Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010690.1 Kokia drynarioides strain JFW-HI SEQ_125636, 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: 7919
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:66 original size:45 final size:45
Alignment explanation
Indices: 2--141 Score: 255
Period size: 45 Copynumber: 3.1 Consensus size: 45
1 G
2 CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
1 CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
47 CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
1 CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
* *
92 CATAATCAATCAAATAATATTTACCATATCATTC-TATCACATAG
1 CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
136 CATAAT
1 CATAAT
142 TACTTAGATA
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
44 14 0.15
45 79 0.85
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (45 bp):
CATAATCAATCAAATAATATTTACCATATCATTCGTATCATATAA
Found at i:5798 original size:11 final size:11
Alignment explanation
Indices: 5781--5844 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 11
5771 GAGCCCCTTT
*
5781 TTTAATTT-AT
1 TTTAATTTAAA
*
5791 TTTAAATTTAGA
1 TTT-AATTTAAA
*
5803 TTTATTTTAAA
1 TTTAATTTAAA
*
5814 TTTAAATTAAA
1 TTTAATTTAAA
5825 TTTAAATTTAAA
1 TTT-AATTTAAA
5837 TTTAATTT
1 TTTAATTT
5845 CAAAATTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.07
11 28 0.64
12 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5807 original size:17 final size:17
Alignment explanation
Indices: 5784--5854 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
5774 CCCCTTTTTT
5784 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
5801 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
5818 AATTAAATTTAAATTTA
1 AATTTATTTTAAATTTA
* *
5835 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
5853 AA
1 AA
5855 AGTCCAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 34 0.76
18 11 0.24
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:5855 original size:6 final size:6
Alignment explanation
Indices: 5791--5854 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
5781 TTTAATTTAT
* *
5791 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
5837 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
5855 AGTCCAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 13 0.27
6 32 0.65
7 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:6509 original size:3 final size:3
Alignment explanation
Indices: 6495--6555 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
6485 TATTACAATA
* *
6495 AAT AAT ATT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6543 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
6556 TTTTTAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:7639 original size:30 final size:30
Alignment explanation
Indices: 7599--7800 Score: 219
Period size: 30 Copynumber: 6.7 Consensus size: 30
7589 AAAGGTCCCT
*
7599 AAACTATCCAAAAATTCCATTTTCAACCCCA
1 AAACT-TCCAAAAATTCCATTTTTAACCCCA
*
7630 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * *
7659 AAACTCCCAAAAATCCCATTTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* *
7689 TAACTTCCAAAAATTCCATTTTTACCCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
*
7719 AAACTTCCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
* * * ** ***
7748 GAACTTCTAAAATTTATATTTTTAACCATG
1 AAACTTCCAAAAATTCCATTTTTAACCCCA
*
7778 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
7801 GCCCCCAAAA
Statistics
Matches: 141, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
29 48 0.34
30 83 0.59
31 10 0.07
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCA
Found at i:7698 original size:59 final size:60
Alignment explanation
Indices: 7606--7747 Score: 223
Period size: 59 Copynumber: 2.4 Consensus size: 60
7596 CCTAAACTAT
*
7606 CCAAAAATTCCATTTTCAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC-AAACTC
1 CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTC
* ** *
7665 CCAAAAATCCCATTTTTAACCCCTTAACTTCCAAAAATTCCATTTTTACCCCCAAAACTT
1 CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTC
*
7725 CCAAAAATTCCATTTTTACCCCC
1 CCAAAAATTCCATTTTTAACCCC
7748 GAACTTCTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
59 49 0.65
60 26 0.35
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (60 bp):
CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTC
Found at i:7753 original size:59 final size:58
Alignment explanation
Indices: 7599--7810 Score: 217
Period size: 59 Copynumber: 3.6 Consensus size: 58
7589 AAAGGTCCCT
*
7599 AAACTATCCAAAAATTCCATTTTCAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTT-TACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * **
7659 AAACTCCCAAAAATCCCATTTTTAACCCCTTAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
** * * ** ***
7718 AAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAATTTATATTTTTAACCATG
1 -AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCC
* **
7778 AAACTTTCAAAAATTACCATTTTGCCCCCAAAA
1 AAACTTCCAAAAATT-CCATTTTTACCCCAAAA
7811 ATTTAAAATT
Statistics
Matches: 127, Mismatches: 21, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
59 85 0.67
60 42 0.33
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.31
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:7769 original size:89 final size:88
Alignment explanation
Indices: 7595--7810 Score: 272
Period size: 89 Copynumber: 2.4 Consensus size: 88
7585 CCCTAAAGGT
* *
7595 CCCTAAACTATCCAAAAATTCCATTTTCAACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCA
1 CCCTAAACT-TCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACCCCCA
*
7660 AACTCCCAAAAATCCCATTTTTAA
65 AACTCCCAAAAATCACATTTTTAA
* *
7684 CCCCTTAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACCCCCG
1 -CCCTAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACCCCCA
* * * * *
7749 AACTTCTAAAATTTATATTTTTAA
65 AACTCCCAAAAATCACATTTTTAA
* * *
7773 CCATGAAACTTTCAAAAATTACCA-TTTTGCCCCCAAAA
1 CCCT-AAACTTCCAAAAATT-CCATTTTTACCCCCAAAA
7811 ATTTAAAATT
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 3 0.03
89 96 0.87
90 11 0.10
ACGTcount: A:0.37, C:0.31, G:0.01, T:0.31
Consensus pattern (88 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAA
ACTCCCAAAAATCACATTTTTAA
Done.