Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010845.1 Kokia drynarioides strain JFW-HI SEQ_125812, 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: 24288
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Found at i:5161 original size:24 final size:24
Alignment explanation
Indices: 5092--5166 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
5082 AGAAATAATC
* **
5092 TTTCAGTTAAACTCTGTTTAACTG
1 TTTCAATTAAACTCTGTTTATTTG
*
5116 TTTCAATTAAACTCTGTCTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
5140 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
5164 TTT
1 TTT
5167 GAGTCAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:5178 original size:18 final size:18
Alignment explanation
Indices: 5155--5191 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5145 ATTAAACTCT
5155 ATTTATTTGTTTGAGTCA
1 ATTTATTTGTTTGAGTCA
5173 ATTTATTTGTTTGAGTCA
1 ATTTATTTGTTTGAGTCA
5191 A
1 A
5192 ACTCTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.16, T:0.54
Consensus pattern (18 bp):
ATTTATTTGTTTGAGTCA
Found at i:8102 original size:33 final size:32
Alignment explanation
Indices: 8041--8151 Score: 100
Period size: 33 Copynumber: 3.4 Consensus size: 32
8031 TCTACATAAG
* *
8041 TGATTGGAACATCTATCAACGCCGCTTCATCAA
1 TGATTGGAACATCTATC-AGGCAGCTTCATCAA
*
8074 TGATTGGAACATCTATCAGTGCAACTTCAT-AA
1 TGATTGGAACATCTATCAG-GCAGCTTCATCAA
* * *
8106 TTGA-TGCGAACATCTCTCAAGGCAGTTTCATCAT
1 -TGATTG-GAACATCTATC-AGGCAGCTTCATCAA
*
8140 TCATTGGAACAT
1 TGATTGGAACAT
8152 TTCTCGAGGG
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
32 5 0.08
33 54 0.84
34 5 0.08
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (32 bp):
TGATTGGAACATCTATCAGGCAGCTTCATCAA
Found at i:10487 original size:33 final size:33
Alignment explanation
Indices: 10368--10500 Score: 124
Period size: 33 Copynumber: 4.0 Consensus size: 33
10358 TCTACATAAG
* * *
10368 TGATTGGAACATTTATCAGTGTC-GCTTCATCAA
1 TGATTGGAACATCTATCAG-GGCAGCTTCATCAT
* *
10401 TGATTGGAACATCTATCAGTGCAACTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* ** *
10434 TGATTCGAACATCTCCCAGGGCAGTTTCATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
* * * * *
10467 TCATTGGAACATTTGTCAGGGCTGCTTGATCAT
1 TGATTGGAACATCTATCAGGGCAGCTTCATCAT
10500 T
1 T
10501 CTGTTTGACT
Statistics
Matches: 80, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
32 1 0.01
33 79 0.99
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (33 bp):
TGATTGGAACATCTATCAGGGCAGCTTCATCAT
Found at i:16375 original size:24 final size:24
Alignment explanation
Indices: 16289--16363 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
16279 AGAAATAATC
* *
16289 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTATTTG
* *
16313 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
16337 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
16361 TTT
1 TTT
16364 GAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:18335 original size:24 final size:24
Alignment explanation
Indices: 18307--18369 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
18297 AGAAATAATC
*
18307 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
*
18331 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTATTTG
* *
18355 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
18370 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTATTTG
Found at i:19482 original size:20 final size:20
Alignment explanation
Indices: 19457--19497 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19447 TATGAAATGT
*
19457 AATTTACAAAATCATAGCTA
1 AATTTACAAAACCATAGCTA
*
19477 AATTTATAAAACCATAGCTA
1 AATTTACAAAACCATAGCTA
19497 A
1 A
19498 GGCAATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (20 bp):
AATTTACAAAACCATAGCTA
Found at i:21047 original size:29 final size:29
Alignment explanation
Indices: 21015--21076 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
21005 AACGACGACA
*
21015 AGGGAGGATAGAAAGGGTGAACGGCAGCT
1 AGGGAGGATAGAAAGGGTGAACAGCAGCT
*
21044 AGGGAGGATAGAAAGGGTGAACAGCGGCT
1 AGGGAGGATAGAAAGGGTGAACAGCAGCT
21073 AGGG
1 AGGG
21077 GAGAAAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.47, T:0.10
Consensus pattern (29 bp):
AGGGAGGATAGAAAGGGTGAACAGCAGCT
Found at i:21199 original size:43 final size:43
Alignment explanation
Indices: 21151--21240 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
21141 TTGGTTATAT
* * *
21151 GGATAGGGTAAGGGAAAGAATGCGCTATTCTTATGTGGGATAG
1 GGATAGGGTAAGGGAAAGAATGCACTATTCCTATATGGGATAG
21194 GGATAGGGTAAGGGAAAGAATGCACTATTCCTATATGGGATAG
1 GGATAGGGTAAGGGAAAGAATGCACTATTCCTATATGGGATAG
21237 GGAT
1 GGAT
21241 TATGGGCAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (43 bp):
GGATAGGGTAAGGGAAAGAATGCACTATTCCTATATGGGATAG
Found at i:21282 original size:61 final size:61
Alignment explanation
Indices: 21207--21329 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
21197 TAGGGTAAGG
*
21207 GAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGATTGTTTAGTTGTAGT
1 GAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGACTGTTTAGTTGTAGT
*
21268 GAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGACTGTTTGGTTGTAGT
1 GAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGACTGTTTAGTTGTAGT
21329 G
1 G
21330 TGATTGTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.33
Consensus pattern (61 bp):
GAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGACTGTTTAGTTGTAGT
Found at i:21383 original size:80 final size:80
Alignment explanation
Indices: 21250--21409 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
21240 TTATGGGCAA
21250 TGATTGTTTAGTTGTAGTGAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGAC
1 TGATTGTTTAGTTGTAGTGAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGAC
21315 TGTTTGGTTGTAGTG
66 TGTTTGGTTGTAGTG
*
21330 TGATTGTTTAGTTGTAGTGAAAGAATGCACTATTCCTATGTGGGATAGGGATTATGGGCAATGAC
1 TGATTGTTTAGTTGTAGTGAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGAC
21395 TGTTTGGTTGTAGTG
66 TGTTTGGTTGTAGTG
21410 ATAAGGGTTT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.38
Consensus pattern (80 bp):
TGATTGTTTAGTTGTAGTGAAAGAATGCACTATTCCTATATGGGATAGGGATTATGGGCAATGAC
TGTTTGGTTGTAGTG
Done.