Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011055.1 Kokia drynarioides strain JFW-HI SEQ_126026, 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: 88769
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:2301 original size:7 final size:7
Alignment explanation
Indices: 2260--2313 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
2250 TATCTGAATG
2260 TTAATAT
1 TTAATAT
* *
2267 AT-ATAA
1 TTAATAT
2273 TTAA-AT
1 TTAATAT
2279 TTAA-AT
1 TTAATAT
2285 TTAAATAT
1 TT-AATAT
*
2293 TTGATAT
1 TTAATAT
2300 TTAATAT
1 TTAATAT
2307 TTAATAT
1 TTAATAT
2314 GTTTTTGCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
6 13 0.34
7 21 0.55
8 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (7 bp):
TTAATAT
Found at i:5785 original size:22 final size:22
Alignment explanation
Indices: 5757--5843 Score: 113
Period size: 22 Copynumber: 4.0 Consensus size: 22
5747 GCAACAGTAG
*
5757 GCACACAAAGTGCTAAACAGAA
1 GCACACAAAGTGCTGAACAGAA
* *
5779 GCACACACAGTGTTGAACAGAA
1 GCACACAAAGTGCTGAACAGAA
* *
5801 GCACACACAGTGTTGAACAGAA
1 GCACACAAAGTGCTGAACAGAA
5823 GCACACATAA-TGCTGAACAGA
1 GCACACA-AAGTGCTGAACAGA
5844 GGGCACGAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 58 0.98
23 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.13
Consensus pattern (22 bp):
GCACACAAAGTGCTGAACAGAA
Found at i:13445 original size:25 final size:25
Alignment explanation
Indices: 13394--13457 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
13384 AGCACGTTTC
**
13394 GTGCCCTCTGTTATTAGCACTTCAT
1 GTGCCCTCTGTTAACAGCACTTCAT
13419 GTGCCCTCTGTTACACAGCACTT-AT
1 GTGCCCTCTGTTA-ACAGCACTTCAT
*
13444 GTGTCCTCTGTTAA
1 GTGCCCTCTGTTAA
13458 GTGCTTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.03
25 27 0.77
26 7 0.20
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (25 bp):
GTGCCCTCTGTTAACAGCACTTCAT
Found at i:30566 original size:27 final size:27
Alignment explanation
Indices: 30543--30658 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
30533 ACGTTGGAAA
30543 ATTACCATCCTTGCCTGGCATTGGCAT
1 ATTACCATCCTTGCCTGGCATTGGCAT
30570 ATTACCATCCTTGCCTGGCATTGGCAT
1 ATTACCATCCTTGCCTGGCATTGGCAT
* * *
30597 GTTACCATCCATGCCTGGAATTGGCACT
1 ATTACCATCCTTGCCTGGCATTGGCA-T
* * * *
30625 -TTACCATCCTTGACTGCCGTTGGTAT
1 ATTACCATCCTTGCCTGGCATTGGCAT
30651 ATTACCAT
1 ATTACCAT
30659 AATTTGGCAC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
26 1 0.01
27 76 0.97
28 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (27 bp):
ATTACCATCCTTGCCTGGCATTGGCAT
Found at i:30596 original size:33 final size:33
Alignment explanation
Indices: 30413--30565 Score: 243
Period size: 33 Copynumber: 4.6 Consensus size: 33
30403 ATGCCTGGAA
*
30413 TACCAGCCATGTCTGGCATTGACATCGGCAAAT
1 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
30446 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
1 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
*
30479 TACCAGCCATGTCTGGCATTGACGTTGGCAAAT
1 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
* *
30512 TACCAGCCATGTCTGGCATTGACGTTGGAAAAT
1 TACCAGCCATGTCTGGCATTGACATTGGCAAAT
* * *
30545 TACCATCCTTGCCTGGCATTG
1 TACCAGCCATGTCTGGCATTG
30566 GCATATTACC
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 114 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (33 bp):
TACCAGCCATGTCTGGCATTGACATTGGCAAAT
Found at i:34603 original size:29 final size:30
Alignment explanation
Indices: 34548--34658 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
34538 ATATCAAAAT
* *
34548 TATACAT-AAACTTTGATTTAATGTGCAATTG
1 TATACATGAAACTTTAATTT--GGTGCAATTG
*
34579 TATACATG-AACTTTAATTTGGTGCAATTA
1 TATACATGAAACTTTAATTTGGTGCAATTG
** * * *
34608 TGCACGTGAAACTTTAATTGTGGTTCAAATG
1 TATACATGAAACTTTAATT-TGGTGCAATTG
*
34639 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
34659 TGATTTAATC
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
29 13 0.20
30 11 0.17
31 41 0.63
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGGTGCAATTG
Found at i:34847 original size:29 final size:30
Alignment explanation
Indices: 34801--34859 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
34791 GAATTGGATT
*
34801 AAATCAAAATTTCATGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
* *
34831 AAATC-AAAGTTCATGTATACAATTGCACA
1 AAATCAAAAGTTCATGTATAAAATTACACA
34860 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATTACACA
Found at i:35014 original size:20 final size:20
Alignment explanation
Indices: 34977--35015 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34967 TTTTAAAAAA
*
34977 TTAAATAAATATATAATATT
1 TTAAATAAATATACAATATT
34997 TTAAATACAATAT-CAATAT
1 TTAAATA-AATATACAATAT
35016 CAGTATGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAATAAATATACAATATT
Done.