Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010400.1 Kokia drynarioides strain JFW-HI SEQ_125281, 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: 51617
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1296 original size:6 final size:6
Alignment explanation
Indices: 1269--1373 Score: 62
Period size: 6 Copynumber: 18.5 Consensus size: 6
1259 ACTTTCAAAG
* * **
1269 TTTAAA TTT-AA TTTAAA -ATAAA TTTAAA TTTACA -TTAAA TCCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
1314 CTCAAA -ATAAA GTTTAAA TTTAAA -GTGAA TTTAAA TTTAAA --TAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
1359 TTTAGA TTTAAA TTT
1 TTTAAA TTTAAA TTT
1374 TAAAAAAATG
Statistics
Matches: 74, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
4 4 0.05
5 19 0.26
6 47 0.64
7 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:1300 original size:17 final size:17
Alignment explanation
Indices: 1271--1370 Score: 96
Period size: 17 Copynumber: 5.9 Consensus size: 17
1261 TTTCAAAGTT
1271 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
* *
1287 TAAATTTAAATTTACAT
1 TAAATTTAAATTTAAAA
** * *
1304 TAAATCCAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
1321 TAAAGTTTAAATTTAAAG
1 TAAA-TTTAAATTTAAAA
*
1339 TGAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
1355 TAAATTTAGATTTAAA
1 TAAATTTAAATTTAAA
1371 TTTTAAAAAA
Statistics
Matches: 64, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
16 20 0.31
17 33 0.52
18 11 0.17
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:1421 original size:16 final size:16
Alignment explanation
Indices: 1400--1433 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1390 ATTTTAAGTG
1400 TTGGGC-TCAACCAAAA
1 TTGGGCTTCAA-CAAAA
1416 TTGGGCTTCAACAAAA
1 TTGGGCTTCAACAAAA
1432 TT
1 TT
1434 TATTTGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (16 bp):
TTGGGCTTCAACAAAA
Found at i:2480 original size:389 final size:391
Alignment explanation
Indices: 1763--2544 Score: 1300
Period size: 389 Copynumber: 2.0 Consensus size: 391
1753 TATATATGTG
1763 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATATAATAATAGTAATTTACATGTTA
1 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATATAATAATAGTAATTTACATGTTA
1828 TTATTTACTATCATAAAAGATTAGCCCAAATTAAAAATGATTTAATTTTGTTAAACTTTATTGGG
66 TTATTTACTATCATAAAAGATTAGCCCAAATTAAAAATGATTTAATTTTGTTAAACTTTATTGGG
*
1893 CTTTAGTTATTATATAAAGTATAGGTCAAATATGTGTAGATACTTTAGTAACTAATTTCTAAATG
131 CTTTAGTTATTATATAAAGTATAGGTCAAATATGTGTAGATACTCTAGTAACTAATTTCTAAATG
* * *
1958 ATGATAGACTGATTAGAAATTAAATTTAATGTGCAAAAGTTATATATGTTGGATAAAATGGACTT
196 ATGATAGACTGATTAAAAATTAAAGTTAATGTGCAAAAGTTATATATGTTAGATAAAATGGACTT
*
2023 TATGGAAACTTTGAGACATATTCTCGATTGGTAAAGGGGAAAATTTGAATAATAAAATTATGGTT
261 TATGGAAACTTTGAGACATATTCTCGATTGGTAAAGGGGAAAATTTGAATAATAAAATTATAGTT
* * *
2088 TTATACTCTACTCCAT-G-ATATGCAATGATATATCATATGCTCAAAATGGTTGAGATGAATGAG
326 TTATACTCTACTCCATAGAATATACAACGATATATCATATACTCAAAATGGTTGAGATGAATGAG
2151 A
391 A
* *
2152 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATGTAATAATAGTAATTTACATTTTA
1 GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATATAATAATAGTAATTTACATGTTA
* *
2217 TTATTTACTATCATAAAAGATTAGTCCAAATTAAAAGTGATTTAATTTTGTTAAACTTTATTGGG
66 TTATTTACTATCATAAAAGATTAGCCCAAATTAAAAATGATTTAATTTTGTTAAACTTTATTGGG
*
2282 CTTTAGTTATTATATAAAGTATAGGTCAAATATGTGTAGATACTCTAGTAACTAATTTCTAATTG
131 CTTTAGTTATTATATAAAGTATAGGTCAAATATGTGTAGATACTCTAGTAACTAATTTCTAAATG
* **
2347 ATGATGGACTGATTAAAAATTAGGGTTAATGTGCAAAAGTTATATATGTTAGA-AAATATGGACT
196 ATGATAGACTGATTAAAAATTAAAGTTAATGTGCAAAAGTTATATATGTTAGATAAA-ATGGACT
* * * * *
2411 TTATGGAAACTTTGAGGCATATTCTCGATTGGTAAATGTGAAGATTTGAATCATAAAATTATAGT
260 TTATGGAAACTTTGAGACATATTCTCGATTGGTAAAGGGGAAAATTTGAATAATAAAATTATAGT
* * *
2476 TTTATATTCTACTCCATGAGACATTTACAACGGTATATCATATACTCAAAATGGTTGAGATGAAT
325 TTTATACTCTACTCCAT-AGA-ATATACAACGATATATCATATACTCAAAATGGTTGAGATGAAT
2541 GAGA
388 GAGA
2545 AATTGATTCT
Statistics
Matches: 364, Mismatches: 24, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
388 3 0.01
389 318 0.87
391 1 0.00
393 42 0.12
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (391 bp):
GTCCAAGTGGGAGATTGTTGGAAAATATGAACATCACATATATAATAATAGTAATTTACATGTTA
TTATTTACTATCATAAAAGATTAGCCCAAATTAAAAATGATTTAATTTTGTTAAACTTTATTGGG
CTTTAGTTATTATATAAAGTATAGGTCAAATATGTGTAGATACTCTAGTAACTAATTTCTAAATG
ATGATAGACTGATTAAAAATTAAAGTTAATGTGCAAAAGTTATATATGTTAGATAAAATGGACTT
TATGGAAACTTTGAGACATATTCTCGATTGGTAAAGGGGAAAATTTGAATAATAAAATTATAGTT
TTATACTCTACTCCATAGAATATACAACGATATATCATATACTCAAAATGGTTGAGATGAATGAG
A
Found at i:4017 original size:31 final size:31
Alignment explanation
Indices: 3947--4017 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
3937 AAAATTTATG
3947 TATTATTATATTAGATTATTTAAATAGCATT
1 TATTATTATATTAGATTATTTAAATAGCATT
* *
3978 AATCATTATATTA-ATTTATTTAAATA-CAATT
1 TATTATTATATTAGA-TTATTTAAATAGC-ATT
4009 TATTATTAT
1 TATTATTAT
4018 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (31 bp):
TATTATTATATTAGATTATTTAAATAGCATT
Found at i:5707 original size:31 final size:29
Alignment explanation
Indices: 5651--5708 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
5641 ATTTGTCTAC
5651 AAGATAAACATTAAATTAAATTTAATATT
1 AAGATAAACATTAAATTAAATTTAATATT
5680 AAGATAATCACATTAATATTAAA-TTAATA
1 AAGATAA--ACATTAA-ATTAAATTTAATA
5709 AATACTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.27
31 13 0.50
32 6 0.23
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
AAGATAAACATTAAATTAAATTTAATATT
Found at i:5760 original size:18 final size:18
Alignment explanation
Indices: 5737--5773 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5727 ATTAAATTAA
5737 TTTTTTATAA-ATGCTTAT
1 TTTTTTA-AATATGCTTAT
5755 TTTTTTAAATATGCTTAT
1 TTTTTTAAATATGCTTAT
5773 T
1 T
5774 ATATTATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTTTAAATATGCTTAT
Found at i:5815 original size:20 final size:20
Alignment explanation
Indices: 5790--5842 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5780 TATGGGACTA
**
5790 GTGGGGATGGAG-AGGGGTTG
1 GTGGGGATGGAGCA-GGGCAG
*
5810 GTGGGGATGGGGCAGGGCAG
1 GTGGGGATGGAGCAGGGCAG
5830 GTGGGGATGGAGC
1 GTGGGGATGGAGC
5843 GGGTACAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.15, C:0.06, G:0.64, T:0.15
Consensus pattern (20 bp):
GTGGGGATGGAGCAGGGCAG
Found at i:11730 original size:41 final size:42
Alignment explanation
Indices: 11685--11887 Score: 180
Period size: 41 Copynumber: 4.9 Consensus size: 42
11675 ATGTCTTAAG
11685 ATGAGCATGAGATTAT-ATTAAAGGAAGACTCAT-ATCTCGGA
1 ATGAGCATGAGATTATGATTAAAGGAAGACTCATGA-CTCGGA
* * *
11726 ATGAGCATGAGAATAT-ATTAAAGGAAGACTCATGTCTCGGG
1 ATGAGCATGAGATTATGATTAAAGGAAGACTCATGACTCGGA
* * * * * *
11767 GTGAGCATCAAATTATGTTTAAATGGAAGACTCGTGACTCAGA
1 ATGAGCATGAGATTATGATTAAA-GGAAGACTCATGACTCGGA
* * * * * *
11810 AAGAGTATGAGATTATGTTTTAAGGAAGACACATGACTCGGG
1 ATGAGCATGAGATTATGATTAAAGGAAGACTCATGACTCGGA
* * * *
11852 ATGAGCATTAAATT-TCATGTAAAGGAAGACTTATGA
1 ATGAGCATGAGATTATGAT-TAAAGGAAGACTCATGA
11888 TTTGGTTGTT
Statistics
Matches: 127, Mismatches: 31, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
41 51 0.40
42 44 0.35
43 32 0.25
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (42 bp):
ATGAGCATGAGATTATGATTAAAGGAAGACTCATGACTCGGA
Found at i:26732 original size:5 final size:5
Alignment explanation
Indices: 26722--26750 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
26712 AAAATATAGA
26722 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
26751 TATATACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:28970 original size:32 final size:32
Alignment explanation
Indices: 28929--28989 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
28919 TAAAAGGCAT
*
28929 AATTGATTATGGT-ATAAAGTTCAATCAAGCAC
1 AATTGATTAT-GTCATAAACTTCAATCAAGCAC
28961 AATTGATTATGTCATAAACTTCAATCAAG
1 AATTGATTATGTCATAAACTTCAATCAAG
28990 TTGAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (32 bp):
AATTGATTATGTCATAAACTTCAATCAAGCAC
Found at i:36986 original size:18 final size:19
Alignment explanation
Indices: 36958--36998 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
36948 TCTAAAGAAA
36958 GGACAAAAAAAGGGAAATG
1 GGACAAAAAAAGGGAAATG
36977 GGACAAAAAAAGGGAAATG
1 GGACAAAAAAAGGGAAATG
36996 GGA
1 GGA
36999 AGATGTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.05, G:0.34, T:0.05
Consensus pattern (19 bp):
GGACAAAAAAAGGGAAATG
Found at i:38433 original size:37 final size:37
Alignment explanation
Indices: 38351--38478 Score: 130
Period size: 37 Copynumber: 3.4 Consensus size: 37
38341 AGAATTTTTG
* * * *
38351 TAGAGAATCATTACTGTTCATCTTCGTTTTTTTCTTTG
1 TAGAGAATCATTATTATTCATCTTCG-TCTTTTCTTTA
* * *
38389 TAAAGAATCTTTATTATTCATCTCCGTCTTTTCTTTA
1 TAGAGAATCATTATTATTCATCTTCGTCTTTTCTTTA
* * * *
38426 TAGAGAATCATCATTATTCATTTTCGTCTTTTATCTTC
1 TAGAGAATCATTATTATTCATCTTCGTCTTTTCT-TTA
*
38464 TAGAGAATCTTTATT
1 TAGAGAATCATTATT
38479 GTTTGGCTTT
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 37 0.51
38 36 0.49
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.51
Consensus pattern (37 bp):
TAGAGAATCATTATTATTCATCTTCGTCTTTTCTTTA
Done.