Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002484.1 Kokia drynarioides strain JFW-HI SEQ_114631, 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: 3634
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:60 original size:3 final size:3
Alignment explanation
Indices: 1--44 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45 ATGGGTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1606 original size:29 final size:29
Alignment explanation
Indices: 1167--1671 Score: 356
Period size: 29 Copynumber: 17.2 Consensus size: 29
1157 CCGTGAAGGT
*
1167 CCCT-AAACTATCCAAAAATTCTATTTTTTA
1 CCCTCAAACT-TCCAAAAATTCCA-TTTTTA
** *
1197 CTCC-CGTACTTCCAAAAATCCCATTTTTGA
1 C-CCTCAAACTTCCAAAAATTCCATTTTT-A
* * *
1227 -CCTCAAAACTTCTAAAAAATCCAATTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
*
1256 GTCC-CAAACTTCCAAAAA-TCACATTTTTTA
1 -CCCTCAAACTTCCAAAAATTC-CA-TTTTTA
* * *
1286 GCCC-AAAACTTCTAAAAATCCCATTTTTA
1 -CCCTCAAACTTCCAAAAATTCCATTTTTA
** *
1315 CCCTCGTACTTCCAAAAATCCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
*
1345 -CCTCGAAACTTCTAAAAATTCCA-TTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
** *
1373 CCCTCAAACTTCCAAAAATAACATTTTTTG
1 CCCTCAAACTTCCAAAAATTCCA-TTTTTA
* *
1403 CCC-CAAAACTTCTAAAAATTCTATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
** * *
1432 CCCTTGAACTTCCAAAAATCCCATTTTAA
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* *
1461 CCC-CAAAATTTCTAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * *
1490 CCCCCGAACATT-CAAAAATCCCATTTTTGA
1 CCCTCAAAC-TTCCAAAAATTCCATTTTT-A
* *
1520 CCC-CAAAACTTCCATAAATTCCATTGTTA
1 CCCTC-AAACTTCCAAAAATTCCATTTTTA
* * *
1549 CCCCCAAACTTTCAAAAAAATCCCATTTTTA
1 CCCTCAAAC-TTC-CAAAAATTCCATTTTTA
* *
1580 CCCTCAAACTT-CAAAAATTCAATTTTTG
1 CCCTCAAACTTCCAAAAATTCCATTTTTA
* * *
1608 GCCTCGAACTTCCAAAAATTCTATTTTTGA
1 CCCTCAAACTTCCAAAAATTCCATTTTT-A
1638 -CCTCAAAACTTCCAAAAATTACCA-TTTTA
1 CCCTC-AAACTTCCAAAAATT-CCATTTTTA
1667 CCCTC
1 CCCTC
1672 GGATGTCCAA
Statistics
Matches: 375, Mismatches: 68, Indels: 64
0.74 0.13 0.13
Matches are distributed among these distances:
28 45 0.12
29 159 0.42
30 140 0.37
31 31 0.08
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTA
Found at i:1672 original size:59 final size:58
Alignment explanation
Indices: 1171--1731 Score: 464
Period size: 59 Copynumber: 9.5 Consensus size: 58
1161 GAAGGTCCCT
* *
1171 AAACTATCCAAAAATTCTATTTTTTACTCC-CGTACTTCCAAAAATCCCATTTTTGACCTCA
1 AAACT-TCCAAAAATTCCA--TTTTAC-CCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * * *
1232 AAACTTCTAAAAAATCCAATTTTAGTCC-CAAACTTCCAAAAATCACATTTTTTAGCC-CA
1 AAACTTCCAAAAATTCC-ATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGA-CCTCA
* * * *
1291 AAACTTCTAAAAATCCCATTTTTACCCTCGTACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * ** *
1350 AAACTTCTAAAAATTCCATTTTACCCTCAAACTTCCAAAAATAACATTTTTTG-CCCCA
1 AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCA-TTTTTGACCTCA
* * * * *
1408 AAACTTCTAAAAATTCTATTTTTACCCTTGAACTTCCAAAAATCCCA-TTTTAACCCCA
1 AAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * *
1466 AAATTTCTAAAAATTCCATTTTTACCCCCGAACATT-CAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTACCCTCGAAC-TTCCAAAAATCCCATTTTTGACCTCA
* * * *
1525 AAACTTCCATAAATTCCATTGTTACCCCCAAACTTTCAAAAAAATCCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATTCCATT-TTACCCTCGAAC-TTC-CAAAAATCCCATTTTTGA-CCTCA
* ** * *
1585 AAACTT-CAAAAATTCAATTTTTGGCCTCGAACTTCCAAAAATTCTATTTTTGACCTCA
1 AAACTTCCAAAAATTCCA-TTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
* * * * *
1643 AAACTTCCAAAAATTACCATTTTACCCTCGGA-TGTCCAAAAA-CTCTATTTTCGACTTCG
1 AAACTTCCAAAAATT-CCATTTTACCCTCGAACT-TCCAAAAATC-CCATTTTTGACCTCA
* *
1702 AAAC-TCTCAAAATTTCCCTTTTACCC-CGAA
1 AAACTTC-CAAAAATTCCATTTTACCCTCGAA
1732 TGTCTAGAAA
Statistics
Matches: 416, Mismatches: 61, Indels: 50
0.79 0.12 0.09
Matches are distributed among these distances:
57 24 0.06
58 119 0.29
59 227 0.55
60 22 0.05
61 24 0.06
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCA
Found at i:3156 original size:13 final size:12
Alignment explanation
Indices: 3127--3157 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3117 GGGAAATACT
3127 ATTTTTAAAATA
1 ATTTTTAAAATA
3139 ATTTTTAAAATA
1 ATTTTTAAAATA
3151 ATTTTTA
1 ATTTTTA
3158 TTATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTTAAAATA
Done.