Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014017.1 Kokia drynarioides strain JFW-HI SEQ_129048, 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: 8155
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:28 original size:17 final size:17
Alignment explanation
Indices: 2--69 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
1 C
*
2 TTAAATTAAATTTAAAT
1 TTAAAATAAATTTAAAT
19 TTAAAATAAATTTAAAAT
1 TTAAAATAAATTT-AAAT
* * *
37 TTTAAACAAATTTAATT
1 TTAAAATAAATTTAAAT
54 TTAAAATAAATTTAAA
1 TTAAAATAAATTTAAA
70 GAGAGTTTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 28 0.65
18 15 0.35
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAATAAATTTAAAT
Found at i:1108 original size:205 final size:204
Alignment explanation
Indices: 481--1152 Score: 827
Period size: 206 Copynumber: 3.3 Consensus size: 204
471 TTTCATCAAG
* * * * *
481 ATTTGGTTCACTTCTCTGTATCTGATCAGGGAGCTAACCACTTTATGGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACC-GTTTATTGCTTCGACCTGCTTCTCA
* * * *
546 GCGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGTTTTGAGCCT-CGTTTG---GGTCTTC
65 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCGTGGGTTTGATTGGTCTTC
* ** * * *
607 TTCTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCATC
130 TTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATTCGCTTCTCTGTATCTCACC
*
672 AGGAAGGCGA
195 AGGAAGACGA
* * * * *
682 ATTTGGTTCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTATTACTTTGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAG
* * *
747 TATCTTC-TCAGGAAGCTGGGGTTCGAAGATTTTGTTCGCTTTGAGCGTGGGTTCGATTTGGT-T
66 TGTC-TCATCAGGAAGCTGGGGTTCGAAGA-TTTGCTCGCTTTGAGCGTGGGTTTGA-TTGGTCT
* * * * * * *
810 CTCTTCCCAGTATCTCGTCAGAAAGATGACCGTATCGCTTGTTTCAATCCACCTCTCTGTATCTT
128 -TCTTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATTCGCTTCTCTGTATCTC
875 ACCAGGAAGACGA
192 ACCAGGAAGACGA
* * * * *
888 ATTTGATTTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTCCGATCTGCTTCTCGG
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAG
* * *
953 TGTCTCATCAGGAAGCTGGGATTCGAAGACTTT-CTCACTTCGAGCGTGGGTTTGACTTGGTCTT
66 TGTCTCATCAGGAAGCTGGGGTTCGAAGA-TTTGCTCGCTTTGAGCGTGGGTTTGA-TTGGTCTT
* * *
1017 CTTCTCAGTATCTCATCAGGAAGATGACTGTATAGCTTGTTTCAATTCGCTTCTTTGTATCTCAC
129 CTTCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATTCGCTTCTCTGTATCTCAC
1082 CAGGAAGACGA
194 CAGGAAGACGA
* * *
1093 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACTGTTTATTGCTTCAATCTGCTT
1 ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTTCGACCTGCTT
1153 TAAGCTGGGA
Statistics
Matches: 399, Mismatches: 62, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
200 46 0.12
201 52 0.13
202 4 0.01
205 148 0.37
206 149 0.37
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (204 bp):
ATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCTTTGAGCGTGGGTTTGATTGGTCTTCT
TCTCAGTATCTCATCAGGAAGATGACCGTATCGCTTGTTTCAATTCGCTTCTCTGTATCTCACCA
GGAAGACGA
Found at i:1763 original size:27 final size:27
Alignment explanation
Indices: 1731--1790 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
1721 TCAAAAATTT
*
1731 TATTAAGAAGAGGATCAAAAGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
*
1758 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
1785 TCATTA
1 T-ATTA
1791 GTTGAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAAGAAACAA
Found at i:3955 original size:48 final size:48
Alignment explanation
Indices: 3884--3980 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
3874 TATAGGCTCA
*
3884 TAGTCTTCTAAAGCCCTACTTGCCAGGAAGTCTGCTATCGCACTTCCT
1 TAGTCTTCTAAAGCCCTACTTGCCAAGAAGTCTGCTATCGCACTTCCT
3932 TAGTCTTCTAAAGCCCTACTTGCCAAGAAGTCTGCTATCGCACTTCCT
1 TAGTCTTCTAAAGCCCTACTTGCCAAGAAGTCTGCTATCGCACTTCCT
3980 T
1 T
3981 TTATTACTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (48 bp):
TAGTCTTCTAAAGCCCTACTTGCCAAGAAGTCTGCTATCGCACTTCCT
Found at i:3963 original size:27 final size:26
Alignment explanation
Indices: 3885--3964 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 26
3875 ATAGGCTCAT
3885 AGTCTTCTAAAGCCCTACTTGCCAGGA
1 AGTCTTCTAAAGCCCTACTTGCCA-GA
* * * **
3912 AGTCTGCT--ATCGC-ACTT-CC-TT
1 AGTCTTCTAAAGCCCTACTTGCCAGA
3933 AGTCTTCTAAAGCCCTACTTGCCAAGA
1 AGTCTTCTAAAGCCCTACTTGCC-AGA
3960 AGTCT
1 AGTCT
3965 GCTATCGCAC
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
21 7 0.19
23 5 0.14
24 8 0.22
25 5 0.14
27 12 0.32
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (26 bp):
AGTCTTCTAAAGCCCTACTTGCCAGA
Done.