Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011944.1 Kokia drynarioides strain JFW-HI SEQ_126942, 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: 66552
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 238 characters in sequence are not A, C, G, or T
Found at i:631 original size:23 final size:22
Alignment explanation
Indices: 601--725 Score: 117
Period size: 23 Copynumber: 5.5 Consensus size: 22
591 ACGCTAACGC
601 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
624 GCTTACTGTTTCGCACTTCT-TGT
1 GCTTACTGTTT-GCACTT-TGTGT
* *
647 GCTTACTGATTTGCGCTATGTGT
1 GCTTACTG-TTTGCACTTTGTGT
* * *
670 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTTTGTGT
* * *
692 GCCTACTGGATTGCACTGTGTGT
1 GCTTACT-GTTTGCACTTTGTGT
*
715 GCTTATTGTTT
1 GCTTACTGTTT
726 TCCCAGCACT
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
22 22 0.25
23 63 0.71
24 4 0.04
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:714 original size:45 final size:46
Alignment explanation
Indices: 604--716 Score: 108
Period size: 45 Copynumber: 2.5 Consensus size: 46
594 CTAACGCGCT
* * * * *
604 TACTG-TTTCGCACTTTGTGTGCTTACTGTTTCGCACTTCTTGTGCT
1 TACTGATTT-GCACTATGTGTGCCTACTGATTCGCACTTCGTGTGCC
*
650 TACTGATTTGCGCTATGTGTGCCTACTGATT-GCACTGT-GTGTGCC
1 TACTGATTTGCACTATGTGTGCCTACTGATTCGCACT-TCGTGTGCC
*
695 TACTGGA-TTGCACTGTGTGTGC
1 TACT-GATTTGCACTATGTGTGC
717 TTATTGTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
45 27 0.48
46 26 0.46
47 3 0.05
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.42
Consensus pattern (46 bp):
TACTGATTTGCACTATGTGTGCCTACTGATTCGCACTTCGTGTGCC
Found at i:1628 original size:19 final size:21
Alignment explanation
Indices: 1606--1650 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1596 TATTTTTATT
1606 TAAAAAAATT-AAATTT-AAA
1 TAAAAAAATTAAAATTTAAAA
**
1625 TAAAAATTTTAAAATTTAAAA
1 TAAAAAAATTAAAATTTAAAA
1646 TAAAA
1 TAAAA
1651 TTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 6 0.27
21 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAAATTAAAATTTAAAA
Found at i:1651 original size:20 final size:21
Alignment explanation
Indices: 1616--1657 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1606 TAAAAAAATT
1616 AAATTTAAATAAAAATT-TTA
1 AAATTTAAATAAAAATTATTA
1636 AAATTTAAA-ATAAAATTATTA
1 AAATTTAAATA-AAAATTATTA
1657 A
1 A
1658 TATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 15 0.75
21 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTTAAATAAAAATTATTA
Found at i:2265 original size:6 final size:6
Alignment explanation
Indices: 2254--2288 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
2244 AAGAGAGAAA
2254 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT CTTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT -TTTT
2289 TAAAAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:2468 original size:30 final size:31
Alignment explanation
Indices: 2409--2475 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2399 AATTAGTAAA
*
2409 GATAAAATTGTACTTTGATCCTCTTAAAAAT
1 GATAAAATTGTACTTTAATCCTCTTAAAAAT
*
2440 GATAAAATTTTGA-TTTAATCCT-TTAAAAAT
1 GATAAAATTGT-ACTTTAATCCTCTTAAAAAT
*
2470 TATAAA
1 GATAAA
2476 GAAATAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.41
31 18 0.56
32 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (31 bp):
GATAAAATTGTACTTTAATCCTCTTAAAAAT
Found at i:8386 original size:2 final size:2
Alignment explanation
Indices: 8379--8409 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
8369 ATATACGTGT
*
8379 AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8410 TTTCTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Found at i:23612 original size:16 final size:16
Alignment explanation
Indices: 23591--23621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23581 ATATAATCAA
23591 ATTTATTCACCCAAAG
1 ATTTATTCACCCAAAG
*
23607 ATTTATTCACTCAAA
1 ATTTATTCACCCAAA
23622 CGAACATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTATTCACCCAAAG
Found at i:28209 original size:63 final size:63
Alignment explanation
Indices: 28030--28181 Score: 241
Period size: 63 Copynumber: 2.4 Consensus size: 63
28020 GATATTGCCA
* * *
28030 ATGAAGCTTTGGTAGTATTGATAAAAGTTGAGGACTTAGAATCTTTAGCATTTAGGTTCATAT
1 ATGAAGTTTTGGTAGTATTGATAAAAGTTGAGGACTTAGAATCTTGAGCATTTAGGTTCAGAT
* **
28093 ATGAAGTTTTGGTAGTATTGATAAAAGTTGAGGACTTGGAATCTTGAGCATTTAGGTTTGGAT
1 ATGAAGTTTTGGTAGTATTGATAAAAGTTGAGGACTTAGAATCTTGAGCATTTAGGTTCAGAT
*
28156 ATGAAGTTTTGGTAGTATCGATAAAA
1 ATGAAGTTTTGGTAGTATTGATAAAA
28182 ATCGAAGATT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 82 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38
Consensus pattern (63 bp):
ATGAAGTTTTGGTAGTATTGATAAAAGTTGAGGACTTAGAATCTTGAGCATTTAGGTTCAGAT
Found at i:32387 original size:48 final size:48
Alignment explanation
Indices: 32323--32422 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 48
32313 AAAATTTTCG
* * * * *
32323 TCAATTTTATCTCTTGATTATAATAAATTTATTAAAATCGTCATTACA
1 TCAACTTTATCTCTTGATCACAAAAAATTTATTAAAATCGTCACTACA
* * *
32371 TCAACTTTGTCTCTTGATCACAAAAAATTTATTAAGATTGTCACTACA
1 TCAACTTTATCTCTTGATCACAAAAAATTTATTAAAATCGTCACTACA
32419 TCAA
1 TCAA
32423 ATTAAAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (48 bp):
TCAACTTTATCTCTTGATCACAAAAAATTTATTAAAATCGTCACTACA
Found at i:32516 original size:23 final size:23
Alignment explanation
Indices: 32490--32534 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
32480 CTTATTACAT
32490 GTATATAATTATTAGGTTTAATA
1 GTATATAATTATTAGGTTTAATA
* *
32513 GTATATATTTTTTAGGTTTAAT
1 GTATATAATTATTAGGTTTAAT
32535 GTTTAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (23 bp):
GTATATAATTATTAGGTTTAATA
Found at i:33517 original size:22 final size:22
Alignment explanation
Indices: 33332--33518 Score: 185
Period size: 22 Copynumber: 8.0 Consensus size: 22
33322 CTGCTTGGGA
*
33332 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
*
33354 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
*
33376 AACAGAAGCACACGCAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* *
33398 ATCAGAAGCACACGCAGTGCTGGGG
1 AACAGAAGCACACACAGTGCT---G
33423 AAACAGAAGCACACACAGTGCTGGGG
1 -AACAGAAGCACACACAGTGCT---G
* * *
33449 AAACAAAAGCACACGCATTGCTAGGG
1 -AACAGAAGCACACACAGTGCT---G
*
33475 AAACAGAAGCACACAAAGTGCTG
1 -AACAGAAGCACACACAGTGCTG
33498 AACAGAAGCACACACAGTGCT
1 AACAGAAGCACACACAGTGCT
33519 TTCCTTAATG
Statistics
Matches: 147, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
22 82 0.56
23 1 0.01
25 1 0.01
26 63 0.43
ACGTcount: A:0.40, C:0.24, G:0.26, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:37845 original size:23 final size:23
Alignment explanation
Indices: 37748--37896 Score: 137
Period size: 23 Copynumber: 6.5 Consensus size: 23
37738 ATACTAACGC
*
37748 GCTCTCTGTTTAGCACGTTT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
*
37771 GC-CTTCTGATTAGCACTTTGTGT
1 GCTC-TCTGTTTAGCACTTTGTGT
* *
37794 GCTCTTTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
37817 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
37840 GCTCTCTGTTGCCCAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACTTTGTGT
*
37865 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
*
37886 GCTCTTTGTTT
1 GCTCTCTGTTT
37897 GTTCCGTATA
Statistics
Matches: 105, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
21 13 0.12
22 8 0.08
23 65 0.62
24 2 0.02
25 12 0.11
26 5 0.05
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:39308 original size:22 final size:22
Alignment explanation
Indices: 39283--39414 Score: 158
Period size: 22 Copynumber: 6.0 Consensus size: 22
39273 CTGCTGGGGA
*
39283 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
*
39305 AACAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
** **
39327 ATTAGAAGCACACGTAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* * *
39349 ATCAGAAAG-ACACGCAGTGCTA
1 AACAG-AAGCACACACAGTGCTG
39371 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
39393 ATCAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
39415 GGGAAATAGA
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
21 3 0.03
22 90 0.94
23 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:39425 original size:26 final size:26
Alignment explanation
Indices: 39374--39463 Score: 100
Period size: 26 Copynumber: 3.6 Consensus size: 26
39364 AGTGCTAAAC
39374 AGAAGCACACACAGTGCT---G--AT
1 AGAAGCACACACAGTGCTGGGGAAAT
39395 CAGAAGCACACACAGTGCTGGGGAAAT
1 -AGAAGCACACACAGTGCTGGGGAAAT
** * *
39422 AGAAGCACACGTAGTACTGGGGAAAC
1 AGAAGCACACACAGTGCTGGGGAAAT
39448 AGAAGCACACACAGTG
1 AGAAGCACACACAGTG
39464 ATAAACAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
22 18 0.32
25 1 0.02
26 35 0.62
27 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (26 bp):
AGAAGCACACACAGTGCTGGGGAAAT
Found at i:39873 original size:22 final size:23
Alignment explanation
Indices: 39839--39939 Score: 100
Period size: 23 Copynumber: 4.4 Consensus size: 23
39829 AATGCTAGGC
* *
39839 AACAGTAGGCACACAAAGTGCTA
1 AACAGAAGGCACACATAGTGCTA
*
39862 AACAGAA-GCACACATAGTGCTG
1 AACAGAAGGCACACATAGTGCTA
*
39884 AACAGAAGGCACACATAGTGCTG
1 AACAGAAGGCACACATAGTGCTA
* *
39907 AATAGAGGGCACGA-A-ACGTGCTA
1 AACAGAAGGCAC-ACATA-GTGCTA
*
39930 AACAGTAGGC
1 AACAGAAGGC
39940 GCGTTAGTGT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
22 21 0.32
23 44 0.67
24 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.13
Consensus pattern (23 bp):
AACAGAAGGCACACATAGTGCTA
Found at i:40041 original size:26 final size:24
Alignment explanation
Indices: 40002--40049 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
39992 TCTACATGGG
*
40002 CATAATCTCTTATATTCATCATTTCT
1 CATAATCTCATATA-TCA-CATTTCT
*
40028 CATAATTTCATATATCACATTT
1 CATAATCTCATATATCACATTT
40050 ACATTTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 3 0.15
26 12 0.60
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (24 bp):
CATAATCTCATATATCACATTTCT
Found at i:41864 original size:14 final size:14
Alignment explanation
Indices: 41841--41886 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
41831 TTAAATTTAT
41841 TTAAAATAAAAATA
1 TTAAAATAAAAATA
*
41855 TT-AAATTAAAAT-
1 TTAAAATAAAAATA
41867 TTAAAATATAAAA-A
1 TTAAAATA-AAAATA
41881 TTAAAA
1 TTAAAA
41887 AATTAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 13 0.48
14 12 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAATAAAAATA
Found at i:41881 original size:21 final size:20
Alignment explanation
Indices: 41841--41909 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 20
41831 TTAAATTTAT
* *
41841 TTAAAATAAAAATAT-TAAA
1 TTAAAATTAAAATATAAAAA
41860 TTAAAATTTAAAATATAAAAA
1 TTAAAA-TTAAAATATAAAAA
* *
41881 TTAAAAAATTAAATATTTAAATA
1 TT--AAAATTAAA-ATATAAAAA
41904 TTAAAA
1 TTAAAA
41910 ACACCTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.15
20 8 0.20
21 9 0.22
22 5 0.12
23 13 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAATTAAAATATAAAAA
Found at i:41906 original size:15 final size:13
Alignment explanation
Indices: 41839--41909 Score: 63
Period size: 15 Copynumber: 5.1 Consensus size: 13
41829 AATTAAATTT
*
41839 ATTTAAAATAAAA
1 ATTTAAAATTAAA
41852 ATATT-AAATTAAA
1 AT-TTAAAATTAAA
41865 ATTTAAAATATAAAA
1 ATTTAAAAT-T-AAA
*
41880 ATTAAAAAATTAAA
1 ATT-TAAAATTAAA
41894 TATTTAAATATTAAA
1 -ATTTAAA-ATTAAA
41909 A
1 A
41910 ACACCTTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
12 2 0.04
13 15 0.31
14 10 0.21
15 16 0.33
16 5 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATTTAAAATTAAA
Found at i:41944 original size:17 final size:18
Alignment explanation
Indices: 41922--41963 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
41912 ACCTTTAACT
41922 TTGATTTTGACTT-ATCA
1 TTGATTTTGACTTAATCA
41939 TTGA--TTGACTTGAATCA
1 TTGATTTTGACTT-AATCA
41956 TTGATTTT
1 TTGATTTT
41964 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.33
17 12 0.57
19 2 0.10
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (18 bp):
TTGATTTTGACTTAATCA
Found at i:41971 original size:7 final size:7
Alignment explanation
Indices: 41959--41984 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41949 TGAATCATTG
41959 ATTTTAA
1 ATTTTAA
41966 ATTTTAA
1 ATTTTAA
41973 ATTTTAA
1 ATTTTAA
41980 ATTTT
1 ATTTT
41985 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATTTTAA
Found at i:43528 original size:2 final size:2
Alignment explanation
Indices: 43523--43548 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43513 ATATATATAT
43523 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
43549 TTTATCTAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48653 original size:3 final size:3
Alignment explanation
Indices: 48645--48673 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48635 AAGTTATTGA
48645 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
48674 TGCATTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:49470 original size:5 final size:5
Alignment explanation
Indices: 49460--49493 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
49450 TTGAAGTGAG
49460 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGG
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT TGGG
49494 GATGACTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (5 bp):
TGGGT
Done.