Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002701.1 Kokia drynarioides strain JFW-HI SEQ_114983, 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: 2146
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Found at i:619 original size:30 final size:30
Alignment explanation
Indices: 585--654 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
575 CAGCGAAGGT
* * *
585 GTCGGATGACAACGCGTGACAGCGACGTGC
1 GTCGGACGACAACGCGCGACAGCGACGCGC
615 GTCGGACGACAACGCGCGACAGCGACGCGC
1 GTCGGACGACAACGCGCGACAGCGACGCGC
645 GTCGGACGAC
1 GTCGGACGAC
655 GATCGAAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.23, C:0.31, G:0.37, T:0.09
Consensus pattern (30 bp):
GTCGGACGACAACGCGCGACAGCGACGCGC
Found at i:1292 original size:29 final size:29
Alignment explanation
Indices: 1248--1717 Score: 349
Period size: 29 Copynumber: 16.6 Consensus size: 29
1238 CTTAAATTTT
1248 CAAAAATTCCATTTTTACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * * * *
1277 TAAAAATCCCAATTTTGACCCTAAAGCTTC
1 CAAAAATTCC-ATTTTTACCCCAAAACTTC
*
1307 CAAAAATTCCATTTTTACCCTC-GAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
* **
1336 CAAAAATTCCATTTTGACTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * *
1365 CAAAAATTCCATTTTTACACTAGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * *
1394 TAAAAATCCCATTTTTTACCCCGAAACTTC
1 CAAAAATTCCA-TTTTTACCCCAAAACTTC
* *
1424 CAAAAATTCCATTTTTACCCTAGAACTTC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
1453 CAAAAATTCAATTTTT-------AAC-CC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* * ** *
1474 CAAAAATTCCATTTTTACCTCGAACTTCC
1 CAAAAATTCCATTTTTACCCCAAAACTTC
* *
1503 AAAAAT-TCCATTTTTAACCCCAAAA-TTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
*
1531 C----A-----TTTTTACCCTC-AAACTTT
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
*
1551 CAAAAATTCTATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
* *
1581 CAAAAAGTCCATTTTTTACCCTC-GAACTTC
1 CAAAAATTCCA-TTTTTACCC-CAAAACTTC
1611 CAAAAA-TCTCATTTTTAACCCCAAAACTTC
1 CAAAAATTC-CATTTTT-ACCCCAAAACTTC
* *
1641 CAAAAATTTCATTTTTACCCTC-GAACTTC
1 CAAAAATTCCATTTTTACCC-CAAAACTTC
** *
1670 CAAAAAACCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTT-ACCCCAAAACTTC
1700 CAAAAATTCCATTTTTAC
1 CAAAAATTCCATTTTTAC
1718 TCTCGAACTT
Statistics
Matches: 347, Mismatches: 59, Indels: 70
0.73 0.12 0.15
Matches are distributed among these distances:
19 7 0.02
20 9 0.03
21 16 0.05
22 3 0.01
24 1 0.00
28 13 0.04
29 160 0.46
30 131 0.38
31 7 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAATTCCATTTTTACCCCAAAACTTC
Found at i:1341 original size:59 final size:58
Alignment explanation
Indices: 1248--1739 Score: 468
Period size: 59 Copynumber: 8.7 Consensus size: 58
1238 CTTAAATTTT
* * *
1248 CAAAAATTCCATTTTTACCC-CAAAACTTCTAAAAATCCCAATTTTGACCCTAAAGCTTC
1 CAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* *
1307 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCC-ATTTTGA-CTTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCT-AAAACTTC
* * * * **
1365 CAAAAATTCCATTTTTACACTAGAACTTCTAAAAATCCCATTTTTTACCCCGAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA-ATTTTACCCTAAAACTTC
* * *
1424 CAAAAATTCCATTTTTACCCTAGAACTTCCAAAAAT-TCAATTTT----T--AAC-CC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
*
1474 CAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCC-ATTTT----T--AAC--C
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
* * * * * * *
1522 CCAAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* * * *
1581 CAAAAAGTCCATTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTAACCCCAAAACTTC
1 CAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATCCCAATTTT-ACCCTAAAACTTC
* * * *
1641 CAAAAATTTCATTTTTACCCTCGAACTTCCAAAAAACCCATTTTTAACCTCAAAACTTC
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCT-AAAACTTC
* *
1700 CAAAAATTCCATTTTTACTCTCGAACTTCTAAAAATCCCA
1 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCA
1740 CTGAACATCC
Statistics
Matches: 370, Mismatches: 44, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
48 17 0.05
49 44 0.12
50 23 0.06
51 3 0.01
57 9 0.02
58 54 0.15
59 162 0.44
60 58 0.16
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCAATTTTACCCTAAAACTTC
Found at i:1516 original size:49 final size:50
Alignment explanation
Indices: 1423--1642 Score: 257
Period size: 49 Copynumber: 4.2 Consensus size: 50
1413 CCCGAAACTT
*
1423 CCAAAAATTCCATTTTTACCCTAGAACTTCCAAAAATTCAATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
*
1473 CCAAAAATTCCATTTTTA-CCTCGAACTTCCAAAAATTCCATTTTTAACC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
* * *
1522 CC-AAAATTCCATTTTTACCCTCAAACTTTCAAAAATTCTATTTTTAACCCCAAAAC
1 CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAA---C----C
*
1578 TTCCAAAAAGTCCATTTTTTACCCTCGAACTTCCAAAAATCTC-ATTTTTAACC
1 --CCAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAAT-TCAATTTTTAACC
*
1631 CCAAAACTTCCA
1 CCAAAAATTCCA
1643 AAAATTTCAT
Statistics
Matches: 147, Mismatches: 10, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
48 15 0.10
49 57 0.39
50 18 0.12
51 10 0.07
52 1 0.01
53 1 0.01
56 1 0.01
57 1 0.01
58 2 0.01
59 8 0.05
60 31 0.21
61 2 0.01
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.34
Consensus pattern (50 bp):
CCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCAATTTTTAACC
Found at i:1541 original size:19 final size:21
Alignment explanation
Indices: 1504--1546 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1494 CGAACTTCCA
1504 AAAATTCCATTTTTAACCC-C
1 AAAATTCCATTTTTAACCCTC
1524 AAAATTCCATTTTT-ACCCTC
1 AAAATTCCATTTTTAACCCTC
1544 AAA
1 AAA
1547 CTTTCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTCCATTTTTAACCCTC
Found at i:1585 original size:30 final size:30
Alignment explanation
Indices: 1524--1735 Score: 231
Period size: 30 Copynumber: 7.2 Consensus size: 30
1514 TTTTAACCCC
*
1524 AAAATTCCATTTTT-ACCCTCAAACTTTCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
*
1553 AAAATTCTATTTTTAACCC-CAAAACTTCCA
1 AAAATTCCATTTTTAACCCTC-AAACTTCCA
* * *
1583 AAAAGTCCATTTTTTACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
1613 AAAA-TCTCATTTTTAACCC-CAAAACTTCCA
1 AAAATTC-CATTTTTAACCCTC-AAACTTCCA
* *
1643 AAAATTTCATTTTT-ACCCTCGAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
**
1672 AAAAACCCATTTTTAA-CCTCAAAACTTCCA
1 AAAATTCCATTTTTAACCCTC-AAACTTCCA
* * *
1702 AAAATTCCATTTTT-ACTCTCGAACTTCTA
1 AAAATTCCATTTTTAACCCTCAAACTTCCA
1731 AAAAT
1 AAAAT
1736 CCCACTGAAC
Statistics
Matches: 154, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
29 57 0.37
30 95 0.62
31 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCTCAAACTTCCA
Done.