Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014831.1 Kokia drynarioides strain JFW-HI SEQ_129873, 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: 33941
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:80 original size:20 final size:21
Alignment explanation
Indices: 55--97 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
45 TACTTACTAC
55 TACTAAC-AATAAAATAAAAT
1 TACTAACTAATAAAATAAAAT
* *
75 TACTAACTAGTAAAATTAAAT
1 TACTAACTAATAAAATAAAAT
96 TA
1 TA
98 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
TACTAACTAATAAAATAAAAT
Found at i:498 original size:21 final size:20
Alignment explanation
Indices: 469--513 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
459 CCTTCTTCCT
*
469 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTCCTTT-TTTC
*
490 TCTTTTTTCTTCCTTTTTTC
1 TCTTCTTTCTTCCTTTTTTC
510 -CTTC
1 TCTTC
514 ATTTTTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.19
21 14 0.67
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTCTTTCTTCCTTTTTTC
Found at i:2244 original size:16 final size:16
Alignment explanation
Indices: 2223--2253 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2213 ATAATGTGAA
2223 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
2239 AATAAAGTTAAAATG
1 AATAAAGATAAAATG
2254 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:3093 original size:26 final size:26
Alignment explanation
Indices: 3050--3100 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
3040 AATTCTGGGC
3050 ATAATTCTGAACACGTTTATGCAACG
1 ATAATTCTGAACACGTTTATGCAACG
*
3076 ATAATTCT-AGACATGTTTATGCAAC
1 ATAATTCTGA-ACACGTTTATGCAAC
3101 AACATTCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (26 bp):
ATAATTCTGAACACGTTTATGCAACG
Found at i:4935 original size:17 final size:17
Alignment explanation
Indices: 4913--4967 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
4903 TTCCTCTTAG
4913 TTTTATTACGTTCATTT
1 TTTTATTACGTTCATTT
*
4930 TTTTA-TA-GTTTCCTCTT
1 TTTTATTACG-TTCAT-TT
4947 AGTTTTATTACGTTCATTT
1 --TTTTATTACGTTCATTT
4966 TT
1 TT
4968 CTTTCTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.03
16 6 0.20
17 9 0.30
19 7 0.23
20 6 0.20
21 1 0.03
ACGTcount: A:0.16, C:0.13, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTTATTACGTTCATTT
Found at i:4954 original size:19 final size:19
Alignment explanation
Indices: 4898--4954 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
4888 AGTTAATTAG
4898 ATAGTTTCCTCTTAGTTTT
1 ATAGTTTCCTCTTAGTTTT
*
4917 ATTACG-TTCAT-TT--TTTT
1 A-TA-GTTTCCTCTTAGTTTT
4934 ATAGTTTCCTCTTAGTTTT
1 ATAGTTTCCTCTTAGTTTT
4953 AT
1 AT
4955 TACGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 1 0.03
16 6 0.20
17 7 0.23
19 9 0.30
20 6 0.20
21 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.60
Consensus pattern (19 bp):
ATAGTTTCCTCTTAGTTTT
Found at i:4989 original size:36 final size:36
Alignment explanation
Indices: 4898--4967 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
4888 AGTTAATTAG
4898 ATAGTTTCCTCTTAGTTTTATTACGTTCATTTTTTT
1 ATAGTTTCCTCTTAGTTTTATTACGTTCATTTTTTT
4934 ATAGTTTCCTCTTAGTTTTATTACGTTCATTTTT
1 ATAGTTTCCTCTTAGTTTTATTACGTTCATTTTT
4968 CTTTCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (36 bp):
ATAGTTTCCTCTTAGTTTTATTACGTTCATTTTTTT
Found at i:5766 original size:43 final size:43
Alignment explanation
Indices: 5694--5809 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
5684 ACACACGGGC
* **
5694 TGGG-CACACGGGTGTGTACCAGATTGTGTGTGTATACTATAT
1 TGGGACACACGGGCGTGTACCAGACCGTGTGTGTATACTATAT
* * *
5736 TGGGACACACGGGCGTGTATCAGACCGTGTGTGTATACTGTCT
1 TGGGACACACGGGCGTGTACCAGACCGTGTGTGTATACTATAT
* * *
5779 TGGGACACACGGGCATGTGCCAGACCATGTG
1 TGGGACACACGGGCGTGTACCAGACCGTGTG
5810 AATACACTGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 4 0.06
43 59 0.94
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.27
Consensus pattern (43 bp):
TGGGACACACGGGCGTGTACCAGACCGTGTGTGTATACTATAT
Found at i:5819 original size:43 final size:43
Alignment explanation
Indices: 5735--5819 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
5725 GTATACTATA
* * * ** *
5735 TTGGGACACACGGGCGTGTATCAGACCGTGTGTGTATACTGTC
1 TTGGGACACACGGGCATGTACCAGACCATGTGAATACACTGTC
*
5778 TTGGGACACACGGGCATGTGCCAGACCATGTGAATACACTGT
1 TTGGGACACACGGGCATGTACCAGACCATGTGAATACACTGT
5820 TTTAGAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (43 bp):
TTGGGACACACGGGCATGTACCAGACCATGTGAATACACTGTC
Found at i:13993 original size:23 final size:24
Alignment explanation
Indices: 13956--14004 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13946 AGTGACAATT
13956 ATTTAACTAATTAGT-ATTTTTATC
1 ATTTAACTAATTAGTAATTTTT-TC
*
13980 ATTTAA-TTATTAGTAATTTTTTC
1 ATTTAACTAATTAGTAATTTTTTC
14003 AT
1 AT
14005 AATTTATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTAACTAATTAGTAATTTTTTC
Found at i:16059 original size:39 final size:39
Alignment explanation
Indices: 15975--16074 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 39
15965 ATAATGAACT
* * * *
15975 GACAGTGACATTGTAAATACTACGAAACCATATTGAACT
1 GACAGTGACATTGTAAACACTACGAAACCATACTAAACA
* * *
16014 GACAGTGAAATTGTAAACACTACGGAACTATACTAAACA
1 GACAGTGACATTGTAAACACTACGAAACCATACTAAACA
* *
16053 GGCAGTGACACTGTAAACACTA
1 GACAGTGACATTGTAAACACTA
16075 TGAAGCTATA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (39 bp):
GACAGTGACATTGTAAACACTACGAAACCATACTAAACA
Found at i:23757 original size:39 final size:39
Alignment explanation
Indices: 23697--23771 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
23687 AGTGATCAAA
* * *
23697 ATACTGAATTAGAAGTGACACTGGAAACATTGCGAAGTT
1 ATACTGAATAAGAAGTAACACTGGAAACACTGCGAAGTT
* *
23736 ATACTGAATAAGCAGTAACACTGTAAACACTGCGAA
1 ATACTGAATAAGAAGTAACACTGGAAACACTGCGAA
23772 ACTACATTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (39 bp):
ATACTGAATAAGAAGTAACACTGGAAACACTGCGAAGTT
Found at i:30244 original size:196 final size:196
Alignment explanation
Indices: 29910--30303 Score: 752
Period size: 196 Copynumber: 2.0 Consensus size: 196
29900 AATGCAAGAA
29910 GATATCTGATATGAGAGATAATGAACAGGCTAGTTTTGAAGAACAGAACTAAAGTCGCTGATTTA
1 GATATCTGATATGAGAGATAATGAACAGGCTAGTTTTGAAGAACAGAACTAAAGTCGCTGATTTA
29975 AAACAAAAGCAATGGTAGACAGCTATTTGAAATGGTATTCAAACATTACCAATTAGCTTGGTATA
66 AAACAAAAGCAATGGTAGACAGCTATTTGAAATGGTATTCAAACATTACCAATTAGCTTGGTATA
*
30040 AATGGTATCCAGCTTACTTATTTTATCCAAAAAGAGGGAGAAGAGAAGGAGCAAGAAATGAGAGA
131 AATGGTATCCAGCTTACTTATTTTATCCAAAAAGAGGGAGAAGAGAAGGAGAAAGAAATGAGAGA
30105 G
196 G
* *
30106 GATATCTGATATGAGAGATAATGAACAGGCTAGTTTTGAAGAACGGAACTAAAGTCGCTGCTTTA
1 GATATCTGATATGAGAGATAATGAACAGGCTAGTTTTGAAGAACAGAACTAAAGTCGCTGATTTA
*
30171 AAACAAAAGCGATGGTAGACAGCTATTTGAAATGGTATTCAAACATTACCAATTAGCTTGGTATA
66 AAACAAAAGCAATGGTAGACAGCTATTTGAAATGGTATTCAAACATTACCAATTAGCTTGGTATA
30236 AATGGTATCCAGCTTACTTATTTTATCCAAAAAGAGGGAGAAGAGAAGGAGAAAGAAATGAGAGA
131 AATGGTATCCAGCTTACTTATTTTATCCAAAAAGAGGGAGAAGAGAAGGAGAAAGAAATGAGAGA
30301 G
196 G
30302 GA
1 GA
30304 ATTTTGGCTG
Statistics
Matches: 194, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
196 194 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (196 bp):
GATATCTGATATGAGAGATAATGAACAGGCTAGTTTTGAAGAACAGAACTAAAGTCGCTGATTTA
AAACAAAAGCAATGGTAGACAGCTATTTGAAATGGTATTCAAACATTACCAATTAGCTTGGTATA
AATGGTATCCAGCTTACTTATTTTATCCAAAAAGAGGGAGAAGAGAAGGAGAAAGAAATGAGAGA
G
Done.