Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011251.1 Kokia drynarioides strain JFW-HI SEQ_126229, 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: 10633
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.25
Warning! 227 characters in sequence are not A, C, G, or T
Found at i:8889 original size:27 final size:26
Alignment explanation
Indices: 8858--8909 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
8848 CAATTAAGGA
*
8858 TTGTTTCCTTTGATCCTCCTTTTAATT
1 TTGTTTCCTTCGATCCT-CTTTTAATT
8885 TTGTTTCCTTCGATCCTCTTTTAAT
1 TTGTTTCCTTCGATCCTCTTTTAAT
8910 AGAATTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.12, C:0.23, G:0.08, T:0.58
Consensus pattern (26 bp):
TTGTTTCCTTCGATCCTCTTTTAATT
Found at i:9826 original size:86 final size:86
Alignment explanation
Indices: 9734--10157 Score: 289
Period size: 86 Copynumber: 5.3 Consensus size: 86
9724 ACTGGTCAGC
* *
9734 TTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
1 TTCCTGATGAGACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
9799 GAAACAAGCGATGTGGTCATT
66 GAAACAAGCGATGTGGTCATT
* * * ** * * * *
9820 TTCCTGATGATACACTGAGAAGAAGACCCAAATGAGAC--ACTGA-GA-A-GC--AG--GTGGA-
1 TTCCTGATGAGACACTGAGAAG-TGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * * **
9875 AGCAATAA---A--TGGTCAAC
65 TGAAACAAGCGATGTGGTCATT
* *
9892 TTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
1 TTCCTGATGAGACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
*
9957 AAAACAAGCGATGTGGTCATT
66 GAAACAAGCGATGTGGTCATT
* * * ** * * ** * *
9978 TTCTTGATGAGACACTGAGAAGAAGACCCAAATGAGAC--ACTGAAAAG-TA-GGTGGAAGC--A
1 TTCCTGATGAGACACTGAGAAG-TGAACCAAATTCGTCTTCCTGATGAGATACAG-AGAAGCGGA
* *
10037 AT--AA-AAG-G-T-TAG-C---
64 TTGAAACAAGCGATGTGGTCATT
* * *
10050 TTACTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
1 TTCCTGATGAGACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
10115 GAAACAAGCGATGTGGTCATT
66 GAAACAAGCGATGTGGTCATT
10136 TTCCTGATGAGACACTGAGAAG
1 TTCCTGATGAGACACTGAGAAG
10158 AAGACCCAAA
Statistics
Matches: 238, Mismatches: 66, Indels: 68
0.64 0.18 0.18
Matches are distributed among these distances:
71 18 0.08
72 45 0.19
73 10 0.04
74 10 0.04
75 3 0.01
76 5 0.02
77 6 0.03
78 9 0.04
79 6 0.03
80 9 0.04
81 5 0.02
82 5 0.02
83 3 0.01
84 10 0.04
85 10 0.04
86 65 0.27
87 19 0.08
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (86 bp):
TTCCTGATGAGACACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATT
GAAACAAGCGATGTGGTCATT
Found at i:10317 original size:158 final size:158
Alignment explanation
Indices: 9700--10283 Score: 1024
Period size: 158 Copynumber: 3.7 Consensus size: 158
9690 TTGAGAAGAT
* * *
9700 ACTGAGAAGCAGGTGGAAGCAATAACTGGTCAGCTTCCTGATGAGATATTGAGAAGTGAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
9765 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
66 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
*
9830 TACACTGAGAAGAAGACCCAAATGAGAC
131 GACACTGAGAAGAAGACCCAAATGAGAC
*
9858 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAACTTCCTGATGAGATACTGAGAAGTAAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
* *
9923 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTAAAACAAGCGATGTGGTCATTTTCTTGATGA
66 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
9988 GACACTGAGAAGAAGACCCAAATGAGAC
131 GACACTGAGAAGAAGACCCAAATGAGAC
* * * * *
10016 ACTGAAAAGTAGGTGGAAGCAATAAAAGGTTAGCTTACTGATGAGATACTGAGAAGTAAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
10081 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
66 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
10146 GACACTGAGAAGAAGACCCAAATGAGAC
131 GACACTGAGAAGAAGACCCAAATGAGAC
* * * *
10174 ACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCCTGATGAGATGCGGAGAAGTGAACCAAA
1 ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
10239 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGA
66 TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGA
10284 CAAACGTAAA
Statistics
Matches: 404, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 404 1.00
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (158 bp):
ACTGAGAAGCAGGTGGAAGCAATAAATGGTCAGCTTCCTGATGAGATACTGAGAAGTAAACCAAA
TTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATGTGGTCATTTTCCTGATGA
GACACTGAGAAGAAGACCCAAATGAGAC
Found at i:10464 original size:11 final size:11
Alignment explanation
Indices: 10448--10503 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
10438 CCATACTCCC
10448 TTTAAATTTAT
1 TTTAAATTTAT
*
10459 TTTAAATTTAAA
1 TTTAAATTT-AT
* *
10471 TTTAAATTAAG
1 TTTAAATTTAT
*
10482 TTTAAAATTAT
1 TTTAAATTTAT
10493 TTTCAAATTTA
1 TTT-AAATTTA
10504 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 21 0.58
12 15 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:10470 original size:17 final size:17
Alignment explanation
Indices: 10448--10510 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
10438 CCATACTCCC
10448 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
** *
10465 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
10482 TTTAAAATTATTTTCAAA
1 TTTAAATTTATTTT-AAA
10500 TTTAAAATTTA
1 TTT-AAATTTA
10511 AAATAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
17 25 0.69
18 5 0.14
19 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:10480 original size:5 final size:6
Alignment explanation
Indices: 10448--10512 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
10438 CCATACTCCC
* * * *
10448 TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA ATT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
10493 TTTCAAA TTTAAAA TTTAAA
1 TTT-AAA TTT-AAA TTTAAA
10513 ATAAATAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
5 11 0.24
6 25 0.54
7 10 0.22
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:10518 original size:18 final size:18
Alignment explanation
Indices: 10460--10518 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
10450 TAAATTTATT
10460 TTAAATTT-AAATTTAAA
1 TTAAATTTAAAATTTAAA
* **
10477 TTAAGTTTAAAA-TTATT
1 TTAAATTTAAAATTTAAA
10494 TTCAAATTTAAAATTTAAA
1 TT-AAATTTAAAATTTAAA
*
10513 ATAAAT
1 TTAAAT
10519 AAAACCCAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.38
18 16 0.50
19 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAAATTTAAAATTTAAA
Done.