Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013690.1 Kokia drynarioides strain JFW-HI SEQ_128718, 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: 6985
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1432 original size:28 final size:28
Alignment explanation
Indices: 1401--1462 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1391 AAAATTTATT
*
1401 TAAAATTAGAAAAAAATTATA-AAAATTA
1 TAAAATT-GAAAAAAATCATACAAAATTA
* * *
1429 TAAAATTTATAAAAATCATACAAAATTT
1 TAAAATTGAAAAAAATCATACAAAATTA
1457 TAAAAT
1 TAAAAT
1463 GCATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAATTGAAAAAAATCATACAAAATTA
Found at i:1438 original size:18 final size:18
Alignment explanation
Indices: 1380--1444 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1370 TTAATAAATG
*
1380 TAAAAATATTTAAAATTTA
1 TAAAAAT-TATAAAATTTA
* * *
1399 TTTAAAATTAGAAAAAAATTA
1 -TAAAAATT--ATAAAATTTA
1420 TAAAAATTATAAAATTTA
1 TAAAAATTATAAAATTTA
1438 TAAAAAT
1 TAAAAAT
1445 CATACAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 15 0.42
19 1 0.03
20 13 0.36
21 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
TAAAAATTATAAAATTTA
Found at i:1467 original size:19 final size:19
Alignment explanation
Indices: 1411--1471 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
1401 TAAAATTAGA
* *
1411 AAAAAATTATAAAAATTAT
1 AAAAATTTATAAAAATCAT
1430 -AAAATTTATAAAAATCAT
1 AAAAATTTATAAAAATCAT
1448 ACAAAATTT-T-AAAATGCAT
1 A-AAAATTTATAAAAAT-CAT
1467 AAAAA
1 AAAAA
1472 AAAAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 25 0.68
19 5 0.14
20 7 0.19
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATTTATAAAAATCAT
Found at i:1472 original size:19 final size:20
Alignment explanation
Indices: 1391--1472 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 20
1381 AAAAATATTT
* * *
1391 AAAATTTATTTAAAATTAGAA
1 AAAATTTA-TAAAAATCATAA
* *
1412 AAAAATTATAAAAAT--TAT
1 AAAATTTATAAAAATCATAA
*
1430 AAAATTTATAAAAATCATAC
1 AAAATTTATAAAAATCATAA
1450 AAAATTT-T-AAAATGCATAA
1 AAAATTTATAAAAAT-CATAA
1469 AAAA
1 AAAA
1473 AAAATTTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
18 20 0.39
19 9 0.18
20 15 0.29
21 7 0.14
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (20 bp):
AAAATTTATAAAAATCATAA
Found at i:1772 original size:9 final size:9
Alignment explanation
Indices: 1760--1878 Score: 64
Period size: 9 Copynumber: 12.7 Consensus size: 9
1750 AAAAAAATCA
1760 ATAAAAATT
1 ATAAAAATT
1769 ATAAAAATT
1 ATAAAAATT
* *
1778 AT-TACATT
1 ATAAAAATT
*
1786 TTAATAAATGT
1 ATAA-AAAT-T
1797 A-AAAATATT
1 ATAAAA-ATT
*
1806 -TAAAATTT
1 ATAAAAATT
*
1814 ATTTAAAATT
1 A-TAAAAATT
*
1824 AGAAAAAAATT
1 --ATAAAAATT
1835 ATAAAAATT
1 ATAAAAATT
*
1844 ATAAAATTTT
1 ATAAAA-ATT
*
1854 ATAAAAATC
1 ATAAAAATT
1863 ATACAAAATT
1 ATA-AAAATT
*
1873 TTAAAA
1 ATAAAA
1879 TGCATAAAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
8 7 0.09
9 39 0.48
10 28 0.34
11 7 0.09
12 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1849 original size:19 final size:19
Alignment explanation
Indices: 1827--1889 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
1817 TAAAATTAGA
*
1827 AAAAAATTATAAAAATTAT
1 AAAAAATTATAAAAATCAT
**
1846 AAAATTTTATAAAAATCAT
1 AAAAAATTATAAAAATCAT
* *
1865 ACAAAATT-TTAAAATGCAT
1 AAAAAATTATAAAAAT-CAT
1884 AAAAAA
1 AAAAAA
1890 AAAATTTAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATTATAAAAATCAT
Found at i:1872 original size:21 final size:19
Alignment explanation
Indices: 1833--1875 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1823 TAGAAAAAAA
*
1833 TTATAAAAATTATAAAATT
1 TTATAAAAATTACAAAATT
1852 TTATAAAAATCATACAAAATT
1 TTATAAAAAT--TACAAAATT
1873 TTA
1 TTA
1876 AAATGCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATAAAAATTACAAAATT
Found at i:5712 original size:5 final size:6
Alignment explanation
Indices: 5695--5719 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5685 ACAATTTATG
5695 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5720 TTGATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:6150 original size:43 final size:43
Alignment explanation
Indices: 6062--6283 Score: 236
Period size: 43 Copynumber: 5.2 Consensus size: 43
6052 TTTGTTAATG
* * * *
6062 TTAGCAGCGTTTGTGGGAAAA-TGCCGATAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
6104 TTAGCGGCGTTTGTGGGAAAAGCGTCACTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCT
* *
6147 TTAGCGGCGTTTGTGAGATAAGTGCCGCTAAAGACCATAG-TCT
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCAT-GTTCT
* * *
6190 TTAGCGACGTTTGTGAGATAAGCGCCGTTAAAGACCATGGTT-T
1 TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCAT-GTTCT
* * * *
6233 TTTGTGGCGTTCGTGCA-AAAAGCGCCGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTG-AGAAAAGCGCCGCTAAAGACCATGTTCT
*
6276 ATAGCGGC
1 TTAGCGGC
6284 ACAAGCGGCG
Statistics
Matches: 151, Mismatches: 24, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
42 23 0.15
43 125 0.83
44 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCT
Done.