Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009582.1 Kokia drynarioides strain JFW-HI SEQ_124296, 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: 16841
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:4998 original size:24 final size:24
Alignment explanation
Indices: 4970--5035 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
4960 TAGACTAATA
*
4970 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
4994 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
5018 AAAGTTTAACT-AAA-AAAT
1 AGAGTTTAACTCAAACAAAT
5036 TATTTCTTAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 3 0.09
23 3 0.09
24 29 0.83
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:7047 original size:24 final size:24
Alignment explanation
Indices: 6974--7048 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
6964 GTTTGACTCT
* *
6974 AACAAATAAACAAAGTTTAATTCA
1 AACAAATAAACAGAGTTTAATTGA
*
6998 AACAAATAAATAGAGATTTAATTGA
1 AACAAATAAACAGAG-TTTAATTGA
* *
7023 AACAATTAAACAGAGTTTAACTGA
1 AACAAATAAACAGAGTTTAATTGA
7047 AA
1 AA
7049 GATTATTTCT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
24 23 0.52
25 21 0.48
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.25
Consensus pattern (24 bp):
AACAAATAAACAGAGTTTAATTGA
Found at i:10396 original size:28 final size:28
Alignment explanation
Indices: 10363--10438 Score: 118
Period size: 28 Copynumber: 2.7 Consensus size: 28
10353 CATATAACAA
*
10363 AGAACAACTAAAAAGGCTTAC-ATATCAG
1 AGAACAACCAAAAAGGCTT-CTATATCAG
10391 AGAACAACCAAAAAGGCTTCTATATCAG
1 AGAACAACCAAAAAGGCTTCTATATCAG
*
10419 AGAACAACCAAAAAGTCTTC
1 AGAACAACCAAAAAGGCTTC
10439 CACATTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (28 bp):
AGAACAACCAAAAAGGCTTCTATATCAG
Found at i:11485 original size:21 final size:21
Alignment explanation
Indices: 11439--11495 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
11429 ATAGTGCAGA
*
11439 CTTCTACCGATACCTATGACAG
1 CTTCTACCGATA-CAATGACAG
11461 -TTCTACCGATACAAGTGA-AG
1 CTTCTACCGATACAA-TGACAG
*
11481 CTTCTACCGAAACAA
1 CTTCTACCGATACAA
11496 ATCATGCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (21 bp):
CTTCTACCGATACAATGACAG
Found at i:11504 original size:21 final size:21
Alignment explanation
Indices: 11461--11504 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
11451 CCTATGACAG
* * *
11461 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
11482 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
11503 TT
1 TT
11505 TTACTGGTAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:12271 original size:28 final size:28
Alignment explanation
Indices: 12230--12284 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
12220 GATATCTGAT
* *
12230 TTACTCCCTGTTGACTCAAAGGTCATGC
1 TTACTCCCTCTTGACCCAAAGGTCATGC
12258 TTACTCCCTCTTGACCCAAAGGTCATG
1 TTACTCCCTCTTGACCCAAAGGTCATG
12285 ATGCTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (28 bp):
TTACTCCCTCTTGACCCAAAGGTCATGC
Found at i:12311 original size:36 final size:36
Alignment explanation
Indices: 12258--12356 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 36
12248 AAGGTCATGC
* *
12258 TTACTCCCTCTTG-ACCCAAAGGTCATGATGCTTATT
1 TTACTCCCT-ATGAACCCAAAGGTCATGATGCTCATT
* *
12294 TTATTCCCTGTGAACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTATGAACCCAAAGGTCATGATGCTCATT
*
12330 TTACTCCCTATTAACCCAAAGGTCATG
1 TTACTCCCTATGAACCCAAAGGTCATG
12357 TCTATTACCA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 2 0.04
36 54 0.96
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (36 bp):
TTACTCCCTATGAACCCAAAGGTCATGATGCTCATT
Found at i:16676 original size:113 final size:113
Alignment explanation
Indices: 16534--16760 Score: 393
Period size: 113 Copynumber: 2.0 Consensus size: 113
16524 ACTTAGCTAC
* *
16534 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTGGGTGCGGAAA
1 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
*
16599 TATCCCAAAATAACTACTACATTTGACGTTAGGTT-AGACATCCCAAAA
66 TATCCCAAAATAACTACTACATTTGACGTCA-GTTCAGACATCCCAAAA
*
16647 TAACTACTGAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
1 TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
*
16712 TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCCAAA
66 TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCAAAA
16760 T
1 T
16761 GCAAAAGTGC
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
112 3 0.03
113 105 0.97
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (113 bp):
TAACTACTAAAAATGTAATAATTAATTATAAAATGCCTAGAAAACAATATCCTTAGGTGCGAAAA
TATCCCAAAATAACTACTACATTTGACGTCAGTTCAGACATCCCAAAA
Done.