Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011465.1 Kokia drynarioides strain JFW-HI SEQ_126449, 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: 4354
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Found at i:210 original size:28 final size:27
Alignment explanation
Indices: 160--220 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
150 TAATTTTCAA
* **
160 TTAATGATTGTTTCCTTTAATCCTCCTT
1 TTAATAATTGTTTCCTACAATCCT-CTT
*
188 TTAATAATTGTTTCCTACGATCCTCTT
1 TTAATAATTGTTTCCTACAATCCTCTT
215 TTAATA
1 TTAATA
221 GAATTCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 9 0.31
28 20 0.69
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.51
Consensus pattern (27 bp):
TTAATAATTGTTTCCTACAATCCTCTT
Found at i:1669 original size:18 final size:18
Alignment explanation
Indices: 1618--1710 Score: 100
Period size: 18 Copynumber: 5.3 Consensus size: 18
1608 CATAGTCCCC
1618 TTAAATTTATTTTAAAA-
1 TTAAATTTATTTTAAAAT
* * *
1635 TTGAATTTGTTTAAAAAT
1 TTAAATTTATTTTAAAAT
1653 TTAAATTTATTTTAAAAT
1 TTAAATTTATTTTAAAAT
* * *
1671 TAAAATTTAATTT-AAGT
1 TTAAATTTATTTTAAAAT
* *
1688 TTAAAATTATTTTCAAAT
1 TTAAATTTATTTTAAAAT
1706 TTAAA
1 TTAAA
1711 GTTAAAAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
17 27 0.44
18 34 0.56
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAAATTTATTTTAAAAT
Found at i:1675 original size:24 final size:24
Alignment explanation
Indices: 1648--1696 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1638 AATTTGTTTA
*
1648 AAAATTTAAATTT-ATTTTAAAATT
1 AAAATTT-AATTTAAGTTTAAAATT
1672 AAAATTTAATTTAAGTTTAAAATT
1 AAAATTTAATTTAAGTTTAAAATT
1696 A
1 A
1697 TTTTCAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AAAATTTAATTTAAGTTTAAAATT
Found at i:1691 original size:35 final size:35
Alignment explanation
Indices: 1618--1715 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
1608 CATAGTCCCC
* *
1618 TTAAATTTATTTTAAAATTGAATTT-GTTTAAAAAT
1 TTAAATTTATTTTAAAATTAAATTTAATTT-AAAAT
*
1653 TTAAATTTATTTTAAAATTAAAATTTAATTT-AAGT
1 TTAAATTTATTTTAAAATT-AAATTTAATTTAAAAT
* * *
1688 TTAAAATTATTTTCAAATTTAAAGTTAA
1 TTAAATTTATTTT-AAAATTAAATTTAA
1716 AAATAAATAC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 41 0.76
36 10 0.19
37 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (35 bp):
TTAAATTTATTTTAAAATTAAATTTAATTTAAAAT
Found at i:1757 original size:19 final size:19
Alignment explanation
Indices: 1715--1756 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1705 TTTAAAGTTA
*
1715 AAAATAAATACAAAGGTCC
1 AAAATAAATACAAAAGTCC
*
1734 AAAATAATTACAAAAAGTCC
1 AAAATAAATAC-AAAAGTCC
1754 AAA
1 AAA
1757 TTACATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAATAAATACAAAAGTCC
Found at i:2478 original size:15 final size:15
Alignment explanation
Indices: 2458--2503 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2448 AAATGTTTTG
2458 ATATTAATAATAATA
1 ATATTAATAATAATA
* *
2473 ATATTAATAATTATT
1 ATATTAATAATAATA
2488 A-ATTAATAATTAATA
1 ATATTAATAA-TAATA
2503 A
1 A
2504 AAAAAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 8 0.31
15 18 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:2490 original size:7 final size:7
Alignment explanation
Indices: 2465--2503 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2455 TTGATATTAA
2465 TAATAA-
1 TAATAAT
2471 TAAT-AT
1 TAATAAT
2477 TAATAAT
1 TAATAAT
*
2484 TATTAAT
1 TAATAAT
2491 TAATAAT
1 TAATAAT
2498 TAATAA
1 TAATAA
2504 AAAAAAGGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATAAT
Found at i:3859 original size:59 final size:59
Alignment explanation
Indices: 3617--4115 Score: 571
Period size: 59 Copynumber: 8.5 Consensus size: 59
3607 GATGTCCCTA
* * * *
3617 AACCTTCTAAAAATTACCATTTTA-CCCTCAAACTTTCAAAAATCTCATTTTTGACCCTG
1 AACCTTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCG
* * * *
3676 AACCTTCC-AAAATTACTATTTTA-CCCTCGAACTTCTAAAAATCCCATTTTTGACCCTG
1 AACCTTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCG
* *
3734 AACCTACCAAAAATTACCATTTTACCCC-AAACTTCCAAAAA-CCCATTTTTTAACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCA-TTTTTGACCCCG
* *
3792 AACCTTCCAAAAATTACCTTTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
3851 AACTTTCCACAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
** * * * *
3910 AACCTTTTAAAAATTATCATTTTACCCCCAAACTTACAAAAATCCCCTTTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAAT-CCCATTTTTGACCCCG
* *
3970 AACCTTCCAAAAATTACCTTTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
** * * * * * ***
4029 AAGTTTCCACAAATTACCATTTTTA-CCTTCGAACTTTCAAAAATCCCACTTTTGATTTCG
1 AACCTTCCAAAAATTACCA-TTTTACCCCT-AAACTTCCAAAAATCCCATTTTTGACCCCG
* * *
4089 AACATT-CAAAAACTACCATTTTGCCCC
1 AACCTTCCAAAAATTACCATTTTACCCC
4116 CGTGCATTCG
Statistics
Matches: 379, Mismatches: 52, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
57 4 0.01
58 103 0.27
59 179 0.47
60 93 0.25
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
AACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCCCG
Found at i:4037 original size:30 final size:29
Alignment explanation
Indices: 3617--4081 Score: 306
Period size: 29 Copynumber: 15.8 Consensus size: 29
3607 GATGTCCCTA
* *
3617 AACCTTCTAAAAATTACCA-TTTTACCCTC-
1 AACCTTCCAAAAA-TCCCATTTTTACCC-CG
* * * *
3646 AAACTTTCAAAAATCTCATTTTTGACCCTG
1 AACCTTCCAAAAATCCCATTTTT-ACCCCG
* * *
3676 AACCTTCCAAAATTACTA-TTTTACCCTCG
1 AACCTTCCAAAAATCCCATTTTTACCC-CG
* *
3705 AA-CTTCTAAAAATCCCATTTTTGACCCTG
1 AACCTTCCAAAAATCCCATTTTT-ACCCCG
* *
3734 AACCTACCAAAAATTACCA-TTTTACCCC-
1 AACCTTCCAAAAA-TCCCATTTTTACCCCG
*
3762 AAACTTCCAAAAA-CCCATTTTTTAACCCCG
1 AACCTTCCAAAAATCCCA-TTTTT-ACCCCG
* *
3792 AACCTTCCAAAAATTACC-TTTTTACCCCT
1 AACCTTCCAAAAA-TCCCATTTTTACCCCG
* *
3821 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AACCTTCCAAAAATCCCATTTTT-ACCCCG
* * * *
3851 AACTTTCCACAAATTACCA-TTTTACCCCC
1 AACCTTCCA-AAAATCCCATTTTTACCCCG
*
3880 AAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATCCCATTTTT-ACCCCG
** ** *
3910 AACCTTTTAAAAATTATCA-TTTTACCCCC
1 AACCTTCCAAAAA-TCCCATTTTTACCCCG
* * *
3939 AAACTTACAAAAATCCCCTTTTTTGACCCCG
1 AACCTTCCAAAAAT-CCCATTTTT-ACCCCG
* *
3970 AACCTTCCAAAAATTACC-TTTTTACCCCC
1 AACCTTCCAAAAA-TCCCATTTTTACCCCG
*
3999 AAACTTCCAAAAATCCCATTTTTGACCCCG
1 AACCTTCCAAAAATCCCATTTTT-ACCCCG
** * * *
4029 AAGTTTCCACAAATTACCATTTTTACCTTCG
1 AACCTTCCA-AAAATCCCATTTTTACC-CCG
* *
4060 AA-CTTTCAAAAATCCCACTTTT
1 AACCTTCCAAAAATCCCATTTTT
4082 GATTTCGAAC
Statistics
Matches: 337, Mismatches: 71, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
26 3 0.01
28 47 0.14
29 124 0.37
30 112 0.33
31 48 0.14
32 3 0.01
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (29 bp):
AACCTTCCAAAAATCCCATTTTTACCCCG
Found at i:4110 original size:29 final size:29
Alignment explanation
Indices: 4056--4111 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4046 CATTTTTACC
* *
4056 TTCGAACTTTCAAAAATCCCACTTTTGAT
1 TTCGAACATTCAAAAATACCACTTTTGAT
4085 TTCGAACATTCAAAAACTACCA-TTTTG
1 TTCGAACATTCAAAAA-TACCACTTTTG
4112 CCCCCGTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (29 bp):
TTCGAACATTCAAAAATACCACTTTTGAT
Done.