Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004998.1 Kokia drynarioides strain JFW-HI SEQ_118756, 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: 84736
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:383 original size:15 final size:14
Alignment explanation
Indices: 358--406 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
348 GTAACATCTG
358 TATTTTTTTATTTT
1 TATTTTTTTATTTT
372 TATTTTTATTATTTT
1 TATTTTT-TTATTTT
* *
387 GTAATTGTTTTATTAT
1 -T-ATTTTTTTATTTT
403 TATT
1 TATT
407 ATCAACGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
16 7 0.23
17 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (14 bp):
TATTTTTTTATTTT
Found at i:579 original size:32 final size:31
Alignment explanation
Indices: 542--607 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
532 ATCCTCAGGC
*
542 TTTTAACACCTGGCATTGATTTGAGGATTGCT
1 TTTTAACACCTGGAATTGATTTG-GGATTGCT
** * *
574 TTTTAACATTTGGAATTGGTTTGGGGTTGCT
1 TTTTAACACCTGGAATTGATTTGGGATTGCT
605 TTT
1 TTT
608 AATATTGGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.34
32 19 0.66
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (31 bp):
TTTTAACACCTGGAATTGATTTGGGATTGCT
Found at i:1703 original size:8 final size:8
Alignment explanation
Indices: 1653--1703 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
1643 TTTATGAGTT
*
1653 TTTTTATA
1 TTTTTAAA
1661 TTTTTAAA
1 TTTTTAAA
*
1669 -TTTTAAT
1 TTTTTAAA
1676 TTTTTAAA
1 TTTTTAAA
1684 TATTTTATAA
1 T-TTTTA-AA
1694 TTTTTAAA
1 TTTTTAAA
1702 TT
1 TT
1704 ACTTGTTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.16
8 18 0.49
9 10 0.27
10 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTTAAA
Found at i:7725 original size:18 final size:18
Alignment explanation
Indices: 7687--7725 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7677 GTTAAAGTTT
*
7687 GTTAATAACAGTTAATTA
1 GTTAATAACAGTTAATCA
* *
7705 GTTAATGACAGTTAGTCA
1 GTTAATAACAGTTAATCA
7723 GTT
1 GTT
7726 GTCATTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (18 bp):
GTTAATAACAGTTAATCA
Found at i:9977 original size:5 final size:5
Alignment explanation
Indices: 9969--9998 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
9959 CTAACATCTG
*
9969 ATTTG ATTTA ATTTA ATTTA ATTTA ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
9999 GCCCCAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (5 bp):
ATTTA
Found at i:19515 original size:31 final size:31
Alignment explanation
Indices: 19480--19541 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
19470 ATATTATTGC
19480 TCGAGGGGATATTGTTGTGAGCAAAGTTAGT
1 TCGAGGGGATATTGTTGTGAGCAAAGTTAGT
19511 TCGAGGGGATATTGTTGTGAGCAAAGTTAGT
1 TCGAGGGGATATTGTTGTGAGCAAAGTTAGT
19542 ACTTTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.35, T:0.32
Consensus pattern (31 bp):
TCGAGGGGATATTGTTGTGAGCAAAGTTAGT
Found at i:19693 original size:17 final size:17
Alignment explanation
Indices: 19671--19709 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
19661 AGGTGGAGAA
* * *
19671 CTTGTTTGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
19688 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
19705 CTTGT
1 CTTGT
19710 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:19792 original size:41 final size:41
Alignment explanation
Indices: 19699--19794 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
19689 TTGTTCGTAG
* * *
19699 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
19740 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
19781 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
19795 AATAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGATGACT
Found at i:26033 original size:24 final size:24
Alignment explanation
Indices: 25979--26040 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 24
25969 ATTAATGAAT
* *
25979 AATTAATTAATAATTTTATATTTA
1 AATTATTTAATAATTTTAAATTTA
*
26003 AATTTATTTAAT-ATTTTAAATATTG
1 AA-TTATTTAATAATTTTAAAT-TTA
*
26028 AATTATTTTATAA
1 AATTATTTAATAA
26041 AATATCGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
AATTATTTAATAATTTTAAATTTA
Found at i:27095 original size:3 final size:3
Alignment explanation
Indices: 27087--27112 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
27077 CCAGAAGCTA
27087 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
27113 CCGTTATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:35679 original size:181 final size:181
Alignment explanation
Indices: 35375--35737 Score: 717
Period size: 181 Copynumber: 2.0 Consensus size: 181
35365 AATTTAAATT
35375 AAAATTAAATAGTAAAATTTAATCAAAAATCAAAGTTTGGTTTCGAAATTGATTCAAAAAAAAAT
1 AAAATTAAATAGTAAAATTTAATCAAAAATCAAAGTTTGGTTTCGAAATTGATTCAAAAAAAAAT
35440 TAAGTGACAAAATTTAATATAAAATTGAAGTGGAGTGATAAATTTACCATTAATTTGAAAGTACG
66 TAAGTGACAAAATTTAATATAAAATTGAAGTGGAGTGATAAATTTACCATTAATTTGAAAGTACG
35505 ATGGCAAATTTATACAATAACCCATTATTACATTTCTATTTAAGCAAATCG
131 ATGGCAAATTTATACAATAACCCATTATTACATTTCTATTTAAGCAAATCG
*
35556 AAAATTAAATAGTAAAATTTAATCAAAAATCAAAGTTTGGTTTCGAAATTGATTCAAATAAAAAT
1 AAAATTAAATAGTAAAATTTAATCAAAAATCAAAGTTTGGTTTCGAAATTGATTCAAAAAAAAAT
35621 TAAGTGACAAAATTTAATATAAAATTGAAGTGGAGTGATAAATTTACCATTAATTTGAAAGTACG
66 TAAGTGACAAAATTTAATATAAAATTGAAGTGGAGTGATAAATTTACCATTAATTTGAAAGTACG
35686 ATGGCAAATTTATACAATAACCCATTATTACATTTCTATTTAAGCAAATCG
131 ATGGCAAATTTATACAATAACCCATTATTACATTTCTATTTAAGCAAATCG
35737 A
1 A
35738 CTGATCAAGT
Statistics
Matches: 181, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 181 1.00
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (181 bp):
AAAATTAAATAGTAAAATTTAATCAAAAATCAAAGTTTGGTTTCGAAATTGATTCAAAAAAAAAT
TAAGTGACAAAATTTAATATAAAATTGAAGTGGAGTGATAAATTTACCATTAATTTGAAAGTACG
ATGGCAAATTTATACAATAACCCATTATTACATTTCTATTTAAGCAAATCG
Found at i:53418 original size:24 final size:23
Alignment explanation
Indices: 53386--53438 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
53376 TAGTTTAGTG
* *
53386 AATTTAGTTTTCTTTTCCTTCCGA
1 AATTCAGTTTT-TTTTACTTCCGA
* *
53410 AATTCAGTTTTTTTTAGTTTCGA
1 AATTCAGTTTTTTTTACTTCCGA
53433 AATTCA
1 AATTCA
53439 TTATTATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (23 bp):
AATTCAGTTTTTTTTACTTCCGA
Found at i:61493 original size:16 final size:17
Alignment explanation
Indices: 61463--61500 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
61453 TTTGAGGTGC
*
61463 TAAAGTGTTACAAATTA
1 TAAAATGTTACAAATTA
*
61480 -AAAATGTTATAAATTA
1 TAAAATGTTACAAATTA
61496 TAAAA
1 TAAAA
61501 GACTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (17 bp):
TAAAATGTTACAAATTA
Found at i:64175 original size:21 final size:22
Alignment explanation
Indices: 64145--64190 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
64135 ATAAACAATA
* *
64145 TAATAGTTTTACCTTTTAA-TT
1 TAATAATTTTAACTTTTAACTT
*
64166 TAATAATTTTAATTTTTAACTT
1 TAATAATTTTAACTTTTAACTT
64188 TAA
1 TAA
64191 AAAATATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TAATAATTTTAACTTTTAACTT
Found at i:67979 original size:72 final size:74
Alignment explanation
Indices: 67881--68018 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 74
67871 AGAAAAGAAG
* ** * *
67881 AAAATAAATTATGGAAGAAATCTATAATTTTTAAT-ATTTTTC-TAGATTTTAAAAATAATT-TT
1 AAAATAAATCATAAAAGAAATCTATAATTTTTAATAATTTTTCGGAAATTTT-AAAATAATTGTT
67943 TGAATCTTTA
65 TGAATCTTTA
*
67953 AAAATAAATCATAAAAGAAATTTATAATTTTTAATAATTTTTCGGAAATTTTAAAATAATTGTTT
1 AAAATAAATCATAAAAGAAATCTATAATTTTTAATAATTTTTCGGAAATTTTAAAATAATTGTTT
68018 G
66 G
68019 TTTTTAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 31 0.54
73 16 0.28
74 10 0.18
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (74 bp):
AAAATAAATCATAAAAGAAATCTATAATTTTTAATAATTTTTCGGAAATTTTAAAATAATTGTTT
GAATCTTTA
Found at i:76498 original size:23 final size:24
Alignment explanation
Indices: 76439--76499 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
76429 ATTAATATCG
76439 TTCATGAACATGTTCAATTATATA
1 TTCATGAACATGTTCAATTATATA
* *
76463 TTCATGAATATGTTCATTTA-ATA
1 TTCATGAACATGTTCAATTATATA
* *
76486 TTCGTGAGCATGTT
1 TTCATGAACATGTT
76500 TGATTAAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 14 0.44
24 18 0.56
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (24 bp):
TTCATGAACATGTTCAATTATATA
Done.