Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006592.1 Kokia drynarioides strain JFW-HI SEQ_121180, 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: 2610
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Found at i:119 original size:47 final size:47
Alignment explanation
Indices: 59--179 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
49 ATTTTGGTAC
* *
59 ACTTCTTTATATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
**
106 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGATGT
1 ACTTCTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGACCT
*
153 ACTTCTCTGTACCTCACCAGGAAGATG
1 ACTTCTCTGTATCTCACCAGGAAGATG
180 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:247 original size:123 final size:123
Alignment explanation
Indices: 110--443 Score: 488
Period size: 123 Copynumber: 2.7 Consensus size: 123
100 TGACCTACTT
* * **
110 CTCTGTATCTCACCAGGAAGATGACCACTTCATTGTTTGATGTACTTCTCTGTACCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
* * * *
175 AGATGGGGTCTGAGGTTTCACTCACATTCGAGTTTTACATCATTATTTTGGTACACTA
66 AGATAGGGTCTGAAGTTTCACTCACATTCGAGCTTTACAGCATTATTTTGGTACACTA
**
233 CTCTGTATCTCACCAGGAAGATGATTGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
* * * * *
298 AGATAGGGTCTAAAGTTTCACTCATATTTGAGCTTTACCGCATTATTTTGGTACACTT
66 AGATAGGGTCTGAAGTTTCACTCACATTCGAGCTTTACAGCATTATTTTGGTACACTA
* * * *
356 CTCTGTATCTCACCAGGAATATGACCGCTTCGTTGTCTGACCTACTTCTCAGTACCTCACTAGGA
1 CTCTGTATCTCACCAGGAAGATGACCGCTTCATTGTCTGACCTACTTCTCTGTACCTCACCAGGA
*
421 AGATAGGGTTTGAAGTTTCACTC
66 AGATAGGGTCTGAAGTTTCACTC
444 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:877 original size:99 final size:97
Alignment explanation
Indices: 774--1382 Score: 410
Period size: 99 Copynumber: 6.4 Consensus size: 97
764 TTGGATTCAT
* *
774 CGTTATGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCAGGTTCGCCGTTATGGCCTCAA
1 CGTTACGGCCTCAA-CCTTTCCCATCACATCTTC-AAGGTACCAGGTTCGCCGTTACGGCCTCAA
*
838 CCTTTCCCTTTACATCTTCATGGTACCAGGTTCGC
64 CCTTTCCC-TTACATCTTCATGGTACCGGGTTCGC
** * * * ** * *
873 CGTTACAACCTCAACCTTTCCCATTACATCTTTTAAGGTACTAAATTTGTCGTTACGGCCTCAAC
1 CGTTACGGCCTCAACCTTTCCCATCACATC-TTCAAGGTACCAGGTTCGCCGTTACGGCCTCAAC
** *
938 CTTT--C---C--CTTCATGGTACTAGGTTCGT
65 CTTTCCCTTACATCTTCATGGTACCGGGTTCGC
* * * * * * * * * *
964 CGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACTATGTTCGCCATTGCGACCTCAACC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACCAGGTTCGCCGTTACGGCCTCAACC
* * *
1029 TTTCCCTT-CA----AATGGTACCGGATTCGT
66 TTTCCCTTACATCTTCATGGTACCGGGTTCGC
* * ***
1056 CGTTACGGCCTCAACCTTTCCC-T-TCATCTT-AATGGTACC-GTGTTCGCCATTGTAGCCTCAA
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCAA-GGTACCAG-GTTCGCCGTTACGGCCTCAA
* * **
1117 CCTTTCCCTTCAAATCTTCATGGTACTGGGTTTTC
64 CCTTTCCCTT-ACATCTTCATGGTACCGGGTTCGC
* ** * * * * * * * *
1152 CATTGTGGCCTCAACCTTTCTCGTCATATCTTCATGGTA-CTGAATTCGTCGTTACGTCCTCAAT
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACCAG-GTTCGCCGTTACGGCCTCAA-
* *
1216 CC-TTCCCATTACATCTTTTAAGGTACCGGGTTCGC
64 CCTTTCCC-TTACATC-TTCATGGTACCGGGTTCGC
* * * * * * *
1251 CATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCTGGTTCGCCGTTGCGGCCTCAACC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACCAGGTTCGCCGTTACGGCCTCAACC
* * *
1316 TTTCCCATCACATTTTCATGGTACCGGGTTCAC
66 TTTCCC-TTACATCTTCATGGTACCGGGTTCGC
** *
1349 TATTACGGCCTCAACCTTTCCCATTACATCTTCA
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCA
1383 TGTTTCTTTT
Statistics
Matches: 400, Mismatches: 86, Indels: 49
0.75 0.16 0.09
Matches are distributed among these distances:
89 1 0.00
90 66 0.17
91 44 0.11
92 35 0.09
93 1 0.00
94 1 0.00
96 29 0.07
97 3 0.01
98 82 0.20
99 133 0.33
100 5 0.01
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.35
Consensus pattern (97 bp):
CGTTACGGCCTCAACCTTTCCCATCACATCTTCAAGGTACCAGGTTCGCCGTTACGGCCTCAACC
TTTCCCTTACATCTTCATGGTACCGGGTTCGC
Found at i:885 original size:49 final size:49
Alignment explanation
Indices: 774--1384 Score: 409
Period size: 49 Copynumber: 12.7 Consensus size: 49
764 TTGGATTCAT
* *
774 CGTTATGGCCTCAATCC-TTCCCATCACATCTTCTAAGGTACCAGGTTCGC
1 CGTTACGGCCTCAA-CCTTTCCCATCACATCTTC-ATGGTACCAGGTTCGC
* * *
824 CGTTATGGCCTCAACCTTTCCCTTTACATCTTCATGGTACCAGGTTCGC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
** * * * * ** * *
873 CGTTACAACCTCAACCTTTCCCATTACATCTTTTAAGGTACTAAATTTGT
1 CGTTACGGCCTCAACCTTTCCCATCACATC-TTCATGGTACCAGGTTCGC
* *
923 CGTTACGGCCTCAACC-TT----TC-C--CTTCATGGTACTAGGTTCGT
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
* * * * * *
964 CGTTGCGACCTCAACCTTTCCCTTCATATCTTCATGGTACTATGTTCGC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
* * * * *
1013 CATTGCGACCTCAACCTTTCCCTTCA-A-----ATGGTACC-GGATTCGT
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGG-TTCGC
* *
1056 CGTTACGGCCTCAACCTTTCCC-T-TCATCTTAATGGTACC-GTGTTCGC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAG-GTTCGC
* *** * * ** **
1103 CATTGTAGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTTC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
* ** * * * * * *
1152 CATTGTGGCCTCAACCTTTCTCGTCATATCTTCATGGTA-CTGAATTCGT
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAG-GTTCGC
* * * * *
1201 CGTTACGTCCTCAATCC-TTCCCATTACATCTTTTAAGGTACCGGGTTCGC
1 CGTTACGGCCTCAA-CCTTTCCCATCACATC-TTCATGGTACCAGGTTCGC
* * * * *
1251 CATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCTGGTTCGC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
* * * *
1300 CGTTGCGGCCTCAACCTTTCCCATCACATTTTCATGGTACCGGGTTCAC
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
** *
1349 TATTACGGCCTCAACCTTTCCCATTACATCTTCATG
1 CGTTACGGCCTCAACCTTTCCCATCACATCTTCATG
1385 TTTCTTTTGT
Statistics
Matches: 444, Mismatches: 91, Indels: 53
0.76 0.15 0.09
Matches are distributed among these distances:
41 28 0.06
42 6 0.01
43 30 0.07
44 1 0.00
45 1 0.00
46 2 0.00
47 31 0.07
48 4 0.01
49 249 0.56
50 90 0.20
51 2 0.00
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.35
Consensus pattern (49 bp):
CGTTACGGCCTCAACCTTTCCCATCACATCTTCATGGTACCAGGTTCGC
Found at i:1091 original size:90 final size:91
Alignment explanation
Indices: 930--1131 Score: 279
Period size: 90 Copynumber: 2.2 Consensus size: 91
920 TGTCGTTACG
*
930 GCCTCAACCTTTCCCTTC--ATGGTACTAGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATAT
1 GCCTCAACCTTTCCCTTCAAATGGTACTAGGTTCGTCGTTACGACCTCAACCTTTCCCTTCA-AT
* *
993 CTTCATGGTACTATGTTCGCCATTGCGA
65 CTTAATGGTACCATGTTCGCCATTG-GA
* *
1021 -CCTCAACCTTTCCCTTCAAATGGTAC-CGGATTCGTCGTTACGGCCTCAACCTTTCCCTTC-AT
1 GCCTCAACCTTTCCCTTCAAATGGTACTAGG-TTCGTCGTTACGACCTCAACCTTTCCCTTCAAT
* *
1083 CTTAATGGTACCGTGTTCGCCATTGTA
65 CTTAATGGTACCATGTTCGCCATTGGA
1110 GCCTCAACCTTTCCCTTCAAAT
1 GCCTCAACCTTTCCCTTCAAAT
1132 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
Found at i:1271 original size:148 final size:142
Alignment explanation
Indices: 727--1380 Score: 462
Period size: 148 Copynumber: 4.5 Consensus size: 142
717 AAGTTTGACG
* * ** * * *
727 TTGCGGCCTCAACCTTTCTTTTTATAT-TTCCATGGTATTGGATTCATCGTTATGGCCTCAATCC
1 TTGCGGCCTCAACCTTTC--CTCATATCTT-CATGGTACCGAATTCGTCGTTACGGCCTCAA-CC
* * * ** * *
791 -TTCCCATCACATCTTCTAA-GGTACCAGGTTCGCCGTTATGGCCTCAACCTTTCCCTTTACATC
62 TTTCCC-T-TCATC-T-TAATGGTACCGGGTTCGCCATTACAGCCTCAACCTTTCCCTTCATATC
* *
854 TTCATGGTACCAGGTTCGCCG
123 TTCATGGTA-CTGGTTCGCCA
* ** * * ** *
875 TTACAACCTCAACCTTTCC-CATTACATCTTTTAAGGTACTAAATTTGTCGTTACGGCCTCAACC
1 TTGCGGCCTCAACCTTTCCTCA-T--ATC-TTCATGGTACCGAATTCGTCGTTACGGCCTCAACC
** * * *
939 TTTCCC-T--TC---ATGGTACTAGGTTCGTCGTTGC-GACCTCAACCTTTCCCTTCATATCTTC
62 TTTCCCTTCATCTTAATGGTACCGGGTTCGCCATTACAG-CCTCAACCTTTCCCTTCATATCTTC
*
997 ATGGTACTATGTTCGCCA
126 ATGGTACT-GGTTCGCCA
* ** *
1015 TTGCGACCTCAACCTTTCC-C-T-TC-AAATGGTACCGGATTCGTCGTTACGGCCTCAACCTTTC
1 TTGCGGCCTCAACCTTTCCTCATATCTTCATGGTACCGAATTCGTCGTTACGGCCTCAACCTTTC
* ** *
1076 CCTTCATCTTAATGGTACCGTGTTCGCCATTGTAGCCTCAACCTTTCCCTTCAAATCTTCATGGT
66 CCTTCATCTTAATGGTACCGGGTTCGCCATTACAGCCTCAACCTTTCCCTTCATATCTTCATGGT
**
1141 ACTGGGTTTTCCA
131 ACT-GGTTCGCCA
* * *
1154 TTGTGGCCTCAACCTTTCTCGTCATATCTTCATGGTACTGAATTCGTCGTTACGTCCTCAATCC-
1 TTGCGGCCTCAACCTTTC-C-TCATATCTTCATGGTACCGAATTCGTCGTTACGGCCTCAA-CCT
*
1218 TTCCCATTACATCTTTTAA-GGTACCGGGTTCGCCATTACGGCCTCAACCTTTCCCTTCATATCT
63 TTCCC-TT-CATC--TTAATGGTACCGGGTTCGCCATTACAGCCTCAACCTTTCCCTTCATATCT
*
1282 TCATGGTATCTGGTTCGCCG
124 TCATGGTA-CTGGTTCGCCA
* * ** * *
1302 TTGCGGCCTCAACCTTTCCCATCACATTTTCATGGTACCGGGTTC-ACTATTACGGCCTCAACCT
1 TTGCGGCCTCAACCTTT-CC-TCATATCTTCATGGTACCGAATTCGTC-GTTACGGCCTCAACCT
1366 TTCCCATTACATCTT
63 TTCCC-TT-CATCTT
1381 CATGTTTCTT
Statistics
Matches: 407, Mismatches: 68, Indels: 64
0.76 0.13 0.12
Matches are distributed among these distances:
133 33 0.08
134 1 0.00
135 2 0.00
136 2 0.00
138 1 0.00
139 73 0.18
140 72 0.18
142 1 0.00
143 1 0.00
144 4 0.01
145 33 0.08
146 7 0.02
147 7 0.02
148 133 0.33
149 35 0.09
150 2 0.00
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (142 bp):
TTGCGGCCTCAACCTTTCCTCATATCTTCATGGTACCGAATTCGTCGTTACGGCCTCAACCTTTC
CCTTCATCTTAATGGTACCGGGTTCGCCATTACAGCCTCAACCTTTCCCTTCATATCTTCATGGT
ACTGGTTCGCCA
Done.