Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001411.1 Kokia drynarioides strain JFW-HI SEQ_112902, 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: 2135
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Found at i:1519 original size:59 final size:58
Alignment explanation
Indices: 1456--1667 Score: 182
Period size: 59 Copynumber: 3.6 Consensus size: 58
1446 GCAAAATGGT
* * * *
1456 AATTTTGGGAAATTTTGGGGTTAAAAATGAAATTTTTAGACATTCGGGGGTAAAAGGGA
1 AATTTTGGGAAATTTCGAGGTTAAAAATGAAATTTTTGGACATTCGGGGGTAAAA-TGA
* * * *
1515 AATTTTGAG-AGTTTCGAGGTTGAAAAAT-AAAGTTTTTGGACATTCGAGGGCAAAATGA
1 AATTTTGGGAAATTTCGAGGTT-AAAAATGAAA-TTTTTGGACATTCGGGGGTAAAATGA
* * * * **
1573 TAATTTT-TGAAAGTTTTGAGGTAAAAAATGAAAATTTTGGAGGTT-GGGGGTAAAAATGA
1 -AATTTTGGGAAA-TTTCGAGGTTAAAAATGAAATTTTTGGACATTCGGGGGT-AAAATGA
* * *
1632 AATTTTTGGAAGTTTCGAGGTT-AAAATGGAATTTTT
1 AATTTTGGGAAATTTCGAGGTTAAAAATGAAATTTTT
1668 TGAAGTTTTA
Statistics
Matches: 122, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
57 12 0.10
58 33 0.27
59 66 0.54
60 11 0.09
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
AATTTTGGGAAATTTCGAGGTTAAAAATGAAATTTTTGGACATTCGGGGGTAAAATGA
Found at i:1639 original size:118 final size:117
Alignment explanation
Indices: 1442--1657 Score: 285
Period size: 118 Copynumber: 1.8 Consensus size: 117
1432 TTGAATTTTT
* * * *
1442 GAGGGCAAAATGGTAATTTTGGGAAATTTTGGGGTTAAAAATGAAATTTTTAGACATTCGGGGGT
1 GAGGGCAAAATGATAATTTTGGGAAATTTTGAGGTAAAAAATGAAAATTTTAGACATTCGGGGGT
*
1507 AAAAGGGAAATTTT-GAGAGTTTCGAGGTTGAAAAATAAAGTTTTTGGACATTC
66 AAAAAGGAAATTTTGGA-AGTTTCGAGGTT-AAAAATAAAGTTTTTGGACATTC
* * **
1560 GAGGGCAAAATGATAATTTT-TGAAAGTTTTGAGGTAAAAAATGAAAATTTTGGAGGTT-GGGGG
1 GAGGGCAAAATGATAATTTTGGGAAA-TTTTGAGGTAAAAAATGAAAATTTTAGACATTCGGGGG
*
1623 TAAAAATGAAATTTTTGGAAGTTTCGAGGTTAAAA
65 TAAAAAGGAAA-TTTTGGAAGTTTCGAGGTTAAAA
1658 TGGAATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
117 22 0.26
118 61 0.72
119 2 0.02
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (117 bp):
GAGGGCAAAATGATAATTTTGGGAAATTTTGAGGTAAAAAATGAAAATTTTAGACATTCGGGGGT
AAAAAGGAAATTTTGGAAGTTTCGAGGTTAAAAATAAAGTTTTTGGACATTC
Found at i:1651 original size:88 final size:88
Alignment explanation
Indices: 1537--1733 Score: 228
Period size: 88 Copynumber: 2.2 Consensus size: 88
1527 TTCGAGGTTG
1537 AAAAAT-AAAGTTTTTGGACA--TTCGAGGGCAAAAT-GATAATTTTTGAAAGTTTT-GAGGTAA
1 AAAAATGAAA-TTTTTGGA-AGTTTCGAGGGCAAAATGGA-AATTTTTG-AAGTTTTAG-GGTAA
*
1597 AAAATGA-AAATTTTGGAGGTT-GGGGGT
61 AAAAT-ATAAATTTTGGAAGTTCGGGGGT
** * *
1624 AAAAATGAAATTTTTGGAAGTTTCGAGGTTAAAATGGAATTTTTTGAAGTTTTAGGGTTAAAAAT
1 AAAAATGAAATTTTTGGAAGTTTCGAGGGCAAAATGGAAATTTTTGAAGTTTTAGGGTAAAAAAT
*
1689 ATAATTTTTGGAAGTTCGGGGGT
66 ATAAATTTTGGAAGTTCGGGGGT
*
1712 AAAAATGGAATTTTTGGAAGTT
1 AAAAATGAAATTTTTGGAAGTT
1734 CTAAGGTCCT
Statistics
Matches: 96, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
86 2 0.02
87 42 0.44
88 50 0.52
89 2 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (88 bp):
AAAAATGAAATTTTTGGAAGTTTCGAGGGCAAAATGGAAATTTTTGAAGTTTTAGGGTAAAAAAT
ATAAATTTTGGAAGTTCGGGGGT
Found at i:1688 original size:59 final size:60
Alignment explanation
Indices: 1566--1733 Score: 184
Period size: 59 Copynumber: 2.9 Consensus size: 60
1556 ATTCGAGGGC
* * ** * * *
1566 AAAATGATAATTTTTGAAAGTTTTGAGGTAAAAAAT-GAAAATTTTGGAG-GTTGGGGGTA
1 AAAATGATAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTTGAAGTTTTAGGGGTA
* *
1625 AAAATGA-AATTTTTGGAAGTTTCGAGGTTAAAATGGAATTTTTTGAAGTTTTAGGGTTA
1 AAAATGATAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAGTTTTAGGGGTA
* *
1684 AAAAT-ATAATTTTTGGAAG-TTCGGGGGTAAAAATGGAATTTTTGGAAGTT
1 AAAATGATAATTTTTGGAAGTTTC-GAGGTAAAAATGGAATTTTTTGAAGTT
1734 CTAAGGTCCT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 5 0.05
58 33 0.35
59 55 0.59
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (60 bp):
AAAATGATAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTTGAAGTTTTAGGGGTA
Found at i:1734 original size:29 final size:29
Alignment explanation
Indices: 1472--1734 Score: 166
Period size: 29 Copynumber: 9.0 Consensus size: 29
1462 GGGAAATTTT
* *
1472 GGGGTTAAAAATGAAATTTTTAGACA-TTC
1 GGGGGTAAAAATGAAATTTTTGGA-AGTTC
**
1501 GGGGGTAAAAGGGAAA-TTTT-GAGAGTTTC
1 GGGGGTAAAAATGAAATTTTTGGA-AG-TTC
* *
1530 GAGGTTGAAAAAT-AAAGTTTTTGGACA-TTC
1 GGGGGT-AAAAATGAAA-TTTTTGGA-AGTTC
* * * *
1560 GAGGG-CAAAATGATAATTTTTGAAAGTTT
1 GGGGGTAAAAATGA-AATTTTTGGAAGTTC
* * * *
1589 TGAGGTAAAAAATGAAAATTTTGGAGGTT-
1 GGGGGT-AAAAATGAAATTTTTGGAAGTTC
1618 GGGGGTAAAAATGAAATTTTTGGAAGTTTC
1 GGGGGTAAAAATGAAATTTTTGGAAG-TTC
* * * * *
1648 -GAGGTTAAAATGGAATTTTTTGAAGTTTT
1 GGGGGTAAAAATGAAATTTTTGGAAG-TTC
* *
1677 AGGGTTAAAAAT-ATAATTTTTGGAAGTTC
1 GGGGGTAAAAATGA-AATTTTTGGAAGTTC
*
1706 GGGGGTAAAAATGGAATTTTTGGAAGTTC
1 GGGGGTAAAAATGAAATTTTTGGAAGTTC
1735 TAAGGTCCTC
Statistics
Matches: 180, Mismatches: 38, Indels: 32
0.72 0.15 0.13
Matches are distributed among these distances:
27 3 0.02
28 28 0.16
29 92 0.51
30 43 0.24
31 11 0.06
32 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGGGTAAAAATGAAATTTTTGGAAGTTC
Done.