Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002375.1 Kokia drynarioides strain JFW-HI SEQ_114455, 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: 4211
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Found at i:1690 original size:23 final size:23
Alignment explanation
Indices: 1647--1690 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1637 AAAGTTAAAT
* *
1647 TGTAATTTTTACAATAATAAAAG
1 TGTAATTTTTAAAAGAATAAAAG
*
1670 TGTAATTTTTAAAAGATTAAA
1 TGTAATTTTTAAAAGAATAAA
1691 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (23 bp):
TGTAATTTTTAAAAGAATAAAAG
Found at i:1708 original size:30 final size:30
Alignment explanation
Indices: 1674--1733 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1664 TAAAAGTGTA
*
1674 ATTTTT-AAAAGATTAAATTAAAATTTTATT
1 ATTTTTAAAAAG-TTAAAATAAAATTTTATT
*
1704 ATTTTTAAAAAGTTAAAATATAATTTTATT
1 ATTTTTAAAAAGTTAAAATAAAATTTTATT
1734 TTTACTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTTTTAAAAAGTTAAAATAAAATTTTATT
Found at i:1961 original size:3 final size:3
Alignment explanation
Indices: 1953--1977 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1943 TAGTTGAGAC
1953 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1978 GTGTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3075 original size:108 final size:108
Alignment explanation
Indices: 2778--3145 Score: 521
Period size: 108 Copynumber: 3.4 Consensus size: 108
2768 TTTAAACGAA
* * * *
2778 ATATTCGATTATTTAGGTTCAAGGTAAAATCACACCGAACATGTTAGGGCACGATTTTTAAAATC
1 ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTAACACGTTAGGACACGATTTTTAAAATC
* * *
2843 CCTTAAAATAACAGAATATTGAGCATTATTTGGTTTTGAATAGG
66 CCCTAAAATAACAGAATATTGAGCATT-TTTAGTTCTGAATAGG
* * *
2887 ATATTTGATTATTTAGGTTCAAGGCAAAATCACA-C---C-CTTTAGGACACGATTTTTTAAATC
1 ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTAACACGTTAGGACACGATTTTTAAAATC
* **
2947 CCCTAAAATAACAGAATATTGAGCATTTTCAGTTCCAAATAGG
66 CCCTAAAATAACAGAATATTGAGCATTTTTAGTTCTGAATAGG
* **
2990 ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTTACACGTTAGGACACGATTTTTCGAATC
1 ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTAACACGTTAGGACACGATTTTTAAAATC
3055 CCCTAAAATAACAGAATATTGAGCATTTTTAGTTCTGAATAGG
66 CCCTAAAATAACAGAATATTGAGCATTTTTAGTTCTGAATAGG
* * *
3098 ATATTCGATTATTTAGGTTCAAAGAAAAATCATACCTAACACGTTAGG
1 ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTAACACGTTAGG
3146 GTATAATTTC
Statistics
Matches: 231, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
103 44 0.19
104 47 0.20
105 1 0.00
107 1 0.00
108 106 0.46
109 32 0.14
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (108 bp):
ATATTCGATTATTTAGGTTCAAGGCAAAATCACACCTAACACGTTAGGACACGATTTTTAAAATC
CCCTAAAATAACAGAATATTGAGCATTTTTAGTTCTGAATAGG
Found at i:3712 original size:30 final size:30
Alignment explanation
Indices: 3619--4005 Score: 135
Period size: 30 Copynumber: 13.1 Consensus size: 30
3609 GGAAGGTTTG
* * * *
3619 GGGTC-AAATTTGAATTTTGGAAAGTTCAA
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* **
3648 -GGTCAAAATATGATTTTT-AGAAAG-ATCG
1 GGGTCAAAATATGATTTTTGA-AAAGTTTAA
3676 GAGGTCAAAATATGATTTTTGAAAAGTTTAA
1 G-GGTCAAAATATGATTTTTGAAAAGTTTAA
* * * * * * *
3707 GGGTC-AATTCTAAAATTTGGGAAAGTTT-G
1 GGGTCAAAATAT-GATTTTTGAAAAGTTTAA
* *
3736 GTGGTCATAATGTAT-TTTTTTG-AAAG-TTAA
1 G-GGTCA-AA-ATATGATTTTTGAAAAGTTTAA
* * * *
3766 GAGTCAAAATGTGATTTCT-AGAAAG-TTAGG
1 GGGTCAAAATATGATTTTTGA-AAAGTTTA-A
* *
3796 GGGTTAAAATATGATTTTTGAAAAGTTTAT
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* * * **
3826 GGGTTAAAATGTAATTTTTGAAAAG--TGC
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
* * * * *
3854 GGGAGCCAAATTTGAATTTTTGGAACGTTT-A
1 GGG-TCAAAATATG-ATTTTTGAAAAGTTTAA
* * * *
3885 GGAGTTAAAATGTAATTTTTTAAAAGTTT-A
1 GG-GTCAAAATATGATTTTTGAAAAGTTTAA
* **
3915 GGGTC-AAA-ATGAATTTTTGAAATGTTTGG
1 GGGTCAAAATATG-ATTTTTGAAAAGTTTAA
3944 GGGTCAAAATATGATTTTTGAAAAGTTTGAA
1 GGGTCAAAATATGATTTTTGAAAAGTTT-AA
* * ** *
3975 -AGTTAAAATATGATTTTAAAAAAGTTCAA
1 GGGTCAAAATATGATTTTTGAAAAGTTTAA
4004 GG
1 GG
4006 ACTTCTTGGA
Statistics
Matches: 260, Mismatches: 69, Indels: 57
0.67 0.18 0.15
Matches are distributed among these distances:
27 3 0.01
28 30 0.12
29 47 0.18
30 153 0.59
31 21 0.08
32 4 0.02
33 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATATGATTTTTGAAAAGTTTAA
Found at i:3851 original size:60 final size:59
Alignment explanation
Indices: 3752--3970 Score: 162
Period size: 60 Copynumber: 3.7 Consensus size: 59
3742 ATAATGTATT
* * * * * *
3752 TTTTTG-AAAGTTAAGAGTCAAAATGTGATTTCT-AGAAAGTTAGGGGGTTAAAATATG-A
1 TTTTTGAAAAGTTTAGGGTTAAAATGTAATTTTTGA-AAAGTTAGGGAG-TAAAATATGAA
** ** *
3810 TTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGGGAGCCAAATTTGAA
1 TTTTTGAAAAGTTTA-GGGTTAAAATGTAATTTTTGAAAAGTTAGGGAGTAAAATATGAA
* * * *
3870 TTTTTGGAACGTTTAGGAGTTAAAATGTAATTTTTTAAAAGTTTA-GG-GTCAAA-ATGAA
1 TTTTTGAAAAGTTTAGG-GTTAAAATGTAATTTTTGAAAAG-TTAGGGAGTAAAATATGAA
* * * * *
3928 TTTTTGAAATGTTTGGGGGTCAAAATATGATTTTTGAAAAGTT
1 TTTTTGAAAAGTTT-AGGGTTAAAATGTAATTTTTGAAAAGTT
3971 TGAAAGTTAA
Statistics
Matches: 129, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
57 2 0.02
58 41 0.32
59 22 0.17
60 62 0.48
61 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (59 bp):
TTTTTGAAAAGTTTAGGGTTAAAATGTAATTTTTGAAAAGTTAGGGAGTAAAATATGAA
Found at i:3874 original size:119 final size:119
Alignment explanation
Indices: 3623--3969 Score: 282
Period size: 119 Copynumber: 2.9 Consensus size: 119
3613 GGTTTGGGGT
* * * * *
3623 CAAATTTGAA-TTTTGGAAAGTTCAAG-GTCAAAATATGATTTTTAGAAAGATCGGAGGTCAAAA
1 CAAATTTGAATTTTTGGAAAGTT-AAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAA
* * * * * * ** *
3686 TATGATTTTTGAAAAGTTTAAGGG-TCAATTCTAAAATTTGGGAAAGTTTGGTGGT
65 TATGATTTTTGAAAAGTTTAAGGGTTAAAATAT-AATTTTTGAAAAGTGCGGTGGC
* * * *
3741 CATAATGT-ATTTTTTTGAAAGTTAAGAGTCAAAATGTGATTTCTAGAAAGTTAGGGGGTTAAAA
1 CA-AATTTGAATTTTTGGAAAGTTAAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAA
* *
3805 TATGATTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGG-GAGC
65 TATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTGCGGTG-GC
* * * * *
3860 CAAATTTGAATTTTTGGAACGTTTAGGAGTTAAAATGTAATTTTTTA-AAAGTTTA--GGG-TCA
1 CAAATTTGAATTTTTGGAAAG-TTAAGAGTCAAAATGTGA-TTTTTAGAAAG-TTAGGGGGTTAA
* ** * *
3921 AA-ATGAATTTTTGAAATGTTTGGGGGTCAAAATATGATTTTTGAAAAGT
63 AATATG-ATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGT
3970 TTGAAAGTTA
Statistics
Matches: 185, Mismatches: 34, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
117 3 0.02
118 52 0.28
119 98 0.53
120 24 0.13
121 8 0.04
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.37
Consensus pattern (119 bp):
CAAATTTGAATTTTTGGAAAGTTAAGAGTCAAAATGTGATTTTTAGAAAGTTAGGGGGTTAAAAT
ATGATTTTTGAAAAGTTTAAGGGTTAAAATATAATTTTTGAAAAGTGCGGTGGC
Found at i:3991 original size:88 final size:90
Alignment explanation
Indices: 3798--4000 Score: 225
Period size: 88 Copynumber: 2.3 Consensus size: 90
3788 AAGTTAGGGG
* * *
3798 GTTAAAATATGATTTTTGAAAAGTTTATGGGTTAAAATGTAATTTTTGAAAAGTGCGGGAGCCAA
1 GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAGCAAA
* * * *
3863 ATTTGAATTTTTGGAACGTTTAGGA
66 ATATGAATTTTTGAAAAGTTTAGAA
* * * * ** *
3888 GTTAAAATGTAATTTTTTAAAAGTTTA-GGGTCAAAATG-AATTTTTGAAATGTTTGGGGGTCAA
1 GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAG-CAA
3951 AATATG-ATTTTTGAAAAGTTT-GAAA
65 AATATGAATTTTTGAAAAGTTTAG-AA
*
3976 GTTAAAATATGATTTTAAAAAAGTT
1 GTTAAAATATGATTTTTAAAAAGTT
4001 CAAGGACTTC
Statistics
Matches: 94, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
87 1 0.01
88 52 0.55
89 17 0.18
90 24 0.26
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (90 bp):
GTTAAAATATGATTTTTAAAAAGTTTATGGGTCAAAATGTAATTTTTGAAAAGTGCGGGAGCAAA
ATATGAATTTTTGAAAAGTTTAGAA
Done.