Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012485.1 Kokia drynarioides strain JFW-HI SEQ_127489, 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: 6769
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:1358 original size:30 final size:30
Alignment explanation
Indices: 1297--1658 Score: 313
Period size: 30 Copynumber: 12.2 Consensus size: 30
1287 TAAGAGGTCC
*
1297 CGAAACTTCCAAAAA-TCACATTTTTTTACCT
1 CGAAACTTCCAAAAATTC-CA-TTTTTGACCT
*
1328 CGAAACTTCTAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
1358 CG-AACTTCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
* * *
1387 CTG-AACTTCCAAAAATCCCATTTTTAACCC
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
*
1417 CAAAACTTCCAAAAATTCCATTTTTGACC-
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* * *
1446 CTAAAACTTCTAAAAATCCCATTTTTGACCT
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
*
1477 CAAAACTTCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
* *
1507 CG-AACTT-CAAAAATTTCATTTTT-ACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* * * * *
1534 CTAAAACTTCAAAAAATTCTAATTTT-ACCC
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
* *
1564 CTG-AACTTCTAAAAACTCCATTTTTGACC-
1 C-GAAACTTCCAAAAATTCCATTTTTGACCT
* *
1593 CTAAACTTCCAAAAATTACCA-TTTTGCCCT
1 CGAAACTTCCAAAAATT-CCATTTTTGACCT
* * *
1623 TG-AA-TGTCCAAAAACTCCATTTTCGACCT
1 CGAAACT-TCCAAAAATTCCATTTTTGACCT
1652 CGAAACT
1 CGAAACT
1659 CTTAAAATTA
Statistics
Matches: 277, Mismatches: 35, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
27 3 0.01
28 21 0.08
29 94 0.34
30 138 0.50
31 19 0.07
32 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:1424 original size:60 final size:60
Alignment explanation
Indices: 1299--1650 Score: 347
Period size: 58 Copynumber: 6.0 Consensus size: 60
1289 AGAGGTCCCG
* * *
1299 AAACTTCCAAAAA-TCACATTTTTTTA-CCTC-GAAACTTCTAAAAATTCCATTTTTGACCTC-
1 AAACTTCCAAAAATTC-CA--TTTTTACCCTCTG-AACTTCCAAAAATCCCATTTTTGACCCCA
* *
1359 GAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
** * *
1419 AAACTTCCAAAAATTCCATTTTTGACCCT-AAAACTTCTAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
**
1479 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTT-CAAAAATTTCATTTTT-ACCCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCC-A
* * * * *
1537 AAACTTCAAAAAATTCTAATTTTACCC-CTGAACTTCTAAAAA-CTCCATTTTTGA-CCCT
1 AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATC-CCATTTTTGACCCCA
* *
1595 AAACTTCCAAAAATTACCA-TTTTGCCCT-TGAA-TGTCCAAAAA-CTCCATTTTCGACC
1 AAACTTCCAAAAATT-CCATTTTTACCCTCTGAACT-TCCAAAAATC-CCATTTTTGACC
1651 TCGAAACTCT
Statistics
Matches: 249, Mismatches: 28, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
57 6 0.02
58 93 0.37
59 56 0.22
60 87 0.35
61 7 0.03
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (60 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCTGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:1686 original size:58 final size:58
Alignment explanation
Indices: 1295--1738 Score: 206
Period size: 58 Copynumber: 7.5 Consensus size: 58
1285 TCTAAGAGGT
* * * *
1295 CCCGAAACTTCCAAAAATCA-CATTTTTTTA-CCTCGAAACT-TCTAAAAATTCCATTTTTGA
1 CCCGAAACTTCCAAAAATTACCA---TTTTACCCTCG-AA-TGTCCAAAAACTCCATTTTCGA
**
1355 CCTCG-AACTTCCAAAAATT-CCATTTTTACCCTCTGAACT-TCCAAAAA-TCCCATTTTTAA
1 CC-CGAAACTTCCAAAAATTACCA-TTTTACCCTC-GAA-TGTCCAAAAACT-CCATTTTCGA
* ** * *
1414 CCCCAAAACTTCCAAAAATT-CCATTTTTGACCCTAAAACT-TCTAAAAA-TCCCATTTTTGA
1 -CCCGAAACTTCCAAAAATTACCA-TTTT-ACCCTCGAA-TGTCCAAAAACT-CCATTTTCGA
* * * *
1474 CCTCAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACT-T-CAAAAATTTCATTTT-TA
1 CC-CGAAACTTCCAAAAATTACCA-TTTTACCCTCGAA-TGTCCAAAAACTCCATTTTCGA
* * * * *
1531 CCCCTAAAACTTCAAAAAATT-CTAATTTTACCC-CTGAACT-TCTAAAAACTCCATTTTTGA
1 -CCC-GAAACTTCCAAAAATTAC-CATTTTACCCTC-GAA-TGTCCAAAAACTCCATTTTCGA
* * *
1591 CCCTAAACTTCCAAAAATTACCATTTTGCCCTTGAATGTCCAAAAACTCCATTTTCGA
1 CCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTCGA
** * * * * **
1649 CCTCGAAAC-TCTTAAAATTACCCTTTTA-CCTCCGAATGTCTAAAAATTCCTTTTTTAA
1 CC-CGAAACTTCCAAAAATTACCATTTTACCCT-CGAATGTCCAAAAACTCCATTTTCGA
** * *
1707 CTCCGAATTTTCCCAAAATTACCATTTCACCC
1 C-CCGAAACTTCCAAAAATTACCATTTTACCC
1739 CCAAGAATCC
Statistics
Matches: 317, Mismatches: 43, Indels: 48
0.78 0.11 0.12
Matches are distributed among these distances:
57 7 0.02
58 135 0.43
59 76 0.24
60 92 0.29
61 7 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
CCCGAAACTTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCCATTTTCGA
Found at i:3756 original size:18 final size:19
Alignment explanation
Indices: 3722--3758 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3712 AAAAAACAAA
3722 TTCAGATTACGTTTTTTAAT
1 TTCAGATTAC-TTTTTTAAT
3742 TTCAGATTA-TTTTTTAA
1 TTCAGATTACTTTTTTAA
3759 AGAGATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (19 bp):
TTCAGATTACTTTTTTAAT
Done.