Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009715.1 Kokia drynarioides strain JFW-HI SEQ_124434, 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: 66140
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3226 original size:21 final size:21
Alignment explanation
Indices: 3200--3243 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3190 ATTAATAAAA
3200 TATATAATTTAT-ATTAATATT
1 TATATAATTTATGATTAA-ATT
*
3221 TATATATTTTATGATTAAATT
1 TATATAATTTATGATTAAATT
3242 TA
1 TA
3244 AATTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATAATTTATGATTAAATT
Found at i:11281 original size:46 final size:46
Alignment explanation
Indices: 11211--11332 Score: 165
Period size: 46 Copynumber: 2.7 Consensus size: 46
11201 ACATTAGCAC
*
11211 GCTCTCTGTTTAGCACGTTT-TGTGCCCTCTTATCAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-TTTGTGTGCTCTCTTATCAGCACTTTGTGT
* * *
11257 GCTCTCTGATTAGCACTTTGTGTGCTCTCTTATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGTGCTCTCTTATCAGCACTTTGTGT
* * *
11303 ACTTTCTGTTTAGCACTGTGTGTGCTCTCT
1 GCTCTCTGTTTAGCACTTTGTGTGCTCTCT
11333 GTTGCCCAGC
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 3 0.04
46 64 0.96
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (46 bp):
GCTCTCTGTTTAGCACTTTGTGTGCTCTCTTATCAGCACTTTGTGT
Found at i:11325 original size:69 final size:66
Alignment explanation
Indices: 11245--11382 Score: 163
Period size: 69 Copynumber: 2.0 Consensus size: 66
11235 CCCTCTTATC
* *
11245 AGCACTTTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTTATTAGTACTTTGTGTACT-TT
1 AGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTC-TATTAGTACTTTG-GTACTCTT
11308 CTGTTT
62 -TGTTT
*
11314 AGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTTT
1 AGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTATTAGTACTTTGGTACTCTTT
11379 GTTT
63 GTTT
11383 GTTCCGTATA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
68 2 0.03
69 29 0.48
70 14 0.23
71 11 0.18
72 5 0.08
ACGTcount: A:0.12, C:0.21, G:0.20, T:0.46
Consensus pattern (66 bp):
AGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTATTAGTACTTTGGTACTCTTTGTT
T
Found at i:11333 original size:23 final size:23
Alignment explanation
Indices: 11211--11382 Score: 140
Period size: 23 Copynumber: 7.5 Consensus size: 23
11201 ACATTAGCAC
11211 GCTCTCTGTTTAGCACGTTT-TGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
* *
11234 GCCCTCT-TATCAGCACTTTGTGT
1 GCTCTCTGT-TTAGCACTTTGTGT
*
11257 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
11280 GCTCTCT-TATTAGTACTTTGTGT
1 GCTCTCTGT-TTAGCACTTTGTGT
* * *
11303 ACTTTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
11326 GCTCTCTGTTGCCCAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACTTTGTGT
*
11351 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
11372 ACTCTTTGTTT
1 GCTCTCTGTTT
11383 GTTCCGTATA
Statistics
Matches: 118, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
21 12 0.10
22 8 0.07
23 79 0.67
24 2 0.02
25 12 0.10
26 5 0.04
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:12828 original size:24 final size:24
Alignment explanation
Indices: 12797--12847 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
12787 AGAAATAATC
*
12797 TTTCAATTAAAATCTGTTTATTTG
1 TTTCAATTAAAATCTGTTTAGTTG
*
12821 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAAATCTGTTTAGTTG
12845 TTT
1 TTT
12848 GAATCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAAATCTGTTTAGTTG
Found at i:12856 original size:24 final size:24
Alignment explanation
Indices: 12797--12859 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
12787 AGAAATAATC
* * *
12797 TTTCAATTAAAATCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTAGTTG
*
12821 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATCAAACTCTGTTTAGTTG
*
12845 TTTGAATCAAACTCT
1 TTTCAATCAAACTCT
12860 TATTTGTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAATCAAACTCTGTTTAGTTG
Found at i:48429 original size:117 final size:118
Alignment explanation
Indices: 48297--48521 Score: 380
Period size: 119 Copynumber: 1.9 Consensus size: 118
48287 CCTAAATCTA
* * *
48297 CTAAACTAAAAACCCTAAAACAACTTTGC-AAAAAGCTCTTAAGCCTTGCCTTAACTTAACTATT
1 CTAAACTAAAAACCCTAAAACAACCTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
* *
48361 TATAAAAGATTTTAGCAACCTTAATTAGGTCAAATACAAGCCTTAAACTAAAC
66 TATAAAAGAGTTTAGAAACCTTAATTAGGTCAAATACAAGCCTTAAACTAAAC
*
48414 CTAAACTAAAAACCCTAAAACAGCCTTGCAAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTAT
1 CTAAACTAAAAACCCTAAAACAACCTTGC-AAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTAT
48479 TTATAAAAGAGTTTAGAAACCTTAATTAGGTCAAATACAAGCC
65 TTATAAAAGAGTTTAGAAACCTTAATTAGGTCAAATACAAGCC
48522 CTAATTACAT
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
117 27 0.27
119 73 0.73
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (118 bp):
CTAAACTAAAAACCCTAAAACAACCTTGCAAAAAAGCTCCTAAGCCTTGCCTCAACTTAACTATT
TATAAAAGAGTTTAGAAACCTTAATTAGGTCAAATACAAGCCTTAAACTAAAC
Found at i:51415 original size:73 final size:73
Alignment explanation
Indices: 51296--51442 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
51286 ATGCACCAAG
51296 GCTATGAATCAACACAAATACAATTATAAATATAGTGGTGTATTACAAGTGTGATAAGTCAGTTG
1 GCTATGAATCAACACAAATACAATTATAAATATAGTGGTGTATTACAAGTGTGATAAGTCAGTTG
51361 TAATATTT
66 TAATATTT
51369 GCTATGAATCAACACAAATACAATTATAAATATAGTGGTGTATTACAAGTGTGATAAGTCAGTTG
1 GCTATGAATCAACACAAATACAATTATAAATATAGTGGTGTATTACAAGTGTGATAAGTCAGTTG
51434 TAATATTT
66 TAATATTT
51442 G
1 G
51443 TAGTATTACA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (73 bp):
GCTATGAATCAACACAAATACAATTATAAATATAGTGGTGTATTACAAGTGTGATAAGTCAGTTG
TAATATTT
Found at i:61628 original size:2 final size:2
Alignment explanation
Indices: 61623--61656 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61613 CGCTAACGAA
61623 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
61657 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:64082 original size:28 final size:28
Alignment explanation
Indices: 64042--64125 Score: 150
Period size: 28 Copynumber: 3.0 Consensus size: 28
64032 GATATCCGAT
*
64042 TTACTCCCTGTTGACCCAAAAGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
64070 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
*
64098 TTACTCCCTATTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAGGTCATGC
64126 CTGTTACCAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAGGTCATGC
Done.