Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005621.1 Kokia drynarioides strain JFW-HI SEQ_119779, 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: 42689
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:4725 original size:53 final size:53
Alignment explanation
Indices: 4615--4861 Score: 334
Period size: 53 Copynumber: 4.6 Consensus size: 53
4605 TTCACGTTTG
* * *
4615 ATAACTCATAATGACATAGAGTCATCGGACCCTTTAATCCATAATAGGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGA-CCTTTAATCCGTAATAGGATTCAT
* *
4669 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAGTAGGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * * *
4722 ATAACTCGTGAT-AGTATAGAGTCATCGAACCTTTAATCCGTAATACGATTCAT
1 ATAACTCATGATGA-CACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * *
4775 ATAACTCATGATGAAACAGAGTCATCAGACCTTTAATTCGTAATAGGATTCAT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* *
4828 ATAACTCACGGTGACACAGAGTCATCGGACCTTT
1 ATAACTCATGATGACACAGAGTCATCGGACCTTT
4862 TGCATTTACG
Statistics
Matches: 168, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
52 1 0.01
53 140 0.83
54 27 0.16
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (53 bp):
ATAACTCATGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
Found at i:5145 original size:18 final size:19
Alignment explanation
Indices: 5122--5157 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5112 ATATTAAATC
5122 ACACAAT-TAGATCATTTA
1 ACACAATGTAGATCATTTA
*
5140 ACACAATGTAGTTCATTT
1 ACACAATGTAGATCATTT
5158 TGGAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
ACACAATGTAGATCATTTA
Found at i:7125 original size:199 final size:199
Alignment explanation
Indices: 6785--7171 Score: 650
Period size: 199 Copynumber: 1.9 Consensus size: 199
6775 CAGTATGTAA
* *
6785 TTTTTTTCCTCAGTAGATATTATTACAAAATCTATTTTAAAATGAAAAATACCTCAATTTGATTT
1 TTTTTTTCCTCAGCAAATATTATTACAAAATCTATTTTAAAATGAAAAATACCTCAATTTGATTT
*
6850 TGTTTCCAATTAAATTGATTTTCGATTTGATTTGATTTTATTCAATTTGATTTCAAGACTCCTTT
66 TGTTTCCAATTAAATTGATTTTCGATTTGATTTGATTTTATTCAATTTGATTTAAAGACTCCTTT
* *
6915 AAATCATATTTGTATCCTTGTTCAAGGAAATTTCCTAAAATCCTCCACATTGAATGCCAATACGT
131 AAATCATATTTGTATCCTTATTCAAGGAAATTTCCTAAAATCCTCAACATTGAATGCCAATACGT
6980 AATT
196 AATT
* * *
6984 TTTTTTTCCTCAGCAAATATTATTACAGAATTTGTTTTAAAATGAAAAATATCC-CAATTTGATT
1 TTTTTTTCCTCAGCAAATATTATTACAAAATCTATTTTAAAATGAAAAATA-CCTCAATTTGATT
* *
7048 TTGTTTCTAATTAAATTGATTTTCGATTTGATTTTATTTTATTCAATTTGATTTAAAGACTCCTT
65 TTGTTTCCAATTAAATTGATTTTCGATTTGATTTGATTTTATTCAATTTGATTTAAAGACTCCTT
* *
7113 TAAATCATATTTGTATCTTTATTCACGGAAATTTCCTAAAATCCTCAACATTGAATGCC
130 TAAATCATATTTGTATCCTTATTCAAGGAAATTTCCTAAAATCCTCAACATTGAATGCC
7172 TATAAAAACC
Statistics
Matches: 175, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
199 173 0.99
200 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (199 bp):
TTTTTTTCCTCAGCAAATATTATTACAAAATCTATTTTAAAATGAAAAATACCTCAATTTGATTT
TGTTTCCAATTAAATTGATTTTCGATTTGATTTGATTTTATTCAATTTGATTTAAAGACTCCTTT
AAATCATATTTGTATCCTTATTCAAGGAAATTTCCTAAAATCCTCAACATTGAATGCCAATACGT
AATT
Found at i:8648 original size:37 final size:37
Alignment explanation
Indices: 8591--8847 Score: 253
Period size: 37 Copynumber: 6.9 Consensus size: 37
8581 GCTTCTAAGA
*
8591 ATTCGGGCTATATGCCTAGCAGGCTTTGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* * * * * *
8628 ATCCGAGCTATGTGCTTAGCAGGCTTTATGTCGTTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* *
8665 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGTCGATGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* * * *
8702 ATTTGGGCTATGTGCCTAGCAGGTTTTGTGACGGCGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
** * * * *
8739 ATTAAGGCTAGGAGCCTAGCAGGATTTGTGCCAGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* * * *
8776 ATTCGGGCTATGTGCCTAACAGGCTTTATGTCAGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
* * * * *
8813 ATTTGGGCTTTGAGCCTAGCAAGCCTTTGTTCCGG
1 ATTCGGGCTATGTGCCTAGC-AGGCTTTGTGCCGG
8848 GGATAGAGGA
Statistics
Matches: 177, Mismatches: 42, Indels: 1
0.80 0.19 0.00
Matches are distributed among these distances:
37 168 0.95
38 9 0.05
ACGTcount: A:0.16, C:0.19, G:0.31, T:0.34
Consensus pattern (37 bp):
ATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGT
Found at i:13982 original size:37 final size:36
Alignment explanation
Indices: 13924--14051 Score: 139
Period size: 37 Copynumber: 3.4 Consensus size: 36
13914 AATTAAAGTT
* *
13924 TAGCAGGCTTCGTGCCGGTGTATTCAGGCTATGTGCC
1 TAGCAGGCTTTGTGCCAGTGTATTC-GGCTATGTGCC
** * *
13961 TAGCAGGCTTTGTGTTAGTGTATTTGGGCTATATGCC
1 TAGCAGGCTTTGTGCCAGTGTA-TTCGGCTATGTGCC
* *
13998 TAGCAGGCTTTGTGCCAATGTATTCGAGCTTTGTGCC
1 TAGCAGGCTTTGTGCCAGTGTATTCG-GCTATGTGCC
*
14035 TAGCAAGCCTTTGTGCC
1 TAGC-AGGCTTTGTGCC
14052 GGTGATAGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 3 0.04
37 59 0.79
38 13 0.17
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (36 bp):
TAGCAGGCTTTGTGCCAGTGTATTCGGCTATGTGCC
Found at i:15108 original size:11 final size:11
Alignment explanation
Indices: 15092--15116 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15082 TCAAGTATGT
15092 GCTCATGAAGG
1 GCTCATGAAGG
15103 GCTCATGAAGG
1 GCTCATGAAGG
15114 GCT
1 GCT
15117 GAAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (11 bp):
GCTCATGAAGG
Found at i:15360 original size:50 final size:52
Alignment explanation
Indices: 15302--15431 Score: 174
Period size: 50 Copynumber: 2.5 Consensus size: 52
15292 GTTTTTTTTT
15302 AGATATGATGTTTTAAATAAATATAAACATTTATTTAATTT-ACTTTGTTCA
1 AGATATGATGTTTTAAATAAATATAAACATTTATTTAATTTGACTTTGTTCA
* * ** *
15353 A-ATATGATGTTTTAAATAAATACAAATATTTATTTAATTTGTTTTTGTTTA
1 AGATATGATGTTTTAAATAAATATAAACATTTATTTAATTTGACTTTGTTCA
* *
15404 AGATATGGTGTTTTTACATAAATATAAA
1 AGATATGATG-TTTTAAATAAATATAAA
15432 TGTTTGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 37 0.54
51 9 0.13
52 7 0.10
53 15 0.22
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (52 bp):
AGATATGATGTTTTAAATAAATATAAACATTTATTTAATTTGACTTTGTTCA
Found at i:15663 original size:82 final size:82
Alignment explanation
Indices: 15526--15689 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
15516 GACGACCTGC
*
15526 ATACTTAATCGTTGGAGGCGAGCCCTCTTAACAAGGTACATAAGTATAACAAGTTTAAATTGGAT
1 ATACTTAATCGTTGGAGGCGAGCCCTCTTAACAAGGTACATAAGTATAACAAGTTTAAATTAGAT
15591 ATATATATATATATATA
66 ATATATATATATATATA
15608 ATACTTAATCGTTGGAGGCGAGCCCTCTTAACAAGGTACATAAGTATAACAAGTTTAAATTAGAT
1 ATACTTAATCGTTGGAGGCGAGCCCTCTTAACAAGGTACATAAGTATAACAAGTTTAAATTAGAT
15673 ATATATATATATATATA
66 ATATATATATATATATA
15690 TTGCATTTGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (82 bp):
ATACTTAATCGTTGGAGGCGAGCCCTCTTAACAAGGTACATAAGTATAACAAGTTTAAATTAGAT
ATATATATATATATATA
Found at i:16198 original size:4 final size:4
Alignment explanation
Indices: 16189--16213 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16179 CTTTTTATAA
16189 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
16214 ATGAATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:23218 original size:18 final size:18
Alignment explanation
Indices: 23195--23230 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23185 AAATAATATT
*
23195 TGCTAGGAGAAAACAATA
1 TGCTAGAAGAAAACAATA
23213 TGCTAGAAGAAAACAATA
1 TGCTAGAAGAAAACAATA
23231 AAATTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.11, G:0.19, T:0.17
Consensus pattern (18 bp):
TGCTAGAAGAAAACAATA
Found at i:24776 original size:126 final size:125
Alignment explanation
Indices: 24552--24805 Score: 454
Period size: 126 Copynumber: 2.0 Consensus size: 125
24542 ATTTAGACAG
24552 TTAGAAGGAAATTCCTTTTAACAGTAGCCCACTGATGCAGGAATAACTAGGTAACGCATAAATAT
1 TTAGAAGGAAATTCCTTTTAACAGTAGCCCACTGATGCAGGAATAACTAGGTAACGCATAAATAT
24617 TTATATTTTGTATCCAAAGGAAAAGGAAAGTACAGCCATCCTAACCTGCGCAACTCATTT
66 TTATATTTTGTATCCAAAGGAAAAGGAAAGTACAGCCATCCTAACCTGCGCAACTCATTT
* * *
24677 TTAGAAGGAAATTCCTTTTTAACAGTAGCCCATTGATGCTGGAATAATTAGGTAACGCATAAATA
1 TTAGAAGGAAATTCC-TTTTAACAGTAGCCCACTGATGCAGGAATAACTAGGTAACGCATAAATA
* *
24742 TTTCTATTTTGTATCCAAAGGAAAAGGGAAGTACAGCCATCCTAACCTGCGCAACTCATTT
65 TTTATATTTTGTATCCAAAGGAAAAGGAAAGTACAGCCATCCTAACCTGCGCAACTCATTT
24803 TTA
1 TTA
24806 CTATTTTTCC
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
125 15 0.12
126 108 0.88
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (125 bp):
TTAGAAGGAAATTCCTTTTAACAGTAGCCCACTGATGCAGGAATAACTAGGTAACGCATAAATAT
TTATATTTTGTATCCAAAGGAAAAGGAAAGTACAGCCATCCTAACCTGCGCAACTCATTT
Found at i:32224 original size:18 final size:18
Alignment explanation
Indices: 32201--32236 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32191 TTCCTGTCAT
32201 ACAGATGTTAAGTTGCAG
1 ACAGATGTTAAGTTGCAG
32219 ACAGATGTTAAGTTGCAG
1 ACAGATGTTAAGTTGCAG
32237 CAAATTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
ACAGATGTTAAGTTGCAG
Found at i:34694 original size:58 final size:58
Alignment explanation
Indices: 34623--34739 Score: 189
Period size: 58 Copynumber: 2.0 Consensus size: 58
34613 TGATAAACTA
*
34623 GTTAAATTAACTCATTTGGATAGTAAAAGATTACAAATTTTTGAAGTATCTTCATTTG
1 GTTAAATTAACTCACTTGGATAGTAAAAGATTACAAATTTTTGAAGTATCTTCATTTG
* * * *
34681 GTTAAATTGACTCACTTGGGTAGTAAAAGATTTCAAATTTTTTAAGTATCTTCATTTG
1 GTTAAATTAACTCACTTGGATAGTAAAAGATTACAAATTTTTGAAGTATCTTCATTTG
34739 G
1 G
34740 GGAAATGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (58 bp):
GTTAAATTAACTCACTTGGATAGTAAAAGATTACAAATTTTTGAAGTATCTTCATTTG
Found at i:34802 original size:13 final size:13
Alignment explanation
Indices: 34786--34826 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
34776 TGTTTTTGAG
*
34786 AAATACTTTTAAA
1 AAATACTTTGAAA
34799 AAATACTTTGAAA
1 AAATACTTTGAAA
*
34812 AAATGATTTTGAAA
1 AAAT-ACTTTGAAA
34826 A
1 A
34827 GTATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (13 bp):
AAATACTTTGAAA
Found at i:35247 original size:17 final size:17
Alignment explanation
Indices: 35225--35267 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
35215 TGTTTAACAT
35225 TATTTTTA-GTTCAAAAA
1 TATTTTTATG-TCAAAAA
35242 TATTTTTTATGTCAAAAA
1 TA-TTTTTATGTCAAAAA
35260 TATTTTTA
1 TATTTTTA
35268 AAAAGGACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 15 0.62
19 1 0.04
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
TATTTTTATGTCAAAAA
Found at i:35881 original size:12 final size:12
Alignment explanation
Indices: 35864--35888 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35854 TATATAAAAA
35864 TAAAATATTTTT
1 TAAAATATTTTT
35876 TAAAATATTTTT
1 TAAAATATTTTT
35888 T
1 T
35889 TTTACAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:37009 original size:23 final size:24
Alignment explanation
Indices: 36955--37012 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
36945 ATTAACATTA
36955 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTCAATTATATG
* **
36979 TTCATGAACATGTTCGTTTA-ATG
1 TTCGTGAACATGTTCAATTATATG
37002 TTCGTGAACAT
1 TTCGTGAACAT
37013 CAAACAAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (24 bp):
TTCGTGAACATGTTCAATTATATG
Done.