Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005807.1 Kokia drynarioides strain JFW-HI SEQ_120089, 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: 14742
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Warning! 157 characters in sequence are not A, C, G, or T
Found at i:5195 original size:207 final size:207
Alignment explanation
Indices: 4846--5443 Score: 877
Period size: 207 Copynumber: 2.9 Consensus size: 207
4836 GAATCCCAGT
* * * * *
4846 TTCCTGATGAGGTACAGAGAAGCGAATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATGC-
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGATGCAGTCATCTTCCTGATGAGATACT
* * * * *
4910 -AG-AGAAG--TATA-CCAACTCAGGGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGAT
66 GAGAAGAAGACCAAATCAAACCCAGGGCTCAATGCGAGCAAATCTTCGAAACCCAGCTTCCTGAT
*
4970 GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTAAGAAGTGG
131 GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGG
5035 ACCAAATTCATC
196 ACCAAATTCATC
* * *
5047 TTCCTGATGAGATACAGAGAAGCAAATTGAAATAAACGATGCAGTCATCTTCCTGATGAGATACT
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGATGCAGTCATCTTCCTGATGAGATACT
*
5112 GAGAAGAAGACCAAATCAAACCCAGGGCTCAATGCGAGCAAATCTTCGAAACCCAACTTCCTGAT
66 GAGAAGAAGACCAAATCAAACCCAGGGCTCAATGCGAGCAAATCTTCGAAACCCAGCTTCCTGAT
*
5177 GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACAAAGAAGTGG
131 GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGG
*
5242 ACCAAATTCGTC
196 ACCAAATTCATC
* *
5254 TTCTTGATGAGATATAGAGAAGCGAATTGAAACAAATGATGCAGTCATCTTCCTGATGAGATACT
1 TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGATGCAGTCATCTTCCTGATGAGATACT
* * * * ** *
5319 GAGAAAAAGACCAAATCAAACCTA-CGCTCGATATGAGCAAATCTTCGAATCCCAGCTTCCTGAT
66 GAGAAGAAGACCAAATCAAACCCAGGGCTCAATGCGAGCAAATCTTCGAAACCCAGCTTCCTGAT
* * * *
5383 GAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCAGATGAGATACTGAGAA
131 GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAA
5444 TAAGACCAAA
Statistics
Matches: 356, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
201 56 0.16
203 2 0.01
204 5 0.01
206 92 0.26
207 201 0.56
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (207 bp):
TTCCTGATGAGATACAGAGAAGCGAATTGAAACAAATGATGCAGTCATCTTCCTGATGAGATACT
GAGAAGAAGACCAAATCAAACCCAGGGCTCAATGCGAGCAAATCTTCGAAACCCAGCTTCCTGAT
GAAATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGG
ACCAAATTCATC
Found at i:5708 original size:6 final size:6
Alignment explanation
Indices: 5694--5763 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
5684 TTTAATTTAT
* *
5694 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
5740 TTTAAA TATAAA TTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
5764 AAGTCCAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
4 2 0.04
5 5 0.10
6 41 0.80
7 3 0.06
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:5710 original size:17 final size:17
Alignment explanation
Indices: 5687--5743 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
5677 GTCCCTTTTT
5687 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
5704 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
5721 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
5738 AATTTA
1 AATTTA
5744 AATATAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:5724 original size:23 final size:24
Alignment explanation
Indices: 5694--5746 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
5684 TTTAATTTAT
*
5694 TTTAAATTTAGAT-TT-ATTTTAAA
1 TTTAAATTTA-ATCTTAAATTTAAA
5717 TTTAAA-TTAATCTTAAATTTAAA
1 TTTAAATTTAATCTTAAATTTAAA
5740 TTTAAAT
1 TTTAAAT
5747 ATAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 19 0.73
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTAAATTTAATCTTAAATTTAAA
Found at i:7252 original size:30 final size:29
Alignment explanation
Indices: 7193--7263 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
7183 NNNNNNNNNN
***
7193 AGGATTTTTTTTTTTTAAATTTCAGAGGAA
1 AGGA-TTTTTTTTTTTAAATGAAAGAGGAA
*
7223 AGGGTTTTTTTTTTTAAATGAAAGAAGGAA
1 AGGATTTTTTTTTTTAAATGAAAG-AGGAA
*
7253 ATGATTTTTTT
1 AGGATTTTTTT
7264 CTAAAGAGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.49
Consensus pattern (29 bp):
AGGATTTTTTTTTTTAAATGAAAGAGGAA
Found at i:7811 original size:29 final size:28
Alignment explanation
Indices: 7764--8023 Score: 114
Period size: 29 Copynumber: 8.9 Consensus size: 28
7754 GAGGTCCCTA
* *
7764 AACTATCCAAAAATTCCATTTTTTCCGTCG
1 AACT-TCCAAAAATCCCATTTTTACC-TCG
*
7794 AACTTCCAAAAATCCCATTTTGACC-CTG
1 AACTTCCAAAAATCCCATTTTTACCTC-G
* * * *
7822 AAATTTCTAAAAATTCCATTTTTACCTCA
1 -AACTTCCAAAAATCCCATTTTTACCTCG
* *
7851 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTT-ACCTC-G
* * * * * *
7881 AATTTCTAAAAATTCTATTTTTACCCCCA
1 AACTTCCAAAAATCCCATTTTTA-CCTCG
* *
7910 AAC-TCCTAAAAATCCCAATTTTGACC-CAAA
1 AACTTCC-AAAAATCCC-ATTTTTACCTC--G
** * *
7940 AACTTCCCAAACTTCCC-CTTTTACCCTCA
1 AACTT-CCAAAAATCCCATTTTTA-CCTCG
**
7969 AACTTTTAAAAATCCCATTTTTGACCTCG
1 AACTTCCAAAAATCCCATTTTT-ACCTCG
* * **
7998 AAACTTCCCAAATTTTCATTTTTACC
1 -AACTTCCAAAAATCCCATTTTTACC
8024 CCCGAACTCT
Statistics
Matches: 176, Mismatches: 37, Indels: 35
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 30 0.17
29 77 0.44
30 57 0.32
31 9 0.05
32 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATCCCATTTTTACCTCG
Found at i:7873 original size:58 final size:59
Alignment explanation
Indices: 7772--7994 Score: 263
Period size: 59 Copynumber: 3.8 Consensus size: 59
7762 TAAACTATCC
* * * **
7772 AAAAATTCCATTTTTTCCGTCGAACTTCCAAAAATCCCA-TTTTGACCCTGAAATTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCAAAAATTTCT
*
7830 AAAAATTCCATTTTTA-CCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTCT
1 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCAAAAATTTCT
* * * * *
7888 AAAAATTCTATTTTTACCCCCAAAC-TCCTAAAAATCCCAATTTTGACCCAAAAACTTCC
1 AAAAATTCCATTTTTACCCTCAAACTTCC-AAAAATCCCATTTTTGACCCAAAAATTTCT
* * ** **
7947 CAAACTTCCCCTTTTACCCTCAAACTTTTAAAAATCCCATTTTTGACC
1 AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACC
7995 TCGAAACTTC
Statistics
Matches: 141, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
57 20 0.14
58 50 0.35
59 70 0.50
60 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCAAAAATTTCT
Found at i:7943 original size:30 final size:29
Alignment explanation
Indices: 7801--7994 Score: 126
Period size: 29 Copynumber: 6.6 Consensus size: 29
7791 TCGAACTTCC
** * *
7801 AAAAATCCCATTTTGACCCTGAAATTTCT
1 AAAAATCCCATTTTGACCCCAAAACTCCT
* * *
7830 AAAAATTCCATTTTTACCTC-AAACTTCC-
1 AAAAATCCCATTTTGACCCCAAAAC-TCCT
* *
7858 AAAAATCCCATTTTTGACCCCAAAATTTCT
1 AAAAATCCCA-TTTTGACCCCAAAACTCCT
* * * *
7888 AAAAATTCTATTTTTACCCCCAAACTCCT
1 AAAAATCCCATTTTGACCCCAAAACTCCT
* *
7917 AAAAATCCCAATTTTGACCCAAAAACTTCCC
1 AAAAATCCC-ATTTTGACCCCAAAAC-TCCT
** * **
7948 AAACTTCCCCTTTT-ACCCTC-AAACTTTT
1 AAAAATCCCATTTTGACCC-CAAAACTCCT
7976 AAAAATCCCATTTTTGACC
1 AAAAATCCCA-TTTTGACC
7995 TCGAAACTTC
Statistics
Matches: 123, Mismatches: 33, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
28 20 0.16
29 62 0.50
30 31 0.25
31 10 0.08
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATCCCATTTTGACCCCAAAACTCCT
Found at i:8002 original size:59 final size:59
Alignment explanation
Indices: 7763--8024 Score: 260
Period size: 59 Copynumber: 4.5 Consensus size: 59
7753 GGAGGTCCCT
* * * * **
7763 AAACTATCCAAAAATTCCATTTTTTCCGTCGAACTTCCAAAAATCCCA-TTTTGACCCTG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCAA
* * * *
7822 AAATTTCTAAAAATTCCATTTTTA-CCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCAA
* * * * * *
7880 AAATTTCTAAAAATTCTATTTTTACCCCCAAACTCCTAAAAATCCCAATTTTGACCCAA
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCAA
* * ** * *
7939 AAACTTCCCAAACTTCCCCTTTTACCCTCAAACTTTTAAAAATCCCATTTTTGACCTC-G
1 AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACC-CAA
* * *
7998 AAACTTCCCAAATTTTCATTTTTACCC
1 AAACTTCCAAAAATTCCATTTTTACCC
8025 CCGAACTCTC
Statistics
Matches: 171, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
57 20 0.12
58 49 0.29
59 101 0.59
60 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCAAACTTCTAAAAATCCCATTTTTGACCCAA
Found at i:8031 original size:29 final size:28
Alignment explanation
Indices: 8003--8057 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
7993 CCTCGAAACT
* * *
8003 TCCCAAATTTTCATTTTTACCCCCGAAC
1 TCCCAAAATTACACTTTTACCCCCGAAC
* *
8031 TCTCAAAATTACCCTTTTACCCCCGAA
1 TCCCAAAATTACACTTTTACCCCCGAA
8058 TGTCTAAGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (28 bp):
TCCCAAAATTACACTTTTACCCCCGAAC
Done.