Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001036.1 Kokia drynarioides strain JFW-HI SEQ_112263, 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: 85219
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:11946 original size:4 final size:4
Alignment explanation
Indices: 11939--11975 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
11929 AATTCAACAA
* *
11939 ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAC ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
11976 ATGTTCATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (4 bp):
ACAT
Found at i:29720 original size:19 final size:21
Alignment explanation
Indices: 29681--29720 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
29671 TTCCCAAAAA
*
29681 CCCTAAAAACATTTTATTTTC
1 CCCTAAAAACATTTTACTTTC
29702 CCCT-AAAAC-TTTTACTTTC
1 CCCTAAAAACATTTTACTTTC
29721 ACCCACTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.42
Consensus pattern (21 bp):
CCCTAAAAACATTTTACTTTC
Found at i:32332 original size:17 final size:18
Alignment explanation
Indices: 32297--32361 Score: 96
Period size: 17 Copynumber: 3.6 Consensus size: 18
32287 GTTTAATTGG
32297 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
*
32315 TTTAAATTTA-TCTTAAA
1 TTTAAATTTATTTTTAAA
32332 TTTAAATTTATTTTTATAAA
1 TTTAAATTTA-TTTT-TAAA
32352 TTTAAATTTA
1 TTTAAATTTA
32362 CTTTAATCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.38
18 10 0.24
19 2 0.05
20 14 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:32374 original size:35 final size:35
Alignment explanation
Indices: 32300--32376 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
32290 TAATTGGTTT
*
32300 AAATTTATTTTTAAATTTAAATTTATCTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTATCTTAAATTC
*
32335 AAATTTATTTTTATAAATTTAAATTTA-CTTTAA-TC
1 AAATTTA-TTTT-TAAATTTAAATTTATCTTAAATTC
32370 AAATTTA
1 AAATTTA
32377 AATGGATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
35 15 0.39
36 9 0.24
37 14 0.37
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTATCTTAAATTC
Found at i:32375 original size:21 final size:20
Alignment explanation
Indices: 32297--32379 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
32287 GTTTAATTGG
*
32297 TTTAAATTTA-TTT-TTAAA
1 TTTAAATTTACTTTAATAAA
*
32315 TTTAAATTTA-TCT--TAAA
1 TTTAAATTTACTTTAATAAA
* *
32332 TTTAAATTTATTTTTATAAA
1 TTTAAATTTACTTTAATAAA
32352 TTTAAATTTACTTTAATCAAA
1 TTTAAATTTACTTTAAT-AAA
32373 TTTAAAT
1 TTTAAAT
32380 GGATTTAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
17 14 0.25
18 14 0.25
20 19 0.33
21 10 0.18
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAATTTACTTTAATAAA
Found at i:32379 original size:6 final size:6
Alignment explanation
Indices: 32297--32361 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
32287 GTTTAATTGG
** **
32297 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA
32345 TTATAAA TTTAAA TTTA
1 TT-TAAA TTTAAA TTTA
32362 CTTTAATCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
6 34 0.74
7 6 0.13
8 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:35579 original size:21 final size:20
Alignment explanation
Indices: 35554--35590 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
35544 AACTATATTT
35554 TAATTAATTTATTTTTTAAC
1 TAATTAATTTATTTTTTAAC
35574 --A-TAATTTATTTTTTAAC
1 TAATTAATTTATTTTTTAAC
35591 ATACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 16 0.94
18 1 0.06
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTAATTTATTTTTTAAC
Found at i:35580 original size:17 final size:17
Alignment explanation
Indices: 35558--35593 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35548 ATATTTTAAT
35558 TAATTTATTTTTTAACA
1 TAATTTATTTTTTAACA
35575 TAATTTATTTTTTAACA
1 TAATTTATTTTTTAACA
35592 TA
1 TA
35594 CTTAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTTATTTTTTAACA
Found at i:38593 original size:43 final size:43
Alignment explanation
Indices: 38545--38631 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
38535 TGGTGGTGCT
38545 TGGATATTTATATGATACGAGTATTGTTTGTTGATATGACATG
1 TGGATATTTATATGATACGAGTATTGTTTGTTGATATGACATG
38588 TGGATATTTATATGATACGAGTATTGTTTGTTGATATGACATG
1 TGGATATTTATATGATACGAGTATTGTTTGTTGATATGACATG
38631 T
1 T
38632 CATGTAGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (43 bp):
TGGATATTTATATGATACGAGTATTGTTTGTTGATATGACATG
Found at i:38624 original size:24 final size:24
Alignment explanation
Indices: 38554--38626 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
38544 TTGGATATTT
38554 ATATGATACGAGTATTGTTTGTTG
1 ATATGATACGAGTATTGTTTGTTG
* * *
38578 ATATG--AC-A-TGTGGATAT-TT-
1 ATATGATACGAGTATTG-TTTGTTG
38597 ATATGATACGAGTATTGTTTGTTG
1 ATATGATACGAGTATTGTTTGTTG
38621 ATATGA
1 ATATGA
38627 CATGTCATGT
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 5 0.14
20 5 0.14
21 5 0.14
22 5 0.14
23 5 0.14
24 11 0.31
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (24 bp):
ATATGATACGAGTATTGTTTGTTG
Found at i:40264 original size:8 final size:8
Alignment explanation
Indices: 40251--40293 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
40241 TGAATTAATC
*
40251 ATAAATAA
1 ATAAATAT
40259 ATAAATAT
1 ATAAATAT
*
40267 ATATATAT
1 ATAAATAT
*
40275 ATATATAT
1 ATAAATAT
40283 ATAAATA-
1 ATAAATAT
40290 ATAA
1 ATAA
40294 GCCTGCCGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 4 0.12
8 28 0.88
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAAATAT
Found at i:44288 original size:34 final size:34
Alignment explanation
Indices: 44250--44314 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
44240 CAAAGTTATA
*
44250 AAAAAAAATTATAAAAGTTATTTAGAAAAACTAT
1 AAAAAAAATTACAAAAGTTATTTAGAAAAACTAT
44284 AAAAAAAATTACAAAAGTTATTTAGAAAAAC
1 AAAAAAAATTACAAAAGTTATTTAGAAAAAC
44315 CAAATTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAAAAAATTACAAAAGTTATTTAGAAAAACTAT
Found at i:54782 original size:30 final size:30
Alignment explanation
Indices: 54742--54812 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
54732 ACCCGCCGCT
*
54742 TCCAAGCCCGCCGCCATTGCTTCCTCCAAG
1 TCCAAACCCGCCGCCATTGCTTCCTCCAAG
54772 TCCAAACCCGCCGCCATTGCTTCCTCCAAG
1 TCCAAACCCGCCGCCATTGCTTCCTCCAAG
54802 TCCAAACCCGC
1 TCCAAACCCGC
54813 TGCTTCCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.20, C:0.48, G:0.14, T:0.18
Consensus pattern (30 bp):
TCCAAACCCGCCGCCATTGCTTCCTCCAAG
Found at i:59732 original size:16 final size:16
Alignment explanation
Indices: 59707--59737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59697 AAAAAATAAT
59707 ATAAAATTTATAATAC
1 ATAAAATTTATAATAC
*
59723 ATAAACTTTATAATA
1 ATAAAATTTATAATA
59738 AAAAAACATT
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:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAAATTTATAATAC
Found at i:60002 original size:15 final size:14
Alignment explanation
Indices: 59982--60013 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
59972 GTGGGAATTA
59982 TTTTTTATAATAAAC
1 TTTTTTATAAT-AAC
59997 TTTTTTATAATAAC
1 TTTTTTATAATAAC
60011 TTT
1 TTT
60014 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTTATAATAAC
Found at i:71048 original size:6 final size:6
Alignment explanation
Indices: 71039--71085 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
71029 ATAAATTAAA
* * *
71039 ATTTAT ATTTAT GTCTAT ATTTAT ATTTAT ATTTAT ATTGAT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
71086 ATAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (6 bp):
ATTTAT
Found at i:84591 original size:22 final size:22
Alignment explanation
Indices: 84566--84608 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
84556 TAAAATTTCA
84566 TAAATCAAAAAAAT-AAATATAC
1 TAAAT-AAAAAAATAAAATATAC
*
84588 TAAATAAAAAATTAAAATATA
1 TAAATAAAAAAATAAAATATA
84609 AAAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAATAAAAAAATAAAATATAC
Done.