Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013148.1 Kokia drynarioides strain JFW-HI SEQ_128167, 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: 10085
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Warning! 101 characters in sequence are not A, C, G, or T
Found at i:1619 original size:2 final size:2
Alignment explanation
Indices: 1612--1641 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1602 CTTAGTTTGA
1612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1642 TAAAAGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2396 original size:22 final size:23
Alignment explanation
Indices: 2346--2401 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2336 ATTTTATGTG
2346 ATATT-TAAAAAATTACTATTTT
1 ATATTATAAAAAATTACTATTTT
*
2368 A-AATATAAAAAATT--TATTTTT
1 ATATTATAAAAAATTACTA-TTTT
2389 ATATTATAAAAAA
1 ATATTATAAAAAA
2402 ATAAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 7 0.24
22 20 0.69
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTATAAAAAATTACTATTTT
Found at i:2416 original size:20 final size:21
Alignment explanation
Indices: 2393--2432 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2383 ATTTTTATAT
2393 TATAAAAAAAT-AAAATAAAA
1 TATAAAAAAATAAAAATAAAA
*
2413 TATAAATAAATAAAAATAAA
1 TATAAAAAAATAAAAATAAA
2433 TTCTATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TATAAAAAAATAAAAATAAAA
Found at i:2928 original size:14 final size:15
Alignment explanation
Indices: 2895--2928 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2885 ATTCGAGGAC
*
2895 AAACTTATTAAATAT
1 AAACTAATTAAATAT
2910 AAACTAATTAAAT-T
1 AAACTAATTAAATAT
2924 AAACT
1 AAACT
2929 TCATATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
AAACTAATTAAATAT
Found at i:3424 original size:25 final size:24
Alignment explanation
Indices: 3374--3425 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
3364 TTAAAATTCC
**
3374 ATTAATAAACTTTCTTTAAATTAA
1 ATTAATAAACTTTCTTTAAAGAAA
3398 ATTATATAAACTTT-TTTAAAAGAAA
1 ATTA-ATAAACTTTCTTT-AAAGAAA
3423 ATT
1 ATT
3426 GTTCACGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (24 bp):
ATTAATAAACTTTCTTTAAAGAAA
Found at i:4106 original size:2 final size:2
Alignment explanation
Indices: 4101--4129 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4091 ACACACACAC
4101 AT AT 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 AT AT A
4130 ATTCCACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6123 original size:8 final size:8
Alignment explanation
Indices: 6110--6173 Score: 67
Period size: 8 Copynumber: 7.5 Consensus size: 8
6100 AGATACAGAA
6110 AAAATTAT
1 AAAATTAT
6118 AAAATTAT
1 AAAATTAT
6126 AAAA-TATT
1 AAAATTA-T
6134 AAAATTGAT
1 AAAATT-AT
6143 ATAAACTTAT
1 A-AAA-TTAT
6153 AAATATTAT
1 AAA-ATTAT
*
6162 AAAAATAT
1 AAAATTAT
6170 AAAA
1 AAAA
6174 GTCTAATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
7 2 0.04
8 25 0.51
9 12 0.24
10 8 0.16
11 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:6754 original size:11 final size:10
Alignment explanation
Indices: 6740--6882 Score: 61
Period size: 10 Copynumber: 14.7 Consensus size: 10
6730 TTTATGATTT
6740 TTTTCATATAA
1 TTTT-ATATAA
6751 TTTT-TATAA
1 TTTTATATAA
*
6760 GTTTATATGAA
1 TTTTATAT-AA
*
6771 TTTTA-ATAT
1 TTTTATATAA
* *
6780 TTTTTTATAT
1 TTTTATATAA
* *
6790 TTTTTTATGA
1 TTTTATATAA
* *
6800 TTTTTTAGAA
1 TTTTATATAA
*
6810 TTTTA-ATGCA
1 TTTTATAT-AA
6820 TTTTATA-AA
1 TTTTATATAA
*
6829 ATTT-TA-AA
1 TTTTATATAA
*
6837 TGTTATATTAA
1 TTTTATA-TAA
6848 TTTTATA-AA
1 TTTTATATAA
6857 TTTT-TAT-A
1 TTTTATATAA
* *
6865 TTTCATTATAT
1 TTTTA-TATAA
6876 TTTTATA
1 TTTTATA
6883 ACGTCATATC
Statistics
Matches: 101, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
8 12 0.12
9 26 0.26
10 40 0.40
11 23 0.23
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTATATAA
Found at i:6833 original size:28 final size:28
Alignment explanation
Indices: 6802--6862 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
6792 TTTTATGATT
* *
6802 TTTTAGAATTTTA-ATGCATTTTATAAAA
1 TTTTA-AATGTTATATGAATTTTATAAAA
* *
6830 TTTTAAATGTTATATTAATTTTATAAAT
1 TTTTAAATGTTATATGAATTTTATAAAA
6858 TTTTA
1 TTTTA
6863 TATTTCATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.56
Consensus pattern (28 bp):
TTTTAAATGTTATATGAATTTTATAAAA
Found at i:6943 original size:18 final size:17
Alignment explanation
Indices: 6920--6973 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
6910 ATATTTGATA
6920 TTTATATTTTTGATAAAT
1 TTTATATTTTT-ATAAAT
* *
6938 TTTATATTATTTATGATT
1 TTTATATT-TTTATAAAT
6956 TTTATAATTTTTTATAAA
1 TTTAT-A-TTTTTATAAA
6974 AAAAATTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 17 0.59
19 10 0.34
20 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (17 bp):
TTTATATTTTTATAAAT
Found at i:6949 original size:34 final size:37
Alignment explanation
Indices: 6902--6973 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
6892 CAATTTTCAT
*
6902 ATTTTTTAATA-TT-TGATATTTAT-ATTTTTGATAA
1 ATTTTATAATATTTATGATATTTATAATTTTTGATAA
* * *
6936 ATTTTATATTATTTATGATTTTTATAATTTTTTATAA
1 ATTTTATAATATTTATGATATTTATAATTTTTGATAA
6973 A
1 A
6974 AAAAATTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 2 0.06
36 9 0.29
37 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (37 bp):
ATTTTATAATATTTATGATATTTATAATTTTTGATAA
Found at i:7881 original size:24 final size:25
Alignment explanation
Indices: 7841--7887 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
7831 TTAATCTATC
7841 TATACTATAATAATTTGT-AATATA
1 TATACTATAATAATTTGTGAATATA
*
7865 TATA-TATATATATTTTGTGAATA
1 TATACTATA-ATAATTTGTGAATA
7888 ATAGTTCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (25 bp):
TATACTATAATAATTTGTGAATATA
Found at i:9942 original size:4 final size:4
Alignment explanation
Indices: 9929--9971 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
9919 AATAATGAAG
*
9929 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
9972 GGAAGAAGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:9993 original size:3 final size:3
Alignment explanation
Indices: 9967--10009 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
9957 GAAAGAAAGA
* * *
9967 AAG AAGG AAG AAG GAG AAG GAG AAG AAG AAG AAG AGG AAG AAG
1 AAG AA-G AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
10010 GAGAGGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10014 original size:12 final size:12
Alignment explanation
Indices: 9967--10017 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
9957 GAAAGAAAGA
9967 AAGAAGGAAGAAGG
1 AAGAAGG-AG-AGG
*
9981 -AGAAGGAGAAG
1 AAGAAGGAGAGG
*
9992 AAGAAGAAGAGG
1 AAGAAGGAGAGG
10004 AAGAAGGAGAGG
1 AAGAAGGAGAGG
10016 AA
1 AA
10018 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 24 0.75
13 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
AAGAAGGAGAGG
Done.