Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015102.1 Kokia drynarioides strain JFW-HI SEQ_130146, 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: 783730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 366 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:695870 original size:15 final size:16
Alignment explanation
Indices: 695852--695881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
695842 CTTCTCTATT
695852 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
695867 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
695882 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:695874 original size:22 final size:22
Alignment explanation
Indices: 695846--695907 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
695836 CTTCGACTTC
695846 TCTATTTTCTATTT-CTTTTAAT
1 TCTATTTTCT-TTTACTTTTAAT
*
695868 TCTATTTTCTTTTATTTTTAAT
1 TCTATTTTCTTTTACTTTTAAT
* *
695890 TCT-GTTTCTTTTATTTTT
1 TCTATTTTCTTTTACTTTT
695908 CCTTAGATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (22 bp):
TCTATTTTCTTTTACTTTTAAT
Found at i:695897 original size:21 final size:22
Alignment explanation
Indices: 695861--695907 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
695851 TTTCTATTTC
*
695861 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
695883 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
695904 TTTT
1 TTTT
695908 CCTTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:697867 original size:19 final size:20
Alignment explanation
Indices: 697826--697878 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
697816 ATATATATAT
* *
697826 ATATATATAAATTATAAAAAA
1 ATATATCTAAA-TCTAAAAAA
*
697847 AT-TATCTAAATCTAAACAA
1 ATATATCTAAATCTAAAAAA
697866 ATAATATCTAAAT
1 AT-ATATCTAAAT
697879 TCAAATAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 11 0.41
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
ATATATCTAAATCTAAAAAA
Found at i:703016 original size:17 final size:18
Alignment explanation
Indices: 702984--703017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
702974 AAAAATTACT
*
702984 AGTTGTTTGCCTTGTTGG
1 AGTTGTATGCCTTGTTGG
703002 AGTTGTATG-CTTGTTG
1 AGTTGTATGCCTTGTTG
703018 TAGGCTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.32, T:0.50
Consensus pattern (18 bp):
AGTTGTATGCCTTGTTGG
Found at i:706138 original size:32 final size:30
Alignment explanation
Indices: 706082--706170 Score: 108
Period size: 32 Copynumber: 2.9 Consensus size: 30
706072 AAATTTTCTT
* *
706082 TCTGCATTTTGGATTTTCTCCAGATTTTGG
1 TCTGCACTTTGGATTTTCTTCAGATTTTGG
*
706112 TTTTGCACTTTGGGATTTTCTTCAGATTTTGG
1 -TCTGCACTTT-GGATTTTCTTCAGATTTTGG
* *
706144 TCTACTCTTTGGATTTTC-TCAGATTTT
1 TCTGCACTTTGGATTTTCTTCAGATTTT
706171 ATTTGGTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
29 9 0.18
30 8 0.16
31 15 0.29
32 19 0.37
ACGTcount: A:0.13, C:0.16, G:0.18, T:0.53
Consensus pattern (30 bp):
TCTGCACTTTGGATTTTCTTCAGATTTTGG
Found at i:708419 original size:8 final size:8
Alignment explanation
Indices: 708397--708430 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
708387 GAGATCATTC
*
708397 TACATACA
1 TACATATA
708405 TACATATA
1 TACATATA
708413 TACATATA
1 TACATATA
*
708421 TATATATA
1 TACATATA
708429 TA
1 TA
708431 TGTATGCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
TACATATA
Found at i:713640 original size:37 final size:35
Alignment explanation
Indices: 713582--713653 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
713572 CGATTCAGTT
713582 AAATTTAAAAAAAAAAATAATTCAATTAATGATTAA
1 AAATTTAAAAAAAAAAATAATTCAATTAATG-TTAA
** *
713618 AAATTTAAAAAATTTAATTAATTCAATTAATGTTAA
1 AAATTTAAAAAA-AAAAATAATTCAATTAATGTTAA
713654 TTCAAATAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 16 0.50
37 16 0.50
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATTTAAAAAAAAAAATAATTCAATTAATGTTAA
Found at i:732615 original size:17 final size:18
Alignment explanation
Indices: 732581--732619 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
732571 TTTCATTTAG
732581 TTGTCATTGCATTTTCAT
1 TTGTCATTGCATTTTCAT
732599 TTGTCATTGCA-TTTCAT
1 TTGTCATTGCATTTTCAT
732616 TTGT
1 TTGT
732620 TAGTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.56
Consensus pattern (18 bp):
TTGTCATTGCATTTTCAT
Found at i:733238 original size:17 final size:17
Alignment explanation
Indices: 733216--733254 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
733206 AAAAAATCAC
733216 AAAAAGAAAGAAAA-AAG
1 AAAAAG-AAGAAAAGAAG
733233 AAAAAGAAGAAAAGAAG
1 AAAAAGAAGAAAAGAAG
733250 AAAAA
1 AAAAA
733255 AAGGAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAAGAAG
Found at i:759407 original size:21 final size:21
Alignment explanation
Indices: 759381--759427 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
759371 CTTGTTTCGA
*
759381 TAGAATTTATGCATGTATCGG
1 TAGAATATATGCATGTATCGG
*
759402 TAGAATATATGCATGTATCGT
1 TAGAATATATGCATGTATCGG
759423 TAGAA
1 TAGAA
759428 GTACAGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (21 bp):
TAGAATATATGCATGTATCGG
Found at i:768011 original size:3 final size:3
Alignment explanation
Indices: 768005--768033 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
767995 TTTTTTTTCT
768005 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
768034 TAGCTGAAAA
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:768467 original size:56 final size:56
Alignment explanation
Indices: 768404--768527 Score: 221
Period size: 56 Copynumber: 2.2 Consensus size: 56
768394 TCCGCTAAGC
768404 TAAAATTGAAATAAAATAGTTAATTTGCATGTTTAAGGCTTAAGGACTAAATTGAA
1 TAAAATTGAAATAAAATAGTTAATTTGCATGTTTAAGGCTTAAGGACTAAATTGAA
* *
768460 TAAAATTGAAATAAAATGGTTAATTTGCATGTTTAAGGCTTAGGGACTAAATTGAA
1 TAAAATTGAAATAAAATAGTTAATTTGCATGTTTAAGGCTTAAGGACTAAATTGAA
*
768516 TAAAATTAAAAT
1 TAAAATTGAAAT
768528 GTTGGAGGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (56 bp):
TAAAATTGAAATAAAATAGTTAATTTGCATGTTTAAGGCTTAAGGACTAAATTGAA
Found at i:769404 original size:43 final size:43
Alignment explanation
Indices: 769338--769500 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 43
769328 GTGAATTCTT
*
769338 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTATA
* *
769381 AATGAAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTATA
* * * * **
769424 AATGGAAGATTTATCTCTCGATTAGAGCATAATATTATTTGCA
1 AATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTATA
* *
769467 AATGGAAGAACTTATGACTCGAATAGAGCATAAG
1 AATGGAAG-ACTTATGTCTCGATTAGAGCATAAG
769501 GTTAACTCAG
Statistics
Matches: 105, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
43 85 0.81
44 20 0.19
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGATTAGAGCATAAGATTGTTTATA
Found at i:774458 original size:16 final size:17
Alignment explanation
Indices: 774434--774466 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
774424 ACTTTATGTA
774434 ATTAATAAAA-AATAAC
1 ATTAATAAAATAATAAC
*
774450 ATTATTAAAATAATAAC
1 ATTAATAAAATAATAAC
774467 TAATTAACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
ATTAATAAAATAATAAC
Found at i:774740 original size:17 final size:18
Alignment explanation
Indices: 774718--774751 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
774708 TTAATTGTAA
774718 TTTAAAT-TGTAATTATT
1 TTTAAATGTGTAATTATT
774735 TTTAAATGTGTAATTAT
1 TTTAAATGTGTAATTAT
774752 CACAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
TTTAAATGTGTAATTATT
Found at i:776708 original size:19 final size:19
Alignment explanation
Indices: 776671--776708 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
776661 TTCTGAGCAA
*
776671 TTTAATTTTTTTATGTTTT
1 TTTAATTTTTTTATATTTT
776690 TTTAATTTTCTTTA-ATTTT
1 TTTAATTTT-TTTATATTTT
776709 CCATTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTAATTTTTTTATATTTT
Found at i:777162 original size:14 final size:16
Alignment explanation
Indices: 777139--777180 Score: 63
Period size: 14 Copynumber: 2.8 Consensus size: 16
777129 AACGTAATTA
777139 ATTAAAATATAATATT
1 ATTAAAATATAATATT
777155 -TT-AAATATAA-ATT
1 ATTAAAATATAATATT
777168 ATTAAAATATAAT
1 ATTAAAATATAAT
777181 CCAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.13
14 10 0.43
15 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTAAAATATAATATT
Found at i:779301 original size:23 final size:23
Alignment explanation
Indices: 779256--779301 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
779246 AATTTAAATT
* * *
779256 TCGAATTATTCTAATTAAATTAA
1 TCGAATTAATCAAATCAAATTAA
*
779279 TCGAATTAATCAAATCAACTTAA
1 TCGAATTAATCAAATCAAATTAA
779302 ATTTTTCTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (23 bp):
TCGAATTAATCAAATCAAATTAA
Found at i:779354 original size:16 final size:16
Alignment explanation
Indices: 779327--779367 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
779317 CAAATCTTTT
779327 ATTTTA-TTCCCAAAA
1 ATTTTACTTCCCAAAA
779342 ATTTTACTTCCCAAAA
1 ATTTTACTTCCCAAAA
779358 ATTTTACTTC
1 ATTTTACTTC
779368 TTACAAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 6 0.24
16 19 0.76
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTACTTCCCAAAA
Found at i:779647 original size:18 final size:17
Alignment explanation
Indices: 779624--779657 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
779614 GTTTATATTA
779624 TTGAATTGTTTAATAATG
1 TTGAATT-TTTAATAATG
*
779642 TTGAATTTTTATTAAT
1 TTGAATTTTTAATAAT
779658 TTCTGTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
TTGAATTTTTAATAATG
Found at i:780086 original size:27 final size:28
Alignment explanation
Indices: 780042--780095 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
780032 AAGTTAACGA
*
780042 TAAAATAAAATTCATTAACTT-GATTAATT
1 TAAAAAAAAATT-ATTAA-TTCGATTAATT
780071 TAAAAAAAAATT-TTAATTCGATTAA
1 TAAAAAAAAATTATTAATTCGATTAA
780096 ACGCCCATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.09
27 10 0.43
29 11 0.48
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (28 bp):
TAAAAAAAAATTATTAATTCGATTAATT
Done.