Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014855.1 Kokia drynarioides strain JFW-HI SEQ_129898, 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: 46377
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--67 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
* * *
1 ATT ATT ATT ATT AGT GTC ATT ATT ATT ATT ATT ATT ATT ATT AATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* *
47 ATT ATT A-T ATA AAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
68 ATAATATAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:37 original size:30 final size:27
Alignment explanation
Indices: 1--72 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
* *
1 ATTATTATTATTAGTGTCATTATTATTATT
1 ATTATTATTATTAAT-T-ATTATTA-TATA
31 ATTATTATTATTAATTATTATTATATA
1 ATTATTATTATTAATTATTATTATATA
* *
58 AATATTATTAATAAT
1 ATTATTATTATTAAT
73 ATAATAATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 16 0.42
28 7 0.18
29 1 0.03
30 14 0.37
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (27 bp):
ATTATTATTATTAATTATTATTATATA
Found at i:824 original size:12 final size:11
Alignment explanation
Indices: 807--863 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
797 ATAGTAATTT
807 TAAATTTGAAAA
1 TAAATTT-AAAA
*
819 TAAATTTAAACT
1 TAAATTTAAA-A
*
831 TAAA-TTAAAT
1 TAAATTTAAAA
841 TAAATTTTTAAAA
1 TAAA--TTTAAAA
854 TAAATTTAAA
1 TAAATTTAAA
864 GAGAATTCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 5 0.13
11 14 0.36
12 11 0.28
13 9 0.23
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:826 original size:35 final size:35
Alignment explanation
Indices: 787--863 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
777 TTTTAACTTT
* * *
787 ATTTAAATTTATAGTAATTTTAAA-TTTGAAAATAA
1 ATTTAAACTTAAAGTAA-ATTAAATTTTGAAAATAA
* *
822 ATTTAAACTTAAATTAAATTAAATTTTTAAAATAA
1 ATTTAAACTTAAAGTAAATTAAATTTTGAAAATAA
857 ATTTAAA
1 ATTTAAA
864 GAGAATTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTTAAACTTAAAGTAAATTAAATTTTGAAAATAA
Found at i:828 original size:18 final size:17
Alignment explanation
Indices: 787--863 Score: 75
Period size: 18 Copynumber: 4.4 Consensus size: 17
777 TTTTAACTTT
* *
787 ATTTAAATTTATAGTAA
1 ATTTAAATTTAAAATAA
*
804 TTTTAAATTTGAAAATAA
1 ATTTAAATTT-AAAATAA
* *
822 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
839 A-TTAAATTTTTAAAATAA
1 ATTTAAA--TTTAAAATAA
857 ATTTAAA
1 ATTTAAA
864 GAGAATTCGG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.10
17 16 0.33
18 22 0.46
19 5 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:5756 original size:13 final size:13
Alignment explanation
Indices: 5738--5763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5728 ATGCTTGAAC
5738 TGCACAAAAACCT
1 TGCACAAAAACCT
5751 TGCACAAAAACCT
1 TGCACAAAAACCT
5764 GGCAAGGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (13 bp):
TGCACAAAAACCT
Found at i:7777 original size:42 final size:42
Alignment explanation
Indices: 7718--7814 Score: 185
Period size: 42 Copynumber: 2.3 Consensus size: 42
7708 ATATGAACCG
*
7718 AGTTTTCATCTATTTCTACAACAACTATTAAGCCTTATTAAC
1 AGTTTCCATCTATTTCTACAACAACTATTAAGCCTTATTAAC
7760 AGTTTCCATCTATTTCTACAACAACTATTAAGCCTTATTAAC
1 AGTTTCCATCTATTTCTACAACAACTATTAAGCCTTATTAAC
7802 AGTTTCCATCTAT
1 AGTTTCCATCTAT
7815 AACAGACACT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (42 bp):
AGTTTCCATCTATTTCTACAACAACTATTAAGCCTTATTAAC
Found at i:9051 original size:23 final size:24
Alignment explanation
Indices: 9024--9076 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
9014 TTATCCATTC
*
9024 AAATATTATAA-CAAAATATTTTT
1 AAATATTATAATCAAAACATTTTT
*
9047 AAATA--ATAATTAAAACATTTTT
1 AAATATTATAATCAAAACATTTTT
9069 AATATATT
1 AA-ATATT
9077 CAACTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.17
22 12 0.50
23 8 0.33
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AAATATTATAATCAAAACATTTTT
Found at i:9225 original size:17 final size:17
Alignment explanation
Indices: 9203--9237 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9193 TATATATTTT
9203 TTATAATT-TTTATTAAA
1 TTATAATTATTT-TTAAA
9220 TTATAATTATTTTTAAA
1 TTATAATTATTTTTAAA
9237 T
1 T
9238 ATATGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATTATTTTTAAA
Found at i:10908 original size:19 final size:18
Alignment explanation
Indices: 10876--10930 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
10866 AATACTTTCA
*
10876 CATAAAAATTATATAAAAAT
1 CATAAAAA-AATAT-AAAAT
10896 CATAAAAAAATATAAAAT
1 CATAAAAAAATATAAAAT
* *
10914 -ATTAAAAAATATGAAAT
1 CATAAAAAAATATAAAAT
10931 TAATATGAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.47
18 5 0.16
19 4 0.12
20 8 0.25
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (18 bp):
CATAAAAAAATATAAAAT
Found at i:10922 original size:17 final size:17
Alignment explanation
Indices: 10886--11005 Score: 55
Period size: 17 Copynumber: 6.6 Consensus size: 17
10876 CATAAAAATT
*
10886 ATATAAAAATCATAAAAAA
1 ATAT-AAAAT-ATTAAAAA
10905 ATATAAAATATTAAAAA
1 ATATAAAATATTAAAAA
* * **
10922 ATATGAAATTAATATGAA
1 ATAT-AAAATATTAAAAA
* *
10940 CT-TATAAATAATAAAAA
1 ATATA-AAATATTAAAAA
* *
10957 TTA-ATAAATTTTAAAAA
1 ATATA-AAATATTAAAAA
10974 ATATTTAAAATATTATAAAA
1 ATA--TAAAATATTA-AAAA
*
10994 TTAATAAAATAT
1 AT-ATAAAATAT
11006 ATTTGAAATA
Statistics
Matches: 78, Mismatches: 15, Indels: 16
0.72 0.14 0.15
Matches are distributed among these distances:
16 1 0.01
17 36 0.46
18 15 0.19
19 19 0.24
20 6 0.08
21 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAAAATATTAAAAA
Found at i:11001 original size:19 final size:18
Alignment explanation
Indices: 10945--11005 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
10935 ATGAACTTAT
*
10945 AAATAATAAAAATTAAT-
1 AAATATTAAAAATTAATA
* * *
10962 AAATTTTAAAAAATATTTA
1 AAATATTAAAAATTA-ATA
10981 AAATATTATAAAATTAATA
1 AAATATTA-AAAATTAATA
11000 AAATAT
1 AAATAT
11006 ATTTGAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
17 12 0.35
18 1 0.03
19 15 0.44
20 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTAAAAATTAATA
Found at i:15026 original size:31 final size:27
Alignment explanation
Indices: 14990--15103 Score: 75
Period size: 31 Copynumber: 3.8 Consensus size: 27
14980 GATTAAATCA
14990 AAATTAAAGTTTCATGTATAGATTTGAACC
1 AAATTAAA-TTTCATGTATA-A-TTGAACC
* *
15020 ATAATTAGAATTTTACGTGTATAATTGCACC
1 A-AATTA-AA-TTT-CATGTATAATTGAACC
* **
15051 AAATTAAAATTCATGTATATAATTGTACATT
1 AAATTAAATTTCATG--TATAATTG-A-ACC
*
15082 AAATCAAATTTCATGTATAATT
1 AAATTAAATTTCATGTATAATT
15104 TTGAGGTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
27 3 0.04
28 2 0.03
29 17 0.25
30 6 0.09
31 26 0.39
32 6 0.09
33 7 0.10
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (27 bp):
AAATTAAATTTCATGTATAATTGAACC
Found at i:24743 original size:29 final size:28
Alignment explanation
Indices: 24710--24825 Score: 101
Period size: 30 Copynumber: 3.9 Consensus size: 28
24700 TAGGGGTAGC
24710 TCATATAAGGGCCAAACTTTTCAAAATAG
1 TCATATAAGGGCCAAACTTTTCAAAAT-G
* * *
24739 TCATATAAGGGCTTAACCTTTACAAAAGTG
1 TCATATAAGGGC-CAAACTTTTCAAAA-TG
* *
24769 CTCAAATGAA-GGTCAAACTTTTCAAAATGG
1 -TCATAT-AAGGGCCAAACTTTTCAAAAT-G
24799 TCGA-ATAAGGGCCAAACCTTTTCAAAA
1 TC-ATATAAGGGCCAAA-CTTTTCAAAA
24826 GCCCTCAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
28 2 0.03
29 23 0.33
30 35 0.50
31 8 0.11
32 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (28 bp):
TCATATAAGGGCCAAACTTTTCAAAATG
Found at i:24772 original size:60 final size:60
Alignment explanation
Indices: 24708--24841 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
24698 TTTAGGGGTA
* ** *
24708 GCTCATATAAGGGCCAAACTTTTCAAAATAGTC-ATATAAGGGCTTAACCTTTACAAAAGT
1 GCTCAAATAAGGGCCAAACTTTTCAAAATAGTCGA-ATAAGGGCCAAACCTTTACAAAAGC
* * *
24768 GCTCAAATGAA-GGTCAAACTTTTCAAAATGGTCGAATAAGGGCCAAACCTTTTCAAAAGC
1 GCTCAAAT-AAGGGCCAAACTTTTCAAAATAGTCGAATAAGGGCCAAACCTTTACAAAAGC
*
24828 CCTCAAATAAGGGC
1 GCTCAAATAAGGGC
24842 TTCTCATATG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 2 0.03
60 57 0.92
61 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (60 bp):
GCTCAAATAAGGGCCAAACTTTTCAAAATAGTCGAATAAGGGCCAAACCTTTACAAAAGC
Found at i:37541 original size:21 final size:21
Alignment explanation
Indices: 37517--37567 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
37507 AGTGCAGACT
37517 GATATAAGTGACAATTCTACC
1 GATATAAGTGACAATTCTACC
* **
37538 GATACAAGTGACTCTTCTACC
1 GATATAAGTGACAATTCTACC
*
37559 GAAATAAGT
1 GATATAAGT
37568 ATTACTTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
GATATAAGTGACAATTCTACC
Found at i:38323 original size:53 final size:53
Alignment explanation
Indices: 38235--38480 Score: 264
Period size: 53 Copynumber: 4.6 Consensus size: 53
38225 TTCACACTTG
* * *
38235 ATAACTCACAATGACACAGAGTCATC-GAACTTTTAATCCGAAATAGGATTCGT
1 ATAACTCACGATGACACAGAGTCATCAG-ACCTTTAATCCGAAATAGGATTCAT
* ** *
38288 ATAACTCACGATGATACAGAGTCATCAGACCTTTAATCC-ATGTTAGGACTCAT
1 ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCCGA-AATAGGATTCAT
* ** *
38341 ATAACTCACGATGATACAGAGTCATGGGA-CTCTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCAGACCT-TTAATCCGAAATAGGATTCAT
* * * ** **
38394 ATAGCTCACGATGACACAAAGTCATCGGACCTTTAATATGTGATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCCGAAATAGGATTCAT
* *
38447 ATAACTCACAATGACACAGAGTCATCAAACCTTT
1 ATAACTCACGATGACACAGAGTCATCAGACCTTT
38481 TTGCATTTAC
Statistics
Matches: 163, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
52 3 0.02
53 157 0.96
54 3 0.02
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCCGAAATAGGATTCAT
Found at i:38425 original size:106 final size:105
Alignment explanation
Indices: 38235--38472 Score: 334
Period size: 106 Copynumber: 2.2 Consensus size: 105
38225 TTCACACTTG
* *
38235 ATAACTCACAATGACACAGAGTCATCGAACTTTTAATCCGAAATAGGATTCGTATAACTCACGAT
1 ATAACTCACAATGACACAGAGTCATCGAACTCTTAATCCGAAATAGGATTCATATAACTCACGAT
* *
38300 GATACAGAGTCATCAGACCTTTAATCCATGT-TAGGACTCAT
66 GACACAAAGTCATCAGACCTTTAAT--ATGTATAGGACTCAT
* * * * * *
38341 ATAACTCACGATGATACAGAGTCATGGGACTCTTAATCCGTAATAGGATTCATATAGCTCACGAT
1 ATAACTCACAATGACACAGAGTCATCGAACTCTTAATCCGAAATAGGATTCATATAACTCACGAT
* *
38406 GACACAAAGTCATCGGACCTTTAATATGTGATAGGATTCAT
66 GACACAAAGTCATCAGACCTTTAATATGT-ATAGGACTCAT
38447 ATAACTCACAATGACACAGAGTCATC
1 ATAACTCACAATGACACAGAGTCATC
38473 AAACCTTTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
104 4 0.03
106 111 0.97
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (105 bp):
ATAACTCACAATGACACAGAGTCATCGAACTCTTAATCCGAAATAGGATTCATATAACTCACGAT
GACACAAAGTCATCAGACCTTTAATATGTATAGGACTCAT
Found at i:43335 original size:4 final size:4
Alignment explanation
Indices: 43326--43393 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
43316 AAATAAACGG
* * *
43326 GAAA GAAA GAAA GAAA -AAA -AAA GAAAA GAAA GGAA GAAG GAGAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GA-AA GAAA
*
43374 GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
43394 GTAATGCGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
3 9 0.17
4 37 0.69
5 8 0.15
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:43379 original size:17 final size:15
Alignment explanation
Indices: 43325--43393 Score: 65
Period size: 15 Copynumber: 4.7 Consensus size: 15
43315 CAAATAAACG
43325 GGAAAGAAAGAAAGAA
1 GGAAAGAAAG-AAGAA
*
43341 --AAAAAAAGAA-AA
1 GGAAAGAAAGAAGAA
*
43353 -GAAAGGAAGAAGGAGA
1 GGAAAGAAAGAA-GA-A
43369 GGAAAGAAAGAAGAA
1 GGAAAGAAAGAAGAA
43384 GGAAAGAAAG
1 GGAAAGAAAG
43394 GTAATGCGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
12 2 0.05
13 10 0.23
14 7 0.16
15 12 0.27
16 3 0.07
17 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
GGAAAGAAAGAAGAA
Done.