Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011579.1 Kokia drynarioides strain JFW-HI SEQ_126568, 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: 60883
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:7507 original size:30 final size:30
Alignment explanation
Indices: 7473--7719 Score: 262
Period size: 30 Copynumber: 8.3 Consensus size: 30
7463 AAATTTATGT
*
7473 TTTGACCCTTAAAATTTCCAAAAATTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
* * **
7503 TTTGACCCTTAAAATTTCC-ATAATTTGAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
*
7532 TTTGACCCCTAAACTTTCCAAAAATTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
* **
7562 TTTAACCCTTAAACTTTTAAAAAATTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
* *
7592 TTTGACCCTTAAACTTTCCAAAATTTTAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
** * * *
7622 TTTGACCCTCGAATTTTTCAAAAATTCCAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
* * * **
7652 TTTGACCGTTAAACTTTCCAAATACTCTGA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
* * *
7682 TTTGACCCTTGAAGTTTCCAAAAGTTCAAA
1 TTTGACCCTTAAACTTTCCAAAAATTCAAA
*
7712 TTTAACCC
1 TTTGACCC
7720 GATTTTAATG
Statistics
Matches: 174, Mismatches: 42, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
29 24 0.14
30 150 0.86
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (30 bp):
TTTGACCCTTAAACTTTCCAAAAATTCAAA
Found at i:9776 original size:31 final size:31
Alignment explanation
Indices: 9741--9816 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
9731 TGCATATGCA
9741 TTCATGAATTCATAAAA-TTTCGCATCGCATT
1 TTCATGAATTCA-AAAAGTTTCGCATCGCATT
* *
9772 TTCATGCATTCAAAAAGTTTTGCATCGCATT
1 TTCATGAATTCAAAAAGTTTCGCATCGCATT
*
9803 TTCATGCATT-AAAA
1 TTCATGAATTCAAAA
9817 TATAGAGAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
30 8 0.19
31 34 0.81
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (31 bp):
TTCATGAATTCAAAAAGTTTCGCATCGCATT
Found at i:14655 original size:50 final size:50
Alignment explanation
Indices: 14560--14655 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
14550 GTAGAGGAAC
* *
14560 AGATTGAAGCCACAATAGCAAATCTCATACACTTAAAGTTGTAGAGAGGT
1 AGATTGAAGCCACAATAGCAAATCTCATACACTTAAAGCTATAGAGAGGT
** * * *
14610 AGATTGAAGCTGCAATGGCGAATCTCATCCA-TCTAAAGCTATAGAG
1 AGATTGAAGCCACAATAGCAAATCTCATACACT-TAAAGCTATAGAG
14656 GGGCAGATGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 1 0.03
50 37 0.97
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACAATAGCAAATCTCATACACTTAAAGCTATAGAGAGGT
Found at i:14787 original size:39 final size:39
Alignment explanation
Indices: 14724--14936 Score: 191
Period size: 39 Copynumber: 5.4 Consensus size: 39
14714 TGTAACCTCT
**
14724 AATCTTTTACCCCGACCATGGGGCAGATTGAAACAATCC
1 AATCTTTTACCCTAACCATGGGGCAGATTGAAACAATCC
* * *
14763 AATCTTTTACCCTAACTA-GAGGGCAAATTGAAGACCATCC
1 AATCTTTTACCCTAACCATG-GGGCAGATTGAA-ACAATCC
* * * *
14803 AATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATTC
1 AATCTTTTACCCTAACCATGGGGCAGATTGAAACAATCC
* * * *
14842 AATCTTTTACCCTAACTA-GAGGGAAAATTGAAGACCAT-C
1 AATCTTTTACCCTAACCATG-GGGCAGATTGAA-ACAATCC
* *
14881 AGATCTCTTACCCCT-ACCATGGGGCAGATTGAAACAATTC
1 A-ATCTTTTA-CCCTAACCATGGGGCAGATTGAAACAATCC
*
14921 AATCTTTAACCTCTAA
1 AATCTTTTACC-CTAA
14937 AGCTATAGAG
Statistics
Matches: 137, Mismatches: 26, Indels: 21
0.74 0.14 0.11
Matches are distributed among these distances:
38 4 0.03
39 69 0.50
40 58 0.42
41 6 0.04
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (39 bp):
AATCTTTTACCCTAACCATGGGGCAGATTGAAACAATCC
Found at i:14813 original size:40 final size:40
Alignment explanation
Indices: 14744--14893 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
14734 CCCGACCATG
* *
14744 GGGCAGATTGAA-ACAATCCAATCTTTTACCCTAACTAGA
1 GGGCAAATTGAAGACAATCCAATCTCTTACCCTAACTAGA
* * *
14783 GGGCAAATTGAAGACCATCCAATCTCTTACCCCAACCATG-
1 GGGCAAATTGAAGACAATCCAATCTCTTACCCTAACTA-GA
* * *
14823 GGGCAGATTGAAG-CAATTCAATCTTTTACCCTAACTAGA
1 GGGCAAATTGAAGACAATCCAATCTCTTACCCTAACTAGA
* *
14862 GGGAAAATTGAAGACCAT-CAGATCTCTTACCC
1 GGGCAAATTGAAGACAATCCA-ATCTCTTACCC
14894 CTACCATGGG
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
38 1 0.01
39 43 0.47
40 46 0.51
41 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
GGGCAAATTGAAGACAATCCAATCTCTTACCCTAACTAGA
Found at i:14821 original size:79 final size:78
Alignment explanation
Indices: 14724--14936 Score: 336
Period size: 79 Copynumber: 2.7 Consensus size: 78
14714 TGTAACCTCT
* * * *
14724 AATCTTTTACCCCGACCATGGGGCAGATTGAAACAATCCAATCTTTTACCCTAACTAGAGGGCAA
1 AATCTCTTACCCCAACCATGGGGCAGATTGAAACAATTCAATCTTTTACCCTAACTAGAGGGAAA
14789 ATTGAAGACCATCC
66 ATTGAAGACCAT-C
*
14803 AATCTCTTACCCCAACCATGGGGCAGATTGAAGCAATTCAATCTTTTACCCTAACTAGAGGGAAA
1 AATCTCTTACCCCAACCATGGGGCAGATTGAAACAATTCAATCTTTTACCCTAACTAGAGGGAAA
14868 ATTGAAGACCATC
66 ATTGAAGACCATC
* *
14881 AGATCTCTTACCCCTACCATGGGGCAGATTGAAACAATTCAATCTTTAACCTCTAA
1 A-ATCTCTTACCCCAACCATGGGGCAGATTGAAACAATTCAATCTTTTACC-CTAA
14937 AGCTATAGAG
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
78 2 0.02
79 118 0.95
80 4 0.03
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.25
Consensus pattern (78 bp):
AATCTCTTACCCCAACCATGGGGCAGATTGAAACAATTCAATCTTTTACCCTAACTAGAGGGAAA
ATTGAAGACCATC
Found at i:28793 original size:30 final size:30
Alignment explanation
Indices: 28757--28833 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
28747 CCTTCACCCA
* *
28757 TGCTCGCAACACGAGTGTTCGAAACATTAG
1 TGCTCGCAACACCAGTGTTCGAAACATGAG
* * **
28787 TGCTCGCAGCTCCAGTGTTCTCAACATGAG
1 TGCTCGCAACACCAGTGTTCGAAACATGAG
*
28817 TGCTCACAACACCAGTG
1 TGCTCGCAACACCAGTG
28834 CTCGCATCTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (30 bp):
TGCTCGCAACACCAGTGTTCGAAACATGAG
Found at i:41157 original size:75 final size:74
Alignment explanation
Indices: 41034--41178 Score: 272
Period size: 75 Copynumber: 1.9 Consensus size: 74
41024 CACATCACCA
*
41034 CCATTGAACCACCAAAACTTCACCGAATAAACATTTTCGCCGCCCTCTACCGTTCGTCGCCACCG
1 CCATTGAACCACCAAAACTTCACCGAATAAACATTTTCGCCGCCCTCTACCGTTCGCCGCCACCG
41099 TTTGACGCC
66 TTTGACGCC
41108 NCCATTGAACCACCAAAACTTCACCGAATAAACATTTTCGCCGCCCTCTACCGTTCGCCGCCACC
1 -CCATTGAACCACCAAAACTTCACCGAATAAACATTTTCGCCGCCCTCTACCGTTCGCCGCCACC
41173 GTTTGA
65 GTTTGA
41179 TGCCGCGAAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.25, C:0.39, G:0.13, T:0.23
Consensus pattern (74 bp):
CCATTGAACCACCAAAACTTCACCGAATAAACATTTTCGCCGCCCTCTACCGTTCGCCGCCACCG
TTTGACGCC
Found at i:43963 original size:17 final size:17
Alignment explanation
Indices: 43941--43976 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
43931 TAGTCAAAAA
43941 TTGTTATTTTCTTATTT
1 TTGTTATTTTCTTATTT
*
43958 TTGTTATTTTTTTATTT
1 TTGTTATTTTCTTATTT
43975 TT
1 TT
43977 TATTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.81
Consensus pattern (17 bp):
TTGTTATTTTCTTATTT
Found at i:45894 original size:30 final size:30
Alignment explanation
Indices: 45847--46088 Score: 202
Period size: 30 Copynumber: 8.1 Consensus size: 30
45837 ATGTTTTGAT
* *
45847 CCCTAAATTTTCTAAAAATTCAAATTTAAC
1 CCCTAAACTTTCCAAAAATTCAAATTTAAC
* * * *
45877 CCTTAAAATTTCCAAAAATTCAAATTTGAT
1 CCCTAAACTTTCCAAAAATTCAAATTTAAC
*
45907 CCCTAAACTTTCCAAAAATTCAAATTTGAC
1 CCCTAAACTTTCCAAAAATTCAAATTTAAC
* *
45937 CCCTAAACTTTCCAAAAAATT-AAACTTGAC
1 CCCTAAACTTTCC-AAAAATTCAAATTTAAC
* * * *
45967 CCCCAAAGTTTCCAAAAAATT-GAATTTTAC
1 CCCTAAACTTTCC-AAAAATTCAAATTTAAC
* * * * *
45997 TCCC-GAATTTTTCAAAAATTCTAATTCAAC
1 -CCCTAAACTTTCCAAAAATTCAAATTTAAC
* * * * *
46027 CCCCAAACTTTCCAAATACTCTAATTTGAC
1 CCCTAAACTTTCCAAAAATTCAAATTTAAC
* * *
46057 CCCTAAAGTTTTCAAAATTTCAAATTTAAC
1 CCCTAAACTTTCCAAAAATTCAAATTTAAC
46087 CC
1 CC
46089 GATTTTAATG
Statistics
Matches: 173, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
29 10 0.06
30 153 0.88
31 10 0.06
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTCAAATTTAAC
Found at i:45984 original size:90 final size:90
Alignment explanation
Indices: 45841--46083 Score: 233
Period size: 90 Copynumber: 2.7 Consensus size: 90
45831 AAAATTATGT
* * * * * *
45841 TTTGATCCCTAAA-TTTTCTAAAAATTCAAATTTAACCCTTAAAATTTCCAAAAATTCAAATTTG
1 TTTGACCCCTAAACTTTCCAAAAAATT-AAATTTGACCCCTAAAGTTTCCAAAAATTCAAATTTG
45905 A-TCCCTAAACTTTCCAAAAATTCAAA
65 ACTCCC-AAACTTTCCAAAAATTCAAA
* * * *
45931 TTTGACCCCTAAACTTTCCAAAAAATTAAACTTGACCCCCAAAGTTTCCAAAAAATT-GAATTTT
1 TTTGACCCCTAAACTTTCCAAAAAATTAAATTTGACCCCTAAAGTTTCC-AAAAATTCAAATTTG
* * * *
45995 ACTCCCGAATTTTTCAAAAATTCTAA
65 ACTCCCAAACTTTCCAAAAATTCAAA
** * * * * *
46021 TTCAACCCCCAAACTTTCCAAATACTCT-AATTTGACCCCTAAAGTTTTCAAAATTTCAAATTT
1 TTTGACCCCTAAACTTTCCAAAAAAT-TAAATTTGACCCCTAAAGTTTCCAAAAATTCAAATTT
46084 AACCCGATTT
Statistics
Matches: 124, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
89 6 0.05
90 95 0.77
91 23 0.19
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (90 bp):
TTTGACCCCTAAACTTTCCAAAAAATTAAATTTGACCCCTAAAGTTTCCAAAAATTCAAATTTGA
CTCCCAAACTTTCCAAAAATTCAAA
Found at i:46177 original size:29 final size:28
Alignment explanation
Indices: 46127--46181 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
46117 TTTTATCCTA
46127 TATGTATATTATTTTATTTTATTGTATTT
1 TATGTATATTATTTTATTTTA-TGTATTT
*
46156 TATGTATA-TATTTTTTTATTATGTAT
1 TATGTATATTATTTTATT-TTATGTAT
46182 ACTTGTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (28 bp):
TATGTATATTATTTTATTTTATGTATTT
Found at i:48177 original size:31 final size:31
Alignment explanation
Indices: 48142--48215 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
48132 TGCATATGCA
* *
48142 TTCATGCATTCATAAAATTTCGCATCGTATT
1 TTCATGCATTAATAAAATTTCGCATCGCATT
* * *
48173 TTCATGCATTAATAAAGTTTTGCATTGCATT
1 TTCATGCATTAATAAAATTTCGCATCGCATT
48204 TTCATGCATTAA
1 TTCATGCATTAA
48216 AATATCGAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (31 bp):
TTCATGCATTAATAAAATTTCGCATCGCATT
Found at i:53188 original size:38 final size:39
Alignment explanation
Indices: 53056--53267 Score: 124
Period size: 39 Copynumber: 5.4 Consensus size: 39
53046 TATAACCTCT
* * *
53056 AATCTTTTACCCTAACCATGGGGCAGAATGAAACAATTC
1 AATCTTTTACCCTAACCATGGGGTAGATTGAAGCAATTC
* * * *
53095 AATCTTTTACCCTAACCA-GAGGGGAGATTAAAGACCATCC
1 AATCTTTTACCCTAACCATG-GGGTAGATTGAAG-CAATTC
* ** ** *
53135 GATCGCTTACCCCGACCATGGGGTAGATTGAAGCAATTA
1 AATCTTTTACCCTAACCATGGGGTAGATTGAAGCAATTC
* ** **
53174 AATCTTTTACCC-GACCATAAGGTAGATTGAAG-ACCGTC
1 AATCTTTTACCCTAACCATGGGGTAGATTGAAGCA-ATTC
* * * * * ** *
53212 AGATCTCTTACGCTGACCATGGGGCAGATAGAAAAAATTT
1 A-ATCTTTTACCCTAACCATGGGGTAGATTGAAGCAATTC
53252 AATCTTTTACCTCTAA
1 AATCTTTTACC-CTAA
53268 AGCTATAGAG
Statistics
Matches: 128, Mismatches: 37, Indels: 15
0.71 0.21 0.08
Matches are distributed among these distances:
37 1 0.01
38 21 0.16
39 56 0.44
40 48 0.38
41 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (39 bp):
AATCTTTTACCCTAACCATGGGGTAGATTGAAGCAATTC
Found at i:53235 original size:78 final size:79
Alignment explanation
Indices: 53070--53267 Score: 227
Period size: 78 Copynumber: 2.5 Consensus size: 79
53060 TTTTACCCTA
* * * *
53070 ACCATGGGGCAGAATGAAACAATTCAATCTTTTACCCTAACCAGAGGGGAGATTAAAGACCATCC
1 ACCATGGGGCAGATTGAAACAATTAAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACCATCA
53135 GATCGCTTACCCCG
66 GATCGCTTACCCCG
* * * * * * *
53149 ACCATGGGGTAGATTGAAGCAATTAAATCTTTTACCC-GACCATAAGGTAGATTGAAGACCGTCA
1 ACCATGGGGCAGATTGAAACAATTAAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACCATCA
* * *
53213 GATCTCTTACGCTG
66 GATCGCTTACCCCG
* * *
53227 ACCATGGGGCAGATAGAAAAAATTTAATCTTTTACCTCTAA
1 ACCATGGGGCAGATTGAAACAATTAAATCTTTTACC-CTAA
53268 AGCTATAGAG
Statistics
Matches: 97, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
78 62 0.64
79 34 0.35
80 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (79 bp):
ACCATGGGGCAGATTGAAACAATTAAATCTTTTACCCTAACCAGAAGGGAGATTAAAGACCATCA
GATCGCTTACCCCG
Found at i:53746 original size:14 final size:15
Alignment explanation
Indices: 53727--53756 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
53717 TTATTATTTT
53727 ATAAATAT-AAATAA
1 ATAAATATAAAATAA
53741 ATAAATATAAAATAA
1 ATAAATATAAAATAA
53756 A
1 A
53757 ATTAACCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
ATAAATATAAAATAA
Found at i:54853 original size:28 final size:28
Alignment explanation
Indices: 54791--54888 Score: 106
Period size: 29 Copynumber: 3.4 Consensus size: 28
54781 AAAAAATTCA
** *
54791 AATTTAACCTCTAAAATTTCCAAAAATTTA
1 AATTTAACC-CTAAACCTTCC-AAAATTTG
*
54821 AATTTAACCCTAATCCTTCCAAAATTTG
1 AATTTAACCCTAAACCTTCCAAAATTTG
* * *
54849 AATTTAACCCCAAACTTTCTAAAAATTTG
1 AATTTAACCCTAAACCTTC-CAAAATTTG
54878 AATTTAACCCT
1 AATTTAACCCT
54889 TAAATTTATC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
28 23 0.40
29 26 0.45
30 9 0.16
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (28 bp):
AATTTAACCCTAAACCTTCCAAAATTTG
Found at i:54973 original size:30 final size:30
Alignment explanation
Indices: 54723--54973 Score: 177
Period size: 30 Copynumber: 8.5 Consensus size: 30
54713 AAATTTTTTT
* * * *
54723 AAAATTGAAATTTGACCCCTAAATTTTCAA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
* * *
54753 AAAATTCAAATTTGATCCCTAAAATTTCAA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
*
54783 AAAATTCAAATTTAACCTCTAAAATTTCCA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
* ***
54813 AAAATTTAAATTTAA-CCCTAATCCTTCC-
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
** * *
54841 AAAATTTGAATTTAACCCC-AAACTTTCTA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
** * *
54870 AAAATTTGAATTTAA-CCCTTAAATTTATCA
1 AAAATTCAAATTTAACCCCTAAAATTT-CCA
** * *
54900 AAAATTCTGATTTGACCCCTAAACTTTCCA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
* ** ** * * *
54930 AATACACTGATTTAACCCCTGAAGTTCCCA
1 AAAATTCAAATTTAACCCCTAAAATTTCCA
54960 AAAATTCAAATTTA
1 AAAATTCAAATTTA
54974 GCCCGATTTT
Statistics
Matches: 177, Mismatches: 39, Indels: 10
0.78 0.17 0.04
Matches are distributed among these distances:
28 23 0.13
29 32 0.18
30 113 0.64
31 9 0.05
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCAAATTTAACCCCTAAAATTTCCA
Found at i:55028 original size:21 final size:20
Alignment explanation
Indices: 55004--55043 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
54994 TTTTATTTAT
55004 TTATTTTATCGTATATGTATA
1 TTATTTTATCGTAT-TGTATA
*
55025 TTATTTTATTGTATTGTAT
1 TTATTTTATCGTATTGTAT
55044 TTTTTGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (20 bp):
TTATTTTATCGTATTGTATA
Found at i:60261 original size:19 final size:20
Alignment explanation
Indices: 60222--60261 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
60212 CCTTAAGCAA
*
60222 ACCTCTACTCCTTTGATTCC
1 ACCTCTACTCCTTTCATTCC
*
60242 ACCTCTCCTCC-TTCATTCC
1 ACCTCTACTCCTTTCATTCC
60261 A
1 A
60262 AATATGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.15, C:0.45, G:0.03, T:0.38
Consensus pattern (20 bp):
ACCTCTACTCCTTTCATTCC
Done.