Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007426.1 Kokia drynarioides strain JFW-HI SEQ_122047, 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: 39363
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:147 original size:28 final size:28
Alignment explanation
Indices: 114--209 Score: 69
Period size: 28 Copynumber: 3.5 Consensus size: 28
104 GTTCAAGTAC
114 CAAATTGGATAAAAAAAAATTTAGGTAA
1 CAAATTGGATAAAAAAAAATTTAGGTAA
* *
142 CAAA-T---T-AAGAAAAATTGTCAAGGTAC
1 CAAATTGGATAAAAAAAAATT-T--AGGTAA
* * *
168 CAAATTGGGTAAAAACAAATTTAGATAA
1 CAAATTGGATAAAAAAAAATTTAGGTAA
196 CAAATTAGGA-AAAA
1 CAAATT-GGATAAAA
210 TATCAAGTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
23 9 0.17
24 2 0.04
26 9 0.17
27 2 0.04
28 18 0.35
29 2 0.04
30 2 0.04
31 8 0.15
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.23
Consensus pattern (28 bp):
CAAATTGGATAAAAAAAAATTTAGGTAA
Found at i:170 original size:54 final size:53
Alignment explanation
Indices: 106--210 Score: 165
Period size: 54 Copynumber: 2.0 Consensus size: 53
96 AATACCAAGT
*
106 TCAAGTACCAAATTGGATAAAAAAAAATTTAGGTAACAAATTAAGAAAAATTG
1 TCAAGTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAATTG
* * *
159 TCAAGGTACCAAATTGGGTAAAAACAAATTTAGATAACAAATTAGGAAAAAT
1 TCAA-GTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAAT
211 ATCAAGTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 4 0.09
54 43 0.91
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.24
Consensus pattern (53 bp):
TCAAGTACCAAATTGGATAAAAAAAAATTTAGATAACAAATTAAGAAAAATTG
Found at i:2864 original size:9 final size:9
Alignment explanation
Indices: 2842--2876 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2832 GATGTCATCA
2842 TTATTTTATT
1 TTATTTT-TT
2852 TTATTTTTT
1 TTATTTTTT
2861 TTA-TTTTT
1 TTATTTTTT
2869 TTATTTTT
1 TTATTTTT
2877 GTTTCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 9 0.38
10 7 0.29
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (9 bp):
TTATTTTTT
Found at i:4169 original size:21 final size:20
Alignment explanation
Indices: 4118--4178 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
4108 TTGACCTTAG
*
4118 GGTTTAG-GGTTTT-AATTA
1 GGTTTAGAGTTTTTAAATTA
4136 GGTTTAGAGTTTTTAAATTA
1 GGTTTAGAGTTTTTAAATTA
4156 GAGTTTA-AGTTTTTAAAATTA
1 G-GTTTAGAGTTTTT-AAATTA
4177 GG
1 GG
4179 GTTCTAGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
18 7 0.18
19 5 0.13
20 14 0.37
21 12 0.32
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (20 bp):
GGTTTAGAGTTTTTAAATTA
Found at i:4191 original size:21 final size:21
Alignment explanation
Indices: 4131--4191 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
4121 TTAGGGTTTT
*
4131 AATTAG-GTTTAGAGT-TTTTA
1 AATTAGAGTTTA-AGTATTTAA
*
4151 AATTAGAGTTTAAGTTTTTAA
1 AATTAGAGTTTAAGTATTTAA
*
4172 AATTAGGGTTCT-AGTATTTA
1 AATTAGAGTT-TAAGTATTTA
4192 TTTTATATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.26
21 25 0.71
22 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.48
Consensus pattern (21 bp):
AATTAGAGTTTAAGTATTTAA
Found at i:6654 original size:12 final size:10
Alignment explanation
Indices: 6631--6704 Score: 55
Period size: 10 Copynumber: 7.4 Consensus size: 10
6621 ACCATTCACA
6631 TAAAAAATAT
1 TAAAAAATAT
6641 T-AAAAA-AT
1 TAAAAAATAT
**
6649 TAATTAA-AT
1 TAAAAAATAT
6658 TATAAAAATAT
1 TA-AAAAATAT
*
6669 TATAAAATAAT
1 TAAAAAAT-AT
* *
6680 TAAATATTAT
1 TAAAAAATAT
6690 TAAAAAATAAT
1 TAAAAAAT-AT
6701 TAAA
1 TAAA
6705 TTATAAAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
8 3 0.06
9 12 0.24
10 17 0.35
11 17 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:6666 original size:18 final size:18
Alignment explanation
Indices: 6639--6714 Score: 53
Period size: 18 Copynumber: 4.6 Consensus size: 18
6629 CATAAAAAAT
6639 ATTA-AAAAATTAATTAA
1 ATTATAAAAATTAATTAA
6656 ATTATAAAAA-T-ATT--
1 ATTATAAAAATTAATTAA
*
6670 A-TA-AAATAATTAA--AT
1 ATTATAAA-AATTAATTAA
*
6685 ATTATTAAAAAATAATTAA
1 ATTA-TAAAAATTAATTAA
6704 ATTATAAAAAT
1 ATTATAAAAAT
6715 AAATAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 21
0.65 0.04 0.30
Matches are distributed among these distances:
12 3 0.07
13 4 0.09
14 2 0.04
15 2 0.04
16 5 0.11
17 10 0.22
18 14 0.31
19 5 0.11
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTATAAAAATTAATTAA
Found at i:6676 original size:19 final size:19
Alignment explanation
Indices: 6634--6727 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 19
6624 ATTCACATAA
*
6634 AAAATATTAAAAA-ATTAAT
1 AAAATAATAAAAATATT-AT
* *
6653 TAAATTATAAAAATATTAT
1 AAAATAATAAAAATATTAT
*
6672 AAAATAAT-TAAATATTATT
1 AAAATAATAAAAATATTA-T
*
6691 AAAA-AATAATTAA-ATTAT
1 AAAATAATAA-AAATATTAT
6709 AAAAATAAATAAATAATAT
1 -AAAAT-AATAAA-AATAT
6728 AAACAAATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
18 12 0.21
19 31 0.54
20 5 0.09
21 7 0.12
22 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATAAAAATATTAT
Found at i:6696 original size:21 final size:21
Alignment explanation
Indices: 6666--6705 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6656 ATTATAAAAA
*
6666 TATTATAAAATAATTAAATAT
1 TATTAAAAAATAATTAAATAT
6687 TATTAAAAAATAATTAAAT
1 TATTAAAAAATAATTAAAT
6706 TATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAAAAATAATTAAATAT
Found at i:6696 original size:31 final size:29
Alignment explanation
Indices: 6630--6704 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 29
6620 AACCATTCAC
6630 ATAAAAAATATTAAAAAATTAATTAAATT
1 ATAAAAAATATTAAAAAATTAATTAAATT
*
6659 AT-AAAAATATTATAAAA-TAATTAAATATT
1 ATAAAAAATATTAAAAAATTAATT-AA-ATT
6688 ATTAAAAAATAATTAAA
1 A-TAAAAAAT-ATTAAA
6705 TTATAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 5 0.13
28 16 0.41
29 6 0.15
30 1 0.03
31 6 0.15
32 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAAAAAATATTAAAAAATTAATTAAATT
Found at i:6704 original size:11 final size:11
Alignment explanation
Indices: 6655--6704 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
6645 AAATTAATTA
6655 AATTATAAAAAT
1 AATTA-AAAAAT
*
6667 -ATTATAAAAT
1 AATTAAAAAAT
*
6677 AATT-AAATAT
1 AATTAAAAAAT
*
6687 TATTAAAAAAT
1 AATTAAAAAAT
6698 AATTAAA
1 AATTAAA
6705 TTATAAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
10 12 0.40
11 18 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTAAAAAAT
Found at i:6718 original size:21 final size:21
Alignment explanation
Indices: 6672--6735 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
6662 AAAATATTAT
*
6672 AAAATAATTAAATATTATTAA
1 AAAATAATTAAATATTATAAA
6693 AAAATAATT-AA-ATTAT--A
1 AAAATAATTAAATATTATAAA
* *
6710 AAAATAAATAAATAATATAAA
1 AAAATAATTAAATATTATAAA
*
6731 CAAAT
1 AAAAT
6736 TTAAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.25
18 2 0.06
19 9 0.25
20 2 0.06
21 14 0.39
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATTAAATATTATAAA
Found at i:8171 original size:30 final size:30
Alignment explanation
Indices: 8062--8312 Score: 212
Period size: 29 Copynumber: 8.5 Consensus size: 30
8052 TTTTAGGGAA
8062 TTTG-GGGTCAAAATGCAATTTTGGAAAAG
1 TTTGAGGGTCAAAATGCAATTTTGGAAAAG
* ** *
8091 TTT-AGGGTTAAAATGTGATTTAGG--AAG
1 TTTGAGGGTCAAAATGCAATTTTGGAAAAG
*
8118 TTTGAGGGTCAAAAATGCAATTTTGGATAAG
1 TTTGAGGGTC-AAAATGCAATTTTGGAAAAG
* * * * *
8149 TTTTAGGATCAAAATGTGATTTTTGG-GAAG
1 TTTGAGGGTCAAAATG-CAATTTTGGAAAAG
* * *
8179 TTTGAGGGTCGAAATACAATTTTGAAAAAG
1 TTTGAGGGTCAAAATGCAATTTTGGAAAAG
* * *
8209 TTTGAGGGTCAAAATGTGATTTTTGG-GAAG
1 TTTGAGGGTCAAAATG-CAATTTTGGAAAAG
* * *
8239 TTTGAGGGTCGAAATACAA-TTTGAAAAAG
1 TTTGAGGGTCAAAATGCAATTTTGGAAAAG
** * *
8268 TTTGAGGGTCAAAATATAATTTTTGAGAAG
1 TTTGAGGGTCAAAATGCAATTTTGGAAAAG
8298 TTTG-GGGTCAAAATG
1 TTTGAGGGTCAAAATG
8313 GGTTTTTTAA
Statistics
Matches: 173, Mismatches: 39, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
27 6 0.03
28 9 0.05
29 68 0.39
30 66 0.38
31 24 0.14
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (30 bp):
TTTGAGGGTCAAAATGCAATTTTGGAAAAG
Found at i:8221 original size:60 final size:60
Alignment explanation
Indices: 8052--8311 Score: 327
Period size: 60 Copynumber: 4.4 Consensus size: 60
8042 GAAAATGAAG
* * * *
8052 TTTTAGGGAA-TTTG-GGGTCAAAATGCAATTTTGGAAAAGTTT-AGGGTTAAAATGTGA
1 TTTTTGGGAAGTTTGAGGGTCAAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
* * * * * *
8109 --TTTAGGAAGTTTGAGGGTCAAAAATGCAATTTTGGATAAGTTTTAGGATCAAAATGTGA
1 TTTTTGGGAAGTTTGAGGGTC-AAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
*
8168 TTTTTGGGAAGTTTGAGGGTCGAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
1 TTTTTGGGAAGTTTGAGGGTCAAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
* * *
8228 TTTTTGGGAAGTTTGAGGGTCGAAATACAA-TTTGAAAAAGTTTGAGGGTCAAAATATAA
1 TTTTTGGGAAGTTTGAGGGTCAAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
*
8287 TTTTTGAGAAGTTTG-GGGTCAAAAT
1 TTTTTGGGAAGTTTGAGGGTCAAAAT
8312 GGGTTTTTTA
Statistics
Matches: 181, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
55 6 0.03
56 4 0.02
57 5 0.03
58 31 0.17
59 54 0.30
60 63 0.35
61 18 0.10
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (60 bp):
TTTTTGGGAAGTTTGAGGGTCAAAATACAATTTTGAAAAAGTTTGAGGGTCAAAATGTGA
Found at i:19875 original size:123 final size:123
Alignment explanation
Indices: 19668--19898 Score: 358
Period size: 123 Copynumber: 1.9 Consensus size: 123
19658 AGAATGATGC
*
19668 TGATAATATCACCAAGGCTAATGATCTTTATTTGACTTTCAATTAGCAAGCATGATCTCATAAAA
1 TGATAATATCACCAAGGCCAATGATCTTTATTTGACTTTCAATTAGCAAGCATGATCTCATAAAA
*
19733 ACTAAGGCACATTACAATATCACTGATAATGATG-AGCTGCAACGATATAGAAAAATGT
66 ACCAAGGCACATTACAATATCACTGATAATGA-GCAGCTGCAACGATATAGAAAAATGT
* * **
19791 TGATAATATCACCAAGGCCATTGATCTTTATTTGA-TGTTCAATTGGCTGGCATGATCTCATAAA
1 TGATAATATCACCAAGGCCAATGATCTTTATTTGACT-TTCAATTAGCAAGCATGATCTCATAAA
* *
19855 ACCCAAGGCACATTATAATATCACTGATAATGAGCAGCTGCAAC
65 AACCAAGGCACATTACAATATCACTGATAATGAGCAGCTGCAAC
19899 AATTTACCTT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
122 2 0.02
123 96 0.98
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (123 bp):
TGATAATATCACCAAGGCCAATGATCTTTATTTGACTTTCAATTAGCAAGCATGATCTCATAAAA
ACCAAGGCACATTACAATATCACTGATAATGAGCAGCTGCAACGATATAGAAAAATGT
Found at i:30966 original size:18 final size:19
Alignment explanation
Indices: 30945--30981 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30935 TTTTAACTTC
30945 TTTTTAT-ATATTTTAAAA
1 TTTTTATAATATTTTAAAA
*
30963 TTTTTATAATTTTTTAAAA
1 TTTTTATAATATTTTAAAA
30982 ATATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATAATATTTTAAAA
Found at i:31024 original size:20 final size:20
Alignment explanation
Indices: 31001--31038 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30991 TTGATTTTTT
31001 ATAAATA-TTTTAAATTTTAA
1 ATAAATACTTTT-AATTTTAA
*
31021 ATAATTACTTTTAATTTT
1 ATAAATACTTTTAATTTT
31039 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAATACTTTTAATTTTAA
Found at i:31046 original size:20 final size:19
Alignment explanation
Indices: 30955--31056 Score: 73
Period size: 19 Copynumber: 5.0 Consensus size: 19
30945 TTTTTATATA
30955 TTTTAAAATT-TTTATAATT
1 TTTTAAAATTATTT-TAATT
* *
30974 TTTTAAAAATATAAAATTTGATT
1 TTTT-AAAAT-T--ATTTTAATT
*
30997 TTTTATAAA-TATTTTAAAT
1 TTTTA-AAATTATTTTAATT
*
31016 TTTAAATAATTACTTTTAATT
1 TTTTAA-AATTA-TTTTAATT
31037 TTTTAAAATTATTTTGAATT
1 TTTTAAAATTATTTT-AATT
31057 ATATTGTATT
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
18 1 0.02
19 20 0.31
20 16 0.25
21 14 0.22
22 1 0.02
23 11 0.17
24 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAAATTATTTTAATT
Found at i:33283 original size:45 final size:45
Alignment explanation
Indices: 33234--33357 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 45
33224 GGTTTATAGT
* *
33234 TTAGGAGTTA-GGACTTCGAATAATGTAGTGTTTATGATTTAGGGC
1 TTAGGAGTTATGG-CTTCGAATAATGTAGGGTTTATAATTTAGGGC
* * * *
33279 TTAGG-GATTATTGTTTTGAATAATGTAGGGTTTATAATTTAGGGT
1 TTAGGAG-TTATGGCTTCGAATAATGTAGGGTTTATAATTTAGGGC
* * * *
33324 TTAGAAATTATGGCTTCGAATAATATAAGGTTTA
1 TTAGGAGTTATGGCTTCGAATAATGTAGGGTTTA
33358 ATGTTTAGGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
44 1 0.02
45 61 0.97
46 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (45 bp):
TTAGGAGTTATGGCTTCGAATAATGTAGGGTTTATAATTTAGGGC
Found at i:33365 original size:45 final size:44
Alignment explanation
Indices: 33247--33402 Score: 127
Period size: 45 Copynumber: 3.5 Consensus size: 44
33237 GGAGTTAGGA
* ** *
33247 CTTCGAATAATGT-AGTGTTTATGATTTAGGGCTTAGGGATTATTG
1 CTTCGAATAATGTAAG-GTTTATG-TTTAGGGTTTAGAAATTATGG
* * * *
33292 TTTTGAATAATGTAGGGTTTATAATTTAGGGTTTAGAAATTATGG
1 CTTCGAATAATGTAAGGTTTAT-GTTTAGGGTTTAGAAATTATGG
* * *
33337 CTTCGAATAATATAAGGTTTAATGTTTAGGGTTTATG-GATTATGA
1 CTTCGAATAATGTAAGGTTT-ATGTTTAGGGTTTA-GAAATTATGG
* * *
33382 TTTTGAATAATGCAAGGTTTA
1 CTTCGAATAATGTAAGGTTTA
33403 GGGTTTTGTT
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
44 1 0.01
45 83 0.94
46 4 0.05
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (44 bp):
CTTCGAATAATGTAAGGTTTATGTTTAGGGTTTAGAAATTATGG
Done.