Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013588.1 Kokia drynarioides strain JFW-HI SEQ_128615, 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: 6843
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:268 original size:11 final size:11
Alignment explanation
Indices: 254--278 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
244 TTCTTTTTAT
254 TTATTAATTAA
1 TTATTAATTAA
265 TTATTAATTAA
1 TTATTAATTAA
276 TTA
1 TTA
279 ATAAATATTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATTAATTAA
Found at i:274 original size:15 final size:15
Alignment explanation
Indices: 250--280 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
240 CGTTTTCTTT
*
250 TTATTTATTAATTAA
1 TTATTAATTAATTAA
265 TTATTAATTAATTAA
1 TTATTAATTAATTAA
280 T
1 T
281 AAATATTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTAATTAATTAA
Found at i:922 original size:30 final size:30
Alignment explanation
Indices: 888--972 Score: 120
Period size: 30 Copynumber: 2.8 Consensus size: 30
878 TAGGCTTAGG
888 GTATTTGGGCTGATTTGGGCCATTT-AGTAT
1 GTATTTGGGCTGATTTGGGCCATTTGA-TAT
* *
918 GTATTTGGGCCGACTTGGGCCATTTGATAT
1 GTATTTGGGCTGATTTGGGCCATTTGATAT
948 GTATTTGGG-TCGATTTGGGCCATTT
1 GTATTTGGGCT-GATTTGGGCCATTT
973 TATTTGTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.41
Consensus pattern (30 bp):
GTATTTGGGCTGATTTGGGCCATTTGATAT
Found at i:1028 original size:28 final size:28
Alignment explanation
Indices: 1000--1079 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
990 TGGACAAAAA
*
1000 TAAATTTTAAAGTTAAATTTATGATAAATT
1 TAAATTTTAAA-TTAAATTTATAATAAA-T
* *
1030 TAAA-TTTCATTTAAATTTATAATAAAT
1 TAAATTTTAAATTAAATTTATAATAAAT
* *
1057 TCAATTTTAAAATAAATTT-TAAT
1 TAAATTTTAAATTAAATTTATAAT
1080 TTTATTGGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 8 0.19
28 26 0.62
29 4 0.10
30 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
TAAATTTTAAATTAAATTTATAATAAAT
Found at i:1044 original size:17 final size:16
Alignment explanation
Indices: 1005--1048 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
995 AAAAATAAAT
*
1005 TTTAAAGTTAAATTTA
1 TTTAAATTTAAATTTA
*
1021 TGATAAATTTAAATTTCA
1 T-TTAAATTTAAATTT-A
1039 TTTAAATTTA
1 TTTAAATTTA
1049 TAATAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.87
18 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:1065 original size:17 final size:18
Alignment explanation
Indices: 1045--1084 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1035 TTCATTTAAA
1045 TTTATAATAAA-TTCAAT
1 TTTATAATAAATTTCAAT
* *
1062 TTTAAAATAAATTTTAAT
1 TTTATAATAAATTTCAAT
1080 TTTAT
1 TTTAT
1085 TGGGCCTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATAATAAATTTCAAT
Found at i:1816 original size:158 final size:159
Alignment explanation
Indices: 1531--1863 Score: 571
Period size: 158 Copynumber: 2.1 Consensus size: 159
1521 ACGCTTCTCA
*
1531 GTATCTCATCAGGCAA-CTGTGGTTCAAAGATTTGCTCACATCGAGCATGGGTTTGGTTTGGTCT
1 GTATCTCATCAGG-AAGCTGTGGTTCAAAGATTTGATCACATCGAGCATGGGTTTGGTTTGGTCT
1595 TTCTTCTCAATATCTCATCAGGAAGATAACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTC
65 TTCTTCTCAATATCTCATCAGGAAGATAACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTC
1660 ATCAGGAAGACGAATTTGGTCTACTTCTAC
130 ATCAGGAAGACGAATTTGGTCTACTTCTAC
* *
1690 GTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGATCACGTCGAGCATGGGTTTGGTTTGGTC-T
1 GTATCTCATCAGGAAGCTGTGGTTCAAAGATTTGATCACATCGAGCATGGGTTTGGTTTGGTCTT
* * * *
1754 TCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCA
66 TCTTCTCAATATCTCATCAGGAAGATAACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTCA
*
1819 TCAGGAAGACGAATTTGGTCTACTTCTCC
131 TCAGGAAGACGAATTTGGTCTACTTCTAC
1848 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
1864 ATAATTACTT
Statistics
Matches: 165, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
158 108 0.65
159 57 0.35
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (159 bp):
GTATCTCATCAGGAAGCTGTGGTTCAAAGATTTGATCACATCGAGCATGGGTTTGGTTTGGTCTT
TCTTCTCAATATCTCATCAGGAAGATAACCGCGTCATTTGTTTCAATCCACTTCTCTGTATCTCA
TCAGGAAGACGAATTTGGTCTACTTCTAC
Found at i:1980 original size:198 final size:199
Alignment explanation
Indices: 1683--2386 Score: 956
Period size: 198 Copynumber: 3.5 Consensus size: 199
1673 ATTTGGTCTA
* * *
1683 CTTCTACGTATCTCATCAGGAAGCTGTGG-TTCGAAGATTTGATCACGTCGAGCATGGGTTTGGT
1 CTTCT-CGTATCTCATCAGGAAGCTGTGGATTCGAAGACTTGCTCACATCGAGCATGGGTTTGGT
1747 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTG
65 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTG
* *
1812 TATCTCATCAGGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGATAA-TTACTT-C
130 TATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACTTA-TTCC
1875 GACACG
194 GACACG
* * *
1881 CTTCTCAGTATCTCATCAGGAAGCTGTGG-TTCGAAGATTTGCTCACGTCGAGCATGAGTTTGGT
1 CTTCTC-GTATCTCATCAGGAAGCTGTGGATTCGAAGACTTGCTCACATCGAGCATGGGTTTGGT
* *
1945 TTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTG
65 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTG
2010 TATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATT
130 TATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAA-C--TTATT
*
2075 CCGATC-TG
192 CCGA-CACG
* * * *
2083 CTTCTCGGTGTGTCATCAGGAAGCT-TGGATTCGAAGACTTGCTCACATCGAGCGTGGGTTCGGT
1 CTTCTC-GTATCTCATCAGGAAGCTGTGGATTCGAAGACTTGCTCACATCGAGCATGGGTTTGGT
* * *
2147 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACAGCGTCGTTTGTTTCAATTCGCTTCTCTA
65 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTG
* * *
2212 TATCTCATCAAGAAGACAAATTTGGTCTACTTCTCCATATCTCATCAGGAAGCTAACCGTTTTTT
130 TATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAA-C---TTAT
*
2277 GCTCCGATC-TG
191 --TCCGA-CACG
* * * * *
2288 TTTCTCGATGTGTCATCAGGAAGTTG-GGATTCGAAGACTTGCTCACATCGAGCCTGGGTTTGGT
1 CTTCTCG-TATCTCATCAGGAAGCTGTGGATTCGAAGACTTGCTCACATCGAGCATGGGTTTGGT
*
2352 TTGGTCTTCTTCTCAATATCTCATCAGGAAGATGA
65 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA
2387 TTGTGCCGTT
Statistics
Matches: 464, Mismatches: 29, Indels: 19
0.91 0.06 0.04
Matches are distributed among these distances:
197 1 0.00
198 177 0.38
201 5 0.01
202 175 0.38
203 5 0.01
204 1 0.00
205 100 0.22
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (199 bp):
CTTCTCGTATCTCATCAGGAAGCTGTGGATTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTT
TGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGT
ATCTCATCAAGAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACTTATTCCGA
CACG
Found at i:2197 original size:202 final size:202
Alignment explanation
Indices: 1695--2386 Score: 1015
Period size: 202 Copynumber: 3.4 Consensus size: 202
1685 TCTACGTATC
* * *
1695 TCATCAGGAAGCTGTGGTTCGAAGATTTGATCACGTCGAGCATGGGTTTGGTTTGGTCTTCTTCT
1 TCATCAGGAAGCTGTGGTTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTCT
* *
1760 CAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGA
66 CAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAAGA
* *
1825 AGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGATAA----TTACTT-CGA-CACGCTT
131 AGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTA-TTCCGATC-TGCTT
* * *
1884 CTCAGTATC
194 CTCGGTGTG
* * *
1893 TCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACGTCGAGCATGAGTTTGGTTTGGTCTTCTTCT
1 TCATCAGGAAGCTGTGGTTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTCT
*
1958 CAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAAGA
66 CAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAAGA
2023 AGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTCCGATCTGCTTCT
131 AGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTCCGATCTGCTTCT
2088 CGGTGTG
196 CGGTGTG
* *
2095 TCATCAGGAAGCT-TGGATTCGAAGACTTGCTCACATCGAGCGTGGGTTCGGTTTGGTCTTCTTC
1 TCATCAGGAAGCTGTGG-TTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTC
* *
2159 TCAGTATCTCATCAGGAAGATGACAGCGTCGTTTGTTTCAAT-TCGCTTCTCTATATCTCATCAA
65 TCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCT-GCTTCTCTGTATCTCATCAA
* * *
2223 GAAGACAAATTTGGTCTACTTCTCCATATCTCATCAGGAAGCTAACCGTTTTTTGCTCCGATCTG
129 GAAGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCG-TTTAT--TCCGATCTG
* *
2288 TTTCTCGATGTG
191 CTTCTCGGTGTG
* *
2300 TCATCAGGAAGTTG-GGATTCGAAGACTTGCTCACATCGAGCCTGGGTTTGGTTTGGTCTTCTTC
1 TCATCAGGAAGCTGTGG-TTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTC
*
2364 TCAATATCTCATCAGGAAGATGA
65 TCAGTATCTCATCAGGAAGATGA
2387 TTGTGCCGTT
Statistics
Matches: 455, Mismatches: 27, Indels: 17
0.91 0.05 0.03
Matches are distributed among these distances:
198 167 0.37
201 6 0.01
202 176 0.39
203 5 0.01
205 101 0.22
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (202 bp):
TCATCAGGAAGCTGTGGTTCGAAGACTTGCTCACATCGAGCATGGGTTTGGTTTGGTCTTCTTCT
CAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTTCTCTGTATCTCATCAAGA
AGACGAATTTGGTCTACTTCTCCGTATCTCATCAGGAAGCTAACCGTTTATTCCGATCTGCTTCT
CGGTGTG
Done.