Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004374.1 Kokia drynarioides strain JFW-HI SEQ_117739, 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: 50381
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:7191 original size:27 final size:27
Alignment explanation
Indices: 7153--7214 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
7143 AAAATAAATT
*
7153 AATTTAACTCTCATTCAATTTTTTATC
1 AATTTAATTCTCATTCAATTTTTTATC
7180 AATTTAATTCTCATTCAATTTTTTATC
1 AATTTAATTCTCATTCAATTTTTTATC
7207 AATTTAAT
1 AATTTAAT
7215 CCTTCTTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTAATTCTCATTCAATTTTTTATC
Found at i:7197 original size:16 final size:16
Alignment explanation
Indices: 7153--7200 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
7143 AAAATAAATT
*
7153 AATTTAACTCTCATTC
1 AATTTAATTCTCATTC
7169 AATTT--TT-T-A-TC
1 AATTTAATTCTCATTC
7180 AATTTAATTCTCATTC
1 AATTTAATTCTCATTC
7196 AATTT
1 AATTT
7201 TTTATCAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 10
0.70 0.03 0.27
Matches are distributed among these distances:
11 7 0.27
12 1 0.04
13 3 0.12
14 2 0.08
15 1 0.04
16 12 0.46
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAATTCTCATTC
Found at i:10414 original size:60 final size:58
Alignment explanation
Indices: 10299--10514 Score: 255
Period size: 60 Copynumber: 3.7 Consensus size: 58
10289 TCAAATGGTT
* *
10299 GACACCCCCTTTTCTC-AAAAAAAATTGC--ATTCTTGGGTGTTGGCCATTGCATGGCC
1 GACACCCCCTTTTCTCGAAAAAAAATT-CAAATTTTTTGGTGTTGGCCATTGCATGGCC
*
10355 GACACCCCCTTTTCTCGAAAAAAAATTTCAAATTTTTTTGGTGTTGGTCA-TGCAATGGCC
1 GACACCCCCTTTTCTCGAAAAAAAA-TTCAAA-TTTTTTGGTGTTGGCCATTGC-ATGGCC
* *
10415 GACACCCCCTTTTCTCGAAAAAAAATT-ACA-TTTTTGGTTGTGGGCCATTGCATGGCC
1 GACACCCCCTTTTCTCGAAAAAAAATTCAAATTTTTTGG-TGTTGGCCATTGCATGGCC
* * *
10472 GATACCCCTTTTTCTTGAAATAAAAATTCAAAATTTTTTGGTG
1 GACACCCCCTTTTCTCGAAA-AAAAATTC-AAATTTTTTGGTG
10515 CTAGCCATGC
Statistics
Matches: 138, Mismatches: 10, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
56 23 0.17
57 39 0.28
58 14 0.10
59 6 0.04
60 49 0.36
61 7 0.05
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (58 bp):
GACACCCCCTTTTCTCGAAAAAAAATTCAAATTTTTTGGTGTTGGCCATTGCATGGCC
Found at i:10502 original size:117 final size:116
Alignment explanation
Indices: 10299--10529 Score: 338
Period size: 117 Copynumber: 2.0 Consensus size: 116
10289 TCAAATGGTT
* *
10299 GACACCCCCTTTTCTCAAAAAAAATTGCATTCTTGGGTGTTGGCCATTGCATGGCCGACACCCCC
1 GACACCCCCTTTTCTCAAAAAAAATTACATTCTTGGGTGTGGGCCATTGCATGGCCGACACCCCC
* * * *
10364 TTTTCTCGAAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGCC
66 TTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGCTAGCCATGCAATGGCC
* * *
10415 GACACCCCCTTTTCTCGAAAAAAAATTACATTTTTGGTTGTGGGCCATTGCATGGCCGATACCCC
1 GACACCCCCTTTTCTC-AAAAAAAATTACATTCTTGGGTGTGGGCCATTGCATGGCCGACACCCC
* *
10480 TTTTTCTTGAAATAAAAA-TTCAAAATTTTTTGGTGCTAGCCATGCAATGG
65 CTTTTCTCGAAA-AAAAATTTCAAAATTTTTTGGTGCTAGCCATGCAATGG
10530 AGGTGTCGGC
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
116 16 0.16
117 81 0.79
118 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (116 bp):
GACACCCCCTTTTCTCAAAAAAAATTACATTCTTGGGTGTGGGCCATTGCATGGCCGACACCCCC
TTTTCTCGAAAAAAAATTTCAAAATTTTTTGGTGCTAGCCATGCAATGGCC
Found at i:14811 original size:6 final size:6
Alignment explanation
Indices: 14800--14829 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
14790 ATCATTACAT
14800 TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC
1 TAGGGC TAGGGC TAGGGC TAGGGC TAGGGC
14830 CAGGTTGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
TAGGGC
Found at i:15255 original size:12 final size:12
Alignment explanation
Indices: 15240--15277 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
15230 GGATTGCTGC
15240 TGCTGTTGTACT
1 TGCTGTTGTACT
*
15252 TGCTGTTGTAAT
1 TGCTGTTGTACT
*
15264 TGCTGTGGTACT
1 TGCTGTTGTACT
15276 TG
1 TG
15278 TTGTGGCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.29, T:0.47
Consensus pattern (12 bp):
TGCTGTTGTACT
Found at i:15282 original size:12 final size:12
Alignment explanation
Indices: 15240--15283 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
15230 GGATTGCTGC
*
15240 TGCTGTTGTACT
1 TGCTGTGGTACT
* *
15252 TGCTGTTGTAAT
1 TGCTGTGGTACT
15264 TGCTGTGGTACT
1 TGCTGTGGTACT
*
15276 TGTTGTGG
1 TGCTGTGG
15284 CCACTGCTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.09, C:0.11, G:0.32, T:0.48
Consensus pattern (12 bp):
TGCTGTGGTACT
Found at i:22820 original size:18 final size:18
Alignment explanation
Indices: 22797--22845 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
22787 GCATTTAATT
22797 AAATTTTTAAAAATTAAA
1 AAATTTTTAAAAATTAAA
**
22815 AAATTTAAAAAAATTAAA
1 AAATTTTTAAAAATTAAA
*
22833 ATCATTTTTAAAA
1 A-AATTTTTAAAA
22846 TTTTAAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTTTAAAAATTAAA
Found at i:22879 original size:18 final size:18
Alignment explanation
Indices: 22840--22885 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
22830 AAAATCATTT
*
22840 TTAAAATT-TTAAAATCG
1 TTAAAATTATTAAAATAG
22857 TTAAAATTATTAAAA-AG
1 TTAAAATTATTAAAATAG
22874 TATAAAAATTAT
1 T-T-AAAATTAT
22886 AATCTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
TTAAAATTATTAAAATAG
Found at i:28664 original size:12 final size:12
Alignment explanation
Indices: 28649--28679 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28639 ATTTTTTCAT
28649 GTCAACCTTCTA
1 GTCAACCTTCTA
*
28661 GTCAACCTTGTA
1 GTCAACCTTCTA
28673 GTCAACC
1 GTCAACC
28680 ACCATGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (12 bp):
GTCAACCTTCTA
Found at i:28806 original size:15 final size:16
Alignment explanation
Indices: 28786--28836 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
28776 ATTTCAATAG
28786 ATTTAAAAAAAAAAC-
1 ATTTAAAAAAAAAACA
**
28801 ATTTAAACCAAAAACA
1 ATTTAAAAAAAAAACA
*
28817 ATCTTAAAAAAAAAAAA
1 AT-TTAAAAAAAAAACA
28834 ATT
1 ATT
28837 GGTATAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 13 0.45
16 3 0.10
17 13 0.45
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.22
Consensus pattern (16 bp):
ATTTAAAAAAAAAACA
Found at i:39158 original size:31 final size:31
Alignment explanation
Indices: 39123--39192 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
39113 ACTTAACGAC
*
39123 TCAGTGACTTAAAT-AAAATCTTTCAAATAGT
1 TCAGTGACTCAAATGAAAA-CTTTCAAATAGT
**
39154 TCAGTGACTCAAATGAAAACTTTTGAATAGT
1 TCAGTGACTCAAATGAAAACTTTCAAATAGT
*
39185 TCAATGAC
1 TCAGTGAC
39193 CATTTTGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 30 0.88
32 4 0.12
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (31 bp):
TCAGTGACTCAAATGAAAACTTTCAAATAGT
Found at i:39382 original size:17 final size:17
Alignment explanation
Indices: 39343--39383 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
39333 ATTTTACTAA
*
39343 TACAAAAGTATTACAAT
1 TACAACAGTATTACAAT
39360 TACAACAGTATTACAAT
1 TACAACAGTATTACAAT
39377 TACAACA
1 TACAACA
39384 ATAAGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (17 bp):
TACAACAGTATTACAAT
Found at i:40802 original size:10 final size:10
Alignment explanation
Indices: 40784--40836 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
40774 AAGTCATTTT
40784 AAATT-TTAA
1 AAATTATTAA
40793 AAATTATTAA
1 AAATTATTAA
*
40803 CAATTA-TAA
1 AAATTATTAA
*
40812 AAATTATAAA
1 AAATTATTAA
40822 AAATATATATAA
1 AAAT-TAT-TAA
40834 AAA
1 AAA
40837 GAACTTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 13 0.36
10 15 0.42
11 3 0.08
12 5 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATTATTAA
Found at i:40816 original size:9 final size:9
Alignment explanation
Indices: 40784--40828 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
40774 AAGTCATTTT
*
40784 AAATTTTAA
1 AAATTATAA
40793 AAATTATTAA
1 AAATTA-TAA
*
40803 CAATTATAA
1 AAATTATAA
40812 AAATTATAA
1 AAATTATAA
*
40821 AAAATATA
1 AAATTATA
40829 TATAAAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:43872 original size:14 final size:15
Alignment explanation
Indices: 43842--43877 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
43832 ATAATTTAAA
*
43842 TTTAATATTTAAATT
1 TTTAATACTTAAATT
*
43857 TTTAATACTTAATTT
1 TTTAATACTTAAATT
43872 TTTAAT
1 TTTAAT
43878 TTAACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATACTTAAATT
Found at i:47533 original size:17 final size:17
Alignment explanation
Indices: 47511--47547 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
47501 TCAAATTTAA
*
47511 AATCACAAAATCAGTTT
1 AATCACAAAATCAATTT
*
47528 AATCACATAATCAATTT
1 AATCACAAAATCAATTT
47545 AAT
1 AAT
47548 TTACACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (17 bp):
AATCACAAAATCAATTT
Done.