Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009492.1 Kokia drynarioides strain JFW-HI SEQ_124201, 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: 9583
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6796 original size:59 final size:57
Alignment explanation
Indices: 6705--6899 Score: 194
Period size: 59 Copynumber: 3.3 Consensus size: 57
6695 CGGCCCCCTT
**
6705 TTTTATCAGATAAAAAA-TTTAATTTTTTGGTGTTGGCCATGCAATGGTCGACACCCC
1 TTTTATCAGATAAAAAACTCAAATTTTTTGGTGTTGGCCATGCAAT-GTCGACACCCC
* * * * *
6762 TATTTATCTGATAAAAAACTCAAATTTTTGGGTGTTGGTCATGCAATGACAGACACTCTC
1 T-TTTATCAGATAAAAAACTCAAATTTTTTGGTGTTGGCCATGCAATGTC-GACAC-CCC
* * ** *
6822 TTTTCTCAAATAAAAAACTTTCAAATTTTTTTGGTGTTGGCCATATAATAATCGACACCCC
1 TTTTATCAGATAAAAAAC--TCAAA-TTTTTTGGTGTTGGCCATGCAAT-GTCGACACCCC
*
6883 TTTTTTCAGATAAAAAA
1 TTTTATCAGATAAAAAA
6900 TTTAAATATT
Statistics
Matches: 111, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
57 1 0.01
58 17 0.15
59 43 0.39
60 3 0.03
61 22 0.20
62 24 0.22
63 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (57 bp):
TTTTATCAGATAAAAAACTCAAATTTTTTGGTGTTGGCCATGCAATGTCGACACCCC
Found at i:7062 original size:84 final size:84
Alignment explanation
Indices: 6900--7251 Score: 546
Period size: 84 Copynumber: 4.2 Consensus size: 84
6890 AGATAAAAAA
*
6900 TTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTTATCAAATAATGTGTTGATTTG
1 TTTAAATATTTAAATAAAAAATTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGATTTG
* *
6965 ATAATATATTATTTATTTAT
65 ATAATACATTATTTATTAAT
* * *
6985 TTTAAATATTTAAAGTACAAAA-TATTATTATATTATAATTTTTATCAAATAATATGTTGATTTG
1 TTTAAATATTTAAA-TAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTG
*
7049 ATAATACATTATTTACTAAT
65 ATAATACATTATTTATTAAT
*
7069 TTTAAATATTTAAACAAAAAAATTTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
1 TTTAAATATTTAAA-TAAAAAA-TTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
* *
7134 AACAATACATTATTTATT-AT
64 GATAATACATTATTTATTAAT
*
7154 TTTAAATATTTAAATAAACAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGA
1 TTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGA
*
7219 TAATATATTATTTATTAAT
66 TAATACATTATTTATTAAT
7238 TTTAAATATTTAAA
1 TTTAAATATTTAAA
7252 GGGGATGTCG
Statistics
Matches: 244, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
83 57 0.23
84 82 0.34
85 45 0.18
86 60 0.25
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (84 bp):
TTTAAATATTTAAATAAAAAATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGA
TAATACATTATTTATTAAT
Found at i:7182 original size:169 final size:169
Alignment explanation
Indices: 6900--7251 Score: 568
Period size: 169 Copynumber: 2.1 Consensus size: 169
6890 AGATAAAAAA
* *
6900 TTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTTATCAAATAATGTGTTGATTTG
1 TTTAAATATTTAAACAAAAAAATATTATTATATTACAATTTTTTATCAAATAATGTGTTGATTTA
* * *
6965 ATAATATATTATTTATTTATTTTAAATATTTAAAGTACAAAATATTATTATATTATAATTTTTAT
66 ACAATACATTATTTATTTATTTTAAATATTTAAAGTACAAAATATTATTATATTACAATTTTTAT
7030 CAAATAATATGTTGATTTGATAATACATTATTTACTAAT
131 CAAATAATATGTTGATTTGATAATACATTATTTACTAAT
7069 TTTAAATATTTAAACAAAAAAATTTATTATTATATTACAA-TTTTTATCAAATAATGTGTTGATT
1 TTTAAATATTTAAACAAAAAAA--TATTATTATATTACAATTTTTTATCAAATAATGTGTTGATT
7133 TAACAATACATTATTTA-TTATTTTAAATATTTAAA-TA-AACAATTATTATTATATTACAATTT
64 TAACAATACATTATTTATTTATTTTAAATATTTAAAGTACAA-AA-TATTATTATATTACAATTT
* * *
7195 TTATCAAATAATGTGTTGATTTGATAATATATTATTTATTAAT
127 TTATCAAATAATATGTTGATTTGATAATACATTATTTACTAAT
7238 TTTAAATATTTAAA
1 TTTAAATATTTAAA
7252 GGGGATGTCG
Statistics
Matches: 171, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
167 2 0.01
168 4 0.02
169 111 0.65
170 38 0.22
171 16 0.09
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (169 bp):
TTTAAATATTTAAACAAAAAAATATTATTATATTACAATTTTTTATCAAATAATGTGTTGATTTA
ACAATACATTATTTATTTATTTTAAATATTTAAAGTACAAAATATTATTATATTACAATTTTTAT
CAAATAATATGTTGATTTGATAATACATTATTTACTAAT
Found at i:7428 original size:98 final size:98
Alignment explanation
Indices: 7251--7447 Score: 249
Period size: 98 Copynumber: 2.0 Consensus size: 98
7241 AAATATTTAA
*
7251 AGGGGATGTCGACCATTATATGACCAACATAAAAAAATTTAAATTTTTTTTATCTGAGAAAAAAG
1 AGGGGATGTCGACCATTACATGACCAACATAAAAAAATTTAAA-TTTTTTTATCTGAGAAAAAAG
*
7316 AGTGTCAGCCATTGCATGACTAACACCCAAAAAAT
65 AGTGTCAGCCATTGCATGACCAACA-CCAAAAAAT
* * * *
7351 AGGGG-TGTCTACCATTGCATGACCAATACT-AAAAAA-TTAAA-TTTTTTATCTGATAAAAAAG
1 AGGGGATGTCGACCATTACATGACCAACA-TAAAAAAATTTAAATTTTTTTATCTGAGAAAAAAG
* *
7412 AGGGTGTCGGTCATTGCATGACCAACACCAAAAAAT
65 A--GTGTCAGCCATTGCATGACCAACACCAAAAAAT
7448 TTGATTTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
96 20 0.23
97 9 0.10
98 26 0.30
99 25 0.29
100 6 0.07
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (98 bp):
AGGGGATGTCGACCATTACATGACCAACATAAAAAAATTTAAATTTTTTTATCTGAGAAAAAAGA
GTGTCAGCCATTGCATGACCAACACCAAAAAAT
Found at i:7445 original size:60 final size:58
Alignment explanation
Indices: 7363--7578 Score: 245
Period size: 58 Copynumber: 3.7 Consensus size: 58
7353 GGGTGTCTAC
* *
7363 CATTGCATGACCAATACTAAAAAATTAAATTTTTTATCTGATAAAAAAGAGGGTGTCGGT
1 CATTGCATGACCAACACCAAAAAATTAAATTTTTTATCTGAT-AAAAA-AGGGTGTCGGT
** *
7423 CATTGCATGACCAACACCAAAAAATTTGATTTTTTTTAT-TAGATAAATAAGGGTGTCGGT
1 CATTGCATGACCAACACCAAAAAA-TT-AAATTTTTTATCT-GATAAAAAAGGGTGTCGGT
* * * * * *
7483 CATTGTATGGCCAACACAAAAAAATTATATTTTTTATCTGACAAAAAAGGATGTCGGT
1 CATTGCATGACCAACACCAAAAAATTAAATTTTTTATCTGATAAAAAAGGGTGTCGGT
* * * *
7541 CATTGCATGGCCAACACCAAAAATTTGATTTTTTTATC
1 CATTGCATGACCAACACCAAAAAATTAAATTTTTTATC
7579 AGATTAAATT
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
58 58 0.43
59 3 0.02
60 54 0.40
61 7 0.05
62 12 0.09
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (58 bp):
CATTGCATGACCAACACCAAAAAATTAAATTTTTTATCTGATAAAAAAGGGTGTCGGT
Found at i:8689 original size:30 final size:30
Alignment explanation
Indices: 8653--8751 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 30
8643 TAAACTTAGC
8653 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ****
8683 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTACCAAAATATAATATAAAAAA
8710 TCATATT-ATTGACCAAAATATAATATAAAAAA
1 T-A-ATTAATT-ACCAAAATATAATATAAAAAA
8742 TAATTAATTA
1 TAATTAATTA
8752 TGAAAATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
27 2 0.04
28 11 0.21
29 8 0.15
30 18 0.35
31 11 0.21
32 2 0.04
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.33
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:8698 original size:16 final size:16
Alignment explanation
Indices: 8653--8702 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
8643 TAAACTTAGC
*
8653 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
8669 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
8683 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
8699 TAAT
1 TAAT
8703 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:8725 original size:59 final size:59
Alignment explanation
Indices: 8662--8787 Score: 234
Period size: 59 Copynumber: 2.1 Consensus size: 59
8652 CTAATTAATT
8662 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
* *
8721 ACCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCATATTATTT
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
8780 ACCAAAAT
1 ACCAAAAT
8788 GGTACAAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (59 bp):
ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
Found at i:8786 original size:29 final size:29
Alignment explanation
Indices: 8685--8787 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
8675 ATAAAAAATA
*
8685 ATTAATTATCAAAATAATATCCCCATCAT
1 ATTAATTACCAAAATAATATCCCCATCAT
** **
8714 ATT-ATTGACCAAAATATAATAT--AAAAAAT
1 ATTAATT-ACC-AAA-ATAATATCCCCATCAT
**
8743 AATTAATTATGAAAATAATATCCCCATCAT
1 -ATTAATTACCAAAATAATATCCCCATCAT
*
8773 ATTATTTACCAAAAT
1 ATTAATTACCAAAAT
8788 GGTACAAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
28 10 0.19
29 23 0.43
30 10 0.19
31 10 0.19
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.34
Consensus pattern (29 bp):
ATTAATTACCAAAATAATATCCCCATCAT
Done.