Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011963.1 Kokia drynarioides strain JFW-HI SEQ_126961, 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: 30461
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3833 original size:35 final size:36
Alignment explanation
Indices: 3794--3862 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
3784 TCATACTCCC
3794 TTTAAATTTATTTTAAATTAAATTT-GTTTAAAGAT
1 TTTAAATTTATTTTAAATTAAATTTAGTTTAAAGAT
*
3829 TTTAAATTTATTTTAAATTTAATTTAAGTTTAAA
1 TTTAAATTTATTTTAAATTAAATTT-AGTTTAAA
3863 ATTATTTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 24 0.77
37 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (36 bp):
TTTAAATTTATTTTAAATTAAATTTAGTTTAAAGAT
Found at i:3843 original size:11 final size:11
Alignment explanation
Indices: 3827--3860 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3817 TTGTTTAAAG
3827 ATTTTAAATTT
1 ATTTTAAATTT
3838 ATTTTAAATTT
1 ATTTTAAATTT
* *
3849 AATTTAAGTTT
1 ATTTTAAATTT
3860 A
1 A
3861 AAATTATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:4655 original size:17 final size:17
Alignment explanation
Indices: 4633--4667 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4623 CGGTTTTCAT
*
4633 AATATTTATTACTAATA
1 AATATTTATTAATAATA
*
4650 AATATTTTTTAATAATA
1 AATATTTATTAATAATA
4667 A
1 A
4668 TTTTAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTATTAATAATA
Found at i:4951 original size:20 final size:22
Alignment explanation
Indices: 4921--4962 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4911 AGGGAAAATC
*
4921 GTTTAGATCTAG-GCTAGATCT
1 GTTTAGATCTAGACCTAGATCT
4942 GTTT-GATCTAGACCTAGATCT
1 GTTTAGATCTAGACCTAGATCT
4963 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (22 bp):
GTTTAGATCTAGACCTAGATCT
Found at i:5803 original size:29 final size:29
Alignment explanation
Indices: 5754--6000 Score: 193
Period size: 29 Copynumber: 8.4 Consensus size: 29
5744 GAGGTCCCTA
* *
5754 AACTGTCCAAAAATTCTATTTTTACCCCCG
1 AACT-TCCAAAAATCCCATTTTTACCCCCG
5784 AACTTCCAAAAATCCCATTTTTGA--CCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* * **
5812 AACCTTCTAAAAATTACCA-NATTACCCCCG
1 AA-CTTCCAAAAA-TCCCATTTTTACCCCCG
* *
5842 AACTTCCAAAAATCCCATTTTTAACCTCG
1 AACTTCCAAAAATCCCATTTTTACCCCCG
* * *
5871 AACCTTCTAAACATTACCA-TTTTACCCCCG
1 AA-CTTCCAAA-AATCCCATTTTTACCCCCG
*
5901 AACTTCCAAAAATCTCATTTTTGA-CCCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
* * * *
5930 AACCTTCCGAAAATTACCA-TTTTACCCTCA
1 AA-CTTCC-AAAAATCCCATTTTTACCCCCG
*
5960 AACTTCCAAAAATCCCATTTTTGA-CTCCG
1 AACTTCCAAAAATCCCATTTTT-ACCCCCG
5989 AACCTTCCAAAA
1 AA-CTTCCAAAA
6001 CTACCATTAT
Statistics
Matches: 170, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
28 23 0.14
29 77 0.45
30 58 0.34
31 12 0.07
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.29
Consensus pattern (29 bp):
AACTTCCAAAAATCCCATTTTTACCCCCG
Found at i:5902 original size:59 final size:58
Alignment explanation
Indices: 5773--6017 Score: 332
Period size: 59 Copynumber: 4.2 Consensus size: 58
5763 AAAATTCTAT
5773 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCTAAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT-AAAATTACCA
** *
5831 NATTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTAAACATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAA-ATTACCA
* * *
5890 TTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACCCCGAACCTTCCGAAAATTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT-CTAAAATTACCA
* * * *
5949 TTTTACCCTCAAACTTCCAAAAATCCCATTTTTGA-CTCCGAACCTTCCAAAACTACCA
1 TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCT-CGAACCTTCTAAAATTACCA
* *
6007 TTATGCCCCCG
1 TTTTACCCCCG
6018 TGCATCCAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
58 55 0.34
59 105 0.64
60 4 0.02
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.29
Consensus pattern (58 bp):
TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAATTACCA
Found at i:10657 original size:4 final size:4
Alignment explanation
Indices: 10650--10688 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
10640 GGTATATATA
* * *
10650 TATG TATG TATG TATG TATG TATG TGTG TGTG TGTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
10689 TTTTTTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:23803 original size:14 final size:15
Alignment explanation
Indices: 23784--23812 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23774 ATTTTAAATA
23784 GATTTAAT-TTTTTG
1 GATTTAATATTTTTG
23798 GATTTAATATTTTTG
1 GATTTAATATTTTTG
23813 TTCGAATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
GATTTAATATTTTTG
Found at i:23979 original size:6 final size:6
Alignment explanation
Indices: 23968--23993 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23958 ATTATTTATG
23968 TATAAA TATAAA TATAAA TATAAA TA
1 TATAAA TATAAA TATAAA TATAAA TA
23994 ATATTACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:24256 original size:28 final size:28
Alignment explanation
Indices: 24223--24279 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
24213 AATAAAACAC
* *
24223 AATCATCCCACATTATAAATAAGATATG
1 AATCATCACACATTATAAATAACATATG
* * *
24251 AATCATGACACGTTATAAATGACATATG
1 AATCATCACACATTATAAATAACATATG
24279 A
1 A
24280 TGTAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (28 bp):
AATCATCACACATTATAAATAACATATG
Found at i:25063 original size:24 final size:24
Alignment explanation
Indices: 25036--25088 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
25026 AGAAAAAATT
*
25036 AATTTA-ATGATTTAAAATTATAAA
1 AATTTAGATGA-TTAAAATGATAAA
* *
25060 AA-TTAGATTATTAAAATGATGAA
1 AATTTAGATGATTAAAATGATAAA
25083 AATTTA
1 AATTTA
25089 TTTTTACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
AATTTAGATGATTAAAATGATAAA
Found at i:25846 original size:11 final size:10
Alignment explanation
Indices: 25831--25855 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25821 TTTTTTCCTA
25831 CTTTTTTTTT
1 CTTTTTTTTT
25841 CTTTTTTTTT
1 CTTTTTTTTT
25851 CTTTT
1 CTTTT
25856 AGTACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:28133 original size:15 final size:15
Alignment explanation
Indices: 28113--28146 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28103 CAAAATCAAT
*
28113 ATTTTTACGATATTC
1 ATTTTTACAATATTC
28128 ATTTTTACAATATTC
1 ATTTTTACAATATTC
28143 ATTT
1 ATTT
28147 CTTTGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTTTACAATATTC
Done.