Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015357.1 Kokia drynarioides strain JFW-HI SEQ_130404, 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: 17203
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 96 characters in sequence are not A, C, G, or T
Found at i:1003 original size:19 final size:19
Alignment explanation
Indices: 981--1017 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
971 CTTTCTCTTT
*
981 CTTTTTCTCTATCCCCTTC
1 CTTTTTCCCTATCCCCTTC
*
1000 CTTTTTCCCTTTCCCCTT
1 CTTTTTCCCTATCCCCTT
1018 GTCACCCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.54
Consensus pattern (19 bp):
CTTTTTCCCTATCCCCTTC
Found at i:2843 original size:19 final size:19
Alignment explanation
Indices: 2819--2855 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2809 CCATTTCGAA
2819 AAATAAAAATAAA-AAAAGC
1 AAATAAAAA-AAACAAAAGC
2838 AAATAAAAAAAACAAAAG
1 AAATAAAAAAAACAAAAG
2856 GGATTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.08
Consensus pattern (19 bp):
AAATAAAAAAAACAAAAGC
Found at i:6698 original size:23 final size:22
Alignment explanation
Indices: 6680--6768 Score: 119
Period size: 23 Copynumber: 3.9 Consensus size: 22
6670 CATTTACACA
6680 ATAATCACATTAACTTTTAAGC
1 ATAATCACATTAACTTTTAAGC
6702 ATAAATCACA-TATACTTTTAAGC
1 AT-AATCACATTA-ACTTTTAAGC
6725 ATAAGTCACATTAACTTTTAAGC
1 ATAA-TCACATTAACTTTTAAGC
6748 ATAAATCACA-TATACTTTTAA
1 AT-AATCACATTA-ACTTTTAA
6769 CACATTTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.13
23 49 0.80
24 4 0.07
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (22 bp):
ATAATCACATTAACTTTTAAGC
Found at i:6734 original size:46 final size:45
Alignment explanation
Indices: 6680--6768 Score: 169
Period size: 46 Copynumber: 2.0 Consensus size: 45
6670 CATTTACACA
6680 ATAATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGC
1 ATAATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGC
6725 ATAAGTCACATTAACTTTTAAGCATAAATCACATATACTTTTAA
1 ATAA-TCACATTAACTTTTAAGCATAAATCACATATACTTTTAA
6769 CACATTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 4 0.09
46 39 0.91
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (45 bp):
ATAATCACATTAACTTTTAAGCATAAATCACATATACTTTTAAGC
Found at i:9646 original size:39 final size:38
Alignment explanation
Indices: 9561--9778 Score: 188
Period size: 39 Copynumber: 5.6 Consensus size: 38
9551 TTTATAACTT
* * **
9561 GCAGTGACACTGCAAACACTACGATAATATTACTGAACTG
1 GCAGTGACACTGTAAACACTACAATGTTA-TACTGAA-TG
* * * *
9601 GCAGTGACAATGTAAACACTAAAATGCTGTACTGAATCG
1 GCAGTGACACTGTAAACACTACAATGTTATACTGAAT-G
* *
9640 GTAGTGACACTGTAAACACTACAATGTTATACGGAAATG
1 GCAGTGACACTGTAAACACTACAATGTTATACTG-AATG
*
9679 GCAATGACACTGTAAACACTACAATGTTATACTGAACTG
1 GCAGTGACACTGTAAACACTACAATGTTATACTGAA-TG
* * * *
9718 GC-GATCACACTGGAAACA-TCGCAATGCTATACTGAAGTG
1 GCAG-TGACACTGTAAACACT-ACAATGTTATACTGAA-TG
* * *
9757 GTAATGACACTGTAGACACTAC
1 GCAGTGACACTGTAAACACTAC
9779 CAGGTTATCA
Statistics
Matches: 143, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
38 4 0.03
39 113 0.79
40 26 0.18
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (38 bp):
GCAGTGACACTGTAAACACTACAATGTTATACTGAATG
Found at i:9735 original size:117 final size:118
Alignment explanation
Indices: 9565--9778 Score: 265
Period size: 117 Copynumber: 1.8 Consensus size: 118
9555 TAACTTGCAG
* * *
9565 TGACACTGCAAACACTACGATAATATTACTGAACTGGCAGTGACAATGTAAACA-CTAAAATGCT
1 TGACACTGCAAACACTACAATAATATTACTGAACTGGCAGTCACAATGGAAACATC-AAAATGCT
* *
9629 GTACTGAA-TCGGTAGTGACACTGTAAACACTACAATGTTATACGGAAATGGCAA
65 ATACTGAAGT-GGTAATGACACTGTAAACACTACAATGTTATACGGAAATGGCAA
* ** * **
9683 TGACACTGTAAACACTACAATGTTA-TACTGAACTGGC-GATCACACTGGAAACATCGCAATGCT
1 TGACACTGCAAACACTACAATAATATTACTGAACTGGCAG-TCACAATGGAAACATCAAAATGCT
*
9746 ATACTGAAGTGGTAATGACACTGTAGACACTAC
65 ATACTGAAGTGGTAATGACACTGTAAACACTAC
9779 CAGGTTATCA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 1 0.01
117 57 0.70
118 23 0.28
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (118 bp):
TGACACTGCAAACACTACAATAATATTACTGAACTGGCAGTCACAATGGAAACATCAAAATGCTA
TACTGAAGTGGTAATGACACTGTAAACACTACAATGTTATACGGAAATGGCAA
Found at i:14064 original size:19 final size:19
Alignment explanation
Indices: 14040--14076 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
14030 CCATTTCGAA
14040 AAATAAAAATAAA-AAAAGC
1 AAATAAAAA-AAACAAAAGC
14059 AAATAAAAAAAACAAAAG
1 AAATAAAAAAAACAAAAG
14077 GGATTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.08
Consensus pattern (19 bp):
AAATAAAAAAAACAAAAGC
Done.