Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014854.1 Kokia drynarioides strain JFW-HI SEQ_129897, 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: 15650
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9100 original size:6 final size:6
Alignment explanation
Indices: 9089--9116 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9079 TAAAGTATCG
9089 ATTTGT ATTTGT ATTTGT ATTTGT ATTT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTT
9117 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.14, T:0.68
Consensus pattern (6 bp):
ATTTGT
Found at i:9314 original size:25 final size:26
Alignment explanation
Indices: 9279--9328 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
9269 TTATTATTAT
9279 TATTTATATTTAGTTG-TTTATTTTGG
1 TATTTATATTTA-TTGATTTATTTTGG
*
9305 TATTTA-ATTTATTGATTTTTTTTG
1 TATTTATATTTATTGATTTATTTTG
9329 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (26 bp):
TATTTATATTTATTGATTTATTTTGG
Found at i:9434 original size:19 final size:19
Alignment explanation
Indices: 9378--9436 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
9368 ATCCCAATTA
9378 TTTTTATTGTTTATATTTGTT
1 TTTTTATT-TTTATATTT-TT
* *
9399 TGTTTA-TTTTAGCATTTTT
1 TTTTTATTTTTA-TATTTTT
*
9418 TTTTTATTTTTTTATTTTT
1 TTTTTATTTTTATATTTTT
9437 GTTTATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 17 0.55
20 9 0.29
21 5 0.16
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTATATTTTT
Found at i:9889 original size:23 final size:23
Alignment explanation
Indices: 9862--9923 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
9852 AATAATACTA
9862 TAATTATATTTTTATTGTGTT-AT
1 TAATT-TATTTTTATTGTGTTCAT
*
9885 TAATTGTA-TTTTATTGTTTTCAT
1 TAATT-TATTTTTATTGTGTTCAT
*
9908 TAAATTTATTTATATT
1 T-AATTTATTTTTATT
9924 CATATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 11 0.33
23 12 0.36
24 10 0.30
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (23 bp):
TAATTTATTTTTATTGTGTTCAT
Found at i:11560 original size:16 final size:18
Alignment explanation
Indices: 11532--11565 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11522 TTAGAATTGG
11532 ATTGAGAAAATT-ATTTA
1 ATTGAGAAAATTAATTTA
11549 ATTGAG-AAATTAATTTA
1 ATTGAGAAAATTAATTTA
11566 TTTAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTGAGAAAATTAATTTA
Found at i:13999 original size:193 final size:193
Alignment explanation
Indices: 13670--14054 Score: 725
Period size: 193 Copynumber: 2.0 Consensus size: 193
13660 ACGGCTTGTT
*
13670 ATGAGTCTTGATTGAATATGAAGACGAGACAAAATGAACTTCATATCAGGACTATTTTTGACATC
1 ATGAGTCTCGATTGAATATGAAGACGAGACAAAATGAACTTCATATCAGGACTATTTTTGACATC
* * *
13735 GAGAAGGAAAGTCCTTGTCTAGATTATTATTGGTAGACTAACGAAATTGGCTCATTTTATTCCGG
66 GAGAAGGAAAGTCCTTATCTAGATTATTATTGATAGACTAACGAAATTGGCTCATTTTATTCCAG
13800 TCAAAACGAATTACTCGTTTAAAAAGCTAGTTGAGTTGTATGTATCAGAGAATATCAGATTGA
131 TCAAAACGAATTACTCGTTTAAAAAGCTAGTTGAGTTGTATGTATCAGAGAATATCAGATTGA
*
13863 ATGAGTCTCGATTGAATATGAAGACGAGACAAAATGAACTTCATATCTGGACTATTTTTGACATC
1 ATGAGTCTCGATTGAATATGAAGACGAGACAAAATGAACTTCATATCAGGACTATTTTTGACATC
13928 GAGAAGGAAAGTCCTTATCTAGATTATTATTGATAGACTAACGAAATTGGCTCATTTTATTCCAG
66 GAGAAGGAAAGTCCTTATCTAGATTATTATTGATAGACTAACGAAATTGGCTCATTTTATTCCAG
13993 TCAAAACGAATTACTCGTTTAAAAAGCTAGTTGAGTTGTATGTATCAGAGAATATCAGATTG
131 TCAAAACGAATTACTCGTTTAAAAAGCTAGTTGAGTTGTATGTATCAGAGAATATCAGATTG
14055 CACAGAGTGT
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 187 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (193 bp):
ATGAGTCTCGATTGAATATGAAGACGAGACAAAATGAACTTCATATCAGGACTATTTTTGACATC
GAGAAGGAAAGTCCTTATCTAGATTATTATTGATAGACTAACGAAATTGGCTCATTTTATTCCAG
TCAAAACGAATTACTCGTTTAAAAAGCTAGTTGAGTTGTATGTATCAGAGAATATCAGATTGA
Found at i:14902 original size:17 final size:17
Alignment explanation
Indices: 14874--14947 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
14864 TTGGAAATTG
14874 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
14890 AGTTTATTTTAAAATTTA
1 AATTTATTTT-AAATTTA
* *
14908 AATTTATTTGAAATCTA
1 AATTTATTTTAAATTTA
* *
14925 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
14942 AATTTA
1 AATTTA
14948 GAAAGTCCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
16 5 0.10
17 28 0.58
18 15 0.31
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:14913 original size:34 final size:34
Alignment explanation
Indices: 14868--14947 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
14858 GACTTATTGG
* * * *
14868 AAATTGAATTTATTT-AAATTTAAGTTTATTTTA
1 AAATTAAATTTATTTGAAATCTAAATTTATTATA
14901 AAATTTAAATTTATTTGAAATCTAAATTTATTATA
1 AAA-TTAAATTTATTTGAAATCTAAATTTATTATA
14936 AAATTAAATTTA
1 AAATTAAATTTA
14948 GAAAGTCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
33 3 0.07
34 20 0.49
35 18 0.44
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (34 bp):
AAATTAAATTTATTTGAAATCTAAATTTATTATA
Found at i:14967 original size:13 final size:14
Alignment explanation
Indices: 14949--14989 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
14939 TTAAATTTAG
14949 AAAGTCCAATTAA-
1 AAAGTCCAATTAAC
14962 AAAGTCCAA--AAC
1 AAAGTCCAATTAAC
14974 AAAGTCCAATT-AC
1 AAAGTCCAATTAAC
14987 AAA
1 AAA
14990 TGRCCCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 14 0.56
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAGTCCAATTAAC
Found at i:15003 original size:15 final size:15
Alignment explanation
Indices: 14979--15049 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
14969 AAAACAAAGT
*
14979 CCAATTACAAATGRC
1 CCAATTACAAATGGC
*
14994 CCAATAACAAATGGC
1 CCAATTACAAATGGC
*
15009 CCAATTACAGATGGC
1 CCAATTACAAATGGC
*
15024 CCAAATACAAATGGC
1 CCAATTACAAATGGC
15039 CCAATTACAAA
1 CCAATTACAAA
15050 CTACCCAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.17
Consensus pattern (15 bp):
CCAATTACAAATGGC
Found at i:15057 original size:30 final size:31
Alignment explanation
Indices: 14979--15058 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
14969 AAAACAAAGT
*
14979 CCAATTACAAATGRCCC-AATAACAAATGGC
1 CCAATTACAAATGACCCAAATAACAAATGGC
* *
15009 CCAATTACAGATGGCCCAAAT-ACAAATGGC
1 CCAATTACAAATGACCCAAATAACAAATGGC
15039 CCAATTACAAACT-ACCCAAA
1 CCAATTACAAA-TGACCCAAA
15059 AGCCCAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 40 0.91
31 4 0.09
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.16
Consensus pattern (31 bp):
CCAATTACAAATGACCCAAATAACAAATGGC
Done.