Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005260.1 Kokia drynarioides strain JFW-HI SEQ_119169, 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: 2282
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Found at i:1118 original size:26 final size:27
Alignment explanation
Indices: 1088--1139 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1078 AATTTCTCAA
1088 AAATTACAA-TTTCCCCCCAAATTCTG
1 AAATTACAATTTTCCCCCCAAATTCTG
** *
1114 AAATTTGAATTTTTCCCCCAAATTCT
1 AAATTACAATTTTCCCCCCAAATTCT
1140 CAAAAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATTACAATTTTCCCCCCAAATTCTG
Found at i:1153 original size:28 final size:29
Alignment explanation
Indices: 1048--1294 Score: 170
Period size: 29 Copynumber: 8.6 Consensus size: 29
1038 TTGACCCTCG
* * *
1048 AACTTCTCAAAAATTACATGTTTACCTCTA
1 AACTTCTCAAAAATTACAT-TTTTCCCCCA
* * *
1078 AATTTCTCAAAAATTACAATTTCCCCCCA
1 AACTTCTCAAAAATTACATTTTTCCCCCA
* *
1107 AA-TTCT-GAAATTTGA-ATTTTTCCCCCA
1 AACTTCTCAAAAATT-ACATTTTTCCCCCA
*
1134 AA-TTCTCAAAAATTACATTTTTGCCCCTA
1 AACTTCTCAAAAATTACATTTTT-CCCCCA
* *
1163 AACTTC-CAAAAATTCCATTTTTACCCCAA
1 AACTTCTCAAAAATTACATTTTT-CCCCCA
* * *
1192 AACTT-TCAAAAATCACATTTTGCCCTCA
1 AACTTCTCAAAAATTACATTTTTCCCCCA
* * * *
1220 AATTTC-CAAAAATTCCATTTTTTCCCTCG
1 AACTTCTCAAAAATTACA-TTTTTCCCCCA
* ** **
1249 AACTTC-CAAAAATTCCAATTTTAACCCTG
1 AACTTCTCAAAAATTAC-ATTTTTCCCCCA
1278 AACTT-TCAAAAATTACA
1 AACTTCTCAAAAATTACA
1295 ATTCTGCTCA
Statistics
Matches: 176, Mismatches: 31, Indels: 22
0.77 0.14 0.10
Matches are distributed among these distances:
27 22 0.12
28 34 0.19
29 99 0.56
30 21 0.12
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
AACTTCTCAAAAATTACATTTTTCCCCCA
Found at i:1213 original size:57 final size:58
Alignment explanation
Indices: 1027--1241 Score: 190
Period size: 57 Copynumber: 3.7 Consensus size: 58
1017 ACACTTTTCC
* * * * * * *
1027 AAAATCACGTTTTGACCCTCGAACTTCTCAAAAATTACATGTTTACCTCTAAATTTCTCA
1 AAAATCACATTTTGCCCCTCAAACTTC-CAAAAATTCCATTTTTACC-CCAAAATTCTCA
* * * ** * ** *
1087 AAAATTACAATTT-CCCCCCAAA-TTCTGAAATTTGAATTTTT-CCCCCAAATTCTCA
1 AAAATCACATTTTGCCCCTCAAACTTCCAAAAATTCCATTTTTACCCCAAAATTCTCA
*
1142 AAAATTACATTTTTGCCCCT-AAACTTCCAAAAATTCCATTTTTACCCCAAAACTT-TCA
1 AAAATCACA-TTTTGCCCCTCAAACTTCCAAAAATTCCATTTTTACCCCAAAA-TTCTCA
*
1200 AAAATCACATTTTG-CCCTCAAATTTCCAAAAATTCCATTTTT
1 AAAATCACATTTTGCCCCTCAAACTTCCAAAAATTCCATTTTT
1242 TCCCTCGAAC
Statistics
Matches: 124, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
55 18 0.15
56 12 0.10
57 55 0.44
58 21 0.17
59 8 0.06
60 10 0.08
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATCACATTTTGCCCCTCAAACTTCCAAAAATTCCATTTTTACCCCAAAATTCTCA
Found at i:1239 original size:86 final size:87
Alignment explanation
Indices: 1121--1356 Score: 248
Period size: 86 Copynumber: 2.7 Consensus size: 87
1111 CTGAAATTTG
* * *
1121 AATTTTTCCCCCAAA-TTCTCAAAAATTACATTTTTGCCCCT-AAACTTCCAAAAATTCCATTTT
1 AATTTTGCCCACAAATTTC-CAAAAATTCCATTTTTG-CCCTAAAACTTCCAAAAATTCCATTTT
*
1184 TACCCCAAAACTTTCAAAAATCAC
64 TAACCCAAAACTTTCAAAAATCAC
* * ** *
1208 -ATTTTGCCCTCAAATTTCCAAAAATTCCATTTTTTCCCTCGAACTTCCAAAAATTCCAATTTTA
1 AATTTTGCCCACAAATTTCCAAAAATTCCATTTTTGCCCTAAAACTTCCAAAAATTCCATTTTTA
** *
1272 ACCCTGAACTTTCAAAAATTAC
66 ACCCAAAACTTTCAAAAATCAC
* * * * *
1294 AATTCTGCTCACGAATTTCC-AAAATTCACATTTTTGTCCTAAAACTTTCC-AAAATTGCATTTT
1 AATTTTGCCCACAAATTTCCAAAAATTC-CATTTTTGCCCTAAAAC-TTCCAAAAATTCCATTTT
1357 AGTCCCAAAC
Statistics
Matches: 124, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
85 4 0.03
86 74 0.60
87 42 0.34
88 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (87 bp):
AATTTTGCCCACAAATTTCCAAAAATTCCATTTTTGCCCTAAAACTTCCAAAAATTCCATTTTTA
ACCCAAAACTTTCAAAAATCAC
Found at i:1259 original size:57 final size:57
Alignment explanation
Indices: 1122--1261 Score: 169
Period size: 57 Copynumber: 2.4 Consensus size: 57
1112 TGAAATTTGA
* *
1122 ATTTTTCCCCCAAA-TTCTCAAAAATTACATTTTTGCCCCTAAACTTCCAAAAATTCC
1 ATTTTTTCCCCAAACTTC-CAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTCC
* * *
1179 ATTTTTACCCCAAAACTTTCAAAAATCACA-TTTTG-CCCTCAAATTTCCAAAAATTCC
1 ATTTTTTCCCC-AAACTTCCAAAAATCACATTTTTGCCCCT-AAACTTCCAAAAATTCC
*
1236 ATTTTTTCCCTCGAACTTCCAAAAAT
1 ATTTTTTCCC-CAAACTTCCAAAAAT
1262 TCCAATTTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
56 4 0.06
57 52 0.72
58 14 0.19
59 2 0.03
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (57 bp):
ATTTTTTCCCCAAACTTCCAAAAATCACATTTTTGCCCCTAAACTTCCAAAAATTCC
Found at i:1793 original size:98 final size:98
Alignment explanation
Indices: 1624--1890 Score: 430
Period size: 98 Copynumber: 2.7 Consensus size: 98
1614 TATTTAAAAT
* * *
1624 CGAGGTAATATTCCTTTATTTCGGGT-TATGAAAATTTGTGTCTTAACTTACTAGGCGCTATTTT
1 CGAGGCAATATTCCTTTATTTCGGGTCT-TGAAAATTTGTGCCTTAACTTACTAGGCGCGATTTT
1688 TTCTTCAAACCGAAATAATCGAGTACCCTTAAAC
65 TTCTTCAAACCGAAATAATCGAGTACCCTTAAAC
*
1722 CGAGGCAATATTCCTTTATTTCGGGTCTTGAAAATTTGTGCCTTAACTCACTAGGCGCGATTTTT
1 CGAGGCAATATTCCTTTATTTCGGGTCTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATTTTT
*
1787 TCTTCAAACCGGAATAATCGAGTACCCTTAAAC
66 TCTTCAAACCGAAATAATCGAGTACCCTTAAAC
* * * *
1820 CGAGGCAATATTCCATTATTTCGAGTCTTGAAAAGTTGTGCCTTAACTTACTAGGCGCGA-CTTT
1 CGAGGCAATATTCCTTTATTTCGGGTCTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATTTTT
1884 TCTTCAA
66 TCTTCAA
1891 TCTGGGATAA
Statistics
Matches: 158, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
97 10 0.06
98 147 0.93
99 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.36
Consensus pattern (98 bp):
CGAGGCAATATTCCTTTATTTCGGGTCTTGAAAATTTGTGCCTTAACTTACTAGGCGCGATTTTT
TCTTCAAACCGAAATAATCGAGTACCCTTAAAC
Done.