Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013140.1 Kokia drynarioides strain JFW-HI SEQ_128159, 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: 52891
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:12126 original size:3 final size:3
Alignment explanation
Indices: 12118--12147 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12108 GGATCAAATG
*
12118 ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12148 TAAGTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:20202 original size:3 final size:3
Alignment explanation
Indices: 20196--20231 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
20186 CTAATAAATC
*
20196 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTC TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
20232 CCATGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:22495 original size:22 final size:22
Alignment explanation
Indices: 22470--22513 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
22460 TATTTATGAG
* *
22470 ATCATTAGTATCGTATTAAAAT
1 ATCATTAATATCATATTAAAAT
22492 ATCATTAATATCATATTAAAAT
1 ATCATTAATATCATATTAAAAT
22514 TTGGTTACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
ATCATTAATATCATATTAAAAT
Found at i:23877 original size:36 final size:36
Alignment explanation
Indices: 23781--23880 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
23771 TGGTAATAGG
* *
23781 CATGACCTTTGGGTCAACAGGGAGAAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
*
23817 CATAACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
23853 CATGACCTTTGGGTCAATAGGGAGTAAA
1 CATGACCTTTGGGTCAATAGGGAGTAAA
23881 TAAGATATCG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAATGAGCAT
Found at i:25661 original size:43 final size:43
Alignment explanation
Indices: 25602--25683 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
25592 AGTTACGTGG
*
25602 AAAAAGCCACATTCAAGAAACGA-AAAAAAAGAAAGCTACATGA
1 AAAAAACCACATTCAAGAAACGACAAAAAAAG-AAGCTACATGA
* * *
25645 AAAAAACCACTTTCAAGAAATGACAAAGAAAGAAGCTAC
1 AAAAAACCACATTCAAGAAACGACAAAAAAAGAAGCTAC
25684 GTGGAAAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 27 0.79
44 7 0.21
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (43 bp):
AAAAAACCACATTCAAGAAACGACAAAAAAAGAAGCTACATGA
Found at i:26145 original size:129 final size:125
Alignment explanation
Indices: 25905--26145 Score: 304
Period size: 125 Copynumber: 1.9 Consensus size: 125
25895 AATTTCCTTT
* * * *
25905 CCTACTTCTAGTTTCATTGTAATCTCACCCACCGTCCTCTTACCCTGAAATTGGTATCAAAGAAG
1 CCTACTTCTAGTTTCATTGTAATCTCACCCACCATCCTCTCACCCTGAAATTGCTATCAAAAAAG
* *
25970 ACTCTAGAATAATTATAGTCCAATTGGAAGAAGCAGTCCTGATTGAATAATTAAAATATC
66 ACCCTAGAATAATTAGAGTCCAATTGGAAGAAGCAGTCCTGATTGAATAATTAAAATATC
* * **
26030 CCTACTTGTAGTTTCATTGTAATCTCATCCACCATCCTCTCACCCTGCTATT-CTAATCATATTA
1 CCTACTTCTAGTTTCATTGTAATCTCACCCACCATCCTCTCACCCTGAAATTGCT-ATCA-A--A
* * * *
26094 AAATATCCCTAGAATAATTAGAGTCCAATTGGGAGAAGCAGTCTTGCTTGAA
62 AAAGA-CCCTAGAATAATTAGAGTCCAATTGGAAGAAGCAGTCCTGATTGAA
26146 GTCTAAAATG
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
124 1 0.01
125 50 0.52
126 1 0.01
128 4 0.04
129 41 0.42
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (125 bp):
CCTACTTCTAGTTTCATTGTAATCTCACCCACCATCCTCTCACCCTGAAATTGCTATCAAAAAAG
ACCCTAGAATAATTAGAGTCCAATTGGAAGAAGCAGTCCTGATTGAATAATTAAAATATC
Found at i:28730 original size:26 final size:26
Alignment explanation
Indices: 28670--28731 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
28660 TTAACATTGT
*
28670 TTTTTGAGAAGTATTTTAAAAAAAAA
1 TTTTTGAAAAGTATTTTAAAAAAAAA
* * * *
28696 TTGTGGAAAAGTGATTTT-GAAAAATA
1 TTTTTGAAAAGT-ATTTTAAAAAAAAA
28722 TTTTTGAAAA
1 TTTTTGAAAA
28732 AATTGATTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (26 bp):
TTTTTGAAAAGTATTTTAAAAAAAAA
Found at i:28998 original size:20 final size:19
Alignment explanation
Indices: 28968--29016 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
28958 TAATTATTCA
*
28968 TAAAATTTAATTTAAATAT
1 TAAAATATAATTTAAATAT
*
28987 ATAAACTATAATTTAAATAT
1 -TAAAATATAATTTAAATAT
29007 TAAAATATAA
1 TAAAATATAA
29017 CTAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATATAATTTAAATAT
Found at i:29037 original size:14 final size:14
Alignment explanation
Indices: 28996--29039 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28986 TATAAACTAT
*
28996 AATTTAAATATTAA
1 AATTTAAATATAAA
* *
29010 AATATAACTAATAAA
1 AATTTAAAT-ATAAA
29025 AATTTAAATATAAA
1 AATTTAAATATAAA
29039 A
1 A
29040 TATTATTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTTAAATATAAA
Found at i:30620 original size:25 final size:22
Alignment explanation
Indices: 30566--30621 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 22
30556 AAGAAATTTA
*
30566 TTTATTTAATTTTTAAATATAT
1 TTTAATTAATTTTTAAATATAT
30588 TTACTAATTAATTTTTATAATAAATAT
1 TT--TAATTAATTTTTA-AAT--ATAT
30615 TTTAATT
1 TTTAATT
30622 CCTTATACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.07
24 12 0.43
25 8 0.29
27 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTAATTAATTTTTAAATATAT
Found at i:37327 original size:51 final size:52
Alignment explanation
Indices: 37234--37335 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 52
37224 AGAAATGGTG
* * *
37234 AAAATGGAGAAATATGAAACATTTGAAAATTATTATGGTTTTCTCCAAAATA
1 AAAATGGAGAAATATGAAACATTTGAAAATGAATATGATTTTCTCCAAAATA
*
37286 AAAATGGAG-AA-ATGAAATCATTTGAAAATGAATGTGATTTTCTCCAAAAT
1 AAAATGGAGAAATATGAAA-CATTTGAAAATGAATATGATTTTCTCCAAAAT
37336 GACAATGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 6 0.13
51 30 0.67
52 9 0.20
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (52 bp):
AAAATGGAGAAATATGAAACATTTGAAAATGAATATGATTTTCTCCAAAATA
Found at i:39368 original size:19 final size:19
Alignment explanation
Indices: 39329--39382 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
39319 CAAGGACACT
39329 GAAGTGCAAATAGGAGCATC
1 GAAGTGCAAATAGG-GCATC
* *
39349 GGAGTGCAAACAGGGCATC
1 GAAGTGCAAATAGGGCATC
39368 GAAGTGCAAATAGGG
1 GAAGTGCAAATAGGG
39383 GCACTCTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.37, C:0.15, G:0.35, T:0.13
Consensus pattern (19 bp):
GAAGTGCAAATAGGGCATC
Found at i:41723 original size:49 final size:49
Alignment explanation
Indices: 41669--41762 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
41659 ACATATCTTG
41669 TGACATTATTTCCAATATTATGGAAATTTCCCTTTGAACAAAACACTTA
1 TGACATTATTTCCAATATTATGGAAATTTCCCTTTGAACAAAACACTTA
41718 TGACATTATTTCCAATATTATGGAAATTTCCCTTTGAACAAAACA
1 TGACATTATTTCCAATATTATGGAAATTTCCCTTTGAACAAAACA
41763 TTCATAAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (49 bp):
TGACATTATTTCCAATATTATGGAAATTTCCCTTTGAACAAAACACTTA
Found at i:46180 original size:24 final size:22
Alignment explanation
Indices: 46139--46188 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
46129 GTCAACCTGA
*
46139 TAAAAAAAATACTTATTCGAA-T
1 TAAAAAAAACACTTATTC-AACT
46161 TAAAAAAAACACTTAAATTCAACT
1 TAAAAAAAACACTT--ATTCAACT
46185 TAAA
1 TAAA
46189 CACACCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 13 0.54
23 2 0.08
24 9 0.38
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAAAAAAACACTTATTCAACT
Found at i:46294 original size:17 final size:19
Alignment explanation
Indices: 46262--46300 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
46252 CAATTTTTTG
46262 TTTTCATTGATCTTTAA-C
1 TTTTCATTGATCTTTAATC
*
46280 TTTTCATT-TTCTTTAATC
1 TTTTCATTGATCTTTAATC
46298 TTT
1 TTT
46301 CATATTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTCATTGATCTTTAATC
Found at i:51785 original size:13 final size:13
Alignment explanation
Indices: 51767--51791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51757 TTTTTTAAAA
51767 TTAATATTGTTAT
1 TTAATATTGTTAT
51780 TTAATATTGTTA
1 TTAATATTGTTA
51792 AAGTATGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TTAATATTGTTAT
Done.