Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014451.1 Kokia drynarioides strain JFW-HI SEQ_129490, 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: 73547
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 93 characters in sequence are not A, C, G, or T
Found at i:5144 original size:216 final size:216
Alignment explanation
Indices: 4770--5199 Score: 722
Period size: 216 Copynumber: 2.0 Consensus size: 216
4760 AGACCATAAT
4770 CCTAATATATATAACTTTGGCACATTAGTCCTAATTCTTAATCAGCCCATCATCAATTAGAAATT
1 CCTAATATATATAACTTTGGCACATTAGTCCTAATTCTTAATCAGCCCATCATCAATTAGAAATT
*
4835 AGTCTTCAATTAGAATTTAGTTACTAGAATATTTACACATATTTATCTCATACTTTATTTAATAA
66 AGTCTTCAATTAGAATTTAGTTACTAGAATATCTACACATATTTATCTCATACTTTATTTAATAA
* * * *
4900 TTAAAGCCCAATAAACTTTAATTAAATTATATCATTTTTAATTTGGGCTAATCTATTATGATAGT
131 TTAAAACCCAATAAACTTTAATTAAATTAGATCATTTTTAATTTGGGCTAATCCATTATGATAAT
4965 AAATAATAACATGTAATTAGC
196 AAATAATAACATGTAATTAGC
** *
4986 CCTAATATACT-TAACTTTGGCACATTAG-CCTTAATTCTTAATCAGTTCATCATCAATTAGGAA
1 CCTAATATA-TATAACTTTGGCACATTAGTCC-TAATTCTTAATCAGCCCATCATCAATTAGAAA
5049 TTAGTCTTCAATTAGAATTTAGTTACTA-AAGTATCTACACATATTTATCTCATACTTTATTTAA
64 TTAGTCTTCAATTAGAATTTAGTTACTAGAA-TATCTACACATATTTATCTCATACTTTATTTAA
*
5113 TAATTAAAACCCAATAAACTTTAATTAAATTAGATCATTTTTAATTTGGGTTAATCCATTATGAT
128 TAATTAAAACCCAATAAACTTTAATTAAATTAGATCATTTTTAATTTGGGCTAATCCATTATGAT
*
5178 AATAATTAATAACATGTAATTA
193 AATAAATAATAACATGTAATTA
5200 CTCTTATTAT
Statistics
Matches: 201, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
215 4 0.02
216 196 0.98
217 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (216 bp):
CCTAATATATATAACTTTGGCACATTAGTCCTAATTCTTAATCAGCCCATCATCAATTAGAAATT
AGTCTTCAATTAGAATTTAGTTACTAGAATATCTACACATATTTATCTCATACTTTATTTAATAA
TTAAAACCCAATAAACTTTAATTAAATTAGATCATTTTTAATTTGGGCTAATCCATTATGATAAT
AAATAATAACATGTAATTAGC
Found at i:6187 original size:17 final size:16
Alignment explanation
Indices: 6167--6209 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
6157 ATAATTATTA
6167 ATATAATTAAATTAAAT
1 ATATAATTAAA-TAAAT
**
6184 ATATAAAGAAATAAAT
1 ATATAATTAAATAAAT
6200 -TATAATTAAA
1 ATATAATTAAA
6210 AATTTGTGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 8 0.36
16 5 0.23
17 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATATAATTAAATAAAT
Found at i:7329 original size:30 final size:29
Alignment explanation
Indices: 7295--7359 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
7285 TAGACTATAT
*
7295 TTTTATAATTTTTA-AAGGATTAAATCAAAA
1 TTTTAT-ATTTTTAGAAGGATAAAAT-AAAA
* *
7325 TTTTATATTTTTAGAAGGGTAAAATACAA
1 TTTTATATTTTTAGAAGGATAAAATAAAA
7354 TTTTAT
1 TTTTAT
7360 CTTTGTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTATATTTTTAGAAGGATAAAATAAAA
Found at i:7337 original size:29 final size:28
Alignment explanation
Indices: 7295--7368 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
7285 TAGACTATAT
*
7295 TTTTATAATTTTTAAAGGATTAAATCAAAA
1 TTTTAT-ATTTTTAAAGGATAAAAT-AAAA
* *
7325 TTTTATATTTTTAGAAGGGTAAAATACAA
1 TTTTATATTTTTA-AAGGATAAAATAAAA
*
7354 TTTTATCTTTGTTAA
1 TTTTATATTT-TTAA
7369 TTAAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (28 bp):
TTTTATATTTTTAAAGGATAAAATAAAA
Found at i:20129 original size:151 final size:148
Alignment explanation
Indices: 19857--20155 Score: 562
Period size: 151 Copynumber: 2.0 Consensus size: 148
19847 TCATTTTTAA
19857 CTCTTTTTTTAATAATTTTATTATAGGTTTTGATCATATCATATTTTTGACAAAATATTTATAAC
1 CTCTTTTTTTAATAATTTTATTATAGGTTTTGATCATATCATATTTTTGACAAAATATTTATAAC
19922 CACACATAGCCCTTCTCCAACTCATAAATAGGAGGATAATACACTTCGGCGCATTCGAACTTATG
66 CACACATAGCCCTTCTCCAACTCATAAATAGGAGGATAATACACTTCGGCGCATTCGAACTTATG
19987 TCCTCCTGCATTAACAAC
131 TCCTCCTGCATTAACAAC
20005 NCTCTTTTTTTAATAATTTTATTATAGGTTTTGATCATATCTGATATTTTTGACAAAATATTTAT
1 -CTCTTTTTTTAATAATTTTATTATAGGTTTTGATCATATC--ATATTTTTGACAAAATATTTAT
*
20070 AACCACACATAGCCCTTCTCCAACTCATAAATAGGAGGATAATGCACTTCGGCGCATTCGAACTT
63 AACCACACATAGCCCTTCTCCAACTCATAAATAGGAGGATAATACACTTCGGCGCATTCGAACTT
20135 ATGTCCTCCTGCATTAACAAC
128 ATGTCCTCCTGCATTAACAAC
20156 AATACTTCTA
Statistics
Matches: 147, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
149 40 0.27
151 107 0.73
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (148 bp):
CTCTTTTTTTAATAATTTTATTATAGGTTTTGATCATATCATATTTTTGACAAAATATTTATAAC
CACACATAGCCCTTCTCCAACTCATAAATAGGAGGATAATACACTTCGGCGCATTCGAACTTATG
TCCTCCTGCATTAACAAC
Found at i:20654 original size:14 final size:14
Alignment explanation
Indices: 20609--20666 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
20599 AAATGGTCTC
*
20609 ATTTCAATTTTTAT
1 ATTTTAATTTTTAT
*
20623 CTTTTAATTATATTTAT
1 ATTTTAA-T-T-TTTAT
20640 ATTTTAATTTTTAT
1 ATTTTAATTTTTAT
20654 ATTTTAATTTTTA
1 ATTTTAATTTTTA
20667 ATATAATTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 23 0.61
15 2 0.05
16 2 0.05
17 11 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTAATTTTTAT
Found at i:26821 original size:18 final size:18
Alignment explanation
Indices: 26798--26834 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26788 AAAGTTTTTA
*
26798 AAAATATAAAAAAAATAG
1 AAAATAGAAAAAAAATAG
*
26816 AAAATAGAAAACAAATAG
1 AAAATAGAAAAAAAATAG
26834 A
1 A
26835 GCCTAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (18 bp):
AAAATAGAAAAAAAATAG
Found at i:31489 original size:21 final size:22
Alignment explanation
Indices: 31448--31489 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
31438 AAGTCCTTAA
*
31448 AGTAAAAAAGAAAATTTATTAC
1 AGTAAAAAAGAAAATTAATTAC
31470 AGTAAAATAA-AAAA-TAATTA
1 AGTAAAA-AAGAAAATTAATTA
31490 TTTTTATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (22 bp):
AGTAAAAAAGAAAATTAATTAC
Found at i:31977 original size:23 final size:23
Alignment explanation
Indices: 31949--31994 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
31939 ATTTAATATT
* *
31949 TATATTTATATTAAATAATATAA
1 TATATTAATATTAAATAAAATAA
31972 TATATTAATATTAAATAAAATAA
1 TATATTAATATTAAATAAAATAA
31995 AATACCACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATTAATATTAAATAAAATAA
Found at i:32359 original size:53 final size:52
Alignment explanation
Indices: 32268--32409 Score: 148
Period size: 53 Copynumber: 2.7 Consensus size: 52
32258 TTTATTGCTT
* *
32268 TATTTTTTAAAAATA-TTTATGTATTTTTATATTTTTTTAAAATTAATA-TAT-
1 TATTTTTCAAAAATATTTTAT-T-TTTTTATATATTTTTAAAATTAATATTATA
* *
32319 TATTTCTTGGCAAAAATATTTTATTTTTTTATATATTTTTAAATTTACTATTATA
1 TATTT-TT--CAAAAATATTTTATTTTTTTATATATTTTTAAAATTAATATTATA
*
32374 TATTTTTC-AAAATATTTATAAATTTTTTATATATTT
1 TATTTTTCAAAAATATTT-T-ATTTTTTTATATATTT
32410 GTTTGTTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 14
0.80 0.05 0.14
Matches are distributed among these distances:
51 14 0.18
52 4 0.05
53 37 0.47
54 13 0.17
55 10 0.13
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (52 bp):
TATTTTTCAAAAATATTTTATTTTTTTATATATTTTTAAAATTAATATTATA
Found at i:32392 original size:20 final size:21
Alignment explanation
Indices: 32346--32400 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
32336 ATTTTATTTT
*
32346 TTTATATATTTTTAAATTTAC
1 TTTATATATTTTTAAATATAC
32367 TATTATATATTTTTCAAA-ATA-
1 T-TTATATATTTTT-AAATATAC
*
32388 TTTATAAATTTTT
1 TTTATATATTTTT
32401 TATATATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.37
21 2 0.07
22 14 0.47
23 3 0.10
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATATATTTTTAAATATAC
Found at i:39260 original size:30 final size:30
Alignment explanation
Indices: 39224--39284 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
39214 TGTTGATTGG
39224 AATAAGGTTTTTCAACCTATAAATAGGCTT
1 AATAAGGTTTTTCAACCTATAAATAGGCTT
39254 AATAAGGTTTTTCAACCTATAAATAGGCTT
1 AATAAGGTTTTTCAACCTATAAATAGGCTT
39284 A
1 A
39285 GTCATCTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (30 bp):
AATAAGGTTTTTCAACCTATAAATAGGCTT
Found at i:53560 original size:3 final size:3
Alignment explanation
Indices: 53552--53604 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
53542 AGAGCGAGAG
* * * *
53552 AGA AGA AGA AGA TGA TGA TGA TGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
53600 AGA AG
1 AGA AG
53605 TGATTTAATC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (3 bp):
AGA
Found at i:54401 original size:40 final size:40
Alignment explanation
Indices: 54335--54416 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
54325 TAAATTTGAG
** * *
54335 TTATAAATTATTATATTATATTCATAAGTACGTATTAGTA
1 TTATAAATTATTATATTATACGCATAAATACATATTAGTA
*
54375 TTATAAATTATTATATTATACGCATAAATATATATTAGTA
1 TTATAAATTATTATATTATACGCATAAATACATATTAGTA
54415 TT
1 TT
54417 TGAGATTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (40 bp):
TTATAAATTATTATATTATACGCATAAATACATATTAGTA
Found at i:55147 original size:17 final size:18
Alignment explanation
Indices: 55125--55158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55115 TTGTTTATAA
55125 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
55142 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
55159 AAATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:55612 original size:10 final size:10
Alignment explanation
Indices: 55597--55630 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
55587 ATAATTATTC
55597 AAAACTATCT
1 AAAACTATCT
*
55607 AAAACTATTT
1 AAAACTATCT
*
55617 AAAACTATCC
1 AAAACTATCT
55627 AAAA
1 AAAA
55631 TTTCTCCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAACTATCT
Found at i:55615 original size:20 final size:20
Alignment explanation
Indices: 55592--55630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55582 TGTCTATAAT
*
55592 TATTCAAAACTATCTAAAAC
1 TATTCAAAACTATCCAAAAC
*
55612 TATTTAAAACTATCCAAAA
1 TATTCAAAACTATCCAAAA
55631 TTTCTCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (20 bp):
TATTCAAAACTATCCAAAAC
Found at i:57764 original size:39 final size:39
Alignment explanation
Indices: 57721--57812 Score: 105
Period size: 39 Copynumber: 2.4 Consensus size: 39
57711 ACTGACAGTG
* **
57721 ACACTATAAACACTGCATTGTTATACTCAATTGG-TAGTA
1 ACACTATAAACACTGCAATACTATACTCAATTGGCT-GTA
* * *
57760 ACACTATGAACACTGCAATACTATACTGAATTGGCTGTG
1 ACACTATAAACACTGCAATACTATACTCAATTGGCTGTA
*
57799 ACACTGTAAACACT
1 ACACTATAAACACT
57813 ACCATGCTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 43 0.98
40 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (39 bp):
ACACTATAAACACTGCAATACTATACTCAATTGGCTGTA
Found at i:65797 original size:15 final size:15
Alignment explanation
Indices: 65777--65805 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
65767 TTTATCTCAT
65777 GTTTTTAATATGATA
1 GTTTTTAATATGATA
65792 GTTTTTAATATGAT
1 GTTTTTAATATGAT
65806 GTTCGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (15 bp):
GTTTTTAATATGATA
Found at i:70238 original size:9 final size:9
Alignment explanation
Indices: 70224--70250 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
70214 AAAAGGAATG
70224 AGAAAGGTT
1 AGAAAGGTT
70233 AGAAAGGTT
1 AGAAAGGTT
70242 AGAAAGGTT
1 AGAAAGGTT
70251 TTAAGGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
AGAAAGGTT
Done.