Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011034.1 Kokia drynarioides strain JFW-HI SEQ_126005, 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: 25242
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:7587 original size:59 final size:59
Alignment explanation
Indices: 7488--7869 Score: 572
Period size: 59 Copynumber: 6.5 Consensus size: 59
7478 CGGATGCACG
* * * * *
7488 GGGGTAAAATGGT-AGTTTTGGAGGGTTCG-GAGTCAAAAATGGGATTTTTGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAG-GTCAAAAATGAGATTTTTGGAAGTTCA
7546 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
* *
7605 AGGGTAAAATGGTAATTTTTAGAAAGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTC-
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
* * * *
7663 GAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTTGAAGTTCA
1 G-GGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
* * *
7723 GGGGTAAGATGGTAATTTTTAGAAGGCTCGAGGTCAAAAATGAGATTTTTGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
* *
7782 GGGGTAAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGAGAATTTTTGTAAGTTCA
1 GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAG-ATTTTTGGAAGTTCA
7842 GGGGTAAAATGGTAATTTTTAGAAGGTT
1 GGGGTAAAATGGTAATTTTTAGAAGGTT
7870 TAGGGACCTC
Statistics
Matches: 294, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
58 13 0.04
59 238 0.81
60 43 0.15
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTAGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCA
Found at i:8568 original size:35 final size:35
Alignment explanation
Indices: 8522--8599 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
8512 CCCGGCGCGT
*
8522 GGCCATCGCGCGTCACCGTCTAGGTTTCTCCGGTG
1 GGCCATCGCGCGTCACCGCCTAGGTTTCTCCGGTG
**
8557 GGCCATCGCGCGTCGTCGCCTAGGTTTCTCCGGTG
1 GGCCATCGCGCGTCACCGCCTAGGTTTCTCCGGTG
8592 GGCCATCG
1 GGCCATCG
8600 AGACCCCGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.08, C:0.35, G:0.33, T:0.24
Consensus pattern (35 bp):
GGCCATCGCGCGTCACCGCCTAGGTTTCTCCGGTG
Found at i:9034 original size:14 final size:16
Alignment explanation
Indices: 9015--9047 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9005 TATTATTATT
9015 ATTATT-TTAA-AAAA
1 ATTATTATTAATAAAA
9029 ATTATTATTAATAAAA
1 ATTATTATTAATAAAA
9045 ATT
1 ATT
9048 TTGAAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 4 0.24
16 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATTATTAATAAAA
Found at i:9038 original size:3 final size:3
Alignment explanation
Indices: 8982--9020 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
8972 ATTTTTTTAT
* *
8982 TTA TTA TTCA TTA ATA TTA TTA ATA TTA TTA TTA TTA TT
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9021 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9727 original size:17 final size:18
Alignment explanation
Indices: 9702--9743 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
9692 GATCGGGCCC
* *
9702 TTTTAGGTTTAGGG-TTA
1 TTTTGGGTTTAGGGCTGA
*
9719 TTTTGGGTTTGGGGCTGA
1 TTTTGGGTTTAGGGCTGA
9737 TTTTGGG
1 TTTTGGG
9744 CCATTTTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (18 bp):
TTTTGGGTTTAGGGCTGA
Found at i:9875 original size:17 final size:18
Alignment explanation
Indices: 9839--9913 Score: 93
Period size: 17 Copynumber: 4.3 Consensus size: 18
9829 ATTTAGCAAT
*
9839 TTTAAATTTGAAAATAAA
1 TTTAAATTTAAAAATAAA
* *
9857 TTTAAACTT-AAATTAAA
1 TTTAAATTTAAAAATAAA
9874 TTTAAA-TTAAAAATAAA
1 TTTAAATTTAAAAATAAA
*
9891 TTTAAATTT-AAAACAAA
1 TTTAAATTTAAAAATAAA
9908 TTTAAA
1 TTTAAA
9914 AAAATGAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
16 2 0.04
17 39 0.76
18 10 0.20
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
TTTAAATTTAAAAATAAA
Found at i:9878 original size:11 final size:11
Alignment explanation
Indices: 9853--9913 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
9843 AATTTGAAAA
*
9853 TAAATTTAAACT
1 TAAA-TTAAATT
9865 TAAATTAAATT
1 TAAATTAAATT
**
9876 TAAATTAAAAA
1 TAAATTAAATT
9887 TAAATTTAAATT
1 TAAA-TTAAATT
**
9899 TAAAACAAATT
1 TAAATTAAATT
9910 TAAA
1 TAAA
9914 AAAATGAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
11 28 0.68
12 13 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:9899 original size:6 final size:6
Alignment explanation
Indices: 9839--9902 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
9829 ATTTAGCAAT
* *
9839 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA -TTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
9885 AATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
9903 ACAAATTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 13 0.27
6 32 0.67
7 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:10615 original size:2 final size:2
Alignment explanation
Indices: 10608--10632 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10598 AACGCAATTA
10608 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
10633 GGCTCGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16386 original size:22 final size:22
Alignment explanation
Indices: 16361--16405 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16351 TTAAACCCAT
16361 AAAAT-TAAATCTAAACTAAAAA
1 AAAATCTAAA-CTAAACTAAAAA
* *
16383 AAAATCTAAACTCAATTAAAAA
1 AAAATCTAAACTAAACTAAAAA
16405 A
1 A
16406 TAAAACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (22 bp):
AAAATCTAAACTAAACTAAAAA
Found at i:16403 original size:17 final size:17
Alignment explanation
Indices: 16362--16403 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16352 TAAACCCATA
16362 AAATT-AAATCTAAACT
1 AAATTAAAATCTAAACT
**
16378 AAAAAAAAATCTAAACT
1 AAATTAAAATCTAAACT
*
16395 CAATTAAAA
1 AAATTAAAA
16404 AATAAAACAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATTAAAATCTAAACT
Found at i:20212 original size:29 final size:28
Alignment explanation
Indices: 20179--20248 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 28
20169 ATAAATATTT
*
20179 AATTAAAAAAACACAATTA-TTAAATTGA
1 AATTAAAAAAACACAAATACTT-AATTGA
*
20207 ACATTAAAACCAAACATAAATACTTAATTGA
1 A-ATTAAAA--AAACACAAATACTTAATTGA
20238 AA-TAAAAAAAC
1 AATTAAAAAAAC
20249 TTACATATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 4 0.11
28 1 0.03
29 12 0.33
30 1 0.03
31 16 0.44
32 2 0.06
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.24
Consensus pattern (28 bp):
AATTAAAAAAACACAAATACTTAATTGA
Found at i:20447 original size:13 final size:14
Alignment explanation
Indices: 20424--20458 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
20414 TTATGTTTCA
*
20424 ATAAATATTGAATC
1 ATAATTATTGAATC
20438 AT-ATTATTGAATC
1 ATAATTATTGAATC
20451 ATAATTAT
1 ATAATTAT
20459 GTTTGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (14 bp):
ATAATTATTGAATC
Found at i:23498 original size:16 final size:16
Alignment explanation
Indices: 23474--23504 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23464 GTTGTTTTAA
*
23474 GTAGTTAATAATATTG
1 GTAGATAATAATATTG
23490 GTAGATAATAATATT
1 GTAGATAATAATATT
23505 TTATTATCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
GTAGATAATAATATTG
Done.