Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014621.1 Kokia drynarioides strain JFW-HI SEQ_129660, 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: 23503
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:3470 original size:26 final size:26
Alignment explanation
Indices: 3418--3468 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3408 TTGGACATGA
* *
3418 AAGAAAATAAAATTAAAACAAATTTG
1 AAGAAAAAAAAATCAAAACAAATTTG
*
3444 AAGAAAAAAAAATCATACACAAATT
1 AAGAAAAAAAAATCA-AAACAAATT
3469 GATGATATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.20
Consensus pattern (26 bp):
AAGAAAAAAAAATCAAAACAAATTTG
Found at i:5684 original size:29 final size:29
Alignment explanation
Indices: 5651--5708 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5641 ATTAAGAGAT
5651 TGGATCAAATTAATCCATT-TAATATTAAA
1 TGGATCAAATTAAT-CATTGTAATATTAAA
* *
5680 TGGATCAATTTAATCATTGTACTATTAAA
1 TGGATCAAATTAATCATTGTAATATTAAA
5709 AAAATAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (29 bp):
TGGATCAAATTAATCATTGTAATATTAAA
Found at i:5758 original size:47 final size:49
Alignment explanation
Indices: 5689--5853 Score: 177
Period size: 47 Copynumber: 3.6 Consensus size: 49
5679 ATGGATCAAT
5689 TTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
1 TTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
* * * * * * *
5738 TTAAT-ATT-TACTGTTTAAAAAAT-AA--CAATTAA-ATG-GATTAAT
1 TTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
*
5780 TTGATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
1 TTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
* *
5829 TTAAT-ATT-TACTGTTTAAAAAATAA
1 TTAATCATTGTACTATTAAAAAAATAA
5854 CAAAAATATT
Statistics
Matches: 91, Mismatches: 18, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
42 8 0.09
43 5 0.05
44 19 0.21
45 2 0.02
46 2 0.02
47 34 0.37
48 8 0.09
49 13 0.14
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (49 bp):
TTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAA
Found at i:5788 original size:91 final size:91
Alignment explanation
Indices: 5674--5856 Score: 348
Period size: 91 Copynumber: 2.0 Consensus size: 91
5664 TCCATTTAAT
5674 ATTAAATGGATCAATTTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAAT
1 ATTAAATGGATCAATTTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAAT
5739 TAATATTTACTGTTTAAAAAATAACA
66 TAATATTTACTGTTTAAAAAATAACA
* *
5765 ATTAAATGGATTAATTTGATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAAT
1 ATTAAATGGATCAATTTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAAT
5830 TAATATTTACTGTTTAAAAAATAACA
66 TAATATTTACTGTTTAAAAAATAACA
5856 A
1 A
5857 AAATATTTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (91 bp):
ATTAAATGGATCAATTTAATCATTGTACTATTAAAAAAATAAATGAAATTAATTTGTTATAAAAT
TAATATTTACTGTTTAAAAAATAACA
Found at i:10636 original size:113 final size:113
Alignment explanation
Indices: 10438--10664 Score: 427
Period size: 113 Copynumber: 2.0 Consensus size: 113
10428 TGGTGGGTCA
10438 CCCCTTGGGGTTTTAGGATTCTGGCCACCCTCATATCATATGGAACCATCCTTAGCCAGGATGCA
1 CCCCTTGGGGTTTTAGGATTCTGGCCACCCTCATATCATATGGAACCATCCTTAGCCAGGATGCA
*
10503 GCCAAGGAACCAACTTGGACCACGACTTGTAGCCTTTCTTATGCTAGG
66 GCCAAGGAACCAACTTGGACCACGACTTGTAGCCTTTCTTATGATAGG
*
10551 CCCCTTGGGGTTTTAGGATTCTGGCCACCCTCATATCATATGGAACCATCCTTAGCCAGGCTGCA
1 CCCCTTGGGGTTTTAGGATTCTGGCCACCCTCATATCATATGGAACCATCCTTAGCCAGGATGCA
*
10616 GCTAAGGAACCAACTTGGACCACGACTTGTAGCCTTTCTTATGATAGG
66 GCCAAGGAACCAACTTGGACCACGACTTGTAGCCTTTCTTATGATAGG
10664 C
1 C
10665 GGACTCCATT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (113 bp):
CCCCTTGGGGTTTTAGGATTCTGGCCACCCTCATATCATATGGAACCATCCTTAGCCAGGATGCA
GCCAAGGAACCAACTTGGACCACGACTTGTAGCCTTTCTTATGATAGG
Found at i:11679 original size:24 final size:26
Alignment explanation
Indices: 11651--11706 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
11641 ATATAATCTT
11651 AATATTT-CC-CAAAAAGATA-TTTTA
1 AATATTTCCCTCAAAAA-ATACTTTTA
11675 AATATTTCCCTCAAAAAATATCTTTTA
1 AATATTTCCCTCAAAAAATA-CTTTTA
11702 AATAT
1 AATAT
11707 ATATTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.25
25 5 0.18
26 6 0.21
27 10 0.36
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (26 bp):
AATATTTCCCTCAAAAAATACTTTTA
Found at i:22970 original size:18 final size:19
Alignment explanation
Indices: 22947--22983 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
22937 AAAAGCATAC
*
22947 CACAAGACA-AANAAAAAT
1 CACAAGACAGAAAAAAAAT
22965 CACAAGACAGAAAAAAAAT
1 CACAAGACAGAAAAAAAAT
22984 GGTGCAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.05
Consensus pattern (19 bp):
CACAAGACAGAAAAAAAAT
Done.