Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015034.1 Kokia drynarioides strain JFW-HI SEQ_130078, 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: 43228
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:2241 original size:19 final size:19
Alignment explanation
Indices: 2217--2261 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2207 TATATTATTT
2217 TAAAATCAA-AATAAAATTA
1 TAAAAT-AAGAATAAAATTA
* *
2236 TAAAATAAGGATTAAATTA
1 TAAAATAAGAATAAAATTA
2255 TAAAATA
1 TAAAATA
2262 TATAAAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAAATAAGAATAAAATTA
Found at i:2714 original size:3 final size:3
Alignment explanation
Indices: 2706--2734 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2696 AACAAAAACT
2706 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
2735 TTATTGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:15782 original size:21 final size:23
Alignment explanation
Indices: 15747--15789 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
15737 GGGTAAAATT
15747 AATTATATAATAAAATTATAAAA
1 AATTATATAATAAAATTATAAAA
*
15770 AATTA-AT-ATAAAATTTTAAA
1 AATTATATAATAAAATTATAAA
15790 TATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTATATAATAAAATTATAAAA
Found at i:21033 original size:37 final size:37
Alignment explanation
Indices: 20981--21058 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 37
20971 GACCCATTGG
20981 TTAAATTTTACCAATTAAGTACAAATTTTAAGCCTTT
1 TTAAATTTTACCAATTAAGTACAAATTTTAAGCCTTT
* * *
21018 TTAATTTTTACCAATTAAGTATAAATTTTAAGCTTTT
1 TTAAATTTTACCAATTAAGTACAAATTTTAAGCCTTT
21055 TTAA
1 TTAA
21059 CTCTTTGGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (37 bp):
TTAAATTTTACCAATTAAGTACAAATTTTAAGCCTTT
Found at i:23054 original size:16 final size:16
Alignment explanation
Indices: 23033--23075 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
23023 ATTATACATG
*
23033 AATTTTGATTTTGTGT
1 AATTTTGATTTTGTGA
23049 AATTTT-A-TTTGTGA
1 AATTTTGATTTTGTGA
*
23063 AATGTTGATTTTG
1 AATTTTGATTTTG
23076 GTTCAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (16 bp):
AATTTTGATTTTGTGA
Found at i:34569 original size:24 final size:22
Alignment explanation
Indices: 34542--34587 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
34532 ATATAAATTT
34542 GCTTATAGTGGAGTTAAACTCATC
1 GCTTATAGT-GAGTTAAAC-CATC
* *
34566 GCTTCTAGTGATTTAAACCATC
1 GCTTATAGTGAGTTAAACCATC
34588 AATTGACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (22 bp):
GCTTATAGTGAGTTAAACCATC
Found at i:35955 original size:21 final size:21
Alignment explanation
Indices: 35931--35975 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
35921 TTTTTATTAA
*
35931 TATGATTATTT-ATATTAATAT
1 TATGATT-TTTGATACTAATAT
*
35952 TATGATTTTTGTTACTAATAT
1 TATGATTTTTGATACTAATAT
35973 TAT
1 TAT
35976 TTTCGTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
TATGATTTTTGATACTAATAT
Found at i:35977 original size:18 final size:18
Alignment explanation
Indices: 35916--35978 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 18
35906 TTTCCACTAT
35916 TATTATTTTTATTAAT-A
1 TATTATTTTTATTAATAA
* *
35933 TGATTATTTATATTAATAT
1 T-ATTATTTTTATTAATAA
* * *
35952 TATGATTTTTGTTACTAA
1 TATTATTTTTATTAATAA
35970 TATTATTTT
1 TATTATTTT
35979 CGTTAGGATC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTATTTTTATTAATAA
Found at i:38342 original size:17 final size:18
Alignment explanation
Indices: 38307--38343 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38297 ACTAAATTTG
38307 ATAGAAAATATACAAAAA
1 ATAGAAAATATACAAAAA
38325 ATAGAAACAT-TA-AAAAA
1 ATAGAAA-ATATACAAAAA
38342 AT
1 AT
38344 CCAAGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 9 0.50
19 2 0.11
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (18 bp):
ATAGAAAATATACAAAAA
Done.