Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007458.1 Kokia drynarioides strain JFW-HI SEQ_122079, 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: 9744
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Found at i:857 original size:20 final size:20
Alignment explanation
Indices: 834--881 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
824 GCAATGGCAA
*
834 GTTGCTGGTGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
854 GTTGCTGATGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
874 GTTGCTGA
1 GTTGCTGA
882 CGTGGCGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.15, G:0.38, T:0.35
Consensus pattern (20 bp):
GTTGCTGATGGTGCAACTTG
Found at i:1089 original size:17 final size:17
Alignment explanation
Indices: 1069--1154 Score: 95
Period size: 17 Copynumber: 5.0 Consensus size: 17
1059 CAATATTGAG
*
1069 TTTAAAAC-CATTTCAAA
1 TTTAAAACAAATTT-AAA
1086 TTT-AAACTAAATTTAAA
1 TTTAAAAC-AAATTTAAA
1103 TTTAAAACAAATTTAAA
1 TTTAAAACAAATTTAAA
*
1120 TTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAA
* *
1137 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
16 4 0.06
17 38 0.61
18 20 0.32
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
TTTAAAACAAATTTAAA
Found at i:1104 original size:6 final size:6
Alignment explanation
Indices: 1078--1182 Score: 60
Period size: 6 Copynumber: 18.2 Consensus size: 6
1068 GTTTAAAACC
* **
1078 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * *
1125 A-ATAA ATTTAA ATTCAA GA-ATAA ATTTAA A-ATGA ATTTAA ACTT-A
1 ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
1170 ATATAA ATTTAA A
1 ATTTAA ATTTAA A
1183 AATCGAAAGT
Statistics
Matches: 71, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
5 18 0.25
6 48 0.68
7 5 0.07
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (6 bp):
ATTTAA
Found at i:1107 original size:34 final size:34
Alignment explanation
Indices: 1069--1154 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1059 CAATATTGAG
* *
1069 TTTAAAAC-CATTTCAAATTTAAACTAAATTTAAA
1 TTTAAAACAAATTT-AAATTTAAAATAAATTTAAA
1103 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
* *
1137 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 31 0.67
35 15 0.33
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
Found at i:1182 original size:17 final size:17
Alignment explanation
Indices: 1078--1154 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
1068 GTTTAAAACC
*
1078 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
*
1096 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAATAA
1113 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
1130 ATTTAAATTCAAGAATAA
1 ATTTAAATTTAA-AATAA
1148 ATTTAAA
1 ATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
17 38 0.70
18 16 0.30
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1185 original size:29 final size:29
Alignment explanation
Indices: 1116--1183 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
1106 AAAACAAATT
1116 TAAATTTAAAATAAATTTAAATTCAAGAA
1 TAAATTTAAAATAAATTTAAATTCAAGAA
* *
1145 TAAATTTAAAATGAATTTAAACTT-AA-TA
1 TAAATTTAAAATAAATTTAAA-TTCAAGAA
1173 TAAATTTAAAA
1 TAAATTTAAAA
1184 ATCGAAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 12 0.33
29 22 0.61
30 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTTAAAATAAATTTAAATTCAAGAA
Found at i:1665 original size:24 final size:23
Alignment explanation
Indices: 1630--1680 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
1620 TAAGAGTGTT
*
1630 AAATTAAAAAATAAAACAAAATA
1 AAATGAAAAAATAAAACAAAATA
**
1653 AAATGAAACAAATAAAGTAAAATA
1 AAATGAAA-AAATAAAACAAAATA
1677 AAAT
1 AAAT
1681 ATTGTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATGAAAAAATAAAACAAAATA
Found at i:5274 original size:24 final size:24
Alignment explanation
Indices: 5241--5288 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5231 ATGTGACTCG
*
5241 ATTGTACAATGATAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
* **
5265 ATTGTGCAATTCCAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
5289 CTAAAGGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
ATTGTACAATGACAGTAGCAGCCA
Found at i:7792 original size:21 final size:22
Alignment explanation
Indices: 7766--7808 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7756 ATCTTCCTTT
*
7766 TAATACTTG-TTTTTATGTTCA
1 TAATACTTGCTTTTTATCTTCA
7787 TAATACTTGCTTTTTATCTTCA
1 TAATACTTGCTTTTTATCTTCA
7809 ACATTTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TAATACTTGCTTTTTATCTTCA
Found at i:8384 original size:18 final size:17
Alignment explanation
Indices: 8346--8384 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
8336 GCTATCTTAG
**
8346 TTTTCCCTTTTTTTGGT
1 TTTTCCCTTTTTTTGCA
8363 TTTTCCCTTTTTCTTGCA
1 TTTTCCCTTTTT-TTGCA
8381 TTTT
1 TTTT
8385 GAGCTTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTTCCCTTTTTTTGCA
Found at i:9046 original size:20 final size:21
Alignment explanation
Indices: 9021--9060 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9011 TTCATTTTTA
*
9021 GCATTTT-TAACTTAGTGATT
1 GCATTTTCTAACTCAGTGATT
9041 GCATTTTCTAACTCAGTGAT
1 GCATTTTCTAACTCAGTGAT
9061 GCTCGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGATT
Done.