Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010644.1 Kokia drynarioides strain JFW-HI SEQ_125587, 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: 32051
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 34 characters in sequence are not A, C, G, or T
Found at i:1807 original size:29 final size:29
Alignment explanation
Indices: 1774--2102 Score: 302
Period size: 29 Copynumber: 11.2 Consensus size: 29
1764 TAAACTTTCT
1774 AAAAATTACCATTTTTACCCCGAACTTCC
1 AAAAATTACCATTTTTACCCCGAACTTCC
* *
1803 AAAAA-TCCCAATTTTAACCCCGAACCTT-C
1 AAAAATTACC-ATTTTTACCCCGAA-CTTCC
1832 AAAAATTACCATTTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTTA-CCCCGAACTTCC
* * *
1862 AAAAA-TCCCATTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTTACCCCGAA-CTTCC
* **
1891 AAAAATTACCA-TTTTACCCCCAAACTTTG
1 AAAAATTACCATTTTTA-CCCCGAACTTCC
* * *
1920 AAAAA-TCCCATTTTTGACCCCAAACCTTCT
1 AAAAATTACCATTTTT-ACCCCGAA-CTTCC
1950 AAAAATTACCA-TTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTTACCC-CGAACTTCC
* *
1979 AAAAA-TCCCATTTTTAACCCCAAACCTTCC
1 AAAAATTACCATTTTT-ACCCCGAA-CTTCC
*
2009 AAAAATTACCA-TTTTACCCCCAAACTTCC
1 AAAAATTACCATTTTTA-CCCCGAACTTCC
**
2038 AAAAA-T-CTCATTTTTAACCCCGAACCTTTA
1 AAAAATTAC-CATTTTT-ACCCCGAA-CTTCC
2068 AAAAATTACCA-TTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTTACCC-CGAACTTCC
2097 AAAAAT
1 AAAAAT
2103 CTCATTTTTG
Statistics
Matches: 249, Mismatches: 26, Indels: 50
0.77 0.08 0.15
Matches are distributed among these distances:
27 1 0.00
28 21 0.08
29 128 0.51
30 87 0.35
31 11 0.04
32 1 0.00
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATTACCATTTTTACCCCGAACTTCC
Found at i:1870 original size:59 final size:58
Alignment explanation
Indices: 1765--2147 Score: 491
Period size: 59 Copynumber: 6.5 Consensus size: 58
1755 GGAAGTCCCT
* *
1765 AAACTTTCTAAAAATTACCATTTTTA-CCCCGAACTTCCAAAAATCCCAATTTTAACCCC
1 AAACCTTC-AAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* *
1824 GAACCTTCAAAAATTACCATTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCC
1 AAACCTTCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * ** *
1882 GAACCTTCTAAAAATTACCATTTTACCCCCAAACTTTGAAAAATCCCATTTTTGACCCC
1 AAACCTTC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
*
1941 AAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCC
1 AAACCTTC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* *
2000 AAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCTCATTTTTAACCCC
1 AAACCTT-CAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * * * *
2059 GAACCTTTAAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCTCATTTTTGACTCC
1 AAACC-TTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
* * * *
2118 AAACCTACCAAAACTACCATTTTGCCCCCG
1 AAACCTTCAAAAATTACCATTTTACCCCCG
2148 TGCATCTGAA
Statistics
Matches: 291, Mismatches: 28, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
58 78 0.27
59 210 0.72
60 3 0.01
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (58 bp):
AAACCTTCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCC
Found at i:3805 original size:21 final size:20
Alignment explanation
Indices: 3771--3809 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3761 TAAACATTTG
3771 AATTAAATAAAATAAAAATC
1 AATTAAATAAAATAAAAATC
*
3791 AATTAAAATATAATAAAAA
1 AATT-AAATAAAATAAAAA
3810 GTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AATTAAATAAAATAAAAATC
Found at i:12198 original size:30 final size:30
Alignment explanation
Indices: 12158--12219 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
12148 TGGTGCTGGA
*
12158 GGAGGAGGTGCAGCATAGTAAG-GCGGAGGT
1 GGAGGAGGTGCACCATA-TAAGTGCGGAGGT
* *
12188 GGAGGCGGTGCACCATATAAGTGCGGTGGT
1 GGAGGAGGTGCACCATATAAGTGCGGAGGT
12218 GG
1 GG
12220 TGGTGGTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.23, C:0.13, G:0.48, T:0.16
Consensus pattern (30 bp):
GGAGGAGGTGCACCATATAAGTGCGGAGGT
Found at i:12220 original size:3 final size:3
Alignment explanation
Indices: 12212--12236 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12202 ATATAAGTGC
12212 GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT G
12237 CAAAAGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:14955 original size:48 final size:48
Alignment explanation
Indices: 14901--15051 Score: 196
Period size: 48 Copynumber: 3.1 Consensus size: 48
14891 TGCCCAAACA
*
14901 GAGGTGGTGCCGGATGCCCTAGCGGTGGTGGAGCAAAGGGGTCTGGTG
1 GAGGTGGTGCCGGATGCCCTAGCGGTGGTGGAGCAAAGGGGTCTGATG
* * **
14949 GAGGTGGAGCCGGATGCCCTGGCGGTGGTGGAGCAAAGGGGTCTGCCG
1 GAGGTGGTGCCGGATGCCCTAGCGGTGGTGGAGCAAAGGGGTCTGATG
* ** * *
14997 GAGGTGTTGCCGGA-GGTCTAGGCGGTGGAGGTGCAAAGGGGTCTGATG
1 GAGGTGGTGCCGGATGCCCTA-GCGGTGGTGGAGCAAAGGGGTCTGATG
15045 GAGGTGG
1 GAGGTGG
15052 GGGATGCCGG
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
47 3 0.03
48 85 0.97
ACGTcount: A:0.15, C:0.16, G:0.51, T:0.18
Consensus pattern (48 bp):
GAGGTGGTGCCGGATGCCCTAGCGGTGGTGGAGCAAAGGGGTCTGATG
Found at i:15002 original size:24 final size:24
Alignment explanation
Indices: 14922--15002 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
14912 GGATGCCCTA
*
14922 GCGGTGGTGGAGCAAAGGGGTCTG
1 GCGGAGGTGGAGCAAAGGGGTCTG
* * **
14946 GTGGAGGTGGAGC--CGGATGCCCTG
1 GCGGAGGTGGAGCAAAGG--GGTCTG
*
14970 GCGGTGGTGGAGCAAAGGGGTCTG
1 GCGGAGGTGGAGCAAAGGGGTCTG
*
14994 CCGGAGGTG
1 GCGGAGGTG
15003 TTGCCGGAGG
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
22 2 0.05
24 37 0.90
26 2 0.05
ACGTcount: A:0.15, C:0.16, G:0.53, T:0.16
Consensus pattern (24 bp):
GCGGAGGTGGAGCAAAGGGGTCTG
Found at i:16995 original size:23 final size:22
Alignment explanation
Indices: 16969--17021 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
16959 TTTTTTTTTT
* *
16969 TTTTTTTTTCCAAAAACATATTG
1 TTTTTTTGT-CAAAAAAATATTG
*
16992 TTTTATTTGTGAAAAAAATATTG
1 TTTT-TTTGTCAAAAAAATATTG
*
17015 CTTTTTT
1 TTTTTTT
17022 AAGCCAACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 18 0.72
24 4 0.16
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.55
Consensus pattern (22 bp):
TTTTTTTGTCAAAAAAATATTG
Found at i:27163 original size:22 final size:21
Alignment explanation
Indices: 27134--27174 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
27124 ATATCTAACT
27134 AGAAATATA-AATATAAATAAA
1 AGAAATATAGAA-ATAAATAAA
27155 AGAATATATAGAAATAAATA
1 AGAA-ATATAGAAATAAATA
27175 TAAAAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 12 0.67
23 2 0.11
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
AGAAATATAGAAATAAATAAA
Found at i:29159 original size:29 final size:29
Alignment explanation
Indices: 29124--29185 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
29114 AATTGAAAAA
29124 AAAATCAGATATAA-TTACTTTTAAAATAT
1 AAAATCAGA-ATAATTTACTTTTAAAATAT
* * * *
29153 AAAATCATAATAATTTTCTTTTTAAATGT
1 AAAATCAGAATAATTTACTTTTAAAATAT
29182 AAAA
1 AAAA
29186 AAGTTATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATCAGAATAATTTACTTTTAAAATAT
Found at i:29707 original size:11 final size:11
Alignment explanation
Indices: 29675--29708 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
29665 ATTGGAGGAA
29675 GAGG-AAGAGG
1 GAGGCAAGAGG
*
29685 AAGGCAAGAGG
1 GAGGCAAGAGG
29696 GAGGCAAGAGG
1 GAGGCAAGAGG
29707 GA
1 GA
29709 AAGGGAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.41, C:0.06, G:0.53, T:0.00
Consensus pattern (11 bp):
GAGGCAAGAGG
Found at i:30445 original size:2 final size:2
Alignment explanation
Indices: 30440--30481 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
30430 CACACACACG
30440 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30482 GAACATTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.