Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009665.1 Kokia drynarioides strain JFW-HI SEQ_124383, 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: 69419
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:29 original size:6 final size:6
Alignment explanation
Indices: 4--48 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1 ATA
* * * *
4 TCACTT TCAATT CCAATT TCATTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
49 ATTTTGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:1080 original size:33 final size:29
Alignment explanation
Indices: 1024--1087 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 29
1014 TTCTCAGACA
*
1024 TTAGCTTTCTCCTTTTCTTTTTCTTCAAT
1 TTAGCTTTCTCCTTTTCTCTTTCTTCAAT
1053 TTAGTCTTTCTCCTTCTTCGCTCTTTCTTCAAT
1 TTAG-CTTTCTCCTT-TT--CTCTTTCTTCAAT
1086 TT
1 TT
1088 CATACAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 10 0.33
31 2 0.07
33 14 0.47
ACGTcount: A:0.09, C:0.27, G:0.05, T:0.59
Consensus pattern (29 bp):
TTAGCTTTCTCCTTTTCTCTTTCTTCAAT
Found at i:2411 original size:48 final size:48
Alignment explanation
Indices: 2340--2435 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
2330 GGGCCAATGG
2340 TTCTCTGAGTTTATAAGAGGTAATCAGATAGTTCCAAAGCCTCCTCCT
1 TTCTCTGAGTTTATAAGAGGTAATCAGATAGTTCCAAAGCCTCCTCCT
2388 TTCTCTGAGTTTATAAGAGGTAATCAGATAGTTCCAAAGCCTCCTCCT
1 TTCTCTGAGTTTATAAGAGGTAATCAGATAGTTCCAAAGCCTCCTCCT
2436 CCACCTATGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (48 bp):
TTCTCTGAGTTTATAAGAGGTAATCAGATAGTTCCAAAGCCTCCTCCT
Found at i:2462 original size:12 final size:12
Alignment explanation
Indices: 2445--2469 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2435 TCCACCTATG
2445 CAACCTATTGCA
1 CAACCTATTGCA
2457 CAACCTATTGCA
1 CAACCTATTGCA
2469 C
1 C
2470 CATCGGTTGT
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:0.32, C:0.36, G:0.08, T:0.24
Consensus pattern (12 bp):
CAACCTATTGCA
Found at i:8151 original size:21 final size:21
Alignment explanation
Indices: 8127--8203 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 21
8117 TAGAGATTTT
*
8127 AGTATCGGTAGAAGCATGTCA
1 AGTATCGGTAGAAGCATCTCA
* * * *
8148 AGTATTGGTAGGAAGTA-CACT
1 AGTATCGGTA-GAAGCATCTCA
* * * *
8169 TGTATCGGTAAAACCATTTCA
1 AGTATCGGTAGAAGCATCTCA
8190 AGTATCGGTAGAAG
1 AGTATCGGTAGAAG
8204 TCTGCTACTA
Statistics
Matches: 38, Mismatches: 16, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
20 3 0.08
21 30 0.79
22 5 0.13
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (21 bp):
AGTATCGGTAGAAGCATCTCA
Found at i:16830 original size:20 final size:20
Alignment explanation
Indices: 16805--16845 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16795 TGTGTGTTTT
16805 CTAGGCATTG-TCGCGACATA
1 CTAGGC-TTGATCGCGACATA
16825 CTAGGCTTGTATCGCGACATA
1 CTAGGCTTG-ATCGCGACATA
16846 GAAGACAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 6 0.32
21 10 0.53
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (20 bp):
CTAGGCTTGATCGCGACATA
Found at i:17400 original size:3 final size:3
Alignment explanation
Indices: 17392--17416 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17382 AAGAAACTAC
17392 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
17417 GTCCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17729 original size:13 final size:13
Alignment explanation
Indices: 17711--17735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17701 TATAAAATCA
17711 AATATAATTATTG
1 AATATAATTATTG
17724 AATATAATTATT
1 AATATAATTATT
17736 TTAAAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AATATAATTATTG
Found at i:18095 original size:13 final size:13
Alignment explanation
Indices: 18079--18118 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
18069 ACTCAAATAA
18079 TAAACCTCAAACC
1 TAAACCTCAAACC
18092 TAAACC-CAAACTC
1 TAAACCTCAAAC-C
*
18105 TAAACTTCAAACC
1 TAAACCTCAAACC
18118 T
1 T
18119 CAAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAACCTCAAACC
Found at i:18209 original size:20 final size:20
Alignment explanation
Indices: 18184--18221 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18174 TCGAGGTTTG
18184 GGTTTAGGTTTCAGGTTCAA
1 GGTTTAGGTTTCAGGTTCAA
*
18204 GGTTTAGGTTTCGGGTTC
1 GGTTTAGGTTTCAGGTTC
18222 GGGATTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.11, G:0.34, T:0.42
Consensus pattern (20 bp):
GGTTTAGGTTTCAGGTTCAA
Found at i:18805 original size:13 final size:14
Alignment explanation
Indices: 18787--18817 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
18777 ATTTATTATG
18787 ATTTTTATTTT-TT
1 ATTTTTATTTTCTT
18800 ATTTTTATTTTCTT
1 ATTTTTATTTTCTT
18814 ATTT
1 ATTT
18818 CTCACTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTTATTTTCTT
Found at i:21435 original size:54 final size:54
Alignment explanation
Indices: 21353--21461 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
21343 ACATATCATT
21353 GCTTTAGAAGGAAAACAAATTTGAATAATTGTACAATTTTAGACTTGTGATTGA
1 GCTTTAGAAGGAAAACAAATTTGAATAATTGTACAATTTTAGACTTGTGATTGA
21407 GCTTTAGAAGGAAAACAAATTTGAATAATTGTACAATTTTAGACTTGTGATTGA
1 GCTTTAGAAGGAAAACAAATTTGAATAATTGTACAATTTTAGACTTGTGATTGA
21461 G
1 G
21462 GTTAACTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.35
Consensus pattern (54 bp):
GCTTTAGAAGGAAAACAAATTTGAATAATTGTACAATTTTAGACTTGTGATTGA
Found at i:24351 original size:26 final size:27
Alignment explanation
Indices: 24322--24373 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
24312 GTTTTCCAAC
* *
24322 TTTTAAAGGG-CCCAATTTTTTTTTAG
1 TTTTAAAGGGTCCAAAATTTTTTTTAG
*
24348 TTTTTAAGGGTCCAAAATTTTTTTTA
1 TTTTAAAGGGTCCAAAATTTTTTTTA
24374 CCAACTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.52
Consensus pattern (27 bp):
TTTTAAAGGGTCCAAAATTTTTTTTAG
Found at i:25991 original size:13 final size:14
Alignment explanation
Indices: 25959--26003 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
25949 ATATTGATTC
*
25959 TTTTAATATGTTTAA
1 TTTTTATAT-TTTAA
*
25974 ATTTTATA-TTTAA
1 TTTTTATATTTTAA
25987 TTTTTATATTTTAA
1 TTTTTATATTTTAA
26001 TTT
1 TTT
26004 CTAACATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 12 0.46
14 8 0.31
15 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTTATATTTTAA
Found at i:26861 original size:18 final size:18
Alignment explanation
Indices: 26838--26880 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
26828 CTTTCAGTTG
26838 TAATTAAGTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
26856 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
26874 TAATTAA
1 TAATTAA
26881 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:32500 original size:56 final size:56
Alignment explanation
Indices: 32440--32622 Score: 147
Period size: 56 Copynumber: 3.1 Consensus size: 56
32430 CTTAAATTTT
32440 AGATTATATAAAATGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTA
1 AGATTATATAAAATGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTA
* * * * ** *
32496 AGATTCAAATTTTCTACTCGTACATGGT-AAAATTTAATTTT-AGTTCTTACTCTA-AGCTTAAA
1 AGATT---A-----TA-T--AAAATGGTCAAATTTTAATTTTGA-TCCTTGTTCTACA-CTCAAA
* *
32558 TTTT
53 TGTA
32562 AGATTATATAAAATGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTA
1 AGATTATATAAAATGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTA
32618 AGATT
1 AGATT
32623 CAAATTTTCT
Statistics
Matches: 93, Mismatches: 18, Indels: 32
0.65 0.13 0.22
Matches are distributed among these distances:
55 6 0.06
56 37 0.40
57 3 0.03
58 2 0.02
59 1 0.01
63 1 0.01
64 2 0.02
65 3 0.03
66 32 0.34
67 6 0.06
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (56 bp):
AGATTATATAAAATGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTA
Found at i:32605 original size:122 final size:122
Alignment explanation
Indices: 32388--32635 Score: 487
Period size: 122 Copynumber: 2.0 Consensus size: 122
32378 ATATTTGAAT
*
32388 TACTCTTACATGGTAAAATTTAATTTTAGTTCTTACTCTAAGCTTAAATTTTAGATTATATAAAA
1 TACTCGTACATGGTAAAATTTAATTTTAGTTCTTACTCTAAGCTTAAATTTTAGATTATATAAAA
32453 TGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTAAGATTCAAATTTTC
66 TGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTAAGATTCAAATTTTC
32510 TACTCGTACATGGTAAAATTTAATTTTAGTTCTTACTCTAAGCTTAAATTTTAGATTATATAAAA
1 TACTCGTACATGGTAAAATTTAATTTTAGTTCTTACTCTAAGCTTAAATTTTAGATTATATAAAA
32575 TGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTAAGATTCAAATTTTC
66 TGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTAAGATTCAAATTTTC
32632 TACT
1 TACT
32636 TCAACTTTTT
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 125 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (122 bp):
TACTCGTACATGGTAAAATTTAATTTTAGTTCTTACTCTAAGCTTAAATTTTAGATTATATAAAA
TGGTCAAATTTTAATTTTGATCCTTGTTCTACACTCAAATGTAAGATTCAAATTTTC
Found at i:32764 original size:32 final size:32
Alignment explanation
Indices: 32728--32795 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
32718 GACGTAACTT
32728 TTAAGATTTATTAATACTGTTAAAATTATTTG
1 TTAAGATTTATTAATACTGTTAAAATTATTTG
32760 TTAAGATTTATTAATACTGTTAAAATTATTTG
1 TTAAGATTTATTAATACTGTTAAAATTATTTG
32792 TTAA
1 TTAA
32796 ATTCAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (32 bp):
TTAAGATTTATTAATACTGTTAAAATTATTTG
Found at i:32782 original size:19 final size:19
Alignment explanation
Indices: 32728--32782 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
32718 GACGTAACTT
32728 TTAAGATTTATTAATACTG
1 TTAAGATTTATTAATACTG
*
32747 TTAA-A---ATT-AT-TTG
1 TTAAGATTTATTAATACTG
32760 TTAAGATTTATTAATACTG
1 TTAAGATTTATTAATACTG
32779 TTAA
1 TTAA
32783 AATTATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
13 6 0.21
14 3 0.11
15 3 0.11
17 3 0.11
18 3 0.11
19 10 0.36
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (19 bp):
TTAAGATTTATTAATACTG
Found at i:35469 original size:10 final size:10
Alignment explanation
Indices: 35454--35481 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
35444 TCTTTTGTTG
35454 ATTCTTTTCA
1 ATTCTTTTCA
35464 ATTCTTTTCA
1 ATTCTTTTCA
35474 ATTCTTTT
1 ATTCTTTT
35482 TAGGTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTCTTTTCA
Found at i:42034 original size:7 final size:7
Alignment explanation
Indices: 42018--42055 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
42008 ATTATCGAAG
*
42018 AAGGAGA
1 AAGGAAA
42025 AAGGAAA
1 AAGGAAA
42032 AAGGAAA
1 AAGGAAA
42039 AAGGAAA
1 AAGGAAA
42046 AAGGAAA
1 AAGGAAA
42053 AAG
1 AAG
42056 AAGGACAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (7 bp):
AAGGAAA
Found at i:51685 original size:24 final size:24
Alignment explanation
Indices: 51658--51712 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
51648 ATGTGAACAA
*
51658 CAATATTCAATAA-CATATTAAAAT
1 CAATATACAATAAGCA-ATTAAAAT
51682 CAATA-ACAATAAGTCAATTAAAAT
1 CAATATACAATAAG-CAATTAAAAT
*
51706 AAATATA
1 CAATATA
51713 TTTTCATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.23
24 17 0.65
25 3 0.12
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (24 bp):
CAATATACAATAAGCAATTAAAAT
Found at i:59401 original size:37 final size:37
Alignment explanation
Indices: 59291--59461 Score: 175
Period size: 37 Copynumber: 4.6 Consensus size: 37
59281 TCCGAAATTA
* *
59291 CGCCCAAACATGTCGCTGCATGAGTACTTCTAGATTA
1 CGCCCAAACATGTCGCTGCATGAGCACTTCTAGATTG
* *
59328 TGCCCAAACATGTCGCTGTATGAGCACTTCTAGATTG
1 CGCCCAAACATGTCGCTGCATGAGCACTTCTAGATTG
* *
59365 CGCCCAAACATGTCGCCGCATGAGCACCTCTAGATTG
1 CGCCCAAACATGTCGCTGCATGAGCACTTCTAGATTG
* * * ** *
59402 CACCTAAAAAAATTGTCGCCACATGAGCACTTCCAGATTG
1 CGCC--CAAACA-TGTCGCTGCATGAGCACTTCTAGATTG
*
59442 C-ACCAAA-ATTGTCGCTGCAT
1 CGCCCAAACA-TGTCGCTGCAT
59462 AAATATTCTT
Statistics
Matches: 113, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
36 11 0.10
37 72 0.64
39 5 0.04
40 25 0.22
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
CGCCCAAACATGTCGCTGCATGAGCACTTCTAGATTG
Found at i:59575 original size:26 final size:26
Alignment explanation
Indices: 59523--59575 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
59513 CACCCAGGAA
* *
59523 TGTCGTTGCATGAACATGTACATAAT
1 TGTCGCTGCATGAACATGTACAGAAT
*
59549 TGTCGCTGCATGAACATGTCCAGAAT
1 TGTCGCTGCATGAACATGTACAGAAT
59575 T
1 T
59576 ACGCTCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (26 bp):
TGTCGCTGCATGAACATGTACAGAAT
Done.