Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003971.1 Kokia drynarioides strain JFW-HI SEQ_117066, 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: 27208
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:802 original size:41 final size:41
Alignment explanation
Indices: 752--898 Score: 197
Period size: 41 Copynumber: 3.6 Consensus size: 41
742 GTTTTTTTAA
*
752 AAGCGTCGCTAATGGTCTGACCTTTAGCGACGTTTTCCCAC
1 AAGCGTCGCTAATGCTCTGACCTTTAGCGACGTTTTCCCAC
* * * *
793 AAGCATCGCTAATGCTTTGACCTTTAGCGACGTTTTACCAT
1 AAGCGTCGCTAATGCTCTGACCTTTAGCGACGTTTTCCCAC
* * * *
834 AAGCGTCGCTAATGCTCAGATCTTTAGCGATGCTTTCCCAC
1 AAGCGTCGCTAATGCTCTGACCTTTAGCGACGTTTTCCCAC
*
875 AAGCGTCGCTAATGCT-TTACCTTT
1 AAGCGTCGCTAATGCTCTGACCTTT
899 TGCGGCATTT
Statistics
Matches: 90, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 5 0.06
41 85 0.94
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (41 bp):
AAGCGTCGCTAATGCTCTGACCTTTAGCGACGTTTTCCCAC
Found at i:1085 original size:15 final size:14
Alignment explanation
Indices: 1065--1110 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
1055 CACATGTTTC
1065 TTTTCTCTCTCTTTT
1 TTTTCT-TCTCTTTT
*
1080 TTTTCTTCT-TTCT
1 TTTTCTTCTCTTTT
*
1093 TTTTCTTTTCTTTT
1 TTTTCTTCTCTTTT
1107 TTTT
1 TTTT
1111 TTAGGTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.41
14 10 0.37
15 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTCTTCTCTTTT
Found at i:1101 original size:18 final size:18
Alignment explanation
Indices: 1061--1112 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 18
1051 ACCTCACATG
*
1061 TTTCTTTTC-TCTCTC-T
1 TTTCTTTTCTTCTTTCTT
1077 TTT-TTTTCTTCTTTCTT
1 TTTCTTTTCTTCTTTCTT
1094 TTTCTTTTCTT-TTT-TT
1 TTTCTTTTCTTCTTTCTT
1110 TTT
1 TTT
1113 AGGTGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.16
16 13 0.41
17 7 0.22
18 7 0.22
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCTTTTCTTCTTTCTT
Found at i:1111 original size:15 final size:15
Alignment explanation
Indices: 1061--1111 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1051 ACCTCACATG
1061 TTTCTTTTCTCTCTCTTT
1 TTTCTTTTCT-T-T-TTT
*
1079 TTT-TTCTTCTTTCTT
1 TTTCTT-TTCTTTTTT
1094 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
1109 TTT
1 TTT
1112 TAGGTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 16 0.55
16 3 0.10
17 3 0.10
18 7 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTCTTTTTT
Found at i:1112 original size:11 final size:11
Alignment explanation
Indices: 1061--1111 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
1051 ACCTCACATG
*
1061 TTTCTTTTCTC
1 TTTCTTTTCTT
* *
1072 TCTCTTTTTTT
1 TTTCTTTTCTT
1083 TCTTC-TTTCTT
1 T-TTCTTTTCTT
1094 TTTCTTTTCTT
1 TTTCTTTTCTT
1105 TTT-TTTT
1 TTTCTTTT
1112 TAGGTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 7 0.21
11 24 0.73
12 2 0.06
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:2332 original size:120 final size:120
Alignment explanation
Indices: 2119--2358 Score: 426
Period size: 120 Copynumber: 2.0 Consensus size: 120
2109 ATATTTAAAA
* *
2119 TTATTAAAATCATTTTGGTCTTCGAAATCAAAAGAAAATGGGTTCGAGAGTCGGTTACGCATGAG
1 TTATTAAAATCATTTTGGTCTTCGAAATCAAAAGAAAATAGATTCGAGAGTCGGTTACGCATGAG
2184 GAAAGATTACCACCCTCATACGCCCAAAATTGATACCTAGTCGATTATTTGATGT
66 GAAAGATTACCACCCTCATACGCCCAAAATTGATACCTAGTCGATTATTTGATGT
* *
2239 TTATTAAAATCATTTTGGTCTTTGAAATCAAAAGAAAATAGATTCGGGAGTCGGTTACGCATGAG
1 TTATTAAAATCATTTTGGTCTTCGAAATCAAAAGAAAATAGATTCGAGAGTCGGTTACGCATGAG
* *
2304 GAAGGATTACCACCCTCATACGCCCAAAATTGGTACCTAGTCGATTATTTGATGT
66 GAAAGATTACCACCCTCATACGCCCAAAATTGATACCTAGTCGATTATTTGATGT
2359 CTTAGTATTG
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 114 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (120 bp):
TTATTAAAATCATTTTGGTCTTCGAAATCAAAAGAAAATAGATTCGAGAGTCGGTTACGCATGAG
GAAAGATTACCACCCTCATACGCCCAAAATTGATACCTAGTCGATTATTTGATGT
Found at i:2678 original size:109 final size:109
Alignment explanation
Indices: 2555--2752 Score: 292
Period size: 109 Copynumber: 1.8 Consensus size: 109
2545 CATTTATTTA
* * **
2555 TTTTAAATAAGATATTCAATTATTTAGG-TTCTAAGAAAAA-CTATACCCTGCACGTTAAGGCAC
1 TTTTAAATAAGATATTCAATTACTTAGGCTT-AAAGAAAAATC-ATACCCAACACGTTAAGGCAC
* * *
2618 AATTTTTTGAGTTCCCTAAAATAAAATAACATTGAACATTTATCGG
64 AATTTCTCGAATTCCCTAAAATAAAATAACATTGAACATTTATCGG
*
2664 TTTTAAATAGGATATTCAATTACTTAGGCTTAAAGAAAAATCATACCCAACACGTTAAGGCACAA
1 TTTTAAATAAGATATTCAATTACTTAGGCTTAAAGAAAAATCATACCCAACACGTTAAGGCACAA
2729 TTTCTCGAATTCCCTAAAATAAAA
66 TTTCTCGAATTCCCTAAAATAAAA
2753 GAAAATTGCC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
109 76 0.96
110 3 0.04
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (109 bp):
TTTTAAATAAGATATTCAATTACTTAGGCTTAAAGAAAAATCATACCCAACACGTTAAGGCACAA
TTTCTCGAATTCCCTAAAATAAAATAACATTGAACATTTATCGG
Found at i:7993 original size:21 final size:21
Alignment explanation
Indices: 7969--8010 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7959 TACTTTAGCC
*
7969 ATTTTTTATTTTTGT-TTTAAT
1 ATTTTTCATTTTT-TATTTAAT
7990 ATTTTTCATTTTTTATTTAAT
1 ATTTTTCATTTTTTATTTAAT
8011 TTTCTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTTTTCATTTTTTATTTAAT
Found at i:21555 original size:21 final size:21
Alignment explanation
Indices: 21531--21572 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
21521 TATTTTTACT
21531 AGAACTTG-AAACAAGATTATC
1 AGAA-TTGCAAACAAGATTATC
**
21552 AGAATTGCAAACCCGATTATC
1 AGAATTGCAAACAAGATTATC
21573 CTCATTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
AGAATTGCAAACAAGATTATC
Found at i:24948 original size:14 final size:13
Alignment explanation
Indices: 24922--24947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24912 TTTACCTATA
24922 GCTTTAATTTTTT
1 GCTTTAATTTTTT
24935 GCTTTAATTTTTT
1 GCTTTAATTTTTT
24948 TTTAACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
GCTTTAATTTTTT
Found at i:24976 original size:23 final size:23
Alignment explanation
Indices: 24940--24996 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
24930 TTTTTGCTTT
*
24940 AATT-TTTTTTTAACTCTTCAAC
1 AATTATTTTTGTAACTCTTCAAC
24962 AATTATTTTTGTAACTCTTCAAC
1 AATTATTTTTGTAACTCTTCAAC
* *
24985 CATTATATTTGT
1 AATTATTTTTGT
24997 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.53
Consensus pattern (23 bp):
AATTATTTTTGTAACTCTTCAAC
Done.