.743 63.158 0.00 0.00 37.13 4.79
3494 3665 1.232621 GGGACGGTGTACAAGGCAAC 61.233 60.000 0.00 0.00 0.00 4.17
3496 3667 0.584876 GACGGTGTACAAGGCAACAC 59.415 55.000 0.00 0.00 44.19 3.32
3534 3705 5.106157 GGTCTTTGCTATAAAGAAGCTTGCA 60.106 40.000 2.10 1.78 40.73 4.08
3543 3714 0.961019 AGAAGCTTGCAATTTCCGCA 59.039 45.000 2.10 0.00 37.68 5.69
3555 3726 3.807631 TTCCGCACGCAGCAGTTCT 62.808 57.895 0.00 0.00 46.13 3.01
3561 3732 1.398960 GCACGCAGCAGTTCTTACAAG 60.399 52.381 0.00 0.00 44.79 3.16
3630 3801 8.518702 AGGAACTTGATAAAGCTGAAAGAATTC 58.481 33.333 0.00 0.00 27.35 2.17
3639 3810 2.751806 GCTGAAAGAATTCTGGGTGAGG 59.248 50.000 9.17 0.00 36.48 3.86
3642 3813 1.760405 AAGAATTCTGGGTGAGGGGT 58.240 50.000 9.17 0.00 0.00 4.95
3681 3852 4.136796 TGTATGACTTTATGGAGCATGGC 58.863 43.478 0.00 0.00 0.00 4.40
3927 4098 0.903454 CTCCACAGTCTACCGGGGTT 60.903 60.000 6.32 0.00 0.00 4.11
3991 4162 7.315142 TGCAAACCATTTCTTGATAGTGAATC 58.685 34.615 0.00 0.00 34.93 2.52
4039 4210 2.234661 TGACAAGCTGATACCTGACAGG 59.765 50.000 20.45 20.45 42.49 4.00
4041 4212 0.543749 AAGCTGATACCTGACAGGCC 59.456 55.000 21.95 11.33 39.63 5.19
4042 4213 1.227380 GCTGATACCTGACAGGCCG 60.227 63.158 21.95 6.57 39.63 6.13
4043 4214 1.961180 GCTGATACCTGACAGGCCGT 61.961 60.000 21.95 7.49 39.63 5.68
4044 4215 0.179100 CTGATACCTGACAGGCCGTG 60.179 60.000 21.95 4.69 39.63 4.94
4045 4216 0.902984 TGATACCTGACAGGCCGTGT 60.903 55.000 21.95 7.46 44.49 4.49
4046 4217 0.249398 GATACCTGACAGGCCGTGTT 59.751 55.000 21.95 3.23 40.56 3.32
4047 4218 0.036388 ATACCTGACAGGCCGTGTTG 60.036 55.000 21.95 0.00 40.56 3.33
4048 4219 1.404479 TACCTGACAGGCCGTGTTGT 61.404 55.000 21.95 2.20 40.56 3.32
4050 4221 1.101049 CCTGACAGGCCGTGTTGTTT 61.101 55.000 8.99 0.00 40.56 2.83
4051 4222 0.307760 CTGACAGGCCGTGTTGTTTC 59.692 55.000 8.90 0.00 40.56 2.78
4066 4237 1.604593 TTTCCTTGCAGAGCTGGCC 60.605 57.895 0.00 0.00 0.00 5.36
4099 4270 3.655276 AACAGTATCAAGACCGACGTT 57.345 42.857 0.00 0.00 0.00 3.99
4144 4315 2.416836 CGAGCTGATAACGGGAAAGACA 60.417 50.000 0.00 0.00 0.00 3.41
4324 4495 1.449601 CCTTAGGTGCACGGCGAAT 60.450 57.895 16.62 0.00 0.00 3.34
4459 4630 1.404851 GGCTCTTCCTGACTGCAGTAC 60.405 57.143 21.73 13.90 40.63 2.73
4460 4631 1.273606 GCTCTTCCTGACTGCAGTACA 59.726 52.381 21.73 17.67 40.63 2.90
4510 4727 1.478510 CATCGGCTAGGTTCTGACTGT 59.521 52.381 0.00 0.00 0.00 3.55
4511 4728 2.502142 TCGGCTAGGTTCTGACTGTA 57.498 50.000 0.00 0.00 0.00 2.74
4512 4729 2.366533 TCGGCTAGGTTCTGACTGTAG 58.633 52.381 0.00 0.00 0.00 2.74
4513 4730 2.093106 CGGCTAGGTTCTGACTGTAGT 58.907 52.381 0.00 0.00 0.00 2.73
4514 4731 2.097791 CGGCTAGGTTCTGACTGTAGTC 59.902 54.545 5.09 5.09 44.97 2.59
4548 4770 6.012658 TGGTAACTGAGTTTTGATGATTGC 57.987 37.500 1.97 0.00 37.61 3.56
4619 4841 1.684983 GAAATCATGTGGCTGGATGGG 59.315 52.381 0.00 0.00 0.00 4.00
4621 4843 1.521764 ATCATGTGGCTGGATGGGTA 58.478 50.000 0.00 0.00 0.00 3.69
4666 4888 6.294675 CCTGTCTTTGGCTGAATACATGAAAA 60.295 38.462 0.00 0.00 0.00 2.29
4671 4893 3.011144 TGGCTGAATACATGAAAAGGGGA 59.989 43.478 0.00 0.00 0.00 4.81
4674 4896 5.394553 GGCTGAATACATGAAAAGGGGAAAG 60.395 44.000 0.00 0.00 0.00 2.62
4683 4905 2.978156 AAAGGGGAAAGTCATCAGCA 57.022 45.000 0.00 0.00 0.00 4.41
4696 4918 3.318275 GTCATCAGCATCATCTTGGCATT 59.682 43.478 0.00 0.00 0.00 3.56
4700 4922 3.512329 TCAGCATCATCTTGGCATTTGTT 59.488 39.130 0.00 0.00 0.00 2.83
4732 4954 2.730183 TTGTCTTCGCTGTTTTGTCG 57.270 45.000 0.00 0.00 0.00 4.35
4766 4992 9.571810 CTTCGATATAGTACTACGTAGATGTCT 57.428 37.037 28.74 19.62 0.00 3.41
4797 5023 3.132824 TCATGTAGCGGTGTGAAGATCAT 59.867 43.478 0.00 0.00 0.00 2.45
4800 5026 0.615331 AGCGGTGTGAAGATCATGGT 59.385 50.000 0.00 0.00 0.00 3.55
4821 5047 0.758734 TTCCTGGCCATACCGATCTG 59.241 55.000 5.51 0.00 43.94 2.90
4845 5071 4.144727 TGGCGGGGTTGGGTTTGT 62.145 61.111 0.00 0.00 0.00 2.83
4853 5079 3.910490 TTGGGTTTGTGCTGGCGC 61.910 61.111 0.00 0.00 0.00 6.53
4959 5185 2.631580 GCGCCGAGAGAGGGGATAG 61.632 68.421 0.00 0.00 45.92 2.08
4995 5222 3.504342 CGACATCGATCGTGCGAG 58.496 61.111 15.94 4.42 44.26 5.03
4996 5223 2.630714 CGACATCGATCGTGCGAGC 61.631 63.158 15.94 0.00 44.26 5.03
4997 5224 1.586303 GACATCGATCGTGCGAGCA 60.586 57.895 15.94 0.00 44.26 4.26
4998 5225 0.936764 GACATCGATCGTGCGAGCAT 60.937 55.000 15.94 0.00 44.26 3.79
4999 5226 0.528466 ACATCGATCGTGCGAGCATT 60.528 50.000 15.94 0.00 44.26 3.56
5000 5227 0.111398 CATCGATCGTGCGAGCATTG 60.111 55.000 15.94 3.17 44.26 2.82
5008 5235 2.575262 GCGAGCATTGCGTCTTGC 60.575 61.111 2.38 0.00 46.70 4.01
5017 5244 4.681978 GCGTCTTGCGTGGTCCCT 62.682 66.667 0.00 0.00 43.66 4.20
5091 5319 2.992689 TGCTCGGCGTGGGACTTA 60.993 61.111 6.85 0.00 0.00 2.24
5110 5338 8.573035 GGGACTTATGTTTGAATTTGAAGTGTA 58.427 33.333 0.00 0.00 0.00 2.90
5111 5339 9.612620 GGACTTATGTTTGAATTTGAAGTGTAG 57.387 33.333 0.00 0.00 0.00 2.74
5191 5420 4.917906 TTAAAATGGGGGTTTGGGAATG 57.082 40.909 0.00 0.00 0.00 2.67
5196 5425 0.040499 GGGGGTTTGGGAATGTGCTA 59.960 55.000 0.00 0.00 0.00 3.49
5278 5507 5.077564 GGTCTCCCATTTTAAGGAAACTGT 58.922 41.667 0.00 0.00 42.68 3.55
5307 5536 3.870633 CTCCTAGGAGCGTAGTGTTTT 57.129 47.619 25.73 0.00 35.31 2.43
5364 5600 8.997621 AAGTTATCGTTATAATATGATGCGGT 57.002 30.769 7.63 0.00 30.42 5.68
5365 5601 8.997621 AGTTATCGTTATAATATGATGCGGTT 57.002 30.769 7.63 0.00 30.42 4.44
5366 5602 8.869897 AGTTATCGTTATAATATGATGCGGTTG 58.130 33.333 7.63 0.00 30.42 3.77
5367 5603 5.524511 TCGTTATAATATGATGCGGTTGC 57.475 39.130 0.00 0.00 43.20 4.17
5394 5631 2.799126 TGAACCAAATATGTCGGCCT 57.201 45.000 0.00 0.00 0.00 5.19
5406 5643 6.859112 ATATGTCGGCCTATGTCTAAAGAT 57.141 37.500 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.351233 TGTATAACAAAAGTCGCTTGGTG 57.649 39.130 0.00 0.00 0.00 4.17
73 74 2.807676 ACAAACAGGGAAATAGCTGGG 58.192 47.619 0.00 0.00 0.00 4.45
87 88 9.567776 TTCTAATGATAAACAGAGGAACAAACA 57.432 29.630 0.00 0.00 0.00 2.83
109 110 5.243060 TGAGTCGAAGTGGTCTGAAATTCTA 59.757 40.000 0.00 0.00 0.00 2.10
118 120 1.581954 CGCTGAGTCGAAGTGGTCT 59.418 57.895 0.00 0.00 0.00 3.85
220 222 8.408043 TGGATACTGAAAAAGTTGATGTCATT 57.592 30.769 0.00 0.00 40.56 2.57
309 473 7.296628 ACTGAGGCTATTAGTAAGAATCAGG 57.703 40.000 13.99 2.98 34.71 3.86
365 529 8.250538 TCAAACAAAAACTTTGAGGTGATTTC 57.749 30.769 6.15 0.00 33.60 2.17
494 659 0.322322 CCACATGGGTGCAAGCATTT 59.678 50.000 0.00 0.00 43.88 2.32
536 701 0.178876 TCCATGAGGTCCCTCCAACA 60.179 55.000 10.77 0.00 42.09 3.33
582 747 6.047231 ACGTCTTATATTTTGGTACTGAGGC 58.953 40.000 0.00 0.00 0.00 4.70
698 868 5.242838 GTGAGTTGGGTTTCATGGTTTATGA 59.757 40.000 0.00 0.00 43.92 2.15
715 885 9.352784 TCTTGAAAAACATAAAACTGTGAGTTG 57.647 29.630 0.00 0.00 38.66 3.16
721 891 9.087424 GCTTTCTCTTGAAAAACATAAAACTGT 57.913 29.630 0.00 0.00 41.09 3.55
776 946 6.630071 ACCATGTACACTCCAAATTATTTGC 58.370 36.000 11.82 0.00 39.31 3.68
784 955 6.183360 GCCTAGTATACCATGTACACTCCAAA 60.183 42.308 0.00 0.00 0.00 3.28
889 1060 2.028112 TGCCTCGCAGATATTACATCCC 60.028 50.000 0.00 0.00 33.89 3.85
908 1079 0.379669 CAATCGATGCCCAGAAGTGC 59.620 55.000 0.00 0.00 0.00 4.40
911 1082 3.411415 GAAACAATCGATGCCCAGAAG 57.589 47.619 0.00 0.00 0.00 2.85
1050 1221 4.690748 TCTGAATTCAAACTCCATGACGAC 59.309 41.667 9.88 0.00 0.00 4.34
1184 1355 7.039313 AGAGAAACCACATTGTTCCTTTTAC 57.961 36.000 0.00 0.00 0.00 2.01
1364 1535 6.004574 GGTATTTCACCAGAAAGGAAGTTCT 58.995 40.000 2.25 0.00 46.13 3.01
1535 1706 3.496884 GCTTGTCGTTTCACCAACTGATA 59.503 43.478 0.00 0.00 32.53 2.15
1550 1721 4.396166 ACCAAAATGATCTAAGGCTTGTCG 59.604 41.667 10.69 0.00 0.00 4.35
1581 1752 4.458397 ACAGACCTCCAGATAATGCATTG 58.542 43.478 22.27 5.63 0.00 2.82
1603 1774 2.892215 TGCAGTTGCCAATTGAATCTGA 59.108 40.909 7.12 0.00 41.18 3.27
1638 1809 3.194542 GCCGATTATCCAGCAGATAGAGT 59.805 47.826 0.00 0.00 38.69 3.24
1660 1831 4.521062 CGGAAGGCTCCCGCTCAG 62.521 72.222 0.00 0.00 40.54 3.35
1695 1866 7.001674 TGGCATCTAAAACTTTCAGTCCTTTA 58.998 34.615 0.00 0.00 0.00 1.85
1822 1993 1.871080 CTACTGCAATTCCCTAGCCG 58.129 55.000 0.00 0.00 0.00 5.52
1899 2070 0.107703 TGAGGTTGCTCAATAGGCCG 60.108 55.000 0.00 0.00 0.00 6.13
2019 2190 2.303022 CTCTTTAGGAACAGTGCCCTCA 59.697 50.000 7.85 0.00 34.11 3.86
2079 2250 2.721167 CCCGGTCAGGCGATTCTCA 61.721 63.158 0.00 0.00 39.21 3.27
2111 2282 2.979678 AGGTACCGGATGCTCCAAATAT 59.020 45.455 9.46 0.00 35.91 1.28
2223 2394 5.414789 TGACTCCGGTGAAGAAATTATCA 57.585 39.130 11.17 0.00 0.00 2.15
2359 2530 7.038088 ACCATTAAGAAGATTGAAGCCCAAAAT 60.038 33.333 0.00 0.00 38.43 1.82
2367 2538 7.040823 GGGATGCTACCATTAAGAAGATTGAAG 60.041 40.741 2.59 0.00 0.00 3.02
2485 2656 2.988859 TGAAATCCATATAGCCCAGCCT 59.011 45.455 0.00 0.00 0.00 4.58
2486 2657 3.245052 ACTGAAATCCATATAGCCCAGCC 60.245 47.826 0.00 0.00 0.00 4.85
2524 2695 2.547211 CCAAGCTTGCTGGAATATCTCG 59.453 50.000 21.43 0.00 35.85 4.04
2640 2811 5.368989 AGACTGTTTTGTGAGAGGTTAAGG 58.631 41.667 0.00 0.00 0.00 2.69
2753 2924 1.609061 GCTTCAGGCTGCTTACTGTCA 60.609 52.381 10.34 0.00 38.06 3.58
2889 3060 8.158025 TCAACTTTCCTAAAGATGAAGGGATA 57.842 34.615 9.17 0.00 44.15 2.59
2898 3069 8.924511 TGAGTTTGATCAACTTTCCTAAAGAT 57.075 30.769 7.89 0.00 46.53 2.40
2901 3072 7.867403 GCAATGAGTTTGATCAACTTTCCTAAA 59.133 33.333 7.89 0.00 46.53 1.85
2946 3117 0.984230 GAAGATCACCCACCAGTCCA 59.016 55.000 0.00 0.00 0.00 4.02
3147 3318 5.392811 GCAGAGACCTGAATTTCCATTGAAG 60.393 44.000 0.00 0.00 43.02 3.02
3150 3321 3.181503 CGCAGAGACCTGAATTTCCATTG 60.182 47.826 0.00 0.00 43.02 2.82
3162 3333 1.589113 GCAAGAGACGCAGAGACCT 59.411 57.895 0.00 0.00 0.00 3.85
3171 3342 1.073964 CACTGTCATGGCAAGAGACG 58.926 55.000 0.00 9.49 35.09 4.18
3172 3343 2.072298 GTCACTGTCATGGCAAGAGAC 58.928 52.381 0.00 6.09 0.00 3.36
3182 3353 3.758755 TGCAAGAAGAGTCACTGTCAT 57.241 42.857 0.00 0.00 0.00 3.06
3192 3363 5.292345 CACATCAGATCTCTTGCAAGAAGAG 59.708 44.000 28.16 17.84 43.85 2.85
3211 3382 1.944024 TCCACACGGTTTCAACACATC 59.056 47.619 0.00 0.00 0.00 3.06
3217 3388 1.418264 TGATCCTCCACACGGTTTCAA 59.582 47.619 0.00 0.00 0.00 2.69
3225 3396 2.879103 TTTTCCCTGATCCTCCACAC 57.121 50.000 0.00 0.00 0.00 3.82
3255 3426 0.865769 GTGCAACCTTGAATCGACGT 59.134 50.000 0.00 0.00 0.00 4.34
3426 3597 7.475840 ACTTGTCATCAAAGTTTTCTGTCTTC 58.524 34.615 0.00 0.00 32.87 2.87
3463 3634 2.665000 CGTCCCATGAGCACCTGT 59.335 61.111 0.00 0.00 0.00 4.00
3480 3651 1.961793 TCAGTGTTGCCTTGTACACC 58.038 50.000 0.00 0.00 44.38 4.16
3494 3665 1.912043 AGACCTCCCCTGAATTCAGTG 59.088 52.381 29.03 20.56 42.27 3.66
3496 3667 3.350833 CAAAGACCTCCCCTGAATTCAG 58.649 50.000 25.75 25.75 43.40 3.02
3543 3714 2.408050 CTCTTGTAAGAACTGCTGCGT 58.592 47.619 0.00 0.00 34.03 5.24
3555 3726 4.405036 AGCTCTCTGATCATGCTCTTGTAA 59.595 41.667 0.00 0.00 0.00 2.41
3630 3801 1.229336 AGAGTCACCCCTCACCCAG 60.229 63.158 0.00 0.00 33.75 4.45
3639 3810 2.093447 CAGTATGAACCCAGAGTCACCC 60.093 54.545 0.00 0.00 39.69 4.61
3642 3813 5.127194 GTCATACAGTATGAACCCAGAGTCA 59.873 44.000 22.51 0.00 45.91 3.41
3681 3852 1.415289 TGCAGGACATCATAGAGGCTG 59.585 52.381 0.00 0.00 0.00 4.85
3768 3939 3.144506 GTCATGGTGAAGATATGCCAGG 58.855 50.000 0.00 0.00 34.18 4.45
3927 4098 3.494223 CCATATATCCAGTTGTGCCGACA 60.494 47.826 0.00 0.00 0.00 4.35
4015 4186 3.257393 GTCAGGTATCAGCTTGTCACTG 58.743 50.000 0.00 0.00 36.44 3.66
4023 4194 1.680522 CGGCCTGTCAGGTATCAGCT 61.681 60.000 20.24 0.00 37.80 4.24
4024 4195 1.227380 CGGCCTGTCAGGTATCAGC 60.227 63.158 20.24 4.44 37.80 4.26
4039 4210 0.594796 CTGCAAGGAAACAACACGGC 60.595 55.000 0.00 0.00 0.00 5.68
4041 4212 1.597937 GCTCTGCAAGGAAACAACACG 60.598 52.381 0.00 0.00 0.00 4.49
4042 4213 1.678101 AGCTCTGCAAGGAAACAACAC 59.322 47.619 0.00 0.00 0.00 3.32
4043 4214 1.677576 CAGCTCTGCAAGGAAACAACA 59.322 47.619 0.00 0.00 0.00 3.33
4044 4215 1.000938 CCAGCTCTGCAAGGAAACAAC 60.001 52.381 0.00 0.00 0.00 3.32
4045 4216 1.321474 CCAGCTCTGCAAGGAAACAA 58.679 50.000 0.00 0.00 0.00 2.83
4046 4217 1.174712 GCCAGCTCTGCAAGGAAACA 61.175 55.000 0.00 0.00 0.00 2.83
4047 4218 1.583477 GCCAGCTCTGCAAGGAAAC 59.417 57.895 0.00 0.00 0.00 2.78
4048 4219 1.604593 GGCCAGCTCTGCAAGGAAA 60.605 57.895 0.00 0.00 0.00 3.13
4050 4221 2.072874 AAAGGCCAGCTCTGCAAGGA 62.073 55.000 5.01 0.00 0.00 3.36
4051 4222 1.183676 AAAAGGCCAGCTCTGCAAGG 61.184 55.000 5.01 0.00 0.00 3.61
4066 4237 6.486657 TCTTGATACTGTTTCTGGTGGAAAAG 59.513 38.462 0.17 0.00 44.34 2.27
4144 4315 2.683933 AACGAGGGATCCACCGCT 60.684 61.111 20.50 9.41 40.11 5.52
4211 4382 2.136878 CGGGCCCTATCTGCTCAGT 61.137 63.158 22.43 0.00 0.00 3.41
4339 4510 1.883084 GACATCGACCATGGACGGC 60.883 63.158 31.05 16.99 36.72 5.68
4459 4630 7.384932 TGACTGTACATTCTATGTTTCACACTG 59.615 37.037 13.66 0.00 41.63 3.66
4460 4631 7.441836 TGACTGTACATTCTATGTTTCACACT 58.558 34.615 13.66 0.00 41.63 3.55
4470 4687 7.374272 CCGATGAATCTGACTGTACATTCTAT 58.626 38.462 13.66 5.55 0.00 1.98
4510 4727 5.427806 TCAGTTACCAGCCTAGACTAGACTA 59.572 44.000 11.27 0.00 0.00 2.59
4511 4728 4.227754 TCAGTTACCAGCCTAGACTAGACT 59.772 45.833 11.27 1.29 0.00 3.24
4512 4729 4.525024 TCAGTTACCAGCCTAGACTAGAC 58.475 47.826 11.27 0.00 0.00 2.59
4513 4730 4.227754 ACTCAGTTACCAGCCTAGACTAGA 59.772 45.833 11.27 0.00 0.00 2.43
4514 4731 4.528920 ACTCAGTTACCAGCCTAGACTAG 58.471 47.826 2.18 2.18 0.00 2.57
4548 4770 4.095483 GCATCCAGTTAGAAATCACCACAG 59.905 45.833 0.00 0.00 0.00 3.66
4659 4881 4.381292 GCTGATGACTTTCCCCTTTTCATG 60.381 45.833 0.00 0.00 0.00 3.07
4666 4888 1.918262 TGATGCTGATGACTTTCCCCT 59.082 47.619 0.00 0.00 0.00 4.79
4671 4893 3.380637 GCCAAGATGATGCTGATGACTTT 59.619 43.478 0.00 0.00 0.00 2.66
4674 4896 2.294979 TGCCAAGATGATGCTGATGAC 58.705 47.619 0.00 0.00 0.00 3.06
4683 4905 4.768448 TCTGTGAACAAATGCCAAGATGAT 59.232 37.500 0.00 0.00 0.00 2.45
4696 4918 6.073602 CGAAGACAATGAGATTCTGTGAACAA 60.074 38.462 0.00 0.00 0.00 2.83
4700 4922 3.928992 GCGAAGACAATGAGATTCTGTGA 59.071 43.478 0.00 0.00 0.00 3.58
4732 4954 6.796072 CGTAGTACTATATCGAAGTTGCCTTC 59.204 42.308 5.75 0.00 43.09 3.46
4735 4957 5.995055 ACGTAGTACTATATCGAAGTTGCC 58.005 41.667 15.81 0.00 41.94 4.52
4766 4992 3.699538 ACACCGCTACATGAGATTCACTA 59.300 43.478 0.00 0.00 0.00 2.74
4797 5023 1.688811 GGTATGGCCAGGAACACCA 59.311 57.895 13.05 0.00 37.99 4.17
4800 5026 0.468226 GATCGGTATGGCCAGGAACA 59.532 55.000 13.05 0.00 36.97 3.18
4827 5053 3.611674 CAAACCCAACCCCGCCAC 61.612 66.667 0.00 0.00 0.00 5.01
4899 5125 3.151958 ATACCTAGCGGCGCACCTG 62.152 63.158 35.02 20.57 0.00 4.00
4900 5126 2.838225 ATACCTAGCGGCGCACCT 60.838 61.111 35.02 16.53 0.00 4.00
4901 5127 2.661866 CATACCTAGCGGCGCACC 60.662 66.667 35.02 4.46 0.00 5.01
4902 5128 2.661866 CCATACCTAGCGGCGCAC 60.662 66.667 35.02 5.34 0.00 5.34
4903 5129 4.602259 GCCATACCTAGCGGCGCA 62.602 66.667 35.02 18.60 35.79 6.09
4989 5216 1.510623 CAAGACGCAATGCTCGCAC 60.511 57.895 2.94 0.00 0.00 5.34
4990 5217 2.862436 CAAGACGCAATGCTCGCA 59.138 55.556 2.94 0.00 0.00 5.10
4991 5218 2.575262 GCAAGACGCAATGCTCGC 60.575 61.111 2.94 0.00 41.79 5.03
4992 5219 2.276244 CGCAAGACGCAATGCTCG 60.276 61.111 2.94 0.00 42.60 5.03
5002 5229 1.235281 GGAAAGGGACCACGCAAGAC 61.235 60.000 0.00 0.00 43.62 3.01
5003 5230 1.072505 GGAAAGGGACCACGCAAGA 59.927 57.895 0.00 0.00 43.62 3.02
5005 5232 2.002018 AAGGGAAAGGGACCACGCAA 62.002 55.000 0.00 0.00 0.00 4.85
5006 5233 2.406002 GAAGGGAAAGGGACCACGCA 62.406 60.000 0.00 0.00 0.00 5.24
5007 5234 1.674651 GAAGGGAAAGGGACCACGC 60.675 63.158 0.00 0.00 0.00 5.34
5008 5235 1.002502 GGAAGGGAAAGGGACCACG 60.003 63.158 0.00 0.00 0.00 4.94
5009 5236 1.140772 AGGGAAGGGAAAGGGACCAC 61.141 60.000 0.00 0.00 0.00 4.16
5010 5237 1.140134 CAGGGAAGGGAAAGGGACCA 61.140 60.000 0.00 0.00 0.00 4.02
5011 5238 1.691823 CAGGGAAGGGAAAGGGACC 59.308 63.158 0.00 0.00 0.00 4.46
5012 5239 0.845102 TCCAGGGAAGGGAAAGGGAC 60.845 60.000 0.00 0.00 0.00 4.46
5013 5240 0.103608 TTCCAGGGAAGGGAAAGGGA 60.104 55.000 0.00 0.00 41.30 4.20
5014 5241 0.332972 CTTCCAGGGAAGGGAAAGGG 59.667 60.000 18.40 0.00 45.60 3.95
5015 5242 3.987594 CTTCCAGGGAAGGGAAAGG 57.012 57.895 18.40 0.00 45.60 3.11
5058 5286 3.190079 CGAGCAGTACTGTACTACGGTA 58.810 50.000 23.44 4.03 38.84 4.02
5065 5293 0.797249 CACGCCGAGCAGTACTGTAC 60.797 60.000 23.44 15.93 0.00 2.90
5066 5294 1.504900 CACGCCGAGCAGTACTGTA 59.495 57.895 23.44 0.00 0.00 2.74
5067 5295 2.258591 CACGCCGAGCAGTACTGT 59.741 61.111 23.44 10.82 0.00 3.55
5068 5296 2.507102 CCACGCCGAGCAGTACTG 60.507 66.667 18.93 18.93 0.00 2.74
5069 5297 3.760035 CCCACGCCGAGCAGTACT 61.760 66.667 0.00 0.00 0.00 2.73
5164 5393 7.590359 TCCCAAACCCCCATTTTAAATTAAT 57.410 32.000 0.00 0.00 0.00 1.40
5172 5401 2.374839 CACATTCCCAAACCCCCATTTT 59.625 45.455 0.00 0.00 0.00 1.82
5207 5436 5.532779 CCTACAGATTTTAGGGATTTCAGGC 59.467 44.000 0.00 0.00 33.57 4.85
5351 5587 2.248280 ACCGCAACCGCATCATATTA 57.752 45.000 0.00 0.00 38.40 0.98
5357 5593 0.798009 CATTCAACCGCAACCGCATC 60.798 55.000 0.00 0.00 38.40 3.91
5361 5597 0.386731 GGTTCATTCAACCGCAACCG 60.387 55.000 0.00 0.00 45.58 4.44
5362 5598 3.489813 GGTTCATTCAACCGCAACC 57.510 52.632 0.00 0.00 45.58 3.77
5390 5627 7.228906 GGTTTTCCTTATCTTTAGACATAGGCC 59.771 40.741 0.00 0.00 36.94 5.19
5394 5631 8.607713 TGGTGGTTTTCCTTATCTTTAGACATA 58.392 33.333 0.00 0.00 41.38 2.29
5406 5643 3.876309 AAGCTCTGGTGGTTTTCCTTA 57.124 42.857 0.00 0.00 41.38 2.69


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

AutoCloner maintained by Alex Coulton.