Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011333.1 Kokia drynarioides strain JFW-HI SEQ_126313, 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: 7269
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Found at i:1870 original size:139 final size:139
Alignment explanation
Indices: 1620--2016 Score: 584
Period size: 139 Copynumber: 2.9 Consensus size: 139
1610 AAACGGTTAG
* * * * *
1620 CTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAACAGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* *
1685 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTGAGAAGAAGACCCAAACGAGGCTTGAAA
66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGAAA
1750 CGAGCAAAT
131 CGAGCAAAT
**
1759 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTTATCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* *
1824 TGAAACAGTGATGGGATCATCTTCTTGATGAGACACTAAAAAGAAGACCCAAACGAGGCTCGAAA
66 TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGAAA
1889 CGAGCAAAT
131 CGAGCAAAT
* * *
1898 CTTCCAGATGAGG-TACTGAGAAGTGAACAAAATTCGTCTACCTGATGAGATACAGAGAAGCGAA
1 CTTCCAGATG-GGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
* * * *
1962 TTGAGACAGACGACGTGG-TCATCTTCCTGATGAGATACTAAGAAGAAGA-CCAAAC
65 TTGAAACAG-TGATG-GGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAAC
2017 CAAACCCACG
Statistics
Matches: 233, Mismatches: 22, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
139 198 0.85
140 33 0.14
141 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (139 bp):
CTTCCAGATGGGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAGTGATGGGATCATCTTCCTGATGAGACACTAAGAAGAAGACCCAAACGAGGCTCGAAA
CGAGCAAAT
Found at i:2498 original size:17 final size:17
Alignment explanation
Indices: 2470--2543 Score: 96
Period size: 17 Copynumber: 4.4 Consensus size: 17
2460 TTGGAAATTG
2470 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
2486 AGTTTATTTTAAAATTTA
1 AATTTATTTT-AAATTTA
*
2504 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
2521 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
2538 AATTTA
1 AATTTA
2544 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
16 5 0.10
17 30 0.60
18 15 0.30
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:2509 original size:34 final size:34
Alignment explanation
Indices: 2464--2543 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
2454 GACTTATTGG
* * *
2464 AAATTGAATTTATTT-AAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTGAAATTTAAATTTATTATA
2497 AAATTTAAATTTATTTGAAATTTAAATTTATTATA
1 AAA-TTAAATTTATTTGAAATTTAAATTTATTATA
2532 AAATTAAATTTA
1 AAATTAAATTTA
2544 GAAAGTCCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.07
34 20 0.48
35 19 0.45
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
AAATTAAATTTATTTGAAATTTAAATTTATTATA
Found at i:2563 original size:13 final size:13
Alignment explanation
Indices: 2545--2596 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 13
2535 TTAAATTTAG
2545 AAAGTCCAATTAA
1 AAAGTCCAATTAA
2558 AAAGTCCAA--AA
1 AAAGTCCAATTAA
2569 CAAAGTCCAATTACA
1 -AAAGTCCAATTA-A
*
2584 AATGGTCCAATTA
1 AA-AGTCCAATTA
2597 CAGATGGCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 2 0.06
12 9 0.27
13 9 0.27
14 3 0.09
15 10 0.30
ACGTcount: A:0.50, C:0.19, G:0.10, T:0.21
Consensus pattern (13 bp):
AAAGTCCAATTAA
Found at i:2593 original size:15 final size:15
Alignment explanation
Indices: 2575--2630 Score: 94
Period size: 15 Copynumber: 3.7 Consensus size: 15
2565 AAAACAAAGT
*
2575 CCAATTACAAATGGT
1 CCAATTACAAATGGC
*
2590 CCAATTACAGATGGC
1 CCAATTACAAATGGC
2605 CCAATTACAAATGGC
1 CCAATTACAAATGGC
2620 CCAATTACAAA
1 CCAATTACAAA
2631 CTACCCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.21
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:2638 original size:30 final size:30
Alignment explanation
Indices: 2575--2638 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2565 AAAACAAAGT
* * *
2575 CCAATTACAAATGGTCCAATTACAGATGGC
1 CCAATTACAAATGGCCCAATTACAAATGAC
2605 CCAATTACAAATGGCCCAATTACAAACT-AC
1 CCAATTACAAATGGCCCAATTACAAA-TGAC
2635 CCAA
1 CCAA
2639 AAGCTCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (30 bp):
CCAATTACAAATGGCCCAATTACAAATGAC
Found at i:4514 original size:59 final size:59
Alignment explanation
Indices: 4422--4948 Score: 679
Period size: 59 Copynumber: 8.9 Consensus size: 59
4412 GAAGGTCCTT
* * *
4422 AAACTTTCC-AAAATTACCATTTTAACCCCGAGCTTCCAAAAATCCCATTTTTAACCTCG
1 AAAC-TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * * * *
4481 AAACTTCCAAAATTTACAATTTTACCCCCGAGCTTCCAAAAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
*
4539 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCTCC-TTTTTGACCTCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CCATTTTTGACCTCG
* * * * *
4598 AAACTTCCAAAAATTACAATTTTACCCTCGAGCTTCCAAAAATCCCATTTTTGACATTG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * *
4657 AAACTTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * *
4716 AAACTTCCAAAAATTACAATTTTACCCCCGAGCTTCCAAAAATCCCATTTTTGACCTTG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
* * * *
4775 AAACTTCTAAAAATTACAATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA-CTCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCT-CG
** * * * * *
4834 AAACCTTTTAAAAA-TACCATTTTACCCTCGAACTTCTAAAAA-CTCCTTTTTTCACCTCA
1 AAA-CTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATC-CCATTTTTGACCTCG
*
4893 AAACTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACC
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC
4949 CTGAATATGC
Statistics
Matches: 409, Mismatches: 49, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
58 65 0.16
59 332 0.81
60 12 0.03
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.31
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
Done.