Multiple sequence alignment - TraesCS7B01G460300

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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 TraesCS7B01G460300 chr7B 100.000 3120 0 0 1 3120 717873696 717876815 0.000000e+00 5762.0
1 TraesCS7B01G460300 chr7B 97.001 667 20 0 2251 2917 718073481 718074147 0.000000e+00 1122.0
2 TraesCS7B01G460300 chr7B 84.138 1160 161 14 787 1942 717984691 717985831 0.000000e+00 1101.0
3 TraesCS7B01G460300 chr7B 87.389 563 52 14 2023 2570 719490646 719490088 2.040000e-176 628.0
4 TraesCS7B01G460300 chr7B 91.563 403 17 1 2735 3120 717543901 717544303 9.840000e-150 540.0
5 TraesCS7B01G460300 chr7B 78.488 688 130 11 1264 1942 719491456 719490778 4.780000e-118 435.0
6 TraesCS7B01G460300 chr7B 89.254 335 36 0 464 798 717984335 717984669 1.340000e-113 420.0
7 TraesCS7B01G460300 chr7B 88.068 352 31 6 2007 2349 717985932 717986281 1.040000e-109 407.0
8 TraesCS7B01G460300 chr7B 90.045 221 5 1 2917 3120 718078878 718079098 1.430000e-68 270.0
9 TraesCS7B01G460300 chr7B 90.811 185 2 4 2559 2742 717542882 717543052 1.870000e-57 233.0
10 TraesCS7B01G460300 chr7B 90.123 162 16 0 2444 2605 717986332 717986493 8.770000e-51 211.0
11 TraesCS7B01G460300 chr7B 79.333 150 25 6 2204 2349 717609752 717609899 1.980000e-17 100.0
12 TraesCS7B01G460300 chr7D 82.626 1485 195 40 310 1769 621862804 621861358 0.000000e+00 1254.0
13 TraesCS7B01G460300 chr7D 80.536 1269 184 30 1093 2349 621962685 621961468 0.000000e+00 917.0
14 TraesCS7B01G460300 chr7D 86.409 802 99 6 310 1101 621969629 621968828 0.000000e+00 869.0
15 TraesCS7B01G460300 chr7D 87.421 318 36 3 1 317 621863155 621862841 2.290000e-96 363.0
16 TraesCS7B01G460300 chr7D 90.361 83 5 3 2000 2079 621861130 621861048 4.260000e-19 106.0
17 TraesCS7B01G460300 chr7D 97.143 35 1 0 2803 2837 621961094 621961060 3.360000e-05 60.2
18 TraesCS7B01G460300 chr7A 85.741 1066 138 11 310 1363 717407325 717406262 0.000000e+00 1114.0
19 TraesCS7B01G460300 chr7A 93.380 574 29 5 2444 3011 717401717 717401147 0.000000e+00 841.0
20 TraesCS7B01G460300 chr7A 84.926 544 65 8 310 844 717365664 717365129 4.580000e-148 534.0
21 TraesCS7B01G460300 chr7A 86.027 365 49 2 1397 1761 717405428 717405066 1.050000e-104 390.0
22 TraesCS7B01G460300 chr7A 85.445 371 38 12 2158 2513 717386855 717386486 3.800000e-99 372.0
23 TraesCS7B01G460300 chr7A 87.500 312 37 2 1 311 717407678 717407368 2.960000e-95 359.0
24 TraesCS7B01G460300 chr7A 86.432 199 20 5 123 317 717365896 717365701 8.770000e-51 211.0
25 TraesCS7B01G460300 chr7A 92.982 57 1 2 2023 2076 717386912 717386856 2.580000e-11 80.5
26 TraesCS7B01G460300 chr2A 88.994 318 33 2 1 317 50690461 50690145 2.920000e-105 392.0


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 TraesCS7B01G460300 chr7B 717873696 717876815 3119 False 5762.000000 5762 100.000000 1 3120 1 chr7B.!!$F2 3119
1 TraesCS7B01G460300 chr7B 718073481 718074147 666 False 1122.000000 1122 97.001000 2251 2917 1 chr7B.!!$F3 666
2 TraesCS7B01G460300 chr7B 717984335 717986493 2158 False 534.750000 1101 87.895750 464 2605 4 chr7B.!!$F6 2141
3 TraesCS7B01G460300 chr7B 719490088 719491456 1368 True 531.500000 628 82.938500 1264 2570 2 chr7B.!!$R1 1306
4 TraesCS7B01G460300 chr7B 717542882 717544303 1421 False 386.500000 540 91.187000 2559 3120 2 chr7B.!!$F5 561
5 TraesCS7B01G460300 chr7D 621968828 621969629 801 True 869.000000 869 86.409000 310 1101 1 chr7D.!!$R1 791
6 TraesCS7B01G460300 chr7D 621861048 621863155 2107 True 574.333333 1254 86.802667 1 2079 3 chr7D.!!$R2 2078
7 TraesCS7B01G460300 chr7D 621961060 621962685 1625 True 488.600000 917 88.839500 1093 2837 2 chr7D.!!$R3 1744
8 TraesCS7B01G460300 chr7A 717401147 717407678 6531 True 676.000000 1114 88.162000 1 3011 4 chr7A.!!$R3 3010
9 TraesCS7B01G460300 chr7A 717365129 717365896 767 True 372.500000 534 85.679000 123 844 2 chr7A.!!$R1 721

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
733 795 1.296715 GGATTGTCAGGGTGCTCGT 59.703 57.895 0.00 0.00 0.00 4.18 F
1512 2420 0.038251 TGAGAATCACGTGCTTCGCT 60.038 50.000 27.74 13.65 42.56 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 5815 0.099436 GTTGATCCATCAGCAACGGC 59.901 55.0 0.0 0.0 37.85 5.68 R
3092 7750 1.246737 GCCCTGCTTTCTCCCTGTTG 61.247 60.0 0.0 0.0 0.00 3.33 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
34 35 8.324306 TGAGTCCTCTTAATGATCAAAACTCAT 58.676 33.333 0.00 0.00 35.70 2.90
74 75 7.711339 CAGTATAGTTGGACAGGTTAATCTTCC 59.289 40.741 9.00 9.00 0.00 3.46
76 77 3.326880 AGTTGGACAGGTTAATCTTCCGT 59.673 43.478 10.49 0.00 0.00 4.69
124 125 8.877864 AATTCTATAAAAATGTGGTGGTCTCA 57.122 30.769 0.00 0.00 0.00 3.27
136 137 2.418197 GGTGGTCTCACGCTTGCTATTA 60.418 50.000 0.00 0.00 44.50 0.98
178 182 3.055819 GGTCAGTCAGCCAACTAGATCAA 60.056 47.826 0.00 0.00 0.00 2.57
180 184 5.163405 GGTCAGTCAGCCAACTAGATCAATA 60.163 44.000 0.00 0.00 0.00 1.90
181 185 5.982516 GTCAGTCAGCCAACTAGATCAATAG 59.017 44.000 0.00 0.00 0.00 1.73
182 186 5.893824 TCAGTCAGCCAACTAGATCAATAGA 59.106 40.000 0.00 0.00 0.00 1.98
183 187 6.040278 TCAGTCAGCCAACTAGATCAATAGAG 59.960 42.308 0.00 0.00 0.00 2.43
193 197 7.609097 ACTAGATCAATAGAGCAATGGAAGA 57.391 36.000 0.00 0.00 30.99 2.87
255 259 2.305927 GACTTTGGAGGGGATGAGACAA 59.694 50.000 0.00 0.00 0.00 3.18
259 263 3.421394 TGGAGGGGATGAGACAAGTAT 57.579 47.619 0.00 0.00 0.00 2.12
287 291 4.806247 CCTTAGCTACAACAATCTTCCTCG 59.194 45.833 0.00 0.00 0.00 4.63
290 294 3.258372 AGCTACAACAATCTTCCTCGTCA 59.742 43.478 0.00 0.00 0.00 4.35
298 302 5.738909 ACAATCTTCCTCGTCATCTCAAAT 58.261 37.500 0.00 0.00 0.00 2.32
303 307 3.461061 TCCTCGTCATCTCAAATCATGC 58.539 45.455 0.00 0.00 0.00 4.06
346 394 1.743394 GTGGCTTAAGGTTTCATCCCG 59.257 52.381 4.29 0.00 0.00 5.14
399 448 5.523916 TCGCTGGAATTACTTTAATGAGCTC 59.476 40.000 6.82 6.82 0.00 4.09
418 467 4.248691 CTCGTCAATAGGAGCATGATCA 57.751 45.455 13.85 0.00 31.38 2.92
429 478 5.324409 AGGAGCATGATCAAACCTACAAAA 58.676 37.500 13.85 0.00 0.00 2.44
433 482 7.603784 GGAGCATGATCAAACCTACAAAAATTT 59.396 33.333 13.85 0.00 0.00 1.82
444 493 9.990360 AAACCTACAAAAATTTGGTATAACAGG 57.010 29.630 10.38 4.97 42.34 4.00
451 500 4.862641 ATTTGGTATAACAGGCAGGTCT 57.137 40.909 0.00 0.00 0.00 3.85
454 503 2.238646 TGGTATAACAGGCAGGTCTTGG 59.761 50.000 0.00 0.00 0.00 3.61
462 511 3.010584 ACAGGCAGGTCTTGGAATGTAAT 59.989 43.478 0.00 0.00 0.00 1.89
516 573 6.926272 TCAGAAGAAGAGAAGTTTCTTAGTGC 59.074 38.462 0.66 0.00 43.07 4.40
575 632 4.083581 AGCAAAGTTCATCGAATTTCCG 57.916 40.909 0.00 0.00 0.00 4.30
586 643 3.468770 TCGAATTTCCGTTCAGTTGGAA 58.531 40.909 0.00 0.00 42.35 3.53
595 652 3.270027 CGTTCAGTTGGAATATGGAGCA 58.730 45.455 0.00 0.00 37.93 4.26
672 734 1.698506 TTTGGCAAGTCCCGTTTCAT 58.301 45.000 0.00 0.00 0.00 2.57
673 735 2.570415 TTGGCAAGTCCCGTTTCATA 57.430 45.000 0.00 0.00 0.00 2.15
733 795 1.296715 GGATTGTCAGGGTGCTCGT 59.703 57.895 0.00 0.00 0.00 4.18
768 830 5.527582 GGATTGACCTCACACCAATATGTAC 59.472 44.000 0.00 0.00 35.41 2.90
806 901 2.507452 TGAGCATCAGCATCCCCG 59.493 61.111 0.00 0.00 42.56 5.73
844 939 4.145052 CCCTTATTCTGCCAACCCTAATC 58.855 47.826 0.00 0.00 0.00 1.75
986 1091 5.250082 CCTGATGGAATTCATAGGATGAGGA 59.750 44.000 7.93 0.00 36.61 3.71
1012 1117 7.036220 CCTACGTACTCTGATGAACTTTGATT 58.964 38.462 0.00 0.00 0.00 2.57
1023 1128 7.156000 TGATGAACTTTGATTTGCACATGAAT 58.844 30.769 0.00 0.00 0.00 2.57
1044 1149 5.767816 ATTCGGTGGATAATTTAACAGGC 57.232 39.130 0.00 0.00 0.00 4.85
1058 1163 7.923414 ATTTAACAGGCCTTAGTGAACTTAG 57.077 36.000 0.00 0.00 0.00 2.18
1090 1195 4.025313 GGTCTCTTAATTTCTGCTGCGATC 60.025 45.833 0.00 0.00 0.00 3.69
1125 1230 1.895131 ACCAGCCAACATGGAATTCAC 59.105 47.619 7.93 0.00 40.96 3.18
1162 1267 2.092429 TGTTCTGTGGCCAAACTTCTCT 60.092 45.455 7.24 0.00 0.00 3.10
1181 1286 4.940046 TCTCTGTTGCAATCTGAGAAATCC 59.060 41.667 23.25 3.29 37.11 3.01
1183 1288 4.698780 TCTGTTGCAATCTGAGAAATCCTG 59.301 41.667 0.59 0.00 0.00 3.86
1188 1293 4.165565 TGCAATCTGAGAAATCCTGGATCT 59.834 41.667 10.14 4.42 0.00 2.75
1190 1295 3.834489 TCTGAGAAATCCTGGATCTGC 57.166 47.619 10.14 2.63 0.00 4.26
1247 1352 5.221402 TGGCTTCTCTGATCACTAGCAATAG 60.221 44.000 12.79 0.00 0.00 1.73
1261 1366 7.353414 ACTAGCAATAGTGAGAGCAATCTTA 57.647 36.000 0.00 0.00 0.00 2.10
1314 1420 0.609131 CGAGGGTGCCAATTTGGACT 60.609 55.000 19.76 10.30 40.96 3.85
1321 1427 2.299867 GTGCCAATTTGGACTGGTCAAT 59.700 45.455 19.76 0.00 40.96 2.57
1322 1428 2.971330 TGCCAATTTGGACTGGTCAATT 59.029 40.909 19.76 0.00 40.96 2.32
1337 1443 3.057245 GGTCAATTCCAAAAGCTCTCCAC 60.057 47.826 0.00 0.00 0.00 4.02
1367 2042 4.771590 TTTGTGTTGAGAAGATGATGCC 57.228 40.909 0.00 0.00 0.00 4.40
1370 2045 1.278985 TGTTGAGAAGATGATGCCGGT 59.721 47.619 1.90 0.00 0.00 5.28
1512 2420 0.038251 TGAGAATCACGTGCTTCGCT 60.038 50.000 27.74 13.65 42.56 4.93
1515 2423 1.696832 GAATCACGTGCTTCGCTCCC 61.697 60.000 15.58 0.00 44.19 4.30
1540 2448 2.441532 CCTTCATGGCAGGGGCAG 60.442 66.667 0.00 0.00 42.43 4.85
1543 2451 2.776370 CTTCATGGCAGGGGCAGTGT 62.776 60.000 0.00 0.00 42.43 3.55
1545 2453 2.937689 ATGGCAGGGGCAGTGTCT 60.938 61.111 0.00 0.00 42.43 3.41
1546 2454 3.278072 ATGGCAGGGGCAGTGTCTG 62.278 63.158 0.00 0.45 42.43 3.51
1557 2465 1.604278 GCAGTGTCTGAACTCCAAACC 59.396 52.381 0.66 0.00 32.44 3.27
1579 2487 4.506271 CCTTGGAACTGGATATCCATGAGG 60.506 50.000 24.73 18.70 46.46 3.86
1612 2520 1.526917 CATGGCCCCTCGACCATTC 60.527 63.158 0.00 0.00 44.37 2.67
1650 2558 1.895798 TCGAGACTCAGGCAAGTTGAT 59.104 47.619 7.16 0.00 0.00 2.57
1660 2568 7.989826 ACTCAGGCAAGTTGATGTTTATATTC 58.010 34.615 7.16 0.00 0.00 1.75
1721 2629 0.102481 GACGCGGAGGCTATCTTGAA 59.898 55.000 12.47 0.00 36.88 2.69
1727 2635 3.742640 GCGGAGGCTATCTTGAAGAATGT 60.743 47.826 0.00 0.00 35.83 2.71
1761 2669 1.021390 CAGGACACCCGAGCATCAAC 61.021 60.000 0.00 0.00 37.58 3.18
1769 3956 1.442526 CCGAGCATCAACATCAGGCC 61.443 60.000 0.00 0.00 33.17 5.19
1771 3958 1.202568 CGAGCATCAACATCAGGCCTA 60.203 52.381 3.98 0.00 33.17 3.93
1772 3959 2.216898 GAGCATCAACATCAGGCCTAC 58.783 52.381 3.98 0.00 33.17 3.18
1789 3976 5.128008 AGGCCTACAGATAACAGAAACTCTC 59.872 44.000 1.29 0.00 0.00 3.20
1792 3979 7.100409 GCCTACAGATAACAGAAACTCTCTTT 58.900 38.462 0.00 0.00 29.07 2.52
1793 3980 7.064016 GCCTACAGATAACAGAAACTCTCTTTG 59.936 40.741 0.00 0.00 29.07 2.77
1794 3981 8.091449 CCTACAGATAACAGAAACTCTCTTTGT 58.909 37.037 0.00 0.00 29.07 2.83
1797 3984 9.482627 ACAGATAACAGAAACTCTCTTTGTAAG 57.517 33.333 0.00 0.00 29.07 2.34
1817 4004 4.916041 AGATCCATGAACTTTCCAGTGA 57.084 40.909 0.00 0.00 31.60 3.41
1820 4007 3.476552 TCCATGAACTTTCCAGTGACAC 58.523 45.455 0.00 0.00 31.60 3.67
1828 4021 5.808366 ACTTTCCAGTGACACTTCTGATA 57.192 39.130 5.04 0.00 34.02 2.15
1841 4034 1.693627 TCTGATAGGGACGAAGAGGC 58.306 55.000 0.00 0.00 0.00 4.70
1845 4038 0.396695 ATAGGGACGAAGAGGCGGAA 60.397 55.000 0.00 0.00 35.12 4.30
1861 4057 2.033424 GCGGAAAGGCAAGGTAATGATC 59.967 50.000 0.00 0.00 0.00 2.92
1889 4085 2.355209 CCCTCCTAGTCAAACTTCTGCC 60.355 54.545 0.00 0.00 0.00 4.85
1895 5533 4.932200 CCTAGTCAAACTTCTGCCTACTTG 59.068 45.833 0.00 0.00 0.00 3.16
1896 5534 4.689612 AGTCAAACTTCTGCCTACTTGA 57.310 40.909 0.00 0.00 0.00 3.02
1904 5569 5.735766 ACTTCTGCCTACTTGAATTCCTAC 58.264 41.667 2.27 0.00 0.00 3.18
1906 5571 5.344743 TCTGCCTACTTGAATTCCTACAG 57.655 43.478 2.27 1.81 0.00 2.74
1907 5572 4.777896 TCTGCCTACTTGAATTCCTACAGT 59.222 41.667 2.27 2.83 0.00 3.55
1912 5577 7.104290 GCCTACTTGAATTCCTACAGTACTTT 58.896 38.462 2.27 0.00 0.00 2.66
1928 5593 8.877864 ACAGTACTTTAATTTGATTCATCCCA 57.122 30.769 0.00 0.00 0.00 4.37
1938 5603 2.027385 GATTCATCCCAGGAAACCAGC 58.973 52.381 0.00 0.00 0.00 4.85
1942 5607 0.685458 ATCCCAGGAAACCAGCATGC 60.685 55.000 10.51 10.51 31.97 4.06
1943 5608 2.703798 CCCAGGAAACCAGCATGCG 61.704 63.158 13.01 7.31 31.97 4.73
1945 5610 2.282391 AGGAAACCAGCATGCGCA 60.282 55.556 14.96 14.96 42.27 6.09
1947 5644 2.629656 GGAAACCAGCATGCGCACT 61.630 57.895 14.90 2.53 42.27 4.40
1974 5677 9.696917 AAATAATTTACTCCTGAAACTTGCTTG 57.303 29.630 0.00 0.00 0.00 4.01
1979 5690 2.951642 CTCCTGAAACTTGCTTGGTTCA 59.048 45.455 9.06 9.06 0.00 3.18
1982 5693 3.068590 CCTGAAACTTGCTTGGTTCATGT 59.931 43.478 9.68 0.00 0.00 3.21
1984 5695 3.446873 TGAAACTTGCTTGGTTCATGTGT 59.553 39.130 6.02 0.00 0.00 3.72
1986 5697 4.470334 AACTTGCTTGGTTCATGTGTTT 57.530 36.364 0.00 0.00 0.00 2.83
1988 5699 2.886862 TGCTTGGTTCATGTGTTTGG 57.113 45.000 0.00 0.00 0.00 3.28
1989 5700 2.106566 TGCTTGGTTCATGTGTTTGGT 58.893 42.857 0.00 0.00 0.00 3.67
1993 5704 4.610945 CTTGGTTCATGTGTTTGGTTCTC 58.389 43.478 0.00 0.00 0.00 2.87
1997 5708 4.261197 GGTTCATGTGTTTGGTTCTCTGTC 60.261 45.833 0.00 0.00 0.00 3.51
1998 5709 3.130633 TCATGTGTTTGGTTCTCTGTCG 58.869 45.455 0.00 0.00 0.00 4.35
2004 5715 4.621886 GTGTTTGGTTCTCTGTCGATCTAC 59.378 45.833 0.00 0.00 0.00 2.59
2005 5716 4.279922 TGTTTGGTTCTCTGTCGATCTACA 59.720 41.667 0.00 0.00 0.00 2.74
2039 5770 7.287696 ACACAACTTTCCTCCTGTTTTTGATAT 59.712 33.333 0.00 0.00 0.00 1.63
2081 5812 3.506096 CAGCCACGCATGCTCCAG 61.506 66.667 17.13 2.03 36.81 3.86
2100 5831 2.537560 CCGCCGTTGCTGATGGATC 61.538 63.158 3.45 0.00 36.44 3.36
2115 5846 4.395854 TGATGGATCAACAAGGAATTCACG 59.604 41.667 7.93 0.00 33.08 4.35
2189 5924 2.299013 TCCACAGATTTCGCACTACACT 59.701 45.455 0.00 0.00 0.00 3.55
2213 5953 5.384336 TCCAAGGATTCATTTCAAGTGTCA 58.616 37.500 0.00 0.00 0.00 3.58
2223 5963 5.241506 TCATTTCAAGTGTCAGACCATTTCC 59.758 40.000 0.00 0.00 0.00 3.13
2243 5983 5.403558 TCCATGGTAGGATAGAGACTGAA 57.596 43.478 12.58 0.00 31.23 3.02
2248 5989 4.402793 TGGTAGGATAGAGACTGAAGTTGC 59.597 45.833 0.00 0.00 0.00 4.17
2253 5994 1.372997 GAGACTGAAGTTGCGGCGA 60.373 57.895 12.98 0.00 0.00 5.54
2264 6005 0.176910 TTGCGGCGATTACCTGATGA 59.823 50.000 12.98 0.00 0.00 2.92
2278 6019 5.426689 ACCTGATGATCTGCTTCTGTTAA 57.573 39.130 0.00 0.00 0.00 2.01
2365 6137 5.925506 TCGGGTCATTAACAGAGTATTGA 57.074 39.130 0.00 0.00 0.00 2.57
2389 6161 3.573558 CGTAAACGGCACAGGCAT 58.426 55.556 0.00 0.00 43.71 4.40
2637 6415 6.322712 AGACCTCTACACAAGATTAGGATGAC 59.677 42.308 0.00 0.00 32.41 3.06
2662 6440 1.745653 GTGATAGCTGAAGTTTGGGCC 59.254 52.381 0.00 0.00 0.00 5.80
2901 7541 8.291032 TGTTAGGATTTTTATTTGGTACACACG 58.709 33.333 0.00 0.00 39.29 4.49
3020 7661 3.394836 GAACCTGAGCTCCGCCCT 61.395 66.667 12.15 0.00 0.00 5.19
3069 7727 0.972471 CACATTGGGGAAGAAGGGGC 60.972 60.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 4.529377 ACGGAAGATTAACCTGTCCAACTA 59.471 41.667 0.00 0.00 0.00 2.24
67 68 7.436673 CGAAATCTCTTCTAATGACGGAAGATT 59.563 37.037 5.97 0.00 44.30 2.40
74 75 7.685532 TCATTCGAAATCTCTTCTAATGACG 57.314 36.000 0.00 0.00 36.40 4.35
106 107 2.550606 GCGTGAGACCACCACATTTTTA 59.449 45.455 0.00 0.00 40.12 1.52
124 125 5.300752 AGCAATACTGATAATAGCAAGCGT 58.699 37.500 0.00 0.00 0.00 5.07
136 137 6.711277 TGACCAAAAGACTAGCAATACTGAT 58.289 36.000 0.00 0.00 0.00 2.90
158 159 5.893824 TCTATTGATCTAGTTGGCTGACTGA 59.106 40.000 0.00 1.90 0.00 3.41
178 182 4.337555 GCACACATTCTTCCATTGCTCTAT 59.662 41.667 0.00 0.00 0.00 1.98
180 184 2.490903 GCACACATTCTTCCATTGCTCT 59.509 45.455 0.00 0.00 0.00 4.09
181 185 2.229543 TGCACACATTCTTCCATTGCTC 59.770 45.455 0.00 0.00 0.00 4.26
182 186 2.241160 TGCACACATTCTTCCATTGCT 58.759 42.857 0.00 0.00 0.00 3.91
183 187 2.728690 TGCACACATTCTTCCATTGC 57.271 45.000 0.00 0.00 0.00 3.56
193 197 6.088016 TGAGCTTAAAGAATTGCACACATT 57.912 33.333 0.00 0.00 0.00 2.71
233 237 2.192263 GTCTCATCCCCTCCAAAGTCT 58.808 52.381 0.00 0.00 0.00 3.24
255 259 8.322091 AGATTGTTGTAGCTAAGGTTCAATACT 58.678 33.333 0.00 1.45 0.00 2.12
259 263 6.430000 GGAAGATTGTTGTAGCTAAGGTTCAA 59.570 38.462 0.00 0.00 0.00 2.69
287 291 4.634184 AGCAAGCATGATTTGAGATGAC 57.366 40.909 12.84 0.00 0.00 3.06
290 294 7.584122 AAAGATAGCAAGCATGATTTGAGAT 57.416 32.000 12.84 6.07 0.00 2.75
298 302 3.379372 GCCTCAAAAGATAGCAAGCATGA 59.621 43.478 0.00 0.00 0.00 3.07
303 307 4.441079 CCCATTGCCTCAAAAGATAGCAAG 60.441 45.833 0.00 0.00 45.67 4.01
332 380 5.486735 TGTACTTTCGGGATGAAACCTTA 57.513 39.130 0.00 0.00 41.59 2.69
346 394 1.678101 GCATCCTGGCCATGTACTTTC 59.322 52.381 5.51 0.00 0.00 2.62
399 448 4.024556 GGTTTGATCATGCTCCTATTGACG 60.025 45.833 0.00 0.00 0.00 4.35
418 467 9.990360 CCTGTTATACCAAATTTTTGTAGGTTT 57.010 29.630 2.78 0.00 36.45 3.27
429 478 5.193099 AGACCTGCCTGTTATACCAAATT 57.807 39.130 0.00 0.00 0.00 1.82
433 482 2.238646 CCAAGACCTGCCTGTTATACCA 59.761 50.000 0.00 0.00 0.00 3.25
438 487 2.375174 ACATTCCAAGACCTGCCTGTTA 59.625 45.455 0.00 0.00 0.00 2.41
441 490 2.787473 TACATTCCAAGACCTGCCTG 57.213 50.000 0.00 0.00 0.00 4.85
442 491 4.322057 AATTACATTCCAAGACCTGCCT 57.678 40.909 0.00 0.00 0.00 4.75
444 493 6.942532 TCATAATTACATTCCAAGACCTGC 57.057 37.500 0.00 0.00 0.00 4.85
481 538 6.547880 ACTTCTCTTCTTCTGAGTTGTGTCTA 59.452 38.462 0.00 0.00 33.59 2.59
486 543 6.883744 AGAAACTTCTCTTCTTCTGAGTTGT 58.116 36.000 0.00 0.00 29.94 3.32
490 547 7.116233 GCACTAAGAAACTTCTCTTCTTCTGAG 59.884 40.741 1.29 0.00 41.21 3.35
493 550 5.923684 CGCACTAAGAAACTTCTCTTCTTCT 59.076 40.000 1.29 0.00 41.21 2.85
516 573 1.607148 TGCCGTGTAGATCATCTACCG 59.393 52.381 20.21 20.31 46.64 4.02
532 589 0.040336 GCAATGCTGAGATCATGCCG 60.040 55.000 0.00 0.00 0.00 5.69
559 616 4.315803 ACTGAACGGAAATTCGATGAACT 58.684 39.130 0.00 0.00 0.00 3.01
575 632 5.643379 TTTGCTCCATATTCCAACTGAAC 57.357 39.130 0.00 0.00 35.31 3.18
586 643 3.634504 TGTGCCTTCATTTGCTCCATAT 58.365 40.909 0.00 0.00 0.00 1.78
595 652 3.754965 TGCTTCTACTGTGCCTTCATTT 58.245 40.909 0.00 0.00 0.00 2.32
673 735 9.911788 ATGGACTTGAGTTCATACATAGAAAAT 57.088 29.630 3.06 0.00 42.23 1.82
778 840 5.286267 TGCTGATGCTCAAATATCTGAGA 57.714 39.130 10.34 0.00 44.82 3.27
806 901 1.671379 GGGTTGCCGTCTGTTCCTC 60.671 63.158 0.00 0.00 0.00 3.71
816 911 2.106844 GGCAGAATAAGGGTTGCCG 58.893 57.895 0.00 0.00 45.68 5.69
844 939 0.887933 CCAAATGTTTCAGGTCCCCG 59.112 55.000 0.00 0.00 0.00 5.73
986 1091 5.475909 TCAAAGTTCATCAGAGTACGTAGGT 59.524 40.000 0.00 0.00 0.00 3.08
1000 1105 7.148705 CGAATTCATGTGCAAATCAAAGTTCAT 60.149 33.333 6.22 0.00 0.00 2.57
1012 1117 1.902938 TCCACCGAATTCATGTGCAA 58.097 45.000 16.05 6.85 0.00 4.08
1023 1128 3.949113 GGCCTGTTAAATTATCCACCGAA 59.051 43.478 0.00 0.00 0.00 4.30
1044 1149 7.616313 ACCTGAGATTTCTAAGTTCACTAAGG 58.384 38.462 0.00 0.00 32.49 2.69
1058 1163 7.552330 AGCAGAAATTAAGAGACCTGAGATTTC 59.448 37.037 0.00 0.00 34.12 2.17
1080 1185 4.120085 TCAGCATGATCGCAGCAG 57.880 55.556 0.00 0.00 42.56 4.24
1125 1230 4.279169 ACAGAACACCAGAAAATGTCCATG 59.721 41.667 0.00 0.00 0.00 3.66
1162 1267 3.760151 CCAGGATTTCTCAGATTGCAACA 59.240 43.478 0.00 0.00 0.00 3.33
1181 1286 8.668510 ACAAAATATGTTACTAGCAGATCCAG 57.331 34.615 0.00 0.00 40.06 3.86
1183 1288 7.934120 AGGACAAAATATGTTACTAGCAGATCC 59.066 37.037 0.00 0.00 44.12 3.36
1188 1293 6.953101 TGGAGGACAAAATATGTTACTAGCA 58.047 36.000 0.00 0.00 44.12 3.49
1190 1295 9.265901 CAGATGGAGGACAAAATATGTTACTAG 57.734 37.037 0.00 0.00 44.12 2.57
1247 1352 4.813697 GGAGTTCCATAAGATTGCTCTCAC 59.186 45.833 0.00 0.00 35.64 3.51
1314 1420 3.157087 GGAGAGCTTTTGGAATTGACCA 58.843 45.455 0.00 0.00 38.24 4.02
1321 1427 2.341846 AACGTGGAGAGCTTTTGGAA 57.658 45.000 0.00 0.00 0.00 3.53
1322 1428 2.289444 CCTAACGTGGAGAGCTTTTGGA 60.289 50.000 0.00 0.00 0.00 3.53
1337 1443 6.539649 TCTTCTCAACACAAATTCCTAACG 57.460 37.500 0.00 0.00 0.00 3.18
1367 2042 2.159517 GCTAGCAAATCAAAGTCCACCG 60.160 50.000 10.63 0.00 0.00 4.94
1370 2045 3.084039 CCTGCTAGCAAATCAAAGTCCA 58.916 45.455 19.86 0.00 0.00 4.02
1466 2372 4.621068 TTTAGAAGCTTGAATGCCATCG 57.379 40.909 2.10 0.00 0.00 3.84
1512 2420 0.918983 CCATGAAGGTTAGGCAGGGA 59.081 55.000 0.00 0.00 35.63 4.20
1540 2448 3.971032 CAAGGTTTGGAGTTCAGACAC 57.029 47.619 0.00 0.00 32.66 3.67
1569 2477 4.639726 CCCCCGTCCTCATGGATA 57.360 61.111 0.00 0.00 45.29 2.59
1650 2558 6.599244 CAGCTCCCTCAAAGTGAATATAAACA 59.401 38.462 0.00 0.00 0.00 2.83
1660 2568 3.196469 TCTGTATCAGCTCCCTCAAAGTG 59.804 47.826 0.00 0.00 0.00 3.16
1721 2629 3.638627 TGGATAGACGCTGATGACATTCT 59.361 43.478 0.00 0.00 0.00 2.40
1727 2635 1.957177 GTCCTGGATAGACGCTGATGA 59.043 52.381 0.00 0.00 0.00 2.92
1761 2669 4.944619 TCTGTTATCTGTAGGCCTGATG 57.055 45.455 17.99 4.83 34.08 3.07
1771 3958 9.482627 CTTACAAAGAGAGTTTCTGTTATCTGT 57.517 33.333 0.00 0.00 35.91 3.41
1772 3959 9.698309 TCTTACAAAGAGAGTTTCTGTTATCTG 57.302 33.333 0.00 0.00 35.91 2.90
1789 3976 7.175641 ACTGGAAAGTTCATGGATCTTACAAAG 59.824 37.037 0.00 0.00 0.00 2.77
1792 3979 5.939883 CACTGGAAAGTTCATGGATCTTACA 59.060 40.000 0.00 0.00 0.00 2.41
1793 3980 6.092807 GTCACTGGAAAGTTCATGGATCTTAC 59.907 42.308 0.00 0.00 0.00 2.34
1794 3981 6.173339 GTCACTGGAAAGTTCATGGATCTTA 58.827 40.000 0.00 0.00 0.00 2.10
1795 3982 5.006386 GTCACTGGAAAGTTCATGGATCTT 58.994 41.667 0.00 0.00 0.00 2.40
1796 3983 4.042062 TGTCACTGGAAAGTTCATGGATCT 59.958 41.667 0.00 0.00 0.00 2.75
1797 3984 4.154918 GTGTCACTGGAAAGTTCATGGATC 59.845 45.833 0.00 0.00 0.00 3.36
1800 3987 3.480470 AGTGTCACTGGAAAGTTCATGG 58.520 45.455 4.21 0.00 0.00 3.66
1817 4004 3.697045 CTCTTCGTCCCTATCAGAAGTGT 59.303 47.826 4.32 0.00 40.49 3.55
1820 4007 2.035321 GCCTCTTCGTCCCTATCAGAAG 59.965 54.545 0.00 0.00 40.85 2.85
1828 4021 1.889530 CTTTCCGCCTCTTCGTCCCT 61.890 60.000 0.00 0.00 0.00 4.20
1841 4034 2.618709 GGATCATTACCTTGCCTTTCCG 59.381 50.000 0.00 0.00 0.00 4.30
1845 4038 2.582636 ACCTGGATCATTACCTTGCCTT 59.417 45.455 0.00 0.00 0.00 4.35
1904 5569 8.408601 CCTGGGATGAATCAAATTAAAGTACTG 58.591 37.037 0.00 0.00 0.00 2.74
1906 5571 8.519799 TCCTGGGATGAATCAAATTAAAGTAC 57.480 34.615 0.00 0.00 0.00 2.73
1907 5572 9.540538 TTTCCTGGGATGAATCAAATTAAAGTA 57.459 29.630 0.00 0.00 0.00 2.24
1912 5577 6.259893 TGGTTTCCTGGGATGAATCAAATTA 58.740 36.000 0.00 0.00 0.00 1.40
1928 5593 2.282391 TGCGCATGCTGGTTTCCT 60.282 55.556 17.13 0.00 43.34 3.36
1938 5603 6.852853 CAGGAGTAAATTATTTAGTGCGCATG 59.147 38.462 15.91 0.00 40.52 4.06
1942 5607 8.665685 AGTTTCAGGAGTAAATTATTTAGTGCG 58.334 33.333 15.07 11.44 40.52 5.34
1970 5673 2.888834 ACCAAACACATGAACCAAGC 57.111 45.000 0.00 0.00 0.00 4.01
1974 5677 3.632145 ACAGAGAACCAAACACATGAACC 59.368 43.478 0.00 0.00 0.00 3.62
1979 5690 3.469008 TCGACAGAGAACCAAACACAT 57.531 42.857 0.00 0.00 0.00 3.21
1982 5693 4.279922 TGTAGATCGACAGAGAACCAAACA 59.720 41.667 4.35 0.00 0.00 2.83
1984 5695 5.462530 TTGTAGATCGACAGAGAACCAAA 57.537 39.130 8.71 0.00 0.00 3.28
1986 5697 4.618460 GCTTTGTAGATCGACAGAGAACCA 60.618 45.833 24.53 1.09 34.29 3.67
1988 5699 3.860536 GGCTTTGTAGATCGACAGAGAAC 59.139 47.826 24.53 14.87 34.29 3.01
1989 5700 3.764434 AGGCTTTGTAGATCGACAGAGAA 59.236 43.478 24.53 10.12 34.29 2.87
1993 5704 4.563184 GTGTTAGGCTTTGTAGATCGACAG 59.437 45.833 8.71 0.23 0.00 3.51
1997 5708 4.929808 AGTTGTGTTAGGCTTTGTAGATCG 59.070 41.667 0.00 0.00 0.00 3.69
1998 5709 6.803154 AAGTTGTGTTAGGCTTTGTAGATC 57.197 37.500 0.00 0.00 0.00 2.75
2004 5715 4.261614 GGAGGAAAGTTGTGTTAGGCTTTG 60.262 45.833 0.00 0.00 32.14 2.77
2005 5716 3.889538 GGAGGAAAGTTGTGTTAGGCTTT 59.110 43.478 0.00 0.00 34.34 3.51
2084 5815 0.099436 GTTGATCCATCAGCAACGGC 59.901 55.000 0.00 0.00 37.85 5.68
2100 5831 2.747446 CCCTACCGTGAATTCCTTGTTG 59.253 50.000 2.27 0.00 0.00 3.33
2156 5887 0.972134 TCTGTGGAGAGCTTGACCAG 59.028 55.000 7.53 2.30 34.21 4.00
2189 5924 5.832595 TGACACTTGAAATGAATCCTTGGAA 59.167 36.000 0.00 0.00 0.00 3.53
2223 5963 6.511416 CAACTTCAGTCTCTATCCTACCATG 58.489 44.000 0.00 0.00 0.00 3.66
2243 5983 0.178068 ATCAGGTAATCGCCGCAACT 59.822 50.000 0.00 0.00 0.00 3.16
2248 5989 2.332104 CAGATCATCAGGTAATCGCCG 58.668 52.381 0.00 0.00 0.00 6.46
2253 5994 5.627182 ACAGAAGCAGATCATCAGGTAAT 57.373 39.130 0.00 0.00 0.00 1.89
2264 6005 3.604582 GCTGGTCTTAACAGAAGCAGAT 58.395 45.455 5.09 0.00 40.14 2.90
2389 6161 4.226394 TCCCTAGTAAACTGGCATTAGCAA 59.774 41.667 0.00 0.00 44.61 3.91
2637 6415 2.279582 AACTTCAGCTATCACGTCCG 57.720 50.000 0.00 0.00 0.00 4.79
2662 6440 5.505173 AAATTTGGAAGTCAGCCGATATG 57.495 39.130 0.00 0.00 0.00 1.78
2901 7541 2.203451 CCATGGCCTGATGCTCCC 60.203 66.667 3.32 0.00 40.92 4.30
3092 7750 1.246737 GCCCTGCTTTCTCCCTGTTG 61.247 60.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.