Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004585.1 Kokia drynarioides strain JFW-HI SEQ_118075, 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: 17772
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:983 original size:29 final size:29
Alignment explanation
Indices: 941--1193 Score: 241
Period size: 29 Copynumber: 8.7 Consensus size: 29
931 ATTTTCTTTG
* *
941 AAAATCACATTTTAATCCC-AAACTTATCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* *
970 AAAATTATATTTTAACCCTAAACTTCTCC
1 AAAATTACATTTTAACCCTAAACTTTTCC
*
999 AAAATCACATTTTAACCCCTAAAC-TTTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
*
1028 TAAAATTACATTTTAACCCCT-AACTTTTCT
1 -AAAATTACATTTTAA-CCCTAAACTTTTCC
*** *
1058 AAAATCGTATTTTAACACTAAAAC--TTCC
1 AAAATTACATTTTAACCCT-AAACTTTTCC
* *
1086 TAAAATCAAATTTTAACCCTAAAACTTTTCC
1 -AAAATTACATTTTAACCCT-AAACTTTTCC
*
1117 AAAATTACATTTTAACCCTAAACTTTTCT
1 AAAATTACATTTTAACCCTAAACTTTTCC
* *
1146 AAAATTACATTTTAACCAC-GAACTTATCC
1 AAAATTACATTTTAACC-CTAAACTTTTCC
1175 AAAATTACCATTTT-ACCCT
1 AAAATTA-CATTTTAACCCT
1194 TGAACATCCA
Statistics
Matches: 190, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
28 10 0.05
29 118 0.62
30 58 0.31
31 4 0.02
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:1041 original size:59 final size:58
Alignment explanation
Indices: 941--1193 Score: 275
Period size: 59 Copynumber: 4.3 Consensus size: 58
931 ATTTTCTTTG
* *
941 AAAATCACATTTTAATCCC-AAACTTATCC-AAAATTATATTTTAACCCTAAACTTCTCC
1 AAAATCACATTTTAA-CCCTAAACTT-TCCTAAAATTACATTTTAACCCTAAACTTTTCC
*
999 AAAATCACATTTTAACCCCTAAACTTTCCTAAAATTACATTTTAACCCCT-AACTTTTCT
1 AAAATCACATTTTAA-CCCTAAACTTTCCTAAAATTACATTTTAA-CCCTAAACTTTTCC
** * * *
1058 AAAATCGTATTTTAACACTAAAAC-TTCCTAAAATCAAATTTTAACCCTAAAACTTTTCC
1 AAAATCACATTTTAACCCT-AAACTTTCCTAAAATTACATTTTAACCCT-AAACTTTTCC
* * * *
1117 AAAATTACATTTTAACCCTAAACTTTTCTAAAATTACATTTTAACCAC-GAACTTATCC
1 AAAATCACATTTTAACCCTAAACTTTCCTAAAATTACATTTTAACC-CTAAACTTTTCC
*
1175 AAAATTACCATTTT-ACCCT
1 AAAATCA-CATTTTAACCCT
1194 TGAACATCCA
Statistics
Matches: 167, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
57 4 0.02
58 66 0.40
59 92 0.55
60 5 0.03
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.36
Consensus pattern (58 bp):
AAAATCACATTTTAACCCTAAACTTTCCTAAAATTACATTTTAACCCTAAACTTTTCC
Found at i:1193 original size:88 final size:88
Alignment explanation
Indices: 941--1193 Score: 281
Period size: 88 Copynumber: 2.9 Consensus size: 88
931 ATTTTCTTTG
* * * *
941 AAAATCACATTTTAATCCC-AAACTTATCCAAAATTATATTTTAACC-CTAAACTTCTCCAAAAT
1 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTATATTTTAACCACTAAACTT-TCCAAAAT
1004 CACATTTTAACCCCTAAACTTTCCT
65 CACATTTTAA-CCCTAAACTTTCCT
**
1029 AAAATTACATTTTAACCCCT-AACTTTTCTAAAATCGTATTTTAA-CACTAAAAC-TTCCTAAAA
1 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTATATTTTAACCACT-AAACTTTCC-AAAA
*
1091 TCAAATTTTAACCCTAAAACTTTTCC-
64 TCACATTTTAACCCT-AAAC-TTTCCT
* *
1117 AAAATTACATTTTAA-CCCTAAACTTTTCTAAAATTACATTTTAACCAC-GAACTTATCCAAAAT
1 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTATATTTTAACCACTAAACTT-TCCAAAAT
*
1180 TACCATTTT-ACCCT
65 CA-CATTTTAACCCT
1194 TGAACATCCA
Statistics
Matches: 141, Mismatches: 13, Indels: 22
0.80 0.07 0.12
Matches are distributed among these distances:
87 15 0.11
88 106 0.75
89 20 0.14
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.36
Consensus pattern (88 bp):
AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTATATTTTAACCACTAAACTTTCCAAAATC
ACATTTTAACCCTAAACTTTCCT
Found at i:1255 original size:29 final size:29
Alignment explanation
Indices: 1200--1258 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1190 CCCTTGAACA
*
1200 TCCAAAAATCACCATTTTGCCCCCAAATT
1 TCCAAAAATCACCATTTTGACCCCAAATT
* *
1229 TCCAAAAGTCA-CATTTTCGACCTCAAATT
1 TCCAAAAATCACCATTTT-GACCCCAAATT
1258 T
1 T
1259 TTGAAAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
TCCAAAAATCACCATTTTGACCCCAAATT
Found at i:7170 original size:23 final size:20
Alignment explanation
Indices: 7143--7186 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
7133 TCTTAAATTG
7143 TTTTATTTA-AAAATTATTA
1 TTTTATTTATAAAATTATTA
*
7162 TTTTATTTATAAGATTATTA
1 TTTTATTTATAAAATTATTA
7182 TTTTA
1 TTTTA
7187 ATAGATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAAAATTATTA
Found at i:7266 original size:22 final size:22
Alignment explanation
Indices: 7241--7282 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7231 TATACTTTTG
*
7241 TATGTAT-TTTTTAATAAAATAT
1 TATGTATATTTATAA-AAAATAT
7263 TATGTATATTTATAAAAAAT
1 TATGTATATTTATAAAAAAT
7283 TAACTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATGTATATTTATAAAAAATAT
Done.