Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014670.1 Kokia drynarioides strain JFW-HI SEQ_129709, 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: 41389
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:6448 original size:63 final size:65
Alignment explanation
Indices: 6375--6506 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 65
6365 ATTGTGTAGC
** *
6375 CTGGTTCATCTGGTGACAAAGATTTGTATATTTCTATAGATGAAACCAAG-TTTTG-TTGAATGT
1 CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
* * * * *
6438 CTGGTTCATCTAATGACAAAGATTTTTATGTTTCAATTGATGAAACTAAGTTTTTGTTTGAATTT
1 CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
6503 CTGG
1 CTGG
6507 ATTGTAGCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 43 0.73
64 5 0.08
65 11 0.19
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (65 bp):
CTGGTTCATCTAATGACAAAGATTTGTATATTTCAATAGATGAAACCAAGTTTTTGTTTGAATGT
Found at i:11014 original size:6 final size:6
Alignment explanation
Indices: 11003--11033 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
10993 TCCAATCTCC
*
11003 ATTTTT ATTTTT ATTTAT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
11034 AAAATTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:20775 original size:35 final size:34
Alignment explanation
Indices: 20729--20829 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 34
20719 AATCCAAATA
20729 AACAGCAAAACATTTCAAATATGCAAGTAAAAGCC
1 AACAGCAAAACATTTCAAA-ATGCAAGTAAAAGCC
* **
20764 AACAGCAAAACATTAT-AAACATGCAAATAGCAG-C
1 AACAGCAAAACATT-TCAAA-ATGCAAGTAAAAGCC
* *
20798 -ACAGGAAAACATTACAAAATGCAAGTAAAAGC
1 AACAGCAAAACATTTCAAAATGCAAGTAAAAGC
20830 AAATGGGTAA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
32 10 0.19
33 15 0.28
34 1 0.02
35 27 0.50
36 1 0.02
ACGTcount: A:0.53, C:0.19, G:0.13, T:0.15
Consensus pattern (34 bp):
AACAGCAAAACATTTCAAAATGCAAGTAAAAGCC
Found at i:24258 original size:3 final size:3
Alignment explanation
Indices: 24250--24277 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
24240 CGGAATGCAG
24250 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
24278 TTTTTAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:30076 original size:28 final size:29
Alignment explanation
Indices: 30015--30080 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
30005 TTTTCTCATT
* *
30015 TTGGTACCTAAACTCTTTTTTTGTTATAA
1 TTGGTACCTAAACTATTTTTTTCTTATAA
* *
30044 ATGGTACCTAAACTATTTTTTTCTTA-AG
1 TTGGTACCTAAACTATTTTTTTCTTATAA
30072 TTGGTACCT
1 TTGGTACCT
30081 TTGTGGTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.48
Consensus pattern (29 bp):
TTGGTACCTAAACTATTTTTTTCTTATAA
Found at i:35021 original size:59 final size:57
Alignment explanation
Indices: 34958--35207 Score: 244
Period size: 59 Copynumber: 4.3 Consensus size: 57
34948 AGACATTTAG
34958 GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTCGA
1 GGGTAAAAT-GTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTT-GA
* * * * * *
35017 GGGTAAAAATGTAATTTTTGGTGAAATCGAGGCCAAAAATGTAATTTTAGAAACTTCGA
1 GGGT-AAAATGTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTT-GA
* * * * *
35076 GGGTAAAATGGTAA-TTTTGGCGAAATAGGGGTTAAAAATGAAATTTTGGAAAGTTTA
1 GGGTAAAAT-GTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTGA
*
35133 GGGTAAAATTGTAA-TTTT-G-GAAAGTTTAGGGG-C--AAATGGTAATTTTGGAAAGTTTA
1 GGGTAAAA-TGTAATTTTTGGTGAAA--TT-GGGGTCAAAAATGG-AATTTTGGAAAGTTGA
35189 GGGGTAAAATGTAATTTTT
1 -GGGTAAAATGTAATTTTT
35208 AAGAAGTTTA
Statistics
Matches: 164, Mismatches: 18, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
55 9 0.05
56 22 0.13
57 30 0.18
58 43 0.26
59 55 0.34
60 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTGGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTGA
Found at i:35136 original size:29 final size:28
Alignment explanation
Indices: 34987--35264 Score: 185
Period size: 28 Copynumber: 9.6 Consensus size: 28
34977 GGTGAAATTG
* *
34987 GGGTCAAAAATGGAATTTTGGAAAGTTCGA
1 GGGT-AAAAATGTAATTTTGGAAAGTT-TA
**
35017 GGGTAAAAATGTAATTTTTGGTGAAA-TCGA
1 GGGTAAAAATGTAA-TTTT-G-GAAAGTTTA
** * * *
35047 GGCCAAAAATGTAATTTTAGAAACTTCGA
1 GGGTAAAAATGTAATTTTGGAAAGTT-TA
35076 GGGT-AAAATGGTAATTTTGGCGAAA---TA
1 GGGTAAAAAT-GTAATTTT-G-GAAAGTTTA
*
35103 GGGGTTAAAAATGAAATTTTGGAAAGTTTA
1 -GGG-TAAAAATGTAATTTTGGAAAGTTTA
*
35133 GGGTAAAATTGTAATTTTGGAAAGTTTA
1 GGGTAAAAATGTAATTTTGGAAAGTTTA
**
35161 GGG-GCAAATGGTAATTTTGGAAAGTTTA
1 GGGTAAAAAT-GTAATTTTGGAAAGTTTA
**
35189 GGGGT-AAAATGTAATTTTTAAGAAGTTTA
1 -GGGTAAAAATGTAATTTTGGA-AAGTTTA
* *
35218 GGGGTAAAAATGTAATTTTTAGAAAGTTTG
1 -GGGTAAAAATGTAA-TTTTGGAAAGTTTA
*
35248 GTGGT-AAAATATAATTT
1 G-GGTAAAAATGTAATTT
35265 CTAGATAATT
Statistics
Matches: 204, Mismatches: 23, Indels: 44
0.75 0.08 0.16
Matches are distributed among these distances:
27 12 0.06
28 66 0.32
29 64 0.31
30 47 0.23
31 11 0.05
32 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTTGGAAAGTTTA
Found at i:35202 original size:56 final size:57
Alignment explanation
Indices: 34953--35264 Score: 194
Period size: 59 Copynumber: 5.4 Consensus size: 57
34943 TTTTTAGACA
** * *
34953 TTTAGGGGTAAAATGGTAATTTTTGGTGAA-ATT-GGGGTCAAAAATGGAATTTTGGAAAG
1 TTTAGGGGTAAAAT-GTAA-TTTTGAAGAAGTTTAGGGG--AAAAATGTAATTTTGGAAAG
* ** * ** ** *
35012 -TTCGAGGGTAAAAATGTAATTTTTGGTGAAATCGAGGCCAAAAATGTAATTTTAGAAA-
1 TTTAG-GGGT-AAAATGTAA-TTTTGAAGAAGTTTAGGGGAAAAATGTAATTTTGGAAAG
* * ** * *
35070 CTTCGAGGGTAAAATGGTAATTTTGGCGAA--ATAGGGGTTAAAAATGAAATTTTGGAAAG
1 TTTAG-GGGTAAAAT-GTAATTTTGAAGAAGTTTAGGGG--AAAAATGTAATTTTGGAAAG
* *
35129 TTTA-GGGTAAAATTGTAATTTTGGA-AAGTTTAGGGG-CAAATGGTAATTTTGGAAAG
1 TTTAGGGGTAAAA-TGTAATTTTGAAGAAGTTTAGGGGAAAAAT-GTAATTTTGGAAAG
* *
35185 TTTAGGGGTAAAATGTAATTTTTAAGAAGTTTAGGGGTAAAAATGTAATTTTTAGAAAG
1 TTTAGGGGTAAAATGTAATTTTGAAGAAGTTTAGGGG-AAAAATGTAA-TTTTGGAAAG
*
35244 TTT-GGTGGTAAAATATAATTT
1 TTTAGG-GGTAAAATGTAATTT
35265 CTAGATAATT
Statistics
Matches: 208, Mismatches: 26, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
55 4 0.02
56 32 0.15
57 37 0.18
58 47 0.23
59 81 0.39
60 5 0.02
61 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (57 bp):
TTTAGGGGTAAAATGTAATTTTGAAGAAGTTTAGGGGAAAAATGTAATTTTGGAAAG
Found at i:35230 original size:30 final size:28
Alignment explanation
Indices: 34953--35264 Score: 189
Period size: 29 Copynumber: 10.8 Consensus size: 28
34943 TTTTTAGACA
34953 TTTAGGGGTAAAATGGTAATTTTTGGTGAAA-
1 TTTAGGGGTAAAAT-GTAA-TTTT-G-GAAAG
*
34984 -TT-GGGGTCAAAAATGGAATTTTGGAAAG
1 TTTAGGGGT--AAAATGTAATTTTGGAAAG
*
35012 -TTCGAGGGTAAAAATGTAATTTTTGGTGAAA-
1 TTTAG-GGGT-AAAATGTAA-TTTT-G-GAAAG
** *** *
35043 TCGAGGCCAAAAATGTAATTTTAGAAA-
1 TTTAGGGGTAAAATGTAATTTTGGAAAG
* *
35070 CTTCGAGGGTAAAATGGTAATTTTGGCGAAA-
1 TTTAG-GGGTAAAAT-GTAATTTT-G-GAAAG
*
35101 --TAGGGGTTAAAAATGAAATTTTGGAAAG
1 TTTAGGGG-T-AAAATGTAATTTTGGAAAG
35129 TTTA-GGGTAAAATTGTAATTTTGGAAAG
1 TTTAGGGGTAAAA-TGTAATTTTGGAAAG
*
35157 TTTAGGGG-CAAATGGTAATTTTGGAAAG
1 TTTAGGGGTAAAAT-GTAATTTTGGAAAG
**
35185 TTTAGGGGTAAAATGTAATTTTTAAGAAG
1 TTTAGGGGTAAAATGTAATTTTGGA-AAG
*
35214 TTTAGGGGTAAAAATGTAATTTTTAGAAAG
1 TTTAGGGGT-AAAATGTAA-TTTTGGAAAG
*
35244 TTT-GGTGGTAAAATATAATTT
1 TTTAGG-GGTAAAATGTAATTT
35265 CTAGATAATT
Statistics
Matches: 228, Mismatches: 27, Indels: 55
0.74 0.09 0.18
Matches are distributed among these distances:
27 18 0.08
28 69 0.30
29 73 0.32
30 47 0.21
31 16 0.07
32 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (28 bp):
TTTAGGGGTAAAATGTAATTTTGGAAAG
Found at i:36364 original size:3 final size:3
Alignment explanation
Indices: 36358--36397 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
36348 TTATAAATAT
*
36358 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTCA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
36398 ATGCTATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:39920 original size:44 final size:44
Alignment explanation
Indices: 39831--39918 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
39821 TAGTGTCGAG
* * *
39831 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
39875 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
39919 TTCAAGGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Done.