Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007381.1 Kokia drynarioides strain JFW-HI SEQ_121997, 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: 19816
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:579 original size:30 final size:29
Alignment explanation
Indices: 512--712 Score: 138
Period size: 30 Copynumber: 6.8 Consensus size: 29
502 GGAGGTCCCT
* *
512 AAACTATCCAAAAATTCTA-TTTTCACCCTC
1 AAACT-TCCAAAAATTCCATTTTTTACCC-C
* * *
542 GAACTTCCAAGAATCCCATTTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCC
* *
571 AAAACTTCCAAAAATTCTA-TTTTCACCCCC
1 -AAACTTCCAAAAATTCCATTTTTTA-CCCC
* * * *
601 GAACTTCTAAAAATTCAATTTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTTACCCC
*
630 GAAACTTCCAAAATTTCCA-TTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTTACCC-C
* * * ** *
660 GAACTTCAAAAAATGCCATTTTTTATATCA
1 AAACTTCCAAAAATTCCATTTTTTA-CCCC
*
690 AAAGTTCCAAAAAATTCCATTTT
1 AAACTTCC-AAAAATTCCATTTT
713 GCCCCCGAAT
Statistics
Matches: 132, Mismatches: 30, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
29 57 0.43
30 61 0.46
31 14 0.11
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTTACCCC
Found at i:585 original size:59 final size:59
Alignment explanation
Indices: 512--712 Score: 231
Period size: 59 Copynumber: 3.4 Consensus size: 59
502 GGAGGTCCCT
* * *
512 AAACTATCCAAAAATTCTATTTTCACCCTCGAACTTCCAAGAATCCCATTTTTTACCCCA
1 AAACT-TCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACCCCA
* * * * * * *
572 AAACTTCCAAAAATTCTATTTTCACCCCCGAACTTCTAAAAATTCAATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACCCCA
* * * ***
631 AAACTTCCAAAATTTCCATTTTTACCCTCGAACTTCAAAAAATGCCATTTTTTATATCA
1 AAACTTCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACCCCA
*
690 AAAGTTCCAAAAAATTCCATTTT
1 AAACTTCC-AAAAATTCCATTTT
713 GCCCCCGAAT
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
59 101 0.85
60 18 0.15
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACCCCA
Found at i:682 original size:29 final size:28
Alignment explanation
Indices: 513--682 Score: 160
Period size: 29 Copynumber: 5.8 Consensus size: 28
503 GAGGTCCCTA
* *
513 AACTATCCAAAAATTCTATTTTCACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCC-CG
* * *
543 AACTTCCAAGAATCCCATTTTTTACCCCAA
1 AACTTCCAAAAATTCCA-TTTTTACCCC-G
* *
573 AACTTCCAAAAATTCTATTTTCACCCCCG
1 AACTTCCAAAAATTCCATTTTTA-CCCCG
* *
602 AACTTCTAAAAATTCAATTTTTAACCCCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
*
631 AAACTTCCAAAATTTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTACCC-CG
* *
661 AACTTCAAAAAATGCCATTTTT
1 AACTTCCAAAAATTCCATTTTT
683 TATATCAAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
29 63 0.55
30 52 0.45
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:683 original size:118 final size:119
Alignment explanation
Indices: 512--743 Score: 299
Period size: 118 Copynumber: 2.0 Consensus size: 119
502 GGAGGTCCCT
* * * *
512 AAACTATCCAAAAATTCTATTTTCACCCTCGAACTTCCAAGAATCCCATTTTTTACCCCAAAACT
1 AAACTATCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACACCAAAACT
*
577 TCC-AAAAATTCTATTTTCACCCCCGAACT-TCTAAAAATTCAATTTTTAACCCCG
66 TCCAAAAAATTCCATTTT-ACCCCCGAA-TGTCTAAAAATTCAATTTTTAACCCCG
* * * * * *
631 AAACT-TCCAAAATTTCCATTTTTACCCTCGAACTTCAAAAAATGCCATTTTTTATATCAAAAGT
1 AAACTATCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACACCAAAACT
* * *
695 TCCAAAAAATTCCATTTTGCCCCCGAATGTCTACAAATTCCATTTTTAA
66 TCCAAAAAATTCCATTTTACCCCCGAATGTCTAAAAATTCAATTTTTAA
744 ACCCTAATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
117 1 0.01
118 78 0.80
119 18 0.19
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (119 bp):
AAACTATCCAAAAATTCCATTTTCACCCTCGAACTTCAAAAAATCCCATTTTTTACACCAAAACT
TCCAAAAAATTCCATTTTACCCCCGAATGTCTAAAAATTCAATTTTTAACCCCG
Found at i:4716 original size:22 final size:21
Alignment explanation
Indices: 4675--4717 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
4665 CCCAGACAGA
*
4675 TAGAAGAAAAATACAGGCGAT
1 TAGAAGAAAAATACACGCGAT
4696 TAGAAGAGAAAAT-CGACGCGAT
1 TAGAAGA-AAAATAC-ACGCGAT
4718 ACAGGGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.49, C:0.12, G:0.26, T:0.14
Consensus pattern (21 bp):
TAGAAGAAAAATACACGCGAT
Found at i:5573 original size:28 final size:29
Alignment explanation
Indices: 5504--5574 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
5494 ATCAAAGTTG
* * * *
5504 AAAATGATATTTTTGGATACTCGGGGGGT
1 AAAATGATAATTTTGGACACTCGGAGGGC
*
5533 AAAATGGTAATTTTGGACACTC-GAGGGC
1 AAAATGATAATTTTGGACACTCGGAGGGC
5561 AAAATGATAATTTT
1 AAAATGATAATTTT
5575 AGGAAAGTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 17 0.47
29 19 0.53
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAATGATAATTTTGGACACTCGGAGGGC
Found at i:5672 original size:58 final size:57
Alignment explanation
Indices: 5610--5985 Score: 360
Period size: 58 Copynumber: 6.5 Consensus size: 57
5600 TTTTATGACA
* * *
5610 TTCGAGGATAAAATGGTAA-TTTTGAAAAAATCGAGATAAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATTG-GAT-AAAAATGGAATTTTTGGAAG
* *
5668 TTCGAGGGT-AAATGGTAATTTTTGGAAAAATTGGAGTTAAAAATGGAATCTTTGGAGG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGGA--TAAAAATGGAATTTTTGGAAG
* * * *
5726 TTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGTAAAAAT-GAAATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATT-GGATAAAAATGGAATTTTTGG-AAG
* * *
5784 TTCAAGGGT-AAATGGTAATTTTTGGAAAAATTGGAGTTAAAAATGGAATCTTTGGAGG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGGA--TAAAAATGGAATTTTTGGAAG
* * * *
5842 TTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGTAAAAAT-GAAATTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAATT-GGATAAAAATGGAATTTTTGG-AAG
**
5900 TTCGAGGGTAAAAT-GTAATTTTTGGAAAGTTCATGG-TCAAAAATGGAA-TTTTGGAAAG
1 TTCGAGGGTAAAATGGTAATTTTTGGAAAAAT--TGGAT-AAAAATGGAATTTTTGG-AAG
*
5958 TTC-ATGGTCAAAAATGG-AA-TTTTGGAAA
1 TTCGAGGGT--AAAATGGTAATTTTTGGAAA
5986 GTTTGGGGGT
Statistics
Matches: 270, Mismatches: 29, Indels: 38
0.80 0.09 0.11
Matches are distributed among these distances:
56 2 0.01
57 69 0.26
58 130 0.48
59 64 0.24
60 5 0.02
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.32
Consensus pattern (57 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAAAATTGGATAAAAATGGAATTTTTGGAAG
Found at i:5878 original size:29 final size:28
Alignment explanation
Indices: 5649--5998 Score: 222
Period size: 29 Copynumber: 12.1 Consensus size: 28
5639 ATCGAGATAA
5649 AAAATGGAATTTTTGG-AAGTTCGAGGGT
1 AAAATGGAATTTTTGGAAAGTTCG-GGGT
* *
5677 -AAATGGTAATTTTTGGAAAAATT-GGAGTT
1 AAAATGG-AATTTTTGG-AAAGTTCGG-GGT
* *
5706 AAAAATGGAATCTTTGG-AGGTTCGGGGGT
1 -AAAATGGAATTTTTGGAAAGTTC-GGGGT
*
5735 AAAATGGTAATTTTTGGAAAACTT-GGGGT
1 AAAATGG-AATTTTTGG-AAAGTTCGGGGT
* *
5764 AAAAAT-GAAATTTTGGAAAGTTCAAGGGT
1 -AAAATGGAATTTTTGGAAAGTTC-GGGGT
* *
5793 -AAATGGTAATTTTTGGAAAAATT-GGAGTT
1 AAAATGG-AATTTTTGG-AAAGTTCGG-GGT
* *
5822 AAAAATGGAATCTTTGG-AGGTTCGGGGGT
1 -AAAATGGAATTTTTGGAAAGTTC-GGGGT
*
5851 AAAATGGTAATTTTTGGAAAACTT-GGGGT
1 AAAATGG-AATTTTTGG-AAAGTTCGGGGT
*
5880 AAAAAT-GAAATTTTGGAAAGTTCGAGGGT
1 -AAAATGGAATTTTTGGAAAGTTCG-GGGT
* **
5909 AAAATGTAATTTTTGGAAAGTTCATGGT
1 AAAATGGAATTTTTGGAAAGTTCGGGGT
**
5937 CAAAAATGGAA-TTTTGGAAAGTTCATGGT
1 --AAAATGGAATTTTTGGAAAGTTCGGGGT
*
5966 CAAAAATGGAA-TTTTGGAAAGTTTGGGGGT
1 --AAAATGGAATTTTTGGAAAG-TTCGGGGT
5996 AAA
1 AAA
5999 CATGAGATTT
Statistics
Matches: 257, Mismatches: 33, Indels: 64
0.73 0.09 0.18
Matches are distributed among these distances:
27 20 0.08
28 60 0.23
29 107 0.42
30 52 0.20
31 18 0.07
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAAGTTCGGGGT
Found at i:6009 original size:116 final size:116
Alignment explanation
Indices: 5648--5927 Score: 510
Period size: 116 Copynumber: 2.4 Consensus size: 116
5638 AATCGAGATA
*
5648 AAAAATGGAATTTTTGG-AAGTTCGAGGGTAAATGGTAATTTTTGGAAAAATTGGAGTTAAAAAT
1 AAAAAT-GAAATTTTGGAAAGTTCGAGGGTAAATGGTAATTTTTGGAAAAATTGGAGTTAAAAAT
5712 GGAATCTTTGGAGGTTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGT
65 GGAATCTTTGGAGGTTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGT
*
5764 AAAAATGAAATTTTGGAAAGTTCAAGGGTAAATGGTAATTTTTGGAAAAATTGGAGTTAAAAATG
1 AAAAATGAAATTTTGGAAAGTTCGAGGGTAAATGGTAATTTTTGGAAAAATTGGAGTTAAAAATG
5829 GAATCTTTGGAGGTTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGT
66 GAATCTTTGGAGGTTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGT
5880 AAAAATGAAATTTTGGAAAGTTCGAGGGTAAAAT-GTAATTTTTGGAAA
1 AAAAATGAAATTTTGGAAAGTTCGAGGGT-AAATGGTAATTTTTGGAAA
5928 GTTCATGGTC
Statistics
Matches: 159, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
115 9 0.06
116 146 0.92
117 4 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.32
Consensus pattern (116 bp):
AAAAATGAAATTTTGGAAAGTTCGAGGGTAAATGGTAATTTTTGGAAAAATTGGAGTTAAAAATG
GAATCTTTGGAGGTTCGGGGGTAAAATGGTAATTTTTGGAAAACTTGGGGT
Found at i:7130 original size:3 final size:3
Alignment explanation
Indices: 7064--7113 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
7054 GACTTTCTTT
* *
7064 TTA TTA TTA ATA TTTA TTA ATA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
7109 TTA TT
1 TTA TT
7114 TAATAACTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:7827 original size:6 final size:6
Alignment explanation
Indices: 7811--7881 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
7801 ATTATTCAAA
* *
7811 TAAATTT TAAATT TAAATTT TTAA-- TAAATT TAAATT TAAA-A TAAATT
1 TAAA-TT TAAATT TAAA-TT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
7858 TAATTT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
7882 TATTGGGCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 31 0.61
7 9 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:7838 original size:17 final size:17
Alignment explanation
Indices: 7818--7883 Score: 98
Period size: 17 Copynumber: 3.9 Consensus size: 17
7808 AAATAAATTT
*
7818 TAAATTTAAATTTTTAA
1 TAAATTTAAATTTTAAA
*
7835 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTTAAA
7852 TAAATTT-AATTTTAAAA
1 TAAATTTAAATTTT-AAA
7869 TAAATTTAAATTTTA
1 TAAATTTAAATTTTA
7884 TTGGGCCCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
16 5 0.11
17 33 0.75
18 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATTTAAATTTTAAA
Found at i:15336 original size:193 final size:193
Alignment explanation
Indices: 14857--15337 Score: 519
Period size: 195 Copynumber: 2.5 Consensus size: 193
14847 CGTGTTTAAA
* * *
14857 AAGAACAATCTTATAATTTATTTAATATATTGGATTCAAATATAAATTATTGT-GTTCATTCATT
1 AAGATCAATCTTATAATTTATTTAATTTATAGGATTCAAATATAAATTATTGTCG-TCATTCATT
* *
14921 CATACGTAGTTCTTTATATTACACGTATTTATGAAGATTGATTCGATAATTGATATGATTTCTAG
65 CATACGTAGTTCTTTAAATTACACGTGTTTATGAAGATTGATTCGATAATTGATATGATTTCTAG
* * *
14986 TGTTAAAATACAAACCATAATATTCATTTATTCTTATGCAATTATTAATATAACACGTGCTTTGC
130 AGTTAAAATACAAACCATAATATTCATTTATTCTTAT-CAATTATTAACATAACACATGCTTTGC
* * ** * *
15051 AAAGATCAATATTATAATTTATTTAATTTA-CGAGATTCAAACGTAAATTATTG-CTGCCATTTA
1 -AAGATCAATCTTATAATTTATTTAATTTATAG-GATTCAAATATAAATTATTGTC-GTCATTCA
* * * * * *
15114 TTCATATGTAGTT-ATCAATATTACACGTGTTTGTGAAGATTGA-TCGTTTAATTGATTTGATTA
63 TTCATACGTAGTTCTTTAA-ATTACACGTGTTTATGAAGATTGATTCG-ATAATTGATATGATT-
* * * * * * * * *
15177 T-TAGAGTTCAAGTACAAACCATCATCTTCATTTATTTTTAT-AGTTCTTAACATTACACATGTT
125 TCTAGAGTTAAAATACAAACCATAATATTCATTTATTCTTATCAATTATTAACATAACACATG-C
*
15240 TTTTC
189 TTTGC
* * *
15245 -AGTATCAATCTTATAGTTTATTTAATTTATAGGATTCAAATAAAAATTATCGTCGTCATTCATT
1 AAG-ATCAATCTTATAATTTATTTAATTTATAGGATTCAAATATAAATTATTGTCGTCATTCATT
15309 CATACGTAGTTCTTTAAATTACACGTGTT
65 CATACGTAGTTCTTTAAATTACACGTGTT
15338 CGTGCAAACA
Statistics
Matches: 234, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
192 2 0.01
193 85 0.36
194 15 0.06
195 130 0.56
196 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (193 bp):
AAGATCAATCTTATAATTTATTTAATTTATAGGATTCAAATATAAATTATTGTCGTCATTCATTC
ATACGTAGTTCTTTAAATTACACGTGTTTATGAAGATTGATTCGATAATTGATATGATTTCTAGA
GTTAAAATACAAACCATAATATTCATTTATTCTTATCAATTATTAACATAACACATGCTTTGC
Done.