Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011294.1 Kokia drynarioides strain JFW-HI SEQ_126274, 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: 27168
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Warning! 52 characters in sequence are not A, C, G, or T
Found at i:857 original size:20 final size:20
Alignment explanation
Indices: 834--881 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
824 GCAATGGCAA
*
834 GTTGCTGGTGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
854 GTTGCTGATGGTGCAACTTG
1 GTTGCTGATGGTGCAACTTG
874 GTTGCTGA
1 GTTGCTGA
882 CGTGGCGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.15, G:0.38, T:0.35
Consensus pattern (20 bp):
GTTGCTGATGGTGCAACTTG
Found at i:1089 original size:17 final size:17
Alignment explanation
Indices: 1069--1154 Score: 95
Period size: 17 Copynumber: 5.0 Consensus size: 17
1059 CAATATTGAG
*
1069 TTTAAAAC-CATTTCAAA
1 TTTAAAACAAATTT-AAA
1086 TTT-AAACTAAATTTAAA
1 TTTAAAAC-AAATTTAAA
1103 TTTAAAACAAATTTAAA
1 TTTAAAACAAATTTAAA
*
1120 TTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAA
* *
1137 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
16 4 0.06
17 38 0.61
18 20 0.32
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
TTTAAAACAAATTTAAA
Found at i:1104 original size:6 final size:6
Alignment explanation
Indices: 1078--1182 Score: 60
Period size: 6 Copynumber: 18.2 Consensus size: 6
1068 GTTTAAAACC
* **
1078 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * * * *
1125 A-ATAA ATTTAA ATTCAA GA-ATAA ATTTAA A-ATGA ATTTAA ACTT-A
1 ATTTAA ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
1170 ATATAA ATTTAA A
1 ATTTAA ATTTAA A
1183 AATCGAAAGT
Statistics
Matches: 71, Mismatches: 20, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
5 18 0.25
6 48 0.68
7 5 0.07
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (6 bp):
ATTTAA
Found at i:1107 original size:34 final size:34
Alignment explanation
Indices: 1069--1154 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 34
1059 CAATATTGAG
* *
1069 TTTAAAAC-CATTTCAAATTTAAACTAAATTTAAA
1 TTTAAAACAAATTT-AAATTTAAAATAAATTTAAA
1103 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
1 TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
* *
1137 TTCAAGAATAAATTTAAA
1 TTTAA-AACAAATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
34 31 0.67
35 15 0.33
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
TTTAAAACAAATTTAAATTTAAAATAAATTTAAA
Found at i:1182 original size:17 final size:17
Alignment explanation
Indices: 1078--1154 Score: 109
Period size: 17 Copynumber: 4.4 Consensus size: 17
1068 GTTTAAAACC
*
1078 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAATAA
*
1096 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAATAA
1113 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
1130 ATTTAAATTCAAGAATAA
1 ATTTAAATTTAA-AATAA
1148 ATTTAAA
1 ATTTAAA
1155 ATGAATTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
17 38 0.70
18 16 0.30
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:1185 original size:29 final size:29
Alignment explanation
Indices: 1116--1183 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
1106 AAAACAAATT
1116 TAAATTTAAAATAAATTTAAATTCAAGAA
1 TAAATTTAAAATAAATTTAAATTCAAGAA
* *
1145 TAAATTTAAAATGAATTTAAACTT-AA-TA
1 TAAATTTAAAATAAATTTAAA-TTCAAGAA
1173 TAAATTTAAAA
1 TAAATTTAAAA
1184 ATCGAAAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 12 0.33
29 22 0.61
30 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TAAATTTAAAATAAATTTAAATTCAAGAA
Found at i:1665 original size:24 final size:23
Alignment explanation
Indices: 1630--1680 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
1620 TAAGAGTGTT
*
1630 AAATTAAAAAATAAAACAAAATA
1 AAATGAAAAAATAAAACAAAATA
**
1653 AAATGAAACAAATAAAGTAAAATA
1 AAATGAAA-AAATAAAACAAAATA
1677 AAAT
1 AAAT
1681 ATTGTTGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (23 bp):
AAATGAAAAAATAAAACAAAATA
Found at i:5277 original size:24 final size:24
Alignment explanation
Indices: 5244--5291 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5234 ATGTGACTCG
*
5244 ATTGTACAATGATAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
* **
5268 ATTGTGCAATTCCAGTAGCAGCCA
1 ATTGTACAATGACAGTAGCAGCCA
5292 CTAAAGGGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
ATTGTACAATGACAGTAGCAGCCA
Found at i:7795 original size:21 final size:22
Alignment explanation
Indices: 7769--7811 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
7759 ATCTTCCTTT
*
7769 TAATACTTG-TTTTTATGTTCA
1 TAATACTTGCTTTTTATCTTCA
7790 TAATACTTGCTTTTTATCTTCA
1 TAATACTTGCTTTTTATCTTCA
7812 ACATTTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (22 bp):
TAATACTTGCTTTTTATCTTCA
Found at i:8387 original size:18 final size:17
Alignment explanation
Indices: 8349--8387 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
8339 GCTATCTTAG
**
8349 TTTTCCCTTTTTTTGGT
1 TTTTCCCTTTTTTTGCA
8366 TTTTCCCTTTTTCTTGCA
1 TTTTCCCTTTTT-TTGCA
8384 TTTT
1 TTTT
8388 GAGCTTCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTTCCCTTTTTTTGCA
Found at i:9049 original size:20 final size:21
Alignment explanation
Indices: 9024--9063 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9014 TTCATTTTTA
*
9024 GCATTTT-TAACTTAGTGATT
1 GCATTTTCTAACTCAGTGATT
9044 GCATTTTCTAACTCAGTGAT
1 GCATTTTCTAACTCAGTGAT
9064 GCTCGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGATT
Found at i:11657 original size:20 final size:18
Alignment explanation
Indices: 11625--11664 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
11615 TATTTTTACC
11625 TTCATTTAATTTTATTTA
1 TTCATTTAATTTTATTTA
11643 TTCATTTATATTTTTATTTA
1 TTCATTTA-A-TTTTATTTA
11663 TT
1 TT
11665 TATATGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCATTTAATTTTATTTA
Found at i:11660 original size:16 final size:16
Alignment explanation
Indices: 11596--11669 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 16
11586 TATTTATTTG
*
11596 TTAT-TTTTTATGCTAT
1 TTATATTTTTATTC-AT
11612 TTATATTTTTACCTTCAT
1 TTATATTTTTA--TTCAT
*
11630 TTAATTTTATTTATTCAT
1 TT-ATATT-TTTATTCAT
*
11648 TTATATTTTTATTTAT
1 TTATATTTTTATTCAT
11664 TTATAT
1 TTATAT
11670 GTCATATTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 18 0.37
17 10 0.20
18 11 0.22
19 6 0.12
20 4 0.08
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (16 bp):
TTATATTTTTATTCAT
Found at i:19680 original size:25 final size:25
Alignment explanation
Indices: 19607--19783 Score: 160
Period size: 25 Copynumber: 7.0 Consensus size: 25
19597 TTAGCTCAAA
* *
19607 CGAGCCCAAACAGAGTTTA-GCTCTTA
1 CGAG-CCAAACAGA-ATTACGCTCTTT
* * ** *
19633 CGAGCCTAGATAGAATTTTGCTCTCT
1 CGAGCC-AAACAGAATTACGCTCTTT
*
19659 CGAGCCAAATAGAATTACGCTCTTT
1 CGAGCCAAACAGAATTACGCTCTTT
* *
19684 CGAGCCAAATAGATTTACGCTCTTT
1 CGAGCCAAACAGAATTACGCTCTTT
* * *
19709 CAAGCCAGACAAAATTACGCTCTTT
1 CGAGCCAAACAGAATTACGCTCTTT
* *
19734 CGAGCCGAACA-AATTTATGCTCTTT
1 CGAGCCAAACAGAA-TTACGCTCTTT
*
19759 CGAGCCAAACAAAATTACGCTCTTT
1 CGAGCCAAACAGAATTACGCTCTTT
19784 TGATCCAGAA
Statistics
Matches: 125, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
24 2 0.02
25 101 0.81
26 22 0.18
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (25 bp):
CGAGCCAAACAGAATTACGCTCTTT
Found at i:23924 original size:123 final size:123
Alignment explanation
Indices: 23705--23951 Score: 449
Period size: 123 Copynumber: 2.0 Consensus size: 123
23695 TTTAGCCACA
*
23705 AGCTTCGAATCATTTTCTTACAACTCTTGAATCCGTTGTAAAAATAACGGTCTCATCCTGAGTTC
1 AGCTTCGAATCATTTTCTTACAACTCTTGAATCCGCTGTAAAAATAACGGTCTCATCCTGAGTTC
* *
23770 AGCAGTGACAGAACCATCACTCCCTAATGACAGGTGAGCATTCATTGCTCTCAACGCG
66 AGCAGTGACAGAACCATCACTCCCCAATGACAGGTGAACATTCATTGCTCTCAACGCG
*
23828 AGCTTCGAATCATTTTCTTACAACTCTTGAATCCGCTGTAAAAATAACGGTCTCGTCCTGAGTTC
1 AGCTTCGAATCATTTTCTTACAACTCTTGAATCCGCTGTAAAAATAACGGTCTCATCCTGAGTTC
*
23893 AGCAGTGACAGAACCATCACTCCCCAATGACAGGTGAACGTTCATTGCTCTCAACGCG
66 AGCAGTGACAGAACCATCACTCCCCAATGACAGGTGAACATTCATTGCTCTCAACGCG
23951 A
1 A
23952 ATAATGACTT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 119 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (123 bp):
AGCTTCGAATCATTTTCTTACAACTCTTGAATCCGCTGTAAAAATAACGGTCTCATCCTGAGTTC
AGCAGTGACAGAACCATCACTCCCCAATGACAGGTGAACATTCATTGCTCTCAACGCG
Found at i:25798 original size:79 final size:78
Alignment explanation
Indices: 25667--25823 Score: 296
Period size: 79 Copynumber: 2.0 Consensus size: 78
25657 TCAAATTCAT
25667 TCGACTCTACCGGTAGTTTCTTATCAGTTGCTAATGCAATGCATATATATGAATGAGTCGACCTT
1 TCGACTCTACCGGTAGTTTCTTATCAGTTGCTAATGCAATGCATATATATGAATGAGTCGACCTT
25732 GGATCAATCAGAG
66 GGATCAATCAGAG
*
25745 NTCGACTCTACCGGTAGTTTCTTATCAGTTGCTAATGCAGTGCATATATATGAATGAGTCGACCT
1 -TCGACTCTACCGGTAGTTTCTTATCAGTTGCTAATGCAATGCATATATATGAATGAGTCGACCT
25810 TGGATCAATCAGAG
65 TGGATCAATCAGAG
25824 CACAGACAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (78 bp):
TCGACTCTACCGGTAGTTTCTTATCAGTTGCTAATGCAATGCATATATATGAATGAGTCGACCTT
GGATCAATCAGAG
Found at i:26656 original size:266 final size:265
Alignment explanation
Indices: 26182--26713 Score: 1019
Period size: 266 Copynumber: 2.0 Consensus size: 265
26172 CCTCGAGATC
*
26182 GCCTGTACTATTGCTCTACCCCGAGTGTTTACCTTTTAACGGAGTAATAGGGGGTTTCGCACTCT
1 GCCTGTACTATTGCTCTACCCCGAGTGTTTACCTTTTAACGGAGTAATAGGAGGTTTCGCACTCT
26247 GATCCTTTTTTACCTTTATAGTCATCAGGCAGTTTCACATGAAATGATTTGTACCCCCACAACAG
66 GATCCTTTTTTACCTTTATAGTCATCAGGCAGTTTCACATGAAATGATTTGTACCCCCACAACAG
*
26312 TAACAAGTTCTTTTTATCTTTCGACACTCACCTGCATGGTATCTTTCGCAATAATCACATTATGG
131 TAACAAGTTCTTTTTATCTTTCGACACTCACCTGCATGGTATCTTTCGCAATAATCACATGATGG
*
26377 GTTCGGCATGATCTGAACACTAGGTATACTAGCTGCAGGACAATTTTGGAATTTAGACTCCAGTG
196 GTTCGGCATGATCTGAACACTAGGTACACTAGCTGCAGGACAATTTTGGAATTTAGACTCCAGTG
26442 GTCCT
261 GTCCT
26447 NGCCTGTACTATTGCTCTACCCCGAGTGTTTACCTTTTAACGGAGTAATAGGAGGTTTCGCACTC
1 -GCCTGTACTATTGCTCTACCCCGAGTGTTTACCTTTTAACGGAGTAATAGGAGGTTTCGCACTC
*
26512 TGATCCTTTTTTACCTTTATAGTCATCAGGCAGTTTCACATGAAATGATTTGTTCCCCCACAACA
65 TGATCCTTTTTTACCTTTATAGTCATCAGGCAGTTTCACATGAAATGATTTGTACCCCCACAACA
26577 GTAACAAGTTCTTTTTATCTTTCGACACTCACCTGCATGGTATCTTTCGCAATAATCACATGATG
130 GTAACAAGTTCTTTTTATCTTTCGACACTCACCTGCATGGTATCTTTCGCAATAATCACATGATG
26642 GGTTCGGCATGATCTGAACACTAGGTACACTAGCTGCAGGACAATTTTGGAATTTAGACTCCAGT
195 GGTTCGGCATGATCTGAACACTAGGTACACTAGCTGCAGGACAATTTTGGAATTTAGACTCCAGT
26707 GGTCCT
260 GGTCCT
26713 G
1 G
26714 ATCTACTTCT
Statistics
Matches: 262, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
265 1 0.00
266 261 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (265 bp):
GCCTGTACTATTGCTCTACCCCGAGTGTTTACCTTTTAACGGAGTAATAGGAGGTTTCGCACTCT
GATCCTTTTTTACCTTTATAGTCATCAGGCAGTTTCACATGAAATGATTTGTACCCCCACAACAG
TAACAAGTTCTTTTTATCTTTCGACACTCACCTGCATGGTATCTTTCGCAATAATCACATGATGG
GTTCGGCATGATCTGAACACTAGGTACACTAGCTGCAGGACAATTTTGGAATTTAGACTCCAGTG
GTCCT
Done.