Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002995.1 Kokia drynarioides strain JFW-HI SEQ_115486, 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: 34239
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:495 original size:23 final size:23
Alignment explanation
Indices: 465--589 Score: 110
Period size: 23 Copynumber: 5.5 Consensus size: 23
455 ACGCTAGCGC
465 GCTTACTGTTTTGCACT-TCGTGT
1 GCTTACTGTTTTGCACTGT-GTGT
* *
488 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTTGCACTGTGTGT
* * * * *
511 GCCTACTGATTTGCGCTATGTGC
1 GCTTACTGTTTTGCACTGTGTGT
* *
534 GCCTACTG-ATTGCACTGTGTGT
1 GCTTACTGTTTTGCACTGTGTGT
* ** *
556 GCATACTGGATTGCACTGTGTAT
1 GCTTACTGTTTTGCACTGTGTGT
579 GCTTACTGTTT
1 GCTTACTGTTT
590 CCCCAGCACT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 17 0.20
23 66 0.79
24 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.42
Consensus pattern (23 bp):
GCTTACTGTTTTGCACTGTGTGT
Found at i:586 original size:45 final size:46
Alignment explanation
Indices: 468--586 Score: 109
Period size: 45 Copynumber: 2.6 Consensus size: 46
458 CTAGCGCGCT
* * * * *
468 TACTGTTTTGCACT-TCGTGTGCTTACTGTTTCGCACTTTGTGTGCC
1 TACTGATTTGCACTAT-GTATGCTTACTGATTCGCACTGTGTGTGCA
* ** *
514 TACTGATTTGCGCTATGTGCGCCTACTGATT-GCACTGTGTGTGCA
1 TACTGATTTGCACTATGTATGCTTACTGATTCGCACTGTGTGTGCA
*
559 TACTGGA-TTGCACTGTGTATGCTTACTG
1 TACT-GATTTGCACTATGTATGCTTACTG
587 TTTCCCCAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
45 32 0.54
46 26 0.44
47 1 0.02
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.40
Consensus pattern (46 bp):
TACTGATTTGCACTATGTATGCTTACTGATTCGCACTGTGTGTGCA
Found at i:1630 original size:17 final size:17
Alignment explanation
Indices: 1602--1676 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 17
1592 ATTTTAAAGT
* *
1602 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
1618 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
1636 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
1653 TTTAAATTTAGAAATAAA
1 TTTAAATTTA-AAATAAA
*
1671 TCTAAA
1 TTTAAA
1677 AATTAATCTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
16 3 0.06
17 31 0.63
18 15 0.31
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:2980 original size:22 final size:23
Alignment explanation
Indices: 2944--2986 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2934 TAATTCGATG
2944 ATTTAAATAAAAATTTCTAAATA
1 ATTTAAATAAAAATTTCTAAATA
* *
2967 ATTT-AATAATAATTTTTAAA
1 ATTTAAATAAAAATTTCTAAA
2987 CTTTTAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAAATAAAAATTTCTAAATA
Found at i:3140 original size:63 final size:63
Alignment explanation
Indices: 3067--3192 Score: 243
Period size: 63 Copynumber: 2.0 Consensus size: 63
3057 ACCACATAAT
*
3067 ATCTTTTATTTTAAGAAAATAAAGTTTTTTAATAATGGTTTTAGTATGGTCTACTTCTTCTTC
1 ATCTTTTATTTTAAGAAAATAAAGTTTTTTAATAATGGTTTTAGTATGGTCTACTTCCTCTTC
3130 ATCTTTTATTTTAAGAAAATAAAGTTTTTTAATAATGGTTTTAGTATGGTCTACTTCCTCTTC
1 ATCTTTTATTTTAAGAAAATAAAGTTTTTTAATAATGGTTTTAGTATGGTCTACTTCCTCTTC
3193 TCTGACCTCT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (63 bp):
ATCTTTTATTTTAAGAAAATAAAGTTTTTTAATAATGGTTTTAGTATGGTCTACTTCCTCTTC
Found at i:8139 original size:6 final size:6
Alignment explanation
Indices: 8128--8161 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
8118 AGCCAAGCAG
* *
8128 CAACAA CAACAA CAACTA CAACTA CAACTA CAAC
1 CAACTA CAACTA CAACTA CAACTA CAACTA CAAC
8162 GAAGGAGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.35, G:0.00, T:0.09
Consensus pattern (6 bp):
CAACTA
Found at i:11064 original size:2 final size:2
Alignment explanation
Indices: 11057--11088 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11047 TGATTTTCTC
11057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11089 TTGGAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13632 original size:24 final size:24
Alignment explanation
Indices: 13597--13651 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
13587 CGGTTGATAA
13597 TATTTTTCTGTTCTG-CTTAAATTT
1 TATTTTTCTGTTC-GACTTAAATTT
*
13621 TATTTTGT-TGTTCGATTTAAATTT
1 TATTTT-TCTGTTCGACTTAAATTT
*
13645 TTTTTTT
1 TATTTTT
13652 TTTTTGTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 2 0.07
24 24 0.89
25 1 0.04
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.67
Consensus pattern (24 bp):
TATTTTTCTGTTCGACTTAAATTT
Found at i:14006 original size:20 final size:20
Alignment explanation
Indices: 13981--14054 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 20
13971 ATTTTAAAAT
13981 TAAAAAATTAAAATATTATA
1 TAAAAAATTAAAATATTATA
** * *
14001 TAAAAACAGAAAAATATAAAAA
1 TAAAAA-ATTAAAATAT-TATA
14023 TAAATAAATAAATAAAATATTATA
1 TAAA-AAAT---TAAAATATTATA
14047 TAAAAAAT
1 TAAAAAAT
14055 CAAATTTTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.15
21 8 0.20
22 7 0.17
23 6 0.15
24 6 0.15
25 7 0.17
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (20 bp):
TAAAAAATTAAAATATTATA
Found at i:14102 original size:2 final size:2
Alignment explanation
Indices: 14095--14122 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14085 CTAAATTCTA
14095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14123 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14196 original size:16 final size:16
Alignment explanation
Indices: 14175--14206 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14165 AAATGCAATT
*
14175 TTTATATAATTTTTTA
1 TTTATATAATATTTTA
14191 TTTATATAATATTTTA
1 TTTATATAATATTTTA
14207 CCTTATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATATAATATTTTA
Found at i:14281 original size:29 final size:32
Alignment explanation
Indices: 14249--14317 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 32
14239 TTTTTAAACT
* *
14249 TTTTTAAAAC-TTTTTAAATGAT-T-TATATA
1 TTTTTAAAACATTTTAAAATAATATATATATA
**
14278 TTTTT-TTACATTTTAAAATAATATATATATA
1 TTTTTAAAACATTTTAAAATAATATATATATA
14309 TTTTTAAAA
1 TTTTTAAAA
14318 GTAATGCGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
28 2 0.07
29 15 0.50
30 1 0.03
31 11 0.37
32 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTTTAAAACATTTTAAAATAATATATATATA
Done.