Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004371.1 Kokia drynarioides strain JFW-HI SEQ_117728, 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: 17506
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:5270 original size:36 final size:36
Alignment explanation
Indices: 5220--5297 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
5210 GCTGTAGGAG
*
5220 CCACACGGGATAAACCATTCCACATGGTCGTGTGAT
1 CCACACAGGATAAACCATTCCACATGGTCGTGTGAT
*
5256 CCACACAGGCTAAACCATTCCACATGGTCGTGTGAT
1 CCACACAGGATAAACCATTCCACATGGTCGTGTGAT
5292 CCACAC
1 CCACAC
5298 GAGCGTGTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (36 bp):
CCACACAGGATAAACCATTCCACATGGTCGTGTGAT
Found at i:7677 original size:2 final size:2
Alignment explanation
Indices: 7672--7723 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
7662 AAAAATCAGA
* *
7672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
7713 AT GT AT AT AT A
1 AT AT AT AT AT A
7724 ATTTATCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8530 original size:30 final size:29
Alignment explanation
Indices: 8494--8804 Score: 294
Period size: 29 Copynumber: 10.6 Consensus size: 29
8484 AAAAATTAAA
* *
8494 TTTTGGAAAGTTCAGGGATAAAAATGAAAT
1 TTTTGGAAAGTTTAGGG-TAAAAATGGAAT
* *
8524 TTTTGG-AAGTTAAGGGACAAAAATGGAA-
1 TTTTGGAAAGTTTAGGG-TAAAAATGGAAT
* *
8552 TTTTGGAAAGTTTAAGGGTAAAATTGTAAT
1 TTTTGGAAAGTTT-AGGGTAAAAATGGAAT
* *
8582 TTTTAGAAAGTTTAGGGTTAAAATGGAA-
1 TTTTGGAAAGTTTAGGGTAAAAATGGAAT
** *
8610 TTTTGGAAAGTTCGGGGGTAAAAATGTAAT
1 TTTTGGAAAGTT-TAGGGTAAAAATGGAAT
*
8640 TTTTGGAAA-TTTCAAGGTTAAAAATGGAAT
1 TTTTGGAAAGTTT--AGGGTAAAAATGGAAT
* *
8670 TTTT-GAAAGTTTATGGGTAAAAATGTATT
1 TTTTGGAAAGTTTA-GGGTAAAAATGGAAT
* * *
8699 TTTTGGAAAATTTGATGTTAAAAATGGAA-
1 TTTTGGAAAGTTT-AGGGTAAAAATGGAAT
* *
8728 TTTTGGAAAGTGTAGGGGTAAAAATGTAAT
1 TTTTGGAAAGTTTA-GGGTAAAAATGGAAT
*
8758 TTTTGTAAAGTTTAGGGTCAAAAATGGAA-
1 TTTTGGAAAGTTTAGGGT-AAAAATGGAAT
8787 TTTTGGAAAAGTTTAGGG
1 TTTTGG-AAAGTTTAGGG
8805 ACTTTCAGGG
Statistics
Matches: 229, Mismatches: 37, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
28 19 0.08
29 109 0.48
30 100 0.44
31 1 0.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTAAAAATGGAAT
Found at i:8678 original size:59 final size:58
Alignment explanation
Indices: 8492--8804 Score: 353
Period size: 59 Copynumber: 5.3 Consensus size: 58
8482 TCAAAAATTA
* * * **
8492 AATTTTGGAAAGTTCAGGGATAAAAATGAAATTTTTGG-AAGTTAAGGGACAAAAATGG
1 AATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGAAATTTAA-GGTTAAAAATGG
* * * * *
8550 AATTTTGGAAAGTTTAAGGGTAAAATTGTAATTTTTAGAAAGTTTAGGGTT-AAAATGG
1 AATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGAAA-TTTAAGGTTAAAAATGG
*
8608 AATTTTGGAAAGTTCGGGGGTAAAAATGTAATTTTTGGAAATTTCAAGGTTAAAAATGG
1 AATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGAAATTT-AAGGTTAAAAATGG
* * * * * *
8667 AATTTTTGAAAGTTTATGGGTAAAAATGTATTTTTTGGAAAATTTGATGTTAAAAATGG
1 AATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGG-AAATTTAAGGTTAAAAATGG
* * *
8726 AATTTTGGAAAGTGT-AGGGGTAAAAATGTAATTTTTGTAAAGTTTAGGGTCAAAAATGG
1 AATTTTGGAAAGT-TCAGGGGTAAAAATGTAATTTTTGGAAA-TTTAAGGTTAAAAATGG
*
8785 AATTTTGGAAAAGTTTAGGG
1 AATTTTGG-AAAGTTCAGGG
8805 ACTTTCAGGG
Statistics
Matches: 215, Mismatches: 31, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
57 3 0.01
58 83 0.39
59 110 0.51
60 19 0.09
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (58 bp):
AATTTTGGAAAGTTCAGGGGTAAAAATGTAATTTTTGGAAATTTAAGGTTAAAAATGG
Found at i:10063 original size:3 final size:3
Alignment explanation
Indices: 10055--10125 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
10045 CTCTTTGCTT
* *
10055 TTA TTA TTA TTA ATA TTAA TTA TTA TTA TTA TTA ATA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * *
10102 TTA -GA TTA ATA TTA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
10126 AATAATCAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
2 1 0.02
3 49 0.89
4 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:10078 original size:16 final size:15
Alignment explanation
Indices: 10057--10153 Score: 69
Period size: 16 Copynumber: 6.5 Consensus size: 15
10047 CTTTGCTTTT
10057 ATTATTATTAATATTA
1 ATTA-TATTAATATTA
*
10073 ATTATTATTATTATTA
1 ATTA-TATTAATATTA
*
10089 A-TAT-TTATTATT-
1 ATTATATTAATATTA
*
10101 ATTAGATTAATATT-
1 ATTATATTAATATTA
*
10115 ATTAATATT-ATAATA
1 ATT-ATATTAATATTA
*
10130 ATCAATATTAATATTA
1 AT-TATATTAATATTA
*
10146 ATGATATT
1 ATTATATT
10154 TACTAATACG
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
12 1 0.01
13 10 0.15
14 15 0.22
15 18 0.27
16 23 0.34
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTATATTAATATTA
Found at i:10140 original size:30 final size:30
Alignment explanation
Indices: 10065--10161 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
10055 TTATTATTAT
* *
10065 TAATATTAATTATTATTATTATTAATATTTA
1 TAATAATAA-TATTAATATTATTAATATTTA
* * * *
10096 TTATTATTAGATTAATATTATTAATA-TTA
1 TAATAATAATATTAATATTATTAATATTTA
* *
10125 TAATAATCAATATTAATATTAATGATATTTA
1 TAATAAT-AATATTAATATTATTAATATTTA
10156 CTAATA
1 -TAATA
10162 CGTTTTGAAA
Statistics
Matches: 51, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
29 8 0.16
30 30 0.59
31 8 0.16
32 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (30 bp):
TAATAATAATATTAATATTATTAATATTTA
Found at i:10142 original size:6 final size:6
Alignment explanation
Indices: 10056--10147 Score: 52
Period size: 6 Copynumber: 16.2 Consensus size: 6
10046 TCTTTGCTTT
* * * *
10056 TATTAT TATTAA TATT-A -ATTAT TATTAT TATTAA TATT-- TATTAT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
* * * * *
10100 TATT-A GATTAA TATTAT TAATAT TA-TAA TAATCAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA T-ATTAA TATTAA TATTAA
10147 T
1 T
10148 GATATTTACT
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
4 7 0.10
5 7 0.10
6 51 0.75
7 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:13371 original size:29 final size:28
Alignment explanation
Indices: 13335--13613 Score: 78
Period size: 28 Copynumber: 9.6 Consensus size: 28
13325 GTCACTCGGG
13335 GGGTAAAATAGTAA-TTTTGGAAAAATTA
1 GGGTAAAATAG-AATTTTTGGAAAAATTA
*
13363 GGGTCAAAAATAGAATTTTTGG--AAGTTCGA
1 GGGT--AAAATAGAATTTTTGGAAAAATT--A
*
13393 GGGTAAAAT-GTTAA-TTTTGGAAAAA-TC
1 GGGTAAAATAG--AATTTTTGGAAAAATTA
* *
13420 GAGGTCAAAATAGAATTTTTGG--AAGTTCGG
1 G-GGT-AAAATAGAATTTTTGGAAAAATT--A
* * * *
13450 GGGTAAAATGGTAATTTTT-GTAAAAGTC
1 GGGTAAAATAG-AATTTTTGGAAAAATTA
* * **
13478 GAGGTCAAAAATGGAATTTTTAG-AAGTTTAA
1 G-GGT--AAAATAGAATTTTTGGAAAAATT-A
* *
13509 GGGTAAAATGGTAATTTTTGGAAAAATCA
1 GGGTAAAATAG-AATTTTTGGAAAAATTA
** * *
13538 GTCTAAAATGGAATTTTTGG--AAGTTCGA
1 GGGTAAAATAGAATTTTTGGAAAAATT--A
* *
13566 GGGTAAAATGGTATTTTTTGGAAAAATTA
1 GGGTAAAATAG-AATTTTTGGAAAAATTA
* *
13595 AGGTCAAAAATGGAATTTT
1 GGGT--AAAATAGAATTTT
13614 GTAAAGTTCG
Statistics
Matches: 191, Mismatches: 27, Indels: 64
0.68 0.10 0.23
Matches are distributed among these distances:
26 3 0.02
27 4 0.02
28 59 0.31
29 59 0.31
30 46 0.24
31 20 0.10
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (28 bp):
GGGTAAAATAGAATTTTTGGAAAAATTA
Found at i:13408 original size:58 final size:57
Alignment explanation
Indices: 13335--13700 Score: 386
Period size: 57 Copynumber: 6.3 Consensus size: 57
13325 GTCACTCGGG
*
13335 GGGTAAAATAGTAATTTTGGAAAAATTAGGGTCAAAAATAGAATTTTTGGAAGTTCGA
1 GGGTAAAAT-GTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* * *
13393 GGGTAAAATGTTAATTTTGGAAAAA-TCGAGGTC-AAAATAGAATTTTTGGAAGTTCGG
1 GGGTAAAATG-TAATTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGA
* * * * * **
13450 GGGTAAAATGGTAATTTTTGTAAAAGTCGAGGTCAAAAATGGAATTTTTAGAAGTTTAA
1 GGGTAAAAT-GTAATTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGA
* *
13509 GGGTAAAATGGTAATTTTTGGAAAAATCA--GTCTAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAAT-GTAA-TTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* * *
13566 GGGTAAAATGGTATTTTTTGGAAAAATTAAGGTCAAAAATGGAA-TTTTGTAAAGTTCGA
1 GGGTAAAAT-GTA-ATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTG-GAAGTTCGA
* * *
13625 GGGCT-AAATGTAATTTATGGAAAAATCAGGGTTAAAAATGGAA-TTTTGGAAAGCTCGA
1 GGG-TAAAATGTAATTT-TGGAAAAATTAGGGTCAAAAATGGAATTTTTGG-AAGTTCGA
13683 GGGCTAAAATGTAATTTT
1 GGG-TAAAATGTAATTTT
13701 TGGACTGTTT
Statistics
Matches: 266, Mismatches: 28, Indels: 28
0.83 0.09 0.09
Matches are distributed among these distances:
57 100 0.38
58 85 0.32
59 71 0.27
60 10 0.04
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:13450 original size:116 final size:113
Alignment explanation
Indices: 13333--13700 Score: 422
Period size: 116 Copynumber: 3.2 Consensus size: 113
13323 TGGTCACTCG
* *
13333 GGGGGTAAAATAGTAATTTTGGAAAAATTAGGGTCAAAAATAGAATTTTTGGAAGTTCGAGGGTA
1 GGGGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
*
13398 AAATGTTAATTTTGGAAAAATCGAGGTCAAAATAGAATTTTTGGAAGTTC
66 AAATG-TAATTTTGGAAAAATC-AGGTCAAAATGGAATTTTTGGAAGTTC
* * * * * **
13448 GGGGGTAAAATGGTAATTTTTGTAAAAGTCGAGGTCAAAAATGGAATTTTTAGAAGTTTAAGGGT
1 GGGGGTAAAATGGTAATTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
13513 AAAATGGTAATTTTTGGAAAAATCA-GTCTAAAATGGAATTTTTGGAAGTTC
65 AAAAT-GTAA-TTTTGGAAAAATCAGGTC-AAAATGGAATTTTTGGAAGTTC
* * * *
13564 GAGGGTAAAATGGTATTTTTTGGAAAAATTAAGGTCAAAAATGGAA-TTTTGTAAAGTTCGAGGG
1 GGGGGTAAAATGGTA-ATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTG-GAAGTTCGAGGG
* *
13628 CT-AAATGTAATTTATGGAAAAATCAGGGTTAAAAATGGAA-TTTTGGAAAGCTC
64 -TAAAATGTAATTT-TGGAAAAATCA-GG-TCAAAATGGAATTTTTGG-AAGTTC
*
13681 GAGGGCTAAAAT-GTAATTTT
1 G-GGGGTAAAATGGTAATTTT
13701 TGGACTGTTT
Statistics
Matches: 214, Mismatches: 26, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
114 3 0.01
115 48 0.22
116 110 0.51
117 44 0.21
118 9 0.04
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (113 bp):
GGGGGTAAAATGGTAATTTTGGAAAAATTAGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTA
AAATGTAATTTTGGAAAAATCAGGTCAAAATGGAATTTTTGGAAGTTC
Found at i:13691 original size:29 final size:29
Alignment explanation
Indices: 13369--13700 Score: 172
Period size: 29 Copynumber: 11.4 Consensus size: 29
13359 ATTAGGGTCA
*
13369 AAAATAGAATTTTTGG-AAGTTCGAGGG-T
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGCT
* ** *
13397 AAAATGTTAATTTTGGAAAAATCGAGGTC-
1 AAAATG-GAATTTTGGAAAGTTCGAGGGCT
* *
13426 AAAATAGAATTTTTGG-AAGTTCG-GGGGT
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGCT
* * *
13454 AAAATGGTAATTTTTGTAAAAG-TCGAGGTCA
1 AAAATGG-AA-TTTTG-GAAAGTTCGAGGGCT
* **
13485 AAAATGGAATTTT-TAGAAGTTTAAGGG-T
1 AAAATGGAATTTTGGA-AAGTTCGAGGGCT
** *
13513 AAAATGGTAATTTTTGGAAAAATC-A-GTCT
1 AAAATGG-AA-TTTTGGAAAGTTCGAGGGCT
13542 AAAATGGAATTTTTGG-AAGTTCGAGGG-T
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGCT
* * * * *
13570 AAAATGGTATTTTTTGGAAAAATT-AAGGTCA
1 AAAATGG-A-ATTTTGG-AAAGTTCGAGGGCT
*
13601 AAAATGGAATTTTGTAAAGTTCGAGGGCT
1 AAAATGGAATTTTGGAAAGTTCGAGGGCT
* ** *
13630 -AAATGTAATTTATGGAAAAATC-AGGGTT
1 AAAATGGAATTT-TGGAAAGTTCGAGGGCT
*
13658 AAAAATGGAATTTTGGAAAGCTCGAGGGCT
1 -AAAATGGAATTTTGGAAAGTTCGAGGGCT
*
13688 AAAATGTAATTTT
1 AAAATGGAATTTT
13701 TGGACTGTTT
Statistics
Matches: 227, Mismatches: 50, Indels: 53
0.69 0.15 0.16
Matches are distributed among these distances:
27 7 0.03
28 73 0.32
29 92 0.41
30 31 0.14
31 24 0.11
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGCT
Found at i:14758 original size:3 final size:3
Alignment explanation
Indices: 14750--14799 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
14740 TATTTTCCTT
*
14750 TTA TTA TTA TT- TTA TTA ATA TTA TTA -TA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
14794 TTA TTA
1 TTA TTA
14800 AAACGTTCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 36 0.86
4 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:15568 original size:17 final size:17
Alignment explanation
Indices: 15547--15607 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
15537 ATTTTATTTA
15547 AAAATAAATTTAAACTT
1 AAAATAAATTTAAACTT
* ** *
15564 CAAATAAGCTTAAATTT
1 AAAATAAATTTAAACTT
*
15581 ATAATAAATTTAAACTT
1 AAAATAAATTTAAACTT
*
15598 AAAATGAATT
1 AAAATAAATT
15608 AAAAATTAAG
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (17 bp):
AAAATAAATTTAAACTT
Found at i:15637 original size:23 final size:24
Alignment explanation
Indices: 15611--15656 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
15601 ATGAATTAAA
15611 AATTAAGATCTAAA-ATTGGGTTT
1 AATTAAGATCTAAATATTGGGTTT
**
15634 AATTTCGATCTAAATATTGGGTT
1 AATTAAGATCTAAATATTGGGTT
15657 CAGTCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (24 bp):
AATTAAGATCTAAATATTGGGTTT
Found at i:16922 original size:17 final size:17
Alignment explanation
Indices: 16893--16956 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
16883 CGGGCCAAAC
*
16893 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTAT
* * *
16910 AAAATTAAGTTTATTCT
1 AAATTTAAATTTATTAT
*
16927 GAATTTAAATTTATTAT
1 AAATTTAAATTTATTAT
16944 AAATTTAAATTTA
1 AAATTTAAATTTA
16957 AAATTTATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTAT
Done.