Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002612.1 Kokia drynarioides strain JFW-HI SEQ_114827, 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: 4201
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Found at i:1548 original size:45 final size:45
Alignment explanation
Indices: 1497--1774 Score: 247
Period size: 45 Copynumber: 6.2 Consensus size: 45
1487 CATCGGTGGC
* * * *
1497 TTCTTTGGAGGCTCATAAACTGGTGATTTGGGCTCTGGTTTTTCT
1 TTCTTTGGAGGTTCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
* * * *
1542 TTCTTT-GACGGTTCATACACTGGTGGTTT-GGATTCAGGCTTCTCT
1 TTCTTTGGA-GGTTCATAAACTGGTGATTTAGG-CTCAGGTTTCTCT
* * * * * *
1587 TTCTTTGAAGGTGCATAAATTGGTGACTTAGGCTCAAGTTTCTCC
1 TTCTTTGGAGGTTCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
* * *
1632 TTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAGGTTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
*** ** *
1677 TTCTTTGGAGGTGT-ATAAACCAATGGCTTAGGTTCAGGTTTCTCT
1 TTCTTTGGAGGT-TCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
* * * * * *
1722 TTTTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCT
1 TTCTTTGGAGGTTCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
1767 TTCTTTGG
1 TTCTTTGG
1775 GTTCAGGTTT
Statistics
Matches: 185, Mismatches: 42, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
44 5 0.03
45 176 0.95
46 4 0.02
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (45 bp):
TTCTTTGGAGGTTCATAAACTGGTGATTTAGGCTCAGGTTTCTCT
Found at i:1645 original size:90 final size:89
Alignment explanation
Indices: 1497--1774 Score: 326
Period size: 90 Copynumber: 3.1 Consensus size: 89
1487 CATCGGTGGC
* * * *
1497 TTCTTTGGAGGCT-CATAAACTGGTGATTTGGGCTCTGGTTTTTCTTTCTTT-GACGGTTCATAC
1 TTCTTTGGAGG-TGCATAAACTGGTGACTTAGGCTCAGGTTTCTCTTTCTTTGGA-GGTTCATAC
*
1560 ACTGGTGGTTTGGATTCAGGCTTCTCT
64 ACTGGTGGTTTGG-TTCAGGTTTCTCT
* * * *
1587 TTCTTTGAAGGTGCATAAATTGGTGACTTAGGCTCAAGTTTCTCCTTCTTTGGAGGTTCATACAC
1 TTCTTTGGAGGTGCATAAACTGGTGACTTAGGCTCAGGTTTCTCTTTCTTTGGAGGTTCATACAC
* *
1652 TGGTGATCTAGGTTCAGGTTTCTCT
66 TGGTGGT-TTGGTTCAGGTTTCTCT
* *** * * * *
1677 TTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAGGTTTCTCTTTTTTTGGTGGTTCATACAC
1 TTCTTTGGAGGTGCATAAACTGGTGACTTAGGCTCAGGTTTCTCTTTCTTTGGAGGTTCATACAC
1742 TGGTGGTTTGGGTTCAGGTTTCTCT
66 TGGTGGTTT-GGTTCAGGTTTCTCT
1767 TTCTTTGG
1 TTCTTTGG
1775 GTTCAGGTTT
Statistics
Matches: 159, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
89 2 0.01
90 152 0.96
91 5 0.03
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (89 bp):
TTCTTTGGAGGTGCATAAACTGGTGACTTAGGCTCAGGTTTCTCTTTCTTTGGAGGTTCATACAC
TGGTGGTTTGGTTCAGGTTTCTCT
Found at i:1746 original size:135 final size:135
Alignment explanation
Indices: 1496--1774 Score: 285
Period size: 135 Copynumber: 2.1 Consensus size: 135
1486 ACATCGGTGG
* * * * *
1496 CTTCTTTGGAGGCTCATAAACTGGTGATTTGGGCTCTGGTTTTTCTTTCTTTGACGGTTCATACA
1 CTTCTTTGGAGGCTCATAAACTGGTGATCTAGGCTCAGGTTTCTCTTTCTTTGACGGTTCATAAA
*** * *
1561 CTGGTGGTTTGGATTCAGGCTTCTCTTTCTTTGAAGGTGCATAAATTGGTGACTTAGGCTCAAGT
66 CCAATGGTTAGGATTCAGGCTTCTCTTTCTTTGAAGGTGCATAAACTGGTGACTTAGGCTCAAGT
1626 TTCTC
131 TTCTC
* * *
1631 CTTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAGGTTTCTCTTTCTTTGGA-GGTGT-ATA
1 CTTCTTTGGAGGCTCATAAACTGGTGATCTAGGCTCAGGTTTCTCTTTCTTT-GACGGT-TCATA
* * ** * * ** * *
1694 AACCAATGGCTTAGG-TTCAGGTTTCTCTTTTTTTGGTGGTTCATACACTGGTGGTTTGGGTTCA
64 AACCAATGG-TTAGGATTCAGGCTTCTCTTTCTTTGAAGGTGCATAAACTGGTGACTTAGGCTCA
*
1758 GGTTTCTC
128 AGTTTCTC
*
1766 TTTCTTTGG
1 CTTCTTTGG
1775 GTTCAGGTTT
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
135 109 0.94
136 7 0.06
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (135 bp):
CTTCTTTGGAGGCTCATAAACTGGTGATCTAGGCTCAGGTTTCTCTTTCTTTGACGGTTCATAAA
CCAATGGTTAGGATTCAGGCTTCTCTTTCTTTGAAGGTGCATAAACTGGTGACTTAGGCTCAAGT
TTCTC
Found at i:1775 original size:22 final size:22
Alignment explanation
Indices: 1748--1796 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1738 ACACTGGTGG
1748 TTTGGGTTCAGGTTTCTCTTTC
1 TTTGGGTTCAGGTTTCTCTTTC
1770 TTTGGGTTCAGGTTTCTCTTTC
1 TTTGGGTTCAGGTTTCTCTTTC
1792 TTTGG
1 TTTGG
1797 TGGTTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.04, C:0.16, G:0.24, T:0.55
Consensus pattern (22 bp):
TTTGGGTTCAGGTTTCTCTTTC
Found at i:1780 original size:67 final size:67
Alignment explanation
Indices: 1707--1841 Score: 243
Period size: 67 Copynumber: 2.0 Consensus size: 67
1697 CAATGGCTTA
* *
1707 GGTTCAGGTTTCTCTTTTTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTT
1 GGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTT
1772 TG
66 TG
*
1774 GGTTCAGGTTTCTCTTTCTTTGGTGGTTCATATACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTT
1 GGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTT
1839 TG
66 TG
1841 G
1 G
1842 AGGTGTATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.50
Consensus pattern (67 bp):
GGTTCAGGTTTCTCTTTCTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTT
TG
Found at i:1820 original size:45 final size:45
Alignment explanation
Indices: 1770--1993 Score: 213
Period size: 45 Copynumber: 5.0 Consensus size: 45
1760 TTTCTCTTTC
* *
1770 TTTGGGTTCAGGTTTCTCTTTCTTTGGTGGTTCATATACTGGTGG
1 TTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTTCATAAACTGGTGG
* * *
1815 TTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT-ATAAATTGGCGG
1 TTTGGGTTCAGGTTTCTCTTTCTTTGGAGGT-TCATAAACTGGTGG
* * * ** * * *
1860 CTTAGGCTCAGACTTCTCCTTCTTCGGAGGTTCATACACTGGTGG
1 TTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTTCATAAACTGGTGG
* *
1905 TTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT-ATAAACAGGTGG
1 TTTGGGTTCAGGTTTCTCTTTCTTTGGAGGT-TCATAAACTGGTGG
* * * *
1950 CTTAGGTTCAGGCTTT-TCTTT-TTTCGGTGGTTCATACACTGGTG
1 TTTGGGTTCAGG-TTTCTCTTTCTTT-GGAGGTTCATAAACTGGTG
1994 ACTTAGATTC
Statistics
Matches: 141, Mismatches: 32, Indels: 12
0.76 0.17 0.06
Matches are distributed among these distances:
44 5 0.04
45 131 0.93
46 5 0.04
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (45 bp):
TTTGGGTTCAGGTTTCTCTTTCTTTGGAGGTTCATAAACTGGTGG
Found at i:1831 original size:157 final size:157
Alignment explanation
Indices: 1624--1931 Score: 436
Period size: 157 Copynumber: 2.0 Consensus size: 157
1614 TTAGGCTCAA
*
1624 GTTTCTCCTTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAGGTTTCTCTTTCTTTGGAGGT
1 GTTTCTCCTTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGT
* * ** * * * *
1689 GTATAAACCAATGGCTTAGGTTCAGGTTTCTCTTTTTTTGGTGGTTCATACACTGGTGGTTTGGG
66 GTATAAACCAACGGCTTAGGCTCAGACTTCTCCTTCTTCGGAGGTTCATACACTGGTGGTTTGGG
*
1754 TTCAGGTTTCTCTTTCTTTGGGTTCAG
131 TTCAAGTTTCTCTTTCTTTGGGTTCAG
* * * * * *
1781 GTTTCTCTTTCTTTGGTGGTTCATATACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGT
1 GTTTCTCCTTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGT
****
1846 GTATAAATTGGCGGCTTAGGCTCAGACTTCTCCTTCTTCGGAGGTTCATACACTGGTGGTTTGGG
66 GTATAAACCAACGGCTTAGGCTCAGACTTCTCCTTCTTCGGAGGTTCATACACTGGTGGTTTGGG
1911 TTCAAGTTTCTCTTTCTTTGG
131 TTCAAGTTTCTCTTTCTTTGG
1932 AGGTGTATAA
Statistics
Matches: 131, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
157 131 1.00
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.44
Consensus pattern (157 bp):
GTTTCTCCTTCTTTGGAGGTTCATACACTGGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGT
GTATAAACCAACGGCTTAGGCTCAGACTTCTCCTTCTTCGGAGGTTCATACACTGGTGGTTTGGG
TTCAAGTTTCTCTTTCTTTGGGTTCAG
Found at i:1877 original size:112 final size:112
Alignment explanation
Indices: 1662--1883 Score: 241
Period size: 112 Copynumber: 2.0 Consensus size: 112
1652 TGGTGATCTA
* *
1662 GGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAGGTTTCTCTTTTTT
1 GGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAAGTTTCTCTTTCTT
* * * * * * ** *
1727 TGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTTTCTTTG
66 TGGAGGTTCATAAACTGGCGGCTTAGGCTCAGACTTCTCCTTCTTTG
* * *** * *
1774 GGTTCAGGTTTCTCTTTCTTTGGTGGT-TCATATACTGGTGGTTTGGGTTCAAGTTTCTCTTTCT
1 GGTTCAGGTTTCTCTTTCTTTGGAGGTGT-ATAAACCAATGGCTTAGGTTCAAGTTTCTCTTTCT
*
1838 TTGGAGGTGT-ATAAATTGGCGGCTTAGGCTCAGACTTCTCCTTCTT
65 TTGGAGGT-TCATAAACTGGCGGCTTAGGCTCAGACTTCTCCTTCTT
1884 CGGAGGTTCA
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
111 1 0.01
112 87 0.98
113 1 0.01
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (112 bp):
GGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAAGTTTCTCTTTCTT
TGGAGGTTCATAAACTGGCGGCTTAGGCTCAGACTTCTCCTTCTTTG
Found at i:1892 original size:90 final size:90
Alignment explanation
Indices: 1783--1993 Score: 323
Period size: 90 Copynumber: 2.3 Consensus size: 90
1773 GGGTTCAGGT
* *
1783 TTCTCTTTCTTTGGTGGTTCATATACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT
1 TTCTCTTTCTTCGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT
**
1848 ATAAATTGGCGGCTTAGGCTCAGAC
66 ATAAACAGGCGGCTTAGGCTCAGAC
* *
1873 TTCTCCTTCTTCGGAGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT
1 TTCTCTTTCTTCGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT
* * *
1938 ATAAACAGGTGGCTTAGGTTCAGGC
66 ATAAACAGGCGGCTTAGGCTCAGAC
* *
1963 TTTTCTTTTTTCGGTGGTTCATACACTGGTG
1 TTCTCTTTCTTCGGTGGTTCATACACTGGTG
1994 ACTTAGATTC
Statistics
Matches: 108, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 108 1.00
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.43
Consensus pattern (90 bp):
TTCTCTTTCTTCGGTGGTTCATACACTGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGT
ATAAACAGGCGGCTTAGGCTCAGAC
Found at i:1981 original size:247 final size:247
Alignment explanation
Indices: 1523--1993 Score: 705
Period size: 247 Copynumber: 1.9 Consensus size: 247
1513 AAACTGGTGA
* * *
1523 TTTGGGCTCTGGTTTTTCTTTCTTTGACGGTTCATACACTGGTGGTTTGGATTCAGGCTTCTCTT
1 TTTGGGCTCAGGTTTCTCTTTCTTTGACGGTTCATACACTGGTGGTTTGGATTCAAGCTTCTCTT
* * *
1588 TCTTTGAAGGTGCATAAATTGGTGACTTAGGCTCAAGTTTCTCCTTCTTTGGAGGTTCATACACT
66 TCTTTGAAGGTGCATAAATTGGCGACTTAGGCTCAAGCTTCTCCTTCTTCGGAGGTTCATACACT
*
1653 GGTGATCTAGGTTCAGGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAGGTTT
131 GGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAGGTTT
*
1718 CTCTTTTTTTGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTTTC
196 CTCTTTTTTCGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTTTC
* ** * * *
1770 TTTGGGTTCAGGTTTCTCTTTCTTTGGTGGTTCATATACTGGTGGTTTGGGTTCAAGTTTCTCTT
1 TTTGGGCTCAGGTTTCTCTTTCTTTGACGGTTCATACACTGGTGGTTTGGATTCAAGCTTCTCTT
* * *
1835 TCTTTGGAGGTGTATAAATTGGCGGCTTAGGCTC-AGACTTCTCCTTCTTCGGAGGTTCATACAC
66 TCTTTGAAGGTGCATAAATTGGCGACTTAGGCTCAAG-CTTCTCCTTCTTCGGAGGTTCATACAC
* * * *
1899 TGGTGGTTTGGGTTCAAGTTTCTCTTTCTTTGGAGGTGTATAAA-CAGGTGGCTTAGGTTCAGGC
130 TGGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGTGTATAAACCA-ATGGCTTAGGTTCAGG-
1963 TTT-TCTTTTTTCGGTGGTTCATACACTGGTG
193 TTTCTCTTTTTTCGGTGGTTCATACACTGGTG
1994 ACTTAGATTC
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
246 4 0.02
247 193 0.96
248 3 0.01
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.43
Consensus pattern (247 bp):
TTTGGGCTCAGGTTTCTCTTTCTTTGACGGTTCATACACTGGTGGTTTGGATTCAAGCTTCTCTT
TCTTTGAAGGTGCATAAATTGGCGACTTAGGCTCAAGCTTCTCCTTCTTCGGAGGTTCATACACT
GGTGATCTAGGTTCAAGTTTCTCTTTCTTTGGAGGTGTATAAACCAATGGCTTAGGTTCAGGTTT
CTCTTTTTTCGGTGGTTCATACACTGGTGGTTTGGGTTCAGGTTTCTCTTTC
Found at i:3746 original size:24 final size:26
Alignment explanation
Indices: 3711--3762 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
3701 AAATATTAAA
3711 AAAATTAATAAATA-AAAAATA-TAT
1 AAAATTAATAAATATAAAAATAGTAT
* *
3735 AAAATTATTAAATATTAAAATAGTAT
1 AAAATTAATAAATATAAAAATAGTAT
3761 AA
1 AA
3763 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 6 0.25
26 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAATTAATAAATATAAAAATAGTAT
Found at i:3786 original size:24 final size:22
Alignment explanation
Indices: 3695--3790 Score: 67
Period size: 24 Copynumber: 4.3 Consensus size: 22
3685 AATATTATTC
*
3695 TAATGTAAATATTAAAAAAAT-
1 TAATATAAATATTAAAAAAATA
3716 T-A-ATAAATA--AAAAATATATA
1 TAATATAAATATTAAAAA-A-ATA
* * *
3736 AAATTATTAAATATTAAAATAGTA
1 TAA-TA-TAAATATTAAAAAAATA
3760 TAATATAAATATTTAAAAAAATAA
1 TAATATAAATA-TTAAAAAAAT-A
3784 TAATATA
1 TAATATA
3791 GGTGAACTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
17 5 0.09
18 1 0.02
19 8 0.14
20 1 0.02
21 2 0.04
22 6 0.11
23 11 0.19
24 18 0.32
25 1 0.02
26 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATATAAATATTAAAAAAATA
Done.