Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000856.1 Kokia drynarioides strain JFW-HI SEQ_111968, 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: 1983
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Found at i:18 original size:6 final size:6
Alignment explanation
Indices: 3--55 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
1 AC
* *
3 TTAAA- TTAAAT TTAAAT TCGAAA- -TAAAT TTAAAT TT-AAT ATAAAT
1 TTAAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAAT TTAAAT TTAAAT
48 TTAAAT TT
1 TTAAAT TT
56 CTACACAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
4 3 0.08
5 9 0.23
6 24 0.62
7 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:55 original size:17 final size:16
Alignment explanation
Indices: 3--55 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 16
1 AC
3 TTAAATTAAATTTAAAT
1 TTAAA-TAAATTTAAAT
*
20 TCGAAATAAATTTAAAT
1 T-TAAATAAATTTAAAT
37 TTAATATAAATTTAAAT
1 TTAA-ATAAATTTAAAT
54 TT
1 TT
56 CTACACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.06
17 27 0.84
18 3 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTAAATAAATTTAAAT
Found at i:881 original size:203 final size:203
Alignment explanation
Indices: 495--1053 Score: 795
Period size: 203 Copynumber: 2.7 Consensus size: 203
485 TTTCATCAGG
** * ** * * *
495 ATTTGGTTCACTTCTCGGTATCTCATCAGGGGGCTAACCACTTTATGGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACC-TTTTATTGCTTCGACCTGCTTCTCA
** ** * * *
560 GCATCTCATCAGGAAGCTGGGGTTAGAAGA-TTTGCTCGTTTTGAGCCTCGTTTGGGTATTTTTT
65 GTGTCTCATCAGGAAGCTGGGGTTA-AAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
* *
624 TCAGTGCCTCATCAGGAAGATGATTACATCGCTGTTTTTTTCAATTCGCTCCTCCGTATATCA-T
129 TCAGTGTCTCATCAGGAAGATGATTACATCACTGTTTTTTTCAATTCGCTCCTCCGTATATCATT
*
688 CTGGAAGACGA
194 C-GAAAGACGA
*
699 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGTTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCAG
* *
764 TGTCTCATCAGGAAGCTAGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGATCTTCTTCT
66 TGTCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* *
829 CAGTGTCTCATCAGG-AGATGATTACATTACTGTTTGTTTT-AATTCGCTCCTCCGTATCTCATT
130 CAGTGTCTCATCAGGAAGATGATTACATCACTGTTT-TTTTCAATTCGCTCCTCCGTATATCATT
892 CGAAAGACGA
194 CGAAAGACGA
*
902 ATTTGGTTCACTTCTCAA-TACCTCATCAGGAAGTTAACCTTATATTGCTTCGACCTGCTTCTCA
1 ATTTGGTTCACTTCT-AAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCA
*
966 GTGTCTCATCAGGAAGCTGGGGTTGAAAGACTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTTC
65 GTGTCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTC
1031 TCAGTGTCTCATCAGGAAGATGA
129 TCAGTGTCTCATCAGGAAGATGA
1054 CCGCGTCGTT
Statistics
Matches: 320, Mismatches: 29, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
203 229 0.72
204 91 0.28
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (203 bp):
ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGCTTCGACCTGCTTCTCAG
TGTCTCATCAGGAAGCTGGGGTTAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGATTACATCACTGTTTTTTTCAATTCGCTCCTCCGTATATCATTCG
AAAGACGA
Found at i:1124 original size:37 final size:37
Alignment explanation
Indices: 1073--1221 Score: 127
Period size: 37 Copynumber: 3.7 Consensus size: 37
1063 TCGTTTCAAC
* *
1073 TCACTTCTCTGTATCTTATCAGGAAGGCGGATTTGGT
1 TCACTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
* *
1110 TCACTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTT
1 TCACTTCTCAGTATCTCATCAGGAAG--G-C-G-G--ATTTGGT
* * *
1154 TCAACTCGCTTCTCTGTATCTCCTCAGGAAGGCGAATTTGGT
1 TC-A----CTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
1196 TCACTTCTCAGTATCTCATCAGGAAG
1 TCACTTCTCAGTATCTCATCAGGAAG
1222 CTAACCTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
37 45 0.51
39 1 0.01
40 1 0.01
41 2 0.02
42 8 0.09
44 7 0.08
45 2 0.02
46 1 0.01
47 1 0.01
49 21 0.24
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (37 bp):
TCACTTCTCAGTATCTCATCAGGAAGGCGGATTTGGT
Found at i:1172 original size:86 final size:86
Alignment explanation
Indices: 1027--1221 Score: 327
Period size: 86 Copynumber: 2.3 Consensus size: 86
1017 TTTGGGTCTT
* *
1027 CTTCTCAGTGTCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTTAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
*
1092 CAGGAAGGCGGATTTGGTTCA
66 CAGGAAGGCGAATTTGGTTCA
* * * *
1113 CTTCTCAGTATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAACTCGCTTCTCTGTATCTCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
1178 CAGGAAGGCGAATTTGGTTCA
66 CAGGAAGGCGAATTTGGTTCA
1199 CTTCTCAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
1222 CTAACCTTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 102 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (86 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTCAT
CAGGAAGGCGAATTTGGTTCA
Found at i:1184 original size:203 final size:198
Alignment explanation
Indices: 495--1135 Score: 741
Period size: 203 Copynumber: 3.2 Consensus size: 198
485 TTTCATCAGG
* * ** * * *
495 ATTTGGTTCACTTCTCGGTATCTCATCAGGGGGCTAACCACTT-TATGGCTTCGACCTGCTTCTC
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAA-C-CTTATATTGTTTCGACCTGCTTCTC
* ** * *
559 AGCATCTCATCAGGAAGCTGGGGTTAGAAGA-TTTGCTCGTTTTGAGCCTCGTTTGGGTATTTTT
64 AGTATCTCATCAGGAAGCTGGGGTTA-AAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTT
* * * *
623 TTCAGTGCCTCATCAGGAAGATGATTACATCGCT-GTTTTTTTCAATTCGCTCCTCCGTATATCA
128 CTCAGTGTCTCATCAGGAAGATG---AC--CGCTCGTTTGTTTCAATTCGCTCCTCCGTATCTCA
687 TCTGGAAGACGA
188 TC-GGAAGACGA
* *
699 ATTTGGTTCACTTCTAAGTACCTCATCAGGAAGTTAACCTTTTATTGTTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
* * *
764 TGTCTCATCAGGAAGCTAGGGTTCAAAGACTTTGCTCACTTTGAGCCTCGTTTGGATCTTCTTCT
66 TATCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* ** *
829 CAGTGTCTCATCAGG-AGATGATTACATTACTGTTTGTTTTAATTCGCTCCTCCGTATCTCATTC
130 CAGTGTCTCATCAGGAAGATGA--CCGCT-C-GTTTGTTTCAATTCGCTCCTCCGTATCTCA-TC
*
893 GAAAGACGA
190 GGAAGACGA
* *
902 ATTTGGTTCACTTCTCAATACCTCATCAGGAAGTTAACCTTATATTGCTTCGACCTGCTTCTCAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
* *
967 TGTCTCATCAGGAAGCTGGGGTTGAAAGACTTTGCTCACTTTGAGCCTCATTTGGGTCTTCTTCT
66 TATCTCATCAGGAAGCTGGGGTT-AAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCT
* * * * * *
1032 CAGTGTCTCATCAGGAAGATGACCGCGTCGTTCGTTTCAACTCACTTCTCTGTATCTTATCAGGA
130 CAGTGTCTCATCAGGAAGATGACCGC-TCGTTTGTTTCAATTCGCTCCTCCGTATCTCATC-GGA
* *
1097 AGGCGG
193 AGACGA
*
1103 ATTTGGTTCACTTCTCAGTATCTCATCAGGAAG
1 ATTTGGTTCACTTCTCAGTACCTCATCAGGAAG
1136 ATGACTGCGT
Statistics
Matches: 377, Mismatches: 48, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
200 5 0.01
201 60 0.16
202 5 0.01
203 224 0.59
204 83 0.22
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (198 bp):
ATTTGGTTCACTTCTCAGTACCTCATCAGGAAGTTAACCTTATATTGTTTCGACCTGCTTCTCAG
TATCTCATCAGGAAGCTGGGGTTAAAGACTTTGCTCACTTTGAGCCTCGTTTGGGTCTTCTTCTC
AGTGTCTCATCAGGAAGATGACCGCTCGTTTGTTTCAATTCGCTCCTCCGTATCTCATCGGAAGA
CGA
Done.