Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012575.1 Kokia drynarioides strain JFW-HI SEQ_127584, 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: 55021
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2856 original size:19 final size:19
Alignment explanation
Indices: 2821--2858 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2811 GATCATTATT
*
2821 ATTTAAAATGTTAAGTAAA
1 ATTTAAAAGGTTAAGTAAA
2840 ATTTAAAAGGATT-AGTAAA
1 ATTTAAAAGG-TTAAGTAAA
2859 TTTCGAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (19 bp):
ATTTAAAAGGTTAAGTAAA
Found at i:7875 original size:31 final size:29
Alignment explanation
Indices: 7840--7911 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 29
7830 TTTGTTTAGT
7840 ATTTATTATTTAAAATT-ATTTGTTTTATTTA
1 ATTTATTATTT-AAATTGATTTG--TTATTTA
7871 ATTTAATT-TTT-AATTGATTTGTTATTTA
1 ATTT-ATTATTTAAATTGATTTGTTATTTA
*
7899 ATATTTTTATTTA
1 AT-TTATTATTTA
7912 GTTGAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
28 11 0.31
29 9 0.26
30 5 0.14
31 7 0.20
32 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (29 bp):
ATTTATTATTTAAATTGATTTGTTATTTA
Found at i:8034 original size:5 final size:5
Alignment explanation
Indices: 8024--8054 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
8014 TAAATTTAAA
8024 TTTAT TTTAT TTTAT TTTAT TTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
8055 CATTAGTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:9318 original size:18 final size:17
Alignment explanation
Indices: 9277--9323 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
9267 ATCAACTTAC
9277 TAAACAAATAAATTTAT
1 TAAACAAATAAATTTAT
* *
9294 GATAACAAATCAATTATAT
1 TA-AACAAATAAATT-TAT
9313 TAAAC-AATAAA
1 TAAACAAATAAA
9324 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (17 bp):
TAAACAAATAAATTTAT
Found at i:9439 original size:4 final size:4
Alignment explanation
Indices: 9432--9478 Score: 67
Period size: 4 Copynumber: 11.0 Consensus size: 4
9422 CCTCTCCTTC
9432 TTCT TTCT TTCT TTCT TTCTT TTCT TTCTT TTCT TTCTT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTC-T TTCT TTC-T TTCT TTCT
9479 ACTTGATGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
4 28 0.70
5 12 0.30
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:9457 original size:9 final size:9
Alignment explanation
Indices: 9435--9478 Score: 81
Period size: 9 Copynumber: 5.0 Consensus size: 9
9425 CTCCTTCTTC
9435 TTTCTTTC-
1 TTTCTTTCT
9443 TTTCTTTCT
1 TTTCTTTCT
9452 TTTCTTTCT
1 TTTCTTTCT
9461 TTTCTTTCT
1 TTTCTTTCT
9470 TTTCTTTCT
1 TTTCTTTCT
9479 ACTTGATGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:9457 original size:13 final size:13
Alignment explanation
Indices: 9432--9478 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
9422 CCTCTCCTTC
9432 TTCTTTCTTTC-T
1 TTCTTTCTTTCTT
9444 TTCTTTCTTT-TCT
1 TTCTTTCTTTCT-T
9457 TTCTTTTCTTTCTT
1 TTC-TTTCTTTCTT
9471 TTCTTTCT
1 TTCTTTCT
9479 ACTTGATGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.32
13 9 0.29
14 11 0.35
15 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTCTTTCTT
Found at i:15892 original size:42 final size:42
Alignment explanation
Indices: 15833--15917 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
15823 ATGATGGGGT
15833 AACTCGGTGGCTCGATTAGGTTGTCAACAGATTTAGCGGCTA
1 AACTCGGTGGCTCGATTAGGTTGTCAACAGATTTAGCGGCTA
*
15875 AACTCGGTGGCTCGATTAGGTTGTCAACAGATTTAGTGGCTA
1 AACTCGGTGGCTCGATTAGGTTGTCAACAGATTTAGCGGCTA
15917 A
1 A
15918 CTTTTCTATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (42 bp):
AACTCGGTGGCTCGATTAGGTTGTCAACAGATTTAGCGGCTA
Found at i:25839 original size:14 final size:14
Alignment explanation
Indices: 25820--25847 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25810 GGGAAAAAAC
25820 ATGTCACAGCGCAA
1 ATGTCACAGCGCAA
25834 ATGTCACAGCGCAA
1 ATGTCACAGCGCAA
25848 TTAACCCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (14 bp):
ATGTCACAGCGCAA
Found at i:27327 original size:3 final size:3
Alignment explanation
Indices: 27319--27343 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27309 GCAAGGAGAT
27319 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
27344 AGAAAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:34139 original size:11 final size:10
Alignment explanation
Indices: 34123--34160 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
34113 TTCATGCTAT
34123 TTTTTATGAA
1 TTTTTATGAA
34133 CTTTTTAT-AA
1 -TTTTTATGAA
*
34143 TTTTTTTGAA
1 TTTTTATGAA
34153 TTTTTATG
1 TTTTTATG
34161 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 6 0.25
10 11 0.46
11 7 0.29
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.66
Consensus pattern (10 bp):
TTTTTATGAA
Found at i:36703 original size:40 final size:40
Alignment explanation
Indices: 36656--36737 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
36646 AAATATGTTT
36656 ATTATGTCTCTTTTGCGATTACTTTATAACTAATGTTCTC
1 ATTATGTCTCTTTTGCGATTACTTTATAACTAATGTTCTC
*
36696 ATTATGTCTCTTTTGCTATTACTTTATAACTAATGTTCTC
1 ATTATGTCTCTTTTGCGATTACTTTATAACTAATGTTCTC
36736 AT
1 AT
36738 GAAACAGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTATGTCTCTTTTGCGATTACTTTATAACTAATGTTCTC
Found at i:37147 original size:28 final size:28
Alignment explanation
Indices: 37079--37158 Score: 74
Period size: 31 Copynumber: 2.7 Consensus size: 28
37069 AAAATTATTA
* *
37079 TTTTAATTTTTTAAAAAATTGTTTAGACTT
1 TTTTAA-TTTTTAAAAAATT-TATAGAATT
37109 TTTTAAAATTTTTAAAAAATTTATA-AATAT
1 TTTT--AATTTTTAAAAAATTTATAGAAT-T
37139 TTTTAA-TTTTAAAAGAATTT
1 TTTTAATTTTTAAAA-AATTT
37159 TTCAAAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
27 8 0.18
28 7 0.16
29 2 0.05
30 12 0.27
31 13 0.30
32 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (28 bp):
TTTTAATTTTTAAAAAATTTATAGAATT
Found at i:37800 original size:60 final size:60
Alignment explanation
Indices: 37721--37871 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
37711 GTAAATCATC
* ** * *
37721 ATTTAAACATGTTTGAAAAAATTTAATCTTTATTTGTACACTTTAAAAAATATGAAATTTTT
1 ATTTGAACAT-TTT-AAAAAATTTAATCTTTATTTAAACACTTTAAAAAAGATGAAATATTT
* * * * * *
37783 ATTTGAACATTTTAAAAAATTTGACCTTTGTTTAAACACTTTTATAAAGATTAAATATTT
1 ATTTGAACATTTTAAAAAATTTAATCTTTATTTAAACACTTTAAAAAAGATGAAATATTT
* *
37843 ATTTG-ACTATTCTAAAAATTTTAATCTTT
1 ATTTGAAC-ATTTTAAAAAATTTAATCTTT
37872 TATAAGTAAT
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
59 2 0.03
60 59 0.81
61 3 0.04
62 9 0.12
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (60 bp):
ATTTGAACATTTTAAAAAATTTAATCTTTATTTAAACACTTTAAAAAAGATGAAATATTT
Found at i:39711 original size:18 final size:17
Alignment explanation
Indices: 39669--39719 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
39659 TCTATTTTTG
*
39669 AAAATTATAAAA-ATTCA
1 AAAATT-TAAAATTTTCA
39686 AAAGATTTAAAATTTTCA
1 AAA-ATTTAAAATTTTCA
39704 TAAAATTTAAAATTTT
1 -AAAATTTAAAATTTT
39720 TGTTTTATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.27
18 19 0.63
19 3 0.10
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
AAAATTTAAAATTTTCA
Found at i:39921 original size:42 final size:42
Alignment explanation
Indices: 39873--39954 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
39863 TTTTTTTACA
39873 AAATTATGAAAATTTCAAAAACATTTAATTATAAACAAACTC
1 AAATTATGAAAATTTCAAAAACATTTAATTATAAACAAACTC
* * *
39915 AAATTATGAAAATTTCAGAAACCTTTAATTCTAAACAAAC
1 AAATTATGAAAATTTCAAAAACATTTAATTATAAACAAAC
39955 GCATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (42 bp):
AAATTATGAAAATTTCAAAAACATTTAATTATAAACAAACTC
Found at i:41535 original size:19 final size:20
Alignment explanation
Indices: 41511--41555 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
41501 ATAAAGCTTG
*
41511 GAATTTTTATAAAT-ATTTT
1 GAATTTTTAAAAATGATTTT
41530 GAA-TTTTAAAAATGATTTT
1 GAATTTTTAAAAATGATTTT
41549 -AATTTTT
1 GAATTTTT
41556 TTTGTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
GAATTTTTAAAAATGATTTT
Found at i:41536 original size:18 final size:18
Alignment explanation
Indices: 41515--41554 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41505 AGCTTGGAAT
*
41515 TTTTATAAAT-ATTTTGAA
1 TTTTAAAAATGATTTT-AA
41533 TTTTAAAAATGATTTTAA
1 TTTTAAAAATGATTTTAA
41551 TTTT
1 TTTT
41555 TTTTGTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTAAAAATGATTTTAA
Found at i:43117 original size:4 final size:4
Alignment explanation
Indices: 43108--43133 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
43098 CCCTGTACCT
43108 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
43134 TATAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:44336 original size:40 final size:40
Alignment explanation
Indices: 44286--44363 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
44276 CGTTGCCAAA
*
44286 TTTTTTTCTAAACCAATGGTGGTGACACAAATAGCAATTT
1 TTTTTTTCTAAACCAATGGTGATGACACAAATAGCAATTT
*
44326 TTTTTTTCTAAACCAATGGTGATGACACCAATAGCAAT
1 TTTTTTTCTAAACCAATGGTGATGACACAAATAGCAAT
44364 GATGTCACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (40 bp):
TTTTTTTCTAAACCAATGGTGATGACACAAATAGCAATTT
Found at i:47973 original size:41 final size:42
Alignment explanation
Indices: 47898--47978 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 42
47888 TTCCCCCTTT
*
47898 TTTTTAAGGAAAATAAATCATTAATTTTTGGAATTTAAATTC
1 TTTTTAAGGAAAATAAATCATTAATTTTTGGAATTGAAATTC
47940 TTTTT-AGGAAAATAAATCATTAA-TTTTGAGAATTGAAAT
1 TTTTTAAGGAAAATAAATCATTAATTTTTG-GAATTGAAAT
47979 AATAGTGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
40 5 0.14
41 27 0.73
42 5 0.14
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (42 bp):
TTTTTAAGGAAAATAAATCATTAATTTTTGGAATTGAAATTC
Found at i:48171 original size:14 final size:14
Alignment explanation
Indices: 48152--48178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48142 TACTTAATTG
48152 AATAAAAAAACAAT
1 AATAAAAAAACAAT
48166 AATAAAAAAACAA
1 AATAAAAAAACAA
48179 AACTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.11
Consensus pattern (14 bp):
AATAAAAAAACAAT
Done.