Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008376.1 Kokia drynarioides strain JFW-HI SEQ_123043, 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: 2861
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Found at i:239 original size:3 final size:3
Alignment explanation
Indices: 233--286 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
223 ATCATTAAAA
* * *
233 ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
279 ATT ATT AT
1 ATT ATT AT
287 ATAAATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:253 original size:15 final size:13
Alignment explanation
Indices: 232--296 Score: 67
Period size: 15 Copynumber: 4.6 Consensus size: 13
222 CATCATTAAA
232 AATTATTATTAGTGT
1 AATTATTATTA-T-T
*
247 CATTATTATTATT
1 AATTATTATTATT
260 ATTATTATTATTATT
1 A--ATTATTATTATT
275 AATTATTATTATAT
1 AATTATTATTAT-T
*
289 AAATATTA
1 AATTATTA
297 ATAATAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.27
14 9 0.20
15 23 0.52
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (13 bp):
AATTATTATTATT
Found at i:1010 original size:23 final size:23
Alignment explanation
Indices: 971--1021 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
961 TTAATTTAAT
* *
971 TTTAACTTAAAATAAACTTAT-A
1 TTTAAATTAAAATAAACTCATAA
*
993 TTTAAATTAAATTCAAACTCATAA
1 TTTAAATTAAAAT-AAACTCATAA
1017 TTTAA
1 TTTAA
1022 TTTTGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.46
23 7 0.29
24 6 0.25
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAATTAAAATAAACTCATAA
Found at i:1023 original size:23 final size:21
Alignment explanation
Indices: 971--1023 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
961 TTAATTTAAT
*
971 TTTAACTTAAAATAAACTTATA
1 TTTAA-TTAAAATAAACTCATA
*
993 TTTAAATTAAATTCAAACTCATAA
1 TTT-AATTAAAAT-AAACTCAT-A
1017 TTTAATT
1 TTTAATT
1024 TTGAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 9 0.35
23 13 0.50
24 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAATTAAAATAAACTCATA
Found at i:1831 original size:159 final size:158
Alignment explanation
Indices: 1543--1882 Score: 592
Period size: 159 Copynumber: 2.1 Consensus size: 158
1533 CTTCGACACG
*
1543 CTTCTCAGTATCTCATCAGGAAGCTATGGTTCGAAAATTTGCTCACATCGAGCATGGGTTTGGTT
1 CTTCTCCGTATCTCATCAGGAAGCTATGGTTCGAAAATTTGCTCACATCGAGCATGGGTTTGGTT
*
1608 TGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGT
66 TGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATTCGCTTCTCTGT
1673 ATCTCATCAGGAAGATGAATTTGGTTTA
131 ATCTCATCAGGAAGATGAATTTGGTTTA
* * *
1701 CTTCTCCGTATCTCATCAGGAAGCTGTGGTTCGAAGATTTGCTCACGTCGAGCATGGGTTTGGGT
1 CTTCTCCGTATCTCATCAGGAAGCTATGGTTCGAAAATTTGCTCACATCGAGCATGGGTTT-GGT
*
1766 TTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATT-GCTTCTCT
65 TTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTC-AATTCGCTTCTCT
*
1830 GTATCTCATCATGAAGATGAATTTGGTTTA
129 GTATCTCATCAGGAAGATGAATTTGGTTTA
1860 CTTCTCCGTATCTCATCAGGAAG
1 CTTCTCCGTATCTCATCAGGAAG
1883 GTGACTGCGT
Statistics
Matches: 173, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
158 57 0.33
159 112 0.65
160 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (158 bp):
CTTCTCCGTATCTCATCAGGAAGCTATGGTTCGAAAATTTGCTCACATCGAGCATGGGTTTGGTT
TGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCACGTCATTTGTTTCAATTCGCTTCTCTGT
ATCTCATCAGGAAGATGAATTTGGTTTA
Found at i:1834 original size:49 final size:47
Alignment explanation
Indices: 1781--1932 Score: 153
Period size: 49 Copynumber: 3.4 Consensus size: 47
1771 CTTCTTCTTA
1781 GTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATTGCTTCTCT
1 GTATCTCATCAGGAAGATGA-CACGTCGTTTGTTTC-AATTGCTTCTCT
* * *
1830 GTATCTCATCATGAAGATGA-A--T--TTGGTTT--A---CTTCTCC
1 GTATCTCATCAGGAAGATGACACGTCGTTTGTTTCAATTGCTTCTCT
* *
1867 GTATCTCATCAGGAAGGTGACTGCGTCGTTTGTTTCAATTCGCTTCTCT
1 GTATCTCATCAGGAAGATGAC-ACGTCGTTTGTTTCAATT-GCTTCTCT
1916 GTATCTCATCAGGAAGA
1 GTATCTCATCAGGAAGA
1933 CGAATTTGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
37 24 0.29
40 1 0.01
41 1 0.01
43 12 0.15
45 2 0.02
47 1 0.01
49 41 0.50
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (47 bp):
GTATCTCATCAGGAAGATGACACGTCGTTTGTTTCAATTGCTTCTCT
Found at i:1912 original size:86 final size:86
Alignment explanation
Indices: 1781--1968 Score: 306
Period size: 86 Copynumber: 2.2 Consensus size: 86
1771 CTTCTTCTTA
*
1781 GTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATTGCTTCTCTGTATCTCATCATGAAG
1 GTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATTGCTTCTCTGTATCTCATCAGGAAG
* *
1846 ATGAATTTGGTTTACTTCTCC
66 ACGAATTTGGTTCACTTCTCC
* **
1867 GTATCTCATCAGGAAGGTGACTGCGTCGTTTGTTTC-AATTCGCTTCTCTGTATCTCATCAGGAA
1 GTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATT-GCTTCTCTGTATCTCATCAGGAA
1931 GACGAATTTGGTTCACTTCTCC
65 GACGAATTTGGTTCACTTCTCC
1953 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
1969 CTGTGGTTCG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (86 bp):
GTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAAATTGCTTCTCTGTATCTCATCAGGAAG
ACGAATTTGGTTCACTTCTCC
Done.