Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003584.1 Kokia drynarioides strain JFW-HI SEQ_116457, 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: 2252
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Found at i:1287 original size:30 final size:29
Alignment explanation
Indices: 1253--1487 Score: 251
Period size: 30 Copynumber: 7.9 Consensus size: 29
1243 ATTTTCTCTA
* *
1253 AAAATCACATTTTAACACCTAAACTTCTCC
1 AAAATTACATTTTAAC-CCTAAACTTTTCC
* *
1283 AAAATTACATTTTGACCCTTAAAATTTTCC
1 AAAATTACATTTTAACCC-TAAACTTTTCC
* * *
1313 AAAAATCACATTTTGACCATTAAACTTTTCC
1 -AAAATTACATTTTAACC-CTAAACTTTTCC
1344 AAAATTACATTTTAACCCATAAACTTTTCC
1 AAAATTACATTTTAACCC-TAAACTTTTCC
*
1374 AAAATTACATTTTAACCCCCT-AACCTTTCC
1 AAAATTACATTTTAA--CCCTAAACTTTTCC
*
1404 AAAATTACATTTTAACCCCTAAACTTCTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* *
1434 GAAATTACCA-TTTAACTCCTAAACTTTTCA
1 AAAATTA-CATTTTAAC-CCTAAACTTTTCC
*
1464 AAAATTACA-TTTGACCCTAAACTT
1 AAAATTACATTTTAACCCTAAACTT
1488 CCCTAAAATT
Statistics
Matches: 178, Mismatches: 18, Indels: 20
0.82 0.08 0.09
Matches are distributed among these distances:
28 9 0.05
29 15 0.08
30 122 0.69
31 29 0.16
32 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:1509 original size:29 final size:27
Alignment explanation
Indices: 1253--1542 Score: 150
Period size: 30 Copynumber: 9.8 Consensus size: 27
1243 ATTTTCTCTA
*
1253 AAAATCACATTTTAACACCTAAACTTCTCC
1 AAAATTACA-TTTAAC-CCTAAACTTC-CC
* * *
1283 AAAATTACATTTTGACCCTTAAAATTTTCCA
1 AAAATTACA-TTTAACCC-T-AAA-CTTCCC
* * * *
1314 AAAATCACATTTTGACCATTAAACTTTTCC
1 AAAATTACA-TTTAACC-CTAAAC-TTCCC
*
1344 AAAATTACATTTTAACCCATAAACTTTTCC
1 AAAATTACA-TTTAACCC-TAAAC-TTCCC
* *
1374 AAAATTACATTTTAACCCCCTAACCTTTCC
1 AAAATTACA-TTTAA--CCCTAAACTTCCC
1404 AAAATTACATTTTAACCCCTAAACTTCTCC
1 AAAATTACA-TTTAA-CCCTAAACTTC-CC
* * *
1434 GAAATTACCATTTAACTCCTAAACTTTTCA
1 AAAATTA-CATTTAAC-CCTAAAC-TTCCC
*
1464 AAAATTACATTTGACCCTAAACTTCCC
1 AAAATTACATTTAACCCTAAACTTCCC
* * * * *
1491 TAAAATTATGATTTTACCCTTGAACATCCA
1 -AAAATTA-CATTTAACCC-TAAACTTCCC
1521 AAAATTACCATTT-ACCACTAAA
1 AAAATTA-CATTTAACC-CTAAA
1543 TTTCTAAAAA
Statistics
Matches: 214, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
27 3 0.01
28 20 0.09
29 40 0.19
30 116 0.54
31 29 0.14
32 6 0.03
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAATTACATTTAACCCTAAACTTCCC
Found at i:1708 original size:10 final size:11
Alignment explanation
Indices: 1688--1712 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1678 TTTGACCCCG
1688 TTTCTTTTTTT
1 TTTCTTTTTTT
1699 TTTCTTTTTTT
1 TTTCTTTTTTT
1710 TTT
1 TTT
1713 GATGTTCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Done.