Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015248.1 Kokia drynarioides strain JFW-HI SEQ_130293, 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: 61452
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 228 characters in sequence are not A, C, G, or T
Found at i:2255 original size:19 final size:21
Alignment explanation
Indices: 2211--2262 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
2201 AAAATTTGAG
*
2211 TTAATCTTATTCAATATTTAAT
1 TTAATATT-TTCAATATTTAAT
2233 TTAAT-TTTTCAAT-TTT-AT
1 TTAATATTTTCAATATTTAAT
2251 ATTAATATTTTC
1 -TTAATATTTTC
2263 TACAATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 8 0.29
20 11 0.39
21 2 0.07
22 5 0.18
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATATTTTCAATATTTAAT
Found at i:2545 original size:27 final size:26
Alignment explanation
Indices: 2472--2563 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 26
2462 TGTACGCTGC
* *
2472 CAGGTAGGCACATTTGGTGCTGCCTGG
1 CAGGTAGGCAC-TTTGGTGCCGCCTGT
** *
2499 CAGGTAGGCACCACTAGTGCCGCCTGT
1 CAGGTAGGCA-CTTTGGTGCCGCCTGT
*
2526 CAGGTAGGCATCTTTGGTGCCGCCTAT
1 CAGGTAGGCA-CTTTGGTGCCGCCTGT
*
2553 CAGATAGGCAC
1 CAGGTAGGCAC
2564 CACCCCTTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
26 1 0.02
27 51 0.96
28 1 0.02
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (26 bp):
CAGGTAGGCACTTTGGTGCCGCCTGT
Found at i:17203 original size:26 final size:26
Alignment explanation
Indices: 17174--17224 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
17164 TTTTATTTTA
* *
17174 TTTTAGTATTTAATATTTTTATATAT
1 TTTTAGTATTAAAAATTTTTATATAT
**
17200 TTTTTTTATTAAAAATTTTTATATA
1 TTTTAGTATTAAAAATTTTTATATA
17225 GACATCTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTAGTATTAAAAATTTTTATATAT
Found at i:22152 original size:10 final size:10
Alignment explanation
Indices: 22137--22170 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
22127 AGTGCCCTAC
*
22137 ATATATGTGT
1 ATATATGTAT
22147 ATATATGTAT
1 ATATATGTAT
*
22157 ATGTATGTAT
1 ATATATGTAT
22167 ATAT
1 ATAT
22171 TAAAGCAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (10 bp):
ATATATGTAT
Found at i:29726 original size:60 final size:60
Alignment explanation
Indices: 29637--29751 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
29627 GACACTTTTT
* * *
29637 CCTAATTTCGTACCTAAACTTAATACTTTTTCTTAAGTTGGTGCTTAAACTTTTTGGGGG
1 CCTAATTTCGTACCTAAACTTAATACTTTTTCCTAAGTTAGTACTTAAACTTTTTGGGGG
* * * * *
29697 CCTAATTTGGTATCTAAACTTGACT-CTTTTTCCTAATTTAGTACTTAATCTTTTT
1 CCTAATTTCGTACCTAAACTT-AATACTTTTTCCTAAGTTAGTACTTAAACTTTTT
29752 TTTGTTCGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (60 bp):
CCTAATTTCGTACCTAAACTTAATACTTTTTCCTAAGTTAGTACTTAAACTTTTTGGGGG
Found at i:30685 original size:30 final size:29
Alignment explanation
Indices: 30640--30734 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 29
30630 AAAATTTTTA
*
30640 AATTTAA-GATTAAAAATAATAAAAATAT
1 AATTTAATTATTAAAAATAATAAAAATAT
* *
30668 AATTTAATCTCTTAAAAAT--TATAAATA-
1 AATTTAAT-TATTAAAAATAATAAAAATAT
*
30695 AA-TAAATTATT-AAAATAATAAAAATAT
1 AATTTAATTATTAAAAATAATAAAAATAT
*
30722 ATTTTAATT-TTAA
1 AATTTAATTATTAA
30735 CTCCTAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.10
25 3 0.06
26 11 0.21
27 5 0.10
28 20 0.38
30 8 0.15
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (29 bp):
AATTTAATTATTAAAAATAATAAAAATAT
Found at i:40683 original size:6 final size:6
Alignment explanation
Indices: 40672--40702 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40662 AAGCTACTCA
40672 AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG A
1 AGCTTG AGCTTG AGCTTG AGCTTG AGCTTG A
40703 TTAAATTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
AGCTTG
Found at i:47098 original size:158 final size:156
Alignment explanation
Indices: 46801--47214 Score: 454
Period size: 158 Copynumber: 2.6 Consensus size: 156
46791 AAAGATACCA
* * * *
46801 TTTTTTTAATTTGTAGTCTAAACCTCAATTATCAATCTAAACAACATATAATATTTGGGTATGCG
1 TTTTTTTAATTTTTAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTT-GGTATG-G
* * * * * **
46866 ATTCAATTCTCATTTTGCGTATGGAACAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGA
64 GTTCGATCCTCGTTCT-CGTATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGA
**
46931 CCTACAGAATGTGGAGGATTAAAT-TTTT
128 CCTACAGAATGCAGAGGATTAAATCTTTT
* *
46959 TTTTTTTAATTTTTAGGCTAAATCTCAATTATCTATGTAAACAACATATAATATCTTGGTATGGG
1 TTTTTTTAATTTTTAGACTAAATCTCAATTATCAATGTAAACAACATATAATAT-TTGGTATGGG
* * * * *
47024 TTCGATCCTCGTTCTCGATATGGAGTAGTTTTATAATTCGTGGTCAGTCTCTATCTTTTATTGGG
65 TTCGATCCTCGTTCTCG-TATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATC-TTTAATGGA
* * * *
47089 CTTATAGAATGCAGATGATTAGATCTTTT
128 CCTACAGAATGCAGAGGATTAAATCTTTT
* *
47118 TTATTTT-ATTTTGTAGACTAAATCTCAATTATCAATGTAAACGACATATAATATTTGGATATGG
1 TTTTTTTAATTTT-TAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTTGG-TATGG
* * * * *
47182 GTTCGTTCCTTGCTCTGGGTATGAAGTAGTTTT
64 GTTCGATCCTCGTTCT-CGTATGGAGTAGTTTT
47215 TTTTTTAATA
Statistics
Matches: 217, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
156 2 0.01
157 44 0.20
158 89 0.41
159 81 0.37
160 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (156 bp):
TTTTTTTAATTTTTAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTTGGTATGGGT
TCGATCCTCGTTCTCGTATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGACCT
ACAGAATGCAGAGGATTAAATCTTTT
Found at i:47170 original size:159 final size:155
Alignment explanation
Indices: 46804--47214 Score: 446
Period size: 159 Copynumber: 2.6 Consensus size: 155
46794 GATACCATTT
* * * * *
46804 TTTTAATTTGTAGTCTAAACCTCAATTATCAATCTAAACAACATATAATATTTGGGTATGCGATT
1 TTTTATTTTGTAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTT-GGTATG-GGTT
* * * * **
46869 CAATTCTCATTTTGCGTATGGAACAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGACCT
64 CGATCCTCGTTCT-CGTATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGACCT
** *
46934 ACAGAATGTGGAGGATTAAATTTTTTTT
128 ACAGAATGCAGAGGATTAAATTTTTTTA
* *
46962 TTTTAATTTT-TAGGCTAAATCTCAATTATCTATGTAAACAACATATAATATCTTGGTATGGGTT
1 TTTT-ATTTTGTAGACTAAATCTCAATTATCAATGTAAACAACATATAATAT-TTGGTATGGGTT
* * * * * *
47026 CGATCCTCGTTCTCGATATGGAGTAGTTTTATAATTCGTGGTCAGTCTCTATCTTTTATTGGGCT
64 CGATCCTCGTTCTCG-TATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATC-TTTAATGGACC
* * *
47091 TATAGAATGCAGATGATTAGATCTTTTTTA
127 TACAGAATGCAGAGGATTAAAT-TTTTTTA
*
47121 TTTTATTTTGTAGACTAAATCTCAATTATCAATGTAAACGACATATAATATTTGGATATGGGTTC
1 TTTTATTTTGTAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTTGG-TATGGGTTC
* * * * *
47186 GTTCCTTGCTCTGGGTATGAAGTAGTTTT
65 GATCCTCGTTCT-CGTATGGAGTAGTTTT
47215 TTTTTTAATA
Statistics
Matches: 213, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
156 2 0.01
157 44 0.21
158 81 0.38
159 85 0.40
160 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (155 bp):
TTTTATTTTGTAGACTAAATCTCAATTATCAATGTAAACAACATATAATATTTGGTATGGGTTCG
ATCCTCGTTCTCGTATGGAGTAGTTTTAAAATTCGTGGTCAATATCTATCTTTAATGGACCTACA
GAATGCAGAGGATTAAATTTTTTTA
Found at i:52515 original size:21 final size:22
Alignment explanation
Indices: 52480--52614 Score: 114
Period size: 23 Copynumber: 5.9 Consensus size: 22
52470 GCACGTCTCA
52480 TGCTCTCTGTTATTAGCAC-TGTG
1 TGCTCTCTG--ATTAGCACTTGTG
52503 TGCTCTCTGATTAGCACTTTGTG
1 TGCTCTCTGATTAGCAC-TTGTG
*
52526 TGCTCTCTGATTAGTACTTTGTG
1 TGCTCTCTGATTAGCAC-TTGTG
* * *
52549 TACTCTATGTTTAGCACTGTGTG
1 TGCTCTCTGATTAGCACT-TGTG
*
52572 TGCTCTCTG-TTGCCCAGCACTTATG
1 TGCTCTCTGATT----AGCACTTGTG
*
52597 TGCTCTCTG-TTAGTACTT
1 TGCTCTCTGATTAGCACTT
52615 TGGTACTCTG
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
21 14 0.15
22 3 0.03
23 59 0.61
25 14 0.15
26 6 0.06
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (22 bp):
TGCTCTCTGATTAGCACTTGTG
Found at i:52530 original size:46 final size:47
Alignment explanation
Indices: 52480--52582 Score: 131
Period size: 46 Copynumber: 2.2 Consensus size: 47
52470 GCACGTCTCA
* * *
52480 TGCTCTCTGTTATTAGCAC-TGTGTGCTCTCTGATTAGCACTTTGTG
1 TGCTCTCTGTTATTAGCACTTGTGTACTCTATGATTAGCACTGTGTG
* *
52526 TGCTCTCTG--ATTAGTACTTTGTGTACTCTATGTTTAGCACTGTGTG
1 TGCTCTCTGTTATTAGCAC-TTGTGTACTCTATGATTAGCACTGTGTG
52572 TGCTCTCTGTT
1 TGCTCTCTGTT
52583 GCCCAGCACT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 7 0.15
46 41 0.85
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (47 bp):
TGCTCTCTGTTATTAGCACTTGTGTACTCTATGATTAGCACTGTGTG
Done.