Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010095.1 Kokia drynarioides strain JFW-HI SEQ_124876, 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: 10067
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1143 original size:30 final size:30
Alignment explanation
Indices: 1108--1444 Score: 307
Period size: 30 Copynumber: 11.4 Consensus size: 30
1098 CTAAATTGTT
* * *
1108 CAAAAATCCCATTTTTAAACTCGAACCTTT
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* * * *
1138 TAAAAATCCTAATTTTAACCCCGAAACTTC
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* * * *
1168 CAAAAATTCTATTTTTACCCTCG-AACTAC
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* *
1197 CAAAAATCCCATTTTTAA-CTCCGAAGCTTT
1 CAAAAATCCCATTTTTAACCT-CGAAACTTC
*
1227 CAAAAATTCCATTTTTAACCTCGAAACTTC
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* * * *
1257 CAAAAATTCCATTTTTACCCCCG-AACTAC
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* * *
1286 CAAAAATCCCATTTTTAACCCCGAAGCTTT
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* *
1316 CAAAAATTCCA-TTTTAACCTCG-AACCTC
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* *
1344 CAAAAATCCCATTTTTGACC-CTAAAACTAT-
1 CAAAAATCCCATTTTTAACCTC-GAAACT-TC
*
1374 C-AAAATCCCATTTTTAACCTCGAAACTTT
1 CAAAAATCCCATTTTTAACCTCGAAACTTC
* *
1403 CAAAAGGT-CCATTTTTACCCTCG-AACTTC
1 CAAAA-ATCCCATTTTTAACCTCGAAACTTC
*
1432 TAAAAATCCCATT
1 CAAAAATCCCATT
1445 GTTGACCTTG
Statistics
Matches: 248, Mismatches: 46, Indels: 27
0.77 0.14 0.08
Matches are distributed among these distances:
28 18 0.07
29 102 0.41
30 124 0.50
31 4 0.02
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (30 bp):
CAAAAATCCCATTTTTAACCTCGAAACTTC
Found at i:1231 original size:59 final size:57
Alignment explanation
Indices: 1108--1444 Score: 295
Period size: 59 Copynumber: 5.7 Consensus size: 57
1098 CTAAATTGTT
* ** ** * *
1108 CAAAAATCCCATTTTTAAACTCGAACCTTTTAAAAATCCTAATTTTAACCCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAA-CTTCCAAAAATCCCATTTTTAA-CCCG-AACTTC
* * *
1168 CAAAAATTCTATTTTTACCCTCGAACTACCAAAAATCCCATTTTTAACTCCGAAGCTTT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAAC-CCGAA-CTTC
* * * *
1227 CAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTAC
1 CAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATCCCATTTTTA-ACCCGAACTTC
* * * *
1286 CAAAAATCCCATTTTTAACCC-CGAAGCTTTCAAAAATTCCA-TTTTAACCTCGAACCTC
1 CAAAAATTCCATTTTT-ACCCTCGAA-CTTCCAAAAATCCCATTTTTAACC-CGAACTTC
* ** *
1344 CAAAAATCCCATTTTTGACCCTAAAACTAT-C-AAAATCCCATTTTTAACCTCGAAACTTT
1 CAAAAATTCCATTTTT-ACCCTCGAACT-TCCAAAAATCCCATTTTTAACC-CG-AACTTC
** *
1403 CAAAAGGTCCATTTTTACCCTCGAACTTCTAAAAATCCCATT
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATT
1445 GTTGACCTTG
Statistics
Matches: 229, Mismatches: 35, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
57 11 0.05
58 59 0.26
59 108 0.47
60 50 0.22
61 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (57 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCGAACTTC
Found at i:1259 original size:89 final size:88
Alignment explanation
Indices: 1108--1444 Score: 423
Period size: 89 Copynumber: 3.8 Consensus size: 88
1098 CTAAATTGTT
* * * *
1108 CAAAAATCCCATTTTTAAACT-CGAACCTTTTAAAAA-TCCTAATTTTAACCCCGAAACTTCCAA
1 CAAAAATCCCATTTTT-AACTCCGAAGCTTTCAAAAATTCC-ATTTTTAACCTCG-AACTTCCAA
*
1171 AAATTCTATTTTTACCCTCGAACTAC
63 AAATTCCATTTTTACCCTCGAACTAC
1197 CAAAAATCCCATTTTTAACTCCGAAGCTTTCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAA
1 CAAAAATCCCATTTTTAACTCCGAAGCTTTCAAAAATTCCATTTTTAACCTCG-AACTTCCAAAA
*
1262 ATTCCATTTTTACCCCCGAACTAC
65 ATTCCATTTTTACCCTCGAACTAC
* *
1286 CAAAAATCCCATTTTTAACCCCGAAGCTTTCAAAAATTCCA-TTTTAACCTCGAACCTCCAAAAA
1 CAAAAATCCCATTTTTAACTCCGAAGCTTTCAAAAATTCCATTTTTAACCTCGAACTTCCAAAAA
* ** *
1350 TCCCATTTTTGACCCTAAAACTAT
66 TTCCATTTTT-ACCCTCGAACTAC
* ** * *
1374 C-AAAATCCCATTTTTAAC-CTCGAAACTTTCAAAAGGTCCATTTTTACCCTCGAACTTCTAAAA
1 CAAAAATCCCATTTTTAACTC-CGAAGCTTTCAAAAATTCCATTTTTAACCTCGAACTTCCAAAA
*
1437 ATCCCATT
65 ATTCCATT
1445 GTTGACCTTG
Statistics
Matches: 224, Mismatches: 19, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
86 1 0.00
87 54 0.24
88 52 0.23
89 114 0.51
90 3 0.01
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.31
Consensus pattern (88 bp):
CAAAAATCCCATTTTTAACTCCGAAGCTTTCAAAAATTCCATTTTTAACCTCGAACTTCCAAAAA
TTCCATTTTTACCCTCGAACTAC
Done.