Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003543.1 Kokia drynarioides strain JFW-HI SEQ_116390, 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: 10586
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:1102 original size:20 final size:21
Alignment explanation
Indices: 1047--1128 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 21
1037 ACTCTAAGTT
*
1047 TAATAATTTATTTTTAAATAA
1 TAATATTTTATTTTTAAATAA
*
1068 TAATATTTTAATTTTAGAAT-A
1 TAATATTTTATTTTTA-AATAA
1089 T-ATATTTTATTTTTTAAA-ATA
1 TAATATTTTA-TTTTTAAATA-A
1110 TAATTATATGTTATTTTTA
1 TAA-TAT-T-TTATTTTTA
1129 CTAATATTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
20 10 0.20
21 23 0.46
22 4 0.08
23 3 0.06
24 7 0.14
25 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TAATATTTTATTTTTAAATAA
Found at i:1110 original size:19 final size:19
Alignment explanation
Indices: 1053--1111 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
1043 AGTTTAATAA
*
1053 TTTATTTTTAAATAATAATAT
1 TTTATTTTTTAA-AAT-ATAT
*
1074 TTTA-ATTTTAGAATATATAT
1 TTTATTTTTTA-AA-ATATAT
1094 TTTATTTTTTAAAATATA
1 TTTATTTTTTAAAATATA
1112 ATTATATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 5 0.16
20 15 0.47
21 12 0.38
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATTTTTTAAAATATAT
Found at i:1691 original size:30 final size:31
Alignment explanation
Indices: 1655--1724 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1645 CATTTAACAC
*
1655 AACAGTCACTCAAC-TT-T-GAAAATGTGATAA
1 AACAGTCACT-AACGTTATCGAAAA-GTGACAA
1685 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCGAAAAGTGACAA
1716 AACAGTCAC
1 AACAGTCAC
1725 CTTATCATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCGAAAAGTGACAA
Found at i:2852 original size:31 final size:32
Alignment explanation
Indices: 2817--2893 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
2807 CCGAGTGGAA
*
2817 AATGTTAGTGATTGTTTTGTCAC-TTTTCGAT
1 AATGTTAGTGACTGTTTTGTCACATTTTCGAT
2848 AATGTTAGTGACTGTTTTGTCACATTTTC-A-
1 AATGTTAGTGACTGTTTTGTCACATTTTCGAT
2878 AA-GTTGAGTGACTGTT
1 AATGTT-AGTGACTGTT
2894 ATGTTAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 3 0.07
30 12 0.28
31 23 0.53
32 5 0.12
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (32 bp):
AATGTTAGTGACTGTTTTGTCACATTTTCGAT
Found at i:4919 original size:26 final size:26
Alignment explanation
Indices: 4852--4920 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
4842 GAATCATATA
*
4852 TGCTCACACGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
4878 TGCTCACACGAGCTGTGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
*
4904 TGCTCACACGACCTGTG
1 TGCTCACACGAGCTGTG
4921 GGTCGAGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGTC
Found at i:5166 original size:158 final size:158
Alignment explanation
Indices: 4878--5210 Score: 463
Period size: 158 Copynumber: 2.1 Consensus size: 158
4868 GAAATGGGTC
*
4878 TGCTCACACGAGCTGTGAAATGGGTCTGCTCACACGACCTGTGGGTCGAGATGTGAGGCTACACG
1 TGCTCACACGAGCTGTGAAATGGCTCTGCTCACACGACCTGTGGGTCGAGATGTGAGGCTACACG
* * * **
4943 ATGCTACTCACACGAGCTGTGGAGTATCCGCAATAAATGTTGGACCTGAGCCATCAGTAAGACAT
66 ATGCTACTCACACGAGCTATGGAGAATCCGCAACAAATGCAGGACCTGAGCCATCAGTAAGACAT
5008 CTAAGACCAACACCCATATAACCTGTAA
131 CTAAGACCAACACCCATATAACCTGTAA
* * **
5036 TGCTCACACGAGCTGTGAAATGAGCT-TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTATGC
1 TGCTCACACGAGCTGTGAAATG-GCTCTGCTCACACGACCTGTGGGTCGAGATGTGAGGCTACAC
* * * * *
5100 GATGCTGCTCACATGAGCTATGGAGAATCCGCAACCAATGCAGGACCAT-AGCCATCGGTAGGAC
65 GATGCTACTCACACGAGCTATGGAGAATCCGCAACAAATGCAGGACC-TGAGCCATCAGTAAGAC
* * * *
5164 ATCTAAGTCCAGCATCCATATAACTTGTAA
129 ATCTAAGACCAACACCCATATAACCTGTAA
5194 TGCTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
5211 GGTCGAGATG
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
158 151 0.98
159 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (158 bp):
TGCTCACACGAGCTGTGAAATGGCTCTGCTCACACGACCTGTGGGTCGAGATGTGAGGCTACACG
ATGCTACTCACACGAGCTATGGAGAATCCGCAACAAATGCAGGACCTGAGCCATCAGTAAGACAT
CTAAGACCAACACCCATATAACCTGTAA
Found at i:5308 original size:132 final size:132
Alignment explanation
Indices: 5062--5312 Score: 344
Period size: 132 Copynumber: 1.9 Consensus size: 132
5052 GAAATGAGCT
* * * *
5062 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTATGCGATGCTGCTCACATGAGCTATGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTAAGCGATGCTGCTCACACGAACTATGGAGAA
* ** * *
5127 TCCGCAACCAATGCAGGACCATAGCCATCGGTAGGACATCTAAGTCCAGCATCCATATAACTTGT
66 TCCGCAACCAATGCAGGACCATAACCATCGACAGGACATCCAAGACCAGCATCCATATAACTTGT
5192 AA
131 AA
* * *
5194 TGCTCACACGAGCTGTGGGTCGAGATGTGGGGCTACAG-GATGCTGCTCACACGAATTGTGGAGA
1 TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTA-AGCGATGCTGCTCACACGAACTATGGAGA
* *
5258 ATTCGCAGCCAATGCAGGACC-TCAACCATCGACAGGACATCCAAGACCAGCATCC
65 ATCCGCAACCAATGCAGGACCAT-AACCATCGACAGGACATCCAAGACCAGCATCC
5313 GGATCTGTAA
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 1 0.01
132 101 0.98
133 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (132 bp):
TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTAAGCGATGCTGCTCACACGAACTATGGAGAA
TCCGCAACCAATGCAGGACCATAACCATCGACAGGACATCCAAGACCAGCATCCATATAACTTGT
AA
Done.