Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012853.1 Kokia drynarioides strain JFW-HI SEQ_127867, 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: 15493
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.25
Warning! 377 characters in sequence are not A, C, G, or T
Found at i:696 original size:35 final size:33
Alignment explanation
Indices: 656--766 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 33
646 CGACGGCCAC
*
656 GCGCCGGGATCGGCGATGCGCGGGCGGCCATACG
1 GCGCC-GGATCGGCGATGCGCGTGCGGCCATACG
*
690 TGCGCCGGAT-GGCGA--CGCATGCGGCC--AC-
1 -GCGCCGGATCGGCGATGCGCGTGCGGCCATACG
718 GCGCCGGGATCGGCGATGCGCGTGCGGCCATACG
1 GCGCC-GGATCGGCGATGCGCGTGCGGCCATACG
752 CGCGCCGGA-CGGCGA
1 -GCGCCGGATCGGCGA
767 CTAGCCTGAC
Statistics
Matches: 65, Mismatches: 3, Indels: 18
0.76 0.03 0.21
Matches are distributed among these distances:
27 5 0.08
28 4 0.06
29 7 0.11
31 19 0.29
33 13 0.20
34 7 0.11
35 10 0.15
ACGTcount: A:0.13, C:0.34, G:0.44, T:0.09
Consensus pattern (33 bp):
GCGCCGGATCGGCGATGCGCGTGCGGCCATACG
Found at i:746 original size:62 final size:62
Alignment explanation
Indices: 649--767 Score: 211
Period size: 62 Copynumber: 1.9 Consensus size: 62
639 CGACACACGA
* *
649 CGGCCACGCGCCGGGATCGGCGATGCGCGGGCGGCCATACGTGCGCCGGATGGCGACGCATG
1 CGGCCACGCGCCGGGATCGGCGATGCGCGGGCGGCCATACGCGCGCCGGACGGCGACGCATG
*
711 CGGCCACGCGCCGGGATCGGCGATGCGCGTGCGGCCATACGCGCGCCGGACGGCGAC
1 CGGCCACGCGCCGGGATCGGCGATGCGCGGGCGGCCATACGCGCGCCGGACGGCGAC
768 TAGCCTGACT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.13, C:0.36, G:0.43, T:0.08
Consensus pattern (62 bp):
CGGCCACGCGCCGGGATCGGCGATGCGCGGGCGGCCATACGCGCGCCGGACGGCGACGCATG
Found at i:1412 original size:29 final size:28
Alignment explanation
Indices: 1378--1479 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
1368 TAAACTTTCT
1378 AAAAATTACCATTTTACCCTTGAACTTCC
1 AAAAA-TACCATTTTACCCTTGAACTTCC
* * *
1407 AAAAATCCCATTTTTGGCCC-TGAACCTTCT
1 AAAAATACCA-TTTT-ACCCTTGAA-CTTCC
* *
1437 AAAAATTACCATTTTACCCTCGAGCTTCC
1 AAAAA-TACCATTTTACCCTTGAACTTCC
*
1466 AAAAATCCCATTTT
1 AAAAATACCATTTT
1480 TGACCTCGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 12 0.20
29 25 0.42
30 18 0.31
31 4 0.07
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.33
Consensus pattern (28 bp):
AAAAATACCATTTTACCCTTGAACTTCC
Found at i:1466 original size:59 final size:59
Alignment explanation
Indices: 1374--1503 Score: 217
Period size: 59 Copynumber: 2.2 Consensus size: 59
1364 TCTCTAAACT
* *
1374 TTCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGGCC-CTGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTC-GAACC
*
1433 TTCTAAAAATTACCATTTTACCCTCGAGCTTCCAAAAATCCCATTTTTGACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
1492 TTCTAAAAATTA
1 TTCTAAAAATTA
1504 NNNNNNNNNN
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
59 66 0.99
60 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (59 bp):
TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
Found at i:1480 original size:29 final size:30
Alignment explanation
Indices: 1389--1501 Score: 110
Period size: 29 Copynumber: 3.8 Consensus size: 30
1379 AAAATTACCA
*
1389 TTTT-ACCCTTGAACTTCCAAAAATCCCAT
1 TTTTGACCCTCGAACTTCCAAAAATCCCAT
* * *
1418 TTTTGGCCCT-GAACCTTCTAAAAATTACCA-
1 TTTTGACCCTCGAA-CTTCCAAAAA-TCCCAT
*
1448 TTTT-ACCCTCGAGCTTCCAAAAATCCCAT
1 TTTTGACCCTCGAACTTCCAAAAATCCCAT
*
1477 TTTTGA-CCTCGAACCTTCTAAAAAT
1 TTTTGACCCTCGAA-CTTCCAAAAAT
1502 TANNNNNNNN
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.06
29 30 0.44
30 30 0.44
31 4 0.06
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.34
Consensus pattern (30 bp):
TTTTGACCCTCGAACTTCCAAAAATCCCAT
Found at i:1655 original size:29 final size:29
Alignment explanation
Indices: 1573--1663 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
1563 NNNNNNNNNN
*
1573 CGAGCTTCCAAAAATCCCATTTTTGACCT
1 CGAGCTTCCAAAAATCCCATTTTTGACCC
* * ** *
1602 CGAACCTTCTAAAAATTAACA-TTTTGCCCC
1 CG-AGCTTCCAAAAA-TCCCATTTTTGACCC
*
1632 CGAGCTTCCAAAAATCCCATTTTTGACTC
1 CGAGCTTCCAAAAATCCCATTTTTGACCC
1661 CGA
1 CGA
1664 ACCCTCCAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
28 3 0.06
29 22 0.47
30 19 0.40
31 3 0.06
ACGTcount: A:0.30, C:0.31, G:0.10, T:0.30
Consensus pattern (29 bp):
CGAGCTTCCAAAAATCCCATTTTTGACCC
Found at i:1665 original size:59 final size:58
Alignment explanation
Indices: 1573--1690 Score: 175
Period size: 59 Copynumber: 2.0 Consensus size: 58
1563 NNNNNNNNNN
* *
1573 CGAGCTTCCAAAAATCCCATTTTTGACCTCGAACCTTCTAAAAATTAACATTTTGCCCC
1 CGAGCTTCCAAAAATCCCATTTTTGACCTCGAACCCTC-AAAAACTAACATTTTGCCCC
* *
1632 CGAGCTTCCAAAAATCCCATTTTTGA-CTCCGAACCCTCCAAAACTACCATTTTGCCCC
1 CGAGCTTCCAAAAATCCCATTTTTGACCT-CGAACCCTCAAAAACTAACATTTTGCCCC
1690 C
1 C
1691 ATGCATTCGA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
58 20 0.37
59 34 0.63
ACGTcount: A:0.29, C:0.35, G:0.08, T:0.28
Consensus pattern (58 bp):
CGAGCTTCCAAAAATCCCATTTTTGACCTCGAACCCTCAAAAACTAACATTTTGCCCC
Found at i:1674 original size:30 final size:29
Alignment explanation
Indices: 1577--1684 Score: 94
Period size: 30 Copynumber: 3.7 Consensus size: 29
1567 NNNNNNCGAG
*
1577 CTTCCAAAAATCCCATTTTTGACCTCGAAC
1 CTTCCAAAAATACCATTTTTGACC-CGAAC
* * * *
1607 CTTCTAAAAATTAACA-TTTTGCCCCCG-AG
1 CTTCCAAAAA-TACCATTTTTG-ACCCGAAC
*
1636 CTTCCAAAAATCCCATTTTTGACTCCGAAC
1 CTTCCAAAAATACCATTTTTGAC-CCGAAC
* *
1666 CCTCCAAAACTACCATTTT
1 CTTCCAAAAATACCATTTT
1685 GCCCCCATGC
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
28 4 0.07
29 18 0.30
30 33 0.55
31 5 0.08
ACGTcount: A:0.31, C:0.32, G:0.06, T:0.31
Consensus pattern (29 bp):
CTTCCAAAAATACCATTTTTGACCCGAAC
Found at i:2164 original size:96 final size:96
Alignment explanation
Indices: 1932--2185 Score: 384
Period size: 96 Copynumber: 2.7 Consensus size: 96
1922 CGGGTTTCGA
*
1932 AAAT-TTGCGCCTTAACTCACTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1 AAATATTGCGCCTTAACTCACTAGGTGCAATCTTTCTTCAAATCGAAATAATCGAATACCCTTAA
1996 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
66 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
********
2027 AAATATTGCGCCTTAACTCACTAGGTGCANNNNNNNNTCAAATCGAAATAATCGAATACCCTTAA
1 AAATATTGCGCCTTAACTCACTAGGTGCAATCTTTCTTCAAATCGAAATAATCGAATACCCTTAA
2092 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
66 TCGAGGCAATGTTTCCTTATCTTCGATTCTG
** * *
2123 AAATATTGCGCCTTAACTCACTAGGTGCAATCTTTCTTCAAATCGGGATAATCAAATATCCTT
1 AAATATTGCGCCTTAACTCACTAGGTGCAATCTTTCTTCAAATCGAAATAATCGAATACCCTT
2186 TTCTCGAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
95 4 0.03
96 134 0.97
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.33
Consensus pattern (96 bp):
AAATATTGCGCCTTAACTCACTAGGTGCAATCTTTCTTCAAATCGAAATAATCGAATACCCTTAA
TCGAGGCAATGTTTCCTTATCTTCGATTCTG
Done.