Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015117.1 Kokia drynarioides strain JFW-HI SEQ_130161, 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: 20845
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:4831 original size:70 final size:73
Alignment explanation
Indices: 4739--4954 Score: 215
Period size: 79 Copynumber: 2.9 Consensus size: 73
4729 GTATCAAATG
* * *
4739 TTTTTGGTTCTTTCCTAAGAAGTGTTTTTTTTTCTGGTCGACTTCTTGCTTCTCATGTTTATTCC
1 TTTTTGGTTCTTTCCTAAGAAGTGTTTTTTTTTCTAGTCGAATTCTTGCTTCTCCTGTTTATTCC
4804 ATGG-T-A
66 ATGGATAA
* * * * *
4810 -TTTTGGTTCTTTCCTAAGAAGTGTTTACTTTTCCTAGTTGAAATCTTGCTTCTCCTGTTCATTC
1 TTTTTGGTTCTTTCCTAAGAAGTGTTT-TTTTTTCTAGTCGAATTCTTGCTTCTCCTGTTTATTC
*
4874 TATGGTATCAGA
65 CATGG-AT-A-A
* * *
4886 TGTTTTTGGTTCCTTCCTAAGAAGAT-TTTTTTTTTCTTCGTCGAGTTCTTGCTTCTCCTGTTCT
1 --TTTTTGGTTCTTTCCTAAGAAG-TGTTTTTTTTTC-TAGTCGAATTCTTGCTTCTCCTGTT-T
4950 ATTCC
61 ATTCC
4955 CAAGTCCTTT
Statistics
Matches: 115, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
70 26 0.23
71 33 0.29
73 1 0.01
76 1 0.01
78 5 0.04
79 44 0.38
80 5 0.04
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (73 bp):
TTTTTGGTTCTTTCCTAAGAAGTGTTTTTTTTTCTAGTCGAATTCTTGCTTCTCCTGTTTATTCC
ATGGATAA
Found at i:12033 original size:286 final size:286
Alignment explanation
Indices: 11515--12083 Score: 1066
Period size: 286 Copynumber: 2.0 Consensus size: 286
11505 TTCATAAACT
11515 TGGAAAAACCCCTGGTATCGCAAATATTAGTTGAAGATGCTGTCCAAAAGGTGGAATATGAGGCC
1 TGGAAAAACCCCTGGTATCGCAAATATTAGTTGAAGATGCTGTCCAAAAGGTGGAATATGAGGCC
*
11580 CTTCCCACCGTTTGTTTTACGTGTGGAAAATATGGGCATGTCAAGGACCTTTGCCCGACGATGGC
66 CTTCCCACCGTTTGCTTTACGTGTGGAAAATATGGGCATGTCAAGGACCTTTGCCCGACGATGGC
11645 GGTAGAATCACACATGGAGCGGAAAGTTGGTGCCACGGAGAAGACACATGAGAATGCTTCCAGAG
131 GGTAGAATCACACATGGAGCGGAAAGTTGGTGCCACGGAGAAGACACATGAGAATGCTTCCAGAG
* *
11710 AAGAACCTCAAGGAGGAAAGATGGATTACGGGCCGTGGATGTTGGTCGAAAGGAGAGGCCGTCTA
196 AAGAACCTCAAGAAGGAAAGATGGATTACGGGCCGTGGATGTTGGTCGAAAGGAGAGGCCGTCGA
11775 GGGCAACGGACACCCCGTGCAAAAGG
261 GGGCAACGGACACCCCGTGCAAAAGG
*
11801 TGGAATAACCCCTGGTATCGCAAATATTAGTTGAAGATGCTGTCCAAAAGGTGGAATATGAGGCC
1 TGGAAAAACCCCTGGTATCGCAAATATTAGTTGAAGATGCTGTCCAAAAGGTGGAATATGAGGCC
11866 CTTCCCACCGTTTGCTTTACGTGTGGAAAATATGGGCATGTCAAGGACCTTTGCCCGACGATGGC
66 CTTCCCACCGTTTGCTTTACGTGTGGAAAATATGGGCATGTCAAGGACCTTTGCCCGACGATGGC
* * * *
11931 TGTAGAATCGCACATGGAGCGGAAAGTTGGTGCCACGGAGAAGACACGTGAGAATGCTTCCATAG
131 GGTAGAATCACACATGGAGCGGAAAGTTGGTGCCACGGAGAAGACACATGAGAATGCTTCCAGAG
11996 AAGAACCTCAAGAAGGAAAGATGGATTACGGGCCGTGGATGTTGGTCGAAAGGAGAGGCCGTCGA
196 AAGAACCTCAAGAAGGAAAGATGGATTACGGGCCGTGGATGTTGGTCGAAAGGAGAGGCCGTCGA
12061 GGGCAACGGACACCCCGTGCAAA
261 GGGCAACGGACACCCCGTGCAAA
12084 CGATGATTCG
Statistics
Matches: 275, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
286 275 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (286 bp):
TGGAAAAACCCCTGGTATCGCAAATATTAGTTGAAGATGCTGTCCAAAAGGTGGAATATGAGGCC
CTTCCCACCGTTTGCTTTACGTGTGGAAAATATGGGCATGTCAAGGACCTTTGCCCGACGATGGC
GGTAGAATCACACATGGAGCGGAAAGTTGGTGCCACGGAGAAGACACATGAGAATGCTTCCAGAG
AAGAACCTCAAGAAGGAAAGATGGATTACGGGCCGTGGATGTTGGTCGAAAGGAGAGGCCGTCGA
GGGCAACGGACACCCCGTGCAAAAGG
Found at i:15007 original size:288 final size:288
Alignment explanation
Indices: 14485--15067 Score: 1157
Period size: 288 Copynumber: 2.0 Consensus size: 288
14475 CTAAAAGCAC
14485 CAGGTAGCGATGGATTCCATGCCTTGTTCTTTCAGAAGCATTGGGATATCGTTGGGAAGGCGGTT
1 CAGGTAGCGATGGATTCCATGCCTTGTTCTTTCAGAAGCATTGGGATATCGTTGGGAAGGCGGTT
14550 TGTGACTGGGTTAAGAAAATATTCAATGAAGGTGTTATTGATGCTAACCTTAATAATACCCTTAT
66 TGTGACTGGGTTAAGAAAATATTCAATGAAGGTGTTATTGATGCTAACCTTAATAATACCCTTAT
14615 TGTTCTCATACCCAAGGTTGCAAATTCGGAGGGGTTTGCTCAGTTTCGTCCCATTAGTATCTACT
131 TGTTCTCATACCCAAGGTTGCAAATTCGGAGGGGTTTGCTCAGTTTCGTCCCATTAGTATCTACT
*
14680 CTGTTTTGTACAAATTAGTGATAAAGGTGATCGTTAATAGATTTAAACTCATTTTCCCTAAGATT
196 CTGTTTTGTACAAATTAGTGATAAAGGTGATCATTAATAGATTTAAACTCATTTTCCCTAAGATT
14745 ATTGCACAGGAGCAGGCTGGCTTTATTG
261 ATTGCACAGGAGCAGGCTGGCTTTATTG
14773 CAGGTAGCGATGGATTCCATGCCTTGTTCTTTCAGAAGCATTGGGATATCGTTGGGAAGGCGGTT
1 CAGGTAGCGATGGATTCCATGCCTTGTTCTTTCAGAAGCATTGGGATATCGTTGGGAAGGCGGTT
14838 TGTGACTGGGTTAAGAAAATATTCAATGAAGGTGTTATTGATGCTAACCTTAATAATACCCTTAT
66 TGTGACTGGGTTAAGAAAATATTCAATGAAGGTGTTATTGATGCTAACCTTAATAATACCCTTAT
14903 TGTTCTCATACCCAAGGTTGCAAATTCGGAGGGGTTTGCTCAGTTTCGTCCCATTAGTATCTACT
131 TGTTCTCATACCCAAGGTTGCAAATTCGGAGGGGTTTGCTCAGTTTCGTCCCATTAGTATCTACT
14968 CTGTTTTGTACAAATTAGTGATAAAGGTGATCATTAATAGATTTAAACTCATTTTCCCTAAGATT
196 CTGTTTTGTACAAATTAGTGATAAAGGTGATCATTAATAGATTTAAACTCATTTTCCCTAAGATT
15033 ATTGCACAGGAGCAGGCTGGCTTTATTG
261 ATTGCACAGGAGCAGGCTGGCTTTATTG
15061 CAGGTAG
1 CAGGTAG
15068 GAACATTACT
Statistics
Matches: 294, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
288 294 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (288 bp):
CAGGTAGCGATGGATTCCATGCCTTGTTCTTTCAGAAGCATTGGGATATCGTTGGGAAGGCGGTT
TGTGACTGGGTTAAGAAAATATTCAATGAAGGTGTTATTGATGCTAACCTTAATAATACCCTTAT
TGTTCTCATACCCAAGGTTGCAAATTCGGAGGGGTTTGCTCAGTTTCGTCCCATTAGTATCTACT
CTGTTTTGTACAAATTAGTGATAAAGGTGATCATTAATAGATTTAAACTCATTTTCCCTAAGATT
ATTGCACAGGAGCAGGCTGGCTTTATTG
Found at i:18779 original size:2 final size:2
Alignment explanation
Indices: 18772--18801 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18762 TAAACAATAC
18772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18802 GCATGTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.