Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010444.1 Kokia drynarioides strain JFW-HI SEQ_125336, 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: 40624
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 103 characters in sequence are not A, C, G, or T
Found at i:12069 original size:23 final size:23
Alignment explanation
Indices: 12024--12069 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12014 TCATTAACAT
**
12024 TGTTCGTGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
12047 TGTTCGTGAATATGTTCAATTAA
1 TGTTCGTGAACATGTTCAATTAA
12070 GTTAAATGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:16867 original size:30 final size:30
Alignment explanation
Indices: 16816--16882 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
16806 TCATATCAAT
*
16816 AAAATTT-AATTTATTTATTTTTA-CTTTC
1 AAAATTTAAATTTATTTATTTTTATATTTC
16844 AAAAATTTAAATTT-TTTACTTTTTATATTTC
1 -AAAATTTAAATTTATTTA-TTTTTATATTTC
16875 AAAATTTA
1 AAAATTTA
16883 TGTTCAACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
29 11 0.32
30 19 0.56
31 4 0.12
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (30 bp):
AAAATTTAAATTTATTTATTTTTATATTTC
Found at i:18068 original size:141 final size:141
Alignment explanation
Indices: 17814--18095 Score: 546
Period size: 141 Copynumber: 2.0 Consensus size: 141
17804 GAGTTCGTGG
*
17814 GTCCAAAATTTCAAATCAGTCCCTGTAATCAAAGACAACTTCCCTGATACTGATAAGATATTTGC
1 GTCCAAAATTTCAAATCAATCCCTGTAATCAAAGACAACTTCCCTGATACTGATAAGATATTTGC
*
17879 TTTGTTGAAACGTCGGAGAGAAATGTTGTTGGCGTCAAAATCGAGTTAGGGTTTGGAATATTGAT
66 TTTGTTGAAACGTCGGAGAGAAATGTTGCTGGCGTCAAAATCGAGTTAGGGTTTGGAATATTGAT
17944 TCCATTTTCTC
131 TCCATTTTCTC
17955 GTCCAAAATTTCAAATCAATCCCTGTAATCAAAGACAACTTCCCTGATACTGATAAGATATTTGC
1 GTCCAAAATTTCAAATCAATCCCTGTAATCAAAGACAACTTCCCTGATACTGATAAGATATTTGC
18020 TTTGTTGAAACGTCGGAGAGAAATGTTGCTGGCGTCAAAATCGAGTTAGGGTTTGGAATATTGAT
66 TTTGTTGAAACGTCGGAGAGAAATGTTGCTGGCGTCAAAATCGAGTTAGGGTTTGGAATATTGAT
18085 TCCATTTTCTC
131 TCCATTTTCTC
18096 CCATGGAAGT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 139 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (141 bp):
GTCCAAAATTTCAAATCAATCCCTGTAATCAAAGACAACTTCCCTGATACTGATAAGATATTTGC
TTTGTTGAAACGTCGGAGAGAAATGTTGCTGGCGTCAAAATCGAGTTAGGGTTTGGAATATTGAT
TCCATTTTCTC
Found at i:29236 original size:21 final size:22
Alignment explanation
Indices: 29210--29262 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
29200 AAAGGAGAGC
*
29210 AGAGGGAGAGGATGGTGG-GGG
1 AGAGGGAGAGGATAGTGGTGGG
*
29231 AGAGGG-G-GAATAGTGGTGGG
1 AGAGGGAGAGGATAGTGGTGGG
29251 AGAGGGATGAGG
1 AGAGGGA-GAGG
29263 TGGGGAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 6 0.24
22 1 0.04
23 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.62, T:0.11
Consensus pattern (22 bp):
AGAGGGAGAGGATAGTGGTGGG
Found at i:29624 original size:35 final size:35
Alignment explanation
Indices: 29585--29669 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 35
29575 TTTTGATGCA
**
29585 TTTTATAAATTTTTTTAATCTTTAATAAAATTTAT
1 TTTTATAAATTTTTTTAAAATTTAATAAAATTTAT
* ***
29620 TTTTAT-ACTTTTTATTAAAATTTAATATTTTTTAT
1 TTTTATAAATTTTT-TTAAAATTTAATAAAATTTAT
29655 TTTT-TATAATTTTTT
1 TTTTATA-AATTTTTT
29670 GCCATATGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
34 7 0.17
35 27 0.68
36 6 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (35 bp):
TTTTATAAATTTTTTTAAAATTTAATAAAATTTAT
Found at i:29657 original size:25 final size:23
Alignment explanation
Indices: 29593--29666 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 23
29583 CATTTTATAA
*
29593 ATTTTTTTAATCTTTAATAAAATTT
1 ATTTTTTT-AT-TTTATTAAAATTT
*
29618 ATTTTTATACTTTTTATTAAAATTT
1 ATTTTTTTA--TTTTATTAAAATTT
*
29643 AATATTTTTTATTTT-TTATAATTT
1 -AT-TTTTTTATTTTATTAAAATTT
29667 TTTGCCATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
24 9 0.22
25 23 0.56
26 3 0.07
27 6 0.15
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTTTATTTTATTAAAATTT
Found at i:32090 original size:24 final size:24
Alignment explanation
Indices: 32058--32116 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
32048 TTAAACTCTG
32058 TCTGGGCTCGTAAGAGCTAATCAC
1 TCTGGGCTCGTAAGAGCTAATCAC
* *
32082 TCTGGGCTCGTAAGAGTTAATCAT
1 TCTGGGCTCGTAAGAGCTAATCAC
*
32106 TCTGGACTCGT
1 TCTGGGCTCGT
32117 GTTAGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAATCAC
Found at i:37425 original size:31 final size:31
Alignment explanation
Indices: 37390--37453 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
37380 TACTGGAACA
* *
37390 TGACTTCAAAGTTCAATTTGGTACCTAAATT
1 TGACTTCAAAGTTCAAATTGATACCTAAATT
** *
37421 TGACTTCTTAGTTCAAATTGATACCTGAATT
1 TGACTTCAAAGTTCAAATTGATACCTAAATT
37452 TG
1 TG
37454 GTTTTTGTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (31 bp):
TGACTTCAAAGTTCAAATTGATACCTAAATT
Done.