Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000094.1 Kokia drynarioides strain JFW-HI SEQ_110722, 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: 3013
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Found at i:1508 original size:28 final size:28
Alignment explanation
Indices: 1477--1538 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1467 AAAATGTGAT
* *
1477 TTTTGGATAC-CCGAGGACAAAATGGTAA
1 TTTTGGACACTCCGAGGA-AAAATAGTAA
* *
1505 TTTTGGACACTCGGGGGAAAAATAGTAA
1 TTTTGGACACTCCGAGGAAAAATAGTAA
1533 TTTTGG
1 TTTTGG
1539 GAAAGTTCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.29
Consensus pattern (28 bp):
TTTTGGACACTCCGAGGAAAAATAGTAA
Found at i:1566 original size:31 final size:30
Alignment explanation
Indices: 1515--1573 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
1505 TTTTGGACAC
1515 TCGGGGGAAAAATAGTAATTTTGGGAAAGT
1 TCGGGGGAAAAATAGTAATTTTGGGAAAGT
*
1545 TCGGGTGGTAAAAAT-GTAATTTTTGGAAA
1 TCGGG-GG-AAAAATAGTAATTTTGGGAAA
1574 AATCAAGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 5 0.19
31 15 0.58
32 6 0.23
ACGTcount: A:0.36, C:0.03, G:0.31, T:0.31
Consensus pattern (30 bp):
TCGGGGGAAAAATAGTAATTTTGGGAAAGT
Found at i:1644 original size:29 final size:30
Alignment explanation
Indices: 1550--1778 Score: 113
Period size: 29 Copynumber: 7.8 Consensus size: 30
1540 AAAGTTCGGG
1550 TGGTAAAAAT-GTAATTTTTGGAAAAATCA
1 TGGTAAAAATGGTAATTTTTGGAAAAATCA
* ** *
1579 AGGTCAAAAATGG-AATTTTTGG-AAGTTCG
1 TGGT-AAAAATGGTAATTTTTGGAAAAATCA
* * *
1608 GGGTTAAAATGGTGATTTTTGGAAAAATCA
1 TGGTAAAAATGGTAATTTTTGGAAAAATCA
* * ***
1638 TGGTAAAAAAT-GAAATTTTGGGAGGTAT-A
1 TGGT-AAAAATGGTAATTTTTGGAAAAATCA
* * * *
1667 AGGGAAAAATGGTATTTTTTGG-AAAATCG
1 TGGTAAAAATGGTAATTTTTGGAAAAATCA
* * **
1696 GGGTTAAAAATAG-AATTTTT-GAAAGTTCGA
1 TGG-TAAAAATGGTAATTTTTGGAAAAATC-A
* *
1726 GGGT-AAAATGGTAATTTTT-GAAAAATTGA
1 TGGTAAAAATGGTAATTTTTGGAAAAA-TCA
1755 -GGTAAAAAATGG-AATTTTTTGGAA
1 TGGT-AAAAATGGTAA-TTTTTGGAA
1779 GTTCGGAGGT
Statistics
Matches: 146, Mismatches: 38, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
28 25 0.17
29 56 0.38
30 56 0.38
31 9 0.06
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
TGGTAAAAATGGTAATTTTTGGAAAAATCA
Found at i:1801 original size:117 final size:117
Alignment explanation
Indices: 1554--1862 Score: 337
Period size: 117 Copynumber: 2.6 Consensus size: 117
1544 TTCGGGTGGT
** *
1554 AAAAAT-GTAA-TTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGTTAAA
1 AAAAATGGTAATTTTTTGG-AAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGAGGG-TAAA
* *
1616 ATGGTGATTTTTGGAAAAATCATGGTAAAAAATGAAATTTTGGGAGGTATAAGGG
64 ATGGTAATTTTT-GAAAAATCATGGTAAAAAATGAAATTTTGGGAAGTATAAGGG
* *
1671 AAAAATGGT-ATTTTTTGGAAAATCGGGGTTAAAAATAGAATTTTTGAAAGTTCGAGGGTAAAAT
1 AAAAATGGTAATTTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAT
* * * *
1735 GGTAATTTTTGAAAAATTGA-GGTAAAAAATGGAATTTTTTGGAAGT-T-CGGAG
66 GGTAATTTTTGAAAAA-TCATGGTAAAAAAT-GAAATTTTGGGAAGTATAAGG-G
** * * * * *
1787 GTAAATGGTAATTTTTAGAAAAATTGGGGTCAAAAATGGAATTTTAGAAAGTTTGAGGGTAAAAA
1 AAAAATGGTAATTTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGT-AAAA
1852 T-GTAATTTTTG
65 TGGTAATTTTTG
1863 GAAAGTTTGG
Statistics
Matches: 164, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
115 2 0.01
116 25 0.15
117 120 0.73
118 17 0.10
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (117 bp):
AAAAATGGTAATTTTTTGGAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGAGGGTAAAAT
GGTAATTTTTGAAAAATCATGGTAAAAAATGAAATTTTGGGAAGTATAAGGG
Found at i:1833 original size:29 final size:29
Alignment explanation
Indices: 1671--1882 Score: 125
Period size: 30 Copynumber: 7.2 Consensus size: 29
1661 GGTATAAGGG
* * * *
1671 AAAAATGGTATTTTTTGGAAAATCGGGGTT
1 AAAAATGGAATTTTTAGAAAAATTGGGG-T
* *
1701 AAAAATAGAATTTTT-G-AAAGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAAAATT-G-GGGT
*
1730 -AAAATGGTAATTTTT-GAAAAATTGAGGT
1 AAAAATGG-AATTTTTAGAAAAATTGGGGT
* * *
1758 AAAAAATGGAATTTTTTG-GAAGTTCGGAGGT
1 -AAAAATGGAATTTTTAGAAAAATT-GG-GGT
1789 --AAATGGTAATTTTTAGAAAAATTGGGGT
1 AAAAATGG-AATTTTTAGAAAAATTGGGGT
**
1817 CAAAAATGGAA-TTTTAGAAAGTTTGAGGGT
1 -AAAAATGGAATTTTTAGAAAAATTG-GGGT
* * **
1847 AAAAATGTAATTTTTGGAAAGTTTGGGGT
1 AAAAATGGAATTTTTAGAAAAATTGGGGT
1876 CAAAAAT
1 -AAAAAT
1883 ATAATTTTGG
Statistics
Matches: 148, Mismatches: 17, Indels: 34
0.74 0.09 0.17
Matches are distributed among these distances:
28 22 0.15
29 58 0.39
30 59 0.40
31 9 0.06
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAAAATTGGGGT
Found at i:1873 original size:59 final size:60
Alignment explanation
Indices: 1539--1921 Score: 331
Period size: 59 Copynumber: 6.5 Consensus size: 60
1529 GTAATTTTGG
* ***
1539 GAAAGTTCGGGTGGTAAAAAT-GTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTT
1 GAAAGTTCGAG-GGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
* * * *** * * *
1599 GGAAGTTCG-GGGTTAAAATGGTGATTTTTGGAAAAATCATGGTAAAAAATGAAATTTTG
1 GAAAGTTCGAGGGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
* * * * * * *
1658 GGAGGTAT-AAGGG-AAAAATGGTATTTTTTGG-AAAATCGGGGTTAAAAATAGAATTTTT
1 GAAAGT-TCGAGGGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
* *
1716 GAAAGTTCGAGGGT-AAAATGGTAATTTTT-GAAAAATTGAGGTAAAAAATGGAATTTTTT
1 GAAAGTTCGAGGGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAA-TTTTT
* * *
1775 GGAAGTTCG-GAGGT--AAATGGTAATTTTTAGAAAAATTGGGGTCAAAAATGGAATTTTA
1 GAAAGTTCGAG-GGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
* ** ** *
1833 GAAAGTTTGAGGGTAAAAAT-GTAATTTTTGGAAAGTTTGGGGTCAAAAATATAATTTTG
1 GAAAGTTCGAGGGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
* * *
1892 GAGAAGTTTGAGGGTCAAAAT-ATAATTTTT
1 GA-AAGTTCGAGGGTAAAAATGGTAATTTTT
1922 TGATAGTTTA
Statistics
Matches: 270, Mismatches: 40, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
57 2 0.01
58 98 0.36
59 129 0.48
60 41 0.15
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (60 bp):
GAAAGTTCGAGGGTAAAAATGGTAATTTTTGGAAAAATTGGGGTCAAAAATGGAATTTTT
Found at i:1888 original size:30 final size:31
Alignment explanation
Indices: 1795--1930 Score: 140
Period size: 30 Copynumber: 4.5 Consensus size: 31
1785 AGGTAAATGG
** *
1795 TAATTTTTAGAAAAATTG-GGGTCAAAAATG
1 TAATTTTTAGAAAGTTTGAGGGTCAAAAATA
* *
1825 GAA-TTTTAGAAAGTTTGAGGGT-AAAAATG
1 TAATTTTTAGAAAGTTTGAGGGTCAAAAATA
*
1854 TAATTTTTGGAAAGTTTG-GGGTCAAAAATA
1 TAATTTTTAGAAAGTTTGAGGGTCAAAAATA
*
1884 TAA-TTTTGGAGAAGTTTGAGGGTC-AAAATA
1 TAATTTTTAGA-AAGTTTGAGGGTCAAAAATA
* *
1914 TAATTTTTTGATAGTTT
1 TAATTTTTAGAAAGTTT
1931 ATTGACCTCT
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
29 32 0.35
30 49 0.53
31 11 0.12
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.38
Consensus pattern (31 bp):
TAATTTTTAGAAAGTTTGAGGGTCAAAAATA
Found at i:1890 original size:29 final size:30
Alignment explanation
Indices: 1813--1920 Score: 141
Period size: 30 Copynumber: 3.6 Consensus size: 30
1803 AGAAAAATTG
** *
1813 GGGTCAAAAATGGAATTTTAGAAAGTTTGA
1 GGGTCAAAAATATAATTTTGGAAAGTTTGA
*
1843 GGGT-AAAAATGTAATTTTTGGAAAGTTTG-
1 GGGTCAAAAATATAA-TTTTGGAAAGTTTGA
1872 GGGTCAAAAATATAATTTTGGAGAAGTTTGA
1 GGGTCAAAAATATAATTTTGGA-AAGTTTGA
1903 GGGTC-AAAATATAATTTT
1 GGGTCAAAAATATAATTTT
1921 TTGATAGTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
29 20 0.28
30 46 0.65
31 5 0.07
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
GGGTCAAAAATATAATTTTGGAAAGTTTGA
Done.