Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013536.1 Kokia drynarioides strain JFW-HI SEQ_128562, 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: 14604
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Found at i:986 original size:6 final size:6
Alignment explanation
Indices: 967--1057 Score: 57
Period size: 6 Copynumber: 15.5 Consensus size: 6
957 AAATCCATTC
** * **
967 AAATTT -AA-TT AAATTT AAATTT AAA-GC AAATTT AAATTAAA AAAGAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT--T AAATTT
**
1014 AAATTT AAATTT AACA--T AAATTT AAATTT AAAAAT AAATTT AAA
1 AAATTT AAATTT AA-ATTT AAATTT AAATTT AAATTT AAATTT AAA
1058 CCAATTTAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
4 3 0.05
5 10 0.16
6 46 0.73
7 1 0.02
8 3 0.05
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (6 bp):
AAATTT
Found at i:999 original size:17 final size:17
Alignment explanation
Indices: 967--1057 Score: 87
Period size: 17 Copynumber: 5.2 Consensus size: 17
957 AAATCCATTC
*
967 AAATTT-AATTAAATTT
1 AAATTTAAAGTAAATTT
*
983 AAATTTAAAGCAAATTT
1 AAATTTAAAGTAAATTT
*
1000 AAATTAAAAAAGATAAATTT
1 AAATT--TAAAG-TAAATTT
1020 AAATTTAACA-TAAATTT
1 AAATTTAA-AGTAAATTT
*
1037 AAATTTAAAAATAAATTT
1 AAATTT-AAAGTAAATTT
1055 AAA
1 AAA
1058 CCAATTTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.10
17 27 0.43
18 14 0.22
19 5 0.08
20 11 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTTAAAGTAAATTT
Found at i:1021 original size:37 final size:35
Alignment explanation
Indices: 976--1057 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
966 CAAATTTAAT
976 TAAATTTAAATTTAA-AGCAAATTTAAATTAAAAAAGA
1 TAAATTTAAATTTAACA-CAAATTTAAATT-AAAAA-A
* *
1013 TAAATTTAAATTTAACATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAACACAAATTTAAATTAAAAAA
1048 TAAATTTAAA
1 TAAATTTAAA
1058 CCAATTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 11 0.26
36 4 0.10
37 26 0.62
38 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (35 bp):
TAAATTTAAATTTAACACAAATTTAAATTAAAAAA
Found at i:7694 original size:14 final size:14
Alignment explanation
Indices: 7675--7703 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7665 ATATGTTTCA
7675 TTCATTAGTGCGCT
1 TTCATTAGTGCGCT
7689 TTCATTAGTGCGCT
1 TTCATTAGTGCGCT
7703 T
1 T
7704 CGATGGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (14 bp):
TTCATTAGTGCGCT
Found at i:13537 original size:30 final size:28
Alignment explanation
Indices: 13502--13906 Score: 166
Period size: 30 Copynumber: 13.8 Consensus size: 28
13492 AAATGGTAAT
13502 TTTTTGGAAGTATCGAGGTCAAAAATGAGA
1 TTTTTGGAAGT-TCGAGGT-AAAAATGAGA
*
13532 TTTTTGGAAGTTCGAGGGT-AAAATGGAAA
1 TTTTTGGAAGTTCGA-GGTAAAAAT-GAGA
* * * *
13561 TTTTTAGAAGTTTTGGGGTTAAAAATGGGA
1 TTTTTGGAAG-TTCGAGG-TAAAAATGAGA
**
13591 TTTTTGGAAGTTTAAGGGT-AAAATG-GTA
1 TTTTTGGAAGTTCGA-GGTAAAAATGAG-A
* * *
13619 ATTTTGGAAGGTTCGGGGTGAAAAATGGGA
1 TTTTTGGAA-GTTCGAGGT-AAAAATGAGA
*
13649 TTTTTGGAAGTTCGGGGGT-AAAATG-GTAA
1 TTTTTGGAAGTTC-GAGGTAAAAATGAG--A
** * **
13678 TTTTAAGAGGTTTTAGGGTTAGAAAATGAGA
1 TTTTTGGAAGTTCGA-GG-TA-AAAATGAGA
*
13709 TTTTTGGAAGTTTGAGGGT-AAAATG-GTAA
1 TTTTTGGAAGTTCGA-GGTAAAAATGAG--A
* * * * *
13738 TTTTAGGAGGTTTTGGGGTTAAAAATGGGA
1 TTTTTGGAAG-TTCGAGG-TAAAAATGAGA
*
13768 TTTTTGGAAGTTCGGGGGT-AAAATG-GTAA
1 TTTTTGGAAGTTC-GAGGTAAAAATGAG--A
* *
13797 TTTTAGGAGGTTTCGAGGTTAAAAATGAGA
1 TTTTTGGAAG-TTCGAGG-TAAAAATGAGA
* *
13827 TTTTT-GAAGTTCGGGGGT-AAAATGATAA
1 TTTTTGGAAGTTC-GAGGTAAAAATGA-GA
* * * * *
13855 TTTTAGGAGGTTTTGGGGTCAAAAATGGGA
1 TTTTTGGAAG-TTCGAGGT-AAAAATGAGA
*
13885 TTTTTGGAAGTTCGGGGTAAAA
1 TTTTTGGAAGTTCGAGGTAAAA
13907 TGGTAATTTT
Statistics
Matches: 292, Mismatches: 45, Indels: 78
0.70 0.11 0.19
Matches are distributed among these distances:
27 11 0.04
28 54 0.18
29 88 0.30
30 91 0.31
31 39 0.13
32 8 0.03
33 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (28 bp):
TTTTTGGAAGTTCGAGGTAAAAATGAGA
Found at i:13593 original size:59 final size:58
Alignment explanation
Indices: 13489--13916 Score: 518
Period size: 59 Copynumber: 7.3 Consensus size: 58
13479 ACATTCGATA
* * * * * *
13489 GTAAAATGGTAATTTTTTGGAAGTATCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGG
1 GTAAAATGGTAA--TTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
* **
13549 GTAAAATGGAAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTAAGG
1 GTAAAATGGTAA-TTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
* * * * *
13608 GTAAAATGGTAATTTTGGAAGGTTCGGGGTGAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
* * * *
13666 GTAAAATGGTAATTTTAAGAGGTTTTAGGGTTAGAAAATGAGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTT-AGAAGTTTTGGGGTTA-AAAATGGGATTTTTGGAAGTTCGAGG
* *
13726 GTAAAATGGTAATTTTAGGAGGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTA-GAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
* * * * *
13785 GTAAAATGGTAATTTTAGGAGGTTTCGAGGTTAAAAATGAGATTTTT-GAAGTTCGGGG
1 GTAAAATGGTAATTTTA-GAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
* * *
13843 GTAAAATGATAATTTTAGGAGGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GG
1 GTAAAATGGTAATTTTA-GAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
13901 GTAAAATGGTAATTTT
1 GTAAAATGGTAATTTT
13917 TGGATAGTTT
Statistics
Matches: 325, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
58 125 0.38
59 136 0.42
60 64 0.20
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (58 bp):
GTAAAATGGTAATTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGG
Found at i:13681 original size:177 final size:175
Alignment explanation
Indices: 13489--13926 Score: 596
Period size: 177 Copynumber: 2.5 Consensus size: 175
13479 ACATTCGATA
* * *
13489 GTAAAATGGTAATTTTTTGGAAGTATCGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAA
1 GTAAAATGGTAA-TTTTAGGAGGT-TTGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAA
* *
13554 ATGGAAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAATGGTA
64 ATGGTAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTA
* *
13619 ATTTT-GGAAGG-TTCGGGGTGAAAAATGGGATTTTTGGAAGTTCGGGG
129 ATTTTAGG-AGGTTTCGAGGTGAAAAATGAGATTTTT-GAAGTTCGGGG
* * * *
13666 GTAAAATGGTAATTTTAAGAGGTTTTAGGGTTAGAAAATGAGATTTTTGGAAGTTTGAGGGTAAA
1 GTAAAATGGTAATTTTAGGAGGTTTGA-GGTCA-AAAATGAGATTTTTGGAAGTTCGAGGGTAAA
* **
13731 ATGGTAA-TTTTAGGAGGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGT
64 ATGGTAATTTTTA-GAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGT
*
13795 AATTTTAGGAGGTTTCGAGGTTAAAAATGAGATTTTTGAAGTTCGGGG
128 AATTTTAGGAGGTTTCGAGGTGAAAAATGAGATTTTTGAAGTTCGGGG
* * *
13843 GTAAAATGATAATTTTAGGAGGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAA
1 GTAAAATGGTAATTTTAGGAGG-TTTGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAA
*
13907 TGGTAATTTTTGGATAGTTT
65 TGGTAATTTTTAGA-AGTTT
13927 AGGGACCTCC
Statistics
Matches: 229, Mismatches: 24, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
175 18 0.08
176 46 0.20
177 139 0.61
178 26 0.11
ACGTcount: A:0.31, C:0.02, G:0.32, T:0.35
Consensus pattern (175 bp):
GTAAAATGGTAATTTTAGGAGGTTTGAGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGTAAAAT
GGTAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCAAGGGTAAAATGGTAAT
TTTAGGAGGTTTCGAGGTGAAAAATGAGATTTTTGAAGTTCGGGG
Done.