Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005797.1 Kokia drynarioides strain JFW-HI SEQ_120070, 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, 865
Length: 1443
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Found at i:1026 original size:29 final size:29
Alignment explanation
Indices: 983--1275 Score: 142
Period size: 30 Copynumber: 10.0 Consensus size: 29
973 TTATACTTTA
*
983 ACCCCCGAACTTTCTAAAAATTACATTTTT
1 ACCCTCGAA-TTTCTAAAAATTACATTTTT
* *
1013 ATCCTTGAATTTCTTAAAAATTACATTTTT
1 ACCCTCGAATTTC-TAAAAATTACATTTTT
*
1043 ACCCTCGAACATTCT-AAAATTGACA-TTTT
1 ACCCTCGAA-TTTCTAAAAATT-ACATTTTT
** * * *
1072 ACTCCTATACTTTC-CAAAATTACAATTTT
1 AC-CCTCGAATTTCTAAAAATTACATTTTT
* *
1101 ACCCTCGAATTT-TCCAAAATTTCATTTTT
1 ACCCTCGAATTTCT-AAAAATTACATTTTT
** *
1130 AATCTCG-ATTTCACGAAAAATTACCA-TTTT
1 ACCCTCGAATTT--CTAAAAATTA-CATTTTT
* * *
1160 ACCCCCGAACTTTC-CAAAATTCCATTTTT
1 ACCCTCGAA-TTTCTAAAAATTACATTTTT
*
1189 A-CCTCGAATTTC-ACCCAAAATTCCATTTTTT
1 ACCCTCGAATTTCTA---AAAATTACA-TTTTT
* * * *
1220 A-TCTTGATTTTTCTAAAAATTATC-GTTTT
1 ACCCTCGA-ATTTCTAAAAATTA-CATTTTT
* *
1249 ACCCTCGAATGTCT-AAAATTCCATTTT
1 ACCCTCGAATTTCTAAAAATTACATTTT
1276 AATCCCCAAA
Statistics
Matches: 201, Mismatches: 38, Indels: 50
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.02
28 31 0.15
29 69 0.34
30 71 0.35
31 17 0.08
32 7 0.03
33 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.41
Consensus pattern (29 bp):
ACCCTCGAATTTCTAAAAATTACATTTTT
Found at i:1061 original size:30 final size:30
Alignment explanation
Indices: 983--1200 Score: 147
Period size: 29 Copynumber: 7.5 Consensus size: 30
973 TTATACTTTA
*
983 ACCCCCGAACTTTCTAAAAATTACATTTTT
1 ACCCTCGAACTTTCTAAAAATTACATTTTT
* *
1013 ATCCTTGAA-TTTCTTAAAAATTACATTTTT
1 ACCCTCGAACTTTC-TAAAAATTACATTTTT
*
1043 ACCCTCGAACATTCT-AAAATTGACA-TTTT
1 ACCCTCGAACTTTCTAAAAATT-ACATTTTT
* *
1072 ACTCCT--ATACTTTC-CAAAATTACAATTTT
1 AC-CCTCGA-ACTTTCTAAAAATTACATTTTT
* * *
1101 ACCCTCGAATTTTC-CAAAATTTCATTTTT
1 ACCCTCGAACTTTCTAAAAATTACATTTTT
** *
1130 AATCTCG-A-TTTCACGAAAAATTACCA-TTTT
1 ACCCTCGAACTTT--CTAAAAATTA-CATTTTT
* * *
1160 ACCCCCGAACTTTC-CAAAATTCCATTTTT
1 ACCCTCGAACTTTCTAAAAATTACATTTTT
1189 A-CCTCGAA-TTTC
1 ACCCTCGAACTTTC
1201 ACCCAAAATT
Statistics
Matches: 152, Mismatches: 20, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
27 7 0.05
28 16 0.11
29 68 0.45
30 52 0.34
31 6 0.04
32 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
ACCCTCGAACTTTCTAAAAATTACATTTTT
Found at i:1150 original size:88 final size:88
Alignment explanation
Indices: 1080--1257 Score: 223
Period size: 89 Copynumber: 2.0 Consensus size: 88
1070 TTACTCCTAT
* *
1080 ACTTTCCAAAATTACAATTTTACCCTCGAATTT-TCCAAAATTTCATTTTTAATCTCGATTTCAC
1 ACTTTCCAAAATTACAATTTTA-CCTCGAATTTACCCAAAATTCCATTTTTAATCTCGATTTCAC
1144 GAAAAATTACCATTTTACCCCCGA
65 GAAAAATTACCATTTTACCCCCGA
* * * * **
1168 ACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCCAAAATTCCATTTTTTATCTTGATTTTTC
1 ACTTTCCAAAATTACAATTTTACCTCGAATTT-ACCCAAAATTCCATTTTTAATCTCGATTTCAC
* * * *
1233 TAAAAATTATCGTTTTACCCTCGA
65 GAAAAATTACCATTTTACCCCCGA
1257 A
1 A
1258 TGTCTAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 10 0.13
88 20 0.26
89 46 0.61
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.40
Consensus pattern (88 bp):
ACTTTCCAAAATTACAATTTTACCTCGAATTTACCCAAAATTCCATTTTTAATCTCGATTTCACG
AAAAATTACCATTTTACCCCCGA
Found at i:1174 original size:59 final size:59
Alignment explanation
Indices: 983--1217 Score: 182
Period size: 59 Copynumber: 4.0 Consensus size: 59
973 TTATACTTTA
* * * **
983 ACCCCCGAACTTTCTAAAAATTACATTTTTATCCTTGAATTTC-TTAAAAATTA-CATTTTT
1 ACCCCCGAACTTTC-CAAAATTCCATTTTTA-CCTCGAATTTCACCAAAAATTACCA-TTTT
* * * * * *
1043 ACCCTCGAACATTCTAAAATTGACA-TTTTA-CTCCTATACTTT--CC-AAAATTACAATTTT
1 ACCCCCGAACTTTCCAAAATT-CCATTTTTACCT-CGA-A-TTTCACCAAAAATTACCATTTT
* * * * *
1101 ACCCTCGAATTTTCCAAAATTTCATTTTTAATCTCG-ATTTCACGAAAAATTACCATTTT
1 ACCCCCGAACTTTCCAAAATTCCATTTTT-ACCTCGAATTTCACCAAAAATTACCATTTT
*
1160 ACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCCAAAATT-CCATTTT
1 ACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCAAAAATTACCATTTT
1218 TTATCTTGAT
Statistics
Matches: 142, Mismatches: 21, Indels: 26
0.75 0.11 0.14
Matches are distributed among these distances:
56 3 0.02
57 5 0.04
58 47 0.33
59 67 0.47
60 20 0.14
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (59 bp):
ACCCCCGAACTTTCCAAAATTCCATTTTTACCTCGAATTTCACCAAAAATTACCATTTT
Found at i:1288 original size:89 final size:89
Alignment explanation
Indices: 1084--1306 Score: 215
Period size: 89 Copynumber: 2.5 Consensus size: 89
1074 TCCTATACTT
* * *
1084 TCCAAAATTACAATTTT-ACCCTCGAATTTT--CCAAAATTTCATTTTTAATCTCGATTTCACGA
1 TCCAAAATT-CCATTTTAACCC-CAAATTTTCACCAAAATTCCATTTTTAATCTCGATTTCACGA
*
1146 AAAATTACCATTTTACCCCCGAACTT
64 AAAATTACCATTTTACCCCCGAACTG
* * * * * ** *
1172 TCCAAAATTCCATTTTTACCTCGAA-TTTCACCCAAAATTCCATTTTTTATCTTGATTTTTCTAA
1 TCCAAAATTCCATTTTAACCCCAAATTTTCA-CCAAAATTCCATTTTTAATCTCGATTTCACGAA
* * *
1236 AAATTATCGTTTTACCCTCGAA-TG
65 AAATTACCATTTTACCCCCGAACTG
*
1260 TCTAAAATTCCATTTTAATCCCCAAATTTTCA-CAAAATTTCCATTTT
1 TCCAAAATTCCATTTTAA-CCCCAAATTTTCACCAAAA-TTCCATTTT
1307 ACCCTCGAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 13
0.79 0.11 0.09
Matches are distributed among these distances:
86 3 0.03
87 10 0.09
88 34 0.30
89 60 0.54
90 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (89 bp):
TCCAAAATTCCATTTTAACCCCAAATTTTCACCAAAATTCCATTTTTAATCTCGATTTCACGAAA
AATTACCATTTTACCCCCGAACTG
Done.