Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009778.1 Kokia drynarioides strain JFW-HI SEQ_124499, 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: 1989
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Found at i:1356 original size:30 final size:29
Alignment explanation
Indices: 1312--1571 Score: 160
Period size: 30 Copynumber: 8.8 Consensus size: 29
1302 GGAGGTCCCT
* *
1312 AAACTGTCTGAAAATTACATTTTCGACCTCA
1 AAACT-TCTAAAAATTCCATTTT-GACCTCA
*
1343 AAACTTCTAAAAATTCCATTTTTGACCTCG
1 AAACTTCTAAAAATTCCA-TTTTGACCTCA
*
1373 AAACTTCTAAAAATTCCATTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTGACCTCA
* *
1402 AAACTTCCAAAAATTCCATTTTTAACC-CTA
1 AAACTTCTAAAAATTCCA-TTTTGACCTC-A
* *
1432 AAACTT-TCAAATATTACCATTTTGCCCTC-
1 AAACTTCT-AAAAATT-CCATTTTGACCTCA
* * *
1461 AAA-TGTCCAAAATTTCCATTTTTAACC-CTA
1 AAACT-TCTAAAAATTCCA-TTTTGACCTC-A
*
1491 AAACTT-TCAAAAATTACCATTTTGCCCTC-
1 AAACTTCT-AAAAATT-CCATTTTGACCTCA
* * * * *
1520 GAA-TGTCCAAAAATTCCTTTTTTAACC-CTG
1 AAACT-TCTAAAAATTCC-ATTTTGACCTC-A
*
1550 AAACTTCCAAAAATTCCATTTT
1 AAACTTCTAAAAATTCCATTTT
1572 TACCCTTGAA
Statistics
Matches: 181, Mismatches: 27, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
28 9 0.05
29 62 0.34
30 91 0.50
31 19 0.10
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (29 bp):
AAACTTCTAAAAATTCCATTTTGACCTCA
Found at i:1414 original size:59 final size:58
Alignment explanation
Indices: 1308--1606 Score: 263
Period size: 59 Copynumber: 5.0 Consensus size: 58
1298 CCTTGGAGGT
* * * * *
1308 CCCT-AAACTGTCTGAAAATTACATTTTCGACCTCAAAACT-TCTAAAAATTCCATTTTTGA
1 CCCTGAAACT-TCTAAAAATTCCATTTT-GACC-CCAAA-TGTCCAAAAATTCCATTTTTAA
1368 -CCTCGAAACTTCTAAAAATTCCATTTTGACCCCAAAACT-TCCAAAAATTCCATTTTTAA
1 CCCT-GAAACTTCTAAAAATTCCATTTTGACCCC-AAA-TGTCCAAAAATTCCATTTTTAA
* * *
1427 CCCTAAAACTT-TCAAATATTACCATTTTG-CCCTCAAATGTCCAAAATTTCCATTTTTAA
1 CCCTGAAACTTCT-AAAAATT-CCATTTTGACCC-CAAATGTCCAAAAATTCCATTTTTAA
* * *
1486 CCCTAAAACTT-TCAAAAATTACCATTTTG-CCCTCGAATGTCCAAAAATTCCTTTTTTAA
1 CCCTGAAACTTCT-AAAAATT-CCATTTTGACCC-CAAATGTCCAAAAATTCCATTTTTAA
* * ** *
1545 CCCTGAAACTTCCAAAAATTCCATTTTTACCCTTGAATGTCTAAAAATTCCATCTTTTAA
1 CCCTGAAACTTCTAAAAATTCCATTTTGACCC-CAAATGTCCAAAAATTCCAT-TTTTAA
1605 CC
1 CC
1607 TCGAACTTCC
Statistics
Matches: 210, Mismatches: 18, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
58 10 0.05
59 160 0.76
60 35 0.17
61 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
CCCTGAAACTTCTAAAAATTCCATTTTGACCCCAAATGTCCAAAAATTCCATTTTTAA
Found at i:1572 original size:30 final size:30
Alignment explanation
Indices: 1343--1606 Score: 210
Period size: 30 Copynumber: 8.9 Consensus size: 30
1333 TTCGACCTCA
* *
1343 AAACTTCTAAAAATTCCATTTTTGA-CCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCT-G
* * **
1373 AAACTTCTAAAAATTCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTAACCCTG
*
1402 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTAACCCTG
* * * *
1432 AAACTTTCAAATATTACCA-TTTT-GCCCTC
1 AAACTTCCAAAAATT-CCATTTTTAACCCTG
* *
1461 AAA-TGTCCAAAATTTCCATTTTTAACCCTA
1 AAACT-TCCAAAAATTCCATTTTTAACCCTG
* *
1491 AAACTTTCAAAAATTACCA-TTTT-GCCCTCG
1 AAACTTCCAAAAATT-CCATTTTTAACCCT-G
*
1521 -AA-TGTCCAAAAATTCCTTTTTTAACCCTG
1 AAACT-TCCAAAAATTCCATTTTTAACCCTG
1550 AAACTTCCAAAAATTCCATTTTT-ACCCTTG
1 AAACTTCCAAAAATTCCATTTTTAACCC-TG
*
1580 -AA-TGTCTAAAAATTCCATCTTTTAACC
1 AAACT-TCCAAAAATTCCAT-TTTTAACC
1607 TCGAACTTCC
Statistics
Matches: 193, Mismatches: 23, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
28 8 0.04
29 80 0.41
30 94 0.49
31 11 0.06
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCTG
Found at i:1660 original size:118 final size:116
Alignment explanation
Indices: 1348--1649 Score: 347
Period size: 118 Copynumber: 2.6 Consensus size: 116
1338 CCTCAAAACT
* * * *
1348 TCTAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAATT-CCATTTTGACCCCAAAACTTCCAA
1 TCTAAAAATTCCATTTTTAACCTCG-AACTTCCAAAAATTACCATTTTG-CCCCGAAA-GTCCAA
* * *
1412 AAATTCCATTTTTAACCCTAAAACTTTCAAATATTACCATTTTGCCCTCAAATG
63 AAATTCCATTTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCTCAAATG
* * ** * *
1466 TCCAAAATTTCCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTGCCCTCGAATGTCCAAA
1 TCTAAAAATTCCATTTTTAA-CCTCGAACTTCCAAAAATTACCATTTTGCCC-CGAAAGTCCAAA
* * **
1531 AATTCCTTTTTTAACCCTGAAACTTCCAAAAATT-CCATTTTTACCCTTGAATG
64 AATTCCATTTTTAACCCTAAAACTTCCAAAAATTACCA-TTTTACCCTCAAATG
* *
1584 TCTAAAAATTCCATCTTTTAACCTCGAACTTCCCCAAAATTACCATCTTGCCCCGAAAGTCCAAA
1 TCTAAAAATTCCAT-TTTTAACCTCGAACTT-CCAAAAATTACCATTTTGCCCCGAAAGTCCAAA
1649 A
64 A
1650 TTAGCATTTT
Statistics
Matches: 153, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
117 3 0.02
118 112 0.73
119 38 0.25
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (116 bp):
TCTAAAAATTCCATTTTTAACCTCGAACTTCCAAAAATTACCATTTTGCCCCGAAAGTCCAAAAA
TTCCATTTTTAACCCTAAAACTTCCAAAAATTACCATTTTACCCTCAAATG
Done.