Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004283.1 Kokia drynarioides strain JFW-HI SEQ_117578, 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: 2381
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.34
Warning! 171 characters in sequence are not A, C, G, or T
Found at i:1475 original size:58 final size:57
Alignment explanation
Indices: 1411--1717 Score: 314
Period size: 58 Copynumber: 5.3 Consensus size: 57
1401 CATAATTCTC
* * *
1411 CAAAAATTACAATTTTAACCTTAAACTTTTTAAAATTCCA-TTTTAACCCTAAATTTT
1 CAAAAATTAC-ATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCCTAAATTTT
* * *
1468 CAAAAAATTACATTTTACACC-CAAAATTTTCCAAAATTCCATTTTTGACCTTAAATTTTT
1 C-AAAAATTACATTTTAC-CCTCAAACTTTT-CAAAATTCCATTTTTAACCCTAAA-TTTT
* * * *
1528 CAAAAATTACATTTTACCCTCGAACTTTTCAAAATCCCATTTTTTACCTTAAATTTT
1 CAAAAATTACATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCCTAAATTTT
* * * *
1585 CTAAAAATTACATTTTACCCTTAAACTTTCCAAAATCCCATTTTTGACCCCTAAA-TTT
1 C-AAAAATTACATTTTACCCTCAAACTTTTCAAAATTCCATTTTT-AACCCTAAATTTT
* * * * * * *
1643 CCAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCAAAAATTC
1 CAAAAATTACA-TTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACC-CTAAATTTT
1702 CAAAAATTACAATTTT
1 CAAAAATTAC-ATTTT
1718 GCCTCTGAAC
Statistics
Matches: 213, Mismatches: 25, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
57 30 0.14
58 122 0.57
59 55 0.26
60 6 0.03
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.39
Consensus pattern (57 bp):
CAAAAATTACATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCCTAAATTTT
Found at i:1629 original size:116 final size:116
Alignment explanation
Indices: 1394--1717 Score: 359
Period size: 116 Copynumber: 2.8 Consensus size: 116
1384 AAATTGTCAG
* * * *
1394 TTTGACCCAT-AATTCTCCAAAAATTACAATTTTAACCTTAAACTTTTTAAAATTCCA-TTTTAA
1 TTTGACCCCTAAATT-T-CAAAAATTAC-ATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAA
* * *
1457 CCCTAAATTTTCAAAAAATTACATTTTACACCCAAAATTTTCCAAAATTCCATT
63 CCTTAAATTTTCAAAAAATTACATTTTACACCCAAAACTTTCCAAAATCCCATT
* * * *
1511 TTTGA-CCTTAAATTTTTCAAAAATTACATTTTACCCTCGAACTTTTCAAAATCCCATTTTTTAC
1 TTTGACCCCTAAA--TTTCAAAAATTACATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAAC
* **
1575 CTTAAATTTTCTAAAAATTACATTTTAC-CCTTAAACTTTCCAAAATCCCATT
64 CTTAAATTTTCAAAAAATTACATTTTACACCCAAAACTTTCCAAAATCCCATT
* * * *
1627 TTTGACCCCTAAATTTCCAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACC
1 TTTGACCCCTAAATTTCAAAAATTACA-TTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACC
* ** *
1692 TCAAAAATTCCAAAAATTACAATTTT
65 TTAAATTTTCAAAAAATTAC-ATTTT
1718 GCCTCTGAAC
Statistics
Matches: 176, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
115 13 0.07
116 100 0.57
117 60 0.34
118 1 0.01
119 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (116 bp):
TTTGACCCCTAAATTTCAAAAATTACATTTTACCCTCAAACTTTTCAAAATTCCATTTTTAACCT
TAAATTTTCAAAAAATTACATTTTACACCCAAAACTTTCCAAAATCCCATT
Found at i:1658 original size:29 final size:29
Alignment explanation
Indices: 1404--1757 Score: 192
Period size: 29 Copynumber: 12.1 Consensus size: 29
1394 TTTGACCCAT
* * * *
1404 AATTCTCCAAAAATTACAATTTTAACCTTA
1 AATTTTCC-AAAATTACATTTTTACCCCTA
* * *
1434 AACTTTT-TAAAATTCCA-TTTTAACCCTA
1 AA-TTTTCCAAAATTACATTTTTACCCCTA
* *
1462 AATTTTCAAAAAATTACA-TTTTACACCCAA
1 AATTTTC-CAAAATTACATTTTTAC-CCCTA
* *
1492 AATTTTCCAAAATTCCATTTTTGA-CCTTA
1 AATTTTCCAAAATTACATTTTT-ACCCCTA
* *
1521 AATTTTTCAAAAATTACA-TTTTACCCTCGA
1 AA-TTTTCCAAAATTACATTTTTACCC-CTA
* ** *
1551 ACTTTT-CAAAATCCCATTTTTTA-CCTTA
1 AATTTTCCAAAATTACA-TTTTTACCCCTA
* *
1579 AATTTTCTAAAAATTACA-TTTTACCCTTA
1 AATTTTC-CAAAATTACATTTTTACCCCTA
* **
1608 AACTTTCCAAAATCCCATTTTTGACCCCTA
1 AATTTTCCAAAATTACATTTTT-ACCCCTA
*
1638 AA-TTTCCAAAATTACATTTTTACCCCCA
1 AATTTTCCAAAATTACATTTTTACCCCTA
* * *
1666 AACTTTCCAAAATTCCATTTTTGACCTC-A
1 AATTTTCCAAAATTACATTTTT-ACCCCTA
** * * * *
1695 AAAATTCCAAAAATTACAATTTTGCCTCTG
1 AATTTTCC-AAAATTACATTTTTACCCCTA
*
1725 AA-CTTCCAAAAATTTAC-TATTTTACCCCTA
1 AATTTTCC-AAAA-TTACAT-TTTTACCCCTA
1755 AAT
1 AAT
1758 GTCTAAAAAT
Statistics
Matches: 254, Mismatches: 47, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
27 4 0.02
28 46 0.18
29 116 0.46
30 84 0.33
31 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.39
Consensus pattern (29 bp):
AATTTTCCAAAATTACATTTTTACCCCTA
Found at i:1732 original size:58 final size:57
Alignment explanation
Indices: 1394--1735 Score: 298
Period size: 58 Copynumber: 5.9 Consensus size: 57
1384 AAATTGTCAG
* * ** *
1394 TTTGACC-CATAATTCTCCAAAAATTACAATTTTAACCTTAAACTTTTTAAAATTCCA-T
1 TTTGACCTCAAAATT-TCCAAAAATTAC-ATTTT-ACCCTAAACTTTCCAAAATCCCATT
* * * * * *
1452 TTTAACC-CTAAATTTTCAAAAAATTACATTTTACACCCAAAATTTTCCAAAATTCCATT
1 TTTGACCTC-AAAATTTCCAAAAATTACATTTT--ACCCTAAACTTTCCAAAATCCCATT
* * * * *
1511 TTTGACCTTAAATTTTTCAAAAATTACATTTTACCCTCGAACTTTTCAAAATCCCATT
1 TTTGACCTCAAAATTTCCAAAAATTACATTTTACCCT-AAACTTTCCAAAATCCCATT
* * * *
1569 TTTTACCTTAAATTTTCTAAAAATTACATTTTACCCTTAAACTTTCCAAAATCCCATT
1 TTTGACCTCAAAATTTCCAAAAATTACATTTTACCC-TAAACTTTCCAAAATCCCATT
* * * *
1627 TTTGACCCCTAAATTTCC-AAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATT
1 TTTGACCTCAAAATTTCCAAAAATTACA-TTTTA-CCCTAAACTTTCCAAAATCCCATT
* * *
1685 TTTGACCTCAAAAATTCCAAAAATTACAATTTTGCCTCTGAAC-TTCCAAAA
1 TTTGACCTCAAAATTTCCAAAAATTAC-ATTTTACC-CTAAACTTTCCAAAA
1736 ATTTACTATT
Statistics
Matches: 235, Mismatches: 38, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
57 18 0.08
58 164 0.70
59 52 0.22
60 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (57 bp):
TTTGACCTCAAAATTTCCAAAAATTACATTTTACCCTAAACTTTCCAAAATCCCATT
Found at i:1766 original size:59 final size:59
Alignment explanation
Indices: 1703--1865 Score: 133
Period size: 59 Copynumber: 2.8 Consensus size: 59
1693 CAAAAATTCC
* * *
1703 AAAAATTA-CAATTTTGCCTCTGAA-CTTCCAAAAATTTACTATTTTACCC-CTAAATGTCT
1 AAAAATTACCAATTTTGACTC-CAACCTTCCAAAAA-TTACCATTTTACCCTC-AAATGTCT
** *
1762 AAAAA-TACCTTTTTTGATTCCAAGCCTTCCAAAAATTACCATTTTACCCTCAAATGTCT
1 AAAAATTACCAATTTTGACTCCAA-CCTTCCAAAAATTACCATTTTACCCTCAAATGTCT
* * *
1821 AAAAATT-CTC--TTTTAAACCTCGAACCTTCTAAAAATTACCATTTT
1 AAAAATTAC-CAATTTT-GA-CTCCAACCTTCCAAAAATTACCATTTT
1866 GTTCCTGAAG
Statistics
Matches: 86, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
58 8 0.09
59 61 0.71
60 17 0.20
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAAATTACCAATTTTGACTCCAACCTTCCAAAAATTACCATTTTACCCTCAAATGTCT
Found at i:1826 original size:29 final size:31
Alignment explanation
Indices: 1792--1865 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 31
1782 CAAGCCTTCC
*
1792 AAAAATTACCATTTT-ACCCTC-AA-ATGTCT
1 AAAAATTACCATTTTAAACCTCGAACAT-TCT
*
1821 AAAAATT-CTC-TTTTAAACCTCGAACCTTCT
1 AAAAATTAC-CATTTTAAACCTCGAACATTCT
1851 AAAAATTACCATTTT
1 AAAAATTACCATTTT
1866 GTTCCTGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 5 0.14
29 13 0.35
30 13 0.35
31 6 0.16
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (31 bp):
AAAAATTACCATTTTAAACCTCGAACATTCT
Done.