Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013263.1 Kokia drynarioides strain JFW-HI SEQ_128284, 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: 35405
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:94 original size:31 final size:28
Alignment explanation
Indices: 57--121 Score: 94
Period size: 31 Copynumber: 2.2 Consensus size: 28
47 ATTTCCTTTT
57 TTATTATTGATATTTATTAATAATAATAATA
1 TTATTATTGATATTTATT-ATAAT--TAATA
*
88 TTATTATTGTTATTTATTATAATTAATA
1 TTATTATTGATATTTATTATAATTAATA
116 TTATTA
1 TTATTA
122 ATGTCATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 11 0.33
30 5 0.15
31 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
TTATTATTGATATTTATTATAATTAATA
Found at i:871 original size:6 final size:6
Alignment explanation
Indices: 860--942 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
850 TCAAATTTGA
** * *
860 TTAAAT TTAAAT TTAAA- GAAAAT TTAAAT TTAAAAAG ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT
* *
909 TTAAGA- -TAAAT TTAAAT TTAAAA ATAAAT TTAAA
1 TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
943 CTAATTTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 1 0.02
5 6 0.10
6 47 0.80
7 1 0.02
8 4 0.07
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:884 original size:17 final size:18
Alignment explanation
Indices: 861--942 Score: 123
Period size: 17 Copynumber: 4.6 Consensus size: 18
851 CAAATTTGAT
861 TAAATTTAAATTTAAAGA
1 TAAATTTAAATTTAAAGA
879 -AAATTTAAATTTAAAAAGA
1 TAAATTTAAATTT--AAAGA
898 TAAATTTAAATTT-AAGA
1 TAAATTTAAATTTAAAGA
*
915 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAGA
933 TAAATTTAAA
1 TAAATTTAAA
943 CTAATTTAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
17 29 0.49
18 13 0.22
19 5 0.08
20 12 0.20
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
TAAATTTAAATTTAAAGA
Found at i:903 original size:37 final size:35
Alignment explanation
Indices: 861--942 Score: 130
Period size: 37 Copynumber: 2.3 Consensus size: 35
851 CAAATTTGAT
861 TAAATTTAAATTTAAAGA-AAATTTAAATTTAAAAAGA
1 TAAATTTAAATTT-AAGATAAATTTAAATTT-AAAA-A
898 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAGATAAATTTAAATTTAAAAA
933 TAAATTTAAA
1 TAAATTTAAA
943 CTAATTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
35 11 0.25
36 8 0.18
37 25 0.57
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (35 bp):
TAAATTTAAATTTAAGATAAATTTAAATTTAAAAA
Found at i:1679 original size:206 final size:206
Alignment explanation
Indices: 1295--1964 Score: 867
Period size: 206 Copynumber: 3.3 Consensus size: 206
1285 TCTGGTTTCA
* * * * *** ** ** *
1295 TTGACTTGGCCTTCTTCTCAGTATCTCATTAGGAAGACGACCATATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * * ** * * * *
1360 CTCTGTGTTTCATCAGGAAGATGGTTTTTGTTCACTTCCCTGTATTTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
1425 TTTATTAGTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
1490 CGAGCGTGGGT
196 CGAGCGTGGGT
* *
1501 TTGATTTGGTCTTC-TCTTCTGTGTCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
1 TTGATTTGGTCTTCTTC-TCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCT
* * **
1565 TCTCTGTATCTCAACAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAATTA
65 TCTCTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
*
1630 TTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCACA
130 TTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
1695 TCGAGCGTGAGT
195 TCGAGCGTGGGT
** * * *
1707 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATTGTGTCGTTTATTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
* * *
1772 CTCTGTATCTCATCAGGCAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAGCC-T
66 CTCTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
** * * * * *
1836 TTTATTGTTTCAACCTACTTTTCAATGTCTCATAAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
1901 CGAGCGTGGGT
196 CGAGCGTGGGT
* * *
1912 TTGATTTGGTCTTCTTCTCAATATCTTATTAGGAAGATGACCGCGTCGTTTGT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGT
1965 GGATAATCGT
Statistics
Matches: 401, Mismatches: 61, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
205 116 0.29
206 283 0.71
207 2 0.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTAGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:8983 original size:153 final size:153
Alignment explanation
Indices: 8743--9051 Score: 566
Period size: 153 Copynumber: 2.0 Consensus size: 153
8733 GGTAATTGCC
*
8743 CATTGGAGTTTTGGGTTGACCTGTCAAGAAGGGTTTGGTGTAGCTAGGTCTGTATATGCTTACGT
1 CATTGAAGTTTTGGGTTGACCTGTCAAGAAGGGTTTGGTGTAGCTAGGTCTGTATATGCTTACGT
8808 TATTGACTTCATTATCCCTTTTTCTAGGGGCAAG-CCTTTTAGGGTTTTCTCCGGTTTCAATCTT
66 TATTGACTTCATTATCCCTTTTTCTAGGGG-AAGACCTTTTAGGGTTTTCTCCGGTTTCAATCTT
8872 GCCAGTCTTGATTGCATTTTCAAT
130 GCCAGTCTTGATTGCATTTTCAAT
*
8896 CATTGAAGTTTTGGGTTGACCTGTCATGAAGGGTTTGGTGTAGCTAGGTCTGTATATGCTTACGT
1 CATTGAAGTTTTGGGTTGACCTGTCAAGAAGGGTTTGGTGTAGCTAGGTCTGTATATGCTTACGT
*
8961 TATTGACTTCATTATCCCTTTTTCTAGGGGTAGACCTTTTAGGGTTTTCTCCGGTTTCAATCTTG
66 TATTGACTTCATTATCCCTTTTTCTAGGGGAAGACCTTTTAGGGTTTTCTCCGGTTTCAATCTTG
*
9026 CCAGTCTTGATTGCATTTTCATT
131 CCAGTCTTGATTGCATTTTCAAT
9049 CAT
1 CAT
9052 CTCCACCGAT
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
152 2 0.01
153 149 0.99
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (153 bp):
CATTGAAGTTTTGGGTTGACCTGTCAAGAAGGGTTTGGTGTAGCTAGGTCTGTATATGCTTACGT
TATTGACTTCATTATCCCTTTTTCTAGGGGAAGACCTTTTAGGGTTTTCTCCGGTTTCAATCTTG
CCAGTCTTGATTGCATTTTCAAT
Found at i:22950 original size:4 final size:4
Alignment explanation
Indices: 22937--22990 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
22927 TAGAAAAAGG
* *
22937 AAAT -AAT AAAT AAAT AGGAT ATA- AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
22984 ATAT AAA
1 AAAT AAA
22991 CATATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
3 5 0.12
4 34 0.81
5 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:27501 original size:21 final size:21
Alignment explanation
Indices: 27472--27511 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27462 TATTTATCGA
* *
27472 TTTCTATTGAGAGAAATTAGT
1 TTTCGATTGAAAGAAATTAGT
*
27493 TTTCGATTGAAAGTAATTA
1 TTTCGATTGAAAGAAATTA
27512 TTAAGGTTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (21 bp):
TTTCGATTGAAAGAAATTAGT
Found at i:30386 original size:31 final size:31
Alignment explanation
Indices: 30346--30413 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
30336 CTTAATACTC
*
30346 TAATAACTTAAATAAAAACTTTCAAATAATT
1 TAATGACTTAAATAAAAACTTTCAAATAATT
* *
30377 TAATGACTTAACTGAAAACTTTCAAATAATT
1 TAATGACTTAAATAAAAACTTTCAAATAATT
*
30408 CAATGA
1 TAATGA
30414 TCATTTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (31 bp):
TAATGACTTAAATAAAAACTTTCAAATAATT
Done.