Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015168.1 Kokia drynarioides strain JFW-HI SEQ_130212, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 92242
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2055 original size:13 final size:14
Alignment explanation
Indices: 2032--2069 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2022 ATGATTTTAA
*
2032 AATTATTAAAAT-T
1 AATTTTTAAAATAT
*
2045 ATTTTTTAAAATAT
1 AATTTTTAAAATAT
2059 AATTTTTAAAA
1 AATTTTTAAAA
2070 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTTAAAATAT
Found at i:2200 original size:34 final size:34
Alignment explanation
Indices: 2161--2268 Score: 146
Period size: 34 Copynumber: 3.1 Consensus size: 34
2151 TTTCATTTTC
2161 TTCTCACCATTTTTCCATCTAACACCACTTCTTT
1 TTCTCACCATTTTTCCATCTAACACCACTTCTTT
* * *
2195 TTCTCACCATTTTTCTATCTAACACCAATTATTCT
1 TTCTCACCATTTTTCCATCTAACACCACTTCTT-T
* *
2230 TCTCTC-CCATTTTTCCATCTAACATCACTTCTTC
1 T-TCTCACCATTTTTCCATCTAACACCACTTCTTT
2264 TTCTC
1 TTCTC
2269 GTCATCCAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
33 4 0.06
34 31 0.48
35 25 0.39
36 4 0.06
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.45
Consensus pattern (34 bp):
TTCTCACCATTTTTCCATCTAACACCACTTCTTT
Found at i:2250 original size:35 final size:35
Alignment explanation
Indices: 2158--2268 Score: 147
Period size: 35 Copynumber: 3.2 Consensus size: 35
2148 CAATTTCATT
*
2158 TTCTTCTC-ACCATTTTTCCATCTAACACCACTTC
1 TTCTTCTCTCCCATTTTTCCATCTAACACCACTTC
* * *
2192 TT-TT-TCTCACCATTTTTCTATCTAACACCAATTA
1 TTCTTCTCTC-CCATTTTTCCATCTAACACCACTTC
*
2226 TTCTTCTCTCCCATTTTTCCATCTAACATCACTTC
1 TTCTTCTCTCCCATTTTTCCATCTAACACCACTTC
2261 TTCTTCTC
1 TTCTTCTC
2269 GTCATCCAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 2 0.03
34 26 0.40
35 31 0.48
36 4 0.06
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.46
Consensus pattern (35 bp):
TTCTTCTCTCCCATTTTTCCATCTAACACCACTTC
Found at i:9076 original size:25 final size:28
Alignment explanation
Indices: 9034--9107 Score: 100
Period size: 25 Copynumber: 2.7 Consensus size: 28
9024 AATGATGAAA
*
9034 GTCCAAAATTACAGGCCCAAATA-AAAT
1 GTCCAAAATTACAAGCCCAAATACAAAT
*
9061 GTCC-AAA-TACAAGCCCAATTACAAAT
1 GTCCAAAATTACAAGCCCAAATACAAAT
9087 GTCCAAAAATTACAAGCCCAA
1 GTCC-AAAATTACAAGCCCAA
9108 CTTGGCCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.29
26 11 0.27
27 4 0.10
28 3 0.07
29 11 0.27
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.18
Consensus pattern (28 bp):
GTCCAAAATTACAAGCCCAAATACAAAT
Found at i:10882 original size:29 final size:29
Alignment explanation
Indices: 10849--11147 Score: 183
Period size: 29 Copynumber: 10.2 Consensus size: 29
10839 AACTATCTAG
*
10849 AAATTACATTTTTACCATCGAACTTTCCA
1 AAATTACATTTTTACCCTCGAACTTTCCA
* *
10878 AAATTCCATTTTTGA-CCTCGAATTTTCCAA
1 AAATTACATTTTT-ACCCTCGAACTTTCC-A
* **
10908 AAAGTACATTTTGCCCCT-GAACTTTCCA
1 AAATTACATTTTTACCCTCGAACTTTCCA
* *
10936 AAATT-CATTTTTGA-CCT-AAATTTTCCAA
1 AAATTACATTTTT-ACCCTCGAACTTTCC-A
* * **
10964 AAATTA-ATTTTTTACCC-CTAAATTTTTTA
1 AAATTACA-TTTTTACCCTC-GAACTTTCCA
* * *
10993 AAATTCCATTTTTGACCCTTGAATTTTCCA
1 AAATTACATTTTT-ACCCTCGAACTTTCCA
*
11023 AAAGTTACATTTTTTCCCTCGAACTTTCCA
1 AAA-TTACATTTTTACCCTCGAACTTTCCA
* * *
11053 AAATT-CTATTTTTAACCACGAACTCTTCGA
1 AAATTAC-ATTTTTACCCTCGAACT-TTCCA
* *
11083 AAATTACCA-TTTTACCCTCGAA-TGTCTAA
1 AAATTA-CATTTTTACCCTCGAACTTTC-CA
11112 AAATT-CTATTTTTAACCC-CGAACCTTT-CA
1 AAATTAC-ATTTTT-ACCCTCGAA-CTTTCCA
11141 AAATTAC
1 AAATTAC
11148 CATTCCCCCT
Statistics
Matches: 211, Mismatches: 34, Indels: 49
0.72 0.12 0.17
Matches are distributed among these distances:
27 17 0.08
28 17 0.08
29 86 0.41
30 78 0.37
31 12 0.06
32 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.39
Consensus pattern (29 bp):
AAATTACATTTTTACCCTCGAACTTTCCA
Found at i:11053 original size:30 final size:29
Alignment explanation
Indices: 10849--11105 Score: 181
Period size: 30 Copynumber: 8.8 Consensus size: 29
10839 AACTATCTAG
* *
10849 AAATTACATTTTTACCATCGAACTTTCCA
1 AAATTACATTTTTACCCTCGAATTTTCCA
*
10878 AAATTCCATTTTTGA-CCTCGAATTTTCCAA
1 AAATTACATTTTT-ACCCTCGAATTTTCC-A
* ** *
10908 AAAGTACATTTTGCCCCT-GAACTTTCCA
1 AAATTACATTTTTACCCTCGAATTTTCCA
*
10936 AAATT-CATTTTTGA-CCT-AAATTTTCCAA
1 AAATTACATTTTT-ACCCTCGAATTTTCC-A
* **
10964 AAATTA-ATTTTTTACCC-CTAAATTTTTTA
1 AAATTACA-TTTTTACCCTC-GAATTTTCCA
* *
10993 AAATTCCATTTTTGACCCTTGAATTTTCCA
1 AAATTACATTTTT-ACCCTCGAATTTTCCA
* *
11023 AAAGTTACATTTTTTCCCTCGAACTTTCCA
1 AAA-TTACATTTTTACCCTCGAATTTTCCA
* * * *
11053 AAATT-CTATTTTTAACCACGAACTCTTCGA
1 AAATTAC-ATTTTTACCCTCGAA-TTTTCCA
11083 AAATTACCA-TTTTACCCTCGAAT
1 AAATTA-CATTTTTACCCTCGAAT
11106 GTCTAAAAAT
Statistics
Matches: 178, Mismatches: 32, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
27 16 0.09
28 14 0.08
29 64 0.36
30 73 0.41
31 10 0.06
32 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATTACATTTTTACCCTCGAATTTTCCA
Found at i:11118 original size:59 final size:57
Alignment explanation
Indices: 11038--11170 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 57
11028 TACATTTTTT
* *
11038 CCCTCGAACTTTCC-AAAATTCTATTTTTAACCACGAA-CTCTTCGAAAATTACCATTTTA
1 CCCTCGAA-TGTCCAAAAATTCTATTTTTAACCACGAACCT-TTC-AAAATTACCA-TTCA
* * *
11097 CCCTCGAATGTCTAAAAATTCTATTTTTAACCCCGAACCTTTCAAAATTACCATTCC
1 CCCTCGAATGTCCAAAAATTCTATTTTTAACCACGAACCTTTCAAAATTACCATTCA
11154 CCCTCGAATGTCCAAAA
1 CCCTCGAATGTCCAAAA
11171 TTATCGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
57 18 0.27
58 13 0.20
59 33 0.50
60 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (57 bp):
CCCTCGAATGTCCAAAAATTCTATTTTTAACCACGAACCTTTCAAAATTACCATTCA
Found at i:13839 original size:20 final size:20
Alignment explanation
Indices: 13800--13839 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13790 TTTTCCCATT
**
13800 TTAATTATAAAAAACTAAAA
1 TTAATTATAAAAAAAAAAAA
*
13820 TTAATTCTAAAAAAAAAAAA
1 TTAATTATAAAAAAAAAAAA
13840 GCAAAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAATTATAAAAAAAAAAAA
Found at i:14751 original size:14 final size:14
Alignment explanation
Indices: 14732--14761 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14722 GAATAAATAT
14732 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
14746 TTAATTAATTAAAA
1 TTAATTAAATAAAA
14760 TT
1 TT
14762 TTTAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:15104 original size:18 final size:16
Alignment explanation
Indices: 15077--15118 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
15067 TTAGGATTTA
*
15077 AAAAATTTAATTAATT
1 AAAAATTTATTTAATT
15093 --AAATTTATTTAATT
1 AAAAATTTATTTAATT
15107 AAAAATTTATTT
1 AAAAATTTATTT
15119 CCATTCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAAATTTATTTAATT
Found at i:15964 original size:18 final size:18
Alignment explanation
Indices: 15933--15970 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
15923 TAAGCTCAAA
*
15933 TATTTTTATGATTTA-TT
1 TATTTTTATAATTTAGTT
15950 TATTTTTCATAATTTAGTT
1 TATTTTT-ATAATTTAGTT
15969 TA
1 TA
15971 ACTACCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TATTTTTATAATTTAGTT
Found at i:16741 original size:2 final size:2
Alignment explanation
Indices: 16734--16766 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16724 TTATATGTTT
16734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16767 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16814 original size:19 final size:19
Alignment explanation
Indices: 16786--16825 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
16776 TGTGTGTGAA
16786 TTTTAAAATTTTAAAATAT
1 TTTTAAAATTTTAAAATAT
* *
16805 TTTTATAATTTTAAATTAT
1 TTTTAAAATTTTAAAATAT
16824 TT
1 TT
16826 ATTGACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTTAAAATAT
Found at i:17368 original size:20 final size:20
Alignment explanation
Indices: 17345--17392 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
17335 TTTAATGAGG
17345 ATAATTTATT-AAATAAAATA
1 ATAATTT-TTAAAATAAAATA
17365 ATAATATTTTAAAAATAAAATA
1 ATAAT-TTTT-AAAATAAAATA
17387 A-AATTT
1 ATAATTT
17393 CAAAATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 9 0.36
21 5 0.20
22 11 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTTTTAAAATAAAATA
Found at i:25000 original size:18 final size:18
Alignment explanation
Indices: 24979--25015 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
24969 GTCATTCGAC
24979 TCATCGATCTCATCATCA
1 TCATCGATCTCATCATCA
*
24997 TCATCGGTCTCATCATCA
1 TCATCGATCTCATCATCA
25015 T
1 T
25016 TATCAACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.35
Consensus pattern (18 bp):
TCATCGATCTCATCATCA
Found at i:26524 original size:23 final size:23
Alignment explanation
Indices: 26497--26573 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
26487 TAACGCAAAT
* *
26497 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
26520 AAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
26543 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
26566 CAGTAAGC
1 CAGTAAGC
26574 GCGCTAGCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.42, C:0.21, G:0.29, T:0.09
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:26674 original size:24 final size:26
Alignment explanation
Indices: 26636--26683 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
26626 TCTACATAGG
26636 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
26662 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
26684 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:30032 original size:27 final size:28
Alignment explanation
Indices: 29976--30032 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
29966 GGACCAATTA
*
29976 TTTAACTAGTAAACAAAGTATAAGATTT
1 TTTAACTAATAAACAAAGTATAAGATTT
30004 TTTAACTATATAAAC-AA-TATAATGATTT
1 TTTAACTA-ATAAACAAAGTATAA-GATTT
30032 T
1 T
30033 ACCTTTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
28 16 0.62
29 5 0.19
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (28 bp):
TTTAACTAATAAACAAAGTATAAGATTT
Found at i:34777 original size:58 final size:55
Alignment explanation
Indices: 34691--35043 Score: 264
Period size: 57 Copynumber: 6.1 Consensus size: 55
34681 GAGGGGAATG
** ** * * *
34691 GTAATTTTGGAAGGTTCGGGGTTAAAAATAGAATTTTTAAACATTCGGGGATAAAAT
1 GTAATTTTGGAAAATTTAGGGTT-AAAATAGAATTTTGAAA-GTTTGGGGATAAAAT
* * * *
34748 GGTAATTTTTGGAGAGTTTGGGGTTAAAATAAAATTTTTGAAAGTTTAGGGGCA-AAAAT
1 -GTAA-TTTTGGAAAATTTAGGGTTAAAATAGAA-TTTTGAAAGTTT-GGGG-ATAAAAT
* * **
34807 GTAATTTTGGAAATTTTAGGGTTAAAATGGAATTTTGGAAAGTTTGAGGGGCAAAAT
1 GTAATTTTGGAAAATTTAGGGTTAAAATAGAATTTT-GAAAGTTTG-GGGATAAAAT
* * *
34864 GTAATTTTTGGAAAATTTAGGGTAAAAATAAAATTTTGAAAGTTTGGGGGTAAAAT
1 GTAA-TTTTGGAAAATTTAGGGTTAAAATAGAATTTTGAAAGTTTGGGGATAAAAT
* * * *
34920 GTAATTTTGGAAAATTTAGGTTTAAAATGGAATTTTAGAAAGTTCGATGG-TAAAAAT
1 GTAATTTTGGAAAATTTAGGGTTAAAATAGAATTTT-GAAAGTTTG-GGGAT-AAAAT
* * * * *
34977 TTACTTTTTGGAAAA-TTCGAGGTCAAAAATAGAATTTTTGAAAGTTCGAGGG-TAAAAAT
1 GTA-ATTTTGGAAAATTTAG-GGT-TAAAATAGAA-TTTTGAAAGTTTG-GGGAT-AAAAT
35036 GTAATTTT
1 GTAATTTT
35044 TAAACAGTTT
Statistics
Matches: 247, Mismatches: 33, Indels: 30
0.80 0.11 0.10
Matches are distributed among these distances:
55 28 0.11
56 27 0.11
57 64 0.26
58 62 0.25
59 61 0.25
60 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (55 bp):
GTAATTTTGGAAAATTTAGGGTTAAAATAGAATTTTGAAAGTTTGGGGATAAAAT
Found at i:34783 original size:29 final size:28
Alignment explanation
Indices: 34693--34963 Score: 179
Period size: 28 Copynumber: 9.5 Consensus size: 28
34683 GGGGAATGGT
* *
34693 AATTTTGGAAGGTTCGGGGTTAAAAAT-A
1 AATTTTGGAAAGTTTGGGGTT-AAAATGA
* * * *
34721 GAATTTT-TAAACATTCGGGGATAAAATGGTA
1 -AATTTTGGAAA-GTTTGGGGTTAAAAT-G-A
* * *
34752 ATTTTTGGAGAGTTTGGGGTTAAAATAA
1 AATTTTGGAAAGTTTGGGGTTAAAATGA
* ** *
34780 AATTTTTGAAAGTTTAGGGGCAAAAATGT
1 AATTTTGGAAAGTTT-GGGGTTAAAATGA
* * *
34809 AATTTTGGAAATTTTAGGGTTAAAATGG
1 AATTTTGGAAAGTTTGGGGTTAAAATGA
**
34837 AATTTTGGAAAGTTTGAGGGGCAAAATGTA
1 AATTTTGGAAAGTTTG-GGGTTAAAATG-A
* * * * *
34867 ATTTTTGGAAAATTTAGGGTAAAAATAA
1 AATTTTGGAAAGTTTGGGGTTAAAATGA
* *
34895 AATTTT-GAAAGTTTGGGGGTAAAATGT
1 AATTTTGGAAAGTTTGGGGTTAAAATGA
* * * *
34922 AATTTTGGAAAATTTAGGTTTAAAATGG
1 AATTTTGGAAAGTTTGGGGTTAAAATGA
*
34950 AATTTTAGAAAGTT
1 AATTTTGGAAAGTT
34964 CGATGGTAAA
Statistics
Matches: 184, Mismatches: 49, Indels: 19
0.73 0.19 0.08
Matches are distributed among these distances:
27 21 0.11
28 77 0.42
29 53 0.29
30 30 0.16
31 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (28 bp):
AATTTTGGAAAGTTTGGGGTTAAAATGA
Found at i:34793 original size:28 final size:28
Alignment explanation
Indices: 34691--35053 Score: 194
Period size: 29 Copynumber: 12.6 Consensus size: 28
34681 GAGGGGAATG
* * *
34691 GTAATTTTGGAAGGTTCGGGGTTAAAAAT
1 GTAATTTTTGAAAGTTTGGGGTT-AAAAT
* * *
34720 AG-AATTTTT-AAACATTCGGGGATAAAAT
1 -GTAATTTTTGAAA-GTTTGGGGTTAAAAT
*
34748 GGTAATTTTTGGAGAGTTTGGGGTTAAAAT
1 -GTAATTTTT-GAAAGTTTGGGGTTAAAAT
** **
34778 AAAATTTTTGAAAGTTTAGGGGCAAAAAT
1 GTAATTTTTGAAAGTTT-GGGGTTAAAAT
* * *
34807 GTAATTTTGGAAATTTTAGGGTTAAAAT
1 GTAATTTTTGAAAGTTTGGGGTTAAAAT
* * **
34835 GGAATTTTGGAAAGTTTGAGGGGCAAAAT
1 GTAATTTTTGAAAGTTTG-GGGTTAAAAT
* * *
34864 GTAATTTTTGGAAAATTTAGGGTAAAAAT
1 GTAATTTTT-GAAAGTTTGGGGTTAAAAT
* * *
34893 -AAAATTTTGAAAGTTTGGGGGTAAAAT
1 GTAATTTTTGAAAGTTTGGGGTTAAAAT
* * * *
34920 GTAATTTTGGAAAATTTAGGTTTAAAAT
1 GTAATTTTTGAAAGTTTGGGGTTAAAAT
* * * * *
34948 GGAATTTTAGAAAGTTCGATGGTAAAAAT
1 GTAATTTTTGAAAGTTTG-GGGTTAAAAT
* * * * * *
34977 TTACTTTTTGGAAAATTCGAGGTCAAAAAT
1 GTAATTTTT-GAAAGTTTGGGGT-TAAAAT
* *
35007 AG-AATTTTTGAAAGTTCGAGGGTAAAAAT
1 -GTAATTTTTGAAAGTTTG-GGGTTAAAAT
*
35036 GTAATTTTTAAACAGTTT
1 GTAATTTTTGAA-AGTTT
35054 AGGGACCTCC
Statistics
Matches: 253, Mismatches: 65, Indels: 30
0.73 0.19 0.09
Matches are distributed among these distances:
27 15 0.06
28 78 0.31
29 111 0.44
30 47 0.19
31 2 0.01
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (28 bp):
GTAATTTTTGAAAGTTTGGGGTTAAAAT
Found at i:36448 original size:30 final size:30
Alignment explanation
Indices: 36406--36496 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
36396 AATAGTTTAT
36406 ATTTTATAATTTTTAAATAATTAAATTAAA
1 ATTTTATAATTTTTAAATAATTAAATTAAA
* * * * *
36436 TTTTTATTATTTTT-AAGAACTAATTTAAA
1 ATTTTATAATTTTTAAATAATTAAATTAAA
* * *
36465 ATTTTATAAATTATAAATAATTTTAATTAAA
1 ATTTTATAATTTTTAAATAA-TTAAATTAAA
36496 A
1 A
36497 AATCATTTTA
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
29 22 0.48
30 16 0.35
31 8 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTTTATAATTTTTAAATAATTAAATTAAA
Found at i:37364 original size:61 final size:62
Alignment explanation
Indices: 37294--37463 Score: 168
Period size: 61 Copynumber: 2.8 Consensus size: 62
37284 CATTAAATCT
* * * * *
37294 CTAACCTCAAAATTAAACCTTATACCCCAAAA-TGATTGAACCCTAAACCCCATTATCATTC
1 CTAATCTCAAAATCAAACCTTAAACCCCAAAACTGATTGAACCTTAAACCCCATTAACATTC
* ** *
37355 CTAATCTCAAAATCAATCCTTAAAATCCAAAACT-ATT-AACCTTGAAACCCTATTAACATTC
1 CTAATCTCAAAATCAAACCTTAAACCCCAAAACTGATTGAACCTT-AAACCCCATTAACATTC
* * * * * *
37416 ATAATCTCGAAATCAAATCATAAACCCTAAAATTG-TTGAACCTTAAAC
1 CTAATCTCAAAATCAAACCTTAAACCCCAAAACTGATTGAACCTTAAAC
37464 TCTTTTTATG
Statistics
Matches: 87, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
60 5 0.06
61 75 0.86
62 7 0.08
ACGTcount: A:0.42, C:0.26, G:0.04, T:0.28
Consensus pattern (62 bp):
CTAATCTCAAAATCAAACCTTAAACCCCAAAACTGATTGAACCTTAAACCCCATTAACATTC
Found at i:43080 original size:31 final size:31
Alignment explanation
Indices: 43042--43103 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
43032 AAACATAATT
43042 TCTTTATTTATTAAATATTTTTCTTTAGCAA
1 TCTTTATTTATTAAATATTTTTCTTTAGCAA
43073 TCTTTATTTATTAAATATTTTTCTTTAGCAA
1 TCTTTATTTATTAAATATTTTTCTTTAGCAA
43104 AAACACACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (31 bp):
TCTTTATTTATTAAATATTTTTCTTTAGCAA
Found at i:44564 original size:18 final size:18
Alignment explanation
Indices: 44543--44582 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
44533 ATTTTAAAAT
*
44543 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTG-A
44561 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
44579 TTTT
1 TTTT
44583 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATTTTGA
Found at i:44564 original size:19 final size:20
Alignment explanation
Indices: 44494--44583 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 20
44484 ATATTCTTTA
* *
44494 GAATTTTTTAAAATTATTAT
1 GAATTTTTAAAAATTATTTT
44514 -AATTTTTTTAAAAATATATATTTT
1 GAA--TTTTT-AAAA-AT-TATTTT
* *
44538 AAAATTTTTATAAA-TATTTT
1 -GAATTTTTAAAAATTATTTT
44558 GAA-TTTTAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
44577 G-ATTTTT
1 GAATTTTT
44584 TTAATTTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
18 9 0.16
19 15 0.27
20 6 0.11
21 5 0.09
22 4 0.07
23 5 0.09
24 10 0.18
26 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:44977 original size:2 final size:2
Alignment explanation
Indices: 44970--45019 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
44960 TTATACATCT
44970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45012 TA TA TA TA
1 TA TA TA TA
45020 ATCAACTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46900 original size:18 final size:18
Alignment explanation
Indices: 46877--46919 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
46867 GAATAATTTG
46877 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
46895 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
46913 TTAATTA
1 TTAATTA
46920 CAACTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:47958 original size:17 final size:17
Alignment explanation
Indices: 47936--47969 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47926 TATGATTTTT
47936 ATTTTAAAATATTTTAA
1 ATTTTAAAATATTTTAA
47953 ATTTTAAAATATTTTAA
1 ATTTTAAAATATTTTAA
47970 TTATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAAAATATTTTAA
Found at i:51180 original size:30 final size:27
Alignment explanation
Indices: 51146--51212 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 27
51136 ACAACTGAAC
51146 TTAAATTTAAAATATGAAAAAGTA-AAGAAA
1 TTAAATTTAAAATA--AAAAA-TATAA-AAA
51176 TTAAATTATTAAAATAAAAAATATAAAAA
1 TTAAA-T-TTAAAATAAAAAATATAAAAA
51205 TTAAATTT
1 TTAAATTT
51213 TAATATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 10 0.29
30 12 0.35
31 1 0.03
32 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (27 bp):
TTAAATTTAAAATAAAAAATATAAAAA
Found at i:51405 original size:19 final size:18
Alignment explanation
Indices: 51381--51423 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
51371 TTGAATTCAT
*
51381 ATATATTTTTATTTTTAAA
1 ATATATTTTT-TTGTTAAA
51400 ATATATTTTTTTGTTAAA
1 ATATATTTTTTTGTTAAA
51418 AT-TATT
1 ATATATT
51424 AAAATTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATATATTTTTTTGTTAAA
Found at i:52837 original size:15 final size:15
Alignment explanation
Indices: 52817--52857 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
52807 GTTACAACTA
52817 TGGCTATGGTGCTGG
1 TGGCTATGGTGCTGG
*
52832 TGGCTATGATGCTGG
1 TGGCTATGGTGCTGG
52847 TGGCTATGGTG
1 TGGCTATGGTG
52858 GTTATGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.44, T:0.34
Consensus pattern (15 bp):
TGGCTATGGTGCTGG
Found at i:52865 original size:15 final size:15
Alignment explanation
Indices: 52816--52870 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
52806 GGTTACAACT
52816 ATGGCTATGGTGCTG
1 ATGGCTATGGTGCTG
* *
52831 GTGGCTATGATGCTG
1 ATGGCTATGGTGCTG
* * *
52846 GTGGCTATGGTGGTT
1 ATGGCTATGGTGCTG
52861 ATGGCTATGG
1 ATGGCTATGG
52871 ATATCCTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.13, C:0.11, G:0.42, T:0.35
Consensus pattern (15 bp):
ATGGCTATGGTGCTG
Found at i:62109 original size:22 final size:22
Alignment explanation
Indices: 62078--62120 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
62068 GTGCTATTGA
*
62078 CTTCTCTATCAGCTTGGTTTTC
1 CTTCTATATCAGCTTGGTTTTC
**
62100 CTTCTATATCATTTTGGTTTT
1 CTTCTATATCAGCTTGGTTTT
62121 GATTGTCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.56
Consensus pattern (22 bp):
CTTCTATATCAGCTTGGTTTTC
Found at i:76499 original size:31 final size:30
Alignment explanation
Indices: 76463--76540 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
76453 TTTTCGATCA
*
76463 AATTTGGTACTTAAATTTAATATATTTTTTT
1 AATTTGGTACTTAAACTTAATAT-TTTTTTT
* *
76494 AATTTGGTATTTAAACTTGATA-TTTTTTT
1 AATTTGGTACTTAAACTTAATATTTTTTTT
* * *
76523 AAGTCGATACTTAAACTT
1 AATTTGGTACTTAAACTT
76541 TTGGAGATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 21 0.52
31 19 0.47
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (30 bp):
AATTTGGTACTTAAACTTAATATTTTTTTT
Found at i:76767 original size:4 final size:4
Alignment explanation
Indices: 76758--76788 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
76748 TACTTTTAGT
*
76758 TTTA TTTA TTTA TTTA TTTA TTTA ATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
76789 TATTAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:77403 original size:3 final size:3
Alignment explanation
Indices: 77391--77420 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
77381 CAACCATCCG
77391 ATC A-C ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
77421 ACAGCATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:79360 original size:21 final size:22
Alignment explanation
Indices: 79345--79389 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
79335 GTCATTCGAC
79345 TCATCGATCTCATCA-TCATCA
1 TCATCGATCTCATCATTCATCA
* *
79366 TCATCGGTCTCATCA-TCATTA
1 TCATCGATCTCATCATTCATCA
79387 TCA
1 TCA
79390 ACCGACACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.07, T:0.36
Consensus pattern (22 bp):
TCATCGATCTCATCATTCATCA
Done.