Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008328.1 Kokia drynarioides strain JFW-HI SEQ_122994, 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, 945
Length: 1576
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Found at i:47 original size:13 final size:13
Alignment explanation
Indices: 28--66 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
18 ATTGATAACT
28 GTATTAATAATTA
1 GTATTAATAATTA
* *
41 TTATTAATAATCA
1 GTATTAATAATTA
*
54 GTATTAATTATTA
1 GTATTAATAATTA
67 AGAATAAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (13 bp):
GTATTAATAATTA
Found at i:1092 original size:29 final size:29
Alignment explanation
Indices: 1060--1430 Score: 266
Period size: 29 Copynumber: 12.6 Consensus size: 29
1050 CTAAACTGTA
1060 CAAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCTCGAACTTC
*
1089 CAAAAA-T-CTCATTTTTTA-CCTCAAAACTTC
1 CAAAAATTAC-CA--TTTTACCCTC-GAACTTC
* *
1119 CTAAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTACCATTTTACCCTCGAACTTC
* **
1148 CAAAAA-TCCCATTTTTGACCCTAAAACTTC
1 CAAAAATTACCA-TTTT-ACCCTCGAACTTC
* * *
1178 CTAAAATTACCA-TTTACCCCCAAACTTC
1 CAAAAATTACCATTTTACCCTCGAACTTC
*
1206 CAAAAA-TCCCATTTTGACCCT-GAACCTTC
1 CAAAAATTACCATTTT-ACCCTCGAA-CTTC
*
1235 CTAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCTCGAACTTC
* *
1264 CAAAAA-TCCCATTTTTTACCC-CAAAACTTC
1 CAAAAATTACCA--TTTTACCCTC-GAACTTC
* * * *
1294 CTAAAATTATCGTTTTACTCTCGAACTTC
1 CAAAAATTACCATTTTACCCTCGAACTTC
*
1323 CAAAAGTT-CCATTTTTTA-CCTCGAAACTTC
1 CAAAAATTACCA--TTTTACCCTCG-AACTTC
* *
1353 TAAAAATTACCATTTTACCCCCGAACTT-
1 CAAAAATTACCATTTTACCCTCGAACTTC
* *
1381 CTAAAAGT-CTCATTTTTAACCCT-GACACTTAC
1 CAAAAATTAC-CA-TTTT-ACCCTCGA-ACTT-C
*
1413 AAAAAATTACCATTTTAC
1 CAAAAATTACCATTTTAC
1431 TTTCGAATGT
Statistics
Matches: 267, Mismatches: 43, Indels: 63
0.72 0.12 0.17
Matches are distributed among these distances:
27 6 0.02
28 40 0.15
29 100 0.37
30 96 0.36
31 16 0.06
32 8 0.03
33 1 0.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAACTTC
Found at i:1154 original size:59 final size:58
Alignment explanation
Indices: 1062--1430 Score: 438
Period size: 59 Copynumber: 6.3 Consensus size: 58
1052 AAACTGTACA
* *
1062 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTTACCTCAAAACTTCCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACC-CAAAACTTCCT
*
1121 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCC-AAAACTTCCT
* * * *
1180 AAAATTACCA-TTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCCTGAACCTTCCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCC-AAAACTTCCT
*
1237 AAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTA-CCCAAAACTTCCT
* * * * * * *
1296 AAAATTATCGTTTTACTCTCGAACTTCCAAAAGTTCCATTTTTTACCTCGAAACTT-CT
1 AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACC-CAAAACTTCCT
* * * * * * **
1354 AAAAATTACCATTTTACCCCCGAACTTCTAAAAGTCTCATTTTTAACCCTGACACTTACAA
1 -AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCC-AAAACTT-CCT
1415 AAAATTACCATTTTAC
1 AAAATTACCATTTTAC
1431 TTTCGAATGT
Statistics
Matches: 273, Mismatches: 28, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
57 28 0.10
58 57 0.21
59 169 0.62
60 19 0.07
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCAAAACTTCCT
Found at i:1361 original size:175 final size:178
Alignment explanation
Indices: 1061--1430 Score: 518
Period size: 175 Copynumber: 2.1 Consensus size: 178
1051 TAAACTGTAC
* *
1061 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTTACCTCAAAACTTCCTAAAAT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCTAAAAT
1126 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCTAAAATTACCA-
66 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCTAAAATTACCAT
* *
1190 TTTACCCCCAAACTTCCAAAAATCCCA-TTTTGACCCTGA-ACCTT-CC
131 TTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTGACA-CTTACA
*
1236 TAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCTAAAAT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCTAAAAT
* * * * * * * *
1301 TATCGTTTTACTCTCGAACTTCCAAAAGTTCCATTTTTTA-CCTCGAAACTT-CTAAAAATTACC
66 TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCT-AAAACTTCCT-AAAATTACC
* * * *
1364 ATTTTACCCCCGAACTTCTAAAAGTCTCATTTTTAACCCTGACACTTACA
129 ATTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTGACACTTACA
1414 AAAAATTACCATTTTAC
1 AAAAATTACCATTTTAC
1431 TTTCGAATGT
Statistics
Matches: 171, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
174 5 0.03
175 111 0.65
176 23 0.13
177 14 0.08
178 18 0.11
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (178 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACCCCAAAACTTCCTAAAAT
TACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCTAAAATTACCAT
TTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCTGACACTTACA
Done.