Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011935.1 Kokia drynarioides strain JFW-HI SEQ_126933, 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: 30995
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 230 characters in sequence are not A, C, G, or T
Found at i:1507 original size:22 final size:22
Alignment explanation
Indices: 1479--1529 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1469 AAATCGGCCC
1479 GGATCCGATTCGACCCGACTCA
1 GGATCCGATTCGACCCGACTCA
1501 GGATCCGATTCGACCCGACTCA
1 GGATCCGATTCGACCCGACTCA
1523 GGATCCG
1 GGATCCG
1530 CGTGTTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
GGATCCGATTCGACCCGACTCA
Found at i:2102 original size:59 final size:58
Alignment explanation
Indices: 1945--2519 Score: 687
Period size: 59 Copynumber: 9.7 Consensus size: 58
1935 AAAACTTCCG
* *
1945 AAATTACCATTTTACCCTCGAACTTTCAAAAATCTCATTTTTGACCCCGAATCTTCCAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAATC-CATTTTTGACCCCGAATCTTCTAA
* *
2004 AAATTTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTT-AGCCCCGAACCTTCTAA
1 AAA-TTACCATTTTACCCTC-GAACTTCCAAAAAT-CCATTTTTGA-CCCCGAATCTTCTAA
* * * *
2064 AAATTACCATTTTACCCTCGCA-TTCCCAAAAATACCATTTTTCACCCCGAATTTTCCAA
1 AAATTACCATTTTACCCTCGAACTT-CCAAAAAT-CCATTTTTGACCCCGAATCTTCTAA
* * * * * *
2123 AAATTACTATTTTACCC-CTAAATTTCAAAAAATCCCATTTTT-AGCCCCGAACCTTTTAA
1 AAATTACCATTTTACCCTC-GAACTTCCAAAAAT-CCATTTTTGA-CCCCGAATCTTCTAA
* * * * *
2182 AAATTACCATTTTACCCCCGCACTCCCAAAAATCTCATTTTTGACCCTGAATCTTTTAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAATC-CATTTTTGACCCCGAATCTTCTAA
* *
2241 AAATTACCTTTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAA-CTTTCTAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAATC-CATTTTTGACCCCGAATC-TTCTAA
* * *
2300 AAATTACAATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCTAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTGACCCCGAATCTTCTAA
* * *
2359 AAATTACCATTTTACCCTCAAACTTCCAAAAATCCTATTTTTGACCTCAAATCTTCTAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAATCC-ATTTTTGACCCCGAATCTTCTAA
* *
2418 AAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCTAA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAAT-CCATTTTTGACCCCGAATCTTCTAA
2477 AAATTACCATTTTACCCTCGAACTTCC-AAAATCCTATTTTTGA
1 AAATTACCATTTTACCCTCGAACTTCCAAAAATCC-ATTTTTGA
2520 TTCCGAACAT
Statistics
Matches: 452, Mismatches: 45, Indels: 39
0.84 0.08 0.07
Matches are distributed among these distances:
57 2 0.00
58 21 0.05
59 369 0.82
60 59 0.13
61 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (58 bp):
AAATTACCATTTTACCCTCGAACTTCCAAAAATCCATTTTTGACCCCGAATCTTCTAA
Found at i:9083 original size:6 final size:6
Alignment explanation
Indices: 9072--9111 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
9062 TTCAGGTCGT
* *
9072 TTTTCA TTTTCA TTTTCA TTTTCA TTTTTA TTTTTA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
9112 GGAGAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCA
Found at i:20029 original size:2 final size:2
Alignment explanation
Indices: 20022--20046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20012 AGGCAGGCGC
20022 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20047 ATATATGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22249 original size:18 final size:20
Alignment explanation
Indices: 22226--22265 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
22216 ATATATCGTT
*
22226 TTCCTCTCTCT-T-TTTCCC
1 TTCCTCTCACTGTATTTCCC
22244 TTCCTCTCACTGTATTTCCC
1 TTCCTCTCACTGTATTTCCC
22264 TT
1 TT
22266 AGAGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.05, C:0.40, G:0.03, T:0.53
Consensus pattern (20 bp):
TTCCTCTCACTGTATTTCCC
Found at i:27539 original size:31 final size:31
Alignment explanation
Indices: 27504--27562 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
27494 TGGTCCAATG
*
27504 ACTTAAATAAAAACTTTCGAATAGTTTAGTA
1 ACTTAAATAAAAACTTTAGAATAGTTTAGTA
* *
27535 ACTTAAATGAAAATTTTAGAATAGTTTA
1 ACTTAAATAAAAACTTTAGAATAGTTTA
27563 AGGATCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTAGAATAGTTTAGTA
Done.