Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009901.1 Kokia drynarioides strain JFW-HI SEQ_124639, 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: 30785
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:153 original size:25 final size:23
Alignment explanation
Indices: 109--158 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
99 ACACTAGCGC
109 GCTCTCTAATTAGCACTGTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
** *
132 GCTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
155 GCTC
1 GCTC
159 AGCACTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTAATTAGCACTGTGTGT
Found at i:176 original size:39 final size:39
Alignment explanation
Indices: 120--197 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
110 CTCTCTAATT
*
120 AGCACTGTGTGTGCTCTCTGTTTAGCACTTTGTGTGCTC
1 AGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
*
159 AGCACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 AGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
198 TCTGTTGCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (39 bp):
AGCACTGTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
Found at i:189 original size:23 final size:23
Alignment explanation
Indices: 159--203 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
149 TTGTGTGCTC
159 AGCACTTTGTGTACTCTCTGTTT
1 AGCACTTTGTGTACTCTCTGTTT
*
182 AGCACTTTGTGTGCTCTCTGTT
1 AGCACTTTGTGTACTCTCTGTT
204 GCCCAGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (23 bp):
AGCACTTTGTGTACTCTCTGTTT
Found at i:5341 original size:26 final size:26
Alignment explanation
Indices: 5295--5344 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
5285 TGTTTATGTG
5295 AAATTGAAGAGAAAAGGAAAGAGACC
1 AAATTGAAGAGAAAAGGAAAGAGACC
*
5321 AAATTGAAGA-CAAAGGAAAAGAGA
1 AAATTGAAGAGAAAAGG-AAAGAGA
5345 AGAGCAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.60, C:0.06, G:0.26, T:0.08
Consensus pattern (26 bp):
AAATTGAAGAGAAAAGGAAAGAGACC
Found at i:7211 original size:30 final size:30
Alignment explanation
Indices: 7177--7237 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
7167 ATGTGTCTCT
*
7177 AATGAATGTGTTACTAATATTGTTTTAAAA
1 AATGAATGGGTTACTAATATTGTTTTAAAA
7207 AATGAATGGGTTACTAATATTGTTTTAAAA
1 AATGAATGGGTTACTAATATTGTTTTAAAA
7237 A
1 A
7238 TTTACATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (30 bp):
AATGAATGGGTTACTAATATTGTTTTAAAA
Found at i:9996 original size:26 final size:25
Alignment explanation
Indices: 9958--10013 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
9948 TAAAAAAAAA
*
9958 TTAAAATACTCAAGATTAATCACAATAT
1 TTAAAATA-TCAAAATT-ATC-CAATAT
*
9986 TTAAAAT-TCAAAATTATCCAATCT
1 TTAAAATATCAAAATTATCCAATAT
10010 TTAA
1 TTAA
10014 CGGGTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.35
25 3 0.12
26 7 0.27
28 7 0.27
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (25 bp):
TTAAAATATCAAAATTATCCAATAT
Found at i:14984 original size:57 final size:57
Alignment explanation
Indices: 14915--15055 Score: 255
Period size: 57 Copynumber: 2.5 Consensus size: 57
14905 CAACAACTAA
*
14915 AGCTGAAGGGGGAAGCAGATTCAAACAACTTGTCATTCCAGAAGGCTCCGCAGTTAG
1 AGCTGAAGGGGGAAGCAGTTTCAAACAACTTGTCATTCCAGAAGGCTCCGCAGTTAG
14972 AGCTGAAGGGGGAAGCAGTTTCAAACAACTTGTCATTCCAGAAGGCTCCGCAGTTAG
1 AGCTGAAGGGGGAAGCAGTTTCAAACAACTTGTCATTCCAGAAGGCTCCGCAGTTAG
* *
15029 AGCTGAAGGTGGAAGTAGTTTCAAACA
1 AGCTGAAGGGGGAAGCAGTTTCAAACA
15056 TTCAGGAACA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 81 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (57 bp):
AGCTGAAGGGGGAAGCAGTTTCAAACAACTTGTCATTCCAGAAGGCTCCGCAGTTAG
Found at i:15546 original size:18 final size:18
Alignment explanation
Indices: 15515--15550 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15505 TTCATTCACA
*
15515 CCAGAAAGACATGAAAAT
1 CCAGAAAGAAATGAAAAT
*
15533 CCAGATAGAAATGAAAAT
1 CCAGAAAGAAATGAAAAT
15551 TATACAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14
Consensus pattern (18 bp):
CCAGAAAGAAATGAAAAT
Found at i:19868 original size:19 final size:18
Alignment explanation
Indices: 19832--19869 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
19822 ATATGAAATA
19832 TATAAAATTTGAAATTTT
1 TATAAAATTTGAAATTTT
19850 TATAAATATCTTG-AATTTT
1 TATAAA-AT-TTGAAATTTT
19869 T
1 T
19870 GAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (18 bp):
TATAAAATTTGAAATTTT
Found at i:19875 original size:19 final size:20
Alignment explanation
Indices: 19844--19889 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
19834 TAAAATTTGA
19844 AATTTTTATAAA-TATCTTG
1 AATTTTTATAAATTATCTTG
* *
19863 AATTTTTGA-AAATTATTTTT
1 AATTTTT-ATAAATTATCTTG
19883 AATTTTT
1 AATTTTT
19890 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
AATTTTTATAAATTATCTTG
Found at i:21469 original size:2 final size:2
Alignment explanation
Indices: 21462--21492 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21452 TTTCGCTTCT
21462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21493 TAACATTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28841 original size:60 final size:57
Alignment explanation
Indices: 28775--29060 Score: 249
Period size: 60 Copynumber: 4.9 Consensus size: 57
28765 ACTCGAGGGC
*
28775 AAAATGGTAATTTTGGGAAAATTAGGGGTCAAAAATGGAATTTTTAGACA-TCTGGGGGGT
1 AAAATGGTAATTTTGGAAAAATTA-GGGTCAAAAATGGAATTTTTAGA-AGT-T-GGGGGT
* * * * *
28835 AAAATGGTACTTTTTGAAATAATCAGGGTCAAAAAT-AAATTTTTAGAAGTTCGGGGT
1 AAAATGGTAATTTTGGAAA-AATTAGGGTCAAAAATGGAATTTTTAGAAGTTGGGGGT
*
28892 AAAATGGTAATTTTTGGAAAAA-TCGTGGTCAAAAATGGAATTTTT-GAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTTAG-AAGTT-GGGGGT
* * * * * **
28951 AAAATGGTAATTTTTGAAAAAAATTATGGTCAAAAATGGAATTTTGAAAAATTCAAGGGT
1 AAAATGGTAA-TTTTG-GAAAAATTAGGGTCAAAAATGGAATTTTTAGAAGTT-GGGGGT
* * ** * *
29011 AATATGGTAATTTTGGAACAATCGGGGT-TAAAATGGAATTTTTGGAAGTT
1 AAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTAGAAGTT
29061 TAGGGGTTAA
Statistics
Matches: 185, Mismatches: 31, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
56 1 0.01
57 44 0.24
58 30 0.16
59 37 0.20
60 68 0.37
61 5 0.03
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTAGAAGTTGGGGGT
Found at i:28934 original size:117 final size:119
Alignment explanation
Indices: 28770--29060 Score: 342
Period size: 117 Copynumber: 2.5 Consensus size: 119
28760 TGGTAACTCG
* * * * * *
28770 AGGGCAAAATGGTAATTTTGGGAAAATTAGGGGTCAAAAATGGAATTTTTAGACA-TCTGGGGGG
1 AGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTT-GAAAGT-TCGGGGG
* * * * *
28834 TAAAATGGTACTTTTTG-AAATAATCAGGGTCAAAAAT-AAATTTTTAGAAGTTC-
64 TAAAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTTGAAAAATTCA
* *
28887 GGGGTAAAATGGTAATTTTTGGAAAAATCGTGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTA
1 AGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTA
* * *
28952 AAATGGTAATTTTTGAAAAAAATTATGGTCAAAAATGGAATTTTGAAAAATTCA
66 AAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTTGAAAAATTCA
* * * *
29006 AGGGTAATATGGTAA-TTTTGGAACAATCGGGGT-TAAAATGGAATTTTTGGAAGTT
1 AGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTT
29061 TAGGGGTTAA
Statistics
Matches: 148, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
116 25 0.17
117 82 0.55
118 28 0.19
119 13 0.09
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (119 bp):
AGGGTAAAATGGTAATTTTTGGAAAAATCGGGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGTA
AAATGGTAATTTTTGAAAAAAATCAGGGTCAAAAATGAAATTTTGAAAAATTCA
Found at i:28966 original size:29 final size:28
Alignment explanation
Indices: 28743--28969 Score: 110
Period size: 29 Copynumber: 7.8 Consensus size: 28
28733 GGATACTCGA
* * * *
28743 GGGTAAAATGGTAATTATGGTAA-CTCG
1 GGGTAAAATGGTAATTTTTGAAAGTTCG
* * * *
28770 AGGGCAAAATGGTAATTTTGGGAAAATTAG
1 -GGGTAAAATGGTAATTTT-TGAAAGTTCG
* *
28800 GGGTCAAAAATGG-AATTTTTAGACA-TCTGGG
1 GGGT--AAAATGGTAATTTTT-GAAAGT-T-CG
* *
28831 GGGTAAAATGGTACTTTTTGAAA-TAATCA
1 GGGTAAAATGGTAATTTTTGAAAGT--TCG
*
28860 GGGTCAAAAAT--AAATTTTT-AGAAGTTCG
1 GGGT--AAAATGGTAATTTTTGA-AAGTTCG
**
28888 GGGTAAAATGGTAATTTTTGGAAAAATCG
1 GGGTAAAATGGTAATTTTT-GAAAGTTCG
*
28917 TGGTCAAAAATGG-AATTTTTGAAAGTTCGG
1 GGGT--AAAATGGTAATTTTTGAAAGTTC-G
28947 GGGTAAAATGGTAATTTTTGAAA
1 GGGTAAAATGGTAATTTTTGAAA
28970 AAAATTATGG
Statistics
Matches: 154, Mismatches: 24, Indels: 41
0.70 0.11 0.19
Matches are distributed among these distances:
26 5 0.03
28 37 0.24
29 56 0.36
30 32 0.21
31 24 0.16
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.31
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGAAAGTTCG
Found at i:29046 original size:29 final size:29
Alignment explanation
Indices: 28775--29057 Score: 116
Period size: 29 Copynumber: 9.6 Consensus size: 29
28765 ACTCGAGGGC
* * * *
28775 AAAATGGTAATTTTGGGAAAATTAGGGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGGGGT-T
* * ** * *
28806 AAAATGGAATTTTTAGACATCTGGGGGGT
1 AAAATGGAATTTTTGGAAAAATCGGGGTT
* * *
28835 AAAATGGTACTTTTT-GAAATAATCAGGGTCA
1 AAAATGG-AATTTTTGGAAA-AATCGGGGT-T
* * **
28866 AAAAT-AAATTTTTAG-AAGTTCGGGG-T
1 AAAATGGAATTTTTGGAAAAATCGGGGTT
* *
28892 AAAATGGTAATTTTTGGAAAAATCGTGGTCA
1 AAAATGG-AATTTTTGGAAAAATCGGGGT-T
** *
28923 AAAATGGAATTTTT-GAAAGTTCGGGGGT
1 AAAATGGAATTTTTGGAAAAATCGGGGTT
* *** *
28951 AAAATGGTAATTTTTGAAAAAAATTATGGTCA
1 AAAATGG-AATTTTTG-GAAAAATCGGGGT-T
*
28983 AAAATGGAA-TTTT-GAAAAATTCAAGGG-T
1 AAAATGGAATTTTTGGAAAAA-TC-GGGGTT
* *
29011 AATATGGTAA-TTTTGGAACAATCGGGGTT
1 AAAATGG-AATTTTTGGAAAAATCGGGGTT
29040 AAAATGGAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
29058 GTTTAGGGGT
Statistics
Matches: 184, Mismatches: 49, Indels: 40
0.67 0.18 0.15
Matches are distributed among these distances:
26 5 0.03
28 36 0.20
29 65 0.35
30 44 0.24
31 27 0.15
32 7 0.04
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAAATCGGGGTT
Found at i:29066 original size:29 final size:30
Alignment explanation
Indices: 29034--29095 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
29024 TGGAACAATC
29034 GGGGTTAAAAT-GGAATTTTTGGA-AGTTTA
1 GGGGTTAAAATAGG-ATTTTTGGACAGTTTA
*
29063 GGGGTTAAAATATGATTTTTGGACAGTTTA
1 GGGGTTAAAATAGGATTTTTGGACAGTTTA
29093 GGG
1 GGG
29096 ACCTATAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.29, C:0.02, G:0.32, T:0.37
Consensus pattern (30 bp):
GGGGTTAAAATAGGATTTTTGGACAGTTTA
Found at i:30024 original size:3 final size:3
Alignment explanation
Indices: 30016--30054 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
30006 TCAGTTTCCT
30016 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30055 ATGTCGTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.