Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014944.1 Kokia drynarioides strain JFW-HI SEQ_129987, 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: 53991
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 466 characters in sequence are not A, C, G, or T
Found at i:2568 original size:29 final size:28
Alignment explanation
Indices: 2531--2585 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
2521 AACTATTGGT
*
2531 AAAATTTCATTTTGATCACATAACTAAA
1 AAAATTTCAATTTGATCACATAACTAAA
* *
2559 AAAAGTTTCAATTTGGTCACGTAACTA
1 AAAA-TTTCAATTTGATCACATAACTA
2586 TTCAAAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAATTTCAATTTGATCACATAACTAAA
Found at i:3254 original size:23 final size:23
Alignment explanation
Indices: 3228--3279 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
3218 TTATATGCCT
**
3228 TTGTGGCATGCTTTTTCTCTACC
1 TTGTGGCACACTTTTTCTCTACC
* * *
3251 TTGTGGTACACTTTTTCTCTGCT
1 TTGTGGCACACTTTTTCTCTACC
3274 TTGTGG
1 TTGTGG
3280 AACGTTTCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.50
Consensus pattern (23 bp):
TTGTGGCACACTTTTTCTCTACC
Found at i:3630 original size:19 final size:19
Alignment explanation
Indices: 3606--3647 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3596 TGATTTGAGA
3606 TTTATTTTTCTAATTTTTT
1 TTTATTTTTCTAATTTTTT
* *
3625 TTTATTTTTTTAGTTTTTT
1 TTTATTTTTCTAATTTTTT
3644 TTTA
1 TTTA
3648 ATTTCTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTATTTTTCTAATTTTTT
Found at i:3650 original size:30 final size:29
Alignment explanation
Indices: 3605--3682 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
3595 CTGATTTGAG
* *
3605 ATTTATTTTTCTAATTTTTTTTTATTTTTTT
1 ATTT-TTTTT-TAATTTTTCTTTATTTTATT
* *
3636 AGTTTTTTTTTAATTTCTCTTTGTTTTATT
1 A-TTTTTTTTTAATTTTTCTTTATTTTATT
*
3666 ATTTTTTGTTATATTTT
1 ATTTTTTTTTA-ATTTT
3683 AATTTCGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 9 0.23
30 21 0.54
31 6 0.15
32 3 0.08
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (29 bp):
ATTTTTTTTTAATTTTTCTTTATTTTATT
Found at i:18605 original size:52 final size:52
Alignment explanation
Indices: 18480--18763 Score: 417
Period size: 52 Copynumber: 5.5 Consensus size: 52
18470 AAAAAGGTTT
* * *
18480 GATGACTGAGTGTCATCGTAAGTATATGAATCCTTTACGGATTA-AAGGTCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* *
18531 GATGACTGAGTGTTATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
*
18583 GATGACTAAGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * * **
18635 GATGACTATGTGCCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTTT
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
18687 GATGACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGATCC
1 GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* *
18739 GATGACCATGTGTCATCGTGAGTAT
1 GATGACTAAGTGTCATCGTGAGTAT
18764 CAAATGAGAA
Statistics
Matches: 212, Mismatches: 20, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 0.20
52 170 0.80
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.34
Consensus pattern (52 bp):
GATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
Found at i:18682 original size:26 final size:26
Alignment explanation
Indices: 18653--18734 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
18643 TGTGCCATCG
18653 TGAGTATATGAATCCTTTATGGATTA
1 TGAGTATATGAATCCTTTATGGATTA
* * * * *
18679 TGAGGT-T-TG-ATGACTATGTGTCATCA
1 TGA-GTATATGAAT-CCTTTATG-GATTA
*
18705 TGAGTATATGAATCCTTTACGGATTA
1 TGAGTATATGAATCCTTTATGGATTA
18731 TGAG
1 TGAG
18735 ATCCGATGAC
Statistics
Matches: 39, Mismatches: 11, Indels: 12
0.63 0.18 0.19
Matches are distributed among these distances:
24 2 0.05
25 9 0.23
26 18 0.46
27 8 0.21
28 2 0.05
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTATGGATTA
Found at i:18802 original size:62 final size:63
Alignment explanation
Indices: 18712--18841 Score: 158
Period size: 62 Copynumber: 2.1 Consensus size: 63
18702 TCATGAGTAT
* * *
18712 ATGAATCCTTTACGGATTATGAGATCCGATGAC-CATGTGTCATCGTGAG-TATCAAATGAGAA
1 ATGAATCCTTTACGGATTATAAGATCCGATGACTC-CGTGTCATCGTGAGTTACCAAATGAGAA
* * *
18774 ATGAATCCTATTATGGATTA-AAGGTCCGATGACTCCGTGTCATCGTGAGTTACCAAATGCGAA
1 ATGAATCCT-TTACGGATTATAAGATCCGATGACTCCGTGTCATCGTGAGTTACCAAATGAGAA
*
18837 TTGAA
1 ATGAA
18842 ACCAACCTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
62 33 0.57
63 25 0.43
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (63 bp):
ATGAATCCTTTACGGATTATAAGATCCGATGACTCCGTGTCATCGTGAGTTACCAAATGAGAA
Found at i:21143 original size:18 final size:18
Alignment explanation
Indices: 21109--21143 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21099 TAGAAGTTGA
*
21109 TTTATTTTTAACAATTAC
1 TTTATTTTAAACAATTAC
*
21127 TTTATTTTAAACTATTA
1 TTTATTTTAAACAATTA
21144 TGCAATTATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATTTTAAACAATTAC
Found at i:30361 original size:21 final size:21
Alignment explanation
Indices: 30312--30369 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
30302 TTATTTGTTT
*
30312 CTTTTAAT-A-TTTTTATAAT
1 CTTTTAATAATTTTTTATAAC
* *
30331 ATTCTAAATAATTTTTTATAAC
1 CTT-TTAATAATTTTTTATAAC
*
30353 CTTTTAATAATTATTTA
1 CTTTTAATAATTTTTTA
30370 AAAGATCATG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 4 0.13
21 13 0.43
22 11 0.37
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
CTTTTAATAATTTTTTATAAC
Found at i:30495 original size:31 final size:32
Alignment explanation
Indices: 30460--30519 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
30450 TCTAGCTTGC
*
30460 ATTTTTAGT-AATTTTTA-AATATTTTTTTAGA
1 ATTTTTAGTAAATTTCTAGAAT-TTTTTTTAGA
*
30491 ATTTTTATTAAATTTCTAGAATTTTTTTT
1 ATTTTTAGTAAATTTCTAGAATTTTTTTT
30520 GTTGATTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 8 0.32
32 14 0.56
33 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (32 bp):
ATTTTTAGTAAATTTCTAGAATTTTTTTTAGA
Found at i:35972 original size:2 final size:2
Alignment explanation
Indices: 35965--36003 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
35955 ATTGATTGAT
35965 TA TA TA TA 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 TA TA TA TA T
36004 NNNNNNNNNN
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40276 original size:22 final size:22
Alignment explanation
Indices: 40216--40277 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
40206 ATTATATTAT
*
40216 TGTTTTGGTG-TTTCTTTTTAC
1 TGTTTTGGTGTTTTTTTTTTAC
* **
40237 TGTTTTGGTATTGGTTTTTTAC
1 TGTTTTGGTGTTTTTTTTTTAC
*
40259 TGTTTTTGTGTTTTTTTTT
1 TGTTTTGGTGTTTTTTTTT
40278 GTTTTGATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 9 0.28
22 23 0.72
ACGTcount: A:0.05, C:0.05, G:0.19, T:0.71
Consensus pattern (22 bp):
TGTTTTGGTGTTTTTTTTTTAC
Found at i:40280 original size:18 final size:21
Alignment explanation
Indices: 40259--40301 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
40249 GGTTTTTTAC
40259 TGTTTTTG-TGTT-TT-TTTT
1 TGTTTTTGATGTTGTTATTTT
40277 TG-TTTTGATGTTGTTATTTT
1 TGTTTTTGATGTTGTTATTTT
40297 TGTTT
1 TGTTT
40302 CTGTTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 2 0.10
20 6 0.29
21 2 0.10
ACGTcount: A:0.05, C:0.00, G:0.19, T:0.77
Consensus pattern (21 bp):
TGTTTTTGATGTTGTTATTTT
Found at i:40312 original size:24 final size:24
Alignment explanation
Indices: 40269--40354 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
40259 TGTTTTTGTG
40269 TTTTT-TTT-TGTTTTGATGTTGTTA
1 TTTTTGTTTCTGTTTT--TGTTGTTA
*
40293 TTTTTGTTTCTGTTTTTGTTGCTA
1 TTTTTGTTTCTGTTTTTGTTGTTA
40317 TTTTTTGTTTTGCTGTTATTTTAGTTGTTA
1 -TTTTTG-TTT-CTG-T-TTTT-GTTGTTA
40347 TTTTTGTT
1 TTTTTGTT
40355 ATTTGGATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
24 12 0.23
25 9 0.17
26 9 0.17
27 3 0.06
28 3 0.06
29 10 0.19
30 6 0.12
ACGTcount: A:0.07, C:0.03, G:0.16, T:0.73
Consensus pattern (24 bp):
TTTTTGTTTCTGTTTTTGTTGTTA
Found at i:40345 original size:45 final size:44
Alignment explanation
Indices: 40258--40345 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
40248 TGGTTTTTTA
* * * *
40258 CTGTTTTTGTGTTTTTTTTTGTTTTGATGTTGTTATTTTTGTTT
1 CTGTTTTTGTGCTATTTTTTGTTTTGATGTTATTATTGTTGTTT
*
40302 CTGTTTTTGTTGCTATTTTTTGTTTTGCTGTTATT-TTAGTTGTT
1 CTGTTTTTG-TGCTATTTTTTGTTTTGATGTTATTATT-GTTGTT
40346 ATTTTTGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.30
45 26 0.70
ACGTcount: A:0.06, C:0.05, G:0.18, T:0.72
Consensus pattern (44 bp):
CTGTTTTTGTGCTATTTTTTGTTTTGATGTTATTATTGTTGTTT
Found at i:40349 original size:30 final size:25
Alignment explanation
Indices: 40258--40351 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 25
40248 TGGTTTTTTA
*
40258 CTGTTTTTG-TGTTTTTTTTTGTTT
1 CTGTTTTTGTTGTTATTTTTTGTTT
*
40282 -TG---ATGTTGTTA-TTTTTGTTT
1 CTGTTTTTGTTGTTATTTTTTGTTT
*
40302 CTGTTTTTGTTGCTATTTTTTGTTTT
1 CTGTTTTTGTTGTTATTTTTTG-TTT
40328 GCTGTTATTTTAGTTGTTATTTTT
1 -CTG-T-TTTT-GTTGTTATTTTT
40352 GTTATTTGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
20 11 0.20
21 6 0.11
23 2 0.04
24 7 0.13
25 6 0.11
26 3 0.06
27 3 0.06
28 1 0.02
29 4 0.07
30 11 0.20
ACGTcount: A:0.06, C:0.04, G:0.17, T:0.72
Consensus pattern (25 bp):
CTGTTTTTGTTGTTATTTTTTGTTT
Found at i:48857 original size:12 final size:12
Alignment explanation
Indices: 48842--48873 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
48832 TTCAGGTCCT
48842 TCTTCATCTTCC
1 TCTTCATCTTCC
*
48854 TCTTCCTCTTCC
1 TCTTCATCTTCC
48866 TCTTCATC
1 TCTTCATC
48874 ATCATCATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (12 bp):
TCTTCATCTTCC
Found at i:53128 original size:6 final size:6
Alignment explanation
Indices: 53112--53140 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
53102 TTGGTAGCAG
53112 CCATA- CCATAC CCATAC CCATAC CCATAC
1 CCATAC CCATAC CCATAC CCATAC CCATAC
53141 GTGTAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATAC
Found at i:53496 original size:20 final size:21
Alignment explanation
Indices: 53468--53507 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
53458 TGTGACAAAA
*
53468 AATATAAAA-AATAAAATTTT
1 AATAAAAAATAATAAAATTTT
*
53488 AATAAAAAATATTAAAATTT
1 AATAAAAAATAATAAAATTT
53508 AGAATTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAAATAATAAAATTTT
Found at i:53513 original size:28 final size:28
Alignment explanation
Indices: 53464--53524 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
53454 GACGTGTGAC
53464 AAAAAATATAAAAAATAAAA-TTTTAAT
1 AAAAAATATAAAAAATAAAATTTTTAAT
** * *
53491 AAAAAATATTAAAATTTAGAATTTTTTAT
1 AAAAAATA-TAAAAAATAAAATTTTTAAT
53520 AAAAA
1 AAAAA
53525 TTGTAAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.29
28 9 0.32
29 11 0.39
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAAAATATAAAAAATAAAATTTTTAAT
Found at i:53563 original size:20 final size:20
Alignment explanation
Indices: 53514--53564 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
53504 ATTTAGAATT
53514 TTTTATAAAAATTGTAAAGA
1 TTTTATAAAAATTGTAAAGA
** *
53534 AATTATAAAAATTGTAAA-C
1 TTTTATAAAAATTGTAAAGA
53553 TTTTATAAAAAT
1 TTTTATAAAAAT
53565 ATTATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
TTTTATAAAAATTGTAAAGA
Done.