Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014972.1 Kokia drynarioides strain JFW-HI SEQ_130016, 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: 90619
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5967 original size:27 final size:27
Alignment explanation
Indices: 5934--5987 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5924 CTTCCATAAG
5934 CTAAAAACCCTAAGAAAATAAGCATAC
1 CTAAAAACCCTAAGAAAATAAGCATAC
5961 CTAAAAACCCTAAGAAAATAAGCATAC
1 CTAAAAACCCTAAGAAAATAAGCATAC
5988 ATATTCAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.07, T:0.15
Consensus pattern (27 bp):
CTAAAAACCCTAAGAAAATAAGCATAC
Found at i:7006 original size:24 final size:24
Alignment explanation
Indices: 6978--7027 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
6968 ATCGTATACT
6978 AGTTAACCATTCTGGGCTCGTAAG
1 AGTTAACCATTCTGGGCTCGTAAG
* *
7002 AGTTAACCTTTCTGGGCTCGTGAG
1 AGTTAACCATTCTGGGCTCGTAAG
7026 AG
1 AG
7028 CTAATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (24 bp):
AGTTAACCATTCTGGGCTCGTAAG
Found at i:11209 original size:54 final size:54
Alignment explanation
Indices: 11127--11243 Score: 225
Period size: 54 Copynumber: 2.2 Consensus size: 54
11117 CTCCTCAAGG
*
11127 TTTGGTTTCATTTCTTGTTGATGAGATTGTTGAAAACTTGGAGGGGTTGTGACA
1 TTTGGTTTCATTTCTTGTTGATGAGATTGTTGAAAACTAGGAGGGGTTGTGACA
11181 TTTGGTTTCATTTCTTGTTGATGAGATTGTTGAAAACTAGGAGGGGTTGTGACA
1 TTTGGTTTCATTTCTTGTTGATGAGATTGTTGAAAACTAGGAGGGGTTGTGACA
11235 TTTGGTTTC
1 TTTGGTTTC
11244 CTTGACCACC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.20, C:0.08, G:0.29, T:0.44
Consensus pattern (54 bp):
TTTGGTTTCATTTCTTGTTGATGAGATTGTTGAAAACTAGGAGGGGTTGTGACA
Found at i:12876 original size:86 final size:81
Alignment explanation
Indices: 12684--12990 Score: 280
Period size: 80 Copynumber: 3.8 Consensus size: 81
12674 TATGATGATG
* ** * * * * * * *
12684 CTCACACAAGCTGTCAAGAATCCATAACATATGCAGGATATCAGCCATCGATACGGACCAT-ATT
1 CTCACACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATC-AGAGGGTCCATAATC
*
12748 ACC-ACTCAT-GATGCTG
65 ACCAACTC-TCGATGCTA
* * * * * * *
12764 CCCACACAAGCTACCAAAAATTCGCAACATATGCAAGATCTCAACCATCAAAGGGTCCATAAATG
1 CTCACACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATCAGAGGGTCCAT-AA--
* * *
12829 TAACACCCACTCTCGATGTTG
63 T--CACCAACTCTCGATGCTA
*
12850 CTCATACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATCAGAGGGTCCAT-ATCA
1 CTCACACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATCAGAGGGTCCATAATCA
12914 CCAACTCTCGATGCTA
66 CCAACTCTCGATGCTA
* * * * *
12930 CTCACACAAGTTGTCAAGAGTCCGCAACACATGTAGGATCTCAACCATCGGAGGGTCCATA
1 CTCACACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATCAGAGGGTCCATA
12991 CAGTCAGTAT
Statistics
Matches: 186, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
79 8 0.04
80 108 0.58
81 1 0.01
82 1 0.01
83 1 0.01
84 1 0.01
85 4 0.02
86 62 0.33
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (81 bp):
CTCACACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATCAGAGGGTCCATAATCA
CCAACTCTCGATGCTA
Found at i:12972 original size:166 final size:166
Alignment explanation
Indices: 12677--12990 Score: 371
Period size: 166 Copynumber: 1.9 Consensus size: 166
12667 ACCAGTATAT
* * * *
12677 GATGATGCTCACACAAGCTGTCAAGAATCCATAACATATGCAGGATATCAGCCATCGATACGGAC
1 GATGATGCTCACACAAGCTATCAAGAATCCACAACATATGCAGGATATCAACCATCGAGACGGAC
* * * *
12742 CATATTACCACTCATGATGCTGCCCACACAAGCTACCAAAAATTCGCAACATATGCAAGATCTCA
66 CATATCACCACTCATGATGCTACCCACACAAGCTACCAAAAATCCGCAACACATGCAAGATCTCA
12807 ACCATCAAAGGGTCCATAAATGTAACACCCACTCTC
131 ACCATCAAAGGGTCCATAAATGTAACACCCACTCTC
* * * * * * *
12843 GATGTTGCTCATACAAGCTATCAAGAATCCGCAACATATGTAGGATCTCAACCATC-AGAGGGTC
1 GATGATGCTCACACAAGCTATCAAGAATCCACAACATATGCAGGATATCAACCATCGAGACGGAC
* * ** * * * *
12907 CATATCACCAACTC-TCGATGCTACTCACACAAGTTGTCAAGAGTCCGCAACACATGTAGGATCT
66 CATATCACC-ACTCAT-GATGCTACCCACACAAGCTACCAAAAATCCGCAACACATGCAAGATCT
**
12971 CAACCATCGGAGGGTCCATA
129 CAACCATCAAAGGGTCCATA
12991 CAGTCAGTAT
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
165 14 0.12
166 107 0.88
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (166 bp):
GATGATGCTCACACAAGCTATCAAGAATCCACAACATATGCAGGATATCAACCATCGAGACGGAC
CATATCACCACTCATGATGCTACCCACACAAGCTACCAAAAATCCGCAACACATGCAAGATCTCA
ACCATCAAAGGGTCCATAAATGTAACACCCACTCTC
Found at i:15475 original size:60 final size:59
Alignment explanation
Indices: 15377--15499 Score: 203
Period size: 60 Copynumber: 2.1 Consensus size: 59
15367 TTTGGGCCTA
*
15377 TAAGCACCGTTAAAAATAGCGACGTTTATGAGGAAAAACCCCGCTATATAATATGGTCT
1 TAAGCACCGTTAAAAATAGCGACGTTTATGAGGAAAAACACCGCTATATAATATGGTCT
*
15436 TAAGCGACCGTTAAAAATAGC-AGCGTTTATGAGGAAAAACACTGCTATATAATATGGTCT
1 TAAGC-ACCGTTAAAAATAGCGA-CGTTTATGAGGAAAAACACCGCTATATAATATGGTCT
15496 TAAG
1 TAAG
15500 TGACACTTTC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 6 0.10
60 54 0.90
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (59 bp):
TAAGCACCGTTAAAAATAGCGACGTTTATGAGGAAAAACACCGCTATATAATATGGTCT
Found at i:15613 original size:43 final size:42
Alignment explanation
Indices: 15502--15626 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
15492 GTCTTAAGTG
*
15502 ACACTTTCCCATAAATGCCGCTAAAGAACATGATCTTTAGCA
1 ACACTTTCCCATAAACGCCGCTAAAGAACATGATCTTTAGCA
* * * * * *
15544 ACGCTTTACCCACAAACGTCGTTAAAGAACATGATTTTTAGCG
1 ACACTTT-CCCATAAACGCCGCTAAAGAACATGATCTTTAGCA
** * *
15587 GTACTTTGCCCATAAACCCCGCTAAAGAATATGATCTTTA
1 ACACTTT-CCCATAAACGCCGCTAAAGAACATGATCTTTA
15627 ACGACGCTTT
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
42 6 0.09
43 59 0.91
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (42 bp):
ACACTTTCCCATAAACGCCGCTAAAGAACATGATCTTTAGCA
Found at i:16048 original size:21 final size:21
Alignment explanation
Indices: 16015--16059 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16005 ACTTCCTTCA
* *
16015 CTTCTCTCGCTGCTGCCTCCG
1 CTTCCCTCACTGCTGCCTCCG
16036 CTTCCCTCACTGCTGCCTCCG
1 CTTCCCTCACTGCTGCCTCCG
16057 CTT
1 CTT
16060 TAAGTTATAG
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:0.02, C:0.49, G:0.16, T:0.33
Consensus pattern (21 bp):
CTTCCCTCACTGCTGCCTCCG
Found at i:17882 original size:219 final size:219
Alignment explanation
Indices: 17503--17941 Score: 860
Period size: 219 Copynumber: 2.0 Consensus size: 219
17493 ACTTTGATTT
*
17503 TCTTCAATTTCCAAAACATTCAAAGATCCAATAGCAATAGTCTGTTGATCACTATTTGTTTCTTC
1 TCTTCAATTTCCAAAACATTCAAAGATCCAATAGCAATAGTATGTTGATCACTATTTGTTTCTTC
17568 CGAATTCGGAGGATTTTGGATAATACTTAGCTCTCGAAATTTTTTTCTAGGCATATTATCTGCAA
66 CGAATTCGGAGGATTTTGGATAATACTTAGCTCTCGAAATTTTTTTCTAGGCATATTATCTGCAA
*
17633 TACACATAAAATAGTTGAAATATTAGTAACTAATTACAATAATAATAGTAATGGATATATTTAAC
131 TACACATAAAATAGTTGAAATATTAGTAACTAATTACAATAAAAATAGTAATGGATATATTTAAC
17698 GAGATCAATATTTAAATTATAATA
196 GAGATCAATATTTAAATTATAATA
17722 TCTTCAATTTCCAAAACATTCAAAGATCCAATAGCAATAGTATGTTGATCACTATTTGTTTCTTC
1 TCTTCAATTTCCAAAACATTCAAAGATCCAATAGCAATAGTATGTTGATCACTATTTGTTTCTTC
17787 CGAATTCGGAGGATTTTGGATAATACTTAGCTCTCGAAATTTTTTTCTAGGCATATTATCTGCAA
66 CGAATTCGGAGGATTTTGGATAATACTTAGCTCTCGAAATTTTTTTCTAGGCATATTATCTGCAA
17852 TACACATAAAATAGTTGAAATATTAGTAACTAATTACAATAAAAATAGTAATGGATATATTTAAC
131 TACACATAAAATAGTTGAAATATTAGTAACTAATTACAATAAAAATAGTAATGGATATATTTAAC
17917 GAGATCAATATTTAAATTATAATA
196 GAGATCAATATTTAAATTATAATA
17941 T
1 T
17942 TACATATTAT
Statistics
Matches: 218, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 218 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (219 bp):
TCTTCAATTTCCAAAACATTCAAAGATCCAATAGCAATAGTATGTTGATCACTATTTGTTTCTTC
CGAATTCGGAGGATTTTGGATAATACTTAGCTCTCGAAATTTTTTTCTAGGCATATTATCTGCAA
TACACATAAAATAGTTGAAATATTAGTAACTAATTACAATAAAAATAGTAATGGATATATTTAAC
GAGATCAATATTTAAATTATAATA
Found at i:18890 original size:24 final size:25
Alignment explanation
Indices: 18863--18912 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
18853 GAAAAAGATG
18863 AATATTTATC-AAATTCTAAAACTT
1 AATATTTATCAAAATTCTAAAACTT
18887 AATATTTATCAAAATTCTAAAACTT
1 AATATTTATCAAAATTCTAAAACTT
18912 A
1 A
18913 CTTGCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
AATATTTATCAAAATTCTAAAACTT
Found at i:22106 original size:121 final size:121
Alignment explanation
Indices: 21953--22299 Score: 544
Period size: 121 Copynumber: 2.9 Consensus size: 121
21943 GGGTTTTATT
* *
21953 TAAC-AATTAAATATGTAATTATTTTAATATTTGTTATGTTTTTAATAATTGAATATTTATTTAA
1 TAACTAATTAAATAT-TAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTTAA
*
22017 TATAATTAAATAATTTAATAGTTTGAATTAAATATTTTGA-TTTAAGG-TTTAATAAA
65 TATAATTAAATAATTTAATATTTTGAATTAAATATTTTGAGTTT-AGGATTTAATAAA
22073 TAACTAATTAAATACTTAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTTAA
1 TAACTAATTAAATA-TTAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTTAA
22138 TATAATTAAATAATTTAATATTTTGAATTAAATA-TTTGAGTTTAGGATTTAATAAA
65 TATAATTAAATAATTTAATATTTTGAATTAAATATTTTGAGTTTAGGATTTAATAAA
*** *
22194 TAACTAATTAAATAATTAATTATTTTAAT-CGAGTTCTATTTTTAATAATTTAATATTTATTTAA
1 TAACTAATTAAAT-ATTAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTTAA
*
22258 TATATTTAAATAATTTAATATTTTGAATTAAATA-TTTGAGTT
65 TATAATTAAATAATTTAATATTTTGAATTAAATATTTTGAGTT
22300 GTTTTTTTTT
Statistics
Matches: 214, Mismatches: 8, Indels: 10
0.92 0.03 0.04
Matches are distributed among these distances:
120 84 0.39
121 128 0.60
122 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (121 bp):
TAACTAATTAAATATTAATTATTTTAATATTTGTTCTATTTTTAATAATTGAATATTTATTTAAT
ATAATTAAATAATTTAATATTTTGAATTAAATATTTTGAGTTTAGGATTTAATAAA
Found at i:24413 original size:20 final size:20
Alignment explanation
Indices: 24355--24405 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
24345 TGGAGAGAAA
24355 GAGAATGAAATGGAGGATTG
1 GAGAATGAAATGGAGGATTG
24375 GAGAATGAAATGGAGGATTG
1 GAGAATGAAATGGAGGATTG
24395 GAGAATGAAAT
1 GAGAATGAAAT
24406 TAGGGATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (20 bp):
GAGAATGAAATGGAGGATTG
Found at i:24793 original size:21 final size:18
Alignment explanation
Indices: 24748--24799 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 18
24738 GTTCTTTCTC
24748 ATATTTTAAATTTTTTAA
1 ATATTTTAAATTTTTTAA
24766 ATTTATTTTCAAATTTTATATAA
1 A--TATTTT-AAATTTT-T-TAA
*
24789 ATATTTAAAAT
1 ATATTTTAAAT
24800 ACATCAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 1 0.04
20 10 0.36
21 12 0.43
22 1 0.04
23 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTTTAAATTTTTTAA
Found at i:26829 original size:41 final size:41
Alignment explanation
Indices: 26668--26837 Score: 196
Period size: 41 Copynumber: 4.1 Consensus size: 41
26658 ACCTAAACGT
* ** * * *
26668 CGCTAATTCTCTGACCTTTAGCGATGTGTATGAGAAAGCAC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGCGC
* *
26709 CGCAAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGAGC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGCGC
** * *
26750 CGCTCTTGCTTTGACCTTTAGCGGCGTTTATGAGAAAGCGC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGCGC
* * *
26791 CGCTAATGCTCTAACTTTTAGCGGCGTTTATTATAAAGCGC
1 CGCTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGCGC
*
26832 CACTAA
1 CGCTAA
26838 ATGTTAGAGC
Statistics
Matches: 107, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (41 bp):
CGCTAATGCTCTGACCTTTAGCGGCGTTTATGATAAAGCGC
Found at i:26853 original size:41 final size:41
Alignment explanation
Indices: 26808--26938 Score: 165
Period size: 41 Copynumber: 3.2 Consensus size: 41
26798 GCTCTAACTT
* *
26808 TTAGCGGCG-TTTATTATAAAGCGCCACTAAATGTTAGAGCA
1 TTAGCGGCGCTTTATCATAAA-CGCCACTAAAGGTTAGAGCA
* ** *
26849 TTAGCGGCGCTTTCTCATAAACGCTGCTAAAGGTCAGAGCA
1 TTAGCGGCGCTTTATCATAAACGCCACTAAAGGTTAGAGCA
* * *
26890 TTAGCGGCGCTTTATCATAAATGCCACTAAAGGTTAGACCT
1 TTAGCGGCGCTTTATCATAAACGCCACTAAAGGTTAGAGCA
26931 TTAGCGGC
1 TTAGCGGC
26939 TTTTTTTATA
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 67 0.88
42 9 0.12
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGCTTTATCATAAACGCCACTAAAGGTTAGAGCA
Found at i:26878 original size:82 final size:81
Alignment explanation
Indices: 26680--26938 Score: 202
Period size: 82 Copynumber: 3.2 Consensus size: 81
26670 CTAATTCTCT
** * * * * * *
26680 GACCTTTAGCGATGTGTATGAGAAAGCACCGCAAATGCTCTGACCTTTAGCGGCGTTTATGATAA
1 GACCTTTAGCGGCGTTTATCAGAAAGCGCCGCTAATGCTCT-AACTTTAGCGGCGTTTATCATAA
* ** *
26745 AGAGCCGCT-CTTGCTTT
65 AGAGCCACTAAATG-TTA
* *
26762 GACCTTTAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCTAACTTTTAGCGGCGTTTATTATAA
1 GACCTTTAGCGGCGTTTATCAGAAAGCGCCGCTAATGCTCTAAC-TTTAGCGGCGTTTATCATAA
*
26827 AGCGCCACTAAATGTTA
65 AGAGCCACTAAATGTTA
* * * * * * * *
26844 GAGCATTAGCGGCGCTTTCTCATAAA-CGCTGCTAAAGGTC-AGAGCATTAGCGGCGCTTTATCA
1 GACCTTTAGCGGCG-TTTATCAGAAAGCGCCGCTAATGCTCTA-A-CTTTAGCGGCG-TTTATCA
* *
26907 TAAA-TGCCACTAAAGGTTA
62 TAAAGAGCCACTAAATGTTA
26926 GACCTTTAGCGGC
1 GACCTTTAGCGGC
26939 TTTTTTTATA
Statistics
Matches: 145, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
81 3 0.02
82 121 0.83
83 21 0.14
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (81 bp):
GACCTTTAGCGGCGTTTATCAGAAAGCGCCGCTAATGCTCTAACTTTAGCGGCGTTTATCATAAA
GAGCCACTAAATGTTA
Found at i:36619 original size:23 final size:23
Alignment explanation
Indices: 36587--36674 Score: 131
Period size: 23 Copynumber: 3.8 Consensus size: 23
36577 GCTGGGGAAA
36587 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
36610 CAGTAGGCACACACAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
* * *
36633 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
36656 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
36675 TGAACAGTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.41, C:0.25, G:0.20, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:36640 original size:46 final size:46
Alignment explanation
Indices: 36584--36685 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
36574 AGTGCTGGGG
*
36584 AAACAGTAAGCACACACAGTGCAAATCAGTAGGCACACACAGTGCA
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCA
* * * *
36630 AAACAGTAAGCACATATAGTGCGAATCAGTAAGCACACACAGTGCT
1 AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCA
*
36676 GAACAGTAAG
1 AAACAGTAAG
36686 TACGCTAGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.14
Consensus pattern (46 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAGTGCA
Found at i:36682 original size:23 final size:22
Alignment explanation
Indices: 36584--36685 Score: 123
Period size: 23 Copynumber: 4.5 Consensus size: 22
36574 AGTGCTGGGG
36584 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
*
36606 AAATCAGTAGGCACACACAGTGC
1 AAA-CAGTAAGCACACACAGTGC
* *
36629 AAAACAGTAAGCACATATAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
36652 GAATCAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
36675 TGAACAGTAAG
1 -AAACAGTAAG
36686 TACGCTAGTG
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
22 3 0.04
23 61 0.91
24 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.14
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:39827 original size:21 final size:22
Alignment explanation
Indices: 39794--39845 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
39784 ATTAGAATGT
*
39794 AAAA-ATT-AAATTAAAA-ACA
1 AAAATATTAAAATTAAAATAAA
39813 AAAATATTAAAATTAAAATAAA
1 AAAATATTAAAATTAAAATAAA
*
39835 AAAATGTTAAA
1 AAAATATTAAA
39846 TCAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 9 0.32
22 12 0.43
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATATTAAAATTAAAATAAA
Found at i:39846 original size:21 final size:21
Alignment explanation
Indices: 39794--39861 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
39784 ATTAGAATGT
*
39794 AAAA-ATTAAATTAAAA-ACA
1 AAAATATTAAATTAAAATAAA
39813 AAAATATTAAAATTAAAATAAA
1 AAAATATT-AAATTAAAATAAA
* * *
39835 AAAATGTTAAATCAATATAAA
1 AAAATATTAAATTAAAATAAA
39856 TAAAAT
1 -AAAAT
39862 TTTCCTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.10
20 3 0.07
21 20 0.49
22 14 0.34
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.26
Consensus pattern (21 bp):
AAAATATTAAATTAAAATAAA
Found at i:40734 original size:20 final size:20
Alignment explanation
Indices: 40709--40752 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
40699 TTTTCCATTA
40709 TTTGGAGTGAAAATCGCAAT
1 TTTGGAGTGAAAATCGCAAT
40729 TTTGGAGTGAAAATCGCAAT
1 TTTGGAGTGAAAATCGCAAT
40749 TTTG
1 TTTG
40753 ACACGGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (20 bp):
TTTGGAGTGAAAATCGCAAT
Found at i:43307 original size:44 final size:44
Alignment explanation
Indices: 43218--43305 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
43208 TAGTGTTGAG
* * * *
43218 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAAAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* * *
43262 TTAAGAATTAAAATGTGTAGTTTAAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAAAATATGTAGTTAAAATAAG-AAGATTAAGAAAA
43306 TTCAAGGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 25 0.69
45 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.28
Consensus pattern (44 bp):
TTAAGAATTAAAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:47034 original size:12 final size:12
Alignment explanation
Indices: 47017--47056 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
47007 ATTTATTAAA
47017 AATATTTATTTT
1 AATATTTATTTT
47029 AATA--T-TTTT
1 AATATTTATTTT
*
47038 AGTATTTATTTT
1 AATATTTATTTT
47050 AATATTT
1 AATATTT
47057 TTTGTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 7 0.30
10 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
AATATTTATTTT
Found at i:47043 original size:21 final size:21
Alignment explanation
Indices: 47019--47058 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
47009 TTATTAAAAA
47019 TATTTATTTTAATATTTTTAG
1 TATTTATTTTAATATTTTTAG
47040 TATTTATTTTAATATTTTT
1 TATTTATTTTAATATTTTT
47059 TGTTGTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TATTTATTTTAATATTTTTAG
Found at i:47664 original size:27 final size:28
Alignment explanation
Indices: 47607--47678 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
47597 ATTATGTACT
* *
47607 AATAATTTTATTATTTTTAAAAAGATTA
1 AATAATTTTATTATATTTAAAAAGATAA
*
47635 AATAATTTT-TTATATTT-AAGAGAATAAA
1 AATAATTTTATTATATTTAAAAAG-AT-AA
47663 ATATAATTTTATTATA
1 A-ATAATTTTATTATA
47679 AATTTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 4 0.11
27 9 0.24
28 11 0.30
29 8 0.22
30 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
AATAATTTTATTATATTTAAAAAGATAA
Found at i:47684 original size:11 final size:11
Alignment explanation
Indices: 47664--47700 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
47654 GAGAATAAAA
47664 TATAATTTTAT
1 TATAATTTTAT
*
47675 TATAAATTTATT
1 TATAATTTTA-T
47687 TATAATTTTAT
1 TATAATTTTAT
47698 TAT
1 TAT
47701 TTCTAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATAATTTTAT
Found at i:47689 original size:12 final size:12
Alignment explanation
Indices: 47664--47698 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
47654 GAGAATAAAA
47664 TATAATTTTA-T
1 TATAATTTTATT
*
47675 TATAAATTTATT
1 TATAATTTTATT
47687 TATAATTTTATT
1 TATAATTTTATT
47699 ATTTCTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TATAATTTTATT
Found at i:48868 original size:6 final size:7
Alignment explanation
Indices: 48847--48871 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
48837 AAATTTTTAA
48847 TTTATTT
1 TTTATTT
48854 TTTATTT
1 TTTATTT
48861 TTTATTT
1 TTTATTT
48868 TTTA
1 TTTA
48872 ATCATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:50343 original size:19 final size:19
Alignment explanation
Indices: 50289--50345 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
50279 ATAGTGTTTA
*
50289 ATTAGTGGAATTGTGCT-TG
1 ATTAGTGGAATCGTG-TGTG
* *
50308 ATTAGTGGAACCATGTGTG
1 ATTAGTGGAATCGTGTGTG
50327 ATTAGTGGAATCGTGTGTG
1 ATTAGTGGAATCGTGTGTG
50346 CATGTAAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 1 0.03
19 31 0.97
ACGTcount: A:0.23, C:0.07, G:0.33, T:0.37
Consensus pattern (19 bp):
ATTAGTGGAATCGTGTGTG
Found at i:56799 original size:18 final size:18
Alignment explanation
Indices: 56776--56812 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
56766 TTTGTGATCA
56776 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
56794 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
56812 A
1 A
56813 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:68034 original size:20 final size:20
Alignment explanation
Indices: 67992--68047 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
67982 TAATTTAATA
**
67992 ATTATCTTAATATT-ATTTT
1 ATTATCTTAATATTAAAGTT
68011 ATTAAT-TTAATATTAAAGTT
1 ATT-ATCTTAATATTAAAGTT
68031 ATTATCTTAATATTAAA
1 ATTATCTTAATATTAAA
68048 TTGAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 13 0.41
20 19 0.59
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATCTTAATATTAAAGTT
Found at i:69136 original size:30 final size:30
Alignment explanation
Indices: 69100--69156 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
69090 ACCTAACCCT
69100 AAACTCGAGAATTCC-AAGATAAAATTTCTG
1 AAACTCGAGAA-TCCGAAGATAAAATTTCTG
* *
69130 AAACTCGGGAATCCGAGGATAAAATTT
1 AAACTCGAGAATCCGAAGATAAAATTT
69157 ACATTTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (30 bp):
AAACTCGAGAATCCGAAGATAAAATTTCTG
Found at i:74609 original size:34 final size:34
Alignment explanation
Indices: 74559--74627 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
74549 GGCCTTTAAA
*
74559 TCTCTCACCATTTTTTTGCTAATGATTGTATTCT
1 TCTCTCACCATTTTTTTACTAATGATTGTATTCT
*
74593 TCTCTCACC-TTCTTTTTACTGATGATTGTATTCT
1 TCTCTCACCATT-TTTTTACTAATGATTGTATTCT
74627 T
1 T
74628 TTCGATGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.16, C:0.22, G:0.09, T:0.54
Consensus pattern (34 bp):
TCTCTCACCATTTTTTTACTAATGATTGTATTCT
Found at i:87085 original size:2 final size:2
Alignment explanation
Indices: 87080--87119 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
87070 AAAAGAGAGG
87080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87120 TAAAACATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88056 original size:16 final size:16
Alignment explanation
Indices: 88017--88060 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
88007 CAATTGAACT
*
88017 AATTTTTTTATTTTAA
1 AATTTTTTAATTTTAA
*
88033 AATATTTTTAATTTTAT
1 AAT-TTTTTAATTTTAA
*
88050 GATTTTTTAAT
1 AATTTTTTAAT
88061 AATTTATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
AATTTTTTAATTTTAA
Found at i:88817 original size:17 final size:18
Alignment explanation
Indices: 88795--88873 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 18
88785 AAATATTCAT
88795 AATATTTAATTAAGCA-A
1 AATATTTAATTAAGCAGA
*
88812 AATATTTAATTAAGCATGC
1 AATATTTAATTAAGCA-GA
* *
88831 AATA-ATAACTTAGGCATGA
1 AATATTTAA-TTAAGCA-GA
88850 TAATATTTAATTAAGCA-A
1 -AATATTTAATTAAGCAGA
88868 AATATT
1 AATATT
88874 CAGGGTCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 22 0.43
18 4 0.08
19 12 0.24
20 10 0.20
21 3 0.06
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (18 bp):
AATATTTAATTAAGCAGA
Found at i:88987 original size:12 final size:12
Alignment explanation
Indices: 88972--88996 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88962 ATTAAAGAAT
88972 TAATAGCATTCA
1 TAATAGCATTCA
88984 TAATAGCATTCA
1 TAATAGCATTCA
88996 T
1 T
88997 CATATAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:90592 original size:2 final size:2
Alignment explanation
Indices: 90585--90619 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
90575 TGTTTTATTT
90585 TA 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 TA T
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.