Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001829.1 Kokia drynarioides strain JFW-HI SEQ_113573, 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: 22144
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:920 original size:17 final size:15
Alignment explanation
Indices: 900--940 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
890 TTCATCTTGC
900 TTTCTTTTTTCTTCCTT
1 TTTCTTTTTTCTT-C-T
917 TTTCTTTTTTTCTTCT
1 TTTC-TTTTTTCTTCT
933 TTTCTTTT
1 TTTCTTTT
941 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 5 0.22
18 9 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:925 original size:18 final size:16
Alignment explanation
Indices: 900--940 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
890 TTCATCTTGC
900 TTTC-TTTTTTCTTCCTT
1 TTTCTTTTTTTCTT-C-T
917 TTTCTTTTTTTCTTCT
1 TTTCTTTTTTTCTTCT
933 TTTCTTTT
1 TTTCTTTT
941 CCCTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTCTTCT
Found at i:1029 original size:19 final size:18
Alignment explanation
Indices: 992--1033 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
982 CTTGACTTTC
992 TTTCTCTTTTTTTCTTCT
1 TTTCTCTTTTTTTCTTCT
1010 TCTTCTCTTTTTTT-TATCT
1 T-TTCTCTTTTTTTCT-TCT
1029 TTTCT
1 TTTCT
1034 TTTAATGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTCTTTTTTTCTTCT
Found at i:5730 original size:30 final size:29
Alignment explanation
Indices: 5696--5987 Score: 247
Period size: 30 Copynumber: 9.9 Consensus size: 29
5686 AATTTCAAAA
*
5696 AAAGTTTAGGGGTAAAAATGTAATTTTAGG
1 AAAGTTTAGGGGTCAAAATGTAATTTT-GG
* * *
5726 AAAGTTT--GGGTTAAAATGTGATTTCGG
1 AAAGTTTAGGGGTCAAAATGTAATTTTGG
*
5753 AGAAGTTT--GGGTCAAAATGTGATTTTTGG
1 A-AAGTTTAGGGGTCAAAATGT-AATTTTGG
* * *
5782 AATAG-TTAAGGGTTAAAATGTGATTTTGG
1 AA-AGTTTAGGGGTCAAAATGTAATTTTGG
* *
5811 AGAAGTTTAGGAGTTAAAATGTAATTTTGG
1 A-AAGTTTAGGGGTCAAAATGTAATTTTGG
**
5841 AAAAGTTTATTGGTCAAAATGTAATTTTGG
1 -AAAGTTTAGGGGTCAAAATGTAATTTTGG
** * *
5871 AAAAGTTTAAAGGTCAAAATATAATTTTGTA
1 -AAAGTTTAGGGGTCAAAATGTAATTTTG-G
* * * *
5902 AAAGTTTAAGGGTTTAAAATGAAATTTTAG
1 AAAGTTT-AGGGGTCAAAATGTAATTTTGG
5932 AGAAGTTT-GGGGTCAAAATGTAATTTTGG
1 A-AAGTTTAGGGGTCAAAATGTAATTTTGG
*
5961 AAAAG-TTAGGGGTCAAAATATAATTTT
1 -AAAGTTTAGGGGTCAAAATGTAATTTT
5988 CAAAGAAAAC
Statistics
Matches: 215, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.01
28 37 0.17
29 55 0.26
30 99 0.46
31 21 0.10
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTGG
Found at i:5862 original size:60 final size:60
Alignment explanation
Indices: 5697--5987 Score: 294
Period size: 60 Copynumber: 4.9 Consensus size: 60
5687 ATTTCAAAAA
* * * *
5697 AAGTTTAGGGGTAAAAATGTAATTTTAGG-AAAGTTT--GGGTTAAAATGTGATTTCGGAG
1 AAGTTTAGGAGTCAAAATGTAATTTT-GGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* * *
5755 AAGTTT-GG-GTCAAAATGTGATTTTTGGAATAG-TTAAGGGTTAAAATGTGATTTTGGAG
1 AAGTTTAGGAGTCAAAATGT-AATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* ** * *
5813 AAGTTTAGGAGTTAAAATGTAATTTTGGAAAAGTTTATTGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
* * * * *
5873 AAGTTTA-AAGGTCAAAATATAATTTTGTAAAAGTTTAAGGGTTTAAAATGAAATTTTAGAG
1 AAGTTTAGGA-GTCAAAATGTAATTTTGGAAAAGTTTAAGGG-TTAAAATGTAATTTTGGAG
* * * *
5934 AAGTTT-GGGGTCAAAATGTAATTTTGGAAAAG-TTAGGGGTCAAAATATAATTTT
1 AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTT
5988 CAAAGAAAAC
Statistics
Matches: 193, Mismatches: 30, Indels: 20
0.79 0.12 0.08
Matches are distributed among these distances:
56 13 0.07
57 10 0.05
58 45 0.23
59 20 0.10
60 84 0.44
61 21 0.11
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
AAGTTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAG
Found at i:5874 original size:15 final size:15
Alignment explanation
Indices: 5826--5874 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5816 TTTAGGAGTT
5826 AAAATGTAATTTTGG
1 AAAATGTAATTTTGG
5841 AAAA-GT--TTATTGG
1 AAAATGTAATT-TTGG
5854 TCAAAATGTAATTTTGG
1 --AAAATGTAATTTTGG
5871 AAAA
1 AAAA
5875 GTTTAAAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 2 0.07
15 12 0.43
16 2 0.07
17 4 0.14
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (15 bp):
AAAATGTAATTTTGG
Found at i:6253 original size:35 final size:35
Alignment explanation
Indices: 6207--6276 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
6197 TGATTCATTT
6207 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
1 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
6242 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
1 TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
6277 AATCCTATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (35 bp):
TCATTTTCCTCATTCTCTTCTTCAAAGAAAACCAA
Found at i:8381 original size:19 final size:19
Alignment explanation
Indices: 8354--8404 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
8344 CTTAAAAACT
*
8354 AAAATTTAAATTATTATTA
1 AAAAATTAAATTATTATTA
*
8373 AAAAATTAAATTATTCTTA
1 AAAAATTAAATTATTATTA
8392 AACAAA-TAAATTA
1 AA-AAATTAAATTA
8405 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 26 0.90
20 3 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAATTAAATTATTATTA
Found at i:12689 original size:22 final size:22
Alignment explanation
Indices: 12664--12708 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12654 TAATTAGGTG
12664 GAGCAACCTTGGATGAAATAGA
1 GAGCAACCTTGGATGAAATAGA
*
12686 GAGCATCCTTGGATGAAATAGA
1 GAGCAACCTTGGATGAAATAGA
12708 G
1 G
12709 GGTATCGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (22 bp):
GAGCAACCTTGGATGAAATAGA
Found at i:21428 original size:13 final size:13
Alignment explanation
Indices: 21388--21428 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
21378 GTTTTCGAAA
21388 AAAGTCAACGATC
1 AAAGTCAACGATC
* * *
21401 AAAGTTAATGGTC
1 AAAGTCAACGATC
21414 AAAGTCAACGATC
1 AAAGTCAACGATC
21427 AA
1 AA
21429 CGGTTGGTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (13 bp):
AAAGTCAACGATC
Done.