Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003485.1 Kokia drynarioides strain JFW-HI SEQ_116297, 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, 975
Length: 1626
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:107 original size:21 final size:23
Alignment explanation
Indices: 78--121 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
68 GGGGAAAATC
*
78 GTTTAGATCTAG-GCTAGATCTG
1 GTTTAGATCTAGACCTAGATCTG
100 GTTT-GATCTAGACCTAGATCTG
1 GTTTAGATCTAGACCTAGATCTG
122 TTCTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (23 bp):
GTTTAGATCTAGACCTAGATCTG
Found at i:1174 original size:59 final size:59
Alignment explanation
Indices: 981--1331 Score: 356
Period size: 59 Copynumber: 5.9 Consensus size: 59
971 CCCTAAATTA
* * * *
981 TTCAACAATCCTATTTTTAACCCCGAAACTTCCAAAAAATCCCATTTTTACCCTC-GAAC-
1 TTCAAAAATCCCATTTTTAACCCCAAAACTTCC-AAAAATCCCATTTTTACCC-CAAAACT
* *
1040 TTCTAGAAATCCCATTTTTAACCCCAAAACTTCCAAAAAATCCCATTTTTACCCTC-GAA-T
1 TTC-AAAAATCCCATTTTTAACCCCAAAACTTCC-AAAAATCCCATTTTTACCC-CAAAACT
*
1100 TTCTAGAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAAAACT
1 TTC-AAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAAAACT
* * * * *
1160 TTCAAAAATACCATTTTTAACCCCGAAACTTCCAAAAATCTCAATTTTAACCCAAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATC-CCATTTTTACCCCAAAACT
* * ** * * *
1220 TCCAAAAATTCCATTTTT-ACCCCCGAACTACAAAAAATCTCATTTTTAACCCCAAAACT
1 TTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTT-ACCCCAAAACT
* * * *
1279 TTCAAAAGGT-CAATTTTT-ACCCCCAAACTTCTAAAAATCCCATTTTTGACCCC
1 TTCAAAA-ATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTT-ACCCC
1332 GAATTTTCCC
Statistics
Matches: 256, Mismatches: 29, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
58 6 0.02
59 128 0.50
60 122 0.48
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (59 bp):
TTCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTACCCCAAAACT
Found at i:1346 original size:30 final size:30
Alignment explanation
Indices: 987--1334 Score: 352
Period size: 30 Copynumber: 11.7 Consensus size: 30
977 ATTATTCAAC
*
987 AATCCTATTTTTAACCCCGAAACTTCCAAAA
1 AATCCCATTTTTAACCCCGAAACTTCC-AAA
* *
1018 AATCCCATTTTT-ACCCTCG-AACTTCTAGA
1 AATCCCATTTTTAACCC-CGAAACTTCCAAA
*
1047 AATCCCATTTTTAACCCCAAAACTTCCAAAA
1 AATCCCATTTTTAACCCCGAAACTTCC-AAA
* * *
1078 AATCCCATTTTT-ACCCTCG-AATTTCTAGA
1 AATCCCATTTTTAACCC-CGAAACTTCCAAA
*
1107 AATCCCATTTTTAACCCCAAAACTTCCAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
* *
1137 AATCCCATTTTT-ACCCCAAAACTTTCAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
*
1166 AATACCATTTTTAACCCCGAAACTTCCAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
* * **
1196 AATCTCAATTTTAACCCAAAAACTTCCAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
* * * *
1226 AATTCCATTTTTACCCCCG-AACTACAAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
* * *
1255 AATCTCATTTTTAACCCCAAAACTTTCAAA
1 AATCCCATTTTTAACCCCGAAACTTCCAAA
* * * *
1285 AGGT-CAATTTTT-ACCCCCAAACTTCTAAA
1 A-ATCCCATTTTTAACCCCGAAACTTCCAAA
*
1314 AATCCCATTTTTGACCCCGAA
1 AATCCCATTTTTAACCCCGAA
1335 TTTTCCCAAA
Statistics
Matches: 258, Mismatches: 47, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.00
29 102 0.40
30 126 0.49
31 29 0.11
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (30 bp):
AATCCCATTTTTAACCCCGAAACTTCCAAA
Done.