Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009294.1 Kokia drynarioides strain JFW-HI SEQ_124000, 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: 2578
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Found at i:1058 original size:42 final size:41
Alignment explanation
Indices: 1011--1130 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 41
1001 GTGTGACTTC
*
1011 AATCTGCCCTTCTGAATTAGGGGTAAAAGATTGGATCGCTTT
1 AATCTGCCCTT-TGAATTAGGGGTAAAAGATTGGATAGCTTT
*
1053 AATCTGCCCATTTGGATTAGGGGTAAAAGATTGGATAGCTTT
1 AATCTGCCC-TTTGAATTAGGGGTAAAAGATTGGATAGCTTT
* *
1095 AATCTTCCCCTTT-AGATTAGGGATAAAAGATTGGAT
1 AATC-TGCCCTTTGA-ATTAGGGGTAAAAGATTGGAT
1131 GGTGGTTTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
42 64 0.91
43 6 0.09
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.33
Consensus pattern (41 bp):
AATCTGCCCTTTGAATTAGGGGTAAAAGATTGGATAGCTTT
Found at i:1160 original size:45 final size:45
Alignment explanation
Indices: 1007--1266 Score: 227
Period size: 45 Copynumber: 5.9 Consensus size: 45
997 TTGTGTGTGA
*
1007 CTTCAATCTGCC-CT-TCTGAATTAGGGGTAAAAGATTGGA---TCG
1 CTTCAATCTGCCTCTCT-TG-ATTAGGGGTAAAAGATTGGATGGTGG
* *
1049 CTTTAATCTGCC-CAT-TTGGATTAGGGGTAAAAGATTGGA---TAG
1 CTTCAATCTGCCTC-TCTT-GATTAGGGGTAAAAGATTGGATGGTGG
* * * *
1091 CTTTAATCTTCCCCT-TTAGATTAGGGATAAAAGATTGGATGGTGG
1 CTTCAATCTGCCTCTCTT-GATTAGGGGTAAAAGATTGGATGGTGG
* * * * * *
1136 TTTCAATCTGCTTTTTTTGATTAGGGGTAAAAGATTAGATGGTAG
1 CTTCAATCTGCCTCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* * * *
1181 CTTCAATCTTCCCCTCTTGACTAAGGGTAAAAGATTGGATGGTGG
1 CTTCAATCTGCCTCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
* *
1226 CTTCAATCTGCCTCACTTGACTAGGGGTAAAAGATTGGATG
1 CTTCAATCTGCCTCTCTTGATTAGGGGTAAAAGATTGGATG
1267 AGGTGATGTA
Statistics
Matches: 182, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
42 69 0.38
43 4 0.02
45 107 0.59
46 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (45 bp):
CTTCAATCTGCCTCTCTTGATTAGGGGTAAAAGATTGGATGGTGG
Found at i:1215 original size:90 final size:89
Alignment explanation
Indices: 1048--1267 Score: 261
Period size: 90 Copynumber: 2.5 Consensus size: 89
1038 AGATTGGATC
* * *
1048 GCTTTAATCTGCC-CATTTGGATTAGGGGTAAAAGATTG--GATAGCTTTAATCTTCCCCTTTAG
1 GCTTCAATCTGCCTCACTT-GATTAGGGGTAAAAGATTGATGATAGCTTCAATCTTCCCCTTTAG
*
1110 ATTAGGGATAAAAGATTGGATGGTG
65 ATAAGGGATAAAAGATTGGATGGTG
* * *** *
1135 GTTTCAATCTGCTTTTTTTGATTAGGGGTAAAAGATTAGATGGTAGCTTCAATCTTCCCCTCTT-
1 GCTTCAATCTGCCTCACTTGATTAGGGGTAAAAGATT-GATGATAGCTTCAATCTTCCCCT-TTA
1199 GACTAAGGG-TAAAAGATTGGATGGTG
64 GA-TAAGGGATAAAAGATTGGATGGTG
*
1225 GCTTCAATCTGCCTCACTTGACTAGGGGTAAAAGATTGGATGA
1 GCTTCAATCTGCCTCACTTGATTAGGGGTAAAAGATT-GATGA
1268 GGTGATGTAG
Statistics
Matches: 111, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
87 28 0.25
88 4 0.04
90 72 0.65
91 7 0.06
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (89 bp):
GCTTCAATCTGCCTCACTTGATTAGGGGTAAAAGATTGATGATAGCTTCAATCTTCCCCTTTAGA
TAAGGGATAAAAGATTGGATGGTG
Found at i:2107 original size:49 final size:49
Alignment explanation
Indices: 1411--2187 Score: 599
Period size: 49 Copynumber: 15.9 Consensus size: 49
1401 TCACGCTATG
* * * * *
1411 AGATTCGCC-TCTGTGGCTTCAATCTTTCCCTCCACATTTCTAGGCTATA
1 AGATTCGCCGT-TGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* ** * * * *
1460 AGGTTCGCTATTGCGGCTTCAACCTTGCCTTCCACATCTTTAGGGTATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * *
1509 AGGTTCGCAGTTGCGGCTTCAACATTTCCCTCTATATCTTTAGGGTATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
** * * *
1558 AGATTCATCGTTGCGG-TGT-AACTTTTCCCTTCATATCTTTAGGGTATA
1 AGATTCGCCGTTGCGGCT-TCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * *
1606 AGATTCGTCGTTACGGCTTTAAACTTTCCCTCCATATCTCTAGGGTATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * *
1655 AGGTTCGCCGTTGAGTCTTCAACCTTTCCCTCCATATCTCTATGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * ** * * * *
1704 AGGTTCGCCATTTTGGCATCAACCTTTCCCTCCATATCTCTAAGGCACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * *
1753 AGGTTCGCCGTTGCAGCTTCAACCTTTCCCTCCATATCTCTAAGGTATG
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * * * * *
1802 AGATTCGTCATTACGACTTCAATCTCTCCCTCCATATCTCTAAGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * * * * * *
1851 AGGTTCACCATTGTGGCTTTAACCTTTCCCTCCATATTTTTGGGGTATG
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
** ** * * * * *
1900 AGATTTTCTATTGCGGCTTCAATCTCTCCCTTCATATCTCTAAGGTACA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * *
1949 AGGTTCGTCGTTGCAGCTTCAATCTTTCCCTCCATATCTCTAGGGTATG
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * *
1998 AGATTCGCCGTTGCGGCTTCAATCTCTCCCTTCATATCCCTAGGGTATA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* ** * * * *
2047 AGTTTTTCCGTTGCGACTTTAACCTTTCCCTTCATATCTCTAGGGTATG
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
* * * * * * * *
2096 AGATTCGCCGTTGTGGCTTTAATCTCTCCCTTCACATCTTTAAGGTATTA
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTA-TA
* * * * * * *
2146 A-ATTCGTCATTGTGGCTTTAATCTTTCCCTTCACATCTCTAG
1 AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAG
2188 AGTGTAGGAT
Statistics
Matches: 586, Mismatches: 137, Indels: 10
0.80 0.19 0.01
Matches are distributed among these distances:
48 42 0.07
49 541 0.92
50 3 0.01
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.37
Consensus pattern (49 bp):
AGATTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCTAGGGTATA
Done.