Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009693.1 Kokia drynarioides strain JFW-HI SEQ_124412, 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: 23196
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:845 original size:30 final size:30
Alignment explanation
Indices: 809--878 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 30
799 AAAATAATTT
809 AATAATTTTAATAATTTTATATTTCAAAAA
1 AATAATTTTAATAATTTTATATTTCAAAAA
*
839 AATAA-TTTAATAATTTTATATTTTAAAAA
1 AATAATTTTAATAATTTTATATTTCAAAAA
868 AATAATTTTAA
1 AATAATTTTAA
879 AATCATTTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 28 0.74
30 10 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
AATAATTTTAATAATTTTATATTTCAAAAA
Found at i:1227 original size:31 final size:29
Alignment explanation
Indices: 1156--1233 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
1146 AAGTTATGGG
* * *
1156 TTTAGTTTATCTACTTTTATTTTATCAAT
1 TTTAGTTTTTATACTTTTATTTGATCAAT
** *
1185 TTTAGACTTTATACTTTTCGATTTGATTAAT
1 TTTAGTTTTTATACTTTT--ATTTGATCAAT
*
1216 TTTAGTTTTTATATTTTT
1 TTTAGTTTTTATACTTTT
1234 TAAAATTTAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 14 0.37
31 24 0.63
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.63
Consensus pattern (29 bp):
TTTAGTTTTTATACTTTTATTTGATCAAT
Found at i:6809 original size:376 final size:376
Alignment explanation
Indices: 6114--6862 Score: 1444
Period size: 376 Copynumber: 2.0 Consensus size: 376
6104 ATGGTTTGTA
6114 TTGTAAATAATGTGAATATTTGTTATAACAATTAAGTTATGCGAAGTGTTAAGAATCGTTAAGGA
1 TTGTAAATAATGTGAATATTTGTTATAACAATTAAGTTATGCGAAGTGTTAAGAATCGTTAAGGA
6179 TGATTTGTATTGTAAATAATGTGAAGAGCTACTAAAAATTATAGAGGATCATGTTGTAAGCGTAT
66 TGATTTGTATTGTAAATAATGTGAAGAGCTACTAAAAATTATAGAGGATCATGTTGTAAGCGTAT
*
6244 AGAGAGCCACCAAGAATGGTTGTTTATCTGAGTTGCGAGGATGTTTGGGAAGAATGTGAGCTATA
131 AGAGAGCCACCAAGAATGATTGTTTATCTGAGTTGCGAGGATGTTTGGGAAGAATGTGAGCTATA
6309 TTTGATCTTGTGTACGTCACTTTTGTTTTGATATTGAAAGGAAGTATTTATTGAAGGAGGTTGGT
196 TTTGATCTTGTGTACGTCACTTTTGTTTTGATATTGAAAGGAAGTATTTATTGAAGGAGGTTGGT
*
6374 TTGGTGTAGATCCTAATCATTAAGTGTTGTATTCTATAGATACGTGTGGTAGAGTGTTGAATTGT
261 TTGGTGTAGATCCTAATCATTAAGTGTTGTACTCTATAGATACGTGTGGTAGAGTGTTGAATTGT
6439 TAGTTAAGATCATTGTAGAGACGATGAGAGAGGACTATGTGAGATGATTTT
326 TAGTTAAGATCATTGTAGAGACGATGAGAGAGGACTATGTGAGATGATTTT
*
6490 TTGTAAATAATGTGAATATTTGTTATAACAATTAAGTTATGCGAAGTGTTAAGAATCGTTAATGA
1 TTGTAAATAATGTGAATATTTGTTATAACAATTAAGTTATGCGAAGTGTTAAGAATCGTTAAGGA
*
6555 TGATTTGTATTGTAAATAATGTGAAGAGCTACTAAAAATTGTAGAGGATCATGTTGTAAGCGTAT
66 TGATTTGTATTGTAAATAATGTGAAGAGCTACTAAAAATTATAGAGGATCATGTTGTAAGCGTAT
6620 AGAGAGCCACCAAGAATGATTGTTTATCTGAGTTGCGAGGATGTTTGGGAAGAATGTGAGCTATA
131 AGAGAGCCACCAAGAATGATTGTTTATCTGAGTTGCGAGGATGTTTGGGAAGAATGTGAGCTATA
6685 TTTGATCTTGTGTACGTCACTTTTGTTTTGATATTGAAAGGAAGTATTTATTGAAGGAGGTTGGT
196 TTTGATCTTGTGTACGTCACTTTTGTTTTGATATTGAAAGGAAGTATTTATTGAAGGAGGTTGGT
*
6750 TTGGTGTAGATCCTAATCATTAAGTGTTGTACTCTATAGATACGTGTGGTAGTGTGTTGAATTGT
261 TTGGTGTAGATCCTAATCATTAAGTGTTGTACTCTATAGATACGTGTGGTAGAGTGTTGAATTGT
*
6815 TAGTTAAGATCATTGTAGAGACGATGAGAGGGGACTATGTGAGATGAT
326 TAGTTAAGATCATTGTAGAGACGATGAGAGAGGACTATGTGAGATGAT
6863 CATTTTAGAG
Statistics
Matches: 367, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
376 367 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (376 bp):
TTGTAAATAATGTGAATATTTGTTATAACAATTAAGTTATGCGAAGTGTTAAGAATCGTTAAGGA
TGATTTGTATTGTAAATAATGTGAAGAGCTACTAAAAATTATAGAGGATCATGTTGTAAGCGTAT
AGAGAGCCACCAAGAATGATTGTTTATCTGAGTTGCGAGGATGTTTGGGAAGAATGTGAGCTATA
TTTGATCTTGTGTACGTCACTTTTGTTTTGATATTGAAAGGAAGTATTTATTGAAGGAGGTTGGT
TTGGTGTAGATCCTAATCATTAAGTGTTGTACTCTATAGATACGTGTGGTAGAGTGTTGAATTGT
TAGTTAAGATCATTGTAGAGACGATGAGAGAGGACTATGTGAGATGATTTT
Found at i:6873 original size:38 final size:38
Alignment explanation
Indices: 6822--6910 Score: 160
Period size: 38 Copynumber: 2.3 Consensus size: 38
6812 TGTTAGTTAA
6822 GATCATTGTAGAGACGATGAGAGGGGACTATGTGAGAT
1 GATCATTGTAGAGACGATGAGAGGGGACTATGTGAGAT
*
6860 GATCATTTTAGAGACGATGAGAGGGGACTATGTGAGAT
1 GATCATTGTAGAGACGATGAGAGGGGACTATGTGAGAT
*
6898 GATCACTGTAGAG
1 GATCATTGTAGAG
6911 GGGACCATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.31, C:0.09, G:0.35, T:0.25
Consensus pattern (38 bp):
GATCATTGTAGAGACGATGAGAGGGGACTATGTGAGAT
Found at i:7539 original size:16 final size:17
Alignment explanation
Indices: 7520--7555 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
7510 CATTAATTTA
7520 AATTAAATAATTTT-TC
1 AATTAAATAATTTTCTC
7536 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
7553 AAT
1 AAT
7556 CCAATTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:9714 original size:31 final size:30
Alignment explanation
Indices: 9679--9880 Score: 99
Period size: 31 Copynumber: 6.8 Consensus size: 30
9669 TAATATTTAA
*
9679 TATCTAAACTTGACAATTTTTTTTATTTTGG
1 TATCTAAACTTGAC-ATTTTTTTTAATTTGG
* *
9710 TATCT-AA-TT----TTTCTGTTCAATTTGG
1 TATCTAAACTTGACATTT-TTTTTAATTTGG
* * *
9735 TATTTAAACTTGACACTTTTTCTTAATTTGA
1 TATCTAAACTTGACA-TTTTTTTTAATTTGG
* * *
9766 TACCTAAACTTGACGTTTTTTTTCTATTTTGG
1 TATCTAAACTTGAC-ATTTTTTT-TAATTTGG
*
9798 TACCT-AA-TT----TTTTTTTGTCCAATTTGG
1 TATCTAAACTTGACATTTTTTT-T--AATTTGG
* *
9825 TA-CATAAACTTGACATTTTTTCCTAATTTAG
1 TATC-TAAACTTGACATTTTTT-TTAATTTGG
9856 TA-CTTAAACTTGACATTTTTTTTAA
1 TATC-TAAACTTGACATTTTTTTTAA
9881 GTTGATAATT
Statistics
Matches: 131, Mismatches: 20, Indels: 41
0.68 0.10 0.21
Matches are distributed among these distances:
24 3 0.02
25 21 0.16
26 3 0.02
27 11 0.08
28 2 0.02
29 4 0.03
30 7 0.05
31 59 0.45
32 14 0.11
33 7 0.05
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.52
Consensus pattern (30 bp):
TATCTAAACTTGACATTTTTTTTAATTTGG
Found at i:9838 original size:90 final size:86
Alignment explanation
Indices: 9673--9878 Score: 259
Period size: 90 Copynumber: 2.3 Consensus size: 86
9663 TTAATATAAT
* * * * *
9673 ATTTAATATCTAAACTTGACAATTTTTTTTATTTTGGTATCTAATTTTTCTGTTCAATTTGGTAT
1 ATTT-ATACCTAAACTTGACATTTTTTTTTATTTTGGTACCTAATTTTTCTGTCCAATTTGGTAC
* *
9738 TTAAACTTGACACTTTTTCTTA
65 ATAAACTTGACACTTTTTCCTA
* *
9760 ATTTGATACCTAAACTTGACGTTTTTTTTCTATTTTGGTACCTAATTTTTTTTTGTCCAATTTGG
1 ATTT-ATACCTAAACTTGACATTTTTTTT-TATTTTGGTACCTAA--TTTTTCTGTCCAATTTGG
*
9825 TACATAAACTTGACATTTTTTCCTA
62 TACATAAACTTGACACTTTTTCCTA
*
9850 ATTTAGTACTTAAACTTGACATTTTTTTT
1 ATTTA-TACCTAAACTTGACATTTTTTTT
9879 AAGTTGATAA
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
87 25 0.25
88 14 0.14
89 1 0.01
90 62 0.61
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.53
Consensus pattern (86 bp):
ATTTATACCTAAACTTGACATTTTTTTTTATTTTGGTACCTAATTTTTCTGTCCAATTTGGTACA
TAAACTTGACACTTTTTCCTA
Found at i:9893 original size:30 final size:31
Alignment explanation
Indices: 9829--9896 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
9819 ATTTGGTACA
* *
9829 TAAACTTGACATTTTTTCCTAATTTAGTACT
1 TAAACTTGACATTTTTTCCTAATTGAGTAAT
*
9860 TAAACTTGACATTTTTT-TTAAGTTGA-TAAT
1 TAAACTTGACATTTTTTCCTAA-TTGAGTAAT
9890 TAAACTT
1 TAAACTT
9897 TTTGGGGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
TAAACTTGACATTTTTTCCTAATTGAGTAAT
Found at i:10201 original size:59 final size:59
Alignment explanation
Indices: 10124--10288 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 59
10114 TTGAATCTTA
* ** * * *
10124 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTGGGTACCAAATTGGGTTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAAGTAACAAATT-AGATC
* * *
10184 -AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGCCATGTTTAAGTAACAAATTAGATC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAAGTAACAAATTAGATC
* *
10242 AAAAAAAGTTTAGGTACTAAATTA-GAAAAAAGTGTCAAGTTCAAGTA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAA-TGTCAAGTTTAAGTA
10289 CCAACTGTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 9 0.10
59 80 0.90
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTTAAGTAACAAATTAGATC
Found at i:11505 original size:16 final size:17
Alignment explanation
Indices: 11477--11508 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11467 AAATAACAAT
11477 TTTCAATTAAAATATTA
1 TTTCAATTAAAATATTA
11494 TTTCAA-TAAAATATT
1 TTTCAATTAAAATATT
11509 GAAATTTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTCAATTAAAATATTA
Found at i:17690 original size:23 final size:23
Alignment explanation
Indices: 17639--17691 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
17629 ATATTTAAAT
*
17639 AAATACTCATATTTATATAATTA
1 AAATATTCATATTTATATAATTA
*
17662 AAATATTCATATTT-TATACTATA
1 AAATATTCATATTTATATAAT-TA
17685 AAATATT
1 AAATATT
17692 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATTCATATTTATATAATTA
Found at i:17723 original size:19 final size:19
Alignment explanation
Indices: 17699--17735 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17689 ATTTAAAAAT
17699 TAAAATATAGATAGATTAG
1 TAAAATATAGATAGATTAG
* *
17718 TAAAATATTGATATATTA
1 TAAAATATAGATAGATTA
17736 AGAATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
TAAAATATAGATAGATTAG
Found at i:17756 original size:28 final size:26
Alignment explanation
Indices: 17720--17771 Score: 61
Period size: 28 Copynumber: 1.9 Consensus size: 26
17710 TAGATTAGTA
*
17720 AAATATTGATATATTAAGAATATTATTTG
1 AAATATTGAAAT-TTAA-AAT-TTATTTG
17749 AAAT-TTGAAATTTAAAATTTATT
1 AAATATTGAAATTTAAAATTTATT
17772 ACTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 5 0.23
26 3 0.14
27 4 0.18
28 6 0.27
29 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (26 bp):
AAATATTGAAATTTAAAATTTATTTG
Done.