Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009810.1 Kokia drynarioides strain JFW-HI SEQ_124531, 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: 61516
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:3880 original size:23 final size:23
Alignment explanation
Indices: 3827--3873 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3817 ACACTATCGC
3827 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCACGTCTCGT
*
3850 GCTCTCTGTTTAGCACGTTTCGT
1 GCTCTCTGTTTAGCACGTCTCGT
3873 G
1 G
3874 TCCTCTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.28, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACGTCTCGT
Found at i:5109 original size:14 final size:15
Alignment explanation
Indices: 5085--5117 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5075 TAACTTGTGA
5085 ATTTAAAAAAATGTC
1 ATTTAAAAAAATGTC
5100 ATTTAAAAAAATGTC
1 ATTTAAAAAAATGTC
5115 ATT
1 ATT
5118 ATCAATGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (15 bp):
ATTTAAAAAAATGTC
Found at i:15681 original size:6 final size:6
Alignment explanation
Indices: 15670--15699 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
15660 TGTCCCCCTT
15670 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTCAA
15700 GTGGCTGAGC
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:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCAA
Found at i:29894 original size:17 final size:18
Alignment explanation
Indices: 29874--29913 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
29864 TTTATTATAT
29874 TTTTTA-AAAATTTAACA
1 TTTTTATAAAATTTAACA
* *
29891 TTTTTATAGAATTTAATA
1 TTTTTATAAAATTTAACA
29909 TTTTT
1 TTTTT
29914 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTTATAAAATTTAACA
Found at i:36184 original size:2 final size:2
Alignment explanation
Indices: 36177--36209 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36167 AAATCATAAA
36177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36210 ATAGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37957 original size:2 final size:2
Alignment explanation
Indices: 37950--37976 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37940 GAAATCTAAA
37950 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
37977 AATTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38019 original size:33 final size:35
Alignment explanation
Indices: 37960--38025 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
37950 ATATATATAT
*
37960 ATATATATATATATATAAATTAAAATTTTTAAAAA
1 ATATATATATATATATAAATTAAAATTTATAAAAA
37995 ATATATA-ATA-AT-TAAATTATAAATTTATAAA
1 ATATATATATATATATAAATTA-AAATTTATAAA
38026 GAATTGATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.24
33 12 0.41
34 3 0.10
35 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (35 bp):
ATATATATATATATATAAATTAAAATTTATAAAAA
Found at i:44793 original size:162 final size:162
Alignment explanation
Indices: 44582--44910 Score: 543
Period size: 162 Copynumber: 2.0 Consensus size: 162
44572 AAGTCTTCTC
* * *
44582 TGCAGGCAGTGGAGTTTCACTCCTATATGTTGTTTGCTTAATTTCATCTGCATTGTTTTCTTCAG
1 TGCAGGCAGTGGAGTTTCACTCCTATATGTTGTTTGCTTAATCTCATCTGCAGTATTTTCTTCAG
44647 GAAAACAGAACTGATGTGGATCAATTTTAGAACTTTTCTTCTCAGTTCT-CTTTTCCTGGGGCAA
66 GAAAACAGAACTGATGTGGATCAATTTTAGAACTTTTCTTCTCAGTTCTCCTTTTCC-GGGGCAA
* *
44711 CAATGAGCCACCATTGACAGTACCAGCTAGCTT
130 CAATGAACCACCATTGACAGAACCAGCTAGCTT
* * *
44744 TGCAGGCGGTGGAGTTTCAGTCCTATATGTTGTTTGCTTAATCTCATCTGCAGTATTTTCTTCGG
1 TGCAGGCAGTGGAGTTTCACTCCTATATGTTGTTTGCTTAATCTCATCTGCAGTATTTTCTTCAG
* *
44809 GAAAACAGACCTGATGTGGATCAATTTTAGAACTTTTCTTCTCAGTTTTCCTTTTCCGGGGCAAC
66 GAAAACAGAACTGATGTGGATCAATTTTAGAACTTTTCTTCTCAGTTCTCCTTTTCCGGGGCAAC
*
44874 AATGAACCACCATTGACAGAACCATCTAGCTT
131 AATGAACCACCATTGACAGAACCAGCTAGCTT
44906 TGCAG
1 TGCAG
44911 ATCTTCCTTC
Statistics
Matches: 155, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
162 148 0.95
163 7 0.05
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (162 bp):
TGCAGGCAGTGGAGTTTCACTCCTATATGTTGTTTGCTTAATCTCATCTGCAGTATTTTCTTCAG
GAAAACAGAACTGATGTGGATCAATTTTAGAACTTTTCTTCTCAGTTCTCCTTTTCCGGGGCAAC
AATGAACCACCATTGACAGAACCAGCTAGCTT
Found at i:49855 original size:270 final size:270
Alignment explanation
Indices: 49374--49910 Score: 1065
Period size: 270 Copynumber: 2.0 Consensus size: 270
49364 TTTTGTTCAG
49374 GTGATGATTGATATCTTTATTCTCTATTATTTATTTTTTTGATTCAAGTTTTTCTTGTAGGAAAC
1 GTGATGATTGATATCTTTATTCTCTATTATTTATTTTTTTGATTCAAGTTTTTCTTGTAGGAAAC
49439 ATTTGTTATTTAATCACTTCTGCGCTGAGCGTCAATTATTACATTCTTTTCAGTCTCAATTACCT
66 ATTTGTTATTTAATCACTTCTGCGCTGAGCGTCAATTATTACATTCTTTTCAGTCTCAATTACCT
49504 TGTCATCATGGCTTGTTAATTGTCCTTATTATCTACTGGCTCTACTGGTCATTTCATAAAAATAT
131 TGTCATCATGGCTTGTTAATTGTCCTTATTATCTACTGGCTCTACTGGTCATTTCATAAAAATAT
49569 TTTGGACATTTCTCTGTTTTATTTGCATTGTTATCAGTTATCATATACATATTTGGGTTAGTTCC
196 TTTGGACATTTCTCTGTTTTATTTGCATTGTTATCAGTTATCATATACATATTTGGGTTAGTTCC
49634 ATGGGATTTT
261 ATGGGATTTT
49644 GTGATGATTGATATCTTTATTCTCTATTATTTATTTTTTTGATTCAAGTTTTTCTTGTAGGAAAC
1 GTGATGATTGATATCTTTATTCTCTATTATTTATTTTTTTGATTCAAGTTTTTCTTGTAGGAAAC
*
49709 ATTTGTTATTTAATCATTTCTGCGCTGAGCGTCAATTATTACATTCTTTTCAGTCTCAATTACCT
66 ATTTGTTATTTAATCACTTCTGCGCTGAGCGTCAATTATTACATTCTTTTCAGTCTCAATTACCT
49774 TGTCATCATGGCTTGTTAATTGTCCTTATTATCTACTGGCTCTACTGGTCATTTCATAAAAATAT
131 TGTCATCATGGCTTGTTAATTGTCCTTATTATCTACTGGCTCTACTGGTCATTTCATAAAAATAT
49839 TTTGGACATTTCTCTGTTTTATTTGCATTGTTATCAGTTATCATATACATATTTGGGTTAGTTCC
196 TTTGGACATTTCTCTGTTTTATTTGCATTGTTATCAGTTATCATATACATATTTGGGTTAGTTCC
49904 ATGGGAT
261 ATGGGAT
49911 CTTGCTCAGA
Statistics
Matches: 266, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
270 266 1.00
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (270 bp):
GTGATGATTGATATCTTTATTCTCTATTATTTATTTTTTTGATTCAAGTTTTTCTTGTAGGAAAC
ATTTGTTATTTAATCACTTCTGCGCTGAGCGTCAATTATTACATTCTTTTCAGTCTCAATTACCT
TGTCATCATGGCTTGTTAATTGTCCTTATTATCTACTGGCTCTACTGGTCATTTCATAAAAATAT
TTTGGACATTTCTCTGTTTTATTTGCATTGTTATCAGTTATCATATACATATTTGGGTTAGTTCC
ATGGGATTTT
Found at i:56092 original size:27 final size:28
Alignment explanation
Indices: 56049--56134 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 28
56039 GTACAAGGGG
* *
56049 TGGTGCCTATCTGACAGGCGGCACCAAA
1 TGGTGCCTACCTAACAGGCGGCACCAAA
* * *
56077 T-GTGCCTACCTAACAGGCAGCA-CTAG
1 TGGTGCCTACCTAACAGGCGGCACCAAA
* *
56103 TGGTGCCTACCTACCAGGCGGCACTAAA
1 TGGTGCCTACCTAACAGGCGGCACCAAA
56131 -GGTG
1 TGGTG
56135 TCTATCTGGC
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
26 3 0.07
27 41 0.89
28 2 0.04
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.19
Consensus pattern (28 bp):
TGGTGCCTACCTAACAGGCGGCACCAAA
Found at i:56224 original size:15 final size:15
Alignment explanation
Indices: 56201--56245 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
56191 TTTTTTACAT
56201 AAATAATACAAAAAA
1 AAATAATACAAAAAA
* **
56216 AAATTATACACCAAA
1 AAATAATACAAAAAA
*
56231 ATATAATACAAAAAA
1 AAATAATACAAAAAA
56246 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAATACAAAAAA
Found at i:56787 original size:26 final size:26
Alignment explanation
Indices: 56700--56777 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
56690 AACAACAAAT
*
56700 TTTTGAAGAAGGAAAGGAAGCAAAAG
1 TTTTGAAGAAGAAAAGGAAGCAAAAG
56726 TTTTGAAGAAGAAAAGGAAGCAAAAG
1 TTTTGAAGAAGAAAAGGAAGCAAAAG
*
56752 TTTTGAAGAAGAAAAGGAAACAAAAG
1 TTTTGAAGAAGAAAAGGAAGCAAAAG
56778 GTTAGCAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.15
Consensus pattern (26 bp):
TTTTGAAGAAGAAAAGGAAGCAAAAG
Found at i:59625 original size:26 final size:26
Alignment explanation
Indices: 59576--59625 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
59566 TCTATTTAAA
**
59576 TTTGAATTTATTTAATAATTTTTATG
1 TTTGAATTTATTTAATAAGGTTTATG
*
59602 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAATTTATTTAATAAGGTTTA
59626 GCAAATGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTTATTTAATAAGGTTTATG
Found at i:61225 original size:18 final size:17
Alignment explanation
Indices: 61202--61237 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
61192 TGAATTTCTA
*
61202 TCCAATTTATATCTTAAT
1 TCCAATTTA-ATCCTAAT
61220 TCCAATTTAATCCTAAT
1 TCCAATTTAATCCTAAT
61237 T
1 T
61238 AACTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TCCAATTTAATCCTAAT
Done.