Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009716.1 Kokia drynarioides strain JFW-HI SEQ_124435, 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: 12428
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:657 original size:29 final size:28
Alignment explanation
Indices: 614--783 Score: 146
Period size: 30 Copynumber: 5.8 Consensus size: 28
604 GGAGGTCCTT
614 AAACTTTCCAAAAATTACCATTTTACCCTC-
1 AAAC-TTCCAAAAA-TACCATTTTACCC-CG
*
644 AAACTTCCAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATACCA--TTTTACCCCG
* * * *
674 AACCTTCTAATAATTACCATTTTTACCCCT
1 AAACTTCCAA-AAATACCA-TTTTACCCCG
*
704 AAACTTCCAAAAATCCCATTTTGACCCCG
1 AAACTTCCAAAAATACCATTTT-ACCCCG
* * *
733 AACCTTTCAAAAATTACCAATTTACCCTCG
1 AAACTTCCAAAAA-TACCATTTTACCC-CG
*
763 -AACTTCCAAAAATCCCATTTT
1 AAACTTCCAAAAATACCATTTT
784 TGATTTCGAA
Statistics
Matches: 114, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
28 15 0.13
29 46 0.40
30 47 0.41
31 6 0.05
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATACCATTTTACCCCG
Found at i:668 original size:30 final size:29
Alignment explanation
Indices: 614--784 Score: 152
Period size: 29 Copynumber: 5.8 Consensus size: 29
604 GGAGGTCCTT
*
614 AAACTTTCCAAAAATTACCA-TTTTACCCTC-
1 AAAC-TTCCAAAAA-TCCCATTTTTACCC-CG
644 AAACTTCCAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCG
* * * * *
674 AACCTTCTAATAATTACCATTTTTACCCCT
1 AAACTTCCAA-AAATCCCATTTTTACCCCG
*
704 AAACTTCCAAAAATCCCATTTTGACCCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCG
* * * *
733 AACCTTTCAAAAATTACCA-ATTTACCCTCG
1 AAACTTCCAAAAA-TCCCATTTTTACCC-CG
763 -AACTTCCAAAAATCCCATTTTT
1 AAACTTCCAAAAATCCCATTTTT
785 GATTTCGAAC
Statistics
Matches: 113, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
28 8 0.07
29 55 0.49
30 44 0.39
31 6 0.05
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:785 original size:59 final size:59
Alignment explanation
Indices: 617--813 Score: 249
Period size: 59 Copynumber: 3.3 Consensus size: 59
607 GGTCCTTAAA
*
617 CTTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTTACCCCGAAC
1 CTTT-CAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
*
677 C-TTCTAATAATTACCATTTTTACCC-CTAAACTTCCAAAAATCCCA-TTTTGACCCCGAAC
1 CTTTC-AAAAATTACCA-TTTTACCCTC-AAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * ***
736 CTTTCAAAAATTACCAATTTACCCTCGAACTTCCAAAAATCCCATTTTTGATTTCGAAC
1 CTTTCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
795 C-TTCCAAAACTACCATTTT
1 CTTTCAAAAATTACCATTTT
814 GCCCCCCGTC
Statistics
Matches: 120, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
58 40 0.33
59 50 0.42
60 30 0.25
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
CTTTCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAAC
Found at i:5242 original size:17 final size:18
Alignment explanation
Indices: 5203--5246 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5193 ATGGATAGCA
* *
5203 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
5221 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
5238 TTTATTTGT
1 TTTATTTGT
5247 TAGTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:8047 original size:68 final size:68
Alignment explanation
Indices: 7937--8109 Score: 238
Period size: 68 Copynumber: 2.5 Consensus size: 68
7927 GTTAAATGCG
* * * *
7937 TGTCATTCGGTTGGATTAAAATCATGTTTCAATGGAAATTAGTTGTTATCCAAAGCTAGACATTT
1 TGTCATTAGGTTGGATTAAAATCATGTTTCAATTGAAATTAGTTGTTATCAAAAGCTAGACAATT
8002 CCA
66 CCA
* * * * * *
8005 TGTCATTTGGCTGGATTAAAATCATGTTTCAATTGAAGTTAGTTGTTGTCAAAAGTTGGACAATT
1 TGTCATTAGGTTGGATTAAAATCATGTTTCAATTGAAATTAGTTGTTATCAAAAGCTAGACAATT
8070 CCA
66 CCA
*
8073 TGTCATTAGGTTAGATTAAAATACATGTTTCAATTGA
1 TGTCATTAGGTTGGATTAAAAT-CATGTTTCAATTGA
8110 TGTTCCAGTG
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
68 78 0.85
69 14 0.15
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (68 bp):
TGTCATTAGGTTGGATTAAAATCATGTTTCAATTGAAATTAGTTGTTATCAAAAGCTAGACAATT
CCA
Found at i:9439 original size:68 final size:68
Alignment explanation
Indices: 9330--9502 Score: 222
Period size: 68 Copynumber: 2.5 Consensus size: 68
9320 GTTAAATGCG
* * * *
9330 TGTCATTCGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCCAAAGCTAG-ACAAT
1 TGTCATTAGGTTGGATTAAATTCATGTTTCAATTGAAGTTAGTTGTTATCAAAAG-TAGAACAAT
9394 TCCA
65 TCCA
* * * *
9398 TGTCATTTGGCTGGATTAAATTCATGTTTCAATTGAAGTTAGTTGTTGTCAAAAGTTGAACAATT
1 TGTCATTAGGTTGGATTAAATTCATGTTTCAATTGAAGTTAGTTGTTATCAAAAGTAGAACAATT
9463 CCA
66 CCA
** *
9466 TGTCATTAGGTTATATTAAAATACATGTTTCAATTGA
1 TGTCATTAGGTTGGATT-AAATTCATGTTTCAATTGA
9503 TGTTGCAGTG
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
67 2 0.02
68 71 0.78
69 18 0.20
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (68 bp):
TGTCATTAGGTTGGATTAAATTCATGTTTCAATTGAAGTTAGTTGTTATCAAAAGTAGAACAATT
CCA
Found at i:10803 original size:68 final size:68
Alignment explanation
Indices: 10723--10892 Score: 225
Period size: 68 Copynumber: 2.5 Consensus size: 68
10713 GTTAAATGCG
* *
10723 TGTCATTCGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCCAAAGCTAG-ACAAT
1 TGTCATTAGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAG-TAGAACAAT
10787 TCCA
65 TCCA
* * * * * *
10791 TGTCATTTGGTTGGATTAAATTCATGTTTCAATTGAAGTTAGTTGTTGTTAAAAGTTGAACAATT
1 TGTCATTAGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAGTAGAACAATT
10856 CCA
66 CCA
**
10859 TGTCATTAGGTTATATTAAAATACATGTTTCAAT
1 TGTCATTAGGTTGGATTAAAAT-CATGTTTCAAT
10893 TGATGTTGCA
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
67 2 0.02
68 76 0.85
69 11 0.12
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (68 bp):
TGTCATTAGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAGTAGAACAATT
CCA
Found at i:12183 original size:68 final size:68
Alignment explanation
Indices: 12095--12266 Score: 236
Period size: 68 Copynumber: 2.5 Consensus size: 68
12085 AAGTTAAATG
* *
12095 CATGTCATTTGGTTGGATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCCAAAGCTAGACAA
1 CATGTCATTTGGTTGAATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAGCTAGACAA
12160 TTC
66 TTC
* * * * *
12163 CATGTCATTTGGCTGAATTAAAATCATGTTTCAATTGAAGTTAGTTGTTGTCAAAAGTTGGACAA
1 CATGTCATTTGGTTGAATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAGCTAGACAA
12228 TTC
66 TTC
* * * *
12231 AATGTCATTAGGTTAAATTTAAATACATGTTTCAAT
1 CATGTCATTTGGTTGAATTAAAAT-CATGTTTCAAT
12267 AGATGTTACA
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
68 80 0.88
69 11 0.12
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (68 bp):
CATGTCATTTGGTTGAATTAAAATCATGTTTCAATGGAAGTTAGTTGTTATCAAAAGCTAGACAA
TTC
Done.