Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010744.1 Kokia drynarioides strain JFW-HI SEQ_125699, 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: 28444
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 41 characters in sequence are not A, C, G, or T
Found at i:740 original size:18 final size:18
Alignment explanation
Indices: 691--752 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
681 GGCGGTTTTC
691 ATAATATTTATTAATAATA
1 ATAATA-TTATTAATAATA
* *
710 GAT-ATTTTCTTAATAATA
1 -ATAATATTATTAATAATA
*
728 ATAATATTATTAATATTA
1 ATAATATTATTAATAATA
746 ATGAATA
1 AT-AATA
753 ATAAAAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.06
18 25 0.71
19 6 0.17
20 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (18 bp):
ATAATATTATTAATAATA
Found at i:811 original size:13 final size:13
Alignment explanation
Indices: 793--821 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
783 TCGGTCAGCC
793 CGCTATCGTCGAT
1 CGCTATCGTCGAT
806 CGCTATCGTCGAT
1 CGCTATCGTCGAT
819 CGC
1 CGC
822 CGTCGCCGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.34, G:0.24, T:0.28
Consensus pattern (13 bp):
CGCTATCGTCGAT
Found at i:2057 original size:29 final size:29
Alignment explanation
Indices: 1816--2048 Score: 251
Period size: 29 Copynumber: 7.9 Consensus size: 29
1806 CCACGAGGGT
*
1816 CCCTAAACTATCCAAAAATTCCATTTTTAC
1 CCCTGAACT-TCCAAAAATTCCATTTTTAC
1846 CCCTGAACTTCCAAAAA-TCCTATTTTTGAC
1 CCCTGAACTTCCAAAAATTCC-ATTTTT-AC
* *
1876 CCC-GAAACTTCCAAGAATTACATTTTTAC
1 CCCTG-AACTTCCAAAAATTCCATTTTTAC
*
1905 CCCCGAACTTCC-AAAATTCCATTTTTGAC
1 CCCTGAACTTCCAAAAATTCCATTTTT-AC
* * *
1934 CTC-GAAACTTCTAAGAATTCCATTTTTAC
1 CCCTG-AACTTCCAAAAATTCCATTTTTAC
* *
1963 CCCCGAACTTCCAAAAATCCCATTTTTGAC
1 CCCTGAACTTCCAAAAATTCCATTTTT-AC
* * *
1993 CTC-GAAACTTCCAAAAATTCTATTTTTAG
1 CCCTG-AACTTCCAAAAATTCCATTTTTAC
2022 CCCTGAACTTCCAAAAATTCCATTTTT
1 CCCTGAACTTCCAAAAATTCCATTTTT
2049 GACACTGAAA
Statistics
Matches: 173, Mismatches: 18, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
28 16 0.09
29 85 0.49
30 70 0.40
31 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.33
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATTCCATTTTTAC
Found at i:2070 original size:30 final size:29
Alignment explanation
Indices: 1820--2078 Score: 212
Period size: 29 Copynumber: 8.8 Consensus size: 29
1810 GAGGGTCCCT
1820 AAACTATCCAAAAATTCCATTTTT-ACCCCTG
1 AAACT-TCCAAAAATTCCATTTTTGA--CCTG
*
1851 -AACTTCCAAAAA-TCCTATTTTTGACCCCG
1 AAACTTCCAAAAATTCC-ATTTTTGA-CCTG
* * *
1880 AAACTTCCAAGAATTACATTTTT-ACCCCCG
1 AAACTTCCAAAAATTCCATTTTTGA--CCTG
1910 -AACTTCC-AAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCT-G
* * *
1938 AAACTTCTAAGAATTCCATTTTT-ACCCCCG
1 AAACTTCCAAAAATTCCATTTTTGA--CCTG
*
1968 -AACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCT-G
* *
1997 AAACTTCCAAAAATTCTATTTTTAGCCCTG
1 AAACTTCCAAAAATTCCATTTTT-GACCTG
2027 -AACTTCCAAAAATTCCATTTTTGACACTG
1 AAACTTCCAAAAATTCCATTTTTGAC-CTG
* **
2056 AAAATTTTAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
2079 ACCCCCGAGT
Statistics
Matches: 189, Mismatches: 21, Indels: 36
0.77 0.09 0.15
Matches are distributed among these distances:
27 2 0.01
28 20 0.11
29 78 0.41
30 74 0.39
31 15 0.08
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCTG
Found at i:2097 original size:59 final size:59
Alignment explanation
Indices: 1820--2086 Score: 353
Period size: 59 Copynumber: 4.5 Consensus size: 59
1810 GAGGGTCCCT
* *
1820 AAACTATCCAAAAATTCCATTTTTACCCCTGAACTTCCAAAAA-TCCTATTTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCC-ATTTTTGACCTCG
* *
1880 AAACTTCCAAGAATTACATTTTTACCCCCGAACTTCC-AAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
1938 AAACTTCTAAGAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
1997 AAACTTCCAAAAATTCTATTTTTAGCCCTGAACTTCCAAAAATTCCATTTTTGACACT-G
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGAC-CTCG
* **
2056 AAAATTTTAAAAATTACCA-TTTTACCCCCGA
1 AAACTTCCAAAAATT-CCATTTTTACCCCCGA
2087 GTATCCAAAA
Statistics
Matches: 184, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
58 51 0.28
59 124 0.67
60 9 0.05
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:14284 original size:206 final size:207
Alignment explanation
Indices: 13812--14354 Score: 653
Period size: 206 Copynumber: 2.6 Consensus size: 207
13802 AGATCGGAGC
* * * *
13812 AATAAACGATTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCTGCCTTCCTGATAAGGTA
1 AATAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGCCTTCCTGATGAGGTA
* * *
13877 CAGAGAAGCGGATTGAAACAAGCGATGCGGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAA
66 CAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAA
*
13942 AATCAAGCCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAA
131 AATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAA
* **
14007 GCAAGTAGAAGC
196 GCAAGCAGAAAA
* * *
14019 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAATCAAGTCCGCCTTCCTGATGAGGTA
1 AATAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGCCTTCCTGATGAGGTA
*
14084 CAAAGAAGC-GAGTTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACC-
66 CAAAGAAGCGGA-TTGAAACAAACGATGCAGTCATCTCCCTGATGAGATACTGAGAAGAAGACCA
* * * * * *
14147 AAATCAAACTCACGCTCGATA-TGAGC-AAATTTTCGAACCCCAGCTTCTTGATGAGACACTGAG
130 AAATCAAACCCACGCTC-AAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAG
* *
14210 AAGCAGGCCGAAAA
194 AAGCAAGCAGAAAA
* * * * ***
14224 AATAAAGTGGTTAGCTCCCTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTGATGAAAC
1 AATAAA-AGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGCCTTCCTGATGAGGT
* ** ** ** * * * * *
14289 ACAGAGAAATGGATCAAAACAAGTGATGCGGCCATCTTCCGGATGAGATACTGAGAAGAAGGCCA
65 ACAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTCCCTGATGAGATACTGAGAAGAAGACCA
14354 A
130 A
14355 GCCAACGAAA
Statistics
Matches: 287, Mismatches: 44, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
205 49 0.17
206 119 0.41
207 119 0.41
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (207 bp):
AATAAAAGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGCCTTCCTGATGAGGTA
CAAAGAAGCGGATTGAAACAAACGATGCAGTCATCTCCCTGATGAGATACTGAGAAGAAGACCAA
AATCAAACCCACGCTCAAAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATAAGACACTGAGAA
GCAAGCAGAAAA
Found at i:14715 original size:17 final size:17
Alignment explanation
Indices: 14692--14790 Score: 78
Period size: 17 Copynumber: 5.8 Consensus size: 17
14682 CAAACTCCCT
14692 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
* * *
14709 ATAAATTT-GTTTAGAAA
1 TTAAATTTATTTTA-AGA
*
14726 TTTAAATTTATATTAA-A
1 -TTAAATTTATTTTAAGA
*
14743 TTTAAATTTATTTCAA-A
1 -TTAAATTTATTTTAAGA
* *
14760 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAGA
14778 TTAAATTTATTTT
1 TTAAATTTATTTT
14791 CTAAATTTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
16 4 0.06
17 51 0.77
18 8 0.12
19 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:14734 original size:6 final size:6
Alignment explanation
Indices: 14723--14800 Score: 74
Period size: 6 Copynumber: 13.3 Consensus size: 6
14713 ATTTGTTTAG
*
14723 AAATTT AAATTT ATA-TT AAATTT AAATTT --ATTT CAAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT
* **
14769 -AATTT AAGTTT AAATTT ATTTTCT AAATTT AA
1 AAATTT AAATTT AAATTT AAATT-T AAATTT AA
14801 GATTATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 37 0.64
7 8 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:15593 original size:3 final size:3
Alignment explanation
Indices: 15587--15626 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
15577 AATATTTTCT
* *
15587 TAA TAA TAA TAA TAT TAA TAA TAT TAA TGAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
15627 AAACGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16737 original size:29 final size:29
Alignment explanation
Indices: 16695--16982 Score: 275
Period size: 29 Copynumber: 9.8 Consensus size: 29
16685 TAAACTGTCC
*
16695 AAAAATTCCATTTTTACCC-CTGAACTACT
1 AAAAATTCCATTTTTACCCTC-GAACTTCT
* *
16724 AAAAA-TCCTATTTTTAACCTCGAAACTTCC
1 AAAAATTCC-ATTTTTACCCTCG-AACTTCT
16754 AAAAATTCCATTTTTACCCTCGAACTTCT
1 AAAAATTCCATTTTTACCCTCGAACTTCT
** *
16783 AAAAATTCCATTTTTGACCCTAAAACTTCC
1 AAAAATTCCATTTTT-ACCCTCGAACTTCT
* *
16813 AAAAATTCCATTTTGACCC-CGAAACTTCC
1 AAAAATTCCATTTTTACCCTCG-AACTTCT
*
16842 AAGAATTCCATTTTTACCCTCGAACTT-T
1 AAAAATTCCATTTTTACCCTCGAACTTCT
* *
16870 CAAAAATCCCATTTTTGACCC-CGAAACTTCC
1 -AAAAATTCCATTTTT-ACCCTCG-AACTTCT
* * *
16901 AAAAATTCTATTTTTAGCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCTCGAACTTCT
* *
16930 AAAAATTCCATTTTTGACACT-GAAACTTTT
1 AAAAATTCCATTTTT-ACCCTCG-AACTTCT
*
16960 GAAAATTACCA-TTTTACCCTCGA
1 AAAAATT-CCATTTTTACCCTCGA
16983 GTATCCAAAA
Statistics
Matches: 216, Mismatches: 27, Indels: 32
0.79 0.10 0.12
Matches are distributed among these distances:
28 3 0.01
29 114 0.53
30 93 0.43
31 6 0.03
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTCGAACTTCT
Found at i:16849 original size:88 final size:87
Alignment explanation
Indices: 16694--16944 Score: 321
Period size: 88 Copynumber: 2.9 Consensus size: 87
16684 CTAAACTGTC
* * *
16694 CAAAAATTCCATTTTT-ACCCCTGAACTACTAAAAA-TCCTATTTTTAACCTCGAAACTTCCAAA
1 CAAAAATTCCATTTTTGA-CCCTAAACTTCCAAAAATTCC-A-TTTTAACCTCGAAACTTCCAAA
16757 AATTCCATTTTTACCCTCGAAC-TT
63 AATTCCATTTTTACCCTCGAACTTT
* * *
16781 CTAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTCCATTTTGACCCCGAAACTTCCAAGA
1 C-AAAAATTCCATTTTTGACCCT-AAACTTCCAAAAATTCCATTTTAACCTCGAAACTTCCAAAA
16846 ATTCCATTTTTACCCTCGAACTTT
64 ATTCCATTTTTACCCTCGAACTTT
* * * *
16870 CAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTAGCCTCG-AACTTCCAAAA
1 CAAAAATTCCATTTTTGA-CCCTAAACTTCCAAAAATTCCA-TTTTAACCTCGAAACTTCCAAAA
16934 ATTCCATTTTT
64 ATTCCATTTTT
16945 GACACTGAAA
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
87 1 0.01
88 114 0.79
89 26 0.18
90 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (87 bp):
CAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTCCATTTTAACCTCGAAACTTCCAAAAAT
TCCATTTTTACCCTCGAACTTT
Found at i:16990 original size:88 final size:87
Alignment explanation
Indices: 16695--17003 Score: 294
Period size: 88 Copynumber: 3.5 Consensus size: 87
16685 TAAACTGTCC
* *
16695 AAAAATTCCATTTTT-ACCC-CTGA-ACTACTAAAAATCCTATTTTTAACCTCGAAACTTCCAAA
1 AAAAATTCCATTTTTGACCCTC-GATA-T-CCAAAAATTCTATTTTT-ACCTCGAAACTTCCAAA
*
16757 AATTCCATTTTTACCCTCGAACTTCT
62 AATTCCATTTTTACCCTCGAACTTTT
* * * * * *
16783 AAAAATTCCATTTTTGACCCT-AAAACTTCCAAAAATTCCATTTTGACCCCGAAACTTCCAAGAA
1 AAAAATTCCATTTTTGACCCTCGATA--TCCAAAAATTCTATTTTTACCTCGAAACTTCCAAAAA
*
16847 TTCCATTTTTACCCTCGAACTTTC
64 TTCCATTTTTACCCTCGAACTTTT
* *
16871 AAAAATCCCATTTTTGACCC-CGAAACTTCCAAAAATTCTATTTTTAGCCTCG-AACTTCCAAAA
1 AAAAATTCCATTTTTGACCCTCGATA--TCCAAAAATTCTATTTTTA-CCTCGAAACTTCCAAAA
*
16934 ATTCCATTTTTGACACT-GAAACTTTT
63 ATTCCATTTTT-ACCCTCG-AACTTTT
* *
16960 GAAAATTACCA-TTTT-ACCCTCGAGTATCCAAAAAGTCTCATTTT
1 AAAAATT-CCATTTTTGACCCTCGA-TATCCAAAAATTCT-ATTTT
17004 CAAACCCGAT
Statistics
Matches: 187, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
88 133 0.71
89 49 0.26
90 5 0.03
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (87 bp):
AAAAATTCCATTTTTGACCCTCGATATCCAAAAATTCTATTTTTACCTCGAAACTTCCAAAAATT
CCATTTTTACCCTCGAACTTTT
Found at i:16993 original size:59 final size:59
Alignment explanation
Indices: 16687--16982 Score: 336
Period size: 59 Copynumber: 5.0 Consensus size: 59
16677 AGGGTCCCTA
* * *
16687 AACTGTCCAAAAATTCCATTTTT-ACCCCTG-AACTACTAAAAA-TCCTATTTTTAACCTCG
1 AACT-TCCAAAAATTCCATTTTTGACCCC-GAAACTTCCAAAAATTCC-ATTTTTACCCTCG
* **
16746 AAACTTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCTAAAAATTCCATTTTTGACCCTAA
1 -AACTTCCAAAAATTCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
*
16806 AACTTCCAAAAATTCCA-TTTTGACCCCGAAACTTCCAAGAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * * *
16864 AACTTTCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCTATTTTTAGCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * ***
16923 AACTTCCAAAAATTCCATTTTTGACACTGAAACTTTTGAAAATTACCA-TTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTTACCCTCG
16982 A
1 A
16983 GTATCCAAAA
Statistics
Matches: 207, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
58 26 0.13
59 167 0.81
60 14 0.07
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (59 bp):
AACTTCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Done.