Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014045.1 Kokia drynarioides strain JFW-HI SEQ_129076, 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: 2808
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Found at i:1456 original size:28 final size:28
Alignment explanation
Indices: 1425--1549 Score: 78
Period size: 28 Copynumber: 4.4 Consensus size: 28
1415 AAAATAGGAT
1425 TTTTAGCAA-CTCGAGGG-TAAAATGGTAA
1 TTTT-GCAAGCTC-AGGGATAAAATGGTAA
* *
1453 TTTTGGAAGTTCAGGGATAAAATGGTAA
1 TTTTGCAAGCTCAGGGATAAAATGGTAA
* * * *
1481 TTTTTGGAAGATTCGGGGTTAAAAATGGT-A
1 -TTTTGCAAG-CTCAGGGAT-AAAATGGTAA
* * *
1511 TTTTGGAAGTCTGAGGG-TAAGATGGTAA
1 TTTTGCAAG-CTCAGGGATAAAATGGTAA
*
1539 TTTTGGAAGCT
1 TTTTGCAAGCT
1550 TCGGGGTAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
27 16 0.20
28 28 0.34
29 22 0.27
30 8 0.10
31 8 0.10
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.34
Consensus pattern (28 bp):
TTTTGCAAGCTCAGGGATAAAATGGTAA
Found at i:1484 original size:86 final size:86
Alignment explanation
Indices: 1385--1560 Score: 200
Period size: 86 Copynumber: 2.0 Consensus size: 86
1375 ACGGAGTGGC
1385 AAAATGGTAA-TTTTAGAATG-TTCGGAATCAAAAATAGG-ATTTTTAGCAACTC-GAGGGTAAA
1 AAAATGGTAATTTTTAGAA-GATTCGGAATCAAAAAT-GGTA-TTTT-GCAACTCTGAGGGTAAA
1446 ATGGTAATTTTGGAAG-TTCAGGGAT
62 ATGGTAATTTTGGAAGCTTC-GGGAT
* ** * * * *
1471 AAAATGGTAATTTTTGGAAGATTCGGGGTTAAAAATGGTATTTTGGAAGTCTGAGGGTAAGATGG
1 AAAATGGTAATTTTTAGAAGATTCGGAATCAAAAATGGTATTTTGCAACTCTGAGGGTAAAATGG
*
1536 TAATTTTGGAAGCTTCGGGGT
66 TAATTTTGGAAGCTTCGGGAT
1557 AAAA
1 AAAA
1561 AAAATGAGAT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
85 5 0.06
86 49 0.64
87 23 0.30
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (86 bp):
AAAATGGTAATTTTTAGAAGATTCGGAATCAAAAATGGTATTTTGCAACTCTGAGGGTAAAATGG
TAATTTTGGAAGCTTCGGGAT
Found at i:1556 original size:28 final size:28
Alignment explanation
Indices: 1439--1823 Score: 220
Period size: 28 Copynumber: 13.1 Consensus size: 28
1429 AGCAACTCGA
1439 GGGTAAAATGGTAATTTTGGAAGTTCAG
1 GGGTAAAATGGTAATTTTGGAAGTTCAG
*
1467 GGATAAAATGGTAATTTTTGGAAGATTC-G
1 GGGTAAAATGGTAA-TTTTGGAAG-TTCAG
*
1496 GGGTTAAAAATGGT-ATTTTGGAAG-TCTG
1 GGG-T-AAAATGGTAATTTTGGAAGTTCAG
*
1524 AGGGTAAGATGGTAATTTTGGAAGCTTC-G
1 -GGGTAAAATGGTAATTTTGGAAG-TTCAG
* *
1553 GGGTAAAAAAAATGAG-ATTTTTGGGAA-TTTAG
1 GGGT----AAAATG-GTAATTTT-GGAAGTTCAG
*
1585 GGGTAAAACGGTAATTTTTGGGAA-TTCAG
1 GGGTAAAATGGTAA-TTTT-GGAAGTTCAG
**
1614 GGGTAAAATGGTAATTTTTGGAAGCTT-TT
1 GGGTAAAATGGTAA-TTTTGGAAG-TTCAG
* * *
1643 GGGTCAAAATTTGGGATTTTTGTGAA-TTTAG
1 GGGT-AAAA--TGGTAATTTTG-GAAGTTCAG
1674 GGGTAAAATGGTAATTTTGGAATGTTC-G
1 GGGTAAAATGGTAATTTTGGAA-GTTCAG
* * *
1702 GGGTCAAAAATGGGATTTTTAGGAA-TTTAG
1 GGGT--AAAATGGTAATTTT-GGAAGTTCAG
*
1732 GGGTAAAACGGTAATTTTGGAAGGTTTTC-G
1 GGGTAAAATGGTAATTTTGGAA-G--TTCAG
* * *
1762 GGGTCAAAAATGGGATTTTTGGGAA-TTCGG
1 GGGT--AAAATGGTAATTTT-GGAAGTTCAG
*
1792 GGGTAAAACGGTAATTTTTGGAAGGTTCAG
1 GGGTAAAATGGTAA-TTTTGGAA-GTTCAG
1822 GG
1 GG
1824 ACCTCCGGGG
Statistics
Matches: 282, Mismatches: 33, Indels: 82
0.71 0.08 0.21
Matches are distributed among these distances:
27 17 0.06
28 75 0.27
29 71 0.25
30 52 0.18
31 25 0.09
32 33 0.12
33 9 0.03
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAGTTCAG
Found at i:1618 original size:89 final size:89
Alignment explanation
Indices: 1525--1691 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
1515 GGAAGTCTGA
*
1525 GGGTAAGATGGTAA-TTTTGGAAGCTTCGGGGTAAAAAAAATGAGATTTTTGGGAATTTAGGGGT
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGT-AAAAAAATGAGATTTTTGGGAATTTAGGGGT
1589 AAAACGGTAATTTTTGGGAATTCAG
65 AAAACGGTAATTTTTGGGAATTCAG
** * ** * *
1614 GGGTAAAATGGTAATTTTTGGAAGCTTTTGGGTCAAAATTTGGGATTTTTGTGAATTTAGGGGTA
1 GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTAAAAAAATGAGATTTTTGGGAATTTAGGGGTA
*
1679 AAATGGTAATTTT
66 AAACGGTAATTTT
1692 GGAATGTTCG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
89 52 0.76
90 16 0.24
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.36
Consensus pattern (89 bp):
GGGTAAAATGGTAATTTTTGGAAGCTTCGGGGTAAAAAAATGAGATTTTTGGGAATTTAGGGGTA
AAACGGTAATTTTTGGGAATTCAG
Found at i:1670 original size:60 final size:57
Alignment explanation
Indices: 1598--1815 Score: 274
Period size: 60 Copynumber: 3.7 Consensus size: 57
1588 TAAAACGGTA
* *
1598 ATTTTTGGGAATTCAGGGGTAAAATGGTAATTTTTGGAAGCTTTTGGGTCAAAATTTGGG
1 ATTTTTGGGAATTCAGGGGTAAAACGGTAA-TTTTGGAAG-TTTTGGGTCAAAA-ATGGG
* * * **
1658 ATTTTTGTGAATTTAGGGGTAAAATGGTAATTTTGGAATGTTCGGGGTCAAAAATGGG
1 ATTTTTGGGAATTCAGGGGTAAAACGGTAATTTTGGAA-GTTTTGGGTCAAAAATGGG
* *
1716 ATTTTTAGGAATTTAGGGGTAAAACGGTAATTTTGGAAGGTTTTCGGGGTCAAAAATGGG
1 ATTTTTGGGAATTCAGGGGTAAAACGGTAATTTTGGAA-GTTTT--GGGTCAAAAATGGG
*
1776 ATTTTTGGGAATTCGGGGGTAAAACGGTAATTTTTGGAAG
1 ATTTTTGGGAATTCAGGGGTAAAACGGTAA-TTTTGGAAG
1816 GTTCAGGGAC
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
58 42 0.30
59 19 0.14
60 71 0.51
61 8 0.06
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (57 bp):
ATTTTTGGGAATTCAGGGGTAAAACGGTAATTTTGGAAGTTTTGGGTCAAAAATGGG
Found at i:1691 original size:118 final size:118
Alignment explanation
Indices: 1569--1812 Score: 300
Period size: 118 Copynumber: 2.1 Consensus size: 118
1559 AAAAAATGAG
* *
1569 ATTTTTGGGAAT-TTAGGGGT-AAAACGGTAATTTTTGGGAATTCAGGGGTAAAATGGTAATTTT
1 ATTTTTGGGAATGTTAGGGGTAAAAACGG-AATTTTTAGGAATTCAGGGGTAAAACGGTAA-TTT
* * * *
1632 TGGAAGCTTTT-GGGTCAAAATTTGGGATTTTTGTGAATTTAGGGGTAAAATGGTA
64 TGGAAGCTTTTCGGGTCAAAA-ATGGGATTTTTGGGAATTCAGGGGTAAAACGGTA
* * * *
1687 A-TTTT-GGAATGTTCGGGGTCAAAAATGGGATTTTTAGGAATTTAGGGGTAAAACGGTAATTTT
1 ATTTTTGGGAATGTTAGGGGT-AAAAACGGAATTTTTAGGAATTCAGGGGTAAAACGGTAATTTT
* *
1750 GGAAGGTTTTCGGGGTCAAAAATGGGATTTTTGGGAATTCGGGGGTAAAACGGTA
65 GGAAGCTTTTC-GGGTCAAAAATGGGATTTTTGGGAATTCAGGGGTAAAACGGTA
1805 ATTTTTGG
1 ATTTTTGG
1813 AAGGTTCAGG
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
116 5 0.05
117 24 0.22
118 58 0.54
119 19 0.18
120 1 0.01
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (118 bp):
ATTTTTGGGAATGTTAGGGGTAAAAACGGAATTTTTAGGAATTCAGGGGTAAAACGGTAATTTTG
GAAGCTTTTCGGGTCAAAAATGGGATTTTTGGGAATTCAGGGGTAAAACGGTA
Done.