Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014727.1 Kokia drynarioides strain JFW-HI SEQ_129766, 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: 10314
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1429 original size:14 final size:15
Alignment explanation
Indices: 1410--1448 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1400 TTCATATTTT
1410 AAATAAAAAC-ATAA
1 AAATAAAAACTATAA
*
1424 AAATAAAAACTTTTAA
1 AAATAAAAAC-TATAA
1440 AAATAAAAA
1 AAATAAAAA
1449 AAATGTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
16 12 0.55
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAAAAACTATAA
Found at i:4784 original size:24 final size:24
Alignment explanation
Indices: 4702--4776 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
4692 AGAAATAATC
* *
4702 TTTCAATTAAACTCTGTTTATTTA
1 TTTCAATTAAACTCTGTTTAGTTG
4726 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
4750 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
4774 TTT
1 TTT
4777 GAGTTAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:6741 original size:24 final size:24
Alignment explanation
Indices: 6713--6763 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
6703 AGAAATAATC
*
6713 TTTCAGTTAAACTCTGTTTAT-TTG
1 TTTCAATTAAACTCTGTTT-TGTTG
6737 TTTCAATTAAACTCTGTTTTGTTG
1 TTTCAATTAAACTCTGTTTTGTTG
6761 TTT
1 TTT
6764 GAGTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTTGTTG
Found at i:8024 original size:15 final size:17
Alignment explanation
Indices: 8001--8033 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
7991 TATTGAAACT
8001 GAGATGCTTGAGA-AAG
1 GAGATGCTTGAGATAAG
8017 GAGA-GCTTGAGATAAG
1 GAGATGCTTGAGATAAG
8033 G
1 G
8034 TTGCAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.06, G:0.39, T:0.18
Consensus pattern (17 bp):
GAGATGCTTGAGATAAG
Found at i:8407 original size:15 final size:17
Alignment explanation
Indices: 8378--8410 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
8368 GGATGCTATT
8378 GAAACGGAGATGCTTGA
1 GAAACGGAGATGCTTGA
8395 GAAA-GGAGA-GCTTGA
1 GAAACGGAGATGCTTGA
8410 G
1 G
8411 CTAGGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.36, C:0.09, G:0.39, T:0.15
Consensus pattern (17 bp):
GAAACGGAGATGCTTGA
Found at i:8588 original size:383 final size:384
Alignment explanation
Indices: 7975--8744 Score: 1328
Period size: 383 Copynumber: 2.0 Consensus size: 384
7965 GAAGAAAAAA
*
7975 CATGGAAATAGGATGCTATTGAAACTGAGATGCTTGAGAAAGGAGAGCTTGAGATAAGGTTGCAA
1 CATGGAAATAGGATGCTATTGAAACGGAGATGCTTGAGAAAGGAGAGCTTGAGATAAGGTTGCAA
* *
8040 CTTGGGGATAATCAAGTTGAAGAAGAAGACTTCAATGACATGCCATTTAGGGGTACGCGACCAAT
66 CTTGGGGATAATCAAGTTGAAAAAGAAGACTTCAATGACATACCATTTAGGGGTACGCGACCAAT
* *
8105 TGTTAAAATTTACCGAAGATTAGAGGTAGCAACTCTTAAACCTATGAACTCCGAAGAAGCTGAAG
131 TGTTAAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCTATGAACTCCGAAGAAGCTGAAG
* *
8170 CAACAAAAGGCTTAAAAGAAGCTATGCAAGCTGAGTTGAATATGATTTGCAAGAACCAG-ATTTG
196 CAACAAAAGGCTTAAAAGAAGCTATGCAAGCTGAGTTAAATATGATTTGCAAGAACCAGAATATG
* *
8234 GGAACTTGTTGATAGGCCATCACACAAAAGGGTTATTAGCATCAAATGGGTGTTCAGAACCGAAC
261 GGAACTTGTTGATAGGCCATCACACAAAAGGGTTATTAGCATCAAATGGGTGTTCAAAACCAAAC
*
8299 TCAA-CGTTGATGGTTCACTCAACAGACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAGT
326 TCAATC-TCGATGGTTCACTCAACAGACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAGT
* * * *
8358 CATGGAAATGGGATGCTATTGAAACGGAGATGCTTGAGAAAGGAGAGCTTGAGCTAGGGTTGTAA
1 CATGGAAATAGGATGCTATTGAAACGGAGATGCTTGAGAAAGGAGAGCTTGAGATAAGGTTGCAA
* *
8423 CTTGGGGATAATCAAGTTGAAAAAGAAGACTTCAATGATATACCATTTAGGGGTACGCGACTAAT
66 CTTGGGGATAATCAAGTTGAAAAAGAAGACTTCAATGACATACCATTTAGGGGTACGCGACCAAT
* * *
8488 TGTTAAAATTTACCAAAGAGTAGAGGTAGCAACTTTTAAATCTGTGAACTCCGAAGAAGCTGAAG
131 TGTTAAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCTATGAACTCCGAAGAAGCTGAAG
* *
8553 CAACAAAAGGCTTGAAAGAAGCTATGCAAGCTGAGTTAAATATGATTTGTAAGAACCAGAATATG
196 CAACAAAAGGCTTAAAAGAAGCTATGCAAGCTGAGTTAAATATGATTTGCAAGAACCAGAATATG
8618 GGAACTTGTTGATAGGCCATCACACAAAAGGGTTATTAGCATCAAATGGGTGTTCAAAACCAAAC
261 GGAACTTGTTGATAGGCCATCACACAAAAGGGTTATTAGCATCAAATGGGTGTTCAAAACCAAAC
8683 TCAATCTCGATGGTTCACTCAACAGACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAGT
326 TCAATCTCGATGGTTCACTCAACAGACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAGT
8742 CAT
1 CAT
8745 CAATATGGGA
Statistics
Matches: 364, Mismatches: 21, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
383 237 0.65
384 126 0.35
385 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (384 bp):
CATGGAAATAGGATGCTATTGAAACGGAGATGCTTGAGAAAGGAGAGCTTGAGATAAGGTTGCAA
CTTGGGGATAATCAAGTTGAAAAAGAAGACTTCAATGACATACCATTTAGGGGTACGCGACCAAT
TGTTAAAATTTACCAAAGAGTAGAGGTAGCAACTCTTAAACCTATGAACTCCGAAGAAGCTGAAG
CAACAAAAGGCTTAAAAGAAGCTATGCAAGCTGAGTTAAATATGATTTGCAAGAACCAGAATATG
GGAACTTGTTGATAGGCCATCACACAAAAGGGTTATTAGCATCAAATGGGTGTTCAAAACCAAAC
TCAATCTCGATGGTTCACTCAACAGACCGAAGGCAAGACTGGTTGTAAAGAGTTTTAGT
Found at i:10082 original size:54 final size:54
Alignment explanation
Indices: 10000--10107 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
9990 AAACACCAGA
*
10000 ATGGCAAACTGTCATTTGGCGAACATGATAAACACTAGAAAAATGGCGAACTAT
1 ATGGCAAACTGTCATTTGGCGAACATGATAAACACCAGAAAAATGGCGAACTAT
*
10054 ATGGCAAACTGTCATTTGGTGAACATGATAAACACCAGAAAAATGGCGAACTAT
1 ATGGCAAACTGTCATTTGGCGAACATGATAAACACCAGAAAAATGGCGAACTAT
10108 GTAGCAGACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (54 bp):
ATGGCAAACTGTCATTTGGCGAACATGATAAACACCAGAAAAATGGCGAACTAT
Done.