Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003023.1 Kokia drynarioides strain JFW-HI SEQ_115538, 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: 4986
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Found at i:230 original size:3 final size:3
Alignment explanation
Indices: 224--290 Score: 73
Period size: 3 Copynumber: 21.7 Consensus size: 3
214 CTTCGTTTTT
* * *
224 TTA TTA TTAA TTA ATA TTA TTA TTA TTA TTA TTA -AA ATA GTTA TTTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
271 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
291 GCTATCAGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 1 0.02
3 46 0.84
4 8 0.15
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:989 original size:6 final size:6
Alignment explanation
Indices: 957--1038 Score: 50
Period size: 6 Copynumber: 14.3 Consensus size: 6
947 ATTTAAATAT
* *
957 ATTTAA ATTTTCA ATTTATA A--TAA ATTTAA ATTT-A A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
1003 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
1039 CTTGTTAGCC
Statistics
Matches: 57, Mismatches: 11, Indels: 16
0.68 0.13 0.19
Matches are distributed among these distances:
4 3 0.05
5 14 0.25
6 33 0.58
7 7 0.12
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:991 original size:17 final size:17
Alignment explanation
Indices: 969--1038 Score: 97
Period size: 17 Copynumber: 4.2 Consensus size: 17
959 TTAAATTTTC
*
969 AATTTATAATAAATTTA
1 AATTTAAAATAAATTTA
*
986 AATTT-AAGTAAATTTA
1 AATTTAAAATAAATTTA
*
1002 AACTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
1019 ATTTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
1036 AAT
1 AAT
1039 CTTGTTAGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.29
17 32 0.71
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:3560 original size:29 final size:28
Alignment explanation
Indices: 3528--3583 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
3518 AAATTATTAT
*
3528 TTTAGATTTTTTTAATTTTTAATATATTC
1 TTTAGATTTTTTAAATTTTT-ATATATTC
3557 TTTAGATTTTTTAAATTTTTATATATT
1 TTTAGATTTTTTAAATTTTTATATATT
3584 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTAGATTTTTTAAATTTTTATATATTC
Found at i:3575 original size:28 final size:29
Alignment explanation
Indices: 3528--3583 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3518 AAATTATTAT
*
3528 TTTAGATTTTTTTAATTTTTAATATATTC
1 TTTAGATTTTTTTAAATTTTAATATATTC
*
3557 TTTAGA-TTTTTTAAATTTTTATATATT
1 TTTAGATTTTTTTAAATTTTAATATATT
3584 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (29 bp):
TTTAGATTTTTTTAAATTTTAATATATTC
Found at i:3903 original size:61 final size:61
Alignment explanation
Indices: 3774--4000 Score: 275
Period size: 61 Copynumber: 3.8 Consensus size: 61
3764 AATTTTTGGC
** * * *
3774 ATGGCCGACACCCCCTTTTTTCAAATAAAAAAATTGC--A-TTTTTTGGTGTTGGCCATACA
1 ATGGCCGACACTTCC-TTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCA
* *
3833 ATGGCCGACACTTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGGCATGCA
1 ATGGCCGACACTTCCTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCA
* * *
3894 ATGGTCGACA-TCCCCTTTTTCAGATAAAAAAA-TTCAAAATTTTTTTGGTGTTGGTCATGCA
1 ATGGCCGACACT-TCCTTTTTCAGATAAAAAAATTTC-AAATTTTTTTGGTGTTGGCCATGCA
* * *
3955 ATGGCCGGCACCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTT
1 ATGGCCGACACTTCCTTTTTCAGATAAAAAAATTTCAAATTTTTTT
4001 CTTTTTCTCT
Statistics
Matches: 145, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
58 19 0.13
59 12 0.08
60 5 0.03
61 106 0.73
62 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (61 bp):
ATGGCCGACACTTCCTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCCATGCA
Found at i:3999 original size:122 final size:120
Alignment explanation
Indices: 3774--4000 Score: 323
Period size: 122 Copynumber: 1.9 Consensus size: 120
3764 AATTTTTGGC
3774 ATGGCCGACACCCCCTTTTTTCAAATAAAAAAATTGCATTTTTTGGTGTTGGCCATACAATGGCC
1 ATGGCCGACACCCCCTTTTTTCAAATAAAAAAATTGCATTTTTTGGTGTTGGCCATACAATGGCC
* * *
3839 GACACTTCTTTTTTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGGCATGCA
66 GACACCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGGCATGCA
* * * * *
3894 ATGGTCGACATCCCC-TTTTTCAGATAAAAAAATT-CAAAATTTTTTTGGTGTTGGTCATGCAAT
1 ATGGCCGACACCCCCTTTTTTCAAATAAAAAAATTGC---A-TTTTTTGGTGTTGGCCATACAAT
*
3957 GGCCGGCACCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTT
62 GGCCGACACCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTT
4001 CTTTTTCTCT
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
118 1 0.01
119 18 0.19
120 13 0.14
121 1 0.01
122 61 0.65
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (120 bp):
ATGGCCGACACCCCCTTTTTTCAAATAAAAAAATTGCATTTTTTGGTGTTGGCCATACAATGGCC
GACACCTCCTTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGGCATGCA
Found at i:4147 original size:37 final size:38
Alignment explanation
Indices: 4070--4179 Score: 149
Period size: 37 Copynumber: 3.0 Consensus size: 38
4060 CCCCTTTTTT
*
4070 AGATAAAAAAATTGC--ATTTTTTGGTGTCGGCCATTGC
1 AGATAAAAAAATTTCAAATTTTTTGGTGTCGGCCA-TGC
4107 AGATAAAAAAATTTCAAAATTTTTTGGTGTCGGCC-T-C
1 AGATAAAAAAATTTC-AAATTTTTTGGTGTCGGCCATGC
*
4144 AGAT-AAAAAATTTCAAATTTTTTGGTGTTGGCCATG
1 AGATAAAAAAATTTCAAATTTTTTGGTGTCGGCCATG
4180 TAATACCTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
35 18 0.27
36 11 0.17
37 19 0.29
38 1 0.02
40 17 0.26
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (38 bp):
AGATAAAAAAATTTCAAATTTTTTGGTGTCGGCCATGC
Found at i:4179 original size:133 final size:132
Alignment explanation
Indices: 3975--4229 Score: 356
Period size: 133 Copynumber: 1.9 Consensus size: 132
3965 CCTCCTTTTT
*** *
3975 CAGATAAAAAAATTTCAAAATTTTTTCTTTTTCTCTGATAAAAAAATTTCAAATTTTTTGGTGTT
1 CAGATAAAAAAATTTCAAAATTTTTTCTTGGCCTCAGATAAAAAAATTTCAAATTTTTTGGTGTT
*
4040 GACCATGCAATGGCC-GACACCCCCTTTTTT-AGATAAAAAAATTGCA-TTTTTTGGTGTCGGCC
66 GACCATGCAAT-ACCTGACACCCCCTTTTTTCAGAT-AAAAAATTGCATTTTTTTGGTGTCGGCC
4102 ATTG
129 ATTG
*
4106 CAGATAAAAAAATTTCAAAATTTTTTGGTGTCGGCCTCAGAT-AAAAAATTTCAAATTTTTTGGT
1 CAGATAAAAAAATTTCAAAATTTTTT-CT-T-GGCCTCAGATAAAAAAATTTCAAATTTTTTGGT
* * *
4170 GTTGGCCATGTAATACCTGACACCCCTTTTTTTCAGATAAAAAATTGCATTTTTTTGGTG
63 GTTGACCATGCAATACCTGACACCCCCTTTTTTCAGATAAAAAATTGCATTTTTTTGGTG
4230 CCAGCCATGC
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
131 26 0.24
132 3 0.03
133 60 0.55
134 20 0.18
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (132 bp):
CAGATAAAAAAATTTCAAAATTTTTTCTTGGCCTCAGATAAAAAAATTTCAAATTTTTTGGTGTT
GACCATGCAATACCTGACACCCCCTTTTTTCAGATAAAAAATTGCATTTTTTTGGTGTCGGCCAT
TG
Found at i:4259 original size:59 final size:60
Alignment explanation
Indices: 4142--4259 Score: 132
Period size: 59 Copynumber: 2.0 Consensus size: 60
4132 GGTGTCGGCC
* *** * *
4142 TCAGATAAAAAATTTCAAATTTTTTGGTGTTGGCCATGTAATACCTGACACCCCTTTTTT
1 TCAGATAAAAAATTGCAAATTTTTTGGTGCCAGCCATGCAATACCTGACACCCATTTTTT
* * *
4202 TCAGATAAAAAATTGC-ATTTTTTTGGTGCCAGCCATGCAATGGCC-GACACCTATTTTT
1 TCAGATAAAAAATTGCAAATTTTTTGGTGCCAGCCATGCAAT-ACCTGACACCCATTTTT
4260 ATTTGGTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
59 31 0.65
60 17 0.35
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (60 bp):
TCAGATAAAAAATTGCAAATTTTTTGGTGCCAGCCATGCAATACCTGACACCCATTTTTT
Found at i:4366 original size:55 final size:55
Alignment explanation
Indices: 4299--4405 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
4289 TGGCCATGTA
* *
4299 ATGGCCGGCACCAACTTCTCCTCATTCTCTATAAATAGGGTTTAGTTTTTTTTAC
1 ATGGCCGACACCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTTTAC
* *
4354 ATGGCCGACACCAATTTCCCCTCATTCTTTATAAATAGGGTTTAGTTTTTTT
1 ATGGCCGACACCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTT
4406 ATTTTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.41
Consensus pattern (55 bp):
ATGGCCGACACCAACTTCCCCTCATTCTCTATAAATAGGGTTTAGTTTTTTTTAC
Done.