Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000657.1 Kokia drynarioides strain JFW-HI SEQ_111637, 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: 8930
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:1161 original size:30 final size:30
Alignment explanation
Indices: 1123--1504 Score: 193
Period size: 29 Copynumber: 13.0 Consensus size: 30
1113 CGTAAAAGGT
* *
1123 CCCT-AAACTTTTCAAAAATCACATTTTGA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* * *
1152 CCCTCAAACTTTTCCAAAATTACGTTTTAA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* ** *
1182 CCCTTATGCTTTTCCAAAATTACA-TTTTA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* * * *
1211 ACCTAAAAAATTTTCAAAAATTATATTTTTA
1 CCCT-CAAACTTTTCAAAAATTACATTTTTA
* * *
1242 -CTTCTAAACTTCTCAAAAATTATATTTTTA
1 CCCTC-AAACTTTTCAAAAATTACATTTTTA
* ** * *
1272 CTCTTGAAC-TTTCAAAAATCACATTTTCA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* *
1301 CCCTCAAACTTCT-GAAAATTACATTTTTA
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* * * *
1330 CCCTCGAA-TTTCCAAAAATCACATTTTTT
1 CCCTCAAACTTTTCAAAAATTACATTTTTA
* *
1359 CCCTCAAAC--TTAAGAAAATCACATTTTTA
1 CCCTCAAACTTTTCA-AAAATTACATTTTTA
* * * *
1388 CCCCCGAAC-ATACAAAAATTACCATTTTGT-
1 CCCTCAAACTTTTCAAAAATTA-CATTTT-TA
* * * *
1418 -CC-CGAA-TATCCAAAAAGATTACCATTTTGA
1 CCCTCAAACTTTTC-AAAA-ATTA-CATTTTTA
*
1448 -CCTCAAACTTTTCTAAAATTACCA-TTTTA
1 CCCTCAAACTTTTCAAAAATTA-CATTTTTA
* * * *
1477 CCCCCGAACGTCT-AAAAATTACATTTTT
1 CCCTCAAACTTTTCAAAAATTACATTTTT
1505 GCCTCCGAAC
Statistics
Matches: 271, Mismatches: 62, Indels: 40
0.73 0.17 0.11
Matches are distributed among these distances:
28 13 0.05
29 121 0.45
30 121 0.45
31 13 0.05
32 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.37
Consensus pattern (30 bp):
CCCTCAAACTTTTCAAAAATTACATTTTTA
Found at i:1286 original size:29 final size:29
Alignment explanation
Indices: 1222--1290 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 29
1212 CCTAAAAAAT
1222 TTTCAAAAATTATATTTTTACTTCTAAAC
1 TTTCAAAAATTATATTTTTACTTCTAAAC
*
1251 TTCTCAAAAATTATATTTTTAC-TCTTGAAC
1 TT-TCAAAAATTATATTTTTACTTC-TAAAC
1281 TTTCAAAAAT
1 TTTCAAAAAT
1291 CACATTTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 12 0.32
30 25 0.68
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.46
Consensus pattern (29 bp):
TTTCAAAAATTATATTTTTACTTCTAAAC
Found at i:1563 original size:29 final size:28
Alignment explanation
Indices: 1389--1566 Score: 153
Period size: 29 Copynumber: 6.1 Consensus size: 28
1379 ACATTTTTAC
*
1389 CCCCGAACATACAAAAATTACCATTTTG
1 CCCCGAACATCCAAAAATTACCATTTTG
* *
1417 TCCCGAATATCCAAAAAGATTACCATTTTG
1 CCCCGAACATCC-AAAA-ATTACCATTTTG
* * * * * *
1447 ACCTCAAACTTTTCTAAAATTACCATTTTAC
1 -CCCCGAAC-ATCCAAAAATTACCATTTT-G
* *
1478 CCCCGAACGTCTAAAAATTA-CATTTTTG
1 CCCCGAACATCCAAAAATTACCA-TTTTG
1506 CCTCCGAACAT-CAAAAATTACCATTTTTG
1 CC-CCGAACATCCAAAAATTACCA-TTTTG
*
1535 CCCCTAAACATCCAAAAATTACCATTTTG
1 CCCC-GAACATCCAAAAATTACCATTTTG
1564 CCC
1 CCC
1567 TCAAATTTCC
Statistics
Matches: 119, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
28 23 0.19
29 46 0.39
30 41 0.34
31 7 0.06
32 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.30
Consensus pattern (28 bp):
CCCCGAACATCCAAAAATTACCATTTTG
Found at i:1620 original size:30 final size:30
Alignment explanation
Indices: 1545--1662 Score: 84
Period size: 29 Copynumber: 4.0 Consensus size: 30
1535 CCCCTAAACA
* * ** *
1545 TCCAAAAATTACCATTTTGCCCTCAAA-TT
1 TCCAAAAATTTCAATTTTAACCTTAAATTT
1574 TCCAAAAA--TCATATTTTCAACCTTAAATTT
1 TCCAAAAATTTCA-ATTTT-AACCTTAAATTT
* * *
1604 TCCAAAAGTTT-GATTTTAATCC-CAAATTT
1 TCCAAAAATTTCAATTTTAA-CCTTAAATTT
*
1633 TCCAAAAATTTCAATTTTGATCCTTAAATT
1 TCCAAAAATTTCAATTTT-AACCTTAAATT
1663 CCTCAAAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.01
28 5 0.07
29 32 0.47
30 23 0.34
31 6 0.09
32 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.40
Consensus pattern (30 bp):
TCCAAAAATTTCAATTTTAACCTTAAATTT
Found at i:6815 original size:12 final size:12
Alignment explanation
Indices: 6790--6875 Score: 68
Period size: 12 Copynumber: 6.9 Consensus size: 12
6780 ATTCAATGAA
*
6790 AAAAAAAAG-TG
1 AAAAAAAAGAAG
6801 AAAAAAAAGAAG
1 AAAAAAAAGAAG
*
6813 AAAAAGCAAAATAAAAG
1 --AAA--AAAA-AGAAG
*
6830 ATAAAAAAGAAG
1 AAAAAAAAGAAG
*
6842 AAAAACAAGAAG
1 AAAAAAAAGAAG
6854 AAAAAAAA-AAG
1 AAAAAAAAGAAG
*
6865 AGAAAAAAGAA
1 AAAAAAAAGAA
6876 AAGGAGAGAT
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
11 19 0.32
12 24 0.40
13 4 0.07
14 3 0.05
15 2 0.03
16 4 0.07
17 4 0.07
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:6816 original size:9 final size:9
Alignment explanation
Indices: 6804--6871 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
6794 AAAAGTGAAA
6804 AAAAAGAAG
1 AAAAAGAAG
*
6813 AAAAAGCAAA
1 AAAAAG-AAG
6823 ATAAAAGATA-
1 A-AAAAGA-AG
6833 AAAAAGAAG
1 AAAAAGAAG
*
6842 AAAAACAAG
1 AAAAAGAAG
6851 AAGAAA-AA-
1 AA-AAAGAAG
6859 AAAAAG-AG
1 AAAAAGAAG
6867 AAAAA
1 AAAAA
6872 AGAAAAGGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
7 4 0.08
8 8 0.16
9 24 0.48
10 8 0.16
11 6 0.12
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:6857 original size:29 final size:27
Alignment explanation
Indices: 6801--6872 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 27
6791 AAAAAAAGTG
*
6801 AAAAAAAAGAAGAAAAAGCAAAATAAA
1 AAAAAAAAGAAGAAAAAGCAAAAGAAA
6828 AGATAAAAAAGAAGAAAAA-CAAGAAGAAA
1 A-A-AAAAAAGAAGAAAAAGCAA-AAGAAA
6857 AAAAAAAGAGAA-AAAA
1 AAAAAAA-AGAAGAAAA
6873 GAAAAGGAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 10 0.25
28 9 0.22
29 21 0.52
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (27 bp):
AAAAAAAAGAAGAAAAAGCAAAAGAAA
Found at i:8604 original size:78 final size:77
Alignment explanation
Indices: 8506--8930 Score: 523
Period size: 78 Copynumber: 5.5 Consensus size: 77
8496 GATATTTTAC
* * * * * *
8506 CCCGAGCTTGGGGTAGATTGCAACCATTCGATTTCTTACCCTGAGCCTAAGGCAGATCACCGTTA
1 CCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAGGGCAAATCACCGTCA
8571 GCCAATCTCTTA
66 GCCAATCTCTTA
* * * * * * * * * *
8583 CTCCAAGCCTGGGGTAAATTGCAGCCATTCGATCTCTTACCCCGAGCTTGGGGTAGATCACCATC
1 C-CCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAGGGCAAATCACCGTC
* *
8648 ATCCAATCTCGTA
65 AGCCAATCTCTTA
* *
8661 CCCCGAGAC-TGGGGTAGATTGCAACCGTTCAATCTCTTACCCCGAGCCT-GAAGCAAATCACCG
1 -CCCGAG-CTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAG-GGCAAATCACCG
*
8724 TCAACCAATCTCTTA
63 TCAGCCAATCTCTTA
* *
8739 CCCGAGCTTGGGGCAGATTGCAACCATTCAATCTCTTACCCCGAGCCT-GGAGCAAATCACCATC
1 CCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAGG-GCAAATCACCGTC
8803 AGCCAATCTCTTA
65 AGCCAATCTCTTA
* * *
8816 CCCAAGCTTGGGGTAGATTGTAACCATTCAATCTCTTACCCCGAGCCTAGGGAAAATCACCGTCA
1 CCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAGGGCAAATCACCGTCA
8881 GCCAATCTCTTA
66 GCCAATCTCTTA
* *
8893 CTCCGAGCTTCGGGTAGATTGCAGCCATTCAATCTCTT
1 C-CCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTT
Statistics
Matches: 300, Mismatches: 40, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
76 1 0.00
77 141 0.47
78 156 0.52
79 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (77 bp):
CCCGAGCTTGGGGTAGATTGCAACCATTCAATCTCTTACCCCGAGCCTAGGGCAAATCACCGTCA
GCCAATCTCTTA
Found at i:8926 original size:39 final size:39
Alignment explanation
Indices: 8502--8930 Score: 241
Period size: 39 Copynumber: 11.1 Consensus size: 39
8492 TTTTGATATT
* * * *
8502 TTACCCCGAGCTTGGGGTAGATTGCAACCATTCGATTTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
* ** * *
8541 TTACCCTGAGCCTAAGGCAGA-T-CA-CCGTTAGCCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATT---CAATCTC
* * * *
8580 TTACTCCAAGCCTGGGGTAAATTGCAGCCATTCGATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
*
8619 TTACCCCGAGCTTGGGGTAGA-T-CA-CCATCATCCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCAT--T-CAATCTC
* * * *
8658 GTACCCCGAGACTGGGGTAGATTGCAACCGTTCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
** * * ** * * **
8697 TTACCCCGAGCCTGAAGCAAATCACCGTCAACCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
* * *
8736 TTA-CCCGAGCTTGGGGCAGATTGCAACCATTCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
* * * *
8774 TTACCCCGAGCCTGGAGCA-AAT-CA-CCATCAGCCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCAT---TCAATCTC
* * * *
8813 TTA-CCCAAGCTTGGGGTAGATTGTAACCATTCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
* * * ** * * **
8851 TTACCCCGAGCCTAGGGAAAATCACCGTCAGCCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
* * *
8890 TTACTCCGAGCTTCGGGTAGATTGCAGCCATTCAATCTC
1 TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
8929 TT
1 TT
Statistics
Matches: 284, Mismatches: 86, Indels: 40
0.69 0.21 0.10
Matches are distributed among these distances:
36 12 0.04
37 6 0.02
38 53 0.19
39 194 0.68
40 4 0.01
41 8 0.03
42 7 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (39 bp):
TTACCCCGAGCCTGGGGTAGATTGCAGCCATTCAATCTC
Done.