Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002811.1 Kokia drynarioides strain JFW-HI SEQ_115164, 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: 35823
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:722 original size:52 final size:52
Alignment explanation
Indices: 607--896 Score: 404
Period size: 52 Copynumber: 5.6 Consensus size: 52
597 TTCCCATTTA
* * * *
607 ATACTCACGATGACATAAAGTCATTGGACCTTA-AATCCGTAAAGGA-TCTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTC-AT
* * *
658 ATGCTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
710 ATACTCATGATGACACATAGCCATCGGACCTCATAATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
762 ATACTCACGATAACACATAGTTATCGGACCTCAAAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
814 ATACTCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAGGATTTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
866 ATACTTACGATGACACATAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
897 TTTTCATTTA
Statistics
Matches: 211, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
51 27 0.13
52 182 0.86
53 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:2847 original size:21 final size:19
Alignment explanation
Indices: 2822--2860 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
2812 CTATAATTTT
2822 TTTATTATTTTAATTTAATTA
1 TTTATTATTTT--TTTAATTA
*
2843 TTTATTCTTTTTTTAATT
1 TTTATTATTTTTTTAATT
2861 TTAACCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTATTTTTTTAATTA
Found at i:2971 original size:30 final size:29
Alignment explanation
Indices: 2928--3025 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 29
2918 TTTTAATTTA
2928 TATTTTTTCAATTTATACTTTATTATTTTCT
1 TATTTTTT-AATTTATACTTTATTATTTT-T
* *
2959 TATTTTTTAATTTAGTCCATTTATTGTTTTT
1 TATTTTTTAATTTA-TAC-TTTATTATTTTT
*
2990 TATTTGTT--TTTATA-TTTATTTATTTTT
1 TATTTTTTAATTTATACTTTA-TTATTTTT
3017 TATTATTTT
1 TATT-TTTT
3026 CTGTTTATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
26 4 0.07
27 11 0.19
28 4 0.07
29 4 0.07
30 6 0.11
31 18 0.32
32 10 0.18
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.71
Consensus pattern (29 bp):
TATTTTTTAATTTATACTTTATTATTTTT
Found at i:3061 original size:20 final size:19
Alignment explanation
Indices: 2978--3061 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 19
2968 ATTTAGTCCA
*
2978 TTTATTGTTTTTTAT-TTGTT
1 TTTATT-TTCTTTATATT-TT
*
2998 TTTATATTTATTTAT-TTTT
1 TTTAT-TTTCTTTATATTTT
*
3017 TATTATTTTCTGTT-TATTATG
1 T-TTATTTTCT-TTATATT-TT
3038 TTTATTTTCTTTAGTATTTT
1 TTTATTTTCTTTA-TATTTT
3058 TTTA
1 TTTA
3062 GTTCATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
19 10 0.19
20 36 0.68
21 7 0.13
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTATTTTCTTTATATTTT
Found at i:6326 original size:21 final size:22
Alignment explanation
Indices: 6294--6347 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
6284 TTTAAATGAT
*
6294 AATTCTTAAAAA-ATTATCAAAA
1 AATTCTTAAAAATA-TATAAAAA
6316 AATTC-TAAAAATATATAAAAA
1 AATTCTTAAAAATATATAAAAA
*
6337 AA-TCTTTAAAA
1 AATTCTTAAAAA
6348 CAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 20 0.71
22 6 0.21
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTCTTAAAAATATATAAAAA
Found at i:6657 original size:20 final size:21
Alignment explanation
Indices: 6618--6671 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
6608 ATAAATAATG
*
6618 TTTTGA-ATTTTTAAAGATTT
1 TTTTGATATTTTTAAACATTT
6638 ATTTT-ATATTTTT-AACATTT
1 -TTTTGATATTTTTAAACATTT
6658 TTTTGATACTTTTT
1 TTTTGATA-TTTTT
6672 TTAGAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 10 0.34
21 15 0.52
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.65
Consensus pattern (21 bp):
TTTTGATATTTTTAAACATTT
Found at i:35213 original size:31 final size:32
Alignment explanation
Indices: 35178--35247 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
35168 GGACCAAAAA
35178 AAGTTTAGA-TCTCAATGTAAGAAAAATTGTC
1 AAGTTTAGAGTCTCAATGTAAGAAAAATTGTC
* * *
35209 AAGTTCA-AGTCTCAATGTGAGAACAATTGTC
1 AAGTTTAGAGTCTCAATGTAAGAAAAATTGTC
35240 AAGTTTAG
1 AAGTTTAG
35248 GACTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 32 0.97
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (32 bp):
AAGTTTAGAGTCTCAATGTAAGAAAAATTGTC
Found at i:35800 original size:6 final size:6
Alignment explanation
Indices: 35789--35823 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
35779 CAATCACCTG
* *
35789 GTGGGA GTGGGA GTGGGA GTGGGT GTGGGT GTGGG
1 GTGGGA GTGGGA GTGGGA GTGGGA GTGGGA GTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.09, C:0.00, G:0.69, T:0.23
Consensus pattern (6 bp):
GTGGGA
Done.