Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006236.1 Kokia drynarioides strain JFW-HI SEQ_120807, 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: 2996
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Found at i:1423 original size:47 final size:47
Alignment explanation
Indices: 1363--1491 Score: 170
Period size: 47 Copynumber: 2.7 Consensus size: 47
1353 TAGCTTCATA
* * *
1363 TTTTGATCTACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTG
1 TTTTG-TCCACTTCTCTGTATCTCACCAGGAAGATGACTACTTTGTTG
*
1411 TTTTGTCCACTTCTCTGTATCTCACCAAGAAGATGACTACTTTGTTG
1 TTTTGTCCACTTCTCTGTATCTCACCAGGAAGATGACTACTTTGTTG
** * *
1458 TTTTACCCACTTCTCTGTATC-AACTAGGAAGATG
1 TTTTGTCCACTTCTCTGTATCTCACCAGGAAGATG
1492 GGGTTTGAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 10 0.14
47 57 0.79
48 5 0.07
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (47 bp):
TTTTGTCCACTTCTCTGTATCTCACCAGGAAGATGACTACTTTGTTG
Found at i:1601 original size:47 final size:47
Alignment explanation
Indices: 1541--1754 Score: 189
Period size: 47 Copynumber: 4.6 Consensus size: 47
1531 ATTTTGGTAC
* * *
1541 ACTTCTTTATATCTCACTAGGAAGATGACCACTTCATTATTTGACCT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTATTTGACCT
* * * **
1588 ACTTCTCTGTATCTCACAAGGAAGATGACCACTTCATTGTTCGATGT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTATTTGACCT
*** ** * *
1635 ACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCC-
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATT-ATTTGACCT
* ** ** * *
1682 ACTTCTCTGTATCTCACCAAGAAGATGACTGCTTTGTTATTTTACCC
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTATTTGACCT
* *
1729 ACTTCTCTGTATC-AACTAGGAAGATG
1 ACTTCTCTGTATCTCACCAGGAAGATG
1755 GGGTTTGAAG
Statistics
Matches: 139, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
46 15 0.11
47 121 0.87
48 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (47 bp):
ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTATTTGACCT
Found at i:1838 original size:263 final size:263
Alignment explanation
Indices: 1371--1924 Score: 1045
Period size: 263 Copynumber: 2.1 Consensus size: 263
1361 TATTTTGATC
1371 TACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCCACTTCTCTGTATCTCAC
1 TACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCCACTTCTCTGTATCTCAC
*
1436 CAAGAAGATGACTACTTTGTTGTTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAA
66 CAAGAAGATGACTACTTTGTTATTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAA
*
1501 GTTTCACTAACATTTAATTTTCACCTCATTATTTTGGTACACTTCTTTATATCTCACTAGGAAGA
131 GTTTCACTAACATTTAATTTTCACCTCATTATTTTGGTACACTTCTTTATATCTCACCAGGAAGA
1566 TGACCACTTCATTATTTGACCTACTTCTCTGTATCTCACAAGGAAGATGACCACTTCATTGTTCG
196 TGACCACTTCATTATTTGACCTACTTCTCTGTATCTCACAAGGAAGATGACCACTTCATTGTTCG
1631 ATG
261 ATG
1634 TACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCCACTTCTCTGTATCTCAC
1 TACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCCACTTCTCTGTATCTCAC
*
1699 CAAGAAGATGACTGCTTTGTTATTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAA
66 CAAGAAGATGACTACTTTGTTATTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAA
1764 GTTTCACTAACATTTAATTTTCACCTCATTATTTTGGTACACTTCTTTATATCTCACCAGGAAGA
131 GTTTCACTAACATTTAATTTTCACCTCATTATTTTGGTACACTTCTTTATATCTCACCAGGAAGA
* * *
1829 TGACCACTTCATTGTTTGACCTACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTG
196 TGACCACTTCATTATTTGACCTACTTCTCTGTATCTCACAAGGAAGATGACCACTTCATTGTTCG
1894 ATG
261 ATG
*
1897 TACTTCTCTGTACCTCACCAGGAAGATG
1 TACTTCTCTGTATCTCACCAGGAAGATG
1925 GGGTCTGAGG
Statistics
Matches: 284, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
263 284 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (263 bp):
TACTTCTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCCACTTCTCTGTATCTCAC
CAAGAAGATGACTACTTTGTTATTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAA
GTTTCACTAACATTTAATTTTCACCTCATTATTTTGGTACACTTCTTTATATCTCACCAGGAAGA
TGACCACTTCATTATTTGACCTACTTCTCTGTATCTCACAAGGAAGATGACCACTTCATTGTTCG
ATG
Found at i:1864 original size:47 final size:47
Alignment explanation
Indices: 1804--1924 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
1794 ATTTTGGTAC
* *
1804 ACTTCTTTATATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
**
1851 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGATGT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
*
1898 ACTTCTCTGTACCTCACCAGGAAGATG
1 ACTTCTCTGTATCTCACCAGGAAGATG
1925 GGGTCTGAGG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (47 bp):
ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
Found at i:1992 original size:123 final size:123
Alignment explanation
Indices: 1855--2188 Score: 488
Period size: 123 Copynumber: 2.7 Consensus size: 123
1845 TGACCTACTT
* * **
1855 CTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGATGTACTTCTCTGTACCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
* * * *
1920 AGATGGGGTCTGAGGTTTCACTCACATTCGAGTTTTACATCATTATTTTGGTACACTA
66 AGATAGGGTCTGAAGTTTCACTCACATTCGAGCTTTACAGCATTATTTTGGTACACTA
**
1978 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
* * * * *
2043 AGATAGGGTCTAAAGTTTCACTCATATTTGAGCTTTACCGCATTATTTTGGTACACTT
66 AGATAGGGTCTGAAGTTTCACTCACATTCGAGCTTTACAGCATTATTTTGGTACACTA
* * * *
2101 CTCTGTATCTCACCAGGAATATGACCGCTTCGTTGTCTGACCTACTTCTCAGTACCTCACTAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
*
2166 AGATAGGGTTTGAAGTTTCACTC
66 AGATAGGGTCTGAAGTTTCACTC
2189 CACTCCACTG
Statistics
Matches: 188, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
123 188 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (123 bp):
CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
AGATAGGGTCTGAAGTTTCACTCACATTCGAGCTTTACAGCATTATTTTGGTACACTA
Found at i:2000 original size:170 final size:169
Alignment explanation
Indices: 1639--2046 Score: 507
Period size: 170 Copynumber: 2.4 Consensus size: 169
1629 CGATGTACTT
** * *
1639 CTCTGTATCTCACCAGGAAGATGATTGCTTTGTTGTTTTGTCC-ACTTCTCTGTATCTCACCAAG
1 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTG-TTTGACCTACTTCTCTGTATCTCACCAGG
** ** * * *
1703 AAGATGACTGCTTTGTTATTTTACCCACTTCTCTGTATCAACTAGGAAGATGGGGTTTGAAGTTT
65 AAGATGACCACTTCATTATTTGACCCACTTCTCTGTATCAACCAGGAAGATGGGGTCTGAAGTTT
* * *
1768 CACTAACATTTAATTTTCACCTCATTATTTTGGTACACTT
130 CACTAACATTGAATTTTCACATCATTATTTTGGTACACTA
* * ***
1808 CTTTATATCTCACCAGGAAGATGACCACTTCATTGTTTGACCTACTTCTCTGTATCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTTTGACCTACTTCTCTGTATCTCACCAGGA
* *** *
1873 AGATGACCACTTCATTGTTTGATGTACTTCTCTGTACCTC-ACCAGGAAGATGGGGTCTGAGGTT
66 AGATGACCACTTCATTATTTGACCCACTTCTCTGTA--TCAACCAGGAAGATGGGGTCTGAAGTT
* *
1937 TCACTCACATTCGAGTTTT-ACATCATTATTTTGGTACACTA
129 TCACTAACATT-GAATTTTCACATCATTATTTTGGTACACTA
* *
1978 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTTTGACCTACTTCTCTGTATCTCACCAGGA
2043 AGAT
66 AGAT
2047 AGGGTCTAAA
Statistics
Matches: 202, Mismatches: 33, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
168 6 0.03
169 76 0.38
170 113 0.56
171 7 0.03
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (169 bp):
CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTTTGACCTACTTCTCTGTATCTCACCAGGA
AGATGACCACTTCATTATTTGACCCACTTCTCTGTATCAACCAGGAAGATGGGGTCTGAAGTTTC
ACTAACATTGAATTTTCACATCATTATTTTGGTACACTA
Found at i:2576 original size:50 final size:50
Alignment explanation
Indices: 2519--2689 Score: 202
Period size: 50 Copynumber: 3.4 Consensus size: 50
2509 TTGGATTCAT
*
2519 CGTTATGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCAGGTTCGC
1 CGTTATGGCCTCAA-CCTTTCCCATTACATCTTCTAAGGTACCAGGTTCGC
* *
2569 CGTTATGGCCTCAACCTTTCCCTTTACATCTTC-ATGGTACCAGGTTCGC
1 CGTTATGGCCTCAACCTTTCCCATTACATCTTCTAAGGTACCAGGTTCGC
*** * * ** * *
2618 CGTTACAACCTCAACCTTTCCCATTACATCTTTTAAGGTACTAAATTTGT
1 CGTTATGGCCTCAACCTTTCCCATTACATCTTCTAAGGTACCAGGTTCGC
*
2668 CGTTACGGCCTCAACCTTTCCC
1 CGTTATGGCCTCAACCTTTCCC
2690 TTCATGGTAC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 45 0.44
50 58 0.56
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (50 bp):
CGTTATGGCCTCAACCTTTCCCATTACATCTTCTAAGGTACCAGGTTCGC
Found at i:2630 original size:49 final size:48
Alignment explanation
Indices: 2519--2996 Score: 263
Period size: 49 Copynumber: 10.0 Consensus size: 48
2509 TTGGATTCAT
* * *
2519 CGTTATGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCAGGTTCGC
1 CGTTACGGCCTCAA-CCTTTCCC-TTACATCTTC-ATGGTACCAGGTTCGC
*
2569 CGTTATGGCCTCAACCTTTCCCTTTACATCTTCATGGTACCAGGTTCGC
1 CGTTACGGCCTCAACCTTTCCC-TTACATCTTCATGGTACCAGGTTCGC
** * * * ** * *
2618 CGTTACAACCTCAACCTTTCCCATTACATCTTTTAAGGTACTAAATTTGT
1 CGTTACGGCCTCAACCTTTCCC-TTACATC-TTCATGGTACCAGGTTCGC
* *
2668 CGTTACGGCCTCAACCTTT--C---C--CTTCATGGTACTAGGTTCGT
1 CGTTACGGCCTCAACCTTTCCCTTACATCTTCATGGTACCAGGTTCGC
* * * * *
2709 CGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACTATGTTCGC
1 CGTTACGGCCTCAACCTTTCCCTT-ACATCTTCATGGTACCAGGTTCGC
* * * * *
2758 CATTGCGACCTCAACCTTTCCCTT-CA----AATGGTACC-GGATTCGT
1 CGTTACGGCCTCAACCTTTCCCTTACATCTTCATGGTACCAGG-TTCGC
*
2801 CGTTACGGCCTCAACCTTTCCCTT-CATCTTAATGGTACC-GTGTTCGC
1 CGTTACGGCCTCAACCTTTCCCTTACATCTTCATGGTACCAG-GTTCGC
* *** * ** **
2848 CATTGTAGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTTC
1 CGTTACGGCCTCAACCTTTCCCTT-ACATCTTCATGGTACCAGGTTCGC
* ** * * * * * *
2897 CATTGTGGCCTCAACCTTTCTCGTCATATCTTCATGGTA-CTGAATTCGT
1 CGTTACGGCCTCAACCTTTC-CCTTACATCTTCATGGTACCAG-GTTCGC
* * * *
2946 CGTTACGTCCTCAATCC-TTCCCATTACATCTTTTAAGGTACCGGGTTCGC
1 CGTTACGGCCTCAA-CCTTTCCC-TTACATC-TTCATGGTACCAGGTTCGC
2996 C
1 C
Statistics
Matches: 336, Mismatches: 67, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
41 31 0.09
42 2 0.01
43 35 0.10
44 1 0.00
47 35 0.10
48 4 0.01
49 152 0.45
50 74 0.22
51 2 0.01
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (48 bp):
CGTTACGGCCTCAACCTTTCCCTTACATCTTCATGGTACCAGGTTCGC
Found at i:2836 original size:90 final size:91
Alignment explanation
Indices: 2675--2876 Score: 279
Period size: 90 Copynumber: 2.2 Consensus size: 91
2665 TGTCGTTACG
*
2675 GCCTCAACCTTTCCCTTC--ATGGTACTAGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATAT
1 GCCTCAACCTTTCCCTTCAAATGGTACTAGGTTCGTCGTTACGACCTCAACCTTTCCCTTCA-AT
* *
2738 CTTCATGGTACTATGTTCGCCATTGCGA
65 CTTAATGGTACCATGTTCGCCATTG-GA
* *
2766 -CCTCAACCTTTCCCTTCAAATGGTAC-CGGATTCGTCGTTACGGCCTCAACCTTTCCCTTC-AT
1 GCCTCAACCTTTCCCTTCAAATGGTACTAGG-TTCGTCGTTACGACCTCAACCTTTCCCTTCAAT
* *
2828 CTTAATGGTACCGTGTTCGCCATTGTA
65 CTTAATGGTACCATGTTCGCCATTGGA
2855 GCCTCAACCTTTCCCTTCAAAT
1 GCCTCAACCTTTCCCTTCAAAT
2877 CTTCATGGTA
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
89 1 0.01
90 62 0.62
91 2 0.02
92 35 0.35
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (91 bp):
GCCTCAACCTTTCCCTTCAAATGGTACTAGGTTCGTCGTTACGACCTCAACCTTTCCCTTCAATC
TTAATGGTACCATGTTCGCCATTGGA
Done.