Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001923.1 Kokia drynarioides strain JFW-HI SEQ_113722, 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: 37391
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 74 characters in sequence are not A, C, G, or T
Found at i:2096 original size:17 final size:17
Alignment explanation
Indices: 2074--2107 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2064 ATTTCTTAAA
2074 ATTAATTTTAATTTTTT
1 ATTAATTTTAATTTTTT
2091 ATTAATTTTAATTTTTT
1 ATTAATTTTAATTTTTT
2108 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTAATTTTAATTTTTT
Found at i:2739 original size:18 final size:19
Alignment explanation
Indices: 2704--2749 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
2694 TTTTTACTTT
* *
2704 ATTTAATATTCTTAT-AAA
1 ATTTAATAATATTATAAAA
*
2722 ATTTAATAATATTTTAAAA
1 ATTTAATAATATTATAAAA
2741 ATTT-ATAAT
1 ATTTAATAAT
2750 TTGAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAATAATATTATAAAA
Found at i:2743 original size:19 final size:20
Alignment explanation
Indices: 2707--2749 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2697 TTACTTTATT
2707 TAATATTCTTATAAAATTTAA
1 TAATATTCTTATAAAATTT-A
2728 TAATATT-TTA-AAAATTTA
1 TAATATTCTTATAAAATTTA
2746 TAAT
1 TAAT
2750 TTGAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 7 0.32
20 3 0.14
21 7 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATATTCTTATAAAATTTA
Found at i:2864 original size:14 final size:15
Alignment explanation
Indices: 2847--2876 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2837 ATTTTTTAAA
2847 AAAATGAT-TTTTTT
1 AAAATGATATTTTTT
2861 AAAATGATATTTTTT
1 AAAATGATATTTTTT
2876 A
1 A
2877 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
AAAATGATATTTTTT
Found at i:2864 original size:15 final size:16
Alignment explanation
Indices: 2836--2876 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
2826 ATATTCATTT
2836 TATTTTTTAAAAAAATGA
1 TATTTTTT--AAAAATGA
2854 T-TTTTTT-AAAATGA
1 TATTTTTTAAAAATGA
2868 TATTTTTTA
1 TATTTTTTA
2877 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
17 6 0.29
18 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (16 bp):
TATTTTTTAAAAATGA
Found at i:2892 original size:20 final size:21
Alignment explanation
Indices: 2855--2901 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
2845 AAAAAATGAT
2855 TTTTTTAAAATGATATTTTTTA
1 TTTTTTAAAATGA-ATTTTTTA
*
2877 TTTTTTAAATTG-ATTTTTTA
1 TTTTTTAAAATGAATTTTTTA
2897 TTTTT
1 TTTTT
2902 ATTGGCGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTTTAAAATGAATTTTTTA
Found at i:8766 original size:21 final size:22
Alignment explanation
Indices: 8742--8786 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
8732 CTTTTTTAGT
* *
8742 TCTTGCTAAATCTTTCAAT-AA
1 TCTTGATAAATCTTTAAATCAA
8763 TCTTGATAAATCTTTAAATCAA
1 TCTTGATAAATCTTTAAATCAA
8785 TC
1 TC
8787 GTTAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (22 bp):
TCTTGATAAATCTTTAAATCAA
Found at i:9628 original size:40 final size:38
Alignment explanation
Indices: 9554--9628 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 38
9544 TTATTTAATT
*
9554 TGCAAATATGTTGTGCATCCACAACAAGTGGCAGTAAC
1 TGCAAATATGTGGTGCATCCACAACAAGTGGCAGTAAC
*
9592 TGCAAATATGTGGTTCGAT-CACGAACCAAGTGGCAGT
1 TGCAAATATGTGGTGC-ATCCAC-AA-CAAGTGGCAGT
9629 CTGTTTAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 17 0.53
39 4 0.12
40 11 0.34
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (38 bp):
TGCAAATATGTGGTGCATCCACAACAAGTGGCAGTAAC
Found at i:9663 original size:85 final size:86
Alignment explanation
Indices: 9506--9683 Score: 227
Period size: 85 Copynumber: 2.1 Consensus size: 86
9496 CAGTTTAATA
* * * * *
9506 TGCAAACAGTGTGGTTCGATCACAAATCAAGTGGTAGTTTATTTAATTTGCAAATATGTTGTGCA
1 TGCAAATAGTGTGGTTCGATCACAAACCAAGTGGCAGTCTATTTAATCTGCAAATATGTTGTGCA
*
9571 TCCACAACAAGTGGCAGTAAC
66 TCCACAACAAGTGACAGTAAC
* * *
9592 TGCAAATA-TGTGGTTCGATCACGAACCAAGTGGCAGTCTGTTTAATCT-CTAAATATGTTGTGT
1 TGCAAATAGTGTGGTTCGATCACAAACCAAGTGGCAGTCTATTTAATCTGC-AAATATGTTGTGC
9655 A-CCTACAACAAGTGACAGTAAC
65 ATCC-ACAACAAGTGACAGTAAC
*
9677 TACAAAT
1 TGCAAAT
9684 CAACGATGGT
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
84 3 0.04
85 70 0.88
86 7 0.09
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (86 bp):
TGCAAATAGTGTGGTTCGATCACAAACCAAGTGGCAGTCTATTTAATCTGCAAATATGTTGTGCA
TCCACAACAAGTGACAGTAAC
Found at i:11376 original size:41 final size:41
Alignment explanation
Indices: 11331--11409 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
11321 TTCATACCAT
* *
11331 TTTTAAAATTTTTAT-ATATTTTAGATTTTTAAAAATACAAA
1 TTTTAAAATTTTTATAATATATTA-AATTTTAAAAATACAAA
**
11372 TTTTAGGATTTTTATAAATATATTAAATTTTAAAAATA
1 TTTTAAAATTTTTAT-AATATATTAAATTTTAAAAATA
11410 ATTTTGATGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 13 0.41
42 12 0.38
43 7 0.22
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
TTTTAAAATTTTTATAATATATTAAATTTTAAAAATACAAA
Found at i:13602 original size:23 final size:22
Alignment explanation
Indices: 13576--13619 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
13566 GTTTTTTTAT
13576 TTCC-ACATAATTTTTAGTATATA
1 TTCCTACA-AATTTTTAG-ATATA
*
13599 TTCCTTCAAATTTTTAGATAT
1 TTCCTACAAATTTTTAGATAT
13620 TCTCTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 13 0.68
24 2 0.11
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (22 bp):
TTCCTACAAATTTTTAGATATA
Found at i:13621 original size:20 final size:21
Alignment explanation
Indices: 13581--13674 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 21
13571 TTTATTTCCA
13581 CATAATTTTTAGTATATAT-TCCTT
1 CATAATTTTTAG-ATAT-TCT-C-T
13605 CA-AATTTTTAGATATTCTCT
1 CATAATTTTTAGATATTCTCT
*
13625 CATAATTTTT-TATATTCTCT
1 CATAATTTTTAGATATTCTCT
* * *
13645 TATAATCTTTAG-TATTGC-AT
1 CATAATTTTTAGATATT-CTCT
13665 CATAATTTTT
1 CATAATTTTT
13675 TGTAAGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
20 33 0.56
21 10 0.17
22 5 0.08
23 9 0.15
24 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.54
Consensus pattern (21 bp):
CATAATTTTTAGATATTCTCT
Found at i:15193 original size:48 final size:48
Alignment explanation
Indices: 15140--15232 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
15130 GCATGAATTT
* *
15140 TTTTATCTTGAGGTGTGAATCACTTTCCT-TATCGCTTTATCTTTTTTC
1 TTTTATCTTGAGGCGTAAATCACTTT-CTATATCGCTTTATCTTTTTTC
*
15188 TTTTATTTTGAGGCGTAAATCACTTTCTATATCGCTTTATCTTTT
1 TTTTATCTTGAGGCGTAAATCACTTTCTATATCGCTTTATCTTTT
15233 GACTGATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 2 0.05
48 39 0.95
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (48 bp):
TTTTATCTTGAGGCGTAAATCACTTTCTATATCGCTTTATCTTTTTTC
Found at i:21864 original size:17 final size:17
Alignment explanation
Indices: 21842--21880 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
21832 AGGTGGAGAA
* *
21842 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
21859 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
21876 CTTGT
1 CTTGT
21881 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:21933 original size:17 final size:18
Alignment explanation
Indices: 21913--21950 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
21903 GGGTGACTAG
21913 AATTC-TTGGTAAAATAA
1 AATTCATTGGTAAAATAA
21930 AATTCATTGGTAAAATAA
1 AATTCATTGGTAAAATAA
21948 AAT
1 AAT
21951 AAAAGTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
AATTCATTGGTAAAATAA
Found at i:23357 original size:20 final size:20
Alignment explanation
Indices: 23328--23372 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
23318 GTCAGCAAAT
23328 AATT-TTAAAATAAATATAA
1 AATTATTAAAATAAATATAA
* * *
23347 AATTATTAAAATTATTTTAA
1 AATTATTAAAATAAATATAA
23367 AATTAT
1 AATTAT
23373 AATCATCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTATTAAAATAAATATAA
Found at i:24102 original size:55 final size:55
Alignment explanation
Indices: 23991--24103 Score: 140
Period size: 55 Copynumber: 2.1 Consensus size: 55
23981 TTTGCATGCG
* *
23991 TGATTCAAACCCAGATGAGGAAATTTGTTTTATAAAGTAAATGGATTTTTTATTT
1 TGATTCAAACCCAGATGAGGAAATTTGTTTTATAAAGCAAATGGATTTTTGATTT
* * * *
24046 TGATTCAAATCCATATGATGAAATTTGTTTTATCAAA-CAAAT-GAGTTTTTGGTTT
1 TGATTCAAACCCAGATGAGGAAATTTGTTTTAT-AAAGCAAATGGA-TTTTTGATTT
24101 TGA
1 TGA
24104 CAGTAATGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
54 2 0.04
55 45 0.90
56 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (55 bp):
TGATTCAAACCCAGATGAGGAAATTTGTTTTATAAAGCAAATGGATTTTTGATTT
Found at i:24235 original size:9 final size:9
Alignment explanation
Indices: 24221--24279 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
24211 ATTAAAATTA
24221 TTTAATAAT
1 TTTAATAAT
24230 TTTAATAAT
1 TTTAATAAT
24239 TTT-AT-AT
1 TTTAATAAT
*
24246 TTTAAAAAAT
1 TTT-AATAAT
*
24256 AATATAATAAT
1 --TTTAATAAT
*
24267 ATTAATAAT
1 TTTAATAAT
24276 TTTA
1 TTTA
24280 TATTTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
7 5 0.13
8 2 0.05
9 23 0.59
10 2 0.05
11 5 0.13
12 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAATAAT
Found at i:24240 original size:17 final size:17
Alignment explanation
Indices: 24220--24279 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
24210 AATTAAAATT
24220 ATTTAATAATTTTAATA
1 ATTTAATAATTTTAATA
*
24237 ATTTTAT-ATTTTAA-A
1 ATTTAATAATTTTAATA
*
24252 A---AATAA-TATAATA
1 ATTTAATAATTTTAATA
24265 ATATTAATAATTTTA
1 AT-TTAATAATTTTA
24280 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 13
0.65 0.08 0.27
Matches are distributed among these distances:
12 6 0.19
13 3 0.09
15 2 0.06
16 7 0.22
17 11 0.34
18 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATAATTTTAATA
Found at i:24256 original size:20 final size:20
Alignment explanation
Indices: 24233--24300 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
24223 TAATAATTTT
24233 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* * *
24253 AATAATATAATAATATT----
1 AATAATTTTAT-ATTTTAAAA
*
24270 AATAATTTTATATTTAAAAA
1 AATAATTTTATATTTTAAAA
24290 AATTAATTTTA
1 AA-TAATTTTA
24301 AAATCATTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 11
0.66 0.13 0.21
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
20 11 0.31
21 12 0.34
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:24264 original size:37 final size:37
Alignment explanation
Indices: 24214--24292 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
24204 CGATGAAATT
* * * *
24214 AAAATTATTTAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATATAATAATATTAATAATTTTATATTTAAA
24251 AAAATAATATAATAATATTAATAATTTTATATTTAAA
1 AAAATAATATAATAATATTAATAATTTTATATTTAAA
24288 AAAAT
1 AAAAT
24293 TAATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAATAATATAATAATATTAATAATTTTATATTTAAA
Found at i:34110 original size:19 final size:19
Alignment explanation
Indices: 34070--34111 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
34060 TTTTAGTTTC
* *
34070 TTTTAATTTTAATTCTTGT
1 TTTTAATTTTAATCCCTGT
34089 TTTTAATTTTAAATCCCT-T
1 TTTTAATTTT-AATCCCTGT
34108 TTTT
1 TTTT
34112 TTTATCGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAATTTTAATCCCTGT
Found at i:34510 original size:3 final size:3
Alignment explanation
Indices: 34502--34541 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
34492 TTGGAAATTT
34502 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
34542 ACCATGAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:34682 original size:6 final size:6
Alignment explanation
Indices: 34673--34698 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34663 GAAGAAGAAA
34673 AAAAGG AAAAGG AAAAGG AAAAGG AA
1 AAAAGG AAAAGG AAAAGG AAAAGG AA
34699 GAAGAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:34791 original size:37 final size:37
Alignment explanation
Indices: 34742--34816 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
34732 AAAATCCAAG
*
34742 TCTTCTTGGCAGGTAAGAAAGGCAACTATAACCACAT
1 TCTTCTTGGCAGGTAAGAAAGGCAACTAAAACCACAT
34779 TCTTCTTGGCAGGTAAGAAAGGCAACTAAAACCACAT
1 TCTTCTTGGCAGGTAAGAAAGGCAACTAAAACCACAT
34816 T
1 T
34817 ACCAAAGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (37 bp):
TCTTCTTGGCAGGTAAGAAAGGCAACTAAAACCACAT
Found at i:37358 original size:2 final size:2
Alignment explanation
Indices: 37353--37391 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37343 TTGAGAGATA
37353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.