Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005482.1 Kokia drynarioides strain JFW-HI SEQ_119539, 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: 29082
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1551 original size:2 final size:2
Alignment explanation
Indices: 1544--1570 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1534 AAGAATGTCA
1544 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 A
1571 AGAAACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2926 original size:66 final size:66
Alignment explanation
Indices: 2843--2983 Score: 259
Period size: 66 Copynumber: 2.2 Consensus size: 66
2833 TGCTTCTAAC
2843 CTAA-CTA-CCGGTGCATAAGTTTCATCATAGTCTATACCTTCCTCTTGGCGATATCCTTTGGCA
1 CTAATCTAGCCGGTGCATAAGTTTCATCATAGTCTATACCTTCCTCTTGGCGATATCCTTTGGCA
2906 A
66 A
*
2907 CTAATCTAGCCGGTGCATAAGTTTCATCATAGTCTATACCTTCCTCTTGGCGATATCCTTTGGGA
1 CTAATCTAGCCGGTGCATAAGTTTCATCATAGTCTATACCTTCCTCTTGGCGATATCCTTTGGCA
2972 A
66 A
2973 CTAATCTAGCC
1 CTAATCTAGCC
2984 TTGTTTCTAA
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
64 4 0.05
65 3 0.04
66 67 0.91
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (66 bp):
CTAATCTAGCCGGTGCATAAGTTTCATCATAGTCTATACCTTCCTCTTGGCGATATCCTTTGGCA
A
Found at i:7087 original size:19 final size:19
Alignment explanation
Indices: 7036--7088 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
7026 AAAAAAATAA
*
7036 AAAATATTAAAA-ATTTCG
1 AAAATATAAAAATATTTCG
*
7054 AAAATGTAAAAAATATTTCG
1 AAAATAT-AAAAATATTTCG
7074 AAAATATAAAAATAT
1 AAAATATAAAAATAT
7089 ATTTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.20
19 12 0.40
20 12 0.40
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (19 bp):
AAAATATAAAAATATTTCG
Found at i:7090 original size:21 final size:20
Alignment explanation
Indices: 7044--7092 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
7034 AAAAAATATT
*
7044 AAAA-ATTTCGAAAATGTAA
1 AAAATATTTCGAAAATATAA
7063 AAAATATTTCGAAAATATAA
1 AAAATATTTCGAAAATATAA
7083 AAATATATTT
1 AAA-ATATTT
7093 AAAAATTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 4 0.15
20 17 0.63
21 6 0.22
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAATATTTCGAAAATATAA
Found at i:7097 original size:20 final size:20
Alignment explanation
Indices: 7017--7098 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 20
7007 GAAAATCAAA
7017 TTCAAAAATA-AAAAAATA-
1 TTCAAAAATATAAAAAATAT
*
7035 ---AAAAATAT-TAAAA-AT
1 TTCAAAAATATAAAAAATAT
* *
7050 TTCGAAAATGTAAAAAATAT
1 TTCAAAAATATAAAAAATAT
*
7070 TTCGAAAATATAAAAATATAT
1 TTCAAAAATATAAAAA-ATAT
7091 TT-AAAAAT
1 TTCAAAAAT
7099 TTGAAATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 1 0.02
15 11 0.22
18 6 0.12
19 4 0.08
20 22 0.44
21 6 0.12
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (20 bp):
TTCAAAAATATAAAAAATAT
Found at i:8580 original size:15 final size:15
Alignment explanation
Indices: 8531--8587 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 15
8521 TTAAATCATT
*
8531 TTTATTTTTTTTGTAA
1 TTTATTTTTTAT-TAA
8547 TTTATTTATTATATTTTAA
1 TTTATTT-TT-TA--TTAA
8566 TTTATTTTTTATTAA
1 TTTATTTTTTATTAA
8581 TTT-TTTT
1 TTTATTTT
8588 GCCCTTGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 4 0.11
15 7 0.19
16 7 0.19
17 4 0.11
18 3 0.08
19 10 0.28
20 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTATTTTTTATTAA
Found at i:8691 original size:6 final size:6
Alignment explanation
Indices: 8669--8777 Score: 73
Period size: 6 Copynumber: 18.3 Consensus size: 6
8659 CTTTTTTTTT
* * * * *
8669 TTTTAA TTTCAA ATTTAC TTTTAA TTTTAA TTCTAA ATTTAA TTTTCAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT-AA
* * * * *
8718 -TTTCA -TTTAA TTTTCA TTTTAA TTGT-A TTTGAAA TTTTAA TTTCAAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT-TAA TTTTAA TTT-TAA
8765 TTTTAA -TTTAA TT
1 TTTTAA TTTTAA TT
8778 ATAAATAAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
5 13 0.17
6 53 0.69
7 11 0.14
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTTAA
Found at i:9127 original size:24 final size:24
Alignment explanation
Indices: 9073--9127 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
9063 ATTTAAATAA
*
9073 AATTTAAAATTTAAAATTTCATATC
1 AATTT-AAATTTAAAATTTCAAATC
* *
9098 ATTTTAAATTT-CAATTTCAAATTC
1 AATTTAAATTTAAAATTTCAAA-TC
9122 AATTTA
1 AATTTA
9128 CACTAGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTTAAATTTAAAATTTCAAATC
Found at i:9397 original size:41 final size:41
Alignment explanation
Indices: 9351--9438 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
9341 AATATAAACT
*
9351 TGTATAATTTGTATACTTTTATAATTTTACAACGTTTTGTA
1 TGTATAATTTGTATACTTTTATAACTTTACAACGTTTTGTA
9392 TGTATAATTTGTATACTTTTATAACTTTACAACGTTTTGTA
1 TGTATAATTTGTATACTTTTATAACTTTACAACGTTTTGTA
9433 TGTATA
1 TGTATA
9439 CTCGTGGACA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (41 bp):
TGTATAATTTGTATACTTTTATAACTTTACAACGTTTTGTA
Found at i:12251 original size:2 final size:2
Alignment explanation
Indices: 12244--12274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12234 AGTAGACAAT
12244 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
12275 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12652 original size:48 final size:48
Alignment explanation
Indices: 12581--12678 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
12571 GCTGTCTTCT
12581 TATTATTTAACTGATCGAATGAAGTGATTGTTTAAAACTAAATTTAAC
1 TATTATTTAACTGATCGAATGAAGTGATTGTTTAAAACTAAATTTAAC
12629 TATTATTTAACTGATCGAATGAAGTGATTGTTTAAAACTAAATTTAAC
1 TATTATTTAACTGATCGAATGAAGTGATTGTTTAAAACTAAATTTAAC
12677 TA
1 TA
12679 AATAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (48 bp):
TATTATTTAACTGATCGAATGAAGTGATTGTTTAAAACTAAATTTAAC
Found at i:13530 original size:25 final size:25
Alignment explanation
Indices: 13502--13565 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
13492 AGTTGGATCC
13502 AAATTAAATTCTAAAAAAATAATTA
1 AAATTAAATTCTAAAAAAATAATTA
13527 AAATTAAATTCTAAAAAAATAATTA
1 AAATTAAATTCTAAAAAAATAATTA
13552 AAATTAAA-TCTAAA
1 AAATTAAATTCTAAA
13566 CAATAATACC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 6 0.15
25 33 0.85
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATTAAATTCTAAAAAAATAATTA
Found at i:14405 original size:13 final size:13
Alignment explanation
Indices: 14387--14411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14377 TTATTCAACT
14387 TAAATAATTTTTG
1 TAAATAATTTTTG
14400 TAAATAATTTTT
1 TAAATAATTTTT
14412 TTCGGATCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TAAATAATTTTTG
Found at i:16650 original size:62 final size:62
Alignment explanation
Indices: 16579--16696 Score: 236
Period size: 62 Copynumber: 1.9 Consensus size: 62
16569 AGTAGTAGTA
16579 CTACTAATCAAATTCCAGAAAAGCAGAAAATTATTCTCATTGATATTCTTGATTTTGTACTG
1 CTACTAATCAAATTCCAGAAAAGCAGAAAATTATTCTCATTGATATTCTTGATTTTGTACTG
16641 CTACTAATCAAATTCCAGAAAAGCAGAAAATTATTCTCATTGATATTCTTGATTTT
1 CTACTAATCAAATTCCAGAAAAGCAGAAAATTATTCTCATTGATATTCTTGATTTT
16697 ATTCTATCCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (62 bp):
CTACTAATCAAATTCCAGAAAAGCAGAAAATTATTCTCATTGATATTCTTGATTTTGTACTG
Found at i:27759 original size:17 final size:17
Alignment explanation
Indices: 27738--27793 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
27728 TGAAAATTGT
27738 ATTTATTTTAAAATTAA
1 ATTTATTTTAAAATTAA
*
27755 GTTTA-TTTAAAATTTAA
1 ATTTATTTTAAAA-TTAA
* *
27772 ATTTATTATAAATTTAA
1 ATTTATTTTAAAATTAA
27789 ATTTA
1 ATTTA
27794 AAATGTCCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.21
17 21 0.64
18 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTATTTTAAAATTAA
Found at i:27857 original size:15 final size:15
Alignment explanation
Indices: 27837--27917 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
27827 ATCAAAACGA
*
27837 CCCAATTACAGATGG
1 CCCAATTACAAATGG
27852 CCCAATTACAAATGG
1 CCCAATTACAAATGG
*
27867 CCCAATT-CTAAACGG
1 CCCAATTAC-AAATGG
* * * **
27882 TCTCAATTATAGATAA
1 -CCCAATTACAAATGG
27898 CCCAATTACAAATGG
1 CCCAATTACAAATGG
27913 CCCAA
1 CCCAA
27918 GATTCCAAAC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
14 1 0.02
15 41 0.82
16 8 0.16
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.22
Consensus pattern (15 bp):
CCCAATTACAAATGG
Found at i:28428 original size:15 final size:15
Alignment explanation
Indices: 28391--28432 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
28381 TTTCCTTTAT
*
28391 TAATAATAATAATTG
1 TAATAATAATAATAG
*
28406 T-TTAAATAATAATAG
1 TAAT-AATAATAATAG
28421 TAATAATAATAA
1 TAATAATAATAA
28433 CATTAATGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:28507 original size:25 final size:26
Alignment explanation
Indices: 28462--28514 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
28452 AAACGAACGG
28462 TTTTCTTAATAATAATTAATAATAAA
1 TTTTCTTAATAATAATTAATAATAAA
*
28488 TTTT-TTAATTAATAA-TAATAATGAA
1 TTTTCTTAA-TAATAATTAATAATAAA
28513 TT
1 TT
28515 AGATATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTTCTTAATAATAATTAATAATAAA
Found at i:28804 original size:10 final size:10
Alignment explanation
Indices: 28789--28821 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28779 ACGTTGCTTA
28789 AAAAAGAAAG
1 AAAAAGAAAG
28799 AAAAAGAAA-
1 AAAAAGAAAG
28808 AAAAAGGAAAG
1 AAAAA-GAAAG
28819 AAA
1 AAA
28822 GGAGAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 13 0.62
11 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Done.