Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001278.1 Kokia drynarioides strain JFW-HI SEQ_112665, 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: 12502
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:314 original size:18 final size:18
Alignment explanation
Indices: 293--329 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
283 GTCATTCGAC
293 TCATCGATCTCATCATCA
1 TCATCGATCTCATCATCA
*
311 TCATCGGTCTCATCATCA
1 TCATCGATCTCATCATCA
329 T
1 T
330 TATCAACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.35
Consensus pattern (18 bp):
TCATCGATCTCATCATCA
Found at i:5123 original size:24 final size:24
Alignment explanation
Indices: 5096--5146 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5086 AGCTTGACTC
*
5096 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
* *
5120 AAACAATTAAACAGATTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
5144 AAA
1 AAA
5147 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:8708 original size:16 final size:16
Alignment explanation
Indices: 8684--8718 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
8674 TAAAAATGCT
8684 AATAATAAAAATA-AA
1 AATAATAAAAATATAA
8699 AATAAGTAAAAATATAA
1 AATAA-TAAAAATATAA
8716 AAT
1 AAT
8719 TTTATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 8 0.44
17 5 0.28
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAATAAAAATATAA
Found at i:8757 original size:20 final size:21
Alignment explanation
Indices: 8732--8786 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
8722 ATAAAGTCAT
8732 AAGAAAATTATAAAAAT-GTA
1 AAGAAAATTATAAAAATCGTA
*
8752 AAG-AAA-TATAAAATTCGTA
1 AAGAAAATTATAAAAATCGTA
8771 AA-AAAATTATAAAAAT
1 AAGAAAATTATAAAAAT
8787 TATGGTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 8 0.27
19 11 0.37
20 11 0.37
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
AAGAAAATTATAAAAATCGTA
Found at i:8975 original size:9 final size:9
Alignment explanation
Indices: 8963--9052 Score: 59
Period size: 9 Copynumber: 10.6 Consensus size: 9
8953 TTTTTGGTGT
8963 TTTTTATAA
1 TTTTTATAA
8972 TTTTTATAA
1 TTTTTATAA
*
8981 TTTTAATAAA
1 TTTTTAT-AA
*
8991 ATTTTA-ATA
1 TTTTTATA-A
9000 TTTTT-T--
1 TTTTTATAA
*
9006 TTATTA-AA
1 TTTTTATAA
*
9014 TTTTAATAA
1 TTTTTATAA
*
9023 TTTTAATAA
1 TTTTTATAA
*
9032 -TTTTA-AT
1 TTTTTATAA
9039 TTTTTATAA
1 TTTTTATAA
9048 TTTTT
1 TTTTT
9053 TTATTTTGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 14 0.23
9 37 0.60
10 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:9013 original size:23 final size:22
Alignment explanation
Indices: 8981--9026 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
8971 ATTTTTATAA
*
8981 TTTTAATAAAATTTTAATATTTT
1 TTTTAAT-AAATTTTAATAATTT
*
9004 TTTTATTAAATTTTAATAATTT
1 TTTTAATAAATTTTAATAATTT
9026 T
1 T
9027 AATAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAATAAATTTTAATAATTT
Found at i:9023 original size:42 final size:37
Alignment explanation
Indices: 8962--9043 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 37
8952 CTTTTTGGTG
*
8962 TTTTTTATAATTTTTATAATTTTAATAAAATTTTAATATT
1 TTTTTTATAATTTTAATAATTTTAAT--AATTTTAAT-TT
9002 TTTTTTATTAAATTTTAATAATTTTAATAATTTTAATTT
1 TTTTTTA-T-AATTTTAATAATTTTAATAATTTTAATTT
9041 TTT
1 TTT
9044 ATAATTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
39 5 0.13
40 16 0.41
41 1 0.03
42 17 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (37 bp):
TTTTTTATAATTTTAATAATTTTAATAATTTTAATTT
Found at i:9025 original size:31 final size:30
Alignment explanation
Indices: 8972--9035 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
8962 TTTTTTATAA
*
8972 TTTTTATAATTTTAATAAAATTTTAATATTT
1 TTTTTATAATTTTAAT-AAATTTTAATAATT
9003 TTTTTATTAAATTTTAAT-AATTTTAATAATT
1 TTTTTA-T-AATTTTAATAAATTTTAATAATT
9034 TT
1 TT
9036 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 20 0.67
32 1 0.03
33 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTATAATTTTAATAAATTTTAATAATT
Found at i:9059 original size:16 final size:18
Alignment explanation
Indices: 9012--9064 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 18
9002 TTTTTTATTA
*
9012 AATTTTAATAATTTTAAT
1 AATTTTAATTATTTTAAT
9030 AATTTTAATT-TTTT-AT
1 AATTTTAATTATTTTAAT
* *
9046 AATTTT-TTTATTTTGAT
1 AATTTTAATTATTTTAAT
9063 AA
1 AA
9065 CTTAAGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 2 0.06
16 12 0.39
17 8 0.26
18 9 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTTAATTATTTTAAT
Found at i:9184 original size:21 final size:20
Alignment explanation
Indices: 9159--9198 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9149 TTAAGTATCA
9159 AATTAAATGTAAAAAAAATTT
1 AATT-AATGTAAAAAAAATTT
* *
9180 AATTATTTTAAAAAAAATT
1 AATTAATGTAAAAAAAATT
9199 GAGGATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
AATTAATGTAAAAAAAATTT
Found at i:9448 original size:41 final size:40
Alignment explanation
Indices: 9388--9466 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
9378 AGGTTTCAAG
*
9388 AATTCAGAATTTTGCCCGTTCTCTTTTCACATCCCTCTTTT
1 AATTCAAAATTTTGCCCGTTCTCTTTTCACAT-CCTCTTTT
* * *
9429 AATTCAAAATTTTGGCCGTTGTCTTTTTACATCCTCTT
1 AATTCAAAATTTTGCCCGTTCTCTTTTCACATCCTCTT
9467 CTTCTCCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 6 0.18
41 28 0.82
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (40 bp):
AATTCAAAATTTTGCCCGTTCTCTTTTCACATCCTCTTTT
Found at i:11694 original size:29 final size:28
Alignment explanation
Indices: 11584--11742 Score: 94
Period size: 28 Copynumber: 5.5 Consensus size: 28
11574 CCTAGTGGTA
11584 AAAATGGTAATTTTG-G-ATTCTCGGGGGT
1 AAAATGGTAATTTTGAGAATT-T-GGGGGT
* * *
11612 GAAATGGTAATTTTGGGAAAATTTGGGGTT
1 AAAATGGTAATTTT--GAGAATTTGGGGGT
*
11642 AAAAATGG-AATTTTCAGACATTTGGGGGT
1 -AAAATGGTAATTTTGAGA-ATTTGGGGGT
* * * *
11671 AAAAGGGTAATTTTGAGAGTTTTGAGGT
1 AAAATGGTAATTTTGAGAATTTGGGGGT
* **
11699 CGAAAATGG-AGTTTTTG-GACATCCGGGGGT
1 --AAAATGGTA-ATTTTGAGA-ATTTGGGGGT
11729 AAAATGGTAATTTT
1 AAAATGGTAATTTT
11743 AGGAAGATAC
Statistics
Matches: 99, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
28 39 0.39
29 22 0.22
30 28 0.28
31 7 0.07
32 3 0.03
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (28 bp):
AAAATGGTAATTTTGAGAATTTGGGGGT
Found at i:11799 original size:29 final size:28
Alignment explanation
Indices: 11701--12010 Score: 186
Period size: 29 Copynumber: 10.6 Consensus size: 28
11691 TTTGAGGTCG
* * *
11701 AAAATGGAGTTTTTGGACATCCGGGGGT-
1 AAAATGGAATTTTTGGA-ATTCGAGGGTA
* * *
11729 AAAATGGTAATTTTAGGAAGATACGA-GGTCG
1 AAAATGG-AATTTTTGG-A-ATTCGAGGGT-A
11760 AAAATGGAATTTTTGGATATTCGAGGGT-
1 AAAATGGAATTTTTGGA-ATTCGAGGGTA
* * **
11788 AAAATGGTAATTTTAGGAAGTTTCGAAGGCG
1 AAAATGG-AATTTTTGGAA--TTCGAGGGTA
* * *
11819 AAAATGGAGTTTTCGGACA-TCTGGGGGT-
1 AAAATGGAATTTTTGGA-ATTC-GAGGGTA
* *
11847 AAAATGGTAATTTTAGGAAGTTTCG-GAGTAA
1 AAAATGG-AATTTTTGGAA--TTCGAGGGT-A
* *
11878 AAAATGGGATTTTTGGAAGTTCG-GGGTT
1 AAAATGGAATTTTTGGAA-TTCGAGGGTA
* *
11906 AAAATGGAATTTTGGGAAGTTTTGA-GGTCA
1 AAAATGGAATTTTTGGAA--TTCGAGGGT-A
* *
11936 AAAATGGGATTTTTGGAAGTTCGAGGCTA
1 AAAATGGAATTTTTGGAA-TTCGAGGGTA
11965 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAA-TTCGAGGGTA
11994 AAAATGGAATTTTTGGA
1 AAAATGGAATTTTTGGA
12011 CAGCTTAGGG
Statistics
Matches: 225, Mismatches: 36, Indels: 41
0.75 0.12 0.14
Matches are distributed among these distances:
28 41 0.18
29 101 0.45
30 59 0.26
31 24 0.11
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAATTCGAGGGTA
Found at i:11856 original size:118 final size:114
Alignment explanation
Indices: 11605--12010 Score: 378
Period size: 117 Copynumber: 3.5 Consensus size: 114
11595 TTTGGATTCT
* * * * * ** *
11605 CGGGGGTGAAATGGTAATTTTGGGAAAATTTGGGGTTAAAAATGGAATTTTCAGACATTTGGGGG
1 CGGGGGTAAAATGGTAATTTTAGGAAGA-TTCGGGTAAAAAATGGAATTTTTGGA-A-TTCGGGG
* * *
11670 TAAAAGGGTAATTTT-GAGAGTTTTGAGGTCGAAAATGGAGTTTTTGGACATC
63 TAAAATGGTAATTTTGGA-AGTTTCGAGGTCGAAAATGGAGTTTTCGGACATC
* **
11722 CGGGGGTAAAATGGTAATTTTAGGAAGATACGAGGTCGAAAATGGAATTTTTGGATATTCGAGGG
1 CGGGGGTAAAATGGTAATTTTAGGAAGATTCG-GGTAAAAAATGGAATTTTTGGA-ATTCG-GGG
11787 TAAAATGGTAATTTTAGGAAGTTTCGAAGG-CGAAAATGGAGTTTTCGGACATC
63 TAAAATGGTAATTTT-GGAAGTTTCG-AGGTCGAAAATGGAGTTTTCGGACATC
* * *
11840 TGGGGGTAAAATGGTAATTTTAGGAAGTTTCGGAGTAAAAAATGGGATTTTTGGAAGTTCGGGGT
1 CGGGGGTAAAATGGTAATTTTAGGAAGATTCGG-GTAAAAAATGGAATTTTTGGAA-TTCGGGG-
* * * *
11905 TAAAATGG-AATTTTGGGAAGTTTTGAGGTCAAAAATGG-GATTTTTGGA-AGTT
63 TAAAATGGTAATTTT-GGAAGTTTCGAGGTCGAAAATGGAG-TTTTCGGACA-TC
* * *
11957 CGAGGCTAAAAATGG-AATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGA
1 CGGGGGT-AAAATGGTAATTTTAGGAAGATTC--GGGTAAAAAATGGAATTTTTGGA
12011 CAGCTTAGGG
Statistics
Matches: 245, Mismatches: 30, Indels: 29
0.81 0.10 0.10
Matches are distributed among these distances:
116 30 0.12
117 114 0.47
118 96 0.39
119 5 0.02
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (114 bp):
CGGGGGTAAAATGGTAATTTTAGGAAGATTCGGGTAAAAAATGGAATTTTTGGAATTCGGGGTAA
AATGGTAATTTTGGAAGTTTCGAGGTCGAAAATGGAGTTTTCGGACATC
Found at i:11939 original size:58 final size:59
Alignment explanation
Indices: 11604--12012 Score: 360
Period size: 59 Copynumber: 7.0 Consensus size: 59
11594 TTTTGGATTC
* * * * * * **
11604 TCGGGGGTGAAATGGTAATTTTGGGAAAATTT-GGGGTTAAAAATGGAATTTTCAGACAT
1 TCGGGGGTAAAATGGTAATTTTAGG-AAGTTTCGAGGTCAAAAATGGGATTTTTGGACAT
* * * *
11663 TTGGGGGTAAAAGGGTAATTTT--GAGAGTTTTGAGGTCGAAAAT-GGAGTTTTTGGACAT
1 TCGGGGGTAAAATGGTAATTTTAGGA-AGTTTCGAGGTCAAAAATGGGA-TTTTTGGACAT
* * * * * *
11721 CCGGGGGTAAAATGGTAATTTTAGGAAGATACGAGGTCGAAAATGGAATTTTTGGATAT
1 TCGGGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGACAT
* * *
11780 TCGAGGGTAAAATGGTAATTTTAGGAAGTTTCGAAGG-CGAAAAT-GGAGTTTTCGGACA-
1 TCGGGGGTAAAATGGTAATTTTAGGAAGTTTCG-AGGTCAAAAATGGGA-TTTTTGGACAT
*
11838 TCTGGGGGTAAAATGGTAATTTTAGGAAGTTTCG-GAGTAAAAAATGGGATTTTTGGA-AGT
1 TC-GGGGGTAAAATGGTAATTTTAGGAAGTTTCGAG-GTCAAAAATGGGATTTTTGGACA-T
* * *
11898 TCGGGGTTAAAATGG-AATTTTGGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGA-AGT
1 TCGGGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGACA-T
* * * *
11956 TCGAGGCTAAAAATGG-AATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTGGACA
1 TCGGGGGT-AAAATGGTAATTTTAGGAAGTTTCGA-GGTCAAAAATGGGATTTTTGGACA
12013 GCTTAGGGAC
Statistics
Matches: 294, Mismatches: 38, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 8 0.03
58 108 0.37
59 165 0.56
60 12 0.04
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGACAT
Done.