Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003970.1 Kokia drynarioides strain JFW-HI SEQ_117065, 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: 67236
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:3483 original size:11 final size:11
Alignment explanation
Indices: 3454--3487 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3444 CCTATTTAAA
3454 AGCTCGTTTATT
1 AGCTCGTTTA-T
*
3466 GGCTCGTTTAT
1 AGCTCGTTTAT
3477 AGCTCGTTTAT
1 AGCTCGTTTAT
3488 TTATTAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (11 bp):
AGCTCGTTTAT
Found at i:3591 original size:12 final size:12
Alignment explanation
Indices: 3574--3616 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3564 TCATTAACAT
3574 TGTTCATGAATA
1 TGTTCATGAATA
*
3586 TGTTCAAT-TATA
1 TGTTC-ATGAATA
*
3598 TGTTCATGAACA
1 TGTTCATGAATA
3610 TGTTCAT
1 TGTTCAT
3617 TTAATGTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (12 bp):
TGTTCATGAATA
Found at i:3601 original size:24 final size:23
Alignment explanation
Indices: 3574--3683 Score: 132
Period size: 23 Copynumber: 4.7 Consensus size: 23
3564 TCATTAACAT
*
3574 TGTTCATGAATATGTTCAATTATA
1 TGTTCATGAACATGTTCAATTA-A
*
3598 TGTTCATGAACATGTTCATTTAA
1 TGTTCATGAACATGTTCAATTAA
* *
3621 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
* *
3644 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATGAACATGTTCAATTAA
*
3667 -GTTAAATGAACATGTTC
1 TGTT-CATGAACATGTTC
3684 GTGAACATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
22 3 0.04
23 55 0.71
24 20 0.26
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCATGAACATGTTCAATTAA
Found at i:3635 original size:12 final size:12
Alignment explanation
Indices: 3597--3661 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
3587 GTTCAATTAT
*
3597 ATGTTCATGAAC
1 ATGTTCGTGAAC
* **
3609 ATGTTCATTTA-
1 ATGTTCGTGAAC
3620 ATGTTCGTGAAC
1 ATGTTCGTGAAC
*
3632 ATGTTCGAT-TA-
1 ATGTTCG-TGAAC
3643 ATGTTCGTGAAC
1 ATGTTCGTGAAC
3655 ATGTTCG
1 ATGTTCG
3662 ATTAAGTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
10 1 0.02
11 16 0.38
12 24 0.57
13 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:3694 original size:23 final size:23
Alignment explanation
Indices: 3650--3695 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3640 TTAATGTTCG
* *
3650 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
3673 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
3696 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:6309 original size:21 final size:19
Alignment explanation
Indices: 6262--6304 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
6252 AAGAAACATA
6262 CAATACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
*
6281 CAATACTGGCTCGTGAGAG
1 CAATACTGGCTCGTAAGAG
6300 CAATA
1 CAATA
6305 TACTGTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (19 bp):
CAATACTGGCTCGTAAGAG
Found at i:16192 original size:16 final size:18
Alignment explanation
Indices: 16153--16186 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16143 TAAGTTTATA
16153 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
16170 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
16187 AATTTAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:17091 original size:24 final size:26
Alignment explanation
Indices: 17064--17115 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
17054 TTCTATAAAC
17064 AAAATTAATAAATA-AAAAAT-ATAT
1 AAAATTAATAAATATAAAAATAATAT
* *
17088 AAAATTATTAAATATTAAAATAATAT
1 AAAATTAATAAATATAAAAATAATAT
17114 AA
1 AA
17116 TATGAGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 5 0.21
26 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATTAATAAATATAAAAATAATAT
Found at i:17985 original size:19 final size:20
Alignment explanation
Indices: 17942--17990 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
17932 AATCAACATG
*
17942 TATTTTATAATTTTTTTGAA
1 TATTTTATAATTTTTATGAA
17962 T-TTTTATAGA-TTTTAT-AA
1 TATTTTATA-ATTTTTATGAA
17980 TATTTTA-AATT
1 TATTTTATAATT
17991 CATTTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
17 1 0.04
18 5 0.20
19 17 0.68
20 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TATTTTATAATTTTTATGAA
Found at i:22644 original size:41 final size:41
Alignment explanation
Indices: 22594--22684 Score: 173
Period size: 41 Copynumber: 2.2 Consensus size: 41
22584 CCTAGTTGAA
22594 CGTGTTTTCTTTAGAATTTTCAAAAAACACTTCTAACTGAG
1 CGTGTTTTCTTTAGAATTTTCAAAAAACACTTCTAACTGAG
*
22635 CGTGCTTTCTTTAGAATTTTCAAAAAACACTTCTAACTGAG
1 CGTGTTTTCTTTAGAATTTTCAAAAAACACTTCTAACTGAG
22676 CGTGTTTTC
1 CGTGTTTTC
22685 CTAATATGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (41 bp):
CGTGTTTTCTTTAGAATTTTCAAAAAACACTTCTAACTGAG
Found at i:25567 original size:23 final size:23
Alignment explanation
Indices: 25535--25578 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
25525 GTGAGTGTTC
25535 TTTTCTAAATTCATTTTGTTTTTG
1 TTTTCTAAATTCATTTT-TTTTTG
*
25559 TTTT-TAAATTGATTTTTTTT
1 TTTTCTAAATTCATTTTTTTT
25579 ATAATATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTTCTAAATTCATTTTTTTTTG
Found at i:26119 original size:2 final size:2
Alignment explanation
Indices: 26114--26143 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
26104 ACTCAATTGT
26114 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26144 GACAATATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:26719 original size:2 final size:2
Alignment explanation
Indices: 26712--26755 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
26702 GTTTCTAGTA
26712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26754 AT
1 AT
26756 GCGAACAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33336 original size:2 final size:2
Alignment explanation
Indices: 33329--33355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33319 CATTCATGTA
33329 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
33356 AATTAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33618 original size:23 final size:23
Alignment explanation
Indices: 33592--33636 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
33582 TCTTAATATT
*
33592 TAGT-ATAAATAATTTTATTTTAA
1 TAGTAATAAA-AATTTAATTTTAA
*
33615 TAGTAATACAAATTTAATTTTA
1 TAGTAATAAAAATTTAATTTTA
33637 TTTTGATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TAGTAATAAAAATTTAATTTTAA
Found at i:33634 original size:28 final size:28
Alignment explanation
Indices: 33601--33657 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
33591 TTAGTATAAA
**
33601 TAATTTTATTTTAATAGTAATACAAATT
1 TAATTTTATTTTAATACCAATACAAATT
*
33629 TAATTTTATTTTGATACCAATACAAATT
1 TAATTTTATTTTAATACCAATACAAATT
33657 T
1 T
33658 TCTCCGACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (28 bp):
TAATTTTATTTTAATACCAATACAAATT
Found at i:33825 original size:24 final size:24
Alignment explanation
Indices: 33785--33835 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
33775 GTTCGGTTTG
33785 ATAAAAAAAAAGTATTAAAAAATTT
1 ATAAAAAAAAAG-ATTAAAAAATTT
*
33810 ATAAAAAATAAA-ATTAAAAATTTT
1 ATAAAAAA-AAAGATTAAAAAATTT
33834 AT
1 AT
33836 TCAATACCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 13 0.54
25 8 0.33
26 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
ATAAAAAAAAAGATTAAAAAATTT
Found at i:40548 original size:29 final size:29
Alignment explanation
Indices: 40506--40562 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
40496 AAAAAGATTA
40506 CTTATTTTATGTGGGAGTTCCACAGAAAT
1 CTTATTTTATGTGGGAGTTCCACAGAAAT
40535 CTTATTTTATGTGGGAGTTCCACAGAAA
1 CTTATTTTATGTGGGAGTTCCACAGAAA
40563 AGAAGAGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (29 bp):
CTTATTTTATGTGGGAGTTCCACAGAAAT
Found at i:55214 original size:33 final size:33
Alignment explanation
Indices: 55146--55217 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
55136 GTACCAACTT
* *
55146 AAAAGTGTCAAGTTTAGGTACCAAATTAAGGAA
1 AAAAATGTCAAGTTTAGGTACCAAATTAAGCAA
*
55179 AAAAATGTCAAGTTT-GAGTATCAAATTATA-CAA
1 AAAAATGTCAAGTTTAG-GTACCAAATTA-AGCAA
55212 AAAAAT
1 AAAAAT
55218 TTAAGTACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 1 0.03
33 32 0.94
34 1 0.03
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.26
Consensus pattern (33 bp):
AAAAATGTCAAGTTTAGGTACCAAATTAAGCAA
Found at i:55590 original size:31 final size:30
Alignment explanation
Indices: 55548--55618 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
55538 ATGTACCAAC
* * *
55548 TTAAAAAAAGTGTCAAGTTTAGGTATCAAA
1 TTAAAAAAAGTGTCAAATTTAAGTATAAAA
55578 TTAAGAAAAAGTGTCAAATTTAAGTATAAAA
1 TTAA-AAAAAGTGTCAAATTTAAGTATAAAA
55609 TTAAACAAAA
1 TTAAA-AAAA
55619 AAAATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.14
31 31 0.86
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.28
Consensus pattern (30 bp):
TTAAAAAAAGTGTCAAATTTAAGTATAAAA
Done.