Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011223.1 Kokia drynarioides strain JFW-HI SEQ_126201, 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: 36027
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:8907 original size:30 final size:30
Alignment explanation
Indices: 8871--8935 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
8861 ACTTATTTTA
8871 TTGTTAATTTTATTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
* *
8901 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
8931 TTGTT
1 TTGTT
8936 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:12729 original size:60 final size:60
Alignment explanation
Indices: 12636--12851 Score: 310
Period size: 60 Copynumber: 3.6 Consensus size: 60
12626 GTTTCAATTC
* * * * * * *
12636 GCATTTGATACTTA-GATGACACAGAGTCATCGGA-CATGTAATTCATAATAGGATTAATT
1 GCATTTAATACTCACGATGACACAAAGTCATCGGACCCT-TAATCCATAATTGGATTCATT
* *
12695 TCATTTAATACTCACGATGACACAAAGTCATCGGACCCTTAATCCATGATTGGATTCATT
1 GCATTTAATACTCACGATGACACAAAGTCATCGGACCCTTAATCCATAATTGGATTCATT
*
12755 GCATTTAATACTCACGATGACACAAAGTCATCGGACCCTTAATCCGTAATTGGATTCATT
1 GCATTTAATACTCACGATGACACAAAGTCATCGGACCCTTAATCCATAATTGGATTCATT
*
12815 GCATTTAATACTCACGATAACACAAAGTCATCGGACC
1 GCATTTAATACTCACGATGACACAAAGTCATCGGACC
12852 TTTTTACATT
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
59 11 0.08
60 129 0.91
61 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (60 bp):
GCATTTAATACTCACGATGACACAAAGTCATCGGACCCTTAATCCATAATTGGATTCATT
Found at i:26143 original size:67 final size:67
Alignment explanation
Indices: 26026--26195 Score: 306
Period size: 67 Copynumber: 2.5 Consensus size: 67
26016 ATGGAAGGGA
*
26026 GGCACGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGACCTTCAACATGGGCAATAATGAAGACAGA
1 GGCAAGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGACCTTCAACATGGGCAATAATGAAGACAGA
26091 AG
66 AG
26093 GGCAAGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGACCTTCAACGA-GGGCAATAATGAAGACAG
1 GGCAAGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGACCTTCAAC-ATGGGCAATAATGAAGACAG
26157 AAG
65 AAG
*
26160 GGCAAGTGGGAGGGGGAAGCAGGTTGGGCCGGGTGA
1 GGCAAGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGA
26196 ATTGGATAGG
Statistics
Matches: 100, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
67 99 0.99
68 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.46, T:0.11
Consensus pattern (67 bp):
GGCAAGTGGGAGGGGGAAGCAGGTAGGGCCGGGTGACCTTCAACATGGGCAATAATGAAGACAGA
AG
Found at i:27396 original size:14 final size:14
Alignment explanation
Indices: 27379--27418 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
27369 TTTATTCAAT
*
27379 TCAACTCTTAACAC
1 TCAACTCTCAACAC
*
27393 TCAACACTCAACAC
1 TCAACTCTCAACAC
*
27407 TCAACTTTCAAC
1 TCAACTCTCAAC
27419 TTTCAACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (14 bp):
TCAACTCTCAACAC
Found at i:28100 original size:32 final size:32
Alignment explanation
Indices: 28042--28114 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
28032 GGGATTTTGG
* *
28042 TTTAGGTTTCAAAAATTTGGAAATTTTTGGGT
1 TTTAGGTTTCAAAAATTTGGAAATTTTCGGGA
* *
28074 TTTAGGTTTCAAAATTTTAGG-GATTTTCGGGA
1 TTTAGGTTTCAAAAATTT-GGAAATTTTCGGGA
*
28106 TTTAAGTTT
1 TTTAGGTTT
28115 GAGGATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (32 bp):
TTTAGGTTTCAAAAATTTGGAAATTTTCGGGA
Found at i:28203 original size:30 final size:30
Alignment explanation
Indices: 28167--28229 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
28157 ATGATTAGTG
*
28167 AAGGTTCATGCTCCAAATCACAGTGAAGAA
1 AAGGTTCATGCTCCAAATCACAGAGAAGAA
*
28197 AAGGTTCATGCTCCAGATCACAGAGAAGAA
1 AAGGTTCATGCTCCAAATCACAGAGAAGAA
28227 AAG
1 AAG
28230 ATACAAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (30 bp):
AAGGTTCATGCTCCAAATCACAGAGAAGAA
Found at i:32153 original size:63 final size:63
Alignment explanation
Indices: 32035--32180 Score: 152
Period size: 63 Copynumber: 2.3 Consensus size: 63
32025 TAATCGCTCT
* * * * * *
32035 TGCATCAACACATACATCACCAATTTATTTTACACGAGCACAACATCACGTGCAAT-TGTTCCC
1 TGCACCAACACATTCATCACCAATGTATTTCACACAAGCACAACATCACGCGCAATCT-TTCCC
* * *
32098 TGCACCAACACATTCATCACCACTGTATTTCACACAAGCACCA-ATACATGCGCAATCTTTCCC
1 TGCACCAACACATTCATCACCAATGTATTTCACACAAGCACAACAT-CACGCGCAATCTTTCCC
* **
32161 TACACTGACACATTCATCAC
1 TGCACCAACACATTCATCAC
32181 AGGTTTATTA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
62 2 0.03
63 66 0.96
64 1 0.01
ACGTcount: A:0.33, C:0.34, G:0.08, T:0.25
Consensus pattern (63 bp):
TGCACCAACACATTCATCACCAATGTATTTCACACAAGCACAACATCACGCGCAATCTTTCCC
Found at i:35982 original size:2 final size:2
Alignment explanation
Indices: 35975--36027 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
35965 GGTAAATGTA
35975 AT AT AT AT AT AT 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 AT AT AT AT AT AT
36017 AT AT AT AT AT A
1 AT AT AT AT AT A
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.